title: HD_siRNA_LGF_s2_rep2

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Trimmed adapter sequences and low quality reads using the Trimmomatic and FASTQ Groomer tools. The filtered reads were then mapped to the human reference genome hg38 (UCSC 2013 release) by using Bowtie2
Duplicate and unmapped reads were removed using SAM Tools
Abundance was measured using featurecounts tool.
Genome_build: hg38 (UCSC 2013 release)
Supplementary_files_format_and_content: tab-delimited text files with count values for each Sample

growth_protocol: Complete neurobasal proliferation medium (HGF files)

extract_protocol:
Total RNA was isolated and purified using the RNeasy Mini kit (Qiagen, 74104) and DNase treated using the DNA-freeTM-DNA removal Kit (Life Technologies, AM1906)
Libraries were prepared by FASTERIS SA (Switzerland) using standard protocols from Illumina and sequenced with the Illumina HiSeq Genome Analyzer

treatment_protocol: FOXO3 was induced in the nucleus by removing bFGF and Leukemia Inhibitory Factor from the culture media for 4 h and treating cells with 20 μM LY294002 for 1 h 30 min (LGF files). Reducing Ryk expression was performed by treating cells with a Ryk siRNA (siRNA) or scrambled RNA (SCR).

value: Ryk siRNA

tag: phenotype

value: Huntington's disease

value: Neural stem cells


title: C116_NTCGF_T_3

status: Public on Jan 30 2021

type: SRA

city: Paris

first: Christian

last: Neri

address: 9 quai St Bernard

department: CNRS UMR 8256, Inserm ERL U1164

country: France

institute: Sorbonne Université, CNRS, INSERM

library_source: transcriptomic

data_processing:
NextSeq Control Software 2.2.0.4 , RTA 2.4.11, bcl2fastq2.17 v2.17.1.14
The raw sequencing reads corresponding to FOXO3 knockdown were pre-processed in order to perform quality control of the reads using fastqc and discard adapter sequences using Clip adapter (Galaxy Version 2.2.0). The reads were then mapped to the human reference genome hg38 (UCSC 2013 release) by using HISAT2. Read distributions were calculated using the featureCounts tool. Sample technical replicates were merged.
Genome_build: hg38 (UCSC 2013 release)
Supplementary_files_format_and_content: tab-delimited text files with count values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Neural stem cells

growth_protocol: Complete neurobasal proliferation medium

extract_protocol:
Total RNA was isolated and purified using the NucleoSpin RNA kit (Macherey-Nagel, 740955.50)
Libraries were prepared by FASTERIS SA (Switzerland) using TruSeq stranded mrna protocols from Illumina and sequenced with the NextSeq Genome Analyzer

treatment_protocol: Reducing FOXO3 expression was performed by treating cells with a FOXO3 siRNAs (ON-target plus smart pool) (siF3) or non-targeting control pool (NTC). 48 h after transfection, complete medium was replaced with medium without bFGF and LIF for 6 h (-GF).

tag: cell type

value: IPS cells differentiated into neural stem cells

tag: passage number

tag: genotype

value: wild type 21Q/19Q

tag: sirna

value: scrambled RNA


title: C116_siFOXO3GF_T_3

value: FOXO3 siRNA


title: HD_siRNA_HGF_s2_rep2

tag: treatment

tag: tissue


title: HD_NTC_T_3


title: HD_siFOXO3_T_3


title: HD_SCR_HGF_s2_rep2


title: C116_siRNA_HGF_s2_rep2

value: control


title: C116_SCR_LGF_s2_rep2


title: CBMC_NOSTIM2

city: Boston

first: Daniel

last: Dwyer

state: MA

address: 60 Fenwood Road

country: USA

institute: Brigham and Women's Hospital

data_processing:
Data for each lane was separated by barcode and concatinated. Transcripts were alligned to GRCh38 (hg38) genome assembly with STAR (Dobin et al 2013) with the following parameter settings: --outSAMstrandField intronMotif --outSJfilterReads Unique --outSJfilterCountUniqueMin 100 1 1 1 --limitSjdbInsertNsj 10000000 --chimSegmentMin 10. Transcripts were quantified with HTseq (Anders et al, 2014).
Data analysis was conducted using Bioconductor for R. Count normalization and differential was conducted using the DESeq2 software package (Love et al., 2014).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw count matrix

source_name: Umbilical cord blood-derived mast cells

growth_protocol: CBMC cultures were maintained in SCF (100 ng/mL), IL-6 (50 ng/mL) and IL-10 (10 ng/mL) until reaching 95% purity based on staining with touidine blue

extract_protocol:
Samples were lysed in TCL buffer (Qiagen)
SmartSeq2 libraries were prepared according to the SmartSeq2 protocol described by Trombetta et al, 2014. Briefly, total RNA was purified using RNA-SPRI beads. cDNA was generated from full-length mRNA transcripts using reverse transcriptase with terminal transferase activity. Combined with a second "template switch" primer, the cDNA was constructed to have two universal priming sequences. Following preamplification, the Nextera XT library construction kit was used to prepare 96 unique indexes specific to each sample. Barcoded cDNA fragments were then pooled prior to sequencing. Sequencing was carried out using an Illumina NextSeq500 as paired- end 2x38bp to a coverage of approximately ~4 million reads per well.

treatment_protocol: Samples were stimulated for 96h with the indicated treatments.

value: Umbilical cord blood-derived mast cells

tag: age

value: 7-9 weeks

value: Saline


title: HD_NTCGF_T_2


title: C116_siFOXO3_T_3


title: HD_siFOXO3GF_T_2


title: C116_SCR_HGF_s2_rep2


title: C116_siFOXO3GF_T_2


title: C116_NTC_T_3


title: HD_siRNA_LGF_s1_rep2


title: HD_SCR_LGF_s1_rep2


title: HD_siFOXO3_T_2


title: C116_siFOXO3_T_2


title: HD_SCR_LGF_s2_rep2


title: HD_SCR_HGF_s1_rep2


title: SKOV3-siNC-1

city: Sungnam-Si

first: Su-Yeon

last: Lee

address: Pangyo-Ro 335

department: Department of Biomedical Science

country: South Korea

institute: CHA University

data_processing:
Quality control of the raw sequencing data was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapter and low-quality reads (<Q20) were removed using FASTX_Trimmer (http://hannonlab.cshl.edu/fastx_toolkit/) and BBMap (https://sourceforge.net/projects/bbmap/).
The n trimmed reads were mapped to the reference genome using TopHat.
Gene expression levels were estimated based on RC (Read Count) and FPKM (fragments per kb per million reads) values calculated using BEDTools and Cufflinks.
The expression values were normalized based on the quantile normalization method using edgeR within R (https://www.r-project.org/).
Genome_build: Hg19

growth_protocol: SKOV3 were maintained in RPMI 1640 containing 10% FBS, 25 mM HEPES and 25 mM NaHCO3. A2780 were maintained in RPMI 1640 containing 10% FBS.

extract_protocol:
Total RNA was harvested using Trizol reagent. The SMARTer Stranded RNA Seq Kit (Clontech Laboratories, Inc., USA) was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA was treated for 48 hours

value: Human ovarian cancer cell line

value: Negative control siRNA transfection


title: C116_siRNA_LGF_s2_rep2


title: C116_siRNA_LGF_s1_rep2


title: C116_NTCGF_T_2


title: HD_NTC_T_2


title: HD_siRNA_HGF_s1_rep2


title: C116_SCR_LGF_s1_rep2


title: HD_siFOXO3GF_T_1


title: C116_siRNA_HGF_s1_rep2


title: HD_NTCGF_T_1


title: C116_siFOXO3GF_T_1


title: HD_siRNA_LGF_s2_rep1


title: HD_siRNA_HGF_s2_rep1


title: HD_SCR_LGF_s2_rep1


title: C116_SCR_HGF_s1_rep2


title: HD_SCR_HGF_s2_rep1


title: HD_siFOXO3_T_1


title: C116_siFOXO3_T_1


title: C116_NTCGF_T_1


title: C116_siRNA_LGF_s2_rep1


title: C116_siRNA_HGF_s2_rep1


title: HD_siFOXO3GF_3


title: HD_NTC_T_1


title: C116_NTC_T_1


title: C116_SCR_HGF_s2_rep1


title: HD_NTCGF_3


title: C116_siFOXO3GF_3


title: C116_SCR_LGF_s2_rep1


title: C116_NTC_T_2


title: HD_siRNA_LGF_s1_rep1


title: C116_NTCGF_3


title: HD_siFOXO3_3


title: HD_SCR_HGF_s1_rep1


title: HD_siRNA_HGF_s1_rep1


title: C116_siRNA_LGF_s1_rep1


title: HD_SCR_LGF_s1_rep1


title: C116_siFOXO3_3


title: C116_NTC_3


title: HD_NTCGF_2


title: HD_siFOXO3GF_2


title: C116_SCR_HGF_s1_rep1


title: C116_siFOXO3GF_2


title: C116_SCR_LGF_s1_rep1


title: HD_HGF_FOXO_SCR_rep1

library_source: genomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Trimmed adapter sequences and low quality reads using the Trimmomatic and FASTQ Groomer tools. The filtered reads were then mapped to the human reference genome hg38 (UCSC 2013 release) by using Bowtie2
Duplicate and unmapped reads were removed using SAM Tools. Background signals corresponding to whole cell extracts were removed first, then the background signals corresponding to immunoprecipitation using mock antibody were removed, followed by removing the background signals corresponding to no induction of FOXO3 in the nucleus.
Peaks were called using MACS2 (bdgpeakcall)
Genome_build: hg38 (UCSC 2013 release)
Supplementary_files_format_and_content: 4 processed tab-delimited files with scores

molecule: genomic DNA

extract_protocol:
Chromatin was immunoprecipitated using a NFL FOXO3 antibody (FOXO files) or mock antibody (IgG files). Whole cell extract files are labelled as WCE for each condition.
Libraries were prepared by FASTERIS SA (Switzerland) using standard protocols from Illumina and sequenced with the Illumina HiSeq Genome Analyzer

tag: chip antibody

value: ChIP-grade anti-FOXO3 antibody “NFL"


title: HD_siFOXO3_2


title: C116_siRNA_HGF_s1_rep1


title: C116_LGF_IgG_si_rep1


title: HD_LGF_IgG_si_rep1


title: HD_NTC_2


title: C116_HGF_FOXO_SCR_rep1


title: HD_LGF_FOXO_SCR_rep2


title: C116_siFOXO3_2


title: C116_NTC_2


title: WCE_HD_LGF_IgG_si_rep2


title: WCE_HD_HGF_FOXO_SCR_rep2


title: HD_NTC_3


title: WCE_C116_LGF_IgG_si_rep2


title: HD_NTCGF_1


title: C116_NTCGF_2


title: WCE_C116_HGF_FOXO_SCR_rep2


title: C116_siFOXO3GF_1


title: HD_siFOXO3_1


title: HD_LGF_IgG_si_rep2


title: C116_LGF_IgG_si_rep2


title: HD_NTC_1


title: C116_HGF_FOXO_SCR_rep2


title: NL-1_Rep5

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

country: Germany

institute: University of Wuerzburg

data_processing:
The generated raw reads were processed using FastQC 0.11.6 for assessing read quality, amount of duplicates and presence of adapter sequences.
After this, the Illumina TruSeq adaptors were cleaved using cutadapt (version 1.16) and resulting reads were further trimmed keeping a quality drop value below a mean of Q20.
Further, the processed sequences were mapped to the human genome using the short read aligner STAR (version-2.5.2b) with genome and annotation files retrieved from GENCODE (GRCh38, V25). For all the studied samples, the proportion of reads mapped to the human reference genome ranged between 83% and 86% in total.
The sequences aligning to specific genes were quantified using bedtools subcommand intersect (version 2.15.0).
Next, the differentially expressed genes were identified using DESeq2 (version 1.16.1). Only the genes having a Benjamini-Hochberg corrected p-value below 0.05 were classified as significantly differentially expressed (DEGs).
To compare the group, genes having p-adjusted values below 0.05 and an absolute log2 fold-change equal or above 2.
Genome_build: The data were visualized as MA plot using DESeq2’s function plotMA.

source_name: subject with nerve lesion

extract_protocol: The cDNA libraries for all 14 samples were prepared using standard Illumina TruSeq protocol, following manufacturer's instructions.  Following this, all libraries were sequenced with High Output 1 x 75 cycles kit using the NextSeq 500 sequencing platform that generated 75 bp long single end reads

value: white blood cells


title: HD_HGF_FOXO_SCR_rep2


title: C116_siFOXO3_1


title: WCE_C116_LGF_FOXO_SCR_rep2


title: C116_NTCGF_1


title: NL-1_Rep2


title: NL-1_Rep3


title: WCE_HD_LGF_FOXO_SCR_rep2


title: NL-1_Rep1


title: C116_NTC_1


title: C116_LGF_FOXO_si_rep2


title: NL-0_Rep4

source_name: subject without neuropathic pain


title: WCE_HD_HGF_FOXO_SCR_rep1


title: NL-1_Rep4


title: WCE_C116_HGF_FOXO_SCR_rep1


title: WCE_HD_LGF_FOXO_si_rep2


title: Control_Rep5

source_name: control subject


title: WCE_C116_LGF_IgG_si_rep1


title: Control_Rep3


title: Control_Rep4


title: WCE_C116_LGF_FOXO_si_rep1


title: WCE_HD_LGF_FOXO_SCR_rep1


title: HD_LGF_FOXO_si_rep1


title: WCE_HD_LGF_FOXO_si_rep1


title: Control_Rep1


title: WCE_C116_LGF_FOXO_SCR_rep1


title: C116_LGF_FOXO_si_rep1


title: NL-0_Rep3


title: C116_LGF_FOXO_SCR_rep1


title: Control_Rep2


title: 28m_GAS_rep7

city: Basel

first: Anastasiya

last: Boersch

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

description:
Sample_98105
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt

data_processing:
RNA-seq reads were subjected to 3’ adapter and poly(A)/poly(T) tail trimming using Cutadapt v1.9.1 from Martin et al., EMBnet.journal, 2011. The following 3’ adapter sequences were utilized for generating RNA-Seq libraries and subsequently trimmed: mate1 5’-AGATCGGAAGAGCACACGTC-3’, mate2 5’-AGATCGGAAGAGCGTCGTGT-3’.
Reads shorter than 30 nucleotides were discarded.
The kallisto v0.43.1 software from Bray et al., Nature Biotechnology, 2016 was used for building transcriptome index and aligning filtered reads. The default options of kallisto were utilized for building transcriptome index. For aligning filtered reads we used options “--rf-stranded” and “--pseudobam”.
Mapped reads were assigned to transcripts in a weighted manner: if a read was uniquely mapped to a transcript, then the transcript’s read count was incremented by 1; if a read was mapped to n different transcripts, each transcript’s read count was incremented by 1/n.
The expression of each transcript was estimated in transcripts per million (TPM) units by dividing its read count by the transcript length and normalizing to the library size. The expression of a gene was obtained by summing up the normalized expression of the transcripts associated with it. For every gene, read counts of transcripts associated with this gene were also summed up and further used for the differential expression analysis.
As the reference mouse transcriptome, we considered sequences of protein coding transcripts with the support level 1-3 based on genome assembly GRCm38 (release 92) and transcript annotations from Ensembl database (see Hubbard et al., Nucleic Acids Research, 2002).
Genome_build: GRCm38
Supplementary_files_format_and_content: counts_mouse_aging_timecourse.txt: Tab-delimited text file includes raw counts at the gene level for each sample.
Supplementary_files_format_and_content: tpms_mouse_aging_timecourse.txt: Tab-delimited text file includes TPM values at the gene level for each sample.

organism: Mus musculus

source_name: Gastrocnemius muscle

growth_protocol: Mice were singly caged throughout the treatment period.

extract_protocol:
Snap frozen muscles were pulverized and lysed in RLT buffer (Qiagen). RNA was extracted using an AccuPure Tissue RNA Mini Kit(R20096) with an iColumn 24 (AccuBioMed). TruSeq Stranded mRNA HT Sample Prep Kit was used for the library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were fed a standardized AIN93M diet.

tag: strain

value: Wild type

value: Gastrocnemius muscle

value: Postnatal month 28


title: 28m_GAS_rep6

description:
Sample_98104
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 28m_GAS_rep8

description:
Sample_98106
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 28m_GAS_rep9

description:
Sample_98107
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 28m_GAS_rep5

description:
Sample_98103
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 28m_GAS_rep4

description:
Sample_98102
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 28m_GAS_rep2

description:
Sample_98100
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 28m_GAS_rep1

description:
Sample_98099
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: WCE_C116_LGF_FOXO_si_rep2

value: Ryk siRNA


title: HD_LGF_FOXO_SCR_rep1

value: Huntington's disease

value: Neural stem cells


title: 26m_GAS_rep8

description:
Sample_98097
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt

value: Postnatal month 26


title: 26m_GAS_rep7

description:
Sample_98096
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 28m_GAS_rep3

description:
Sample_98101
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 26m_GAS_rep9

description:
Sample_98098
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: SoLo_1

city: New Haven

first: Marc

last: Hammarlund

state: Connecticut

address: 295 Congress Ave

department: Genetics

institute: Yale University

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics.
Barrett_GEO_counts.txt

data_processing:
fastq files were aligned to the WBcel235 genome using STAR on default settings, and duplicate reads were removed using samtools markup.
BAM files resulting from the alignments were summarized to genes using the featureCounts tool.
Genome_build: WBcel235 C. elegans reference genome from Ensembl (labeled WS235 on WormBase).
Supplementary_files_format_and_content: Barrett_GEO_counts.txt: Space-delimited text file includes raw counts from featureCounts.

organism: Caenorhabditis elegans

source_name: FACS C. elegans neurons

growth_protocol: Worms were grown on 8P nutrient agar 150 mm plates seeded with E. coli strain NA22.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were prepared using Tecan SoLo Ovation RNAseq library or Tekara SMARTseq V4/Illumina Nextera XT kits.

treatment_protocol: Sorting: Fluorescence Activated Cell Sorting (FACS) was performed on a BD FACSAria™ III equipped with a 70-micron diameter nozzle. Cells were sorted into Trizol reagent LS.

tag: background strain

value: otIs355 [rab-3(prom1)::2xNLS-TagRFP] IV

value: untreated

value: Neurons


title: NL-0_Rep2


title: SMARTseq_2

description:
Library built using SMARTseq V4 kit from Tekara, and Nextera XT kit from Illumina.
Barrett_GEO_counts.txt


title: 26m_GAS_rep6

description:
Sample_98095
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: SMARTseq_1


title: SMARTseq_4


title: hb_vivo_m_H4

city: Berlin

first: Vera

last: van der Weijden

address: Ihnestraße 63-73

department: Department of Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description:
Porcine_embryos_in_vivo.xlsx
Porcine_embryos_hatched_blastocysts.xlsx

data_processing:
Basic read statistics and read quality was evaluated based on FastQC reports and a MultiQC overview report of all samples was generated.
Adaptors were clipped, sequences shorter than 20 bp were removed, and a low-quality end score of 20 was applied with the Trim Galore! tool
The trimmed reads were aligned against the porcine genome (Sus scrofa 11.1) with HISAT2
The sex of the morulae and hatched blastocysts was assigned based on the expression of DDX3Y, EIF1AY and EIF2S3Y
Differential gene expression analyses was conducted with EdgeR. A false discovery rate (FDR) of < 0.1% and an absolute log2FC > 1 was applied to identify the differentially expressed genes (DEGs)
Genome_build: Sus scrofa 11.1
Supplementary_files_format_and_content: Porcine_embryos_in_vivo.xlsx contains CPM of in vivo developed embryos at the 4-cell, morula and hatched blastocyst stage, including EdgeR DEG analyses results
Supplementary_files_format_and_content: Porcine_embryos_in_vitro.xlsx contains CPM of in vitro produced embryos at the 4-cell, morula and hatched blastocyst stage, including EdgeR DEG analyses results
Supplementary_files_format_and_content: Porcine_embryos_hatched_blastocysts.xlsx contains CPM of in vivo developed and in vitro produced hatched blastocysts, including EdgeR DEG analyses of source-induced differences and sex-specific differences

organism: Sus scrofa

source_name: vivo: hatched blastocyst

extract_protocol:
whole embryo lysis in buffer containing dNTPs and tailed oligo-dT oligonucleotides (30 nt poly-dT stretch and 25 nt universal 5’anchor sequence) plus 3.1 µl PBS
Illumina smart-seq2 according to Picelli et al., (2014)

tag: developmental stage

value: Embryo

tag: embryo stage

value: hatched blastocyst

tag: group

value: in vivo developed

tag: Sex

value: male


title: SoLo_3


title: SoLo_4


title: SMARTseq_3


title: HD_LGF_FOXO_si_rep2

value: IPS cells differentiated into neural stem cells


title: mor_vivo_m_H2

source_name: vivo: morula

value: morula


title: mor_vivo_f_H1

value: female


title: 26m_GAS_rep5

description:
Sample_98094
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt

value: Wild type


title: 26m_GAS_rep4

description:
Sample_98093
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt

value: Gastrocnemius muscle


title: SoLo_2


title: mor_vivo_f_G1


title: 26m_GAS_rep1

description:
Sample_98090
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: hb_vivo_f_G3


title: hb_vivo_m_F4


title: 26m_GAS_rep2

description:
Sample_98091
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: hb_vivo_m_F3


title: 24m_GAS_rep7

description:
Sample_98088
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt

value: Postnatal month 24


title: mor_vivo_f_F1


title: mor_vivo_m_E2


title: 24m_GAS_rep5

description:
Sample_98086
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: mor_vivo_f_D2


title: hb_vivo_m_D3


title: 26m_GAS_rep3

description:
Sample_98092
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: WCE_HD_LGF_IgG_si_rep1

value: ChIP-grade anti-FOXO3 antibody “NFL"

value: Ryk siRNA


title: 24m_GAS_rep1

description:
Sample_98082
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 24m_GAS_rep3

description:
Sample_98084
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 24m_GAS_rep4

description:
Sample_98085
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 24m_GAS_rep2

description:
Sample_98083
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 22m_GAS_rep8

description:
Sample_98081
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt

value: Postnatal month 22


title: 22m_GAS_rep7

description:
Sample_98080
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 4C_vivo_E1

source_name: vivo: 4-cell

value: 4-cell stage


title: 24m_GAS_rep8

description:
Sample_98089
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 24m_GAS_rep6

description:
Sample_98087
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: hb_vivo_f_B4


title: 22m_GAS_rep5

description:
Sample_98078
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 22m_GAS_rep6

description:
Sample_98079
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: mor_vivo_m_C2


title: mor_vivo_m_B2


title: 22m_GAS_rep2

description:
Sample_98075
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 22m_GAS_rep1

description:
Sample_98074
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 4C_vivo_B1


title: 22m_GAS_rep3

description:
Sample_98076
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 4C_vivo_D1


title: mor_vivo_f_A3


title: 18m_GAS_rep8

description:
Sample_98073
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt

value: Postnatal month 18


title: 18m_GAS_rep6

description:
Sample_98071
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: HD_siFOXO3GF_1

value: FOXO3 siRNA


title: mor_vivo_m_A2


title: 4C_vivo_A1


title: Adipose-KO-A13

city: Bergen

first: Laurence

middle: William-Joseph

last: Dyer

address: Haukelandsveien 22

department: Clinical Institute

country: Norway

institute: University of Bergen

data_processing:
Illumina Casava v1.8
Reads were aligned to the Zebrafish reference genome (GRCz10) using HiSat (Version 2.05), with options “hisat2-align-s --wrapper basic-0 -p 140”
Aligned reads were then put into featureCounts (Version 1.5.2) with options “featureCounts -T 64 -p -t exon -g gene_id”
Differential expression analysis was performed via DESeq2 (Version 1.14.1)
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalised counts for each Sample ...

organism: Danio rerio

source_name: Adipose

growth_protocol: Zebrafish were housed in 3 litre tanks for a period of 4 months and subsequently housed for a further 2 months in 1.5 litre tanks with 3 individuals per tank.

extract_protocol:
Tissue biopsies from three fish in each tank were pooled together, snap-frozen and processed for kit-based extraction of RNA, using the RNeasy kit (QIAGEN), and quality checked via spectrophotometer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Individuals were overfed for a period of 2 months on GEMMA Micro 500 (Skretting, USA) 3 times per day and given 3 drops of freshly hatched Artemia once per day.

value: ASC-1 KO

value: 6 months

value: Adipose


title: 18m_GAS_rep5

description:
Sample_98070
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: hb_vivo_m_A5

description:
Porcine_embryos_in_vivo.xlsx
Porcine_embryos_hatched_blastocysts.xlsx

value: Embryo

value: hatched blastocyst

value: in vivo developed


title: 18m_GAS_rep7

description:
Sample_98072
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: Adipose-KO-A12


title: mor_vitro_m_H1

source_name: vitro: morula

value: morula

value: in vitro produced

value: male


title: Adipose-KO-A11


title: 4C_vivo_C1


title: hb_vivo_f_E4

value: female


title: hb_vivo_m_B3


title: 18m_GAS_rep4

description:
Sample_98069
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt

value: Wild type

value: Gastrocnemius muscle


title: Adipose-KO-A10


title: hb_vitro_m_G4

description:
Porcine_embryos_in_vitro.xlsx
Porcine_embryos_hatched_blastocysts.xlsx

source_name: vitro: hatched blastocyst


title: Adipose-KO-A9


title: 22m_GAS_rep4

description:
Sample_98077
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: Adipose-KO-A8


title: Adipose-KO-A7


title: Adipose-KO-A6


title: Adipose-KO-A5


title: mor_vitro_m_G2


title: 18m_GAS_rep2

description:
Sample_98067
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 18m_GAS_rep1

description:
Sample_98066
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: Adipose-KO-A4


title: hb_vitro_m_G3


title: hb_vitro_m_F4


title: Adipose-KO-A1


title: Adipose-WT-A11

value: WT


title: 8m_GAS_rep8

description:
Sample_98065
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt

value: Postnatal month 8


title: Adipose-WT-A10


title: mor_vitro_f_F2


title: 8m_GAS_rep6

description:
Sample_98063
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: Adipose-WT-A9


title: mor_vitro_m_F1


title: Adipose-WT-A8


title: hb_vitro_f_E4


title: 8m_GAS_rep5

description:
Sample_98062
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 8m_GAS_rep7

description:
Sample_98064
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: Adipose-WT-A6


title: hb_vitro_m_E3


title: Adipose-WT-A7


title: mor_vitro_m_G1


title: 8m_GAS_rep3

description:
Sample_98060
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: 8m_GAS_rep4

description:
Sample_98061
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: Adipose-WT-A5


title: Adipose-KO-A3


title: Adipose-KO-A2


title: Adipose-WT-A4


title: Adipose-WT-A3


title: mor_vitro_f_E2


title: Adipose-WT-A2


title: 8m_GAS_rep2

description:
Sample_98059
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: ce_vitro_E1

source_name: vitro: 4-cell

value: 4-cell stage


title: 8m_GAS_rep1

description:
Sample_98058
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt


title: hb_vitro_f_D3


title: Input E17.5 Rep 3

city: Rensselaer

first: Sally

last: Temple

state: NY

address: One Discovery Drive

institute: Neural Stem Cell Institute

description:
e17_pos_results_pvalpeak_filtered.bed
e17_neg_results_pvalpeak_filtered.bed

data_processing:
fastq files mapped to mm10 genome using Tophat 2.0.9
tophat .bam files were normalized by average number of mapped reads to create scaled bedgraph files using BedTools 2.17.0
triplicate controls vs STAU2 RIPs were analyzed per genomic locus to produce a -10log10 transformed pValue using a one way t-test
peaks were generated using a threshold of 20 (pVal=.01), max gap =26, and min run =77
peaks were reanalyzed using a Java program (SeqPeakStatisticalAnalyzer) to apply a tTest to the average signal in treatments versus controls to generate pVals and qVals (Benjamini-Hochberg), scores were assigned using a combined metric where 80% was based on qVal and 20% on differential signal
peaks were aligned against RefSeq annotation for mm10 and RIP signal was assigned to various transcript regions (full transcript, intron, exon, CDS and UTRs) based on peak score and coverage (also, cufflinks version 2.2.1 was run on input samples to generate fpkm values)
Genome_build: mm10

source_name: Embryonic Day 17.5 Cortex

extract_protocol:
RIPs were performed with the MAGNA-RIP kit (Millipore, 17-700). For each RIP, 15 μl of Protein A/G beads were blocked with 2% UltraPure BSA (ThermoFisher, AM2616) at room temperature (RT) for 1-2 hours (hrs) before overnight incubation with 5-10 ug of either mouse anti-STAU2 (Abcam ab60724) or mouse anti-T7 (Novagen/Millipore 69522-3) monoclonal antibodies. For generation of the RIP-seq dataset, STAU2 RIP results were compared directly to input samples. After generation of the RIP-Seq dataset, a small number of select targets were compared with results from negative control T7-RIPs, using qPCR rather than direct sequencing. RNA was purified using TRIzol (ThermoFisher) and RNeasy Micro (Qiagen, 74004) or RNA Clean and Concentrator (Zymo, R1014) Kits, with DNase treatment. For RIPs performed on whole cortical lysate, pooled cortical tissue from a whole litter of embryos was used as starting material for each independent experiment (i.e. biological replicate). For RIPs performed on TBR2+ GFP-high cells, cell fractions obtained from two separate FACS collections were pooled and used as starting material for each independent experiment (i.e. biological replicate).
Libraries for RNA-seq were prepared using ‘ScriptSeq™ Complete Kit (Human/Mouse/Rat)-Low Input from Epicentre/Illumina using manufacturer’s instructions.

tag: sample type

value: input

tag: time point


title: mor_vitro_m_D2


title: Input E17.5 Rep 2


title: Input E17.5 Rep 1


title: Hela cells, SRSF10-overexpression, rep1

city: Wuhan

first: Chenhui

last: Wang

state: Hubei

address: 1037 Luoyu Rd

country: China

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
RSEM software was used to calculate gene expression level (FPKM).
Genome_build: GRCh38.p12, GCF_000001405.38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Gene IDs are NCBI Gene IDs.

source_name: Hela cells

growth_protocol: The Hela cells of control and SRSF10-overexpression were digested with trypsin,and then divided into 3 6cm-dishes respectively. Cell were harvested after 24h culturing in DMEM medium plus 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
The medium were removed and cells were washed with ice PBS buffer. RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

tag: cell line

value: HeLa

value: untreated


title: Hela cells, control, rep2

value: Vector


title: Hela cells, SRSF10-overexpression, rep2


title: Hela cells, control, rep3


title: ce_vitro_D1


title: hb_vitro_m_C3


title: Hela cells, SRSF10-overexpression, rep3


title: Adipose-WT-A1

value: 6 months

value: Adipose


title: Stau2 E17.5 Rep 3

description:
Total RNA after RIP
e17_pos_results_pvalpeak_filtered.bed
e17_neg_results_pvalpeak_filtered.bed


title: Hela cells, control, rep1


title: Stau2 E17.5 Rep 2


title: Stau2 E17.5 Rep 1


title: hb_vitro_m_C4

value: Embryo

value: hatched blastocyst


title: 25_S

type: RNA

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

description:
severe BPD
sample name in data files:
25

data_processing:
Data were analyzed in excel using Ct values for each sample,  normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.
Matrix normalized template shows miRNA Ct values normalized to global mean ΔCt = (Ct_miRNA − Ct_global mean)
For fold change calculations, ΔΔCt based fold-change values were obtained using an average of control sample Ct values (2^-ΔΔCt, where -ΔΔCt = -[ΔCtsample -ΔCtavgcontrol])). A fold change of 25 was considered as cutoff.
Matrix non-normalized are raw Ct values. Matrix normalized are normalized to the global mean.
Fold changes are calculated with the livak method (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol]).  Sample  1 was used as control for most miRNAs, except when the expression was below the detection limit, in which case we used other samples (2, 3, 4, 5, 20).

label: SYBR Green

source_name: tracheal aspirate

label_protocol: Small RNAs were retro-transcribed from 200 ng of total RNA using the miScript II RT kit (Qiagen). The expression of 1066 human miRNAs was assayed with the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z).

extract_protocol: MicroRNAs were purified from 0.5 mL of TAs with the Plasma/Serum RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada).

treatment_protocol: Tracheal aspirates were obtained from premature patients with bronchopulmonary dysplasia. Total RNA was purified from TAs and the expression of 1066 human miRNAs was detected with a PCR array.

tag: diagnosis

value: bronchopulmonary dysplasia (BPD)

value: tracheal aspirate

tag: mild/moderate bpd

value: no

tag: severe bpd

value: yes


title: 23_S

description:
severe BPD
sample name in data files:
23


title: C116_LGF_FOXO_SCR_rep2

source_name: Neural stem cells

value: ChIP-grade anti-FOXO3 antibody “NFL"

tag: phenotype

value: control

tag: sirna

value: scrambled RNA

value: Neural stem cells

tag: cell type

value: IPS cells differentiated into neural stem cells

tag: passage number

tag: genotype


title: 22_S

description:
severe BPD
sample name in data files:
22

tag: tissue


title: 21_M

description:
moderate BPD
sample name in data files:
21


title: Input E15.5 Rep 1

description:
e15_pos_results_pvalpeak_filtered.bed
e15_neg_results_pvalpeak_filtered.bed

source_name: Embryonic Day 15.5 Cortex

value: input


title: Input E15.5 Rep 2


title: 24_M

description:
moderate BPD
sample name in data files:
24


title: 4C_vitro_B1

value: 4-cell stage

value: in vitro produced


title: hb_vitro_m_B4

description:
Porcine_embryos_in_vitro.xlsx
Porcine_embryos_hatched_blastocysts.xlsx

value: male


title: mor_vitro_f_B2

value: morula

value: female


title: mor_vitro_m_C2

value: Embryo


title: Stau2 E15.5 Rep 3

description:
Total RNA after RIP
e15_pos_results_pvalpeak_filtered.bed
e15_neg_results_pvalpeak_filtered.bed


title: ce_vitro_C1


title: Macrophages treated with LPS_2

city: Changsha

first: Songqing

last: Tang

state: Hunan

address: Tianma Road

department: Department of pharmacy

institute: Hunan University

description: Biological replicate 2 of LPS treatment group, Gene expression data from mouse peritoneal macrophages treated with 100 ng/ml LPS for 6 hours.

hyb_protocol: Labelled cDNA Were hybridized in shaking water bath for 16 h at 50 °C. Arrays then washed in 2x SSC (+0.2 % SDS), 2x SSC and 0.2x SSC, each at 42 °C for 5 min prior to drying and scanning.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Data analysis was carried out using Rosetta Resolver R System (Rosetta Biosoftware).

source_name: mouse peritoneal macrophages

label_protocol: 1μg total RNA has been used to perform amplification process and labelled with Cy5, using Onearray Amino Allyl aRNA Amplification Kit as manufacturers instructions.

growth_protocol: Mouse peritoneal macrophages were grown in 6-well plate with the CO2 levels were 5% and the temperature maintained at 37 °C.

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

treatment_protocol: Mouse peritoneal macrophages were treated with 100 ng/ml LPS.

tag: strain

value: peritoneal macrophages

tag: treatment

value: LPS


title: Macrophages treated with PBS_1

description: Biological replicate 1 of Control group, Gene expression data from mouse peritoneal macrophages treated with PBS for 6 hours.

value: PBS (control)


title: Input E15.5 Rep 3


title: Macrophages treated with LPS_1

description: Biological replicate 1 of LPS treatment group, Gene expression data from mouse peritoneal macrophages treated with 100 ng/ml LPS for 6 hours.


title: Macrophages treated with PBS_2

description: Biological replicate 2 of Control group, Gene expression data from mouse peritoneal macrophages treated with PBS for 6 hours.


title: 19_S

description:
severe BPD
sample name in data files:
19

value: bronchopulmonary dysplasia (BPD)

value: tracheal aspirate

value: no


title: 20_M

description:
moderate BPD
sample name in data files:
20

value: yes


title: 18_M

description:
moderate BPD
sample name in data files:
18


title: hb_vitro_f_A4

tag: developmental stage

tag: embryo stage

value: hatched blastocyst


title: 16_M

description:
moderate BPD
sample name in data files:
16


title: 17_S

description:
severe BPD
sample name in data files:
17


title: 15_S

description:
severe BPD
sample name in data files:
15


title: 18m_GAS_rep3

description:
Sample_98068
PolyA RNA
direction_1st_mate: antisense
direction_2nd_mate: sense
processed data file: counts_mouse_aging_timecourse.txt
processed data file: tpms_mouse_aging_timecourse.txt

value: Wild type

value: Gastrocnemius muscle

tag: age

value: Postnatal month 18


title: NL-0_Rep1

source_name: subject without neuropathic pain

value: white blood cells


title: 14_S

description:
severe BPD
sample name in data files:
14


title: Stau2 E15.5 Rep 1

tag: sample type


title: Input E13.5 Rep 3

description:
e13_pos_results_pvalpeak_filtered.bed
e13_neg_results_pvalpeak_filtered.bed

source_name: Embryonic Day 13.5 Cortex

value: input

tag: time point


title: 13_S

description:
severe BPD
sample name in data files:
13


title: Stau2 E15.5 Rep 2


title: 4C_vitro_A1

value: 4-cell stage

tag: group

value: in vitro produced


title: Input E13.5 Rep 2


title: 8_S

description:
severe BPD
sample name in data files:
8

tag: diagnosis


title: ASD_MIPP-seq4

first: Ryan

middle: N

last: Doan

address: 3 Blackfan Circle, CLS 15040

institute: Boston Children's Hospital

description: SNVs and INDELS in ASD Part 4

data_processing:
Library strategy: MIPP-seq
See MIPP-seq publication
First, all BAMs were converted to fastq using bedtool’s bamtofastq tool. Next, the samples were demultiplexed using the unique 15nt barcodes (5nt of the primer and 10nt index) using FASTX toolkit’s fastx_barcode_splitter (--bol --mismatches 3) resulting in fastq files for each primer set.
Indel correction was performed using Pollux[44] (-n false -d false -h true -s false -f false), and barcode and quality trimming were performed using the cutadapt [45]tool (-u 10 -q 10).
aligned to the reference genome using default settings in BWA-mem with local indel realignment being performed with GATK 3.7 IndelRealigner[46] (-greedy 1200 -maxReads 2000000 -maxInMemory 1500000) with indels present in gnomAD being used as a reference. Primer binding sites were removed using the bamclipper tool[47] with default settings. Variants were called across the length of each amplicon using Samtools mPileup with the settings: q=20, Q=20.
Genome_build: hg19
Supplementary_files_format_and_content: text TDT files containing all primers sites, sequences and the allelic fractions of mutations and correseponding background error rates

source_name: panel of Autism and control brain tissues specimens

extract_protocol: MIPP-Seq: Unique primers are designed to prevent sharing binding sites and avoiding known mutations in the individual and general population but are within 250 nucleotides of the target mutation. Once designed, unique 10nt barcodes are appended to the reverse primer, along with the standard Ion Torrent platform specific adapters.  The primers designed above amplify targets using reduced cycling  (20cycles) with a high-fildelity enzyme and minimal amount of DNA (25-50ng). As all primers are unique and can be identified using the primer sequence, recations from up to 96 differnet mutations are pooled and PCR purified, before being diluted to 100pm for sequencing on the Ion Torrent S5 with 400nt reads platform for ultra-deep coverage.

value: Autsim cases and controls, brain tissue

tag: experiment

value: novel allele validation


title: 10_S

description:
severe BPD
sample name in data files:
10

tag: mild/moderate bpd

tag: severe bpd


title: 9_S

description:
severe BPD
sample name in data files:
9


title: 12_S

description:
severe BPD
sample name in data files:
12


title: 11_S

description:
severe BPD
sample name in data files:
11


title: ASD_MIPP-seq5

description: SNVs and INDELS in ASD Part 5


title: ASD_MIPP-seq3

description: SNVs and INDELS in ASD Part 3


title: InP/ZnS QD treated yeast rep3

city: Springfield

first: Kyoungtae

last: Kim

state: Missouri

address: 901 S National Ave

institute: MISSOURI STATE UNIVERSITY

description: Strain used systematic sequencing project, contains reference sequence

data_processing:
Data from cDNA sequencing was analyzed using Galaxy, a website platform for analyzing sequenced data (www.usegalaxy.org).
The data obtained from Kansas Medical Genome Center was uploaded to the Galaxy server where sequences that were separated when sent to us were concatenated back together so the full reads could be analyzed.
A quality check was carried out on each file of sequence data to check the quality of the reads and ensure good samples and that the data is interpreted correctly. The files were then re-formatted into Sanger which is necessary for the steps to follow.
To achieve high fidelity, the files were trimmed based on quality, and bases with a quality score below 20 were removed from the reads. For eliminating bias of primers and to ensure the removal of adapters, 12 bases were trimmed from the 5’ end of the reads.
The remaining reads were then filtered to remove any reads less than 80 base pairs. Next, reads were aligned to the wild type Saccharomyces cerevisiae reference genome (S288C) obtained from the Saccharomyces Genome Database (SGD) (YeastGenome.org) with Tophat in Galaxy.
With Cufflink, the transcriptome was assembled using the reference annotation by comparing the reads to the reference genome.
Lastly, using Cuffdiff, the aligned sequence expression rates were compared between sample conditions, creating a list of differentially expressed genes (DEGs). When the final differential gene data was obtained, genes with a q-value greater than 0.05 were not included in the final list of genes analyzed. The remaining genes were grouped based on correlating Gene Ontology (GO) Terms obtained from GOrilla.
Supplementary_files_format_and_content: Excel files that include cuffdiff output (fold-changes, p-values, q-values, and rpkm).

organism: Saccharomyces cerevisiae

source_name: InP/ZnS QD treated yeast rep3

growth_protocol: Saccharomyces cerevisiae (S288C) cells were cultured in SD-Glucose media to mid log phase. The OD was determined at a wavelength of 600 nm and fell in the mid log phase OD range 0.3-0.6.

extract_protocol:
TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA) was used to isolate mRNA from the total RNA.
The kit provided SuperScript II Reverse Transcriptase that was used to synthesize the first cDNA strands from the newly purified mRNA, followed promptly by the synthesis of the second cDNA strand. Using unique adaptors ligated to each cDNA sample, the samples could be distinguished when sequenced and then amplified on both ends for 15 cycles in a T100TM Thermal Cycler (BIO RAD). The cDNA of each sample was suspended in 30 mL of Resuspension Buffer with a concentration of approximately 50 ng/mL.

treatment_protocol: From mid log phase, some samples were treated with InP/ZnS-QDs. The cells were incubated at 220 rmp at 30°C for six hours in a shaking incubator and brought to a concentration of 100 mg/mL InP/ZnS-QDs.

tag: agent

value: InP/ZnS


title: ASD_MIPP-seq2

description: SNVs and INDELS in ASD Part 2


title: 7_M

description:
moderate BPD
sample name in data files:
7


title: InP/ZnS QD treated yeast rep2

source_name: InP/ZnS QD treated yeast rep2


title: mor_vitro_m_A3

value: Embryo

value: morula

tag: Sex

value: male


title: Stau2 E13.5 Rep 2

description:
Total RNA after RIP
e13_pos_results_pvalpeak_filtered.bed
e13_neg_results_pvalpeak_filtered.bed


title: Input E13.5 Rep 1


title: ASD_MIPP-seq1

description: SNVs and INDELS in ASD Part 1


title: InP/ZnS QD treated yeast rep1

source_name: InP/ZnS QD treated yeast rep1


title: hb_vivo_f_G4

description:
Porcine_embryos_in_vivo.xlsx
Porcine_embryos_hatched_blastocysts.xlsx

source_name: vivo: hatched blastocyst

value: in vivo developed

value: female


title: Stau2 E13.5 Rep 1


title: 4_S

description:
severe BPD
sample name in data files:
4

value: bronchopulmonary dysplasia (BPD)

value: tracheal aspirate

value: no

value: yes


title: 6_S

description:
severe BPD
sample name in data files:
6


title: 2_M

description:
mild BPD
sample name in data files:
2


title: Input E11.5 Rep 3

description:
e11_pos_results_pvalpeak_filtered.bed
e11_neg_results_pvalpeak_filtered.bed

source_name: Embryonic Day 11.5 Cortex


title: 1_S

description:
severe BPD
sample name in data files:
1


title: CdSe/ZnS QD treated yeast rep3

source_name: CdSe/ZnS QD treated yeast rep3

value: CdSe/ZnS QD


title: 3_S

description:
severe BPD
sample name in data files:
3


title: Sensitivity_Testing_MIPP-seq3

description: 25ng Sensivitiy Testing Part 1

source_name: 25ng Sensivitiy Testing Part 1

value: blood and cell line derived genomic DNA

value: Dilution series


title: Input E11.5 Rep 2

value: input


title: Sensitivity_Testing_MIPP-seq2

description: 50ng Sensivitiy Testing Part 2

source_name: 50ng Sensivitiy Testing Part 2


title: CdSe/ZnS QD treated yeast rep1

source_name: CdSe/ZnS QD treated yeast rep1


title: Stau2 E13.5 Rep 3


title: Library 1 with Polylinker DNA plasmid pool

city: St. Louis

first: Michael

middle: Aaron

last: White

state: MO

address: 4515 McKinley Ave, Campus Box 8510

institute: Washington University School of Medicine

description: Demultiplexing barcode sequence of 'ATAGTGGACA' upstream of a spacer sequence 'CACCTGTTCCTGTAGGCATGC' followed by a 9 bp barcode for library elements

data_processing:
Library strategy: Massively Parallel Reporter Assay
All raw reads were processed regardless of quality score. Reads with the expected in-line multiplexing barcode for each sample followed by the spacer sequence were identified. Demultiplexed reads were then used to determine the number of unique occurances of 9 bp sequences in the barcoded region of the reporter construct. Barcodes that exactly matched designed sequences were written to file along with the sequence identifier and the barcode's count. All other reads and barcodes were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: First column contains unique 9 bp barcode, second column contains sequence identifier, third column contains number of reads with the corresponding barcode. Sequences were named using the following nomenclature: "chrom-start-stop_annotations_variant". "Chrom", "start", and "stop" correspond to the mm10 genomic coordinates of the sequences in BED format. "Annotations" is a four letter string where the first position indicates CRX binding status ("C" ChIP-seq peak or "U" Unbound), the second position indicates CRX motif status ("P" PWM hit, "S" Shape motif, or "B" Both PWM and shape motif), the third position indicates ATAC-seq status ("R" peak in Rods but not cones, "C" peak in Cones but not rods, "P" peak in both rod and cone Photoreceptors, or "N" peak in None of the above), and the fourth position indicates histone ChIP-seq status ("E" Enhancer marked with H3K27Ac+H3K4me3-, "P" Promoter marked with H3K27Ac+H3K4me3+, "Q" H3K27Ac-H3K4me3+, or "N" Neither mark). "Variant" indicates whether the sequence is genomic ("WT"), mutated CRX sites ("MUT-allCrxSites"), scrambled shape motif ("MUT-shape"), or a scrambled control ("scrambled").

organism: Escherichia coli

source_name: Bacterial culture

growth_protocol: Retinas were isolated from P0 newborn CD-1 mice and electroporated in a solution with 30 micrograms library and 30 micrograms Rho-GFP as described previously (Hsiau et al., 2007; Hughes et al., 2018; Kwasnieski et al., 2012; White et al., 2013, 2016). Electroporated retinas were cultured for eight days, at which point they were harvested, washed three times with HBSS (Gibco), and stored in TRIzol (Invitrogen) at -80C. Five retinas were pooled for each biological replicate and three replicates were performed for each experiment.

extract_protocol:
Target library reporter sequences were amplified using primers 'GTGGAGCAGTACGAGCG' and 'TAGCCAGAAGTCAGATGCTCAAG' for 30 cycles (NEB Q5) at an annealing temperature of 67C and then purified with the Monarch PCR kit. Illumina adaptors were then added via two further rounds of PCR. First, custom P1 indexing barcodes were tailed on for 5 cycles at an annealing temperature of 55C followed by 5 cycles with no annealing step (NEB Q5). PE2 indexing barcodes were then tailed on by amplifying 2 microliters of the previous reaction for 5 cycles at an annealing temperature of 66C followed by 5 cycles with no annealing step (NEB Q5) and then purified with the Monarch PCR kit. Samples were mixed at equal concentration and sequenced on the Illumina NextSeq platform.
RNA was extracted from TRIzol according to manufacturer instructions and treated with TURBO DNase (Invitrogen). cDNA was prepared using SuperScript RT III (Invitrogen) with oligo dT primers.


title: Library 2 with Polylinker DNA plasmid pool


title: Library 2 with Rho DNA plasmid pool

description: Demultiplexing barcode sequence of 'ATAGTGGACA' upstream of a spacer sequence 'CATGC' followed by a 9 bp barcode for library elements

extract_protocol:
Target library reporter sequences were amplified using primers 'CACCTGTTCCTGTAGGCATGC' and 'TATTACAATTGTAGCCAGAAGTCAGATGCTCAAG' for 6 cycles at an annealing temperature of 66C followed by 18 cycles with no annealing step (NEB Phusion) and then purified with the Monarch PCR kit (NEB). PCR amplicons were digested using MfeI-HF and SphI-HF (NEB) and ligated to custom annealed adaptors with PE2 indexing barcodes and phased P1 barcodes. The final enrichment PCR used primers 'AATGATACGGCGACCACCGAG' and 'CAAGCAGAAGACGGCATACGA' for 20 cycles at an annealing temperature of 66C (NEB Phusion), followed by purification with the Monarch PCR kit. Samples were mixed at equal concentration and sequenced on the Illumina NextSeq platform.
RNA was extracted from TRIzol according to manufacturer instructions and treated with TURBO DNase (Invitrogen). cDNA was prepared using SuperScript RT III (Invitrogen) with oligo dT primers.


title: Input E11.5 Rep 1


title: Stau2 E11.5 Rep 3

description:
Total RNA after RIP
e11_pos_results_pvalpeak_filtered.bed
e11_neg_results_pvalpeak_filtered.bed


title: Library 1 with Rho DNA plasmid pool


title: non-treated yeast rep3

source_name: non-treated yeast rep3


title: Sample D708

city: QingDao

first: Qilai

last: Huang

address: Binhai road 72#

institute: Shandong University

data_processing:
The next-generation sequencing Data quality statistical software Cutadapt (version 1.9.1) was used to remove the adapters and low-quality sequences from the original sequencing Data (Pass Filter Data) to obtain Clean Data for subsequent information analysis.
The overlap area between read1 and read2 of Clean Reads was combined using Pandaseq (version 2.7) to produce complete sequences.
According to the Barcode sequence of read1 of each sample, the spliced Tag starting position is split into the corresponding sample with perfect matching, and the result is saved in FASTQ file.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every barcode and every sample

molecule: other

organism:
Homo sapiens
synthetic construct

source_name: prostate cancer cell line LNCaP, plasmid library

extract_protocol:
Twenty-four hours post-transfection, cells were washed twice and harvested in 1 × PBS, and Total RNA was extracted from all surviving cells using RNeasy Plus Mini Kit (74136, QIAGEN). We treated the mRNA with RapidOut DNA Removal Kit (K2981, Thermo Scientific) to remove the trace amount of genomic DNA residue according to the product manual. The purified RNA was then subjected to reverse transcription with High-Capacity cDNA Reverse Transcription Kits (4374967, Applied Biosystems). Briefly, 1.5μg RNA was added into 10μl of 2× RT Master Mix and made up to the final 20μl with nuclease-free water. The reactions were incubated at 25°C for 10 min, followed by 120 min at 37°C, then were inactivated Reverse Transcriptase by heating to 85°C for 5 min. The cDNA products were stored at -20°C or -80°C and ready for qPCR analysis and preparing the NGS sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: multiplexed

tag: molecule

value: total RNA and plasmid mixture


title: non-treated yeast rep2

source_name: non-treated yeast rep2


title: Sensitivity_Testing_MIPP-seq1

description: 50ng Sensivitiy Testing Part 1

source_name: 50ng Sensivitiy Testing Part 1


title: Stau2 E11.5 Rep 2


title: Sensitivity_Testing_MIPP-seq4

description: 25ng Sensivitiy Testing Part 2

source_name: 25ng Sensivitiy Testing Part 2


title: Sample D704

value: prostate cancer cell line LNCaP, plasmid library


title: Stau2 E11.5 Rep 1


title: CdSe/ZnS QD treated yeast rep2

source_name: CdSe/ZnS QD treated yeast rep2


title: Radix Paeoniae Rubra decoctio 4 mg/mL

city: Beijing

first: Zhao

last: Xiaomng

address: Beinong Road num 6

institute: Beijing university of agriculture

data_processing:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies).
Quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific) and a Bioanalyzer 2100 system (Agilent). For mRNA sequening, Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA).
Random oligonucleotides and SuperScript III were used to synthesize the first strand cDNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization.
To select cDNA fragments of the preferred 300 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).
The sequencing library was then sequenced on a NextSeq 500 platform (Illumina) .
Supplementary_files_format_and_content: The control group was compared with the genome build. A table with raw gene build for every gene and every sample

organism: Staphylococcus aureus

source_name: co-culture

extract_protocol:
Lysin and lysozyme are added to break up the ATCC-29213 after co-culture, then RNA was harvested by Trizol reagent for examination.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: treated with Radix Paeoniae Rubra decoction for 12 hours


title: Radix Paeoniae Rubra decoctio 2 mg/mL


title: H3K27Ac_H4

city: Hangzhou

first: Yin-Li

last: Zhang

address: No. 3 Qingchun East Road, Jianggan District

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mouse genome mm10 using Bowtie (Version 2.0) with the default parameters
Significant enrichments were identified using MACS2.0. Bamcoverage was used to generate the bigWig files.
Peak annotation was performed using R and the ChIPseeker package
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files
Supplementary_files_format_and_content: peak text files

source_name: Mouse ovary

extract_protocol:
Ovary lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. ChIP was performed using a commercial kit (CST, 9003)
Libraries were prepared for the ChIP DNA experiments with a TruSeq DNA LT/HT Sample Prep Kit (Illumina) and were subjected to quality control on a Bioanalyzer (Agilent 2200). Illumina sequencing was performed on an Illumina HiSeq 2000 Sequencing system at RiboBio Co., Ltd.

treatment_protocol: Immature female mice were primed with pregnant mare chorionic gonadotropin (PMSG) to stimulate follicular growth, injected with human chorionic gonadotropin (hCG) 48h later to induce ovulation.At 0h, 1h and 4h after hCG treatment, mice were killed and ovaries were collected for ChIP.

value: ICR

value: PMSG 48h + 4h after hCG)

tag: chip antibody


title: Radix Paeoniae Rubra decoctio 1 mg/mL


title: H3K27Ac_H1

value: PMSG 48h + 1h after hCG)


title: Q300

city: Seoul

first: Eunkyong

last: Ko

address: Gwanak ro

institute: Seoul National University

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
To estimate expression levels, the RNA–seq reads were mapped to the human genome using TopHat v.1.3.3 (Johns Hopkins University, Baltimore, MD, USA). The reference genome sequence (hg19, Genome Reference Consortium GRCh37) and annotation data were downloaded from the UCSC website (http://genome.uscs.edu). The transcript counts at the gene level were calculated, and the relative transcript abundances were measured in fragments per kilobase of exon per million fragments mapped using the Cuffdiff software, which tests the observed log fold change in the expression of a gene against the null hypothesis of no change (version 1.2.1). The false discovery rate was controlled by adjusting P values with the Benjamini–Hochberg algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: HCC, H2O2

growth_protocol: Cell lines were grown in Dulbecco’s modified Eagle’s medium (DMEM; Welgene, Gyeongsan-si, Korea) supplemented with 10 % fetal bovine serum (FBS; GenDepot, Barker, TX, USA) and cultured in a humidified 5 % CO2 incubator at 37°C, as previously described.

extract_protocol:
RNA was extracted from mock- and 300 μM H2O2-treated Huh7 cells using the NucleoSpin® TriPrep Kit (740966.250, Macherey-Nagel). Total RNA quality and quantity were verified using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Library construction was performed by Macrogen Inc. (Macrogen, Seoul, Korea). One microgram of total RNA was used to construct cDNA libraries with the TruSeq RNA library kit (Illumina, San Diego, CA, USA).
Library construction was performed by Macrogen Inc. (Macrogen, Seoul, Korea).

treatment_protocol: Culture media were replaced daily, and cells were incubated for 4 days in 300 M, or the indicated concentration, of H2O2 (H1009, Sigma).

tag: cell line

value: HCC cell line Huh7

tag: treatment day

value: 4 days

tag: treatment method

value: daily media change


title: Q0

source_name: HCC, mock

tag: treatment

value: mock


title: H3K27Ac_H0

tag: strain

value: PMSG 48h (0h after hCG)


title: contrast

source_name: control

value: untreated


title: H300


title: non-treated yeast rep1

source_name: non-treated yeast rep1


title: H0


title: Input DNA


title: EV-human myoblast 3

city: Tampa

first: Wanling

last: xuan

state: FL

address: 12901 Bruce B Down Blvd

department: DPS

institute: University of South Florida

hyb_protocol: The labeled samples were then hybridized to the GeneChip miRNA 4.0 array (Thermofisher) that contains 2,578 and 2,025 human mature and premature miRNA

scan_protocol: Scanning of the arrays were carried out according to Affymetrix’s recommendations

data_processing: The CEL files were imported into Partek Genomic Suites version 6.6 (Partek, St. Louis, MO) using standard import tool with RMA normalization

label: multiplexed DNA tags (miR-tag)

source_name: skeletal muscle

label_protocol: 130 ng of total RNA was labeled with biotin using the FlashTag Biotin HSR RNA Labeling Kit (Applied Biosystems) according to manufacturer’s procedure.

extract_protocol: Conditioned medium was collected and EV were isolated by centrifugation at 3000 rpm for 30 min to remove cells and debris, followed by filtration through a 0.22 μm filter to remove the remaining debris. Then the medium was further concentrated to 500 μl using Amicon Ultra-15 100 kDa centrifugal filter units (Millipore). Isolation of exosomes in the concentrated medium was carried out through qEV size exclusion columns (Izon Science). Exosome fractions were collected and concentrated by Amicon Ultra-4 10 KDa centrifugal filter units to a final volume of <100 μl.

treatment_protocol: Human iPS cell line (CYS0105, ATCC), primary human myoblasts (CC-2580, Lonza) and iPS-derived muscle progenitors  induced by givinostat were cultured and their EV were isolated.

tag: tissue

value: extracellular vesicles

tag: cell type

value: human myoblasts


title: Liver_251_BLKO_DF_22B

status: Public on Jan 29 2021

city: Rehovot

first: Gal

last: Manella

state: Israel

address: 234 Herzel St.

country: Israel

institute: Weizmann Institute of Science

description:
288
Liver_BLKO_reads.xlsx

data_processing:
Illumina bcl2fastq software used for basecalling.
The rest of analysis was done through the UTAP pipline. Reads were trimmed using cutadapt
Reads were mapped to genome (/shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index) using STAR (default parameters)
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases)
Counting was done using htseq-count (union mode)
Normalization of the counts was performed using DESeq2 with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files containing for each gene and sample the raw counts and normalized counts

source_name: Liver

growth_protocol: 3mo mice were housed under standard light-dark conditions (12h/12h) for 2 weeks before the experiment, and during the experiment.

extract_protocol:
Tissues were snap-frozen in liquid nitrogen immediately after dissection and stored at -80°C till used. For RNA extraction, the tissues were soaked in TRI-reagent (Sigma) and were homogenized by bead beater (Bead Ruptor e24, OMNI), and then proceeded by a standard TRI-reagent based RNA extraction protocol. RNA concentration was determined using NanoDrop™ 2000 Spectrophotometer (Thermo Fisher Scientific). RNA Integrity was validated using 2200 TapeStation (Agilent).
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina HiSeq 1500.
3' RNA-seq for digital gene expression quantitation

treatment_protocol: Mice were fed either Ad Libitum (AL), or exclusively during the light-phase (DF) for 30 days. Food restriction was performed manually.

value: Liver

tag: genotype

value: Alb-Cre, Bmal fl/fl (BLKO)

tag: feeding regimen

value: DF


title: EV-Givi-MPC 3

source_name: iPS

value: givinostat indcued muscle progenitor cells


title: EV-Givi-MPC 1


title: EV-Givi-MPC 2


title: Liver_251_BLKO_DF_16A

description:
281
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_20A

description:
285
Liver_BLKO_reads.xlsx


title: EV-human myoblast 2


title: Liver_251_BLKO_DF_14B

description:
280
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_16B

description:
282
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_18B

description:
284
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_20B

description:
286
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_18A

description:
283
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_10A

description:
275
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_12A

description:
277
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_10B

description:
276
Liver_BLKO_reads.xlsx


title: EV-human myoblast 1


title: Liver_251_BLKO_DF_22A

description:
287
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_14A

description:
279
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_8B

description:
274
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_8A

description:
273
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_6B

description:
272
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_6A

description:
271
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_2A

description:
267
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_4A

description:
269
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_12B

description:
278
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_0B

description:
266
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_20B

description:
262
Liver_BLKO_reads.xlsx

value: AL


title: Liver_250_BLKO_AL_22B

description:
264
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_12B

description:
254
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_18B

description:
260
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_18A

description:
259
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_22A

description:
263
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_10B

description:
252
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_20A

description:
261
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_14B

description:
256
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_16B

description:
258
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_12A

description:
253
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_8B

description:
250
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_4B

description:
246
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_10A

description:
251
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_6A

description:
247
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_6B

description:
248
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_4A

description:
245
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_14A

description:
255
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_2B

description:
244
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_2A

description:
243
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_8A

description:
249
Liver_BLKO_reads.xlsx


title: Liver_250_BLKO_AL_0A

description:
241
Liver_BLKO_reads.xlsx


title: 251_BLKO_DF_22B

data_processing:
Illumina bcl2fastq software used for basecalling.
The rest of analysis was done through the UTAP pipline. Reads were trimmed using cutadapt
Reads were mapped to genome (/shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index) using STAR (default parameters)
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases)
Counting was done using htseq-count (union mode)
Normalization of the counts was performed using DESeq2 with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files containing the normalized raw counts for each gene and sample

source_name: Lung

extract_protocol:
Tissues were snap-frozen in liquid nitrogen immediately after dissection and stored at -80°C till used. For RNA extraction, the tissues were soaked in TRI-reagent (Sigma) and were homogenized by bead beater (Bead Ruptor e24, OMNI), and then proceeded by a standard TRI-reagent based RNA extraction protocol. RNA concentration was determined using NanoDrop™ 2000 Spectrophotometer (Thermo Fisher Scientific). RNA Integrity was validated using 2200 TapeStation (Agilent).
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina HiSeq 1500.

value: Lung


title: 251_BLKO_DF_22A


title: Liver_250_BLKO_AL_16A

description:
257
Liver_BLKO_reads.xlsx


title: Liver_251_BLKO_DF_0A

description:
265
Liver_BLKO_reads.xlsx


title: 251_BLKO_DF_16B


title: Liver_250_BLKO_AL_0B

description:
242
Liver_BLKO_reads.xlsx


title: 251_BLKO_DF_18A


title: 251_BLKO_DF_16A


title: 251_BLKO_DF_18B


title: 251_BLKO_DF_20B


title: 251_BLKO_DF_14A


title: 250_BLKO_AL_22B


title: 251_BLKO_DF_8B


title: 251_BLKO_DF_10B


title: 251_BLKO_DF_6B


title: 251_BLKO_DF_12A


title: 251_BLKO_DF_10A


title: 251_BLKO_DF_12B


title: 250_BLKO_AL_22A


title: 251_BLKO_DF_6A


title: Liver_251_BLKO_DF_2B

description:
268
Liver_BLKO_reads.xlsx


title: 251_BLKO_DF_8A


title: 251_BLKO_DF_4B


title: 251_BLKO_DF_4A


title: Liver_251_BLKO_DF_4B

description:
270
Liver_BLKO_reads.xlsx


title: 251_BLKO_DF_2B


title: 251_BLKO_DF_2A


title: 250_BLKO_AL_20A


title: 250_BLKO_AL_20B


title: 251_BLKO_DF_20A


title: 251_BLKO_DF_14B


title: 251_BLKO_DF_0B


title: 251_BLKO_DF_0A


title: 250_BLKO_AL_18B


title: 250_BLKO_AL_18A


title: 250_BLKO_AL_16A


title: 250_BLKO_AL_14B


title: 250_BLKO_AL_12B


title: 250_BLKO_AL_16B


title: 250_BLKO_AL_10B


title: 250_BLKO_AL_8A


title: 250_BLKO_AL_8B


title: 250_BLKO_AL_0B


title: 252_albcre_DF_22B

value: Alb-Cre


title: 250_BLKO_AL_6A


title: 250_BLKO_AL_6B


title: 250_BLKO_AL_2B


title: 250_BLKO_AL_4B


title: 250_BLKO_AL_0A


title: 250_BLKO_AL_12A


title: 252_albcre_DF_22A


title: 250_BLKO_AL_4A


title: 252_albcre_DF_20A


title: 252_albcre_DF_16B


title: 252_albcre_DF_18A


title: 252_albcre_DF_18B


title: 252_albcre_DF_16A


title: 252_albcre_DF_14B


title: 250_BLKO_AL_14A


title: 252_albcre_DF_12B


title: 250_BLKO_AL_2A


title: 252_albcre_DF_20B


title: 252_albcre_DF_10A


title: 250_BLKO_AL_10A


title: 252_albcre_DF_14A


title: 252_albcre_DF_12A


title: 252_albcre_DF_10B


title: 252_albcre_DF_6A


title: 252_albcre_DF_4B


title: 252_albcre_DF_2B


title: 252_albcre_DF_4A


title: 252_albcre_DF_2A


title: 5_M

description:
mild BPD
sample name in data files:
5

source_name: tracheal aspirate

tag: diagnosis

value: bronchopulmonary dysplasia (BPD)

value: tracheal aspirate

value: yes

value: no


title: 252_albcre_DF_0A


title: 276_albcre_AL_18B


title: 276_albcre_AL_22A


title: 276_albcre_AL_20A


title: 276_albcre_AL_20B


title: 276_albcre_AL_22B


title: 276_albcre_AL_16A


title: 276_albcre_AL_16B


title: 252_albcre_DF_0B


title: 252_albcre_DF_6B


title: 276_albcre_AL_18A


title: 276_albcre_AL_14A


title: 276_albcre_AL_14B


title: 276_albcre_AL_12B


title: 276_albcre_AL_12A


title: 252_albcre_DF_8B


title: 252_albcre_DF_8A


title: 276_albcre_AL_6A


title: 276_albcre_AL_10A


title: 276_albcre_AL_8A


title: 276_albcre_AL_8B


title: 276_albcre_AL_6B


title: 276_albcre_AL_10B


title: 276_albcre_AL_4A


title: 276_albcre_AL_2B


title: 276_albcre_AL_4B


title: 276_albcre_AL_2A


title: 276_albcre_AL_0B


title: WAT_251_BLKO_DF_22A

source_name: WAT

value: WAT


title: WAT_251_BLKO_DF_22B


title: WAT_251_BLKO_DF_20A


title: WAT_251_BLKO_DF_20B


title: WAT_251_BLKO_DF_18B


title: WAT_251_BLKO_DF_14A


title: WAT_251_BLKO_DF_16B


title: WAT_251_BLKO_DF_16A


title: WAT_251_BLKO_DF_14B


title: 276_albcre_AL_0A


title: WAT_251_BLKO_DF_18A


title: WAT_251_BLKO_DF_8B


title: WAT_251_BLKO_DF_6B


title: WAT_251_BLKO_DF_12A


title: WAT_251_BLKO_DF_8A


title: WAT_251_BLKO_DF_12B


title: WAT_251_BLKO_DF_10A


title: WAT_251_BLKO_DF_6A


title: WAT_251_BLKO_DF_10B


title: WAT_251_BLKO_DF_4A


title: WAT_251_BLKO_DF_2B


title: WAT_251_BLKO_DF_4B


title: WAT_251_BLKO_DF_0A


title: WAT_250_BLKO_AL_22B


title: WAT_251_BLKO_DF_2A


title: WAT_250_BLKO_AL_20A


title: WAT_250_BLKO_AL_22A


title: WAT_250_BLKO_AL_20B


title: WAT_250_BLKO_AL_10A


title: WAT_250_BLKO_AL_16B


title: WAT_250_BLKO_AL_12B


title: WAT_250_BLKO_AL_14B


title: WAT_250_BLKO_AL_18A


title: WAT_250_BLKO_AL_10B


title: WAT_250_BLKO_AL_16A


title: WAT_250_BLKO_AL_14A


title: WAT_250_BLKO_AL_18B


title: WAT_250_BLKO_AL_8B


title: WAT_250_BLKO_AL_8A


title: WAT_250_BLKO_AL_4B


title: WAT_252_albcre_DF_22B


title: WAT_250_BLKO_AL_4A


title: WAT_250_BLKO_AL_0A


title: WAT_250_BLKO_AL_6B


title: WAT_251_BLKO_DF_0B


title: WAT_250_BLKO_AL_6A


title: WAT_250_BLKO_AL_2A


title: WAT_252_albcre_DF_20B


title: WAT_252_albcre_DF_22A


title: WAT_252_albcre_DF_20A


title: WAT_250_BLKO_AL_0B


title: WAT_252_albcre_DF_14B


title: WAT_252_albcre_DF_18B


title: WAT_252_albcre_DF_16B


title: WAT_250_BLKO_AL_12A


title: WAT_252_albcre_DF_12A


title: WAT_252_albcre_DF_14A


title: WAT_250_BLKO_AL_2B


title: WAT_252_albcre_DF_12B


title: WAT_252_albcre_DF_4A


title: WAT_252_albcre_DF_10A


title: WAT_252_albcre_DF_8B


title: WAT_252_albcre_DF_8A


title: WAT_252_albcre_DF_6A


title: WAT_252_albcre_DF_2B


title: WAT_252_albcre_DF_2A


title: WAT_252_albcre_DF_10B


title: WAT_276_albcre_AL_22A


title: WAT_276_albcre_AL_20B


title: WAT_252_albcre_DF_0B


title: WAT_252_albcre_DF_0A


title: WAT_252_albcre_DF_18A


title: WAT_276_albcre_AL_20A


title: WAT_276_albcre_AL_18A


title: WAT_276_albcre_AL_16A


title: WAT_276_albcre_AL_14B


title: WAT_276_albcre_AL_16B


title: WAT_276_albcre_AL_12B


title: WAT_276_albcre_AL_12A


title: WAT_276_albcre_AL_14A


title: WAT_252_albcre_DF_4B


title: WAT_252_albcre_DF_6B


title: WAT_276_albcre_AL_22B


title: WAT_276_albcre_AL_10B


title: WAT_276_albcre_AL_8B


title: WAT_276_albcre_AL_10A


title: WAT_276_albcre_AL_18B


title: WAT_276_albcre_AL_0B


title: Liver_252_albcre_DF_22B


title: WAT_276_albcre_AL_0A


title: Liver_252_albcre_DF_22A


title: WAT_276_albcre_AL_2A


title: WAT_276_albcre_AL_4A


title: WAT_276_albcre_AL_2B


title: WAT_276_albcre_AL_6A


title: WAT_276_albcre_AL_4B


title: WAT_276_albcre_AL_8A


title: WAT_276_albcre_AL_6B


title: WAT_252_albcre_DF_16A


title: Liver_252_albcre_DF_14B


title: Liver_252_albcre_DF_16A


title: Liver_252_albcre_DF_20A


title: Liver_252_albcre_DF_20B


title: Liver_252_albcre_DF_18A


title: Liver_252_albcre_DF_18B


title: Liver_252_albcre_DF_14A


title: Liver_252_albcre_DF_16B


title: Liver_252_albcre_DF_10B


title: Liver_252_albcre_DF_12A


title: Liver_252_albcre_DF_12B


title: EKV

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description:
Neuron from left side of DMV in Naive Rat
BioMark-RTqPCR

data_processing:
Samples were normalized through centering aound the median of the 35 genes with highest expression values across all samples.
Raw Matrix contains raw Ct values for genes and control RNA dilution series

label: EvaGreen

organism: Rattus norvegicus

source_name: DMV neuron

label_protocol: cDNA labeled with SYBR green according to manufacture's protocol.

extract_protocol: Brainstems were extracted and frozen in OCT, sectioned on a cryostat at 10 um, sections were prepared with rapid IHC for DAPI and NeuN in less than 15 minutes, single neurons were captured using Arcturus CapSure system according to manufacture protocols.  Single cells or cell pools (2-5 single cells) were indiviually lysed and PCR performed according to Fluidigm's Biomark preparation protocols.

treatment_protocol: Male sprague dawley rats were subjected to remote ischemia preconditioning (rIPC) through ligation of bilateral femoral arteries or sham operation incluing ketamine/xylazine anesthesia and surgical exposure without ligation. n=3 biological replicates. All samples were collected 2.5 hours after referfusion.

tag: condition

value: left side of DMV in Naive Rat

value: Male

value: Sprague Dawley

value: Naive Rat

tag: animal number

tag: single cells/sample

tag: side of the brainstem

value: Left Side of DMV


title: EKZ

description:
Neuron from right side of DMV in Naive Rat
BioMark-RTqPCR

value: right side of DMV in Naive Rat

tag: Sex

value: Reft Side of DMV


title: Liver_252_albcre_DF_10A

value: Liver

value: DF


title: Liver_252_albcre_DF_6B


title: Liver_252_albcre_DF_8B


title: Liver_252_albcre_DF_8A


title: Liver_252_albcre_DF_6A


title: Liver_252_albcre_DF_4B


title: EK9


title: EKB


title: EK74


title: EKE


title: EKH


title: EK77


title: EK72


title: EK81


title: EK80


title: EKU


title: EKP


title: EK79


title: EK73


title: EK76


title: EKI


title: EKO


title: EKK


title: EK69


title: EK70


title: Liver_252_albcre_DF_2B


title: Liver_252_albcre_DF_2A


title: Liver_252_albcre_DF_0B


title: Liver_252_albcre_DF_4A


title: Liver_252_albcre_DF_0A


title: EK68


title: Liver_276_albcre_AL_20A

value: AL


title: Liver_276_albcre_AL_22A


title: Liver_276_albcre_AL_22B


title: Liver_276_albcre_AL_18B


title: Liver_276_albcre_AL_18A


title: Liver_276_albcre_AL_20B


title: EK65


title: EK64


title: EK66


title: EK78


title: Liver_276_albcre_AL_14B


title: Liver_276_albcre_AL_14A


title: Liver_276_albcre_AL_16A


title: Liver_276_albcre_AL_16B


title: EK6


title: EK59


title: EK56


title: EK60


title: EK58


title: EK54


title: EK55


title: EK61


title: Liver_276_albcre_AL_12B


title: Liver_276_albcre_AL_12A


title: Liver_276_albcre_AL_10B


title: EK57


title: Liver_276_albcre_AL_10A


title: EK67


title: Liver_276_albcre_AL_8B


title: Liver_276_albcre_AL_8A


title: Liver_276_albcre_AL_6B


title: EK50


title: EK51


title: EK50-replicate


title: EK49


title: EK48


title: EK53


title: Liver_276_albcre_AL_4B


title: Liver_276_albcre_AL_4A


title: Liver_276_albcre_AL_2B


title: Liver_276_albcre_AL_0A


title: Liver_276_albcre_AL_2A


title: Liver_276_albcre_AL_0B


title: Liver_276_albcre_AL_6A


title: EK45