title: Δihf_2

status: Public on Feb 28 2021

type: SRA

city: Uppsala

first: Ankita

last: Pal

address: Husargatan 3

department: Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

library_source: transcriptomic

data_processing:
Illumina Hi-seq 4000 used for sequencing
CUTADAPT used for removing adapter sequence and low-quality reads (q >= 20)
BWA used for reads mapping and alignment to reference genome (GenBank accession no. NC_000913.3)
Samtools used for compressing alignment files and sorting
FeatureCounts used for assigning counts at gene level
EdgeR used for differential gene expression analysis
Genome_build: Reference genome used: E.coli K12 MG1655, accession number : NC_000913.3
Supplementary_files_format_and_content: tab delimited .txt file containing raw reads count (Raw_counts_msi.txt)

molecule: total RNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacteria grown in M9 + glucose  under anaerobic fermentative conditions

growth_protocol: Escherichia coli cells grown in a bioreactor under anaerobic fermentation conditions with M9 + glucose at 37 degree Celcius and 150 rpm till exponential phase

extract_protocol:
Total RNA extraction was done using the TRIzol-chloroform method. DNase treatment was done to remove any DNA contamination. Dnase treated RNA was treated with MEGAclear to remove small-RNA and produce high-quality RNA after which enrichment for mRNA was done using the MicrobExpress Kit.
Paired-end, strand specific libraries for RNA sequencing were prepared using NEBNext Ultra Directional RNA library kit.The sequencing was carried out on HiSeq 4000  using 2x150 bp paired-end reads.

treatment_protocol: Escherichia coli cells grown in a bioreactor under anaerobic conditions with M9+glucose at 37 degree Celcius and 150 rpm and total RNA extracted at exponential phase

tag: growth phase

value: exponential phase of growth

tag: genotype

value: ihf


title: WT_2

value: WT


title: WT_1


title: Δihf_1


title: Del_46-54-Cas12a-3

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

country: China

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

library_source: genomic

data_processing:
Library strategy: Nanopore sequncing
Then High-throughput sequencing was performed on the MinION
Porechop (version 0.2.4) was used to remove adapter sequences from Nanopore reads.
Minimap2 (version 2.17-r941) was used to map long reads to human genome.
Samtools (version 1.9) was used to process bam files.
bamCoverage (version 3.3.0) was used to convert bam files to bigwig files.
Genome_build: hg38

molecule: genomic DNA

organism: Homo sapiens

source_name: Muscle-derived stem cells

growth_protocol: Human muscle-derived stem cells were isolated using a modified version of the pre-plate technique as previously described(29). Briefly, 2 h after seeding the cells in the flask (pre-plate [PP]1), non-adherent cells and medium were transferred to a fresh flask, re-collected, and transferred to another flask 24 h later (PP2). Serial pre-plating was thus performed to separate cells until PP6; these cells were deemed as MDSCs

extract_protocol:
The cells were trypsinized and collected, and genomic DNA was extracted using the Cell Genome Extraction kit (Tiangen Biotech, Beijing, China)
The libraries for each sample were constructed by Oxford Nanopore Technology EXP-NBD103 for barcoding and Ligation Sequencing Kit 1D (SQK-LSK108) for sequencing.

tag: tissue

value: Muscle

tag: passages


title: Del_46-54-Cas12a-2


title: Del_46-54-Cas12a-1


title: Del_46-54_Cas9-1


title: Del_46-54_Cas9-2


title: Del_45-55_Cas9-2


title: ΔarcA_2

value: arcA


title: ΔarcA_1


title: Δfnr_2

value: fnr


title: Δfnr_1


title: Sa187-F-Rt rep2

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

description:
Variety: Karim
Endospehare of Wheat Root inculated with SA187

data_processing:
Microbiome data was analyzed using the software MOTHUR (version 1.42.3) (Schloss et al., 2009) by using 16S rRNA sequence editing and analysis following methods described by Röthig, Roik (Röthig et al., 2017).
Reads were demultiplexed, quality trimmed, afterwards pre-clustered depend on 2 bp differences (Huse et al., 2010), Singletons were removed and the residual sequences were aligned against the SILVA database release 119 (Schloss et al., 2009).
Chimeric sequences were removed using UCHIME as preformed in Mothur (Edgar et al., 2011), as well as undesirables sequences such as chloroplasts, mitochondria, archaea and eukaryotes. Sequences were classified against Greengenes database using bootstrapping of 60 (release gg_13_8_99; bootstrap = 60) (McDonald et al., 2012).
Then, phylogenetically classified sequences were used to generate bacterial taxonomic composition of samples and plotted into Phylum and family level using the means of relative abundances from three replicated samples of Soil, Control Root and Root treated with SA187.
For further analyses, sequences were subsampled to 20816 sequences per sample and were then clustered into Operational Taxonomic Units (OTUs) using a 97% similarity cutoff.
Genome_build: SILVA 119 release
Supplementary_files_format_and_content: excel, OTUs

organism: Triticum aestivum

growth_protocol: The experiment was conducted using a randomized complete block design; each plot is 5 m2 with three replications. Ten-row plots were prepared with intra- and inter row distances of 20 cm and 50 cm, respectively. All the plots were irrigated with water EC= 0.3 dS m-1, the average value for the soil pH was 7.45 and the salinity of soil was EC=1.9 dS m-1

extract_protocol:
Total DNA extraction of endophytic bacterial community was performed as described by (Eida et al., 2018),
accourding to Eid al etal 2018

treatment_protocol: Inoculation was performed by coating the seeds of the durum wheat local variety Karim with a mixture containing broth culture, sugar solution (10%) with a rate of 2x109 cell/kg seed.

value: root

tag: cell type

value: endosphere

tag: agent

value: Enterobacter sp. SA187

tag: cultivar

value: Karim


title: Del_46-54-Cas12a-4


title: Sa187-F-Rt rep1

source_name: Endospehare of Wheat Root inculated with SA187


title: C-S-Rt rep3

description:
Variety: Karim
Endospehare of Wheat Root

source_name: Endospehare of Wheat Root


title: Del_46-54_Cas9-4


title: Del_46-54_Cas9-3


title: C-S-Rt rep2


title: C-S-Rt rep1


title: BMECs 3

city: Changchun

first: Lixin

last: Xia

state: Jilin

address: No.5333 Xi'an Road,Luyuan District

department: College of Animal Science

institute: Jilin University

data_processing:
Library preparation for Transcriptome sequencing A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Clustering and sequencing (Novogene Experimental Department) The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

organism: Bos taurus

source_name: mammary epithelial cells

growth_protocol: The BMECs were isolated from bovine breast tissue by tissue culture method, and the primary breast epithelial cells were obtained by enzyme digestion.The kruppel-like factors 6 (KLF6) gene was completely knocked out in BMECs using CRISPR/Cas9.

extract_protocol: The sequencing library of each RNA sample was prepared by using Ion Total RNA-Seq Kit v2

treatment_protocol: Total RNA from KLF6-KO and wild type BMECs was extracted using TRIzol reagent. Total RNA was further treated with RNase-free DNase I, and RNA longer than 18 nucleotides was recovered. The quality was assessed by the Agilent2200 (Agilent, USA).

value: Bovine Primary Mammary Epithelial Cells

value: wild type

tag: breed

value: Holstein


title: Del_45-55_Cas9-4


title: BMECs 2


title: BMECs 1


title: KLF6-KO BMECs 2

value: KLF6 knockout


title: KLF6-KO BMECs 1


title: Del_45-55_Cas9-1


title: 54_cancer_136+139

city: Rehovot

first: Ruth

last: Scherz-Shouval

address: 234 Herzl street

department: Biomolecular Science

country: Israel

institute: Weizmann Institute of Science

description: This sample contains a mixture of  CAFs from 2 gastric cancer mice.

data_processing:
Illumina NextSeq 500
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome /shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of RefSeq annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream):
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg (DOI: 10.1111/j.2517-6161.1995.tb02031.x).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

organism: Mus musculus

source_name: Stomach CAFs

growth_protocol: 8 weeks-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Briefly, dissected stomachs were washed in cold PBS and incubated in dissociation (HBSS with 5 mM EDTA, 10 mM HEPES) solution at 37°C for 20 min. Stomachs were then digested with collagenase A. CAFs were collected by usign FACS sorting after removing endothelial cells (gating for CD31), immune cells (gating for CD45), epithelial cells (gating for EpCAM)and selecting for live/podoplanin positive cells. RNA was extracted and sequencing was carried out as described in Jaitin et al, 2014.
MARS-seq was used as described in Jaitin et al, 2014.

treatment_protocol: 8 weeks old  iLgr5;GLI2A mice were treated with tamoxifen in corn oil administered for 5 days by oral gavage. Mice were then fed doxycycline containing chow  for 3 weeks after which they were sacrificed. For the first 3 days of doxycycline induction, mice also received doxycycline in their drinking water with 5% sucrose. After 3 weeks mice were sacrificed and CAFs were isolated from their stomachs. Control mice received corn oil as control and they were not given doxycyline.

tag: strain

value: Triple-transgenic iLgr5;GLI2A gastric cancer mice as described in Syu et al, 2016

tag: mouse age

value: 8 weeks

tag: treatment

value: Cancer was induced as described in Syu et al, 2016

value: Stomach

value: cancer-associated fibroblasts (CAFs)


title: 50_normal_2

description: This sample contains normal fibroblasts from 1 mouse.

source_name: Normal stomach fibroblasts

value: Mice received corn oil as control and they were not treated with tamoxifen and doxycycline

value: normal fibroblasts


title: Sa187-F-Rt rep3


title: 49_normal_1


title: 52_cancer_109

description: This sample contains CAFs from 1 gastric cancer mouse.


title: 53_cancer_118+121


title: IL4+IL10-injected 5

city: Utrecht

first: Niels

last: Eijkelkamp

address: Lundlaan 6

department: Center for Translational Immunology

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Perform quality control on FastQ files (using FastQC)
Align reads of each sample in a run against reference genome using STAR
Count reads in features (using HTSeq-count)
Normalize read counts (using DESeq2)
Perform DE analysis for standard designs (using DESeq2)
Genome_build: GRCm38
Supplementary_files_format_and_content: VSD normalized data

source_name: DRG

extract_protocol:
DRG were removed, kepst in RNA-later, and RNA was harvested using Trizol reagent.
RNA libraries were prepared with the poly A selection method.

treatment_protocol: Persistent inflammatory pain was induced by an intraplantar injection of 20ul of 2% carrageenan. Six days later mice received an intrathecal injection of vehicle (PBS), IL4+IL10 (0.5 μg each) or IL4-10 FP (1μg). Six hours after intrathecal injection, lumbar DRGs (L3-L5) were isolated.

value: DRG

tag: inflammatory model

value: Carageenan 2percent


title: IL4+IL10-injected 3


title: IL4+IL10-injected 1


title: IL4+IL10-injected 4


title: IL4-10 FP-injected 4

value: IL4-10 FP


title: IL4+IL10-injected 2


title: IL4-10 FP-injected 5


title: IL4-10 FP-injected 2


title: Vehicle-injected 5

value: PBS


title: IL4-10 FP-injected 1


title: IL4-10 FP-injected 3


title: KLF6-KO BMECs 3


title: 51_normal_103+104

description: This sample contains normal fibroblasts from a mixture of 2 mice.


title: IL4-10 FP-injected 6


title: Vehicle-injected 4


title: Vehicle-injected 2


title: Rep161_WT_ATAC_Rep2

city: Frederick

first: GuoJun

last: Yu

state: MD

address: 560 CHANDLER STREET

department: Cell Biology

country: USA

institute: National Institutes of Health

data_processing:
Adaptors and low-quality reads were filtered out using Trim Galore (version 0.3.7)
For whole genome analysis, clean reads were aligned to the human genome from GENCODE (GRCh38 v30) with STAR (v 2.7.6a, --alignIntronMax 1 --seedSearchStartLmax 25 --outFilterMultimapNmax 2 --outFilterMismatchNmax 1).
Samtools was used to remove the reads mapped to mitochondria and duplicated reads were filtered out using Picard.
Macs2 (v2.2.7.1) was adopted to call peaks for all the samples and the differential peaks were determined using featureCounts and DEseq2 with threshold: foldchange >=2 and Padj <= 005.
bamCoverage was used to generate the bigwig files and the ATAC-seq profile for each sample was plotted using computeMatrix and plotProfile command from deeptools.
The genomic track of ATAC-seq for Ig locus was plotted using pyGenomeTracks program.
Genome_build: GRCh38 v30
Supplementary_files_format_and_content: genome browser track

source_name: human B cell line Ramos-Rep161-WT

growth_protocol: The cells were cultured with Iscove’s modified Dulbecco’s medium (BioWhittaker) supplemented with 10% (vol/vol) FBS (Atlanta Biologicals) and 100 U/mL penicillin-streptomycin (Mediatech).

extract_protocol:
The nuclei from each group were treated with Tn5 transposase and the accessible DNA regions were collected and amplified.
Liabries were prepared under the standard Omni-ATAC protocol using Illumina Tagment DNA Enzyme and Buffer Small Kit.

treatment_protocol: The Dot1L was knocked out using CRISPR-Cas9 and positive clones were screend using western blotting and sanger sequencing.

tag: cell line

value: B cell

tag: aid level

value: endogenous AID is undectable

tag: aid-er

value: Ectopic AID-ER is stably transfected

value: WT


title: Vehicle-injected 1


title: Rep161_WT_ATAC_Rep1


title: Rep161_Dot1L_KO_ATAC_Rep1

source_name: human B cell line Ramos-Rep161-Dot1L_KO

value: Dot1L KO by CRISPR/Cas9


title: WES PBS rep2

data_processing:
Library strategy: Whole Exome Sequencing
High-throughput sequencing was performed on the Agilent V6.
Trimmed reads were obtained by removing adapter sequences, and reads with low complexity or of low quality were removed.
quality filtered reads were mapped to the human reference genome using hisat2.
SNPs and indels were detected and filtered using gatk4.
SNPs and indels were annotated using ANNOVAR.
Genome_build: hg38

extract_protocol:
The cells were trypsinized and collected, and genomic DNA was extracted using the Cell Genome Extraction kit (Tiangen Biotech, Beijing, China)
The libraries for each sample were constructed using Agilent V6 Kit for sequencing.

value: Muscle


title: WES PBS rep1


title: WES Unedited rep1


title: Control_sEVs-1

city: Niigata

first: Atsunori

last: Tsuchiya

state: %null%

address: 1-757, Asahimachi-dori, Chuo-ku, Niigata

country: Japan

institute: Niigata University

description: miRNA

data_processing:
Duplicated reads were removed from raw reads using seqkit (ver. 0.10.1), and adapter sequence was trimmed with cutadapt (ver. 1.16).
Trimmed reads were mapped to the human and mouse genomes (genome assemblies used were GRCh38.p13 and GRCm38.p6, respectively) using STAR (ver. 2.7.2b) with the following parameters: --alignEndsType EndToEnd --outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --outReadsUnmapped None --outSAMtype BAM Unsorted --outFilterMultimapNmax 10 --outSAMunmapped Within --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000 --alignIntronMax 1.
Reads mapped to miRNA genes were quantified using featureCounts of the Subread package (ver. 1.6.1) with the following parameters: -s 1 -O -M -p -C -B -T.
Differential gene expression analysis and GO analysis were performed using DESeq2 (ver. 1.18.1) and clusterProfiler (ver. 3.6.0), respectively.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Tab-delimited text files include Count or FPKM values for each sample

source_name: adipose tissue

growth_protocol: MSCs were cultured with or withour IFN-γ. Then exosomes were harvested and their miRNAs were analyzed.

extract_protocol:
miRNA was extracted from the isolated exosome samples using miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany).
miRNA-seq library was prepared using QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) following the manufacturer’s instruction.

value: mesenchymal stem cell

tag: type

value: exosome

value: without IFN-γ stimulation


title: Case_γ-sEVs-2

description: miRNA

value: with IFN-γ stimulation


title: Control_sEVs-2

description: miRNA


title: Case_γ-sEVs-1

description: miRNA


title: Vehicle-injected 3


title: WES ∆46–54/Cas12a rep2


title: WES ∆46–54/Cas12a rep1


title: WES ∆46–54/Cas9 rep2


title: WES INDEL50/Cas9 rep1


title: WES INDEL50/Cas9 rep2


title: WES Cas9 rep1


title: WES Cas9 rep2


title: WES ∆45–55/Cas9 rep2


title: Rep161_Dot1L_KO_ATAC_Rep2


title: D3-P-COV1_S10

city: Los Angeles

first: Dhruv

last: Sareen

state: CA California

address: 8700 Beverly Blvd

department: Board of Governors Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
Reads were mapped and quantified using the STAR alligner
Genome_build: GRCh38 human reference transcriptome based on human GENCODE version 33
Supplementary_files_format_and_content: Processed data includes raw read counts and normalized transcripts per million reads

source_name: iPan iPSC-derived pancreatic cells

growth_protocol: iPSCs were maintained in mTeSR+ prior to differentiation via sequential GSK signaling, BMP signaling, SHH signaling, Notch signaling, and EGF signaling

extract_protocol:
QIAGEN RNeasy Micro RNA extraction kit
Illumina TruSeq Stranded mRNA library preparation kit

value: iPan iPSC-derived pancreatic cells

tag: infection status

value: SARS-CoV-2 infected

tag: time point


title: D3-P-COV3_S12


title: D3-P-COV2_S11


title: D3-Mock-3_S9

value: Mock


title: D3-Mock-2_S8


title: WES Unedited rep2


title: D1-P-COV1_S4


title: D3-Mock-1_S7


title: D1-P-COV3_S6


title: D1-P-COV2_S5


title: D1-Mock-3_S3


title: D1-Mock-1_S1


title: D1-Mock-2_S2


title: 1518442 cancer sample 9

description: RAW counts.csv

data_processing:
Illumina NextSeq 500
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) and mapped to genome /shareDB/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_index using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (default parameters).
The pipeline quantifies the genes annotated in RefSeq: /home/labs/bioservices/services/ngs/support/gtf/hg38.genes.gtf.
Counting was done using STAR.
Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2
Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Genome_build: Pipeline was constructed using Snakemake (DOI: 10.1093/bioinformatics/bts480).
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Patient data

extract_protocol:
FFPE slides were deparaffinized and stained using Arcturus Paradise Plus Staining kit (#KIT0312J, Thermo-Fischer) according to the instructions of the manufacturer. Slides were then left to dry for 5 min at RT followed by microdissection using the Arcturus (XT) laser microdissection instrument (#010013097, Thermo-Fischer). Infrared capture was used to minimize RNA damage. CapSure Macro LCM caps (#LCM0211, Thermo-Fischer) were used to capture microdissected tissue. RNA isolation was carried out using the RNeasy FFPE kit (#73504, Qiagen) following the instructions of the manufacturer with one modification- proteinase K digestion at 56°C was carried out for 1 h.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq v2-Pico Input Mammalian kit (#634415, Takara Bio USA) according to the instructions of the manufacturer.

tag: patient outcome

value: good

tag: tumor stage

value: stage 2

value: Stomach

tag: lauren classification

value: intestinal


title: WES ∆45–55/Cas9 rep1

tag: tissue

tag: passages


title: LT: long-term treatment

city: Taigu

first: Chunlei

last: Zou

address: No.1 Mingxian Road

institute: Shanxi Agricultural University

description: Five-week-old sugar beet (Beta vulgaris L.) seedlings were treated with Hoagland solution, containing 75 mM mixed alkaline solution (Na2CO3:NaHCO3, 1:2) for 0 day (control, designated as C), 3 days (short-term treatment, designated as ST) and 7 days (long-term treatment, designated as LT).

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas (clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing poly A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRbase20.0 was used as reference, modified software mirdeep2 (Friedländer et al., 2012) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specific species itself.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Beta+vulgaris+L

organism: Beta vulgaris

source_name: Five-week-old sugar beet (Beta vulgaris L.) seedlings were treated with Hoagland solution, containing 75 mM mixed alkaline solution (Na2CO3:NaHCO3, 1:2) for 7 days

growth_protocol: Pelleted seeds of sugar beet (Beta vulgaris L.) cultivar “KWS0143”, supplied by KWS company, Germany, were germinated in vermiculite with distilled water for a week, transferred to Hoagland solution, and kept in a culture room for 3 weeks under a 16 h light/8 h dark cycle at room temperature.

extract_protocol:
Total RNA was isolated from leaves with using the CAUltra Clean Plant RNA isolation kit (MO BIO Laboratories, USA) according to the manufacturer’s instructions.
After quantification and qualification, all RNA samples were submitted to Novogene (Shenzhen, China) for high-throughput sequencing. The sequences of 3 libraries were obtained using the Illumina Hiseq 2500 platform.

treatment_protocol: Five-week-old seedlings were treated with Hoagland solution, containing 75 mM mixed alkaline solution (Na2CO3:NaHCO3, 1:2) for 0 day (control, designated as C), 3 days (short-term treatment, designated as ST) and 7 days (long-term treatment, designated as LT). Fresh leaves from the same position of seedlings at different treatments were collected. Sample from each treatment represented a pool of more than 10 independent individuals. All the harvested leaves were immediately frozen in liquid nitrogen after collection and stored at −80 °C for RNA-seq

value: Sugar beet leaves

tag: treatment time


title: 1223760 cancer sample 2

description: RAW counts.csv

value: bad


title: 1321847 cancer sample 6

description: RAW counts.csv

value: signet cell ring


title: 1322532 cancer sample 7

description: RAW counts.csv

value: intestinal,signet cell ring


title: 1510356 cancer sample 3

description: RAW counts.csv

value: stage 3


title: 1411657 stroma sample 8

description: RAW counts.csv

value: diffuse


title: 1517598 cancer sample 4

description: RAW counts.csv


title: 1520565 cancer sample 1

description: RAW counts.csv


title: C: control

source_name: Five-week-old sugar beet (Beta vulgaris L.) seedlings

value: 0 day (control, designated as C)


title: 1322532 stroma sample 7

description: RAW counts.csv


title: 1404943 stroma sample 5

description: RAW counts.csv


title: 1321847 stroma sample 6

description: RAW counts.csv


title: 1517598 stroma sample 4

description: RAW counts.csv


title: V4

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

description: Parental human K562 leukemia cells

data_processing:
RNA-seq raw reads  were mapped to the human reference genome GRCh38 using HISAT2 v2.1.0 with default parameters
Counts on genes were generated using subread-1.5.1 featureCounts and ensembl gene annotation GRCh38.92
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression counts in a tab delimmited text file

source_name: K/VP.5 cells

growth_protocol: K562, K/VP.5 and KVP.5/Edit-3 cells were maintained in DMEM/10% FBS with etoposide (0.5 µM) added every other week.

extract_protocol:
DNA-free RNA was isolated from K562, K/VP.5, and K/VP.5/edit-3 cells using the RNA Easy Plus Mini Kit with on-column digestion with RNase-Free DNase (cat. no. 79254). Two rounds of purification were utilized to assure high purity and DNase free RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Etoposide resistant K/VP.5 cells were transfected with purified Cas9, gRNA, and single strand oligonucleotide repair template that equally spans the TOP2α E19/I19 boundary and harbors two nucleotide changes to enhance the recgnition of this splice site by the splicing machinery. Genomic qPCR using a probe specific for the edited TOP2α E19/I19 5' splice site was used to screen for clones that harbored edited alleles.

tag: parental cell line

tag: cell type

value: Human leukemia

tag: condition

value: Etoposide resistant human K562 leukemia cells


title: V3

description: Parental human K562 leukemia cells


title: WES ∆46–54/Cas9 rep1

value: Muscle


title: 1404943 cancer sample 5

description: RAW counts.csv


title: 1510356 stroma sample 3

description: RAW counts.csv


title: V2

description: Parental human K562 leukemia cells


title: 1520565 stroma sample 1

description: RAW counts.csv


title: K4

description: Parental human K562 leukemia cells

source_name: K562 cells

value: Parental human K562 leukemia cells


title: MM1.S-shRNA2  IRF3_rep2

city: London

first: Kanagaraju

last: Ponnusamy

address: 4th Floor common wealth building, Du Cane Road

department: Hematology

country: United Kingdom

institute: Imperial College London

data_processing:
reads were aligned using Salmon (v0.12.0) on GRCh38 (hg38) genome assembly
Differential expression analysis was performed using DESeq2 (v1.24.0)
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: tab-delimited text files include differentially expressed genes

source_name: Myeloma cell line

growth_protocol: cells were cultured in RPMI 1640 medium with 10% FBS

extract_protocol:
Total RNA was isolated using Nucleospin RNA kit (Macherey-Nagel) and poly A-tail mRNA was enriched using NEBNext poly(A) mRNA Magnetic Isolation Module
Libraries were prepared using NEBNext Ultra II RNA library prep kits (New Engand Biolabs) according to manufacturer's protocol

treatment_protocol: cells were transduced with lentivirus to express scramble control or shRNAs

tag: shRNA

value: anti- IRF3 shRNA 2


title: 1223760 stroma sample 2

description: RAW counts.csv


title: MM1.S-shRNA1  IRF3_rep2

value: anti- IRF3 shRNA 1


title: K1

description: Parental human K562 leukemia cells


title: 1411657 cancer sample 8

description: RAW counts.csv

value: good


title: MM1.S-shRNA2  IRF3_rep1


title: E3.4

description: Parental human K562 leukemia cells

source_name: K/VP.5/edit-3 cells

value: Etoposide resistant human leukemia cells with the TOP2alpha gene exon-19/intron-19 5' splice site CRISPR/Cas9 edited.


title: MM1.S-shRNA1 IRF3_rep1


title: K2

description: Parental human K562 leukemia cells


title: K3

description: Parental human K562 leukemia cells


title: MM.1S-scramble_rep1

value: scramble control


title: MM.1S-scramble_rep2


title: E3.3

description: Parental human K562 leukemia cells


title: E3.2

description: Parental human K562 leukemia cells


title: E3.1

description: Parental human K562 leukemia cells


title: Spp1_gRNA_2

city: San Francisco

first: Simone

last: Giacometti

address: 513 Parnassus Avenue

institute: UCSF

description:
RNA-Seq
counts_all_genes.tsv

data_processing:
For scRNA-Seq: data was generated on the 10X platform (10X Genomics, Pleasanton, CA) according to Single Cell 3’ protocol (v2 Chemistry) recommended by the manufacturer .The Cell Ranger software pipeline (version 2.1.1) was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and produce a  matrix of gene counts versus cells. The R package Seurat (version 3.1.1) was used to process the unique molecular identifier (UMI) count matrix, and to perform data normalization (gene expression measurements for each cell were normalized by total expression, and log-transformed), dimensionality reduction, clustering, and differential expression analysis. DE analysis was performed with the R packages DESeq2 (v.1.16.0) and MAST. Gene-set enrichment analysis was performed on the identified differentially expressed genes with the GSEA software in the pre-ranked mode.
Genome_build: GRCm38
Supplementary_files_format_and_content: C57BL6J_matrix.mtx: a gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: C57BL6J_gene.tsv: gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: C57BL6J_cell.tsv: cell names (colname names of the sparse count matrix)
For RNA-Seq: Quality of raw FASTQ sequences was assessed using FASTQC. To process RNA-Seq libraries,  adaptor sequences were trimmed using Cutadapt version 1.14 (requiring a length greater than 10 nt after trimming) and quality-filtered by requiring all bases to have a minimum score of 20 (-m 20 -q 20). Only reads that passed the quality or length threshold on both strands were considered for mapping. Reads were aligned to the human genome GRCh38 (hg38) with the STAR Aligner (version 020201). Ensembl reference annotation version 89 was used to define gene models for mapping quantification. Uniquely mapped reads for each gene model were produced using STAR parameter “--quantMode GeneCounts”. Differential expression analysis was performed in R using DESeq2 (v.1.16.0) with the default parameters, including the Cook’s distance treatment to remove outliers.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts_all_genes.tsv: tab-delimited file containing the raw reads count matrix

source_name: Immortalized pancreatic duct cells

growth_protocol: For RNA-Seq: 10% FBS, 1X P/S, DMEM

extract_protocol:
Qiagen RNeasy kit
For RNA-Seq: Eukaryotic stranded library
DBA-lectin based generation of single cell suspension of pancreatic duct cells
Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v2

treatment_protocol: Viral transduction of gRNA followed by stable selection with puromycin

tag: strain

value: HPDE E6/E7

value: pancreas

tag: age

value: 63 years


title: Spp1_gRNA_3

description:
RNA-Seq
counts_all_genes.tsv


title: Spp1_gRNA_4

description:
RNA-Seq
counts_all_genes.tsv


title: Spp1_gRNA_1

description:
RNA-Seq
counts_all_genes.tsv


title: scr_gRNA_3

description:
RNA-Seq
counts_all_genes.tsv


title: ZM-RNH1

city: Charlottesville

first: Erin

last: Moran

state: VA

address: 1340 Jefferson Park Avenue, Pinn 6014

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: DRIP-seq

data_processing:
Raw sequence files were filtered for quality using Prinseq and downsampled to 6.5M reads each
Spike-in quantification was performed by aligning reads to the SacCer3 genome using BWA-MEM (HEK293T samples were also aligned to determine a background level of alignment)
Reads were aligned using BWA-MEM paired end options to hg38 genome
Model build using MACS2 estimated ~290 as a shift between paired end sequences. Peaks were called using paired end settings using a -d value of 290.
Repetitive elements from DLD1 cells were determined de novo using the RepeatExplorer package and a subset of the reads from both input files (~1M reads from each)
Count tables of DRIP enrichments within repetitive elements was determined using ChIP-seq mapper (Neumann et al., 2012), a BLASTN style mapper to determine reads within repetitive contigs.
Count tables were then normalized based on Spike-in quantification scale factors, found in table 4 of the Materials and methods section of Moran et al
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files
Supplementary_files_format_and_content: NarrowPeak bed files were created from individual alignment files using MACS2 callpeaks -pe
Supplementary_files_format_and_content: Inputs, treatment files across duplicates were compiled after alignment using BWA-MEM using Samtools. Compiled files were used to call peaks using MACS2 callpeak.

growth_protocol: DLD1 cells grown in RPMI-1640 with 10% FBS

extract_protocol:
Nucleic acids were extracted from sonicated chromatin, and RNA-DNA hybrids were precipitated with the S9.6 hybridoma.
Libraries were prepared using Takara SMARTer ThruPLEX DNA seq using Illumina compatible DNA HT dual Index kit N1-N12. Sonicated yeast DNA was spiked in at a 10% rate prior to library preparation.

tag: precipitating antibody

value: S9.6 hybridoma

tag: treatment

value: Colcemid, ZM447439 2 uM

tag: rnaseh1 treatment


title: AZD-RNH1

description: DRIP-seq

value: Colcemid, AZD1152 500 nM


title: V1

description: Parental human K562 leukemia cells


title: scr_gRNA_2

description:
RNA-Seq
counts_all_genes.tsv


title: RB 400 µM, rep2

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

description:
6G
RB 3-2

data_processing:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20  -m 30 )
The remaining reads (raw data submitted)  were mapped to the Arabidopsis thaliana genome (Araport11) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from Araport release), which was modified to contain a window surrounding the 3' UTR.
Genes were filtered out if thier sum counts   <=5 .  Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: Araport11
Supplementary_files_format_and_content: Deseq_raw_norm_no_UMI_filter_Trans2X_RB.xlsx  contains raw,  normalized counts and  log2 normalized counts (rld) done by DESeq2 for 13,307 gene remained after filtering based on expression levels (sum normalized count in all samples greater than 5) .

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Plants were grown on standing square Petri dishes on 1/2MS + 1% sucrose, pH5.8. Growth room with a 16h light/8h dark cycle, and temperature of 22oC

extract_protocol:
Standard Trizol RNA extraction
Total RNA was eluted with 50ul of UPW and stored at -80C.For library preparation RNA was used for the bulk MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: Plants were equilibrated for at least 1hour in ddw in petri dishes, then sorted into a set of 12-well plates with ddw in preparation for treatment. Samples were shifted from these holding plates to plates containing various concentrations of RB, and incubated in the light for 2h

value: whole seedlings

value: RB 400 µM

tag: genotype

value: wild type

value: 2 week old

tag: ecotype


title: RB 400 µM, rep3

description:
6H
RB 3-3


title: scr_gRNA_1

description:
RNA-Seq
counts_all_genes.tsv


title: RB 400 µM, rep1

description:
6F
RB 3-1


title: RB 100 µM, rep1

description:
6C
RB 2-1

value: RB 100 µM


title: RB 100 µM, rep3

description:
6E
RB 2-3


title: RB 100 µM, rep2

description:
6D
RB 2-2


title: RB 10 µM, rep3

description:
6B
RB 1-3

value: RB 10 µM


title: RB 10 µM, rep1

description:
5H
RB 1-1


title: RB 0 µM, rep3

description:
5G
RB 0-3

value: RB 0 µM


title: RB 0 µM, rep1

description:
5E
RB 0-1


title: RB 10 µM, rep2

description:
6A
RB 1-2


title: CHX 100 µM, rep3

description:
CHX 3-3
11D

data_processing:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20  -m 30 )
The remaining reads (raw data submitted)  were mapped to the Arabidopsis thaliana genome (Araport11) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from Araport release), which was modified to contain a window surrounding the 3' UTR.
Genes were filtered out if thier sum counts   <=5 .  Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: Araport11
Supplementary_files_format_and_content: Deseq_raw_norm_no_UMI_filter_SO19J.xlsx  contains raw, normalized counts and log2 normalized counts (rld) computed by HTSeq and DESeq2 for 12,905  gene remained after filtering based on expression levels (sum normalized count in all samples greater than 5)

treatment_protocol: Plants were equilibrated for at least 1hour in ddw in petri dishes, then sorted into a set of 12-well plates with ddw in preparation for treatment. Samples were shifted from these holding plates to plates containing various concentrations of CHX, and incubated in the light for 2h

value: CHX 100 µM


title: CHX 100 µM, rep2

description:
CHX 3-2
11C


title: CHX 100 µM, rep1

description:
CHX 3-1
11B


title: RB 0 µM, rep2

description:
5F
RB 0-2


title: CHX 10 µM, rep2

description:
CHX 2-2
10H

value: CHX 10 µM


title: CHX 10 µM, rep1

description:
CHX 2-1
10G


title: CHX 10 µM, rep3

description:
CHX 2-3
11A


title: CHX 1 µM, rep2

description:
CHX 1-2
10E

value: CHX 1 µM


title: CHX 1 µM, rep1

description:
CHX 1-1
10D


title: CHX 1 µM, rep3

description:
CHX 1-3
10F


title: CHX 0 µM, rep3

description:
CHX 0-3
10C

value: CHX 0 µM


title: CHX 0 µM, rep2

description:
CHX 0-2
10B


title: ST: short-term treatment

source_name: Five-week-old sugar beet (Beta vulgaris L.) seedlings were treated with Hoagland solution, containing 75 mM mixed alkaline solution (Na2CO3:NaHCO3, 1:2) for 3 days

value: Sugar beet leaves

value: 3 days (short-term treatment, designated as ST)


title: CHX 0 µM, rep1

description:
CHX 0-1
10A


title: DCMU 4h, rep2

description:
5C
DCMU 3-2

data_processing:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20  -m 30 )
The remaining reads (raw data submitted)  were mapped to the Arabidopsis thaliana genome (Araport11) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from Araport release), which was modified to contain a window surrounding the 3' UTR.
Genes were filtered out if thier sum counts   <=5 .  Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: Araport11
Supplementary_files_format_and_content: Deseq_raw_norm_no_UMI_filter_Trans2X_DCMU.xlsx  contains raw and normalized counts  and  log2 normalized counts (rld) calculated  by HTSeq and DESeq2 for 13,836 gene remained after filtering based on expression levels (sum normalized count in all samples greater than 5).

treatment_protocol: Plants were equilibrated for at least 1hour in ddw in petri dishes, then sorted into a set of 12-well plates with ddw in preparation for treatment. Samples were shifted from these holding plates to plates containing 100 µM of DCMU and incubated in the dark for 1h, and then incubated in the light (30 µE) for 0, 1, 2, 4h

value: DCMU 4h


title: DCMU 4h, rep1

description:
5B
DCMU 3-1


title: DCMU 4h, rep3

description:
5D
DCMU 3-3


title: DCMU 2h, rep2

description:
4H
DCMU 2-2

value: DCMU 2h


title: DCMU 2h, rep3

description:
5A
DCMU 2-3


title: DCMU 2h, rep1

description:
4G
DCMU 2-1


title: DCMU 1h, rep3

description:
4F
DCMU 1-3

value: DCMU 1h


title: DCMU 1h, rep1

description:
4D
DCMU 1-1


title: DCMU 0h, rep3

description:
4C
DCMU 0-3

value: DCMU 0h


title: DCMU 0h, rep2

description:
4B
DCMU 0-2

value: whole seedlings


title: DCMU 1h, rep2

description:
4E
DCMU 1-2


title: DCMU 0h, rep1

description:
4A
DCMU 0-1


title: flu 4h, rep1

description:
12C
flu 2-1

data_processing:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20  -m 30 )
The remaining reads (raw data submitted)  were mapped to the Arabidopsis thaliana genome (Araport11) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from Araport release), which was modified to contain a window surrounding the 3' UTR.
Genes were filtered out if thier sum counts   <=5 .  Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: Araport11
Supplementary_files_format_and_content: Deseq_raw_norm_no_UMI_filter_Flu1b.xlsx  contains raw, normalized counts and log2 normalized counts (rld) computed by HTSeq and DESeq2 for 11,167 gene remained after filtering based on expression levels (sum normalized count in all samples greater than 5 .

growth_protocol: Plants were grown on standing square Petri dishes on 1/2MS + 1% sucrose, pH5.8. Growth chamber with a 24h continuous light cycle, and temperature of 22oC

treatment_protocol: Plants were equilibrated for at least 1hour in ddw in petri dishes, then sorted into a set of 12-well plates with ddw in preparation for treatment. Samples were shifted from these holding plates to plates containing ddw and incubated in the dark for 0, 4h, and then exposed to light (30 µE) for 30min

value: 4h exposure to light

value: flu 1-1 mutant


title: flu 4h, rep3

description:
12E
flu 2-3

value: 2 week old


title: flu 4h, rep2

description:
12D
flu 2-2


title: Unedited rep2

data_processing:
High-throughput sequencing was performed on the HiSeq 2500 system (Illumina).
Trimmed reads were obtained by removing adapter sequences, and reads with low complexity or of low quality were removed.
quality filtered reads were mapped to the human reference genome using Salmon v.0.8.2.
Genome_build: hg38
Supplementary_files_format_and_content: comma-delimited csv files include Raw reads counts for each Sample ...

source_name: Muscle-derived stem cells

extract_protocol:
The cells were trypsinized and collected, and total mRNA was extracted using TRIzol reagent
The TruSeq RNA Sample Preparation kit (Illumina) was used to construct RNA-seq libraries

value: Muscle


title: flu 0h, rep2

description:
11F
flu 0-2

value: 0h exposure to light


title: flu 0h, rep3

description:
11G
flu 0-3


title: Unedited rep1


title: flu 0h, rep1

description:
11E
flu 0-1


title: Cas9 rep1


title: PBS rep2


title: PBS rep1


title: Cas9 rep2


title: INDEL50 rep2


title: ∆46–54/Cas9 rep2


title: ∆46–54/Cas12a rep2


title: ∆46–54/Cas12a rep1


title: Female WT

type: RNA

city: Southampton

first: Aikta

last: Sharma

state: Hampshire

address: Life Sciences Building 85, University Road

department: Biological Sciences

institute: University of Southampton

description: Control

data_processing:
All data analysis, including data normalisation were performed according to the manufacturers instructions using their web-based data analysis software: https://geneglobe.qiagen.com/gb/analyze/
Target gene expression levels were normalised to the housekeeping genes using the 2^-delta Ct method where the Ct of the target - Ct of the housekeeper.
Calculation of the deltadeltaCt based fold change in expression between groups was performed using the web-based analysis software using the raw threshold cycle values.

label: SYBR Green

source_name: Female osteoblast

label_protocol: 500 ng total RNA was reverse transcribed using the GoScript Reverse Transcriptase kit (Promega, USA). RT-qPCR arrays were performed using the Extracellular Matrix and Adhesion Molecule RT2 Profiler PCR Array (PAMM-013Z, 332031 Qiagen, Germany) following the manufacturer's instructions.

growth_protocol: Osteoblasts were isolated from male and female Vegffl/fl mice using the 4-step sequential digest (collagenase-collagenase-EDTA-collagenase) method and cultured separately in basal Minimum Essential Medium α, supplemented with 10% FBS, 0.1% gentamicin, 100 U/ml penicillin and 100 μg/ml streptomycin. All cells were maintained at 37 °C and 5% CO2 until 80% confluent and used at passage 1.

extract_protocol: Total RNA was extracted from Vegf expressing and deficient male and female osteoblasts using the Monarch® Total RNA Miniprep Kit (New England Biolabs, USA).

treatment_protocol: Male and female osteoblasts were cultured separately prior to transduction with either an adenovirus expressing Cre-recombinase or an adenovirus expressing GFP for six days in 10% FBS basal medium. After this culture period, osteoblasts were stepped down in 1% FBS containing basal medium for 24 hours, after which the conditioned medium was collected for knockdown validation.

tag: transduction

value: Adenovirus-GFP

tag: vegf expression

value: Expressing


title: Nucleoplasmic RNAs

city: Seoul

first: Boyoun

last: Park

address: 50 Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

description:
Immunoprecipitated RNA
Exclude cytosolic fractions

data_processing:
Paired end sequencing reads (101bp) generated from a HiSeq2000 instrument were verified its sequence quality with FastQC (version 0.10.0).
Trimmomatic (version 0.32) was used to remove adapter sequences and bases with base quality lower than 3 from the ends reads.
Afterwards, reads with minimum length of 36bp were removed to produce clear data.
A pseudo value of 0.1 FPKM was added to all genes of RNA-IP-seq to avoid division by zero.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: text files include RPKM values for each Sample

source_name: RAW 264.7 macrophages

growth_protocol: mRrp6-depleted macrophages were grown in Dulbecco's Modified Eagle Medium containing 10% fetal bovine serum and penicillin/streptomycin in a  humidifed incubator with 5% CO2 at 37°C.

extract_protocol:
After mRrp6-depleted macrophages were exposed to 80 ng/ml LPS for 12 h, nuclei were fractionated with a hypotonic buffer (10 mM HEPES, 1.5 mM MgCl2, 10 mM KCl, 0.5 mM dithiothreitol [DTT], 0.05% nonyl phenoxypolyethoxyethanol [NP]-40, pH 7.9) containing the protease inhibitor cocktail (Roche) and 40 units of recombinant RNase inhibitor (#2313A, TaKaRa, Otsu, Japan). Isolated nuclei were resuspended in 500 µl RIP buffer (50 mM Tris-HCl, 0.05% NP-40, 100 mM NaCl, pH 7.4) that was supplemented with 40 units of recombinant RNase inhibitor and the protease inhibitor cocktail. The samples were incubated on ice for 30 min, and the tubes were vortexed vigorously every 10 min. Nuclear extracts were transferred to new tubes, followed by centrifugation at 13,000 rpm for 10 min at 4°C. The extracts were then incubated with the anti-nucleolin antibody for 5 h at 4°C. The primary antibody was pulled down by protein G-Sepharose beads (Sigma) for 1 h, and the beads were washed 3 times with RIP buffer. RNA was eluted from the beads by the RNA purification kit (GeneAll), according to the manufacturer’s instructions.
Nuclear RNA immunoprecipitated with anti-rabbit IgG or anti-nucleolin antibodies was incubated with DNaseI, reverse transcribed, and synthesized to double stranded cDNA using Second strand cDNA synthesis kit (Applied Biological Material Inc.) according to the manufacturers’ instructions. cDNAs were fragmented by sonication until the size of DNA below the 500bp.

treatment_protocol: Cells were stimulated with LPS (80ng/ml) for 12h.

tag: cell line

value: RAW 264.7 macrophages

tag: stimulation

value: LPS 12h


title: IgG control


title: Female OBVEGFKO

description: Test

value: Adenovirus-Cre-GFP

value: Deficient


title: ∆45–55/Cas9 rep1

tag: tissue

tag: passages


title: ∆46–54/Cas9 rep1


title: ∆45–55/Cas9 rep2


title: Normal rep4


title: Normal rep3


title: Male WT

description: Control

source_name: Male osteoblast


title: Normal rep2


title: Nucleolar RNA-seq

description: Nucleolar RNAs

data_processing:
Sequencing was performed by Illumina HiSeq2000 using 50-bp paired-end readings.
Before aligning to the reference genes, raw data were analyzed by the FastQC tool for quality control.
Trimmomatic (version 0.32) was used to remove adapter sequences and bases with base quality lower than 3 from the ends reads.
Afterwards, reads with minimum length of 36bp were removed to produce clear data.
a pseudo value of FPKM was added to all genes of RNA-seq to avoid division by zero.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: text files include RPKM values for each Sample

growth_protocol: Murine RAW 264.7 macrophages were grown in Dulbecco's Modified Eagle Medium containing 10% fetal bovine serum and penicillin/streptomycin in a  humidifed incubator with 5% CO2 at 37°C.

extract_protocol:
Nucleoli were isolated from LPS stimulated macrophages (1~2 × 107) as previously described (http://www.lamondlab.com/f5nucleolarprotocol.htm). The cells were then suspended with 3 ml cold hypotonic buffer for 10 min on ice. Cells were vortexed vigorously for 10 sec and centrifuged at 218 g for 5 min at 4°C. The nuclear pellet suspended in 3 ml S1 solution (0.25 M sucrose, 10 mM MgCl2, protease inhibitor cocktail) and layered over 3 ml S2 solution (0.35 M sucrose, 0.5 mM MgCl2, protease inhibitor cocktail). Nuclei were pelleted by centrifugation at 1430 g for 5 min at 4°C, and the supernatant was carefully transferred. Pure nuclei were suspended in 3 ml S2 solution and sonicated on ice for 5-sec pulses with 4-sec intervals between each pulse using a VCX 500 sonicator with a 3-mm tapered microtip (Sonics and Materials, Newtown, CT) at 35% amplitude. After sonication, extracted nucleoli were observed by phase contrast microscopy. The sonicated samples were layered over 3 ml S3 solution (0.88 M sucrose, 0.5 mM MgCl2, protease inhibitor cocktail) and centrifuged at 3000 g for 10 min at 4°C. Purified nucleoli were washed in 500 μl S2 solution, followed by centrifugation at 1430 g for 5 min at 4°C. After nucleoli were suspended in RNase-free distilled water on ice, nucleoli were completely dissolved in five volumes of TRIzol reagent (Life technologies). Nucleolar RNA was extracted from nucleoli, according to the manufacturer’s protocol.
Whole-transcriptome sequencing of nucleolar RNA was carried out by Illumina HiSeq 2000. According to the manufacturer’s instructions, rRNA in nucleolar RNA was twice depleted by the Ribo-Zero kit. The RNA was then fragmented and primed for cDNA synthesis. RNA fragments were copied into first-strand cDNA using reverse transcriptase and random hexamers. Second-strand cDNA was synthesized using DNA polymerase I, RNase H, and dUTP. After the ends of cDNA fragments were polished, a single adenine base was added at the 3’ end, and Illumina-supplied adaptors were ligated. The products were then purified and enriched with the PCR reaction to create the final cDNA library.


title: Male OBVEGFKO

description: Test


title: Normal rep1

growth_protocol: Human muscle-derived stem cells were isolated using a modified version of the pre-plate technique as previously described(29). Briefly, 2 h after seeding the cells in the flask (pre-plate [PP]1), non-adherent cells and medium were transferred to a fresh flask, re-collected, and transferred to another flask 24 h later (PP2). Serial pre-plating was thus performed to separate cells until PP6; these cells were deemed as MDSCs


title: INDEL50 rep1


title: Nucleolar RNA-seq LPS 12h

description: Nucleolar RNAs


title: S-Soil rep2

description: Soil

data_processing:
Microbiome data was analyzed using the software MOTHUR (version 1.42.3) (Schloss et al., 2009) by using 16S rRNA sequence editing and analysis following methods described by Röthig, Roik (Röthig et al., 2017).
Reads were demultiplexed, quality trimmed, afterwards pre-clustered depend on 2 bp differences (Huse et al., 2010), Singletons were removed and the residual sequences were aligned against the SILVA database release 119 (Schloss et al., 2009).
Chimeric sequences were removed using UCHIME as preformed in Mothur (Edgar et al., 2011), as well as undesirables sequences such as chloroplasts, mitochondria, archaea and eukaryotes. Sequences were classified against Greengenes database using bootstrapping of 60 (release gg_13_8_99; bootstrap = 60) (McDonald et al., 2012).
Then, phylogenetically classified sequences were used to generate bacterial taxonomic composition of samples and plotted into Phylum and family level using the means of relative abundances from three replicated samples of Soil, Control Root and Root treated with SA187.
For further analyses, sequences were subsampled to 20816 sequences per sample and were then clustered into Operational Taxonomic Units (OTUs) using a 97% similarity cutoff.
Genome_build: SILVA 119 release
Supplementary_files_format_and_content: excel, OTUs

organism: unidentified soil bacteria

source_name: Soil

growth_protocol: The experiment was conducted using a randomized complete block design; each plot is 5 m2 with three replications. Ten-row plots were prepared with intra- and inter row distances of 20 cm and 50 cm, respectively. All the plots were irrigated with water EC= 0.3 dS m-1, the average value for the soil pH was 7.45 and the salinity of soil was EC=1.9 dS m-1

extract_protocol:
Total DNA extraction of endophytic bacterial community was performed as described by (Eida et al., 2018),
accourding to Eid al etal 2018

value: soil

tag: agent


title: smSP_KO1

city: La Jolla

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

data_processing:
Trim adapter sequences, removed unpaired reads; Trimmomatic v0.36; options: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Align reads to genome; STAR v2.5.4b; options: --runThreadN 6 --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outBAMcompression 6 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.06 --outFilterMatchNminOverLread 0.55 --outFilterMatchNmin 30 --alignIntronMax 1 --alignEndsType Local
Sort by name; samtools v1.10; options: sort -@ 4 -n
Fix mate information; samtools v1.10; options: fixmate -rm
Sort by coordinate; samtools v1.10; options: sort -@ 4
Remove duplicate reads; samtools v1.10; options: markdup -l 1500 -r -d 100
Sort by name; samtools v1.10; options: sort -@ 4 -n
Call peaks by celltype and genotype; Genrich v0.5dev; options: -j -d 25 -g 5 -e chrM -v -q 0.01 -a 280
Merge peak atlases; R v3.6.3; custom script
Count reads against atlas; R (GenomicAlignments v1.20.1) v3.6.3; custom script
Normalize read counts, analyze differential accessibility; R (DESeq2 v1.24.0) v3.6.3; custom script
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of sample by peak (including coordinates of each peak) matrix of normalized counts as determined by Genrich, custom R scripts, GenomicAlignments, and DESeq2

source_name: Thymic semimature CD4SP

extract_protocol:
Combined protocol for extraction and library preparation, see below
cells were pelleted in a fixed rotor benchtop centrifuge at 500g for 5 minutes at 4°C. Cells were then washed in 1ml cold 1x PBS and pelleted again. Supernatant was aspirated and cells were resuspended in 50µl ice-cold cell lysis buffer (10mM Tris-Cl pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% NP-40) to disrupt plasma membranes. Nuclei were pelleted at 1000g for 10 minutes. Supernatant was aspirated and nuclei were resuspended in 50µl transposition reaction mixture (25µl TD buffer; 2.5µl TDE1; 22.5µl ddH2O; llumina, 20034197). Samples were incubated in a ThermoMixer at 1100rpm for 45 minutes at 42°C. DNA was then purified using a MinElute PCR Purification Kit (QIAGEN, 28004), per manufacturer instructions. DNA was eluted in 10µl buffer EB. Libraries were then barcoded and amplified with NEBNext High-Fidelity Master Mix and primers from (Buenrostro et al., 2013) (50µl reaction with 10µl DNA and 2.5µl of 25µM primers - 1 cycle of 5min at 72°C, 30sec at 98°C; 5 cycles of 10sec at 98°C, 20sec at 63°C, 1min at 72°C). A qPCR on the product determined that an additional 7 cycles (10sec at 98°C, 20sec at 63°C, 1min at 72°C) were required. Library was purified and size selected with AMPure beads (Beckman Coulter, A63881): 45µl of PCR product was incubated with 18µl beads and supernatant was collected (beads bound larger >2000bp fragments). Supernatant (63µl) was then incubated with an additional 63µl of beads for 5 minutes, supernatant was removed, beads were washed 2x with 75% ethanol, and DNA was eluted into 50µl H2O by incubating for 2 minutes.

tag: strain background

tag: mouse id

value: Thymus

tag: cell type

value: semimature CD4 single positive


title: smSP_KO2


title: smSP_FL2


title: E50-gRNA_P

first: Shixue

last: Gou

data_processing:
Library strategy: GUIDE-seq
MDSCs were transfected with Cas9, Cas12a and sgRNA plasmids, as well as phosphorothioate-modified double-stranded oligodeoxynucleotide (dsODN).
Restriction fragment length polymorphism (RFLP) analyses were performed to determine frequency of dsODN-tag integration frequencies.
T7E1 assays were performed to quantify on-target Cas9 mutagenesis frequencies.
dsODN tag-specific amplification and library preparation was performed prior to high-throughput sequencing using an Illumina MiSeq Sequencer
When mapping potential off-target sites, the cut-off for alignment to the on-target spacer sequence was set at 8 mismatches for 21 nucleotide spacers, 9 mismatches for 22 nucleotide spacers,and 10 mismatches for 23 nucleotide spacers.
Genome_build: hg38

extract_protocol:
The cells were trypsinized and collected, and genomic DNA was extracted using the Cell Genome Extraction kit (Tiangen Biotech, Beijing, China)
The GeneRulor NGS Library Prep Kit was used to construct RGUIDE-seq libraries

value: edited by E50-gRNA


title: S-Soil rep3

first: Prof. Heribert

last: HIRT

description: Soil


title: mSP_KO2

source_name: Thymic mature CD4SP

value: mature CD4 single positive


title: E50-gRNA_N


title: smSP_FL1


title: mSP_KO1


title: mSP_FL2


title: IN54-Cas12a-gRNA_P

value: edited by IN54-Cas12a-gRNA


title: S-Soil rep1

description: Soil


title: sgKAT8

first: Aliaksandra

last: Radzisheuskaya

address: 237 Fulham road

department: Cancer Biology

institute: The Institute of Cancer Research

data_processing:
Quality assessment and pre-processing of the raw data was performed using the R/Bioconductor library ShortRead v.1.38.0 and the standard R infrastructure.
Mapping using subjunc from the R/Bioconductor library Rsubread v.1.22.3 using default settings of the function subjunc and collected only uniquely mapped reads with the maximum of 3 mismatched bases in the alignment.
Differential gene expression was performed using DESeq2 and edgeR/limma
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Excel table with average CPM expression for each gene and the results of the differential gene expression analysis

molecule: polyA RNA

source_name: Acute myeloid leukemia cell line

extract_protocol:
The total RNA was extracted using Qiagen Rneasy kit
Illumina Truseq v2 kit

treatment_protocol: The cells were transduced with the lentiviruses driving the corresponding sgRNA expression and collected for sequencing 3 days post-transduction

value: monocyte

value: peripheral blood

tag: culture type

value: suspension


title: SSB_BPH_3

city: Xinyang

first: Qingsong

last: Liu

state: Henan

address: No. 237, Nanhu road

institute: Xinyang Normal University

data_processing:
For transcriptome data, raw Illumina data of fastq format were first processed using in-house perl scripts. After removing reads containing adaptors, reads containing poly-N and low-quality reads from raw data, we obtained the clean data. The Q20, Q30, GC (guanine-cytosine)-content and sequence duplication level of the clean data were calculated. The clean reads were aligned to the reference genome IRGSP-1.0 (https://rapdb.dna.affrc.go.jp)using HISAT2 tools (version 2.09)
Feature Counts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. Gene expression levels were estimated using fragments per kilobase of transcript per million mapped reads (FPKM) based on the length of the gene and reads count mapped to this gene. Differentially expressed genes analysis was performed using the DESeq2 R package.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each sample.

organism: Oryza sativa

source_name: Rice plant stems

growth_protocol: Rice plants (Oryza sativa, cultivar Minghui63) were grown in a greenhouse at 27 ± 3 °C with 75 ± 10% RH (relative humidity) and a photoperiod of 16:8 hr L:D (light:dark).

extract_protocol:
Total RNA from rice leaves samples was isolated using TRIzol Reagent (Life Technologies, Grand Island, NY, USA) following to the manufacturer’s instructions.
Libraries were prepared using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA USA) according to the manufacturer’s instructions.

treatment_protocol: i) Control plants (Control), meaning that potted rice plants remained intact without insect infestation; (ii) SSB-infested plants (SSB), each potted rice plant was artificially infested with one 3rd instar SSB larva that had been starved for  3 hr for 48 hr; iii) BPH-infested plants (BPH), each potted rice plant was artificially infested with a mix of fifteen 3rd and 4th instars BPH nymphs for 48 hr; iv) SSB_BPH-infested plants (SSB_BPH), each potted rice plant was simultaneously infested with one SSB larva and 15 BPH nymphs for 48 hr. After 48h, the stems of the plants were harvested and frozen in liquid nitrogen. Samples from 5 individual plants of the same treatment were pooled together as one biological replicate, and three replicates were collected for each treatment.

value: Rice plant stems

tag: age

value: 44–49 days after sowing

tag: stress


title: IN54-Cas12a-gRNA_N

city: Guangzhou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

value: Muscle

tag: treatment


title: sgKANSL3


title: SSB_BPH_2


title: IN45-Cas12a-gRNA_P

value: edited by IN45-Cas12a-gRNA


title: sgKANSL2


title: mSP_FL1


title: IN45-Cas12a-gRNA_N


title: sgNegCtrl


title: preTreg_FL2

source_name: Thymic Treg cell precursors

value: Treg cell precursor


title: preTreg_KO2


title: IN54-Cas9-gRNA_N

value: edited by IN54-Cas9-gRNA


title: SSB_BPH_1


title: preTreg_FL1


title: preTreg_KO1


title: IN45-Cas9-gRNA_P

value: edited by IN45-Cas9-gRNA


title: IN54-Cas9-gRNA_P


title: SSB_3

value: SSB


title: SSB_1


title: SSB_2


title: Treg_KO2

source_name: Thymic regulatory T cells

value: regulatory T cell


title: ATAC_sgNegCtrl

data_processing:
The reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.4.5), with a quality setting of 15, and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in Picard Tools (v2.16.0).
The BEDTools suite (http://bedtools.readthedocs.io) was used to create normalized read density profiles with no read extension
A global peak atlas was created by first removing blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz) then merging all peaks within 500 bp and counting reads with version 1.6.1 of featureCounts (http://subread.sourceforge.net). Comparison of intra vs inter-group clustering in principle component analysis was used to determine normalization strategy, using either the median ratio method of DESeq2 or a sequencing depth-based factor normalized to ten million uniquely mapped fragments. Differential enrichment was scored using DESeq2 for all pairwise group contrasts. Peak-gene associations were created using linear genomic distance to transcription start site.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Excel table with the results of the differential ATAC-seq peak analysis

extract_protocol:
50, 000 cells per condition were washed in PBS, resuspended in 50 ul of the ice-cold ATAC-RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) with the addition of 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin and incubated on ice for 3 min. Then, 1 ml of ice-cold ATAC-RSB buffer with the addition of 0.1% Tween-20 was added to each sample and gently mixed by inverting the tubes. The nuclei were then pelleted at 500g for 10 min at 4C, resuspended in 50 ul of the transposition mix (25ul 2x TD buffer from Illumina, 2.5 ul Tn5 from Illumina, 16.5 ul PBS, 0.5 ul 1% Digitonin, 0.5 ul 10% Tween-20, 5 ul water) and incubated for 30 min at 37C with shaking. DNA fragments were isolated using QIAQuick PCR purification kit (QIAGEN)
Amplification using NEBNext® High-Fidelity 2X PCR Master Mix

treatment_protocol: The cells were transduced with the lentiviruses driving the corresponding sgRNA expression and after selection in culture were collected for the experiment

value: control


title: IN45-Cas9-gRNA_N


title: ATAC_sgMSL1_KO

value: knockout of MSL1


title: Treg_KO1

value: Thymus


title: BPH_3

value: BPH


title: No_Stretch_No_RASAG_Day_3

city: Heverlee

first: Adrian

last: Ranga

state: Flanders

address: Celestijnenlaan 200F - Room 03.349

department: Mechanical Engineering

country: Belgium

institute: KU Leuven

data_processing:
Raw sequencing data was demultiplexed using the mkfastq pipeline of CellRanger 3.0.2.
Alignment, barcode assignment and UMI quantification was performed using the count pipeline of CellRanger 3.0.2 and mapped to the hg38 genome
Genome_build: hg38
Supplementary_files_format_and_content: processed raw count text file was generated from the Seurat object on R, and contains the raw count of each gene for every cell that remained after the QC step
Supplementary_files_format_and_content: metadata text file was generated from the Seurat object on R, and contains the metadata of each cell that remained after the QC step

source_name: Human iPSC derived neural tube organoids

growth_protocol: single iPSCs were embedded in PEG hydrogels with a stiffness of 2 kPa and grown on top of elastomeric membranes connected to mechanical stretching devices. The cells were kept in neurobasal medium for 11 days with media changes every 2 days after the first 3 days.

extract_protocol:
PEG gels were detached from elastomeric membranes and dissociated using TrypLE for 6 to 7 minutes at 37 degrees Celsius and with mechanical agitation. This process also dissociated the embedded organoids into single cells. The TrypLE was neutralized using DMEM with 20% FBS. The single cells were spun down and washed twice with PBS before filtering and loading into the 10X Genomics Chromium Single Cell 3' Kit.
Library preparations for the scRNA-seq was performed using 10X Genomics Chromium Single Cell 3’ Kit, v3 (10X Genomics, Pleasanton, CA, USA). The cell count and the viability of the samples were accessed using LUNA dual fluorescence cell counter (Logos Biosystems) and a targeted cell recovery of 6000 cells was aimed for all the samples. Post cell count and QC, the samples were immediately loaded onto the Chromium Controller. Single cell RNAseq libraries were prepared using manufacturers recommendations (Single cell 3’ reagent kits v3 user guide; CG00052 Rev B), and at the different check points, the library quality was accessed using Qubit  (ThermoFisher) and Bioanalyzer (Agilent). With a sequencing coverage targeted for 50,000 reads per cell, single cell libraries were sequenced either on Illumina’s NovaSeq 6000 or NovaSeq 500 platforms using paired-end sequencing workflow and with recommended 10X; v3 read parameters (28-8-0-91 cycles).

treatment_protocol: Rock inhibitor (Y-27632) was supplemented to the media for the first 3 days to help increase survival. From day 3 to 5 a treatment of retinoic acid (RA) and smoothened agonist (SAG) are supplemented to the media. During this treatment period, stretched samples (samples 1 and 3) underwent an equibiaxial stretch that increased the surface area of the membrane by 100%.

tag: tissue/cell type

tag: experimental time

value: Day 3

value: Untreated

tag: stretch state

value: unstretched


title: No_Stretch_RASAG_Day_5

value: Human iPSC derived neural tube organoids

value: Day 5

value: Treated with RA and SAG


title: BPH_2

value: Rice plant stems

value: 44–49 days after sowing


title: IN55-gRNA_P

value: Muscle

value: edited by IN55-gRNA


title: Treg_FL2

tag: genotype


title: Stretch_RASAG_Day_5

value: stretched


title: BPH_1


title: IN55-gRNA_N


title: Treg_FL1


title: METTL18_KO_haploid_rep3

city: Bern

first: Yeji

last: Kim

address: Freiestrasse 3

department: Department of Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

data_processing:
Adaptors were clipped and trimmed using FASTx toolkit
Reads were aligned to human rRNA to remove rRNA-derived reads and mapped to the human genome hg38 using bowtie
Reads for each individual transcript were counted using a custom script
Genome_build: hg38
Supplementary_files_format_and_content: CSV file containing raw counts per transcript for the three biological replicates

source_name: haploid cells

extract_protocol:
Cells were washed with ice-cold PBS and flash frozen in liquid nitrogen. Subsequently, the dish was transferred to ice, 400 µl lysis buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM MgCl2, 1 % Triton X-100, 0.5 mM DTT, 0.5 % deoxycholate (w/v) and 100 µg/ml CHX) was dripped onto the cells and cells were scraped after lysis buffer had thawed. Next, samples were centrifuged for 5 min at 4 °C and 10,000 g.
Ribosome protected fragments were generated by digesting 10 A260 units of the cleared lysate with 900 U RNase I (ThermoFisher) at 22 °C. The reaction was stopped after 1 h by addition of 15 µl SuperaseIn (ThermoFisher) and loaded on a 10-50% (w/v) sucrose gradient in 50 mM Tris pH 7.5, 50 mM NH4Cl, 12 mM MgCl2, 0.5 mM DTT, 100 µg/ml CHX and centrifuged for 3 h at 35,000 rpm and 4 °C in a TH-641 rotor (Thermo Scientific). Monosomes were fractionated and total RNA isolated. Subsequently,RNA was separated on 15% polyacrylamide gels (8 M urea, 1 x TBE) and 28-32nt ribosome footprints were extracted from the gel. Finally, libraries were generated as described by Ingolia and coworkers (Ingolia et al. 2012) but using adenylated 3’-adapters that contained 4 randomized nucleotides to reduce ligation biases (Lecanda et al. 2016).

value: HAP1 cells

value: METTL18 knockout


title: Del_45-55_Cas9-3

data_processing:
Library strategy: Nanopore sequncing
Then High-throughput sequencing was performed on the MinION
Porechop (version 0.2.4) was used to remove adapter sequences from Nanopore reads.
Minimap2 (version 2.17-r941) was used to map long reads to human genome.
Samtools (version 1.9) was used to process bam files.
bamCoverage (version 3.3.0) was used to convert bam files to bigwig files.
Genome_build: hg38

extract_protocol:
The cells were trypsinized and collected, and genomic DNA was extracted using the Cell Genome Extraction kit (Tiangen Biotech, Beijing, China)
The libraries for each sample were constructed by Oxford Nanopore Technology EXP-NBD103 for barcoding and Ligation Sequencing Kit 1D (SQK-LSK108) for sequencing.


title: Control_3

value: Control


title: IN44-gRNA_P

value: edited by IN44-gRNA


title: METTL18_KO_haploid_rep2


title: METTL18_KO_haploid_rep1


title: Wildtype_haploid_rep2

value: Wild type


title: Wildtype_haploid_rep1


title: Control_2


title: IN44-gRNA_N


title: Control_1


title: E50-gRNA-unedited-1

description: Quantification_of_editing_reads_counts_and_frequency.xls

data_processing:
Library strategy: Amplicon-seq
High-throughput sequencing was performed on NOVA SEQ system (Illumina).
Trimmed reads were obtained by removing adapter sequences, and reads with low complexity or of low quality were removed.
The types and proportions of SNVS are analyzed using customized shell scripts
Genome_build: hg38

extract_protocol:
The cells were trypsinized and collected, and genomic DNA was extracted using the TIANamp Genomic DNA Kit (TIANGEN)
Amplification primers containing Illumina forward and reverse adapters were used for a first round of PCR (PCR 1) amplifying the genomic region of interest. Unique Illumina barcoding primer pairs were  added to each sample in a secondary PCR reaction (PCR 2).

value: E50-gRNA untreated


title: E50-gRNA-target-1

value: E50-gRNA gRNA+Cas9


title: E50-gRNA-unedited-2


title: H929-shRNA2 ZBP1_rep2

data_processing:
reads were aligned using STAR (v2.5.3a) on GRCh38 (hg38) genome assembly
Differential expression analysis was performed using DESeq2 (v1.24.0)
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
Supplementary_files_format_and_content: tab-delimited text files include differentially expressed genes

source_name: Myeloma cell line

extract_protocol:
Total RNA was isolated using Nucleospin RNA kit (Macherey-Nagel) and poly A-tail mRNA was enriched using NEBNext poly(A) mRNA Magnetic Isolation Module
Libraries were prepared using NEBNext Ultra II RNA library prep kits (New Engand Biolabs) according to manufacturer's protocol

tag: shRNA

value: anti-ZBP1 shRNA 2


title: E50-gRNA-mock-3

value: E50-gRNA mock (pbs)


title: E50-gRNA-target-3


title: E50-gRNA-target-2


title: E50-gRNA-unedited-3


title: 1518442 stroma sample 9

city: Rehovot

first: Ruth

last: Scherz-Shouval

address: 234 Herzl street

institute: Weizmann Institute of Science

description: RAW counts.csv

data_processing:
Illumina NextSeq 500
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) and mapped to genome /shareDB/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_index using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (default parameters).
The pipeline quantifies the genes annotated in RefSeq: /home/labs/bioservices/services/ngs/support/gtf/hg38.genes.gtf.
Counting was done using STAR.
Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2
Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Genome_build: Pipeline was constructed using Snakemake (DOI: 10.1093/bioinformatics/bts480).
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Patient data

extract_protocol:
FFPE slides were deparaffinized and stained using Arcturus Paradise Plus Staining kit (#KIT0312J, Thermo-Fischer) according to the instructions of the manufacturer. Slides were then left to dry for 5 min at RT followed by microdissection using the Arcturus (XT) laser microdissection instrument (#010013097, Thermo-Fischer). Infrared capture was used to minimize RNA damage. CapSure Macro LCM caps (#LCM0211, Thermo-Fischer) were used to capture microdissected tissue. RNA isolation was carried out using the RNeasy FFPE kit (#73504, Qiagen) following the instructions of the manufacturer with one modification- proteinase K digestion at 56°C was carried out for 1 h.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq v2-Pico Input Mammalian kit (#634415, Takara Bio USA) according to the instructions of the manufacturer.

tag: patient outcome

value: good

tag: tumor stage

value: stage 2

value: Stomach

tag: lauren classification

value: intestinal


title: H929-scramble control for shRNA2_rep2

value: scramble control

tag: cell line


title: H929-scramble control for shRNA1_rep2


title: H929-shRNA2 ZBP1_rep1


title: E50-gRNA-mock-2

tag: tissue

value: Muscle

tag: passages


title: E50-gRNA-cas9-2

value: E50-gRNA cas9 only


title: E50-gRNA-mock-1


title: H929-shRNA1 ZBP1_rep1

value: anti-ZBP1 shRNA 1


title: E50-gRNA-cas9-1


title: IN54-Cas9-gRNA-unedited-3

value: IN54-Cas9-gRNA untreated


title: H929-scramble control for shRNA2_rep1


title: H929-scramble control for shRNA1_rep1


title: standard RIBO-Seq from mESCs, replicate 3

city: Povo (TN)

first: Fabio

last: Lauria

address: Via alla Cascata 56

country: Italy

institute: Institute of Biophysics (Italian National Research Council)

description: standard RIBO-Seq from mouse embryonic stem cells, biological replicate 3

data_processing:
Library strategy: RIBO-seq
Reads were processed by removing 5ʼ adapters, discarding reads shorter than 20 nucleotides and trimming the first nucleotide of the remaining ones (using Trimmomatic v0.36). Reads mapping on the collection of M. musculus rRNAs (from the SILVA rRNA database, release 119) and tRNAs (from the Genomic tRNA database: gtrnadb.ucsc.edu/) were removed. Remaining reads were mapped on the mouse transcriptome (using the Gencode M17 transcript annotations). Antisense and duplicate reads were removed. All alignments were performed with STAR (v020201) employing default settings.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with read counts before and after deduplication for each transript and sample

source_name: mouse embryonic stem cells, standard RIBO-Seq, biological replicate 3

growth_protocol: mESCs were maintained in mESC self-renewal medium composed of Glasgow’s MEM (Thermo Scientific #11710-035) supplemented with 1000 units/ml ESGRO Recombinant Mouse LIF protein (Millipore #ESG1107), 10% fetal bovine serum, 55 μM 2-Mercaptoethanol, 1mM Sodium Pyruvate (Thermo Scientific #11360070), MEM Non-Essential Amino Acids (Thermo Scientific #11140050), GlutaMax (Thermo Scientific #35050061), and penicillin/streptomycin. For passaging, mESCs were washed twice with 1x PBS, detached using 0.02-0.05% trypsin-EDTA and spun down at 260 x g for 3 minutes. Pellet was resuspended in fresh medium and plated onto 0.1% gelatin-coated culture vessels.

extract_protocol:
Standard RIBO-seq. 80S ribosomes were isolated by centrifuging lysates through a 30% sucrose standard at 95000 rpm, for 2 h at 4°C. The standard was resuspended in W-buffer and treated with SDS 10% (final 1%) and 5 µL of proteinase K (20mg/mL), and incubated at 37 °C in a water bath for 75 min before acid phenol:chlorophorm:isoamyl alcohol (pH 4.5) RNA extraction.  AHARIBO RIBO-seq. The lysates was incubated with Dibenzocyclooctyne-PEG4-biotin conjugate (Sigma-Aldrich #760749; 50 µM final concentration) in a reaction volume of 100 µl for 1 h on a rotator in slow motion (9 rpm) at 4°C. Lysates were then incubated with 50 µl of eMagSi-cN beads (IMMAGINA BioTechnology #018-eMS-001) for 30 min at 4°C on the rotator in slow motion (9 rpm). Subsequently, samples were taken off the rotator and placed on a magnetic rack on ice, and supernatants were discarded. Beads were washed two times with 500 µl of 1x PBS supplemented with 0.1 % Triton-X100, 1x sBlock and 1:10,000 RiboLock RNase Inhibitor (Thermo Scientific #EO0381) on the rotator in slow motion at 4 °C, removing supernatants from the tubes sitting on the magnetic rack and gently adding new washing solution each time. After the final wash, beads were resuspended in 200 µl of W-buffer and transferred to a new vial. Then, 20 µl of 10% SDS and 5 ul of Proteinase K (Qiagen #19131) were added to each sample, and samples were incubated at 37 °C for 75 min in a water bath. Subsequently, suspensions were transferred to a new vial and acid phenol:chloroform:isoamyl alcohol (pH 4.5) RNA extraction was performed.
Extracted RNA was then resolved by electrophoresis through denaturing TBE-urea gels, and fragments between 25 nt and 35 nt were excised. Libraries were prepared using the RiboLace kit_module 2 (IMMAGINA BioTechnolgy #RL001_mod2) and sequenced on an Illumina HiSeq 2500 sequencer with a single-end 50 base pair run.

treatment_protocol: mESCs at 80 % confluence were pre-treated with the elongation inhibitor cycloheximide before rapid harvest on ice and cell lysis (lysis buffer, IMMAGINA BioTechnology #RL001-1). Clarified cell lysates (1.7 total a.u., measured by Nanodrop) were treated with 1.3 U of RNase I (Thermo, #AM2295) in W-buffer (IMMAGINA BioTechnology #RL001-4) containing 1x sBlock to digest RNA not protected by ribosomes. Digestion was performed for 45 min at RT and then stopped with Superase-In RNase Inhibitor (Thermo Scientific #AM2696) for 10 min on ice.

value: embryonic stem cells

value: untreated

tag: replicate


title: standard RIBO-Seq from mESCs, replicate 2

description: standard RIBO-Seq from mouse embryonic stem cells, biological replicate 2

source_name: mouse embryonic stem cells, standard RIBO-Seq, biological replicate 2

tag: cell type


title: MM1.S-shRNA2 ZBP1_rep2


title: AHARIBO RIBO-Seq from mESCs, replicate 1

description: AHARIBO RIBO-Seq from mouse embryonic stem cells, biological replicate 1

source_name: mouse embryonic stem cells, AHARIBO RIBO-Seq, biological replicate 1


title: H929-shRNA1 ZBP1_rep2


title: IN54-Cas9-gRNA-unedited-1

source_name: Muscle-derived stem cells


title: standard RIBO-Seq from mESCs, replicate 1

description: standard RIBO-Seq from mouse embryonic stem cells, biological replicate 1

source_name: mouse embryonic stem cells, standard RIBO-Seq, biological replicate 1


title: MM.1S-scramble_control rep2


title: MM1.S-shRNA1 ZBP1_rep2


title: IN54-Cas9-gRNA-mock-3

value: IN54-Cas9-gRNA mock (pbs)


title: IN54-Cas9-gRNA-target-1

value: IN54-Cas9-gRNA gRNA+Cas9


title: AHARIBO RIBO-Seq from mESCs, replicate 2

description: AHARIBO RIBO-Seq from mouse embryonic stem cells, biological replicate 2

source_name: mouse embryonic stem cells, AHARIBO RIBO-Seq, biological replicate 2


title: MM1.S-shRNA2 ZBP1_rep1


title: MM1.S-shRNA1 ZBP1_rep1


title: MM.1S-scramble_control rep1


title: IN54-Cas9-gRNA-mock-1


title: E50-gRNA-cas9-3


title: healthy control NeuN-positive Rep1

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description:
RNA-seq of healthy control cortical neuronal nuceli
Ctrl_NueNngeVSNueNpos_GeneCounts.csv
4907NeuNpos

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Reads were mapped to hg38 whole genome using tophat2 (2.0.11) with argument “--library-type fr-firststrand"
Gene annotations were obtained from iGenome UCSC hg38. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: hg38
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

source_name: cortical neuronal nuclei

extract_protocol:
RNA was purified using the PicoPure RNA isolation kit (ThermoFisher) following the manufacturer's instructions.
40ng of total RNA was used to prepare libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (ribozero ribosomal RNA depletion), following the manufacturer recommendations. Library quality and quantity were assessed on a Bionalayser and Qubit respectively. Libraries were sequenced on an Illumina Hiseq2500 (v4 chemistry) and at least 40million paired end 100bp reads per sample were generated per library..

treatment_protocol: Isolation of nuclei was performed as previously described (Krishnaswami et al., 2016) with minor modifications. Briefly, 50-250mg of pre-frontal cortical grey matter was homogenised in homogenisation buffer (250mM sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris buffer pH 8.0, 1μM DTT, 1X Proteinase Inhibitor w/o EDTA (Roche), 0.4U μl-1 RNaseIn (ThermoFisher) 0.2U μl-1 Superasin (ThermoFisher), 1μM DAPI) and centrifuged through an iodixanol gradient (Sigma). Pelleted nuclei were washed and then stained with NeuN antibody (Abcam, ab190195) in staining buffer (PBS, 1%BSA, 0.2U/μl RNaseIn (Thermofisher), NeuN antibody (1:200)) for one hour at 4oC. For negative controls antibody was excluded. Nuclei were then sorted on BD Fusion, and collected in wash buffer (PBS, 1%BSA, 0.2U/μl RNaseIn (Thermofisher)), before proceeding to downstream RNA extraction.

tag: disorder

value: healthy control

value: NeuN-positive


title: healthy control NeuN-positive Rep2

description:
RNA-seq of healthy control cortical neuronal nuceli
Ctrl_NueNngeVSNueNpos_GeneCounts.csv
1739NeuNpos


title: healthy control NeuN-positive Rep3

description:
RNA-seq of healthy control cortical neuronal nuceli
Ctrl_NueNngeVSNueNpos_GeneCounts.csv
1499NeuNpos


title: healthy control NeuN-negative Rep3

description:
RNA-seq of healthy control cortical non-neuronal nuceli
Ctrl_NueNngeVSNueNpos_GeneCounts.csv
1499NeuNneg

source_name: cortical non-neuronal nuclei

value: NeuN-negative


title: IN54-Cas9-gRNA-cas9-1

value: IN54-Cas9-gRNA cas9 only


title: Rad21tev+etoh_72h_primary_neuron_culture Rep3

description:
RNA-seq of ethanol-treated Rad21-Tev primary neuron transduced with ERT2-TEV
TEV_ETOH_72H_Rep3

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
The reads were aligned to mouse genome mm9 using Tophat2 with arguments  “--library-type fr-firststrand --b2-very-sensitive --b2-L 25” with gene annotation from Ensembl version 67
Number of reads counts on exons were summarised using Rsubread.
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

source_name: Primary neuron

growth_protocol: Mouse cortices were dissected and dissociated from individual E14.5 mouse embryos as described in (Beaudoin et al., 2012) with minor modifications. Dissociated neurons were maintained in Neurobasal medium with B27 supplement (Invitrogen), 1 mM L-glutamine, and 100 U/mL penicillin/streptomycin for 10 days in vitro (DIV10). Cells were plated at a density of 2.5 × 10e05 cells per well on 24-well plates pre-coated overnight with 0.1 mg/ml poly-D-lysine (Millipore) and half of the media in each well was replaced every 3 days. Cells were transduced after 3 days in culture with lentivirus encoding NLS-TEV at a multiplicity of infection of 1. AraC was added 2 days later. Following ten days in culture cultures were treated with 500nM 4-OHT or EtOH for 24 or 72 hours as indicated.

extract_protocol:
RNA was purified using the PicoPure RNA isolation kit (ThermoFisher) following the manufacturer's instructions.
200ng of total RNA was used to prepare libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (polyA enrichment), following the manufacturer recommendations. Library quality and quantity were assessed on a Bionalayser and Qubit respectively. Libraries were sequenced on an Illumina Hiseq2500 (v4 chemistry) and at least 40million paired end 100bp reads per sample were generated per library.

treatment_protocol: On DIV10 500nM 4-hydroxy tamoxifen or ethanol (as indicated in each individual sample) was added to the cells for 24 or 72 hours as indicated.

value: ethanol


title: Rad21tev+etoh_72h_primary_neuron_culture Rep1

description:
RNA-seq of ethanol-treated Rad21-Tev primary neuron transduced with ERT2-TEV
TEV_ETOH_72H_Rep1


title: IN45-Cas9-gRNA-unedited-1

value: IN45-Cas9-gRNA untreated


title: IN45-Cas9-gRNA-unedited-2


title: IN54-Cas9-gRNA-target-3


title: Rad21tev+4OHT_72h_primary_neuron_culture Rep3

description:
RNA-seq of tamoxifen-treated Rad21-Tev primary neuron transduced with ERT2-TEV
TEV_4OHT_72H_Rep3

value: 4-hydroxy tamoxifen


title: CdLS Patient744P [NeuN-pos RNAseq]

description:
RNA-seq of CdLS cortical neuronal nuceli
CdLS.NeuN.positive_GeneCounts.csv
CDL_744P

value: CdLS

tag: age

tag: gender

value: Female


title: IN54-Cas9-gRNA-target-2

value: Muscle

tag: treatment


title: Rad21tev+4OHT_72h_primary_neuron_culture Rep2

description:
RNA-seq of tamoxifen-treated Rad21-Tev primary neuron transduced with ERT2-TEV
TEV_4OHT_72H_Rep2


title: IN54-Cas9-gRNA-cas9-3


title: CdLS Patient380P [NeuN-pos RNAseq]

description:
RNA-seq of CdLS cortical neuronal nuceli
CdLS.NeuN.positive_GeneCounts.csv
CDL_380P

value: Male


title: Rad21tev+4OHT_72h_primary_neuron_culture Rep1

description:
RNA-seq of tamoxifen-treated Rad21-Tev primary neuron transduced with ERT2-TEV
TEV_4OHT_72H_Rep1


title: IN45-Cas9-gRNA-target-2

description: Quantification_of_editing_reads_counts_and_frequency.xls

value: IN45-Cas9-gRNA gRNA+Cas9


title: IN54-Cas9-gRNA-mock-2


title: healthy control Patient3011 [NeuN-pos RNAseq]

description:
RNA-seq of healthy control cortical neuronal nuceli
CdLS.NeuN.positive_GeneCounts.csv
SD030_11


title: IN45-Cas9-gRNA-target-1


title: healthy control Patient2308 [NeuN-pos RNAseq]

description:
RNA-seq of healthy control cortical neuronal nuceli
CdLS.NeuN.positive_GeneCounts.csv
SD023_08


title: Rad21tev+VEH24H_6DWASH_primary_neuron_culture Rep3

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Reads were mapped to mm9 whole genome using tophat2 (2.0.11) with argument  “--library-type fr-firststrand"
Gene annotations were obtained from iGenome NCBIM37. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

growth_protocol: Mouse cortices were dissected and dissociated from individual E14.5 mouse embryos as described in (Beaudoin et al., 2012) with minor modifications. Dissociated neurons were maintained in Neurobasal medium with B27 supplement (Invitrogen), 1 mM L-glutamine, and 100 U/mL penicillin/streptomycin for 10 days in vitro (DIV10). Cells were plated at a density of 2.5 × 10e05 cells per well on 24-well plates pre-coated overnight with 0.1 mg/ml poly-D-lysine (Millipore) and half of the media in each well was replaced every 3 days. Cells were transduced after 3 days in culture with lentivirus encoding NLS-TEV at a multiplicity of infection of 1. AraC was added 2 days later. Following 10 days in culture either 100ug/ml doxycyline or carrier (water) were added and samples collected 7 days later

extract_protocol:
RNA was purified using the PicoPure RNA isolation kit (ThermoFisher) following the manufacturer's instructions.
200ng of total RNA was used to prepare libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (ribozero ribosomal RNA depletion), following the manufacturer recommendations. Library quality and quantity were assessed on a Bionalayser and Qubit respectively. Libraries were sequenced on an Illumina Hiseq2500 (v4 chemistry) and at least 40million paired end 100bp reads per sample were generated per library..

treatment_protocol: On DIV10 1ug/ml doxycycline or water (as indicated in each individual sample) was added to the cells for 24 hours, and samples collected 7 days following beginning of treatment

value: water


title: IN45-Cas9-gRNA-target-3


title: Rad21tev+VEH24H_6DWASH_primary_neuron_culture Rep2


title: healthy control Patient4715 [NeuN-pos RNAseq]

description:
RNA-seq of healthy control cortical neuronal nuceli
CdLS.NeuN.positive_GeneCounts.csv
SD047_15


title: IN54-Cas9-gRNA-cas9-2


title: healthy control NeuN-negative Rep2

description:
RNA-seq of healthy control cortical non-neuronal nuceli
Ctrl_NueNngeVSNueNpos_GeneCounts.csv
1739NeuNneg


title: healthy control NeuN-negative Rep1

description:
RNA-seq of healthy control cortical non-neuronal nuceli
Ctrl_NueNngeVSNueNpos_GeneCounts.csv
4907NeuNneg


title: IN45-Cas9-gRNA-unedited-3


title: Rad21tev+etoh_72h_primary_neuron_culture Rep2

description:
RNA-seq of ethanol-treated Rad21-Tev primary neuron transduced with ERT2-TEV
TEV_ETOH_72H_Rep2


title: IN45-Cas9-gRNA-mock-2

value: IN45-Cas9-gRNA mock (pbs)


title: CdLS Patient764P [NeuN-pos RNAseq]

description:
RNA-seq of CdLS cortical neuronal nuceli
CdLS.NeuN.positive_GeneCounts.csv
CDL_764P


title: IN54-Cas9-gRNA-unedited-2

value: IN54-Cas9-gRNA untreated


title: Rad21tev+1UGDOX24H_6DWASH_primary_neuron_culture Rep3

value: doxycycline


title: healthy control Patient1739 [NeuN-pos RNAseq]

description:
RNA-seq of healthy control cortical neuronal nuceli
CdLS.NeuN.positive_GeneCounts.csv
1739


title: CdLS Patient2082 [NeuN-pos RNAseq]

description:
RNA-seq of CdLS cortical neuronal nuceli
CdLS.NeuN.positive_GeneCounts.csv
2082


title: IN45-Cas9-gRNA-mock-3


title: IN45-Cas9-gRNA-cas9-2

value: IN45-Cas9-gRNA cas9 only


title: healthy control Patient4788 [NeuN-pos RNAseq]

description:
RNA-seq of healthy control cortical neuronal nuceli
CdLS.NeuN.positive_GeneCounts.csv
4788

value: healthy control