title: WOXINTS

description:
Solanum lycopersicum cv. M82
Random primed libraries
S08
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: Tissue NeoCortex GCGR-NS13 - 13.5 pcw

status: Public on Mar 24 2021

type: SRA

city: Edinburgh

first: Ben

last: Southgate

address: Little France Dr

country: United Kingdom

institute: University of Edinburgh

description:
Tissue
GCGR_NS_normalised_counts.txt

library_source: transcriptomic

data_processing:
Paired end RNA sequencing reads were trimmed with Cutadapt (version 1.14) with default parameters and aligned to hg38 genome using Kallisto (version 0.43.1).
Read counts were summarised via the package Tximport (version 1.8.0) and subsequent normalisation was completed via DESeq2 (version 1.27.32) as regularised-logarithm transformation (rlog).
Genome_build: hg38
Supplementary_files_format_and_content: Three sets of tab-delimited files for pHGG, NSCs, and engineered NSCs containing raw counts, and normalised counts as calculated by DESeq2 (rlog and FPM).
Supplementary_files_format_and_content: DESeq2 fpm
Supplementary_files_format_and_content: DESeq2 normalised counts rlog
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Neocortex

growth_protocol: Cultures were maintained in DMEM/HAMS-F12 serum-free basal medium supplemented with N2 and B27 (Life Technologies), laminin (Sigma, 1 µg/ml) and growth factors EGF and bFGF (Peprotech, 10 ng/ml)

extract_protocol:
total RNA was extracted with Qiagen Rneasy plus mini kit
Libraries were generated with 200ng of RNA input using the KAPA mRNA HyperPrep kit and KAPA SeqCap adapters. Fragmentation was carried out at 94°C for 6 minutes and libraries amplified for 12 cycles
Pooled libraries were diluted and processed for sequencing using the Illumina HiSeq 2500 platform.

tag: tissue

value: NeoCortex

tag: embryo

value: GCGR-NS13 - 13.5 pcw

tag: disease state

value: Normal


title: Paediatric glioblastoma cell GBM002-P2D3 v5-tag G34R rep2

library_source: genomic

data_processing:
ChIP-seq reads were quality and adapter trimmed with Cutadapt (version 1.14), before being aligned to the human hg38 genome with bowtie2 (version 2.3.5) using default parameters.
Resulting BAM files were sorted and indexed with samtools and reads were filtered from ENCODE blacklist regions with samtools view (version 1.9) and bedtools intersect (version 2.29.0).
PCR duplicates were filtered with picard tools MarkDuplicates (version 2.18.26).
Peaks were called on filtered input and control BAM files with MAC2 set to broadPeak (H3.3, H3K36me3, H3K27me3), and narrowPeak (H3K4me3). Narrow peaks were called using MACS2 (version 2.1.2) with the following command line parameters: macs2 callpeak -t Input.bam -c Control.bam -f BAMPE -g 2701495761 -s 50 --keep-dup all -B --SPMR --nomodel --shift 0 --extsize 146 -q 0.05. Broad peaks were called with the additional parameters --broad --broad-cutoff 0.1 instead of -q 0.05.
RPM normalised bedgraph files were generated via MACS2 following peak calling. Subtracted coverage files were generated using MACS2 bdgcmp between input and control BAMs - where negative values were set to 0.
BigWig coverage files were generated using bedGraphToBigWig (version 4) from MACS2 resulting bedgraphs.
Where merged samples are reported (_0), samtools merge was used on filtered BAMs across sample replicates before undergoing the same peak calling, bedgraph, and bigWig generation process.
Coverage of each histone mark over gene regions for boxplots were summarised using bedtools multicov on filtered and processed BAM files, and normalised to RPKM using gene length
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 Peakfiles
Supplementary_files_format_and_content: Bigwig files of histone marks
Supplementary_files_format_and_content: RPKM histone coverage over genes

molecule: genomic DNA

source_name: pHGG

growth_protocol: Cultures were maintained in DMEM/HAMS-F12 serum-free basal medium supplemented with N2 and B27 (Life Technologies), laminin (Sigma, 1 µg/ml) and growth factors EGF and FGF2 (Peprotech, 10 ng/ml)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone/protein-DNA complexes were isolated using antibodies.
Libraries were constructed using the NEBNext Ultra II DNA Library Kit and NEBNextdual index primer sets for Illumina (Cat. #E7645S and #E7600S) in accordance with the manufacturers instructions.

tag: cell type

value: Paediatric glioblastoma cell

value: pHGG

tag: cell line

value: Cancer

tag: chip antibody

tag: genotype


title: 20μMGW9662-EB-D10

city: Beijing

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

country: China

institute: Peking University

data_processing:
For PolyA(+) RNA-seq,Adapteor was removed by trimmomatic-0.39, HISAT2 software was used to align sequencing reads to reference mRNA.
For polyA(+) RNA-seq,mouse Cdna database(UCSC, NCBI37)  was used for alignment.
Reads per Million was calculated for the normalization
Genome_build: mm9
Supplementary_files_format_and_content: RPM

organism: Mus musculus

source_name: mESC cultured in Differentiation medium containing 20μM GW9662  for EB induction for 10 day

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina)。

tag: cell type source

value: mESCs

value: WT

tag: treatment

value: cultured in Differentiation medium containing 20uM GW9662 for EB induction for 10 day

value: Embryoid bodies


title: DMSO-EB-D13

source_name: mESC cultured in Differentiation medium containing DMSO for  EB induction for 13 day


title: WOXINTK

city: Davis

first: Siobhan

last: Brady

state: CA

address: 451 Health Sciences Dr

department: Genome Center and Plant Biology

country: USA

institute: University of California Davis

description:
Solanum lycopersicum cv. M82
Random primed libraries
K07
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

data_processing:
Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to ITAG3.2 transcriptome (cDNA) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values.
ATAC-seq raw reads were aligned to each species' corresponding genome using Bowtie2 with default parameters.
ATAC-seq mapped reads were filtered to remove 1) reads that mapped to organelle genomes and 2) reads with a mapping quality score of q<2.
Transposase Hypersensitive Sites were identified using the Findpeaks function of the HOMER package, with the parameters "-minDist 150" "-region" and "-regionRes 1".
Filtered ATAC-seq bam files for each sample were converted to the bigwig format using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
For accurate visualization, all filtered ATAC-seq bam files for a given tissue were scaled to the same number of reads and combined per condition to create a single merged bam file for a condition in a tissue type. The merged bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Filtered ATAC-seq bam files from genomic DNA samples were scaled to the total number of reads present in the merged bam files for a given tissue type. The scaled bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Rice TRAP-seq. Barcoded libraries were pooled together and sequenced on Illumina HiSeq 3000 at the UC Davis DNA Technologies Core to obtain 50-bp reads.
Rice TRAP-seq. R/Bioconductor (version 3.2.1) and FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) were used in short read quality control and grep for filtering of oligo dT for PolyA RNA libraries.
Rice TRAP-seq. Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to IRGSP-1.0 transcriptome (CDS, https://rapdb.dna.affrc.go.jp/index.html) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values. Splice variants were summed to assess transcript values.
Genome_build: Tomato: SOLANUM LYCOPERSICUM: ITAG3.20 (ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/)
Genome_build: Rice: IRGSP-1.0 (https://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Supplementary_files_format_and_content: .bed files contain Transposase Hypersensitive Site (THS) coordinates for individual samples or for each tissue type they are organized as (All) all the replicated THSs identified in that sample set in either control or submergence samples, (Up) THSs upregulated in submergence samples, and (Down) THSs downregulated in submergence samples.
Supplementary_files_format_and_content: .bw files contain aligned reads for individual samples, or combined samples for a specific condition of a given tissue, at a resolution of 1 bp bin sized windows.
Supplementary_files_format_and_content: .csv files contain raw counts.

organism: Solanum lycopersicum

source_name: 3-5 days-old seedling 1 cm roots tips

growth_protocol:
growth protocol 1: Transgenic Solanum lycopersicum seeds from transgenic lines were surface sterilized in 50% (v/v) bleach solution for 20 min (S. lycopersicum) and then rinsed three times with sterile distilled water. Seven seeds were plated on 10 cm x 10 cm plates containing full-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose and germination was scored daily after plating. Seedlings were grown for 3-5 days after germination in a growth chamber (16 h day / 8 h night;  at 22°C/22°C day/night; 60-65 ?Em-2s-1) and 1cm primary root tips were harvested and flash frozen into liquid nitrogen.
growth protocol 2: 1-month-old control plants: Transgenic Solanum lycopersicum seeds were germinated on 1xMS media with 1% sucrose and 200ug/ml Kanamycin. After 7d, seedlings were transplanted into pots with Turface Athletic Profile Field & Fairway clay substrate (Turface Athletics, 2017) that was pre-wetted with a nutrient water solution containing 4% nitrogen, 18% phosphoric acid, and 38% soluble potash. Plants were grown in a randomized design for 31 d in a Conviron Growth Chamber at 22°C, 70% RH, 16/8 h light/dark cycle, light intensity of 150-200 µmol/m2/s.
growth protocol 3: Field: Transgenic Solanum lycopersicum seeds were germinated on 1xMS plate (0-7d), screened for correct GFP pattern from root tip, transplanted on soil and grown in a growth chamber for one week (7-14d) ,  grown in a screenhouse for two weeks (14-28d), and finally transplanted into the field and grown for one month (29-60d)  with drip watering and weekly removal of flower buds.
growth protocol 4: Rice seeds from transgenic lines were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min and then rinsed with sterile distilled water. Seedlings were grown on plates (10 cm x 10 cm) containing half-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose, during 7 days in a growth chamber (16 h day / 8 h night;  at 28°C/25°C day/night; 110 ?Em-2s-1). The whole root system was placed immediately into liquid nitrogen upon harvesting.

extract_protocol:
extract protocol 1: Translating Ribosome Affinity Purification (TRAP) was performed as previously described (Reynoso et al, 2019).
extract protocol 2: Nuclei were purified from frozen and pulverized tissue as previously described (Reynoso et al, 2019). Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of  streptavidin-coated beads (NEB) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet  to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
extract protocol 3: For Rice: TRAP was performed as previously described (Reynoso et al, 2019)
library construction protocol 1: RNA-seq libraries  were prepared from poly(A)+ selected total and TRAP mRNA as described by Townsley et al. (2014) for random primer primed libraries.
library construction protocol 2: RNA-seq libraries  were prepared from poly(A)+ selected total and TRAP mRNA as described by Townsley et al. (2014) for random primer primed libraries.

tag: cultivar

tag: line

tag: age

value: 3-5 days

value: Roots tips


title: DMSO-EB-D10

source_name: mESC cultured in Differentiation medium containing DMSO for EB induction for 10 day


title: Tissue Spinalcord GCGR-NS19 - 19.3 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Spinalcord

value: Spinalcord

value: GCGR-NS19 - 19.3 pcw


title: VINTR

description:
Solanum lycopersicum cv. M82
Random primed libraries
R08
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: SlSHRpro:WPP:GFP:BLRP / SlACT2pro:mBirA


title: Paediatric glioblastoma cell GBM002-P2D3 input DNA G34R rep2


title: Paediatric glioblastoma cell GBM002-P2D3 H3K4me3 G34R KO rep1

value: G34R KO


title: Tissue Anterior Brainstem GCGR-NS19 - 19.3 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Anterior Brainstem

value: Anterior Brainstem


title: Paediatric glioblastoma cell GBM002-P2D3 v5-tag G34R rep1


title: Paediatric glioblastoma cell GBM002-P2D3 input DNA G34R rep1


title: miRNA-mESC-ΔSL1-rep1

data_processing:
For PolyA(+) RNA-seq,Adapteor was removed by trimmomatic-0.39, HISAT2 software was used to align sequencing reads to reference mRNA. For small RNA-seq, homemade PERL software was used to  remove adaptor sequences, and Bowtie sofeware was used to align sequencing reads to miRNA database
For polyA(+) RNA-seq,mouse Cdna database(UCSC, NCBI37)  was used for alignment. For small RNA-seq, 20-25nt small RNAs was aligned to known mature miRNA sequences(miRBase)
Both polyA(+) and small RNA-seq, Reads per Million was calculated for the normalization
Genome_build: mm9
Supplementary_files_format_and_content: csv

source_name: mESC cultured in serum/lif medium

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina)。Small RNA-seq libraries preparation using NEBNext® Small RNA Library Prep Set for Illumina kit。

value: mESC


title: WOXINTP

description:
Solanum lycopersicum cv. M82
Random primed libraries
P06
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: 20μMGW9662-EB-D13

source_name: mESC cultured in Differentiation medium containing 20μM GW9662  for EB induction for 13 day

value: cultured in Differentiation medium containing 20uM GW9662  for EB induction for 13 day


title: Paediatric glioblastoma cell GBM002-P2D3 H3K27me3 G34R KO rep1


title: Tissue Cerebellum GCGR-NS19 - 19.3 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Cerebellum

value: Cerebellum

value: Normal


title: WOXINTO

description:
Solanum lycopersicum cv. M82
Random primed libraries
O08
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: miRNA-mESC-WT-rep2


title: VINTM

description:
Solanum lycopersicum cv. M82
Random primed libraries
M08
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: miRNA-mESC-WT-rep1


title: Tissue Posterior Brainstem GCGR-NS19 - 19.3 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Posterior Brainstem

value: Posterior Brainstem


title: Tissue Diencephalon GCGR-NS19 - 19.3 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Diencephalon

value: Diencephalon


title: Paediatric glioblastoma cell GBM002-P2D3 H3K4me3 G34R rep2

value: Paediatric glioblastoma cell

value: pHGG

value: Cancer


title: Tissue Midbrain GCGR-NS19 - 19.3 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Midbrain

value: Midbrain


title: Paediatric glioblastoma cell GBM002-P2D3 H3K36me3 G34R rep2


title: Paediatric glioblastoma cell GBM002-P2D3 H3K4me3 G34R rep1


title: Tissue Striatum GCGR-NS19 - 19.3 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Striatum

value: Striatum


title: VINTJ

description:
Solanum lycopersicum cv. M82
Random primed libraries
J07
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: 3-5 days

value: Roots tips


title: VINTI

description:
Solanum lycopersicum cv. M82
Random primed libraries
I05
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: EB-D10-ΔSL1

description: RNA_seq_EB_differentiation_Neutal_differentiation.csv

source_name: mESC cultured in Differentiation medium for EB induction for 10 day

value: Embryoid bodies


title: PHINTQ

description:
Solanum lycopersicum cv. M82
Random primed libraries
Q05
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: S32pro:WPP:GFP:BLRP / SlACT2pro:mBirA


title: PHINTM

description:
Solanum lycopersicum cv. M82
Random primed libraries
M07
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: EB-D12-ΔSL1

source_name: mESC cultured in Differentiation medium for EB induction for 12 day


title: miRNA-mESC-ΔSL1-rep2


title: BGC823 cells, NO631

city: beijing

first: guo

last: ting

address: 52 Fucheng Road, Haidian District

institute: Peking University Cancer Hospital & Institute, Beijing

data_processing:
Basecalls performed using CASAVA version 1.4
aligned to the hg19 genome assembly using BWA .
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
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: hg19
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: BGC823 cells

extract_protocol:
Total RNA was harvested using Qiagen Kit.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The BGC823 cells were transfected by ISL1 Lentivirus and scramble lentivirus as control.

value: gastric cancer cell line BGC823

tag: passage

value: ISL1 knockdown


title: Paediatric glioblastoma cell GBM002-P2D3 H3K27me3 G34R rep2

source_name: pHGG


title: Paediatric glioblastoma cell GBM002-P2D3 H3K36me3 G34R rep1


title: PHINTL

description:
Solanum lycopersicum cv. M82
Random primed libraries
L06
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: EB-D6-ΔSL1

source_name: mESC cultured in Differentiation medium for EB induction for 6 day


title: Tissue NeoCortex GCGR-NS19 - 19.3 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Neocortex

value: NeoCortex

value: GCGR-NS19 - 19.3 pcw


title: BGC823 cells, Scramble

value: control


title: Paediatric glioblastoma cell GBM002-P2D3 H3K27me3 G34R rep1


title: MZINTS

description:
Solanum lycopersicum cv. M82
Random primed libraries
S03
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

source_name: 3-5 days-old seedling 1 cm roots tips


title: PHINTI

description:
Solanum lycopersicum cv. M82
Random primed libraries
I06
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: BGC823 cells, NO110


title: Paediatric glioblastoma cell GBM002-P1C8 input DNA G34R KO rep2

value: G34R KO


title: MZINTO

description:
Solanum lycopersicum cv. M82
Random primed libraries
O09
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: MZINTR

description:
Solanum lycopersicum cv. M82
Random primed libraries
R09
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: Paediatric glioblastoma cell GBM002-P1C8 input DNA G34R KO rep1


title: EB-D12-WT

value: WT


title: EB-D10-WT


title: Paediatric glioblastoma cell GBM002-P1C8 H3K4me3 G34R KO rep2


title: MZINTL

description:
Solanum lycopersicum cv. M82
Random primed libraries
L07
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: EB-D8-ΔSL1

source_name: mESC cultured in Differentiation medium for EB induction for 8 day


title: G48_DMEM

city: Campinas

first: Luciana

middle: Souto

last: Mofatto

state: Sao Paulo

address: R. Carl Von Linaeus

department: Genetics, Evolution and Bioagents

country: Brazil

institute: Institute of Biology - University of Campinas

data_processing:
For RNA-seq data, quality of raw data was evaluated by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Data was filtered by quality using Perl scripts, with quality cut over 20. The adapters were removed with Cutadapt (Martin 2011) and trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Filtered reads of RNA library were mapped against the human genome (GRCh38) using the pipeline Tophat2-Cufflinks (Trapnell et al. 2012).
Number of reads aligned per genes (read counts) and fragments per kilobase of transcript per million mapped reads (FPKM) were calculated by RSEM program (Li and Dewey 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM output file with transcript length, effective_length, expected_count, TPM, FPKM values for each Sample.

source_name: periodontal ligament

growth_protocol: Cell clones were cultivated in Dulbecco’s modified Eagle medium high glucose (DMEM) supplemented with 10% FBS, penicillin (100 U/ml) and streptomycin (100 mg/mL) (Gibco, USA)

extract_protocol:
TRIzol (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA from confluent C-O and C-F clones when were cultivated during 14 days. Phenol-Chloroform protocol was used to extract RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each cell clone were seeded (2x10^5cells/well) in 24-well plates with medium that was composed by Dulbecco’s modified Eagle medium high glucose (DMEM) supplemented with 10% FBS, penicillin (100 U/ml) and streptomycin (100 mg/mL) (Gibco, USA) and incubated for 24 hours. Cells were cultivated in this medium condition for 14 days, with medium change every 2-3 days.

value: Periodontal Ligament Primary Cell Clone With Osteo/Cementoblastic Phenotype


title: G13_DMEM


title: Paediatric glioblastoma cell GBM002-P1C8 H3K4me3 G34R KO rep1

value: Paediatric glioblastoma cell


title: G23_DMEM

value: Periodontal Ligament Primary Cell Clone With Fibroblastic Phenotype


title: Paediatric glioblastoma cell GBM002-P1C8 H3K36me3 G34R KO rep2

value: pHGG

value: Cancer


title: EB-D6-WT


title: MCOINTP

description:
Solanum lycopersicum cv. M82
Random primed libraries
P05
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: SlCO2pro:WPP:GFP:BLRP / SlACT2pro:mBirA


title: MCOINTM

description:
Solanum lycopersicum cv. M82
Random primed libraries
M06
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: 3-5 days


title: Neural-D6-ΔSL1

source_name: mESC cultured in Nerual differentiation medium for 6 day

value: neural progenitor cells


title: G16_DMEM


title: Paediatric glioblastoma cell GBM002-P1C8 H3K36me3 G34R KO rep1


title: MCOINTK

description:
Solanum lycopersicum cv. M82
Random primed libraries
K05
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: Roots tips


title: Neural-D6-WT


title: MCOINTI

description:
Solanum lycopersicum cv. M82
Random primed libraries
I08
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: adipocyte WT  (Bisulfite-Seq)

city: Seoul

first: Yoon Jeong

last: Park

address: San 56-1, Sillim-Dong, Gwanak-Gu

country: South Korea

institute: Seoul National University

description: WT

data_processing:
For WGBS data, sequenced reads were trimmed with adaptor sequences and performed quality control using TrimGalore v0.5.0. Then, the trimmed reads were mapped to the mouse genome (GRCm38) using Bismark v0.22.1. Cytosines that were mapped less than five reads were discarded for downstream analyses. Methylation levels of individual CpGs were determined using Bismark Methylation Extractor.
For RNA-seq data, Sequenced reads of  adipocytes were trimmed with adaptor sequences and performed quality control by using trim galore. The trimmed reads were mapped to the mouse genome (GRCm38) using Rsubread v2.0.1. Raw read counts per genes were measured using featurecounts program in Rsubread with the builid-in mouse genome annotation (GRCm38).
Genome_build: mm10
Supplementary_files_format_and_content: wig files include CpG methylation values for each sample
Supplementary_files_format_and_content: Excel file include FPKM values for every genes and every adipocyte WT replicates.

source_name: adipocytes

extract_protocol:
Briefly, primary adipocytes were lysed for 1 h in lysis buffer at 37°C and digested with 10 g/mL proteinase K for 3 h at 50°C. After cell lysis, DNA and RNA was isolated by phenol-chloroform extraction and using trizol, respectively.
For WGBS library construction, 100ng of genomic DNA was treated with the EZ DNA Methylation-Gold kit (Zymo Research, Orange, CA, USA) for bisulfite conversion. Then, the sequencing libraries were prepared according to the manufacturer’s instructions of TruSeq DNA Methylation Library Preparation Kits (Illumina, #EGMK91396). Briefly, bisulfite-converted DNA is random-primed using a polymerase to synthesize DNA containing a specific sequence tag. The 3’ ends of the newly synthesized DNA strands are tagged with a second specific sequence. The di-tagged DNA molecules are amplified using FailSafe PCR Enzyme (Epicentre, #FSE51100) and TruSeq Index PCR Primer. The final purified product is quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using the Agilent Technologies 2100 Bioanalyzer (Agilent). Finally, sequencing was performed using the HiSeqX platform (Illumina). In case of RNA-seq,   RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: epididymal adipose tissue

value: adipocytes

value: 17wks old

value: wild type


title: adipocyte Dnmt1 AKO (Bisulfite-Seq)

description: AKO

value: Dnmt1 AKO


title: Paediatric glioblastoma cell GBM002-P1C8 H3K27me3 G34R KO rep2


title: EB-D8-WT

value: Embryoid bodies


title: EXOINTP

description:
Solanum lycopersicum cv. M82
Random primed libraries
P04
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: SlPEPpro:WPP:GFP:BLRP / SlACT2pro:mBirA


title: Paediatric glioblastoma cell GBM002-P1C8 H3K27me3 G34R KO rep1

value: G34R KO


title: EXOINTS

description:
Solanum lycopersicum cv. M82
Random primed libraries
S05
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: Paediatric glioblastoma cell GBM002-P1C8 G34R G34R KO rep2


title: Paediatric glioblastoma cell GBM002-P1C8 G34R G34R KO rep1


title: Wistar WU 15

city: Pécs

first: Kovács-Valasek

last: Andrea

state: Baranya

address: Ifjusag utja 6

country: Hungary

institute: University of Pécs

data_processing:
Ion Torrent Suite Platform was used to trim the raw sequence data and remove any residual sequencing adapter fragments that remained on the 5′ or 3′ ends.
Reads were mapped to the non-coding RNAs from ENSEMBL [Rnor_6.0 (GCA_000001895.4)] using TMAP algorithm
Further analysis was carried out on Galaxy Web-based platform (Afgan, 2018) via Cufflinks, Cuffmerge and Cuffdiff (Version 2.2.1.3) application (Trapnell, 2010).
Genome_build: rno6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; gtf

organism: Rattus norvegicus

source_name: retina

growth_protocol: Animals were maintained on a 12:12 light/dark cycle and were provided with food and water ad libitum. The day of birth is recorded as postnatal day 0 (P0).

extract_protocol:
Retinas were removed, flash frozen on dry ice, and total RNA was extracted using NucleoSpin miRNA kit (Macherey–Nagel, Düren, Germany) following manufacturer's instructions.
Small RNA library construction from pooled retinal samples (N=3, in each age-group) were carried out according to the Ion Total RNA-Seq Kit v2 protocol (Revision E) with slight modification. Enzymatic reaction was performed in half reaction volume, while cleaning procedures were executed with the accurate final volume according to the protocol.

treatment_protocol: no treatment was applied

value: Wistar WU

value: retina

value: postnatal day 15


title: EXOINTM

description:
Solanum lycopersicum cv. M82
Random primed libraries
M05
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: si-EIF5A2 rep3

city: Jinan

first: Kun

last: Wang

address: WenHua west road 107

institute: Shandong University qilu hospital

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: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human ovarian cancer cell line

extract_protocol:
Total RNA was extracted from theSKOV3 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Wistar WU 10

value: postnatal day 10


title: EXOINTJ

description:
Solanum lycopersicum cv. M82
Random primed libraries
J06
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: si-EIF5A2 rep2


title: Decidua from 4th pregnancy of control mouse 2

type: RNA

city: Guangzhou

first: Ren-Wei

last: Su

state: Guangdong

address: 483 Wushan Road

department: Histology and Embryology

institute: South China Agricultural University

description: SAMPLE 5

hyb_protocol: Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94°C for 35 min prior to cRNA chip hybridization. Samples were hybridized with GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) .

scan_protocol: Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Raw data were processed using Affymetrix GCOS version 1.4

label: biotin

source_name: Decidua from Pgr+/+Notch1f/f mouse on E7.5 of 4th pregnancy

label_protocol: Approximately 1 micrograms of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol

growth_protocol: Female mice were caged with males and decidua were collected on E7.5 of pregnancy, myometrium and embryonic tissues were removed under dissecting microscope

extract_protocol: All RNA samples were isolated using the RNeasy kit from QIAGEN (Valencia, CA).

tag: mouse id

tag: gender

value: Female

value: Decidua

tag: no. of pregnancies


title: Wistar WU 7

tag: tissue

value: postnatal day 7


title: EPINTQ

description:
Solanum lycopersicum cv. M82
Random primed libraries
Q07
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: AtWERpro:WPP:GFP:BLRP / SlACT2pro:mBirA

value: 3-5 days


title: Wistar WU 5

value: postnatal day 5


title: EPINTS

description:
Solanum lycopersicum cv. M82
Random primed libraries
S07
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: Roots tips


title: Wistar WU 3

value: postnatal day 3


title: Paediatric glioblastoma cell GBM002-Parental H3K27me3 G34R rep1

value: Paediatric glioblastoma cell

value: pHGG

value: Cancer


title: Wistar WU 21

value: postnatal day 21


title: NC rep3

value: NC


title: Decidua from 1st pregnancy of control mouse 5

description: SAMPLE 11

source_name: Decidua from Pgr+/+Notch1f/f mouse on E7.5 of 1st pregnancy


title: EPINTJ

description:
Solanum lycopersicum cv. M82
Random primed libraries
J05
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: NC rep2


title: Wistar WU 1

value: Wistar WU

value: postnatal day 1


title: EPINTN

description:
Solanum lycopersicum cv. M82
Random primed libraries
N04
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: Decidua from 4th pregnancy of knock mouse 2

description: SAMPLE 3

source_name: Decidua from PgrCre/+Notch1f/f mouse on E7.5 of 4th pregnancy


title: Decidua from 4th pregnancy of control mouse 1

description: SAMPLE 4


title: Decidua from 4th pregnancy of knock mouse 1

description: SAMPLE 2


title: NC rep1


title: Decidua from 1st pregnancy of control mouse 4

description: SAMPLE 10


title: Decidua from 1st pregnancy of control mouse 3

description: SAMPLE 9


title: siNLRC5_3

city: Shanghai

first: Yefei

last: Shi

address: 1239 Siping Road

institute: Tongji University School of Medicine

data_processing:
data filtering was performed using trim Galore(version 0.3.7)
reads were aligned to the hg38 using STAR(version 2.5)
sequence assembly was performed using cufflinks(version 2.2.1)
differentially expressed genes were screened using DESeq(version 1.22.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (passage 2-8) were cultured in endothelial cells medium (Cat#1001, Sciencell) with 5% FBS (Cat#0025, ScienCell), 1% endothelial cells growth supplement (Cat#at#1052, ScienCell), 1% penicillin and streptomycin (Cat#Cat#0503, ScienCel). They were incubated at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent, Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human umbilical vein endothelial cells were transfected with siRNA (siNLRC5 or negative control, 50 nM) for 48 h. After starvation for 12 h, VEGFA-165 (50 ng/mL) was used to stimulate HUVECs for 12 h.

value: human umbilical vein endothelial cells

value: wild type


title: si-EIF5A2 rep1


title: Decidua from 1st pregnancy of knock mouse 3

description: SAMPLE 8

source_name: Decidua from PgrCre/+Notch1f/f mouse on E7.5 of 1st pregnancy

value: Female


title: Decidua from 1st pregnancy of knock mouse 2

description: SAMPLE 7

value: Decidua


title: Decidua from 1st pregnancy of knock mouse 1

description: SAMPLE 6


title: siNLRC5_1


title: ENINTN

description:
Solanum lycopersicum cv. M82
Random primed libraries
N06
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: SlSCRpro:WPP:GFP:BLRP / SlACT2pro:mBirA


title: ENINTL

description:
Solanum lycopersicum cv. M82
Random primed libraries
L05
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: siNLRC5_2


title: siNC_3

value: siNC


title: siNC_2


title: CORINTS

description:
Solanum lycopersicum cv. M82
Random primed libraries
S06
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: AtPEPpro:WPP:GFP:BLRP / SlACT2pro:mBirA

value: 3-5 days


title: ENINTS

description:
Solanum lycopersicum cv. M82
Random primed libraries
S09
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

value: Roots tips


title: siNC_1


title: FT194 OCV-1c

city: Tampa

first: Meera

last: Nanjundan

state: Florida

address: 4202 East Fowler Avenue, ISA2015

institute: University of South Florida

hyb_protocol: Incubated 20x Hyb Controls at 65°C for 5 min then Assembled Hyb Cocktail. Volume for 14 samples (µl):  2X Hyb Mix (875ul), 27.5% Formadine (256ul), DMSO (170ul), 20X Hyb Controls (88.2ul), B2 Control Oligo (3nM, 29.4ul), and water (32.2ul) for a total volume of 1.45ml. Add 103.5µl of Hyb Cocktail to 21.5µl of Poly A Biotin Labeled RNA, mix and spin. Store in -20°C for 2 hrs then process Hyb for first 4 samples, then subsequent groups of 4 every two hours (3 total). Thaw on ice, incubate 95°C for 5 min, then 45°C for 5 minutes. Then transfer to hyb dish and hybridize 48°C for 20 hours. Following hybridization, Chips were washed and stained using robotics.

scan_protocol: Chips were scanned in the Geneatlas system scan head. Generating the following files: .arr -->sample attribute (Contains sample attributes and Chip information); .AUDIT --> Audit file (Record of chip processing); .dat --> Image file (For gridding, contains the pixel densities); .cel --> Intensity file (Expression data corresponding to pixel density); .chp --> Probe file (Normalized expression data)

data_processing:
Algorithms applied using TAC. Robust Multi-Array Average (RMA) & Detection above background (DABG)
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

label: Biotin

source_name: FTSECs_Oncogenic Cocktail Virus Infected

label_protocol: FlashTag Biotin RNA Labeling Procedure: Each sample thawed on ice, 550µg was removed and diluted to 8µl with RNase free water. 2µl RNA Spike °Control Oligo's added. ATP diluted from 1mM to 2µM in 1M Tris pH 8.8. MasterMix assembled on Ice for Poly Adenylation of RNA: 10X reaction buffer (21ul), 25mM MbCl2 (21ul), 2uM ATP (14ul), and PAP Enzyme (14ul) for a total of 70ul. 5µl added to each sample, gently mixed and briefly. 37°C incubation for 15 minutes. Repeat mix and spin. Added 4 µl 5x Flash Tag Biotin HSR Ligation Mix to each. Added 2µl DNA Ligase to each sample. Repeat mix and spin. Incubate 25°C for 30 min. Add 2µl Stop solution to each sample. Stored at -20°C for ~6hrs.

growth_protocol: Human immortalized FTSECs (FT194) were provided by Dr. Ronald Drapkin (Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA). These cells were immortalized by SV40 LTAg and hTERT, and were maintained in DMEM:F12 (1:1, #15–090-CV, Corning Incorporated, Corning, NY, USA) with phenol red, supplemented with 2% Ultroser G Serum Substitute (#67042, Crescent Chemical Company, Islandia, NY, USA) and 1% penicillin-streptomycin. Long-term FAC treated and the corresponding Untreated FT194 cells were maintained in phenol red-free DMEM:F12 (1:1, #21041-025, ThermoFisher, Waltham, MA, USA) with 8% charcoal dextran-stripped FBS and 1% penicillin/streptomycin (denoted as -PR media). Cells were incubated at 37°C in a 5% CO2 environment. Cell lines were tested for mycoplasma and confirmed to be negative. Chronic iron-treated (250 nM for greater than 60 days) immortalized FT194 cells were maintained in 250 nM ferric ammonium citrate (FAC) (day 111 to 129 and p=30-38). Oncogenic cocktail virus infected (OCV) and control virus infected FT194 cells (CV) cells generated by retroviral transduction of c-MycT58A, H-RasV12A, and SV40 LTAg cDNAs were generated previously and were used herein at passages of RV+11).

extract_protocol: Total RNA was isolated from FT194 cells maintained in 250 nM FAC for 104 days (p=31) along with parental untreated FT194 cell line cultured simultaneously. In addition, total RNA was isolated from CV and OCV-infected FT194 cell lines (p=RV+12). RNA isolation was performed using the RNeasy Kit (#74106, QIAGEN, Valencia, CA, USA) according to manufacturer’s instructions. Total RNA was quantified by Nanodrop and then analyzed using the GeneChip 4.1 Array (#902409, ThermoFisher Scientific, Waltham, MA, USA).

treatment_protocol: We previously reported the generation of a transformed-like FTSEC cell line following chronic iron overload (with 250 nM Ferric Ammonium Citrate (FAC) for > 60 days in culture) which was characterized by alterations in oncogene expression (based on a focused approach) and survivability as well as oncogenically transformed FT194 cells generated by stable overexpression of c-MycT58A, H-RasV12A, and SV40 LTAg (10). To further characterize global changes in an unbiased manner, we. E prepared experimental samples from Untreated, FAC-treated, control virus (CV), and oncogenic cocktail virus (OCV) infected FT194 cells; these were utilized for both noncoding RNA microarray and proteomic analysis.

value: Immortalized Fallopian Tube Secretory Epithelial Cells (FTSECs)

value: Oncogenic Cocktail Virus Infected


title: FT194 OCV-1b


title: CORINTR

description:
Solanum lycopersicum cv. M82
Random primed libraries
R07
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: CORINTO

description:
Solanum lycopersicum cv. M82
Random primed libraries
O07
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: FT194 CV-1b

source_name: FTSECs_Control Virus Infected

value: Control Virus Infected


title: CORINTK

description:
Solanum lycopersicum cv. M82
Random primed libraries
K06
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: FT194 OCV-1a


title: Liver_Met_E

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: Michigan

address: 1500 E Medical Center Drive

department: Surgery

institute: University of Michigan

data_processing:
Samples OT_Tumor_1, Control_Scaff_B and iKras_p53_Scaff were run on HiSeq 4000. All other samples were run on the NovaSeq 6000 (Illumina). All samples were run using paired end 50 cycle reads to a depth of 100,000 reads.
The raw data were processed and aligned by the University of Michigan DNA Sequencing Core. Cellranger count version 2.2.0, 3.0.0, or 3.1.0 with default settings was used, with an initial expected cell count of 10,000.
Genome_build: Mouse samples were aligned to the mouse genome mm10-3.0.0 using Cell Ranger. Human samples were aligned to the human genome hg19-3.0.0.
Supplementary_files_format_and_content: Zipped GZ archive file containing barcodes.tsv, genes.tsv/features.tsv, and matrix.mtx files, and .h5 files for reading into R using the Seurat Pipeline.

source_name: Liver metastasis

growth_protocol: 7940b cells were grown in DMEM supplemented with 10% FBS and 1% Pen-Strep. Mouse tumors were harvested after three weeks. Biomaterial scaffolds were harvested three weeks after tumor cell implantation.

extract_protocol:
Samples were mechanically and enzymatically (Collagenase P; 1mg/mL in DMEM) digested under constant agitation. Single cell suspension was obtained by filtering through a 40 µm mesh. Dead cells were removed using MACS®Dead Cell Removal Kit (Miltenyi Biotec Inc.).
Single-cell cDNA libraries were prepared and sequenced using the 10x Genomics Platform at the University of Michigan Advanced Genomics Core.

treatment_protocol: iKras* and iKras* p53*mice were administered doxycycline chow (BioServ, F3949) to induce expression of KrasG12D for 72 hours, followed by two days of 8 intraperitoneal injections of caerulein (Sigma, 75 ?g/kg) to induce pancreatitis. Doxycycline chow was continuously administered until experiment endpoint.

tag: condition

value: pancreatic cancer (PDA)

value: human liver metastasis sample


title: HM2

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
raw data file:
HM1_HM2_US83300186_252665510917_S01_GE2_1200_Dec17_1_1.txt
Gene expression in cortex of adult female mouse

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) mouse (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

source_name: Hippocampus of MRL/MpJ mouse_replicate 2

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: hippocampus was isolated from adult female mice and  minced in ice

value: MRL/MpJ

tag: Sex

value: female

value: Hippocampus

tag: develomental stage

value: adult


title: Liver_Met_D


title: Liver_Met_C


title: FT194 CV-1a

tag: cell type


title: HM4

description:
raw data file:
HM3_HM4_US83300186_252665510917_S01_GE2_1200_Dec17_1_2.txt
Gene expression in cortex of adult female mouse

source_name: Hippocampus of MRL/MpJ mouse_replicate 4


title: HM1

source_name: Hippocampus of MRL/MpJ mouse_replicate 1


title: HK4

description:
raw data file:
HK3_HK4_US83300186_252665510916_S01_GE2_1200_Dec17_1_4.txt
Gene expression in cortex of adult female mouse

source_name: Hippocampus of Fn14koMRL mouse_replicate 4


title: FT194 FAC-1b

source_name: FTSECs_Chronic Iron treatment

value: Chronic Iron treatment


title: HM3

source_name: Hippocampus of MRL/MpJ mouse_replicate 3


title: FT194 CV-1c


title: HK1

description:
raw data file:
HK1_HK2_US83300186_252665510916_S01_GE2_1200_Dec17_1_3.txt
Gene expression in cortex of adult female mouse

source_name: Hippocampus of Fn14koMRL mouse_replicate 1


title: Liver_Met_B


title: HK3

source_name: Hippocampus of Fn14koMRL mouse_replicate 3


title: JM121-250315-IP_S37_L002_R1_001 [SB5]

city: Edgebaston

first: Saverio

last: Brogna

state: West midlands

address: School of Biosciences, University of Birmingham

department: School of Biosciences

institute: University of Birmingham

description:
Rpb3
Pol II core subuni

data_processing:
Trimming using Trimmomatic (SE setting, sliding window and minimum read length set to 4:22 and 32, respectively)
Aligned using Bowtie2, with "--no-unal" option
Single base resolution coverage for each sample was obtained using custom Python scripts, which also carried out normalisations for metagene plots
Genome_build: Schizosaccharomyces pombe (Ensembl EF2)
Supplementary_files_format_and_content: ChIPseqProcessedDataTable.txt : Tab-delimited table, with each gene-averaged, base specific coverage values of each of the 4 immunoprecipitation files (normalised by the control file and sequencing depth), corresponding to the y-axis values in the main metagene plot (figure 4A), with one file per row and each of the corresponding position values (x-axis values in the metagene plots) in the first row, starting with the 1000bp upstream of the TSS, then 0-100% through the gene body, and ending with the 1000bp downstream of the TES

organism: Schizosaccharomyces pombe

source_name: wt

growth_protocol: 30ºC in 400 ml YES with an OD600 of 0.8

extract_protocol:
DNA were purified using MinElute PCR Purification Kit (QIAGEN).
10 ng of DNA was used for DNA library construction with the NEBNext Ultra II DNA Library Prep Kit (New England Biolab E7645L), indexed using NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S) and sequenced simultaneously using a Illumina HiSeq4000 System.

value: wt

tag: antibody

value: antiFlag M2 - sigma


title: Liver_Met_A


title: JM131-140115-IP_S35_L002_R1_001 [SB3]

description:
Rpb3
Pol II core subuni

source_name: upf1 deletion

tag: genotype

value: upf1 deletion


title: JM94-090215-Input_S42_L002_R1_001 [SB10]


title: JM121-140115-IP_S33_L002_R1_001 [SB1]

description:
Rpb3
Pol II core subuni


title: FT194 FAC-1a


title: FT194 UNT-1b

source_name: FTSECs_No treatment

value: No treatment


title: FT194 UNT-1c


title: JM131-250315-IP_S39_L002_R1_001 [SB7]

description:
Rpb3
Pol II core subuni


title: FT194 UNT-1a


title: FT194 FAC-1c


title: HK2

source_name: Hippocampus of Fn14koMRL mouse_replicate 2


title: Enriched monocytes (healthy infants and KD infants)

city: Hangzhou

first: Fangqi

last: Gong

address: Binsheng Road

institute: Children's Hospital, Zhejiang University School of Medicine

description:
Enriched monocytes - HI1 (female)
Enriched monocytes - HI2 (male)
Enriched monocytes - KD1 (male)
Enriched monocytes - KD2 (female)

data_processing:
Raw sequencing reads of cDNA library and sample tag library were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline (Early access), which included filtering by reads quality, annotating reads, annotating molecules, determining putative cells and generating single-cell expression matrix. Briefly, read pairs with low sequencing quality were firstly removed. The quality-filtered R1 reads were analyzed to identify sequence of cell labels, UMI sequence, and poly-dT tail sequence, meanwhile the quality-filtered R2 reads were mapped to Genome Reference Consortium Human Build 38 (GRCh38) using STAR (version 2.5.2b) in reads annotation step.
Further adjustment was performed with the recursive substitution error correction (RSEC) and distribution-based error correction (DBEC) algorithms to remove artifact molecules due to amplification bias in molecules annotation step. Putative cells were distinguished from background noise with second derivative analysis in putative cell determination step.
Finally, putative cells information was combined together with molecules adjusted by the recursive substitution error correction and distribution-based error correction algorithms to generate a single-cell expression matrix.
The pipeline also determined sample origin of every single cells via sample determination algorithm according to the sequencing reads of sample tag library. The algorithm classified all putative single cell into three categories: “multiplet”, two or more sample tag exceed their minimum thresholds, indicating more than one actual cell in one microwell; “undetermined”, not enough sample tag reads for determining the sample origin; “sample tag 01 - 12”, only one sample tag exceed their minimum thresholds. Among all the output files, matrix for UMI counts per cell corrected by DBEC and sample tag annotation result were used for downstream clustering analysis. The 8880 data rows correspond to the four starting samples, which was labled with Sample Tag 6 ("Enriched monocytes - HI1"), Sample Tag 7 ("Enriched monocytes - HI2"), Sample Tag 8 ("Enriched monocytes - KD1") and Sample Tag 9 ("Enriched monocytes - KD2") respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: Peripheral blood

extract_protocol:
Peripheral blood samples (2 ml each sample) were collected from 2 healthy infants and 2 KD patients at acute stage before intravenous immunoglobulin treatment. Peripheral blood mononuclear cells were isolated using Ficoll-Paque PLUS (GE Healthcare Biosciences AB) according to the manufacturer’s protocol. Then peripheral blood monocytes were separated from peripheral blood mononuclear cells by negative magnetic sorting techniques using Pan Monocyte Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s instructions.
Enriched monocytes of each sample were sequentially labeled with BD Human Single-Cell Multiplexing Kit which utilizing an innovative antibody-oligo technology mainly to provide higher sample throughput and eliminate batch effect for single cell library preparation and sequencing. A set of 12 antibodies in this kit recognize the same universally expressed cell-surface antigen of human cells. Each antibody is conjugated with a sample tag, a unique 45-nucleotide barcode sequence. Cells from each sample were labeled by antibodies with different sample tags respectively before pooling all samples together. The following sample Tags were used: Sample Tag 6—TTACCCGCAGGAAGACGTATACCCCTCGTGCCAGGCGACCAATGC (used to lable "Enriched monocytes - HI1"); Sample Tag 7—TGTCTACGTCGGACCGCAAGAAGTGAGTCAGAGGCTGCACGCTGT (used to lable "Enriched monocytes - HI2"); Sample Tag 8—CCCCACCAGGTTGCTTTGTCGGACGAGCCCGCACAGCGCTAGGAT (used to lable "Enriched monocytes - KD1"); Sample Tag 9—GTGATCCGCGCAGGCACACATACCGACTCAGATGGGTTGTCCAGG (used to lable "Enriched monocytes - KD2"). BD Rhapsody Express system was utilized for single cell transcriptomics capturation. Pooled samples were then loaded in one BD Rhapsody™ Cartridge that was primed and treated strictly following the manufacturers protocol (BD Biosciences).  Then cells were lysed, cell capture beads were retrieved and washed prior to performing reverse transcription and treatment with exonuclease I. Transcriptomic and sample tag information of single cells was obtained through BD Rhapsody System. Microbeads-captured single cell transcriptome and sample tag sequences were generated into cDNA library and sample tag library separately containing cell labels and unique molecular identifiers (UMI) information respectively.
OTHER: sample tag library, AMPLICON; cDNA library, RNA-Seq.

value: 10 months

value: monocytes


title: HL4

description:
raw data file:
HL3_HL4_US83300186_252665512245_S01_GE2_1200_Dec17_1_4.txt
Gene expression in cortex of adult female mouse

source_name: Hippocampus of MRL/lpr mouse_replicate 4

value: MRL/lpr


title: HL3

source_name: Hippocampus of MRL/lpr mouse_replicate 3


title: HL1

description:
raw data file:
HL1_HL2_US83300186_252665512245_S01_GE2_1200_Dec17_1_3.txt
Gene expression in cortex of adult female mouse

source_name: Hippocampus of MRL/lpr mouse_replicate 1


title: HL2

source_name: Hippocampus of MRL/lpr mouse_replicate 2


title: S. aureus and HUVEC 16hpi, Replicate 2

status: Public on Mar 23 2021

city: Hoersholm

first: Christian

last: Garde

address: Dr Neergaards Vej 5F

country: Denmark

institute: Evaxion Biotech

description:
4994
29213.tsv.gz, HUVEC.tsv.gz

data_processing:
Fastq files were preprocessed using cutadapt and base qualities checked using fastqc.
The reads were mapped against the human reference genome hg38 using STAR. Unmapped reads were mapped to the NC_007795.1 reference genome using bwa mem.
Gene read coverages were computed using featureCounts.
Differential gene expression analysis was conducted using the DESeq2 workflow with the BH corrected Wald test and log2FC skrinkage
Genome_build: hg38, NC_007795.1
Supplementary_files_format_and_content: Tab separated text files with gene read coverages.

organism:
Staphylococcus aureus
Homo sapiens

source_name: ATCC 29213, HUVEC

growth_protocol: The Staphylococcus aureus ATCC29213 reference strain and primary human umbilical cord endothelial cells (HUVEC from pooled donors, passage 2-3, PromoCell) were used for all experiments. Prior to experiments, the bacteria were grown until exponential growth phase in tryptic soy broth (2½h at 37°C), and bacterial stock solution could then be prepared by centrifugation and resuspension of pellet in phosphate buffered saline (PBS) followed by adjustment to OD600=0.1. HUVECs were grown until confluence in basal medium (Endothelial Cell Growth Medium 2, PromoCell) with fetal bovine serum (FBS) and penicillin-streptomycin (PS) and then split into microtiter plates. Prior to experiments, the confluent HUVEC microtiter plates were washed 3 times in PBS and filled with 0.5 ml basal medium+FBS without PS.

extract_protocol:
Pellets were resuspended in 700 μl acetate buffer (20 mM NaOAc, 1 mM EDTA, 0.5% SDS, pH 4.5) and transferred to FastPrep tubes containing lysing matrix B. Cells were lysed in a Thermo Savant FastPrep FP120 Cell Homogenizer at 6.0 m/sec for 3 x 40 sec with 1 min pause on ice in between runs, and then centrifuged for 5 min at 20,000 g. Lysate was transferred to tubes containing 500 μl phenol solution (2:1 phenol in water adjusted to pH 4.5 with NaOAc) and 100 μl chloroform followed by incubation at 65 °C at 1100 rpm in a thermomixer for 15 min with vortexing every 2 min. After centrifugation, the aqueous phase was transferred into tubes containing 500 μl chloroform followed by vortexing, centrifugation, and transferring to new tubes. The RNA was precipitated using 96% EtOH and 10vol% 3M NaOAc on ice for ≥1 hour. Tubes were centrifuged for 60 min at 4°C, and pellets were washed in ice cold 70% EtOH followed by centrifugation for 10 min. Supernatant was removed and pellets were then air-dried and dissolved in sterile ddH2O. RNA quantity was measured using Nanodrop spectrophotometer, and RNA quality was then verified by fragment analysis using a Fragment Analyzer (Agilent), followed by RiboZero Gold (MRZE724, Epidemiology/Illumina) treatment on the 3 samples from each group to remove both human and bacterial rRNA.
After DNase treatment, library preparation was performed using the NebNext® UltraTM Library prep kit (NEB) followed by quality assessment by the fragment analyzer

treatment_protocol: Microtiter plates were inoculated with 20 μl of bacterial stock suspension corresponding to a multiplicity of infection (MOI) of 16, followed by centrifugation at 300g for 5 min to sediment the bacteria. After 1½ hours post-infection (hpi), wells were supplemented with lysostaphin (10 μg/ml) + gentamicin (100 μg/ml). HUVEC samples were collected by washing 3 times in PBS followed by trypsination for 10 min, centrifugation, and washing the pellet followed by centrifugation and resuspension of the pellet in 100 μl PBS. Samples were then snap-frozen in liquid nitrogen and kept at -80°C until RNA isolation.

tag: group

value: Sixteen hours post infection

tag: s. aureus strain


title: S. aureus and HUVEC 16hpi, Replicate 3

description:
4995
29213.tsv.gz, HUVEC.tsv.gz


title: S. aureus and HUVEC 16hpi, Replicate 1

description:
4993
29213.tsv.gz, HUVEC.tsv.gz


title: S. aureus and HUVEC 1hpi, Replicate 2

description:
4991
29213.tsv.gz, HUVEC.tsv.gz

value: One hour post infection


title: Plasma_ESCC patient_rep2

first: Fen

last: Liu

address: Youanmenwai Street

department: Department of Epidemiology and Health Statistics

institute: Capital Medical University

description: circular RNAs expression in plasma from ESCC patients

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

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

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 5 out of 10 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: Plasma, ESCC patient, pre-operative

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from 1mL plasma using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacture’s protocol. The integrity of RNA was evaluated by 1% denaturing agarose gel electrophoresis. The concentration and purity of total RNA were then measured using the NanoDrop ND-1000 spectrophotometer (Wilmington, DE, USA).

treatment_protocol: 5 mL venous blood (usually in the morning) were collected from each participant in  EDTA tubes. Blood samples were allowed to stand for 1 hour at room temperature or kept at 4℃ and processed within 24 hours after collection and plasma separation was accomplished by centrifugation at 820g for 10 min at 4℃. Then the plasma samples were transferred into new tubes and stored at -80℃ for next procedure.

value: plasma

value: male

tag: disease state

value: ESCC


title: S. aureus and HUVEC 1hpi, Replicate 1

description:
4990
29213.tsv.gz, HUVEC.tsv.gz


title: Plasma_Healthy control_rep4

description: circular RNAs expression in plasma from healthy controls

source_name: Plasma, Healthy control, Matched by age and sex

value: control


title: Plasma_ESCC patient_rep1


title: Plasma_ESCC patient_rep4

value: female


title: Plasma_Healthy control_rep1


title: Plasma_Healthy control_rep3


title: Plasma_ESCC patient_rep5


title: Plasma_ESCC patient_rep3


title: Plasma_Healthy control_rep2


title: Plasma_Healthy control_rep5


title: Mammary tumor vs. adjacent normal mammary gland, replicate 3 dye swap

city: Houston

first: Yue

last: Lu

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: Biological replicate 3 of 4 dye swap. Mammary tumors arose in parous BK5.ATF3 transgenic females between 6 and 12 months of age, and animals were sacrificed when their tumors reached 1.5 cm in their longest dimension. Mammary tumor was directly compared to adjacent normal mammary gland.

hyb_protocol: Labeled samples were mixed pairwise and Hybridized to the array (provided slides by Exiqon) using Tecan HS400 following the manufacturer's instructions.

scan_protocol: Scanned with GenePix 4200A 01 scanner. Images were quantified using GenePix Pro 6.0.1.25 software.

data_processing: R limma package used as follows: Low quality and control spots removed, between array normalization using vsn performed on background subtracted data. After within-array duplicate spot correlation was determined, fold change estimates and standard errors calculated with lmFit. Empirical Bayes smoothing was applied to standard error values and p-values were adjusted with Benjamini and Hochberg method.

source_name: adjacent normal mammary gland

label_protocol: RNA molecules labeled using Hy5 or Hy3 fluorescent-labed using miRCURY LNA microRNA Array.

growth_protocol: Transgenic female BK5.ATF3 mice were bred and raised in an A AALAC-accredited facility on standard lab chow.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions

treatment_protocol: Females were allowed to breed and raise one litter of pups. Mammary tumors arose in most transgenic mice between 6 months and 12 months of age. When tumors reached 1.5 cm in length, animals were sacrificed under CO2 and the tumor was quickly dissected. Adjacent normal mammary glands were obtained from each tumor-bearing mouse.

value: normal

value: BK5.ATF3 transgenic

source_name: mammary tumor

value: tumor


title: S. aureus and HUVEC 1hpi, Replicate 3

description:
4992
29213.tsv.gz, HUVEC.tsv.gz


title: Mammary tumor vs. adjacent normal mammary gland, replicate 3.

description: Biological replicate 3 of 4. Mammary tumors arose in parous BK5.ATF3 transgenic females between 6 and 12 months of age, and animals were sacrificed when their tumors reached 1.5 cm in their longest dimension. Mammary tumor was directly compared to adjacent normal mammary gland.


title: Mammary tumor vs. adjacent normal mammary gland, replicate 4.

description: Biological replicate 4 of 4. Mammary tumors arose in parous BK5.ATF3 transgenic females between 6 and 12 months of age, and animals were sacrificed when their tumors reached 1.5 cm in their longest dimension. Mammary tumor was directly compared to adjacent normal mammary gland.


title: Mammary tumor vs. adjacent normal mammary gland, replicate 2.

description: Biological replicate 2 of 4. Mammary tumors arose in parous BK5.ATF3 transgenic females between 6 and 12 months of age, and animals were sacrificed when their tumors reached 1.5 cm in their longest dimension. Mammary tumor was directly compared to adjacent normal mammary gland.


title: AHF070

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

description: Bacterial rRNA amplified and sequenced

data_processing:
During the read pre-processing step, sequencing adapters and PCR primers were first removed using the ILLUMINACLIP step in Trimmomatic(v0.35) run in paired-end mode.
Paired-end reads were then joined using FLASh (v1.2.11) with a maximum overlap of 250 bp, before quality trimming (qtrim = rl; trimq = 30) using BBDuk of BBTools (v35.85) and finally filtered for at least 50 bp using the MINLEN step in Trimmomatic run in single-end mode.
After preprocessing, 16S samples were mapped against the SILVA (v.123) database.
The pick_closed_reference_otus.py script in QIIME (v1.8.0), implementing the usearch (v7.0.1090) algorithm, was used for OTU picking, enabling reverse strand matching and requiring a minimum similarity of 99%.
Genome_build: NA
Supplementary_files_format_and_content: Operational taxonomic units (OTUs) occurring only once (singletons) were removed from the entire dataset. Samples with fewer than 500 reads were removed. Alpha- (Shannon and Chao1 indices) and beta-diversity analyses (Bray-Curtis and weighted UniFrac distances) were performed in QIIME(Caporaso et al., 2010) (v1.8.0) on OTU tables that had been rarefied to 1,000 reads per sample for 10 times.

organism: human gut metagenome

source_name: Human fetal tissues

extract_protocol:
DNA from fetal tissues was extracted according to the protocol as previously described(Rancati et al., 2008), except that the volume of Breaking Buffer and phenol/chloroform/IAA used was 400μL. Three consecutive phenol/chloroform/isoamylalcohol extractions were performed to reduce protein contamination. A final chloroform extraction was performed to remove phenol contamination, prior to ethanol precipitation. RNA contamination was removed by treating the gDNA samples with 70 ng/μl affinity-purified RNAse A (Ambion) for 1 h at +37 °C. Final yields were quantified with a ND- 1000 spectrophotometer (NanoDrop). Fetal microbiome reagent and environmental controls were concurrently performed during the DNA extraction process.
Genomic DNA isolated from fetal tissues and control samples were treated with McrBC restriction enzyme (New England BioLabs) according to manufacturer’s instructions, to remove host DNA and to enrich for microbial DNA. The treated DNA samples were purified using 0.8X ratio of AMPure XP beads (Beckman Coulter). The McrBC-treated, purified gDNA was quantified using Quant-iT TM Picogreen® dsDNA Assay kit (Invitrogen). For amplification of the 16S rRNA gene-variable regions three rounds of amplification were performed using 100ng of McrBC-treated gDNA with LongAmp Taq DNA polymerase (New England Biolabs) according to manufacturer’s instructions. The first step aimed at enriching microbial sequences was performed using primers that amplify V2-V6 regions (Table S3). PCR cycling parameters consisted of initial denaturation step for 30s at 94°C, followed by 12 cycles of 15s at 94°C, 30s at 45°C, and 1min at 65°C with a final extension for 10 min at 65°C. Subsequently a nested PCR was performed targeting V4-V5 regions using the enriched V2-V6 amplicon as template. PCR Cycling parameters for amplifying V4-V5 regions were similar to V2- V6 PCR cycling profile, except that the extension was for 30s at 65 °C. The final amplification step involved addition of barcodes for identifying, de-multiplexing individual samples and Illumina adapter sequences to the V4-V5 enriched product using communal primers. Communal PCR amplification consisted of initial denaturation step for 30 s at 94 °C, followed by 30 cycles of 15s at 94 °C, 30s at 45°C, and 1 min at 65°C with a final extension for 10 min at 65°C. Equimolar concentrations of the prepared libraries were pooled and electrophoresed using 1% agarose gel. Pooled amplicon libraries were gel-purified using the Qiaquick Gel Extraction Kit (Qiagen). Integrity of gel-purified libraries were validated using the High Sensitivity DNA kit (Agilent Technologies). The libraries were quantified using KAPA Library Quantification Kit (Kapa Biosystems) to ascertain the loading concentration and sequenced on a HiSeq 2500 System (Illumina) operated in Rapid Run Mode to generate 2 ×250 bp paired-end reads
16S rRNA sequencing on HiSeq 2500 System (Illumina)

value: Fetal gut, lungs, skin, thymus, spleen and placenta

value: Bacterial


title: AHF068

description: Bacterial rRNA amplified and sequenced


title: Mammary tumor vs. adjacent normal mammary gland, replicate 1 dye swap

description: Biological replicate 1 of 4 dye swap. Mammary tumors arose in parous BK5.ATF3 transgenic females between 6 and 12 months of age, and animals were sacrificed when their tumors reached 1.5 cm in their longest dimension. Mammary tumor was directly compared to adjacent normal mammary gland.


title: AHF073

description: Bacterial rRNA amplified and sequenced


title: AHF072

description: Bacterial rRNA amplified and sequenced


title: AHF067

description: Bacterial rRNA amplified and sequenced


title: AHF071

description: Bacterial rRNA amplified and sequenced


title: AHF066

description: Bacterial rRNA amplified and sequenced


title: Mammary tumor vs. adjacent normal mammary gland, replicate 2 dye swap

description: Biological replicate 2 of 4 dye swap. Mammary tumors arose in parous BK5.ATF3 transgenic females between 6 and 12 months of age, and animals were sacrificed when their tumors reached 1.5 cm in their longest dimension. Mammary tumor was directly compared to adjacent normal mammary gland.


title: AHF069

description: Bacterial rRNA amplified and sequenced


title: AHF065

description: Bacterial rRNA amplified and sequenced


title: AHF063

description: Bacterial rRNA amplified and sequenced


title: AHF060

description: Bacterial rRNA amplified and sequenced


title: AHF061

description: Bacterial rRNA amplified and sequenced


title: AHF064

description: Bacterial rRNA amplified and sequenced


title: AHF057

description: Bacterial rRNA amplified and sequenced


title: AHF058

description: Bacterial rRNA amplified and sequenced


title: AHF059

description: Bacterial rRNA amplified and sequenced


title: AHF055

description: Bacterial rRNA amplified and sequenced


title: AHF056

description: Bacterial rRNA amplified and sequenced


title: AHF052

description: Bacterial rRNA amplified and sequenced


title: AHF049

description: Bacterial rRNA amplified and sequenced


title: AHF047

description: Bacterial rRNA amplified and sequenced


title: AHF044

description: Bacterial rRNA amplified and sequenced


title: AHF046

description: Bacterial rRNA amplified and sequenced


title: Mammary tumor vs. adjacent normal mammary gland, replicate 1.

description: Biological replicate 1 of 4. Mammary tumors arose in parous BK5.ATF3 transgenic females between 6 and 12 months of age, and animals were sacrificed when their tumors reached 1.5 cm in their longest dimension. Mammary tumor was directly compared to adjacent normal mammary gland.


title: AHF045

description: Bacterial rRNA amplified and sequenced


title: AHF053

description: Bacterial rRNA amplified and sequenced


title: AHF041

description: Bacterial rRNA amplified and sequenced


title: AHF039

description: Bacterial rRNA amplified and sequenced


title: AHF042

description: Bacterial rRNA amplified and sequenced


title: AHF036

description: Bacterial rRNA amplified and sequenced


title: AHF043

description: Bacterial rRNA amplified and sequenced


title: AHF035

description: Bacterial rRNA amplified and sequenced


title: AHF034

description: Bacterial rRNA amplified and sequenced


title: AHF062

description: Bacterial rRNA amplified and sequenced


title: AHF032

description: Bacterial rRNA amplified and sequenced


title: AHF031

description: Bacterial rRNA amplified and sequenced


title: AHF030

description: Bacterial rRNA amplified and sequenced


title: AHF029

description: Bacterial rRNA amplified and sequenced


title: AHF028

description: Bacterial rRNA amplified and sequenced


title: AHF026

description: Bacterial rRNA amplified and sequenced


title: AHF025

description: Bacterial rRNA amplified and sequenced


title: AHF050

description: Bacterial rRNA amplified and sequenced


title: AHF048

description: Bacterial rRNA amplified and sequenced


title: AHF027

description: Bacterial rRNA amplified and sequenced


title: AHF040

description: Bacterial rRNA amplified and sequenced


title: AHF038

description: Bacterial rRNA amplified and sequenced


title: AHF037

description: Bacterial rRNA amplified and sequenced


title: AHF024

description: Bacterial rRNA amplified and sequenced


title: AHF022

description: Bacterial rRNA amplified and sequenced


title: AHF023

description: Bacterial rRNA amplified and sequenced


title: AHF005

description: Bacterial rRNA amplified and sequenced


title: AHF021

description: Bacterial rRNA amplified and sequenced


title: AHF008

description: Bacterial rRNA amplified and sequenced


title: ENINTR

first: Siobhan

last: Brady

address: 451 Health Sciences Dr

institute: University of California Davis

description:
Solanum lycopersicum cv. M82
Random primed libraries
R06
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

data_processing:
Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to ITAG3.2 transcriptome (cDNA) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values.
ATAC-seq raw reads were aligned to each species' corresponding genome using Bowtie2 with default parameters.
ATAC-seq mapped reads were filtered to remove 1) reads that mapped to organelle genomes and 2) reads with a mapping quality score of q<2.
Transposase Hypersensitive Sites were identified using the Findpeaks function of the HOMER package, with the parameters "-minDist 150" "-region" and "-regionRes 1".
Filtered ATAC-seq bam files for each sample were converted to the bigwig format using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
For accurate visualization, all filtered ATAC-seq bam files for a given tissue were scaled to the same number of reads and combined per condition to create a single merged bam file for a condition in a tissue type. The merged bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Filtered ATAC-seq bam files from genomic DNA samples were scaled to the total number of reads present in the merged bam files for a given tissue type. The scaled bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Rice TRAP-seq. Barcoded libraries were pooled together and sequenced on Illumina HiSeq 3000 at the UC Davis DNA Technologies Core to obtain 50-bp reads.
Rice TRAP-seq. R/Bioconductor (version 3.2.1) and FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) were used in short read quality control and grep for filtering of oligo dT for PolyA RNA libraries.
Rice TRAP-seq. Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to IRGSP-1.0 transcriptome (CDS, https://rapdb.dna.affrc.go.jp/index.html) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values. Splice variants were summed to assess transcript values.
Genome_build: Tomato: SOLANUM LYCOPERSICUM: ITAG3.20 (ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/)
Genome_build: Rice: IRGSP-1.0 (https://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Supplementary_files_format_and_content: .bed files contain Transposase Hypersensitive Site (THS) coordinates for individual samples or for each tissue type they are organized as (All) all the replicated THSs identified in that sample set in either control or submergence samples, (Up) THSs upregulated in submergence samples, and (Down) THSs downregulated in submergence samples.
Supplementary_files_format_and_content: .bw files contain aligned reads for individual samples, or combined samples for a specific condition of a given tissue, at a resolution of 1 bp bin sized windows.
Supplementary_files_format_and_content: .csv files contain raw counts.

source_name: 3-5 days-old seedling 1 cm roots tips

extract_protocol:
extract protocol 1: Translating Ribosome Affinity Purification (TRAP) was performed as previously described (Reynoso et al, 2019).
extract protocol 2: Nuclei were purified from frozen and pulverized tissue as previously described (Reynoso et al, 2019). Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of  streptavidin-coated beads (NEB) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet  to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
extract protocol 3: For Rice: TRAP was performed as previously described (Reynoso et al, 2019)
library construction protocol 1: RNA-seq libraries  were prepared from poly(A)+ selected total and TRAP mRNA as described by Townsley et al. (2014) for random primer primed libraries.
library construction protocol 2: RNA-seq libraries  were prepared from poly(A)+ selected total and TRAP mRNA as described by Townsley et al. (2014) for random primer primed libraries.

tag: cultivar

tag: line

value: SlSCRpro:WPP:GFP:BLRP / SlACT2pro:mBirA

value: 3-5 days

value: Roots tips


title: AHM011

description: Bacterial rRNA amplified and sequenced


title: AHM008

description: Bacterial rRNA amplified and sequenced


title: AHM014

description: Bacterial rRNA amplified and sequenced


title: AHM009

description: Bacterial rRNA amplified and sequenced


title: AHM007

description: Bacterial rRNA amplified and sequenced


title: AHM004

description: Bacterial rRNA amplified and sequenced


title: AHM012

description: Bacterial rRNA amplified and sequenced


title: AHF003

description: Bacterial rRNA amplified and sequenced


title: AHF004

description: Bacterial rRNA amplified and sequenced


title: AHM002

description: Bacterial rRNA amplified and sequenced


title: AHM005

description: Bacterial rRNA amplified and sequenced


title: AHM003

description: Bacterial rRNA amplified and sequenced


title: AHH20860

description: Bacterial rRNA amplified and sequenced


title: AHM001

description: Bacterial rRNA amplified and sequenced


title: AHH20859

description: Bacterial rRNA amplified and sequenced


title: AHM013

description: Bacterial rRNA amplified and sequenced


title: AHM006

description: Bacterial rRNA amplified and sequenced


title: AHH20855

description: Bacterial rRNA amplified and sequenced


title: AHH20858

description: Bacterial rRNA amplified and sequenced


title: AHH20857

description: Bacterial rRNA amplified and sequenced


title: AHH20853

description: Bacterial rRNA amplified and sequenced


title: AHH20851

description: Bacterial rRNA amplified and sequenced


title: AHH20850

description: Bacterial rRNA amplified and sequenced


title: AHH20854

description: Bacterial rRNA amplified and sequenced


title: AHH20852

description: Bacterial rRNA amplified and sequenced


title: AHF033

description: Bacterial rRNA amplified and sequenced


title: AHH20856

description: Bacterial rRNA amplified and sequenced


title: AHH20849

description: Bacterial rRNA amplified and sequenced


title: AHH20847

description: Bacterial rRNA amplified and sequenced


title: AHH20844

description: Bacterial rRNA amplified and sequenced


title: AHH20846

description: Bacterial rRNA amplified and sequenced


title: AHH20848

description: Bacterial rRNA amplified and sequenced


title: AHH20843

description: Bacterial rRNA amplified and sequenced


title: AHH20842

description: Bacterial rRNA amplified and sequenced


title: AHH20845

description: Bacterial rRNA amplified and sequenced


title: AHH20838

description: Bacterial rRNA amplified and sequenced


title: AHH20841

description: Bacterial rRNA amplified and sequenced


title: AHH20839

description: Bacterial rRNA amplified and sequenced


title: AHH20840

description: Bacterial rRNA amplified and sequenced


title: AHF361

description: Bacterial rRNA amplified and sequenced


title: AHH20837

description: Bacterial rRNA amplified and sequenced


title: AHF360

description: Bacterial rRNA amplified and sequenced


title: AHF359

description: Bacterial rRNA amplified and sequenced


title: AHF358

description: Bacterial rRNA amplified and sequenced


title: AHF357

description: Bacterial rRNA amplified and sequenced


title: AHF344

description: Bacterial rRNA amplified and sequenced


title: AHF348

description: Bacterial rRNA amplified and sequenced


title: AHF356

description: Bacterial rRNA amplified and sequenced


title: AHF347

description: Bacterial rRNA amplified and sequenced


title: AHF349

description: Bacterial rRNA amplified and sequenced


title: AHF353

description: Bacterial rRNA amplified and sequenced


title: AHF342

description: Bacterial rRNA amplified and sequenced


title: AHF346

description: Bacterial rRNA amplified and sequenced


title: AHF355

description: Bacterial rRNA amplified and sequenced


title: AHF341

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 27°C_Mature stage, T28_M3

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Genome mapping against Arabidopsis reference transcriptome Araport v11 using Salmon algorithm
Clean reads were mapped to the reference transcritome araport v11  and quantified using Salmon algorithm to calculate gene expression level in counts
Genome_build: Araport11_genes.201606.cdna.fasta downlaoded from arabidopsis.org
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample

organism: Arabidopsis thaliana

growth_protocol: Plants were grown in a culture room in trays containing a sterile  soil at 20°C/18°C, with a 16 h light photoperiod at 200 μmol photons m -²s-².

extract_protocol:
Total RNAs were extracted from the frozen grinded tissues lots using the Macherey-Nagel NucleoSpin RNA Plus kit (Macherey-Nagel, GmbH & Co. KG, Germany) following manufacturer’s instructions
Samples were sent to BGI, Hong Kong, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on Illumina Hiseq 2500 platform, generating an average 24M reads of 50bp per sample

treatment_protocol: After bolting and first flowers, control plants were grown at the same temperature condition 24°C/22°C (23°C) but stressed plants were transferred to another culture room with mild stress conditions 26°C/24°C (25°C) and severe stress conditions 28°C/26°C (27°C)

tag: ecotype

tag: developmental stage

value: seed Mature stage

tag: treatment

value: growing severe heat stress conditions 27°C

value: entire seed


title: AHF345

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 27°C_Bent stage, T28_B2

value: seed Bent stage


title: RNAs from seed produced at 27°C_Mature stage, T28_M1


title: RNAs from seed produced at 27°C_Mature stage, T28_M2


title: RNAs from seed produced at 27°C_Bent stage, T28_B3


title: AHF337

description: Bacterial rRNA amplified and sequenced


title: AHF338

description: Bacterial rRNA amplified and sequenced


title: AHF340

description: Bacterial rRNA amplified and sequenced


title: AHF335

description: Bacterial rRNA amplified and sequenced


title: AHF334

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 27°C_Bent stage, T28_B1


title: AHF336

description: Bacterial rRNA amplified and sequenced


title: AHF343

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 27°C_Heart stage, T28_H3

value: seed heart stage


title: AHF333

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 27°C_Heart stage, T28_H2


title: AHF332

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 25°C_Mature stage, T26_M1

value: growing mild heat stress conditions 25°C


title: RNAs from seed produced at 25°C_Mature stage, T26_M2


title: RNAs from seed produced at 25°C_Mature stage, T26_M3


title: RNAs from seed produced at 25°C_Bent stage, T26_B3


title: RNAs from seed produced at 27°C_Heart stage, T28_H1


title: AHF319

description: Bacterial rRNA amplified and sequenced


title: AHF321

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 25°C_Bent stage, T26_B2


title: AHF320

description: Bacterial rRNA amplified and sequenced


title: AHF318

description: Bacterial rRNA amplified and sequenced


title: AHF317

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 25°C_Heart stage, T26_H2


title: RNAs from seed produced at 25°C_Bent stage, T26_B1


title: AHF304

description: Bacterial rRNA amplified and sequenced


title: AHF303

description: Bacterial rRNA amplified and sequenced


title: AHF302

description: Bacterial rRNA amplified and sequenced


title: AHF331

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 23°C_Mature stage, T24_M1

value: growing control conditions 23°C


title: AHF339

description: Bacterial rRNA amplified and sequenced


title: AHF301

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 23°C_Bent stage, T24_B3


title: AHF299

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 23°C_Bent stage, T24_B1


title: AHF300

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 23°C_Bent stage, T24_B2


title: AHF316

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 25°C_Heart stage, T26_H3


title: AHF315

description: Bacterial rRNA amplified and sequenced


title: AHF290

description: Bacterial rRNA amplified and sequenced


title: AHF289

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 23°C_Heart stage, T24_H1


title: RNAs from seed produced at 23°C_Mature stage, T24_M3


title: AHF305

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 23°C_Heart stage, T24_H2


title: AHF287

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 23°C_Mature stage, T24_M2


title: RNAs from seed produced at 25°C_Heart stage, T26_H1


title: AHF288

description: Bacterial rRNA amplified and sequenced


title: AHF286

description: Bacterial rRNA amplified and sequenced


title: AHF285

description: Bacterial rRNA amplified and sequenced


title: AHF283

description: Bacterial rRNA amplified and sequenced


title: AHF284

description: Bacterial rRNA amplified and sequenced


title: AHF269

description: Bacterial rRNA amplified and sequenced


title: RNAs from seed produced at 23°C_Heart stage, T24_H3


title: AHF268

description: Bacterial rRNA amplified and sequenced


title: AHF267

description: Bacterial rRNA amplified and sequenced


title: AHF265

description: Bacterial rRNA amplified and sequenced


title: AHF264

description: Bacterial rRNA amplified and sequenced


title: AHF266

description: Bacterial rRNA amplified and sequenced


title: hiMyc miR-32 vs. hiMyc dye-swap replicate

city: Kuopio

first: Leena

last: Latonen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

hyb_protocol: The labeled RNA was purified using Quiagen Rneasy mini spin columns and quantified using NanoDrop UV-VIS Spectrophotometer ver. The hybridization was performed in Agilent 2X GE Hybridization Buffer HI-RPM according to Agilent guidelines in Agilent hybridization oven at 65 degrees C 10rpm for 21 hours.

scan_protocol: Scanned on Agilent scanner G2565CA. Images were quantified using Agilent Feature Extraction ver. 11.0.1.1

data_processing:
Normalization was performed to sample-wise means. Genes detected in both samples, and with an expression fold change over the threshold of 2 were considered significantly altered
values: Normalized logratio representing hiMyc miR-32/hiMyc mice

source_name: mouse prostate

label_protocol: 100ng of total RNA were labeled using the Agilent Low Input Quick Amp labeling kit according to the manufacturer’s protocol

growth_protocol: Generation of transgenic mir-32 mice in FVB/N background has been previously described in Latonen et al. 2017 (doi: 10.1016/j.ajpath.2017.07.012). Mice transgenic for oncogenic Myc (hiMyc mice) in FVB/N background have been previously described by Ellwood-Yen et al., 2003 (doi: 10.1016/s1535-6108(03)00197-1).

extract_protocol: Tissues for RNA extraction were collected and stored in RNAlater® (ThermoFischer Scientific Inc.). RNA was extracted with manual homogenization by pressing a sample repeatedly through 20G - 22G needles and using TriReagent® (Sigma-Aldrich) according to manufacturer’s instructions.

value: hiMyc miR-32

tag: tisssue

value: prostate

value: hiMyc


title: hiMyc miR-32 vs. hiMyc dye-swap

description: hiMyc miR-32 vs. hiMyc dye-swap


title: AHM010

description: Bacterial rRNA amplified and sequenced


title: hiMyc miR-32 vs. hiMyc replicate

description: hiMyc miR-32 vs. hiMyc replicate


title: AHF263

description: Bacterial rRNA amplified and sequenced


title: AHF257

description: Bacterial rRNA amplified and sequenced


title: AHF261

description: Bacterial rRNA amplified and sequenced


title: AHF262

description: Bacterial rRNA amplified and sequenced


title: AHF256

description: Bacterial rRNA amplified and sequenced


title: AHF255

description: Bacterial rRNA amplified and sequenced


title: hiMyc miR-32 vs. hiMyc

description: hiMyc miR-32 vs. hiMyc


title: AHF253

description: Bacterial rRNA amplified and sequenced


title: AHF254

description: Bacterial rRNA amplified and sequenced


title: PBMCs in control 02

city: Zhenjiang

first: shihe

last: shao

state: Jiangsu Province

address: 301 Xuefu Road

institute: School of Medicine, Jiangsu University

description:
lncRNA and mRNA
Gene expression data from  PBMCs in healthy control

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Affymetrix Expression Console (DABG)

source_name: PBMCs from healthy control

label_protocol: not provided

growth_protocol: For all participants, blood samples were collected the cubital vein after an overnight fasting for at least 10 hours

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

treatment_protocol: The obtained whole blood was added with erythrocyte lysate to obtain PBMCs, Trizol was added and stored at -80 ℃

value: nondiabetic

value: PBMCs


title: PBMCs in type 2 diabetes 02

description:
lncRNA and mRNA
Gene expression data from  PBMCs in type 2 diabetes

source_name: PBMCs from type 2 diabetes

value: diabetic


title: PBMCs in control 01


title: PBMCs in type 2 diabetes 01


title: AHF248

description: Bacterial rRNA amplified and sequenced

value: Fetal gut, lungs, skin, thymus, spleen and placenta

value: Bacterial


title: AHF251

description: Bacterial rRNA amplified and sequenced


title: AHF250

description: Bacterial rRNA amplified and sequenced


title: AHF252

description: Bacterial rRNA amplified and sequenced


title: AHF249

description: Bacterial rRNA amplified and sequenced


title: AHF246

description: Bacterial rRNA amplified and sequenced


title: AHF234

description: Bacterial rRNA amplified and sequenced


title: AHF247

description: Bacterial rRNA amplified and sequenced


title: AHF229

description: Bacterial rRNA amplified and sequenced


title: AHF228

description: Bacterial rRNA amplified and sequenced


title: AHF233

description: Bacterial rRNA amplified and sequenced


title: AHF231

description: Bacterial rRNA amplified and sequenced


title: AHF230

description: Bacterial rRNA amplified and sequenced


title: AHF232

description: Bacterial rRNA amplified and sequenced