title: CTRLsiRNA_1

description: control siRNAs replicate 1


title: EDTA plasma, T1D, rep1

status: Public on Oct 18 2023

type: RNA

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
RT-qPCR miRNA data was normalized to UniSp4 spike in Cq-values.
Delta Cq-values are provided in the "Matrix normalized" Sheet.

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: EDTA plasma

label_protocol: cDNA was synthesized using the Universal cDNA Synthesis Kit II using reaction conditions provided by the manufacturer (Exiqon, Denmark). In total, 2 µL of total RNA were used as input per 10 µL reverse transcription (RT) reaction mix. Cel-miR-39-3p was added to each RT reaction to monitor RT efficiency. PCR amplification was performed in a 384-well plate format using custom Pick&Mix plates (Exiqon, Denmark) in a Roche LC480 II instrument (Roche, Germany) and EXiLENT SYBR Green mastermix (Exiqon, Denmark) with the following settings: 95°C for 10 min, 45 cycles of 95°C for 10 s and 60°C for 60 s, followed by melting curve analysis. Cycle of quantification values (Cq-values) were determined using the second derivative method as provided by the Roche LC480 software. Data quality was assessed by visual inspection of spike-in control data. Hemolysis was assessed in all samples using the ratio of miR-23a-3p versus miR-451a and applying a cut-off of >7 to the ratio for calling a sample hemolytic.

growth_protocol: Twelve adolescents aged 15.0–17.9 years, 7 males and 5 females, with a long-term T1D duration of at least 8 years (8.0-15.0 years) were included in this case-control study. These individuals were followed regularly at the Queen Silvia Children’s Hospital in Gothenburg, Sweden. They were identified from the Swedish Pediatric Diabetes Quality Registry (SWEDIABKIDS). The control group, comprised 12 age-matched healthy adolescents, 15.0–17.5 years, 6 females and 6 males, living in the Gothenburg area. The current study commenced in April 2019, and was completed by October 2019.

extract_protocol: Total RNA extraction from 200 µL plasma samples was performed using the miRNeasy Mini Kit (Qiagen, Germany)12. Plasma was thawed on ice and centrifuged at 12,000×g for 5 min to remove any cellular debris. For sample lysis, 200 µL of plasma were mixed with 1000 µL Qiazol to which 1 µL spike-in controls had been added (Exiqon, Denmark). Following incubation at room temperature for 10 min, 200 µL chloroform were added to the lysates. After centrifugation at 12,000×g for 15 min at 4°C, 650 µL of the upper aqueous phase were obtained and mixed with 7 µL glycogen (50 mg/mL) to enhance precipitation. The aqueous phase was then transferred to a miRNeasy mini column, and RNA was precipitated by adding 750 µL ethanol. Washing with RPE and RWT buffer was performed in a QiaCube liquid handling robot (Qiagen, Germany). In the last step, total RNA was eluted in 30 µL nuclease free water and stored at -80°C until further analysis.

tag: group

tag: gender

value: F


title: EDTA plasma, T1D, rep2

value: M


title: B cell GSK343 rep1

type: genomic

city: London

first: Frederick

middle: Andrew

last: Dick

state: ON

address: 790 Commissioners Road E

department: Pathology

country: Canada

institute: Western University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation 285k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

label: Cy5 and Cy3

molecule: genomic DNA

organism: Mus musculus

source_name: B1 GSK

label_protocol: Standard Illumina protocol

growth_protocol: To separate CD43- from CD43+ cells, washed splenic lymphocytes (5e7) were resuspended in 450 µL FACS buffer and stained with 50 µL CD43 microbeads on ice for 30 min. Cells were washed once, resuspended in 500 µL FACS buffer and passed through an LD column in a VarioMACS separator as per manufacturer’s recommendation. CD43 microbead-labelled non-B cells were eluted from the column by applying the plunger. Purified B cells in the flow-through were incubated in RPMI-1640  supplemented with 10% (v/v) FBS, 55 µM 2-ME, 2 mM L-glutamine, penicillin and streptomycin plus 2 ng/mL IL-4 and BAFF at 37 °C in 5% CO2.

extract_protocol: Genomic DNA was extracted using Monarch genomic DNA purification kit

treatment_protocol: CD43- or CD43+ cells were treated with DMSO or 1 uM GSK343 for 48 hours

tag: strain


title: 2cell embryo 5 wild-type scBS-seq

type: SRA

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

library_source: transcriptomic

data_processing:
A total of 96 scBS-seq libraries were processed for analysis. The first 6 bp containing the N portion of the random primers, adapters and bases called with poor quality (Phred score <20) were removed using Trim Galore version 0.4.4 (Krueger, 2017) in single-end mode. Only the good quality reads were used for the alignment to the Genome Reference Consortium mouse genome build 39 (GRCm39) using Bismark version 0.18.2 (Krueger & Andrews, 2011) with single-end and non-directional mode followed by deduplication and methylation calling using Bismark functions. The MII scBS-seq libraries having a mapping efficiency <10% or fewer than 500,000 CpGs covered were removed (Supp. Table S20-21). To investigate a possible somatic cell DNA contamination in MII oocytes, we compared the global CpG methylation rates with the methylation of X-chromosome CpG islands, removing the samples with X-chromosome CpG island mean methylation > 12 % (Fig. S5a-c; Castillo-Fernandez et al. 2020); there was no difference in the proportion of oocytes excluded on this basis between Padi6P620A/P620A and control. In total, out of 44 MII oocytes, we kept 10 cells for downstream analysis. The embryos scBS-seq libraries having fewer than 100,000 reads were removed. In total, out of 44 embryos, we kept for 29 the downstream analysis (Fig. S5d,e). The methylation profile for each feature was calculated by the Bisulfite methylation pipeline implemented in SeqMonk.
Assembly: mm39
Supplementary files format and content: Bismark coverage file

molecule: polyA RNA

source_name: embryo

growth_protocol: For the experiment, males of 8-12 weeks of age and females of 4-8 weeks of age were used. The day before the start of the experiment, the males were separated. On day 1, at 2 pm, intraperitoneal injections of pregnant mare serum gonadotropin (PMSG) were given to the females. After approximately 52 hours, the same females received intraperitoneal injections of human chorionic gonadotropin (hCG). Male was sacrificed approximately 12 hours after the female hCG injection. The cauda epididymis and vasa deferentia were dissected and the spermatozoa were collected in the human tubal fluid medium (HTF) (EmbryoMax® HTF MR-070-D). Spermatozoa were counted and incubated at 37°C within a humidified atmosphere of 5% CO2 in air. Females were sacrificed approximately 13 hours after the hCG injection. Ampullae were placed in hyaluronidase 1mg/ml (H6254-500MG) drops to break down the oocyte-cumulus complex and collect MII oocyte. The oocytes were moved to the HTF medium and a 2x106 sperm/ml concentration of spermatozoa were added. After 4 - 6 hours of incubation at 37°C within a humidified atmosphere of 5% CO2 in air, the fertilised oocytes were washed, to remove the spermatozoa e debris, transferred in KSOM medium and incubated overnight at 37°C within a humidified atmosphere of 5% CO2 in air. The embryos' status was evaluated in the morning and the next 120 hours.

extract_protocol:
MII oocytes and 2-cell embryos were collected as described before. For 2-cell embryos, the zona pellucida was removed with Tyrode’s solution (SIGMA-ALDRICH), the blastomeres were separated and the polar body was discarded. Then single oocytes and blastomeres were picked and put into a lysis buffer (Buffer RLT Plus Qiagen). DNA and RNA from lysate were separated using the G&T protocol (Angermueller et al. 2016). The magnetic beads (MyOne C1, Life Technologies) were washed and then annealed to oligo dTs. These were used to capture polyadenylated mRNA from individual cell lysate. The supernatant containing the DNA was transferred to a new tube and the beads washed three times in 1xFSS buffer (Superscript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma) and 0.4 U/μl of RNAsin (Promega) to remove all DNA residue. Each washing solution was added to the DNA tube to maximise recovery.
The scBS-seq libraries were generated as described (Clark et al., 2017). The DNA was purified from the lysated using a 0.9:1 ratio of Ampure XP Beads (Beckman Coulter) and eluted into 10 μl of water. DNA purified from single cells was treated with the EZ Methylation Direct Kit (Zymo) for bisulfite-conversion following the manufacturer's instructions. First-strand synthesis was performed in five rounds. Initially, the bisulfite-treated DNA was mixed with 40 μl first-strand synthesis mastermix (1 × Blue Buffer (Enzymatics), 0.4 mM dNTP mix (Roche), 0.4 μM 6NF oligo (IDT)) and heated to 65 °C for 2 min and cooled on ice, followed by the addition of 50U of Klenow exo- and incubation at 37 °C for 30 minutes after slowly ramping from 4 °C. This process was repeated four more times with additional reaction mixture added each time, and the final round was incubated for 90 minutes at 37 °C. Exonuclease digestion was carried out by adding 20U of exonuclease I (NEB) in a total volume of 100 μl, at 37 °C for 1 h. The resulting samples were purified using AMPure XP beads with a 0.8:1 ratio. The beads were mixed with 50 μl second-strand master mix (1× Blue Buffer (Enzymatics), 0.4 mM dNTP mix (Roche), 0.4 μM 6NF oligo (IDT). The mixture was heated to 98 °C for 1 min and cooled on ice. Then, 50U of Klenow exo- (Enzymatics) were added. The mixture was incubated on a thermocycler at 37 °C for 90 min after slowly ramping from 4 °C. The resulting samples were purified using a 0.8:1 ratio of AMPure XP beads, and libraries were amplified using a 50 μl PCR mastermix (1× KAPA HiFi Readymix, 0.2 μM PE1.0 primer, 0.2 μM iTAG index primer) The amplification process involved a 2 min step at 95 °C, followed by 14 cycles of 80 s at 94 °C, 30 s at 65 °C, and 30 s at 72 °C, with a final extension for 3 min at 72 °C. Finally, the scBS-seq libraries were subjected to purification using a 0.7:1 ratio of AMPure XP beads. After purification, the libraries were eluted in 15 µl of water, pooled together, and sequenced. The sequencing process involved the generation of pools of 48 libraries, which were sequenced on an Illumina HiSeq 2500 platform. On average, the libraries were sequenced to generate 13.0 million paired-end reads with a read-length of 75 bp.

tag: cell type

value: embryo

tag: genotype


title: Case 30: Giant cell tumor of the bone

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description: Giant cell tumor of the bone

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
Average Beta

label: Cy3 and Cy5

source_name: Giant cell tumor of the bone

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE


title: B cell DMSO rep2

source_name: B2 DMSO


title: HUVEC, CYR61-5, rep5

city: Saint Louis

first: Joseph

last: Lin

state: MO

address: 660 South Euclid Ave, MSC-8096-06-07

department: Ophthalmology & Visual Sciences

country: USA

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: Ensembl release 101 primary assembly
Supplementary files format and content: group_CYR61_0.05_Differential_Expression.tsv: Differential gene expression performed comparing control vs. CYR61 0.05.
Supplementary files format and content: group_CYR61_0.5_Differential_Expression.tsv: Differential gene expression performed comparing control vs. CYR61 0.5.
Supplementary files format and content: group_CYR61_5_Differential_Expression.tsv: Differential gene expression performed comparing control vs. CYR61 5.
Supplementary files format and content: all.gene_counts.tsv: Raw counts.

growth_protocol: We used primary human umbilical vein endothelial cells (HUVECs) from ATCC (PCS-100-010). These cells were maintained according to the manufacturer's recommended instructions.

extract_protocol:
After incubation, we washed cells twice with PBS, then used TRIzol (Ambion) and RNeasy Plus Mini Kit (Qiagen) to extract RNA following the manufacturer's recommended protocol.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: We treated HUVECs with recombinant human CYR61 (PeproTech 120-25): 0.00, 0.05, 0.50, and 5.00 μg/ml for 24 hr.

tag: treatment

value: CYR61, 5 ug/ml


title: 2cell embryo 4 wild-type scBS-seq


title: CD43 cell DMSO rep1

source_name: CD43-1 DMSO


title: S228Arep1

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

country: China

institute: Hubei university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to sacCer3 whole genome using bowtie v0.12.2 with parameters -q -p 5 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: sacCer3

organism: Saccharomyces cerevisiae S288C

growth_protocol: Cells were grown in YPD until mid-log phase

extract_protocol:
Lysates were clarified from sonicated yeast cell pellets and histone-DNA complexes were isolated with antibody against  H3 (ab1791, Abcam),H3K4me3 (Abclonal; A2357),FLAG (F1804-1MG; Sigma-Aldrich),Rpd3 (sc-514160; Santa Cruz Biotechnology)
Libraries were prepared using the HTP KAPA kit

treatment_protocol: No treatment

value: Set1 S228A


title: Case 29: Giant cell tumor of the bone

description: Giant cell tumor of the bone


title: HUVEC, CYR61-5, rep3

source_name: primary human umbilical vein endothelial cells


title: 2cell embryo 3 wild-type scBS-seq


title: Case 28: Giant cell tumor of the bone

description: Giant cell tumor of the bone


title: HUVEC, CYR61-5, rep2

value: primary human umbilical vein endothelial cells


title: Case 32: Giant cell tumor of the bone

description: Giant cell tumor of the bone


title: HUVEC, CYR61-5, rep1


title: Case 27: Giant cell tumor of the bone

description: Giant cell tumor of the bone


title: HUVEC, CYR61-0.5, rep5

value: CYR61, 0.5 ug/ml


title: 2cell embryo 2 wild-type scBS-seq


title: SAH3

city: Chongqing

first: Zhaosi

last: Zhang

state: Chongqing

address: No.1 Youyi Road, Yuzhong District

institute: The First Affiliated Hospital of Chongqing medical university

description: Biological replicate 3 of 3. SAH

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version10.7.1.1, Agilent Technologies).

organism: Rattus norvegicus

source_name: plasma, SAH

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: The rats were kept in constant temperature 22-24°C and humidity 60 -65% on a 12 h day/night cycle and free access to food and water.

extract_protocol: Plasma exosome extracted: Blood was collected through the abdominal aorta. The sample was subjected to gradient centrifugation (2000 × g, 30 min; 10000 × g, 45 min; 10,000 × g, 45 min), supernatant underwent ultracentrifugation (100,000 × g, 70 min). resuspend the resulting pellet, suspensions were centrifuged by ultracentrifugation (100,000 × g, 70 min). Total RNA extracted: using Trizol following manufacturer's instructions

treatment_protocol: SAH model establishing based on endovascular perforation of the internal carotid artery. Sham-operated rats underwent the same procedure without puncturing the internal carotid artery.

tag: tissue

value: blood

tag: age

value: 8-12 weeks

tag: time of plasma collection

value: Day 3 after SAH

value: Sprague-Dawley


title: SAH2

description: Biological replicate 2 of 3. SAH


title: Negative control4 48 Negative scBS-seq

source_name: control

value: control


title: Negative control3 47 Negative scBS-seq


title: HUVEC, CYR61-0.5, rep4


title: CD4 memory T, 16C283+16C301+16C235, week 6, VDJ-derived cDNA

city: Bethesda

first: Chaim

middle: A

last: Schramm

state: MD

address: 40 Convent Dr

department: Vaccine Research Center

institute: NIAID, NIH

description: TRA/TRB enriched from polyA RNA via 10x Chromimum

library_source: transcriptomic single cell

data_processing:
The counts matrix was generated with Cellranger v3.1.0, using the protein-coding genes of the rhesus macaque reference genome from Ensembl (Mmul10, release #101). The filtered feature/barcode matrices were imported into Seurat v4.0.1 using R v4.0.4. Cells absent from either the gene expression or antibody capture datasets were eliminated, along with cells expressing zero counts of hash oligos. For hash demultiplexing, Seurat’s HTOdemux function was applied, and only singlets were retained for subsequent analyses. The filters based on percent mitochondrial genes and number of genes expressed varied between sample, but the upper threshold for percent mitochondrial genes ranged from 4-10%; the minimum for number of genes expressed was 200 genes for each sample; the upper threshold for number of genes expressed ranged from 1500-2500. The raw counts of each individual sample were merged.  For the innate cell sorts, clusters of contaminating B and T cells (identified using Seurat’s FindClusters and RunUMAP) were removed and not included in downstream analysis. The merged and filtered data matrix was then corrected for sparseness using DeepImpute with tensorflow v2.1.0 and default parameters. The imputed matrix was then re-imported into Seurat.  For both innate and T cells, Seurat was used to normalize the (imputed) count matrix, find variable genes, and regress out technical factors. Principle compents (PCs) were then calculated and used as input to Harmony to remove batch effects between samples. The integrated output was clustered using FindClusters and marker genes were identified with FindAllMarkers. Canonical marker genes were used to annotate the detected clusters.  Gene set enrichment analysis of the innate cell data was conducted using the R library fgsea. The data were broken down by cell type and time point, and differential expression analysis of all 21,369 genes was conducted using FindMarkers between each subset. Finally, the statistically significant (adjusted p < 0.05) pathways were detected by inputting the genes, ranked by average log fold change, into the function fgsea. The Hallmark gene set databases originated from MSigDB.  Signature scores for 50 pro-inflammatory genes previously determined to be predictive of antibody responses to a variety of vaccines were calculated using AddModuleScore in Seurat.
cellranger vdj (10x Genomics) was used to assign TCR annotations for each read-pair. TCR alpha recovery was minimal and not followed up further. An in-house shell script was used to filter for productive TCR betas. All subsequent analyses were done in R (v4.0.2). Cells with duplicated barcodes were discarded, and the TCR data was merged with the T cell transcriptomics Seurat (v4.0.1) object metadata for hash demultiplexing. Usage of each TRBV gene was compared between the S-specific and non-specific T cells from each animal using a paired samples Wilcoxon test in R.
SmartSeq sequencing reads were trimmed with Trimmomatic v 0.39, trimming nucleotides with Phred score below 20 and removing reads with resulting length less than 50 nucleotides. Alignment of reads to macaque protein-coding reference build Mmul10 was performed using Spliced Transcript to a Reference (STAR) v. 2.5.1b. Gene quantifications of reads as transcripts per million (TPM) were computed with Stringtie v. 1.33. Individual cells were removed from the analysis based on trimming and alignment metrics, as well as read quantity, feature quantity, quantity of mitochondrial reads, and diversity of transcripts.   Seurat was used to calculate principal component analysis, which was used as input to integrate the data by batch with Harmony. PCA, cell clustering and UMAP dimensionality reductions were conducted in Seurat. A single cluster was identified as likely T cells by its more than triple the expression of CD3E than the next highest cluster and so was removed from the analysis. Clustering and dimensionality reduction was repeated after this cell filter.   Differential expression of cell clusters was conducted with Seurat's function FindAllMarkers, and FindMarkers was used for comparison of timepoints week 2 and week 6. Those results were used as input to Gene set enrichment analysis conducted with the R package fgsea and the hallmark pathwaysfrom MSigDB.
Full-length V(D)J sequences from were reconstructed from SmartSeq data using BALDR and filtered using filterBALDR.pl (https://github.com/scharch/filterBALDR). Gene annotation and clonal assignment were done using SONAR v4.2 in single cell mode. Clonal flow diagrams were plotted using the ggalluvial package in R v4.2.1. Public clone were identified by clustering CDR H3 amino acid sequences using usearch as previously described . Members of the human public clone were identified from CovAbDab sequences downloaded as of January 24th, 2023 meeting the following criteria: (1) derived from IGHV3-30, IGHV3-30-3, or IGHV3-30-5; (2) 14 amino acid CDR H3 with Gly at position 6 and Tyr at position 8; (3) originating from a human; (4) not annotated as binding to any RBD or NTD epitope. This resulted in 326 public clone sequences, which were plotted using ggseqlogo.
Assembly: Mmul10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: tab-delimited HTO assignments for each cell
Supplementary files format and content: comma-delimited values of gene expression in TPM
Supplementary files format and content: AIRR-formated VDJ sequences recovered from B cells
Supplementary files format and content: 10x Genomics output files: TR VDJ contigs with annotations
Supplementary files format and content: RDS-formatted R data files with complete Seurat objects

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Frozen rhesus macaque PBMCs were thawed into warm R10 media (RPMI + 10% Fetal Bovine Serum + 2 mL L-Glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin; all reagents from Gibco) containing DNase I (MilliporeSigma), followed by one wash with R10 and one wash with FACS buffer (PBS with 2% FBS). For B and innate cell staining, cells were resuspended in 100µL of Live/Dead Fixable Blue Dead Cell Stain Kit (Invitrogen, cat# L23105) diluted 1:200 in PBS for 10 min at room temperature. Cells were washed with FACS buffer and incubated for 20 min with the staining cocktail consisting of antibodies and probes. Additionally, each sample was labelled with 1µl of TotalSeq-C Hashtag antibodies (Biolegend) that was incubated together with the staining cocktail. After incubation, cells were washed twice with FACS buffer and resuspended in R10 for sort.  From each sample, 10,000-60,000 innate cells were sorted into a tube containing FBS according to the gating strategy showed in Fig. S1B. From baseline samples, 50 thousand naïve B cells were also sorted in a separate tube. From week 2 and 6 samples, antigen-specific cells were single-cell sorted into 96-well plates containing 5 µL of TCL buffer (Qiagen) with 1% b-mercaptoethanol for sequencing by SmartSeq. All sorts were performed using a BD FACSymphony S6 Cell Sorter (BD Biosciences) with BD FACSDiva Software version 9.5.1 (BD Biosciences) and data were analyzed using Flowjo v10.8.1.
Frozen rhesus macaque PBMC were thawed into warm R10 media (RPMI + 10% Fetal Bovine Serum + 2 mL L-Glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin; all reagents from Gibco) containing DNase I (MilliporeSigma) and rested for 1 hour at 37oC / 5% CO2.  Cells were stimulated with two peptide pools corresponding to S1 and S2 of the vaccine insert SARS-CoV-2 S protein (JPT Peptide Technologies) at 2 µg/mL of each peptide for 6 hours at 37oC / 5% CO2.  A DMSO only control was included for each sample.  Anti-CD154 BV421(Biolegend, clone 24-31, cat# 310824) was included during the 6-hour culture and GolgiStop (BD Biosciences) was added after 2 hours of stimulation.  Following stimulation, cells were washed and stained with Aqua LIVE/DEAD dye (ThermoFisher) for 10 minutes, and subsequently stained with antibody mix. In addition, cells were incubated with TotalSeqTM Hashtag antibodies (Biolegend) with separate antibodies applied to the DMSO only condition and the stimulated conditions. For each animal, 1000-2000 memory CD4 cells from the DMSO only condition were sorted and combined with memory cells expressing CD154 and CD69 from each S pool stimulation for processing for 10X Genomics.
Bulk-sorted cells were pooled into a tube and loaded on the 10x Genomics Chromium Chip according to the manufacturer’s protocol for the Next GEM Single Cell 5’ Kit v1.1 (10x Genomics, PN-1000165). To sequence single-cell gene expression and cell surface oligonucleotides (from Hashtag antibodies), libraries were prepared according to manufacturer’s instructions using the Chromium Single Cell 5' Library Construction Kit (10x Genomics, PN-1000020) and Chromium Single Cell 5' Feature Barcode Library Kit (10x Genomics, PN-1000080), respectively. To sequence TCR repertoire libraries were prepared using the Chromium Single Cell V(D)J Enrichment Kit (10x Genomics, PN- PN-1000005). These libraries were sequenced on an Illumina NovaSeq platform (Illumina). To sequence BCR repertoire, heavy and light chains were amplified from the cDNA using IgG_REV, IgA_REV, IgK_REV or IgL_REV primers (Table S3) with the addition of Illumina sequences as detailed in (25). These Illumina-ready libraries were sequenced using 2x300 paired-end reads on an Illumina MiSeq
Full-length transcriptomes were sequenced using a modified SMART-Seq protocol. Heavy and light chain variable regions were enriched by amplifying cDNA with a forward primer complementary to the TSO and IgA/IgG_REV or IgK/IgL_REV primer pools.
OTHER: scRNA-seq with FeatureSeq and scAIRR-seq

value: PBMC

value: CD4 memory T cells

tag: library type

value: mRNA

tag: tags

value: mRNA-1273 vaccination

tag: time

value: week 6


title: 2cell embryo 1 wild-type scBS-seq


title: CD4 memory T, 16C303+36186+16C222, week 6,VDJ-derived cDNA


title: HUVEC, CYR61-0.5, rep2


title: CD4 memory T, 16C237+34941, week 6, VDJ-derived cDNA


title: B cell DMSO rep1

source_name: B1 DMSO


title: MII oocyte 46 Mutant scBS-seq

source_name: oocyte

value: oocyte


title: CCseq_VG402_sae2Dtel1D_6h_rep1B

city: Brighton

first: Matthew

last: Neale

address: Science Park Road

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

description:
MATa/alpha ho::LYS2/”, lys2/”, ura3/”, arg4-nsp/”, leu2::hisG,/” his4X::LEU2/”, nuc1::LEU2/”, sae2∆::KanMX4/”, tel1∆::HphMX4/”
Chr=Chromosome; Pos=Position in reference;Watson=Top-strand reads; Crick=Bottom-strand reads

library_source: genomic

data_processing:
FASTQ reads were aligned to the reference genome (SacCer3H4L2; which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 S. cerevisiae genome build as described in Gittens 2019) via Bowtie2, using TermMapper as previously described in Gittens 2019 (https://github.com/Neale-Lab/terminalMapper)
Assembly: SacCer3H4L2 which includes the HIS4::LEU2 and leu2::hisG loci inserted into the Cer3 R64 S. cerevisiae genome build
Supplementary files format and content: Sparse table of positions (Pos) of read frequencies of 5' ends of Read 1 molecules mapping to the top (Watson) and bottom (Crick) strand of each chromosome (Chrom) of the reference genome
Library strategy: CC-seq

organism: Saccharomyces cerevisiae

source_name: MATa/alpha ho::LYS2/", lys2/", ura3/", arg4-nsp/", leu2::hisG,/" his4X::LEU2/", nuc1::LEU2/", sae2delta::KanMX4/", tel1delta::HphMX4/"

growth_protocol: For meiosis induction, a single colony was inoculated in 4mL of YPD medium (1% yeast extract, 2% peptone, 2% glucose supplemented with 0.5 mM adenine and 0.4 mM uracil) and incubated at 30 °C, 250 rpm for a day to reach saturation, then diluted to OD600 of 0.2 in a volume of 200 mL of either YPA (1% yeast extract, 2% peptone, 1% potassium acetate) or SPS (0.5% yeast extract, 1% peptone, 0.67% Yeast Nitrogen Base without amino acids, 1% potassium acetate, 0.05M Potassium Hydrogen phthalate, 0.001% Antifoam 204) pre-sporulation medium. Cultures were incubated at 30 °C, 250 rpm for 14–16 hours, then washed and resuspended in 200 mL pre-warmed SPM sporulation medium (2% potassium acetate supplemented with diluted amino acids) and incubated at 30°C, 250rpm for the duration of the time course.

extract_protocol:
Protein-DNA Covalent-Complex Mapping (CC-seq) in yeast followed a method previously described (Gittens 2019). Briefly, meiotic cell samples are chilled and frozen at -20˚C for at least 8 hours, then thawed and spheroplasted (in 1 M sorbitol, 50 mM NaHPO4, 10 mM EDTA, 30 min at 37˚C), fixed in 70% ice-cold ethanol, collected by centrifugation, dried briefly, then lysed in STE (2% SDS, 0.5 M Tris, 10 mM EDTA). Genomic DNA was extracted via Phenol/Chloroform/IAA extraction (25:24:1 ratio) at room temperature, with aqueous material carefully collected, precipitated with ethanol, washed, dried, then resuspended in 1xTE buffer (10 mM Tris/1 mM EDTA). Total genomic DNA was sonicated to <500 bp average length using a Covaris M220 before equilibrating to a final concentration of 0.3 M NaCl, 0.1% TritonX100, 0.05% Sarkosyl. Covalent complexes were enriched on silica columns (Qiagen) via centrifugation, washed with TEN solution (10 mM Tris / 1 mM EDTA / 0.3 M NaCl), before eluted with TES buffer (10 mM Tris / 1 mM EDTA / 1% SDS). Samples were treated with Proteinase K at 50˚C, and purified by ethanol precipitation.
DNA ends were filled and repaired using NEB Ultra II end-repair module (NEB #E7645), with adapters ligated sequentially to the sonicated, then blocked, ends with recombinant TDP2 treatment in between these steps to remove the 5-phosphotyrosyl-linked Spo11 peptide. Ampure bead cleanups were used to facilitate sequential reactions. PCR-amplified libraries were quantified on a Bioanalyser and appropriately diluted and multiplexed for deep sequencing (Illumina MiSeq 2x75 bp).

treatment_protocol: 50 mL of culture was taken at t = 6 hours. Samples were centrifuged at 3000 x g for 5 minutes, supernatant discarded and pellet frozen at -20 °C until use.

tag: cell line

value: Meiotic

value: 6 hour


title: CCseq_VG402_sae2Dtel1D_6h_rep3


title: CCseq_VG402_sae2Dtel1D_6h_rep4


title: CD4 memory T, 16C303+36186+16C222+16C283, week 2, VDJ-derived cDNA

value: week 2


title: HUVEC, CYR61-0.5, rep1


title: CCseq_VG402_sae2Dtel1D_6h_rep2


title: HUVEC, CYR61-0.05, rep5


title: MII oocyte 44 Mutant scBS-seq


title: MII oocyte 45 Mutant scBS-seq


title: CD4 memory T, 16C301+16C235+16C237+34941, week 2, VDJ-derived cDNA


title: CCseq_MJ965_sae2Dndt80Dtel1D_6h_rep5

description:
MATa/alpha ho::LYS2/”, lys2/”, ura3/”, arg4-nsp/”, leu2::hisG,/” his4X::LEU2/”, nuc1::LEU2/”, sae2∆::KanMX6/”, ndt80∆::LEU2/’’, tel1∆::HYG/’’
Chr=Chromosome; Pos=Position in reference;Watson=Top-strand reads; Crick=Bottom-strand reads

source_name: MATa/alpha ho::LYS2/", lys2/", ura3/", arg4-nsp/", leu2::hisG,/" his4X::LEU2/", nuc1::LEU2/", sae2delta::KanMX6/", ndt80delta::LEU2/", tel1delta::HYG/’'


title: MII oocyte 43 Mutant scBS-seq


title: HUVEC, CYR61-0.05, rep4


title: innate PBMC, 16C301, week -1, mRNA-derived cDNA

description: poly A RNA via 10x Chromium

value: monocytes/natural killer/dendritic

value: week -1


title: MII oocyte 42 Mutant scBS-seq


title: CCseq_VG402_sae2Dtel1D_6h_rep1A


title: SAH1

description: Biological replicate 1 of 3. SAH


title: HUVEC, CYR61-0.5, rep3

value: primary human umbilical vein endothelial cells

value: CYR61, 0.5 ug/ml


title: CCseq_MJ965_sae2Dndt80Dtel1D_6h_rep4


title: MII oocyte 41 Mutant scBS-seq


title: HUVEC, CYR61-0.05, rep3


title: Sham1

description: Biological replicate 1 of 3. Sham

source_name: plasma, sham

value: blood

value: 8-12 weeks

value: Day 3 after sham operation


title: innate PBMC, 16C283, week -1, mRNA-derived cDNA

description: poly A RNA via 10x Chromium


title: NTsiRNA_1

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: control siRNAs replicate 1

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg38 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for all 116 samples

source_name: human HEK293T cells treated with siRNAs

extract_protocol:
Cells were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase. RNA sequencing was performed as previously described from from human HEK293T cells treated with siRNAs targetingUBA1 and E2 ubiquitin-conjugating enzymes compared to control treatment with non-targeting (NT) siRNAs
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina NovaSeq 6000 platform.

value: control siRNAs


title: CCseq_MJ965_sae2Dndt80Dtel1D_6h_rep3


title: Sham3

description: Biological replicate 3 of 3. Sham

value: Sprague-Dawley


title: Sham2

description: Biological replicate 2 of 3. Sham


title: HUVEC, CYR61-0.05, rep2


title: iSOX9KO (no Dox)

city: San Francisco

first: Sapna

last: Puri

address: 513 Parnassus Avenue

institute: UCSF

data_processing:
Sequencing data were generated on the 10X platform (10X Genomics, Pleasanton, CA) according to Single Cell 3’ protocol (v2 Chemistry) as per manufacturer's recommendations. Cell Ranger outputs a .mtx file with the gene (prior to Cell Ranger 3.0) or feature (after Cell Ranger 3.0)-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cell Ranger. The matrix is in market exchange format while the row (gene or feature) and columns (cell barcodes) are provided as TSV files. File formats are documented in the Cell Ranger software manual.
The raw files for both samples (DOX/NO DOX) were pseudoaligned to the Ensembl GRCh38 cdna reference transcriptome using the kallisto bus command (version 0.46.1) and the transcript compatibility counts (TCCs) were generated with bustools (version 0.40.0), filtering out reads that were multi-mapping across genes. Gene counts were also generated by aggregating TCCs to genes using bustools with the --genecounts flag. We subsequently filtered out 1) low quality cells based on their total UMI counts (60,848 cells kept) and 2) rare TCCs that were either detected in less than 1% of the cells or had a mean expression of less than 0.01 (61,006 equivalence classes kept). Doublets were removed based on the gene count data using Scrublet with the default parameters. Scanpy was used for downstream clustering and visualization. Gene counts were log-normalized, highly variable genes were selected with scanpy’s pp.highly_variable_genes function (flavor=’seurat’) with the default parameters (2410 genes kept) and both total UMI counts and mitochondrial count percentages were regressed out. UMAP dimensionality reduction was performed on the nearest neighbor graph computed with bbknn on the PCA-reduced gene expression matrix (50 principal components). Clustering was performed with the Leiden algorithm implemented within scanpy with resolution parameter set to 0.2 and 0.5 to generate coarse and fine-grained resolution cluster labels. Cell types were annotated based on known gene markers and genes identified from a standard differential expression analysis with sc.tl.rank_genes_groups with the default parameters. The resulting gene lists were first filtered based on their p values (<10e-5) and then sorted based on their log-fold change. We then performed a high-dimensional TCC differential expression test between DOX and NO DOX treated beta-cells, including all TCCs mapping to SRSF5 with mean expression above 0.05 in both conditions. The resulting raw p-value was extremely small (2e-50) which even after Bonferroni correction across all genes would indicate a significant change in the splicing patterns of SRSF5 in DOX-treated eBCs. For reference, testing for gene-level expression changes in SRSF5 between the same groups results in a raw p-value of 0.99.
Assembly: GRCh38
Supplementary files format and content: Processed data files are in tsv format and mtx format

source_name: Stem cell derivatives

growth_protocol: CMRL containing 1:100 B27 (or 10% FBS), 1:100 Glutamax (Gibco), 1:100 NEAA (Gibco), 10 μm ALKi II (Axxora), 0.5 mM Vitamin C, 1 μM T3 (Sigma-Aldrich), 1 mM N-acetyl Cysteine (Sigma-Aldrich), 10 μM zinc sulfate (Sigma-Aldrich) and 10 μg/ml of Heparin sulfate in humidified atmosphere supplemented with 5% CO2 at 37ºC.

extract_protocol:
Total RNA was extracted from isolated islets using the Rneasy Mini kit from Qiagen as per manufacturer's instructions.
Eukaryotic stranded library

treatment_protocol: Starting day 12 of the differentiation, just prior to endocrine specification but after the pancreatic lineage has been determined, cells were treated with with or without 2 ug/ml doxycycline.

value: Stem cell derivatives

value: Differentiated Stem Cells

value: NO DOX


title: iSOX9KO (+DOX)

value: PLUS DOX


title: MII oocyte 40 Mutant scBS-seq

value: oocyte


title: MII oocyte 39 Mutant scBS-seq


title: MII oocyte 38 Mutant scBS-seq


title: CCseq_MJ965_sae2Dndt80Dtel1D_6h_rep2

value: Meiotic


title: HUVEC, control, rep5

value: control


title: HUVEC, CYR61-0.05, rep1


title: CCseq_MJ962_sae2Dndt80D_6h_rep4

description:
MATa/alpha ho::LYS2/”, lys2/”, ura3/”, arg4-nsp/”, leu2::hisG,/” his4X::LEU2/”, nuc1::LEU2/”, sae2∆::KanMX6/”, ndt80∆::LEU2/’’
Chr=Chromosome; Pos=Position in reference;Watson=Top-strand reads; Crick=Bottom-strand reads

source_name: MATa/alpha ho::LYS2/", lys2/", ura3/", arg4-nsp/", leu2::hisG,/" his4X::LEU2/", nuc1::LEU2/", sae2delta::KanMX6/", ndt80delta::LEU2/’'

value: 6 hour


title: MII oocyte 36 Mutant scBS-seq


title: CCseq_MJ965_sae2Dndt80Dtel1D_6h_rep1


title: MII oocyte 37 Mutant scBS-seq


title: si3033_Stimulated_4Days_4

city: Worcester

first: Samuel

last: Hilebrand

state: MA

address: 368 Plantation Street AS4.1016

department: RNA Therapeutics Institute

institute: University of Massachusetts Chan Medical School

data_processing:
The sequenced reads were mapped to the human genome (hg38) using STAR v.2.7.10a under default settings
Transcripts were quantified using RSEM v1.3.3 under default settings
Assembly: hg38
Supplementary files format and content: RSEM isoform quantification output

source_name: Skin

growth_protocol: De-identified surgically discarded fresh abdominal skin was obtained from UMass Chan Biospecimen, Tissue, and Tumor Bank. The siRNA treatments were conducted within 24 h after the excision of human specimens. Subcutaneous fat was fully removed and all skin specimens were cultured in Iscove′s Modified Dulbecco′s Media (Sigma-Aldrich; #I3390) containing 10% FBS, 100 U/ml penicillin-streptomycin, and 50 μM 2-mercaptoethanol.

extract_protocol:
Total RNA was extracted from 30 mg of skin sample using RNAeasy Fibrous Tissue Mini Kit (QIAGEN, #74704) following the manufacturer’s instructions and the purified total RNA was eluted into RNase-free water for RNAseq.
Illumina RNA with PolyA Selection

treatment_protocol: 8-mm skin biopsies were taken and injected intradermally with 0.13 mg of siRNAs in a volume of 50 mL. For silencing studies, the skin biopsies were cultured in a 24-well plate with 2 mL of media per punch for 96 h at 37 °C. To induce CXCL9, 10, and 11 expression, after 96 h of siRNA treatment, skin biopsies were treated with new media containing 10 ng/mL recombinant human IFN-g protein (R&D System, #285-IF-100) and 10 ng/mL recombinant human TNF-a protein (R&D System, #210-TA-020)

value: Skin

tag: stimulation

value: Stimulated

tag: timepoint


title: HUVEC, control, rep4

value: primary human umbilical vein endothelial cells


title: Org2

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description: 10X Genomics

data_processing:
Reads were aligned to hg19 human genome by Cellranger (v3.0.2).
Assembly: hg19
Supplementary files format and content: Read count matrix was formated by mtx. Barcodes and genes were provided by tsv format.

source_name: Liver organoid

extract_protocol: Library was constructed by the manufacter's protocol (Chromium reagent 3' v2, 10X Genomics)

value: Liver organoid

value: H1 hESCs

value: 48 days


title: CCseq_MJ962_sae2Dndt80D_6h_rep1


title: HUVEC, control, rep2


title: CCseq_MJ962_sae2Dndt80D_6h_rep3


title: si3033_Stimulated_4Days_3


title: si3033_Stimulated_4Days_2


title: MII oocyte 35 Mutant scBS-seq


title: CCseq_MJ962_sae2Dndt80D_6h_rep2


title: Org1

description: 10X Genomics


title: HUVEC, control, rep3


title: HUVEC, CYR61-BMDM, rep6

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: Ensembl release 101 primary assembly
Supplementary files format and content: group_CYR61BMDM-group_control_Differential_Expression.tsv: Differential gene expression performed comparing HUVECs incubated with BMDM-free control vs. CYR61-activated BMDMs.
Supplementary files format and content: group_CYR61BMDM-group_naiveBDM_Differential_Expression.tsv: Differential gene expression performed comparing HUVECs incubated with naïve BMDMs vs. CYR61-activated BMDMs.
Supplementary files format and content: group_naiveBDM-group_control_Differential_Expression.tsv: Differential gene expression performed comparing HUVECs incubated with BMDM-free control vs. naïve BMDMs.
Supplementary files format and content: all.gene_counts.tsv: Raw counts.

growth_protocol: We used primary human umbilical vein endothelial cells (HUVECs) from ATCC (PCS-100-010). We maintained HUVECs according to the manufacturer's recommended instructions. We isolated bone marrow from the tibias and femurs of C57BL/6J mice (2-5 months old). Bone marrow cells were incubated for 5-6 days in macrophage differentiation media: DMEM + 10% FBS + 10% CMG-conditioned media + 1% penicillin/streptomycin + 1% L-glutamine. After differentiation, macrophages were switched to mature macrophage media: DMEM + 10% FBS + 2% CMG-conditioned media + 1% penicillin/streptomycin + 1% L-glutamine.

extract_protocol:
After co-incubation for 24 hrs, we washed HUVECs twice with PBS, then used TRIzol (Ambion) and RNeasy Plus Mini Kit (Qiagen) to extract RNA following the manufacturer's recommended protocol.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: We plated HUVECs in the bottom compartments of 24-well transwell plates (0.4 μm pore size) along with the following in the top compartments: 1) cell-free (n=6 wells); 2) naïve BMDMs (n=6 wells); or 3) CYR61-treated BMDMs (0.5 μg/ml, 24 hr, n=6 wells).

value: CYR61-activated BMDM


title: MII oocyte 33 Mutant scBS-seq


title: CCseq_MJ315_sae2D_6h_rep7C

description:
MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, sae2∆::KanMX6/’
Chr=Chromosome; Pos=Position in reference;Watson=Top-strand reads; Crick=Bottom-strand reads

source_name: MATa/alpha ho::LYS2/’, lys2/’, ura3/’, arg4-nsp/’, leu2::hisG/’, his4X::LEU2/’, nuc1::LEU2/’, sae2delta::KanMX6/'


title: MII oocyte 34 Mutant scBS-seq


title: si3033_Stimulated_4Days_1


title: MII oocyte 31 Mutant scBS-seq


title: HUVEC, CYR61-BMDM, rep4


title: HUVEC, CYR61-BMDM, rep5


title: MII oocyte 32 Mutant scBS-seq


title: siNTC_Stimulated_4Days_3

value: NTC siRNA


title: HUVEC, CYR61-BMDM, rep3


title: CCseq_MJ315_sae2D_6h_rep3


title: CCseq_MJ315_sae2D_6h_rep7B


title: CCseq_MJ315_sae2D_6h_rep5


title: MII oocyte 30 Mutant scBS-seq


title: HUVEC, control, rep1


title: siNTC_Stimulated_4Days_2


title: siNTC_Stimulated_4Days_1


title: HUVEC, CYR61-BMDM, rep2


title: PBS_Stimulated_4Days_4

value: PBS


title: MII oocyte 28 Mutant scBS-seq


title: MII oocyte 29 Mutant scBS-seq


title: HUVEC, naïve-BMDM, rep6

value: naive BMDM


title: CCseq_GB21_sae2Dspo11Y135F_6h_rep1

description:
MATa/alpha ho::LYS2/”, lys2/”, ura3/”, arg4-nsp/”, leu2::hisG,/” his4X::LEU2/”, sae2∆::KanMX6/”, ndt80∆::LEU2/’’, spo11(Y135F)::KanMX4/”
Chr=Chromosome; Pos=Position in reference;Watson=Top-strand reads; Crick=Bottom-strand reads

source_name: MATa/alpha ho::LYS2/", lys2/", ura3/", arg4-nsp/", leu2::hisG,/" his4X::LEU2/", sae2delta::KanMX6/", ndt80delta::LEU2/", spo11(Y135F)::KanMX4/"


title: CCseq_MJ315_sae2D_6h_rep1


title: HUVEC, naïve-BMDM, rep5


title: CCseq_MJ315_sae2D_6h_rep2A


title: HUVEC, CYR61-BMDM, rep1


title: PBS_Stimulated_4Days_3


title: MII oocyte 27 Mutant scBS-seq


title: PBS_Stimulated_4Days_2


title: MII oocyte 26 Mutant scBS-seq


title: IgD- B, 34941, week 6, plates 5&6 & 16C237, week 6, plate 4

description: poly A RNA via SmartSeq

value: PBMC

value: IgD- memory B cells

value: mRNA

value: 34941_wk6_5/Nextera UDI set C ; 34941_wk6_6/Nextera UDI set D ; 16C237_wk6_4/Nextera UDI set A

value: mRNA-1273 vaccination

value: week 6


title: siNTC_Stimulated_4Days_4


title: IgD- B, 16C222, week 2, plates 1&2 & 16C283, week 2, plate 2

description: poly A RNA via SmartSeq

value: 16C222_wk2_1/Nextera UDI set A ; 16C222_wk2_2/Nextera UDI set D ; 16C283_wk2_2/Nextera UDI set B

value: week 2


title: IgD- B, 34941, week 6, plate 4 & 36186, week 2, plate 3

description: poly A RNA via SmartSeq

value: 34941_wk6_4/Nextera UDI set D ; 36186_wk2_3/Nextera UDI set A

value: week 2 & week 6


title: HUVEC, naïve-BMDM, rep4

value: primary human umbilical vein endothelial cells


title: IgD+ B, 16C303+16C222+16C237+16C235, week -1, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: IgD+ naive B cells

value: HTO

value: Anti CD298 + Anti beta2-microglobulin:16C303/TotalSeq-C0251 ; 16C222/TotalSeq-C0252 ; 16C237/TotalSeq-C0253 ; 16C235/TotalSeq-C0254

value: week -1


title: Negative control2 24 Negative scBS-seq

value: control


title: MII oocyte 25 Mutant scBS-seq

value: oocyte


title: HUVEC, naïve-BMDM, rep3

value: naive BMDM


title: si3033_Unstimulated_4Days_4

value: Skin

value: Unstimulated


title: HUVEC, naïve-BMDM, rep2


title: Negative control1 23 Negative scBS-seq


title: CD4 memory T, 16C283+16C301+16C235, week 6, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: PBMC

value: CD4 memory T cells

value: Anti CD298 + Anti beta2-microglobulin:16C283-nostim/TotalSeq-C0251 ; 16C283-stim/TotalSeq-C0252 ; 16C301-nostim/TotalSeq-C0253 ; 16C301-stim/TotalSeq-C0254 ; 16C235-nostim/TotalSeq-C0255 ; 16C235-stim/TotalSeq-C0256


title: si3033_Unstimulated_4Days_3


title: HUVEC, naïve-BMDM, rep1


title: CD4 memory T, 16C283+16C301+16C235, week 6, mRNA-derived cDNA

description: poly A RNA via 10x Chromium

value: mRNA

value: mRNA-1273 vaccination

value: week 6


title: HUVEC, BMDM-free, rep6

value: BMDM-free control


title: MII oocyte 22 wild-type scBS-seq


title: MII oocyte 21 wild-type scBS-seq


title: si3033_Unstimulated_4Days_1


title: siNTC_Unstimulated_4Days_4

value: NTC siRNA


title: HUVEC, BMDM-free, rep4

value: primary human umbilical vein endothelial cells


title: HUVEC, BMDM-free, rep5


title: CD4 memory T, 16C303+36186+16C222, week 6, mRNA-derived cDNA

description: poly A RNA via 10x Chromium


title: siNTC_Unstimulated_4Days_3


title: innate PBMC, 16C303+36186+16C222+16C283, week 6, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: monocytes/natural killer/dendritic

value: HTO

value: Anti CD298 + Anti beta2-microglobulin:16C303/TotalSeq-C0251 ; 36186/TotalSeq-C0252 ; 16C222/TotalSeq-C0253 ; 16C283/TotalSeq-C0254


title: HUVEC, BMDM-free, rep3


title: si3033_Unstimulated_4Days_2


title: MII oocyte 19 wild-type scBS-seq


title: MII oocyte 20 wild-type scBS-seq


title: PBS_Stimulated_4Days_1

value: PBS

value: Stimulated


title: MII oocyte 18 wild-type scBS-seq

value: oocyte


title: siNTC_Unstimulated_4Days_2

value: Skin


title: CD4 memory T, 16C303+36186+16C222, week 6, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: Anti CD298 + Anti beta2-microglobulin:16C303-nostim/TotalSeq-C0251 ; 16C303-stim/TotalSeq-C0252 ; 36186-nostim/TotalSeq-C0253 ; 36186-stim/TotalSeq-C0254 ; 16C222-nostim/TotalSeq-C0255 ; 16C222-stim/TotalSeq-C0256


title: siNTC_Unstimulated_4Days_1

value: Unstimulated


title: MII oocyte 17 wild-type scBS-seq


title: CD4 memory T, 16C237+34941, week 6, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: PBMC

value: CD4 memory T cells

value: Anti CD298 + Anti beta2-microglobulin:16C237-nostim/TotalSeq-C0255 ; 16C237-stim/TotalSeq-C0256 ; 34941-nostim/TotalSeq-C0257 ; 34941-stim/TotalSeq-C0258


title: HUVEC, BMDM-free, rep1


title: MII oocyte 16 wild-type scBS-seq


title: innate PBMC, 16C303+36186+16C222+16C283, week 6, mRNA-derived cDNA

description: poly A RNA via 10x Chromium

value: mRNA

value: mRNA-1273 vaccination


title: MII oocyte 15 wild-type scBS-seq


title: HEK293T cells, dox-induced RBFOX2-Apobec fusion replicate 3

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
STAR aligned original fastqs to hg19 reference build
Run SAILOR to identify editing sites. Code available at: https://github.com/YeoLab/FLARE
Run FLARE to identify regions of enriched editing. Code available at: https://github.com/YeoLab/FLARE
Assembly: hg19
Supplementary files format and content: Peak files are tab delimited and include peak coordinates, edit fraction, fraction of reads edited, and score

growth_protocol: All stable STAMP HEK293T cell lines were generated using human lenti-X HEK293T cells (HEK293XT, Takara Bio) which are derived from transformed female human embryonic kidney tissue. Cells were maintained in DMEM (4.5 g/L D-glucose) supplemented with 10% FBS (Gibco) at 37o C with 5% CO2. Cells were periodically passaged once at 70-90% confluency by dissociating with TrypLE Express Enzyme (Gibco) at a ratio of 1:10.

extract_protocol:
Trizol extraction (Fisher) and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol
Illumina TruSeq stranded mRNA or total RNA
TruSeq

value: Human embryonic kidney

value: WT

value: Transient transfection


title: HUVEC, BMDM-free, rep2

value: primary human umbilical vein endothelial cells

value: BMDM-free control


title: PBS_Unstimulated_4Days_4


title: CD4 memory T, 16C237+34941, week 6, mRNA-derived cDNA

description: poly A RNA via 10x Chromium

value: week 6


title: innate PBMC, 16C301+16C235+16C237+34941, week 6, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: monocytes/natural killer/dendritic

value: HTO

value: Anti CD298 + Anti beta2-microglobulin:16C301/TotalSeq-C0251 ; 16C235/TotalSeq-C0252 ; 16C237/TotalSeq-C0253 ; 34941/TotalSeq-C0254


title: PBS_Unstimulated_4Days_3

value: Skin

value: PBS


title: HEK293T cells, dox-induced RBFOX2-Apobec fusion replicate 2

value: 72 hrs


title: MII oocyte 14 wild-type scBS-seq

value: oocyte


title: innate PBMC, 16C301+16C235+16C237+34941, week 6, mRNA-derived cDNA

description: poly A RNA via 10x Chromium

value: PBMC


title: HEK293T cells, dox-induced RBFOX2-Apobec fusion replicate 1


title: PBS_Unstimulated_4Days_2

value: Unstimulated


title: PBS_Unstimulated_4Days_1


title: CD4 memory T, 16C303+36186+16C222+16C283, week 2, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: CD4 memory T cells

value: Anti CD298 + Anti beta2-microglobulin:16C303-nostim/TotalSeq-C0251 ; 16C303-stim/TotalSeq-C0252 ; 36186-nostim/TotalSeq-C0253 ; 36186-stim/TotalSeq-C0254 ; 16C222-nostim/TotalSeq-C0255 ; 16C222-stim/TotalSeq-C0256 ; 16C283-nostim/TotalSeq-C0257 ; 16C283-stim/TotalSeq-C0258

value: week 2


title: MII oocyte 13 wild-type scBS-seq


title: ActD_8hr_RNA_rep2

city: Beijing

first: Yue

last: Huo

state: Beijing

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

description: control Poly(A)+ RNA-seq after ActD treatment 8hr with ERCC spike-in

data_processing:
For Poly(A)+ RNA-seq with ActD treatment: Analysis of RNA-seq data, reads were aligned to Homo sapiens genome using Tophat2 PE mode with the default parameter, and uniquely mapped reads were retained for further analysis filtered by SAMtools. HTSeq-counts or featureCounts were used for calculating annotated gene counts. Differential gene expression analysis was conducted using DESeq2 with the P-value<0.05, and all genes with non-zero counts in the samples were considered.
genome build: Ensembl GRCh38.p12
processed data files format and content: raw counts

source_name: K562 cell line

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen).
For RNA sequencing, an equal amount of ERCC RNA spike-in control (Thermo Scientific, Waltham, MA) was added to the total RNA samples as internal control before library construction. Sequencing libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit. RNA stability assay was generated from two biological replicates.

treatment_protocol: For Poly(A)+ RNA-seq with ActD treatment: K562 cells were treated with 1 µg/ml actinomycin D and collected at indicated time points.

tag: lncrna probes

value: ActD 8hr

value: K562 cell line

tag: sequencing type

value: Poly(A)+ RNA-seq


title: CD4 memory T, 16C303+36186+16C222+16C283, week 2, mRNA-derived cDNA

description: poly A RNA via 10x Chromium

value: mRNA

value: mRNA-1273 vaccination


title: Naive_Unstimulated_4Days_3

value: Naive


title: MII oocyte 12 wild-type scBS-seq


title: ActD_8hr_RNA_rep1


title: Naive_Unstimulated_4Days_4


title: innate PBMC, 16C303+36186+16C222+16C283, week 2, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: monocytes/natural killer/dendritic

value: HTO

value: Anti CD298 + Anti beta2-microglobulin:16C303/TotalSeq-C0251 ; 36186/TotalSeq-C0252 ; 16C222/TotalSeq-C0253 ; 16C283/TotalSeq-C0254


title: MII oocyte 11 wild-type scBS-seq


title: MII oocyte 10 wild-type scBS-seq


title: ActD_6hr_RNA_rep2

description: control Poly(A)+ RNA-seq after ActD treatment 6hr with ERCC spike-in

value: ActD 6hr


title: ActD_6hr_RNA_rep1


title: Naive_Unstimulated_4Days_1

value: Skin


title: Naive_Unstimulated_4Days_2


title: MII oocyte 9 wild-type scBS-seq

value: oocyte


title: MII oocyte 8 wild-type scBS-seq


title: CD4 memory T, 16C301+16C235+16C237+34941, week 2, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: PBMC

value: Anti CD298 + Anti beta2-microglobulin:16C301-nostim/TotalSeq-C0251 ; 16C301-stim/TotalSeq-C0252 ; 16C235-nostim/TotalSeq-C0253 ; 16C235-stim/TotalSeq-C0254 ; 16C237-nostim/TotalSeq-C0255 ; 16C237-stim/TotalSeq-C0256 ; 34941-nostim/TotalSeq-C0257 ; 34941-stim/TotalSeq-C0258


title: CD4 memory T, 16C301+16C235+16C237+34941, week 2, mRNA-derived cDNA

description: poly A RNA via 10x Chromium

value: CD4 memory T cells


title: CB-5083-4

city: Guangzhou

first: Fang

state: None Selected

address: 601 Huangpu Avenue West

institute: Jinan university

data_processing:
IIIumina Casava1.4 software used for basecalling.
Data were filtered the low-quality sequence, including adapter sequence and low-quality bases (mass value <=20) using the software FASTP
Reads were reference to the henome using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) software
Reads were calculated using fragment per kilobase of exon per million fragments mapped (FPKM) software
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HCT116 cells, Control

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard IIIumina protocol.

value: Large intestine, Colon

value: Colorectal Cancer cell


title: ActD_3hr_RNA_rep1

description: control Poly(A)+ RNA-seq after ActD treatment 3hr with ERCC spike-in

value: ActD 3hr


title: ActD_3hr_RNA_rep2

value: K562 cell line


title: MII oocyte 7 wild-type scBS-seq


title: CB-5083-2


title: ActD_0hr_RNA_rep2

description: control Poly(A)+ RNA-seq with ERCC spike-in

value: Poly(A)+ RNA-seq


title: innate PBMC, 16C301+16C235+16C237+34941, week 2, mRNA-derived cDNA

description: poly A RNA via 10x Chromium

value: mRNA

value: week 2


title: MII oocyte 5 wild-type scBS-seq


title: CB-5083-1


title: innate PBMC, 16C301+16C235+16C237+34941, week 2, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: Anti CD298 + Anti beta2-microglobulin:16C301/TotalSeq-C0251 ; 16C235/TotalSeq-C0252 ; 16C237/TotalSeq-C0253 ; 34941/TotalSeq-C0254

value: mRNA-1273 vaccination


title: innate PBMC, 16C303+16C222+16C237+16C235, week -1, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: monocytes/natural killer/dendritic

value: HTO

value: Anti CD298 + Anti beta2-microglobulin:16C303/TotalSeq-C0251 ; 16C222/TotalSeq-C0252 ; 16C237/TotalSeq-C0253 ; 16C235/TotalSeq-C0254

value: week -1


title: Control-4

value: untreatment


title: shSMARCA5_shB_rep2

description: Poly(A)+ RNA-seq after SMARCA5 knockdown

data_processing:
For Poly(A)+ shRNA-seq in K562 cell line: Analysis of RNA-seq data, reads were aligned to Homo sapiens genome using Tophat2 PE mode with the default parameter, and uniquely mapped reads were retained for further analysis filtered by SAMtools. HTSeq-counts or featureCounts were used for calculating annotated gene counts. Differential gene expression analysis was conducted using DESeq2 with the P-value<0.05, and all genes with non-zero counts in the samples were considered.
genome build: Ensembl GRCh38.p5
processed data files format and content: raw counts

extract_protocol:
For Poly(A)+ shRNA-seq in K562 cell line: The cells were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: SMARCA5 knockdown


title: MII oocyte 4 wild-type scBS-seq

value: oocyte


title: innate PBMC, 16C303+36186+16C222+16C283, week 2, mRNA-derived cDNA

description: poly A RNA via 10x Chromium

value: PBMC


title: innate PBMC, 16C303+16C222+16C237+16C235, week -1, mRNA-derived cDNA

description: poly A RNA via 10x Chromium


title: shSMARCA5_shB_rep1


title: MII oocyte 3 wild-type scBS-seq


title: innate PBMC, 34941, week -1, mRNA-derived cDNA

description: poly A RNA via 10x Chromium


title: MII oocyte 2 wild-type scBS-seq


title: Control-2

value: Large intestine, Colon


title: shSMARCA5_shA_rep2


title: CB-5083-3

value: Colorectal Cancer cell


title: MII oocyte 1 wild-type scBS-seq


title: MII oocyte 6 wild-type scBS-seq


title: Drosophila_stage5-10_wt

city: Pasadena

first: Angelike

last: Stathopoulos

address: 1200 E Calif Blvd

institute: Caltech

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Single-cell RNA-seq data were processed using 10X Cellranger 7 software. Customized dm6-transgene reference annotations were loaded to the pipeline for read mapping and gene quantification.
Assembly: dm6 with mCD8-GFP transgene
Supplementary files format and content: Tab separated txt and tsv table files and matrix files

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
manual homogenization with Douncer, 5min Accumax treatment, wash, 30µm filter, magnetic beads-based dead cell removal
standard protocol as recommended by 10x Genomics
single cell RNA-seq library preparation was performed with 10x Chromium v3

value: embryo


title: Control-1


title: shSMARCA5_shA_rep1

value: K562 cell line


title: ActD_0hr_RNA_rep1

value: Poly(A)+ RNA-seq


title: RNA_techrep2_K562_promoters_v2_30k_rep1_S136

status: Public on Oct 17 2023

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

institute: University of Montreal

description: Bulk MPRA

data_processing:
Sequencing data was demultiplexed using bcl2fastq. Raw fastq files were processed first by trimming unnecessary cycles from the 3’ end using seqtk (https://github.com/lh3/seqtk). Forward and reverse mBC reads were joined and error corrected with PEAR (options -v 15 -m 15 -n 15 -t 15). Using custom python and R scripts, successfully assembled barcode reads were combined with UMI reads, mBC/UMI pairs were counted, and the read counts and UMI count per mBC was determined.
Assembly: N/A
Supplementary files format and content: bulk_MPRA_counts_promoters_architecture_positional_effects: summary count tables for bulk MPRA data. Column 1: originating library short identifier column 2: reporter architecture identifier column 3: reporter ORF column 4: promoter id column 5: logical boolean indicating whether U6/oBC cassette is present on construct column 6: logical boolean indicating whether cHS4 insulators are present on construct column 7: mBC column 8: cell line  column 9: bottleneck replicate (3k, 10k, 30k, two replicates per) column 10: technical replicate identifier column 11-16: UMI and read counts for RNA, DNA as well as normalised UMI counts (UMI divided by total UMI count in sample [individual normalization pe rsample])
Library strategy: Bulk MPRA

growth_protocol: K562 cells were grown in RPMI 1640 medium (ThermoFisher, cat. num. 11875119), supplemented with 10% FBS and 1x Penicillin/streptomycin (ThermoFisher, cat. num. 15140122). HEK293T cells were grown in DMEM (ThermoFisher, cat. num. 10313021) with 10% FBS and 1x Penicillin/streptomycin. Cells were kept at 37C and 5% CO2, and passaged every two days (K562, HEK293T), except for clonal expansion.  All cells were transfected in mid-exponential phase. K562 cells were transfected using Nucleofector (V4XC-2024, protocol FF12) following manufacturer’s protocol (6.5 M cells, with 9 ug reporter plasmid mix, 0.4 ug hyPBase). 2M HEK293 cells were transfected using lipofectamine 2000 (ThermoFisher) with 8 ug of reporter plasmid mix and 0.4 ug hyPBase. Cells were allowed to recover for five days post-transfection and passaged upon confluence (HEK293) or reaching 1 M/mL (K562). Following five days, 2 ug/mL puromycin selection was applied for another 7 days to select for piggyBac-mediated genomic integration of reporter transposons (which contained the GFP-P2A-puromycin resistance ORF). After dilution of the unintegrated plasmids (12 days post transfection), polyclonal cell populations were seeded at an estimated starting number of clones of 3k, 10k, and 30k each in biological duplicates. After expansion of populations to approximately 5M cells (7 to 9 days), cells were harvested, fixed in 80% methanol, and stored at -80C until extraction.

extract_protocol:
DNA and RNA were extracted from methanol fixed samples using the AllPrep kit (Qiagen) following manufacturer's instructions.
RNA and DNA was extracted from methanol fixed cells (AllPrep kit, Qiagen). MPRA libraries were constructed as follows: for RNA libraries, 5 ug of RNA was reverse transcribed with UMI containing primer oJBL753 using SuperScript IV (10 uL 500 ng/uL RNA mixed with 2 uL 1 uM oJBL753; 5 min at 65C, ice for >2 min; followed by addition of 4 uL 5x buffer, 1 uL 0.1M DTT, 1 uL 10 mM dNTPs, 1 uL water, 1 uL SSIV as a master mix for 20 uL total reaction; 55C for 60 min, 80C for 10 min). The cDNA was taken directly as template for PCR1 (25 uL reactions, 10 uL cDNA, primers oJBL039+Nextera v2 P7 indexed primers; 4 elongation cycles). Following the first PCR, reactions were cleaned up with 1x Ampure XP beads, eluted in 12 uL 10 mM Tris 8. 4 uL of PCR1 eluates were taken to PCR2 (10 uL reactions, primers oJBL077+oJBL359, tracked with qPCR and SYBr green, stopped at cycles 9-15 depending on reaction’s inflection point). Reactions were again purified with 1x Ampure XP and eluted in a final volume of 10 uL 10 mM Tris 8. For DNA, approximately 10 ug genomic DNA was amplified in 25 uL reactions (primers oJBL039+oJBL753; 4 cycles). Following 1x Ampure XP cleanup and elution in 12 uL 10 mM Tris 8, 4 uL of the eluate was amplified in a second round of PCR (10 uL reactions, 15 elongation cycles; primers oJBL360+Nextera v2 P7 indexed primers), cleaned up with 1x Ampure XP, and eluted in 10 uL 10 mM Tris 8. Each biological replicate was process in technical duplicate, for a total of 48 libraries (2 cell lines ⨉ 2 library types RNA/DNA ⨉ 3 bottlenecking factors ⨉ 2 biological replicates ⨉ 2 technical replicates). All reactions were performed in 96-well plates. To quantify final amplicon concentrations, a real-time qPCR experiment was performed using P5 and P7 primers (oJBL076, oJBL077 respectively).   Samples were pooled according to their concentration as determined by qPCR and sequenced on a Nextseq2000 using custom set of primers (read 1: oJBL369, 15 cycles to read mBC; index 1: oJBL335 [Nextera index 1], 10 cycles to read the sample index; read 2: oJBL494 [Nextera read 2], 10 cycles to read the pseudo-UMI; index 2: oJBL371, 15 cycles to read the reverse complement of the mBC).

value: Erythroleukemia

value: high MOI integration via piggyBac of MPRA reporter promoter series with varying architecture. Cellular pool bottlenecked to different complexity


title: RNA_techrep2_K562_promoters_v2_10k_rep1_S138

description: Bulk MPRA


title: RNA_techrep2_K562_promoters_v2_30k_rep2_S137

description: Bulk MPRA


title: RNA_techrep2_K562_promoters_v2_10k_rep2_S139

description: Bulk MPRA


title: RNA_techrep2_HEK293_promoters_v2_30k_rep2_S143

description: Bulk MPRA

value: Embryonic kidney


title: RNA_techrep2_K562_promoters_v2_03k_rep1_S140

description: Bulk MPRA


title: Control-3


title: RNA_techrep2_K562_promoters_v2_03k_rep2_S141

description: Bulk MPRA


title: innate PBMC, 36186, week -1, mRNA-derived cDNA

description: poly A RNA via 10x Chromium

value: mRNA

value: mRNA-1273 vaccination


title: RNA_techrep2_HEK293_promoters_v2_10k_rep2_S145

description: Bulk MPRA


title: RNA_techrep2_HEK293_promoters_v2_30k_rep1_S142

description: Bulk MPRA


title: RNA_techrep2_HEK293_promoters_v2_03k_rep2_S147

description: Bulk MPRA


title: RNA_techrep2_HEK293_promoters_v2_10k_rep1_S144

description: Bulk MPRA


title: Replicate 2 DCLK1 KO

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

data_processing: Normalization of housekeeping genes for the quantification of gene expression levels, normalization of the positive control for background correction, and data analysis were performed using the nSolverTM analysis software (NanoString Technologies).

label: NanoString

source_name: Ovarian Cancer

growth_protocol: Spheroids were grown on poly-HEMA coated plates. The spheroid were allowed to form for 48 h

extract_protocol: Total RNA was extracted from the cell pellets using TRIzol reagent (Invitrogen, 15596026) and purified using Monarch RNA Cleanup Kit (New England BioLabs, T2050L). RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

tag: histology

value: HGSOC cell line


title: Replicate 3 Control


title: Replicate 3 DCLK1 KO


title: Replicate 1 DCLK1 KO


title: Replicate 2 Control


title: DNA_techrep2_HEK293_promoters_v2_30k_rep1_S52

description: Bulk MPRA


title: DNA_techrep2_HEK293_promoters_v2_10k_rep2_S55

description: Bulk MPRA


title: DNA_techrep2_HEK293_promoters_v2_10k_rep1_S54

description: Bulk MPRA


title: DNA_techrep2_K562_promoters_v2_10k_rep1_S48

description: Bulk MPRA


title: DNA_techrep2_K562_promoters_v2_30k_rep1_S46

description: Bulk MPRA


title: DNA_techrep2_K562_promoters_v2_30k_rep2_S47

description: Bulk MPRA


title: RNA_techrep1_HEK293_promoters_v2_03k_rep1_S101

description: Bulk MPRA


title: RNA_techrep1_K562_promoters_v2_03k_rep2_S96

description: Bulk MPRA


title: DNA_techrep2_K562_promoters_v2_10k_rep2_S49

description: Bulk MPRA


title: RNA_techrep1_HEK293_promoters_v2_30k_rep1_S97

description: Bulk MPRA


title: RNA_techrep1_K562_promoters_v2_10k_rep1_S93

description: Bulk MPRA


title: DNA_techrep2_K562_promoters_v2_03k_rep1_S50

description: Bulk MPRA


title: RNA_techrep1_K562_promoters_v2_30k_rep1_S91

description: Bulk MPRA


title: RNA_techrep1_HEK293_promoters_v2_10k_rep2_S100

description: Bulk MPRA


title: RNA_techrep2_HEK293_promoters_v2_03k_rep1_S146

description: Bulk MPRA


title: RNA_techrep1_HEK293_promoters_v2_10k_rep1_S99

description: Bulk MPRA


title: DNA_techrep2_K562_promoters_v2_03k_rep2_S51

description: Bulk MPRA


title: RNA_techrep1_HEK293_promoters_v2_30k_rep2_S98

description: Bulk MPRA


title: RNA_techrep1_K562_promoters_v2_30k_rep2_S92

description: Bulk MPRA


title: RNA_techrep1_K562_promoters_v2_10k_rep2_S94

description: Bulk MPRA


title: RNA_techrep1_K562_promoters_v2_03k_rep1_S95

description: Bulk MPRA


title: DNA_techrep2_HEK293_promoters_v2_30k_rep2_S53

description: Bulk MPRA


title: Replicate 1 Control


title: RNA_techrep1_HEK293_promoters_v2_03k_rep2_S102

description: Bulk MPRA


title: DNA_techrep1_K562_promoters_v2_30k_rep2_S2

description: Bulk MPRA


title: DNA_techrep2_HEK293_promoters_v2_03k_rep1_S56

description: Bulk MPRA


title: DNA_techrep2_HEK293_promoters_v2_03k_rep2_S57

description: Bulk MPRA


title: DNA_techrep1_K562_promoters_v2_10k_rep1_S3

description: Bulk MPRA


title: DNA_techrep1_K562_promoters_v2_03k_rep2_S6

description: Bulk MPRA


title: DNA_techrep1_HEK293_promoters_v2_30k_rep2_S8

description: Bulk MPRA


title: DNA_techrep1_K562_promoters_v2_03k_rep1_S5

description: Bulk MPRA


title: DNA_techrep1_K562_promoters_v2_10k_rep2_S4

description: Bulk MPRA


title: TO_3141

city: Kyoto

first: Yasuhiro

last: Takashima

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
The sequenced data were preprocessed and quantified for gene expression using STAR aligner (v2.5.1b) and RSEM (v1.3.1) tool.
Assembly: GRCh38-3.0.0
Supplementary files format and content: text file includes TPM values for each sample.

extract_protocol:
Bilaminoids (D6) were manually picked. Each bilaminoid was transferred in a drop of Accutase and incubated at 37℃ for 15-20 min, then dissociated into single cells by repeated pipetting using glass capillaries. Each single cell was transferred into individual PCR tubes and immediately frozen in Smart-seq HT lysis buffer. To collect amnion-like cells(AMLCs), PGC-like cells(PGCLCs), and hematoendothelial progenitor-like cells(HEPLCs), CER1-GFP+ anterior visceral endoderm-like cells(AVELCs) were sorted as single-cells and immediately frozen in Smart-seq HT lysis buffer.
The libraries for scRNA-seq were prepared using the SMART-seq HT kit (Z4436N, Takara), following the manufacture’s instruction. The libraries were then sequenced on an NovaSeq 6000 or NextSeq 2000 with paired-end sequencing.

tag: analysis method

value: scRNA-seq

value: 585B1 iPSCs

value: Bilaminoid Day9

tag: transgenes

value: Blimp1-tdTomato, TFAP2C-EGFP

tag: protocol

value: FACS:Blimp1-tdTomato and TFAP2C-EGFP+


title: TO_3096

tag: cell type


title: TO_3147


title: TO_3146


title: TO_3085


title: TO_3137


title: DNA_techrep1_K562_promoters_v2_30k_rep1_S1

description: Bulk MPRA

tag: genotype


title: Ip_IgG_Lm_3

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

data_processing:
On Galaxy, sequence reads were aligned to the 5s pre ribosomal RNA sequence with Bowtie.2 and unaligned reads were kept to deplete remaining ribosomal reads from the data set.
On Galaxy, sequence reads were aligned to the 45s pre ribosomal RNA sequence with Bowtie.2 and unaligned reads were kept to deplete remaining ribosomal reads from the data set.
On Galaxy, filtered sequence reads were mapped to GrCh38 using RNA Star with GrcH38 gencode annotation index (v39)  as gene model.
On Galaxy, read count extraction was performed using featureCounts with GrcH38 gencode annotation index (v39) and default parameters.
Assembly: grch 38
Supplementary files format and content: tab-delimited text files include counts per gene for each Sample

source_name: Colon metastasis

growth_protocol: LoVo cells were maintained in DMEM low glucose (1g/L) + Glutamax supplemented with 10% fetal bovine serum (FBS)  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
LoVo cells were grown to 70–85% confluence in 75 cm2 flasks (2 per condition) and infected or not with Lm LL195 as described above. Flasks were snap-frozen in liquid nitrogen at 10 h p.i., and then stored at −80°C until further use.  RNA-immunoprecipitation was performed as described in Kwon et al., 2021, Nature Comm.
10% of the lysate was taken as Control Inputs, and acid phenol was used to extract total mRNA from the input fractions and RNA from the immuno-precipitated fractions, either with an anti-CIRBP antibody or a control anti IgG antibody. Purified RNA duplicates were pooled after the DNAse step and phenol/chloroform precipitation for every condition.
Purified RNAs were stored at −80°C and further used in sequencing library construction. Each time course was reproduced at a 1-week interval, thus producing biological triplicates.
Library were built following the Illumina Stranded mRNA ligation protocol and then sequenced on an Illumina NextSeq2000 sequencer and  with 2 P2 flowcells.  SR100 reads were generated.

treatment_protocol: Infection was performed on 90% confluent cells, using an overnight bacterial culture ( OD600nm +/- 3) and a Multiplicity Of Infection of 30

tag: tissue

value: Colon metastasis

value: LoVo

value: colon cancer cells

tag: infection

value: Infected by Lm for 10h

tag: treatment

value: Immunoprecipitation of control IgG

tag: rip antibody

value: IgG


title: TO_3145


title: TO_3136


title: DNA_techrep1_HEK293_promoters_v2_03k_rep1_S11

description: Bulk MPRA


title: DNA_techrep1_HEK293_promoters_v2_10k_rep1_S9

description: Bulk MPRA


title: DNA_techrep1_HEK293_promoters_v2_03k_rep2_S12

description: Bulk MPRA


title: Ip_IgG_NI_3

value: Non Infected


title: TO_3084


title: DNA_techrep1_HEK293_promoters_v2_10k_rep2_S10

description: Bulk MPRA

value: high MOI integration via piggyBac of MPRA reporter promoter series with varying architecture. Cellular pool bottlenecked to different complexity


title: DNA_techrep1_HEK293_promoters_v2_30k_rep1_S7

description: Bulk MPRA

value: Embryonic kidney


title: Ip_CIRBP_NI_3

value: Immunoprecipitation of CIRBP

value: CIRBP


title: Input_Lm_3

value: Control Input


title: Ip_IgG_NI_2


title: Ip_IgG_Lm_2


title: Ip_CIRBP_Lm_2


title: Ip_CIRBP_Lm_3


title: Input_NI_3


title: Ip_CIRBP_NI_2


title: Input_NI_2


title: Ip_CIRBP_NI_1


title: Ip_CIRBP_Lm_1


title: Input_NI_1


title: Ip_IgG_NI_1


title: Lm_5-17

data_processing:
library strategy: Long Read RNA-Seq (ONT)
On Galaxy, sequence reads were aligned to the 5s pre ribosomal RNA sequence with Bowtie.2 and unaligned reads were kept to deplete remaining ribosomal reads from the data set.
On Galaxy, sequence reads were aligned to the 45s pre ribosomal RNA sequence with Bowtie.2 and unaligned reads were kept to deplete remaining ribosomal reads from the data set.
On Galaxy, filtered sequence reads were mapped to GrCh38 using Minimap2 with GrcH38 gencode annotation index (v36)  and enabled spliced alignments (-- splice)
On R, read count extraction was performed using featureCounts from the Rsubread package, GrcH38 gencode annotation index (v36) and default parameters.
Assembly: grch 38
Supplementary files format and content: tab-delimited text files include counts per gene for each Sample

extract_protocol:
LoVo cells were grown to 70–85% confluence in 75 cm2 flasks and infected with Lm LL195 as described above. Flasks were snap-frozen in liquid nitrogen before infection (0 h) and at 2, 5, and 10 h p.i., and then stored at −80°C until further use. Lysis buffer (20 mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 25 U/ml TurboDNase) was added to the frozen monolayer, which was then scrapped and transferred to an Eppendorf tube and processed.
A portion of the lysate was taken, and acid phenol was used to extract total mRNA, which was stored at −80°C and further used in sequencing library construction. Each time course was reproduced twice at a 1-week interval, thus producing biological triplicates.
Libraries were built from total RNA using the 1D PCR Barcoding cDNA kit from Oxford Nanopore Technologies (ONT). They were multiplexed by 4 and then sequenced on 3 flowcells FLO-MIN106 with SQK-LSK108 sequencing kit. MinKnow version 1.7.10 and then 1.10.23 managed the MinION mk1b ONT sequencer. Data were basecalled with guppy 3.6.1.

value: Cancer cells

value: Infected by L. monocytogenes

tag: molecule subtype

value: Cytoplasmic total RNA


title: Lm_2-17

tag: time


title: NI_0-17

tag: cell line

value: Control


title: Lm_10-16


title: Lm_2-16


title: NI_0-16


title: Lm_5-16


title: Lm_10-14


title: NI_0-14


title: Input_Lm_2


title: RNA_techrep2_mEB_bulk_v2_repB3_d22_S177

description: Bulk MPRA

data_processing:
Sequencing data was demultiplexed using bcl2fastq. Raw fastq files were processed first by trimming unnecessary cycles from the 3’ end using seqtk (https://github.com/lh3/seqtk). Forward and reverse mBC reads were joined and error corrected with PEAR (options -v 15 -m 15 -n 15 -t 15). Using custom python and R scripts, successfully assembled barcode reads were combined with UMI reads, mBC/UMI pairs were counted, and the read counts and UMI count per mBC was determined.
Supplementary files format and content: bulk_MPRA_counts_mEB_v2_poolA and bulk_MPRA_counts_mEB_v2_poolB: summary count tables for bulk MPRA data.  column 1: originating library short identifier, column 2: reporter architecture identifier, column 3: position of CRE relative to reporter, column 4: reporter ORF, column 5: promoter id, column 6: logical boolean indicating whether U6/oBC cassette is present on construct, column 7: logical boolean indicating whether cHS4 insulators are present on construct, column 8: pool id, column 9: CRE class, column 10: CRE id, column 11: mBC, column 12: biological replicate, column 13: technical replicate identifier, column 14: harvest day, column 15-20: UMI and read counts for RNA, DNA as well as normalised UMI counts (UMI divided by total UMI count in sample [individual normalization pe rsample])
Library strategy: Bulk MPRA

source_name: WD44 (mouse embryonic stem cells)

growth_protocol: The two respective library pools (A and B, see manuscript for details) were reverse transfected (lipofectamine 2000) in mESCs. Specifically, each pool was transfected in 6 separate reactions (2M cells transfected and plated in 6 cm plates) with 400 ng hyPBase plasmid, 8 ug of reporter pool. Following recovery of cells for 2 days, cells from pairs of transfection replicates from each pool were combined (from 6 to 3 plates of cells), and the resulting three set of cells were hereafter maintained separately, constituting our biological triplicates. Puromycin (2 ug/mL) selective pressure was applied 3 days post transfection and until induction of mEBs, which happened 11 days post transfection. mEB induction proceeded as described below, with 15M of cells split in 5 plates (3M/plate) for each biological replicate. 3M of cells per replicate were also sampled for the day 0 time point. Plates from the same replicates were mixed at each medium change (once every two days). One plate’s worth of mEB was harvested on days 4, 18, 20, and 22. At harvest, cells/mEBs were fixed in 80% methanol and placed at -80C until RNA/DNA extraction for library preparation.  EB induction: exponentially growing mESCs are lifted from the plate (aspirate medium, wash with PBS, add 2.5 mL [for 10 cm plate] 0.05% trypsin , incubate 2 minutes at 37C, deactivate trypsin and triturate to a single-cell suspension with 10 mL pre-warmed SL medium). Cells are then counted and spun down (5 min at 300 g). Supernatant is aspirated and cells are resuspended to 2 M/mL in CA medium (medium for EB induction: DMEM, 10% FBS, 1x MEM non-essential amino-acids, 1x Glutamax , 10-5 beta-mercaptoethanol). Cells are counted again, and density adjusted to 1 M/mL with CA medium. 3 mL (3 M cells) are added to 12 mL of CA medium in 10 cm plates (non gelatinized, non adherent). One the next day, plates are gently agitated to promote cell aggregation. Following induction, embryoid bodies (mEBs) are passaged every two days (no daily medium change). mEBs are collected using a serological pipette and transferred to a 50 mL conical tube (typically three plates are pooled). Leftover mEBs on plates are recovered by a CA medium wash and pooled with in the conical tube. mEBs are left to settle (initially up to 15-20 min, faster as the mEBs grow in size). Once mEBs have settled, medium is aspirated from the top, carefully avoiding disturbing the loose pellet. Fresh, pre-warmed, CA medium is then added to 15 mL/plate and mEBs redistributed to plates.

value: WD44 (mouse embryonic stem cells)

value: Mouse embryoid bodies

value: monoclonal CRISPRi (dCAS9-KRAB) cell line, high MOI (polyclonal) single-cell reporter cassette (89% devCRE library + 10% promoter series + 1% EEF1A1-mCherry) delivered by piggyBac

tag: day

value: Day 22


title: RNA_techrep2_mEB_bulk_v2_repB3_d04_S174

description: Bulk MPRA

value: Day 04


title: RNA_techrep2_mEB_bulk_v2_repB3_d18_S175

description: Bulk MPRA

value: Day 18


title: RNA_techrep2_mEB_bulk_v2_repB3_d20_S176

description: Bulk MPRA

value: Day 20


title: Lm_10-17

value: Colon metastasis

value: LoVo


title: Ip_IgG_Lm_1

value: colon cancer cells

value: Infected by Lm for 10h

value: Immunoprecipitation of control IgG

value: IgG


title: RNA_techrep2_mEB_bulk_v2_repB3_d00_S173

description: Bulk MPRA

value: Day 00


title: RNA_techrep2_mEB_bulk_v2_repB2_d18_S170

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repB2_d20_S171

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repB2_d04_S169

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repB2_d00_S168

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repB2_d22_S172

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repB1_d22_S162

description: Bulk MPRA


title: Input_Lm_1

value: Control Input


title: Lm_2-14

value: Cancer cells

value: Infected by L. monocytogenes

value: Cytoplasmic total RNA


title: RNA_techrep2_mEB_bulk_v2_repB1_d18_S160

description: Bulk MPRA

value: WD44 (mouse embryonic stem cells)

value: Mouse embryoid bodies


title: Lm_5-14


title: RNA_techrep2_mEB_bulk_v2_repB1_d20_S161

description: Bulk MPRA

value: monoclonal CRISPRi (dCAS9-KRAB) cell line, high MOI (polyclonal) single-cell reporter cassette (89% devCRE library + 10% promoter series + 1% EEF1A1-mCherry) delivered by piggyBac


title: RNA_techrep2_mEB_bulk_v2_repB1_d04_S159

description: Bulk MPRA

value: Day 04


title: RNA_techrep2_mEB_bulk_v2_repA3_d22_S167

description: Bulk MPRA

value: Day 22


title: RNA_techrep2_mEB_bulk_v2_repB1_d00_S158

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA2_d22_S157

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA3_d04_S164

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA2_d20_S156

description: Bulk MPRA

value: Day 20


title: RNA_techrep2_mEB_bulk_v2_repA3_d00_S163

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA2_d04_S154

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA3_d18_S165

description: Bulk MPRA

value: Day 18


title: RNA_techrep2_mEB_bulk_v2_repA2_d00_S153

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA1_d04_S149

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA1_d20_S151

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA1_d18_S150

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB3_d18_S130

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB3_d20_S131

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA2_d18_S155

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB2_d22_S127

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB3_d00_S128

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA3_d20_S166

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB3_d04_S129

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB3_d22_S132

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB2_d04_S124

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB2_d00_S123

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA1_d00_S148

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB2_d20_S126

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB1_d22_S117

description: Bulk MPRA


title: RNA_techrep2_mEB_bulk_v2_repA1_d22_S152

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB1_d18_S115

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB1_d20_S116

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB1_d00_S113

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA3_d04_S119

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA3_d22_S122

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA3_d18_S120

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA3_d20_S121

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA2_d20_S111

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA2_d22_S112

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB2_d18_S125

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA2_d18_S110

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA2_d04_S109

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA2_d00_S108

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA1_d22_S107

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA1_d20_S106

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA1_d00_S103

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB3_d22_S87

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB3_d20_S86

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA1_d04_S104

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB3_d04_S84

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB3_d00_S83

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB2_d22_S82

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB2_d20_S81

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB2_d18_S80

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB2_d04_S79

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB2_d00_S78

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB1_d22_S72

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB1_d18_S70

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA3_d20_S76

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA3_d18_S75

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB1_d00_S68

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA3_d00_S73

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA3_d22_S77

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA3_d04_S74

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repB1_d04_S114

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA2_d22_S67

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA1_d18_S105

description: Bulk MPRA


title: RNA_techrep1_mEB_bulk_v2_repA3_d00_S118

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA2_d20_S66

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB3_d18_S85

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA2_d18_S65

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA2_d04_S64

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB1_d04_S69

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repB1_d20_S71

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA2_d00_S63

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA1_d20_S61

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA1_d18_S60

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA1_d22_S62

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA1_d04_S59

description: Bulk MPRA


title: DNA_techrep2_mEB_bulk_v2_repA1_d00_S58

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB3_d18_S40

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB3_d22_S42

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB3_d20_S41

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB3_d04_S39

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB2_d22_S37

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB3_d00_S38

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB2_d20_S36

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB2_d18_S35

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB2_d04_S34

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB2_d00_S33

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB1_d20_S26

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB1_d22_S27

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB1_d18_S25

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB1_d00_S23

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA3_d20_S31

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA3_d18_S30

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repB1_d04_S24

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA3_d22_S32

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA3_d00_S28

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA3_d04_S29

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA2_d22_S22

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA2_d00_S18

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA2_d18_S20

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA2_d04_S19

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA2_d20_S21

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA1_d22_S17

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA1_d18_S15

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA1_d04_S14

description: Bulk MPRA


title: DNA_techrep1_mEB_bulk_v2_repA1_d20_S16

description: Bulk MPRA