title: Sample_24hr-rep1


title: Sert_Pet1_dlDR_9

status: Public on Feb 09 2020

type: SRA

city: Boston

first: Benjamin

last: Okaty

state: MA

address: 77 Avenue Louis Pasteur

country: USA

institute: Harvard Medical School

description: Sample 9

library_source: transcriptomic

data_processing:
Illumina 2.2.0.4 - RTA 2.4.11 software for base calling (except for samples 34-38, which used 2.2.68 - RTA 1.18.66.3)
For samples 1-70, transcript mapping to the mm10 genome assembly and feature counts were performed using STAR (version 2.5.4) (Dobin and Gingeras, 2016). For samples 71-72, transcriptome mapping and demultiplexing were performed using the 10X Genomics Cell Ranger software (version  3.0.2). Several data-filtering steps were performed on the matrix of transcript counts   (using R version 3.5.3) prior to further analysis, as described in Okaty, Sturrock, et al. 2020 BioRxiv doi: https://doi.org/10.1101/2020.01.28.923375.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files containing transcript counts

molecule: polyA RNA

organism: Mus musculus

source_name: Acutely dissociated dorsal raphe (DR) single neuron

extract_protocol:
Brain tissue was harvested from  transgenic animals and fluorescently labeled cells were sorted as described in (Okaty, Sturrock, et al. 2020). Samples 1-70 were manually sorted and samples 71-72 were sorted using the On-Chip Sorter.
Samples 1-70 were constructed using the SMART-Seq v4 Ultra Low Input RNA kit, followed by Nextera XT  1212 DNA Library Preparation Kit. Samples 71 and 72 were constructed using 10X Genomics Chromium Single Cell 3’ v3 kit.

tag: cell type

tag: genotype

tag: dr subdomain

value: dorsolateral

tag: age

value: postnatal day 90


title: Mut43-RNAseq-rep2

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

data_processing:
RNA-seq basecalls performed by BGI, Shenzhen
ChIP-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ChIP reads were mapped to UCSC mm10 genome by Bowtie2 (2.3.4.2)
ChIP data were filtered using samtools rmdup to remove potential PCR duplicates
RNA-Seq data were mapped to UCSC mm10 by STAR aligner and quantitified by DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files of ChIP-seq data were generated using deepTools v3.3.0 with library size normalized to 10 million read pairs.
Supplementary_files_format_and_content: Raw read counts of RNA-seq for each gene were calculated by summarizeOverlaps method from GenomicAlignments v1.8.4 and stored as tab separated texts.

molecule: total RNA

extract_protocol:
For mRNA-seq, total RNA was directly extracted from cells cultured in 3.5 cm dishes by TRIzol reagent with two biological replicates for each cell line.
For ChIP-seq, Cells were harvested in PBS and cross-linked with 1% formaldehyde for 9 min at room temperature, cells prepared for RNA pol II were pre-cross-linked with 0.2 mM disuccinimidyl glutarate (DSG, ProtecoChem, c1104) for 30 min at room temperature. Reaction was terminated by adding glycine to a final concentration of 125 mM, incubated at room temperature for 5 min. After washing with PBS twice, cells were resuspended in 5 mL of Lysis Buffer 1 (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25%Triton X-100), incubated on ice for 10 min. After centrifuge at 2,000 rpm at 4 ˚C for 5 min, cells were then resuspended in 5 mL of Lysis Buffer 2 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA), incubated at room temperature for 10 min. The lysate was centrifuged at 4,000 rpm for 5 min at 4 ˚C. The chromatin fraction was resuspended in 1 mL of Lysis Buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% sodium N-lauroylsarcosine, 1x proteinase inhibitor (Merck, 5892970001)). Chromatin was then sonicated into 200-400 bp fragments (Covaris M220), in assistance with 0.1% sodium dodecyl sulfate (SDS) or 0.5% SDS (for double cross-linked sample). Supernatant after centrifuging at 12,000 rpm for 10 min at 4 ˚C were flash freezed and kept in -80 ˚C refrigerator.    Keep 10% of chromatin as input, the fragments were immunoprecipitated overnight with antibodies against histone modifications or RNA pol II. Pre-washed Dynabeads protein A or G (ThermoFisher 10002D, or 10004D) was added to the Protein-antibody complexes, and incubated at 4 ˚C for 1 hour. The beads were sequentially washed with buffers as follows: FA-lysis buffer (150 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5 mM sodium deoxycholate), FA high salt buffer (500 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5% sodium deoxycholate) for twice, LiCl buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl, pH 8.0), TE buffer (10 mM Tris-HCl, pH8.0, 1 mM EDTA) for twice. Each washing step was incubated for 5 min at 4 ˚C with rotation. Protein-DNA complexes were eluted by incubation with 250 µl of elution buffer (1% SDS, 100 mM NaHCO3, freshly made) for 15 min at 55 ˚C with periodic gentle vortex. This step was repeated once and eluted sample was combined.    Eluted DNA, as well as input, was reverse cross-linked from protein by adding 20 µl of 5M NaCl to the 500 µl of elution, incubated at 65 ˚C over 8 hours. After digested with RNase at 37 ˚C, proteinase K at 55 ˚C, DNA was extracted by phenol-chloroform method.
RNA-seq library construction: Poly-A tailed mRNA molecules were captured using attached oligo-dT and subjected to library construction according to the manufacturer’s recommendations.
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).

tag: strain background

tag: developmental stage

value: embryo, blastocyst

tag: cell line

tag: source tissue

value: inner cell mass

value: embryonic stem (ES) cell

tag: genotype/variation

tag: tissue


title: Sert_Pet1_dlDR_7

description: Sample 7

value: Acutely dissociated dorsal raphe (DR) single neuron


title: Sert_Pet1_dlDR_8

description: Sample 8


title: Mut43-RNAseq-rep1


title: Crh_Pet1_rDR_4

description: Sample 66

value: rostral

value: postnatal day 119


title: Sert_Pet1_dlDR_6

description: Sample 6


title: Mut18-RNAseq-rep2


title: Sert_Pet1_dlDR_4

description: Sample 4

value: postnatal day 63


title: Mut18-RNAseq-rep1


title: Sert_Pet1_dlDR_3

description: Sample 3


title: WT-RNAseq-rep2

source_name: WT-RNA

value: wild type


title: Sample_6hr-rep1

city: Riverside

first: Heba

middle: A. H. M.

last: Zaghloul

state: CA

address: 900 University Ave

department: Entomology

institute: University of California, Riverside

data_processing:
Illumina adapter sequences were removed and low quality sequencing reads removed using Trimmomatic software
Ribosomal contaminant sequences were removed using sortMeRNA software
Reads were aligned to reference genome using Bowtie2 software
Transcript expression was estimated using RSEM software and reported as TPMs
Genome_build: Spodoptera frugiperda mitochondrion genome: NCBI accesssion KM362176; Spodoptera frugiperda chromosomal genome assembly reported by  Gouin et al. (2017) doi:10.1038/s41598-017-10461-4
Supplementary_files_format_and_content: Transcript expression values are reported as TPM values in Microsoft Excel spreadsheet format

organism: Spodoptera frugiperda

source_name: SfAV-1a 6h infected 3rd instar caterpillar

extract_protocol:
Total RNA was isolated from the entire body of each healthy or SfAV-1a infected Spodoptera frugiperda larva and homogenized separately by mechanical trituration in TRIzol (Invitrogen), followed by DNase-treatment using the RNA Clean and Concentrator TM-5 kit (ZYMO RESEARCH) and eluted in ultra pure distilled water (Invitrogen).
The NEBNextPoly(A) mRNA magnetic isolation module kit (New England Biolabs) was used to enrich the mRNA first from the DNase-treated total RNA samples.The libraries were then prepared following the manufacturer’s instructions of the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs)

tag: infection

value: Wild type SfAv-1a

tag: time point

value: whole insect body


title: Sert_Pet1_dlDR_2

description: Sample 2


title: Sample_6hr-rep2


title: Sert_Pet1_dlDR_1

description: Sample 1


title: WT-RNAseq-rep1


title: P2ry1_Pet1_cDR_2

description: Sample 35

value: caudal

value: postnatal day 62


title: P2ry1_Pet1_cDR_1

description: Sample 34

value: postnatal day 74


title: P2ry1_Pet1_cDR_5

description: Sample 38

value: postnatal day 64


title: P2ry1_Pet1_cDR_4

description: Sample 37


title: P2ry1_Pet1_cDR_3

description: Sample 36


title: Sample_0hr-rep1

source_name: Uninfected, 3rd instar caterpillar

value: uninfected


title: Sample_0hr-rep2


title: Sample_12hr-rep2

source_name: SfAV-1a 12 h infected 3rd instar caterpillar


title: s_deep6403

city: Guangzhou

first: wu

middle: jing

last: wen

state: Guangdong

address: TianHe

department: Department of Animal Genetics, Breeding and Reproduction

institute: South China Agricultural University

data_processing:
The sequencing data was filtered with SOAPnuke(v1.5.2)
The clean reads were mapped to the reference genome using HISAT2(v2.0.4)
Bowtie2(v2.2.5) was applied to align the clean reads to the reference coding gene set,then expression level of gene was calculated by RSEM(v1.1.12)
The heatmap was dramn by pheatmap(v1.0.8)according to the gene expression in different samples.Essentially,differenial expression analysis was performed using the DESeq2(v1.4.5) with Q value≤0.05.
Genome_build: GCF_000002315.4_Gallus_gallus-5.0
Supplementary_files_format_and_content: XLS files include RPKM values for each Sample ...

organism: Gallus gallus

source_name: Ma-Huang chickens

extract_protocol:
A piece of skin (8 mm in diameter) were isolated from cloaca and then snap frozen in liquid nitrogen prior to use,and RNA was harvested using Trizol reagent.cDNA library construction and illumine HiSeeq4000 sequencing were conducted at BGI Institute.
RNA libraries were prepared for sequencing using illumine HiSeeq4000 sequencing

value: skin

tag: cloaca yellowness

value: high yellowness (s_deep)


title: Sample_12hr-rep1

source_name: SfAV-1a 12h infected 3rd instar caterpillar


title: Sert_Pet1_dlDR_5

description: Sample 5

value: dorsolateral

value: postnatal day 90


title: s_light6971

value: low yellowness (s_light)


title: s_deep7858


title: Sample_48hr-rep3

data_processing:
Illumina adapter sequences were removed and low quality sequencing reads removed using Trimmomatic software
Ribosomal contaminant sequences were removed using sortMeRNA software
Reads were aligned to reference genome using Bowtie2 software
Transcript expression was estimated using RSEM software and reported as TPMs
Genome_build: Spodoptera frugiperda mitochondrion genome: NCBI accession KM362176; Spodoptera frugiperda chromosomal genome assembly reported by Gouin et al. (2017) doi:10.1038/s41598-017-10461-4
Supplementary_files_format_and_content: Transcript expression values are reported as TPM values in Microsoft Excel spreadsheet format

source_name: SfAV-1a 48h infected 3rd instar caterpillar

extract_protocol:
Total RNA was isolated from the entire body of each healthy or SfAV-1a infected Spodoptera frugiperda larva and homogenized separately by mechanical trituration in TRIzol (Invitrogen), followed by DNase-treatment using the RNA Clean and Concentrator TM-5 kit (ZYMO RESEARCH) and eluted in ultra pure distilled water (Invitrogen).
The NEBNextPoly(A) mRNA magnetic isolation module kit (New England Biolabs) was used to enrich the mRNA first from the DNase-treated total RNA samples. The libraries were then prepared following the manufacturer’s instructions of the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs)


title: Sample_4thday-rep3

source_name: SfAV-1a 4 days infected 3rd instar caterpillar

value: 4 days


title: Sample_24hr-rep3

source_name: SfAV-1a 24h infected 3rd instar caterpillar


title: s_deep6402


title: Sample_12hr-rep3


title: Sample_6hr-rep3


title: s_light6575


title: bpm235_repl5

type: RNA

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

hyb_protocol: 825 ng of Cy3 probes were hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation.

scan_protocol: Images for the Cy3 channel were captured with an Agilent DNA Microarray Scanner at a resolution of 2 µm, and spots quantified using Agilent Feature Extraction Software.

data_processing: Background correction and quantile normalization of expression data were performed using LIMMA (Smyth and Speed, 2003; Smyth, 2004).

organism: Arabidopsis thaliana

source_name: seedlings

label_protocol: Total RNA (500 ng each) was amplified and Cyanine 3- (Cy3-) labeled using One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer´s instructions.

growth_protocol: Seedlings were grown 3 weeks under a 16-h light/8-h dark cycle at 21ºC in 0,5xMS1 solid

extract_protocol: Plant tissue (~100 mg) was ground in liquid nitrogen and total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with RNeasy mini kit (Qiagen, 74104).

value: seedlings


title: Sample_7thday-rep3

source_name: SfAV-1a 7 days infected 3rd instar caterpillar

value: 7 days


title: Sample_0hr-rep3


title: s_light8275


title: bpm235_repl3


title: bpm235_repl2


title: pregnant (Days 15-16) vs. cyclic (Days 15-16 of the estrous cycle) 3

city: Olsztyn

first: Agata

last: Zmijewska

address: Oczapowski 1a

department: Demartment of Animal Anatomy and Physiology

country: Poland

institute: Univeristy of Warmia and Mazury

hyb_protocol: Two differentially labelled samples (from pregnant and cyclic gilts) were placed on each array (one slide, n = 4) in a balanced block design with dye swaps. Hybridization was carried out in an Agilent hybridization oven for 17 h at 60°C. After the hybridization process, the microarrays were washed.

scan_protocol: Microarrays were scanned at 5 μm resolution with an Agilent’s High-Resolution C Microarray Scanner according to the manufacturers' protocol.

data_processing: The TIFF image, generated after the scanning process, was used for: data extraction and detailed analysis, background subtraction from features, and dye normalizations (linear and LOWESS); in the Feature Extraction Software. Gene expression data were analysed in GeneSpring GX 12 software (Agilent Technologies, USA) to identify the genes that were differentially expressed in pregnant and cyclic pigs.

organism: Sus scrofa domesticus

source_name: Anterior pituitary of pregnant pigs

label_protocol: The RNA isolated from the pituitary of pregnant and cyclic females were labelled with Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5), respectively. Quantity and purity of obtained cRNA were measured with NanoQuant plates on the Infinite M200 Pro plate reader. 825 ng of Cy-3 and 825 ng of Cy-5-labeled cRNA were mixed together (for each microarray). According to the microarray manufacturer’s protocol, cRNA was fragmented and mixed with hybridization buffer.

growth_protocol: Eight mature gilts (Large White x Polish Landrace, weighing 90-110 kg) were used in the study (n = 8). All individuals were descended from private breeding farm. Day 0 was a day indicating the beginning of estrus. Cyclic animals (n=4) were sacrificed on days 15-16.  Days of the estrous cycle were confirmed on the morphology of ovaries. Gilts assigned to the early pregnancy group (n = 4) were naturally bred twice on the first and the second days of the estrous  and sacrificed on days 15-16 of pregnancy. Pregnancy was confirmed by the presence of conceptuses. Animals were slaughtered by qualified abattoir worker.

extract_protocol: Total RNA was isolated from porcine pituitaries using the RNeasy Mini Kit (Qiagen, USA), according to manufacture procedure.RNA purity and quantity were measured spectrophotometrically. RNA quality was checked using RNA 6000 Nano Assay Kit on an Agilent 2100 Bioanalyzer. RNA integrity number (RIN) score between 7.5 and 10. The obtained nucleic acid was used for microarray analysis and quantitative real-time PCR (qPCR) experiments. RNAs were stored at −80 °C until the microarray analysis.

tag: reproductive status

value: Early pregnancy

tag: race

value: Large White x Polish Landrace

tag: days

value: days 15 to 16

source_name: Anterior pituitary of cyclic pigs

value: The estrous cycle


title: bpm235_repl1


title: pregnant (Days 15-16) vs. cyclic (Days 15-16 of the estrous cycle) 4


title: pregnant (Days 15-16) vs. cyclic (Days 15-16 of the estrous cycle) 2


title: pregnant (Days 15-16) vs. cyclic (Days 15-16 of the estrous cycle) 1


title: bpm235_repl4


title: Col-0_repl2


title: Col-0_repl3


title: 12 month RGE_2

status: Public on Feb 08 2020

city: seongnam si,

first: Boo-yong

last: Lee

state: kyungggi do

address: pangyoro 335, seongnam si, kyungggi do

country: South Korea

institute: CHA university

description: Gene expression data from 12 month old mice ovarian tissue with RGE 10 mg/mL

hyb_protocol: Turn Affymetrix® Hybridization Oven on, set the temperature to 45°C and set the RPM to 60. Turn the rotation on and allow the oven to preheat. Equilibrate the arrays to room. Prepare hybridization master mix and hybridization cocktatil(add the appropriate amount of Hybridization Master Mix to each fragmented and biotin-labeled ss-cDNA sample). Inject the appropriate amount of the specific sample into the array through one of the septa. Place the arrays into hybridization oven trays. Load the trays into the hybridization oven and incubate with rotation at 60 rpm for 16hr at 45℃. temperature immediately before use. Label the array with the name of the sample that will be hybridized. Register the sample and array information into AGCC. Prepare hybridization master mix and hybridization cocktatil(add the appropriate amount of Hybridization Master Mix to each fragmented and biotin-labeled ss-cDNA sample). Inject the appropriate amount of the specific sample into the array through one of the septa. Place the arrays into hybridization oven trays. Load the trays into the hybridization oven and incubate with rotation at 60 rpm for 16hr at 45℃.

scan_protocol: Image was acquired with Affymetrix GeneChip® Scanner 3000DX and data extracted using by Affymetrix GeneChip® Command Console® Software (AGCC) 4.0

data_processing: After robust multi-array Average (RMA) normalization using Expression Console 1.4, differentially expressed gene (DEG) analysis was performed, involving fold change filtering and statistical filtering using Clusster 3.0, TreeView software, GeneSpring GX14.9.

label: biotin

source_name: 12 month mice ovarian tissue + 10mg/mL RGE_2

label_protocol: In this procedure, the purified, sense-strand cDNA was fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that was covalently linked to biotin. 250ng of singlestranded cDNA was required for fragmentation and labeling.

growth_protocol: The ovarian tissue was isolated from 6 and 12 month old female mice and cultured with DMEM medium (Hyclone) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Thermo Fisher Scientific).

extract_protocol: Total RNA was extracted using TRIzol reagent and processed for quality control of total RNA using ND-1000 spectrophotometer (Thermo Scientific).

treatment_protocol: The ovarian tissue were treated with DMSO or 10mg/mL RGE for 24 hours.

value: ovary

tag: Sex

value: female

value: 12 month


title: 12 month RGE_1

source_name: 12 month mice ovarian tissue + 10mg/mL RGE_1


title: 12 month Control_3

description: Gene expression data from 12 month old mice ovarian tissue without RGE 10 mg/mL

source_name: 12 month mice ovarian tissue_3


title: 6 month RGE_2

description: Gene expression data from 6 month old mice ovarian tissue with RGE 10 mg/mL

source_name: 6 month mice ovarian tissue + 10mg/mL RGE_2

value: 6 month


title: 12 month RGE_3

source_name: 12 month mice ovarian tissue + 10mg/mL RGE_3


title: I-AbΔIEC Inf3

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

description: Gene expression data from the colon of C. rodentium-infected  I-AbΔIEC mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC to GeneChip™ Mouse Gene 2.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: .cel files were inmported into GeneSpring 14.9 software (Agilent).

source_name: infected knockout

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

extract_protocol: Trizol extraction of total RNA and column clean-up was performed according to the manufacturer's instructions.

treatment_protocol: Colon tissue samples from uninfected (Ctrl) and infected (Inf) I-AbWT and I-AbΔIEC mice were collected on day 9 post-infection and RNA used for microarray gene expression analysis using GeneChip™ Mouse Gene 2.0 ST arrays

value: colon

value: I-Ab{delta}IEC

tag: treatment

value: Infected


title: 12 month Control_2

source_name: 12 month mice ovarian tissue_2


title: 12 month Control_1

source_name: 12 month mice ovarian tissue_1


title: 6 month RGE_1

source_name: 6 month mice ovarian tissue + 10mg/mL RGE_1


title: 6 month RGE_3

source_name: 6 month mice ovarian tissue + 10mg/mL RGE_3


title: I-AbΔIEC Ctrl3

description: Gene expression data from the colon of healthy I-AbΔIEC mice

source_name: uninfected knockout

tag: genotype

value: Control


title: 6 month Control_2

description: Gene expression data from 6 month old mice ovarian tissue without RGE 10 mg/mL

source_name: 6 month mice ovarian tissue_2


title: I-AbΔIEC Ctrl2


title: 6 month Control_3

source_name: 6 month mice ovarian tissue_3


title: I-AbΔIEC Inf1


title: I-AbΔIEC Ctrl1


title: I-AbWT Inf1

description: Gene expression data from the colon of C. rodentium-infected   I-AbWT mice

source_name: infected wild-type

value: I-AbWT


title: I-AbWT Inf2


title: I-AbWT Inf3


title: 6 month Control_1

source_name: 6 month mice ovarian tissue_1


title: I-AbWT Ctrl1

description: Gene expression data from the colon of healthy I-AbWT mice

source_name: uninfected wild-type


title: I-AbWT Ctrl2


title: I-AbΔIEC Inf2


title: CARFIB_2

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
The primary sequence data were generated using the Illumina bcl2fastq 1.8.4 pipeline.
Reads were trimmed for quality using a minimum phred value of 20 and minimum length of 18 using Skewer version 0.2.2
Reads were mapped with STAR v2.5.2b to the Ensembl version 90 human reference genome (Homo_sapiens.GRCh38.90.gtf) to generate a count matrix.
Genome_build: Homo_sapiens.GRCh38.90
Supplementary_files_format_and_content: Tab separated gene expression count matrix

organism: Homo sapiens

source_name: Primary fibroblast

growth_protocol: Human primary dermal fibroblasts were cultured in DMEM medium (Cat. #11995-065, Thermo Fisher Scientific) containing 25 mM D-glucose and supplemented with 10% FBS, 1 x GlutaMAX, 100 units/mL penicillin, and 100 µg/mL streptomycin, all from Thermo Fisher Scientific. All samples were randomized, experiments performed in large batches and analyses blinded to sample identity.

extract_protocol:
Total RNA was extracted from three independent fibroblast cell lines for each experimental group using the miRNeasy RNA extraction kit (Qiagen, Cat. #217004) with an on-column DNase I (Qiagen) treatment to eliminate contaminating genomic DNA, according to manufacturer’s instructions.
Transcriptome-wide mRNA sequencing was performed by the Australian Genome Research Facility (Melbourne, Australia). RNA purity and integrity were confirmed by BioAnalyser (Agilent, CA). Libraries were created with TruSeq RNA v2 kit (Illumina), barcoded and sequenced on a HiSeq 2000 sequencer (Illumina), producing 100 bp single-end reads, with a depth of at least 20 million reads per sample.

tag: lhon status

value: Carrier

tag: cell type

value: Primary fibroblast


title: CARFIB_3


title: CTRFIB_2


title: CTRFIB_3


title: I-AbWT Ctrl3


title: CARFIB_1


title: AFFFIB_2

value: Affected


title: CTRFIB_1


title: AFFFIB_3


title: AFFFIB_1


title: HGSC3

city: Montréal

first: Claude

last: Perreault

state: Quebec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal

data_processing:
Basecalls performed using Illumina RTA 1.18.66.3 for HiSEQ samples and Illumina RTA 2.4.11 for NextSEQ samples.
Samples demultiplexed using bcl2fastq 2.19
Sequenced reads were trimmed for sequencing adapters and low quality extrimities using Trimmomatic 0.35 and then mapped to the reference transcriptome using kallisto 0.43.0, taking into account that libraries are stranded.
TPM values were computed by kallisto 0.43.0 using a transcriptome index built on human genome GRCh38 along with Ensembl 88 annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression files are tab delimited with columns 1) Ensembl transcript identifier, 2) transcript length , 3) effective transcript length, 4) estimated counts, and 5) transcript per million reads sequenced (TPM).

source_name: ovary

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) or the AllPrep DNA/RNA/miRNA Universal kit (Qiagen) as recommended by the manufacturer.
cDNA libraries were prepared from polyA-enriched mRNA using the KAPA Stranded mRNA-Seq Kit and were further amplified for sequencing.

tag: disease

value: Ovarian cancer

value: Ovary


title: HGSC1


title: HGSC2


title: M1_CNT: middle-aged LT-HSC rep 1

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: Maine

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

data_processing:
Trimmed alignment files (with trimmed base quality value < 30, and 70% of read bases surpassing that threshold) were processed using the RSEM (v1.2.12; RNA-Seq by Expectation-Maximization) software and the Mus musculus reference GRCm38. This software estimates gene (and isoform) expression levels from RNA-Seq data with a statistical model that considers reads that map to multiple positions. Alignment was completed using Bowtie 2 (v2.2.0) and processed using SAMtools (v0.1.18). Fragment length mean was set to 280 and standard deviation to 50.
Expected read counts per gene produced by RSEM were rounded to integer values, filtered to include only genes that have at least two samples within a sample group having a cpm > 1.0, and were passed to edgeR (v3.5.3) for differential expression analysis.
A negative binomial generalized log-linear model was fit to the read counts for each gene.  The dispersion trend was estimated by Cox-Reid approximate profile likelihood followed by empirical Bayes estimate of the negative binomial dispersion parameter for each tag, with expression levels specified by a log-linear model. Likelihood ratio tests for coefficient contrasts in the linear model were evaluated producing a p-value per contrast.
The Benjamini and Hochberg’s algorithm (p-value adjustment) was used to control the false discovery rate (FDR). Features with an FDR-adjusted p-value < 0.05 were declared significantly differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts produced by RSEM (v1.2.12) for each sample stored in tab-delimited, text format

source_name: bone marrow

extract_protocol:
Total RNA was isolated from cells using the RNeasy Micro kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: young and middle-aged LT-HSCs from 3 independent replicates of pooled mice were sorted directly into a 96-well plate for 18hrs in StemSpan SFEM II, SCF (100 ng/ml), TPO (50 ng/ml), Pen-Strep (1%) with vehicle (.1% BSA/PBS) or IGF1 (100ng/ml) stimulation at 37oC and 5% CO2 before being spun down and resuspended in RLT buffer

tag: strain

value: LT-HSC


title: M2_CNT: middle-aged LT-HSC rep 2


title: M1_IGF1: middle-aged LT-HSC + IGF1 rep 1


title: M3_CNT: middle-aged LT-HSC rep 3


title: M3_IGF1: middle-aged LT-HSC + IGF1 rep 3


title: M2_IGF1: middle-aged LT-HSC + IGF1 rep 2


title: Y1_CNT: young LT-HSCs rep 1


title: Y2_CNT: young LT-HSCs rep 2


title: Y3_CNT: young LT-HSCs rep 3


title: 98-OOY: re-isolated LT-HSC from MMY TX

extract_protocol:
LT-HSC were re-isolated from TX mice and sorted directly into RLT buffer. Total RNA was isolated from cells using the RNeasy Micro kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tx #


title: 41-OOO: re-isolated LT-HSC from MMM TX


title: 65-YYY: re-isolated LT-HSC from YYY TX


title: 95-OOY: re-isolated LT-HSC from MMY TX


title: 94-OOY: re-isolated LT-HSC from MMY TX


title: 67-YYY: re-isolated LT-HSC from YYY TX


title: 35-OOO: re-isolated LT-HSC from MMM TX


title: 43-OOO: re-isolated LT-HSC from MMM TX


title: OV633

source_name: HGS Ascites fluid cells

value: Ascites fluid cells


title: OV642


title: 38-OOO: re-isolated LT-HSC from MMM TX


title: OV606


title: HGSC5


title: HGSC6


title: Pancreactic islets from 12-week old hIAPP-Tg mouse 6

city: Barcelona

first: Gema

last: Alcarraz-Vizán

address: Rossello 149

department: Diabetes & Obesity Laboratory

institute: IDIBAPS

description: Global gene expression of pancreactic islets from 12-week old hIAPP-Tg mouse

hyb_protocol: Following fragmentation, cRNA was hybridized to Genechip Mouse 430 2.0 Affymetrix arrays, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: Expression data were normalized with Robust Multi-array Average (RMA)  from the affy package (www.bioconductor.org)

source_name: Pancreatic islets

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (150 ng starting total RNA).

growth_protocol: Islets from wild type and hIAPP-Tg mice were isolated at week 12.

extract_protocol: RNA was extracted with Trizol (R) reagent according to manufacturer protocol.

treatment_protocol: Wild type and hIAPP-Tg mice were fed ad libitum with standard chow diet for 12 weeks.

value: Islets of Langerhans

value: hIAPP Tg

tag: age

value: 12 weeks


title: Pancreactic islets from 12-week old hIAPP-Tg mouse 4


title: Pancreactic islets from 12-week old wild type mouse 2

description: Global gene expression of pancreactic islets from 12-week old wild type mouse

value: wild type


title: Pancreactic islets from 12-week old hIAPP-Tg mouse 5


title: HGSC4


title: D_L18

city: Yangzhou

first: chunhong

last: zhu

address: Cangjie Rd.58

institute: Jiangsu Institute of Poultry Science

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using Hisat2v2.0.5
Genome_build: IASCAAS_PekingDuck_PBH1.5 (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/850/225/GCF_003850225.1_IASCAAS_PekingDuck_PBH1.5/GCF_003850225.1_IASCAAS_PekingDuck_PBH1.5_genomic.fna.gz)
Supplementary_files_format_and_content: FPKM,expected number of Fragments Per Kilo base of transcript sequence per Millions base pairs sequenced,considers the effect of  sequencing depth and gene length for the reads count at the same time

organism: Anas platyrhynchos

source_name: liver tissue

extract_protocol:
The liver tissue was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: variety

value: domestica

value: high ammonia

value: liver


title: A_L13

value: low ammonia

tag: tissue


title: Pancreactic islets from 12-week old wild type mouse 1


title: A_L15


title: D_L17


title: Pancreactic islets from 12-week old wild type mouse 3


title: D_L16


title: A_L18


title: CTL-70.5 h-replicate 1

type: mixed

city: León

first: Antonio

last: Rodríguez-García

address: Avenida Real 1

institute: INBIOTEC

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_CTL.70.5.r1

hyb_protocol: Mixes of Cy3-cDNA (300 ng) and Cy5-gDNA (4 pmol) in a volume of 18.8 μl were denaturalized (94 °C, 3 min), pulse centrifuged and added to 31.2 μl of 1.6 × hybridization solution (PMID 19146703). Forty microlitres of this solution were applied on each microarray surface. The slides were placed in an Agilent hybridization chamber and rotated at 4 rpm and 55 °C for 64–67 h. Washing, stabilization and drying of the slides were carried out as indicated previously (PMID 23555999).

scan_protocol: A G2565BA scanner (Agilent), in extended dynamic mode, and the FeatureExtraction v9.5.1 software (CGH protocol) were used to quantify the hybridization signals.

data_processing:
The limma package v3.20 (Bioconductor 2.14) was used for normalization of the signal intensities and for statistical analyses. Net fluorescence signals were calculated as the subtraction of the median of background pixels from the mean of foreground pixels. When this mean value was negative or lower than the background standard deviation, the background standard deviation was used as the surrogate signal. Mg values were calculated as the log2 of Cy3-cDNA/Cy5-gDNA net signals and then normalized using cyclic loess and global median. For both normalization processes, probes were weighted to exclude tiling probes (fkb cluster) in the calculus of the normalization factors.
Mg values are the normalized log2 ratio (Cy3/Cy5) representing, respectively, the fluorescence intensities of labelled cDNA and labelled gDNA. A Mg value is an approximate measure of the abundance of the transcripts for a particular gene with respect to its genomic copies (PMID 18628968, 18078514). The locus tags indicated correspond to the protein coding genes as annotated in the GenBank assembly accession GCA_000297155.1

organism: Streptomyces tsukubensis NRRL18488

source_name: Culture no. 2, 70.5 h of culture, control

label_protocol: Total RNA samples were labelled using random hexamers (Invitrogen), SuperScript III reverse transcriptase (Invitrogen) and Cy3-dCTP (GE Healthcare Life Sciences) as indicated previously (PMID 17623301). Then, remnant RNAwas hydrolyzed with NaOH at 70 °C and the synthesized Cy3-cDNA was purified using the MinElute PCR Purification Kit (Qiagen). gDNA from S. tsukubaensis NRRL 18488 was labelled with Cy5-dCTP (GE Healthcare Life Sciences) using the BioPrime Array CGH Genomic Labeling Module (Invitrogen) and the Cy5-gDNA was purified with the MinElute kit (Qiagen). The incorporation of Cy3/Cy5- dCTP was quantified with NanoDrop spectrophotometer and kept at −20 °C. Only samples with a specific activity greater than 40 pmol μg−1 were used in the microarray hybridization.

growth_protocol: Streptomyces tsukubensis  NRRL 18488 was grown at 28 ºC on ISP4 (Difco™) medium for spore preparation. 10e9 spores were inoculated into 0.5-l flasks containing 100 ml of MGm-2.5 media (PMID 22990582) and incubated at 28 ºC and 220 rpm.

extract_protocol: Frozen samples were thawed on ice, suspended in 170 μl of lysozyme solution (15 mg ml−1 in TE buffer) and incubated at room temperature for 10 min. Cell suspensions were transferred to lysing matrix B columns (MP Biochemicals), cooled on ice and lysed on a FastPrep FP120 homogenizer (Thermo Electron). Two pulses of 30 s at speed 6.5 m s−1 were applied, cooling down the tubes on ice for 1 min between pulses. After centrifugation, the aqueous solution was prepurified by fenolization. RNA was extracted using RNeasy Mini Spin columns and treated on-column with DNase I (both from Qiagen). After elution, RNA concentration, purity and integrity were determined using a ND-1000 spectrophotometer, the RNA 6000 Nano LabChip kit and a 2100 Bioanalyzer (Agilent)

treatment_protocol: Culture samples ranging from 0.4 to 1 ml were taken and immediately mixed with two volumes of RNAprotect Bacteria Reagent (Qiagen), vortexed for 30 s and kept for 5 min at room temperature for stabilization of RNA. After centrifugation, the supernatant was discarded and the pellets were kept at −80 °C until further processed

tag: agent

tag: time

molecule: genomic DNA

source_name: Total DNA extracted from a stationary-phase culture

tag: reference


title: CTL-71 h-replicate 1

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_CTL.71.r1

source_name: Culture no. 2, 71 h of culture, control


title: CTL-71 h-replicate 2

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_CTL.71.r2

source_name: Culture no. 4, 71 h of culture, control


title: PBMC_MECFS_27

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

hyb_protocol: performed according to manufacturer's instructions (NanoString Technologies)

source_name: PBMC, MECFS patient

extract_protocol: total RNA was extracted using RNAzol (Molecular Research Center) according to manufacturer's instructions

tag: condition

value: MECFS

tag: pbmc/ev

value: PBMC


title: PBMC_MECFS_28

scan_protocol: performed according to manufacturer's instructions (NanoString Technologies)


title: CTL-72 h-replicate 1

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_CTL.72.r1

source_name: Culture no. 2, 72 h of culture, control


title: CTL-70.5 h-replicate 2

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_CTL.70.5.r2

source_name: Culture no. 4, 70.5 h of culture, control


title: PBMC_MECFS_30

data_processing: performed according to manufacturer's instructions (NanoString Technologies)


title: NAG-70 h-replicate 1

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_NAG.70.r1

source_name: Culture no. 1, 70 h of culture, N-acetylglucosamine added

value: N-acetylglucosamine


title: CTL-72 h-replicate 2

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_CTL.72.r2

source_name: Culture no. 4, 72 h of culture, control


title: NAG-72 h-replicate 2

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_NAG.72.r2

source_name: Culture no. 3, 72 h of culture, N-acetylglucosamine added


title: NAG-70 h-replicate 2

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_NAG.70.r2

source_name: Culture no. 3, 70 h of culture, N-acetylglucosamine added


title: CTL-70 h-replicate 1

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_CTL.70.r1

source_name: Culture no. 2, 70 h of culture, control


title: NAG-71 h-replicate 1

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_NAG.71.r1

source_name: Culture no. 1, 71 h of culture, N-acetylglucosamine added


title: NAG-70.5 h-replicate 2

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_NAG.70.5.r2

source_name: Culture no. 3, 70.5 h of culture, N-acetylglucosamine added


title: NAG-70.5 h-replicate 1

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_NAG.70.5.r1

source_name: Culture no. 1, 70.5 h of culture, N-acetylglucosamine added


title: CTL-70 h-replicate 2

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_CTL.70.r2

source_name: Culture no. 4, 70 h of culture, control


title: PBMC_HC_23

source_name: PBMC, healthy control

label_protocol: performed according to manufacturer's instructions (NanoString Technologies)

value: Healthy Control


title: PBMC_HC_22


title: NAG-71 h-replicate 2

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_NAG.71.r2

source_name: Culture no. 3, 71 h of culture, N-acetylglucosamine added


title: PBMC_MECFS_19


title: NAG-72 h-replicate 1

description:
Hybridization of Cy3-labelled cDNA from total RNA together with Cy5-labelled genomic DNA used as the reference; the same reference sample for all the hybridizations of the experiment
MgLoc_NAG.72.r1

source_name: Culture no. 1, 72 h of culture, N-acetylglucosamine added

source_name: Total DNA extracted from a stationary-phase culture


title: PBMC_HC_17


title: PBMC_MECFS_20


title: PBMC_HC_24


title: PBMC_MECFS_18


title: PBMC_MECFS_29


title: PBMC_MECFS_16


title: PBMC_HC_26


title: PBMC_HC_14


title: PBMC_HC_13


title: CycC cKO 3

city: Iowa City

first: Chad

last: Grueter

state: Iowa

address: 285 Newton Rd, 4332 PBDB, 285 Newton Rd

institute: University of Iowa

data_processing:
Illumina HiSeq platform
Basespace applications were used for trimming and sequence alignments
Raw files were uploaded into Illumina's BaseSpace hub (basespace.illumina.com) and aligned to mus musculus mm10 genome using the TopHat Alignment Version 1.0.0 App and selecting "Trim TruSeq Adapters" option.
Transcripts were assembled and differential expression was determined using the BaseSpace Cufflinks Assembly and DE Version 1.1.0 App selecting mm10 reference genome and "Stranded" polyA enriched sequences.
FPKM tables and CuffDiff results of differential gene expression of were downloaded and significantly expressed genes (FDR<0.05, FPKM>5) were used for analyses
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample and CuffDiff output

source_name: heart

extract_protocol:
hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq RNA Library prep kit V2

value: heart

value: 6 weeks old

tag: background strain

value: fl/fl; aMHC cre


title: PBMC_HC_10


title: PBMC_MECFS_7

source_name: PBMC, MECFS patient


title: PBMC_HC_9


title: PBMC_HC_12


title: PBMC_HC_11


title: PBMC_MECFS_6


title: PBMC_MECFS_3


title: PBMC_MECFS_4


title: PBMC_MECFS_5


title: PBMC_MECFS_8


title: CycC cKO 2


title: CycC cKO 1


title: CycC fl/fl 3

value: fl/fl


title: RNA-seq of dng701/4 zygote replicate 1

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

description: 14-vs-DJ-Z-gene_exp.diff, q1: WT-Z, q2: dng701/4-Z

data_processing:
For RNA-seq, sequencing reads were mapped to genome (RGAP, version 7.0) by Hisat software, cufflinks suite was used to splice transcripts and calculate gene expression fold changes. Genes with fold change higher than 2 and P value less than 0.01 were considered as differentially expressed genes. For Bisulfite-seq, clean reads were mapped to the rice genome (RGAP, version 7.0) by BS-seeker2 (v.2.1.8). Uniquely mapped reads were retained for further analysis. Mean nuclear methylation levels were calculated by averaging methylation of individual cytosine in each context as described.
Genome_build: RGAP version 7.0
Supplementary_files_format_and_content: tab-delimited text file containing differentially expressed gene information and cytosine methylation information

organism: Oryza sativa Japonica Group

source_name: unicellular zygote

growth_protocol: Rice plants were grown in either greenhouse or paddy field

extract_protocol:
Rice gametes and unicellular zygotes were isolated from mature anthers and ovaries as reported. Briefly, mature anthers were soaked in 45% (w/v) sucrose and then transferred into 15% (w/v) sucrose to release sperm pairs. For isolation of eggs and unicellular zygotes, ovaries of non-pollinated and pollinated florets (about 6.5 h after pollination) were manually dissected under a dissection microscope. The dissociated ovules were then transferred into fresh 0.53 M mannitol and broken to release eggs or zygotes. All isolated cells were stained by FDA (Fluoresceinc diacetate, Sangon, 596-09-8) and collected by a micromanipulator system (Eppendorf, TransferMan® 4r).
For RNA-seq library construction, mRNA isolated from egg, sperm, and unicellular zygote were reverse transcribed and amplified by utilizing SMART-Seq® v4 Ultra® Low Input RNA Kit (TAKARA, Cat. No.634889), cDNAs were sheared into 200-400 bp DNA fragments followed by purification using Agencourt AMPure Beads (Beckman Coulter, USA A63881). The rest steps were performed using the Truseq ChIP DNA library preparation kit (Illumina .IP-202-1012). BS-seq libraries were constructed using reported protocol (Clark et al., 2017).

value: unicellular zygote isolated from ovule at 6.5 hours after pollination

tag: genotype/variation

tag: cultivar

value: DongJin


title: CycC fl/fl 1

tag: genotype


title: RNA-seq of dng701/4 zygote replicate 2


title: RNA-seq of dng701/4 egg replicate 1

description: 14-vs-DJ-E-gene_exp.diff, q1: WT-E, q2: dng701/4-E

source_name: egg

value: mature egg isolated from ovule


title: EXO_MECFS_27

source_name: Extracellular vesicles, MECFS patient

value: EV


title: EXO_HC_30

source_name: Extracellular vesicles, healthy control


title: PBMC_HC_1


title: EXO_MECFS_29


title: RNA-seq of dng702 egg replicate 1

description: 2-vs-DJ-E-gene_exp.diff, q1: WT-E, q2: dng702-E


title: RNA-seq of dng702 egg replicate 2


title: DAEO84: D.discoideum _Bs Rep4

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

data_processing:
Reads were mapped to the D.discoideum genome using tophat (version 2.0.13) and bowtie2 (version 2.2.4) softwares
The read counts per gene were generated using HTSeq software (version 0.6.1) and the GFF annotation downloaded from dictybase (February 2019)
The genes were filtered for minimal expression, by removing genes with an average through all samples lower than 5 reads
Normalization factors to scale the libraries sizes were calculated using edgeR. The read counts were then log-transformed and variance stabilized
The log-transformed counts were then batch-corrected for date effect using the R package limma and the removeBatchEffect function
Genome_build: 05-13-2009 13:53
Supplementary_files_format_and_content: Tab delimited containing the raw counts or the normalized counts

organism: Dictyostelium discoideum

source_name: amoeba

growth_protocol: Wild-type D. discoideum cells (4 x 106) were washed and resuspended in 1mL of HL5c medium containing 15 µg/mL of tetracycline. Bacteria were added at a multiplicity of infection (MOI) of 500. Alternatively, 1 mM of folate was added. The cells were then incubated at 21°C at 120 rpm for 4 h. As a control, D. discoideum cells were cultured separately in HL5c medium containing 15 µg/mL of tetracycline.

extract_protocol:
RNA was extracted from cells using the directzol RNA extraction kit (Zymo research) following the manufacturer’s instructions for total RNA isolation. To remove contaminating genomic DNA, samples were treated with 0.25U of DNase I (Zymo) per 1 μg of RNA for 15 min at 25°C. RNA was quantified using Qubit 4.0 (Invitrogen) and its quality was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies). The quality of the libraries was monitored by TapeStation (Agilent, High Sensitivity D1000 ScreenTape, # 5067–5584). Samples were pooled in approximately equimolar amounts and analyzed in 50 bp single read flow cells (Illumina, # 15022187; Hiseq 4000).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After co-incubation between bacteria and wild-type D. discoideum cells, the uningested bacteria were removed by centrifugation at 1000 g for 2 min

tag: amoebal strain

tag: bacteria strain

value: Bacillus subtilis 36.1 (Bs)


title: RNA-seq of WT zygote replicate 2

value: WT


title: DAEO79: D.discoideum (Control) Rep13


title: DAEO80: D.discoideum (Control) Rep14


title: DAEO82: D.discoideum _KpGe Rep5

value: Klebsiella pneumoniae (KpGe)


title: PBMC_MECFS_2


title: RNA-seq of dng701/4 egg replicate 2


title: CycC fl/fl 2


title: EXO_MECFS_25


title: EXO_MECFS_24


title: RNA-seq of WT egg replicate 2

description:
2-vs-DJ-E-gene_exp.diff, q1: WT-E, q2: dng702-E
14-vs-DJ-E-gene_exp.diff, q1: WT-E, q2: dng701/4-E


title: EXO_HC_28


title: DAEO78: D.discoideum (Control) Rep12


title: EXO_MECFS_23


title: EXO_MECFS_22


title: PBMC_HC_15


title: AI008_MDA-MB-231_siSHC1_48h

city: Chicago

first: Geoffrey

last: Greene

state: IL

address: 929 East 57th Street

department: Ben May Department for Cancer Research

institute: University of Chicago

data_processing:
Data analysis
RNA sequencing data analysis was performed using Artificial Intelligene’s (AI, www.artificialintelligene.com) RNAseq analysis platform. Briefly, short reads were aligned to the hg19 human genome using STAR. Subsequently cufflinks packages were used to perform transcript assemblies. Downstream differential gene expression calling on the reference and experimental groups of interest was performed using DESeq2. To perform clustering analyses on a group of samples, a union of all the genes and their expression RPKM values within that group was generated to build a read count matrix for the group of interest. Various unsupervised and other machine learning techniques were applied to this composite read count matrix of interest. The sample-sample correlation heatmaps represent the correlation observed between any two samples. The sample-feature heatmaps represent the signal intensity of a feature for any given sample. ggplot2, heatmap.2 and Pheatmap packages in R were used to build various heatmaps. Functional analysis was performed using gene set enrichment analyses.
Genome_build: hg19
Supplementary_files_format_and_content: read counts

source_name: Breast Cancer

extract_protocol:
RNA was harvested using Trizol. KAPA Stranded mRNA-Seq kit (Illumina Platforms Cat#KR0960) was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with different siRNAs and collected at 24 and 48 h after treansfection.

tag: cell line

tag: receptor status

value: triple negative

tag: treatment

value: 48 hours


title: DAEO77: D.discoideum (Control) Rep11


title: AI008_MDA-MB-231_siNCOA3_48h


title: BS-seq of dng701/4 zygote replicate 2

library_source: genomic


title: RNA-seq of WT egg replicate 1


title: DAEO66: D.discoideum _Mm Rep5

value: Mycobacterium marinum M strain (Mm)


title: RNA-seq of WT zygote replicate 1


title: EXO_MECFS_20

value: MECFS


title: BS-seq of dng701/4 zygote replicate 1


title: EXO_MECFS_26


title: DAEO65: D.discoideum _Mm Rep4


title: AI008_MDA-MB-231_siControl_48h

value: siControl


title: Col-0_repl1

source_name: seedlings

value: seedlings


title: EXO_MECFS_19


title: DAEO64: D.discoideum _Bs Rep3


title: BS-seq of dng701/4 sperm replicate 2

source_name: sperm

value: mature sperm isolated from pollen


title: AI008_MDA-MB-231_siSHC1_24h

value: 24 hours


title: EXO_HC_18

value: Healthy Control


title: AI008_MDA-MB-231_siNCOA3_24h


title: DAEO62: D.discoideum _KpGe Rep4


title: EXO_MECFS_21


title: DAEO60: D.discoideum (Control) Rep10


title: BS-seq of dng701/4 sperm replicate 1


title: EXO_HC_17


title: BS-seq of dng701/4 egg replicate 1


title: DAEO59: D.discoideum (Control) Rep9


title: EXO_HC_16


title: EXO_HC_15


title: Melanocyte3 30J UVB

city: MADISON

first: Vijayasaradhi

last: Setaluri

address: 1300 University Avenue

department: Dermatology

institute: University of Wisconsin-Madison

data_processing:
Raw FASTQ files were analyzed for quality using FASTQC, and low quality reads and adaptors were filtered and trimmed using cut-adapt. RSEM was used to map the reads to transcripts from human genome version hg19 and call isoform level expression.
Genome_build: hg19
Supplementary_files_format_and_content: Excel File:  contains information on reads per million.

source_name: Human Neonatal Foreskin

growth_protocol: Matched melanocytes, keratinocytes and fibroblasts were obtained from 3 individual donors and cultured in M254, M154 and DMEM with 10% FBS respectively.

extract_protocol:
Cells were harvested in QiaZol Lysis reagent (Qiagen, Redwood City, CA) at 0h and 24h post-irradiation. RNA was isolated using miRNEasy Isolation kit (Qiagen, Cat. No. 217004) for all melanocyte, fibroblast and keratinocyte samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4 X 105 melanocytes were plated in 6 well dishes for UVB exposure. 12h-24h post-plating, the cells were exposed to mock, 10mJ/cm2 or 30mJ/cm2 UVB integrated over 10s using a Daavlin Research Irradiator (Daavlin Company, Bryan, OH).

tag: cell type

value: Melanocyte

tag: uvb treatment


title: DAEO58: D.discoideum (Control) Rep8


title: BS-seq of dng702 sperm replicate 2

tag: tissue


title: Melanocyte3 10J UVB


title: BS-seq of dng702 sperm replicate 1


title: Melanocyte3 control


title: DAEO57: D.discoideum (Control) Rep7


title: Melanocyte2 30J UVB


title: BS-seq of dng702 egg replicate 2


title: BS-seq of dng701/4 egg replicate 2


title: Melanocyte2 10J UVB


title: DAEO31: D.discoideum _Mm Rep2


title: EXO_HC_12


title: EXO_HC_13


title: EXO_HC_11


title: Melanocyte2 control


title: BS-seq of WT zygote replicate 2

value: unicellular zygote isolated from ovule at 6.5 hours after pollination


title: EXO_HC_14


title: DAEO30: D.discoideum _Bs Rep2


title: EXO_HC_10


title: EXO_HC_9


title: BS-seq of WT zygote replicate 1

value: DongJin


title: DAEO29: D.discoideum _Bs Rep1


title: Melanocyte 1 30J UVB


title: BS-seq of WT sperm replicate 2


title: BS-seq of WT sperm replicate 1


title: Melanocyte1 10J UVB


title: DAEO28: D.discoideum _KpGe Rep3


title: Melanocyte1 control


title: AI008_MDA-MB-231_siControl_24h


title: DAEO27: D.discoideum _KpGe Rep2


title: DAEO32: D.discoideum _Mm Rep3


title: BS-seq of dng702 egg replicate 1

value: mature egg isolated from ovule


title: EXO_HC_8

value: EV


title: BS-seq of WT egg replicate 2


title: EXO_HC_7


title: DAEO26: D.discoideum (Control) Rep6


title: Melanocyte 3


title: EXO_HC_6


title: BS-seq of WT egg replicate 1


title: EXO_MECFS_5


title: DAEO25: D.discoideum (Control) Rep5


title: DAEO24: D.discoideum (Control) Rep4


title: EXO_MECFS_3


title: Keratinocyte 3

value: Keratinocyte


title: DADJ09: D.discoideum _Kp21 Rep2

value: Klebsiella pneumoniae (Kp21)


title: DADJ08: D.discoideum _KpGe Rep1

value: Klebsiella pneumoniae (KpGe)


title: Keratinocyte 2


title: Keratinocyte 1


title: Fibroblast 3

value: Fibroblast


title: Fibroblast 2


title: DADJ02n: D.discoideum _Ml Rep2

value: Micrococcus luteus (Ml)


title: NLS_Venus_GFP_ChIP_Fe_minus_Rep1

city: Manchester

first: Michael

middle: J

last: Bromley

state: Greater Manchester

address: 46 Grafton Street

department: Division of Infection, Immunity, and Respiratory mediciney

country: United Kingdom

institute: The University of Manchester

data_processing:
Raw sequencing reads were quality controlled with Illumina chastity filter and fastqc v0.11.3.
Illumina adapters were trimmed from them using Trimmomatic v0.32.
The resulting reads were aligned to the Aspergillus fumigatus A1163 CADRE genome from Ensemble fungi, version 28 using Bowtie2 v2.2.3.
Peak calling was carried out using a Model-based Analysis for ChIP-Sequencing (MACS2) version 2.1.0.20140616 with a q-value cutoff of 0.01.
Genome_build: Aspergillus fumigatus A1163 CADRE genome from Ensemble fungi, version 28
Supplementary_files_format_and_content: bigWig file were generated using bedGraphToBigWig v305

organism: Aspergillus fumigatus

source_name: Mycelia

growth_protocol: 1x106 spores/ml of the NLS-Venus expressing strain were grown in 50 ml of Aspergillus minimal medium (AMM) in the presence and the absence of iron for 24 h at 37 °C with constant shaking at 180 rpm.

extract_protocol:
Cross-linked mycelia were ground to a fine powder under liquid nitrogen. Samples were suspended in a ChIP lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Deoxycholate (Sigma D6750), 0.1% SDS, 1 mM PMSF, and fungal proteinase inhibitor cocktail (Sigma)), and then sonicated with a Q125 sonicator (Qsonica, USA). The sheared chromatin was immunoprecipitated with a GFP-polyclonal antibody (A-11122, Thermo Fischer Scientific) on Dynabeads Protein A magnetic beads (Thermo Fischer Scientific). Immunoprecipitated DNA was reverse cross-linked, treated with RNase A (Sigma), and then purified using a MinElute PCR purification kit (QIAGEN).
Libraries were constructed following the manufacture's instractions for Illumina TruSeq ChIP-seq samplepreparation kit.

treatment_protocol: Cross-linking was carried out by the addition of formaldehyde to a final concentration of 1.0 % followed by incubation at 37°C for 20 min. Fixation was stopped by adding glycine to a final concentration of 125 mM and continuing shaking for 10 min at 37 °C.

tag: strain

value: A1160pyrG+, {delta}atfA::NLS-Venus

tag: chip antibody

value: GFP Tag polyclonal antibody (ThermoFischerScientific, A-11122)

value: Mycelia


title: Melanocyte 2


title: NLS_Venus_GFP_ChIP_Fe_minus_Rep2


title: DAAX28: D.discoideum _Ml Rep1


title: Fibroblast 1


title: DAAX29: D.discoideum (Control) Rep1


title: NLS_Venus_GFP_ChIP_Fe_plus_Rep1


title: NLS_Venus_GFP_ChIP_Fe_plus_Rep2


title: EXO_MECFS_1

value: MECFS


title: sample-42: 96 H-2

status: Public on Feb 07 2020

city: St Augustine

first: Leonid

middle: L

last: Moroz

state: FL

address: 9505 Ocean Shore Blvd

institute: University of Florida

description:
Single-cell sequencing
Read 1, 26 cycles;i7 Index, 8 cycles;i5 Index,0 cycles;Read 2, 98 cycles

data_processing:
Chromium, v2 was used
The Cell Ranger Single Cell Software vs 2.1 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting
Downstream processing was performed with a custom pipeline
Genome_build: Genome release version 6.13
Supplementary_files_format_and_content: File description and contents are described at http://software.10xgenomics.com/single-cell/overview/welcome

organism: Drosophila melanogaster

extract_protocol:
CNS was disected then dissociated in 1% Neutral Protease (Dispase) (cat# LS02109, Worthington) at room temperature (21 °C).
Library protocol was followed according 10x genomics using Chromium Single Cell 3′ Library & Gel Bead Kit


title: sample-40: 96 H


title: sample-39: 4 CNS 3rd instarcontrol

source_name: 48H ALH

value: 4 CNS 3rd instar


title: Melanocyte 1


title: EXO_MECFS_4


title: sample-43: 96 H paired

source_name: 96 H paired

value: 96 H paired


title: sample-41: 96 H unpaired

source_name: 96 H unpaired

value: 96 H unpaired


title: sample-38: 4 CNS 3rd instartrained


title: sample-36: 10 brain 3rd instartrained

value: 10 brain 3rd instar


title: sample-37: 10 brain 3rd instarcontrol


title: sample-35: 4 CNS 3rd instarcontrol


title: DADJ07: D.discoideum _Ml Rep3


title: EXO_MECFS_2


title: sample-34: 4 CNS 3rd instartrained


title: sample-33: 10 brain 3rd instarcontrol


title: sample-30: 1st instar4 CNS

source_name: 1st instar 1H

value: 4 CNS


title: sample-31: 1st instar5 CNS

value: 5 CNS


title: sample-32: 10 brain 3rd instartrained


title: sample-29: adult male3 VNC

source_name: adult male

value: 3 VNC


title: sample-28: 48H ALHSalivary Gland

value: Salivary Gland


title: sample-25: 48H ALHimaginal disc

value: imaginal disc


title: sample-24: 24H ALH6 brains

source_name: 24H ALH

value: 6 brains


title: sample-21: 24H ALH10 brains

value: 10 brains


title: sample-23: 48H ALH8 brains

value: 8 brains


title: sample-27: adult male1 VNC

value: 1 VNC


title: sample-22: 24H ALH6 VNC

value: 6 VNC


title: sample-26: adult male1 VNC


title: sample-19: 24H ALH10 brains


title: sample-17: 48H ALH6 brains


title: sample-6: 48H ALH1 CNS

value: 1 CNS


title: sample-3: 48H ALH2 CNS

value: 2 CNS


title: sample-7: 48H ALH1 CNS


title: sample-1: 48H ALH1 CNS


title: sample-18: 48H ALH4 VNC

value: 4 VNC


title: sample-8: 48H ALH1 CNS


title: sample-2: 48H ALH1 CNS


title: sample-4: 48H ALH1 CNS


title: RA5108K3-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 8.2

city: Oslo

first: Kari

last: Guderud

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

description: MSP1 fragmented DNA

data_processing:
Primary base calling and quality scoring was performed using BSMAP v.2.90 (-p4, -D C-CGG, -v2, -n1, -q28)
getting methylation ratios in methratio.py with samtools
Getting CGs: grep -c "CG" sorted_*.txt
Methratio format to RnBeads format were transformed with a custom R-script
Call methylation differences: RnBeads v.1.10.8  No SNPs, cov treshold=10, min.group.size=5, no sex chromosomes)
Genome_build: hg19

source_name: CD4+ naïve t cell

extract_protocol:
RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
Diagenode RRBS, In house mRRBS

value: CD4+ naïve t cell

tag: library prep kit

value: mRRBS

tag: disease state

value: Newly diagnosed Rheumatoid Arthritis

tag: replicate


title: RA5514B-4m: Treated Rheumatoid Arthritis patient CD4mem 14

description: MSP1 fragmented DNA

source_name: CD4+ memory t cell

value: CD4+ memory t cell

value: Treated Rheumatoid Arthritis


title: RA5513B-4m: Treated Rheumatoid Arthritis patient CD4mem 13

description: MSP1 fragmented DNA


title: RA5519B-4m: Treated Rheumatoid Arthritis patient CD4mem 19

description: MSP1 fragmented DNA


title: RA5516B-4m: Treated Rheumatoid Arthritis patient CD4mem 16

description: MSP1 fragmented DNA


title: RA5515B-4m: Treated Rheumatoid Arthritis patient CD4mem 15

description: MSP1 fragmented DNA


title: RA5512B-4m: Treated Rheumatoid Arthritis patient CD4mem 12

description: MSP1 fragmented DNA


title: RA5509B-4m: Treated Rheumatoid Arthritis patient CD4mem 9

description: MSP1 fragmented DNA


title: RA5517B-4m: Treated Rheumatoid Arthritis patient CD4mem 17

description: MSP1 fragmented DNA


title: RA5511B-4m: Treated Rheumatoid Arthritis patient CD4mem 11

description: MSP1 fragmented DNA


title: RA5518B-4m: Treated Rheumatoid Arthritis patient CD4mem 18

description: MSP1 fragmented DNA


title: sample-20: 24H ALH6 VNC


title: RA5508B-4m: Treated Rheumatoid Arthritis patient CD4mem 8

description: MSP1 fragmented DNA


title: RA5502B-4m: Treated Rheumatoid Arthritis patient CD4mem 2

description: MSP1 fragmented DNA


title: RA5505B-4m: Treated Rheumatoid Arthritis patient CD4mem 5

description: MSP1 fragmented DNA


title: RA5506B-4m: Treated Rheumatoid Arthritis patient CD4mem 6

description: MSP1 fragmented DNA


title: RA5111B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 11.1

description: MSP1 fragmented DNA


title: RA5111K3-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 11.2

description: MSP1 fragmented DNA


title: RA5507B-4m: Treated Rheumatoid Arthritis patient CD4mem 7

description: MSP1 fragmented DNA


title: RA5503B-4m: Treated Rheumatoid Arthritis patient CD4mem 3

description: MSP1 fragmented DNA


title: RA5110B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 10.1

description: MSP1 fragmented DNA


title: RA5109K3-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 9.2

description: MSP1 fragmented DNA


title: RA5107K3-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 7.2

description: MSP1 fragmented DNA

value: Diagenode mRRBS


title: RA5105K3-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 5.2

description: MSP1 fragmented DNA


title: RA5109B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 9.1

description: MSP1 fragmented DNA


title: RA5108K3-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 8.2

description: MSP1 fragmented DNA


title: RA5106B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 6

description: MSP1 fragmented DNA


title: RA5107B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 7.1

description: MSP1 fragmented DNA


title: RA5105B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 5.1

description: MSP1 fragmented DNA


title: RA5510B-4m: Treated Rheumatoid Arthritis patient CD4mem 10

description: MSP1 fragmented DNA


title: IRC5111A-4m: Control CD4mem 11

description: MSP1 fragmented DNA

value: Healthy control


title: RA5101B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 1.1

description: MSP1 fragmented DNA


title: RA5102B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 2.1

description: MSP1 fragmented DNA


title: RA5102K3-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 2.2

description: MSP1 fragmented DNA


title: RA5104B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 4.1

description: MSP1 fragmented DNA


title: IRC5110A-4m: Control CD4mem 10

description: MSP1 fragmented DNA


title: IRC5109A-4m: Control CD4mem 9

description: MSP1 fragmented DNA


title: IRC5107A-4m: Control CD4mem 7

description: MSP1 fragmented DNA


title: RA5101K3-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 1.2

description: MSP1 fragmented DNA


title: RA5110K3-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 10.2

description: MSP1 fragmented DNA


title: IRC5102A-4m: Control CD4mem 2

description: MSP1 fragmented DNA


title: IRC5104A-4m: Control CD4mem 4

description: MSP1 fragmented DNA


title: IRC5103A-4m: Control CD4mem 3

description: MSP1 fragmented DNA


title: IRC5101A-4m: Control CD4mem 1

description: MSP1 fragmented DNA


title: CBP93

city: Bronx

first: Maureen

last: Charron

state: NY

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

description: HpaII test for HELP-tagging

data_processing:
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (ELAND - 1.7.0).  Initial data processing was performed using the default read length of 37 or 42 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions. To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Illumina Casava was used for basecalling.
After the sequence data was obtained from Illumina HiSeq 2500, we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again  (ELAND - 1.7.0) on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).
The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.
To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: hg19
Supplementary_files_format_and_content: Format: bedGraph; content: Chromosome, start, end, processed angle value

source_name: human CD3+ T-cell

extract_protocol:
High molecular weight genomic DNA was extracted from CD3+ T-cell from human cord blood.
Custom adapters were created for HELP-tagging, referred to as AE and AS Index. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence, and adapter AS contains index sequences for multiplexing .  Adapter AS contains an Illumina sequencing primer sequence.  Five hundred nanograms of genomic DNA were digested with HpaII in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, HpaII-digested DNA, 0.5 μl of Adapter AE (0.1 μM), 1 μl of Quick Ligase in a final volume of 10 μl).  After AE ligation, the products were purified using AMpure XP (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (12.5 μl of 2x Quick ligase buffer, 1.25 μl of Adapter AS (1 μM), 1.25 μl of Quick Ligase in a final volume 25 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).

tag: offspring gender

value: male

tag: gestational age (weeks)

tag: birth weight (g)

tag: maternal age (years)

tag: bmi at term

tag: weight at term (lbs)

value: CD3+ T-cell


title: CBP87

description: HpaII test for HELP-tagging

value: female


title: CBP90

description: HpaII test for HELP-tagging


title: CBP92

description: HpaII test for HELP-tagging


title: CBP82

description: HpaII test for HELP-tagging


title: CBP96

description: HpaII test for HELP-tagging


title: CBP80

description: HpaII test for HELP-tagging


title: RA5103K3-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 3.2

description: MSP1 fragmented DNA


title: CBP77

description: HpaII test for HELP-tagging


title: RA5103B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 3.1

description: MSP1 fragmented DNA


title: CBP65

description: HpaII test for HELP-tagging


title: CBP68

description: HpaII test for HELP-tagging


title: CBP64

description: HpaII test for HELP-tagging


title: CBP66

description: HpaII test for HELP-tagging


title: CBP71

description: HpaII test for HELP-tagging


title: CBP63

description: HpaII test for HELP-tagging


title: CBP70

description: HpaII test for HELP-tagging


title: IRC5106A-4m: Control CD4mem 6

description: MSP1 fragmented DNA


title: CBP95

description: HpaII test for HELP-tagging


title: CBP62

description: HpaII test for HELP-tagging


title: CBP57

description: HpaII test for HELP-tagging


title: CBP61

description: HpaII test for HELP-tagging


title: CBP84

description: HpaII test for HELP-tagging


title: CBP58

description: HpaII test for HELP-tagging


title: CBP60

description: HpaII test for HELP-tagging


title: CBP88

description: HpaII test for HELP-tagging


title: CBP81

description: HpaII test for HELP-tagging


title: CBP79

description: HpaII test for HELP-tagging


title: CBP56

description: HpaII test for HELP-tagging


title: CBP55

description: HpaII test for HELP-tagging


title: CBP52

description: HpaII test for HELP-tagging


title: CBP54

description: HpaII test for HELP-tagging


title: CBP51

description: HpaII test for HELP-tagging


title: CBP53

description: HpaII test for HELP-tagging


title: CBP48

description: HpaII test for HELP-tagging


title: CBP50

description: HpaII test for HELP-tagging


title: CBP43

description: HpaII test for HELP-tagging


title: CBP45

description: HpaII test for HELP-tagging


title: CBP44

description: HpaII test for HELP-tagging


title: CBP47

description: HpaII test for HELP-tagging


title: CBP42

description: HpaII test for HELP-tagging


title: CBP40

description: HpaII test for HELP-tagging


title: CBP41

description: HpaII test for HELP-tagging


title: CBP39

description: HpaII test for HELP-tagging


title: CBP38

description: HpaII test for HELP-tagging


title: CBP36

description: HpaII test for HELP-tagging


title: CBP32

description: HpaII test for HELP-tagging


title: CBP37

description: HpaII test for HELP-tagging


title: CBP33

description: HpaII test for HELP-tagging


title: CBP34

description: HpaII test for HELP-tagging


title: CBP26

description: HpaII test for HELP-tagging


title: CBP30

description: HpaII test for HELP-tagging


title: CBP27

description: HpaII test for HELP-tagging


title: CBP35

description: HpaII test for HELP-tagging


title: CBP31

description: HpaII test for HELP-tagging


title: CBP25

description: HpaII test for HELP-tagging


title: CBP24

description: HpaII test for HELP-tagging


title: CBP23

description: HpaII test for HELP-tagging


title: CBP22

description: HpaII test for HELP-tagging


title: CBP20

description: HpaII test for HELP-tagging


title: CBP19

description: HpaII test for HELP-tagging


title: CBP17

description: HpaII test for HELP-tagging


title: CBP18

description: HpaII test for HELP-tagging


title: CBP12

description: HpaII test for HELP-tagging


title: CBP13

description: HpaII test for HELP-tagging


title: CBP9

description: HpaII test for HELP-tagging


title: CBP8

description: HpaII test for HELP-tagging


title: CBP14

description: HpaII test for HELP-tagging


title: CBP11

description: HpaII test for HELP-tagging


title: CBP10

description: HpaII test for HELP-tagging


title: CBP6

description: HpaII test for HELP-tagging


title: CBP5

description: HpaII test for HELP-tagging


title: CBP3

description: HpaII test for HELP-tagging


title: 21 dpi 4

city: Coralville

first: Alan

middle: Jacob

last: Sariol

state: IA

address: 2868 Coral Ct., Apt 201

department: Microbiology and Immunology

data_processing:
Libraries were loaded onto a NextSeq 550 (single read, Illumina) cartridge, where clustering occurred on-board the instrument. After clustering, sequencing was commenced using Illumina’s 2-color SBS chemistry. Following sequencing, Base call (.bcl) files for each cycle of sequencing were generated by Illumina Real Time Analysis software. Primary analysis and de-multiplexing were performed using Illumina’s CASAVA software 1.8.2. The end result of the CASAVA workflow was de-multiplexed FASTQ files for subsequent analysis.
75bp FastQ single-end reads (19.7-25.9 million reads per sample) were trimmed using Trimmomatic (version 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control of raw sequence data for each sample was performed using FastQC. Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (mm10) as reference. Gene quantification was performed using Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen) using raw read counts. We filtered the generated list on the basis of a minimum 2 absolute fold change after log2 transformation and an FDR corrected p value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files

source_name: Spinal cord

extract_protocol:
Microglia were isolated by FACS-sorting. Total RNA was extracted by RNeasy Micro Kit (Qiagen) per manufacturer's instructions
Libraries were prepared using a SMARTer Stranded Total RNA-Seq v2 – Pico Mammalian kit (Takara) per manufacturer's instructions. Briefly, between 250pg-10ng of total RNA was fragmented and then reverse transcribed into cDNA using random primers, with a template switching oligo incorporated during cDNA synthesis to allow for full length cDNA synthesis and retain strand specificity. Illumina sequencing adapters and barcodes were then added to the cDNA by PCR, followed by cleavage of ribosomal cDNA. Uncleaved fragments were then enriched by PCR for 12-16 cycles. Final library size distribution was again validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen). Indexed libraries were then normalized and pooled for sequencing.

treatment_protocol: Mice were infected with 700 PFU of the rJ2.2 variant of JHMV in 30 uL DMEM or mock infected with 30 uL DMEM alone. Spinal cords were harvested and immune cells isolated at the indicated days post-infection. Microglia (CD45 intermediate, CD11b+) were sorted by FACS.

value: spinal cord

value: microglia

tag: age

value: 8 weeks

tag: infection status

value: infected


title: CBP2

description: HpaII test for HELP-tagging


title: 21 dpi 2


title: 21 dpi 3


title: 21 dpi 1


title: 14 dpi 4


title: CBP1

description: HpaII test for HELP-tagging


title: 14 dpi 2


title: CBP15

description: HpaII test for HELP-tagging


title: 14 dpi 1


title: Mock-infected 2

value: naive


title: Mock-infected 3


title: CBP7

description: HpaII test for HELP-tagging


title: Pig 7704 – Naive – Sac day 28

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

description: Pig heart tissue, naive, tissue collected on day 28

data_processing:
Trimming: Paired-end fastq files were evaluated with the trim-galore [48] package for quality assessments of the input sequencing files
Mapping: mapping was conducted with the Ensembl pig genome assembly (Sscrofa11.1) and STAR package v2.5.2 to produce the sorted BAM (Binary Alignment Map) file format.
Convert from BAM format to SAM format: SAMtool
Counting: mapped transcripts (raw expression) were counted with the HTSeq/0.6.1 package
Normalization: Expression levels were normalized and differential gene expressions (log2 of the fold-change ) were analyzed with Deseq2
Genome_build: Ensembl pig genome assembly (Sscrofa11.1)
Supplementary_files_format_and_content: tab-delimited text files include expression values for each sample.

organism: Sus scrofa

source_name: Naive Heart

growth_protocol: Pigs (Prestage Farms, Inc, West Point, MS) were fed every 4 hours with bovine colostrum on P1-P2, with a 1:1 ratio of colostrum:sow’s milk on P3, and with cow’s milk from P4 until sample collection. Supplemental iron was provided on P7, and the animals were housed in an incubator at ~85 °F with room air until P28 days of age.

extract_protocol:
RNA was isolated from tissue samples (~30 mg) colle cted from the border zone of ischemia in the hearts of MI animals and from the corresponding region of hearts in Age-matched normal  animals.
Libraries were quantified via qPCR with equal amounts of RNA for all samples, and RNA concentrations were diluted to 3 nM before loading equimolar amounts onto the flow cells.

treatment_protocol: MI was induced via permanent ligation of the left descending coronary artery, and animals in the Age-matched normals  group underwent all surgical procedures for MI induction except the ligation step.

tag: injured / naive

value: Naive

tag: injured postnatal day

tag: age at tissue collection (day)


title: Pig 7706 – Naive – Sac day 28


title: Pig 7698 – Naive – Sac day 7

description: Pig heart tissue, naive, tissue collected on day 7


title: Pig 7711 – Naive – Sac day 1

description: Pig heart tissue, naive, tissue collected on day 1


title: Pig 7699 – Naive – Sac day 7


title: Pig 7705 – Naive – Sac day 28


title: Pig 7700 – Naive – Sac day 7


title: Pig 7703 – Naive – Sac day 14

description: Pig heart tissue, naive, tissue collected on day 14


title: Pig 7702 – Naive – Sac day 14


title: Pig 7701 – Naive – Sac day 14


title: Pig 7697 – Naive – Sac day 3

description: Pig heart tissue, naive, tissue collected on day 3


title: Pig 7693 – Naive – Sac day 1


title: 14 dpi 3

tag: tissue

tag: cell type


title: Pig 7656 – Naive – Sac day 3


title: Pig 7728 – MI – Sac day 7

description: Pig heart tissue, injured on postnatal day 1, tissue collected on day 7

source_name: MI Heart

value: Injured


title: Pig 7729 – MI – Sac day 7


title: Pig 7731 – MI – Sac day 7


title: Mock-infected 4

tag: strain


title: Mock-infected 1


title: Pig 7690 – MI – Sac day 28

description: Pig heart tissue, injured on postnatal day 1, tissue collected on day 28


title: Pig 7640 – MI – Sac day 28


title: Pig 7715 – MI – Sac day 14

description: Pig heart tissue, injured on postnatal day 1, tissue collected on day 14


title: Pig 7713 – MI – Sac day 14


title: Pig 7712 – MI – Sac day 14


title: Veh.8h.3

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
RNA-seq reads were aligned to the reference genome by using STAR.
Reads were counted with Subread featureCounts.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file of raw counts

source_name: Brown preadipocytes

extract_protocol:
Total RNA was isolated using Direct-zol™ RNA miniprep Kits (Zymo Research, Irvine, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Brown preadipocytes

tag: treatment

value: Veh

tag: time


title: Con_Mes3

city: Los Angeles

first: Zijun

last: Zhang

state: CA

address: 650 Charles E. Young Drive South

institute: UCLA

description: Barcodes: AGTCAA

data_processing:
fastq reads were aligned using STAR (v2.5.2a) to mm10 reference genome
alternative splicing events were analyzed by rMATS (v4.0.1)
gene expression levels (TPM) were quantified by Kallisto(v0.43.0) with gencodevM13 as index
Genome_build: mm10
Supplementary_files_format_and_content: rMATS.zip, TPM.tsv

source_name: Wild-type Mesenchyme

extract_protocol:
E12.0 mouse embryos were dissected, and the ectodermal and mesenchymal tissue layers of the prominences were separated and collected for wild-type and Esrp1-/- mice for a total of 4 pools of 6 to 7 mice in each category. The facial ectoderm and mesenchyme of each embryo was separated using a described surgical protocol (Li and Williams, J Vis Exp. 74. 2013). RNA from dissected ectoderm and mesenchyme samples was harvested using Trizol.
RNA libraries were prepared by the Penn Next Generation Sequencing Core facility using standard Illumina protocols

tag: genotype

value: Wild-type

tag: region

value: Facial prominences

value: Mesenchyme

value: Embryonic day 12 (E12)


title: KO_Mes1

description: Barcodes: GAGATTCC-CCTATCCT

source_name: Esrp1 KO Mesenchyme

value: Esrp1 KO


title: KO_Mes2

description: Barcodes: ATTCAGAA-CCTATCCT


title: Con_Mes1

description: Barcodes: CAGATC


title: Con_Epi4

description: Barcodes: ATTACTCG-CCTATCCT

source_name: Wild-type Ectoderm

value: Ectoderm


title: KO_Epi4

description: Barcodes: CGCTCATT-CCTATCCT

source_name: Esrp1 KO Ectoderm


title: KO_Mes4

description: Barcodes: GTCCGC


title: Con_Epi1

description: Barcodes: CGATGT


title: Veh.8h.2


title: KO_Epi1

description: Barcodes: TCCGGAGA-CCTATCCT


title: KO_Mes3

description: Barcodes: GTGAAA


title: Con_Mes2

description: Barcodes: CTTGTA


title: Con_Mes4

description: Barcodes: AGTTCC


title: Veh.8h.1


title: Veh.4h.3


title: Con_Epi2

description: Barcodes: TGACCA


title: Con_Epi3

description: Barcodes: ATGTCA


title: Veh.4h.1


title: Veh.4h.2


title: Veh.24h.3


title: Veh.24h.1


title: FGF6.8h.3


title: Veh.24h.2


title: FGF6.8h.2


title: KO_Epi2

description: Barcodes: GCCAAT


title: KO_Epi3

description: Barcodes: CCGTCC


title: FGF6.4h.3


title: FGF6.4h.1


title: FGF6.24h.2


title: FGF6.24h.1


title: FGF6.24h.3


title: FGF6.4h.2


title: FGF6.8h.1


title: RBG27688_IL3_Day4_ME-Parental

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were aligned to Mus musculus genome (GRCm38.81) using G-SNAP (version 2015-09-29) with the following parameters: –B 5 –n 1 –N 1 –Q. HTSeq-count (version 0.6.0) was run to assign mapped reads to Ensembl genes (GRCm38.81).
Genome_build: GRCm38.81
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

source_name: Hoxb8 Cell line

growth_protocol: Conditionally immortalised early hematopoietic progenitor cells (Hoxb8-FL cells) (Redecke et al., 2013) were cultured in RPMI 1640 medium (Sigma-R8758) supplemented with 10% Fetal Bovine Serum (FBS) (HyCloneTM GE Healthcare), 5% Flt3L conditional medium, 1% Penicillin/Streptomycin (Sigma-P0781), 1% L-Glutamine (Sigma-G7513), 0.1% 2-Mercaptoethanol (50mM stock)(Gibco®), 0.001% β-estradiol (10mM stock) at 37 ̊C and 5% CO2.

extract_protocol:
GFP positive and DAPI negative cells were FACS sorted into individual wells of a 96 well plates containing lysis buffer and processed using Smart-Seq2 protocol as previously described (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 4000.
Libraries were prepared using the Illumina Nextera XT Libraries were prepared using the Illumina Nextera XT DNA preparation kit.

tag: day

tag: batch

tag: condition

value: ME-Parental


title: RBG27700_IL3_Day4_ME-Parental


title: RBG27901_IL3_Day7_ME-Parental


title: RBG27948_IL3_Day7_ME-Parental


title: RBG27676_IL3_Day4_ME-Parental


title: RBG27724_IL3_Day4_ME-Parental


title: RBG27748_IL3_Day4_ME-Parental


title: RBG27889_IL3_Day7_ME-Parental


title: RBG27736_IL3_Day4_ME-Parental


title: RBG27913_IL3_Day7_ME-Parental


title: RBG27912_IL3_Day7_ME-Parental


title: RBG27924_IL3_Day7_ME-Parental


title: RBG27949_IL3_Day7_ME-Parental


title: RBG27712_IL3_Day4_ME-Parental


title: RBG27925_IL3_Day7_ME-Parental


title: RBG27936_IL3_Day7_ME-Parental


title: RBG27888_IL3_Day7_ME-Parental


title: RBG27937_IL3_Day7_ME-Parental


title: RBG27864_IL3_Day7_ME-Parental


title: RBG27877_IL3_Day7_ME-Parental


title: RBG27865_IL3_Day7_ME-Parental


title: RBG27756_IL3_Day4_ME-Parental


title: RBG27900_IL3_Day7_ME-Parental


title: RBG27735_IL3_Day4_ME-Parental


title: RBG27699_IL3_Day4_ME-Parental


title: RBG27935_IL3_Day7_ME-Parental


title: RBG27755_IL3_Day4_ME-Parental


title: RBG27674_IL3_Day4_ME-Parental


title: RBG27687_IL3_Day4_ME-Parental


title: CBP78

description: HpaII test for HELP-tagging

tag: offspring gender

value: male

tag: gestational age (weeks)

tag: birth weight (g)

tag: maternal age (years)

tag: bmi at term

value: CD3+ T-cell


title: RBG27698_IL3_Day4_ME-Parental


title: RBG27675_IL3_Day4_ME-Parental


title: CBP72

description: HpaII test for HELP-tagging

value: female

tag: weight at term (lbs)


title: RBG27922_IL3_Day7_ME-Parental


title: RBG27947_IL3_Day7_ME-Parental


title: RBG27899_IL3_Day7_ME-Parental


title: RBG27874_IL3_Day7_ME-Parental


title: RBG27686_IL3_Day4_ME-Parental


title: RBG27911_IL3_Day7_ME-Parental


title: RBG27746_IL3_Day4_ME-Parental


title: RBG27709_IL3_Day4_ME-Parental


title: RBG27721_IL3_Day4_ME-Parental


title: RBG27862_IL3_Day7_ME-Parental


title: RBG27697_IL3_Day4_ME-Parental


title: RBG27733_IL3_Day4_ME-Parental


title: RBG27745_IL3_Day4_ME-Parental


title: RBG27723_IL3_Day4_ME-Parental


title: RBG27685_IL3_Day4_ME-Parental


title: RBG27711_IL3_Day4_ME-Parental


title: RBG27747_IL3_Day4_ME-Parental


title: RBG27921_IL3_Day7_ME-Parental


title: RBG27673_IL3_Day4_ME-Parental


title: RBG27909_IL3_Day7_ME-Parental


title: RBG27710_IL3_Day4_ME-Parental


title: RBG27722_IL3_Day4_ME-Parental


title: RBG27897_IL3_Day7_ME-Parental


title: RBG27885_IL3_Day7_ME-Parental


title: RBG27754_IL3_Day4_ME-Parental


title: RBG27708_IL3_Day4_ME-Parental


title: RBG27684_IL3_Day4_ME-Parental


title: RBG27720_IL3_Day4_ME-Parental


title: RBG27944_IL3_Day7_ME-Parental


title: RBG27920_IL3_Day7_ME-Parental


title: RBG27696_IL3_Day4_ME-Parental


title: RBG27744_IL3_Day4_ME-Parental


title: RBG27672_IL3_Day4_ME-Parental


title: RBG27743_IL3_Day4_ME-Parental


title: RBG27719_IL3_Day4_ME-Parental


title: RBG27908_IL3_Day7_ME-Parental


title: RBG27731_IL3_Day4_ME-Parental


title: RBG27932_IL3_Day7_ME-Parental


title: RBG27683_IL3_Day4_ME-Parental


title: RBG27695_IL3_Day4_ME-Parental


title: RBG27671_IL3_Day4_ME-Parental


title: RBG27706_IL3_Day4_Parental

value: Parental


title: RBG27872_IL3_Day7_ME-Parental


title: RBG27694_IL3_Day4_Parental


title: RBG27682_IL3_Day4_Parental


title: RBG27707_IL3_Day4_ME-Parental


title: RBG27894_IL3_Day7_Parental


title: RBG27870_IL3_Day7_Parental


title: RBG27705_IL3_Day4_Parental


title: RBG27882_IL3_Day7_Parental


title: RBG27693_IL3_Day4_Parental


title: RBG27681_IL3_Day4_Parental


title: RBG27669_IL3_Day4_Parental


title: RBG27917_IL3_Day7_Parental


title: RBG27941_IL3_Day7_Parental


title: RBG27893_IL3_Day7_Parental


title: RBG27857_IL3_Day7_Parental


title: RBG27728_IL3_Day4_Parental


title: RBG27881_IL3_Day7_Parental


title: RBG27940_IL3_Day7_Parental


title: RBG27715_IL3_Day4_Parental


title: RBG27739_IL3_Day4_Parental


title: RBG27680_IL3_Day4_Parental


title: RBG27856_IL3_Day7_Parental


title: RBG27916_IL3_Day7_Parental


title: RBG27691_IL3_Day4_Parental


title: RBG27668_IL3_Day4_Parental


title: RBG27904_IL3_Day7_Parental


title: RBG27928_IL3_Day7_Parental


title: RBG27679_IL3_Day4_Parental


title: RBG27703_IL3_Day4_Parental


title: RBG27727_IL3_Day4_Parental


title: RBG27868_IL3_Day7_Parental


title: RBG27667_IL3_Day4_Parental


title: RBG27927_IL3_Day7_Parental


title: RBG27929_IL3_Day7_Parental


title: RBG27915_IL3_Day7_Parental


title: RBG27903_IL3_Day7_Parental


title: RBG27869_IL3_Day7_Parental


title: RBG27716_IL3_Day4_Parental


title: RBG27891_IL3_Day7_Parental


title: RBG27692_IL3_Day4_Parental


title: RBG27855_IL3_Day7_Parental


title: RBG27879_IL3_Day7_Parental


title: RBG27750_IL3_Day4_Parental


title: RBG27714_IL3_Day4_Parental


title: RBG27704_IL3_Day4_Parental


title: RBG27678_IL3_Day4_Parental


title: RBG27666_IL3_Day4_Parental


title: RBG27690_IL3_Day4_Parental


title: RBG27702_IL3_Day4_Parental


title: RBG27749_IL3_Day4_Parental


title: RBG27689_IL3_Day4_Parental


title: RBG27902_IL3_Day7_Parental


title: RBG27926_IL3_Day7_Parental


title: RBG27939_IL3_Day7_Parental


title: RBG27713_IL3_Day4_Parental


title: RBG27914_IL3_Day7_Parental


title: RBG27677_IL3_Day4_Parental


title: RBG27817_IL3_Day11_ME-Parental


title: RBG27805_IL3_Day11_ME-Parental


title: RBG27841_IL3_Day11_ME-Parental


title: RBG27829_IL3_Day11_ME-Parental


title: RBG27853_IL3_Day11_ME-Parental


title: RBG27665_IL3_Day4_Parental


title: RBG27781_IL3_Day11_ME-Parental


title: RBG27769_IL3_Day11_ME-Parental


title: RBG27652_ME-Parental


title: RBG27793_IL3_Day11_ME-Parental


title: RBG27628_ME-Parental


title: RBG27664_ME-Parental


title: RBG27604_ME-Parental


title: RBG27592_ME-Parental


title: RBG27580_ME-Parental


title: RBG27840_IL3_Day11_ME-Parental


title: RBG27792_IL3_Day11_ME-Parental


title: RBG27663_ME-Parental


title: RBG27651_ME-Parental


title: RBG27780_IL3_Day11_ME-Parental


title: RBG27768_IL3_Day11_ME-Parental


title: RBG27828_IL3_Day11_ME-Parental


title: RBG27603_ME-Parental


title: RBG27627_ME-Parental


title: RBG27591_ME-Parental


title: RBG27851_IL3_Day11_ME-Parental


title: RBG27615_ME-Parental


title: RBG27639_ME-Parental


title: RBG27839_IL3_Day11_ME-Parental


title: RBG27803_IL3_Day11_ME-Parental


title: RBG27791_IL3_Day11_ME-Parental


title: RBG27779_IL3_Day11_ME-Parental


title: RBG27579_ME-Parental


title: RBG27640_ME-Parental


title: RBG27827_IL3_Day11_ME-Parental


title: RBG27616_ME-Parental


title: RBG27815_IL3_Day11_ME-Parental


title: RBG27650_ME-Parental


title: RBG27767_IL3_Day11_ME-Parental


title: RBG27662_ME-Parental


title: RBG27638_ME-Parental


title: RBG27590_ME-Parental


title: RBG27578_ME-Parental


title: RBG27838_IL3_Day11_ME-Parental


title: RBG27826_IL3_Day11_ME-Parental


title: RBG27661_ME-Parental


title: RBG27802_IL3_Day11_ME-Parental


title: RBG27766_IL3_Day11_ME-Parental


title: RBG27778_IL3_Day11_ME-Parental


title: RBG27649_ME-Parental


title: RBG27790_IL3_Day11_ME-Parental


title: RBG27625_ME-Parental


title: RBG27589_ME-Parental


title: RBG27601_ME-Parental


title: RBG27837_IL3_Day11_ME-Parental


title: RBG27813_IL3_Day11_ME-Parental


title: RBG27816_IL3_Day11_ME-Parental


title: RBG27849_IL3_Day11_ME-Parental


title: RBG27825_IL3_Day11_ME-Parental


title: RBG27626_ME-Parental


title: RBG27660_ME-Parental


title: RBG27648_ME-Parental


title: RBG27801_IL3_Day11_ME-Parental


title: RBG27614_ME-Parental


title: RBG27636_ME-Parental


title: RBG27624_ME-Parental


title: RBG27612_ME-Parental


title: RBG27577_ME-Parental


title: RBG27600_ME-Parental


title: RBG27637_ME-Parental


title: RBG27613_ME-Parental


title: RBG27848_IL3_Day11_ME-Parental


title: RBG27836_IL3_Day11_ME-Parental


title: RBG27588_ME-Parental


title: RBG27764_IL3_Day11_ME-Parental


title: RBG27824_IL3_Day11_ME-Parental


title: RBG27576_ME-Parental


title: RBG27812_IL3_Day11_ME-Parental


title: RBG27776_IL3_Day11_ME-Parental


title: RBG27789_IL3_Day11_ME-Parental


title: RBG27777_IL3_Day11_ME-Parental


title: RBG27623_ME-Parental


title: RBG27599_ME-Parental


title: RBG27835_IL3_Day11_Parental


title: RBG27587_ME-Parental


title: RBG27847_IL3_Day11_Parental


title: RBG27647_ME-Parental


title: RBG27787_IL3_Day11_Parental


title: RBG27659_ME-Parental


title: RBG27575_ME-Parental


title: RBG27823_IL3_Day11_Parental


title: RBG27634_Parental


title: RBG27611_ME-Parental


title: RBG27788_IL3_Day11_ME-Parental


title: RBG27763_IL3_Day11_Parental


title: RBG27799_IL3_Day11_Parental


title: RBG27658_Parental


title: RBG27610_Parental


title: RBG27598_Parental


title: RBG27574_Parental


title: RBG27834_IL3_Day11_Parental


title: RBG27586_Parental


title: RBG27822_IL3_Day11_Parental


title: RBG27786_IL3_Day11_Parental


title: RBG27657_Parental


title: RBG27774_IL3_Day11_Parental


title: RBG27762_IL3_Day11_Parental


title: RBG27597_Parental


title: RBG27573_Parental


title: RBG27585_Parental


title: RBG27635_ME-Parental


title: RBG27609_Parental


title: RBG27785_IL3_Day11_Parental


title: RBG27797_IL3_Day11_Parental


title: RBG27809_IL3_Day11_Parental


title: RBG27584_Parental


title: RBG27608_Parental


title: RBG27572_Parental


title: RBG27596_Parental


title: RBG27844_IL3_Day11_Parental


title: RBG27644_Parental


title: RBG27821_IL3_Day11_Parental


title: RBG27808_IL3_Day11_Parental


title: RBG27784_IL3_Day11_Parental


title: RBG27760_IL3_Day11_Parental


title: RBG27655_Parental


title: RBG27619_Parental


title: RBG27607_Parental


title: RBG27583_Parental


title: RBG27595_Parental


title: RBG27571_Parental


title: RBG27773_IL3_Day11_Parental


title: RBG27831_IL3_Day11_Parental


title: RBG27819_IL3_Day11_Parental


title: RBG27771_IL3_Day11_Parental


title: RBG27654_Parental


title: RBG27807_IL3_Day11_Parental


title: RBG27642_Parental


title: RBG27783_IL3_Day11_Parental


title: RBG27759_IL3_Day11_Parental


title: RBG27620_Parental


title: RBG27772_IL3_Day11_Parental


title: RBG27594_Parental


title: RBG27582_Parental


title: RBG27830_IL3_Day11_Parental


title: RBG27794_IL3_Day11_Parental


title: RBG27770_IL3_Day11_Parental


title: RBG27653_Parental