title: Athaliana+Boleracea+Csativa,seedling,rep2

description: Library name: NNAWO

organism:
Arabidopsis thaliana
Brassica oleracea
Camelina sativa

source_name: whole seedling

value: whole seedling

value: frozen


title: T cells, transduced unedited, Donor 1

status: Public on Jun 05 2025

type: SRA

city: New York

first: Zachary

last: Walsh

state: New York

address: 650 West 168th Street, Rm 1708

department: Hematology/Oncology

country: USA

institute: Columbia University

description:
Library name: D1_U
Control for baseline sgRNA library distribution pre-editing; serves as baseline for ABE8e and ABE9 screens as the same donors/cells were edited with each editor

library_source: genomic

data_processing:
.bases files were converted to FASTQ and samples were demultiplexed using Element's Bases2Fastq platform.
FASTQ files were trimmed with Cutadapt with the input: CTTGTGGAAAGGACGAAACACCG.
sgRNA enrichment analysis was performed using MAGeCK. For each sample, MAGeCK’s ‘count’ command was used to determine the number of sequencing reads mapped to each sgRNA. Across all sequenced samples, the mean reads per sample was 5,613,368 (range 2,842,507 to 9,279,031), mean percent of reads mapping to the sgRNA dictionary was 89.5% (range 88.0% to 91.7%), and mean Gini index was 0.066 (range 0.040 to 0.097).
MAGeCK’s ‘test’ command with default parameters was used to determine enriched and depleted guides in “treated” versus “control” conditions. For the pAKT/pS6 screen, “control” was defined as the pAKT/pS6-negative sort bin and “treated” was defined as the pAKT/pS6-high sort bin. For the proliferation screen, “control” was defined as a sampling timepoint immediately post-base editing and “treated” was defined as a sampling timepoint 14 days after T cell re-expansion. sgRNAs with low coverage (defined as MAGeCK median normalized read count <30 in the control group) were filtered from downstream analyses. A two-sided MAGeCK P value cutoff rather than a log2(fold change) cutoff was used to score significance to incorporate consideration of both sgRNA effect size and read count. sgRNAs were scored as significant if the MAGeCK two-sided P value was < 0.05.
Assembly: The custom sgRNA dictionary file was used to map sgRNA read counts per sample in MAGeCK count.
Supplementary files format and content: Raw sgRNA count outputs form MAGeCK count for each sample.
Library strategy: CRISPR Screen

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary Human T cells

growth_protocol: All T cell cultures were performed with OpTmizer SFM (Gibco #A1048501) supplemented with 1:40 OpTmizer Supplement (Gibco #A1048501), 1:100 GlutaMAX (Gibco #35050061), and 300 IU/ml IL-2 (Chiron) using a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
For unfixed samples (proliferation screen), DNA was extracted from library-edited T cells using a DNeasy Blood & Tissue Kit (Qiagen, #69504) per to the manufacturer’s protocols with buffer AL, and eluted in 100 µl buffer EB (Qiagen, #19086) per 5e6 T cells. For fixed samples (pAKT/pS6 screen), DNA was extracted as above with the following modification: samples were incubated overnight at 65 °C in buffer AL and proteinase K with shaking at 1000 RPM.
Sample amplification and indexing PCR was performed with ExTaq polymerase (Takara Bio, #RR001A): for unfixed and unsorted samples, 10 µg gDNA input per 100 µl PCR with 24 cycles; for fixed samples, 1µg gDNA input per 100 µl PCR with 24 cycles. Each gDNA sample was split across 8 parallel PCRs and then products were pooled after PCR to minimize library skewing. Pooled PCR products for each sample were cleaned up with 1x SPRI, quantified by D5000 Tapestation (Agilent, #5067-5588), and then pooled targeting 1000x read coverage per sgRNA per library and sequenced with a CloudBreak Freestyle Kit (Element Biosciences, #860-00015), 75 bp Read 1, 8 bp Index 1 on an Element AVITI sequencer (Element Bioscience).

treatment_protocol: Proliferation screen: T cells were restimulated with Immunocult CD3/CD28/CD2 T cell activation cocktail and expanded in G-REX 6-well plates for 14 days. Every 2-4 days, IL-2 and media were refreshed. After 14 days, T cells were harvested for DNA extraction and sequencing. AKT/S6 Screen: A total of 100e6 library-edited T cells per donor were stimulated in 96-well plates (with crosslinked anti-CD3/CD28 antibodies) for 20 minutes with approximately 1e6 T cells per well, to ensure high library coverage. Cells were then fixed, permeabilized, and stained with anti-pAKT (pS473) and anti-pS6 (pS235/pS236). Cells were sorted using an MA-900 cell sorter (Sony) with the 100µm nozzle, binned into the top 15% and bottom 15% of pAKT/pS6 expression, and collected in FACS buffer. Following the sort, the DNA extraction protocol was immediately initiated.

tag: cell type

value: Primary Human T cells

tag: genotype

value: Wild-type (unedited)

tag: treatment

value: Transduced, unedited

tag: batch

value: Day 0


title: Arabidopsis thaliana, H3.14 myc, antimyc, NaCl, biol rep 1

city: Madrid

first: Crisanto

last: Gutierrez

address: Nicolas Cabrera 1

department: Genome Dynamics and Function

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

data_processing:
ChIP-Seq raw reads were trimmed with Trimmomatic (v 0.39) to remove adapters and small sequences.
FastQC (v 0.11.9) was used to assess the quality control of the reads.
Trimmed reads were then aligned to the A. thaliana reference genome (TAIR10) using Bowtie2 (v 2.3.4.3) with default parameters.
Duplicate reads were removed with Picard MarkDuplicates (v 2.7.1)
Unmapped reads and unwanted regions (transposons, miRNA) were removed with SAMtools (v 1.9)
Narrow peaks were called with MACS2 (v 2.2.6, additional parameters -p 0.05 -s 150). DeepTools bamCompare (v 3.5.1) was used to normalize reads with CPM and against H3.
Assembly: Read pileup plots were generated with deepTools.
Supplementary files format and content: TAIR10
Supplementary files format and content: bam file for each sample

organism: Arabidopsis thaliana

source_name: Root tips

growth_protocol: Arabidopsis thaliana seedlings were grown in Murashige and Skoog (MS) with 1% sucrose and 1% agar medium. Seedlings were synchronized in long days (16h light 8h dark) at 22ºC.

extract_protocol:
Samples were fixed in 1% formaldehyde solution under vacuum (16% Formaldehyde (w/v), Methanol-free, ThermoFisher) for a total of 12 minutes. After nuclei extraction and lysis, soluble chromatin was incubated overnight at 4ºC with anti-myc. Conjugates were immunoprecipitated for 4 hours at 4ºC with protein G Dynabeads™ (ThermoFisher).
Libraries were generated using the Ovation® Ultralow V2 DNA-Seq Library Preparation Kit (Tecan), following manufacturer´s instructions. Total ChIPed DNA was resuspended in 10 µL of nuclease-free water and quantified by Qubit HS dsDNA assay (ThermoScientific) before the amplification step. 7 to 16 amplification cycles were used after taking in consideration ChIPed DNA concentration.

treatment_protocol: pHTR14::gHTR14::myc seedlings were treated with 140 mM NaCl during 4 hours 5 days after sowing.

tag: tissue

value: Root tips

tag: ecotype

tag: chip antibody

value: anti-myc

value: 4 h 140 mM NaCl


title: brassica-mix,leaf,rep1

city: Berkeley

first: Sharon

last: Greenblum

state: CA

address: 1 Cyclotron Road

institute: DOE Joint Genome Institute

description: Library name: OCHBH

library_source: transcriptomic single cell

data_processing:
Raw fastq files for each library were filtered using BBTools v38.96 bbduk.sh to remove read pairs with 31-mers in read 2 matching common ribosomal 31-mers. Filtered fastq files from 10X Chromium libraries were processed with Cellranger count v7.0.1, and filtered fastqs from BD Rhapsody libraries were processed with BD Rhapsody CWL pipeline (v2.2, available at bitbucket.org/CRSwDev/cwl) with default parameters. For libraries containing multiplexed species, combined-species reference genome and gene annotation files with species name preprended to the chromosome name were provided. Both processing workflows performed barcode identification, alignment, UMI de-duplication, gene aggregation, and final DGE matrix construction. Custom scripts were used to differentiate cell barcodes containing nuclei from each species (or multiple species in the case of doublets), as well as putatively empty droplets/wells and perform QC filtering. Demultiplexed libraries from the same species and tissue were integrated and clustered using Seurat v5.0 to create final atlases for a subset of species (available here as 14 Supplementary .RDS files).
Assembly: Arabidopsis thaliana Col-0 TAIR/Araport via Phytozome
Assembly: Arabidopsis lyrata MN47 Phytozome v2.1
Assembly: Brassica oleracea TO1000DH3 NCBI RefSeq GCF_000695525.1
Assembly: Capsella rubella Monte_Gargano Phytozome v1.1
Assembly: Sorghum bicolor RTx430 Phytozome v2.1
Assembly: Camelina sativa DH55 (via cruciferseq)
Assembly: Panicum hallii var. FIL2 Phytozome v3.2
Assembly: Brachypodium distachyon Bd21 Phytozome v3.2
Assembly: Thlaspi arvense MN106 NCBI GCA_911865555.2
Supplementary files format and content: Tab-separated values files and matrix files summarising transcript counts of each gene associated with each cell barcode (raw counts before any barcode filtering)

molecule: polyA RNA

organism:
Arabidopsis thaliana
Brassica oleracea
Arabidopsis lyrata
Capsella rubella

source_name: leaf

growth_protocol: Seeds from each species were surface sterilized before planting vertically on agar plates containing 3 mM Ca(NO3)2, 1.5 mM MgSO4, 1.25 mM NH4H2PO4, 1 mM KCl, 1x micronutrients (Murashige and Skoog Micronutrient Salts 100x, MSP18-10LT), in 0.8% agar with pH 5.7. Seedling root and shoot tissues from A. thaliana, A. lyrata, C. rubella, and B. oleracea were harvested at the 5-7 day old growth stage, and  root and shoot samples from S. bicolor were harvested from 3 day old seedlings. For mature leaves, we sampled the youngest fully expanded rosette leaf from plants grown in soil in a plant grow room or cold room. For floral buds, we sampled young buds on the main stem from plants grown in soil, where the petal was just emerging (~1 mm visible). Plant tissue samples were either processed immediately after harvest or flash frozen in liquid nitrogen.

extract_protocol:
Nuclei were isolated by chopping 20-100 mg fresh or frozen tissue for 3 minutes using a razor blade on a glass plate with 100-200 μl buffer in a cold room at 4°C. For multiplexed samples, tissues from different species were weighed separately before being combined and chopped together. The samples were then transferred to a 48-well filter plate. The filtered nuclei solution was centrifuged at 500x g for 10 minutes at 4°C to pellet the nuclei, after which the supernatant was discarded.
For profiling with 10X Chromium, the nuclei suspension was diluted to a concentration of 700-1000 nuclei/μl, then single nuclei were partitioned and barcoded using a Chromium system (10x Genomics) with the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index). Approximately 20,000 nuclei in total were loaded for single species samples, and up to 60,000 nuclei for multiplexed species samples. Library creation was carried out following the manufacturer’s protocol. For profiling with BD Rhapsody, the pooled nuclei suspension was diluted to a concentration of 600-900 total nuclei/μl, then single nuclei were partitioned and barcoded on a BD Rhapsody system (BD Rhapsody HT Xpress, BD Rhapsody Scanner), using the BD Rhapsody WTA V3 kit and cartridge, loading 50,000-150,000 total nuclei per lane. Library creation was carried out following the manufacturer’s protocol.

value: leaf

tag: tissue condition

value: fresh

tag: platform

value: 10X Chromium

tag: number of_multiplexed_species


title: Naïve microglia WT2

city: Bethesda

first: Anup

last: Dey

address: 9000 Rockville Pike

department: DDB

institute: NIH/NICHD

library_source: transcriptomic

data_processing:
RNA-seq data was analyzed using CCBR pipeliner and RENEE (RNA sequencing analysis pipeline).
These pipelines allowed determination of sequence quality before and after adaptor trimming (Fastqc), adaptor trimming (Cutadapt), align reads against reference genome (STAR), convert STAR aligned bam file into forward and reverse strand bigwigs, suitable for genome track viewer,
Pipelines include quantification of gene expression (RSEM) and differential expression profiling (DESeq2, edgeR)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each sample
Supplementary files format and content: BigWig files for each sample

molecule: total RNA

organism: Mus musculus

source_name: Microglia

growth_protocol: Tamoxifen 2mg/mouse was injected intraperitoneally  at 7-8 weeks old female mice

extract_protocol:
10,000 to 40,000 Mononuclear cells were prepared from brain and spinal cord using percoll gradient. CD11b/CD45/TMEM119 postive microglia cells were FACS sorted. Total RNA was extracted using Trizol/chloroform. RNA was precipitated with isopropanol, washed with ETOH, dried and subjected for library preparation.
For library preparation from small input RNA, Smart-Seq v4 RNA-seq library kit was used  Nexttera XT-DNA library prep kit was used for Adaptor ligation and library normalization.

treatment_protocol: For active immunization 11-12 weeks old Mice were immunized with MOG35-55/CFA and PTX following the instruction of Hooke laboratory (http://hooklabs.com)

value: Microglia

value: WT

value: No treatment


description: Library name: AT4G25490_S_lycopersicum_Heinz-1706-BG_DAPi712A08-ORGi5039-96P220

data_processing:
Fastq files were quality filtered and adapters were trimmed using BBTools v38.96 bbduk.sh62 with parameters k=21 mink=11 ktrim=r tbo tpe qtrim=r trimq=6 maq=10, and then aligned to the corresponding reference genome using bowtie2 v2.4.2 and parameters --no-mixed --no-discordant. Bam files from negative control wells were merged using the samtools v1.15.1 merge command, to generate a single background file for each 96-well plate. The MACS3 v3.0.0a6 callpeak command was used to generate narrowPeak files, using the merged background as the control, with the parameters --call-summits --keep-dup 1 and –gsize with the total fasta genome size. Bigwig files were generated using deeptools v3.5.2 bamCoverage with parameters --extendReads --binSize 1 --ignoreDuplicates --maxFragmentLength 600 --normalizeUsing RPGC, and --effectiveGenomeSize with the total fasta genome assembly size of each species.
Assembly: Solanum lycopersicum Heinz-1706-BG:: SGN/ITAG via Phytozome ITAG4.0
Supplementary files format and content: narrowPeak are tab-delimited extended bed format files that contain peak regions identified by MACS3, using the matched negative controls on each 96 well plate to dentify regions that were enriched for by each transcription factor. The identified peaks represent putative transcription factor binding sites.
Supplementary files format and content: bigwig files show the genome coverage of each DAP-seq library. They can be used to compare coverage between different libraries and to view peaks in a genome browser. Note that they should be compared to the matched negative control libraries from the same plate.
Library strategy: DAP-seq

organism: Solanum lycopersicum

source_name: plant

growth_protocol: Various growth protocols and tissues were used for gDNA extraction depending on the plant species, however gDNA libraries were PCR amplified upstream of DAP-seq to remove condition/tissue-specific DNA modifications.

extract_protocol:
CTAB protocol for gDNA extraction
Genomic DNA fragment libraries were constructed with an average shearing size at 150 bp. Different species were labeled by unique Illumina i5 index adapters to enable multiplexing following the multiDAP method. Upstream of the DAP-seq assay, fragment libraries were amplified for 10 cycles to remove any DNA modifications. After performing the DAP-seq enrichment in 96-well plates with each well containing a single in vitro expressed transcription factor, the libraries were amplified with i7 index primers to attach a unique i7 adapter corresponding to each well.

value: plant

tag: tf id

tag: tf family

tag: multidap sample_id

tag: 96 well_plate_id

tag: tf source_species


title: T cells, ABE8e edited, baseline, Donor 1

description:
Library name: D1_ABE8e_baseline
Control for baseline sgRNA library distribution immediately post-editing (ABE8e)

value: Base edited (PIK3CD/PIK3R1 library)

value: Transduced, edited (ABE8e)

value: Day 4


description: Library name: AT1G49480_S_lycopersicum_Heinz-1706-BG_DAPi712A04-ORGi5039-96P220

value: REM


title: NP_2hrs_Rep1

status: Public on Jun 04 2025

type: protein

city: Keelung City

first: Yu-Chiau

last: Shyu

address: No. 200, Ln. 208, Jijin 1st Rd., Anle Dist.

country: Taiwan

institute: Chang Gung Memorial Hosipital

hyb_protocol: Array Buffer 6 is added to a 4-Well Multi-dish followed by placing individual membranes with their numbers facing up. After an hour of incubation, samples are prepared and added to the wells, followed by an overnight incubation at a cold temperature.    The membranes are then washed multiple times before a Detection Antibody Cocktail is added and incubated. Subsequent washes are performed, followed by the addition of Streptavidin-HRP and another incubation step. Further washes ensure the removal of excess reagents.    The membranes are then prepared for imaging by adding Chemi Reagent Mix and covering them with plastic sheet protectors. Excess reagent is removed before carefully wrapping the membranes in plastic

scan_protocol: The arrays were analyzed using the UVP imaging system and exposed for 10 min, with one picture recorded every 3 min. The results were quantified using ImageJ software (JAVA 1.8.0, USA)

data_processing: The raw intensity values from the cytokine array were normalized using a widely recognized global adjustment method. Specifically, for each array, we calculated a replicate-specific normalization factor (F_i) based on the mean intensity across three positive references (R ̅_i), each measured in duplicate spots, using the formula F_i=(min(1,R ̅_((i%2)+1))⁄R ̅_i ). Here, i represents the index of the replicate, which is either 1 or 2, min refers to taking the minimum between values, and % represents the modulo operation. Subsequently, we multiplied each raw intensity value by the normalization factor of the corresponding replicate to obtain the normalized intensity value. The expression fold change (FC) of a specific gene under an experimental condition (AP or NP at 0.5, 2, or 16 hours) was determined as the ratio relative to the control group (AP at 0 hours) using the average of the normalized intensity values across replicates. In addition, each gene profiled on the array was classified into one of five distinct functional groups: hemostasis (3 genes), inflammation (43 genes), inflammation & proliferation (20 genes), proliferation (26 genes), and remodeling (7 genes). When calculating the FC for each functional group, we computed the mean FC across all gene members within the same group.

label: Antibody

molecule: protein

source_name: Serum

label_protocol: Serum cytokine levels were analyzed using the mouse XL cytokine array (R&D Systems, USA) according to the manufacturer’s instructions. Serum samples (20 µL) from the AP or NP groups were combined for each test for a final volume of 100 µL for each array membrane.

extract_protocol: We collected 500 µL of blood in 1.5 mL Eppendorf tubes from the cheeks of the mice after AP or NP treatment before euthanasia. After setting for 0.5-2 hrs, centrifugation was performed at 1,500 g and 4°C for 10 min. The supernatant was transferred into a new tube and centrifuged at 13,000 and at 4°C for 3 min to obtain the serum.

tag: strain

value: Serum

tag: age

value: Eight-week-old

tag: Sex

value: Male


title: NP_16hrs_Rep1


title: NP_0.5hr_Rep2


title: AP_16hrs_Rep2


title: NP_0.5hr_Rep1


title: NP_16hrs_Rep2


title: AP_2hrs_Rep2


title: AP_16hrs_Rep1


title: AP_2hrs_Rep1


title: CTRL_0hr_Rep2


title: NP_2hrs_Rep2


title: S48

city: Stanford

first: Daniel

last: Richard

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

description:
Library name: S48
Eptesicus fuscus EF_LU -treatment- infect_24

data_processing:
TrimGalore! read trimming
STAR transcriptome alignment
DESEQ2 analysis
Assembly: GRCh38.100, GCF_000308155.1
Supplementary files format and content: CSV of aligned read counts

organism: Eptesicus fuscus

extract_protocol:
RNA was isolated from whole cell lysates using RNeasy Mini kit (Qiagen, 74106).
Sequencing was conducted at the McMaster Genomics Facility, Farncombe Institute at McMaster University. RNA quality was first verified using a Bioanalyzer (Agilent), followed by poly(A) enrichment (NEBNext Poly(a) mRNA Magnetic Isolation Module; NEB). Library were prepared (NEBNext Ultra II Directional RNA Library Prep Kit; NEB) and library fragment size distribution was verified (Agilent TapeSection D1000; Agilent). Libraries were quantified by qPCR and pooled in equimolar amounts. Subsequently, qPCR and fragment size distribution were verified. Libraries were then sequenced on an Illumina HiSeq 1500 across 12 HiSeq Rapid v2 flow cells in 6 lanes (Illumina) using a paired end, 2x50 bp configuration, with onboard cluster generation averaging 80M clusters per biological replicate.

treatment_protocol: Clinical isolate of ancestral SARS-CoV-2 (SARS-CoV-2/SB2) was used for infections. Cells at ~80% confluence were infected with SARS-CoV-2 at indicated multiplicity of infection (MOI). Control cells were treated with serum-free DMEM alone (mock infected). Infected and mock infected cells were incubated at 37 °C for 1 h with gentle rocking every 15 min. After 1 h, the virus inoculum was aspirated, cells were washed 1x with phosphate-buffered saline (PBS), and complete growth medium was added. Cells were infected with SARS-CoV-2 at an MOI of 0.1 for 12 and 24 h. Time-matched, sham infected cells served as controls.

tag: cell line

tag: cell type


title: AP_0.5hr_Rep1

tag: treatment


title: S46

description:
Library name: S46
Eptesicus fuscus EF_LU -treatment- infect_24

tag: tissue

tag: batch


title: S45

description:
Library name: S45
Eptesicus fuscus efk3B -treatment- infect_24


title: S47

description:
Library name: S47
Eptesicus fuscus EF_LU -treatment- infect_24


title: S44

description:
Library name: S44
Eptesicus fuscus efk3B -treatment- infect_24


title: S35

description:
Library name: S35
Eptesicus fuscus EF_LU -treatment- infect_12


title: S36

description:
Library name: S36
Eptesicus fuscus EF_LU -treatment- infect_12


title: S33

description:
Library name: S33
Eptesicus fuscus efk3B -treatment- infect_12


title: S32

description:
Library name: S32
Eptesicus fuscus efk3B -treatment- infect_12


title: S31

description:
Library name: S31
Eptesicus fuscus efk3B -treatment- infect_12


title: S43

description:
Library name: S43
Eptesicus fuscus efk3B -treatment- infect_24


title: S24

description:
Library name: S24
Eptesicus fuscus EF_LU -treatment- mock_24


title: S22

description:
Library name: S22
Eptesicus fuscus EF_LU -treatment- mock_24


title: S23

description:
Library name: S23
Eptesicus fuscus EF_LU -treatment- mock_24


title: S34

description:
Library name: S34
Eptesicus fuscus EF_LU -treatment- infect_12


title: AP_0.5hr_Rep2


title: S21

description:
Library name: S21
Eptesicus fuscus efk3B -treatment- mock_24


title: S20

description:
Library name: S20
Eptesicus fuscus efk3B -treatment- mock_24


title: S10

description:
Library name: S10
Eptesicus fuscus EF_LU -treatment- mock_12


title: S12

description:
Library name: S12
Eptesicus fuscus EF_LU -treatment- mock_12


title: S9

description:
Library name: S9
Eptesicus fuscus efk3B -treatment- mock_12


title: S19

description:
Library name: S19
Eptesicus fuscus efk3B -treatment- mock_24


title: S7

description:
Library name: S7
Eptesicus fuscus efk3B -treatment- mock_12


title: Stickleback brain, juvenile

city: La Jolla

first: Benjamin

middle: D

last: Gastfriend

address: 9500 Gilman Dr

institute: University of California, San Diego

description: Library name: Stickleback_juvenile_brain

data_processing:
Basecalling was performed by the NovaSeq X Plus.
Reads were aligned and UMIs quantified using CellRanger (v9.0.1).
Assembly: GCF_016920845.1_GAculeatus_UGA_version5 (NCBI)
Supplementary files format and content: Filtered feature/barcode matrices produced by CellRanger in h5 archive format.

organism: Gasterosteus aculeatus

source_name: Brain

extract_protocol:
Nuclei were isolated from flash-frozen brain tissue via iodixanol gradient centrifugation.
Libraries were prepared using the Chromium GEM-X Single Cell 3' Reagent Kit v4 (10X Genomics).

value: Brain


title: MecrKO_Rep3

city: Nashville

first: Denis

last: Mogilenko

state: Tennessee

address: 1161 21st Ave S, MCN A3208B, Mogilenko Lab

department: Medicine

institute: Vanderbilt University Medical Cente

data_processing:
Sequence reads were trimmed for adapter sequence (Illumina, TruSeq3-PE.fa) and low quality reads using Trimmomatic with parameters: MINLEN 36; LEADING 3; TRAILING 3; SLIDINGWINDOW 4:20; ILLUMINACLIP_SETTINGS 2:30:10
Trimmed sequences were aligned to GRCm39/mm39 (GCF_000001635.27) using STAR in twoPass basic mode paired-end mode with sjdbOverhang = 100
Raw counts matrix was calculated using featureCounts with parameters  -p \ --countReadPairs \  -B \  -C \  -s 2 \   -t exon \
Assembly: mm39
Supplementary files format and content: Tab-delimeted txt file with raw counts matrix

source_name: Spleen

growth_protocol: Donor cells were prepared by isolating naïve CD4+ T cells (CD4+ CD44-) by magnetic bead isolation (Miltenyi, 130-104-453) from Mecrfl/fl; Cd4cre – (WT) or + (Mecr-KO) mice. 400,000 live naïve CD4+ WT or Mecr-KO T cells were transferred into Rag1-/-mice by i.p. injection. Following weight monitoring and IBD development, mice were euthanized after 8 weeks and the spleens were harvested and CD4+ T cells were isolated from the spleens of  Rag1-/- mice using Stem Cell Easy Sep Mouse CD4+ T cell Isolation Kit (Stem Cell 19852) according to the manufacturer’s protocol.

extract_protocol:
RNA was extracted from CD4+ T cells using Rneasy Plus mini kit (Qiagen)
The Vanderbilt Technologies for Advanced Genomics Core (VANTAGE) performed mRNA enrichment and cDNA library preparation utilizing the stranded mRNA (polyA-selected) library preparation kit.

treatment_protocol: Mecr fl/fl Cd4 cre - (WT) or Mecr fl/fl Cd4 cre + (Mecr-KO)

value: Spleen

value: CD4+ T cell

tag: genotype

value: Mecr fl/fl Cd4 cre +


title: S8

description:
Library name: S8
Eptesicus fuscus efk3B -treatment- mock_12


title: Pseudomonas donghuensis HYS fur mutant, growth on NGM plate, 24h

city: WuHan

first: Donghao

last: Gao

state: Hubei

address: College of Life Sciences, Wuhan University, 299 Bayi Road, Wuchang District, Wuhan, Hubei Province, China.

department: College of Life Sciences

country: China

institute: WuHan University

description: Library name: Sample5

data_processing:
Raw sequencing data were first quality-controlled using FASTX_TOOLKIT (Version 0.0.14), evaluated with FASTAQ (0.19.5), and ribosomal RNA contamination assessed via Rfam database (Version14.8). Sequence alignment was performed using STAR (Version 2.7.1a). Gene annotation utilized NR database (Version 2022.10), Pfam database (Version 35.0), KEGG database (Version 2022.10), eggNOG database (Version 2020.06), Swiss-prot database (Version 2022.10), and GO database (Version 2022.0915). Expression analysis was conducted using Salmon (Version 1.3.0) and differential expression statistics with DEseq2 (Version 1.24.0). Gene enrichment analysis was performed using KEGG, GO, and COG databases.
Assembly: Pseudomonas donghuensis HYS  AJJP00000000.1;  Caenorhabditis elegans GCA_000002985.3.
Supplementary files format and content: csv files include TPM values for each sample

organism: Pseudomonas donghuensis

source_name: bacteria

growth_protocol: Escherichia coli OP50 cultured in LB medium at 37℃ . HYS and the fur-deletion strain were cultured in LB medium at 30℃. Wild-type N2 Bristol strain Caenorhabditis elegans were fed with E. coli OP50 on NGM plates at 22 ℃.

extract_protocol:
For the Caenorhabditis elegans  samples, collected nematodes were ground rapidly from liquid nitrogen and processed using an RNA extraction kit (Nanjing, Vazyme, RC112). Ground nematodes were resuspended in lysis buffer, added to a genomic DNA removal column, centrifuged at 12,000 rpm for 1 minute, filtrate collected, and RNA adsorbed, washed twice, and eluted using RNase-free water. For bacteria samples, mRNA was extracted using the Trizol method. Following the lysis of bacterial cells, guanidine isothiocyanate in Trizol was employed to denature proteins and inhibit RNase activity. RNA was then separated from the aqueous phase through chloroform partitioning, and total RNA (including mRNA) was precipitated with isopropanol. Subsequently, impurities were removed by ethanol washing, and the final product was dissolved in nuclease-free water.
For the Caenorhabditis elegans samples, including the Dual-RNA seq samples, the enriched mRNA consisted of complete RNA sequences, which were randomly fragmented by adding fragmentation buffer to generate small fragments of approximately 300 bp. Under the action of reverse transcriptase, random primers were utilized to synthesize a single strand of cDNA using mRNA as the template, followed by the synthesis of the second strand to form a stable double-stranded structure. The double-stranded cDNA structure featured sticky ends, which were converted to blunt ends by adding End Repair Mix. Subsequently, an A base was added to the 3' end, and the products were purified and size-selected after adapter ligation, followed by PCR amplification of the selected products to obtain the final library. For the bacterial samples, the TruSeq™ Stranded Total RNA Library Prep Kit was employed to construct the library. In the synthesis of the second strand of cDNA, dUTP was used in place of dTTP in the dNTP reagent, resulting in the incorporation of A/U/C/G bases in the second strand of cDNA. Prior to PCR amplification, UNG enzyme was utilized to digest the second strand of cDNA, ensuring that the library contained only the first strand of cDNA.

treatment_protocol: 1000 adult nematodes were transferred to NGM plates smeared with pathogenic bacteria(HYS，and fur mutant)and OP50, incubated at 22 ℃ for 24 hours

value: bacteria

value: bacteria cell

value: Pseudomonas donghuensis HYS fur mutant

value: growth on NGM plate


title: Pseudomonas donghuensis HYS, growth on NGM plate, 24h

description: Library name: Sample4

value: WT


title: MecrKO_Rep1


title: Stickleback brain, adult

description: Library name: Stickleback_adult_brain


title: WT_Rep3

value: Mecr fl/fl Cd4 cre -


title: CTRL_0hr_Rep1


title: WT_Rep2


title: WT_Rep1


title: SC5314, Cinnamaldehyde, replicate3

city: Hefei

first: Wenqian

last: Li

address: Longzihu Road

institute: Anhui University of Chinese Medicine

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (0.19.5) with default parameters.Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (Version 2.1.0) software. The mapped reads of each sample were assembled by StringTie (Version2.1.2) in a reference-based approach.
The expression level of each transcript was  calculated  according  to  the  transcripts per million  reads  (TPM)  method.  RSEM (Version 1.3.3) was used to quantify  gene  abundances.
Assembly: GCF_000182965.3
Supplementary files format and content: table-delimited text file includes read counts for each sample
Supplementary files format and content: table-delimited text file includes tpm for each sample

organism: Candida albicans SC5314

source_name: fungi

growth_protocol: C. albicans strain SC5314 was grown in YPD medium at 37 ℃

extract_protocol:
Total RNA was extracted using MJZol total RNA extraction kit (Shanghai Majorbio Bio-pharm Technology Co.,Ltd) according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo (dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150 bp read length).

treatment_protocol: C. albicans strain SC5314 was cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 2 × 10^5 CFU/mL and incubated at 37 ℃ for 24 hours in the presence of cinnamaldehyde at 31.25 μg/mL. The 5% DMSO-treated group was used as a control.

value: fungi

value: fungal cell

value: wild type

value: incubated at 37 degreeC for 24 hours in the presence of cinnamaldehyde at 31.25 mirogram/mL


title: MecrKO_Rep2


title: SC5314, Control, replicate2

value: incubated at 37 degreeC for 24 hours in the presence of 5 percent DMSO


title: NJ30

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: raw counts

data_processing:
The fastQ resulting from sequencing were imported into the QIIME 2 environment (ver 2023.7)
Assembly: Greengenes
Supplementary files format and content: raw counts
Library strategy: 16S amplicon sequencing

extract_protocol:
The microbic DNA was extracted with the QIAsymphony DSP/ Virus/pathogen Midi (QIAGEN) used on the QIAsymphony SP instrument (QIAGEN)
16S rRNA gene amplicons libraries were generated with ION 16S Metagenomics kit (Thermo Fisher Scientific)

value: M

tag: age (years)

tag: bmi

value: previously

tag: pathology

value: other

value: no


title: NJ60

description: raw counts

value: negative

value: yes


title: SC5314, Control, replicate1


title: NI90

description: raw counts

value: F

value: positive


title: MY58

description: raw counts


title: SC5314, Cinnamaldehyde, replicate1


title: SC5314, Control, replicate3


title: S11

description:
Library name: S11
Eptesicus fuscus EF_LU -treatment- mock_12


title: MY43

description: raw counts


title: MP23

description: raw counts


title: MO78

description: raw counts


title: MM07

description: raw counts

value: CNS tumor


title: MH61

description: raw counts


title: MH31

description: raw counts


title: MH81

description: raw counts


title: MH76

description: raw counts


title: MY28

description: raw counts


title: MM02

description: raw counts


title: MB67

description: raw counts


title: MH01

description: raw counts


title: MH11

description: raw counts


title: MB52

description: raw counts


title: MY98

description: raw counts


title: MI26

description: raw counts


title: MB12

description: raw counts


title: MA92

description: raw counts


title: MA77

description: raw counts


title: MA37

description: raw counts


title: MA42

description: raw counts


title: MA52

description: raw counts


title: MA97

description: raw counts


title: MI01

description: raw counts


title: LZ82

description: raw counts


title: LZ72

description: raw counts


title: ischemia reperfusion acute kidney injury, 30 min, with MTAPi, rep4

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Library name: Sample_126

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 algorithm (v2.1.0)
gene count measurements were obtained using FeatureCounts using refseq annotation
Assembly: mm10
Supplementary files format and content: Tab-delimited text file with columns: 1) GeneID, 2) Chr; 3) transcript start position; 4) transcript end position; 5) Strand; 6) Length of transcript; 7) read counts

source_name: Kidney

extract_protocol:
Total RNA was extracted using Qiagen Rneasy MiniKit (Cat# 74104) from tumor and quantified using nanodrop and Agilent bioanalyzer.
Total RNA samples  were used for sequencing library preparation according to Illumina stranded mRNA sample preparation guide. Each library was bar-coded and then pooled for sequencing run with 100bp paired-read sequencing protocol.

treatment_protocol: Ten- to twelve-week-old male C57BL/6J mice were used for the study. Mice were anesthetized by inhalation of isoflurane (3% in oxygen). All procedures were performed on anesthetized mice on controlled heating pads with body temperatures monitored and maintained at 36-37 °C. Bilateral renal ischemia-reperfusion (IR) was conducted. Briefly, the renal pedicles were identified via flank incisions and clamped for 30 or 35 min with small nontraumatic vascular aneurysm clips. After clamp removal, reperfusion was confirmed by observing restoration of kidney color, indicating arterial blood flow. All mice were sacrificed 24 hours after surgery.

value: Kidney

value: Bilateral renal ischemia-reperfusion (IR) was conducted for 30 min with small nontraumatic vascular aneurysm clips, with  MTAP inhibitor (20mg/kg)  intraperitoneal injection 4.5 hours before ischemia.


title: ischemia reperfusion acute kidney injury, 30 min, with MTAPi, rep5

description: Library name: Sample_134


title: ischemia reperfusion acute kidney injury, 30 min, with MTAPi, rep1

description: Library name: Sample_120


title: ischemia reperfusion acute kidney injury, 30 min, with vehicle,  rep3

description: Library name: Sample_129

value: Bilateral renal ischemia-reperfusion (IR) was conducted for 30 min with small nontraumatic vascular aneurysm clips, mice were treated with vehicle 4.5 hours prior to ischemia (10% DMSO in 1XPBS)


title: MO73

description: raw counts


title: ischemia reperfusion acute kidney injury, 30 min, with vehicle,  rep1

description: Library name: Sample_122


title: ischemia reperfusion acute kidney injury, 30 min, with vehicle,  rep6

description: Library name: Sample_141


title: ischemia reperfusion acute kidney injury, 30 min, with vehicle,  rep4

description: Library name: Sample_139


title: ischemia reperfusion acute kidney injury, 30 min, with MTAPi, rep3

description: Library name: Sample_125


title: MB03

description: raw counts


title: Sham, Rep5

description: Library name: Sample_25

value: Sham-operated mice underwent an identical procedure with no pedicle clamping


title: ischemia reperfusion acute kidney injury, 30 min, with MTAPi, rep2

description: Library name: Sample_121


title: ischemia reperfusion acute kidney injury, 30 min, with vehicle,  rep5

description: Library name: Sample_140


title: Sham, Rep6

description: Library name: Sample_26


title: ischemia reperfusion acute kidney injury, 30 min, with vehicle,  rep2

description: Library name: Sample_123


title: Sham, Rep4

description: Library name: Sample_15


title: Sham, Rep2

description: Library name: Sample_115


title: Sham, Rep1

description: Library name: Sample_103


title: Primary hepatocyte cells, PHH, Replicate1

city: Sao Paulo

first: Kayque

last: Alves Telles Silva

address: 106 Matao St.

country: Brazil

institute: University of Sao Paulo

description: Library name: Sample 5

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ ≥ 13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
Assembly: hg38
Supplementary files format and content: Processed data include peak files for each sample.

source_name: PHH

extract_protocol:
Nuclei was extracted from samples. The nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min.
Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. Hi-C library preparation was performed according to the Hi-C 2.0 protocol with minor modifications. Briefly, 1–5 million cells were incubated in trypsin for 15 minutes to facilitate detachment, then pelleted by centrifugation at 500g, washed twice with PBS, and fixed in 1% formaldehyde for 10–12 minutes. Fixation was quenched with glycine, after which cells were pelleted, washed, and stored at –80°C. For library preparation, frozen cells were thawed on ice, lysed, and digested overnight with 300 U of DpnII. The resulting DNA ends were labeled with biotin-14-dCTP using Klenow fragment and ligated overnight with T4 DNA ligase. Crosslinks were reversed by Proteinase K treatment at 65°C overnight, followed by ethanol precipitation. Unligated biotinylated ends were removed using T4 DNA polymerase.Next-generation sequencing (NGS) libraries were prepared using the KAPA HyperPlus Kit. Biotin-labeled ligation products were selectively enriched using Dynabeads MyOne Streptavidin C1 beads prior to library amplification. Sequencing was performed using 150 bp paired-end reads.

value: PHH

value: Hepatocyte cells


title: Hepatocyte-like cells, Etoposide, Replicate1

description: Library name: Sample 3

value: Hepatocyte-like cells


title: WT-4

city: Shanghai

first: Shujuan

last: Chang

address: siping road 1239

institute: tongji university

description: Library name: Sample4

data_processing:
bcl2fastq software used for basecalling.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: hippocampus

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

value: WT


title: Sirt6 KO-4

description: Library name: Sample8

value: Sirt6 KO


title: Sham, Rep3

description: Library name: Sample_116


title: Sirt6 KO-3

description: Library name: Sample7


title: Sirt6 KO-2

description: Library name: Sample6


title: Sirt6 KO-1

description: Library name: Sample5


title: T cells, ABE9 edited, pAKT/pS6 high, Donor 1

description:
Library name: D1_ABE9_AKTS6hi
pAKT/pS6 screen (ABE9)

value: Primary Human T cells

value: Base edited (PIK3CD/PIK3R1 library)

value: Transduced, edited (ABE9), acutely stimulated, pAKT/pS6-sorted

value: Day 11


title: Hepatocyte-like cells, Control, Replicate2

description: Library name: Sample 2


title: ILA3

city: nanjing

first: Shizhen

last: Zhou

state: jiangsu

address: 鼓楼区汉口路58号

institute: Department of General Surgery, Nanjing Drum Tower Hospital

data_processing:
Data filtering:
The raw data was filtered with SOAPnuke (v1.6.5) [1] by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping：
The clean data were mapped to the reference genome by HISAT (v2.2.1) [2].
Reference gene mapping:
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5) [3]. The expression level of genes was calculated by RSEM (v1.3.1) [4].
New transcript prediction:
StringTie (v2.2.1) was used to reconstruct transcripts, and Cuffmerge was used to integrate the assembled transcripts. Cuffcompare was used to compare the integrated transcripts to a reference annotation. The transcripts with class code types u, i, o, j were selected as new transcripts. The protein-coding potential of new transcripts was predicted by CPC (v0.1).
Gene Annotation:
Using public database (KEGG, GO, etc.) to annotate the genes.
Time Series and WGCNA analysis:
Time Series analysis was performed by Mfuzz (v2.60.0) [5], and gene co-expression network analysis was performed by WGCNA (v1.71).
Differential Gene Expression:
Between-group differential gene analysis was performed using DEseq2[6]/DEGSeq [7] under the conditions of Fold Change ≥ 2 and Adjusted Pvalue ≤ 0.001 (Depends on projects). PoissonDis was performed between-sample differential gene analysis under the conditions of Fold Change ≥ 2 and FDR ≤ 0.001(Depends on projects). Using the pheatmap function on the differential gene set to draw a heatmap of differential gene clusters. According to the GO and KEGG annotation results and official classification, the differentially expressed genes were functionally classified, and the phyper in R software was used for KEGG enrichment analysis, and the TermFinder package was used for GO Enrichment analysis. With Qvalue ≤ 0.05 as the threshold, candidate genes that met this condition was defined as being significantly enriched.

extract_protocol:
2. Experimental Procedures 2.1 Sample Lysis 2.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 2.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 2.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 2.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 2.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 2.2 DNA Purification  2.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 2.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 2.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 2.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 2.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 2.3 RNA Purification 2.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 2.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 2.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 2.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 2.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 2.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 2.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 2.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).
2. Experimental Procedures
2.1 Sample Lysis
2.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107).
2.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min.
2.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column.
2.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification.
2.1.5 Transfer the DNA spin column to the new collection tube for DNA purification.
2.2 DNA Purification
2.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate.
2.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate.
2.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube.
2.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min.
2.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA.
2.3 RNA Purification
2.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting.
2.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow.
2.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
2.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
2.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
2.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube.
2.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min.
2.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
2.1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2.2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
2.3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
2.4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
2.5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
2.6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
2.7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
2.8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
2.9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: ILA (1mM)


title: ILA2


title: WT-3

description: Library name: Sample3


title: ILA1


title: WT-2

description: Library name: Sample2


title: liver,rep5

city: shanghai

first: Yueying

last: Yang

state: shanghai

address: No. 85/86, Wujin Road, Hongkou District, Shanghai

institute: Shanghai General Hospital

description: Library name: db_1[MeRIP-Seq]

data_processing:
To prepare the RNA samples for sequencing, ribosomal RNA (rRNA) was selectively removed using an rRNA depletion kit, or alternatively, mRNA was enriched using a specialized mRNA enrichment kit.
Following this step, the resulting samples—either rRNA-depleted total RNA or enriched mRNA—underwent bisulfite conversion using the EZ RNA Methylation Kit from Zymo Research.
Post-conversion, strand-specific RNA libraries were constructed.
The quality of these libraries was rigorously assessed using a fragment analyzer and Qubit quantification, ensuring they met stringent standards before proceeding to next-generation high-throughput sequencing.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: MeRIP-Seq

source_name: liver

extract_protocol:
According to the manufacturer's instructions, liver total RNA in mice was extracted from TRIzol (Invitrogen, CA, USA).
Both input samples without IP and m5C IP samples were used to generate the RNA-seq library using the EZ RNA methylation Kit (Zymo Research).

value: liver


title: liver,rep7

description: Library name: db_3[MeRIP-Seq]


title: liver,rep8

description: Library name: db_4[MeRIP-Seq]


title: CON3

value: DMSO


title: CON2


title: CON1


title: WT-1

description: Library name: Sample1


title: liver,rep6

description: Library name: db_2[MeRIP-Seq]


title: liver,rep4

description: Library name: db_C5[MeRIP-Seq]


title: Hepatocyte-like cells, Etoposide, Replicate2

description: Library name: Sample 4


title: heart, ko mouse 4

city: Leipzig

first: Linnaeus

middle: Tapia

last: Bundalian

address: 15 Albert-Scwheitzer Str.

country: Germany

institute: Universitatklinikum Leipzig

description: Library name: Sample 8

data_processing:
adapters were trimmed from the reads and reads < 60 bp were removed
Reads were mapped to the mouse genome (July 2007 NCBI37/mm9) with Ensembl v66 annotations using TopHat 1.3.3
The transcription level for each gene was obtained by intersecting mapping results with gene annotations using BEDTools.
Assembly: mouse genome (July 2007 NCBI37/mm9) with Ensembl v66 annotations
Supplementary files format and content: xlsx file includes fpkm values of each sample

source_name: heart

growth_protocol: Mice were maintained under specific pathogen-free conditions with a 12 hour light/dark cycle, at 21-24°C, and 55% humidity with unrestricted access to food and water.

extract_protocol:
TRI Reagent (Sigma-Aldrich) according to the manufacturer’s instructions. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260/280 nm (A260/A280) using a NanoDrop spectrophotometer.
Indexed cDNA libraries were generated using TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol, constructing libraries with an average size of 300bp as evaluated on the Agilent 2100 bioanalyzer with DNA 1000 Chips.

treatment_protocol: no treatment - adult mice

value: heart


title: liver,rep3

description: Library name: db_C4[MeRIP-Seq]


title: heart, ko mouse 3

description: Library name: Sample 7


title: heart, ko mouse 1

description: Library name: Sample 5


title: heart, wt mouse 5

description: Library name: Sample 4

value: wt


title: Hepatocyte-like cells, Control, Replicate1

description: Library name: Sample 1


title: heart, wt mouse 4

description: Library name: Sample 3


title: liver,rep2

description: Library name: db_C3[MeRIP-Seq]


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 28, pegRNA library, rep 2

city: Cambridge

first: Kathryn

last: Yost

state: Massachusetts

address: 455 Main St

department: Biology

institute: Whitehead Institute

description: Library name: PEtracer_B16F10_kinetics_D28_rep2_pegRNA

data_processing:
All scRNA-seq data was processed using the Cellranger software package (version 7.1.0). To capture lineage information a custom reference genome was constructed by appending the 2171 lineage tracing cassette sequences to the human hg38 genome build. Both gene expression and lineage tracing cassette libraries were then aligned to this reference using default parameters. Since the reference contains all 2171 30bp barcode sequences the integration barcode (intBC) of each lineage tracing cassette read can be determined based on which element in the reference it aligns to. A custom Python script was used to extract lineage information from the bam alignment file generated by Cellranger. This script iterated through all reads aligned to a tracing cassette sequence. For each read the lineage mark (LM) sequence at each edit site was determined based on the alignment. For each UMI the number of supporting reads was calculated and the LM for each site set to the LM with the most read support (ties broken randomly). UMIs were then aggregated by intBC, cellBC, and the set of LMs detected across the three edit sites to generate a final LM table. scRNA-seq data for puromycin and blasticidin barcode libraries was aligned using Cellranger to a custom reference. This reference included puromycin and blasticidin resistance cassette sequences with ‘N’s indicating the positions of the 10nt random barcodes. A custom Python script was used to extract the barcode sequence from each read aligned to these elements, generate a consensus barcode for each UMI, and aggregate UMIs by barcode for each cell. To separate barcode calls corresponding to real integrations from sequencing errors and ambient RNA, for each 10x capture a Gaussian mixture model was fitted to the distribution of UMIs per barcode per cell. Barcode calls corresponding to the lower peak were excluded as likely errors. pegRNA libraries were processed using the “CRISPR Guide Capture” feature of Cellranger. pegRNA protospacer mismatch calls supported by <3 UMIs were filtered out and careful quality control performed to exclude cells with multiple pegRNA integrations as these cells could confound our estimation of protospacer mismatch kinetics. Cells with multiple pegRNA calls were removed as well as cells with lineage cassette reads where more than one edit site had an LM installed.
Assembly: mm10
Supplementary files format and content: Processed data barcodes/features/matrix and filtered_counts.h5 files contain the filtered_feature_bc_matrix transcript count matrix outputs from Cellranger. BlastBC_counts.csv, PuroBC_counts.csv, allele_counts.csv, and mapping_counts.csv files contain unfiltered static barcode, lineage tracing cassette allele, and intBC mapping count data.

extract_protocol:
Single cell suspensions were washed with PBS + 0.04% BSA and captured using the 10X Genomics Next GEM Single Cell 3ʹ Kit v3.1
Gene expression libraries were prepared using the 10X Genomics Next GEM Single Cell 3ʹ Kit v3.1 according to the manufacturer's instructions. Targeted lineage tracing cassette, puromycin/blasticidin barcode, and pegRNA libraries were prepared from amplified cDNA using two or three rounds of PCR with target-specific amplification primers and sample indexing primers.


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 28, gene expression library, rep 2

description: Library name: PEtracer_B16F10_kinetics_D28_rep2_GEX


title: heart, wt mouse 3

description: Library name: Sample 2


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 28, lineage tracing cassette library, rep 2

description: Library name: PEtracer_B16F10_kinetics_D28_rep2_LTC


title: liver,rep1

description: Library name: db_C2[MeRIP-Seq]


title: heart, wt mouse 2

description: Library name: Sample 1


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 21, lineage tracing cassette library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D21_rep1_LTC


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 28, gene expression library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D28_rep1_GEX


title: mAdu1

city: Heidelberg

first: Stephanie

last: Gehrs

address: Im Neuenheimer Feld

institute: DKFZ

description: Library name: mAdu1

data_processing:
ATAC-seq reads were processed using the ENCODE ATAC-seq pipeline kundajelab/atac_dnase_pipelines v1, unless otherwise specified (Lee et al., 2016). As a reference, the mm10 genome was used. Reads were trimmed using Cutadapt and the parameters -e 0.1 -m 5 and aligned using bowtie2 allowing 0 multimapping and -X2000 --mm –local parameters. Duplicated reads were marked using picard and mitochondrial reads were removed from the analysis.
Assembly: mm10
Supplementary files format and content: ATAC peak list per samples as txt file.

source_name: lung

extract_protocol:
Murine pulmonary EC were subjected to FACS, pelleted for 7 min at 500 × g in a prechilled (4°C) fixed-angle centrifuge, and resuspended in 50 µl of cold lysis buffer (10 mM Tris-HCL (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween20, 0.01% Digitonin). The nuclei isolation reaction was incubated for 3 min at room temperature. After lysis, 1 ml of ATAC-RSB (10 mM Tris-HCL (pH 7.4), 10 mM NaCl, and 3 mM MgCl2) containing 0.1% Tween20 was added and mixed. Nuclei were pelleted for 10 min at 500 × g at 4°C and resuspended in 50 µl of transposition buffer (10 mM Tris-HCl (pH 7.6), 5 mM MgCl2, 10% Dimethyl Formamide, 2.5µl Transposase (100 nM final concentration), 0.1% Tween20, 0.01% Digitonin, 16.5 µl PBS, 5 µl H2O). Transposition reaction was incubated for 30 min at 37°C in a thermomixer shaking at 1000 r.p.m. The reaction was stopped with 20 µl of 5 M guanidinium thiocyanate, the ATAC raw material was purified with a 2x volume of Ampure XP DNA purification beads, and the DNA was eluted in 25 µl of H2O.
The DNA eluate was PCR amplified using 1x NEBNext High Fidelity Mix in a total volume of 50 µl. The number of cycles used for library amplification depended on the observed amplification curve and varied between 10 and 15 cycles. ATAC libraries were purified with a 1.4x volume of Ampure XP DNA purification beads, and the DNA was eluted in 12 µl of elution buffer.

value: lung

value: endothelial cell


title: yAdu3

description: Library name: yAdu3


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 28, pegRNA library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D28_rep1_pegRNA


title: MA02

description: raw counts

value: M

value: negative

value: CNS tumor

value: yes


title: yAdu2

description: Library name: yAdu2


title: yAdu1

description: Library name: yAdu1


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 21, gene expression library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D21_rep1_GEX


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 14, lineage tracing cassette library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D14_rep1_LTC


title: Inf3

description: Library name: Inf3


title: SC5314, Cinnamaldehyde, replicate2

value: fungi

value: fungal cell

value: wild type

value: incubated at 37 degreeC for 24 hours in the presence of cinnamaldehyde at 31.25 mirogram/mL


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 14, gene expression library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D14_rep1_GEX


title: mAdu2

description: Library name: mAdu2


title: Inf2

description: Library name: Inf2


title: mAdu3

description: Library name: mAdu3


title: Inf1

description: Library name: Inf1


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 14, pegRNA library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D14_rep1_pegRNA


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 28, lineage tracing cassette library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D28_rep1_LTC


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 10, lineage tracing cassette library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D10_rep1_LTC


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 10, gene expression library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D10_rep1_GEX


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 10, pegRNA library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D10_rep1_pegRNA


title: PC-12

city: qingdao

first: chengwen

last: gao

state: shandong

address: Huangdao Qingdao Shandong

institute: Affiliated Hospital of Qingdao University

description: Library name: PC-12

data_processing:
*library strategy: modified STARR-seq
Expression data for the SNP fragments were processed by converting raw counts to Transcripts Per Million (TPM) and filtering out low-expressed fragments. Residual log expression normalization and hierarchical clustering were performed to assess sample quality, with outliers identified based on D-statistics and removed from the dataset. Pairwise global alignments compared relevant sequences, summarizing results with alignment scores. The filtered expression data and sequence alignment outputs were saved for further analysis.Enhancer activity analysis followed the method described by Tippens et al.66 Raw sequencing reads were processed using the "voom" function from the R limma package (v3.40.6). Input and output samples were treated as separate experimental conditions, and eSNPs were identified based on significantly higher expression in the output compared to the input. A false discovery rate (FDR)-adjusted p-value less than 0.05 and a fold change greater than 1.5 (log₂FC > 0.585) defined eSNPs (Table S2). SNPs showing significantly reduced expression were classified as candidate silencer SNPs.To identify baaSNPs among the eSNPs, differential allelic regulatory activity was calculated using the mpra package (v1.14.0)43. The analysis employed the `mpralm()` function, which uses a linear model to measure differential regulatory activity between two alleles. This provided summary statistics for each variant, including t-statistics, p-values, log fold changes, B-statistics, and average expression .
Supplementary files format and content: csv files include counts for each cell lines

extract_protocol:
Neuro-2a, SH-SY5Y, HEK-293T, and PC-12 cells were cultured to logarithmic growth phase, reaching a density of 2×107 cells on the day of transfection. Transfections were performed using Xfect™ Transfection Reagent (Takara, Cat. No. 631317, China) under optimized conditions established from preliminary experiments. The purified plasmid DNA from the constructed library was transfected into the cells, and each experiment was conducted in triplicate to ensure reproducibility.
Before cell transfection, the plasmid library was used to construct the input sequencing library. For the initial PCR, 100 ng of the plasmid library underwent a one-step PCR. The purified products were then subjected to two additional rounds of PCR with sample index primers. High-fidelity KAPA HiFi HotStart ReadyMix (Roche, Cat. No. KK2601, USA) was used in all PCR steps to ensure accurate amplification. The final products were prepared for paired-end sequencing on the Illumina NovaSeq 6000 platform. After transfection, total RNA was extracted using the E.Z.N.A.® Total RNA Midiprep Kit (Omega Bio-Tek, Cat. No. R6664, USA). Polyadenylated RNA was isolated using VAHTS mRNA Capture Beads (Vazyme, Cat. No. N401, China) and reverse-transcribed with the HiScript III 1st Strand cDNA Synthesis Kit (Vazyme, Cat. No. R312-02, China). The resulting cDNA was treated with RNase A and purified using AMPure XP beads. Two rounds of PCR amplification were performed, with products purified using Agencourt SPRIselect Reagent (Beckman Coulter, Cat. No. B23318, USA). Three biological replicates were prepared for both input and output sequencing libraries, which were then sequenced using paired-end 150 bp reads on the Illumina NovaSeq 6000 platform.


title: HB3-3

city: Beijing

first: yongpan

last: an

address: xueyuanlu

institute: Peking University

data_processing:
Illumina Casava software used for basecalling.
Read quality was checked for each sample using fastx_toolkit_0.0.14.
High-quality reads were then imported into HISAT2 to get mapped reads.
Mapped Reads are spliced using StringTie software, based on the selected reference genome sequence.
The functional annotations of gene/transcript in NR, Swiss-PROt, Pfam, EggNOG, GO and KEGG were summarized.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: kidney

growth_protocol: The animals were housed in a temperature-controlled animal room (24 ± 2 ℃) with a relative humidity of 60-80%.

extract_protocol:
Kidney were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Survival curves: We selected 11-month-old male ICR mice, dissolved 3HB-Na in drinking water (1 g/L), and administered 3HB-Na to 11-month-old mice in drinking water until the mice died naturally, and recorded the body weights and survival conditions.

value: kidney

value: 20 month


title: HB3-2


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 6, lineage tracing cassette library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D6_rep1_LTC


title: HB3-1


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 21, pegRNA library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D21_rep1_pegRNA


title: C-3

value: no


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 6, pegRNA library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D6_rep1_pegRNA


title: Y-2

description: youngvsold

value: 2 month


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 4, lineage tracing cassette library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D4_rep1_LTC


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 28, gene expression library, rep 1

description: Library name: PEtracer_4T1_kinetics_D28_rep1_GEX


title: Y-1

description: youngvsold


title: C-2


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 4, gene expression library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D4_rep1_GEX


title: Y-3

description: youngvsold


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 28, pegRNA library, rep 1

description: Library name: PEtracer_4T1_kinetics_D28_rep1_pegRNA


title: S42

description:
Library name: S42
human a549 -treatment- infect_24


title: S41

description:
Library name: S41
human a549 -treatment- infect_24


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 21, gene expression library, rep 1

description: Library name: PEtracer_4T1_kinetics_D21_rep1_GEX


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 21, lineage tracing cassette library, rep 1

description: Library name: PEtracer_4T1_kinetics_D21_rep1_LTC


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 6, gene expression library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D6_rep1_GEX


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 28, lineage tracing cassette library, rep 1

description: Library name: PEtracer_4T1_kinetics_D28_rep1_LTC


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 21, pegRNA library, rep 1

description: Library name: PEtracer_4T1_kinetics_D21_rep1_pegRNA


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, gene expression library, rep 4

description: Library name: PEtracer_4T1_kinetics_D14_rep4_GEX


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, lineage tracing cassette library, rep 4

description: Library name: PEtracer_4T1_kinetics_D14_rep4_LTC


title: S38

description:
Library name: S38
human calu3 -treatment- infect_24


title: S37

description:
Library name: S37
human calu3 -treatment- infect_24


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, pegRNA library, rep 4

description: Library name: PEtracer_4T1_kinetics_D14_rep4_pegRNA


title: S40

description:
Library name: S40
human a549 -treatment- infect_24


title: S30

description:
Library name: S30
human a549 -treatment- infect_12


title: C-1


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, lineage tracing cassette library, rep 3

description: Library name: PEtracer_4T1_kinetics_D14_rep3_LTC


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, gene expression library, rep 3

description: Library name: PEtracer_4T1_kinetics_D14_rep3_GEX


title: S28

description:
Library name: S28
human a549 -treatment- infect_12


title: B16F10 cells, PEtracer mismatch kinetic screening, Day 4, pegRNA library, rep 1

description: Library name: PEtracer_B16F10_kinetics_D4_rep1_pegRNA


title: S29

description:
Library name: S29
human a549 -treatment- infect_12


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, lineage tracing cassette library, rep 2

description: Library name: PEtracer_4T1_kinetics_D14_rep2_LTC


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, pegRNA library, rep 3

description: Library name: PEtracer_4T1_kinetics_D14_rep3_pegRNA


title: S26

description:
Library name: S26
human calu3 -treatment- infect_12


title: S27

description:
Library name: S27
human calu3 -treatment- infect_12


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, gene expression library, rep 2

description: Library name: PEtracer_4T1_kinetics_D14_rep2_GEX


title: S25

description:
Library name: S25
human calu3 -treatment- infect_12


title: Neuro-2a

description: Library name: Neuro-2a


title: S39

description:
Library name: S39
human calu3 -treatment- infect_24


title: S18

description:
Library name: S18
human a549 -treatment- mock_24


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, pegRNA library, rep 1

description: Library name: PEtracer_4T1_kinetics_D14_rep1_pegRNA


title: S16

description:
Library name: S16
human a549 -treatment- mock_24


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, pegRNA library, rep 2

description: Library name: PEtracer_4T1_kinetics_D14_rep2_pegRNA


title: S17

description:
Library name: S17
human a549 -treatment- mock_24


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 10, lineage tracing cassette library, rep 1

description: Library name: PEtracer_4T1_kinetics_D10_rep1_LTC


title: S15

description:
Library name: S15
human calu3 -treatment- mock_24


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, gene expression library, rep 1

description: Library name: PEtracer_4T1_kinetics_D14_rep1_GEX


title: S13

description:
Library name: S13
human calu3 -treatment- mock_24


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 10, pegRNA library, rep 1

description: Library name: PEtracer_4T1_kinetics_D10_rep1_pegRNA


title: S14

description:
Library name: S14
human calu3 -treatment- mock_24


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 14, lineage tracing cassette library, rep 1

description: Library name: PEtracer_4T1_kinetics_D14_rep1_LTC


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 10, gene expression library, rep 1

description: Library name: PEtracer_4T1_kinetics_D10_rep1_GEX


title: S6

description:
Library name: S6
human a549 -treatment- mock_12


title: S5

description:
Library name: S5
human a549 -treatment- mock_12


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 6, lineage tracing cassette library, rep 1

description: Library name: PEtracer_4T1_kinetics_D6_rep1_LTC


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 6, gene expression library, rep 1

description: Library name: PEtracer_4T1_kinetics_D6_rep1_GEX


title: S3

description:
Library name: S3
human calu3 -treatment- mock_12


title: Lung cells, BALB/cJ mice with primary 4T1 tumor, gene expression library

description: Library name: Lung_4T1_primary_GEX

source_name: Lung

value: Lung


title: S1

description:
Library name: S1
human calu3 -treatment- mock_12


title: S2

description:
Library name: S2
human calu3 -treatment- mock_12


title: transcriptome of myocardium of a patient with HCMP - id X9H

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

country: Russia

institute: National Research Center «Kurchatov Institute»

data_processing:
Pipelines was used for data processing.
Pipeline – Ambiguous and low-quality bases were removed from the files obtained during the FASTQ sequencing process. Removal was done with AdapterRemoval V2. The trimmed files were aligned to the human reference genome GRCH38 and GRCH38.92 gene annotation using RSEM with rsem-prepare-reference and rsem-calculate-expression commands  and the -star option to also generate STAR indices.
Assembly: GRCH38
Supplementary files format and content: Processed count files  were obtained using RSEM pseudo counts output from (rsem-calculate-expression) with --star option enabled..

source_name: myocardium

extract_protocol:
Total RNA isolation was conducted using a Direct-Zol RNA Mini-Prep Kit (ZymoResearch) according to the manufacturer's recommendations. The concentration of total RNA isolated was measured using a Quant-iT RNA BR Assay Kit and a Qubit fluorimeter (Invitrogen). RNA quality was monitored using an Experion automated electrophoresis system (Bio-Rad Laboratories).
Poly-a fraction of RNA was extracted from total RNA for RNA-seq. Sequencing libraries were prepared using NEBNext® mRNA Library Perp Reagent Set (NEB, USA). Sequencing was performed using HiSeq1500 (Illumina, USA), obtaining no less then 15 mln. reads of 50 length per library.

value: myocardium

value: f

tag: hight

tag: weight

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

value: rough systolic

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

value: HCMP

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics

value: CC


title: 4T1 cells, PEtracer mismatch kinetic screening, Day 6, pegRNA library, rep 1

description: Library name: PEtracer_4T1_kinetics_D6_rep1_pegRNA

tag: cell line

tag: treatment


title: Tumor cells, BALB/cJ mice with primary 4T1 tumor, gene expression library

description: Library name: Tumor_4T1_primary_GEX

source_name: Tumor

tag: tissue

value: Tumor


title: transcriptome of myocardium of a patient with HCMP - id X81H

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

value: systolic

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: bmi

value: CT


title: whole brain, PLDP Diet Group No.26

city: Saga city

first: Taiga

last: Kurihara

state: Saga (佐賀県)

address: 5-1-1 Nabeshima

country: Japan

institute: Saga University

description: Library name: P26

data_processing:
Raw reads with low quality and adapter sequences were removed using Cutadapt v.2.9.
Those remaining reads were then mapped to the human genome (GRCh38 version 101) by HISAT2 v.2.2.0 (PMID: 25751142), and gene expression was quantified using the R package featureCounts v.2.6.0 (PMID: 24227677).
Consequently, differentially expressed genes (DEGs) were identified based on differences in expression levels (|log2 fold-change| > 1 and adjusted p-value < 0.05) between samples after removing those genes with zero read counts using DESeq2 v.1.6.3 (PMID: 25516281).
Assembly: GRCm38
Supplementary files format and content: Processed data files are tab-delimited text files (.txt) containing normalized gene expression levels for each sample.

source_name: whole brain

growth_protocol: Mice were fed either a PLDP-containing diet (PLDP mice: n = 13) or a control diet (control mice: n = 13) for 16 weeks. Food intake and body weight were measured every alternate week. After the 16-week diet period, the mice underwent a series of behavioral experiments.

extract_protocol:
Total RNA was extracted from mouse brains following behavioral experiments using TRIZOL reagent (Thermo Fisher Scientific, USA) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads to achieve a coverage of approximately 6 Gb per sample.

treatment_protocol: The PLDP-containing diet was prepared by Oriental Yeast Co., Ltd. (Tokyo, Japan) and consisted of a modified AIN-93M diet with 20% PLDP. The control diet consisted of a modified AIN-93M diet with an adjusted total caloric content to match the PLDP-containing diet.

value: whole brain

tag: genotype

tag: treatment

value: PLDP diet-fed


title: whole brain, PLDP Diet Group No.22

description: Library name: P22

tag: tissue


title: whole brain, Control Diet Group No.5

description: Library name: C5

value: Control diet-fed


title: transcriptome of myocardium of a patient with HCMP - id X7H

tag: batch

tag: Sex

value: yes

tag: perindopril

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: S4

city: Stanford

first: Daniel

last: Richard

address: 290 Jane Stanford Way

institute: Stanford University

description:
Library name: S4
human a549 -treatment- mock_12

data_processing:
TrimGalore! read trimming
STAR transcriptome alignment
DESEQ2 analysis
Assembly: GRCh38.100, GCF_000308155.1
Supplementary files format and content: CSV of aligned read counts

extract_protocol:
RNA was isolated from whole cell lysates using RNeasy Mini kit (Qiagen, 74106).
Sequencing was conducted at the McMaster Genomics Facility, Farncombe Institute at McMaster University. RNA quality was first verified using a Bioanalyzer (Agilent), followed by poly(A) enrichment (NEBNext Poly(a) mRNA Magnetic Isolation Module; NEB). Library were prepared (NEBNext Ultra II Directional RNA Library Prep Kit; NEB) and library fragment size distribution was verified (Agilent TapeSection D1000; Agilent). Libraries were quantified by qPCR and pooled in equimolar amounts. Subsequently, qPCR and fragment size distribution were verified. Libraries were then sequenced on an Illumina HiSeq 1500 across 12 HiSeq Rapid v2 flow cells in 6 lanes (Illumina) using a paired end, 2x50 bp configuration, with onboard cluster generation averaging 80M clusters per biological replicate.

tag: cell line

tag: cell type

tag: treatment


title: Liver cells, BALB/cJ mice with primary 4T1 tumor, gene expression library

description: Library name: Liver_4T1_primary_GEX

source_name: Liver

tag: tissue

value: Liver


title: whole brain, Control Diet Group No.10

description: Library name: C10

tag: genotype


title: transcriptome of myocardium of a patient with HCMP - id X80H

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: bmi


title: transcriptome of myocardium of a patient with HCMP - id X78H

tag: tissue

tag: batch

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: liver, Input1

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

description: Library name: 7_0A73_01BHBaylor_Pooled-Liver_Input

data_processing:
ChIP-Seq and initial data processing were carried out using the Active Motif analysis pipeline.
The generated 75-nt single-end (SE75) reads were mapped to the Mus musculus genome (mm10) using the BWA algorithm with default parameters, and alignment data for each read was stored in BAM format.
PCR duplicates were removed to ensure data quality. ChIP samples were normalized to their respective input controls and converted to bigWig format for visualization in the Integrative Genomics Viewer (IGV).
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
ChIP-Seq was conducted using 100 mg of liver tissue from 6-month-old Atp7b−/− and WT mice (n=3 mice per group) with an FXR antibody (H-130X, Santa Cruz Biotechnology).
Active motif ChIP-Seq Kit

value: liver

tag: genotype

value: Input


title: transcriptome of myocardium of a patient with HCMP - id X76H

tag: Sex

value: m

tag: hight

tag: weight

tag: age

tag: vss family_history

value: no

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril


title: transcriptome of myocardium of a patient with HCMP - id X75H

tag: tissue

value: myocardium

tag: batch

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants


title: transcriptome of myocardium of a patient with HCMP - id X74H

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: antiarrytmics


title: liver, KO2

description: Library name: 5_s1624-KO_FXR_mm10

tag: tissue

tag: genotype

value: Atp7b KO


title: transcriptome of myocardium of a patient with HCMP - id X71H

tag: batch

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins


title: liver, KO1

description: Library name: 4_s1636-KO_FXR_mm10


title: liver, WT2

description: Library name: 2_s1625-WT_FXR_mm10

value: wild-type


title: transcriptome of myocardium of a patient with HCMP - id X70H

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

value: HCMP

tag: anticoagulants

tag: antiarrytmics


title: transcriptome of myocardium of a patient with HCMP - id X6H

tag: tissue

tag: batch

value: f

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

value: CC


title: MIN6 fresh cells

city: Hatfield

first: Floryne

middle: Ottilie

last: Buishand

address: Hawkshead Lane

department: Clinical Science and Service

country: United Kingdom

institute: Royal Veterinary College

description: Library name: MIN6

data_processing:
CellRanger (version 7.1.0, 10x Genomics) was used to process raw FASTQ files and to align reads to either the canine CanFam3.1, human GRCh38, murine GRMch38/mm10, or rat mRatBN7.2 genome.
Assembly: CanFam3.1 for canINS-fresh and canINS-cryo, human GRCh38 for CM-fresh and CM-cryo, murine GRMch38/mm10 for MIN6, or rat mRatBN7.2 for INS-1
Supplementary files format and content: Cell Ranger software output files: barcodes.tsv, features.tsv, matrix.mtx

extract_protocol:
The canine insulinoma cell line canINS was cultured in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS) (Invitrogen), 1% penicillin-streptomycin (Invitrogen) and 200 ng/mL growth hormone (GH) (ProSpec). The human insulinoma cell line CM was cultured in RPMI-1640 supplemented with 10% FBS and 1% penicillin-streptomycin. The mouse insulinoma cell line MIN6 was cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco) containing 25 mM glucose, supplemented with 15% FBS, 0.05 mM beta-mercaptoethanol (Life Technologies) and 1% penicillin-streptomycin. The rat insulinoma cell line INS-1 was cultured in RPMI-1640 + Glutamax (Gibco) supplemented with 10% FBS, 1mM sodium pyruvate (Life Tech), 10mM HEPES (Life Tech), and 0.05 mM beta-mercaptoethanol. All cell lines were cultured at 37°C with 5% CO2, and cells were passaged on reaching 70–80% confluence.
Cell cryopreservation
Freezing medium, consisting out of 90% FCS and 10% dimethyl sulfoxide (DMSO) (Sigma-Aldrich) was added to aliquots of 1 x 106 cells/mL of the canINS and CM cell lines and cells were transferred to cryogenic vials. The vials were put into a CoolCell cell freezing vial container (Corning) and stored at -80°C overnight. Vials of the frozen cell lines were then taken out of the CoolCell containers and stored at -80°C for four weeks until use.
Sample preparation
Cryopreserved cells were thawed in a 37 °C water bath, after which they were washed using pre-warmed 1x phosphate-buffered saline (PBS) (Gibco) supplemented with 0.04% bovine serum albumin (BSA) (Sigma-Aldrich). Single cell suspensions of both fresh and cryopreserved cells were created at a concentration of 1 x 106 cells/mL in 1x PBS + 0.04% BSA according to the Cell Preparation for Single Cell Protocols Handbook CG00053 (10x Genomics). Using trypan blue exclusion, all cell suspensions were confirmed to have a viability greater than 90%. Samples were partitioned on a Chromium Controller (10x Genomics) within 30 min of preparation.
Single-cell 3’ gene expression libraries were prepared for each sample using a Chromium NEXT Gem Single Cell 3 v3.1 Kit and dual index library construction kit (10x Genomics) targeting 10,000 cells per sample. Sequencing was performed on a NovaSeq 6000 sequencer (Illumina) using a 28 x 10 x 10 x 90 bp configuration.

tag: cell line

tag: cell type

value: insulinoma


title: transcriptome of myocardium of a patient with IHD plus tension stenocardy - id X69H

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: diuretics

tag: statins

tag: anticoagulants


title: transcriptome of myocardium of a patient with HCMP - id X79H

tag: tissue

tag: batch

value: systolic

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: antiarrytmics


title: whole brain, PLDP Diet Group No.17

description: Library name: P17

value: whole brain

tag: genotype

tag: treatment


title: whole brain, Control Diet Group No.2

description: Library name: C2


title: transcriptome of myocardium of a patient with HCMP - id X77H

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: diuretics

tag: statins

tag: anticoagulants


title: liver, Input2

description: Library name: 8_0EW6_022KBCM_Pooled-Liver_Input

tag: tissue

tag: genotype


title: liver, KO3

description: Library name: 6_s1146-KO_FXR_mm10


title: transcriptome of myocardium of a patient with IHD plus tension stenocardy - id X68H

tag: batch

tag: Sex

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: antiarrytmics


title: transcriptome of myocardium of a patient with IHD - id X66H

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

value: IHD

tag: diuretics

tag: statins

tag: anticoagulants


title: transcriptome of myocardium of a patient with IHD plus tension stenocardy - id X67H

tag: tissue

tag: batch

tag: Sex

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi


title: HFD3

city: Qingdao

first: Xueqiang

last: Wang

state: China

address: 369 Dengyun Road, High-tech Zone

institute: University of Health and Rehabilitation Sciences

description: Library name: HFD3

data_processing:
CLC Genomics Workbench V11.0.1
Sequence reads were trimmed for adaptor seguence/low-qualty sequence using CLC genomic benchwork (parameter- Qualty limit. 0.05)
Timmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost:2 inseion cost:3 deleion cost:3 length faction:0.8 simlanity fraction:0.8)
Read count extraction and normalization were performed usina CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Mouse were fed a HFD 4 weeks of age,then supplemented with allantoin in their drinking water at the concentrations of 0.06 mg/mL and 0.3mg/mL for additional 4 weeks

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5ug of total RNA was uesed for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Allantoin was supplemented  in their drinking water at the concentrations of 0.06 mg/mL and 0.3mg/mL for additional 4 weeks under HFD

tag: genotype

value: WT

tag: treatment

value: HFD


title: transcriptome of myocardium of a patient with HCMP - id X73H

tag: hight

tag: weight

tag: age

value: yes

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: dyspnea

tag: diuretics

tag: statins

tag: antiarrytmics


title: HFD2

description: Library name: HFD2

tag: tissue

value: Liver

tag: genotype


title: transcriptome of myocardium of a patient with unstable stenocardy - id X65H

tag: batch

tag: Sex

tag: hight

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: anticoagulants


title: liver, WT3

description: Library name: 3_s2913-WT_FXR_mm10

value: liver


title: HAH5

description: Library name: HAH5

tag: treatment

value: HFD+allantoin


title: HAH4

description: Library name: HAH4

tag: tissue


title: transcriptome of myocardium of a patient with HCMP - id X64H

value: m

tag: weight

tag: age

value: no

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: dyspnea

tag: diuretics

tag: statins

tag: antiarrytmics


title: transcriptome of myocardium of a patient with HCMP - id X72H

value: myocardium

tag: batch

tag: Sex

tag: hight

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: anticoagulants


title: transcriptome of myocardium of a patient with HCMP - id X62H

tag: tissue

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: dyspnea

tag: diuretics