title: 3m-HFD miR-223KO 4

city: Rockville

first: Yong

last: He

address: 5625 Fishers lane Room 2S-12

institute: NIAAA/NIH

hyb_protocol: Blocking buffer and Hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software. Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: miR-223KO mouse liver with HFD fed for 3 months

label_protocol: cDNA was generated with SuperScript® Indirect cDNA Labeling Core kit (Invitrogen) and labeled with Cy3/Cy5-mono reactive dye pack (GE healthcare), and the labeled cDNA was purified with Qiagen kit (#28004).

extract_protocol: Total RNA extracted using Trizol from liver and purified with QIAGEN kit (#74104) following manufacturer's instructions.

treatment_protocol: Collected tissues from fresh liver.

tag: strain/background

value: miR-223 KO

tag: gender

value: Male

value: Liver

value: High-fat diet

source_name: Ambion Mouse Assorted Total RNA

extract_protocol: Ambion Mouse Assorted Total RNA reference.

tag: sample type

value: Reference

value: Mixed


title: Cortex-rTg4510-Dox-1

status: Public on Mar 30 2019

type: RNA

city: Gainesville

first: Jose

middle: F

last: Abisambra

state: FL

address: 1275 Center Dr

department: Department of Neuroscience & Center for Translational Research in Neurodegenerative Research

country: USA

institute: University of Florida

description:
rTg4510 Dox 1
Tg(Camk2a-tTA)1Mmay Tg(tetO-MAPT*P301L)4510Kha/J fed doxycycline feed to suppress transgenic tau expression. Expresses human 0N4R P301L tau at approx 5-8x endongenous murine tau levels.

hyb_protocol: Commercially analyzed by ThermoFisher

scan_protocol: Commercially analyzed by ThermoFisher

data_processing: Signal intensities were calculated using SST-RMA and are reported on the log 2 scale. Transcript clusters were annotated to gene symbols using NetAffx annotation files (Release 36).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Brain cortex in rTg4510 mouse, Doxycycline (200ppm) feed

label_protocol: Commercially analyzed by ThermoFisher

growth_protocol: Standard housing in a 14 hr light/10 hr dark cycle at a constant temperature (23°C±2°C) with food and water available ad libitum

extract_protocol: Trizol extraction according to manufacturer's instructions from LN2 frozen brain samples.

treatment_protocol: Either normal feed or feed treated with Doxycycline (200ppm) for 35d

tag: strain

tag: genotype/variation

tag: Sex

value: M

tag: treatment

value: Doxycycline (200ppm) for 35d

tag: tissue

value: brain cortex


title: Cortex-rTg4510-Dox-2

description:
rTg4510 Dox 2
Tg(Camk2a-tTA)1Mmay Tg(tetO-MAPT*P301L)4510Kha/J fed doxycycline feed to suppress transgenic tau expression. Expresses human 0N4R P301L tau at approx 5-8x endongenous murine tau levels.

value: F


title: Cortex-Non-Veh-3

description:
Non Veh 3
FVB/NJ. Normal wildtype mouse.

source_name: Brain cortex in Nontg mouse, Normal feed

value: FVB/NJ

value: wild type

value: none (normal feed)


title: 17-0126_E1Pos

type: SRA

city: Columbus

first: Dean

last: Lee

state: Ohio

address: 700 Children’s Drive

department: Hematology & Oncology

institute: Nationwide Children’s Hospital

description:
processed data file: AllData_N_E_StimVsUnstim_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx
processed data file: AllData_NvsE_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx
processed data file: AllData_Overprocessed data file: All_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx

library_source: transcriptomic

data_processing:
Each sample was aligned to the GRCh38.p9 assembly of the Homo sapiens reference from NCBI (http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.35/) using version 2.5.2b of the RNA-Seq aligner STAR.
Features were identified from the GFF file that came with the assembly from NCBI.
Feature coverage counts were calculated using version 0.6.1p1 of HTSeq -count.
Differentially expressed features were calculated using DESeq2.
Genome_build: human NCBI GRCh38.p9
Supplementary_files_format_and_content: Excel spreadsheets containing normalized read counts for each sample and differential expression data for each feature. File AllData_N_E_StimVsUnstim_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx contains "N+ vs. N-" & "E+ vs. E-" comparisons. File AllData_NvsE_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx contains "N+ vs. E+" & "N- vs. E-" comparisons. File AllData_Overall_170515_RNASeq_TruSeqStranded_CHAKRAVARTI_Results.xlsx contains the "Allstim(N+,E+,Pooled) vs. AllUnstim(N-,E-)" comparison.

organism: Homo sapiens

source_name: Norm_17-0126_E1Pos- Expanded NK cells, Donor 1, yes IL-21

extract_protocol:
Total RNA was prepared using the Total RNA Purification Plus Kit (Norgen Biotek, Ontario, ON, Canada). rRNA was removed from 800ng with TruSeq Stranded Total RNA with Ribo-Zero Gold  kit (Illumina, CA).
Libraries were constructed from first strand cDNA using TruSeq Stranded Total RNA with Ribo-Zero Gold removal kit (Illumina, CA).

tag: cell type

value: Expanded NK cells

tag: donor

tag: disease status

value: Healthy


title: Cortex-Non-Dox-1

description:
Non Dox 1
FVB/NJ. Normal wildtype mouse treated with doxycycline for 35d.

source_name: Brain cortex in Nontg mouse, Doxycycline (200ppm) feed


title: Cortex-rTg4510-Veh-3

description:
rTg4510 Veh 3
Tg(Camk2a-tTA)1Mmay Tg(tetO-MAPT*P301L)4510Kha/J fed normal feed. Expresses human 0N4R P301L tau at approx 13x endongenous murine tau levels.

source_name: Brain cortex in rTg4510 mouse, Normal feed


title: Cortex-rTg4510-Veh-4

description:
rTg4510 Veh 4
Tg(Camk2a-tTA)1Mmay Tg(tetO-MAPT*P301L)4510Kha/J fed normal feed. Expresses human 0N4R P301L tau at approx 13x endongenous murine tau levels.


title: Mutant_2

city: Boston

first: Sahar

last: Nissim

state: MA

address: 77 Ave Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description:
PolyA RNA
processed data file: diff_exp_deseq2_gene.txt

data_processing:
Paired end reads were aligned using Star v2.3 to the zebrafish genome (Zv9). The mapped reads were counted using HTSeq-count (v0.6.0) and gene models from Ensembl transcriptome. Analysis of differential gene expression was performed using DESeq2. Orthology to human genes was determined using Ensembl and supplemented by performing BLAST. GSEA was performed using normalized counts.
Genome_build: Zv9
Supplementary_files_format_and_content: diff_exp_deseq2_gene.txt: Tab-delimited text file; differential expression table that includes DESeq2 normalized data, statistics, and human orthologs.

organism: Danio rerio

source_name: Whole fish

extract_protocol:
RNA was extracted using TRIzol reagent (Life Technologies) from wild-type and mutant larval zebrafish at 3 weeks post-fertilization according to the manufacturer's instructions. RNA quality was checked by Agilent Bioanalyzer. Sequencing was performed after library construction on an Illumina HiSeq.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Tubingen

value: Homozygous rabl3-TR41 mutant

value: Whole fish

tag: age

value: 3 weeks post-fertilization


title: Cortex-Non-Dox-2

description:
Non Dox 2
FVB/NJ. Normal wildtype mouse treated with doxycycline for 35d.


title: Cortex-rTg4510-Veh-2

description:
rTg4510 Veh 2
Tg(Camk2a-tTA)1Mmay Tg(tetO-MAPT*P301L)4510Kha/J fed normal feed. Expresses human 0N4R P301L tau at approx 13x endongenous murine tau levels.


title: Donor3_P1_Rep3_RNA

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Gene quantifications for Gencode v19 were summarized using the --quantMode GeneCounts parameter in STAR.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression counts for hg19 / Gencode v19 annotations

source_name: CD34+ hematopoietic cells

growth_protocol: CD34+ hematopoietic cells were cultured in IMDM supplemented with Erytrhopoietin, SCF, IL-3 as described by Hu et al. (Blood 2013)

extract_protocol:
Qiagen RCL lysis buffer supplemented with beta-mercaptoethanol
Smart-seq2; Nextera-based indexing

tag: population


title: 3m-HFD miR-223KO 2

state: MD

value: miR-223 KO

value: Male

value: Liver


title: 17-0125_E1Neg

source_name: Norm_17-0125_E1Neg- Expanded NK cells, Donor 1, no IL-21


title: Donor2_P4_Rep2_RNA


title: 3m-HFD miR-223KO 3

value: High-fat diet

value: Reference

value: Mixed


title: 17-0124_N2Pos

source_name: Norm_17-0124_N2Pos- Naïve NK cells, Donor 2, yes IL-21

value: Naive NK cells


title: Donor2_P3_Rep2_RNA


title: Mutant_1


title: Cortex-rTg4510-Veh-1

description:
rTg4510 Veh 1
Tg(Camk2a-tTA)1Mmay Tg(tetO-MAPT*P301L)4510Kha/J fed normal feed. Expresses human 0N4R P301L tau at approx 13x endongenous murine tau levels.

value: M

value: brain cortex


title: 17-0123_N2Neg

source_name: Norm_17-0123_N2Neg- Naïve NK cells, Donor 2, no IL-21


title: Cortex-Non-Veh-2

description:
Non Veh 2
FVB/NJ. Normal wildtype mouse.

value: FVB/NJ

value: wild type


title: WT_2

value: WT


title: 3m-HFD miR-223KO 1


title: WT_4


title: 17-0121_N1Neg

source_name: Norm_17-0121_N1Neg- Naïve NK cells, Donor 1, no IL-21

value: Healthy


title: WT_3

value: Tubingen


title: 3m-HFD WT 4

source_name: WT mouse liver with HFD fed for 3 months


title: WT_1


title: Cortex-Non-Veh-1

description:
Non Veh 1
FVB/NJ. Normal wildtype mouse.

value: F

value: none (normal feed)


title: Donor2_P1_Rep2_RNA


title: RNA150202CC_9_UDR1

city: Portland

first: Cecilia

middle: Y

last: Cheung

state: Or

address: 3181 SW Sam Jackson Park Road

department: Obstetrics & Gynecology

institute: Oregon Health & Science University

data_processing:
FastQC software (v.0.11.3) was used to evaluate the quality of the fastq files.
Fast- and SNP-tolerant detection of complex variants as well as splicing in short reads were used to align the reads to the sheep genome (Oar_v.3.1).
HTSeq-count (v0.6.1) was used to count the number of reads per unique gene_id.  The union option was selected so that reads that ambiguously map to multiple gene_ids were discarded.
Normalized counts for all samples were merged into one file and imported into Bioconductor’s (v3.1) DESeq2 to determine differential expression.
The only factor included in the statistical model was experimental condition, and pairwise comparisons were performed between the control and each of the 3 experimental conditions.
Genome_build: Oar_v.3.1 from Ensembl
Supplementary_files_format_and_content: tab delimited text file containing the raw counts for each gene (Ensembl Gene ID) in each sample

organism: Ovis aries

source_name: amnion tissue

growth_protocol: On gestational age 121 ± 0.5 (mean ± SE) days (term = 145-150 days), sixteen late gestation time-dated pregnant sheep with singleton fetuses were instrumented with chronic maternal and fetal vascular catheters as well as amniotic fluid and fetal bladder catheters

extract_protocol:
Ovine tissue samples for multiomics analysis were obtained immediately after the 2-day experimental protocols. Total RNA was extracted from amnion tissues using an RNeasy Kit (Qiagen, Inc., Valencia, CA).
Illumina TruSeq RNA-Seq. Briefly, Poly(A)+ RNA was extracted from total RNA, chemically fragmented and converted to double stranded cDNA by random hexamer priming.  The 3’ adenylated fragments were ligated to indexed adaptors.  The libraries were amplified by 10 rounds of polymerase chain reaction (PCR), profiled on the Bioanalyzer and mixed for multiplexing.  Following concentration determination by real time PCR (Kapa Biosystems, Sigma-Aldrich, St. Louis, MO), the mixes were denatured and sequenced on the HiSeq 2000 (Illumina).

treatment_protocol: control (C, n=4), urine drainage without fluid replacement (UD, n=4), urine drainage and isovolumic fluid replacement with lactated Ringer’s solution (UDR, n=4), and continuous intra-amniotic fluid infusion of lactated Ringer’s solution at 2 liters/day (IA, n=4).  Two-day experimental protocols were used.

value: amnion

value: UDR

tag: treatment description

value: urine drainage and isovolumic fluid replacement with lactated Ringer’s solution (UDR)


title: Donor1_P7_Rep2_RNA


title: Donor1_P8_Rep2_RNA


title: Donor1_P6_Rep2_RNA


title: RNA150202CC_7_UD3

value: UD

value: urine drainage without fluid replacement (UD)


title: Donor1_P5_Rep2_RNA


title: RNA150202CC_8_UD4


title: dram1_mutant_infected_300cfu_rep3

city: Leiden

first: Gabriel

last: Forn-Cuní

state: Zuid-Holland

address: Einsteinweg 55

department: IBL-ASH-CO

country: Netherlands

institute: Universiteit Leiden

data_processing:
Image analysis and base calling was done by the Illumina HCS version 2.2.68.
Filtered reads were mapped to Ensembl genome GRCz10 annotation version 80 using Tophat version 2.0.13, Samtools and HTSeq version 0.6.1p1.
Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq2 package (version 1.18.1) available in Bioconductor (version 3.6).
Genome_build: D. rerio GRCz10.80 reference genome (http://www.ensembl.org/info/data/ftp/index.html )
Supplementary_files_format_and_content: tab-delimited text files include read values for each gene in each Sample

source_name: zebrafish dram1 mutant embryos infected with 300CFU of M. marinum, 4 dpi

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were kept in egg water (60µg/ml Instant Ocean sea salts) containing 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) at 28.5°C.

extract_protocol:
Pools of embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 0,7 ml of QIAzol® Reagent (Qiagen) and subsequently total RNA was extracted and on-column DNase digestion was performed with a RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
A total of 0.5 μg of RNA was used to make RNAseq libraries using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina Inc., San Diego, USA). The resulting mRNA-Seq library was sequenced using an Illumina HiSeq2500 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.

treatment_protocol: Zebrafish embryos from three independent crosses were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the blood island with 150 or 300 CFU of M. marinum strain M bacteria suspended in PBS/2%PVP or mock-injected with PBS/2%PVP as a control. Embryos were treated with 0.02% ethyl 3-aminobenzoate methanesulfonate (Tricaine, SIGMA-ALDRICH) for anesthesia before bacterial injections and RNA extraction. At 5 days post fertilization (4 days post infection), total RNA from pools of 20 embryos for treatment group was isolated using QIAzol® Reagent (Qiagen).

value: dram1{delta}19N mutation

tag: treatment (blood island injection at 28 hpf)

value: M. marinum, M strain 300 cfu

tag: developmental stage (rna isolation)

value: 4 dpi


title: RNA150202CC_6_UD2


title: dram1_mutant_infected_300cfu_rep2


title: 3m-HFD WT 3

value: Male

value: Liver

value: High-fat diet

value: Reference

value: Mixed


title: dram1_mutant_infected_300cfu_rep1


title: 3m-HFD WT 2

value: WT


title: 3m-HFD WT 1


title: Donor1_P8_Rep1_RNA


title: Donor2_P2_Rep2_RNA


title: dram1_mutant_infected_150cfu_rep3

source_name: zebrafish dram1 mutant embryos infected with 150CFU of M. marinum, 4 dpi

value: M. marinum, M strain 150 cfu


title: dram1_mutant_infected_150cfu_rep2


title: RNA150202CC_5_UD1


title: RNA150202CC_4_C4

value: C

value: control


title: Donor1_P7_Rep1_RNA


title: dram1_mutant_infected_150cfu_rep1


title: Donor1_P6_Rep1_RNA


title: SUPB15: RNAseq

city: MEMPHIS

first: John

last: Diedrich

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Peaks were called using MACS2 peak caller
ATACseq an RNAseq reads were aligned to the hg19 human genome using Bowtie2
Genome_build: hg19

growth_protocol: Leukemia cells were routinely generated by culturing (typically 20–30 × 106 cells into a T75 flask) in RPMI1640 +10%FBS+1%P/S  and 10,000 cells were used for ATAC transposition

extract_protocol:
DNA was transposed using the FAST-ATAC protocol and mini-elute reaction cleanup kit was used to isolate the transposed DNA
Library was constructed using illumina barcodes and SPRI bead size selection

value: Human-Derived ALL Cell Line

tag: cell line


title: dram1_mutant_uninfected_rep3

source_name: zebrafish dram1 mutant embryos injected with PBS, 4dpi


title: 17-0122_N1Pos

source_name: Norm_17-0122_N1Pos- Naïve NK cells, Donor 1, yes IL-21

value: Naive NK cells

value: Healthy


title: RNA150202CC_3_C3

value: amnion


title: RNA150202CC_2_C2


title: Donor1_P4_Rep1_RNA


title: Donor1_P5_Rep1_RNA


title: dram1_mutant_uninfected_rep2


title: Donor1_P3_Rep1_RNA


title: dram1_mutant_uninfected_rep1


title: control_infected_300cfu_rep3

source_name: zebrafish control embryo infected with 300CFU of M. marinum, 4 dpi

value: Non-mutant


title: RNA150202CC_1_C1


title: Donor1_P2_Rep1_RNA


title: Donor1_P1_Rep1_RNA


title: control_infected_300cfu_rep2


title: RNA150202CC_16_S4

value: IA

value: continuous intra-amniotic fluid infusion of lactated Ringer’s solution at 2 liters/day (IA)


title: control_infected_300cfu_rep1

value: M. marinum, M strain 300 cfu

value: 4 dpi


title: control_uninfected_rep3

source_name: zebrafish control embryos injected with PBS, 4dpi


title: RNA150202CC_15_S3


title: RNA150202CC_13_S1


title: RNA150202CC_14_S2


title: Donor3_P8_Rep3_ATAC

library_source: genomic

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
We used MACS2 to call all reported ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues. For all subsequent analysis we discarded peaks falling within these regions.
A consensus peak set was called for of fixed 250bp using all summits proritized by the maximum -log10 FDR per sample using an iterative algorithm. Individual samples were scored
Genome_build: hg19
Supplementary_files_format_and_content: Raw chromatin accessibility counts over a comprehensive peak set for each sample

molecule: genomic DNA

extract_protocol:
Digitonin-based lysis
FAST-ATAC-seq


title: Donor3_P8_Rep4_ATAC


title: RNA150202CC_12_UDR4

value: UDR

value: urine drainage and isovolumic fluid replacement with lactated Ringer’s solution (UDR)


title: control_uninfected_rep2


title: RNA150202CC_11_UDR3


title: Donor3_P7_Rep4_ATAC


title: Donor3_P7_Rep3_ATAC


title: control_uninfected_rep1


title: Donor3_P6_Rep4_ATAC


title: RNA150202CC_10_UDR2


title: Wei-plate7

first: wei

last: wang

state: NY

address: 100 washington square east

department: Biology

institute: New York University

data_processing:
Barcodes in Read1 fastq files. Sequenced reads were mapped to JoinedScaffold (http://ghost.zool.kyoto-u.ac.jp/datas/JoinedScaffold.zip) whole genome using star/intel/2.5.2b with default parameters.
Reads count were calculated using featureCounts function in Rsubread package with parameters as annot.ext="KH.KHGene.2013.gtf",isGTFAnnotationFile = TRUE,GTF.featureType = "exon",GTF.attrType = "gene_id"
Supplementary_files_format_and_content: Expression matrix ready for single cell RNA-seq analysis.tab-delimited text files include raw FPKMs for each gene per cell. Rows:Gene_id, Columns: cell_id.

molecule: polyA RNA

organism: Ciona robusta

source_name: TVC progeny

growth_protocol: Juvenile cultured in FASW in agarose coated plastic Petri dishes at 18°C.

extract_protocol: RNA libraries were prepared for sequencing SMART-seq 2 protocol.

tag: developmental stage

value: Stage 38 juveniles

value: FACS purified Mesp+ cells


title: Wei-plate6


title: Wei-plate5


title: Wei-plate8


title: Wei-plate4


title: Donor3_P6_Rep3_ATAC


title: Wei-plate3


title: Sham-1

city: Changsha

first: Weijun

last: Peng

address: No.139 Middle Renmin Road

department: The Second Xiangya Hospital

country: China

institute: Central South University

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor.  Expressed data were normalized using the Median normalization.

organism: Rattus norvegicus

source_name: hippocampal tissue

label_protocol: After quality Sham, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: In this experiment, we utilized an intracerebroventricular(ICV) injection of Aβ1–42 oligomers into the cerebral ventricles of the animals to induce a validated AD model. For the Sham group, the vehicle was injected bilaterally into the lateral ventricles through a stainless steel cannula.

tag: gender

value: male


title: Donor3_P4_Rep3_ATAC


title: Sham-2


title: Sham-3


title: Donor3_P3_Rep3_ATAC


title: AD-3


title: Wei-plate2


title: Donor3_P5_Rep3_ATAC


title: Donor3_P5_Rep4_ATAC


title: Donor3_P2_Rep3_ATAC


title: T20_heads_embryos_RNAseq

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

data_processing:
RNA-seq: Reads were mapped to the sea lamprey germline genome assembly using STAR (v2.4.2 )63 (STAR --genomeDir $GENOME --readFilesIn $R1.fastq $R2.fastq --runThreadN 4 --outFileNamePrefix $PREFIX --readFilesCommand zcat --outSAMstrandField intronMotif --alignEndsType EndToEnd --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate). Separate transcriptomes for dorsal neural tube sample datasets or head and embryo sample datasets were assembled de novo with Cufflinks followed by Cuffmerge using default parameters to make a consensus transcriptome from all the datasets. Read counts for dorsal neural tube datasets were obtained with Subread featureCounts (v1.4.6-p4) using the Cuffmerge consensus transcriptome in SAF format as a reference (featureCounts -p -B -M -F SAF -s 2 -T 4 -a $SAF -o $OUT $IN.bam). Differential expression analysis was performed on the dorsal neural tube read count datasets using DESeq2 (v.1.8.2)
ATAC-seq: Reads were mapped to the sea lamprey germline genome assembly using Bowtie2 (bowtie2 --phred33 -p 4 -X 2000 --very-sensitive -x $GENOME -1 $R1.fastq -2 $R2.fastq -S $OUT.sam). Duplicates were removed with Picard (v1.83) MarkDuplicates and the distribution of fragment sizes assessed with Picard (v1.83) CollectInsertSizeMetrics. Replicate bam files for each developmental stage were merged with SAMtools and filtered with BamTools to remove unpaired reads and reads mapped to the mitochondrial chromosome. Filtered bam files were down-sampled to match the file with the lowest number of reads using Picard (v1.83) DownsampleSam. Down-sampled bam files were sorted by name using SAMtools and paired-end bed files were obtained using bedtools(v.2.15.0) bamtobed bedpe. Reads were extended to a read length of 100bp. Peak-calling was performed using MACS2 (macs2 callpeak -t $IN.bed –f BED –name $IN.macs2 --outdir $OUT --shiftsize=100 --nomodel --slocal 1000). Output peak files (.xls) for each developmental stage were converted to bed format and merged with bedtools merge to create one consensus peak set.
Genome_build: Petromyzon marinus germline genome
Supplementary_files_format_and_content: RNAseq_transcriptome.gtf: Separate transcriptomes for dorsal neural tube sample datasets or head and embryo sample datasets were assembled de novo with Cufflinks followed by Cuffmerge using default parameters to make a consensus transcriptome from all the datasets.
Supplementary_files_format_and_content: RNAseq_Featurecounts.txt: a matrix of readcounts for the dorsal neural tube RNA-seq datasets generated with featureCounts
Supplementary_files_format_and_content: RNAseq_DESeq2_normalised_counts.txt:  a matrix of normlaised readcounts for the dorsal neural tube RNA-seq datasets generated with DESeq2
Supplementary_files_format_and_content: Pm_ATAC_consensus_peaks.bb: Output peak files from MACS2 (.xls) for each developmental stage were converted to bed format and merged with bedtools merge to create one consensus peak set. Bed files were converted to bigBed with KentUtilities's bedToBigBed
Supplementary_files_format_and_content: Lp_ATAC_consensus_peaks.bb: Output peak files from MACS2 (.xls) for each developmental stage were converted to bed format and merged with bedtools merge to create one consensus peak set. Bed files were converted to bigBed with KentUtilities's bedToBigBed

organism: Petromyzon marinus

source_name: heads and whole embryos

extract_protocol:
T18, T20 and T21 dorsal neural tubes including premigratory, migrating and/or post-migratory neural crest cells were dissected from the head using an eye-lash knife. T20 and T23 heads were dissected using forceps.
For RNA-seq, tissue was lysed in the Ambion RNaqueous Total RNA Isolation kit lysis buffer (AM1931), set on ice for 15 minutes with occasional vortexing, flash frozen in liquid nitrogen and stored at -80°C. RNA was extracted using the Ambion RNAqueous Micro Total RNA isolation kit and assessed using the Agilent Bioanalyser.
For ATAC-seq, groups of dissected tissue were collected into L-15 medium (Lifetech) with 10% fetal bovine serum at 19°C. Tissue was first dissociated in dispase (1.5 mg/ml in DMEM; 10mM Hepes, pH 7.5), followed by the addition of an equal volume of trypsin (0.05% Trypsin; 0.53mM EDTA in HBSS) at room temperature for a total of up to 15 minutes. Dissociated cells were passed over a 40 μm cell strainer into Hanks’ solution (1xHBSS; 10mMHepes; 0.25%BSA) and centrifuged at 500 x g for 7 minutes at room temperature. The supernatant was removed and fresh Hank’s solution applied. 50 000 cells were counted out and centrifuged for 5 minutes at 500 × g at 4°C and washed with cold 2/3 phosphate buffered saline (PBS) by centrifugation for 5 minutes at 500 × g, 4°C.
RNA-seq libraries were prepared from 100 ng RNA per sample using the NEBNExt Ultra Directional RNA Library Prep Kit for Illumina (E7420) in combination with the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext High-Fidelity 2X PCR Master Mix (M0451S). Libraries were indexed and enriched by 15 cycles of amplification. Library preparation was assessed using the Agilent TapeStation and libraries quantified by Qubit. The concentration of library pools was assessed with the KAPA Library Quantification Kit (KK4835).
For ATAC-seq, dissociated cells were lysed (10mM Tris-HCl, pH7.4; 10mM NaCl; 3mM MgCl2; 0.1% Igepal) and tagmented using the Illumina Nextera kit (FC-121-1030) for 30 minutes at 37°C as previously described (Buenrostro et al. 2015 Curr Protoc Mol Biol 109, 21 29 21-29, doi:10.1002/0471142727.mb2129s109), with the addition of a tagmentation-stop step by the addition of EDTA to final concentration of 50 nM and incubation at 50°C for 30 minutes. Tagmented DNA was amplified using the NEB Q5 High-Fidelity 2X Master Mix (M0492S) for 14 cycles. Tagmentation efficiency was assessed using Agilent TapeStation and libraries quantified by Qubit. The concentration of ATAC library pools was assessed with the KAPA Library Quantification Kit (KK4835).

tag: Stage

value: heads and whole embryos

tag: number of individuals per sample

value: 2 groups of 20 heads; two groups of 10 embryos


title: 2 mM sialic acid

city: Cambridge

first: Benjamin

last: Wang

address: 31 Ames Street

institute: MIT

data_processing:
Single-end reads mapped to PA14 genome using bowtie2 with default settings.
Genes with fewer than 200 read counts were eliminated. To normalize data, the total number of reads across all genes was calculated for + and - sialic acid conditions. The normalized read count for each gene was calculated by dividing each raw read count by the total read count for both + and - sialic acid conditions.
To calculate fold change of each gene, the ratio between the normalized read count of each gene in the + sialic acid vs. the - sialic acid condition was calculated. Data in the paper is shown as the log2 transformation of this data.
Genome_build: NC_008463.1
Supplementary_files_format_and_content: All_RNAseqdata_20min.csv is a file containing the counts of all genes from the processed RNA-seq data in both + and - sialic acid conditions.

organism: Pseudomonas aeruginosa

source_name: Bacterial liquid culture

growth_protocol: Separate P. aeruginosa colonies were picked from LB agar plates. Overnight cultures (12-16 hrs) were grown at 37°C in LB. Cultures were back diluted 1:100 in the morning and grown up to OD~0.6 before the addition of sialic acid.

extract_protocol:
RNA was extracted using the MasterPure Complete DNA and RNA Purification Kit (see publication for more details).
Purified RNA was submitted to the MIT MicroBio core for processing and library construction.

treatment_protocol: Sialic acid was made as a 100 mM stock and then dissolved 1:100 into cultures for a final concentration of 1 mM at OD~0.6. Sialic acid was incubated for 20 minutes with cultures before RNA extraction.

tag: strain

value: WT

tag: time induction

value: 20 minutes

value: 2 mM sialic acid


title: AD-2


title: Donor3_P1_Rep3_ATAC

source_name: CD34+ hematopoietic cells


title: 0 mM sialic acid

tag: treatment

value: 0 mM sialic acid


title: Donor2_P4_Rep2_ATAC


title: T23_heads_Pm_ATACseq_3

source_name: heads

tag: tissue

value: heads


title: AD-1


title: T23_heads_Pm_ATACseq_2


title: Run+ISO4

type: protein

city: Beijing

first: Cao

last: Ning

address: 49 Huayuan North Road

institute: Peking university

description: SAMPLE 16

hyb_protocol: Then aspirated the remaining, added heart lysates containing equal amounts of protein to each sub-array, incubated arrays for 2 hours. Aspirated samples from sub-arrays and washed gently

scan_protocol: The signals were detected with a laser scanner (Innopsys’ InnoScan®) using Cy3 or "green" channel (excitation frequency = 532 nm) to get gray values of every cytokines

data_processing:
The gray values were calculated by ImageJ version 1.8.0 to be as the raw data of cytokines expression.
These Raw data were normalized with the expression file creator module from the GenePattern software package.

label: Biotin-antibody

molecule: protein

source_name: cardiac ventricle

label_protocol: Added 1X Biotin-conjugated Anti-Cytokines to each sub-array, incubated for 2 hours. Repeated the aspirate and wash procedures. Added 1X Streptavidin-Fluor to each sub-array, incubated for 2 hours, aspirated and washed again

growth_protocol: 10-week old male C57BL/6 mice (body weight 25-30 g). Mice were housed in a specific pathogen-free environment under the controlled temperature of 23°C, relative humidity of 65%, and illumination of 12 hr light/ 12hr dark cycle, and received standard rodent food.

extract_protocol:
1. Weigh the tissue and cut small pieces into the tube.
2. Protein extraction reagents containing inhibitors were prepared.
3. Add precooled protein extraction reagent containing inhibitor (add 1 ml extraction reagent in 250 mg tissue).
4. Use a homogenizer to homogenize at a low speed for 30 seconds at a time, and take an ice bath for 1 minute between homogenates until the tissue is completely cracked.
5. The lysate was centrifuged by 14,000 xg for 15 minutes in a pre-cooled centrifuge.The supernatant was immediately transferred into a new centrifuge tube for storage.

treatment_protocol: The mice were subjected to running training group and sedentary control group randomly. Running group ran on a treadmill for 90 min/day, 6 days/week, for 6 weeks. We choose the velocity of 80% VO2max, which is 15cm/s as the speed based on the exercise tolerance of the mice. ISO group was given subcutaneous injections of ISO (Sigma-Aldrich, St. Louis, MO, USA) at a dose of 5 mg/kg body weight. Control group was injected subcutaneously with an equal volume of saline

value: 10 weeks old

tag: Sex

value: Run+ISO

value: cardiac ventricle


title: Run+ISO3

description: SAMPLE 15


title: T23_heads_Pm_ATACseq_1


title: T23_heads_Lp_ATACseq_2

organism: Lampetra planeri


title: T21_dnt_Pm_ATACseq_3

source_name: dorsal neural tube (dnt)

value: dorsal neural tube (dnt)


title: T23_heads_Lp_ATACseq_1


title: Donor2_P2_Rep2_ATAC


title: Run+ISO2

description: SAMPLE 14


title: T21_dnt_Lp_ATACseq_4


title: Donor2_P3_Rep2_ATAC


title: Run+ISO1

description: SAMPLE 13


title: Donor1_P8_Rep2_ATAC


title: T21_dnt_Pm_ATACseq_1


title: Donor2_P1_Rep2_ATAC


title: T21_dnt_Lp_ATACseq_3


title: Sed+ISO4

description: SAMPLE 12

value: Sed+ISO


title: Sed+ISO3

description: SAMPLE 11


title: T20_dnt_Pm_ATACseq_3


title: Sed+ISO2

description: SAMPLE 10


title: T21_dnt_Pm_ATACseq_2


title: Donor1_P6_Rep2_ATAC


title: T23_heads_Lp_ATACseq_3


title: T20_dnt_Pm_ATACseq_2


title: T21_dnt_Lp_ATACseq_1


title: Donor1_P5_Rep2_ATAC


title: Donor1_P7_Rep2_ATAC


title: T20_dnt_Pm_ATACseq_1


title: T20_dnt_Lp_ATACseq_3


title: Sed+ISO1

description: SAMPLE 9


title: Donor1_P8_Rep1_ATAC


title: T21_dnt_RNAseq_3

description:
RNAseq_transcriptome.gtf
RNAseq_Featurecounts.txt
RNAseq_DESeq2_normalised_counts.txt


title: Run4

description: SAMPLE 8

value: Run


title: T20_dnt_Lp_ATACseq_2


title: T20_dnt_Lp_ATACseq_1


title: Run3

description: SAMPLE 7


title: T21_dnt_RNAseq_2


title: T21_dnt_Lp_ATACseq_2


title: Donor1_P6_Rep1_ATAC


title: Donor1_P7_Rep1_ATAC


title: T21_dnt_RNAseq_1


title: Run2

description: SAMPLE 6


title: Run1

description: SAMPLE 5


title: Ctrl4

description: SAMPLE 4

value: Ctrl


title: T20_dnt_RNAseq_1


title: Ctrl3

description: SAMPLE 3


title: Donor1_P2_Rep1_ATAC


title: Donor1_P3_Rep1_ATAC


title: Donor1_P5_Rep1_ATAC


title: Ctrl2

description: SAMPLE 2


title: T18_dnt_RNAseq_2


title: T18_dnt_RNAseq_3


title: Sham-1

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Rat circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. Then, a series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 9 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

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

treatment_protocol: In this experiment, we utilized an intracerebroventricular(ICV) injection of Aβ1–42 oligomers into the cerebral ventricles of the animals to induce a validated AD model. For the sham group, the vehicle was injected bilaterally into the lateral ventricles through a stainless steel cannula.


title: AD-3


title: T18_dnt_RNAseq_1


title: Donor1_P1_Rep1_ATAC


title: Sham-2


title: AD-2


title: Sham-3


title: Ctrl1

description: SAMPLE 1


title: T20_dnt_RNAseq_2


title: Donor1_P4_Rep1_ATAC


title: siRNA_SNHG15_rep3 [S3]

status: Public on Mar 29 2019

city: Pamplona

first: Morvarid

last: Saeinasab

state: Navarra

address: Avda. Pío XII, 55

department: Gene Therapy

country: Spain

institute: Center for Applied Medical Research (CIMA)

data_processing:
Sequence reads were aligned to the genome assembly hg19 using STAR (Dobin et al., 2013) with default parameters
Reads were counted in each gene with featureCount (Liao Y et al., 2014)
Genome_build: hg19
Supplementary_files_format_and_content: one tab-delimited text matrix including raw counts values of each gene in each sample

growth_protocol: Human colorectal cancer cell line LoVo was cultured in Roswell Park Memorial Institute (RPMI-1640) medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin (Lonza).

extract_protocol:
Total RNAs were isolated from cultured cells using TRIzol Reagent (Invitrogen) following the manufacturer’s instructions.
Library preparation was performed with the TruSeq Stranded mRNA kit (Illumina).
Libraries were then sequenced on an Illumina NextSeq (75 bp paired-end).

treatment_protocol: LoVo  cells were plated into 6 well plate (150 × 103 cells per well) and transfected with siRNAs at a final concentration of 25 nM for 48 h, using Lipofectamine 2000 (Invitrogen, USA) according to manufacturer’s protocol.

value: LoVo

tag: cell type

value: Human colorectal cancer cell line

value: siRNA_SNHG15 transfected


title: AD-1

value: male


title: Day3Old3: middle-aged injured - mRNA

city: Calgary

first: V. Wee

last: Yong

state: AB

address: 3330 Hospital Dr. NW

country: Canada

institute: University of Calgary

data_processing:
RNA quality determined using the Agilent 2200 TapeStation, only samples with a RIN greater than 8 were used for sequencing
RNA was amplified with REPLI-g protocol
Sequencing performed on the Illumina NextSeq500 platform
Sequencing reads assessed for quality using FastQC version 0.11.4
Reads mapped to the genome using TopHat version 2.0.10 with bowtie version 1.1.2 as an internal aligner
Raw read counts were calculated using featureCounts at the gene level
Genome_build: Ensembl, GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes read counts for each sample

source_name: middle-aged injured

extract_protocol:
PBS perfusion followed by laser capture microdissection of the spinal cord white matter region of interest
Sequences read, assessed for quality using FastQC, mapped to the genome (Ensembl, GRCm38) using TopHat with bowtie

treatment_protocol: Injured animals were injected with lysolecithin into the ventrolateral white matter

value: spinal cord white matter


title: Day3Old2: middle-aged injured - mRNA


title: SCRAMBLE_rep3 [S6]

source_name: LoVo_SCRAMBLE siRNA

value: SCRAMBLE siRNA transfected


title: SCRAMBLE_rep1 [S4]


title: SCRAMBLE_rep2 [S5]


title: Day3Young2: young injured - mRNA

source_name: young injured


title: Day3Young1: young injured - mRNA


title: siRNA_SNHG15_rep1 [S1]


title: Day3Old1: middle-aged injured - mRNA


title: Day3Young3: young injured - mRNA


title: NaiveOld1: middle-aged naive - mRNA

source_name: middle-aged naïve


title: NaiveOld3: middle-aged naive - mRNA


title: NaiveYoung2: young naïve - mRNA

source_name: young naïve


title: NaiveOld2: middle-aged naive - mRNA


title: NaiveYoung3: young naïve - mRNA


title: siRNA_SNHG15_rep2 [S2]


title: S21_KG-CD44High

city: Monterotondo

first: Christophe

last: Lancrin

state: RM

address: Via Ramarini 32

department: EMBL Rome

country: Italy

institute: EMBL

data_processing:
Quality check with Fastqc
Adaptor clipping with FASTX-clipper version 1.0.1
Synchronisation of clipped files with FASTQ-paired-end-joiner version 2.0.0
Splitting with FASTQ-paired-end-splitter version 1.0.0
Mapping with RNA star
Genome_build: mm10
Supplementary_files_format_and_content: Htseq-count text file with raw count numbers for each sample

growth_protocol: Not applicable. The cells were not grown.

extract_protocol:
Cells from C57Bl/6 Aorta-Gonad-Mesonephros (AGM) region at E9.5, E10 and E11 stages of embryonic development were FACS sorted into tube strips with lysis buffer containing 0.2% Triton X-100, oligo-dT Primer and dNTP mix and after snap frozen on dry-ice. RT & template-switching, PCR preamplification (14 cycles of amplification) were performed as described in the Smart-seq2 protocol (Picelli S et al, 2014, PMID: 24385147 )
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Not applicable. The cells were not treated.

tag: embryonic time point

value: HSPC

tag: number of cells


title: S18_KG-CD44LoKitPos

value: Pre-HSPC


title: S17_KG-CD44LoKitPos


title: S14_CD44LoKitNeg

value: Hemogenic Endothelial Cell


title: S13_CD44LoKitNeg


title: S16_CD44LoKitNeg


title: S15_CD44LoKitNeg


title: S10_CD44Neg

value: Endothelial Cell


title: S11_CD44LoKitNeg


title: S8_CD44Neg


title: S9_CD44Neg


title: S6_CD44Neg


title: S5_CD44Neg


title: S4_CD44Neg


title: S3_CD44Neg


title: Splenic monocytes from naïve donors, replicate 1

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files containing 75-80bp paired-end reads were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread 1.22.3.
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in NCBI annotation.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: spleen

extract_protocol:
RNA was isolated from freshly sorted cells with the RNeasyPlus Mini kit (Qiagen).
mRNA reverse transcription cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

value: spleen

tag: background strain

value: naïve

value: splenic monocytes

tag: ccr2 marker

value: positive

tag: mhc-ii marker


title: S22_KG-CD44High


title: S1_CD44Neg


title: Cardiac macrophage population R3 from CAWS challenged donors, replicate 2

source_name: heart

value: heart

value: CAWS challenged

value: cardiac macrophages

value: high


title: NaiveYoung1: young naïve - mRNA


title: Splenic monocytes from naïve donors, replicate 3


title: Splenic monocytes from naïve donors, replicate 2


title: Cardiac macrophage population R3 from CAWS challenged donors, replicate 3


title: Cardiac macrophage population R3 from CAWS challenged donors, replicate 1


title: S20_KG-CD44High


title: S19_KG-CD44LoKitPos


title: S12_CD44LoKitNeg


title: Cardiac macrophage population R2 from CAWS challenged donors, replicate 3

value: negative


title: S7_CD44Neg


title: S2_CD44Neg


title: Cardiac macrophage population R2 from naïve donors, replicate 3


title: Cardiac macrophage population R3 from naïve donors, replicate 1


title: Cardiac macrophage population R3 from naïve donors, replicate 2


title: Cardiac macrophage population R1 from CAWS challenged donors, replicate 2

value: low


title: Cardiac macrophage population R2 from CAWS challenged donors, replicate 1


title: Cardiac macrophage population R1 from CAWS challenged donors, replicate 3


title: Cardiac macrophage population R1 from naïve donors, replicate 1


title: RNA-Seq CD11b+CD45_CK3

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

description: SMART-Seq v4 Ultra Low Input RNA Kit

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using STAR. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). The GTF annotation files for UCSC mm9 was used for gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: Text file for FPKM values of each individual sample.

source_name: microglia from wild type control mice

growth_protocol: P301S mice (Tg(Prnp-MAPT*P301S)PS19)- 8months age; CK-p25 mice (Camk2a-tTA bred with tetO-CDK5R1/GFP) - 6 weeks p25 induced

extract_protocol:
FACS sorted (Neun antibody staining for neuron; CD11b+CD45 antibody staining for microglia); Total RNA extracted
According to the manufacturer instruction. Microglia- SMART-Seq v4 Ultra Low Input RNA Kit. Neuron- SMARTer Stranded Total RNA-Seq Kit - Pico Input

treatment_protocol: 22 days GENUS for P301S; 43 days GENUS for CK-p25 mice

value: Visual cortex

value: microglia

tag: rna fraction

value: Total RNA


title: RNA-Seq CD11b+CD45_CK-p25_NoStim4

description: SMART-Seq v4 Ultra Low Input RNA Kit

source_name: microglia from CK-p25 mice that did not under go any stimulation


title: RNA-Seq CD11b+CD45_CK-p25_GENUS2

description: SMART-Seq v4 Ultra Low Input RNA Kit

source_name: microglia from Ck-p25 mice that were stimulated with 40 Hz visual stimulation


title: RNA-Seq CD11b+CD45_CK2

description: SMART-Seq v4 Ultra Low Input RNA Kit


title: RNA-Seq CD11b+CD45_CK-p25_NoStim1

description: SMART-Seq v4 Ultra Low Input RNA Kit


title: RNA-Seq CD11b+CD45_CK-p25_GENUS1

description: SMART-Seq v4 Ultra Low Input RNA Kit


title: RNA-Seq CD11b+CD45_CK4

description: SMART-Seq v4 Ultra Low Input RNA Kit


title: RNA-Seq CD11b+CD45_CK-p25_GENUS3

description: SMART-Seq v4 Ultra Low Input RNA Kit


title: Cardiac macrophage population R1 from CAWS challenged donors, replicate 1


title: RNA-Seq CD11b+CD45_CK-p25_GENUS4

description: SMART-Seq v4 Ultra Low Input RNA Kit


title: Cardiac macrophage population R2 from CAWS challenged donors, replicate 2


title: RNA-Seq CD11b+CD45_CK1

description: SMART-Seq v4 Ultra Low Input RNA Kit


title: RNA-Seq NeuN nuclei_P301S_GENUS4

description: SMARTer Stranded Total RNA-Seq Kit - Pico Input

source_name: P301S +GENUS = P301S mice that was stimulated with 40 Hz visual stimulation

value: Neurons

value: Nuclear RNA


title: RNA-Seq NeuN nuclei_P301S_GENUS3


title: Cardiac macrophage population R1 from naïve donors, replicate 3


title: RNA-Seq NeuN nuclei_P301S_GENUS5


title: Cardiac macrophage population R1 from naïve donors, replicate 2


title: Cardiac macrophage population R2 from naïve donors, replicate 1


title: RNA-Seq CD11b+CD45_CK-p25_NoStim3

description: SMART-Seq v4 Ultra Low Input RNA Kit


title: Cardiac macrophage population R2 from naïve donors, replicate 2


title: RNA-Seq NeuN nuclei_P301S_NoStim5

source_name: P301S + No Stim = P301S mice that did not under go any stimulation


title: RNA-Seq NeuN nuclei_P301S_GENUS2


title: RNA-Seq CD11b+CD45_CK-p25_NoStim2

description: SMART-Seq v4 Ultra Low Input RNA Kit


title: RNA-Seq NeuN nuclei_P301S_NoStim4


title: RNA-Seq NeuN nuclei_P301S_NoStim3


title: Cardiac macrophage population R3 from naïve donors, replicate 3


title: RNA-Seq NeuN nuclei_P301S_NoStim2


title: RNA-Seq NeuN nuclei_P301S_NoStim1


title: RNA-Seq NeuN nuclei_WT6

source_name: wild type control mice


title: RNA-Seq NeuN nuclei_WT5


title: RNA-Seq NeuN nuclei_WT2


title: RNA-Seq NeuN nuclei_WT1


title: RNA-Seq NeuN nuclei_CK-p25_GENUS4

source_name: CK-p25 +GENUS = Ck-p25 mice that were stimulated with 40 Hz visual stimulation


title: RNA-Seq NeuN nuclei_CK-p25_GENUS2


title: RNA-Seq NeuN nuclei_CK-p25_GENUS3


title: RNA-Seq NeuN nuclei_CK-p25_NoStim5

source_name: CK-p25 + No Stim = CK-p25 mice that did not under go any stimulation


title: RNA-Seq NeuN nuclei_WT3


title: RNA-Seq NeuN nuclei_CK-p25_NoStim4


title: RNA-Seq NeuN nuclei_WT4


title: RNA-Seq NeuN nuclei_CK-p25_NoStim2


title: RNA-Seq NeuN nuclei_CK-p25_NoStim3


title: RNA-Seq NeuN nuclei_CK5

source_name: CK = wild type control mice


title: RNA-Seq NeuN nuclei_P301S_NoStim6


title: RNA-Seq NeuN nuclei_CK-p25_GENUS1


title: RNA-Seq NeuN nuclei_P301S_GENUS1


title: RNA-Seq NeuN nuclei_CK3


title: RNA-Seq NeuN nuclei_CK-p25_NoStim1


title: me1

city: Valencia

first: Joaquin

last: Panadero

state: Valencia

address: Avenida Fernando Abril Martorell, 106 Torre A

department: Genomics

institute: Instituto Investigación Sanitaria La Fe

data_processing:
Read trimming and filtering with Cutadapt version
Read alignment against GRCh38 ncRNAs (Ensembl) with Tophat2 version
Selection of those reads classified as miRNAs
Read count, normalization and differential expression with R Bioconductor
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are in CSV format containing the read counts and the differential expression results
Supplementary_files_format_and_content: S1: miRNA precursor raw counts
Supplementary_files_format_and_content: S2: miRNA mature raw counts
Supplementary_files_format_and_content: S7: miRNA precursor differential expression
Supplementary_files_format_and_content: S8: miRNA mature differential expression

source_name: osteosarcoma 143B cells (cybrids) containing 100% mutant (m.3243A>G) mtDNA

growth_protocol: Cybrids were cultured in high glucose Dulbecco’s modified Eagle medium (Gibco) containing 10% fetal bovine serum, 1 mM sodium pyruvate, 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM glutamine and 1mM non-essential amino acids.

extract_protocol: Total RNA from cybrid cells was isolated using Trizol reagent (Invitrogen) according to manufacturer's protocol

tag: genotype/variation

value: 100 percent mutant (m.3243A>G) mtDNA


title: RNA-Seq NeuN nuclei_CK4


title: me2


title: me3


title: RNA-Seq NeuN nuclei_CK1


title: wt2

source_name: osteosarcoma 143B cells (cybrids) containing the wild type counterpart

value: wild type


title: wt3


title: wt1


title: RNA-Seq NeuN nuclei_CK2


title: T3SD2, T3SD2XOC

city: Nanning

first: Sheng

last: Huang

state: Guangxi

address: 100 Daxue Road

department: College of Life Science and Technology

institute: Guangxi University

description:
T3SD2
T3SD2XOC

data_processing:
After removing reads containing the adapter, reads containing poly-N, and low-quality reads, clean reads were obtained. The Q20, Q30 and GC contents of the clean reads were calculated.
Paired-end clean reads from Xoc-rice mixed sample were aligned to the rice reference genome Oryza sativa Japonica Group (Assembly ID=22512) using TopHat v2.0.9.
Clean reads from Xoc-rice mixed sample that cann't aligned on rice genome were subsequently aligned to the Xoc reference genome Xoc BLS256 (Assembly ID=357911) using Bowtie v2.0.6
Paired-end clean from Xoc liquid culture sample that were aligned to the Xoc reference genome Xoc BLS256 (Assembly ID=357911) using Bowtie v2.0.6
Cuffdiff (v2.1.1) was used to calculate the FPKMs of the genes in each sample (Trapnell, C. et al. 2010).
Genome_build: Oryza sativa Japonica Group (Assembly ID=22512), Xanthomonas oryzae pv. oryzicola BLS256 (Assembly ID=357911)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa

source_name: rice leaves, in planta bacteria

growth_protocol: Rice (Oryza sativa L. cv. Nipponbare) seeds were germinated by submersion in water, followed by incubation in the dark for two days at 37°C. Five germinated seeds were planted in a small pot containing autoclaved soil. The plants were grown in the greenhouse under a 14/10-h light/dark cycle with a temperature controlled between 28°C and 30°C till the fourth leaf begins sprouting (about 14 days). Xoc strains were grown in rich medium named nutrient broth (NB) at 28°C (Yang and Bogdanove, 2013).

extract_protocol:
Infiltrated leaf part was collected 24 h after inoculation, snap frozen in liquid nitrogen, and stored at −80°C immediately. Bacteria cultures were collected by centrifugation and the medium discarded. Snap frozen the cell pellets in liquid nitrogen, then stored at −80°C immediately.
Before cDNA library preparation, ribosomal RNA was removed using the Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and the rRNA-free residue was cleaned by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations. Briefly fragmentation was performed using divalent cations under elevated temperatures in NEB Next First Strand Synthesis Reaction Buffer. First-strand cDNA was synthesized using random hexamer primers and the M-MuLV Reverse Transcriptase (RNaseH-). Second-strand cDNA synthesis was performed subsequently using DNA Polymerase I and RNase H. In the reaction buffer dNTPs, dTTP was replaced with dUTP. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activity. After adenylation of the DNA fragment 3’ ends, the NEBNext Adaptor with a hairpin loop structure was ligated to prepare for hybridization.   To preferentially select cDNA fragments 150-200 bp in length, the library fragments were purified with the AM Pure XP system (Beckman Coulter, Beverly, MA, USA). After that, 3 μL of the USER Enzyme (NEB, USA) was incubated with size-selected, adaptor-ligated cDNA at 37°C for 15 min, followed by incubation for 5 min at 95°C prior to the PCR. The PCR was performed with the Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.   Finally, the products were purified (AM Pure XP system), and the library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Before inoculated, Xoc strains were grown for 24 h at 28°C in NB medium, and the cells were collected by centrifugation and re-suspended in DI water. The concentration of the Xoc suspension was adjusted to O.D.600=0.5 (approximately 5.0 × 107 CFU/mL) prior to infiltration. Two-week-old rice seedlings were inoculated with the Xoc suspension using a syringe infiltration method (Zou et al., 2011). For each plant, the second and third leaves were picked, and 2/3 of the leaf surface was infiltrated. To prepare Xoc bacterial cultures for RNA-seq, Xoc strains were grown for 24 h at 28°C in NB medium, and the cells were collected by centrifugation and re-suspended in DI water. Xoc suspension was adjusted to Optical Density (O.D.)600=1 (approximately 1.0 × 108 CFU/mL), 100 μL of the Xoc suspension was added into 10 mL fresh NB medium and grown for 24 h at 28°C.

tag: agent

value: Xanthomonas oryzae pv. oryzicola

tag: infiltrated strain

value: GX01 type three-secretion system defective mutant

tag: cultivar

value: Nipponbare


title: WT2, WT2XOC

description:
WT2
WT2XOC

value: GX01 wild type


title: ymr111c/euc1∆_ExpA_Rep1

city: Martinsried/Munich

first: Markus

last: Höpfler

address: Am Klopferspitz 18

department: Molecular Cell Biology

country: Germany

institute: Max-Planck Institute of Biochemistry

hyb_protocol: 5 μg of labelled and fragmented aRNA was hybridised on a GeneChIP Yeast Genome 2.0 array (Affymetrix) using the GeneChip Hybridization Wash and Stain Kit (Affymetrix). Array washing and staining procedures were performed with a GeneChip Fluidics Station 450 using the GeneChip Hybridization Wash and Stain Kit (Affymetrix) according to the manufacturer's instructions.

scan_protocol: Scanning was performed with a GeneChip scanner 3000 (Affymetrix) according to the manufacturer's instructions

data_processing: For data analysis, R/Bioconductor was used (Gentleman et al, 2004). First, raw gene expression intensities were normalized by Robust Multiarray Analysis (RMA) (Irizarry et al, 2003) and the affyPLM and simpleaffy packages were used for quality control (Gentleman et al, 2004; Wilson & Miller, 2005). Limma and affy microarray packages (Gautier et al, 2004) were then used for low-level analysis and gene annotation was obtained from R/Bioconductor metadata packages and biomaRt repository (Durinck et al, 2005; 2009). For differential expression comparison between two strains a fixed linear model was fitted for individual features to estimate expression differences between the two sample groups. Standard errors of M-values were moderated by using an empirical Bayes approach. Finally, a moderated t-statistics, raw and adjusted p-values (Benjamini and Hochberg FDR control) were obtained for each feature.

organism: Saccharomyces cerevisiae

source_name: Total RNA from ymr111c/euc1∆ strain (Exp.A)

label_protocol: Biotin labelled antisense RNA (aRNA) was produced from 300 ng total yeast RNA using the GeneChip 3’ IVT Express Kit (Affymetrix) and fragmented according to the manufacturer’s instructions.

growth_protocol: Yeast cell precultures were grown over-night in YP+2% glucose medium and 1.5 OD600-units of main cultures were harvested in mid-log-phase (OD600 0.7-1). All cultures were grown under constant shaking at 30°C.

extract_protocol: Yeast total RNA was isolated form 1.5 OD600 units of yeast cells using the RNeasy Kit (Qiagen) following the manufacturer’s instruction, with beat-beating (MM301, Retsch GmbH) for cell lysis using zirconia/silica beads (BioSpec Inc.) and DNase I digest performed on-column.


title: testes_transgenic with active HSF1_15-day-old_rep2

city: Gliwice

first: Wiesława

middle: Elżbieta

last: Widłak

address: Wybrzeże Armii Krajowej 15

country: Poland

institute: Maria Sklodowska-Curie Institute – Oncology Center, Gliwice Branch

description: Gene expression data from juvenile transgenic testes, shortly after the transgene activation in spermatocytes, before apoptosis induction

hyb_protocol: Biotin-labeled cRNA probe samples were purified, fragmented and hybridized at 45°C overnight to the Affymetrix GeneChip® Mouse Genome 430A Array. The arrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The arrays were scanned using a microarray scanner, which is component of the Affymetrix GeneChip Instrument System

data_processing: The data was analyzed with R/Bioconductor and Matlab softwares, RMA algorithm with Dai annotation were used for data normalization.

source_name: testes from 15-day-old transgenic mouse expressing active HSF1 in spermatocytes

label_protocol: cDNA was synthesized from 8 μg of total RNA using the Superscript Choice System (Invitrogen) with an oligo-dT primer containing a T7 promoter sequence (Amersham Pharmacia Biotech) and then reverse-transcribed with a T7 RNA polymerase incorporating biotin-labeled nucleotides using the BioArray RNA Transcript Labeling Kit (Enzo Diagnostic).

growth_protocol: Transgenic mice were generated by DNA microinjection into the pronuclei of zygotes from FVB/N females by standard procedures. All animal experiments were approved by the Committee of Ethics and Animal Experimentation.

extract_protocol: Total RNA was isolated using RNeasy® Mini Kit spin columns (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Not applicable

value: FVB/N

tag: gender

value: male

tag: age

value: testes


title: ymr111c/euc1-K231R_ExpB_Rep2

source_name: Total RNA from ymr111c/euc1-K231R strain (Exp.B)

tag: strain


title: ymr111c/euc1∆_ExpA_Rep3


title: ymr111c/euc1-K231R_ExpB_Rep3


title: WT_ExpA_Rep3

source_name: Total RNA from wild-type strain (Exp.A)


title: ymr111c/euc1∆_ExpA_Rep2


title: WT_ExpB_Rep1

source_name: Total RNA from wild-type strain (Exp.B)


title: WT_ExpA_Rep1


title: testes_wild-type_15-day-old_rep4

description: Gene expression data from control, wild-type testes

source_name: testes from 15-day-old wild-type mouse


title: testes_transgenic with active HSF1_15-day-old_rep1


title: WT1, WT1XOC

description:
WT1
WT1XOC

value: Xanthomonas oryzae pv. Oryzicola


title: WT_ExpA_Rep2


title: WT_ExpB_Rep3


title: YMR111C/EUC1-OE_pGAL-EUC1_Exp2_Rep2

description:
M2
Cells were gronw in YP+raffinose to OD=0.5 and 2% galactose was added for 3h

data_processing:
Sequencing reads were aligned to the yeast transcriptome (ENSEMBL R64-1-1, annotation version 94) using STAR (v. 2.6.0a)
Read counts per gene were provided by STAR and TPM expression values were calculated with RSEM (v. 1.3.0)
Genome_build: ENSEMBL R64-1-1, annotation version 94
Supplementary_files_format_and_content: processed data (TPM-values) are provided as single matrix for all samples

source_name: Total RNA from pGAL-EUC1 strain (Exp.2)

growth_protocol: Cells ere grown in YP+glucose to mid-log-phase (Exp1) or YP-raffinose to OD=0.5 and 2% galactose was added for 3h (Exp2)

extract_protocol:
Yeast total RNA was isolated form 4 OD600 units of yeast cells using the RNeasy Kit (Qiagen) following the manufacturer’s instruction, with beat-beating for cell lysis and DNase I digest performed on-column.
polyA RNA was enriched (NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490), libraries were prepared for sequencing (NEBNext Ultra II RNA library prep Set for Illumina #E7770L) and barcoded (NEBNext Multiplex Oligo for Illumina #E7335L, #E7500L, #E7710L, #E7730L), all according to the manufacturer’s instructions.

treatment_protocol: Galactose induction (2%, 3h) for Exp2

tag: genotype

value: W303a RAD5 ymr111c::natNT2 YIplac211-pGAL-EUC1::URA3


title: Control_pEUC1-EUC1_Exp2_Rep2

description:
L2
Cells were gronw in YP+raffinose to OD=0.5 and 2% galactose was added for 3h

source_name: Total RNA from pEUC1-EUC1 control strain (Exp.2)

value: W303a RAD5 ymr111c::natNT2 YIplac211-pEUC1-EUC1::URA3


title: YMR111C/EUC1-OE_pGAL-EUC1_Exp2_Rep1

description:
M1
Cells were gronw in YP+raffinose to OD=0.5 and 2% galactose was added for 3h


title: Control_pEUC1-EUC1_Exp2_Rep3

description:
K3
Cells were gronw in YP+raffinose to OD=0.5 and 2% galactose was added for 3h


title: YMR111C/EUC1-OE_pGAL-EUC1_Exp2_Rep3

description:
L3
Cells were gronw in YP+raffinose to OD=0.5 and 2% galactose was added for 3h


title: testes_wild-type_15-day-old_rep3

tag: tissue


title: ymr111c/euc1-K231R_ExpB_Rep1


title: Control_pEUC1-EUC1_Exp2_Rep1

description:
L1
Cells were gronw in YP+raffinose to OD=0.5 and 2% galactose was added for 3h


title: ymr111c/euc1∆_Exp1_Rep3

description:
B3
Cells were grown in YP+glucose to mid-log phase

source_name: Total RNA from ymr111c/euc1∆ strain (Exp.1)


title: testes_wild-type_15-day-old_rep1


title: WT_ExpB_Rep2


title: ymr111c/euc1∆_Exp1_Rep1

description:
B1
Cells were grown in YP+glucose to mid-log phase


title: WT_Exp1_Rep2

description:
A2
Cells were grown in YP+glucose to mid-log phase

source_name: Total RNA from wild-type strain (Exp.1)

value: DF5a YIplac211-MED11::URA3


title: WT_Exp1_Rep1

description:
A1
Cells were grown in YP+glucose to mid-log phase


title: t2 BrdU_limit (90 min) (control input)

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

description: Illumina sequencing reads from control input sample

data_processing:
Illumina: sequencing reads were demultiplexed and the barcode sequences were trimmed using the FASTX toolkit
Illumina: Sequencing reads were mapped to the sacCer3 genome assembly using bowtie2
Illumina: Read tag counts were determined for the 5’ end of uniquely mapping reads without mismatches in 100 bp nonoverlapping regions
Illumina: The ratio between IP and Input sample was calculated for each bin, excluding bins that had less than 20% of the expected number of reads in the input sample
Illumina: Ratios were median-smoothed over 1 kb windows
Nanopore: Basecalling was perform with Albacore
Nanopore: Aligned reads to sacCer3 reference using minimap2
Nanopore: Detected BrdU in reads using D-NAscent
Nanopore: D-NAscent converts called BrdU sites to psl files
Nanopore: D-NAscent converts regions of called BrdU into bedgraphs
Genome_build: sacCer3
Supplementary_files_format_and_content: bed files show either BrdU-seq data or D-Nascent origin calls
Supplementary_files_format_and_content: bedgraphs show either BrdU calls or fork direction
Supplementary_files_format_and_content: psl files show hard call BrdU detectiondata

source_name: genomic DNA from cells released into media containing 40 ug/ml BrdU for 90 min in the presenc of nocodazole

extract_protocol:
Cells were harvested, spun down, washed in water,  and then resuspended in 500 µL of 1.2 M sorbitol, 200 mM Tris-HCl (pH7.5), 20 mM EDTA, 0.1% b-mercaptoethanol. Cells were spheroplasted with Zymolyase and then treated with SDS, Proteinase K and RNase A. DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to Illumina and ONT instructions.

tag: relevant genotype


title: t2 BrdU_limit (90 min)

description: Illumina sequencing reads from BrdU-IP sample and processed file with the IP/input ratios in 100 bp median-smoothed windows


title: WT_Exp1_Rep3

description:
A3
Cells were grown in YP+glucose to mid-log phase


title: 100% BrdU media

description: Illumina sequencing reads from BrdU-IP sample and processed file with the IP/input ratios in 5 kb median-smoothed windows

source_name: genomic DNA from cells grown in YPG media containing 100 uM of BrdU for 24 hours

value: MATa ADE2 cdc21::kanMX leu2::LEU2-GAL-hENT1 LYS2 RAD5 trp1::TRP1-GAL-dNK ura3-1


title: t4 HU (130 min) (control input)

source_name: genomic DNA from cells released synchronously into media containing 0.2 M HU and 40 ug/ml BrdU for 60 min, and then chased with 400 ug/ml thymidine for 70 min


title: hemi-labelled gDNA 100 min after release (control input)

source_name: genomic DNA from cells released into one round of S phase in media containing 400 ug/ml BrdU


title: hemi-labelled gDNA 100 min after release


title: t4 HU (130 min)


title: 100% BrdU media (control input)


title: 80% BrdU / 20% T media (control input)

source_name: genomic DNA from cells grown in  YPG media containing 100 uM of 80% BrdU and 20% thymidine for 24 hours


title: testes_wild-type_15-day-old_rep2


title: 60% BrdU / 40% T media (control input)

source_name: genomic DNA from cells grown in YPG media containing  100 uM of 60% BrdU and 40% thymidine for 24 hours


title: 80% BrdU / 20% T media


title: 60% BrdU / 40% T media


title: ymr111c/euc1∆_Exp1_Rep2

description:
B2
Cells were grown in YP+glucose to mid-log phase


title: WBJPE170996159

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
alignment was conducted with Tophat
The final gene expression data was normalized using Cuffnorm and represented as counts
Genome_build: mm9,hg19
Supplementary_files_format_and_content: Excel files include raw counts of each gene from each sample. Columns are sample name, rows are genes.

source_name: MUSC HA-2

extract_protocol:
Trizol for RNAextraction,  reverse transcription for 1st cDNA strand, second strand kit for double strand DNA synthesis.
3' end enrichment with Illumina Nextera XT

treatment_protocol: We collected tissues of heart, liver, spleen, kidney, skeletal muscle, peripheral blood mononuclear cells (PBMC) as well as tissue specific (stem) cells of skeletal muscle derived stem cells (MUSC), Human bone marrow derived stem cells (hBMSC), Human primary umbilical vein endothelial cell lines (HUVEC) for RNA-seq after treated with the two groups (PBS control and HA solution) for 24hours, respectively.

value: muscle stem cell

tag: ages

tag: treatment

value: HA


title: WBJPE170996160

source_name: MUSC HA-3


title: AD-3

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.

scan_protocol: Slides were scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using homemade scripts.

source_name: hippocampal tissue

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3′ bias via a random priming method (Arraystar Flash RNA Labelling Kit, Arraystar). The labelled cRNAs were purified using an RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labelled cRNAs (pmol Cy3/μg cRNA) were measured using the NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from each hippocampal tissue sample by soaking the tissue samples in TRIzol Reagent (Invitrogen, Grand Island, NY, USA) in accordance with the manufacturer’s instructions.

treatment_protocol: In this experiment, we utilized an intracerebroventricular (ICV) injection of Aβ1–42 oligomers into the cerebral ventricles of the animals to induce a validated AD model. For the control group, the vehicle was injected bilaterally into the lateral ventricles through a stainless steel cannula.

tag: group

value: Alzheimer's disease

value: Hippocampus

tag: strain/background

value: SD

value: Male


title: Control-1

value: Control


title: AD-2


title: WBJPE170996158

source_name: MUSC HA-1


title: Control-3


title: AD-1


title: WBJPE170996156

source_name: MUSC CTR-2

value: control


title: 40% BrdU / 60% T media

source_name: genomic DNA from cells grown in YPG media containing 100 uM of 40% BrdU and 60% thymidine for 24 hours


title: 40% BrdU / 60% T media (control input)


title: DS5_MEF

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
Libraries were sequenced using Illumina's Hiseq 2500 (100bp paired end sequencing)
Base calling was performed using the Illumina default pipeline
Sample demultiplexing was performed by the Advanced Sequencing Facility, The Francis Crick Institute
Reads were trimmed to remove adapter sequences using Trim Galore
Reads were mapped using Tophat (version 2.0.12) to the GRCm38 mouse assembly
Read counts for each gene were generated in htseq-count: transcripts from the same gene were collapsed into a single transcript containing all exons
Differences in the abundance of transcripts between KO and control samples were calculated in the R/Bioconductor program DESeq2 (version 1.6.3).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw and normalised read counts for each sample amd DESeq2 output

source_name: E14.5 mouse embryos

growth_protocol: DMEM, 10% FBS, penicillin/streptomycin, 50mM 2-mercaptoethanol

extract_protocol:
Trizol
TruSeq Stranded mRNA Sample Prep kit (Illumina)

treatment_protocol: MEFs were dissociated with trypsin during MEF generation and passaging

tag: cell type

value: Mouse embryonic fibroblasts


title: DS4_MEF


title: Thymidine media

description: Illumina sequencing reads from BrdU-IP sample

source_name: genomic DNA from cells grown in YPG media containing 100 uM thymidine


title: Thymidine media (control input)


title: WBJPE170996089

value: muscle


title: DS2_MEF


title: WBJPE170996087


title: Control-2


title: WBJPE170996088


title: WBJPE170996090


title: WBJPE170996157

source_name: MUSC CTR-3


title: DS3_MEF


title: testes_transgenic with active HSF1_15-day-old_rep3

description: Gene expression data from juvenile transgenic testes, shortly after the transgene activation in spermatocytes, before apoptosis induction

source_name: testes from 15-day-old transgenic mouse expressing active HSF1 in spermatocytes

value: FVB/N

value: male


title: LD_pos_4: Glia with high levels of LDs replicate 4

city: Ashburn

first: Zhe

last: Liu

state: Virginia

address: 19700 Helix Dr.

department: Janelia Farm Research Campus

institute: Howard Hughes Medical Institute

description: mRNA-seq

data_processing:
Reads Mapping: Bowtie 2
Differential Gene expression analysis: Cuffdiff
Significance Thresholding: R
Genome_build: rn6
Supplementary_files_format_and_content: Table containing differential gene expression information

source_name: hippocampal glia culture P0

growth_protocol: Astrocyte cultures were grown in Basal Eagle Media containing 10% fetal bovine serum, 0.45% glucose, 1 mM sodium pyruvate, 2 mM glutamax supplement and antibiotic-antimycotic and used at DIV 3-5

extract_protocol:
RNA was extracted using PicoPure RNA Isolation kit
cDNA was amplified using Ovation RNA-seq v2 kit and the Ovation Rapid DR Multiplexing kit was used to make the sequencing library

treatment_protocol: Nile red staining

value: hippocampal glia

tag: developmental stage


title: WBJPE170996083


title: WBJPE170996070

value: spleen


title: WT4_MEF

value: Wild-type


title: DS1_MEF


title: LD_pos_3: Glia with high levels of LDs replicate 3

description: mRNA-seq


title: LD_pos_2: Glia with high levels of LDs replicate 2

description: mRNA-seq


title: WBJPE170996068


title: WT2_MEF


title: LD_pos_1: Glia with high levels of LDs replicate 1

description: mRNA-seq


title: Carpel_vernalized_rep2

city: Jeonju-si

first: Soo In

last: Lee

state: Jeollabuk-do

address: Nongsaengmyeong-ro, Wansan-gu

department: Agricultural Biotechnology

country: South Korea

institute: National Institute of Agricultural Sciences (NAS)

description: This sample is of carpel tissues collected from vernalised (7 weeks) B.rapa plants maintained at greenhouse after vernalization. It is the second of two biological replicates used in this study

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Brassica rapa

source_name: Carpel_Brassica rapa

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Chinese cabbage (B. rapa ssp. pekinensis, inbred line ‘Chiifu’) plants were grown at greenhouse conditions (22/18 °C, 16/8 h light/dark) for 4 weeks. For vernalization, plants were transferred to 4 °C cold chamber for 7 weeks and then transferred to the greenhouse for flowering. Microarray analysis, tissues were collected from the vernalized small (< 2 mm) early floral buds (FB2), large (2-4 mm) early floral buds (FB4), stamens (ST), carpels (CP), and non-vernalized leaves (4-weeks old) as control (CON).

extract_protocol: The total RNA was extracted using RNeasy plant mini kit (Qiagen) according to manufacturer’s instruction and the quantity and quality were examined with a spectrophotometer

tag: tissue types

value: Carpel

tag: morphology

value: Normal

value: vernalized


title: WBJPE170996067


title: LD_neg_4: Glia with low levels of LDs replicate 4

description: mRNA-seq


title: WT3_MEF


title: Carpel_vernalized_rep1

description: This sample is of carpel tissues collected from vernalised (7 weeks) B.rapa plants maintained at greenhouse after vernalization. It is the first of two biological replicates used in this study

treatment_protocol: For vernalization, plants were transferred to 4 °C cold chamber for 7 weeks and then transferred to the greenhouse for flowering

value: B. rapa ssp. pekinensis, inbred line ‘Chiifu’


title: LD_neg_3: Glia with low levels of LDs replicate 3

description: mRNA-seq


title: WBJPE170996155

source_name: MUSC CTR-1

value: muscle stem cell


title: WBJPE170996066


title: Stamen_Vernalised_rep1

description: This sample is of stamen tissues collected from vernalised (7 weeks) B.rapa plants maintained at greenhouse after vernalization. It is the first of two biological replicates used in this study

source_name: Stamen_Brassica rapa

value: Stamen


title: WT1_MEF


title: WBJPE170996065


title: eds1_Pathogen_rep3

city: Cologne

first: Takaki

last: Maekawa

address: Carl-von-Linne Weg 10

institute: Max-Planck Institute for Plant Breeding Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
The sequence of Illumina adapters were trimmed using BBMap_37.28.
Sequenced reads were mapped to the genome of Arabidopsis thaliana (TAIR10) using the tool 'RNA-Seq Analysis' in CLC Genomics Workbench (10.1.2)  with the default setting.
TPM (Transcripts Per Kilobase Million) per gene per sample were obtained using the tool 'RNA-Seq Analysis' in CLC Genomics Workbench (10.1.2) with the default setting.
Genome_build: TAIR10 (Arabidopsis)
Supplementary_files_format_and_content: tab-delimited text file including TPM (Transcripts Per Kilobase Million) per gene per sample

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: The plants were initially grown on MS-agar plates for 2 weeks under sterile conditions and subsequently transferred to Jiffy pots supplemented with a fertilizer, Wuxal TopN (Aglukon Spezialdünger), and grown for an additional 2-3 weeks under short day conditions. Similar-seized 4-5 week-old plants were used for the analysis.

extract_protocol:
RNA extraction was performed using the RNeasy Plant Mini Kit (Qiagen) according to the manufacurer's instruction, including an on-column DNA digestion.
RNA-seq libraries were prepared from polyA-enriched RNA by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq RNA sample preparation v2 guide (Illumina).

treatment_protocol: Plants were challenged with conidia of Golovinomyces orontii using a settling tower. Pathogen-challenged plants and plants without conidia inoculations (mock) were placed in the same phytochamber until sample collection.

tag: line

tag: library

value: Pathogen


title: eds1_Pathogen_rep2


title: Flowerbuds (≤ 2mm)_Vernalized_rep2

description: This sample is of early small floral buds (≤ 2mm) collected from vernalised (7 weeks) B.rapa plants maintained at greenhouse after vernalization. It is the second of two biological replicates used in this study

source_name: Flowerbuds (≤ 2mm)_Brassica rapa

value: Flower buds

value: early small flower buds (≤ 2mm)


title: WBJPE170996069

value: HA


title: LD_neg_1: Glia with low levels of LDs replicate 1

description: mRNA-seq


title: WBJPE170996061

value: pbmc


title: Flowerbuds (≤ 4mm)_Vernalized_rep2

description: This sample is of early large floral buds (≤ 4mm) collected from vernalised (7 weeks) B.rapa plants maintained at greenhouse after vernalization. It is the second of two biological replicates used in this study

source_name: Flowerbuds (≤ 4mm)_Brassica rapa

value: early large flower buds (≤ 4mm)


title: Flowerbuds (≤ 4mm)_Vernalized_rep1

description: This sample is of early large floral buds (≤ 4mm) collected from vernalised (7 weeks) B.rapa plants maintained at greenhouse after vernalization. It is the first of two biological replicates used in this study


title: LD_neg_2: Glia with low levels of LDs replicate 2

description: mRNA-seq


title: eds1_Pathogen_rep1


title: WBJPE170996060


title: WBJPE170996059


title: Atmlkl123_Pathogen_rep3


title: Flowerbuds (≤ 2mm)_Vernalized_rep1

description: This sample is of early small floral buds (≤ 2mm) collected from vernalised (7 weeks) B.rapa plants maintained at greenhouse after vernalization. It is the first of two biological replicates used in this study


title: Stamen_Vernalised_rep2

description: This sample is of stamen tissues collected from vernalised (7 weeks) B.rapa plants maintained at greenhouse after vernalization. It is the second of two biological replicates used in this study


title: Atmlkl123_Pathogen_rep2


title: M4

city: New York

first: Charles

last: Murphy

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
genes-fpkm.csv
HTSeq.gene.counts.csv

data_processing:
The quality of the raw FASTQ files were checked with FastQC. Raw FASTQ reads were mapped to mouse reference GRCm38 using STAR two-pass alignment (v2.4.1d; --outFilterMismatchNmax 5), estimated gene expression using cufflinks (v2.2.1, default parameters), and quantified per-gene counts using HTseq (v0.6.0, default parameters).
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-delimited file containing FPKM values for each sample. Comma-delimited file containing per-gene counts for each sample.

source_name: Control, untreated, small intestines

extract_protocol:
RNA was extracted using TRIzol according to the manufacturers instructions and contaminating DNA was removed by DNase treatment for 10 mins and column purification (Qiagen RNAeasy). cDNA was prepared from 1 µg total RNA using qScript reverse transcription kit (Quantabio, #95047).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: APC mutant

value: Small intestines


title: M3

description:
genes-fpkm.csv
HTSeq.gene.counts.csv


title: T3SD1, T3SD1XOC

description:
T3SD1
T3SD1XOC

source_name: rice leaves, in planta bacteria

tag: agent

value: Xanthomonas oryzae pv. oryzicola

tag: infiltrated strain

value: GX01 type three-secretion system defective mutant

tag: cultivar

value: Nipponbare


title: WBJPE170996058

tag: strain

value: control


title: DS4

description:
Dp1_4
ANY751A32_S21_L006

data_processing:
Libraries were sequenced using Illumina's Hiseq 4000 (75 bases paired end sequencing)
Base calling was performed using the Illumina default pipeline
Sample demultiplexing was performed by the Advanced Sequencing Facility, The Francis Crick Institute
Reads were trimmed to remove adapter sequences using Trim Galore
Reads were mapped using Tophat (version 2.0.12) to the GRCm38 mouse assembly including ERCC spike in sequences
Read counts for each gene were generated in htseq-count: transcripts from the same gene were collapsed into a single transcript containing all exons
Count data was normalised against ERCC spike ins using R?Bioconductor package RUVSeq (version 1.0.0). Differences in the abundance of transcripts between DS and control samples were calculated in the R/Bioconductor program DESeq2 (version 1.6.3).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw and normalised read counts for each sample

source_name: Dp1Tyb_E14.5 mouse embryos

tag: strain background

tag: genotype/variation

value: Mouse embryonic fibroblasts


title: Leaves_Non-vernalized_rep3

description: This sample is of of 6 weeks old non-vernalised leaves collected from B.rapa grown at greenhouse conditions. It is the third of three biological replicates used in this study

source_name: Leaves_Brassica rapa

value: Leaves

value: 4 weeks old leaves

value: non-vernalized


title: Atmlkl123_Pathogen_rep1


title: WBJPE170996054

tag: tissue


title: M2

description:
genes-fpkm.csv
HTSeq.gene.counts.csv

tag: genotype


title: TMCC2_guide2_Rep1_RNA

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Gene quantifications for Gencode v19 were summarized using the --quantMode GeneCounts parameter in STAR.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression counts for hg19 / Gencode v19 annotations

growth_protocol: HUDEP-2 cells were cultured in StemSpan SFEM supplemented with hSCF (50 ng/ml), erythropoietin (3 IU/ml), dexamethasone (10-6 M) and doxycycline (1 μg/ml), lentivirally infected and then differetiated in erythroid differentiation media (IMDM, 2% human AB plasma, 3% human AB serum, 1 mg/mL Holo-human transferrin, 3 IU/mL heparin,10 μg/mL insulin and 3 IU/mL erythropoietin) for 72 h followed by RNA extraction and RNA-seq

extract_protocol:
Qiagen RCL lysis buffer supplemented with beta-mercaptoethanol
Smart-seq2; Nextera-based indexing

treatment_protocol: CRISPRi nontargeting vs. guide RNAs targeting a TMCC2 enhancer

tag: cell line

tag: grna treatment

value: CCATCCTTCAGAGTAAACAG

tag: grna annotation

value: TMCC2 enhancer - gRNA 2


title: M1

description:
genes-fpkm.csv
HTSeq.gene.counts.csv

tag: treatment


title: Leaves_Non-vernalized_rep1

description: This sample is of of 4 weeks old non-vernalised leaves collected from B.rapa grown at greenhouse conditions. It is the first of three biological replicates used in this study

value: B. rapa ssp. pekinensis, inbred line ‘Chiifu’


title: DS3

description:
Dp1_3
ANY751A31_S20_L006

tag: developmental stage

tag: cell type


title: Atmlkl23_Pathogen_rep3

value: Pathogen


title: C4

description:
genes-fpkm.csv
HTSeq.gene.counts.csv

source_name: Control, untreated tumor

value: Tumor


title: WBJPE170996049

value: bone

tag: ages

value: HA


title: DS1

description:
Dp1_1
ANY751A29_S18_L006


title: Leaves_Non-vernalized_rep2

description: This sample is of of 5 weeks old non-vernalised leaves collected from B.rapa grown at greenhouse conditions. It is the second  of three biological replicates used in this study

tag: tissue types

tag: morphology


title: Atmlkl23_Pathogen_rep2

tag: line

tag: library


title: WBJPE170996048


title: WBJPE170996047


title: Atmlkl23_Pathogen_rep1


title: DS2

description:
Dp1_2
ANY751A30_S19_L006


title: C3

description:
genes-fpkm.csv
HTSeq.gene.counts.csv

value: APC mutant


title: WT_Pathogen_rep3


title: C2

description:
genes-fpkm.csv
HTSeq.gene.counts.csv


title: C1

description:
genes-fpkm.csv
HTSeq.gene.counts.csv


title: WT3

description:
Dp1_WT_3
ANY751A27_S16_L006

source_name: WT_E14.5 mouse embryos

value: Wild-type


title: WBJPE170996045


title: WBJPE170996046


title: WT2

description:
Dp1_WT_2
ANY751A26_S15_L006


title: WT1

description:
Dp1_WT_1
ANY751A25_S14_L006


title: WBJPE170996036

value: liver


title: WT_Pathogen_rep2


title: Col-0_Pathogen_rep3


title: WBJPE170996035


title: WT5_hippocampus

data_processing:
Libraries were sequenced using Illumina's Hiseq 4000 (75p paired end sequencing)
Basecalling was performed using the Illumina default pipeline
Sample demultiplexing was performed by the Advanced Sequencing Facility, The Francis Crick Institute
Reads were trimmed to remove adapter sequences using Trim Galore
Reads were mapped using Tophat (version 2.0.12) to the GRCm38 mouse assembly
Read counts for each gene were generated in htseq-count: transcripts from the same gene were collapsed into a single transcript containing all exons
Differences in the abundance of transcripts between KO and control samples were calculated in the R/Bioconductor program DESeq2 (version 1.6.3).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw and normalised read counts for each sample and DESeq2 output

source_name: Adult mouse aged 18 weeks

extract_protocol:
Qiagen miRNeasy kit
TruSeq Stranded mRNA Sample Prep kit (Illumina)

value: Total hippocampus

tag: age

value: 18 weeks


title: Col-0_Pathogen_rep2


title: WT4

description:
Dp1_WT_4
ANY751A28_S17_L006


title: WT4_hippocampus

tag: strain


title: WBJPE170996033

value: control


title: Dp1Tyb5_hippocampus


title: WBJPE170996034


title: eds1_Mock_rep3

value: Mock


title: Dp1Tyb4_hippocampus


title: WBJPE170996031


title: Col-0_Pathogen_rep1


title: CNOT6L KO hepatocytes for IP, biological rep3

city: San Antonio

first: Masahiro

last: Morita

state: Texas

address: 4939 Charles Katz Drive

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

description: Immunoprecipitated RNA data from CNOT6L KO primary hepatocytes

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16hr at 45C on Gene Chip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: For analysis of microarray data, we extracted and normalized data using robust multi-array averaging implemented in the R package “affy” (www.r-project.org). We used updated probe set definitions because these provide improved precision and accuracy (Sandberg and Larsson, 2007). To identify immunoprecipitated mRNAs, we used analysis of partial variance (APV) and applied the random variance model (RVM) as implemented in the anota R package (Larsson et al., 2010, 2011). In anota we applied the following settings (as defined in the anotaPlotSigGenes function) for gene selection: slopeP=0.01; maxSlope=2; minSlope=(-2); selDeltaP=0.5; selDeltaPT=0.5 and maxRvmP=0.01. This identified genes showing enrichment in immunoprecipitated mRNA from WT cells independent of steady-state mRNA level. The resulting genes were further filtered to identify those enriched in immunoprecipitated mRNA from WT cells (i.e. removed those that were depleted).

label: Biotin

source_name: Immunoprecipitated RNA of primary hepatocytes from CNOT6L KO mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Primary hepatocytes were isolated from 8-week-old wild-type and Cnot6l KO mice.

extract_protocol: RNA were extracted with Trizol Reagent and GlycoBlue Coprecipitant (Invitrogen) and purified with an RNeasy Kit (Qiagen) according to the manufacturer’s instructions. The quality of RNA was determined using the Bioanalyzer nano chip (Agilent Technologies, Inc.).

tag: gender

value: Male

value: CNOT6L KO

value: Isolated primary hepatocytes


title: eds1_Mock_rep2


title: WBJPE170996030

value: kidney


title: WT3_hippocampus


title: Dp1Tyb3_hippocampus


title: Atmlkl123_Mock_rep3


title: CNOT6L KO hepatocytes for IP, biological rep1


title: WBJPE170996029


title: Dp1Tyb2_hippocampus


title: CNOT6L KO hepatocytes for Input, biological rep3

description: Gene expression data from CNOT6L KO primary hepatocytes

source_name: Total RNA of primary hepatocytes from CNOT6L KO mice


title: CNOT6L KO hepatocytes for IP, biological rep2


title: CNOT6L KO hepatocytes for Input, biological rep1


title: WT_Pathogen_rep1


title: CNOT6L WT hepatocytes for IP, biological rep3

description: Immunoprecipitated RNA data from wild-type primary hepatocytes

source_name: Immunoprecipitated RNA of primary hepatocytes from CNOT6L WT mice


title: WT2_hippocampus


title: WBJPE170996027


title: CNOT6L WT hepatocytes for IP, biological rep2


title: Atmlkl23_Mock_rep3


title: WBJPE170996026


title: WT1_hippocampus


title: WBJPE170996025


title: Atmlkl123_Mock_rep2


title: CNOT6L WT hepatocytes for IP, biological rep1


title: eds1_Mock_rep1


title: Atmlkl123_Mock_rep1


title: Atmlkl23_Mock_rep1


title: WBJPE170996028


title: Dp1Tyb1_hippocampus


title: CNOT6L WT hepatocytes for Input, biological rep3

description: Gene expression data from wild-type primary hepatocytes

source_name: Total RNA of primary hepatocytes from CNOT6L WT mice


title: WT_Mock_rep3


title: WBJPE170996021

value: heart


title: Atmlkl23_Mock_rep2


title: WT_Mock_rep2


title: WBJPE170996032


title: CNOT6L KO hepatocytes for Input, biological rep2


title: WBJPE170996020


title: WBJPE170996019


title: WT_Mock_rep1


title: Col-0_Mock_rep3


title: WBJPE170996017


title: Col-0_Mock_rep1


title: WBJPE170996013


title: DM-2

city: Guangzhou

first: chen

last: genghua

address: WuShan

institute: South China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to gga5 whole genome using HISAT with default parameters.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using HTSeq.
Genome_build: gga5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Gallus gallus

source_name: chicken embryo myoblast

growth_protocol: chicken primary myoblasts were growed in growth medium containing RPMI-1640, 15% FBS and 2% pen/srep

extract_protocol:
Total RNA of the proliferating myoblasts or differentiated myotubes were harvested using Trizol reagent according to the manufacturer’s direction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: chicken primary myoblasts were induced to differentiation by culturing in differentiation medium (RPMI-1640, 2% horse serum and 2% pen/strep)

value: chicken embryo skeletal muscle derived myotubes

value: differentiated myotube

tag: passages


title: DM-3


title: DM-1


title: Col-0_Mock_rep2


title: SH-SY5Y cells_CSBmut rep2

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

data_processing:
FastQC was conducted for Quality control (QC) of RNA-seq reads
Trimming was performed by seqtk for known Illumina TruSeq adapter sequences, poor reads, and ribosomal RNA reads
Trimmed reads were mapped to the Homo Sapiens reference genome by the Hisat 2(version:2.0.4)
String Tie(version:1.3.0) was performed for each gene count from trimmed reads
Gene counts were normalized by trimmed mean of M-values, and fragments per kilobase of transcript per million mapped reads (FPKM) in Perl script
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CSBmut, neuroblastoma cell line

growth_protocol: neuroblastoma cells were transduced with lentivirus expressing shRNAs targeting CSA, CSB or control, selected in complete DMEM/F12 containing puromycin and cultured for 2-3 weeks

extract_protocol:
Culture medium was removed and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: neuroblastoma cells

value: CSBmut


title: SH-SY5Y cells_CSAmut rep2

source_name: CSAmut, neuroblastoma cell line

value: CSAmut


title: SH-SY5Y cells_CSBmut rep1


title: GM-3

value: chicken embryo skeletal muscle derived myoblasts

value: proliferating myoblast


title: CNOT6L WT hepatocytes for Input, biological rep1

value: Wild-type

tag: tissue


title: SH-SY5Y cells_CSAmut rep1

tag: genotype


title: WBJPE170996018


title: CNOT6L WT hepatocytes for Input, biological rep2


title: SH-SY5Y cells_WT rep2

source_name: WT, neuroblastoma cell line

tag: cell line

value: WT


title: S19 CD8.12wk.ctrl

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: Illumina whole-genome gene expression direct hybridization assay protocol.

scan_protocol: Illumina BeadArray Reader scanning protocol.

data_processing: The data were background corrected normalised using negative control probes and quantile normalized using negative and positive control probes with neqc in R.

label_protocol: cDNA was labeled with biotin following the Encore Biotin IL labeling protocol.

extract_protocol: Total RNAs from T-cells were extracted using Trizol.

tag: genotype/variation

value: ctrl, NOD-Lox

value: CD8+ T-cells


title: GM-2


title: GM-1


title: S15 Treg.12wk.ctrl

source_name: Treg

value: Treg


title: S21 CD8.12wk.ctrl


title: S16 Treg.12wk.MIP

value: MIP, NOD-LIRKO


title: S13 Treg.12wk.ctrl


title: S18 Treg.12wk.MIP


title: SH-SY5Y cells_WT rep1