title: HEK293 miRNA from control nuclear fraction biol rep 1


title: HEK293 miRNA from virus infected nuclear fraction biol rep 4

status: Public on Mar 13 2025

type: SRA

city: Goteborg

first: Davide

last: Angeletti

address: Medicinaregatan 7a

country: Sweden

institute: University of Gothenburg

library_source: other

data_processing:
Illumina Nova-seq 6000 platform was used for sequencing
sequences were aligned to human miRNAs using bowtie2 and quantified using bedtools coverage
normalized counts in excel file
Assembly: hg38
Supplementary files format and content: raw counts file

molecule: other

organism: Homo sapiens

growth_protocol: HEK293 cells were cultured in DMEM media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin.

extract_protocol:
After PR8 infection for 16 hrs, cells were fractionated into cytplasmic and nuclear fractions. First AGO proteins were enriched by immunoprecipitation with T6B peptide. The RNA was isolated and small RNA libraries were genereated.
Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: PR8 IAV virus treatment at MOI 10

tag: ip molecule

value: T6B peptide

tag: cell line

tag: genotype

value: PR8 IAV infection

tag: fraction

value: nuclear fraction


title: HEK293 miRNA from virus infected nuclear fraction biol rep 2


title: Mouse colon, Control 2

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

country: USA

institute: UTMB NGS Core

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed for low quality bases and Illumina adapters using cutadapt v1.15.
STAR 2.7.10a
DESeq2 v1.38.3
Gene ontology and KEGG pathway enrichment of gene lists was completed with Enrichr.
Assembly: GRCm39
Supplementary files format and content: Excel files containing gene lists, id, mean base, log2 fold change, and p-values.

molecule: total RNA

organism: Mus musculus

source_name: Colon

growth_protocol: Six-week-old male C57BL/6J mice were housed in the UTMB Animal Facility with a 12-hour light/dark cycle, temperature range of 24-26°C, and a relative humidity of 40-70%.

extract_protocol:
Mice were euthanized under anesthesia and their colon tissues snap-frozen in liquid nitrogen. Total RNAs were isolated from pulverized frozen colon tissue using the PureLink RNA Mini Kit (Thermo Fisher).
RNA libraries were prepared using the NEBNext Ultra II RNA Kit per manufacturer's protocol.

treatment_protocol: There were three groups of 4 mice receiving the following treatments: (1) vehicle control mice received AIN-93G basal diet, (2) CAC mice were additionally subjected to AOM 7.4 mg/kg i.p. followed by 2.5% DSS in drinking water for 2 cycles of 7 days each with intermittent 2-week intervals of normal drinking water, and (3) CAC+Erl70 mice received the same AOM/DSS regimen but were fed AIN-93G diet containing 70 ppm erlotinib.

tag: tissue

value: Colon

tag: cell type

value: Colonocytes

value: WT

tag: strain

tag: Sex

value: Male

tag: treatment

value: AIN-93G Diet


title: HEK293 miRNA from control cytoplasmic fraction biol rep 3

value: Control cells

value: cytoplasmic fraction


title: HEK293 miRNA from control cytoplasmic fraction biol rep 4


title: HEK293 miRNA from control cytoplasmic fraction biol rep 2


title: Mouse colon, CAC+Erl70 2

value: AOM/DSS + AIN-93G Diet pre-mixed with Erlotinb 70 ppm


title: Mouse colon, Control 4


title: cepd, LN, rep4

city: Göttingen

first: Christiane

last: Gatz

state: Lower Saxony

address: Julia-Lermontowa-Weg 3

department: Plant Molecular Biology and Physiology

country: Germany

institute: Georg-August-University Göttingen

description: Library name: cepd_4

data_processing:
Sequence images were transformed with the Illumina BaseCaller software to BCL files, which were subsequently demultiplexed to FASTQ files with CASAVA (v1.8.2).
Using a Galaxy platform (Afgan et al., 2018), mapping of reads to the Arabidopsis thaliana genome reference sequence (TAIR10 release-51, ftp://ftp.ensemblgenomes.org/pub/plants/release-51) was carried out with RNA STAR (Galaxy version 2.5.2b-2 (Afgan et al., 2018)) and aligned reads to the feature type “exon” were quantified using HTSeq-count (Galaxy version 0.9.1 (Anders et al., 2015)). Normalization and differential expression analysis was performed with DESeq2 (Galaxy version 2.11.40.6+galaxy1 (Love et al., 2014)) to obtain log2-fold changes and adjusted p values (Benjamini-Hochberg-corrected).
Assembly: Arabidopsis thaliana (TAIR10 release-51; https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-51/fasta/arabidopsis_thaliana/)
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Surface-sterilized seeds were grown in vertically oriented 10 x 10 x 2 cm square plastic Petri dishes (10 seeds per plate). The basal media composition was 3 mM KH2PO4/K2HPO4, pH 5.8, 4 mM CaCl2, 1 mM MgSO4, 2 mM K2SO4, 3 mM MES, pH 5.8, 0.5% (w/v) sucrose, and microelements (i.e. 40 μM Na2FeEDTA, 60 μM H3BO3, 14 μM MnSO4, 1 μM ZnSO4, 0.6 μM CuSO4, 0.4 μM NiCl2, 0.3 μM Na2MoO4, 20 nM CoCl2). For growth on full nutrition (FN), 2 mM KNO3, 1 mM NH4NO3, 1 mM L-glutamine, was added, for growth on low N (LN) 0.1 mM KNO3, 50 μm NH4NO3, and 3 mM KCl was added (Scheible et al., 2004). Petri dishes were stored at 4°C for 24 to 48 hours with the lid facing upwards. Subsequently, plants were cultivated at 22°C with continuous light at a photon flux of 70 to 80 µmol·m–2·s–1.

extract_protocol:
Total RNA was extracted using Trizol.
TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: For gene expression analysis in roots under LN doses, plants were first grown for 7 days on FN medium. Subsequently, they were transferred to LN medium and incubated for two days before harvest.

value: Roots

value: LN


title: cepd, LN, rep2

description: Library name: cepd_2


title: HEK293 miRNA from control cytoplasmic fraction biol rep 1


title: HEK293 miRNA from virus infected cytoplasmic fraction biol rep 1


title: Col-0, LN, rep4

description: Library name: Col0_4

value: Col-0 wild-type


title: cepd, LN, rep1

description: Library name: cepd_1


title: cepd, LN, rep3

description: Library name: cepd_3


title: 111_T1D_BCR

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

description: 10x Genomics

data_processing:
Sequences from scRNA-seq were processed using 10x Genomics Cellranger v 7.1.0 software using the human 10x genomics refdata-gex-GRCh38-2020-A reference. V(D)J data was aligned using the 10x genomics reference refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.  Raw data generated by Cellranger were then read into R v4.2.3 using the Seurat (30) v4.3.0 R package with at least 200 genes per cell and at least 3 cells. Cells were further filtered based on the number of genes per cell and the percent of mitochondrial reads per cell by finding outliers using `perCellQCMetrics` and `perCellQCFilters` from `scuttle` based on total RNA and ADT reads and features and percent mitochondria. The data were normalized by using `NormalizeData`. For each sample, variable genes were found by using `FindVariableFeatures` followed by removal of the immunoglobulin genes from the set and data was scaled using `ScaleData`.
Doublets were removed using `DoubletFinder` using the default values except for pK, nExp, and PCs. The pK was identified using the pK associated with the maximum BCmetric value after running `find.pK` from doublet finder. All samples used PCs 1:20. The normalized and raw count tables provided are after doublet removal.
Because we noticed high amounts of tetramer expression in empty droplets, we performed scar (single cell ambient remover) on each sample individually. To run scar, we followed the recommended steps (https://scar-tutorials.readthedocs.io/en/latest/tutorials/scAR_tutorial_ambient_profile.html). The scar ADT file is the ADTs post scar background correction.
Libra seq normalization was performed on each sample individually as previously described. We read in the corrected tetramer matrices from running scar ambient background removal. Results of the libra score  are in libra_score.rda
Because we also had non-B cells captured in our sample, we used these to generate a second “Quantile” tetramer score. Within each cell type individually, we used the cell types determined above and subset to only the non-B cells. We then read in the corrected tetramer matrices from running scar ambient background removal and identified the cutoff based on the 95th quartile. We generated our score by dividing each tetramer count for each cell by the cutoff determined for the given tetramer. In this way, like the Libra score, any score greater than 1 is considered positive for a given tetramer while any score less than 1 is considered negative. This score is in the quantile_score.rda
The 16 samples were merged using the `merge` function from Seurat. The merged data was then normalized and scaled using `NormalizeData`, `FindVariableFeatures` followed by removal of the immunoglobulin genes, and `ScaleData` as described above. Dimensionality reduction and clustering were performed using `RunPCA`, `FindNeighbors`, `FindClusters`, and `RunUMAP`. `RunPCA` was run using the default values except all variable features were used for the features argument (except for immunoglobulin genes). `FindNeighbors` was run with default parameters except for the dims argument (dims=1:30). `FindClusters` was run with default parameters except for the resolution argument (resolution=0.8). `RunUMAP` was run with default parameters except for the dims and metric arguments (dims=1:30, metric=”correlation”).
We used `mnn` with the default values for batch correction methods on our data. The corrected UMAP values are in umap.csv
We made a first pass at naming clusters existing PBMC datasets as references and determined cluster identity using `clustifyr`. To identify markers of each cluster, `FindAllMarkers` was run. Genes were called differentially expressed if the adjusted p-value was less than 0.05 and the log fold change was greater than 0.5. We inspected these marker genes to determine if the cell types determined above were correct. These cell types are in the metadata.csv file.
V(D)J data was read in using `import_vdj` from `djvdj`.  Clones were identified using the `AssignGenes.py`, `MakeDb.py` and `DefineClones.py` from the Change-O package in the immcantation suite. These values are all in themetadata.csv file.
Assembly: For more information regarding data processing and the contents of these files, please visit our github https://github.com/CUAnschutzBDC/smith_nicholas_sc_antigen
Supplementary files format and content: Tab separated barcodes, features, and matrix files from cellranger output
Supplementary files format and content: Tab and comma seprated values for vdj output

molecule: polyA RNA

source_name: peripheral blood mononuclear cells

extract_protocol:
Cells were thawed in a 37 C waterbath, washed twice with 10 mL 1X PBS, and kept on ice for cell staining. Cells were stained with LIVE/DEADTM Fixable Near-IR Dead Cell Stain Kit at a 1:1500 dilution (ThermoFisher, Cat#L34975) in FACS buffer (1% BSA in 1X PBS) for 15 minutes on ice in the dark. Then, 2 ug of INS tetramer, 1 ug of IA2 and TET tetramers, and 0.75 ug of GAD and Empty tetramers in addition to 1:200 anti-human CD19-BV421 (BioLegend, Cat#363017) and 1:100 anti-human CD3-FITC (BioLegend, Cat#317305) were added to ~30e6 PBMCs in 1 mL total volume. Cells were stained on ice for 20 minutes in the dark. Finally, cells were washed twice in FACS buffer (400 x g for 5 minutes) prior to analysis on the cell sorter. After tetramer and antibody staining, cells were immediately brought to the CU Cancer Center Flow Cytometry Core. PE-binding B cells were sorted as Live/singlet/lymphocyte/CD19+/CD3-/PE+ cells into 100 uL of FACS buffer. Up to 20,000 B cells were collected, and in some instances, PE-negative binding B cells were also sorted to increase the overall yield of B cells to be captured. After the cells were sorted, they were stained with 1 uL each of the following TotalSeqC surface antibodies: anti-human IgM (BioLegend, Cat#314547), anti-human IgD (BioLegend, Cat#348245), anti-human CD27 (BioLegend, Cat#302853), anti-human CD21 (BioLegend, Cat#354923), and anti-human CXCR5 (BioLegend, Cat#356939). Cells were stained for 15 minutes on ice in the dark, washed once  (400 x g for 5 minutes), and then loaded onto the 10X Genomics system for cell capture at the CU Genomics Core.
The 10X Genomics Chromium system was used for 5’ mRNA capture with chip K according to user guide CG000330_ChromiumNextGEMSingleCell5-v2_CellSurfaceProtein_UserGuide_RevF.pdf.  The deviations from this protocol included: 1.) Overloading the chip with up to 20,000 cells per well depending on the sample, and 2.) Using the Feature Barcode Kit Primer 4 (Cat# 2000277) to detect and amplify TotalSeq C barcodes. Otherwise, the protocol was followed as written to produce gene expression, BCR V(D)J, and Feature Barcode Cell Surface Protein libraries for sequencing analysis. Library quality and quantity was determined using Agilent High Sensitivity D1000 TapeStation Screentape (Cat# 5067-5584), Reagents (Cat# 5067-5585), and Qubit DNA Quantification Assay (Cat# Q32851).

value: peripheral blood mononuclear cells

value: male

tag: age (years)

tag: ethnicity

value: not hispanic or latino

value: B cells

tag: disease stage

value: recent onset type 1 diabetic


title: 119_T1D_BCR

description: 10x Genomics


title: Col-0, LN, rep3

description: Library name: Col0_3


title: 112_T1D_BCR

description: 10x Genomics

value: female


title: 109_T1D_BCR

description: 10x Genomics

value: hispanic or latino


title: 102_T1D_BCR

description: 10x Genomics


title: Col-0, LN, rep1

description: Library name: Col0_1


title: 105_AAB_BCR

description: 10x Genomics

value: autoantibody positive


title: CS14 Ventral hind brain biological replicate1

city: London

first: Andrea

last: Streit

address: Great Maze Pond

department: CCRB

country: United Kingdom

institute: King's college London

data_processing:
sequence reads quality check using FastQC
adapter sequences and low quality reads were trimmed (FASTQ quality control)
paired end reads were aligned to human genome GRCh38 using HiSAT2 with the default parameters in the Galaxy web serve (https://usegalaxy.org/) and using GTF (downloaded from Ensembl database ) version GRCh38.105 as reference annotation file
Transcript quantification  was performed using FeatureCounts which generates the raw counts
The raw counts from all samples were normalised and differential analysis was performed using DESeq2 in R
Assembly: human GRCh38 genome
Supplementary files format and content: raw-counts-all.txt :  A tab delimited text file with the raw counts for all the samples for all the genes as generated by FeatureCounts
Supplementary files format and content: normalised-counts-OVandDHB.txt:  A tab delimited text file with the normalised counts for Otic Vesicle and dorsal hind brain for both stages for all the transcripts as generated by DESeq2 using sizefactor that account for differences in sequencing depth and library size across samples
Supplementary files format and content: normalised-counts-all.txt:  A tab delimited text file with the normalised counts for all the samples for all the transcripts as generated by DESeq2 using sizefactor that account for differences in sequencing depth and library size across samples using Dorsal hind brain (DHB) as baseline
Supplementary files format and content: OVvsDHB-CS13-deseq-results.txt:  A tab delimited text file with Differential analysis results (DESeq2 output) of the pairwise comparision of otic vesicle and dorsal hind brain from CS13 stage including all the respective biological replicates using normalised-counts-OVand DHB.txt as input
Supplementary files format and content: OVvsDHB-CS15-deseq-results.txt:  A tab delimited text file with Differential analysis results (DESeq2 output) of the pairwise comparision of otic vesicle and dorsal hind brain from CS15 stage including all the respective biological replicates  using normalised-counts-OVand DHB.txt as input
Supplementary files format and content: OVvsVHB-CS13-deseq-results.txt:  A tab delimited text file with Differential analysis results (DESeq2 output) of the pairwise comparision of otic vesicle and ventral hind brain from CS13 stage including all the respective biological replicates using normalised-counts-all.txt as input
Supplementary files format and content: OVvsVHB-CS14-deseq-results.txt:  A tab delimited text file with Differential analysis results (DESeq2 output) of the pairwise comparision of otic vesicle and dorsal hind brain from CS15 stage including all the respective biological replicates  using normalised-counts-all.txt as input
Supplementary files format and content: Gene annotation.txt:  A tab delimited text file with annotation file for cross refer the Genenames in other processed files to the ENSEMBL stable GeneID extracted from the gtf version GRCh38.105
Supplementary files format and content: sampleinfo.txt: A tab delimited text file which is an meta data file information of the tissue, stage  and sample name used in the raw count and normalised file header

source_name: Ventral hind brain

extract_protocol:
Samples were collected for two biological replicates on independent occasions . Otic vesicles (left and right) and dorsal hindbrain were isolated from CS13 and CS14 human embryos in cold L-15 medium (Thermofisher, 21083027). Tissues were collected into low-binding tubes with 40ul NEB protection buffer (T2010) on ice and frozen straight way at −80 °C. All the samples were stored at −80 °C before they were sent to Novogene for RNA sequencing.
RNA purification, library preparation and RNA Sequencing were carried out at Novogene (www.novogen.com). Generally, tissues were processed using the NEB Monarch kit (T2010) for RNA isolation. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. RNA and cDNA quality were checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina HiSeq 4000, 150bp paired end sequencing
Bulk RNA seq

value: Ventral hind brain

tag: developmental stage

value: WT


title: CS14 ventral hind brain biological replicate2


title: CS14 dorsal hind brain biological replicate1

description: for the CS14 dorsal hind brain only one biological replicate passed the QC for further processing

source_name: Dorsal hind brain

value: Dorsal hind brain


title: 114_AAB_BCR

description: 10x Genomics


title: CS14 otic vesicle biological replicate2

source_name: Otic vesicle

value: Otic vesicle


title: 118_AAB_BCR

description: 10x Genomics


title: 115_AAB_BCR

description: 10x Genomics


title: CS14 otic vesicle biological replicate1


title: CS13 Ventral hind brain biological replicate2


title: 117_AAB_BCR

description: 10x Genomics


title: CS13 ventral hind brain biological replicate1


title: CS13 dorsal hind brain biological replicate1


title: 116_ND_BCR

description: 10x Genomics

value: nondiabetic first degree relative


title: IER3 knockdown in SK-N-BE(2) RNA-seq Replicate 1

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

data_processing:
FASTQ files were mapped against a reference human genome hg38 with the splice-aware aligner STAR (v2.7.10a) to generate BAM files
Obtained aligned files (BAM format) were subjected to quantification using featureCounts from Subread package (v2.0.3). The reads were quantified for Gencode transcript annotation release v46 (corresponds to genome hg38).
Generated matrix file from read quantification was then used for differential expression (DE) analysis. DE analysis was performed using Bioconductor package DESeq2.
Assembly: hg38
Supplementary files format and content: Matrix containing tab-delimited data includes raw read count values for individual genes in each Sample.

source_name: cell line

growth_protocol: SH-SY5Y, SKNBE2 and HeLa cells were routinely cultured in DMEM media supplemented with 10% FBS.

extract_protocol:
The cells from both contrl and IER3sh stable cell lines were collected  and Total RNA extraction was carried out using ReliaPrep RNA Cell Miniprep System. For RNA sequencing.
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero from Illumina (Cat # RS-122-2201). mRNA sequencing on 100PE of DNBseq platform.

treatment_protocol: Stable shRNA cells were generated after lentival transduction of the shRNA particle followed by puromycin selection.

value: cell line

value: ShRNA


title: 106_AAB_BCR

description: 10x Genomics


title: 113_ND_BCR

description: 10x Genomics


title: CS13 dorsal hind brain biological replicate2


title: 112_T1D_ADT

description:
10x Genomics
112_barcodes.tsv.gz
112_features.tsv.gz
112_matrix.mtx.gz


title: HP253_d21_neg_c

city: Leuven

first: Ioannis

last: Papantoniou

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Protocol Quality control of raw reads was performed with FastQC v0.11.7
Adapters were filtered with Trimmomatic v0.39
Splice-aware alignment was performed with STAR against the reference genome using the default parameters
Reads mapping to multiple loci in the reference genome were discarded
Quantification of reads per gene was performed with FeatureCounts from Subread package
Assembly: hg38
Supplementary files format and content: txt file contains tab delimited tekst file with processed not normalized count matrix
Supplementary files format and content: individual tab delimited files contain counts per sample

source_name: periosteum derived cells

growth_protocol: donor derived human periosteum derived cells were cultured to P8 and seeded in microwells in either chondrogenic differentiation medium or basal medium as organoids for 21 days

extract_protocol:
RNA was isolated using the Rneasy kit (Qiagen) according to the manufacturers instructions
Library preparation was performed with the Lexogen QuantSeq FWD Sample Preparation Kit, according to the manufacturer’s protocol

tag: donor

tag: age

value: basal

tag: phenotype

tag: timepoint

value: periosteum derived cells


title: HP248_d21_mod_b

value: chondrogenic

value: HyC


title: 109_T1D_ADT

description:
10x Genomics
109_barcodes.tsv.gz
109_features.tsv.gz
109_matrix.mtx.gz

value: peripheral blood mononuclear cells


title: 105_AAB_ADT

description:
10x Genomics
105_barcodes.tsv.gz
105_features.tsv.gz
105_matrix.mtx.gz

value: male

value: not hispanic or latino

value: B cells


title: Dark, Time 8 hours, rep 2

city: Richland

first: Lindsey

middle: N

last: Anderson

state: WA

address: 3300 Stevens Dr

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

description:
Library name: sample 10 R2
D_T8_B

data_processing:
Rsubread v2.16.1
Assembly: NC007604.1 (16-NOV-2022), NC_007595.1 (16-NOV-2022), NC_004990.1 (29-OCT-2022)
Supplementary files format and content: .csv counts

organism: Synechococcus elongatus

source_name: strain PCC 7942 (FACHB-805)

growth_protocol: Cultures were maintained at 29 ± 2°C in 1.2 L Roux culture flasks containing 0.4-0.6 L of BG-11 medium supplemented with 1 g L⁻¹ HEPES (pH 8.4, adjusted with NaOH), 25 mg L⁻¹ chloramphenicol, and 25 mg L⁻¹ kanamycin to maintain cscB and sps. Cultures were diluted to OD₇₅₀ 0.2 every 4 days. Mixing was achieved using PFTE Octagon Spinbar Magnetic Stirring Bars (9.5 mm × 25.4 mm) at approximately 200 rpm, and cultures were sparged with nitrogen gas containing 2% CO₂. Light intensity at the flask surface was maintained at approximately 200 μE m⁻² s⁻¹ using Monios-L LED Full Spectrum Grow Lights. Culture samples (10 mL) were collected at 0, 2, 4, and 8 hours.

extract_protocol:
RNA was isolated using RNeasy Plus kit and QiaShredder (QIAGEN, Hilden, Germany). Frozen cell pellets were resuspended in RLT buffer containing 1% β-mercaptoethanol, passed through a QiaShredder column, and mixed with an equal volume of 70% ethanol. Subsequent RNA extraction was performed according to the manufacturer's protocol, followed by DNase treatment and quality assessment.
RNA sequencing was performed by Azenta U.S., including rRNA depletion, additional quality assessment and Illumina sequencing (2 × 150 bp, ~350M PE reads, ~105 GB, single index per lane).
RNA-Seq with rRNA depletion

treatment_protocol: Cultures were adapted to a 14:10 light-dark (LD) cycle (light period 06:00-20:00) for approximately 6 months. At time of study cells were washed and diluted to OD₇₅₀ 0.2 in fresh BG-11 and split into two cultures to enable measurements during subjective day and subjective night periods. Expression of the sucrose synthesis pathway (sps) and export system (cscB) was activated 24 hours prior to sampling by adding 1 mM IPTG. At time 0, cultures were adjusted to OD₇₅₀ 0.1 with BG-11 containing IPTG to ensure even light distribution, then divided into three biological replicates of 0.85 L per flask.

value: strain PCC 7942 (FACHB-805)

value: cscB-sps

value: night induced sucrose production 8h circadian time 20h


title: HP240_d21_neg_a


title: 114_AAB_ADT

description:
10x Genomics
114_barcodes.tsv.gz
114_features.tsv.gz
114_matrix.mtx.gz

value: female

value: autoantibody positive


title: Dark, Time 8 hours, rep 1

description:
Library name: sample 10 R1
D_T8_A


title: CS13 otic vesicle biological replicate2

value: Otic vesicle

value: WT


title: 107_ND_BCR

description: 10x Genomics

value: hispanic or latino

value: nondiabetic first degree relative


title: 110_ND_BCR

description: 10x Genomics


title: CS13 otic vesicle biological replicate1


title: 115_AAB_ADT

description:
10x Genomics
115_barcodes.tsv.gz
115_features.tsv.gz
115_matrix.mtx.gz


title: 108_ND_BCR

description: 10x Genomics


title: Dark, Time 4 hours, rep 3

description:
Library name: sample 9 R3
D_T4_C

value: night induced sucrose production 4h circadian time 16h


title: 119_T1D_ADT

description:
10x Genomics
119_barcodes.tsv.gz
119_features.tsv.gz
119_matrix.mtx.gz

value: recent onset type 1 diabetic


title: HP268_d21_mod_a

value: chondrogenic

value: FiC

value: periosteum derived cells


title: HP248_d21_neg_b

value: basal


title: 102_T1D_ADT

description:
10x Genomics
102_barcodes.tsv.gz
102_features.tsv.gz
102_matrix.mtx.gz

value: peripheral blood mononuclear cells

value: male

value: not hispanic or latino


title: HP225_d21_neg_c


title: 111_T1D_ADT

description:
10x Genomics
111_barcodes.tsv.gz
111_features.tsv.gz
111_matrix.mtx.gz

value: B cells


title: Dark, Time 8 hours, rep 3

description:
Library name: sample 10 R3
D_T8_C

value: strain PCC 7942 (FACHB-805)

value: cscB-sps

value: night induced sucrose production 8h circadian time 20h


title: 110_ND_ADT

description:
10x Genomics
110_barcodes.tsv.gz
110_features.tsv.gz
110_matrix.mtx.gz

value: female


title: 118_AAB_ADT

description:
10x Genomics
118_barcodes.tsv.gz
118_features.tsv.gz
118_matrix.mtx.gz

value: autoantibody positive


title: HP240_d21_mod_c

value: HyC


title: Dark, Time 4 hours, rep 1

description:
Library name: sample 9 R1
D_T4_A


title: 107_ND_ADT

description:
10x Genomics
107_barcodes.tsv.gz
107_features.tsv.gz
107_matrix.mtx.gz

value: hispanic or latino

value: nondiabetic first degree relative


title: 108_ND_ADT

description:
10x Genomics
108_barcodes.tsv.gz
108_features.tsv.gz
108_matrix.mtx.gz


title: Dark, Time 2 hours, rep 3

description:
Library name: sample 8 R3
D_T2_C

value: night induced sucrose production 2h circadian time 14h


title: HP449_D21a

value: chondrogenic


title: HP431_D21_neg_a


title: 113_ND_ADT

description:
10x Genomics
113_barcodes.tsv.gz
113_features.tsv.gz
113_matrix.mtx.gz


title: 117_AAB_ADT

description:
10x Genomics
117_barcodes.tsv.gz
117_features.tsv.gz
117_matrix.mtx.gz


title: 112_T1D_GEX

value: recent onset type 1 diabetic


title: 119_T1D_GEX


title: Dark, Time 2 hours, rep 2

description:
Library name: sample 8 R2
D_T2_B


title: 102_T1D_GEX


title: Dark, Time 2 hours, rep 1

description:
Library name: sample 8 R1
D_T2_A


title: HP489_D21a

value: periosteum derived cells


title: 111_T1D_GEX


title: Dark, Time 4 hours, rep 2

description:
Library name: sample 9 R2
D_T4_B

value: night induced sucrose production 4h circadian time 16h


title: HP293_D21a

value: FiC


title: HP256_D21a

value: male


title: 105_AAB_GEX

value: peripheral blood mononuclear cells

value: not hispanic or latino


title: 106_AAB_ADT

description:
10x Genomics
106_barcodes.tsv.gz
106_features.tsv.gz
106_matrix.mtx.gz

value: B cells


title: 118_AAB_GEX


title: Dark, Time 0 hours, rep 3

description:
Library name: sample 7 R3
D_T0_C

value: strain PCC 7942 (FACHB-805)

value: cscB-sps

value: night induced sucrose production 0h circadian time 12h


title: 109_T1D_GEX

value: female


title: HP431_D21_mod_c

value: HyC


title: 116_ND_ADT

description:
10x Genomics
116_barcodes.tsv.gz
116_features.tsv.gz
116_matrix.mtx.gz


title: HP495_D21_A2


title: Dark, Time 0 hours, rep 2

description:
Library name: sample 7 R2
D_T0_B


title: 114_AAB_GEX

value: autoantibody positive


title: 115_AAB_GEX

value: hispanic or latino


title: HP494_D21_A3


title: 117_AAB_GEX


title: Light, Time 16 hours, rep 3

description:
Library name: sample 6 R3
L_T16_C

value: day induced sucrose production 16h circadian time 20h


title: Dark, Time 0 hours, rep 1

description:
Library name: sample 7 R1
D_T0_A


title: 106_AAB_GEX


title: cepd tga1 tga4, LN, rep4

description: Library name: cepdtga1tga4LN_4

data_processing:
Sequence images were transformed with the Illumina BaseCaller software to BCL files, which were subsequently demultiplexed to FASTQ files with CASAVA (v1.8.2).
Using a Galaxy platform (Afgan et al., 2018), mapping of reads to the Arabidopsis thaliana genome reference sequence (TAIR10 release-51, ftp://ftp.ensemblgenomes.org/pub/plants/release-51) was carried out with RNA STAR (Galaxy version 2.5.2b-2 (Afgan et al., 2018)) and aligned reads to the feature type “exon” were quantified using HTSeq-count (Galaxy version 0.9.1 (Anders et al., 2015)). Normalization and differential expression analysis was performed with DESeq2 (Galaxy version 2.11.40.6+galaxy2 (Love et al., 2014)) to obtain log2-fold changes and adjusted p values (Benjamini-Hochberg-corrected).
Assembly: Arabidopsis thaliana (TAIR10 release-51; https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-51/fasta/arabidopsis_thaliana/)
Supplementary files format and content: tab-delimited text files include raw counts for each sample

extract_protocol:
Total RNA was extracted using Trizol.
Illumina Stranded mRNA Library Prep

treatment_protocol: For gene expression analysis in roots under FN or LN doses, plants were first grown for 7 days on FN medium. Subsequently, plants were either transferred to FN or to LN medium and incubated for two days before harvest.

value: Roots

value: tga1 tga 4 roxy6,7,8,9

value: LN


title: 113_ND_GEX

value: nondiabetic first degree relative


title: 110_ND_GEX


title: cepd tga1 tga4, LN, rep3

description: Library name: cepdtga1tga4LN_3


title: Light, Time 16 hours, rep 2

description:
Library name: sample 6 R2
L_T16_B


title: 107_ND_GEX


title: 116_ND_GEX


title: Light, Time 16 hours, rep 1

description:
Library name: sample 6 R1
L_T16_A


title: 108_ND_GEX


title: cepd tga1 tga4, LN, rep1

description: Library name: cepdtga1tga4LN_1


title: Lu139_NEUROD1_2

city: Hamamatsu

first: HIROFUMI

last: WATANABE

state: Select State

country: Japan

institute: Hamamatsu University of Medicine

library_source: genomic

data_processing:
The quality of the raw paired-end sequence reads was checked using FastQC27 version 0.11.7, and these files were trimmed to remove Illumina Nextera adapter sequence by Skewer version 0.2.2. The trimmed reads were aligned to the reference genome (hg38 assembly of the human genome) using Bowtie2 version 2.3.4.2. Then, sequence reads mapped to the mitochondrial chromosome and blacklist regions were removed by Samtools version 1.9, and PCR duplicates were removed by Picard version 2.18.11 (http://broadinstitute.github.io/picard/). Peak calling was carried out using MACS2 version 2.1.2 with parameters “—shift-75 –extsize 150 – nomodel -q 0.01”, and the called peaks of all samples were merged with Bedtools version 2.27.1. A matrix of peak counts is created with featureCounts34 version 1.6.3. The raw read counts were normalized by Trimmed mean of M values.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

growth_protocol: Cells were maintained in a 5% CO2 and 95% air incubator at 37°C.

extract_protocol:
ATAC-seq was performed using ATAC-Seq Kit (Active Motif) according to the manufacturer’s protocol.
Samples were  sequenced on the NovaSeq 6000 (Illumina).

treatment_protocol: Lu139-NEUROD1 cells, Lu139-EGFP cells, H524-ASCL1 cells, and H524-EGFP cells were treated with doxycycline for 72 hours and were collected at 2.0 × 105 cells/tube in duplicate at 4°C.

value: small cell lung cancer cell


title: Lu139_NEUROD1_1


title: Light, Time 12 hours, rep 3

description:
Library name: sample 5 R3
L_T12_C

value: day induced sucrose production 12h circadian time 16h


title: Light, Time 12 hours, rep 2

description:
Library name: sample 5 R2
L_T12_B


title: Lu139_EGFP_2


title: cepd, LN, rep3

description: Library name: cepdLN_3

value: roxy6 roxy7 roxy8 roxy9


title: Light, Time 12 hours, rep 1

description:
Library name: sample 5 R1
L_T12_A


title: Lu139_EGFP_1


title: DKO8 cells transfected with lentiviurs carrying mutant DNMT3L E103R [mE103R]

type: genomic

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Center of Epigenetics

institute: Van Andel Research Institute

description: Biological replicate 1

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
SeSAMe R package on Bioconductor V1.24.0
Average Beta

label: Cy3 and Cy5

label_protocol: Standard Illumina protocol

growth_protocol: The DKO8 cells, obtained from Dr. Stephen Baylin’s laboratory at Johns Hopkins University, were cultured in McCoy’s 5A medium (Gibco) containing 10% FBS and 1% penicillin/streptomycin. All cells were maintained at 37°C in a humidified incubator with 5% CO2 and routinely verified to be free of Mycoplasma contamination.

extract_protocol: Genomic DNA was extracted using Phenol-chloroform

treatment_protocol: To infect DKO8 cells, lentivirus was added to the culture media with 8 μg/mL polybrene (Sigma H9268). Forty-eight hours post-infection, cells were selected with 2 μg/mL puromycin until harvesting.


title: DKO8 cells transfected with lentiviurs carrying mutant DNMT3L E103R [nE103R3L]

description: Biological replicate 2


title: H524_EGFP_2


title: DKO8 cells transfected with lentiviurs carrying mutant DNMT3L with deletion of a Helix loop (Del E341 – K354) [lHEX3L]

description: Biological replicate 2


title: Light, Time 8 hours, rep 3

description:
Library name: sample 4 R3
L_T8_C

value: day induced sucrose production 8h circadian time 12h


title: cepd, LN, rep1

description: Library name: cepdLN_1


title: tga1 tga4, LN, rep4

description: Library name: tga1tga4LN_4

value: tga1 tga4


title: H524_ASCL1_2


title: DKO8 cells transfected with lentiviurs carrying mutant DNMT3L with deletion of a Beta loop (Del D311 – N319) [jBETA3L]

description: Biological replicate 2


title: cepd tga1 tga4, LN, rep2

description: Library name: cepdtga1tga4LN_2


title: cepd, LN, rep2

description: Library name: cepdLN_2


title: H524_EGFP_1


title: Light, Time 8 hours, rep 1

description:
Library name: sample 4 R1
L_T8_A

value: strain PCC 7942 (FACHB-805)


title: tga1 tga4, LN, rep3

description: Library name: tga1tga4LN_3


title: H524_ASCL1_1


title: DKO8 cells transfected with lentiviurs carrying mutant DNMT3L with deletion of a Beta loop (Del D311 – N319) [iBeta3L]

description: Biological replicate 1


title: Light, Time 4 hours, rep 3

description:
Library name: sample 3 R3
L_T4_C

value: cscB-sps

value: day induced sucrose production 4h circadian time 8h


title: cepd, LN, rep4

description: Library name: cepdLN_4


title: DKO8 cells transfected with lentiviurs carrying mutant DNMT3L with deletion of ADD domain (Del M1-E173) [hADD3L]

description: Biological replicate 2


title: Light, Time 4 hours, rep 2

description:
Library name: sample 3 R2
L_T4_B


title: OE_LARP6_3

city: YinChuan

first: Li

last: Guo

address: Victory Street

country: China

institute: Ningxia Medical University

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13).
The short reads less than 16nt were also dropped. After that, clean reads were aligned to the GRCh38 genome by HISAT2 allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
The R Bioconductor package DESeq2 was utilized to screen out the differentially expressed genes (DEGs).
The P value for correction <0.05 and fold change>2 or < 0.1.5 were set as the cut-off criteria for identifying DEGs.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified by using the ABLas pipeline as RNA binding protein connects the future described previously. In brief, ABLas detection of ten types of ASEs was based on the splice junction reads.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: MDA-MB-231 cells

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Nanodrop one (Thermo). The integrity of RNA was further verified by 1.0% agarose gel electrophoresis.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: MDA-MB-231 cells

value: LARP6 overexpression


title: tga1 tga4, LN, rep2

description: Library name: tga1tga4LN_2


title: OE_LARP6_2


title: DKO8 cells transfected with lentiviurs carrying mutant DNMT3L with deletion of ADD domain (Del M1-E173) [gADD3L]

description: Biological replicate 1


title: tga1 tga4, LN, rep1

description: Library name: tga1tga4LN_1


title: Light, Time 4 hours, rep 1

description:
Library name: sample 3 R1
L_T4_A


title: DKO8 cells transfected with lentiviurs carrying mutant DNMT3L with deletion of a Helix loop (Del E341 – K354) [kHex3L]

description: Biological replicate 1


title: DKO8 cells transfected with lentiviurs carrying wildtype DNMT3L [fWT3L]

description: Biological replicate 2


title: Light, Time 8 hours, rep 2

description:
Library name: sample 4 R2
L_T8_B


title: OE_LARP6_1


title: NC_3

value: No-load control


title: Col-0, LN, rep4

description: Library name: Col0LN_4

value: Col-0 wild-type


title: Light, Time 2 hours, rep 3

description:
Library name: sample 2 R3
L_T2_C

value: day induced sucrose production 2h circadian time 6h


title: DKO8 cells transfected with lentiviurs carrying wildtype DNMT3L [eWT3L]

description: Biological replicate 1


title: Light, Time 2 hours, rep 2

description:
Library name: sample 2 R2
L_T2_B


title: NC_2


title: DKO8 cells transfected with lentiviural empty vector [dEVDKO8]

description: Biological replicate 2


title: Col-0, LN, rep2

description: Library name: Col0LN_2

value: Roots


title: NC_1


title: Light, Time 2 hours, rep 1

description:
Library name: sample 2 R1
L_T2_A


title: DKO8 cells transfected with lentiviural empty vector [cEVDKO8]

description: Biological replicate 1


title: Light, Time 0 hours, rep 3

description:
Library name: sample 1 R3
L_T0_C

value: day induced sucrose production 0h circadian time 4h


title: LARP6-IP-2

data_processing:
Illumina NovaSeq system 6000 used for 150 nt paired-end sequencing.
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
After reads were aligned onto the genome with HISAT2 (Kim, Langmead et al 2015), the unique comparison on the genome was finally obtained, and the comparison result of PCR duplicate was removed.
After reads were aligned onto the genome, we used “ABLIRC” strategy to identify the binding regions.
The target genes of IP were finally determined by the peaks and the binding motifs of IP protein were called by HOMER software.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.

growth_protocol: The MDA-MB-231 cells line (CL-0150, Procell Life Science & Technology Co., Ltd., China) were cultured at 37℃ with 5% CO2 in DMEM (PM150210, Procell Life Science & Technology Co., Ltd., China) with 10% fetal bovine serum (FBS) (10091148, Gibco, China), 100 µg/ml streptomycin, 100 U/ml penicillin (SV30010, Hyclone, USA).

extract_protocol:
The LARP6-bound RNA was isolated from the immunoprecipitation of anti-LARP6 using Trizol (Invitrogen).
Complementary DNA (cDNA) libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8541) according the manufacturer’s procedure. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq system 6000 for 150 nt paired-end sequencing.

value: MDA-MB-231 cells (IP)


title: cepd tga1 tga4, FN, rep4

description: Library name: cepdtga1tga4FN_4

value: tga1 tga 4 roxy6,7,8,9

value: FN


title: AC18-R3

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

country: Spain

institute: University of Cordoba

data_processing:
A total of 50±10 million of reads were obtained  in two sequencing for each one of the libraries which corresponded to approximately 40-50X coverage of the total haploid genome size. These were analyzed with FastQC and trimmed with Trimmomatic when required to get rid of low-quality bases and/or adapters. Reads were then mapped to the fasta coding sequences corresponding to Olea europaea var. sylvestris genome (v1.0) using Kallisto v0.46.1.
Assembly: Olea europaea var. sylvestris genome (v1.0).
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

organism: Olea europaea var. sylvestris

source_name: stem

growth_protocol: The self-rooted plants, 6-10 month old and 40–52 cm tall, were propagated by “Plantas Continental, S.A.”, a commercial nursery located in the province of Córdoba (southern Spain), by rooting leafy stem cuttings in a pasteurised potting mix (peat:sand, 2:1, v/v) under mist conditions in plastic tunnels. Before starting the experiments, the plants were acclimated for 2 months in a greenhouse under natural lighting at a temperature of 23 ± 4◦C and a relative humidity ranging from 40% (day) to 80% (night).

extract_protocol:
Total RNA was isolated and purified from three independent biological replicates using an automated extraction system Maxwell® 16 Lev Plant RSC Instrument (manufactured by Promega Corporation, Wisconsin, USA) using a Maxwell® RSC RNA FFPE kit (AS1440, Promega, Wisconsin, USA). The process was conducted according to the manufacturer’s instructions.
Illumina’s TruSeq Stranded mRNA Library Prep Kit was used to prepare the libraries following the manufacturer’s instructions.
Briefly, each sample was enriched in mRNA by selection 3’ poly(A) tails using poly(T) magnetic beads. Captured mRNAs were then converted into cDNA, and sequencing adaptors were added to their ends to make the molecules ready for sequencing. Samples were dual-indexed for post-sequencing demultiplexing. The fragment size distribution and concentration of the libraries were checked in an Agilent 2100 Bioanalyzer using the Agilent DNA 1000 kit. These were sequenced into a HiSeq-4000 Illumina platform as 2x100b paired-end sequences.

treatment_protocol: non-treated plants

value: stem

value: non-treated plants


title: Light, Time 0 hours, rep 1

description:
Library name: sample 1 R1
L_T0_A


title: cepd tga1 tga4, FN, rep3

description: Library name: cepdtga1tga4FN_3


title: Light, Time 0 hours, rep 2

description:
Library name: sample 1 R2
L_T0_B


title: LARP6-IP-1


title: AC18-R2


title: LARP6-Input-2

value: MDA-MB-231 cells (input)


title: cepd tga1 tga4, FN, rep2

description: Library name: cepdtga1tga4FN_2


title: AC18-R1


title: Col-0, LN, rep3

description: Library name: Col0LN_3

value: LN


title: AC15-R3


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO7-Duplicate

city: Munich

first: Omar

last: El Bounkari

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia Research (ISD)

institute: LMU Klinikum

description: Library name: sampler 28

data_processing:
zUMIs pipeline
Assembly: Mus musculus: mm10
Supplementary files format and content: Tab-delimited text files contain raw counts for each WT and DKO sample als duplicates.

source_name: Liver

growth_protocol: Livers were isolated from WT and DKO mice fed a high-fat diet (HFD) for 12 weeks and were immediatly frozen in liquid nitrogen.

extract_protocol:
RNA was isolated from liver tissue using the RNeasy Mini kit (Qiagen).
Prime Seq

treatment_protocol: Tissues were dissected and placed in buffer RLT with β-mercaptoethanol, then homogenized using the TissueLyser LT (Qiagen). After centrifugation, the supernatant was mixed with 70% ethanol and processed on an RNeasy spin column for RNA isolation (Qiagen). RNA was eluted in RNase-free water, and its concentration and purity were evaluated using the Qubit RNA IQ Assay kit (Invitrogen).

value: Liver

value: Female

value: DKO

value: 12 weeks of HFD


title: LARP6-Input-1

value: MDA-MB-231 cells

value: LARP6 overexpression


title: cepd, FN, rep4

description: Library name: cepdFN_4

value: roxy6 roxy7 roxy8 roxy9


title: cepd tga1 tga4, FN, rep1

description: Library name: cepdtga1tga4FN_1


title: Apoe-/-, 12 weeks  HFD, WT2-Duplicate

description: Library name: sampler 4

value: ApoeKO

value: WT


title: Mouse colon, Control 1

value: Colon

value: Colonocytes

value: Male

value: AIN-93G Diet


title: AC15-R2

value: stem


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO7

description: Library name: sampler 27


title: CJ9 cells, endoderm differentiation, Day 4, Rep 3

city: Ankara

first: Nihal

middle: Terzi

last: Terzi Cizmecioglu

state: Select...

address: Universiteler Mah., Dumlupinar Bulvari No:1

department: Biological Sciences

country: Turkey

institute: Middle East Technical University

data_processing:
Sequence reads were trimmed for adaptor sequence and low-quality sequences via Trimmomatic tool.
Trimmed sequences were aligned to Mus musculus reference genome M25 via HISAT2 tool.
Assembly: Mus musculus M25 (GRCm38.p6)
Supplementary files format and content: Raw counts of the transcripts in a tab-delimited .txt formatted file. The first and the last columns include ensmbl gene ids and gene names, respectively.

growth_protocol: mESCs were maintained in ESC medium supplemented with LIF and antibiotics on mitotically inactivated MEFs in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA is isolated using RNeasy Plus Mini Kit (Qiagen).
PolyA+ library construction

treatment_protocol: mESCs were separated from MEFs, and passaged into 10-cm Petri dishes in Serum-free endoderm differentiation medium for 2 days. On day 2, single cell suspension is obtained and the cells are passaged into 6-cm Petri dishes in Serum-free endoderm differentiation medium supplemented with Activin A (Peprotech).

value: embryonic stem cell

value: Wild-type

value: endoderm differentiation

tag: time

value: Day 4


title: CJ9 cells, endoderm differentiation, Day 3, Rep 3

tag: cell line

value: Day 3


title: Col-0, LN, rep1

description: Library name: Col0LN_1

value: Roots

tag: genotype

value: Col-0 wild-type

value: LN


title: cepd, FN, rep3

description: Library name: cepdFN_3

value: FN


title: CJ9 cells, endoderm differentiation, Day 2, Rep 3

value: Day 2


title: AC15-R1

value: non-treated plants


title: cepd, FN, rep2

description: Library name: cepdFN_2

value: roxy6 roxy7 roxy8 roxy9


title: CJ9 cells, endoderm differentiation, Day 0, Rep 3

value: Day 0


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO6

description: Library name: sampler 25

value: Liver

value: Female

value: DKO

value: 12 weeks of HFD


title: FLOX-7

city: Shanghai

first: Hong

last: Zhang

address: 600 Yishan Road

department: Shanghai Diabetes Institute

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: Samples 8

data_processing:
The cleaned reads were aligned to the index file of the mm10 genome generated by HISAT2 version 2.0.5. Read counts for each gene were calculated by HTSeq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: BMDM

extract_protocol:
Total RNA was extracted from islets via TRIzol reagent (Thermo Fisher).
RNA libraries were constructed using VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina Vazyme, according to the manufacturer’s protocol, and paired-end reads were obtained on the NovaSeq 6000 platform.

value: BMDM

value: primary cell

value: OPA1f/f mice


title: cepd, FN, rep1

description: Library name: cepdFN_1


title: setd3Δ cells, endoderm differentiation, Day 4, Rep 3

value: embryonic stem cell

value: Setd3 knock-out

value: endoderm differentiation

value: Day 4


title: tga1 tga4, FN, rep4

description: Library name: tga1tga4FN_4

value: Roots

value: tga1 tga4


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO5

description: Library name: sampler 23


title: setd3Δ cells, endoderm differentiation, Day 3, Rep 3

value: Day 3


title: FLOX-4

description: Library name: Samples 6


title: FLOX-6

description: Library name: Samples 7


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO5-Duplicate

description: Library name: sampler 24


title: tga1 tga4, FN, rep3

description: Library name: tga1tga4FN_3

value: FN


title: FLOX-3

description: Library name: Samples 5


title: setd3Δ cells, endoderm differentiation, Day 2, Rep 3

value: Day 2


title: CKO-8

description: Library name: Samples 4

value: OPA1f/f; Lyz2-Cre mice


title: setd3Δ cells, endoderm differentiation, Day 0, Rep 3

value: Day 0


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO4

description: Library name: sampler 21

value: Liver

value: Female


title: tga1 tga4, FN, rep1

description: Library name: tga1tga4FN_1


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO4-Duplicate

description: Library name: sampler 22

value: DKO

value: 12 weeks of HFD


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO3-Duplicate

description: Library name: sampler 20


title: tga1 tga4, FN, rep2

description: Library name: tga1tga4FN_2


title: CKO-7

description: Library name: Samples 3

value: BMDM

value: primary cell


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO6-Duplicate

description: Library name: sampler 26


title: Col-0, FN, rep3

description: Library name: Col0FN_3

value: Col-0 wild-type


title: CJ9 cells, endoderm differentiation, Day 2, Rep 2

value: embryonic stem cell

value: Wild-type


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO2-Duplicate

description: Library name: sampler 18


title: CKO-6

description: Library name: Samples 2


title: CVAF_26.1d_Separate_1E12

city: Cambridge

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

institute: University of Cambridge

description: Library name: i724-i522

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to ChrM (GRCm39)
Samtools mpileup and Cutadapt to count nucleotides surrounding the editing site
Assembly: GRCm39
Supplementary files format and content: .xlsx

source_name: Skeletal muscle

extract_protocol:
Total DNA was extracted from mouse skeletal muscle using a QIAGEN blood and tissue kit as per manufaturer's instructions
Illumina NexteraXT

value: Skeletal muscle

value: mt-tRNAAla (m.5024C>T)


title: Col-0, FN, rep1

description: Library name: Col0FN_1

value: Roots


title: CVAF_26.1c_Separate_1E12

description: Library name: i723-i522


title: S72hpf_trunks

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina sequencing reads were aligned to the zebrafish mRNA reference genome (GRCz11) using the 10x Genomics CellRanger pipeline (version 3.0.2) with default parameters.
Assembly: GRCz11
Supplementary files format and content: zip compressed  files include filtered_gene_bc_matrices after running CellRanger pipeline

organism: Danio rerio

source_name: zebrafish hearts

growth_protocol: Dechorionated zebrafish embryos were maintained in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h light/dark.

extract_protocol:
A total of 1000 hearts dissected from Tg(myl7:mCherry) embryos at 72 hpf were digested in 0.25% trypsin-EDTA solution at 37 °C for 30 min.
Single-cell RNA-seq library construction was performed using a droplet-based library prep platform Chromium (10x Genomics) with a Chromium Single Cell Reagent Kit according to the manufacturer’s instructions.
Single cell RNA-Seq (10x)

value: zebrafish hearts

value: Tg(myl7:mCherry) heart cells

value: zebrafish heart cells


title: CJ9 cells, endoderm differentiation, Day 0, Rep 2

value: endoderm differentiation


title: CJ9 cells, endoderm differentiation, Day 4, Rep 2

value: Day 4


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO1-Duplicate

description: Library name: sampler 16

value: Liver


title: CVAF_26.1a_Separate_1E12

description: Library name: i721-i522


title: CVAF_26.1b_Separate_1E12

description: Library name: i722-i522


title: DAPT_2

data_processing:
Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 (GRCz11) using STAR v2.7.1a, and the aligned reads were assigned to each gene using featureCounts v1.6.0.
For each embryo, gene counts of each slice were merged into a count matrix, and the genes that received more than 0.5 counts per million reads (CPM) in at least 3 slices were retained.
The count matrixes with slice position information were constructed into DGEList objects using edgeR, which were saved in rds format.
Assembly: GRCz11
Supplementary files format and content: Expression matrix  between treatment samples and wild-type samples.

source_name: hearts

growth_protocol: Transgenic Tg(myl7:mCherry) zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h.

extract_protocol:
1 μg total RNA was extracted from Tg(myl7:mCherry) zebrafish hearts using TRIzol following the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 60 hpf Tg(myl7:mCherry) zebrafish embryos were treated with DMSO or DAPT (100 μM)  to 96 hpf.

value: hearts

value: 96 hpf

value: DAPT


title: setd3Δ cells, endoderm differentiation, Day 2, Rep 2

value: Setd3 knock-out

value: Day 2


title: CKO-2

description: Library name: Samples 1

value: BMDM

value: primary cell

value: OPA1f/f; Lyz2-Cre mice


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO1

description: Library name: sampler 15

value: Female

value: DKO

value: 12 weeks of HFD


title: CVAF_33.1c_Separate_1E12

description: Library name: i720-i522

value: Skeletal muscle

value: mt-tRNAAla (m.5024C>T)


title: Apoe-/-, 12 weeks  HFD, WT7

description: Library name: sampler 13

value: ApoeKO

value: WT


title: Col-0, FN, rep4

description: Library name: Col0FN_4

value: Roots

value: Col-0 wild-type

value: FN


title: CJ9 cells, endoderm differentiation, Day 3, Rep 2

value: embryonic stem cell

value: Wild-type

value: endoderm differentiation

value: Day 3


title: DAPT_1

value: hearts

value: 96 hpf

value: DAPT


title: Col-0, FN, rep2

description: Library name: Col0FN_2


title: setd3Δ cells, endoderm differentiation, Day 3, Rep 2

value: Setd3 knock-out


title: CVAF_32.1d_Separate_1E12

description: Library name: i719-i522


title: Apoe-/-, 12 weeks  HFD, WT6-Duplicate

description: Library name: sampler 12

value: Liver

value: Female


title: DMSO_3

value: DMSO


title: CVAF_33.1j_Separate_1E12

description: Library name: i718-i522

value: Skeletal muscle

value: mt-tRNAAla (m.5024C>T)


title: CJ9 cells, endoderm differentiation, Day 4, Rep 1

value: Day 4


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO2

description: Library name: sampler 17

value: DKO

value: 12 weeks of HFD


title: setd3Δ cells, endoderm differentiation, Day 4, Rep 2


title: CJ9 cells, endoderm differentiation, Day 3, Rep 1


title: Apoe-/-, 12 weeks  HFD, WT6

description: Library name: sampler 11

value: ApoeKO

value: WT


title: CVAF_33.1f_Separate_1E12

description: Library name: i716-i522


title: DAPT_3


title: CJ9 cells, endoderm differentiation, Day 2, Rep 1

value: embryonic stem cell

value: Wild-type

value: Day 2


title: Mif-2-/- Apoe-/-, 12 weeks HFD, DKO3

description: Library name: sampler 19


title: Apoe-/-, 12 weeks  HFD, WT5-Duplicate

description: Library name: sampler 10


title: DMSO_1

value: hearts


title: CJ9 cells, endoderm differentiation, Day 0, Rep 1

value: endoderm differentiation

value: Day 0


title: CVAF_25.1d_T2A_5E11

description: Library name: i724-i521


title: setd3Δ cells, endoderm differentiation, Day 0, Rep 2

value: Setd3 knock-out


title: setd3Δ cells, endoderm differentiation, Day 4, Rep 1


title: Apoe-/-, 12 weeks  HFD, WT5

description: Library name: sampler 9

value: Liver


title: 3M-KI-M07

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

description: Library name: 20

data_processing:
The reads were mapped to the mouse genome mm10, and raw gene read counts were generated using the Mayo Clinic RNA-sequencing analytic pipeline, MAP-RSeq
Conditional quantile normalization (CQN) on the raw gene counts was used to correct for GC bias and gene length differences and obtain similar quantile-by-quantile distributions of gene expression levels across samples.
Assembly: mm10
Supplementary files format and content: .tsv file with raw gene counts

source_name: Cortex

growth_protocol: Abca7 p.A693S knockin mice were crossed with transgenic 5xFAD amyloid model mice, and male littermates of control (5xFAD+/-; Abca7WT/WT), heterozygous knockin (5xFAD+/-; Abca7WT/KI), and homozygous knockin (5xFAD+/-; Abca7KI/KI) mice with 5xFAD background were analyzed at 3 and 10 months of age.

extract_protocol:
Total RNAs were extracted from the samples using TRIzol RNA Isolation Reagents (Thermo Fisher Scientific) and RNeasy Mini Kit with DNase (QIAGEN)
RNA libraries were prepared and sequenced with Illumina HiSeq 4000 at the Mayo Clinic Center for Individualized Medicine’s Medical Genome Facility.

value: Cortex

value: KI


title: Apoe-/-, 12 weeks  HFD, WT4-Duplicate

description: Library name: sampler 8

value: Female


title: CVAF_25.1c_T2A_5E11

description: Library name: i723-i521

value: Skeletal muscle

value: mt-tRNAAla (m.5024C>T)


title: setd3Δ cells, endoderm differentiation, Day 3, Rep 1

value: Day 3


title: 3M-KI-M06

description: Library name: 19


title: Apoe-/-, 12 weeks  HFD, WT4

description: Library name: sampler 7

value: 12 weeks of HFD


title: 3M-KI-M05

description: Library name: 18


title: CVAF_25.1b_T2A_5E11

description: Library name: i722-i521


title: Apoe-/-, 12 weeks  HFD, WT3-Duplicate

description: Library name: sampler 6

value: ApoeKO


title: setd3Δ cells, endoderm differentiation, Day 2, Rep 1


title: DMSO_2

value: 96 hpf

value: DMSO


title: setd3Δ cells, endoderm differentiation, Day 0, Rep 1

value: embryonic stem cell


title: 3M-KI-M03

description: Library name: 16


title: 3M-WT-M10

description: Library name: 15

value: Control


title: Apoe-/-, 12 weeks  HFD, WT1-Duplictate

description: Library name: sampler 2

value: WT


title: CVAF_30.1b_T2A_5E11

description: Library name: i718-i521


title: CVAF_30.1c_T2A_5E11

description: Library name: i719-i521


title: 3M-KI-M04

description: Library name: 17


title: Apoe-/-, 12 weeks  HFD, WT3

description: Library name: sampler 5


title: Apoe-/-, 12 weeks  HFD, WT1

description: Library name: sampler 1


title: 3M-WT-M8

description: Library name: 13


title: Control, replicate2, snRNAseq

city: Philadelphia

first: Klaudia

last: Kuranda

state: PA

address: 3737 Market St

department: Data Sciences

institute: Spark Therapeutics

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10 + EGFP
Supplementary files format and content: Tab-separated value files and matrix files

molecule: nuclear RNA

source_name: Striatum

extract_protocol:
Both striata from each mouse were pooled prior to nuclear isolation. Nuclei were isolated using the 10x Genomics Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) with minor modifications. First, flash-frozen tissue was transferred to ice-cold lysis buffer (from the Nuclei Isolation Kit) in a 1mL glass tissue homogenizer (Wheaton). After douncing, the tissue lysate was resuspended and left to incubate for 10min on ice. Additional steps followed the manufacturer’s instructions. During the first wash (after debris removal), the nuclear suspension was incubated with rotation for 20min at 4oC with DAPI staining solution (Abcam) at a final concentration of 5µM. Following a spin and final resuspension, nuclei with 2N DNA content were purified by fluorescence-activated nuclear sorting (Sony Cell Sorter) based on DAPI-fluorescence and collected in Wash and Resuspension Buffer (PBS, 0.5% BSA, and 0.2U/µl RNase Inhibitor - prepared according to kit instructions). Sorted 2N nuclei event count and final volume was used to inform sample loading volume, and the nuclei were immediately loaded onto 10x Chromium Single Cell 3’ Kit v3.1 chips at ~20k nuclei per sample (this loading concentration was optimized based on sorter nuclear count and 10x nuclear recovery).
Libraries were generated following the manufacturer’s protocol (single cell 3' v3 protocol, 10x Genomics)

value: Striatum

value: male

value: 9 weeks old

value: vehicle injection


title: CVAF_30.1a_T2A_5E11

description: Library name: i716-i521


title: CVAF_35.2b_T2A_2.5E11

description: Library name: i724-i520


title: Vastus Sample 15

type: RNA

city: Nashville

first: Jamey

middle: Dale

last: Young

state: Tennessee

address: 2414 Highland Ave

department: Chemical and Biomolecular Engineering

institute: Vanderbilt University

description: Animal Group is KO WD and Tissue type is Vastus

hyb_protocol: Hybridization reactions were set up by adding 10 μL of hybridization buffer, 5 μL of TagSet Master mix, 5 μL of Extension TagSet, 1 μL of 30x working probe A pool, 1 μL of 30x working probe B pool, 3 μL of DNase/RNase free water and 5 μL of RNA Sample (20 ng/μL), for a total volume of 30 μL to each sample tube. The samples were hybridized at 67°C for 16 hours

scan_protocol: The hybridized samples were then analyzed using the FLEX system’s nCounter Prep Station, and the cartridge was scanned using an nCounter Digital Analyzer to generate RCC files

data_processing:
Raw counts were processed using NanoString nSolver software. Counts were normalized to internal reference genes, and fold changes were calculated.
The reported values correspond to normalized RNA counts after background correction and normalization to internal reference genes.

label: NanoString probes

source_name: Vastus

label_protocol: No enzymatic labeling was performed. RNA was hybridized directly to NanoString nCounter custom codeset probes according to the manufacturer's standard protocol.

extract_protocol: RNA was isolated from ~30 mg of heart, gastrocnemius, and vastus using Trizol reagent (Invitrogen), according to manufacturer protocols. To eliminate phenolic impurities carried over from the Trizol extraction, we further processed the samples using a RNeasy mini kit (Qiagen, Hilden, Germany). RNA yield from each sample was determined using a NanoDrop ND-100 spectrophotometer (Thermo Scientific, Wilmington, DE), and RNA integrity was determined using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Vastus

value: MC4R KO

tag: diet

value: Western Diet


title: Vastus Sample 14

tag: tissue


title: 3M-WT-M9

description: Library name: 14

value: Cortex


title: Apoe-/-, 12 weeks  HFD, WT7-Duplicate

description: Library name: sampler 14

value: Liver

tag: cell type

value: Female


title: Vastus Sample 13


title: CVAF_25.1a_T2A_5E11

description: Library name: i721-i521

value: Skeletal muscle

value: mt-tRNAAla (m.5024C>T)


title: 3M-WT-M7

description: Library name: 12


title: Control, replicate1, snRNAseq

description: 10x Genomics

tag: strain


title: CVAF_30.2b_T2A_5E11

description: Library name: i720-i521


title: Vastus Sample 12


title: Apoe-/-, 12 weeks  HFD, WT2

description: Library name: sampler 3

value: ApoeKO

value: 12 weeks of HFD


title: CVAF_35.2d_T2A_2.5E11

description: Library name: i723-i520


title: 3M-WT-M6

description: Library name: 11


title: AAV9, replicate 2, snRNAseq

description: 10x Genomics

tag: Sex

value: AAV9-CAG-GFP injection


title: 10M-KI-M07

description: Library name: 10

value: KI


title: CVAF_34.2e_T2A_2.5E11

description: Library name: i721-i520


title: Vastus Sample 10


title: CVAF_35.1h_T2A_2.5E11

description: Library name: i720-i520


title: 10M-KI-M06

description: Library name: 9


title: AAV9, replicate 1, snRNAseq

description: 10x Genomics

tag: treatment


title: ArmYFP (epridermis) replicate 1, Stage 10-12 embryos, YFP+ cells flow cytometry sc-RNAseq

first: Katja

last: Röper

state: Cambridgeshire

address: Cambridge Biomedical Campus,, Francis Crick Ave

department: Cell Biology Division

institute: MRC LMB

description: 10X genomics

data_processing:
The demultiplexing, modified genome alignment, barcoded processing, gene counting were generated using the CellRanger software 5.0.1
Assembly: dmel6.32 (modified to include GFP and YFP sequence)
Supplementary files format and content: Tab seperated value files and matrix files

organism: Drosophila melanogaster

source_name: Drosophila embryo

extract_protocol:
Initial 3 x 1-hour pre-lay collections were discarded, then embryos were collected in 1 and 2-hour intervals on apple juice agar plates, plates were removed and left to age for 5 hours 15 minutes. Aged embryos were dechorinated in 50% bleach for 3 minutes and throughly washed in deionsied water. Embryos were screened for embryonic stage, stage 10-12 were retained and embryos beyond this stage discarded. Embryos were dissociated in a dounce homogonizer (8 strokes of loose pestle, 10 gentle passes through 16G 2-inch needle) and filtered through a 50um filter. Propidium iodide was added to the single cell suspension was sorted for negaitve propidium iodide and positive flourecent tag singal (GFP or YFP). Sorted suspension was kept on ice before library construction.
Library was constructed following manufacturers instruction (single cell 3' v3 (SrcGFP_1 and ArmYFP_1) and v3.1 (SrcGFP_2), 10X genomics)

value: Drosophila embryo

value: Epidermis

value: Isolated for Propidium iodide(-) and YFP(+) signal by Flow cytometry


title: 10M-KI-M05

description: Library name: 8


title: CVAF_35.1g_T2A_2.5E11

description: Library name: i719-i520


title: CVAF_35.2c_T2A_2.5E11

description: Library name: i722-i520


title: 10M-KI-M04

description: Library name: 7


title: CVAF_35.1e_T2A_2.5E11

description: Library name: i718-i520


title: SrcGFP (salivary gland) replicate 1, Stage 10-12 embryos, GFP+ cells flow cytometry, sc-RNAseq

description: 10X genomics

value: Salivary gland

value: w;;fkhGal4 x UAS-srcGFP

value: Isolated for Propidium iodide(-) and GFP(+) signal by Flow cytometry


title: Vastus Sample 8

description: Animal Group is KO Chow and Tissue type is Vastus

value: Vastus

value: MC4R KO

value: Chow


title: Vastus Sample 9


title: 10M-KI-M03

description: Library name: 6

value: Cortex


title: CVAF_35.1d_T2A_2.5E11

description: Library name: i716-i520


title: 10M-WT-M10

description: Library name: 5

value: Control


title: CVAF_20.1f_Vehicle

description: Library name: i720-i518

value: Skeletal muscle


title: Vastus Sample 11

value: Western Diet


title: BXD75 3

city: Los Angeles

first: Christine

last: Quach

state: CA

address: 1450 Biggy St NRT 5509

institute: University of Southern California

description:
Library name: Sample 6
21079R-05-89

data_processing:
RNA-seq data analysis was done using Partek Flow v 12.2
Sequence reads were trimmed based on quality score (min quality score 20, min length 25)
Trimmed sequence reads were mapped using STAR 2.7.3a to both genome (mm39) and transcriptome (Ensembl release109 v2)
Aligned sequence reads were quantified to Ensembl release109 v2 using Partek E/M
Gene-level read counts were filtered to exclude low-expressed genes (exclude genes where maximum <=10) and normalized (add 1 then upper quartile normalization)
Differential expression analysis was done using Partek's Gene-Specfic Analysis (GSA) analysis
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include raw read counts for each WT and BXD75 sample

source_name: Lung

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen).
10ng of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Mice were immunized with house dust mite (HDM) in Alhydrogel and 7 days later were intranasally administered HDM for 3 consecutive days.

value: Lung

value: CD4+ T cells

value: helper T cells

value: House Dust Mite


title: Vastus Sample 6


title: BXD75 2

description:
Library name: Sample 5
21079R-05-87


title: CVAF_20.1e_Vehicle

description: Library name: i719-i518

value: mt-tRNAAla (m.5024C>T)


title: 10M-WT-M9

description: Library name: 4


title: BXD75 1

description:
Library name: Sample 4
21079R-05-85


title: 10M-WT-M8

description: Library name: 3


title: Vastus Sample 4

description: Animal Group is WT Chow and Tissue type is Vastus

value: WT


title: Vastus Sample 5


title: CVAF_22.1d_Vehicle

description: Library name: i718-i518


title: WT 3

description:
Library name: Sample 3
21079R-05-83


title: Vastus Sample 3


title: SrcGFP (salivary gland) replicate 2, Stage 10-12 embryos, GFP+ cells flow cytometry, sc-RNAseq

description: 10X genomics

value: Drosophila embryo


title: WT 2

description:
Library name: Sample 2
21079R-05-81


title: CVAF_20.1a_Vehicle

description: Library name: i716-i518


title: Vastus Sample 7


title: 10M-WT-M7

description: Library name: 2


title: Vastus Sample 2


title: 10M-WT-M6

description: Library name: 1


title: WT 1

description:
Library name: Sample 1
21079R-05-79


title: Neuron, KO, ATACseq, rep1

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description: Library name: 9ATACseq_rep1d6KO

data_processing:
To remove adapter sequences from the sequencing data, raw sequencing reads were trimmed using TrimGalore (www.bioinformatics.babraham.ac.uk/).
The raw trimmed reads were aligned to the mm10 mouse genome using the bowtie2 aligner (http://bowtie-bio.sourceforge.net/).
bigWig files were generated using Galaxy (usegalaxy.org)
Assembly: mm10
Supplementary files format and content: BIGWIG (wiggle type files using the program wigToBigWig)

source_name: mESC-derived motor neuron

growth_protocol: Motor neuron differentiation of mouse embryonic stem (ES) cells was performed as described previously (Jaura and Yeh et al., Nat. Commun, 2022) with some modifications.

extract_protocol:
Cells were lysed and chromatin pellets were isolated, and then treated with Tn5 transposase.
ChIP-seq libraries were prepared according to the standard Illumina protocols. After LM-PCR amplification, library DNA was gel-purified. The purified DNA libraries were sequenced following the manufacturer's protocols.

treatment_protocol: ES cells were trypsinized and seeded at 8 x 10^4 cells per mL on day 0.1 uM retinoic acid and 0.25 uM Sonic Hedgehog Agonist were added to the medium on day 2.5 uM gamma-secretase inhibitors were added on days 4 and 5.

value: mESC-derived motor neuron


title: 6 h following Insulin exposure_rep3

city: Baltimore

first: Norman

last: Haughey

state: MD

address: 2912 Saint Paul St

institute: Johns Hopkins School of Medicine

data_processing:
Illumina HiSeq read samples at 2 x 100
Base calling with RTA version 2.4.11
BCL files were demultiplexed and converted to compressed FASTQ with filtering to strip adapters with bcl2fastq
The data were aligned to the GRCm38 reference genome using the CLCGenomicsServer with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 9.1.3 as above
FPKM vaues log2 converted (FPKM = 0 ignored as NULL) and quantile normalized with Partek Genomics Suite v6.7
Assembly: NCBI GRCm38 reference genome
Supplementary files format and content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples, contains NULLs.

source_name: Hippocampus

growth_protocol: Male C3-C57B1/6J Mus musculus were obtained from the Jackson Laboratory (Bar Harbor, ME, USA). Animals were single-housed in a temperature and humidity-controlled room under a 12 h light cycle with food and water available ad libitum. All animal procedures were approved by the Johns Hopkins University Animal Care and Use Committee.

extract_protocol:
Total RNA was extracted  from Mus musculus hippocampus using a RNeasy Mini Kit following the manufacturer's protocol (Qiagen, Venlo, Limburg)
Illumina TruSeq Stranded Total RNA kit using standard paired-end protocol.

treatment_protocol: Male C3-C57B1/6J (2-3 months of age) Mus musculus were treated with 5 ml of saline or insulin (2.4 IU) per nare at time points 0, 15 minutes, 1 h and 6 h (N=3). At the end of each time point, mice were anesthetized using isoflurane, brains were extracted, and hippocampus tissue was isolated. Tissues were flash frozen in liquid nitrogen, then stored in -80’C until further analysis.Whole genome sequencing (RNAseq) was performed on hippocampus, a brain region involved in learning and memory.

value: Hippocampus

tag: time point

value: 6 h

value: Intranasal insulin exposure


title: Vastus Sample 1

value: Vastus


title: Liver, Mif-2-/- Apoe-/-, 12 weeks HFD, DKO3

data_processing:
Galaxy platform (https://usegalaxy.org/)
FastQC software assessed the sequence quality of the raw data files. Post-quality control, the fragments underwent 5′ and 3′ adaptor trimming and were filtered to include only reads ≤20 bp using cutadapt software. The resulting trimmed reads were aligned to a reference mouse genome using HISAT2 software
The trimmed reads were aligned to a reference mouse genome using HISAT2 software
Assembly: Mus musculus: mm10
Supplementary files format and content: Tab-delimited text files contain raw counts for each WT and DKO sample.

growth_protocol: Livers were isolated from WT and DKO mice fed a high-fat diet (HFD) for 12 weeks, embedded in Tissue-Tek optimal cutting temperature (O.C.T.) compound, and immediately frozen on dry ice. Serial frozen sections, each eight micrometers thick, were then prepared.

extract_protocol:
RNA was purified from the lysates and washed with oligo dT25 magnetic beads (Thermo FisherScientific)
Smart-seq2 protocol

treatment_protocol: liver sections were treated with 50 μL of freshly prepared RNA isolation buffer containing 20% proteinase K (Qiagen) in buffer PKD (Thermo FisherScientific)

value: Liver

value: Female

tag: group

value: DKO

value: 12 weeks of HFD


title: Neuron, KO, ATACseq, rep2

description: Library name: 10ATACseq_rep2d6KO


title: Liver, Mif-2-/- Apoe-/-, 12 weeks HFD, DKO4


title: Gastroc Sample 15

description: Animal Group is KO WD and Tissue type is Gastroc

source_name: Gastrocnemius

value: Gastrocnemius

value: MC4R KO

value: Western Diet


title: 6 h following Insulin exposure_rep2


title: Gastroc Sample 14


title: Liver, Mif-2-/- Apoe-/-, 12 weeks HFD, DKO2


title: Neuron, wt, ATACseq, rep2

description: Library name: 8ATACseq_rep2d6


title: Neuron, wt, ATACseq, rep1

description: Library name: 7ATACseq_rep1d6


title: Gastroc Sample 13


title: 6 h following Insulin exposure_rep1


title: Liver, Mif-2-/- Apoe-/-, 12 weeks HFD, DKO1


title: Neuron, wt, RNAseq, day5, rep2

description: Library name: 6RNAseq_day5_rep2

data_processing:
To remove adapter sequences from the sequencing data, raw sequencing reads were trimmed using Trim Galore (www.bioinformatics.babraham.ac.uk/).
The raw trimmed reads were aligned to the mm10 mouse genome using the RNA STAR using Galaxy (www.usegalaxy.org).
BAM files were generated using Galaxy (www.usegalaxy.org)
FPKM values were generated using Cufflinks using Galaxy (www.usegalaxy.org)
Tabular files were generated using Galaxy (www.usegalaxy.org)
Assembly: mm10
Supplementary files format and content: tabular (FPKM, Fragments Per Kilobase per Million mapped fragments)

extract_protocol:
Cells were collected, poly(A)+ RNA was homogenized in a phenol-containing solution, and the sample was isolated by standard ethanol precipitation.
RNA-seq libraries were prepared according to the standard Illumina protocols. Briefly, cDNA was synthesized from RNA, end-repaired, and ligated to sequencing adaptors, then PCR amplified and gel purified. The purified DNA libraries were sequenced following the manufacturer's protocols.

treatment_protocol: ES cells were trypsinized and seeded at 8 x 10^4 cells per mL on day 0. 1 uM retinoic acid and 0.25 uM Sonic Hedgehog Agonist were added to the medium on day 2. 5 uM gamma-secretase inhibitors were added on days 4 and 5.


title: Gastroc Sample 12


title: 1 h following Insulin exposure_rep3

value: 1 h


title: Liver, Apoe-/-, 12 weeks  HFD, WT5

value: Apoe-/-


title: Neuron, wt, RNAseq, day5, rep1

description: Library name: 5RNAseq_day5_rep1


title: Gastroc Sample 11


title: 1 h following Insulin exposure_rep2


title: Neuron, wt, RNAseq, day4, rep3

description: Library name: 4RNAseq_day4_rep3


title: Liver, Apoe-/-, 12 weeks  HFD, WT4


title: Gastroc Sample 10


title: 1 h following Insulin exposure_rep1


title: Liver, Apoe-/-, 12 weeks  HFD, WT3


title: Neuron, wt, RNAseq, day4, rep2

description: Library name: 3RNAseq_day4_rep2


title: Liver, Apoe-/-, 12 weeks  HFD, WT2


title: Neuron, wt, RNAseq, day4, rep1

description: Library name: 2RNAseq_day4_rep1


title: Gastroc Sample 9

description: Animal Group is KO Chow and Tissue type is Gastroc

value: Chow


title: 15 min following Insulin exposure_rep3

value: 15 min


title: 15 min following Insulin exposure_rep1


title: Liver, Apoe-/-, 12 weeks  HFD, WT1

value: WT


title: Gastroc Sample 8


title: Control (treated with saline)_rep2

value: 0 min

value: Untreated


title: Control (treated with saline)_rep3

value: Hippocampus


title: Neuron, wt, RNAseq, day0, rep1

description: Library name: 1RNAseq_day0_rep1

value: mESC-derived motor neuron


title: Prickle1 f/f, uterus

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: 10x Genomics Chromium Single Cell Gene Expression data

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-6.1.1).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference (refdata-gex-mm10-2020-A) and analyzed using "cellranger count".
Assembly: mm10
Supplementary files format and content: cellranger generated unfiltered feature-barcode matrix file.

source_name: uterus

extract_protocol:
Uteri were processed by mincing the tissue and digesting in DMEM (Gibco, Waltham, MA), 10% FBS (Atlanta Biologicals, Flower Branch, GA), 1.5mg/ml collagenase (Gibco, Waltham, MA), and 2400U of DNaseI (NEB, Ipswich, MA) for 5 hours in a shaking water bath at 37°C. After digestion, cells were centrifuged at 300g for 5 minutes and treated with ACK lysis buffer followed by two washes with 1X PBS and 2% FBS. Cells were passed through a 100um cell strainer and resuspended in 1X PBS and 2% FBS. Cells were passed through a 40um cell strainer and resuspended in 1X PBS and 2% FBS.
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).
Single Cell RNA-seq (10X Genomics Chromium Single Cell 3' v3)

value: uterus

value: female

value: wild-type


title: Gastroc Sample 7


title: Prickle1 f/f MiC, uterus


title: hippocampus, 6month,knockout-3

city: beijing

first: HAN

last: WANG

state: beijing

address: peking university

institute: peking university

data_processing:
The sequencing quality were assessed with FastQC (v0.11.5)[1] and then low quality data were filtered using NGSQC (v2.3.3)
Gene expression analyses were performed using StringTie (v1.3.3b), and differential gene expression was assessed with DESeq (v1.28.0).
p-values were corrected by FDR method, and Corrected p-values (q-values) were calculated by correcting using BH method. Both p-values and q-values were used for significance analysis, with significantly differentially expressed genes defined as those with p ≤ 0.05.
The annotations of the DEGs were performed based on the information obtained from the database of ENSEMBL, NCBI, Uniprot, GO, and KEGG.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: hippocampus

growth_protocol: WT C57BL/6 mice  and SSTR3-/- mice were were maintained in compliance with the Animal Care and Use guidelines of Peking University (approval no. LSC-ZhangY-1),  according to standard guidelines with ad libitum access to food and water under a 12::12 hr light/dark cycle.

extract_protocol:
Total RNA was extracted from freshly dissected tissue using the TRNzol Reagent kit (DP405, Tiangen) according to the manufacturer's instructions.
Total RNA samples that meet the following requirements were used in subsequent experiments: RNA integrity number (RIN) > 7.0 and a 28S:18S ratio > 1.8.RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China). The triplicate samples of all assays were constructed an independent library, and do the following sequencing and analysis. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing. NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit was used to enrich the poly(A) tailed mRNA molecules from 1 μg total RNA.

value: hippocampus

tag: strain background

value: SSTR3 knockout


title: hippocampus, 6month,knockout-2


title: Gastroc Sample 4

description: Animal Group is WT Chow and Tissue type is Gastroc

value: Gastrocnemius


title: Gastroc Sample 5

value: MC4R KO


title: H427_SCAT_diff_adip

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

institute: CIMA

description: Library name: Sample 23

data_processing:
Samples were aligned to the Human genome (GRCh38) with STAR (v2.6.1). Gene expression was quantified with quant3p (github.com/ctlab/quant3p).
Downstream analyses were performed in R (v3.6.2). Data transformation, normalization, and differential gene expression analysis were performed with DESeq2. Genes were considered adjusted p value (p-adj)<0.05 and absolute log transformed fold-change (|log2FC|)>1, unless otherwise indicated. vst expression values were used for data visualization and unsupervised analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes filtered counts for all the cell types, treated and control.

source_name: subcutaneous adipose tissue (gluteus-femoral zone)

growth_protocol: Adipocytes and MSCs were harvested from the bone marrow portion of the femoral head and metaphysis and from the SCAT of OA patients. Tissues were minced into small pieces and treated with collagenase. Collection of the floating layer after each centrifugation provided a pure fraction of floating adipocytes and were used directly for total RNA isolation. The pellets containing MSCs after the first wash were placed in 5 cm2 cell culture flasks with DMEM medium supplemented with 10% FBS, 1% Pen-Strep, 1% L-Glutamine and basicFGF 5mg/mL in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions. The transcriptome of very low input (<10ng), degraded or high integrity samples was examined using Takara’s SMARTer Stranded Total RNA-Seq Kit v2 as indicated by the manufacturer.
RNA was fragmented according to the integrity of the sample, then reverse-transcribed (including a template-switching step) and PCR-amplified with primers bearing Illumina adapters and indexes. Next, cDNA originating from rRNA (18S, 28S as well as mitochondrial m12S and m16S) was depleted and the remaining molecules amplified through PCR. Libraries were quantified with Qubit dsDNA HS Assay Kit and their profile was examined using Agilent’s HS D1000 ScreenTape Assay.

treatment_protocol: For differentiation assays, MSCs (5x105/cm2) were cultured in DMEM High Glucose, 10% FBS, 1% Pen-Strep, 1% L-Glutamine supplemented with IBMX (3-isobutyl-1-méthylxanthine) 0.5mM, Dexamethasone 1μM and Indomethacin 50 μM.

value: primary cell line

value: adipocytes

value: Osteoarthritis donor

value: adipogenic differentiation


title: hippocampus, 6month,knockout-1


title: H427_META_primary_adip

description: Library name: Sample 22

source_name: metaphyseal bone (femoral neck)

value: metaphyseal bone (femoral neck)

value: primary cell


title: Gastroc Sample 3

value: WT

value: Chow


title: Gastroc Sample 2


title: Gastroc Sample 6


title: H427_META_diff_adip

description: Library name: Sample 21


title: Gastroc Sample 1


title: hippocampus, 6month,control-2

value: control


title: H427_EPI_primary_adip

description: Library name: Sample 20

source_name: epiphyseal bone (femoral head)

value: epiphyseal bone (femoral head)


title: Control (treated with saline)_rep1

value: Hippocampus

value: 0 min

value: Untreated


title: Heart Sample 15

description: Animal Group is KO WD and Tissue type is Heart

source_name: Heart

value: Heart

value: Western Diet


title: Lu139 NEUROD1 dox+ #2

city: Hamamatsu

first: HIROFUMI

last: WATANABE

institute: Hamamatsu University of Medicine

description: Gene expression data from SCLC cells

hyb_protocol: Incubate the array at 45℃ for 16 hours (60 rpm) using the GeneChip™ Hybridization Oven 645 (Thermo Fisher Scientific) according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned using the GeneChip™ Scanner 3000 7G  (Thermo Fisher Scientific).

data_processing: Expression Console™ Software  (Thermo Fisher Scientific) was used.Raw data of expression values were normalized by Signal Space Transformation-Robust Multiarray Analysis (SST-RMA) method.

label: biotin

source_name: Lu139 NEUROD1 dox+

label_protocol: Total RNA (250 ng) was isolated. Fragmented and labeled cDNA samples were prepared using the GeneChip™ WT PLUS Reagent Kit (#902281, Thermo Fisher Scientific) according to the  the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (#74136, QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: RNA was extracted from Lu139-NEUROD1 cells, Lu139-EGFP cells, H524-ASCL1 cells, and H524-EGFP cells with or without doxycycline treatment for 72 hours (triplicate for each cell line).

value: small cell lung cancer


title: Lu139 NEUROD1 dox+ #1

description: Gene expression data from SCLC cells


title: hippocampus, 6month,control-1

value: hippocampus


title: H427_EPI_diff_adip

description: Library name: Sample 19

value: primary cell line


title: H427_SCAT_primary_adip

description: Library name: Sample 24

value: subcutaneous adipose tissue (gluteus-femoral zone)

value: adipocytes


title: Lu139 NEUROD1 dox- #3

description: Gene expression data from SCLC cells

source_name: Lu139 NEUROD1 dox-


title: Lu139 NEUROD1 dox+ #3

description: Gene expression data from SCLC cells


title: Heart Sample 13

value: MC4R KO


title: Heart Sample 14


title: Lu139 NEUROD1 dox- #2

description: Gene expression data from SCLC cells


title: Lu139 EGFP dox+ #2

description: Gene expression data from SCLC cells

source_name: Lu139 EGFP dox+


title: 783 785 RIP REP2

city: Buffalo

first: John

middle: C.

last: Panepinto

state: NY

address: 955 Main Street Suite 5240

department: Microbiology and Immunology

institute: University at Buffalo

description: IP RNA

data_processing:
Adapter sequences were trimmed and quality filtering performed using Cutadapt (-q 20 -m 1 -a AGATCGGAAGAG -A AGATCGGAAGAG).
Trimmed reads were then checked for quality using FastQC.
Reads were mapped to the genome using STAR aligner (--runThreadN 6 --runMode alignReads).
Transcipt counts were quantified usin RSEM. (-p 12)
Differential expression was determined using DeSeq2 in R.
Assembly: FungiDB-54_CneoformansH99
Supplementary files format and content: Quant_all.xlsx - contains all counts from RSEM

organism: Cryptococcus neoformans

source_name: Puf4FLAG- 783/785 RtoK mutant

growth_protocol: Cells were grown overnigt to OD600 of 1.5-18 stage in YPD at 30 ˚C.

extract_protocol:
RNA was extracted using low pH phenol chloroform and Dnase treated using Ambion DNA free kit.
Library prep was performed using NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: Untreated

value: Puf4FLAG- 783/785 RtoK mutant


title: H426_SCAT_primary_adip

description: Library name: Sample 18

value: Osteoarthritis donor

value: primary cell


title: hippocampus, 6month,control-3

value: WT


title: H426_SCAT_diff_adip

description: Library name: Sample 17

value: adipogenic differentiation


title: 462 RIP REP2

description: IP RNA

source_name: Puf4FLAG- 462 RtoK mutant

value: Puf4FLAG- 462 RtoK mutant


title: Lu139 EGFP dox+ #3

description: Gene expression data from SCLC cells


title: Heart Sample 12


title: Lu139 EGFP dox+ #1

description: Gene expression data from SCLC cells


title: Heart Sample 11


title: H426_META_primary_adip

description: Library name: Sample 16

value: metaphyseal bone (femoral neck)


title: H426_META_diff_adip

description: Library name: Sample 15


title: H99 RIP REP2

description: IP RNA


title: Heart Sample 10


title: Lu139 NEUROD1 dox- #1

description: Gene expression data from SCLC cells


title: 462 INPUT REP2

description: Total RNA


title: PUF4FLAG RIP REP2

description: IP RNA


title: Lu139 EGFP dox- #2

description: Gene expression data from SCLC cells

source_name: Lu139 EGFP dox-


title: H426_EPI_primary_adip

description: Library name: Sample 14

value: epiphyseal bone (femoral head)


title: Heart Sample 8

description: Animal Group is KO Chow and Tissue type is Heart

value: Chow


title: 783 785 INPUT REP2

description: Total RNA


title: Heart Sample 9

value: Heart


title: H426_EPI_diff_adip

description: Library name: Sample 13


title: Heart Sample 7


title: H411_SCAT_primary_adip

description: Library name: Sample 12


title: Lu139 EGFP dox- #3

description: Gene expression data from SCLC cells


title: Lu139 EGFP dox- #1

description: Gene expression data from SCLC cells


title: H411_SCAT_diff_adip

description: Library name: Sample 11


title: PUF4FLAG INPUT REP2

description: Total RNA


title: H524 EGFP dox+ #2

description: Gene expression data from SCLC cells

source_name: H524 EGFP dox+


title: H524 EGFP dox+ #3

description: Gene expression data from SCLC cells


title: 783 785 RIP REP1

description: IP RNA


title: Heart Sample 5


title: H411_META_primary_adip

description: Library name: Sample 10


title: H524 EGFP dox+ #1

description: Gene expression data from SCLC cells


title: H99 INPUT REP2

description: Total RNA


title: 462 RIP REP1

description: IP RNA


title: H411_META_diff_adip

description: Library name: Sample 9


title: Heart Sample 4

description: Animal Group is WT Chow and Tissue type is Heart


title: H524 EGFP dox- #2

description: Gene expression data from SCLC cells

source_name: H524 EGFP dox-


title: PUF4FLAG RIP REP1

description: IP RNA


title: Heart Sample 3


title: H411_EPI_primary_adip

description: Library name: Sample 8


title: H524 EGFP dox- #3

description: Gene expression data from SCLC cells


title: H99 RIP REP1

description: IP RNA


title: H411_EPI_diff_adip

description: Library name: Sample 7


title: Heart Sample 2


title: 783 785 INPUT REP1

description: Total RNA


title: Heart Sample 1


title: 462 INPUT REP1

description: Total RNA


title: H524 EGFP dox- #1

description: Gene expression data from SCLC cells


title: Output pool, covST282A, Biological Replicate 1

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description:
Library name: T282A_rep1
PCR
SuppTableS4_revision.xlsx

data_processing:
2FAST2Q v 2.6 was used to extract and quantify the protospacer abundance in each sample (parameters: Phred score 30, no mismatches allowed).
Count data were analyzed using R version 4.0.5 and the Bioconductor package DESeq2 version 1.30.1 with default parameters (alpha 0.05, log2FCtest 1). Pairwise comparison was performed for WT, Delta CovR, CovRD53A and CovST282A samples (2 biological replicates), and raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and protospacer with an adjusted p-value lower than 0.05 were considered differentially distributed. (2 biological replicates). Sequencing data from the vectors (input pool) have been used for normalisation.
Supplementary files format and content: 2fast2q output and DESeq 2 output matrix
Library strategy: Amplicon-seq

organism: Streptococcus agalactiae

source_name: bacterial cell

growth_protocol: Input pools in E. coli were grown in LB supplemented with 25 µg/ml kanamycin. Ouput pools in GBS were selected on THY supplemented with 500 µg/ml kanamycin.

extract_protocol:
Plasmid purification were done with QIEprep Spin Miniprep (Qiagen) following instructions for large vector (>10kb).
PCR amplification (25 cycles) were done with Phusion+ high fidelity polymerase (NEB). PCR products were gel purified (QIAquick PCR, Qiagen). Illumina adaptaters were added (PCR-free) following provider workflow (Novogen).

value: bacterial cell


title: H524 ASCL1 dox+ #3

description: Gene expression data from SCLC cells

source_name: H524 ASCL1 dox+

value: small cell lung cancer


title: H410_SCAT_diff_adip

description: Library name: Sample 5


title: PUF4FLAG INPUT REP1

description: Total RNA


title: Output pool, covRD53A, Biological Replicate 2

description:
Library name: D53A_rep2
PCR
SuppTableS4_revision.xlsx


title: Output pool, covST282A, Biological Replicate 2

description:
Library name: T282A_rep2
PCR
SuppTableS4_revision.xlsx


title: Heart Sample 6


title: H524 ASCL1 dox+ #1

description: Gene expression data from SCLC cells


title: H410_META_diff_adip

description: Library name: Sample 3


title: H524 ASCL1 dox- #3

description: Gene expression data from SCLC cells

source_name: H524 ASCL1 dox-


title: H524 ASCL1 dox+ #2

description: Gene expression data from SCLC cells


title: H99 INPUT REP1

description: Total RNA


title: Input pool, technical replicate 5

description:
Library name: Input_rep5
PCR
SuppTableS4_revision.xlsx

organism: Escherichia coli