title: Mixture_C1_24_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-48hpf, 43.1 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-48hpf, 43.1 micromol per liter


title: human Primary Muller Glial cells_2

status: Public on Feb 11 2021

type: SRA

city: Paris

first: Xavier

last: Guillonneau

address: 17 rue Moreau

department: Institut de la vision

country: France

institute: INSERM

library_source: transcriptomic

data_processing:
Raw reads were filtered with Trimmomatic to obatin Pass-filtered reads
Pass-filtered reads were mapped using HiSAT2 and aligned to human reference genome GRCh38.95
The count table of the gene features was obtained using HTSeq
Normalization and differential expression analysis values were computed with DESeq2
TPM were determined using Libinorm using htseq mode
Genome_build: GRCh38.95
Supplementary_files_format_and_content: The MGCs_raw_counts.tsv file contains, raw counts and  RPKM, TPM for the processed 6 samples. Data are in a tab-separated format
Supplementary_files_format_and_content: The  hiMGC_vs_pMGC_DE_&_TPM_FC.tsv contains fold change values with pavalues <0.05 generated by Desq2. Data are in a tab-separated format

molecule: total RNA

organism: Homo sapiens

source_name: Muller Glial cell

growth_protocol: pMGCs and hiMGCs were plated at 50 000 cell/cm² in T-25 cm² flask previously coated with Geltrex matrix (ThermoFischer Scientific) and incubated at 37°C in a standard 5% CO2 / 95% air incubator. Medium was changed every 2-3 days until cell processing

extract_protocol:
Total RNA were extracted from  hiMGCs and pMGCsusing the Nucleospin RNA II kit (Macherey-Nagel) according to the manufacturer’s protocol, RNA quality and quantity were evaluated using BioAnalyzer 2100 (Agilent Technologies,) with the RNA 6000 Nano Kit (Agilent Technologies)
RNA sequencing libraries were constructed from 1 μg of total RNA using a modified TruSeq RNA Sample preparation kit protocol

tag: cell type

value: primary cells


title: Caco-2_Control_mRNA_rep1

city: Moscow

first: Stepan

last: Nersisyan

address: Vavilova str 7

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

description:
mRNA_counts.tsv
mRNA_RPKM.tsv

data_processing:
Quality of FASTQ files were assessed with FastQC v0.11.9, three miRNA-seq replicates (Caco-2_Control_miRNA_rep3, HT-29_CoCl2_miRNA_rep1 and HT-29_Oxy_miRNA_rep3) had not passed the quality control
Adapters were trimmed with cutadapt v2.10
Trimmed mRNA-seq reads were mapped on the reference human genome (GENCODE GRCh38.p13) with STAR v2.7.5b, GENCODE genome annotation (release 34) was used to generate the count matrix.
MiRNA count matrix was generated by miRDeep2 v2.0.1.2 with the use of bowtie v1.1.1 and miRBase v22.1
Sequencing library sizes were normalized with the Trimmed Mean of M-values (TMM) algorithm available in edgeR v3.30.3 package. The same package was used to generate TMM-normalized Reads Per Kilobase of transcript per Million mapped reads (RPKM) and Counts Per Million mapped reads (CPM) matrices for mRNA-seq and miRNA-seq data, respectively.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Tab-separated matrices containing raw read counts and TMM-normalized (edgeR) RPKM and RPM values

source_name: Caco-2 cells

growth_protocol: HT-29 cells  (ATCC, Manassas, VA, USA) were grown in McCoy's 5A medium, supplemented with 10% fetal bovine serum, 2 mM glutamine, 1% non-essential amino acids, penicillin (100 U/mL) and streptomycin (100 mg/mL).  Caco-2 cells were obtained from the Russian Vertebrate Cell Culture Collection (Institute of Cytology, Russian Academy of Sciences, Russia). The cells were incubated under conditions for differentiation for 21 days in Eagle’s MEM with 20% FBS, 2 mM glutamine, 0.1 mM non-essential amino acids, 0.1% penicillin-streptomycin.  All cell culture reagents were obtained from Gibco, Waltham, MA, USA. Both cell lines were maintained in a humidified atmosphere at 37ºC and 5% CO2, changing medium every 3 days.

extract_protocol:
Cells were lysed with the Qiazol Lysis Reagent (Qiagen, Hilden, Germany) for subsequent extraction of RNA using the Qiagen miRNeasy Mini Kit (Qiagen, Hilden, Germany). Nanodrop (Thermo Fisher Scientific, Waltham, MA, USA) was used to assess quality (260/280) and quantity. Total RNA samples were also QC checked using the Agilent High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA).
Libraries for mRNA sequencing were prepared from total RNA samples using Illumina Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). Each sample was sequenced on the Illumina NextSeq 550 to generate single-end 75 nucleotide reads. Libraries for miRNA sequencing were prepared from total RNA samples using NEBNext Multiplex Small RNA Library Prep Kit for Illumina. Each sample was sequenced on the Illumina NextSeq 550 to generate single-end 50 nucleotide reads.

treatment_protocol: A fresh stock solution 0.3 M cobalt chloride (CoCl2) was prepared in water and added to the medium to obtain desired final concentration 300 µM for 24 hours. The second treatment included a fresh portion containing oxyquinoline derivative 4896-3212 (ChemDiv Research Institute, Khimki, Russia) in DMSO (10 mM). The final concentration of oxyquinoline in the medium was 5 μM (0.5 μl of the solution in DMSO per 1 ml medium). In the control, the cells were incubated in a medium with 0.5 μl DMSO per 1 ml medium (without CoCl2 or oxyquinoline).

tag: treatment

value: No treatment

tag: cell line


title: human Primary Muller Glial cells_1


title: SLE active_CDR-65_IGF0005594

city: London

first: Marina

last: Botto

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

data_processing:
RawData production and quality check: Illumina bcl2fastq software used for basecalling and using FastQC (v.0.11.2)
Clean read :Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic(v.0.36)
Alignment tools and ref genome and annotation using tophat2(v.2.1.0: -b2-sensitive,--library-type fr-firststrand )
Genome_build: GRCh38.primary_assembly.genome.fa
Genome_build: gencode.v25.annotation.gtf
Quality check after alignment using four tools:using FastQC (v.0.11.2),samtools(v.1.2),picard(v.2.6.0) and rseqc(2.6.4)  for mapping quality or rate, duplicates metric,read distribution, gene body coverage and GC content and rRNA contamination
Tools and parameter for get raw counting of genes usings HT-Seq-count (Anders et al. 201, v 0.6.1 ) with strict "-m intersection-strict” mode
Tools and parameter for diff exp and platform,using DESeq2 (Love et al. 2014,v. 1.14.1)
Threshold selection for significant gene exp lists,using fold change at 1.5 times and below 1 % FDR level
Supplementary_files_format_and_content: text file of count.table of each sample

source_name: SLE Active_Peripheral blood

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kits (Qiagen)  based on the manufacturer’s instruction. Total RNA quality and concentration was analysed using a NanoDrop 1000 spectrophotometer (ThermoFisher Scientific) and verified using Qubit meter (Invitrogen). All total RNA samples were subjected to level of degradation measurement using Agilent 2100 Bioanalyzer (Agilent Tech Inc.) and RIN values for all samples were ≥ 9.0.
RNA libraries were prepared for sequencing using standard Illumina protocols: TruSeq Stranded mRNA HT kits (Catlogue No:RS-122-2103)

tag: disease status

value: SLE Active

tag: tissue

value: Peripheral blood

tag: cell

value: T cell


title: FUOV1 pMSCV Flag-RAD51

city: Singapore

first: Michal

middle: Marek

last: Hoppe

address: 14 Medical Dr

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

description: FUOV1 with stable integration of the pMSCV Flag-RAD51 overexpression plasmid

data_processing:
Raw read counts are provided by HTSeq-count 0.13.5
Mapping is using STAR
Gene expression quantification is based on featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: high grade serious ovarian carcinoma

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s Medium High Glucose with addition of puromycin (1μg/ml), penicillin (100 I.U./mL) and streptomycin (100 μg/mL)  at 37°C and 5% CO2

extract_protocol:
Qiagen RNAeasy Kit with DNase digestion
Bio-Rad iScript cDNA Synthesis Kit

treatment_protocol: no additional treatments

value: high grade serious ovarian carcinoma

value: Overexpression


title: SLE active_CDR-67_IGF0005596


title: IDC2

city: Houston

first: Nicholas

last: Navin

state: tx

address: 6767Bertner AVE

country: USA

institute: UT MD Anderson

description:
10X genomics
5'-scRNAseq

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger V3.0 mkfastq
cellranger V3.0 count
reads are mapped to hg20
UMI counts are summarized are gene expression levels
Genome_build: hg20
Supplementary_files_format_and_content: tab-delimited text files include cell type prediction and UMI values for each Sample

growth_protocol: Single cell suspensions are made from fresh tumors

extract_protocol:
RNAs are extracted from single cell suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3’ protocol (PN-1000075)

treatment_protocol: samples are collected before treatment

value: fresh tumor

tag: sample type

value: biopsy


title: SLE active_CDR-60_IGF0005593


title: FUOV1 pMSCV Flag

description: FUOV1 with stable integration of the pMSCV Flag control plasmid

value: Control


title: COV362 pMSCV Flag-RAD51

description: COV362 with stable integration of the pMSCV Flag-RAD51 overexpression plasmid


title: SLE active_CDR-69_IGF0005598


title: Mixture_C3_48_T.1

type: RNA

city: Koblenz

first: Andreas

last: Schüttler

address: Am Mainzer Tor 1

department: Department Biochemistry and Ecotoxicology

country: Germany

institute: German Federal Institute of Hydrology

description: whole zebrafish embryo, exposed to Mixture, 24hpf-72hpf, 86.49 micromol per liter

hyb_protocol: Agilent Gene Expression Hybridisation Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)

scan_protocol: Agilent DNA Microarray Scanner and Agilent Feature Extraction Software V11.5.1.1, according to manufacturer's protocol.

data_processing: Cyclic loess normalization between all arrays. Software for data normalization: R v3.3.1.

organism: Danio rerio

source_name: whole embryo, exposed to Mixture, 24hpf-72hpf, 86.49 micromol per liter

label_protocol: One-Color Quick Amp Labeling Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)

extract_protocol: Trizol followed by RNeasy MiniKit cleanup (Qiagen) using the manufacturers’ protocols

tag: substance

value: Mixture


title: Mixture_C3_48_T


title: Mixture_C2_48_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-72hpf, 61.06 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-72hpf, 61.06 micromol per liter


title: Mixture_C1_48_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-72hpf, 43.1 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-72hpf, 43.1 micromol per liter


title: Cloz_6

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

data_processing:
The ten libraries were sequenced in one batch and all passed Novogene’s post-sequencing quality control
paired-end reads were aligned to human reference genome GRCH38 by Hisat2 version 2.1.0 (Kim et al., 2019). Samtools 1.9 (Li et al., 2009) produced corresponding BAM files
Stringtie 2.0.3 (Pertea et al., 2015) was used to assemble and estimate the abundance of transcripts based on GRCh38 human gene annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file of transcripts by sample

source_name: Cloz

extract_protocol:
Zymo Quick RNA Miniprep kit
RiboMinus™ technology (ThermoFisher Scientific) was used to deplete ribosomal RNA. Illumina’s TruSeq RNA v2 protocol was used to generate libraries

treatment_protocol: Four  to six replicates were exposed to 300 ng/ul clozapine and the remaining to methanol which was the solvent of clozapine

value: Ngn2 induced excitatory neurons

value: clozapine exposed


title: Cloz_5


title: SLE active_CDR-35_IGF0005591


title: SLE active_CDR-36_IGF0005592


title: Mixture_C2_48_T


title: Caov-3 pMSCV Flag

description: Caov-3 with stable integration of the pMSCV Flag control plasmid


title: IDC1

description:
10X genomics
5'-scRNAseq


title: Caov-3 pMSCV Flag-RAD51

description: Caov-3 with stable integration of the pMSCV Flag-RAD51 overexpression plasmid


title: SLE active_CDR-27_IGF0005590


title: SLE active_CDR-24_IGF0005588


title: Cloz_2


title: Cloz_4


title: LP-1-HRP2

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

country: China

institute: Tianjin Medical University

library_source: genomic

data_processing:
Basecalls performed using HiSeqX
ChIP-seq reads were aligned to the hg38 genome assembly using BWA version 0.7.13 with the following configurations -q 5 -l 32 -k 2
Data were filtered using Picard-tools version 1.126
peaks were called using macs2 version 2.1.1 with the following setting: -pvalue 0.01 --keep-dup all --extsize -1 --shift 0
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated by deeptools

molecule: genomic DNA

growth_protocol: LP-1 cell was cultured in RPMI-1640 medium with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to the TruePrep® DNA Library Prep Kit V2 for Illumina (TD503-02). Briefly, TruePrep Tagment Enzyme Mix (TTEMix) contains transposase and two kinds of adapters (Adapter 1 and Adapter 2) with equal molar. Input DNA are fragmented and linked with adapters on both ends just by mixing with TTE Mix, followed by a 10-minute incubation at 55℃. The tagged DNA fragments can be further amplified with two pairs of primers N5 (N5XX) / N7 (N7XX) and P5 / P7 (PCR Primer Mix, PPM).  After adapter ligation DNA was PCR amplified with Illumina primers for 8 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.

treatment_protocol: LP-1 cells were infected with lentivirus carrying HRP2 sgRNA.

value: B lymphoblast

tag: tumor type

value: multiple myeloma

tag: chip antibody

value: HDGF2 Polyclonal antibody (Proteintech,Cat no :15134-1-AP)

value: untreated


title: SLE active_CDR-25_IGF0005589


title: TYK-nu pMSCV Flag-RAD51

description: TYK-nu with stable integration of the pMSCV Flag-RAD51 overexpression plasmid

value: TYK-nu


title: Cloz_3


title: COV362 pMSCV Flag

description: COV362 with stable integration of the pMSCV Flag control plasmid


title: SLE active_CDR-21_IGF0005587


title: Cloz_1


title: Ctrl_LHC-7_IGF0005620

source_name: Ctrl_Peripheral blood

value: Ctrl


title: TYK-nu pMSCV Flag

description: TYK-nu with stable integration of the pMSCV Flag control plasmid


title: Mixture_Control_24_C

description: whole zebrafish embryo, exposed to Mixture, 24hpf-48hpf, 0 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-48hpf, 0 micromol per liter


title: Ctrl_LHC-8_IGF0005621


title: Mixture_C2_72_R

description: whole zebrafish embryo, exposed to Mixture, 61.06 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf

source_name: whole embryo, exposed to Mixture, 24hpf-96hpf, 61.06 micromol per liter


title: Mixture_C5_24_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-48hpf, 122.51 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-48hpf, 122.51 micromol per liter


title: Mixture_C1_48_T


title: Mixture_Control_48_C.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-72hpf, 0 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-72hpf, 0 micromol per liter


title: SLE active_CDR-20_IGF0005586

value: SLE Active


title: CH3OHA_3

value: methanol exposed


title: CH3OHA_1


title: SLE active_CDR-6_IGF0005585

value: Peripheral blood

value: T cell


title: CH3OHA_2


title: LP-1-V2-H3K27me3

value: Non-target control


title: LP-1-V2-Input


title: LP-1-HK-Input

value: Knockdown HRP2


title: SLE active_CDR-2_IGF0005584


title: LP-1-Input


title: N3752_WT_BSseq

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

data_processing:
The BRAT-BW software package (compbio.cs.ucr.edu/brat/; Harris et al, 2012) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping.
BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged.
A python script (bidensity) was written to calculate the average 5mC level over a 500bp sliding window across the genome, producing a .wig file
.wig files were displayed on IGV (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011)
Genome_build: Ncrassa version12
Supplementary_files_format_and_content: .wig files show the ratio (0-1.0; 0 is DNA that is not cytosine methylated, 1.0 is DNA where all of the cytosines are methylated) of methylated cytosines to unmethylated cytosines as peaks of cytosine methylation enrichment

organism: Neurospora crassa

source_name: N3752 WT Ncrassa (Selker)

growth_protocol: grown under standard dark cycle in 1xVogels medium + 1.5% sucrose (minimum medium) or minimum medium supplemented with histidine (0.5mg/mL [final]) for 48 hours on rocking shaker at 32oC

extract_protocol:
Genomic DNA was isolated using a protocol modified from (Oakley et al, 1987). Genomic DNA (50ng) was treated with bisulfite using the EZ DNA Methylation LightningTM kit (ZYMO Research) per the manufacturer's protocol.
Kit (Epicentre cat #EGMK91324) and EpiGnomeTM Index PCR Primers (Epicentre cat# EGIDX81312) per the manufacturer's protocol, purified with Agencourt AMPure XP beads (Beckman Coulter) per the manufacturer's protocol, Qubit HS Assay quantified (Life Technologies) per the manufacturer's protocol, visualized on the Fragment AnalyzerTM (Advanced Analytical) per the manufacturer's protocol, and sequenced on a Illumina HiSeq 2000

tag: strain

value: wildtype

tag: time point in light cycle

tag: growth medium

value: 1xVogels, 1.5% sucrose (minimum)

tag: bisulfite treated

value: bisulfite


title: injured_with_aLFA1_VLA4_rep3

status: Public on Feb 10 2021

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing.
Post deplexing, the paired-end sequence files (.fastq) per sample were quality inspected using the FastQC tool 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) then adaptor clipped (TruSeq3-PE-2.fa:2:30:10) and trimmed to remove 5' nucleotide bias (HEADCROP:11) and low quality calls (TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:15) using the Trimmomatic tool 0.39 (http://www.usadellab.org/cms/?page=trimmomatic). Surviving intact pairs of reads per sample were then imported into the CLCbio Genomics Workbench 11 (https://www.qiagenbioinformatics.com/), down-sampled to 40M read pairs per sample, then reference mapped by sample in stranded fashion against the current instance of the mouse genome (GRCm38) using the "RNA-Seq Analysis" tool supported therein under default parameters. Expression per known annotated gene (Mus_musculus.GRCm38.83.chr.gtf) in Transcripts Per Kilobase Million (TPM) units was then exported from the Workbench.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files containing enumerated expression per sample sequenced.

organism: Mus musculus

source_name: Brain tissue

extract_protocol:
At day 20 following injury, mice were perfused with normal saline, and a 3 x 3 x 3 mm cube of injured tissue was harvested and snap frozen using dry ice. The tissues were stored at -80oC until use. Total RNA was extracted with Qiagen kit following the manufacturer’s protocol, and RNA quantity and integrity was assessed by the Bioanalyzer (Agilent, Santa Clara, CA).
500 ng of total RNA was used in conjunction with the TruSeq® Stranded Total RNA Library Prep kit (Illumina, San Diego, CA). The libraries quality was checked by the Bioanalyzer and quantitated by the Qubit (ThermoFisher Scientific). Equimolar quantities from each sample library was pooled and run on a Highoutput Next-Seq550 kit.

treatment_protocol: B6 mice were divided into 3 groups (uninjured, injured, continuous αLFA1/VLA4) with 4 mice per group.

tag: sample group

tag: technical replicate

value: No

tag: biological replicate

value: Yes

tag: gender

value: Male

tag: age

value: 13 Weeks


title: LP-1-HK-H3K27me3

tag: cell type

value: B lymphoblast

value: multiple myeloma

tag: treatment

tag: cell line


title: injured_with_aLFA1_VLA4_rep4


title: CH3OHA_4

value: Ngn2 induced excitatory neurons


title: injured_with_aLFA1_VLA4_rep1


title: injured_with_aLFA1_VLA4_rep2


title: injured_rep4

description: injured

value: injured


title: Mixture_C5_48_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-72hpf, 122.51 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-72hpf, 122.51 micromol per liter

value: Mixture


title: injured_rep2

description: injured


title: Mixture_Control_48_C


title: Mixture_C5_48_T


title: Mixture_C4_48_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-72hpf, 102.93 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-72hpf, 102.93 micromol per liter


title: uninjured_rep3

description: uninjured

value: uninjured


title: Mixture_C4_48_T


title: uninjured_rep2

description: uninjured


title: uninjured_rep4

description: uninjured


title: L1 with CR-tdTomato d2 rep1

city: Kyoto

first: Satoshi

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

data_processing:
RNA-seq base calls were converted into FASTQ file format by bcl2fastq2 conversion software v2.20 (Illumina).
RNA-seq reads from the FASTQ files were then aligned to the reference mouse genome GRCm38/mm10 using TopHat2 v2.1.0 after performing quality control (QC) with FASTX Toolkit v0.0.13, FastQC v0.11.2, and PRINSEQ lite v0.20.4.
Gene expression analysis was performed based on the fragments per kilobase million (FPKM) values calculated using the RNA-seq data by Cufflinks v2.2.1.

growth_protocol: 3T3-L1 preadipocytes were grown in DMEM with 10% FBS and 1% antibiotics.

extract_protocol:
Total RNA was extracted from each samples using the TRIzol Reagent (Life technologies, Inc.) and Direct-zol™ RNA MiniPrep Kit (Zymo Research).
Libraries for next-generation sequencing were constructed using a TruSeq Stranded Total RNA Sample Prep LS Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Cells (2e5/well in 6 well plate) were seeded. Next day, cells were differentiated into adipocytes using adipococktail (IBMX, Dexamethasone, and Insulin). Two days after induction, cells were harvested for RNA-seq.

tag: breed

value: Swiss albino

tag: group

value: CR-tdTomato 3T3L1


title: L1 with CR-tdTomato d0 rep3


title: L1 with CR-tdTomato d2 rep3


title: L1 with CR-tdTomato d0 rep1


title: uninjured_rep1

description: uninjured


title: L1 with CR-Ddx6 d2 rep1

value: CR-Ddx6 3T3L1


title: L1 with CR-Ddx6 d2 rep3


title: injured_rep3

description: injured


title: SF-2-18H

city: Guangzhou

first: shimei

last: zhuang

state: Guangdong

address: Xin Gang Xi Road 135#

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality sequence, then mapped to Genome(Hg38) whole genome using STAR.
Fragments Per Kilobase of exon per Million of library size (FPKM) were calculated using RSEM.
Genome_build: Human genome (Hg38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: human skin fibroblasts

growth_protocol: SF cells were cultured in RPMI 1604 medium supplemented with 10% FBS, 100 mg/mL streptomycin and 100 U/mL penicillin in a humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
The Total RNA was isolated using  Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols. The samples were sequenced by deep sequencing using Illumina Hiseq-PE150 by a 2X150 bp run at Beijing Novel Bioinformatics Co., Ltd. (https://en.novogene.com/).

treatment_protocol: SF1 or SF2 cells were serum-deprived for 48 hours and then cultured in the 15% FBS-containing medium for 0, 4 or 18 hours.

value: fibroblasts

value: serum starvation-stimulation


title: L1 with CR-Ddx6 d0 rep1


title: SF-1-0H


title: SF-1-18H


title: SF-1-4H


title: SF-2-0H


title: Mixture_C1_72_R

description: whole zebrafish embryo, exposed to Mixture, 43.1 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf

source_name: whole embryo, exposed to Mixture, 24hpf-96hpf, 43.1 micromol per liter

tag: substance


title: injured_rep1

description: injured


title: TH3

city: LEXINGTON

first: Yohan

last: Choi

state: KY

address: 800 Rose St, UKMC MS341

institute: University of Kentucky

data_processing:
Fastq files were generated and demultiplexed with the bcl2fast1 v1.8.4 Conversion Software (Illumina). Adaptor sequences were trimmed from raw RNA sequencing reads.
The quality of raw data was checked on the FASTQ files using FASTQC (version 0.11.4) software.
Trimmomatic (version 0.33) was used to trim any residual adapter content and low-quality bases, and trimmed data were qualified again on the trimmed FASTQ files using FASTQC (version 0.11.4) software.
Each set of RNA sequencing reads was aligned with the NCBI annotation of the human genome reference sequence (GRCh38.p6_genomic.fna) using the alignment software, STAR (version 2.5.0a).
RNA sequencing data were analyzed in R (version 3.3.1) using packages as described below. Briefly, the number of reads per genes was normalized using the trimmed mean of M-values (TMM values) normalization method in the edgeR package (version 3.15.0). Principal components analysis (PCA) was performed for the clustering of the samples to determine whether any samples are outliers and/or if there are overall treatment differences or batch effects. Next, statistical analysis was applied to the 13,539 genes left after filtering and performed to determine differential expression between the treatments using edgeR (version 3.15.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: Granulosa cells

growth_protocol: Cells were obatined from IVF patients at the time of oocyte retrieval and subjected to a Percoll gradient. Isolated granulosa cells were plated and incubated in Opti-MEM + 1x antibiotics/antimycotics and 10% fetal bovine serum for 6 days to regain the responsiveness to hCG.

extract_protocol:
Total RNA was isolated from the cultured cells using a Rneasy mini kit (Qiagen) and eluted in 30 ul of nuclease-free water.
The strand-specific RNA sequencing libraries for 8 individual samples were prepared using a TruSeq Stranded RNA Sample Prep Kit (Illumina). These samples represent four independent experiments for each of the two conditions examined. Libraries were pooled in equimolar concentration, and the pool was quantitated by quantitative PCR and sequenced on three lanes for 101 cycles on a HiSeq2500 (Illumina) using a HiSeq SBS sequencing kit version 2.

treatment_protocol: After the acclimation period, the cells were incubated without serum and treated with hCG in the presence or absence of T-5224 for 12 hours.

tag: tissue

value: Ovary

value: Primary human granulosa-lutein cells

tag: treatments


title: TH4


title: H4

value: hCG


title: H3


title: TH2


title: TH1


title: L1 with CR-Ddx6 d0 rep2


title: SF-2-4H


title: H1


title: A2_1_KO

city: DALLAS

first: David

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Road

department: Pharmacology

institute: UT-Southwestern Medical Center at Dallas

description: eCLIP_immunoprecipitated RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, raw sequencing reads were adapter-trimmed and then mapped to hg38/Gencode v27 transcriptome using STAR-2.5.3a. Gene quantification and differential analysis were carried with Salmon (0.11.0) and DeSeq2. CLIPper and in-house scripts were used for eCLIP-seq peak calling and normalization.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

growth_protocol: McCoy’s 5a Medium (GIBCO # 16600) + 10% FBS was used as the growth media for all the cell lines studies.

extract_protocol:
For RNA_seq samples, RNA was harvested using Trizol reagent. Illumina Whole Transcriptome RNA Sample Prep Kit (strand specific) was used with 50 ng-1 ug of total RNA for the construction of library. For the eCLIP-seq, cell cytoplasmic fraction was obtained wtih hypotonic buffer from 10 million cell and used for immunprecipitation or size-matched input samples.
RNA libraries were prepared for sequencing using standard Illumina protocols or eCLIP-seq protocol (Van Nostrand, et. al, Nature Methods, 2016, 13, 508-514)

value: human colon cancer cell

value: HCT 116

tag: passages

tag: eclip antibody

value: Aint_Ago2_3148 (gift from Jay A. Nelson lab, OHSU)

tag: genotype


title: I_2_KO

description: eCLIP_size_matched input RNA


title: I_1_KO

description: eCLIP_size_matched input RNA


title: A2_2_KO

description: eCLIP_immunoprecipitated RNA


title: I_1_WT

description: eCLIP_size_matched input RNA

value: wild type(Nuc)


title: A2_1_WT

description: eCLIP_immunoprecipitated RNA


title: RNA-seq of p53 WT 5-FU 300um treated 30min rep2

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
sequnced using Illumina Hiseq platform
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using STAR v2.5.1 with parameters --sjdbOverhang 100 --twopassMode Basic --chimSegmentMin 20 --quantMode TranscriptomeSAM
Fragments Per Kilobase Million (FPKM), Transcripts Per Kilobase Million(TPM) and raw counts were calculated using RSEM
Genome_build: hg19
Supplementary_files_format_and_content: RSEM output files including raw counts, FPKM, TPM values

source_name: p53 WT 5-FU 300um treated 30min

extract_protocol:
Cells were PBS washed, and RNA was harvested and isolated using Hybrid-R Total RNA kits (Gene All Biotechnology) and rRNAs were depleted by using the NEBNext rRNA Depletion Kit (NEB #E6350).
NEBNext Ultra RNA library prep kit (NEB #7770) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: cell line background

value: colorectal carcinoma cell line

tag: genotype/variation

tag: tissue source

value: colon

tag: morphology

value: epithelial

value: treated with 5-FU 30min


title: I_2_WT

description: eCLIP_size_matched input RNA


title: A2_2_WT

description: eCLIP_immunoprecipitated RNA


title: RNA-seq of p53 WT 5-FU 300um treated 2h rep2

source_name: p53 WT 5-FU 300um treated 2h

value: treated with 5-FU 2hr


title: RNA-seq of p53 WT 5-FU 300um treated 24h rep1

source_name: p53 WT 5-FU 300um treated 24h

value: treated with 5-FU 24hr


title: RNA-seq of p53 WT 5-FU non treated rep2

source_name: p53 WT 5-FU non treated

value: treated with 5-FU 0hr


title: RNA-seq of p53 KO 5-FU 300um treated 30min rep2

source_name: p53 KO 5-FU 300um treated 30min


title: RNA-seq of p53 WT 5-FU non treated rep1


title: RNA-seq of p53 KO 5-FU 300um treated 30min rep1


title: RNA-seq of p53 KO 5-FU 300um treated 2h rep1

source_name: p53 KO 5-FU 300um treated 2h


title: RNA-seq of p53 WT 5-FU 300um treated 24h rep2


title: RNA-seq of p53 WT 5-FU 300um treated 2h rep1


title: H2


title: RNA-seq of p53 KO 5-FU 300um treated 24h rep2

source_name: p53 KO 5-FU 300um treated 24h


title: p53 WT 5-FU 300um treated 24h

data_processing:
sequnced using Illumina Hiseq2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the hg19 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ < 30 and sorting, deduplication were processed using PICARD  v1.77
peaks were called using macs2 v2.1.2
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.1.3
Genome_build: hg19
Supplementary_files_format_and_content: CPM normalized bigwig; peak files (narrowPeak)

source_name: colorectal carcinoma cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and p53-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Samples were prepared with 5-FU treated and non-treated TP53-WT HCT116 cells. Regarding the 5-FU treated samples, TP53-WT HCT116 cells were treated with 300uM 5-FU for 24hr.

tag: chip antibody

value: p53 (Santa Cruz, #sc-126, lot XXXX)


title: p53 WT 5-FU non treated


title: RNA-seq of p53 KO 5-FU non treated rep1

source_name: p53 KO 5-FU non treated


title: RNA-seq of p53 KO 5-FU 300um treated 2h rep2


title: RNA-seq of p53 WT 5-FU 300um treated 30min rep1


title: p53 WT 5-FU 300um treated 24h rep2 [ATAC-seq]

data_processing:
sequnced using Illumina Hiseq2500 platform
Raw reads were trimmed for adaptor sequence, and aligned to the hg19 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD  v1.77
merged replicate1 BAM files & replicate2 BAM files to one BAM file
Peak calling: peak called by MACS2 v2.1.2 using rep1 rep2 merged BAM files
Differential peaks analysis: HOMER mergePeaks and getDifferentialPeaks
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.1.3
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files; peak files (bed)

extract_protocol:
Cells were washed with PBS once, and pelleted down by centrifugation. Nuclei were isolated and accessible DNA tagmented and purified throgh the previous ATAC-seq protocol (Buenrostro et al., 2015). DNA fragments 100 bp - 1 kb were purified with AMPure XP beads and amplified by PCR prior to pooling and sequencing.
ATAC-seq libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, tagmented accessile DNA was purified by AMPure XP beads, then end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers. Then, the purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Cells were treated with 300uM 5-FU for 0hr, 30min, 2hr and 24hr.


title: p53 KO 5-FU 300um treated 24h rep2 [ATAC-seq]


title: p53 KO 5-FU non treated rep2 [ATAC-seq]


title: p53 WT 5-FU non treated rep2 [ATAC-seq]


title: Exosomes from Hs8

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Exosomes from Hs8

data_processing:
FASTQ files were trimmed with Quality Score method
We used bowtie 1.01 to align reads against the human genome (hg38) with zero mismatch
Mapped reads were quantificed to  uisng Partek E/M method using mature mirBase (v22)
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: read counts miRNA

source_name: Primary human hepatocytes supernatant

growth_protocol: Hepatocytes freshly isolated were cultured O/N in standard conditions

extract_protocol:
Total RNA was isolated using miRVANA Paris Kit (Ambion, Thermoscientific) from 50 µg of EV preparation, and 2µl of 1nM C. Each sample was spiked with Caenorhabditis elegans miR-39-5p.
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).

treatment_protocol: No treatments. After 16h of culture, supernatant was collected and exosomes were purified by ultracentrifugation

value: Decompensated Cirrhosis

value: Exosomes


title: Exosomes from H47CLB

description: Exosomes from H47CLB


title: Exosomes from Hs7

description: Exosomes from Hs7

value: Control


title: p53 WT 5-FU 300um treated 24h rep1 [ATAC-seq]


title: p53 KO 5-FU non treated rep1 [ATAC-seq]


title: Exosomes from Hs5

description: Exosomes from Hs5


title: p53 KO 5-FU 300um treated 24h rep1 [ATAC-seq]


title: Exosomes from H39CL

description: Exosomes from H39CL


title: RNA-seq of p53 KO 5-FU 300um treated 24h rep1


title: RNA-seq of p53 KO 5-FU non treated rep2


title: Exosomes from H30CL

description: Exosomes from H30CL


title: RNA-seq LNCaP BRG1 KD 144h siRNA2 Replicate 1

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

data_processing:
100bp paired-end reads were normalised using ERCC spike-ins, processed using Trim Galore (version 0.11.2) for adapter trimming (parameter settings: --fastqc --paired --retain_unpaired --length 16) and STAR (version 2.4.0j) for mapping reads to the hg19/GRCh37 human genome build with GENCODE v21 used as a reference transcriptome (parameter settings: --quantMode TranscriptomeSAM --outFilterMatchNmin 101).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: normalized transcript abundance measurment

source_name: LNCaP

growth_protocol: Lymph Node Cancer of the Prostate (LNCaP) cells (ATCC CRL-1740) were maintained in T-medium (Gibco, customized formula) supplemented with 10% foetal bovine serum (FBS; Thermo Fisher Scientific, #SH3007103), 20mM L-Glutamine (Gibco, #25030) and Penicillin (50,000 units)/ Streptomycin (50mg) solution (Pen/strep; Gibco, #15070).  The cells were grown at 37 degrees celcius and 5% CO2. Cells were routinely passaged at 80%-90% confluence. All cell lines were authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.

extract_protocol:
Total RNA was isolated with TRIzol reagent. 500ng of total RNA was spiked with external controls (ERCC RNA spike-in Mix, Thermo Fischer #4456740) and libraries constructed with the Illumina TruSeq Stranded mRNA sample preparation kit (ref. RS-930-1001, Illumina).
Illumina TruSeq Stranded mRNA sample preparation kit (ref. RS-930-1001, Illumina

treatment_protocol: LNCaP cells were seeded into 6-well plates at a density of 2.5x105 cells per well or 10cm dishes at 1.5x106 cells per dish. The cells were transfected with either on target SMARCA4 siRNA (Horizon, #J-010431-06-0005 or #J-010431-07-0005) or the non-targeting control siRNA pool (Horizon, #D-001810-10-05) 24 hours after seeding the cells using DharmaFECT 2 (Thermo Scientific, #T-2002-03) as per the manufacturer’s instructions. To maintain the knockdown over a 6-day period, at 72 hours post transfection the cells were harvested, split at a ratio of 1:2 into two new wells, and reverse-transfected with siRNA. The cells were then incubated for a further 72 hrs before collection.

value: BRG1 KD 144h siRNA2

value: prostate

value: LNCaP cells (ATCC CRL-1740)


title: RNA-seq LNCaP BRG1 KD 144h siRNA2 Replicate 2


title: RNA-seq LNCaP BRG1 KD 72h siRNA2 Replicate 2

value: BRG1 KD 72h siRNA2


title: RNA-seq LNCaP BRG1 KD 144h siRNA1 Replicate 1

value: BRG1 KD 144h siRNA1


title: RNA-seq LNCaP BRG1 KD 72h non-targeting Replicate 2

value: BRG1 KD 72h non-targeting


title: RNA-seq LNCaP BRG1 KD 72h siRNA1 Replicate 2

value: BRG1 KD 72h siRNA1


title: Clone B1 - KO rep1 d28 cortical organoids differentiated from H9 hESC

city: Santa Cruz

first: Ali

middle: S

last: Shariati

state: CA

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

data_processing:
Fastq files were trimmed using Trimmomatic (Galaxy v0.36.5) with parameters “ILLUMINACLIP: Truseq v3 paired-end, SLIDINGWINDOW: window=4, qual=20 and MINLEN: 30”.
Reads passing QC were mapped onto the hg38 reference genome using HISAT2 (Galaxy v2.1.0) with paired-end settings: “strand information: reverse -RF, mate orientation: --fr” and using the GENCODE v27 .gtf file for known splice sites, and parameters “-k 20 and --max-seeds 20”.
Raw read counts were generated with featurecounts (Galaxy v1.6.1.0) using GENCODE v27 annotation with settings “stranded -reverse, count fragments instead of reads, only allow fragments with both reads mapped, exclude chimeric reads, minimum mapping quality 12”.
Read count normalization and paired wild-type versus knock-out statistics were done using DESeq2 (Galaxy v2.11.40.2).
Coverage tracks in bigwig format were made using deepTools bamCoverage (Galaxy v3.0.2.0) with settings “bin size 1, do not normalize or scale, ignore missing data, minimum mapping quality 1”, separating data into two files containing reads from either forward or reverse strand only.
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts: featurecounts output. Normalized counts: DESeq2 normalized read counts output

source_name: KO d28 cortical organoids differentiated from H9 hESC

growth_protocol: Cell Culture: H9 human embryonic stem cells (hESCs, WiCell WA09) were grown as colonies on a feeder layer of mouse embryonic fibroblasts (MEFs, Thermofisher A34958). MEFs were seeded on 0.1% gelatin coated plates 24 hours before hESCs were passaged hESCs were grown in DMEM/F12 + L-glutamine (Thermofisher 11320074), supplemented with 20% Knock-out serum replacement (Thermofisher 10828028), 100U/ml Pen/Strep, 1x non-essential amino acids and 100μM beta-mercaptoethanol. The medium was sterile filtered (Merck SCGPU05RE) and 8 ng/ml recombinant FGF2 was added fresh before use each time (Sigma F0291). For routine passaging, hESC colonies were manually cut into pieces with a 273/4 gauge needle, and lifted from the plate using a cell lifter (VWR 734-1526). The cell lifter was cut using sterile scissors to decrease the size to 1-2mm width. Cell clumps were pipetted gently to a new plate already seeded with MEFs the day before. Medium was replaced daily. CRISPR-Cas9 of H9 human embryonic stem cells:  Cells were prepared using a modified published protocol (Hendriks et al. 2015). H9 hESCs colonies growing on MEFs were passaged to Matrigel (Corning 354277) coated dishes. For culture on matrigel, hESCs were grown in MEF-condition hESC medium. This was generated by adding hESC medium without FGF2 to a MEF feeder layer for 24 hours, then collecting and filtering the conditioned medium. This was used directly or stored at -20 and used within 3 months. FGF2 was added freshly before adding conditioned hESC medium to hESC cultures on matrigel. 24 hours before transfection, hESC cultures on matrigel were passaged using Accutase (Sigma A6964) to obtain a single cell culture and 2μM Thiazovivin (Sigma SML1045) was added to the medium to increase survival. On 1 60mm dish, 770000 cells were seeded. 1 hour before transfection, medium was replaced with hESC medium without pen/strep. Transfection mixes were made according to the Lipofectamine Stem protocol (Thermofisher STEM00003). For 1 60mm dish, 1250ng of pX330-sgRNA1_ZNF675, 1250ng pX330-sgRNA2_ZNF675 and 500ng of pCAG-GFP were mixed in 75μl of OptiMEM. In a separate tube, 12.5μl of Lipofectamine STEM was mixed with 62.5μl of OptiMEM. The 2 solutions were mixed and incubated 20 minutes at room temperature and the transfection complex was added to the 60mm dish. 16 hours after transfection medium was replaced. 48 hours after transfection, hESCs were prepared for FACS. A single-cell solution was made using Accutase. PBS was added to dilute Accutase, and cells were centrifuged at 1000xg to pellet cells, following one more wash in PBS. Then, cells were resuspended in cold 1x PBS + 2μM Thiazovin. The cell suspension was applied to a 30μm cell strainer (Sysmex ZPS40464) column to remove remaining cell clumps, and collected in a Falcon tube (Corning 352058). During these steps, cells were kept on ice, and cell sorting and collection was done at 4°C. A FACSAria III (BD Biosciences) was used for sorting, at 20psi and using a 100μm nozzle. Non-transfected cells were used to set the gates for GFP-negative cells. 60000-80000 transfected cells (GFP+, 4%-10% of total cells) were collected in one well of a Matrigel coated 6-well plate, and cultured in hESC+MEF-conditioned hESC medium with 2μM Thiazovivin and 20mM HEPES pH7.4 for the first 24 hours. The next days, medium was replaced with MEF-condition hESC medium until ready to passage. Single cell clones were grown by seeding 800 cells in hESC medium with 2μM Thiazovivin on a 60mm dish containing a MEF feeder layer. After 24 hours, medium was replaced containing no Thiazovivin. Individual colonies were picked at about 1mm size, and transferred in MEF-conditioned hESC medium to a Matrigel coated 96-wells plate. By pipetting up and down in the well, each colony was broken up into smaller pieces. When hESC colonies recovered, they were passaged again using Accutase, 1/10 to a new 96-well plate for further culturing, and 1/3 to a new 96-well plate for DNA isolation and genotyping. Selected clones according to genotyping were cultured on a MEF-feeder layer, by seeding 800 cells on a 60mm dish as described before, and cultured as colonies according to the regular protocol.

extract_protocol:
Per replicate, 8-12 organoids were pooled and dissolved in 1ml TRIzol reagent, stored at -80°C for later use. RNA was isolated from TRIzol using Direct-zol RNA microprep with DNAseI treatment.
RNA samples were prepared for sequencing using the NEBNext Ultra Library prep kit, and sequenced on an Illumina HiSeq 4000 platform with paired-end 150bp reads (GenomeScan).

treatment_protocol: H9 hESCs were grown as colonies on a MEF feeder layer. Before organoid formation, medium was replaced to hESC medium + 1x sodium pyruvate and without FGF2. Colonies sized 1.5-2mm on a 100mm dish were scooped using a cell lifter, which was cut using sterile scissors to decrease the size to 2-3mm width. The suspension was transferred to a 60mm ultra-low attachment dish (Sigma CLS3261) by gentle pipetting with a wide-bore tip. The dish was then placed overnight in the incubator for organoids to form. Then, 50% of the medium was replaced with differentiation medium consisting of DMEM/F12 + 2mM L-glutamine, 20% KOSR, 100u/ml Pen/Strep, 1x non-essential amino acids, 1x sodium pyruvate and 4 small molecule inhibitors: 1μM Dorsomorphin (Sigma P5499), 10μM SB431542 (Sigma S4317), 3μM IWR-1 (Sigma I0161) and 1μM Cyclopamine (Sigma C4116). For the initial 50% medium replacement, concentration of the 4 inhibitors was doubled to achieve the required concentration for each in the final volume. Thereafter the medium was replaced every other day with differentiation medium until day 18. At this stage medium was replaced to Neurobasal medium (Thermofisher 21103049), supplemented with 2mM L-glutamine (Thermofisher 25030024), 100u/ml Pen/Strep and 1x N2 supplement (Thermofisher 17502048). Until day 24, 1μM Cyclopamine was added. At day 28, organoids were harvested for RNA isolation.

value: WA09 (H9) human embryonicstem cells

tag: znf675 genotype

value: KO

value: Transction of CRISPR-Cas9 constructs followed by clonal expansion and cortical organoid differentiation


title: Clone B1 - KO rep2 d28 cortical organoids differentiated from H9 hESC

tag: cell type


title: RNA-seq LNCaP BRG1 KD 72h non-targeting Replicate 1

tag: treatment


title: RNA-seq LNCaP BRG1 KD 144h non-targeting Replicate 2

value: BRG1 KD 144h non-targeting

tag: cell line


title: RNA-seq LNCaP BRG1 KD 72h siRNA2 Replicate 1


title: RNA-seq LNCaP BRG1 KD 144h siRNA1 Replicate 2


title: RNA-seq LNCaP BRG1 KD 144h non-targeting Replicate 1


title: Clone G10 - Het rep2 d28 cortical organoids differentiated from H9 hESC

source_name: Het d28 cortical organoids differentiated from H9 hESC

value: Het


title: Clone G5 - WT rep2 d28 cortical organoids differentiated from H9 hESC

source_name: WT d28 cortical organoids differentiated from H9 hESC

value: WT


title: Clone G5 - WT rep1 d28 cortical organoids differentiated from H9 hESC


title: Clone F5 - KO rep1 d28 cortical organoids differentiated from H9 hESC


title: Clone F5 - KO rep2 d28 cortical organoids differentiated from H9 hESC


title: Clone E5 - WT rep2 d28 cortical organoids differentiated from H9 hESC


title: Clone E5 - WT rep1 d28 cortical organoids differentiated from H9 hESC


title: p53 WT 5-FU non treated rep1 [ATAC-seq]

value: colorectal carcinoma cell line

value: colon

value: epithelial

value: treated with 5-FU 0hr


title: RNA-seq LNCaP BRG1 KD 72h siRNA1 Replicate 1


title: teloHAEC_CRISPRa_sgRNA_06939_replicate2

city: Montreal

first: Florian

last: Wuennemann

address: 5000 Rue Bélanger

country: Canada

institute: Montreal Heart Institute

description: sgRNA targeting CAD locus

data_processing:
Fastq files were quality controlled using FASTQC and multiqc.
Transcript abundances were quantified from paired-end fastq files using kallisto (v. 0.46.0) against ENSEMBL reference transcripts (release 94) followed by tximport to estimate gene-level counts.
Gene level counts that were used in DESeq2 for differential expression analysis are provided.
Genome_build: Ensemble release 94
Supplementary_files_format_and_content: teloHAEC_CRISPR.RNAseq.counts.tsv.gz contains gene-level estimated counts for all samples from tximport.

source_name: teloHAEC

growth_protocol: TeloHAEC stably expressing either Cas9 or dCas9-VP64 (CRISPRa) were cultured in vascular cell basal medium (ATCC PCS-100-030).

extract_protocol:
RNA was extracted using the RNeasy plus mini kit from Qiagen.
RNA-seq experiments were carried out by the Centre d’Expertise et de Services Genome Quebec (GC) using rRNA-depleted TruSeq stranded (HMR) libraries (Illumina) on an Illumina Hiseq 4000 instrument (paired-ends, 100-bp reads) and by The Center for applied Genomics (TCAG, Toronto) using rRNA-deletion library prep on an Illumina NovaSeq-SP flow cell.

treatment_protocol: TeloHAEC stably expressing either Cas9 or dCas9-VP64 (CRISPRa) were infected with lentiviruses containing safe-harbor sgRNA as control or sgRNA targeting candidate coronary artery disease loci in the genome, at a multiplicity of 0.3. Cells were cultured for 5 (CRISPRa) or 7 days (Cas) respectively. Cas9 experiments were treated with TNFɑ (10ng/ul])  for four hours to induce a pro-inflammatory response.

value: teloHAEC

tag: cas9 variant

value: CRISPRa

tag: sgrna

value: GQ


title: teloHAEC_Cas9_sgRNA_10966_replicate1

description: sgRNA targeting CAD locus


title: teloHAEC_Cas9_safe_001_replicate4

description: Safe-harbor control sgRNA for experiment 4

value: safe


title: teloHAEC_Cas9_sgRNA_10966_replicate2

description: sgRNA targeting CAD locus


title: teloHAEC_CRISPRa_MS2_safe_002_replicate1

description: Safe-harbor control sgRNA for experiment 1


title: teloHAEC_CRISPRa_MS2_safe_002_replicate2


title: CRISPRa_sgRNA_library

description: plasmid library

data_processing:
Library strategy: DNA-seq
Raw sequencing data from Illumina sequencers was processed from the BCL to the FASTQ format using bcl2fastq.
sgRNA abundances were quantified using MAGECK count (v.0.5.9) against a list of sgRNA sequences in the library.
Supplementary_files_format_and_content: teloHAEC_Endoscreen_sgRNA_counts.tsv.gz

source_name: plasmid

growth_protocol: TeloHAEC stably expressing either Cas9, dCas9-KRAB or dCas9-VP64 (CRISPRa) were cultured in vascular cell basal medium (ATCC PCS-100-030).

extract_protocol:
Genomic DNA from both top and bottom 10% cell fractions separately (around 5M cells in each fraction) using the QIAGEN DNeasy Blood and Tissue kit (Cat No. 69504) according to manufacturer’s instructions.
SgRNA sequences were amplified from genomic DNA via PCR, followed by a cleanup step using the QIAGEN QIAquick PCR purification kit (Cat-#: 28104) according to the manufacturer's instructions. Sequencing libraries were created using Illumina TruSeq adapters according to the manufacturer’s protocols.

treatment_protocol: TeloHAEC cell lines (Cas9, dCas9-KRAB, dCas9-VP64) were infected with lentiviruses at a multiplicity of infection of 0.3. Following viral infection, we cells were selected using zeocin (teloHAEC-dCas9-VP64) or G418 (Cas9/dCas9-KRAB) for five (dCas9-VP64) or seven days (Cas9/-dCas9-KRAB) in vascular cell basal medium (ATCC PCS-100-030) to remove any cells that did not incorporate a vector. After selection, cells expressing Cas9 or dCas9-KRAB were stimulated using TNFɑ (10ng/μl) for four hours to induce a pro-inflammatory response. Following stimulation or culture, cells were immunostained for one of three adhesion molecules (E-SELECTIN, ICAM1, VCAM1) or incubated with fluorescent dye-based reagents for endothelial signaling markers (NO,ROS,Ca2+). Stained cells were sorted by flow cytometry to collect the top and bottom 10% of fluorescently labeled cells (Top, Bottom).

value: plasmid

tag: replicate

value: X


title: teloHAEC_CRISPRi_ROS_Bottom_r2

description: PCR amplified sgRNA sequences

value: CRISPRi

value: ROS

value: Bottom


title: teloHAEC_CRISPRi_ROS_Top_r3

description: PCR amplified sgRNA sequences

value: Top


title: teloHAEC_CRISPRi_ROS_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_ROS_Bottom_r4

description: PCR amplified sgRNA sequences


title: Cas9_CRISPRi_sgRNA_library

description: plasmid library


title: teloHAEC_CRISPRi_ROS_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_Ca2+_Top_r5

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_Ca2+_Bottom_r5

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_NO_Bottom_r4

description: PCR amplified sgRNA sequences

value: NO


title: teloHAEC_CRISPRi_VCAM1_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_VCAM1_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_safe_001_replicate3


title: teloHAEC_CRISPRi_ROS_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_NO_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_sgRNA_06939_replicate1

description: sgRNA targeting CAD locus


title: teloHAEC_CRISPRi_NO_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_VCAM1_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_Ca2+_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_NO_Bottom_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_ROS_Top_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_VCAM1_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_VCAM1_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_ROS_Bottom_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_VCAM1_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_NO_Top_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_NO_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_Ca2+_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ROS_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_NO_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_ICAM1_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ROS_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ROS_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_ICAM1_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_NO_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_Ca2+_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_ICAM1_Top_r5

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_Ca2+_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_Ca2+_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_ICAM1_Bottom_r5

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ROS_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_Ca2+_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_VCAM1_Top_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_ICAM1_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_ICAM1_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_NO_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_VCAM1_Bottom_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_NO_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ROS_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ROS_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_NO_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ROS_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ROS_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_Ca2+_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_Ca2+_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_NO_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_Ca2+_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_Ca2+_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_Ca2+_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_Ca2+_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_Ca2+_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_NO_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_NO_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_Ca2+_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ROS_Bottom_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ROS_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ROS_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_Ca2+_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ROS_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ROS_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_NO_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_NO_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ICAM1_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ICAM1_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_VCAM1_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_VCAM1_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_Ca2+_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_VCAM1_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_VCAM1_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ICAM1_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_VCAM1_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ROS_Top_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ICAM1_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_Ca2+_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_VCAM1_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ICAM1_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_Ca2+_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_VCAM1_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_VCAM1_Bottom_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_VCAM1_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_VCAM1_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ROS_Top_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_VCAM1_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ROS_Bottom_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ICAM1_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ICAM1_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ICAM1_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_VCAM1_Top_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_NO_Bottom_r3

description: PCR amplified sgRNA sequences


title: Bp_cytoplasm_rep2

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

institute: University of Hawaii at Manoa

description: Biological replicate 2 of 3

hyb_protocol: 1. Prepare hybridization solution    Hybridization solution mix recipe for two-color B. pseudomallei microarray assay  Component Volume Final Concentration  100% Formamide 400 μl 40%  20x SSC 250 μl 5x  10% SDS 10 μl 0.1%  0.1M DTT 1 μl 0.1 mM  Total Volume 1 ml     2. Filter the hybridization buffer using a 1 ml syringe and 0.45 μm filter.  3. Add 60 μl of Salmon Sperm DNA.  4. Add 50 μl of 1x hybridization buffer to the Cy3/Cy5 probe mixture, heat at 95°C for 10 minutes.  5. Apply the entire labeled probe mixture on to the microarray slides with coverslips, hybridize in the hybridization chamber for 20 hours at 42°C.   6. Following hybridization, the wash procedures are carried out as in the established protocols (http://pfgrc.jcvi.org/index.php/microarray/protocols.html).

scan_protocol: Scan slides immediately in a GenePix 4000B scanner using GenePix Pro software 5.1 at the resolution of 10 μm/pixel and wavelength of 532 nm and 635 nm.

data_processing: Individual TIFF images from each channel were processed with Spotfinder software 3.2.1 (available at http://www.tm4.org) to generate mev data. Microarray data were then normalized by low intensity filtering, LOWESS normalization, standard diviation regularization, and in-slide replicate analysis using MIDAS software 2.21 (available at http://www.tm4.org).  Finally, the mev files from MIDAS were used to generate the data table in MEV software 4.5.1 (available at http://www.tm4.org).

organism: Burkholderia pseudomallei

source_name: Single Bp cell from host cytoplasm

label_protocol: The synthesized cDNA were labeled with Cy3 or Cy5 dye following the established protocols (http://pfgrc.jcvi.org/index.php/microarray/protocols.html).

growth_protocol: First, the RAW264.7 cells were grown in a Corning cell culture flask with the CellBIND surface to enhance cell attachment and growth. After the macrophages reached ~80% confluence, they were gently scraped off the flask and seeded onto 0.17 mm PET membrane coated MembraneSlides (Carl Zeiss) which were pretreated with UV and poly-L-lysine. The macrophages were then incubated overnight to ensure attachment to the membrane and used for B. pseudomallei infection. The RFP-tagged B. pseudomallei strain was first grown overnight in LB medium, diluted 100x into fresh LB medium and grown to mid-log phase (OD600 ~0.8). The bacteria were then harvested, washed with 1x M9 minimal medium, and resuspended in the same volume of 1x M9 medium. The cell densities were estimated and diluted to approximately 4x105 CFU/ml in DMEM medium. Five hundred ml of the diluted B. pseudomallei culture was then added to each macrophage attached membrane slide to achieve approximate multiplicity of infection (MOI) of 0.2 (1 bacterium per 5 macrophage cells). The initial infection was then carried out for 30 min for internalization of the bacteria, and extracellular B. pseudomallei were then washed away with 1x PBS (phosphate buffered saline) solution. Fresh DMEM medium supplemented with 10% FBS was then added to the membrane slides and the infection was carried on for various amounts of time.

extract_protocol: The sections of membrane containing single bacterium at different infection stages were cut by the focused laser and catapulted with unfocused low-intensity laser into the 0.2 ml PCR tube lid. To obtain the in vitro control as the baseline for microarray comparison, the same diluted B. pseudomallei culture as above was incubated in DMEM for 1 h, harvested quickly by centrifugation and resuspended immediately in 1% (w/v) paraformaldehyde for 5 min. The fixed bacteria were then washed with 1x PBS and smeared on to the membrane slides. These slides were treated with 70% (v/v) ethanol for 30 min, and single B. pseudomallei cells were catapulted into one 0.2 ml PCR tube lid. The cDNA synthesis and amplification from single bacterium total RNA were then performed as described (PMC3106325 and PMC4494743). For the in vivo condition, individual B. pseudomallei cells were isolated into each PCR tube. However, for the in vitro condition, a total of nine B. pseudomallei cells were catapulted into the same PCR tube. And for the total transcript amplification from these nine in vitro cells, the steps including i) reverse transcription, ii) single-stranded cDNA ligation, and iii) initial MPRCA were performed in the same tube. Afterwards, the initially amplified cDNA was aliquoted into nine PCR tubes, and additional reagents were added for the second round of MPRCA. Eventually, all nine amplification reactions were combined again and aliquots were used for comparison between the individual in vivo cells.

treatment_protocol: At 1, 2 and 6 h post-infection, the membrane slides were washed quickly with 1x PBS solution and fixed immediately with 1% (w/v) paraformaldehyde for 5 min followed by 70% (v/v) ethanol for 30 min. After fixation, the slides were safe to be removed from the BSL-3 facility. To visualize B. pseudomallei at different stages during macrophage infection, we stained the macrophage endo-vesicle membrane and actin with FM 4-64FX lipophilic dye and Oregon Green 488 phalloidin (Invitrogen), respectively. The fluorescent images were obtained on a Zeiss PALM Laser Microdissection system with 100x oil immersion objective.

tag: host cell compartment/infection stage

value: Cytoplasm

source_name: Bp grown in vitro in DMEM

value: Bp grown in vitro in DMEM


title: Bp_protrusion_rep1

description: Biological replicate 1 of 3

source_name: Single Bp cell from protrusion stage

value: Protrusion


title: Bp_protrusion_rep2

description: Biological replicate 2 of 3


title: Bp_protrusion_rep3

description: Biological replicate 3 of 3


title: Bp_cytoplasm_rep1

description: Biological replicate 1 of 3


title: teloHAEC_CRISPRa_NO_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_NO_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_VCAM1_Bottom_r2

description: PCR amplified sgRNA sequences


title: Bp_vacuole_rep3

description: Biological replicate 3 of 3

source_name: Single Bp cell from host vacuole

value: Vacuole


title: teloHAEC_Cas9_VCAM1_Bottom_r1

description: PCR amplified sgRNA sequences


title: Bp_vacuole_rep2

description: Biological replicate 2 of 3


title: teloHAEC_CRISPRi_ICAM1_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_VCAM1_Bottom_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_ICAM1_Top_r2

description: PCR amplified sgRNA sequences


title: Bp_vacuole_rep1

description: Biological replicate 1 of 3

extract_protocol: The sections of membrane containing single bacterium at different infection stages were cut by the focused laser and catapulted with unfocused low-intensity laser into the 0.2 ml PCR tube lid. To obtain the in vitro control as the baseline for microarray comparison, the same diluted B. pseudomallei culture as above was incubated in DMEM for 1 h, harvested quickly by centrifugation and resuspended immediately in 1% (w/v) paraformaldehyde for 5 min. The fixed bacteria were then washed with 1x PBS and smeared on to the membrane slides. These slides were treated with 70% (v/v) ethanol for 30 min, and single B. pseudomallei cells were catapulted into one 0.2 ml PCR tube lid. The cDNA synthesis and amplification from single bacterium total RNA were then performed as previously described (PMC3106325 and PMC4494743). For the in vivo condition, individual B. pseudomallei cells were isolated into each PCR tube. However, for the in vitro condition, a total of nine B. pseudomallei cells were catapulted into the same PCR tube. And for the total transcript amplification from these nine in vitro cells, the steps including i) reverse transcription, ii) single-stranded cDNA ligation, and iii) initial MPRCA were performed in the same tube. Afterwards, the initially amplified cDNA was aliquoted into nine PCR tubes, and additional reagents were added for the second round of MPRCA. Eventually, all nine amplification reactions were combined again and aliquots were used for comparison between the individual in vivo cells.


title: Bp_cytoplasm_rep3

description: Biological replicate 3 of 3


title: teloHAEC_CRISPRi_Ca2+_Top_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_Ca2+_Bottom_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_NO_Bottom_r2

description: PCR amplified sgRNA sequences


title: Iso-α-acids, biological rep 4

city: Bunkyo-ku, Tokyo

first: Shinji

last: Okada

address: 1-1-1 Yayoi

institute: The University of Tokyo

description: Gene expression data of the livers in mouse with 0.5% iso-α-acids supplemented diets intake

hyb_protocol: The cDNAs were subsequently hybridized to a Clariom S Mouse Array (Thermo Fisher Scientific). The arrays were washed and labeled with streptavidin–phycoerythrin using a GeneChip Hybridization, Wash and Stain Kit and Fluidics Station 450 system (Thermo Fisher Scientific).

scan_protocol: Fluorescence was detected using a GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: Affymetrix GeneChip Command Console software was used to reduce the array images to the intensity of each probe (CEL files). The CEL files were quantified using the Factor Analysis for Robust Microarray Summarization algorithm (quantile normalization, qFARMS) with the statistical packages R and Bioconductor.

label: biotin

source_name: Murine livers with iso-α-acids supplemented diets intake

label_protocol: Biotinylated single-stranded complementary DNA (cDNA) was synthesized from 100 ng of total RNA using the GeneChip WT PLUS reagent kit (Thermo Fisher Scientific).

growth_protocol: Eight-week-old male C57BL/6NCrSlc mice were purchased from Japan SLC (Shizuoka, Japan) and were housed in controlled temperature (24±1°C), humidity (50-70%), and light (12 h light-dark cycle) conditions. They were fed the AIN-93G diet (Oriental Yeast, Tokyo, Japan) for a week and then were divided into two groups based on similar average body weight.

extract_protocol: Total RNA was isolated from each liver sample using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) and was subsequently purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany) and RNase-Free DNase Set (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: The control diet group was fed the AIN-93G diet, and the iso-α-acids diet group was fed the AIN-93G diet containing iso-α-acids (0.5%, w/w). Mice in the control group were pair-fed the control diet to the ad libitum intake of the iso-α-acid group for a week. After a week feeding period, animals were treated with an intraperitoneal (i.p.) injection of acetaldehyde (200 mg/kg). Tail vein blood samples were collected at 1, 2, and 5 h after the acetaldehyde injection. Liver samples were collected after blood sampling under deep anesthesia.

tag: strain

tag: age

value: 8 weeks

tag: Sex

value: male

value: iso-α-acids supplemented diets intake

tag: tissue

value: liver


title: HeLa_DDX41_1st

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue < = 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene reads and FPKM values for each Sample

source_name: HeLa_DDX41 overexpression

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
The HeLa cells were ground into fine powder before RNA extraction. Total RNA was extracted by the hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina HiSeq Xten was used to collect data from 150-bp pair-end sequencing.

treatment_protocol: overexpression plasmid transfection of HeLa cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for q-PCR analysis.

value: HeLa

value: DDX41 overexpression


title: HeLa_Ctrl_2nd

value: control


title: teloHAEC_CRISPRa_ICAM1_Bottom_r2

description: PCR amplified sgRNA sequences

value: teloHAEC

value: CRISPRa


title: teloHAEC_Cas9_ICAM1_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ICAM1_Top_r2

description: PCR amplified sgRNA sequences


title: HeLa_Ctrl_1st


title: HeLa_DDX41_2nd


title: teloHAEC_CRISPRi_ICAM1_Bottom_r1

description: PCR amplified sgRNA sequences

value: CRISPRi


title: Cotrol, biological rep 5

description: Gene expression data of the livers in mouse with contorl diets intake

source_name: Murine livers with control diets intake

value: control diets intake


title: Iso-α-acids, biological rep 3


title: teloHAEC_CRISPRa_ICAM1_Top_r2

description: PCR amplified sgRNA sequences

value: Top


title: Iso-α-acids, biological rep 5


title: Iso-α-acids, biological rep 2


title: teloHAEC_CRISPRa_VCAM1_Top_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ICAM1_Bottom_r1

description: PCR amplified sgRNA sequences

value: Bottom


title: Cotrol, biological rep 4


title: Cotrol, biological rep 3


title: teloHAEC_CRISPRi_ICAM1_Top_r1

description: PCR amplified sgRNA sequences


title: Cotrol, biological rep 2


title: Iso-α-acids, biological rep 1


title: teloHAEC_Cas9_ICAM1_Bottom_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_ICAM1_Top_r1

description: PCR amplified sgRNA sequences


title: Cotrol, biological rep 1


title: teloHAEC_Cas9_Ca2+_Bottom_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_ICAM1_Top_r1

description: PCR amplified sgRNA sequences


title: Folr1-/-, biological rep 2

city: LOUISVILLE

first: Partha

last: Mukhopadhyay

address: 501 S PRESTON ST

department: Division of Craniofacial Development & Anomalies

institute: University of Louisville

description: Gene (messenger RNA) expression data from GD-9.5, Folr1-/- (Knockout) embryos

hyb_protocol: Fifteen µg of labeled cRNA was fragmented in 40 µL of 1X fragmentation buffer (40 mM Tris-acetate pH 8.1, 100 mM K-acetate, 30 mM Mg-acetate) for 35 min at 94°C and assessed by agarose gel electrophoresis.  Fragmented cRNA was brought to a total volume of 300 µL with 1X hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01%Tween 20), 100 µg/mL herring sperm DNA, 500 µg/mL acetylated BSA, 50 pM biotinylated control oligonucleotide B2 and 1X eukaryotic hybridization controls (1.5 pM BioB, 5.0 pM BioC, 25 pM BioD and 100 pM cre; Affymetrix).  Each cRNA preparation derived from either Folr1+/+ or Folr1-/- embryos was hybridized to an individual GeneChip® from an identical lot of Affymetrix Mouse Expression Array 430A for 16 hours.  GeneChip® arrays were washed and stained using antibody-mediated signal amplification and the Affymetrix Fluidics Station’s standard Eukaryotic GE Wash 2 protocol.

scan_protocol: GeneChips were scanned and the  fluorescence intensities were determined using an Affymetrix GeneChip Scanner 3000.

data_processing: Individual GeneChip® arrays were scanned with the GeneChip® Scanner 3000 (Affymetrix) and images were processed using Affymetrix Microarray Analysis Suite (MAS) 5.0 software, according to Affymetrix protocols. For analysis of microarray data, the GeneChip® images of the gd9.5, Folr1-/- embryo samples were normalized to the corresponding images of the gd9.5, Folr1+/+ embryo samples across all probe pair sets.  The full dataset (difference call, fold change, average difference value, and absolute call data) from each of the two KO or three WT samples  was obtained using Affymetrix MAS 5.0 and contained expression levels for all 23,000 genes and expressed sequence tags (ESTs), as well as logarithm (base 2) of the estimated fold changes. It is to be noted that although a total of six samples and six GeneChips were used, one chip from Folr1-/- embryos failed quality control tests and did not yield any usable data.

source_name: Mouse embryos of gestation day 9.5, Folr1-/-

label_protocol: The double stranded cDNA was transcribed in vitro using the High-Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY) according to the manufacturer's instructions using biotinylated CTP and UTP (Affymetrix, Santa Clara, CA).  The resultant biotin-labeled cRNA was purified with RNeasy columns (Qiagen) and eluted in 40 µL of RNase-free water.  The quality and quantity of biotin-labeled cRNA was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

growth_protocol: Animals were housed by an American Association for Accreditation of Laboratory Animal Care (AAALAC)-approved facility, in a climate-controlled room with a 12-hour alternating light/dark cycle, and maintained on standard Purina Mouse Chow #5015 and water ad libitum. Mature male and female mice were mated overnight. The presence of a vaginal plug the following morning was considered evidence of mating and was designated as gd0. Folr1-/- mice were generated by mating female Folr1+/- mice, maintained on folate supplemented diet for 2 weeks, prior to mating with Folr1+/- sires.  Pregnant mice were maintained on this diet throughout gestation.  Animal protocols utilized were reviewed and approved by the University of Louisville Institutional Animal Care and Use Committee (IACUC).

extract_protocol: Total RNA from embryos was isolated using the Picopure RNA isolation kit (Arcturus, Mountain View, CA) following the manufacturer’s recommendations. Antisense RNA (aRNA) was produced using the RiboAmp OA Amplification Kit (Arcturus) according to the manufacturer’s protocols.  The RNA was subjected to one round of first strand cDNA synthesis, followed by second strand cDNA synthesis and in vitro transcription.  This was followed by another round of first and second strand cDNA synthesis.

treatment_protocol: Pregnant female mice were euthanized by carbon dioxide asphyxiation followed by cervical dislocation and Folr1-/- and Folr1+/+ embryos collected on gd9.5.  Embryos were harvested by caesarian section, placed in ice cold phosphate-buffered saline (PBS) and dissected free from the decidual capsule, chorion, and amnion. Folr1-/- and Folr1+/+ embryos were genotyped by tail PCR. Embryos were examined under a Nikon SMZ1500 stereomicroscope and documented by digital photomicroscopy using a Nikon DXM1200 digital camera (Nikon, Japan).

tag: genotype

value: Folr1 KO

value: whole embryo

value: Embryonic day 9.5


title: teloHAEC_Cas9_Ca2+_Top_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_Ca2+_Bottom_r1

description: PCR amplified sgRNA sequences


title: Folr1-/-, biological rep 1


title: Folr1+/+, biological rep 2

description: Gene (messenger RNA) expression data from GD-9.5, Folr1+/+ (Wild type) embryos

source_name: Mouse embryos of gestation day 9.5, Folr1+/+

value: Folr1 WT


title: teloHAEC_CRISPRa_NO_Bottom_r1

description: PCR amplified sgRNA sequences

value: NO


title: Folr1+/+, biological rep 3


title: teloHAEC_Cas9_NO_Bottom_r1

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_E-SELECTIN_Bottom_r4

description: PCR amplified sgRNA sequences

value: E-SELECTIN


title: teloHAEC_Cas9_NO_Top_r1

description: PCR amplified sgRNA sequences


title: ATAC_Non_Activated_2

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
RNA-seq: GRCm38.90 Reference Transcriptome was indexed from RSem (Li B et al. 2011) and sequence reads were aligned using RSem.
RNA-seq: Expected expression counts were then processed with an analysis pipeline using Bioconductor package Limma for normalization (TMM method) and differential expression testing
Supplementary_files_format_and_content: RNA-seq: Tab-delimited text files include raw, TPM and RPKM (Reads Per Kilobase Million) values for each sample.
ATAC-seq: Pre-processed ATAC-Seq reads were mapped against reference genome with a pipeline that used BWA MEM as aligner, Piccard to mark duplicate alignments, and samtools to eliminate duplicates, chimerics and sub-optimally multi-mapped alignments.
ATAC-seq: TSS enrichment values, calculated with HOMER's annotate Peaks function had values between 4 and 11 for any of the samples. Once filtered alignments had been obtained, peaks (accessible DNA regions) were called with MACS2, using parameters "--nomodel --shift -100 --extsize 200", and "-q 0.05" as the false discovery rate cut-off. Around 100 000 peaks were detected for any of the samples.
Supplementary_files_format_and_content: ATAC-seq: BW files includen mapped fragments
Genome_build: Mus sequenced genome GRCm38

source_name: Bone marrow-derived

extract_protocol:
RNA-seq: Total RNA was isolated using RNeasy Micro Kit (Qiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
RNA-seq: 200 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Library size was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration determined using the Qubit® fluorometer (Life Technologies).
ATAC-seq: A number of 5x104 synaptic DCs were sorted and lysed (10 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.1% IGEPAL CA-630) for 15 min at 4ºC while centrifuging at 500 x g.  Supernatant was discard and nuclei were resuspended in transposase reaction buffer with transposase5 (Tn5) and incubated for 1 hour at 37 ºC and 7 min at 4ºC. Later, 0.1 % SDS  was added to stop the reaction (5 min, RT) and DNA was isolated with Agencourt AMPure XP.Beckman Coulter (SPRI beads, 2x) and measured with Qbit Kit. For DNA library generation qPCR with i5 and i7 primers (barcoding) was performed (98ºC 2´, 98ºC 20¨, 63ºC 30¨, 72 ºC 1´, 4ºC ∞; 9 cycles). A size cut off was conducted (0.65 x SPRI beads) and DNA was isolated with 1.8x SPRI beads Finally, another qPCR was performed with i5 and i7 primers with a 6-7 cycles for 0.9 ng/ul or with 5 cycles for more than 0.9 ng/ul (98ºC 2´, 98ºC 20¨, 63 ºC 30¨, 72 ºC 1´ and 4ºC ∞) and amplified DNA was isolated with SPRI beads (2x) and its concentration measured by Qbit . As control we used qPCR for Actb promoter (open) and Cryaa promoter (closed). Agilent Pico 6000 bionalyzer was performed to assess peak sizes and percentages.
RNA-seq: Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.
ATAC-seq: Libraries were applied to an Illumina flow cell for cluster generation (PE Cluster Kit cBot) and sequence-by-synthesis paired reads of 100 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. ATAC-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: Bone marrow-derived dendritic cells

tag: stimulated

value: No

value: CD11c+ MHCIIhigh dendritic cells


title: teloHAEC_CRISPRi_E-SELECTIN_Bottom_r4

description: PCR amplified sgRNA sequences


title: Folr1+/+, biological rep 1


title: teloHAEC_CRISPRi_E-SELECTIN_Top_r4

description: PCR amplified sgRNA sequences


title: ATAC_Non_Activated_1


title: teloHAEC_Cas9_E-SELECTIN_Top_r4

description: PCR amplified sgRNA sequences


title: ATAC_Activated_2

value: Yes (LPS)


title: Blood_PT+HS_rep2

city: Ulm

first: Markus

last: Huber-Lang

address: Helmholtzstrasse 8/1

department: Institute of Clinical and Experimental Trauma-Immunology

institute: University Hospital Ulm

description:
Blood_PT_HS_2
Gene expression data from C57BL/6 mice 4 hours after trauma or control treatment

hyb_protocol: 2µg of total RNA were used for the One-Cycle target labeling assay, further processed and hybridized to the GeneChip® Mouse 430 2.0 array from Affymetrix according to manufacturer’s instructions.

scan_protocol: The Arrays were washed using Affymetrix fluidics station FS450, and scanned using the Gene Chip Scanner 3000.

data_processing: BRB Array Tools

source_name: Peripheral blood, polytrauma+hemorrhage

label_protocol: One Cycle Target Labelling Protocol

growth_protocol: C57BL/6 mice purchased from Jackson Laboratories (Bar Harbour, USA) with a mean body weight of 25 g (±2.5 g) and an age of 8 to 9 weeks were used.

extract_protocol: Blood was collected in RNAprotect Animal Blood Tubes and RNA was isolated using the RNeasy Protect Animal Blood Kit.

treatment_protocol: The polytrauma included a traumatic brain injury, a closed transverse femoral fracture with soft tissue injury and a blunt bilateral chest trauma. Hemorrhage was induced one hour after trauma through controlled blood loss until a mean arterial blood pressure (MAP) of 30 mmHg (±5 mmHg) was reached and then maintained at this level for 60 mins. Afterwards, fluid resuscitation with balanced electrolyte solution four times the volume of blood taken was performed over 30 mins. Cardiac puncture was performed four hours after the induction of trauma in trauma groups and directly after the induction of anesthesia in control animals.

value: polytrauma+hemorrhage

value: peripheral blood


title: Blood_PT+HS_rep3

description:
Blood_PT_HS_3
Gene expression data from C57BL/6 mice 4 hours after trauma or control treatment


title: teloHAEC_CRISPRa_NO_Top_r1

description: PCR amplified sgRNA sequences

value: teloHAEC

value: CRISPRa


title: Blood_PT+HS_rep1

description:
Blood_PT_HS_1
Gene expression data from C57BL/6 mice 4 hours after trauma or control treatment


title: teloHAEC_Cas9_E-SELECTIN_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_Ca2+_Top_r1

description: PCR amplified sgRNA sequences


title: Blood_PT_rep3

description:
Blood_PT_3
Gene expression data from C57BL/6 mice 4 hours after trauma or control treatment

source_name: Peripheral blood, polytrauma

value: polytrauma


title: ATAC_Activated_1


title: Blood_PT_rep2

description:
Blood_PT_2
Gene expression data from C57BL/6 mice 4 hours after trauma or control treatment


title: RNA_Non_Activated_3


title: Blood_PT_rep1

description:
Blood_PT_1
Gene expression data from C57BL/6 mice 4 hours after trauma or control treatment


title: RNA_Non_Activated_1


title: RNA_Non_Activated_2


title: Blood_Ctrl_rep1

description:
Blood_C_1
Gene expression data from C57BL/6 mice 4 hours after trauma or control treatment

source_name: Peripheral blood, control treatment

value: control treatment


title: Blood_Ctrl_rep2

description:
Blood_C_2
Gene expression data from C57BL/6 mice 4 hours after trauma or control treatment


title: teloHAEC_CRISPRi_E-SELECTIN_Top_r3

description: PCR amplified sgRNA sequences

value: CRISPRi

value: Top


title: teloHAEC_CRISPRa_E-SELECTIN_Bottom_r4

description: PCR amplified sgRNA sequences

value: Bottom


title: Blood_Ctrl_rep3

description:
Blood_C_3
Gene expression data from C57BL/6 mice 4 hours after trauma or control treatment


title: teloHAEC_CRISPRi_E-SELECTIN_Bottom_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_E-SELECTIN_Top_r3

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_E-SELECTIN_Top_r4

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRi_E-SELECTIN_Bottom_r2

description: PCR amplified sgRNA sequences


title: RNA_Activated_2


title: RNA_Activated_1


title: teloHAEC_CRISPRi_E-SELECTIN_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_E-SELECTIN_Bottom_r3

description: PCR amplified sgRNA sequences


title: Neural progenitor cells - cKO_Day9_rep2

city: Dresden

first: Tomohisa

last: Toda

address: Tazberg 41

institute: German Center for Neurodegenerative Diseases

description:
LmnB1_gene_count_D9.txt
LmnB1_gene_tpm_D9.txt

data_processing:
RNA-sequencing reads were trimmed for low base-quality using SolexaQA++ dynamic trim, v.3.1.3 and aligned to mm10 using RSEM rsem-calculate-expression ( v.1.2.18) with bowtie2 version 4.8.4 expected counts (counts) and normalized transcripts per million (TPM) were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: The counts file is the raw RNA-seq file, and the tpm file is the normalized RNA-seq data.

molecule: polyA RNA

source_name: Neural progenitor cells

growth_protocol: Mouse NPC cells were cultured in DMEM/F12 supplemented with modified N2/B27 and 10 ng/ml of both EGF and FGF-2.

extract_protocol: EYFP+ cells were sorted by FACS and RNA is isolated using Trizol with Dnase Turbo treatment

value: LaminB1fl/fl; Ai3 derived neural progenitor cells

value: Lentivirus:pSox2-Cre 9 days


title: Neural progenitor cells - cKO_Day9_rep3


title: teloHAEC_CRISPRa_E-SELECTIN_Top_r3

description: PCR amplified sgRNA sequences


title: RNA_Activated_3


title: teloHAEC_Cas9_E-SELECTIN_Bottom_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_Cas9_E-SELECTIN_Top_r2

description: PCR amplified sgRNA sequences


title: teloHAEC_CRISPRa_E-SELECTIN_Bottom_r2

description: PCR amplified sgRNA sequences


title: Neural progenitor cells - WT_Day9_rep3

value: LaminB1+/+; Ai3 derived neural progenitor cells


title: Neural progenitor cells - WT_Day9_rep2


title: Neural progenitor cells - cKO_Day5_rep2

description:
LmnB1_gene_count_D5.txt
LmnB1_gene_tpm_D5.txt

value: Lentivirus:pSox2-Cre 5 days


title: Neural progenitor cells - cKO_Day5_rep3


title: teloHAEC_Cas9_E-SELECTIN_Bottom_r1

description: PCR amplified sgRNA sequences

value: E-SELECTIN


title: Neural progenitor cells - WT_Day5_rep3


title: teloHAEC_Cas9_E-SELECTIN_Top_r1

description: PCR amplified sgRNA sequences


title: Neural progenitor cells - WT_Day9_rep1


title: Neural progenitor cells - cKO_Day5_rep1


title: teloHAEC_CRISPRi_E-SELECTIN_Bottom_r1

description: PCR amplified sgRNA sequences


title: Neural progenitor cells - WT_Day5_rep1


title: m25dwt_SP_Whole

city: Bar Harbor

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

data_processing:
Single-end sequencing was performed on the HiSeq2500 System using TruSeq SBS Kit v4 reagents (Illumina).
Sequence reads were aligned and quantified with the Jackson Laboratory Computational Sciences Civet Single-end RNA-seq Analysis Pipeline (https://github.com/TheJacksonLaboratory/civet/).
Briefly, sequences were preprocessed with an in-house python script that filtered sequences with less than seventy percent of the bases passing a quality threshold of 30, trimmed end bases with quality score less than 30, and filtered sequences where the remaining length was less than seventy percent of the starting length.
The resulting reads were mapped to mouse transcriptome (ENSEMBL version GRCm38.84) using bowtie v2.2.0 (default parameters) and subsequent expression estimates were obtained using rsem-calculate-expression v1.2.19 (default parameters) and counts were third-quartile normalized with an in-house script.
Count matrix normalization (rlog transformation) and differential expression analysis was performed with DESeq2.
Genome_build: GRCm38.84 Genome Reference Consortium Mus musculus Build 38
Supplementary_files_format_and_content: Tab-delimited text file includes third-quantile normalized log2counts for each sample

source_name: Whole mouse

growth_protocol: All mice were maintained in climate- and light cycle-controlled animal facilities at The Jackson Laboratory. Acidified water and 5K52 chow (PMI LabDiet) were provided ad libitum. All experiments were performed in accordance with National Institutes of Health Laboratory Animal Care Guidelines and were approved by the Animal Care and Use Committee (ACUC) of The Jackson Laboratory. All mouse strains used in this study are given in Supplemental Table S1.

extract_protocol:
Stem and myeloid (SMP) progenitor cells (Lin-Sca-Kit+CD34+, CD16_32lo) cells from spleen and bone marrow were sorted as described by Bumm et al., Cancer research 66, 11156-11165, 2006. Megakaryocyte-erythroid progenitors (MEP) were isolated as described in Challen et al., Cytometry A 75, 14-24, 2009. Total RNA was prepared using the PureLink RNA Mini Kit (Invitrogen). Libraries were checked for quality and concentration using the D5000 ScreenTape assay (Agilent Technologies) and quantitative PCR (KAPA Biosystems), according to the manufacturer’s instructions
RNA-seq libraries prepared using the KAPA mRNA HyperPrep Kit (KAPA Biosystems) according to the manufacturer’s instructions.

value: CbyJ.Cby-Rasa3(scat)/Llp +/+

value: spleen

value: Whole tissue

value: wt

tag: disease state

tag: Stage

value: I

tag: age in days


title: teloHAEC_CRISPRi_E-SELECTIN_Top_r1

description: PCR amplified sgRNA sequences

source_name: teloHAEC

value: teloHAEC


title: teloHAEC_CRISPRa_E-SELECTIN_Top_r2

description: PCR amplified sgRNA sequences

value: CRISPRa


title: teloHAEC_CRISPRa_E-SELECTIN_Top_r1

description: PCR amplified sgRNA sequences


title: m25dwt_BM_SMP

value: bone marrow

value: SMP


title: Neural progenitor cells - WT_Day5_rep2