title: HG01770 cell line replicate 3


title: 2063A_flower_bud_H3K4me3_rep2

status: Public on Jan 31 2021

type: SRA

city: WuHan

first: Guan

middle: Peng

last: Peng

state: HuBei

address: shizishan street

department: college of informatics

country: China

institute: Huazhong Agricultural University

library_source: genomic

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak
Genome_build: Download the genome from www.genoscope.cns.fr/brassicanapus
Supplementary_files_format_and_content: bogWig file by deepTools bamCoverage

molecule: genomic DNA

organism: Brassica napus

growth_protocol: Germinating seeds were obtained by placed on moist paper for 7 d at 22 °C. For roots and young leaves, the germinated seeds were grown in a phytotron with the day/night cycle set at 16 h/8 h and a temperature of 22 °C/18 °C. Roots were obtained 7 d after planting on moist filter paper, and young leaves were obtained from 2-week-old plants cultured hydroponically as described. Approximately 20-d-old seedlings were transplanted to the field and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. flower bud buds and siliques were harvested.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads).

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 10 min and quenched with 0.2 M glycine at room temperature.

tag: cultivar

tag: developmental stage

value: flower buds (<= 2 mm)

tag: tissue

value: flower bud

tag: chip antibody


title: MYB-/-YFP+ve_day6rep2

city: Guangzhou

first: ZAHIR

last: SHAH

state: Guangdong

address: 190 Kaiyuan avenue, Haungpu district, Guangzhou, China

department: Stem Cells and Regenerative Medicines

institute: GIBH,CAS, China

library_source: transcriptomic

data_processing:
Samples were checked with FastQC software with no considerable issues found. Reads were trimmed and filtered with BBduk tool from the Bbmap package (used parameters: qtrim=rl trimq=20 maq=20 minlen=50). This procedure keeps 94.98-97.02% bases and 98.64-99.8% reads per sample.
Trimmed reads were mapped to the GRCh38 human genome with Gencode v.24 gene annotation (Harrow 2012) using the --quantMode GeneCounts option of the STAR v.2.5.3ab software (Dobin 2013). After removing of ~15,000 pseudogenes and 552 rRNA genes the STAR output tallies raw read per gene counts, that is total read counts for each of 46,214 transcripts, 19,844 of them representing protein-coding genes. According to the STAR manual, “with --quantMode GeneCounts option STAR will count number reads per gene while mapping. EdgeR was used to convert raw read per gene counts to CPM (counts per million reads) matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: mRNA expression raw counts
Supplementary_files_format_and_content: mRNA expression counts per million reads
Supplementary_files_format_and_content: description of genes_ntc_expression_raw_cpm_GEO.txt file

molecule: total RNA

organism: Homo sapiens

source_name: in vitro hematopoietic cells

growth_protocol: hESC cells–derived hematopoietic cells were routinely generated using EBs-based hematopoietci development in our established serum-free and cytokine-free hematopoietic system (un-published), with initial mesodermal patterning by BMP4 and VEGF supplimentations.

extract_protocol:
Differentiated cells were harvested at different time points, filtered and incubated with cell surface markers on ice. The washed cells were collected into Trizol reagent directly from Aria II-cell sorter.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: hESC-derived hematopoietic progenitors

tag: passage

tag: day of differentiation

value: Day 6

tag: genotype

value: MYB-/-


title: MYB-/-YFP+ve_day6rep1


title: P1183RA

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

country: USA

institute: University of Virginia

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 29 using STAR (v2.6.1d
Briefly, 100bp paired-end reads were trimmed and aligned to the GENCODE reference transcriptome using STAR and reads were quantified using HT-Seq. Gene counts were generated for each sample and collated into a singular matrix for paired regression analysis in DESeq2.
Genome_build: GrCh38, GENCODE release 29
Supplementary_files_format_and_content: "Pheno.csv" contains sample metadata, "Asp_Counts.csv" contains raw counts, "SummaryStats.csv" contains the number and percentages of reads mapped for each samples

molecule: polyA RNA

source_name: Colon Organoid

growth_protocol: Normal 3D colon organoids included in the study were developed from biopsies of either distal or proximal colon using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates.

extract_protocol:
For RNA isolation, media was gently removed and 200μl RNA lysis Solution RA1 with TCEP (Machery-Nagel; Cat No: 740902.50) was added to each well. The lysate was collected in a 1.5ml Eppendorf tube. Each tube was vortexed vigorously and placed on ice. Further steps were carried out according to manufacturer’s protocol of the Machel-Nagel RNA XS kit. RNA was checked for quality using the Agilent 4200 Tapestation. Samples with RIN > =8.5 were considered for library preparation and sequencing using the Illumina NovoSeq
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II).  Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103).  All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area are failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized.  Successful libraries are normalized to 10nM for submission to sequencing.

treatment_protocol: Normal colon 3D organoid lines were thawed, grown and passaged as required in 48-well culture plates. Organoid lines were plated at a density of approximately 105 cells per well and allowed to grow for approximately 3 days prior to treatment with aspirin. Cells within the treatment group were treated with 0.5μL aspirin (100mM Sigma A5376) per 1mL complex media, equating to a 50μM dose of aspirin. Vehicle control samples were treated with an equal amount of 1M Tris pH7.2 with a final concentration of 50μM in complex media

value: Colon Organoid

tag: Sex

value: F

tag: treatment

value: Case

tag: pair

tag: age

value: R

tag: center

value: UVA

tag: smokingstatus

value: Current


title: P1208LAC

value: CTL

value: L

value: Never


title: MYB-/-YFP-ve_day6rep2


title: 2063A_flower_bud_H3K4me3_rep1


title: 2063A_young_leaf_RNAPII_rep2

value: young leaves from two-week seedlings

value: young leaf

value: RNAPII


title: MYB-/-YFP-ve_day12rep2

value: Day 12


title: P1174RA


title: P1179RA


title: 2063A_young_leaf_RNAPII_rep1


title: 2063A_flower_bud_H3K27ac_rep2

value: flower buds (<= 2 mm)

value: flower bud


title: HG01757 cell line replicate 2

type: genomic

city: New York

first: Jeremiah

last: Li

state: NY

address: 430 E 29th St 14th Floor, 14th Floor

institute: Gencove

description: Genomic DNA extracted from B-lymphocytes by Coriell and genotyped using Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)

hyb_protocol: samples were incubated at 48C overnight before undergoing enzymatic base extension and fluorescent staining

scan_protocol: the beadchips were scanned using the iScan system (Illumina)

data_processing: genomic DNA was genotyped using the Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)

label: 2D barcodes

source_name: purified gDNA

label_protocol: sample vials containing gDNA extract were stored and individually labeled with unique 2D-barcodes

extract_protocol: an automated magnetic bead purification protocol (Hamilton Microlab STAR w/ Promega ReliaPrep Isolation system) was used to extract genomic DNA that was eluted in TE buffer (pH 8.0, 1mM EDTA)

tag: cell line


title: HG01757 cell line replicate 3


title: HG01761 cell line replicate 2


title: P1174RAC


title: HG01757 cell line replicate 1


title: 2063A_young_leaf_H3K9me2_rep2


title: MYB-/-YFP-ve_day6rep1

value: hESC-derived hematopoietic progenitors

value: Day 6


title: P1173RAC

value: Colon Organoid


title: HG01756 cell line replicate 2


title: HG01756 cell line replicate 3


title: P1171LA

value: M


title: 2063A_young_leaf_H3K4me1_rep2


title: HG01761 cell line replicate 1


title: 2063A_young_leaf_H3K4me1_rep1


title: HG01756 cell line replicate 1


title: Negtive Control-3

city: Kunming

first: Jing

last: Sun

state: Yunnan

address: NO. 935,JIAO LIN ROAD

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
microRNA-seq reads from single-end libraries.
The sequencing data was filtered with cutadapt.
The clean reads were mapped to the mm9 genome using Bowtie.
After reads were aligned to the genome, we annotated and quantified the expression with featureCounts (Pertea et al., 2016).
Differntal miRNA expression was analyzed using the DESeq(v.1.12.1)
Genome_build: mm9

organism: Mus musculus

source_name: splenocyte

growth_protocol: Mice splenocytes were  were cultured in 1640 containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 U/mL streptomycin

extract_protocol:
Total RNA was extracted using the RNAfast200 kit according to the manufacturer’s protocol.
The strand-specific RNA-seq libraries were prepared using a NEBNext® Ultra™ I RNA Library Prep Kit for Illumina (NEB, MA, USA) following the manufacturer’s instructions.

treatment_protocol: Mice splenocytes were harvested and washed two times with PBS containing 2% BSA. Cells were then adjusted to the concentration of 1×106/ml and incubated for 12 h at 37℃ and 5% CO2 with Kynurenine  (40μg/ml).

value: spleen

tag: strain

value: Balb/C

value: 6 weeks

value: untreated


title: Negtive Control-4


title: Kynurenine stimulated -4

value: treat with the Kynurenine


title: Negtive Control-2


title: P1170LAC

value: F

value: CTL

value: L

value: UVA


title: 2063A_young_leaf_H3K27me3_rep2

value: young leaves from two-week seedlings

value: young leaf


title: HG01699 cell line replicate 3


title: Kynurenine stimulated -3


title: P1170LA

value: Case

value: Never


title: 2063A_young_leaf_H3K27me3_rep1


title: HG01699 cell line replicate 2


title: Kynurenine stimulated -2


title: P1168RAC

value: R


title: P1173RA


title: 2063A_young_leaf_H3K27ac_rep2


title: Kynurenine stimulated -1


title: HG01699 cell line replicate 1


title: 2063A_young_leaf_H3K9me2_rep1


title: P1171LAC

value: Current


title: Negtive Control-1


title: 2063A_young_leaf_H3K27ac_rep1


title: HG01697 cell line replicate 3


title: 2063A_young_leaf_H3K4me3_rep2


title: HG01697 cell line replicate 2


title: HG01500 cell line replicate 3


title: 2063A_young_leaf_H3K4me3_rep1


title: ePOUSox17EKd131RNA

first: Chen

last: yanpu

state: guangdong

address: Kaiyuan No. 190, Luogang district

department: drug discovery pipelines

institute: Guangzhou Institute of Biomedicine and Health

data_processing:
The 150bp paired end raw reads were aligned to the mm10 transcriptome using RSEM and integrated bowtie 2.0.Per-gene read counts were calculated using RSEM.
The read counts were GC normalized using EDAseq (Risso et al., 2011). Genes with mean read counts over all traits and replicates of less than 20 were discarded leading to a final set of 13,703 genes.
This gene set was used for differential gene expression analysis by DESeq2 and further downstream analysis. The criteria for differential gene expression used was fold change >0.5 and p value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files

growth_protocol: OG2 MEF cells (3 x 10^4 cells per sample) were transduced with ePOU/SKM,Oct4/SKM,ePOU/Sox17EK/KM, and Oct4/Sox17EK/KM retroviral cocktails  twice in 24 h intervals, and cultured in mES medium with 50μg/ml Vitamin C upto the indicated day

extract_protocol:
RNA was extracted using Trizol reagent.
TruSeq Nano RNA sample prep kit (Illumina; # FC-121-4001) was used for library constructions with standard illumina protocols

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct4 promoter with transduced reprogramming factors

value: ePOU, Sox17EK, Klf4, cMyc

tag: day of reprogramming


title: ePOUSox17EKd132RNA


title: ePOUSox17EKd61RNA


title: ePOUSox17EKd62RNA


title: HG01697 cell line replicate 1


title: HG01500 cell line replicate 2


title: ePOUSox17EKd41RNA


title: P1155LA

value: Colon Organoid

value: Former


title: P1153RAC

value: M


title: HG01500 cell line replicate 1


title: P1157RAC


title: P1155LAC


title: HG00384 cell line replicate 3


title: P1153RA


title: P1152LAC


title: ePOUSox17EKd22RNA


title: ePOUSox17EKd42RNA


title: ePOUSox17EKd21RNA


title: ePOUSox17EKd02RNA


title: HG00384 cell line replicate 1


title: HG00384 cell line replicate 2


title: P1168RA


title: P1157RA


title: P1151LAC


title: P1152LA


title: P1151LA


title: ePOUSox17EKd01RNA


title: HG00365 cell line replicate 2


title: P1145LAC


title: Oct4Sox17EKd131RNA

value: Oct4, Sox17EK, Klf4, cMyc


title: HG00365 cell line replicate 1


title: P1145LA


title: HG00364 cell line replicate 3


title: Oct4Sox17EKd62RNA


title: HG00364 cell line replicate 2


title: Oct4Sox17EKd61RNA


title: Oct4Sox17EKd42RNA


title: P1128LAC


title: P1138LAC


title: P1138LA


title: HG00360 cell line replicate 3


title: HG00360 cell line replicate 2


title: P1122LAC


title: Oct4Sox17EKd22RNA


title: P1128LA


title: HG00364 cell line replicate 1


title: HG00365 cell line replicate 3


title: Oct4Sox17EKd21RNA


title: P1122LA


title: Oct4Sox17EKd132RNA


title: HG00360 cell line replicate 1


title: Oct4Sox17EKd02RNA


title: HG00330 cell line replicate 3


title: P1119RAC


title: Oct4Sox17EKd01RNA


title: HG00330 cell line replicate 2


title: P1119RA


title: HG00330 cell line replicate 1


title: ePOUSox2d132RNA

value: ePOU, Sox2, Klf4, cMyc


title: ePOUSox2d131RNA


title: P1116LAC

value: F


title: HG00268 cell line replicate 3


title: HG00268 cell line replicate 2


title: ePOUSox2d62RNA


title: HG00268 cell line replicate 1


title: P1116LA


title: P1114RAC

value: CTL


title: ePOUSox2d61RNA


title: Oct4Sox17EKd41RNA


title: ePOUSox2d32RNA


title: HG00262 cell line replicate 3


title: P1109RAC


title: P1114RA


title: ePOUSox2d31RNA


title: exp2_15°C_42day_G140

type: RNA

city: Hitachi

first: Mine

last: Nose

state: Ibaraki

address: 3809-1 Ishi, Juo

country: Japan

institute: Forest Tree Breeding Center

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Gene Expression Custom 8×60K Array (G4102A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on SureScan Microarray Scanner G4900DA using one color scan setting for 8x60k array slides (AgilentG3_HiSen_GX_1Color).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (Protocol: GE1_1105_Oct12 and Grid: 056873_D_F_20130730) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Cryptomeria japonica

source_name: experiment 2, 15°C, 42 day, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from  200 ng total RNA using the One-Color Low Input Quick Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cuttings of a Japanese cedar clone grown in the natural condition were used to investigate the annual transcriptome dynamics. The cuttings grown in the photoperiod and temperature controlled conditions were used to investigate the effects of each environmental factor.

extract_protocol: The total RNA of seasonal samples was extracted from 500 mg samples as Gehrig et al. (2000) reported using an RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), and a DNase digestion was performed on-column using an RNase-free DNase Set (Qiagen).The total RNA of cuttings placed at the controlled-environmental chamber was extracted by LiCl precipitation as described in le Provost et al. (2007), and subsequently extracted using RNeasy Plant Mini Kit as described above.

treatment_protocol: All samples were immediately frozen in liquid nitrogen and stored at -80 °C until use.

value: shoot

tag: condition

value: Experimental condition 2

tag: photoperiod

value: LD

tag: temperature

tag: day of sampling

value: 42 days


title: exp2_15°C_90day_G073

source_name: experiment 2, 15°C, 90 day, replicate 1

tag: tissue

value: 90 days


title: exp2_15°C_90day_G086

source_name: experiment 2, 15°C, 90 day, replicate 2


title: exp2_15°C_63day_G137

source_name: experiment 2, 15°C, 63 day, replicate 1

value: 63 days


title: exp2_15°C_21day_G139

source_name: experiment 2, 15°C, 21 day, replicate 1

value: 21 days


title: exp2_15°C_7day_G140

source_name: experiment 2, 15°C, 7 day, replicate 2

value: 7 days


title: exp2_15°C_63day_G139

source_name: experiment 2, 15°C, 63 day, replicate 2


title: exp2_15°C_21day_G140

source_name: experiment 2, 15°C, 21 day, replicate 2


title: P1109RA

tag: cell type

value: Case

value: R

value: UVA

value: Never


title: ePOUSox2d22RNA

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct4 promoter with transduced reprogramming factors


title: P1102RAC

value: Colon Organoid


title: ePOUSox2d21RNA

value: ePOU, Sox2, Klf4, cMyc


title: HG00255 cell line replicate 3


title: HG00255 cell line replicate 2


title: ePOUSox2d02RNA


title: ePOUSox2d01RNA


title: P1096RAC

value: M


title: P1102RA

value: F


title: HG00255 cell line replicate 1


title: exp2_25°C_90day_G091

source_name: experiment 2, 25°C, 90 day, replicate 2

value: shoot


title: HG00262 cell line replicate 2


title: P1096RA


title: HG00262 cell line replicate 1


title: HG00251 cell line replicate 3


title: Oct4Sox2d132RNA

value: Oct4, Sox2, Klf4, cMyc


title: P1083RAC

value: CTL


title: exp2_25°C_90day_G062

source_name: experiment 2, 25°C, 90 day, replicate 1

value: Experimental condition 2

value: LD


title: HG00251 cell line replicate 1


title: HG00251 cell line replicate 2


title: Oct4Sox2d131RNA


title: Oct4Sox2d62RNA


title: exp2_15°C_42day_G137

source_name: experiment 2, 15°C, 42 day, replicate 1

value: 42 days


title: P1082LAC

value: L

value: Current


title: P1083RA

value: Case


title: exp2_25°C_63day_G041

source_name: experiment 2, 25°C, 63 day, replicate 1

value: 63 days


title: exp2_25°C_42day_G114

source_name: experiment 2, 25°C, 42 day, replicate 2


title: exp2_25°C_21day_G114

source_name: experiment 2, 25°C, 21 day, replicate 2

value: 21 days


title: HG00250 cell line replicate 3


title: exp2_25°C_63day_G114

source_name: experiment 2, 25°C, 63 day, replicate 2


title: Oct4Sox2d61RNA


title: P1082LA

source_name: Colon Organoid

value: UVA


title: exp2_25°C_42day_G056

source_name: experiment 2, 25°C, 42 day, replicate 1


title: Oct4Sox2d42RNA

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct4 promoter with transduced reprogramming factors


title: exp2_25°C_21day_G041

source_name: experiment 2, 25°C, 21 day, replicate 1


title: P1081RAC

value: Colon Organoid

value: R

value: Never


title: HG00250 cell line replicate 2

source_name: purified gDNA


title: HG00250 cell line replicate 1


title: Oct4Sox2d41RNA


title: Oct4Sox2d32RNA


title: HG00244 cell line replicate 3


title: P1081RA

value: M


title: P1074RAC

value: Former


title: exp2_25°C_7day_G091

source_name: experiment 2, 25°C, 7 day, replicate 1

value: shoot

value: 7 days


title: Oct4Sox2d31RNA

value: Oct4, Sox2, Klf4, cMyc


title: HG00244 cell line replicate 2


title: exp2_15°C_7day_G086

source_name: experiment 2, 15°C, 7 day, replicate 1

value: Experimental condition 2

value: LD


title: exp2_25°C_7day_G114

source_name: experiment 2, 25°C, 7 day, replicate 2


title: P1055LAC

value: F

value: CTL

value: L


title: HG00244 cell line replicate 1


title: P1074RA

value: Case


title: HG00242 cell line replicate 3


title: exp2_25°C_0day_G093

source_name: experiment 2, 25°C, 0 day, replicate 2

value: 0 day


title: P1055LA

value: UVA


title: exp2_25°C_0day_G072

source_name: experiment 2, 25°C, 0 day, replicate 1


title: HG00242 cell line replicate 2


title: Oct4Sox2d02RNA

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct4 promoter with transduced reprogramming factors


title: Oct4Sox2d01RNA


title: HG00242 cell line replicate 1


title: CHZ 36 Bx3 V2 Milk

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

description:
Ribosome Protected RNA fragments
Ribo-Seq

data_processing:
Adapter sequences were trimmed (FASTX- Toolkit hannonlab.cshl.edu/fastx_toolkit/) and contaminating rRNA sequences were removed (alignment to the human 45s rRNA repeat sequence using bowtie). Uniquely mapping sequences were identified by alignments using bowtie to Reference Sequence database (RefSeq) mRNA entries obtained from the University of California, Santa Cruz browser (Hg38 human genome reference assembly) in which all mRNAs derived from the same gene were reduced to a single entry corresponding to the longest isoform.
Normalization factors based on the trimmed mean of M-values were determined the Bioconductor package edgeR for ribosome profiling and RNA-Seq. Dispersion estimates were obtained prior to likelihood ratio tests (glmFit and glmLRT functions of edgeR) to determine significance of the log2 fold change in RPFs or RNA for all transcripts with ≥1 count/million in all samples.

source_name: Muscle Biopsy

extract_protocol:
Muscle biopsies were disrupted using a bead beater homogenizer. Total RNA was extracted in qiazol and Ribosomes isolated in a buffer containing 10mM MgCl2.
NEBNext rRNA removal kit was used to remove rRNA. Heat fragmented total RNA for RNA-Seq and ribosome protected RNA fragments were treated with T4 PNK and libraries constructed using the NEBNext Small RNA Library kit. Libraries were size selected for 25-35 nt fragments by native PAGE.

value: Muscle Biopsy

tag: food

value: Ingest Milk

tag: time course

value: 180 Min Post Ingestion

tag: patient


title: exp1_SD_70day_G54

source_name: experiment 1, SD, 70 day, replicate 2

value: Experimental condition 1

value: SD

value: 70 days


title: CHZ 36 Bx2 V2 Milk

value: 60 Min Post Ingestion


title: OSKM-D6-2_ATAC

data_processing:
trmming adapter and fastqc
Read were aligned to mouse genome assembly (mm10) using bowtie2 (--very-sensitive --end-to-end --no-unal --no-mixed).
Low quality mapped reads were removed and sorted using samtools (view –q 30|sort).
PCR duplicates were removed using samtools (rmdup) to keep uniquely mapped reads.
Genome_build: mm10

growth_protocol: OG2-MEF cells were transduced twice by pMX-Sox2, Klf4, c-Myc along with Oct4 or engineered Oct4 (ePOU) retroviruses produced using PlatE cells in DMEM + 10% FBS media supplemented with 1x NEAA and Glutamax. After second viral transduction, the medium was switched to mouse Embryonic Stem Cell(mES) medium with 50μg/ml VC reprogramming medium. The media switch day was defined as day 0 and cells were further cultured with daily media change.

extract_protocol: The libraries were generated using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme)

value: reprogramming cells

tag: timepoint


title: exp1_SD_70day_G50

source_name: experiment 1, SD, 70 day, replicate 1

value: shoot


title: HG00240 cell line replicate 3


title: CHZ 36 Bx1 V2 Milk

value: 0 min


title: OSKM-D3-R2_ATAC


title: Oct4Sox2d21RNA

tag: genotype

value: Oct4, Sox2, Klf4, cMyc


title: OSKM-D2_ATAC


title: CHZ 36 Bx3 V1 Cheese

value: Ingest Cheese


title: exp1_SD_35day_G27

source_name: experiment 1, SD, 35 day, replicate 2

value: 35 days


title: ESKM-D6-1_ATAC


title: HG00240 cell line replicate 2


title: HG00239 cell line replicate 3


title: CHZ 36 Bx2 V1 Cheese


title: ESKM-D3-R2_ATAC


title: CHZ 36 Bx1 V1 Cheese


title: ESKM-D2-1_ATAC


title: HG00239 cell line replicate 2


title: CHZ 30 Bx3 V2 Cheese


title: ES-D3-R1_ATAC


title: exp1_SD_35day_G17

source_name: experiment 1, SD, 35 day, replicate 1


title: exp1_SD_21day_G27

source_name: experiment 1, SD, 21 day, replicate 2

value: 21 days


title: EK-D3-R1_ATAC


title: exp1_SD_49day_G27

source_name: experiment 1, SD, 49 day, replicate 1

value: 49 days


title: CHZ 30 Bx2 V2 Cheese


title: HG00234 cell line replicate 3


title: exp1_SD_7day_G54

source_name: experiment 1, SD, 7 day, replicate 2

value: 7 days


title: HG00240 cell line replicate 1


title: CHZ 30 Bx3 V1 Milk


title: exp1_LD_70day_G22

source_name: experiment 1, LD, 70 day, replicate 2

value: LD


title: O-D3-1-8_ATAC


title: CHZ 30 Bx1 V2 Cheese

value: Muscle Biopsy


title: exp1_SD_21day_G17

source_name: experiment 1, SD, 21 day, replicate 1


title: exp1_SD_49day_G54

source_name: experiment 1, SD, 49 day, replicate 2


title: exp1_SD_7day_G17

source_name: experiment 1, SD, 7 day, replicate 1


title: HG00239 cell line replicate 1

source_name: purified gDNA


title: HG00234 cell line replicate 1


title: CHZ 30 Bx2 V1 Milk

value: Ingest Milk


title: CHZ 30 Bx1 V1 Milk


title: ES-D3-1-1_ATAC


title: HG00160 cell line replicate 3


title: HG00160 cell line replicate 2


title: O-D3-1-3_ATAC


title: CHZ 27 Bx3 V2 Cheese

value: 180 Min Post Ingestion


title: exp1_LD_49day_G09

source_name: experiment 1, LD, 49 day, replicate 1

value: Experimental condition 1


title: CHZ 27 Bx2 V2 Cheese


title: HG00234 cell line replicate 2


title: HG00160 cell line replicate 1


title: exp1_LD_70day_G09

source_name: experiment 1, LD, 70 day, replicate 1


title: HG00145 cell line replicate 3


title: E-D3-1-2_ATAC


title: exp1_LD_35day_G12

source_name: experiment 1, LD, 35 day, replicate 2


title: HG00145 cell line replicate 2


title: CHZ 27 Bx3 V1 Milk


title: OS-D3-1-9_ATAC


title: CHZ 27 Bx1 V2 Cheese


title: exp1_LD_35day_G09

source_name: experiment 1, LD, 35 day, replicate 1


title: OS-D3-1-4_ATAC


title: exp1_LD_49day_G12

source_name: experiment 1, LD, 49 day, replicate 2


title: exp1_LD_21day_G12

source_name: experiment 1, LD, 21 day, replicate 2


title: HG00145 cell line replicate 1


title: exp1_LD_7day_G12

source_name: experiment 1, LD, 7 day, replicate 2


title: exp1_LD_21day_G02

source_name: experiment 1, LD, 21 day, replicate 1


title: CHZ 27 Bx2 V1 Milk

source_name: Muscle Biopsy


title: EK-D3-1-6_ATAC


title: exp1_LD_7day_G02

source_name: experiment 1, LD, 7 day, replicate 1


title: HG00132 cell line replicate 3


title: E-D3-1-7_ATAC


title: CHZ 20 Bx3 V2 Milk


title: HG00132 cell line replicate 2


title: CHZ 27 Bx1 V1 Milk


title: HG00132 cell line replicate 1


title: RNAseq_day3_reprogramming_ePOUSKM_rep1

data_processing:
The 150bp paired end raw reads were aligned to the mm10 transcriptome using RSEM and integrated bowtie 2.0.Per-gene read counts were calculated using RSEM.
The read counts were GC normalized using EDAseq (Risso et al., 2011). Genes with mean read counts over all traits and replicates of less than 20 were discarded leading to a final set of 10,787 genes.
This gene set was used for differential gene expression analysis by DESeq2 and further downstream analysis. The criteria for differential gene expression used was fold change >0.5 and p value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: reprogramming intermediate after 3days of transduction

growth_protocol: OG2 MEF cells (3 x 10^4 cells per sample) were transduced with ePOU/SKM and Oct4/SKM cocktails twice per 24 h respectively, and cultured in mES medium with 50μg/ml VC, then cells were collect after 3 day culturing.

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct4 promoter with transduced reprogramming factors

value: ePOU, Sox2, Klf4, cMyc


title: exp1_LD_0day_G47

source_name: experiment 1, LD, 0 day, replicate 2

value: 0 day


title: RNAseq_day3_reprogramming_ePOUSKM_rep2


title: CHZ 20 Bx2 V2 Milk

value: 60 Min Post Ingestion


title: HG00131 cell line replicate 3


title: CHZ 20 Bx1 V2 Milk


title: HG00131 cell line replicate 2


title: Season_Jun-14_G7

source_name: season, Jun-14,  replicate 2

value: shoot

tag: clone

value: Natural condition


title: RNAseq_day3_reprogramming_OSKM_rep1

source_name: reprogramming intermediate at 3days of induction

value: Oct4, Sox2, Klf4, cMyc


title: RNAseq_day3_reprogramming_OSKM_rep2


title: CHZ 20 Bx3 V1 Cheese

value: Ingest Cheese


title: HG00119 cell line replicate 3


title: CHZ 20 Bx1 V1 Cheese

value: 0 min


title: CHZ 20 Bx2 V1 Cheese


title: Flyorf-TaDa-MRG15_n1

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

country: Australia

institute: Menzies Institute for Medical Research

data_processing:
Library strategy: DamID-seq
FASTQ files were processed using damidseq_pipeline, default options.
Peaks were called on the averaged binding track via a three-state hidden markov model using hmm.peak.caller (https://github.com/owenjm/hmm.peak.caller)
Genome_build: DmBDGP6
Supplementary_files_format_and_content: gatc.bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution.  Score represents the normalised log2(Dam-fusion/Dam) enrichment.  MRG15 bound peaks are provided in GFF format. The files MRG15-vs-Dam.average.gatc.bedgraph and MRG15-vs-Dam.peaks.gff include data from all samples.

organism: Drosophila melanogaster

source_name: dissected 3rd instar larval brain

extract_protocol:
Larval brains were dissected in PBS, and processed for DamID-seq as previously described (Marshall et al., 2016; Marshall and Brand, 2017) with the following modifications. Briefly, DNA was extracted using a Quick-DNA Miniprep plus kit (Zymo), digested with DpnI (NEB) overnight and cleaned-up with a PCR purification kit (Machery-Nagel), DamID adaptors were ligated, digested with DpnII (NEB) for 2 hours, and amplified via PCR using MyTaq DNA polymerase (Bioline).
2 µg DNA was sonicated in a Bioruptor Plus (Diagenode). DamID adaptors were removed by AlwI digestion, and 500 ng of the resulting fragments end-repaired with a mix of enzymes (T4 DNA ligase (NEB) + Klenow Fragment (NEB) + T4 polynucleotide kinase (NEB)), A-tailed with Klenow 3’ to 5’ exo- (NEB), ligated to Illumina Truseq LT adaptors using Quick Ligase enzyme (NEB) and amplified via PCR with NEBNext Hi-fidelity enzyme (NEB).

value: brain

tag: developmental stage

value: 3rd instar larvae

tag: construct


title: Flyorf-TaDa-MRG15_n2


title: Flyorf-TaDa-Dam_n2

value: Flyorf-TaDa-Dam


title: Flyorf-TaDa-Dam_n1


title: HG00119 cell line replicate 2

tag: cell line


title: Season_Jun-14_G4

source_name: season, Jun-14,  replicate 1


title: Season_May-14_G5

source_name: season, May-14,  replicate 2


title: OK-D3-1-10_ATAC

value: reprogramming cells


title: RNAseq sample 3: PAO1 Pf4 prophage knockout with pPf4r complemented (R3)

city: Singapore

first: Muhammad Hafiz

last: Ismail

state: Singapore

address: Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27

country: Singapore

institute: Nanyang Technological University / Singapore Centre for Environmental Life Sciences Engineering (SCELSE)

description: RNAseq data

data_processing:
Raw reads were quality and adapter trimmed using bbduk
Ribosomal RNA reads were depleted in silico using SortMeRNA version 2.1
The mRNA reads were mapped using bowtie 2 v 2.2.6 to the reference genome and feature counts were obtained using htseq-count
Differential expression was determined using DESeq2
processed data files format and content: Text file containing raw counts of sequencing reads for each sample
processed data files format and content: Normalized abundance (using trimmed means of M values)
processed data files format and content: Sample metadata csv file used in DGE analysis in DESeq2
Genome_build: Pseudomonas aeruginosa PAO1 (NC_002516.2)

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1 ΔPf4 with pPf4r

growth_protocol: Cells were grown overnight in M9 minimal media before being diluted to be used as an inoculum to grow biofilms in a continuous flow biofilm reactor. The biofilm was allowed to grow for 2 days at room temperature with a media flow rate of 9 mL/h before the biofilm was collected for RNA extraction

extract_protocol:
The biofilm was treated with RNAprotect Bacteria Reagent (Qiagen) before RNA was extracted using the RNeasy Mini Kit (Qiagen) as per manufacturer's protocol. Contaminating DNA was removed using TURBO Dnase (Ambion) and purified using the RNA Clean & Concentrator (Zymo Research)
The total RNA was converted to double stranded cDNA and made into libraries using the TruSeq Stranded mRNA Sample Preparation as per manufacturer's instruction but without the oligo dT purification. The sequencing was done using the HiSeq Rapid SBS Kit V2 200 cycles.

value: Bacteria biofilm

value: {delta}Pf4 + pPf4r


title: Season_Apr-14_G8

source_name: season, Apr-14,  replicate 2


title: SLE_Jurkat_RNA_TNFa_5

city: Cincinnati

first: Xiaoming

last: Lu

state: Ohio

address: 3333 Burnet Ave

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Library strategy: Massively parallel reporter assay (MPRA)
Paired-end, 125 bp reads were first quality filtered through Trimmomatic-0.3864 (flags: PE -phred33, LEADING:25, TRAILING:25, MINLEN:80). Read 1 was then separated into the 20bp barcode region and the oligo-matching region. The trimmed oligo-matching region of Read 1 and Read 2 were mapped back to the synthesized oligo sequences using Bowtie265 (flags: -X 250, --very-sensitive, -p 16). Barcodes were then associated with the oligo sequences using the read ID. Only uniquely mapped barcodes were used for downstream analysis.
Single end reads were first quality filtered using Trimmomatic-0.3864 (flags: PE -phred33, LEADING:3, TRAILING:3, MINLEN:70). Each read was then separated into the 20bp barcode region and the constant region. The trimmed constant regions of the reads were mapped back to the constant regions within the GFP 3’ UTR using Bowtie265 (flags: --very-sensitive, -p 16). Only reads with Levenshtein distance of 4 or less within the constant region and perfect matches to the two bases directly adjacent to the barcode were kept. Barcodes were then associated with the retained reads using the read ID. Only barcodes that met our quality threshold requirements were used for downstream analysis.
We followed the procedures described in the “Identification of Regulatory Oligos” section of Tewhey et al (PMID: 27259153) with minor modifications. In brief, oligos (alleles) with 30 or more unique barcodes from the plasmid control were included for analysis. Barcode count totals for each oligo, including SLE variants and the 20 control variants, were passed into DESeq2 (R version 3.5.367) to estimate the fold change and significance between plasmid controls and the triplicate experiments. An adjusted p-value of less than 0.05 was required for significance. Only significant alleles with greater than or equal to a 1.5x fold change were identified as enhancer alleles (enAlleles). A variant was identified as an enhancer variant (enVar) if any allele of this variant was an enAllele. Results for the 20 control variants were compared to data from Tewhey et al (PMID: 27259153) to estimate accuracy, sensitivity, and specificity.
Only enVars were considered for allelic analysis. The barcode counts from every allele of enVars were used for calculating p-values by comparing the log2 ratios of the non-reference allele vs the reference allele, normalized by plasmid controls, using Student’s t-test (PMID: 27259153). P-values were adjusted with the Benjamini-Hochberg FDR-based procedure. A corrected p-value of less than 0.05 was required for significance. Only significant alleles with 25%-fold changes or greater were identified as allelic enVars. We have created an R package (mpraprofiler) for performing this analysis, which is available on the Weirauch lab GitHub page (https://github.com/WeirauchLab/).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file: barcodes and count for each element, enhancer sequences. xlsx: summarized counts from all data

source_name: Jurkat cell line

growth_protocol: Jurkat cell line was grown in RPMI medium supplemented with 10% FBS, 100 units/mL of penicillin, and 100 µg/mL of streptomycin. Cells were seeded at a density of 5 x 10E5 cells/mL the day before transfection.

extract_protocol:
Total DNA and RNA of transfected cells were extracted by the Qiagen ALLPrep DNA/RNA Mini Kit following the manufacturer’s instruction
Extracted RNA was subjected to DNase treatment in a 375 L system with 2.5 L Turbo DNase, and 37.5 L Turbo DNase Buffer at 37°C for 1 hr.  3.75 L 10% SDS and 37.5 L 0.5M EDTA was added to stop DNase with 5 mins of incubation at 75°C. The whole volume was used for eGFP probe hybridization in an 1800 L system, with 450 l 20X SSC Buffer, 900 L Formamide, and 1 L of each 100 M Biotin-labeled GFP probe One to Three. The probe hybridization was performed through incubation at 65°C for 2.5 hrs. 200 l Dynabeads™ MyOne™ Streptavidin C1 was prepared according to the manufacturer’s instructions. The beads were suspended in 250 L 20X SSC Buffer and incubated with the above probe hybridization reaction at room temperature for 15 mins. Beads were then collected on a magnet and washed with 1X SSC Buffer once, and 0.1X SSC Buffer twice. eGFP mRNA was eluted first through adding 12.5 L ddH2O, heating at 70°C for 2 mins and collecting on a magnet, then adding another 12.5 L ddH2O, heating at 80°C for 2 mins and collecting on a magnet. All collected elution was performed with another DNase treatment in a 30 L system containing 0.5 L Turbo DNase, and 3 L Turbo DNase Buffer at 37°C for 1 hr.  0.5 L 10% SDS was added to halt DNase reactions. Eluted mRNA was purified through RNA Clean SPRI Beads. mRNA was reverse transcribed to cDNA using SuperScript™ IV First-Strand Synthesis System with specific primer MPRA_v3_Amp2Sc_R, following the manufacturer’s instructions. cDNA, extracted DNA and plasmid control were then used for building sequencing libraries following Tag-seq Library Construction section in the paper of Tewhey et al (PMID: 27259153). A total of two PCR rounds were needed for building the sequencing library. The first PCR was performed with TruSeq_TruSeq_Universal_Adapter_P5 and MPRA_V3_Illumina_GFP_F. The second PCR was performed with TruSeq_TruSeq_Universal_Adapter_P5 and index primer. Samples were purified, molar pooled and sequenced using Illumina 1x100bp on Illumina Novaseq 6000

treatment_protocol: For each experimental group, we collected a total of 5 x 10E7 cells per replicate for 5 replicates. Cells were then suspended with 50 g transfection library plasmid in 400 L Buffer R. Electroporation was performed with the Neon transfection system in 100l needles with 3 pulses of 1350V, 10 ms each. After transfection, cells were recovered in 50 mL pre-warmed RPMI medium supplemented only with 10% FBS for 24 hrs. After recovery, cells were supplemented with or without 100ng/ml TNF for 24 hrs. Cells were then collected for preparation of the sequencing library for barcode counting.

tag: replicate

value: Jurkat

tag: disease state

value: Systemic Lupus Erythematosus (SLE)


title: HG00119 cell line replicate 1

source_name: purified gDNA


title: HG00116 cell line replicate 3


title: Season_Apr-14_G7

source_name: season, Apr-14,  replicate 1

tag: condition


title: SLE_Jurkat_RNA_TNFa_4


title: HG00116 cell line replicate 2


title: HG00131 cell line replicate 1


title: SLE_Jurkat_RNA_TNFa_3


title: RNAseq sample 3: PAO1 Pf4 prophage knockout with pPf4r complemented (R2)

description: RNAseq data


title: Season_Mar-14_G7

source_name: season, Mar-14,  replicate 2

tag: photoperiod


title: exp1_LD_0day_G32

source_name: experiment 1, LD, 0 day, replicate 1

value: Experimental condition 1

value: LD

tag: temperature


title: Season_Mar-14_G1

source_name: season, Mar-14,  replicate 1

tag: day of sampling


title: Season_May-14_G3

source_name: season, May-14,  replicate 1

tag: tissue


title: RNAseq sample 2: PAO1 Pf4 prophage knockout (P3)

description: RNAseq data

source_name: Pseudomonas aeruginosa PAO1 ΔPf4


title: SLE_Jurkat_RNA_TNFa_2


title: RNAseq sample 3: PAO1 Pf4 prophage knockout with pPf4r complemented (R1)

description: RNAseq data


title: RNAseq sample 2: PAO1 Pf4 prophage knockout (P2)

description: RNAseq data


title: SLE_Jurkat_DNA_TNFa_5


title: Season_Feb-14_G5

source_name: season, Feb-14,  replicate 2


title: HG00111 cell line replicate 2


title: SLE_Jurkat_RNA_TNFa_1


title: SLE_Jurkat_DNA_TNFa_4


title: HG00111 cell line replicate 3


title: HG00111 cell line replicate 1


title: RNAseq sample 2: PAO1 Pf4 prophage knockout (P1)

description: RNAseq data


title: SLE_Jurkat_DNA_TNFa_3


title: HG00110 cell line replicate 3


title: RNAseq sample 1: PAO1 (W3)

description: RNAseq data

source_name: Pseudomonas aeruginosa PAO1

value: wild type


title: RNAseq sample 1: PAO1 (W2)

description: RNAseq data


title: HG00116 cell line replicate 1


title: RNAseq sample 1: PAO1 (W1)

description: RNAseq data


title: HG00110 cell line replicate 2


title: SLE_Jurkat_DNA_TNFa_2


title: SLE_Jurkat_RNA_4


title: SLE_Jurkat_RNA_5


title: HG00108 cell line replicate 3


title: HG00108 cell line replicate 2


title: Season_Dec-13_G6

source_name: season, Dec-13,  replicate 2


title: Season_Jan-14_G4

source_name: season, Jan-14,  replicate 2


title: Season_Feb-14_G2

source_name: season, Feb-14,  replicate 1


title: SLE_Jurkat_RNA_3


title: Season_Dec-13_G4

source_name: season, Dec-13,  replicate 1


title: SLE_Jurkat_RNA_2


title: HG00108 cell line replicate 1


title: Season_Jan-14_G3

source_name: season, Jan-14,  replicate 1


title: HG00107 cell line replicate 2


title: HG00110 cell line replicate 1


title: SLE_Jurkat_DNA_TNFa_1


title: Season_Nov-13_G2

source_name: season, Nov-13,  replicate 1


title: SLE_Jurkat_DNA_5


title: SLE_Jurkat_DNA_4


title: CPAA-3

city: Bloemfontein

first: Carolina

middle: H

last: Pohl

state: Free State

address: 205 Nelson Mandela avenue, Park West

department: Department of Microbial, Biochemical and Food Biotechnology

country: South Africa

institute: University of the Free State

description:
processed data file:
Supplementary Table S3

data_processing:
Base calling by Illumina Nextseq 500 RTA v2
fastq files (150 bp; paired-end) were analysed for quality by FastQC (v0.11.5; Andrews, 2010)
low-quality reads and bases were discarded using PRINSEQ-lite (v0.20.4; Schmieder & Edwards, 2011) with -min_len 20 -ns_max_n 0 -min_qual_mean 20 -trim_qual_right 30 -trim_qual_type min -trim_qual_rule lt -trim_qual_window 5 -trim_qual_step 3
Alignment to Candida albicans SC5314 genome (assembly 21; The Candida Genome Database; Skrzypek et al., 2017) using TopHat2 fr-secondstrand (Dutton et al., 2016)
BAM files sorted and indexed with SAMtools (Li et al., 2009)
Gene expression count tables created with BEDTools multicov command (Quinlan et al., 2010)
Differential expression analysis done with DESeq2 (Love et al., 2014)
Genome_build: Candida albicans SC5314 genome (assembly 21; The Candida Genome Database; Skrzypek et al., 2017)
Supplementary_files_format_and_content: xlsx file containing assembly 21 identifier, systematic name, log2fold change and padj value. In addition, normalised gene counts are given. Data is filtered according to padj value (padj < 0,05) in sheet2 and log2fold change <-1 and >1 in sheet 3

organism:
Pseudomonas aeruginosa
Candida albicans

source_name: In vitro polymicrobial biofilm

growth_protocol: 24 h cultures (Yeast nitrogen base for C. albicans @ 30°C; Luria-Bertani for P. aeruginosa @ 37°C) were washed with phosphate buffered saline (3X) and diluted (1x10^6 cells/mL for C. albicans; OD600 of 0,05 for P. aeruginosa) in 20 mL sterile RPMI-1640 medium and incubated for 6 hours @ 37°C.

extract_protocol:
Supernatant was removed and cells were scraped off and suspended in RNAlater. Samples were stored @ -80°C until extraction. Total RNA was extracted using Rneasy protect Mini kit (Qiagen) and quality control was done using NanoDrop ND1000, Qubit RNA HS Assay Kit and Agilent Bioanalyzer XP Kit. A total of 1 µg RNA was treated with Illumina Ribo-Zero rRNA removal kit to remove rRNA
indexed libraries were prepared using the ScriptSeqTM v2 RNA-Seq Library Preparation Kit and ScriptSeqTM Index PCR Primers – Set 1 (Illumina). The sizes of the libraries were profiled with the Bioanalyzer High Sensitivity Assay Kit (Agilent) and quantified (Qubit HS DNA Assay Kit). Samples were diluted and a 1 % Phix control library (Illumina) was spiked into samples. Sequencing was completed on the Nextseq 500 (Illumina) using Nextseq 500 High Output (150 cycle) Kits which yielded paired-end reads

treatment_protocol: 100 µM arachidonic acid or equivalent ethanol control (0,076 % ethanol) were added to RPMI-1640 medium with cells prior to incubation

tag: constituants

value: yeast and bacteria

tag: strains

tag: treatment

value: C. albicans + P. aeruginosa + 100 µM arachidonic acid

tag: amount of biofilms pooled per sample

value: 5 X 20 mL petri dish (90 mm)

tag: biofilm age

value: 6 hours


title: Season_Nov-13_G3

source_name: season, Nov-13,  replicate 2

value: shoot

value: Natural condition


title: Season_Oct-13_G1

source_name: season, Oct-13,  replicate 1


title: Season_Sep-13_G6

source_name: season, Sep-13,  replicate 2


title: SLE_Jurkat_RNA_1

source_name: Jurkat cell line


title: Season_Oct-13_G6

source_name: season, Oct-13,  replicate 2


title: Season_Sep-13_G5

source_name: season, Sep-13,  replicate 1


title: CPAA-1


title: SLE_Jurkat_DNA_3


title: Season_Aug-13_G5

source_name: season, Aug-13,  replicate 2


title: SLE_Jurkat_DNA_2


title: KLU_E7_B

city: Bandung

first: Fenny

last: Dwivany

address: Jl. Ganesha No. 10

country: Indonesia

institute: Institut Teknologi Bandung

data_processing:
Raw paired-end reads were examined for a possible low base score, Illumina adapter, and PCR contaminations using FastQC ver. 0.11.8
Illumina adapter was cut using Trimmomatic ver. 0.38.0
Clean reads were mapped against genome reference using TopHat-Cufflink pipeline (Trapnell et al. 2012)
Reads that aligned to annotated loci were quantified and normalized with FPKM value using Cufflinks V2.2.2.1 (Trapnell et al. 2012)
Genome_build: Musa balbisiana DH PKW v.1.1 (available at https://banana-genome-hub.southgreen.fr) (Wang et al., 2019)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Musa balbisiana

source_name: 100μl/L ethylene treatment replicate 2

extract_protocol:
Total RNA were extracted from the fruit pulp using RNA isolation method according to Cordeiro et al. (2008)
RNA libraries were prepared for sequencing using standars Illumina protocols

treatment_protocol: Banana fruit was treated in two conditions, i.e. control and ethylene-treatment. Control is fruits without ethylene treatment. Ethylene-treatment is fruits which were exposed by 100μl/L exogenous ethylene gas and carried out in a glass container.

tag: cultivar

value: Klutuk Wulung (BB group)

tag: Stage

value: Day 7 of fruit ripening

value: 100μl/L ethylene treatment

value: fruit pulp


title: KLU_E7_C

source_name: 100μl/L ethylene treatment replicate 3


title: HG00105 cell line replicate 2

source_name: purified gDNA


title: HG00105 cell line replicate 1


title: Season_Aug-13_G4

source_name: season, Aug-13,  replicate 1

tag: clone


title: CPET-3

description:
processed data file:
Supplementary Table S1
Supplementary Table S3

value: C. albicans + P. aeruginosa + 0,076 % ethanol


title: HG00102 cell line replicate 3


title: SLE_Jurkat_DNA_1


title: KLU_E7_A

source_name: 100μl/L ethylene treatment replicate 1


title: Season_Jun-13_G2

source_name: season, Jun-13,  replicate 2


title: CPET-2


title: HG00105 cell line replicate 3


title: HG00102 cell line replicate 2


title: DM1 Treated 218 3

city: Burjassot

first: Ruben

last: Artero

state: Valencia

address: C/ Doctor Moliner, 50

department: Genetics

country: Spain

institute: Universidad de Valencia

data_processing:
Concadenate and Sort using the linux terminal
Quality control was performed with FASTQC (version 0.11.9)
Aligment was performed with STAR (version 2.7.1a)
Gene counts were performed with using RSEM (1.3.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Total RNA from Myoblast

growth_protocol: Fibroblast cells were grown in DMEM with 4.5 g L−1 glucose, 1% P/S, and 10% FBS (Sigma). To transdifferentiate fibroblasts into myoblasts by inducing MyoD expression, the cells were plated in muscle differentiation medium (MDM) containing DMEM with 4.5 g L−1 glucose, 1% P/S, 2% horse serum, 1% apo-transferrin (10 mg ml−1), 0.1% insulin (10 mg ml−1), and 0.02% doxycycline (10 mg ml−1). In all cases, the cells were grown at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA from human myoblasts was isolated using the miRNeasy Mini Kit (Qiagen; Valencia, CA) according to the manufacturer’s instructions.
Library preparation was performed using TruSeq Stranded mRNA Library prep kit from Illumina without any change

treatment_protocol: Control fibroblasts were seeded into 96-well plates (1 × 10e5 cells per well), transfected with different antagomiR concentrations (from 1 nM to 1 µM) and transdifferentiated into myoblasts for 96 h in MDM medium

tag: cell type

value: normal (iCDF) skin fibroblasts transdifferentiated into myoblast


title: DM1 Treated 218 2


title: KLU_E1_C

value: Day 1 of fruit ripening


title: CPET-1


title: CPAA-2


title: Season_Jun-13_G1

source_name: season, Jun-13,  replicate 1


title: DM1 Treated 218 1


title: HG00102 cell line replicate 1

tag: cell line


title: HG00101 cell line replicate 3


title: KLU_E1_A


title: DM1 3


title: N2_Inf_3

city: Houston

first: Benson

last: Otarigho

state: Texas

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

data_processing:
fq.gz file dataset were uploaded into Galaxy Tool Version 2.11.40.2 that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
Sequences were mapped to W275 C elegans genome
The htseq-count were further analyesd for the differentially expressed features from count tables using DESeq2
Genome_build: Genome_build: Caenorhabditis elegans genome WS275
Supplementary_files_format_and_content: tabular files include htseq-count/values for each Sample

organism: Caenorhabditis elegans

source_name: C. elegans whole animal

growth_protocol: Approximately 40 gravid animals were placed for 3 hours on 10-cm NGM plates (seeded with E. coli OP50) in order to have a synchronized population, which developed and grew to L4 larval stage at 20 C and 4 hours Pseudomonas aeruginosa infection was done at 25 C

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Residual genomic DNA was removed using TURBO DNase (Life Technologies, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were washed off the plates with M9 and frozen in QIAzol by ethanol/dry ice and stored at -80 prior to RNA extraction.

tag: strain

value: Wild type (N2)

value: whole animal

tag: age

tag: infection status

value: P. aeruginosa infected

tag: genotype


title: KLU_K7_C

source_name: Control (non-treatment) replicate 3

value: Control (non-treatment)


title: KLU_K7_B

source_name: Control (non-treatment) replicate 2


title: DM1 2

tag: disease state


title: HG00101 cell line replicate 1


title: HG00101 cell line replicate 2


title: HG00096 cell line replicate 3


title: KLU_K7_A

source_name: Control (non-treatment) replicate 1


title: DM1 1


title: N2_Inf_1


title: U30_If_3


title: Healthy 3

value: Healthy


title: KLU_K1_B


title: HG00096 cell line replicate 2


title: U30_If_2


title: Healthy 2


title: HG00096 cell line replicate 1


title: KLU_K1_A


title: U30_If_1


title: Healthy 1


title: N2_Inf_2


title: pLV-gag21

status: Public on Jan 30 2021

city: London

first: Chad

last: Swanson

state: Select...

address: Great Maze Pond

department: Infectious Diseases

country: United Kingdom

institute: King's College London

data_processing:
Basecalling and debarcoding using GUPPY basecaller version 3.1.5
Reads aligned to the human genome (hg38) and the lentiviral vector genome using minimap2
Near-full length vector genome reads (reads that contain at least 1 nucleotide upstream of SD1) were selected using samtools
Lentiviral vector-mapping junction-spanning reads were isolated using regtools
The percentage of HIV-1 junction-spanning reads was calculated by dividing the number of reads for each junction by the total number of junction-spanning reads in the library.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with number of reads per junction

growth_protocol: HEK293Tsa cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) plus Gluta-Max (Life Technologies) supplemented with 10% FBS and 1% penicillin-streptomycin. Cells were maintained in a humidified atmosphere with 5% CO2 at 37°C. Cells were subcultured to a fresh culture plate when growth reached 70-90% confluence (every 2-3 days).

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen). Polyadenylated mRNA was isolated from approximately 10 µg of total RNA using the Dynabeads mRNA purification kit (ThermoFisher Scientific) following the manufacturer’s instructions.
Nanopore libraries were prepared with 100 ng of poly(A)+ RNA using the Direct cDNA Sequencing kit (SQK-DCS109) with Native Barcoding (EXP-NB104) following the manufacturer’s instructions (Oxford Nanopore Technologies). The final library was loaded onto an R9.4.1 MinION flow cell (FLO-MIN111, Oxford Nanopore Technologies) and sequenced for 72 hours.
Oxford Nanopore Sequencing Direct cDNA Sequencing kit (SQK-DCS109)

treatment_protocol: Cells were seeded 24 hours prior to transfection at a density of 10^6 cells per well in a six-well plate. Plasmids for transfection was prepared in Opti-MEM. Each well was co-transfected with 1 µg vector genome, 1 µg packaging plasmid (pCMV∆R8.91) and 0.5 µg pVSV-G using PEI at a DNA/PEI ratio of 1:3.

value: Human embryonic kidney

value: HEK293Tsa cells transfected with pLV-gag21, pCMVdeltaR8.91 and pVSV-G


title: pLV

value: HEK293Tsa cells transfected with pLV, pCMVdeltaR8.91 and pVSV-G


title: pLV-RRE

value: HEK293Tsa cells transfected with pLV-RRE, pCMVdeltaR8.91 and pVSV-G


title: pLV-RREgag60

value: HEK293Tsa cells transfected with pLV-RREgag60, pCMVdeltaR8.91 and pVSV-G


title: pLV-RREgag21

value: HEK293Tsa cells transfected with pLV-RREgag21, pCMVdeltaR8.91 and pVSV-G


title: C_5_S30_L001_R1_001

city: Lincoln

first: Kyle

last: Harrison

state: Nebraska

address: 1700 E Campus Mall

department: Entomology

institute: USDA-ARS

data_processing:
Sequence cluster identification, quality prefiltering, base calling, and uncertainty assessment were done in real time using Illumina’s HCS 2.2.38 and RTA 1.18.61 software with default parameter settings.
Alignment using HISAT2-index-align2.1 on the CyVerse platform mapping to the S. lycopersicum genome (vSL3.0)
Assembly using StringTie-1.3.3 on the CyVerse platform mapping hits to known transcripts based on the S. lycopersicum genome vITAG3.2 annotation and made non-redundant with StringTie-Merge
Ballgown analysis of FPKM values for each Sample using R
Genome_build: Solanum lycopersicum genome (vSL3.0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Solanum lycopersicum

source_name: Stem and leaf tissue

growth_protocol: Grown from seed in Metro-Mix 900 (Sun Gro Horticulture, Agawam, MA) soil and individually transplanted to 10 x 10 cm square pots four weeks later. Plants were watered every other day and fertilized weekly according to the manufacturer’s recommendation (Miracle-Gro® Water Soluble Tomato Plant Food; 18-18-21 NPK). All experiments were conducted at the same photoperiod (16: 8) and temperature (22±2°C).

extract_protocol:
Total RNA extraction was performed on leaf tissue harvested three weeks after psyllid infestation using the Plant RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s protocol. Three biological replicates were sequenced per treatment (i.e., uninfested and psyllid-infested, six samples total). One fully-develop leaf and petiole were removed per biological replicate using sterilized razor blades. The top-most leaf was sampled to ensure that the gene expression changes observed were more likely to be associated with a plant systemic response. Samples were ground using sterilized plastic pestles. RNA samples were treated with RNase-Free DNase (Qiagen). Any remaining DNA was removed using the TURBO DNA-free™ Kit (Life Technologies, Carlsbad, CA). All remaining RNA was stored at -80°C for downstream quantitative reverse transcription PCR (RT-qPCR) validation. The isolated RNA was submitted to the Texas A&M Genomics and Bioinformatic Service for quality analysis, library preparation, and sequencing.
cDNA libraries were developed using the TruSeq RNA Library Prep Kit v2 (Illumina ®; San Diego, CA) following the manufacturer’s protocol, generating 2 Х 150 bp read lengths

treatment_protocol: Psyllid infestation were initiated when plants were six weeks old. Leaves branching below the apical meristem (i.e., leaves like the ones sampled for the transcriptome analysis) were caged with a small, white organza bag (amazon.com). Restricting psyllids to these leaves exposed them to systemic response of the plant to any prior infestation. Each bag either had no psyllids (control plants) or three adult male psyllids (psyllid-infested plants). Males were chosen to avoid the potentially confounding effect of oviposition on tomato gene expression. Seven days after infestation, caged tomato leaves were removed with a bleach-sterilized razor blade. Three weeks later, the top-most, fully developed leaf was sampled from each plant and immediately flash-frozen in liquid nitrogen. Samples were transferred to Eppendorf tubes and kept submerged under liquid nitrogen while ground with plastic, RNase-free pestles.

value: Stem and leaf tissue

value: untreated

value: Moneymaker


title: C_3_S28_L001_R1_001


title: J1_5_S33_L001_R1_001

value: previously infested with B. cockerelli


title: J1_3_S31_L001_R1_001


title: J1_4_S32_L001_R1_001


title: C_4_S29_L001_R1_001


title: 470140_repl3

city: Vienna

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

country: Austria

institute: Max Perutz Labs

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v1.18 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1)
The reads were then mapped to C. auris genome (B11221 GCF_002775015.1) using NextGenMap (Sedlazeck et al., 2013), settings: -b -Q 30.
Optical read duplicates were removed using Picard tools (Broad Institute, https://broadinstitute.github.io/picard/, settings: MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT).  Read counting was done using HTseq (Anders et al., 2014) in the union mode and the genomic annotation from C. auris B11221 (settings: -f bam  -t gene -i ID).
Differential gene expression analysis was done using pair-wise comparisons in edgeR (Robinson et al., 2009)
Genome_build: C. auris genome (B11221 GCF_002775015.1)
Supplementary_files_format_and_content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)

organism: Candidozyma auris

source_name: 470140_fungal cells

extract_protocol:
Total RNA was purified using Genejet RNA purification kit (Thermo Scientific). Quality of RNA was assessed on a Bioanalyzer using the RNA6000 Nanochip (Agilent), mRNA was enriched using oligo(dT) beads (NEB) and subsequently, double-stranded cDNA libraries were generated by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.
The qualified libraries were subjected to Illumina sequencing with a 75 bp paired-read length at the Novogene (Novogene, USA) sequencing facility.

tag: genotype/clinical isolate


title: 470147_repl3

source_name: 470147_fungal cells


title: CBS10913_repl2

source_name: CBS10913_fungal cells


title: 470154_repl1

source_name: 470154_fungal cells


title: CBS10913_repl13


title: CBS10913_repl1


title: 470154_repl3


title: 470140_repl1


title: 470147_repl2


title: 470154_repl2


title: 470140_repl2


title: Alport treated with metformin replicate 2

city: Kumammoto

first: Kohei

last: Omachi

address: 5-1, Oe-honmachi

department: Molecular Medicine

institute: Kumamoto University

description: Alport M2

hyb_protocol: Following fragmentation, 5.2 ug of ssDNA were hybridized for 16 hr at 45C on Clariom S Array Chips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0 (TAC4.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Alport treated with metformin, kidney

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Manual target preparation for GeneChip Whole Transcript (WT), Affymetrix).

growth_protocol: wild type mice and Alport mice were sacrificed at 16-week-old.

extract_protocol: Total RNA was isolated from mouse kidney tissue using Rneasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Metformin was orally administered via drinking water at a dose of 2.5 mg/mL for 6 to 11 weeks-old, and 5 mg/mL for 12 to 20 weeks-old AS mice. Losartan was co-administered via drinking water at a dose of 125 µg/mL for 6 to 11 weeks-old, and 250 µg/mL from 12 to 20 weeks-old AS mice.  The water containing these compounds was replenished twice a week.

tag: tissue

value: whole kidney

value: COL4A5 nonsense (G5X) hemi


title: Alport treated with metformin replicate 3

description: Alport M3


title: 470147_repl1


title: Sample D710

city: QingDao

first: Qilai

last: Huang

address: Binhai road 72#

institute: Shandong University

data_processing:
The next-generation sequencing Data quality statistical software Cutadapt (version 1.9.1) was used to remove the adapters and low-quality sequences from the original sequencing Data (Pass Filter Data) to obtain Clean Data for subsequent information analysis.
The overlap area between read1 and read2 of Clean Reads was combined using Pandaseq (version 2.7) to produce complete sequences.
According to the Barcode sequence of read1 of each sample, the spliced Tag starting position is split into the corresponding sample with perfect matching, and the result is saved in FASTQ file.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every barcode and every sample

molecule: other

organism: synthetic construct

source_name: plasmid library

extract_protocol:
Twenty-four hours post-transfection, cells were washed twice and harvested in 1 × PBS, and Total RNA was extracted from all surviving cells using RNeasy Plus Mini Kit (74136, QIAGEN). We treated the mRNA with RapidOut DNA Removal Kit (K2981, Thermo Scientific) to remove the trace amount of genomic DNA residue according to the product manual. The purified RNA was then subjected to reverse transcription with High-Capacity cDNA Reverse Transcription Kits (4374967, Applied Biosystems). Briefly, 1.5μg RNA was added into 10μl of 2× RT Master Mix and made up to the final 20μl with nuclease-free water. The reactions were incubated at 25°C for 10 min, followed by 120 min at 37°C, then were inactivated Reverse Transcriptase by heating to 85°C for 5 min. The cDNA products were stored at -20°C or -80°C and ready for qPCR analysis and preparing the NGS sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: plasmid library

tag: sample type

value: multiplexed

tag: molecule

value: plasmid mixture


title: Sample D703


title: Sample D711


title: Alport treated with losartan replicate 3

description: Alport L3

source_name: Alport treated with llosartan, kidney


title: Alport treated with vehicle replicate 3

description: Alport CON3

source_name: Alport treated with vehicle, kidney


title: Alport treated with vehicle replicate 1

description: Alport CON1


title: Alport treated with losartan replicate 1

description: Alport L1


title: Alport treated with vehicle replicate 2

description: Alport CON2


title: Alport treated with losartan replicate 2

description: Alport L2


title: Sample D707

source_name: prostate cancer cell line LNCaP

value: prostate cancer cell line LNCaP

value: total RNA


title: Sample D706


title: Sample D702

source_name: breast cancer cell line MCF7

value: breast cancer cell line MCF7


title: Sample D701


title: Sample D705


title: Alport treated with metformin replicate 1

description: Alport M1


title: Sample D709


title: water-rep 2

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

description: wheat seedling (without root) 1 day post water treatment

data_processing:
Basecalls performed using CASAVA version 1.8
Sequencing reads were preprocessed using Trim Galore to trim the adapter sequence
mRNA-seq reads were aligned to the genome sequence assembly Triticum aestivum IWGSC 47 (ftp://ftp.ensemblgenomes.org/pub/plants/release-47/fasta/triticum_aestivum/dna/) using HISAT2 (Kim et al., 2015) with strand-specific information (--rna-strandness RF) and otherwise default settings.
Only the uniquely mapped reads were used to create count matrix using featureCounts
Differential gene expression analysis was performed using the DESeq2
Genome_build: Triticum aestivum Chinesespring genome sequence IWGSC 47
Supplementary_files_format_and_content: Differential gene expression analysis was performed using the DESeq2

organism: Triticum aestivum

source_name: wheat seedling (without root)

growth_protocol: Wheat seeds were soaked in water overnight at room temperature, and then the imbibed seeds in a medical enamel tray containing 2 layers of wet gauze and geminate in the dark for 1 day at 25 °C. Grow the wheat seedlings in the growth chamber for 2 days under controlled environment conditions at 25 °C with a 12 h light/12 h dark photoperiod.Then these 3-day-old seedlings were treated by NHP or water, and continue to grow for 1 day at 25 °C with a 12 h light/12 h dark photoperiod before RNA extraction.

extract_protocol:
Total RNA was extracted using EasyPure Plant RNA kit (Transgen biotech) according to the manufacturer’s protocol. RNA quality was evaluated using the Bioanalyzer 2100 (Agilent Technology).
The RNA sequencing was performed at Sinotech Genomics. The libraries for sequencing were prepared using SureSelect Strand-Specific RNA Component kit.

treatment_protocol: The top 1-2 mm of each coleoptile of 3-day-old seedlings were cut off, 1 μL 1 mM NHP or 1 μL water per seedling were added on the wound site of each coleoptile for NHP treated samples or water treated samples respectively.

value: Zhongyuan 98-68

value: 4-day-old seedlings

tag: treatment

value: 1 day post water


title: wild type treated with vehicle replicate 2

source_name: wild type treated with vehicle, kidney

value: WT


title: NHP-rep 2

description: wheat seedling (without root) 1 day post NHP treatment

value: 1 day post NHP


title: water-rep 3


title: NHP-rep 1


title: water-rep 1


title: NHP-rep 3


title: HG00107 cell line replicate 1

city: New York

first: Jeremiah

last: Li

address: 430 E 29th St 14th Floor, 14th Floor

institute: Gencove

data_processing: genomic DNA was genotyped using the Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)

source_name: purified gDNA

extract_protocol: an automated magnetic bead purification protocol (Hamilton Microlab STAR w/ Promega ReliaPrep Isolation system) was used to extract genomic DNA that was eluted in TE buffer (pH 8.0, 1mM EDTA)


title: wild type treated with vehicle replicate 1


title: HG00107 cell line replicate 3


title: Treg_CNS_icKO mouse rep1

city: Paris

first: Benoit

middle: L

last: Salomon

address: 91 Bd de l'hopital

country: France

institute: Inserm

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including expecting counts, TPM and FPKM

source_name: CD4+Foxp3+ Treg from the CNS

extract_protocol:
RNA was extracted from highly purified Treg and Tconv cells using the NucleoSpin RNA XS kit from Macherey-Nagel, quantified using a ND-1000 NanoDrop spectrophotometer (NanoDrop Technologies) and purity/integrity was assessed using disposable RNA chips (Agilent High Sensitivity RNA ScreenTape) and an Agilent 2200 Tapestation (Agilent Technologies, Waldbrunn, Germany).
Libraries were prepared from the extracted RNA using the Smartseq V4 TAKARA followed by Nextera library preparation

value: CNS

value: Treg

value: Foxp3Cre-ERT2 x Tnfrsf1bFlox/Flox

value: Induction of active EAE

value: Tamoxifen from d7 to d14


title: Treg_CNS_Ctrl mouse rep3


title: wild type treated with vehicle replicate 3

value: whole kidney


title: Tconv_dLN_icKOl mouse rep3

source_name: CD4+Foxp3- Tconv from the dLN

value: draining Lymph node

value: Tconv


title: Tconv_dLN_Ctrl mouse rep3


title: Tconv_dLN_Ctrl mouse rep2


title: Treg_dLN_icKOl mouse rep1

source_name: CD4+Foxp3+ Treg from the dLN


title: Tconv_dLN_Ctrl mouse rep1


title: Treg_dLN_icKOl mouse rep3


title: Treg_dLN_icKOl mouse rep2


title: Treg_CNS_icKO mouse rep3


title: Tconv_CNS_icKO mouse rep2

source_name: CD4+Foxp3- Tconv from the CNS


title: Tconv_CNS_icKO mouse rep3


title: Treg_dLN_Ctrl mouse rep1


title: Treg_dLN_Ctrl mouse rep2


title: Tconv_CNS_Ctrl mouse rep4


title: Tconv_CNS_Ctrl mouse rep2


title: Tconv_CNS_icKO mouse rep1


title: Tconv_CNS_icKO mouse rep4


title: Tconv_CNS_Ctrl mouse rep3


title: Treg_dLN_Ctrl mouse rep3


title: Tconv_dLN_icKOl mouse rep2


title: Tconv_CNS_Ctrl mouse rep1


title: Treg_CNS_Ctrl mouse rep2


title: Tconv_dLN_icKOl mouse rep1


title: Treg_CNS_Ctrl mouse rep1


title: Library 2 with Polylinker Rep3 RNA

city: St. Louis

middle: Aaron

last: White

state: MO

address: 4515 McKinley Ave, Campus Box 8510

institute: Washington University School of Medicine

description: Demultiplexing barcode sequence of 'CGCTACCCT' upstream of a spacer sequence 'CACCTGTTCCTGTAGGCATGC' followed by a 9 bp barcode for library elements

data_processing:
Library strategy: Massively Parallel Reporter Assay
All raw reads were processed regardless of quality score. Reads with the expected in-line multiplexing barcode for each sample followed by the spacer sequence were identified. Demultiplexed reads were then used to determine the number of unique occurances of 9 bp sequences in the barcoded region of the reporter construct. Barcodes that exactly matched designed sequences were written to file along with the sequence identifier and the barcode's count. All other reads and barcodes were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: First column contains unique 9 bp barcode, second column contains sequence identifier, third column contains number of reads with the corresponding barcode. Sequences were named using the following nomenclature: "chrom-start-stop_annotations_variant". "Chrom", "start", and "stop" correspond to the mm10 genomic coordinates of the sequences in BED format. "Annotations" is a four letter string where the first position indicates CRX binding status ("C" ChIP-seq peak or "U" Unbound), the second position indicates CRX motif status ("P" PWM hit, "S" Shape motif, or "B" Both PWM and shape motif), the third position indicates ATAC-seq status ("R" peak in Rods but not cones, "C" peak in Cones but not rods, "P" peak in both rod and cone Photoreceptors, or "N" peak in None of the above), and the fourth position indicates histone ChIP-seq status ("E" Enhancer marked with H3K27Ac+H3K4me3-, "P" Promoter marked with H3K27Ac+H3K4me3+, "Q" H3K27Ac-H3K4me3+, or "N" Neither mark). "Variant" indicates whether the sequence is genomic ("WT"), mutated CRX sites ("MUT-allCrxSites"), scrambled shape motif ("MUT-shape"), or a scrambled control ("scrambled").

source_name: Retina

growth_protocol: Retinas were isolated from P0 newborn CD-1 mice and electroporated in a solution with 30 micrograms library and 30 micrograms Rho-GFP as described previously (Hsiau et al., 2007; Hughes et al., 2018; Kwasnieski et al., 2012; White et al., 2013, 2016). Electroporated retinas were cultured for eight days, at which point they were harvested, washed three times with HBSS (Gibco), and stored in TRIzol (Invitrogen) at -80C. Five retinas were pooled for each biological replicate and three replicates were performed for each experiment.

extract_protocol:
Target library reporter sequences were amplified using primers 'GTGGAGCAGTACGAGCG' and 'TAGCCAGAAGTCAGATGCTCAAG' for 30 cycles (NEB Q5) at an annealing temperature of 67C and then purified with the Monarch PCR kit. Illumina adaptors were then added via two further rounds of PCR. First, custom P1 indexing barcodes were tailed on for 5 cycles at an annealing temperature of 55C followed by 5 cycles with no annealing step (NEB Q5). PE2 indexing barcodes were then tailed on by amplifying 2 microliters of the previous reaction for 5 cycles at an annealing temperature of 66C followed by 5 cycles with no annealing step (NEB Q5) and then purified with the Monarch PCR kit. Samples were mixed at equal concentration and sequenced on the Illumina NextSeq platform.
RNA was extracted from TRIzol according to manufacturer instructions and treated with TURBO DNase (Invitrogen). cDNA was prepared using SuperScript RT III (Invitrogen) with oligo dT primers.

value: retina

value: postnatal day 8


title: Library 2 with Polylinker Rep2 RNA

description: Demultiplexing barcode sequence of 'TAGACTAT' upstream of a spacer sequence 'CACCTGTTCCTGTAGGCATGC' followed by a 9 bp barcode for library elements


title: Treg_CNS_icKO mouse rep2


title: Library 1 with Polylinker Rep3 RNA


title: Library 1 with Polylinker Rep2 RNA


title: Library 1 with Polylinker Rep1 RNA

description: Demultiplexing barcode sequence of 'GCTCGAT' upstream of a spacer sequence 'CACCTGTTCCTGTAGGCATGC' followed by a 9 bp barcode for library elements


title: Library 2 with Rho Rep3 RNA

description: Demultiplexing barcode sequence of 'CGCTACCCT' upstream of a spacer sequence 'CATGC' followed by a 9 bp barcode for library elements

extract_protocol:
Target library reporter sequences were amplified using primers 'CACCTGTTCCTGTAGGCATGC' and 'TATTACAATTGTAGCCAGAAGTCAGATGCTCAAG' for 6 cycles at an annealing temperature of 66C followed by 18 cycles with no annealing step (NEB Phusion) and then purified with the Monarch PCR kit (NEB). PCR amplicons were digested using MfeI-HF and SphI-HF (NEB) and ligated to custom annealed adaptors with PE2 indexing barcodes and phased P1 barcodes. The final enrichment PCR used primers 'AATGATACGGCGACCACCGAG' and 'CAAGCAGAAGACGGCATACGA' for 20 cycles at an annealing temperature of 66C (NEB Phusion), followed by purification with the Monarch PCR kit. Samples were mixed at equal concentration and sequenced on the Illumina NextSeq platform.
RNA was extracted from TRIzol according to manufacturer instructions and treated with TURBO DNase (Invitrogen). cDNA was prepared using SuperScript RT III (Invitrogen) with oligo dT primers.


title: MS_ko_P66_Cohort_2_Num_53

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

country: Germany

institute: University of Wuerzburg

data_processing:
The raw reads were processed using FastQC 0.11.4 for assessing read quality, amount of duplicates and presence of adapter sequences
After this, the Illumina TruSeq adaptors were cleaved using cutadapt version 1.16 and resulting reads were further trimmed keeping a quality drop value below a mean of Q20
Reads were then further processed using edge R (3.20.9) and first converted into an edgeR file.
Genes with no reads were excluded from the analysis, followed by a log2FC transformation.
The two different age groups were analysed separatly. Mean variance trends were calculated using the voom function from the limma package (3.34.9), and ananylsed using lmFit and eBayes from the same package.
The results of individual factors (gene and environment) were then filtered by selecting all genes that had a p-value smaller than 0.01 and a log2 Fold Change (log2FC) higher than 0.2 or lower than -0.2.
Genome_build: Mus.musculus (v1.3.1)
Supplementary_files_format_and_content: abundance measurements: text format

source_name: Hippocampus

growth_protocol: Pups were weaned at postnatal day 22 (P22), half of the animals were sacrificed right at this time, while the other half was left undisturbed till postnatal day 66 (P66) when they reached adulthood.Due to limited capacity for breeding animals, two rounds of breedings were conducted (cohort_1 and cohort_2). Only male animals were used in this experiment. Number (Num_x) refer to individual animals in each cohort and environmental group and are not continuous.

extract_protocol:
Mice of both age, genotype and treatment group were sacrificed by isoflurane. Brains were then quickly dissected and frozen in dry ice cooled 2-methylbutane (-50°C) and stored at -80°C. The hippocampus, alongside five other brain regions (not investigated here), was extracted from approximately 1 mm-thick brain slices on a sterile pre-cooled plate (-8.5°C) using the Allen Brain Atlas as a reference.
Standard Illumina protocols were used to prepare RNA libraries

treatment_protocol: Pregnant dams were single housed aproximatly 1 week prior to birth. From P1 till P14 half of the litters were daily separated for 3h at a random time during the light cycle (12h/12h), while control litters were handled and otherwise not distrubed.

value: Hippocampus

tag: environment

value: maternal separation

value: Cdh13 knockout

value: postnatal day 66


title: MS_ko_P66_Cohort_2_Num_84


title: MS_ko_P66_Cohort_1_Num_56


title: MS_ko_P66_Cohort_1_Num_54


title: MS_ko_P66_Cohort_1_Num_2


title: Ctr_ko_P66_Cohort_2_Num_61

value: control


title: Ctr_ko_P66_Cohort_2_Num_76


title: Library 1 with Rho Rep2 RNA

first: Michael

description: Demultiplexing barcode sequence of 'TAGACTAT' upstream of a spacer sequence 'CATGC' followed by a 9 bp barcode for library elements


title: Ctr_ko_P66_Cohort_2_Num_42


title: Library 2 with Rho Rep2 RNA


title: Library 2 with Rho Rep1 RNA

description: Demultiplexing barcode sequence of 'GCTCGAT' upstream of a spacer sequence 'CATGC' followed by a 9 bp barcode for library elements


title: Library 1 with Rho Rep1 RNA


title: MS_ko_P66_Cohort_1_Num_58


title: Library 1 with Rho Rep3 RNA


title: MS_ko_P66_Cohort_1_Num_3


title: Ctr_ko_P66_Cohort_1_Num_24


title: MS_wt_P66_Cohort_2_Num_66

value: wildtype


title: Ctr_ko_P66_Cohort_1_Num_22


title: MS_wt_P66_Cohort_2_Num_64


title: Ctr_ko_P66_Cohort_1_Num_30


title: Ctr_ko_P66_Cohort_2_Num_41


title: MS_wt_P66_Cohort_1_Num_55


title: MS_wt_P66_Cohort_1_Num_53


title: MS_wt_P66_Cohort_1_Num_14


title: MS_wt_P66_Cohort_1_Num_30


title: MS_wt_P66_Cohort_2_Num_55


title: MS_wt_P66_Cohort_2_Num_42


title: MS_wt_P66_Cohort_1_Num_57


title: Ctr_wt_P66_Cohort_2_Num_19


title: Library 2 with Polylinker Rep1 RNA


title: Ctr_wt_P66_Cohort_1_Num_6


title: Ctr_wt_P66_Cohort_1_Num_15


title: MS_ko_P22_Cohort_2_Num_63

value: postnatal day 22


title: MS_ko_P22_Cohort_2_Num_9


title: MS_ko_P22_Cohort_2_Num_36


title: Ctr_ko_P22_Cohort_2_Num_96


title: MS_ko_P22_Cohort_1_Num_61


title: Ctr_wt_P66_Cohort_2_Num_84


title: Ctr_wt_P66_Cohort_2_Num_86


title: Ctr_ko_P22_Cohort_2_Num_77


title: MS_ko_P22_Cohort_2_Num_92


title: MS_ko_P22_Cohort_2_Num_74


title: Ctr_ko_P22_Cohort_2_Num_43


title: MS_ko_P22_Cohort_2_Num_77


title: Ctr_ko_P22_Cohort_2_Num_34


title: MS_ko_P22_Cohort_2_Num_23


title: MS_ko_P22_Cohort_2_Num_12


title: MS_ko_P22_Cohort_1_Num_52


title: MS_wt_P66_Cohort_1_Num_46


title: MS_wt_P22_Cohort_2_Num_75


title: Ctr_wt_P66_Cohort_2_Num_58


title: Ctr_ko_P22_Cohort_2_Num_10


title: Ctr_ko_P22_Cohort_1_Num_21


title: MS_wt_P22_Cohort_1_Num_39


title: Ctr_ko_P22_Cohort_1_Num_55


title: MS_wt_P22_Cohort_2_Num_62


title: Ctr_wt_P66_Cohort_1_Num_58


title: MS_wt_P22_Cohort_1_Num_1


title: Ctr_wt_P22_Cohort_2_Num_97


title: MS_wt_P22_Cohort_1_Num_51


title: MS_wt_P22_Cohort_1_Num_43


title: Ctr_ko_P22_Cohort_1_Num_51


title: MS_wt_P22_Cohort_2_Num_90


title: Ctr_wt_P22_Cohort_2_Num_27


title: MS_wt_P22_Cohort_2_Num_35


title: MS_wt_P22_Cohort_1_Num_29


title: Ctr_wt_P22_Cohort_2_Num_85


title: Ctr_ko_P22_Cohort_1_Num_4


title: Ctr_wt_P22_Cohort_1_Num_56


title: MS_wt_P22_Cohort_2_Num_21


title: WT_Striatum_Rep7

data_processing:
The raw reads were processed using FastQC 0.11.4 for assessing read quality, amount of duplicates and presence of adapter sequences
After this, the Illumina TruSeq adaptors were cleaved using cutadapt version 1.16 and resulting reads were further trimmed keeping a quality drop value below a mean of Q20
Further, the processed sequences were mapped to the murine genome (mm16, GRCm38) using the short read aligner STAR-2.5.2b with genome and annotation files retrieved from GENCODE
For all the studied samples, the proportion of reads mapped to the mouse reference genome ranged between 89% and 91% in total
The sequences aligning to specific genes were quantified using bedtools subcommand intersect
Each brain regions was analysed independently to identify differentially expressed genes using DESeq2 version 1.16.1,
For the combined brain region analysis read counts were summed across the three brain regions prior to the analysis with DESeq2.
Only the genes having a Benjamini-Hochberg corrected p-value below 0.05 were classified as significantly differentially expressed (DEGs)
Genome_build: murine genome (mm16, GRCm38)
Supplementary_files_format_and_content: abundance measurements (text format)

extract_protocol:
12 Lphn3 +/+ and 12 Lphn3 -/- mice were sacrificed between P65 and P76 (Mean=P67.15, SD=3.468). Brains were frozen immediately and stored at -20°C until microdissection. The prefrontal cortex, hippocampus and straitum were separated and homogenized for RNA collection.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adgrl3 +/+

value: Brain

tag: tissue region

value: Striatum


title: Ctr_wt_P22_Cohort_1_Num_32


title: Ctr_wt_P22_Cohort_1_Num_12


title: Ctr_wt_P22_Cohort_2_Num_51


title: WT_Striatum_Rep4


title: WT_Striatum_Rep9


title: WT_Striatum_Rep5


title: WT_Striatum_Rep10


title: WT_Striatum_Rep2


title: WT_Striatum_Rep3


title: WT_Striatum_Rep1


title: WT_Prefrontal-Cortex_Rep10

value: Prefrontal-Cortex


title: Ctr_wt_P22_Cohort_1_Num_50


title: MS_wt_P22_Cohort_1_Num_11


title: WT_Prefrontal-Cortex_Rep9


title: WT_Striatum_Rep8


title: WT_Prefrontal-Cortex_Rep4


title: WT_Prefrontal-Cortex_Rep3


title: WT_Prefrontal-Cortex_Rep8


title: WT_Prefrontal-Cortex_Rep5


title: WT_Prefrontal-Cortex_Rep6


title: WT_Prefrontal-Cortex_Rep1


title: WT_Prefrontal-Cortex_Rep2


title: WT_Hippocampus_Rep10


title: WT_Hippocampus_Rep8


title: WT_Hippocampus_Rep9


title: WT_Hippocampus_Rep6


title: WT_Hippocampus_Rep5


title: WT_Hippocampus_Rep4


title: WT_Striatum_Rep6


title: WT_Hippocampus_Rep3


title: WT_Hippocampus_Rep7


title: KO_Striatum_Rep3

value: Adgrl3 -/-


title: WT_Hippocampus_Rep2


title: KO_Striatum_Rep9


title: KO_Striatum_Rep6


title: WT_Hippocampus_Rep1


title: KO_Striatum_Rep8


title: KO_Striatum_Rep4


title: WT_Prefrontal-Cortex_Rep7


title: KO_Striatum_Rep2


title: KO_Prefrontal-Cortex_Rep10


title: KO_Striatum_Rep1


title: KO_Striatum_Rep5


title: KO_Prefrontal-Cortex_Rep9


title: KO_Prefrontal-Cortex_Rep8


title: KO_Striatum_Rep7


title: KO_Prefrontal-Cortex_Rep4


title: KO_Prefrontal-Cortex_Rep5


title: KO_Hippocampus_Rep9


title: KO_Prefrontal-Cortex_Rep1


title: KO_Prefrontal-Cortex_Rep3


title: KO_Prefrontal-Cortex_Rep6


title: KO_Striatum_Rep10


title: KO_Hippocampus_Rep7


title: KO_Hippocampus_Rep6


title: KO_Hippocampus_Rep8


title: KO_Hippocampus_Rep5


title: KO_Hippocampus_Rep4


title: KO_Hippocampus_Rep3


title: KO_Hippocampus_Rep2


title: KO_Hippocampus_Rep1


title: KO_Prefrontal-Cortex_Rep7


title: KO_Prefrontal-Cortex_Rep2


title: LUHMES_Day2_Rep1

first: Matthew

middle: A

last: Lalli

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description:
Replicate 1
Timecourse_LUHMES_counts.csv

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: LUHMES cells

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuronal

value: wild type

value: LUHMES cells

value: Day 2 differentiation


title: LUHMES_Day6_Rep1

value: Day 6 differentiation


title: LUHMES_Day2_Rep2

description:
Replicate 2
Timecourse_LUHMES_counts.csv


title: LUHMES_Day6_Rep2


title: LUHMES_Day0_Rep1

value: Day 0 differentiation


title: LUHMES_Day8_Rep1

value: Day 8 differentiation


title: LUHMES_Day0_Rep2


title: LUHMES_Day4_Rep1

value: Day 4 differentiation


title: Decending aorta patient Ao8B

city: Boston

first: Amelia

middle: Weber

last: Hall

state: MA

address: 185 Cambridge St

department: Cardiology

institute: Massachusetts General Hospital

description:
Ao8B_S4
processed file is an h5ad file containing output from all samples

data_processing:
FASTQ construction done with CellRanger 3.0.2 mkfastq
Reads trimmed for switch oligo and homopolymers using cutadapt, demultiplexed and aligned to pre-mRNA transcriptome using CellRanger 3.0.2 count
Nuclei were removed if they had 1) <500 UMI, or greater than 3rd quartile + 1.5*interquartile range (IQR); 2) <250 genes, or greater than 3rd quartile + 1.5*IQR; 3) >=0.5% mitochondrial reads; 4) proportion of strictly exonic reads >=20; 5) predicted doublet score >= 0.25; 6) entropy <8 or >10.
Remaining nuclei were combined across samples
Genome_build: GRCh38
Supplementary_files_format_and_content: h5ad file containing output from all samples

source_name: Descending aorta

growth_protocol: N/A primary human tissue

extract_protocol:
Ascending and descending human aortas were obtained from 5 human patients collected in compliance with all relevant ethical regulations for human research participants with patient consent following a rapid autopsy protocol (DFHCC IRB #13-416) within 4 hours of cardiac death. Aortic segments from the aortic root, ascending aorta, descending thoracic aorta and infrarenal abdominal aorta were surgically collected by a single operator and immediately frozen and stored at -80°C until use. For nuclei isolation, aortas were mounted frozen on OCT and sectioned. Cut tissues were incubated in ice cold nuclei isolation buffer and then liberated by dounce homogenization in isolation buffer. Homogenates were centrifuged and filtered to isolate nuclei. Nuclei, stained with Trypan blue, were manually counted using a hemocytometer (inCyto.com). 7,000 nuclei (5,000 recovery) per aorta were used for droplet generation and library construction according to manufacturer’s protocol (10x Genomics, V3).
10x genomics 3' capture v3

treatment_protocol: N/A primary human tissue

value: Descending aorta

tag: data type

value: 10x genomics v3 single cell 3' capture


title: Decending aorta patient Ao12B

description:
Ao12B_S2
processed file is an h5ad file containing output from all samples


title: Ascending aorta patient Ao4A

description:
Ao4A_S1
processed file is an h5ad file containing output from all samples

source_name: Ascending aorta

value: Ascending aorta


title: Decending aorta patient Ao4B

description:
Ao4B_S2
processed file is an h5ad file containing output from all samples


title: Ascending aorta patient Ao8A

description:
Ao8A_S3
processed file is an h5ad file containing output from all samples


title: LUHMES_Day8_Rep2


title: LUHMES_Day4_Rep2


title: KO_Hippocampus_Rep10

value: Hippocampus


title: CBMC_IL4STIM1

first: Daniel

last: Dwyer

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

data_processing:
Data for each lane was separated by barcode and concatinated. Transcripts were alligned to GRCh38 (hg38) genome assembly with STAR (Dobin et al 2013) with the following parameter settings: --outSAMstrandField intronMotif --outSJfilterReads Unique --outSJfilterCountUniqueMin 100 1 1 1 --limitSjdbInsertNsj 10000000 --chimSegmentMin 10. Transcripts were quantified with HTseq (Anders et al, 2014).
Data analysis was conducted using Bioconductor for R. Count normalization and differential was conducted using the DESeq2 software package (Love et al., 2014).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw count matrix

source_name: Umbilical cord blood-derived mast cells

growth_protocol: CBMC cultures were maintained in SCF (100 ng/mL), IL-6 (50 ng/mL) and IL-10 (10 ng/mL) until reaching 95% purity based on staining with touidine blue

extract_protocol:
Samples were lysed in TCL buffer (Qiagen)
SmartSeq2 libraries were prepared according to the SmartSeq2 protocol described by Trombetta et al, 2014. Briefly, total RNA was purified using RNA-SPRI beads. cDNA was generated from full-length mRNA transcripts using reverse transcriptase with terminal transferase activity. Combined with a second "template switch" primer, the cDNA was constructed to have two universal priming sequences. Following preamplification, the Nextera XT library construction kit was used to prepare 96 unique indexes specific to each sample. Barcoded cDNA fragments were then pooled prior to sequencing. Sequencing was carried out using an Illumina NextSeq500 as paired- end 2x38bp to a coverage of approximately ~4 million reads per well.

treatment_protocol: Samples were stimulated for 96h with the indicated treatments.

value: Umbilical cord blood-derived mast cells

value: 7-9 weeks


title: A2780-siNC-1

city: Sungnam-Si

first: Su-Yeon

last: Lee

address: Pangyo-Ro 335

department: Department of Biomedical Science

country: South Korea

institute: CHA University

data_processing:
Quality control of the raw sequencing data was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapter and low-quality reads (<Q20) were removed using FASTX_Trimmer (http://hannonlab.cshl.edu/fastx_toolkit/) and BBMap (https://sourceforge.net/projects/bbmap/).
The n trimmed reads were mapped to the reference genome using TopHat.
Gene expression levels were estimated based on RC (Read Count) and FPKM (fragments per kb per million reads) values calculated using BEDTools and Cufflinks.
The expression values were normalized based on the quantile normalization method using edgeR within R (https://www.r-project.org/).
Genome_build: Hg19

growth_protocol: SKOV3 were maintained in RPMI 1640 containing 10% FBS, 25 mM HEPES and 25 mM NaHCO3. A2780 were maintained in RPMI 1640 containing 10% FBS.

extract_protocol:
Total RNA was harvested using Trizol reagent. The SMARTer Stranded RNA Seq Kit (Clontech Laboratories, Inc., USA) was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA was treated for 48 hours

value: Human ovarian cancer cell line

value: Negative control siRNA transfection


title: A2780-siBcl2l10-2

value: Bcl2l10 siRNA transfection


title: A2780-siBcl2l10-1


title: A2780-siNC-2


title: CBMC_IL4STIM2


title: SKOV3-siBcl2l10-2


title: SKOV3-siBcl2l10-1


title: HD_siFOXO3GF_T_3

first: Christian

last: Neri

address: 9 quai St Bernard

department: CNRS UMR 8256, Inserm ERL U1164

institute: Sorbonne Université, CNRS, INSERM

data_processing:
NextSeq Control Software 2.2.0.4 , RTA 2.4.11, bcl2fastq2.17 v2.17.1.14
The raw sequencing reads corresponding to FOXO3 knockdown were pre-processed in order to perform quality control of the reads using fastqc and discard adapter sequences using Clip adapter (Galaxy Version 2.2.0). The reads were then mapped to the human reference genome hg38 (UCSC 2013 release) by using HISAT2. Read distributions were calculated using the featureCounts tool. Sample technical replicates were merged.
Genome_build: hg38 (UCSC 2013 release)
Supplementary_files_format_and_content: tab-delimited text files with count values for each Sample

source_name: Neural stem cells

growth_protocol: Complete neurobasal proliferation medium

extract_protocol:
Total RNA was isolated and purified using the NucleoSpin RNA kit (Macherey-Nagel, 740955.50)
Libraries were prepared by FASTERIS SA (Switzerland) using TruSeq stranded mrna protocols from Illumina and sequenced with the NextSeq Genome Analyzer

treatment_protocol: Reducing FOXO3 expression was performed by treating cells with a FOXO3 siRNAs (ON-target plus smart pool) (siF3) or non-targeting control pool (NTC). 48 h after transfection, complete medium was replaced with medium without bFGF and LIF for 6 h (-GF).

value: IPS cells differentiated into neural stem cells

tag: passage number

tag: sirna

value: FOXO3 siRNA


title: Ascending aorta patient Ao12A

description:
Ao12A_S1
processed file is an h5ad file containing output from all samples


title: SKOV3-siNC-2

tag: cell type


title: CBMC_NOSTIM1

value: Saline


title: HD_NTCGF_T_3

value: scrambled RNA