title: PC3-T-E7107-rep5

description: Sample 32

source_name: Xenograft

growth_protocol: Early passages of LNCaP and PC3 cells (obtained from ATCC) were grown in RPMI1640 medium supplemented with 7% serum. LAPC9-AI and PC3 xenograft models were maintained in castrated NSG male mice.

extract_protocol:
Cell cultures (LNCaP and PC3) treated with DMSO (D) or E7107 (E) for 6hrs in vitro, and tumors (LAPC9-AI and PC3) harvested 4hrs after Vehicle (C) or E7107 (E) injection were subject to total RNA extraction by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) 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: Cell cultures were treated with E7107 at 10nM for 6 hrs, and tumors were treated with E7107 at 5mg/kg/day for 5 days.

tag: disease state

value: Prostate cancer

tag: xenograft

tag: animal treatment

value: E7107 5mg/kg/day


title: rgs1-0h-2

status: Public on Mar 04 2020

type: SRA

city: Nanjing

first: Ying

last: Li

department: College of Plant protection

country: China

institute: Nanjing Agricultural University

library_source: transcriptomic

data_processing:
Isolation of Poly (A) mRNA from total RNA and construction of cDNA libraries were preformed according to Dong et al. (Dong et al., 2015). Finally, the cDNA libraries were loaded onto the flow cell channels of an Illumina HiSeqTM 4000 platform for paired-end 151 bp x 2 sequencing at the Beijing Genomics Institute (BGI), Shenzhen, China (Zhang et al., 2013).
After discarding low-quality raw reads (contain the connectors and discarded the reads whose content had more than 5% unknown bases.), the clean reads from each library were assembled to M. oryzae. Gene expression levels were measured in the RNA-Seq analysis as reads per kb of exon model per million mapped reads (RPKM) (Mortazavi et al., 2008).
Differentially expressed genes and their corresponding P-values were determined using the DEG. Fold changes (Log2 Ratio) were estimated according to the normalized gene expression level in each sample. We used the absolute value of Log2Ratio>1, p-values<0.001, q-value<0.001 as the threshold to judge differentially expressed genes.
Genome_build: novel_coding_transcript.gtf
Supplementary_files_format_and_content: transcript.fpkm

molecule: total RNA

organism: Pyricularia oryzae

extract_protocol:
The samples of the inoculated rice leaves with conidial suspensions were immediately frozen in liquid nitrogen, total RNA was extracted using an Invitrogen kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: Magnaporthe oryzae and rice leaves mixed sample

tag: strain background

tag: genotype/variation

value: {deleta}Morgs1 mutants

tag: timepoint

value: Conidia were inoculated onto rice leaves for 0 h


title: PC3-siNC-rep2

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

description:
growth condition: RPMI1640+FBS
Sample2

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.5.2).
The number of fragments in each known gene from GENCODE (version 25) was enumerated using STAR QuantMode (GeneCounts) function.
The normalized fragment count for each gene was calculated by R/Bioconductor package DESeq2 (version 1.18.1).
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq2) for all the samples.

organism: Homo sapiens

growth_protocol: Early passages of PC3 cells (obtained from ATCC) were grown in RPMI1640 medium supplemented with 7% serum.

extract_protocol:
PC3 cells treated with siRNAs for 8-10hrs in vitro and RNA harvested 48-72hrs after transfection by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) 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: Cell cultures (~75% confluence) were transfected with siRNAs at 20nM for 8-10 hrs in Opti-MEM, then cultured in normal medium for 48-72 hrs before RNA isolation.

tag: cell type

value: Prostate cancer cell line

tag: sirna treatment

value: negative control

tag: cell line

tag: ar status

value: AR-


title: rgs1-0h-3


title: PC3-T-E7107-rep3

description: Sample 30


title: PC3-T-E7107-rep4

description: Sample 31


title: rgs1-0h-1


title: PC3-T-Veh-rep5

description: Sample 27

value: Vehicle


title: PC3-T-E7107-rep1

description: Sample 28


title: HET_48h_R3

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

country: USA

institute: University of California Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Low count genes were filtered. Normalization by TMM. PC1 and PC2 of sequencing QC produced by Picardtools were regressed out. Differential expression analysis was done using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Complete_geneList_EdgeR.csv

organism: Mus musculus

tag: genotype

tag: time point


title: PC3-T-Veh-rep4

description: Sample 26


title: PC3-T-Veh-rep1

description: Sample 23


title: PC3-siNC-rep1

description:
growth condition: RPMI1640+FBS
Sample1


title: Guy11-24h-3

value: wild type

value: Conidia were inoculated onto rice leaves for 24 h


title: LAPC9-AI-E7107-rep5

description: Sample 22


title: LAPC9-AI-E7107-rep4

description: Sample 21


title: HET_24h_R5


title: PC3-T-Veh-rep3

description: Sample 25


title: LAPC9-AI-E7107-rep2

description: Sample 19


title: HET_48h_R2


title: Guy11-4h-3

value: Conidia were inoculated onto rice leaves for 4 h


title: PC3-T-Veh-rep2

description: Sample 24


title: Guy11-24h-1


title: HET_24h_R1


title: LAPC9-AI-Veh-rep4

description: Sample 16


title: Guy11-4h-1


title: LAPC9-AI-Veh-rep5

description: Sample 17


title: LAPC9-AI-Veh-rep2

description: Sample 14


title: PC3-T-E7107-rep2

description: Sample 29


title: HET_24h_R2


title: HET_48h_R1


title: LAPC9-AI-E7107-rep3

description: Sample 20


title: LAPC9-AI-E7107-rep1

description: Sample 18


title: LAPC9-AI-Veh-rep3

description: Sample 15


title: LAPC9-AI-Veh-rep1

description: Sample 13


title: Guy11-1h-2

value: Conidia were inoculated onto rice leaves for 1 h


title: HET_12h_R5


title: PC3-E7107-6h-rep2

description: Sample 11

source_name: Prostate cancer cell line

tag: growth condition


title: HET_12h_R1


title: Guy11-24h-2


title: Guy11-1h-1


title: PC3-DMSO-6h-rep2

description: Sample 8

value: FBS


title: Guy11-0h-3


title: WT_48h_R2

value: Wild type


title: Guy11-1h-3


title: HET_12h_R2


title: LNCAP-E7107-6h-rep2

description: Sample 5

value: LNCaP

value: AR+


title: Guy11-0h-2


title: PC3-E7107-6h-rep3

description: Sample 12

value: Prostate cancer


title: LNCAP-E7107-6h-rep3

description: Sample 6


title: Guy11-4h-2


title: WT_48h_R1


title: PC3-DMSO-6h-rep1

description: Sample 7


title: WT_24h_R5


title: LNCAP-DMSO-6h-rep3

description: Sample 3


title: PC3-E7107-6h-rep1

description: Sample 10


title: LNCAP-DMSO-6h-rep2

description: Sample 2


title: PC3-DMSO-6h-rep3

description: Sample 9


title: WT-H3K27me3-rep1

city: Beijing

first: Zhuqiang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

library_source: genomic

data_processing:
ATAC-seq/ChIP-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ChIP reads were mapped to UCSC mm10 genome by Bowtie2 (2.3.4.2)
ChIP data were filtered using samtools rmdup to remove potential PCR duplicates
Genome_build: mm10
Supplementary_files_format_and_content: Wig files of ChIP-seq data were generated using deepTools v3.3.0 with library size normalized to 10 million read pairs.
Supplementary_files_format_and_content: Peaks of ATAC-seq were called by MACS2 software and stored in narrowPeaks text format.

molecule: genomic DNA

extract_protocol:
ATAC-seq was performed as the following decription. Briefly, 50,000 cells were washed once with 50 μl of ice-cold PBS, then lysed with 50 μl of ice-cold lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) by incubating on ice for 10 min. The pellet was washed once with 1 ml of washing buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Tansposition reaction was performed in 50 μl of reaction mix containing 10 μl of 5× TTBL (Vazyme, TD501), 5 μl of TTE Mix V50 (Vazyme, TD501), 16.5 μl of PBS, 0.5 μl of 10% Tween-20, 0.5 μl of 1% digitonin, and 17.5 μl of PCR-grade water. The mixture was incubated at 37 ˚C for 30 min on a thermomixer with shaking at 1,000 rpm. Then, DNA was extracted by phenol-chloroform and amplified by KAPA HiFi HotStart ReadyMix (KAPA Biosystems, KK2611) with barcoded primers (Vazyme, TD202). DNA fragments ranging from 200 bp to 1,000 bp were selected for deep sequencing.
For ChIP-seq, Cells were harvested in PBS and cross-linked with 1% formaldehyde for 9 min at room temperature, cells prepared for RNA pol II were pre-cross-linked with 0.2 mM disuccinimidyl glutarate (DSG, ProtecoChem, c1104) for 30 min at room temperature. Reaction was terminated by adding glycine to a final concentration of 125 mM, incubated at room temperature for 5 min. After washing with PBS twice, cells were resuspended in 5 mL of Lysis Buffer 1 (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25%Triton X-100), incubated on ice for 10 min. After centrifuge at 2,000 rpm at 4 ˚C for 5 min, cells were then resuspended in 5 mL of Lysis Buffer 2 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA), incubated at room temperature for 10 min. The lysate was centrifuged at 4,000 rpm for 5 min at 4 ˚C. The chromatin fraction was resuspended in 1 mL of Lysis Buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% sodium N-lauroylsarcosine, 1x proteinase inhibitor (Merck, 5892970001)). Chromatin was then sonicated into 200-400 bp fragments (Covaris M220), in assistance with 0.1% sodium dodecyl sulfate (SDS) or 0.5% SDS (for double cross-linked sample). Supernatant after centrifuging at 12,000 rpm for 10 min at 4 ˚C were flash freezed and kept in -80 ˚C refrigerator.    Keep 10% of chromatin as input, the fragments were immunoprecipitated overnight with antibodies against histone modifications or RNA pol II. Pre-washed Dynabeads protein A or G (ThermoFisher 10002D, or 10004D) was added to the Protein-antibody complexes, and incubated at 4 ˚C for 1 hour. The beads were sequentially washed with buffers as follows: FA-lysis buffer (150 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5 mM sodium deoxycholate), FA high salt buffer (500 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5% sodium deoxycholate) for twice, LiCl buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl, pH 8.0), TE buffer (10 mM Tris-HCl, pH8.0, 1 mM EDTA) for twice. Each washing step was incubated for 5 min at 4 ˚C with rotation. Protein-DNA complexes were eluted by incubation with 250 µl of elution buffer (1% SDS, 100 mM NaHCO3, freshly made) for 15 min at 55 ˚C with periodic gentle vortex. This step was repeated once and eluted sample was combined.    Eluted DNA, as well as input, was reverse cross-linked from protein by adding 20 µl of 5M NaCl to the 500 µl of elution, incubated at 65 ˚C over 8 hours. After digested with RNase at 37 ˚C, proteinase K at 55 ˚C, DNA was extracted by phenol-chloroform method.
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).

value: J1 mouse ES cell

value: embryonic stem cell

tag: tissue

value: inner cell mass

tag: developmental stage

value: embryo, blastocyst

tag: antibody

value: Cell Signaling, 9733S


title: LNCAP-DMSO-6h-rep1

description: Sample 1

tag: disease state


title: WT_24h_R2


title: WT_48h_R3


title: WT_24h_R1


title: WT_12h_R2


title: LNCAP-E7107-6h-rep1

description: Sample 4


title: olrn-1(ums9) rep4

city: Worcester

first: Read

last: Pukkila-Worley

state: MA

address: 364 Plantation Street

department: Medicine

institute: University of Massachusetts Medical School

data_processing:
The quality of raw sequencing data was evaluated by FastQC (Version 0.11.8) and multiqc (Version 1.7). Low-quality reads were trimmed using Trimmomatic (version 0.36). The trimmed reads were mapped to the C.elegans reference genome (WS220/ce11 on UCSC genome website) using HISAT2 (version 2.1.0). Then we use samtools (Version 1.3.1) to convert SAM files to sorted BAM files. GTF (WS220/ce11) annotation file was downloaded from UCSC genome website. The assembled gft file will be generated for each sample by using stringtie (Version 1.3.4). Stringtie will compare each sample against merged assembly and estimate it transcript abundance. Finally, we used stringtie to generate count table for Ballgown analysis. We use Ballgown package from the Bioconductor (Version 3.8) software suite and run custom R script in R console (R Version is 3.5) to analyze the gene differential expression, including: data visualization and inspection, statistical tests for differential expression, and multiple test correction. Differential gene expression was assessed on the multiple samples with the following parameters: fold change (FC) > 2 fold, adjusted P value < 0.05 and RPKM>1.
Genome_build: WS220/ce11
Supplementary_files_format_and_content: excel files include FPKM values for each sequenced sample

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Gravid wild-type and olrn-1(ums9) animals treated with 6% bleach and 5M NaOH to isolate eggs. Eggs from olrn-1(ums9) animals were harvested 18 hours before N2 due to the strain having a developmental delay. Animals were dropped to NGM plates seeded with OP50 and incubated at 20 degrees celcius untill the L4 stage when they were harvested.

extract_protocol:
RNA was isolated using TriReagent (Molecular Research Center, Inc.) and purified with RNeasy columns (Qiagen)
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers were used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

tag: strain


title: 18_108a_mut1

type: RNA

city: Cologne

first: Manolis

last: Pasparakis

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Institute for Genetics

country: Germany

institute: University of Cologne

hyb_protocol: accoring to GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays protocol(thermo Fisher, 2017) for 16h at 45°C, hybridization was performed in a GeneChip Hybridization Oven 645

scan_protocol: Gene chips were scanned using the GeneChip Scanner 7G

data_processing: Array analysis was performed using Affymetrix Expression Console and Transcriptome Analysis Console Software (TAC).

label: biotin

source_name: mouse colon tissue at week 11

label_protocol: labelled ssc-DNA was prepared according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays protocol(thermo Fisher, 2017) from 100 ng total RNA

growth_protocol: Mice were maintained at an SPF animal facility uner a 12h light cycle and given a regular chow diet

extract_protocol: Colon tissues were disrupted using a Precellys 24 (Bertin technologies) and total RNA was extracted using a Nucelospin RNA kit (Macherey-Nagel) according to manufacturer's instructions.

treatment_protocol: Colon tissues were frozen on dry ice immeadiately after collection.

value: NEMO IEC-KO Ripk1 wt/wt

value: colon

tag: age

value: 11 weeks-old


title: HSC-4 EV

city: Chengdu

first: Qianming

last: Chen

state: Sichuan

address: Renmin Nan Street Section 3 NO.14

department: oral medicine

institute: Sichuan University

description:
Gene expression in EV set of OSCC cells
C V

hyb_protocol: Labeled controls and test samples with Cy3-dCTP were dissolved in 80 L hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was performed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA)

data_processing: The array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V12 (Agilent)

source_name: Human oral cancer cell line HSC-4 EV

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction upon using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio)

growth_protocol: Culture oral squamous cell carcinoma cell line (HSC-3 and HSC-4) in Dulbecco’s modified Eagle’s medium (DMEM) supplied with 10% fetal bovine serum and penicilin /streptomycin.

extract_protocol: Total RNA was extracted using Trizol isolation system (Invitrogen) according to manufacturer’s instructions. Total RNA quality was then determined. Reverse transcription was performed using High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems) to get cDNA.

treatment_protocol: HSC-3 and HSC-4 were infected with lentivral EV or overexpressed ORAOV1-B, stably cell lines were generated by puromycin selection.

value: oral squamous cell carcinoma

value: EV lentivirus (control)


title: olrn-1(ums9) rep3


title: BR_2

first: Zhang

last: Huan

address: 2 yuanmingyuan west road

institute: China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference genome of the hexaploid sweet potato Taizhong 6 (https://www.ipomoea-genome.org/) using HISAT 2.0.4.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010.
Genome_build: Taizhong 6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Ipomoea batatas

source_name: leaves

growth_protocol: Plants were cultivated in a greenhouse under a regime of 16 h light and 8 h darkness (28 °C) for one month.

extract_protocol:
Total RNA samples were extracted from the leaves using the TRIzol method (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT, IbBBX24-OE, and IbBBX24-RNAi plants were treated by the spore infection method at 1 dpi.

value: IbBBX24-RNAi line


title: 12_30a_mut1


title: WT_12h_R1


title: 13_31a_mut1


title: 15_107a_mut1


title: 11_16a_mut1


title: OPDA4_kleb

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

data_processing:
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with HISAT2
Summarization of reads was performed with HTSeq-count program
Normalization and differential expression analysis with DESeq2
Genome_build: klebsormidium_Scaffolds_v1.0
http://www.plantmorphogenesis.bio.titech.ac.jp/~algae_genome_project/klebsormidium/
Supplementary_files_format_and_content: Text format with two columns: gene_ID and raw reads per gene

organism: Klebsormidium nitens

source_name: algal suspension

growth_protocol: Droplets of algal suspension from a fully-grown plate were plated on fresh 0.5 Gamborg’s B5 plates and incubated for one month

extract_protocol:
Total RNA was extracted with the Favorgen plant RNA extraction kit including DNAse treatment
The RNA-seq library was prepared by the Beijing Genomics Institute, using standard Illumina protocols.

treatment_protocol: Algal discs were  transferred to a 12-well plate containing 2 ml liquid 0.5 Gamborg’s B5 mock or OPDA 25 µM, incubated for 2 hours on a shaker (120 rpm) and then the algae were frozen in liquid nitrogen and ground to a fine powder.

tag: treatment

value: OPDA

value: 2 hours


title: HSC-4 ORAOV1-B overexpression

description:
Gene expression in ORAOV1-B set of OSCC cells
C V_1

source_name: Human oral cancer cell line HSC-4 overexpressed ORAOV1-B

value: ORAOV1-B overexpression lentivirus


title: 10_55a_WT


title: BR_1


title: BRO11b

type: genomic

city: FIRENZE

first: Stefano

last: MOCALI

state: FI

address: VIA di Lanciola 12/a

department: AA

country: Italy

institute: CREA

hyb_protocol: The labeled target was re-suspended in 120 µl hybridization solution containing 50% formamide, 3 x SSC, 10 µg of unlabeled herring sperm DNA (Promega, Madison, WI), and 0.1% SDS, and the mix was denatured at 95°C for 5 min and kept at 50°C until it was deposited directly onto a microarray. Hybridizations were performed with a TECAN Hybridization Station HS4800 Pro (TECAN, US) according to the manufacturer’s recommended method.

scan_protocol: The hybridized GeoChip 3.0 was scanned with a ScanArray 5000 (Perkin-Elmer, Wellesley, MA, USA) at 95% laser energy and 85% photomultiplier tube gain, and digitally analyzed using Imagene software (6.0 premium version, Biodiscovery, El Segundo, CA, USA)

data_processing: Microarray slides were scanned by a NimbleGen MS200 scanner (Madison, WI, USA) and the signal intensities were digitized from the raw images data, which were uploaded and analyzed using the data analysis pipeline at IEG (http://ieg.ou.edu/microarray) as described previously

organism: soil metagenome

source_name: Vineyard

label_protocol: The DNA was labeled by Cy5 as described by He et al., 2007 (He, Z., Gentry, T. J., Schadt, C. W., Wu, L., Liebich, J., Chong, S. C., ... & Criddle, C. (2007). GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. The ISME journal, 1(1), 67-77.)

extract_protocol: The total genomic DNA was extracted directly from a 5 g soil sample by using a protocol that included liquid nitrogen grinding, freezing and thawing, and treatment with sodium dodecyl sulfate for cell lysis, according with Richard et al., 2001 (Richard AH, Qiu XY, Wu LY, Roh Y, Palumbo AV, Tiedje JM, Zhou JZ: Simultaneous recovery of RNA and DNA from soils and sediments. Appl Environ Microbiol 2001, 67:4495–4503)

tag: soil

tag: derived wine quality

value: Low quality wine (VPS=62)


title: BRO12b

value: High quality wine (VPS=81)


title: BRO11c


title: BO_1

tag: genotype/variation

value: IbBBX24-overexpression line


title: HSC-3 ORAOV1-B overexpression

description:
Gene expression in ORAOV1-B set of OSCC cells
B V_1

source_name: Human oral cancer cell line HSC-3 overexpressed ORAOV1-B

tag: cell type


title: olrn-1(ums9) rep2


title: olrn-1(ums9) rep1


title: BRO11a


title: BRO12c


title: WT_12h_R5

value: Wild type


title: BO_2


title: 8_28a_WT

value: NEMO FL


title: HSC-3 EV

description:
Gene expression in EV set of OSCC cells
B V

source_name: Human oral cancer cell line HSC-3 EV


title: BRO12a


title: OPDA2_kleb


title: N2 rep3

value: wild-type


title: BCK_1

value: wild type


title: 7_22a_WT


title: OPDA1_kleb


title: Mock3_kleb

value: mock


title: N2 rep2


title: 5_56a_mut2

value: NEMO IEC-KO Ripk1 S166A/S166A


title: 6_18a_WT

value: colon


title: 9_29a_WT

value: 11 weeks-old


title: Mock2_kleb


title: Mock1_kleb


title: top2_td_input_rep1

status: Public on Mar 03 2020

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

description:
processed data file:
e46r-top2td-BYAK172-noco_R64_rpa_RPA_nodupl_to_input_SPMR_FE.bedgraph_binned_50_norm.wig

data_processing:
FASTQ files were generated by Illumina basespace   (https://basespace.illumina.com/home/index).
The resulting sequences were aligned to a reference genome (R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database) using Bowtie 2 generating a SAM output file for each sample (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Reads from MySeq were trimmed 25 bp from 3’ and 1 bp from the 5’ end, while reads from NextSeq were  not trimmed.  Command for MySeq reads:   bowtie2 -p 14 -x [path to index folder]  --trim3 25 --trim5 1 -1 [Path and name of R1 fastq file] -2 [Path and name of R2 fastq file] -S [name of the resulting .sam file]     Command for NextSeq reads:   bowtie2 -p 14 -x [path to index folder]  --trim3 0 --trim5 0 -1 [Path and name of R1 fastq file] -2 [Path and name of R2 fastq file] -S [name of the resulting .sam file]
SAM files were then converted into sorted BAM files by using SAMtools (http://samtools.sourceforge.net/):    samtools sort [name of the .sam file generated with bowtie2] -o [name for the resulting .bam file] -O bam -T [name for resulting .bam file wo .bam]
BAM files were used for Model-based Analysis of ChIP-Seq (MACS2). We used the ‘call peak’ function which also generates genome wide score data. These were used to generate fold enrichment tracks. Example command:     macs2 callpeak -t [sorted BAM file from yh2a data]-c  [sorted BAM file from h2a data]-f BAMPE -g 12100000 -n [name for output file] -B -q 0.01 --SPMR
The data then was sorted into 50 bp bins and used for meta data analysis using custom made R programs.
Genome_build: R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database
Supplementary_files_format_and_content: wig

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: top2-td cell cultures for alpha factor release experiments were prepared as described previously -S. A. Schalbetter, S. Mansoubi, A. L. Chambers, J. A. Downs, J. Baxter, Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability. Proceedings of the National Academy of Sciences. 112, E4565–70 (2015).

extract_protocol:
Pellets from 50 ml culture were resuspended in 500 μl SDS buffer (1% SDS, 10 mM EDTA, 5M Tris HCl, cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)). Cells were lysed in a FASTPREP machine, 5 rounds of 1 min at 6.5 power, with 200 μl of 0.5 mm silica beads. Lysate was spun out and IP buffer (0.1% SDS, 1.1% Triton-X-100, 1.2 mM EDTA, 16.7 mM TRIS HCl (pH8), cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)) was added to a final volume of 1 ml. Samples were sonicated using the Focused-Ultrasonicator (Covaris, M220) (Average incident power – 7.5 Watts, Peak Incident Power – 75 Watts, Duty Factor – 10 %, Cycles/Burst – 200, Duration – 20 min). The sample was centrifuged for 20 min at 13,000 rpm at 4°C. Supernatant was then diluted to 1:10 (5 ml total).  50 μl protein A Dynabeads (Invitrogen, 10002D) and 50 μl protein G Dynabeads (Invitrogen, 10004D), were washed 3 times in IP buffer followed by adding to the sample and incubating for 2 h at 4°C. Supernatant was split, with 2X 2 ml being taken to 15 ml Falcon tubes, and 1 ml being kept at -20°C as an input sample. To the two 2 ml samples antibody was added, either H2A 1:500 (active motif) or 1.6 μg/ml H2AP (Abcam), and these were placed on a rotating wheel at 4°C for 15 – 20 h. For experiments where RPA1 ChIP was performed on the same sample, 75 ml starting cultures were used meaning supernatant could be split into 3X 2ml and 1 ml for input, with RPA1 antibody (1:10000, Agrisera) added to one 2 ml aliquot. For experiments where RPA1 ChIP was exclusively performed, 25 ml starting cultures were used to make a split of 1X 2ml for antibody addition and 1ml for input.
A preparation of Dynabeads (Invitrogen), Protein A (30 μl) and Protein G (30 μl), was washed 3 times in IP buffer. This was added to each sample and incubated at 4°C for 4 h. Supernatant was removed and beads were washed at 4°C for 6 min in TSE-150 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 150 mM NaCl), followed by TSE-500 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 500 mM NaCl), followed by LiCl wash (0.25 M LiCl, 1% NP-40, 1% dioxycholate, 1 mM EDTA, 10 mM Tris HCl (pH8)) and finally Tris-EDTA (TE pH8). Elution was carried out in 400 μl elution buffer, for 30 min at room temperature. At the same time 50 μl from the input sample was added to 150 μl of elution buffer. 20 μl of 5 M NaCl and 10 μl of 10 mg/ml proteinase K (Invitrogen) was then added to the input, and 40 μl and 20 μl to the IP samples respectively. These were incubated at 65°C overnight. Then 10 μl of DNase-free RNase (Roche) was added to the input and 20 μl to the IP samples, and they were left at 37°C for 30 min. All DNA was purified with a Qiagen PCR purification kit and eluted in 50 μl for H2A or H2AP or 40 μl for RPA1. DNA amount was measured using the Qubit 2.0 Fluorometer (Life technologies) as per the manufacturer’s instructions.            For H2A or H2AP samples, libraries were prepared using the NEBnext Ultra II library kit (NEB) as per the manufacturer’s instructions. PCR enrichment required 13 cycles. PCR purification was carried out using AMPure XP beads. For RPA1 library preparation 34 ul from the RPA1 samples and 1 ng DNA in 34 ul water from the input were used. 5 µl 10 x NEB2.1 buffer and 5 µl of  random  primers  (8N,  3  mg/ml  stock)  were  added  and  the  samples  were  boiled  at  95°C  for  5  minutes  and  immediately placed  to  ice  for  5  minutes. 5 µl 10 x dNTP with dUTP instead of  dTTP (2  mM each)  and 1 µl T4  polymerase  (NEB)  were  added  and  the  mixture  was  incubated  at 37°C  in  a  thermal  cycler  for  20  min,  and  5  µl  0.5  M  EDTA (pH  8)  was  immediately  added  to  stop  the  reaction.  The resulting dsDNA was used to create libraries using the Ultra II library kit (NEB) as  per  the  manufacturer’s  instructions.

treatment_protocol: Cultures were fixed at 25°C  in  YP  + 1%  formaldehyde  (Sigma)  for  45  min. 125 mM glycine was then added for 5 min. Cells were washed with PBS before being pelleted and frozen in liquid nitrogen.

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100   UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)   leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3   top2-td TOP2 5prime upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub -DHFRL80P-ts - Myc -linker )

tag: chip antibody


title: top2_td_RPA1_rep1


title: top2_td_input_rep3

description:
processed data file:
e57-top2td-BYAK172-noco_R64_rpa_RPA_nodupl_to_input_SPMR_FE.bedgraph_binned_50_norm.wig


title: top2_td_RPA1_rep3


title: top2_td_RPA1_rep2

description:
processed data file:
e54-top2td-BYAK172-noco_R64_rpa_RPA_nodupl_to_input_SPMR_FE.bedgraph_binned_50_norm.wig


title: top2_td_input_rep2


title: 4_27a_mut2


title: degron_background_wt_input_rep3

description:
processed data file:
e56-wt-BYAK171-noco_R64_rpa_RPA_nodupl_to_input_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3


title: N2 rep1


title: degron_background_wt_RPA1_ rep1

description:
processed data file:
e46r-wt-BYAK171-noco_R64_rpa_RPA_nodupl_to_input_SPMR_FE.bedgraph_binned_50_norm.wig


title: IbBBX24_ChIPSeq

data_processing:
Sequencing reads of 100 bp were mapped to the genome of the hexaploid sweet potato Taizhong 6 (http://www.ipomoea-genome.org/) using BWA v0.7.12
Model-based Analysis of ChIP-Seq version (MACS) 2.1.0 was used to implement a peak-finding algorithm to identify regions of IP enrichment
https://www.ipomoea-genome.org/
Genome_build: Taizhong 6
Supplementary_files_format_and_content: wig files were generated

extract_protocol:
The leaves of the OE-16 line infected with Fob at 1 dpi  were ground to a powder in liquid nitrogen and subjected to nuclear isolation   and protein-DNA complexes were isolated with IbBBX24 antibody.
The leaves of the OE-16 line infected with Fob at 1 dpi were used for the ChIP assay. In brief, leaves (approximately 2 g) were cross-linked in 1% formaldehyde under a vacuum. The cross-linking was stopped with 0.125 M Gly. The sample was ground to a powder in liquid nitrogen and subjected to nuclear isolation. Anti-IbBBX24 (1:150 dilutions) antibodies were used to immunoprecipitate the protein-DNA complex, and the precipitated DNA was recovered. The precipitated DNA was sequenced using the Illumina HiSeq 2500 SE50 system according to the manufacturer  s instructions.

treatment_protocol: IbBBX24-OE plants were treated by the spore infection method at 1 dpi.

value: OE-16 line


title: degron_background_wt_RPA1_ rep2

description:
processed data file:
e54-wt-BYAK171-noco_R64_rpa_RPA_nodupl_to_input_SPMR_FE.bedgraph_binned_50_norm.wig


title: cdc45_td_yH2A_rep1

description:
processed data file:
e62-cdc45td-BYAK263-noco_R64_1_1_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100   UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)   leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3   CDC45::cdc45-td (CUP1p-Ub-DHFRts-HA-CDC45)(TRP1)

value: yH2A (1.6 ug/ml final concentration, Abcam, ab181447)


title: degron_background_wt_input_rep2


title: cdc45_td_H2A_rep1


title: GAL1_SMC2_K38I_smc2_td_top2_td_H2A_rep1

description:
processed data file:
N181002_smc2td-k38i-noco_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100    UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)    Leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3    trp1-1::SDM-pFA6a-GAL1-SMC2-K39I-6HA, TRP1    smc2-td SMC2 5prime upstream-100 to -1 replaced with kanMX-tTA (tetR-VP16) -tetO2 -Ub -DHFRts -3xHA extended linker)   top2-td TOP2 5prime upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)


title: 1_94a_mut2


title: 3_33a_mut2


title: coi1opr3_mock vs coi1opr3_OPDA_rep3

hyb_protocol: 825 ng of Cy3 and Hy5 probes were mixed and hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation

scan_protocol: Images were scanned at 2um resolution in an Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and  were with Feature Extraction 9.0 software (Agilent Technologies).

data_processing: Raw intensities were background-subtracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were  normalized by LOWESS algorithm followed by quantile normalization

organism: Arabidopsis thaliana

source_name: 9 day-old seedlings, mock

label_protocol: 200 ng of total RNA were reverse transcribed used T7 primer and the cDNA converted to aRNA using T7 RNA polymerase, incorporating cyanine 3- or cyanine 5-labeled CTP, according to 'Two color Microarray-Based Gene Expression Analysis Protocol' (Agilent)

growth_protocol: Seeds of the double mutant opr3-3 coi1-1 were germinated in Johnson media supplemented with 0.5 µM coronatine, to select homozygous coi1-1 plants, at 21°C under long-day conditions (16-h light/8-h dark)

extract_protocol: Plant tissue (~100 mg) was ground in liquid nitrogen and total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with RNeasy mini kit (Qiagen, 74104).

treatment_protocol: Nine-day-old double homozygous opr3-3 coi1-1 mutant seedlings (N = 20) were transferred in liquid mock solution or in presence of 50 µM OPDA and collected 1 hour after treatment

value: opr3-3 coi1-1

tag: agent

source_name: 9 day-old seedlings, OPDA

value: 50 uM OPDA


title: coi1opr3_mock vs coi1opr3_OPDA_rep1


title: GAL1_SMC2_K38I_smc2_td_top2_td_yH2A_rep1


title: degron_background_wt_RPA1_ rep3


title: GAL1_SMC2_K38I_smc2_td_yH2A_rep1

description:
processed data file:
e61_smc2_td_K38I_500-noco_R64_1_1_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100    UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)    Leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3    trp1-1::SDM-pFA6a-GAL1-SMC2-K39I-6HA, TRP1    smc2-td SMC2 5prime upstream-100 to -1 replaced with kanMX-tTA (tetR-VP16) -tetO2 -Ub -DHFRts -3xHA extended linker)


title: degron_background_wt_input_rep1


title: FSS-HepG2 [1]

first: hongchi

last: Yu

address: No.24 South Section 1, Yihuan Road

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

growth_protocol: All cell lines were cultured under an atmosphere of 5% CO2 at 37°C. HepG2 were cultured in DMEM (GIBCO) medium. The medium is supplemented with 10% fetal bovine serum (FBS, GIBCO), penicillin (100 U/ml), and streptomycin (100 mg/ml).

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions
After agarose gel electrophoresis for quality control and NANODROP check for quantification, total RNA was used to prepare the sequencing library. The quality control of library were conducted by Agilent 2100 and quantified by qPCR.

treatment_protocol: The HepG2 cells were exposed to Fluid shear stress for 8h and the static cultured HepG2 used as control

tag: cell line

value: hepatocellular carcinoma cells

tag: passage

value: fluid shear stress (FSS)


title: HepG2 [HepG2]

value: control


title: sgKLHL14 DMSO 1 24h Rep1

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

data_processing:
Illuma bcl2fastq was used for base calling and demultiplexing
STAR for genome alignment
Htseq-Count for read count
In-house script for normalization as described in manuscript
Genome_build: hg19
Supplementary_files_format_and_content: text file with normalized gene expression values in log2 scale

source_name: ABC DLBCL cell line

growth_protocol: TMD8 Cas-9 cells were established with stable expression of control gRNA or gRNA targeting KLHL14 and cultured in RPMI supplemented with fetal bovine serum and 1% penicillin/streptomycin and 1% L-glutamine.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN, #74104). TruSeq Stranded mRNA Library Prep (illumina) was used with total 1ug to construct seqeuncing libraries.
RNA libraries were prepared with standard illumina manufacture's protocol.

treatment_protocol: Cells were treated with DMSO or Ibrutinib 2nM for 24h before cell lysis for RNA extraction

value: TMD8 cells

tag: genotype

tag: cas9 expression

value: Lentivirally transduced to express Cas9

value: DMSO


title: sgCTRL Ibrutinib 2nM 24h Rep2

value: Ibrutinib 2nM


title: sgKLHL14 Ibrutinib 2nM 24h Rep1


title: sgKLHL14 Ibrutinib 2nM 24h Rep2


title: sgKLHL14 DMSO 1 24h Rep2


title: sgCTRL DMSO 1 24h Rep2


title: sgCTRL Ibrutinib 2nM 24h Rep1


title: GAL1_SMC2_K38I_smc2_td_H2A_rep1


title: sgCTRL DMSO 1 24h Rep1


title: PREMIERE-Trans-SV-007 [scRNA-seq]

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

description: kidney biospecimen were placed in 1 ml Hypothermasol™ (Stemcell Technologies) and immediately transferred to the laboratory and cryopreserved in DMSO containing Cryostor CS 10 (Stemcell Technologies) solution for long term storage in liquid nitrogen

data_processing:
Further data analyses were performed on the CellRanger output data files using Seurat 3 R package. As a quality control step, cells with less than 500 genes per cell were filtered out. The percentage of mitochondrial gene read content has emerged as a quality measure for the cell viability in single-cell studies. High percentage of mitochondrial reads indicates that the cells are less viable, as much of their cytoplasmic mRNAs were lost due to the breakage of plasma membrane during dissociation process. For the tumor-nephrectomy data generated by 10Xgenomics version2, a threshold of < 20% mitochondrial reads per cell was used, whereas, a cutoff of < 50% mitochondrial reads per cell was applied for the data from 10X genomics version 3. It has been observed by us and other groups that for certain tissues, including kidney, 10X genomics version 3 chemistry results in higher percentage of mitochondrial reads irrespective of the viability status of the cells. This issue was circumvented by deeper sequencing of the samples to obtain more genes per cell. After the quality control step, the data from the three sample types (tumor-nephrectomy, surveillance biopsy and pre-perfusion biopsy) were merged and further analyzed. In order to exclude cells that were doublets or multiplets from the analysis, we used a cutoff of > 500 and < 5000 genes per cell.
Genome_build: Grch38
Supplementary_files_format_and_content: read counts

source_name: Surveillance biopsy

extract_protocol:
For tissue dissociation, samples were quickly thawed in a 37˚C waterbath for one minute, transferred to a small dish containing 1 ml DMEM/F12 medium (with L-Glutamine, HEPES, and high glucose) supplemented with 10% heat inactivated FBS, and incubated for 10 minutes at room temperature. Tissue/biopsy samples were cut into 1 mm3 small pieces to increase the surface area before they were transferred to a 1.5 ml tube containing 500 µl DMEM/F12 digestion media containing 125 ng Liberase TL (Sigma) enzyme (conc.: 0.25 mg/mL). Samples were incubated on an orbital shaker (500 rpm) for 12 minutes at 37˚C with a mild trituration step using a wide bore 1000P tip applied after 6 minutes. Digestion was stopped by adding 500 µl DMEM/F12 medium containing 10% FBS and incubated at room temperature for 1 minute. The cell suspension was then filtered through a 30 µl strainer (Milteny Biotech) into a 15 ml conical tube. Remaining solid tissue was passed through the nylon mesh using the rubber end of a 5 ml syringe pestle and the filter was washed with 10 ml DMEM/F12/10%FBS medium. Cells were pelleted by centrifugation for 10 minutes at 200 x g and 4˚C. The supernatant was immediately, completely removed by vacuum suction using a glass Pasteur pipet. The cell pellet was then gently re-suspended in 55 µl DMEM/F12/10%FBS medium and cell viability was analyzed with a Countess II FL automated cell counter exploiting the Trypan Blue dye exclusion method.
Single cell samples were immediately transferred to the University of Michigan Sequencing Core facility (in up to 46 µl DMEM/F12/10%FBS) per sample were added to each channel of a chip on the droplet based high-throughput 10XGenomics™ Chromium™ platform allowing cell lysis, individual cell barcoding, and reverse RNA transcription. We used the 10X Single Cell 3' GEX – version 2 chemistry for all tumor-nephrectomy samples and the enhanced 10X Single Cell 3' GEX – version3 for the more recently processed transplant surveillance biopsies and pre-perfusion biopsies. Single cell library preparation based on 10X Genomics technology  included emulsion breakage, PCR amplification, cDNA fragmentation, oligo adapter and Illumina sample index addition. Libraries have been pooled and sequenced on an Illumina HiSeq4000 platform as asymmetric paired end runs (26x115 bases) with a median of 100 million raw sequencing reads per sample. The output from the sequencer was first processed by CellRanger, the proprietary 10X Chromium single cell gene expression analysis software
Bulk glomerular RNAseq expression data were obtained for 74 participants with biopsy proven FSGS enrolled in the NEPTUNE study. Briefly, mRNA samples were prepared using the Illumina TruSeq mRNA Sample Prep v2 kit (Illumina, San Diego, CA, USA). Multiplex amplification was used to prepare cDNA with a paired‐end read length of 100 bases using an Illumina HiSeq2000 (Illumina Inc., San Diego, CA, USA). RNA‐sequencing was performed by the University of Michigan DNA Sequencing Core (http://seqcore.brcf.med.umich.edu/). Quality of the sequencing data was assessed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Read counts were extracted from the fastq files using HTSeq (version 0.11). The objectives and study design of NEPTUNE can be found in the clinicaltrials.gov database under NCT1209000 (42).

tag: subject status

value: normal/healthy

tag: tissue

value: adult kidney


title: PREMIERE-TN116-17-116-Lib-4a [scRNA-seq]

source_name: Tumor-nephrectory


title: PREMIERE-Trans-SV-005 [scRNA-seq]


title: PREMIERE-TN120-18-696-4 [scRNA-seq]


title: PREMIERE-TN121-18-696-10 [scRNA-seq]


title: PREMIERE-TN117-17-116-Lib-4b [scRNA-seq]


title: PREMIERE-SamplePRE038-1 [scRNA-seq]

source_name: Living donor


title: PREMIERE-SampleTransPRE19025 [scRNA-seq]


title: PREMIERE-SamplePRE027-1 [scRNA-seq]


title: PREMIERE-Hkid-PH-2017-08-25 [scRNA-seq]


title: PREMIERE-Hkid-YY-2017-08-25 [scRNA-seq]


title: PREMIERE-KPMP_Pilot_18342 [scRNA-seq]


title: PREMIERE-Trans-SV-006 [scRNA-seq]


title: PREMIERE-2017-06-28-TN-1 [scRNA-seq]


title: PREMIERE-2017-06-28-TN-2 [scRNA-seq]


title: PREMIERE-17-1606-2-0 [scRNA-seq]


title: G523 NDP second knockdown construct replicate 1

city: Montreal

first: Francois

last: Lefebvre

state: QC

address: 845 Sherbrooke St W

department: Human Genetics

country: Canada

institute: McGill University

description:
C2
PolyA RNA
processed data file: expressions.csv

data_processing:
Illumina HiSeq 4000 PE100 Run Standard processing with HTA, fastq files generation with bcl2fastq.
Quality trimming and adapter clipping with Trimmomatic version 0.36. Parameters ILLUMINACLIP:adapters.fa:2:30:15:8:true TRAILING:30 MINLEN:32
Two-passes alignment with STAR v2.5.3a. Default parameters. Junctions from GRCh37 Ensembl 75.
Htseq count version 0.6.0. -m intersection-nonempty. Exons from GRCh37 Ensembl 75 GTF file.
Genome_build: GRCh37
Supplementary_files_format_and_content: expressions.csv: Comma-separated (no quotes) file containing counts generated by HTseq-count.

source_name: G523 GBM stem cell line

growth_protocol: Standard protocol for expanding patient-derived GBM stem cells in a monolayer culture (see Pollard et al., Cell Stem Cel, 2009).

extract_protocol:
RNeasy mini kit from Qiagen (Cat No./ID: 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols at Génome Québec.

treatment_protocol: Gene knockdown through lentiviral transduction of short-hairpin shRNA constructs.

value: Patient-derived glioblastoma stem cell line

value: NDP second knockdown construct (shNDP-C)


title: G523 NDP second knockdown construct replicate 2

description:
C3
PolyA RNA
processed data file: expressions.csv


title: G523 NDP second knockdown construct replicate 0

description:
C1
PolyA RNA
processed data file: expressions.csv


title: RNAseq-KspCreDKO-3W-WK-2

city: Philadelphia

first: Hongbo

last: Liu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
For WGBS data, after trimming adapter and low-quality reads by Trim Galore Bismark was used for alignment to mouse genome (mm10), deduplication and quantification of methylation level for each CpG site.
For RRBS data, after trimming adapter and low-quality reads by Trim Galore v0.5.0 with option '--rrbs, Bismark v0.19.1 was used for align reads to mouse genome (mm10).
For RNA-seq data, sequencing reads were aligned to mouse genome using STAR v2.2.1 and gene expression was quantified by RSEM v1.3.1. Comprehensive gene annotation (gencode.vM18.annotation.gtf) was obtained from GENCODE database.
Genome_build: mm10
Supplementary_files_format_and_content: For WGBS and RRBS, Bismark coverage file. For RNA-seq, tab-delimited text files include TPM values for each Sample.

source_name: Whole kidney

extract_protocol:
Total RNA from whole kidneys were isolated using the RNeasy mini kit (Qiagen).
Total RNA was used to isolate poly A purified mRNA using the Illumina TruSeq RNA Preparation Kit.

value: kidney

value: post natal day 21

value: KspCre Dnmt3ab f/f


title: G523 scrambled control replicate 0

description:
R3
PolyA RNA
processed data file: expressions.csv

value: scrambled control


title: PREMIERE-17-1606-2-1 [scRNA-seq]


title: YKO1 24 stim

city: Baltimore

first: Liam

last: Chung

address: 400 N Broadway FL5001

department: Oncology

institute: Johns Hopkins University

data_processing:
Raw data QA and preprocessing
Sequence alignment and secondary QA
Data exploration and QA on gene expression
Quantificaton of differentiatl experession and exploratory analysis
Downstream functional analysis
Genome_build: mm9
Supplementary_files_format_and_content: count matrix from each sample

source_name: spleen and lymph node

extract_protocol:
RNA extracted from cell culture
Illumina MiSeq platform

value: Yap KO


title: RNAseq-KspCreDKO-3W-WK-1


title: PREMIERE-18142-5-1 [scRNA-seq]


title: PREMIERE-18-162 [scRNA-seq]


title: PREMIERE-18142-5-2 [scRNA-seq]


title: G523 scrambled control replicate 1

description:
R1
PolyA RNA
processed data file: expressions.csv


title: PREMIERE-18-139 [scRNA-seq]


title: WT1 24 stim

value: WT


title: coi1opr3_mock vs coi1opr3_OPDA_rep2

value: opr3-3 coi1-1

value: mock

value: 50 uM OPDA


title: G523 NDP knockdown construct replicate 2

description:
A1
PolyA RNA
processed data file: expressions.csv

value: NDP first knockdown construct (shNDP-A)


title: PREMIERE-TN109-18-242-Lib [scRNA-seq]


title: WT1 unstim


title: G523 NDP knockdown construct replicate 1

description:
A3
PolyA RNA
processed data file: expressions.csv


title: PREMIERE-Trans-SV-004 [scRNA-seq]


title: BCK_2

value: wild type


title: G523 scrambled control replicate 2

description:
R2
PolyA RNA
processed data file: expressions.csv


title: G411 scrambled control replicate 1

description:
R8
PolyA RNA
processed data file: expressions.csv

source_name: G411 GBM stem cell line


title: RRBS-Six2CreDKO-3W-WK-2

extract_protocol:
Genomic DNA from whole kidney was isolated using DNeasy kit (Qiagen).
Library was generated with isolated DNA using Premium Reduced Representation Bisulfite Sequencing Kit (Diagenode) following manufacturer’s instruction.

value: Six2Cre Dnmt3ab f/f


title: G523 NDP knockdown construct replicate 0

description:
A2
PolyA RNA
processed data file: expressions.csv


title: G411 scrambled control replicate 0

description:
R6
PolyA RNA
processed data file: expressions.csv


title: RNAseq-Control-3W-WK-2

value: Dnmt3ab f/f


title: RNAseq-Control-3W-WK-3


title: G411 NDP knockdown construct replicate 2

description:
A7
PolyA RNA
processed data file: expressions.csv


title: RRBS-Six2CreDKO-3W-WK-1


title: G411 scrambled control replicate 2

description:
R5
PolyA RNA
processed data file: expressions.csv


title: RRBS-Six2CreDKO-3W-WK-3


title: RRBS-KspCreDKO-3W-WK-1


title: G411 NDP second knockdown construct replicate 2

description:
C7
PolyA RNA
processed data file: expressions.csv


title: RRBS-Control-3W-WK-5


title: G411 NDP second knockdown construct replicate 1

description:
C5
PolyA RNA
processed data file: expressions.csv


title: G411 NDP knockdown construct replicate 1

description:
A5
PolyA RNA
processed data file: expressions.csv


title: RRBS-KspCreDKO-3W-WK-3


title: WT rep3

city: Bronx

first: Julio

last: Madrigal-Matute

state: New York

address: 1300 Morris Park Ave, C504

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

data_processing:
The R statistical software environment was used to run the Bioconductor package, DESeq2 to analyze the RNA-Seq data set for differential expression between groups.
Supplementary_files_format_and_content: tab-delimited excel file include RPKM values for each Sample, baseMean, log2FoldChange, lfcSE, stat, pvalue and padj.

source_name: VSMCs

growth_protocol: Aortic vascular smooth muscle cells (VSMC) were isolated from aorta of wild-type (WT). Briefly, adhering fat and connective tissue were removed by blunt dissection from the thoracic aorta. Vessels were opened longitudinally and preincubated in DMEM (Whitaker) containing 1 mg/mL collagenase (type II, 290 U/mg), penicillin (100 U/mL), streptomycin (100 lg/mL), and glutamine (2 mmol/L) (Sigma) for 15 to 20 minutes at 37°C in 95% air/5% CO2. Then aortas were minced into 1-mm pieces, incubated for an additional 1.5 to 2 hours, and rinsed twice with PBS to remove the cells, which were counted and seeded at a concentration of 104 cells/cm2 in plastic culture flashes (Costar) in DMEM with 10% FBS. Cells were harvested for passaging at 2- to 3-day intervals and used between the second and seventh passages. For experimental analysis, cells were made quiescent by 24-hour incubation in medium with 0.5% FBS.

extract_protocol:
VSMCs were harvested using Trizol reagent. Rnaeasy plus mini kit was used to isolate RNA. 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: VSMCs were grown to confluence in growth medium and then serum deprived for 24 h. Then, cells were incubated  with vehicle or with rTWEAK (100 ng/mL) plus 0.5% FBS for 24h.

value: Aortic vascular smooth muscle cells

tag: passages


title: TWEAK rep1

value: wild type +rTWEAK


title: RRBS-KspCreDKO-3W-WK-2


title: G411 NDP second knockdown construct replicate 0

description:
C6
PolyA RNA
processed data file: expressions.csv

value: Patient-derived glioblastoma stem cell line


title: Skin biopsy, PT1163lesional skinDay0

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: One Gustave L. Levy Place, Box 1077

department: Population Health Science and Policy

institute: Icahn School of Medicine at Mount Sinai

description: PF-06700841 100 MG QD (P)

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: preprocessed using GCRMA packages in R/Bioconductor. Adjustement for batch was done using sva::ComBat function.

source_name: lesional skinDay0PF.100

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

tag: subjid

value: lesional skin

tag: time

tag: Sex

value: Male

tag: race

value: ASIAN

tag: ethnicity

value: NOT HISPANIC/LATINO


title: Skin biopsy, PT1163non-lesional skinDay0

description: PF-06700841 100 MG QD (P)

source_name: non-lesional skinDay0PF.100

value: non-lesional skin

tag: treatment

tag: age


title: RRBS-Control-3W-WK-6

tag: strain

value: kidney

value: post natal day 21


title: G411 NDP knockdown construct replicate 0

description:
A8
PolyA RNA
processed data file: expressions.csv

tag: cell type

tag: genotype/variation


title: RRBS-Control-3W-WK-4


title: RRBS-Control-3W-WK-3


title: Skin biopsy, PT1162lesional skinDay0

description: PF-06700841 100 MG QD (P)

value: WHITE


title: Skin biopsy, PT1162lesional skinDay14

description: PF-06700841 100 MG QD (P)

source_name: lesional skinDay14PF.100


title: RRBS-Control-3W-WK-1


title: TWEAK rep3


title: RRBS-Control-3W-WK-2


title: WT rep1


title: MESO18651

city: shenzhen

first: qian

last: he

state: guangdong

address: liuyibu ,luo hu region ,shen zhen city

institute: shenzhen poeple's hospital

data_processing:
Basecalls performed using bcl2fastq version 2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.1.0 with parameters  --dta -t -p 4
Data were filtered using the following specifications:picard-tools-1.115/MarkDuplicates.jar |samtools view -q 20
Fragments Per Kilobase per Million Mapped Fragments (FPKM) were calculated using HTSeq_v0.6.0 from Simon Anders et al., Bioinformatics, 2015. In short, as the script is designed specifically for differential expression analysis, only reads mapping unambiguously to a single gene are counted, whereas reads aligned to multiple positions or overlapping with more than one gene are discarded.
Genome build: hg38
tab-delimited text files include FPKM values for each Sample.

growth_protocol: Trilineage endoderm, mesoderm, and ectoderm differentiation was performed using STEMdiff™ Trilineage specification Kit (STEMCELL Technologies, #05230). Briefly, hESCs were dissociated into single cells by TrypLE™ (ThermoFisher, 12604021) and resuspended in DMEM/F-12 (ThermoFisher, 11330057). After centrifuge at 300 g for 5 minutes, cell pellets were resuspended in mTeSR™1/ Ectoderm Medium with 10 μM Y-27632. The Endoderm /Mesoderm/ Ectoderm Medium was replaced once a day. Endoderm and mesoderm lineages were harvested at day 5, while ectoderm lineage was harvested at day 7.

extract_protocol:
1x10^6 cells, Total RNA was extracted from the harvested cells after by using Trizol (ThermoFisher, 15596026) and the concentration of the total RNA was measured by NanoDrop 2000 (ThermoFisher).NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530L，NEB) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: the IFI16 target sequence sh1865 and its correspondence negative control shNC were inserted into the hU6-MCS-CMV-Puromycin (GV112) plasmid for lentivirus package. The shNC and sh1865 lentivirus were introduced to H9 at MOI of 100.

tag: cell line

value: human embryonic stem cell H9

value: mesoderm

tag: gender

value: female

value: IFI16 knockdown


title: TWEAK rep2


title: Skin biopsy, PT1166non-lesional skinDay0

description: PF-06700841 100 MG QD (P)

value: HISPANIC/LATINO


title: WT rep2

value: wild type


title: Skin biopsy, PT1149lesional skinDay0

description: PF-06700841 100 MG QD (P)


title: ENDO187652

source_name: H9-endoderm_ IFI16sh1865

value: endoderm


title: Skin biopsy, PT1161lesional skinDay14

description: PF-06700841 100 MG QD (P)


title: Skin biopsy, PT1161lesional skinDay0

description: PF-06700841 100 MG QD (P)


title: Skin biopsy, PT1093non-lesional skinDay0

description: PF-06700841 30 MG QD (P)

source_name: non-lesional skinDay0PF.30

value: Female


title: H918652


title: Skin biopsy, PT1162non-lesional skinDay0

description: PF-06700841 100 MG QD (P)


title: ECTO18652

value: ectoderm


title: Skin biopsy, PT1149lesional skinDay28

description: PF-06700841 100 MG QD (P)

source_name: lesional skinDay28PF.100

value: lesional skin


title: ECTO18651


title: Skin biopsy, PT1149lesional skinDay14

description: PF-06700841 100 MG QD (P)

value: Male


title: Skin biopsy, PT1161non-lesional skinDay0

description: PF-06700841 100 MG QD (P)


title: Skin biopsy, PT1161lesional skinDay28

description: PF-06700841 100 MG QD (P)


title: ECTOINPUT

data_processing:
Basecalls performed using bcl2fastq version 2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie2 v2.1.0 with parameters  –N 1 -1 -2
Data were filtered using the following specifications:picard-tools-1.115/MarkDuplicates.jar |samtools view -q 20
peaks were called using macs2 version 2.1.1 with the following setting: -log10(pvalue) (5), Enrichment Fold (1.1), -log10(qvalue) (2.2).
Genome build: hg38
peak files were generated using macs2 v2.1.1

extract_protocol:
1x10^7 cells, fragmentation by sonicator, p53-DNA complexes were enriched with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (IP-202-1024).

tag: antibody


title: MESO18652


title: Skin biopsy, PT1147lesional skinDay14

description: PF-06700841 100 MG QD (P)


title: ENDOINPUT


title: Skin biopsy, PT1147non-lesional skinDay0

description: PF-06700841 100 MG QD (P)


title: ENDO18651


title: H918651


title: ECTO1865_2

source_name: H9-ectoderm_p53_ IFI16sh1865

value: p53 (Santa Cruz, sc-126)


title: ECTONC_2

source_name: H9-ectoderm_p53_ IFI16shNC


title: Skin biopsy, PT1145lesional skinDay14

description: Placebo QD (P)

source_name: lesional skinDay14Placebo

value: Placebo

value: BLACK

value: NOT HISPANIC/LATINO


title: ECTONC_1


title: MESO1865_2

source_name: H9-mesoderm_p53_ IFI16sh1865


title: MESO1865_1


title: Skin biopsy, PT1149non-lesional skinDay0

description: PF-06700841 100 MG QD (P)

value: non-lesional skin


title: Skin biopsy, PT1147lesional skinDay28

description: PF-06700841 100 MG QD (P)

value: WHITE


title: MESOINPUT

value: human embryonic stem cell H9


title: ECTO1865_1


title: MESONC_1

source_name: H9-mesoderm_p53_ IFI16shNC

value: mesoderm


title: Skin biopsy, PT1144lesional skinDay28

description: PF-06700841 100 MG QD (P)

value: OTHER (Pacific Islander)


title: Skin biopsy, PT1147lesional skinDay0

description: PF-06700841 100 MG QD (P)


title: Skin biopsy, PT1145lesional skinDay28

description: Placebo QD (P)

source_name: lesional skinDay28Placebo


title: Skin biopsy, PT1145lesional skinDay0

description: Placebo QD (P)

source_name: lesional skinDay0Placebo


title: Skin biopsy, PT1144non-lesional skinDay0

description: PF-06700841 100 MG QD (P)


title: Skin biopsy, PT1092lesional skinDay28

description: PF-06700841 30 MG QD (P)

source_name: lesional skinDay28PF.30

value: ASIAN


title: Skin biopsy, PT1144lesional skinDay0

description: PF-06700841 100 MG QD (P)


title: S_468_0

city: Vienna

first: Stefanie

last: Berger

address: Schwarzspanierstraße 17

country: Austria

institute: Medical University Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquistion on the sequencing instrument.
On-instrument basecalling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam tools 1.17 (https://github.com/wtsi-npg/illumina2bam)
NGS reads passing vendor quality filtering were aligned to the mm10 reference genome assembly provided by the UCSC Genome Browser based on Genome Reference Consortium GRCm38 with the TopHat2 (v2.1.1, http://genomebiology.com/2013/14/4/R36/abstract) splice junction mapper utilising the Bowtie2 short read aligner (v2.2.9 http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1923.html).
"basic" Ensembl transcript annotation from version e87 (December 2016) served as reference transcriptome. Cufflinks (v2.1.1, http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) allowed for transcriptome assembly, customary including novel transcript structures, on the basis of the reference transcriptome and spliced read alignments, as well as raw transcript quantification.
Before differential expression calling with Cuffdiff (included in Cufflinks v2.1.1, http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html), transcriptome sets of each sample of each group to be compared were combined via the Cuffmerge algorithm.
Finally, the cummeRbund (https://bioconductor.org/packages/release/bioc/html/cummeRbund.html), biomaRt (https://bioconductor.org/packages/release/bioc/html/biomaRt.html) and rtracklayer (https://bioconductor.org/packages/release/bioc/html/rtracklayer.html) Bioconductor packages were utilised in custom R scripts to perform quality assessment and further refine analysis results.
Genome_build: GRCm38 (mm10)

source_name: hippocampus

extract_protocol:
Hipocampus was dissected out of the murine brains. For RNA extraction, Qiagen's miRNEasy Mini kit was used according to manufactors protocol
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

tag: strain background

value: KI (HMBS-deficient)

value: male

value: midbrain dorsal raphe


title: S_502_0


title: ENDO1865_2

source_name: H9-endoderm_p53_ IFI16sh1865

value: endoderm

value: female

value: IFI16 knockdown


title: S_463_0

value: WT (control)


title: S_661_0


title: S_474_0


title: MESONC_2

value: p53 (Santa Cruz, sc-126)


title: S_462_0


title: S_507_0


title: RNAseq-Control-3W-WK-1

source_name: Whole kidney

value: kidney

value: post natal day 21

tag: genotype

value: Dnmt3ab f/f


title: S_652_0

tag: tissue


title: RQ1249


title: S_450_0


title: Skin biopsy, PT1145non-lesional skinDay0

description: Placebo QD (P)

source_name: non-lesional skinDay0Placebo

value: non-lesional skin

value: Placebo

value: Male

value: BLACK

value: NOT HISPANIC/LATINO


title: ENDO1865_1

value: human embryonic stem cell H9


title: Skin biopsy, PT1144lesional skinDay14

description: PF-06700841 100 MG QD (P)

value: lesional skin

value: OTHER (Pacific Islander)


title: Skin biopsy, PT1143lesional skinDay28

description: Placebo QD (P)

value: ASIAN


title: Skin biopsy, PT1143lesional skinDay14

description: Placebo QD (P)


title: ENDONC_2

source_name: H9-endoderm_p53_ IFI16shNC

value: endoderm


title: S_448_0

value: male

value: midbrain dorsal raphe


title: Skin biopsy, PT1143lesional skinDay0

description: Placebo QD (P)


title: S_662_0

value: KI (HMBS-deficient)


title: B73_8dpi_6-1

city: College Station

first: Man

middle: S

last: Kim

state: TX

address: 202N  LF Peterson, Texas A&M Univ., Plant Pathology & Microbiology

department: Plant Pathology & Microbiology

institute: Texas A&M University

data_processing:
RNA sequencing reads were aligned to 'Fusarium verticillioides strain 7600' using TopHat2 and subsequently quantified using HTSeq
Reference genome: Fusarium verticillioides 7600 (Ma et al., 2010)
Since files are paired-end, two corresponding fastq files result in one processed file (i.e., B73_2dpi_1-1_R1.fastq & B73_2dpi_1-1_R2.fastq -> B73_2dpi_1-1.txt)
Supplementary_files_format_and_content: Format is txt and content is read counts

organism: Fusarium verticillioides

source_name: fungal spores

growth_protocol: Maize inbred B73 kernels and maize hybrid 33k44 kernels were inoculated with F. verticillioides wild type and incubated for 2, 4, 6, 8 days

extract_protocol:
For each replicate, 10 inoculated kernels were pooled, and total RNA from kernels was extracted.
Standard QA/QC procedure for RNA samples was implemented and library construction was performed at the Texas A&M AgriLife Research Genomics and Bioinformatics Service (College Station, TX).

treatment_protocol: Fungal spores were inculated directed into maize kernels through sterile needle wounds

tag: inoculum

value: fungal spores

value: infected maize inbred B73 kernels


title: B73_8dpi_4-2


title: B73_8dpi_7-2


title: YKO1 unstim

source_name: spleen and lymph node

value: Yap KO


title: B73_8dpi_7-1


title: B73_8dpi_5-2


title: FSG69 [bulk RNA-seq]

description: Raw reads extracted using HTSeq from the  single end fastq files generated from glomerular fraction of disease biopsy tissue of FSGS patient

source_name: disease biopsy

tag: subject status

value: patient with Focal Segmental Glomerulosclerosis (FSGS) glomerular disease

value: adult kidney


title: FSG70 [bulk RNA-seq]


title: B73_8dpi_3-2


title: B73_8dpi_5-1


title: B73_8dpi_3-1


title: B73_8dpi_4-1


title: Skin biopsy, PT1092lesional skinDay14

description: PF-06700841 30 MG QD (P)

source_name: lesional skinDay14PF.30

tag: subjid

tag: time

value: Female


title: FSG74 [bulk RNA-seq]


title: Skin biopsy, PT1130lesional skinDay14

description: Placebo QD (P)

value: Placebo

tag: Sex

value: Male

tag: race

value: WHITE

value: HISPANIC/LATINO


title: B73_8dpi_2-2


title: Skin biopsy, PT1130lesional skinDay28

description: Placebo QD (P)

value: lesional skin

tag: treatment

tag: ethnicity


title: FSG71 [bulk RNA-seq]


title: FSG67 [bulk RNA-seq]


title: ENDONC_1

value: human embryonic stem cell H9

value: female

value: p53 (Santa Cruz, sc-126)


title: B73_8dpi_6-2


title: B73_6dpi_6-1


title: FSG66 [bulk RNA-seq]


title: FSG65 [bulk RNA-seq]


title: B73_8dpi_1-1


title: B73_6dpi_6-2


title: B73_6dpi_5-2


title: B73_8dpi_1-2


title: Skin biopsy, PT1129lesional skinDay28

description: PF-06700841 30 MG QD (P)

tag: age

value: NOT HISPANIC/LATINO


title: Skin biopsy, PT1129lesional skinDay14

description: PF-06700841 30 MG QD (P)


title: B73_6dpi_5-1


title: Skin biopsy, PT1130non-lesional skinDay0

description: Placebo QD (P)

value: non-lesional skin


title: Skin biopsy, PT1129lesional skinDay0

description: PF-06700841 30 MG QD (P)

source_name: lesional skinDay0PF.30


title: B73_8dpi_2-1


title: B73_6dpi_4-2


title: B73_6dpi_4-1


title: FSG64 [bulk RNA-seq]


title: B73_6dpi_3-2


title: FSG63 [bulk RNA-seq]


title: B73_6dpi_3-1


title: B73_6dpi_2-2


title: Skin biopsy, PT1143non-lesional skinDay0

description: Placebo QD (P)

value: ASIAN


title: Skin biopsy, PT1129non-lesional skinDay0

description: PF-06700841 30 MG QD (P)

source_name: non-lesional skinDay0PF.30


title: Skin biopsy, PT1127lesional skinDay28

description: PF-06700841 30 MG QD (P)


title: FSG62 [bulk RNA-seq]


title: B73_6dpi_2-1

value: fungal spores


title: B73_6dpi_1-2

value: infected maize inbred B73 kernels


title: B73_6dpi_1-1


title: FSG59 [bulk RNA-seq]


title: Skin biopsy, PT1127lesional skinDay14

description: PF-06700841 30 MG QD (P)


title: FSG60 [bulk RNA-seq]


title: FSG61 [bulk RNA-seq]


title: Skin biopsy, PT1092lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: FSG58 [bulk RNA-seq]


title: B73_4dpi_6-2


title: B73_4dpi_7-2


title: 2_95a_mut2

first: Manolis

last: Pasparakis

address: Joseph Stelzmann Strasse, 26

data_processing: Array analysis was performed using Affymetrix Expression Console and Transcriptome Analysis Console Software (TAC).

source_name: mouse colon tissue at week 11

extract_protocol: Colon tissues were disrupted using a Precellys 24 (Bertin technologies) and total RNA was extracted using a Nucelospin RNA kit (Macherey-Nagel) according to manufacturer's instructions.

value: NEMO IEC-KO Ripk1 S166A/S166A

value: colon

value: 11 weeks-old


title: B73_4dpi_6-1


title: Skin biopsy, PT1127lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: FSG57 [bulk RNA-seq]

value: patient with Focal Segmental Glomerulosclerosis (FSGS) glomerular disease

value: adult kidney


title: B73_4dpi_5-2


title: B73_4dpi_7-1


title: B73_4dpi_4-2


title: FSG56 [bulk RNA-seq]


title: Skin biopsy, PT1130lesional skinDay0

description: Placebo QD (P)

value: Placebo

value: Male


title: B73_4dpi_3-2


title: B73_4dpi_4-1


title: Skin biopsy, PT1127non-lesional skinDay0

description: PF-06700841 30 MG QD (P)

value: WHITE


title: Skin biopsy, PT1120lesional skinDay28

description: PF-06700841 30 MG QD (P)

value: lesional skin


title: Skin biopsy, PT1120lesional skinDay14

description: PF-06700841 30 MG QD (P)


title: Skin biopsy, PT1120non-lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: B73_4dpi_2-2


title: FSG51 [bulk RNA-seq]


title: FSG52 [bulk RNA-seq]


title: B73_4dpi_2-1


title: B73_4dpi_1-1


title: B73_4dpi_5-1


title: B73_2dpi_7-1


title: FSG49 [bulk RNA-seq]


title: FSG50 [bulk RNA-seq]


title: Skin biopsy, PT1120lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: B73_2dpi_7-2


title: B73_2dpi_6-1


title: B73_2dpi_5-2


title: B73_2dpi_6-2


title: FSG54 [bulk RNA-seq]


title: FSG48 [bulk RNA-seq]


title: B73_2dpi_5-1


title: B73_4dpi_3-1


title: FSG47 [bulk RNA-seq]


title: B73_2dpi_4-2


title: FSG45 [bulk RNA-seq]


title: B73_2dpi_3-2


title: B73_4dpi_1-2


title: B73_2dpi_2-2


title: B73_2dpi_2-1


title: B73_2dpi_1-2


title: B73_2dpi_3-1


title: 33K44_8dpi_7-2

value: infected maize hybrid 33k44 kernels


title: 33K44_8dpi_6-2


title: 33K44_8dpi_7-1


title: B73_2dpi_4-1


title: 33K44_8dpi_6-1


title: 33K44_8dpi_5-2


title: 33K44_8dpi_5-1


title: 33K44_8dpi_4-2


title: FSG44 [bulk RNA-seq]


title: FSG42 [bulk RNA-seq]


title: FSG41 [bulk RNA-seq]


title: FSG40 [bulk RNA-seq]


title: FSG39 [bulk RNA-seq]


title: B73_2dpi_1-1


title: FSG43 [bulk RNA-seq]


title: 33K44_8dpi_4-1


title: 33K44_8dpi_3-2


title: FSG38 [bulk RNA-seq]


title: Skin biopsy, PT1118lesional skinDay28

description: Placebo QD (P)

value: BLACK


title: FSG37 [bulk RNA-seq]


title: 33K44_8dpi_3-1


title: 33K44_8dpi_2-2


title: 33K44_8dpi_2-1


title: 33K44_6dpi_6-2


title: 33K44_8dpi_1-2


title: Skin biopsy, PT1117non-lesional skinDay0

description: PF-06700841 30 MG QD (P)

value: HISPANIC/LATINO


title: 33K44_8dpi_1-1


title: Skin biopsy, PT1118non-lesional skinDay0

description: Placebo QD (P)

value: NOT HISPANIC/LATINO


title: Skin biopsy, PT1112lesional skinDay0

description: Placebo QD (P)


title: Skin biopsy, PT1092non-lesional skinDay0

description: PF-06700841 30 MG QD (P)

value: non-lesional skin

value: Female


title: 33K44_6dpi_5-2

value: fungal spores


title: 33K44_6dpi_5-1


title: Skin biopsy, PT1117lesional skinDay28

description: PF-06700841 30 MG QD (P)


title: Skin biopsy, PT1112lesional skinDay14

description: Placebo QD (P)

source_name: lesional skinDay14Placebo

value: ASIAN


title: Skin biopsy, PT1112lesional skinDay28

description: Placebo QD (P)


title: FSG35 [bulk RNA-seq]


title: Skin biopsy, PT1118lesional skinDay0

description: Placebo QD (P)


title: FSG36 [bulk RNA-seq]


title: FSG34 [bulk RNA-seq]


title: FSG33 [bulk RNA-seq]


title: 33K44_6dpi_4-2


title: Skin biopsy, PT1109lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: Skin biopsy, PT1117lesional skinDay14

description: PF-06700841 30 MG QD (P)


title: Skin biopsy, PT1108lesional skinDay14

description: Placebo QD (P)


title: Skin biopsy, PT1117lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: Skin biopsy, PT1112non-lesional skinDay0

description: Placebo QD (P)


title: Skin biopsy, PT1109non-lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: Skin biopsy, PT1118lesional skinDay14

description: Placebo QD (P)


title: Skin biopsy, PT1091lesional skinDay28

description: PF-06700841 30 MG QD (P)


title: Skin biopsy, PT1108lesional skinDay0

description: Placebo QD (P)


title: Skin biopsy, PT1108lesional skinDay28

description: Placebo QD (P)


title: 33K44_6dpi_4-1


title: FSG32 [bulk RNA-seq]


title: 33K44_6dpi_6-1


title: 33K44_6dpi_3-2


title: 33K44_6dpi_3-1


title: FSG31 [bulk RNA-seq]


title: 33K44_6dpi_2-2


title: 33K44_6dpi_2-1


title: 33K44_6dpi_1-1


title: FSG30 [bulk RNA-seq]


title: 33K44_4dpi_7-2


title: 33K44_4dpi_7-1


title: 33K44_4dpi_6-2


title: FSG27 [bulk RNA-seq]


title: FSG28 [bulk RNA-seq]


title: 33K44_4dpi_6-1


title: 33K44_4dpi_5-2


title: FSG26 [bulk RNA-seq]


title: 33K44_4dpi_5-1


title: nf1-pat

city: St Louis

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

description: run_1409_s_6_withindex_sequence.txt_CCGATTA

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
The raw gene count matrix was imported into Partek Flow software, version 8.0. Normalization size factors were calculated for all gene counts by CPM to adjust for differences in sequencing depth. Ribosomal genes and genes not expressed in the smallest group size minus samples greater than one count-per-million were excluded from further analysis.
Gene-specific analysis was then performed using the lognormal with shrinkage model (limma-trend method) to analyze for differential expression between the three groups of samples
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing normalized gene counts for each sample and also output from GSA differential analysis

source_name: hiPSC-derived NPCs_nf1

growth_protocol: Cells were grown in NPC maturation media (50% DMEM/F12, 50% Neurobasal medium supplemented with N2, B27, 2mM GlutaMax, 10ng/mL hLIF, 3µM CHIR99021 and 2µM SB431541)

extract_protocol:
QIAGEN Rneasy mini kit
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq

treatment_protocol: no treatment

tag: cell type

value: hiPSC-derived neural progenitor cells

tag: passage

value: NF1 mutation (1185+1G>A)


title: ctl-pat

description: run_1409_s_6_withindex_sequence.txt_CTTGGAA

source_name: hiPSC-derived NPCs_control

tag: genotype/variation

value: no NF1 mutation (control; CTL)


title: nf8-pat

description: run_1409_s_6_withindex_sequence.txt_GGCAGCG

source_name: hiPSC-derived NPCs_nf8

value: NF1 mutation (16513T>A)


title: 33K44_6dpi_1-2


title: FSG29 [bulk RNA-seq]

value: patient with Focal Segmental Glomerulosclerosis (FSGS) glomerular disease

value: adult kidney


title: 33K44_4dpi_4-2


title: nf8-2

description: nf8-2.CAGAAGTTAG-GAAGCGGTCA.CAGAAGTTAG-GAAGCGGTCA_S26

value: NF1 mutation (6513T>A)


title: nf8-3

description: nf8-3.CCACTGAGCT-ACCTGTCTTG.CCACTGAGCT-ACCTGTCTTG_S35


title: Skin biopsy, PT1108non-lesional skinDay0

description: Placebo QD (P)

value: Placebo

value: Male

value: WHITE


title: FSG24 [bulk RNA-seq]


title: 33K44_4dpi_4-1

value: infected maize hybrid 33k44 kernels


title: FSG23 [bulk RNA-seq]


title: nf8-1

description: nf8-1.GCTCATTGTA-TATGGTTCTC.GCTCATTGTA-TATGGTTCTC_S59


title: Skin biopsy, PT1104lesional skinDay14

description: PF-06700841 30 MG QD (P)

value: lesional skin


title: Skin biopsy, PT1106lesional skinDay14

description: PF-06700841 30 MG QD (P)

value: NOT HISPANIC/LATINO


title: Skin biopsy, PT1104lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: FSG25 [bulk RNA-seq]


title: Skin biopsy, PT1106lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: nf1-3

description: nf1-3.TCTAGAGTGC-TTCCTCACGT.TCTAGAGTGC-TTCCTCACGT_S73


title: Skin biopsy, PT1106non-lesional skinDay0

description: PF-06700841 30 MG QD (P)

value: non-lesional skin


title: Skin biopsy, PT1091lesional skinDay14

description: PF-06700841 30 MG QD (P)

value: HISPANIC/LATINO


title: FSG21 [bulk RNA-seq]


title: FSG20 [bulk RNA-seq]


title: 33K44_4dpi_3-1

value: fungal spores


title: Skin biopsy, PT1102lesional skinDay14

description: PF-06700841 30 MG QD (P)

value: ASIAN


title: nf1-2

description: nf1-3.AACTCCAAGA-CTCACTACTC.AACTCCAAGA-CTCACTACTC_S4

value: hiPSC-derived neural progenitor cells


title: Skin biopsy, PT1104non-lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: 33K44_4dpi_2-2


title: FSG19 [bulk RNA-seq]


title: Skin biopsy, PT1102non-lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: ctl-3

description: ctl-3.GTACCGGATA-AGTGAAGCGC.GTACCGGATA-AGTGAAGCGC_S61


title: 33K44_4dpi_1-2


title: nf1-1

description: nf1-2.CGGAGCGATA-CTTAACAAGG.CGGAGCGATA-CTTAACAAGG_S57

value: NF1 mutation (1185+1G>A)


title: 33K44_4dpi_3-2


title: FSG22 [bulk RNA-seq]


title: FSG18 [bulk RNA-seq]


title: FSG17 [bulk RNA-seq]


title: ctl-2

description: ctl-2.AAGGACCGCA-ATGAGAGAGA.AAGGACCGCA-ATGAGAGAGA_S5

value: no NF1 mutation (control; CTL)


title: 33K44_4dpi_1-1


title: 33K44_2dpi_7-2


title: Skin biopsy, PT1102lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: Skin biopsy, PT1100non-lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: Skin biopsy, PT1100lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: 33K44_4dpi_2-1


title: eco1_1_top2_td_H2A_rep2

description:
processed data file:
N180214_eco1-top2td-2_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

data_processing:
FASTQ files were generated by Illumina basespace   (https://basespace.illumina.com/home/index).
The resulting sequences were aligned to a reference genome (R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database) using Bowtie 2 generating a SAM output file for each sample (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Reads from MySeq were trimmed 25 bp from 3’ and 1 bp from the 5’ end, while reads from NextSeq were  not trimmed.  Command for MySeq reads:   bowtie2 -p 14 -x [path to index folder]  --trim3 25 --trim5 1 -1 [Path and name of R1 fastq file] -2 [Path and name of R2 fastq file] -S [name of the resulting .sam file]     Command for NextSeq reads:   bowtie2 -p 14 -x [path to index folder]  --trim3 0 --trim5 0 -1 [Path and name of R1 fastq file] -2 [Path and name of R2 fastq file] -S [name of the resulting .sam file]
SAM files were then converted into sorted BAM files by using SAMtools (http://samtools.sourceforge.net/):    samtools sort [name of the .sam file generated with bowtie2] -o [name for the resulting .bam file] -O bam -T [name for resulting .bam file wo .bam]
BAM files were used for Model-based Analysis of ChIP-Seq (MACS2). We used the ‘call peak’ function which also generates genome wide score data. These were used to generate fold enrichment tracks. Example command:     macs2 callpeak -t [sorted BAM file from yh2a data]-c  [sorted BAM file from h2a data]-f BAMPE -g 12100000 -n [name for output file] -B -q 0.01 --SPMR
The data then was sorted into 50 bp bins and used for meta data analysis using custom made R programs.
Genome_build: R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database
Supplementary_files_format_and_content: wig

source_name: Saccharomyces cerevisiae

extract_protocol:
Pellets from 50 ml culture were resuspended in 500 μl SDS buffer (1% SDS, 10 mM EDTA, 5M Tris HCl, cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)). Cells were lysed in a FASTPREP machine, 5 rounds of 1 min at 6.5 power, with 200 μl of 0.5 mm silica beads. Lysate was spun out and IP buffer (0.1% SDS, 1.1% Triton-X-100, 1.2 mM EDTA, 16.7 mM TRIS HCl (pH8), cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)) was added to a final volume of 1 ml. Samples were sonicated using the Focused-Ultrasonicator (Covaris, M220) (Average incident power – 7.5 Watts, Peak Incident Power – 75 Watts, Duty Factor – 10 %, Cycles/Burst – 200, Duration – 20 min). The sample was centrifuged for 20 min at 13,000 rpm at 4°C. Supernatant was then diluted to 1:10 (5 ml total).  50 μl protein A Dynabeads (Invitrogen, 10002D) and 50 μl protein G Dynabeads (Invitrogen, 10004D), were washed 3 times in IP buffer followed by adding to the sample and incubating for 2 h at 4°C. Supernatant was split, with 2X 2 ml being taken to 15 ml Falcon tubes, and 1 ml being kept at -20°C as an input sample. To the two 2 ml samples antibody was added, either H2A 1:500 (active motif) or 1.6 μg/ml H2AP (Abcam), and these were placed on a rotating wheel at 4°C for 15 – 20 h. For experiments where RPA1 ChIP was performed on the same sample, 75 ml starting cultures were used meaning supernatant could be split into 3X 2ml and 1 ml for input, with RPA1 antibody (1:10000, Agrisera) added to one 2 ml aliquot. For experiments where RPA1 ChIP was exclusively performed, 25 ml starting cultures were used to make a split of 1X 2ml for antibody addition and 1ml for input.
A preparation of Dynabeads (Invitrogen), Protein A (30 μl) and Protein G (30 μl), was washed 3 times in IP buffer. This was added to each sample and incubated at 4°C for 4 h. Supernatant was removed and beads were washed at 4°C for 6 min in TSE-150 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 150 mM NaCl), followed by TSE-500 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 500 mM NaCl), followed by LiCl wash (0.25 M LiCl, 1% NP-40, 1% dioxycholate, 1 mM EDTA, 10 mM Tris HCl (pH8)) and finally Tris-EDTA (TE pH8). Elution was carried out in 400 μl elution buffer, for 30 min at room temperature. At the same time 50 μl from the input sample was added to 150 μl of elution buffer. 20 μl of 5 M NaCl and 10 μl of 10 mg/ml proteinase K (Invitrogen) was then added to the input, and 40 μl and 20 μl to the IP samples respectively. These were incubated at 65°C overnight. Then 10 μl of DNase-free RNase (Roche) was added to the input and 20 μl to the IP samples, and they were left at 37°C for 30 min. All DNA was purified with a Qiagen PCR purification kit and eluted in 50 μl for H2A or H2AP or 40 μl for RPA1. DNA amount was measured using the Qubit 2.0 Fluorometer (Life technologies) as per the manufacturer’s instructions.            For H2A or H2AP samples, libraries were prepared using the NEBnext Ultra II library kit (NEB) as per the manufacturer’s instructions. PCR enrichment required 13 cycles. PCR purification was carried out using AMPure XP beads. For RPA1 library preparation 34 ul from the RPA1 samples and 1 ng DNA in 34 ul water from the input were used. 5 µl 10 x NEB2.1 buffer and 5 µl of  random  primers  (8N,  3  mg/ml  stock)  were  added  and  the  samples  were  boiled  at  95°C  for  5  minutes  and  immediately placed  to  ice  for  5  minutes. 5 µl 10 x dNTP with dUTP instead of  dTTP (2  mM each)  and 1 µl T4  polymerase  (NEB)  were  added  and  the  mixture  was  incubated  at 37°C  in  a  thermal  cycler  for  20  min,  and  5  µl  0.5  M  EDTA (pH  8)  was  immediately  added  to  stop  the  reaction.  The resulting dsDNA was used to create libraries using the Ultra II library kit (NEB) as  per  the  manufacturer’s  instructions.

tag: strain

value: Mata ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3  top2-td TOP2 5prime upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)  eco1-1 (G211H)

tag: chip antibody


title: FSG15 [bulk RNA-seq]

value: patient with Focal Segmental Glomerulosclerosis (FSGS) glomerular disease


title: Skin biopsy, PT1098lesional skinDay28

description: PF-06700841 30 MG QD (P)

source_name: lesional skinDay28PF.30


title: 33K44_2dpi_7-1


title: Skin biopsy, PT1098lesional skinDay14

description: PF-06700841 30 MG QD (P)


title: eco1_1_top2_td_yH2A_rep2

value: yH2A (1.6 ug/ml final concentration, Abcam, ab181447)


title: 33K44_2dpi_6-2


title: FSG14 [bulk RNA-seq]

value: adult kidney


title: eco1_1_top2_td_H2A_rep1

description:
processed data file:
N180124_eco1-top2td_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig


title: Skin biopsy, PT1098lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: 33K44_2dpi_6-1


title: FSG12 [bulk RNA-seq]


title: Skin biopsy, PT1098non-lesional skinDay0

description: PF-06700841 30 MG QD (P)


title: eco1_1_top2_td_yH2A_rep1


title: ctl-1

description: ctl-1.TCTCTAGCGC-CTGCTTGACG.TCTCTAGCGC-CTGCTTGACG_S76


title: FSG13 [bulk RNA-seq]


title: FSG11 [bulk RNA-seq]


title: 33K44_2dpi_5-1


title: Skin biopsy, PT1097lesional skinDay28

description: Placebo QD (P)

source_name: lesional skinDay28Placebo

value: Placebo

value: Female


title: Skin biopsy, PT1091lesional skinDay0

description: PF-06700841 30 MG QD (P)

value: Male

value: WHITE


title: 33K44_2dpi_4-2

value: infected maize hybrid 33k44 kernels


title: FSG10 [bulk RNA-seq]


title: eco1_1_yH2A_rep2

description:
processed data file:
N180214_eco1-830-2_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3  eco1-1 (G211H)


title: Skin biopsy, PT1097lesional skinDay0

description: Placebo QD (P)

source_name: lesional skinDay0Placebo

value: lesional skin


title: FSG9 [bulk RNA-seq]


title: eco1_1_H2A_rep1

description:
processed data file:
N180124_eco1-830_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig


title: eco1_1_yH2A_rep1


title: FSG8 [bulk RNA-seq]

description: Raw reads extracted using HTSeq from the  single end fastq files generated from glomerular fraction of disease biopsy tissue of FSGS patient


title: 33K44_2dpi_5-2


title: 33K44_2dpi_3-2


title: degron_background_wt_RPA1_ HU

description:
Cells were released from alpha factor block to 200 mM HU for 60 mins
processed data file:
e53_60min_BYAK171-wt-HU_to_wt_rpa_nodupl_to_input_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3


title: degron_background_wt_input_HU


title: FSG6 [bulk RNA-seq]


title: 33K44_2dpi_3-1

value: fungal spores


title: Skin biopsy, PT1097lesional skinDay14

description: Placebo QD (P)

value: HISPANIC/LATINO


title: 33K44_2dpi_2-2


title: 33K44_2dpi_4-1


title: FSG7 [bulk RNA-seq]


title: cdc45_td_top2_td_H2A_rep2

description:
processed data file:
N190226_AK265-cdc45td-top2td-noco-2_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100   UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)   leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3   CDC45::cdc45-td (CUP1p-Ub-DHFRts-HA-CDC45)(TRP1)   top2-td TOP2 5prime upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)


title: FSG5 [bulk RNA-seq]


title: 33K44_2dpi_2-1


title: FSG4 [bulk RNA-seq]


title: Skin biopsy, PT1095lesional skinDay28

description: Placebo QD (P)


title: 33K44_2dpi_1-1


title: Skin biopsy, PT1095lesional skinDay0

description: Placebo QD (P)


title: Skin biopsy, PT1095lesional skinDay14

description: Placebo QD (P)


title: cdc45_td_top2_td_H2A_rep1

description:
processed data file:
N190123_AK265-cdc45-top2_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig


title: FSG3 [bulk RNA-seq]


title: Skin biopsy, PT1094lesional skinDay0

description: PF-06700841 30 MG QD (P)

value: BLACK

value: NOT HISPANIC/LATINO


title: Skin biopsy, PT1097non-lesional skinDay0

description: Placebo QD (P)

source_name: non-lesional skinDay0Placebo

value: non-lesional skin


title: P5 Sox9Cre; Ror2f/f rep3

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

institute: University of California, San Francisco

description: Sox9Cre-Ror2 at P5.txt

data_processing:
Remove adaptor, align the reading to genome and create table counts
Generate DEG table with DeSeq2 in R
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: lung left lobe

extract_protocol:
The left lung lobe from control and mutant mice were homogenized in 1 ml TRIzol(Life Technologies) and 200 μl chloroform was then added. After centrifugation, the upper aqueous layer was removed and mixed with an equal volume of 70% ethanol. RNA was extracted with the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA quality was evaluated using the Agilent 2100 Bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse lung

tag: developmental stage

value: postnatal day 5

value: Sox9Cre/+; Ror2f/f


title: Skin biopsy, PT1095non-lesional skinDay0

description: Placebo QD (P)

value: Placebo


title: cdc45_td_top2_td_yH2A_rep1

tag: genotype

value: yH2A (1.6 ug/ml final concentration, Abcam, ab181447)


title: FSG2 [bulk RNA-seq]

value: patient with Focal Segmental Glomerulosclerosis (FSGS) glomerular disease

tag: tissue

value: adult kidney


title: Skin biopsy, PT1094non-lesional skinDay0

description: PF-06700841 30 MG QD (P)

value: Male


title: P5 Sox9Cre; Ror2f/f rep2

description: Sox9Cre-Ror2 at P5.txt


title: cdc45_td_H2A_rep2

description:
processed data file:
N190425_ak263-cdc45td-noco_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100   UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)   leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3   CDC45::cdc45-td (CUP1p-Ub-DHFRts-HA-CDC45)(TRP1)


title: FSG1 [bulk RNA-seq]


title: P5 Sox9Cre; Ror2f/f rep1

description: Sox9Cre-Ror2 at P5.txt


title: cdc45_td_yH2A_rep2


title: cdc45_td_top2_td_yH2A_rep2


title: GAL1_SMC2_K38I_smc2_td_top2_td_H2A_rep2

description:
processed data file:
N181002_smc2td-k38i-top2td-noco_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100    UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)    Leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3    trp1-1::SDM-pFA6a-GAL1-SMC2-K39I-6HA, TRP1    smc2-td SMC2 5prime upstream-100 to -1 replaced with kanMX-tTA (tetR-VP16) -tetO2 -Ub -DHFRts -3xHA extended linker)   top2-td TOP2 5prime upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)


title: P5 Control(Ror2) rep3

description: Sox9Cre-Ror2 at P5.txt

value: WT


title: Skin biopsy, PT1167lesional skinDay14

description: Placebo QD (P)

value: lesional skin

value: WHITE


title: P5 Control(Ror2) rep2

description: Sox9Cre-Ror2 at P5.txt


title: E. multilocularis- infected mouse 2

city: bern

first: Ghalia

last: Boubaker

state: Bern

address: Länggassstrasse, 122

department: INSTITUT OF PARASITOLOGY

country: Switzerland

institute: UNIVERSITY OF BERN

data_processing:
de-multiplexing and trimming of the TriLink adapter residuals (Illumina bcl2fastq v2 analysis software.
Quality of reads was checked with the software FastQC (v. 0.11.5)
Clean reads of samples derived from the same experimental group (AE-1pm or ctr-1pm) were pooled together and then dereplicated using the software usearch (v. 8.1.1681). This resulted in a list of unique sequences that were annotated and recorded based on their frequency of occurrence.
Mapping of cleaned reads using the RNA mapping software STAR (v. 2.5.1b).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: 1-month E. multilocularis- infected mice

growth_protocol: Ten 8-week-old female C57BL/6 mice

extract_protocol:
The obtained liver tissues were minced quickly, mixed at a ratio of 1:10 with QIAzol lysis reagent and homogenized by bead beating. Total RNA was extracted according to the manufacturer’s instruction of the QIAzol lysis reagent with the exception that chloroform was replaced by 1-bromo-3-chloropropane for the phase separation step. To remove genomic DNA contamination in RNA samples, an enzymatic digestion step using DNase I was carried out. Finally, total RNA was re-suspended in RNase-free water. RNA quantity and RNA quality number (RQN ≥ 8) was determined by the Fragment Analyzer CE12.
Five libraries were generated from five mice (three mice from E. multilocularis-infected group and two mice from the uninfected control group). The total RNA was checked on an Agilent 2100 Bioanalyzer instrument for degradation. Subsequently, the CleanTag Ligation Kit (was used to prepare small RNA stranded libraries from total RNA (1µg RNA per library). Libraries were analyzed a second time on the Bioanalyzer to check for the expected miRNAs fragment peak at 141 bp and subsequently a Sage Science Pippin Prep instrument was used to select the expected fragment size range. In a last step before the deep sequencing, the quality and concentration of each final library (the eluted 141 bp band) were submitted to PicoGreen analysis.

treatment_protocol: The animals were divided into two groups: The control group remained uninfected, and the other group was orally infected with E. multilocularis eggs.

value: female

value: E. multilocularis- infected

tag: infection stage

value: 1 month

value: liver

tag: molecule subtype

value: small RNA


title: E. multilocularis- infected mouse 5


title: GAL1_SMC2_K38I_smc2_td_top2_td_yH2A_rep2


title: Skin biopsy, PT1167non-lesional skinDay0

description: Placebo QD (P)

tag: subjid

value: non-lesional skin

value: NOT HISPANIC/LATINO


title: Skin biopsy, PT1167lesional skinDay0

description: Placebo QD (P)

tag: time

value: Placebo


title: Skin biopsy, PT1166lesional skinDay28

description: PF-06700841 100 MG QD (P)

source_name: lesional skinDay28PF.100

tag: Sex

value: HISPANIC/LATINO


title: P5 Control(Ror2) rep1

description: Sox9Cre-Ror2 at P5.txt

value: mouse lung

value: postnatal day 5


title: E. multilocularis- infected mouse 3


title: Skin biopsy, PT1166lesional skinDay0

description: PF-06700841 100 MG QD (P)

source_name: lesional skinDay0PF.100

value: Male

tag: race


title: Skin biopsy, PT1166lesional skinDay14

description: PF-06700841 100 MG QD (P)

source_name: lesional skinDay14PF.100

tag: treatment


title: P5 Sox9Cre; Vangl2f/f rep3

description: Sox9Cre-Vangl2 at P5.txt

value: Sox9Cre/+; Ror2f/f


title: GAL1_SMC2_K38I_smc2_td_H2A_rep2

description:
processed data file:
e61_smc2_td_K38I_top2_BYAK302-noco_R64_1_1_to_H2A_SPMR_FE.bedgraph_binned_50_norm.wig

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100    UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)    Leu2-3::pCM244 (CMVp-tetRprime-SSN6, LEU2) x3    trp1-1::SDM-pFA6a-GAL1-SMC2-K39I-6HA, TRP1    smc2-td SMC2 5prime upstream-100 to -1 replaced with kanMX-tTA (tetR-VP16) -tetO2 -Ub -DHFRts -3xHA extended linker)


title: uninfected control mouse 4

source_name: 1-month non-infected mice

value: uninfected


title: P5 Sox9Cre; Vangl2f/f rep2

description: Sox9Cre-Vangl2 at P5.txt