title: Plasma_cells_Multiple_Myeloma [T01910]


title: Plasma_cells_Multiple_Myeloma [T01888]

status: Public on Dec 14 2022

type: genomic

city: Toulouse

first: Laura

last: Do Souto Ferreira

address: 1 Av. Irène Joliot-Curie

country: France

institute: IUCT

hyb_protocol: Cytoscan HD arrays (Affymetrix)

scan_protocol: Scanner Affymetrix  GCS 3000 7G

data_processing: analysis with the logarithm of ChAS software

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: sorted Plasma cells, from bone marrow of newly diagnosed multiple myeloma patients

label_protocol: Cytoscan Affymetrix Label (DNA labeling reagent)

extract_protocol: Nucleospin Tissue Macherey Nagel

treatment_protocol: sorted plasma cells (CD138+) then frozen (-80°C)

tag: subject id

tag: diagnosis

value: multiple myeloma

tag: Sex

value: female

tag: age

tag: del1p32 status

tag: treatment

value: RD

tag: tissue

value: bone marrow

tag: cell type

value: sorted plasma cells (CD138+)


title: S1_2_66

type: SRA

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

library_source: transcriptomic

data_processing:
Raw reads were aligned to the mouse reference genome GRCm39v26 downloaded from GENCODE using STAR-2.7.5a with default parameters.
Transcript quantification was performed with RSEM program version 1.3.0 and the mouse GENCODE gene annotation version M27
Quality control and outlier cell detection was performed using Seurat R package.
Assembly: GRCm39
Supplementary files format and content: tab delimited TPM table

molecule: total RNA

organism: Mus musculus

source_name: CD8 T cells

extract_protocol:
cells were sorted in 96 well plates directly in lysis buffer with a FACS Aria III sorter (BD Biosciences)
SMARTSeq v2 protocol with Illumina Nextera XT

tag: strain

value: C57BL/6J (RRID:IMSR_JAX:000664)

value: CD8 T cells

tag: disease state

value: Zika


title: S1_2_65


title: S1_2_63


title: Plasma_cells_Multiple_Myeloma [T01887]

value: VCD-HDM


title: S1_2_64


title: Plasma_cells_Multiple_Myeloma [T01884]


title: Plasma_cells_Multiple_Myeloma [T01880]

value: MPV


title: S1_2_62


title: S1_2_60


title: Plasma_cells_Multiple_Myeloma [T01854]

value: male


title: S1_2_6


title: Plasma_cells_Multiple_Myeloma [T01847]


title: S1_2_58


title: S1_2_57


title: S1_2_56


title: Plasma_cells_Multiple_Myeloma [T01839]


title: S1_2_53


title: Plasma_cells_Multiple_Myeloma [T01837]


title: S1_2_54


title: Plasma_cells_Multiple_Myeloma [T01801]


title: Plasma_cells_Multiple_Myeloma [T01778]


title: Plasma_cells_Multiple_Myeloma [T01781]


title: Plasma_cells_Multiple_Myeloma [T01790]


title: S1_2_50


title: S1_2_52


title: S1_2_5


title: S1_2_51


title: Plasma_cells_Multiple_Myeloma [T01871]


title: Plasma_cells_Multiple_Myeloma [T01777]

value: MPT


title: S1_2_49


title: S1_2_48


title: Plasma_cells_Multiple_Myeloma [T01763]


title: Plasma_cells_Multiple_Myeloma [T01761]


title: S1_2_47


title: Plasma_cells_Multiple_Myeloma [T01746]


title: Plasma_cells_Multiple_Myeloma [T01804]


title: S1_2_46


title: Plasma_cells_Multiple_Myeloma [T01700]


title: S1_2_44


title: Plasma_cells_Multiple_Myeloma [T01723]


title: S1_2_45


title: Plasma_cells_Multiple_Myeloma [T01784]


title: Plasma_cells_Multiple_Myeloma [T01669]


title: Plasma_cells_Multiple_Myeloma [T01699]


title: S1_2_42


title: Plasma_cells_Multiple_Myeloma [T01668]


title: Plasma_cells_Multiple_Myeloma [T01772]


title: S1_2_41


title: S1_2_4


title: Plasma_cells_Multiple_Myeloma [T01657]


title: S1_2_39


title: Plasma_cells_Multiple_Myeloma [T01655]


title: Plasma_cells_Multiple_Myeloma [T01647]


title: Plasma_cells_Multiple_Myeloma [T01634]


title: S1_2_37


title: Plasma_cells_Multiple_Myeloma [T01626]


title: S1_2_36


title: S1_2_35


title: Plasma_cells_Multiple_Myeloma [T01588]


title: S1_2_43


title: Plasma_cells_Multiple_Myeloma [T01604]


title: S1_2_33


title: S1_2_32


title: Plasma_cells_Multiple_Myeloma [T01587]


title: S1_2_3


title: Plasma_cells_Multiple_Myeloma [T01570]


title: Plasma_cells_Multiple_Myeloma [T01575]


title: Plasma_cells_Multiple_Myeloma [T01577]


title: S1_2_23


title: S1_2_38


title: S1_2_26


title: Plasma_cells_Multiple_Myeloma [T01537]


title: Plasma_cells_Multiple_Myeloma [T01625]

value: VCD


title: Plasma_cells_Multiple_Myeloma [T01566]


title: S1_2_2


title: S1_2_25


title: Plasma_cells_Multiple_Myeloma [T01499]


title: S1_2_22


title: S1_2_34


title: S1_2_17


title: S1_2_30


title: Plasma_cells_Multiple_Myeloma [T01583]


title: S1_2_18


title: Plasma_cells_Multiple_Myeloma [T01490]


title: S1_2_15


title: Plasma_cells_Multiple_Myeloma [T01468]


title: S1_2_19


title: Plasma_cells_Multiple_Myeloma [T01473]

value: MP


title: Plasma_cells_Multiple_Myeloma [T01465]


title: S1_2_16


title: Plasma_cells_Multiple_Myeloma [T01453]


title: S1_2_14


title: S1_2_12


title: Plasma_cells_Multiple_Myeloma [T01514]


title: S1_2_13


title: S1_2_11


title: Plasma_cells_Multiple_Myeloma [T01513]


title: Plasma_cells_Multiple_Myeloma [T01447]


title: S1_1_93


title: S1_2_28


title: Plasma_cells_Multiple_Myeloma [T01427]


title: Plasma_cells_Multiple_Myeloma [T01437]


title: S1_2_1


title: S1_1_89


title: S1_1_84


title: Plasma_cells_Multiple_Myeloma [T01392]


title: Plasma_cells_Multiple_Myeloma [T01443]

value: VD


title: S1_1_91


title: Plasma_cells_Multiple_Myeloma [T01411]


title: Plasma_cells_Multiple_Myeloma [T01398]


title: S1_1_87


title: Plasma_cells_Multiple_Myeloma [T01352]


title: S1_1_82


title: Plasma_cells_Multiple_Myeloma [T01422]


title: Plasma_cells_Multiple_Myeloma [T01390]


title: Plasma_cells_Multiple_Myeloma [T01323]


title: Plasma_cells_Multiple_Myeloma [T01321]


title: S1_1_77


title: S1_1_83


title: Plasma_cells_Multiple_Myeloma [T01300]


title: S1_1_8


title: S1_1_73


title: S1_1_78


title: Plasma_cells_Multiple_Myeloma [T01290]


title: Plasma_cells_Multiple_Myeloma [T01383]


title: S1_1_75


title: S1_1_70


title: S1_1_68


title: S1_1_72


title: Plasma_cells_Multiple_Myeloma [T01283]


title: S1_1_71


title: Plasma_cells_Multiple_Myeloma [T01339]


title: Plasma_cells_Multiple_Myeloma [T01385]


title: Plasma_cells_Multiple_Myeloma [T01258]


title: S1_1_76


title: S1_1_64


title: Plasma_cells_Multiple_Myeloma [T01200]


title: Plasma_cells_Multiple_Myeloma [T01234]


title: S1_1_61


title: S1_1_67


title: Plasma_cells_Multiple_Myeloma [T01163]

value: VTD


title: Plasma_cells_Multiple_Myeloma [T01232]


title: Plasma_cells_Multiple_Myeloma [T01266]


title: S1_1_63


title: Plasma_cells_Multiple_Myeloma [T01183]


title: S1_1_66


title: S1_1_56


title: S1_1_58


title: Plasma_cells_Multiple_Myeloma [T01129]


title: S1_1_54


title: Plasma_cells_Multiple_Myeloma [T01217]


title: S1_1_62


title: S1_1_57


title: S1_1_60


title: Plasma_cells_Multiple_Myeloma [T01218]


title: S1_1_59


title: Plasma_cells_Multiple_Myeloma [T01103]


title: Plasma_cells_Multiple_Myeloma [T01114]


title: S1_1_53


title: Plasma_cells_Multiple_Myeloma [T01087]


title: Plasma_cells_Multiple_Myeloma [T01074]


title: Plasma_cells_Multiple_Myeloma [T01057]


title: Plasma_cells_Multiple_Myeloma [T01128]


title: S1_1_55


title: Plasma_cells_Multiple_Myeloma [T01035]


title: Plasma_cells_Multiple_Myeloma [T01006]


title: Plasma_cells_Multiple_Myeloma [T01140]


title: S1_1_6


title: S1_1_50


title: Plasma_cells_Multiple_Myeloma [T01117]


title: Plasma_cells_Multiple_Myeloma [T00986]


title: Plasma_cells_Multiple_Myeloma [T00977]


title: Plasma_cells_Multiple_Myeloma [T00980]


title: S1_1_48


title: S1_1_45


title: S1_1_49


title: Plasma_cells_Multiple_Myeloma [T00982]


title: S1_1_41


title: S1_1_43


title: Plasma_cells_Multiple_Myeloma [T00976]


title: S1_1_4


title: Plasma_cells_Multiple_Myeloma [T00949]


title: S1_1_51


title: S1_1_39


title: S1_1_40


title: Plasma_cells_Multiple_Myeloma [T00939]


title: Plasma_cells_Multiple_Myeloma [T00928]


title: S1_1_35


title: S1_1_5


title: S1_1_33


title: S1_1_36


title: S1_1_32


title: S1_1_31


title: S1_1_30


title: S1_1_27


title: S1_1_3


title: S1_1_34


title: S1_1_24


title: S1_1_28


title: S1_1_19


title: S1_1_20


title: S1_1_21


title: S1_1_18


title: S1_1_29


title: INS1E cells siRNA Srrm3 replicate 3

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

description: polyA-selected RNA

data_processing:
Raw reads were mapped with vast-tools align v2.5.1.
Assembly: hg38 (GRCh38), mm10 (GRCm38), rn6 (Rnor_6.0)
Supplementary files format and content: *.cRPKM.txt: Files with raw read counts and cRPKMs for each human, mouse or rat gene in Ensembl.

organism: Rattus norvegicus

source_name: INS1E cells

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
Illumina strand-specific
Strand-specific polyA-selected

tag: cell line

tag: sirna

value: siRNA Srrm3


title: S1_1_14


title: S1_1_16


title: INS1E cells siRNA Srrm3 replicate 2

description: polyA-selected RNA


title: S1_1_17


title: INS1E cells siRNA Srrm3 replicate 1

description: polyA-selected RNA


title: S1_1_1


title: INS1E cells siRNA control replicate 2

description: polyA-selected RNA

value: siRNA control


title: INS1E cells siRNA control replicate 3

description: polyA-selected RNA


title: S1_1_13


title: S1_1


title: INS1E cells siRNA control replicate 1

description: polyA-selected RNA


title: Areg-flox wildtype control AECint Sample 4

city: New York

first: Nicholas

last: Arpaia

state: NY

address: 701 W 168TH ST HHSC 910C

department: Microbiology & Immunology

country: USA

institute: Columbia University Irving Medical Center

data_processing:
Fastq files were ran through fastqc to check for sequencing quality. QC was visualized using MultiQC (Ewels et al Bioinformatics 2016)
Salmon (Patro et al Nature Methods 2017) was used to generate an index of the CHR Gencode mouse transcriptome (gencode.vM24.annotation.gff3)
Salmon was used to quanitfy transcripts against the mouse transcriptome reference. Flags used were for automatic library type detection -l A (unstranded, single-end), --seqBias, --gcBias, and --validateMappings
Transcript quantification files (quants.sf) were convereted to gene level counts using TxImport (Soneson et al. F1000Research 2015)
Differential expresison on gene level counts was performed using DESeq2 (Love et al Genome Biology 2014). Results were generated using the lfcShrink and contrast functions, making pairwise comparsions on the indicated groups. Alpha threshold set to 0.05 and lfcThreshold to 1.
Genome_build: Gencode GRCm38 primary assembly genome sequence
Supplementary_files_format_and_content: Differential expression files include log2 fold changes generated by DESeq2 for each indicated comparison (with all samples from a given group identified utilized in the differential expression test). These files are listed as .csv files. Counts for each gene is provided with the DESeq2 analysis.

source_name: Mouse lung

growth_protocol: Fresh alveolar epithelial cells were isolated from lungs followed by enzymatic digestion, negative enrichment using magnetic biotinylated beads for depletion of CD45+, CD31+, and Ter119+ cells, then sorted by FACs.

extract_protocol:
Cells were pelleted and flash frozen. RNA extraction performed using Qiagen kit by Genewiz.
Library preparation was performed by Genewiz / Illumina protocol of ultra-low input RNA value package.
Paired-end 150bp HiSeq

treatment_protocol: Mice were infected with 400TCID50 PR8/H1N1 and lungs were harvested at day 5 post infection.

value: Lung alveolar epithelial cells from influenza-infected mice

tag: genotype

value: Areg-flox/flox

value: H1N1/PR8 at day 5 post infection


title: 205772280168_R07C01

city: Oslo

first: Adam

middle: P

last: Sharples

address: 220 Sognsveien

country: Norway

institute: Norwegian School of Sport Sciences

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: BeadChips were imaged using the Illumina iScan System

data_processing:
Partek Genomic Suite V7 (Using MethylationEPIC_v-1-0_B4 manifest file)
Data is normalised via functional normalisation (with noob background correction)

label: Cy3, Cy5

source_name: DNA from Vastus Lateralis Muscle

label_protocol: Labels (Condition (80 FAIL & 30 FAIL), Timepoint (Baseline, 3hrs post exercise, 6hrs post exercise), Partricipant number (training status - all trained)

extract_protocol: Genomic DNA was extracted via the Qiagen DNA Easy Kit in accordance with  manufacturers guidelines. The DNA was then bisulfite converted using the EZ DNA Methylation Kit, Zymo Research, CA, United States, as per manufacturer’s instructions.

tag: condition

value: 80 FAIL

tag: timepoint

tag: participant number

value: Trained 17

tag: gender

value: Male

value: Skeletal Muscle - Vastus Lateralis


title: Areg-flox CD4-Cre AECint Sample 4

value: CD4-cre Areg-flox/flox


title: Areg-flox CD4-Cre AECint Sample 3


title: Areg-flox wildtype control AECint Sample 3


title: 205772280168_R03C01

value: 30 FAIL


title: 205772280168_R04C01


title: Areg-flox CD4-Cre AECint Sample 2


title: 205772280168_R02C01

value: Baseline


title: 205772280168_R01C01

value: Trained 16


title: S1_1_10

value: C57BL/6J (RRID:IMSR_JAX:000664)

value: CD8 T cells

value: Zika


title: Areg-flox wildtype control AECint Sample 2


title: Areg-flox wildtype control AECint Sample 1


title: 205772280168_R05C01


title: 205772280151_R07C01

value: Trained 15


title: Areg-flox wildtype control AT2 Sample 4


title: 205772280151_R06C01


title: 205772280151_R05C01

value: Trained 14


title: Areg-flox wildtype control AT2 Sample 3


title: Areg-flox CD4-Cre AECint Sample 1


title: 205772280168_R06C01


title: Areg-flox wildtype control AT2 Sample 2


title: Areg-flox wildtype control AT2 Sample 1


title: 205772280151_R03C01


title: 205772280151_R04C01


title: 205772280139_R07C01


title: NSC11 GSCs GFP in the RH, biological replicate 3

city: Besthesda

first: Charlotte

middle: M

last: Degorre

state: Maryland

address: 10 Center drive

department: NCI

institute: NIH

data_processing:
Basecalling software : RTA 2.11.3
Demultiplexing Software : Bcl2fastq v2.17
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt 1.18 before alignment with the reference genome (Human_hg38) and the annotated transcripts using STAR 2.7.0f.
Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility 2.18.26.
In addition, the gene expression quantification analysis was performed for all samples using STAR/RSEM tools 1.3.1.
Assembly: hg38
Supplementary files format and content: rawreadcount - rsemgenes - .xlsx file

source_name: Human tumor from the murine Right hemisphere

growth_protocol: NSC11 GSCs GFP were maintained in DMEM/F12 supplemented with B27, EGF and FGF in humidified atmosphere with 5% CO2/5%O2 at 37C

extract_protocol:
OB and RH tumor were scoop from the brain using the GFP signal and flash frozen in liquid nitrogen. RNA was then exctracted using the Allprep DNA/RNA/protein mini kit (Qiagen) . The resulting RNA was digested using the one column clean up protocol present in the QIAGEN Rneasy Mini Kit.
200 ng of RNA was used as input for mRNA capture with oligo-dT coated magnetic beads.  The mRNA was fragmented, followed by random-primed cDNA synthesis.  The resulting double-stranded cDNA was used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification to generate a sequencing ready library

tag: breed

value: NCr nu/nu

value: Female

value: NSC11 Gliobastoma stem like cells transfected with GFP

value: WT


title: 205772280151_R08C01


title: 205772280139_R08C01


title: NSC11 GSCs GFP in the RH, biological replicate 1

value: Human tumor from the murine Right hemisphere


title: NSC11 GSCs GFP in the RH, biological replicate 2


title: 205772280139_R06C01

value: 80 FAIL


title: NSC11 GSCs GFP in the OB, biological replicate 3

source_name: Human tumor from the murin Olfactory Bulb


title: NSC11 GSCs GFP in the OB, biological replicate 1

value: Human tumor from the murin Olfactory Bulb


title: pSS_22 cDC2s

city: Utrecht

first: Ana

middle: Pinheiro

last: Lopes

state: Utrecht

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Reads were aligned using STAR aligner using the default parameters to the 65,217 annotated genes obtained from the GrCh38 (v79) built of the human genome.
The read counts per gene were quantified by the Python package HTSeq.
Variance stabilizing transformation (VST) was applied to obtain normalized gene counts.
Assembly: GrCh38 (v79)
Supplementary files format and content: Matrix table with normalized gene counts (VST) for every gene across all samples_Discovery
Supplementary files format and content: Matrix table with normalized gene counts (VST) for every gene across all samples_Replication

source_name: peripheral blood

extract_protocol:
CD1c-expressing cDC2s were isolated from peripheral blood mononuclear cells with the CD1c (BDCA-1)+ Dendritic Cell Isolation Kit (Miltenyi) according to manufacturer's instruction. Cells were lysed in RLTplus buffer (Qiagen) supplemented with beta-mercaptoethanol (1%). Total RNA was purified using AllPrep Universal Kit (Qiagen), according to the manufacturer’s instructions. RNA integrity was measured by capillary electrophoresis using a Bioanalyzer (Agilent), and the RNA 6000 Nano Kit (Agilent Technologies); all samples had RIN-score >7.0.
RNA libraries were prepared according to the standard Illumina protocols

tag: group

value: primary Sjogren's syndrome

tag: cohort type

value: Replication


title: NSC11 GSCs GFP in the OB, biological replicate 4

tag: Sex


title: 205676800146_R08C01

value: Trained 1

value: Male

value: Skeletal Muscle - Vastus Lateralis


title: pSS_20 cDC2s

tag: age


title: pSS_21 cDC2s


title: pSS_19 cDC2s


title: 205676800146_R06C01

value: 30 FAIL


title: pSS_18 cDC2s


title: 205772280139_R03C01


title: pSS_23 cDC2s


title: 205772280139_R04C01

value: Baseline

value: Trained 16


title: 205676800146_R07C01


title: 205772280139_R05C01


title: 205676800146_R05C01


title: 205772280139_R01C01

value: Trained 15


title: 205772280139_R02C01


title: 205676800081_R08C01

value: Trained 2


title: NB23 (aCGH)

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

description: Affymetrix CytoScan HD

hyb_protocol: DNA extraction from neuroblastoma samples was performed using the DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol. DNA quality was assessed using the Tapestation platform (Agilent).

scan_protocol: The Arrays were washed using affymetrix fluidics stations FS450 and scanned using the Gene Chip Scanner 3000.

data_processing: SNP microarray analysis was performed using the Cytoscan HD Array (Affymetrix) and data was processed using the Chromosome Analysis Suite version 3.3.0.139.

source_name: neuroblastoma

label_protocol: Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the diagested DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Cytoscan HD array kit and reagent kit bundle, (Affymetrix, Santa Clara, CA,US) to obtain biotin labeled DNA, as per manufacturer’s instruction.

tag: risk group

value: Intermediate

tag: tumor type

value: Primary


title: NB19 (aCGH)

description: Affymetrix CytoScan HD

extract_protocol: DNA extraction from neuroblastoma samples was performed using the DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol. DNA quality was assessed using the Tapestation platform (Agilent).

value: Low


title: NB21 (aCGH)

description: Affymetrix CytoScan HD

value: High


title: pSS_17 cDC2s

value: Female


title: pSS_16 cDC2s


title: NB12 (aCGH)

description: Affymetrix CytoScan HD


title: NB16 (aCGH)

description: Affymetrix CytoScan HD


title: SupFig9 maize vCasphi lc gRNA9 rep2

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

library_source: genomic

data_processing:
Amplicon sequencing:  Reads were first quality and adaptor trimmed using Trim Galore and then mapped to the target genomic region by the BWA aligner. Sorted and indexed bam files were used as input files for further analysis by the CrispRvariants R package. Each mutation pattern with corresponding read counts was exported by the CrispRvariants R package. After assessing all control samples, a criterion to classify reads as edited reads was established: only reads with a >= 3 bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 100 read counts from a sample were counted as edited reads. This criterion is established due to the observation of 1 bp indels and occasionally 2 bp indels with read numbers >100 in control samples. Also, larger indels that occur at very low frequencies (much lower than 100 reads) were observed in control samples. These observations indicate that occasional PCR inaccuracy and low-quality sequencing in a small fraction of reads can result in the indel patterns with corresponding read number ranges as stated above in control samples with the typical sequencing depth in our experiments (1-5 million reads/sample). By employing such stringent criteria, it is believed that the editing signals counted are true signals indicating editing events. Additionally, for FWA gRNA5 and gRNA6 targeted regions, there are long stretches of adenines near these target regions. Due to the high error rate of polymerases amplifying long stretches of adenines, reads with indels only within these stretches of adenines were not counted as true deletions. For amplicon sequencing result analysis of maize protoplast, the criterion to classify reads as edited reads was established: only reads with a >= 3bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 10 read counts from a sample were counted as edited reads. The adjustment of the criterion was based on the fact that these amplicon sequencing was of less depth (performed by the iSeq 100) compared to the amplicon libraries of Arabidopsis protoplasts.
Whole genome sequencing for off-target analysis: For variant calling, whole genome sequencing reads were aligned to the TAIR10 reference genome using BWA mem (v0.7.17)53 with default parameters. GATK (4.2.0.0)39 MarkDuplicatesSpark was used to remove PCR duplicate reads. Then GATK HaplotypeCaller was used to call raw variants. Raw SNPs were filtered with QD < 2.0, FS > 60.0, MQ < 40.0, and SOR > 4.0. Raw InDels were filtered with QD < 2.0, FS > 200.0, and SOR > 10.0 and used for base quality score recalibration. The recalibrated bam file was further applied to GATK and Strelka (v2.9.2)40 for SNPs/InDel calling. Only SNPs/InDels called by both GATK and Strelka were used for further analysis. The intersection of GATK and Strelka  SNPs/InDels were filtered by removing identical SNPs/InDels in the rdr6-15 background by BedTools (v2.26.0)54. Variants with coverage lower than 30 reads were removed. Variant loci at which the ratio of the reads with the WT allele over the reads with variant allele larger than three were removed. For heterozygous alleles, at a coverage level of 30 reads, the chance of observing WT reads /mutation allele reads >3 is 0.26% (binomial distribution, one-tailed P=0.0026).
Assembly: tair10
Supplementary files format and content: Crispvariant_result, with detected SNV and indels in amplicon sequencing  vcf, raw variants called with GATK or strelka2 comparing to tair10 reference genome sequence
Library strategy: amplicon sequencing

organism: Zea mays

source_name: maize mesophyll protoplast

growth_protocol: To grow Arabidopsis plants for protoplast preparation, Col-0 and fwa-4 epi-mutant plants were grown under a 12-hour light/12-hour dark photoperiod and with low light condition for 3-4 weeks. To grow maize plants for protoplast isolation, B73 seeds were soaked in water overnight and planted in half peat moss and half vermiculite. After three days of light incubation, emerged seedlings were transferred to dark until the 2nd leaf was 10-15 cm long.   Transgenic T1 plants were screened with half MS plates with 40 μg/ml hygromycin B. For 28 °C treatment of T1 plants, stratified seeds on half MS plates with hygromycin B were incubated at 28 °C and resistant T1 plants were transferred to soil after about a week, and put back to 28 °C for a total of two weeks incubation at 28 °C. T1 plants were then moved to a greenhouse (23 °C) for the rest of the life cycle.  To support the growth of albino seedlings in T2 generation, 3% sucrose was supplemented to half MS plates when needed.

extract_protocol:
Amplicon sequencing: DNA was extracted from protoplast samples and leaves of transgenic plants with Qiagen DNeasy plant mini kit. The amplicon was obtained using two rounds of PCR. Amplification primers for the first round of PCR were designed to have the 3’ sequence of the primers flanking a 200-300 bp fragment of the genomic area targeted by the guide RNA of interest. The 5’ part of the primer contained a sequence which will be bound by common sequencing primers. After 25 cycles of the first round of PCR amplification, the reaction was purified using 1x Ampure XP beads (Beckman Coulter A63881). The eluate was used as template for the second round of PCR using the Phusion enzyme and 12 cycles of amplification. The second round of PCR was designed so that indexes were added to each sample. The samples were then purified using 0.8x Ampure XP beads. Part of the purified libraries were run on a 2% agarose gel to check for size and absence of primer dimer (fragments below 200 bp considered as primer dimer). Then amplicons were sent for sequencing with NovaSeq 6000 or iSeq 100 platform.
Whole genome sequencing: DNA from single Arabidopsis seedlings was extracted with the Qiagen DNeasy plant mini kit and sheared to 300 bp size with a Covaris. Library preparation was performed with Tecan Ovation Ultralow V2 DNA-seq kit. The libraries were sequenced with the NovaSeq 6000 platform.

tag: tissue

value: mysophyll protoplast

tag: developmental stage

tag: target locus

value: Lc


title: nSS_11 cDC2s

value: non-Sjogren's sicca


title: SupFig9 maize vCasphi lc gRNA9 rep1

tag: strain


title: NB22 (aCGH)

description: Affymetrix CytoScan HD


title: nSS_12 cDC2s

value: Replication


title: 205676800081_R06C01


title: 205676800081_R07C01


title: HC_18 cDC2s

value: healthy control


title: 205676800081_R04C01

value: 80 FAIL

value: Male


title: NB18 (aCGH)

description: Affymetrix CytoScan HD


title: 205676800081_R05C01

value: Skeletal Muscle - Vastus Lateralis


title: nSS_15 cDC2s


title: nSS_13 cDC2s


title: nSS_10 cDC2s


title: 205676800081_R03C01

value: Baseline


title: NB20 (aCGH)

description: Affymetrix CytoScan HD


title: SupFig9 maize vCasphi lc gRNA8 rep1


title: NB24 (aCGH)

description: Affymetrix CytoScan HD


title: nSS_14 cDC2s


title: NB01 (aCGH)

description: Affymetrix CytoScan HD


title: pSS_15 cDC2s

value: primary Sjogren's syndrome


title: NB26 (aCGH)

description: Affymetrix CytoScan HD


title: SupFig9 maize vCasphi lc gRNA8 rep2


title: 205676800081_R01C01

value: Trained 1


title: HC_14 cDC2s


title: HC_16 cDC2s


title: NB02 (aCGH)

description: Affymetrix CytoScan HD


title: 205676800081_R02C01


title: NB14 (aCGH)

description: Affymetrix CytoScan HD


title: HC_15 cDC2s


title: HC_17 cDC2s


title: 205676380101_R08C01

value: 30 FAIL

value: Trained 10


title: HC_12 cDC2s


title: SupFig9 maize vCasphi lc gRNA7 rep2


title: pSS13

data_processing:
Reads were aligned using STAR aligner using the default parameters to the 65,217 annotated genes obtained from the GrCh38 (v79) built of the human genome.
The read counts per gene were quantified by the Python package HTSeq.
Variance stabilizing transformation (VST) was applied to obtain normalized gene counts.
Assembly: GrCh38 (v79)
Supplementary files format and content: Matrix table with normalized gene counts (VST) for every gene across all samples

extract_protocol:
CD19-expressing B cells were isolated from peripheral blood mononuclear cells with the CD1c (BDCA-1)+ Dendritic Cell Isolation Kit (Miltenyi) according to manufacturer's instruction. Cells were lysed in RLTplus buffer (Qiagen) supplemented with beta-mercaptoethanol (1%). Total RNA was purified using AllPrep Universal Kit (Qiagen), according to the manufacturer’s instructions. RNA integrity was measured by capillary electrophoresis using a Bioanalyzer (Agilent), and the RNA 6000 Nano Kit (Agilent Technologies); all samples had RIN-score >7.0.
RNA libraries were prepared according to the standard Illumina protocols

tag: cell type

value: CD19+ B cells


title: 205676380101_R07C01


title: HC_11 cDC2s


title: SupFig9 maize vCasphi lc gRNA6 rep1


title: NB17 (aCGH)

description: Affymetrix CytoScan HD

value: Primary


title: pSS14


title: HC_09 cDC2s


title: 205676380101_R04C01

value: Trained 5


title: HC_10 cDC2s

value: Female


title: 205676380101_R06C01


title: 205676380101_R05C01


title: pSS12


title: pSS11


title: NB13 (aCGH)

description: Affymetrix CytoScan HD

value: High

value: Recurrence


title: pSS10


title: SupFig9 maize vCasphi lc gRNA5 rep2

value: mysophyll protoplast

value: Lc


title: 205676380101_R03C01


title: NB09 (aCGH)

description: Affymetrix CytoScan HD


title: pSS9


title: NB11 (aCGH)

description: Affymetrix CytoScan HD


title: SupFig9 maize vCasphi lc gRNA6 rep2


title: SupFig9 maize vCasphi lc gRNA4 rep2


title: 205676380101_R02C01


title: SupFig9 maize vCasphi lc gRNA4 rep1


title: pSS7


title: pSS8


title: pSS6


title: HC_13 cDC2s

value: healthy control

value: Replication


title: pSS4


title: SupFig9 maize vCasphi lc gRNA7 rep1


title: 205676380101_R01C01

value: Male


title: pSS3


title: 205676380100_R07C01

value: Skeletal Muscle - Vastus Lateralis


title: SupFig9 maize vCasphi lc gRNA3 rep1


title: SupFig9 maize vCasphi lc gRNA3 rep2


title: pSS1


title: nSS10

value: non-Sjogren's sicca


title: 205676380100_R06C01

value: Trained 4


title: SupFig9 maize vCasphi lc gRNA2 rep1


title: SupFig9 maize vCasphi lc gRNA2 rep2


title: nSS11


title: nSS8


title: SupFig9 maize vCasphi lc gRNA1 rep2


title: nSS9


title: pSS2

value: primary Sjogren's syndrome


title: nSS6


title: 205676380100_R04C01

value: 30 FAIL

value: Baseline


title: nSS5

value: CD19+ B cells


title: 205676380100_R05C01


title: nSS7


title: 205676380100_R08C01


title: pSS5


title: 205676380100_R03C01

value: 80 FAIL


title: 205676380100_R02C01


title: nSS1


title: SupFig9 maize vCasphi lc gRNA11 rep2


title: nSS2


title: HC13


title: SupFig9 maize vCasphi lc gRNA11 rep1


title: 205676380080_R08C01

value: Trained 11


title: 205676380100_R01C01


title: HC12

value: Female


title: nSS4


title: SupFig9 maize vCasphi lc gRNA10 rep1


title: SupFig9 maize nCasphi lc gRNA9 rep1


title: SupFig9 maize nCasphi lc gRNA9 rep2


title: HC10


title: HC11


title: HC6


title: nSS3


title: SupFig9 maize vCasphi lc gRNA1 rep1


title: 205676380080_R07C01


title: SupFig9 maize nCasphi lc gRNA8 rep2


title: HC5


title: HC8


title: HC7


title: 205676380080_R06C01


title: HC4


title: 205676380080_R04C01


title: HC3


title: SupFig9 maize vCasphi lc gRNA10 rep2


title: 205676380080_R03C01


title: SupFig9 maize nCasphi lc gRNA8 rep1


title: HC1


title: SupFig9 maize nCasphi lc gRNA7 rep2


title: SupFig9 maize nCasphi lc gRNA7 rep1


title: 205676380080_R05C01


title: 205676380080_R02C01

value: Trained 10


title: SupFig9 maize nCasphi lc gRNA6 rep2


title: HC9


title: iAst, P4, untreated, rep3, L002

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.20.0
alignment to GRCh38 genome using STAR v2.7.1a
reads counted on GENCODE release 27 gene models with htseq-count 0.9.1
Genome_build: GRCh38
Supplementary_files_format_and_content: htseq-count output, two-column text file with Ensembl gene identifier and read count columns

molecule: polyA RNA

source_name: induced astrocytes

growth_protocol: Patient and healthy fibroblasts were directly converted to neurons using small molecules. Skin fibroblasts were directly converted to induced neuronal progenitor cells (iNPCs) and differentiated into astrocytes with DMEM/Glutamax media containing 10% FBS and 0.2% N2.

extract_protocol:
Cell pellets were flash frozen on dry ice. RNA was extracte using Qiagen Rneasy mini Kit. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Healthy and patient iAs were treated with 1 µM CuATSM or same volume of DMSO beginning day 2 of their differentiation for 4 days.

value: induced astrocytes

tag: disease state

value: NEDAMSS patient

tag: cuatsm drug treatment

value: untreated


title: iAst, P4, treated, rep2, L002

value: treated


title: 205676380080_R01C01

tag: condition

tag: timepoint


title: iAst, P4, treated, rep2, L001


title: iAst, P4, untreated, rep3, L001


title: iAst, P4, treated, rep3, L001


title: SupFig9 maize nCasphi lc gRNA5 rep2

value: mysophyll protoplast

value: Lc


title: 205676380052_R07C01

tag: participant number

value: Trained 14

tag: gender

value: Male

value: Skeletal Muscle - Vastus Lateralis


title: SupFig9 maize nCasphi lc gRNA6 rep1


title: 205676380052_R06C01


title: iAst, P4, untreated, rep2, L002


title: iAst, P4, treated, rep1, L001


title: SupFig9 maize nCasphi lc gRNA5 rep1


title: iAst, P4, treated, rep1, L002


title: iAst, P4, treated, rep3, L002


title: iAst, P4, untreated, rep2, L001


title: iAst, P4, untreated, rep1, L001


title: iAst, P2, treated, rep3, L002


title: 205676380052_R03C01

value: Trained 12


title: HC2

tag: group

value: healthy control


title: iAst, P2, untreated, rep3, L002


title: SupFig9 maize nCasphi lc gRNA3 rep2


title: iAst, P4, untreated, rep1, L002


title: iAst, P2, treated, rep2, L002


title: SupFig9 maize nCasphi lc gRNA4 rep2


title: SupFig9 maize nCasphi lc gRNA4 rep1


title: 205676380052_R05C01

value: Baseline


title: iAst, P2, untreated, rep2, L002


title: iAst, P2, treated, rep3, L001


title: iAst, P2, untreated, rep2, L001


title: 205676380052_R02C01


title: SupFig9 maize nCasphi lc gRNA2 rep1


title: iAst, P2, untreated, rep3, L001


title: 205676380052_R04C01

value: 30 FAIL


title: SupFig9 maize nCasphi lc gRNA3 rep1


title: iAst, P2, treated, rep1, L002


title: iAst, P2, treated, rep2, L001


title: SupFig9 maize nCasphi lc gRNA2 rep2


title: iAst, P2, untreated, rep1, L002


title: iAst, P2, untreated, rep1, L001


title: iAst, P2, treated, rep1, L001


title: iAst, P3, treated, rep3, L002


title: SupFig9 maize nCasphi lc gRNA1 rep2


title: SupFig9 maize nCasphi lc gRNA1 rep1


title: iAst, P3, treated, rep3, L001


title: iAst, P3, untreated, rep3, L002


title: iAst, P3, untreated, rep3, L001


title: iAst, P3, treated, rep2, L002


title: 205676380052_R01C01

value: 80 FAIL


title: SupFig9 maize nCasphi lc gRNA11 rep2


title: iAst, P3, treated, rep2, L001


title: iAst, P3, untreated, rep2, L002


title: iAst, P3, treated, rep1, L002


title: SupFig9 maize nCasphi lc gRNA11 rep1


title: SupFig9 maize nCasphi lc gRNA10 rep1


title: iAst, P3, treated, rep1, L001


title: iAst, P3, untreated, rep1, L001


title: iAst, P3, untreated, rep1, L002


title: SupFig9 maize vCasphi lc gRNA5 rep1


title: iAst, P1, treated, rep3, L001


title: SupFig9 maize WTCasphi lc gRNA9 rep2


title: SupFig9 maize WTCasphi lc gRNA9 rep1


title: iAst, P1, untreated, rep3, L002


title: iAst, P3, untreated, rep2, L001


title: SupFig9 maize WTCasphi lc gRNA8 rep2


title: SupFig9 maize nCasphi lc gRNA10 rep2


title: iAst, P1, untreated, rep3, L001


title: iAst, P1, treated, rep3, L002


title: iAst, P1, treated, rep2, L002


title: iAst, P1, treated, rep2, L001


title: iAst, P1, untreated, rep2, L001


title: iAst, P1, untreated, rep2, L002


title: SupFig9 maize WTCasphi lc gRNA8 rep1


title: SupFig9 maize WTCasphi lc gRNA7 rep2


title: iAst, P1, treated, rep1, L002


title: SupFig9 maize WTCasphi lc gRNA7 rep1


title: iAst, P1, treated, rep1, L001


title: shPRMT2/4, rep 3

city: Charleston

first: Wenjian

last: Gan

state: SC

address: 173 Ashley Ave, BSB507

institute: Medical University of South Carolina

data_processing:
Raw reads were filtered by software SOAPnuke to remove reads with adaptors, reads in which unknown bases(N) are more than 0.1%, and low-quality reads that are defined as the percentage of base which quality is lesser than 20 is greater than 40% in a read
Clean reads were mapped to the human genome with HISAT2 and Bowtie2
Gene expression level was calculated with RSEM
Differentially expression genes were detected with DEseq2
FPKM=(1000000*C)/(N*L/1000), C represents the amount of fragment which mapped to the specific transcripts, N represents the amount of fragment which mapped to any transcripts. L represents the base amount of the specific transcripts.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MCF7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin and maintained at 37°C and 5% CO2

extract_protocol:
Total RNAs were prepared using a NucleoSpin RNA Plus kit (TaKaRa, 740984.50)
The poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. The PCR yield was quantified by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

tag: cell line

value: breast cancer cells

tag: genotype

value: PRMT2/4 knockdown


title: iAst, P1, untreated, rep1, L001


title: shPRMT2/4, rep 2


title: iAst, P1, untreated, rep1, L002


title: iAst, H1, treated, rep3, L002

value: heatlhy control


title: iAst, H1, treated, rep3, L001

value: induced astrocytes


title: shPRMT2/4, rep 1


title: iAst, H1, untreated, rep3, L002


title: shBRD4, rep 3

value: BRD4 knockdown


title: SupFig9 maize WTCasphi lc gRNA6 rep2


title: SupFig9 maize WTCasphi lc gRNA6 rep1


title: SupFig9 maize WTCasphi lc gRNA5 rep1


title: shBRD4, rep 2


title: iAst, H1, untreated, rep3, L001

value: untreated


title: iAst, H1, treated, rep2, L001

value: treated


title: iAst, H1, untreated, rep2, L002


title: shBRD4, rep 1


title: SupFig9 maize WTCasphi lc gRNA4 rep2

value: mysophyll protoplast


title: iAst, H1, untreated, rep2, L001


title: iAst, H1, treated, rep1, L002


title: SupFig9 maize WTCasphi lc gRNA4 rep1

value: Lc


title: iAst, H1, treated, rep1, L001


title: iAst, H1, treated, rep2, L002


title: SupFig9 maize WTCasphi lc gRNA3 rep2


title: iAst, H1, untreated, rep1, L001


title: SupFig9 maize WTCasphi lc gRNA5 rep2


title: iAst, H3, treated, rep3, L001


title: iAst, H1, untreated, rep1, L002


title: iAst, H3, untreated, rep3, L002


title: Ctrl, rep 2

value: WT


title: SupFig9 maize WTCasphi lc gRNA3 rep1


title: Ctrl, rep 1


title: iAst, H3, untreated, rep3, L001


title: hbs-1RNASeqRep1

city: Santa Cruz

first: Joshua

last: Arribere

state: CA

address: 1156 High St

department: Department of Molecular, Cell, and Developmental Biology

institute: University of California at Santa Cruz

description:
ribo-depleted RNA
RNA-seq of unc-54(srf1004); hbs-1(srf0730) C. elegans

data_processing:
Reads were mapped to a custom C. elegans genome including annotated splice junctions using STAR v2.5.4b allowing for zero mismatches
All downstream analyses were restricted to uniquely mapping reads
Assembly: Ensembl, WBCel235
Supplementary files format and content: processed jam file containing uniquely-mapping reads with additional information pertaining to gene assignment

organism: Caenorhabditis elegans

growth_protocol: Animals were synchronized by hypochlorite treatment, propagated on NGM plates with OP50 at 16C, and harvested at the L4/young adult stage. Animals were washed off with N50, passed through a 5% sucrose cushion in N50 to remove E. coli, and snap frozen in liquid nitrogen.

extract_protocol:
Animals were lysed by grinding in a mortar and pestle cooled in liquid nitrogen in the presence of frozen PLB (20mM Tris pH8.0, 140mM KCl, 1.5mM MgCl2, 1% Triton). RNA was extracted by trizol.
RNA extracted, rRNA depleted by C. elegans-specific hybridization oligos, libraries  prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina sequencing

value: young adult

tag: Sex

value: hermaphrodite

value: whole body

tag: growth conditions

value: NGM + OP50


title: SupFig9 maize WTCasphi lc gRNA2 rep2


title: SupFig9 maize WTCasphi lc gRNA2 rep1


title: AS-5

city: Moscow

first: Ivan

middle: S

last: Kiselev

address: Ostrovitianov st. 1

country: Russia

institute: Pirogov Russian National Research Medical Universitty

description: secondary hypertrophied left ventricle sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Illumina iScan array scanner and standard software with recommended Illumina scanner setting

data_processing: ChAMP R package v. 3.14

source_name: heart left ventricle

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from left ventricle samples samples using Qiagen DNA Mini Kit according to standard instructions.

value: male

tag: age

value: AS


title: iAst, H3, treated, rep2, L002


title: iAst, H3, treated, rep2, L001


title: iAst, H3, untreated, rep2, L002


title: SupFig9 maize WTCasphi lc gRNA1 rep2

tag: tissue


title: iAst, H3, untreated, rep2, L001


title: znf-598RNASeqRep1

description:
ribo-depleted RNA
RNA-seq of unc-54(srf1004); znf-598(srf2119) C. elegans

tag: developmental stage


title: SupFig9 maize WTCasphi lc gRNA1 rep1

tag: target locus


title: nonu-1RNASeqRep1

description:
ribo-depleted RNA
RNA-seq of unc-54(srf1004); nonu-1(srf3015) C. elegans

tag: strain


title: iAst, H3, treated, rep1, L002

tag: cell type


title: iAst, H3, treated, rep1, L001

tag: disease state


title: SupFig9 maize WTCasphi lc gRNA11 rep2


title: wildtypeRNASeqRep1

description:
ribo-depleted RNA
RNA-seq of unc-54(srf1004) C. elegans

source_name: unc-54(srf1004) C. elegans


title: iAst, H3, untreated, rep1, L002

tag: cuatsm drug treatment


title: iAst, H3, untreated, rep1, L001


title: SupFig9 maize WTCasphi lc gRNA11 rep1


title: iAst, H2, treated, rep3, L002


title: iAst, H2, treated, rep3, L001


title: siHDAC3 rep2

city: Shanghai

first: Liangling

last: Shen

address: 389 Xincun Road

country: China

institute: Tongji Hospital, Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Helicoverpa armigera

source_name: whole worm

extract_protocol:
The whole worm flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole worm


title: iAst, H2, untreated, rep3, L002


title: siHDAC3 rep3


title: SupFig9 maize WTCasphi lc gRNA10 rep2


title: siHDAC3 rep1


title: iAst, H2, untreated, rep3, L001


title: SupFig9 maize WTCasphi lc gRNA10 rep1


title: HCM-8

description: primary hypertrophied left ventricle sample

value: female

value: HCM


title: iAst, H3, treated, rep3, L002

value: heatlhy control


title: iAst, H2, treated, rep2, L002

value: induced astrocytes


title: iAst, H2, treated, rep2, L001


title: siNC rep3


title: iAst, H2, untreated, rep2, L002


title: SupFig9 maize Casphi lc gRNA9, gRNA10, gRNA11 control


title: Ctrl, rep 3

value: breast cancer cells


title: iAst, H2, untreated, rep2, L001

value: untreated


title: siNC rep2


title: iAst, H2, treated, rep1, L002

value: treated


title: SupFig9 maize Casphi lc gRNA6, gRNA7, gRNA8 control

value: mysophyll protoplast


title: AS-3


title: iAst, H2, treated, rep1, L001


title: AS-4


title: HCM-7


title: AS-1


title: iAst, H2, untreated, rep1, L002


title: SupFig9 maize Casphi lc gRNA4, gRNA5 control

value: Lc


title: iAst, H2, untreated, rep1, L001


title: TM Rec7_7 met

city: Olomouc

first: Maciej

last: Majka

state: Please select a region, state or province.

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany AS CR

description:
AB 3730xL Genetic Analyzer
Rec7 part 7

data_processing:
Geneious Prime version 2020.2.4
Bisulfate sequencing reads obtained for forward and reverse primers were aligned and trimmed.
Assembly: Wheat Chinese Spring IWGSC RefSeq v1.0 genome assembly (2018)
Supplementary files format and content: FASTA format text files.

organism: Triticum timopheevii subsp. timopheevii

source_name: Second leaf

extract_protocol:
DNA was extracted from 100 mg lyophilized leaf segments disrupted with two 5 mm glass beads in sealed 96-well 2ml plates. Lysis was performed in 1 ml of lysis buffer at 65°C for 45 min. Subsequently, plates were centrifuged at 1300 × g for 10 min at 4°C. DNA purification was done at a Biomek® NXP automated workstation. A 100 µl of lysate was transferred to a new PCR plate and mixed with 70 µl of isopropanol and 5 µl of Agencourt® Genfind® v2 magnetic beads and incubated for 5 min at RT. Subsequent steps comprised 5 min incubation at the magnet, supernatant discarding, and three-time wash with 100 µl of 70% ethanol. Elution was done in 100 µl of H20 with 10 min incubation at RT and 10 min incubation at the magnet. Eluted DNA was transferred to a new PCR plate.
DNA methylation in the regions with recombination events was determined using the EZ DNA Methylation-Gold Kit (Zymo Research, USA). 400 ng of genomic DNA was bisulfite converted and purified according to the manufacturer's instruction (ver. 1.0.1). For amplification of the bisulfite converted DNA, a set of new primers was designed.
For amplification and sequencing of the Hotspot region part 1 after CT-conversion we used: Hot1_Met_F 5’-TTGTGTGTGTAGTTAGGTATAAAAAGT-3’ and Hot1_Met _R 5’-ACTTCTTCTCCATACATCCTAATC-3’
For amplification and sequencing of the Hotspot region part 2 after CT-conversion we used: Hot2_Met_F 5’- TTGTTTATTTTTTTTATTTAGTGT -3’ and Hot2_Met _R 5’-AAACRAATACCAAAATTTTTCATTCTCTAT-3’
For amplification and sequencing of the Hotspot region part 3 after CT-conversion we used: Hot3_Met_F 5’- TTAAATTTTTAAAGAAGATAAAGAGAG -3’ and Hot3_Met _R 5’- ATATTCCTCCATCACCATCACACTAC -3’
For amplification and sequencing of the Hotspot region part 4 after CT-conversion we used: Hot4_Met_F 5’- TAATAAGATGYGTTGGGTAGAGGTG -3’ and Hot4_Met _R 5’- CTTCTAAACRCCATTAAAAACTTCATTA -3’
For amplification and sequencing of the Rec7 region part 1 after CT-conversion we used: Rec7_1F_Met 5’- GAATGTTATTTGTTAGTAGA -3’ and Rec7_1R_Met 5’- AAACTAAAAACTTTAAAACTTATCAT -3’
For amplification and sequencing of the Rec7 region part 2 after CT-conversion we used: Rec7_2F_Met 5’- TAGTATGAAATATGATATGTTTTT -3’ and Rec7_2R_Met 5’- ATAAATACAACTCAACCAAC -3’
For amplification and sequencing of the Rec7 region part 3 after CT-conversion we used: Rec7_3F_Met 5’- AAAGATAGTAATAGAAGTAATAAGT -3’ and Rec7_3R_Met 5’- TAAAACCTTACAATCCAACA -3’
For amplification and sequencing of the Rec7 region part 4 after CT-conversion we used: Rec7_4F2_Met 5’- TTTGAGTTGTTGTTATAATT -3’ and Rec7_4R4_Met 5’- CTTCACCAACRACTCCAA -3’
For amplification and sequencing of the Rec7 region part 5 after CT-conversion we used: Rec7_5F4_Met 5’- ATTTAATAAAGTTTAGAGTTYG -3’ and Rec7_5R3_Met 5’- ACACCCRCCATACCTTAA -3’
For amplification and sequencing of the Rec7 region part 6 after CT-conversion we used: Rec7_6F_Met 5’- TTTGTTAAAAATTAAGGTATGG -3’ and Rec7_6R_Met 5’- ATATTTTCATACCTAAATCACATAAA -3’
For amplification and sequencing of the Rec7 region part 7 after CT-conversion we used: Rec7_7F_Met 5’- TGAAGAAAATTTTGAAAAATATGAA -3’ and Rec7_7R_Met 5’- ATTCCRACAATTTATTTTTA -3’

value: Second leaf


title: iAst, H4, treated, rep3, L002


title: HCM-6


title: siNC rep1


title: SupFig9 maize Casphi lc gRNA1, gRNA2, gRNA3 control


title: iAst, H4, treated, rep3, L001


title: TM Rec7_6 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 6


title: iAst, H4, untreated, rep3, L002


title: iAst, H4, untreated, rep3, L001


title: Repeat 2: BUD23 targetting shRNA - ribosome footprint RNA

city: Leeds

first: James

last: Murphy

state: West Yorkshire

address: Claredon Way

department: Faculty of Biological Sciences

country: United Kingdom

institute: University of Leeds

description:
kshv-RPFcounts-input4RiboRex.tsv
a8

data_processing:
Library strategy: Ribo-Seq
Raw sequencing data was demultiplexed and single-end sequencing quality control was assessed through FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). Both adapters and low-quality bases (QV < 20) were trimmed from reads’ extremities using Cutadapt (v3.2) with minimum read length of 25bp, and untrimmed outputs discarded for Ribo-Seq reads.
All libraries were mapped against Human hg38 rRNAs (Gencode v36) and tRNA sequences (GtRNAdb 18.1) using Bowtie2 v.2.3.4.2 (--sensitive-local -N1 -k1), and then removed using Samtools v1.9 with the -f 4 option.
STAR aligner with default parameters was used for alignments of each QC-processed library against both Human  and KSHV genomes, separately.
STAR-generated BAM output files were used for assigning read counts to CDS features in each genome with featureCounts, disregarding multi-mapper reads (not invoking -M option) and assigning reads to all overlapped features (invoking -O option).
Read counts’ tables generated by featureCounts for each organism were then used as input for differential translation (DT) analyses with RiboRex relying on the DeSeq2 negative binomial distribution model and a 0.05 FDR threshold. Both genome-aligned read count assessments were submitted to a multi-dimensional scaling analysis using the plotMDS function from the EdgeR package. Those tools were run under the R environment version 4.0.4.
Assembly: Human genome (Gencode v36 - GRCh38p13 primary assembly) and annotation file (Gencode v36 primary assembly gtf) and Kaposi’s sarcoma-associated herpesvirus genome (NCBI - GQ994935.1) and annotation file (KSHV 2.0 - Arias et al. 2014)
Supplementary files format and content: kshv-RNAcounts-input4RiboRex.tsv, kshv-RPFcounts-input4RiboRex.tsv

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: TREx BCBL1-Rta

growth_protocol: TREx BCBL1-Rta cells were grown in RPMI1640 growth medium with glutamine (Gibco®), supplemented with 10% foetal bovine serum (FBS, Gibco®), 1% penicillin-streptomycin (Gibco®) and 100 mg/mL hygromycin B (Thermo Scientific) at 37°C in 5% CO2.

extract_protocol:
Cells were treated with cycloheximide (Sigma) at 100 μg/ml for 3 min at 37°C. A total of ∼50 × 10^6 cells were pelleted and washed (1 x PBS, 100 μg/ml cycloheximide) then lysed in ice cold buffer [50 mM Tris-HCl pH8, 150 mM NaCl, 10mM MgCl2, 1 mM DTT, 1% IGEPAL, 100 μg/ml cycloheximide, Turbo DNase 24 U/mL (Invitrogen), RNasin Plus RNase Inhibitor 90 U (Promega), 1 × protease inhibitor cocktail (Roche)] for 45 minutes. Lysates were clarified by centrifugation (12,000 × g, 10 min, 4°C) and 20% saved as a total mRNA input for downstream processing and analysis. The resulting supernatants were applied to continuous sucrose gradients of either 5% − 45% or GFP-ORF11 lysates applied to 5% − 30% (10 mM MgCl2, 50 mM Tris/HCl (pH 7.6), 150 mM NaCl, 1 mM DTT, 100 μg/ml cycloheximide and 1× protease inhibitor cocktail). Gradients were then subjected to ultracentrifugation (121,355 × g 3.5h, 4°C) in SW-40 rotor. Fractions from each gradient were collected using a Gradient Fractionator (BioComp) and the RNA profile was measured by absorbance (254 nm) across the gradient in real time using an EM-1 Econo UV Monitor (Bio-Rad). Total nucleic acid was extracted from input samples using TRIzol™ LS (Invitrogen™), as described by the manufacturer. Sucrose fractions containing 80S and polysome ribosomes were used for poly-ribo-seq. Fractions for each sample were pooled and diluted (100 mM Tris/HCl (pH 7.6), 30 mM NaCl and 10 mM MgCl2) to a 10% sucrose concentration and ribosomes footprinted with 1 U/1×10^6 cells RNase I (Thermo Fischer), rotating overnight at 4°C. The reaction was stopped with SuperRNaseIN (200U/gradient, Thermo Fischer), rotating for 5 minutes at room temperature. Sucrose samples were concentrated with 30 kDa cut off filter units (Millipore) and loaded onto 5% − 45% sucrose gradients. Gradients were processed as described above and just the 80S fraction collected containing footprinted ribosomes and the RNA precipitated 1:1 isopropanol, 300 mM NaCl and glycoblue, overnight at -80°C. Fractions for each were pooled through resuspension in 100 μl Nuclease-Free Water, and the same done for the mRNA input samples. Samples were treated with TURBO DNase (Thermo Fischer) according to manufacturer’s instructions and the RNA purified with TRIzol™ LS (Invitrogen™), as described by the manufacture. PolyA RNA was selected from input mRNA samples using a Dynabeads™ mRNA DIRECT™ Purification Kit (Invitrogen™), according to manufacturer’s instructions and the RNA fragmented in 2 mM EDTA, 10mM Na2CO3 and 90mM NaHCO3 for 20 minutes at 95°C. 28–34 nt ribosome footprints and 50-80 nt polyA RNA samples were gel purified in 10% (w/v) polyacrylamide-TBE-urea gel at 300 V for 3.5 h in 1X TBE. Fragment ends were repaired using T4 PNK treatment (New England Biolabs) as described by the manufacturer. Ribosome footprints were subjected to rRNA depletion using a NEBNext® rRNA depletion kit (New England Biolabs) according to the manufacturers protocol.
The NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs) was used to generate the libraries for next generation sequencing. Resulting cDNA was PCR amplified and gel purified prior to sequencing.

treatment_protocol: Lytic replication of KSHV induced using 2 mg/mL doxycycline hyclate (Sigma-Aldrich) 36 hours prior to sample collection.

value: TREx BCBL1-Rta

value: Stably expressing a shRNA targetting BUD23

tag: time

value: 36 hours post KSHV lytic induction

tag: rna fraction

value: Ribosome footprint RNA


title: iAst, H4, treated, rep2, L002


title: TM Rec7_5 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 5


title: AS-2

value: male


title: HCM-4


title: TM Rec7_4 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 4


title: iAst, H4, treated, rep2, L001


title: HCM-5


title: iAst, H4, untreated, rep2, L002


title: Repeat 2: Scrambled shRNA - ribosome footprint RNA

description:
kshv-RPFcounts-input4RiboRex.tsv
a7

value: Stably expressing a scrambled control shRNA


title: Repeat 2: BUD23 targetting shRNA - polyA RNA

description:
kshv-RNAcounts-input4RiboRex.tsv
a6

data_processing:
Raw sequencing data was demultiplexed and single-end sequencing quality control was assessed through FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). Both adapters and low-quality bases (QV < 20) were trimmed from reads’ extremities using Cutadapt (v3.2) with minimum read length of 25bp, and untrimmed outputs discarded for Ribo-Seq reads.
All libraries were mapped against Human hg38 rRNAs (Gencode v36) and tRNA sequences (GtRNAdb 18.1) using Bowtie2 v.2.3.4.2 (--sensitive-local -N1 -k1), and then removed using Samtools v1.9 with the -f 4 option.
STAR aligner with default parameters was used for alignments of each QC-processed library against both Human  and KSHV genomes, separately.
STAR-generated BAM output files were used for assigning read counts to CDS features in each genome with featureCounts, disregarding multi-mapper reads (not invoking -M option) and assigning reads to all overlapped features (invoking -O option).
Read counts’ tables generated by featureCounts for each organism were then used as input for differential translation (DT) analyses with RiboRex relying on the DeSeq2 negative binomial distribution model and a 0.05 FDR threshold. Both genome-aligned read count assessments were submitted to a multi-dimensional scaling analysis using the plotMDS function from the EdgeR package. Those tools were run under the R environment version 4.0.4.
Assembly: Human genome (Gencode v36 - GRCh38p13 primary assembly) and annotation file (Gencode v36 primary assembly gtf) and Kaposi’s sarcoma-associated herpesvirus genome (NCBI - GQ994935.1) and annotation file (KSHV 2.0 - Arias et al. 2014)
Supplementary files format and content: kshv-RNAcounts-input4RiboRex.tsv, kshv-RPFcounts-input4RiboRex.tsv

value: polyA RNA


title: iAst, H4, untreated, rep2, L001


title: TM Rec7_3 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 3


title: Repeat 2: Scrambled shRNA - polyA RNA

description:
kshv-RNAcounts-input4RiboRex.tsv
a5


title: iAst, H4, treated, rep1, L001


title: TM Rec7_2 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 2


title: iAst, H4, untreated, rep1, L001


title: HCM-2


title: Repeat 1: BUD23 targetting shRNA - ribosome footprint RNA

description:
kshv-RPFcounts-input4RiboRex.tsv
a4


title: iAst, H4, untreated, rep1, L002


title: Repeat 1: Scrambled shRNA - ribosome footprint RNA

description:
kshv-RPFcounts-input4RiboRex.tsv
a3


title: rdr6 vCasphi U6PDS3gR10 line2 T2 transgene-free albino seedling

data_processing:
Amplicon sequencing:  Reads were first quality and adaptor trimmed using Trim Galore and then mapped to the target genomic region by the BWA aligner. Sorted and indexed bam files were used as input files for further analysis by the CrispRvariants R package. Each mutation pattern with corresponding read counts was exported by the CrispRvariants R package. After assessing all control samples, a criterion to classify reads as edited reads was established: only reads with a >= 3 bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 100 read counts from a sample were counted as edited reads. This criterion is established due to the observation of 1 bp indels and occasionally 2 bp indels with read numbers >100 in control samples. Also, larger indels that occur at very low frequencies (much lower than 100 reads) were observed in control samples. These observations indicate that occasional PCR inaccuracy and low-quality sequencing in a small fraction of reads can result in the indel patterns with corresponding read number ranges as stated above in control samples with the typical sequencing depth in our experiments (1-5 million reads/sample). By employing such stringent criteria, it is believed that the editing signals counted are true signals indicating editing events. Additionally, for FWA gRNA5 and gRNA6 targeted regions, there are long stretches of adenines near these target regions. Due to the high error rate of polymerases amplifying long stretches of adenines, reads with indels only within these stretches of adenines were not counted as true deletions. For amplicon sequencing result analysis of maize protoplast, the criterion to classify reads as edited reads was established: only reads with a >= 3bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 10 read counts from a sample were counted as edited reads. The adjustment of the criterion was based on the fact that these amplicon sequencing was of less depth (performed by the iSeq 100) compared to the amplicon libraries of Arabidopsis protoplasts.
Whole genome sequencing for off-target analysis: For variant calling, whole genome sequencing reads were aligned to the TAIR10 reference genome using BWA mem (v0.7.17)53 with default parameters. GATK (4.2.0.0)39 MarkDuplicatesSpark was used to remove PCR duplicate reads. Then GATK HaplotypeCaller was used to call raw variants. Raw SNPs were filtered with QD < 2.0, FS > 60.0, MQ < 40.0, and SOR > 4.0. Raw InDels were filtered with QD < 2.0, FS > 200.0, and SOR > 10.0 and used for base quality score recalibration. The recalibrated bam file was further applied to GATK and Strelka (v2.9.2)40 for SNPs/InDel calling. Only SNPs/InDels called by both GATK and Strelka were used for further analysis. The intersection of GATK and Strelka  SNPs/InDels were filtered by removing identical SNPs/InDels in the rdr6-15 background by BedTools (v2.26.0)54. Variants with coverage lower than 30 reads were removed. Variant loci at which the ratio of the reads with the WT allele over the reads with variant allele larger than three were removed. For heterozygous alleles, at a coverage level of 30 reads, the chance of observing WT reads /mutation allele reads >3 is 0.26% (binomial distribution, one-tailed P=0.0026).
Assembly: tair10
Supplementary files format and content: Crispvariant_result, with detected SNV and indels in amplicon sequencing  vcf, raw variants called with GATK or strelka2 comparing to tair10 reference genome sequence
Library strategy: whole genome sequencing

organism: Arabidopsis thaliana

source_name: Arabidopsis whole seedling

value: whole seedling

value: 14 days

tag: background genotype


title: rdr6 vCasphi U6PDS3gR10 line3 T2 transgene-free albino seedling


title: TM Rec7_1 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 1


title: TM Hot4 met

description:
AB 3730xL Genetic Analyzer
H1 part 4


title: rdr6 vCasphi U6PDS3gR10 line1 T2 transgene-free albino seedling


title: HCM-3

value: HCM


title: HCM-1


title: rdr6 control seedling 4


title: Repeat 1: BUD23 targetting shRNA - polyA RNA

description:
kshv-RNAcounts-input4RiboRex.tsv
a2


title: TM Hot3 met

description:
AB 3730xL Genetic Analyzer
H1 part 3


title: Repeat 1: Scrambled shRNA - polyA RNA

description:
kshv-RNAcounts-input4RiboRex.tsv
a1


title: TM Hot2 met

description:
AB 3730xL Genetic Analyzer
H1 part 2


title: rdr6 control seedling 1


title: rdr6 control seedling 2


title: rdr6 nCasphi U6PDS3gR10 line3 T2 transgene-free albino seedling


title: TM Hot1 met

description:
AB 3730xL Genetic Analyzer
H1 part 1


title: rdr6 nCasphi U6PDS3gR10 line1 T2 transgene-free albino seedling


title: iAst, H4, treated, rep1, L002

value: induced astrocytes

value: heatlhy control


title: pdac_ff_057

type: RNA

city: Rotterdam

first: Willem

last: de Koning

state: Zuid-Holland

address: Doctor Molewaterplein 40

institute: Erasmus University Medical Center

hyb_protocol: For each sample, 200 ng of RNA was hybridized with the PanCancer Immune Profiling probes for 17 hours at 65⁰C, following the manufacturing procedure (NanoString Technologies Inc., Seattle, WA, USA).

scan_protocol: The nCounter FLEX platform was used and genes were counted by scanning 490 Fields-of-view (FOV).

data_processing: Data analysis was performed using the advanced analysis module (version 2.0) of nSolver software (version 4.0, NanoString Technology).

source_name: pdac

extract_protocol: Fresh Frozen (FF) tumor samples of the included PDAC patients were sectioned with 5 μM thickness, stained with hematoxylin and eosin (H&E), and examined by a pathologist who highlighted the location of the tumor-rich areas. Each sample was then further sectioned, and a total of 60 μM was used for RNA isolation using the Fresh Frozen Micro Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. The quality and quantity of RNA samples were examined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA). RNA concentration was corrected to include the proportion of the sample that was >300 base pairs.

tag: short/long

value: Short

tag: age at surgery

value: Male

tag: tumor location

value: Head

tag: operation procedure

value: Whipple

tag: tumor differentiation

value: Poor

tag: lymph node metastasis

value: Yes

tag: margin status

tag: t-stage

tag: sii

tag: adjuvant systemic therapy

value: No

tag: cea (ng/ml)


title: pdac_ff_056

value: Female


title: primary human oral keratinocytes_24_h_rep3

first: Yiting

last: Guo

address: 399 Middle Yanchang Road

institute: Tongji University

data_processing:
Data quality was assessed, gene annotation was performed for the obtained sequences, and the reads count of each gene was calculated using HTSeq software.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: oral cavity

growth_protocol: The primary human oral keratinocytes were cultured in Dulbecco's modified Eagle's medium (DMEM; GIBCO, USA) supplemented with 10% fetal bovine serum (FBS; GIBCO) in a humidified atmosphere with 5% CO2 and 95% air at 37°C.

extract_protocol:
The cells were lysed with Trizol to obtain total RNA and verification for purity and integrity of total RNA was conducted
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Sample RNA was segmented, the segmented RNA was reverse-transcribed to generate double-stranded DNA, and the double-stranded DNA ends were processed for PCR amplification.
The products amplified by PCR were terminologically denatured to form single strands, which were cycled and a single strand circular DNA library was established.
High-throughput transcriptome sequencing was performed with Illumina Nova6000 sequencing platform for the DNA library, and the original data of transcriptome sequencing was finally obtained.

treatment_protocol: Replaced the old medium with serum-free DMEM medium, for each group added 10 μL bacteria suspension, so that the MOI was 10, co-cultured for 4 h or 24 h at 37 ℃ and 5% CO2.

tag: tissue

value: oral mucosa

tag: cell line

value: primary human oral keratinocytes

tag: cell type

value: keratinocytes

tag: genotype

value: WT

tag: treatment

value: co-cultured with Prevotella melaninogenica for 24 h in MOI=10


title: TemperatureTest protoplast incubate without 37 Celsius pulse PDS3gR10

source_name: Arabidopsis mesophyll protoplast

value: mysophyll protoplast

tag: developmental stage

value: 3-4 weeks

tag: strain

tag: background genotype

value: wild type

tag: target locus


title: TemperatureTest protoplast incubate with 37 Celsius pulse PDS3gR10


title: SupFig6A fwa protoplast vCasphi RNP scramble gRNA control for FWAgR6

value: FWA


title: SupFig6A fwa protoplast vCasphi RNP scramble gRNA control for FWAgR4


title: primary human oral keratinocytes_24_h_rep2


title: primary human oral keratinocytes_24_h_rep1


title: pdac_ff_055

tag: short/long

value: Short

tag: age at surgery

tag: tumor location

tag: operation procedure


title: primary human oral keratinocytes_4_h_rep3

value: co-cultured with Prevotella melaninogenica for 4 h in MOI=10


title: SupFig6A fwa protoplast vCasphi RNP scramble gRNA control for FWAgR1


title: SupFig6A fwa protoplast vCasphi RNP scramble gRNA control for FWAgR5


title: pdac_ff_053

value: Head

tag: tumor differentiation

value: Moderate

tag: lymph node metastasis

tag: margin status

tag: t-stage


title: primary human oral keratinocytes_4_h_rep2

tag: tissue


title: SupFig6A fwa protoplast vCasphi RNP FWAgR6 rep4


title: pdac_ff_052

value: Male

value: Whipple

tag: adjuvant systemic therapy

tag: cea (ng/ml)


title: SupFig6A fwa protoplast vCasphi RNP FWAgR6 rep3


title: SupFig6A fwa protoplast vCasphi RNP FWAgR6 rep1


title: rdr6 control seedling 3

value: whole seedling

value: 14 days


title: SupFig6A fwa protoplast vCasphi RNP FWAgR6 rep2


title: pdac_ff_049

value: Long

value: Body

value: No

tag: sii

value: Yes


title: primary human oral keratinocytes_4_h_rep1

value: oral mucosa

tag: cell line

value: primary human oral keratinocytes

tag: cell type

value: keratinocytes

tag: genotype

value: WT

tag: treatment


title: rdr6 nCasphi U6PDS3gR10 line2 T2 transgene-free albino seedling

tag: developmental stage

tag: strain

tag: background genotype


title: SupFig6A fwa protoplast vCasphi RNP FWAgR5 rep4

value: mysophyll protoplast

value: 3-4 weeks

tag: target locus

value: FWA


title: SupFig6A fwa protoplast vCasphi RNP FWAgR5 rep3


title: SupFig6A fwa protoplast vCasphi RNP FWAgR5 rep2


title: primary human oral keratinocytes_control group_rep3

value: no treatment


title: pdac_ff_048

tag: short/long

value: Short

tag: age at surgery

tag: tumor location

value: Head

tag: operation procedure

value: Poor


title: primary human oral keratinocytes_control group_rep2


title: SupFig6A fwa protoplast vCasphi RNP FWAgR4 rep4


title: SupFig6A fwa protoplast vCasphi RNP FWAgR5 rep1


title: primary human oral keratinocytes_control group_rep1


title: pdac_ff_050

value: Female

value: Whipple

tag: tumor differentiation

tag: lymph node metastasis

tag: margin status

tag: t-stage


title: SupFig6A fwa protoplast vCasphi RNP FWAgR4 rep3

tag: tissue


title: P24_TN

city: New York City

first: Syed

middle: M. Shoiab

last: Bukhari

state: New York

department: Medicine

institute: Columbia University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
The GEX, FB and HTO libraries were sequenced on the NovaSeq 6000 100cycle kit with sequencing parameters 28x8x60
Assembly: not provided
Supplementary files format and content: Tab-separated values files and matrix file

source_name: Blood

extract_protocol:
We used RosetteSep T cell enrichment kit (StemCell) to isolate untouched CD3 T cells. Each sample was washed once with RPMI and 3 times with PBS + 2% BSA before labeling and pooling. Specimens were then filtered through 70 um strainers (Fisher). Cell concentration, singularity, and viability were confirmed with a hematocytometer before submission for scRNA-Seq (10X Genomics).
This experiment was done using the Chromium Single Cell V(D)J Reagent Kits (v1 Chemistry) AKA 5'

value: Human T cells

value: Blood

tag: disease

value: No irAE

tag: condition

value: Baseline


title: SupFig6A fwa protoplast vCasphi RNP FWAgR4 rep1


title: SupFig6A fwa protoplast vCasphi RNP FWAgR1 rep3


title: SupFig6A fwa protoplast vCasphi RNP FWAgR1 rep4


title: pdac_ff_047

value: Yes

tag: adjuvant systemic therapy

value: No

tag: cea (ng/ml)


title: SupFig6A fwa protoplast vCasphi RNP FWAgR1 rep1

tag: developmental stage


title: P24_T

description: 10x Genomics

tag: cell type

value: On treatment


title: SupFig6A fwa protoplast nCasphi RNP scramble gRNA control for FWAgR5

tag: strain

tag: background genotype


title: SupFig6A fwa protoplast vCasphi RNP FWAgR4 rep2

tag: target locus


title: SupFig6A fwa protoplast vCasphi RNP FWAgR1 rep2


title: P22_TN

description: 10x Genomics


title: SupFig6A fwa protoplast nCasphi RNP scramble gRNA control for FWAgR6


title: P23_T

description: 10x Genomics


title: SupFig6A fwa protoplast nCasphi RNP scramble gRNA control for FWAgR1


title: pdac_ff_023

tag: short/long

value: Long

tag: age at surgery

value: Tail

value: Distal pancreatecomy+splenectomy

value: Moderate


title: SupFig6A fwa protoplast nCasphi RNP FWAgR6 rep2

value: mysophyll protoplast

value: 3-4 weeks

value: FWA


title: SupFig6A fwa protoplast nCasphi RNP FWAgR6 rep4


title: SupFig6A fwa protoplast nCasphi RNP scramble gRNA control for FWAgR4


title: pdac_ff_038

value: Short

tag: tumor location

value: Body

tag: operation procedure

tag: sii


title: SupFig6A fwa protoplast nCasphi RNP FWAgR6 rep3


title: pdac_ff_024

value: Female

value: Head

value: Whipple

tag: tumor differentiation

tag: lymph node metastasis

tag: margin status


title: pdac_ff_018

value: Good

tag: t-stage


title: pdac_ff_020


title: SupFig6A fwa protoplast nCasphi RNP FWAgR5 rep4

tag: tissue


title: pdac_ff_021

value: Male

tag: adjuvant systemic therapy


title: P21_T

description: 10x Genomics

value: Human T cells

value: Blood

tag: disease

value: No irAE

tag: condition


title: pdac_ff_035

value: Poor

value: Yes

value: No

tag: cea (ng/ml)


title: P22_T

description: 10x Genomics

tag: cell type

value: On treatment


title: P20_TN

description: 10x Genomics

value: Baseline


title: SupFig6A fwa protoplast nCasphi RNP FWAgR6 rep1

value: mysophyll protoplast

tag: developmental stage

value: 3-4 weeks

tag: strain

tag: background genotype


title: P21_TN

description: 10x Genomics


title: pdac_ff_017

tag: short/long

value: Long

tag: age at surgery

value: Moderate


title: P23_TN

description: 10x Genomics


title: SupFig6A fwa protoplast nCasphi RNP FWAgR4 rep3

tag: target locus

value: FWA


title: pdac_ff_011

tag: tumor location

value: Tail

tag: operation procedure

value: Distal pancreatecomy+splenectomy

tag: sii


title: SupFig6A fwa protoplast nCasphi RNP FWAgR5 rep3


title: SupFig6A fwa protoplast nCasphi RNP FWAgR5 rep2


title: SupFig6A fwa protoplast nCasphi RNP FWAgR4 rep1


title: pdac_ff_013

value: Female

value: Head

value: Whipple

tag: tumor differentiation

tag: lymph node metastasis

tag: margin status


title: MC38 tumor, PB-020+anti-PD-1_2

city: Hangzhou

first: Yingjie

last: Wang

state: Zhejiang

address: Research Center C701,School of Medicine,Zhejiang University,866 Yuhangtang Road

department: Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine

institute: Zhejiang University

data_processing:
Raw reads mapped to genome by HISAT
and mapped to single gene by Bowtie2
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited xls file include FPKM values for each Sample ...

source_name: MC38 tumor

growth_protocol: MC38 cells were injected subcutaneously to C57BL/6 mice to form tumor

extract_protocol:
grind in liquid nitrogen
BGI protocol

treatment_protocol: After tumor formation, mice were randomly divided into four groups and treated with vhicle, PB-020, anti-PD-1 and PB-020+anti-PD-1

tag: treatment

tag: tissue

value: MC38 tumor


title: P16_T

description: 10x Genomics

value: Human T cells

value: Blood

tag: disease

value: Colitis/ Neurotoxicity

tag: condition


title: P16_TN

description: 10x Genomics

tag: cell type


title: SupFig6A fwa protoplast nCasphi RNP FWAgR5 rep1

tag: developmental stage


title: SupFig6A fwa protoplast nCasphi RNP FWAgR1 rep1

tag: strain


title: SupFig6A fwa protoplast nCasphi RNP FWAgR4 rep4

tag: background genotype


title: P15_TN

description: 10x Genomics

value: Thyroiditis/ Neurotoxicity / Nephritis


title: MC38 tumor, PB-020+anti-PD-1_3


title: P20_T

description: 10x Genomics

value: No irAE

value: On treatment


title: SupFig6A fwa protoplast WTCasphi RNP scramble gRNA control for FWAgR5

value: mysophyll protoplast


title: SupFig6A fwa protoplast nCasphi RNP FWAgR4 rep2

value: 3-4 weeks


title: SupFig6A fwa protoplast nCasphi RNP FWAgR1 rep4


title: SupFig6A fwa protoplast nCasphi RNP FWAgR1 rep3


title: MC38 tumor, PB-020+anti-PD-1_1


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR6 rep4


title: P15_T

description: 10x Genomics

value: Thyroiditis/ Neurotoxicity/ Nephritis


title: pdac_ff_016

tag: short/long

value: Long

value: Male

value: Poor

value: No

tag: t-stage

tag: adjuvant systemic therapy

tag: cea (ng/ml)


title: MC38 tumor, anti-PD-1_3


title: SupFig6A fwa protoplast nCasphi RNP FWAgR1 rep2

tag: target locus

value: FWA


title: MC38 tumor, anti-PD-1_1


title: SupFig6A fwa protoplast WTCasphi RNP scramble gRNA control for FWAgR4


title: MC38 tumor, PB-020_3


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR6 rep2


title: MC38 tumor, anti-PD-1_2


title: P14_T

description: 10x Genomics

value: Pneumonitis


title: SupFig6A fwa protoplast WTCasphi RNP scramble gRNA control for FWAgR1


title: P14_TN

description: 10x Genomics

value: Baseline


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR6 rep3


title: SupFig6A fwa protoplast WTCasphi RNP scramble gRNAcontrol for FWAgR6


title: MC38 tumor, PB-020_2

value: MC38 tumor


title: P13_T

description: 10x Genomics

value: Human T cells


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR5 rep2


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR5 rep3


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR5 rep4


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR4 rep3


title: MC38 tumor, PB-020_1


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR4 rep4


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR4 rep2


title: P12_TN

description: 10x Genomics

value: Blood


title: MC38 tumor, CK_1

value: CK


title: P13_TN

description: 10x Genomics


title: MC38 tumor, CK_2


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR4 rep1


title: P12_T

description: 10x Genomics


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR1 rep4


title: P6_TN

description: 10x Genomics

value: Thyroiditis/ Nephritis


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR1 rep1


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR1 rep2


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR6 rep1


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR1 rep3


title: P19_TN

description: 10x Genomics

value: No irAE


title: SupFig6A fwa protoplast WTCasphi RNP FWAgR5 rep1


title: SupFig6A WT protoplast vCasphi RNP scramble gRNA control for PDS3gR8

value: wild type


title: P6_T

description: 10x Genomics

value: On treatment


title: P19_T

description: 10x Genomics


title: MC38 tumor, CK_3


title: SupFig6A WT protoplast vCasphi RNP PDS3gR8 rep3

value: mysophyll protoplast

value: 3-4 weeks


title: SupFig6A WT protoplast vCasphi RNP scramble gRNA control for PDS3gR10


title: KLF5 treat_3

city: shijiazhuang

first: Xinhua

last: Zhang

state: Hebei

address: ZhongshanRoad NO.361

department: Biochemistry and Molecular Biology

institute: Hebei Medical University

description: circRNA expression KLF5 treat_3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: KLF5 treat_3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the  RNA Purification kit (Tiangen, China) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: smooth muscle cells

tag: treat


title: SupFig6A WT protoplast vCasphi RNP PDS3gR8 rep2


title: P18_TN

description: 10x Genomics


title: P18_T

description: 10x Genomics


title: SupFig6A WT protoplast vCasphi RNP PDS3gR10 rep4


title: SupFig6A WT protoplast vCasphi RNP PDS3gR10 rep2


title: P11_TN

description: 10x Genomics


title: SupFig6A WT protoplast vCasphi RNP PDS3gR10 rep1


title: P10_TN

description: 10x Genomics


title: KLF5 treat_1

description: circRNA expression KLF5 treat_1

source_name: KLF5 treat_1


title: KLF5 treat_2

description: circRNA expression KLF5 treat_2

source_name: KLF5 treat_2


title: P10_T

description: 10x Genomics


title: SupFig6A WT protoplast nCasphi RNP PDS3gR8 rep4


title: SupFig6A WT protoplast nCasphi RNP scramble gRNA control for PDS3gR10


title: SupFig6A WT protoplast nCasphi RNP scramble gRNA control for PDS3gR8


title: KLF4 treat_1

description: circRNA expression KLF4 treat_1

source_name: KLF4 treat_1


title: KLF4 treat_2

description: circRNA expression KLF4 treat_2

source_name: KLF4 treat_2


title: SupFig6A WT protoplast nCasphi RNP PDS3gR8 rep2


title: KLF4 treat_3

description: circRNA expression KLF4 treat_3

source_name: KLF4 treat_3


title: SupFig6A WT protoplast nCasphi RNP PDS3gR8 rep1


title: SupFig6A WT protoplast vCasphi RNP PDS3gR8 rep4


title: P9_TN

description: 10x Genomics


title: SupFig6A WT protoplast vCasphi RNP PDS3gR8 rep1


title: P11_T

description: 10x Genomics


title: SupFig6A WT protoplast nCasphi RNP PDS3gR10 rep4


title: GFPtreat_2

description: circRNA expression GFPtreat_2

value: GFP


title: SupFig6A WT protoplast nCasphi RNP PDS3gR10 rep1


title: GFPtreat_1

description: circRNA expression GFPtreat_1


title: GFPtreat_3

description: circRNA expression GFPtreat_3


title: SupFig6A WT protoplast nCasphi RNP PDS3gR10 rep2


title: SupFig6A WT protoplast nCasphi RNP PDS3gR8 rep3


title: P9_T

description: 10x Genomics


title: SupFig6A WT protoplast WTCasphi RNP scramble gRNA control for PDS3gR8


title: control2

description: circRNA expression control2

value: control


title: P8_TN

description: 10x Genomics


title: SupFig6A WT protoplast WTCasphi RNP scramble gRNA control for PDS3gR10


title: P3_T

description: 10x Genomics

value: Arthritis


title: SupFig6A WT protoplast WTCasphi RNP PDS3gR8 rep2


title: SupFig6A WT protoplast WTCasphi RNP PDS3gR10 rep4


title: SupFig6A WT protoplast WTCasphi RNP PDS3gR10 rep3


title: control1

description: circRNA expression control1


title: SupFig6A WT protoplast WTCasphi RNP PDS3gR10 rep2


title: P8_T

description: 10x Genomics


title: P3_TN

description: 10x Genomics


title: SupFig6A WT protoplast nCasphi RNP PDS3gR10 rep3


title: Chern_City_128

city: Bethesda

first: Alexander

middle: Christian

last: Harris

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

organism: Canis lupus familiaris

source_name: Whole Blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: location

value: Chernobyl City

value: Whole Blood

tag: breed

value: Mixed Breed


title: Chern_City_127


title: SupFig6A WT protoplast WTCasphi RNP PDS3gR8 rep1

data_processing:
Amplicon sequencing:  Reads were first quality and adaptor trimmed using Trim Galore and then mapped to the target genomic region by the BWA aligner. Sorted and indexed bam files were used as input files for further analysis by the CrispRvariants R package. Each mutation pattern with corresponding read counts was exported by the CrispRvariants R package. After assessing all control samples, a criterion to classify reads as edited reads was established: only reads with a >= 3 bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 100 read counts from a sample were counted as edited reads. This criterion is established due to the observation of 1 bp indels and occasionally 2 bp indels with read numbers >100 in control samples. Also, larger indels that occur at very low frequencies (much lower than 100 reads) were observed in control samples. These observations indicate that occasional PCR inaccuracy and low-quality sequencing in a small fraction of reads can result in the indel patterns with corresponding read number ranges as stated above in control samples with the typical sequencing depth in our experiments (1-5 million reads/sample). By employing such stringent criteria, it is believed that the editing signals counted are true signals indicating editing events. Additionally, for FWA gRNA5 and gRNA6 targeted regions, there are long stretches of adenines near these target regions. Due to the high error rate of polymerases amplifying long stretches of adenines, reads with indels only within these stretches of adenines were not counted as true deletions. For amplicon sequencing result analysis of maize protoplast, the criterion to classify reads as edited reads was established: only reads with a >= 3bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 10 read counts from a sample were counted as edited reads. The adjustment of the criterion was based on the fact that these amplicon sequencing was of less depth (performed by the iSeq 100) compared to the amplicon libraries of Arabidopsis protoplasts.
Whole genome sequencing for off-target analysis: For variant calling, whole genome sequencing reads were aligned to the TAIR10 reference genome using BWA mem (v0.7.17)53 with default parameters. GATK (4.2.0.0)39 MarkDuplicatesSpark was used to remove PCR duplicate reads. Then GATK HaplotypeCaller was used to call raw variants. Raw SNPs were filtered with QD < 2.0, FS > 60.0, MQ < 40.0, and SOR > 4.0. Raw InDels were filtered with QD < 2.0, FS > 200.0, and SOR > 10.0 and used for base quality score recalibration. The recalibrated bam file was further applied to GATK and Strelka (v2.9.2)40 for SNPs/InDel calling. Only SNPs/InDels called by both GATK and Strelka were used for further analysis. The intersection of GATK and Strelka  SNPs/InDels were filtered by removing identical SNPs/InDels in the rdr6-15 background by BedTools (v2.26.0)54. Variants with coverage lower than 30 reads were removed. Variant loci at which the ratio of the reads with the WT allele over the reads with variant allele larger than three were removed. For heterozygous alleles, at a coverage level of 30 reads, the chance of observing WT reads /mutation allele reads >3 is 0.26% (binomial distribution, one-tailed P=0.0026).
Assembly: tair10
Supplementary files format and content: Crispvariant_result, with detected SNV and indels in amplicon sequencing  vcf, raw variants called with GATK or strelka2 comparing to tair10 reference genome sequence
Library strategy: amplicon sequencing


title: SupFig6A WT protoplast WTCasphi RNP PDS3gR8 rep3


title: P7_TN

description: 10x Genomics

value: Baseline


title: Chern_City_124


title: Chern_City_123


title: P17_TN

description: 10x Genomics

value: Human T cells


title: Chern_City_126


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 07

source_name: Arabidopsis leaf tissue

value: leaf tissue


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 08


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 06


title: SupFig6A WT protoplast WTCasphi RNP PDS3gR10 rep1


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 05


title: P5_T

description: 10x Genomics

value: Blood

value: Thyroiditis


title: Chern_City_121


title: P17_T

description: 10x Genomics

value: No irAE


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 09


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 12


title: Chern_City_125


title: SupFig6A WT protoplast WTCasphi RNP PDS3gR8 rep4

value: wild type


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 11


title: Chern_City_129


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 10


title: SupFig3D 28 Celsius rdr6 background version1 T1 plant 07


title: SupFig3D 28 Celsius rdr6 background version1 T1 plant 09


title: P7_T

description: 10x Genomics

value: On treatment


title: SupFig3D 28 Celsius rdr6 background version1 T1 plant 06


title: P5_TN

description: 10x Genomics


title: Chern_City_120


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 03


title: SupFig3D 28 Celsius rdr6 background version1 T1 plant 05


title: P4_TN

description: 10x Genomics


title: P1_TN

description: 10x Genomics


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 04


title: SupFig3D 28 Celsius rdr6 background version1 T1 plant 10


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 01


title: Chern_City_122


title: P4_T

description: 10x Genomics


title: Chern_City_118


title: SupFig3D 28 Celsius rdr6 background version1 T1 plant 04


title: Chern_City_119


title: P2_T

description: 10x Genomics


title: SupFig3D 28 Celsius rdr6 background version1 T1 plant 01


title: SupFig3D 28 Celsius rdr6 background version2 T1 plant 02


title: SupFig3C 28 Celsius WT background version2 T1 plant 10


title: Rh4_PAX3-FOXO1-FKBP cells PRO-seq_dTAG4hr_rep4

first: Susu

address: 360 Longwood Ave, LC6102

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Adaptors were trimmed and short/low quality sequence filtered by Trimmomatic-0.32: ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15 MINLEN:15
Reverse complement sequence was generated using fastx_reverse_complement from the FASTX toolkit(v 0.0.13)
Reverse complement sequences were aligned to the human genome (hg19)+ S2 genome  using bowtie2 (v2.2.2)
samtools -view  generated .bam file with hg19 chromosomes
Differential transcript analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - pause_PROseq.pl with DESeq normalization
Differential eRNA analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - eRNA.pl
Assembly: hg19
Supplementary files format and content: Homer-generated bedgraph files, differential gene transcription analysis generated by NRSA
Library strategy: PRO-seq

source_name: Rh4 cell line

growth_protocol: Cells were cultured in RPMI-1640 containing 10% FetalPlex and supplemented with 1% L-Glutamine and 1% penicillin/streptomycin.

extract_protocol:
following nuclear run-on, total RNA was isolated by Trizol extraction and biotinylated RNA isolated by streptavidin bead binding
follwing hydrolysis of RNA, 3'adaptors were ligated to biotinylated RNA fragments. After 5'Cap removal and end repair, 5' adaptors were also ligated. Adaptor-ligated RNA fragments were reverse transcribed and cDNA libraries amplified using indexed primers.

treatment_protocol: 500 nM dTAG47

tag: cell line

value: Rh4 cell line

value: 500nM dTAG47


title: Rh4_PAX3-FOXO1-FKBP cells PRO-seq_dTAG2hr_rep1

tag: treatment


title: control3

description: circRNA expression control3

value: smooth muscle cells


title: SupFig3C 28 Celsius WT background version2 T1 plant 02

tag: tissue

value: 3-4 weeks


title: SupFig3C 28 Celsius WT background version2 T1 plant 01


title: Chern_City_109


title: Chern_City_112


title: Chern_City_117


title: P2_TN

description: 10x Genomics

tag: disease


title: SupFig3D 28 Celsius rdr6 background version1 T1 plant 08


title: SupFig3D 28 Celsius rdr6 background version1 T1 plant 02


title: Chern_City_116


title: SupFig3D 28 Celsius rdr6 background version1 T1 plant 03


title: P1_T

description: 10x Genomics

tag: condition


title: Chern_City_114


title: SupFig3C 28 Celsius WT background version2 T1 plant 09


title: Rh4_PAX3-FOXO1-FKBP cells PRO-seq_dTAG4hr_rep3


title: SupFig3C 28 Celsius WT background version2 T1 plant 08


title: Chern_City_113


title: SupFig3C 28 Celsius WT background version2 T1 plant 07


title: SupFig3C 28 Celsius WT background version2 T1 plant 06


title: SupFig3C 28 Celsius WT background version2 T1 plant 05


title: Chern_City_111


title: Rh4_PAX3-FOXO1-FKBP cells PRO-seq_dTAG2hr_rep2


title: SupFig3C 28 Celsius WT background version2 T1 plant 04


title: Chern_City_115


title: SupFig3C 28 Celsius WT background version2 T1 plant 03


title: Rh4_PAX3-FOXO1-FKBP cells PRO-seq_DMSO_rep1

value: DMOS


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS5_ChIP-seq_dTAG4hr_rep2

data_processing:
Raw FASTQ data were trimmed by Trimmomatic (v0.32).
Paired end reads were aligned to a concatenated human and Drosophila genome (hg19 and dm3) using Bowtie2.
Peaks were called using MACS2.
Differential analysis was performed using DiffBind and DESeq2.
BigWig files were generated and normalized using DESeq2 normalization factor
Assembly: hg19 and dm3
Supplementary files format and content: bigWig file
Supplementary files format and content: peak file

source_name: Rh30 cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: DMSO, 500 nM dTAG47

value: Rh30 cell line

tag: antibody

value: anti-PolII-Ser5 (Abcam, #ab5131)


title: Rh4_PAX3-FOXO1-FKBP cells PRO-seq_dTAG1hr_rep2


title: Chern_City_110

value: Chernobyl City

value: Whole Blood


title: Chern_City_106

value: Mixed Breed


title: SupFig3C 28 Celsius WT background version1 T1 plant 11

extract_protocol:
Amplicon sequencing: DNA was extracted from protoplast samples and leaves of transgenic plants with Qiagen DNeasy plant mini kit. The amplicon was obtained using two rounds of PCR. Amplification primers for the first round of PCR were designed to have the 3’ sequence of the primers flanking a 200-300 bp fragment of the genomic area targeted by the guide RNA of interest. The 5’ part of the primer contained a sequence which will be bound by common sequencing primers. After 25 cycles of the first round of PCR amplification, the reaction was purified using 1x Ampure XP beads (Beckman Coulter A63881). The eluate was used as template for the second round of PCR using the Phusion enzyme and 12 cycles of amplification. The second round of PCR was designed so that indexes were added to each sample. The samples were then purified using 0.8x Ampure XP beads. Part of the purified libraries were run on a 2% agarose gel to check for size and absence of primer dimer (fragments below 200 bp considered as primer dimer). Then amplicons were sent for sequencing with NovaSeq 6000 or iSeq 100 platform.
Whole genome sequencing: DNA from single Arabidopsis seedlings was extracted with the Qiagen DNeasy plant mini kit and sheared to 300 bp size with a Covaris. Library preparation was performed with Tecan Ovation Ultralow V2 DNA-seq kit. The libraries were sequenced with the NovaSeq 6000 platform.

tag: developmental stage


title: SupFig3C 28 Celsius WT background version1 T1 plant 12

tag: strain


title: Rh4_PAX3-FOXO1-FKBP cells PRO-seq_dTAG1hr_rep1


title: Chern_City_107


title: SupFig3C 28 Celsius WT background version1 T1 plant 15

tag: background genotype


title: SupFig3C 28 Celsius WT background version1 T1 plant 13


title: Chern_City_108


title: Rh4_PAX3-FOXO1-FKBP cells PRO-seq_DMSO_rep2


title: SupFig3C 28 Celsius WT background version1 T1 plant 10


title: SupFig3C 28 Celsius WT background version1 T1 plant 09


title: Chern_City_104


title: Chern_City_102


title: SupFig3C 28 Celsius WT background version1 T1 plant 04


title: SupFig3C 28 Celsius WT background version1 T1 plant 03


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS5_ChIP-seq_DMSO_rep1

value: DMSO


title: SupFig3C 28 Celsius WT background version1 T1 plant 14

value: leaf tissue


title: SupFig3C 28 Celsius WT background version1 T1 plant 01


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS5_ChIP-seq_dTAG4hr_rep1


title: SupFig3C 28 Celsius WT background version1 T1 plant 06


title: SupFig3C 28 Celsius WT background version1 T1 plant 07