title: 5XFAD_12mo_3

description:
Total RNA was extracted from cortex at 12 months of age.
SJMMALZ058779_G1

value: 12 months


title: 5XFAD_12mo_1

status: Public on Dec 04 2019

type: SRA

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

country: USA

institute: St Jude Children's Research Hospital

description:
Total RNA was extracted from cortex at 12 months of age.
SJMMALZ058780_G1

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped by StrongARM, an internal mapping pipeline that performs STAR and bwa mapping.
reads were counted using an internal perl script and converted to FPKM using mm9
Genome_build: mm9

molecule: polyA RNA

organism: Mus musculus

source_name: 5XFAD transgenic mice

extract_protocol:
RNAs were extracted by Trizol (Invitrogen) from about 20 mg aliquots of the same tumor samples for proteomics analyses.
For RNAseq, libraries were generated from ~1 µg total RNA using the Illumina Stranded Total RNA kit with the Human/Mouse/Rat Ribo-Zero Gold ribosomal reduction kit. Libraries were sequenced on an Illumina HiSeq 2500 using paired-end 100 bp sequencing chemistry

tag: age

tag: tissue

value: Cortex

tag: genotype

value: amyloid deposition expresses five familial AD (FAD) mutations

tag: strain


title: WT_6mo_2

description:
Total RNA was extracted from cortex 6 months of age.
SJMMALZ058772_G1

source_name: Non transgenic control

value: 6 months

value: control


title: WT_12mo_3

description:
Total RNA was extracted from cortex at 12 months of age.
SJMMALZ058782_G1


title: WT_6mo_3

description:
Total RNA was extracted from cortex 6 months of age.
SJMMALZ058773_G1


title: WT_6mo_1

description:
Total RNA was extracted from cortex 6 months of age.
SJMMALZ058771_G1


title: 5XFAD_6mo_1

description:
Total RNA was extracted from cortex 6 months of age.
SJMMALZ058774_G1


title: WT_12mo_2

description:
Total RNA was extracted from cortex at 12 months of age.
SJMMALZ058778_G1


title: 5XFAD_3mo_1

description:
Total RNA was extracted from cortex 3 months of age.
SJMMALZ058768_G1

value: 3 months


title: 5XFAD_12mo_2

description:
Total RNA was extracted from cortex at 12 months of age.
SJMMALZ058781_G1


title: WT_3mo_2

description:
Total RNA was extracted from cortex 3 months of age.
SJMMALZ058766_G1


title: Zfp36ΔIEC Rep3

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
Bcl converion and demultiplexing using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. Adapter masked fastq files were generated.
Quality filter by FASTX Toolkit 0.0.13 (fastq_quality_filter: -Q33 -q 20 -p 80 was used as a parameter, fastq_quality_trimmer: -Q33 -t 20 -l 10 was used as a parameter). Fastq files were generated.
Read alignment using Tophat 2.0.9 using mm10 reference genome. BAM files were generated.
FPKM calculation using Cufflinks 2.2.1. Plain text (can be read by excel) files were generated. Both Tophat and Cufflinks used GRCm38.78.gtf file as guided annotation file.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: xls files for FPKM values for each sample and result of differential gene expression analysis

source_name: colon tissue

extract_protocol:
RNA was isolated from 2 cm of full thickness colonic tissue by pestle homogenization in TRIzol according to the manufacturer’s instructions. RNA concentrations were measured on a NanoDrop (ThermoFisher) apparatus.
The cDNA libraries were prepared using the NEXTflex™ Rapid RNA Sequencing Kit and NEXTflex™ RNA-Seq Barcodes – 24 Kit (BioO Scientific) as per the manufacturer’s instructions. The final product was assessed for its size distribution using Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). The samples were sequenced using a HiSeq 2500 that was set to run for 50 cycles using a single-read recipe (TruSeq SBS Kit v3, FC-401-3002) according to the manufacturer’s instructions.

value: Colon


title: WT_3mo_1

description:
Total RNA was extracted from cortex 3 months of age.
SJMMALZ058765_G1


title: Zfp36ΔIEC Rep1


title: 5XFAD_3mo_2

description:
Total RNA was extracted from cortex 3 months of age.
SJMMALZ058769_G1


title: Zfp36ΔIEC Rep2


title: Zfp36fl/fl Rep2


title: Zfp36fl/fl Rep3


title: P0SAC1

city: Los Angeles

first: Yi-Rong

last: Peng

state: CA

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

institute: University of California, Los Angeles

data_processing:
ScRNA-seq data was analyzed as previously described (Peng et al., 2019; Karthik et al., 2016). Briefly, sequenced reads were aligned to the mouse genome mm10, and count matrix of sequenced cells was generated using the Cell Ranger software (version 2.1.0, 10X Genomics).
Only cells with the expression of > 600 gene were used for further analysis. We then preprocessed the count data following normalization to median UMI counts, regression out mitochondrial and ribosome genes, and extraction of all the SACs with scoring for gene signatures of SACs – Sox2, Megf10, Megf11, Chat, and Slc18a3.
Lastly, we clustered SACs with graph-based clustering using significant PCs and visualized the clustering result in 2D via t-distributed stochastic neighbor embedding (t-SNE).
Genome_build: mm10
Supplementary_files_format_and_content: count data for each SACs

molecule: total RNA

source_name: Mus musculus retina, P0

extract_protocol:
P0 ChATCre:Thy1-STP-YFP (line#15) retinas were digested with papain (Worthington, LS003126) at 37°C for 10 mins. Retinas were then dissociated and triturated into single cell suspensions. YFP labeled SACs were further isolated by FACS.
Single SAC suspensions were loaded into 10X Chromium Single Cell A Chips at a concentration of ~1,000 cells/µL. Single cell libraries were prepared using the Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA).

value: Retina

tag: cell type

value: Cholinergic interneurons


title: ATAC-Ramos.1

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

library_source: genomic

data_processing:
ATAC-seq reads were aligned to the GRCh37/hg19 genome assembly
Alignment done using Bowtie (version 1.1.2) with seed length 50 and 2, 3, and 3 mismatches allowed, respectively
Peaks were called using MACS 1.4.3 (Zhang et al., 2008). Default parameters were used (p value cutoff for peak detection = 1x10e-5;–keep-dup = auto). No control was used, and the parameters were tuned to fit broader peaks (–nolambda,–nomodel) (Feng et al., 2011).
human GRCh37/hg19
Aligned-reads bed files were first converted to bedgraph files using bedtools genomecov (Quinlan and Hall, 2010) following by bedGraphToBigWig to make a bigwig file (Kent et al., 2010).

molecule: genomic DNA

organism: Homo sapiens

source_name: Ramos cell line

growth_protocol: Ramos cells were propagated in RPMI 1640 medium (Sigma) supplemented with 10% fetal calf serum (GIBCO) and antibiotic mixture (Sigma) in a 5% CO2 atmosphere at 37°C

extract_protocol:
Cells were resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three  times.  This  cell  lysis  reaction  was  incubated  on  ice  for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without  NP40  or  digitonin)  was  added,  and  the  tubes  were inverted to mix. Nuclei were then centrifuged for 10 min at 500 r.c.f. in a pre-chilled (4 °C) fixed-angle centrifuge. Supernatant was removed with two pipetting steps, as described before, and nuclei were  resuspended  in  50 μl  of  transposition  mix  (25 μl  2×  TD buffer (recipe in Supplementary Protocol 1) 2.5 μl transposase (100  nM  final),  16.5 μl  PBS,  0.5 μl  1%  digitonin,  0.5 μl  10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns.
All libraries were amplified with a target concentration of 20 μl at 4 nM, which is equivalent to 80 femtomoles of product. Following amplification, libraries were purified with Ampure XP beads using two-sided size selection to remove primer dimers and fragments >1000 bp.

treatment_protocol: Cells were pretreated with 200 U/ml DNase for 30 min at 37 °C to remove free-floating DNA and to digest DNA from dead cells.  This medium was then washed out, and the cells were resuspended in cold PBS.

value: B lymphocyte

value: WT

value: Burkitt's lymphoma-derived cell line, EBV-negative

value: Unknown

tag: Sex

value: male


title: HTISA.WT.NONSELECTED.2

data_processing:
fastq raw reads files were split into the individual Total and GFP-negative libraries by their barcodes, using fastqx toolkit fastx_barcode_splitter.pl program with ---bol --exact parameters (search exact match of barcode at the beginning of the read).
For each library, the viral LTR sequence spanning the first 41 base-pairs of the read was trimmed and processed reads were mapped to the human grch37/hg19 genome build using Bowtie (version 1.1.2) software with seed length 25 and 3 mismatches allowed. To reduce background, integration sites with only a single read were discarded.
The genome was divided into 25 kb bins and the number of reads for each bin was counted. Covered bins were defined as those with at least 3 unique integration sites and total 50 or more reads. Bins that did not match these criteria were discarded from the analysis. For each covered bin, enrichment of reads in the GFP-negative population was determined as follows. First, the reads that were mapped to Ig loci were discarded. Next, the reads in the Total population were normalized to have the same total number of reads as the GFP-negative population. The resulting normalized number of reads per bin in the total population was used as the Poisson l parameter against which the number of reads in the GFP-negative population at the same bin were compared in the Poisson test.  This generated an array of p-value to which we applied Benjamini-Hochberg criteria using FDR of 0.05 to determine the significant GFP-negative enriched bins for this pair of Total/GFP-negative libraries.
human GRCh37/hg19
Aligned-reads bed files were first converted to bedgraph files using bedtools genomecov (Quinlan and Hall, 2010) following by bedGraphToBigWig to make a bigwig file (Kent et al., 2010).

extract_protocol:
Total and GFP-negative cultures were harvested for genomic DNA isolation on the same day so that culture times after infection with GFP7 were the same. Genomic DNA was isolated using a salt-extraction method (Aljanabi and Martinez, 1997).
HTISA libraries were prepared and sequenced from GFP-negative and Total populations ("B" culture genomic DNAs were combined to yield a GFP-negative "Pool" library and a Total "Pool" library, so that finally, we obtained one pooled and 4 separate GFP-negative samples and one pooled and 4 separate Total samples). We used a linear amplification–PCR protocol based on a previously published high-throughput, genome-wide, translocation sequencing (HTGTS) method (Frock et al., 2015). The adaptation of the protocol was as follows: Retroviral integration sites were linearly amplified from the vector 5' LTR using biotinylated Bio_L7a (HIV-derived vector integrations) or Bio_A7a (ASLV-derived vector integrations) primers. Nested PCR was performed with barcoded inner primer I5_bar75_L7a (HIV-derived vector integrations) or I5_bar75_A7a (ASLV-derived vector integrations). The blocking digestion of the nested PCR product was omitted. The resulting PCR product were gel purified and sequenced using a NextSeq500 (Illumina) sequencer.

treatment_protocol: 10e7 Ramos cells were infected (4 independent infections) with no-DIVAC GFP7 vector at low multiplicity resulting in 0.5-1% GFP-positive cells 2 days after infection. Blasticidin (final concentration 5 µg/ml) was added 2 days post infection. Three days post infection the blasticidin concentration was increased to 6.5 µg/ml and kept until the 5th day. Seven days post infection, GFP positive cells were sorted and cultured for two days. Nine days post infection, GFP-positive cells were sorted again. Each culture was split in half to create duplicate "A" and "B" cultures. After 20 days of propagation, the culture was selected with blasticidin (12 µg/ml) to remove cells with silenced vector. After 4 days of blasticidin selection, GFP-negative cells (containing mostly vectors integrated into SHM-susceptible sites) were then sorted from each of the 8 cultures ("A" and "B" duplicates of 4 infections) and sorted again 3 days later to remove the remaining GFP-positive cells.


title: HIC2608

data_processing:
Hi-C reads were aligned to the GRCh37/hg19 genome assembly
Juicer software was used to filter reads and subsequently normalize the ligation frequency matrices as previously published (Rao et al., 2014). All of the normalized data corresponds to matrices balanced using the Knight-Ruiz algorithm as described (Rao et al., 2014).
We next used the juicebox dump function to extract the normalized matrices from the inter_30.hic file (Durand et al., 2016). For this analysis, we used 5kb resolution matrices. We then used juicer software to call loops with the default parameters.
human GRCh37/hg19
see RAMOS.HIC.hic

extract_protocol:
Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume.
After reversal of crosslinks, ligated DNA was purified and sheared to a length of 400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing.

treatment_protocol: Two to five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature.


title: HTISA.AIDKO.NONSELECTED.2

value: AID-/-


title: HTISA.AIDKO.NONSELECTED.1


title: HTISA.WT.NONSELECTED.1


title: HIC2606


title: HIC2607


title: HTISA.SD11.gneg.4


title: HIC2605

data_processing:
Hi-C reads were aligned to the GRCh37/hg19 genome assembly
Juicer software was used to filter reads and subsequently normalize the ligation frequency matrices as previously published (Rao et al., 2014). All of the normalized data corresponds to matrices balanced using the Knight-Ruiz algorithm as described (Rao et al., 2014).
We next used the juicebox dump function to extract the normalized matrices from the inter_30.hic file (Durand et al., 2016). For this analysis, we used 5kb resolution matrices. We then used juicer software to call loops with the default parameters.
human GRCh37/hg19
RAMOS.HIC.hic


title: THY_IF JB13

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The reads with good quality were aligned to several human reference databases including hg19 human genome, exon, splicing-junction segments, and contamination database including ribosome and mitochondrial sequences using BWA alignment algorithm.
After filtering reads mapped to the contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 miss-matches for each transcript were then counted as expression level for the corresponding transcripts.
Supplementary_files_format_and_content: counts

source_name: Human primary thyrocytes

growth_protocol: Cells werre routinely cultured. ML-1 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM), Human hepatocyte cell line Huh7.5 in DMEM, and primary thyrocytes in  medium E199/EBSS .

extract_protocol: RNA from cells in culture was extracted using TriZol.

treatment_protocol: Huh7.5JFH1 which releases HCV genotype 2a virions into cell culture supernatant were used to produce HCV virions in order to infect cells.

tag: condition

value: Infected


title: HTISA.SD11.gneg.1


title: HTISA.SD11.gneg.2


title: THY_IF JB14


title: Zfp36fl/fl Rep1


title: HTISA.SD11.total.3


title: THY_IF JB12


title: HTISA.SD11.total.4


title: THY_UNIF JB10

value: Uninfected


title: HTISA.SD11.total.2


title: ATAC-Ramos.2


title: HUH_IF JB8

source_name: Human hepatocyte cell line Huh7.5


title: THY_UNIF JB11


title: HTISA.SD22.gneg.3


title: HUH_IF JB7


title: HTISA.SD22.gneg.4


title: THY_UNIF JB9


title: HTISA.SD11.total.1


title: HTISA.SD22.gneg.2


title: HUH_UNIF JB6


title: HUH_UNIF JB5


title: HTISA.SD22.gneg.1


title: HTISA.SD22.total.4


title: HTISA.SD11.gneg.3


title: ML1_IF JB4

source_name: Human thyroid cell line ML-1


title: ML1_IF JB3


title: HTISA.SD22.total.2


title: ML1_UNIF JB2


title: HTISA.SD22.total.1


title: ML1_UNIF JB1


title: HTISA.gneg.pool


title: CPSF1_Term_2

status: Public on Dec 05 2019

city: Beijing

first: Lei

last: Yue

address: NO.1 Beichen West Road, Chaoyang District

department: Institute if Microbiology

country: China

institute: Chinese academy of science

data_processing:
For RNA-seq raw reads of fastq format were firstly processed through in-house perl scripts to remove low quality reads and those containing adapter or ploy-N. The clean reads were mapped against predicted transcripts of the M. maripaludis S2 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_005791.1/) by using Bowtie2-2.2.3. HTSeq v0.6.1 was used to count the read numbers mapped to each gene, and then the FPKM was calculated based on the gene length and mapped read counts.
Genome_build: M. maripaludis S2 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_005791.1/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample of RNA_seq. The TESs for each stain identified in duplicate and the average head reads (reads number of -1 site minus +1 site) and ratio1_1 (ratio of -1 site to +1 site) are listed in tab-delimited text files.

organism: Methanococcus maripaludis

source_name: Neural strain cells

growth_protocol: The Methanococcus maripaludis strains were grew until mid-log phase and harvested

extract_protocol:
RNA was harvested using Trizol reagent. 3 ug of total RNA was used for RNA-seq and 5 ug of total RNA was used for Term-seq .
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aCPSF1 depletion

tag: growth period

value: mid-log phase


title: CAFO_hiseq [OxBS] 2

city: Bronx

first: Amit

last: Verma

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

data_processing:
Library strategy: OxBS-seq (Oxidative bisulfite sequencing)
adapters were trimmed from fastq files using trim_galore 0.4.0 with default parameters
reads were aligned to the PhiX RTA genome using bowtie2 with parameters: -N 1   Mapped reads were filtered away.
bisulfite mapping was performed with Bismark version 0.14.5 using default parameters.
Duplicate reads were marked with picard-tools 1.92.
number of methylated reads were counted  at each loci with mpileup2methylation.py
Genome_build: hg19
Supplementary_files_format_and_content: The output files are in bedGraph-like format with columns:  Chromosome, Position of C (0-based), Position of C +1, Percentage reads methylated, Count methylated reads, Total read count, Strand

source_name: CAFs

growth_protocol: CAFs were generated by exposure of MSCs to conditioned media from Panc1 cells

extract_protocol:
Qiagen Gentra Puregene DNA isolation protocol
https://www.qiagen.com/us/resources/resourcedetail?id=a9e6a609-4600-4b03-afbd-974318590ce5&lang=en
TrueMethyl® oxBS Module - NuGEN Technologies
https://www.nugen.com/sites/default/files/M01481_v2_User_Guide-TrueMethyl_oxBS_module_4977.pdf

treatment_protocol: 2-3 weeks of exposure of MSCs to conditioned media

tag: experiment type

value: OxBS

value: CAF


title: HTISA.gneg.3


title: HTISA.gneg.2


title: MSCO_hiseq [OxBS] 2

source_name: MSCs

value: MSC


title: HTISA.SD22.total.3


title: MSCC_hiseq [BS] 2

data_processing:
adapters were trimmed from fastq files using trim_galore 0.4.0 with default parameters
reads were aligned to the PhiX RTA genome using bowtie2 with parameters: -N 1   Mapped reads were filtered away.
bisulfite mapping was performed with Bismark version 0.14.5 using default parameters.
Duplicate reads were marked with picard-tools 1.92.
number of methylated reads were counted  at each loci with mpileup2methylation.py
Genome_build: hg19
Supplementary_files_format_and_content: The output files are in bedGraph-like format with columns:  Chromosome, Position of C (0-based), Position of C +1, Percentage reads methylated, Count methylated reads, Total read count, Strand

value: BS


title: HTISA.gneg.1


title: Case no. 54; primary GIST

type: RNA

city: Sunto-gun

first: Keiichi

last: Ohshima

state: Shizuoka

address: 1007 Shimonagakubo, Nagaizumi-cho

department: Medical Genetics Division

country: Japan

institute: Shizuoka Cancer Center Research Institute

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC for 30 min, and hybridized to Agilent SurePrint G3 Human Gene Expression 8×60K v2 microarrays at 65º C for 17 hours in a rotating Agilent hybridization oven. The hybridized slides were washed using Agilent Gene Expression wash buffers.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2505C Microarray Scanner System.

data_processing: The scanned images were analyzed with Feature Extraction Software (version 10.7.3.1, Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: primary GIST

label_protocol: RNA samples with RNA integrity number ≥ 6.0 was used for microarray analysis. Total RNA (100 ng) was amplified and fluorescence-labeled using the One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies).

extract_protocol: Tissue samples were submerged in RNAlater solution (Thermo Fisher Scientific), minced, and stored overnight at 4°C before RNA extraction. Total RNA was extracted from approximately 10 mg of minced tissue samples using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Initially, tissue samples were mixed with QIAzol reagent from the kit and then ground with a TissueLyzer II (Qiagen) using a 5-mm zirconia bead for 10 min at room temperature.

value: gastrointestinal stromal tumor

tag: gender

value: F

tag: primary tumor site

value: stomach

tag: metastatic tumor site

tag: risk

value: very low

tag: tumor stage

value: IA

tag: kit/pdgfra mutation type

value: KIT

tag: kit/pdgfra mutation site


title: Case no. 61; primary GIST


title: Case no. 58; primary GIST


title: Case no. 64; primary GIST

value: M

value: duodenum

value: I


title: HTISA.gneg.4

value: B lymphocyte

value: WT

value: Burkitt's lymphoma-derived cell line, EBV-negative

value: Unknown

value: male


title: CAFO_hiseq [OxBS] 1

value: OxBS

value: CAF


title: Case no. 53; primary GIST

value: small intestine

value: low


title: Case no. 55; primary GIST

value: gastrointestinal stromal tumor


title: CAFC_hiseq [BS] 2

value: BS


title: Case no. 56; primary GIST

value: stomach

value: very low


title: HTISA.total.pool


title: Case no. 52; primary GIST

value: KIT


title: Case no. 63; primary GIST

value: M

value: IA


title: CAFC_hiseq [BS] 1


title: Case no. 62; primary GIST


title: HTISA.total.4


title: Case no. 50; primary GIST

value: F

value: duodenum

value: I


title: Case no. 60; primary GIST


title: Case no. 59; primary GIST


title: Case no. 51; primary GIST

value: colon (rectum)


title: Case no. 57; primary GIST


title: MSCO_hiseq [OxBS] 1

value: MSC


title: Case no. 46; primary GIST

value: PDGFRA


title: Case no. 48; primary GIST


title: Case no. 49; primary GIST


title: Case no. 47; primary GIST


title: Case no. 45; primary GIST


title: MSCC_hiseq [BS] 1


title: HTISA.total.3

value: B lymphocyte

value: WT

value: Burkitt's lymphoma-derived cell line, EBV-negative

value: Unknown

value: male


title: Case no. 43; primary GIST

value: gastrointestinal stromal tumor

value: low


title: HTISA.total.1


title: Case no. 44; primary GIST

value: stomach


title: HTISA.total.2


title: CAFO_hiseq [OxBS]

value: OxBS

value: CAF


title: CAFC_hiseq [BS]

value: BS


title: MSCO_hiseq [OxBS]


title: PBS, Control

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

data_processing:
The fastq files were aligned to zebrafish transcript (Ensembl Version 91)by using STAR.
The BAM files were as input for Cell Ranger (10X genmoics) to generate processed data files that include gene names (row names) and cell names (column names) and counts.
Further analysis done by using Seurat package in R.
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited file, with gene names in rows and cell names and counts in columns.

organism: Danio rerio

source_name: Telencephalon

growth_protocol: Fish were kept at 28 °C water system with 14/10 hours light/dark cycles

extract_protocol:
Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number.
The library preparation was performed by 10X Genomics as per manufactur protocol

treatment_protocol: Fish were injected PBS by CVMI.

tag: treatment

value: PBS, Control


title: Case no. 42; primary GIST

tag: age

value: M

value: IA

value: KIT


title: H6-3mRNA

city: Ithaca

first: Joel

middle: D

last: Baines

address: 235 Hungerfordhill Rd

institute: Cornell University

data_processing:
All processing steps were done using the Danko lab template for PRO-seq alignment/QC found at https://github.com/Danko-Lab/utils/tree/master/proseq with instructions at https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md
Pre-processing reads and sequence adapter trimming are done with cutadapt
Reads are mapped to the bwa index reference genome using bowtie
BAM files are converted to BigWig using Kentsource
BigWig can be viewed using IGV, and BAM files analyzed with DESeq2 statistics using SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/.  SeqMonk data is reported in Xcel files as supporting/supplemental information in the publication
Genome_build: HSV-1 reference genome-GU734771.1, the hg38 human genome build, and the dm3 Drosophila melanogaster genome build
Supplementary_files_format_and_content: bigwig

source_name: HEp-2 Cells

growth_protocol:
Hep-2 cells--grown at 37 degrees C in 5% CO2 in DMEM 10% Newborn calf serum supplemented with Penn/Strep
Drosophila S2 cells--grown at 20 degrees C on bench top in Schneider's Drosophila Medium with 10% FBS and Penn/Strep

extract_protocol:
mRNA seq: Cytoplasmic fractions were collected using the nuclei isolation protocol.  The extracts were subjected to oligodT selection of polyadenylated mRNA using poly-A coated magnetic beads.
PRO-seq: Nuclei isolation followed by Nuclear Run-on in the presence of biotinylated nucleotides (A, U, G, C).  Biotinylated transcripts were isolated using streptavadin coated magnetic beads
mRNA seq: Libraries were constructed by Camille Abshire at Louisiana State University Health Science Center in Shreveport in the Genomics Core using the TruSeq Stranded mRNA LS kit.
PRO-seq: Libraries were constructed following the protocol outlined by Mahat et al. 2016. "Base-pair-resolution genome-wide mapping of active RNA Polymerases using precision nuclear run-on (PRO-seq).  Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086

treatment_protocol:
mRNA-seq: Hep-2 cells were infected with HSV-1 F strain at an MOI of 5 and infection progressed for either 3 or 6 hours post infection.
PRO-seq: Hep-2 cells were infected with HSV-1 F strain at an MOI of 5, and treated at 1 hour post infection with either 10µM Acyclovir, or at the time of infection with 0.01% DMSO, or 0.01% DMSO with 450nM Flavopiridol. Nuclei were isolated at 6 hours post infection.  S2 cells were left untreated before nuclei isolation, and spiked-in to isolated Hep-2 nuclei (1 drosophila nuclei/10,000 Hep-2 nuclei)

tag: cell line

value: HEp-2 Cells

value: lung epithelial cells from a carcinoma

tag: viral infeciton

value: Herpes Simplex virus 1 infection for 6 hours post infeciton

tag: drug treatment

tag: processing

value: cytoplasmic fractionation followed by polyA selection with oligo dT

tag: molecule subtype

value: cytoplasmic mRNA


title: interleukin-4

treatment_protocol: Fish were injected interleukin-4 by CVMI.


title: MSCC_hiseq [BS]

tag: cell type

value: MSC


title: Case no. 41; primary GIST

tag: tissue

value: F


title: amyloid-beta 42

treatment_protocol: Fish were injected amyloid-beta 42 by CVMI.

value: amyloid-beta 42


title: H6-1mRNA


title: iPSC_saC9_R1_spC9_AAVS1_Rep1

city: Stanford

first: Richard

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

description: Processed data file: iPSC_saC9_R1_spC9_AAVS1.txt (Filtered Junctions)

data_processing:
Library strategy: LAM-HTGTS
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

source_name: IPS cells

growth_protocol: Feeder-free essential 8 medium

extract_protocol:
Genomic DNA was isolated using the Dneasy Blood & Tissue kit
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203) using RAG1 primers described in Frock et al., 2015 Nature Biotechnology (PMC4320661) and Illumina Miseq sequencing

treatment_protocol:
48 hour culture post transfection
Genomic DNA was collected 48 hours after delivery of nuclease

value: IPS cells

tag: genotype

value: WT

tag: nuclease delivery

tag: target locus

value: RAG1 (saCas9:RAG1.1 gRNA)

tag: extract protocol (dna fragmentation/blocking methods)

value: Sonication


title: H3-3mRNA

value: Herpes Simplex virus 1 infection for 3 hours post infeciton


title: iPSC_saC9_R1_spC9D10A_AAVS1_Rep1

description: Processed data file: iPSC_saC9_R1_spC9D10A_AAVS1.txt (Filtered Junctions)


title: H3-2mRNA


title: H3-1mRNA


title: iPSC_saC9_R1_Rep1

description: Processed data file: iPSC_saC9_R1.txt (Filtered Junctions)

value: Nucleofection; saCas9:RAG1.1


title: ChIP-ZEB1

data_processing:
ChIP-seq reads were aligned to the GRCh37/hg19 genome assembly
Alignment done using Bowtie (version 1.1.2) with seed length 50 and 2, 3, and 3 mismatches allowed, respectively
Peaks were called using MACS 1.4.3 (Zhang et al., 2008). Default parameters were used (p value cutoff for peak detection = 1x10e-5;–keep-dup = auto), with corresponding DNA input as a control.
Genome_build: human GRCh37/hg19
Supplementary_files_format_and_content: Aligned-reads bed files were first converted to bedgraph files using bedtools genomecov (Quinlan and Hall, 2010) following by bedGraphToBigWig to make a bigwig file (Kent et al., 2010).

extract_protocol:
Chromatin Immunoprecipitation was performed with the SimpleChIP Enzymatic Chromatin IP Kit (#9003) according to the manufacturer’s protocol with minor modifications. In brief, 40 x 10e6 Ramos cells were spun down at 90xg for 10 min before the pellet was reconstituted in 9 ml of RPMI with 2% FBS in a 15 ml conical tube. Then, 0.6 ml of 16% Formaldehyde (Pierce/ThermoFisher #28906) was added and the cells were placed on a rocker for 10 min at RT. One ml of 10x glycine solution was added to quench the reaction, and the cells were then returned to the rocker for 5 min at RT before being spun down at 300xg and washed 2x with PBS. All following steps were performed on ice or at 4°C unless otherwise noted. Cells were reconstituted in 10 ml of Buffer A with protease inhibitors and allowed to rest for 10 minutes and the lysed cells were spun down at 2000xg for 5 min to pellet nuclei. Pelleted nuclei were washed with 10 ml of Buffer B, pelleted at 2000xg for 5 min, and then resuspended in 1 ml of Buffer B. 1.7 µl of micrococcal nuclease (CST #10011) was added to the nuclei and the tube incubated in a 37°C water bath for 20 min. The reaction was stopped with 100 µl of 0.5 ml of EDTA, and the nuclei pelleted at 16,000xg for 1 min. The pellet was then resuspended in 1 ml of 1x ChIP Buffer with protease inhibitors and sonicated in 200 µl aliquots in a Qsonica sonicator for 2 cycles of 15 s on, 45 s off at 20% power. The lysate was then clarified at 10,000xg for 10 min before the supernatant was removed and diluted five-fold in 1x ChIP Buffer with protease inhibitors. For each ChIP, 500 µl of chromatin was incubated with 1-2 µg of antibody in a 1.5 ml Eppendorf tube at 4°C overnight on a rotator. The next day, 30 µl of Protein G Magnetic beads (CST #70024) was added to each tube and the mixture incubated at 4°C for 2 hours on a rotator. The beads were pelleted using a magnetic separation rack and the supernatant discarded.  The beads were then washed 3x with a low-salt wash and 1x with a high-salt wash using 5 min incubations on a rotator. Chromatin was eluted from beads with the addition of 150 µl of 1x Elution Buffer and incubation at 1200 rpm on a thermal mixer for 2 hours at 65°C. The beads were pelleted and the supernatant was moved to a new 1.5 ml Eppendorf tube and 2 µl of Proteinase K (CST #10012) added. The mixture was incubated for 2 hr at 65°C and then DNA was purified using SimpleChIP DNA Purification Buffers and Columns (CST #14209) and eluted in a volume of 50 µl.
libraries were prepared from 50 ng of eluted DNA using the Ultra II DNA Library Prep Kit for Illumina (NEB #E7645) following the manufacturer’s protocol

value: Ramos

value: Burkitt's lymphoma-derived cell line, EBV-negative

tag: cell line source gender

value: male

tag: chip antibody

tag: chip antibody vendor

value: Proteintech

tag: chip antibody cat. #

tag: input sample used


title: H6-2mRNA

value: HEp-2 Cells

value: lung epithelial cells from a carcinoma


title: MSCO_miseq [OxBS]

tag: experiment type

value: OxBS


title: R_neurons_1

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: MDD patient_SSRI remitter

data_processing:
Low quality ends and adapter removal/trimming were performed using cutadapt. Trimmed reads were mapped using STAR30 and assigned to genes with featurecounts31, and normalized counts and differential expression and statistics were calculated using the DESeq2 R package32
Genome_build: hg19
Supplementary_files_format_and_content: csv file with raw counts

source_name: MDD patient_SSRI remitter

growth_protocol: The growth protocols have been described in our study (Vadodaria et al)- forebrain neurons were derived from patient iPSCs. In vitro derivation of neurons from human iPSC with dual SMAD inhibition.

extract_protocol:
RNA was extracted with trizol and phenol chloroform precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatments were performed

tag: diagnosis

value: MDD

value: iPSC-derived neurons

tag: age

value: adult


title: ChIP-YY2

tag: cell line

value: Sigma


title: R_neurons_3

description: MDD patient_SSRI remitter


title: Case no. 39; primary GIST

value: gastrointestinal stromal tumor

tag: gender

value: F

tag: primary tumor site

value: stomach

tag: metastatic tumor site

tag: risk

value: low

tag: tumor stage

value: IA

tag: kit/pdgfra mutation type

value: KIT

tag: kit/pdgfra mutation site


title: Case no. 37; primary GIST

tag: tissue


title: NR_neurons_1

description: MDD patient_SSRI nonremitter

source_name: MDD patient_SSRI nonremitter


title: MSCC_miseq [BS]

value: BS

tag: cell type

value: MSC


title: R_neurons_2

description: MDD patient_SSRI remitter


title: Case no. 38; primary GIST

value: M


title: ChIP-YY1

value: Ramos

value: Burkitt's lymphoma-derived cell line, EBV-negative

tag: genotype

value: WT

tag: cell line source gender

value: male

tag: chip antibody

value: Santa Cruz Biotechnology


title: CAFO_miseq [OxBS]

value: OxBS

value: CAF


title: Case no. 35; primary GIST


title: H_neurons_3

description: neurotypical healthy control

source_name: neurotypical healthy control

value: healthy

value: iPSC-derived neurons

value: adult


title: Case no. 40; primary GIST

value: gastrointestinal stromal tumor

value: F

value: stomach


title: Case no. 33; primary GIST

value: low

value: IA

value: KIT


title: Case no. 36; primary GIST


title: Case no. 32; primary GIST


title: Case no. 34; primary GIST

value: M


title: Case no. 31; primary GIST

value: intermediate

value: IB


title: ChIP-SPT5

value: Ramos

value: Burkitt's lymphoma-derived cell line, EBV-negative

value: WT

tag: chip antibody vendor

tag: chip antibody cat. #

tag: input sample used


title: Case no. 30; primary GIST

tag: age


title: NR_neurons_3

description: MDD patient_SSRI nonremitter

tag: diagnosis

value: MDD


title: H_neurons_2

description: neurotypical healthy control


title: CAFC_miseq [BS]

tag: experiment type

value: BS

value: CAF


title: Case no. 29; primary GIST

tag: gender

tag: primary tumor site


title: NR_neurons_2

description: MDD patient_SSRI nonremitter

value: iPSC-derived neurons


title: ChIP-Ser5p

tag: cell line

value: male

value: anti-Ser5P PolII

value: Abcam


title: H_neurons_1

description: neurotypical healthy control

value: healthy

value: adult


title: ChIP-RAD21


title: saC9_R1_spC9D10A_AAVS1_Rep3

description: Processed data file: saC9_R1_spC9D10A_AAVS1_s3.txt (Filtered Junctions)

source_name: 293T-Embryonic Kidney

growth_protocol: DMEM; 10% Fetal calf serum

value: 293T-Embryonic Kidney

tag: nuclease delivery

value: PEI; saCas9:RAG1.1; spCas9D10A:AAVS1

tag: target locus

value: RAG1 (saCas9:RAG1.1 gRNA)

tag: extract protocol (dna fragmentation/blocking methods)

value: Sonication


title: saC9_R1_Rep3

description: Processed data file: saC9_R1_s3.txt (Filtered Junctions)

value: PEI; saCas9:RAG1.1


title: Case no. 28; primary GIST

tag: tissue

value: gastrointestinal stromal tumor

value: F

value: stomach

tag: metastatic tumor site

tag: risk

value: intermediate

tag: tumor stage

value: IB

tag: kit/pdgfra mutation type

value: KIT

tag: kit/pdgfra mutation site


title: ChIP-PU1

value: Ramos

tag: cell type

value: Burkitt's lymphoma-derived cell line, EBV-negative

tag: genotype

value: WT

tag: cell line source gender

tag: chip antibody

tag: chip antibody vendor

value: Cell Signaling Technology

tag: chip antibody cat. #


title: CAPU_Treated_BiologicalRepC

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

data_processing:
Base calling was performed using the RTA v2 software built into the Illumina NextSeq 500 instrument.
Demultiplexing and FASTQ file generation was performed with Illumina’s Basespace informatics platform
Data analysis was performed using the Qiagen CLC Genomics Workbench (CLCGxWB) version 11 software. Sequencing reads were mapped to the S. cerevisiae reference genome (R64-1-1 release), using default parameters with a strand-specific alignment protocol. The mapping results generated values for Fragments Per Kilobase of exon per Million reads mapped (FPKM) for each gene. The “Differential Expression for RNA-Seq” tool in CLCGxWB software was used, using default parameters, to identify differentially expressed genes between drug-treated and solvent-treated samples.
Genome_build: Saccharomyces cerevisiae S288C reference genome R64-1-1 release
Supplementary_files_format_and_content: Excel file showing FPKM values for each Sample.

organism: Saccharomyces cerevisiae

source_name: Yeast cells treated with CAS + PUUP

growth_protocol: All cultures were grown in SD broth (2% dextrose, 0.67% yeast nitrogen base without amino acids, MOPS buffered, pH 7.0) at 30 degrees, with shaking at 200 rpm.

extract_protocol:
Qiagen RNeasy Mini kit was used for total RNA extraction. An on-column RNase-free DNase I treatment was included. RNA quality was assessed on the Agilent 2100 Bioanalyzer.
Sequencing libraries were generated with 4 µg of RNA using the Illumina TruSeq Stranded mRNA Sample Preparation Kit. The libraries were assessed for size and purity using the Agilent 2100 Bioanalyzer, and quantitated by qPCR using a KAPA Biosystems Library Quantitation kit. Libraries were normalized, pooled, and diluted to a loading concentration of 1.8 pM, loaded on an Illumina Mid-Output Flow Cell, and sequenced on the Illumina NextSeq 500 instrument.

treatment_protocol: Cultures of S. cerevisiae strain S288C were started at OD600 of 0.1, allowed to grow to OD600 of 0.2, then treated with CAS (0.03 µg/ml), PUUP (0.87 µg/ml), or CAS + PUUP (0.03 µg/ml CAS + 0.87 µg/ml PUUP), with the concentrations used corresponding to the IC50 value of each compound. When OD600 of 0.5 was reached (~4 h), cells were harvested and frozen.  In all experiments, three biological replicate cultures were grown for each treatment, and RNA from each replicate was used to generate sequencing libraries.

tag: strain


title: CAPU_Treated_BiologicalRepB


title: ChIP-POL2

tag: cell line

value: male

value: PolII

value: Santa Cruz Biotechnology

value: N20x; Cat#sc-899x

tag: input sample used


title: saC9_R1_spC9_AAVS1_Rep2

description: Processed data file: saC9_R1_spC9_AAVS1_s3.txt (Filtered Junctions)

value: 293T-Embryonic Kidney

tag: nuclease delivery

value: PEI; saCas9:RAG1.1; spCas9:AAVS1

tag: target locus

value: RAG1 (saCas9:RAG1.1 gRNA)


title: ChIP-PAX5

value: Novus


title: CAPU_Treated_BiologicalRepA


title: saC9_R1_spC9D10A_AAVS1_Rep2

value: PEI; saCas9:RAG1.1; spCas9D10A:AAVS1

tag: extract protocol (dna fragmentation/blocking methods)

value: Sonication


title: ChIP-P65


title: Case no. 25; primary GIST

tag: tissue

value: gastrointestinal stromal tumor

tag: age

tag: gender

value: M

tag: primary tumor site

value: stomach

tag: metastatic tumor site

value: intermediate

value: II

value: PDGFRA


title: ChIP-NPC

value: Ramos

tag: cell type

value: Burkitt's lymphoma-derived cell line, EBV-negative

value: WT

value: Nuclear Pore Proteins

value: Abcam


title: saC9_R1_spC9_AAVS1_Rep3

value: 293T-Embryonic Kidney

tag: genotype


title: Case no. 23; primary GIST

value: F

tag: risk

tag: tumor stage

tag: kit/pdgfra mutation type

value: KIT

tag: kit/pdgfra mutation site


title: CA_Treated_BiologicalRepA

source_name: Yeast cells treated with CAS

tag: strain


title: ChIP-NFKB1

source_name: Ramos cell line

tag: cell line

tag: cell line source gender

value: male

tag: chip antibody

tag: chip antibody vendor

value: Cell Signaling Technology

tag: chip antibody cat. #


title: Case no. 22; primary GIST

tag: tissue

value: duodenum

value: high


title: Case no. 26; primary GIST

value: gastrointestinal stromal tumor

tag: age

value: M

value: IB


title: Case no. 21; primary GIST

tag: gender

value: stomach

value: II


title: Case no. 27; primary GIST

tag: primary tumor site

value: intermediate


title: saC9_R1_spC9D10A_AAVS1_Rep1

tag: nuclease delivery

value: PEI; saCas9:RAG1.1; spCas9D10A:AAVS1

tag: target locus

value: RAG1 (saCas9:RAG1.1 gRNA)

tag: extract protocol (dna fragmentation/blocking methods)

value: Sonication


title: PU_Treated_BiologicalRepC

source_name: Yeast cells treated with PUUP


title: ChIP-MEF2B

value: Ramos

tag: cell type

value: Burkitt's lymphoma-derived cell line, EBV-negative

tag: genotype

value: WT

value: Abcam

tag: input sample used


title: Case no. 20; primary GIST

value: colon (rectum)

tag: metastatic tumor site

tag: risk

tag: tumor stage

tag: kit/pdgfra mutation type

value: KIT

tag: kit/pdgfra mutation site


title: ChIP-IRF8

tag: cell line

tag: cell line source gender

value: male

tag: chip antibody

tag: chip antibody vendor

value: Cell Signaling Technology


title: CA_Treated_BiologicalRepB

tag: strain


title: PU_Treated_BiologicalRepB


title: PU_Treated_BiologicalRepA


title: saC9_R1_Rep2

value: 293T-Embryonic Kidney

value: PEI; saCas9:RAG1.1


title: CA_Treated_BiologicalRepC


title: DMSO_Control_BiologicalRepC

source_name: Yeast cells treated with DMSO


title: ChIP-IRF4

tag: chip antibody cat. #


title: P5_after

city: Saint Petersburg

first: Oksana

last: Ivanova

address: 2 Akkuratova street

department: Institute of Molecular Biology and Genetics

country: Russia

institute: Almazov National Medical Research Centre

data_processing:
Read quality was checked for each sample using FastQC v0.11.5.
Sequenced reads were mapped to the genome using mapper STAR v2.5 with reference genome GRCh38.p12 and annotation Gencode v28.
Aligned reads were count with featureCounts program.
Further analysis were made using DESeq2 and fGSEA R packages, as well as MSigDB and phantasus online tools.
Genome_build: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary_files_format_and_content: tab-delimited text file includes matrix of counts for each of 6 Samples

source_name: Gastrocnemius muscle

extract_protocol:
Gastrocnemius muscle samples were removed, put on ice and saved in liquid nitrogen for storage. RNA was extracted using ExtractRNA reagent (Evrogen, Moscow,Russia, Cat#BC032) and quantified with Bioanalyser 2100 instrument  (Agilent Technologies, Palo Alto, CA) using BA RNA nano kit.
3' mRNA libraries were prepared using QuantSeq 3‘mRNA-Seq Library Prep Kit for Illumina (FWD) (Lexogen, Vienna, Austria, Cat#015) from 1mkg of total RNA and PCR anplified for 15 cycles. Libraries were sequenced on MiSeq using kit MiSeq Reagent Kit v3 2x75 (Cat#MS-102-3001) in the single-end read mode.

tag: tissue

value: gastrocnemius muscle

tag: Sex

tag: age

tag: bmi

tag: disorder

value: Heart failure

tag: training period

value: 12 weeks

tag: treatment

value: individual exercise rehabilitation programm


title: Case no. 24; primary GIST

value: gastrointestinal stromal tumor

tag: gender

value: M

tag: primary tumor site

value: stomach

tag: metastatic tumor site

tag: risk

value: intermediate

value: II

value: PDGFRA


title: P5_before

value: 0 weeks


title: P4_after


title: Case no. 19; primary GIST

value: esophagus

value: high

tag: tumor stage

tag: kit/pdgfra mutation type

tag: kit/pdgfra mutation site


title: ChIP-INPUT2

tag: cell line

value: Ramos

tag: cell type

value: Burkitt's lymphoma-derived cell line, EBV-negative

tag: genotype

value: WT

tag: cell line source gender

value: male

tag: chip antibody

value: normal rabbit IgG

tag: chip antibody vendor

value: EMD Millipore


title: saC9_R1_spC9_AAVS1_Rep1

value: 293T-Embryonic Kidney

tag: nuclease delivery

value: PEI; saCas9:RAG1.1; spCas9:AAVS1

tag: target locus

value: RAG1 (saCas9:RAG1.1 gRNA)

tag: extract protocol (dna fragmentation/blocking methods)

value: Sonication


title: Case no. 18; primary GIST

tag: tissue

value: gastrointestinal stromal tumor

tag: age

value: M

value: stomach

value: KIT


title: DMSO_Control_BiologicalRepB

tag: strain


title: P4_before

value: gastrocnemius muscle

tag: Sex

tag: bmi

tag: disorder

value: Heart failure

tag: training period

value: 0 weeks

tag: treatment


title: DMSO_Control_BiologicalRepA


title: ChIP-INPUT1

tag: cell line

value: Ramos

tag: chip antibody cat. #


title: ChIP-IKAROS

tag: cell type

value: Burkitt's lymphoma-derived cell line, EBV-negative

tag: genotype

value: Ikaros D10E5 Rabbit mAb

value: Cell Signaling Technology

tag: input sample used


title: P1_after

value: male

value: 12 weeks

value: individual exercise rehabilitation programm


title: 454C

city: New Haven

first: Micha Sam

middle: Brickman

last: Raredon

state: Connecticut

address: 10 Amistad Street

department: Biomedical Engineering

institute: Yale University

description: 10x Genomics

data_processing:
FASTQ read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 30 bp long were discarded.
Downstream processing was conducted with zUMIs v 0.4 (44) with the default parameters; the top 10,000 cell barcodes ranked by reads were output for each sample.
Cells were accepted with greater than 500 and fewer than 10000 unique mapped genes. Analysis was performed on cells with less than 5% mitochondrial mapping for the mouse, rat, and pig samples and less than 8% for the human samples.
Genome_build: Ensembl GRCm38 release 92, Ensembl Rnor6.0 release 92, Ensembl Sscrofa11.1 release 92, and Ensembl GRCh38 release 91 were used to align the mouse, rat, pig, and human data respectively.
Supplementary_files_format_and_content: sparse matrix file of raw counts; genelist (rownames for .mtx file); barcodes (column names for .mtx file)

source_name: Lung

extract_protocol:
Lungs were exracted and perfused/inflated with an enzyme mixture containing collagenase, elastase, dispase, and DNAse. Following a 20-40 minute incubation, tissue was pushed through a metal strainer to dissociate.  All subsequent steps performed on ice. Total time from tissue perfusion to library preparation <2 hours.
Single-cell libraries were prepped using the standard 10x Genomics v2 processing workflow. Cell loadings were designed to yield ~5000 cells per library.
10x genomics standard library preparation. Sequencing on Illumina HiSeq 4000 sequencers, indexed to yield a mean read depth of ~88,000 reads per cell. Read 1 sequencing was 26 bp long, read 2 sequencing was 98 bp long.

value: 48 years

value: female

value: Lung


title: Case no. 17; primary GIST

value: gastrointestinal stromal tumor

tag: gender

tag: primary tumor site

tag: metastatic tumor site

tag: risk

value: high

tag: tumor stage

value: IIIA

tag: kit/pdgfra mutation type

tag: kit/pdgfra mutation site


title: saC9_R1_Rep1

value: 293T-Embryonic Kidney

value: WT

tag: nuclease delivery

value: PEI; saCas9:RAG1.1

tag: target locus

value: RAG1 (saCas9:RAG1.1 gRNA)

tag: extract protocol (dna fragmentation/blocking methods)

value: Sonication


title: Case no. 16; primary GIST

tag: tissue

tag: age

value: F

value: colon (ascending)

value: KIT


title: Case no. 15; primary GIST

value: M

value: stomach


title: ChIP-HELIOS

tag: cell line

value: Ramos

value: Burkitt's lymphoma-derived cell line, EBV-negative

tag: cell line source gender

value: male

tag: chip antibody

value: Helios D8W4X

tag: chip antibody vendor

value: Cell Signaling Technology


title: P1_before

value: gastrocnemius muscle

tag: Sex

tag: bmi

tag: disorder

value: Heart failure

tag: training period

value: 0 weeks

tag: treatment


title: Case no. 14; primary GIST

value: gastrointestinal stromal tumor

tag: gender

tag: primary tumor site

value: colon (rectum)

tag: metastatic tumor site

tag: risk

value: high

tag: tumor stage

value: IIIB


title: 388C

description: 10x Genomics

value: 61 years

value: Lung


title: ChIP-H3K27Ac

tag: cell type

tag: genotype

value: WT

value: Abcam

tag: chip antibody cat. #

tag: input sample used


title: TOF-22_RV_smallRNA

city: Berlin

first: Silke

last: Sperling

state: Berlin

address: Lindenberger Weg 80

department: Cardiovascular Genetics

institute: Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine

description: Small RNA-Seq.

data_processing:
Sequencing reads were extracted from the image files using the open source Firecrest and Bustard applications (Illumina Genome Analyzer pipeline 1.3.2). MicroRNA reads were mapped to the human reference genome (NCBI v36.1; hg18) using MicroRazerS with the following parameters: -m 20 -pa -sL 18 -sE. Multimatched reads were proportionally assigned to their loci. Using annotations from miRBase database 14.0, reads could be assigned to known mature microRNA sequences. Read count normalization for microRNAs was performed using the RNA composition adjustment by trimmed mean of M-values (TMM) and quantile-to-quantile count adjustment implemented in the edgeR package.

Processed data files are linked to the Series record as supplementary files.

source_name: right ventricle from TOF human heart

extract_protocol: Total RNA was isolated from human heart samples using TRIzol reagent. Small RNAs were isolated from total RNA and prepared for microRNA sequencing using Illumina Kit FG-102-1009 according to the manufacturer's protocol (Preparing Samples for Analysis of Small RNA Illumina 2007). The sequencing libraries were generated using a non-strand-specific library construction method.

tag: tissue

value: heart, right ventricle

tag: disease state

value: Tetralogy of Fallot (TOF)


title: ChIP-H3

tag: cell line

value: Ramos

value: Burkitt's lymphoma-derived cell line, EBV-negative

tag: cell line source gender

tag: chip antibody

value: anti-H3 antibody

tag: chip antibody vendor


title: 244C

description: 10x Genomics

tag: age

value: 50 years

tag: Sex

value: male


title: 222C

description: 10x Genomics

value: 65 years


title: ChIP-ELF2

value: Invitrogen


title: TOF-20_RV_smallRNA

description: Small RNA-Seq.


title: 160C

description: 10x Genomics

value: 64 years


title: 192C

description: 10x Genomics

value: 62 years

value: female


title: ChIP-ELF1

value: Bethyl


title: ChIP-E2A

value: Cell Signaling Technology


title: Case no. 13; primary GIST

value: gastrointestinal stromal tumor

tag: gender

value: F

value: colon (rectum)

value: high

value: IIIB

tag: kit/pdgfra mutation type

value: KIT

tag: kit/pdgfra mutation site


title: TOF-19_RV_smallRNA

description: Small RNA-Seq.

value: heart, right ventricle

value: Tetralogy of Fallot (TOF)


title: TOF-18_RV_smallRNA

description: Small RNA-Seq.


title: TOF-17_RV_smallRNA

description: Small RNA-Seq.


title: ChIP-CREL

value: Ramos

value: Burkitt's lymphoma-derived cell line, EBV-negative

value: WT

value: c-Rel


title: Case no. 9; primary GIST

tag: primary tumor site

value: stomach

tag: metastatic tumor site

tag: risk


title: Case no. 10; primary GIST

value: M

tag: tumor stage


title: Case no. 12; primary GIST

value: small intestine


title: ChIP-BCL6

tag: cell type

tag: genotype

value: male

tag: chip antibody cat. #


title: Case no. 8; primary GIST

tag: tissue

value: IV


title: TOF-21_RV_smallRNA

description: Small RNA-Seq.

tag: disease state


title: TOF-16_RV_smallRNA

description: Small RNA-Seq.


title: 1372C

description: 10x Genomics

value: 21 years

value: female

value: Lung


title: Case no. 11; primary GIST

value: gastrointestinal stromal tumor

value: duodenum

value: high


title: 133C

description: 10x Genomics

value: 32 years


title: TOF-15_RV_smallRNA

description: Small RNA-Seq.

value: heart, right ventricle

value: Tetralogy of Fallot (TOF)


title: 098C

description: 10x Genomics

value: 41 years


title: HeLa hypoxia rep2

city: Frankfurt am Main

first: Kathi

last: Zarnack

address: Max-von-Laue-Str. 15

institute: BMLS - Buchmann Institute for Molecular Life Sciences

data_processing:
Stranded RNA sequencing (RNA-seq) libraries were sequenced on Illumina NextSeq sequencer (75-nt single-end), yielding ca. 60 million reads per sample.
Reads were filtered based on sequencing quality (Phred score > 20) and read length (> 20 nt) using Flexbar (version 2.5).
Sequencing qualities were checked before and after trimming using FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the human genome (hg38/GRCh38) and its annotation (GENCODE release 24) (Harrow et al., 2012) using the splice-aware aliger STAR (version 2.4.5a) (Dobin et al., 2013) allowing up to 2 mismatches and with parameters --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15 for chimeric reads detection. For circRNA detection using find_circ, the same reads were also mapped using Bowtie2 as described in (Memczak et al., 2013).
Uniquely mapped reads from STAR were summarized per gene using htseq-count  from the python package HTSeq (version 0.6.1) (Anders et al., 2015). Chimeric reads from STAR were used to quantify circRNA expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include raw back-splicing read counts for each sample.

source_name: HeLa hypoxia

growth_protocol: HeLa cells were cultured in 10 cm2 plates in high glucose (4.5 g/l) DMEM medium (Sigma Aldrich) supplemented with 10% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin (PenStrep, all Thermo Fisher Scientific).

extract_protocol:
Total RNA was isolated using the miRNeasy Mini kit (Qiagen), including the optional on-column DNA digestion with the RNase-Free DNase Set (Qiagen).
After isolation, 500 ng RNA were quality checked on a 1% agarose gel. rRNA was depleted using the RiboZero kit (Zymo). Libraries were prepared and sequenced on a Illumina NextSeq sequencer with HighOutput

treatment_protocol: For hypoxia treatment, HeLa cells were plated and grown in a normal incubator until they reached 60% confluency (21% O2, 37°C, 5% CO2), then either kept in the normal incubator for normoxic conditions or transferred to a hypoxia chamber (0.2% O2, 37°C, 5% CO2) for 24 h.

tag: cell line

value: HeLa

tag: oxygen condition

value: hypoxia


title: TOF-14_RV_smallRNA

description: Small RNA-Seq.


title: 048C

description: 10x Genomics

value: 35 years


title: ChIP-AIOLOS

value: Ramos

value: Burkitt's lymphoma-derived cell line, EBV-negative

value: WT

tag: cell line source gender

tag: chip antibody

value: Aiolos D1C1E Rabbit mAb

tag: chip antibody vendor

value: Cell Signaling Technology

tag: input sample used


title: TOF-13_RV_smallRNA

description: Small RNA-Seq.


title: 001C

description: 10x Genomics

tag: age

value: 22 years

tag: Sex

value: male


title: HeLa hypoxia rep1


title: 137C

description: 10x Genomics

value: 54 years

value: Lung


title: HeLa normoxia rep3

source_name: HeLa normoxia

value: normoxia


title: Case no. 6.2; primary GIST

source_name: primary GIST

value: gastrointestinal stromal tumor

tag: gender

value: M

tag: primary tumor site

value: stomach

value: high

value: IV

tag: kit/pdgfra mutation type

value: PDGFRA

tag: kit/pdgfra mutation site


title: TOF-12_RV_smallRNA

description: Small RNA-Seq.

value: heart, right ventricle

value: Tetralogy of Fallot (TOF)


title: Case no. 6.1; metastatic GIST

source_name: metastatic GIST

tag: metastatic tumor site

value: peritoneum

tag: risk

tag: tumor stage


title: Case no. 5; metastatic GIST

tag: tissue

value: omentum

value: liver


title: Case no. 7; primary GIST

value: F

value: KIT


title: HeLa normoxia rep2

value: HeLa


title: HeLa normoxia rep1


title: TOF-10_RV_smallRNA

description: Small RNA-Seq.

tag: disease state


title: TOF-11_RV_smallRNA

description: Small RNA-Seq.


title: Case no. 4; metastatic GIST

value: small intestine


title: Case no. 3; metastatic GIST


title: NDRI_1b

description: 10x Genomics

data_processing:
FASTQ read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 30 bp long were discarded.
Downstream processing was conducted with zUMIs v 0.4 (44) with the default parameters; the top 10,000 cell barcodes ranked by reads were output for each sample.
Cells were accepted with greater than 500 and fewer than 10000 unique mapped genes. Analysis was performed on cells with less than 5% mitochondrial mapping for the mouse, rat, and pig samples and less than 8% for the human samples.
Genome_build: Ensembl GRCm38 release 92, Ensembl Rnor6.0 release 92, Ensembl Sscrofa11.1 release 92, and Ensembl GRCh38 release 91 were used to align the mouse, rat, pig, and human data respectively.

value: 88 years

value: female


title: fMouse

description: 10x Genomics

extract_protocol:
Lungs were exracted and perfused/inflated with an enzyme mixture containing collagenase, elastase, dispase, and DNAse. Following a 20-40 minute incubation, tissue was pushed through a metal strainer to dissociate.  All subsequent steps performed on ice. Total time from tissue perfusion to library preparation <2 hours.
Single-cell libraries were prepped using the standard 10x Genomics v3 processing workflow. Cell loadings were designed to yield ~5000 cells per library.
10x genomics standard library preparation. Sequencing on Illumina HiSeq 4000 sequencers, indexed to yield a mean read depth of ~88,000 reads per cell. Read 1 sequencing was 26 bp long, read 2 sequencing was 98 bp long.

value: 9 weeks


title: HC1

description: 10x Genomics

value: 76 years


title: mMouse

description: 10x Genomics

value: male


title: Case no. 1; metastatic GIST

value: gastrointestinal stromal tumor

value: M

value: duodenum


title: TOF-08_RV_smallRNA

description: Small RNA-Seq.

value: heart, right ventricle


title: iM2_CCR5_2

city: Bethesda

first: Manfred

last: Boehm

state: MD

address: 9000 Rockbille Pike

institute: NHLBI

data_processing:
RNA-seq data quality was assessed using FastQC
Reads obtained for each sample were aligned to the hg19 human reference genome using STAR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include total counts values for all samples

source_name: skin biopsy

growth_protocol: 5 Control and 3 CCR5-delta  mutation patient-derived fibroblasts lines were generated from 3-4-mm skin biopsies following informed consent under protocols approved by NHLBI IRB. Fibroblasts derived from individuals with the homozygous CCR5Δ32 variant and healthy volunteers were collected from explants of 4-mm skin punch biopsy specimens and grown in Dulbecco's mod-ifiedEagle'smedium(DMEM)containing10%fetalcalfserumand1%penicillin-streptomycin,aspreviouslydescribed(Jinetal.,2016).After1-2weeks, fibroblast outgrowths from thee-xplants were passaged. Fibroblasts from individuals with the homozygous CCR5Δ32 variant were reprogrammed to generate iPSC lines by transduction with the Human STEMCCA Cre-Excisable Constitutive Polycistronic (OKSM) Lentivirus Reprogramming Kit(Millipore).iPSC colonies were collected at 21days post-transduction, and expanded in a typical hESC/iPSC culture condition. hiPSCs were differentiated to iPS-derived monocytes(iMono) and macrophages(iMac) using the step-wise protocol to drive hiPSCs prone into mesoderm precursors in feeder free and chemical defined condition, following by specifically linage commitment and maturation (described in the manuscript).

extract_protocol:
Total RNA integrity was assessed using automated capillary electrophoresis on a Fragment Analyzer (Roche, Indianapolis, IN)
For all samples RQI > 8.0, a total RNA amount of 500 ng was used as input for library preparation using the TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA, USA).

treatment_protocol: Monocytes (iPS-drived monocytes and primary monocytes) were subsequently either differentiated into macrophages in the presence of M-CSF in vitro and further polarized into M0, M1 and M2 macrophages. In particular, For M0 polarization, macrophages were cultured for 24h with RPMI1640 complete (+ 10% FBS + 2mmol/L L-Glutammine + 100U/mL penicillin and 100ug/mL streptomycin. For M1 polarization, macrophages were cultured for 24h in presence of LPS (100 ng/mL; Sigma, from E.coli 055:B5) and rhIFN-gamma (20ng/mL). For M2 polarization, macrophages were cultured for 24 h in presence of rhIL-4 (20 ng/mL).

tag: individual

value: CCR5 Patient

tag: isolated cell type

value: skin fibroblasts

tag: final cell type


title: KO_3

first: Marco

last: Seandel

department: Surgery

institute: Weill Cornell Medical College

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (for RNA-seq samples) (Andrews 2010, Hartley and Mullikin (2015)).
Sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38) using STAR (Dobin et al. 2013). Gene expression estimates were obtained with featureCounts using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M3) (Liao, Smyth, and Shi 2014, Harrow et al. (2012)).
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: cultured adult spermatogonial stem cells

growth_protocol: SSCs are cultured in media consisting of StemPro-34 with additional supplements and growth factors as described in Yamada M et al., 2019

extract_protocol:
RNA was isolated using QIAGEN RNeasy Micro Kit
Directional RNA-seq libraries were prepared from 450ng total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: SSCs were electroporated with a plasmid expressing a GFP reporter with or without an sgRNA targeting Ephb2. GFP positive cells were then sorted, sub-cloned and sequenced to create 3 WT cell lines and 3 KO cell lines.

value: adult

tag: passage

tag: genotype/variation


title: KO_2


title: Case no. 2; metastatic GIST

value: liver

value: IV


title: iM2_CCR5_1


title: TOF-07_RV_smallRNA

description: Small RNA-Seq.

value: Tetralogy of Fallot (TOF)


title: KO_1


title: S_T8_ceres2_rep2

city: MADRID

first: M.

middle: MAR

last: CASTELLANO

address: Crta. de la Coruña, km 7,5

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA (CBGP)

description: processed data file: DEF_24_30_NOR_DE_TE_deseq2_GEO.xls

data_processing:
TopHat (version 2.1.0)
featureCounts (Version 1.6.2)
DESeq2 R package (version 1.1.14)
Genome_build: Arabidopsis thaliana Ensembl Genomes release 27
Supplementary_files_format_and_content: DEF_24_30_NOR_DE_TE_deseq2_GEO.xls: Excel file with counts and differential expression values.

organism: Arabidopsis thaliana

source_name: 9-day-old seedlings

growth_protocol: 9-day-old Arabidopsis seedlings form Col-0 and ceres-1, ceres-2 mutants.

extract_protocol: TruSeq Ribo Profile (Mammalian) Library Prep Kit.

treatment_protocol: Grown under control conditions. Seedlings were harvested at Zeitgeber time 5 (ZT5).

tag: ecotype/background

value: Seedlings

value: 9 days


title: TOF-09_RV_smallRNA

description: Small RNA-Seq.


title: WT_3

tag: age

value: wild type


title: iM1_CCR5_3


title: TOF-06_RV_smallRNA

description: Small RNA-Seq.


title: iM1_CCR5_2


title: S_T7_ceres2_rep1


title: WT_2


title: TOF-05_RV_smallRNA

description: Small RNA-Seq.


title: S_T6_ceres1_rep3


title: iM2_CCR5_3


title: iM1_CCR5_1


title: WT_1


title: S_T5_ceres1_rep2


title: TOF-04_RV_smallRNA

description: Small RNA-Seq.


title: TOF-03_RV_smallRNA

description: Small RNA-Seq.


title: S_T9_ceres2_rep3


title: iM0_CCR5_3


title: TOF-02_RV_smallRNA

description: Small RNA-Seq.


title: iM0_CCR5_2


title: S_T4_ceres1_rep1


title: iM0_CCR5_1


title: S_T3_COL_0_rep3

value: WT


title: TOF-01_RV_smallRNA

description: Small RNA-Seq.


title: S_T2_COL_0_rep2


title: NH-08_RV_smallRNA

description: Small RNA-Seq.

source_name: right ventricle from normal human heart

value: healthy


title: S_T1_COL_0_rep1


title: pM2_ctrl_7

source_name: peripheral blood

value: Healthy Control

value: PBMC


title: pM2_ctrl_1


title: pM2_ctrl_8


title: NH-07_LV_smallRNA

description: Small RNA-Seq.

source_name: left ventricle from normal human heart

value: heart, left ventricle


title: NH-06_RV_smallRNA

description: Small RNA-Seq.


title: S_R8_ceres2_rep2

description:
mRNA ribosome footprint
processed data file: DEF_24_30_NOR_DE_TE_deseq2_GEO.xls

data_processing:
Library strategy: Ribo-seq
TopHat (version 2.1.0)
featureCounts (Version 1.6.2)
DESeq2 R package (version 1.1.14)
Genome_build: Arabidopsis thaliana Ensembl Genomes release 27
Supplementary_files_format_and_content: DEF_24_30_NOR_DE_TE_deseq2_GEO.xls: Excel file with counts and differential expression values.


title: NH-05_LV_smallRNA

description: Small RNA-Seq.


title: S_R7_ceres2_rep1


title: pM1_ctrl_8


title: pM1_ctrl_7


title: NH-04_RV_smallRNA

description: Small RNA-Seq.


title: S_R6_ceres1_rep3


title: pM1_ctrl_2


title: NH-03_LV_smallRNA

description: Small RNA-Seq.


title: S_R5_ceres1_rep2


title: pM1_ctrl_1


title: NH-02_RV_smallRNA

description: Small RNA-Seq.


title: S_R4_ceres1_rep1


title: pM0_ctrl_8


title: NH-01_LV_smallRNA

description: Small RNA-Seq.


title: S_R3_COL_0_rep3


title: pM0_ctrl_7


title: S_R2_COL_0_rep2


title: pM0_ctrl_1


title: S_R1_COL_0_rep1


title: S_R9_ceres2_rep3


title: Noff_stem_air_2d_R3

city: Bayreuth

first: Angelika

last: Mustroph

address: Universitaetsstr. 30, NWI

department: Plant Physiology

institute: University Bayreuth

data_processing:
Adapters were trimmed from the FASTQ files using the BBDuk algorithm.
Quantification of aligned reads to the published transcriptome by Voutsina et al., 2016 was performed using Kallisto (Bray et al., 2016).
Differential expression analysis was performed with the edgeR and limma Bioconductor packages in R. Log2 Fold Changes and Benjamini-Hochberg-corrected P-values were calculated fitting a negative binomial generalized log-linear model with a full factorial design matrix of treatment and tissue.
Genome_build: PRJNA284126
Supplementary_files_format_and_content: tab-separated text files include length of transcript, est_counts and tpm for each sample

organism: Nasturtium officinale

source_name: stems of 3-week-old plants

growth_protocol: For germination, several seeds were sown in the same pot on sterilized soil. After 6-7 d, germinated seedlings were transplanted to single pots. Plants grew under short-day conditions (8 h light/ 16 h dark cycle), 23 °C, and 100 μmol photons m-2 s-1 for about two more weeks.

extract_protocol:
Frozen samples of three replicates were ground for 3 min in 2 ml tubes with Zirconia/Silica beads using Mini-Beadbeater (BioSpec Products, Bartlesville, OK, USA) in plates frozen with liquid nitrogen. After grinding, 1 ml Lysis binding buffer (Dynabeads mRNA Direct Kit, Thermo Fisher Scientific, Waltham, MA, USA) was added and samples were homogenized with this buffer for an additional 2 min in the Mini-Beadbeater. Homogenized samples were centrifuged at 10,000 rpm for 3 min and loaded onto a homogenizer spin column (Omega Bio-Tek, Norcross, GA, USA) and centrifuged to remove excess tissue. Lysates were transferred to a 96-well plate and stored at -80°C until library preparations.
RNA-seq libraries were constructed using BrAD-seq protocol for non-strand specific libraries (Townsley et al., 2015). 200 μl of lysates were used for mRNA isolation, following manufacturer’s instructions (Dynabeads mRNA Direct Kit, Thermo Fisher Scientific, Waltham, MA, USA). Isolated mRNA was fragmented by RT buffer for 90 sec at 94°C (RevertAid RT enzyme, Thermo Fisher Scientific, Waltham, MA, USA), and cDNA synthesis was done on the fragmented mRNA. Second strand synthesis was done according to BrAD-seq protocol and was followed by adapter ligation. PCR enrichment was performed using unique indexed oligos for multiplexing. After purification, sample concentration was measured on a plate reader (with SYBR Green I Nucleic Acid Gel Stain, Invitrogen, Carlsbad, CA, USA) and sample concentrations for multiplexing were adjusted accordingly. Multiplexing within the plate was done in a completely randomized design. Multiplexed samples were analyzed on a Bioanalyzer for contamination and size confirmation. The size of the fragments varied between 200 and 500 bps. Samples were sequenced on Hiseq4000 with 100 bp paired-end mode.

treatment_protocol: Plants of the 5-6 leaf stage were selected for developmental homogeneity before the start of the experiments. Two hours after the start of the photoperiod, plants were completely submerged under short-day conditions in plastic tubs, filled with temperature-adjusted water, or kept in air in similar plastic tubs. Stems and petioles of air and submerged plants (five plants pooled per sample) were harvested separately after 1 and 2 days and frozen in liquid nitrogen.

tag: treatment

value: air

tag: treatment duration

value: 2 days


title: pmono_ctrl_2

value: pmono


title: pmono_ctrl_1


title: Noff_stem_sub_2d_R3

value: submergence


title: Noff_pet_sub_2d_R3

source_name: petioles of 3-week-old plants


title: Noff_stem_air_1d_R3

value: 1 day


title: iM2_ctrl_5

value: skin fibroblasts


title: iM2_ctrl_4


title: Noff_pet_air_1d_R3


title: iM2_ctrl_3


title: Fezf1Hete_No26

city: Los Angeles

first: Yi-Rong

last: Peng

address: 100 Stein Plaza Driveway, B-133

institute: University of California, Los Angeles

description: lgTPM-allSACs.txt

data_processing:
Reads were aligned to a reference genome (mm10 Ensembl) using Tophat v2.0.10
Expression levels were quantified using cufflinks (inferred counts and tpm values)
FPKM was transformed into log10(TPM)
Genome_build: mm10
Supplementary_files_format_and_content: One tab-delimited text file include lgTPM values for all the samples

source_name: Mus musculus retina, E17.5

extract_protocol:
E17.5 Fezf1GFP/+ and Fezf1GFP/GFP SACs were isolated by FACS in pools of 100 cells. 13 replicates were collected from either Fezf1GFP/+ or Fezf1GFP/GFP retinas. cDNA libraries were prepared with Smart-seq2 and Nextera XT (Picelli et al., 2014).
NexteraXT

tag: strain

tag: genotype

value: Retina

tag: cell type

value: Cholinergic interneurons


title: Noff_stem_sub_1d_R3


title: Noff_pet_air_2d_R3


title: Noff_pet_sub_1d_R3


title: Fezf1Hete_No24

description: lgTPM-allSACs.txt


title: Water treated_water3

city: Mar del Plata

first: Mariana

middle: Laura

last: Feldman

state: Buenos Aires

address: Funes 3250 4to nivel

country: Argentina

institute: IIB-CONICET- Univ. Nac. de Mar del Plata

hyb_protocol: The aRNAs were then fragmented in 200 nt fragments, and 15 ug of these fragmented and labeled aRNAs were used as probes for Array hybridization (Fluidic Station 450, Affymetrix). For each treatment, the hybridization was done three times.

scan_protocol: Scanning of fluorescent signals was done with a GeneChip Scaner 3000 7G, according to the Affymetrix GeneChip Expression Analysis Technical manual

data_processing: Data pre-processing was performed using the rma function implemented in the affy package (Gautier et al., 2004) of R (R Core Team, 2015). Between-arrays normalization was performed using quantile equalization method. Finally, gene expression values were transformed to log2 scale to produce a 10209 genes by 12 arrays (3 replicates for each of the 4 treatments) data matrix.  Statistical analysis was performed using a set of ad hoc R routines to fit, gene by gene, a linear effect model, assuming a completely randomized design of 2 by 2 factorial experiments, being the factors: infection (yes-no) and phosphite treatment (KPhi-control). The routines were based on the nlme package (Pinheiro et al., 2015) and implemented in InfoStat statistical software (Di Rienzo et al., 2015). Preliminary candidate genes were selected by the p-value criterion using a p-value threshold of 0.05 for either the main or the interaction effects. A linear model of fixed effects was adjusted, including the effects of Infection, Phosphite and their interaction.

label: biotin

organism: Solanum tuberosum

source_name: Leaves

label_protocol: Total RNAs obtained during the tissue extraction were processed to obtain dsDNAs. In vitro transcription was performed to generate antisense cRNAs (aRNAs) using biotin-modified nucleotides.

growth_protocol: Solanum tuberosum seed tubers (cv. Shepody) were planted in pots containing a pasteurized mixture of soil and vermiculite (3:1, v/v). Pots were maintained under greenhouse conditions (18°C day-night temperature, 16 h of light per day).

extract_protocol: Total RNAs were extracted from leaf tissue using the Trizol reagent according to the manufacturer's instructions (Invitrogen), and treated with DNAse (Promega) to avoid DNA contamination. RNAs were processed for use on an Affymetrix Tomato Gene Chip.

treatment_protocol: Potassium phosphite (KPhi), 1% (v/v) water solution of the commercial product (Afital Potassium Phosphite, Agro-EMCODI SA) was applied to the foliage at 5 mL per plant (3 L/ha) by using an atomizer (ESAC SA) operating at 200 kPa, 21 days after emergence and leaves were harvested after 72h. Control samples were treated with water. Three days after KPhi or water treatment, two leaflets per plant were detached from ten plants per treatment. These leaflets were immediately placed on a wet filter paper in Petri dishes and artificially inoculated with a zoospore suspension (2×104 zoospores mL -1) of P. infestans or H2O by spray. The inoculated leaflets were then incubated at 18◦C. At 24 h post-inoculation, leaves were used for RNA extraction.

tag: agent

value: Water treated_water

tag: cultivated variety

value: Shepody

value: 21 days post emergency


title: iM2_ctrl_2


title: Noff_stem_air_2d_R2


title: Kphi treated_Infected3

value: Kphi treated_Infected


title: iM2_ctrl_1


title: pmono_ctrl_7


title: Fezf1Hete_No23

description: lgTPM-allSACs.txt


title: iM1_ctrl_5


title: iM1_ctrl_4


title: Water treated_Infected3

value: Water treated_Infected


title: Noff_stem_sub_2d_R2


title: Kphi treated_water2

value: Kphi treated_water


title: Noff_pet_air_2d_R2


title: Kphi treated_water3


title: Fezf1KO_No22

description: lgTPM-allSACs.txt


title: Fezf1KO_No21

description: lgTPM-allSACs.txt


title: Water treated_Infected2


title: Noff_pet_sub_2d_R2


title: iM1_ctrl_3

value: Healthy Control


title: Fezf1KO_No19

description: lgTPM-allSACs.txt


title: Fezf1Hete_No25

description: lgTPM-allSACs.txt


title: Fezf1KO_No20

description: lgTPM-allSACs.txt


title: Water treated_water2


title: iM1_ctrl_1


title: iM1_ctrl_2


title: iM0_ctrl_5


title: Noff_stem_sub_1d_R2


title: Kphi treated_water1


title: Fezf1Hete_No18

description: lgTPM-allSACs.txt


title: Noff_pet_air_1d_R2


title: Noff_stem_air_1d_R2


title: Fezf1Hete_No17

description: lgTPM-allSACs.txt


title: Kphi treated_Infected1


title: Water treated_Infected1


title: Control (NC) replicate 3

city: 杭州

first: Zhe

last: Zhang

state: 浙江

address: Yuhangtang Road 866

institute: Zhe Jiang University

data_processing:
Reads were trimmed to remove the bases with low quality and adapter sequences
The trimmed reads were assigned directly to transcripts and counted with Salmon software
Gene expression level was quantified and normalized by Salmon
Differentially expressed genes between 4 genotypes and NC overexpression groups were selected by DESeq2 with Padj. <0.05 and fold change (FC) of >1.2 or <-1.2
Genome_build: 11.1
Supplementary_files_format_and_content: txt

organism: Sus scrofa

source_name: Cell line

extract_protocol:
Total RNA was isolated using MiniBEST Universal RNA extraction kit (Takara)
mRNAs were separated with oligo(dT)25 beads from total RNA. mRNA was fragmented and reverse transcribed. The cDNA library was subjected to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.

treatment_protocol: The different treatments of samples were undertaken by overexpression of different mutants of PKD2 (genotypes) via transfection of different plasmids. FLAG-floxP-neo-pH11 is the plasmid used.

tag: cell line

value: LLC-PK1 cells

tag: overexpression

value: FLAG-floxP-neo-pH11 with no PKD2 gene


title: Noff_pet_sub_1d_R2


title: Control (NC) replicate 1


title: iM0_ctrl_4


title: Fezf1Hete_No16

description: lgTPM-allSACs.txt

tag: tissue


title: Noff_stem_air_2d_R1

value: air


title: Genotype 3 (WT) replicate 3

value: FLAG-floxP-neo-pH11 with WT PKD2


title: Water treated_water1


title: Noff_pet_air_2d_R1

value: 2 days


title: Fezf1KO_No15

description: lgTPM-allSACs.txt


title: Control (NC) replicate 2


title: iM0_ctrl_2

tag: individual


title: Fezf1KO_No14

description: lgTPM-allSACs.txt


title: Fezf1KO_No13

description: lgTPM-allSACs.txt


title: Genotype 3 (WT) replicate 2


title: Genotype 3 (WT) replicate 1


title: iM0_ctrl_1

tag: isolated cell type


title: Noff_pet_sub_2d_R1

value: submergence


title: imono_ctrl_5

tag: final cell type

value: imono


title: Genotype 3 (Tg3) replicate 3

value: FLAG-floxP-neo-pH11 with mutant PKD2 (c.C2224T/p.R742X-3)


title: Fezf1Hete_No12

description: lgTPM-allSACs.txt

value: Retina


title: Noff_pet_air_1d_R1

value: 1 day


title: Noff_stem_sub_2d_R1


title: Genotype 3 (Tg3) replicate 2


title: iM0_ctrl_3

value: skin fibroblasts


title: Fezf1Hete_No11

description: lgTPM-allSACs.txt

value: Cholinergic interneurons


title: imono_ctrl_2


title: imono_ctrl_1


title: iPS_ctrl_6

value: iPS


title: Noff_pet_sub_1d_R1


title: Fezf1Hete_No10

description: lgTPM-allSACs.txt


title: Genotype 3 (Tg3) replicate 1


title: iPS_ctrl_4


title: Fezf1Hete_No8

description: lgTPM-allSACs.txt


title: Genotype 2 (Tg2) replicate 2

value: FLAG-floxP-neo-pH11 with mutant PKD2 (c.T1967G/p.L656W-3)


title: iPS_ctrl_3


title: PB1+Pi1 M.oryzae Treated BR3_24hpi

city: New Delhi

first: T

middle: R

last: Sharma

state: Delhi

address: Pusa Campus New

country: India

institute: NRCPB

description: Each Sample has an acceptable hits (aligned) bam file and an unmapped bam file.

data_processing:
CASAVA pipeline 1.7 was used for data processing, demultiplexing and bcl conversion for all samples
The spliced read mapper Tophat v2.0.9 and Bowtie was used to map reads indiviually of each biological replicate(BR) in resistant and suceptible lines against O. sativa Japonica Group cultivar Nipponbare; MSU release 7.
The aligned reads obtained from tophat were analyzed using Qualimap. The aligned reads were visualized on IGV. Cufflink v2.1.1 was used to  assemble aligned reads into transcript. Cufflink measures abundance in fragments per kilobase of exon per million fragments mapped (FPKM).  Cuffdiff was used to quantify transcript using the merged transcript assembly obtained from cuffmerge and to detect differentially expressed genes.
Genome_build: O. sativa Japonica Group cultivar Nipponbare; MSU release 7.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

source_name: Leaf

growth_protocol: Growth conditions of 16 h light (115 μ Mol m–2 s–1) and 8 h dark photoperiod at 25 ± 2°C

extract_protocol:
Rice leaves were collected  after M.oryzae infection from resistant and suceptible line, frozen on liquid nitrogen, and RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: M.oryzae conidia concentration was adjusted to 105spores/ml

value: Indica

value: Leaves from 4 leaf stage rice plant

value: 24 hours after M.oryzae spray

value: PB1+ Pi1


title: Genotype 2 (Tg2) replicate 1

value: LLC-PK1 cells


title: Noff_stem_air_1d_R1

value: air


title: PB1+Pi1 M.oryzae Treated BR2_24hpi


title: C-miR146a3

city: Duarte

first: Marcin

last: Kortylewski

address: 1500 E. Duarte Road

institute: City of Hope National Medical Center

description: test

data_processing: Qiagen Gene Globe Data Analysis for RT2 Profiler PCR Data Analysis, Ct cut-off =37, normalized by Arithmetci mean using ACTB, B2M, GAPDH, HPRT1, and RPLP0 as housekeeping genes

label: SYBR Green

source_name: Bone marrow cells containing HL-60 cancer cells

label_protocol: Qiagen RT2 First Strand Kit followed by RT2 Profiler PCR Array (Human NFkB Signaling Pathway Cat. no. 330231 PAHS-025ZA)

growth_protocol: NOD/SCID/IL-2RgKO (NSG) and NSG Tg(CMV-IL3,CSF2,KITLG)1Eav/MloySzJ (SGM3) mice from Jackson Laboratory. All animal experiments were following institutional guidance and approved protocols from the institutional animal care and use committee (COH).

extract_protocol: Total RNA was isolated from bone marrow cells using the Maxwell RSC miRNA tissue kit in combination with the Maxwell system (Promega).

treatment_protocol: For the systemic leukemia xenograft models, SGM3 mice were injected intravenously with 2×106 of HL-60LUC cells. Tumor progression was monitored using bioluminescent imaging on AmiX (Spectral Instruments). From day 9, mice were injected retro-orbitally with 10mg/kg of C-miR146a or C-scrRNA every other day for 10 days.

tag: mouse strain

value: bone marrow

value: 10mg/kg of C-miR146a

tag: tumor engrafed

value: HL-60 cancer cell engrafted


title: Genotype 1 (Tg1) replicate 3

value: FLAG-floxP-neo-pH11 with mutant PKD2 (c.A1532T/p.D511V-3)


title: C-miR146a2

description: test


title: Fezf1KO_No6

description: lgTPM-allSACs.txt


title: PB1+Pi1 M.oryzae Treated BR1_24hpi


title: Fezf1KO_No4

description: lgTPM-allSACs.txt


title: Noff_stem_sub_1d_R1

value: submergence


title: PB1+Pi1 Mock BR3_24hpi

value: 24 hours after Gelatin spray


title: PB1+Pi1 Mock BR2_24hpi


title: C-scrRNA3

description: scramble

value: 10mg/kg of C-scrRNA


title: Genotype 2 (Tg2) replicate 3


title: Genotype 1 (Tg1) replicate 1


title: Fezf1KO_No3

description: lgTPM-allSACs.txt

value: Retina


title: C-scrRNA2

description: scramble


title: Fezf1Hete_No9

description: lgTPM-allSACs.txt

value: Cholinergic interneurons


title: PB1+Pi1 Mock BR1_24hpi


title: F2

first: Joel

last: Baines

institute: Cornell University

data_processing:
All processing steps were done using the Danko lab template for PRO-seq alignment/QC found at https://github.com/Danko-Lab/utils/tree/master/proseq with instructions at https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md
Pre-processing reads and sequence adapter trimming are done with cutadapt
Reads are mapped to the bwa index reference genome using bowtie
BAM files are converted to BigWig using Kentsource
BigWig can be viewed using IGV, and BAM files analyzed with DESeq2 statistics using SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/.  SeqMonk data is reported in Xcel files as supporting/supplemental information in the publication
Genome_build: HSV-1 reference genome-GU734771.1, the hg38 human genome build, and the dm3 Drosophila melanogaster genome build
Supplementary_files_format_and_content: bigwig

organism:
Drosophila melanogaster
Homo sapiens

source_name: HEP-2 Cells and Drosophila S2 Cells

extract_protocol:
mRNA seq: Cytoplasmic fractions were collected using the nuclei isolation protocol.  The extracts were subjected to oligodT selection of polyadenylated mRNA using poly-A coated magnetic beads.
PRO-seq: Nuclei isolation followed by Nuclear Run-on in the presence of biotinylated nucleotides (A, U, G, C).  Biotinylated transcripts were isolated using streptavadin coated magnetic beads
mRNA seq: Libraries were constructed by Camille Abshire at Louisiana State University Health Science Center in Shreveport in the Genomics Core using the TruSeq Stranded mRNA LS kit.
PRO-seq: Libraries were constructed following the protocol outlined by Mahat et al. 2016. "Base-pair-resolution genome-wide mapping of active RNA Polymerases using precision nuclear run-on (PRO-seq).  Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086

value: HEP-2 Cells and Drosophila S2 Cells

value: lung epithelial cells from a carcinoma

value: epithelial, late stage embryo

tag: viral infeciton

value: Herpes Simplex virus 1 infection for 6 hours post infeciton

tag: drug treatment

value: Flavopiridol (450nM)

tag: processing

value: nuclei isolation after nuclear run-on

tag: molecule subtype

value: biotinylated RNA


title: Fezf1Hete_No7

description: lgTPM-allSACs.txt

tag: strain

tag: age


title: C-scrRNA1

description: scramble

tag: treatment


title: PB1+Pi54 M.oryzae Treated BR3_72hpi

value: Indica

value: Leaves from 4 leaf stage rice plant

value: 72 hours after M.oryzae spray

tag: genotype

value: PB1+ Pi54


title: Fezf1KO_No1

description: lgTPM-allSACs.txt

tag: cell type


title: F1

tag: cell line


title: Fezf1KO_No2

description: lgTPM-allSACs.txt


title: PB1+Pi54 M.oryzae Treated BR2_72hpi


title: C-miR146a1

description: test

value: bone marrow

value: 10mg/kg of C-miR146a

value: HL-60 cancer cell engrafted


title: PBS3

description: control

value: PBS


title: D2


title: Genotype 1 (Tg1) replicate 2

value: LLC-PK1 cells

tag: overexpression

value: FLAG-floxP-neo-pH11 with mutant PKD2 (c.A1532T/p.D511V-3)


title: PBS2

description: control

tag: tissue


title: Fezf1KO_No5

description: lgTPM-allSACs.txt

value: Retina

value: Cholinergic interneurons


title: D1

value: HEP-2 Cells and Drosophila S2 Cells

value: lung epithelial cells from a carcinoma

value: epithelial, late stage embryo


title: PB1+Pi54 M.oryzae Treated BR1_72hpi


title: PB1+Pi54 Mock BR3_72hpi

value: 72 hours after Gelatin spray


title: A2

value: Herpes Simplex virus 1 infection for 6 hours post infeciton

value: acyclovir 10µM

value: nuclei isolation after nuclear run-on

value: biotinylated RNA


title: PB1+Pi54 Mock BR2_72hpi

value: Indica

value: Leaves from 4 leaf stage rice plant

value: PB1+ Pi54


title: A1


title: PB1+Pi54 M.oryzae Treated BR3_24hpi

value: 24 hours after M.oryzae spray


title: PB1+Pi54 Mock BR1_72hpi


title: HSV-1 6hpi PAA rep 2

description:
reverse transcribed RNA from a nuclear run-on reaction
Precision Nuclear Run-on
The Drosophila S2 nuclei used as normalization control.

data_processing:
Library strategy: PRO-seq
All processing steps were done using the Danko lab template for PRO-seq alignment/QC found at https://github.com/Danko-Lab/utils/tree/master/proseq with instructions at https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md
Pre-processing reads and sequence adapter trimming are done with cutadapt
Reads are mapped to the bwa index reference genome using bowtie
BAM files are converted to BigWig using Kentsource
BigWig can be viewed using IGV, and BAM files analyzed with DESeq2 statistics using SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/.
Genome_build: hg 38, dm3, HSV-1 F strain
Supplementary_files_format_and_content: big wig

source_name: HEp-2 cells

growth_protocol: Hep-2 cells--grown at 37 degrees C in 5% CO2 in DMEM 10% Newborn calf serum supplemented with Penn/Strep

extract_protocol:
Hep-2 cells were infected with HSV-1 F strain at an MOI of 5.  S2 cells were left untreated before nuclei isolation, and spiked-in to isolated Hep-2 nuclei (1 drosophila nuclei/10,000 Hep-2 nuclei)
Nuclei isolation followed by Nuclear Run-on in the presence of biotinylated nucleotides (A, U, G, C).  Biotinylated transcripts were isolated using streptavadin coated magnetic beads
Libraries were constructed following the protocol outlined by Mahat et al. 2016. "Base-pair-resolution genome-wide mapping of active RNA Polymerases using precision nuclear run-on (PRO-seq).  Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086

treatment_protocol: Drosophila S2 cells--grown at 20 degrees C on bench top in Schneider's Drosophila Medium with 10% FBS and Penn/Strep

value: phosophonoacetic acid

value: epithelial cells

value: HEp-2 cells

tag: viral infection

value: Infected with HSV-1 (F) for 6 hours

tag: stock source

value: ATCC


title: PB1+Pi54 M.oryzae Treated BR2_24hpi


title: WT2

city: Shenzhen

first: CNSA

last: CNGBdb

state: Guangdong

address: Jinsha Road

institute: CNGB

data_processing:
Basecalls performed using Bcl2fastq (v2.17.1.14)
Filter Dataset using Cutadapt（version 1.9.1）

organism: Oryctolagus cuniculus

source_name: rabbit skin

growth_protocol: All rabbit experiments were conducted under the approval of the Animal Care Center and Use Committee of Jilin University. The rabbits were housed under standard laboratory conditions of a 12-h light and 12-h dark cycle in individual cages and were fed twice a day with commercial rabbit basic diet (Animal center of Jilin University) and water ad libitum.

extract_protocol:
Skin were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
NEBNext Ultra RNA library Prep Kit for Illumina

value: skin

value: 30 days

value: wild type


title: WT1


title: HSV-1 3hpi CHX rep 3

city: Ithaca

address: 235 Hungerfordhill Rd

value: cycloheximide

value: Infected with HSV-1 (F) for 3 hours


title: Kphi treated_Infected2

tag: agent

value: Kphi treated_Infected

tag: cultivated variety

value: Shepody

value: 21 days post emergency


title: PRSS53-3


title: PB1+Pi54 M.oryzae Treated BR1_24hpi

value: Indica


title: PRSS53-2


title: PBS1

description: control

tag: mouse strain

value: bone marrow

value: PBS

tag: tumor engrafed

value: HL-60 cancer cell engrafted


title: HSV-1 3hpi CHX rep 2


title: WT3


title: PB1+Pi54 Mock BR3_24hpi

value: Leaves from 4 leaf stage rice plant

value: 24 hours after Gelatin spray

value: PB1+ Pi54


title: Healthy Control 5

city: Wuhan

first: yun

last: fan

address: 1095 Jie Fang Avenue

department: Tongji Hospital，Tongji Medical College

institute: Huazhong University of Science and Technology

description: lncRNA and mRNA expression profiles of circulating leukocytes of Healthy Control 5

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

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

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

source_name: Whole Blood

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Blood samples were collected from 5 PD patients and 5 healthy controls for microarray. A neurologist specialized in movement disorders made the diagnosis of PD based on the International Parkinson and Movement Disorder Society (MDS) clinical diagnostic criteria for PD (Postuma et al., 2015). Exclusion criteria were as follows: (1) the presence of other neurologic illness or injury (traumatic brain injury, stroke, epilepsy); (2) the presence of chronic inflammatory disease; (3) the presence of previous malignancies or cardiac events; and (4) unstable psychiatric disorders such as schizophrenia or major depression.  Blood samples were collected between 6–10 a.m.. Red blood cells were removed immediately using red blood cell lysis buffer (Haoyang Biology, Tianjin, China). The leukocyte-enriched samples were immediately added into RNAiso Plus (TaKaRa, Dalian, China) and stored at -80℃.

tag: disease state

value: healthy control

value: circulating leukocytes


title: Healthy Control 3

description: lncRNA and mRNA expression profiles of circulating leukocytes of Healthy Control 3


title: Healthy Control 4

description: lncRNA and mRNA expression profiles of circulating leukocytes of Healthy Control 4


title: Healthy Control 2

description: lncRNA and mRNA expression profiles of circulating leukocytes of Healthy Control 2


title: PRSS53-1

value: skin