title: patient29_whole-blood_day0 [p29D0]

value: whole-blood cells


title: Rag1ko/ko_Bone_Marrow_ProB_rep1_Experiment_2

status: Public on Dec 29 2020

type: SRA

city: Amsterdam

first: Heinz

last: jacobs

address: Plesmanlaan 121

country: Netherlands

institute: NKI

library_source: transcriptomic

data_processing:
Sample 1-16: The 51 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 37) using TopHat (version 2.0.6).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 66. Additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using HTSeq-count.
Sample 17-40: The 51/65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script that gives the same output as HTSeq-count.
Genome_build: Ensembl build 37 / build 38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

molecule: total RNA

organism: Mus musculus

growth_protocol: Single cells suspensions were prepared from the Bone Marrow of 6-8-week-old mice and subjected to erylysis.

extract_protocol:
Pro or PreB cells were flow cytometrically sorted and resuspended in Trizol (Ambion Life Technologies) for the subsequent extraction of total RNA using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001). Total RNA was extracted using according to the manufacturer’s protocol.
Library preparation was performed on RNA samples with a measured RNA Integrity Number (RIN) between 8.0 and 10.0 as assessed by the 2100 Bioanalyzer using a Nano chip (Agilent). Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.) according to manufacturer’s instructions (Illumina, Part # 15031047 Rev. E). RNA libraries were prepared using standard Illumina protocols, analyzed for size and quantity of cDNAs on a 2100 Bioanalyzer using a DNA 7500 chip (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

treatment_protocol: Following erythrocyte lysis, Bone marrow cells were stained with flourescence conjugated monoclonal atibodies against CD19, B220, IgM, c-Kit and CD25 to identify their cell surface expression. ProB cells were identified as CD19+B220+IgM-c-Kit+CD25- and PreB cells were identified as CD19+B220+IgM-c-Kit-CD25+.

tag: strain

tag: tissue

value: Bone Marrow

tag: cell type

tag: genotype


title: GSC11

city: La Jolla

first: Tao

last: Long

state: CA

address: 9500 Gilman Dr

department: Medicine

country: USA

institute: University of California at San Diego

description: PTEN-NULL

data_processing:
QC of raw fastq files with MultiQC
Alignment with STAR
TPM calling with RSEM
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: text files include TPM values for each gene

organism: Homo sapiens

growth_protocol: GBM-neurospheres were cultured in DMEM/F12 medium supplemented with B27 (GIBCO/Life Technologies) and human recombinant EGF (20 ng/ml), bFGF (10 ng/ml) and 2 mg/mL heparin (Stemcell Technologies), and dissociated with Accutase (Stemcell Technologies).

extract_protocol:
Total RNA was extracted from GBM-spheres using RNeasy Plus Mini Kit (Qiagen # 74134). 2000 ng of total RNA dissolved in RNase-free ddH2O was shipped for sequencing to Novogene Corporation Inc.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
The qualified libraries are fed into HiSeq/MiSeq sequencers after pooling according to its effective concentration and expected data volume.

value: Glioblastoma stem cells

value: Brain

tag: disease state

value: Cancer (glioblastoma)

tag: treatment

value: Untreated

value: PTEN-NULL


title: patient27_whole-blood_day60 [p27D60]

type: RNA

city: Paris

first: Jeremy

last: Manry

address: 24 boulevard du Montparnasse

country: France

institute: INSERM, Institut Imagine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
We used the lumi package of R for variance-stabilization transformation (VST) and quantile normalization of the crude data. Only probes corresponding to autosomes, mapping to unique locations and expressed at levels above background noise (p-value < 0.05) in at least 10 samples (10%) were retained. Probes not matching any unique Ensembl gene or Hugo ID were excluded. For genes with several probes, we retained the median expression value.
quantile normalized. Probes with Detection P val < 0.05 in at least 10 samples were kept for analysis.

label: biotin

source_name: whole-blood cells, day 60 after start of treatment

label_protocol: RNA samples were labeled with the Illumina TotalPrep RNA Amplification Kit from Ambion

extract_protocol: Total RNA was extracted with the Tempus Sample kit (Applied Biosystem).

tag: subject id

tag: subject status

value: patient diagnosed with Buruli ulcer

tag: age

tag: gender

value: female

tag: time point

value: day 60 after start of treatment

tag: tissue/cell type


title: IghTer5 /wt;Rag1ko/ko_Bone_Marrow_ProB_rep2_Experiment_2

source_name: IghTer5 /wt;Rag1ko/ko_Bone_Marrow

value: IghTer5 /wt;Rag1ko/ko


title: HCM4

city: Guangzhou

first: Qi

last: Guo

address: Yanjiangxi Road

country: China

institute: Sun Yat-sen University

description: Gene expression in hypertrophic cardiomyopathy patient plasma

hyb_protocol: The biotinylated cRNA targets were then hybridized with the slides.

scan_protocol: After hybridization, slides were scanned on the Agilent Microarray Scanner (Agilent Technologies, Santa Clara, USA).

data_processing: Data were extracted with Feature Extraction software 12.0.3.1 (Agilent Technologies, Santa Clara, USA).

source_name: plasma, hypretrophic cardiomyopathy4

label_protocol: RNA samples from each group were then used to generate biotinylated cRNA targets for the LC Human ceRNA array (version 1.0).

extract_protocol: Total RNA was isolated using a Plasma RNA Purification Mini Kit (Norgen, Thorold, Canada) according to the manufacturer’s instructions and purified using an RNeasy Mini Kit (Qiagen, GmBH, Germany).

treatment_protocol: Whole blood was collected in venous blood collection tubes containing EDTA after fasting overnight, and plasma was separated by centrifugation.

tag: disease

value: hypretrophic cardiomyopathy

value: plasma


title: HCM8

source_name: plasma, hypretrophic cardiomyopathy8

value: male


title: patient27_whole-blood_day90 [p27D90]

source_name: whole-blood cells, day 90 after start of treatment

value: day 90 after start of treatment


title: HCM7

source_name: plasma, hypretrophic cardiomyopathy7


title: patient26_whole-blood_day110 [p26D110]

source_name: whole-blood cells, day 110 after start of treatment

value: day 110 after start of treatment


title: HCM6

source_name: plasma, hypretrophic cardiomyopathy6


title: HCM2

source_name: plasma, hypretrophic cardiomyopathy2


title: patient27_whole-blood_day0 [p27D0]

source_name: whole-blood cells, day 0 after start of treatment

value: day 0 after start of treatment


title: Rag1ko/ko_Bone_Marrow_ProB_rep3_Experiment_2


title: HCM1

source_name: plasma, hypretrophic cardiomyopathy1


title: patient26_whole-blood_day90 [p26D90]

value: whole-blood cells


title: patient26_whole-blood_day60 [p26D60]


title: patient26_whole-blood_day0 [p26D0]


title: HCM5

source_name: plasma, hypretrophic cardiomyopathy5


title: WT_Bone_Marrow_PreB_rep1_Experiment_2

source_name: WT Bone Marrow

value: Bone Marrow

value: WT


title: WT_Bone_Marrow_PreB_rep3_Experiment_2


title: GSC23-PTEN

description: PTEN-OVEREXPRESSION

value: Glioblastoma stem cells

value: Brain

value: PTEN-OVEREXPRESSION


title: MED13 KO #17 MMS rep. 3

city: Trondheim

first: Barbara

last: van Loon

address: Erling Skjalgssons gt 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
Sequenced reads were mapped to GRCh38.84 whole genome using STAR v2.4.0 with parameters --chimSegmentMin 30 --runThreadN 12 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000
Counting was performed using HTSeq (Anders et a., 2015 Bioinformatics) v0.6.0 (htseq-count) counting exon features and reporting Ensembl Gene Ids.
Data normalization and differential expression analysis was performed using limma v3.32.10 (Ritchie et al., 2015 Nucleic Acids Research), in R v 3.4.1, filtering out genes with expression (total normalized read counts) less than the number of samples.
Genome_build: GRCh38.84
Supplementary_files_format_and_content: Voom normalized count matrix output from HTSeq and limma (details above).

source_name: HAP1 cells

growth_protocol: All cells were cultured under 5% CO2 and 37ºC in Iscove's Modified Dulbecco's Medium with supplementation of 10% FBS, 1% PenStrep and 1% L-glutamine.

extract_protocol:
Total RNA was purified with RNeasy mini kit  and DNase I digested (Qiagen) according to the manufacturer's protocol.
Stranded mRNA Library(B02), performed by BGI
100bp, PE. Sequencing on BGISEQ platform, performed by BGIs

treatment_protocol: HAP1 WT, HAP1 MED KO #10 and #17 cells were continuously treated for 72h with 125 µM MMS or media alone.

value: HAP1 cells

tag: sample number

value: 125 µM MMS treated

value: MED13 KO


title: patient26_whole-blood_day210 [p26D210]

source_name: whole-blood cells, day 210 after start of treatment

value: patient diagnosed with Buruli ulcer

value: day 210 after start of treatment


title: HK281

description: PTEN-NULL

value: Cancer (glioblastoma)

value: Untreated

value: PTEN-NULL


title: WT_Bone_Marrow_PreB_rep2_Experiment_2


title: GSC23

description: PTEN-NULL


title: HCM3

source_name: plasma, hypretrophic cardiomyopathy3

value: hypretrophic cardiomyopathy

value: plasma

value: female


title: MED13 KO #17 NT rep. 3

value: no treated


title: MED13 KO #17 MMS rep. 2


title: patient24_whole-blood_day56 [p24D56]

source_name: whole-blood cells, day 56 after start of treatment

value: male

value: day 56 after start of treatment

value: whole-blood cells


title: patient24_whole-blood_day120 [p24D120]

source_name: whole-blood cells, day 120 after start of treatment

value: day 120 after start of treatment


title: PD1_Plus_PE_Minus_4

city: Seattle

first: Benjamin

middle: Henry

last: Gern

state: WA

address: 307 Westlake Ave N

department: Center for Global Infectious Diseases Research

institute: Seattle Children's Research Institute

data_processing:
Illumina Casava software used for basecalling
Spliced Transcripts Alignment to a Reference (STAR) tool was used to map the RNASeq reads to University of California Santa Cruz (UCSC) mouse genome.
Aligned reads were sorted and mapped to transcripts and counts were output into a matrix using htseq-count
Genome_build: mm10
Supplementary_files_format_and_content: gexp_counts.csv

source_name: Parenchymal pulmonary T cells

extract_protocol:
The cells were sorted using the BD-Aria directly into a buffer containing trizol. Samples were shipped to Expression Analysis (Durham, NC), RNA was isolated and amplified linearly followed by RNA sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6 mice infected with Mtb. Labeled intravascularly with PE label. Cell suspension generated from lungs. Mtb-specific T cells sorted with MHCII tetramer for epitope on the secreted Mtb antigen, ESAT=6

value: Parenchymal pulmonary T cells

tag: t cell activation status

value: Activated

tag: tissue location

value: Parenchymal

tag: receptor expression


title: PD1_Plus_PE_Minus_5


title: patient24_whole-blood_day90 [p24D90]

value: day 90 after start of treatment


title: m6A_seq_4OHT_rep1

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

description: total RNA

data_processing:
The adaptor of all sequencing data was removed by Cutadapt.
For all sequencing data expect for the Ribo-seq and QTI-seq in METTL3 knockdown cells, the adaptor AAAAAAAAAA was used. The trimmed reads with length <15 nt were excluded. The trimmed reads were aligned to transcriptome using bowtie with parameters: -a --best -m1 --strata -S --sam-nohead.  For Ribo-seq and QTI-seq in METTL3 knockdown cells,  The adaptor CTGTAGGCACCATCAAT was used. The first SIX nucleotides (3 randome nucleotides + 3-word barcode sequence) and the last FOUR nucleotides were removed (3 random nucleotides). PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab or Comma separated RPKM (Ribo-seq) , m6A peaks and coverage values. For Ribo-seq and RNA-seq, the RPKM table was provided. The first column is the Ensembl transcript ID, the second column is the RPKM value. For QTI-seq, read counts at individual sites on mRNAs were provided. The first column is the Ensembl transcript ID, the remaining columns are read count at individual mRNA sites from the 5' end to the 3' end of mRNA. For m6A-seq, the coverage files contain tab separated sequencing read count at individual mRNA sites. The first column is the ENSEMBL transcript ID. The other columns are read count at individual mRNA sites from the 5' end to the 3' end of mRNA. The m6A peak files contain identified m6A peaks on individual mRNAs. Each row of the m6A peak file represents an identified m6A peak on individual mRNAs. The first column is the Ensembl transcript ID, the second and third columns are the start position and end position of the sliding window used to identify m6A peak. The fourth column is the peak submit, and the remaining columns are the POI and POM values.

source_name: Human embryonic kidney cells

growth_protocol: HEK-TtH-ER:HRASG12V cells were grown in high glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 1X Penicillin-Streptomycin-Glutamine at 37°C and 5% CO2.

extract_protocol:
For cell lysates, at least four 10 cm dishes of cells were harvested in 400 µl ice-cold polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2) containing CHX (100 µg ml-1, for Ribo-seq) or LTM (5 µM, for QTI-seq), cells were then disrupted by vortexing six times for 20s using lysing matrix D (Fisher), followed by a 40 s interval each time on ice, then centrifuged at 12,000g, 4 °C for 10 min. For QTI-seq, to dissociate non-initiating ribosomes, cell lysates were incubated in a solution containing 16 mM HEPES buffer, pH 7.4, 10 mM creatine phosphate, 0.1 mM spermidine, 40 µg ml-1 creatine phosphokinase, 0.8 mM ATP, and 25 µM puromycin at 35 °C for 15 min. Samples were then subjected to sucrose gradient sedimentation.  Sucrose solutions were prepared in polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2 and 2% Triton X-100). A 15%-45% (w/v) sucrose density gradients were freshly prepared in SW41 ultracentrifuge tubes (Backman) using a Gradient Master (BioComp Instruments). 500 µl of supernatant from cell lysates prepared as described above was loaded onto sucrose gradients followed by centrifugation for 2.5 hr at 32,000 rpm, 4 °C in a SW41 rotor. Separated samples were fractionated at 1.5 ml min-1 through an automated fractionation system (Isco) that continually monitors OD254 values.   For RNA-seq, total RNA was first isolated using Trizol reagent followed by fragmentation using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2). 5 µg fragmented RNA was saved as input control. For m6A immunoprecipitation, 1 mg fragmented RNA was incubated with 15 μg anti-m6A antibody (Millipore ABE572) in 1× IP buffer (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, and 0.1% Igepal CA-630) for 2 hr at 4°C. The m6A-IP mixture was then incubated with Protein A beads for additional 2 hr at 4 °C on a rotating wheel. After washing 3 times with IP buffer, bound RNA was eluted using 100 μl elution buffer (6.7 mM N6-Methyladenosine 5’-monophosphate sodium salt in 1 × IP buffer), followed by ethanol precipitation. Precipitated RNA was used for cDNA library construction and high-throughput sequencing.
For Ribo-seq and QTI-seq, to convert the polysome into monosome, E. coli RNase I (750 U per 100 A260 units) was added into the pooled fractions from ribosome profiling and incubated at 4 °C for 1 hr, then total RNAs were extracted using Trizol reagent. RNA extracts (Ribo-seq and QTI-seq), fragmented RNAs (RNA-seq) and m6A-IP elutes (m6A-seq) were dephosphorylated for 2 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel and visualized using SYBR Gold. Selected regions in the gel corresponding to 40-60 nt (for RNA-seq and m6A-seq) or 25-35 nt (for Ribo-seq and QTI-seq) were excised. The gel slices were disrupted by using centrifugation through the holes at the bottom of the tube. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.2 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. Poly-(A) tailing reaction was carried out for 45 min at 37 °C (1 × poly-(A) polymerase buffer, 1 mM ATP, 0.75 U μl-1 SUPERase_In and 3 U E. coli polyA polymerase). For reverse transcription, the following oligos containing barcodes were used:   MCA:5’-pCAGATCGTCGGACTGTAGAACTCTØCAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’;   LGT:5’-pGTGATCGTCGGACTGTAGAACTCTØCAACAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’;   YAG:5’-pAGGATCGTCGGACTGTAGAACTCTØCAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’;   HTC:5’-pTCGATCGTCGGACTGTAGAACTCTØCAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’,  where Ø represents abasic residue.  In brief, the tailed-RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 65 °C for 5 min, followed by incubation on ice for 5 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer’s instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 100 nt, and the corresponding region was excised. The cDNA was recovered by using DNA gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer’s instructions. The oligonucleotide primers qNTI200 (5’-CAAGCAGAAGACGGCATA-3’) and qNTI201 (5’-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG-3’) were used to create DNA suitable for sequencing. The PCR contains 1× HF buffer, 0.2 mM dNTP, 0.5 µM oligonucleotide primers, and 0.5 U Phusion polymerase. PCR was carried out with an initial 30 s denaturation at 98 °C, followed by 12 cycles of 10 s denaturation at 98 °C, 20 s annealing at 60 °C, and 10 s extension at 72 °C. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 120 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer5’-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3’ (Illumina HiSeq).

treatment_protocol: HEK-TtH-ER:HRASG12V cells were treated with or without 4-OHT for 48 hours and METTL3 or FTO knockdown using sh-RNA

value: HEK-TtH cells stably expressing fused ER:HRasG12V


title: MED13 KO #10 MMS rep. 2

value: HAP1 cells

value: 125 µM MMS treated

value: MED13 KO


title: MED13 KO #17 MMS rep. 1


title: RNA_seq_4OHT

description: total RNA


title: patient24_whole-blood_day0 [p24D0]

value: patient diagnosed with Buruli ulcer

value: day 0 after start of treatment


title: MED13 KO #17 NT rep. 2


title: PD1_Plus_PE_Minus_3


title: m6A_seq_Control_rep1

description: total RNA


title: m6A_seq_4OHT_rep2

description: total RNA


title: patient23_whole-blood_day120 [p23D120]


title: m6A_seq_Control_rep2

description: total RNA


title: MED13 KO #17 NT rep. 1


title: RNA_seq_Control

description: total RNA


title: KLRG1_Plus_PE_Minus_3


title: MED13 KO #10 MMS rep. 3


title: PD1_Plus_PE_Minus_1


title: KLRG1_Plus_PE_Minus_2


title: QTI_seq_shMETTL3_4OHT

description: ribosome protected RNA


title: PD1_Plus_PE_Minus_2


title: MED13 KO #10 NT rep. 3


title: QTI_seq_shMETTL3

description: ribosome protected RNA


title: Ribo_seq_shMETTL3_4OHT

description: ribosome protected RNA


title: KLRG1_Plus_PE_Minus_1


title: MED13 KO #10 MMS rep. 1


title: KLRG1_Plus_PE_Plus_5

source_name: Intravascular pulmonary T cells

value: Intravascular pulmonary T cells

value: Intravascular


title: MED13 KO #10 NT rep. 2

value: no treated


title: KLRG1_Plus_PE_Plus_4


title: MED13 KO #10 NT rep. 1


title: WT MMS rep. 3

value: WT


title: KLRG1_Plus_PE_Plus_2


title: KLRG1_Plus_PE_Plus_3


title: WT MMS rep. 2


title: WT MMS rep. 1


title: QTI_seq_shFTO_rep3

description: ribosome protected RNA


title: Ribo_seq_shMETTL3

description: ribosome protected RNA


title: QTI_seq_shScram_rep3

description: ribosome protected RNA


title: patient23_whole-blood_day56 [p23D56]

value: male

value: day 56 after start of treatment


title: patient23_whole-blood_day0 [p23D0]

value: whole-blood cells


title: patient22_whole-blood_day56 [p22D56]

value: female


title: patient22_whole-blood_day120 [p22D120]

value: day 120 after start of treatment


title: patient23_whole-blood_day80 [p23D80]

source_name: whole-blood cells, day 80 after start of treatment

value: day 80 after start of treatment


title: patient22_whole-blood_day90 [p22D90]

source_name: whole-blood cells, day 90 after start of treatment

value: day 90 after start of treatment


title: patient20_whole-blood_day90 [p20D90]


title: Ribo_seq_shFTO_rep3

description: ribosome protected RNA


title: KLRG1_Plus_PE_Plus_1

value: Activated


title: WT NT rep. 2

value: HAP1 cells


title: WT NT rep. 3


title: CD44low_5

source_name: Naïve pulmonary T cells

value: pulmonary T cells

value: Naïve

value: Lung


title: WT NT rep. 1


title: patient22_whole-blood_day0 [p22D0]

value: patient diagnosed with Buruli ulcer

value: day 0 after start of treatment


title: patient20_whole-blood_day56 [p20D56]


title: CD44low_3


title: CD44low_4


title: Ribo_seq_shScram_rep3

description: ribosome protected RNA


title: ZFP541 ChIP_Antibody1

city: Chuo-ku

first: Kei-ichiro

last: Ishiguro

state: Kumamoto

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto university

description: ZFP541 ChIP-DNA

library_source: genomic

data_processing:
The trimmed ChIP-seq reads ware mapped to the UCSC mm10 genome assemblies using Bowtie2 v2.3.4.1 with default parameters.
BigWig files were generated using deepTools (v3.1.0).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: wild type testes

growth_protocol: Wild type testes were prepared from postnatal day 18-19.

extract_protocol:
Sonicated DNA from cells was pulled down with antibody.
Libraries were prepared according to KAPA Biosystems's instructions.

treatment_protocol: ChIP-seq experiments were carried out following standard procedures.

tag: strain

value: testis

value: Wild type

tag: developmental stage

value: postnatal day 18-19 (P18-19)

tag: chip antibody


title: patient20_whole-blood_day0 [p20D0]


title: QTI_seq_OE_GFP_rep2

description: ribosome protected RNA

tag: cell type


title: Ribo_seq_OE_FTO_rep2

description: ribosome protected RNA


title: patient19_whole-blood_day56 [p19D56]


title: CD44low_1


title: QTI_seq_OE_FTO_rep2

description: ribosome protected RNA


title: Ribo_seq_OE_GFP_rep2

description: ribosome protected RNA


title: CD44low_2


title: ZFP541 ChIP_Antibody2

description: ZFP541 ChIP-DNA

tag: tissue

tag: genotype


title: patient19_whole-blood_day75 [p19D75]

source_name: whole-blood cells, day 75 after start of treatment

tag: subject id

value: day 75 after start of treatment


title: B72h_rep3

city: Beijing

first: Duo

last: Su

address: Street Dongdajie

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10. Discard those reads that can not form paired. The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this.
Fragments per kilobase of exon model per million reads mapped (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung tissue challenged with BoNT/A after 72h

extract_protocol:
Lung tissues were for RNA extraction and subsequent RNA sequencing. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were intratracheal inoculation with a single doses of BoNT/A

value: Balb/C

value: lung


title: QTI_seq_OE_FTO_rep1

description: ribosome protected RNA


title: QTI_seq_OE_GFP_rep1

description: ribosome protected RNA


title: input

description: input genome DNA

value: none (input)


title: B72h_rep1


title: FH-AGO2_PARCLIP_plusUreaPAGE_1Uul_RNaseT1_repB

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
Bcl2fastq (v2.20.0) was used to demultiplex and convert BCL basecall files from the sequencer to fastq files
Cutadapt (cutadapt 1.15 with Python 3.6.4) (19) was used to demultiplex adapter barcoded samples (without removing adapters). For demultiplexing libraries with a 5’ adapter barcode, the 5’ adapter barcode anchored to the 5’ end of the read was removed during demultiplexing (without removing UMIs)
PARpipe (https://github.com/ohlerlab/PARpipe) was used for further pre-processing, implementation of paralyzer
To allow the use of additional UMIs in the new protocol and preserve the true number of reads in the final bam file, during preprocessing fastq sequences were collapsed prior to adapter and UMI removal to remove potential PCR duplicates.
Genome_build: hg38
Supplementary_files_format_and_content: clusters(binding sites) csv files

growth_protocol: Flp-In™ 293 T-REx cells with stably integrated transgenic FLAG-HA tagged RBP of interest were cultured at 80% confluency in DMEM supplemented with 10% FBS and1x Pen/Strep

extract_protocol:
Following crosslinking, cells were collected in PBS and centrifuged at 500 x g for 5 minutes at 4°C. For chromatin associated RNPs (e.g U2AF1) cells were lysed by gentle resuspension in a modified HLB buffer (10 mM Tris at pH 7.5, 50 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 10% glycerol) for 2 min and spun for 2 min at 200 x g. The nuclei were washed twice with the same buffer and extracted using MWS buffer (10 mM Tris-HCl at pH 7.0, 4 mM EDTA, 0.3 M NaCl, 1 M urea, and 1% [v/v] NP-40). The chromatin pellet was washed twice in MWS buffer and resuspended in RIPA buffer(10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1%, sodium deoxycholate, 0.1% SDS, 140 mM NaCl supplemented with protease inhibitor cocktail (cOmplete, Sigma Aldrich 4693159001) followed by sonication in a bath sonicator (Bioruptor 300, Diagenode) 3 times for 30 seconds at medium amplitude at 4°C. 0.1 U/µl RNase I was added and incubation for 10 min at 22°C. For KHSRP, the cell pellet was lysed in 3 volumes of RIPA buffer and sonicated followed by addition of 0.1 U/µl RNase I and incubation for 10 min at 22°C. For cytoplasmic RBPs, cells were lysed in 3 volumes of NP40 lysis buffer (20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% (v/v) NP40, 0.5 mM DTT) on ice for 15 minutes with optional addition of 0.1 U/µl RNase I and incubation for 10 min at 22°C. The cell extract was cleared at 15,000 x g for 15 minutes at 4°C.
Library conctraction was performed either with the radiolabel protocol or with fPAR-CLIP protocol

treatment_protocol: 8-12 hours before crosslinking, 4-thiouridine (4SU) was added to the cell culture medium at a final concentration of 100 µM. For U2AF1 PAR-CLIP, 4SU-labeling was reduced to 2 hours at a final concentration of 250 µM. Cells were washed once with 1x PBS and crosslinked with 0.3 J/cm2 of 312 or 365 nm UVA or UVB light for PAR-CLIP or 0.3 J/cm2 of 254 nm UVC light for regular CLIP in a Spectrolinker XL-1500 (Spectronics Corporation) or comparable instrument equipped with the appropriate UV lamps

tag: cell line

value: Flp-In T-REx 293

tag: protein

tag: protocol

value: PAR-CLIP-Seq

tag: clip antibody

value: Anti-FLAG® M2 Magnetic Beads, Millipore, M8823

value: NNTGACTGTGGAATTCTCGGGTGCCAAGG


title: B72h_rep2


title: FH-U2AF1_15Uml_RNaseAT1

value: fPAR-CLIP-Seq


title: FH-U2AF1_1.5Uml_RNaseAT1


title: Ribo_seq_OE_FTO_rep1

description: ribosome protected RNA


title: B48h_rep3

source_name: Lung tissue challenged with BoNT/A after 48h


title: Ribo_seq_OE_GFP_rep1

description: ribosome protected RNA


title: FH-AGO2_PARCLIP_plusUreaPAGE_1Uul_RNaseT1_repA


title: patient17_whole-blood_day56 [p17D56]

tag: subject status

tag: age

tag: gender

value: male

tag: time point

value: day 56 after start of treatment

tag: tissue/cell type

value: whole-blood cells


title: QTI_seq_shScram_rep2

description: ribosome protected RNA


title: patient19_whole-blood_day0 [p19D0]

source_name: whole-blood cells, day 0 after start of treatment

value: patient diagnosed with Buruli ulcer

value: female


title: patient17_whole-blood_day80 [p17D80]

value: day 80 after start of treatment


title: patient17_whole-blood_day120 [p17D120]

value: day 120 after start of treatment


title: patient16_whole-blood_day90 [p16D90]

value: day 90 after start of treatment


title: AgedNulliparous_D

city: Boston

first: Joan

middle: S.

last: Brugge

state: MA

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

description:
Li_Brugge_10XscRNAseq_GeneCellMatrix_RNAcounts_GEO.csv
Li_Brugge_10XscRNAseq_Metadata_GEO.csv

data_processing:
Paired-end reads from Illumina HiSeq were processed and mapped to the mm10 mouse genome using Cell Ranger v2.0.
The following filters were used to eliminate cells with (1) UMI counts < 1,000 or > 60,000, (2) gene counts < 500 or > 2,500, and (3) mitochondrial gene ratio > 10%.
Genome_build: mm10
Supplementary_files_format_and_content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample
Supplementary_files_format_and_content: Metadata table containing meta data information for each cell, including sample of origin and designated cell type.

molecule: polyA RNA

source_name: Mammary tissue

extract_protocol:
Abdominal #4 mammary glands, with lymph nodes removed, were finely minced and then incubated in a digestion solution containing DMEM/F12 (Gibco 11330), 10% heat-inactivated fetal bovine serum, 2 mg/ml collagenase XI (Sigma C9407), and 0.1 mg/ml hyaluronidase (Sigma H3506) for 1.5 hours at 37°C with constant shaking at 150 rpm. The dissociated cells were then subjected to red blood cell lysis (Biolegend 420301), a 5-minute treatment with 1 U/ml dispase (Stem Cell Technologies 07913) and 0.1 mg/ml DNase (Stem Cell Technologies 7470), a 5-minute treatment with TrypLE (Gibco 12605010), and filtered through a 40 µm cell strainer. Cells were resuspended in PBS containing 0.04% BSA, counted manually under the microscope, and adjusted for loading 7,000 viable cells for single-cell RNA sequencing.
Single cell capturing and cDNA library generation were performed using the 10X Chromium 3’ library construction kit v2 following the manufacturer’s instruction.

tag: tissue type

value: Mammary glands (#4, abdominal glands)

tag: Sex

value: Female

tag: age group

value: Aged (13-14 months)


title: FH-AGO2_PARCLIP_noUreaPAGE_1Uul_RNaseT1_repA


title: FH-AGO2_PARCLIP_noUreaPAGE_1Uul_RNaseT1_repB


title: QTI_seq_shFTO_rep2

description: ribosome protected RNA


title: Ribo_seq_shFTO_rep2

description: ribosome protected RNA


title: patient17_whole-blood_day0 [p17D0]

value: day 0 after start of treatment


title: B48h_rep2

tag: strain

value: Balb/C

value: lung

value: Wild type


title: B48h_rep1


title: B24h_rep3

source_name: Lung tissue challenged with BoNT/A after 24h


title: patient16_whole-blood_day56 [p16D56]


title: B24h_rep1


title: AgedNulliparous_C


title: patient16_whole-blood_day0 [p16D0]


title: B12h_rep3

source_name: Lung tissue challenged with BoNT/A after 12h


title: patient13_whole-blood_day200 [p13D200]

source_name: whole-blood cells, day 200 after start of treatment

value: day 200 after start of treatment


title: patient13_whole-blood_day150 [p13D150]

source_name: whole-blood cells, day 150 after start of treatment

value: day 150 after start of treatment


title: Ribo_seq_shScram_rep2

description: ribosome protected RNA

tag: cell type


title: B12h_rep2

tag: tissue


title: B24h_rep2

tag: genotype


title: AgedNulliparous_B


title: AgedNulliparous_A


title: QTI_seq_shFTO_rep1

description: ribosome protected RNA


title: QTI_seq_shScram_rep1

description: ribosome protected RNA


title: Ribo_seq_shScram_rep1

description: ribosome protected RNA


title: B12h_rep1


title: patient13_whole-blood_day90 [p13D90]

tag: subject id

value: male


title: patient13_whole-blood_day110 [p13D110]

source_name: whole-blood cells, day 110 after start of treatment

value: day 110 after start of treatment


title: patient13_whole-blood_day56 [p13D56]

source_name: whole-blood cells, day 56 after start of treatment

value: day 56 after start of treatment

value: whole-blood cells


title: Ctrl_rep2

source_name: Lung tissue challenged with PBS


title: Ribo_seq_shFTO_rep1

description: ribosome protected RNA

source_name: Human embryonic kidney cells


title: YoungNulliparous_C

value: Young (3-4 months)


title: YoungNulliparous_B


title: YoungNulliparous_A


title: Ribo_seq_4OHT_rep2

description: ribosome protected RNA

value: HEK-TtH cells stably expressing fused ER:HRasG12V


title: QTI_seq_Control_rep2

description: ribosome protected RNA


title: patient13_whole-blood_day0 [p13D0]

value: patient diagnosed with Buruli ulcer


title: Ctrl_rep1


title: Brain, Autism-2

city: Harbin

first: Yanan

last: Jiang

address: 157 Baojian Road

department: Pharmacology

institute: Harbin Medical University

description: circRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were filtered according to the following rules: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.0.3.12), respectively. After aligned with reference genome, the reads that could be mapped to the genomes were discarded, and the unmapped reads were then collected for circRNA identification.
20mers from both ends of the unmapped reads were extracted and aligned to the reference genome to find unique anchor positions within splice site. Anchor reads that aligned in the reversed orientation (head-to tail) indicated circRNA splicing and then were subjected to find_circ to identify circRNAs. The anchor alignments were then extended such that the complete read aligns and the breakpoints were flanked by GU/AG splice sites. A candidate circRNA was called if it was supported by at least two unique back spliced reads at least in one sample.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain, Autism

extract_protocol:
Brains were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. After extracted, total RNAs were treated with RNase R to degrade the linear RNAs, and purified using RNeasy MinElute Cleanup Kit (Qiagen).
Strand-specific library was constructed using VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina following the manufacture’s instructions.

value: 1 month

value: Brain

tag: condition

value: autism


title: Brain, Autism-3

description: circRNA


title: patient12_whole-blood_day0 [p12D0]

value: female


title: Brain, Autism-1

description: circRNA


title: patient12_whole-blood_day90 [p12D90]

source_name: whole-blood cells, day 90 after start of treatment

value: day 90 after start of treatment


title: Ctrl_rep3

value: Balb/C


title: Ribo_seq_Control_rep2

description: ribosome protected RNA


title: QTI_seq_4OHT_rep1

description: ribosome protected RNA


title: QTI_seq_4OHT_rep2

description: ribosome protected RNA


title: patient12_whole-blood_day120 [p12D120]

source_name: whole-blood cells, day 120 after start of treatment

value: day 120 after start of treatment


title: QTI_seq_Control_rep1

description: ribosome protected RNA


title: Ribo_seq_4OHT_rep1

description: ribosome protected RNA


title: Brain, Control-2

description: circRNA

source_name: Brain, Control

value: control


title: Brain, Control-1

description: circRNA


title: HFHS flox_y 388

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

institute: Okayama University

description: Gene expression data from epididymal fat tissues in mir221/222 flox/y C57BL/6J mice with HFHS

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip™ Mouse Gene 2.0 ST Array (Thermo Fisher Scientific, Inc., cat.# 902118). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Data Analysis Tool Ver3.2 (Filgen).

label: Biotin

source_name: Epididymal fat tissues from mir342wt/wt C57BL/6J mice fed with STD

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip WT PLUS Reagent Kit UserGuide).

growth_protocol: 5-week-old male C57BL/6J mice were housed in cages, and maintained on a 12-hour light-dark cycle.

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

treatment_protocol: The mice were fed with standard diet (STD) and high fat-high sucrose diet (HFHS) and thier epididymal adipose tissues were obtained at 16 weeks of age.

value: Epididymal fat tissue

value: mir221/222 flox/y

value: 16 weeks of age


title: STD AdipoKO 387

description: Gene expression data from epididymal fat tissues in mir221/222 AdipoKO C57BL/6J mice with STD

source_name: Epididymal fat tissues from mi342-/- C57BL/6J mice fed with STD

value: mir221/222 AdipoKO


title: Ribo_seq_Control_rep1

description: ribosome protected RNA


title: Plasma_Stressed_3

status: Public on Dec 28 2020

city: Waterloo

first: Heather

last: Ikert

state: Ontario

address: 200 University Ave W

department: Biology

country: Canada

institute: University of Waterloo

description: size_trimmed_adapterless_SV18263_0024_S14_R1_001

data_processing:
Adapter removal and filtering was performed using cutadapt (2.10; used under python3.8). The adapter was removed and any bases below a quality score of 28 were trimmed (cutadapt -j 4 --nextseq-trim=28  -a TGGAATTCTCGGGTGCCAAGG -o "output file" "input file"). Next, sequencing files were filtered to remove any sequences shorter than 18 bases or longer than 35 bases, as they are not useful in microRNA analysis (cutadapt -j 4 -m 18 -M 35 -o "output file" "input file").
Alignment was performed within miARma-Seq (version 1.7.2) using bowtie 1 (version 1.1.1) and annotation and read counting using mirDeep2 (2.0.1.2). Parameters given in the miARma-Seq configuration file include: "General" - type=miRNA, organism=RainbowTrout, threads=8, strand=no, "DeNovo" - bowtie1index="location of bowtie1 index created from Oncorhynchus mykiss genome (GCF_002163495.1_Omyk_1.0_genomic.fna)", adapter=TGGAATTCTCGGGTGCCAAGG, mature_miRNA_file= "mature Salmo salar miRNA from mirbase.org", precursor_miRNA_file="hairpin Salmo salar miRNA from mirbase.org", genome="previously mentioned O. mykiss genome", bowtiemiss=1, bowtie1parameter=--best --strata, threads=8. The miARma-Seq script uses the following miRDeep2 tools and options (mapper.pl -e -h -i -j -n -m -k -o -p -s -t). Refer to the miRDeep2 documentation (https://github.com/rajewsky-lab/mirdeep2) for the meaning of the options. Also, it is crucial to note that miRDeep2 will count reads twice that originate from different precursors. miARma-Seq corrects for this by averaging the number of counts of mature microRNA from different precursors so that all the tags (microRNA) are unique in the readcount file. This allows for more accurate differential expression analysis.
For edgeR analysis, the read count file was split by sample type so that the library normalization wouldn’t be affected by the different sample types. Samples were normalized by treatment groups and lowly expressed genes were filtered. MDS plots were used to ensure that samples separated by treatment. Exact edgeR tests were conducted for mucus and plasma because they have two treatment groups (control vs stressed) and samples aren’t paired. For water, however, the samples were paired therefore the data were analyzed using a generalized linear model (glm) using the fish number as the blocking factor. All results were exported after being sorted by p-value in order to identify significantly differentially expressed microRNA (p < 0.1).
For analysis using DESeq2, the read count file was split by sample type so that the library normalization wouldn’t be affected by the different sample types. Following this, the DESeq data set was created from the matrix of read counts. This step filters and normalizes the read counts. For plasma and mucus, the design is solely based on the treatment (control vs stressed), but due to the paired nature of the water samples, the fish number is added in as a blocking factor. These DESeq datasets are then used to conduct differential expression analysis. Results are obtained and ordered via adjusted p value (FDR) and exported so that significant results (p < 0.1) can be identified. Analysis via apeglm (Approximate Posterior Estimation for the GLM, Zhu et al., 2019) was conducted for visualization of results.
Genome_build: Omyk_1.0
Supplementary_files_format_and_content: miRNAs_finalized.tab - tab delimited matrix of all 18 samples and the read counts aligned to genomic features of the Oncorhynchus mykiss genome or mature Salmo salar microRNA.
Supplementary_files_format_and_content: Oncorhynchus_mykiss_acute_stress_miRNASeq.edgeR_DESeq2_results.xlsx - excel spreadsheet containing the differential expression data generated using edgeR and DESeq2 for each sample type (plasma, mucus, water). Data from edgeR analysis includes microRNA name (Salmo salar) or genomic location (Oncorhynchus mykiss), logFC, logCPM, p-value, and FDR. Data from DESeq2 includes microRNA name (Salmo salar) or genomic location (Oncorhynchus mykiss), baseMean, log2FoldChange, lfcSE, stat, p-value, and padj (adjusted p-value).

organism: Oncorhynchus mykiss

source_name: Blood plasma

growth_protocol: Rainbow trout (Oncorhynchus mykiss) this experiment were sourced from Silver Creek Aquaculture (Erin, Ontario, Canada) or donated by the Ontario Ministry of Natural Resources and Forestry (AUPP #40315). They were housed in the University of Waterloo Aquatic Facility (Waterloo, ON, Canada). They were fed daily with EWOS Vita (Floating Complete Fish Food for Salmonids) to satiety. Water chemistry was maintained at 13.5 +/- 0.7 °C, pH 8.85, ~2000 μS, in well-aerated water. Fish were maintained at a density of four fish per 200L tank. Experimental fish had an average length of 30.5 +/- 3.9 cm and a weight of 322 +/- 138 g. Water flow was maintained at 3.6 +/- 0.1 L/min.

extract_protocol:
Plasma microRNA were extracted using the Norgen Plasma/Serum RNA Purification Mini Kit (CAT 55000). The manufacturer’s directions were followed with exception of the following. Plasma aliquots were thawed on ice and centrifuged for two minutes at 400 x g and 200 μL of clear supernatant was used for the extraction. During the elutions, 25 μL elution solution A was applied to the column and the eluate was transferred to the column again for maximum recovery of RNA. Following this, the extracted RNAs was further processed using the Norgen RNA Clean-Up and Concentration Micro-Elute Kit (CAT 61000). With this kit, 75 μL RNAse free water was added to 25 μL extracted RNA to bring the starting volume to 100 μL. Samples were vortexed for 10 seconds and spun at 14,000 x g. Due to the fact that that isolated RNA was from plasma, 350 μL 96-100% ethanol was used. During the elution, 15 μL of eluate was used and a second elution was performed into a separate tube for maximum recovery. RNA quantification occurred using the SoftMax SpectroDrop microplate.
Library prep and sequencing were performed by Norgen Biotek (Thorold, ON, Canada) using the Norgen Biotek Small RNA Library Prep Kit (CAT 63600).

treatment_protocol: Three experimental replicates of the air stress experiment occurred. Blood plasma, epidermal mucus, and water samples were collected before (control) and one hour following exposure of rainbow trout to three minutes of air (stressed). Fish were euthanized in a buffered MS-222 solution (0.5 g/L MS-222 in 1 g/L NaHCO3).

tag: treatment

value: Stressed

tag: sample collection

value: Blood was collected by caudal puncture a 23G needle and 1mL syringes pre-coated with 0.5M EDTA. Blood was placed in 2mL microcentrifuge tubes (1mL blood was added to 10 μL 0.5M EDTA to prevent coagulation). Blood was stored on ice until spun for 10 mins at 1,300 x g at 4 °C to collect plasma. Plasma was aliquoted into 200 μL amounts and stored at -80 °C until RNA extraction.


title: patient11_whole-blood_day90 [p11D90]

value: whole-blood cells


title: Brain, Control-3

description: circRNA


title: HFHS AdipoKO 384

description: Gene expression data from epididymal fat tissues in mir221/222 AdipoKO C57BL/6J mice with HFHS

source_name: Epididymal fat tissues from mir342wt/wt C57BL/6J mice fed with HFHS


title: patient11_whole-blood_day0 [p11D0]

source_name: whole-blood cells, day 0 after start of treatment

value: day 0 after start of treatment


title: STD flox_y 378

description: Gene expression data from epididymal fat tissues in mir221/222 flox/y C57BL/6J mice with STD

source_name: Epididymal fat tissues from mi342-/- C57BL/6J mice with HFHS


title: patient8_whole-blood_day56 [p8D56]

value: patient diagnosed with Buruli ulcer

value: day 56 after start of treatment


title: Plasma_Stressed_1

description: size_trimmed_adapterless_SV18263_0020_S10_R1_001


title: Plasma_Control_2

description: size_trimmed_adapterless_SV18263_0021_S11_R1_001

value: Control


title: Plasma_Control_1

description: size_trimmed_adapterless_SV18263_0019_S9_R1_001


title: Water_Stressed_3

description: size_trimmed_adapterless_SV18263_0018_S30_R1_001

source_name: Water

extract_protocol:
Water microRNA was extracted using the Norgen Water RNA/DNA Purification Kit (CAT 26480). The manufacturer’s directions were followed with exception of the following specifics. Since the filters were stored in 5 mL tubes, the beads were transferred to the 5 mL tube and 1 mL lysis buffer E was added. These tubes were vortexed for five minutes on a flatbed vortexer at maximum speed. The initial one minute spin at 20,000 x g was replaced with a seven minute spin at 3000 x g (maximum allowable speed on centrifuge). Due to this modification, visual separation of lysate and filter was ensured before removing the supernatant for use in the remainder of the protocol. The optional DNAse treatment was applied (Norgen RNase-Free DNase I Kit - CAT 25710) in order to ensure only RNA was present for sequencing. The optional addition of 50 μL elution solution to maximize yield was performed. RNA quantification occurred using the RiboGreenAssay by Norgen Biotek.
Library prep and sequencing were performed by Norgen Biotek (Thorold, ON, Canada) using the Norgen Biotek Small RNA Library Prep Kit (CAT 63600).

value: Water was collected in 1 L sterile amber bottles sterilized with 10% bleach for 20 mins, rinsed 3x with milliQ water, and autoclaved. Care was given to collect water from the tank aseptically and ensure that no human DNA/RNA was present. For example, the fish net used to stress the fish for three minutes was placed into the water before control water samples were collected so that there would be no new nucleic acids introduced from the net. The water samples were stored at 4 °C until filtered within 3 hours of collection. Samples were filtered onto 0.45 μm cellulose nitrate filters (Thermo Scientific™ 1450045) in a sterilized laminar flow hood using peristaltic pumps. The filters were placed in 5 mL tubes on dry ice and stored for future analysis at -80 °C.


title: Plasma_Stressed_2

description: size_trimmed_adapterless_SV18263_0022_S12_R1_001


title: patient5_whole-blood_day56 [p5D56]

value: male


title: patient5_whole-blood_day0 [p5D0]


title: Water_Stressed_1

description: size_trimmed_adapterless_SV18263_0014_S26_R1_001


title: Water _Control_3

description: size_trimmed_adapterless_SV18263_0017_S29_R1_001


title: Water _Control_1

description: size_trimmed_adapterless_SV18263_0013_S25_R1_001


title: Mucus_Control_2

description: size_trimmed_adapterless_SV18263_0009_S21_R1_001

source_name: Epidermal mucus

extract_protocol:
Mucus microRNA were extracted using the Qiagen miRNeasy Serum/Plasma Advanced Kit (CAT 217204). The manufacturer’s directions were followed with the exception of using 200 μL of mucus for the extraction. For any non-specified centrifuge speed, 12,000 x g was used. RNA quantification occurred using the RiboGreenAssay by Norgen Biotek.
Library prep and sequencing were performed by Norgen Biotek (Thorold, ON, Canada) using the Norgen Biotek Small RNA Library Prep Kit (CAT 63600).

value: Mucus was collected by aseptically scraping the epidermal mucus from the left side of the rainbow trout . This was accomplished by using a new pair of gloves, cleaned with 70% ethanol, and using one hand to secure the trout by holding by the mouth and gill operculum, using the other hand to scrape the mucus into a 2 mL cryotube. The mucus was stored on dry ice and then moved to the -80 °C for future analysis.


title: Mucus_Control_1

description: size_trimmed_adapterless_SV18263_0007_S19_R1_001


title: Mucus_Stressed_3

description: size_trimmed_adapterless_SV18263_0012_S24_R1_001


title: Mucus_Control_3

description: size_trimmed_adapterless_SV18263_0011_S23_R1_001


title: Water _Control_2

description: size_trimmed_adapterless_SV18263_0015_S27_R1_001


title: patient8_whole-blood_day0 [p8D0]

value: female


title: Mucus_Stressed_2

description: size_trimmed_adapterless_SV18263_0010_S22_R1_001


title: Mucus_Stressed_1

description: size_trimmed_adapterless_SV18263_0008_S20_R1_001


title: Plasma_Control_3

description: size_trimmed_adapterless_SV18263_0023_S13_R1_001


title: NDV-resistant EJ28_rep3

city: Serdang

first: Lee Chin

last: Chan

state: Selangor

address: Jalan Sapucaya

department: Microbiology

country: Malaysia

institute: Universiti Putra Malaysia

description:
replicate 3
200769980019_L

hyb_protocol: The BeadChip was hybridized for 18 hr 24 min at 58 °C, and the detection was carried out using Cy3-Streptavidin (Invitrogen).

scan_protocol: Scanning of the microarray BeadChip was done with an iScan (illumina).

data_processing:
The edgeR program was used to select genes that had significant changes (Padj < 1e-10) with an absolute log2 fold-change of 2 by setting the follwing parameters: Padj < 1e-10 & absolute log2 fold-change of 2.
absolute log2 fold-change of 2 by setting the follwing parameters: Padj < 1e-10 & absolute log2 fold-change of 2

source_name: Bladder cancer

label_protocol: Biotinylated cRNA were prepared with TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip.

growth_protocol: NDV-resistant bladder cancer cell EJ28 and parental EJ28 were culture in Dulbeco

extract_protocol: Total RNA of EJ28 and EJ28P cells were extracted using RNeasy MinEluteTM Kit according to the manufacturer’s protocol. The RNA integrity of the samples were determined by agilent bioanalyzer.

value: Bladder cancer

tag: cell line

tag: phenotype

value: NDV resistant


title: NDV-resistant EJ28_rep1

description:
replicate 1
200769980019_J


title: EJ28_rep2

description:
replicate 2
200769980019_H

value: parental


title: EJ28_rep3

description:
replicate 3
200769980019_I


title: NDV-resistant EJ28_rep2

description:
replicate 2
200769980019_K


title: EJ28_rep1

description:
replicate 1
200769980019_G


title: Water_Stressed_2

description: size_trimmed_adapterless_SV18263_0016_S28_R1_001


title: WBJPE161032-550

first: Zi

last: Yin

address: YuHangTang Road N0.866

data_processing:
Illumina Casava1.7 software used for basecalling.
alignment was conducted with Tophat
use the FindAllMarkers function in the Seurat(version 2.3.4)to find markers for every cluster compared to all remaining cells
Genome_build: mm9
Supplementary_files_format_and_content: Excel files include markers for every cluster compared to all remaining cells;p_val:p_val (unadjusted);avg_logFC : log fold-chage of the average expression between the two groups. Positive values indicate that the feature is more highly expressed in the first group;p_val_adj : Adjusted p-value, based on bonferroni correction using all features in the dataset.

source_name: E15.5_hind limb

extract_protocol:
Single-cell capture, RNA extraction and cDNA preparation were performed following the methods described in the Fluidigm protocol (PN 100-9886, Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing).
3' end enrichment with Illumina Nextera XT

treatment_protocol: We collected single cell suspension from embryonic SCX-GFP mouse hindlimb at E10.5, E12.5 and E15.5.

value: C57BL/6 Transgenic Mouse

tag: genotype/variation

value: SCX-GFP mouse

tag: developmental stage

value: hind limb


title: WBJPE161032-547


title: WBJPE161032-545


title: WBJPE161032-548


title: WBJPE161032-552


title: WBJPE161032-556


title: WBJPE161032-557


title: WBJPE161032-549


title: WBJPE161032-553


title: WBJPE161032-560


title: WBJPE161032-559


title: WBJPE161032-558


title: WBJPE161032-555


title: WBJPE161032-554


title: WBJPE161032-541


title: mir342-/- C57BL/6J mice with HFHS

description: Gene expression data from epididymal fat tissues in mir342-/- C57BL/6J mice with HFHS

source_name: Epididymal fat tissues from mir342-/- C57BL/6J mice with HFHS

value: Epididymal fat tissues

tag: age

value: 16 weeks of age

tag: diet

value: HFHS


title: WBJPE161032-538


title: mir342wt/wt C57BL/6J mice fed with STD

description: Gene expression data from epididymal fat tissues in mir342wt/wt C57BL/6J mice fed with STD

value: STD


title: mir342wt/wt C57BL/6J mice fed with HFHS

description: Gene expression data from epididymal fat tissues in mir342wt/wt C57BL/6J mice fed with HFHS


title: WBJPE161032-536


title: WBJPE161032-551


title: mir342-/- C57BL/6J mice fed with STD

description: Gene expression data from epididymal fat tissues in mir342-/- C57BL/6J mice fed with STD

source_name: Epididymal fat tissues from mir342-/- C57BL/6J mice fed with STD


title: WBJPE161032-546


title: WBJPE161032-544


title: WBJPE161032-543


title: WBJPE161032-542


title: WBJPE161032-531


title: WBJPE161032-529


title: WBJPE161032-540


title: WBJPE161032-539


title: WBJPE161032-524


title: WBJPE161032-533


title: WBJPE161032-522


title: WBJPE161032-537


title: WBJPE161032-530


title: WBJPE161032-526


title: WBJPE161032-535


title: WBJPE161032-523


title: WBJPE161032-521


title: WBJPE161032-520


title: WBJPE161032-518


title: WBJPE161032-534


title: WBJPE161032-532


title: WBJPE161032-525


title: WBJPE161032-517


title: WBJPE161032-527


title: WBJPE161032-515


title: WBJPE161032-514


title: WBJPE161032-519


title: WBJPE161032-511


title: WBJPE161032-513


title: WBJPE161032-516


title: WBJPE161032-512


title: WBJPE161032-505


title: WBJPE161032-504


title: WBJPE161032-509


title: WBJPE161032-502


title: WBJPE161032-499


title: WBJPE161032-510


title: WBJPE161032-528


title: WBJPE161032-508


title: WBJPE161032-503


title: WBJPE161032-507


title: WBJPE161032-501


title: WBJPE161032-500


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title: WBJPE161032-494


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title: WBJPE161032-473


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title: WBJPE161032-422


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title: WBJPE161032-395


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title: WBJPE161032-386


title: WBJPE161032-364


title: WBJPE161032-384


title: WBJPE161032-359


title: WBJPE161032-361


title: WBJPE161032-355


title: WBJPE161032-353


title: WBJPE161032-354


title: WBJPE161032-352


title: WBJPE161032-351


title: WBJPE161032-356


title: WBJPE161032-357


title: WBJPE161032-346


title: WBJPE161032-348


title: WBJPE161032-366


title: WBJPE161032-345


title: WBJPE161032-347


title: WBJPE161032-342


title: WBJPE161032-343


title: WBJPE161032-341


title: WBJPE161032-358


title: WBJPE161032-340


title: WBJPE161032-338


title: WBJPE161032-337


title: WBJPE161032-334


title: WBJPE161032-333


title: WBJPE161032-330


title: WBJPE161032-331


title: WBJPE161032-350


title: WBJPE161032-339


title: WBJPE161032-324


title: WBJPE161032-329


title: WBJPE161032-332


title: WBJPE161032-327


title: WBJPE161032-349


title: WBJPE161032-326


title: WBJPE161032-323


title: WBJPE161032-328


title: WBJPE161032-322


title: WBJPE161032-321


title: WBJPE161032-319


title: WBJPE161032-325


title: WBJPE161032-320


title: WBJPE161032-318


title: WBJPE161032-316


title: WBJPE161032-317


title: WBJPE161032-315


title: WBJPE161032-311


title: WBJPE161032-313


title: WBJPE161032-314


title: WBJPE161032-312


title: WBJPE161032-344


title: WBJPE161032-335


title: WBJPE161032-336


title: WBJPE161032-309


title: WBJPE161032-310


title: WBJPE161032-307


title: WBJPE161032-306


title: WBJPE161032-305


title: WBJPE161032-303


title: WBJPE161032-301


title: WBJPE161032-302


title: WBJPE161032-304


title: WBJPE161032-300


title: WBJPE161032-296


title: WBJPE161032-293


title: WBJPE161032-297


title: WBJPE161032-295


title: WBJPE161032-291


title: WBJPE161032-294


title: WBJPE161032-308


title: WBJPE161032-292


title: WBJPE161032-287


title: WBJPE161032-286


title: WBJPE161032-289


title: WBJPE161032-285


title: WBJPE161032-284


title: WBJPE161032-281


title: WBJPE161032-280


title: WBJPE161032-290


title: WBJPE161032-283


title: WBJPE161032-279


title: WBJPE161032-278


title: WBJPE161032-299


title: WBJPE161032-282


title: WBJPE161032-298


title: WBJPE161032-288


title: WBJPE161032-276


title: WBJPE161032-275


title: WBJPE161032-277


title: WBJPE161032-273


title: WBJPE161032-270


title: WBJPE161032-271


title: WBJPE161032-274


title: WBJPE161032-272


title: WBJPE161032-268


title: WBJPE161032-269


title: WBJPE161032-267


title: WBJPE161032-266


title: WBJPE161032-264


title: WBJPE161032-263


title: WBJPE161032-262


title: WBJPE161032-259


title: WBJPE161032-260


title: WBJPE161032-256


title: WBJPE161032-258


title: WBJPE161032-252


title: WBJPE161032-253


title: WBJPE161032-254


title: WBJPE161032-250


title: WBJPE161032-257


title: WBJPE161032-255


title: WBJPE161032-245


title: WBJPE161032-251


title: WBJPE161032-246


title: WBJPE161032-249


title: WBJPE161032-248


title: WBJPE161032-244


title: WBJPE161032-242


title: WBJPE161032-243


title: WBJPE161032-241


title: WBJPE161032-240

source_name: E12.5_hind limb


title: WBJPE161032-239


title: WBJPE161032-238


title: WBJPE161032-265


title: WBJPE161032-237


title: WBJPE161032-236


title: WBJPE161032-261


title: WBJPE161032-234


title: WBJPE161032-235


title: WBJPE161032-233


title: WBJPE161032-247


title: WBJPE161032-231


title: WBJPE161032-230


title: WBJPE161032-226


title: WBJPE161032-227


title: WBJPE161032-225


title: WBJPE161032-228


title: WBJPE161032-229


title: WBJPE161032-224


title: WBJPE161032-223


title: WBJPE161032-221


title: WBJPE161032-222


title: WBJPE161032-217


title: WBJPE161032-220


title: WBJPE161032-218


title: WBJPE161032-216


title: WBJPE161032-214


title: WBJPE161032-219


title: WBJPE161032-212


title: WBJPE161032-211


title: WBJPE161032-210


title: WBJPE161032-213


title: WBJPE161032-209


title: WBJPE161032-207


title: WBJPE161032-208


title: WBJPE161032-206


title: WBJPE161032-205


title: WBJPE161032-204


title: WBJPE161032-202


title: WBJPE161032-203


title: WBJPE161032-197


title: WBJPE161032-199


title: WBJPE161032-201


title: WBJPE161032-195


title: WBJPE161032-200


title: WBJPE161032-191


title: WBJPE161032-196


title: WBJPE161032-193


title: WBJPE161032-215


title: WBJPE161032-190


title: WBJPE161032-189


title: WBJPE161032-188


title: WBJPE161032-198


title: WBJPE161032-187


title: WBJPE161032-185


title: WBJPE161032-194


title: WBJPE161032-186


title: WBJPE161032-192


title: WBJPE161032-184


title: WBJPE161032-232


title: WBJPE161032-181


title: WBJPE161032-183


title: WBJPE161032-182


title: WBJPE161032-180


title: WBJPE161032-178


title: WBJPE161032-177


title: WBJPE161032-176


title: WBJPE161032-175


title: WBJPE161032-173


title: WBJPE161032-171


title: WBJPE161032-172


title: WBJPE161032-170


title: WBJPE161032-174


title: WBJPE161032-169


title: WBJPE161032-168


title: WBJPE161032-166


title: WBJPE161032-165


title: WBJPE161032-164


title: WBJPE161032-162


title: WBJPE161032-161


title: WBJPE161032-160

source_name: E10.5_hind limb


title: WBJPE161032-157


title: WBJPE161032-154


title: WBJPE161032-153


title: WBJPE161032-152


title: WBJPE161032-151


title: WBJPE161032-179


title: WBJPE161032-150


title: WBJPE161032-149


title: WBJPE161032-156


title: WBJPE161032-147


title: WBJPE161032-145


title: WBJPE161032-167


title: WBJPE161032-143


title: WBJPE161032-142


title: WBJPE161032-140


title: WBJPE161032-148


title: WBJPE161032-141


title: WBJPE161032-139


title: WBJPE161032-138


title: WBJPE161032-137


title: WBJPE161032-135


title: WBJPE161032-159


title: WBJPE161032-158


title: WBJPE161032-155


title: WBJPE161032-134


title: WBJPE161032-131


title: WBJPE161032-132


title: WBJPE161032-128


title: WBJPE161032-127


title: WBJPE161032-130


title: WBJPE161032-126


title: WBJPE161032-129


title: WBJPE161032-124


title: WBJPE161032-125


title: WBJPE161032-146


title: WBJPE161032-144


title: WBJPE161032-163


title: WBJPE161032-136


title: WBJPE161032-120


title: WBJPE161032-118


title: WBJPE161032-117


title: WBJPE161032-119


title: WBJPE161032-114


title: WBJPE161032-121


title: WBJPE161032-116


title: WBJPE161032-113


title: WBJPE161032-133


title: WBJPE161032-115


title: WBJPE161032-111


title: WBJPE161032-112


title: WBJPE161032-109


title: WBJPE161032-110


title: WBJPE161032-106


title: WBJPE161032-107


title: WBJPE161032-104


title: WBJPE161032-102


title: WBJPE161032-108


title: WBJPE161032-100


title: WBJPE161032-122


title: WBJPE161032-123


title: WBJPE161032-97


title: WBJPE161032-101


title: WBJPE161032-95


title: WBJPE161032-94


title: WBJPE161032-96


title: WBJPE161032-93


title: WBJPE161032-88


title: WBJPE161032-99


title: WBJPE161032-98


title: WBJPE161032-90


title: WBJPE161032-87


title: WBJPE161032-89


title: WBJPE161032-86


title: WBJPE161032-85


title: WBJPE161032-84


title: WBJPE161032-103


title: WBJPE161032-83


title: WBJPE161032-82


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title: WBJPE161032-80


title: WBJPE161032-75


title: WBJPE161032-74


title: WBJPE161032-72


title: WBJPE161032-71


title: WBJPE161032-91


title: WBJPE161032-73


title: WBJPE161032-70


title: WBJPE161032-92


title: WBJPE161032-67


title: WBJPE161032-68


title: WBJPE161032-66


title: WBJPE161032-64


title: WBJPE161032-62


title: WBJPE161032-65


title: WBJPE161032-63


title: WBJPE161032-61


title: WBJPE161032-60


title: WBJPE161032-58


title: WBJPE161032-57


title: WBJPE161032-56


title: WBJPE161032-54


title: WBJPE161032-55


title: WBJPE161032-53


title: WBJPE161032-52


title: WBJPE161032-76


title: WBJPE161032-49


title: WBJPE161032-51


title: WBJPE161032-50


title: WBJPE161032-69


title: WBJPE161032-48


title: WBJPE161032-46


title: WBJPE161032-47


title: WBJPE161032-44


title: WBJPE161032-45


title: WBJPE161032-43


title: WBJPE161032-40


title: WBJPE161032-39


title: WBJPE161032-59


title: WBJPE161032-42


title: WBJPE161032-38


title: WBJPE161032-37


title: WBJPE161032-35


title: WBJPE161032-34


title: WBJPE161032-32


title: WBJPE161032-31


title: WBJPE161032-33


title: WBJPE161032-27


title: WBJPE161032-28


title: WBJPE161032-25


title: WBJPE161032-29


title: WBJPE161032-22


title: WBJPE161032-26


title: WBJPE161032-23


title: WBJPE161032-20


title: WBJPE161032-15


title: WBJPE161032-11


title: WBJPE161032-19


title: WBJPE161032-18


title: WBJPE161032-14


title: WBJPE161032-17


title: WBJPE161032-21


title: WBJPE161032-16


title: WBJPE161032-30


title: WBJPE161032-8


title: WBJPE161032-7


title: WBJPE161032-6


title: WBJPE161032-9


title: WBJPE161032-4


title: WBJPE161032-36


title: WBJPE161032-12


title: WBJPE161032-13


title: WBJPE161032-5


title: WBJPE161032-1


title: WBJPE161032-24


title: WBJPE161032-2


title: WBJPE161032-41


title: WBJPE161032-10


title: WBJPE161031-559


title: WBJPE161031-560


title: WBJPE161031-558


title: WBJPE161031-557


title: WBJPE161031-556


title: WBJPE161031-554


title: WBJPE161031-555


title: WBJPE161032-3


title: WBJPE161031-553


title: WBJPE161031-552


title: WBJPE161031-551


title: WBJPE161031-550


title: WBJPE161031-549


title: WBJPE161031-540


title: WBJPE161031-542


title: WBJPE161031-548


title: WBJPE161031-547


title: WBJPE161031-541


title: WBJPE161031-543


title: WBJPE161031-544


title: WBJPE161031-538


title: WBJPE161031-539


title: WBJPE161031-536


title: WBJPE161031-545


title: WBJPE161031-537


title: WBJPE161031-535


title: WBJPE161031-533


title: WBJPE161031-534


title: WBJPE161031-531


title: WBJPE161031-530


title: WBJPE161031-529


title: WBJPE161031-528


title: WBJPE161031-546


title: WBJPE161031-526


title: WBJPE161031-524


title: WBJPE161031-523


title: WBJPE161031-525


title: WBJPE161031-521


title: WBJPE161031-520


title: WBJPE161031-519


title: WBJPE161031-517


title: WBJPE161031-522


title: WBJPE161031-516


title: WBJPE161031-515


title: WBJPE161031-514


title: WBJPE161031-513


title: WBJPE161031-512


title: WBJPE161031-532


title: WBJPE161031-518


title: WBJPE161031-510


title: WBJPE161031-506


title: WBJPE161031-511


title: WBJPE161031-509


title: WBJPE161031-507


title: WBJPE161031-504


title: WBJPE161031-508


title: WBJPE161031-505


title: WBJPE161031-503


title: WBJPE161031-527


title: WBJPE161031-501


title: WBJPE161031-500


title: WBJPE161031-499


title: WBJPE161031-495


title: WBJPE161031-497


title: WBJPE161031-496


title: WBJPE161031-493


title: WBJPE161031-494


title: WBJPE161031-491


title: WBJPE161031-492


title: WBJPE161031-490


title: WBJPE161031-489


title: WBJPE161031-484


title: WBJPE161031-486


title: WBJPE161031-488


title: WBJPE161031-485


title: WBJPE161031-482


title: WBJPE161031-502


title: WBJPE161031-480


title: WBJPE161032-105


title: WBJPE161031-477


title: WBJPE161031-487


title: WBJPE161031-478


title: WBJPE161031-483


title: WBJPE161031-479


title: WBJPE161031-475


title: WBJPE161031-476


title: WBJPE161031-474


title: WBJPE161031-473


title: WBJPE161031-498


title: WBJPE161031-472


title: WBJPE161031-470


title: WBJPE161031-469


title: WBJPE161031-468


title: WBJPE161031-471


title: WBJPE161031-467


title: WBJPE161031-466


title: WBJPE161031-465


title: WBJPE161031-464


title: WBJPE161031-463


title: WBJPE161031-481


title: WBJPE161031-456


title: WBJPE161031-458


title: WBJPE161031-462


title: WBJPE161031-453


title: WBJPE161031-460


title: WBJPE161031-455


title: WBJPE161031-452


title: WBJPE161031-451


title: WBJPE161031-449


title: WBJPE161031-450


title: WBJPE161031-448


title: WBJPE161031-457


title: WBJPE161031-454


title: WBJPE161031-461


title: WBJPE161031-447


title: WBJPE161031-444


title: WBJPE161031-446


title: WBJPE161031-443


title: WBJPE161031-445


title: WBJPE161031-442


title: WBJPE161031-436


title: WBJPE161031-440


title: WBJPE161031-438


title: WBJPE161031-439


title: WBJPE161031-441


title: WBJPE161031-437


title: WBJPE161031-435


title: WBJPE161031-459


title: WBJPE161031-434


title: WBJPE161031-433


title: WBJPE161031-430


title: WBJPE161031-431


title: WBJPE161031-432


title: WBJPE161031-429


title: WBJPE161031-428


title: WBJPE161031-423


title: WBJPE161031-424


title: WBJPE161031-426


title: WBJPE161031-427


title: WBJPE161031-425


title: WBJPE161031-422


title: WBJPE161031-421


title: WBJPE161031-420


title: Subject ID: IN.USW.1041_IgG

type: protein

city: Irvine

first: Joseph

middle: John

last: Campo

address: 1 Technology Dr., STE E309

institute: Antigen Discovery, Inc.

hyb_protocol: Milk samples were diluted 1:5 in a 1.5 mg/mL E. coli lysate solution (Antigen Discovery, Inc., Irvine, CA) in protein arraying buffer (GVS, Cat. 10485356, Sanford, ME) and incubated at room temperature for 30 min. For milk samples previously diluted in preservative solution, samples were diluted 1:2.5 in the lysate solution. Microarray slides were hydrated in arraying buffer and then probed with 250 µL of the preincubated milk samples using sealed, fitted slide chambers to avoid cross-contamination between arrays. Arrays were incubated overnight at 4°C with agitation, washed three times with Tris-buffered saline (TBS)-0.05% Tween 20 (Thermo Scientific, J77500K8, diluted 20x in molecular grade water), and incubated with Cy3-conjugated anti-human IgG diluted 1:200 in arraying buffer and biotin-conjugated anti-Human IgA diluted 1:1000 (Jackson ImmunoResearch, Cat. 709-165-098 and Cat. 109-065-011, West Grove, PA). Arrays were washed three times with TBS–0.05% Tween 20 and incubated with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Cat. D7-2212, Frederick, MD) at room temperature, protected from light. Arrays were washed 3x with TBS–0.05% Tween 20, 3x with TBS, and once with water and then air dried by being centrifuged at 1,000 x g for 4 min and left overnight in a desiccator before scanning.

scan_protocol: Probed microarrays were scanned using a GenePix 4300A high-resolution microarray scanner (Molecular Devices, Sunnyvale, CA), and an image file (.tiff) was saved for each array using GenePix pro 7 software. The signals in the scanned images were quantified using Mapix software (Innopsys).

data_processing: All further data processing was performed in R (http://www.R-project.org). Data were normalized by first transforming raw values using the base 2 logarithm. Next, the data set was normalized to remove systematic effects by subtracting the median signal intensity of the IVTT control spots from the IVTT antigen spots for each sample. Since the IVTT control spots carry not only the chip, sample, and batch-level systematic effects, but also antibody background reactivity to the E. coli cell-free IVTT system, this procedure normalizes the data and provides a relative measure of the specific antibody binding versus the nonspecific antibody binding to the IVTT controls. With the normalized data, a value of 0.0 means that the intensity is no different than that of the IVTT controls, a value of 1.0 indicates a doubling (2-fold) with respect to IVTT control spots, a value of 2.0 indicates 4-fold, 3.0 indicates 8-fold, etc. The normalized signal intensity of the purified protein spots is represented as the base 2 logarithm of the raw signal intensities.

label: Cy3-conjugated anti-human IgG

molecule: protein

source_name: human breast milk

label_protocol: Cy3-conjugated anti-human IgG (Jackson ImmunoResearch, Cat. 709-165-098, West Grove, PA)

extract_protocol: Sampling protocol: In PE, SW, USC, and USW, milk was collected using an electric breast pump. In all other cohorts, milk was manually expressed. Except for those collected in ETR, samples were immediately placed on ice, aliquoted within 30 min, and frozen at −20°C. Milk collected in ETR was preserved in a 1:1 ratio with Milk Preservation Solution (Norgen Biotek, Cat. 44800, Thorold, Ontario) and frozen within 6 d. We have shown previously that this method can maintain bacterial DNA integrity in human milk held at 37°C for at least 2 wk (34). All samples were shipped on dry ice to the University of Idaho, where they were immediately frozen at −20°C.

tag: region

value: U.S. Washington

tag: mother's age

tag: infant's sex

tag: time post-partum

tag: parity

tag: delivery

value: Vaginal

tag: bmi

tag: bmi code

value: NORMAL

tag: mother's height (cm)

tag: companion animals

value: YES

tag: agricultural animals

value: NO

tag: adjusted household density

tag: molecule type

value: IgG


title: Subject ID: IN.USW.1038_IgG


title: Subject ID: IN.USW.1037_IgG

value: OVERWEIGHT


title: Subject ID: IN.USW.1036_IgG


title: Subject ID: IN.USW.1040_IgG


title: WBJPE161031-419

tag: strain

tag: genotype/variation

tag: tissue


title: WBJPE161031-418

tag: developmental stage


title: Subject ID: IN.USW.1035_IgG

tag: region


title: WBJPE161031-416


title: WBJPE161031-417


title: Subject ID: IN.USW.1034_IgG

tag: mother's age

value: cSection


title: Subject ID: IN.USW.1031_IgG

tag: infant's sex


title: WBJPE161031-414


title: Subject ID: IN.USW.1032_IgG

tag: time post-partum


title: Subject ID: IN.USW.1033_IgG

tag: parity


title: Subject ID: IN.USW.1030_IgG

tag: delivery


title: WBJPE161031-415


title: WBJPE161031-413


title: Subject ID: IN.USW.1039_IgG

tag: bmi


title: WBJPE161031-410


title: WBJPE161031-412


title: Subject ID: IN.USW.1029_IgG

tag: bmi code


title: Subject ID: IN.USW.1028_IgG

tag: mother's height (cm)


title: WBJPE161031-409


title: Subject ID: IN.USW.1027_IgG

tag: companion animals


title: Subject ID: IN.USW.1024_IgG

tag: agricultural animals


title: Subject ID: IN.USW.1026_IgG

tag: adjusted household density


title: WBJPE161031-407


title: Subject ID: IN.USW.1023_IgG

tag: molecule type


title: Subject ID: IN.USW.1021_IgG

value: OBESE


title: Subject ID: IN.USW.1019_IgG


title: WBJPE161031-404

tag: strain


title: Subject ID: IN.USW.1022_IgG


title: WBJPE161031-402

tag: genotype/variation


title: WBJPE161031-401

tag: tissue


title: Subject ID: IN.USW.1020_IgG


title: WBJPE161031-400

tag: developmental stage


title: WBJPE161031-411


title: Subject ID: IN.USW.1025_IgG

tag: region


title: Subject ID: IN.USW.1017_IgG

tag: mother's age


title: WBJPE161031-399


title: Subject ID: IN.USW.1015_IgG

tag: infant's sex


title: WBJPE161031-397


title: Subject ID: IN.USW.1013_IgG

tag: time post-partum


title: WBJPE161031-396


title: Subject ID: IN.USW.1018_IgG

tag: parity


title: WBJPE161031-408


title: Subject ID: IN.USW.1012_IgG

tag: delivery


title: WBJPE161031-405


title: WBJPE161031-406


title: Subject ID: IN.USW.1014_IgG

tag: bmi


title: WBJPE161031-403


title: Subject ID: IN.USW.1010_IgG

tag: bmi code


title: Subject ID: IN.USW.1011_IgG

tag: mother's height (cm)


title: Subject ID: IN.USW.1009_IgG

tag: companion animals


title: WBJPE161031-392


title: WBJPE161031-390


title: WBJPE161031-398


title: WBJPE161031-391


title: Subject ID: IN.USW.1016_IgG

tag: agricultural animals


title: WBJPE161031-389


title: Subject ID: IN.USW.1007_IgG

tag: adjusted household density


title: Subject ID: IN.USW.1008_IgG

tag: molecule type


title: Subject ID: IN.USW.1006_IgG


title: WBJPE161031-395

tag: strain


title: WBJPE161031-388

tag: genotype/variation


title: Subject ID: IN.USW.1004_IgG


title: Subject ID: IN.USW.1003_IgG


title: WBJPE161031-387

tag: tissue


title: WBJPE161031-384

tag: developmental stage


title: Subject ID: IN.USW.1002_IgG

tag: region


title: WBJPE161031-383


title: Subject ID: IN.USW.1005_IgG

tag: mother's age


title: Subject ID: IN.USW.1001_IgG

tag: infant's sex


title: Subject ID: IN.USC.1125_IgG

value: U.S. California

tag: time post-partum


title: Subject ID: IN.USC.1126_IgG

tag: parity


title: WBJPE161031-393

value: C57BL/6 Transgenic Mouse


title: WBJPE161031-381

value: SCX-GFP mouse


title: WBJPE161031-382

value: hind limb


title: Subject ID: IN.USC.1124_IgG

tag: delivery


title: Subject ID: IN.USC.1122_IgG

tag: bmi


title: WBJPE161031-380


title: WBJPE161031-385


title: Subject ID: IN.USC.1121_IgG

tag: bmi code


title: Subject ID: IN.USC.1123_IgG

tag: mother's height (cm)


title: WBJPE161031-379


title: WBJPE161031-394


title: WBJPE161031-378


title: WBJPE161031-377


title: WBJPE161031-386


title: Subject ID: IN.USC.1120_IgG

tag: companion animals


title: Subject ID: IN.USC.1119_IgG

tag: agricultural animals


title: WBJPE161031-376


title: WBJPE161031-375


title: WBJPE161031-374


title: WBJPE161031-372


title: WBJPE161031-373


title: Subject ID: IN.USC.1118_IgG

tag: adjusted household density


title: Subject ID: IN.USC.1116_IgG

tag: molecule type


title: Subject ID: IN.USC.1115_IgG


title: WBJPE161031-371

tag: strain


title: Subject ID: IN.USC.1108_IgG


title: WBJPE161031-370

tag: genotype/variation


title: Subject ID: IN.USC.1101_IgG


title: WBJPE161031-369

tag: tissue


title: WBJPE161031-367

tag: developmental stage


title: WBJPE161031-368


title: Subject ID: IN.SW.925_IgG

tag: region

value: Sweden


title: WBJPE161031-366


title: WBJPE161031-365


title: Subject ID: IN.SW.924_IgG

tag: mother's age


title: Subject ID: IN.SW.923_IgG

tag: infant's sex


title: WBJPE161031-364


title: WBJPE161031-363


title: Subject ID: IN.SW.922_IgG

tag: time post-partum


title: Subject ID: IN.SW.921_IgG

tag: parity


title: WBJPE161031-362


title: Subject ID: IN.SW.918_IgG

tag: delivery


title: WBJPE161031-361


title: Subject ID: IN.USC.1102_IgG

tag: bmi


title: Subject ID: IN.SW.917_IgG

tag: bmi code


title: WBJPE161031-360


title: Subject ID: IN.SW.916_IgG

tag: mother's height (cm)


title: WBJPE161031-358


title: Subject ID: IN.SW.915_IgG

tag: companion animals


title: WBJPE161031-357


title: WBJPE161031-359


title: Subject ID: IN.SW.913_IgG

tag: agricultural animals


title: Subject ID: IN.SW.911_IgG

tag: adjusted household density


title: Subject ID: IN.SW.912_IgG

tag: molecule type


title: Subject ID: IN.USC.1109_IgG


title: WBJPE161031-356

tag: strain


title: Subject ID: IN.SW.909_IgG


title: Subject ID: IN.SW.910_IgG


title: Subject ID: IN.SW.920_IgG


title: WBJPE161031-355

tag: genotype/variation


title: WBJPE161031-353

tag: tissue


title: WBJPE161031-352

tag: developmental stage


title: Subject ID: IN.SW.908_IgG

tag: region


title: Subject ID: IN.SW.905_IgG

tag: mother's age


title: Subject ID: IN.SW.906_IgG

tag: infant's sex


title: WBJPE161031-350


title: WBJPE161031-351


title: Subject ID: IN.SW.904_IgG

tag: time post-partum


title: Subject ID: IN.SW.903_IgG

tag: parity


title: WBJPE161031-349


title: WBJPE161031-348


title: Subject ID: IN.SW.902_IgG

tag: delivery


title: WBJPE161031-346


title: WBJPE161031-347


title: WBJPE161031-345


title: Subject ID: IN.SW.901_IgG

tag: bmi


title: WBJPE161031-343


title: WBJPE161031-344


title: Subject ID: IN.SP.840_IgG

value: Spain

tag: bmi code


title: Subject ID: IN.SP.839_IgG

tag: mother's height (cm)


title: WBJPE161031-341


title: Subject ID: IN.SP.838_IgG

tag: companion animals


title: Subject ID: IN.SP.841_IgG

tag: agricultural animals


title: Subject ID: IN.SW.907_IgG

tag: adjusted household density


title: WBJPE161031-339


title: Subject ID: IN.SP.837_IgG

tag: molecule type


title: Subject ID: IN.SP.836_IgG


title: WBJPE161031-338

tag: strain


title: WBJPE161031-337

tag: genotype/variation


title: Subject ID: IN.SP.835_IgG


title: Subject ID: IN.SP.834_IgG


title: WBJPE161031-336

tag: tissue


title: Subject ID: IN.SP.843_IgG


title: Subject ID: IN.SP.833_IgG


title: Subject ID: IN.SP.842_IgG


title: Subject ID: IN.SP.832_IgG


title: Subject ID: IN.SP.831_IgG


title: WBJPE161031-335

tag: developmental stage


title: WBJPE161031-334


title: WBJPE161031-342


title: WBJPE161031-333


title: WBJPE161031-332


title: Subject ID: IN.SP.829_IgG

tag: region


title: WBJPE161031-340


title: Subject ID: IN.SP.830_IgG

tag: mother's age


title: WBJPE161031-330


title: Subject ID: IN.SP.828_IgG

tag: infant's sex


title: Subject ID: IN.SP.827_IgG

tag: time post-partum


title: WBJPE161031-329


title: Subject ID: IN.SP.826_IgG

tag: parity


title: Subject ID: IN.SP.825_IgG

tag: delivery


title: WBJPE161031-326


title: WBJPE161031-328


title: WBJPE161031-325


title: Subject ID: IN.SP.822_IgG

tag: bmi


title: Subject ID: IN.SP.821_IgG

tag: bmi code


title: WBJPE161031-324


title: Subject ID: IN.SP.824_IgG

tag: mother's height (cm)


title: WBJPE161031-323


title: Subject ID: IN.SP.823_IgG

tag: companion animals


title: WBJPE161031-322


title: Subject ID: IN.SP.820_IgG

tag: agricultural animals


title: Subject ID: IN.SP.819_IgG

tag: adjusted household density


title: WBJPE161031-321


title: WBJPE161031-331


title: Subject ID: IN.SP.818_IgG

tag: molecule type


title: WBJPE161031-319

tag: strain


title: WBJPE161031-317

tag: genotype/variation


title: WBJPE161031-318

tag: tissue


title: Subject ID: IN.SP.817_IgG


title: WBJPE161031-327

tag: developmental stage


title: Subject ID: IN.SP.813_IgG

tag: region


title: WBJPE161031-316


title: Subject ID: IN.SP.815_IgG

tag: mother's age


title: Subject ID: IN.SP.812_IgG

tag: infant's sex


title: Subject ID: IN.SP.811_IgG

tag: time post-partum


title: Subject ID: IN.SP.810_IgG

tag: parity


title: WBJPE161031-315


title: WBJPE161031-314


title: Subject ID: IN.SP.809_IgG

tag: delivery


title: WBJPE161031-313


title: Subject ID: IN.SP.807_IgG

tag: bmi


title: WBJPE161031-312


title: WBJPE161031-320


title: Subject ID: IN.SP.808_IgG

tag: bmi code


title: WBJPE161031-311


title: Subject ID: IN.SP.805_IgG

tag: mother's height (cm)


title: WBJPE161031-309


title: WBJPE161031-308


title: Subject ID: IN.SP.804_IgG

tag: companion animals


title: WBJPE161031-307


title: Subject ID: IN.SP.803_IgG

tag: agricultural animals


title: WBJPE161031-306


title: Subject ID: IN.SP.802_IgG

tag: adjusted household density


title: WBJPE161031-305


title: WBJPE161031-304


title: Subject ID: IN.SP.801_IgG

tag: molecule type


title: WBJPE161031-354

tag: strain


title: WBJPE161031-302

tag: genotype/variation


title: Subject ID: IN.PE.742_IgG

value: Peru


title: WBJPE161031-303

tag: tissue


title: Subject ID: IN.PE.743_IgG


title: WBJPE161031-301

tag: developmental stage


title: Subject ID: IN.PE.741_IgG

tag: region


title: Subject ID: IN.PE.740_IgG

tag: mother's age


title: Subject ID: IN.PE.739_IgG

tag: infant's sex


title: WBJPE161031-310


title: Subject ID: IN.PE.737_IgG

tag: time post-partum


title: WBJPE161031-300


title: Subject ID: IN.SP.806_IgG

tag: parity


title: Subject ID: IN.PE.735_IgG

tag: delivery


title: Subject ID: IN.PE.736_IgG

tag: bmi


title: WBJPE161031-297


title: WBJPE161031-299


title: Subject ID: IN.PE.734_IgG

tag: bmi code


title: WBJPE161031-296


title: WBJPE161031-295


title: Subject ID: IN.PE.733_IgG

tag: mother's height (cm)


title: Subject ID: IN.PE.732_IgG

tag: companion animals


title: WBJPE161031-294


title: WBJPE161031-292


title: WBJPE161031-293


title: Subject ID: IN.PE.730_IgG

tag: agricultural animals


title: Subject ID: IN.PE.738_IgG

tag: adjusted household density


title: Subject ID: IN.PE.729_IgG

tag: molecule type


title: WBJPE161031-290

tag: strain


title: WBJPE161031-289

tag: genotype/variation


title: WBJPE161031-288

tag: tissue


title: Subject ID: IN.PE.728_IgG


title: WBJPE161031-291

tag: developmental stage


title: Subject ID: IN.PE.727_IgG

tag: region


title: WBJPE161031-298


title: Subject ID: IN.PE.726_IgG

tag: mother's age


title: WBJPE161031-286


title: Subject ID: IN.PE.725_IgG

tag: infant's sex


title: WBJPE161031-287


title: WBJPE161031-284


title: WBJPE161031-283


title: WBJPE161031-285


title: Subject ID: IN.PE.723_IgG

tag: time post-partum


title: WBJPE161031-282


title: Subject ID: IN.PE.722_IgG

tag: parity


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tag: delivery


title: Subject ID: IN.PE.720_IgG

tag: bmi


title: WBJPE161031-281


title: Subject ID: IN.PE.721_IgG

tag: bmi code


title: WBJPE161031-280


title: Subject ID: IN.PE.731_IgG

tag: mother's height (cm)


title: Subject ID: IN.PE.717_IgG

tag: companion animals


title: WBJPE161031-279


title: Subject ID: IN.PE.719_IgG

tag: agricultural animals


title: Subject ID: IN.PE.718_IgG

tag: adjusted household density


title: WBJPE161031-277


title: WBJPE161031-278


title: Subject ID: IN.PE.716_IgG

tag: molecule type


title: Subject ID: IN.PE.714_IgG


title: WBJPE161031-276

tag: strain


title: WBJPE161031-275

tag: genotype/variation


title: Subject ID: IN.PE.715_IgG


title: WBJPE161031-274

tag: tissue


title: Subject ID: IN.PE.713_IgG


title: WBJPE161031-273

tag: developmental stage


title: Subject ID: IN.PE.712_IgG

tag: region


title: WBJPE161031-272


title: WBJPE161031-271


title: WBJPE161031-270


title: WBJPE161031-269


title: Subject ID: IN.PE.711_IgG

tag: mother's age


title: Subject ID: IN.PE.709_IgG

tag: infant's sex


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tag: time post-partum


title: Subject ID: IN.PE.705_IgG

tag: parity


title: Subject ID: IN.PE.706_IgG

tag: delivery


title: Subject ID: IN.PE.708_IgG

tag: bmi


title: Subject ID: IN.PE.704_IgG

tag: bmi code


title: WBJPE161031-266


title: WBJPE161031-268


title: WBJPE161031-265


title: WBJPE161031-267


title: WBJPE161031-264


title: Subject ID: IN.PE.702_IgG

tag: mother's height (cm)


title: Subject ID: IN.PE.703_IgG

tag: companion animals


title: WBJPE161031-263


title: Subject ID: IN.KE.644_IgG

value: Kenya

tag: agricultural animals


title: WBJPE161031-262


title: WBJPE161031-261


title: WBJPE161031-260


title: Subject ID: IN.KE.643_IgG

tag: adjusted household density


title: Subject ID: IN.PE.701_IgG

tag: molecule type


title: Subject ID: IN.KE.642_IgG


title: Subject ID: IN.PE.707_IgG


title: WBJPE161031-258

tag: strain


title: Subject ID: IN.KE.639_IgG


title: Subject ID: IN.KE.641_IgG


title: WBJPE161031-257

tag: genotype/variation


title: Subject ID: IN.KE.637_IgG


title: Subject ID: IN.KE.638_IgG


title: WBJPE161031-256

tag: tissue


title: WBJPE161031-255

tag: developmental stage


title: WBJPE161031-254


title: Subject ID: IN.KE.635_IgG

tag: region


title: Subject ID: IN.KE.634_IgG

tag: mother's age


title: WBJPE161031-252


title: Subject ID: IN.KE.631_IgG

tag: infant's sex


title: WBJPE161031-250


title: Subject ID: IN.KE.632_IgG

tag: time post-partum


title: WBJPE161031-249


title: Subject ID: IN.KE.636_IgG

tag: parity


title: WBJPE161031-259


title: WBJPE161031-248


title: WBJPE161031-247


title: Subject ID: IN.KE.629_IgG

tag: delivery


title: WBJPE161031-246


title: Subject ID: IN.KE.628_IgG

tag: bmi


title: Subject ID: IN.KE.627_IgG

tag: bmi code


title: WBJPE161031-245


title: WBJPE161031-244


title: Subject ID: IN.KE.624_IgG

value: UNDERWEIGHT

tag: mother's height (cm)


title: Subject ID: IN.KE.626_IgG

tag: companion animals


title: WBJPE161031-242


title: Subject ID: IN.KE.623_IgG

value: Vaginal

tag: agricultural animals


title: Subject ID: IN.KE.625_IgG

value: NORMAL

tag: adjusted household density


title: WBJPE161031-253


title: WBJPE161031-241


title: WBJPE161031-251


title: Subject ID: IN.KE.622_IgG

value: YES

tag: molecule type


title: Subject ID: IN.KE.621_IgG

value: NO


title: WBJPE161031-240

tag: strain


title: Subject ID: IN.KE.630_IgG

value: IgG


title: Subject ID: IN.KE.620_IgG


title: WBJPE161031-237

tag: genotype/variation


title: Subject ID: IN.KE.619_IgG


title: Subject ID: IN.KE.617_IgG

value: OVERWEIGHT


title: WBJPE161031-236

tag: tissue


title: WBJPE161031-235

tag: developmental stage


title: WBJPE161031-234


title: WBJPE161031-233


title: WBJPE161031-243


title: Subject ID: IN.KE.614_IgG

tag: region


title: Subject ID: IN.KE.615_IgG

tag: mother's age


title: Subject ID: IN.KE.612_IgG

tag: infant's sex

value: cSection


title: Subject ID: IN.KE.611_IgG

tag: time post-partum


title: WBJPE161031-231


title: Subject ID: IN.KE.633_IgG

tag: parity


title: WBJPE161031-232


title: WBJPE161031-230


title: Subject ID: IN.KE.613_IgG

tag: delivery


title: WBJPE161031-229


title: WBJPE161031-239


title: Subject ID: IN.KE.608_IgG

tag: bmi


title: Subject ID: IN.KE.609_IgG

tag: bmi code

value: OBESE


title: WBJPE161031-228


title: WBJPE161031-238


title: WBJPE161031-227


title: Subject ID: IN.KE.607_IgG

tag: mother's height (cm)


title: Subject ID: IN.KE.606_IgG

tag: companion animals


title: Subject ID: IN.KE.616_IgG

tag: agricultural animals


title: Subject ID: IN.KE.605_IgG

tag: adjusted household density


title: WBJPE161031-225


title: WBJPE161031-224


title: Subject ID: IN.KE.603_IgG

tag: molecule type


title: WBJPE161031-223

tag: strain


title: Subject ID: IN.KE.604_IgG


title: Subject ID: IN.KE.602_IgG


title: WBJPE161031-221

tag: genotype/variation


title: WBJPE161031-222

tag: tissue


title: Subject ID: IN.KE.610_IgG


title: Subject ID: IN.GN.544_IgG

value: Ghana


title: WBJPE161031-218

value: C57BL/6 Transgenic Mouse

tag: developmental stage


title: WBJPE161031-220

value: SCX-GFP mouse


title: Subject ID: IN.KE.601_IgG

tag: region


title: Subject ID: IN.GN.540_IgG

tag: mother's age


title: Subject ID: IN.GN.542_IgG

tag: infant's sex


title: Subject ID: IN.GN.541_IgG

tag: time post-partum


title: WBJPE161031-215

value: hind limb


title: WBJPE161031-217


title: WBJPE161031-226


title: WBJPE161031-214


title: Subject ID: IN.GN.538_IgG

tag: parity


title: WBJPE161031-216


title: WBJPE161031-212


title: Subject ID: IN.GN.535_IgG

tag: delivery


title: WBJPE161031-211


title: Subject ID: IN.GN.536_IgG

tag: bmi


title: WBJPE161031-210


title: Subject ID: IN.GN.537_IgG

tag: bmi code


title: WBJPE161031-219


title: WBJPE161031-213


title: Subject ID: IN.GN.532_IgG

tag: mother's height (cm)


title: WBJPE161031-209


title: WBJPE161031-208


title: Subject ID: IN.GN.531_IgG

tag: companion animals


title: WBJPE161031-207


title: Subject ID: IN.GN.533_IgG

tag: agricultural animals


title: Subject ID: IN.GN.530_IgG

tag: adjusted household density


title: Subject ID: IN.GN.539_IgG

tag: molecule type


title: WBJPE161031-204

tag: strain


title: Subject ID: IN.GN.528_IgG


title: Subject ID: IN.GN.529_IgG


title: Subject ID: IN.GN.523_IgG


title: Subject ID: IN.GN.527_IgG


title: Subject ID: IN.GN.525_IgG


title: WBJPE161031-203

tag: genotype/variation


title: WBJPE161031-202

tag: tissue


title: Subject ID: IN.GN.522_IgG


title: WBJPE161031-201

tag: developmental stage


title: WBJPE161031-200


title: WBJPE161031-199


title: Subject ID: IN.GN.520_IgG

tag: region


title: WBJPE161031-197


title: WBJPE161031-196


title: Subject ID: IN.GN.519_IgG

tag: mother's age


title: Subject ID: IN.GN.516_IgG

tag: infant's sex


title: Subject ID: IN.GN.517_IgG

tag: time post-partum


title: Subject ID: IN.GN.515_IgG

tag: parity


title: WBJPE161031-206


title: WBJPE161031-195


title: WBJPE161031-194


title: WBJPE161031-205


title: Subject ID: IN.GN.521_IgG

tag: delivery


title: Subject ID: IN.GN.534_IgG

tag: bmi


title: WBJPE161031-193


title: Subject ID: IN.GN.513_IgG

tag: bmi code


title: Subject ID: IN.GN.514_IgG

tag: mother's height (cm)


title: WBJPE161031-189


title: WBJPE161031-190


title: WBJPE161031-192


title: WBJPE161031-188


title: Subject ID: IN.GN.511_IgG

tag: companion animals


title: WBJPE161031-198


title: WBJPE161031-187


title: Subject ID: IN.GN.512_IgG

tag: agricultural animals


title: Subject ID: IN.GN.508_IgG

tag: adjusted household density


title: Subject ID: IN.GN.510_IgG

tag: molecule type


title: Subject ID: IN.GN.505_IgG


title: Subject ID: IN.GN.518_IgG


title: Subject ID: IN.GN.504_IgG


title: WBJPE161031-185

tag: strain


title: Subject ID: IN.GN.506_IgG


title: WBJPE161031-182

tag: genotype/variation


title: WBJPE161031-181

tag: tissue


title: WBJPE161031-180

tag: developmental stage


title: WBJPE161031-184


title: WBJPE161031-183


title: Subject ID: IN.GN.503_IgG

tag: region


title: WBJPE161031-177


title: WBJPE161031-191


title: Subject ID: IN.GN.502_IgG

tag: mother's age


title: Subject ID: IN.GBU.440_IgG

value: The Gambia, urban

tag: infant's sex


title: Subject ID: IN.GBU.444_IgG

tag: time post-partum


title: Subject ID: IN.GN.501_IgG

tag: parity


title: Subject ID: IN.GBU.436_IgG

tag: delivery


title: WBJPE161031-176


title: WBJPE161031-173


title: Subject ID: IN.GBU.437_IgG

tag: bmi


title: Subject ID: IN.GBU.435_IgG

tag: bmi code


title: WBJPE161031-174


title: WBJPE161031-175


title: Subject ID: IN.GBU.434_IgG

tag: mother's height (cm)


title: Subject ID: IN.GBU.438_IgG

tag: companion animals


title: Subject ID: IN.GBU.433_IgG

tag: agricultural animals


title: WBJPE161031-172


title: Subject ID: IN.GN.509_IgG

tag: adjusted household density


title: Subject ID: IN.GBU.431_IgG

tag: molecule type


title: WBJPE161031-186

tag: strain


title: WBJPE161031-179

tag: genotype/variation


title: WBJPE161031-178

tag: tissue