title: 22531-64

type: genomic

city: North Brunswick Township

first: Jia

last: Xu

state: NJ

address: 675 US Highway One

institute: Genomic Prediction, Inc.

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #14 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

data_processing:
Affymetrix UK Biobank Axiom Array Manufacturer's Protocol
Primary data description: DNA copy number and genotyping

label: biotin

source_name: Blastomere from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D4

growth_protocol: Thawing of human 2PN zygotes was performed using the Qinn's Advantage warming kit or using a one-step protocol with GMOPS-plus depending on the method of cryopreservation. Donated oocytes were warmed using the Cryotech warming kit. Embryos were cultured in Global total.

extract_protocol: Single cells, single polar bodies, or cytoplasmic fragments were placed into single PCR tubes containing 2 ul of Genomic Prediction's loading Buffer. Genomic DNA amplification was performed using amplification kit as indicated for each sample.

treatment_protocol: Cas9 or ABE ribonucleoprotein complex was assembled in vitro and injected at fertilization or at the 1-cell stage of embryo development. Zygotes were either at the 2PN stage or at the entry into the first mitosis.

value: Preimplantation embryo


title: eq_OA_Ctrl_GJA16

status: Public on Jun 18 2026

type: SRA

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

country: USA

institute: Colorado State University

description: Library name: sample37

library_source: transcriptomic

data_processing:
All paired end RNA-seq reads were assessed for quality using Partek® Flow® software (Illumina, San Diego, CA). Low quality reads (Q ≤ 20) were filtered and adapter sequences were trimmed with CUTadapt (version 1.12)
Filtered reads were mapped to the Equcab 3.0 reference genome (GCA_002863925.1; https://www.ensembl.org/Equus_caballus/Info/Index) using STAR (version 2.7.3a)
HTSeq (version 0.11.0)[54] was used to count the number of reads aligning to annotated genes. Genes with read counts greater than 10 and expressed in ≥ 10 horses (~50% of OA group) were retained for downstream analysi
Reads were normalized using Remove Unwanted Variation from RNA-Seq Data (RUVSeq) accounting for residuals (RUVr)
Differential expression analysis was performed with limma-voom (version 3.64.1) in RStudio (version 2024.04.2) [59,60] with correction for multiple testing (Padj ≤ 0.05, 1.5 ≤ Log2Fold Change ≤ -1.5)
Assembly: Equcab 3.0
Supplementary files format and content: csv file includes raw counts from each sample

molecule: polyA RNA

organism: Equus caballus

source_name: PBMC

growth_protocol: peripheral blood mononuclear cells (PBMC) isolated using ficol gradient.

extract_protocol:
Ficol gradiant seperation from whole blood
Library construction was performed with a polyA capture protocol with the ABclonal mRNA-seq Lib Prep Kit for Illumina (ABclonal Technology, Woburn MA).

treatment_protocol: healthy horse PBMC compared to horses with naturally occuring OA

tag: cell type

value: PBMC

tag: treatment

value: Ctrl


title: eq_OA_Ctrl_GJA15

description: Library name: sample36


title: Replicate 3 of FMRP-KO RNA using M protocol

city: Montreal

first: Senthilkumar

last: Kailasam

state: Quebec

address: 740 Dr. Penfield Avenue, #4200

department: Human Genetics

country: Canada

institute: McGill University

description:
Library name: FMRP_RNA_M_rep3
Third replicate of RNA from FMRP knockout mice, using M protocol.

data_processing:
The raw reads were trimmed with Cutadapt 2.10, removing adapters and bases below quality thresholds, and then demultiplexed using UMI barcodes (ID1=ATCGT, ID2=AGCTA, ID3=CGTAA) with specific options for base trimming and sequence length.
Reads mapping to non-coding and ribosomal RNAs were filtered using Bowtie2 (version 2.3.5) against the Mus musculus reference (GRCm38, Ensembl release 102), set for high sensitivity. Remaining reads were aligned to the Mus musculus genome with STAR aligner 2.7.8a, outputting sorted BAM files. PCR duplicates were marked and removed using Picard MarkDuplicates (version 2.26.6) and samtools (version 1.19.2).
Raw counts were obtained using featurecounts (version 2.2.0).
Assembly: Mus musculus GRCm38, Ensembl release 102.
Supplementary files format and content: bed files
Supplementary files format and content: Comma-separated values (.csv) file includes information for all the samples.

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
The RNA of RC and RG was extracted through the trizole chloroform method followed by isopropanol precipitation to concentrate the samples. The samples were loaded onto Urea gel (catalog # EC68852Box, #EC68752Box, #EC62152Box, ThermoFisher) to select for RPF size. Segments between 25b and just above 40b were excised and retrieved to account for the possible longer fragments of the RPFs. The excised gels were frozen for 30 minutes on ice and then thawed overnight at room temperature. The RNA was extracted again with trizole chloroform extraction.
The steps were adopted from Glincy & Ingolia, 2017. The concentration from the RNA footprint was calculated from Bioanalyzer small RNA kid (catalog # 5067-1548, Agilent). An equal amount of RNA was calculated and transferred to a new tube for each sample to ensure each sample has a relatively equal amount after pooling. 3 different linkers (NI-810, NI-811, BI-812) were attached to each of the replicates. The samples were first dephosphorylated with T4PNK linker (catalog # M0351L, NEB), and then pre-adenylated linkers are attached through T4 Rnl2 (catalog # M0351L, NEB). The linked RNA was purified through excision of urea gel between 50bp and 70bp. Samples in the same variables were then pooled together with their gel fragment combined. The RNA was extracted from the gel with the steps stated previously containing all three replicates, followed by Reverse transcription. MyOne Streptavidin C1 DynaBeads (catalog#65001, ThermoFisher) was used for rRNA depletion. Lastly, PCR was performed. The samples were sequenced through the McGill University Genome Center on NovaSeq S1/2 flow cells.

treatment_protocol: All preparations used brains that were flashed frozen using either liquid nitrogen or ethanol dry ice bath after dissection. 10 mouse brains from postnatal day 5 C57BL/6 mouse and FMR1-KO mouse from Charles Rivers Laboratory were used. Samples were homogenized in either the previous (Anadolu et al, 2023) RNA Granule Buffer (20 mM Tris-HCl pH 7.4 (catalog #BP152-1, Thermo Fisher Scientific), 150 mM NaCl (catalog # BP358-212, Thermo Fisher Scientific), 2.5 mM MgCl2 (catalog# M33-500, Thermo Fisher Scientific)) or high Mg2+ RNA Granule Buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 10 mM MgCl2. These buffers were supplemented with 1mM DTT (catalog #D9163, Sigma-Aldrich), and 1mM EGTA (catalog # E8145 Sigma-Aldrich) for homogenization. The homogenate was centrifuged 15min in a Thermo Fisher Scientific T865 fixed-angle rotor at 6117 x g at 4oC to separate debris, such as lipid and extracellular matrix, from the ribosomes. The supernatant was collected with some set aside as starter fraction. The rest of the supernatant was then clarified with 1% iGEPAL CA-630 (catalog #04693132001, Roche) for 5 min at 4 C. Sucrose solution was produced by suspending sucrose (catalog #8550, Calbiochem) with RNA Granule buffer. The samples were loaded onto a 60% sucrose pad in a Sorvall 36 ml tube (Kendro, catalog #3141, Thermo Fisher Scientific) and centrifuged at 56,660 x g for two hours in AH-629 swing-bucket rotor to retrieve the polyribosomes. The polyribosome was resuspended in RNA Granule buffer then reloaded onto 15%-60% sucrose gradient and centrifuged at 56,660 xg for 45 min to separate the ribosomes into monosomes, ribosomal clusters (RC) and RNA Granule (RG). Each fraction was 3.5 ml and collected from the top. We retrieved RCs from fraction 5 and 6, RNA Granules from the pellet. The RC samples were loaded onto a 60% sucrose pad and centrifuged to concentrate the samples, while the RG samples were resuspended with 2ml of normal Granule buffer or high Mg2+ buffer. For normal nuclease treatment groups, 1µl of RNase I (100U/µ l; catalog #AM2294, Thermo Fisher Scientific) was administered to the RC and RG and rotated at 4ºC for 30min. Then, 4ul of SuperaseIN (20U/µl; catalog # AM2969, Invitrogen) was added to the solution to halt the reaction. The samples are then loaded onto 15% to 60% sucrose gradient and centrifuged at 56,660 x g for 45 minutes to retrieve the monosomes from fraction 2 and 3. For high nuclease treatment group, RNase I (10 U/ul, catalog #N6901K, Epicentre) was adjusted to the concentration of RC and RG via the A260 read from the Nanodrop. The OD obtained from the A260 read equals 6 unit. In other words, the amount of nuclease (µl) added equals A260 * 6 (U)/ 10 (µl/U). In addition, the samples are incubated at room temperature for 30min instead of 4 ºC. Then, 6ul of SuperaseIN were added to halt the reaction. The samples were then spin at 68,000 xg for 3hrs on a Beckman tabletop ultracentrifuge to concentrate the monosomes, which pellets.

tag: tissue

value: brain

tag: genotype

value: M-protocol


title: Replicate 1 of Wild Type RNA using M protocol

description:
Library name: WT_RNA_M_rep1
First replicate of RNA from wild type mice, using M protocol.

value: WT


title: Cortical organoids. isogenic control for MECP2[R306C], rep2

city: Cambridge

first: Tatsuya

last: Osaki

state: MA

address: 43 Vassar street, 46-6227

department: Picower Institute for Learning and Memory

institute: Massachusetts Institute of Technology

description:
Library name: CO_isogenic_control_for_R306C_2
Feature_count_matirx

data_processing:
Fastq files were combined and aligned with STAR 2.0.4b Gene counts derived with Subread:featureCount 1.45. RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: GRCh37/hg19
Supplementary files format and content: Feature counts matrix
Supplementary files format and content: Differential_gene_expression_data

organism: Homo sapiens

growth_protocol: All hiPS cells were maintained on Matrigel-coated 6-well plates in mTeSR Plus medium (STEMCELL Technologies) with 10 μM Y-23632 (Rock inhibiter, STEMCELL Technologies) for the first day after each passage and subcultured every 5–7 days using ReLeSR reagent (STEMCELL Technologies). To generate cerebral organoids, two mutant hiPS cell lines and isogenic control iPS cells on 6-well plates were dissociated into single cells with TrypLE express and then plated at 30,000 cells per well on U-bottom ultra-low attachment 96-well plates (Corning) with mTeSR Plus supplemented with 20 μM of Y-23632. After 24 h, the culture medium was replaced with neural induction medium (knockout DMEM-F12, 15% (v/v) knockout serum replacement, 1% (v/v) MEM-NEAA, 1% (v/v) GlutaMAX, 100 nM LDN-193189, 10 μM SB431542, and 10 μM XAV939) and changed every other day. After 10 days of culture, the culture medium was replaced with 1:1 mixture of knockout DMEM/F12 and neurobasal medium supplemented with 0.5% (v/v) N2 supplement, 1% (v/v) B27 plus supplement with vitamin A, 1% (v/v) GlutaMAX, 1% (v/v) MEM-NEAA, and 2.5 ng/ml (v/v) human insulin solution. This medium was changed every 2 days until 18 days of culture had elapsed. After 18 days, the organoids were transferred to flat-bottom ultra-low attachment 24-well plates (Corning) on a rocking shaker (120 rpm) and switched to a maintenance medium (Neurobasal medium supplemented with 1% (v/v) N2 supplement, 2% (v/v) B27 supplement with vitamin A, 1% (v/v) GlutaMAX, 1% (v/v) MEM-NEAA, 0.25 mg/ml (v/v) human insulin solution, 20 ng/ml BDNF, 200 μM ascorbic acid, 100 μM dibutyryl-cAMP (Sigma-Aldrich), and 1% (v/v) Penicillin/Streptomycin). After 30 days from differentiation, the culture medium was changed twice per week with BrainPhys medium supplemented with 2% (v/v) B27 supplement with vitamin A, 1% (v/v) GlutaMAX, 20 ng/ml BDNF, 20 ng/ml GDNF, and 1%(v/v) Penicillin/Streptomycin until the time of imaging.

extract_protocol:
Total RNA was isolated from the cells from 2D culture using RNAeasy Mini Kit (Qiagen) following manufacture protocol.
NA libraries for RNA sequencing were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin library prep kit according to the manufacturer’s instructions.

tag: Sex

value: Female

tag: cell line

value: Cortical organoids

tag: replicate

value: biol rep2


title: HAP1 SFPQ intronic deletion hgRNA 2, replicate 1

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

description: Library name: H011_IDel.SFPQ.G171_r1

data_processing:
Base-calling Q-scores were obtained with RTA 3.4.4. Demultiplexing of raw sequencing data was performed using Illumina’s bclfastq.
Alternative splicing analysis was performed as follows: RNA-Seq data were processed using the vast-tools pipeline, version 2.5.1 https://github.com/vastgroup/vast-tools (Braunschweig et al., 2014; Irimia et al., 2014; Tapial et al., 2017). From primary output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW/VLOW for cassette exon [CE], microexon [MIC], and alternative 5' or 3' splice site [Alt5/3] events or coverage less than 10 reads for intron retention [IR] events; score 4 other than OK/B1/B2/Bl/Bn for CE and MIC events and score 5 of less than 0.05 for IR events). If more than one replicate was present, the point estimate from vast-tools diff was used and if the coverage/balance filtering step failed for an event in more than half of the replicates, its value was set to NA. Differential AS was assessed through the vast-tools diff module available with the main pipeline. Changes were considered significant if they were greater than 10 dPSI/dPIR and the expected minimum change was different from zero at p > 0.95 according to vast-tools’ diff module.
Gene expression changes were analyzed by pseudo-aligning pre-trimmed reads to GENCODE v43 transcripts using Salmon v1.10 (Patro et al., 2017) and aggregated per gene using the R package tximport (Soneson et al., 2015). Differential expression was then assessed using the classic mode (exactTest) edgeR (McCarthy et al., 2012), and genes with an FDR < 0.05 and a greater than 2-fold change were considered differential. For each comparison, only genes expressed at a minimum of 5 RPKM in one or both conditions were considered.
RNAseq.HAP1_vastTools.tab.gz is a tab-delimited file and contains vast-tools output, i.e. event information and raw percent-spliced-in values and quality scores per sample. See https://github.com/vastgroup/vast-tools#combine-output-format.
Assembly: GENCODE v43
Supplementary files format and content: RNAseq.HAP1_vastTools.tab.gz is a tab-delimited file and contains vast-tools output, i.e. event information and raw percent-spliced-in values and quality scores per sample. See https://github.com/vastgroup/vast-tools#combine-output-format.
Supplementary files format and content: RNAseq.HAP1_altSplicing.tab.gzz is a tab-delimited file and contains mean percent-spliced-in values per treatment and significance calls for the difference vs intergenic hgRNA control.
Supplementary files format and content: Expression_HAP1.tab.gz is a tab-delimited file and contains RPKM, log2 fold-change and p-values per treatment vs intergenic hgRNA control.

source_name: HAP1 chronic myelogenous leukemia

growth_protocol: HAP1 cells (clone C631; male, with Y chromosome loss; Horizon Genomics, RRID: CVCL_Y019) were maintained under standard sterile cell culture conditions at 37°C in a humidified incubator containing 5% CO2 at subconfluent densities (50-70%). HAP1 cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM; Gibco, #12440053) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Gibco, #26140079) and penicillin/streptomycin (Gibco, #15140-122).

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen #74106). Briefly, cells were washed in PBS twice and lysed directly in the vessel using RLT buffer supplemented with reducing agent β-Mercaptoethanol (Milipore #444203-250ML). All RNA samples were DNase-treated using RNase-Free DNase Set (Qiagen #79256) according to the manufacturer's protocol.
Biological duplicates were processed for RNA-Seq. Stranded/directional total RNA-Seq (ribo-depletion) libraries were prepared as follows. RNA concentration was measured using Qubit RNA BR (cat # Q10211, Thermo Fisher Scientific Inc., Waltham, USA) and RNA quality was assessed from 1 ng input on the Bioanalyzer RNA 6000 Pico kit (cat # 5067-1513, Agilent Technologies Inc., Santa Clara, USA). RIN score ranged from 8.4- 9.8 ; with a median RIN score of 9.6. For library preparation, 300 ng of DNase-treated RNA per sample was first subjected to rRNA depletion (H/M/R) and then processed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (cat #E7760L; New England Biolabs; protocol 6.0_7/24), with 7.5 minutes of fragmentation at 94 °C and 12 cycles of amplification. To assess final library quality, 1 μl of the library was analyzed on the Agilent Bioanalyzer dsDNA High Sensitivity chip (cat # 5067-4626, Agilent Technologies Inc., Santa Clara, USA). The libraries were quantified using the Qubit 1X dsDNA HS (cat # Q33231, Thermo Fisher Scientific Inc., Waltham, USA) and were pooled at equimolar ratios after adjusting for fragment size. The final pool, with an average library size of ~395 bp was run on the Bioanalyzer and quantified using NEBNext Library Quant Kit for Illumina (cat # E7630L, New England Biolabs, Ipswich, USA).

treatment_protocol: For CHyMErA deletions, cells were transduced at an estimated MOI < 1 with lentivirus encoding the indicated hgRNAs in pLCHKO-EGFP-P2A-Puro vector. Cells were subsequently selected for the integration of the CHyMErA cassette by puromycin (Gibco A11138-03) at 1 µg/ml for 48 hours. At T0, puromycin was removed from the medium and cells were grown for three days prior to harvesting RNA at 60-80% confluency. For siRNA-mediated knockdowns, reverse transfection was performed for 350K HAP1 cells using 80 pmoles of siRNA and 6 µL of Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, #13778100). RNA was harvested 48 hours post-transfection.

value: HAP1 chronic myelogenous leukemia

value: Intronic deletion in SFPQ generated with hybrid guide RNA comprising Cas9 guide ATCAGTTGAACTGGTATGAG and Cas12a guide ACATCAGATTAACCCACTGAAAA.


title: WT parental, untreated, rep2

first: Whitney

last: Henry

address: 500 Main St

department: Biology

institute: MIT

description: Library name: 1099_2

data_processing:
Mapping was performed with STAR (2.7.1a) using the canonical chromosomes from GRCm38/mm10, with an index built with genes from Ensembl 96 and '--sjdbOverhang 49'.
Gene counts were obtained using featureCounts (v1.6.2) and Ensembl 96 gene annotations and '-s 2'.
Gene counts were normalized and differential expression assayed with DESeq2 (v1.26.0), using 'independentFiltering=FALSE'.
Assembly: GRCm38/mm10
Supplementary files format and content: Ensembl gene ID, raw counts
Supplementary files format and content: Ensembl gene ID, matrix of DESeq2-normalized counts

source_name: Breast

growth_protocol: Cells were cultured in DMEM high glucose supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 1% glutamine.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Libraries were prepared for RNA-Seq using Roche Diagnostics KAPA mRNA HyperPrep Kit, according to manufacturer’s directions.

treatment_protocol: Cells were treated with 2 ng/ml TGF- β treatment for 10 days

value: Breast

value: PyMT-1099 parental

value: Untreated


title: HAP1 PFN1 intronic deletion hgRNA 2, replicate 1

description: Library name: H007_IDel.PFN1.G163_r1

value: Intronic deletion in PFN1 generated with hybrid guide RNA comprising Cas9 guide CGTAGGTCCTATGCCCCAGG and Cas12a guide GATGTCAGTGTTAATGGGGAAAG.


title: HAP1 SFPQ intronic deletion hgRNA 1, replicate 2

description: Library name: H010_IDel.SFPQ.G170_r2

value: Intronic deletion in SFPQ generated with hybrid guide RNA comprising Cas9 guide TTGGTAGGGGAAACTAAAAG and Cas12a guide GCACTACAGGGAAGATCTGTTCT.


title: Replicate 1 of FMRP-KO RNA using M protocol

description:
Library name: FMRP_RNA_M_rep1
First replicate of RNA from FMRP knockout mice, using M protocol.


title: eq_OA_Ctrl_GJA07

description: Library name: sample33


title: FMR1-KO Polysome Sample single-end, replicate 3

description:
Library name: FMR1_KO_Polysome_rep3
Polysome sample from FMR1-knockout mouse, processed with single-end sequencing.

library_source: other

data_processing:
The raw reads were trimmed with Cutadapt 2.10, removing adapters and bases below quality thresholds, and then demultiplexed using UMI barcodes (ID1=ATCGT, ID2=AGCTA, ID3=CGTAA) with specific options for base trimming and sequence length.
Reads mapping to non-coding and ribosomal RNAs were filtered using Bowtie2 (version 2.3.5) against the Mus musculus reference (GRCm38, Ensembl release 102), set for high sensitivity. Remaining reads were aligned to the Mus musculus genome with STAR aligner 2.7.8a, outputting sorted BAM files. PCR duplicates were marked and removed using Picard MarkDuplicates (version 2.26.6) and samtools (version 1.19.2).
Raw counts were obtained using featurecounts (version 2.2.0).
Assembly: Mus musculus GRCm38, Ensembl release 102.
Supplementary files format and content: bed files
Supplementary files format and content: Comma-separated values (.csv) file includes information for all the samples.
Library strategy: Ribo-Seq

molecule: other

value: Polysome

value: control


title: eq_OA_OA_GJA73

description: Library name: sample30

value: PBMC

value: OA


title: HAP1 SFPQ intronic deletion hgRNA 1, replicate 1

description: Library name: H009_IDel.SFPQ.G170_r1


title: Cortical organoids. isogenic control for MECP2[R306C], rep1

description:
Library name: CO_isogenic_control_for_R306C_1
Feature_count_matirx

value: biol rep1


title: FMR1-KO Polysome Sample single-end, replicate 2

description:
Library name: FMR1_KO_Polysome_rep2
Polysome sample from FMR1-knockout mouse, processed with single-end sequencing.

value: brain


title: eq_OA_OA_GJA72

description: Library name: sample29


title: Cortical organoids. MECP2[V247X] mutation, rep2

description:
Library name: CO_Rett_patient-derived_V247X_2
Feature_count_matirx


title: eq_OA_OA_GJA76

description: Library name: sample32


title: HAP1 PFN1 intronic deletion hgRNA 1, replicate 1

description: Library name: H005_IDel.PFN1.G162_r1

value: Intronic deletion in PFN1 generated with hybrid guide RNA comprising Cas9 guide CTTTCCCGGAAAGCCCCCAG and Cas12a guide CTGGGGATTGGGATTGAGAGGGG.


title: FMR1-KO Polysome Sample single-end, replicate 1

description:
Library name: FMR1_KO_Polysome_rep1
Polysome sample from FMR1-knockout mouse, processed with single-end sequencing.


title: eq_OA_OA_GJA71

description: Library name: sample28


title: Cortical organoids. MECP2[V247X] mutation, rep1

description:
Library name: CO_Rett_patient-derived_V247X_1
Feature_count_matirx

value: Female


title: WT Polysome Sample single-end, replicate 3

description:
Library name: WT_Polysome_rep3
Polysome sample from wild-type mouse, processed with single-end sequencing.

value: WT


title: HAP1 intergenic control hgRNA 2, replicate 2

description: Library name: H004_IDel.ctrl.gui2_r2

value: Intergenic-intergenic control hybrid guide RNA comprising Cas9 guide TCCGTTAGCTTCATCCTATC and Cas12a guide GCCTGAGACCTAAAGGGCTATTG.


title: Cortical organoids. isogenic control for MECP2[V247X], rep2

description:
Library name: CO_isogenic_control_for_V247X_2
Feature_count_matirx

value: Cortical organoids

value: biol rep2


title: eq_OA_Ctrl_GJA06

description: Library name: sample26

value: Ctrl


title: HAP1 intergenic control hgRNA 2, replicate 1

description: Library name: H003_IDel.ctrl.gui2_r1

value: HAP1 chronic myelogenous leukemia


title: WT Polysome Sample single-end, replicate 2

description:
Library name: WT_Polysome_rep2
Polysome sample from wild-type mouse, processed with single-end sequencing.


title: Cortical organoids. isogenic control for MECP2[V247X], rep1

description:
Library name: CO_isogenic_control_for_V247X_1
Feature_count_matirx


title: HAP1 intergenic control hgRNA 1, replicate 1

description: Library name: H001_IDel.ctrl.gui1_r1

value: Intergenic-intergenic control hybrid guide RNA comprising Cas9 guide CTATCCAGAGTAGATCATTA and Cas12a guide AAACCCAGTCCCCAATGTGATGA.


title: HAP1 intergenic control hgRNA 1, replicate 2

description: Library name: H002_IDel.ctrl.gui1_r2


title: WT Polysome Sample single-end, replicate 1

description:
Library name: WT_Polysome_rep1
Polysome sample from wild-type mouse, processed with single-end sequencing.


title: FMR1-KO Granule Sample single-end, replicate 3

description:
Library name: FMR1_KO_Granule_rep3
Granule sample from FMR1-knockout mouse, processed with single-end sequencing.

value: Granule


title: eq_OA_OA_GJA68

description: Library name: sample25


title: HAP1 PFN1 intronic deletion hgRNA 2, replicate 2

description: Library name: H008_IDel.PFN1.G163_r2

value: Intronic deletion in PFN1 generated with hybrid guide RNA comprising Cas9 guide CGTAGGTCCTATGCCCCAGG and Cas12a guide GATGTCAGTGTTAATGGGGAAAG.


title: DMS114DDP, cisplatin-induced, rep3

city: Guangzhou

first: Qiong

last: Lyu

state: Guang Dong

address: 253 GongYe Road

department: Oncology

country: China

institute: Zhujiang Hospital, Southern Medical University

description: Library name: DMS114-DDP-3

data_processing:
Raw reads were quality-checked with FastQC (v0.11.9) and adapter-trimmed using Trim Galore (v0.6.7). High-quality reads were aligned to the GRCh38 human reference genome (Ensembl release 107) using HISAT2 (v2.2.1). Gene-level read counts were obtained using featureCounts (Subread v2.0.1). Counts were normalized to TPM (Transcripts Per Million), and differential expression analysis was performed using the limma package (v3.54.2) in R.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

source_name: pleural effusion

growth_protocol: All cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS) and antibiotics in an incubator at 37˚C with 5% CO2. The chemoresistant cell lines H82DDP and DMS114DDP were cultured with addional cisplatin necessary to maintain their chemoresistance.

extract_protocol:
Total RNA was extracted using a magnetic bead-based universal RNA extraction kit (Beijing Meijimei Biotechnology Co., R6623-02)
Sequencing libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604) and VAHTS mRNA Capture Beads 2.0 (Vazyme, N403-01).

value: pleural effusion

value: Small cell lung cancer

value: RPMI-1640 medium containing 10% fetal calf serum,cisplatin


title: DMS114DDP, cisplatin-induced, rep2

description: Library name: DMS114-DDP-2


title: HAP1 DMSO control treatment, replicate 3

description: Library name: HAP1_DMSO_3

data_processing:
Base-calling Q-scores were obtained with RTA 3.4.4
Alternative splicing analysis was performed as follows: RNA-Seq data were processed using the vast-tools pipeline, version 2.5.1 https://github.com/vastgroup/vast-tools (Braunschweig et al., 2014; Irimia et al., 2014; Tapial et al., 2017). From primary output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW/VLOW for cassette exon [CE], microexon [MIC], and alternative 5' or 3' splice site [Alt5/3] events or coverage less than 10 reads for intron retention [IR] events; score 4 other than OK/B1/B2/Bl/Bn for CE and MIC events and score 5 of less than 0.05 for IR events). If more than one replicate was present, the point estimate from vast-tools diff was used and if the coverage/balance filtering step failed for an event in more than half of the replicates, its value was set to NA. Differential AS was assessed through the vast-tools diff module available with the main pipeline. Changes were considered significant if they were greater than 10 dPSI/dPIR and the expected minimum change was different from zero at p > 0.95 according to vast-tools’ diff module.
In parallel to vast-tools analysis, alternative splicing was analyzed with rMATS v4.1.2 (Shen, Park et al.,  2014) based on reads from which Illumina adaptors had been trimmed off the 3'-end using Trimmomatic v0.33 (Bolger et al., 2014). rMATs was run using options --lipType fr-firststrand --variable-read-length --anchorLength 8 --novelSS with a GENCODE v43 index and annotation.
Gene expression changes were analyzed by pseudo-aligning pre-trimmed reads to GENCODE v43 transcripts using Salmon v1.10 (Patro et al., 2017) and aggregated per gene using the R package tximport (Soneson et al., 2015). Differential expression was then assessed using the classic mode (exactTest) edgeR (McCarthy et al., 2012), and genes with an FDR < 0.05 and a greater than 2-fold change were considered differential. For each comparison, only genes expressed at a minimum of 5 RPKM in one or both conditions were considered.
Assembly: GENCODE v43
Supplementary files format and content: RNAseq.RPE1_vastTools.tab.gz is a tab-delimited file and contains vast-tools output, i.e. event information and raw percent-spliced-in values and quality scores per sample. See https://github.com/vastgroup/vast-tools#combine-output-format.
Supplementary files format and content: RNAseq.RPE1_altSplicing.tab.gz is a tab-delimited file and contains mean percent-spliced-in values per treatment and significance calls for the difference vs intergenic hgRNA control.
Supplementary files format and content: Files names rMATS.[cell line]_[event type].MATS.JC.txt are tab-delimited files containing primary rMATS output (i.e., splicing event coordinates, read counts and splicing information). Files named rMATS.[cell line]_sigEvents.csv are comma-separated files with combined information from all splicing event types and filtered for a mimium of 10 junction reads, FDR < 0.05 and inclusion level difference >= 0.1.
Supplementary files format and content: Expression_RPE1.tab.gz is a tab-delimited file and contains RPKM, log2 fold-change and p-values per treatment vs intergenic hgRNA control.

growth_protocol: HAP1 cells (clone C631; male, with Y chromosome loss; Horizon Genomics, RRID: CVCL_Y019), and hTERT-RPE-1 cells (ATCC, CRL-4000) were maintained under standard sterile cell culture conditions at subconfluent densities (50-70%) and incubated at 37°C in a humidified incubator containing 5% CO2. HAP1 cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM; Gibco, #12440053) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Gibco, #26140079) and penicillin/streptomycin (Gibco, #15140-122). RPE-1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; Sigma-Aldrich, #D5796)  supplemented with 10% heat-inactivated FBS, penicillin/streptomycin, and sodium pyruvate (Gibco, #11360070).

extract_protocol:
Total RNA was extracted from HAP1 and RPE-1 cells using the RNeasy Mini Kit (Qiagen #74106). Briefly, cells were washed twice in PBS and lysed directly in the culture vessel using RLT buffer supplemented with the reducing agent β-mercaptoethanol (Milipore, #444203-250ML). All RNA samples were DNase-treated using RNase-Free DNase Set (Qiagen, #79256) according to the manufacturer's protocol.
Stranded/directional mRNA-Seq libraries were prepared as follows. DNase-treated total RNA was assessed using Qubit RNA BR (cat # Q10211, Thermo Fisher Scientific Inc., Waltham, USA) and RNA integrity was evaluated using the Bioanalyzer RNA 6000 Pico kit (cat # 5067-1513, Agilent Technologies Inc., Santa Clara, USA) with all samples exhibiting high quality (RIN ≥ 9, median RIN = 9.7). For each sample, 500 ng of total RNA was used to prepare libraries with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (cat # E7760L; New England Biolabs; protocol 6.0_7/24) incorporating Poly (A) selection, with 7.5 minutes of fragmentation at 94 °C and 11 cycles of amplification. Library quality was verified by running 1 μl of each final library on an Agilent Bioanalyzer using the High Sensitivity dsDNA chip (cat #5067-4626, Agilent Technologies). The libraries were quantified using the Quant-iT dsDNA high-sensitivity (cat # Q33120, Thermo Fisher Scientific Inc., Waltham, USA), then normalized and pooled at equimolar ratios after size-adjustment. The pooled library had an average library size of 502 bp.

treatment_protocol: To indirectly inhibit nonsense-mediated mRNA decay through translation inhibition, HAP1 and RPE-1 cells were seeded and cultured at sub-confluent densities for 48 hours prior to treatment. Cells were then incubated for 6 hours in media supplemented with either vehicle control (DMSO; Fisher BioReagents™, BP231-100) or 50 µM cycloheximide (Sigma-Aldrich, 01810) solubilized in DMSO. Cells were harvested immediately following treatment at a final confluency of ~70% .


title: eq_OA_OA_GJA66

description: Library name: sample23

value: PBMC

value: OA


title: FMR1-KO Granule Sample single-end, replicate 2

description:
Library name: FMR1_KO_Granule_rep2
Granule sample from FMR1-knockout mouse, processed with single-end sequencing.

value: brain

value: control


title: DMS114DDP, cisplatin-induced, rep1

description: Library name: DMS114-DDP-1


title: eq_OA_OA_GJA64

description: Library name: sample22


title: FMR1-KO Granule Sample single-end, replicate 1

description:
Library name: FMR1_KO_Granule_rep1
Granule sample from FMR1-knockout mouse, processed with single-end sequencing.


title: HAP1 DMSO control treatment, replicate 1

description: Library name: HAP1_DMSO_1


title: DMS114, parental, rep3

description: Library name: DMS114-N-3

value: RPMI-1640 medium containing 10% fetal calf serum


title: DMS114, parental, rep2

description: Library name: DMS114-N-2

value: WT


title: eq_OA_OA_GJA63

description: Library name: sample21


title: WT Granule Sample single-end, replicate 3

description:
Library name: WT_Granule_rep3
Granule sample from wild-type mouse, processed with single-end sequencing.


title: WT Granule Sample single-end, replicate 2

description:
Library name: WT_Granule_rep2
Granule sample from wild-type mouse, processed with single-end sequencing.


title: DMS114, parental, rep1

description: Library name: DMS114-N-1


title: eq_OA_OA_GJA61

description: Library name: sample19


title: WT Granule Sample single-end, replicate 1

description:
Library name: WT_Granule_rep1
Granule sample from wild-type mouse, processed with single-end sequencing.


title: H82DDP, cisplatin-induced, rep3

description: Library name: H82-DDP-3


title: eq_OA_OA_GJA50

description: Library name: sample18


title: H82DDP, cisplatin-induced, rep2

description: Library name: H82-DDP-2


title: M-FMR1-KO Polysome Sample single-end M-protocol, replicate 3

description:
Library name: FMR1_KO_Polysome_M_rep3
Polysome sample from FMR1-knockout mouse, processed with single-end M-protocol.

value: Polysome

value: M-protocol


title: eq_OA_Ctrl_GJA45

description: Library name: sample17


title: RPE-1 DMSO control treatment, replicate 3

description: Library name: RPE1_DMSO_3

source_name: RPE-1 retinal pigment epithelium

value: RPE-1 retinal pigment epithelium


title: M-FMR1-KO Polysome Sample single-end M-protocol, replicate 2

description:
Library name: FMR1_KO_Polysome_M_rep2
Polysome sample from FMR1-knockout mouse, processed with single-end M-protocol.


title: RPE-1 DMSO control treatment, replicate 2

description: Library name: RPE1_DMSO_2


title: eq_OA_Ctrl_GJA44

description: Library name: sample16

value: Ctrl


title: M-FMR1-KO Polysome Sample single-end M-protocol, replicate 1

description:
Library name: FMR1_KO_Polysome_M_rep1
Polysome sample from FMR1-knockout mouse, processed with single-end M-protocol.


title: RPE-1 DMSO control treatment, replicate 1

description: Library name: RPE1_DMSO_1


title: H82, parental, rep3

description: Library name: H82-N-3


title: eq_OA_Ctrl_GJA43

description: Library name: sample15


title: M-WT Polysome Sample single-end M-protocol, replicate 3

description:
Library name: WT_Polysome_M_rep3
Polysome sample from wild-type mouse, processed with single-end M-protocol.


title: H82, parental, rep2

description: Library name: H82-N-2


title: eq_OA_Ctrl_GJA42

description: Library name: sample14


title: M-WT Polysome Sample single-end M-protocol, replicate 2

description:
Library name: WT_Polysome_M_rep2
Polysome sample from wild-type mouse, processed with single-end M-protocol.


title: H82, parental, rep1

description: Library name: H82-N-1


title: eq_OA_Ctrl_GJA41

description: Library name: sample13


title: M-WT Polysome Sample single-end M-protocol, replicate 1

description:
Library name: WT_Polysome_M_rep1
Polysome sample from wild-type mouse, processed with single-end M-protocol.


title: CMK_KO3

city: Wilmington

first: Anilkumar

last: Gopalakrishnapillai

state: DE

address: 200 Powder Mill road

institute: Nemours Children's Health

description:
Library name: Sample 6
A6

data_processing:
HiSeq Control Software for base calling.
RNA-Seq reads were aligned to human reference genome hg38 with STAR.
Number of read counts per gene locus was summarized using 'featureCounts' using hg38 annotation.
Read counts normalized using TMM normalization (edgeR).
Assembly: Genome_build: hg38
Supplementary files format and content: csv file with TMM normalized read counts

source_name: CMK

extract_protocol:
Total RNA extracted by RNeasy Plus Micro kit
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit. RNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA).

value: CMK

value: DS-AML


title: RPE-1 cycloheximinde treatment, replicate 1

description: Library name: RPE1_CHX_1


title: M-FMR1-KO Granule Sample single-end M-protocol, replicate 3

description:
Library name: FMR1_KO_Granule_M_rep3
Granule sample from FMR1-knockout mouse, processed with single-end M-protocol.

value: Granule


title: eq_OA_Ctrl_GJA03

description: Library name: sample12


title: eq_OA_Ctrl_GJA39

description: Library name: sample11


title: M-FMR1-KO Granule Sample single-end M-protocol, replicate 2

description:
Library name: FMR1_KO_Granule_M_rep2
Granule sample from FMR1-knockout mouse, processed with single-end M-protocol.


title: CHyMErA in RPE-1 cells, T27 post infection, DMSO control treatment, replicate B

description: Library name: RPE1_T27_DMSO_B

library_source: genomic

data_processing:
Demultiplexing of raw sequencing data was performed using Illumina’s bclfastq.
A library FASTA file was generated by placing the Cas9 and Cas12a guides, extracted from the library annotation file, into the sequence context of hgRNA construct.  Specifically, the following was used:  CGAGGTACCG + <Cas9.sgRNA> + GTTTCAGAGCTACTAAGTGTAGAT + <Cas12a.sgRNA> + TTTTTTTTGAATTCTCT. The FASTA file was then indexed by bowtie-build. Reads in FASTQ format were pre-processing using a bespoke Perl script designed to identify the 5’ or 3’ end of the Cas12a direct repeat sequence, and extract the adjacent 23bp upstream sequence (Cas12a guide) from read1 and 20bp downstream sequence (Cas12a) from read2 for mapping. The extracted sequences were written to a new FASTQ file, and aligned to the prepared FASTA file with bowtie (v0.12.1) using the following parameters: -p 16 -v 3 -l 18 --chunkmbs 256 -t intronKnockoutLibrary. Alignments to each hgRNA construct were enumerated from the resulting SAM file using a bespoke Perl script, written to a text file for each sample, and merged with the library annotations in R.
Read counts were depth normalized by summing the mapped reads for each sample, then dividing the count for each hgRNA construct by the total counts and multiplying by 1x10^6.
Assembly: Custom reference, see data processing.
Supplementary files format and content: IntCHyMErA.library.design.tab.gz is a tab-delimited file containing library design information for the CRISPR guide RNA library used in every sample. Each hybdrid guide RNA contains a Cas9 and a Cas12a part.
Supplementary files format and content: IntCHyMErA_counts_raw.txt.gz is a tab-delimited file containing raw hgRNA counts in each sample.
Supplementary files format and content: IntCHyMErA_counts_norm.txt.gz is a tab-delimited file containing read counts normalized to million reads in the library (RPM).

molecule: genomic DNA

growth_protocol: All cells were maintained under standard sterile cell culture conditions at subconfluent densities (50-70%) at 37°C and in a humidified incubator containing 5% CO2. HAP1 cells (clone C631; male, with Y chromosome loss; Horizon Genomics, RRID: CVCL_Y019) were cultured in Iscove's Modified Dulbecco's Medium (IMDM; Gibco, #12440053) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Gibco, #26140079) and penicillin/streptomycin (Gibco, #15140-122). hTERT-RPE-1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; Sigma-Aldrich, #D5796) supplemented with 10% heat-inactivated FBS, penicillin/streptomycin, and sodium pyruvate (Gibco, #11360070).

extract_protocol:
CRISPR sequencing libraries were prepared as previously described (PMID: 32249828). Briefly, at each timepoint, cells were collected at 100-fold of library coverage, washed in PBS, and stored at -80 until processing. Genomic DNA was extracted using the Wizard™ Genomic DNA Purification Kit (Promega #A1125) according to the manufacturer's protocol. DNA concentration was determined using the Qubit dsDNA Broad Range Assay kit (Invitrogen).
For PCR amplification of hgRNA sequences, the following primers were used to amplify the integrated library from genomic DNA at >95-fold coverage, using NEBNext Ultra II Q5 Master Mix (NEB #M0544L). PCR1_Hybrid_Outer_F2: TGAAGAATCGCAAAACCAGCA PCR1_Hybrid_Outer_R1: GAGGGCCTATTTCCCATGATTC The resulting products were analyzed by gel electrophoresis for size and quality. PCR products were then pooled and subjected to indexing by PCR using Illumina TruSeq i5 and i7 barcoded adapters. Sequencing libraries were analyzed by agarose gel electrophoresis. Gel extraction was performed for the correct PCR product using PureLink™ PCR Purification Kit (Invitrogen, #K310001).Sequencing libraries were submitted for quality control analysis and high-throughput sequencing at the Donnelly Sequencing Centre (DSC). 1 μl top stock of each purified library was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip (cat # 5067-4626, Agilent Technologies Inc., Santa Clara, USA). The libraries were quantified using the Quant-iT dsDNA high-sensitivity (cat # Q33120, Thermo Fisher Scientific Inc., Waltham, USA) and were pooled at equimolar ratios after size-adjustment. The final pool was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip and quantified using NEBNext Library Quant Kit for Illumina (cat # E7630L, New England Biolabs, Ipswich, USA). The quantified pool was hybridized at a final concentration of 350 pM and sequenced at a depth of 50 M reads/sample on the Illumina NovaSeq 6000 platform using a SP flow cell of the following parameters: DC1: 29bp, R1: 33bp, IR1: 8bp, IR2: 8bp, DC2:20bp, R2: 32bp.

treatment_protocol: Cells were transduced at a multiplicity of infection of < 0.3 in media supplemented with 8 µg/ml Hexadimethrine bromide. Cells were infected at >400-fold library coverage. Twenty-four hours post-transduction, media was replaced with fresh media supplemented with 1 μg/ml puromycin for HAP1 and 20 µg/ml puromycin for RPE-1 cells (Gibco, A11138-03). Selection was complete for HAP1 cells after 48 hours. To ensure complete selection, RPE-1 cells were trypsinized and re-seeded after 48 hours of puromycin selection and selected for an additional day. At T0, puromycin was removed and the desired MOI (less than 0.3) was confirmed. Subsequently, each screen was divided into three replicates (replicates A, B and C at 250-fold coverage). Non-treated (NT) cells were grown in culture for >20 doublings while maintaining a 250-fold coverage and up to T18 and T27 for HAP1 and RPE-1 cells respectively and were maintained every 3 days. At T3 for HAP1, two treatment arms were separated from each replicate and were treated with either DMSO or TG003 (Sigma T5575-25MG) from T3 to T18 at IC50 (inhibitory dose by 50%, at 30µM - please note the discrepancy with the naming of the samples). For RPE-1 cells, at T6, each replicate arm was divided into a DMSO or TG003 treatment arms at 172-fold coverage. For RPE-1 cells, TG-003 was performed at IC20 (50µM) up to T27. Biological triplicates were sampled for sequencing at T12 and T18 for HAP1 and T21 and T27 for RPE-1 non-treated condition (NT); DMSO-treated condition (DMSO); IC50/IC20 TG-003 treated cells (C20).

tag: time point


title: CMK_KO1

description:
Library name: Sample 4
A4


title: eq_OA_Ctrl_GJA38

description: Library name: sample10


title: M-FMR1-KO Granule Sample single-end M-protocol, replicate 1

description:
Library name: FMR1_KO_Granule_M_rep1
Granule sample from FMR1-knockout mouse, processed with single-end M-protocol.


title: CHyMErA in RPE-1 cells, T27 post infection, DMSO control treatment, replicate A

description: Library name: RPE1_T27_DMSO_A


title: CMK_WT3

description:
Library name: Sample 3
A3


title: eq_OA_Ctrl_GJA37

description: Library name: sample9


title: CMK_WT2

description:
Library name: Sample 2
A2


title: CHyMErA in RPE-1 cells, T27 post infection, TG003 treatment, replicate C

description: Library name: RPE1_T27_IC20_C


title: eq_OA_Ctrl_GJA36

description: Library name: sample8


title: CMK_WT1

description:
Library name: Sample 1
A1


title: M-WT Granule Sample single-end M-protocol, replicate 2

description:
Library name: WT_Granule_M_rep2
Granule sample from wild-type mouse, processed with single-end M-protocol.


title: CHyMErA in RPE-1 cells, T27 post infection, TG003 treatment, replicate B

description: Library name: RPE1_T27_IC20_B


title: M-WT Granule Sample single-end M-protocol, replicate 1

description:
Library name: WT_Granule_M_rep1
Granule sample from wild-type mouse, processed with single-end M-protocol.


title: CHyMErA in RPE-1 cells, T27 post infection, TG003 treatment, replicate A

description: Library name: RPE1_T27_IC20_A


title: eq_OA_Ctrl_GJA34

description: Library name: sample6


title: M-WT Granule Sample single-end M-protocol, replicate 3

description:
Library name: WT_Granule_M_rep3
Granule sample from wild-type mouse, processed with single-end M-protocol.


title: Uninjected GHR-/- (KO), Female: KC14-134

city: Singapore

first: Kian Chuan

last: Sia

address: MD11, Basement 1, 10 Medical Drive, Singapore 117597

country: Singapore

institute: Department of Surgery, National University of Singapore

description: Library name: KC14_134

data_processing:
Quality control was first performed by removing reads with adapter contamination and reads with high content on uncertain nucleotides (N > 10%) and low-quality nucleotides (base quality less than 5 constituting more than 50% of the read). Mapping to the mm39 mouse genome was performed with HISTAT2. FeatureCounts v1.5.0-p3 was used to count reads mapping to each gene, and FPKM values of each gene (Fragments Per Kilobase of transcript sequence per Million mapped reads) were calculated based on the gene length and read counts mapping to the gene. FPKM values considered the effect of sequencing depth and gene length for the reads count, and is commonly used to express gene expression levels.
Assembly: Mus Musculus(mm39)
Supplementary files format and content: deseq

source_name: Liver

extract_protocol:
Total RNA from the livers of treated mice was isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN), according to the manufacturer’s instructions.
polyA-RNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers and second strand cDNA was synthesized using dUTP to obtain a directional (stranded) sequencing library was obtained after end repair, A-tailing, adapter ligation, size selection, enzymatic digestion, amplification, and purification. Libraries were quantified with Qubit and real-time PCR and Bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on an Illumina NovaSeq 6000 instrument at Novogene-AIT Genomics, Singapore.

value: Liver

tag: group

value: Uninjected GHR-/- (KO)

value: Female


title: HAP1 PFN1 intronic deletion hgRNA 1, replicate 2

description: Library name: H006_IDel.PFN1.G162_r2

value: HAP1 chronic myelogenous leukemia

value: Intronic deletion in PFN1 generated with hybrid guide RNA comprising Cas9 guide CTTTCCCGGAAAGCCCCCAG and Cas12a guide CTGGGGATTGGGATTGAGAGGGG.


title: eq_OA_OA_GJA70

description: Library name: sample27

value: PBMC

value: OA


title: CD34.4_1

data_processing:
HiSeq Control Software for base calling.
RNA-Seq reads were aligned to human reference genome hg38 with STAR.
Number of read counts per gene locus was summarized using 'featureCounts' using hg38 annotation.
Read counts normalized using TMM normalization (edgeR).
Assembly: Genome_build: hg38
Supplementary files format and content: xlsx file with TMM normalized read counts

source_name: bone marrow-derived CD34 cells

value: bone marrow-derived CD34 cells

value: normal


title: CHyMErA in RPE-1 cells, T27 post infection, no treatment, replicate C

description: Library name: RPE1_T27_NT_C


title: eq_OA_Ctrl_GJA33

description: Library name: sample5


title: eq_OA_OA_GJA67

description: Library name: sample24


title: Uninjected GHR-/- (KO), Female: KC14-132

description: Library name: KC14_132


title: CHyMErA in RPE-1 cells, T27 post infection, no treatment, replicate B

description: Library name: RPE1_T27_NT_B


title: eq_OA_Ctrl_GJA35

description: Library name: sample7


title: CD34.3_2


title: HAP1 DMSO control treatment, replicate 2

description: Library name: HAP1_DMSO_2


title: eq_OA_Ctrl_GJA84

description: Library name: sample4


title: HAP1 cycloheximinde treatment, replicate 3

description: Library name: HAP1_CHX_3


title: CD34.4_2


title: Uninjected GHR-/- (KO), Female: KC14-131

description: Library name: KC14_131


title: CD34.3_1


title: eq_OA_OA_GJA62

description: Library name: sample20


title: HAP1 cycloheximinde treatment, replicate 2

description: Library name: HAP1_CHX_2


title: Uninjected GHR+/+ (WT), Female: KC14-121

description: Library name: KC14_121

value: Uninjected GHR+/+ (WT)


title: eq_OA_Ctrl_GJA81

description: Library name: sample3


title: CD34.2_2


title: CHyMErA in RPE-1 cells, T21 post infection, DMSO control treatment, replicate C

description: Library name: RPE1_T21_DMSO_C


title: eq_OA_Ctrl_GJA80

description: Library name: sample2


title: CD34.2_1


title: Uninjected GHR+/+ (WT), Female: KC14-120

description: Library name: KC14_120


title: CHyMErA in RPE-1 cells, T21 post infection, DMSO control treatment, replicate B

description: Library name: RPE1_T21_DMSO_B


title: HAP1 cycloheximinde treatment, replicate 1

description: Library name: HAP1_CHX_1


title: eq_OA_Ctrl_GJA78

description: Library name: sample1


title: Uninjected GHR+/+ (WT), Female: KC14-119

description: Library name: KC14_119


title: CD34.1_2


title: CHyMErA in RPE-1 cells, T21 post infection, DMSO control treatment, replicate A

description: Library name: RPE1_T21_DMSO_A


title: AAV8-HLP-mGHR (4E10 vg), Female: KC14-024

description: Library name: KC14_024

value: AAV8-HLP-mGHR (4E10 vg)


title: H82DDP, cisplatin-induced, rep1

description: Library name: H82-DDP-1

value: pleural effusion

value: Small cell lung cancer

value: WT

value: RPMI-1640 medium containing 10% fetal calf serum,cisplatin


title: CUTeTag-E85-HF_B6_AAmin_female_TP303-5_H3K27me3

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 651

department: Deparment of Human Genetics

country: Belgium

institute: KU Leuven

description: Library name: CT_L122

data_processing:
reads were trimmed with cutadapt, aligned with Bowtie2, deduplicated using Picard, and peaks called using Seacr.
Assembly: mm10
Supplementary files format and content: bigwig file
Supplementary files format and content: bed file containting peaks
Library strategy: CUT&Tag

source_name: E8.5 headfold

growth_protocol: Supply VitC at 3.3 g/l in drinkin water for +VitC (AAplus) samples, or  nothing for -VitC Aamin) samples

extract_protocol:
E8.5 headfold tissues were dissociated in 0.05% Trypsin-EDTA (5 min, 37°C, 300 rpm), quenched with MEF medium, and cryopreserved in 1:1 MEF medium / 20% DMSO. Cryopreserved cells were thawed (37°C water bath) and washed in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl). Concanavalin A-coated magnetic beads (BioMag Plus, Bangs Laboratories #BP531; 3.3 µl/reaction) were activated in Bead Binding Buffer (20 mM HEPES-KOH pH 7.8, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) and incubated with cells for 10 min at RT. Bead-bound cells were incubated overnight at 4°C in antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 2 mM EDTA, 0.1% BSA, protease inhibitor) with anti-H3K27me3 (0.5 µg, Invitrogen MA5-11198) or IgG control (Merck 12-370). One headfold per reaction. Secondary anti-rabbit antibody (Antibodies Online ABIN101961) was added in Digitonin 150 buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, protease inhibitor) for 30 min at RT. After two washes in Digitonin 150 buffer, samples were incubated with pAG-Tn5 (Epicypher 15-1017) in Digitonin 300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, protease inhibitor) for 1 hour at RT. After two washes, tagmentation was performed in Digitonin 300 buffer supplemented with 10 mM MgCl2 for 1 hour at 37°C.
Samples were washed in TAPS buffer (10 mM TAPS pH 8.5, 0.2 mM EDTA) and resuspended in SDS release buffer (0.1% SDS, 10 mM TAPS pH 8.5) for 1 hour at 58°C. SDS was quenched with Triton-X100 (final 0.5%). Libraries were amplified using NEBNext 2x Master Mix (NEB M0541S) with indexed i5/i7 primers (58°C 5 min, 72°C 5 min, 98°C 45 sec, 14 cycles of 98°C 15 sec / 63°C 10 sec, 72°C 1 min). Libraries were purified with 1.3x Ampure XP beads (Beckman Coulter A63881) and eluted in 15 µl TE (1 mM Tris-HCl pH 8, 0.1 mM EDTA).

value: E8.5 headfold

tag: background

tag: condition

value: AAmin

value: female

tag: timed pregnancy

tag: cut&tag antibody


title: CD34.1_1


title: CHyMErA in RPE-1 cells, T21 post infection, TG003 treatment, replicate C

description: Library name: RPE1_T21_IC20_C

value: RPE-1 retinal pigment epithelium


title: AAV8-HLP-mGHR (4E10 vg), Female: KC14-022

description: Library name: KC14_022

value: Liver

value: Female


title: CHyMErA in RPE-1 cells, T21 post infection, TG003 treatment, replicate B

description: Library name: RPE1_T21_IC20_B


title: CUTeTag-E85-HF_B6_AAplus_female_TP290-9_H3K27me3

description: Library name: CT_L121

value: AAplus


title: CUTeTag-E85-HF_B6_AAmin_female_TP270-7_H3K27me3

description: Library name: CT_L118


title: RPE-1 cycloheximinde treatment, replicate 3

description: Library name: RPE1_CHX_3


title: NTPL-60_1

source_name: PDX

value: PDX

value: ML-DS


title: AAV8-HLP-mGHR (4E10 vg), Female: KC14-019

description: Library name: KC14_019


title: AAV8-HLP-Luc (4E10 vg), Female: KC14-017

description: Library name: KC14_017

value: AAV8-HLP-Luc (4E10 vg)


title: CUTeTag-E85-HF_B6_AAplus_female_TP298-4_H3K27me3

description: Library name: CT_L117


title: CPCT-0010_2


title: CUTeTag-E85-HF_B6_AAmin_male_TP270-5_IgG

description: Library name: CT_L114

value: male

value: IgG


title: CHyMErA in RPE-1 cells, T21 post infection, no treatment, replicate C

description: Library name: RPE1_T21_NT_C


title: CHyMErA in RPE-1 cells, T21 post infection, TG003 treatment, replicate A

description: Library name: RPE1_T21_IC20_A


title: NTPL-60_2


title: AAV8-HLP-Luc (4E10 vg), Female: KC14-016

description: Library name: KC14_016


title: CPCT-0010_1


title: CHyMErA in RPE-1 cells, T21 post infection, no treatment, replicate B

description: Library name: RPE1_T21_NT_B


title: CUTeTag-E85-HF_B6_AAplus_male_TP290-4_IgG

description: Library name: CT_L109


title: AAV8-HLP-Luc (4E10 vg), Female: KC14-015

description: Library name: KC14_015


title: CHyMErA in RPE-1 cells, T21 post infection, no treatment, replicate A

description: Library name: RPE1_T21_NT_A


title: CUTeTag-E85-HF_B6_AAmin_female_TP270-6_H3K27me3

description: Library name: CT_L108


title: NTPL-386_2


title: NTPL-386_1


title: CHyMErA in RPE-1 cells, T0 post infection

description: Library name: RPE1_T0


title: Uninjected GHR-/- (KO), Male: KC14-136

description: Library name: KC14_136

value: Uninjected GHR-/- (KO)

value: Male


title: Uninjected GHR-/- (KO), Male: KC14-114

description: Library name: KC14_114


title: CUTeTag-E85-HF_B6_AAplus_female_TP290-2_H3K27me3

description: Library name: CT_L107


title: CMK_2

value: CMK


title: CHyMErA in RPE-1 cells, T27 post infection, no treatment, replicate A

description: Library name: RPE1_T27_NT_A


title: CUTeTag-E85-HF_B6_AAmin_male_TP248-1_H3K27me3

description: Library name: CT_L106


title: Uninjected GHR-/- (KO), Male: KC14-113

description: Library name: KC14_113


title: CMK_1


title: CUTeTag-E85-HF_129_AAmin_male_TP241-5_IgG

description: Library name: CT_L96


title: CHyMErA in HAP1 cells, T18 post infection, DMSO control treatment, replicate B

description: Library name: HAP1_T18_DMSO_B

value: HAP1 chronic myelogenous leukemia


title: CHyMErA in HAP1 cells, T18 post infection, DMSO control treatment, replicate A

description: Library name: HAP1_T18_DMSO_A


title: CUTeTag-E85-HF_B6_AAplus_male_TP290-1_H3K27me3

description: Library name: CT_L105


title: 16002_2


title: Uninjected GHR+/+ (WT), Male: KC14-102

description:
Library name: KC14_102
DE-gene (.xlsx) and Geneset enrichment (.txt) for GHR vs LUC in female

value: Uninjected GHR+/+ (WT)


title: 16002_1


title: CUTeTag-E85-HF_129_AAmin_male_TP242-3_H3K27me3

description: Library name: CT_L85

value: E8.5 headfold


title: Limb_PosteriorBlast_ERKi_5

city: Dallas

first: Alexander

middle: J

last: Trostle

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern

description: Library name: P38D-34

data_processing:
Raw reads trimmed with trimmomatic-0.39 at default parameters
Trimmed reads aligned to reference with STAR 2.7.3a at default parameters
Assembly: UKY_AmexF1_1
Supplementary files format and content: Counts generated by STAR, tab file contains quantification per sample

organism: Ambystoma mexicanum

source_name: Forelimb

growth_protocol: Blastemas were induced with nerve deviation and  harvested with the wound epithelium intact 10 days post-injury

extract_protocol:
NEB Ultra II
Qiagen RNeasy Plus Mini Kit

treatment_protocol: 25 uM ERK inhibitor (U0126), or no treatment (Holtfreter's solution) and DMSO

value: Forelimb

value: d/d

value: ERKi


title: CHyMErA in HAP1 cells, T18 post infection, TG003 treatment, replicate B

description: Library name: HAP1_T18_IC20_B


title: CUTeTag-E85-HF_129_AAplus_male_TP240-4_H3K27me3

description: Library name: CT_L84


title: CHyMErA in HAP1 cells, T18 post infection, TG003 treatment, replicate A

description: Library name: HAP1_T18_IC20_A


title: CUTeTag-E85-HF_129_AAplus_female_TP245-1_H3K27me3

description: Library name: CT_L83

value: female


title: AAV8-HLP-mGHR (4E10 vg), Male: KC14-008

description:
Library name: KC14_008
DE-gene (.xlsx) and Geneset enrichment (.txt) for male WT vs female WT

value: Liver

value: AAV8-HLP-mGHR (4E10 vg)


title: Limb_PosteriorBlast_4

description: Library name: P36D-29


title: CHyMErA in HAP1 cells, T18 post infection, no treatment, replicate C

description: Library name: HAP1_T18_NT_C


title: CUTeTag-E85-HF_129_AAmin_female_TP243-6_H3K27me3

description: Library name: CT_L82

value: AAmin


title: AAV8-HLP-mGHR (4E10 vg), Male: KC14-007

description:
Library name: KC14_007
DE-gene (.xlsx) and Geneset enrichment (.txt) for WT vs KO


title: CHyMErA in HAP1 cells, T18 post infection, no treatment, replicate B

description: Library name: HAP1_T18_NT_B


title: AAV8-HLP-Luc (4E10 vg), Male: KC14-005

description:
Library name: KC14_005
DE-gene (.xlsx) and Geneset enrichment (.txt) for WT v sGHR


title: CUTeTag-E85-HF_129_AAplus_female_TP237-2_IgG

description: Library name: CT_L75

value: AAplus


title: Limb_PosteriorBlast_ERKi_3

description: Library name: P29D-32


title: CHyMErA in HAP1 cells, T18 post infection, no treatment, replicate A

description: Library name: HAP1_T18_NT_A


title: CUTeTag-E85-HF_129_AAmin_female_TP241-3 _H3K27me3

description: Library name: CT_L74


title: AAV8-HLP-Luc (4E10 vg), Male: KC14-002

description:
Library name: KC14_002
DE-gene (.xlsx) and Geneset enrichment (.txt) for GHR vs LUC

value: AAV8-HLP-Luc (4E10 vg)


title: Limb_PosteriorBlast_2

description: Library name: P25D-27


title: CUTeTag-E85-HF_129_AAplus_female_TP237-1 _H3K27me3

description: Library name: CT_L73


title: AAV8-HLP-Luc (4E10 vg), Male: KC14-001

description:
Library name: KC14_001
DE-gene (.xlsx) and Geneset enrichment (.txt) for LUC vs KO


title: CHyMErA in HAP1 cells, T12 post infection, DMSO control treatment, replicate C

description: Library name: HAP1_T12_DMSO_C


title: Limb_PosteriorBlast_1

description: Library name: P21D-26


title: CHyMErA in HAP1 cells, T12 post infection, DMSO control treatment, replicate B

description: Library name: HAP1_T12_DMSO_B


title: female germline stem cells, FGSCs. C2.IP

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: C2.IP

data_processing:
Cutadapt used for triming reads. It can bin reads based on mapping to multiple references at once
Mapping sequencing RNA reads to align genome assembly using sofeware Hisat2
Peak calling was performed independently for each sample using MACS2
Differential acetylation genes were identified using diffReps. Peaks located on mRNA exons were screened using in-house programs and annotated accordingly
Assembly: MM10
Supplementary files format and content: Tab-delimited text files include the number of reads, relative RPKM values, and P-values for control and experimental group Sample.

source_name: Ovary

extract_protocol:
total RNA was isolated from FGSCs and Dif-FGCs.NEBNext rRNA Depletion Kit v2 was used to remove rRNA and the GenSeq® ac4C-IP Kit was used to immuneprecipitate RNA.
For library preparation, RNA Fragmentation Reagents were used to fragment the RNA to ~200 nt. Then The RNA fragments incubated with the protein A beads/ ac4C antibody complexes for 4 h at 4 °C. Eluted the ac4C-enriched RNA fragments off the beads by proteinase K digestion, and purify the RNA fragments by phenol-chloroform. Subsequently, the RNA fragments used for the RNA library construction.

value: Ovary

value: FGSCs

value: germ stem cells

value: control group


title: SE-BDEV Treated 3

city: Atlanta

first: Samantha

middle: Reed

last: Lynn

state: GA

address: 615 Michael St

department: Department of Human Genetics

institute: Emory University

description: Library name: EV Pilo 2C4

data_processing:
mapped to the mouse genome (mm9) using TopHat2
gene expression quantification and differential expression analysis using Cuffdiff (FDR<0.05). Cells treated with either BDEV treatment were compared to vehicle treated cells
Assembly: mm9
Supplementary files format and content: txt files include the fkpm used in the differential expression analysis (one file for each comparison)
Supplementary files format and content: csv files include the differential expression analysis comparing either BDEV treatment to vehicle treated cells (one file for each comparison)

source_name: N2a cells

extract_protocol:
Total RNA was isolated with ReliaPrep RNA Cell Miniprep System per manufacturer’s instructions (Promega Z6011)
NEB Ultra II Directional RNA library Prep kit with PolyA selection

value: N2a cells


title: Mouse heart tissue, treated with naked-VEGFA, rep 3

city: Skövde

first: Jane

last: Synnergren

address: Högskolevägen 1

country: Sweden

institute: University of Skövde

description:
P25704_118
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with a 151nt(Read1)-19nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell.
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite.
The quality scale used is Sanger / phred33 / Illumina 1.8+. Processing of FASTQ files was carried out by the SciLifeLab National Genomics Infrastructure at the Uppsala Multidisciplinary Center for Advanced Computational Science, Sweden.
The processed reads were then aligned to the reference genome of Mus musculus (build GRCm38) with the STAR aligner.
Read counts for genes were generated using the feature Counts library and normalized TPM values calculated with StringTie, and raw gene read counts were generated by Salmon.
Technical documentation on the RNA-seq pipeline can be accessed here: https://github.com/nf-core/rnaseq.
Assembly: Mus musculus (build GRCm38)
Supplementary files format and content: tab-separated text file with raw gene counts for every gene and every sample
Supplementary files format and content: tab-separated text file with transcript-per-million (TPM) values for every gene and every sample

source_name: Heart

extract_protocol:
The mice were sacrificed 6h post injection, and the heart, liver and blood were collected. For the heart, the area of injection in the left ventricle was dissected and separated from the rest of the heart and snap-frozen. The remaining parts of the heart (remote left ventricle, right ventricle and atria) was snap-frozen in a second tube and referred to as remote non-injected area for further analysis. Total RNA were isolated using miRNeasy Mini Kit.
Library construction was performed using Takara SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian kit - V3, which is specifically designed for very low input total RNA samples

treatment_protocol: C57BL/6Ncrl mice at 10-12 weeks of age and weight of ~25 g purchased from Charles river. The mice were subjected to a left thoracotomy at the fourth intercostal space ~2 to 3 mm to the left of the sternum. A rib spreader was used to keep the incision open. The pericardium was opened, the heart was held using an USP 8-0 suture and 40 µL of EVs, LNPs, naked RNA or PBS (no mRNA) treatments were injected in one single site in the myocardium of the left ventricle using an insulin syringe

value: Heart

value: Naked-VEGFA injection


title: Limb_PosteriorBlast_ERKi_2

description: Library name: P18D-31


title: CON-BDEV Treated 3

description: Library name: EV Saline 2B4


title: CHyMErA in HAP1 cells, T12 post infection, DMSO control treatment, replicate A

description: Library name: HAP1_T12_DMSO_A

value: HAP1 chronic myelogenous leukemia


title: CHyMErA in HAP1 cells, T18 post infection, DMSO control treatment, replicate C

description: Library name: HAP1_T18_DMSO_C


title: Mouse heart tissue, treated with naked-VEGFA, rep 2

description:
P25704_117
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv


title: Replicate 3 of FMRP-KO RNA

description:
Library name: FMRP_RNA_rep3
Third replicate of RNA from FMRP knockout mice.

value: brain

value: control


title: Limb_PosteriorBlast_ERKi_1

description: Library name: P08D-30

value: Forelimb

value: d/d

value: ERKi


title: Uninjected GHR+/+ (WT), Male: KC14-103

description:
Library name: KC14_103
DE-gene (.xlsx) and Geneset enrichment (.txt) for WT vs KO in female

value: Liver

value: Uninjected GHR+/+ (WT)

value: Male


title: CHyMErA in HAP1 cells, T12 post infection, TG003 treatment, replicate C

description: Library name: HAP1_T12_IC20_C


title: CON-BDEV Treated 2

description: Library name: EV Saline 2B3


title: Mouse heart tissue, treated with naked-VEGFA, rep 1

description:
P25704_116
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv


title: Limb_AnteriorBlast_5

description: Library name: A47D-25


title: SE-BDEV Treated 2

description: Library name: EV Pilo 2B2


title: CHyMErA in HAP1 cells, T18 post infection, TG003 treatment, replicate C

description: Library name: HAP1_T18_IC20_C


title: CHyMErA in HAP1 cells, T12 post infection, TG003 treatment, replicate B

description: Library name: HAP1_T12_IC20_B


title: Uninjected GHR+/+ (WT), Male: KC14-101

description:
Library name: KC14_101
DE-gene (.xlsx) and Geneset enrichment (.txt) for WT vs KO in male


title: Mouse heart tissue, treated with LNPs, rep 3

description:
P25704_115
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv

value: LNP injection


title: Limb_AnteriorBlast_4

description: Library name: A42D-23


title: CHyMErA in HAP1 cells, T12 post infection, TG003 treatment, replicate A

description: Library name: HAP1_T12_IC20_A


title: HAP1 SFPQ intronic deletion hgRNA 2, replicate 2

description: Library name: H012_IDel.SFPQ.G171_r2

value: Intronic deletion in SFPQ generated with hybrid guide RNA comprising Cas9 guide ATCAGTTGAACTGGTATGAG and Cas12a guide ACATCAGATTAACCCACTGAAAA.


title: Mouse heart tissue, treated with LNPs, rep 2

description:
P25704_114
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv


title: AAV8-HLP-mGHR (4E10 vg), Male: KC14-012

description:
Library name: KC14_012
DE-gene (.xlsx) and Geneset enrichment (.txt) for GHR vs LUC in male

value: AAV8-HLP-mGHR (4E10 vg)


title: CHyMErA in HAP1 cells, T12 post infection, no treatment, replicate C

description: Library name: HAP1_T12_NT_C


title: Limb_Uninjured_3

description: Library name: A41M-37


title: Vehicle Treated 3

description: Library name: CON 2A2


title: SE-BDEV Treated 1

description: Library name: EV Pilo 1C2


title: Mouse heart tissue, treated with LNPs, rep 1

description:
P25704_113
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv


title: Limb_PosteriorBlast_3

description: Library name: P33D-28


title: CHyMErA in HAP1 cells, T12 post infection, no treatment, replicate B

description: Library name: HAP1_T12_NT_B


title: Limb_AnteriorBlast_3

description: Library name: A41D-22


title: CON-BDEV Treated 1

description: Library name: EV Saline 1C1


title: Mouse heart tissue, treated with CPC-Evs, rep 3

description:
P25704_112
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv

value: CPC-EV injection


title: Limb_Uninjured_2

description: Library name: A16M-36


title: Replicate 3 of Wild Type RNA using M protocol

description:
Library name: WT_RNA_M_rep3
Third replicate of RNA from wild type mice, using M protocol.

value: WT

value: M-protocol


title: Limb_PosteriorBlast_ERKi_4

description: Library name: P31D-33


title: Vehicle Treated 2

description: Library name: CON 1B4

value: N2a cells


title: CHyMErA in HAP1 cells, T12 post infection, no treatment, replicate A

description: Library name: HAP1_T12_NT_A


title: Mouse heart tissue, treated with CPC-Evs, rep 2

description:
P25704_111
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv

value: Heart


title: Limb_AnteriorBlast_2

description: Library name: A16D-21


title: Vehicle Treated 1

description: Library name: CON 1B3


title: Limb_Uninjured_1

description: Library name: A07M-35


title: Mouse heart tissue, treated with CPC-Evs, rep 1

description:
P25704_110
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv


title: CHyMErA in HAP1 cells, T0 post infection

description: Library name: HAP1_T0

value: HAP1 chronic myelogenous leukemia


title: HTS cell (replicate 3)

city: Kansas City

first: Soumen

last: Paul

state: KS

address: Hemenway Building 3901 Rainbow Boulevard

department: Department of Pathology & Laboratory Medicine

institute: University of Kansas Medical Center

description: Library name: Sample6

data_processing:
Illumina bcl2fastq2 conversion software used for basecalling.
reads were aligned using the STAR (2.6.1c) software.
raw read counts were obtained using RSEM-1.3.1
differential expression was obtained using DESeq2
Assembly: GRCh38.rel92
Supplementary files format and content: tab-delimited text files of raw count values for each Sample

source_name: Placenta

growth_protocol: Cell culture protocol was published earlier (Saha et al. Proc Natl Acad Sci U S A. 2020 Jul 28;117(30):17864-17875. doi: 10.1073/pnas.2002449117)

extract_protocol:
For RNA extraction we used Qiagen RNeasy Kit (Catalog#74104) following manufacturer's protocol. For each experimental conditions, 1 million cells were used to isolate total RNA.
For sequencing, libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) designed for transcriptome analysis from samples as small as a single cell.  For library preparation, the mRNA fraction was enriched, fragmented, sized, reverse transcribed into cDNA and ligated with the appropriate adaptors. Finally, deep sequencing was performed using the Illumine NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate pair-end reads with read length 101 bp.

value: Placenta


title: Vehicle-Treated 4

description: Library name: N2A_EV_RNA_12


title: Mouse heart tissue, treated with HUVEC-Evs, rep 3

description:
P25704_109
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv

value: HUVEC-EV injection


title: Limb_AnteriorBlast_1

description: Library name: A07D-20

value: Forelimb


title: Vehicle-Treated 3

description: Library name: N2A_EV_RNA_11


title: HTS cell (replicate 2)

description: Library name: Sample5


title: Mouse heart tissue, treated with HUVEC-Evs, rep 2

description:
P25704_108
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv


title: E. coli HCF2CAD2 grown in a minimal medium at 24 h, replicate 3

city: Incheon

first: Hyungyu

last: Lim

address: Inha ro 100

country: South Korea

institute: Inha University

description: Library name: HCF_3

data_processing:
Raw read data was processed by running a bacterial transcriptome profiling pipeline utilizing Bowtie2, summarizeOverlaps, and DEseq2 to obtain transcripts per million (TPM) values for each gene. A reference genome was created to include two heterologous genes (i.e., phlF and cad) based on the E. coli W chromosome and its two native plasmids obtained from GenBank.
Assembly: CP002185, CP002186, CP002187
Supplementary files format and content: csv

organism: Escherichia coli W

source_name: bacteria

growth_protocol: E. coli W single colonies of each strain were inoculated into 5 mL of medium in a 15 mL test tube. After 18 h of cultivation, the seed culture was re-inoculated into 150 mL of fresh medium in the 400-mL Erlenmeyer flasks at an optical density at 600 nm (OD600) of 0.05. In case of itaconate production, isopropyl-β-D-thiogalactopyranoside (IPTG) was added to the medium at 10 mM to induce the expression of cad. Cell cultivations were carried out in a shaker at 220 rpm and 30 °C. pH was monitored using an Orion™ 8103BN ROSS™ pH meter (Thermo Scientific) and 5 M HCl was added to maintain the pH below 7.0. All experiments were conducted in triplicate.

extract_protocol:
Cells were treated using the Qiagen RNA-protect bacterial reagent (Hilden, Germany) according to the instruction from the manufacturer. Pelleted cells were stored at -80oC, and after cell resuspension and partial lysis, they were ruptured with a beat beater. Subsequently, the total RNA was extracted using a Qiagen RNA purification kit. After total RNA extraction, ribosomal RNA was removed.
Prepared RNA libraries were prepard by using a TruSeq Stranded Total RNA kit (Illumina, San Diego, CA, USA) and were sequenced by using an Illumina NovaSeq X machine.

value: bacteria

value: W DpykA DpykF DptsG Dedd DaceA Dicd (Picd::PBBa_J23108-phlO-icd) / pPCDF_PPC_GLTA / pACYC_ACKA_PTA / pCADP2


title: Vehicle-Treated 2

description: Library name: N2A_EV_RNA_10


title: HTS cell (replicate 1)

description: Library name: Sample4


title: E. coli HCF2CAD2 grown in a minimal medium at 24 h, replicate 2

description: Library name: HCF_2


title: Mouse heart tissue, treated with HUVEC-Evs, rep 1

description:
P25704_107
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv


title: Vehicle-Treated 1

description: Library name: N2A_EV_RNA_9


title: Mouse heart tissue, treated with HTB-Evs, rep 3

description:
P25704_106
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv

value: HTB-EV injection


title: CON-BDEV-Treated 4

description: Library name: N2A_EV_RNA_8


title: E. coli HCF2CAD2 grown in a minimal medium at 24 h, replicate 1

description: Library name: HCF_1


title: EVT cell (replicate 2)

description: Library name: Sample2


title: EVT cell (replicate 3)

description: Library name: Sample3


title: EVT cell (replicate 1)

description: Library name: Sample1


title: E. coli WCAD grown in a minimal medium at 24 h, replicate 3

description: Library name: WT_3

value: W / pCAD


title: SE-BDEV-Treated 4

description: Library name: N2A_EV_RNA_7


title: Mouse heart tissue, treated with HTB-Evs, rep 1

description:
P25704_104
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv


title: E. coli WCAD grown in a minimal medium at 24 h, replicate 2

description: Library name: WT_2


title: A549, MOA-seq Control4, Rep2

city: Tallahassee

first: Ayush

last: Singh

state: Florida

address: 319 Stadium Dr,

department: Department of Biological Science

institute: Flordia State University

description: Library name: MOA4_Ctrl_Rep2

data_processing:
Sequence reads (FASTQ format) were trimmed for adapters using Cutadapt with default parameters. For the MOA control, SeqPurge was used with default parameters.
Trimmed paired-end reads were merged using FLASh with the parameters -t 40 --cap-mismatch-quals -M 100 -d -q
Merged reads were aligned to the human reference genome (hg38) using the bwa-mem2 mem function with the parameters -M -t 40. Alignment files (SAM) were converted to BAM format using SAMtools, and filtering was applied to retain reads with a mapping quality score (MAPQ) of 20 or greater. PCR duplicates were removed.
BAM files were converted to BED files using bamToBed in Bedtools.
Fragment center tracks ("frenters") were created by shortening mapped reads to their central 20 bp using a custom awk command. Bedgraphs were generated using genomeCoverageBed in Bedtools with a counts-per-million (CPM) scaling factor for sequencing depth normalization.
BigWig files for UCSC Genome Browser visualization were produced using bedGraphToBigWig.
Peak calling was performed using MACS3. Fragment center BED files for each biological replicate pair per treatment were used as input to the callpeak function. The Irreproducibility Discovery Rate (IDR) framework was applied to identify consistent peaks between biological replicates, which were designated as within-sample peaks. To minimize artifacts, within-sample peaks were filtered using intersect in Bedtools. ENCODE blacklist  regions and MOA control regions (chromatin-free total DNA light digests with MNase) were used as exclusion criteria. For MOA control, peak calling was performed using only MACS3 callpeak.
Differential peak calling was performed using bdgdiff in MACS3, comparing each hypoxia time point (1h, 3h, 24h) to the normoxic sample. The optimal likelihood ratio (LHR) cutoff was determined using the elbow method to maximize sensitivity while minimizing noise.
Assembly: hg38
Supplementary files format and content: The narrowPeak file includes genomic peak data with associated scores and significance metrics for each region.
Supplementary files format and content: The BigWig file includes continuous data, such as the MOA-seq signal intensity, across a genomic region.
Supplementary files format and content: The differential peak BED file stores genomic regions with varying enrichment between hypoxia and normoxic conditions, categorizing peaks as gained, lost, or shared. Each entry represents a genomic region, with the last column containing the log10 likelihood ratio, quantifying the likelihood that the observed signal originates from one condition over the other. Regions enriched in hypoxia compared to normoxic are classified as gained peaks, while those enriched in normoxic conditions are lost peaks. Shared peaks represent regions with similar enrichment in both conditions, where the difference is not statistically significant.

source_name: lung carcinoma

extract_protocol:
HUVEC cells were cultured to 90–95% confluency and subjected to induced hypoxia (2% O₂) for 1, 3, or 24 hours. MOA-seq was performed on formaldehyde-fixed cells collected at each time point. Fixed cells were dispersed using a hand mixer and a 5/8-gauge needle, followed by nuclei isolation using Nucleus Isolation Buffer (NIB) containing 0.3 M sucrose, 2 mM MgOAc, 2.1% Triton X-100, 10 mM HEPES (pH 7.4), and 1 mM CaCl₂. Nuclei purity and density were assessed by fluorescence microscopy after staining with Vectashield DAPI mounting medium. For MOA control libraries, A549 human DNA (ATCC, CCL-185) was used. Cells were cultured in F12K media supplemented with fetal bovine serum, 1% L-glutamine, and 1% penicillin-streptomycin. DNA was isolated using the TRIzol Reagent protocol (cat no. 15596026). Qualitative and quantitative checks were performed on the samples received. Initially, 1 µL of DNA was run on a 1% agarose 1X TBE gel, confirming the presence of high molecular weight total naked DNA. DNA concentration was further assessed using a NanoDrop UV spectrophotometer.
MNase digestion was performed on isolated nuclei using serial dilutions of MNase enzymes (ranging from 1280 U/mL to 0 U/mL) at 37ºC for 15 minutes. Reactions were stopped with 0.5 M EGTA-NaOH (pH 8.0). DNA was decrosslinked overnight at 65°C in the presence of SDS, NaCl, Proteinase K, and ddH₂O. Following decrosslinking, DNA was purified via sequential phase extraction using Tris-saturated phenol, phenol:chloroform, and chloroform. Purified DNA was precipitated with sodium acetate, linear polyacrylamide (LPA), and ethanol, washed with 70% ethanol, and resuspended in TE buffer containing RNase A. After RNase treatment, DNA was re-precipitated, washed, and air-dried before final resuspension in TE buffer. DNA quality was assessed by spectrophotometry, and digestion patterns were visualized using gel electrophoresis on a 1% agarose, 1X TBE gel. DNA was further quality-controlled using an Agilent 2100 Bioanalyzer, Q-PCR, and a Qubit 2.0 Fluorometer. Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep kits (Cat. E7103S). Indexed libraries were size-selected to enrich for sub-nucleosomal (<150 bp) genomic insert sequences and submitted for paired-end 150 bp reads on the Illumina HiSeq or NovaSeq (FSU College of Medicine, Translational Science Lab). Two biological replicates were analyzed per condition. For MOA control libraries, DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7103). After adapter ligation, samples were flash frozen, and library-specific index sequences (dual indices method) were added by the NGS Library Facility, Department of Biological Science, FSU.

value: lung carcinoma

value: epithelial cell


title: CON-BDEV-Treated 3

description: Library name: N2A_EV_RNA_6


title: A549, MOA-seq Control4, Rep1

description: Library name: MOA4_Ctrl_Rep1


title: Mouse heart tissue, treated with HTB-Evs, rep 2

description:
P25704_105
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv


title: SE-BDEV-Treated 3

description: Library name: N2A_EV_RNA_5


title: WT-8

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

description: Library name: A2536

data_processing:
Noncoding RNA library data were aligned and quality checked by STAR (v 2.5.3a) and analyzed with COMPSRA (v 1.0.3) and DESeq2 (v 1.42.1). Selected gene targets were analyzed using TargetScanMouse 8.0.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet containing ncRNA overall reads generated from Compsra COMPSRA (v 1.0.3)

source_name: brain

extract_protocol:
10 mg of frozen prefrontal cortex was dissociated in RLT buffer (#74106, Qiagen RNeasy Mini Kit, Germany) with 10% beta-mercaptoethanol and ncRNA was isolated using the Norgen MicroRNA Isolation Kit (#21300, Canada) according to manufacturer's protocol.
Small ncRNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set (#E7560S, NEB, MA).

value: brain


title: CON-BDEV-Treated 2

description: Library name: N2A_EV_RNA_4


title: Mouse heart tissue, untreated, rep2

description:
P25704_102
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv

value: Untreated


title: A549, MOA-seq Control3, Rep2

description: Library name: MOA3_Ctrl_Rep2


title: Mouse heart tissue, untreated, rep1

description:
P25704_101
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv


title: A549, MOA-seq Control3, Rep1

description: Library name: MOA3_Ctrl_Rep1


title: SE-BDEV-Treated 2

description: Library name: N2A_EV_RNA_3


title: Animal cap, BEX3, gastrula

city: Portsmouth

first: Colin

middle: Richard

last: Sharpe

state: Hampshire

address: King Henry Building, King Henry I Street

department: School of Environment and Life Sciences

country: United Kingdom

institute: University of Portsmouth

description:
Library name: Sample9
Column name in all_genes_count.txt: BEX3

data_processing:
Clean reads were obtained by removing adapter sequences, low-quality reads, and reads containing ambiguous bases.
Clean reads were aligned to the Xenopus laevis reference genome using HISAT2.
Gene-level read counts were generated from aligned reads for each sample.
Differential expression analysis was performed using DESeq2.
P-values were adjusted using the Benjamini-Hochberg method to control the false discovery rate.
Assembly: Xenopus laevis genome assembly version 10 (Xenbase v10)
Supplementary files format and content: Tab-delimited text files (.xls format) include gene-level raw read counts for each sample.
Supplementary files format and content: Tab-delimited text files (.xls format) include differential expression results with log2FoldChange, p-value, adjusted p-value (FDR), and gene annotation.

organism: Xenopus laevis

source_name: Ectoderm

growth_protocol: Xenopus laevis embryos were maintained in MBS and staged according to Nieuwkoop and Faber. Animal caps were dissected from NF stage 9-10 embryos in 1x MBS, maintained as paired explants, and cultured for 4 h at 21°C until control embryos reached approximately NF stage 12.

extract_protocol:
Total RNA was extracted from frozen animal cap explants by homogenisation in NETS buffer followed by phenol-chloroform extraction and ethanol precipitation. DNA was removed using DNase I treatment, and RNA was re-purified by phenol–chloroform extraction and ethanol precipitation. RNA quantity was assessed by spectrophotometry and integrity confirmed by agarose gel electrophoresis.
RNA-seq libraries were prepared by Novogene using standard Illumina-compatible protocols following poly(A) RNA enrichment and fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

treatment_protocol: Treatment protocol WT - ACWT  Untreated animal cap explants were generated from uninjected embryos. Three pairs of animal caps were pooled per biological replicate, with three biological replicates prepared.  treatment protocol - NGRX  Embryos were injected at the two-cell stage with synthetic Noggin and RXRβ mRNA. Animal caps were dissected at NF stage 9-10 and cultured without bexarotene until approximately NF stage 12.  treatment protocol - BEX  Embryos were injected at the two-cell stage with synthetic Noggin and RXRβ mRNA. Animal caps were dissected at NF stage 9-10 and cultured in 100 nM bexarotene until approximately NF stage 12.

value: Ectoderm

value: Co-inject Noggin, RXRβ mRNA with Bexarotene

tag: batch

value: Repeat 3 BEX


title: WT-6

description: Library name: F2719

value: WT


title: A549, MOA-seq Control2, Rep2

description: Library name: MOA2_Ctrl_Rep2


title: CON-BDEV-Treated 1

description: Library name: N2A_EV_RNA_2

value: N2a cells


title: Animal cap, BEX2, gastrula

description:
Library name: Sample8
Column name in all_genes_count.txt: BEX2

value: Repeat 2 BEX


title: A549, MOA-seq Control2, Rep1

description: Library name: MOA2_Ctrl_Rep1


title: WT-5

description: Library name: F2608


title: SE-BDEV-Treated 1

description: Library name: N2A_EV_RNA_1


title: A549, MOA-seq Control1, Rep2

description: Library name: MOA1_Ctrl_Rep2


title: Animal cap, BEX1, gastrula

description:
Library name: Sample7
Column name in all_genes_count.txt: BEX1

value: Repeat 1 BEX


title: Animal cap, NGRX3, gastrula

description:
Library name: Sample6
Column name in all_genes_count.txt: NGRX3

value: Co-inject Noggin and RXRβ mRNA

value: Repeat 3 NGRX


title: 10 Day SE-BDEV 3

description: Library name: Sample 6

data_processing:
Small RNA-sequencing data was mapped to the mouse miRNA database with miRge 2.0
Differential expression analysis of miRNAs was performed by DESeq2 (FDR < 0.05)
Assembly: mm9
Supplementary files format and content: 10day_miRNA_RPM.csv file includes reads per million mapped reads for all samples
Supplementary files format and content: 10day_miRNA_Deseq2.cvs includes differential expression analysis comparing miRNA abundence in SE-BDEVs and CON-BDEVs

source_name: Brain-Derived Extracellular Vesicles

extract_protocol:
miRNeasy Micro Kit (Qiagen 21708) with DNase treatment (Qiagen 79254)
QIAseq miRNA Library Kit

value: Brain-Derived Extracellular Vesicles


title: Animal cap, NGRX2, gastrula

description:
Library name: Sample5
Column name in all_genes_count.txt: NGRX2

value: Repeat 2 NGRX


title: 10 Day CON-BDEV 3

description: Library name: Sample 5


title: A549, MOA-seq Control1, Rep1

description: Library name: MOA1_Ctrl_Rep1


title: WT-2

description: Library name: G0698


title: 10 Day SE-BDEV 2

description: Library name: Sample 4


title: HL-60 cells, mock3

city: Gent

first: Laurens

last: Van Camp

address: C. Heymanslaan 10

institute: Ghent University

description:
Library name: Sample 11
Column name in processed_data_OE_CD68.xlsx:  MOCK3

data_processing:
R, DEseq2 package
Assembly: NCBI hg38
Supplementary files format and content: csv files include RPKM values for each sample

growth_protocol: cell culture according to standard guidelines

extract_protocol:
To overexpress CD68, a constitutive Lenti-hCMV-ORF-P2A-eGFP-IRES-Puromycin vector was used with an empty lentiviral open reading frame vector as a control, both provided as a bacterial glycerol stocks (Transomic). For the knockdown models, three shERWOOD UltramiR short hairpin RNA targeting CD68, and one non-targeting shRNA (NTC), were purchased as glycerol stocks at Transomic (TLHSU1452). The OE and KD vector backbones allowed for selection of retroviral integration based on GFP and mCherry fluorescent expression, respectively, and puromycin-enriched medium. Plasmid DNA (pDNA) was extracted from bacterial cultures started from the glycerol stock of the constructs using a DNA Midiprep extraction kit (Qiagen) following manufacturer’s guidelines. The pDNA concentrations were measured by Nanodrop (ThermoFisher Scientific BVBA, Merelbeke, Belgium) and DNA quality cutoff values were set at a 260/230 ratio of 1.80 and a 280/230 ratio of 2. HEK293T cells were transfected using JetPEI reagens (Polyplus transfection, Illkirch, France) and the following plasmids: KD or OE vector (3µg), a pCMV-VSV-G envelope (0.3µg), and the packaging vector p8.91 (2.7µg) in 250µL NaCl. The third day after transfection, virus was harvested and concentrated by adding PEG-it virus precipitation solution (Sanbio) and centrifugating the mix after >12h of incubation at 4°C. Concentrated virus was aliquoted and stored at −80 °C. Leukemic cells were spin-infected in a centrifuge at 32° for 90 min at 2300 rpm and puromycin selection (0.5 µg/mL) was initiated 24 hours after transduction. After incubation with puromycin selection of 48h, transduction efficacy was measured through GFP or mCherry fluorescence by flow cytometry (BD Lyrica), using the parental non-transduced cell lines (HL-60 and THP-1) as a control. Puromycin selection was continued in case the transduction efficacy was less than 95%.
Total RNA of the CD68 OE HL-60 cell line (HL-60CD68 OE) and an empty vector control HL-60 cell line (HL-60mock) as well as the CD68 KD THP1 cell line (THP-1CD68 KD) the NTC THP-1 cell line (THP-1NTC) were checked for purity and integrity on a electrophoresis gel. RNA sequencing was done in triplicate for every cell line by Eurofins (Eurofins Genomics, Ebersberg, Germany).

treatment_protocol: lentiviral transduction

value: myeloid cells

value: mock


title: Animal cap, NGRX1, gastrula

description:
Library name: Sample4
Column name in all_genes_count.txt: NGRX1

value: Repeat 1 NGRX


title: HL-60 cells, mock2

description:
Library name: Sample 10
Column name in processed_data_OE_CD68.xlsx:  MOCK2


title: Animal cap, ACWT3 wild type, gastrula

description:
Library name: Sample3
Column name in all_genes_count.txt: ACWT3

value: Repeat 3 WT


title: 10 Day SE-BDEV 1

description: Library name: Sample 2


title: Animal cap, ACWT2 wild type, gastrula

description:
Library name: Sample2
Column name in all_genes_count.txt: ACWT2

value: Repeat 2 WT


title: HL-60 cells, mock1

description:
Library name: Sample 9
Column name in processed_data_OE_CD68.xlsx:  MOCK1


title: HL-60 cells, CD68 OE3

description:
Library name: Sample 8
Column name in processed_data_OE_CD68.xlsx:  OE3

value: CD68 OE


title: 10 Day CON-BDEV 1

description: Library name: Sample 1


title: Animal cap, ACWT1 wild type, gastrula

description:
Library name: Sample1
Column name in all_genes_count.txt: ACWT1

value: Ectoderm

value: Repeat 1 WT


title: HL-60 cells, CD68 OE2

description:
Library name: Sample 7
Column name in processed_data_OE_CD68.xlsx:  OE2


title: SE-BDEV 3

description: Library name: Sample F

data_processing:
Small RNA-sequencing data was mapped to the mouse miRNA database with miRge 2.0
Differential expression analysis of miRNAs was performed by DESeq2 (FDR < 0.05)
Assembly: mm9
Supplementary files format and content: 24hr_miRNA_RPM.csv file includes reads per million mapped reads for all samples
Supplementary files format and content: 24hr_miRNA_Deseq2.cvs includes differential expression analysis comparing miRNA abundence in SE-BDEVs and CON-BDEVs


title: SN_9

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

description: Library name: SN_9

data_processing:
The quality control (QC) and read statistics of the raw sequencing data were verified using FastQC v0.11.9  and aggregated with MultiQC v1.12. The quality of the reads was evaluated based on parameters such as average read length, adapter content, over-represented sequences, and Phred sequence quality scores. Reads were mapped with the STAR aligner v2.7.5 to the Ensembl ARS-UCD 1.3 Bos taurus reference genome. The read quantification was performed using the STAR aligner with the -quantMode gene counts flag and annotation file from Ensembl (release 113). Read counts with zero or low count expression were filtered out using the filterByExpr function from edgeR v3.28.1. A principal component analysis (PCA) using the factoextra v1.0.7 R-package was performed for exploratory analysis. The DEGs were identified using DESeq2.
Matrix table with raw gene counts for every gene and every sample
Assembly: ARS-UCD1.3, Ensembl (release 113).
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample. TXT file
Supplementary files format and content: .TXT file

organism: Bos taurus

source_name: liver

extract_protocol:
Total RNA isolation was carried out using Trizol in conjunction with an on-column DNase digestion step, as per the manufacturer’s guidelines.
Strand-specific libraries were then constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs®, Ipswich, MA, USA).

value: liver

value: S

value: M


title: Tau-5

description: Library name: G0722

value: brain


title: SN_18

description: Library name: SN_18

value: F


title: Tau-4

description: Library name: G0522


title: THP-1 cells, NTC3

description:
Library name: Sample 5
Column name in processed_data_KD_CD68.xlsx:  NTC3

value: non targetable control


title: SE-BDEV 2

description: Library name: Sample D


title: SN_15

description: Library name: SN_15


title: Tau-3

description: Library name: G0725


title: CON-BDEV 2

description: Library name: Sample C


title: SN_12

description: Library name: SN_12


title: Tau-2

description: Library name: G0712


title: THP-1 cells, NTC1

description:
Library name: Sample 3
Column name in processed_data_KD_CD68.xlsx:  NTC1


title: SN_1

description: Library name: SN_1


title: SE-BDEV 1

description: Library name: Sample B


title: THP-1 cells, CD68 KD2

description:
Library name: Sample 2
Column name in processed_data_KD_CD68.xlsx:  KD2

value: CD68 KD


title: CON-BDEV 1

description: Library name: Sample A

value: Brain-Derived Extracellular Vesicles


title: WT-8

description: Library name: A2536

source_name: plasma-derived EVs

extract_protocol:
pEVs were isolated from 200 µL plasma using the Total Exosome Isolation Kit (#4484450, Invitrogen, Vilnius, Lithuania) following manufacturer’s protocol. EV RNA was extracted using the ExoQuick Exosome RNA Purification Column Kit (EQ808A, SBI, CA).
Small ncRNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set (#E7560S, NEB, MA).

value: plasma-derived EVs

value: WT


title: THP-1 cells, CD68 KD1

description:
Library name: Sample 1
Column name in processed_data_KD_CD68.xlsx:  KD1

value: myeloid cells