title: Peritoneal macrophages, obtained from Angptl4-/- mice, intralipid, 3 pooled samples.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization, washing, and scanning of Affymetrix GeneChip Mouse Gene 1.0 ST Arrays were carried out according to standard Affymetrix protocols.

scan_protocol: Scanning of the Affymetrix GeneChip Mouse Gene 1.0 ST arrays was carried out according to standard Affymetrix protocols on a GeneChip 3000-7G  Scanner (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.46.0).

source_name: Peritoneal macrophages were obtained from Angptl4-/- mice and incubated with intralipid (0.5mM) for 6 hrs in the absence of recombinant ANGPTL4. Pooled RNA of 3 samples.

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Peritoneal macrophages were obtained from male purebred Angptl4-/- mice (C57Bl/6 background strain).

extract_protocol: Total RNA was isolated from samples using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer’s protocol. RNA quality was verified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) using 6000 Nano Chips according to manufacturer’s instructions. RNA was considered suitable for array hybridization only if RNA integrity number exceeded 8.0. RNA from 3 samples per group was pooled for microarray analysis.

treatment_protocol: To obtain peritoneal macrophages, mice were injected intraperitoneally with 1 mL 4% thioglycollate. Three days later, the animals were anesthesized with isoflurane, bled via orbital puncture, and their peritoneal cavities washed using 10 mL ice-cold RPMI medium supplemented with 100 U/mL penicillin, and 100 µg/mL streptomycin (Lonza, Verviers, Belgium). Cell pellets were incubated with RBC lysis buffer on ice for 5 min and subsequently washed with RPMI medium supplemented with 10% fetal bovine serum (FBS) (Lonza, Verviers, Belgium) and antibiotics, re-pelletized and seeded at a density of 3×105 cells/cm2. Two hours later, the cells were washed twice with PBS to remove non-adherent cells and provided with medium. Two days later, the cells were exposed to PBS, intralipid at a triglyceride concentration of 0.5 mM for 6 hours preceded by pre-incubation with either 20 µM Orlistat (Sigma Zwijndrecht, The Netherlands) or 2.5 µg/mL mouse recombinant Angptl4 (R&D Systems, Abingdon, United Kingdom) for 1.5 hours.

tag: agent

value: Intralipid (0.5mm)


title: N4 primed OT-I, biological rep3

status: Public on Aug 24 2019

type: RNA

city: Shimotogari, Nagaizumi-cho

first: Akihiro

last: Tokunaga

state: Shizuoka

country: Japan

institute: Kyowa kirin Co., Ltd

hyb_protocol: Following fragmentation, ssDNA were hybridized for 17 hr on GeneChip Clariom D Array, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Clariom D Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Raw data were processed with the Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST) algorithms prior to Robust Multiarray Average (RMA) using Expresson Console Software (ThermoFisher Scientific) according to the default analysis settings (Exon Level-SST-Alt Splice Analysis).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: N4 primed, 4 days

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 5.5 ug ssDNA.

growth_protocol: OT-I cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum and 4 mmol/L of L-glutamine.

extract_protocol: Total RNA was isolated with the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: OT-I cells were stimulated with N4 or Y3 peptide and treated with corticosteroids in vitro for 4 days.

tag: cell type

value: splenocyte

tag: cell line

value: OT-I


title: N4 primed OT-I, biological rep1


title: N4 primed OT-I, biological rep2


title: KO3: 62-441_RNA_mut

type: SRA

city: Montreal

first: Anna

middle: K

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
Trimming and filtering, TRIMMOMATIC v0.36
Alignment to mm10, STAR v2.5.3a
Mark duplicates, Picard v2.9.0
Produce raw counts, HTSeq-Count v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: CSV, Raw Counts

source_name: lung

extract_protocol: Trizol extraction followed by purification with RNAeasy (Qiagen, NL)

tag: strain

tag: tissue

value: lung

tag: time

tag: genotype/variation

value: Zpbp2 KO


title: N4 primed OT-I with corticosteroid, biological rep2

source_name: N4 primed, corticosteroid treated, 4 days


title: HepG2.2.15 cells Sp110 siRNA treated Set 3

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: Array hybridization were performed per recommended specifications (Asuragen, Austin, TX).

scan_protocol: Scanning were performed per recommended specifications (Asuragen, Austin, TX).

data_processing: Genechip PrimeView Human Arrays were utilized (Affymetrix, Santa Clara, CA). CEL files were analyzed utilizing R/Bioconductor package, oneChannelGUI. Briefly, normalization of expression values was performed utilizing the “Expresso” option, selecting “RMA” as the background correction, “quantiles” as normalization, “pmonly” as the PM correction, and “MAS” as the expression. Probes were filtered with IQR settings of 0.25. P values were calculated using a two-tailed Student’s t-test.

organism: Homo sapiens

source_name: HepG2.2.15 cells Sp110 siRNA treated

label_protocol: Per Affymetrix Protocol

growth_protocol: HepG2.2.15 cells were maintained in RPMI1640 supplemented with 12% FBS and 1% Pen-Step at 37⁰C and 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were transiently transfected with Control siRNA or Sp110 siRNA using Interferrin transfection reagent (Polyplus)

tag: gender

value: Male

tag: disease state

value: hepatocellular carcinoma

value: Liver

value: HepG2.2.15 (a HBV expressing cell-line)

tag: genotype

value: Sp110 knockdown


title: GATA1_HUDEP2: HUDEP2 cells

city: Boston

first: Stuart

last: Orkin

state: MA

address: 1 Blackfan Circle

department: Hematology and Oncology

country: USA

institute: Boston Childrens Hospital

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Reads are of size 42bp.
Trimmomatic v.0.33 was run to trim away adapter sequences (ILLUMINACLIP:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25)
Untrimmed reads were further removed 6bp from the 3’ end to further rid of remaining adapter bases not trimmed by Trimmomatic. Deposited raw reads (FASTQ) have been trimmed.
Bowtie2 was used to align reads to reference genome assembly (hg19) with settings -p 2 --dovetail –phred33
Aligned reads are marked for duplicates with Picard MarkDuplicates function.
Afterward, the BAM file was filtered with SAMtools to discard reads, mates that were unmapped, or PCR/optical duplicates (-f 3 –F 4 –F 8 –F 1024).
MACS version 2.1 was used to call peaks from the fragment-size selected and duplicate-removed reads with narrowPeak setting, P-value cutoff of 1e-5, and with –SPMR which normalizes the signal intensity to facilitate comparison between tracks.  Low-complexity regions as outlined in the ENCODE blacklist file were also removed.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak – peaks generated with MACS v2 (callpeak -g hs -f BAMPE -q 0.01) and we filtered peaks centered on blacklisted regions (ENCODE)

molecule: genomic DNA

source_name: human umbilical cord blood-derived erythroid progenitor (HUDEP)

extract_protocol:
CUT&RUN experiments were carried out as described(Skene and Henikoff, 2017) with minor changes. Briefly, nuclei from 2 million cells were isolated and incubated with primary antibody for 2 hours. After washing away unbound antibody, protein A-MNase was added at a 1:1000 ratio and incubated for 1 hour. The nuclei were washed again and placed in a 0°C metal block. To activate protein A-MNase, CaCl2 was added to a final concentration of 2mM. The reaction was carried out for different time courses and stopped by chelating Ca2+. The protein-DNA complex was released by centrifugation and then digested by proteinase K at 50°C overnight. DNA was extracted by ethanol precipitation, followed by Qubit and bioanalyzer quality control. Protein A-MNase (batch 5) was kindly provided by Dr. Steve Henikoff.  The antibodies used were: GATA1, ab11852, abcam; KLF1, HPA051850, sigma; TAL1, ab155195, abcam.
For library preparation, we modified the protocol of NEBNext® Ultra™ II DNA Library Prep Kit, NEB (Ipswich, USA), aiming to preserve small DNA fragments (30-80bp). Briefly, dA-tailing temperature was decreased to 50°C to avoid DNA melting, and the reaction time was increased to 1 hour to compensate for lower enzymatic activity. After adapter ligation, 2.1x volume of AMPure XP beads was added to the reaction to ensure high recovery efficiency of small fragments. After 12 cycle of PCR amplification, the reaction was cleaned up with 1.2x volume of AMPure XP beads. 16-24 barcoded libraries were quantified, mixed and denatured according to the standard protocol from Illumina. 1.3mL of 1.8pM diluted library was loaded to a NextSeq® 500/550 High Output Kit v2 (75 cycles), and sequenced in the NextSeq 500 platform with paired-end sequencing.

value: erythroid

tag: differentiation days

tag: replicate

tag: antibody


title: KLF1 HUDEP2: HUDEP2 differentiated

value: human umbilical cord blood-derived erythroid progenitor (HUDEP)


title: KO1: 62-435_RNA_mut


title: Th0 plus stim WT1

first: Takayuki

last: Katsuyama

address: 3 Blackfan Circle, CLS-948

department: Rheumatology and Clinical Immunology

institute: Beth Israel Deaconess Medical Center

data_processing:
Samples were sequenced on an Illumina NextSeq500 run with single-end 75-bp reads.
Cufflinks
STAR Align
STAR Gene counts
Genome_build: mm9

source_name: Th0 Effector CD4 T cells

growth_protocol: Naïve CD4 T cells were isolated from spleens using CD4+CD62L+ T cell isolation kit II (Miltenyi)

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stimulated with anti-CD3 (0.5μg/mL) and anti-CD28 (1μg/mL) for 72 hours, and re-stimulated with PMA (100ng/mL) and Ionomycin (1μM) for 4 hours.

value: spleen

value: Th0 Effector CD4 T cells

tag: age

value: 7 week

value: WT


title: Peritoneal macrophages, obtained from Angptl4-/- mice, intralipid + recANGPTL4, 3 pooled samples.

source_name: Peritoneal macrophages were obtained from Angptl4-/- mice and incubated with intralipid (0.5mM) for 6 hrs in the presence of recombinant ANGPTL4 (2.5 μg/mL). Pooled RNA of 3 samples.

value: Intralipid (0.5mm) + recombinant ANGPTL (2.5 microg/mL)


title: Eye disc rep 1

city: Baltimore

first: Robert

last: Johnston

state: Maryland

address: 3400 N. Charles St.

department: Biology

institute: Johns Hopkins University

description:
Eye_disc_all_reps.cool.gz
Eye_disc_all_reps_DI.bedgraph
Eye_disc_all_reps_TADs.bed

data_processing:
Hi-C fastq reads were trimmed of the adapter sequence ‘GATCGAGCTCGAGAATTCTCGAGCTCGATC’. Read ends were then independently aligned using Bowtie2 v2.3.4.2 and default parameters. Pairing of mapped reads was done by custom script that removed PCR duplicates and filtered out reads aligning to more than two restriction enzyme fragments.
Hi-C read pairs were processed using HiFive, v1.4. Reads were filtered for a maximum insert size of 500bp, followed by filter of fragment-ends with fewer than 10 valid intra-chromosomal interactions larger than 100Kb. Linearly-interpolated log-log distance curves were calculated across 90 bins with a minimum interaction size of 200 and a maximum equal to the largest chromosome. Fragment-end corrections were calculated using the ‘express’ algorithm, an iterative correction procedure that removes distance effects prior to normalization. This was done using intra-chromosomal interactions only for 1000 iterations or until the largest parameter change was smaller than 1e-4.
TAD calls were performed using Hifive based on the directionality index (DI). DI was found using a 15Kb window considering interactions up to 100Kb tong. DI was calculated for each 5Kb step along the genome. TADs were called using a 3-state, 3-part Gaussian mixture model HMM initialized with an upstream, neutral, and downstream bias state. All mixture model components had variance of one and means in 0.5 increments centered on 1.0, 0.0, and -1.0 for the three states, respectively. Transitions to states (0, 1, 2) were set to (0.8, 0.05, 0.15), (0.25, 0.5, 0.25), and (0.15, 0.05, 0.8) for the downstream, neutral, and upstream states, respectively. Initial state frequencies were set at 0.3, 0.4, and 0.3. Parameters were learned from all chromosome DI scores after dividing each chromosome DI score set by its standard deviation. TADs were defined as starting at the first downstream bias state following an upstream bias state with any number of intervening neutral states.  TADs extended through the last upstream bias state followed by a downstream bias state with any number of intervening neutral states.
Genome_build: dm6
Supplementary_files_format_and_content: Hi-C files are in the cool format (https://github.com/mirnylab/cooler) and were created using a HiFive to Cool converter. Directionality Index (DI) files are in a BEDGRAPH format, and TADs are in BED format, both created using HiFive.

organism: Drosophila melanogaster

source_name: Eye disc

extract_protocol:
Larval eye discs and antennal discs were prepared for Hi-C using the following steps: 3 replicates of 125 third instar larval eye or antennal discs (i.e. N=3, n=125) were dissected in 1X PBS and stored in 1X PBS on ice until fixation. Eye and antennal discs were separated manually by dissection. After all discs were collected, discs were centrifuged at 17,600g for 1 minute and PBS was removed. Residual PBS was removed with a pipette, and discs were left to air dry for 3 minutes. Fixative (750 uL heptane, 237.4 uL cross-linking solution, 12uL fresh 37% formaldehyde) was added to the discs, and discs were fixed for 15 minutes with vigorous shaking. Discs were then centrifuged at 17,600g for 1 minute and fixative was removed. 1 mL of glycine solution (125 mM glycine, 0.1% Triton in PBS) was added to the discs, and the discs were incubated for 1 minute with vigorous shaking to quench the crosslinking reaction. Discs were then centrifuged at 17,600g for 1 minute and glycine solution was removed. Discs were then washed 2X with 1 mL of ice-cold PBX and centrifuged at 17,600g for 1 minute. PBX was removed, and discs were then centrifuged again at 17,600g for 1 minute. Any residual PBX was removed with a pipette, and discs were air dried for 3 minutes. Discs were then snap-frozen in liquid nitrogen and stored at -80 degrees C. Cross-linking solution: 50 mM Hepes (11.92 g), 1 mM EDTA (0.292 g), 0.5 mM EGTA (0.19 g), 100 mM NaCl (5.844 g) in 1L ultra-pure water. Solution was brought to pH 8, sterile filtered, and stored at room temperature. Glycine solution: 0.14 g glycine, 15 mL 1X PBS, 15 mL Triton-X. Solution was made fresh for each experiment and was stored at 4 degrees C until use.
Prior to the Hi-C experiment, biotinylated bridge oligos were prepared as follows: 10 μl 10X NEBuffer 2 was mixed with 90 μl of a 100 μM mixture of the two oligos (Bridge oligo forward: GATCGAGCTCGAGAA/iBiodT/T, Bridge oligo reverse: CTCGAGCTC). The mixture was heated to 98°C for 6 min, then ramped down to RT at -0.1°C / sec and stored at -20°C until use. Antennal and eye discs were thawed on ice and 1 ml of lysis buffer (10 mM Tris-Cl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, 1x cOmplete protease inhibitor (Roche, Cat. No. 11 873 580 001)) was added. Samples were incubated on ice for 30 min and then spun at 1000g at 4°C for 5 min. The supernatant was removed and pellets were resuspended in 200 μl of 0.5% SDS and incubated at 65°C for 10 min. The SDS was then quenched by adding 100 μl of 10% Triton X-100 and incubating at 37°C for 15 min. 50 μl of 10x NEBuffer 3.1, 130 μl nuclease-free H2O and 8 μl of DpnII (NEB) were added and samples were incubated at 37°C overnight. Tubes were centrifuged for 5 min at 1000g at RT and pellets were resuspended in 30 μl nuclease-free H2O. 5 μl biotinylated bridge oligos (90 uM) were ligated to the DNA fragments overnight at 16°C using 1 μl of T4 DNA ligase HC (Thermo Fisher), 5 μl ligation buffer, 4 μl 10x BSA, and 5 μl PEG 4000. After adding 2.5 μl of 0.5 M EDTA, the samples were centrifuged at 1000g at RT for 5 min and resuspended in 300 μl 1x BSA and 0.2% SDS in water. The pellets were centrifuged again at 1000xg at RT for 5 min and the pellets were resuspended in 300 μl 1x BSA and 0.1% SDS in water. This step was repeated for a second time. After another centrifugation, the samples were resuspended in 245 μl of 1.22x BSA and 0.2% Triton X-100 in water. The bridge oligos were phosphorylated by adding 30 μl 10x T4 ligase buffer (Thermo Fisher) and 20 μl PNK (10 U/ μl, NEB). Tubes were incubated at 37°C for 1h. Bridge oligos were ligated to each other using 5 μl T4 DNA ligase HC (Thermo Fisher), 70 μl 10x T4 ligase buffer, 7 μl 100x BSA and 618 μl nuclease-free H2O. Samples were incubated for 4 h at RT. The samples were then spun down at 1000g at 4°C for 5 min and the pellet was resuspended in 500 μL of extraction buffer (50 mM Tris-Cl pH 8.0, 50 mM NaCl, 1 mM EDTA, 1% SDS). To digest proteins, 20 μL of 20 mg/ml Proteinase K (Invitrogen) was added and the mixture was incubated at 55°C at 1000 rpm on a thermal shaker for 30 min. For decrosslinking, 130 μL of 5 M sodium chloride were added and the mixture was incubated at 68°C at 1000 on a thermal shaker overnight. To precipitate DNA, 63 μL of 3 M sodium acetate pH 5.2, 2 μL of 15 mg/ml GlycoBlue (Thermo Fisher) and 1000 μL of absolute ethanol were mixed with the sample, followed by incubation at -80°C for 1 hour. The samples were then spun at 20,000xg at 4°C for one hour. The supernatant was removed and the DNA pellet was washed two times using 800 μL of 70% ethanol. All traces of remaining supernatant were removed; the was pellet air-dried for 2 min and then solubilized in 99 μl of 10 mM Tris-Cl pH 8.0. RNA was digested by incubation with 1 μL of 10 mg/ml RNase A at 37°C for 15 min. The DNA was sheared in a total volume of 100μl to ∼200-400 bp with Diagenode Bioruptor Pico (4°C, ON/OFF 30’’/90’’, 8 cycles). DNA fragments were size-selected with SPRIselect Beads (Beckman Coulter) following the manufacturer’s instructions. For right side size selection, 0.6x volume of beads were used, and for left side size selection 1x was used. DNA was eluted in 100μL of 10mM Tris-Cl pH 8.0. For biotin enrichment, 30 μl of Dynabeads Streptavidin M-280 (Life Technologies) per sample were prepared following the manufacturer’s instructions and added to the purified DNA. The biotinylated bridge oligos were allowed to bind to the beads for 20 min at RT. The beads were washed 4 times with 200 μL each of 1x B&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) + 0.1% Tween-20. This was followed by 2 washes with 10 mM Tris-Cl pH 8.0. The beads were then resuspended in 40 μL of the same solution. Library preparation was performed using the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit, with the following modification: throughout the library preparation there was no SPRIselect clean-up performed. Instead, the samples were washed using the already bound Streptavidin beads. Each of the SPRI steps were replaced by the washes described hereafter: Samples were placed against the magnet and incubated until the solution was clear. The supernatant was discarded and samples removed from the magnet. Beads were resuspended in 150 μL of 1x B&W buffer + 0.1% Tween-20, and incubated at 55°C in a thermal cycler for 2 min. This wash step was repeated a second time. An additional wash step with 100μL of 10 mM Tris-Cl pH 8.0 was performed. Here, the samples were immediately put against the magnet after resuspension, without any incubation. The supernatant was discarded and samples removed from the magnet. Beads were resuspended in the mixes as described in the Swift Biosciences Library Kit for Repair II, Ligation I and Ligation II. After Ligation II and the above described washes, beads were resuspended in 20μL of 10 mM Tris-Cl pH 8.0.

tag: developmental stage

value: third instar larvae

value: eye imaginal disc


title: Peritoneal macrophages, obtained from Angptl4-/- mice, PBS, 3 pooled samples.

source_name: Peritoneal macrophages were obtained from Angptl4-/- mice and incubated with phosphate-buffered saline (PBS) for 6 hrs. Pooled RNA of 3 samples.

value: PBS


title: KO2: 62-436_RNA_mut

value: lung


title: GATA1_CD34_rep2: CD34+ differentiated

source_name: CD34+ HSPC derived erythroid precursors

value: CD34+ HSPC derived erythroid precursors


title: AGM_144neg45+_rep3

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® MouseGene1.0st and MouseGene2.0st (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V19 was used for annotation.

source_name: E11.5 mouse AGM

label_protocol: around 5ng of total RNA is reverse transcribed  following the Ovation Pico System V2  (Nugen) Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3,6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen). After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MouseGene1.0st and MouseGene2.0st  (Affymetrix) at 45°C for 17 hours.

extract_protocol: RNeasy Plus Micro Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: AGM

tag: sorted cell


title: WT2: B6-17a_RNA_wt


title: HepG2.2.15 cells Sp110 siRNA treated Set 2

value: Male

value: hepatocellular carcinoma


title: AGM_144+45+_rep3


title: AGM_144+45neg_rep3


title: HepG2.2.15 cells Control siRNA treated Set 3

source_name: HepG2.2.15 cells Control siRNA treated

value: Liver

value: HepG2.2.15 (a HBV expressing cell-line)

value: control


title: WT1: B6-16b_RNA_wt


title: AGM_144+45+_rep2


title: HepG2.2.15 cells Sp110 siRNA treated Set 1

value: Sp110 knockdown


title: AGM_144neg45+_rep1


title: MDA-MB-231: Low Glucose vs High Glucose

city: Estado de Mexico

first: Rubi

last: Viedma

state: Estado de Mexico

address: Av. de los Barrios 1, Los Reyes Ixtacala,  Tlalnepantla,

department: bioquimica

country: Mexico

institute: unam

hyb_protocol: Similar quantities of fluorophores labeled cDNA were hybridized on the oligonucleotides collection 50-mer Human10K from MWG Biotech Oligo Bio Sets (Germany).

scan_protocol: Images of the microarrays were acquired and quantified in a Scan Array 4000 using the Quant Array software from Packard BioChips (USA).

data_processing:
A first analysis of the images and the data was performed using the Array-Pro Analyzer software from Media Cybernetics (USA).  Microarray data analysis was performed using the free software program genArise, allowing background correction, normalization, intensity filter, replicate analysis, and selection of differentially expressed genes; this program was developed in the Computing Unit of the Cellular Physiology Institute of the UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed.
The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean.
zi = (Ri – mean(R)) / sd(R)
Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.

source_name: high glucose

label_protocol: 10 μg of total RNA were obtained and used for cDNA synthesis and labeling with a Super Script II kit Invitrogen, using the dUTP-Cy3 incorporation array for BG (control) and dUTP-Cy5 for HG. Incorporation efficiency was analyzed measuring absorbance at 555 nm for Cy3 and 655 nm for Cy5.

growth_protocol: The cells were cultured in BG and HG media;

extract_protocol: total RNA extraction

source_name: low glucose


title: HepG2.2.15 cells Control siRNA treated Set 1


title: PC8_NoIndex_L006

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

data_processing:
50 bp Paired-read sequencing was performed on Illumina Genome Analyzer IIx.
Agilent Tapestation 2200 for library quality
Trimmed reads were then aligned using BWA (version 0.5.9, settings aln -o 1 -e 10 -i 5 -k 2 -t 8) against the Pneumocystis murina genome (courtesy of the Broad Institute) in geneSifter Analysis Edition for Next Generation Seqeucning (Geospiza, Seattle, WA)
Genome_build: Pneumocystis murina
Supplementary_files_format_and_content: Fastq files

organism: Pneumocystis murina

source_name: Trophs

growth_protocol: Pneumocystis was grown in the lungs of Rag2-/-Il2rg-/-  mice and isolated by BAL.

extract_protocol:
RNA was extracted from separated troph and asci life froms using the Illumina TruSeq Stranded mRNA sample preparation kit
The cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by using dUTP in the Second Strand Marking Mix, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H
cDNA libraries were validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorometer

treatment_protocol: Troph isolation was aided by the treamtent of Rag2-/-Il2rg-/- mice with micafungin, an echinocandin shown previously to deplete asci

tag: host strain

value: Rag2-/-Il2rg-/-  mice

tag: life form

value: Trophs


title: WT3: B6-18b_RNA_wt


title: GATA1_CD34_rep1: CD34+ differentiated

tag: cell type

value: erythroid


title: AGM_144neg45+_rep2


title: AGM_144+45+_rep1


title: AGM_144+45neg_rep1


title: AGM_144+45neg_rep2


title: PC2_NoIndex_L001

source_name: Asci

value: Asci


title: Wildtype control rep2

status: Public on Aug 23 2019

city: Tsukuba

first: Shogo

last: Matoba

state: Ibaraki

address: 3-1-1, Koyadai

institute: RIKEN BioResource Research Center

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (G4852B) at 65°C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images of microarray slides were processed using Feature Extraction software (Agilent Technologies). All raw data were loaded into Gene Spring GX 14.5 (Agilent Technologies) and signal intensities were normalized by shift to 75 percentile. Baseline was set to the median of all samples. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: placenta, E13.5, wildtype, B6N background

label_protocol: Total RNA (200 ng) was amplified and labeled with a Low Input Quick Amp Gene Expression Labeling Kit (#5190-2305, Agilent Technologies).

growth_protocol: C57BL/6N (B6N) mice were purchased from Japan Slc Inc.  The mutant mice for Slc38a4 allele were generated by using CRISPR/Cas9 system. They were housed under controlled lighting conditions (daily light period 07:00 to 21:00).

extract_protocol: Total RNA was extracted from E13.5 placentas using an RNeasy Mini Kit (Qiagen).

treatment_protocol: Whole placentas collected at E13.5 were cut into a half or quarter size.

tag: slc38a4 allele

value: wildtype


title: Paternal KO rep2

source_name: placenta, E13.5, Slc38a4 PKO, B6N background

tag: strain

value: heterozygous paternal knockout


title: CP-40_miRNA

city: Murcia

first: Angel

last: Esteban-Gil

state: Murcia

address: Campus de Ciencias de la Salud Carretera Buenavista s/n

department: Biomedical Informatics and Bioinformatics Platform

country: Spain

institute: Institute for Biomedical Research of Murcia (IMIB)

description: miRNA

data_processing: The Affymetrix raw data were normalized using the robust multichip average algorithm from ‘oligo’ Bioconductor package in R version 3.0.1. Normalized miRNA expression data were evaluated using Bioconductor LIMMA differential expression analysis.

source_name: Colorectal tissue

label_protocol: Total RNA was quantified by spectrometry (NanoDrop ND1000, NanoDrop Technologies, Wilminton, Delaware USA) and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies, Palo Alto, California USA) assay. Using NanoDrop measurements, an approximately 50 ng/ul dilution was prepared from each total RNA sample. All steps of the procedure were performed according to the Affymetrix standardized protocol for miRNA 3.0 arrays.

extract_protocol: A volume of approximately 10mm3 was extracted from each frozen tissue using the disposable sterile biopsy punch Acupunch 2mm (Acuderm Inc, Lauderdale, FL, USA). RNA was extracted following the manufacturer´s instructions (Qiagen, Hilden, Germany). Briefly, tissue was disrupted and homogenized in 700µl of Qiazol (Qiagen ref:1023537) using a Tissueruptor by Qiagen for 20 seconds. The homogenate was incubated at room temperature for 5 minutes. After adding 140µl of chloroform and centrifuging at 12,000xg for 15 minutes at 4ºC, 350µl of the aqueous phase was subjected to automatic total RNA extraction using the Qiacube equipment and the miRNeasy Mini Kit (ref:217004), both provided by Qiagen.

treatment_protocol: The clinico-pathological features of the patients have been previously reported. Updated follow-up information was obtained from cancer registry files and approval for the study was granted by the Local Ethical Board. SACs were diagnosed on the basis of criteria proposed by Mäkinen et al., and hmMSI-Hs according to prior established criteria (mucinous, signet-ring cell, and medullary carcinoma, tumor infiltrating and peritumoral lymphocytes, “Crohn-like” inflammatory response, poor differentiation, tumor heterogeneity, and “pushing” tumor border) and later cofirm using MSI-H testing (MSI Analysis System, version 1.2 provided by Promega (Madison, USA)).

tag: tissue

value: colorectal carcinomas

tag: Sex

value: female

tag: tumor type

value: Serrated Adenocarcinoma


title: CP-57_miRNA

description: miRNA

hyb_protocol: All steps of the procedure were performed according to the Affymetrix standardized protocol for miRNA 3.0 arrays.

value: Microsatellite Instable


title: CP-55_miRNA

description: miRNA

scan_protocol: All steps of the procedure were performed according to the Affymetrix standardized protocol for miRNA 3.0 arrays.

value: male


title: CP-33_miRNA

description: miRNA

value: Conventional Carcinoma


title: Null rep2

source_name: placenta, E13.5, Slc38a4 Null, B6N background

value: homozygous knockout


title: Paternal KO rep1


title: CP-51_miRNA

description: miRNA


title: Wildtype control rep1


title: Maternal KO rep2

source_name: placenta, E13.5, Slc38a4 MKO, B6N background

value: heterozygous maternal knockout


title: CP-43_miRNA

description: miRNA


title: CP-39_miRNA

description: miRNA


title: CP-59_miRNA

description: miRNA


title: CP-72_miRNA

description: miRNA


title: CP-82_miRNA

description: miRNA


title: CP-50_miRNA

description: miRNA


title: Null rep1


title: CP-28_miRNA

description: miRNA


title: CP-44_miRNA

description: miRNA


title: CP-41_miRNA

description: miRNA


title: CP-47_miRNA

description: miRNA


title: A12

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Data were analyzed using Cell Ranger™ v1.3 pipelines and were visualized by Loupe™ Cell Browser. Both are available in 10x Genomics website.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: h5 format: Contains the per molecule read information from Cell Ranger. The instructions to read the matrix in hdf5 format can be found here: https://support.10xgenomics.com/single-cell/software/pipelines/latest/advanced/h5_matrices

source_name: total aorta without macroscopically visible atherosclerotic plaques

extract_protocol: Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10x Genomics). The detailed protocol was provided by 10x Genomics.

treatment_protocol: Macroscopically visible atherosclerotic plaques were manually removed from the aorta any enzymatically digested before CD45+ cell sorting

tag: genotype/variation

value: Ldlr-/-

tag: cell marker

tag: treatment

value: 10 weeks high fat, high cholesterol diet


title: A11

source_name: plaque tissue


title: Maternal KO rep1


title: CP-52_miRNA

description: miRNA


title: CP-32_miRNA

description: miRNA


title: CP-37_miRNA

description: miRNA


title: CP-35_miRNA

description: miRNA


title: input DNA (5257)

first: William

last: Muller

state: Quebec

address: 1160 Avenue des Pins

description: 5257 +DMSO

data_processing:
After isolation of the DNA, it was sequenced using AAA base pair Paired end sequencing and reported as .fastq files
Data was assayed for quality through the use of FASTQC and processed using trimmomatic
Drosophila and mouse DNA was aligned to the BDGP6 and mm10 reference genomes respectively through the use of BWA
As previously described the mouse data was normalized to remove background noise through the removal of random reads through the use of the drosophila data
Genome_build: mm10
Supplementary_files_format_and_content: After the removal of PCR bias and other artifacts through the use of SAMtools and PICARD tools using default parameters, broad peaks were called through the use of MACS2 with default parameters

source_name: NIC mouse model

growth_protocol: Breast cancer cell lines were established from the MMTV-NIC (ErbB2-IRES-Cre) model (PMID: 18273058, Ursini-Siegel et al.) and routinely cultured in DMEM supplemented with 5% FBS, EGF (5 ng/ml), Hydrocortisone (1 μg/ml), Insulin (5 μg/ml) and Bovine Pituitary Extract (BPE) (35μg/ml)). Cells were grown in a humidified, 5% CO2, 37°C incubator

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody (Millopre H3K27me3, Cat# 07-449)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were treated with 2uM GSK-126 or DMSO for 96 hours prior to cross linking

value: Mouse Mammary Tumor cells

tag: passages

value: 10-15 passages

value: FVB/N

tag: chip antibody

value: DMSO


title: CP-36_miRNA

description: miRNA


title: H3K27me3_ChIPSeq (9822) GSK-126

description: 9822+ GSK-126

value: H3K27me3 (Millipore, Cat# 07-449)


title: H3K27me3_ChIPSeq (5257) GSK-126

description: 5257 + GSK-126


title: H3K27me3_ChIPSeq (5257) DMSO

description: 5257 +DMSO


title: H3K27me3_ChIPSeq (9822) DMSO

description: 9822 +DMSO


title: CP-30_miRNA

description: miRNA


title: CP-27_miRNA

description: miRNA


title: PFHT1_ROW40_9_R2

city: Genève 4

first: Quentin

last: Lo Giudice

state: switzerland

address: 1 rue Michel Servet

department: Department of Basic Neurosciences

country: Switzerland

institute: University of Geneva

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using star.
After the counting, Seurat package version 2.3 (Butler et al., 2018) was used to import in R version 3.4.4 (R Core Team) to perform downstream analysis. The left part of the chip (column 1-10) are Tomato positive sorted cells. Column 11-20 are Tomato negative.
For NormalizedCounts, Read Per Million scaling was performed, Cells considered expressed at least 200 genes, and genes kept are expressed in a minimum of 3 cells.  Cells expressing more than 0.25 mitochindrial genes were removed. Dataset was Log-normalized.
Genome_build: mm10
Supplementary_files_format_and_content: CountsC1.csv : comma-delimited text files (csv) including counts values for each cells.

source_name: Retinal E15.5 cells

extract_protocol:
Coordinated pregnant mice of 12 to 30 weeks were ethically sacrificed to extract E15.5 embryos eyes. Thirty retinas were extracted in ice-cold L15, micro-dissected under a stereomicroscope and incubated in 200µl single cell dissociation solution consisting in a papain (1mg/ml) enriched HBSS at 37°C for 12 minutes with trituration every 2 minutes. At the end of the incubation time, cells were further dissociated via gentle up-and-down pipetting. Reaction was stopped with the addition of 400µl of ovalbumin enriched cold HBSS and the cell suspension was then passed on a 40µm cell strainer to remove cellular aggregates.  Cells were then centrifuged 5 min at 500 G at 4°C. After removal of the liquid, the pellet was suspended in 250µl of cold HBSS and the resulting solution was finally FAC-sorted on a MoFloAstrios device (Beckman) to reach a concentration of 410 cells /µl.
The libraries of single-cells were prepared using the SmartSeq2 platform following the manufacturer’s protocol.

value: retina

value: embryonic E15.5

tag: genotype

value: Tomato+


title: CP-3_miRNA

description: miRNA

value: colorectal carcinomas

tag: age


title: CP-26_miRNA

description: miRNA

value: female


title: PFHT1_ROW40_7_R2

tag: developmental stage


title: PFHT1_ROW40_6_R2


title: CP-12_miRNA

description: miRNA

value: Microsatellite Instable


title: CP-14_miRNA

description: miRNA

value: male

value: Serrated Adenocarcinoma


title: HepG2.2.15 cells Control siRNA treated Set 2

tag: gender

value: Male

tag: disease state

value: hepatocellular carcinoma

value: Liver

tag: cell line

value: HepG2.2.15 (a HBV expressing cell-line)

value: control


title: input DNA (9822)

tag: cell type

value: Mouse Mammary Tumor cells

value: 10-15 passages


title: CP-23_miRNA

description: miRNA


title: PFHT1_ROW40_4_R2


title: CP-5_miRNA

description: miRNA


title: CP-1_miRNA

description: miRNA


title: PFHT1_ROW40_5_R2


title: CP-16_miRNA

description: miRNA

value: Conventional Carcinoma


title: PFHT1_ROW40_8_R2


title: PFHT1_ROW40_20_R2

value: Tomato-


title: PFHT1_ROW40_2_R2

value: retina


title: PFHT1_ROW40_1_R2

value: embryonic E15.5


title: PFHT1_ROW40_3_R2

value: Tomato+


title: PFHT1_ROW40_19_R2


title: PFHT1_ROW40_18_R2


title: PFHT1_ROW40_16_R2


title: PFHT1_ROW40_15_R2


title: PFHT1_ROW40_12_R2


title: PFHT1_ROW40_11_R2


title: PFHT1_ROW39_9_R2


title: PFHT1_ROW39_7_R2


title: PFHT1_ROW39_8_R2


title: PFHT1_ROW39_6_R2


title: PFHT1_ROW39_5_R2


title: PFHT1_ROW39_3_R2


title: PFHT1_ROW39_20_R2


title: PFHT1_ROW39_2_R2


title: PFHT1_ROW39_18_R2


title: PFHT1_ROW39_19_R2


title: PFHT1_ROW39_16_R2


title: PFHT1_ROW39_17_R2


title: PFHT1_ROW40_14_R2


title: PFHT1_ROW40_13_R2


title: PFHT1_ROW39_15_R2


title: PFHT1_ROW39_12_R2


title: PFHT1_ROW39_14_R2


title: PFHT1_ROW39_10_R2


title: PFHT1_ROW39_13_R2


title: PFHT1_ROW38_7_R2


title: PFHT1_ROW38_8_R2


title: PFHT1_ROW38_6_R2


title: PFHT1_ROW40_10_R2


title: PFHT1_ROW39_4_R2


title: PFHT1_ROW38_4_R2


title: PFHT1_ROW38_2_R2


title: PFHT1_ROW38_3_R2


title: PFHT1_ROW38_20_R2


title: PFHT1_ROW38_19_R2


title: PFHT1_ROW39_1_R2


title: PFHT1_ROW38_1_R2


title: PFHT1_ROW39_11_R2


title: PFHT1_ROW38_15_R2


title: PFHT1_ROW38_17_R2


title: PFHT1_ROW38_18_R2


title: PFHT1_ROW38_16_R2


title: PFHT1_ROW38_14_R2


title: PFHT1_ROW38_10_R2


title: PFHT1_ROW38_9_R2


title: PFHT1_ROW37_7_R2


title: PFHT1_ROW37_8_R2


title: PFHT1_ROW37_6_R2


title: PFHT1_ROW40_17_R2


title: PFHT1_ROW38_12_R2


title: PFHT1_ROW38_5_R2


title: PFHT1_ROW38_13_R2


title: PFHT1_ROW37_9_R2


title: PFHT1_ROW38_11_R2


title: PFHT1_ROW37_3_R2


title: PFHT1_ROW37_2_R2


title: PFHT1_ROW37_5_R2


title: PFHT1_ROW37_4_R2


title: PFHT1_ROW37_20_R2


title: PFHT1_ROW37_1_R2


title: PFHT1_ROW37_18_R2


title: PFHT1_ROW37_19_R2


title: PFHT1_ROW37_17_R2


title: PFHT1_ROW37_15_R2


title: PFHT1_ROW37_11_R2


title: PFHT1_ROW37_12_R2


title: PFHT1_ROW37_13_R2


title: PFHT1_ROW36_9_R2


title: PFHT1_ROW37_10_R2


title: PFHT1_ROW36_5_R2


title: PFHT1_ROW36_4_R2


title: PFHT1_ROW36_7_R2


title: PFHT1_ROW36_3_R2


title: PFHT1_ROW36_20_R2


title: PFHT1_ROW36_8_R2


title: PFHT1_ROW36_6_R2


title: PFHT1_ROW36_17_R2


title: PFHT1_ROW36_16_R2


title: PFHT1_ROW36_19_R2


title: PFHT1_ROW36_1_R2


title: PFHT1_ROW36_15_R2


title: PFHT1_ROW36_18_R2


title: PFHT1_ROW36_14_R2


title: PFHT1_ROW37_16_R2


title: PFHT1_ROW36_12_R2


title: PFHT1_ROW36_13_R2


title: PFHT1_ROW36_11_R2


title: PFHT1_ROW35_9_R2


title: PFHT1_ROW36_10_R2


title: PFHT1_ROW37_14_R2


title: PFHT1_ROW35_8_R2


title: PFHT1_ROW35_6_R2


title: PFHT1_ROW35_5_R2


title: PFHT1_ROW35_4_R2


title: PFHT1_ROW35_7_R2


title: PFHT1_ROW36_2_R2


title: PFHT1_ROW35_3_R2


title: PFHT1_ROW35_20_R2


title: PFHT1_ROW35_19_R2


title: PFHT1_ROW35_16_R2


title: PFHT1_ROW35_18_R2


title: PFHT1_ROW35_17_R2


title: PFHT1_ROW35_15_R2


title: PFHT1_ROW35_14_R2


title: PFHT1_ROW35_1_R2


title: PFHT1_ROW35_12_R2


title: PFHT1_ROW35_11_R2


title: PFHT1_ROW35_13_R2


title: PFHT1_ROW35_10_R2


title: PFHT1_ROW34_9_R2


title: PFHT1_ROW34_8_R2


title: PFHT1_ROW34_7_R2


title: PFHT1_ROW34_5_R2


title: PFHT1_ROW34_6_R2


title: PFHT1_ROW34_4_R2


title: PFHT1_ROW34_3_R2


title: PFHT1_ROW34_2_R2


title: PFHT1_ROW34_20_R2


title: PFHT1_ROW35_2_R2


title: PFHT1_ROW34_17_R2


title: PFHT1_ROW34_1_R2


title: PFHT1_ROW34_19_R2


title: PFHT1_ROW34_16_R2


title: PFHT1_ROW34_18_R2


title: PFHT1_ROW34_13_R2


title: PFHT1_ROW34_10_R2


title: PFHT1_ROW33_9_R2


title: PFHT1_ROW34_12_R2


title: PFHT1_ROW34_15_R2


title: PFHT1_ROW34_11_R2


title: PFHT1_ROW33_8_R2


title: PFHT1_ROW33_6_R2


title: PFHT1_ROW33_5_R2


title: PFHT1_ROW33_3_R2


title: PFHT1_ROW33_20_R2


title: PFHT1_ROW33_4_R2


title: PFHT1_ROW33_2_R2


title: PFHT1_ROW33_7_R2


title: PFHT1_ROW33_16_R2


title: PFHT1_ROW33_19_R2


title: PFHT1_ROW33_17_R2


title: PFHT1_ROW33_18_R2


title: PFHT1_ROW33_15_R2


title: PFHT1_ROW33_13_R2


title: PFHT1_ROW34_14_R2


title: PFHT1_ROW33_12_R2


title: PFHT1_ROW33_10_R2


title: PFHT1_ROW33_11_R2


title: PFHT1_ROW32_9_R2


title: PFHT1_ROW32_7_R2


title: PFHT1_ROW32_8_R2


title: PFHT1_ROW32_6_R2


title: PFHT1_ROW32_5_R2


title: PFHT1_ROW32_2_R2


title: PFHT1_ROW32_1_R2


title: PFHT1_ROW32_3_R2


title: PFHT1_ROW33_1_R2


title: PFHT1_ROW32_4_R2


title: PFHT1_ROW32_15_R2


title: PFHT1_ROW32_18_R2


title: PFHT1_ROW32_16_R2


title: PFHT1_ROW32_19_R2


title: PFHT1_ROW32_17_R2


title: PFHT1_ROW32_14_R2


title: PFHT1_ROW33_14_R2


title: PFHT1_ROW32_13_R2


title: TAL1_HUDEP2: HUDEP2 differentiated

source_name: human umbilical cord blood-derived erythroid progenitor (HUDEP)

value: erythroid

tag: differentiation days

tag: replicate

tag: antibody


title: PFHT1_ROW32_10_R2

tag: strain

tag: tissue


title: PFHT1_ROW32_11_R2


title: PFHT1_ROW31_9_R2


title: PFHT1_ROW31_8_R2


title: PFHT1_ROW31_7_R2


title: PFHT1_ROW31_6_R2


title: PFHT1_ROW31_5_R2


title: PFHT1_ROW31_1_R2


title: PFHT1_ROW31_20_R2


title: PFHT1_ROW31_2_R2


title: PFHT1_ROW31_3_R2


title: PFHT1_ROW32_20_R2


title: PFHT1_ROW31_19_R2


title: PFHT1_ROW31_18_R2


title: PFHT1_ROW31_16_R2


title: PFHT1_ROW31_17_R2


title: PFHT1_ROW31_15_R2


title: PFHT1_ROW31_14_R2


title: PFHT1_ROW31_11_R2


title: PFHT1_ROW32_12_R2


title: PFHT1_ROW30_9_R2


title: PFHT1_ROW31_12_R2


title: PFHT1_ROW30_8_R2


title: PFHT1_ROW31_13_R2


title: PFHT1_ROW30_6_R2


title: PFHT1_ROW30_2_R2


title: PFHT1_ROW30_7_R2


title: PFHT1_ROW30_5_R2


title: PFHT1_ROW30_3_R2


title: PFHT1_ROW30_20_R2


title: PFHT1_ROW30_19_R2


title: PFHT1_ROW30_4_R2


title: PFHT1_ROW31_4_R2


title: PFHT1_ROW30_15_R2


title: PFHT1_ROW30_16_R2


title: PFHT1_ROW30_17_R2


title: PFHT1_ROW30_18_R2


title: PFHT1_ROW30_14_R2


title: PFHT1_ROW30_13_R2


title: PFHT1_ROW30_12_R2


title: PFHT1_ROW30_11_R2


title: PFHT1_ROW31_10_R2


title: PFHT1_ROW29_9_R2


title: PFHT1_ROW29_8_R2


title: PFHT1_ROW29_7_R2


title: PFHT1_ROW29_6_R2


title: PFHT1_ROW29_3_R2


title: PFHT1_ROW29_2_R2


title: PFHT1_ROW29_4_R2


title: PFHT1_ROW29_1_R2


title: PFHT1_ROW30_1_R2


title: PFHT1_ROW29_19_R2


title: PFHT1_ROW29_17_R2


title: PFHT1_ROW29_15_R2


title: PFHT1_ROW29_16_R2


title: PFHT1_ROW29_13_R2


title: PFHT1_ROW29_18_R2


title: PFHT1_ROW29_12_R2


title: PFHT1_ROW29_11_R2


title: PFHT1_ROW28_8_R2


title: PFHT1_ROW28_9_R2


title: PFHT1_ROW29_10_R2


title: PFHT1_ROW28_7_R2


title: PFHT1_ROW28_6_R2


title: PFHT1_ROW30_10_R2


title: PFHT1_ROW28_4_R2


title: PFHT1_ROW28_5_R2


title: PFHT1_ROW28_2_R2


title: PFHT1_ROW29_5_R2


title: PFHT1_ROW28_20_R2


title: PFHT1_ROW28_1_R2


title: PFHT1_ROW29_20_R2


title: PFHT1_ROW28_19_R2


title: PFHT1_ROW28_17_R2


title: PFHT1_ROW28_16_R2


title: PFHT1_ROW28_15_R2


title: PFHT1_ROW29_14_R2


title: PFHT1_ROW28_13_R2


title: PFHT1_ROW28_14_R2


title: PFHT1_ROW28_18_R2


title: PFHT1_ROW27_7_R2


title: PFHT1_ROW27_6_R2


title: PFHT1_ROW28_10_R2


title: PFHT1_ROW27_8_R2


title: PFHT1_ROW28_12_R2


title: PFHT1_ROW28_11_R2


title: PFHT1_ROW27_9_R2


title: PFHT1_ROW27_3_R2


title: PFHT1_ROW27_4_R2


title: PFHT1_ROW27_20_R2


title: PFHT1_ROW27_1_R2


title: PFHT1_ROW28_3_R2


title: PFHT1_ROW27_5_R2


title: PFHT1_ROW27_19_R2


title: PFHT1_ROW27_18_R2


title: PFHT1_ROW27_15_R2


title: PFHT1_ROW27_12_R2


title: PFHT1_ROW27_16_R2


title: PFHT1_ROW27_13_R2


title: PFHT1_ROW27_17_R2


title: PFHT1_ROW27_14_R2


title: PFHT1_ROW27_11_R2


title: PFHT1_ROW26_8_R2


title: PFHT1_ROW26_7_R2


title: PFHT1_ROW26_6_R2


title: PFHT1_ROW26_5_R2


title: PFHT1_ROW26_9_R2


title: PFHT1_ROW26_4_R2


title: PFHT1_ROW27_2_R2


title: PFHT1_ROW26_20_R2


title: PFHT1_ROW26_1_R2


title: PFHT1_ROW26_19_R2


title: PFHT1_ROW26_2_R2


title: PFHT1_ROW26_17_R2


title: PFHT1_ROW26_18_R2


title: PFHT1_ROW26_14_R2


title: PFHT1_ROW26_15_R2


title: PFHT1_ROW26_3_R2


title: PFHT1_ROW26_12_R2


title: PFHT1_ROW26_11_R2


title: PFHT1_ROW26_16_R2


title: PFHT1_ROW26_10_R2


title: PFHT1_ROW25_9_R2


title: PFHT1_ROW25_7_R2


title: PFHT1_ROW25_8_R2


title: PFHT1_ROW27_10_R2


title: PFHT1_ROW25_6_R2


title: PFHT1_ROW25_5_R2


title: PFHT1_ROW25_4_R2


title: PFHT1_ROW25_3_R2


title: PFHT1_ROW25_1_R2


title: PFHT1_ROW25_20_R2


title: PFHT1_ROW25_19_R2


title: PFHT1_ROW25_18_R2


title: PFHT1_ROW25_17_R2


title: PFHT1_ROW26_13_R2


title: PFHT1_ROW25_16_R2


title: PFHT1_ROW25_12_R2


title: PFHT1_ROW25_11_R2


title: PFHT1_ROW25_10_R2


title: PFHT1_ROW24_9_R2


title: PFHT1_ROW25_13_R2


title: PFHT1_ROW24_4_R2


title: PFHT1_ROW24_2_R2


title: PFHT1_ROW24_6_R2


title: PFHT1_ROW25_15_R2


title: PFHT1_ROW24_5_R2


title: PFHT1_ROW25_14_R2


title: PFHT1_ROW24_3_R2


title: PFHT1_ROW24_7_R2


title: PFHT1_ROW24_8_R2


title: PFHT1_ROW24_20_R2


title: PFHT1_ROW25_2_R2


title: PFHT1_ROW24_19_R2


title: PFHT1_ROW24_17_R2


title: PFHT1_ROW24_16_R2


title: PFHT1_ROW24_18_R2


title: PFHT1_ROW24_13_R2


title: PFHT1_ROW24_11_R2


title: PFHT1_ROW24_15_R2


title: PFHT1_ROW24_12_R2


title: PFHT1_ROW24_1_R2


title: PFHT1_ROW24_14_R2


title: PFHT1_ROW23_9_R2


title: PFHT1_ROW23_7_R2


title: PFHT1_ROW23_8_R2


title: PFHT1_ROW23_6_R2


title: PFHT1_ROW23_2_R2


title: PFHT1_ROW23_1_R2


title: PFHT1_ROW23_20_R2


title: PFHT1_ROW23_18_R2


title: PFHT1_ROW23_14_R2


title: PFHT1_ROW23_19_R2


title: PFHT1_ROW23_13_R2


title: PFHT1_ROW23_17_R2


title: PFHT1_ROW24_10_R2


title: PFHT1_ROW23_10_R2


title: PFHT1_ROW22_9_R2


title: PFHT1_ROW23_12_R2


title: PFHT1_ROW22_8_R2


title: PFHT1_ROW23_11_R2


title: PFHT1_ROW22_7_R2


title: PFHT1_ROW22_6_R2


title: PFHT1_ROW22_5_R2


title: PFHT1_ROW22_3_R2


title: PFHT1_ROW22_2_R2


title: PFHT1_ROW23_4_R2


title: PFHT1_ROW23_3_R2


title: PFHT1_ROW23_5_R2


title: PFHT1_ROW23_15_R2


title: PFHT1_ROW23_16_R2


title: PFHT1_ROW22_13_R2


title: PFHT1_ROW22_12_R2


title: PFHT1_ROW22_11_R2


title: PFHT1_ROW22_14_R2


title: PFHT1_ROW22_17_R2


title: PFHT1_ROW22_10_R2


title: PFHT1_ROW22_18_R2


title: PFHT1_ROW22_16_R2


title: PFHT1_ROW21_9_R2


title: PFHT1_ROW22_19_R2


title: PFHT1_ROW22_15_R2


title: PFHT1_ROW21_6_R2


title: PFHT1_ROW21_5_R2


title: PFHT1_ROW21_4_R2


title: PFHT1_ROW21_7_R2


title: PFHT1_ROW21_3_R2


title: PFHT1_ROW22_4_R2


title: PFHT1_ROW21_2_R2


title: PFHT1_ROW21_1_R2


title: PFHT1_ROW21_8_R2


title: PFHT1_ROW22_20_R2


title: PFHT1_ROW22_1_R2


title: PFHT1_ROW21_20_R2


title: PFHT1_ROW21_19_R2


title: PFHT1_ROW21_18_R2


title: PFHT1_ROW21_16_R2


title: PFHT1_ROW21_17_R2


title: PFHT1_ROW21_14_R2


title: PFHT1_ROW21_15_R2


title: PFHT1_ROW21_13_R2


title: PFHT1_ROW21_11_R2


title: PFHT1_ROW20_7_R2


title: PFHT1_ROW20_6_R2


title: PFHT1_ROW20_9_R2


title: PFHT1_ROW20_8_R2


title: PFHT1_ROW20_3_R2


title: PFHT1_ROW20_2_R2


title: PFHT1_ROW21_12_R2


title: PFHT1_ROW20_20_R2


title: PFHT1_ROW20_18_R2


title: PFHT1_ROW20_4_R2


title: PFHT1_ROW20_1_R2


title: PFHT1_ROW20_17_R2


title: PFHT1_ROW20_14_R2


title: PFHT1_ROW20_15_R2


title: PFHT1_ROW20_11_R2


title: PFHT1_ROW20_16_R2


title: PFHT1_ROW19_9_R2


title: PFHT1_ROW20_10_R2


title: PFHT1_ROW20_13_R2


title: PFHT1_ROW20_12_R2


title: PFHT1_ROW19_8_R2


title: PFHT1_ROW19_6_R2


title: PFHT1_ROW19_7_R2


title: PFHT1_ROW19_5_R2


title: PFHT1_ROW19_4_R2


title: PFHT1_ROW20_5_R2


title: PFHT1_ROW21_10_R2


title: PFHT1_ROW20_19_R2


title: PFHT1_ROW19_20_R2


title: PFHT1_ROW19_3_R2


title: PFHT1_ROW19_18_R2


title: PFHT1_ROW19_1_R2


title: PFHT1_ROW19_19_R2


title: PFHT1_ROW19_17_R2


title: PFHT1_ROW19_14_R2


title: PFHT1_ROW19_16_R2


title: PFHT1_ROW19_13_R2


title: PFHT1_ROW19_15_R2


title: PFHT1_ROW19_10_R2


title: PFHT1_ROW19_12_R2


title: PFHT1_ROW19_11_R2


title: PFHT1_ROW18_8_R2


title: PFHT1_ROW18_6_R2


title: PFHT1_ROW18_5_R2


title: PFHT1_ROW18_4_R2


title: PFHT1_ROW18_2_R2


title: PFHT1_ROW18_7_R2


title: PFHT1_ROW18_9_R2


title: PFHT1_ROW18_3_R2


title: PFHT1_ROW18_18_R2


title: PFHT1_ROW18_19_R2


title: PFHT1_ROW18_17_R2


title: PFHT1_ROW18_20_R2


title: PFHT1_ROW19_2_R2


title: PFHT1_ROW18_1_R2


title: PFHT1_ROW18_14_R2


title: PFHT1_ROW18_15_R2


title: PFHT1_ROW18_16_R2


title: PFHT1_ROW18_12_R2


title: PFHT1_ROW18_11_R2


title: PFHT1_ROW17_9_R2


title: PFHT1_ROW17_8_R2


title: PFHT1_ROW17_7_R2


title: PFHT1_ROW18_10_R2


title: PFHT1_ROW17_4_R2


title: PFHT1_ROW17_2_R2


title: PFHT1_ROW17_5_R2


title: PFHT1_ROW17_6_R2


title: PFHT1_ROW17_3_R2


title: PFHT1_ROW17_20_R2


title: PFHT1_ROW17_18_R2


title: PFHT1_ROW17_19_R2


title: PFHT1_ROW17_16_R2


title: PFHT1_ROW17_17_R2


title: PFHT1_ROW17_1_R2


title: PFHT1_ROW17_15_R2


title: PFHT1_ROW17_11_R2


title: PFHT1_ROW17_12_R2


title: PFHT1_ROW17_14_R2


title: PFHT1_ROW17_13_R2


title: PFHT1_ROW17_10_R2


title: PFHT1_ROW16_9_R2


title: PFHT1_ROW16_8_R2


title: PFHT1_ROW18_13_R2


title: PFHT1_ROW16_7_R2


title: PFHT1_ROW16_6_R2


title: PFHT1_ROW16_5_R2


title: PFHT1_ROW16_3_R2


title: PFHT1_ROW16_4_R2


title: PFHT1_ROW16_19_R2


title: PFHT1_ROW16_18_R2


title: PFHT1_ROW16_20_R2


title: PFHT1_ROW16_16_R2


title: PFHT1_ROW16_17_R2


title: PFHT1_ROW16_14_R2


title: PFHT1_ROW16_15_R2


title: PFHT1_ROW16_10_R2


title: PFHT1_ROW16_13_R2


title: PFHT1_ROW15_9_R2


title: PFHT1_ROW15_8_R2


title: PFHT1_ROW15_7_R2


title: PFHT1_ROW15_6_R2


title: PFHT1_ROW15_2_R2


title: PFHT1_ROW15_5_R2


title: PFHT1_ROW15_4_R2


title: PFHT1_ROW15_3_R2


title: PFHT1_ROW15_20_R2


title: PFHT1_ROW15_1_R2


title: PFHT1_ROW15_19_R2


title: PFHT1_ROW15_18_R2


title: PFHT1_ROW16_2_R2


title: PFHT1_ROW16_1_R2


title: PFHT1_ROW15_16_R2


title: PFHT1_ROW15_15_R2


title: PFHT1_ROW15_17_R2


title: PFHT1_ROW15_14_R2


title: PFHT1_ROW15_13_R2


title: PFHT1_ROW16_12_R2


title: PFHT1_ROW15_11_R2


title: PFHT1_ROW14_9_R2


title: PFHT1_ROW14_8_R2


title: PFHT1_ROW16_11_R2


title: PFHT1_ROW14_7_R2


title: PFHT1_ROW14_6_R2


title: PFHT1_ROW14_3_R2


title: PFHT1_ROW14_2_R2


title: PFHT1_ROW14_20_R2


title: PFHT1_ROW14_1_R2


title: PFHT1_ROW14_5_R2


title: PFHT1_ROW14_17_R2


title: PFHT1_ROW14_19_R2


title: PFHT1_ROW14_18_R2


title: PFHT1_ROW14_4_R2


title: PFHT1_ROW14_14_R2


title: PFHT1_ROW14_15_R2


title: PFHT1_ROW14_13_R2


title: PFHT1_ROW14_10_R2


title: PFHT1_ROW14_12_R2


title: PFHT1_ROW13_7_R2


title: PFHT1_ROW13_9_R2


title: PFHT1_ROW13_6_R2


title: PFHT1_ROW14_11_R2


title: PFHT1_ROW13_8_R2


title: PFHT1_ROW13_5_R2


title: PFHT1_ROW13_4_R2


title: PFHT1_ROW13_1_R2


title: PFHT1_ROW15_10_R2


title: PFHT1_ROW13_20_R2


title: PFHT1_ROW13_2_R2


title: PFHT1_ROW13_3_R2


title: PFHT1_ROW14_16_R2


title: PFHT1_ROW13_12_R2


title: PFHT1_ROW13_15_R2


title: PFHT1_ROW13_11_R2


title: PFHT1_ROW13_17_R2


title: PFHT1_ROW12_9_R2


title: PFHT1_ROW13_10_R2


title: PFHT1_ROW13_13_R2


title: PFHT1_ROW13_14_R2


title: PFHT1_ROW12_7_R2


title: PFHT1_ROW12_6_R2


title: PFHT1_ROW12_4_R2


title: PFHT1_ROW12_3_R2


title: PFHT1_ROW12_5_R2


title: PFHT1_ROW12_20_R2


title: PFHT1_ROW12_2_R2


title: PFHT1_ROW12_17_R2


title: PFHT1_ROW13_18_R2


title: PFHT1_ROW13_19_R2


title: PFHT1_ROW12_19_R2


title: PFHT1_ROW12_18_R2


title: PFHT1_ROW12_16_R2


title: PFHT1_ROW12_14_R2


title: PFHT1_ROW12_15_R2


title: PFHT1_ROW12_12_R2


title: PFHT1_ROW13_16_R2


title: PFHT1_ROW12_11_R2


title: PFHT1_ROW12_8_R2


title: PFHT1_ROW11_7_R2


title: PFHT1_ROW12_10_R2


title: PFHT1_ROW11_3_R2


title: PFHT1_ROW11_8_R2


title: PFHT1_ROW11_6_R2


title: PFHT1_ROW11_4_R2


title: PFHT1_ROW11_9_R2


title: PFHT1_ROW11_5_R2


title: PFHT1_ROW11_1_R2


title: PFHT1_ROW12_13_R2


title: PFHT1_ROW11_20_R2


title: PFHT1_ROW11_19_R2


title: PFHT1_ROW11_18_R2


title: PFHT1_ROW11_2_R2


title: PFHT1_ROW11_16_R2


title: PFHT1_ROW11_17_R2


title: PFHT1_ROW11_13_R2


title: PFHT1_ROW11_11_R2


title: PFHT1_ROW11_15_R2


title: PFHT1_ROW11_14_R2


title: PFHT1_ROW11_10_R2


title: PFHT1_ROW11_12_R2


title: PFHT1_ROW10_7_R2


title: PFHT1_ROW10_8_R2


title: PFHT1_ROW10_6_R2


title: PFHT1_ROW10_4_R2


title: PFHT1_ROW10_5_R2


title: PFHT1_ROW10_3_R2


title: PFHT1_ROW10_2_R2


title: PFHT1_ROW10_18_R2


title: PFHT1_ROW10_16_R2


title: PFHT1_ROW10_19_R2


title: PFHT1_ROW10_1_R2


title: PFHT1_ROW10_15_R2


title: PFHT1_ROW10_20_R2


title: PFHT1_ROW10_11_R2


title: PFHT1_ROW10_10_R2


title: PFHT1_ROW09_8_R2


title: PFHT1_ROW10_13_R2


title: PFHT1_ROW09_9_R2


title: PFHT1_ROW10_9_R2


title: PFHT1_ROW10_12_R2


title: PFHT1_ROW10_14_R2


title: PFHT1_ROW09_5_R2


title: PFHT1_ROW09_4_R2


title: PFHT1_ROW09_6_R2


title: PFHT1_ROW09_2_R2


title: PFHT1_ROW09_3_R2


title: PFHT1_ROW09_7_R2


title: PFHT1_ROW09_1_R2


title: PFHT1_ROW09_19_R2


title: PFHT1_ROW09_17_R2


title: PFHT1_ROW09_18_R2


title: PFHT1_ROW09_16_R2


title: PFHT1_ROW09_15_R2


title: PFHT1_ROW09_14_R2


title: PFHT1_ROW09_10_R2


title: PFHT1_ROW09_13_R2


title: PFHT1_ROW10_17_R2


title: PFHT1_ROW09_11_R2


title: PFHT1_ROW08_5_R2


title: PFHT1_ROW08_9_R2


title: PFHT1_ROW08_8_R2


title: PFHT1_ROW08_2_R2


title: PFHT1_ROW08_4_R2


title: PFHT1_ROW08_20_R2


title: PFHT1_ROW08_3_R2


title: PFHT1_ROW08_7_R2


title: PFHT1_ROW08_19_R2


title: PFHT1_ROW08_15_R2


title: PFHT1_ROW08_17_R2


title: PFHT1_ROW08_14_R2


title: PFHT1_ROW08_1_R2


title: PFHT1_ROW08_18_R2


title: PFHT1_ROW08_6_R2


title: PFHT1_ROW08_13_R2


title: PFHT1_ROW08_12_R2


title: PFHT1_ROW09_12_R2


title: PFHT1_ROW08_10_R2


title: PFHT1_ROW08_11_R2


title: PFHT1_ROW07_8_R2


title: PFHT1_ROW07_7_R2


title: PFHT1_ROW09_20_R2


title: PFHT1_ROW08_16_R2


title: PFHT1_ROW07_5_R2


title: PFHT1_ROW07_2_R2


title: PFHT1_ROW07_20_R2


title: PFHT1_ROW07_3_R2


title: PFHT1_ROW07_19_R2


title: PFHT1_ROW15_12_R2


title: PFHT1_ROW07_18_R2


title: PFHT1_ROW07_17_R2


title: PFHT1_ROW07_12_R2


title: PFHT1_ROW07_13_R2


title: PFHT1_ROW07_11_R2


title: PFHT1_ROW07_10_R2


title: PFHT1_ROW06_8_R2


title: PFHT1_ROW07_14_R2


title: PFHT1_ROW06_7_R2


title: PFHT1_ROW07_9_R2


title: PFHT1_ROW07_6_R2


title: PFHT1_ROW06_4_R2


title: PFHT1_ROW06_6_R2


title: PFHT1_ROW06_2_R2


title: PFHT1_ROW07_4_R2


title: PFHT1_ROW06_19_R2


title: PFHT1_ROW07_1_R2


title: PFHT1_ROW06_20_R2


title: PFHT1_ROW06_1_R2


title: PFHT1_ROW06_17_R2


title: PFHT1_ROW07_16_R2


title: PFHT1_ROW06_15_R2


title: PFHT1_ROW06_14_R2


title: PFHT1_ROW06_16_R2


title: PFHT1_ROW12_1_R2


title: PFHT1_ROW06_9_R2


title: PFHT1_ROW06_12_R2


title: PFHT1_ROW06_13_R2


title: PFHT1_ROW06_11_R2


title: PFHT1_ROW06_10_R2


title: PFHT1_ROW05_8_R2


title: PFHT1_ROW05_7_R2


title: PFHT1_ROW05_6_R2


title: PFHT1_ROW05_5_R2


title: PFHT1_ROW05_4_R2


title: PFHT1_ROW05_9_R2


title: PFHT1_ROW06_3_R2


title: PFHT1_ROW07_15_R2


title: PFHT1_ROW05_3_R2


title: PFHT1_ROW05_20_R2


title: PFHT1_ROW06_5_R2


title: PFHT1_ROW05_2_R2


title: PFHT1_ROW05_1_R2


title: PFHT1_ROW06_18_R2


title: PFHT1_ROW05_19_R2


title: PFHT1_ROW05_18_R2


title: PFHT1_ROW05_16_R2


title: PFHT1_ROW05_15_R2


title: PFHT1_ROW05_13_R2


title: PFHT1_ROW05_17_R2


title: PFHT1_ROW05_14_R2


title: PFHT1_ROW05_11_R2


title: PFHT1_ROW04_9_R2


title: PFHT1_ROW04_8_R2


title: PFHT1_ROW04_7_R2


title: PFHT1_ROW05_10_R2


title: PFHT1_ROW04_6_R2


title: PFHT1_ROW04_5_R2


title: PFHT1_ROW04_2_R2


title: PFHT1_ROW04_18_R2


title: PFHT1_ROW04_20_R2


title: PFHT1_ROW04_1_R2


title: PFHT1_ROW04_19_R2


title: PFHT1_ROW04_16_R2


title: PFHT1_ROW04_14_R2


title: PFHT1_ROW04_13_R2


title: PFHT1_ROW04_11_R2


title: PFHT1_ROW04_10_R2


title: PFHT1_ROW05_12_R2


title: PFHT1_ROW03_7_R2


title: PFHT1_ROW03_4_R2


title: PFHT1_ROW03_5_R2


title: PFHT1_ROW03_3_R2


title: PFHT1_ROW03_6_R2


title: PFHT1_ROW04_12_R2


title: PFHT1_ROW03_2_R2


title: PFHT1_ROW04_15_R2


title: PFHT1_ROW03_8_R2


title: PFHT1_ROW03_20_R2


title: PFHT1_ROW04_4_R2


title: PFHT1_ROW03_1_R2


title: PFHT1_ROW03_19_R2


title: PFHT1_ROW03_9_R2


title: PFHT1_ROW04_3_R2


title: PFHT1_ROW03_17_R2


title: PFHT1_ROW03_16_R2


title: PFHT1_ROW03_13_R2


title: PFHT1_ROW03_12_R2


title: PFHT1_ROW03_11_R2


title: PFHT1_ROW03_10_R2


title: PFHT1_ROW03_14_R2


title: PFHT1_ROW03_15_R2


title: PFHT1_ROW02_8_R2


title: PFHT1_ROW02_9_R2


title: PFHT1_ROW02_5_R2


title: PFHT1_ROW02_6_R2


title: PFHT1_ROW03_18_R2


title: PFHT1_ROW02_20_R2


title: PFHT1_ROW02_2_R2


title: PFHT1_ROW02_3_R2


title: PFHT1_ROW02_4_R2


title: PFHT1_ROW02_1_R2


title: PFHT1_ROW02_13_R2


title: PFHT1_ROW02_17_R2


title: PFHT1_ROW02_11_R2


title: PFHT1_ROW02_19_R2


title: PFHT1_ROW02_18_R2


title: PFHT1_ROW02_10_R2


title: PFHT1_ROW02_14_R2


title: PFHT1_ROW01_9_R2


title: PFHT1_ROW02_16_R2


title: PFHT1_ROW02_15_R2


title: PFHT1_ROW01_7_R2


title: PFHT1_ROW02_12_R2


title: PFHT1_ROW01_4_R2


title: PFHT1_ROW01_6_R2


title: PFHT1_ROW01_5_R2


title: PFHT1_ROW02_7_R2


title: PFHT1_ROW01_8_R2


title: PFHT1_ROW01_2_R2


title: PFHT1_ROW01_3_R2


title: PFHT1_ROW01_20_R2


title: PFHT1_ROW01_1_R2


title: PFHT1_ROW01_19_R2


title: PFHT1_ROW01_18_R2


title: PFHT1_ROW01_17_R2


title: PFHT1_ROW01_14_R2


title: PFHT1_ROW01_15_R2


title: PFHT1_ROW01_13_R2


title: PFHT1_ROW01_10_R2


title: PFHT1_ROW01_11_R2


title: PFHT1_ROW01_12_R2


title: CD49f+TOM+814

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

description:
SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) & Nextera XT DNA Library Prep Kit" (Illumina)
Unstranded RNA-seq

data_processing:
RNA-seq processing:
51 base single-end reads were analyzed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Sequencing quality was checked with FastQC v0.11.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the human genome (NCBI37/mm9) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.1.9, allowing two mismatches and twenty multihits.
Transcripts quantification and differential expression were calculated with Cufflinks 2.2.1, using the human GRCm38/mm10 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Tabulated text file with gene FPKM values

molecule: polyA RNA

source_name: Ear skin

growth_protocol: To obtain fresh dissociated epidermal cells from ear skin of psoriasis-like and control mice, the epidermis was separated from the dermis by trypsin digestion (0.75%) for 1 hour at 37ºC.  After mechanical dissociation, the cell suspension was filtered through a 70 μm cell strainer and centrifuged 5 min at 1500 rpm. Epidermal cells were counted and resuspended in PBS with 1% chelated FBS and 1% BSA (staining buffer), and stained for 30-45 min at 4ºC with the following conjugated surface markers: CD45-APC-Cy7, CD49f-PE-Cy7, CD34-Alexa-647. After staining, cells were washed with staining buffer, dye with Dapi to exclude dead cells and different epidermal subpopulations were sorted, CD45-Cd49fhighCD34- (basal keratinocytes) and CD45-Cd49fhighCD34+ (hair follicle stem cells). Sorting procedures were done excluding dead cells and doublets. GFP+ and Tomato+ epidermal basal keratinocytes and hair follicle stem cells were purified into Trizol LS for RNA isolation.

extract_protocol:
After FACS sorting, each purified epidermal subpopulation was collected in Trizol-LS (ref) for further RNA isolation as described manufacturer´s instructions
Variable amounts of total RNA samples, between 4 and 10 ng, were processed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) by following manufacturer instructions. Briefly, oligo(dT) primes preferentially reverse transcription on poly(A) RNA in the presence of a template switching oligonucleotide, then limited-cycle PCR produces double stranded cDNA. Resulting cDNA was subsequently processed with the "Nextera XT DNA Library Prep Kit" (Illumina), which fragments and inserts Illumina adapters. Adapter-ligated non-directional libraries were completed by 12 cycles of PCR.  The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq 2500 following manufacturer's protocols.

value: Ear skin

value: Basal Keratinocytes

value: psoriatic-like DKO* mice

value: mT/mG mouse


title: CD49f+TOM+817


title: CD49f+TOM+815


title: CD49f+GFP+817


title: PC3_Si4B-3

city: Miami

first: Karoline

last: Briegel

state: FL

address: 1600 NW 10th Ave

department: Surgery

institute: University of Miami

data_processing:
After sequencing, the analysis was performed using the in-house developed RNAv9 pipeline which uses a variety of internally developed and open source programs. Many of the tools used were developed at EA | Q² Solutions and are available on the Google code website https://github.com/ExpressionAnalysis/ea-utils/.
Any read that has one particular base at ≥ 95% frequency (homopolymer filtering), or has more than 4 Ns within its sequence, or has an average Q score below 25, or has sa equence corresponding to a Illumina adapters, or are shorter than 25 nt in length, was removed.  Samples were aligned to  the human genome using STAR software version 2.4 and quantified using RSEM version 1.2.14
Genome_build: hg19
Supplementary_files_format_and_content: Comparison-Genes (TXT file) contains multiple matrices that summarize the data based on gene counts across all of samples.  Field_Descriptions (TXT file) contains descriptions of column headers in Comparison-Genes.txt

source_name: PC3, siARID4B

growth_protocol: PC3 cells were grown in RPMI 1640 medium containing 10% FBS, and supplemented with penicillin (100 units/ml) and streptomycin (100 µg/ml)

extract_protocol:
Total RNA was purified using an RNeasy plus kit (Qiagen), and was treated by DNase I (Qiagen).
Samples were prepared and sequenced according to EA | Q² Solutions standard TS Stranded mRNA sequencing protocol using HiSeq - 2x50bp-PE sequencing on an Illumina sequencing platform.  RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103), and with dUTP utilized in place of dTTP in the second strand master mix. Forked barcode adaptors were attached to the cDNAs via ligation.  The resulting molecules were PCR amplified. Since only the second strand included the dUTP base, stalling the polymerase, the only viable template was the first strand, thereby preserving the strand information. Final libraries are quantified, normalized and pooled for sequencing.

treatment_protocol: PC3 cells were incubated at 37°C in 5% CO2 and grown to 50% confluence before transfected with siRNA against ARID4B (si4B) or with a control scrambled siRNA (sic) for 72 hours.

value: metastatic prostate cancer cells

tag: sirna treatment

value: ARID4B siRNA


title: 131CTX

first: Gabsang

last: Lee

state: MD

address: 733 North Broadway, Suite 747

department: Department of Neurology and Neuroscience

institute: Institute for Cell Engineering, Johns Hopkins University

data_processing:
After library QC with the Caliber LabChip Gx and quantification with QPCR, libraries were loaded on HiSeq 2000 for paired-end 100X2 bp sequencing. Reads were aligned with Tophat2 (v2.0.9) to the mm10 genome build guided by (e.g. –G flag) the Ensembl Mus_musculus.GRCm38.82 transcriptome GTF file. Aligned reads overlapping genes in this GTF were quantified with the featureCounts tool.
Genome_build: GRCm38
Supplementary_files_format_and_content: gene-level read count

source_name: Mouse Prefrontal cortex tissue

growth_protocol: The mPFC region was isolated from 2, 6, 10, and 22 weeks old mice, and was homologized by TissueLyser LT (Qiagen, Germany). The total RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, 80224) with QIAcube (Qiagen, Germany). 300 ng of total RNA extracted from mouse tissue was used for each library prep. RNAseq libraries were prepared using the TruSeq Stranded Total RNA Library Preparation kit with Ribo-Zero Gold ribosomal RNA depletion from Illumina (catalog number RS-122-2303) according to the manufacturer’s instructions. The Invitrogen SuperScript III Reverse Transcriptase from ThermoFisher (catalog number 18080093) was used for cDNA synthesis. After library QC with the Caliber LabChip Gx and quantification with QPCR, libraries were loaded on HiSeq 2000 for paired-end 100X2 bp sequencing.

extract_protocol:
TissueLyser LT
The mPFC region was isolated from 2, 6, 10, and 22 weeks old mice, and was homologized by TissueLyser LT (Qiagen, Germany). The total RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, 80224) with QIAcube (Qiagen, Germany). 300 ng of total RNA extracted from mouse tissue was used for each library prep. RNAseq libraries were prepared using the TruSeq Stranded Total RNA Library Preparation kit with Ribo-Zero Gold ribosomal RNA depletion from Illumina (catalog number RS-122-2303) according to the manufacturer’s instructions. The Invitrogen SuperScript III Reverse Transcriptase from ThermoFisher (catalog number 18080093) was used for cDNA synthesis.

value: Male

value: Prefrontal cortex tissue


title: 130CTX


title: 124CTX


title: CD49f+GFP+814


title: CD49f+GFP+815


title: CD49f+825

value: Control


title: D223


title: PC3_Si4B-2


title: PFHT1_ROW01_16_R2


title: CD49f+810


title: D222


title: PC3_Si4B-1


title: D397


title: D395


title: PC3_SiC-3

source_name: PC3, sicontrol

value: Control scrambled siRNA


title: D136


title: CD49f+828


title: lentiviral vector alone_2

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

hyb_protocol: The obtained cRNAs were hybridized on a HumanHT-12 v4 Expression BeadChip according to the Standard Illumina hybridization protocol.

scan_protocol: Hybridized chips were then scanned and the background subtracted intensities were generated by GenomeStudio Software, according to the standard Illumina scanning protocol.

data_processing: Between arrays normalization (quantile) and differential expression analysis were performed by limma package (Bioconductor, RStudio v 0.98.501).

source_name: HAOEC

label_protocol: Biotinylated cRNA was prepared using the Ambion Illumina RNA amplification kit.

growth_protocol: HAOEC were grown in EGM-2 (Lonza) containing 2% FBS.

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HAOEC were infected with lentiviral particles for vector alone (pReceiver-Lv105) or for BACE1-AS cDNA (Genecopeia Inc) and selected with 1µg/ml Puromycin.

value: aorta endothelial cells

value: Negative Control

tag: experiment id


title: lentiviral_BACE1AS_2

tag: treatment

value: Overexpression BACE1AS


title: 213CTX


title: CD34+TOM+815

value: Hair follicle stem cells


title: 122CTX


title: lentiviral vector alone_1


title: 129CTX


title: PC3_SiC-1


title: 123CTX


title: 104CTX


title: ESS 101

type: genomic

city: Stockholm

first: Joseph

middle: Woodward

last: Carlson

address: P1:02 Radiumhemmet

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

hyb_protocol: standard Affymetrix protocol

scan_protocol: Wash and stain on Fluidics Station 450 and arrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were normalized with the default settings on Thermo Fishers OncoScan Console 1.3 Software.

source_name: sarcoma

label_protocol: OncoScan® FFPE Assay Kit, P/N 703175

extract_protocol: none provided by the submitter

value: Undifferentiated Uterine Sarcomas


title: lentiviral_BACE1AS_3


title: D303


title: CD34+GFP+817


title: D304


title: lentiviral_BACE1AS_1


title: ESS 100


title: PFHT1_ROW04_17_R2

value: retina

value: embryonic E15.5

value: Tomato-


title: CD34+TOM+817

value: Ear skin


title: D605


title: ESS 97


title: D301


title: D604


title: CD34+GFP+814

value: psoriatic-like DKO* mice


title: ESS 96


title: D603


title: D602


title: PC3_SiC-2


title: CD34+TOM+814

value: mT/mG mouse


title: D586


title: CD34+825


title: D307

value: Female


title: D588


title: D580


title: D309


title: ESS 89


title: ESS 91


title: CD34+810


title: 15


title: ESS 87


title: CD34+GFP+815


title: ESS 86


title: ESS 83


title: D686


title: 14


title: CD34+828


title: ESS 78


title: D684


title: D685


title: D687


title: D592


title: D581


title: mammary tumor 9063R1

first: Tung

last: Bui

address: 1160 Pine Ave. W, R507

department: Biochemistry

institute: McGill University

description: Gene expression data

hyb_protocol: 3.5µg DNA target was hybridized on GeneChip® Mouse Gene 2.0 ST Array (Affymetrix) and incubated at 45oC in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm

scan_protocol: The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix)

data_processing: Raw data were first processed to perform gene-level normalization and quality control using Affymetrix Expression Console software (Affymetrix). Processed data were next subjected to Gene Level Differential Expression Analysis using Affymetrix Transcriptome

label: Biotin

source_name: Mammary tumor

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix)

extract_protocol: Rneasy RNA extraction kit Qiagen

value: Mammary tumor

value: NIC WT


title: D728

value: Male

value: Prefrontal cortex tissue


title: D727


title: D725


title: ESS 76


title: mammary tumor 9568R1

description: Gene expression data


title: mammary tumor 8919

description: Gene expression data

value: NIC itgb3 fl/fl (beta 3 integrin KO)


title: ESS 75


title: 326CTX


title: ESS 72


title: 13

value: Control


title: D724


title: mammary tumor 6666

description: Gene expression data


title: mammary tumor 8604

description: Gene expression data

value: NIC itgb1 fl/fl (beta 1 integrin KO)


title: D333


title: ESS 71


title: ESS 70


title: D741


title: D331


title: mammary tumor 6191R5

description: Gene expression data


title: D738


title: D740


title: ESS 69


title: D726


title: ESS 73


title: D693


title: mammary tumor 2898R2

description: Gene expression data


title: D692


title: mammary tumor 5648L23

description: Gene expression data


title: mammary tumor 5780R4

description: Gene expression data

value: NIC itgb1 fl/fl itgb3 fl/fl (beta 1/3 integrin DKO)


title: ESS 67


title: 324CTX


title: ESS 62


title: ESS 63


title: 21


title: P14_19


title: P14_27


title: ESS 60


title: mammary tumor 2811R2

description: Gene expression data


title: P14_25


title: P14_15


title: P14_21


title: mammary tumor 5769R23

description: Gene expression data


title: ESS 59


title: mammary tumor 2445L23

description: Gene expression data


title: mammary tumor 2474R3

description: Gene expression data


title: mammary tumor 2333R2

description: Gene expression data


title: P14_14


title: ESS 58


title: 332CTX


title: mammary tumor 2330R2

description: Gene expression data


title: 22


title: ESS 55


title: 325CTX


title: P14_10


title: ESS 53


title: P14_2


title: P14_1


title: P14_29


title: P14_12


title: mammary tumor 2328L2

description: Gene expression data


title: ESS 51


title: mammary tumor 2234R2

description: Gene expression data


title: mammary tumor 2212NT

description: Gene expression data


title: mammary tumor 1833R2

description: Gene expression data


title: P14_28


title: P14_24


title: ESS 47


title: P14_23


title: P14_5


title: ESS 46


title: BAT_KO_Cold6hr_2

city: Singapore

first: Lei

last: Sun

address: 8 College Road

country: Singapore

institute: Duke-NUS

description:
Each replicate is pooled from 2 mice
BAT_WT and KO_RNA-seq_FPKM.xlsx

data_processing:
Reads were aligned to mm10, using Tophat and genes were quantified using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: FPKM of the genes

source_name: Brown fat

growth_protocol: adipose tissue depots were digested in 0.2% collagenase at 37°C for 25–30 min. Digested tissues were filtered through a 100-mm membrane, and SVF cells were collected by centrifugation at 1,500 rpm for 5 min. After centrifugation, the mature adipocytes floating on top were collected for genotyping analysis. The freshly iso- lated SVF cells were seeded and cultured in DMEM con- taining 10% newborn calf serum and 0.5% penicillin/ streptomycin at 37°C with 5% CO2. On confluence, the cells were induced to differentiate for 2 days with DMEM containing 10% FBS, 850 nmol/L insulin, 0.5 mmol/L dexamethasone (Sigma-Aldrich), 250 mmol/L of 3-isobutyl- methylxanthine (Sigma-Aldrich) and 1 mmol/L rosiglita- zone (Sigma-Aldrich) in DMEM. The induction medium was replaced with DMEM containing 10% FBS and 160 nmol/L insulin for 2 days. Then cells were incubated in DMEM with 10% FBS

extract_protocol:
Total RNA from primary cells or mouse tissues were extracted with miRNeasy Mini Kit (Qiagen).
NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: NSA (CF-1)

value: 8-9 week old

value: brown fat


title: BAT_KO_Cold6hr_3


title: P14_13


title: ESS 45

value: Undifferentiated Uterine Sarcomas


title: P14_11


title: ESS 43


title: BAT_KO_Cold6hr_1


title: Cells with solids, repl2

first: Antonio

middle: David

last: Moreno

address: Avda. Complutense 40

department: Department of Energy

institute: CIEMAT

description:
Gene expression data from cells collected after 4 h of fermentation in presence of insoluble solids
Solids_4h-B

hyb_protocol: Labeled cDNAs were processed with GeneChip® IVT PLUS Reagent Kit (Affymetrix®) and hybridized with GeneChip™ Yeast Genome 2.0 Array

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix®)

data_processing:
Raw data were processed with RMA algorithm included in Affymetrix® Expression Console™ for normalization and gene level analysis. Fold changes between experimental conditions were calculated as a quotient between the mean of the gene expression signals. Statistical analysis was performed with LIMMA package included in Babelomics software package.
Raw data were processed with Bioconductor online Piano software, using FDR for multiple testing adjustment and a P-value cuttoff of 0.001
Summary topTable() with False Discovery Rate adjustment.

organism: Saccharomyces cerevisiae

source_name: Cells with solids

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol

growth_protocol: Fermentation was performed in YNB medium (Conda, Cat.1553.00) supplemented with 20 g/L glucose and 7.5 g/L (NH4)2SO4 in presence/absence 40% (w/w) insoluble solids

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: BAT_KO_2


title: Cells with solids, repl3

description:
Gene expression data from cells collected after 4 h of fermentation in presence of insoluble solids
Solids_4h-C


title: BAT_KO_1


title: BAT_KO_3


title: BAT_WT_Cold6hr_3


title: ESS 41


title: Cells with solids, repl1

description:
Gene expression data from cells collected after 4 h of fermentation in presence of insoluble solids
Solids_4h-A


title: BAT_WT_Cold6hr_1


title: BAT_WT_Cold6hr_2


title: ESS 49


title: ESS 40


title: Cells without solids, repl3

description:
Gene expression data from cells collected after 4 h of fermentation in absence of insoluble solids
No_solids_4h-C

source_name: Cells without solids


title: BAT_WT_3


title: BAT_WT_2


title: ESS 39


title: Cells without solids, repl2

description:
Gene expression data from cells collected after 4 h of fermentation in absence of insoluble solids
No_solids_4h-B


title: BAT_D5_YBX2KO

description: AdipocyteD5_WT and KO_RNA-seq_FPKM.xlsx

tag: sample type

value: primary brown adipocyte culture from SVF derived from 3 weeks mice


title: ESS 38


title: BAT_D5_WT

description: AdipocyteD5_WT and KO_RNA-seq_FPKM.xlsx


title: WAT_YBX2_RIP

source_name: inguinal white fat

value: primary iWAT adipocyte culture from SVF derived from 3 weeks mice

value: inguinal white fat


title: Cells without solids, repl1

description:
Gene expression data from cells collected after 4 h of fermentation in absence of insoluble solids
No_solids_4h-A


title: ESS 37


title: WAT_IGG_RIP


title: ESS 35


title: BAT_IGG_RIP


title: BAT_YBX2_RIP


title: ESS 34


title: M2: Male rep2

city: Bethesda

first: Patrick

middle: Allen

last: Fletcher

address: 9000 Rockville Pike

institute: NIDDK

data_processing:
Custom extension of 3'UTR annotations for NCBI Rnor6.0 reference transcriptome
CellRanger (v2.1) count for each sample: De-multiplexing, alignment to reference transcriptome and UMI collapsing
CellRanger (v2.1) aggr to merge samples into a common matrix
Genome_build: Rnor6.0 (NCBI annotation)
Supplementary_files_format_and_content: CellRanger generated text file containing merged UMI counts for all four samples (Matrix Market exchange format) with tab-separated list of barcodes and genes

organism: Rattus norvegicus

source_name: Anterior pituitary

extract_protocol:
Anterior pituitaries were quickly collected from postpubertal rats and dispersed using a trypsin/EDTA based method. Four pituitaries per sex were collected, pooled, dispersed and counted, then two samples per sex were loaded into a total of four lanes of the Chromium Single Cell Controller (10X Genomics)
Single-cell cDNAs and barcoded sequencing libraries were constructed from the output of the Chromium Single Cell Controller using a Chromium Single Cell 3’ Reagent Kit v2 according to the manufacturer’s protocol (10X Genomics)
Each library received a different sample index; these were multiplexed and sequenced together. Barcodes = cell barcodes

value: Sprague Dawley

value: Anterior pituitary

value: post natal day 59

tag: estrus cycle stage

tag: Sex

value: male


title: M1: Male rep1

tag: age


title: F2: Female rep2

value: post natal day 44

value: Diestrus

value: female


title: F1: Female rep1


title: ESS 32


title: BAT_WT_1


title: P4NS: Normal skin

city: Luxembourg

first: Arnaud

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

data_processing:
Reads have been trimmed with Trim Galore! with main focus on adapter trimming (options: --fastqc -q 10 --length 35 --paired --retain_unpaired; unpaired reads have been discarded from further analysis)
Next, we followed the GDC bioinformatics pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/) with minor modifications. The reference file used is: star.index.genome.d1.vd1.gtfv22.tar.gz and the annotation is: gencode.v22.annotation.gtf.gz.
Alignment of fastq-files 1st pass with STAR (v2.5.2b).
Intermediate index generation with STAR.
Alignment 2nd pass.
Counting reads of mapped counts has been achieved directly during the 2nd alignment pass of STAR by applying the option –quantMode TTTranscriptomeSAM GeneCounts.
We normalized expression data by the FPKM method provided by GDC (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#fpkm), wherein gene length data used to process TCGA sample have been kindly provided by GDC on demand.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files that contain the raw sequence counts for each gene (Ensembl gene identifier) produced by the program STAR as well as TPM and FPKM.

source_name: Normal skin

extract_protocol:
Total RNA were extracted using the Qiagen’s AllPrep Mini Kit according to supplied protocols. Quality and quantity of samples were measured with Nandrop, gel electrophoresis and Qubit High Sensitivity Kit. RNA integrity was determined using the Agilent Bioanalyzer Nano chip.
Library preparation was performed using Illumina’s TruSeq Sample Prep Kit, amplification was done on Illumina’s cBot Cluster Generation System. Paired-end reads (2x 83 bp) were generated on the Illumina HiSeq 2000

tag: biomaterial type

value: biopsy

tag: patient

value: Normal skin


title: Synovial tissues_Mod_NS_rep2

city: Beijing

first: Yanqiong

last: Zhang

address: No 16, Nanxiaojie, Dongzhimennei

country: China

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Synovial tissues_Model_rep2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

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

treatment_protocol: Briefly, the rats were immunized intradermally at the base of the tail with 0.1 mL Freund’s complete adjuvant (CFA) (1 mg of heat-killed Mycobacterium tuberculosis suspended in 0.1 mL paraffin oil). Rats in the normal control group were injected with an equal volume of saline instead of CFA.

tag: disease state

value: antigen-induced arthritis (AIA) model

value: Synovial tissues


title: P2PM: Melanoma primary tumor

source_name: Melanoma primary tumor

tag: cell line

value: Melanoma primary tumor


title: P6PM: Melanoma primary tumor


title: NHEM: Human Epidermal Melanocytes

source_name: Human Epidermal Melanocytes

value: cell line

value: NHEM

value: Melanocyte


title: e12.5 GC 10x

city: San Francisco

first: Daniel

last: Nguyen

address: 513 Parnassus Ave

institute: University of California San Francisco

description:
E12.5 male germ cells
Single cell RNA-seq

data_processing:
Sequenced on Illumina HiSeq 4000.
Reads were processed on 10X Cell Ranger and mapped to mm10 genome.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *csv: Comma-separated text files for cell by gene raw reads matrix.

source_name: male germ cells

extract_protocol:
Oct4GFP+ germ cells were isolated by FACS and RNA was isolated according to 10x protocol.
Libraries were prepared according to 10x v2 protocol.

tag: strain/background

tag: gender

tag: cell type

value: germ cells

tag: developmental stage


title: ESS 33

value: Undifferentiated Uterine Sarcomas


title: e13.5 GC 10x

description:
E13.5 male germ cells
Single cell RNA-seq


title: ARID4B ChIP-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm (default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg19
Supplementary_files_format_and_content: 005JGWU_ARID4B_PC3_ucsctracks (BED file) contains MACS peaks file in text format. 005JGWU_ARID4B_PC3_bigWig_URLs (TXT file) contains peak shape information in the form of a signal histogram.

source_name: PC3, ChIP fraction

extract_protocol:
Cell lysates were clarified from sonicated nuclei and the ARID4B-DNA complexes were isolated with the anti-ARID4B antibody (CAT#: A302-233A, LOT#: A302-233A-1, Bethyl Laboratories).
Libraries were prepared for sequencing using standard Illumina protocols.

value: metastatic prostate cancer cells

tag: chip antibody

value: anti-ARID4B antibody (CAT#:A302-233A, LOT#:A302-233A-1,Bethyl Laboratories)


title: Synovial tissues_Mod_NS_rep1

source_name: Synovial tissues_Model_rep1

tag: tissue


title: P4PM: Melanoma primary tumor


title: Synovial tissues_Con_NS_rep3

source_name: Synovial tissues_normal control_rep3

value: control


title: Synovial tissues_Mod_NS_rep3

source_name: Synovial tissues_Model_rep3


title: Input control

source_name: PC3, input


title: ESS 97

description: Thermo Fisher Scientific Human Gene 2.1 ST Array

hyb_protocol: GeneTitan™ Instrument User Guide for Expression  ArrayPlates, P/N 702933

scan_protocol: standard Affymetrix protocol

data_processing: The data were normalized with the default settings on Thermo Fishers Expression Console 1.4.1.46 Software.

label: biotiin

source_name: Sarcomas

label_protocol: SensationPlus™ FFPE Amplification and WT Labeling Kit, P/N 703089

extract_protocol: none provided by submitter

tag: mitotic index group

value: High

tag: hormone receptor expression

value: Negative

tag: rna group

value: Developmental

tag: nuclear atypia

value: No Data

tag: cnv group

tag: cell density

value: no info

tag: time to last follow up (months)

tag: status at last follow up

value: Dead


title: mouse LSK, LC190

city: Cambridge

first: Luyi

last: Tian

address: 415 main st Cambridge

institute: Broad institute

description: index sorted hematopoietic stem and progenitor cells from Dach1 reporter mice, FACS value in FACS_annotation.csv

data_processing:
cellular barcode: 8bp as in cell_barcode.csv
barcode position: R1 first eight base
umi position: 6bp after the cell barcode
gene counting matrix generated using scPipe 1.3.0
reads were aligned using Rsubread 1.29.6
Genome_build: ENSEMBL Homo_sapiens.GRCh38.88
Supplementary_files_format_and_content: gene counting matrix, rows repsent genes and each column is a well

source_name: hematopoietic stem and progenitor cells

growth_protocol: All mice were bred and maintained under specific pathogen-free conditions at WEHI, according to institutional guidelines. C57BL/6 (CD45.2), C57BL/6 Pep3b (CD45.1), Cas9-Tg or Dach1-GFP mice aged between 8-16 weeks were used.

extract_protocol:
marrow cells from either C57BL/6 mice or Dach1-GFP mice were harvested, made into a single cell suspension, incubated with red cell removal buffer (NH4Cl), followed by incubation with anti-CD117-APC, then incubation with anti-APC magnetic beads, followed by purification on a LS column (Miltenyit biotech). This enriched fraction was then stained with a cocktail of antibodies including anti-Sca1, anti-Il7Ra-biotin, anti-CD16/32, anti-CD135-PE, anti-CD150, anti-CD48. Cells were sorted either in bulk or using the single cell mode of a BD Fusion cell sorter.
For CEL-seq2, Single cells were flow sorted into chilled 384-well PCR plates containing 1.2ul of primer/ERCC mix using a BD FACSAria III flow cytometer. Sorted plates were sealed and immediately frozen upside down at -80C. Then these plates, together with the mRNA mixture plates, were taken from -80C and processed using an adapted Cel-Seq2 protocol with the following variations. We pooled the samples after the first strand synthesis and the second strand synthesis was performed using NEBNext Second Strand Synthesis module. NucleoMag NGS Clean-up and Size select magnetic beads were used for all DNA purification and size selection steps.

treatment_protocol: A targeting vector was constructed in which sequence encoding a biotin tag was inserted immediately prior to the stop codon in exon 12 of the Dach1 gene, along with an IRES-GFP-frt-flanked neomycin resistance cassette following the stop codon. This targeting vector was linearized and electroporated into C57BL/6 embryonic stem cells. Transfected cells were selected in G418 and resistant clones picked and expanded. Clones in which the targeting vector had recombined with the endogenous Dach1 locus were identified by southern blot analysis and a targeted ES cell clone was injected into Balb/c blastocysts to generate chimeric mice. Male chimeras were mated with C57BL/6 females to yield mice heterozygous for the targeted Dach1 allele (Dach1T); these were then bred with mice expressing Flpe recombinase to excise the neomycin resistance cassette generating mice carrying the Dach1bio-GFP locus.

value: bone marrow

value: hematopoietic stem and progenitor cells


title: ESS 100

value: Low

value: Alive


title: ESS 101


title: Synovial tissues_Con_NS_rep2

source_name: Synovial tissues_normal control_rep2

value: Synovial tissues


title: mouse LSK, LC189


title: ESS 78

value: ECM

value: Uniform


title: ESS 86

value: Undifferentiated Uterine Sarcomas

value: Pleomorphic


title: mouse LSK, LC187


title: ESS 96

value: Positive


title: ESS 74

value: Proliferative


title: ESS 75


title: ESS 91


title: ESS 87

value: High


title: CC from tonsil 5

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

institute: Rennes University Hospital

description: CD19posCD38hiCD10posIgDnegCXCR4neg cells

hyb_protocol: Following fragmentation, cARN were hybridized on GeneChip Human U133Plus2.0 arrays

scan_protocol: GeneChips were scanned using the Genechip Scanner Affymetrix 3000

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC). Normalization was performed by the GC-RMA algorithm. Dataset was then filtering by eliminating PS with no expression in all dataset and/or no gene symbol annotations

source_name: Centrocyte purified from human non tumorla tonsil

label_protocol: Biotinylated cRNA were amplified according to the small sample labeling protocol (Affymetrix, Santa Clara, CA)

extract_protocol: RNA extraction was performed using Qiazol (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Cells were purified by FACSARIA sorting strategy from non tumoral tonsils using following phenotypes : CD19posCD38hiCD10posIgDnegCXCR4pos for CB or CXCR4neg for CC

value: Centrocyte

tag: disease

value: Healthy donor

value: Tonsil


title: Synovial tissues_Con_NS_rep1

source_name: Synovial tissues_normal control_rep1

tag: disease state

value: control


title: CC from tonsil 6


title: ESS 76

value: Negative

value: LMS-like

value: Dead


title: ESS 89

value: No Data

value: Developmental

value: Low


title: mouse LSK, LC188

value: bone marrow

value: hematopoietic stem and progenitor cells


title: CC from tonsil 2


title: ESS 72

value: Undifferentiated Uterine Sarcomas

value: Uniform


title: ESS 71

value: Positive

value: Alive


title: S15

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were mapped to the mouse genome (mm10, Genome Reference Consortium GRCm38)  in the strand-specific mode using HISAT2.
Number of uniquely aligned reads (q > 10) to the exonic region of each gene were counted using HTSeq based on the GenCode annotation version M16 (Ensembl v91)
Genes that achieved at least one read count per million reads (cpm) in at least four samples (i.e., number of samples per group) were kept. Conditional quantile normalisation (cqn) was then performed accounting for gene length and GC content, and a log2 transformed RPKM expression matrix was subsequently generated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each Sample

source_name: Ang + Low dose Cil

growth_protocol: Primary mouse cardiomyocyte cells were isolated from the whole hearts of 1-3-day old C57/BL6 wild-type mice.Following 5 days incubation at 37°C, 5% CO2, primary mouse cardiomyocytes were serum starved for 24 hours in a 0.5% FBS-DMEM media. Cells were then washed and recoated with complete cardiomyocyte growth media. For cardiomyocyte hypertrophy assessment 1uM angiotensin II (Alfa Aesar) was added to cardiomyocyte growth media post serum starvation (i.e. day 6 post-culture), and this was repeated the next day. In tandem to angiotensin II treatment, cells were either treated with vehicle or low dose Cilengitide (20nM) (Bachem). After 8-day culture and treatment, cardiomyocytes were either lysed for RNA analysis.

extract_protocol:
RNA was prepared from cell cultures using the RNeasy Mini Kit and the RNase free DNase set (Qiagen)
Extracted RNA samples were sent to the Bart's and the London Genome Centre for processing. Library preps were made using PolyA-capture.

value: cardiomyocytes

tag: treatment

value: Ang II (1uM) + Low dose Cil (20nM)

tag: strain

tag: genotype/variation

value: wild-type


title: ESS 83


title: ESS 73

value: Proliferative

value: High

value: no info