title: Liver_VEG_tank29_fish3

city: St. John's

first: Albert

last: Caballero Solares

state: NL

address: 0 Marine Lab Road

department: Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: For each array, an equal quantity (825 ng) of an individual Cy5-labeled and a reference Cy3-labeled aRNA sample were fragmented and co-hybridized to a consortium for Genomic Research on All Salmonids Project (cGRASP)-designed Agilent 44K salmonid oligonucleotide microarray (GEOaccession #GPL11299), following manufacturer instructions (Agilent, Mississauga, ON). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately after hybridization as per the manufacturer's instructions.

scan_protocol: The microarray slides were scanned at 5 µm resolution with 90% laser power using a ScanArray Gx Plus scanner and ScanExpress v4.0 software (Perkin Elmer, Waltham, Massachusetts, USA), and the Cy3 and Cy5 channel photomultiplier tube (PMT) settings were adjusted to balance the fluorescence signal.

data_processing: The raw data contained in the TIFF images resulted from the scanning was extracted using Imagene 9.0 (BioDiscovery, El Segundo, California, USA). The removal of low-quality/flagged spots on the microarray, as well as the background signal correction, the log2-transformation and Loess-normalization of the data, were performed using R and the Bioconductor package mArray. Features absent in more than 30% of the arrays were discarded, and the missing values were imputed using the EM_array method and the LSimpute package.

organism: Salmo salar

source_name: Juvenile fish_liver_VEG

label_protocol: Each of the three dietary groups (MAR, ABP, and VEG) contributed liver RNA samples of eight individual fish (two from each quadruplicate tank) to the microarray experiment (i.e., 24 fish in total). Differences among dietary groups in the liver transcriptome of fish were assessed by contrasting individual RNA samples against a common reference pool of equal quantities of RNA from all 24 fish. Twenty-four arrays were used for the experiment: one array for each individual/common reference RNA hybridization. The microarray experiment was performed as described in Xue et al. [32]. Briefly, anti-sense amplified RNA (aRNA) was in vitro transcribed from 1 μg of each experimental RNA or reference RNA pool using Ambion's Amino Allyl MessageAmpTM II aRNA Amplification kit (Life Technologies), following the manufacturer's instructions. The quality and quantity of aRNA were assessed using NanoDrop spectrophotometry and agarose gel electrophoresis. Twenty micrograms of aRNA was subsequently precipitated overnight following standard molecular biology procedures and re-suspended in coupling buffer. Individual aRNA samples were labeled with Cy5, whereas reference aRNA samples were labeled with Cy3 (GE HealthCare, Mississauga, ON), following the manufacturer's instructions. The labeling efficiency was measured using the “microarray” function of the NanoDrop spectrophotometer.

growth_protocol: Atlantic salmon smolts were randomly distributed in 620-L tanks, four tanks per dietary treatment, and 40 fish in each tank. Salmon were acclimated to holding conditions (flow-through seawater system, 12-h light photoperiod, and water temperature of ~12 °C) for two weeks, after which feeding switched from the commercial diet (Nutra Transfer NP, 3mm, Skretting Canada, St. Andrews, NB, Canada) to the experimental diets. Salmon (average initial weight 179 g) were manually fed the experimental diets to apparent satiation twice a day for 14 weeks. Apparent feed intake, and water temperature and oxygen levels, were recorded daily. Salmon weight was measured at the beginning and at the end of the feeding trial to monitor differences in growth performance. At the end of the trial, salmon were starved for 24 h and then five individuals per tank were euthanized with an overdose of MS-222 (400 mg/L; Syndel Laboratories, Vancouver, BC, Canada) and dissected for tissue collection. After collection, liver samples of 50-100 mg were immediately flash-frozen in liquid nitrogen and stored at -80ºC until processing for RNA extraction.

extract_protocol: Liver samples were homogenized in 400 µL of TRIzol Reagent (Invitrogen/Life Technologies, Burlington, Canada) with stainless steel beads (5 mm; QIAGEN, Mississauga, ON) using a TissueLyser (QIAGEN). An additional 400 µL of TRIzol Reagent were added and mixed by pipetting. The homogenates were then passed through QIAshredder (QIAGEN) spin columns, and TRIzol total RNA extractions completed following manufacturer instructions. Due to low 260/230 ratios (i.e., less than 1.2) following TRIzol extraction, all RNA samples were re-extracted using the following phenol-chloroform phase separation method. Ten µL of each crude RNA were diluted 10 times using nuclease-free water (Invitrogen). Two hundred µL of Acid Phenol:Chloroform:IAA (25:24:1, v/v; pH 6.6; Ambion, Burlington, ON) were then added, and after mixing, phases were separated by centrifugation at 15,000 × g at 4°C for 20 min. The RNA was then precipitated from the aqueous phase with a mixture of 20 µL 3M sodium acetate (pH 5.2; Ambion) and 400 µL 95% ethanol (Greenfield, Toronto, ON) and incubated at -80°C for one hour, followed by centrifugation at 15,000 × g at 4°C for 30 min. The resulting RNA pellet was washed by adding 500 µL of 70% ethanol and centrifuging at 15,000 × g at 4°C for 20 min followed by removal of the supernatant, and then air-dried at room temperature for 10 min and dissolved in 30 µL of nuclease-free water (Invitrogen). Thirty µg of each total RNA sample were treated with 6.8 Kunitz units of DNaseI (RNase-Free DNase Set, QIAGEN) with the manufacturer’s buffer (1X final concentration) at room temperature for 10 min to degrade any residual genomic DNA. DNase-treated RNA samples were column-purified using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions. RNA integrity was verified by 1% agarose gel electrophoresis, and RNA purity was assessed by A260/280 and A260/230 NanoDrop UV spectrophotometry (NanoDrop, Wilmington, DE, USA) at all stages of the RNA preparation (i.e., after Trizol-extraction, after re-extraction, and post column-purification). Column-purified RNA samples had A260/280 ratios between 2.1 and 2.3 and A260/230 ratios between 1.9 and 2.4.

tag: life stage

value: Juvenile

tag: diet

value: vegetable meal/oil-based diet (VEG)

value: Liver

source_name: pool of RNAs from liver tissues included in the microarray experiment (i.e., MAR, ABP, and VEG groups)

tag: sample type

value: reference pool


title: HiC_PnM_slmb_rep2

status: Public on Oct 16 2018

type: SRA

city: Cambridge

first: Anton

last: Goloborodko

state: Massachusetts

address: 77 Massachusetts Ave., E25-524

department: Physics

country: USA

institute: MIT

library_source: genomic

data_processing:
Mapping Hi-C data: using the standard mode of seqtk trimfq v.1.2-r94, we trimmed low-quality base pairs at both ends of each side of sequenced of Hi-C molecules. This was followed by mapping the trimmed sequences using bwa mem v.0.7.15 with flags -SP.
Making Hi-C pairs: we used the pairtools parse command line tool (https://github.com/mirnylab/pairtools), to extract the coordinates of Hi-C contacts, kept read pairs that mapped uniquely to one of the two homologs, and used the standard mode of the pairtools dedup command line tool to remove PCR duplicates.
Mapping RNA-seq data: We mapped the raw RNA-seq data using STAR following the same procedure as used by the ENCODE consortium (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/tree/master/dnanexus). The uniquely mapped alignments were then aggregated into bigWig files for the plus and minus strands of the genome separately.
Genome_build: dm3
Supplementary_files_format_and_content: pairs: a tab separated file containing the coordinates of Hi-C contacts (https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md)

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Hybrid PatnMat (PnM) cells were cultured as clone8 cells with supplemented M3 media (supplemented M3 media (M3 Insect Media, 10% Fetal Bovine Serum (JRH), 2.5% Fly Extract (DGRC), 0.5 mg/ml Insulin (Sigma), 1:100 Pen-Strep (Gibco)), according to standard protocols at 25C in small culture dishes (100x 20 mm), with the following modifications: the cells were trypsinized and split at 1:5, or 1:10 every other day, and the media was replaced every day after they are washed with 1X PBS. Prior to any experiment, to ensure the cells were in log phase, the cells were split 12-18 hrs earlier.

extract_protocol:
Hi-C: This protocol was adapted from a previously published protocol (Rao et.al., Cell, 2014) with modifications. Unless otherwise specified, 75T flasks of PnM cells were cultured to 70% confluency, then washed with FBS-free Schneider's medium, and then crosslinked with 1% formaldehyde for 10 min at room temperature. Fixation was quenched with 1M glycine solution, and the cells were scraped gently off the flask, spun down at 1200 rpm, and washed once more with 1X PBS. Supernatant was removed, and cells were resuspended in 1x PBS and then counted 2.5 million cells to be used for the protocol. Nuclei were permeabilized with ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0. 2% Igepal supplemented with 5x Complete, EDTA-free Protease inhibitors (Roche). DNA was digested with 500 units of DpnII, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ~700 bp with QSonica sonicator (30% power, 30 sec on, 30 off for 20 minutes, at which point ligation junctions were pulled down with Dynabeads MyOne Streptavidin beads (Invitrogen) and prepped for Illumina sequencing. Aliquots at different steps were taken to measure the concentration with Qubit dsDNA HS assay kit, and run on a 2% agarose gel with SYBR Gold nucleic acid gel stain (1:10000) to ensure quality control of the sample prepared, and to ensure efficient digest, ligation, and binding to beads.    RNA-seq: Total PnM RNA was purified from around 8 million cells per replicate using TRIzol (Life Technologies), followed by chloroform extraction, DNase treatment with RNase free DNase I recombinant (Roche), and clean up with RNeasy Mini kit (Qiagen). The quality of total RNA was determined using Agilent RNA 6000 Pico assay on a 2100 Bioanalyzer system (Agilent Technologies).
Hi-C: we used BioNEXTFLEX adaptors (Bioo Scientific) and followed manufacturer recommendations, and amplified our final library with Q5 HIFI Hot Start High Fidelity PCR and Biooscientific primer mix for 6 cycles on the beads. The final product was then diluted to 250 ul with 1 mM Tris-HCl, and separated on a magnet then transferred the supernatant to a new tube and purified with 0.7X AMPure XP bead (Beckman Coulter #A63880). Incubation times are extended to 15 minutes to maximize library recovery. To remove traces of short products, we resuspend beads in 100μl of 1X Tris buffer and add another 70μl of AMPure XP beads. Mix by pipetting 20x and incubated at room temperature for 15 min, and separated for another 15 min, and continue with the washes and drying as previously. Once the beads are dry we resuspended in 20 uL 1X Tris-HCl, incubated for 15 min, then separated for another 15 min on the magnet and transferred the final library to a fresh tube. Two replicates were prepared per sample. The library quality was assessed using the High Sensitivity DNA assay on a 2100 Bioanalyzer system (Agilent Technologies).     RNA-seq: RNA-Seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions. Poly(A)+ RNA was enriched from 1 ug of total RNA, fragmented for 10 min at 94C, and reverse transcribed in the first strand cDNA synthesis with random primers. After adaptor ligation, cDNA was size selected between 400-600 bp with Agencourt AMPure XP beads, and amplified for 12 PCR cycles. The library quality was assessed using the High Sensitivity DNA assay on a 2100 Bioanalyzer system (Agilent Technologies).

treatment_protocol: In the RNAi experiments, the synthesis of dsRNA was carried out according to standard protocols (see www.flyrnai.org for more details). Control cells were treated with blank dionized water. The dsRNA was administered to the cells using a calcium phosphate transfection kit (Invitrogen) in 60-mm well plates. PnM cells were seeded at 1e6/ml and treated with 30 ug dsRNA on the first and third day, and then harvested on the fourth. Cells from the knockdowns were counted and an aliquot was taken for RNA isolation, and once knockdown of mRNA was confirmed cells were split to be fixed for Hi-C, and for FISH.

tag: cell line

value: PnM

tag: RNAi

value: Slmb RNAi

tag: replicate


title: Liver_VEG_tank27_fish2

type: RNA

molecule: total RNA

tag: tissue


title: HiC_PnM_slmb_rep1


title: Liver_VEG_tank25_fish1


title: HiC_PnM_mock_rep2

value: mock


title: Liver_VEG_tank29_fish2


title: Liver_VEG_tank27_fish1


title: Liver_VEG_tank1_fish2


title: Liver_VEG_tank1_fish1


title: HiC_PnM_mock_rep1


title: Liver_ABP_tank37_fish1

source_name: Juvenile fish_liver_ABP

value: animal by-product meal (ABP) diet


title: Liver_ABP_tank37_fish2


title: Liver_ABP_tank30_fish2


title: HiC_PnM_WT_rep1

value: n/a (WT)


title: Liver_ABP_tank28_fish1


title: HiC_PnM_WT_rep2


title: Liver_ABP_tank28_fish5


title: HiC_057_439_embryo_rep2

data_processing:
Mapping Hi-C data: we trimmed low-quality base pairs at both ends of each side using the standard mode of seqtk trimfq v.1.2-r94. Then we mapped the trimmed sequences using bwa mem v.0.7.15 with flags -SP.
Making Hi-C pairs: we extracted the coordinates of Hi-C contacts using the pairtools parse command line tool (https://github.com/mirnylab/pairtools). We only kept read pairs that mapped uniquely to one of the two homologous chromosomes and removed PCR duplicates using the standard mode of the pairtools dedup command line tool.
Genome_build: dm3
Supplementary_files_format_and_content: pairs: a tab separated file containing the coordinates of Hi-C contacts (https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md)

source_name: whole 2-4h fly embryo

growth_protocol: The hybrid F1 embryos, obtained by crossing the DGRP-057 (maternal) and 439 (paternal) lines, were collected and fixed after 3 pre-lays, followed by aging for 2-4 h time-point at 25C as previously described (Sandmann et al. 2006). A small aliquot (~100 embryos) per collection was set aside, devitellinised, and stored in methanol at -20C to verify developmental stages of collection under microscope. The remaining embryos from collections were snap-frozen in liquid nitrogen and stored at -80C.

extract_protocol:
Hi-C: Hi-C protocol from Rao et al. (Cell, 2014) was adapted for 30 mg of the snap-frozen, fixed fly embryos using 500 U of DpnII restriction enzyme. Upon ligation, RNA was degraded by adding 5 microliters of 10 mg/ml RNase A (ThermoFisher Scientific) followed by incubation for 30 min at 37C. DNA was sheared to around 400-600 bp with a Qsonica Instrument (Q800R) using the following parameters: 30 sec on/off, 15x cycles, 70% ampl. DNA around 500 bp was retained following size-selection.
Hi-C: The library preparation was performed as previously described (Rao et al. Cell, 2014) with the following modifications. The adapter ligation was performed using NEXTflex DNA Barcode Adapter (25 microM, NEXTflex DNA Barcodes -6, Bioo Scientific #514101). PCR was run using the program: 98C, 30 sec, (98C, 10 sec, 65C, 75 sec) repeated 7 times, 65C, 5 min, hold at 4C. The library quality was assessed using the High Sensitivity DNA assay on a 2100 Bioanalyzer system (Agilent Technologies).

tag: strain

value: DGRP-057 (maternal)/DGRP-439 (paternal)

tag: developmental stage

value: 2-4h embryo


title: HiC_057_439_embryo_rep1


title: Sm-ntrX18-S

city: Shanghai

first: Shenghui

last: Xing

address: nancheng road 333

country: China

institute: shanghai university

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Agrobacterium_fabrum_C58 whole genome using bowtie2(version: 2-2.0.5).
HTSeq was used to count the number of fragments of each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) method, and finally the FPKM value of each gene was calculated.
Genome_build: Agrobacterium_fabrum_C58
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Sinorhizobium meliloti

extract_protocol:
Retinas 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 standard Illumina protocols

treatment_protocol: Synchronized cells were obtained by culturing for 270 min in a medium lacking a carbon source

tag: genotype

value: ntrX knock-down mutation

tag: phase

value: cell cycle S phase


title: Sm-ntrX18-G2

value: cell cycle G2 phase


title: Sm-ntrX18-G1

value: cell cycle G1 phase


title: H3K27me3_ChIPseq_2

city: Amsterdam

first: Like

last: Fokkens

department: Swammerdam Institute of Life Sciences

country: Netherlands

institute: University of Amsterdam

data_processing:
ChIP-seq reads were sorted by adapter and adapter sequences were removed, quality scores were converted to Sanger format with the MAQ sol2sanger command if needed.
Reads were aligned to the genome of Fol4287 using ‘bwa aln’, bwa version 0.7.12
Duplicate reads were removed with Picard tools version 1.134 (http://broadinstitute.github.io/picard, MarkDuplicates)
Domains of enrichment were predicted using RSEG (version 0.4.8) with default settings except we provided a bedfile with gaps in the assembly (N’s in the DNA sequence) as ‘deadzones’.
Genome_build: ASM14995v1: Accessions DS231696:DS231812 (Supercontig level)
Supplementary_files_format_and_content: bedfiles containing domains of enrichment, per ChIP-seq experiment. See data processing step4

organism: Fusarium oxysporum

source_name: mycelium

growth_protocol: Fusarium oxysporum f. sp. lycopersici 4287 was stored as a monoconidial culture at -80 °C and revitalized on potato dextrose agar (PDA) plates at 25 °C. An overgrown agar piece was used to inoculate 100 ml NO3-medium (0.17% yeast nitrogen base, 3% sucrose, 100 nM KNO3). After 3-5 days at 25 °C shaking at 250 rpm, spores were harvested by filtering through miracloth (Merck, pore size of 22-27 μM). Spores were centrifuged for 10 minutes at 2000 rpm, resuspended in sterile MilliQ water and counted. We inoculated 100 ml of fresh NO3-medium with 10^7 spores and cultured for 2 days at 25 °C and shaking at 250 rpm.

extract_protocol:
As described in https://doi.org/10.1016/j.fgb.2015.03.006 (Supplemental Methods)
Illumina TruSeq adapters, libraries were size-selected between 200-400 bp, amplified with standard Illumina TruSeq PCR primers. Libraries were sequenced on the OSU CGRB Illumina HiSeq2500 machine.

treatment_protocol: The ChIP-seq protocol was adapted from the protocol that is extensively described in https://doi.org/10.1016/j.fgb.2015.03.006 and was similar to those used for S. pombe and Neurospora crassa. to important changes made for F. oxysporum strains. To the 2-day old cultures 20% formaldehyde (final concentration ~0.8%) was added directly to the flask and incubated for 15 min at room temperature while shaking at 100 rpm. After formaldehyde quenching, 100-200 mg of the cell pellets were ground in liquid nitrogen. Too much cell mass will decrease ChIP efficiency. Digestion with micrococcal nuclease to release mostly mono- or dinucleosomes was performed as described in https://doi.org/10.1016/j.fgb.2015.03.006 (Supplemental Methods)

value: Fusarium oxysporum f. sp. lycopersici 4287 (FGSC9935)

tag: condition

value: in vitro (liquid culture)


title: H3K4me2_ChIPseq_2


title: Liver_ABP_tank21_fish1

value: Juvenile


title: Liver_MAR_tank36_fish4

source_name: Juvenile fish_liver_MAR

value: fish meal or fish oil (FM/FO)-based diet (MAR)


title: Sm-1021-G2

value: wild type


title: Liver_MAR_tank22_fish4

value: Liver

value: reference pool


title: Liver_ABP_tank21_fish3


title: Liver_MAR_tank22_fish3


title: Liver_ABP_tank30_fish1


title: H3K27me3_ChIPseq_1


title: Liver_MAR_tank36_fish5


title: Sm-1021-G1


title: Sm-1021-S


title: H3K4me2_ChIPseq_1


title: Liver_MAR_tank2_fish4


title: control_HLA_DR

status: Public on Oct 15 2018

first: Navpreet

last: Ranu

state: MA

address: 415 Main Street

institute: Broad Institute

description: Each sample represents 3 replicates.

data_processing:
10X cell ranger-1.3.1 to generate a UMI table and gene expression profiles from fastq
UMI counts for enriched samples were determined by bootstrapping the previous UMI table at an appropriate sequencing depth
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing UMI expression counts for enriched barcodes, key='10X'

organism: Homo sapiens

source_name: FACS sorted HLA_DR

extract_protocol: Single-cell RNA-seq library preparation was performed with the Chromium Single Cell 3’ method (10X Genomics) according to the manufacturer's protocol

value: Blood


title: control_CD_19

description: Each sample represents 3 replicates.

source_name: FACS sorted CD19


title: Liver_MAR_tank4_fish1


title: Liver_MAR_tank2_fish1


title: E11.5 MAC (fetal liver)

city: Hangzhou

first: ZHI

middle: QING

last: LI

address: 866 Yuhangtang Road

institute: Zhejiang University School of Medicine

description:
E115MAC
Early EMP-derived macrophages in the fetal liver at E11.5 were sorted using Csf1r-iCre fate-mapping model.
processed data file: mast cell development.FPKM.txt

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome (UCSC_mm10) using Bowtie2.
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-Seq by Expectation Maximization (RSEM).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: mast cell development.FPKM.txt: Tab-delimited text file includes FPKMs.

organism: Mus musculus

source_name: fetal liver

extract_protocol:
Total RNA was extracted from sorted cells using TRIzol reagent (Invitrogen) according to manufacturer’s protocol.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

treatment_protocol: Early EMP-derived MCPs/mast cells and macrophages during embryogenesis were sorted using Csf1r-iCre fate-mapping model.

tag: strain/background

tag: age

tag: cell type

value: fetal liver MAC


title: E11.5 MCPs (limb)

description:
E11_5_Limb
Early EMP-derived MCPs in the limbs at E11.5 were sorted using Csf1r-iCre fate-mapping model.
processed data file: mast cell development.FPKM.txt

source_name: limb

value: limb MCP


title: E16.5 MCPs (skin)

description:
E16dot5
Early EMP-derived mast cells in the skin at E16.5 were sorted using Csf1r-iCre fate-mapping model.
processed data file: mast cell development.FPKM.txt

source_name: skin

value: skin MCP


title: E11.5 EMP (fetal liver)

description:
E11_5_LiB7_neg
Early EMPs at E11.5 were sorted using Csf1r-iCre fate-mapping model.
processed data file: mast cell development.FPKM.txt

value: fetal liver EMP


title: E11.5 MCPs (fetal liver)

description:
E11_5_LiB7_pos
Early EMP-derived MCPs in the fetal liver at E11.5 were sorted using Csf1r-iCre fate-mapping model.
processed data file: mast cell development.FPKM.txt

value: fetal liver MCP


title: Liver_MAR_tank4_fish2


title: FSGS_Tub1

city: Nanjing

first: Hao

last: Bao

state: Jiangsu

address: 305 East Zhong Shan Road

department: National Clinical Research Center of Kidney Diseases, Jinling Hospital

institute: Nanjing university

description: expression value derived from Expression Console software

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing: Raw data were processed with Expression Console software (Affymetrix) for background correction and normalization.

label: biotin

source_name: renal tubular tissue

label_protocol: Total RNA was amplified, labeled and purified by Ovation® Pico WTA System V2(Cat#3302, NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200, NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Tissues were kept in RNAlater at 4°C.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Microdissection of tubular tissues was performed manually under a stereomicroscope using two dissection needle holders in RNAlater at 4°C.

value: renal tubular tissue

tag: disease state

value: Focal segmental glomerulosclerosis (FSGS)


title: Control_Tub4

value: control


title: MNase-Nut-WT-exp1

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

data_processing:
Base calling was performed using RTA version 2.
Fragments were trimmed with sickle (-q 20 -t sanger) and aligned to the mm10 genome assembly using Bowtie version 2.2.9 with default arguments.
Fragments with mapping quality below 30 were removed.
Bigwigs of coverage were generated with deepTools bamCoverage version 3.1.0 (--binSize 20 –normalizeUsing RPKM –extendReads)
Contingency tables of fragment size were created with R table() on the ninth column of sam files for reads between 50 and 400bp.
Genome_build: mm10
Supplementary_files_format_and_content: tsv contain counts of fragment size in tabulated format
Supplementary_files_format_and_content: bw contain RPKM-normalized bigwig

source_name: Nut-WT, round-elongating spermatids

extract_protocol: Paired-end sequencing 2*75bp was performed using Illumina NextSeq 500.

treatment_protocol: Mononucleosomes were prepared from fractionated round-elongating spermatids as previously described (Goudarzi et al 2016, pmid 27105113).

value: Nut-WT

value: round-elongating spermatids


title: MNase-Nut-KO-exp1

source_name: Nut-KO, round-elongating spermatids

value: Nut-KO


title: Control_Tub3


title: Control_Tub1


title: MNase-Nut-WT-exp2


title: FSGS_Tub5


title: 4C-seq E11.5 branchial arch Twist1 4C-seq

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

data_processing:
Library strategy: 4C
Sequenced reads were split into libraries based on their barcodes, and then by their primer (P1 or P2 for each library), resulting in about 1.5 million reads per library/primer. Bait sequences were then trimmed and the remaining sequences were mapped to the mouse genome (mm9, limited to chr12) using Bowtie [Langmead et al, 2009]. In addition, we used 4Cseqpipe [van de Werken et al, 2012] to generate 4C-seq contact profiles, using "-map -read_length 50" and "-nearcis -calc_from 34150000 -calc_to 35650000 -stat_type log_mean -trend_resolution 10000" parameters
Genome_build: mm9
Supplementary_files_format_and_content: Trimmed FASTQ files analyzed by 4Cseqpipe
Supplementary_files_format_and_content: 4Cseqpipe rawdata, 4Cseqpipe scale

source_name: Mouse E11.5 branchial arch

growth_protocol: C57Black mice were grown under IACCA guidelines

extract_protocol:
Limb bud and branchial arch tissues of mouse E11.5 embryos were micro-dissected and dissociated into single cells that were fixed with 2% formaldehyde. Nuclear DNA was digested using DpnII and BfaI (4-bp cutters) as primary and secondary restriction enzymes, respectively, followed by ligation using T4 DNA ligase.
Ligated fragments were amplified by inverse PCR for each viewpoint. PCR products were sequenced with a 50-bp single-end read on Illumina HiSeq machine.

treatment_protocol: Tissues were micro-dissected at E11.5

value: Branchial arch


title: 4C-seq E11.5 forelimb bud Twist1 4C-seq

description: 4C-seq E11.5 forelimb bud Twist1 4C-seq

source_name: Mouse E11.5 forelimb buds

value: Forelimb bud


title: 4C-seq E11.5 forelimb bud Hdac9 4C-seq

description: 4C-seq E11.5 forelimb bud Hdac9 4C-seq


title: Control_Tub5


title: FSGS_Tub2


title: FSGS_Tub4


title: E14.5 MCPs (limb)

description:
E145
Early EMP-derived MCPs in the limbs at E14.5 were sorted using Csf1r-iCre fate-mapping model.
processed data file: mast cell development.FPKM.txt


title: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4589-3L-ILC]

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

hyb_protocol: Overnight hybridization to agilent microarray- G4862A.

scan_protocol: Microarrays were scanned on a Agilent microarray scanner and analyzed using Agilent feature extraction software.

data_processing: Gene expression was calculated as log2 Cy5/Cy3 ratios, keeping only probes with Lowess normalized intensity values greater than 10 in both Cy5 and Cy3 channels.

source_name: Mouse Ref cRNA 2ug

label_protocol: Total RNA was labeled with cyanine-5 (Cy5) dye for tumor samples and cyanine-3 (Cy3) dye for mouse reference samples 51 using the Agilent Low RNA Input Fluorescent Linear Amplification Kit. For both mouse reference RNA and tumor RNA, 2ug of labeled RNA was co-hybridized overnight to Agilent microarrays (platform G4862A).

growth_protocol: Transgenic mouse model

extract_protocol: Tumors frozen in RNAlater (Qiagen 76106) were thawed and homogenized by Qiagen TissueRupter (Qiagen 9001271). RNA was extracted using Qiagen RNeasy mini kit (Qiagen 74104). RNA quantification was determined using the Nanodrop spectrophotometer and RNA quality for microarray was determined using the Agilent Bioanalyzer.

treatment_protocol: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre mice were monitored for tumor progression.

tag: reference

value: total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups.

source_name: B4589-3L-ILC tumor cRNA 2ug.

value: Mammary tumor


title: FSGS_Tub3


title: MNase-Nut-KO-exp2


title: Control_Tub2


title: 4C-seq E11.5 branchial arch Hdac9 4C-seq


title: Hetero_Scale_E9_Mesenchyme_R20

city: Taichung

first: Yung-Chih

last: Lai

address: 7F., No. 6, Xueshi Road, North District

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

data_processing:
Low quality of sequencing bases were trimmed based on the Phred+33 quality score (> 20) from both of the 5'- and 3'-ends of reads. After trimming, reads are discarded, if they are shorter than 30bp, or have one or more ambiguous base.
Ensembl Release81 annotation were downloaded from the UCSC Genome Browser on 2016.2.6. Keratin (KRT) gene annotation and epidermal differentiation complex (EDC) gene annotation were added into the Ensembl annotation manually.
The alignment, quantification, normalization, and differential expression analysis were performed by STAR 2.4.1d, htseq-count 0.6.0, TMM, and edgeR 3, respectively.
Genes with count-per-million (CPM) values above 1 in at least two samples were retained, and genes with no or low expression levels were discarded.
Genome_build: UCSC galGal4
Supplementary_files_format_and_content: The tab-delimited text files: (1) 16 files with count values of 17289 genes for each sample produced by htseq-count (2) 1 file with count-per-million (CPM) values of 12899 genes produced by edgeR

molecule: polyA RNA

organism: Gallus gallus

source_name: chicken embryonic recombined skin explant

growth_protocol: Skin explant culture in an incubator with 5% CO2 at 37°C

extract_protocol:
TRIzol
Illumina TruSeq RNA sample Prep kit v2

tag: quality score

tag: recombination

value: Heterotypic

value: E9 scale dermis

tag: sample label

tag: phenotype

value: Feather-like


title: Hetero_Scale_E9_Epithelium_R17

value: E9 scale epidermis


title: Hetero_Scale_E9_Epithelium_R49


title: Hetero_Scale_E9_Mesenchyme_R52


title: Hetero_Feather_E7_Mesenchyme_R18

value: E7 feather dermis

value: Scale-like


title: Hetero_Feather_E7_Mesenchyme_R50


title: Hetero_Feather_E7_Epithelium_R51

value: E7 feather epidermis


title: Hetero_Feather_E7_Epithelium_R19


title: Homo_Scale_E9_Mesenchyme_R48

value: Homotypic

value: Scale


title: HB6_CGN-DOT1Linh

city: Freiburg

first: Patrick

middle: Piero

last: Bovio

address: Albertstr. 19

department: Department of Molecular Embryology

country: Germany

institute: Albert-Ludwigs University Freiburg, Institute of Anatomy and Cell Biology

description: CGN (+FBS) DIV1, 44 h with DOT1L inhibition with SGC09446

hyb_protocol: Labeled targets were hybridised to the arrays according to the manufacturers protocol (Affymetrix). Arrays were washed and stained using the Affymetrix Hyb and Stain kit

scan_protocol: Arrays were scanned using the Affymetrix Scanner 3000 7G and CEL files were processed using Command Console software (Affymetrix)

data_processing: We used Partek Genomics Suite software for further analysis: Pre-background Adjustment was done for GC Content and probe sequence. We used RMA background correction and Quantile normalization. Probes were log2 transformed and probeset summarization was done with median polish. Probe values were log2 transformed.

source_name: murine cerebellum NMRI WT

label_protocol: We used the Affymetrix WT Plus kit for labeling as described by the manufacturer.

growth_protocol: detailed information in JoVE56631R1 Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

extract_protocol: detailed information in JoVE56631R1. Density for CGNP/CGN 2* 6well pooled with 3*10⁶ cells/6well; Quiagen RNeasy #74106 Kit following manufacturer manual.

treatment_protocol: CGNP treated 4 h at DIV1; CGN treated 44 h DIV0–DIV2 with 5mM SGC09446 or DMSO ctrl.

value: cerebellum, granular neurons

tag: differentiation state in vitro

tag: mouse number


title: HB3_CGN-DMSO

description: CGN (+FBS) DIV1, 44 h with DMSO

tag: tissue


title: 29_DOT1Linh-CGNP

description: CGNP (+SHH) DIV1, 4 h with DOT1L inhibition with SGC0946

value: cerebellum, granular neuron progenitors


title: HB5_CGN-DOT1Linh

description: CGN (+FBS) DIV1, 44 h with DMSO


title: HB1_CGN-DMSO

description: CGN (+FBS) DIV1, 44 h with DMSO


title: HB4_CGN-DOT1Linh


title: 30_DOT1Linh-CGNP


title: 29.30_DOT1Linh-CGNP


title: 29.30_DMSO-CGNP

description: CGNP (+SHH) DIV1, 4 h with DMSO


title: 2843-Dot1l-ff_Atoh1-wt

description: cerebellum of Dot1l_f/f::Atoh1_+/+; control animals

source_name: murine cerebellum BL6/J ctrl

value: cerebellum


title: 30_DMSO-CGNP

description: CGNP (+SHH) DIV1, 4 h with DMSO


title: Homo_Scale_E9_Epithelium_R47


title: HB2_CGN-DMSO


title: Liver_VEG_tank25_fish3

source_name: Juvenile fish_liver_VEG

tag: life stage

value: Juvenile

tag: diet

value: vegetable meal/oil-based diet (VEG)

value: Liver

source_name: pool of RNAs from liver tissues included in the microarray experiment (i.e., MAR, ABP, and VEG groups)

tag: sample type

value: reference pool


title: 29_DMSO-CGNP

description: CGNP (+SHH) DIV1, 4 h with DMSO


title: 2848-Dot1l-ff_Atoh1-wt

description: cerebellum of Dot1l_f/+::Atoh1_+/+; control animals


title: 2842-Dot1l-ff_Atoh1-cre

description: cerebellum of Dot1l_f/f::Atoh1_cre/+; Dot1l-cKO in cerebellar granular neuron progenitor (CGNP)

source_name: murine cerebellum BL6/J mutant


title: 2844-Dot1l-ff_Atoh1-cre


title: 2847-Dot1l-ff_Atoh1-cre


title: 2846-Dot1l-ff_Atoh1-wt


title: Homo_Feather_E7_Mesenchyme_R44

value: Feather


title: Homo_Scale_E9_Epithelium_R45


title: Homo_Feather_E7_Mesenchyme_R42


title: Homo_Feather_E7_Epithelium_R41


title: Homo_Scale_E9_Mesenchyme_R46


title: Homo_Feather_E7_Epithelium_R43


title: PBMC_SLE2132_v2

city: GRANADA

first: Daniel

last: Toro

state: Spain

address: Avenida de la Ilustracion

department: Bioinformatics

country: Spain

institute: GENYO

description: Gene expression microarray from a patient in a visit

hyb_protocol: Standard Affymetrix protcol.

scan_protocol: HTAPS scan was used.

data_processing: Data was normalized using rma R package.

label: Biotin

label_protocol: NuGEN Ovation.

growth_protocol: Whole Blood samples in collected fom PAXgene tubes.

extract_protocol: The RNA was extracted with Trizol reagent (Life Technologies) and cleaned up with RNA easy (Qiagen) according to the manufacturer’s protocols.

treatment_protocol: Standard.

value: Systemic Lupus Erythematosus

tag: patient id

tag: sledai

tag: visit date

value: PBMC

tag: imputed neutrophil percentage


title: PBMC_SLE2132_v3


title: PBMC_SLE2128_v4


title: PBMC_SLE2129_v3


title: PBMC_SLE2128_v2


title: PBMC_SLE2128_v1


title: PBMC_SLE2128_v6


title: PBMC_SLE2128_v7


title: PBMC_SLE2129_v1


title: PBMC_SLE2104_v1

description: Gene expression microarray from patient number 2129, visit date: 15/10/2009


title: PBMC_SLE2132_v4


title: PBMC_SLE2129_v2


title: PBMC_SLE2132_v1


title: PBMC_SLE2128_v5


title: PBMC_SLE2122_v1


title: PBMC_SLE2128_v3


title: PBMC_SLE2122_v2


title: PBMC_SLE2119_v5


title: PBMC_SLE2122_v3


title: PBMC_SLE2129_v4


title: PBMC_SLE2104_v2

description: Gene expression microarray from patient number 2129, visit date: 19/11/2009


title: PBMC_SLE2129_v5


title: PBMC_SLE2104_v4

description: Gene expression microarray from patient number 2129, visit date: 11/10/2010


title: PBMC_SLE2119_v1

description: Gene expression microarray from patient number 2132, visit date: 30/11/2009


title: PBMC_SLE2104_v3

description: Gene expression microarray from patient number 2129, visit date: 15/02/2010


title: PBMC_SLE2119_v2

description: Gene expression microarray from patient number 2132, visit date: 22/02/2010


title: PBMC_SLE2104_v5

description: Gene expression microarray from patient number 2129, visit date: 13/01/2011


title: PBMC_SLE2119_v4

description: Gene expression microarray from patient number 2132, visit date: 15/12/2010


title: PBMC_SLE2119_v3

description: Gene expression microarray from patient number 2132, visit date: 24/05/2010


title: PBMC_SLE2103_v7

description: Gene expression microarray from patient number 2128, visit date: 03/11/2011


title: PBMC_SLE2103_v6

description: Gene expression microarray from patient number 2128, visit date: 18/08/2011


title: PBMC_SLE2103_v5

description: Gene expression microarray from patient number 2128, visit date: 27/06/2011


title: PBMC_SLE2020_v6

description: Gene expression microarray from patient number 2119, visit date: 18/03/2010


title: PBMC_SLE2020_v5

description: Gene expression microarray from patient number 2119, visit date: 17/12/2009


title: PBMC_SLE2067_v3

description: Gene expression microarray from patient number 2122, visit date: 29/07/2010


title: PBMC_SLE2103_v1

description: Gene expression microarray from patient number 2128, visit date: 05/11/2009


title: PBMC_SLE2103_v3

description: Gene expression microarray from patient number 2128, visit date: 18/11/2010


title: PBMC_SLE2067_v1

description: Gene expression microarray from patient number 2119, visit date: 13/12/2010


title: PBMC_SLE2103_v4

description: Gene expression microarray from patient number 2128, visit date: 10/03/2011


title: PBMC_SLE2020_v1

description: Gene expression microarray from patient number 2104, visit date: 22/07/2010


title: PBMC_SLE2067_v4

description: Gene expression microarray from patient number 2122, visit date: 10/10/2011


title: PBMC_SLE2067_v5

description: Gene expression microarray from patient number 2122, visit date: 11/06/2012


title: PBMC_SLE2103_v2

description: Gene expression microarray from patient number 2128, visit date: 15/02/2010


title: PBMC_SLE1944_v2

description: Gene expression microarray from patient number 2103, visit date: 11/03/2010


title: PBMC_SLE2020_v2

description: Gene expression microarray from patient number 2104, visit date: 27/09/2010


title: PBMC_SLE2067_v2

description: Gene expression microarray from patient number 2119, visit date: 18/04/2011


title: PBMC_SLE2016_v4

description: Gene expression microarray from patient number 2104, visit date: 22/02/2010


title: PBMC_SLE2020_v4

description: Gene expression microarray from patient number 2119, visit date: 28/09/2009


title: PBMC_SLE1938_v5

description: Gene expression microarray from patient number 2103, visit date: 05/11/2009


title: PBMC_SLE2016_v2

description: Gene expression microarray from patient number 2103, visit date: 04/08/2011


title: PBMC_SLE1938_v4

description: Gene expression microarray from patient number 2067, visit date: 12/12/2011


title: PBMC_SLE1938_v2

description: Gene expression microarray from patient number 2067, visit date: 31/03/2011


title: PBMC_SLE2016_v1

description: Gene expression microarray from patient number 2103, visit date: 29/11/2010


title: PBMC_SLE1944_v1

description: Gene expression microarray from patient number 2103, visit date: 10/12/2009


title: PBMC_SLE1944_v3

description: Gene expression microarray from patient number 2103, visit date: 14/06/2010


title: PBMC_SLE2020_v3

description: Gene expression microarray from patient number 2104, visit date: 20/06/2011


title: PBMC_SLE1944_v4

description: Gene expression microarray from patient number 2103, visit date: 30/08/2010


title: PBMC_SLE2016_v3

description: Gene expression microarray from patient number 2104, visit date: 07/12/2009


title: PBMC_SLE1938_v3

description: Gene expression microarray from patient number 2067, visit date: 30/06/2011


title: PBMC_SLE1938_v1

description: Gene expression microarray from patient number 2067, visit date: 04/03/2010


title: PBMC_SLE1924_v4

description: Gene expression microarray from patient number 2016, visit date: 06/12/2010


title: PBMC_SLE1924_v5

description: Gene expression microarray from patient number 2020, visit date: 16/11/2009


title: PBMC_SLE1871_v4

description: Gene expression microarray from patient number 1944, visit date: 29/10/2009


title: PBMC_SLE1927_v4

description: Gene expression microarray from patient number 2067, visit date: 10/12/2009


title: PBMC_SLE1927_v2

description: Gene expression microarray from patient number 2020, visit date: 07/03/2011


title: PBMC_SLE1924_v6

description: Gene expression microarray from patient number 2020, visit date: 14/12/2009


title: PBMC_SLE1927_v3

description: Gene expression microarray from patient number 2020, visit date: 13/06/2011


title: PBMC_SLE1924_v7

description: Gene expression microarray from patient number 2020, visit date: 15/03/2010


title: PBMC_SLE1869_v1

description: Gene expression microarray from patient number 1927, visit date: 12/08/2010


title: PBMC_SLE1842_v2

description: Gene expression microarray from patient number 1927, visit date: 28/01/2010


title: PBMC_SLE1807_v4

description: Gene expression microarray from patient number 1924, visit date: 28/11/2011


title: PBMC_SLE1913_v3

description: Gene expression microarray from patient number 1944, visit date: 21/06/2010


title: PBMC_SLE1927_v1

description: Gene expression microarray from patient number 2020, visit date: 27/09/2010


title: PBMC_SLE1807_v1

description: Gene expression microarray from patient number 1924, visit date: 27/06/2011


title: PBMC_SLE1871_v1

description: Gene expression microarray from patient number 1938, visit date: 12/04/2010


title: PBMC_SLE1869_v3

description: Gene expression microarray from patient number 1938, visit date: 25/01/2010


title: PBMC_SLE1924_v3

description: Gene expression microarray from patient number 2016, visit date: 10/06/2010


title: PBMC_SLE1842_v1

description: Gene expression microarray from patient number 1927, visit date: 22/10/2009


title: PBMC_SLE1913_v2

description: Gene expression microarray from patient number 1944, visit date: 08/03/2010


title: PBMC_SLE1842_v3

description: Gene expression microarray from patient number 1927, visit date: 29/04/2010


title: PBMC_SLE1792_v4

description: Gene expression microarray from patient number 1924, visit date: 21/03/2011


title: PBMC_SLE1869_v2

description: Gene expression microarray from patient number 1938, visit date: 12/10/2009


title: PBMC_SLE1871_v3

description: Gene expression microarray from patient number 1938, visit date: 09/05/2011


title: PBMC_SLE1807_v2

description: Gene expression microarray from patient number 1924, visit date: 25/07/2011


title: PBMC_SLE1871_v2

description: Gene expression microarray from patient number 1938, visit date: 06/07/2010


title: PBMC_SLE1913_v1

description: Gene expression microarray from patient number 1944, visit date: 03/12/2009


title: PBMC_SLE1924_v2

description: Gene expression microarray from patient number 2016, visit date: 04/03/2010


title: PBMC_SLE1792_v3

description: Gene expression microarray from patient number 1924, visit date: 15/03/2010


title: PBMC_SLE1924_v1

description: Gene expression microarray from patient number 2016, visit date: 03/12/2009


title: PBMC_SLE1807_v3

description: Gene expression microarray from patient number 1924, visit date: 29/08/2011


title: PBMC_SLE1764_v3

description: Gene expression microarray from patient number 1913, visit date: 29/10/2009


title: PBMC_SLE1764_v1

description: Gene expression microarray from patient number 1871, visit date: 21/03/2011


title: PBMC_SLE1620_v5

description: Gene expression microarray from patient number 1792, visit date: 12/11/2009


title: PBMC_SLE1764_v4

description: Gene expression microarray from patient number 1913, visit date: 16/12/2009


title: PBMC_SLE1792_v1

description: Gene expression microarray from patient number 1913, visit date: 18/03/2010


title: PBMC_SLE1705_v5

description: Gene expression microarray from patient number 1871, visit date: 21/01/2010


title: PBMC_SLE1792_v2

description: Gene expression microarray from patient number 1924, visit date: 26/10/2009


title: PBMC_SLE1699_v4

description: Gene expression microarray from patient number 1807, visit date: 06/05/2010


title: PBMC_SLE1679_v1

description: Gene expression microarray from patient number 1792, visit date: 18/02/2010


title: PBMC_SLE1764_v2

description: Gene expression microarray from patient number 1871, visit date: 03/10/2011


title: PBMC_SLE1705_v4

description: Gene expression microarray from patient number 1871, visit date: 08/10/2009


title: PBMC_SLE1699_v3

description: Gene expression microarray from patient number 1807, visit date: 22/02/2010


title: PBMC_SLE1702_v1

description: Gene expression microarray from patient number 1842, visit date: 22/10/2009


title: PBMC_SLE1699_v2

description: Gene expression microarray from patient number 1807, visit date: 30/10/2009


title: PBMC_SLE1702_v2

description: Gene expression microarray from patient number 1842, visit date: 03/12/2009


title: PBMC_SLE1705_v1

description: Gene expression microarray from patient number 1869, visit date: 12/10/2009


title: PBMC_SLE1537_v5

description: Gene expression microarray from patient number 1705, visit date: 08/06/2010


title: PBMC_SLE1620_v2

description: Gene expression microarray from patient number 1764, visit date: 17/12/2009


title: PBMC_SLE1537_v2

description: Gene expression microarray from patient number 1705, visit date: 21/12/2009


title: PBMC_SLE1537_v4

description: Gene expression microarray from patient number 1705, visit date: 22/04/2010


title: PBMC_SLE1699_v1

description: Gene expression microarray from patient number 1807, visit date: 29/10/2009


title: PBMC_SLE1705_v2

description: Gene expression microarray from patient number 1869, visit date: 11/01/2010


title: PBMC_SLE1537_v3

description: Gene expression microarray from patient number 1705, visit date: 25/03/2010


title: PBMC_SLE1705_v3

description: Gene expression microarray from patient number 1869, visit date: 05/08/2010


title: PBMC_SLE1679_v2

description: Gene expression microarray from patient number 1792, visit date: 27/05/2010


title: PBMC_SLE1620_v1

description: Gene expression microarray from patient number 1764, visit date: 01/10/2009


title: PBMC_SLE1620_v4

description: Gene expression microarray from patient number 1764, visit date: 03/10/2011


title: PBMC_SLE1679_v3

description: Gene expression microarray from patient number 1792, visit date: 09/09/2010


title: PBMC_SLE1702_v3

description: Gene expression microarray from patient number 1842, visit date: 04/03/2010


title: PBMC_SLE1520_v6

description: Gene expression microarray from patient number 1702, visit date: 28/01/2010


title: PBMC_SLE1620_v3

description: Gene expression microarray from patient number 1764, visit date: 07/02/2011


title: PBMC_SLE1520_v4

description: Gene expression microarray from patient number 1702, visit date: 29/10/2009


title: PBMC_SLE1520_v2

description: Gene expression microarray from patient number 1699, visit date: 18/02/2010


title: PBMC_SLE1520_v3

description: Gene expression microarray from patient number 1699, visit date: 18/03/2010


title: PBMC_SLE1480_v3

description: Gene expression microarray from patient number 1679, visit date: 16/02/2010


title: PBMC_SLE1480_v2

description: Gene expression microarray from patient number 1679, visit date: 14/12/2009


title: PBMC_SLE1409_v2

description: Gene expression microarray from patient number 1480, visit date: 25/10/2010


title: PBMC_SLE1409_v3

description: Gene expression microarray from patient number 1480, visit date: 20/01/2011


title: PBMC_SLE1537_v1

description: Gene expression microarray from patient number 1705, visit date: 08/10/2009


title: PBMC_SLE1520_v1

description: Gene expression microarray from patient number 1699, visit date: 19/11/2009


title: PBMC_SLE1463_v1

description: Gene expression microarray from patient number 1537, visit date: 13/01/2011


title: PBMC_SLE1520_v5

description: Gene expression microarray from patient number 1702, visit date: 09/11/2009


title: PBMC_SLE1478_v3

description: Gene expression microarray from patient number 1620, visit date: 10/05/2010


title: PBMC_SLE1478_v1

description: Gene expression microarray from patient number 1620, visit date: 15/10/2009


title: PBMC_SLE1478_v5

description: Gene expression microarray from patient number 1620, visit date: 06/12/2010


title: PBMC_SLE1480_v1

description: Gene expression microarray from patient number 1679, visit date: 22/10/2009


title: PBMC_SLE1424_v2

description: Gene expression microarray from patient number 1520, visit date: 16/02/2010


title: PBMC_SLE1478_v4

description: Gene expression microarray from patient number 1620, visit date: 12/08/2010


title: PBMC_SLE1463_v2

description: Gene expression microarray from patient number 1537, visit date: 04/05/2011


title: PBMC_SLE1480_v4

description: Gene expression microarray from patient number 1699, visit date: 22/10/2009


title: PBMC_SLE1436_v2

description: Gene expression microarray from patient number 1520, visit date: 30/06/2011


title: PBMC_SLE1436_v3

description: Gene expression microarray from patient number 1537, visit date: 14/12/2009


title: PBMC_SLE1436_v4

description: Gene expression microarray from patient number 1537, visit date: 15/03/2010


title: PBMC_SLE1436_v1

description: Gene expression microarray from patient number 1520, visit date: 19/05/2011


title: PBMC_SLE1424_v3

description: Gene expression microarray from patient number 1520, visit date: 09/08/2010


title: PBMC_SLE1478_v2

description: Gene expression microarray from patient number 1620, visit date: 28/01/2010


title: PBMC_SLE1424_v1

description: Gene expression microarray from patient number 1520, visit date: 02/11/2009


title: PBMC_SLE1424_v4

description: Gene expression microarray from patient number 1520, visit date: 17/02/2011


title: PBMC_SLE1463_v3

description: Gene expression microarray from patient number 1537, visit date: 01/09/2011


title: PBMC_SLE1269_v3

description: Gene expression microarray from patient number 1463, visit date: 07/01/2010


title: PBMC_SLE1263_v5

description: Gene expression microarray from patient number 1436, visit date: 13/01/2011


title: PBMC_SLE1263_v3

description: Gene expression microarray from patient number 1436, visit date: 10/12/2009


title: PBMC_SLE1269_v1

description: Gene expression microarray from patient number 1436, visit date: 17/03/2011


title: PBMC_SLE1263_v4

description: Gene expression microarray from patient number 1436, visit date: 11/03/2010


title: PBMC_SLE1335_v7

description: Gene expression microarray from patient number 1480, visit date: 28/09/2009


title: PBMC_SLE1335_v1

description: Gene expression microarray from patient number 1463, visit date: 18/02/2010


title: PBMC_SLE1335_v2

description: Gene expression microarray from patient number 1478, visit date: 10/11/2009


title: PBMC_SLE1335_v3

description: Gene expression microarray from patient number 1478, visit date: 22/02/2010


title: PBMC_SLE1335_v4

description: Gene expression microarray from patient number 1478, visit date: 24/05/2010


title: PBMC_SLE1269_v2

description: Gene expression microarray from patient number 1463, visit date: 29/10/2009


title: PBMC_SLE1409_v1

description: Gene expression microarray from patient number 1480, visit date: 07/01/2010


title: PBMC_SLE1335_v5

description: Gene expression microarray from patient number 1478, visit date: 29/11/2010


title: PBMC_SLE1335_v6

description: Gene expression microarray from patient number 1478, visit date: 21/02/2011


title: PBMC_SLE1182_v3

description: Gene expression microarray from patient number 1335, visit date: 04/01/2010


title: PBMC_SLE1179_v1

description: Gene expression microarray from patient number 1269, visit date: 21/12/2009


title: PBMC_SLE1227_v3

description: Gene expression microarray from patient number 1424, visit date: 24/02/2011


title: PBMC_SLE1179_v3

description: Gene expression microarray from patient number 1335, visit date: 12/10/2009


title: PBMC_SLE1206_v2

description: Gene expression microarray from patient number 1335, visit date: 04/11/2010


title: PBMC_SLE1263_v1

description: Gene expression microarray from patient number 1424, visit date: 19/05/2011


title: PBMC_SLE1206_v1

description: Gene expression microarray from patient number 1335, visit date: 26/07/2010


title: PBMC_SLE1227_v2

description: Gene expression microarray from patient number 1424, visit date: 12/11/2009


title: PBMC_SLE1206_v3

description: Gene expression microarray from patient number 1335, visit date: 10/02/2011


title: PBMC_SLE1227_v1

description: Gene expression microarray from patient number 1409, visit date: 26/07/2010


title: PBMC_SLE1206_v4

description: Gene expression microarray from patient number 1409, visit date: 12/10/2009


title: PBMC_SLE1179_v2

description: Gene expression microarray from patient number 1269, visit date: 18/03/2010


title: PBMC_SLE1182_v2

description: Gene expression microarray from patient number 1335, visit date: 10/12/2009


title: PBMC_SLE1263_v2

description: Gene expression microarray from patient number 1424, visit date: 18/08/2011


title: PBMC_SLE1206_v5

description: Gene expression microarray from patient number 1409, visit date: 14/01/2010


title: PBMC_SLE1182_v1

description: Gene expression microarray from patient number 1335, visit date: 09/11/2009


title: PBMC_SLE1178_v6

description: Gene expression microarray from patient number 1263, visit date: 09/07/2010


title: PBMC_SLE1178_v7

description: Gene expression microarray from patient number 1269, visit date: 24/09/2009


title: PBMC_SLE1178_v3

description: Gene expression microarray from patient number 1263, visit date: 07/01/2010


title: PBMC_SLE1178_v5

description: Gene expression microarray from patient number 1263, visit date: 10/05/2010


title: PBMC_SLE1178_v1

description: Gene expression microarray from patient number 1227, visit date: 09/02/2012


title: 2-ad-exp

city: Richmond

first: Amanda

last: Dickinson

state: VA

address: 1000 W. Cary St. Rm 339

department: Biology

institute: Virginia Commonwealth University

hyb_protocol: VCU core standard protocols

scan_protocol: VCU core standard protocols

data_processing: RMA

organism: Xenopus laevis

source_name: Facial tissue from Xenopus embryos at st 29/30 (35 hours post fertilization)

label_protocol: VCU core standard protocols

growth_protocol: Eggs were collected from females injected with HGC, fertilized in vitro with testes isolated from a male frog and cultured until stage 24 (26 hours post fertilization) at 23 or 15 degrees celsius

extract_protocol: Facial tissue was microdissected and pooled in TriReagent.  Total RNA was extracted using standard protocols and lithium chloride precipitations.

treatment_protocol: Embros were cultured in 1% DMSO or 1 micromolar BMS453 in 1% DMSO st 24-29/30 (26-35 hpf)

value: isolated facial tissue

tag: treatment

value: 1 micromolar BMS453

tag: developmental stage


title: 1-ad-con

value: 1% DMSO

value: embryos at st 29/30 (35 hours post fertilization)


title: PBMC_SLE1176_v7

description: Gene expression microarray from patient number 1227, visit date: 18/08/2011

tag: disease state


title: 1-ad-con2


title: CD71pos Immune Non-Responders d4.16

city: Cleveland

first: AARTHI

last: TALLA

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University School of Medicine

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label_protocol: standard Illumina protocol

extract_protocol: none provided by submitter

tag: donorid

tag: donor class

value: Immune Non-Responders


title: PBMC_SLE1176_v6

description: Gene expression microarray from patient number 1227, visit date: 11/05/2011


title: 2-ad-exp2


title: CD71pos Immune Non-Responders d4.15


title: PBMC_SLE1174_v3

description: Gene expression microarray from patient number 1182, visit date: 29/04/2010


title: PBMC_SLE1176_v1

description: Gene expression microarray from patient number 1206, visit date: 02/11/2009


title: CD71neg Immune Non-Responders d4.9


title: PBMC_SLE1176_v4

description: Gene expression microarray from patient number 1206, visit date: 10/03/2011


title: PBMC_SLE1178_v4

description: Gene expression microarray from patient number 1263, visit date: 24/02/2010


title: CD71neg Immune Non-Responders d4.14


title: CD71pos Immune Non-Responders d4.9


title: PBMC_SLE1174_v2

description: Gene expression microarray from patient number 1182, visit date: 21/01/2010


title: PBMC_SLE1176_v5

description: Gene expression microarray from patient number 1206, visit date: 03/05/2011


title: PBMC_SLE1176_v2

description: Gene expression microarray from patient number 1206, visit date: 05/11/2009


title: PBMC_SLE1178_v2

description: Gene expression microarray from patient number 1263, visit date: 02/11/2009


title: CD71neg Immune Non-Responders d4.16


title: CD71pos Immune Non-Responders d4.14


title: PBMC_SLE1176_v3

description: Gene expression microarray from patient number 1206, visit date: 22/02/2010


title: PBMC_SLE1174_v1

description: Gene expression microarray from patient number 1182, visit date: 12/10/2009


title: CD71neg Immune Non-Responders d4.15


title: CD71pos Immune Non-Responders d4.7


title: CD71pos Immune Non-Responders d4.8


title: PBMC_SLE1052_v4

description: Gene expression microarray from patient number 1179, visit date: 05/10/2009


title: CD71neg Immune Responders d3.19

value: Immune Responders


title: CD71neg Immune Non-Responders d4.8


title: CD71neg Immune Responders d3.17


title: CD71pos Immune Responders d3.17


title: PBMC_SLE1052_v2

description: Gene expression microarray from patient number 1178, visit date: 10/10/2011


title: PBMC_SLE1052_v1

description: Gene expression microarray from patient number 1178, visit date: 24/03/2011


title: PBMC_SLE1052_v5

description: Gene expression microarray from patient number 1179, visit date: 07/01/2010


title: PBMC_SLE1041_v2

description: Gene expression microarray from patient number 1178, visit date: 02/09/2010


title: CD71neg Immune Non-Responders d4.7


title: PBMC_SLE1052_v3

description: Gene expression microarray from patient number 1179, visit date: 01/10/2009


title: CD71pos Immune Responders d3.19


title: CD71neg Immune Responders d3.16


title: CD71pos Immune Responders d3.14


title: PBMC_SLE1041_v1

description: Gene expression microarray from patient number 1178, visit date: 07/06/2010


title: PBMC_SLE981_v1

description: Gene expression microarray from patient number 1176, visit date: 31/03/2011


title: PBMC_SLE1001_v3

description: Gene expression microarray from patient number 1178, visit date: 28/01/2010


title: CD71pos Immune Responders d3.16


title: PBMC_SLE1001_v1

description: Gene expression microarray from patient number 1176, visit date: 19/09/2011


title: PBMC_SLE1001_v2

description: Gene expression microarray from patient number 1178, visit date: 12/10/2009


title: PBMC_SLE981_v2

description: Gene expression microarray from patient number 1176, visit date: 23/06/2011


title: PBMC_SLE1041_v3

description: Gene expression microarray from patient number 1178, visit date: 09/12/2010


title: CD71neg Immune Responders d3.14


title: CD71pos Immune Responders d3.1


title: CD71pos Immune Responders d3.13


title: CD71neg Immune Responders d3.13


title: PBMC_SLE981_v3

description: Gene expression microarray from patient number 1176, visit date: 12/07/2011


title: CD71neg Immune Responders d3.1


title: CD71pos Healthy Donors d5.13

value: Healthy Donors


title: CD71pos Healthy Donors d5.11


title: PBMC_SLE966_v3

description: Gene expression microarray from patient number 1176, visit date: 11/03/2010


title: Tumor_S3

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
All reads were aligned to mouse reference genome (mm10) using hisat2 with default setting.
Stringtie was used to calculate transcriptional expression level as fragments per kilobase per million (FPKM). Differential gene expression was defined if fold change > 1.5 and p < 0.05 between tumor versus normal samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene

source_name: mouse breast cancer

growth_protocol: We collected  samples from  5 month old tumor burden female FVB/NJ; MMTV-Tg (LINK-A) mice and same aged female FVB/NJ; Tg (LINK-A) mice.

extract_protocol:
Total RNA was harvested used the RNeasy PLUS mini kit (Qiagen, cat. no. 74136). Contaminating genomic DNA was removed from the RNA by treating with the Turbo DNA-free kit(Ambion, cat. no. AM1907M).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent combing RNeasy PLUS mini kit (Qiagen, cat. no. 74136).

tag: strain

value: FVB/NJ; MMTV-Tg(LINK-A)

value: mouse breast cancer

tag: Stage

value: 5 month


title: Tumor_S2


title: Tumor_S1


title: CD71neg Healthy Donors d5.13


title: PBMC_SLE966_v4

description: Gene expression microarray from patient number 1176, visit date: 15/03/2010


title: PBMC_SLE911_v4

description: Gene expression microarray from patient number 1174, visit date: 16/11/2009


title: PBMC_SLE911_v2

description: Gene expression microarray from patient number 1052, visit date: 24/02/2011


title: CD71pos Healthy Donors d5.7


title: PBMC_SLE966_v1

description: Gene expression microarray from patient number 1174, visit date: 15/03/2010


title: CD71neg Healthy Donors d5.11


title: PBMC_SLE911_v3

description: Gene expression microarray from patient number 1174, visit date: 08/10/2009


title: CD71neg Healthy Donors d5.2


title: PBMC_SLE759_v4

description: Gene expression microarray from patient number 1052, visit date: 22/07/2010


title: CD71pos Healthy Donors d5.1


title: CD71pos Healthy Donors d5.10


title: PBMC_SLE911_v1

description: Gene expression microarray from patient number 1052, visit date: 04/11/2010


title: CD71pos Healthy Donors d5.2


title: CD71neg Healthy Donors d5.1


title: PBMC_SLE759_v2

description: Gene expression microarray from patient number 1052, visit date: 01/10/2009


title: Normal_S3

source_name: mammary gland

value: FVB/NJ; Tg(LINK-A)

value: mouse mammary gland


title: WN-11-21b

city: Berlin

first: Erich

last: Wanker

state: Berlin

address: Robert-Rössle-Str. 10

institute: MDC Berlin

description: wt, untreated

hyb_protocol: To perform whole genome expression analysis MouseWG-6 v2.0 Expression BeadChips, were incubated with biotin labeled cRNA for 18 h at 58°C in a hybridization oven under humidity-controlled conditions. After hybridization, the Illumina® Sentrix BeadChips were washed using buffers provided by the kit. 2.5 µl (1 mg/ml) of Streptavidin-Cy3 (per Chip) diluted in 2.5 ml blocking buffer were incubated per Chip for 10 minutes under gentle shaking conditions to allow binding of cRNA to gene-specific probes. After washing, Illumina® Sentrix BeadChips were dried and scanned using the Illumina BeadArray Reader GX (Illumina, San Diego, USA).

scan_protocol: Chips were scanned using the Illumina BeadArray Reader GX (Illumina, San Diego, USA). To quantify gene expression signal levels we used the Illumina’s BeadStudio software (Illumina, San Diego, USA) package.

data_processing: The analysis was carried out using the limma package in R.

source_name: Mouse cortex

label_protocol: 500 ng of total RNA in 11 µl RNase free water was used as starting material for the generation of biotin-labeled cRNA with the Illumina® TotalPrep™ RNA Amplification Kit (ThermoFisher Scientific, Dreieich,  Germany), following supplier instructions. cRNA was cleaned up with cRNA filter cartridges before use for subsequent hybridization on Illumina® Sentrix BeadChips (Illumina, San Diego, USA).

growth_protocol: Mice were group-housed (5/cage) with wood shavings. Environmental enrichment was achieved by providing each cage with a play tunnel, shredded paper and a wood block. Food and water were provided ad libitum.

extract_protocol: Freshly isolated mouse brains were dissected and cortex was isolated. RNA was prepared from mouse tissues using the „RNeasy Lipid Tissue Mini Kit“ (Qiagen, Hilden, Germany). DNA was removed from the RNA sample using the „RNase-Free DNase Set“ kit from Qiagen (Hilden, Germany). The quality and yield of extracted total RNAs were analyzed on Agilent RNA 6000 Nano Chips by the 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) and on the NanoDrop ND-1000 UV-Vis Spectrophotometer (Thermo Scientific, Darmstadt, Germany).

treatment_protocol: DO1 was administered orally for 8 months to 6-week-old mice. All mice in the DO1 group received DO1-supplemented pelleted mouse chow at a concentration of 0.652 g/kg food.

tag: age

value: 9.5 months

value: cortex

tag: genotype/variation

value: wild type

value: untreated


title: PBMC_SLE725_v6

description: Gene expression microarray from patient number 1041, visit date: 10/12/2009

value: Systemic Lupus Erythematosus

tag: tissue

value: PBMC


title: PBMC_SLE759_v3

description: Gene expression microarray from patient number 1052, visit date: 05/04/2010


title: Normal_S2


title: WN-11-19

description: wt, untreated


title: PBMC_SLE759_v1

description: Gene expression microarray from patient number 1041, visit date: 11/03/2010


title: CD71neg Healthy Donors d5.7


title: Normal_S1


title: PBMC_SLE966_v2

description: Gene expression microarray from patient number 1176, visit date: 10/12/2009


title: WN-11-23

description: wt, untreated


title: CD71neg Healthy Donors d5.10


title: PBMC_SLE725_v5

description: Gene expression microarray from patient number 1041, visit date: 24/09/2009


title: PBMC_SLE725_v3

description: Gene expression microarray from patient number 1001, visit date: 11/01/2010


title: PBMC_SLE725_v1

description: Gene expression microarray from patient number 981, visit date: 14/03/2011


title: WN-11-14

description: tg, untreated


title: PBMC_SLE704_v6

description: Gene expression microarray from patient number 981, visit date: 15/11/2010


title: PBMC_SLE704_v5

description: Gene expression microarray from patient number 981, visit date: 16/11/2009


title: WN-11-17

description: tg, untreated


title: WN-11-16

description: tg, untreated


title: WN-11-05

description: tg, treated


title: PBMC_SLE725_v4

description: Gene expression microarray from patient number 1001, visit date: 29/03/2010


title: WN-11-13

description: tg, untreated


title: PBMC_SLE704_v3

description: Gene expression microarray from patient number 966, visit date: 28/11/2011


title: WN-11-01

description: tg, treated


title: WN-11-03

description: tg, treated


title: WN-11-15

description: tg, untreated


title: WN-11-04

description: tg, treated


title: WN-11-09

description: wt, treated


title: WN-11-08

description: wt, treated


title: WN-11-12

description: wt, treated


title: PBMC_SLE704_v2

description: Gene expression microarray from patient number 966, visit date: 22/08/2011


title: PBMC_SLE699_v5

description: Gene expression microarray from patient number 911, visit date: 29/11/2010


title: PBMC_SLE699_v3

description: Gene expression microarray from patient number 911, visit date: 18/02/2010


title: PBMC_SLE699_v4

description: Gene expression microarray from patient number 911, visit date: 16/08/2010


title: PBMC_SLE704_v1

description: Gene expression microarray from patient number 966, visit date: 01/09/2010


title: WN-11-02

description: tg, treated


title: WN-11-06

description: tg, treated


title: PBMC_SLE725_v2

description: Gene expression microarray from patient number 1001, visit date: 08/10/2009


title: Infant2_scRNA-seq_rep2

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v1.2.1). Three types of fastq files were generated: I1 contains 8 bp sample index; R1 contains 26 bp (10 cell + 16 UMI) index and R2 contains 100 bp cDNA sequence. Fastq files were then run with count application (Cell Ranger v1.2.1) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Testicular cells

extract_protocol:
Testicular tissues were firstly minced into small pieces mechanically, and subject to trypsin digestion for ~25 min at 37 C. Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina 2500 instrument. Each sample was sequenced in one separate sequencing lane.
10X Genomics single cell RNA sequencing

tag: gender

value: male

value: 13 months

value: Testicle

tag: cell type

value: Testicular cells


title: KIT+_spermatogonia_ATAC_seq_rep2

data_processing:
Raw ATAC-seq reads were aligned to the hg19 genome using Novoalign (v2.8, Novocraft) using the following options: -o Sam -r Random.
Sam files were then combined due to high correlation between technical and biological replicates.
Peak calling was performed using callpeak application (v2.1.1.20160309, macs2) using the following parameters: -g 2.7e9 --call-summit –f BAMPE –nomodel –B –SPMR –extsize 200
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using macs2, yielding single-base pair peak summits

extract_protocol:
Collected cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and the nuclei were pelleted and resuspended in Transposase buffer. The Tn5 enzyme was made in house and the transposition reaction was carried out for 30 minutes at 37°C.
Following purification, the Nextera libraries were amplified for 12 cycles using the NEBnext PCR master mix and purified using the Qiagen PCR cleanup kit. All libraries were sequenced on a 125-cycle paired-end run on an Illumina HiSeq 2500 instrument.

value: adult

value: testicle

value: Testicular cell

tag: marker

value: KIT


title: Infant2_scRNA-seq_rep1


title: Infant1_scRNA-seq_rep2


title: PBMC_SLE704_v4

description: Gene expression microarray from patient number 966, visit date: 27/02/2012

tag: patient id


title: WN-11-07

description: wt, treated


title: Infant1_scRNA-seq_rep1


title: PBMC_SLE582_v6

description: Gene expression microarray from patient number 759, visit date: 21/04/2011

tag: sledai


title: PBMC_SLE699_v2

description: Gene expression microarray from patient number 911, visit date: 19/11/2009

tag: visit date


title: WN-11-11

description: wt, treated


title: WN-11-22

description: wt, untreated


title: WN-11-10

description: wt, treated


title: PBMC_SLE582_v4

description: Gene expression microarray from patient number 759, visit date: 10/12/2009

tag: imputed neutrophil percentage


title: PBMC_SLE582_v3

description: Gene expression microarray from patient number 725, visit date: 21/11/2011


title: WN-11-21

description: wt, untreated

tag: treatment


title: PBMC_SLE699_v1

description: Gene expression microarray from patient number 759, visit date: 27/06/2011


title: PBMC_SLE582_v1

description: Gene expression microarray from patient number 725, visit date: 02/05/2011


title: PBMC_SLE458_v3

description: Gene expression microarray from patient number 725, visit date: 02/12/2010


title: KIT+_spermatogonia_ATAC_seq_rep1


title: PBMC_SLE453_v4

description: Gene expression microarray from patient number 704, visit date: 09/01/2012


title: WN-11-20

description: wt, untreated


title: PBMC_SLE582_v5

description: Gene expression microarray from patient number 759, visit date: 18/03/2010


title: PBMC_SLE453_v3

description: Gene expression microarray from patient number 704, visit date: 25/07/2011


title: PBMC_SLE453_v2

description: Gene expression microarray from patient number 704, visit date: 06/12/2010


title: PBMC_SLE458_v2

description: Gene expression microarray from patient number 725, visit date: 15/03/2010


title: bebv_input

city: London

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Alignments were performed by hisat2, v2.0.3 or v2.0.5, with the --no-spliced-alignment option
Reads were filtered by alignment to nine vertebrate genomes, including human, and assigned to the best-matching genome.
Peak calling was by MACS2, and analysis of colocalisation was by the R package ChIPpeakAnno
Normalisation and subtraction was done using the deepTools 2.5.4 bamCompare function with option string  --outFileFormat bigwig --scaleFactorsMethod readCount --ratio subtract --binSize 50 --normalizeTo1x 3100000000 --minMappingQuality 30
Genome_build: hg38
Supplementary_files_format_and_content: A bigWig graph representing difference between ChIP and input, with the difference calculated after ChIP and input had each been normalised to 1x coverage genome-wide

source_name: EBV-transformed B lymphoblast

extract_protocol:
as described by Pope SH et al, Eur J Haematol 64:292-303, 2000
library construction was provided by Oxford Genomics Centre, or by Edinburgh Genomics

value: EBV-transformed B lymphoblast

tag: chip antibody

value: no antibody

tag: number of sonications


title: ery_UTX

source_name: erythroblast

growth_protocol: as described by Pope SH et al, Eur J Haematol 64:292-303, 2000

value: Adult erythroblasts

value: UTX (A302-374A) from Bethyl Labs


title: ery_RBBP5

treatment_protocol: as described by Pope SH et al, Eur J Haematol 64:292-303, 2000


title: PBMC_SLE458_v1

description: Gene expression microarray from patient number 725, visit date: 09/11/2009

tag: disease state


title: ery_DNaseHS


title: ery_H3K27me3

value: H3K27me3 (07-449) from Millipore


title: PBMC_SLE582_v2

description: Gene expression microarray from patient number 725, visit date: 15/08/2011


title: PBMC_SLE371_v4

description: Gene expression microarray from patient number 704, visit date: 08/06/2010


title: PBMC_SLE453_v1

description: Gene expression microarray from patient number 704, visit date: 02/09/2010


title: PBMC_SLE371_v2

description: Gene expression microarray from patient number 699, visit date: 21/04/2011


title: PBMC_SLE371_v3

description: Gene expression microarray from patient number 704, visit date: 14/12/2009


title: PBMC_SLE371_v1

description: Gene expression microarray from patient number 699, visit date: 13/01/2011


title: PBMC_SLE365_v5

description: Gene expression microarray from patient number 699, visit date: 18/10/2010


title: PBMC_SLE365_v4

description: Gene expression microarray from patient number 699, visit date: 09/11/2009


title: PBMC_SLE365_v3

description: Gene expression microarray from patient number 699, visit date: 22/10/2009


title: PBMC_SLE365_v1

description: Gene expression microarray from patient number 582, visit date: 21/04/2011


title: PBMC_SLE345_v3

description: Gene expression microarray from patient number 582, visit date: 06/01/2011


title: PBMC_SLE317_v5

description: Gene expression microarray from patient number 458, visit date: 10/12/2009


title: PBMC_SLE345_v2

description: Gene expression microarray from patient number 582, visit date: 04/10/2010


title: PBMC_SLE345_v1

description: Gene expression microarray from patient number 582, visit date: 25/01/2010


title: PBMC_SLE317_v7

description: Gene expression microarray from patient number 458, visit date: 18/11/2010


title: PBMC_SLE317_v8

description: Gene expression microarray from patient number 582, visit date: 26/10/2009


title: PBMC_SLE317_v6

description: Gene expression microarray from patient number 458, visit date: 12/08/2010


title: PBMC_SLE317_v3

description: Gene expression microarray from patient number 453, visit date: 21/06/2010


title: PBMC_SLE244_v5

description: Gene expression microarray from patient number 371, visit date: 13/06/2011


title: PBMC_SLE317_v4

description: Gene expression microarray from patient number 453, visit date: 07/10/2010


title: PBMC_SLE317_v1

description: Gene expression microarray from patient number 453, visit date: 14/12/2009


title: PBMC_SLE317_v2

description: Gene expression microarray from patient number 453, visit date: 05/04/2010


title: PBMC_SLE244_v3

description: Gene expression microarray from patient number 371, visit date: 10/11/2009


title: PBMC_SLE244_v1

description: Gene expression microarray from patient number 365, visit date: 06/12/2010


title: PBMC_SLE244_v2

description: Gene expression microarray from patient number 365, visit date: 30/06/2011


title: PBMC_SLE365_v2

description: Gene expression microarray from patient number 582, visit date: 21/07/2011


title: PBMC_SLE113_v4

description: Gene expression microarray from patient number 365, visit date: 17/05/2010


title: PBMC_SLE113_v5

description: Gene expression microarray from patient number 365, visit date: 04/10/2010


title: PBMC_SLE113_v3

description: Gene expression microarray from patient number 365, visit date: 12/11/2009


title: PBMC_SLE244_v4

description: Gene expression microarray from patient number 371, visit date: 28/01/2010


title: PBMC_SLE113_v2

description: Gene expression microarray from patient number 345, visit date: 06/01/2011


title: PBMC_SLE113_v1

description: Gene expression microarray from patient number 345, visit date: 30/08/2010


title: PBMC_SLE46_v1

description: Gene expression microarray from patient number 317, visit date: 11/05/2011


title: F_EPi_R415

city: Los Angeles

first: Randall

middle: B.

last: Widelitz

state: California

address: 2011 Zonal Ave HMR 305

department: Department of Pathology

institute: University of Southern California

data_processing:
Low quality of sequencing bases were trimmed based on the Phred+33 quality score (> 20) from both of the 5'- and 3'-ends of reads. After trimming, reads are discarded, if they are shorter than 50bp, or have one or more ambiguous base.
Ensembl Release81 annotation were downloaded from the UCSC Genome Browser
The alignment, quantification, normalization, and differential expression analysis were performed by STAR 2.4.1d, htseq-count 0.6.0, TMM, and edgeR 3, respectively.
Genes with count-per-million (CPM) values above 1 in at least two samples were retained, and genes with no or low expression levels were discarded.
Genome_build: UCSC galGal4
Supplementary_files_format_and_content: The tab-delimited text files: 24 files with count values of 17108 genes for each sample produced by htseq-count

source_name: female_collar epithelium

tag: individual

tag: Sex

value: female

value: collar epithelium

tag: quality score


title: F_LFS_R412

source_name: female_lower follicle sheath

value: lower follicle sheath


title: M_DP_R411

source_name: male_dermal papilla

value: dermal papilla


title: M_PE_R410

source_name: male_papilla ectoderm

value: male

value: papilla ectoderm


title: F_DP_R417

source_name: female_dermal papilla


title: F_UFS_R413

source_name: female_upper follicle sheath

value: upper follicle sheath


title: F_PE_R416

source_name: female_papilla ectoderm


title: PBMC_SLE24_v5

description: Gene expression microarray from patient number 317, visit date: 07/02/2011

value: Systemic Lupus Erythematosus

value: PBMC


title: PBMC_SLE46_v2

description: Gene expression microarray from patient number 317, visit date: 27/06/2011


title: M_EPi_R409

source_name: male_collar epithelium


title: PBMC_SLE46_v3

description: Gene expression microarray from patient number 317, visit date: 31/10/2011


title: PBMC_SLE24_v3

description: Gene expression microarray from patient number 317, visit date: 17/12/2009


title: PBMC_SLE24_v4

description: Gene expression microarray from patient number 317, visit date: 18/03/2010


title: M_PP_R408

value: pulp


title: PBMC_SLE46_v4

description: Gene expression microarray from patient number 345, visit date: 01/03/2010


title: PBMC_SLE24_v2

description: Gene expression microarray from patient number 317, visit date: 12/11/2009


title: M_UFS_R407

source_name: male_upper follicle sheath


title: PBMC_SLE244_v6

description: Gene expression microarray from patient number 371, visit date: 09/01/2012


title: PBMC_Healthy19

description: Gene expression microarray from patient number 244, visit date: 17/02/2011

value: Healthy


title: PBMC_Healthy20

description: Gene expression microarray from patient number 244, visit date: 10/11/2011


title: F_DP_R405


title: M_LFS_R406

source_name: male_lower follicle sheath


title: OCM-1A cells control exp3

city: Saint Louis

first: Michael

middle: D

last: Onken

state: MO

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

institute: Washington University School of Medicine

data_processing:
FastQ files aligned with STAR
Biologic replicates analyzed by edgeR and Sailfish for gene-level features
normalized abundance measurements generated from edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of edgeR normalized abundance measurements

source_name: OCM-1A uveal melanoma cell line

growth_protocol: 5% CO2, 37˚C, RPMI 1640 with 10% FBS

extract_protocol:
Qiagen RNeasy mini kit
RNA-polyA

treatment_protocol: Lentiviral constructs expressing shRNA

tag: cell line

value: uveal melanoma

value: shGFP (control)

tag: time

value: 6 days


title: OCM-1A cells control exp1

tag: tissue


title: PBMC_Healthy18

description: Gene expression microarray from patient number 244, visit date: 16/08/2010


title: F_EPi_R403


title: F_PP_R402


title: F_UFS_R401


title: OCM-1A cells shBAP1 exp2


title: OCM-1A cells shBAP1 exp3


title: M_DP_R399


title: PBMC_Healthy16

description: Gene expression microarray from patient number 244, visit date: 07/06/2010


title: PBMC_Healthy17

description: Gene expression microarray from patient number 244, visit date: 15/07/2010


title: OCM-1A cells control exp2


title: M_PE_R398


title: OCM-1A cells shBAP1 exp1


title: F_PE_R404


title: M_EPi_R397


title: PBMC_Healthy11

description: Gene expression microarray from patient number 113, visit date: 21/01/2010


title: PBMC_Healthy15

description: Gene expression microarray from patient number 244, visit date: 25/02/2010


title: PBMC_Healthy13

description: Gene expression microarray from patient number 113, visit date: 22/04/2010


title: M_PP_R396


title: human blastocyst stage embryo, biological rep4

city: manchester

first: Helen

middle: Louise

last: Smith

address: oxford road

institute: The University of Manchester

description: Gene expression data from a blastocyst stage embryo, isolated on day 5

hyb_protocol: Labelled PolyAcRNA was hybridised to Affymetrix Human Genome U133 Plus 2.0 arrays

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Gene expression analysis and normalisation MAS 5.0 method (Affymetrix. Affymetrix Microarray Suite User Guide. Affymetrix, Santa Clara, CA, version 5 edition, 2001) were performed using Bioconductor

source_name: Embryos at the blastocyst stage

label_protocol: PolyAcDNA was then subjected to a second round of amplification and biotin-16-dUTP labelling using EpiStem’s proprietary PolyAPCR based systems, EpiAmp™ (PolyAPCR based amplification) and EpiLabel™ (PolyA-PCR labelling), according to the Manufacturer’s instructions.

growth_protocol: For detailed description of the material see Shaw et.al. 2013. Embryos were cultured in G1 medium (Vitrolife, Goteborg, Sweden) covered with a thin layer of mineral oil (Ovoil, Origio, Malov, Denmark) until day 3, followed by G2 medium (Vitrolife) from day 3 to blastocyst at 37˚C, 6% CO2 in a humidified atmosphere.

extract_protocol: cDNA was prepared by polyAPCR amplification

treatment_protocol: A single embryo was transferred in a minimum volume of culture medium (<0.5 μl) to 4.5 μl complete lysis buffer. The reaction was overlaid with mineral oil, heated to 65°C for 1 min, cooled to room temperature for 3 min then placed on ice. The RNA was reverse transcribed. One volume of tailing buffer (0.33 mol/l potassium cacodylate, 6.7 mmol/l COCl2, 0.67 mmol/l DTT, 0.16 mmol/l dATP, 0.45 units/μl rTdT; Invitrogen) was then added and the reaction was incubated at 37°C for 15 min, 65°C for 10 min and then cooled on ice. This step polyadenylates the first strand cDNA allowing subsequent global amplification of cDNA using a single Not1dT24 oligonucleotide primer.

value: Pre-implantation Embryo


title: human blastocyst stage embryo, biological rep3

tag: developmental stage

value: blastocyst


title: F_LFS_R400


title: PBMC_SLE24_v1

description: Gene expression microarray from patient number 317, visit date: 15/10/2009


title: PBMC_Healthy09

description: Gene expression microarray from patient number 46, visit date: 26/08/2010


title: PBMC_Healthy12

description: Gene expression microarray from patient number 113, visit date: 08/03/2010


title: PBMC_Healthy14

description: Gene expression microarray from patient number 113, visit date: 29/07/2010


title: M_UFS_R395


title: M_LFS_R394


title: RA_ATAC-G7-9

data_processing:
Reads were aligned onto the galGal4 reference genome using bowtie2
Greater than 19 million reads were obtained for each library, and reads mapping to mitochondrial DNA were excluded
Coverage tracks (i.e. bigWig format) were produced by deepTools2
Genome_build: UCSC galGal4
Supplementary_files_format_and_content: bigWig

source_name: chicken embryonic metatarsal skin

growth_protocol: Chicken eggs were incubated at 37℃ in an incubator with humidity control

extract_protocol:
ATAC Lysis Buffer
Nextera DNA Library Preparation Kit

treatment_protocol: RCAS-CTNNB1, RCAS-GFP, and retinoic acid

tag: treat

value: Retinoic acid

value: E12 metatarsal skin

tag: phenotype

value: ptilopody


title: human blastocyst stage embryo, biological rep2


title: PBMC_Healthy07

description: Gene expression microarray from patient number 46, visit date: 16/02/2010

tag: patient id


title: human 8-cell stage embryo, biological rep3

description: Gene expression data from an 8-cell stage embryo, isolated on day 3

source_name: Embryos at the eight-cell stage

value: 8-cell stage


title: human 8-cell stage embryo, biological rep2


title: RA_ATAC-G7-7


title: PBMC_Healthy08

description: Gene expression microarray from patient number 46, visit date: 10/05/2010

tag: sledai


title: PBMC_Healthy10

description: Gene expression microarray from patient number 113, visit date: 12/11/2009

tag: visit date


title: PBMC_Healthy05

description: Gene expression microarray from patient number 24, visit date: 08/03/2010

tag: imputed neutrophil percentage


title: PBMC_Healthy06

description: Gene expression microarray from patient number 46, visit date: 29/10/2009


title: GFP_ATAC-G7-3

value: RCAS-GFP

value: scale


title: human blastocyst stage embryo, biological rep1


title: CTNNB1_ATAC-G8-14


title: CTNNB1_ATAC-G8-13


title: human 8-cell stage embryo, biological rep1


title: bebv_CFP1_AbcamAb

tag: cell type

value: EBV-transformed B lymphoblast

value: CFP1 (ab56035), from Abcam


title: PBMC_Healthy04

description: Gene expression microarray from patient number 24, visit date: 19/02/2010


title: GFP_ATAC-G7-1


title: bebv_CFP1_nonComAb

tag: chip antibody

value: CFP1, non-commercial Ab from Bob Roeder


title: human individual blastomere from 8-cell embryo (B7)

description: Gene expression data from an individual blastomere isolated from an 8-cell stage embryo on day 3

source_name: Individual blastomere 7 isolated from a single 8-cell stage embryo


title: human individual blastomere from 8-cell embryo (B6)

source_name: Individual blastomere 6 isolated from a single 8-cell stage embryo


title: human individual blastomere from 8-cell embryo (B8)

source_name: Individual blastomere 8 isolated from a single 8-cell stage embryo


title: Rif1^PP1 SG/CyO replicate 2

city: Nashville

first: Jared

last: Nordman

state: TN

address: 465 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

data_processing:
Library strategy: DNA-seq
Reads were mapped to the Drosophila genome (BDGP Release 6) using BWA using default parameters
Normalized read counts (RPKM) were generated using bamCoverage using default parameters for the stage 13 samples. For salivary gland data sets (and 0-2h embryo control) normalized read counts (RPKM) were generated using bamCoverage rom Deeptools v2.5.0. Bin size 75 bases, smoothed for 225 bases. Minimum mapping quality required of 1 to only call uniquely mapped reads. Ignore duplicates flag set to true. Scaling method was RPKM, and excluded Chromosome 4 and X for normalization.
CNVnator 0.3.3 was used for the detection of underreplicated regions using a bin size of 1000
log2 ratios were generated using bamCompare from deepTool 2.5.0 by comparing stage 13 follicle cell profiles to a 0-2h embryo sample.
Genome_build: dm6

source_name: 3rd instar larvae

extract_protocol:
Salivary glands were extracted from wandering 3rd instar larvae. Ovaries were dissected from females fattened for 2 days on wet yeast and stage 13 egg chambers were isolated by hand dissection. Tissue was disrupted by douncing and then sonicated to fragment the genomic DNA. Genomic DNA extracted using a standard phenol chloroform extraction protocol.
Illumina libraries were prepared using NEB DNA Ultra II (New England Biolabs) following the manufacturers protocol. Barcoded libraries were sequenced using Illumina NextSeq500 platform.

value: salivary gland

tag: genotype


title: Rif1^PP1 SG replicate 2


title: Rif1^PP1 SG replicate 1


title: Rif1^PP1 SG/CyO replicate 1


title: human individual blastomere from 8-cell embryo (B3)

source_name: Individual blastomere 3 isolated from a single 8-cell stage embryo


title: human individual blastomere from 8-cell embryo (B4)

source_name: Individual blastomere 4 isolated from a single 8-cell stage embryo


title: human individual blastomere from 8-cell embryo (B5)

source_name: Individual blastomere 5 isolated from a single 8-cell stage embryo


title: human individual blastomere from 8-cell embryo (B2)

source_name: Individual blastomere 2 isolated from a single 8-cell stage embryo


title: PBMC_Healthy02

description: Gene expression microarray from patient number 24, visit date: 07/12/2009

tag: disease state

value: PBMC


title: human individual blastomere from 8-cell embryo (B1)

source_name: Individual blastomere 1 isolated from a single 8-cell stage embryo


title: PBMC_Healthy03

description: Gene expression microarray from patient number 24, visit date: 07/01/2010

value: Healthy


title: F_PP_R414

tag: individual

value: female

value: pulp


title: Wild type 0-2h embryo

data_processing:
Reads were mapped to the Drosophila genome (BDGP Release 6) using BWA using default parameters
Normalized read counts (RPKM) were generated using bamCoverage using default parameters for the stage 13 samples. For salivary gland data sets (and 0-2h embryo control) normalized read counts (RPKM) were generated using bamCoverage rom Deeptools v2.5.0. Bin size 75 bases, smoothed for 225 bases. Minimum mapping quality required of 1 to only call uniquely mapped reads. Ignore duplicates flag set to true. Scaling method was RPKM, and excluded Chromosome 4 and X for normalization.
CNVnator 0.3.3 was used for the detection of underreplicated regions using a bin size of 1000
log2 ratios were generated using bamCompare from deepTool 2.5.0 by comparing stage 13 follicle cell profiles to a 0-2h embryo sample.
Genome_build: dm6

source_name: 0-2h embryo

value: embryo

value: wildtype


title: ery_CFP1_nonComAb

source_name: erythroblast

value: Adult erythroblasts

tag: number of sonications


title: PBMC_Healthy01

description: Gene expression microarray from patient number 24, visit date: 15/10/2009


title: human 4-cell stage embryo, biological rep3

description: Gene expression data from a 4-cell stage embryo, isolated on day 2

source_name: Embryos at the four-cell stage

value: Pre-implantation Embryo

value: four-cell stage


title: ery_CFP1_AbcamAb


title: Rif1 st13 replicate 2

source_name: Adult females

value: ovary


title: spermatocyte_WT_rep5

description: SK

hyb_protocol: Hybridization, staining and detection of cRNAs on Illumina Mouse WG-6 v2 Expression BeadChips were performed according to the manufacturer’s protocol.

scan_protocol: The Illumina I-Scan system was used to scan Expression BeadChips, according to Illumina recommendations.

data_processing: The data were normalised using quantile normalisation.

label_protocol: The starting amount of total RNA used for the reactions was 200 nanograms per sample. The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations.

extract_protocol: Total RNA was extracted using Trizol reagent. 0.5-1 μg RNA was reverse transcribed with the SuperScriptTM III First-Strand Synthesis SuperMix (Invitrogen). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA). Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA). A RNA integrity number (RIN) greater or equal to 7.00 was achieved for all samples.

treatment_protocol:
cell enrichment protocol: Fractions enriched in spermatogenic cells at different stages of maturation, including post meiotic round/early elongating spermatids were obtained by sedimentation on a BSA gradient as detailed in a recent dedicated method publication (Buchou et al., 2017; PMID: 27761820)
samples (replicates) preparation: RNAs for transcriptomic analyses were prepared from three independent experiments corresponding to three independent cell fractionations for each genotype. For each fractionation, cell suspensions from testes from two WT mice or three Nut KO mice were used. For each genotype (WT and Nut KO), 6 samples were prepared as follows. Samples 1, 2 and 3 were directly prepared from the three above-mentioned fractionations and three additional samples were obtained by respectively mixing samples 1 with 2, 2 with 3, and 1 with 3.

tag: strain background

tag: genotype/variation

value: WT

tag: Sex

value: male

tag: age

value: adult

value: adult testis

value: male germ cells

tag: cell stage

value: spermatocytes


title: SuUR st13

tag: tissue

value: SuUR


title: Wild type st13


title: human 4-cell stage embryo, biological rep2

tag: developmental stage