title: Pancreatic islet, HI-070719-BFA

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

description:
Raw counts and FPKM normalized counts of mRNAs for all samples are provided in  the same text file; results are in DE gene list
Rawcounts_filtered.txt
FPKM normalized_log transformed.txt
DE gene list.xlsx
HI-070719-BFA_S29

data_processing:
Sequencing reads were aligned to the human genome hg19 using STAR aligner v 2.5.3a.  To account for the negative values during log transformation in the gene RPKM expression, a pseudocount of 1 was added.
Analysis performed using bioconductor packages EdgeR and Limma
Corrected p-values (<0.05) were taken as threshold for significant difference in gene expression.  In addition, the log fold change (FC) of a gene must be 1.5 to be considered as a differentially expressed gene.  A gene was selected as up-regulated or down-regulated if at least 80% islet samples had its expression changed significantly in one direction and none in the opposite direction
Genome_build: hg19
Supplementary_files_format_and_content: .txt files for raw counts and variance stabilized normalized counts

source_name: Pancreatic islet

extract_protocol:
After 24 hours of Brefeldin A treatment, islets were collected, washed once with PBS, lysed in Trizol. Total RNA was isolated using the miRNAeasy kit (Qiagen).
Total RNA sequencing utilized 100 ng of RNA as input. Libraries for total RNA sequencing were prepared using KAPA mRNA Hyperprep Kit (Roche Sequencing & Life Science). Sequencing was performed using Illumina NovaSeq 6000 (2x100 bp paired-end reads), generating 30 million reads per library

treatment_protocol: Cadaveric islets were cultured overnight in standard islet medium (phenol red-free DMEM containing 10% FBS, 10 mM HEPES, 2 mM L-glutamate, 100 U/0.1 mg/L Penicillin/Streptomycin ). To induce Golgi apparatus stress, islets were treated with or without 0.1 ug/mL brefeldin A for 24 hours.

tag: tissue type

value: Islet

value: Brefeldin A treated

tag: age

value: Male

tag: ethnicity

value: White

tag: bmi


title: Pancreatic islet, HI-070719-DMSO

status: Public on Sep 17 2020

type: SRA

country: USA

description:
Raw counts and FPKM normalized counts of mRNAs for all samples are provided in  the same text file; results are in DE gene list
Rawcounts_filtered.txt
FPKM normalized_log transformed.txt
DE gene list.xlsx
HI-070719-DMSO_S28

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment

value: control

tag: Sex


title: SK-N-SH_16

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

department: Medical Faculty

country: Germany

institute: University Heidelberg

description: single-cell RNA-seq (MARS-seq)

data_processing:
Pool barcode, cell-specific tags and UMIs were extracted and reads with ambiguous plate/cell-specific tags were filtered
Sequenced reads were trimmed for adaptor sequence, and mapped to hg19 whole genome combined with ERCC spike-in pseudo-assembly using Bowtie2 v2.1.0  and the standard parameters “-m 1 -t --best --chunkmbs 64 –strata”
Sequence reads were filtered for reads mapping to a range of -1000 to +200 bp from a known transcription termination site
Genome_build: hg19
Supplementary_files_format_and_content: dgCMatrix object with counts as an RDS file R file

molecule: polyA RNA

source_name: Neuroblastoma cell lines

growth_protocol: SK-N-SH cells were cultured in RPMI1640 medium supplemented with 10% fetal calf serum and 1% penicillin/streptomycin at 37°C and 5% CO2 and subcultured every 3-4 days.

extract_protocol:
Cells were harvested using versene and single-cells were sorted into 384-well plates.
Libraries were prepared as described previously (Jaitin et al., 2014)

treatment_protocol: Cells were not treated.

tag: type

value: cell line

tag: cell line

value: SK-N-SH


title: IPD3

city: Berlin

first: Malte

last: Spielmann

address: Ihnestraße 63

institute: Max Planck Institute for Molecular Genetics

data_processing:
Cell Ranger v3 mkfastq
Cell Ranger v3 count
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw UMI count matrix, gene metdata and cell metadata

extract_protocol:
The left hemi-midbrain was removed. This midbrain block was then snap-frozen at -120°C and cryosectioned at ~15 μm thickness in the transverse plane. The resulting sections were stored at -80°C. Addapted 10x Genomics protocol for nuclei isolation was used to extract the nuclei. Sorted nuclei were processed using the Chromium Next GEM Single Cell 3’ Kit v3.1 to generate the cDNA libraries
The sample was prepared for sequencing using standard Illumina protocol and sequenced on Illumina NovaSeq 6000-S2

tag: disease state

value: Idiopathic Parkinson's disease (IPD)

tag: age at death

value: M

tag: pmi (h)

tag: tissue

value: Midbrain

tag: molecule subtype

value: nuclear RNA


title: SK-N-SH_18

description: single-cell RNA-seq (MARS-seq)


title: U87_DPF3V_3 RNA-seq

city: GuangZhou

first: liu

last: xincheng

address: zhongshan Road 74

country: China

institute: sysu

data_processing:
We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value,28S/18S and the fragment length distribution.
We use internal software SOAPnuke to filter reads
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression  level with RSEM
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: The cells were cultured according to the guideline of ATCC

extract_protocol:
Total RNA was isolated from cultured cell lines. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers ere used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced using Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U87 cells were treated with bulk control/combination of 0.5mM 8-cpt-cAMP and 1nM MS275  for 48 hours. Total RNA was extracted from 1×10^6 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent for RNA sequencing

tag: genotype/variation

value: U87 cells transfer plasmid containing DPF3 gene.


title: U87_NCV_3 RNA-seq

value: Control

value: U87 cells transfer empty plasmid as a control


title: SK-N-SH_15

description: single-cell RNA-seq (MARS-seq)


title: SK-N-SH_17

description: single-cell RNA-seq (MARS-seq)


title: Pancreatic islet, HI-061119-BFA

description:
Raw counts and FPKM normalized counts of mRNAs for all samples are provided in  the same text file; results are in DE gene list
Rawcounts_filtered.txt
FPKM normalized_log transformed.txt
DE gene list.xlsx
HI-061119-BFA_S27


title: U87_DPF3V_2 RNA-seq


title: IPD2


title: late_pressure_R_49_133R_a3_hypo

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

hyb_protocol: cRNA was hybridized to a pig genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2505C Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction and GeneSpring v.10.1 (Agilent Technologies, Inc., CA) software was used to conduct the preliminary data filtration and statistical analysis.

organism: Sus scrofa domesticus

label_protocol: Total RNA (200-2000ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labeled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

extract_protocol: RNA was isolated using the RNeasy Fibrous Tissue Kit based on the manufacturer’s protocol (Qiagen).

tag: breed/model

value: red Duroc swine scar model

tag: gender

value: Juvenile

tag: pigmentation phenotype

value: hypo

value: Skin

source_name: Zyagen Universal Pig Reference Total RNA

value: Unknown

tag: sample type

value: Reference


title: late_pressure_R_50_126R_a3_hypo

value: Male

tag: age


title: late_pressure_R_49_133R_a1_hyper

value: hyper


title: Pancreatic islet, HI-061119-DMSO

description:
Raw counts and FPKM normalized counts of mRNAs for all samples are provided in  the same text file; results are in DE gene list
Rawcounts_filtered.txt
FPKM normalized_log transformed.txt
DE gene list.xlsx
HI-061119-DMSO_S26

tag: tissue type

value: Islet

value: control

tag: ethnicity

value: White


title: SK-N-SH_14

description: single-cell RNA-seq (MARS-seq)

value: cell line

value: SK-N-SH


title: U87_NCV_2 RNA-seq

tag: treatment


title: late_sham_L_50_119L_a1_hyper


title: U87_NCCM_2 RNA-seq

value: U87 cells transfer empty plasmid as a control and treated with 0.5mM 8-cpt-cAMP and 1nM MS275 for 48hr.


title: U87_NCCM_1 RNA-seq


title: SK-N-SH_13

description: single-cell RNA-seq (MARS-seq)


title: U87_NCV_1 RNA-seq


title: late_sham_L_49_133L_a3_hypo


title: late_sham_L_50_119L_a3_hypo


title: Pancreatic islet, HI-043019-DMSO

description:
Raw counts and FPKM normalized counts of mRNAs for all samples are provided in  the same text file; results are in DE gene list
Rawcounts_filtered.txt
FPKM normalized_log transformed.txt
DE gene list.xlsx
HI-043019-DMSO_S24

tag: Sex

value: Female

value: Black/African American

tag: bmi


title: SK-N-SH_12

description: single-cell RNA-seq (MARS-seq)

tag: type

tag: cell line


title: Pancreatic islet, HI-042519-BFA

description:
Raw counts and FPKM normalized counts of mRNAs for all samples are provided in  the same text file; results are in DE gene list
Rawcounts_filtered.txt
FPKM normalized_log transformed.txt
DE gene list.xlsx
HI-042519-BFA_S23

value: Brefeldin A treated


title: SK-N-SH_11

description: single-cell RNA-seq (MARS-seq)


title: SK-N-SH_9

description: single-cell RNA-seq (MARS-seq)


title: SK-N-SH_10

description: single-cell RNA-seq (MARS-seq)


title: CS16 Trunk Ao

city: Edinburgh

first: Edie

last: Crosse

address: 5 Little France Road

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

data_processing:
Cell Ranger 2.1.0 (10x Genomics) analysis pipeline
Loompy: Conversion of expression data into loom file
SCANPY: Filtering cells with less than 200 genes, filtering out genes in less than 3 cells, filtering cells with a high percentage of mitochondrial genes (>0.05) and number of genes (>3500), normalising reads per cell.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: CSV, filtered raw count matrices with GENE ID as row names and Cell ID as column names

source_name: Dorsal aorta - mid (around vitelline artery)

extract_protocol:
The dorsal aortae (Ao) were dissected from human embryos CS16 - sample 1 was further bisected into ventral (AoV) and dorsal (AoD) portions with only AoV taken for analysis, sample 2 was trimmed to the mid portion of the Ao. Tissues were dissociated into single cells in 1mg/ml Collagenase-Dispase. For sample 1 CD34+ cells were enriched using the human CD34 MicroBead Kit and LS MACS Columns (both Miltenyi Biotec). For sample 2, live cells were sorted using a FACS Aria-II (BD Bioscience) using 7AAD as a marker of dead cells.
Libraries were prepared using the Single Cell 3’ Reagent Kit v2 (10x Genomics) according to manufacturer's protocol.

tag: embryo

tag: developmental stage

tag: cell population

value: Total


title: Pancreatic islet, HI-043019-BFA

description:
Raw counts and FPKM normalized counts of mRNAs for all samples are provided in  the same text file; results are in DE gene list
Rawcounts_filtered.txt
FPKM normalized_log transformed.txt
DE gene list.xlsx
HI-043019-BFA_S25


title: SN01-006-T

city: Mumbai

first: Sreelaja

last: Nair

state: Maharashtra

address: IIT Bombay campus, Powai

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Bombay

data_processing:
All analysis was performed using Galaxy open source online analysis tool at www.usegalaxy.org. Raw FASTQ files were assessed for their quality using FASTQC. Files that cleared the quality check were then trimmed in Trim Galore! where "Trim low quality ends from reads in addition to adapter removal" = 20, "Overlap with adapter sequence required to trim a sequence" = 1, "Maximum allowed error rate"= 0.1, "Discard reads that become shorter than length INT"=20 and "Unpaired single-end read length cutoff needed for read 1 to be written"= 35.
The trimmed reads were aligned using HISAT2 with Danio_rerio.GRCz10 as the reference genome. Parameters were "Maximum mismatch penalty"=6, " Minimum mismatch penalty"=2, "Penalty for canonical splice sites"=0, "Penalty for non-canonical splice sites"=3, "Penalty for long introns with canonical splice sites"= Constant, constant term(y)=0, coefficient(z)=0, "Penalty for long intron with non-canonical splice sites"= Natural logarithm [f(x) = y + z * log(x)], constant term(y)=-8, coefficient(z)=1, "Minimum intron length"=20, Maximum inton length= 500000, "Specify strand information"= First strand (R/RF).
The abundance of aligned reads was measured using Cufflinks software. Parameters: "Max intron length"= 300000, "Min isoform fraction"=0.1, "Pre mRNA fraction"=0.15, "Inner mean distance"=45, "Inner distance standard deviation"=20, "Max MLE iterations"=5000, "Alpha vaue for the binomial test used during false positive spliced alignment filtration"=0.001, "percent read overhang taken as suspiciously small"=0.09, "intronic overhang tolerance"=8, "maximum genomic length of a given bundle"= 3500000, "maximum number of fragments pe locus"=1000000, "Minimum allowed intron size"=50, "Minimum average coverage required to attempt 3prime trimming"=10
The differential expression levels were computed as FPKM values using Cuffdiff software with two methods of normalization- geometric and quartile. Other parameters were "Dispersion estimation method"= per-condition, "false discovery rate"=0.05, "Min alignment count"=10, "Max ME iterations"=5000, "Hits included in normalization"=Compatible hits, "Maximum number of fragments per locus"= 500000, "Number of fragment genration samples"=100, "Number of fragment assignment samples per generation"= 50, "Minimum replicates for isoform shift testing"=3.
Genome_build: Danio_rerio.GRCz10
Supplementary_files_format_and_content: FPKM

organism: Danio rerio

source_name: zebrafish embryo

growth_protocol: Zebrafish were maintained as per standard conditions at 28°C

extract_protocol:
RNA was extracted from embryos using Trizol reagent. Quality was assesed using Agarose gel electrophoresis and on Agilent Bioanalyzer. Samples with RIN 9 or above were used for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Haploid and tetraploid embryos were generated as per Menon and Nair, Dev Dyn, 2018, doi:10.1002/dvdy.24640.

value: 3 hpf

tag: ploidy

value: Tetraploid

tag: genotype (f*m)

value: TJH*Tu


title: SN01-021-T


title: CS16_D_Outer_3

data_processing:
Adapter trimming Flexbar/2.5
Alignment STAR/2.5.1b
Gene counts with bedtools multicov, gtf = Homo_sapiens.GRCh38.86.gtf.gz
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: .txt, raw read count matrices are provided with ENSEMBL_ID row names, sample column names

source_name: Embryo dorsal aorta and surrounding mesenchyme

extract_protocol:
Human embryos embedded in OCT were sectioned in a caudal-to-rostral direction using a cryotome FSE cryostat (Thermo Scientific).  Sections were stained using a rapid Haematoxylin and Eosin staining protocol - 3 minutes (min) in 70% ethanol, 1 min H2O, 4 min Mayer’s Haematoxylin Solution (Sigma-Aldrich), 2 min tap H2O, 15 seconds Eosin Y (Sigma-Aldrich), 1 min 70% ethanol, 1 min 90% ethanol, 3 mins 100% ethanol. All H2O was treated with diethyl pyrocarbonate (DEPC) and all reagents were pre-cooled in ice except 100% ethanol which was room temperature. The laser capture microscope used was the PALM microbeam (Zeiss). The microscope and surrounding area were sprayed down with RNaseAWAY ® (Sigma-Aldrich). Sections were viewed and microdissected in brightfield using a 10X objective. The microdissected regions were collected into the caps of AdhesiveCap 500 opaque (Zeiss) 500µl PCR tubes. 15µl lysis buffer (0.2% Triton X-100 (Sigma-Aldrich), 2U/µl RNase inhibitor (Takara), Phosphate Buffer Solution (PBS, (Nichterwitz et al., 2016)) was added directly on top of the dissected tissue in the tube caps and the tubes closes in an inverted position. PicoPure RNA Isolation Kit was used to extract RNA for samples 1-12. Samples 13-30 were directly amplified from lysed material
SMARTer® Stranded Total RNA-Seq Kit v2 -Pico Input Mammalian kit (Takara) for samples 1-12, LCM-Seq (Picelli et al., 2014) for samples 13-30.

tag: tissue

value: dorsal aorta and surrounding mesenchyme

tag: subdomain

value: Dorsal Outer (D_Outer)


title: SK-N-SH_7

description: single-cell RNA-seq (MARS-seq)


title: mid_pressure_R_50_99R_a3_hypo

tag: breed/model

value: red Duroc swine scar model

tag: gender

value: Male

value: Juvenile

tag: pigmentation phenotype

value: hypo

value: Skin

value: Unknown

value: Reference


title: late_pressure_R_50_119R_a1_hyper

tag: age

value: hyper

tag: sample type


title: late_sham_L_49_119L_a1_hyper


title: mid_pressure_R_49_91R_a3_hypo


title: mid_sham_L_50_91L_a3_hypo


title: mid_sham_L_49_98L_a3_hypo


title: CS16_D_Mid_3

value: Dorsal Mid (D_Mid)


title: SN01-003-T


title: Pancreatic islet, HI-042519-DMSO

description:
Raw counts and FPKM normalized counts of mRNAs for all samples are provided in  the same text file; results are in DE gene list
Rawcounts_filtered.txt
FPKM normalized_log transformed.txt
DE gene list.xlsx
HI-042519-DMSO_S22

tag: tissue type

value: Islet

tag: treatment

value: control

value: Female

tag: ethnicity

value: White


title: SN01-020-H

value: 3 hpf

value: Haploid


title: SK-N-SH_6

description: single-cell RNA-seq (MARS-seq)

tag: type

value: cell line

value: SK-N-SH


title: SK-N-SH_8

description: single-cell RNA-seq (MARS-seq)

tag: cell line


title: CS16_V_Outer_3

tag: embryo

value: dorsal aorta and surrounding mesenchyme

value: Ventral Outer (V_Outer)


title: CS16_V_Mid_3

tag: developmental stage

value: Ventral Mid (V_Mid)


title: early_sham_L_50_49L_a3_hypo

value: red Duroc swine scar model

value: Male

value: Juvenile

value: hypo


title: mid_sham_L_49_91L_a1_hyper

value: hyper

value: Skin

value: Unknown

value: Reference


title: mid_pressure_R_50_91R_a1_hyper


title: mid_pressure_R_49_91R_a1_hyper


title: SN01-005-H

value: TJH*Tu


title: mid_sham_L_50_105L_a1_hyper


title: CS16_D_Outer_2

value: Dorsal Outer (D_Outer)


title: early_sham_L_49_49L_a3_hypo


title: early_sham_R_50_49R_a3_hypo


title: CS16_V_Outer_2


title: Chick_Nematode_Treated

city: CHENNAI

first: Florida

last: Tilton

state: Tamil Nadu

address: 7, Leo Muthu Street, Kalaimagal Nagar, Ekkaduthangal

institute: Biozone Research Technologies

description: processed data file: Both_Control_&_Treated_Chick.txt

data_processing:
All the 150bp paired end raw reads (IlluminaNextSeq500) were quality checked for low quality bases and adapter sequences (Processing of raw reads). Quality check and processing was done using In-house perl scripts.
All processed reads were assembled into transcripts without any reference (De-novo) both samples independently using Trinity software (trinityrnaseq-r20140413p1).
Unigenes were generated after clustering the merged sequences from both Control and Treated samples using CD-HIT.
The reads for the samples were separately aligned to the corresponding unigene sequences and read count profiles were generated. DESeq "R" package was used for differential gene expression.
Genome_build: fasta files
Supplementary_files_format_and_content: Both_Control_&_Treated_Chick.txt: Tab-delimited text file with abundance measurements.
Supplementary_files_format_and_content: Both_Control_&_Treated_Sheep.txt: Tab-delimited text file with abundance measurements.

organism: Ascaridia galli

source_name: Intestine

growth_protocol: Collection of parasites (Nematodes of Poultry): For the present study, the desired parasites are Ascaridia galli which parasitizes chicken. The intestines of freshly slaughtered fowls, were collected from local slaughterhouse and washed with normal saline solution. These intestines were then dissected and the nematodes were extracted. The average size of the nematode was found to be 5 cm. These parasitic worms, were used to test the anthelmintic activity with bryophyte extracts in vitro. The identification of nematodes was done in the department of Zoology, OUCW, Koti, Hyderabad by using Phase contrast microscope.

extract_protocol:
Preparations of Aqueous extract (Maceration method) Bryophyte, Pottia lanceolata samples were cleaned removing soil debris, by thorough washings with water. The active ingredient was extracted, using cold maceration method dried in shade, powdered using mortar and pestle. The crude aqueous extract was centrifuged, at 5,000 rpm for 5 minutes, using Remi centrifuge. The clear supernatant was used for the treatment and the precipitate was discarded. Piperazine citrate (glaxo smithkline) was used as the standard anthelmintic drug during the experimentation.
To study the gene expression pattern, the control and treated (bryophyte extract Pottia lanceolata) parasites were preserved in RNA later solution, and were subjected to RNA extraction and isolation using RNA mini easy kit. The Extraction was performed as per the protocol, provided by the manufacturer. Extracted RNA was subjected to quality and quantity check, prior to library construction. Library preparation was performed following NEB Next Ultra RNA Library Prep Kit (#E7490L). In brief, approximately 110-350 ng of Total RNA was used to isolate mRNA using Poly dT beads. mRNA was fragmented and converted to cDNA according to the protocol. cDNA was end repaired and purified using Ampure XP beads. Cleaned DNA was adapter ligated and purified using Ampure XP beads. These adapter ligated fragments were subjected to 12cycles of PCR using primers provided in the kit. The PCR products were purified using Ampure XP beads. Quantification and size distribution of the prepared library was determined using Qubit fluorometer (Table 1) and Agilent Tape station D1000 Kit (Agilent Technologies) according to the manufacturer’s instructions. The steps followed to generate the FastQ reads from Total RNA libraries are as follows: 1. The pooled/multiplexed libraries were put into the Illumina Hiseq Sequencer for sequencing which generated raw data in the bcl format. 2. Bcl files were De-multiplexed using sample wise Barcode information to get the sample specific sequences. 3. De-multiplexing resulted into raw reads in FastQ format, which was used for downstream analysis.

treatment_protocol: Anthelmintic activity assay was carried out as per the method of Ajaiyeoba et al., 2001. The assay was performed in vitro, using cestodes and nematodes of sheep and poultry. Test samples of the extract was prepared at the concentrations, 10, 20 and 50 mg/ml of bryophyte extract dissolved in distilled water. Six worms, each of chicken nematodes Ascaridia galli and sheep nematodes Trychostrongyles were placed in petri dish measuring 9 cm in diameter. Similarly cestode parasites Railletina tetragona, which parasitizes chicken and sheep cestode Moniezia expansa were placed in petri dishes and 25 ml of bryophyte extract was added to the petri dishes. Piperazine citrate of concentration 10mg/ml was prepared and used as reference standard and double distilled water was used as control. Extract solution and standard solution were freshly prepared, prior to experimentation. Observations were made and the time taken for paralysis was noted when no movement of any sort could be observed. Time of death of worms were recorded after ascertaining that worms neither moved when shaken vigorously nor when dipped in warm water. It was observed that at higher concentrations of bryophyte extract produced paralytic effect much earlier and the time taken for death was shorter for all types of worms. Aqueous extract of bryophyte exhibited anthelmintic activity in dose dependent manner showing maximum efficacy at 20 mg/ml concentration on cestodes and nematodes. However the plant extract exhibited more potent activity at lowest concentration 10mg/ml against Ascaridia galli. Anthelmintic activity of the extract was compared with standard drug piperazine citrate. These results suggest that Pottia lanceolata bryophyte extract exhibited significant anthelmintic activity when compared to Tortula subulata.

tag: host

value: Gallus gallus

tag: host tissue

value: Intestine

value: Whole body

value: Pottia lanceolata bryophyte extract


title: SK-N-SH_5

description: single-cell RNA-seq (MARS-seq)

value: cell line

value: SK-N-SH


title: SN01-002-H

value: 3 hpf

tag: ploidy

value: Haploid

tag: genotype (f*m)


title: CS16_D_Mid_2

tag: tissue

value: dorsal aorta and surrounding mesenchyme

tag: subdomain

value: Dorsal Mid (D_Mid)


title: SK-N-SH_1

description: single-cell RNA-seq (MARS-seq)


title: CS16_D_Inner_3

value: Dorsal Inner (D_Inner)


title: SK-N-SH_4

description: single-cell RNA-seq (MARS-seq)


title: early_sham_L_50_49L_a1_hyper

tag: breed/model

value: red Duroc swine scar model

tag: gender

value: Male

value: Juvenile

value: hyper


title: CS16_V_Inner_3

value: Ventral Inner (V_Inner)


title: SN01-004-D

value: Diploid

value: TJH*Tu


title: SN01-019-D


title: SK-N-SH_3

description: single-cell RNA-seq (MARS-seq)


title: early_sham_R_49_49R_a3_hypo

tag: age

tag: pigmentation phenotype

value: hypo

value: Skin

value: Unknown

value: Reference


title: early_sham_R_50_49R_a1_hyper

tag: sample type


title: SK-N-SH_2

description: single-cell RNA-seq (MARS-seq)

value: cell line

value: SK-N-SH


title: SN01-001-D

value: 3 hpf


title: NPC_1mln_rep2_MTS

first: Elisa

last: Barbieri

address: 5 Little France Drive

description: nascent-RNA profiling with fastGRO was performed in NPC differentiated cells

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (RNAseq, chromatin RNA-seq): STAR
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: NPC differentiated cells

growth_protocol: NPC differentated cells were mainted in 50% Neurobasal Medium/50% advanced DMEM with 1x Neural Induction Supplement

extract_protocol: NEBNext ChIP-Seq ULTRAII RNA Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: NPC differentated cells were treated with PSC Neural Induction Medium for 7 days and then expanding using Neural Expansion Medium for 6 days

value: NPC

tag: experiment

value: fastGRO

tag: agent


title: low metastatic cell line co-cultured with astrocytes, replicate 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
BrM2.cocul.2
processed data file: QingChen_melanoma_raw_counts.txt

data_processing:
RNA-Seq data was aligned using bowtie2 against hg38 version of genome and rsem (ver. 1.2.12) with Ensembl v84 transcriptome information used for gene count.
DESeq2 was used for differential expression analysis.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: QingChen_melanoma_raw_counts.txt: Processed data file contains the raw counts for each gene.

source_name: derivative from melanoma cell line WM4265.2

extract_protocol:
RNA was extracted with Trizol (Invitrogen) and subsequently cleaned and DNase-treated using RNeasy columns (Qiagen).
Libraries for RNA-seq were prepared with Lexogen QuantSeq 3’mRNA-Seq library prep kit at the Wistar Institute Genomics Facility and subjected to a 75 bp single-end sequencing run on NextSeq 500, using Illumina’s NextSeq 500 high output sequencing kit following the manufacturer’s instructions.

tag: cell type

value: Derivative from melanoma cell line WM4265.2

tag: metastatic potential

value: Low

tag: culture

value: Co-cultured with astrocytes

tag: replicate


title: ILF3_IPB

city: Los Angeles

first: Xinshu

last: Xiao

state: CA

address: 610 Charles E. Young Drive S

institute: University of California, Los Angeles

description: ILF3_A549.both_reps_and_alu.gene_annotated.alu_annotated.bed

data_processing:
De-multiplex in-line barcodes (Van Nostrand et al., Nature Methods 13, 508-514. 2016)
Trim adapters using cutadapt in two rounds for each barcode used  (Van Nostrand et al., Nature Methods 13, 508-514. 2016)
Align reads in multiple rounds with STAR. Round 1 of alignment: reads mapped to rRNA sequences discarded. STAR --runMode alignReads --runThreadN 16 --genomeDir rRNA.index --genomeLoad NoSharedMemory --readFilesIn $fastqPT --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outFileNamePrefix $rrna_out_sam --outSAMattributes All  --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd
Round 2 of alignment: remaining reads mapped to Alu sequences, allowing for multi-mapping of up to 100 locations per read. STAR --runMode alignReads --runThreadN 16 --genomeDir Alu.extended.index --genomeLoad NoSharedMemory --readFilesIn $fastqPT --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFilterMismatchNoverLmax 0.05 --outFileNamePrefix $alu_out_sam --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --alignEndsType EndToEnd --outSAMprimaryFlag AllBestScore
Round 3 of alignment: remaining reads uniquely mapped to genome. STAR --runMode alignReads --runThreadN 16 --genomeDir genome.index --genomeLoad NoSharedMemory --readFilesIn $fastqPT --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterMismatchNoverLmax 0.05 --outFileNamePrefix $genome_out_sam --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --alignEndsType EndToEnd
Call peaks of enriched reads, considering genome and Alu-mapped reads, in sliding window of 50 nt by Poisson model. (Bahn et al., Nature Communications 6, 2015 ; Quinones-Valdez et al., Communications Biology 2, 2019)
Normalization by size-matched input: calculate coverage enrichment at peaks (Quinones-Valdez et al., Communications Biology 2, 2019)
Genome_build: hg19
Supplementary_files_format_and_content: bed format includes input-normalized peaks, with at least 4-fold enrichment, merged across two replicates

source_name: A549 cells

growth_protocol: A549 cells were maintained in F12/K media with 10% fetal bovine serum, 100units/mL peniciilin, 100ug/mL streptomycin in 5% CO2 at 37°C.

extract_protocol:
After lysing cells in iCLIP lysis buffer and limited digestion with RNase I (Ambion), ILF3-RNA complexes were immunoprecipitated (ILF3/NF90 antibody from Bethyl Laboratories, A303-651A), and washes were performed. Following RNA dephosphorylation, a barcoded RNA adapter is added to the 3’ end. Then after protein gel electrophoresis and nitrocellulose membrane transfer, RNA is isolated from the region of interest by proteinase K treatment. Reverse transcription is performed, and a DNA adapter is added to the cDNA 3’ end. (Van Nostrand et al., Nature Methods 13, 508-514. 2016)
eCLIP libraries were constructed following previously published ENOCDE eCLIP standard protocol (Van Nostrand et al., Nature Methods 13, 508-514. 2016)

treatment_protocol: 10 million A549 cells were ultraviolet crosslinked at 254 nm (800 mJ cm-2).

tag: cell line

tag: barcodes

tag: eclip antibody

value: ILF3/NF90 antibody (Bethyl Laboratories, A303-651A)


title: early_sham_R_49_49R_a1_hyper

value: red Duroc swine scar model

value: Male

value: Juvenile

value: hyper


title: CS16_V_Mid_2

tag: embryo

tag: developmental stage

value: dorsal aorta and surrounding mesenchyme

value: Ventral Mid (V_Mid)


title: low metastatic cell line co-cultured with astrocytes, replicate 3

description:
BrM2.cocul.3
processed data file: QingChen_melanoma_raw_counts.txt


title: SMInput


title: CS16_D_Inner_2

tag: tissue

tag: subdomain

value: Dorsal Inner (D_Inner)


title: low metastatic cell line cultured alone, replicate 3

description:
BrM2.alone.3
processed data file: QingChen_melanoma_raw_counts.txt

value: Alone


title: low metastatic cell line co-cultured with astrocytes, replicate 1

description:
BrM2.cocul.1
processed data file: QingChen_melanoma_raw_counts.txt


title: CS16_V_Mid_1


title: low metastatic cell line cultured alone, replicate 2

description:
BrM2.alone.2
processed data file: QingChen_melanoma_raw_counts.txt


title: CS16_D_Outer_1

value: Dorsal Outer (D_Outer)


title: CS16_V_Inner_2

value: Ventral Inner (V_Inner)


title: ILF3_IPA


title: low metastatic cell line cultured alone, replicate 4

description:
BrM2.alone.4
processed data file: QingChen_melanoma_raw_counts.txt


title: CS16_V_Outer_1

value: Ventral Outer (V_Outer)


title: 293E, Rep#2, siERH-#5

city: Hong Kong

first: S. Chul

last: Kwon

address: L1-05, Laboratory Block, 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description:
siERH-5
count_ERH.txt
RPM_ERH_txt

data_processing:
The base calling was done by RTA (Real Time Analysis. v1.18)
In the preprocessing step, low-quality base-calling reads were discarded using fastq_quality_filter (-q 20 –p 90). Next, reads containing a 3′ Illumina adapter sequence were filtered and the adapter sequence was removed using cutadapt (-a TGGAATTCTCGGGTGCCAAGG --trimmed-only). Then, PCR duplicate sequences were removed using fastx_collapser. Random tetramer sequences were trimmed at both the 5′ and 3′-ends to reduce the ligation bias and reads within the miRNA size range were obtained using cutadapt (-u 4 -u -4 -m 18 -M 26).
In the alignment and read counting steps, reads were mapped onto the hg38 human genome using bowtie2, allowing no mismatches, deletions, or insertions at all but the terminal modification with at most 2 (-f --local -p 4 --score-min L,-4,2 --ma 2 -k 5). The mapped reads to the miRNA hairpin annotation in miRBase v21 were used to count miRNA reads using bedtools.
The normalization was done by RPM (reads per million).
Genome_build: hg38
Supplementary_files_format_and_content: Provided are tab-delimited text files containing read counts.

growth_protocol: HEK293E was cultured in DMEM (Welgene) supplemented with 9% fetal bovine serum (Welgene). K562 was cultured in RPMI1640 (Welgene) supplemented with 9% fetal bovine serum (Welgene).

extract_protocol:
Total RNA was purified using TRIzol (Thermo Fisher).
10 μg of total RNA was mixed with 30 spike-in RNAs (Nucleic Acids Res. (2019) 47:2630); then, 18–30-nt fragments were purified through a 15% urea-polyacrylamide gel. Subsequently, a 3′ adapter containing 4 random nucleotides at the 5′-end was ligated, and gel purification was performed to purify 40–55-nt RNAs. The purified RNA was ligated with a 5′ adapter that also contained 4 random nucleotides at the 3′-end. Reverse transcription, PCR, and gel purification were performed following a general Illumina protocol.

treatment_protocol: HEK293E cells were tandemly transfected with siRNAs using Lipofectamine 2000 (Thermo Fisher) on days 0 and 3. On day 5, HEK293E cells were harvested for RNA preparation. K562 cells were resuspended in OPTI-MEM (Thermo Fisher) and transfected with siRNAs using Neon (Thermo Fisher) with the condition of 1450 V, 10 ms, 3 pulses. Four days after transfection, K562 cells were harvested.

tag: transfected gene

tag: experimental group

value: Group 2


title: K562, Rep#1, siERH-#5

description:
siERH-5
count_ERH.txt
RPM_ERH_txt

value: Group 3


title: Chick_Nematode_Control

tag: host

value: Gallus gallus

tag: host tissue

value: Intestine

value: Whole body

tag: treatment

value: Control


title: K562, Rep#1, siGFP

description:
siGFP
count_ERH.txt
RPM_ERH_txt

value: siGFP


title: early_sham_L_49_49L_a1_hyper

tag: breed/model

value: red Duroc swine scar model

tag: gender

value: Male

tag: age

tag: pigmentation phenotype

value: Skin

value: Unknown

tag: sample type

value: Reference


title: CS16_D_Mid_1

value: dorsal aorta and surrounding mesenchyme

value: Dorsal Mid (D_Mid)


title: 293E, Rep#2, siERH-#3

description:
siERH-3
count_ERH.txt
RPM_ERH_txt

tag: cell line


title: D_CD45_2

description: Total RNA (ribosome depleted)

source_name: Dorsal aorta sorted hematoendothelial populations

extract_protocol:
The dorsal aortae were dissected from human embryos CS15-16 (N=2) then further bisected into ventral and dorsal portions (AoV and AoD respectively). Tissues were dissociated into single cells in 1mg/ml Collagenase-Dispase (Roche) and 0.12 mg/ml of DNase I (Roche) for 35 min in a 37 oC rotating water bath and stained with conjugated antibodies anti-human VE-Cadherin-PE (Beckman Coulter, 5µg/ml), anti-human CD45 –v450 (Clone: HI30, BioLegend, 6µg/ml) and anti-human CD235A – APC (BD Bioscience, 0.2µg/ml) for 1 hour at 4 oC. Dead cells and erythroid cells were excluded by 7AAD and CD235A staining respectively. VC+CD45-, VC+CD45+ and VC-CD45+ populations were sorted using a FACS Aria-II (BD Bioscience) into Eppendorf tubes containing RLT buffer from the RNeasy Micro kit ready for RNA purification. RNA was purified using the RNeasy Micro kit.
SMARTer® Stranded Total RNA-Seq Kit v2 -Pico Input Mammalian kit (Takara) for samples 1-12

value: Dorsal aorta

tag: population

value: Dorsal hematopoietic (VC-CD45+)


title: low metastatic cell line cultured alone, replicate 1

description:
BrM2.alone.1
processed data file: QingChen_melanoma_raw_counts.txt

tag: cell type

value: Derivative from melanoma cell line WM4265.2

tag: metastatic potential

value: Low

tag: culture

value: Alone

tag: replicate


title: CS16_D_Inner_1

tag: embryo

tag: developmental stage

tag: tissue

tag: subdomain

value: Dorsal Inner (D_Inner)


title: high metastatic cell line co-cultured with astrocytes, replicate 4

description:
BrM1.cocul.4
processed data file: QingChen_melanoma_raw_counts.txt

value: High

value: Co-cultured with astrocytes


title: CS16_V_Inner_1

value: Ventral Inner (V_Inner)


title: SR1Oe_III_RC4_rep2

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

hyb_protocol: Affymetrix Rat Gene 1.0 ST arrays were hybridized with 5 microgramme of labeled, amplified cDNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) in Affymetrix Expression Console software.

label: biotin

organism: Rattus norvegicus

source_name: oesophagus cells after first transplantation into skin, bulk

label_protocol: 100 nanogram of total RNA were amplified and labeled using Affymetrix whole transcript sense target labeling protocol (kits #900673, #900671)

growth_protocol: Various tissues were dissected from PN200 EFGP rat. Dissected tissues were harvested and kept in cold Dulbecco Modified Eagle's Medium (DMEM) supplemented with 10% Bovine Serum during dissection. Tissues  were mechanically minced before being dissociated in 0.05% trypsin solution containing 0.1% EDTA at 37°C with a gentle stirring. Skin grafts containing GFP-positive hair follicles were carefully dissected from the back of recipient nude mice and dissociated in 30 ml of 0.05% trypsin containing 0.1% EDTA at 37°C for 60 to 120 min.

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (QIAGEN Inc.)

treatment_protocol: Tissues and hair follicle cells were cultivated on a feeder layer of irradiated 3T3-J2 cells in a 3:1 DMEM F12 medium supplemented as described (Bonfanti et al., 2010). EGFP-positive cells were FACS-sorted for analysis.

tag: genotype

value: constitutively express the Enhanced Green Fluorescent protein (EGPF) (green rat CZ-004” SDTgN (act-EGFP)obsCZ-004)

tag: background strain

value: Sprague-Dawley

value: oesophagus


title: control_BL_R_49_BL_R_BL

tag: breed/model

value: red Duroc swine scar model

value: Male

value: Juvenile

value: Skin


title: control_BL_R_50_BL_R_BL

tag: gender

value: Unknown

value: Reference


title: control_BL_L_49_BL_L_BL

tag: age


title: SR1TR_I_RC4_rep2

source_name: trachea cells after first transplantation into skin, bulk

value: trachea


title: SR1FP_III_RC4_rep1

source_name: foot pad cells after first transplantation into skin, bulk

value: foot pad


title: 293E, Rep#2, siGFP

description:
siGFP
count_ERH.txt
RPM_ERH_txt

tag: transfected gene

value: siGFP

tag: experimental group

value: Group 2


title: D_VC_2

description: Total RNA (ribosome depleted)

value: Dorsal aorta

value: Dorsal endothelial (VC+CD45-)


title: SR1TR_I_RC4_rep1


title: 293E, Rep#1, siERH-#3

description:
siERH-3
count_ERH.txt
RPM_ERH_txt

tag: cell line

value: Group 1


title: high metastatic cell line co-cultured with astrocytes, replicate 2

description:
BrM1.cocul.2
processed data file: QingChen_melanoma_raw_counts.txt

value: Derivative from melanoma cell line WM4265.2

value: High

value: Co-cultured with astrocytes


title: control_BL_L_50_BL_L_BL

tag: sample type


title: SR1FP_III_RC4_rep2

value: constitutively express the Enhanced Green Fluorescent protein (EGPF) (green rat CZ-004” SDTgN (act-EGFP)obsCZ-004)

value: Sprague-Dawley


title: 293E, Rep#1, siGFP

description:
siGFP
count_ERH.txt
RPM_ERH_txt


title: SR1Va_IV_RC5_rep1

source_name: vagina cells after first transplantation into skin, bulk

value: vagina


title: 293E, Rep#1, siControl

description:
siControl
count_ERH.txt
RPM_ERH_txt

value: siControl


title: high metastatic cell line cultured alone, replicate 3

description:
BrM1.alone.3
processed data file: QingChen_melanoma_raw_counts.txt

tag: cell type

value: Alone


title: 293E, Rep#2, siControl

description:
siControl
count_ERH.txt
RPM_ERH_txt


title: V_VC_CD45_2

description: Total RNA (ribosome depleted)

tag: population

value: Ventral hematopoietic stem/progenitor cells (VC+CD45+)


title: ∆perR H2O2 3

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description: S. mutans ∆perR grown to OD600 = 0.4 in BHI medium, then exposed to 0.5mM H2O2 for 5 min Replicate 3

data_processing:
Read mapping was performed on a Galalxy server hosted by the University of Florida Research Computer
Map with Bowtie for Illumina was used to map the reads to the S. mutans UA159 genome (NC_004350.2)
htseq-count was used to tabulate the reads per open reading frame
Degust was used to make final comparisons in counts between cells grown in the complete versus the metal-depleted media.
Genome_build: NC_004350.2
Supplementary_files_format_and_content: The processed .csv data files list the numbers of reads for each gene of the S. mutans genome (SMU).

organism: Streptococcus mutans UA159

source_name: Streptococcus mutans ∆perR mutant

growth_protocol: Cells were grown to OD600 = 0.4

extract_protocol:
Harvested cells were resuspended in 1mL of RNA Protect Bacteria Reagent (Qiagen). Total RNA was isolated from homogenized S. mutans cell lysates by acid-phenol:chloroform extractions.  The nucleic acid was subjected to DNase I digestion (Ambion).   The RNA was then purified using the Qiagen RNeasy colum purification kit, including an additional on-column DNase digest.  Total RNA was subjected to two rounds of mRNA enrichment using the MICROBExpress Bacterial mRNA Purification kit (ThermoFisher).
cDNA libraries with unique barcoes were generated from 100ng enriched mRNA using the NEB Next UltraII Directional RNA Library Prep kit for Illumina (New England Biolabs).
Pooled libraries were subjected to RNA deep sequencing at the University of Florida Interdisciplinary Center for Biotechnology Research using the Illumina NextSeq500 platform.

treatment_protocol: At the desired OD600, samples were split in two.  Control samples were incubated an additional 5 minutes.   H2O2 samples were exposed to 0.5mM H2O2 for 5 mintues.

tag: genotype/variation

value: perR mutant

tag: culture

value: Cells were grown to OD600 of 0.4, exposed to 0.5mM H2O2 for 5 min, then harvested by centrifugation.  Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use


title: D_VC_CD45_2

description: Total RNA (ribosome depleted)

tag: embryo

value: Dorsal hematopoietic stem/progenitor cells (VC+CD45+)


title: V_VC_2

description: Total RNA (ribosome depleted)

tag: developmental stage

value: Ventral endothelial (VC+CD45-)


title: high metastatic cell line co-cultured with astrocytes, replicate 1

description:
BrM1.cocul.1
processed data file: QingChen_melanoma_raw_counts.txt

tag: metastatic potential

tag: replicate


title: high metastatic cell line cultured alone, replicate 1

description:
BrM1.alone.1
processed data file: QingChen_melanoma_raw_counts.txt


title: high metastatic cell line co-cultured with astrocytes, replicate 3

description:
BrM1.cocul.3
processed data file: QingChen_melanoma_raw_counts.txt


title: ∆perR Control 3

description: S. mutans ∆perR grown to OD600 = 0.4 in BHI medium Replicate 3

value: Cells were grown to OD600 of 0.4, then harvested by centrifugation.  Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use


title: SR1Va_IV_RC5_rep2

tag: genotype

tag: tissue


title: high metastatic cell line cultured alone, replicate 4

description:
BrM1.alone.4
processed data file: QingChen_melanoma_raw_counts.txt


title: V_CD45_2

description: Total RNA (ribosome depleted)

value: Dorsal aorta

value: Ventral hematopoietic (VC-CD45+)


title: SR1BC_III_RC5_rep1

source_name: oral mucosa cell after first transplantation into skin, bulk

tag: background strain

value: oral mucosa


title: ducts Lats1/2 KO rep2

city: Daejeon

first: David

last: Eisenbarth

address: 335 Gwahak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-seperated value files include raw counts.

organism: Mus musculus

source_name: Pancreas

extract_protocol:
RNA was harvested using an easy-BLUE total RNA extraction kit. Clontech SMARTer Stranded RNA-Seq kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: pancreas

value: ductal

value: Lats1fl/fl; Lats2fl/fl; Sox9-CreER


title: ∆perR H2O2 2

description: S. mutans ∆perR grown to OD600 = 0.4 in BHI medium, then exposed to 0.5mM H2O2 for 5 min Replicate 2


title: high metastatic cell line cultured alone, replicate 2

description:
BrM1.alone.2
processed data file: QingChen_melanoma_raw_counts.txt

value: Derivative from melanoma cell line WM4265.2

value: High


title: D_VC_1

description: Total RNA (ribosome depleted)

value: Dorsal endothelial (VC+CD45-)


title: ducts WT rep2

value: wild type


title: SR1BC_III_RC5_rep2

value: constitutively express the Enhanced Green Fluorescent protein (EGPF) (green rat CZ-004” SDTgN (act-EGFP)obsCZ-004)

value: Sprague-Dawley


title: ∆perR H2O2 1

description: S. mutans ∆perR grown to OD600 = 0.4 in BHI medium, then exposed to 0.5mM H2O2 for 5 min Replicate 1

value: perR mutant


title: SR1FP_IV_rep2

source_name: foot pad cells bulk, adult

value: foot pad


title: D_CD45_1

description: Total RNA (ribosome depleted)

value: Dorsal hematopoietic (VC-CD45+)


title: ∆perR Control 2

description: S. mutans ∆perR grown to OD600 = 0.4 in BHI medium Replicate 2


title: ducts WT rep1


title: ducts Lats1/2 KO rep1


title: SR1Oe_V_rep2

source_name: oesophagus cells bulk, adult

value: oesophagus


title: SR1Tr_V_rep2

source_name: trachea cells bulk, adult

value: trachea


title: ∆perR Control 1

description: S. mutans ∆perR grown to OD600 = 0.4 in BHI medium Replicate 1

value: Cells were grown to OD600 of 0.4, then harvested by centrifugation.  Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use


title: V_CD45_1

description: Total RNA (ribosome depleted)

value: Dorsal aorta

value: Ventral hematopoietic (VC-CD45+)


title: V_VC_CD45_1

description: Total RNA (ribosome depleted)

value: Ventral hematopoietic stem/progenitor cells (VC+CD45+)


title: SR1Tr_V_rep1


title: UA159 H2O2 2

description: S. mutans UA159 grown to OD600 = 0.4 in BHI medium, then exposed to 0.5mM H2O2 for 5 min Replicate 2

source_name: Streptococcus mutans UA159 wild type

value: Cells were grown to OD600 of 0.4, exposed to 0.5mM H2O2 for 5 min, then harvested by centrifugation.  Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use


title: SR1FP_IV_rep1


title: D_VC_CD45_1

description: Total RNA (ribosome depleted)

value: Dorsal hematopoietic stem/progenitor cells (VC+CD45+)


title: UA159 H2O2 1

description: S. mutans UA159 grown to OD600 = 0.4 in BHI medium, then exposed to 0.5mM H2O2 for 5 min Replicate 1


title: UA159 Control 3

description: S. mutans UA159 grown to OD600 = 0.4 in BHI medium Replicate 3


title: UA159 H2O2 3

description: S. mutans UA159 grown to OD600 = 0.4 in BHI medium, then exposed to 0.5mM H2O2 for 5 min Replicate 3


title: U2OSdcp1a_isotonic_replicate 2

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description: bru-labeled RNA

data_processing:
Library strategy: BruSeq
Illumina Casava v1.8.2 software used for basecalling.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3)
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Uniquely mapped reads were counted in 1kb genomic bins and bin RPKM values calculated as previously described (Paulsen et. al. 2013)
Genome_build: hg38
Supplementary_files_format_and_content: The columns of the genes.bed files are: (1) chromosome; (2) start; (3) end; (4) name; (5) strand; (6) gene length  (7) read count (8) RPKM

growth_protocol: Cells were propagated in McCoy’s 5A medium supplemented with 10% fetal bovine serum and Penicillin-Streptomycin (GIBCO, #15140), and were kept under positive selection for GFP-DCP1A expression with 100 μg/mL G418.

extract_protocol:
Cells were labeled with 2 mM Bromouridine (Sigma Aldrich) for 30 min, total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013 (Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response. Proc. Natl. Acad. Sci. U.S.A. 2013; 110:2240–2245)
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: Hypertonic medium (300 mM Na+) was prepared by supplementing regular growth medium with 10x PBS such that the appropriate sodium concentration was achieved. Isotonic medium (150 mM Na+) was prepared by mock supplementing regular growth medium with 1x PBS, whose volumes matched that of 10x PBS in hypertonic medium.

value: stably overexpressing GFP-DCP1a

tag: treatment

value: U2OS-GFP-DCP1a cell line treated with isotonic media

tag: bru labeling time

value: 0.5 hours

tag: assay

value: bruseq

tag: time between end of bru labeling and rna extraction

value: 0 hours

tag: labeling agent

value: Bromouridine (Bru)


title: V_VC_1

description: Total RNA (ribosome depleted)

value: Ventral endothelial (VC+CD45-)


title: U2OSdcp1a_isotonic_replicate 1

description: bru-labeled RNA

tag: cell line


title: SR1Va_IV_rep1

source_name: vagina cells bulk, adult

value: constitutively express the Enhanced Green Fluorescent protein (EGPF) (green rat CZ-004” SDTgN (act-EGFP)obsCZ-004)

value: Sprague-Dawley

value: vagina


title: U2OSdcp1a_hypertonic_replicate 2

description: bru-labeled RNA

value: U2OS-GFP-DCP1a cell line treated with hypertonic media


title: UA159 Control 2

description: S. mutans UA159 grown to OD600 = 0.4 in BHI medium Replicate 2

value: wild type

value: Cells were grown to OD600 of 0.4, then harvested by centrifugation.  Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use


title: eCLIP_2

city: Boston

first: Yang

last: Shi

state: Massachusetts

address: 320 LONGWOOD AVE

department: NEWBORN MEDICINE

institute: BOSTON CHILDREN'S HOSPITAL

description:
Purified RNA from eCLIP
eCLIP_replicate_2

data_processing:
After adapter-trimming and quality-filtering, reads were mapped to human specific version of rRNAs with RNA-seq aligner STAR,then the unmapped reads from last step were taken out to map to Human genome with STAR,the downstream analysis for rRNA enrichment was carried out as decribed(Van Nostrand et al. 2016; Kaiser et al. 2019).
Genome_build: hg19
Supplementary_files_format_and_content: xlsx

growth_protocol: Human 293T cells were grown in standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)).

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with  anti-HA Dynabeads, and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) .Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: While plated, 293T cells were crosslinked with UV (254 nm, 400 mJ/cm2). 293T cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen.

value: METTL5-HA stable cell lines

tag: sample type

value: eCLIP


title: SR1Va_IV_rep2


title: U2OSdcp1a_hypertonic_replicate 1

description: bru-labeled RNA


title: Input

description:
Purified RNA from Input
Input

value: WT

value: Input


title: eCLIP_1

description:
Purified RNA from eCLIP
eCLIP_replicate_1


title: UA159 Control 1

description: S. mutans UA159 grown to OD600 = 0.4 in BHI medium Replicate 1

tag: genotype/variation


title: SR1BC_V_rep2

source_name: oral mucosa cells bulk, adult

value: oral mucosa


title: UninjCtrl_st9.2_Rep2

status: Public on Sep 16 2020

city: Irvine

first: Kitt

middle: D.

last: Paraiso

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

description: Ctnnb1 (bcat) control stage 9.5 embryo RNA-seq replicate 2

data_processing:
ChIP-seq raw reads were assessed by FastQC and trimmed with Trimmomatic.
Reads were aligned to the Xenopus tropicalis genome assembly version 9.0 using bowtie2 v2.3.4.7.
Duplicate and multi-mapped reads were removed by Picard and samtools.
Peaks were called with MACS2 against NF10.5 input DNA with default options.
Peaks were associated with genes using the HOMER “nearest TSS function.
High confidence ChIP-seq peaks were identified using Irreproducible discovery rate (IDR) analysis sing a threshold of 0.01.
RNA-seq raw reads were assessed using FastQC and adapters/low quality reads were removed with Trimmomatic.
Reads were mapped to the Xenopus tropicalis genome version 9.0 with bowtie2.
Mapped reads were quantified using RSEM and reported in transcripts per million (TPM).
Differentially expressed genes (LogFC ><= |1| and FDR <= 0.05) were identified by a pairwise comparison between control-MO and Sox17-MO, control-MO and Bcat-MO embryos at each stage using RUVSeq (R package).
Genome_build: Xenopus tropicalis v9.0

organism: Xenopus tropicalis

source_name: Whole embryos

growth_protocol: Developmentally synchronized embryos were generated by in vitro fertilization using standard protocols. Embryos were incubated in agarose-coated dishes in 1/9thX MMR at 25oC until needed.

extract_protocol: Embryos were injected with Total RNA was isolated at indicated stages using a Nucleo-spin RNA kit (Machery-Nagel). RNA-seq libraries were generated using Smart-seq2 cDNA synthesis followed by tagmentation (Picelli et al., 2014).

tag: tissue type

value: whole embryos at N&F stage 9.5

tag: organism strain

value: Nigerian strain


title: bcatMO_st9.1_Rep2

description: Ctnnb1 (bcat) MO-injected stage 9 embryo RNA-seq replicate 2

value: whole embryos at N&F stage 9


title: bcatMO_st9.2_Rep2

description: Ctnnb1 (bcat) MO-injected stage 9.5 embryo RNA-seq replicate 2


title: UninjCtrl_st9.1_Rep2

description: Ctnnb1 (bcat) control stage 9 embryo RNA-seq replicate 2


title: UninjCtrl_st8_Rep2

description: Ctnnb1 (bcat) control stage 8 embryo RNA-seq replicate 2

value: whole embryos at N&F stage 8


title: bcatMO_st10.5_Rep2

description: Ctnnb1 (bcat) MO-injected stage 10.5 embryo RNA-seq replicate 2

value: whole embryos at N&F stage 10.5


title: bcatMO_st10_Rep2

description: Ctnnb1 (bcat) MO-injected stage 10 embryo RNA-seq replicate 2

value: whole embryos at N&F stage 10


title: UninjCtrl_st10.5_Rep2

description: Ctnnb1 (bcat) control stage 10.5 embryo RNA-seq replicate 2


title: bcatMO_st8_Rep2

description: Ctnnb1 (bcat) MO-injected stage 8 embryo RNA-seq replicate 2


title: UninjCtrl_st7_Rep2

description: Ctnnb1 (bcat) control stage 7 embryo RNA-seq replicate 2

value: whole embryos at N&F stage 7


title: bcatMO_st7_Rep2

description: Ctnnb1 (bcat) MO-injected stage 7 embryo RNA-seq replicate 2


title: sox17MO_UninjCtrl_st12_Rep2

description: Sox17 control stage 12 embryo RNA-seq replicate 2

value: whole embryos at N&F stage 12


title: Sox17MO_st12_Rep2

description: Sox17 MO-injected stage 12 embryo RNA-seq replicate 2


title: SR1BC_V_rep1

value: constitutively express the Enhanced Green Fluorescent protein (EGPF) (green rat CZ-004” SDTgN (act-EGFP)obsCZ-004)

value: Sprague-Dawley


title: sox17MO_UninjCtrl_st10.5_Rep2

description: Sox17 control stage 10.5 embryo RNA-seq replicate 2


title: Sox17MO_st10_Rep2

description: Sox17 MO-injected stage 10 embryo RNA-seq replicate 2


title: sox17MO_UninjCtrl_st10_Rep2

description: Sox17 control stage 10 embryo RNA-seq replicate 2


title: Sox17MO_st11_Rep2

description: Sox17 MO-injected stage 11 embryo RNA-seq replicate 2

value: whole embryos at N&F stage 11


title: sox17MO_UninjCtrl_st11_Rep2

description: Sox17 control stage 11 embryo RNA-seq replicate 2


title: sox17MO_UninjCtrl_st9.2_Rep2

description: Sox17 control stage 9.5 embryo RNA-seq replicate 2


title: Sox17MO_st9.2_Rep2

description: Sox17 MO-injected stage 9.5 embryo RNA-seq replicate 2


title: UninjCtrl_st12_Rep1

description: Ctnnb1 (bcat) control stage 12 embryo RNA-seq replicate 1


title: Sox17MO_st9.1_Rep2

description: Sox17 MO-injected stage 9 embryo RNA-seq replicate 2


title: sox17MO_UninjCtrl_st9.1_Rep2

description: Sox17 control stage 9 embryo RNA-seq replicate 2


title: bcatMO_st12_Rep1

description: Ctnnb1 (bcat) MO-injected stage 12 embryo RNA-seq replicate 1


title: UninjCtrl_st11_Rep1

description: Ctnnb1 (bcat) control stage 11 embryo RNA-seq replicate 1


title: UninjCtrl_st10_Rep2

description: Ctnnb1 (bcat) control stage 10 embryo RNA-seq replicate 2


title: bcatMO_st11_Rep1

description: Ctnnb1 (bcat) MO-injected stage 11 embryo RNA-seq replicate 1


title: UninjCtrl_st9.2_Rep1

description: Ctnnb1 (bcat) control stage 9.5 embryo RNA-seq replicate 1


title: bcatMO_st9.2_Rep1

description: Ctnnb1 (bcat) MO-injected stage 9.5 embryo RNA-seq replicate 1


title: bcatMO_st7_Rep1

description: Ctnnb1 (bcat) MO-injected stage 7 embryo RNA-seq replicate 1


title: UninjCtrl_st10.5_Rep1

description: Ctnnb1 (bcat) control stage 10.5 embryo RNA-seq replicate 1


title: bcatMO_st9.1_Rep1

description: Ctnnb1 (bcat) MO-injected stage 9 embryo RNA-seq replicate 1


title: UninjCtrl_st8_Rep1

description: Ctnnb1 (bcat) control stage 8 embryo RNA-seq replicate 1


title: bcatMO_st10_Rep1

description: Ctnnb1 (bcat) MO-injected stage 10 embryo RNA-seq replicate 1


title: bcatMO_st10.5_Rep1

description: Ctnnb1 (bcat) MO-injected stage 10.5 embryo RNA-seq replicate 1


title: UninjCtrl_st9.1_Rep1

description: Ctnnb1 (bcat) control stage 9 embryo RNA-seq replicate 1


title: sox17MO_UninjCtrl_st12_Rep1

description: Sox17 control stage 12 embryo RNA-seq replicate 1


title: UninjCtrl_st7_Rep1

description: Ctnnb1 (bcat) control stage 7 embryo RNA-seq replicate 1


title: UninjCtrl_st10_Rep1

description: Ctnnb1 (bcat) control stage 10 embryo RNA-seq replicate 1


title: bcatMO_st8_Rep1

description: Ctnnb1 (bcat) MO-injected stage 8 embryo RNA-seq replicate 1


title: Sox17MO_st12_Rep1

description: Sox17 MO-injected stage 12 embryo RNA-seq replicate 1


title: sox17MO_UninjCtrl_st10_Rep1

description: Sox17 control stage 10 embryo RNA-seq replicate 1


title: Sox17MO_st11_Rep1

description: Sox17 MO-injected stage 11 embryo RNA-seq replicate 1


title: sox17MO_UninjCtrl_st10.5_Rep1

description: Sox17 control stage 10.5 embryo RNA-seq replicate 1


title: Sox17MO_st10_Rep1

description: Sox17 MO-injected stage 10 embryo RNA-seq replicate 1


title: sox17MO_UninjCtrl_st11_Rep1

description: Sox17 control stage 11 embryo RNA-seq replicate 1


title: sox17MO_UninjCtrl_st9.2_Rep1

description: Sox17 control stage 9.5 embryo RNA-seq replicate 1


title: Sox17MO_st9.2_Rep1

description: Sox17 MO-injected stage 9.5 embryo RNA-seq replicate 1


title: Sox17MO_st9.1_Rep1

description: Sox17 MO-injected stage 9 embryo RNA-seq replicate 1


title: sox17MO_UninjCtrl_st9.1_Rep1

description: Sox17 control stage 9 embryo RNA-seq replicate 1


title: Sox17ChIP_St10.5_Rep2

description: Sox17 ChIP-seq replicate 2

library_source: genomic

molecule: genomic DNA

extract_protocol: Chromatin for ChIP-seq was obtained after formaldehyde fixation of embryos and sonication as previously described (Chiu et al., 2014) using custom rabbit peptide anti-Sox17-C-terminal antibody (affinity purified by Bethyl labs). ChIP-seq libraries were generated using Bioo Scientific Nextflex ChIP-seq library preparation kit  (Catalog #NOVA-5143-01) and Nextflex barcodes (Catalog #51410).


title: Sox17ChIP_St10.5_Rep1

description: Sox17 ChIP-seq replicate 1


title: Sox17MO_st10.5_Rep1

description: Sox17 MO-injected stage 10.5 embryo RNA-seq replicate 1


title: Splenocyte_10x_scRNA-seq

city: Stanford

first: Jesse

middle: M

last: Engreitz

address: Biomedical Innovation Building Rm 3700

institute: Stanford University

description: scRNA-seq of polyA mRNA from primary mouse splenocytes

data_processing:
Library strategy: scRNA-seq
Align and deduplicate and count with CellRanger (3.0.2)
Pre-process and cluster the count matrix with Seurat (3.1.4)
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix in HDF5 format.
Supplementary_files_format_and_content: Cluster assignments

source_name: Murine Spleen

growth_protocol: C57BL/6 mice from Jackson Laboratory

extract_protocol:
We dissected mice and harvested the spleens on ice in (1x PBS Gibco, 10010-023). We washed spleens in RPMI media (Gibco, 22400-089) and using a scalpel individually cut the spleens into small pieces. We digested the tissue with a 10x collagenase D (Sigma Aldrich 11088866001) / DNase I (Qiagen, 79524) solution (0.05g collagenase D and 10ul DNase I in 1ml of 1 x PBS) diluted to 1x in RPMI by incubation at 37°C shaking (400 rpm) for 30 minutes. We transferred the dissociated tissue onto a 70µm cell strainer (Falcon, 352350) and carefully used a 3ml syringe plunger (BD, 309578) to compress the tissue through the filter. The filtered solution was centrifuged for 10 minutes at 300g and 4°C and we resuspended and incubated the subsequent pellet in ACK lysis buffer (Gibco, A1049201) for 10 minutes at room temperature to lyse the red blood. We quenched the reaction with RPMI media and centrifuged the cells again. We washed twice with cold PBS and used this for final resuspension. We filtered the cells through a 40µm filter (pluriSelect, 43-50040-01) prior to counting the cells using a disposable hemocytometer (INCYTO, DHC-N01-2). We controlled for cell viability using a live/dead stain (Invitrogen, S34860).
10x Chromium Single Cell 3' v3

tag: cell type

value: primary splenocytes

value: Spleen


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H8_ad007

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: DG

tag: Sex

value: male

tag: age


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H8_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H8_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H8_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H9_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H9_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H8_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H9_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H9_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H9_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H9_ad012


title: Plasma_flight_+_ACVR2B/Fc

type: protein

city: Farmington

first: Harshpreet

last: Chandok

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

description: Plasma isolated from mouse maintained in microgravity on the International Space Station and injected with the decoy ACVR2B/Fc decoy receptor

hyb_protocol: SOMAmer–protein complexes are released from the beads by photocleavage of the linker with UV light. Incubation in a buffer containing a polyanionic competitor selectively disrupts nonspecific interactions. SOMAmer–protein complexes are recaptured on a second set of streptavidin- coated beads through biotin-tagged proteins followed by additional washing steps that facilitate further removal of nonspecifically bound SOMAmer reagents.

scan_protocol: A SOMAmer-protein binding step is followed by a series of partitioning and wash steps that converts relative protein concentrations into measurable nucleic acid signals that are quantified using DNA detection technology, which for the SOMAscan assay with over 1,300 SOMAmer reagents is by hybridization to custom DNA microarrays.

data_processing: The SOMAscan assay quantitatively transforms the proteins present in a biological sample into a specific SOMAmer-based DNA signal.

molecule: protein

source_name: Plasma

label_protocol: SOMAmer reagents labeled with a 5’ fluorophore, photocleavable linker, and biotin are immobilized on streptavidin (SA)-coated beads and incubated with samples containing a complex mixture of proteins.Cognate and noncognate SOMAmer–target protein complexes form on the beads. The beads are washed, removing the unbound proteins and the proteins are tagged with biotin.

extract_protocol: SomaScan analysis was performed as described in Williams et al., Nature Medicine 25:1851-1857, 2019.  The entire procedure is described in detail in the Methods section.

treatment_protocol: Flight mice were sent to the International Space Station and maintained in microgravity for 33 days.  Flight recovery mice were maintained at Explora Biolabs in California for two weeks after return from space.  Ground mice were maintained under the identical environmental conditions as the flight mice at Kennedy Space Center in Orlando, FL and then transferred by ground transport to Explora Biolobas for analysis.  Vivarium mice were maintained at the University of Connecticut in Farmington, CT.  ACVR2B/Fc refers to a myostatin/activin A inhibitor that was administered by intraperitoeal injection.  Details of each of these groups of mice can be found in the associated manuscript (Targeting myostatin/activin A protects against skeletal muscle and bone loss during spaceflight, Proceedings of the National Academy of Sciences, USA, in press).

tag: gender

value: female

value: flight + ACVR2B/Fc

tag: tissue

value: plasma


title: Plasma_flight_recovery_uninjected

description: Plasma isolated from uninjected mouse maintained in microgravity at Explora BioLabs

tag: strain

value: flight recovery uninjected


title: Plasma_flight_recovery_+_ACVR2B/Fc

description: Plasma isolated from mouse maintained in microgravity at Explora BioLabs and injected with the decoy ACVR2B/Fc decoy receptor

tag: treatment

value: flight recovery + ACVR2B/Fc


title: Plasma_ground_uninjected

description: Plasma isolated from uninjected mouse maintained on Earth

value: ground uninjected


title: Plasma_vivarium_+_ACVR2B/Fc_1_week

description: Plasma isolated from injected mouse maintained for 1 week at UConn Health

value: vivarium + ACVR2B/Fc 1 week


title: Plasma_flight_uninjected

description: Plasma isolated from uninjected mouse maintained in microgravity on the International Space Station

value: flight uninjected


title: Pasma_vivarium_uninjected_1_week

description: Plasma isolated from uninjected mouse maintained for 1 week at UConn Health

value: vivarium uninjected 1 week


title: Plasma_vivarium_uninjected_2_weeks

description: Plasma isolated from uninjected mouse maintained for 2 weeks at UConn Health

value: vivarium uninjected 2 weeks


title: SR1Oe_V_rep1

tag: genotype

value: constitutively express the Enhanced Green Fluorescent protein (EGPF) (green rat CZ-004” SDTgN (act-EGFP)obsCZ-004)

tag: background strain

value: oesophagus


title: Plasma_vivarium_+_ACVR2B/Fc_2_weeks

description: Plasma isolated from injected mouse maintained for 2 weeks at UConn Health

value: vivarium + ACVR2B/Fc 2 weeks


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H7_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H7_ad010


title: Plasma_ground_+_ACVR2B/Fc

description: Plasma isolated from mouse maintained on Earth and injected with the decoy ACVR2B/Fc decoy receptor

value: ground + ACVR2B/Fc


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H8_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H8_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H7_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H7_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H7_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H7_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H6_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H5_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H6_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H5_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H6_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H6_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H7_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H7_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H5_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H5_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H6_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H5_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H4_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H4_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H4_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H5_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H4_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H4_ad004


title: SR1Oe_III_RC4_rep1

source_name: oesophagus cells after first transplantation into skin, bulk

value: Sprague-Dawley


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H4_ad007

value: DG


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H4_ad001

value: male


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H6_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H5_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H6_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H3_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H3_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H3_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H2_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H4_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H3_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H9_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H2_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H12_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H3_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H2_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H2_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H2_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H2_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H12_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H2_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H12_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H12_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H12_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H12_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H11_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H3_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H11_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H11_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H2_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H3_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H11_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H11_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H11_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H12_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H10_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H10_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H10_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H10_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H10_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H1_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H1_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H10_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H1_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G9_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G9_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G9_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H1_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G9_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H1_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H1_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G8_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G9_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G8_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G8_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H11_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_H1_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G7_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G7_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G6_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G6_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G8_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G8_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G7_ad008


title: Sox17MO_st10.5_Rep2

description: Sox17 MO-injected stage 10.5 embryo RNA-seq replicate 2

value: whole embryos at N&F stage 10.5

value: Nigerian strain


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G5_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G7_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G6_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G7_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G6_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G5_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G5_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G6_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G5_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G5_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G4_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G3_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G4_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G4_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G4_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G4_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G3_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G3_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G5_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G3_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G3_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G4_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G8_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G2_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G3_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G4_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G3_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G12_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G5_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G4_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G2_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G2_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G2_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G12_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G2_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G2_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G12_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G12_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G11_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G2_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G11_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G11_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G11_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G10_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G12_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G11_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G10_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G11_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G10_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G1_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G10_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F9_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F9_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G11_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F9_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G10_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G10_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G1_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G1_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G12_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F9_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F8_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F8_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F9_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F8_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F9_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F8_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F7_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G11_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F7_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F9_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F7_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F8_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F7_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G2_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F6_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F7_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F7_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F8_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F6_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F7_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_G1_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F5_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F6_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F5_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F8_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F6_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F6_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F6_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F5_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F5_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F5_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F5_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F6_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F6_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F4_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F4_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F4_ad008


title: peripheral blood buffy coat, A1178

type: genomic

city: Singapore

first: Jonathan

middle: Yinhao

last: Huang

state: « choose one »

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
GenomeStudio; R/Rstudio
green (RAW_ID_Grn.idat) and red (RAW_ID_Red.idat) channels provided
[value definition] chip position, DNA extraction, and bisulfite conversion batch, and celltype-adjusted residuals provided

label: Cy3, Cy5

source_name: peripheral blood buffy coat

label_protocol: Standard Illumina Protocol

extract_protocol: QIASymphony SP was used for automated purification of (buffy coat/cord tissue) DNA in combination with QIASymphony DSP DNA Midi Kit (Qiagen #937255) and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

value: peripheral blood buffy coat

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)

tag: pre-pregnancy bmi (kg/m^2)


title: peripheral blood buffy coat, A1177


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F4_ad004


title: peripheral blood buffy coat, A1176


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F4_ad007


title: peripheral blood buffy coat, A1175


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F4_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F4_ad001


title: peripheral blood buffy coat, A1174


title: peripheral blood buffy coat, A1172


title: peripheral blood buffy coat, A1170


title: peripheral blood buffy coat, A1173


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F3_ad010


title: Limousin semitendinosus muscle_Cy5 vs Holstein-Friesian semitendinosus muscle_Cy3_4

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 4 of 4. Limousin semitendinosus muscle_Cy5 vs Holstein-Friesian semitendinosus muscle_Cy3_rep 4

hyb_protocol: Probe were hybridized using Gene Expression Hybridization Kit (Agilent Technologies, USA) according to the manufacturers protocol. RNA Spike In Kit (Agilent Technologies, USA) was used as an internal control.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using the Agilent DNA microarray scanner and Agilent Feature Extraction software 10.7.3.1. according to the standard manufacturer’s procedures and LOWESS normalization.

data_processing: Linear Lowess normalized. The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3.

organism: Bos taurus

source_name: Limousin muscle_Cy5

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA).

extract_protocol: Total RNA was isolated by using a total RNA kit (A&A BIOTECHNOLOGY, Poland). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9 were included into the analysis.

tag: breed

value: Limousin

value: 15 month old

value: m. semitendinosus

source_name: Holstein-Friesian muscle_Cy3

value: Holstein-Friesian


title: Limousin semitendinosus muscle_Cy5 vs Holstein-Friesian semitendinosus muscle_Cy3_1

description: Biological replicate 1 of 4. Limousin semitendinosus muscle_Cy5 vs Holstein-Friesian semitendinosus muscle_Cy3_rep 1


title: Limousin semitendinosus muscle_Cy5 vs Holstein-Friesian semitendinosus muscle_Cy3_2

description: Biological replicate 2 of 4. Limousin semitendinosus muscle_Cy5 vs Holstein-Friesian semitendinosus muscle_Cy3_rep 2


title: peripheral blood buffy coat, A1169


title: peripheral blood buffy coat, S1167


title: peripheral blood buffy coat, S1166


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F3_ad007


title: peripheral blood buffy coat, S1164


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F3_ad008


title: peripheral blood buffy coat, S1168


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F4_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F2_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F3_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F3_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F3_ad001


title: peripheral blood buffy coat, S1163


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F3_ad002


title: Limousin semitendinosus muscle_Cy5 vs Holstein-Friesian semitendinosus muscle_Cy3_3

description: Biological replicate 3 of 4. Limousin semitendinosus muscle_Cy5 vs Holstein-Friesian semitendinosus muscle_Cy3_rep 3


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F3_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F2_ad008


title: peripheral blood buffy coat, S1158


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F2_ad007


title: peripheral blood buffy coat, S1157


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F2_ad006


title: peripheral blood buffy coat, S1162


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F2_ad001


title: peripheral blood buffy coat, S1149


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F2_ad010


title: peripheral blood buffy coat, S1159


title: peripheral blood buffy coat, S1148


title: peripheral blood buffy coat, S1147


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F12_ad010


title: peripheral blood buffy coat, S1145


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F12_ad002


title: peripheral blood buffy coat, S1156


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F2_ad004


title: peripheral blood buffy coat, S1155


title: peripheral blood buffy coat, S1140


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F2_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F11_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F12_ad001


title: peripheral blood buffy coat, S1138


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F11_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F11_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F12_ad012


title: peripheral blood buffy coat, S1146


title: peripheral blood buffy coat, S1153


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F12_ad008


title: peripheral blood buffy coat, S1132


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F11_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F12_ad007


title: peripheral blood buffy coat, S1161


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F12_ad004


title: peripheral blood buffy coat, S1144


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F12_ad006


title: peripheral blood buffy coat, S1143


title: peripheral blood buffy coat, S1129


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F11_ad001


title: peripheral blood buffy coat, S1135


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F10_ad010


title: peripheral blood buffy coat, S1142


title: peripheral blood buffy coat, S1139


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F11_ad012


title: peripheral blood buffy coat, S1126


title: peripheral blood buffy coat, S1137


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F11_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F11_ad008


title: peripheral blood buffy coat, S1125


title: peripheral blood buffy coat, S1134


title: peripheral blood buffy coat, S1123


title: peripheral blood buffy coat, S1131


title: peripheral blood buffy coat, S1121


title: peripheral blood buffy coat, S1124


title: peripheral blood buffy coat, S1122


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F10_ad004


title: peripheral blood buffy coat, S1120


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F10_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F10_ad008


title: peripheral blood buffy coat, S1128


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F10_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F1_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F10_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F1_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F1_ad006


title: peripheral blood buffy coat, S1117


title: peripheral blood buffy coat, S1115


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F10_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F1_ad008


title: peripheral blood buffy coat, S1114


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F1_ad004


title: peripheral blood buffy coat, S1119


title: peripheral blood buffy coat, S1113


title: peripheral blood buffy coat, S1112


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E9_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F1_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E9_ad008


title: peripheral blood buffy coat, S1110


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E9_ad004


title: peripheral blood buffy coat, S1118


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E9_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_F1_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E9_ad012


title: peripheral blood buffy coat, S1111


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E9_ad006


title: peripheral blood buffy coat, S1109


title: peripheral blood buffy coat, S1107


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E9_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E8_ad012


title: peripheral blood buffy coat, S1105


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E8_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E8_ad004


title: peripheral blood buffy coat, S1099


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E8_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E8_ad002


title: peripheral blood buffy coat, S1096


title: peripheral blood buffy coat, S1103


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E8_ad001


title: peripheral blood buffy coat, S1097


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E7_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E7_ad010


title: peripheral blood buffy coat, S1108


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E7_ad007


title: peripheral blood buffy coat, S1093


title: peripheral blood buffy coat, S1094


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E7_ad004


title: peripheral blood buffy coat, S1095


title: peripheral blood buffy coat, S1092


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E7_ad006


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E7_ad002


title: peripheral blood buffy coat, S1101


title: peripheral blood buffy coat, S1106


title: peripheral blood buffy coat, S1102


title: peripheral blood buffy coat, S1091


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E8_ad006


title: peripheral blood buffy coat, S1090


title: peripheral blood buffy coat, S1079


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E6_ad004


title: peripheral blood buffy coat, S1083


title: peripheral blood buffy coat, S1084


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E6_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E6_ad012


title: peripheral blood buffy coat, S1078


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E6_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E6_ad006


title: peripheral blood buffy coat, S1086


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E5_ad010


title: peripheral blood buffy coat, S1087


title: peripheral blood buffy coat, S1076


title: peripheral blood buffy coat, S1077


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E5_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E5_ad012


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E6_ad008


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E5_ad002


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E7_ad001


title: peripheral blood buffy coat, S1070


title: peripheral blood buffy coat, S1071


title: peripheral blood buffy coat, S1072


title: peripheral blood buffy coat, S1068


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E5_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E4_ad010


title: peripheral blood buffy coat, S1088


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E6_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E6_ad002


title: peripheral blood buffy coat, S1067


title: peripheral blood buffy coat, S1066


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E4_ad007


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E4_ad006


title: peripheral blood buffy coat, S1062


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E4_ad004


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E4_ad008


title: peripheral blood buffy coat, S1064


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E3_ad010


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E4_ad001


title: CEMBA190625_10F_3_CEMBA190625_10F_4_E3_ad008