title: Spermidine-fed 1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression_minus manganase_3

hyb_protocol: 2000ng ng of labeled cRNA sample were fragmented at 60° C and hybridized on to a Agilent custom Microarray Gene expression 8x15k Array (AMADID: 068043). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Raw data was normalized using  quantile normalization method using R Scripts (https://cran.r-project.org/). Gene based analysis was performed.

source_name: Bacteria_LB grown_3

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Overnight culture of DspeG strain was diluted to 1:100 in Luria broth and grown for 1.5 hours followed by addition of spermidine (3.8 mM), whereever required, for 2.5 hours at 37°C. 2.5 ml stop solution (5% phenol in ethanol) was added in 25 ml of growing culture for 10 minutes to prevent the RNA degradation and the cell pellets were collected by centrifuging at 5000 rpm for 10 minutes at 4°C.

extract_protocol: RNA Extraction was perforemd using Qiagen RNeasy Mini kit (Cat. No. 74106) as per the manufacturer's recommendations.

treatment_protocol: The cells were grown in the presence or absence of 3.8mM of spermidine for 2.5 hours at 37°C

value: delta-speG


title: PANNE008

status: Public on Mar 01 2022

type: SRA

city: Vancouver

first: Robert

middle: E. W.

last: Hancock

state: British Columbia

address: 2259 - Lower Mall Research Station

department: Department of Microbiology & Immunology

country: Canada

institute: University of British Columbia

library_source: transcriptomic

data_processing:
BBDuk (version 38.26) was used to trim adapter sequences and polyA tails (trimpolya=10)
STAR (version 2.6.1b) was used to align trimmed reads to the indexed human genome.
SAMtools (version 1.9) was used to merge alignments or samples sequenced across multiple lanes of the flowcell.
HTSeq-count (version 0.9.1) was used to generate raw count data from alignments using the "union" mode and "reverse" stranded options.
Genome_build: GRCh38/hg38 (version 94) from Ensembl
Supplementary_files_format_and_content: Tab-delimited count matrix of raw counts for all samples from HTSeq-count

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
2.5ml of whole blood was collected from each participant into PAXgene Blood RNA tubes (PreAnalytiX GmbH, Switzerland). RNA was isolated from each samples using the RiboPure RNA purification kit (Ambion ThermoFisher; Waltham, MA, USA) following the manufacturer’s protocol. Quantification and quality assessment of total RNA was performed using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA). Poly-adenylated RNA was captured using the NEBNext Poly(A) mRNA Magnetic Isolation Module (catalogue no.: E7409L, NEB; Ipswich, MA, USA).
Strand-specific cDNA libraries were generated from poly-adenylated RNA using the KAPA Stranded RNA-Seq Library Preparation Kit (cat. no.: 07277253001, Roche; Basel, Switzerland).

tag: tissue

value: whole blood

tag: pathology

value: Mild AP


title: Control 2_unfed (control for Spermidine-fed)

type: RNA

description: Gene expression_minus manganase_2

organism: Escherichia coli

source_name: Bacteria_LB grown_2

tag: strain


title: PANNE011

value: Moderately-severe AP


title: CPUL149_2

city: NANJING

first: yue

last: yang

address: 639 LONGMIAN AVENUE

country: China

institute: china pharmaceutical university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: breast cancer cells

growth_protocol: Cells were cultured in DMEM medium (Gibco, Grand Island, NY, USA) at 37 °C under a humidified atmosphere with 5% CO2, and supplemented with 10% FBS (Gibco), 80 U/ml penicillin, and 0.08 mg/ml streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 cells were treated with CPUL119(4.5 μM), CPUL129(1.8 μM), CPUL149(0.9 μM) for 48 h, and subjected to  deep sequencing, in triplicate, using Illumina GAIIx.

tag: cell type

value: Breast cancer cell line


title: PANNE006


title: WT rep2

city: Washington DC

first: huadong

last: Pei

state: District of Columbia

address: 800 22ND ST NW

country: USA

institute: BioChemistry and Molecular Medicine

data_processing:
Illumina 1.9 solfware was used for base-calling
STAR 2.7.0 with reference genome(GRCh38) and annotation file (GRCh38.95) were used for sequence alignment.
If the quality of alignment file meets standard QC, HT-Seq 0.11.2 was used to count the gene expression
Differential expression analysis is done using DE-Seq 1.22.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files of gene expression normalized counts for samples were generated.

source_name: MCF7 (ATCC® HTB-22)

extract_protocol:
MCF7 were harvsted , flash frozen on dry ice, mRNA were extracted mannually . NEBNext Ultra RNA library Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: shRNA

value: stably expressing shRNA targeting SRPK2 (PLKO.1-puro-shSRPK2-7）

tag: genotype/variation

value: stably overexpressing SRPK2 WT

tag: cell line


title: Control 1_unfed (control for Spermidine-fed)

description: Gene expression_minus manganase_1

source_name: Bacteria_LB grown_1


title: CPUL129_1


title: CPUL129_2


title: WT rep3


title: Spermidine-fed_2

description: Gene expression_Plus manganase_1

source_name: Bacteria_LB_1 mM manganese grown_1


title: Control - 28 hpi - replicate 3

city: Leuven

first: Matthias

last: Naets

address: Willem de Croylaan 42

country: Belgium

institute: KU Leuven

description: Malus x domestica Borkh.

data_processing:
Remove adaptor, low Q
Remove polyA/T
Remove rRNA
Remove virus
Genome_build: MJAX00000000.1

molecule: polyA RNA

organism: Malus domestica

source_name: Peel and cortex tissue of fruit at its equator. Cylinder with diameter 13.75 mm and depth 15 mm.

extract_protocol:
Total RNA was extracted by adding 800 µL of CTAB extraction buffer (2 % CTAB, 2 % PVP40, 100 mM Tris-HCl (pH8), 25 mM EDTA, 2 M NaCl, 0.5 g L-1 spermidine, 1 % β-mercaptoethanol) to 150-200 mg finely crushed tissue sample. Subsequently, 80 µL N-laurylsarcosine sodium salt (20 %) and a glass bead were added, and the mixture was incubated for 10 min in a thermomixer set at 70 °C and 1400 rpm. Next, 900 µL chloroform:isoamylalcohol (24:1) was added and the samples were centrifuged at 21500 G and 22 °C for 10 min. The supernatant was transferred to the gDNA eliminator spin column of the RNeasy Plus Mini kit from Qiagen (Manchester, UK). From here on, the manufacturer’s guidelines for the kit were followed. Quality and concentration of the extracts were verified using a NanodropTM2000 (Leusden, Netherlands) and by gel electrophoresis. Equal amounts of RNA were pooled across experiments to obtain three unique replicates per treatment per time point. The pooled RNA was precipitated by adding 2 vol 100 % ethanol and 0.1 vol 3 M sodium acetate (pH5.2-5.5), incubating at -80 °C overnight, and centrifugating at 21500 G. The precipitate was washed twice with 70 % ethanol before being resuspended in nuclease free water. All A260/A280 and A260/A230 ratios were above 2.
A stranded library was constructed for each sample with fragment lengths of 75 bp, as described by Zhong and coworkers (Zhong et al., 2011). Sequencing was performed on an Illumina Nextseq500 platform (San Diego, USA). Generated reads were cleaned up and subsequently aligned to the ‘Golden Delicious’ apple genome (Daccord et al., 2017).

treatment_protocol: Three wounds were made on the shadow side of the fruit at its equator with a depth of 10.5 mm and a diameter of 1.8 mm. Each wound was inoculated with either 2 µL of the spore suspension containing 10^6 conidia mL-1 of B. cinerea in 12 g L-1 PDB, or 12 g L-1 PDB (mock inoculated). The control consisted of samples from non-treated fruit (not wounded, not inoculated). The middle one of the three inoculated spots was sampled at specific time points post inoculation using a cork borer of size 8 (13.75 mm diameter). Samples were cut off at a depth of 15 mm and were immediately quenched in liquid nitrogen.

tag: apple cultivar

value: Jonagold

tag: apple tissue

value: Peel and cortex


title: Control - 28 hpi - replicate 2

description: Malus x domestica Borkh.


title: PANNE002


title: PANNE005


title: CPUL119_1


title: PANNE004


title: Control - 28 hpi - replicate 1

description: Malus x domestica Borkh.


title: WT rep1


title: 4A rep2

value: stably overexpressing SRPK2 4A


title: 797S

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and FPKM values for each gene per sample

source_name: Knee Joint

growth_protocol: All tissue specimens were placed in Advanced Minimum Essential medium (MEM) (Gibco/Thermo Fisher Scientific, Waltham, MA) supplemented with 10% Fetal Bovine Serum (FBS) (R&D Systems, Minneapolis, MN), 1% Penicillin/Streptomycin (Gibco/Thermo Fisher Scientific, Waltham, MA) and 1% Glutamax (Gibco/Thermo Fisher Scientific, Waltham, MA) under 37°C, 95% humidity, 21% O2, and 5% CO2 conditions to establish outgrowth cell cultures. Close to 100% cell confluency, cells were detached from T175 flasks by trypsinization using TrypLE Express (Gibco/Thermo Fisher Scientific, Waltham, MA), expanded in growth medium, and banked using Cryostor (Sigma-Aldrich, St. Louis, MO) in liquid nitrogen at various passages.

extract_protocol:
RNA was extracted using the miRNeasy mini kit (Qiagen, Germantown, MD) according to the manufacturer's protocol from confluent passage 4 outhgrowth cells.
mRNA version 2 library prep kit (Illumina)

tag: subject status

value: patients undergoing primary TKA

tag: subject id

value: patient no. 797

value: Suprapatellar Pouch

tag: Sex

value: Male


title: PANNE003


title: CPUL119_2


title: Mock inoculated - 28 hpi - replicate 1

description: Malus x domestica Borkh.


title: NPS CoV2 5

city: Galveston

first: Xiaoyong

last: Bao

state: TX

address: 301 University Boulevard

department: Pediatrics

institute: University of Texas Medical Branch

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
Sequenced reads were trimmed for adaptor sequences using cutadapt v1.18 with the options: cutadapt -m 15 -u 3
Trimmed sequences were mapped to a list of known small RNA sequences compiled from UCSC genome browser for hg38 using bowtie2 v2.4.1 with the options: bowtie2 -N 1
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited txt files with raw counts for small RNAs for each sample
Supplementary_files_format_and_content: tab delimited matrix file with raw counts for small RNAs for all samples
Supplementary_files_format_and_content: tab delimited matrix file with DESeq2 normalized expression levels for small RNAs for all samples

source_name: Nasopharyngeal swab

extract_protocol:
Nasopharyngeal swabs (NPS) transported in universal viral transport media and tested for SARS-CoV-2. RNA was extracted from 1 ml of NPS per sample using the mirVana PARIS kit from Invitrogen according to manufacturer protocol. At the elution step, samples were incubated on the column for 5 minutes at 65C and the RNA was eluted with 45 ul of nuclease free water. Prior to library construction, each sample was pretreated with 10 units of T4 PNK, with 14 ul of extracted RNAs in a final reaction volume of 50 ul. This was incubated at 37 C for 30 minutes and then heat inactivated at 65 C for 20 minutes. Next the RNA was purified and concentrated within 6 ul of nuclease-free water using Zymo's RNA Clean & Concentrator 5 kit.
Ligation-based small RNA libraries were prepared with the 6 ul input using the NEBNext Multiplex Small RNA Library Prep Set for Illumina.

tag: disease state


title: 797Q

value: Quadriceps Tendon


title: Mock inoculated - 28 hpi - replicate 3

description: Malus x domestica Borkh.


title: Mock inoculated - 28 hpi - replicate 2

description: Malus x domestica Borkh.


title: Triptonide_1

city: Nanchang

first: Xiaoning

last: Zhang

address: 999 Xuefu R.D., Nanchang

institute: Nanchang University

data_processing:
The raw data produced by the Illumina HiSeq™ X Ten platform was subjected to quality control tests.
The clean reads were aligned to reference sequences using STAR and then assembled by StringTie
The coding capacity of transcripts was predicted by PLEX, CPAT and CNCI
The gene expression level was calculated using the fragments per kilobase of exon per million fragments mapped (FPKM) method. Differentially expressed lncRNAs and mRNAs were identified via fold change filtering based on DEGseq software.
Genome_build: hg19
Supplementary_files_format_and_content: excel files include transcript_id(s), FPKM values for each Sample

organism: Mus musculus

source_name: spermatocyte cell line (GC2)

growth_protocol: The GC2-spd cell line was obtained from the Kunming Institute of Zoology, Chinese Academy of Sciences. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sijiqing, Hangzhou, China) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Penn/Strep), and maintained in a humidified atmosphere containing 95% air and 5% CO2 incubator at 37 oC.

extract_protocol:
Total RNA was isolated using TaKaRa RNAiso Plus (TaKaRa, Dalian, China) according to the manufacturer’s protocol.
After the rRNA was depleted from total RNA using Ribo-Zero™ rRNA removal Kit (Illumina, San Diego, CA, USA), next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®). Sequencing was carried out using a 2 x 150 paired-end (PE) configuration. The sequences were processed and analyzed  by Genergy Biotechnology(Genergy Biotechnology, Shanghai, China).

treatment_protocol: Briefly, cells were cultured in a 6-well plate (100000 cells/well) in a final volume of 2 mL of culture medium for 12 h and then treated with triptolide ( 0.1μM) for 24 h.

tag: agent

value: Triptonide

value: spermatocyte cell line (GC2)


title: NPS CoV2 7


title: Tiptolide_2

value: Tiptolide


title: Control - 12 hpi - replicate 1

description: Malus x domestica Borkh.


title: NPS CoV2 8


title: NPS CN 3

value: Control


title: NPS CoV2 6


title: 565Q

value: patient no. 565

value: Female


title: Control - 12 hpi - replicate 3

description: Malus x domestica Borkh.


title: Control - 12 hpi - replicate 2

description: Malus x domestica Borkh.


title: Tiptolide_1


title: 565P

value: Posterior Capsule


title: 565S


title: Mock inoculated - 12 hpi - replicate 3

description: Malus x domestica Borkh.


title: 256S

value: patient no. 256


title: Con_2

value: control


title: NPS CN 4


title: Triptonide_2


title: Mock inoculated - 12 hpi - replicate 1

description: Malus x domestica Borkh.

value: Jonagold


title: Control - 1 hpi - replicate 3

description: Malus x domestica Borkh.

value: Peel and cortex


title: NPS CN 1


title: DSP-1001250007868-B-D11

city: Seattle

first: Stephanie

last: Zimmerman

state: WA

address: 530 Fairview Ave N

institute: NanoString Technologies

description: RNA ISH

data_processing:
Library strategy: GeoMx-Seq
GeoMx NGS Pipeline v2.3.3.10 with the following parameters: quality-trim-score = 20, 2color-trimming = True, adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3, barcode-max-mismatch = 1, stitching-max-mismatch = 2
Genome_build: NA
Supplementary_files_format_and_content: Digital Count Conversion (DCC) files: format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Kidney_Sample_Annotations.txt: txt file containing sample annotations
Supplementary_files_format_and_content: Kidney_Raw_BioProbeCountMatrix.txt: txt file containing raw probe counts for each AOI
Supplementary_files_format_and_content: Kidney_Raw_TargetCountMatrix.txt: txt file containing collapsed target-level counts for each AOI
Supplementary_files_format_and_content: Kidney_Q3Norm_TargetCountMatrix.txt: txt file containing Q3 normalized target-level counts for each AOI

source_name: Human FFPE kidney

extract_protocol:
Samples were incubated with the human Whole Transcriptome Atlas RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: slide name

tag: class

value: DKD

tag: region

value: glomerulus

value: abnormal

tag: nuclei


title: Con_1


title: NPS CN 2


title: 256Q

value: patients undergoing primary TKA

tag: tissue


title: Control - 1 hpi - replicate 2

description: Malus x domestica Borkh.


title: 797P

value: patient no. 797

value: Male


title: Mock inoculated - 12 hpi - replicate 2

description: Malus x domestica Borkh.


title: 256P


title: DSP-1001250007868-B-D10

description: RNA ISH

tag: pathology


title: Hypoosmotic_t180_n4

city: Düsseldorf

first: David

last: Schöler

address: Moorenstr. 5

country: Germany

institute: University Hospital Düsseldorf

description: Gene expression data from hypoosmotic perfused rat liver

hyb_protocol: Hybridization were carried out in a SciGene 777 Microarray Oven (50 rpm, 45 °C for 16 hours).Hybridized Affymetrix Arrays were washed by Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Microarrays scanning and acquisition of signal intensities were performed on the Affymetrix GeneChip Scanner GCS3000 System.

data_processing: Quality control assessment was carried out through the Expression Console software (Affymetrix). Statistical analysis of microarray data was performed by Transcriptome Analysis Console 4.0 (TAC 4.0). CEL files were imported to TAC and the data was preprocessed and normalized using the RMA (Robust Multichip Average) algorithm.

label: biotin

organism: Rattus norvegicus

source_name: perfused rat liver

label_protocol: Biotinylated cDNA for hybridization to Affymetrix GeneChip arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).

growth_protocol: Male wistar rats were kept under normal husbandry conditions.

extract_protocol: RNA was isolated from homogenized liver samples with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Rat liver perfusions were conducted as previously described by Sies et al. [https://doi.org/10.1016/s0076-6879(78)52005-3.]

tag: time point

value: liver

tag: strain

value: wistar

tag: buffer

value: hypoosmotic (225 mosm/L)


title: DSP-1001250007868-B-D12

description: RNA ISH


title: DSP-1001250007868-B-D09

description: RNA ISH


title: 030S

value: patient no. 030

value: Suprapatellar Pouch


title: DSP-1001250007868-B-D08

description: RNA ISH


title: Control - 1 hpi - replicate 1

description: Malus x domestica Borkh.


title: Mock inoculated - 1 hpi - replicate 2

description: Malus x domestica Borkh.


title: 030Q

value: Quadriceps Tendon

value: Female


title: Hypoosmotic_t180_n2


title: Mock inoculated - 1 hpi - replicate 3

description: Malus x domestica Borkh.


title: Normoosmotic_t180_n4

description: Gene expression data from normoosmotic perfused rat liver

value: normo- (305 mosm/L)


title: Sample_15A_UCa epithelium

city: Trondheim

first: Atle

middle: van  Beelen

last: Granlund

address: Postboks 8905 MTFS

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
Base calling was done on the HiSeq instrument by RTA 1.17.21.3.
FASTQ files were generated using CASAVA 1.8.2 (Illumina, Inc. San Diego, CA, USA).
Transcript expression values were generated by quasi alignment using Salmon (Patro, Duggal, Love, Irizarry, & Kingsford, 2017) and the Ensembl (GRCh38) human transcriptome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file with raw counts per gene

source_name: Colon epithelium

extract_protocol:
After isolating cells corresponding to an area of 1 mm2 (approx. 10 000 cells), the sample was lysed by adding 300µl lysis buffer, followed by vortexing (30 sec) and centrifugation (5 sec). The lysed sample was immediately frozen and stored (-80oC) for later RNA isolation. Total RNA isolation was performed using RNeasy plus micro (cat. No 74034, Qiagen, Venlo, Netherlands) following manufacturers protocol. The quality of isolated RNA was assessed using Bioanalyzer 2100 (Agilent, CA, USA), evaluating the fraction of RNA fragments longer than 200 nt, DV200 analysis. All samples yielded more than 75% fragments >200 nt, with an average DV200 = 82%, all deemed to be suitable for subsequent RNA sequencing.
RNA sequencing libraries were prepared using TruSeq RNA Access library kit (Illumina, Inc., San Diego, CA, USA) according to manufacturer`s protocol. In brief, RNA samples (100 ng total RNA) were fragmented at 94°C for 8 minutes on a thermal cycler. First strand cDNA syntheses were performed at 25°C for 10 minutes, 42°C for 15 minutes and 70°C for 15 minutes, using random hexameres and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific Inc., Waltham, MA, USA). In a second strand cDNA synthesis the RNA templates were removed and a second replacement strand was generated by incorporation dUTP (in place of dTTP, to keep strand information) to generate ds cDNA. AMPure XP beads (Beckman Coulter, Inc., Indianapolis, IN, USA) were used to clean up the blunt-ended cDNA from the second strand reaction mix. The 3`ends of the cDNA were then adenylated to facilitate adaptor ligation in the next step. After ligation of indexing adaptors, AMPure XP beads were used to clean up the libraries. In a first PCR amplification step, PCR (15 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) were used to selectively enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. After validation of the libraries the first hybridization step were performed using exome capture probes. Before hybridization a 4-plex pool of libraries were made, by combining 200 ng of each DNA library. The hybridization was performed by 18 cycles of 1 minute incubation, starting at 94°C, and then decreasing 2°C per cycle. Then streptavidin coated magnetic beads were used to capture probes hybridized to the target regions. The enriched libraries were then eluted from the beads and prepared for a second round of hybridization. This second hybridization (18 cycles of 1 minute incubation, starting at 94°C, and then decreasing 2°C per cycle) were required to ensure high specificity of the capture regions. A second capture with streptavidin coated beads were performed, followed by two heated wash procedures to remove non-specific binding form the beads. The enriched libraries where then eluted from the beads and cleaned up by AMPure XP beads prior to a second PCR amplification. The amplification step were performed by 10 cycles (98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) followed by a second PCR clean up using AMPure XP beads. Libraries were normalized to 22 pM and single read sequencing was performed for 50 cycles on a HiSeq2500 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions.

treatment_protocol: Inflamed samples were taken from maximally inflamed area with intact epithelial monolayer. Uninflamed samples from IBD patients and healthy controls were all taken from hepatic flexure. Four closely adjacent biopsies were taken from each area. Two were snap frozen and stored in N2 for subsequent Laser capture microdissection and RNA isolation. Inflammatory status was verified trough inspection of haemotoxylin and eosin-stained sections, and classified by an experienced pathologist into normal, Inactive or active inflammation. For LCM analysis, each sample was handled individually. All equipment was cleaned using RNAse Zap (Life Technologies, CA, USA) (room temperature) or 70% EtOH (Cryotome) prior to procedures. Samples were removed from N2 inside cooled cryotome chamber, and directly mounted in Tissue-Tek O.C.T. compound embedding medium (Sakura Finetek, CA, USA). The mounted sample was left to equilibrate inside cryotome for 30 minutes. 10 µm cryosections were made using a Leica CM3050 S (Leica, Wetzlar, Germany) and directly placed on a pre-chilled LCM membrane slide. When membrane slide were filled with sections, the slide was briefly exposed to room temperature in order to let sections adhere to the membrane surface, and subsequently placed in 100% EtOH (30 sec). The following staining protocol was modified from the Histogene LCM staining kit (Cat. No. KIT0401, Life Technologies, CA, USA). Sections were washed twice (5 sec.) with dH2O with added ProtectRNA RNase inhibitor (Cat. No. R7397, Sigma-Alrich, MO, USA) followed by staining with Histogene staining solution. After subsequent washing steps (3* 30 sec. 100% EtOH, 2* 2 minutes Xylene, 1* 5 minutes Xylene) sections were air dried (30 sec.) and placed in desiccator (30 minutes). After drying, the membrane slide was placed in an LCM microscope (MMI CellCut on Olympus IX71, Eching, Germany).

value: Colon

tag: collection method

value: Laser capture microdissected epithelium

value: UCa


title: Hypoosmotic_t180_n1


title: DSP-1001250007868-B-D06

description: RNA ISH

value: DKD

value: normal


title: Control - 0 hpi - replicate 3

description: Malus x domestica Borkh.

tag: apple cultivar

value: Jonagold

value: Peel and cortex


title: DSP-1001250007868-B-D04

description: RNA ISH

value: glomerulus


title: DSP-1001250007868-B-D07

description: RNA ISH

value: abnormal


title: Sample_8A_CDu epithelium

value: CDu


title: DSP-1001250007868-B-D05

description: RNA ISH


title: Control - 0 hpi - replicate 2

description: Malus x domestica Borkh.

tag: apple tissue


title: DSP-1001250007868-B-D03

description: RNA ISH


title: Control - 0 hpi - replicate 1

description: Malus x domestica Borkh.


title: Hypoosmotic_t120_n4

hyb_protocol: Hybridization and washing were carried out in a SciGene 777 Microarray Oven (50 rpm, 45 °C for 16 hours) and in an Affymetrix GeneChip 450 Washer.

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

label_protocol: cDNA synthesis and labeling were performed according to the Affymetrix protocol.

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

value: liver

value: wistar

value: Male


title: DSP-1001250007868-B-D02

description: RNA ISH


title: Mock inoculated - 1 hpi - replicate 1

description: Malus x domestica Borkh.


title: Normoosmotic_t180_n1


title: Sample_14A_CDu epithelium


title: Normoosmotic_t180_n3


title: Sample_28A_CDa epithelium

value: CDa


title: Hypoosmotic_t120_n2

value: hypoosmotic (225 mosm/L)


title: DSP-1001250007868-B-D01

description: RNA ISH


title: Sample_11A_UCa epithelium


title: 030P

tag: subject status

value: patients undergoing primary TKA

value: patient no. 030

value: Posterior Capsule

value: Female


title: Sample_22A_UCa epithelium

value: Colon

value: Laser capture microdissected epithelium

value: UCa


title: Sample_20A_UCu epithelium

value: UCu


title: I656tgF

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

description:
Marmoset
Generated using the lentivirus vector pLenti6_4_EF_Aswind_2AKO.
Whole genome sequencing (WGS)

library_source: genomic

data_processing:
Library strategy: WGS
Data of WGS (fastq file format) were quality-checked.
The remaining reads were mapped to the marmoset genome (cj1700) using bowtie2.
Discordant and Split reads were used to identify transgene insertion regions.
Genome_build: cj1700
Supplementary_files_format_and_content: Insertion_site.xlsx describes the transgene integration sites in the genome.

molecule: genomic DNA

organism: Callithrix jacchus

source_name: Hair root

extract_protocol:
Standard genomic DNA extraction and purification.
DNA libraries were prepared for sequencing using standard MGI protocols performed by Azenta Life Sciences, Japan.

tag: genotype

value: Transgene

value: Hair root

tag: cell type

value: Fibroblasts


title: Normoosmotic_t180_n2

tag: Sex

value: normo- (305 mosm/L)


title: Sample_21A_UCa epithelium

tag: disease state


title: Sample_19A_HC epithelium

value: HC


title: Mock inoculated - 0 hpi - replicate 3

description: Malus x domestica Borkh.

value: Jonagold

value: Peel and cortex


title: Mock inoculated - 0 hpi - replicate 2

description: Malus x domestica Borkh.


title: Hypoosmotic_t120_n1

value: liver

value: wistar

value: Male


title: DSP-1001250007868-B-C12

description: RNA ISH

tag: slide name

value: DKD

value: tubule


title: Mock inoculated - 0 hpi - replicate 1

description: Malus x domestica Borkh.


title: Sample_24A_HC epithelium


title: DSP-1001250007868-B-C11

description: RNA ISH

tag: class


title: Hypoosmotic_t120_n3

value: hypoosmotic (225 mosm/L)


title: Normoosmotic_t120_n4


title: DSP-1001250007868-B-C09

description: RNA ISH

tag: region


title: I655tgF


title: Sample_31A_CDu epithelium

value: Colon

value: CDu


title: Hypoosmotic_t180_n3


title: calu3_072h_ctrl_zn129

city: Santa Cruz

first: Jeremy

last: Sanford

state: CA

address: 1156 High St

department: Molecular, Cell and Developmental Biology

institute: UC Santa Cruz

description: mRNA (150bp)

data_processing:
Reads were mapped against human/African Green Monkey repeat elements in their respective genomes for initial repeat-filtering using Bowtie 2
Repeat-filtered reads were then mapped against their respective STAR indexes (joint hg38-wuhCor1 or chlSab2-wuhCor1) using STAR v2.5.3a "--alignEndsType EndToEnd" option
Gene-level quantification and comparisons using DESeq2
Called peaks in sRNA-seq data mapped to wuhCor1 using Piranha v1.2.1
Quantified unique wuhCor1-mapped sRNA-seq coordinates using in-house python script
Predicted duplexes between host (human or African Green Monkey) transcripts and SARS-CoV-2 sRNAs using RNAhybrid v2.1.2
Genome_build: UCSC (hg18, chlSab2 and wuhCor1)
Supplementary_files_format_and_content: Gene-level counts [mRNA mapping to host quantified with DESeq2 (.csv), sRNA mapping to host quantified with DESeq2 (.csv), sRNA mapping to SARS-CoV-2 quantified with in-house script (.csv)], SARS-CoV-2 sRNA peaks [called with Piranha (.bed)], sRNA Interactions [predicted with RNAhybrid (.csv)]

source_name: lung cancer cells – Calu-3

growth_protocol: DMEM + 1% heat inactivated FBS, 100U/mL penicillin, 100 μg/mL streptomycin in 5% CO2 at 37°C

extract_protocol:
Trypsin-EDTA 0.25% (ThermoFIsher Scientific), then 250 μl Trizol
NEXTFLEX Poly(A) Beads Kit 2.0, then NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (Perkin Elmer Applied Genomics)

tag: cell line

value: lung cancer

tag: treatment

value: control (uninfected)

tag: hours post-treatment

tag: moi


title: calu3_072h_ctrl_zn130

description: mRNA (150bp)


title: Normoosmotic_t120_n2

tag: time point

tag: tissue

tag: strain


title: Normoosmotic_t120_n1

tag: buffer


title: DSP-1001250007868-B-C10

description: RNA ISH

tag: pathology

tag: nuclei


title: calu3_072h_ctrl_zn128

description: mRNA (150bp)


title: DSP-1001250007868-B-C08

description: RNA ISH


title: DSP-1001250007868-B-C07

description: RNA ISH


title: Sample_25A_CDu epithelium

tag: collection method

value: Laser capture microdissected epithelium


title: DSP-1001250007868-B-C06

description: RNA ISH


title: calu3_072h_cov2_zn127

description: mRNA (150bp)

tag: cell type

value: Infected – SARS-CoV-2


title: calu3_072h_cov2_zn126

description: mRNA (150bp)


title: CAF68

city: Yushima, Bunkyo-ku

first: Yoshimi

last: Yasukawa

institute: national cancer center research institute, Japan

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1xAgilent fragmentation buffer and 2xAgilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2xAgilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent Technologies) 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 Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

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

source_name: Cancer-associated fibroblasts

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Normal fibroblasts and CAFs were maintained in a MF-medium.

extract_protocol: Total RNA was extracted using the ReliaPrep™ RNA Cell Miniprep System (Promega, Madison, WI).

value: gastric fibroblasts from cancerous tissues of scirrhous gastric cancer patient

tag: pathological type

tag: tumor stage


title: DSP-1001250007868-B-C05

description: RNA ISH

tag: slide name


title: Sample_7A_CDa epithelium

tag: disease state

value: CDa


title: Normoosmotic_t120_n3

tag: Sex

value: normo- (305 mosm/L)


title: DSP-1001250007868-B-C04

description: RNA ISH

tag: class

tag: region


title: CAF67


title: Sample_17A_UCa epithelium

value: UCa


title: calu3_048h_ctrl_zn123

description: mRNA (150bp)

tag: cell line

tag: treatment

tag: hours post-treatment


title: CAF50

tag: tissue


title: Sample_9A_CDu epithelium


title: calu3_048h_ctrl_zn124

description: mRNA (150bp)

tag: moi


title: calu3_072h_cov2_zn125

description: mRNA (150bp)


title: CAF66


title: DSP-1001250007868-B-C03

description: RNA ISH


title: Sample_27A_UCu epithelium

value: UCu


title: calu3_048h_cov2_zn120

description: mRNA (150bp)


title: Sample_5A_UCu epithelium


title: NF67

source_name: Normal fibroblasts

value: gastric fibroblasts from non-cancerous tissues of scirrhous gastric cancer patient


title: Sample_30A_UCu epithelium


title: DSP-1001250007868-B-C02

description: RNA ISH


title: calu3_048h_cov2_zn119

description: mRNA (150bp)


title: Sample_10A_CDa epithelium


title: CAF36


title: DSP-1001250007868-B-B10

description: RNA ISH

value: glomerulus


title: DSP-1001250007868-B-B11

description: RNA ISH


title: calu3_048h_ctrl_zn122

description: mRNA (150bp)


title: calu3_024h_ctrl_zn118

description: mRNA (150bp)


title: CAF63


title: DSP-1001250007868-B-C01

description: RNA ISH


title: NF66


title: calu3_048h_cov2_zn121

description: mRNA (150bp)


title: NF50


title: Sample_12A_UCa epithelium


title: DSP-1001250007868-B-B08

description: RNA ISH


title: DSP-1001250007868-B-B12

description: RNA ISH


title: NF68


title: Sample_29A_HC epithelium

value: HC


title: Sample_6A_UCu epithelium


title: NF63


title: DSP-1001250007868-B-B07

description: RNA ISH

value: DKD


title: Sample_16A_HC epithelium


title: calu3_024h_cov2_zn115

description: mRNA (150bp)


title: Sample_18A_CDa epithelium


title: DSP-1001250007868-B-B06

description: RNA ISH


title: Sample_13A_UCu epithelium


title: CAF42

value: gastric fibroblasts from cancerous tissues of non-scirrhous gastric cancer patient


title: calu3_024h_ctrl_zn116

description: mRNA (150bp)


title: CAF45


title: Sample_2A_UCa epithelium


title: DSP-1001250007868-B-B05

description: RNA ISH


title: Sample_23A_CDa epithelium


title: calu3_024h_cov2_zn114

description: mRNA (150bp)


title: CAF30


title: calu3_024h_cov2_zn113

description: mRNA (150bp)


title: NF45

value: gastric fibroblasts from non-cancerous tissues of non-scirrhous gastric cancer patient


title: DSP-1001250007868-B-B04

description: RNA ISH


title: Sample_3A_HC epithelium

value: Colon


title: DSP-1001250007868-B-B09

description: RNA ISH


title: calu3_012h_ctrl_zn112

description: mRNA (150bp)


title: calu3_024h_ctrl_zn117

description: mRNA (150bp)


title: Sample_1A_HC epithelium


title: CAF19


title: calu3_012h_ctrl_zn110

description: mRNA (150bp)


title: DSP-1001250007868-B-B03

description: RNA ISH


title: T47D GFOGER_10wt%_D40 replicate 3

city: Newark

first: Shawn

middle: William

last: Polson

state: DE

institute: University of Delaware

data_processing:
Analysis was performed by the University of Delaware Bioinformatics Core Facility using a modified MAPRseq pipeline implemented on the BioMix compute cluster at the Center for Bioinformatics and Computational Biology/Delaware Biotechnology Institute
Sequence quality was assessed using FASTQC
Sequences were end-trimmed (Q30) and filtered (no ambiguous nucleotides, 35bp minimum length after trimming) using Trim Galore (v0.4.4)
Trimmed reads were aligned to the reference genome using Tophat v2.1.0
Mapping quality was assessed using RSeQC v2.3.7 and metrics extracted from BedTools v2.17 and SamTools v1.4
Feature counts were extracted using HtSeq v0.6.1p1
Pairwise differential expression analysis was performed on features with >1 cpm in at least 2 samples using EdgeR v 3.16.5
Genome_build: Hg19-37.1
Supplementary_files_format_and_content: tab-delimited w/ the following columns: Chr,GeneID,Start,Stop,CodingLength,samples

source_name: Mammary Gland/Breast; Derived From Metastatic Site: Pleural Effusion

growth_protocol: MDA-MB-231 and T47Ds were cultured in DMEM (Corning 10-013CV) + 10% FBS + Pen/strep + Fungizone. Media was replaced every 2-3 days. Cells encapsulated within hydrogels were cultured in 48-well plates with 500 µL of culture media.

extract_protocol:
Hydrogels were degraded by incubating gels with 250 U collagenase for 20 minutes at 37 ℃ and 5% CO2. After gel degadation, cells were pelleted by centrifugation at 1000 RPM for 5 minutes, and PEG was removed. RNA was then extracted from cells by a Nucleospin miRNA kit (Takara), where cells were first placed into lysis buffer. Three gels of the same composition was used for one replicate of RNA. DNase treatment was performed duing RNA isolation.
RNA Indexed libraries were constructed from 100-500 ng of total RNA using the Universal Plus mRNA-seq Workflow Kit (Nugen)

treatment_protocol: Cells were encapsulated in a hydrogel: 5 µL of the gel precusor solution with a single cell suspension of 5,000 cells/µL was polymersized on top of a pre-formed 15 µL base hydrogel without encapsulated cells (20 uL total hydrogel volume formed in 1-mL sterile syringe with end removed). Cells were formed by free-radical step growth-polymerization 'thiol-ene' click chemistry of a 4-arm PEG-SH and cell-degradable crosslinker (GPQGIWGQ) difunctional with allyloxycarbonyl groups. Two treatments per cell line were performed, consisting of a collagen (GFOGER peptide) or laminin (IKVAV peptide) environment.

value: Mammary Gland/Breast; Derived From Metastatic Site:Pleural Effusion

value: epithelial

tag: disease

value: Ductal Carcinoma

tag: day

tag: growth matrix peptide

value: GFOGER


title: calu3_012h_cov2_zn108

description: mRNA (150bp)

value: lung cancer

value: Infected – SARS-CoV-2


title: DSP-1001250007868-B-B01

description: RNA ISH

tag: pathology

tag: nuclei


title: calu3_012h_cov2_zn109

description: mRNA (150bp)

tag: cell type


title: DSP-1001250007868-B-A01

description: RNA ISH

value: No Template Control


title: T47D GFOGER_10wt%_D40 replicate 2

department: Center for Bioinformatics and Computational Biology


title: T47D GFOGER_10wt%_D40 replicate 1


title: T47D GFOGER_D40 replicate 2


title: T47D GFOGER_D40 replicate 3


title: calu3_012h_cov2_zn107

description: mRNA (150bp)


title: DSP-1002510007866-C-F07

description: RNA ISH

value: normal

value: abnormal


title: DSP-1002510007866-C-F05

description: RNA ISH


title: calu3_012h_ctrl_zn111

description: mRNA (150bp)

value: control (uninfected)


title: DSP-1001250007868-B-B02

description: RNA ISH


title: T47D GFOGER_D40 replicate 1


title: DSP-1002510007866-C-F06

description: RNA ISH


title: calu3_000h_ctrl_zn104

description: mRNA (150bp)


title: calu3_000h_ctrl_zn105

description: mRNA (150bp)


title: DSP-1002510007866-C-F04

description: RNA ISH


title: DSP-1001250007868-B-A12

description: RNA ISH


title: NF36

value: gastric fibroblasts from non-cancerous tissues of scirrhous gastric cancer patient

tag: pathological type

tag: tumor stage


title: NF19


title: TCam2, rep 4

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

description: SAMPLE 8

hyb_protocol: Purified Cy3-labeled antisense RNA was hybridized overnight to Agilent 60-mer oligonucleotide spotted microarray slides.Hybridization and subsequent washing and drying of the slides were performed following the Agilent hybridization protocol.

scan_protocol: The slides were scanned using a GenePix 4100A Scanner (Axon Instruments at a resolution of 2 µm/pixel.

data_processing: Image analysis was performed using GenePix Pro 5.1 software (Axon Instruments) followed by data evaluation using the R software and the Bioconductor limma package [57, 58]. The log of the mean spot signals was recorded for further analysis. Signals of replicate spots (same probes) within arrays were averaged. Intensity data were normalized using quantile normalization before calculating the average probe intensity of the array. Genes were ranked for differential expression using a moderated t-statistic.

source_name: TCam2 cells

label_protocol: After assessing RNA quality by capillary electrophoresis on a 2100 Bioanalyzer (Agilent Technologies), purified total RNA was amplified and labeled with Cy3 using a dual-color LIRAK kit (Agilent Technologies) according to manufacturer’s instructions. Briefly, the RNA samples (500 ng/ reaction) were labeled with Cy3.

growth_protocol:
Cell lines and cell culture
The human Sertoli cell line FS1 [FS1] was provided by Dr. V. Schumacher (Boston Children’s Hospital, Department of Urology; Harvard Medical School, Department of Surgery, Boston, MA, USA). The Sertoli cells were obtained from the testes of a 19 years old patient with Frazier syndrome, characterized by insufficient action of WT1 causing reduction of the downstream SOX9 expression, and with focal GCNIS. FS1 has been immortalized with both the wildtype large T-antigen and the temperature sensitive large T-antigen. FS1 was cultured in medium I, comprising Dulbecco’s modified Eagle medium (Invitrogen), supplemented with 4.5 g/l D-glucose, 40 µM L-glutamine (Sigma), 1% sodium pyruvate (Gibco, by Life Technologies), 20% fetal calf serum (PAA Laboratories GmbH), 1% nonessential amino acids, and 1% penicillin/ streptomycin (Biochrom GmbH).
The human seminoma cell line TCam-2 [TCam2] was provided by Prof. Dr. H. Schorle (University Hospital Bonn, Department of Developmental Pathology, Institute of Pathology, Bonn, Germany). It was cultured in medium II, comprising Rosewell Park Memorial Institute 1640 medium (Gibco) supplemented with 2 mM L-glutamine, 10% fetal calf serum, and 1% penicillin/streptomycin). Each cell line was incubated in 75-cm2 flasks (1 x 106 cells/flask) at 37°C in a humidified incubator with 5% CO2, with medium changes every 2 or 3 days. Cells reaching 80% of confluency were used in subsequent experiments. The cell lines were authenticated by the providers and checked for mycoplasma, using a LookOut® Mycoplasma PCR Detection Kit (Sigma-Aldrich).
Cell co-culture model
For direct co-culture, a defined number of FS1 cells (passages 14-16) were cultured in a 6-well plate. After 24 hours, medium was replaced by a 1:1 mixture of medium I and II and a defined number of TCam-2 cells was added. For insert co-culture, FS1 (passages 14-16) (50,000 cells/well) and TCam-2 cells (50,000 cells/well) were co-cultured for 3 weeks in medium I (1.5 ml) and medium II (2 ml) using 6 well ThinCert™ cell culture inserts (Greiner Bio-One). The medium was changed on every third day.
For control, FS1 cells were cultured in direct and in indirect co-culture with equine bone marrow derived mesenchymal stromal cells, eBM-MSC (kindly provided by Prof. Dr. C. Staszyk, Department of Veterinary Anatomy, Histology and Embryology, Justus-Liebig-University, Giessen, Germany). For further controls, monocultures of FS1 and TCam-2 cells were used. All control groups were cultured under the same conditions as the experimental group. For each condition, four biological replicates were generated. The co-culture experiments were repeated at least 10 times.
References:
[FS1] Schumacher, V.; Gueler, B.; Looijenga, L.H.; Becker, J.U.; Amann, K.; Engers, R.; Dotsch, J.; Stoop, H.; Schulz, W.; Royer-Pokora, B. Characteristics of testicular dysgenesis syndrome and decreased expression of SRY and SOX9 in Frasier syndrome. Mol Reprod Dev, 2008, 75, 1484-1494. DOI: 10.1002/mrd.20889
[TCam2] Eckert, D.; Nettersheim, D.; Heukamp, L.C.; Kitazawa, S.; Biermann, K.; Schorle, H. TCam-2 but not JKT-cells resemble seminoma in cell culture. Cell Tissue Res, 2008, 331, 529-538. DOI: 10.1007/s00441-007-0527-y

extract_protocol: RNA was extracted from the cell cultures using the peqGOLD Total RNA Kit (Peqlab Biotechnologie GmbH) and purified with a RNeasy Mini Kit (Qiagen) according to the manufacture instructions.

tag: culture

value: monoculture

tag: cell line(s)


title: T47D IKVAV_D40 replicate 2

value: IKVAV


title: NF30


title: NF42


title: calu3_000h_cov2_zn103

description: mRNA (150bp)


title: T47D IKVAV_D40 replicate 3


title: TCam2_FS1, rep 4

description: SAMPLE 7

value: co-culture


title: TCam2_FS1, rep 3

description: SAMPLE 6


title: TCam2, rep 3

description: SAMPLE 5


title: DSP-1002510007866-C-F03

description: RNA ISH

tag: slide name

tag: class

value: glomerulus


title: calu3_000h_ctrl_zn106

description: mRNA (150bp)

tag: cell line


title: DSP-1002510007866-C-F02

description: RNA ISH

tag: region


title: calu3_000h_cov2_zn101

description: mRNA (150bp)

tag: treatment

tag: hours post-treatment


title: MDA-MB-231 GFOGER_10wt%_D40 replicate 3

tag: tissue

value: Adenocarcinoma


title: T47D IKVAV_D40 replicate 1

tag: disease


title: DSP-1002510007866-C-E12

description: RNA ISH


title: calu3_000h_cov2_zn102

description: mRNA (150bp)

tag: moi


title: 12w_CDS_4

city: Zurich

first: Sina-Maria

last: Schalbetter

address: Winterthurerstrasse 260

country: Switzerland

institute: Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse

data_processing:
RNA Seq reads were mapped to mouse genome (GRCm38.p5) with STAR-version 2.7.3a (Dobin et al., 2013) using the default parameters.
Reads were assigned to genes with featureCounts (Liao et al., 2014) with folowing parameters: -t exon -g gene_id, gene annotation - Gencode GRCm38/vM12.
The differential expression analysis was carried out with DESeq2-version 1.22.1 (Love et al., 2014) using the deafult parameters. We kept genes that have at least 5 reads in at least 5 samples
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: XLSX file contains results of the differential expression analysis (Log2FC) and q-values

source_name: brain tissue

extract_protocol:
The medial prefrontal cortex was removed from frozen brain specimens. Total RNA was isolated using the SPLIT RNA Extraction Kit (Lexogen), according to the manufacturer's instructions.
The TruSeq Stranded Total RNA Library prep kit (Illumina) with Ribosomal depletion, and dual barcoding (2x10 base pairs) was used to produce library constructs with an input of 400 ng total RNA.

tag: strain

value: CDS

value: medial prefrontal cortex

tag: age

value: post natal day 84


title: MDA-MB-231 GFOGER_10wt%_D40 replicate 1

value: Mammary Gland/Breast; Derived From Metastatic Site:Pleural Effusion

value: epithelial

tag: day

tag: growth matrix peptide


title: DSP-1002510007866-C-F01

description: RNA ISH

tag: pathology

tag: nuclei


title: DSP-1002510007866-C-E11

description: RNA ISH


title: 12w_CDS_5


title: DSP-1002510007866-C-E10

description: RNA ISH


title: DSP-1002510007866-C-E09

description: RNA ISH

value: tubule


title: SUM159PT_sgSTING_STING_2 [S40]

city: Seoul

first: Kyung-min

last: Lee

address: 222 Wangsimni-ro

country: South Korea

institute: Hanyang University

description:
processed data file:
159_STING_OE_NormalizedCount.txt

data_processing:
In the raw fastq files, the ends of sequences with remaining adapter or quality scores <25 were trimmed. Any sequence less than 35bp was removed.
The trimmed fastq files were aligned to the selected reference genome using HiSAT2.
After marking duplicates using SAMBAMBA, genes, transcripts and exons were counted using featureCounts and StringTie.
DESeq2 package was used for analysis of differentially expressed genes and normalization of counts.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: NormalizedCount

extract_protocol:
RNA were extracted using Maxwell® RSC simplyRNA Cells Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: STING sgRNA+STING ORF


title: TCam2, rep 2

description: SAMPLE 4

tag: culture

tag: cell line(s)


title: TCam2_FS1, rep 2

description: SAMPLE 3


title: TCam2, rep 1

description: SAMPLE 1


title: MDA-MB-231 GFOGER_D40 replicate 1

tag: cell type

value: GFOGER


title: TCam2_FS1, rep 1

description: SAMPLE 2


title: SUM159PT_sgSTING_STING_1 [S39]

tag: cell line


title: 12w_CDS_2


title: MDA-MB-231 GFOGER_D40 replicate 2


title: 12w_CDS_3


title: SUM159PT_sgSTING_GFP_2 [S38]

value: STING sgRNA+GFP ORF


title: SUM159PT_sgSTING_GFP_1 [S37]


title: MDA-MB-231 GFOGER_10wt%_D40 replicate 2


title: MDA-MB-436_sgSTING_GFP_2 [S34]

description:
processed data file:
436_STING_OE_NormalizedCount.txt


title: 12w_PBS_3

value: PBS


title: DSP-1002510007866-C-E08

description: RNA ISH

tag: slide name

tag: class

value: normal

tag: region


title: 12w_CDS_1

tag: treatment

tag: tissue


title: MDA-MB-231 GFOGER_D40 replicate 3

tag: disease


title: 12w_PBS_5

tag: strain


title: MDA-MB-231 IKVAV_D40 replicate 3


title: 12w_PBS_4

tag: age


title: MDA-MB-436_sgSTING_GFP_1 [S33]


title: DSP-1002510007866-C-E07

description: RNA ISH


title: MDA-MB-231 IKVAV_D40 replicate 1

tag: day


title: MDA-MB-436_sgSTING_STING_1 [S35]


title: 12w_PBS_2


title: MDA-MB-231 IKVAV_D40 replicate 2

tag: growth matrix peptide


title: DSP-1002510007866-C-E05

description: RNA ISH

tag: pathology


title: SUM159PT_sgSTING_C2_2 [S32]

description:
processed data file:
159_sgSTING_NormalizedCount.txt

value: STING sgRNA


title: DSP-1002510007866-C-E06

description: RNA ISH

tag: nuclei


title: T47D GFOGER_10wt%_D3 replicate 3

value: Ductal Carcinoma


title: DSP-1002510007866-C-E04

description: RNA ISH


title: T47D GFOGER_10wt%_D3 replicate 2


title: SUM159PT_sgSTING_C2_1 [S31]

tag: genotype


title: DSP-1002510007866-C-E03

description: RNA ISH


title: DSP-1002510007866-C-E02

description: RNA ISH


title: CM_rep2

city: nanjing

first: liu

middle: xiao

last: min

state: jiangsu

address: longmiandadao

department: College of life science and technology

institute: China Pharmaceutical University

data_processing:
Trim Galore (v.0.6.6) was used to trim the low quality sequences.
The paired-end reads were aligned to mouse genome (GRCm38) with HISAT2 aligner (v2.2.1) with --rna-strandness RF parameters and Ensemble genes (GRCm38.102) transcriptome annotation.
Then gene expression were quantified using featureCounts (v2.0.1) with -s 2 parameter[3], and differentially expressed genes were identifified using DESeq2 (v1.34.0) R package.
The FoldChange > 2 or < 0.5 and ajusted p-value < 0.05 genes were considered as differentially expressed genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: mESC

growth_protocol: ESCs were grown in gelatin-coated dishes with 15% KnockOut Serum Replacement (Gibco), 1% non-essential amino acids (Gibco), 1% Glutamax (Gibco), 1% Penn-Strep (Life technologies), 0.1 mM β-mercaptoethanol (Invitrogen) and 1000 U/ml ESGRO Recombinant Mouse LIF Protein (Millipore). For cardiomyocyte differentiation, EBs were plated onto 0.2% gelatin-coated dishes in cardiomyocyte differentiation media (CMD) supplemented with DMEM (Gibco), 15% FBS (Gibco), 1% Penn-Strep, 1% non-essential amino acids (Gibco), 1% Glutamine (Gibco), 0.1 mM β-mercaptoethanol and 1mM Ascorbic Acid (Sigma).

extract_protocol:
Isolation of total RNA using TRIzol reagent.
The ribosomal RNA was removed after isolation of total RNA using TRIzol reagent (Invitrogen). The remaining RNA was used for library preparation and sequencing, which were subsequently performed at the Annoroad Gene Technology (Beijing, China). Two biological replicates were prepared for each differentiation phases. The libraries were sequenced on an Illumina Novaseq 6000 system using the 2 × 150-bp paired-end read mode.

treatment_protocol: 1mM ascorbic acid was added to CMD medium to improve cardiomyocyte differentiation efficiency.

value: mESC-derived CM Day10

value: treated with ascorbic acid


title: T47D GFOGER_10wt%_D3 replicate 1


title: SUM159PT_sgSTING_C1_2 [S30]


title: DSP-1002510007866-C-E01

description: RNA ISH


title: MDA-MB-231 GFOGER_10wt%_D3 replicate 3


title: SUM159PT_Par_for_CRISPR_2 [S28]

value: Mock


title: SUM159PT_sgSTING_C1_1 [S29]


title: MDA-MB-231 GFOGER_10wt%_D3 replicate 2

value: Adenocarcinoma


title: DSP-1002510007866-C-D12

description: RNA ISH


title: MDA-MB-231 GFOGER_10wt%_D3 replicate 1


title: CP_rep2

value: mESC-derived CM Day6


title: MDA-MB-436_sgSTING_C2_2 [S26]

description:
processed data file:
436_sgSTING_NormalizedCount.txt


title: MES_rep1

value: mESC-derived CM Day4


title: CP_rep1


title: SUM159PT_Par_for_CRISPR_1 [S27]


title: MES_rep2


title: MDA-MB-436_sgSTING_C2_1 [S25]


title: ESC_rep2

value: mESC Day0

value: untreated


title: DSP-1002510007866-C-D09

description: RNA ISH

value: glomerulus


title: DSP-1002510007866-C-D11

description: RNA ISH

value: tubule


title: Toledo_JO1

city: Taipei

first: Muh-Hwa

last: Yang

address: No. 155, Sec. 2, Li-Nong Street

country: Taiwan

institute: National Yang-Ming University

description:
GA612_RNAseq_GE.csv
GA612_RNAseq_TE.csv

data_processing:
Illumina Casava 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, first 12 nucleotide of 5' end, and low-quality sequence (< Q20), then mapped to GRCh38 reference genome using RNA-seq analysis tool of CLC Genomics Workbench v11.0 with default setting.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using RNA-seq analysis tool of CLC Genomics Workbench v11.0 based on the  lengths of the transcripts provided by the annotated mRNA track
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: a comma-separated values cvs files include RPKM values for each sample

source_name: Toledo

growth_protocol: SU-DHL-5 and Toledo cells were cultured in RPMI1640 medium supplemend with 10% FBS,  and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Total RNA 4 µg/sample in both cell lines were used as input material for the RNA  sample preparations. Sequencing Libraries were generated using Illumina TruSeq Stranded mRNA Sample Prep Kit and limited cycles of PCR by KAPA HiFi Polymerase
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Both cells were treated with either JQ1 (1 µM) or DMSO  for 6 h.

value: B lymphocyte

value: Toledo


title: 12w_PBS_1

value: medial prefrontal cortex

value: post natal day 84


title: DSP-1002510007866-C-D08

description: RNA ISH

value: normal


title: MDA-MB-436_sgSTING_C1_1 [S23]

value: STING sgRNA


title: ESC_rep1


title: DSP-1002510007866-C-D07

description: RNA ISH


title: CM_rep1


title: Toledo_DMSO

description:
GA612_RNAseq_GE.csv
GA612_RNAseq_TE.csv

value: DMSO


title: SU-DHL-5_JO1

description:
GA612_RNAseq_GE.csv
GA612_RNAseq_TE.csv


title: SU-DHL-5_DMSO

description:
GA612_RNAseq_GE.csv
GA612_RNAseq_TE.csv


title: MDA-MB-436_Par_for_CRISPR_2 [S22]


title: MDA-MB-436_Par_for_CRISPR_1 [S21]


title: DSP-1002510007866-C-D10

description: RNA ISH


title: T47D IKVAV_D3 replicate 4

value: Mammary Gland/Breast; Derived From Metastatic Site:Pleural Effusion

value: epithelial

value: Ductal Carcinoma

value: IKVAV


title: MDA-MB-231 IKVAV_D3 replicate 4

value: Adenocarcinoma


title: DSP-1002510007866-C-D06

description: RNA ISH


title: 02_KO_GB

city: San Francisco

first: Richard

last: Locksley

address: 513 Parnassus Ave

department: Medicine

institute: UCSF

data_processing:
Sequencing and base-calling by Illumina NovaSeq 6000
Raw data was processed with 10X Cellranger and analysis was done using Seurat v3.
Sequence data from WT and KO were merged.
Cells were filtered to only keep those that had less than 7% mitochondrial genes with numbers of features greater than 1800 and numbers of counts greater than 7500.
The principal component analysis was performed, a shared nearest neighbor graph was constructed, and clusters were identifed at a resolution of 0.4.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: a .h5 file containing cellranger filtered cell barcodes and gene expression counts

source_name: gallbladder/extrahepatic duct total digest

extract_protocol:
Stromal, epithelial, and immune cells were isolated from gallbladder/extrahepatic ducts and live single cells were sorted on Moflo XDP
10X Chromium Single Cell 3′ Reagent Kit (v3 Chemistry)

value: gallbladder/extrahepatic duct

value: stromal, immune, epithelial cells

value: adult mouse, untreated


title: SUM159PT_Tax-R_siMYC2_2 [S20]

description:
processed data file:
159_siMYC_NormalizedCount.txt

value: MYC siRNA-2


title: 01_WT_GB

value: WT


title: E4F1_Gemcitabine_ChiPseq_repC

city: montpellier

first: stanislas

middle: P

last: du manoir

address: 280 rue des apothicaires

country: France

institute: IRCM

description:
12_IpGMC_S28
processed data file:
Sum159ChIPE4F1-Gem.txt
Sum159ChIPE4F1-Gem.bed
Sum159ChIPE4F1-Gem_annotatedpeaks.txt

data_processing:
Image analysis by HiSeq Control software (Illumina)
Base calling by Real Time Analysis software (Illumina)
Demultiplexing by bcl2fastq
Quality checks Sequencing Analysis Viewer FASTQC
Mapping with bowtie2 -t  -q -p 6 on hg38, sam files were then converted to bam and sorted
Peak were called with HOMER findPeaks (default parameters) with replicates A and C, HOMER peak list (*.txt files) are converted to bed files (*.bed) with pos2bed.pl and peaks were annotated (*.annotatedpeaks.txt)with annotatedPeaks.pl
Bigwig were processed with deeptools bamCoverage (--outFileFormat bigwig --normalizeTo1x 2451960000 --normalizeUsingRPKM --skipNonCoveredRegions --extendReads 300 --ignoreDuplicates)
Genome_build: hg38

extract_protocol:
Lysates were clarified from sonicated nuclei and E4F1-DNA complexes were isolated with antibody.
Libraries construction by TruSeq ChIP Sample Preparation kit (Illumina) and Sequence By Synthesis sequencing using HiSeq 2500 (Illumina)

treatment_protocol: Cells were treated at 40-60% of confluence for 24h with 140nM of Gemcitabine (Sandoz®) corresponding to the IC30 established at lab.

tag: tissue source

value: primary mammary gland; breast tumor

value: Triple negative breast cancer cell type

value: 140nM of Gemcitabine

tag: chip antibody

value: Affinity-purified polyclonal Rabbit


title: DSP-1002510007866-C-D05

description: RNA ISH

value: normal

value: glomerulus


title: DSP-1002510007866-C-D04

description: RNA ISH


title: E4F1_Gemcitabine_Input_repC

description:
11_InGMC_S27
processed data file:
Sum159ChIPE4F1-Gem.txt
Sum159ChIPE4F1-Gem.bed
Sum159ChIPE4F1-Gem_annotatedpeaks.txt

tag: cell type


title: Arid4 Ltf iCre/+ Arid1a f/f 4

city: Research Triangle Park

first: Ryan

middle: M

last: Marquardt

state: NC

address: 111 T.W. Alexander Dr, Bldg 101, Room C-416, Mail Drop C-401

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

description:
Ltf iCre/+ Arid1a f/f 4
Gene expression data from uterus at gestation day 3.5

data_processing:
Raw reads were trimmed with cutadapt v1.18 and Trim Galore! v0.6.4_dev.
Quality control analysis was performed using FastQC v0.11.9.
Trimmed reads were aligned to the GRCm38 genome assembly using STAR v2.7.3a, and feature counting was performed using the command ‘--quantMode GeneCounts’.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for each gene and sample

source_name: Uterus of Ltf iCre/+ Arid1a f/f adult mouse at gestation day 3.5

growth_protocol: Collect uteri from intact adult female mice on the third morning after detection of a vaginal mucus plug (gestation day 3.5).

extract_protocol:
RNA was extracted from the uterine tissues using the RNeasy Mini Kit for total RNA isolation (Qiagen, Valencia, CA, USA).
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA mRNA Hyperprep kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT Illumina UDI dual Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNF-474 HS fragment kit (Agilent Technologies, Inc.) using a Fragment Analyzer (Agilent Technologies, Inc.), and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA).  Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2, 100 bp sequencing kit (Illumina Inc., San Diego, CA, USA) to an average depth of 50M reads per sample. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

tag: Sex

value: Female

value: Ltf iCre/+ Arid1a f/f


title: SUM159PT_Tax-R_siMYC2_1 [S19]

tag: cell line


title: MDA-MB-436_sgSTING_C1_2 [S24]

value: STING sgRNA


title: Arid3 Ltf iCre/+ Arid1a f/f 3

description:
Ltf iCre/+ Arid1a f/f 3
Gene expression data from uterus at gestation day 3.5


title: E4F1_NonTreated_ChiPseq_repC

description:
10_IpNTC_S26
processed data file:
Sum159ChIPE4F1-Ctrl.txt
Sum159ChIPE4F1-Ctrl.bed
Sum159ChIPE4F1-Ctrl_annotatedpeaks.txt


title: DSP-1002510007866-C-D02

description: RNA ISH

tag: slide name

tag: class


title: E4F1_NonTreated_Input_repC

description:
9_InNTC_S25
processed data file:
Sum159ChIPE4F1-Ctrl.txt
Sum159ChIPE4F1-Ctrl.bed
Sum159ChIPE4F1-Ctrl_annotatedpeaks.txt


title: Arid1 Ltf iCre/+ Arid1a f/f 1

description:
Ltf iCre/+ Arid1a f/f 1
Gene expression data from uterus at gestation day 3.5


title: DSP-1002510007866-C-D01

description: RNA ISH

tag: region


title: Arid2 Ltf iCre/+ Arid1a f/f 2

description:
Ltf iCre/+ Arid1a f/f 2
Gene expression data from uterus at gestation day 3.5


title: E4F1_Gemcitabine_ChiPseq_repA

description:
4_IpGMA_S20
processed data file:
Sum159ChIPE4F1-Gem.txt
Sum159ChIPE4F1-Gem.bed
Sum159ChIPE4F1-Gem_annotatedpeaks.txt

tag: treatment


title: Arid5 Ltf iCre/+ Arid1a f/f 5

description:
Ltf iCre/+ Arid1a f/f 5
Gene expression data from uterus at gestation day 3.5


title: DSP-1002510007866-C-C12

description: RNA ISH


title: SUM159PT_Tax-R_siC_2 [S16]

value: control siRNA


title: DSP-1002510007866-C-C11

description: RNA ISH


title: Ctrl3 Arid1a f/f 3

description:
Arid1a f/f 3
Gene expression data from uterus at gestation day 3.5

source_name: Uterus of Arid1a f/f adult mouse at gestation day 3.5

value: Arid1a f/f


title: SUM159PT_Tax-R_siC_1 [S15]


title: E4F1_Gemcitabine_Input_repA

description:
3_InGMA_S19
processed data file:
Sum159ChIPE4F1-Gem.txt
Sum159ChIPE4F1-Gem.bed
Sum159ChIPE4F1-Gem_annotatedpeaks.txt


title: E4F1_NonTreated_Input_repA

description:
1_InNTA_S17
processed data file:
Sum159ChIPE4F1-Ctrl.txt
Sum159ChIPE4F1-Ctrl.bed
Sum159ChIPE4F1-Ctrl_annotatedpeaks.txt


title: SUM159PT_Tax-R_siMYC1_2 [S18]

value: MYC siRNA-1


title: MDA-MB-436_Tax-R_siMYC2_1 [S13]

description:
processed data file:
436_siMYC_NormalizedCount.txt


title: DSP-1002510007866-C-C10

description: RNA ISH


title: MDA-MB-436_Tax-R_siMYC1_2 [S12]


title: Ctrl4 Arid1a f/f 4

description:
Arid1a f/f 4
Gene expression data from uterus at gestation day 3.5


title: MDA-MB-436_Tax-R_siMYC2_2 [S14]


title: E4F1_NonTreated_ChiPseq_repA

description:
2_IpNTA_S18
processed data file:
Sum159ChIPE4F1-Ctrl.txt
Sum159ChIPE4F1-Ctrl.bed
Sum159ChIPE4F1-Ctrl_annotatedpeaks.txt


title: Ctrl2 Arid1a f/f 2

description:
Arid1a f/f 2
Gene expression data from uterus at gestation day 3.5


title: Ctrl1 Arid1a f/f 1

description:
Arid1a f/f 1
Gene expression data from uterus at gestation day 3.5


title: DSP-1002510007866-C-D03

description: RNA ISH


title: DSP-1002510007866-C-C09

description: RNA ISH


title: SUM159_shE4F1_GEM_rep3

data_processing:
Sequencing on a HiSeq 2500
Image analysis by HiSeq Control software (Illumina)
Base calling by Real Time Analysis software (Illumina)
Demultiplexing by bcl2fastq
Quality checks Sequencing Analysis Viewer FASTQC
Contaminant screening by FastQ screen using Bowtie2 v2.2.9
Splice junction mapping TopHat2 v2.1.1
Counting HTSeq-count (version 0.9.0)
Normalization DESeq2 v1.14.1 and R version 3.4.0
Differential Analysis DESeq2
Genome_build: GRCh38
Genome_build: GENECODE Release 25 (GRCh38.p7)
Supplementary_files_format_and_content: rawCounts and DESeq2 output

source_name: SUM159 cells

growth_protocol: SUM159 cells were routinely generated by re-plating d 3-4 adherent cells (typically 2–3 × 10^6 cells into a T150 dish) in Ham's F12 media (Gibco) supplemented with 5% fetal bovine serum, hydrocortisone (1µg/ml), human insulin (10,5 µg/ml).

extract_protocol:
Cells  were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Preparation Kit  was used with 2 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated (GEM) at 40-60% of confluence for 24h with 140nM of Gemcitabine (Sandoz®) corresponding to the IC30 established at lab.Cells were treated (GEM).

tag: tissue

value: mammary gland; breast

tag: subtype

value: Triple negative breast cancer

tag: tumor source

value: Primary tumor

value: Breast cancer cell line

tag: transfection

tag: genotype/variation

value: down regulation E4F1

value: Gemcitabine treated


title: SUM159_shE4F1_NT_rep3

value: Untreated


title: SUM159_shCTRL_GEM_rep3

value: shCTRL


title: MDA-MB-436_Tax-R_siC_2 [S10]


title: SUM159PT_Tax-R_siMYC1_1 [S17]

description:
processed data file:
159_siMYC_NormalizedCount.txt


title: h-Dpi6-3

city: Guangzhou

first: Xiao Xiao

last: Tang

address: No195,Dongfeng Xi Road

institute: Guangzhou Medical University

description: Ad5-hACE2-Dpi6-replicate 3

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome (GRCm38.91) using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis. This choice is motivated by the decision to maximize the sensitivity of this analysis, in order to perform a massive screening and identify candidate genes to be validated with a wider sample population with real-time PCR analysis.
We performed a Gene Ontology (GO) analysis for biological processes, cellular components and molecular function and a KEGG pathway analysis (Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg) via enrich R package.
Genome_build: GRCm38.91
Supplementary_files_format_and_content: Excel files include FPKM values and counts for each Sample .

source_name: lung tissue

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.

value: lung

tag: strain

value: wild type


title: MDA-MB-436_Tax-R_siMYC1_1 [S11]


title: h-Dpi6-2

description: Ad5-hACE2-Dpi6-replicate 2


title: DSP-1002510007866-C-C05

description: RNA ISH

data_processing:
Library strategy: GeoMx-Seq
GeoMx NGS Pipeline v2.3.3.10 with the following parameters: quality-trim-score = 20, 2color-trimming = True, adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3, barcode-max-mismatch = 1, stitching-max-mismatch = 2
Genome_build: NA
Supplementary_files_format_and_content: Digital Count Conversion (DCC) files: format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Kidney_Sample_Annotations.txt: txt file containing sample annotations
Supplementary_files_format_and_content: Kidney_Raw_BioProbeCountMatrix.txt: txt file containing raw probe counts for each AOI
Supplementary_files_format_and_content: Kidney_Raw_TargetCountMatrix.txt: txt file containing collapsed target-level counts for each AOI
Supplementary_files_format_and_content: Kidney_Q3Norm_TargetCountMatrix.txt: txt file containing Q3 normalized target-level counts for each AOI

source_name: Human FFPE kidney

extract_protocol:
Samples were incubated with the human Whole Transcriptome Atlas RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: normal

value: glomerulus

tag: pathology

tag: nuclei


title: Nifurtimox_30uM_rep_3

city: Beijing

first: Ying

last: Guo

address: 1 Xian Nong Tan Street

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Real-Time Analysis (RTA) software  (version v3.4.4) was used for basecalling and bcl2fastq2 software (version 2.20.0.422) was used to converts base call files into FASTQ files.
The adapters of raw data (raw reads) in fastq format were trimmed using Trimmomatic (version 0.36) with parameters LEADING:3 TRAILING:3 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8:true SLIDINGWINDOW:4:15 MINLEN:50.
The clean reads were mapped to the human genome (GRCh38) using HISAT2 (version 2.2.1.0)  with parameters --rna-strandness rf --fr.
Abundance measurement (FPKM) of each gene was calculated using Cufflinks (version 2.2.1) with parameters --library-type fr-firststrand, and the read counts of each gene were obtained by htseq-count (version 0.9.1) with parameters -s reverse.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: A549 cell line

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in humidified incubators at 37℃ with 5% CO2.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (ThermoFisher, USA, Cat. No. 15596026) according to the manufacturer’s protocol.
RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) and three multiplexed libraries for each group were constructed using TruSeq Stranded mRNA LT Sam-ple Prep Kit (Illumina, USA).

treatment_protocol: A549 cells were treated with chrysin or nifurtimox at a final concentration of 30 μM for 40 h. Vehicle controls were treated with 0.1% v/v DMSO. Both treatments and their own vehicle controls were performed in biological triplicate.

tag: cell-line

value: adenocarcinomic human alveolar basal epithelial cells

value: Nifurtimox 30uM


title: SUM159_shE4F1_NT_rep2


title: MDA-MB-436_Tax-R_siC_1 [S9]

value: control siRNA


title: DSP-1002510007866-C-C06

city: Seattle

first: Stephanie

last: Zimmerman

institute: NanoString Technologies

description: RNA ISH


title: Ctrl5 Arid1a f/f 5

description:
Arid1a f/f 5
Gene expression data from uterus at gestation day 3.5

value: Female

tag: genotype

value: Arid1a f/f


title: Nifurtimox_30uM_rep_2

tag: cell type


title: h-Dpi6-1

description: Ad5-hACE2-Dpi6-replicate 1


title: SUM159_shE4F1_GEM_rep2

value: mammary gland; breast


title: DSP-1002510007866-C-C03

description: RNA ISH


title: SUM159_shCTRL_NT_rep3

value: Triple negative breast cancer


title: E-Dpi6-3

description: Ad5-Empty-Dpi6-replicate 3


title: DSP-1002510007866-C-C04

description: RNA ISH


title: SUM159_shCTRL_GEM_rep2

value: Primary tumor


title: DSP-1002510007866-C-C08

description: RNA ISH

value: tubule


title: MDA-MB-436_sgSTING_STING_2 [S36]

description:
processed data file:
436_STING_OE_NormalizedCount.txt

value: STING sgRNA+STING ORF


title: Control_for_nifurtimox_rep_3

value: DMSO


title: DSP-1002510007866-C-C02

description: RNA ISH


title: E-Dpi6-1

description: Ad5-Empty-Dpi6-replicate 1


title: E-Dpi6-2

description: Ad5-Empty-Dpi6-replicate 2


title: Nifurtimox_30uM_rep_1


title: SUM159_shCTRL_NT_rep2

value: Breast cancer cell line

value: Untreated


title: DSP-1002510007866-C-C07

description: RNA ISH


title: DSP-1002510007866-C-B12

description: RNA ISH


title: h-Dpi4-3

description: Ad5-hACE2-Dpi4-replicate 3

value: lung


title: SUM159_shE4F1_GEM_rep1

value: down regulation E4F1

value: Gemcitabine treated


title: h-Dpi4-2

description: Ad5-hACE2-Dpi4-replicate 2

value: wild type


title: Control_for_nifurtimox_rep_2

value: adenocarcinomic human alveolar basal epithelial cells


title: h-Dpi4-1

description: Ad5-hACE2-Dpi4-replicate 1


title: DSP-1002510007866-C-B11

description: RNA ISH

value: normal


title: Chrysin_30uM_rep_3

value: Chrysin 30uM


title: SUM159_shE4F1_NT_rep1


title: E-Dpi4-3

description: Ad5-Empty-Dpi4-replicate 3


title: DSP-1002510007866-C-B10

description: RNA ISH


title: SUM159_shCTRL_GEM_rep1

value: shCTRL


title: DSP-1002510007866-C-B09

description: RNA ISH


title: Chrysin_30uM_rep_1


title: Chrysin_30uM_rep_2


title: DSP-1002510007866-C-B08

description: RNA ISH


title: MDA-MB-231_MEL-18 T334A_FLAG IP

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

institute: College of Medicine, Hanyang University

data_processing:
Illumina Casava 1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.32
Trimmed reads were mapped to hg19 whole genome using bowtie v1.1.1
Peak calling by MACS2 (v2.1.1.20160309)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using MACS2 for each sample

source_name: breast cancer cell line

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Lysates from cells cross-linked with 1% formaldehype were sonicated and incubated with anti-FLAG antibody to isolate the FLAG-tagged protein-DNA complexes. The purified genomic DNA were quantified using Quant-IT PicoGreen (Invitrogen) and qualified using the Agilent High Sensitivity DNA Kit and the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
The sequencing libraries were prepared according to the manufacturer’s instructions of the TruSeq ChIP Sample Preparation Kit (Illumina). The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantification kits for Illumina Sequencing platforms) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, Waldbronn, Germany). Indexed libraries were then sequenced using the HiSeq2500 platform (Illumina).

treatment_protocol: MDA-MB-231 cells were infected with lentiviruses encoding either MEL-18 wild type (pLVX-MEL-18 WT-FLAG) or MEL-18 T334A (pLVX-MEL-18 T334A-FLAG)

value: mammary gland/breast

value: epithelial

tag: lentivirus

value: pLVX-MEL-18 T334A-FLAG

tag: disease

value: adenocarcinoma

tag: chip antibody

value: FLAG antibody (Sigma, F3165)


title: Control_for_chrysin_rep_3


title: E-Dpi4-1

description: Ad5-Empty-Dpi4-replicate 1


title: h-Dpi2-3

description: Ad5-hACE2-Dpi2-replicate 3


title: DSP-1002510007866-C-C01

description: RNA ISH

tag: slide name

tag: class

value: glomerulus


title: DSP-1002510007866-C-B07

description: RNA ISH

tag: region

value: tubule


title: DSP-1002510007866-C-B05

description: RNA ISH


title: h-Dpi2-2

description: Ad5-hACE2-Dpi2-replicate 2

tag: tissue

tag: treatment


title: MDA-MB-231_MEL-18 WT_Input

tag: cell line

value: pLVX-MEL-18 WT-FLAG


title: h-Dpi2-1

description: Ad5-hACE2-Dpi2-replicate 1


title: Control_for_chrysin_rep_2

value: DMSO


title: Control_for_nifurtimox_rep_1


title: ALKBH3 CLIP_2

city: Chicago

first: Guan-Zheng

last: Luo

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

data_processing:
Library strategy: CLIP-seq
Raw reads from CLIP samples were first trimmed according to recommended settings  using cutadpt with a minimum length of 15 nucleotides
Processed  reads were combined to unique sequences then mapped to the human small RNA database (Rfam)
tRNA hits were extracted based on the annotation.
Genome_build: hg19
Supplementary_files_format_and_content: text file with two columns; the first column represents the reads, and the second column represents the corresponding tRNA.

source_name: HeLa cells

growth_protocol: Human cancer cells HeLa  were purchased from American Type Culture Collection (ATCC, Manassas, VA) and maintained in our lab with Dulbecco’s modified Eagle medium (DMEM, GIBCO, Carlsbad, CA, USA) with 10 % fetal bovine serum, and 1 % penicillin/streptomycin (Invitrogen).

extract_protocol:
The CLIP procedures were conducted using HeLa cells according to the previous study (Liu et al., 2016) with slight modifications. Briefly, 4 plates of HeLa cells in 15 cm dishes were transfected with pPB/ALKBH3 plasmid for 48 h to reach about 90% cell confluency. After washing twice with ice-cold PBS, cells were irradiated twice with 400 mJ/cm2 at 254 nm by Stratalinker on ice. Cells were lysed in high salt lysis buffer (300 mM NaCl, 0.2% NP-40, 20 mM Tris-HCl PH 7.6, 0.5 mM DTT, protease inhibitor cocktail (1 tablet/50 ml), and RNase inhibitor (1:200)) at 4°C for 30 min. Supernatant was collected after centrifuged at 17,000 g at 4°C for 15 min and further treated with 1 U RNase T1 for 15 min at 24 °C. After centrifugation and filtration through 0.22 µM filter, 10% supernatant was collected as input for further sequencing analysis. Anti-Flag M2 beads (Sigma-Aldrich, St. Louis, MO, 80 μl) were washed three times with lysis buffer and incubated with the filtered supernatant at 4°C for 4 hrs. After removing the flow through by magnetic rack, beads and input were further incubated with 10 U RNase T1 exactly for 8 min. Samples were treated with 95 µL commercial PNK buffer and 0.5 U PNK for 15 min at 37 °C. After treatments, final concentration of 100 µM ATP and 1 U PNK were added and incubated at 37 °C for another 30 min. The RNA/protein complexes were eluted by NuPAGE 1 × loading buffer and fractionated by neutral NuPAGE 4–12% bis-tris gel. After cutting the gel, RNAs were recovered by proteinase K digestion in proteinase K buffer, followed by phenol/chloroform extraction using glycogen as carrier.  The RNA fragments were ligated to adapter and established library by NEB small RNA library preparation kit (E7330S).
The RNA fragments were ligated to adapter and established library by NEB small RNA library preparation kit (E7330S).

treatment_protocol: For cell lines stably overexpressed ALKBH3: HeLa cells transfected with double-tagged ALKBH3 (N terminal Flag and HA in tandem) in pPB-CAG vector were selected by 2 μg/ml puromycin for two weeks. Control cell lines were created similarly with vector only expressing N-terminal Flag and HA in tandem. The ALKBH3 stable overexpression and control cells were cultured in medium supplemented with 2 μg/ml puromycin. Cells were incubated with medium without puromycin for four days before experiments.

value: HeLa

tag: passages

value: Anti-ALKBH3 Antibody (Millipore, Cat. No. 09-882)


title: E-Dpi2-3

description: Ad5-Empty-Dpi2-replicate 3

value: lung


title: HBECs, B56, 48 IAV

city: Hong Kong

first: Renee Wan Yi

last: Chan

state: Select a State

address: 1 Shing Cheong Road, Kowloon Bay, Hong Kong

department: Paediatrics

country: Hong Kong

institute: Chinese University of Hong Kong

data_processing:
Raw reads were trimmed using the Quality Score method and mapped to hg38 (Ensembl 104) using STAR
Aligned reads were quantified using the Partek E/M method. Low count features were excluded with total count  <=10
Differential expression were performed on normalized reads (TMM) using DESeq2 algorithm
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including TMM values for each Sample

source_name: HBEC

growth_protocol: HBEC were differentiated in Air Liquid Interface for 30 days

extract_protocol:
Total RNA from one transwell was extracted using RNAeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols with polyA enrichment

treatment_protocol: Cells infected with 0.01 MOI of RV, IAV or mock inoculated for two hours followed by extensive washing. Total mRNA was harvested at 48 hours post-infection

value: HBEC

tag: donor

tag: infection

value: influenza (IAV)

tag: post-treatment


title: E-Dpi4-2

description: Ad5-Empty-Dpi4-replicate 2

tag: strain

value: wild type


title: E-Dpi2-2

description: Ad5-Empty-Dpi2-replicate 2


title: DSP-1002510007866-C-B03

address: 530 Fairview Ave N

description: RNA ISH

value: normal

tag: pathology

tag: nuclei


title: DSP-1002510007866-C-B04

description: RNA ISH


title: HBECs, B56, 48 Mock1

tag: cell type


title: MDA-MB-231_MEL-18 WT_FLAG IP

tag: lentivirus


title: HBECs, B56, 48 Mock2


title: E-Dpi2-1

description: Ad5-Empty-Dpi2-replicate 1

tag: genotype


title: ALKBH3 CLIP_1

tag: chip antibody


title: 4T1_siMYC2_3 [T9]

description:
processed data file:
4T1_siMYC_NormalizedCount.txt

value: MYC siRNA-2


title: DSP-1002510007866-C-B02

description: RNA ISH

tag: slide name


title: DSP-1002510007866-C-B01

description: RNA ISH

tag: class


title: Input_1


title: HBECs, B56, 48 RV

value: rhinovirus (RV)


title: PA-treated root rep 3 [P3R]

city: Ghent

first: Willem

last: Desmedt

address: Valentin Vaerwyckweg 1

department: Plants and Crops

institute: Ghent University

data_processing:
Quality assesment using FastQC v0.11.8
Trimming with Trimmomatic v0.38 (Phred > 20, length > 40)
Mapping to tomato reference genome (ITAG 4.0) using STAR v2.6.1d
Counting reads using R GenomicAlignments package (summarizeOverlaps function)
Normalization and differential expression analysis using the R DeSeq2 package
Genome_build: ITAG 4.0
Supplementary_files_format_and_content: count table (after normalization using DeSeq2), in .csv format

organism: Solanum lycopersicum

source_name: PA-treated root

growth_protocol: Tomato seedlings (cv. Moneymaker) were routinely germinated, transplanted to individual pots 4 days after germination and placed in a growth chamber (24°C, 16 hours of light)

extract_protocol:
Plants were washed, pooled (4 plants per sample) and root and shoot tissues were ground seperately in liquid nitrogen. RNA was extracted using a Zymo Plant RNA kit as per manufacturer's instructions (Zymo Research).
QuantSeq 3′mRNA-Seq Library Prep Kit (Lexogen) as per manufacturer's instruction, starting from 2 µg RNA.

treatment_protocol: Plants were foliarly sprayed with a solution containing 300 µM PA and 0.1 v/v% Tween 20 or a corresponding mock solution at two time points: 7 and 14 days post transplantation.

tag: cultivar

value: cv. Moneymaker

tag: age

value: 15 days post transplantation

value: Piperonylic acid (300 µM)

tag: treatment time

value: 7 and 14 days post transplantation

value: Root


title: DSP-1002510007866-C-B06

description: RNA ISH

tag: region

value: tubule


title: HBECs, B47, 48 Mock1


title: MDA-MB-231_MEL-18 T334A_Input

tag: tissue

value: mammary gland/breast

value: epithelial

tag: cell line

value: pLVX-MEL-18 T334A-FLAG

tag: disease

value: adenocarcinoma


title: Control_for_chrysin_rep_1

tag: cell-line

value: adenocarcinomic human alveolar basal epithelial cells

tag: treatment

value: DMSO


title: 4T1_siMYC2_2 [T8]


title: DSP-1002510007866-C-A12

description: RNA ISH

tag: pathology


title: DSP-1002510007866-C-A11

description: RNA ISH

value: glomerulus

tag: nuclei


title: PA-treated root rep 2 [P2R]


title: PA-treated root rep 1 [P1R]


title: Input_2

value: HeLa

tag: passages

value: Anti-ALKBH3 Antibody (Millipore, Cat. No. 09-882)


title: HBECs, B47, 48 Mock2

tag: cell type

value: HBEC

tag: donor

tag: infection

tag: post-treatment


title: DSP-1002510007866-C-A10

description: RNA ISH

tag: slide name

tag: class

value: normal


title: HBECs, B47, 48 RV

value: rhinovirus (RV)


title: 4T1_siMYC1_3 [T6]

value: MYC siRNA-1


title: DSP-1002510007866-C-A09

description: RNA ISH


title: 4T1_siMYC1_2 [T5]


title: 4T1_siMYC1_1 [T4]


title: DSP-1002510007866-C-A08

description: RNA ISH


title: Mock-treated root rep 3 [C3R]

source_name: Mock-treated root

tag: cultivar

value: cv. Moneymaker

tag: age

value: 15 days post transplantation

value: Mock


title: HBECs, B46, 48 Mock1


title: Mock-treated root rep 2 [C2R]

tag: treatment time

value: 7 and 14 days post transplantation

value: Root


title: Mock-treated root rep 1 [C1R]

tag: tissue


title: 4T1_siC_3 [T3]

tag: cell line

value: control siRNA


title: DSP-1002510007866-C-A07

description: RNA ISH

tag: region


title: PA-treated shoot rep 3 [P3S]

source_name: PA-treated shoot

value: Piperonylic acid (300 µM)

value: Shoot


title: HBECs, B46, 48 Mock2


title: 4T1_siC_2 [T2]


title: HBECs, B46, 48 RV


title: PA-treated shoot rep 2 [P2S]


title: DSP-1002510007866-C-A06

description: RNA ISH


title: HBECs, B47, 48 IAV

value: influenza (IAV)


title: 4T1_siC_1 [T1]


title: DSP-1002510007866-C-A05

description: RNA ISH


title: 4T1_siMYC2_1 [T7]

value: MYC siRNA-2


title: PA-treated shoot rep 1 [P1S]


title: DSP-1002510007866-C-A04

description: RNA ISH

value: glomerulus


title: Py230_shSting1_Dox(+)_3 [P6]

description:
processed data file:
Py230_shSting1_NormalizedCount.txt

value: Doxycycline

tag: genotype

value: Sting1 shRNA


title: SUM159_shCTRL_NT_rep1

value: mammary gland; breast

tag: subtype

value: Triple negative breast cancer

tag: tumor source

value: Primary tumor

value: Breast cancer cell line

tag: transfection

value: shCTRL

tag: treatment

value: Untreated


title: Mock-treated shoot rep 3 [C3S]

source_name: Mock-treated shoot

value: cv. Moneymaker

value: 15 days post transplantation

value: Mock


title: si-SF3B4#3

city: Jinan

first: Chen

last: Zhao

state: China

address: 107 Wenhua Xi Road

department: Department of Obstetrics and Gynecology

institute: Qilu Hospital, Shandong University

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were first filtered to obtain clean reads using FASTX-Toolkit
High-quality reads were mapped to the human reference genome hg19 using HISAT2 software with default parameters
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded
Based on the value of reads per kilobase per million mapped reads, gene expression levels were determined using Cufflinks software

source_name: HEY

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

tag: sample type

value: ovarian cancer cell line


title: Py230_shSting1_Dox(+)_2 [P5]


title: si-SF3B4#2


title: DSP-1002510007866-C-A03

description: RNA ISH

value: normal

tag: pathology

tag: nuclei


title: si-SF3B4#1


title: HBECs, B46, 48 IAV

tag: cell type

value: HBEC

tag: donor

tag: infection

tag: post-treatment


title: si-NC#3 (SF3B4 control)

value: si-NC


title: Mock-treated shoot rep 1 [C1S]

tag: cultivar

tag: age

value: 7 and 14 days post transplantation

value: Shoot


title: Mock-treated shoot rep 2 [C2S]

tag: treatment time

tag: tissue


title: Py230_shSting1_Dox(+)_1 [P4]

tag: cell line

value: Doxycycline


title: DSP-1002510007866-C-A01

description: RNA ISH

tag: slide name

value: No Template Control


title: Py230_shSting1_Dox(-)_3 [P3]

value: Vehicle

tag: genotype

value: Sting1 shRNA


title: DSP-1001250007864-D-H12

description: RNA ISH

tag: class

value: DKD

tag: region

value: tubule


title: si-NC#2 (SF3B4 control)

tag: treatment


title: Py230_shSting1_Dox(-)_2 [P2]


title: si-NC#1 (SF3B4 control)

tag: sample type


title: Py230_shSting1_Dox(-)_1 [P1]


title: DSP-1001250007864-D-H11

description: RNA ISH

tag: pathology


title: UUO5d rep3

city: Jinhua

first: Weiqiang

last: Lin

state: Zhejiang

address: Shangcheng street N1

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were build index by hisat2, and masked for low-complexity or low-quality sequence
Mapped to mm9 whole genome using hisat2 and  exported StringTie readable format files
Expression values for all genes in each sample (FPKM) were calculated by StringTie
Differentially expressed miRNAs between the paired groups were analyzed by using DEGseq
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from each tissue sample using Trizol method
RNA libraries were prepared for sequencing using standard illumina protocls

value: Mouse kidneys

tag: group

value: unilateral ureteral obstruction (UUO)

value: 8~10 weeks

tag: strain


title: DSP-1001250007864-D-H10

description: RNA ISH

tag: nuclei


title: Amazonia_FMTHVD-118,124

city: Ribeirao Preto

first: Victor

middle: Hugo

last: Aquino

state: Sao Paulo

address: Avenida do Cafe, s/n

department: Fculty of Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

hyb_protocol: PCR products were hybridized against the DNA microarray using the Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent, USA), following manufacturer’s recommendations.

scan_protocol: The slides were scanned with the Axon GenePix 4000B scanner (Molecular Devices, USA) at a 532 nm wavelength with a pixel size of 10-μm resolution.

data_processing: The median fluorescence intensity of each spot with local background subtraction was calculated from the scanned images using GenePix Pro 7 software (Molecular Devices, USA). The raw data of the sports were normalized against the negative control probes, which were randomly distributed on each sub-array. The normalized data were log2-transformed to reduce variability. The spots containing the probes for each virus species were grouped, and the mean signal intensity of all groups was calculated. The mean signal intensity of the group of probes corresponding to each virus species was compared to the mean signal intensity of the negative control probes, using the Welch’s t-test. A virus was considered present in an analyzed sample when the mean signal intensity of the group of probes was significantly (p<0.05) higher than the mean signal intensity of the negative control probes and showed a normalized mean intensity of at least 2, i.e., it was at least fourfold higher than the mean signal intensity of the negative control probes, thus reducing the chance of virus misidentification due to cross-hybridization.

source_name: Peripheral Blood

label_protocol: Individual or pool of equimolar amount of cDNAs were used for a random PCR amplification, which contained 1 nmol of the fluorescent labelling Cy3-dUTP (SIGMA ALDRICH, USA).

extract_protocol: Total RNA was purified from 200 µL of serum samples, using the PureLink Viral RNA/DNA Mini Kit (Invitrogen, USA), following manufacturer’s recommendations.

value: Whole blood

tag: subject 1

tag: subject 1 gender

value: Female

tag: subject 1 age

value: 58 years

tag: subject 2

tag: subject 2 gender

tag: subject 2 age