title: CD8 Spleen 1

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description: CD8+ T cell_Spleen_Rep1

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.5).
Filtered adaptor and poor quality sequences respectively, using cutadapt (v. 1.8.3) (minimum phred quality score = 20).
The reference genome (mm10) based alignment of clean reads were performed using STAR (v. 2.6.0c) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts packgae by subread/1.6.2 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Genome_build: Mus musculus reference genome (mm10).
Supplementary_files_format_and_content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: Spleen

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols, using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takata Cat# 634894).

treatment_protocol: Cells were surfaced stained using antibodies for flow cytometry and sorted on BD FacsAria

tag: strain

value: MRL/lpr (MRL.Faslpr)

value: Spleen

value: CD8+ T cell

tag: age

value: 23 week old


title: CD8 Spleen 2

status: Public on Aug 09 2018

type: SRA

country: USA

description: CD8+ T cell_Spleen_Rep2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type


title: CD4 Spleen 3

description: CD4+ T cell_Spleen_Rep3

value: CD4+ T cell


title: CD8 Spleen 3

description: CD8+ T cell_Spleen_Rep3


title: CD4 Spleen 2

description: CD4+ T cell_Spleen_Rep2


title: CD8 Kidney 3

description: CD8+ T cell_Kidney_Rep3

source_name: Kidney

value: Kidney


title: Kawasaki_58

type: RNA

city: London

first: Michael

last: Levin

address: South Kensington Campus

department: Paediatrics

country: United Kingdom

institute: Imperial College London

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using RSN, after background subtraction. The software used for data normalization was 'R' Language and Environment for Statistical Computing (R) 3.2.2

label: biotin

organism: Homo sapiens

source_name: Whole Blood from patient with KD

label_protocol: Standard Illumina TotalPrep RNA Amplification kits (Applied Biosystems).

extract_protocol: Standard PAXgene® blood RNA extraction kit protocol (Qiagen).

tag: category

value: KD

tag: dataset

value: Discovery

tag: gender

value: Female


title: CD8 Kidney 2

description: CD8+ T cell_Kidney_Rep2


title: Kawasaki_57

value: Male


title: Kawasaki_56


title: CD4 Spleen 1

description: CD4+ T cell_Spleen_Rep1


title: Kawasaki_59


title: Kawasaki_54


title: Kawasaki_50


title: Kawasaki_62


title: CD4 Kidney 3

description: CD4+ T cell_Kidney_Rep3


title: Kawasaki_49


title: Kawasaki_55


title: Kawasaki_53


title: CD4 Kidney 2

description: CD4+ T cell_Kidney_Rep2


title: CD4 Kidney 1

description: CD4+ T cell_Kidney_Rep1


title: Kawasaki_48


title: Kawasaki_52


title: CD8 Kidney 1

description: CD8+ T cell_Kidney_Rep1


title: Kawasaki_51


title: Kawasaki_45


title: Kawasaki_43


title: Kawasaki_46


title: Kawasaki_47


title: Kawasaki_44


title: piwi-sKD,dcr2-sKD

city: MONTPELLIER

first: SEVERINE

last: CHAMBEYRON

address: 141, rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: CNRS

description:
Chambeyron_16_4_949-Dicer-28_S33_L005_R1_001
Manual anion-exchange chromatography (HiTrapQ column) purification

data_processing:
Sequenced reads were stripped of the adapter in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (dm3) according to sequencing quality using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed (one mismatch was nevertheless allowed on low-sequencing quality nucleotides).
After subtracting reads matching abundant cellular species rRNAs, tRNAs and snRNAs identified by mapping on dataset retrieved from modEncode (http://www.modencode.org/ (Celniker et al. 2009), the 18-30 nt long reads were kept.
Small RNAs mapping on piRNA clusters , ovary siRNA clusters , TEs or 3'UTR of coding genes (ftp://ftp.flybase.net/), and not to rRNAs or miRNAs were defined.
Candidate piRNAs were a subset of the above defined reads with a size between 23 and 30 nucleotides. Candidate siRNA were a subset of the above defined reads with 21nt. Unique mappers were defined as reads for which only one best-score alignment existed in the genome.
Candidate piRNAs were mapped again to piRNA cluster sequences and canonical TE sequences. Candidate siRNA were mapped again to ovarian siRNA cluster sequences and canonical TE sequences.
Data were normalized using the unique mapper reads of piRNA cluster 1 (42AB). Our full analysis pipeline is available at https://bitbucket.org/blaiseli/pirna-pipeline.
Genome_build: Drosophila melanogaster genome (dm3)
Supplementary_files_format_and_content: .txt files with read counts for piRNA- and/or siRNA-candidate reads for each analysed TE in different mapping categories (F=sense read, R= antisense read, mm=mismatch) (#ref = TE-family, total = sense and antisense reads with up to 4 mismatches, total_F = all sense reads, total_R = all antisense reads , F_0mm = sense reads with 0 mismatches , R_0mm = antisense reads with 0 mismatches , F_mm = sense reads with 1 ore more mismatches, R_mm = antisense reads with 1 ore more mismatches, F_1_mm = sense reads with 1 mismatch, R_1_mm = antisense reads with 1 mismatch, F_2_mm = sense reads with 2 mismatches, R_2_mm = antisense reads with 2 mismatches, F_3_mm = sense reads with 3 mismatches, R_3_mm = antisense reads with 3 mismatches, F_4_mm = sense reads with 4 mismatches, R_4_mm = antisense reads with 4 mismatches) for each sequenced condition.

organism: Drosophila melanogaster

source_name: Drosophila ovaries

growth_protocol:
[no-KD] Flies were grown at 20°C
[piwi-sKD] Flies were grown at 20°C exept in the last 5 days (25°C)

extract_protocol:
Small RNAs (18-30nt) were isolated by manual anion exchange chromatography procedure
Extracted small RNAs were size selected by BGI (China) for no-KD and piwi-sKD and by Donnelly sequencing Center (Toronto) for piwi-sKD,dcr2-sKD and piwi-sKD,ctrl-sKD.

tag: genotype

value: tj-GAL4 / + ; GAL80[ts] sh-piwi / sh-dcr2

value: Drosophila ovaries


title: piwi-sKD,ctrl-sKD

description:
Chambeyron_15_3_949-white-28_S32_L005_R1_001
Manual anion-exchange chromatography (HiTrapQ column) purification

value: tj-GAL4 / + ; GAL80[ts] sh-piwi / sh-w


title: Kawasaki_41


title: Kawasaki_42


title: Kawasaki_39


title: piwi-sKD,dcr2-sKD-rep2

description:
Chambeyron___12_949_D_28_rep2_S73_L008_R1_001
comptes_normalises_ET_dicer.txt

data_processing:
RNA-seq reads were trimmed for quality using UrQt (using parameter --t 20)
trimmed reads were aligned against D. melanogaster genes using TopHat2 (Kim et al., 2013). To generate a gene count table alignment, counts were performed on sorted bam files using eXpress.
TE read count table were generated using the TEcount module of TEtools (Lerat et al., 2017).
Gene count table and TE count table were then concatenated for normalization purposes and analyzed using DESeq2 (version 1.10.) and normalized read count tables were generated.
Genome_build: Drosophila melanogaster genome (dm3)
Supplementary_files_format_and_content: one .txt file with normalized read counts for no-KD-rep1, no-KD-rep2, piwi-sKD-rep1 and piwi-sKD-rep2 for each analysed TE. one .txt file with normalized read counts for piwi-sKD,ctrl-sKD-rep1, piwi-sKD,ctrl-sKD-rep2, piwi-sKD,dcr2-sKD-rep1 and piwi-sKD,dcr2-sKD-rep2 for each analysed TE.

growth_protocol:
[no-KD] Flies were grown at 20°C
[piwi-sKD, piwi-sKD,ctrl-sKD  and piwi-sKD,dcr2-sKD] Flies were grown at 20°C exept in the last 5 days (25°C)

extract_protocol:
Total RNA from Drosophila ovaries were Trizol extrated and enrichted in polyA  mRNAs using the OligodT Dynabeads procedure.
Purified PolyA mRNA were cloned by Donnelly Sequencing Center (Toronto)
TruSeq stranded libraries

tag: temperature


title: piwi-sKD,dcr2-sKD-rep1

description:
Chambeyron___11_949_D_28_rep1_S72_L008_R1_001
comptes_normalises_ET_dicer.txt


title: Kawasaki_40


title: Kawasaki_38


title: Kawasaki_37


title: Kawasaki_36


title: Kawasaki_34


title: Kawasaki_30


title: Kawasaki_35


title: Kawasaki_33


title: piwi-sKD,ctrl-sKD-rep2

description:
Chambeyron___10_949_w_28_rep2_S71_L008_R1_001
comptes_normalises_ET_dicer.txt


title: Kawasaki_26


title: Kawasaki_28


title: Kawasaki_31


title: Kawasaki_32


title: Kawasaki_24


title: Kawasaki_21


title: Kawasaki_29


title: piwi-sKD,ctrl-sKD-rep1

description:
Chambeyron___9_949_w_28_rep1_S70_L008_R1_001
comptes_normalises_ET_dicer.txt


title: Kawasaki_25


title: Kawasaki_27


title: piwi-sKD-rep2

description:
Chambeyron___8_C2_25_rep2_S69_L008_R1_001
comptes_normalises_ET.txt

value: w ; tj-GAL4 ; tubP-GAL80[ts] sh-piwi


title: Kawasaki_23


title: Kawasaki_22


title: Kawasaki_20


title: Kawasaki_19


title: piwi-sKD-rep1

description:
Chambeyron___7_C2_25_rep1_S68_L008_R1_001
comptes_normalises_ET.txt


title: no-KD-rep2

description:
Chambeyron___6_C2_20_rep2_S67_L008_R1_001
comptes_normalises_ET.txt


title: Kawasaki_17


title: Kawasaki_18


title: Kawasaki_16


title: no-KD-rep1

description:
Chambeyron___5_C2_20_rep1_S66_L008_R1_001
comptes_normalises_ET.txt


title: piwi-sKD-singleFly-rep10

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence and then mapped against the D. melanogaster genome (dm6) with BWA version 0.7.5a-r405 for the pooled embryo sequencing experiments (one no-KD and one piwi-sKD library), and with BWA version 0.7.10-r789 for the 12 single fly piwi-sKD sequencing experiments.
De novo TE insertions for all experiments were determined using the T-lex de novo pipeline with a minimum read threshold of 2 (Fiston-Lavier et al., 2014; Kelley et al., 2014).
Genome_build: Drosophila melanogaster genome (dm6)
Supplementary_files_format_and_content: Bed file containing the new detected TE insertions (chromosome, start, end, TE-name, read count).

molecule: genomic DNA

source_name: Drosophila adult fly

extract_protocol:
[embryonic gDNA] DNA from 50 ul of 3-17h embryos was extracted with the PureLink Genomic DNA Mini Kit (Invitrogen cat.K1820-01).
[adult single fly gDNA] DNA from individual adult flies was isolated using the GenElute Kit (Sigma G1N70)
[embryonic gDNA] gDNA were cloned by BGI (China)
[adult single fly gDNA] Library was prepared using the NEXTflex™ Small RNA-Seq Kit v3 by MGX (France)
[embryonic gDNA] 100 nt paired-end sequencing on a Illumina Hiseq 2500 by BGI (China)
[adult single fly gDNA] 125 nt paired-end sequencing on a Illumina Hiseq 2500 by MGX (France)

value: Drosophila adult fly


title: piwi-sKD-singleFly-rep11


title: piwi-sKD-singleFly-rep12


title: piwi-sKD-singleFly-rep9


title: piwi-sKD-singleFly-rep8


title: piwi-sKD-singleFly-rep7


title: Kawasaki_15


title: Kawasaki_13


title: Kawasaki_12


title: Kawasaki_04


title: Kawasaki_11


title: Kawasaki_02


title: Kawasaki_09


title: piwi-sKD-singleFly-rep5


title: Kawasaki_08


title: Kawasaki_07


title: piwi-sKD-singleFly-rep4


title: Kawasaki_14


title: piwi-sKD-singleFly-rep6


title: Kawasaki_10


title: piwi-sKD-singleFly-rep3


title: Kawasaki_03


title: Kawasaki_06


title: Inflammatory_84

source_name: Whole Blood from patient with JIA

value: JIA


title: Inflammatory_79


title: Inflammatory_82


title: Inflammatory_80


title: Kawasaki_05


title: Inflammatory_76


title: Kawasaki_01


title: Inflammatory_81


title: Inflammatory_83


title: Inflammatory_74


title: Inflammatory_75


title: Inflammatory_78


title: piwi-sKD

description: 150102_I595_FCC5W8BACXX_L1_wHAIPI014964-112


title: 9090701

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

data_processing:
Alignment and quantification of transcriptomic and epigenomic features. De-multiplexed FASTQ files were mapped with STAR version 2.4.0i in 2-pass mode{Dobin:2013fg} over the hg19 reference genome. Prior to expression quantification, we filtered our reads prone to mapping bias using WASP {vandeGeijn:2014wg}. Total read counts and RPKM were calculated with RNA-SeQC v1.1.8{Deluca:2012dp} using default parameters with additional flags “-n 1000 -noDoC -strictMode” over GENCODE v19 reference. Allele-specific read counts were generated with the createASVCF module in RASQUAL{Kumasaka:2016fn}. We quantified intron excision levels using LeafCutter intron-spanning reads{Li:2016wz}. In brief, we converted bam files to splice junction files using the bam2junc.sh script, and defined intron clusters using leafcutter_cluster.py with default parameters, which requires at least 30 reads supporting each intron and allows intron to have a maximum size of 100kb. We used the ENCODE ATAC-seq pipeline to perform alignment and peak calling(https://github.com/kundajelab/atac_dnase_pipelines){Sloan:2016hy}. FASTQ files were trimmed with Cutadapt v1.9{Martin:2011va} and aligned with Bowtie2 v2.2.6{Langmead:2012jh}. MACS2 v2.0.8 {Zhang:2008gm} was used to call peaks with default parameters. Irreproducible Discovery Rate (IDR){Li:2011gg} analyses were performed based on pseudo-replicates (subsample of reads) with a cutoff of 0.1 to output an IDR call set, which was used for downstream analysis. We used WASP {vandeGeijn:2014wg} to filter out reads that are prone to mapping bias.
Genome_build: hg19

source_name: coronary artery smooth muscle cell

growth_protocol: Sample acquisition and cell culture. A total of 52 primary human coronary artery smooth muscle cell (HCASMC) lines collected from donor hearts were purchased from PromoCell (catalog # C-12511, n = 19), Cell Applications (catalog # 350-05a, n = 25), Lonza (catalog # CC-2583, n = 3), Lifeline Cell Technology (catalog # FC-0031, n = 3), and ATCC (catalog # PCS-100-021, n = 2). All lines were stained with smooth muscle alpha actin to check for smooth muscle content and all lines tested negative for mycoplasma (Table S1).

extract_protocol: Library preparation and sequencing. RNA was extracted using Qiagen miRNeasy Mini Prep Kit (catalog # 74106). Quality of RNA was assessed on the Agilent 2100 Bioanalyzer. Samples with RIN greater than or equal to 8 were sent to the Next-Generation Sequencing Core at the Perelman School of Medicine at the University of Pennsylvania. Libraries were made using Illumina TruSeq Stranded Total RNA Library Prep Kit (catalog # 20020597) and sequenced using 125bp paired-end on HiSeq 2500 Platform. We used ATAC-seq to assess chromatin accessibility with slight modifications to the published protocol {Buenrostro:2015be}. Approximately 5e4 fresh cells were collected at 500 g, washed in PBS, and nuclei extracted with cold lysis buffer. Pellets were subjected to transposition containing Tn5 transposases (Illumina) at 37 °C for 30 min, followed by purification using the DNA Clean-up and Concentration kit (Zymo). Libraries were PCR amplified using Nextera barcodes, with the total # of cycles empirically determined using SYBR qPCR. Amplified libraries were purified and quantified using bioanalyzer, nanodrop and qPCR (KAPA) analysis. Libraries were multiplexed and 2x75 bp sequencing was performed using an Illumina NextSeq 500.

treatment_protocol: All cell lines were cultured in smooth muscle growth medium (Lonza catalog # CC-3182) supplemented with hEGF, insulin, hFGF-b, and 5% FBS, according to Lonza instructions. All HCASMC lines were expanded to passage 5-6 prior to extraction.

tag: sample type

value: cell culture

tag: cell line


title: no-KD

description: 150102_I595_FCC5W8BACXX_L1_wHAIPI014963-113

source_name: Drosophila 3-17h embryos

value: Drosophila 3-17h embryos


title: Inflammatory_72


title: piwi-sKD-singleFly-rep2


title: 9052004


title: 9071501


title: Inflammatory_73


title: Inflammatory_77


title: piwi-sKD-singleFly-rep1


title: Inflammatory_68


title: Inflammatory_70


title: Inflammatory_67


title: 8100901


title: Inflammatory_64


title: Inflammatory_66


title: Inflammatory_71


title: Inflammatory_60


title: Inflammatory_69


title: 8072501


title: Inflammatory_65


title: 59386145


title: 7103002


title: Inflammatory_63


title: Inflammatory_61


title: Inflammatory_59


title: Inflammatory_62


title: Inflammatory_57


title: 59885590


title: Inflammatory_58


title: 317155


title: Inflammatory_56


title: Inflammatory_53


title: 3101801


title: 3100203


title: 3003


title: Inflammatory_52


title: Inflammatory_48


title: 2999


title: Inflammatory_50


title: Inflammatory_51


title: Inflammatory_54


title: Inflammatory_46


title: 2989


title: 2510


title: Inflammatory_49


title: Inflammatory_47


title: TLR-DKO_NAc microglia_R-SDS_rep 4

city: Kobe

first: Tomoyuki

last: Furuyashiki

state: Hyogo

address: 7-5-1, Kusunokicho, Chuo-ku

department: Pharmacology

country: Japan

institute: Kobe University Graduate School of Medicine

description: Gene expression in NAc microglia  of TLR-DKO mice at 1.5 hr after the last session of R-SDS

hyb_protocol: 3 ug of Cy3-labeled cDNA was hybridized with a SurePrint G3 Mouse GE 8×60K Microarray.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid: 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: nucleus accumbens, TLR-DKO_R-SDS, replicate 4

label_protocol: 500 pg of RNA was amplified and converted to cDNA using an Ovation RNA Amplification System V2. The cDNA samples were used to synthesize Cy3-labeled cDNA using a SureTag DNA Labeling Kit.

extract_protocol: The mPFC and NAc were collected using a 1.5 mm biopsy punch. EGFP-positive cells were isolated using a FACS AriaIII. Microglia isolated from the mPFC or NAc of 3-6 mice were pooled for each sample to obtain 500 pg of total RNA. Total RNA was prepared using an RNeasy Plus Mini kit.

treatment_protocol: CX3CR1EGFP/+ mice and TLR-DKO; CX3CR1EGFP/+ mice were subjected to repeated social defeat stress or cage transfer as a naive condition. At 90 min after the last stress exposure, mice were transcardially perfused with ice-cold D-PBS under deep anesthesia with i.p. injection of sodium pentobarbital.

value: microglia

value: TLR-DKO; CX3CR1EGFP/+

tag: brain area

value: nucleus accumbens

tag: treatment

value: repeated social defeat stress

tag: behavioral phenotype

value: resilient


title: Inflammatory_43


title: Inflammatory_45


title: 2463


title: TLR-DKO_NAc microglia_naïve_rep 3

description: Gene expression in NAc microglia  of TLR-DKO mice at 1.5 hr after the last session of cage transfer

source_name: nucleus accumbens, TLR-DKO_naïve, replicate 3

value: cage transfer

value: naive


title: TLR-DKO_NAc microglia_R-SDS_rep 3

source_name: nucleus accumbens, TLR-DKO_R-SDS, replicate 3


title: TLR-DKO_NAc microglia_R-SDS_rep 2

source_name: nucleus accumbens, TLR-DKO_R-SDS, replicate 2


title: Inflammatory_44

value: Discovery

value: Female


title: Inflammatory_42


title: TLR-DKO_NAc microglia_R-SDS_rep 1

source_name: nucleus accumbens, TLR-DKO_R-SDS, replicate 1


title: 2435


title: Inflammatory_38

value: Male


title: Inflammatory_40


title: TLR-DKO_NAc microglia_naïve_rep 1

source_name: nucleus accumbens, TLR-DKO_naïve, replicate 1


title: Inflammatory_39


title: Inflammatory_41


title: Inflammatory_37


title: Inflammatory_36


title: Inflammatory_35


title: Inflammatory_33


title: 2315


title: TLR-DKO_NAc microglia_naïve_rep 2

source_name: nucleus accumbens, TLR-DKO_naïve, replicate 2


title: 2305


title: Inflammatory_30


title: Inflammatory_32


title: WT_NAc microglia_R-SDS(sus)_rep 1

description: Gene expression in NAc microglia  of wild-type mice at 1.5 hr after the last session of R-SDS

source_name: nucleus accumbens, WT_R-SDS(sus), replicate 1

value: susceptible


title: Inflammatory_34


title: 2282


title: 2139


title: WT_NAc microglia_R-SDS(sus)_rep 3

source_name: nucleus accumbens, WT_R-SDS(sus), replicate 3


title: 2228


title: WT_NAc microglia_R-SDS(sus)_rep 2

source_name: nucleus accumbens, WT_R-SDS(sus), replicate 2


title: WT_NAc microglia_naïve_rep 3

description: Gene expression in NAc microglia  of wild-type mice at 1.5 hr after the last session of cage transfer

source_name: nucleus accumbens, WT_naïve, replicate 3


title: Inflammatory_29


title: 2105


title: Inflammatory_31


title: Inflammatory_26


title: Inflammatory_28


title: Inflammatory_24


title: Inflammatory_25


title: WT_NAc microglia_naïve_rep 2

source_name: nucleus accumbens, WT_naïve, replicate 2


title: Inflammatory_22


title: WT_NAc microglia_naïve_rep 1

source_name: nucleus accumbens, WT_naïve, replicate 1


title: TLR-DKO_mPFC microglia_R-SDS_rep 3

description: Gene expression in mPFC microglia  of TLR-DKO mice at 1.5 hr after the last session of R-SDS

source_name: medial prefrontal cortex, TLR-DKO_R-SDS, replicate 3

value: medial prefrontal cortex


title: 20805


title: Inflammatory_23

source_name: Whole Blood from patient with JIA


title: Inflammatory_20


title: 2356

source_name: coronary artery smooth muscle cell


title: 2040401


title: 200212


title: 2030801


title: 1795


title: 177089


title: 1596


title: 1587


title: Inflammatory_19


title: Inflammatory_18

source_name: Whole Blood from patient with HSP

value: HSP


title: Inflammatory_21


title: TLR-DKO_mPFC microglia_R-SDS_rep 2

source_name: medial prefrontal cortex, TLR-DKO_R-SDS, replicate 2


title: Inflammatory_55


title: TLR-DKO_mPFC microglia_R-SDS_rep 1

source_name: medial prefrontal cortex, TLR-DKO_R-SDS, replicate 1


title: WT_mPFC microglia_R-SDS(sus)_rep 2

description: Gene expression in mPFC microglia  of wild-type mice at 1.5 hr after the last session of R-SDS

source_name: medial prefrontal cortex, WT_R-SDS(sus), replicate 2


title: TLR-DKO_mPFC microglia_naïve_rep 1

description: Gene expression in mPFC microglia  of TLR-DKO mice at 1.5 hr after the last session of cage transfer

source_name: medial prefrontal cortex, TLR-DKO_naïve, replicate 1


title: 1576


title: TLR-DKO_mPFC microglia_naïve_rep 4

source_name: medial prefrontal cortex, TLR-DKO_naïve, replicate 4


title: Inflammatory_09


title: Inflammatory_03


title: Inflammatory_14


title: Inflammatory_12


title: WT_mPFC microglia_R-SDS(sus)_rep 3

source_name: medial prefrontal cortex, WT_R-SDS(sus), replicate 3


title: Inflammatory_16


title: Inflammatory_27


title: Inflammatory_05


title: Inflammatory_10


title: TLR-DKO_mPFC microglia_naïve_rep 2

source_name: medial prefrontal cortex, TLR-DKO_naïve, replicate 2


title: Inflammatory_17


title: Inflammatory_08


title: WT_mPFC microglia_R-SDS(sus)_rep 1

source_name: medial prefrontal cortex, WT_R-SDS(sus), replicate 1


title: Inflammatory_13


title: Inflammatory_06


title: Inflammatory_01


title: WT_mPFC microglia_naïve_rep 3

description: Gene expression in mPFC microglia  of wild-type mice at 1.5 hr after the last session of cage transfer

source_name: medial prefrontal cortex, WT_naïve, replicate 3


title: Inflammatory_15


title: Inflammatory_07


title: Inflammatory_11


title: Inflammatory_04


title: Definite Viral_94

source_name: Whole Blood from patient with Definite Viral infection

value: Definite Viral


title: Inflammatory_02


title: 1559


title: 1508


title: 1483


title: 1522


title: Definite Viral_93


title: 1401


title: 1386


title: 1448


title: WT_mPFC microglia_naïve_rep 1

source_name: medial prefrontal cortex, WT_naïve, replicate 1


title: Definite Viral_92


title: WT_mPFC microglia_naïve_rep 2

source_name: medial prefrontal cortex, WT_naïve, replicate 2


title: Definite Viral_90


title: TLR-DKO_mPFC microglia_naïve_rep 3

source_name: medial prefrontal cortex, TLR-DKO_naïve, replicate 3


title: WT_mPFC_res_rep 2

description: Gene expression in mPFC of resilient wild-type mice at 4 hr after the last session of R-SDS

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented and hybridized with a SurePrint G3 Mouse GE 8×60K Microarray.

source_name: medial prefrontal cortex, resilient, replicate 2

label_protocol: The resultant RNA (35 ng per array isolated from the mPFC of an individual mouse) was converted to cDNA using a Low Input Quick Amp Labeling Kit. The cDNA samples were used to synthesize Cy3-labeled cRNA using a Low Input Quick Amp Labeling Kit.

extract_protocol: mPFC was collected in RNAlater using a 1.5 mm biopsy punch. Total RNA was prepared using an RNeasy Plus Mini kit.

treatment_protocol: Wild-type mice were subjected to repeated social defeat stress or cage transfer as a naive condition. At 4 h after the last stress exposure, mice were transcardially perfused with ice-cold D-PBS under deep anesthesia with i.p. injection of sodium pentobarbital.


title: Definite Viral_88


title: WT_mPFC_res_rep 3

source_name: medial prefrontal cortex, resilient, replicate 3


title: Definite Viral_91


title: Definite Viral_86


title: Definite Viral_89


title: Definite Viral_84


title: Definite Viral_87


title: Definite Viral_85


title: Definite Viral_83


title: WT_mPFC_sus_rep 4

description: Gene expression in mPFC of susceptible wild-type mice at 4 hr after the last session of R-SDS

source_name: medial prefrontal cortex, susceptible, replicate 4


title: 1346

source_name: coronary artery smooth muscle cell


title: 1278


title: 1369


title: 1347


title: WT_mPFC_sus_rep 6

source_name: medial prefrontal cortex, susceptible, replicate 6


title: WT_mPFC_res_rep 1

source_name: medial prefrontal cortex, resilient, replicate 1


title: Definite Viral_79


title: WT_mPFC_sus_rep 3

source_name: medial prefrontal cortex, susceptible, replicate 3


title: WT_mPFC_sus_rep 5

source_name: medial prefrontal cortex, susceptible, replicate 5


title: 112201


title: Definite Viral_82


title: Definite Viral_81


title: WT_mPFC_sus_rep 1

source_name: medial prefrontal cortex, susceptible, replicate 1


title: WT_mPFC_sus_rep 2

source_name: medial prefrontal cortex, susceptible, replicate 2


title: Definite Viral_78


title: Definite Viral_75


title: 10705


title: Definite Viral_80


title: Definite Viral_76


title: Definite Viral_71


title: Definite Viral_73


title: WT_mPFC_naïve_rep 5

description: Gene expression in mPFC of wild-type mice at 4 hr after the last session of cage transfer

source_name: medial prefrontal cortex, naïve, replicate 5


title: Definite Viral_72


title: Definite Viral_77


title: Definite Viral_69


title: Definite Viral_70


title: 1051601


title: Definite Viral_74


title: WT_mPFC_naïve_rep 4

description: Gene expression in mPFC  of wild-type mice at 4 hr after the last session of cage transfer

source_name: medial prefrontal cortex, naïve, replicate 4


title: 1060602


title: TTSeq_R360_L6_1_H04_ACGCTGAA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis. We rejected cells that had less than 2000 mRNA molecules, more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Alignments were made with the STAR aligner and default settings
Molecule counting was made with velocyto (http://velocyto.org/velocyto.py/index.html)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited file of molecule counts

molecule: polyA RNA

source_name: Hek293 cells

growth_protocol: As described in Schwalb et al, Science. 2016 Jun 3;352(6290):1225-8

extract_protocol: As described in Islam et al, Genome Res. 2011 Jul;21(7):1160-7

tag: timepoint (minutes)


title: 102901


title: 1020301


title: TTSeq_R360_L6_1_H02_ACGGCTTA


title: TTSeq_R360_L6_1_H03_CGGATTAC


title: WT_mPFC_naïve_rep 3

source_name: medial prefrontal cortex, naïve, replicate 3


title: Definite Viral_66

source_name: Whole Blood from patient with Definite Viral infection


title: Definite Viral_68


title: WT_mPFC_naïve_rep 2

source_name: medial prefrontal cortex, naïve, replicate 2


title: TTSeq_R360_L6_1_H01_ATCGTGGT


title: TTSeq_R360_L6_1_G04_CTCAAGTC


title: Definite Viral_62


title: Definite Viral_65


title: Definite Viral_67


title: WT_mPFC_naïve_rep 1

source_name: medial prefrontal cortex, naïve, replicate 1


title: Definite Viral_64


title: Definite Viral_60


title: TTSeq_R360_L6_1_G03_GGATAGTG


title: Definite Viral_61


title: Definite Viral_58


title: Definite Viral_57


title: mouse subdomain KL1 expression vector rep3

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: Gene expression

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip Expression Wash, Stain and Scan protocol.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner according to the instruction manual.

data_processing: RNA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.6)).

source_name: human colorectal cancer cell lines HCT 116

label_protocol: Samples were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol and Affymetrix WT Terminal Labeling Kit from 100 ng total RNA starting material

growth_protocol: Cells were obtained from the ATCC (Manassas, VA, USA).  Cells were cultured at 37°C in a humidified 5% CO2 atmosphere in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% fetal calf serum (FCS), 1% penicillin/streptomycin and 1% L-glutamine solution. All experiments were conducted using cells with passage number less than 40.

extract_protocol: Total RNA was extracted 24 hours after transfection using TRIzol® Reagent (15596026; Life Technologies, Carlsbad, CA, USA). RNA was quantitated by measuring absorption at 260/280 and 260/230 nm using a NanoDrop 2000 spectrophotometer  110 (Thermo Fisher Scientific, Wilmington, DE, USA).

treatment_protocol: HCT 116 cells were transfected with either KL-FL, KL1 or control vector (pcDNA3). Transfections were done with either JetPEI (Polyplus Transfection, New York, NY, USA) or Polyethylenimine (Polysciences Inc, Warrington, PA, USA) prepared as described (Longo PA, Kavran JM, Kim MS, Leahy DJ. Transient mammalian cell transfection with polyethylenimine (PEI). Methods in enzymology 2013; 529: 227-240.).

value: colorectal cancer cell line HCT 116

value: KL1 overexpression


title: TTSeq_R360_L6_1_G02_CCTGTTCT


title: Definite Viral_59


title: Definite Viral_56


title: Definite Viral_54


title: Definite Viral_55


title: Definite Viral_53


title: mouse subdomain KL1 expression vector rep2

description: Gene expression


title: Definite Viral_52


title: TTSeq_R360_L6_1_G01_CTCACAGA


title: mouse KL-FL (full-length klotho) rep3

description: Gene expression

value: KL-FL overexpression


title: TTSeq_R360_L6_1_F03_ACTCACCA


title: TTSeq_R360_L6_1_F04_GGTAGCTA


title: TTSeq_R360_L6_1_F02_CATGGTTG


title: TTSeq_R360_L6_1_F01_TCAACCGA


title: control vector rep3

description: Gene expression

value: control


title: piwi-sKD

description:
150122_I709_FCC63L2ACXX_L2_WHDROsqrSAABTAASE-T-241
Manual anion-exchange chromatography (HiTrapQ column) purification

source_name: Drosophila ovaries

value: w ; tj-GAL4 ; tubP-GAL80[ts] sh-piwi

value: Drosophila ovaries


title: TTSeq_R360_L6_1_E04_TCACCAAC


title: control vector rep2

description: Gene expression


title: Definite Viral_49


title: Definite Viral_47


title: Definite Viral_45


title: Definite Viral_44


title: no-KD

description:
150122_I709_FCC63L2ACXX_L2_WHDROsqrSAAATAASE-T-240
Manual anion-exchange chromatography (HiTrapQ column) purification


title: Definite Viral_43


title: Definite Viral_41


title: mouse subdomain KL1 expression vector rep1

description: Gene expression


title: TTSeq_R360_L6_1_E03_GAAGAAGC


title: Definite Viral_46


title: control vector rep1

description: Gene expression


title: Definite Viral_48


title: Definite Viral_39


title: Definite Viral_42


title: mouse KL-FL (full-length klotho) rep1

description: Gene expression


title: Definite Viral_37


title: Definite Viral_51


title: Definite Viral_40


title: Definite Viral_38


title: Definite Viral_36


title: TTSeq_R360_L6_1_E01_TCCATCCT


title: TTSeq_R360_L6_1_D04_CCCGAATA


title: TTSeq_R360_L6_1_D03_CTTCGATC


title: TTSeq_R360_L6_1_E02_AAGCGGTT


title: 1042702

value: cell culture


title: Definite Viral_35


title: TTSeq_R360_L6_1_D02_TGCTCCTT


title: TTSeq_R360_L6_1_D01_AGGATCGT


title: mouse KL-FL (full-length klotho) rep2

description: Gene expression


title: Definite Viral_34


title: Unknown_79

source_name: Whole Blood from patient with infection of uncertain bacterial or viral aetiology

value: Uncertain

value: Validation


title: Unknown_77


title: Definite Viral_28


title: Definite Viral_33


title: Definite Viral_27


title: Definite Viral_25


title: Definite Viral_63


title: Definite Viral_32


title: Unknown_76


title: TTSeq_R360_L6_1_C03_AGGTGATC


title: Definite Viral_29


title: Unknown_73


title: Definite Viral_30


title: Definite Viral_31


title: Definite Viral_26


title: Unknown_75


title: Unknown_78


title: TTSeq_R360_L6_1_C02_GTGACATG


title: TTSeq_R360_L6_1_C04_GACAGGTA


title: TTSeq_R360_L6_1_C01_AAATGCGG


title: Definite Viral_21


title: TTSeq_R360_L6_1_B04_TTAGACGG


title: TTSeq_R360_L6_1_B03_GGAACTAG


title: Unknown_74


title: Unknown_72


title: TTSeq_R360_L6_1_B02_GTGCAGTA


title: Definite Viral_18


title: Definite Viral_24


title: Unknown_71


title: Definite Viral_16


title: Definite Viral_22


title: Definite Viral_50


title: Definite Viral_23


title: Definite Viral_17


title: Definite Viral_15


title: Definite Viral_19


title: Definite Viral_13


title: Definite Viral_12


title: Unknown_70


title: Unknown_69


title: Definite Viral_14


title: Definite Viral_10


title: Definite Viral_11


title: Definite Viral_08


title: TTSeq_R360_L6_1_A04_GCTATCTG


title: Definite Viral_20


title: Unknown_67


title: TTSeq_R360_L6_1_A03_AGAGCATC


title: Unknown_68


title: Definite Viral_09


title: TTSeq_R360_L6_1_A02_ATAGAGCC


title: Unknown_66


title: Unknown_65


title: Definite Viral_06


title: Definite Viral_05


title: TTSeq_R360_L6_1_A01_CTTTCTGG


title: Unknown_64


title: Definite Viral_03


title: Definite Viral_02


title: Definite Viral_07


title: Definite Viral_01


title: Definite Viral_04


title: N4_H3K27me3_ChIPseq

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

description:
N4_H3K27me3_ChIPseq
W_CAGATC

data_processing:
Illumina Casava software used for basecalling
Individual 50bp reads were filtered if they contained 5 base calls with quality Phred score less than 30, or if they contained any undetermined bases. The remaining reads were mapped to the hg19 reference genome using Bowtie2
Reads were further filtered so that a maximum of one uniquely-mapped read was kept for each genomic co-ordinate. All reads mapping to the DAC Consensus Excluded Regions were discarded
Locations of significant peaks of enriched DNA in each of the ChIP samples were identified using MACS v1.4.2 using a p-value cutoff of 1e-4
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated from macs2 peak calling

source_name: Normal fallopian tube epithelium

extract_protocol:
Each sample was washed twice with ice-cold phosphate-buffered saline and then lysed in lysis buffer (25 mM Hepes pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, freshly added protease inhibitor from Sigma, St Louis, MO, USA), homogenized on ice and spun at 3000 g for 5 min at 4 °C. The pellet was re-suspended in sonication buffer (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, freshly added protease inhibitors) and sonicated for at least 20 min. The sample was then spun down for 10 min at 4 °C. The chromatin containing supernatant was stored at −80 °C until immunoprecipitation.
End-repair of DNA, adding ‘A’ bases to the DNA, ligation of sequencing adaptors to DNA fragments and amplification of adaptor modified DNA by PCR was done according to the recommended Illumina protocol. For gel purification of the ‘SolexaPreGel for ChIPSeq’ a 2% agarose Tris-acetate-EDTA gel was loaded with the entire sample using loading buffer containing Xylene cyanol (Sigma, X4126). Band fragments of 200–300 bp were excised using a Dark Reader and DNA was purified with the Qiagen MinElute Gel Extraction Kit (Qiagen, West Sussex, UK). DNA was eluted with 15 μl EB preheated to 50 °C.

value: Normal fallopian tube epithelium


title: Unknown_63


title: Unknown_61


title: Definite Bacterial_51

source_name: Whole Blood from patient with Definite Bacterial infection

value: Definite Bacterial

value: Discovery


title: N3_inputDNA

description:
N3_inputDNA
U_GTGAAA

source_name: Normal ovarian surface epithelium

value: Normal ovarian surface epithelium


title: Definite Bacterial_52

value: Female


title: Unknown_62


title: TTSeq_R360_L6_1_B01_GTCGTAAG


title: N3_H3K27me3_ChIPseq

description:
N3_H3K27me3_ChIPseq
T_CAGATC


title: Unknown_60

value: Male


title: Definite Bacterial_47


title: Definite Bacterial_45


title: N3_H3K4me3_ChIPseq

description:
N3_H3K4me3_ChIPseq
S_CGATGT


title: Definite Bacterial_48


title: Definite Bacterial_50


title: Definite Bacterial_46


title: Definite Bacterial_43


title: Definite Bacterial_44


title: Definite Bacterial_41


title: Unknown_59


title: Unknown_58


title: N2_inputDNA

description:
N2_inputDNA
R_GTGAAA


title: N4_H3K4me3_ChIPseq

description:
N4_H3K4me3_ChIPseq
V_CGATGT


title: Unknown_57


title: N2_H3K27me3_ChIPseq

description:
N2_H3K27me3_ChIPseq
Q_CAGATC


title: Definite Bacterial_42


title: N2_H3K4me3_ChIPseq

description:
N2_H3K4me3_ChIPseq
P_CGATGT


title: Definite Bacterial_49


title: Definite Bacterial_40


title: Definite Bacterial_38


title: Definite Bacterial_39


title: Definite Bacterial_37


title: Unknown_53


title: Definite Bacterial_36


title: N1_H3K4me3_ChIPseq

description:
N1_H3K4me3_ChIPseq
M_CGATGT


title: Definite Bacterial_34


title: N1_inputDNA

description:
N1_inputDNA
O_GTGAAA


title: Definite Bacterial_35


title: Unknown_55


title: Unknown_56


title: Unknown_52


title: Definite Bacterial_26


title: N4_inputDNA

description:
N4_inputDNA
X_GTGAAA


title: Unknown_51


title: T4_inputDNA

description:
T4_inputDNA
L_GTGAAA

source_name: Serous epithelial ovarian carcinoma

value: Serous epithelial ovarian carcinoma


title: Definite Bacterial_32


title: Definite Bacterial_31


title: Definite Bacterial_29


title: Definite Bacterial_28


title: Unknown_49


title: Unknown_50


title: Definite Bacterial_33


title: Definite Bacterial_27


title: Unknown_54


title: T3_inputDNA

description:
T3_inputDNA
I_GTGAAA


title: T4_H3K4me3_ChIPseq

description:
T4_H3K4me3_ChIPseq
J_CGATGT


title: Definite Bacterial_23


title: T3_H3K27me3_ChIPseq

description:
T3_H3K27me3_ChIPseq
H_CAGATC


title: Unknown_48


title: Unknown_47


title: T3_H3K4me3_ChIPseq

description:
T3_H3K4me3_ChIPseq
G_CGATGT


title: Definite Bacterial_30


title: T4_H3K27me3_ChIPseq

description:
T4_H3K27me3_ChIPseq
K_CAGATC


title: Definite Bacterial_25


title: T2_inputDNA

description:
T2_inputDNA
F_GTGAAA


title: Definite Bacterial_24


title: Unknown_46


title: Unknown_45


title: Definite Bacterial_21


title: T2_H3K27me3_ChIPseq

description:
T2_H3K27me3_ChIPseq
E_CAGATC


title: Unknown_44


title: Definite Bacterial_19


title: T1_inputDNA

description:
T1_inputDNA
C_GTGAAA


title: Definite Bacterial_22


title: Definite Bacterial_16


title: Definite Bacterial_14


title: Definite Bacterial_15


title: Definite Bacterial_18


title: Definite Bacterial_12


title: Definite Bacterial_17


title: Definite Bacterial_20


title: Definite Bacterial_13


title: Unknown_43


title: Definite Bacterial_11


title: T2_H3K4me3_ChIPseq

description:
T2_H3K4me3_ChIPseq
D_CGATGT


title: Unknown_40


title: Definite Bacterial_10


title: Definite Bacterial_07


title: Unknown_42


title: Unknown_41


title: Unknown_39


title: T1_H3K4me3_ChIPseq

description:
T1_H3K4me3_ChIPseq
A_CGATGT


title: Definite Bacterial_09


title: T1_H3K27me3_ChIPseq

description:
T1_H3K27me3_ChIPseq
B_CAGATC


title: Definite Bacterial_08


title: Definite Bacterial_03


title: Definite Bacterial_06


title: Definite Bacterial_01


title: Definite Bacterial_05


title: Unknown_38


title: Definite Bacterial_04


title: Unknown_37


title: Control_48

source_name: Whole Blood from healthy control patient

value: Control


title: Definite Bacterial_02


title: Control_55


title: Control_52


title: Control_54


title: Unknown_34


title: Control_53


title: Unknown_32


title: Unknown_36


title: Control_45


title: Unknown_35


title: Unknown_31


title: Control_47


title: N1_H3K27me3_ChIPseq

description:
N1_H3K27me3_ChIPseq
N_CAGATC


title: Unknown_33


title: Control_51


title: Control_50


title: Control_44


title: Control_46


title: Control_49


title: Unknown_30


title: Rhesus macaque placenta 2 RNA-seq

city: Cincinnati

first: Caitlin

middle: E

last: Dunn

state: Ohio

address: 3333 Burnet Avenue

department: Division of Human Genetics

institute: Cincinnati Children's Hospital Medical Center

description: RNA-seq

data_processing:
Reads were aligned to the human genome (hg19) using Tophat
Transcript assembly and quantification using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of FPKM values from Cufflinks

organism: Macaca mulatta

source_name: villous placenta approx. 80% gestation

extract_protocol:
RNA was extracted from placental biopsies with the TRIzol reagent (ThermoFisher Scientific) according to manufacturer's instructions.
PolyA stranded RNA-seq was performed on an Illumina HiSeq machine using a paired-end approach with 50 bp reads, generating approximately 15 million paired reads per sample.

treatment_protocol: Two macaque placentas were collected by cesarean section at 128 days and 131 days gestational age (80% completed gestation).

value: placenta


title: Rhesus macaque placenta 1 RNA-seq

description: RNA-seq


title: Control_43


title: Control_38


title: Unknown_29


title: Control_42


title: Control_36


title: Control_41


title: Control_40


title: Unknown_25


title: Unknown_26


title: Unknown_28


title: Unknown_27


title: Unknown_24


title: Control_39


title: Control_34


title: Unknown_23


title: Control_32


title: Control_30


title: Control_33


title: Control_37


title: Control_28


title: Unknown_21


title: Unknown_22


title: Control_35


title: Control_26


title: Control_27


title: Control_24


title: Control_31


title: Control_29


title: Control_23


title: Control_25


title: Control_22


title: Control_21


title: Unknown_19


title: Unknown_18


title: Control_17


title: Control_16


title: Control_20


title: Unknown_20


title: Control_15


title: Unknown_17


title: Control_13


title: macrophages_COPD [P 703]

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

hyb_protocol: Following fragmentaion, single-stranded cDNA were hybridized for 20 hours at 48 ℃ with HuGene2.1ST Array Strip (Affymetrix) and GeneChip Expression 3'-Amplification Reagents Hybridization Control kit (Affymetrix).

scan_protocol: The array was scanned using Imaging Station (Affymetrix) according to the manufacture's instructions.

data_processing: R 3.4.1, rma function from oligo package, version 1.40.2, default options, target=probeset

source_name: induced sputum

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Amplification Kit Module 1(Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: The total RNA was isolated using Tri reagent/chloroform method (Sigma-Aldrich, Saint Louis, USA).

treatment_protocol: A FITC Positive Selection Kit (StemCell, Vancouver, Canada) was used for induced sputum macrophages separation. The immunomagnetic separation of cells labeled with CD68+ FITC antibody (ThermoFisher, Waltham, USA) was performed according to the manufacturer’s instruction.

value: induced sputum

value: macrophage

tag: diagnosis

value: COPD

tag: inhale corticosteroid treatment

tag: smoking status

value: active smoker


title: macrophages_COPD [P 696]


title: Control_14


title: Unknown_14


title: Control_11


title: Unknown_16


title: Unknown_15


title: Control_18


title: Unknown_13


title: Control_12


title: macrophages_COPD [P 676]


title: Control_09


title: Control_06


title: macrophages_control [K 672]

value: control

value: never smoker


title: macrophages_COPD [P 652]


title: Control_07


title: Control_10


title: Control_08


title: Unknown_12

value: Uncertain


title: Control_05


title: Control_04


title: macrophages_control [K 634]


title: Unknown_10

value: Validation


title: Control_03


title: macrophages_asthma [A_685]

value: asthma

value: ICS naïve


title: macrophages_control [K 691]


title: macrophages_control [KP 677]


title: Control_01

value: Discovery


title: Control_02


title: piwi-sKD (C2GnS1)

description:
extra chromosomal circular DNA (eccDNA)
S8_S7_L001

data_processing:
Mobilome reads were mapped with Bowtie2 version 2.2.4 (using parameters -k 10 -N 1) on the Drosophila melanogaster genome (dm3) complemented with canonical TE sequences.
TE annotated reads were re-mapped again using canonical TEs as references, with Bowtie2 version 2.2.4 (using parameters -k 10 -N 1), to attribute each read to a TE family.
Our full analysis pipeline is available at https://bitbucket.org/blaiseli/pirna-pipeline /mobilome.
Genome_build: Drosophila melanogaster genome (dm3)
Supplementary_files_format_and_content: .txt files with read counts for TEmapping reads for each analysed TE in different mapping categories (F=sense read, R= antisense read, mm=mismatch) (#ref = TE-family, total = sense and antisense reads with up to 4 mismatches, total_F = all sense reads, total_R = all antisense reads , F_0mm = sense reads with 0 mismatches , R_0mm = antisense reads with 0 mismatches , F_mm = sense reads with 1 ore more mismatches, R_mm = antisense reads with 1 ore more mismatches, F_1_mm = sense reads with 1 mismatch, R_1_mm = antisense reads with 1 mismatch, F_2_mm = sense reads with 2 mismatches, R_2_mm = antisense reads with 2 mismatches, F_3_mm = sense reads with 3 mismatches, R_3_mm = antisense reads with 3 mismatches) for each sequenced condition.

molecule: other

source_name: Drosophila 0-2 h embryos

extract_protocol:
DNA was extracted from 0-2 h embryos using the DNeasy Blood & Tissue Kit (Qiagen) and further purified with the PCR purification kit (Qiagen). Linear genomic DNA was digested with Plasmid-Safe™ ATP-Dependent DNase (Lucigen) and the remaining eccDNA molecules were then amplified by rolling circle amplification (RCA) using Illustra TempliPhi kit (GE Healthcare) and random primers.
The libraries were prepared with Nextera XT library kit (Illumina).
250 nucleotides paired-end sequencing was performed on a MiSeq platform (Illumina) by Plateau de Génotypage CIRAD (France).

value: w ; tj-GAL4 ; tubP-GAL80[ts] sh-piwi

value: Drosophila 0-2 h embryos


title: no-KD (C2Gn)

description:
extra chromosomal circular DNA (eccDNA)
S7_S6_L001


title: miR-130b overexpressed A549 cells

city: Suita

first: Kentaro

last: Jingushi

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

description: mRNA expression data immunoprecipitated with anti-Ago2 antibody from miR-130b overexpressed A549 cells.

hyb_protocol: After creating the hybridization cocktail, biotinylated cDNA were hybridized with GeneChip Human Exon 1.0 ST Array (Affymetrix) for 17 hours.

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: Scanned data were processed using the Agilent GeneSpring GX software.

source_name: miR-130b overexpressed A549 cells

label_protocol: Total RNA 100 ng were subjected to cDNA synthesis by Ambion WT Expression Kit (Life technologies). Obtained 5.5 μg cDNA were biotinylated and then fragmented by GeneChip WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Following excision, the tissue samples were immediately immersed in RNAlater, (QIAGEN) and stored at −20°C until RNA extraction. miRNAs were purified using the miRNeasy mini kit (QIAGEN).

tag: transfection


title: macrophages_asthma [A_639]

tag: tissue


title: macrophages_asthma [AS 654]

tag: cell type

value: ICS treated


title: Control_19

tag: category

value: Male


title: Unknown_08

tag: dataset


title: HC374 treated with Fg. at 4 dpi rep3

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

description: HCFg 4d3

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package from Stanford University (http://sfg.stanford.edu/)
RAN-seq reads were aligned to the pan-genome of Chinese Spring (IWGSC RefSeq v1.0) from the IWGSC sequence repository hosted by URGI-INRA (https://wheat-urgi.versailles.inra.fr/) and Fusarium graminearum reference genome (Fusarium graminearum str. PH-1) from EnsemblFungi (http://fungi.ensembl.org/, Release 35) using STAR v2.5.3a
R package DESeq2 was used for data normalization and to generate differentially expressed gene (DEG)
Genome_build: IWGSC RefSeq v1.0; Fusarium graminearum str. PH-1
Supplementary_files_format_and_content: Raw read counts data; Normalized read counts data

organism: Triticum aestivum

source_name: spikelets

growth_protocol: Wheat plants were grown in controlled-environment cabinets with 16h light at 20°C and 8h dark at 16°C until mid-anthesis then transferred to growth chambers at anthesis;

extract_protocol:
RNA was extracted using the TriReagent (Molecular Research Center Inc ) followed by a treatment with DNase I (RNase-Free DNase set, Qiagen) onto columns (RNeasy Mini kit, Quiagen) according to instructions provided by the manufacturer
Libraries were prepared according to Illumina's instructions, using the TruSeq RNA v2 LT kit and sequenced on the Genome Analyzer following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf).

treatment_protocol: heads at mid-anthesis were point inoculated with either water (W; control), or F. graminearum (strain DAOM233423).

value: spikelets

value: F. graminearum inoculation

tag: time point (dpi)


title: Unknown_11

tag: gender


title: HC374 treated with Fg. at 4 dpi rep2

description: HCFg 4d2

tag: genotype


title: empty vector-transfected A549 cells

description: mRNA expression data immunoprecipitated with anti-Ago2 antibody from empty vector-transfected A549 cells.

source_name: empty vector-transfected A549 cells

value: empty vector


title: HC374 treated with Fg. at 4 dpi rep1

description: HCFg 4d1


title: macrophages_asthma [AS 653]

value: induced sputum

value: macrophage


title: Unknown_06


title: Unknown_04

value: Female


title: HC374 treated with Fg. at 2 dpi rep3

description: HCFg 2d3


title: HC374 treated with Fg. at 2 dpi rep2

description: HCFg 2d2


title: macrophages_asthma [AS 625]


title: Unknown_07


title: HC374 treated with H2O at 4 dpi rep3

description: HCH20 4d3

value: water (mock) inoculation


title: Unknown_05


title: HC374 treated with Fg. at 2 dpi rep1

description: HCFg 2d1


title: HC374 treated with H2O at 4 dpi rep2

description: HCH20 4d2


title: Unknown_03


title: Input

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie (-5 3 -m 1 --best --strata)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files generated from bam files using Deeptools

source_name: villous placenta >39 weeks gestational age

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody using the MAGnify ChIP kit (Thermo Fisher)
Libraries were prepared using the DNA Smart ChIP-seq library kit (Takara).

treatment_protocol: Two human placentas were collected by cesarean section at 39 weeks 1 day and 39 weeks 4 days gestational age (IRB protocol: CCHMC IRB 2013-2243).

tag: chip antibody


title: H3K4me1

value: villous placenta >39 weeks gestational age

value: H3K4me1 (abcam 8895)


title: HC374 treated with H2O at 4 dpi rep1

description: HCH20 4d1


title: H3K27ac

value: H3K27ac (abcam 4729)


title: Unknown_02

value: Uncertain

value: Validation


title: macrophages_asthma [A 695]

value: asthma

value: ICS naïve

value: never smoker


title: Kawasaki_01

source_name: Whole Blood from patient with Kawasaki Disease

value: Kawasaki Disease


title: HC374 treated with H2O at 2 dpi rep2

description: HCH20 2d2


title: Human placenta 2 Capture-seq

description: Capture-seq

data_processing:
Reads were aligned to the human genome (hg19) using Tophat2 ( -I 100000 --max-segment-intron 100000 -r 300)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files generated from bam files using Deeptools

extract_protocol:
Total RNA was purified from term placentas using a combination of TRIzol and Qiagen columns.
RNA-seq libraries were prepared using the SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing kit (Agilent). For capture-sequencing, pre-amplified RNA-seq libraries were enriched for THE1B containing transcripts using a custom panel of 120 nt THE1B RNA oligos and the SureSelectXT RNA Target Enrichment kit (Agilent). Libraries were sequenced as 75 bp paired-end reads on an Illumina HiSeq machine.

treatment_protocol: Two human placentas were collected by cesarean section at 39 weeks 1 day and 39 weeks 2 days gestational age (IRB protocol: CCHMC IRB 2013-2243).

value: placenta


title: Human placenta 1 Capture-seq

description: Capture-seq


title: HC374 treated with H2O at 2 dpi rep1

description: HCH20 2d1

value: spikelets


title: Unknown_01

extract_protocol: Standard PAXgene® blood RNA extraction kit protocol (Qiagen).

value: Male


title: Definite Viral_28

source_name: Whole Blood from patient with Definite Viral infection

value: Definite Viral


title: Human placenta 2 RNA-seq

description: RNA-seq


title: Shaw treated with Fg. at 4 dpi rep3

description: SFg 4d3

value: Shaw

value: F. graminearum inoculation


title: HC374 treated with H2O at 2 dpi rep3

description: HCH20 2d3


title: Human placenta 1 RNA-seq

description: RNA-seq


title: Shaw treated with Fg. at 4 dpi rep2

description: SFg 4d2


title: Definite Viral_27

value: Female


title: macrophages_asthma [A 693]

value: induced sputum

value: macrophage


title: Shaw treated with Fg. at 2 dpi rep3

description: SFg 2d3


title: Shaw treated with Fg. at 4 dpi rep1

description: SFg 4d1


title: Ging 2: TCRgd cells from the gingiva

city: Manchester

first: Joanne

middle: Elizabeth

last: Konkel

address: AV Hill Building, Oxford Road

department: DIIRM

institute: University of Manchester

data_processing:
Raw files trimmed with Trimmomatic using defualt setting
Timmed Fastqs aligned with STAR (v2.5.3) using default settings
Aligned reads were counted with HTseq
Counts were normalized and analysed with DeSeq2
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Normalized read counts from DeSeq2

source_name: TCRgd cells from the gingiva

growth_protocol: Single cell suspensions were prepared from the different organs before antibody staining for Fluorescence-activated cell sorting (FACS). Samples were FACS sorted using an Aria (BD) using the following antibody cocktail: CD45-AF700, Live/Dead BV510, and TCRgd-APC. 1500 cells were sorted per sample.

extract_protocol:
RNA was isolated from cells using the Norgen Biotek Corp Single Cell RNA Purification Kit (Cat. 51800)
Total RNA was sent to LC Sciences for sequencing service. The quantity and purity of total RNAs were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Inc., Wilmington, DE, USA). The integrity of total RNAs was analyzed using an Agilent 2100 Bioanalyzer system and RNA Pico Chip (Agilent Tech, Santa Clara, CA, USA). The cDNAs were constructed from total RNA (0.7 ng of each sample) using the SMART-Seq v4 Ultra Low Input RNA Kit from Clontech/Takara according to the manufacturer's protocol. The amplified and purified cDNAs were validated using the Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit).  The libraries for sequencing were prepared using Nextera XT DNA Sample Preparation kit from Illumina and following the manufacturer’s protocol (input cDNA: 1ng).   Before sequencing, libraries were qualified on the Bioanalyzer High Sensitivity DNA Chip. Libraries were subsequently pooled and sequenced on the HiSeq X Ten platform in the 150 bp PE configuration.

tag: strain

tag: Sex

tag: age

value: Adult

value: Gingiva


title: Ging 3: TCRgd cells from the gingiva


title: Ging 1: TCRgd cells from the gingiva


title: Shaw treated with Fg. at 2 dpi rep2

description: SFg 2d2

tag: treatment


title: Shaw treated with Fg. at 2 dpi rep1

description: SFg 2d1


title: Shaw treated with H2O at 4 dpi rep2

description: SH20 4d2

value: water (mock) inoculation


title: IEL 2: TCRgd cells from the gut

source_name: TCRgd cells from the gut

value: Gut IEL


title: Definite Viral_24

data_processing: The data were normalised using RSN, after background subtraction. The software used for data normalization was 'R' Language and Environment for Statistical Computing (R) 3.2.2

value: Validation


title: Definite Viral_25


title: Definite Viral_21


title: IEL 1: TCRgd cells from the gut


title: Definite Viral_23


title: Definite Viral_22


title: Spleen 3: TCRgd cells from spleen

source_name: TCRgd cells from spleen

value: Spleen


title: Definite Viral_19


title: Definite Viral_18


title: Spleen 2: TCRgd cells from spleen


title: IEL 3: TCRgd cells from the gut


title: Shaw treated with H2O at 2 dpi rep3

description: SH20 2d3


title: Shaw treated with H2O at 2 dpi rep2

description: SH20 2d2


title: Shaw treated with H2O at 2 dpi rep1

description: SH20 2d1


title: Spleen 1: TCRgd cells from spleen


title: Definite Viral_17


title: Shaw treated with H2O at 4 dpi rep3

description: SH20 4d3


title: Shaw treated with H2O at 4 dpi rep1

description: SH20 4d1


title: Definite Viral_16


title: 4168_3

city: Edmonton

last: Steele

state: AB

address: 116 St. and 85 Ave.

institute: University of Alberta

data_processing:
Illumina Casava1.7 software used for basecalling.
Filtered reads were aligned to the reference bovine genome (UMD 3.1) using Tophat 2.1.1.
The BAM alignment files generated from Tophat were sorted using Samtools (v1.4) and converted to SAM files.
The SAM files were analyzed using HTSeq-count to obtain gene read counts based on the annotation from ENSEMBL bovine genes.
Genome_build: UMD3.1
Supplementary_files_format_and_content: a text file include count number for each sample

organism: Bos taurus

extract_protocol:
Tissues were collected after dissection of calves, flash frozen on liquid nitrogen, and RNA was harvested using a mirVana total RNA Isolation Kit (Ambion, Carlsbad, CA, USA).
TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA, USA) was used with 100 ng of total RNA for the construction of sequencing libraries.The RNA libraries were prepared using standard Illumina protocols

tag: breed

value: Holstein

value: male

tag: developmental stage

value: newborn

value: 51 h of age

tag: feeding strategy

value: colostrum fed 12 h after birth

value: colon


title: Definite Viral_15

value: Definite Viral


title: 4159_3


title: NuyBai treated with Fg. at 4 dpi rep3

description: NFg 4d3

value: NuyBai

value: spikelets

value: F. graminearum inoculation


title: Definite Viral_14

value: Female


title: macrophages_asthma [AS 651]

value: induced sputum

value: macrophage

tag: diagnosis

value: asthma

tag: inhale corticosteroid treatment

value: ICS treated

tag: smoking status

value: never smoker


title: Definite Viral_26

value: Validation


title: NuyBai treated with Fg. at 4 dpi rep2

description: NFg 4d2

tag: tissue


title: 4147_3

value: Holstein


title: NuyBai treated with Fg. at 4 dpi rep1

description: NFg 4d1


title: Definite Viral_12

tag: category

value: Male


title: Definite Viral_20

tag: dataset


title: NuyBai treated with Fg. at 2 dpi rep3

description: NFg 2d3

tag: time point (dpi)


title: 4158_3

tag: gender

value: male

value: newborn


title: NuyBai treated with H2O at 4 dpi rep3

description: NH20 4d3

tag: genotype

value: water (mock) inoculation


title: NuyBai treated with Fg. at 2 dpi rep1

description: NFg 2d1


title: NuyBai treated with H2O at 4 dpi rep2

description: NH20 4d2


title: NuyBai treated with Fg. at 2 dpi rep2

description: NFg 2d2


title: NuyBai treated with H2O at 2 dpi rep2

description: NH20 2d2


title: 4139_3

value: 51 h of age

value: colostrum fed 12 h after birth

value: colon


title: 4117_3


title: 4128_3


title: 4154_2

value: colostrum fed 6 h after birth


title: 4151_2


title: 4145_3


title: 4146_2


title: NuyBai treated with H2O at 2 dpi rep3

description: NH20 2d3

value: NuyBai

value: spikelets


title: Definite Viral_11

value: Definite Viral


title: 4126_3


title: Definite Viral_10

value: Female


title: Definite Viral_13


title: Definite Viral_09


title: Definite Viral_08


title: Unknown_09

source_name: Whole Blood from patient with infection of uncertain bacterial or viral aetiology

value: Uncertain


title: Definite Viral_04


title: 4144_2


title: Definite Viral_06


title: NuyBai treated with H2O at 2 dpi rep1

description: NH20 2d1


title: 4140_2


title: Definite Viral_02


title: Definite Viral_07


title: Wuhan 1 treated with Fg. at 4 dpi rep3

description: WFg 4d3

value: Wuhan 1

value: F. graminearum inoculation


title: NuyBai treated with H2O at 4 dpi rep1

description: NH20 4d1


title: Definite Viral_01

value: Validation


title: 4134_2

value: Holstein


title: 4122_2


title: 4125_2


title: 4114_2


title: 4164_1

value: colostrum fed immediately after birth


title: 4149_1

value: male


title: Wuhan 1 treated with Fg. at 4 dpi rep2

description: WFg 4d2


title: Wuhan 1 treated with Fg. at 4 dpi rep1

description: WFg 4d1


title: Definite Bacterial_23

source_name: Whole Blood from patient with Definite Bacterial infection

value: Definite Bacterial

value: Male


title: Wuhan 1 treated with H2O at 4 dpi rep3

description: WH20 4d3

value: water (mock) inoculation


title: Wuhan 1 treated with Fg. at 2 dpi rep1

description: WFg 2d1


title: Wuhan 1 treated with Fg. at 2 dpi rep3

description: WFg 2d3


title: Wuhan 1 treated with Fg. at 2 dpi rep2

description: WFg 2d2


title: 4143_1

value: newborn

value: 51 h of age


title: Wuhan 1 treated with H2O at 4 dpi rep2

description: WH20 4d2


title: Definite Viral_03


title: 4135_1

value: colon


title: Wuhan 1 treated with H2O at 4 dpi rep1

description: WH20 4d1


title: Definite Bacterial_22


title: Definite Bacterial_17


title: Definite Bacterial_20


title: Definite Bacterial_16


title: Wuhan 1 treated with H2O at 2 dpi rep3

description: WH20 2d3


title: 4133_1


title: Definite Bacterial_14


title: Wuhan 1 treated with H2O at 2 dpi rep2

description: WH20 2d2


title: 4127_1


title: Definite Bacterial_21


title: Definite Viral_05


title: Wuhan 1 treated with H2O at 2 dpi rep1

description: WH20 2d1


title: 4124_1


title: 4138_1


title: Definite Bacterial_18


title: RNA-Seq_heads of newly eclosed, orphaned bees rep3

city: Griffin

first: Brendan

middle: G.

last: Hunt

state: GA

address: 125 Redding Building, Griffin Campus, 1109 Experiment Street

department: Entomology

institute: University of Georgia

description: mRNA from heads of newly eclosed, orphaned bees rep3

data_processing:
Data were mapped to the Ceratina calcarata v1.1 genome
For RNA-seq data:RNA-seq reads were checked for biases using FastQC (v0.11.4) (Andrews, 2010) and then trimmed using Trimmomatic (v0.32) (Bolger, Lohse, & Usadel, 2014). Reads were then aligned to the C. calcarata reference assembly (v1.1) (Rehan et al., 2016) using Tophat (Trapnell et al., 2012) with parameters “--no-mixed --no-discordant” to filter out read pairs that did not have both reads mapping or had a read pair mapping discordantly. Aligned reads were counted against annotated gene models (Rehan et al. 2016) using Rsubread. Gene models were generated previously as described in Rehan et al. 2016.
For Bisulfite-sequencing data: We trimmed adapters and removed low-quality reads using Trimmomatic (v0.32) (Bolger et al., 2014). Reads were then aligned to the reference genome using Bismark (v0.14.5) (Krueger & Andrews, 2011). Bismark was also used to remove duplicate reads and to extract and quantify the per-site methylation level.
Genome_build: Ceratina calcarata v1.1 reference genome
Supplementary_files_format_and_content: For RNA-seq data: Tab delimited file: <gene_symbol> <aligned reads count>.
For Bisulfite-sequencing data: <chromosome/scaffold> <position> <strand> <reads mapped> <% methylated C> <% unmethylated C>

organism: Ceratina calcarata

extract_protocol: mRNA (for RNA-seq) was extracted and prepared using the Truseq library preparation protocol. Bisulfite conversion and illumina sequencing was performed by the Beijing Genomics Institute.

tag: ecotype

value: Collected in their nests (stems of Rhus typhina) from Durham, NH in June 2015 at 8am and brought to the lab. Mother was removed and offspring were reared to adulthood

value: 3 pooled heads

value: newly eclosed adult


title: 4108_1


title: RNA-Seq_heads of newly eclosed, orphaned bees rep1

description: mRNA from heads of newly eclosed, orphaned bees rep1


title: RNA-Seq_heads of newly eclosed, maternally cared for bees rep3

description: mRNA from heads of newly eclosed, maternally cared for bees rep3

value: Collected in their nests (stems of Rhus typhina) from Durham, NH in June 2015 at 8am and brought to the lab to rear brood to adulthood in the presence of their mother


title: Definite Bacterial_19


title: RNA-Seq_heads of newly eclosed, maternally cared for bees rep2

description: mRNA from heads of newly eclosed, maternally cared for bees rep2


title: RNA-Seq_heads of newly eclosed, maternally cared for bees rep1

description: mRNA from heads of newly eclosed, maternally cared for bees rep1


title: 24hr 24

city: Birmingham

first: Poppy

last: Sephton Clark

state: West Midlands

address: University of Birmingham

department: IMI

institute: University of Birmingham

data_processing:
Alignment: Hisat2
Count: HTSeq
EdgeR: Analysis
Genome_build: Rhizopus delemar strain RA 99-880
Supplementary_files_format_and_content: Count Matrix

organism: Rhizopus delemar

source_name: Rhizopus delemar culture

growth_protocol: Sabouraud dextrose agar or broth (10 g/L mycological peptone, 20 g/L dextrose)

extract_protocol:
Trizol, RNEasy Total RNA Extraction, followed by PolyA+ Purification
NEBNextera

tag: strain


title: 24hr 24p

treatment_protocol: Sabouraud dextrose agar or broth (10 g/L mycological peptone, 20 g/L dextrose)


title: 16hr 16a


title: 12hr 12p


title: 16hr 16


title: 16hr 16p


title: Definite Bacterial_12


title: Definite Bacterial_11

value: Female


title: Definite Bacterial_09


title: Definite Bacterial_10


title: Definite Bacterial_03


title: Definite Bacterial_07


title: Definite Bacterial_08


title: Definite Bacterial_13


title: Control_15

value: Control


title: Definite Bacterial_05


title: 12hr 12a


title: Control_14


title: Definite Bacterial_01


title: Definite Bacterial_06


title: 6hr 6p


title: 12hr 12


title: Definite Bacterial_02


title: 6hr 6a


title: Control_13


title: 6hr 6


title: 5hr 5p


title: 5hr 5a


title: 24hr 24a


title: Control_16


title: 4hr 4p


title: 5hr 5


title: 4hr 4a


title: Control_10


title: Control_11


title: 4hr 4


title: 3hr 3p


title: 3hr 3a


title: 3hr 3


title: 2hr 2p


title: Control_09


title: Control_05


title: Control_06


title: Control_07


title: Definite Bacterial_04


title: Control_08


title: Control_04


title: Control_02


title: 2hr 2


title: 1hr 1


title: 1hr 1a


title: MethylC-seq_heads of newly eclosed, orphaned bees rep1

description: bisulfite-treated DNA from heads of newly eclosed, orphaned bees rep1

value: 9 pooled heads


title: MethylC-seq_heads of newly eclosed, maternally cared for bees rep3

description: bisulfite-treated DNA from heads of newly eclosed, maternally cared for bees rep3


title: 2hr 2a


title: MethylC-seq_heads of newly eclosed, orphaned bees rep3

description: bisulfite-treated DNA from heads of newly eclosed, orphaned bees rep3


title: MethylC-seq_heads of newly eclosed, orphaned bees rep2

description: bisulfite-treated DNA from heads of newly eclosed, orphaned bees rep2


title: 0hr 0b


title: MethylC-seq_heads of newly eclosed, maternally cared for bees rep2

description: bisulfite-treated DNA from heads of newly eclosed, maternally cared for bees rep2


title: 0hr 0a


title: 0hr 0

description: zero


title: 1hr 1p


title: MethylC-seq_heads of newly eclosed, maternally cared for bees rep1

description: bisulfite-treated DNA from heads of newly eclosed, maternally cared for bees rep1


title: Patient 4 serous epithelial ovarian carcinoma

description: tumour tissue

hyb_protocol: Genome Institute of Singapore

scan_protocol: Genome Institute of Singapore

data_processing: mas5 implemented in Affy package of Bioconductor was used to obtain P/M/A calls

source_name: Serous epithelial ovarian carcinoma

label_protocol: Genome Institute of Singapore

extract_protocol: Genome Institute of Singapore

value: Serous epithelial ovarian carcinoma

tag: patient number


title: Patient 3 serous epithelial ovarian carcinoma

description: tumour tissue


title: Control_03

source_name: Whole Blood from healthy control patient

value: Validation


title: Patient 1 serous epithelial ovarian carcinoma

description: tumour tissue


title: Control_01


title: Control_12


title: Patient 2 serous epithelial ovarian carcinoma

description: tumour tissue


title: Heart_LPS_rep4

status: Public on Aug 08 2018

city: Shanghai

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

country: China

institute: Shanghai University

description:
LPS caused reduced cardiac fractional shortening and ejection fraction as measured with echocardialgraphy.
LPS5

hyb_protocol: The labeled RNA were hybridized for 20 hr at 55°C on Agilent-038112 Array. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 12.5; Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 75.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis.
Differentially expressed miRNAs were identified through fold change as well as P value calculated using t-test.

source_name: Heart, LPS (i.p 5 mg/kg), 7-9 hr post injection

label_protocol: Total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP.

growth_protocol: Heart samples were harvested 7-9 hr post LPS or Saline injection and snap frozen in liquide nitrogen.

extract_protocol: Total RNA were isolated using mirVanaTM RNA Isolation Kit according to the manufacturer's instructions.

tag: age

value: 10-12 weeks old


title: Heart_Normal_rep5

description:
Saline injection did not change cardiac function as measured with echocardialgraphy.
N6

source_name: Heart, Saline (i.p), 7-9 hr post injection

value: male


title: Heart_LPS_rep3

description:
LPS caused reduced cardiac fractional shortening and ejection fraction as measured with echocardialgraphy.
LPS4


title: Heart_Normal_rep4

description:
Saline injection did not change cardiac function as measured with echocardialgraphy.
N5


title: Heart_LPS_rep1

description:
LPS caused reduced cardiac fractional shortening and ejection fraction as measured with echocardialgraphy.
LPS1


title: Heart_Normal_rep6

description:
Saline injection did not change cardiac function as measured with echocardialgraphy.
N8


title: Heart_LPS_rep2

description:
LPS caused reduced cardiac fractional shortening and ejection fraction as measured with echocardialgraphy.
LPS2


title: Heart_Normal_rep3

description:
Saline injection did not change cardiac function as measured with echocardialgraphy.
N3


title: Heart_LPS_rep5

description:
LPS caused reduced cardiac fractional shortening and ejection fraction as measured with echocardialgraphy.
LPS7


title: Heart_LPS_rep6

description:
LPS caused reduced cardiac fractional shortening and ejection fraction as measured with echocardialgraphy.
LPS11


title: Heart_Normal_rep2

description:
Saline injection did not change cardiac function as measured with echocardialgraphy.
N2


title: Heart_Normal_rep1

description:
Saline injection did not change cardiac function as measured with echocardialgraphy.
N1


title: Raw264.7 NT 48h vs Reference

city: Bhubaneswar

first: Biswaranjan

last: Pradhan

state: ODISHA

address: Jatni

department: Biological Sciences

country: India

institute: National Institute of Science Education and Research Bhubaneswar

description: RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India

hyb_protocol: 825 ng each of test and reference Cy dye  labeled RNA was mixed together and was fragmented using Agilent fragmentation kit in the presence of blocking reagent for 30 minutes in 60 degree celsius. Equal volume of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture to stop the reaction. 100 μl of the mixture was added to each of the chamber of the hybridization gasket and the array slide was sandwitched over it. The hybridization reaction was done for 17 hours in 65 degree celsius with moist condition in a hybridization oven.

scan_protocol: Scanned on an Agilent G2505C scanner using Agilent Scan control (version 8.3.1.1). Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: RAW 264.7 cells

label_protocol: 500 ng of total RNA were primed with 1.2 µl (3rd dilution) of  T7 promoter primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of MMLV Rtase. The c-DNA was then transcribed by T7 RNA Polymerase in the presence of NTPs and labeled with Cy3-CTP (For Rererence) and Cy5-CTP (For test).

growth_protocol: Cells were grown in DMEM medium (Himedia, India) supplemented with 10% heat inactivated fetal bovine serum (Himedia, India) (without any antibiotic) in 75 cm2 tissue culture flasks (BD Biosciences, USA) at 37 degree Celcius in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA extracted using Qiagen RNEasy mini kit following manufacturer's instructions

tag: cell line

tag: treatment

value: Untreated Raw264.7 cells co-cultured with 3T3L-1 for 48 hours

source_name: Reference

tag: sample type

value: Reference


title: Raw264.7 S100 48h vs Reference

value: Raw264.7 cells co-cultured with 3T3L-1 cells and treated with 100 μMolar Serotonin for 48 hours


title: 3T3L-1 C100 48h vs Reference

description: 3T3L-1 fibroblast cells, originated from mouse  embryonic tissue, purchased from NCCS, India

source_name: 3T3L-1 fibroblast cells

value: 3T3L-1 cells co-cultured with Raw264.7 cells and treated with 100 μMolar Cortisol for 48 hours


title: Raw264.7 CS100 48h vs Reference

value: Raw264.7 cells co-cultured with 3T3L-1 cells and treated with 100 μMolar each of Serotonin and Cortisol for 48 hours


title: 3T3L-1 NT 48h vs Reference

value: Untreated 3T3L-1 cells co-cultured with Raw264.7 for 48 hours


title: 3T3L-1_CS100_48h

value: 3T3L-1 cells co-cultured with Raw264.7 cells and treated with 100 μMolar each of Serotonin and Cortisol for 48 hours

value: 3T3L-1 cells grown alone and treated with 100 μMolar each of Serotonin and Cortisol for 48 hours.


title: 3T3L-1 CS100 48h vs Reference


title: Definite Bacterial_15

last: Levin

address: South Kensington Campus

value: Definite Bacterial


title: 3T3L-1_NT_48h

value: Untreated 3T3L-1 cells grown alone for 48 hours.


title: 3T3L-1_S100_48h

value: 3T3L-1 cells co-cultured with Raw264.7 cells and treated with 100 μMolar Serotonin for 48 hours

value: 3T3L-1 cells grown alone and treated with 100 μMolar Serotonin for 48 hours.


title: 3T3L-1 S100 48h vs Reference


title: Raw264.7 C100 48h vs Reference

value: Raw264.7 cells co-cultured with 3T3L-1 cells and treated with 100 μMolar Cortisol for 48 hours


title: 3T3L-1_S100_24h

value: 3T3L-1 cells co-cultured with Raw264.7 cells and treated with 100 μMolar Serotonin for 24 hours

value: 3T3L-1 cells grown alone and treated with 100 μMolar Serotonin for 24 hours.


title: 3T3L-1_CS100_24h

value: 3T3L-1 cells co-cultured with Raw264.7 cells and treated with 100 μMolar each of Serotonin and Cortisol for 24 hours

value: 3T3L-1 cells grown alone and treated with 100 μMolar each of Serotonin and Cortisol for 24 hours.


title: 3T3L-1_C100_24h

value: 3T3L-1 cells co-cultured with Raw264.7 cells and treated with 100 μMolar Cortisol for 24 hours

value: 3T3L-1 cells grown alone and treated with 100 μMolar Cortisol for 24 hours.


title: 3T3L-1_NT_24h

value: Untreated 3T3L-1 cells co-cultured with Raw264.7 for 24 hours

value: Untreated 3T3L-1 cells grown alone for 24 hours.


title: 3T3L-1_CS100_6h

value: 3T3L-1 cells co-cultured with Raw264.7 cells and treated with 100 μMolar each of Serotonin and Cortisol for 6 hours

value: 3T3L-1 cells grown alone and treated with 100 μMolar each of Serotonin and Cortisol for 6 hours.


title: 3T3L-1_C100_48h

value: 3T3L-1 cells co-cultured with Raw264.7 cells and treated with 100 μMolar Cortisol for 48 hours

value: 3T3L-1 cells grown alone and treated with 100 μMolar Cortisol for 48 hours.


title: 3T3L-1_S100_6h

value: 3T3L-1 cells co-cultured with Raw264.7 cells and treated with 100 μMolar Serotonin for 6 hours

value: 3T3L-1 cells grown alone and treated with 100 μMolar Serotonin for 6 hours.


title: YX5-HBV-pos

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip™ C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Partek genomic suites using RMA  normalization method.

source_name: HBV-pos

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: primary human hepatocytes

value: HBV-pos


title: 3T3L-1_NT_6h

value: Untreated 3T3L-1 cells co-cultured with Raw264.7 for 6 hours

value: Untreated 3T3L-1 cells grown alone for 6 hours.


title: YX2-HBV-neg

source_name: HBV-neg

value: HBV-neg


title: YX6-HBV-pos


title: 3T3L-1_C100_6h

value: 3T3L-1 cells co-cultured with Raw264.7 cells and treated with 100 μMolar Cortisol for 6 hours

value: 3T3L-1 cells grown alone and treated with 100 μMolar Cortisol for 6 hours.


title: YX4-HBV-pos


title: Cugbp1 Brain KO Ctrl 1

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

description: brain tissue obtained at 1 day of age from Cugbp1 KO C57BL6 mouse no treatment

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1) was used to read out and process the microarray image files.

source_name: Brain

label_protocol: RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Cugbp1 KO mice were generated using BayGenomic ES cells, which contain the insertion of the trap vector in from of the AUG codon of the Cugbp1 gene. These cells were microinjected into C57BL6 mice.

extract_protocol: Total RNA was isolated using RNEasy Plus mini kit according to the manufacturer's instructions.

value: Cugbp1 KO

tag: background strain

value: Brain

tag: age at tissue collection

value: 1 day


title: Cugbp1 Brain KO Ctrl 4


title: Cugbp1 Brain WT Ctrl 4

description: brain tissue obtained at 1 day of age from WT C57BL6 mouse treated with no treatment

value: WT


title: YX1-HBV-neg


title: Cugbp1 Brain WT Ctrl 2


title: Cugbp1 SM KO Ctrl 3

description: skeletal muscle obtained at 1 day of age from Cugbp1 KO C57BL6 mouse no treatment

source_name: skeletal muscle

value: skeletal muscle


title: Cugbp1 Brain KO Ctrl 2


title: Cugbp1 Brain WT Ctrl 1


title: Cugbp1 Brain KO Ctrl 3


title: Cugbp1 Brain WT Ctrl 3


title: YX3-HBV-neg


title: ALCL29

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

description: Gene expression data from human anaplastic large cell lymphoma biopsies

hyb_protocol: Following fragmentation, cRNA were hybridized to a HG-133_Plus_2 gene chip. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneArray Scanner.

data_processing: CEL files were processed to extract perfect match probes (PMPs) and raw intensities were normalized using robust multi-array average (RMA) with background correction. Normalized intensities were log2-transformed prior to further analysis

source_name: Lymphnode biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

extract_protocol: Total RNA was extracted from frozen tumor tissue using PerfectPure (5 PR IME, Gaithersburg, MD). RNA quality was confirmed on an Agilent Bioanalyzer (Agilent Technologies,Santa Clara, CA).

treatment_protocol: Tissue biopsies were fixed in OCT and frozen.

tag: age/gender

tag: who diagnosis

value: ALCL, ALK negative

tag: genetic subtype


title: ALCL30

value: ALCL, cutaneous

value: Other


title: ALCL27

value: ALCL, ALK positive

value: ALK


title: ALCL28


title: ALCL31


title: ALCL24


title: ALCL25


title: ALCL23


title: Cugbp1 SM WT Ctrl 3

description: skeletal muscle obtained at 1 day of age from WT C57BL6 mouse treated with no treatment

tag: tissue


title: Cugbp1 SM KO Ctrl 1


title: ALCL22


title: ALCL21


title: Cugbp1 SM WT Ctrl 2


title: ALCL20


title: Cugbp1 SM WT Ctrl 1


title: ALCL16


title: Cugbp1 SM KO Ctrl 2


title: ALCL18


title: ALCL26


title: ALCL19


title: ALCL14


title: Si-Mock 5637PR mRNA

city: Tokyo

first: Naoya

last: Niwa

address: 35, Shinanomachi, Shinjuku-ku

institute: Keio University School of Medicine

hyb_protocol: Sample labeling and hybridization followed the exact Affymetrix procedures

scan_protocol: Standard Affymetric protocol

data_processing: The data were analyzed with GeneSplicing GX Version 12.6 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: platinum resistance cells

extract_protocol: Total RNA from cultured cells was isolated using RNAiso Plus (Takara Bio) according to the manufacturer’s protocol.

tag: cell type

tag: transfection

value: si-mock


title: si-TNFAIP2 5637PR mRNA

label_protocol: Sample labeling and hybridization followed the exact Affymetrix procedures


title: ALCL15


title: ALCL17


title: RNA-Seq_heads of newly eclosed, orphaned bees rep2

description: mRNA from heads of newly eclosed, orphaned bees rep2

value: Collected in their nests (stems of Rhus typhina) from Durham, NH in June 2015 at 8am and brought to the lab. Mother was removed and offspring were reared to adulthood

value: 3 pooled heads

value: newly eclosed adult


title: ALCL13


title: E-CM2

city: Daegue

first: Jae-Ryong

last: Kim

address: Hyunchung-Ro

country: South Korea

institute: Yeungnam University

hyb_protocol: Hybridization were prepared according to the standard Affymetrix hybridization system.

scan_protocol: GeneChips were scanned using the Affymetrics 7G scaner.

data_processing: These raw data sets were separately analyzed using R/Bioconductor package affy, Robust Multi-array Average (RMA) and cluster 3.0, TreeView software followed by differential miRNA expression, fold change & cluster analysis.

source_name: mouse embryonic stem cell

growth_protocol: CM was collected from ESCs in OPTI-MEM on gelatin without feeder, FBS or other supplements. We have used CM to define ESC-specific secretory factors excluding potential factors from FBS and MEFs Gelatin coating was used to feeder free conditions, but some feeder cells may remain in culture. M-CM was used as a control to exclude remaining feeder cell effects. We collected conditioned media from MEF (mouse embryonic fibroblast) cells cultured in OPTI-MEM.

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

tag: conditioned media

value: mouse embryonic stem cell conditioned media

value: mouse embryonic stem cell


title: ALCL11


title: 8174 Testis, Cre+

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

description: Gene expression data from the testis of Cre+ TGFbR2fl/fl males

hyb_protocol: According to manufacturer's (Affymetrix) protocol

data_processing: The data were analyzed with GeneSpring 14.9, using  ExonRMA16 summarization algorithm; quantile sample normalization with baseline transformation to median of all samples

source_name: mouse testis

growth_protocol: 8-10 week old mice housed in  a barrier animal facility monitored and free of common murine pathogens (MHV, MPV, MVM, TMEV, Mycoplasma pulmonis, Sendai, EDIM, MNV, and eco- and endoparasites)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by column purification (Qiagen Mini RNA kit)

treatment_protocol: Anaysis was performed at baseline, with no treatment

value: testis

tag: genotype

value: Cre+

value: untreated


title: ALCL09


title: M-CM

source_name: mouse embryonic fibroblast

value: mouse embryonic fibroblast conditioned media

value: mouse embryonic fibroblast


title: ALCL06


title: 8175 Testis, Cre+

scan_protocol: According to manufacturer's (Affymetrix) protocol


title: E-CM1


title: ALCL08


title: ALCL10


title: 8172 Testis, Cre-

description: Gene expression data from the testis of Cre- TGFbR2fl/fl males

label_protocol: According to manufacturer's (Affymetrix) protocol

value: Cre-


title: 8170 Testis, Cre-


title: 7185 Epididymis, Cre+

description: Gene expression data from the epididymis of Cre+ TGFbR2fl/fl males

source_name: mouse epididymis

value: epididymis


title: ALCL12

value: ALCL, cutaneous


title: 7184 Epididymis, Cre+


title: ALCL07


title: ALCL03


title: 7053 Epididymis, Cre+


title: ALCL01

value: ALCL, ALK negative


title: 7454 Epididymis, Cre-

description: Gene expression data from the epididymis of Cre- TGFbR2fl/fl males


title: 7052 Epididymis, Cre-


title: 8171 Testis, Cre-


title: ALCL04

value: ALCL, ALK positive


title: ALCL05

value: Other


title: Dvpdf_nonaRNAi_REP2_expressions

city: waltham

first: weifei

last: luo

state: MA

address: 415 South st

department: Department of Biology

institute: Brandeis University

data_processing:
RNA sequencing data were analyzed as described in (Rodriguez et al., 2012; McMahon et al., 2016)
Scripts available on GitHub (https://github.com/rosbashlab/).
Alignment to dm3 genome was done with Tophat v2.1.1 with referenence annotation in gtf format. Multimapped reads are removed. Expression levels were quantified by cufflinks (Trapnell et al., 2012).
Genome_build: Release 5/dm3
Supplementary_files_format_and_content: RNA editing sites are provided in bedgraph file format

source_name: brains

extract_protocol:
mRNAs extraction and amplification were prepared according to Nagoshi 2010 et al and Abruzzi et al 2016
Libraries were prepared using using illumina Truseq kits

treatment_protocol: nonA is downregulated by RNA interference in dvpdf cells in fly brains

value: dvpdf neurons

tag: rna

value: mRNA

value: NonA RNAi


title: 8173 Testis, Cre+


title: Dvpdf_nonaRNAi_REP1_expressions


title: Dvpdf_con_REP2_expressions

value: control


title: Dvpdf_con_REP1_expressions


title: FVB testis replicate 1

city: Newark

first: Bin

last: Tian

state: NJ

address: 205 South Orange Ave.

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers New Jersey Medical School

data_processing:
Adpter trimming performed using Cutadapt
3'READs reads were aligned to mm9/rn5 using bowtie2
For 3'READs data, reads with a mapping quality score (MAPQ) ?10 were kept for further analysis. Reads with ?2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
Genome_build: mm9 for mouse, rn5 for rat
Supplementary_files_format_and_content: tab-delimited text files include reads count for each PAS position

source_name: testis

extract_protocol:
TRIzol
See the "extraction protocol" column in the SAMPLES section.
3'READS: The 3’READS procedure has been described in (Zheng et al., 2016). Briefly, Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 10 µl of oligo(dT)25 magnetic beads in 100 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 °C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn, and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1. After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H at 37 °C for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 °C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version) at 22 °C for 1 h in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase, followed by PCR amplification using Phusion high-fidelity DNA polymerase and bar-coded PCR primers for 13-18 cycles (13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg).   PCR products were size-selected twice with AMPure XP beads, using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina NextSeq 500 (1x75 bases).

tag: protocol

tag: purpose

value: Analysis of APA in heart, testis and heart between mouse and rat

tag: strain

value: FVB/NJ


title: C57 testis replicate 2

value: testis


title: C57 testis replicate 1


title: 60_HM_1_FC2

city: Chicago

first: Bryan

middle: J

last: Pavlovic

state: IL

department: Human Genetics

institute: University of Chicago

data_processing:
100 bp single-end RNA-seq reads from each species were mapped to the appropriate genome (hg38 or panTro5) using Hisat2 (version 2.0.4) (Kim et al. 2015). Only reads that mapped uniquely were used.
The number of reads falling into orthologous meta-exons across 44,125  Ensembl genes from hg38, panTro5 was determined using featureCounts within SubRead (version 1.5.1) (Liao et al. 2014).
Genome_build: hg38 & panTro5
Supplementary_files_format_and_content: RNA-seq counts for orthologous genes for all individuals

source_name: induced pluripotent stem cells

growth_protocol: Feeder free iPSC cultures were initially maintained on Growth Factor Reduced Matrigel using Essential 8 Medium (E8) as previously described. After 10 passages in E8, all cell lines were transitioned to a 50/50% ratio of iDEAL/E8 feeder free medium that was prepared in house as specified previously (Marinho et al. 2015). Cell culture was conducted at 37°C, 5% CO2, and atmospheric O2.

extract_protocol:
RNA was extracted using the ZR-Duet DNA/RNA MiniPrep kit (Zymo) with the addition of an on column DNAse I treatment step prior to RNA elution.
Samples were pooled together in 8 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit v2.  100 bp sing-end RNA-seq libraries were sequenced on the HiSeq4000 following the manufacturer's protocols.Samples were pooled  in 8 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit v2.  100 bp sing-end RNA-seq libraries were sequenced on the HiSeq4000 following the manufacturer's protocols.

treatment_protocol: Cardiomyocytes were generated following a recently protocol ((Rana et al. 2012; Burridge et al. 2014; Burridge et al. 2015)) with minimal modification. At 12 hours prior to initiating differentiation, iPSC lines at 70-90% confluence were seeded to achieve a starting density of 150,000-250,000 cells/cm2. Differentiations were initiated by removing stem cell maintenance media and adding RPMI base media (with HEPES LifeTechnologies# 22400105) supplemented with 6 μM CHIR9902 (LClabs# C-6556), 0.5 mg/mL BSA (Sigma-Aldrich# A2153), 0.213 mg/mL ascorbic acid (Santa Cruz Bio# sc-228390), 0.3 μg/mL sodium selenite (Sigma-Aldrich# S5261), 5 μg/mL Holo-transferrin (Sigma-Aldrich# T3705), 1 μg/mL Linolenic acid (Sigma-Aldrich# L2376), 1 μg/mL Linoleic acid (Sigma-Aldrich# 1012) and 1x Pen/Strep (Days 0-1 media). After 48 hours the media was changed to RPMI base media (with HEPES LifeTechnologies# 22400105) supplemented with 2 μM Wnt-c59 (Tocris# 5148), 0.5 mg/mL BSA (Sigma-Aldrich# A2153), 0.213 mg/mL ascorbic acid (Santa Cruz Bio# sc-228390 and 1x Pen/Strep (Days 2-3 media).  After another 48 hours, the media was changed to RPMI base (with HEPES LifeTechnologies# 22400105) supplemented 0.5 mg/mL BSA (Sigma-Aldrich# A2153), 0.213 mg/mL ascorbic acid (Santa Cruz Bio# sc-228390) and 1x Pen/Strep. Media was changed every 48 hours until day 10 (total of 2 additional media changes). At day 10 the media was switched to RPMI media (no glucose, Cellgro#10-043-CV) supplemented with 5 mM Sodium D/L Lactate (Sigma-Aldrich# L4263), 0.5 mg/mL BSA (Sigma-Aldrich# A2153), 0.213 mg/mL ascorbic acid (Santa Cruz Bio# sc-228390) and 1x Pen/Strep, media was changed every 48 hours (total of 2 additional media changes). At day 15, cells were dissociated using TrypLE and split to a density of 0.4 x 106 cells/cm2 onto Matrigel coated dishes. Cells were replated in RPMI media (no glucose, Cellgro#10-043-CV) supplemented with 5% FBS, 10 mM D-galactose (Sigma-Aldrich# G5388), 1 mM Sodium Pyruvate (LifeTechnologies# 11360070), 1X NEAA (LifeTechnologies# 11140076), 5 mM HEPES (LifeTechnologies# 15630080), mM Sodium D/L Lactate (Sigma-Aldrich# L4263), 0.5 mg/mL BSA (Sigma-Aldrich# A2153), 0.213 mg/mL ascorbic acid (Santa Cruz Bio# sc-228390) and 1x Pen/Strep (Galactose media). After 24 hours, the media was changed to Galactose media without FBS. Media was changed every 48 hours (total of 1 additional media change). At day 20 media was changed to Galactose media supplemented with 3 ng/mL Triiodothyronine (T3, Sigma-Aldrich# T6397). Media was changed every 48 hours until cells were harvested at day 27 (total of 3 additional media changes). For the first two media changes (Days 0 and 2) cultures were supplies with an excess of media (0.499 mL/cm2), all other days media was added at (0.2495 mL/cm2).

tag: cell line

tag: Sex

value: Male

tag: population

value: Caucasian

value: induced pluripotent stem cells