title: 89_Normal_NN_dermis_Hiroshi

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: 89 Normal NN dermis Hiroshi

label_protocol: Affymetrix double amplification protocol

extract_protocol: QIAGEN Rneasy Kit

tag: patient id

tag: method

value: LCM

tag: diagnosis

value: Normal

value: NN

tag: region

value: dermis


title: 100_Normal_NN_whole_tissue_Hiroshi

status: Public on Oct 02 2018

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 100 Normal NN whole tissue Hiroshi

tag: tissue


title: 57_Normal_NN_dermis_Hiroshi

source_name: 57 Normal NN dermis Hiroshi


title: 98_Normal_NN_epidermis_Hiroshi

source_name: 98 Normal NN epidermis Hiroshi

value: epidermis


title: 76_Normal_NN_dermis_Hiroshi

source_name: 76 Normal NN dermis Hiroshi


title: 68_Normal_NN_epidermis_Hiroshi

source_name: 68 Normal NN epidermis Hiroshi


title: 84_Normal_NN_epidermis_Hiroshi

source_name: 84 Normal NN epidermis Hiroshi


title: 75_Normal_NN_epidermis_Hiroshi

source_name: 75 Normal NN epidermis Hiroshi


title: 44_Normal_NN_epidermis_Hiroshi

source_name: 44 Normal NN epidermis Hiroshi


title: 9_AD_NL_epidermis_Hitokazu

source_name: 9 AD NL epidermis Hitokazu

value: AD

value: NL


title: 53_Normal_NN_whole_tissue_Hiroshi

source_name: 53 Normal NN whole tissue Hiroshi


title: 46_Normal_NN_epidermis_Hiroshi

source_name: 46 Normal NN epidermis Hiroshi


title: 9_AD_NL_dermis_Hitokazu

source_name: 9 AD NL dermis Hitokazu


title: 60_Normal_NN_whole_tissue_Hiroshi

source_name: 60 Normal NN whole tissue Hiroshi


title: 28_Normal_NN_epidermis_Hiroshi

source_name: 28 Normal NN epidermis Hiroshi


title: 10_Normal_NN_whole_tissue_Hiroshi

source_name: 10 Normal NN whole tissue Hiroshi


title: 20_Normal_NN_epidermis_Hiroshi

source_name: 20 Normal NN epidermis Hiroshi


title: 25_Normal_NN_dermis_Hiroshi

source_name: 25 Normal NN dermis Hiroshi


title: 9_AD_NL_whole_tissue_Hitokazu

source_name: 9 AD NL whole tissue Hitokazu


title: 52_Normal_NN_epidermis_Hiroshi

source_name: 52 Normal NN epidermis Hiroshi


title: 61_Normal_NN_dermis_Hiroshi

source_name: 61 Normal NN dermis Hiroshi


title: 37_Normal_NN_whole_tissue_Hiroshi

source_name: 37 Normal NN whole tissue Hiroshi


title: 3_Normal_NN_dermis_Hiroshi

source_name: 3 Normal NN dermis Hiroshi


title: 40_Normal_NN_epidermis_Hiroshi

source_name: 40 Normal NN epidermis Hiroshi


title: 9_AD_LS_whole_tissue_Hitokazu

source_name: 9 AD LS whole tissue Hitokazu

value: LS


title: 22_Normal_NN_whole_tissue_Hiroshi

source_name: 22 Normal NN whole tissue Hiroshi


title: 9_AD_LS_epidermis_Hitokazu

source_name: 9 AD LS epidermis Hitokazu


title: 8_AD_NL_epidermis_Hitokazu

source_name: 8 AD NL epidermis Hitokazu


title: 8_AD_NL_whole_tissue_Hitokazu

source_name: 8 AD NL whole tissue Hitokazu


title: 8_AD_NL_dermis_Hitokazu

source_name: 8 AD NL dermis Hitokazu


title: 9_AD_LS_dermis_Hitokazu

source_name: 9 AD LS dermis Hitokazu


title: 6_AD_NL_epidermis_Hitokazu

source_name: 6 AD NL epidermis Hitokazu


title: 8_AD_LS_whole_tissue_Hitokazu

source_name: 8 AD LS whole tissue Hitokazu


title: 8_AD_LS_epidermis_Hitokazu

source_name: 8 AD LS epidermis Hitokazu


title: 6_AD_NL_dermis_Hitokazu

source_name: 6 AD NL dermis Hitokazu


title: 6_AD_LS_whole_tissue_Hitokazu

source_name: 6 AD LS whole tissue Hitokazu


title: 5_AD_NL_epidermis_Hitokazu

source_name: 5 AD NL epidermis Hitokazu


title: 5_AD_NL_whole_tissue_Hitokazu

source_name: 5 AD NL whole tissue Hitokazu


title: 6_AD_LS_epidermis_Hitokazu

source_name: 6 AD LS epidermis Hitokazu


title: 5_AD_LS_whole_tissue_Hitokazu

source_name: 5 AD LS whole tissue Hitokazu


title: 5_AD_LS_dermis_Hitokazu

source_name: 5 AD LS dermis Hitokazu


title: 5_AD_LS_epidermis_Hitokazu

source_name: 5 AD LS epidermis Hitokazu


title: 5_AD_NL_dermis_Hitokazu

source_name: 5 AD NL dermis Hitokazu


title: 4_AD_NL_epidermis_Hitokazu

source_name: 4 AD NL epidermis Hitokazu


title: 6_AD_NL_whole_tissue_Hitokazu

source_name: 6 AD NL whole tissue Hitokazu


title: 6_AD_LS_dermis_Hitokazu

source_name: 6 AD LS dermis Hitokazu


title: 4_AD_NL_dermis_Hitokazu

source_name: 4 AD NL dermis Hitokazu


title: LTP 90 minutes

type: SRA

city: NEW YORK

first: Chiara

last: Mariottini

address: 1425 Madison Ave, Room 12-52

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
For the RNA-Seq data analysis Tophat 2.0.13, bowtie 2.1.0 , samtool 0.1.7 and cufflinks 1.3.0  were used. The rn5-bowtie2 index was generated with the command 'bowtie2-build rn5.fa rn5'. The 'rn5.fa'-file was downloaded from the UCSC genome browser. The mm10-bowtie2 index was downloaded from http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml.  RefSeq geneTracks and GTF-files for the rn5 and mm10 genome assembly were downloaded from UCSC genome browser. Common gene ids in the GTF-files were matched to individual transcript_ids using the corresponding official symbols obtained from the geneTracks files.
Reads were aligned to the rn5  genome using Tophat with the option '--no-novel-juncs' and the refSeq-GTF-file (the option '--solexa1.3-quals' was additionally chosen in case of the rat samples).
Differentially expressed genes were identified using Cuffdiff with the options '--upper-quartile-norm', '--frag-bias-correct' against the rn5 genome and '--multi-read-correct' and the refSeq-GTF-file.
Genome_build: rn5
processed data files format and content: tab-delimited text files include RPKM values for each Sample
processed data files format and content: final TXT file that contains log2 fold changes of significantly differentially expressed genes

organism: Rattus norvegicus

source_name: CA1 region

extract_protocol:
The tissue was flash frozen immediately after the recordings and the CA1 regions from each hippocampla slices were dissected. Approximately 10 CA1 regions obtained from at least 3 different rats were pooled together for each condition. RNA was harvested using Trizol reagent.The seq library was prepared using TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA) and approximately 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We used field electrophysiology stimulation with a strong high frequency stimulation protocol (HFS: 2 trains of 100 stimuli delivered at 100 Hz at an intensity of 75-80% of the spike treshold). The stimulating electrode was placed in CA3 region while the recording electrode was placed in CA1 region.

tag: strain

value: Sprague Dawley

value: hippocampus

tag: age

value: 3-6 months old

tag: genotype

value: Nrl-/-


title: Control (unstimulated)

value: wild type


title: 4_AD_LS_epidermis_Hitokazu

source_name: 4 AD LS epidermis Hitokazu


title: 4_AD_LS_whole_tissue_Hitokazu

source_name: 4 AD LS whole tissue Hitokazu


title: 4_AD_NL_whole_tissue_Hitokazu

source_name: 4 AD NL whole tissue Hitokazu


title: 4_AD_LS_dermis_Hitokazu

source_name: 4 AD LS dermis Hitokazu


title: sre_dhfr_R1-DP

city: Los Angeles

first: Kimberly

last: Insigne

state: CA

department: Biochemistry

institute: UCLA

description:
Minigene reporter for exon skipping. DNA-sequencing of three FACS-sorted bins, in replicate
processed data file: sre_dhfr_bin_counts.csv

library_source: genomic

data_processing:
library strategy: Multiplexed Functional Assay of Splicing using Sort-seq (MFASS)
Paired-end reads merged with bbmerge version 38 and default parameters
Reads were aligned using custom aligner script, requiring only perfect matches
Used custom script to aggregate raw read counts across bins for each sequence, where each bin is a separate column, for downstream analysis
Genome_build: hg19
Supplementary_files_format_and_content: Each row corresponds to a sequence in the synthetic oligo library. Each column corresponds to the raw read counts for that sequence in that individual bin. 0 count means the sequence was not observed.

molecule: genomic DNA

growth_protocol: RCA7 cells were grown under standard adherent tissue culture conditions for HEK293T-derivatives.

extract_protocol:
We extracted genomic DNA for the sorted populations using blood and cell culture DNA midi kit (Qiagen).
We amplified each sublibrary for ~300-fold amplicon coverage, and reactions were performed in 96-well format in 50 μL reactions for each sublibrary proportional to bin size using Kapa HiFi DNA polymerase.
Custom libraries were constructed using standard adapters from Illumina and paired-end sequenced with custom sequencing primers. Samples were indexed with i7 indices compatible with Illumina paired-end protocols.

tag: cell line

tag: cell type

tag: synthetic oligo library

value: SRE library in DHFR backbone

tag: sorted fraction

value: double positive (DP); both GFP and mCherry are present, correspond to exon skipping


title: sre_dhfr_R1-INT

value: Intermediate (INT); intermediate levels of GFP and mCherry


title: sre_dhfr_R2-INT


title: healthy control 17

city: Beijing

first: Yong

last: Shao

address: 27 Taiping Road

country: China

institute: Beijing Institute of Radiation Medicine

description:
NC47
cinvsn.txt,ccvsn.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Raw reads of fastq format were firstly processed through Trimmomatic-0.36. Clean reads were obtained by removing short reads of less than 50 bp, low quality reads with an average base mass of less than 15, reads containing adapter or ploy-N from raw reads.
Index of the reference genome was built using Hisat2-2.0.0 and paired-end clean reads were aligned to the reference genome using Hisat2-2.0.0.
StringTie-1.3.3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package.
Genome_build: grcm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: peripheral blood cells

extract_protocol:
PAXgene blood RNA tubes were used to collect 2.5ml blood. Total RNA was extracted using the PAXgene Blood RNA Kit. NEBNext® Ultra RNA Library Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, mRNA was captured from 2μg total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature to make mRNA approximate 200 bp inserts. First and second strand cDNA were synthesized, then purified using AMPure XP beads. After end repair, an Illumina adapter was ligated to the sticky 5’end, then different i5 and i7 primers were added to each sample library, following 12 cycles of linear PCR amplification.

value: peripheral blood cells

tag: disease state

value: healthy control


title: healthy control 15

description:
NC44
cinvsn.txt,ccvsn.txt


title: sre_dhfr_R1-SP

value: Single positive (SP); no GFP present but mCherry present, corresponds to exon inclusion


title: healthy control 18

description:
NC48
cinvsn.txt,ccvsn.txt


title: healthy control 14

description:
NC43
cinvsn.txt,ccvsn.txt


title: healthy control 16

description:
NC46
cinvsn.txt,ccvsn.txt


title: sre_dhfr_R2-DP


title: Ptpro-KO rep2

city: Guangzhou

first: Hong

middle: mei

last: Dong

state: Guangdong

address: 601 Huangpu Avenue West

department: Institute of Precision Cancer and Pathology

institute: Jinan University Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Mus musculus

source_name: Esophagus

growth_protocol: To induce tumorigenesis in the esophagus, 100 mg/mL of the water-soluble carcinogen 4NQO (Sigma-Aldrich) was added to the drinking water of 6-week-old mice for 16 weeks. The mice were sacrificed when body weight loss >1/3; otherwise, they were sacrificed 12 weeks after completion of 4NQO treatment.

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent  (Cat#9109, TAKARA)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Esophageal squamous cell carcinoma

value: post natal week 6

value: Ptpro-/-


title: WT rep3

treatment_protocol: To induce tumorigenesis in the esophagus, 100 mg/mL of the water-soluble carcinogen 4NQO (Sigma-Aldrich) was added to the drinking water of 6-week-old mice for 16 weeks. The mice were sacrificed when body weight loss >1/3; otherwise, they were sacrificed 12 weeks after completion of 4NQO treatment.


title: Ptpro-KO rep3


title: WT rep2


title: healthy control 19

description:
NC49
cinvsn.txt,ccvsn.txt


title: WT rep1


title: healthy control 12

description:
NC41
cinvsn.txt,ccvsn.txt


title: healthy control 11

description:
NC40
cinvsn.txt,ccvsn.txt


title: healthy control 13

description:
NC42
cinvsn.txt,ccvsn.txt


title: Ptpro-KO rep1


title: healthy control 9

description:
NC38
cinvsn.txt,ccvsn.txt


title: BLM_EHP_2

city: Córdoba

first: Eduardo

last: Muñoz

address: Avda Menéndez Pidal s/n

country: Spain

institute: Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), University of Córdoba

data_processing:
Pre-processing: Sequences were pre-processed with Trimmomatic v0.36
Alignment: Pre-processed sequences were algined to mouse genome assembly mm10 using HISAT2 v2.1.0
Counts per gene were obtained with featureCounts v1.6.1 using the in-built RefSeq annotation for mm10 genome assembly
The raw counts were then analyzed with DESeq2 v1.20.0 excluding those genes with less than 10 counts across all samples
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include raw counts obtained from featureCounts

source_name: Skin

extract_protocol:
Total RNA was isolated from mice frozen skin tissue using QIAzol lysis reagent (Qiagen, Hilden, Germany) and purified with RNeasy mini kit (Qiagen).
Transcriptome libraries were constructed with TruSeq Stranded Total RNA LT Sample Prep Kit (with Ribo-Zero Human/Mouse/Rat, #RS-122-2201). In brief, 300 ng of total RNA from each Sample was used to construct a cDNA library, followed by sequencing on the Illumina Hiseq 2500 with single end 50 bp reads and ~30 millions of reads per sample.

value: BALB/c

value: Six-eight weeks

value: skin

tag: group


title: BLM_2

value: bleomycin


title: BLM_EHP_1


title: BLM_1


title: healthy control 6

description:
NC34
cinvsn.txt,ccvsn.txt


title: Control_2

value: control


title: WM without 6q del-4

city: Tachikawa

first: NAOHIRO

last: SEKIGUCHI

state: Tokyo

address: 3256, Midori

department: Hematology

country: Japan

institute: Disaster Medical Center

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with MBEI (Li and Wong, 2001 PNAS, 98, 31-36) using GeneSpring software (Agilent technologies).

source_name: WM without 6q del-4

label_protocol: Biotinylated cRNA were prepared using Ovation FFPE WTA System and Encore Biotin Module (NuGEN Technologies, Inc) according to the manufacturer's protocol from 100 ng total RNA.

extract_protocol: Total RNA were extracted from FFPE-embedded bone marrow samples using RNeasy FFPE kit (Qiagen) according to manufacturer’s manual.

treatment_protocol: formalin-fixed parrafin-embedded bone marrow biopsied specimen

value: bone marrow

tag: disease

value: waldenstrom macroglobulinemia


title: WM without 6q del-1

source_name: WM without 6q del-1


title: healthy control 10

description:
NC39
cinvsn.txt,ccvsn.txt


title: WM with 6q del-2

source_name: WM with 6q del-2


title: WM without 6q del-5

source_name: WM without 6q del-5


title: WM with 6q del-3

source_name: WM with 6q del-3


title: healthy control 3

description:
NC9
cinvsn.txt,ccvsn.txt


title: healthy control 4

description:
NC10
cinvsn.txt,ccvsn.txt


title: WM with 6q del-1

source_name: WM with 6q del-1


title: WM without 6q del-2

source_name: WM without 6q del-2


title: healthy control 8

description:
NC37
cinvsn.txt,ccvsn.txt


title: healthy control 5

description:
NC33
cinvsn.txt,ccvsn.txt


title: WM without 6q del-3

source_name: WM without 6q del-3


title: healthy control 1

description:
NC1
cinvsn.txt,ccvsn.txt


title: cervical cancer 11

description:
C57
ccvscin.txt,ccvsn.txt

value: cervical cancer


title: P0.5fiber rep2

city: Bronx

first: Ales

last: Cvekl

address: 1300 Morris Park Avenue, Ullman 123

department: The Departments Ophthalmology and Visual Sciences, Genetics

institute: Albert Einstein College of Medicine

data_processing:
Raw reads are filtered with trim_galore(version 0.4.1)
Trimmed RNAseq reads were aligned to mm10 with Tophat (version 2.0.13)
The number of RNA-seq fragments mapped to each gene in the Refseq gene annotation (downloaded from the UCSC genome browser in 03/2017) was then counted using HTseq (version 0.6.1)
The Cuffdiff in the cufflinks package (version 2.2.1) was also used to generate the normalized gene-expression level, FPKMs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts number for each gene in each sample.

source_name: lens fiber

extract_protocol:
Lens were extracted and microdissected into lens epithelium and fiber. Trizol was then used to extract RNA.
KAPA RNA HyperPrep Kits with RiboErase (HMR) for RNA-seq library preparation according to the manufacturer’s instructions.
stranded total RNAseq

value: lens fiber

tag: developmental stage


title: P0.5epi rep3

source_name: lens epithelium

value: lens epithelium


title: healthy control 7

description:
NC36
cinvsn.txt,ccvsn.txt


title: Control_1


title: P0.5fiber rep3


title: P0.5fiber rep1


title: P0.5epi rep2


title: healthy control 2

description:
NC6
cinvsn.txt,ccvsn.txt


title: P0.5epi rep1


title: E18.5fiber rep3


title: cervical cancer 10

description:
C56
ccvscin.txt,ccvsn.txt


title: E18.5fiber rep2


title: sre_smn1_R2-SP

description:
Minigene reporter for exon skipping. DNA-sequencing of three FACS-sorted bins, in replicate
processed data file: sre_smn1_bin_counts.csv

value: SRE library in SMN1 backbone


title: sre_smn1_R2-INT

value: Intermediate (INT); intermediate levels of GFP and mCherry


title: cervical cancer 8

description:
C54
ccvscin.txt,ccvsn.txt

value: peripheral blood cells


title: cervical cancer 9

description:
C55
ccvscin.txt,ccvsn.txt


title: E18.5fiber rep1


title: PANC-1_1.5 μM Ika-treated_24 hr_rep2

city: Shanghai

first: Shuheng

last: Jiang

address: 800 Dongchuan Road

institute: Shanghai Cancer Institute

description: Gene expression data from 1.5 μM Ika-treated PANC-1 pancreatic cancer cell lines

hyb_protocol: Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned on the Agilent Scanner G2505C using one color scan setting for 8x60k array slides (Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Expression signals were calculated using the Agilent Feature Extraction software (version 10.7.3.1 Agilent Technologies, Santa Clara, CA).

source_name: PANC-1 Pancreatic Cancer Cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: PANC-1 cells were maintained in DMEM medium with 2 mM glutamine, 5 mM glucose supplemented with 1% penicillin, and streptomycin and tested for mycoplasma contamination.

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Cells were treated with 500 nM or 1.5 μM Ika for 24 hr.

tag: treatment

value: 1.5 μM Ika-treated 24 hr


title: sre_smn1_R1-INT


title: 8_AD_LS_dermis_Hitokazu

source_name: 8 AD LS dermis Hitokazu

tag: patient id

value: LCM

value: AD

value: LS

value: dermis


title: sre_dhfr_R2-SP

value: SRE library in DHFR backbone

value: Single positive (SP); no GFP present but mCherry present, corresponds to exon inclusion


title: E18.5epi rep3


title: PANC-1_500 nM Ika-treated_24 hr_rep3

description: Gene expression data from 500 nM Ika-treated PANC-1 pancreatic cancer cell lines

value: 500 nM Ika-treated 24 hr


title: sre_smn1_R1-DP

value: double positive (DP); both GFP and mCherry are present, correspond to exon skipping


title: sre_smn1_R2-DP


title: cervical cancer 4

description:
C50
ccvscin.txt,ccvsn.txt


title: sre_smn1_R1-SP


title: PANC-1_1.5 μM Ika-treated_24 hr_rep1


title: E18.5epi rep1


title: cervical cancer 6

description:
C52
ccvscin.txt,ccvsn.txt


title: cervical cancer 5

description:
C51
ccvscin.txt,ccvsn.txt


title: cervical cancer 1

description:
C46
ccvscin.txt,ccvsn.txt


title: E16.5epi rep3


title: TGFb_72_Nint_R6

city: Pennington

first: Ron

last: Ammar

state: New Jersey

address: 311 Pennington Rocky Hill Road

institute: Bristol-Myers Squibb

data_processing:
Reads were aligned to the Rattus norvegicus Rnor_6.0 reference genome (NCBI assembly accession GCF_000001895.5) with the Omicsoft Sequence Aligner.
Gene and transcript abundance was determined with Ensembl R89 rat gene models using RSEM.
All RNA-Seq data were processed in R with Bioconductor packages.
RNA-Seq samples were TMM normalized with the edgeR package.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Tab-delimited text files of counts and log2CPM

source_name: ex-vivo slice

extract_protocol:
Total RNA was prepared from PCLSs using the RNeasy 96 kit (Qiagen, Germany) according to the manufacturer's instructions. cDNA synthesis was performed with high capacity RNA to cDNA kit (Life Technologies, Carlsbad, CA). Sequencing libraries were generated using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina, San Diego, CA) following manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

tag: replicate group


title: None_0_None_R3


title: E16.5epi rep2


title: cervical intraepithelial neoplasia 20

description:
C44
ccvscin.txt,cinvsn.txt

value: cervical intraepithelial neoplasia


title: cervical intraepithelial neoplasia 21

description:
C45
ccvscin.txt,cinvsn.txt


title: None_72_None_R1


title: E16.5fiber rep2


title: cervical cancer 3

description:
C49
ccvscin.txt,ccvsn.txt

value: cervical cancer


title: cervical intraepithelial neoplasia 19

description:
C43
ccvscin.txt,cinvsn.txt


title: E16.5epi rep1


title: E16.5fiber rep1

value: lens fiber


title: E16.5fiber rep3


title: cervical cancer 2

description:
C48
ccvscin.txt,ccvsn.txt


title: PANC-1_1.5 μM Ika-treated_24 hr_rep3


title: TGFb_72_Pirf_R4


title: PANC-1_500 nM Ika-treated_24 hr_rep1


title: None_0_None_R2


title: cervical intraepithelial neoplasia 17

description:
C41
ccvscin.txt,cinvsn.txt


title: PANC-1_500 nM Ika-treated_24 hr_rep2


title: 371916A07_SLOT03_S01_Green.xys

city: Vigo

first: Humberto

last: Quesada

address: Campus As Lagoas-Marcosende

department: Departamento de Bioquímica, Genética e Inmunología,

institute: Universidad de Vigo

description: This is a wild sample of Littorina saxatilis crab ecotype

hyb_protocol: For each pool, 4 μg of Cy3 labeled cDNA was resuspended in 12 μL of hybridization solution, of which 6 μL was applied onto a subarray. Pools were randomly distributed in the subarrays.   Hybridization was carried out at 42°C for 19 h on a NimbleGen Hybridization System with continuous mixing. After hybridization, the arrays were washed in buffers of various stringencies using the NimbleGen Washing kit

scan_protocol: Arrays were scanned using an Agilent G2565AA microarray scanner (Agilent Technologies) with a resolution of 2 μm

data_processing:
Data were extracted after quality control using NimbleScan software (NimbleGen/Roche) and analyzed in the R/Bioconductor statistical environment. The pdfInfoBuilder and oligo (Carvalho and Irizarry 2010. Bioinformatics 26: 2363-2367) packages were used for data handling and pre-processing, with the robust multichip average (RMA) method (Irizarry et al. 2003. Biostatistics 4: 249-264) used for background correction, quantile normalization and probelevel summarization of the microarray samples.
A single value was obtained for each gene, resulting from each summarization probe-level data. To decide whether a gene was expressed, a threshold level representing the “background signal” was calculated based on the average hybridization signal of the empty spots present in the array. Genes for which less than 80% of the probes had an average hybridization signal lower than the “background signal” were disregarded.

organism: Littorina saxatilis

source_name: Foot muscle

label_protocol: Cy3 labeling was performed with the NimbleGen One-Color DNA labeling kit (Roche) using a starting amount of 1 μg of cDNA per pool

extract_protocol: Total RNA was isolated from the foot muscle tissue of single females using TRIZOL reagent (Invitrogen) according to the manufacturer´s instructions. The Turbo DNA-freeTM kit (Ambion) was used to remove   any remaining DNA from RNA extractions. Genomic DNA was isolated from the foot muscle tissue of single snails using a CTAB extraction method (Wilding et al. 2001. Evol Biol. 14: 611-619) modified to include RNAse treatment.   DNA samples were further cleaned with NucleoSpin columns (Macherey- Nagel) following manufacturer´s instructions. RNA and DNA purity was assessed using a NanoDrop spectrophotometer   (NanoDrop Tech. Inc., Wilmington, DE). All extractions were standardized to 100ng/μL after checking their integrity in agarose gels.

tag: pool

tag: ecotype

value: RB

tag: locality

value: Roncudo


title: 371916A12_SLOT03_S01_Green.xys


title: PANC-1_untreated control_24 hr_rep3

description: Gene expression data from untreated PANC-1 pancreatic cancer cell lines

value: untreated control


title: cervical intraepithelial neoplasia 16

description:
C40
ccvscin.txt,cinvsn.txt

source_name: peripheral blood cells

tag: tissue

value: peripheral blood cells


title: E14.5fiber rep2

tag: strain


title: cervical intraepithelial neoplasia 18

description:
C42
ccvscin.txt,cinvsn.txt


title: E14.5fiber rep3


title: None_72_None_R2


title: None_0_None_R5


title: 371916A09_SLOT03_S01_Green.xys

description: This is a wild sample of Littorina saxatilis wave ecotype

value: SU

value: Silleiro


title: cervical intraepithelial neoplasia 15

description:
C39
ccvscin.txt,cinvsn.txt


title: 371916A08_SLOT03_S01_Green.xys


title: 371916A11_SLOT03_S01_Green.xys

value: Burela


title: 371916A06_SLOT03_S01_Green.xys


title: 371916A10_SLOT03_S01_Green.xys


title: PANC-1_untreated control_24 hr_rep1


title: TGFb_72_None_R3


title: E14.5epi rep3

value: lens epithelium


title: E14.5fiber rep1


title: cervical intraepithelial neoplasia 14

description:
C38
ccvscin.txt,cinvsn.txt


title: TGFb_72_Nint_R3


title: E14.5epi rep1


title: Kupffer cells isolated from Wild type mouse #5  CCl4-12 h rep4

city: augusta

first: Anatolij

last: Horuzsko

state: Georgia

address: 1410 Laney Walker Boulevard

institute: georgia cancer center

description:
55-BC88-t15_S15_L004
55_BC88_t15-43909172.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

data_processing:
The resultant library was sequenced on Illumina NextSeq 500 using 75 cycles High Output Kit v2 (#FC-404-2005)
Bcl files were converted to fastq files on Basespace (Illumina) and were further processed on NIH Biowulf computer cluster. Briefly, sequences were preprocessed using Trimmomatic (Suppl. Ref.2) and aligned to the mouse genome (mm10 annotation), and reads per gene/feature were counted using STAR 2.5.1a). Resultant expression tables were imported into Partek 6.6, (Partek Inc., St. Louis, MO, USA). Data was log2 transformed, quantile-normalized and analyzed using one-way ANOVA. p-values were corrected for multiple testing and genes with q-values < 0.05 and fold change >|2| were selected for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: gene count

extract_protocol:
Total RNA was isolated with TRIzol® Reagent according to the manufacturer’s recommendations.
An RNA-seq library was prepared using Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina (#015.96) according to the manufacturer’s protocol.

treatment_protocol: 8-week-old male Trem1-deficient or WT mice were injected with one dose of corn oil (control) or CCl4 (2 μl/g, diluted 1:4 in corn oil) and sacrificed at 12 h post-treatment. Kupffer cells were isolated by collagenase type I digestion in vivo and in vitro, HISTOPAQUE®-1083 density gradient centrifugation and MACS magnetic bead separation as follows. Livers were perfused with calcium and magnesium-free 40°C prewarmed HBSS solution and digested with collagenase type I. The cell suspension was filtered through a 70 μm cell strainer and then centrifuged at 50g for 5 min at 4°C to eliminate hepatocytes. Cells remaining in the supernatant were layered on HISTOPAQUE®-1083 and centrifuged at 1000g for 15 min at 4°C without a brake. The non-parenchymal cell fraction was washed once with PBS at 300g  for 10 min at 4°C. Kupffer cells were isolated from the non-parenchymal cell fraction using (i) APC-conjugated rat anti-mouse CD11b and anti-APC magnetic beads and then (ii) the depleted CD11b fraction was stained with APC-conjugated rat anti-mouse F4/80 antibody and anti-APC magnetic beads. Total RNA was isolated with TRIzol® Reagent according to the manufacturer’s recommendations.

tag: age

tag: Sex

value: male

tag: genotype/variation

value: wild type

tag: injected with

value: carbon tetracloride (CCl4)

value: Liver

value: Kupffer cells


title: PANC-1_untreated control_24 hr_rep2

tag: cell line


title: TGFb_72_None_R6

value: Lung


title: TGFb_72_Pirf_R6


title: 371916A05_SLOT03_S01_Green.xys


title: cervical intraepithelial neoplasia 13

description:
C36
ccvscin.txt,cinvsn.txt

tag: disease state

value: cervical intraepithelial neoplasia


title: 371916A02_SLOT03_S01_Green.xys


title: E14.5epi rep2


title: None_72_None_R6


title: Kupffer cells isolated from Wild type mouse #5  CCl4-12 h rep3

description:
55-BC88-t15_S15_L003
55_BC88_t15-43909172.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

tag: cell type


title: TGFb_72_Nint_R4


title: cervical intraepithelial neoplasia 12

description:
C35
ccvscin.txt,cinvsn.txt


title: cervical intraepithelial neoplasia 11

description:
C34
ccvscin.txt,cinvsn.txt


title: Kupffer cells isolated from Wild type mouse #5  CCl4-12 h rep2

description:
55-BC88-t15_S15_L002
55_BC88_t15-43909172.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: 371916A04_SLOT03_S01_Green.xys


title: TGFb_72_None_R4


title: 371916A03_SLOT03_S01_Green.xys


title: TGFb_72_Nint_R2


title: 371727A12_SLOT02_S01_Green.xys


title: Kupffer cells isolated from Wild type mouse #5  CCl4-12 h rep1

description:
55-BC88-t15_S15_L001
55_BC88_t15-43909172.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: cervical intraepithelial neoplasia 9

description:
C31
ccvscin.txt,cinvsn.txt


title: 371727A10_SLOT02_S01_Green.xys


title: 371916A01_SLOT03_S01_Green.xys


title: 371727A09_SLOT02_S01_Green.xys


title: None_72_None_R5


title: 371727A06_SLOT02_S01_Green.xys


title: 371727A08_SLOT02_S01_Green.xys


title: cervical intraepithelial neoplasia 7

description:
C29
ccvscin.txt,cinvsn.txt


title: cervical intraepithelial neoplasia 10

description:
C32
ccvscin.txt,cinvsn.txt


title: Kupffer cells isolated from Wild type mouse #4  CCl4-12 h rep3

description:
54-BC76-t14_S14_L003
54_BC76_t14-43910193.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: TGFb_72_None_R1


title: Kupffer cells isolated from Wild type mouse #4  CCl4-12 h rep2

description:
54-BC76-t14_S14_L002
54_BC76_t14-43910193.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: TGFb_72_Sora_R2


title: cervical intraepithelial neoplasia 5

description:
C27
ccvscin.txt,cinvsn.txt


title: cervical intraepithelial neoplasia 6

description:
C28
ccvscin.txt,cinvsn.txt


title: cervical intraepithelial neoplasia 8

description:
C30
ccvscin.txt,cinvsn.txt


title: cervical intraepithelial neoplasia 4

description:
C26
ccvscin.txt,cinvsn.txt


title: TGFb_72_Pirf_R3


title: Kupffer cells isolated from Wild type mouse #4  CCl4-12 h rep1

description:
54-BC76-t14_S14_L001
54_BC76_t14-43910193.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: 371727A05_SLOT02_S01_Green.xys


title: Kupffer cells isolated from Wild type mouse #4  CCl4-12 h rep4

description:
54-BC76-t14_S14_L004
54_BC76_t14-43910193.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Kupffer cells isolated from Wild type mouse #3  CCl4-12 h rep3

description:
53-BC64-t13_S13_L003
53_BC64_t13-43913176.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: cervical intraepithelial neoplasia 3

description:
C25
ccvscin.txt,cinvsn.txt


title: None_72_None_R3


title: cervical intraepithelial neoplasia 2

description:
C22
ccvscin.txt,cinvsn.txt


title: cervical cancer 7

description:
C53
ccvscin.txt,ccvsn.txt

value: cervical cancer


title: 371727A02_SLOT02_S01_Green.xys


title: Kupffer cells isolated from Wild type mouse #3  CCl4-12 h rep2

description:
53-BC64-t13_S13_L002
53_BC64_t13-43913176.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Kupffer cells isolated from Wild type mouse #3  CCl4-12 h rep4

description:
53-BC64-t13_S13_L004
53_BC64_t13-43913176.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: E18.5epi rep2


title: TGFb_72_Sora_R1


title: 371727A04_SLOT02_S01_Green.xys


title: TGFb_72_None_R5


title: Kupffer cells isolated from Wild type mouse #3  CCl4-12 h rep1

description:
53-BC64-t13_S13_L001
53_BC64_t13-43913176.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Kupffer cells isolated from Wild type mouse #2  CCl4-12 h rep4

description:
52-BC52-t12_S12_L004
52_BC52_t12-43908159.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: None_72_None_R4


title: ImmatureB_ped_2

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

state: PA

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
STAR version 020201 (--alignSJoverhangMin 8)
MAJIQ version 1.05
HTSeq version 0.6.0 (-m intersection-strict)
Genome_build: hg19
Supplementary_files_format_and_content: read counts per gene

extract_protocol:
Mononuclear cells from fresh non-leukemic bone marrow specimens were purified via Ficoll gradient separation.  Bone marrow fractions were separated via flow cytometry directly into RLT lysis buffer. Total RNA was extracted using Qiagen Rneasy Micro spin columns.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

tag: age (yrs)

value: Bone Marrow

tag: purification

value: Ficoll gradient

tag: surface antigen


title: ImmatureB_ped_1

value: female


title: Kupffer cells isolated from Wild type mouse #2  CCl4-12 h rep2

description:
52-BC52-t12_S12_L002
52_BC52_t12-43908159.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: TGFb_72_Pirf_R1

tag: replicate group


title: 371727A03_SLOT02_S01_Green.xys

description: This is a wild sample of Littorina saxatilis crab ecotype

tag: pool

value: RB


title: Kupffer cells isolated from Wild type mouse #2  CCl4-12 h rep1

description:
52-BC52-t12_S12_L001
52_BC52_t12-43908159.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Kupffer cells isolated from Wild type mouse #1  CCl4-12 h rep3

description:
51-BC40-t11_S11_L003
51_BC40_t11-43910192.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: 371727A01_SLOT02_S01_Green.xys

description: This is a wild sample of Littorina saxatilis wave ecotype

tag: ecotype

value: Roncudo


title: cervical intraepithelial neoplasia 1

description:
C21
ccvscin.txt,cinvsn.txt

value: peripheral blood cells


title: Kupffer cells isolated from Wild type mouse #1  CCl4-12 h rep4

description:
51-BC40-t11_S11_L004
51_BC40_t11-43910192.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: TGFb_72_Sora_R6


title: Kupffer cells isolated from Wild type mouse #2  CCl4-12 h rep3

description:
52-BC52-t12_S12_L003
52_BC52_t12-43908159.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: EarlyB_ped_2


title: EarlyB_ped_1


title: Kupffer cells isolated from Trem1-deficient mouse #5  CCl4-12 h rep4

description:
45-BC28-t10_S10_L004
45_BC28_t10-43917084.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: None_0_None_R1


title: TGFb_72_Sora_R4


title: None_0_None_R6


title: ImmatureB_2

source_name: ImmatureB


title: Kupffer cells isolated from Wild type mouse #1  CCl4-12 h rep1

description:
51-BC40-t11_S11_L001
51_BC40_t11-43910192.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Kupffer cells isolated from Trem1-deficient mouse #5  CCl4-12 h rep3

description:
45-BC28-t10_S10_L003
45_BC28_t10-43917084.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: ImmatureB_1


title: None_0_None_R4


title: TGFb_72_Nint_R1


title: TGFb_72_None_R2


title: TGFb_72_Sora_R3


title: TGFb_72_Sora_R5


title: TGFb_72_Nint_R5


title: TGFb_72_Pirf_R5


title: Kupffer cells isolated from Trem1-deficient mouse #4  CCl4-12 h rep3

description:
44-BC16-t9_S9_L003
44_BC16_t9-43919079.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: EarlyB_2

source_name: EarlyB


title: TGFb_72_Pirf_R2


title: Kupffer cells isolated from Trem1-deficient mouse #4  CCl4-12 h rep4

description:
44-BC16-t9_S9_L004
44_BC16_t9-43919079.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Control, wild type (untrained) 2

data_processing:
For the RNA-Seq data analysis Tophat 2.0.13, bowtie 2.1.0 , samtool 0.1.7 and cufflinks 1.3.0  were used. The mm10-bowtie2 index was downloaded from http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml.  RefSeq geneTracks and GTF-files for the rn5 and mm10 genome assembly were downloaded from UCSC genome browser. Common gene ids in the GTF-files were matched to individual transcript_ids using the corresponding official symbols obtained from the geneTracks files.
Reads were aligned to the mm10  genome using Tophat with the option '--no-novel-juncs' and the refSeq-GTF-file (the option '--solexa1.3-quals' was additionally chosen in case of the rat samples).
Differentially expressed genes were identified using Cuffdiff with the options '--upper-quartile-norm', '--frag-bias-correct' against the rn5 genome and '--multi-read-correct' and the refSeq-GTF-file.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Brain hippocampus

growth_protocol: Wt1∆ mice expressed a truncated and non-functional Wilm's Tumor 1 (WT1) protein strating at P21.

extract_protocol:
The brains were dissected from naïve untrained animals (Wt1∆ mice and wild type littermates, n=2 each group) and the hippocampus was dissected and flash frozen immediately. RNA was harvested using Trizol reagent.The seq library was prepared using TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA) and approximately 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Although the recombination allele is expressed in the forebrain of these animals, we dissected out their hippocampi and studied their hippocampal expression profile.

value: C57BL6 background

value: hippocampus

value: 3-6 months old

tag: genotype


title: Kupffer cells isolated from Trem1-deficient mouse #5  CCl4-12 h rep1

description:
45-BC28-t10_S10_L001
45_BC28_t10-43917084.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: male

tag: tissue


title: Kupffer cells isolated from Wild type mouse #1  CCl4-12 h rep2

description:
51-BC40-t11_S11_L002
51_BC40_t11-43910192.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

tag: strain

value: wild type


title: Kupffer cells isolated from Trem1-deficient mouse #3  CCl4-12 h rep2

description:
43-BC04-t8_S8_L002
43_BC04_t8-43910191.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

tag: age

value: carbon tetracloride (CCl4)


title: Kupffer cells isolated from Trem1-deficient mouse #3  CCl4-12 h rep4

description:
43-BC04-t8_S8_L004
43_BC04_t8-43910191.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

tag: Sex

value: Liver


title: Kupffer cells isolated from Trem1-deficient mouse #3  CCl4-12 h rep1

description:
43-BC04-t8_S8_L001
43_BC04_t8-43910191.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

tag: genotype/variation

value: Kupffer cells


title: Kupffer cells isolated from Trem1-deficient mouse #5  CCl4-12 h rep2

description:
45-BC28-t10_S10_L002
45_BC28_t10-43917084.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

tag: injected with


title: Kupffer cells isolated from Trem1-deficient mouse #2  CCl4-12 h rep4

description:
42-BC87-t7_S7_L004
42_BC87_t7-43921083.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Kupffer cells isolated from Trem1-deficient mouse #4  CCl4-12 h rep1

description:
44-BC16-t9_S9_L001
44_BC16_t9-43919079.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Wt1∆ (untrained) 1

value: Nrl-/-


title: Kupffer cells isolated from Trem1-deficient mouse #4  CCl4-12 h rep2

description:
44-BC16-t9_S9_L002
44_BC16_t9-43919079.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Myotubes Ash1L silenced Rep1

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description:
Mouse C3H muscle myotubes
limma.dge_results.Ash1L_knock_down.xls

data_processing:
alignment with STAR_2.5.3a (--outFilterMismatchNmax 14)
counting reads with featureCounts
Differential Gene Expression with LIMMA
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: bigWig from deduplicated bam files containing the coverage data from the deduplicated bam alignments for ChIP-Seq data
Supplementary_files_format_and_content: xls with 2 sheet tables with differential expression results from LIMMA for myoblasts and myotubes (kd vs wt)
Supplementary_files_format_and_content: bed file for Ash1L peaks called with MACS2, individual replicates and merged (universe)

growth_protocol: Murine C2C12 cells were cultured in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
Total RNA was extracted using RNA spin columns (PureLink RNA Mini Kit, Ambion). RNA quantification as carried out using Qubit Fluorimetric Quantification (Life Technologies) and 500ng of RNA were used to prepare the library.
QuantSeq 3’ mRNA-Seq Library Prep Kit. The procedure was initiated by oligo-dT priming, then the First-strand synthesis and RNA removal was followed by random-primed synthesis of the complementary strand. The resulting double-stranded cDNA was purified with magnetic beads, in order to remove all reaction components. The adapter sequences were added by library PCR amplification, the proper cycle number was previously determined by qPCR. The library was purified from PCR components using purification beads

treatment_protocol: For differentiation experiments, C2C12 cells were plated in collagen-coated dishes and were differentiated for 3 days in DMEM containing 2% donor horse serum (EuroClone).

tag: treatment 1

value: SMARTpool:ON-TARGETplus ASH1L siRNA L-041891 (mouse) Dharmacon

tag: treatment 2

value: DMEM containing 2% donor horse serum (EuroClone)_ 72 hours (day3)

value: myotubes


title: Myoblasts Ash1L silenced Rep3

description:
Mouse C3H muscle myoblast
limma.dge_results.Ash1L_knock_down.xls

tag: cell type

value: myoblasts


title: EarlyB_1

tag: gender

value: female

value: Bone Marrow

value: Ficoll gradient


title: Myoblasts Ash1L silenced Rep2


title: Kupffer cells isolated from Trem1-deficient mouse #3  CCl4-12 h rep3

description:
43-BC04-t8_S8_L003
43_BC04_t8-43910191.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: P493-6_hnRNPA2-KD

data_processing:
STAR version 020201 (--alignSJoverhangMin 8)
MAJIQ version 1.05
HTSeq version 0.6.0 (-m intersection-strict)
Genome_build: hg19
Supplementary_files_format_and_content: counts_tmm_cpm.txt, RNA-seq was quantified by HTSeq using the ENSEMBLE gene annotations. Normalization of the raw counts was then performed using the trimmed mean of M-values (TMM) with counts per million (CPM) reported.

growth_protocol: P493-6 cells were grown in tetracycline free RPMI

extract_protocol:
Total RNA was extracted using Qiagen Rneasy spin columns.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: P493-6 cells were transfected with either non-targeting control (133nM) or hnRNPA1 targeting (300nM) siRNA by electroporation with Amaxa program O-006.

tag: cell line

value: EBV-transformed B-lymphoblastoid cells

value: hnRNPA1 knockdown


title: Control, wild type (untrained) 1

value: C57BL6 background

value: hippocampus


title: Myoblasts Ash1L silenced Rep1


title: Kupffer cells isolated from Trem1-deficient mouse #2  CCl4-12 h rep2

description:
42-BC87-t7_S7_L002
42_BC87_t7-43921083.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: male


title: P493-6_Ctrl2

value: hnRNPA1 Ctrl


title: P493-6_Ctrl1


title: PHL8414

source_name: pediatric B-cell acute lymphoblastic leukemias

extract_protocol:
Mononuclear cells from peripheral blood or fresh bone marrow specimens were purified via Ficoll gradient separation.  Total RNA was extracted using Qiagen Rneasy spin columns.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age at diagnosis in years

tag: tumor stage

value: Relapse

tag: risk status

value: high

value: peripheral blood or bone marrow

value: mononuclear cells

tag: purification


title: PHL50

value: Diagnosis


title: Myotubes Not Silenced Rep3

value: Non-Targeting Pool D-001810; Dharmacon

value: DMEM containing 2% donor horse serum (EuroClone)_ 72 hours (day3)


title: Myotubes Not Silenced Rep2

value: myotubes


title: Myotubes Ash1L silenced Rep2

value: SMARTpool:ON-TARGETplus ASH1L siRNA L-041891 (mouse) Dharmacon


title: P493-6_hnRNPA1-KD


title: PHL222


title: Kupffer cells isolated from Trem1-deficient mouse #1  CCl4-12 h rep3

description:
41-BC75-t6_S6_L003
41_BC75_t6-43909171.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: carbon tetracloride (CCl4)

value: Liver

value: Kupffer cells


title: PHL54

value: standard

value: Ficoll gradient


title: Wt1∆ (untrained) 2

value: C57BL6 background

value: hippocampus

value: 3-6 months old

value: Nrl-/-


title: Myotubes Ash1L silenced Rep3


title: PHL161

value: male

value: high


title: PHL158

value: female

value: peripheral blood or bone marrow

value: mononuclear cells


title: Kupffer cells isolated from wild type mouse #5 oil-12 h  (control) rep4

description:
35-BC63-t5_S5_L004
35_BC63_t5-43918078.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: wild type

value: oil (control)


title: Kupffer cells isolated from Trem1-deficient mouse #2  CCl4-12 h rep1

description:
42-BC87-t7_S7_L001
42_BC87_t7-43921083.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: PHL8494

value: Diagnosis


title: PHL540


title: Kupffer cells isolated from Trem1-deficient mouse #2  CCl4-12 h rep3

description:
42-BC87-t7_S7_L003
42_BC87_t7-43921083.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: carbon tetracloride (CCl4)


title: Kupffer cells isolated from Trem1-deficient mouse #1  CCl4-12 h rep4

description:
41-BC75-t6_S6_L004
41_BC75_t6-43909171.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: Liver


title: PHL151


title: Kupffer cells isolated from Trem1-deficient mouse #1  CCl4-12 h rep1

description:
41-BC75-t6_S6_L001
41_BC75_t6-43909171.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: Kupffer cells


title: PHL145


title: Myoblasts Not Silenced Rep3

value: Non-Targeting Pool D-001810; Dharmacon

value: myoblasts


title: Histone3 ChIP-Seq

description: Mouse C3H muscle myoblast

data_processing:
trimming of reads with cutadapt 1.17
alignment with bwa mem 0.7.21
remove duplicates; filter for properly paired (Picard Tools and samtools)
peak calling with MACS8
merge peaks with bedTools
bigWig from filtered bam using deeptools8
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: bigWig from deduplicated bam files containing the coverage data from the deduplicated bam alignments for ChIP-Seq data
Supplementary_files_format_and_content: xls with 2 sheet tables with differential expression results from LIMMA for myoblasts and myotubes (kd vs wt)
Supplementary_files_format_and_content: bed file for Ash1L peaks called with MACS2, individual replicates and merged (universe)

extract_protocol:
For DNA purification, the QIAquick PCR purification kit was used (Qiagen). DNA was further sonicated after elution, using the Ultra-Sonicator E220 (CovarisTM) at 10 V for 90 seconds, and the fragments sizes were evaluated by the Bioanalyzer (Agilent Technologies)
Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences)

value: DMEM containing 2% donor horse serum (EuroClone)_ 24 hours (day1)

tag: chip antibody

value: Rabbit anti-H3 (#Ab1791; Abcam)


title: Kupffer cells isolated from wild type mouse #4 oil-12 h  (control) rep4

description:
34-BC51-t4_S4_L004
34_BC51_t4-43915164.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: ChIP INPUT control

description: Mouse C3H muscle myoblast

data_processing:
trimming of reads with cutadapt 1.18
alignment with bwa mem 0.7.22
remove duplicates; filter for properly paired (Picard Tools and samtools)
peak calling with MACS9
merge peaks with bedTools
bigWig from filtered bam using deeptools9
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: bigWig from deduplicated bam files containing the coverage data from the deduplicated bam alignments for ChIP-Seq data
Supplementary_files_format_and_content: xls with 2 sheet tables with differential expression results from LIMMA for myoblasts and myotubes (kd vs wt)
Supplementary_files_format_and_content: bed file for Ash1L peaks called with MACS2, individual replicates and merged (universe)


title: Myoblasts Not Silenced Rep1


title: PHL156

value: Ficoll gradient


title: Myotubes Not Silenced Rep1

value: DMEM containing 2% donor horse serum (EuroClone)_ 72 hours (day3)

value: myotubes


title: H3K36me2 ChIP-Seq Rep2

description: Mouse C3H muscle myoblast

data_processing:
trimming of reads with cutadapt 1.15
alignment with bwa mem 0.7.19
remove duplicates; filter for properly paired (Picard Tools and samtools)
peak calling with MACS6
merge peaks with bedTools
bigWig from filtered bam using deeptools6
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: bigWig from deduplicated bam files containing the coverage data from the deduplicated bam alignments for ChIP-Seq data
Supplementary_files_format_and_content: xls with 2 sheet tables with differential expression results from LIMMA for myoblasts and myotubes (kd vs wt)
Supplementary_files_format_and_content: bed file for Ash1L peaks called with MACS2, individual replicates and merged (universe)

value: Rabbit anti-dimethyl-Histone H3 (Lys 36) (#07-369; Millipore)


title: PHL149

value: female

value: high


title: IgG ChIP-Seq control

description: Mouse C3H muscle myoblast

data_processing:
trimming of reads with cutadapt 1.19
alignment with bwa mem 0.7.23
remove duplicates; filter for properly paired (Picard Tools and samtools)
peak calling with MACS10
merge peaks with bedTools
bigWig from filtered bam using deeptools10
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: bigWig from deduplicated bam files containing the coverage data from the deduplicated bam alignments for ChIP-Seq data
Supplementary_files_format_and_content: xls with 2 sheet tables with differential expression results from LIMMA for myoblasts and myotubes (kd vs wt)
Supplementary_files_format_and_content: bed file for Ash1L peaks called with MACS2, individual replicates and merged (universe)

value: Rabbit IgG (#011-000-003; Jackson Immunoresearch)


title: Kupffer cells isolated from wild type mouse #5 oil-12 h  (control) rep3

description:
35-BC63-t5_S5_L003
35_BC63_t5-43918078.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: male

value: wild type


title: Kupffer cells isolated from wild type mouse #5 oil-12 h  (control) rep1

description:
35-BC63-t5_S5_L001
35_BC63_t5-43918078.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: oil (control)


title: Kupffer cells isolated from wild type mouse #4 oil-12 h  (control) rep2

description:
34-BC51-t4_S4_L002
34_BC51_t4-43915164.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: PHL163

value: Diagnosis

value: standard

value: peripheral blood or bone marrow

value: mononuclear cells


title: Kupffer cells isolated from Trem1-deficient mouse #1  CCl4-12 h rep2

description:
41-BC75-t6_S6_L002
41_BC75_t6-43909171.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: carbon tetracloride (CCl4)

value: Liver

value: Kupffer cells


title: Myoblasts Not Silenced Rep2

value: Non-Targeting Pool D-001810; Dharmacon

value: myoblasts


title: Kupffer cells isolated from wild type mouse #5 oil-12 h  (control) rep2

description:
35-BC63-t5_S5_L002
35_BC63_t5-43918078.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: PHL1074

value: Ficoll gradient


title: H3K36me2 ChIP-Seq Rep3

description: Mouse C3H muscle myoblast

data_processing:
trimming of reads with cutadapt 1.16
alignment with bwa mem 0.7.20
remove duplicates; filter for properly paired (Picard Tools and samtools)
peak calling with MACS7
merge peaks with bedTools
bigWig from filtered bam using deeptools7
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: bigWig from deduplicated bam files containing the coverage data from the deduplicated bam alignments for ChIP-Seq data
Supplementary_files_format_and_content: xls with 2 sheet tables with differential expression results from LIMMA for myoblasts and myotubes (kd vs wt)
Supplementary_files_format_and_content: bed file for Ash1L peaks called with MACS2, individual replicates and merged (universe)

value: DMEM containing 2% donor horse serum (EuroClone)_ 24 hours (day1)

value: Rabbit anti-dimethyl-Histone H3 (Lys 36) (#07-369; Millipore)


title: Kupffer cells isolated from wild type mouse #4 oil-12 h  (control) rep3

description:
34-BC51-t4_S4_L003
34_BC51_t4-43915164.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Kupffer cells isolated from wild type mouse #2 oil-12 h  (control) rep4

description:
32-BC27-t2_S2_L004
32_BC27_t2-43913173.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: PHL1200


title: Kupffer cells isolated from wild type mouse #3 oil-12 h  (control) rep4

description:
33-BC39-t3_S3_L004
33_BC39_t3-43913174.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: H3K36me2 ChIP-Seq Rep1

description: Mouse C3H muscle myoblast

data_processing:
trimming of reads with cutadapt 1.14
alignment with bwa mem 0.7.18
remove duplicates; filter for properly paired (Picard Tools and samtools)
peak calling with MACS5
merge peaks with bedTools
bigWig from filtered bam using deeptools5
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: bigWig from deduplicated bam files containing the coverage data from the deduplicated bam alignments for ChIP-Seq data
Supplementary_files_format_and_content: xls with 2 sheet tables with differential expression results from LIMMA for myoblasts and myotubes (kd vs wt)
Supplementary_files_format_and_content: bed file for Ash1L peaks called with MACS2, individual replicates and merged (universe)


title: Kupffer cells isolated from wild type mouse #2 oil-12 h  (control) rep1

description:
32-BC27-t2_S2_L001
32_BC27_t2-43913173.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Ash1L ChIP-Seq Rep2

description: Mouse C3H muscle myoblast

data_processing:
trimming of reads with cutadapt 1.12
alignment with bwa mem 0.7.16
remove duplicates; filter for properly paired (Picard Tools and samtools)
peak calling with MACS3
merge peaks with bedTools
bigWig from filtered bam using deeptools3
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: bigWig from deduplicated bam files containing the coverage data from the deduplicated bam alignments for ChIP-Seq data
Supplementary_files_format_and_content: xls with 2 sheet tables with differential expression results from LIMMA for myoblasts and myotubes (kd vs wt)
Supplementary_files_format_and_content: bed file for Ash1L peaks called with MACS2, individual replicates and merged (universe)

value: Rabbit anti-Ash1L (#A301-749A; Bethyl laboratories)


title: PHL102

value: female


title: Kupffer cells isolated from wild type mouse #1 oil-12 h  (control) rep4

description:
31-BC15-t1_S1_L004
31_BC15_t1-43911195.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: male


title: PHL11

value: Relapse


title: PHL105


title: Kupffer cells isolated from wild type mouse #1 oil-12 h  (control) rep3

description:
31-BC15-t1_S1_L003
31_BC15_t1-43911195.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

value: wild type

value: oil (control)


title: KI_11

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

data_processing:
quality checked for potential sequencing issues and contaminants using FastQC
Sequence reads were clipped from the invariant portions of both 5’ and 3’ adapters to remove the 4 randomized nucleotides in the adapters
Sequencing analysis was done using MAP-RSeq workflow developed at the Mayo Clinic Bioinformatics Core
RNA-seq results were included if ≥100,000 reads mapped to the  transcriptome, and the number of reads mapping to annotated transcripts represented at least 50% of the number of reads mapping to the murine genome
Genome_build: mm10

source_name: liver

extract_protocol:
RNA was extracted from mouse livers using TRIzol.
Illumina Tru-Seq libraries and indexed using NEBNext Small RNA Library prep kit

treatment_protocol: response to PD-1

tag: background strain

value: FVB/NJ

tag: treatment

tag: treatment reponse

value: non treatment

value: liver

tag: disease state

value: HCC induced by MET/ β-catenin expression


title: Ash1L ChIP-Seq Rep3

description: Mouse C3H muscle myoblast

data_processing:
trimming of reads with cutadapt 1.13
alignment with bwa mem 0.7.17
remove duplicates; filter for properly paired (Picard Tools and samtools)
peak calling with MACS4
merge peaks with bedTools
bigWig from filtered bam using deeptools4
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: bigWig from deduplicated bam files containing the coverage data from the deduplicated bam alignments for ChIP-Seq data
Supplementary_files_format_and_content: xls with 2 sheet tables with differential expression results from LIMMA for myoblasts and myotubes (kd vs wt)
Supplementary_files_format_and_content: bed file for Ash1L peaks called with MACS2, individual replicates and merged (universe)


title: Kupffer cells isolated from wild type mouse #3 oil-12 h  (control) rep2

description:
33-BC39-t3_S3_L002
33_BC39_t3-43913174.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

tag: strain

tag: age

tag: Sex

tag: tissue

value: Liver


title: Kupffer cells isolated from wild type mouse #3 oil-12 h  (control) rep3

description:
33-BC39-t3_S3_L003
33_BC39_t3-43913174.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

tag: genotype/variation

tag: injected with

value: Kupffer cells


title: Kupffer cells isolated from wild type mouse #2 oil-12 h  (control) rep3

description:
32-BC27-t2_S2_L003
32_BC27_t2-43913173.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count

tag: cell type


title: Kupffer cells isolated from wild type mouse #4 oil-12 h  (control) rep1

description:
34-BC51-t4_S4_L001
34_BC51_t4-43915164.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Kupffer cells isolated from wild type mouse #1 oil-12 h  (control) rep1

description:
31-BC15-t1_S1_L001
31_BC15_t1-43911195.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: Ash1L ChIP-Seq Rep1

description: Mouse C3H muscle myoblast

data_processing:
trimming of reads with cutadapt 1.11
alignment with bwa mem 0.7.15
remove duplicates; filter for properly paired (Picard Tools and samtools)
peak calling with MACS2
merge peaks with bedTools
bigWig from filtered bam using deeptools2
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: bigWig from deduplicated bam files containing the coverage data from the deduplicated bam alignments for ChIP-Seq data
Supplementary_files_format_and_content: xls with 2 sheet tables with differential expression results from LIMMA for myoblasts and myotubes (kd vs wt)
Supplementary_files_format_and_content: bed file for Ash1L peaks called with MACS2, individual replicates and merged (universe)

tag: treatment 1


title: Kupffer cells isolated from wild type mouse #2 oil-12 h  (control) rep2

description:
32-BC27-t2_S2_L002
32_BC27_t2-43913173.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: RNAseq_POD5_SSC2

city: Stanford

first: Howard

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Dermatology

institute: Stanford University

data_processing:
Reads were mapped to the mm9 genome using TopHat and assigned to transcripts from UCSC and RefSeq.
FeatureCounts was used to count the number of reads per transcript and remove reads mapping to tRNA and rRNA.
DESeq2 was used to calculate differential expression between conditions.
Genome_build: mm9
Supplementary_files_format_and_content: *.counts.featureCounts.txt: Tab-delimited tables with Gene name, gene length, counts, rpk, fpkm, tpm, and percent.

source_name: Mouse mandible

growth_protocol: in vivo

extract_protocol:
RNA was extracted from FACS-sorted SSCs, BCSPs, and OPs using the Qiagen RNeasy micro kit. Cells were sorted into 350-700 uL buffer RLT plus and RNA was extracted following kit instructions.
1.5 ng PolyA+ RNA was reverse transcribed following the SmartSeq protocol. 1 ng cDNA/sample was then transposed with Nextera Amplicon Tagment Mix to fragment and add adapters. Libraries were then PCR amplified for 11 cycles and sequenced on an Illumina Nextseq.

treatment_protocol: Same as ATAC-seq.

tag: strain/background

tag: gender

tag: tissue source

value: mandible

value: SSC

value: Mandibular Fracture

tag: post-operative day


title: Kupffer cells isolated from wild type mouse #1 oil-12 h  (control) rep2

description:
31-BC15-t1_S1_L002
31_BC15_t1-43911195.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: KI_30

value: non-responder


title: Kupffer cells isolated from wild type mouse #3 oil-12 h  (control) rep1

description:
33-BC39-t3_S3_L001
33_BC39_t3-43913174.cat.fastq.gz.fqReadsPerGene.out.tab.bl:Count


title: 516143A12_2um_20._Red_al

type: genomic

description: DNA pool fropm British populations used in the array design

hyb_protocol: For each sample 20 μg of Cy3 (and Cy5) labeled cDNA was resuspended in 12 μL of hybridization solution, of which 6 μL was applied onto a subarray. Samples were randomly distributed in the subarrays.   Hybridization was carried out at 42°C for 72 h on a NimbleGen Hybridization System with continuous mixing. After hybridization, the arrays were washed in buffers of various stringencies using the NimbleGen Washing kit.

scan_protocol: Arrays were scanned using an Agilent G2565AA microarray scanner (Agilent Technologies) with a resolution of 2 μm.

data_processing:
For the analysis of variation in genomic sequence, each subarray hosted the DNA of one single individual and the DNA of a common reference sample. The data from scanning pictures generated by NimbleScan were parsed using ringo   (Toedling et al. 2007.BMC Bioinformatics 8, p. 221), an R/Bioconductor package.
The signal intensity data for each channel was corrected for the local background signal using the normexp + offset method (Ritchie et al. 2007. Bioinformatics 23: 2700-2707), log2-transformed, and quantile normalized using the method proposed   by Yang and Thome 2003. Notes Monogr Ser. 40: 403-418 for two channels, as implemented in the package limma for R/Bioconductor (Smyth 2005. Linear Models for Microarray Data). We performed a probe-level data analysis to test DNA sequence   differences between the distinct gene fragments included in a probe set and the hybridized DNA. To exclude probes that were not accurately detected in the array, probes with an average hybridization signal lower than the “background signal” of each   channel were disregarded. Only genes containing probes that simultaneously passed genome and expression profiling filters were used in the subsequent analyses.

source_name: Foot muscle CGH

label_protocol: The NimbleGen/Roche Dual label kit was used to label the reference sample (Cy5 dye) and the DNA of each specimen (Cy3 dye) following manufacturer´s instructions.

extract_protocol: Genomic DNA was isolated from the foot muscle tissue of single snails using a CTAB extraction method (Wilding et al. 2001. Evol Biol. 14: 611-619) modified to include RNAse treatment. DNA samples were further cleaned with NucleoSpin columns   (Macherey- Nagel) following manufacturer´s instructions. DNA purity was assessed using a NanoDrop spectrophotometer (NanoDrop Tech. Inc., Wilmington, DE). All extractions were standardized to 100ng/μL after checking their integrity in agarose gels.

tag: sample number

tag: ecotype

value: SU

tag: locality

value: Silleiro

tag: reference

value: DNA pool of 100 snails from two British L. saxatilis populations (Dunvar and Thornwick)


title: KI_37

tag: background strain

tag: treatment

tag: treatment reponse

tag: disease state


title: RNAseq_POD5_SSC1

value: male


title: 516143A10_2um_20._Red_al

value: Burela


title: KI_26

tag: tissue


title: RNAseq_POD5_OP2

value: OP


title: KI_32


title: KI_29

value: responder


title: 516143A08_2um_20._Red_al

value: RB


title: 516143A07_2um_20._Red_al

value: Roncudo


title: 516143A06_2um_20._Red_al


title: KI_16

value: FVB/NJ

value: liver


title: KI_13

value: HCC induced by MET/ β-catenin expression


title: 516143A11_2um_20._Red_al


title: 516143A09_2um_20._Red_al


title: RNAseq_POD5_OP1


title: RNAseq_POD15_Fx_SSC2


title: KI_9


title: RNAseq_POD5_BCSP1

value: BCSP


title: KI_3


title: 516143A03_2um_20._Red_al


title: KI_1


title: RNAseq_POD5_BCSP2

value: mandible


title: RNAseq_POD15_Fx_SSC1

value: SSC


title: RNAseq_POD15_Fx_OP2

value: Mandibular Fracture


title: 516143A05_2um_20._Red_al


title: KO_CNS2_rep2

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

data_processing:
The sequenced reads were trimmed by quality (Phred quality score cutoff 20) using Trim Galore (version 0.4.2, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with Cutadapt (version1.12).
The trimmed reads were mapped to amplicon sequences using Bismark (version 0.17.0; Felix and Simon, Bioinformatics 2011).
The ratio of methylated and unmethylated CpG at each CpG site was calculated from the Bismark analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Text file (methylation percentage)

source_name: Foxp1 deficient itreg cells

growth_protocol: CD4+ cells were prepared from Foxp1+/+Foxp3IRES-YFP-Cre or Foxp1fl/flFoxp3IRES-YFP-Cre by negative selection of total lypmphocyte from Spleen and peripheral lymph nodes using MACS LD columns (Miltenyi Biotec). The enriched cells were sorted using MOFLO ASTRIOS Flow Cytometer System (Beckman Coulter) to isolate naïve CD4+CD62Lhi (YFP- for Foxp3IRES-YFP-Cre reporter mice) T-cells from the total CD4+ cells. The purity of sorted T- cell populations routinely exceeded 99%. These cells were activated with plate bound anti-CD3(1μg/ml) and anti-CD28 (1μg/ml) in the presence of 2ng/ml premium grade human TGFβ (Miltenyi Biotec) and 50 IU/ml of recombinant human IL2 (Miltenyi Biotec) and cultured in complete RPMI1640. For prolonged cultures till 6 to 8 days, cells were split daily, starting from 2 days after TGFβ treatment in complete RPMI1640 supplemented with 50 IU/ml IL2.

extract_protocol: Total genomic DNA from in vitro induced Treg cells at day 7 in culture was isolated using Accuprep Genomic DNA Extraction Kit (Bioneer). Bisulfite conversion of DNA was performed with MethylEasy Xceed kit (Human Genetic Signature). PCR amplicon from loci of interest was generated from this treated DNA using the following primers: -1.5kb (forward - TGTTAGGGTATTAAAGGTTGGAAGTT and reverse - CCAATTTTCCTAAAACCAACAATAT), CNS2 (forward - ATTTGAATTGGATATGGTTTGT and reverse - AACCTTAAACCCCTCTAACATC), and Promoter (forward - TATATTTTTAGATGATTTGTAAAGGGTAAA and reverse - ATCAACCTAACTTATAAAAAACTACCACAT). After electrophoresis to confirm the size these PCR products were then purified from agarose gel using HiGene Gel and PCR purification system (Biofact). Library was contructed using manufacture's protocol accompanying the kit TruSeq Nano DNA LT Library Preparation Kit - Set A : FC-121-4001,  Nextera DNA Library Prep Kit (24 samples) : FC-121-1030, Nextera Index Kit (24 indexes, 96 samples) : FC-121-1011.

treatment_protocol: iTreg cells were induced by tratment of TGFb in presence of IL2 and plate bound anti-CD3, anti-CD28 as mentioned in the growth protocol.

tag: strain

value: In vitro induced iTreg cells by TGFb, sorted 7 days after induction.

tag: genotype


title: 516142A12_2um_20._Red_al


title: 516143A01_2um_20._Red_al


title: RNAseq_POD15_Fx_BCSP2

tag: cell type


title: KO_PRO_rep2


title: WT_PRO_rep2

source_name: Foxp1 suffiecient itreg cells

value: wild type


title: 516143A02_2um_20._Red_al

value: SU


title: RNAseq_POD15_Fx_BCSP1


title: 516142A11_2um_20._Red_al

value: DNA pool of 100 snails from two British L. saxatilis populations (Dunvar and Thornwick)


title: RNAseq_POD15_DO_SSC2

value: male

value: Mandibular Distraction


title: WT_CNS2_rep2


title: 516142A10_2um_20._Red_al

value: Silleiro


title: RNAseq_POD15_DO_OP1

value: OP


title: WT_-1.5kb_rep2


title: KO_CNS2_rep1


title: RNAseq_POD15_Fx_OP1


title: RNAseq_POD15_DO_BCSP2


title: KO_-1.5kb_rep2


title: 516142A06_2um_20._Red_al


title: 516142A04_2um_20._Red_al


title: RNAseq_POD15_DO_BCSP1


title: RNAseq_POD10_Fx_SSC2


title: WT_CNS2_rep1


title: KO_-1.5kb_rep1


title: 516142A08_2um_20._Red_al

value: RB


title: RNAseq_POD15_DO_OP2


title: WT_PRO_rep1


title: 516142A02_2um_20._Red_al


title: 516142A01_2um_20._Red_al

value: Burela


title: RNAseq_POD10_Fx_OP2


title: RNAseq_POD10_Fx_SSC1


title: KO_PRO_rep1


title: 516142A03_2um_20._Red_al


title: 515539A10_SLOT02_S01_Red_al


title: 515539A09_SLOT02_S01_Red_al


title: RNAseq_POD10_Fx_OP1


title: RNAseq_POD10_Fx_BCSP1


title: 515539A12_SLOT02_S01_Red_al

value: Roncudo


title: RNAseq_POD10_Fx_BCSP2


title: WT_-1.5kb_rep1


title: dKO_Input_rep2

city: LEICESTER

first: RICHARD

middle: DAVID WILLIAM

last: KELLY

address: LANCASTER ROAD

department: BIOCHEMISTRY

country: United Kingdom

institute: UNIVERSITY OF LEICESTER

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using BWA-mem.
Reads were filtered by quality, and deduplicated.
Peaks were called using MACS (version 2.1.1.20160309) with default parameters.
Heat maps, computeMatrix and bamCoverage were generated using deepTools (version 2.5.4).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.bw: bigWig files

source_name: embryonic stem cell

growth_protocol: ESCs were plated onto gelatin coated dish in 15% FCS and LIF (M15).

extract_protocol:
Briefly, cell pellets were swollen in 0.3M Sucrose, 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 15mM Tris-HCl, pH 7.5 and EDTA-free protease inhibitors (Sigma-Aldrich, UK). Nuclei were extracted using an equal volume of 0.3M sucrose, 60 mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 15mM Tris-HCl, pH 7.5, 0.4% NP-40, 0.5 mM DTT and protease inhibitors at 4C for 10 min. The cell suspension was applied to a sucrose cushion containing 1.2M sucrose, 60 mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 15 mM Tris-HC pH 7.5 and centrifuge at 1500 rcf for 30min at 4C. Nuclei were resuspended in MNase Digestion Buffer containing 0.32M sucrose, 50mM Tris-HCl, pH 7.5, 4mM MgCl2, 1mM CaCl2 and protease inhibitors. Chromatin was then digested using 2UN/ml-1 Micrococcal nuclease (MNase) for 10-12min at 37C on a thermal shaker. The reaction was stopped with 5 μM EDTA/EGTA and cleared at 20,000 rcf for 10 min at 4C. The supernatant (S1 fraction) was stored a 4C and the pellet was dialysed with 1mM Tris-HCl, pH 7.5 and 0.2mM EDTA overnight at 4C. The dialysed pellet (S2 fraction) was cleared at 20,000 rcf for 10 min at 4C and combined with S1 fraction for immunoprecipitation. Chromatin was immunoprecipitated using 8 μg H3K18ac (Catalog No: 39755; Active Motif) or 8 μg H3K18cr (PTM-Biolabs 517) conjugated to 50 uL Dynabeads Protein G overnight at 4C. Bead were washed for 5min in wash buffer A (50mM Tris-HCl, pH 7.5, 10mM EDTA, 75mM NaCl), wash buffer B (50mM Tris-HCl, pH 7.5, 10mM EDTA, 125mM NaCl), and wash buffer C (50mM Tris-HCl, pH 7.5, 10mM EDTA, 175mM NaCl). DNA was purified using IPure kit v2 (Diagenode, Belgium) according to the manufacturer’s instructions.
For next-generation sequencing, automated library preparation were prepared from 10 ng of ChIP and input DNA using the Apollo prep system (Wafergen, PrepX ILMN 32i, 96 sample kit) and standard Illumina multiplexing adapters following manufacturer’s protocol up to pre-PCR amplification. Libraries were PCR amplified (18 cycles) on a Tetrad (Bio-Rad) using the NEBNext High-Fidelity 2X PCR Master Mix (NEB) and in-house (Oxford Genomics Centre) dual indexing primers (based on DOI: 10.1186/1472-6750-13-104).

treatment_protocol: To induce the deletion of Hdac1/2, DKO ES cells were cultured with 1 μM tamoxifen (OHT) for 24h to activate the CreER fusion protein. Ctrl samples were untreated. dKO samples were sampled 3 days after the addition of OHT.

value: embryonic stem cells

tag: genotype/variation

value: HDAC1 and HDAC2 conditional knockout

value: 1 uM tamoxifen (OHT) for 24h followed by 2 days culture in M15

tag: chip antibody


title: 515539A08_SLOT02_S01_Red_al


title: dKO_H3K18cr_rep2

tag: strain/background

value: H3K18cr (PTM-Biolabs 517)


title: 515539A06_SLOT02_S01_Red_al


title: dKO_H3K18cr_rep1


title: 515539A04_SLOT02_S01_Red_al


title: 515539A05_SLOT02_S01_Red_al


title: 515539A11_SLOT02_S01_Red_al


title: dKO_H3K18ac_rep1

value: H3K18ac (Catalog No:39755; Active Motif)


title: 515539A07_SLOT02_S01_Red_al


title: RNAseq_POD10_DO_OP2

tag: gender

tag: tissue source

value: mandible


title: RNAseq_POD15_DO_SSC1

value: SSC

tag: post-operative day


title: RNAseq_POD10_DO_SSC1


title: RNAseq_POD10_DO_SSC2


title: dKO_Input_rep1


title: Ctrl_Input_rep2

value: untreated


title: RNAseq_POD10_DO_OP1


title: Ctrl_H3K18cr_rep2


title: Ctrl_H3K18cr_rep1


title: Ctrl_H3K18ac_rep1


title: RNAseq_POD10_DO_BCSP1

value: BCSP


title: 515539A03_SLOT02_S01_Red_al

tag: sample number

tag: ecotype

value: DNA pool of 100 snails from two British L. saxatilis populations (Dunvar and Thornwick)


title: 515534A12_SLOT04_S01_Red_al

value: SU

tag: locality

tag: reference


title: 516142A09_2um_20._Red_al


title: Ctrl_Input_rep1

tag: treatment


title: 515534A11_SLOT04_S01_Red_al


title: shRNA-NC C3

first: Ming

middle: zhe

last: Ma

state: Shanghai

address: 270 DongAn Road

department: Department of Gastric Surgery

institute: Fudan University Shanghai Cancer Center

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 hg19 whole genome
Fragments per kilobase Million (FPKM) were calculated using the formula:(total exon reads)/[mapped reads(million)*exon length (kb)]
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: gastric cancer cell line SGC7901

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: control


title: 515539A02_SLOT02_S01_Red_al


title: RNAseq_POD10_DO_BCSP2

value: male

value: Mandibular Distraction


title: 515539A01_SLOT02_S01_Red_al

value: RB

value: Silleiro


title: shRNA-NC C2


title: shRNA 10603

value: transfected with ENST00000431060 shRNA


title: shRNA 10601


title: 515534A07_SLOT04_S01_Red_al


title: shRNA-NC C1


title: shRNA 10602


title: Si OGG1

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

description:
Control
SAMPLE 3

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, RPLP0.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control ratios.

label: SYBR Green

source_name: Cell lysate

label_protocol: PCR assays were performed using the Qiagen Human Inflammatory Cytokines & Receptors PCR Array PAHS-011Z (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 1µg total RNA using the Superscript® IIIFirst Strand Synthesis System (Invitrogen)

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Cells were treated with  control Si RNA or Si OGG1 RNA for 48 hour, then exposed to 20 ng/ml TNF for 30 minutes.

value: Si OGG1


title: 515534A06_SLOT04_S01_Red_al

value: Burela


title: 515534A08_SLOT04_S01_Red_al


title: 515534A09_SLOT04_S01_Red_al

value: Roncudo


title: Si OGG1+20ng/ml TNF

description:
Test
SAMPLE 4

value: Si OGG1+20ng/ml TNF


title: Si Negative control

description:
Control
SAMPLE 1

value: Si Negative control


title: 515534A10_SLOT04_S01_Red_al


title: 13-0-SpinalCord_S13

city: Vancouver

first: Jordan

middle: W

last: Squair

state: BC

address: 818 West 10th Avenue

country: Canada

institute: University of British Columbia

data_processing:
Quality control: FastQC
Pseudoalignment: Salmon (version 0.8.2)
Genome_build: Rnor_6.0.89
Supplementary_files_format_and_content: pseudocounts

source_name: Spinal cord_0

extract_protocol:
Total RNA was purified using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions, eluting in 30 μL of water.
500 ng RNA was used for library preparation with Illumina’s TruSeq Stranded mRNA kit (Illumina, San Diego, CA).

value: Wistar

tag: severity

value: Spinal cord


title: 14-0-SpinalCord_S14

tag: tissue


title: Si Negative control+20ng/ml TNF

description:
Test
SAMPLE 2

value: Si Negative control+20ng/ml TNF


title: 515534A03_SLOT04_S01_Red_al


title: 15-0-SpinalCord_S15

tag: strain


title: 11-0-SpinalCord_S11


title: 515534A04_SLOT04_S01_Red_al


title: 515403A11_SLOT01_S01_Red_al


title: 10-100-SpinalCord_S10

source_name: Spinal cord_100


title: 515534A01_SLOT04_S01_Red_al


title: 8-100-SpinalCord_S8


title: 7-100-SpinalCord_S7


title: 515534A05_SLOT04_S01_Red_al


title: 515534A02_SLOT04_S01_Red_al


title: 515403A09_SLOT01_S01_Red_al


title: 9-100-SpinalCord_S9


title: 12-0-SpinalCord_S12


title: 6-100-SpinalCord_S6


title: 515403A07_SLOT01_S01_Red_al


title: snv_Lo-R1

city: Los Angeles

first: Kimberly

last: Insigne

institute: UCLA

description:
Minigene reporter for exon skipping. DNA-sequencing of four FACS-sorted bins, in replicate
processed data file: snv_bin_counts.csv

data_processing:
library strategy: Multiplexed Functional Assay of Splicing using Sort-seq (MFASS)
Paired-end reads merged with bbmerge version 38 and default parameters
Reads were aligned using custom aligner script, requiring only perfect matches
Used custom script to aggregate raw read counts across bins for each sequence, where each bin is a separate column, for downstream analysis
Genome_build: hg19
Supplementary_files_format_and_content: Each row corresponds to a sequence in the synthetic oligo library. Each column corresponds to the raw read counts for that sequence in that individual bin. 0 count means the sequence was not observed.

extract_protocol:
We extracted genomic DNA for the sorted populations using blood and cell culture DNA midi kit (Qiagen).
We amplified each sublibrary for ~300-fold amplicon coverage, and reactions were performed in 96-well format in 50 μL reactions for each sublibrary proportional to bin size using Kapa HiFi DNA polymerase.
Custom libraries were constructed using standard adapters from Illumina and paired-end sequenced with custom sequencing primers. Samples were indexed with i7 indices compatible with Illumina paired-end protocols.

tag: synthetic oligo library

value: SNV library

tag: sorted fraction

value: Lo; no GFP present but mCherry present


title: 3-200-SpinalCord_S3

source_name: Spinal cord_200


title: 515403A06_SLOT01_S01_Red_al

value: DNA pool of 100 snails from two British L. saxatilis populations (Dunvar and Thornwick)


title: snv_Lo-R2

tag: cell type


title: 515403A10_SLOT01_S01_Red_al

value: SU


title: 5-200-SpinalCord_S5


title: 515403A08_SLOT01_S01_Red_al


title: 515403A05_SLOT01_S01_Red_al


title: 515403A03_SLOT01_S01_Red_al


title: snv_IntLo-R1

value: Int-Lo; intermediate bins


title: 4-200-SpinalCord_S4


title: 2-200-SpinalCord_S2


title: 1-200-SpinalCord_S1


title: 515396A12_SLOT03_S01_Red_al


title: 515403A04_SLOT01_S01_Red_al


title: WT_Hsv

city: Beijing

first: Zeming

last: Zhang

address: 38 Xueyuan Rd , Haidian District,Beijing,China

institute: Institude of Systems Biomedicine

data_processing:
RNA sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), and sequenced on an Illumina Novaseq platform.
Illumina Casava 1.8 software used for basecalling and raw reads were gained.
After eliminating low-quality reads and reads with adaptors, clean reads were mapped to mouse genome reference sequence (GRCm38/mm10 Ensembl release 81) using HISAT2.
Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM) algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ensemble gene ID and RPKM values for each Sample

source_name: Bone marrow

growth_protocol: For bone marrow derived macrophages (BMDM), bone marrow cells were isolated from femurs and tibiae of 10 week old C57BL/6 mice. Cells were cultured in DMEM containing 10% FBS, 1% glutamine, 1% streptomycin-penicillin and 20 ng/mL recombinant murine GM-CSF (Peprotech) in a 10 cm dish for 7 days before experiments. Mature macrophages were harvested by incubating with PBS-EDTA for 10 minutes and cultured on 6-well for further experiments.

extract_protocol:
Supernatant was removed and cells were covered with 350ul Buffer RLT at the end of treatment. Total RNA was extracted following the strandard protocol of RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected by HSV-1(17 strain) for 0 or 6 hours

value: Bone marrow derived macrophages

tag: age

value: 10 weeks

value: HSV-1(17 strain) for 6 hours


title: 515396A08_SLOT03_S01_Red_al

value: RB


title: snv_IntHi-R1

value: Int-Hi; intermediate bins


title: 515403A01_SLOT01_S01_Red_al


title: 515396A07_SLOT03_S01_Red_al


title: 515396A11_SLOT03_S01_Red_al

value: Burela


title: snv_IntHi-R2


title: snv_IntLo-R2


title: snv_Hi-R2

value: Hi; both GFP and mCherry


title: 515396A09_SLOT03_S01_Red_al


title: WT_Mock

value: untreated


title: snv_Hi-R1


title: wt_MOCK

city: BEIJING

first: Peiyan

last: Wang

state: 北京

address: NO.38 ROAD XUEYUAN, DISTRICT HAIDIAN, BEIJING, CHINA, 北京市海淀区学院路38号北京大学医学部

institute: Peking University

growth_protocol: Immortalized bone marrow derived macrophages were cultured in DMEM containing 10% FBS, 1% glutamine, 1% streptomycin-penicillin on 6-well for further experiments.

treatment_protocol: Cells were infected by VSV for 0 or 6 hours

value: Bone marrow

tag: genotype

value: wild type

tag: infection

value: mock


title: BM-MSCs induced 2

city: Thuwal

first: Gerardo

last: Ramos-Mandujano

department: Biological and Environmental Science and Engineering Division

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description: Analysis used BM-MSCs control (CTL) for comparison to BM-MSCs induced with small molecules cocktail (EXP).

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix from Molecular Devices. All images were captured using 10µm resolution.

data_processing:
For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics. Microarray data analysis was performed with genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes.
GenArise software identified differential expressed genes by calculating an intensity-dependent z-score between samples and reference (HDF).
The 'log2_lowess_ratio_data.txt'  values were obtained by SWAP comparisons (experimental/control);
Sample 1: H10KA_07_28 UCB_CTL_Alexa555_EXP_Alexa647 vs.  H10KA_07_29 UCB_EXP_Alexa555_CTL_Alexa647.
Sample 2: H10KA_07_30 BM_CTL_Alexa555_EXP_Alexa647 vs. H10KA_07_31 BM_EXP_Alexa555_CTL_Alexa647.
and the normalization of the SWAP experiments was conducted using lowess log2 ratio

source_name: BM-MSCs induced with a six small molecules cocktail

label_protocol: 10 µg of total RNA was used for cDNA synthesis, incorporating dUTP-Alexa555 or dUTP-Alexa647. Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: UCB-MSCs and BM-MSCs in control condition (DMEM-low glucose supplemented with FBS-10%) were re-plated and induced with neuronal inductioon medium and six smal molecules cocktail.

extract_protocol: Total RNA samples from cultures were extracted with the GeneElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich St. Louis, MO, USA) according to the manufacturer's instructions.

treatment_protocol: Treatment protocol for UCB-MSCs and BM-MSCs consisted in neuronal medium plus six small molecules (I-BET151, CHIR99021, Forskolin, RepSox, Y-27632, and dbcAMP) during 4 or 8 days.

value: Bone marrow (BM)

value: Mesenchymal stem cells (MSCs)

tag: culture condition

value: neuronal induction medium plus six small molecules

source_name: BM-MSCs control

value: mesenchymal medium


title: UCB-MSCs induced 2

description: Analysis used UCB-MSCs control (CTL) for comparison to UCB-MSCs induced with small molecules cocktail (EXP).

source_name: UCB-MSCs induced with a six small molecules cocktail

value: Umbilical Cord Blood (UCB)

source_name: UCB-MSCs control


title: marmoset_liver_adult_male2

status: Public on Oct 01 2018

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

institute: University of Cambridge

description: sample id: 5787sTS

data_processing:
RNA-seq reads were aligned to the assembled genomes of their corresponding species using STAR (version 2.2.1) using the 2-pass mapping mode and standard settings.
Aligned reads from all replicates of each organ were used to reconstruct transcripts through a genome-guided de novo transcriptome assembly using StringTie (version 1.3.4d) with the following parameters: -j 5 –g 50.
Assembled transcripts from each organ were then merged using Cuffmerge to define a unique set of transcripts. Expression levels (measured in FPKM) of the assembled transcripts were calculated with Cuffnorm (version 2.2.1) with --library-norm-method classic-fpkm.
Genome_build: human: hg38; macaque: rheMac8; marmoset: calJac3; mouse: mm10; rat: rn6; rabbit: oryCun2
Supplementary_files_format_and_content: *sample_name*.Signal.UniqueMultiple.str*N*.out.bw: STAR-generated bigWig tracks of the RPM-normalized read coverage from each sample. Files represent reads mapped on the forward (N=1) or reverse (N=2) strand.

molecule: polyA RNA

organism: Callithrix jacchus

source_name: Adult liver

extract_protocol:
QIAGEN RNeasy Kit
Single-end strand-specific RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT kit according to manufacturer instructions. Libraries were sequenced using the Illumina HiSeq 2500.

value: liver

tag: Sex

value: male

tag: developmenta stage

value: adult


title: marmoset_liver_adult_male1

description: sample id: 983sTS


title: 515396A05_SLOT03_S01_Red_al

tag: sample number

tag: ecotype

value: SU

value: Silleiro

value: DNA pool of 100 snails from two British L. saxatilis populations (Dunvar and Thornwick)


title: 515396A04_SLOT03_S01_Red_al

value: RB

tag: locality

value: Roncudo

tag: reference


title: BM-MSCs induced 1


title: UCB-MSCs induced 1


title: marmoset_kidney_adult_female1

description: sample id: 1493sTS

source_name: Adult kidney

value: kidney

value: female


title: marmoset_kidney_adult_male2

description: sample id: 5786sTS


title: marmoset_kidney_adult_male1

description: sample id: 981sTS


title: marmoset_heart_adult_male2

description: sample id: 5795sTS

source_name: Adult heart

value: heart


title: 515396A10_SLOT03_S01_Red_al

source_name: Foot muscle CGH


title: marmoset_heart_adult_female1

description: sample id: 1492sTS


title: 515396A06_SLOT03_S01_Red_al


title: marmoset_brain_adult_male2

description: sample id: 5788sTS

source_name: Adult brain

value: brain


title: marmoset_heart_adult_male1

description: sample id: 5814sTS


title: marmoset_liver_adult_female1

description: sample id: 1491sTS


title: marmoset_brain_adult_male1

description: sample id: 5801sTS


title: 515396A03_SLOT03_S01_Red_al


title: Silc1+/+, sham, rep2

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Three replicates were combined for all the analysis into four groups (WT/KO, injury/sham).
Reads were mapped to the mouse genome (mm10 assembly) using Bowtie2 with the “-X 2000” parameter.
As ATAC-seq libraries typically contain multimodal fragment length distributions, and those were slightly different for different repeats, we performed the following subsampling procedure to unify the fragment length distribution. All the reads were first binned by their inferred insert length (obtained from the BAM file). We then traversed the bins, and kept in each bin an equal number of reads from each of the four groups (matching the read number in each bin to number of reads in the group which had the least reads in the bin), subsampling reads at random. This procedure resulted in 73,944,617 paired-end read mappings per group.
Peaks of accessible chromatin where then found in each group using MACS2 with the following parameters “callpeak -B -format BAMPE -g mm”.
Genome_build: mm10
Supplementary_files_format_and_content: bed files with peak coordinates and score

source_name: DRG

growth_protocol: The study was conducted in accordance with the guidelines of the Weizmann Institutional Animal Care and Use Committee (IACUC). C57black6 Ola HSD male mice were purchased from Harlan Laboratories (Rehovot, Israel). All other mouse strains were bred and maintained at the Veterinary Resources Department of the Weizmann Institute.

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013) with minor adjustment for application to tissue material. Six fresh L4-L6 DRGs were extracted in 100 µl ice cold cell lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.5% IGEPAL CA-630) for 5 minutes on ice, then a 21g needle on a 1 mL syringe was used to shear the tissue through the needle 5 times.
As in Buenrstro et al. 2013

treatment_protocol: Mice were anesthetized with an intraperitoneal injection of xylazine and ketamine (10 mg/kg body weight). A 1-cm-long incision was made in the skin of the thigh perpendicular to the femur. A small incision was made between the thigh muscles and the muscles were separated by insertion and opening of the tip of the scissors between the muscles. The sciatic nerve was identified and pulled out using 45º forceps.  The tissue was crushed using fine forceps (Dumont no. 4) two times for 30 seconds at mid- thigh level. The sciatic was positioned back in its place by gently pooling the hind leg. The incision was closed using reflex wound clips.    Adult mouse DRGs were dissociated for neuron cultures with 100 U of papain followed by 1 mg/ml collagenase-II and 1.2 mg/ml dispase. The ganglia were then triturated in HBSS, 10 mM glucose, and 5 mM HEPES (pH 7.35). Neurons were recovered through percoll, plated on laminin, and grown in F12 medium for 48 hours (Hanz et al., 2003; Perlson et al., 2005; Rishal et al., 2010). Adult mouse DRG cultures were transfected with siGenome siRNAs using DharmaFect 4 (Dharmacon), replated 24 hr later

value: dorsal root ganglia (DRG)

value: wildtype

tag: treatment

value: sham


title: 515396A02_SLOT03_S01_Red_al

first: Humberto

last: Quesada

institute: Universidad de Vigo


title: 515403A02_SLOT01_S01_Red_al

value: Burela


title: marmoset_brain_adult_female1

description: sample id: 5791sTS


title: Silc1+/+, injury, rep2

value: injured


title: 515396A01_SLOT03_S01_Red_al


title: Silc1-/-, sham, rep3


title: Silc1+/+, injury, rep3


title: Silc1-/-, injury, rep2