title: RNA-seq Ad-ShCebpb dual 8h 3

treatment_protocol: primary hepatocytes were isolated from male, 8-10 weeks-old mice (strain C57BL/6JOlaHsd). Three hours after plating, PMH were infected with adenovirus: Ad-ShCebpb. After 12 h, hormones (Glucagon 100 nM , corticosterone 1 µM or a dual treatment)  were added for 8h and downstream experiments.

tag: infection

value: Ad-ShCebpb

value: dual 8h


title: naah_line,rep1,d4

status: Public on Aug 18 2024

type: SRA

city: Poznan

first: Ireneusz

last: Stolarek

address: Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry Polish Academy of Sciences

library_source: transcriptomic

data_processing:
Data were quality trimmed with TrimGalore
FASTQ files were quasialigned to the gencode v39 human reference transcriptome with salmon
Assembly: Gencode v39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: naah

growth_protocol: The Pluripotency rate of the obtained cells was characterized by Sox2 and Nanog immunochemistry. The induced pluripotent stem cells (iPSCs) were cultured on the GeltrexTM (Thermo Fisher Scientific A1413301) coated 12-well plates in Essential 8™ Medium (ThermoFisher Scientific A1517001).

extract_protocol:
The RNA was extracted from the iCMs on day four and day 30. Cells were first washed with PBS and dissociated from the plate either by 3 minutes incubation in 37°C with PBS with EDTA (4 days iCMs) or 5-10 minutes incubation with TrypLE™ (Thermo Fisher Scientific 12604013) (30 days iCMs). Dissociated cells were washed with medium from the plate and collected in 15ml falcon tubes. The centrifugation for 3min/1300rpm/RT allowed us to obtain the cell pellet. The supernatant was discarded, and the cell pellet was washed with cold PBS twice and centrifuged at 4min/2000rpm/4°C. Finally, the cell pellet was resuspended in 1ml of TRIzol™ Reagent (Thermo Fisher Scientific 15596026) or 200µl of RNAlater (Sigma-Aldrich R-0901) and stored at -20°C for further RNA extraction. Standard phenol/chloroform protocol was used to isolate RNA from TRIzol™ Reagent samples. Total RNA isolation from RNAlater collected samples was conducted with mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific AM1561). The obtained RNAs' amount and quality were measured on a Multiskan SkyHigh Microplate Spectrophotometer (Thermo Scientific). The 500ng of RNA was used as a template to generate complementary DNA with SuperScript™ IV First-Strand Synthesis System with ezDNase™ Enzyme (Thermo Fisher Scientific 18091150). Reverse transcription was conducted using a thermal cycling program: 23°C/10 minutes, 55°C/10min, and 80°C/10 min on T100 Thermal Cycler (Bio-Rad).
For each sample, RNA libraries were prepared from 100 ng RNA using the KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems) according to manufacturer’s protocol, followed by quality check using Fragment Analyzer (Agilent). The libraries were normalized and pooled, and then sequenced using NovaSeq6000 platform (Illumina) to an average of 120 M 151 bp paired-end reads per sample.

treatment_protocol: iPSCs next differentiated to iCMs using the PSC Cardiomyocyte Differentiation Kit according to the manufacturer's instructions (ThermoFisher Scientific A2921201). After eight days, cells became contracting iCMs and were further cultured in PSC Cardiomyocyte Maintenance Medium (Thermo Fisher Scientific A2920801) for at least 30 days. TNNT2 expression was used as a measure of differentiation efficiency. All cells in culture were maintained at 37°C in incubators with 5% CO2.

tag: cell line

value: naah

tag: cell type

value: iPSC-iCM

tag: genotype

value: WT

tag: treatment

value: cardiomyocyte differentiation


title: RNA-seq Ad-ShCebpb dual 8h 2

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Assembly: mm10
Supplementary files format and content: BAM files contain aligned reads

organism: Mus musculus

source_name: primary hepatocytes

extract_protocol:
Total RNA was isolated from primary mouse hepatocytes using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer’s protocol.
For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421).

value: primary hepatocytes

value: wt


title: non-stimulated cardiac fibroblasts, A

city: NYC

first: Izabela

last: Tuleta

state: NY

address: 1300 Morris Park Avenue

department: Cardiology

country: USA

institute: Albert Einstein College of Medicine

description:
EVA
Mouse cardiac fibroblasts at passage 2 were cultured with empty plasmid.

data_processing:
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads by CASAVA base recognition (Base Calling).
The library preparations were sequenced on Illumina NovaSeq 6000 devices, generating 100 bp paired end reads. Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis
Quality Phred Scores, Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (December 2011 release of the mouse musculus reference genome (mm10; GRCm38.p6) from Ensembl) using TopHat2 algorithm alignment program v.2.0.
Mapped reads were assembled using both Scripture (beta2) and Cufflinks v.2.1.1 algorithm
HTSeq software v.0.6.1 was used to count the number of reads mapped to each gene. Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM), was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length
Assembly: mm10
Supplementary files format and content: excel files including raw gene counts for every gene and every sample
Supplementary files format and content: excel files including FPKM values counts for every gene and every sample

molecule: polyA RNA

source_name: Cardiac fibroblasts

extract_protocol:
RNA was extracted with Trizol reagent.
RNA sequencing was performed by Novogene. RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq. Library preparation was performed by Novogene, Inc., using at least 1 ug high-quality total RNA input per sample. mRNA enrichment was performed with poly-T oligo-attached magnetic beads. Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: Transformed E. coli bacteria in stab culture were used as a source of plasmids: 1. plasmid containing murine THBS4 ( pAAV.CMV.SV40.THBS4-HA.SV40(polyA), #155193, Addgene, Watertown, MA) and 2. empty plasmid serving as a control (pAAV-CA, #69616, Addgene, Watertown, MA). After transfection, medium with plasmid was discarded and replaced by standard medium without antibiotics for 12 hours. Thereafter, cells were serum deprived for 24h (for RNA) or 48h (for proteins) and collected for subsequent experiments. Efficiency of TSP-4 overexpression was confirmed using western blotting.

value: cardiac fibroblasts

tag: strain

value: Cardiac fibroblasts were cultured in the presence of empty plasmid


title: ATAC_ddmsn_B

first: Naama

last: Barkai

address: Herztel 234

department: Molecular genetics

institute: Weizmann institute of science

description: ATAC-seq msn2/4 double deletion sample 2

library_source: genomic

data_processing:
Reads were aligned to the S. cerevisiae genome (SacerR64) using bowtie2 with parameters: --very-sensitive --trim-to 30 –dovetail.
The coverage was calculated on the 5’ position of each read.
Reads larger than 140 bps were discarded using genome coverage and the repetitive region in chromosome 12 (451600:489500) was removed.
Reads of each sample were normalized to 10^7.
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: csv files containing signalacroos each chromosome (columns)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: BY4741; ddmsn

extract_protocol:
The main steps of our ATAC-seq protocol are outlined here; for detailed information, please refer to the Methods section. Cells were cultured as described in the MPBA protocol until reaching an OD600 of 4, then spheroplasted using lyticase. The resulting spheroplasts were treated with RNase-A. Subsequently, a tagmentation reaction was performed using in-house produced Tn5 transposase loaded with Tn5MEDS-A/B oligonucleotides. The reaction was terminated after 1 hour using SDS and Proteinase K
The eluted samples were used as a template for a PCR reaction for amplifying Tn5 tagmented fragments and sample barcoding (2× Kappa HIFI [Roche], 5 μL nextera primers F: i5, R: i7; 12 cycles; see primer list in Supplementary Table 4). Next, samples were 0.65x reversed SPRI cleaned and resuspended in 22 μL elution buffer (10mM Tris-HCl, pH 8), then concentrations and library quality were validated using Qubit and tape station (Agilent).
ATAC-seq; Libraries were sequenced using the NovaSeq 6000 machine. Runs were performed with the S1 kit (20028319), parameters: R1 - 61 cycles, Index1 - 8 cycles, Index2 - 8 cycles, R2 - 61 cycles.

value: BY4741; ddmsn

value: msn2/4 double deletion


title: non-stimulated cardiac fibroblasts, D

description:
CtrlD
Mouse cardiac fibroblasts at passage 2 were cultured in the absence of recombinant mouse TSP-4

growth_protocol: Cardiac fibroblasts were isolated from 12-week old mouse (C57BL/6) hearts.

treatment_protocol: Following serum starvation overnight mouse cardiac fibroblasts at passage 2 were cultured in the presence or absence of recombinant mouse TSP-4 (10ng/ml, AF2390-SP, R&D Systems). At the end of the experiment, cells were washed 2x with PBS and TRIzol was added to extract RNA.

value: Cardiac fibroblasts were cultured in the absence of TSP-4 (10ng/ml)


title: naah_line,rep2,d2


title: RNA-seq Ad-ShCebpb dual 8h 1


title: cardiac fibroblasts with TSP-4 overexpression, C

description:
THBS4plC
Mouse cardiac fibroblasts at passage 2 were cultured with TSP-4 plasmid.

value: Cardiac fibroblasts were cultured in the presence of TSP-4 plasmid


title: non-stimulated cardiac fibroblasts, C

description:
CtrlC
Mouse cardiac fibroblasts at passage 2 were cultured in the absence of recombinant mouse TSP-4


title: RNA-seq cort 8h 2

treatment_protocol: Primary hepatocytes were isolated from male, 8-10 weeks-old mice (strain C57BL/6JOlaHsd). Three hours after plating, media was changed to Williams E media. After 18 h, hormones (corticosterone 1 µM, Wy14643 10 µM or a dual treatment)  were added for 8h.

value: 1uM cort 2 8h


title: ATAC_ddmsn_A

description: ATAC-seq msn2/4 double deletion sample 1


title: fem_line,rep2,d30

source_name: fem

value: fem


title: ATAC_BY_B

description: ATAC-seq wild-type sample 2

value: Wild-type


title: ATAC_BY_A

description: ATAC-seq wild-type sample 1


title: RNA-seq Ad-ShCebpb cort 8h 3

value: Ad-ShCebpb

value: cort 8h


title: RNA-seq Ad-ShCebpb cort 8h 2


title: non-stimulated cardiac fibroblasts, B

description:
CtrlB
Mouse cardiac fibroblasts at passage 2 were cultured in the absence of recombinant mouse TSP-4


title: non-stimulated cardiac fibroblasts, A

description:
CtrlA
Mouse cardiac fibroblasts at passage 2 were cultured in the absence of recombinant mouse TSP-4


title: fem_line,rep2,d15


title: RNA-seq Ad-ShCebpb cort 8h 1


title: MP1_subset28_pool2_S1

library_source: other

data_processing:
demultiplexing with bcl2fastq
forward primer removal using 'cutadapt'
sample demultiplexing using adapter removal
count number of read for each library variant
generate csv files
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: csv. Each file contains data for of all timepoint and repeats for TF a given library in a given experiment
Library strategy: Massively Parallel Binding Assay (Amplicon based PCR)

molecule: other

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
In this method we extract plasmid DNA from yeast, serving as a template for by a PCR reaction which is the first step of the library preparation protocol. Plasmid DNA was extracted using the MasterPure Yeast DNA Purification Kit (Lucigen Corporation, MPY80200), with some modifications. Briefly, 300 ul of lysis buffer supplemented with RNase A (as recommended) were added to each sample. Following 15 minutes of incubation in 65 C, cells were moved into LoBind microcentrifuge tubes (Eppendorf®, 022431021) containing 0.5mm Zirconium Oxide beads (ZrOB05, Next Advance) and blended using the Bullet Blender 24 (Next Advance) for a single cycle of 3 minutes in level 8. Samples were cooled over ice and lysates were moved to 1.5 ml tubes, vortexed, and supplemented with 300 ul MPC buffer. Samples were vortexed vigorously and centrifuged for 10 minutes (17,000g). Supernatant was moved to 1.5 ml tubes containing 500 ul isopropanol. Samples were vortexed vigorously and DNA was precipitated (10 minutes, 17,000g). Isopropanol was removed, and pellets were washed in 70% EtOH, then air dried and finally resuspended in TE buffer.
Following DNA extraction, samples were 1.5 X SPRI (AMPure XP, A63881) cleaned and resuspended in 30 ul elution buffer (10mM Tris-HCl, pH 8) and then diluted 1:20. 1 ul was used as a template for PCR reaction for amplifying noncleaved variants and sample barcoding (28 cycles) using the Phusion® High-Fidelity PCR Master Mix (NEB, M0531L). Samples were verified using gel electrophoresis, and 0.5 reversed-SPRI cleaned. DNA concentrations were measured using Qubit™ Flex Fluorometer (Invitrogen), and samples were normalized to equal amounts, then pooled together. 1 ng was taken as a template for a PCR reaction using KAPA HiFi HotStart ReadyMix (Roche, KK2602) for adding iIlumina indices and machine adapters. Samples were 1X SPRI cleaned, then concentrations and library quality were validated using Qubit and tape station (Agilent).

treatment_protocol: Massively Parallel Binding Assay (MPBA), a novel method allowing parallel measurement of transcription factor (TF) binding to thousands of DNA sequence-variants within cells. In this project we apply it to quantify binding of dozens of TFs to libraries of mutated regulatory regions, systematically screening all motif combinations. In brief, we integrate a library of DNA variants into a designed plasmid and transform it into cells carrying an endogenous TF of interest fused to a Micrococcal Nuclease (MNase), which allows triggering the cleavage of TF-bound DNA upon a short calcium pulse. Next, after growing the culture to the desired condition, those cells are subjected to a short calcium pulse, triggering the cleavage of TF-bound plasmids. Following this step, variants are PCR amplified, thereby capturing only the non-cleaved (unbound) sequences. Then, the frequency of each variant is defined using high-throughput sequencing and compared to untreated culture.


title: fem_line,rep1,d15


title: cardiac fibroblasts stimulated with TSP-4, D

description:
THBS4D
Mouse cardiac fibroblasts at passage 2 were cultured in the presence of recombinant mouse TSP-4

value: Cardiac fibroblasts were cultured in the presence of TSP-4 (10ng/ml)


title: cardiac fibroblasts stimulated with TSP-4, B

description:
THBS4B
Mouse cardiac fibroblasts at passage 2 were cultured in the presence of recombinant mouse TSP-4


title: RNA-seq Ad-ShCebpb gluc 8h 3

value: gluc 8h


title: MP1_subset28_pool1_S1


title: fem_line,rep2,d7

value: iPSC-iCM

value: WT


title: RNA-seq Ad-ShCebpb gluc 8h 2

value: primary hepatocytes


title: cardiac fibroblasts stimulated with TSP-4, A

description:
THBS4A
Mouse cardiac fibroblasts at passage 2 were cultured in the presence of recombinant mouse TSP-4


title: MP1_subset30_pool3_S140


title: cardiac fibroblasts from Smad3 KO lean animals, 3

description:
PLS3KOH3
Cardiac fibroblasts were isolated from animals at 6 months of age.

source_name: cardiac fibroblasts isolated from Smad3 KO lean mice

treatment_protocol: Intraperitoneal injections of tamoxifen in all mice were administered twice at 8 weeks and 16 weeks of age at a dosage of 100mg/kg, daily over a course of 5 consecutive days. Therafter, PDGFRa pos cardiac fibroblasts out of a non-CD31/non-CD45 cell population were sorted for subsequent analyses.

value: Cardiac fibroblasts

value: Smad3 KO lean mice

value: animal was subjected to tamoxifen injection


title: fem_line,rep1,d7

value: cardiomyocyte differentiation


title: RNA-seq Ad-ShCebpb gluc 8h 1

value: wt


title: fem_line,rep1,d30


title: cardiac fibroblasts from Smad3 KO lean animals, 2

description:
PLS3KOH2
Cardiac fibroblasts were isolated from animals at 6 months of age.


title: RNA-seq Ad-ShCebpb nt 8h 3

value: nt 8h


title: MP1_subset30_pool2_S139


title: naah_line,rep1,d2

value: naah


title: RNA-seq Ad-ShCebpb nt 8h 2


title: fem_line,rep2,d4


title: MP1_subset30_pool1_S138


title: fem_line,rep1,d4


title: fem_line,rep2,d2


title: MP1_subset31_pool1_S136


title: cardiac fibroblasts from Smad3 KO db/db animals, 3

description:
PLS3KOdbH3
Cardiac fibroblasts were isolated from animals at 6 months of age.

source_name: cardiac fibroblasts isolated from Smad3 KO db/db mice

value: Smad3 KO db/db mice


title: RNA-seq AdControl dual 8h 2

value: AdControl

value: dual 8h


title: cardiac fibroblasts from Smad3 KO db/db animals, 2

description:
PLS3KOdbH2
Cardiac fibroblasts were isolated from animals at 6 months of age.


title: RNA-seq AdControl dual 8h 3


title: cardiac fibroblasts from Smad3 KO lean animals, 1

description:
PLS3KOH1
Cardiac fibroblasts were isolated from animals at 6 months of age.


title: MP1_subset29_pool1_S1


title: RNA-seq Ad-ShCebpb nt 8h 1

value: Ad-ShCebpb


title: RNA-seq AdControl dual 8h 1


title: MP1_subset29_pool2_S1


title: cardiac fibroblasts from Smad3 KO db/db animals, 1

description:
PLS3KOdbH1
Cardiac fibroblasts were isolated from animals at 6 months of age.


title: fem_line,rep2,d0

value: fem

value: iPSC


title: fem_line,rep1,d2


title: E16 FT+1H neural tube cells rep3

city: Genève

first: Natalia

last: Baumann

state: Genève

address: Michel-Servet 1

department: Fundamental Neuroscience

country: Switzerland

institute: Université de Genève

description: E16 rep3

library_source: transcriptomic single cell

data_processing:
Pre processing using cellranger.
Assembly: mm10
Supplementary files format and content: Gene expression count as a matrix with genes in rows and cells in columns (.txt).

source_name: FT+1H Apical progenitors

extract_protocol:
10x Genomics Chromium Single Cell 3ʹ GEM kit v3.
10x Genomics Chromium Single Cell 3ʹ library kit v3.

tag: developmental stage

value: FT+1H Apical progenitors


title: cardiac fibroblasts from Smad3 fl/fl lean animals, 2

description:
PLS3H2
Cardiac fibroblasts were isolated from animals at 6 months of age.

source_name: cardiac fibroblasts isolated from Smad3 floxed lean mice

value: Smad3 floxed lean mice


title: cardiac fibroblasts from Smad3 fl/fl lean animals, 3

description:
PLS3H3
Cardiac fibroblasts were isolated from animals at 6 months of age.


title: fem_line,rep1,d0

value: WT


title: E16 FT+1H neural tube cells rep1

description: E16 rep1


title: E16 FT+1H neural tube cells rep2

description: E16 rep2


title: cardiac fibroblasts from Smad3 fl/fl db/db animals, 3

description:
PLS3dbH3
Cardiac fibroblasts were isolated from animals at 6 months of age.

source_name: cardiac fibroblasts isolated from Smad3 floxed db/db mice

value: Smad3 floxed db/db mice


title: RNA-seq AdControl cort 8h 3

value: primary hepatocytes

value: cort 8h


title: AC30_rep3

city: Basel

first: Grégoire

middle: M

last: Vernaz

address: Vesalgasse 1

institute: University of Basel

description:
Total RNA from homogenised whole embryo tissues
GeneCount_ensembl_deseq2Norm.txt.gz
TEquant_deseq2Norm_transposonOnly.txt.gz
lncR_deseq2Norm.txt.gz

data_processing:
Sequenced reads were trimmed for adapter sequence and low-quality sequence using TrimGalore
Reads were then mapped to the A.calliptera 1.2 ref genome assembly (Ensembl) using STAR
A gene count matrix was generated using STAR-in built HTSeq and gene count were normalised using DESeq2
Transposon expression was quantified using STAR and TEcount (deseq2 normalised count)
lncRNA were quantified using STAR/HTseq2 (deseq2 normalised count)
Assembly: AstCal1.2_ensembl_GCA_900246225.3, Astatotilapia_calliptera.fAstCal1.2.105.gff3, GCF_900246225.1_fAstCal1.2_genomic.gff
Supplementary files format and content: GeneCount_ensembl_deseq2Norm.txt.gz: tab-sep text files with DESeq2-normalised protein-coding gene count for each sample (column) and each gene (row)
Supplementary files format and content: TEquant_deseq2Norm_transposonOnly.txt.gz: tab-sep text files with DESeq2-normalised TE gene count for each sample (column) and each gene (row)
Supplementary files format and content: lncR_deseq2Norm.txt.gz: tab-sep text files with DESeq2-normalised long-non-coding gene count for each sample (column) and each gene (row)

organism: Astatotilapia calliptera

source_name: whole embryo

extract_protocol:
RNA was extracted using Direct-Zol RNA Microprep Kit (Zymo) according to manufacturer's instruction
RNA libraries were preped (stranded, polyA enriched) and sequenced on NovaSeq6000 (paired end 150bp)

tag: tissue

value: whole embryo

tag: developemental stage

value: whole embryo ; somite stage 30

value: wild-type

value: tank-reared


title: E14 FT+1H neural tube cells rep2

description: E14 rep2


title: RNA-seq AdControl cort 8h 2

value: wt


title: RNA-seq AdControl cort 8h 1


title: melw_line,rep2,d30

source_name: melw

value: melw

value: iPSC-iCM

value: cardiomyocyte differentiation


title: cardiac fibroblasts from Smad3 fl/fl lean animals, 1

description:
PLS3H1
Cardiac fibroblasts were isolated from animals at 6 months of age.

value: Cardiac fibroblasts

value: animal was subjected to tamoxifen injection


title: melw_line,rep2,d15


title: RNA-seq AdControl gluc 8h 3

value: AdControl

value: gluc 8h


title: melw_line,rep1,d15


title: E14 FT+1H neural tube cells rep1

description: E14 rep1

value: FT+1H Apical progenitors


title: cardiac fibroblasts from Smad3 fl/fl db/db animals, 1

description:
PLS3dbH1
Cardiac fibroblasts were isolated from animals at 6 months of age.


title: cardiac fibroblasts from Smad3 fl/fl db/db animals, 2

description:
PLS3dbH2
Cardiac fibroblasts were isolated from animals at 6 months of age.


title: E14 FT+1H neural tube cells rep3

description: E14 rep3


title: RNA-seq AdControl gluc 8h 1


title: RCC PD1+CD45RA- CD4 TILS VDJ Patient K416

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

description: 10X Genomics of PD1+CD45RA- CD4 T cells from kidney cancer patient

data_processing:
Aligned using Cellranger and differential gene expression and clustering performed with Seurat.
Assembly: hg38
Supplementary files format and content: tsv.gz
Supplementary files format and content: input for scRNAseq analysis.

source_name: primary tumor

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions. RNA was extracted using qiagen all-prep kits. Samples were loaded onto the 10X Genomics Chromium Controller according to manufacturer's protocol.
Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit

value: primary tumor

value: CD4 T cells

value: previously untreated disease

tag: cancer type

value: Kidney cancer


title: melw_line,rep2,d7

value: WT


title: E12 FT+1H neural tube cells rep2

description: E12 rep2


title: RNA-seq AdControl gluc 8h 2

value: primary hepatocytes


title: E12 FT+1H neural tube cells rep3

description: E12 rep3


title: RCC PD1+CD45RA- CD4 TILS VDJ Patient K297


title: E12 FT+1H Hindbrain cells

description: E12 rep1 HB


title: RCC PD1+CD45RA- CD4 TILS GEX Patient K416


title: melw_line,rep1,d30


title: RNA-seq AdControl nt 8h 1

value: nt 8h


title: melw_line,rep1,d7


title: RNA-seq AdControl nt 8h 2


title: E12 FT+1H Forebrain cells

description: E12 rep1 FB


title: RCC PD1+CD45RA- CD4 TILS GEX Patient K297


title: E12 FT+1H Midbrain cells

description: E12 rep1 MB


title: melw_line,rep1,d4


title: naah_line,rep2,d0

value: naah

value: iPSC


title: RNA-seq AdControl nt 8h 3

value: wt


title: melw_line,rep2,d4

value: melw

value: iPSC-iCM


title: 06HUVEC_INPUT_siRNF20_rep3

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

data_processing:
Visualization of raw reads was done using FASTX-ToolKit, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014), min lengh of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3.
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 default settings
samtools were used to convert sam files to bam files, after sorted bam files
bamToBed -i file_sort.bam > file_sort.bed
peaks were called by macs14 using p1e5 settings
bamCoverage was used to create bigWig files with the following settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
Peaks were annotated with annotatePeaks.pl default setting
Assembly: hg38

source_name: primary cells

growth_protocol: HUVEC cells were fixed and harvested on the plate 60h after TF with siCTR/siRNF20

extract_protocol:
Nuclei were isolated and the chromatin was sheared to yield fragment sizes ranging from 100-400bp. Sheared chromatin was precleared (sepharose G fast flow 4) beads and followed by antibody incubation over night at 4°C. Lysates were incubated with sepharose G fast flow 4 beads at 4°C for  3 h bound DNA washed  2x with low salt, 1x high salt, 1x LiCl and 2x Te buffer. AFter proteinase K digestion and reverse crosslinking DNA was cleaned up with the Zymo kit
Libraries were prepared with the NEBNext Ultra II DANN Library Prep Kit for Illumina with the  NEBNext® Multiplex Oligos for Illumina® (96 Index Primers)

tag: cells

value: HUVEC

tag: antibody


title: E10 FT+1H neural tube cells replicate 2

description: E10 rep2


title: melw_line,rep2,d2

value: cardiomyocyte differentiation


title: 06HUVEC_INPUT_siRNF20_rep2


title: 06HUVEC_INPUT_siRNF20_rep1


title: PC3_0 μM [PC3_C_S1]

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

data_processing:
1. trim adapter: trimmomatic
2. Alignment: Hisat2
3. Expression profiling: stringtie
Assembly: Homo_sapiens.GRCh38
hisat2_index: V97
Supplementary files format and content: fpkm

source_name: Prostate cancer cells (PC3)

growth_protocol: 22Rv1 cells were cultured in RPMI medium, whereas PC3 cells were cultured in F12 medium. All media were supplemented with 10% heat-inactivated fetal bovine serum, 100 U/mL penicillin and 0.1 mg/mL streptomycin.

extract_protocol:
Total RNA was extracted using Qiagen RNAeasy mini kit. The quality of total RNA was analyzed by the Agilent 2100 bioanalyzer with the RNA 6000 Nano LabChip kit.
RNA-seq libraries were prepared using Illumina® TruSeq RNA Library Prep Kit v2 and were sequenced using Illumina® Hiseq2500 to obtain 150-bp paired-end reads.

treatment_protocol: 22Rv1 and PC3 cells were treated with or without 75 and 46 uM morusin respectively for 6 hr.

value: Prostate cancer cells


title: E10 FT+1H neural tube cells replicate 1

description: E10 rep1


title: T3 at weeks 3 [Myeloid]

type: RNA

city: Taipei

first: Chung-Hsing

last: Chen

address: No.1 Ai-Guo West Road

department: Department of Mathematics

institute: University of Taipei

hyb_protocol: Hydridized according to the manufacturer's protocol.

scan_protocol: Scanned according to the manufacturer's protocol.

data_processing: We merged these samples in different panels into one dataset for subsequent data normalization. Data normalization similar to that described by the nCounter Advanced Analysis user manual (version 2.0, NanoString Technologies) was applied. Each count was transformed to a log2 scale and then normalized using positive control probes and housekeeping genes identified by geNorm algorithmt to reduce variations. We also calculated means of paired normal mice at weeks 3 and weeks 5 to 7 to scale mice (paired normal, tumor-bearing mice, and recurrence mice) at these two time points.

label: NanoString oligonucleotide probe

source_name: PBMC from tumor-bearing mouse 3 at weeks 3

label_protocol: Labeled according to the manufacturer's protocol.

extract_protocol: Mouse blood was collected with Microtainer® (BD) with EDTA and incubated with 3 ml ACK lysis buffer (Gibco) for 5 min at room temperature to lyse red blood cells. PBMC were spun down by centrifugation at 1500 rpm for 10 min at 4℃ and washed twice with phosphate-buffered saline (PBS). RNA of PBMC was isolated by using Direct-Zol RNA Miniprep Kits (ZYMO RESEARCH) according to manufacturer instructions.

value: BALB/c

tag: group

value: Tumor


title: T1 at weeks 3 [Myeloid]

source_name: PBMC from tumor-bearing mouse 1 at weeks 3


title: T2 at weeks 3 [Myeloid]

source_name: PBMC from tumor-bearing mouse 2 at weeks 3


title: 05HUVEC_INPUT_siCTR_rep1


title: naah_line,rep2,d30

source_name: naah


title: melw_line,rep1,d0


title: PC3_46 μM [PC3_T_S2]

value: 46 μM morusin for 6hrs


title: R2 at weeks 5-7 [Myeloid]

source_name: PBMC from recurrence mouse 2 at weeks 5-7

value: Recurrence


title: 05HUVEC_INPUT_siCTR_rep3


title: 22Rv1_0 μM [P22RV1_C_S3]

source_name: Prostate cancer cells (22Rv1)


title: 22Rv1_75 μM [P22RV1_T_S4]

value: 75 μM morusin for 6hrs


title: 05HUVEC_INPUT_siCTR_rep2


title: 04HUVEC_POL2_IP_siRNF20_rep2

description: 04HUVEC_POL2_IP_siRNF20_MER_RPKM_hg38.bw

value: Pol II antibody Rpb1 NTD (D8L4Y) Cell Signalling


title: R3 at weeks 5-7 [Myeloid]

source_name: PBMC from recurrence mouse 3 at weeks 5-7


title: naah_line,rep1,d30

value: WT


title: 04HUVEC_POL2_IP_siRNF20_rep3


title: R1 at weeks 5-7 [Myeloid]

source_name: PBMC from recurrence mouse 1 at weeks 5-7


title: naah_line,rep2,d15


title: melw_line,rep1,d2


title: naah_line,rep1,d0


title: CSC rep3

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

description:
Treat-CSC: 3062__CSC-3
CSC-3_S5_L002_R1_001.fastq_115214

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison

growth_protocol: SUM149 human TNBC cell lines was provided by Dr. Stephen Ethier at Medical university of South Carolina. The cells were cultured and maintained as previously described (Neve RM, et al. Cancer Cell 2006; 10: 515-27).

extract_protocol:
RNA samples were extracted using an RNeasy mini kit (Qiagen) according the manufacturer's protocol.
Total RNA was extracted using standard methods. RNA quality was determined utilizing an Agilent TapeStation, (Santa Clara, CA). Illumina’s Truseq mRNA non-stranded library protocol
100 ng of RNA was used to prepare sequencing libraries following the manufacture’s protocol with the exception of using half reactions (Illumina, San Diego, CA).
Sequencing was performed on a HiSeq2500 Rapid Run (version 2) single read sequencing (1X50 cycles), (Illumina, San Diego, CA).  Fastq files were generated using Illumina’s bcl2fastq conversion software v2.17.1.14.

treatment_protocol: CSCs and NSCs were sorted from SUM149 cells using a flow cytometry cell sorter.

value: triple-negative breast cancer (TNBC) cells

tag: cell subtype

value: Cancer stem cells (CSCs)


title: NSC rep3

description:
Cntrl-NSC: 3063__NSC-3
NSC-3_S6_L002_R1_001.fastq_115218

value: non-stem cancer cells (NSCs)


title: 04HUVEC_POL2_IP_siRNF20_rep1


title: N3 at weeks 3 [Myeloid]

source_name: PBMC from normal mouse 1 at weeks 3

value: Normal


title: N2 at weeks 3 [Myeloid]


title: melw_line,rep2,d0

value: iPSC


title: N1 at weeks 3 [Myeloid]


title: chipv2

city: Tianjin

first: zilong

last: fan

address: 22 Weidai Road, Heping District

country: China

institute: Tianjin Medical University

data_processing:
Quality control of sequencing data by fastqc-v0.12.1.
Low-quality bases were removed using trim_galore-v0.6.10 with a quality threshold of 25, Phred33, and a minimum length of 35 for the output reads, allowing for a maximum number of 3 mismatched bases.
Alignment of chipseq reads to the hg38 genome of UCSC by bowtie2-v2.5.1 using a local most sensitive hybrid comparison model.
Sequencing depths in BAM files were calculated using the samtools-v1.18 package and converted to bw files with a window size of 50bp for calculating sequencing depths, which were normalised using the RPKM method.
Peaks were called uing MACS v2.2.9.1 with the significance cut-off g-value <=0.01
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: oesophagus

growth_protocol: DMEM,10% FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin in 5% CO2 at 37℃.

extract_protocol:
Cells were fixed with 1% formaldehyde at RT for 10 min, and the fixation was stopped by 125 mM glycine at RT for 5 min. The chromatin pellets were extracted from cells by lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40), and resuspended with 0.8 ml of RIPA buffer.
10ng DNA was used as starting material for input and ip samples.After the DNA samples quality control，the purified DNA was used NEBNext Ultra II
DNA Library Prep Kit （NEB, USA, Catalog #: E7645L）for ChIP-seq library preparation.

value: oesophagus

value: esophageal squamous cell carcinoma


title: 03HUVEC_POL2_IP_siCTR_rep2

value: HUVEC


title: NSC rep2

description:
Cntrl-NSC: 3061__NSC-2
NSC-2_S4_L001_R1_001.fastq_115210


title: inputV2


title: inputsg3


title: N3 at weeks 5-7 [Myeloid]

source_name: PBMC from normal mouse 3 at weeks 5-7


title: 03HUVEC_POL2_IP_siCTR_rep3


title: NSC rep1

description:
Cntrl-NSC: 3059__NSC-1
NSC-1_S2_L001_R1_001.fastq_115202


title: CSC rep2

description:
Treat-CSC: 3060__CSC-2
CSC-2_S3_L001_R1_001.fastq_115206


title: chipsg3


title: CSC rep1

description:
Treat-CSC: 3058__CSC-1
CSC-1_S1_L001_R1_001.fastq_115198


title: N1 at weeks 5-7 [Myeloid]

source_name: PBMC from normal mouse 1 at weeks 5-7


title: 19_DGZV_Infect14d_PBMC

status: Public on Aug 17 2024

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.5.2b.(Dobin et al.)
Transcripts were annotated using the UNMC rhesus annotation v 7.6.8
Transcript abundance was estimated in STAR during alignment using the algorithm or htseq-count
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf available at https://www.unmc.edu/rhesusgenechip/index.htm)
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
RNA was isolated from the frontal cortex tissue preserved in RNAlater using the RNeasy Mini kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent Bioanalyzer and 10 ng of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions.
Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina HiSeq3000 at 100SR

treatment_protocol: Macaques were infected intrarectally with a single high dose challenge of SIVmac239X as described previously [Del Prete et al., J Virol 2014]

tag: subjectid

value: DGZV

tag: condition

value: Infected

tag: sampleday


title: 16_G71P_Infect7d_PBMC


title: 20_G72G_control_PBMC

value: Control


title: N2 at weeks 5-7 [Myeloid]

source_name: PBMC from normal mouse 2 at weeks 5-7

value: BALB/c


title: 21_J709_control_PBMC


title: 14_W103_Infect7d_PBMC


title: 11_G72G_control_FC

source_name: frontal cortex


title: 13_J709_control_FC


title: 9_DGZV_Infect14d_TH

source_name: thalamus


title: 8_DGZV_Infect14d_FC


title: 12_J979_control_FC


title: 7_J617_Infect14d_FC


title: 6_G71G_Infect14d_FC


title: 03HUVEC_POL2_IP_siCTR_rep1

source_name: primary cells


title: 4_W27_Infect14d_FC


title: 5_W72_Infect14d_FC


title: 1_W103_Infect7d_FC


title: 18_J617_Infect14d_PBMC


title: 3_G71P_Infect7d_FC


title: 17_W27_Infect14d_PBMC


title: MSA GP-7

city: Toronto

first: Gabor

last: Kovacs

state: Ontario

address: 60 Leonard Ave, Room 6KD414

country: Canada

institute: University of Toronto

hyb_protocol: According to Nanostring manufactuer's protocol

scan_protocol: 100ng of RNA from each sample were analyzed using Nanostring nCounter assay (Nanostring Technologies)

data_processing: Probe counts were normalized against three housekeeping genes (UBE2D2, GUSB, and RPL13) and a blood marker gene (ALAS2) (Vanni S, et al. 2018) using the standard protocol in nSolver software (ver. 4)

source_name: Brain

extract_protocol: Approximately 25mg of dissected brain tissue were dissociated using the gentleMACS Octo Dissociator (Miltenyi Biotec) and RNA was extracted using the Qiagen Lipid Tissue Mini Kit (Qiagen GmbH) according to the manufacturer's protocol.

treatment_protocol: Frozen at -80C during storage

tag: Sex

value: M


title: MSA FC-7


title: CONTROL GP-6

value: F


title: CONTROL FC-6


title: MSA SN-7


title: CONTROL PUT-6


title: CONTROL SN-6


title: CONTROL GP-5


title: CONTROL GP-1


title: 10_DGZV_Infect14d_BG

source_name: basal ganglia


title: 2_G71D_Infect7d_FC


title: CONTROL PUT-5


title: 15_G71D_Infect7d_PBMC


title: CONTROL SN-5


title: CONTROL FC-4


title: CONTROL SN-4


title: CONTROL FC-5


title: CONTROL GP-4


title: MSA FC-6


title: MSA GP-6


title: CONTROL FC-1


title: CONTROL PUT-4


title: MSA FC-5


title: MSA GP-5


title: MSA PUT-7


title: nasal turbinates, PandB10

first: Jingjing

last: Liu

address: Herzl 234

institute: Weizmann Institute of Science

description: MARS-seq bulk RNAseq

data_processing:
Reads were quality trimmed using cutadapt. Mapped to the genome using STAR.
Htseq count was used to create count matrix
Assembly: mm10
Supplementary files format and content: counts: xlsx file with counts per sample per gene (PandB5, PandB7, and PandB8 exhibited outlier markers within the group. Consequently, they were excluded from final analysis.)

source_name: nasal turbinates

extract_protocol:
Whole tissue RNA extraction utilized the Direct-zolTM RNA MiniPrep Plus Kit (Zymo Research)
A bulk adaptation of the massively parallel single-cell RNA sequencing protocol (MARS-seq) was used (Jaitin et al. Science 2014) to generate RNA-seq libraries for transcriptomic analysis.

value: nasal turbinates

value: PandB


title: nasal turbinates, PandB3

description: MARS-seq bulk RNAseq


title: nasal turbinates, PandB9

description: MARS-seq bulk RNAseq


title: nasal turbinates, PandB4

description: MARS-seq bulk RNAseq


title: MSA PUT-6


title: CONTROL SN-1


title: MSA PUT-5


title: MSA FC-4


title: MSA GP-4


title: MSA SN-5


title: nasal turbinates, prime5

description: MARS-seq bulk RNAseq

value: prime


title: MSA PUT-3


title: nasal turbinates, PandB6

description: MARS-seq bulk RNAseq


title: nasal turbinates, PandB2

description: MARS-seq bulk RNAseq


title: nasal turbinates, prime3

description: MARS-seq bulk RNAseq


title: nasal turbinates, PandB1

description: MARS-seq bulk RNAseq


title: MSA SN-4


title: MSA SN-6


title: nasal turbinates, prime4

description: MARS-seq bulk RNAseq


title: MSA GP-3


title: nasal turbinates, prime2

description: MARS-seq bulk RNAseq


title: nasal turbinates, prime1

description: MARS-seq bulk RNAseq


title: MSA FC-2


title: nasal turbinates, naive5

description: MARS-seq bulk RNAseq

value: naïve


title: nasal turbinates, naive4

description: MARS-seq bulk RNAseq


title: MSA GP-2


title: MSA PUT-1


title: nasal turbinates, naive1

description: MARS-seq bulk RNAseq


title: nasal turbinates, naive2

description: MARS-seq bulk RNAseq


title: MSA GP-1


title: MSA SN-3


title: MSA FC-3


title: SGFD3

city: CHONGQING

first: Chaonan

address: Gaotanyan Street

institute: the Army Medical University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Mus musculus GRCm38.
The mapped reads of each sample were then assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
All the transcriptomes were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating FPKM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow

growth_protocol: All mice used were randomized, background-matched. All mice used were housed in specific pathogen-free (SPF) conditions and fed with autoclaved water and food.

extract_protocol:
LT-HSCs were sorted from the BM of mice with control diet (CD) or  serine/glycine-free diet (SGFD)  for 3 months. RNA was extracted from sorted cells using a RNeasy Micro Kit (QIAGEN) following the manufacturer's introductions. The concentration and integrity of extracted RNA were evaluated by an Agilent 2100 Bioanalyzer with an Agilent RNA 6000 Nano Kit.
Libraries for RNA-seq were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Bone marrow

value: hematopoietic stem cells

value: WT

value: serine/glycine-free diet (SGFD)


title: U251 cells without SLCDS, control 3

city: Guangzhou

first: Wenqiang

last: Che

state: Guangdong Province

address: No. 613, West Huangpu Avenue, Tianhe District, Guangzhou

department: Neurosurgery

institute: Jinan university

data_processing:
CLC genomics workbench v11.01
Sequence reads were trimmed for adaptor sequence/low-quality using CLC genomic workbench (oarameter-Quality limit: 0.05)
Trimmed sequence raeads were mapped to GrCM38/mm10 using CLC genomic benchwork (oarameters-mismath: 2 insertion cost: 3 deletion cost : length fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-deliminted text files include RPKM values for each Sample

source_name: cell line

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: cell line

tag: cell line

value: glioma

value: PBS


title: MSA PUT-2


title: CONTROL SN-3


title: CONTROL PUT-3


title: CONTROL GP-3


title: SGFD2

tag: cell type


title: U251 cells without SLCDS, control 1

tag: genotype


title: U251 cells without SLCDS, control 2

tag: treatment


title: CONTROL FC-3


title: CONTROL SN-2


title: CONTROL PUT-2


title: CONTROL GP-2


title: CONTROL FC-2


title: SGFD1


title: U251 cells incubated SLCDS, experimental sample3

value: SLCDS


title: MSA FC-1


title: CD3

value: control  diet (CD)


title: Single_PDMS

city: Hangzhou

first: Xianchi

last: Zhou

address: Yuhangtang road

institute: Zhejiang University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit fiollowing manufacturer's protocols.

value: skin


title: Single_Mock


title: CD2


title: CONTROL PUT-1


title: Macro_PDMS_r2


title: U251 cells incubated SLCDS, experimental sample1


title: U251 cells incubated SLCDS, experimental sample2


title: MSA PUT-4


title: Macro_PDMS_r1


title: Macro_PDMS


title: CD1


title: Heart_failure_4

first: Qingbo

last: Xu

state: Zhejiang

address: 79 Qingchun Road

department: Department of Cardiology

institute: First Affiliated Hospital, Zhejiang University School of Medicine

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were using the Cell Range software v5.0.0 (http://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: TSV data for genes and barcodes; MTX data for gene expression matrix

source_name: human heart

extract_protocol:
After collecting the human heart, the tissue was minced into fine pieces using a scalpel and transferred into a glass vial with 1.5 ml of cold digestion buffer (Liberase, Roche). The tissues were digested by either using a shaking (100 rpm) 37°C waterbath for 15 min. The obtained cell suspension was gently pipetted up and down (10 x) and transferred onto a 70μm cell strainer placed on top of a 50ml Falcon tube. The tissue was gently rubbed through the strainer using the plunger of a 1ml syringe, after which the strainer was rinsed with 8.5ml of DMEM to obtain a total volume of 10 ml, which was centrifuged for 6 min at 4°C at 300 xg. After the supernatant was removed, non-cardiomyocytes samples pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS, cells were filtered with 40 μm filter and then centrifuged at 300xg for 5 minutes. Cells resuspended in PBS were stained with LIVE/DEAD Fixable Near-IR (APC/Cy7 channel) Dead Cell Stain Kit (Invitrogen; L34975, 1:1000) and Hoechst 33342 (Invitrogen; H3570, 1:1000) for 20 minutes. Unstained cells and cells staining with only 1 fluorochrome prepared concomitantly served as control. After 1 wash in PBS for 5 minutes, cells were resuspended in PBS and then sorted by Flow Cytometer. Nucleated live cells (Hoechst+/APC/Cy7− population) were sorted into PBS with 0.04% BSA for subsequent scRNA-seq.
RNA libraries were prepared with Chromium™ Single Cell 3′ Reagent Kit v3 chemistry (10× Genomics) according to the manufacturer's protocol.

value: heart

value: Total non-cardiomyocytes

tag: disease state

value: heart failure

value: heart failure with a history of coronary heart disease (Hyperlipidaemia) and hypertension


title: Heart_failure_3

description: 10X Genomics


title: T265_corin_1

city: Boston

first: Robert

last: Fisher

state: MA

address: 609 Albany St

department: Dermatology

institute: Boston University

data_processing:
Reads were trimmed and low- quality reads were removed using Trimmomatic v.0.36
Reads were mapped to the GRCh38 reference genome using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Counts were used for differential analysis using DESeq2. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: hg38
Supplementary files format and content: TXT - hitcounts

growth_protocol: Cell lines were cultured in high glucose DMEM with pyruvate (Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin.  Cells were maintained at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen)
Library was prepared and sequenced by Azenta Life Sciences.

value: MPNST

value: corin


title: Macro_P90_r1


title: Heart_failure_2

description: 10X Genomics

value: heart failure with a history of coronary heart disease (Hyperlipidaemia)


title: AngII_CD34 cells

data_processing:
Data were processed following standard protocols using Cell Ranger version 6.0.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting, UMI counting, and to generate feature-barcode matices.
Assembly: mm10
Supplementary files format and content: TSV data for genes and barcodes; MTX data for gene expression matrix

source_name: CD34+ cells isolated from ApoE-/- mice hearts 4 weeks after AngII surgery

extract_protocol:
After collecting the heart of ApoE-/- or AngII-operated mice hearts, the tissue was minced into fine pieces using a scalpel and transferred into a glass vial with 1.5 ml of cold digestion buffer (Liberase, Roche). The tissues were digested by either using a shaking (100 rpm) 37°C waterbath for 15 min. The obtained cell suspension was gently pipetted up and down (10 x) and transferred onto a 70μm cell strainer placed on top of a 50ml Falcon tube. The tissue was gently rubbed through the strainer using the plunger of a 1ml syringe, after which the strainer was rinsed with 8.5ml of DMEM to obtain a total volume of 10 ml, which was centrifuged for 6 min at 4°C at 300 xg. After the supernatant was removed, non-cardiomyocytes samples pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS, cells were filtered with 40 μm filter and then centrifuged at 300xg for 5 minutes. Cells resuspended in PBS were stained with LIVE/DEAD Fixable Near-IR (APC/Cy7 channel) Dead Cell Stain Kit (Invitrogen; L34975, 1:1000) and Hoechst 33342 (Invitrogen; H3570, 1:1000) for 20 minutes. Unstained cells and cells staining with only 1 fluorochrome prepared concomitantly served as control. After 1 wash in PBS for 5 minutes, cells were resuspended in PBS and then sorted by Flow Cytometer. Nucleated live cells (Hoechst+/APC/Cy7− population) were sorted into PBS with 0.04% BSA for subsequent scRNA-seq. For isolation of single CD34+ cells from the heart, a similar protocol was used as describe above.
RNA libraries were prepared with Chromium™ Single Cell 3′ Reagent Kit v3 chemistry (10× Genomics) according to the manufacturer's protocol.

tag: strain

value: CD34+ cells

value: AngII surgery


title: Macro_P90_r2

tag: tissue


title: AngII_Total non-cardiomyocytes

source_name: Total non-cardiomyocytes isolated from ApoE-/- mice hearts 4 weeks after AngII surgery

value: total non-cardiomyocytes


title: ApoE_CD34 cells

source_name: CD34+ cells isolated from ApoE-/- mice hearts

value: no surgery


title: Heart_failure_1

description: 10X Genomics


title: T265_corin_2


title: Macro_P90


title: Single_H90


title: T265_DMSO_2

value: DMSO


title: ApoE_Total non-cardiomyocytes

source_name: Total non-cardiomyocytes isolated from ApoE-/- mice hearts


title: STS26T_corin_2


title: STS26T_corin_1


title: Control_1

description: 10X Genomics

value: Normal

value: donor heart


title: T265_DMSO_1


title: fndc1_4

city: Yangling, Shaanxi

first: xin

middle: rui

last: zhang

address: Yangling, Shaanxi

institute: Northwest A&F University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Supplementary files format and content: Mus_musculus.GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: C2C12 cells were cultured in DMEM medium supplemented with 20% FBS

extract_protocol:
Differentiated for 4 days in high glucose medium with 2% horse serum, samples were collected.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C2C12 cells were transfected with 100nM siRNA in a 6 well plate using 4ul of RNAiMAX (Invitrogen) following manufacturer protocol

value: Myoblast

value: Fndc1 knock down

value: Four days after differentiation


title: Control_2

description: 10X Genomics

value: heart


title: con_3

city: Shanghai

first: Senlin

last: Zhao

address: 270 Dong An Road

department: Colorectal Surgery

institute: Cancer Hospital, Fudan University

description: commen method

data_processing:
Illumina bcf2fastq v2.20 software used for basecalling.
fastp version 0.20.1 software was first used for adpter removing, then low-quality  bases and N-bases or low-quality reads were filtered out.Then sequencing reads were mapped to the Rat genome （Hg38.p13) using HISAT2 version 2.2.1.0 with parameters --rna-strandness rf --fr
Counts and Fragments Per Kilobase of exon model per Million mapped fragments(FPKM) of each gene was calculated using htseq-count version 0.11.2
Assembly: Hg38
Supplementary files format and content: Matrix table with raw counts for every gene and every sample.

extract_protocol:
Total RNA from heart samples was extracted using the mirVana™ miRNA Isolation Kit (Ambion, AM1561) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: CRC cells

value: WT

value: CON


title: STS26T_DMSO_2

value: MPNST


title: fndc1_5


title: STS26T_DMSO_1


title: nasal turbinates, naive3

city: Rehovot

description: MARS-seq bulk RNAseq

value: nasal turbinates

value: naïve


title: In vivo_X902

value: skin

value: In vivo_X90


title: fndc1_3


title: In vivo_X901


title: fndc1_2


title: In vivo_PDMS3

value: In vivo_PDMS


title: In vivo_PDMS2


title: con_1

description: commen method


title: S462_corin_2

value: corin


title: fndc1_1


title: S462_corin_1


title: In vivo_PDMS1


title: In vivo_X903


title: S462_DMSO_2

value: DMSO


title: fa_2

description: commen method

value: GCA


title: nc4

value: control


title: S462_DMSO_1


title: In vivo_mock3

value: In vivo_mock


title: fa_1

description: commen method


title: In vivo_mock2


title: nc3

value: Myoblast


title: In vivo_mock1


title: MPNST724_corin_1


title: sh-NC Input

city: Nanjing

first: Yuan

last: Fang

address: guangzhou road

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
MACS2(version 2.1.0.20151222)/exomePeak was employed to perform m6A peak calling.Then using Hommer(version:4.8)  to annotate the m6A Peaks.The nucleotides in m6A Peaks region were used for detection of the consensus  m6A motif by DREME (version:4.11.1) . Motif central enrichment was performed by  CentriMo (version:4.11.1).Differential methylation was determined by MetDiff.
Genome_build: hg19
Supplementary_files_format_and_content: a tabular file which contains information about called peaks

source_name: Gastric cancer cells

growth_protocol: BGC-823 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Total RNAs were extracted from stable transfected GC cells with TRIzol (Invitrogen, USA). Fragmented RNAs were  incubated with m6A antibody for immunoprecipitation by a Magna MeRIP RNA-Bindin Protein Immunoprecipitation Kit according to the manufacturer’s instructions (Millipore, USA)(#17–10,499,Merck Millipore, MA, USA).
RNA libraries were prepared  using NEBNext® Ultra™ RNA Library Prep Kit for Illumina

treatment_protocol: BGC-823 cells were conducted with  stably silenced ALKBH5 and the corresponding NC  by transducing with letiviruses

tag: source

tag: transfection

value: sh-NC

tag: merip antibody


title: nc1

value: Four days after differentiation


title: con_2

description: commen method

value: CRC cells


title: MPNST724_DMSO_2


title: fa_3

description: commen method

value: WT


title: BGC-823 Input

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
MACS2(version 2.1.0.20151222)/exomePeak was employed to perform m6A peak calling.Then using Hommer(version:4.8)  to annotate the m6A Peaks.The nucleotides in m6A Peaks region were used for detection of the consensus  m6A motif by DREME (version:4.11.1) . Motif central enrichment was performed by  CentriMo (version:4.11.1).
Genome_build: hg19
Supplementary_files_format_and_content: a tabular file which contains information about called peaks


title: RNA-seq, mouse brain mPFC-LHB projection neurons, CRS-4

city: Beijing

first: Zhiyuan

address: YIKE Road

institute: Chinese Institute for Brain Research, Beijing(CIBR)

data_processing:
Quality control was performed by FastQC. The RNA-seq data with high quality was aligned to reference genome (GRCm38) by HISAT. The gene read couts were calculated by featureCounts.
The differentially expressed genes were detected by DESeq2, with p-value less than 0.001 and the log2 fold change largter than 1. The volcano plot was generated by ggplot2 package in R.
The heatmap is generated with gene expression levels normalized by z-score. Gene Ontology (GO) enrichment analysis was perfomed  by ClusterProfiler package in R, remaining terms with FDR less than 0.001.
Assembly: Hisat2 GRCm38
Supplementary files format and content: Deseq2 normalized count, RNA seq_1.csv

source_name: Brain, P90

extract_protocol:
Total RNA was extracted from mPFC-LHB projection neurons using RNeasy Micro Kit (Qiagen, DP420).
DNA library for sequencing was prepared following the protocol of TruePrep DNA Library Prep Kit V2.

value: Brain, P90

value: CRS


title: BGC-823 MeRIP


title: sh-NC MeRIP


title: MPNST724_DMSO_1

value: MPNST


title: RNA-seq, mouse brain mPFC-LHB projection neurons, CRS-3


title: Corin--set-2

data_processing:
Reads were trimmed using the fastp command in fastp v.0.23.4
Reads were aligned with GRCh38 reference genome using bowtie2 v.2.4.2.
Sam files were filtered to retain the mapped reads only and converted to BAM files using Samtools v.1.12.
Peaks were called using Macs2 v.2.2.7.1 with the nomodel, and nolambda options.
Assembly: hg38
Supplementary files format and content: TXT - hitcounts

extract_protocol:
DNA was extracted, tagmented, purified, and adapter ligated using the ATAC-seq Kit (53150) according to the manufacturer’s instructions (Active Motif).
Library was prepared using ATAC-seq Kit (53150). Sequencing was conducted by Azenta Life Sciences.

treatment_protocol: 1uM, 24h (DMSO, HDACi, Corin)


title: shALKBH5 Input


title: nc5


title: shLINC00659 sample-3

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM/counts for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared  using NEBNext® Ultra™ RNA Library Prep Kit after mRNA was enriched by oligo dT according to instructions of NEB Next® Poly(A) mRNA Magnetic Isolation Module


title: Corin-set-1


title: CES2_2

city: guangzhou

first: xianyue

last: Ren

state: guangdong

address: 55 Lingyuan West Road, Guangzhou

institute: Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University

data_processing:
The libraries were loaded on cBot (Illumina) to generate cluster and sequenced on the Illumina HiSeqXten platform.
The RNA-seq reads were mapped to the human reference genome sequence (hg38) assembly by Hisat2 (Version 2.1.0).
Stringtie (version 1.3.3) was used to count the number of fragments of each known gene downloaded from Ensembl (Homo sapiens GRCh38).
After mapping, we removed genes with fewer than 10 fragments in all of the samples and performed differential expression analysis using R/Bioconductor package edgeR (version 3.0.8).
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

growth_protocol: CAL33 and 293FT cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Gibco).

extract_protocol:
For total RNA extraction, Trizol reagent (Invitrogen) was used to lysis cells. Chloroform was added into the mixture. After centrifuging, RNA was precipitated by isopropanol, washed by ethanol and resolved into RNase-free H2O.  Nanodrop One spectrophotometer (Thermo Scientific) and Agilent 2100 bioanalyzer were used to quantify and qualify the RNA.
we constructed Illumina sequencing libraries according to the modified strand-specific RNA sequencing protocol. Briefly, we isolated non-coding RNA and coding RNA from 3 μg of purified total RNA using a ribo-zero kit for rRNA removal. After isolation, we eluted and fragmented the RNA samples at 94°C for 8 min with Elute-Prime-Fragment Mix. Subsequently, we performed first-strand cDNA synthesis using SuperScriptII (Invitrogen, Carlsbad, CA. USA). The product with Second Strand Marking Master Mix were incubated at 16°C for 1 hour to synthesize the second-strand cDNA. After 3’ ends adenylation, we ligated the DNA fragments with TruSeq adapters and the product was amplified using TruSeq PCR primers.

treatment_protocol: The pSin-EF2-empty vector or pSin-EF2-CES2-FLAG overexpression plasmids and the lentivirus packaging plasmids (pMD2.G and psPAX2) were co-transfected into 293FT cells using the calcium phosphate method. Lentivirus particles were harvested and infected into the Cal33 cells. The stably transfected Cal33 cells were selected using puromycin (0.5ug/ml) (Sigma).

value: oral squamous cell carcinoma

value: CES2 overexpression


title: shLINC00659 sample-2


title: nc2


title: MPNST724_corin_2


title: CES2_1


title: RNA-seq, mouse brain mPFC-LHB projection neurons, CRS-1


title: Vector_3

value: Vector


title: shLINC00659 sample-1


title: RNA-seq, mouse brain mPFC-LHB projection neurons, noCRS-3

value: noCRS


title: Vector_2


title: RNA-seq, mouse brain mPFC-LHB projection neurons, noCRS-2


title: DMSO-set-2


title: sh-NC sample-3

value: shNC


title: CES2_3


title: HDACi-set-1


title: shALKBH5 MeRIP


title: sh-NC sample-2


title: DMSO-set-1


title: sh-NC sample-1


title: RNA-seq, mouse brain mPFC-LHB projection neurons, noCRS-1


title: Vector_1


title: 16hpf, replicate 2, scRNAseq

status: Public on Aug 16 2024

city: Bergen

first: Simon

last: Henriet

address: Thormøhlensgate 55

country: Norway

institute: University of Bergen

description: 10x Genomics

data_processing:
The reads were mapped against the O. dioica reference genome generated by our group, and processed with the 10x Genomics Cellranger 5.0.1 pipeline for alignment, barcode and UMI counting. Filtering and clustering were done in Seurat v3.2.328.
Assembly: Oikopleura dioica genome assembly version 3.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Oikopleura dioica

source_name: whole animal

extract_protocol:
O.dioica larvae were washed several times with CASW. In the case of 8-16hpf, a 40um strainer was used for washing and collecting the animals. Meanwhile, 2ml EDTA-CASW (5Mm EDTA in calcium-free ASW) was pre-warmed at 37C for 10min before preparing the enzymatic mix. Early (4-6hpf) and late (8-16hpf) larvae were transferred to individual 1%BSA pre-soaked glass wells. After this, 2ml of filtered enzymatic cocktail (either Pronase 0,5% for early larvae, or Pronase 0,25% + Trypsin 1,25% + Cellulase 10mg/ml for late larvae, in warm EDTA-CASW) were added to each well and gently mixed at room temperature. The animals were left for 5min (for early larvae) or 10min (for late larvae). After this, 1ml of solution was removed. The remaining 1ml solution was mixed by pipetting up and down (5-10 min aprox) until all larvae were completely triturated. The enzymatic reaction was stopped by adding 3ml ice cold 0,5%BSA EDTA-CASW (enriched with 2mg/ml glycine). Dissociation was refined by pipetting up and down with a low-retention tip for 1 more minute under the microscope to avoid presence of cell aggregates. The final suspension was filtered with a 20um Pluriselect strainer into a 50ml falcon tube (previously soaked in 1%BSA-CASW). After filtering, an additional wash with 0,5%BSA EDTA-CASW was done to recover the maximum quantity of cells from the strainer. The final volume in the falcon tube did not exceed more than 20ml. The solution was centrifuged at 300G for 15 minutes, and the supernatant was discarded afterwards. The pellet was gently resuspended in 1ml 0,2%BSA MCASW (Magnesium/Calcium-free ASW). An additional wash was performed in samples from 8-16hpf due to the presence of more cellulose debris in the samples. Cell count and viability was checked using Acridine orange and Propidium iodide stain in the LUNA-FL dual fluorescence cell counter. Viability in all samples was not lower than 80% before fixation. For fixation,  a volume of 500ul of cell suspension was transferred to a 15ml falcon tube. Fixation and cryopreservation were carried out following a variation of the ACME protocol (Garcia-Castro et al., 2021) after enzymatic dissociation. Salinity of 1xPBS in ACME solution was previously increased to 32ppt using a 10X salt compensation buffer (3,42M NaCl 0,05M KCl 0,25M Na2SO4 0,32M NaHCO3) to avoid osmotic shock of dissociated cells. Cryopreserved cells were stored at -80C and posteriosly recovered and resuspended in 1%BSA 1XPBS to a concentration of 500cells/ul before proceeding with the cell barcoding.
Libraries were produced following manufacturer’s recommendations for the 10x Genomics Chromium controller (corresponding to the Chromium Single Cell 3' GEM Kit v3.1 user guide; CG000204 Rev D). The library quality was assessed using Qubit (ThermoFisher) and Bioanalyzer (Agilent). Eleven libraries (2x4hpf, 2x6hpf,2x8hpf, 1x11hpf, 2x12hpf and 2x16hpf) were pair-ended sequenced at the Norwegian Sequencing centre (Oslo, Norway) using Illumina Novaseq sp flowcell (2x100bp) with an expected target of 200K reads per library.

value: whole animal

value: Wildtype

tag: age


title: 8hpf, replicate 2, scRNAseq

description: 10x Genomics


title: 12hpf, replicate 2, scRNAseq

description: 10x Genomics


title: RNA-seq, mouse brain mPFC-LHB projection neurons, CRS-2


title: 16hpf, replicate 1, scRNAseq

description: 10x Genomics


title: 6hpf, replicate 2, scRNAseq

description: 10x Genomics


title: 6hpf, replicate 1, scRNAseq

description: 10x Genomics


title: 8hpf, replicate 1, scRNAseq

description: 10x Genomics


title: 4hpf, replicate 2, scRNAseq

description: 10x Genomics


title: HDACi-set-2


title: 11hpf, replicate 1, scRNAseq

description: 10x Genomics


title: 3h30pf, replicate 1, scRNAseq

description: 10x Genomics


title: 4hpf, replicate 1, scRNAseq

description: 10x Genomics


title: 3hpf, replicate 2, scRNAseq

description: 10x Genomics


title: 12hpf, replicate 1, scRNAseq

description: 10x Genomics


title: 3h30pf, replicate 2, scRNAseq

description: 10x Genomics


title: 3hpf, replicate 1, scRNAseq

description: 10x Genomics


title: 2h30pf, replicate 2, scRNAseq

description: 10x Genomics


title: 2h30pf, replicate 1, scRNAseq

description: 10x Genomics


title: 𝛾𝛿-TCR blockage - KO_𝛾𝛿TCR_3

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

institute: Goethe-University

data_processing:
raw data were processed using the blue-bee pipeline (https://lexogen.bluebee.com/quantseq/)
Trimming: bbduk v35.92
Alignment: STAR Aligner with modified ENCODE settings
Gene Read Counting: HTSeq-count with kit-specic options (FWD)
Differential Analysis: DESeq2 Pipeline
Assembly: Mus musculus (GRCm39)
Supplementary files format and content: text files containing the normalized counts for IL-38 neuralization (wtiggvskoantiil38) and γδ-TCR blockage (koiggvskoantigdtcr)

source_name: PyMT tumors

extract_protocol:
Total RNA from PyMT tumors was isolated using TRIzol Reagent (Life Technologies), followed by RNA purification with RNA Clean & Concentrator-5 (Zymo Research). RNA quality was evaluated in Agilent Tape Station 4150 with RNA Screen Tape (Agilent) and concentration measured by Qubit HS RNA Assay Kit (Thermo Fisher Scientific).
Libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD from Illumina (Lexogen)

treatment_protocol: For the in vivo IL-38 neutralization, PyMT WT mice were divided into two groups according to treatment (anti-IL-38, samples 1-6; IgG, samples 1-5). For the in vivo γδ-TCR blockage, PyMT WT mice were treated with IgG (WT_IgG, samples 1-4) and PyMT IL-38 KO were treated with either IgG (KO_IgG, samples 1-4) or anti-γδ-TCR antibodies (KO_γδTCR, samples 1-4). All the mice were treated once a week for 5 weeks and tumors were harvested in the end point experiment. Afterwards, total RNA from PyMT tumors were isolated by TRIzol followed by RNA purification.

value: PyMT IL-38 KO

value: Treated with anti-γδ-TCR antibodies once a week for 5 weeks

value: PyMT tumors


title: 𝛾𝛿-TCR blockage - KO_𝛾𝛿TCR_4


title: 2hpf, replicate 2, scRNAseq

description: 10x Genomics


title: 2hpf, replicate 1, scRNAseq

description: 10x Genomics


title: 𝛾𝛿-TCR blockage - KO_𝛾𝛿TCR_1


title: 𝛾𝛿-TCR blockage - KO_IgG_4

value: Treated with IgG once a week for 5 weeks


title: 2019_0204_Le2

city: Fukuoka

first: Akiko

last: Satake

address: Motooka 744

country: Japan

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Custom Gene Expression 8x60K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities for each probe were calculated from the hybridization intensities using GeneSpring Software. The raw signal intensities of all samples were  normalized by the 75 percentile shift algorithm with the GeneSpring.
75 percentile shift normalized signal (log2).

organism: Lithocarpus edulis

source_name: leaf and bud

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA from leaf and bud samples was extracted using hexadecyltrimethylammonium bromide (CTAB) buffer (3% CTAB, 1.4 M NaCl, 20 mM EDTA, 100 mM Tris–HCl pH 8.0, 0.2% b-mercaptoethanol) and was purified using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany)

value: leaf and bud


title: 𝛾𝛿-TCR blockage - KO_𝛾𝛿TCR_2


title: 2019_0204_Le1


title: 𝛾𝛿-TCR blockage - KO_IgG_1


title: 2019_0109_Le3


title: 𝛾𝛿-TCR blockage - KO_IgG_3


title: 2018_1213_Le2


title: 2018_1213_Le1


title: 𝛾𝛿-TCR blockage - KO_IgG_2


title: 2019_0204_Le3


title: 2019_0109_Le1


title: 2018_1213_Le3


title: 𝛾𝛿-TCR blockage - WT_IgG_2

value: PyMT WT


title: 2019_0109_Le2


title: 𝛾𝛿-TCR blockage - WT_IgG_4


title: 2018_1115_Le1


title: 2018_1017_Le2


title: 2018_1115_Le3


title: 2018_0919_Le3


title: 2018_1017_Le3


title: 2018_1017_Le1


title: 2018_0919_Le1


title: 𝛾𝛿-TCR blockage - WT_IgG_3


title: 2018_0821_Le1


title: 2018_1115_Le2


title: 2018_0919_Le2


title: IL-38 neutralization - anti-IL-38_2

value: Treated with anti-IL-38 antibodies once a week for 5 weeks


title: IL-38 neutralization - anti-IL-38_6


title: IL-38 neutralization - anti-IL-38_3


title: 2018_0821_Le2


title: IL-38 neutralization - anti-IL-38_5


title: IL-38 neutralization - anti-IL-38_1


title: 2018_0725_Le2


title: 𝛾𝛿-TCR blockage - WT_IgG_1


title: IL-38 neutralization - IgG_5


title: IL-38 neutralization - IgG_4


title: IL-38 neutralization - IgG_1


title: 2018_0725_Le1


title: 2018_0627_Le3


title: 2018_0821_Le3


title: IL-38 neutralization - IgG_2


title: IL-38 neutralization - IgG_3


title: 2018_0725_Le3


title: 2018_0531_Le3


title: 2018_0627_Le1


title: REC-1, Ibrutinib Resistant, H3K27ac ChIP, Repeat 2

city: Philadelphia

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

data_processing:
Reads were trimmed with Trim Galore (version 0.4.1) with parameters -q 5 --phred33 --gzip --stringency 5 -e 0.1 --length 20 --paired. Trimmed reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (Li and Durbin, 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 12. Paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.29.1) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 369).
Assembly: hg19
Supplementary files format and content: bigWig files for genome browser viewing

growth_protocol: RPMI 1640  supplemented with 10% fetal bovine serum , 2 mM L-glutamine, 100 U/mL and 100 μg/mL penicillin/streptomycin, 100 mM nonessential amino acids, 1mM sodium pyruvate and 0.1mM of 2-mercaptoethanol

extract_protocol:
ChIP-seq was performed using previously published protocol (PMID: 30745086) using H3K27ac antibody (Active Motif, cat# 39133)
NEBNext Ultra II DNA library Prep Kit

treatment_protocol: Parental and resistant cells were treated with DMSO (parental) or ibrutinib (resistant) for 24 hours followed by BCR crosslinking with IgM for 5min. Cells used for ChIP-seq were subsequently fixed with 1% formaldehyde

value: Mantle Cell Lymphoma

value: Ibrutinib


title: REC-1, DMSO, H3K27ac ChIP-seq, Repeat 2

value: DMSO


title: REC-1, Ibrutinib Resistant, H3K27ac ChIP, Repeat 1


title: 2018_0531_Le1


title: Donor 8

city: Trondheim

first: Atle

middle: van  Beelen

last: Granlund

address: Postboks 8905 MTFS

institute: Norwegian University of Science and Technology

data_processing:
Base calling was done on the NextSeq 500 instrument by RTA 2.4.6
FASTQ files were generated using bcl2fastq2 Conversion Software v2.20.0.422 (Illumina, Inc. San Diego, CA, USA). FASTQ files quality controlled with fastqc (v0.11.9), then filtered and trimmed by fastp (v0.20.1).
Transcript counts were generated using quasi alignment (Salmon v1.7.0) to the GRCh38 transcriptome reference sequences. Transcript counts were imported into the R statistical software and aggregated to gene counts using the tximport (v1.120) bioconductor package for downstream statistical analysis.
Assembly: GRCh38
Supplementary files format and content: Text file with raw counts per gene

source_name: Colon organoid

growth_protocol: Colonoids were grown according to protocol published by Gopalakrishnan et al.( Gopalakrishnan, Shreya, et al. "Comprehensive protocols for culturing and molecular biological analysis of IBD patient-derived colon epithelial organoids." Frontiers in Immunology 14 (2023): 1097383.)  In preparation for experiments, single cell suspensions in matrigel (160-200 celles/µl) was prepared, and plated on pre-warmed 24-well plates. For the nine first days, the organoids were grown in a complete medium, encouraging organoid growth. After day nine and until harvestin on day 14, they were grown in differentiation medium to encourage epithelial differentiation. All cultures plates were kept in incubators at 2% O2/5%CO2, in order to better recapture oxygen saturation levels seen in vivo (as described in Walaas, G. A et al. “Physiological hypoxia improves growth and functional differentiation of human intestinal epithelial organoids”. Frontiers in Immunology 14 (2023), 1095812).

extract_protocol:
Medium was removed, and colonoids were washed with PBS (37oC), and plates were subsequently placed on ice. Matrigel domes containing colonoids were lysed in each well (275µL lysis buffer per well). Total RNA was then isolated using mirVana total RNA isolation kit (Invitrogen) according to manufacturer’s protocol. Isolated RNA was stored at -80oC or below until analysis.
RNA sequencing libraries were generated Illumina Stranded mRNA prep (ligation) kit (Illumina, San Diego, CA, USA) according to manufacturer’s instructions. Libraries were normalized and pooled to 2.3 pM and subjected to clustering on a NextSeq 500 HO flowcell (Illumina, San Diego, CA, USA). Paired end read sequencing was performed for 2X148 cycles on a NextSeq 500 instrument (Illumina, Inc. San Diego, CA, USA).

treatment_protocol: From each donor, three wells were seeded. Four donors were ERAP2 proficient, while four were ERAP2 deficient. Thirteen days after seeding, media was exchanged to a differentiation medium containing 10 ng/mL IFNg, and with A-83-01 removed. The whole experiment was repeated four times, with two donors per round (one ERAP2 proficient, one ERAP2 deficient).

value: Colon organoid

value: Epithelial

value: 10 ng/mL IFNg


title: 2018_0501_Le2


title: 2018_0501_Le3


title: REC-1, DMSO, H3K27ac ChIP-seq, Repeat 1


title: 2018_0531_Le2


title: Donor 6


title: Donor 5


title: Donor 3


title: Donor 7


title: Donor 2


title: Donor 1


title: Donor 4


title: 2018_0404_Le3


title: 2018_0501_Le1


title: MB157-Cas9, SOX9 KO sgRNA, RNA-seq, Rep 3

data_processing:
RNA-seq data was aligned to Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using STAR (version 2.7.10a) with parameters–outFilterIntronMotifs RemoveNoncanonicalUnannotated–alignIntronMax 100000–outSAMstrandField intronMotif–outSAMunmapped Within–chimSegmentMin 25 –chimJunctionOverhangMin 25.
Strand-specific read counts were quantified using Subread (version 1.6.2) featureCounts with parameters -t exon -g gene_id -s 1 -T 6 and used as input to differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files with read count

growth_protocol: MB157-Cas9 cells were maintained in DMEM supplemented with 10% FBS, 100 U/mL and 100 µg/mL penicillin/streptomycin and 2mM L-glutamine with 2μM puromycin

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (QIAGEN)
Libraries were prepared using the SMARTer® Stranded Total RNA-seq Kit v2- Pico Input Mammalian kit (Takara). Three technical replicates were generated for each experiment.

value: Triple Negative Breast Cancer

tag: guide rna

value: SOX9 KO sgRNA


title: 2018_0404_Le1


title: 2018_0309_Le1


title: 2018_0404_Le2


title: 2018_0309_Le2


title: 2018_0208_Le3


title: 2018_0114_Le3


title: MB157-Cas9, SOX9 KO sgRNA, RNA-seq, Rep 1


title: 2018_0114_Le1


title: MB157-Cas9, control sgRNA, RNA-seq, Rep 3

value: control sgRNA


title: MB157-Cas9, control sgRNA, RNA-seq, Rep 2


title: 2018_0114_Le2


title: 2018_0208_Le2


title: 2018_0309_Le3


title: MB157-Cas9, IgG, Cut & Run

data_processing:
reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (Li and Durbin, 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 6. Paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.30.0) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 2.9).
Assembly: hg19
Supplementary files format and content: bigWig files for genome browser viewing
Library strategy: Cut & Run

extract_protocol:
Cut & Run experiments were performed using CUTANA™ ChIC / CUT&RUN Kit 48 rnx (CUTANA  #14-1048) according to manufacturer’s instructions version 3.5. Nuclei were extracted according to manufacturer’s instructions. Nuclei integrity was examined under light microscopy and immediately proceeded with activated ConA bead binding and antibody binding. 100,000 nuclei and 1 µL H3K27ac antibody (Active Motif #39133) were used per replicate and incubated overnight at 4℃ with nutation. Following binding of pAG-MNase and targeted chromatin digestion and release, purified DNA was quantified with Qubit 4 fluorometer.
Library preparation was performed using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB #E7645L) with modifications included in CUTANA protocol. Final libraries were quantified with Tapestation (Agilent # 5067-5583) and KAPA (Roche #KK4824) and paired-end sequenced on Nextseq 500/550.

tag: chip antibody

value: anti-IgG


title: 2017_1213_Le2


title: MB157-Cas9, control sgRNA, RNA-seq, Rep 1


title: 2017_1115_Le3


title: MB157-Cas9, SOX9 KO sgRNA, H3K27ac, Cut & Run, Rep 1


title: 2018_0208_Le1


title: 2017_1213_Le3


title: 2017_1115_Le2


title: 2017_1213_Le1


title: MB157-Cas9, control sgRNA, H3K27ac, Cut & Run, Rep 2


title: MB157-Cas9, SOX9 KO sgRNA, RNA-seq, Rep 2


title: MB157-Cas9, SOX9 KO sgRNA, H3K27ac, Cut & Run, Rep 2


title: MB157, SOX9.EC3, H3K9me3, ChIP-seq

data_processing:
reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (Li and Durbin, 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 6. Paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.30.0) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 2.9).
Assembly: hg19
Supplementary files format and content: bigWig files for genome browser viewing

growth_protocol: MB157-dCas9 cells were maintained in DMEM supplemented with 10% FBS, 100 U/mL and 100 µg/mL penicillin/streptomycin and 2mM L-glutamine with 2μM puromycin

extract_protocol:
ChIP-seq for histone marks was performed as previously described (Petrovic et al., 2019). Briefly, 1 x 10ˆ7 cells were crosslinked with 1% formaldehyde and lysed. Nuclei were extracted and resuspended in 1% SDS and sonicated using Brandson 450 sonicator with 25% amplitude, 0.5s on, 1s off for a total of 4min 30s on. Solubilized chromatin was then diluted and cleared with IgG (CST cat# 2729S) and recombinant protein G–conjugated Agarose beads (Invitrogen #15920-010) for 1 hour at 4°C. The cleared supernatant was subsequently immunoprecipitated with antibodies recognizing H3K27ac (Active Motif cat# 39133) or H3K9me3 (Active Motif cat#39161) overnight at 4°C. Buffers in all steps above were supplemented with protease inhibitors (Roche cat# 11697498001). Antibody-chromatin complexes were captured with recombinant protein G–conjugated Agarose beads, washed with low salt wash buffer, high salt wash buffer, LiCl wash buffer and TE buffer with 50mM NaCl and eluted. Input sample was prepared by the same approach without immunoprecipitation. ChIP-seq for transcription factors was performed as previously described (Bossen et al., 2015). Briefly, Dynabeads Protein G (ThermoFisherScientific cat# 10003D) was incubated with antibodies recognizing Flag (NETA/SIGMA ALDRICH cat#F1804-5MG) for 8-12 hours in PBS+0.5% BSA at 4°C. 4 x 10ˆ7 cells were crosslinked with 1% formaldehyde and 1.5mM EGS (ThermoFisherScientific cat# 21565) and sonicated using Brandson 450 sonicator with 17% amplitude, 10s on, 1min off for 10 times. Lysate was then cleared by centrifuging for 5min at 16 Kg, 4°C and incubated with antibody-bound beads and 1% Triton Tx-100 (Roche cat# 10789704001) overnight at 4°C. Buffers in all steps above were supplemented with protease inhibitors (Roche cat# 11697498001). Antibody-chromatin complexes captured on beads were then separated on magnet and washed with wash buffer 1, 2, 3, LiCl wash Buffer and TE buffer and eluted.Following elution of histone mark and transcription factor samples, RNase (Roche cat# 10109169001) and Proteinase K (Invitrogen cat# 25530-049) treatments were performed, and reverse crosslinked at 65°C overnight. DNA was purified with QiaQuick PCR Purification Kit (Qiagen, cat# 28106)
Libraries were then prepared using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB cat# E7645S) with single (NEB cat# E7335, cat# E7710) or dual (NEB cat# E7600, cat# E7780) indexing. Two replicates were performed for each condition. Indexed libraries were validated for quality and size distribution using a TapeStation 4150 (Agilent), quantified by KAPA Library Quantification Kit (Roche cat# KK4824) and paired-end sequenced (38 bp+38 bp) on Illumina NextSeq 550.

value: SOX9.EC3 sgRNA,


title: MB157, SOX9.EC2, H3K9me3, ChIP-seq

value: SOX9.EC2 sgRNA


title: 2017_1115_Le1


title: MB157-Cas9, control sgRNA, H3K27ac, Cut & Run, Rep 1


title: MB157, SOX9.EC3 sgRNA, H3K27ac, ChIP-seq


title: MB157, SOX9.EC1, H3K9me3, ChIP-seq

value: SOX9.EC1 sgRNA


title: 2017_1018_Le2


title: MB157, control sgRNA, H3K9me3, ChIP-seq


title: 2017_1018_Le3


title: 2017_1018_Le1


title: MB157, SOX9.EC2 sgRNA, H3K27ac, ChIP-seq


title: 2017_0920_Le2


title: MB157, control sgRNA, H3K27ac, ChIP-seq


title: MB157, SOX9.EC1 sgRNA, H3K27ac, ChIP-seq


title: 2017_0920_Le3


title: MB157, SOX9.EC3 sgRNA, FLAG, ChIP-seq

value: anti-FLAG


title: 2017_0824_Le1

value: leaf and bud


title: 2017_0726_Le3


title: MB157, SOX9.EC2 sgRNA, FLAG, ChIP-seq


title: MB157, SOX9.EC1 sgRNA, FLAG, ChIP-seq


title: 2017_0824_Le3


title: MB157, control sgRNA, FLAG, ChIP-seq


title: opossum, adult, 7

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: polyA RNA-seq

data_processing:
Assembly: ASM229v1
RNA-seq libraries were aligned using HISAT 2.2.1 (Kim et al., 2019) with Ensembl (Yates et al., 2020) release 104 as a reference and -data output type. Output files were converted from SAM format to sorted BAM format using SAMtools-1.12 (Danecek et al., 2021; Li et al., 2009; Murat et al., 2021). Raw count values and FPKM were obtained using StringTie 2.1.4 (Pertea et al., 2016) with the -e and -G options and Ensembl (Yates et al., 2020) ASM229 release 104 or GRCM39 release 104 reference files for opossum and mouse, respectively.
Supplementary files format and content: scRNA-seq: filtered index (.tsv), feature (.tsv), and matrix (.mtx) files
Supplementary files format and content: bulk RNA-seq: tab-delimited text files with FPKM values by gene

organism: Monodelphis domestica

source_name: testis

growth_protocol: Animals were grown under standard laboratory conditions and euthanized at the indicated developmental time points.

extract_protocol:
Bulk RNA-seq libraries were prepared using KAPA mRNA HyperPrep Kit (Roche # 08098123702) and sequenced on an Illumina NovaSeq
Testes from gray short-tailed opossums at Yale or adult (8-16 week old) male C57BL6/J mice purchased from Jackson Laboratories were harvested and dissociated into single-cell suspension for RNA isolation using collagenase and trypsin. Briefly, testes were removed from the scrotum, decapsulated from the tunica albuginea, and incubated in 0.75mg/mL collagenase in Dulbecco’s Modified Eagle Medium (Gibco 11965-09L; Thermo Fisher Scientific, Inc.) at 37oC. DMEM was added to dilute collagenase and samples were centrifuged for 5 minutes at 400 x g at room temperature. Supernatant was discarded and samples were washed in DMEM. Samples were resuspended in 0.05% trypsin-EDTA (Gibco 25300-054; Thermo Fisher Scientific Inc.) with DNAse (1:10,000; Stem Cell Technologies #07900, Vancouver BC, Canada). The reaction was quenched with 10% Cosmic Calf Serum (Sigma-Aldrich #C8056, Burlington, MA, USA) in DMEM (CCS-DMEM) and centrifuged. Samples were resuspended in CCS-DMEM and filtered through a 100-micron filter. Cell concentration was determined by hemocytometer.

value: testis

value: adult


title: 2017_0726_Le2


title: opossum, adult, 4

description: polyA RNA-seq


title: 2017_0824_Le2


title: opossum, adult, 5

description: polyA RNA-seq


title: 2017_0920_Le1


title: 2017_0628_Le2


title: 2017_0628_Le1


title: 2017_0726_Le1


title: 2017_0628_Le3


title: 2017_0601_Le3


title: 2017_0601_Le2


title: 2017_0503_Le3


title: WT3

first: Yunjun

last: Yin

address: 2 Yuanmingyuan West Road

institute: China Agricultural University

data_processing:
SOAPnuke  v1.5.2
HISAT2 v2.0.4 was used to align the clean reads to the reference genome.
Bowtie2 was used to align the clean reads to the reference genes.
Assembly: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: txt file includes gene id, gene symbol, FPKM, TPM, Read count, average FPKM, average TPM and average Read count.

organism: Sus scrofa

source_name: liver

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Optimal Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

value: liver

value: WT


title: 2017_0601_Le1


title: 2017_0503_Le1


title: WT1


title: WT2


title: opossum, adult, 1

description: polyA RNA-seq


title: opossum, adult, 3

description: polyA RNA-seq


title: opossum, adult, 6

description: polyA RNA-seq


title: opossum, 4M, 2

description: polyA RNA-seq

value: 4 months


title: 2017_0503_Le2


title: S05


title: opossum, 4M, 1

description: polyA RNA-seq


title: S03


title: IL-38 neutralization - anti-IL-38_4

value: PyMT WT

value: Treated with anti-IL-38 antibodies once a week for 5 weeks

value: PyMT tumors


title: 2018_0627_Le2


title: opossum, 3M, 4

description: polyA RNA-seq

value: 3 months


title: opossum, 3M, 3

description: polyA RNA-seq


title: Ribo_body_KO2_2

city: Wako city

first: Shintaro

last: Iwasaki

address: 2-1, Hirosawa

department: CPR

institute: RIKEN

data_processing:
Library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: dm6
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

organism: Drosophila melanogaster

source_name: body

extract_protocol:
Testes were dissected from 2-3-day-adult-males in ice-cold PBS with 100 µg/ml cycloheximide. Dissected testes were immediately frozen with liquid nitrogen and stored at −80°C. We prepared 600 pairs of testes per sample. We prepared two replicates from WT (y1 w1118) and Mettl1-KO (Mettl1KO1) males, respectively.
Ribo-seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. RNA-seq: the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).

value: body


title: opossum, adult, 2

description: rRNA depleted RNA-seq

extract_protocol:
Bulk RNA-seq libraries were prepared usingKAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche # 08098140702) and sequenced on an Illumina NovaSeq
Testes from gray short-tailed opossums at Yale or adult (8-16 week old) male C57BL6/J mice purchased from Jackson Laboratories were harvested and dissociated into single-cell suspension for RNA isolation using collagenase and trypsin. Briefly, testes were removed from the scrotum, decapsulated from the tunica albuginea, and incubated in 0.75mg/mL collagenase in Dulbecco’s Modified Eagle Medium (Gibco 11965-09L; Thermo Fisher Scientific, Inc.) at 37oC. DMEM was added to dilute collagenase and samples were centrifuged for 5 minutes at 400 x g at room temperature. Supernatant was discarded and samples were washed in DMEM. Samples were resuspended in 0.05% trypsin-EDTA (Gibco 25300-054; Thermo Fisher Scientific Inc.) with DNAse (1:10,000; Stem Cell Technologies #07900, Vancouver BC, Canada). The reaction was quenched with 10% Cosmic Calf Serum (Sigma-Aldrich #C8056, Burlington, MA, USA) in DMEM (CCS-DMEM) and centrifuged. Samples were resuspended in CCS-DMEM and filtered through a 100-micron filter. Cell concentration was determined by hemocytometer.


title: Ribo_body_KO2_1


title: Ribo_body_KO1_2


title: opossum, 3M, 2

description: polyA RNA-seq


title: opossum, 3M, 1

description: polyA RNA-seq


title: opossum, 4M, 3

description: polyA RNA-seq


title: Ribo_body_WT1_2

value: CT


title: S04


title: opossum, 2M, 3

description: rRNA depleted RNA-seq

value: 2 months


title: Ribo_body_WT1_1


title: opossum, 2M, 2

description: rRNA depleted RNA-seq


title: opossum, 1M, 2

description: polyA RNA-seq

value: 1 month


title: Ribo_testis_KO1_2


title: Ribo_testis_WT2_2


title: opossum, 1M, 1

description: polyA RNA-seq


title: Ribo_testis_KO2_2


title: Ribo_testis_WT1_2


title: opossum, 2M, 1

description: polyA RNA-seq