title: Pol II Ser2_ChIPseq in Wild type 2

description: Pol II Ser2 ChIP in Normal S2 cells-Repeat 2

data_processing:
The ChIP-seq BAM files were converted to bedgraph files by using the genome Coverage Bed command and options bga and ibam from the Bedtools v2.26.0 suite.
Custom Perl scripts were then used to filter the Dm6 annotations either for genes separated by a minimum distance to avoid overlapping signals or RNA-seq expression levels.
Further custom scripts were used to extract the signal from the bedgraph files for each entry in the filtered gene list.
Single base resolution was used for flanking regions, while the signal in gene bodies was binned into 16 bins to take account of different gene lengths.
Each dataset was normalized by the total mapped sequencing reads in that dataset.
Cross-referencing between different datasets was done based on the ‘name’ field, after filtering the annotations for multiple entries with identical name.
Genome_build: Dm6
Supplementary_files_format_and_content: bedgraph

source_name: Pol II Ser2 ChIP in Normal S2 cells

extract_protocol:
Lysates were clarified from sonicated cells and DNA complexes were isolated with antibody.
ChIP-DNA libraries were produced using the NEBNext Ultra II DNA Library Prep Kit (NEB E7645L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (NEB E7600S), using provided protocols with 10ng of fragmented ChIP DNA

tag: genotype/variation

value: wild type

tag: chip antibody

value: Pol II Ser2 (ab5095, Abcam)


title: UPF1_ChIPseq 2

status: Public on Apr 01 2019

type: SRA

city: Birmingham

first: Anand

middle: Kumar

last: Singh

state: West Midlands

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: UPF1 ChIP DNA from normal S2 cells-Repeat 2

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: UPF1 ChIP DNA from normal S2 cells

growth_protocol: Drosophila Embryonic S2 cells were cultured in Insect–XPRESS media (Lonza) supplemented with 10% Fetal Bovine Serum (FBS) and 1% Penicillin-Streptomycin-Glutamine mix (P/S/G) (Invitrogen) at 27°C

treatment_protocol: For RNAi, dsRNA Specific for UPF1 transcripts were used

tag: cell line

tag: cell origin

value: Embryonic cell line

tag: passages

value: UPF1 Antibody (Generated in Lab)


title: C5_V2_C62

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

institute: Newcastle University

description: rawCounts.csv

library_source: transcriptomic

data_processing:
Trimming: Trimmomatic version 0.33, trailing = 20, minlength = 60 and end = “PE
Alignment: STAR 2.4.0, Default parameters
Quantification: HTSEQ 0.6., -f bam, -r name, -a 4, -i gene_id, -m union
Genome_build: Human reference genome GRCh38.p7 version 25 from GenCode

molecule: polyA RNA

organism: Homo sapiens

source_name: human ESC

growth_protocol: human ESC line (CRX-GFP) was expanded in mTeSR™1 (StemCell Technologies) at 37°C and 5% CO2 on 6 well plates pre-coated with Low Growth Factor Matrigel (Corning) as described in our previous publication (Collin et al. 2015, , Collin et al.Stem Cells. 2016 Feb;34:311-21) ). Differentiation to retinal organoids was performed as described in Mellough et al. 2015 (Stem Cells. 2015 Aug;33(8):2416-30) with minor modifications which included addition of 10µM Y27632 dihydrochloride for the first 48 hours of differentiation.

extract_protocol: Full length cDNA libraries were prepared using the Illumina Nextera XT DNA library preparation kit (Illumina). External RNA Control Consortium (ERCC) RNA spike-in Mix  (Ambion) was added to each cell sample prior to sequencing. Libraries were multiplexed as 24-48 libraries per lane and 75 bp single end reads were sequenced on the Ilumina HiSeq 2500.

treatment_protocol: Retinal organoids at day 90 of differentiation were disassociated to single cells using the embryoid body disassociation kit (Miltenyi Biotech) following the manufacturer’s instructions. CRX-GFP+ cells were sorted using a FACS-ARIA flow cytometric activated cell sorter (BD Biosciences). Single cells were loaded onto the C1 Single-Cell Auto Prep fluidic circuit (Fluidigm). Cell capture efficiency was assessed using the Zeiss Axiovert imaging system and empty sites, or sites with more than one cell were excluded from further analysis. Cell lysis, reverse transcription, cDNA amplification were performed using the SMARTer PCR cDNA synthesis kit (Clontech).

tag: condition

value: day 90 of retinal organoid differentiation

tag: cell type

value: human ESC (CRX-GFP line)


title: Pol II Ser2_ChIPseq in Wild type 1

description: Pol II Ser2 ChIP in Normal S2 cells-Repeat 1


title: C6_V2_C63

description: rawCounts.csv


title: D10_V2_C70

description: rawCounts.csv


title: UPF1_ChIPseq 1

description: UPF1 ChIP DNA from normal S2 cells-Repeat 1


title: C4_V2_C61

description: rawCounts.csv


title: C3_V2_C13

description: rawCounts.csv


title: Wild type Input DNA

description: Input DNA from normal S2 cells

source_name: Input DNA from normal S2 cells


title: Wild type Nascent RNA 2

description: FCHKJ7YBBXX_L3_CHKPEI85217080039_indexTCCGGAGA_1_CN2

data_processing:
For RNA-seq data, the BAM files were converted to bedgraph files. This was carried out with the genomeCoverageBed command and options -bga and -ibam from the Bedtools v2.26.0 suite.
Custom Perl scripts were then used to filter the Dm6 annotations either for genes separated by a minimum distance to avoid overlapping signals or RNA-seq expression levels.
Further custom scripts were used to extract the signal from the bedgraph files for each entry in the filtered gene list.
Each dataset was normalized by the total mapped sequencing reads in that dataset
Cross-referencing between different datasets was done based on the ‘name’ field, after filtering the annotations for multiple entries with identical name.
Genome_build: Dm6

molecule: total RNA

source_name: S2_WT_nascent RNA

extract_protocol:
Nascent RNA were isolated following Khodor et al, 2011 using NUN buffer.
All RNA libraries prepared using a NEBNext Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols.

tag: molecule subtype

value: Nascent RNA


title: C2_V2_C14

description: rawCounts.csv


title: Patient 45

type: RNA

city: Boston

first: SAUMYA

last: Das

state: MA

address: 185 Cambridge Street

country: USA

institute: MGH

description:
Test
SAMPLE 45

data_processing: The study does not have the normalized Ct values. This is because raw CT values after applying a threshold (Ct<=22) was used.

label: FAM

source_name: Plasma extracelular RNA

label_protocol: According to BioMark System protocol.

extract_protocol: RNA was extracted from plasma (331 patients, OMEGA-REMODEL trial) using miRCURY RNA Isolation Kit – Biofluids (Exiqon) and reverse transcribed using miScript II RT Kit (Qiagen, Fredrick, MD, USA). cDNA samples were pre-amplified with miScript Microfluidics PreAMP Kit (Qiagen, Fredrick, MD, USA) and RT-qPCR miRNA profiling analyses performed on the BioMark System (Fluidigm Corp. South San Francisco, CA) using miScript miRNA Assays (Qiagen, Fredrick, MD, USA) and Dynamic Array 96.96 (Fluidigm Corp. South San Francisco, CA). A Ct value of 23 was set as the cut-off point for detectable miRNA species.

tag: individual

value: patient who underwent a myocardial infarction

tag: tissue

value: plasma

tag: gender

value: Male

tag: race

value: Caucasian

tag: diabetes

tag: omega-3 fatty acid therapy

tag: age


title: Patient 40

description:
Test
SAMPLE 40


title: Patient 41

description:
Test
SAMPLE 41


title: Patient 42

description:
Test
SAMPLE 42


title: Patient 44

description:
Test
SAMPLE 44


title: C1_V2_C15

description: rawCounts.csv


title: 4_7DL

city: Farmington

first: Peter

last: Setlow

state: CT

address: 263 Farmington Ave.

department: MBB

institute: UConn Health

data_processing:
Analysis of raw data was performed using the Assembler module in MacVector (v16.0.9) (MacVector, Inc., Apex, NC) using default parameters.
Raw paired-end read data from each library were aligned to the B. subtilis strain 168 reference genome (accession number AL009126.3) using Bowtie.
Depth of coverage, read count, Reads Per Kilobase of transcript per Million mapped reads (RPKM), and Transcripts Per Kilobase Million (TPM) values for each library were exported as text for comparison.
Mapped reads were visualized over the reference genome using the Map option in MacVector to obtain the coverage of reads over individual genes or putative operons.
Genome_build: Bacillus subtilis strain 168 reference genome (NCBI GenBank accession number AL009126.3)
Supplementary_files_format_and_content: abundance measurements

organism: Bacillus subtilis

growth_protocol: Spores were routinely sporulated at 37°C on 2xSG medium agar plates for 24 hrs or ~ 2 d, and harvested. Sporulation plates were also incubated for 24 h or ~2 days, spores harvested. Spores were purified over ~ 7 days by daily multiple washes with 4°C water and intermittent sonication for 1 min, obvious contaminating material washed off surfaces of spore pellets with a gentle stream of water, followed by centrifugation through 50% Histodenz (highly purified) or only washed 3 times by centrifugation with 4°C water with sonication in between centrifugation ("less well purified"). Spores also were prepared at 37°C in liquid 2xSG medium for 2 d, which is the minimum time to get release from the sporangium of > 90% of the spores from sporulating cells and then purified as descibed above for spores from plates.

extract_protocol:
RNA was extracted and purified from spores using Ambion RiboPure-Bacteria Kit (product # AM1925). RNA quality was analyzed on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA, USA) using the RNA High Sensitivity assay.  Only samples with Ribosomal Integrity Numbers (RINe) values above 7.0 were considered for library preparation
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Sample Preparation kit. Libraries were validated for length and adapter dimer removal using the Agilent TapeStation 4200 D1000 High Sensitivity assay, and then quantified and normalized using the dsDNA High Sensitivity Assay for Qubit 3.0 (Life Technologies, Carlsbad, CA, USA).
Illumina MiSeq v3 chemistry (paired end 2 x 75bp read length).  Sequencing read depth was targeted at 10-15 million total paired end reads/sample.

treatment_protocol: For chemical decoating,  highly purified spore preparations were treated for 30 min at 70°C in 0.1 M DTT, 0.1 M NaCl, 0.1 M NaOH, 0.5% SDS, washed 6x at 4°C with 0.15 M NaCl and then with water.

tag: strain

value: dormant spores prepared in liquid

tag: sample type

value: highly purified over 7 days

tag: tissue type

value: chemically decoated spores


title: Patient 43

description:
Test
SAMPLE 43


title: C12_V2_C66

description: rawCounts.csv


title: Patient 39

description:
Test
SAMPLE 39


title: 1_1DPL

value: dormant spores prepared on plates

value: purified for only 1 day


title: 2_7DPL


title: Patient 38

description:
Test
SAMPLE 38


title: C10_V2_C64

description: rawCounts.csv


title: C11_V2_C65

description: rawCounts.csv


title: Patient 49

description:
Test
SAMPLE 49


title: Setlow_2018_10_31_S3

value: intact spores


title: Setlow_2018_10_31_S2

value: less well purified over 7 days


title: Patient 36

description:
Test
SAMPLE 36


title: Setlow_2018_10_31_S1


title: B8_V2_C11

description: rawCounts.csv


title: Setlow_2018_08_27_S2


title: Patient 37

description:
Test
SAMPLE 37

value: Female

value: African American


title: B6_V2_C57

description: rawCounts.csv


title: Setlow_2018_08_27_S1


title: Patient 33

description:
Test
SAMPLE 33


title: Patient 35

description:
Test
SAMPLE 35


title: Patient 32

description:
Test
SAMPLE 32


title: B9_V2_C10

description: rawCounts.csv


title: Patient 34

description:
Test
SAMPLE 34


title: Setlow_2018_08_27_S3


title: B7_V2_C12

description: rawCounts.csv


title: B5_V2_C56

description: rawCounts.csv


title: Patient 31

description:
Test
SAMPLE 31


title: B3_V1_C38

description: rawCounts.csv


title: IDG_E2

city: Bunkyo-ku

first: Mikihito

last: Hayashi

state: Tokyo

address: 1-5-45 Yushima

department: Graduate School of Medical and Dental Sciences

country: Japan

institute: Tokyo Medical and Dental University

hyb_protocol: Labeled samples were hybridized for 18 h at 48°C to GeneChip miRNA 4.0 Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA for Affymetrix data as normalization method.

label: biotin

organism: Mus musculus

source_name: IDG-SW3 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 800ng total RNA.

growth_protocol: IDG-SW3 cells (Woo et al., 2011), courtesy of Dr. Lynda Bonewald (University of Indiana) were maintained in normal growth medium (a-MEM  with 10% FBS ) throughout the experiment. Cells were seeded 24 hours prior to the stimulation.

extract_protocol: Total RNA was isolated using TRI Reagent according to the manufacturer’s instructions.

treatment_protocol: IDG-SW3 cells were stimulated with or without 10–7M E2 for 48 h.

value: Murine osteocyte

tag: treatment

value: 10–7M E2 for 48 h


title: B2_V2_C08

description: rawCounts.csv

value: day 90 of retinal organoid differentiation

value: human ESC (CRX-GFP line)


title: B4_V2_C55

description: rawCounts.csv


title: Patient 30

description:
Test
SAMPLE 30

value: patient who underwent a myocardial infarction


title: Patient 29

description:
Test
SAMPLE 29

value: plasma

value: Other


title: IDG_vehicle

tag: cell line

value: Vehicle control


title: FT3

city: Longyan

first: Yanfa

last: Sun

state: Fujian

address: Dongxiao North Road No. 1, Xinluo District

department: College of Life Science

country: China

institute: Longyan University

description:
fpkm.anno.txt
XC3

data_processing:
Raw reads of each sample were obtained from Illumina sequencing through removing low-quality reads, adaptor sequences and high content of unknown base N sequences.
The clean reads were mapped to the chicken reference genome using HISAT software . The map rate of genes was statistics after clean reads mapped to the chicken reference genome using Bowtie2 and the expression levels of gene were calculated by RSEM.
The genes differentially expressed genes (DEGs) between the FC and FT groups were identified using the DEseq2 method described . Genes with absolute value of log2(FT/FC) fold-Change ≥ 2.00 and adjusted P-value ≤ 0.05 were DEGs in this study. Pearson correlation plot of fragments per kilobase of exon per million fragments mapped (FPKM) values for DEGs of each sample was performed in R 3.4.3 software.
Genome_build: GCA_000002315.3
Supplementary_files_format_and_content: FPKMs

organism: Gallus gallus

source_name: abdominal fat tissue

extract_protocol:
Total RNA was isolated from abdominal fat tissue with the RNAsimple Total RNA kit (Tiangen Biotech Inc., Beijing, China) in accordance with the manufacturer’s instructions.
mRNA was enriched from total RNA samples using oligo (DT) magnetic beads (Invitrogen, USA). Purified mRNA was first fragmented by RNA fragmentation kit (Ambion, USA), then first-strand cDNA was synthesized. Then the second-strand cDNA were synthesized according to the manufacturer’s instructions. The cDNA library was assessed with Agilent 2100 Bioanalyzer and ABI Step One Plus Real-Time PCR System.

treatment_protocol: The treated chickens  were fed basal diet supplemented with 50 mg/kg dietary DL-α-tocopheryl acetate (Xinchang Hebao biotechnology Co., Ltd, Xinchang, China), respectively in 42-day trial period.

tag: agent

value: vitamin E

value: abdominal fat tissue


title: B12_V2_C60

description: rawCounts.csv


title: B1_V2_C09

description: rawCounts.csv


title: unfertilized eggs_F1_female 18

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 18

hyb_protocol: A total of 600 ng of Cy3-cRNA of each sample was randomly distributed onto four slides. After 17h of hybridization at 65°C, the slides were washed and dried.

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent).

organism: Perca fluviatilis

source_name: unfertilized eggs, F1, female 18

label_protocol: The “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol” was followed for the sample preparation, hybridization, wash and scan of the slides and data extractions. Briefly, 150 ng of total RNA were used in the amplification/Cy3-labeling step. After this process, the samples were purified (RNeasy mini kit, Qiagen) and quantified using a NanoDrop (ND-1000). Samples exhibiting a yield higher than 1.03 µg of cRNA and a specific activity higher than 10.30 pmol cy3/µg of cRNA were fragmented and used to hybridize the arrays.

growth_protocol: Fish were handled in accordance with national and international guidelines for the protection of the animal welfare (Directive 2010/63/EU). Two populations of three years old perch originated from artificial reproductions in November 2011 were used. They correspond to (i) fish in a more advanced stage of the domestication process coming from breeders reared in recirculating aquaculture systems (RAS) for several generations (Fx population) and (ii) F1 perch originating from breeders collected in the Geneva Lake at the embryonic stage and reared in RAS conditions (F1 population). All animals used in the experiment have been reared in the fishfarm “Lucas Perches” until the fingerling (weaned juvenile) stages (Hampont, France) and were transferred to our indoor facilities in February 2012 (mean weight of 3.78 ± 1.07 g). They grew up until they attained the mean weight of 287 ± 89 g in the same RAS conditions, meaning a constant photoperiod (L:D - 16:8) and the temperature between 20°C and 21°C. In these conditions the oogenesis is not stimulated, remaining the fish at sexual rest (Migaud et al., 2004; Abdulfatah et al., 2011). About two months before the beginning of the experiment (May 2014), the 654 perch (313 from the Fx and 341 from the F1 populations) were divided into 6 independent groups (3 per population with equivalent number of fish in each group). Fish were put into 6 identical rooms called “ecotron” and containing each a similar RAS (3000 liters) on which the lightening conditions (photoperiod, light intensity) and temperature were controlled. During the adaptation phase, the environmental conditions correspond to a constant photoperiod (L:D - 16:8) with a light intensity of 300 lx at the water surface and the temperature was kept between 20°C and 21°C. To trigger the induction of the gonadogenesis, breeders were submitted to a photothermal program allowing effective induction of reproduction cycle (Fontaine, Wang & Hermelink, 2015) from the 18th August 2014 to June 22nd 2015. Water levels of pH (9.53 ± 0.07 and 9.73 ± 0.12), dissolved oxygen (7.55 ± 0.10 mg/L and 7.47 ± 0.00 mg/L), nitrite (0.29 ± 0.14 mg/L and 0.09 ± 0.01 mg/L) and ammonium (0.67 ± 0.22 mg/L and 0.27 ± 0.02 mg/L) were monitored twice a week and kept under the respective thresholds in breeders’ tanks (for F1 and Fx populations, respectively). At the beginning of the experiment, all animals were individually marked with PIT-Tags (Transponder ISO 2 x 12 mm, Biolog-id) to individualize the follow up of their history all along the experiment.  All fish were fed twice a day to satiation five days a week. In alternation, they were fed three days with commercial pellets (Sturgeon Grower N°5, Le Gouessant) and two days with frozen squids and shrimps (Pomona). On Saturdays and Sundays they were fed once with the commercial pellets ad libitum.

extract_protocol: Total RNA were extracted from 32 samples (19F1 and 13Fx; mean weight of 100 mg) of, non-fertilized frozen eggs using TRIzol reagent (Life Technologies) at a ratio of 100mg per mL of reagent and following the manufacturer's instructions with some modifications. Indeed, a step of milling was added during the homogenizing step to get rid more easily of the gelatinous envelope and the chorion surrounding the eggs. To do so, a bullet blender (Next Advance) and zirconium oxide beads 1.0mm were used. In addition, a supplementary centrifugation (4°C, 30min. 13000rpm) was performed before the addition of the chloroform to remove the high lipids content in the eggs. A NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies) was used to evaluate the quantity of total RNA and an Agilent 2100 Bioanalyzer (Agilent Technologies) was used to evaluate the integrity of the RNA extracted. Samples exhibited an integrity score higher than 7 and were used for the microarray analysis.

treatment_protocol: Gametes collection and fertilization - Before the spawning season, all the females were caught to take some oocytes using a catheter and determine their level of oocytes maturation according to (Żarski et al., 2011, 2017). The spawning season took place from May 29th to June 22nd 2015. All females of a tank were monitored depending on scale elaborated by (Żarski et al., 2011), to analyze the oocytes maturation progression. Spawn were collected and separated into two parts. The first one was fertilized as described in (Żarski et al., 2012) with a mixture of sperm from 3 males (total volume of 100 µl sperm/g dry eggs). All males used to perform the fertilization came from the F1 population because they presented a higher quality (motility estimated under light upright optical microscope (Nikon Eclipse Ni-U). The other part of the spawn was immediately frozen in liquid nitrogen and then it was kept at -80°C for the subsequent transcriptomic analysis. Study of reproductive performance - In total 32 spawn (13 from the population Fx and 19 from the F1) were studied to determine the early developmental performance. The following description was performed for each spawn. Just after the fertilization, three samples of around 100 eggs were taken randomly in the spawn and used to determine the survival rate at 24, 48, 72 and 120h as described in (Alix et al., 2017). In addition, three other samples of 100 eggs/sample were kept apart until the hatching period. They were used to determine the hatching rate and the deformities rates according to (Alix et al., 2017). Total (Dr) and specific deformities rates were studied in the axis (Ad), yolk (Yd), cardiac (Cd), mouth (Md), eyes (Ed) and others (Od). They were calculated in reference to the total number of embryos showing some type of deformity.

value: unfertilized eggs

tag: population

value: female


title: unfertilized eggs_F1_female 17

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 17

source_name: unfertilized eggs, F1, female 17


title: Patient 28

description:
Test
SAMPLE 28

value: Male

value: Caucasian


title: unfertilized eggs_F1_female 16

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 16

source_name: unfertilized eggs, F1, female 16


title: Patient 27

description:
Test
SAMPLE 27


title: FT2

description:
fpkm.anno.txt
XC2


title: B11_V2_C59

description: rawCounts.csv

tag: condition


title: Patient 26

description:
Test
SAMPLE 26


title: FT1

description:
fpkm.anno.txt
XC1


title: B10_V2_C58

description: rawCounts.csv

tag: cell type


title: FC3

description:
fpkm.anno.txt
FC3

value: control


title: unfertilized eggs_Fx_female 13

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 13

source_name: unfertilized eggs, Fx, female 13

value: Fx


title: A9_V2_C04

description: rawCounts.csv


title: unfertilized eggs_Fx_female 12

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 12

source_name: unfertilized eggs, Fx, female 12


title: Patient 24

description:
Test
SAMPLE 24


title: FC2

description:
fpkm.anno.txt
FC2


title: unfertilized eggs_Fx_female 11

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 11

source_name: unfertilized eggs, Fx, female 11


title: A8_V1_C49

description: rawCounts.csv


title: FC1

description:
fpkm.anno.txt
FC1


title: Patient 23

description:
Test
SAMPLE 23

value: Female


title: A7_V2_C06

description: rawCounts.csv


title: unfertilized eggs_Fx_female 10

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 10

source_name: unfertilized eggs, Fx, female 10


title: 10775_HC4met

city: Gainesville

first: Laurence

last: Morel

state: FL

address: 1395 Center Drive, D6-6

department: Pathology and Immunology

institute: University of Florida

hyb_protocol: Labeled cDNA was hybridized to microarrays according to Affymetrix (currently Thermo Fisher) instructions. Prehybridization mix was applied for 30 minutes to all microarray, after which  5.2 ug of ss-DNA was injected and hybridized for 16 hours at 45C at 60 rpm.

scan_protocol: GeneChip Scanner 3000 7G using AGCC software

data_processing: Data was analyzed using Partek Genomic Suite version 6.6. Raw CEL files were imported and normalized with the RMA procedure with quantile normalization.  and median polish. Statistical testing was performed with ANOVA for all groups and paired t-test for HC vs HC metformin treated or SLE vs SLE metformin treated.

source_name: Control CD4 T cell

label_protocol: Amplified cDNA was fragmented with UDG and APE1 enzymes according to Affymetrix instructions. Labeling was performed with TdT with biotin reagent followed by streptavidin/phycoerythrin.

growth_protocol: complete RPMI media with 10% FBS, antibiotc/antimycotic

extract_protocol: (Qiagen Rneasy Mini Kit). CD4 T cells lysed in RLT buffer with Beta-mercaptoethanol.  RNA was eluted with ddH20 and stored at -80c until further use.

treatment_protocol: stimulation with CD3 and CD28 antibody in culture for 24 hours, treatment with 1mM Metformin.

value: CD4 T cell

tag: diagnosis

value: healthy

tag: sledai

tag: ethnicity

tag: prednisone use


title: unfertilized eggs_F1_female 15

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 15

source_name: unfertilized eggs, F1, female 15

tag: gender


title: Patient 22

description:
Test
SAMPLE 22

tag: individual

tag: tissue

tag: race

tag: diabetes


title: A6_V2_C51

description: rawCounts.csv

value: day 90 of retinal organoid differentiation


title: H1N1-infected MOI 5 A549 (rep3)

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps University Marburg

data_processing:
Raw Ct data are shown in non-normalized_data.txt (linked to the Series record). miR-ath-159a was used for normalization, yielding deltaCt values.
Fold changes were calculated with the the ddCt method (2^-ddCt)

label: FAM/NFQ-MGB

source_name: H1N1 Infection, MOI 5, 12 h

label_protocol: RNA was reverse transcribed with the Life Technologies miR RT kit wiith megaplex primers. Reverse transcribed RNA was then run on a TLDA plate with FAM-labelled primers

growth_protocol: A549 cells were routinely grown in RPMI1640 + 10% FCS

extract_protocol: Total RNA was isolated by cell lysis in Trizol and subsequent phenol/chloroform precipitation. miR-ath-159a was spiked in.

treatment_protocol: Cells were infected with Influenza H1N1 MOI 0.1 or MOI 5 for 12 h or left uninfected

value: A549, ATCC-purchased

tag: infection

tag: moi


title: 10769_HC3

tag: age


title: 10770_HC4


title: unfertilized eggs_F1_female 14

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 14

source_name: unfertilized eggs, F1, female 14


title: Patient 21

description:
Test
SAMPLE 21

value: patient who underwent a myocardial infarction

tag: omega-3 fatty acid therapy


title: 10773_HC2met

value: African American


title: 10772_HC1met


title: 10771_HC5


title: 10774_HC3met


title: 10776_HC5met


title: Patient 20

description:
Test
SAMPLE 20

value: plasma


title: H1N1-infected MOI 5 A549 (rep2)

tag: cell line


title: A5_V1_C80

description: rawCounts.csv

source_name: human ESC

value: human ESC (CRX-GFP line)


title: unfertilized eggs_F1_female 13

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 13

source_name: unfertilized eggs, F1, female 13

tag: population


title: A4_V2_C49

description: rawCounts.csv

tag: condition


title: 10765_SLE4met

source_name: Lupus CD4 T cell

tag: cell type

value: systemic lupus erythematosus (SLE)

value: No


title: unfertilized eggs_F1_female 12

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 12

source_name: unfertilized eggs, F1, female 12

value: unfertilized eggs


title: 10766_SLE5met

value: female

tag: diagnosis


title: 10760_SLE4

tag: sledai


title: Patient 18

description:
Test
SAMPLE 18

source_name: Plasma extracelular RNA

value: Male


title: A2_V2_C02

description: rawCounts.csv


title: Patient 17

description:
Test
SAMPLE 17

value: Caucasian


title: Patient 25

description:
Test
SAMPLE 25


title: A3_V2_C01

description: rawCounts.csv


title: Patient 19

description:
Test
SAMPLE 19


title: H1N1-infected MOI 0.1 A549 (rep2)

source_name: H1N1 Infection, MOI 0.1, 12 h


title: 10758_SLE2

tag: ethnicity


title: A1_V2_C03

description: rawCounts.csv


title: unfertilized eggs_F1_female 11

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 11

source_name: unfertilized eggs, F1, female 11


title: Patient 16

description:
Test
SAMPLE 16


title: 10763_SLE2met

tag: prednisone use


title: 10762_SLE1met

tag: gender

value: Yes


title: unfertilized eggs_Fx_female 9

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 9

source_name: unfertilized eggs, Fx, female 9

value: Fx


title: uninfected A549 (rep3)

source_name: mock

value: mock


title: 10759_SLE3

value: CD4 T cell


title: A12_V2_C54

description: rawCounts.csv


title: Patient 15

description:
Test
SAMPLE 15

tag: individual

value: Female


title: Patient 14

description:
Test
SAMPLE 14

tag: tissue


title: A11_V2_C53

description: rawCounts.csv

value: day 90 of retinal organoid differentiation


title: 10761_SLE5


title: A10_V2_C52

description: rawCounts.csv


title: Patient 13

description:
Test
SAMPLE 13

tag: race


title: uninfected A549 (rep1)

value: A549, ATCC-purchased


title: unfertilized eggs_Fx_female 7

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 7

source_name: unfertilized eggs, Fx, female 7


title: 10757_SLE1


title: unfertilized eggs_Fx_female 8

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 8

source_name: unfertilized eggs, Fx, female 8


title: unfertilized eggs_F1_female 10

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 10

source_name: unfertilized eggs, F1, female 10


title: H1N1-infected MOI 0.1 A549 (rep3)


title: uninfected A549 (rep2)


title: Patient 12

description:
Test
SAMPLE 12

value: patient who underwent a myocardial infarction

tag: diabetes


title: suppressor B cells 3

city: Brest

first: Sophie

last: Hillion

address: Felix le Dantec

institute: INSERM U1227

data_processing:
Fastq files are mapped to hg19 whole genome using STAR and annoted using FeatureCount v1.4.6-p4 and Ensembl 75
Genome_build: hg19
Supplementary_files_format_and_content: tsv files include raw counts and gene length generated by FeatureCount

source_name: Blood

growth_protocol: For the co-culture 4 conditions were carried out: Naive CD4+ T cells alone, Memory CD4+ T cells alone, Naive CD4+ T cells + B cells and memory CD4+ T cells + B cells with 1:1 ratio. All cells were putted in a plate 96 wells coated with F(ab’)2 fragment goat anti-mouse IgG (Jackson ImmunoReasearch) and in RPMI 1640 medium (SIGMA) containing 10% SVF, 100 U/ml penicillin G, 100 μg/ml streptomycin and 2 mM L-glutamine. CD4+ T cells were stimulated with mouse antibodies anti-CD3 (1000 ng/ml, OKT3, Biolegend) and mouse antibodies anti-CD28 (200ng/ml, CD28.2, Beckman coulter). After 4 or 5 days, B cell were sorted by flow cytometry.

extract_protocol:
RNA from sorted B cells were extracted using the  Guanidine Isothiocyanate method.The starting material (1 µg) of total RNA was mRNA enriched using the oligodT bead system. Illumina TruSeq® Stranded mRNA sample preparation kit was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: suppressor B cell

tag: culture condition

value: cultured with CD3/28 stimulated memory blood T cells during 5 days


title: unfertilized eggs_F1_female 9

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 9

source_name: unfertilized eggs, F1, female 9


title: suppressor B cells 2


title: unfertilized eggs_F1_female 8

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 8

source_name: unfertilized eggs, F1, female 8


title: Patient 11

description:
Test
SAMPLE 11

value: plasma


title: suppressor B cells 1


title: Patient 10

description:
Test
SAMPLE 10


title: Patient 9

description:
Test
SAMPLE 9


title: Patient 8

description:
Test
SAMPLE 8


title: effector B cells 3

value: effector B cell

value: cultured with CD3/28 stimulated naive blood T cells during 5 days


title: effector B cells 1


title: Patient 7

description:
Test
SAMPLE 7


title: effector B cells 2


title: 10768_HC2

source_name: Control CD4 T cell

value: healthy

value: African American


title: unfertilized eggs_F1_female 7

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 7

source_name: unfertilized eggs, F1, female 7

value: unfertilized eggs

value: female


title: Patient 6

description:
Test
SAMPLE 6

value: Hispanic


title: unfertilized eggs_F1_female 6

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 6

source_name: unfertilized eggs, F1, female 6


title: unfertilized eggs_Fx_female 6

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 6

source_name: unfertilized eggs, Fx, female 6

value: Fx


title: Ipme17-2

city: Amiens

first: Christopher

last: Wattier

state: Somme

address: 33 rue Saint Leu

department: Faculté des Sciences

institute: Université de Picardie Jules Verne

description: pme17 infected biological replicate 2 technical replicate 1

hyb_protocol: Hybridization was performed overnight at 42°C using a 4-position NimbleGen hybridization station

scan_protocol: Slides were scanned using an Axon GenePix 4400 A scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) piloted by GenePix pro software (Axon). Scanned images were then imported into NimbleScan software or DEVA software (NimbleGen Systems, Inc. Madison, WI, USA) for grid alignment and expression data analyses.

data_processing: Raw data (.pair files)  were normalized using intra-array (RMA background correction) and inter-array (quantile) normalizations using  ANAIS software (Simon & Biot, 2010)

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana pme17 infected

label_protocol: Labeling was performed following NimbleGen One-color labeling kit instructions (Roche)

growth_protocol: Leaves of Columbia-0 (Col), Wassilewskija (WS) and pme17 (KO mutant) were used, grown at 23°C in a Percival growth room during three weeks.

extract_protocol: Total RNA was extract according to Gehrig et al. 2000 and Verwoerd et al. 1989  and DNA was removed using the Ambion TURBO-DNAfree kit. RNA was quantified using Nanodrop 1000 spectrophotometer (Thermo Scientific) and RNA quality was assessed using Eukaryote total RNA Standard Sensitivity chips on the Experion system (Biorad). All extract protocols were performed at the Centre de Ressources Régionales en Biologie Moléculaire (Université de Picardie Jules Verne, Amiens).

treatment_protocol: Three mature leaves of Col, WS or pme17 were infested with 60 adults of Myzus persicae during 24h, in a growth chamber at 23°C.

tag: ecotype

value: Wassilewskija-0 (WS)

tag: genotype/variation

value: pme17 (KO mutant)

tag: infected with

value: 60 adults of Myzus persicae


title: Ipme17-4

description: pme17 infected biological replicate 3 technical replicate 2


title: Ipme17-3

description: pme17 infected biological replicate 3 technical replicate 1


title: Patient 5

description:
Test
SAMPLE 5

value: Male

value: Caucasian

tag: omega-3 fatty acid therapy

tag: age


title: 10767_HC1

value: CD4 T cell


title: 10764_SLE3met

source_name: Lupus CD4 T cell

value: systemic lupus erythematosus (SLE)

value: Yes


title: Ipme17-1

description: pme17 infected biological replicate 1 technical replicate 1


title: Patient 4

description:
Test
SAMPLE 4

source_name: Plasma extracelular RNA

value: patient who underwent a myocardial infarction

value: plasma

value: Female

value: Other


title: unfertilized eggs_Fx_female 4

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 4

source_name: unfertilized eggs, Fx, female 4

tag: population


title: unfertilized eggs_F1_female 3

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 3

source_name: unfertilized eggs, F1, female 3

tag: cell type


title: unfertilized eggs_F1_female 4

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 4

source_name: unfertilized eggs, F1, female 4


title: H1N1-infected MOI 0.1 A549 (rep1)

source_name: H1N1 Infection, MOI 0.1, 12 h

tag: cell line

value: A549, ATCC-purchased

tag: infection

tag: moi


title: pme17-5

description: pme17 control biological replicate 3 technical replicate 2

source_name: Arabidopsis thaliana pme17 control

value: none (control)


title: pme17-4

description: pme17 control biological replicate 3 technical replicate 1


title: H1299 Omomyc biological replica 5

city: Barcelona

first: Marie-Eve

last: Beaulieu

state: Catalunya

address: Natzaret 115-117

country: Spain

institute: Peptomyc

hyb_protocol: Total RNA was linearly amplified using WT Plus (Affymetrix). The resulting ssDNA was used to hybridize Affimetrix microarrays. Hybridization data was acquired using the Affimetrix GeneChip/GeneTitan platforms. Transcriptomes were determined on a genome wide Clariom S Human HT (Affimetrix).

scan_protocol: Arrays were scanned on a Affymetrix GeneTitan instrument (ThermoFisher Scientific-Affymetrix) according to the manufacturer’s protocol.

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology and analyzed using Partek Genomic Suite followed by GSEA 3.0 software from Broad Institute.

label: Biotin

label_protocol: Labeling of samples was carried out according to the manufacturer’s standard protocol

growth_protocol: Cells were grown at 37ºC, 5% CO2 in RPMI1640 supplemented with glutamine and 10% FBS

extract_protocol: Total RNA were extracted using TRIzol following manufacturer's procedures. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were plated and after overnight incubation, vehicle or 12.8 µM Omomyc treatement were added

tag: tumor type

value: lung carcinoma

tag: treatment

value: Omomyc


title: Patient 3

description:
Test
SAMPLE 3

tag: individual

tag: gender


title: unfertilized eggs_Fx_female 5

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 5

source_name: unfertilized eggs, Fx, female 5

value: unfertilized eggs

value: Fx

value: female


title: unfertilized eggs_F1_female 5

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 5

source_name: unfertilized eggs, F1, female 5


title: pme17-3

description: pme17 control biological replicate 2 technical replicate 2

value: Wassilewskija-0 (WS)

value: pme17 (KO mutant)


title: H1299 Omomyc biological replica 4


title: Patient 2

description:
Test
SAMPLE 2

tag: tissue

value: Male

tag: race

value: Caucasian


title: Patient 1

description:
Test
SAMPLE 1

tag: diabetes


title: H1N1-infected MOI 5 A549 (rep1)

source_name: H1N1 Infection, MOI 5, 12 h


title: pme17-2

description: pme17 control biological replicate 2 technical replicate 1

tag: ecotype


title: High 2 (2000-3)

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

data_processing:
base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Escherichia coli K-12

source_name: E. coli bacteria + P. putida bacteria + IncPα plasmid

growth_protocol: liquid LB culture at 37 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed wild-type strains E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid were cultured in triplicate in 10 mL PBS containing 0, 0.02, 20 and 2000 μg/L triclosan for 2h, at 25 °C, without shaking

tag: strain

value: E. coli K12 LE392


title: High 1 (2000-2)


title: Medium 2 (20-3)


title: unfertilized eggs_F1_female 1

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 1

source_name: unfertilized eggs, F1, female 1


title: unfertilized eggs_F1_female 2

description:
cRNA
Gene expression in unfertilized eggs from population F1, female 2

source_name: unfertilized eggs, F1, female 2


title: pme17-1

description: pme17 control biological replicate 1 technical replicate 1

tag: genotype/variation

tag: infected with


title: InfCol-6

description: Col infected biological replicate 3 technical replicate 2

source_name: Arabidopsis thaliana COL infected

value: Columbia-0 (Col)

value: wild type

value: 60 adults of Myzus persicae


title: H1299 Omomyc biological replica 3


title: H1299 Omomyc biological replica 2


title: cKO_MPP_mouse9

city: Rozzano

first: Francesca

last: Ficara

state: MI

address: via Manzoni 56

country: Italy

institute: CNR/Istituto Clinico Humanitas

description:
cKO_MPP
SAMPLE 18

data_processing:
Non-expressed miRNAs (Ct level ≥35) were filtered out, whereas miRNAs expressed in at least one of the four groups were further analyzed.
Quantile normalization
Differential expression analysis was performed by Statistical Analysis of Microarray (SAM) (FDR with q-value <0.1)

source_name: Bone Marrow

label_protocol: TaqMan Megaplex™ Pools system, RT coupled with Preamplification, Rodent Pools A (Megaplex™ RT Primers catalog number 4399970; Megaplex™ PreAmp Primers catalog number 4399203)

extract_protocol: MirVana isolation kit

treatment_protocol: 7 poly(I:C) injections every other day, 5 weeks prior to cell sorting

value: Bone Marrow

value: Flk2neg MPP

tag: genotype

value: Mx1Cre+ Pbx1f/f


title: cKO_HSC_mouse9

description:
cKO_HSC
SAMPLE 17

value: HSC


title: Medium 1 (20-2)


title: InfCol-5

description: Col infected biological replicate 3 technical replicate 1


title: cKO_MPP_mouse8

description:
cKO_MPP
SAMPLE 16


title: H1299 PBS biological replica 2

value: lung carcinoma

value: PBS


title: H1299 PBS biological replica 1


title: H1299 PBS biological replica 5


title: H1299 PBS biological replica 3


title: H1299 Omomyc biological replica 1

value: Omomyc


title: H1299 PBS biological replica 4


title: unfertilized eggs_Fx_female 3

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 3

source_name: unfertilized eggs, Fx, female 3

value: unfertilized eggs

tag: population

value: Fx


title: cKO_HSC_mouse8

description:
cKO_HSC
SAMPLE 15

tag: cell type


title: unfertilized eggs_Fx_female 2

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 2

source_name: unfertilized eggs, Fx, female 2

value: female


title: Low 2 (0_02-2)


title: unfertilized eggs_Fx_female 1

description:
cRNA
Gene expression in unfertilized eggs from population Fx, female 1

source_name: unfertilized eggs, Fx, female 1


title: InfCol-3

description: Col infected biological replicate 2 technical replicate 1


title: Col-6

description: Col control biological replicate 3 technical replicate 2

source_name: Arabidopsis thaliana COL control

value: none (control)


title: InfCol-2

description: Col infected biological replicate 1 technical replicate 2


title: InfCol-4

description: Col infected biological replicate 2 technical replicate 2


title: A549 Omomyc biological replica 3

tag: cell line


title: Low 1 (0_02-1)


title: cKO_MPP_mouse7

description:
cKO_MPP
SAMPLE 14


title: Col-5

description: Col control biological replicate 3 technical replicate 1


title: InfCol-1

description: Col infected biological replicate 1 technical replicate 1


title: Con 1


title: Con 2


title: A549 Omomyc biological replica 2


title: cKO_HSC_mouse7

description:
cKO_HSC
SAMPLE 13


title: Col-4

description: Col control biological replicate 2 technical replicate 2


title: cKO_HSC_mouse6

description:
cKO_HSC
SAMPLE 11


title: cKO_MPP_mouse6

description:
cKO_MPP
SAMPLE 12


title: cKO_MPP_mouse5

description:
cKO_MPP
SAMPLE 10


title: cKO_HSC_mouse5

description:
cKO_HSC
SAMPLE 9


title: A549 PBS biological replica 3


title: Cont_HSC_mouse4

description:
Cont_HSC
SAMPLE 7

value: Mx1Cre- Pbx1f/f


title: Patient 3_clusters_rep2

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

institute: AltraBio

description: Gene expression data from young human skin obtained from abdominoplasty

hyb_protocol: hybridization, washing and staining were performed using an Affymetrix GeneTitan system

scan_protocol: scanning was performed using an Affymetrix GeneTitan system

data_processing: Affymetrix CEL files were analyzed in R using the Bioconductor suite of packages. Raw probe signals were background-corrected using the maximum likelihood estimation of the normal-exponential mixture model and normalized using the quantile normalization. For summarization, probe signals for each probe set of each sample were summarized into a single value using the summarization step of the Robust Multichip Average (RMA) approach

source_name: cell clusters from human papillary dermis

label_protocol: RNA were biotinylated using the following kits C&E Version ExpressArt TRinucleotide mRNA amplification Pico kit (AmpTech) and ExpressArt® Biotin Add-On (AmpTech) according to manufacturer instructions.

growth_protocol: Skin biopsies from women abdominoplasty were collected following the French Health National Authority approval and informed consent from donors.  12 mm punches were performed from six different donors aged between 23 and 41 and used for laser microdissection experiments after adipose tissue removal.

extract_protocol: RNA extraction was performed using Arcturus PicoPure® RNA Isolation Kit (Thermo Fisher Scientific), according to manufacturer instructions.

treatment_protocol: Laser Capture Microdissection was performed on 8 µm thick sections of frozen human adult skin to isolate the cells. Laser capture was performed using CapSure® LCM MacroCap caps (Excilone, France) for cell clusters or CapSure® LCM HS caps (Excilone, France) for single cells. Microdissection efficiency was evaluated by examining the cap after capture and the remaining tissue before and after lifting off the cap. For single cells, 20-50 cells/cap were captured. For cell clusters, around 20-30 clusters/cap were captured.

value: adult skin

tag: age

value: Young donors between 24 and 33 years old


title: A549 PBS biological replica 1


title: Col-3

description: Col control biological replicate 2 technical replicate 1

value: Columbia-0 (Col)


title: A549 Omomyc biological replica 1


title: A549 PBS biological replica 4


title: H1975 Omomyc biological replica 5

value: lung adenocarcinoma


title: Patient 3_reticular_rep2

source_name: single cells from human reticular dermis


title: Col-2

description: Col control biological replicate 1 technical replicate 2

value: wild type


title: Cont_HSC_mouse3

description:
Cont_HSC
SAMPLE 5

value: Bone Marrow


title: Cont_MPP_mouse3

description:
Cont_MPP
SAMPLE 6

value: Flk2neg MPP


title: InfWS-5

description: WS infected biological replicate 3 technical replicate 1

source_name: Arabidopsis thaliana WS infected

value: Wassilewskija-0 (WS)

value: 60 adults of Myzus persicae


title: InfWS-3

description: WS infected biological replicate 2 technical replicate 1


title: Col-1

description: Col control biological replicate 1 technical replicate 1


title: H1975 Omomyc biological replica 4


title: Cont_MPP_mouse4

description:
Cont_MPP
SAMPLE 8


title: A549 PBS biological replica 2

value: lung carcinoma


title: InfWS-2

description: WS infected biological replicate 1 technical replicate 2


title: Patient 3_reticular_rep1


title: Patient 3_single cells_rep2

source_name: single cells from human papillary dermis


title: H1975 Omomyc biological replica 3


title: InfWS-1

description: WS infected biological replicate 1 technical replicate 1


title: Cont_MPP_mouse2

description:
Cont_MPP
SAMPLE 4


title: Patient 2_reticular_rep2


title: Cont_MPP_mouse1

description:
Cont_MPP
SAMPLE 2


title: Patient 3_clusters_rep1


title: HOPX-knockdown-3

city: La Jolla

first: Bryan

state: CA

address: 9500 Gilman Drive MC 0869

institute: UC San Diego

data_processing:
Removal of adaptor sequences and low-quality reads
Read alignment using STAR (2.5.3a).
Quantification by Partek E/M annotation model onto hg19 - RefSeq Transcripts v87
Genome_build: hg19
Supplementary_files_format_and_content: Counts, ratio

source_name: Neonatal foreskin

growth_protocol: Normal primary human keratinocytes were isolated from neonatal foreskins and cultured in a 50:50 mixture of 154 medium and KSFM medium (Life Technologies) with recommended manufacturer supplements, penicillin/streptomycin, and amphotericin.

extract_protocol:
Total RNA from shCTRL and shHOPX differentiated keratinocytes was extracted with Trizol reagent and purified using the Direct-zol RNA Miniprep Kit (Zymo Research, R2052).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Primary keratinocytes were infected with lentivirus expressing scramble control short hairpin RNA (shCTRL) or HOPX-targeting short hairpn RNA (shHOPX), selected with puromycin for two days, then differentiated for six days by plating keratinocytes in culture confluence in the presence of 1.2 mM calcium.

value: Primary human epidermal keratinocytes

value: shHOPX

tag: passage


title: InfWS-4

description: WS infected biological replicate 2 technical replicate 2


title: Cont_HSC_mouse1

description:
Cont_HSC
SAMPLE 1

value: HSC


title: Patient 2_clusters_rep2


title: H1975 PBS biological replica 4

tag: tumor type

value: PBS


title: H1975 Omomyc biological replica 1

tag: treatment

value: Omomyc


title: Patient 2_reticular_rep1


title: WS-4

description: WS control biological replicate 3 technical replicate 1

source_name: Arabidopsis thaliana WS control

value: none (control)


title: H1975 Omomyc biological replica 2


title: Cont_HSC_mouse2

description:
Cont_HSC
SAMPLE 3

value: Mx1Cre- Pbx1f/f


title: H1975 PBS biological replica 3


title: WS-2

description: WS control biological replicate 2 technical replicate 1


title: 11AC2HUA

city: Palo Alto

first: Ngan

last: Huang

address: 3801 Miranda Avenue

department: Cardiothoracic Surgery

institute: Stanford University

data_processing:
The raw data were checked for quality with FastQC (Version 0.11.7) and results were aggregated with MultiQC and were aligned to the mouse genome (GRCm38) using STAR (Version 2.5.3a) with ENCODE options for long RNA-seq pipeline.
The alignment results were assessed using Samtools and aggregated with MultiQC (Version 1.5) and the differential gene expression analysis of the uniquely mapped reads/raw counts was performed using the DESeq2 package (Version 1.20.0).
Each DE analysis was composed of a pairwise comparison between an experimental group and the control group. Differentially expressed genes were identified after false discovery rate (FDR = 0.05) correction.
Genome_build: mouse genome (GRCm38)
Supplementary_files_format_and_content: txt files contain DE comparison analysis as described above

organism:
Homo sapiens
Mus musculus

source_name: muscle and endothelial cells

growth_protocol: Mouse myoblasts (C2C12, ATCC) were expanded in a high serum DMEM with 20% FBS. Human microvascular ECs (Center for Disease Control) were expanded in 10% FBS and 1% penicillin/streptomycin in DMEM. All cell culture was performed with 1% penicillin/streptomycin at 37°C and 5% CO2. Where indicated, mouse myoblasts were lentivirally transduced to express GFP under the control of ubiquitin promoter.  For in vitro studies, four conditions were assessed: 1) randomly-oriented scaffold seeded with myoblasts; 2) randomly-oriented scaffolds seeded with myoblasts + ECs; 3) aligned scaffold seeded with myoblasts only; 4) aligned scaffold seeded with myoblasts + ECs. Collagen scaffold strips (25mm x 1mm) were sterilized with 70% ethanol and rehydrated with 3 washes with 1X PBS.  Mouse myoblasts (5x105) were seeded into each scaffold and cultured in a high serum DMEM with 20% FBS.  After 24 hours (Day 0), the growth medium was switched to DMEM containing 2% horse serum to induce differentiation and fusion of myoblasts. After 5 days of differentiation (Day 5) during which myoblasts have fused to form myotubes, ECs were cocultured into the myoblast-seeded scaffolds (5x105 cells/scaffold). For conditions with myoblasts only, no ECs were added. For all conditions, media was switched to a maintenance medium (DMEM supplemented with 2% horse serum and 3% FBS), and constructs were culture for an additional 4 days (Day 9).

extract_protocol:
RNA was isolated from cell lysates from engineered muscle and endothelialized engineering muscle on randomly-oriented or aligned scaffolds (n=3) according to the manufacture’s protocol (GeneJet RNA Purification Kit, Thermo Fisher). At least 1000ng of total RNA was pelleted per sample.
Library preparation and RNA Sequencing was performed by Novogene Corporation using the NovaSeq 6000 (Illumina) sequencing platform, and 150-bp paired-end reads were generated (20-30 million reads per sample). Briefly, RNA integrity was assessed (RNA Nano 6000 Assay Kit, Bioanalyzer 2100, Aligent Technologies, CA) and 3ug RNA per sample was used to generate sequencing libraries (NEBNext Ultra RNA Library Prep Kit for Illumina) according to manufacturer’s recommendations. Library fragments were purified (AMPure XP system, Beckman Coulter, Beverly) to select cDNA fragments (150-200 bp in length). PCR was performed with Phusion High-Fidelity DNA polymerase, and purified by the AMPure XP system and assessed for quality on the Agilent Bioanalyzer 2100 system.

value: C2C12 mouse myoblasts and human microvascular endothelial cells (HMEC-1)

tag: passages


title: Brain_trehalose_10day_sample3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Mice were housed in groups of three mice per cage at 22°C in a 12h light/dark cycle and given free access to diet and water.

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

treatment_protocol: Brain tissue (the cerebral cortex and neocortex area) were harvested after 6h starved condition.

tag: gender

value: male

value: 9-weeks old

tag: agent

value: trehalose

tag: time

value: Brain


title: Patient 2_single cells_rep1

tag: tissue

value: adult skin

value: Young donors between 24 and 33 years old


title: Patient 2_single cells_rep2


title: H1975 PBS biological replica 1

value: lung adenocarcinoma


title: Patient 2_clusters_rep1


title: H1975 PBS biological replica 2


title: Brain_trehalose_1day_sample3


title: Patient 1_reticular_rep2


title: 10AC1HUA


title: WS-1

description: WS control biological replicate 1 technical replicate 1

tag: ecotype

value: Wassilewskija-0 (WS)

value: wild type


title: HOPX-knockdown-1

value: Primary human epidermal keratinocytes


title: 9RC3HUA

tag: strain


title: Patient 1_clusters_rep2


title: Brain_trehalose_10day_sample2


title: HOPX-knockdown-2

tag: genotype/variation

value: shHOPX


title: 8RC2HUA


title: Control-2

value: shCTRL


title: Control-1


title: 7RC1HUA


title: Patient 1_single cells_rep2


title: Brain_trehalose_0day_sample2

value: control


title: Brain_trehalose_1day_sample2


title: Patient 1_reticular_rep1


title: GM20390 (ATAC-seq)

status: Public on Mar 31 2019

first: Arko

last: Sen

state: California

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
processing pipeline IGC core
For analysis all replicates were aligned to hg19 genome assembly and the resulting bam files were combined for downstream analysis. RPKM normalized bigWig files from merged bam files were generated using Deeptools
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigWig

source_name: blood derived tumor cells

growth_protocol: Cell lines Jurkat, MOLT-4, CCRF-CEM, RPMI-8402, and K-562 were grown in RPMI 1640 + L-glutamine (Gibco cat #11875-085) with HI-FBS (Heat Inactivated Fetal Bovine Serum, GemCell cat # 100-500, lot A22F) 5% for Jurkat and 15% for all other cells lines.  Cells were maintained within their optimal growth range by dilution with fresh media as needed in T75 untreated suspension cell culture flasks with vented caps, at 37C, 5% CO2.

extract_protocol:
ATAC-seq experiments for the Jurkat, MOLT-4, CCRF-CEM, RPMI-8402 and K-562 cell lines were performed using the Omni-ATAC-seq method. In each experiment, 1 x10^5 cells were centrifuged at 1000 x g for 10 min at 4 ºC. Following aspiration, a cell count of the supernatant was performed, the remaining cell number was calculated, and all further reagents in the protocol were titrated to this cell number.
Library construction was conducted using the Omni-ATAC-seq method.  For every 5 x 10^5 cells, nuclei were isolated in 50 ul cold ATAC-Resuspension Buffer (RSB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin, and pipet-mixed up-and-down at least 5 times. Nuclei isolation mix was incubated on ice for 3 exactly minutes, washed in 1 ml of cold ATAC-RSB containing 0.1% Tween-20 (but no NP40 or Digitonin) and centrifuged at 1000 x g for 10 min at 4 ºC. Nuclear DNA was tagmented in 50 ul Transposition mix (25ul 2 × TD buffer, 2.5ul transposase (100nM final), 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 16.5 ul PBS and 5 ul diH2O), and incubated in a thermomixer at 37°C, 1000 x g for 30 min. Tagmented DNA was purified with Zymo DNA Clean and Concentrator-5 Kit (cat# D4014). Library amplification was performed using custom indexing Nextera primers from IDT in a 50 ul Kapa Hi Fi Hot Start PCR reaction (cat# KK2602). Following 3 initial cycles 1 ul of PCR reaction was diluted in 1 ml buffer (10mM Tris-HCl pH 8.0, 0.05% Tween) and 4 ul of each dilution were run in triplicate 20uL quantitative PCR (Kapa qPCR Library Quantitation Kit cat# KK4824) to calculate the optimum number of final amplification cycles. Library amplification was followed by SPRI size selection with Kapa Pure Beads (cat# KK8002) to retain only fragments between 80-1,200 bp. Library size was obtained on an Aglient Bio-Analyzer or TapeStation using a High Sensitivity DNA kit and factored into final Kapa qPCR results to calculate the final size-adjusted molarity of each library.
ATAC-seq libraries were pooled by size adjusted molarity and sequenced to obtain a minimum of 30 to 50 million reads from each cell line in paired-end 42 x 42 confirugration.

treatment_protocol: no treatment

tag: disease state

value: Childhood B acute lymphoblastic leukemia


title: KLC (ATAC-seq)

value: KLC

value: B acute lymphoblastic leukemia


title: Control-3


title: MOLM-13 (ATAC-seq)

value: Adult acute myeloid leukemia


title: RPMI-8402 (ATAC-seq)

value: Childhood T acute lymphoblastic leukemia


title: K-562 (ATAC-seq)

value: Chronic myelogenous leukemia


title: CCRF-CEM (ATAC-seq)

value: CCRF-CEM


title: MV4-11 (ATAC-seq)

value: Childhood acute monocytic leukemia


title: WS-3

description: WS control biological replicate 2 technical replicate 2

tag: infected with

value: none (control)


title: Brain_trehalose_10day_sample1

value: male

value: 9-weeks old

value: trehalose

value: Brain


title: MOLT-4 (ATAC-seq)

value: Adult T acute lymphoblastic leukemia


title: IPFl_IgG_ChIPSeq

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

institute: University of Bath

data_processing:
FASTQ sequencing data from control (n=5) and IPF (n=5) fibroblasts was aligned to hg38 using Bowtie 2: bowtie2 -q --very-fast <reference_genome.gtf>  -U <file_name.fastq> -S <output_file.sam>.
Output SAM files were then sorted and converted to BAM files (samtools sort -@ 8 –o output.bam output.sam), indexed (samtools index –b output.bam) in Samtools and then converted to BigWig format using BamCoverage (which is part of the deepTools suite) using the following command line: bamCoverage -b <input_bam.bam> --normalize UsingRPKM --binSize 30 --smoothLength 300 -p 10 --extendReads 200 -o <output_file.bw>.
Significant ChIPseq peaks (q = <0.1) in each sample were called with MACS2 using the broadpeak options: macs2 callpeak –t <sample> -c <backgrounf_igG> --broad - <output_files> -g hs.
The differential expression of H3K4me1 peaks was determined by inputing the individual Bam files (Bowtie2) and BED files (Broadpeaks output - MACS2) for control and IPF samples into Diffbind (version 2.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: BigWig

growth_protocol: 1 x 10^4 cells were plated in 96 cell culture wells on day 1 and allowed to adhere overnight. On day 2, cells were serum-deprived by reducing FBS to 0.1% in 200μl of starvation media.

extract_protocol:
Chromatin immunoprecipitation (ChIP) using a H3K4me1 antibody (Diagenode, C15410037) and the iDeal ChIP-seq kit for Histones kit (Diagenode, C01010051) was performed on the 5 control and 5 IPF fibroblast samples. In addition, we performed ChIP on a single control and IPF using an IgG antibody to provide a background control.
Paired-end 75bp sequencing data was obtained using the Illumina HiSeq4000 at the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (funded by Wellcome Trust grant reference 203141/Z/16/Z).

tag: subject status

value: idiopathetic pulmonary fibrosis (IPF) patient

tag: tissue/cell type

value: lung fibroblasts

tag: chip antibody

value: IgG antibody


title: Patient 1_single cells_rep1

value: adult skin

tag: age

value: Young donors between 24 and 33 years old


title: IPF_H3K4me1_ChIPSeq_3

value: Anti-H3K4me1 (Diagenode, C15410037)


title: Patient 1_clusters_rep1


title: IPF_H3K4me1_ChIPSeq_4


title: IPF_H3K4me1_ChIPSeq_1


title: control_IgG_ChIPSeq

value: Control


title: control_H3K4me1_ChIPSeq_2


title: control_H3K4me1_ChIPSeq_3


title: control_H3K4me1_ChIPSeq_5


title: Brain_trehalose_0day_sample1

value: control


title: Brain_trehalose_1day_sample1


title: JURKAT (ATAC-seq)

tag: cell line

value: JURKAT

value: Childhood T acute lymphoblastic leukemia


title: control_H3K4me1_ChIPSeq_1


title: IPF_H3K4me1_ChIPSeq_5


title: IPF_H3K4me1_ChIPSeq_2


title: control_H3K4me1_ChIPSeq_4


title: DN3-H3K4me3-2

city: Hershey

first: Sinisa

last: Dovat

state: PA

address: 500 University Dr

institute: Penn State University

description: ChIP-seq for H3K4me3

data_processing:
qc of fastq data,FastQC,version 0.11.4, cutoff 28
mapping,BWA,version 0.7.13, bwa aln -q 5 -l 32 -k 2
qc of mapped data, samtools,version 1.2, MAPQ > 30
qc of mapped data, PICARD, version 2.0.1
peak call, MACS2, version 2.1.1, q < 0.05
Genome_build: mm9
Supplementary_files_format_and_content: processed chip-seq files are in .bed format for peaks information and bigwig file for signal information

source_name: JE131 cell line (DN3 cells)

growth_protocol: cells were cultured in RPMI1640 with 10% FBS at 37℃ with 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions for KAPA HyperPrep kit.

treatment_protocol: DN3 cells were transduced with retrovirus that contains HA-tagged wild-type murine Ikaros for 1 day, 2 days and 3 days.

tag: cell type

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

tag: cell treatment

value: DN3 cells without transduction

value: anti-H3K4me3 (Abcam, ab8580)


title: DN3(IK)-H3K4me3-3d-2

description: ChIP-seq for H3K4me1

value: DN3 cells transduced with Ikaros for 3 days


title: DN3(IK)-H3K4me3-3d-1

description: ChIP-seq for H3K4me3


title: DN3-H3K4me3-1

description: ChIP-seq for H3K4me3


title: DN3(IK)-HA-2d-1

description: ChIP-seq for HA-tagged Ikaros

value: DN3 cells transduced with Ikaros for 2 days

value: anti-HA tag (Abcam, ab9110)


title: DN3(IK)-HA-3d-1

description: ChIP-seq for HA-tagged Ikaros


title: DN3(IK)-HA-1d-1

description: ChIP-seq for HA-tagged Ikaros

value: DN3 cells transduced with Ikaros for 1 day


title: AM_2 (mm10_2)

city: San Francisco

first: Ari

middle: B

last: Molofsky

address: 513 Parnassus Ave, HSW1201

department: Laboratory Medicine

institute: UCSF

data_processing:
Indexed BAM file containing position-sorted reads aligned to the genome and transcriptome using 10x Genomics Cell Ranger pipeline. See their website for their proprietary steps
Genome_build: mm10
Supplementary_files_format_and_content: The raw reads from the scRNA seq for each cell is the processed output: matrix.mtx is sparse matrix file of reads, the row and column names are attached together as barcodes.tsv and genes.tsv as annotated for each dataset.

source_name: CD45- Il33mcherry+ cells

extract_protocol:
10X Chromium Single Cell 3' v1
10X Chromium Single Cell 3' v1

treatment_protocol: IL-33 reporter mice on wild-type C57BL/6 background were used to prepare single cell suspensions from lung and gonadal adipose tissue (GAT) as previously described (Molofsky AB et al, Immunity 2015, Van Dyken SJ et al, Immunity 2014; Molofsky AB et al, J. Exp Med 2013).

tag: strain background

tag: status

value: Naive

value: Lung

value: CD45- Il33mcherry+ cells


title: AM_1 (mm10_1)

source_name: Total CD45- cells

value: Total CD45- cells


title: AM_4 (mm10_4)

value: 4 weeks post N.brasiliensis infection


title: AM_8 (mm10_8)

value: Naive (female)

value: Gonadal adipose tissue


title: DN3(IK)-HA-3d-2

description: ChIP-seq for HA-tagged Ikaros


title: Raji-stimulated CAR-T cells 1

city: New York

first: Kam

last: Leong

state: NY

address: 3600 Broadway, RM450C

department: Biomedical Engineering

institute: Columbia University

data_processing:
Sequencing data was generated on Illumina HiSeq 2500 instrument, same as GSE109535.
Casava 1.8.2 and bcl2fastq2 v2.19.0 were used for fastq generation.
Sequenced reads were trimmed for adaptor sequence, preprocessed for cell barcodes and unique molecular index, and  then mapped to hg19 genome(STAR v2.5.2b).
Genome_build: hg19
Supplementary_files_format_and_content: Text files of expression matrix used in analysis.  The Seurat package (V2.3.0) in R (V3.4.1) was applied to identify differentially expressed genes among 3817 single cells. Cells were considered in the analysis only if they met the following quality control criteria: low expression of mitochondrial genes (<10% of total counts in a cell). The name of each column is the cell barcode.

growth_protocol: Human anti-CD19scFv-CD28-4-1BB-CD3ζ (Promab) T cells were cultured in complete X-Vivo 10 (Lonza) medium supplemented with IL2 (10 ng/mL, Biolegend) at a concentration of 0.5 x 10e6 cells/mL.

extract_protocol:
CAR-T cells were loaded to a microwell-based chip (sc-FTDseq) for mRNA capture by uniquely barcoded beads. The cells were lysed using three cycles of freeze-thaw .
The single cell mRNA libraries were prepared using the DropSeq protocol (GSE63473), tagged with Illumina nextera single indexes (N701, N702, N703, N704, N705, N706). We used the same protocol as in scFTD-seq(GSE109535), where each mRNA captured was end-paired with an unique molecular index(UMI) and a cell barcode.

treatment_protocol: T cells were isolated from three healthy donors. CAR-T cells used in this study were manufactured through ex vivo transduction of autologous T cells with a CD19-BB-28-3z CAR construct, expansion for ~10 days using CD3/CD28 Dynabeads, and then purification by bead removal and enrichment for CAR expression. CAR-T cells were co-incubated with Raji cells for 6 hours at a 1:1 ratio and then extracted using CD19+ (Raji) positive selection.

value: healthy donor

value: Blood

value: CAR-T cells

tag: activation state

value: Raji-stimulated CAR-T cells


title: Raji-stimulated CAR-T cells 2


title: unstimulated CAR-T cells

value: unstimulated CAR-T cells


title: TRAP_2_IP

city: Darlinghurst

first: CHI KIN

last: IP

state: NSW

address: 384 Victoria Street, Garvan Institute of Medical Research

department: Neuroscience division

institute: Garvan Institute of Medical Research

data_processing:
Raw reads were generated by HiSeq HT chemistry- Single Read (50/100), Illumina sequencing with 100 bp single reads, lane
Quality of the reads were checked by FastQC (Andrew S. 2010)
Read alignment was performed using TopHat (Trapnell et al., 2012) with default parameter, and iGenome (http://cole-trapnell-lab.github.io/cufflinks//igenome_table/ index.html) mm10 UCSC transcriptome annotation
Differential expression was determined by Cufflinks and Cuffdiff analysis
Genome_build: Mouse (Mus musculus): mm10

source_name: Immunoprecipitated RNA samples of the amygdala isolated from the NpyCre/+;TRAPlox/lox  mice replicate 1

extract_protocol: TruSeq RNA Library Prep Kit was used to generate library following manufacturer's standard protocol

value: amygdala

value: NpyCre/+;TRAPlox/lox


title: DN3(IK)-1d-2

hyb_protocol: Hybridization was performed on the GeneChip mouse genome 430 2.0 array as recommended by manufacturer.

scan_protocol: Scanning was performed as recommended by manufacturer.

data_processing: Raw CEL files were pre-processed and normalized with affy10 R package (version 1.52.0). Probe ID was annotated using mouse4302.db11 R package to assign to genes annotated in the mm9 reference genome. Symbol conversion was conducted through biomaRt12 package (version 2.30.0). Differential gene expression analysis was conducted using limma13 R packages (version 3.30.13). Gene expression heatmap and hierarchical clustering analysis was achieved using pheatmap R package.

label_protocol: cDNA were transcribed and biotinylated as recommended by manufacturer.

extract_protocol: Cells were harvested and total RNA was extracted using QIAGEN RNeasy Mini Kit (Qiagen, 74104). Total RNA were sent to UCLA clinical microarray core facility. Labling, hybridization and scanning were done following manufacturer's instructions.


title: DN3(IK)-2d-2

value: DN3 cells transduced with Ikaros for 2 days


title: DN3(IK)-1d-1


title: DN3-1

value: DN3 cells without transduction


title: DN3-2


title: DN3(IK)-2d-3


title: DN3(IK)-2d-1


title: DN3(IK)-3d-2

value: DN3 cells transduced with Ikaros for 3 days


title: DN3(IK)-3d-1


title: DN3-3


title: TRAP_1_IP


title: DN3(IK)-1d-3

value: DN3 cells transduced with Ikaros for 1 day


title: DN3(IK)-3d-3


title: TRAP_2_INPUT

source_name: Total input RNA samples of the amygdala isolated from the NpyCre/+;TRAPlox/lox  mice replicate 2


title: HepG2-RNF2-R33A-rep3

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh38/hg38) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Variants associated with BE treatment were called using the GATK best practices pipeline using GATK 3.8.1 and Picard 2.7 and downstream custom pipelines
No samples were excluded from bioinformatics analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene expression counts per gene estimated by STAR

growth_protocol: HEK293T cells (CRL-3216, obtained from ATCC) were grown in culture using media consisting of DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco). HepG2 cells (HB80-65, obtained from ATCC) were grown in EMEM (ATCC) supplemented with 10% FBS and 0.5% penicillin-streptomycin (Gibco).  Both cell lines were used for experiments until passage 20 for HEK293T and passage 12 for HepG2. Cells were passaged at ~80% confluency every 2-4 days to maintain an actively growing population and avoid anoxic conditions. Cells  were tested for mycoplasma bi-weekly.

extract_protocol:
RNA was extracted with Macherey-Nagel’s  NucleoSpin RNA Plus kit.
Illumina TruSeq Stranded Total RNA Gold, IDT-ILM unique dual indices for barcoding.

treatment_protocol: Transfections were performed using 50ug of transfection quality plasmid DNA (Qiagen Maxiprep) encoding desired BE3-P2A-EGFP, variants thereof or nCas9-UGI-NLS-P2A-EGFP and gRNAs (nuclease-to-gRNA ratio 75:25%). 6x10E6 HEK293T or 15x10E6 HepG2 were seeded into TC-treated 150mm plates 18-24h prior to transfection to yield  ~60-80 % confluency on the day of transfection. Cells were transfected using 150uL TransIT-293 (HEK293T, Mirus) or 150uL transfeX (HepG2, ATCC) reagents per plate, according to the manufacturers’ protocols (mixing DNA and reagent in 5mL Optimem, 30min incubation). Cells were sorted 36-40h after transfection, for either top 5% or all-GFP after doublet-exlusion and gating for the cell population on a BD FACSARIA II.

tag: treatment

tag: guide

value: RNF2 site 1:GTCATCTTAGTCATTACCTG(AGG)

tag: gfp

value: Top 5%


title: DN3(IK)-H3K27Ac-3d-2

description: ChIP-seq for H3K27ac

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

value: anti-H3K27ac (Abcam, ab4729)


title: DN3(IK)-H3K27Ac-1d-2

description: ChIP-seq for H3K27ac


title: HEK293T-RNF2-R33A-rep3


title: DN3(IK)-H3K27Ac-1d-1

description: ChIP-seq for H3K27ac


title: DN3-H3K27Ac-2

description: ChIP-seq for H3K27ac


title: DN3(IK)-H3K27Ac-2d-2

description: ChIP-seq for H3K27ac


title: DN3(IK)-H3K27Ac-3d-1

description: ChIP-seq for H3K27ac


title: DN3(IK)-H3K27Ac-2d-1

description: ChIP-seq for H3K27ac


title: DN3-H3K27Ac-1

description: ChIP-seq for H3K27ac


title: HEK293T-RNF2-controlSECURE-rep3


title: HEK293T-RNF2-R33A-rep2


title: DN3(IK)-H3K4me1-3d-1

description: ChIP-seq for H3K4me1

value: anti-H3K4me1(Abcam, ab8895)


title: DN3(IK)-H3K4me1-2d-1

description: ChIP-seq for H3K4me1


title: HEK293T-RNF2-controlSECURE-rep2


title: DN3(IK)-H3K4me1-1d-1

description: ChIP-seq for H3K4me1


title: TRAP_1_INPUT

source_name: Total input RNA samples of the amygdala isolated from the NpyCre/+;TRAPlox/lox  mice replicate 1

tag: tissue


title: HEK293T-RNF2-R33A-rep1


title: DN3(IK)-H3K4me3-2d-1

description: ChIP-seq for H3K4me3

value: anti-H3K4me3 (Abcam, ab8580)


title: HepG2-RNF2-R33A-rep2


title: HEK293T-RNF2-controlSECURE-rep1


title: DN3-H3K4me1-2

description: ChIP-seq for H3K4me1


title: DN3(IK)-H3K4me3-1d-2

description: ChIP-seq for H3K4me3


title: HepG2-RNF2-R33A-rep1


title: DN3(IK)-H3K4me3-1d-1

description: ChIP-seq for H3K4me3


title: DN3(IK)-H3K4me1-3d-2

description: ChIP-seq for H3K4me1


title: DN3(IK)-HA-2d-2

description: ChIP-seq for HA-tagged Ikaros

value: anti-HA tag (Abcam, ab9110)


title: DN3(IK)-ATAC-3d-2

data_processing:
qc of fastq data,FastQC,version 0.11.4, cutoff 28; triim file, CUTADAPT, version 1.9.1
mapping,Bowtie2,version 2.2.6, -k -X2000 --local --mm --threads -x
qc of mapped data, samtools,version 1.2, MAPQ > 30
qc of mapped data, PICARD, version 2.0.1
peak call, MACS2, version 2.1.1, q < 0.05
Genome_build: mm9
Supplementary_files_format_and_content: processed chip-seq files are in .bed format for peaks information and bigwig file for signal information

extract_protocol:
Approximately 50k cells for each sample were collected, washed using PBS and lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).
Isolated nuclei were incubated with transposition reaction mix at 37℃ for 30 min. DNA was purified using Qiagen MinElute Kit immediately following transposition. Transposed DNA fragments were amplified by PCR for the number of cycles required to obtain 20-40nM of DNA. Barcode primers Ad2.1, Ad2.2, Ad2.3 and Ad2.4 were used for DN3-wt, DN3 (IK)-day 1, DN3 (IK)-day 2 and DN3 (IK)-day 3, respectively. Amplified libraries were then purified by Agencourt AMPure XP beads and QC was performed by BioAnalyzer.


title: AllGFP-HEK293T-RNF2-treated-rep3

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh38/hg38) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Variants associated with BE treatment were called using the GATK best practices pipeline using GATK 3.8.1 and Picard 2.7.
No samples were excluded from bioinformatics analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene expression counts per gene estimated by STAR

value: All GFP


title: AllGFP-HEK293T-RNF2-control-rep3


title: AllGFP-HEK293T-RNF2-treated-rep2


title: DN3(IK)-ATAC-3d-1


title: DN3(IK)-H3K4me1-2d-2

description: ChIP-seq for H3K4me1


title: DN3(IK)-ATAC-2d-1


title: DN3(IK)-H3K4me1-1d-2

description: ChIP-seq for H3K4me1


title: DN3(IK)-ATAC-1d-2


title: DN3-ATAC-2


title: DN3-ATAC-1


title: AllGFP-HEK293T-RNF2-treated-rep1


title: AllGFP-HEK293T-RNF2-control-rep1


title: DN3-H3K4me1-1

description: ChIP-seq for H3K4me1


title: DN3(IK)-ATAC-1d-1


title: DN3(IK)-H3K4me3-2d-2

description: ChIP-seq for H3K4me3


title: AllGFP-HEK293T-RNF2-control-rep2


title: HEK293T-RNF2-treated-rep2


title: HEK293T-RNF2-treated-rep1


title: HEK293T-RNF2-control-rep1


title: DN3(IK)-HA-1d-2

description: ChIP-seq for HA-tagged Ikaros


title: DN3(IK)-ATAC-2d-2


title: HEK293T-RNF2-control-rep2


title: Tumor breast tissue_patient with obesity_non-hereditary breast cancer (Patient 6)

type: genomic

city: Ciudad de México

first: Nishi

middle: Alan

last: Adams-Reyes

state: Cuidad de México

address: AV. UNIVERSIDAD 3000

department: Faculty of Medicine

country: Mexico

institute: Universidad Nacional Autónoma de México

description: Selective amplication of mtDNA

hyb_protocol: Prehybridization, hybridization, washing, and scanning of the MitoChip were performed as described in the Affymetrix CustomSeq Resequencing protocol. The prehybridizations  were performed for 15 minutes in 80-l (for v2.0 chips)  solution containing 3 mol/L tetramethylammonium chloride, 0.1% Tween 20, and 10 mmol/L Tris, pH 7.8. The chips were hybridized for 16 hours at 48°C with 60 rpm rotation in a hybridization solution containing 3 mol/L tetramethylammonium chloride, 100 g/ml herring sperm DNA, 500 g/ml bovine serum albumin, 10 mmol/L Tris, pH 7.8, 0.01% Tween 20, and 200 pmol/L control oligo. The chips were then washed on the Affymetrix fluidics station 450 using the program Mini_DNAArray_WS5_450_FELXMini_DNAArray_WS5_450.

scan_protocol: Chips were scanned in Affymetrix GeneChip Scanner 3000  and data acquisition was performed using the Affymetrix Genechip Command Console (AGCC) software.

data_processing: Analysis of microarray data from the MitoChips v2.0 was carried out using the GeneChip Sequence Analysis Software (GSEQ) v4.0, in order to assign to each position, the basis that meets the quality criteria in the mitochondrial genome. Mitochondrial tumor DNA sequence was compared to matched leukocyte mitochondrial DNA sequence in order to identify true mutations rather than polymorphisms.  Data analysis was carried out with GSEQ 4.1 with “model type” set at diploid to enable the detection of heteroplasmy and “quality score threshold” set at 3 to provide the best base calling accuracy and rate. The other parameters used by the algorithm were No Signal Threshold= 2, Weak Signal Fold Threshold= 20, Large SNR Threshold= 12, Min Fraction of Calls of Samples = 0.5, Trace Threshold = 1, Sequence Profile Threshold = -0.175

source_name: Tumor breast tissue from a patient with obesity diagnosed with non-hereditary breast cancer (Patient 6)

label_protocol: The entire mitochondrial DNA sequence was amplified in three overlapping long PCR fragments, with each reaction containing 50 ng of genomic DNA. The primers for PCR amplification were the same as in the previous report for MitoChip V2.1. Affymetrix fragmentation reagent (0.2 U of DNase I/g DNA), 5 l of OnePhorAll buffer (Amersham Life Sciences, Arlington Heights, IL), and EB buffer. Samples were then incubated at 95°C for 15 minutes to inactivate DNase I. Fragmented DNA was labeled by adding 2.0 l of GeneChip DNA labeling  reagent and 3.4 l of 30 U/l terminal deoxynucleotidyl transferase (both from Affymetrix).

extract_protocol: Genomic DNA of all patients was isolated from blood leukocytes using the salting out procedure described by Miller et al., (17); DNA from tumor tissue samples was obtained from surgical specimens, using the DNeasy Blood & Tissue Kit (QIAGEN GmbH, Hilden, Germany), following those conditions recommended by the manufacturer.

treatment_protocol: The samples were obtained through the Instituto FUCAM AC. All patients signed informed consent letter. The sample of tumor tissue was used both for the diagnosis of breast cancer and for this research protocol.

tag: individual

value: Patient 6

value: Breast tumor tissue

tag: bmi

value: Obese BMI

value: non-hereditary breast cancer


title: PA3 ::gp68 cultured with glusose_rep1

city: Chongqing

first: zichen

last: yang

address: Gaotanyan

institute: Army Medical University (Third Military Medical University)

data_processing:
The sequenced libraries were mapped against predicted  transcripts from the Pseudomonas aeruginosa PAO1 genome using TopHat v2.0.4
The transcript  abundance (FPKM, Fragments Per Kilobase of exon per  Million fragments mapped) and significant changes in  transcript expression were estimated using Cufflinks  v2.0.2
Transcripts with p-values less than 0.05,  determined using CuffDiff
Genome_build: NC_002516.2 were used as the reference genomes
Supplementary_files_format_and_content: abundance measurements

organism: Pseudomonas aeruginosa

source_name: PA3 ::gp68 cultured with glusose

growth_protocol: PA3 ::gp68 was grown in Luria-Bertani (LB) broth medium aerobically.

extract_protocol:
Total RNA was isolated using SV Total RNA Isolation System (Promega) according to the manufacturer’s instructions and   checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer   2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further   purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and   RNase-Free DNase Set    (Cat#79254, QIAGEN, GmBH, Germany).
Barcoded sequencing libraries
Pooled libraries were enriched for the exome using hybridization (TruSeq Exome Enrichment Kit, Illumina), quantified using quantitative PCR and pooled in 1:1 ratio for pairedend sequencing on a HiSeq2500 (Illumina)

treatment_protocol: PA3 ::gp68 was cultured with arabinose or glucose (as control).

tag: genotype/variation

value: transformed with pHerdB20T-gp68

tag: culture condition

value: glucose (control)


title: PA3 ::gp68 cultured with arabinose_rep1

source_name: PA3 ::gp68 cultured with arabinose

value: arabinose


title: PA3 ::gp68 cultured with arabinose_rep3


title: PA3 ::gp68 cultured with arabinose_rep2


title: BAP_ARRII_3: Cytokinin treated transition cambium, biological replicate 3

city: Seoul

first: Ji-Young

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: Expression profile of the cells in transition from procambium to cambium from the middle one third of root sections from 8 day old seedlings after treatment of cytokinin for 48 hours

hyb_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

data_processing: The CEL files were processed and normalized at the probe level using the GC content based robust multi-array algorithm (GCRMA; Wu et al., 2004).

source_name: Arabidopsis roots of 8 day old seedlings

label_protocol: Biotinylated cRNA was prepared using the two-cycle amplification protocol by Affymetrix.

growth_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on standard media. Standard media prepared in square plates include 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar, which were adjusted to pH 5.7 with KOH. Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh. Seedlings were germinated and grown on upright position in the lighted growth chamber with the cycle of 16 hr in the light and 8 hr in the dark.

extract_protocol: RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH)

treatment_protocol: 1. One third long segments were harvested separatedly and placed in the protoplast solution as described in Birnbaum et al. (2005) published in Nat. Methods. GFP expressing protoplasts were isolated from Fluorescence Activated Cell Sorter to collect total RNA. 2. For cytokinin treatment, growth media including 100nM of synthetic cytokinin (BAP) were prepared. Then the mesh with seedlings on regular growth media was transferred to the cytokinin containing media. Seedlings were grown on the regular media for 6 days and then on BAP containing media for 48 hours.

value: transition from procambium to cambium from the middle one third of root section after treatment of cytokinin for 48 hours

tag: organ

value: root

tag: develpmental stage

value: 8 day old seedling

tag: genotype

value: Wild type columbia expressing ARR15::GFP (ER-localized)


title: Tumor breast tissue_patient with obesity_non-hereditary breast cancer (Patient 5)

description: Selective amplication of mtDNA

source_name: Tumor breast tissue from a patient with obesity diagnosed with non-hereditary breast cancer (Patient 5)

value: Patient 5

tag: disease state


title: Blood sample of patient with obesity_non-hereditary breast cancer (Patient 6; control)

description: Selective amplication of mtDNA

source_name: Blood sample of patient with obesity diagnosed with non-hereditary breast cancer (Patient 6; control)

value: blood


title: Blood sample of patient with obesity_non-hereditary breast cancer (Patient 5; control)

description: Selective amplication of mtDNA

source_name: Blood sample of patient with obesity diagnosed with non-hereditary breast cancer (Patient 5; control)


title: ARRI_3: Cambium, biological replicate 3

description: Expression profile of cambium from the basal one third of root sections from 8 day old seedlings

scan_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.


title: BAP_ARRIII_2: Cytokinin treated procambium, biological replicate 2

description: Expression profile of procambium from the apical one third of root sections from 8 day old seedlings after treatment of cytokinin for 48 hours

value: procambium from the apical one third of root section after treatment of cytokinin for 48 hours


title: BAP_ARRI_3: Cytokinin treated cambium, biological replicate 3

description: Expression profiles of cambium from the basal one third of root sections from 8 day old seedlings after treatment of cytokinin for 48 hours

value: cambium from the basal one third of root section after treatment of cytokinin for 48 hours


title: BAP_ARRIII_3: Cytokinin treated procambium, biological replicate 3


title: ARRII_1: Transition cambium, biological replicate 1

description: Expression profiles of the cells in transition from procambium to cambium from the middle one third of root sections from 8 day old seedlings


title: ARRI_1: Cambium, biological replicate 1

value: cambium from the basal one third of root section


title: ARRIII_3: Procambium, biological replicate 2

description: Expression profiles of procambium from the apical one third root sections from 8 day old seedlings

value: procambium from the apical one third of root section


title: BAP_ARRIII_1: Cytokinin treated procambium, biological replicate 1


title: Tumor breast tissue_patient with obesity_non-hereditary breast cancer (Patient 4)

description: Selective amplication of mtDNA

source_name: Tumor breast tissue from a patient with obesity diagnosed with non-hereditary breast cancer (Patient 3)

value: Patient 4


title: ARRIII_1: Procambium, biological replicate 1


title: A8-3: procambium, biological replicate 2

description: Expression profile of procambium and lateral root cap marked by ARR5::GFP

source_name: Arabidopsis roots of 6 day old seedlings

treatment_protocol: For A8, protoplast and cell sorting from a bottom half of roots were proceeded without the dissection of a root into three parts.

value: procambium and lateral root cap

value: 6 day old seedling

value: Wild type columbia expressing ARR5::GFP (ER-localized)


title: ARRI_2: Cambium, biological replicate 2


title: PA3 ::gp68 cultured with glusose_rep2

value: transformed with pHerdB20T-gp68


title: ARRII_2: Transition cambium, biological replicate 2

value: transition from procambium to cambium from the middle one third of root sections


title: PA3 ::gp68 cultured with glusose_rep3

value: glucose (control)


title: BAP_ARRI_2: Cytokinin treated cambium, biological replicate 2


title: BAP_ARRII_1: Cytokinin treated transition cambium, biological replicate 1

value: transition from procambium to cambium from the middle one third of root section after treatment of cytokinin for 48 hours


title: A8-2: procambium, biological replicate 1

value: root


title: BAP_ARRI_1: Cytokinin treated cambium, biological replicate 1

value: 8 day old seedling


title: Blood sample of patient with obesity_non-hereditary breast cancer (Patient 4; control)

description: Selective amplication of mtDNA

source_name: Blood sample of patient with obesity diagnosed with non-hereditary breast cancer (Patient 4; control)

value: Obese BMI

value: non-hereditary breast cancer


title: Tumor breast tissue_patient with a normal body mass index_non-hereditary breast cancer (Patient 3)

description: Selective amplication of mtDNA

source_name: Tumor breast tissue from a patient with a normal body mass index diagnosed with non-hereditary breast cancer (Patient 3)

value: Patient 3

value: Breast tumor tissue

value: Normal BMI


title: BAP_ARRII_2: Cytokinin treated transition cambium, biological replicate 2

value: Wild type columbia expressing ARR15::GFP (ER-localized)


title: Blood sample_patient with normal body mass index_non-hereditary breast cancer (Patient 3; control)

description: Selective amplication of mtDNA

source_name: Blood sample, from patient with normal body mass index diagnosed with non-hereditary breast cancer (Patient 3; control)

value: blood


title: Tumor breast tissue_patient with a normal body mass index_non-hereditary breast cancer (Patient 1)

description: Selective amplication of mtDNA

source_name: Tumor breast tissue from a patient with a normal body mass index diagnosed with non-hereditary breast cancer (Patient 1)

value: Patient 1


title: Tumor breast tissue_patient with a normal body mass index_non-hereditary breast cancer (Patient 2)

description: Selective amplication of mtDNA

source_name: Tumor breast tissue from a patient with a normal body mass index diagnosed with non-hereditary breast cancer (Patient 2)

value: Patient 2


title: Blood sample_patient with normal body mass index_non-hereditary breast cancer (Patient 2; control)

description: Selective amplication of mtDNA

source_name: Blood sample, from patient with normal body mass index diagnosed with non-hereditary breast cancer (Patient 2; control)


title: Blood sample_patient with normal body mass index_non-hereditary breast cancer (Patient 1; control)

description: Selective amplication of mtDNA

source_name: Blood sample, from patient with normal body mass index diagnosed with non-hereditary breast cancer (Patient 1; control)


title: A375 WTOE + IFNG_RNA-seq

city: Singapore

first: SIQIN

last: ZHOU

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
RNA-seq aligned to reference transcript using bowtie2.
RNA-seq aligned to hg19 using HISAT(version 2.0.1-beta).
Gene expression level quantified by RSEM.
Bigwig generated after normalization.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

source_name: LNK overexpressing cells treated with interferon gamma

extract_protocol:
RNA was harvested using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard BGISEQ500 protocols

treatment_protocol: A375 cells were growth until 90% confluent, and then either treated with or without IFNG  (2000 U/ml)  for 24 hours.

tag: cell line

tag: cell type

value: Human melanoma cell line

value: overexpressing LNK

value: IFNG  (2000 U/ml)  for 24 h


title: A375_RNA-seq

source_name: control cells

value: control