title: DM Villi, replicate 3

city: Hoboken

first: ansu

last: perekatt

address: 507 River street

department: CCB

institute: Stevens Institute of Technology

data_processing:
Raw sequencing reads were cleaned by Novogene using in-house Perl scripts
Clean reads were aligned to the mm9 reference genome using Hisat2
Aligned reads were quantified by featureCounts
The aligned reads were quantified for gene expression levels using featureCounts
Assembly: mm9
Supplementary files format and content: tab-delimited file includes raw counts for each Sample

source_name: duodenum epithelium

growth_protocol: The mice were maintained on standared chow diet, temperature, and humidity controlled animal facility with 12 hour light/dark cycle

extract_protocol:
After the final villi pellet was gathered, any remaining PBS was aspirated prior to solubilizing in TRIzol. After which, RNA extraction proceeded as per the manufacturer’s recommendation.
The PolyA enrichment procedure was used for library preparation

treatment_protocol: The duodenum was freshly harvested and flushed with PBS, filleted open, and cut into ~ 1 cm pieces. The epithelium was separated from the underlying mesenchyme by EDTA chelation using 0.5 mM EDTA/PBS. After 10 minutes  of EDTA/PBS incubation at 4ºC rotating, the intestine pieces were shaken  to separate the epithelium from the underlying mesenchyme. The intestinal villi were then collected by decanting this shaken solution through a 70-micron filter. The large villi were contained within the filter and washed through a 6-well plate filled with ice-cold PBS. The villi were then collected in the ice-cold PBS and pelleted by spinning at 200 rcf at 4ºC for two minutes. This process of 10-minute incubation with EDTA/PBS followed by shaking, washing and pelleting of the villi, was repeated 2 more times until all villi were collected from the tissue.

value: duodenum epithelium

value: villi cells

value: Smad4 knockout; beta-catenin GOF

value: Female


title: SKBR3 human breast cancer cell line,DMSO, rep2 (H3K27me3 ChIP)

status: Public on Oct 27 2025

type: SRA

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Av des Pins O

department: Biochemistry

country: Canada

institute: McGill University

description: Library name: P-D_rep2_IP

library_source: genomic

data_processing:
ChIP-seq reads were first trimmed for adapter sequences and low quality score bases using Trimmomatic (Bolger et al., 2014). The resulting reads were mapped to their respective reference genomes (mouse mm10 or human GRCh38) using BWA-MEM (Li and Durbin, 2009) in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were marked using Picard tools (http://broadinstitute.github.io/picard/). Reads mapping to ENCODE blacklist regions (Amemiya et al., 2019) were further removed.
For spike-in normalization, reads were aligned separately to the D. melanogaster BDGP6 genome. For each sample, count the number of reads that align to the spike-in DNA and identify the sample with the lowest number of spike-in reads. The scale factor for each sample is calculated by dividing the minimum spike-in read count by the number of spike-in reads in that sample.
Assembly: mouse mm10 or human GRCh38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: human cell line

growth_protocol: DMEM (Wisent) for SK-BR-3 supplemented with 10% FBS, 1% penicillin/streptomycin (Wisent), 1% Amphotericin B (Wisent) and 0.1% Gentamycin (Wisent) and incubated at 37°C in 5% CO2.

extract_protocol:
Tissue samples were first minced and resuspended in ice-cold PBS with protease inhibitor cocktail before further being disaggregated with a dounce homogenizer, then filtered through a 70mm filter to collect a single cell suspension. Collected cell pellets were resuspended in PBS containing 1% of formaldehyde for 10 min and the cross-linking reaction was quenched with glycine.
Libraries were generated with NEBNext Ultra II DNA Library Prep kits (NEB, E7103L)

treatment_protocol: cells were treated with DMSO and 2μM EPZ6438 for 7 days, medium and drug were replenished every 2-3 days

tag: tissue

value: human cell line

tag: cell line

tag: cell type

value: Human breast cancer

tag: treatment

value: DMSO treatment for 7 days


title: CTR_48h_2

city: Tallinn

first: Indrek

last: Koppel

address: Akadeemia tee 15-241

department: Department of Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

library_source: transcriptomic

data_processing:
fastq files were generated by the usage bcl2fastq (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the mouse genome build GRCm38 using STAR
Counting reads on reference genome GRCm38, Ensembl realese 82, was done with HTSeq-count
Differential analysis was carried out using DESeq2
Assembly: GRCm38
Supplementary files format and content: processed1_raw_counts.xlsx
Supplementary files format and content: processed2_normalized_counts.xlsx

molecule: total RNA

growth_protocol: NIH-3T33T3 cells (mouse embryonic fibroblasts) were grown at 37°C and 5% CO2 in DMEM (Gibco), supplemented with 10% fetal bovine serum (Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Biological Industries).

extract_protocol:
RNA was extracted using RNeasy Mini kit (Qiagen) according to manufacturer’s instructions. RNA integrity was verified using TapeStation analysis (Agilent) and high intergrity samples (RIN > 9) were processed.
Inhouse polyA based RNA seq

treatment_protocol: AS1411 (GGTGGTGGTGGTTGTGGTGGTGGTGG) and control DNA (CCTCCTCCTCCTTCTCCTCCTCCTCC) oligonucleotides (Integrated DNA Technologies) were dissolved in culture medium as 10x stock solutions and used at 10 µM final concentrations.

tag: time point

value: fibroblast

tag: genotype

value: WT

value: Control aptamer


title: Wild-type sample, lactate condition, replicate 3

city: Farmington

first: Xihua

last: Qiu

state: CT

address: 263 Farmington Ave

department: Biomedical Engineering

country: USA

institute: University of Connecticut

description: Library name: YL10_3

data_processing:
Alignment with GRCh38
Gene counting with featureCounts
Transcripts per Million calculations
Assembly: GRCh38
Supplementary files format and content: TPM values in Excel

molecule: polyA RNA

organism: Homo sapiens

source_name: Breast

extract_protocol:
mRNA Extraction
Standard Illumina mRNA library prep

value: Breast

value: Epithelial

value: Wild-type

value: lactate


title: DM Villi, replicate 1

state: NJ

tag: Sex

value: Male


title: SKBR3 human breast cancer cell line,DMSO, rep1 (H3K27me3 ChIP)

description: Library name: P-D_rep1_IP


title: Wild-type sample, lactate condition, replicate 2

description: Library name: YL10_2


title: SKBR3 human breast cancer cell line, EPZ6438, rep1 (Input)

description: Library name: P-E_rep1_Input

value: EPZ6438 treatment for 7 days


title: CTR_48h_1


title: Mouse tumor, EZH2wildtype, biol rep2 (Input)

description: Library name: 2943WTInput

source_name: Mouse mammary gland tumors

value: Mouse mammary gland tumors

value: EIC EZH2wildtype

value: Doxycycline induced at age 8-12weeks until tumor reach endpoint


title: WT Villi, replicate 3

value: duodenum epithelium

value: villi cells

value: Wildtype


title: CTR_24h_3


title: Wild-type sample, lactate condition, replicate 1

description: Library name: YL10_1


title: WT Villi, replicate 2

value: Female


title: CTR_24h_2


title: Mouse tumor, EZH2wildtype, biol rep1 (Input)

description: Library name: 2883WTInput


title: WT Villi, replicate 1


title: Wild-type sample, hypoxia condition, replicate 3

description: Library name: YL9_3

value: hypoxia


title: Mouse tumor, EZH2knockout, biol rep2 (Input)

description: Library name: 4161KOInput

value: EIC EZH2knockout


title: CTR_24h_1

value: fibroblast

value: WT


title: Wild-type sample, hypoxia condition, replicate 2

description: Library name: YL9_2

value: Breast


title: lumbarSpine, gp120gal3KO, scRNAseq

city: Stony Brook

first: Shao-Jun

last: Tang

state: New York

address: 101 Nicolls Road

institute: Renaissance School of Medicine at Stony Brook 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 v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lumbar spinal cord

extract_protocol:
We collected three lumbar spinal sections from each group and pooled them together for nuclei dissociation. To isolate nuclei for snRNA-seq, we used the detergent-mechanical cell lysis method. In brief, the lumbar spinal sections were placed in a pre-chilled Dounce homogenizer, and 500 μl of pre-chilled detergent lysis buffer was added. The detergent lysis buffer was prepared by adding 3µl of 20% Triton-X to 600 µl of low sucrose buffer (sucrose: 0.32 M; HEPES (pH = 8.0):10 mM; CaCl2: 5 mM; MgAc: 3 mM; EDTA: 0.1 mM; DTT: 1 mM). We homogenized the tissue first by 5 strokes with pestle A (‘loose’ pestle), then 5-10 strokes with pestle B (‘tight’ pestle) to prepare crude nuclei. We did not lift pestles out of the lysis buffer between strokes to minimize bubble creation during homogenization. We added 1 ml of low sucrose buffer to the Dounce homogenizer containing the crude nuclei and mixed gently by pipetting 2–3 times. We passed the crude nuclei preparation through a 40 µm strainer (Fisher scientific, cat. no. 08-771-1) into a pre-chilled 50 ml conical tube containing 1 ml of low sucrose buffer. Then, an additional 1 ml of low sucrose buffer was passed through the strainer, which brought the volume of the nucleus preparation to 3.5 ml (3 ml of low sucrose buffer and 500 μl of lysis buffer). We centrifuged the samples for 10 min (3,200g; 4 °C), and resuspended the pellets using 3 ml of low sucrose buffer by gently swirling to wash the pellet off the wall. The suspension was put on ice for 2 min and then transferred to an Oak Ridge tube. We homogenized the suspended nuclei for 30 s on ice using a homogenizer (IKA, Ultra Turrax T8; at setting 1). We carefully added 12.5 ml of density sucrose buffer (sucrose: 1 M; HEPES (pH = 8.0): 10 mM; MgAc: 3 mM; DTT: 1 mM) underneath the low sucrose buffer homogenate using a serological pipette to prevent creating any bubbles that could disrupt the density layers. We then centrifuged the Oak Ridge tube at 3,200 x g for 20 min at 4 °C. Once the centrifugation was complete, we immediately decanted the supernatant in a flicking motion. The nuclei remaining on the wall were resuspended with 500 µl of resuspension solution (BSA: 0.4 mg/ml; RNAse Inhibitor: 0.2 U/μl). The sample was then passed through a 40 μm Flowmi pipette tip filter (Sigma-Aldrich, cat no: H13680-004)
Library was performed according to the manufacter’s instructions (Chromium protocol CG000185 Rev). Briefly, nuclei were loaded onto the Chromium controller for library preparation and sequencing. GEMs were captured and underwent reverse transcription by incubating at in a thermal cycler. Next, GEMs were broken, and the sample cDNA was recovered and cleaned according to the instructions. Then 10 µl of purified cDNA sample was enzymatically fragmented and size-selected using SPRIselect magnetic beads. Illumina sequencing adapters were then ligated to the size-selected fragments and cleaned up using SPRIselect magnetic beads. Sample indices were selected and amplified, followed  by a double-sided size selection using SPRIselect magnetic bead

value: lumbar spinal cord

value: Gp120Tg + gal3 knockout

tag: age

value: 5 month old


title: AS_48h_2


title: Mouse tumor, EZH2wildtype, biol rep2 (H3K27me3 ChIP)

description: Library name: 2943WTChIP


title: Mouse tumor, EZH2knockout, biol rep1 (Input)

description: Library name: 0384KOInput


title: lumbarSpine, gal3KO, scRNAseq

description: 10x Genomics

value: gal3 knockout


title: Wild-type sample, normoxia condition, replicate 3

description: Library name: YL8_3

value: Epithelial

value: Wild-type

value: normoxia


title: Wild-type sample, hypoxia condition, replicate 1

description: Library name: YL9_1


title: Mouse tumor, EZH2wildtype, biol rep1 (H3K27me3 ChIP)

description: Library name: 2883WTChIP

value: Mouse mammary gland tumors

value: EIC EZH2wildtype

value: Doxycycline induced at age 8-12weeks until tumor reach endpoint


title: AS_48h_1


title: DM Villi, replicate 2

value: duodenum epithelium

value: villi cells

value: Smad4 knockout; beta-catenin GOF


title: AS_24h_3


title: Wild-type sample, normoxia condition, replicate 2

description: Library name: YL8_2


title: AS_24h_2


title: Wild-type sample, normoxia condition, replicate 1

description: Library name: YL8_1


title: lumbarSpine, gp120, scRNAseq

description: 10x Genomics


title: Mouse tumor, EZH2knockout, biol rep1 (H3K27me3 ChIP)

description: Library name: 0384KOChIP

value: EIC EZH2knockout


title: lumbarSpine, wt, scRNAseq

description: 10x Genomics

value: wt


title: Mouse tumor, EZH2knockout, biol rep2 (H3K27me3 ChIP)

description: Library name: 4161KOChIP


title: AS_24h_1

value: fibroblast

value: WT


title: Fly heads

city: Lisbon

first: Gili

last: Ezra

address: Av. Brasília

country: Portugal

institute: Champalimaud foundation

data_processing:
Demultiplexing and alignment were done as described in Alpern et al., 2019, using genome assembly version: drosophila_melanogaster BDGP6.28 (dm6) (Ensembl release 100).
Samples processing and alignment was performed in 2021 at Alithea© using their MERCURIUS service for bulk RNA barcoding and sequencing (BRB-seq; Alpern et al., 2019).
Assembly: drosophila_melanogaster BDGP6.28 (dm6)
Supplementary files format and content: tab-deliminated text file includes raw counts
Supplementary files format and content: tab-deliminated text file includes column data, raw counts and size facors based on DEseq2 analysis for all valid samples

organism: Drosophila melanogaster

source_name: 10 fly heads

extract_protocol:
10 heads were dissected from mated axenic females maintained on each dietary condition. Samples were homogenized for 30s in 350μl of PureZOL and RNA was extracted according to manufacturer´s instructions (Direct-zol RNA MicroPrep #R2062, Zymo research). Samples were eluted in 50 μl of distilled RNase/DNase-free water.
Transcriptomics analysis was performed using bulk RNA barcoding and sequencing (BRB-seq; Alpern et al., 2019).

value: 10 fly heads

value: female

value: w1118 axenic


title: shPGR3

status: Public on Oct 26 2025

city: Shanghai

first: Xiaoya

last: Zhao

state: -- None selected --

address: No. 910, Hengshan Rd

country: China

institute: School of Medicine, Shanghai Jiaotong University

data_processing:
The raw sequencing data are also evaluated by FAST-QC including quality distribution of nucleotides, position specific sequencing quality, GC content, the proportion of PCR duplication, kmer frequency etc. These evaluation metrics may help us understand the nature of data deeper before subsequent variant evaluation.
GO analysis was applied to analyze the main function of the differential expression genes according to the Gene Ontology which is the Wey functional classification of NCBI.
Pathway analysis was used to find out the significant pathway of the differential genes. Pathway annotations of Microarray genes were download from KEGG.
Assembly: hg38
Supplementary files format and content: All.counts.xlsx
Supplementary files format and content: All.fpkm.xlsx

source_name: villi

extract_protocol:
Each type of trophoblast stem cells were collected to isolate total RNA using the TRIzol reagent (Enzyme,  Jiangsu, China) following the manufacturer's instructions. The quality of RNA was assessed using an Agilent 2100 Bioanalyzer.
RNA-seq libraries were constructed by NovelBio Bio-Pharm Technology (Shanghai, China). Subsequently, samples were treated with the Illumina mRNA-Seq Sample Preparation Kit (containing 1 box, part # 1004814, and 1 bag, part # 1004815) according to the manufacturer's protocol (Cat # RS-930-1001). mRNA was isolated from 5 μg of total RNA using oligo-dT magnetic beads and fragmented into small pieces at 94°C with divalent cations. The fragmented RNA was then converted into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase. The resulting cDNA fragments underwent end repair, addition of a single A base, and adapter ligation. After purification and PCR enrichment, a final cDNA library was generated. Each RNA-seq library was sequenced with 100 bp paired-end reads using the Illumina Genome Analyzer IIx.

value: villi

value: Trophoblast stem cells

value: knockdown of PGR (shPGR)


title: Control3

value: knockdown of luciferase (Control)


title: Control2


title: Control1


title: shPGR1


title: shPGR2


title: b2m,HEK293T,pTET_ultra-tight,untreated,10days,rep1

city: South San Francisco

first: Hetal

last: Patel

state: California

address: 1 DNA Way

institute: Genentech

description: Library name: ptTetB2m-304_94738260175r3_031021_CD81

data_processing:
Sequencing reads were demultiplexed using i5 and i7 index barcodes, allowing up to one mismatch per index. Reads were then filtered to retain only those with a minimum Phred quality score of 30. For each reaction, reads were aligned to the expected amplicon sequence using BWA-MEM2 69. Alignment results were parsed using custom software to extract the CIGAR string (which encodes how each read aligns to the  reference,  including  matches,  insertions,  and  deletions).  From  this,  the  total  number  of aligned reads, the number of exact matches to the wild-type sequence, the number of reads with indels, and the number of partially aligned or non-matching reads were determined. Exact matches were classified as wild-type  (unmodified),  and  reads  with  indels  were  classified  as  edited  (reflecting  sgRNA  activity). Partially  matched  or  non-specific  reads  were  excluded  from  downstream  analysis.  Wild-type  and indel-containing reads were then reported as a percentage of the total number of high-quality, specific alignments.
The expected amplicon sequence is represented in the .fa file, which was used as a reference file to do the alignment with BWA-MEM2.  The .fa file associated with the alignment for each of the sample has been provided.  The samples that are looking at the same target region have the same amplicon sequence, hence some files are identical.
Supplementary files format and content: iCRISPR_paper_NGS_processed_data_071125.csv
Library strategy: CRISPR Screen

growth_protocol: For 293T, DMEM + 10% TET-free FBS + 1% NEAA + 2mM L-Glutamine; 1X pen-strep. For HAP1 IMDM + 10% Tet-free FBS + 2mM L-Glutamine; 1X pen-strep

extract_protocol:
Genomic  DNA  was  extracted  from  cells  using  the  Agencourt  DNAdvance  Kit  (Beckman  Coulter).
PCR primers  flanking  the  target  site  were  designed  to  amplify  200-300bp  amplicon  using  a  2  stage  PCR method.   Primer sequences for amplicon sequencing are provided in Table 5. The PCR includes genomic DNA,  i5  and  i7  indexed  adapters,  target specific primers with universal adapters, and PrimeTime Gene Expression  Master  Mix  (IDT).   The  first stage of PCR amplifies the target specific amplicons with target specific  primers  flanked  by  universal  adapters  at  60°C  Tm  for  30  cycles.  The  second  stage  of  PCR incorporates the indexed sequencing adapters in the target specific amplicons at  55°C for 4 cycles.  We use  dual  end  indexing  by  incorporating  i5  and  i7  10bp  indexes  by  IDT  to  uniquely  label  amplicons produced  from  each  PCR.   The  PCRs  are  assembled  using Echo 525 Acoustic Liquid Handler (Beckman Coulter).  Following  PCR,  the  amplicons  from  all  of  the  reactions  are  pooled  together.   The  amplicon library  pool  is  cleaned  twice  using  KAPA  Pure  Beads(Kapa)  at  1:1 ratio to remove unused primers and index  adapters.   The  quality  and  quantity  of  the  clean amplicon library pool is determined using 4200 TapeStation  System  (Agillent)  and High Sensitivity D1000 DNA ScreenTape. The amplicon library pool is diluted  to  15pM  with  5%  PhiX as per Illumina MiSeq library preparation procedure, and sequenced on Illumina MiSeq, dual read, 150/150 cycles to produce 300bp sequences using the Miseq V2 kit (Illumina). Primer sequences used for amplicon sequencing are listed in Supplementary Table 5.

treatment_protocol: pTET cells were treated with 2μg/ml Dox;  pTET:Ultra-tight cells were treated with 2μg/ml Dox and 1μM Shield1; Xon-Cas9 cells were treated with 20nM Branaplam; Xon-Cas9;AcrIIA4-FKBP cells were treated with 20nM branaplam and 1μM dTagv-1


title: b2m,HEK293T,pTET_ultra-tight,Dox-shield,10days,rep3

description: Library name: ptTetB2m-312_94738260183r3_031021_CD81


title: b2m,HEK293T,pTET,Dox,10days,rep1

description: Library name: ptTetB2m-307_94738260178r3_031021_CD81


title: b2m,HEK293T,pTET_ultra-tight,untreated,10days,rep2

description: Library name: ptTetB2m-305_126752280094r2_419941_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,10days,rep2

description: Library name: pTet-171_94738260353r3_214948_CD81


title: b2m,HEK293T,pTET_ultra-tight,Dox-shield,10days,rep2

description: Library name: ptTetB2m-311_94738260182r3_031021_CD81


title: b2m,HEK293T,pTET,Dox,10days,rep2

description: Library name: ptTetB2m-308_94738260179r3_031021_CD81


title: b2m,HEK293T,pTET_ultra-tight,untreated,10days,rep3

description: Library name: ptTetB2m-306_94738260177r3_031021_CD81


title: b2m,HEK293T,pTET_ultra-tight,Dox-shield,10days,rep1

description: Library name: ptTetB2m-310_94738260181r3_031021_CD81


title: b2m,HEK293T,pTET,untreated,10days,rep3

description: Library name: ptTetB2m-303_94738260174r3_031021_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,10days,rep1

description: Library name: pTet-170_126752280149r2_964334_CD81


title: b2m,HEK293T,pTET,Dox,10days,rep3

description: Library name: ptTetB2m-309_94738260180r3_031021_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,10days,rep3

description: Library name: pTet-172_126752280150r2_964334_CD81


title: b2m,HEK293T,pTET,untreated,10days,rep2

description: Library name: ptTetB2m-302_126752280093r2_419941_CD81


title: b2m,HEK293T,pTET,untreated,10days,rep1

description: Library name: ptTetB2m-301_94738260172r3_031021_CD81


title: CD81,HEK293T,pTET,Dox,10days,rep3

description: Library name: pTet-169_126752280148r2_964334_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,10days,rep3

description: Library name: pTet-166_126752280146r2_964334_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,10days,rep1

description: Library name: pTet-164_94738260346r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,10days,rep2

description: Library name: pTet-168_126752280147r2_964334_CD81


title: CD81,HEK293T,pTET,untreated,10days,rep3

description: Library name: pTet-163_94738260345r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,10days,rep2

description: Library name: pTet-162_94738260344r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,10days,rep1

description: Library name: pTet-167_94738260349r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,6days,rep2

description: Library name: pTet-159_94738260341r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,10days,rep1

description: Library name: pTet-161_94738260343r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,6days,rep3

description: Library name: pTet-160_126752280144r2_964334_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,6days,rep1

description: Library name: pTet-158_126752280143r2_964334_CD81


title: CD81,HEK293T,pTET,Dox,6days,rep3

description: Library name: pTet-157_94738260339r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,6days,rep2

description: Library name: pTet-156_94738260338r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,6days,rep3

description: Library name: pTet-154_94738260336r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,6days,rep3

description: Library name: pTet-151_126752280141r2_964334_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,6days,rep2

description: Library name: pTet-153_94738260335r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,72hrs,rep3

description: Library name: pTet-148_94738260330r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,6days,rep2

description: Library name: pTet-150_94738260332r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,72hrs,rep3

description: Library name: pTet-142_94738260324r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,6days,rep1

description: Library name: pTet-149_94738260331r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,6days,rep1

description: Library name: pTet-152_94738260334r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,72hrs,rep2

description: Library name: pTet-141_94738260323r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,72hrs,rep3

description: Library name: pTet-145_94738260327r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,72hrs,rep1

description: Library name: pTet-140_94738260322r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,72hrs,rep3

description: Library name: pTet-139_94738260321r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,48hrs,rep3

description: Library name: pTet-136_94738260318r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,72hrs,rep2

description: Library name: pTet-147_94738260329r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,72hrs,rep2

description: Library name: pTet-138_94738260320r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,72hrs,rep2

description: Library name: pTet-144_94738260326r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,48hrs,rep3

description: Library name: pTet-133_126752280140r2_964334_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,48hrs,rep2

description: Library name: pTet-135_94738260317r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,48hrs,rep1

description: Library name: pTet-134_94738260316r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,48hrs,rep3

description: Library name: pTet-130_94738260312r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,6days,rep1

description: Library name: pTet-155_94738260337r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,72hrs,rep1

description: Library name: pTet-146_94738260328r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,48hrs,rep2

description: Library name: pTet-129_94738260311r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,48hrs,rep2

description: Library name: pTet-132_94738260314r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,48hrs,rep1

description: Library name: pTet-128_94738260310r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,48hrs,rep3

description: Library name: pTet-127_126752280139r2_964334_CD81


title: CD81,HEK293T,pTET,untreated,48hrs,rep2

description: Library name: pTet-126_94738260308r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,72hrs,rep1

description: Library name: pTet-143_94738260325r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,72hrs,rep1

description: Library name: pTet-137_94738260319r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,24hrs,rep3

description: Library name: pTet-124_94738260306r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,24hrs,rep1

description: Library name: pTet-122_94738260304r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,24hrs,rep3

description: Library name: pTet-115_94738260297r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,24hrs,rep1

description: Library name: pTet-116_94738260298r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,24hrs,rep3

description: Library name: pTet-118_94738260300r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,24hrs,rep3

description: Library name: pTet-121_94738260303r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,24hrs,rep1

description: Library name: pTet-119_94738260301r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,24hrs,rep2

description: Library name: pTet-123_94738260305r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,24hrs,rep2

description: Library name: pTet-120_94738260302r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,24hrs,rep1

description: Library name: pTet-113_94738260295r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,6hrs,rep3

description: Library name: pTet-112_94738260294r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,24hrs,rep2

description: Library name: pTet-114_94738260296r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,6hrs,rep1

description: Library name: pTet-110_126752280138r2_964334_CD81


title: CD81,HEK293T,pTET,Dox,48hrs,rep1

description: Library name: pTet-131_94738260313r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,48hrs,rep1

description: Library name: pTet-125_94738260307r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,6hrs,rep2

description: Library name: pTet-108_94738260290r3_214948_CD81


title: CD81,HEK293T,pTET,Dox,6hrs,rep3

description: Library name: pTet-109_126752280137r2_964334_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,6hrs,rep3

description: Library name: pTet-106_94738260288r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,6hrs,rep1

description: Library name: pTet-104_94738260286r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,6hrs,rep2

description: Library name: pTet-105_94738260287r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,6hrs,rep2

description: Library name: pTet-102_126752280134r2_964334_CD81


title: CD81,HEK293T,pTET,untreated,6hrs,rep1

description: Library name: pTet-101_94738260283r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,10days,rep2

description: Library name: Xon-271_94738260280r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,10days,rep1

description: Library name: Xon-270_94738260279r3_214948_CD81


title: CD81,HEK293T,pTET_ultra-tight,untreated,24hrs,rep2

description: Library name: pTet-117_94738260299r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,10days,rep3

description: Library name: Xon-269_94738260278r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,10days,rep2

description: Library name: Xon-268_94738260277r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,10days,rep1

description: Library name: Xon-267_126752280132r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,10days,rep3

description: Library name: Xon-263_94738260272r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,10days,rep2

description: Library name: Xon-262_94738260271r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,10days,rep2

description: Library name: Xon-265_94738260274r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,10days,rep1

description: Library name: Xon-261_94738260270r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,10days,rep1

description: Library name: Xon-264_126752280131r2_964334_CD81


title: CD81,HEK293T,pTET_ultra-tight,Dox-shield,6hrs,rep2

description: Library name: pTet-111_94738260293r3_214948_CD81


title: CD81,HEK293T,pTET,untreated,6hrs,rep3

description: Library name: pTet-103_126752280135r2_964334_CD81


title: CD81,HEK293T,pTET,Dox,6hrs,rep1

description: Library name: pTet-107_126752280136r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,6days,rep3

description: Library name: Xon-257_94738260266r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,6days,rep2

description: Library name: Xon-259_94738260268r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,6days,rep3

description: Library name: Xon-260_94738260269r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,6days,rep1

description: Library name: Xon-258_94738260267r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,6days,rep3

description: Library name: Xon-254_94738260263r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,6days,rep2

description: Library name: Xon-256_94738260265r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,6days,rep2

description: Library name: Xon-253_94738260262r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,6days,rep1

description: Library name: Xon-252_94738260261r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,6days,rep2

description: Library name: Xon-250_94738260259r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,72hrs,rep3

description: Library name: Xon-248_94738260257r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,10days,rep3

description: Library name: Xon-272_94738260281r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,6days,rep1

description: Library name: Xon-249_94738260258r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,72hrs,rep1

description: Library name: Xon-246_94738260255r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,72hrs,rep3

description: Library name: Xon-245_126752280128r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,72hrs,rep2

description: Library name: Xon-244_94738260253r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,10days,rep3

description: Library name: Xon-266_94738260275r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,72hrs,rep1

description: Library name: Xon-243_94738260252r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,72hrs,rep3

description: Library name: Xon-239_94738260248r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,72hrs,rep1

description: Library name: Xon-240_94738260249r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,72hrs,rep1

description: Library name: Xon-237_94738260246r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,48hrs,rep1

description: Library name: Xon-234_94738260243r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,48hrs,rep2

description: Library name: Xon-235_126752280127r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,6days,rep3

description: Library name: Xon-251_94738260260r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,48hrs,rep2

description: Library name: Xon-232_94738260241r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,48hrs,rep3

description: Library name: Xon-230_94738260239r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,72hrs,rep2

description: Library name: Xon-247_126752280129r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,6days,rep1

description: Library name: Xon-255_126752280130r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,48hrs,rep3

description: Library name: Xon-233_94738260242r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,48hrs,rep1

description: Library name: Xon-231_126752280126r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,48hrs,rep3

description: Library name: Xon-227_94738260236r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,48hrs,rep1

description: Library name: Xon-225_126752280124r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,48hrs,rep2

description: Library name: Xon-226_126752280125r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,24hrs,rep3

description: Library name: Xon-224_94738260233r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,24hrs,rep1

description: Library name: Xon-222_94738260231r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,48hrs,rep1

description: Library name: Xon-228_94738260237r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,24hrs,rep2

description: Library name: Xon-223_94738260232r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,24hrs,rep3

description: Library name: Xon-221_126752280123r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,24hrs,rep2

description: Library name: Xon-220_94738260229r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,24hrs,rep1

description: Library name: Xon-219_94738260228r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,24hrs,rep3

description: Library name: Xon-218_126752280122r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,72hrs,rep3

description: Library name: Xon-242_94738260251r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,24hrs,rep2

description: Library name: Xon-217_94738260226r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,72hrs,rep2

description: Library name: Xon-241_94738260250r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,72hrs,rep2

description: Library name: Xon-238_94738260247r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,48hrs,rep3

description: Library name: Xon-236_94738260245r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,24hrs,rep3

description: Library name: Xon-215_94738260224r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,24hrs,rep1

description: Library name: Xon-216_94738260225r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,24hrs,rep2

description: Library name: Xon-214_94738260223r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,24hrs,rep1

description: Library name: Xon-213_94738260222r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,48hrs,rep2

description: Library name: Xon-229_94738260238r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,6hrs,rep3

description: Library name: Xon-212_94738260221r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,6hrs,rep2

description: Library name: Xon-211_94738260220r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,6hrs,rep3

description: Library name: Xon-206_94738260215r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,6hrs,rep1

description: Library name: Xon-207_126752280119r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,branaplam-dTagV1,6hrs,rep1

description: Library name: Xon-210_94738260219r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,6hrs,rep2

description: Library name: Xon-205_94738260214r3_214948_CD81


title: CD81,HEK293T,Xon-Cas9,branaplam,6hrs,rep3

description: Library name: Xon-209_126752280121r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9-AcrIIA4-FKBP,untreated,6hrs,rep1

description: Library name: Xon-204_126752280118r2_964334_CD81


title: CD81,HEK293T,Xon-Cas9,untreated,6hrs,rep3

description: Library name: Xon-203_126752280117r2_964334_CD81


title: RNA-seq from quadratus femoris muscle of young adult male mouse at 8 wks post-AAV9-RECODE-P[I83I] administration (rep 3)

city: Fukuoka City

first: Soichi

last: Ozaki

state: Fukuoka

address: West Zone 5 #430, Kyushu University, 744 Motooka, Nishi-ku,

country: Japan

institute: EditForce, Inc.

description:
Library name: QF-RECODE-PG-I83I-3
RNA-seq from quadratus femoris muscle of young adult male Mus musculus at 8 weeks post-AAV9-RECODE-P[I83I] administration (replicate 3)
RECODE-P_I83I.vcf

data_processing:
Raw sequence reads were mapped to customized reference sequence including GRCm39 (Ensembl) and each AAV-RECODE sequences, using STAR (v2.7.10). Alignment parameters included: --quantMode TranscriptomeSAM –outFilterType BySJout –outFilterMultimapNmax 1 –outSAMstrandField intronMotif –outSAMattributes All. After removing PCR duplicates with Picard MarkDuplicates tool, RNA editing candidate sites were identified using REDItools (v1.3) using the following parameters -t 17 -e -d -l -U [AG,TC,CT,GA] -G path/to/gtf -p -u -m 30 -T 6-0 -W -v 10 -n 0 -g 2 -s 1 removing the sites with a read count less than 10 and minimum mapping quality score of less than 30. Base frequencies were counted at all positions in the transcript sequences. Positions with significant differences in base frequency compared to the reference were identified using Fisher’s exact test with Benjamini-Hochberg correction (p-value < 0.01).
Assembly: GRCm39
Supplementary files format and content: VCF

source_name: quadratus femoris

growth_protocol: Mice were kept under the non-SPF condition and were maintained on a 12-hour light/dark cycle at a controlled room temperature of 21.2–23.0°C with humidity of 40–57%

extract_protocol:
Eight weeks after administration, the mice were euthanized by exsanguination under isoflurane inhalation anesthesia (2.0–4.0%; Isoflurane Inhalation Anesthetic Solution “VTRS,” Mylan EPD LLC), and various tissues were collected and flash-frozen in liquid nitrogen. 10 mg of piece of organs were homogenized in 250 µL of the 1- Thioglycerol/Homogenization buffer (supplied with the Maxwell RSC simplyRNA Tissue Kit; Promega) using a BioMasher tube (Funakoshi). The homogenate was centrifuged at 14,000 rpm for 15 min at 4ºC, and 200 µL of supernatant were collected. 200 µL Lysis buffer were added before extracting total RNA using Maxwell RSC simplyRNA Tissue Kit (Promega)
NGS libraries were prepared from total RNA using poly(A) enrichment

treatment_protocol: Each of three groups of three 8-week-old male WT mice (FVB/NJcl) were administreted a single intravenous dose of the test substance (AAV9-RECODE-WW[F75F] or AAV9-RECODE-PG[I83I]) at a dose of 3×10^14 vg/kg or the same volume of PBS as the AAV preparation as the control substance.

value: quadratus femoris

value: young adult

value: male


title: CD81,HEK293T,Xon-Cas9,untreated,6hrs,rep2

description: Library name: Xon-202_126752280116r2_964334_CD81


title: lung adenocarcinoma(LUAD) sputum specimens circRNA 2

type: RNA

city: 天津市

first: 娜

last: 赵

address: 河西区天塔街道卫津南路天津市肿瘤医院

institute: 天津医科大学肿瘤医院

description: circRNA expression lung adenocarcinoma(LUAD) sputum specimens

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least half of samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, circ.)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Sputum specimens  from patients and promptly frozen in liquid nitrogen.

value: sputum

tag: gender

value: 5 males and 5 females


title: lung adenocarcinoma(LUAD) sputum specimens circRNA 1

address: 河西区天塔街道卫津南路天津市肿瘤医院


title: CD81,HEK293T,Xon-Cas9,untreated,6hrs,rep1

description: Library name: Xon-201_126752280115r2_964334_CD81


title: infection sputum specimens circRNA

address: 河西区天塔街道卫津南路天津市肿瘤医院

description: circRNA expression data from Homo sapiens lung infection

source_name: infection sputum specimens


title: RNA-seq from quadratus femoris muscle of young adult male mouse at 8 wks post-AAV9-RECODE-P[I83I] administration (rep 1)

description:
Library name: QF-RECODE-PG-I83I-1
RNA-seq from quadratus femoris muscle of young adult male Mus musculus at 8 weeks post-AAV9-RECODE-P[I83I] administration (replicate 1)
RECODE-P_I83I.vcf


title: CD81,HEK293T,KA1.74,untreated,10days,rep3

description: Library name: KA174-403_126752280113r2_964334_CD81


title: CD81,HEK293T,KA1.74,untreated,10days,rep2

description: Library name: KA174-402_94738260207r3_214948_CD81


title: RNA-seq from quadratus femoris muscle of young adult male mouse at 8 wks post-AAV9-RECODE-P[I83I] administration (rep 2)

description:
Library name: QF-RECODE-PG-I83I-2
RNA-seq from quadratus femoris muscle of young adult male Mus musculus at 8 weeks post-AAV9-RECODE-P[I83I] administration (replicate 2)
RECODE-P_I83I.vcf


title: RNA-seq from quadratus femoris muscle of young adult male mouse at 8 wks post-AAV9-RECODE-W[F75F] administration (rep 3)

description:
Library name: QF-RECODE-WW-F75F-3
RNA-seq from quadratus femoris muscle of young adult male Mus musculus at 8 weeks post-AAV9-RECODE-W[F75F] administration (replicate 3)
RECODE-W_F75F.vcf


title: normal sputum specimens circRNA

address: 河西区天塔街道卫津南路天津市肿瘤医院

description: circRNA expression data from Homo sapiens lung

source_name: normal sputum specimens


title: RNA-seq from quadratus femoris muscle of young adult male mouse at 8 wks post-AAV9-RECODE-W[F75F] administration (rep 2)

description:
Library name: QF-RECODE-WW-F75F-2
RNA-seq from quadratus femoris muscle of young adult male Mus musculus at 8 weeks post-AAV9-RECODE-W[F75F] administration (replicate 2)
RECODE-W_F75F.vcf


title: CD81,HEK293T,KA1.74,untreated,10days,rep1

description: Library name: KA174-401_94738260206r3_214948_CD81


title: CD81,HAP1,NTC,untreated,10days,rep3

description: Library name: HAP1-515_94738260203r3_214948_CD81

value: myeloid leukemia


title: CD81,HEK293T,Xon-Cas9,branaplam,6hrs,rep2

description: Library name: Xon-208_126752280120r2_964334_CD81


title: CD81,HAP1,NTC,untreated,10days,rep1

description: Library name: HAP1-513_126752280109r2_964334_CD81


title: CD81,HAP1,NTC,untreated,10days,rep2

description: Library name: HAP1-514_126752280110r2_964334_CD81


title: RNA-seq from quadratus femoris muscle of young adult male mouse at 8 wks post-AAV9-RECODE-W[F75F] administration (rep 1)

description:
Library name: QF-RECODE-WW-F75F-1
RNA-seq from quadratus femoris muscle of young adult male Mus musculus at 8 weeks post-AAV9-RECODE-W[F75F] administration (replicate 1)
RECODE-W_F75F.vcf


title: RNA-seq from quadratus femoris muscle of young adult male mouse at 8 wks post-PBS administration (rep 2)

description:
Library name: QF-PBS-2
RNA-seq from quadratus femoris muscle of young adult male Mus musculus at 8 weeks post-PBS administration (replicate 2)

value: at 8 weeks post-PBS administration


title: CD81,HAP1,pTET_ultra-tight,Dox-shield,10days,rep3

description: Library name: HAP1-512_126752280108r2_964334_CD81


title: RNA-seq from quadratus femoris muscle of young adult male mouse at 8 wks post-PBS administration (rep 1)

description:
Library name: QF-PBS-1
RNA-seq from quadratus femoris muscle of young adult male Mus musculus at 8 weeks post-PBS administration (replicate 1)


title: CD81,HAP1,pTET_ultra-tight,untreated,10days,rep3

description: Library name: HAP1-506_126752280103r2_964334_CD81


title: CD81,HAP1,pTET,Dox,10days,rep3

description: Library name: HAP1-509_94738260197r3_214948_CD81


title: CD81,HAP1,pTET,Dox,10days,rep1

description: Library name: HAP1-507_126752280104r2_964334_CD81


title: HF_9016_eWAT

city: Harbin

first: Mingming

last: Wu

state: Heilongjiang

address: 23 Youzheng St

department: Departments of Cardiology

institute: The First Affiliated Hospital of Harbin Medical University

description:
Library name: Sample 6
Column name in counts_All_Samples.csv and FPKM_All_Samples.csv:  HF_9016_eWAT

data_processing:
Raw fastq data was processed with fastp to get clean reads, with Q20, Q30 and GC content calculated
Reference genome index was built with Hisat2 v2.0.5, and clean reads were aligned to it using the same tool
Mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach
featureCounts v1.5.0-p3 counted reads mapped to each gene, and FPKM was calculated based on gene length and read count
Assembly: mm10
Supplementary files format and content: csv files include FPKM values for each Sample
Supplementary files format and content: csv files include counts values for each Sample

source_name: Epididymal white adipose tissue

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system, and total RNA was used as input for library preparation
mRNA purified from total RNA was fragmented, converted to cDNA, processed for adaptor ligation, size-selected, amplified by PCR, and quality-assessed

value: Epididymal white adipose tissue

value: littermated control

tag: diet

value: High-fat diet

tag: time

value: 16 weeks


title: lung adenocarcinoma(LUAD) sputum specimens circRNA 3

address: 河西区天塔街道卫津南路天津市肿瘤医院

description: circRNA expression lung adenocarcinoma(LUAD) sputum specimens


title: HF_7688_eWAT

description:
Library name: Sample 4
Column name in counts_All_Samples.csv and FPKM_All_Samples.csv:  HF_7688_eWAT


title: CD81,HAP1,pTET_ultra-tight,untreated,10days,rep2

description: Library name: HAP1-505_126752280102r2_964334_CD81


title: HC_9017_eWAT

description:
Library name: Sample 3
Column name in counts_All_Samples.csv and FPKM_All_Samples.csv:  HC_9017_eWAT

value: Myeloid-specific PD-1 KO


title: CD81,HAP1,pTET_ultra-tight,untreated,10days,rep1

description: Library name: HAP1-504_94738260192r3_214948_CD81


title: HC_5568_eWAT

description:
Library name: Sample 2
Column name in counts_All_Samples.csv and FPKM_All_Samples.csv:  HC_5568_eWAT


title: CD81,HAP1,pTET,untreated,10days,rep3

description: Library name: HAP1-503_126752280101r2_964334_CD81


title: HC_5566_eWAT

description:
Library name: Sample 1
Column name in counts_All_Samples.csv and FPKM_All_Samples.csv:  HC_5566_eWAT


title: aPD1, rep 4

city: Boston

first: Dan

last: Duda

state: MA

address: 55 Fruit St

department: Radiation Oncology

institute: Massachusetts General Hospital

description: Library name: Sample 18

data_processing:
The quality control of RNA-seq raw data was performed by FastQC.
After quality control, the low-quality bases and adaptors contamination was removed by Cutadapt.
Next, the clean data were aligned to mouse reference genome mm39 by STAR under two-pass mode.
After data mapping, samtools and featureCounts were used to count the number of reads aligned to the gene features.
Assembly: mm39
Supplementary files format and content: R data serialization file includes count values for each sample

source_name: tumor

extract_protocol:
Total RNA was extracted from the tumor tissues using Qiagen kits.
RNA libraries for RNA-seq were prepared using Qiagen Stranded RNA Library Kits following manufacturer's protocols.

value: tumor


title: aPD1, rep 3

description: Library name: Sample 17


title: CD81,HAP1,pTET,untreated,10days,rep2

description: Library name: HAP1-502_126752280100r2_964334_CD81


title: CD81,HEK293T,Wt,untreated,,rep3

description: Library name: 293T-603_126752280098r2_964334_CD81

value: fibroblast


title: CD81,HEK293T,Wt,untreated,,rep2

description: Library name: 293T-602_126752280097r2_964334_CD81


title: RNA-seq from quadratus femoris muscle of young adult male mouse at 8 wks post-PBS administration (rep 3)

description:
Library name: QF-PBS-3
RNA-seq from quadratus femoris muscle of young adult male Mus musculus at 8 weeks post-PBS administration (replicate 3)


title: CD81,HAP1,pTET,untreated,10days,rep1

description: Library name: HAP1-501_94738260189r3_214948_CD81


title: RNA-seq of HEK293T, RESCUE-S, rep3

description:
Library name: RESCUE-S-3
RESCUE-S.vcf

data_processing:
Raw sequence reads were mapped to customized reference sequence including GRCh38.105 (Ensembl) and the RECODE sequences, using STAR (v2.7.10). Alignment parameters included: --quantMode TranscriptomeSAM –outFilterType BySJout –outFilterMultimapNmax 1 –outSAMstrandField intronMotif –outSAMattributes All. After removing PCR duplicates with Picard MarkDuplicates tool, RNA editing candidate sites were identified using REDItools (v1.3) using the following parameters -t 17 -e -d -l -U [AG,TC,CT,GA] -G path/to/gtf -p -u -m 30 -T 6-0 -W -v 10 -n 0 -g 2 -s 1 removing the sites with a read count less than 10 and minimum mapping quality score of less than 30. Base frequencies were counted at all positions in the transcript sequences. Positions with significant differences in base frequency compared to the reference were identified using Fisher’s exact test with Benjamini-Hochberg correction (p-value < 0.01).
Assembly: GRCh38.105
Supplementary files format and content: VCF

growth_protocol: HEK293T cells were maintained in cultured using DMEM supplemented with 10% fetal bovine serum and 1× penicillin-streptomycin. Cells were incubated at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from transfected cells using the Maxwell® RSC simplyRNA Tissue Kit (Promega).
NGS libraries were prepared from total RNA using poly(A) enrichment.

treatment_protocol: 700 ng RECODE plasmid, 450 ng RESCUE-S / 900 ng gRNA plasmids or 700 ng of an empty vector was transfected with 2.5 µL of FuGENE® HD Transfection Reagent (Promega) to cells plated in 24-well plates and incubated at 37ºC for 48 hrs.

value: RESCUE-S


title: aPD1, rep 1

description: Library name: Sample 15


title: combination, rep 5

description: Library name: Sample 14


title: RNA-seq of HEK293T, RESCUE-S, rep2

description:
Library name: RESCUE-S-2
RESCUE-S.vcf


title: combination, rep 4

description: Library name: Sample 13


title: RNA-seq of HEK293T, RESCUE-S, rep1

description:
Library name: RESCUE-S-1
RESCUE-S.vcf


title: combination, rep 3

description: Library name: Sample 12


title: HF_7690_eWAT

description:
Library name: Sample 5
Column name in counts_All_Samples.csv and FPKM_All_Samples.csv:  HF_7690_eWAT


title: RNA-seq of HEK293T, RECODE-WW2-PPRm2, rep3

description:
Library name: RECODE-WW2-PPRm2-3
RECODE-W2-PPRm2.vcf


title: combination, rep 2

description: Library name: Sample 11


title: RNA-seq of HEK293T, RECODE-WW2-PPRm1, rep3

description:
Library name: RECODE-WW2-PPRm1-3
RECODE-W2-PPRm1.vcf


title: combination_aCD4, rep 4

description: Library name: Sample 8


title: combination_aCD4, rep 5

description: Library name: Sample 9


title: RNA-seq of HEK293T, RECODE-WW2-PPRm1, rep2

description:
Library name: RECODE-WW2-PPRm1-2
RECODE-W2-PPRm1.vcf


title: combination_aCD4, rep 3

description: Library name: Sample 7


title: combination, rep 1

description: Library name: Sample 10


title: RNA-seq of HEK293T, RECODE-WW2-PPRm2, rep1

description:
Library name: RECODE-WW2-PPRm2-1
RECODE-W2-PPRm2.vcf


title: aPD1, rep 2

description: Library name: Sample 16


title: combination_aCD4, rep 2

description: Library name: Sample 6


title: RNA-seq of HEK293T, RECODE-WW2-PPRm1, rep1

description:
Library name: RECODE-WW2-PPRm1-1
RECODE-W2-PPRm1.vcf


title: combination_aCD4, rep 1

description: Library name: Sample 5


title: RNA-seq of HEK293T, RECODE-WW2, rep2

description:
Library name: RECODE-WW2-2
RECODE-W2.vcf


title: RNA-seq of HEK293T, RECODE-WW2, rep1

description:
Library name: RECODE-WW2-1
RECODE-W2.vcf


title: control, rep 3

description: Library name: Sample 3


title: control, rep 4

description: Library name: Sample 4


title: control, rep 2

description: Library name: Sample 2


title: RNA-seq of HEK293T, RECODE-WW, rep2

description:
Library name: RECODE-WW-2
RECODE-W.vcf

value: RECODE-WW


title: PD1, rep 3

description: Library name: Sample 12


title: RNA-seq of HEK293T, RECODE-WW, rep1

description:
Library name: RECODE-WW-1
RECODE-W.vcf


title: RNA-seq of HEK293T, RECODE-WW, rep3

description:
Library name: RECODE-WW-3
RECODE-W.vcf


title: control, rep 1

description: Library name: Sample 1


title: RNA-seq of HEK293T, RECODE-PG2, rep3

description:
Library name: RECODE-PG2-3
RECODE-P2.vcf


title: RNA-seq of HEK293T, RECODE-PG2, rep2

description:
Library name: RECODE-PG2-2
RECODE-P2.vcf


title: PD1, rep 1

description: Library name: Sample 10


title: RNA-seq of HEK293T, RECODE-PG2, rep1

description:
Library name: RECODE-PG2-1
RECODE-P2.vcf


title: PD1, rep 2

description: Library name: Sample 11


title: low_rego_PD1, rep 3

description: Library name: Sample 9


title: RNA-seq of HEK293T, RECODE-WW2-PPRm2, rep2

description:
Library name: RECODE-WW2-PPRm2-2
RECODE-W2-PPRm2.vcf


title: Differentiated HUDEP-2 cells, D12, rep 2

city: Seoul

first: Heesoo

last: Kim

address: 50 Yonsei-ro, Seodaemun-gu

department: Department of Systems Biology

country: South Korea

institute: Yonsei University

data_processing:
Trimmomatic 0.38, HISAT2 version 2.1.0, StringTie version 2.1.3b
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic 0.38
Trimmed sequence reads were mapped to the hg38 human reference genome by HISAT2 version 2.1.0
Read count extraction and normalization were performed using StringTie version 2.1.3b
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts, RPKM, TPM values for each Sample

source_name: Umbilical cord blood-derived

growth_protocol: HUDEP-2 erythroid cells were maintained in StemSpan SFEM supplemented with 3 U/ml EPO, 100 ng/ml SCF, 1 μg/ml Doxycycline and antibiotics in humidified atmosphere with 5 % CO2 at 37 °C

extract_protocol:
Total RNA was isolated from HUDEP-2 cells using RNA preparation kit (Enzynomics) according to manufacturer’s protocol. To remove contaminated DNA, we cleaned the extracted RNAs using RNeasy mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: To induce erythroid differentiation, HUDEP-2 cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (SH30259, HyClone) supplemented with 330 μg/ml human holo-transferrin (T0665, Sigma-Aldrich), 5 % AB human serum (H5667, Sigma-Aldrich), 2 U/ml heparin (H3149, Sigma-Aldrich), 10 μg/ml human insulin (I9278, Sigma-Aldrich), 2 mM L-Glutamine, 3 U/ml EPO, 100 ng/ml SCF, 1 μg/ml Doxycycline and antibiotics. SCF was excluded from the differentiation media on day 6, followed by the removal of doxycycline on day 8.

value: Umbilical cord blood-derived

value: Erythroid progenitor cell

value: WT

value: Erythroid differentiation


title: RNA-seq of HEK293T, RECODE-PG, rep3

description:
Library name: RECODE-PG-3
RECODE-P.vcf

value: RECODE-PG


title: Differentiated HUDEP-2 cells, D12, rep 1


title: RNA-seq of HEK293T, RECODE-WW2, rep3

description:
Library name: RECODE-WW2-3
RECODE-W2.vcf


title: Differentiated HUDEP-2 cells, D8, rep 2


title: low_rego_PD1, rep 2

description: Library name: Sample 8


title: Differentiated HUDEP-2 cells, D8, rep 1


title: RNA-seq of HEK293T, RECODE-PG, rep2

description:
Library name: RECODE-PG-2
RECODE-P.vcf


title: low_rego_PD1, rep 1

description: Library name: Sample 7


title: Differentiated HUDEP-2 cells, D7, rep 1


title: Differentiated HUDEP-2 cells, D6, rep 2


title: RNA-seq of HEK293T, empty vector, rep3

description: Library name: EV-3

value: empty vector


title: high_rego_PD1, rep 3

description: Library name: Sample 6


title: high_rego_PD1, rep 2

description: Library name: Sample 5


title: Differentiated HUDEP-2 cells, D5, rep 2


title: Differentiated HUDEP-2 cells, D5, rep 1


title: Differentiated HUDEP-2 cells, D6, rep 1


title: high_rego_PD1, rep 1

description: Library name: Sample 4


title: Differentiated HUDEP-2 cells, D4, rep 2


title: Differentiated HUDEP-2 cells, D3, rep 2


title: RNA-seq of HEK293T, empty vector, rep1

description: Library name: EV-1


title: RNA-seq of HEK293T, empty vector, rep2

description: Library name: EV-2


title: control, rep 3

description: Library name: Sample 3


title: Differentiated HUDEP-2 cells, D3, rep 1


title: Differentiated HUDEP-2 cells, D4, rep 1


title: Differentiated HUDEP-2 cells, D2, rep 2


title: control, rep 2

description: Library name: Sample 2


title: Differentiated HUDEP-2 cells, D2, rep 1


title: Differentiated HUDEP-2 cells, D7, rep 2


title: GD3-sh50-rep2

city: Hong Kong

first: Tiantian

last: QIN

address: Tat Chee Avenue, Kowloon

institute: City University of Hong Kong

description:
Library name: Sample37
P2_GD3_sh50

data_processing:
mice: Raw RNA-seq reads were trimmed, filtered and assessed using Trim Galore (version: 0.6.10). High-quality reads were then mapped to the mouse genome (GRCm38/mm10) using Hisat2 (version: 2.2.1). Read counts were calculated by HTSeq (version: 0.11.3). DESeq2 package was used to perform the different expression analyses for different sample groups. Gene Set Enrichment Analysis (GSEA) was performed using the GSEA software (version:4.3.3) available at http://software.broadinstitute.org/gsea/downloads.jsp with the option pre-ranked and default parameters. Gene Ontology (GO) analysis was performed on the online platform DAVID 23 and visualized by Prism GraphPad. cell line : The raw sequencing data were processed using Trimmomatic (RRID:SCR_011848) to remove low-quality reads and adapters . The cleaned reads were then aligned to the human reference genome (hg38) and annotated using GENCODE version M20 for Homo sapiens, employing the STAR aligner (version 2.7.7a) with default parameters 30. Gene expression quantification and differential expression analysis were conducted using Cufflinks (version 2.2.1) .
Flag CUT&RUN-seq data analysis: yeast chromatin was employed as a spike-in control for normalization. FASTQ files were preprocessed using Trimmomatic (v0.39)  to remove adapter sequences and low-quality reads. Sequencing reads were aligned to a composite reference genome, integrating the human genome (hg38) and the yeast genome (Sac3). A custom Bowtie2 library was constructed using Bowtie2-build (v2.4.2) , and reads were mapped to the reference using default parameters. After alignment, paired-end reads were segregated by species. Spike-in-derived reads were used to compute a normalization factor to account for technical variability. Peak calling was performed using MACS2 (v2.2.5) with a significance threshold of p<0.001 . Normalized read counts within peaks were quantified using BEDTools .
CRISPR screen data analysis was performed using the MAGeCK algorithm(doi.org/10.1186/s13059-014-0554-4).All the candidates with Log2FC<0 (indicating a decrease in gDNA abundance over time) were used to calculate Log2FC difference (Log2FC_diff) between GD32 and WT7: Log2FC_diff =Log2FC(GD32)- log2FC(WT7). Candidates with Log2FC_diff>-0.5 are shown in the heatmap.
Assembly: mice: GRCm38/mm10 cell line: hg38
Supplementary files format and content: mice RNA seq excel file include read counts value for each sample knock-in cell  RNAseq: excel file include FPKM value for each sample CUT&RUN: bw file showing the CUT&RUN peaks CRISPR Screen: excel include the raw counts from each sample

source_name: cell line

growth_protocol: mouse RNA-seq: All mice were raised in the laboratory animal research unit (LARU) at the City University of Hong Kong with enough food and water. KI cell lines" All cells were cultured in 37 °C incubator with 5% CO2.Cells cultured in DMEM (Gibco, 12100061) with 10% fetal bovine serum (Biosera, FB-1001).

extract_protocol:
RNA was extracted from primary tumor and liver metastasis tissue by RNA Extraction Kit (Takara, 9597) following manufacturer’s instructions. KI cell line CUT&RUN seq: CUT&RUN experiment was conducted following Skene et al’s protocol (doi.org/10.17504/protocols.io.zcpf2vn) KI cell line CUT&RUN seq: Genomic DNA was extracted using the Blood & Cell Culture DNA Midi Kit (Qiagen, 13343). KI cell line CRISPR screen: CRISPR screen was conducted following zhang feng's protocal(doi: 10.1126/science.1247005). genomic DNA was extracted using the Blood & Cell Culture DNA Midi Kit (Qiagen, 13343).
RNA-seq: 1 μg total RNA was used for following library preparation by VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605). The libraries were sequenced on a NovaSeq 6000 System using 2x150 bp paired-end configuration. KI cell line CUT&RUN seq: Libraries were prepared using the Ovation Ultralow System V2 (Invitrogen, Q32854) KI cell line CRISPR screen: The sgRNA regions within the genomic DNA were amplified with Next® Ultra™ II Q5® Master Mix (NEB, M0544X) and sequenced  on the Illumina platform

treatment_protocol: mice: no treatment KI cell line RNA-seq and CUT&RUN seq : H2B-WT-FLAG and H2BG53D-FLAG knockin cells were infected with either shNT or shSPT16 lentivirus. The infected cells were selected with 3 µg/mL puromycin for 48 hours. KI cell line CRISPR screen: no treat

value: cell line

value: PDAC cancer cell line

value: H2BG53D-FLAG knock-in cell

value: SPT16 knockdown sh50


title: control, rep 1

description: Library name: Sample 1


title: Differentiated HUDEP-2 cells, D1, rep 2


title: WT16-sh50-rep2

description:
Library name: Sample36
P2_WT16_sh50

value: H2B_WT-FLAG knock-in cell


title: RNA-seq of HEK293T, RECODE-PG, rep1

description:
Library name: RECODE-PG-1
RECODE-P.vcf


title: Differentiated HUDEP-2 cells, D1, rep 1


title: combination, rep 2

description: Library name: Sample 11


title: Differentiated HUDEP-2 cells, D0, rep 1


title: WT7-sh50-rep2

description:
Library name: Sample35
P2_WT7_sh50


title: eL31_KO, DD48, rep, Ribo-Seq 2

city: College Station

first: Deborah

last: Bell-Pedersen

state: TX

address: Mail Stop 3258, BSBW210

department: Biology

institute: Texas A&M University

data_processing:
Basecalling was performed using Illumina BaseSpace app using the FASTQ generation application ver. 1.0.0 and bcl2fastq.
Ribosome profiling (ribo-seq) reads were trimmed using Cutadapt (Martin, 2011) to remove the 3′ adapter of the reads (adapter sequence – CTGTAGGCACCATCAAT).
Adapter-trimmed ribo-seq reads were size-filtered to the 28-34 nt range using Trimmomatic (Bolger et al., 2014).
Ribo-seq reads were aligned to the N. crassa genome FungiDB Release 38 using STAR (Dobin et al., 2013).
To calculate the ribo-seq read coverage over the 5’ UTR, 3’ UTR, or CDS regions, the geneBody_coverage2.py program from the RSeQC package (Wnag et al., 2012) was used.
Ribosome-protected footprint (RPF) features such as read length distribution and sub-codon phasing were determined using NGS toolkit Plastid (Dunn et al, 2016).
The RPF originating only from the coding sequences (CDS) were extracted and quantified using HTSeq-count (Anders et al., 2015). The counted reads were normalized using the median of ratios method employed in the DESeq2 analysis workflow (Love et al., 2014).
The normalized RPF time series was analyzed using the following Extended Circadian Harmonic Oscillation (ECHO, De Los Santos et al., 2019) settings: two unpaired replicates, smoothing function enabled, unexpressed genes excluded from the analysis at the default 70% threshold. Genes were considered rhythmic if they had Benjamini-Hochberg p-values < 0.05, and oscillation types harmonic, damped or forced.
Assembly: N. crassa genome FungiDB Release 38
Supplementary files format and content: Output from normalized HTSeq-count done on the reads originating from the CDS and saved as plain text files containing ribosome-occupancy reads, non-normalized read counts are also included.
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Mycelial disks in Vogel’s minimal media containing 2% glucose (pH 6.0) were synchronized to the same time of day by a shift from 30°C constant light (LL) to 25°C constant dark (DD). The cultures were grown in LL for a minimum of 4 h and transferred to DD on day 1 (for collection at DD 36, 40, 44, 48, 52), day 2 (for collection at DD 12, 16, 20, 24, 28, 32), day 3 (for collection at DD8), and harvested either at 9:00 a.m. (DD 12, 16, 20, 36, 40, 44) or 5:00 p.m. (DD 8, 24, 28, 32, 48, 52) on day 3.

extract_protocol:
Tissue was harvested in the dark, pressed in between paper towels to remove excess media, and immediately frozen in liquid N2. Ribosomes were pelleted by sucrose-density centrifugation and ribosome-protected mRNAs were isolated from the pelleted cell extracts using the Qiagen miRNeasy Mini Kit (Cat. # 217004).
All subsequent steps up to step 46 in the published ribosome profiling protocol (Ingolia et al., 2012) were followed as described. An rRNA depletion step was not performed, but instead after heat-inactivation of CircLigase, 2.0 μL of GlycoBlueTM, 6.0 μL 5 M NaCl, 74 μL of DEPC water, and 150 μL of isopropanol were added to each tube and precipitation was carried out overnight at -80°C. The DNA was pelleted by centrifugation for 30 min at 20,000 g at 4°C. The pellets were washed with 70% ethanol and allowed to air-dry for 10 min. The pellet was then resuspended in 5.0 μL of 10 mM Tris (pH 8.0), and cDNA synthesis using SuperScript™ III Reverse Transcriptase, followed by barcode addition by PCR amplification using Phusion Hot Start High-Fidelity DNA Polymerase were performed as described (101). Sequencing libraries were quantified and checked for quality on a 2100 Bioanalyzer using a DNA high sensitivity chip per the manufacturer’s instructions.

value: mycelia

value: fungal

value: eL31/rpl-31(deltancu08344::hph) knockout, mat A, 74OR23-IV background

tag: treatment(hours in_the_dark)

tag: batch


title: PD1, rep 3

description: Library name: Sample 9

value: tumor


title: combination, rep 1

description: Library name: Sample 10


title: GD32-sh49-rep2

description:
Library name: Sample34
P2_GD32_sh49

value: SPT16 knockdown sh49


title: eL31_KO, DD40, rep, Ribo-Seq 2


title: eL31_KO, DD44, rep, Ribo-Seq 2


title: eL31_KO, DD36, rep, Ribo-Seq 2


title: GD3-sh49-rep2

description:
Library name: Sample33
P2_GD3_sh49


title: eL31_KO, DD28, rep, Ribo-Seq 2


title: eL31_KO, DD32, rep, Ribo-Seq 2


title: PD1, rep 2

description: Library name: Sample 8


title: WT16-sh49-rep2

description:
Library name: Sample32
P2_WT16_sh49


title: WT7-sh49-rep2

description:
Library name: Sample31
P2_WT7_sh49


title: PD1, rep 1

description: Library name: Sample 7


title: GD32-sh50-rep2

description:
Library name: Sample38
P2_GD32_sh50


title: eL31_KO, DD24, rep, Ribo-Seq 2


title: eL31_KO, DD16, rep, Ribo-Seq 2


title: Differentiated HUDEP-2 cells, D0, rep 2


title: p53_nanotherapy, rep 3

description: Library name: Sample 6


title: eL31_KO, DD12, rep, Ribo-Seq 2


title: GD32-NT-rep2

description:
Library name: Sample30
P2_GD32_NT

value: non-targeting control


title: p53_nanotherapy, rep 2

description: Library name: Sample 5


title: eL31_KO, DD40, rep, Ribo-Seq 1


title: GD3-NT-rep2

description:
Library name: Sample29
P2_GD3_NT


title: eL31_KO, DD44, rep, Ribo-Seq 1


title: p53_nanotherapy, rep 1

description: Library name: Sample 4


title: eL31_KO, DD48, rep, Ribo-Seq 1


title: eL31_KO, DD36, rep, Ribo-Seq 1


title: WT16-NT-rep2

description:
Library name: Sample28
P2_WT16_NT


title: WT7-NT-rep2

description:
Library name: Sample27
P2_WT7_NT


title: eL31_KO, DD32, rep, Ribo-Seq 1


title: eL31_KO, DD28, rep, Ribo-Seq 1


title: control_nanotherapy, rep 2

description: Library name: Sample 2


title: eL31_KO, DD24, rep, Ribo-Seq 1


title: eL31_KO, DD20, rep, Ribo-Seq 2


title: GD32-sh50-rep1

description:
Library name: Sample26
P1_GD32_sh50


title: control_nanotherapy, rep 3

description: Library name: Sample 3


title: eL31_KO, DD20, rep, Ribo-Seq 1


title: control_nanotherapy, rep 1

description: Library name: Sample 1


title: GD3-sh50-rep1

description:
Library name: Sample25
P1_GD3_sh50


title: eL31_KO, DD44, rep2

data_processing:
Basecalling was performed using Illumina BaseSpace app using the FASTQ generation application ver. 1.0.0 and bcl2fastq.
RNA-seq reads were aligned to the N. crassa genome FungiDB Release 38 using STAR (Dobin et al, 2013).
Mapped RNA-seq reads were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) values using Cufflinks (Trapnell et al., 2010; 2012).
The RNA-seq time series was analyzed using the following Extended Circadian Harmonic Oscillation (ECHO, De Los Santos et al., 2019) settings: two unpaired replicates, smoothing function enabled, unexpressed genes excluded from the analysis at the default 70% threshold, and OE/RE cutoff of 1.25. Genes were considered rhythmic if they had Benjamini-Hochberg p-values < 0.05, and oscillation types harmonic, damped or forced.
Assembly: N. crassa genome FungiDB Release 38
Supplementary files format and content: Output from Cufflinks in generic FPKM tracking format saved as plain text files containing the estimated gene-level expression values.

extract_protocol:
Tissue was harvested in the dark, pressed in between paper towels to remove excess media, and immediately frozen in liquid N2. polyA+ RNA was isolated from 100 μg of total RNA with NEB Oligo d(T)25 Magnetic Beads.
Purified mRNA (8 ng) was used as the input to generate RNA-seq libraries using the Lexogen SENSE Total RNA-seq Library Preparation Kit (Cat. #009).


title: eL31_KO, DD16, rep, Ribo-Seq 1


title: eL31_KO, DD48, rep2


title: in_vitro_cGAMP_aTIM1, rep 3

description: Library name: Sample 54

source_name: isolated splenic B cells

extract_protocol:
Total RNA was extracted from the tumor/liver tissues or cultured cells using Qiagen kits.
RNA libraries for RNA-seq were prepared using Qiagen Stranded RNA Library Kits following manufacturer's protocols.

value: isolated splenic B cells


title: WT16-sh50-rep1

description:
Library name: Sample24
P1_WT16_sh50


title: eL31_KO, DD12, rep, Ribo-Seq 1


title: eL31_KO, DD40, rep2


title: in_vitro_cGAMP_aTIM1, rep 2

description: Library name: Sample 53


title: eL31_KO, DD36, rep2


title: WT7-sh50-rep1

description:
Library name: Sample23
P1_WT7_sh50


title: eL31_KO, DD28, rep2


title: eL31_KO, DD32, rep2


title: in_vitro_cGAMP_aTIM1, rep 1

description: Library name: Sample 52


title: GD32-sh49-rep1

description:
Library name: Sample22
P1_GD32_sh49


title: GD3-sh49-rep1

description:
Library name: Sample21
P1_GD3_sh49


title: eL31_KO, DD24, rep2


title: in_vitro_cGAMP_IgG, rep 1

description: Library name: Sample 49


title: WT16-sh49-rep1

description:
Library name: Sample20
P1_WT16_sh49


title: eL31_KO, DD48, rep1


title: in_vitro_cGAMP_IgG, rep 2

description: Library name: Sample 50


title: eL31_KO, DD16, rep2


title: eL31_KO, DD20, rep2


title: in_vitro_cGAMP_IgG, rep 3

description: Library name: Sample 51


title: eL31_KO, DD12, rep2


title: eL31_KO, DD36, rep1


title: in_vitro_STING_aTIM1, rep 2

description: Library name: Sample 47


title: WT7-sh49-rep1

description:
Library name: Sample19
P1_WT7_sh49


title: eL31_KO, DD40, rep1


title: eL31_KO, DD44, rep1


title: eL31_KO, DD20, rep1


title: eL31_KO, DD28, rep1


title: GD32-NT-rep1

description:
Library name: Sample18
P1_GD32_NT


title: in_vitro_STING_aTIM1, rep 3

description: Library name: Sample 48


title: eL31_KO, DD32, rep1


title: in_vitro_STING_aTIM1, rep 1

description: Library name: Sample 46


title: GD3-NT-rep1

description:
Library name: Sample17
P1_GD3_NT


title: eL31_KO, DD24, rep1


title: WT16-NT-rep1

description:
Library name: Sample16
P1_WT16_NT


title: WT7-NT-rep1

description:
Library name: Sample15
P1_WT7_NT


title: eL31_KO, DD16, rep1


title: in_vitro_STING_IgG, rep 2

description: Library name: Sample 44


title: eL31_KO, DD12, rep1


title: in_vitro_STING_IgG, rep 3

description: Library name: Sample 45


title: DMSO Replicate 5

city: Missoula

first: Travis

last: Hughes

state: MT

address: 32 Campus Drive, Skaggs BLDG RM 472

institute: University of Montana

description:
Novogene contract only says Illumina platform
gene_count_matrix_3hr.csv

data_processing:
Align to GRCh38  with HISAT2 v. 2.2.0
Convert from sam to bam files with SAMtools v. 1.15.1
Assemble with StringTie v. 2.2.1.Linux_x86_64 with GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.gtf as the reference annotation.  Only mRNA annotations were included
convert to a count table with prepDE.py from http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
Genes with less than 10 reads in each replicate for at least one condtion were removed
Run DESeq2 v. 1.32.0  in R
Assembly: GRCh38
Supplementary files format and content: comma seperated value files for differential expression analyses
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Adult Stem Cells - Zenbio

growth_protocol: Cells were grown and differentiated IAW ZenBio protocols.  They were thawed and passaged in Preadipocyte medium (PM-1) until differentiation.  They were differentiated in Differentiation Medium lacking PPARγ agonist (DM-2-PPG) supplemented with 3 μM pioglitazone.  After differentiation for 7 days, they were transferred to Adipocyte Medium (AM-1) for maintenance.

extract_protocol:
Cells were lysed with Trizol and RNA was purified using the Invitrogen RNA was isolated using the TRIzol™Plus RNA Purification Kit (Invitrogen #12183555) treated with the on-column Purelink® DNase Treatment (Invitrogen)
Total RNA was sent to Novogene

treatment_protocol: Cells were treated with PPARγ ligands or controls for 3 hours with or without a 3 hour T0070907 pretreatment or for 24 hours

value: Adult Stem Cells - Zenbio

value: Adipoctye

value: DMSO 3hr


title: T0070907 Replicate 5

value: WT

value: T007 3hr followed by DMSO 3hr


title: T0070907 Replicate 4


title: in_vitro_STING_IgG, rep 1

description: Library name: Sample 43


title: T0070907 pretreated Rosiglitazone Replicate 4

value: T0070907 3hr followed by Rosiglitazone 3hr


title: in_vitro_aTIM1, rep 3

description: Library name: Sample 42


title: Explant 1 all cells

city: New York

first: Sarah

middle: B

last: See

address: 1300 York Ave

institute: WCM

description: Library name: EZ16_GEX

data_processing:
Single-cell sequencing reads were processed and aligned to the human reference genome GRCh38-5.0.0 using the CellRanger v5.0.1 or v6.1.2 or Cell Ranger V(D)J v6.1.1 or v6.1.2 pipelines
Assembly: GRCh38-5.0.0
Supplementary files format and content: tab-separated values files and matrix files

source_name: explanted heart with CAV

extract_protocol:
Samples from the proximal, mid and distal regions of each coronary artery from explanted cardia grafts with CAV were collected. Cells from the dissociated explants were stained with aqua viability dye (Invitrogen) and anti-CD45 antibody (Biolegend). All viable cells as well as viable CD45+ cells were sorted on an Influx cell sorter.
10x Genomics Chromium Next GEM single cell 5' and V(D)J expression libraries were generated from sorted cells

value: cardiac


title: T0070907 pretreated  GW1929 Replicate 4

value: T0070907 3hr followed by GW1929 3hr


title: Rosiglitazone Replicate 4

value: Rosiglitazone 3hr


title: in_vitro_aTIM1, rep 2

description: Library name: Sample 41


title: Explant 1 CD45+ enriched cells

description: Library name: EZ17_GEX


title: DMSO Replicate 3


title: GW1929 Replicate 4


title: in_vitro_aTIM1, rep 1

description: Library name: Sample 40


title: 293T cells, PRRC2B guides, EBSS 48hrs, replicate4

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

description: KO EBSS 4

data_processing:
Data was performed using the UTAP pipeline (Kohen R et al. BMC Bioinformatics. 2019) . The analysis includes adapter treaming with cutadapt and alignment to hg38 with STAR.
UMI reduction was performed with UTAP. DESeq2 was used to generate the count matrix and to test for differential expression.
Assembly: hg38
Supplementary files format and content: raw count matrix, csv file

growth_protocol: Cells were grown in DMEM media (01-055-1A)

extract_protocol:
RNA was harvested using Monarch Total RNA Miniprep Kit
Illumina TruSeq Stranded mRNA
RNA-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science. Libraries were prepared using the TruSeq Stranded mRNA-seq kit (Illumina) according to the manufacturing protocol. Briefly, the polyA fraction (mRNA) was purified from 500 ng of total input RNA followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Sequencing was done on Novaseq Plus X 1.5B 300 cycles kit, allocating ~50M reads per sample (Illumina; paired end sequencing

treatment_protocol: DMEM media was replaced with EBSS (02-010-1A) for 48hrs

value: PRRC2B KO

value: Starvation


title: T0070907 Replicate 3


title: Explant 5 CD45+ enriched cells for V(D)J sequencing

description: Library name: EZ09_BCR

data_processing:
Single-cell sequencing reads were processed and aligned to the human reference genome GRCh38-5.0.0 using the CellRanger v5.0.1 or v6.1.2 or Cell Ranger V(D)J v6.1.1 or v6.1.2 pipelines
Assembly: GRCh38-5.0.0
Supplementary files format and content: tab-separated values files and matrix files
Library strategy: BCR-seq


title: in_vitro_IgG, rep 3

description: Library name: Sample 39


title: 293T cells, PRRC2B guides, EBSS 48hrs, replicate3

description: KO EBSS 3


title: Explant 5 all cells

description: Library name: EZ08_GEX


title: Explant 1 CD45+ enriched cells V(D)J sequencing

description: Library name: EZ17_BCR


title: Explant 5 CD45+ enriched cells

description: Library name: EZ09_GEX


title: Rosiglitazone Replicate 3


title: Explant 4 CD45+ enriched cells for V(D)J sequencing

description: Library name: EZ07_BCR


title: 293T cells, PRRC2B guides, EBSS 48hrs, replicate2

description: KO EBSS 2


title: in_vitro_IgG, rep 1

description: Library name: Sample 37


title: T0070907 pretreated  GW1929 Replicate 3


title: DMSO Replicate 4


title: in_vitro_IgG, rep 2

description: Library name: Sample 38


title: Explant 4 CD45+ enriched cells

description: Library name: EZ07_GEX


title: 293T cells, PRRC2B guides, EBSS 48hrs, replicate1

description: KO EBSS 1


title: GW1929 Replicate 3


title: 293T cells, NT guide, EBSS 48hrs, replicate4

description: NT EBSS 4


title: Explant 3 CD45+ enriched cells for V(D)J sequencing

description: Library name: EZ05_BCR


title: DMSO Replicate 2


title: RIL175_Combination_N, rep 1

description: Library name: Sample 34

source_name: liver

value: liver


title: 293T cells, NT guide, EBSS 48hrs, replicate3

description: NT EBSS 3


title: RIL175_Combination_N, rep 2

description: Library name: Sample 35


title: 293T cells, NT guide, EBSS 48hrs, replicate2

description: NT EBSS 2


title: RIL175_PD1_VEGFR2_N, rep 3

description: Library name: Sample 33


title: T0070907 pretreated Rosiglitazone Replicate 3


title: Explant 3 CD45+ enriched cells

description: Library name: EZ05_GEX


title: 293T cells, NT guide, EBSS 48hrs, replicate1

description: NT EBSS 1


title: Explant 3 all cells for V(D)J sequencing

description: Library name: EZ04_BCR


title: Rosiglitazone Replicate 2


title: T0070907 Replicate 2


title: 293T cells, PRRC2B guides, DMEM, replicate4

description: KO Basal 4

value: Regular growth


title: Explant 2 V(D)J sequencing

description: Library name: EZ02_BCR


title: 293T cells, PRRC2B guides, DMEM, replicate3

description: KO Basal 3


title: RIL175_Combination_N, rep 3

description: Library name: Sample 36


title: RIL175_STING_N, rep 3

description: Library name: Sample 30


title: GW1929 Replicate 2


title: Explant 2

description: Library name: EZ02_GEX


title: RIL175_STING_N, rep 2

description: Library name: Sample 29


title: Explant 3 all cells

description: Library name: EZ04_GEX


title: Explant 4 all cells

description: Library name: EZ06_GEX


title: DMSO Replicate 1


title: 293T cells, PRRC2B guides, DMEM, replicate2

description: KO Basal 2


title: Adipoctye,DMSO,24hr,Replicate,24hr,8

description:
Novogene contract only says NovaSeq
gene_count_matrix_24hr.csv

value: DMSO 24 hr


title: 293T cells, PRRC2B guides, DMEM, replicate1

description: KO Basal 1


title: T0070907 Replicate 1


title: RIL175_STING_N, rep 1

description: Library name: Sample 28


title: Adipoctye,MRL24,24hr,Replicate,24hr,8

value: MRL24 24 hr


title: T0070907 pretreated Rosiglitazone Replicate 2


title: RIL175_Control_N, rep 3

description: Library name: Sample 27


title: RIL175_PD1_VEGFR2_N, rep 2

description: Library name: Sample 32


title: 293T cells, NT guide, DMEM, replicate2

description: NT Basal 3


title: T0070907 pretreated Rosiglitazone Replicate 1


title: Adipoctye,Rosiglitazone,24hr,Replicate,24hr,8

value: Rosiglitazone 24 hr


title: RIL175_Control_N, rep 2

description: Library name: Sample 26


title: RIL175_PD1_VEGFR2_N, rep 1

description: Library name: Sample 31


title: 293T cells, NT guide, DMEM, replicate1

description: NT Basal 1


title: Adipoctye,GW1929,24hr,Replicate,24hr,8


title: T0070907 pretreated  GW1929 Replicate 2


title: RIL175_Control_N, rep 1

description: Library name: Sample 25


title: T0070907 pretreated  GW1929 Replicate 1


title: RIL175_Combination_T, rep 3

description: Library name: Sample 24

value: tumor


title: GW1929 Replicate 1

value: Adult Stem Cells - Zenbio


title: RIL175_Combination_T, rep 2

description: Library name: Sample 23


title: Adipoctye,MRL24,24hr,Replicate,24hr,7

value: Adipoctye


title: MA-VSMCs, calcium medium, LV-Vector, rep3

city: Jinan

first: Fengyang

last: Xu

state: Shandong

address: Wen Hua Xi Road

department: Qilu Hospital

institute: Shandong

data_processing:
Quality control was performed by the generation of FASTQ sequence files by Illumina’s CASAVA 1.8.2 software.
Reads were mapped against the mouse reference genome (GRCm38) with STAR v.2.4.
Normalization and differential expression analyses were done with DESeq2 (v.3.12) calling genes with a minimal 2-fold change and FDR-adjusted P<0.05 differentially expressed.
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa
Supplementary files format and content: tab-delimited text flie includes raw conuts for each sample
Supplementary files format and content: tab-delimited text flie includes RPKM values for each Sample

source_name: primary  aortic vascular smooth muscle cells

growth_protocol: Primary mouse aortic vascular smooth muscle cells (MA-VSMCs) were isolated from the aortas of 5- to 6-week-old C57BL/6J mice. Briefly, the adventitia and endothelium of the thoracic arteries were removed, and the remaining tissue was cut into approximately 1 mm2 sections. The sections of the aorta were then placed in cell culture dishes containing vascular cell basal medium (DMEM with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin). After being cultured in a 37℃ incubator with 5% CO2 for 5 to 7 days, the VSMCs migrated from the explants and then expanded. Cells between passages 5 and 8 were used in the subsequent experiments.

extract_protocol:
RNA was purified using RNeasy Mini Kits (QIAGEN, 74104) from MA-VSMCs after treatment with calcification medium or without it, combined with or without αKlotho lentiviral vector transfection (each in triplicate). RNA was quantified using an Agilent 2100 Bioanalyzer Instrument (Agilent Technologies, USA).
RNA sequencing libraries were prepared and sequenced at the Illumina facility.

treatment_protocol: MA-VSMCs were transfected with lentiviral empty vector (Vector) or αKlotho vector (αKlotho) and with or without exposure to calcification medium (containing 3.0mM sodium phosphate, Pi)for 7 days.

value: primary cells

value: calcium medium, LV-Vector transfection


title: MA-VSMCs, calcium medium, LV-Vector, rep2

value: primary  aortic vascular smooth muscle cells

value: WT


title: AEVs

city: Nanjing

first: xuhui

last: Ge

address: Hanzhong Road

institute: Nanjing medical university

description:
Library name: Sample 2
SeekGene

data_processing:
The raw sequencing data was processed by Fastp firstly to trim primer sequences and low-quality bases. Subsequently, Seeksoul tools (Seekgene, v1.2.1) was used to process the resting data, demultiplex cellular barcodes and map reads to the mouse mm10 reference genome to generate a feature-barcode matrix, which was used for the downstream analyses
Analysis was performed in R using the Seurat package. Nuclei with inadequate features (less than 200 expressed genes) and with mitochondrial genes higher than 20% were excluded. Genes expressed in less than 10 nuclei were removed and DoubletFinder package was used to remove doublets. Filtered gene expression matrices were then transformed, log normalized, scaled using 2000 most highly variable genes, and integrated through anchors. 30 principal components were then selected for cell clustering and UMAP was used for cluster visualization with a resolution of 0.3. Marker genes of each cluster were created via ‘FindMarkers’ function, and cell type annotation was performed according to canonical marker genes with SingleR package.
Assembly: Mouse mm10
Supplementary files format and content: PBS_barcodes.tsv.gz,PBS_matrix.mtx.gz,features.tsv.gz
Supplementary files format and content: AEVs_barcodes.tsv.gz,AEVs_matrix.mtx.gz,features.tsv.gz

source_name: spinal cord cells

growth_protocol: Mice were housed in a temperature-controlled room (22°C) on a 12-hour light/dark cycle with ad libitum access to food and water.

extract_protocol:
Nuclei were isolated from injured mouse spinal cords at day 7 post-injury for snRNA-seq. Briefly, mice were euthanized and spinal cord was rapidly dissected and frozen in liquid nitrogen. The nucleus was isolated using IGEPAL® CA-630 (Sigma I8896) as instructions. The samples were cut and transferred to a 5 mL tube containing lysate, mixed and lysed for 2 min on ice, then filtered through a 40 μm filter. Nucleus count and viability was estimated using SeekMate Tinitan Fluorescence Cell Counter (SeekGene M002C) with AO/PI reagent. Subsequent experiments were performed if the nuclear envelope was intact and there were fewer impurities.
libraries were prepared using SeekOne® DD Single Cell 3’ library preparation kit (SeekGene). Briefly, appropriate number of cell nucleus were mixed with reverse transcription reagent and then added to the sample well in SeekOne® DD Chip S3. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip S3. After emulsion droplet generation reverse transcription were performed at 42 ℃ for 90 minutes and inactivated at 85 ℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were cleanup with VAHTS DNA Clean Beads (Vazyme, N411-01), analyzed by Qubit (Thermo Fisher Scientific, Q33226) and Bio-Fragment Analyzer (Bioptic, Qsep400). The libraries were then sequenced on illumina NovaSeq X Plus with PE150 read length.

treatment_protocol: After isoflurane-induced anesthesia, mice were anesthetized with sodium pentobarbital intraperitoneally. The mice were then fixed in a prone position to localize the T10 spine. After skin preparation, the dorsal operative area was sterilized with 75% alcohol and draped. The epidermis was incised to separate the muscle and define the T10 spine. The T10 spinous process and vertebral plate were occluded to expose the spinal dural sac. A 5-gram rod (1-mm diameter, Reward, Shenzhen, China) was used to cause spinal cord impact contusion by dropping it from a height of 6 cm. Animals were administered a prophylactic dose of antibiotics prior to surgery and continued to receive them daily for 5 days post-surgery. Postoperatively, animals underwent daily artificial drainage of the bladder until signs indicating normal bladder function became apparent. Mice received daily tail-vein injections of AEVs (containing 100 μg of total protein from EVs in 100 μL of PBS) or PBS alone as a control (100 μL) for five consecutive days after SCI.

value: spinal cord

value: Mixed spinal cord cells

value: C57BL/6 (wild-type)

value: SCI and AEVs


title: Adipoctye,GW1929,24hr,Replicate,24hr,7


title: 293T cells, NT guide, DMEM, replicate3

description: NT Basal 4


title: N. punctiforme cells, Light24, bio rep 3

city: Woods Hole

first: Blair

last: Paul

address: 7 MBL St

institute: Marine Biological Laboratory

data_processing:
Alignment, normalization, and transcript abundance was performed using the Rockhopper software package with default settings.
Assembly: GCA_000020025.1
Supplementary files format and content: comma-separated text file includes each replicate's upper quartile normalized gene counts and the time point's smoothed local regression estimate of gene expression

organism: Nostoc punctiforme PCC 73102

growth_protocol: All replicate cultures contained an initial biomass equivalent to ~47 μg chlorophyll ɑ in 25 mL of Allan and Arnon standard growth media, diluted fourfold (AA/4). Cultures were grown at 28℃ under constant shaking (130 rpm) for 12 hours of light (40 - 50 μmol photons m-2s-1), followed by 12 hours of darkness. Following 192 hours of diurnal growth, cultures were subjected to 24 hours of light (Light24), wherein Dark24 cultures were wrapped in tin foil to occlude light.

extract_protocol:
Flash-frozen sample pellets were subjected to mechanical lysis, lithium chloride precipitation, and RNeasy Plus Mini Kit and on-column DNase treatment (QIAGEN).
Bacterial mRNA enrichment was performed with NEBNext rRNA Depletion Kit (Bacteria) and RNA Sample Purification Beads. Non-directional cDNA libraries were synthesized using Invitrogen SuperScript IV First-Strand Synthesis System before library preparation with the Tecan Life Sciences Ovation Ultralow V2 DNA-Seq Library Preparation Kit. Samples were ran with the Illumina NextSeq 500/550 High Output Kit v2.5 (150 cycles).

tag: Stage

tag: light state

value: Light

value: 216 hours


title: RIL175_Combination_T, rep 1

description: Library name: Sample 22


title: Adipoctye,DMSO,24hr,Replicate,24hr,6


title: MA-VSMCs, calcium medium, LV-Vector, rep1


title: Rosiglitazone Replicate 1

value: Rosiglitazone 3hr


title: Adipoctye,MRL24,24hr,Replicate,24hr,6


title: RIL175_PD1_VEGFR2_T, rep 1

description: Library name: Sample 19


title: N. punctiforme cells, Light24, bio rep 1


title: MA-VSMCs, calcium medium, LV-Klotho, rep2

value: calcium medium, LV-Klotho transfection


title: Adipoctye,DMSO,24hr,Replicate,24hr,7

value: DMSO 24 hr


title: MA-VSMCs, calcium medium, rep3

value: calcium medium (containing 3.0mM sodium phosphate, Pi)


title: MA-VSMCs, calcium medium, LV-Klotho, rep1


title: RIL175_STING_T, rep 3

description: Library name: Sample 18

value: tumor


title: Adipoctye,Rosiglitazone,24hr,Replicate,24hr,6

value: Adult Stem Cells - Zenbio

value: Rosiglitazone 24 hr


title: N. punctiforme cells, Dark24, bio rep 3

value: Dark


title: Adipoctye,Rosiglitazone,24hr,Replicate,24hr,7

value: Adipoctye


title: RIL175_STING_T, rep 2

description: Library name: Sample 17


title: Adipoctye,GW1929,24hr,Replicate,24hr,6


title: MA-VSMCs, calcium medium, rep2

value: primary  aortic vascular smooth muscle cells

value: primary cells


title: N. punctiforme cells, Dark24, bio rep 2


title: RIL175_PD1_VEGFR2_T, rep 3

description: Library name: Sample 21


title: PBS

description:
Library name: Sample 1
SeekGene

value: spinal cord

value: SCI and PBS


title: Adipoctye,DMSO,24hr,Replicate,24hr,5

value: WT


title: N. punctiforme cells, Dark24, bio rep 1


title: MA-VSMCs, calcium medium, LV-Klotho, rep3


title: N. punctiforme cells, Light24, bio rep 2


title: RIL175_STING_T, rep 1

description: Library name: Sample 16


title: MA-VSMCs, calcium medium, rep1


title: MA-VSMCs, Control, rep3

value: basal medium


title: RIL175_Control_T, rep 2

description: Library name: Sample 14


title: Adipoctye,MRL24,24hr,Replicate,24hr,5

value: MRL24 24 hr


title: RIL175_Control_T, rep 3

description: Library name: Sample 15


title: RIL175_PD1_VEGFR2_T, rep 2

description: Library name: Sample 20


title: N. punctiforme cells, Dusk2, bio rep 3

value: Pre-Dusk

value: Light

value: 192 hours


title: Adipoctye,Rosiglitazone,24hr,Replicate,24hr,5


title: MA-VSMCs, Control, rep2


title: Adipoctye,DMSO,24hr,Replicate,24hr,4

value: DMSO 24 hr


title: N. punctiforme cells, Dusk2, bio rep 2


title: Adipoctye,GW1929,24hr,Replicate,24hr,5


title: N. punctiforme cells, Dusk2, bio rep 1


title: N. punctiforme cells, MidLight2, bio rep 3

value: Mid-Light

value: 186 hours


title: RIL175_Control_T, rep 1

description: Library name: Sample 13

value: tumor


title: MA-VSMCs, Control, rep1