title: d_14d_3

description:
circRNA_normalizedcounts.txt
lncRNA_normalizedcounts.txt
mRNA_normalizedcounts.txt
circRNA_raw_counts.txt
lncRNA_raw_counts.txt
mRNA_raw_counts.txt

value: post natal day 28

value: dexamethasone intraperitoneal injection at a dose of 2.0 mg/kg/d for 14 days


title: GRNY2

status: Public on Dec 01 2022

type: SRA

city: apex

first: Lyle

last: Burgoon

state: nc

address: 216 kelly west dr

department: Environmental Laboratory

country: USA

institute: US Army Engineer Research and Development Center

library_source: transcriptomic

data_processing:
Our RNA-sequencing analysis pipeline is focused on measuring the abundance of gene transcripts, giving us a measure of gene expression. We start by using Salmon to align and measure the number of RNA molecules. Gene-specific transcript abundance is then calculated using the tximport package in R. We narrowed down the genes to those represented in our Adverse Outcome Pathway Networks for steatosis, energy balance, cell cycle, and cell death. We focused on these networks as they serve as the precursor for liver tumor formation (tumorigenesis) and cancer (carcinogenesis), as well as yields insights into energy availability, which may impact fitness and population health.
Genome_build: GRCh38
Supplementary_files_format_and_content: Table/matrix where first column is the gene symbol, subsequent columns are the sites where water samples were obtained. CONTROL is a control water sample from a reference laboratory.

molecule: total RNA

organism: Homo sapiens

growth_protocol: HepG2 cells (ATCC, Manassas, VA) were cultivated at 37 °C in a humidified 5% CO2 atmosphere as monolayer cultures in Dulbecco's modified Eagle's medium (DMEM, Fisher Scientific, Pittsburgh, PA) supplemented with 100 units/mL penicillin, 100 g/mL streptomycin, 15 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES, Fisher Scientific), and 10% (v/v) heat inactivated fetal bovine serum (FBS, Atlanta Biological, Atlanta, GA). To prepare HepG2 cells for exposure, two T225 flasks of cells were harvested after they reached 80-90% confluence. Cells were combined and evenly distributed to 88 6-cm dishes (there were 4 biological replicates for each of 16 sampling locations, 16 replicates for the laboratory controls, and 8 spare dishes) for precultivation in 5% CO2 at 37 °C for 72 hours.

extract_protocol:
After the 48-hour exposure, cells were harvested with RNALater (Sigma-Aldrich, St. Louis, MO). Briefly, exposure medium was quickly removed from the culture dish and 1 mL RNALater was added to each dish. The cells were detached from the dish bottom with a cell lifter and transferred to a 2-mL centrifuge tube. The harvested cells were kept at 4 °C for 2 hours before stored at -80 °C.
RNA was shipped to BioSpyder for sequencing using their TempO-Seq platform. We received FASTQ files from BioSpyder that contained our sequencing results.

treatment_protocol: For cell exposure experiments, exposure medium was prepared by mixing stock medium with the field-collected grab samples. Specifically, a DMEM with a four-fold higher concentration (4x stock) was prepared with all above supplements, plus 0.4 mg/mL normocin (Invivogen, San Diego, CA). This 4x stock medium was mixed in a ratio of 1:3 with a filtered (0.7 µm) water sample from each field site, or with purified water (ultrapure type 1, 18.2 MΩ.cm, 0.1-µm filtered, Aqua Solutions, Jasper, GA) that served as the laboratory control. The final concentrations of environmental samples in the exposure medium were 75% of the initial field-collected water samples. Cells were then incubated in 5% CO2 at 37 °C for 48 hours before quench.

tag: cell line

tag: cell type

value: hepatoma cell line

tag: surface water site

value: GRNY

tag: protocol

value: TempO-Seq


title: APP allergy, scRNAseq

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Brain

extract_protocol:
Mice were anesthetized by inhalation with isoflurane, and after PBS perfusion, the brain parenchyma was removed and homogenized in 2% FBS/RPMI solution containing glucose and HEPES. After straining and centrifugation at 400 x g for 5 minutes, the pellet was resuspended in 37% Percoll (Cytiva), cells were isolated by centrifugation with slow acceleration/deceleration 800 x g for 20 minutes and resuspended with filtered 0.5% BSA/PBS. Totalseq-Hashtag antibody (BioLegend) was incubated with each sample, and CD45.2+ cells were sorted by FACSMelody (BD Biosciences).
Libraries were prepared according to the protocol of the Chromuim Next GEM Single Cell 5' Reagent Kits v2 (Dual Index, 10x Genomics, Pleasanton, CA, USA) using a Chromium controller (10x Genomics). Briefly, GEMs were prepared by loading barcoded Single Cell VDJ 5' Gel Beads, master mix containing cells and RT enzymes, and Oil onto Chromium Next GEM Chip K. Barcoded cDNA was then generated from the GEM. This cDNA was amplified by PCR reaction to generate V(D)J, 5' Gene Expression and Feature Barcode libraries.

treatment_protocol: WT and APPNL-G-F mice were housed in cages according to experimental group. The control groups received only water, the acute colitis groups received DSS (2%, w/v, MW = 36–50 kDa; MP Biomedicals, LLS, Santa Ana, CA, USA) in their drinking water for one week, and the chronic colitis group received three cycles of alternating 2% DSS then only water, each for five days.

value: Immune cells

tag: tissue

value: Brain

tag: strain

value: APPNL-G-F

tag: age

value: 16 weeks old


title: RNA-Seq H1299-R213X5FUR-4

city: Utrecht

first: Sebastiaan

last: van Heesch

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

data_processing:
use cutadapt v3.4 to trim the data to 29 NT and remove low-quality reads with the following parameters:
STAR v2.7.8a with reference assembly ensembl 102 and the following parameters: --outFilterMismatchNmax 6; --outFilterMultimapNmax 10; --alignSJoverhangMin 10 --outFilterScoreMinOverLread 0.75
run FeatureCount v2.0.2 with the following parameters: -t "CDS"  -g "gene_id" -O  -s 1
use cutadapt v3.4 with --hardtrim5 29 to trim RNA-seq reads to ribo-seq length and follow ribo-seq data processing protocol
Genome_build: hg38
Supplementary_files_format_and_content: count files with raw gene counts for all data generated by FeatureCount

molecule: polyA RNA

source_name: epithelial

growth_protocol: H1299 human lung adenocarcinoma parental cells (ATCC, USA), which are p53 null, were stably transfected with R213X nonsense mutant TP53, Empty Vector (EV) as a control, or other plasmid constructs as described (Zhang et al., Front Oncol 2018). Stably transfected cells were cultured in RPMI-1640 medium (Hyclone, USA) supplemented with 25 mM HEPES Buffer solution (Gibco, USA) and 10% fetal bovine serum (Gibco, USA).

extract_protocol:
Total RNA was isolated from 200 µl of lysate using 750 µl of TRIzol LS and purified using the Zymo RNA Clean and Concentrator-5 kit with modifications to the manufacturer's instructions: Recovered RNA was treated with DNAse I at 37°C for 10 min prior to addition of RNA Binding Buffer, and isolated RNA was eluted in 15 µl nuclease-free water. Prior to library preparation, purified RNA was quantified and checked for RNA integrity with Agilent Bioanalyzer 2100 using the RNA 6000 Nano kit according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded at a density of 0.3 x 106 cells/15 cm dish for non-treated and G418-treated conditions or at a density of 2.3 x 106 cells/15 cm dish for FUr-treated condition in a final volume of 32 ml. One day after seeding the cells, they were treated with 100 µM of G418 or 3 µM of 5-Fluorouridine for 72h, respectively, using four replicate treatments per condition. Next, medium was aspirated, cells were washed once with 5 ml of ice-cold Dulbecco’s Phosphate Buffered Saline (DPBS), and plates were snap frozen with liquid nitrogen.

tag: vector

tag: treatment

value: FUr


title: c_7d_1_samll

city: Shanghai

first: Yuan

last: Xiao

address: No.197, Rui Jin Er Road

department: Department of Pediatrics

country: China

institute: Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine,

description:
miRNA_normalizedcounts.txt
miRNA_raw_counts.txt

data_processing:
Illumina Bustard used for basecalling.
For lncRNA sequences, the clean reads were aligned to the rat reference genome (rattus norvegicus genome obtained from Ensembl Rnor_6.0) with the software Hisat2 (version 2.0.5; main parameter: --no-unal -t --phred33 --rna-strandness RF --dta-cufflinks --un-conc-gz). For small RNA sequences, the small RNA tags were mapped to reference sequence by Bowtie (version 0.12.9; main parameter: -v 0 -k 1) and miRBase20.0 (rattus norvegicus) was used as reference.
Quantification of the transcripts was performed using StringTie software and Fragments Per Kilobase of transcript per Millions base pairs sequenced (FPKM) was use to determine the expression level of mRNAs and lncRNAs. miRNA and circRNA expression levels were estimated by transcript per million (TPM) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000.
Genome_build: rattus norvegicus genome obtained from Ensembl (Rnor_6.0) and miRBase20.0 (rattus norvegicus)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of mRNA and lncRNA for each Sample; tab-delimited text files include TPM values of miRNA and circRNA for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: proximal tibia growth plate

extract_protocol:
The proximal tibia growth plates were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA Library Prep Plant/Gold/Globin +NEBNext® Ultra Directional RNA Library Prep Kit (Cat#RS-122-2303) was used with total RNA for the construction of lncRNA sequencing libraries. NEB Next® Multiplex Small RNA Library Prep Set for Illumina® (Set 1) (Cat#E7300) was used with total RNA for the construction of small RNA sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SD rats at postnatal 14 days were treated with 2 mg/kg/d of dexamethasone for 7 or 14 days (intraperitoneal injection), after which growth plate tissue was obtained from the rat proximal tibia. Control rats received the same volume of saline.

value: Sprague-Dawley

value: proximal tibia growth plate

value: post natal day 21

value: saline intraperitoneal injection at a dose of 2.0 mg/kg/d for 7 days


title: RNA-Seq H1299-R213X5FUR-1


title: d_14d_2


title: GRNY1


title: RNA-Seq H1299-R213XG418-3


title: GRMI4

value: GRMI


title: APP chronic, scRNAseq

description: 10x Genomics


title: d_14d_1


title: RNA-Seq H1299-R213XG418-5


title: WT chronic, scRNAseq

description: 10x Genomics


title: APP acute, scRNAseq

description: 10x Genomics


title: c_14d_2

value: saline intraperitoneal injection at a dose of 2.0 mg/kg/d for 14 days


title: APP control, scRNAseq

description: 10x Genomics


title: RNA-Seq H1299-R213XG418-2


title: c_14d_3


title: GRMI11


title: RNA-Seq H1299-R213X5FUR-2


title: WT allergy, scRNAseq

description: 10x Genomics


title: d_7d_3

value: dexamethasone intraperitoneal injection at a dose of 2.0 mg/kg/d for 7 days


title: RNA-Seq H1299-R213X-5

value: untreated


title: RNA-Seq H1299-R213X-3


title: FRWI4

value: FRWI


title: RNA-Seq H1299-R213X-2


title: WT acute, scRNAseq

description: 10x Genomics


title: GRMI3

value: hepatoma cell line


title: RNA-Seq H1299-R213X-1


title: WT control, scRNAseq

description: 10x Genomics


title: FRWI3


title: Cardiomyocyte, AdGFP, Biol Rep 3

city: San Francisco

first: Antonio

last: Cuevas-Navarro

state: CA

department: HDFCCC

institute: UCSF

description: matrix column name: AdGFP_3

data_processing:
Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: matrix inlcudes FPKM values for all samples

source_name: neonatal heart

growth_protocol: Primary cardiomyocytes were isloated and maintained in DMEM supplemented with 10% FBS, 10% Nu serum (Corning), 1x Penicillin-Streptomycin (Gibco), 1x Glutamax (Gibco), 1x ITS liquid medium supplement (Sigma), and 10 mM HEPES (Gibco) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

treatment_protocol: On day 3 post-isolation, infected with 2 x 10^8 adenoviral particles encoding GFP (AdGFP) or GFP-Cre (AdCre).

value: neonatal heart

value: primary cardiomyocytes

value: cardiac myocytes

tag: genotype

value: GFP control adenovirus


title: d_7d_2


title: FRWI2

value: TempO-Seq


title: RNA-Seq H1299-R213XG418-1


title: d_7d_1


title: Cardiomyocyte, AdGFP, Biol Rep 2

description: matrix column name: AdGFP_2


title: FRWI1


title: GRMI2


title: CTRL8

value: CTRL


title: c_14d_1

value: post natal day 28


title: RNA-Seq H1299-EV5FUR-4

value: EV

value: FUr


title: CTRL7


title: Cardiomyocyte, AdCre, Biol Rep 3

description: matrix column name: AdCre_3

value: Rit1 M90I/+

value: Cre Recombinase adenovirus


title: RNA-Seq H1299-EV5FUR-3


title: RNA-Seq H1299-EV5FUR-2


title: Cardiomyocyte, AdGFP, Biol Rep 1

description: matrix column name: AdGFP_1


title: Cardiomyocyte, AdCre, Biol Rep 2

description: matrix column name: AdCre_2


title: c_7d_2

value: Sprague-Dawley

value: proximal tibia growth plate

value: post natal day 21

value: saline intraperitoneal injection at a dose of 2.0 mg/kg/d for 7 days


title: Cardiomyocyte, AdCre, Biol Rep 1

description: matrix column name: AdCre_1


title: c_7d_1


title: RNA-Seq H1299-EV5FUR-1


title: RNA-Seq H1299-EVG418-5


title: c_7d_3


title: RNA-Seq H1299-EVG418-2


title: GC_VH1-2_VK1-33-CS_TdT_D8_Vk1-33_3

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

description: LAM-HTGTS-Rep-SHM-Seq

library_source: genomic

data_processing:
HTGTS-rep-seq and LAM-HTGTS-Rep-SHM-Seq data analysis was done by the LAM-HTGTS-Rep-SHM-Seq bioinformatics pipeline (Github address: https://github.com/Yyx2626/HTGTSrep), using IgBLAST with default parameters for qualified reads mapping. Only reads with more than 98% of the sequences having a sequencing Quality Score ≥20 were kept; only joined reads (R1 and R2 had an overlap region ≥10 bp and mismatch rate ≤8%) were kept.
Assembly: mm9
Supplementary files format and content: .db.txt files were generated using LAM-HTGTS-Rep-SHM-Seq pipeline (IgBLAST).

molecule: genomic DNA

source_name: spleen

extract_protocol:
Splenic B cells used for HTGTS-rep-seq were purified from unimmunized 5-8 weeks old mice by MACS® Microbeads according to the manufacturer’s protocol. In brief, spleens were dissected out from unimmunized mice, prepared into single cell suspensions and stained with anti-B220 Microbeads for 20 minutes at 4°C. The splenic B cells were collected using the LS column and MACSTM Separater. GC B cells used for LAM-HTGTS-Rep-SHM-Seq were purified from 8-12 weeks old mice after eOD-GT8 60mer immunization. GC B cells were sorted for the phenotype B220+ (BV711: BioLegend 103255), CD95+ (PE-Cy7: eBioscience 557653) and GL7+ (PE: BioLegend 144607). Genomic DNA from sorted cells was prepared using a DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer’s protocol.
The libraries of LAM-HTGTS-Rep-SHM-Seq was constructed as previous described (Chen et al., 2020) and the libraries of HTGTS-Rep-seq was constructed as previous described (Lin et al., PNAS 2016)

value: splenic GC B cells (GL7+, CD95+)

value: C57BL/6 and 129/Sv mix

value: spleen

tag: locus (ig heavy-chain or light-chain)

value: IgK

tag: conditions

value: Day 8 post-immunization with eOD-GT8 60mer

tag: primers


title: CTRL5

value: hepatoma cell line


title: CTRL4

value: TempO-Seq


title: RNA-Seq H1299-EVG418-4


title: Heart, Trametinib, Biol Rep 3

description: matrix column name: T3

source_name: Heart

value: Heart

value: cardiac tissue

value: Trametinib (MEKi)


title: Heart, Trametinib, Biol Rep 4

description: matrix column name: T4


title: CTRL2

value: CTRL


title: GC_VH1-2_VK1-33-CS_TdT_D8_Vk1-33_2

description: LAM-HTGTS-Rep-SHM-Seq


title: CTRL3


title: GC_VH1-2_VK1-33-CS_TdT_D8_Vk1-33_1

description: LAM-HTGTS-Rep-SHM-Seq


title: Heart, Trametinib, Biol Rep 1

description: matrix column name: T1

value: Rit1 M90I/+


title: RNA-Seq H1299-EV-4

value: EV

value: untreated


title: GC_VH1-2_VK1-33-CS_D8_Vk1-33_2

description: LAM-HTGTS-Rep-SHM-Seq


title: GC_VH1-2_VK1-33-CS_D8_Vk1-33_1

description: LAM-HTGTS-Rep-SHM-Seq


title: Heart, Trametinib, Biol Rep 2

description: matrix column name: T2


title: RNA-Seq H1299-EVG418-1


title: CROH4

value: CROH


title: CROH3


title: Heart, Trametinib, Biol Rep 5

description: matrix column name: T5


title: RNA-Seq H1299-EV-5


title: Heart, Vehicle, Biol Rep 4

description: matrix column name: V4

value: Vehicle control


title: CTRL6


title: iMacrophage_oxENDseq

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
bigwig files were made for positive (*.pos.bw) and negativ (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig
Assembly: hg19 for human, mm10 for mourse.
Library strategy: END-seq

source_name: iMacrophage

growth_protocol: For neuronal differentiation, 20–25 million iPSCs were plated on day 0 onto a 15-cm plate in N2 medium (knockout Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium; Life Technologies Corporation, cat. no. 12660012) with N2 supplement (Life Technologies, cat. no. 17502048), 1× GlutaMAX (Thermofisher Scientific, cat. no. 35050061), 1× MEM nonessential amino acids (NEAA) (Thermofisher Scientific, cat. no. 11140050), 10 μM ROCK inhibitor (Y-27632; Selleckchem, cat. no. S1049), and 2 μg/ml doxycycline (Clontech, cat. no. 631311). N2 medium was changed once a day for two more days. On day 3, cells were replated onto freshly prepared dishes coated with freshly prepared poly-L-ornithine (PLO; 0.1 mg/ml; Sigma, cat. no. P3655-10MG). Pre-neuron cells were cultured in i3Neuron Culture Media: BrainPhys media (Stemcell Technologies, cat. no. 05790) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific, cat. no. A3582801), 10 ng ml−1 BDNF (PeproTech, cat. no. 450-02), 10 ng ml−1 NT-3 (PeproTech, cat. no. 450-03), 1 μg ml−1 mouse laminin (Sigma, cat. no. L2020-1MG), and 2 μg ml−1 doxycycline (Clontech, cat. no. 631311). i3Neurons were then fed by half media change on day 6 and then, collected on day 7. For the pre-B-to-macrophage transdifferentiation, C10 cells were induced to reprogram by the addition of 100 nM of β-estradiol (Sigma-Aldrich; Cat. #E8875) and grown with 10 ng/ml of IL-3 (Peprotech; Cat. #213-13), CSF-1 (Peprotech; Cat. #315-02) and 350 nM Ascorbic acid (Sigma-Aldrich; Cat. # A8960) and then collected on day 2.

extract_protocol:
For END-seq, live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing. For S1-END-seq, cells were collected and embedded in 1% agarose plugs, lysed and digested with Proteinase K (1 hour at 50°C, followed by 7 hours at 37°C), washed with TE buffer, and then treated with RNAse A for 1 hour at 37°C. Plugs were then washed in EB and equilibrated in S1 nuclease buffer (40 mM sodium acetate pH 5.2, 300 mM NaCl, 2 mM ZnSO4) for 30 minutes. 1.8 U of S1 nuclease was added to 100 µL of S1 nuclease buffer per plug and incubated on ice for 15 minutes to allow for the enzyme to diffuse into the plug. The reaction mix was then placed at 37°C for 20 minutes before addition of EDTA (10 mM final concentration) to terminate the reaction. Finally, plugs were processed through the standard END-seq protocol
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).

treatment_protocol: In the indicated experiments cells were treated with the following compounds: For iMacrophages, Aphidicolin (APH; 4 μM) 4 hours before EdU incubation; PARPi (Olaparib; 5 μM) and ddC (20 µM) were added 20 hours prior to harvest. For chain-terminating nucleosides, 20 µM of each of ddA, ddT, ddG and ddC was added to cells for 18 hours prior to cell harvesting for END-seq and S1-END-seq.

value: TDG-/-

value: pyridine borane 3hrs

tag: dose

tag: in-situ treatment

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37°C for 20 mins. 5 U of USER @15 mins on ice, followed by 37°C for 1 hour.

tag: harvested day


title: GC_VH1-2_VK1-33-CS_D8_Vk1-33_3

description: LAM-HTGTS-Rep-SHM-Seq

value: splenic GC B cells (GL7+, CD95+)

value: C57BL/6 and 129/Sv mix

value: spleen


title: GC_VH1-2_VK1-33_VK3-20_TdT_D36_VK3-20_2

description: LAM-HTGTS-Rep-SHM-Seq

value: IgK

value: Day 36 post-immunization with eOD-GT8 60mer


title: RNA-Seq H1299-EV-1


title: RNA-Seq H1299-EV-3


title: GC_VH1-2_VK1-33_VK3-20_TdT_D36_VK3-20_3

description: LAM-HTGTS-Rep-SHM-Seq


title: CRMI3

value: hepatoma cell line

value: CRMI

value: TempO-Seq


title: Heart, Vehicle, Biol Rep 5

description: matrix column name: V5

value: Heart

value: cardiac tissue


title: CROH2


title: GC_VH1-2_VK1-33_VK3-20_TdT_D36_VH1-2_2

description: LAM-HTGTS-Rep-SHM-Seq

value: IgH


title: GC_VH1-2_VK1-33_VK3-20_TdT_D36_VH1-2_1

description: LAM-HTGTS-Rep-SHM-Seq


title: Heart, Vehicle, Biol Rep 3

description: matrix column name: V3

value: Rit1 M90I/+


title: CROH1

value: CROH


title: Liver_RECTAS_2

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

data_processing:
Basecalling was performed with RTAVersion v3.3.3
The seuqence data was mapped to the genome sequence with HISAT2 ver. 2.2.0.
Assembly: GRCm38
Supplementary files format and content: Expression TPM values of refseq gene models were calculated with RSEM ver. 1.3.0.

source_name: C57BL/6N mouse

growth_protocol: C57BL/6N mice were maintained in animal facility of Kyoto University Graduate School of Medicine.

extract_protocol:
Tissues were homogenized in TRIzol reagent, and extracted with chloroform.
TruSeq stranded mRNA Library kit was used.

treatment_protocol: 7-weeks old C57BL/6N mice were per os administered with 100 mg/kg body weight RECTAS in 0.5% CMC or 0.5% CMC only with 4 h interval. Tissues were collected 8 h after the first administration.

tag: condition

value: 100 mg/kg body weight RECTAS in 0.5percent CMC po administration for 8 h

value: liver


title: RNA_CR_111

city: Lausanne

first: kevin

last: perez

address: rue du Bugnon 27

country: Switzerland

institute: University of Lausanne

data_processing:
Adapter trimming: Trim Galore! version 0.6.6 in paired end mode
Alignment: Bowtie2 version 2.2.5, bowtie2 --very-sensitive -k 10 -X 1000 --dovetail
Filtering: remove multi-mapping, improper pairs Samtools version 1.9, samtools view -f 0x2 -F 0x100
Filtering: remove duplicates, Picard tools version 2.25.6, MarkDuplicates --REMOVE_DUPLICATES true
Peak calling: Genrich version 0.6.1 in atac mode, ignoring ENCODE blacklist, outputting tn5 cut site BED files, q < 0.05
Count matrix: Bedtools version 2.30.0, count the number of tn5 cut sites intersecting (bedtools intersect -c) the union peakset (bedtools merge of individual peaksets)
Alignment: STAR aligner (v2.7.9a) with '--sjdbOverhang 100'.
Counting: featureCounts, Subread package (v2.0.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated from whole blood using histopaque.
RNA libraries were constructed using standard Illumina protocols

value: Peripheral blood mononuclear cells

tag: gender

value: M


title: RNA_CR_107

tag: cell type

value: F


title: CRMI1

tag: cell line

tag: surface water site


title: CTRL1

value: CTRL

tag: protocol


title: BRWI4

value: BRWI


title: GC_VH1-2_VK1-33_VK3-20_TdT_D36_VK3-20_1

description: LAM-HTGTS-Rep-SHM-Seq

value: splenic GC B cells (GL7+, CD95+)

tag: strain

value: C57BL/6 and 129/Sv mix

tag: tissue

value: spleen

value: IgK


title: Heart, Vehicle, Biol Rep 2

description: matrix column name: V2

value: Vehicle control


title: VH1-2_VK1-33-CS_VK3-20_TdT_SP_IgK_1

description: HTGTS-Rep-Seq

value: splenic B220+ B cells

value: naïve


title: Liver_Veh_3

value: 0.5percent CMC po administration  for 8 h


title: CRMI4

value: hepatoma cell line

value: CRMI

value: TempO-Seq


title: RNA_CR_105

tag: age


title: RNA_CR_110


title: BRWI3


title: Liver_Veh_2

value: liver


title: GC_VH1-2_VK1-33_VK3-20_TdT_D36_VH1-2_3

description: LAM-HTGTS-Rep-SHM-Seq

value: IgH

value: Day 36 post-immunization with eOD-GT8 60mer


title: Heart, Vehicle, Biol Rep 1

description: matrix column name: V1

value: Heart

value: cardiac tissue

value: Rit1 M90I/+

tag: treatment


title: Liver_RECTAS_3

value: 100 mg/kg body weight RECTAS in 0.5percent CMC po administration for 8 h


title: BRWI2

value: BRWI


title: CRMI2


title: RNA_CR_108

value: Peripheral blood mononuclear cells

value: M


title: Liver_Veh_1


title: VH1-2_VK1-33_VK3-20_TdT_SP_IgK_2

description: HTGTS-Rep-Seq

value: C57BL/6 and 129/Sv mix

value: spleen

value: IgK


title: RNA_CR_106

value: F


title: BRWI1

value: hepatoma cell line


title: Liver_RECTAS_1


title: VH1-2_VK3-20_TdT_SP_IgK_3

description: HTGTS-Rep-Seq

value: splenic B220+ B cells

value: naïve


title: Lung_RECTAS_2

value: lung


title: RNA_CR_109


title: RNA_CR_104


title: VH1-2_VK1-33_VK3-20_TdT_SP_IgK_1

description: HTGTS-Rep-Seq


title: VH1-2_VK1-33-CS_VK3-20_TdT_SP_IgK_2

description: HTGTS-Rep-Seq


title: Lung_RECTAS_3


title: RNA_CR_101


title: Krishnan_786-0_Everolimus_4hr_5

city: Chapel Hill

first: Bhavani

last: Krishnan

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina

data_processing:
75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to the human reference genome using MapSplice
The alignment profile was determined by Picard Tools v1.64 (http://broadinstitute.github.io/picard/).
Aligned reads were sorted and indexed using SAMtools and translated to transcriptome coordinates then filtered for indels, large inserts, and zero mapping quality using UBU v1.0 (https://github.com/mozack/ubu).
Transcript abundance estimates for each sample were performed using RSEM, an expectation-maximization algorithm using the UCSC knownGene transcript and gene definitions.
Raw RSEM read counts for all RNAseq samples were normalized to the overall upper quartile
genome build: hg19
Supplementary_files_format_and_content: Excel file includes normalized RSEM values for each sample

source_name: 786-0 cellline

growth_protocol: 786-0 cell were cultered in DMEM

extract_protocol:
RNA was extracted with Qiagen Rneasy Kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)

treatment_protocol: 786-0 cells were treated with either a DMSO vehicle or 10um Everolimus in DMSO for 4 hours

value: renal cell carcinoma

value: 4hr Everolimus


title: Krishnan_786-0_Everolimus_4hr_4


title: RNA_CR_102


title: Lung_RECTAS_1


title: VH1-2_VK1-33_VK3-20_TdT_SP_IgK_3

description: HTGTS-Rep-Seq


title: VH1-2_VK3-20_TdT_SP_IgK_2

description: HTGTS-Rep-Seq


title: VH1-2_VK3-20_TdT_SP_IgK_1

description: HTGTS-Rep-Seq


title: RNA_CR_100


title: Krishnan_786-0_Everolimus_4hr_3


title: Krishnan_786-0_Everolimus_4hr_2


title: RNA_CR_099


title: VH1-2_VK1-33-CS_TdT_SP_IgK_5

description: HTGTS-Rep-Seq


title: Lung_Veh_3

value: 0.5percent CMC po administration  for 8 h


title: RNA_CR_098


title: RNA_CR_103


title: Lung_Veh_2


title: Krishnan_786-0_Everolimus_4hr_1


title: VH1-2_VK1-33-CS_TdT_SP_IgK_4

description: HTGTS-Rep-Seq


title: Lung_Veh_1


title: Krishnan_786-0_Control_6

value: Control


title: RNA_CR_097


title: RNA_CR_096


title: VH1-2_VK1-33-CS_TdT_SP_IgK_2

description: HTGTS-Rep-Seq


title: Colon_RECTAS_3

value: colon


title: Colon_RECTAS_2

value: 100 mg/kg body weight RECTAS in 0.5percent CMC po administration for 8 h


title: VH1-2_VK1-33-CS_TdT_SP_IgK_3

description: HTGTS-Rep-Seq


title: Krishnan_786-0_Control_5


title: Krishnan_786-0_Control_4


title: RNA_CR_095


title: Krishnan_786-0_Control_3


title: Krishnan_786-0_Control_2


title: VH1-2_VK3-20_SP_IgK_3

description: HTGTS-Rep-Seq


title: RNA_CR_094


title: RNA_CR_093


title: VH1-2_VK1-33-CS_TdT_SP_IgK_1

description: HTGTS-Rep-Seq


title: Colon_RECTAS_1


title: VH1-2_VK3-20_SP_IgK_2

description: HTGTS-Rep-Seq


title: Krishnan_786-0_Control_1


title: VH1-2_VK3-20_SP_IgK_1

description: HTGTS-Rep-Seq


title: Colon_Veh_1


title: Colon_Veh_3


title: Colon_Veh_2


title: VH1-2_VK1-33-CS_SP_IgK_5

description: HTGTS-Rep-Seq


title: RNA_CR_091


title: exe2-14-0_9

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

data_processing:
Alignment to reference assembly mm10 using Tuxedo bowtie
Mapping results filtering performed using Tuxedo cuffquant
Read counting for each gene and normalization to FPKM values performed using Tuxedo cuffnorm
Assembly: mm10
Supplementary files format and content: FPKM value for each gene in csv table format

source_name: Dorsal Hippocampus

extract_protocol:
RNeasy minikit (Qiagen, 74104)
TruSeq RNA Sample Preparation Kit (Illumina)

tag: developmental stage

value: adult

tag: Sex

value: male

tag: exercise parameters

tag: olm

value: Yes

tag: harvest cohort

value: hippocampus


title: exe2-14-0_8


title: VH1-2_VK1-33-CS_SP_IgK_4

description: HTGTS-Rep-Seq

value: C57BL/6 and 129/Sv mix

value: spleen

tag: locus (ig heavy-chain or light-chain)

tag: conditions

tag: primers


title: exe2-14-0_7


title: RNA_CR_089

value: Peripheral blood mononuclear cells

tag: gender

value: M


title: RNA_CR_088

tag: cell type


title: LPS and PAD4 inhibitor YW3-56 dual treatment group lung tissue [LPS-YW-2]

city: Kaifeng

first: Huanling

last: Yao

state: Henan

address: Jin Ming Avenue

department: School of Life Sciences

institute: Henan University

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument.
Sequence reads were filtered for quality using the fastqc v 0.11.9 and the trim_galore softwares v 0.6.7 (parameter---length 36,--max_n 3)
Trimmed sequence reads were mapped to the ENSEMBL reference genome Mus_musculus GRCm39 using the Hisat2 software v2.2.1
Gene expression quantity were analyzed by the featureCounts software v2.0.1.
Assembly: the ENSEMBL reference genome Mus_musculus GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: lung tissue

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent/RNeasy Mini Kit (Qiagen)/other kits.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR andP5/ P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: lung tissue


title: LPS and PAD4 inhibitor YW3-56 dual treatment group lung tissue [LPS-YW-5]


title: exe2-14-0_6


title: LPS group lung tissue [LPS-7]

value: LPS


title: exe2-14-0_5


title: RNA_CR_092

value: F


title: exe2-14-0_4


title: RNA_CR_086


title: VH1-2_VK1-33-CS_SP_IgK_2

description: HTGTS-Rep-Seq

value: splenic B220+ B cells

value: IgK

value: naïve


title: VH1-2_VK1-33_VK3-20_TdT_SP_IgH_3

description: HTGTS-Rep-Seq

value: IgH


title: VH1-2_VK1-33-CS_SP_IgK_1

description: HTGTS-Rep-Seq


title: RNA_CR_087


title: LPS group lung tissue [LPS-1]


title: RNA_CR_085


title: VH1-2_VK1-33-CS_SP_IgK_3

description: HTGTS-Rep-Seq


title: exe2-14-0_3


title: control group lung tissue [Control-4]

value: control


title: VH1-2_VK1-33_VK3-20_TdT_SP_IgH_2

description: HTGTS-Rep-Seq


title: exe2-14-0_2


title: control group lung tissue [Control-2]


title: RNA_CR_084


title: exe2-14-0_1


title: VH1-2_VK1-33_VK3-20_TdT_SP_IgH_1

description: HTGTS-Rep-Seq


title: RNA_CR_090


title: control group lung tissue [Control-1]


title: exe2-14-0_0


title: VH1-2_VK3-20_TdT_SP_IgH_3

description: HTGTS-Rep-Seq


title: VH1-2_VK3-20_TdT_SP_IgH_2

description: HTGTS-Rep-Seq


title: RNA_CR_082


title: CTL3_CD31

city: Montreal

first: Olivier

last: Tastet

address: 900 Saint-Denis

country: Canada

institute: crCHUM

description: sequencing batch #2

data_processing:
cell ranger analysis pipeline
Reads aligned to mouse reference genome GRCm38
Seurat processing
SCTransform for normalization + integration of sequencing batch
Public genesets for cell identification guidance
Assembly: mm10
Supplementary files format and content: cellranger output files and annotation of cells remaining after QC.  Cellranger outputs are compressed directories (tar.gz) containing all 3 cellranger output files required for downstream analysis.

source_name: C57BL/6, naive

extract_protocol:
cells were harvested, filtered and processed for single cell capture (1 sample per chip)
cDNA libraries were created using the Chromium Single Cell 3' technology

treatment_protocol: For EAE induction, see H. Kebir et al., Ann Neurol 2009

value: brain

tag: disease state

value: No disease

value: Endothelial cells isolation(CD31 positive selection)


title: CTL2_CD31

description: sequencing batch #2


title: RNA_CR_081


title: exe2-7-2_9

value: adult

value: male

value: Yes


title: exe2-7-2_8

value: hippocampus


title: EAE2_CD31

description: sequencing batch #2

source_name: C57BL/6, Experimental autoimmune encephalomyelitis

value: Peak of the disease


title: VH1-2_VK1-33-CS_TdT_SP_IgH_3

description: HTGTS-Rep-Seq

value: C57BL/6 and 129/Sv mix

value: spleen


title: RNA_CR_080

value: Peripheral blood mononuclear cells


title: CTL3_total

description: sequencing batch #2

value: total brain cells


title: VH1-2_VK3-20_TdT_SP_IgH_1

description: HTGTS-Rep-Seq

value: splenic B220+ B cells


title: CTL2_total

description: sequencing batch #2


title: exe2-7-2_6


title: RNA_CR_078

value: M


title: exe2-7-2_7


title: RNA_CR_083


title: VH1-2_VK1-33-CS_TdT_SP_IgH_1

description: HTGTS-Rep-Seq

value: naïve


title: EAE3_total

description: sequencing batch #2


title: RNA_CR_079


title: VH1-2_VK1-33-CS_TdT_SP_IgH_2

description: HTGTS-Rep-Seq

value: IgH


title: exe2-7-2_5


title: RNA_CR_077


title: exe2-7-2_4


title: VH1-2_VK3-20_SP_IgH_2

description: HTGTS-Rep-Seq


title: RNA_CR_076


title: CTL1_CD31

description: sequencing batch #1


title: exe2-7-2_3


title: VH1-2_VK3-20_SP_IgH_1

description: HTGTS-Rep-Seq


title: exe2-7-2_2


title: VH1-2_VK1-33-CS_SP_IgH_3

description: HTGTS-Rep-Seq


title: CTL1_total

description: sequencing batch #1


title: RNA_CR_074


title: exe2-7-2_1


title: EAE2_total

description: sequencing batch #1


title: RNA_CR_073


title: VH1-2_VK1-33-CS_SP_IgH_2

description: HTGTS-Rep-Seq


title: VH1-2_VK3-20_SP_IgH_3

description: HTGTS-Rep-Seq


title: VH1-2_VK1-33-CS_SP_IgH_1

description: HTGTS-Rep-Seq


title: RNA_CR_072

value: F


title: EAE1_total

description: sequencing batch #1

value: brain


title: exe2-7-0_9


title: exe2-7-0_8


title: Cersis_del_SP_IgK_3

description: HTGTS-Rep-Seq

value: IgK


title: Cersis_del_SP_IgK_2

description: HTGTS-Rep-Seq


title: zscan4+mervl+ cells rep3

first: Yanping

last: zhang

address: Siping Road 1239

institute: Tongji University

description: Normalized tag counts

data_processing:
RNA-seq reads were first removed adapters and low-quality base calls by trim_galore (version 0.6.4) using the default parameters.
RNA-seq reads were aligned to the mouse genome  using Hisat2 (version 2.1.0) with the parameters:--dta-cufflinks.
The expression levels for all Refseq genes were quantified to FPKM by Cufflinks (version 2.2.1).
Assembly: mm9
Supplementary files format and content: Signal track for each sample were generated using the “bamCoverage” function of deeptools and were normalized by calculating the reads per kilobase of transcript per million mapped reads (RPKM)

source_name: Cells

growth_protocol: ESCs and 2C-like Cells were cultured in ESM containing DMEM supplemented with 15% (v/v) FBS, 1 mM L-glutamine, 0.1 mM b-mercaptoethanol, 1% nonessential amino acid stock, and 1000 U/ml LIF.

extract_protocol:
RNAs in embryos lysis with a polyadenylated tail were captured, reverse transcripted and preamplified following the protocol for Smart-seq2 sequence library generation RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were prepared for sequencing using standard Illumina protocols

value: zscan4+mervl+ cells


title: zscan4+mervl+ cells rep2

description: Normalized tag counts


title: RNA_CR_071


title: RNA_CR_070


title: RNA_CR_069


title: exe2-7-0_7

value: adult


title: Cersis_del_SP_IgK_1

description: HTGTS-Rep-Seq


title: zscan4+mervl+ cells rep1

description: Normalized tag counts


title: EAE1_CD31

description: sequencing batch #1

value: Endothelial cells isolation(CD31 positive selection)


title: RNA_CR_075


title: exe2-7-0_6

value: male

value: Yes


title: RNA_CR_068


title: exe2-7-0_5

value: hippocampus


title: zscan4+mervl+ cells rep4

description: Normalized tag counts


title: zscan4+ cells rep4

description: Normalized tag counts

value: zscan4+ cells


title: exe2-7-0_4


title: exe2-7-2_0


title: zscan4+ cells rep3

description: Normalized tag counts


title: Zscan4+ cells rep2

description: Normalized tag counts

value: Zscan4+ cells


title: RNA_CR_066

value: Peripheral blood mononuclear cells


title: RNA_CR_065


title: exe2-7-0_2


title: RNA_CR_064


title: Zscan4+ cells rep1

description: Normalized tag counts


title: R-S136_S36

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description: Naive P14 cells

data_processing:
The fastqs were aligned using STAR 2.5.2a and mm10 genome
The aligned files were processed using PORT gene-based normalization ( https://github.com/itmat/Normalization )
The differential gene expression was done with limma
Assembly: mm10
Supplementary files format and content: text file with limma-voom normalized counts for each sample

source_name: naive

extract_protocol:
RNA was isolated using the Qiagen RNeasy micro kit (#74034) according to the manufacturer's protocol
RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) per manufacturer’s instructions
The libraries were sequenced on an Illumina NextSeq machine using a 150 cycle high output flow cell

value: Spleen

tag: characteristic

value: cell density:NA


title: R-S135_S35

description: Naive P14 cells


title: R-S132_S32

description: in vitro acutely stimulated P14 cells, day 7

value: cell density:invitro culture 50k/well cell density


title: R-S133_S33

description: Naive P14 cells


title: R-S134_S34

description: Naive P14 cells


title: Embryonic stem cells rep4

description: Normalized tag counts

value: Embryonic stem cells


title: R-S131_S31


title: exe2-7-0_0


title: R-S130_S30

description: in vitro chronically stimulated P14 cells, day 7


title: Embryonic stem cells rep2

description: Normalized tag counts


title: exe2-7-0_1


title: RNA_CR_063

value: M


title: RNA_CR_062

value: F


title: exe0-0-2_9


title: Embryonic stem cells rep3

description: Normalized tag counts


title: RNA_CR_067


title: exe0-0-2_8


title: RNA_CR_060


title: R-S128_S28


title: R-S129_S29


title: Embryonic stem cells  rep1

description: Normalized tag counts


title: zscan4+mervl+ cells - input

description: Normalized tag counts

data_processing:
ChIP-seq reads were first removed adapters and low-quality base calls by trim_galore (version 0.6.4) using the default parameters.
Chip-seq reads were aligned to the mouse genome  using Bowtie2 v.2.3.5.1 with the parameters: --no-mixed --no-discordant.
Multiple mapped reads and PCR duplicates were removed by Picard.
ChIP-seq peaks were called with MACS2 with the parameters  –nomodel --nolambda –keep-dup all  over input files
Assembly: mm9
Supplementary files format and content: Signal track for each sample were generated using the “bamCoverage” function of deeptools and were normalized by calculating the reads per kilobase of transcript per million mapped reads (RPKM)

growth_protocol: ESCs and 2C-like Cells were cultured in ESM containing DMEM supplemented  with 15% (v/v) FBS, 1 mM L-glutamine, 0.1 mM b-mercaptoethanol, 1% nonessential amino acid stock, and 1000 U/ml LIF.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody


title: RNA_CR_059


title: exe0-0-2_7


title: R-S127_S27


title: zscan4+mervl+ cells - H3K9me3_rep2

description: Normalized tag counts

tag: strain

value: H3K9me3 (Cell Signaling Technology no.9727S)


title: exe0-0-2_6

tag: tissue


title: exe0-0-2_5


title: R-S126_S26


title: R-S125_S25


title: RNA_CR_057

tag: age


title: zscan4+ cells - input

description: Normalized tag counts


title: exe0-0-2_4


title: RNA_CR_061


title: zscan4+mervl+ cells - H3K9me3_rep1

description: Normalized tag counts


title: R-S124_S24

value: cell density:invitro culture 100k/well cell density


title: exe2-7-0_3


title: Zscan4+ cells - H3K9me3_rep2

description: Normalized tag counts


title: exe0-0-2_3


title: RNA_CR_056


title: R-S123_S23


title: RNA_CR_054


title: Zscan4+ cells - H3K9me3_rep1

description: Normalized tag counts


title: exe0-0-2_2


title: R-S122_S22


title: Embryonic stem cells - input

description: Normalized tag counts


title: exe0-0-2_1


title: R-S121_S21


title: Embryonic stem cells - H3K9me3_rep2

description: Normalized tag counts


title: RNA_CR_053


title: RNA_CR_052


title: Embryonic stem cells - H3K9me3_rep1

description: Normalized tag counts


title: RNA_CR_058


title: exe2-0-0_9


title: R-S119_S19


title: R-S118_S18


title: RNA_CR_050


title: RNA_CR_055


title: RNA_CR_051


title: Young Plantaris PoWeR [PV839_43]

city: Lexington

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

data_processing:
Sequenced reads were mapped to mm10 mouse genome assembly using STAR 2.7.3a with default parameters.
Aligned reads were quantified for gene counts, filtered to exclude genes  with high noise or a maximum count of less than or equal to 50.
The filtered counts were median ratio normalized and tested for statistical significance using DESeq2.
All steps were performed using the Partek® Flow® Software.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Plantaris

extract_protocol:
Plantaris RNA was isolated using TRIzol and the Zymo MicroPrep Kit and prepared for RNA-sequencing
Conducted at NovoGene

treatment_protocol: Adult female mice were subjected to progressive weighted wheel running (PoWeR) for 8 weeks. Age-matched mice served as controls.

value: Skeletal Muscle

tag: group

value: Progressive weighted wheel run (PoWeR)

tag: tag

value: 6 mo


title: exe2-0-0_7

tag: developmental stage

value: adult

tag: Sex

value: male


title: Young Plantaris PoWeR [PV827_38]


title: RNA_CR_048


title: RNA_CR_049


title: Young Plantaris PoWeR [PV810_13]


title: Young Plantaris PoWeR [PV83_7]


title: exe2-0-0_5

tag: exercise parameters

tag: olm

value: Yes

value: hippocampus


title: exe2-0-0_6

tag: harvest cohort


title: R-S115_S15

description: in vitro acutely stimulated P14 cells, day 4


title: exe2-0-0_3


title: R-S114_S14

description: in vitro chronically stimulated P14 cells, day 4


title: R-S120_S20


title: Young Plantaris Control [SV41_21]

value: Sedentary


title: R-S116_S16


title: RNA_CR_047

value: Peripheral blood mononuclear cells


title: RNA_CR_045


title: RNA_CR_046


title: exe0-0-2_0


title: Young Plantaris Control [SV17_44]


title: Young Plantaris Control [SV40_42]


title: RNA_CR_044


title: R-S117_S17

value: Spleen


title: exe2-0-0_4


title: R-S113_S13


title: exe2-0-0_1


title: exe2-0-0_8


title: exe2-0-0_2


title: R-S112_S12


title: Young Soleus PoWeR [s_3PV]

source_name: Soleus


title: RNA_CR_043


title: exe2-0-0_0


title: RNA_CR_042


title: Young Soleus PoWeR [s_1327PV]


title: sed_9


title: Young Plantaris Control [SV1_5]


title: R-S111_S11


title: R-S110_S10


title: RNA_CR_041


title: R-S109_S9


title: sed_8


title: RNA_CR_040


title: R-S108_S8


title: R-S107_S7


title: Young Soleus Control [s_4041SV]


title: Young Soleus Control [s_4244SV]


title: sed_5


title: RNA_CR_037


title: sed_6


title: R-S106_S6


title: RNA_CR_038


title: Young Soleus Control [s_1221SV]


title: R-S105_S5


title: Young Soleus Control [s_15SV]


title: R-S103_S3


title: RNA_CR_034


title: R-S102_S2


title: Aged Soleus PoWeR [PoW15_p]

value: 24 mo


title: sed_2


title: RNA_CR_035


title: R-S104_S4


title: sed_3


title: sed_7


title: Aged Soleus PoWeR [PoW14_p]


title: RNA_CR_039


title: Aged Soleus PoWeR [PoW12_p]


title: Young Soleus PoWeR [s_710PV]


title: R-S101_S1


title: Young Soleus PoWeR [s_3839PV]


title: sed_0


title: RNA_CR_031


title: RNA_CR_030


title: Aged Soleus PoWeR [PoW10_p]


title: D.S136_S30

description: Naive P14 cells

data_processing:
The fastqs were aligned to mm10 using bowtie2.
Unmapped, unpaired, and mitochondrial reads were removed using samtools.
ENCODE Blacklist regions were removed.
PCR duplicates were removed using Picard.
Peak calling was performed with MACS2 with a FDR q-value < 0.01.
Normalization and differential accessibility analysis was done with DESeq2.
Batch correction was performed using combat in sva function
Assembly: mm10
Supplementary files format and content: chromatin accessbility counts file

extract_protocol:
Briefly, nuclei from 50,000 cells were isolated using a lysis solution composed of 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, and 0.1% IGEPAL CA-630,Immediately following cell lysis, nuclei were pelleted in low-bind 1.5ml tubes (Eppendorf) and resuspended in TD Buffer with Tn5 transposase (Illumina). Transposition reaction was performed at 37°C for 45 minutes. DNA fragments were purified from enzyme solution using MinElute Enzyme Reaction Cleanup Kit (Qiagen).
Libraries were barcoded (Nextera Index Kit, Illumina) and amplified with NEBNext High Fidelity PCR Mix (New England Biolabs). Library quality was assessed using a TapeStation instrument. RNA and ATAC libraries were quantified using a KAPA Library Quantification Kit
The libraries were sequenced on an Illumina NextSeq machine using a 150 cycle high output flow cell

tag: cell subset

value: naive

value: cell density:NA


title: HC_9

value: No


title: RNA_CR_036

value: F


title: HC_8


title: D.S134_S28

description: Naive P14 cells


title: Aged Soleus Control [Con16_p]


title: D.S133_S27

description: Naive P14 cells


title: HC_7


title: sed_1


title: Aged Soleus Control [Con14_p]


title: Aged Soleus Control [Con15_p]


title: RNA_CR_032

value: M


title: RNA_CR_027


title: RNA_CR_028


title: HC_6


title: D.S123_S16

value: cell density:invitro culture 100k/well cell density


title: Aged Soleus Control [Con13_p]

value: Skeletal Muscle


title: HC_5


title: ATAC_CR_186

data_processing:
Adapter trimming: Trim Galore! version 0.6.6 in paired end mode
Alignment: Bowtie2 version 2.2.5, bowtie2 --very-sensitive -k 10 -X 1000 --dovetail
Filtering: remove multi-mapping, improper pairs Samtools version 1.9, samtools view -f 0x2 -F 0x100
Filtering: remove duplicates, Picard tools version 2.25.6, MarkDuplicates --REMOVE_DUPLICATES true
Peak calling: Genrich version 0.6.1 in atac mode, ignoring ENCODE blacklist, outputting tn5 cut site BED files, q < 0.05
Count matrix: Bedtools version 2.30.0, count the number of tn5 cut sites intersecting (bedtools intersect -c) the union peakset (bedtools merge of individual peaksets)
Alignment: STAR aligner (v2.7.9a) with '--sjdbOverhang 100'.
Counting: featureCounts, Subread package (v2.0.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw matrix table representing the number of tn5 cut sites overlapping each peak for each sample

extract_protocol:
PBMCs were isolated from whole blood using histopaque.
Omni-ATAC protocol (Corces, 2017) was used to construct the ATAC-seq libraries.


title: HC_4


title: ATAC_CR_185


title: Aged Soleus Control [Con12_p]


title: Aged Soleus PoWeR [PoW15_s]

value: Progressive weighted wheel run (PoWeR)


title: D.S121_S14


title: RNA_CR_029


title: ATAC_CR_184


title: D.S120_S13


title: ATAC_CR_183


title: HC_2


title: Aged Soleus PoWeR [PoW14_s]


title: HC_1


title: D.S124_S17


title: ATAC_CR_182


title: Aged Soleus PoWeR [PoW10_s]


title: HC_0


title: ATAC_CR_181


title: Aged Soleus Control [Con16_s]


title: D.S117_S9


title: D.S122_S15


title: ATAC_CR_180


title: D.S118_S10


title: D.S108_S43


title: Chrm6A-seq_CM Mettl3-ko

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

description: Chromatin-associated RNA m6A in Mettl3-KO differentiated CMs

data_processing:
The sequencing adaptors were removed by Cutadapt.
For ATAC-seq, the trimmed reads were aligned to mouse genome using Bowtie. The PCR duplicates were removed using Picard. Peak calling was done by MACS2.
For RNA-seq, the trimmed reads were aligned using HISAT2. Reads on individual genes and m6A peak calling were done using house-hold Perl scripts.
Genome_build: mm10
Supplementary_files_format_and_content: For ATAC-seq, the processed data files are bed-format files containing all peaks identified by MACS2. For RNA-seq, the processed data files are RPKM table. The first coloum is gene name, the second coloum is RPKM value. For m6A-seq, the processed data files are m6A peaks.  The first coloumn is gene name, the second coloum is the position of m6A motif, the third coloumn is the m6A motif.

source_name: Differentiated cardiomyocyte

growth_protocol: ESCs were cultured the medium containing DMEM, 15% fetal bovine serum, 1% penicillin/streptomycin, 1% GlutaMax  and 1 mM ascorbic acid to induce embryoid body (EB) formation. EBs were resuspended in fresh cardiomyocyte differentiation medium and replated on 0.2% gelatin coated dishes to trigger cardiomyocyte formation.

extract_protocol:
Cells were trypsinized, washed, and resuspended in ice cold PBS. ATAC-seq was performed on 100,000 cells with the following modifications: The transposition reaction was inactivated by adding 200 μl SDS Buffer (100 mM Tris-HCl pH 7.4, 50 mM NaCl, 10 mM EDTA, 0.5% SDS, 100 μg Proteinase K) at 55°C for 30 minutes followed by isopropanol precipitation. The pellet was resuspended in 10 mM Tris-HCl, pH 8.0. Libraries were size-selected using Ampure XP beads (large fragments were removed using a 0.5× selection followed by a 1.8× selection) followed by PCR on half the product using Q5 High-Fidelity DNA Polymerase (New England Biolabs), Program: 98°C 30 s, 10 cycles of (98°C 10 s; 63°C 30 s; 72°C 1 min), 72°C 1 min. Amplified libraries were purified using Ampure XP beads (1.8×). Single end sequencing was performed using 75 bp reads on a NextSeq 500.
For ATAC-seq, cells were trypsinized, washed, and resuspended in ice cold PBS. ATAC-seq was performed on 100,000 cells with the following modifications: The transposition reaction was inactivated by adding 200 μl SDS Buffer (100 mM Tris-HCl pH 7.4, 50 mM NaCl, 10 mM EDTA, 0.5% SDS, 100 μg Proteinase K) at 55°C for 30 minutes followed by isopropanol precipitation. The pellet was resuspended in 10 mM Tris-HCl, pH 8.0. Libraries were size-selected using Ampure XP beads (large fragments were removed using a 0.5× selection followed by a 1.8× selection) followed by PCR on half the product using Q5 High-Fidelity DNA Polymerase (New England Biolabs), Program: 98°C 30 s, 10 cycles of (98°C 10 s; 63°C 30 s; 72°C 1 min), 72°C 1 min. Amplified libraries were purified using Ampure XP beads (1.8×). Single end sequencing was performed using 75 bp reads on a NextSeq 500. For RNA-seq, RNAs associated with chromatin were purified and fragmented. Fragmented ChrRNA or m6A-containing ChrRNA was dephosphorylation in the 15 μl mixture containing 1× T4 poly-nucleotide kinase buffer, 10 U SUPERase-In, and 20 U T4 polynucleotide kinase at 37°C for 1 h. RNA was separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions of the gel corresponding to 40-60 nucleotides (nt) were excised and disrupted by using centrifugation through the holes at the bottom of the tube. Then the gel pieces were dissolved by soaking overnight in 400 μL RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, and 0.1 U ml−1 SUPERase-In). After removal of gel debris using Spin-X column (Corning), RNA was precipitated by one-tenth volumes of 3 M sodium acetate (pH 5.2), 100 μg ml−1 glycogen, and 3 volumes of 100% ethanol overnight. RNA pellets were precipitated by centrifuging at 15,000 rpm for 20 min and washed by 70% ethanol. Purified RNA fragments were re-suspended in nuclease-free water. Poly-(A) tailing reaction was carried out for 45 min at 37°C (1× poly-(A) polymerase buffer, 1 mM ATP, 0.75 U/ml SUPERase_ In and 3 U E. coli poly-(A) polymerase).  For reverse transcription, the primers containing barcodes were listed as follows (Ø represents an abasic residue):  MCA02, 5’-pCAGATCGTCGGACTGTAGAACTCTØCAAGCAGAAGACGGCATACGATT TTTTTTTTTTTTTTTTTTVN-3’;   LGT03, 5′-pGTGATCGTCGGACTGTAGAACTCTØCAAGCAGAAGACGGCATACGATTT TTTTTTTTTTTTTTTTTVN-3′;   YAG04, 5′-pAGGATCGTCGGACTGTAGAACTCTØCAAGCAGAAGACGGCATACGATT TTTTTTTTTTTTTTTTTTVN-3′;   HTC05, 5′-pTCGATCGTCGGACTGTAGAACTCTØCAAGCAGAAGACGGCATACGATT TTTTTTTTTTTTTTTTTTVN-3′.  The tailed-RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 65°C for 5 min, followed by incubation on ice for 5 min. The reaction mix was then added with 1 X SuperScript III buffer, 10mM DTT, 40 U RNaseOUT and 200 U SuperScript III and incubated at 50°C for 50 min. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel and the corresponding region was excised as described earlier. The cDNA was recovered by using DNA gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in a mixture containing 1× CircLigase buffer, 2.5 mM MnCl2, 1 M Betaine, and 100 U CircLigase II (Epicenter) at 60 °C for 1 h. The reaction was heat inactivated at 80°C for 10 min followed by ethanol precipitation.

tag: genotype

value: ESC-derived cardiomyocyte

tag: antibody

value: m6A (Millipore, ABE572 and Synaptic Systems, 202 003)


title: Chrm6A-seq_ESC Mettl3-KO

description: Chromatin-associated RNA m6A in Mettl3-KO ESCs

source_name: Embryonic stem cell

tag: cell type

value: ESC


title: Aged Soleus Control [Con15_s]


title: HC_3

value: adult

value: male


title: ATAC_CR_179

tag: gender


title: D.S107_S42

tag: characteristic


title: Aged Soleus Control [Con14_s]

value: Sedentary


title: Aged Soleus Control [Con13_s]


title: D.S119_S11


title: Chrm6A-seq_ESC WT

description: Chromatin-associated RNA m6A in WT ESCs

value: WT


title: ATAC_CR_178

value: Peripheral blood mononuclear cells


title: Chrm6A-seq_CM WT

description: Chromatin-associated RNA m6A in WT differentiated CMs


title: D.S106_S41

value: Spleen


title: Aged Soleus PoWeR [PoW12_s]

value: 24 mo


title: Aged Soleus Control [Con12_s]


title: ATAC_CR_177


title: ChrRNA-seq_CM Mettl3-KO

description: Chromatin-associated RNA in Mettl3-KO differentiated CMs


title: D.S103_S23


title: D.S105_S40


title: ATAC_CR_175


title: ATAC_CR_176


title: Tumor EA_B

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

data_processing:
Reads were aligned to the mouse reference genome using HISAT2
Read Counting: HTSeq
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv, raw counts matrix (genes x samples)

source_name: C3-TAg Tumor 1339-org line

growth_protocol: Organoids were grown in 100% matrigel overlaid with serum free DMEM/F-12 media with 1X ITS, 10 ng/ml FGFb, 50 ng/ml EGF, 1X B27, 500 nM A8301, 5 uM Y27632, 1X non-essential amino acids, 1.25 uM N-Acetyl-L-cysteine

extract_protocol:
Organoid/ECM gels were collected in 15 mL conical tubes, snap frozen and stored in -80 C freezer. For RNA extraction, the gels were thawed on ice and disintegrated in 500 uL Trizol by repeatedly passing the mixture through a 23G needle. RNA was then further purified using the PureLinkâ„¢ RNA Mini Kit (Invitrogen, 12183025) following the manufacturer's protocol.
The cDNA libraries were prepared and indexed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L).

treatment_protocol: 250,000 1339-org organoids were embedded in a 100 µl ECM mixture (2.4 mg/ml Collagen I and 2 mg/ml Matrigel or Cultrex) and plated on top of a 200 µl ECM base layer in 6 cm dishes. Organoids were overlaid with serum starved media +/- treatments

tag: majority phenotype

value: Non-invasive

tag: treatment

value: 5 ng/ml EGF + 500 nM A8301 (2 days)

value: Tumor


title: ChrRNA-seq_CM WT

description: Chromatin-associated RNA in WT differentiated CMs

tag: strain


title: Tumor EA_A

tag: tissue


title: D.S102_S12


title: ChrRNA-seq_ESC Mettl3-KO

description: Chromatin-associated RNA in Mettl3-KO ESCs


title: ATAC_CR_174

tag: age

value: F


title: Tumor E_B

value: Invasive

value: 5 ng/ml EGF (2 days)


title: D.S101_S1

value: cell density:invitro culture 100k/well cell density


title: ChrRNA-seq_ESC WT

description: Chromatin-associated RNA in WT ESCs


title: sed_4

value: Yes

value: hippocampus


title: ATAC_CR_173


title: Tumor E_A


title: iMacrophage_TDGKO_72h_RNA-seq_rep2

institute: Center for Excellence in Molecular Cell Science

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
For RNA-seq, fragments per kilobase of Read per million mapped reads (RPKM) was calculated by cufflinks based on the annotation from GENCODE v33 for iNeuron. And count was used for iMacrophage using GENCODEvM24.
Assembly: hg19 for human, mm10 for mourse.

growth_protocol: For neuronal differentiation, 20–25 million iPSCs were plated on day 0 onto a 15-cm plate in N2 medium (knockout Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium; Life Technologies Corporation, cat. no. 12660012) with N2 supplement (Life Technologies, cat. no. 17502048), 1× GlutaMAX (Thermofisher Scientific, cat. no. 35050061), 1× MEM nonessential amino acids (NEAA) (Thermofisher Scientific, cat. no. 11140050), 10 μM ROCK inhibitor (Y-27632; Selleckchem, cat. no. S1049), and 2 μg/ml doxycycline (Clontech, cat. no. 631311). N2 medium was changed once a day for two more days. On day 3, cells were replated onto freshly prepared dishes coated with freshly prepared poly-L-ornithine (PLO; 0.1 mg/ml; Sigma, cat. no. P3655-10MG). Pre-neuron cells were cultured in i3Neuron Culture Media: BrainPhys media (Stemcell Technologies, cat. no. 05790) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific, cat. no. A3582801), 10 ng ml−1 BDNF (PeproTech, cat. no. 450-02), 10 ng ml−1 NT-3 (PeproTech, cat. no. 450-03), 1 μg ml−1 mouse laminin (Sigma, cat. no. L2020-1MG), and 2 μg ml−1 doxycycline (Clontech, cat. no. 631311). i3Neurons were then fed by half media change on day 6 and then, collected on day 7. For iMacrophage transdifferentiation, 10 million C10 cells were induced to reprogram by the addition of 100 nM of β-estradiol (Sigma-Aldrich; Cat. #E8875) and grown with 10 ng/ml of IL-3 (Peprotech; Cat. #213-13), CSF-1 (Peprotech; Cat. #315-02) and 350 nM Ascorbic acid (Sigma-Aldrich; Cat. # A8960) and then collected on day 1, day 2 and day3.

extract_protocol: To extract RNA, cells were plated on 6-well dishes, washed with PBS, and then 500 L of tri-reagent (Zymo research corporation, Cat. No. R2050-1-200) was added directly to the cells. The lysed cells were collected using a cell scraper. To isolate RNA, we used a Direct-zol RNA miniprep kit (Zymo Research Corporation, Cat. No. R2052), following manufacturer’s instructions including the optional DNAse step.For RNA sequencing, two biological replicates were sequenced. Total RNA was enriched for polyA and sequenced 2x75 bp on a NextSeq550 machine.

tag: harvested day

value: TDG-/-

value: NT

tag: dose


title: GCN2-/- MEFs_input_Leu

city: Chicago

first: Soroush

last: Tahmasebi

state: IL

address: 909 S Wolcott Ave

department: Department of Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

data_processing:
Reads were aligned to the mouse genome assembly mm10 using BWA v0.7.12.
Peaks were called using MACS v2.1.0 with default parameters (mfold=[5,50]; FDR cutoff=0.05, --nomodel) using sequenced libraries of either WT or GCN2 KO input DNA as control.
Peak annotations, tag directory, bed files and de novo motif discovery were performed using HOMER v4.7.
Peak list intersections were done using the R package GenomicRanges v1.26.4.
Binding intensity heatmaps and tag density plots were generated using the R package Genomation v1.9.3 with an estimated fragment length of 200.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraphs for input and ChIPs as well as peak text files corrected using input controls

source_name: Mouse embryonic fibroblasts (MEFs)

growth_protocol: WT or GCN2 KO MEFs were grown in DMEM +/- Leucine fo 24h.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with an NRF2-specific antibody.
Libraries were prepared at the Genome Quebec Innovation Centre (McGill University) using the TruSeq DNA sample preparation kit according to Illumina's recommendations and sequenced as single 50bp reads on an Illumina HiSeq 2500 sequencer.

value: Complete DMEM for 24h

tag: chip antibody


title: iMacrophage_WT_72h_RNA-seq_rep2


title: ATAC_CR_172


title: Tumor TR_B

value: 2 ng/ml TGFI1 + 1 uM Erlotinib (2 days)


title: ATAC_CR_171

value: M


title: iMacrophage_TDGKO_48h_RNA-seq_rep2


title: Wild-type MEFs_input_Leu

value: Wild-type


title: Tumor TR_A


title: GCN2 KO MEFs_NRF2 ChIP-seq_No Leu

value: DMEM without Leucine for 24h

value: NRF2 (ab62352, Abcam)


title: ATAC_CR_170

value: Peripheral blood mononuclear cells


title: iMacrophage_WT_48h_RNA-seq_rep2

value: WT


title: Tumor T_B

value: 2 ng/ml TGFI1 (2 days)

value: Tumor


title: GCN2 KO MEFs_NRF2 ChIP-seq_Leu


title: iMacrophage_TDGKO_24h_RNA-seq_rep2


title: Tumor Ctrl_2_B

value: Non-invasive

value: untreated


title: WT MEFs_NRF2 ChIP-seq_Leu


title: ATAC_CR_167

value: F


title: iMacrophage_WT_24h_RNA-seq_rep2


title: WT MEFs_NRF2 ChIP-seq_No Leu


title: Tumor Ctrl_2_A


title: ATAC_CR_166


title: ATAC_CR_168


title: Tumor T_A

value: Invasive


title: Auts2-/- NPC infected with Auts2-S-△ virus

city: Hershey

first: Zhonghua

last: Gao

address: 500 University Drive

department: Department of Biochemistry and Molecular Biology

institute: Penn State University College of Medicine

description: Auts2-/- neural prohenitor cells differentiatied fromESCs and infected with Auts2-S-△ virus

data_processing:
Libraries were loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500.
These cells were run for 50 cycles using either a single-read or pair-end recipe according to the manufacturer's instructions.
Raw reads were aligned to the Mus musculus genome (UCSC mm10) using TopHat (version 2.1.1) (14) with default parameters. Subsequently, the relative abundances (FPKM/TPM) of the transcripts and genes were estimated with Cufflinks (version 2.2.1)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files of FPKM/TPM values for each sample

source_name: NPC differentiated from mESC

growth_protocol: E14 mouse ES cells or their derived CRISPR-engineered cells were cultured in DMEM medium, supplemented with 15% FBS, LIF, non-essential amino acids, b-mercaptoethanol, L-glutamine, penicillin/streptomycin, sodium pyruvate, and two small molecule kinase (Mek and GSK3) inhibitors  penicillin/streptomycin, sodium pyruvate, and two small molecule kinase (Mek and GSK3) inhibitors.

extract_protocol:
Total RNA was extracted using TriPure reagent, based on the manufacturer's instructions.
cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions

treatment_protocol: Lentivirus was generated in HEK293T cells through co-transfection of psPAX2, pMD136, and pLV-EF1a-IRES-Blast plasmid carrying genes of interest (empty; Auts2-S: lentiviral vector carrying Auts2 short isoform; Auts2-S-delta: lentiviral vector carrying truncated Auts2 short isoform) using lipofectamine 2000 (Invitrogen, 11668019). Media containing lentivirus was collected, centrifuged at 4,000 g/4 °C for 15 minutes, and the resulting supernatant was concentrated on a spin column (EMD Millpore Corp, UFC910008). Concentrated lentivirus was aliquoted, fast-frozen in liquid nitrogen and stored at -80 °C. To infect mESCs with lentivirus, 300 l condensed lentivirus was added to 6 ml ES media with 48 g polybrene (EMD Millpore Corp, TR-1002-G). After 6 hours incubation, media was removed and the cells were incubated overnight with a mixture of 10 ml media, 500 l lentivirus and 80 mg polybrene. The next day, infected mESCs were ready for further experiments.

value: NPC

value: cells treated with truncated Auts2 short isoform lentivirus


title: Tumor T_d22_B

data_processing:
Reads were aligned to the reference genome using HISAT2
Read Counting: HTSeq
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv, raw counts matrix (genes x samples)

treatment_protocol: 250,000 1339-org organoids were embedded in a 100 µl ECM mixture (2.4 mg/ml Collagen I and 2 mg/ml Matrigel or Cultrex) and plated on top of a 200 µl ECM base layer in 6 cm dishes. Organoids were overlaid with serum starved media +/- TGFi1

tag: phenotype

value: Highly Invasive

tag: conditions

value: Organoids were grown in 100% matrigel overlaid with serum free DMEM/F-12 media with 1X ITS, 10 ng/ml FGFb, 50 ng/ml EGF, 1X B27, 5 uM Y27632, 1X non-essential amino acids, 1.25 uM N-Acetyl-L-cysteine

value: 2ng/ml TGFi1 without A8301 (22 days)


title: iMacrophage_WT_0h_RNA-seq_rep2

source_name: iMacrophage

value: NT


title: Auts2-/- NPC infected with empty virus

description: Auts2-/- neural prohenitor cells differentiatied fromESCs and infected with empty virus

value: cells treated with empty lentiviral


title: iMacrophage_TDGKO_72h_RNA-seq_rep1

value: TDG-/-


title: ATAC_CR_164

value: M


title: Auts2-/- NPC infected with Auts2-S virus

description: Auts2-/- neural prohenitor cells differentiatied fromESCs and infected with Auts2-S virus

value: cells treated with Auts2 short isoform lentivirus


title: ATAC_CR_165

value: Peripheral blood mononuclear cells


title: Tumor T_d22_A


title: iMacrophage_WT_72h_RNA-seq_rep1

value: WT


title: Tumor T_d7_B

value: 2ng/ml TGFi1 without A8301 (7 days)

value: Tumor


title: Tumor T_d7_A


title: iMacrophage_TDGKO_48h_RNA-seq_rep1


title: ATAC_CR_162


title: Auts2-/- ESC infected with Auts2-S-△ virus

description: Auts2-/- mouse embyronic stem cells infected with Auts2-S-△ virus

source_name: mESC

value: ESC


title: E14 NPC infected with empty virus

description: Wild type neural prohenitor cells differentiatied fromESCs and infected with empty virus


title: ATAC_CR_163

source_name: Peripheral blood mononuclear cells


title: ATAC_CR_169


title: iMacrophage_TDGKO_0h_RNA-seq_rep2


title: iMacrophage_WT_48h_RNA-seq_rep1


title: Tumor T_d2_B

value: Moderately Invasive

value: Organoids were grown in 100% matrigel overlaid with serum free DMEM/F-12 media with 1X ITS, 10 ng/ml FGFb, 50 ng/ml EGF, 1X B27, 500 nM A8301, 5 uM Y27632, 1X non-essential amino acids, 1.25 uM N-Acetyl-L-cysteine

value: 2ng/ml TGFi1 without A8301 (2 days)


title: Auts2-/- ESC infected with Auts2-S virus

description: Auts2-/- mouse embyronic stem cells infected with Auts2-S virus


title: iMacrophage_TDGKO_24h_RNA-seq_rep1


title: Auts2-/- ESC infected with empty virus

description: Auts2-/- mouse embyronic stem cells infected with empty virus

value: cells treated with empty lentivirus


title: Tumor T_d2_A


title: ATAC_CR_161


title: ATAC_CR_160


title: iMacrophage_WT_24h_RNA-seq_rep1


title: Tumor Ctrl_1_B

value: Non-invasive

value: untreated


title: ATAC_CR_159

value: F


title: iMacrophage_TDGKO_0h_RNA-seq_rep1

value: NT


title: Tumor Ctrl_1_A


title: E14 ESC infected with empty virus

description: Wild type mouse embyronic stem cells infected with empty virus


title: Auts2-/- NPC rep2

description: Auts2-/- neural progenitor cells differentiated from ESC

value: NPC


title: ATAC_CR_158


title: ATAC_CR_157


title: WEHI3_RECTAS_rep3

data_processing:
Basecalling was performed with RTAVersion v3.3.3
The seuqence data was mapped to the genome sequence with HISAT2 ver. 2.2.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with RSEM ver. 1.3.0.

source_name: WEHI3 leukemia cells

growth_protocol: Cells were cultured in the following frowth media; B16, DMEM + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; CT26, RPMI-1640 + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; EG7, DMEM + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; LLC, DMEM + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; MC38, RPMI-1640 + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; Pan02, DMEM + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin; WEHI3, DMEM + 10% fetal bovine serum + 100 U/mL penicillin + 100 µg/mL streptomycin + 4 µL/L 2-mercaptoethanol. All cell lines were maintained in an incubator at 37oC with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini kit (QIAGEN) according to the manufacturer’s protocol.
TruSeq stranded mRNA Library kit was used.

treatment_protocol: Cells were treated with 0.1% DMSO or 10 μM RECTAS in 0.1% DMSO for 6 h.

tag: condition

value: Treatment with 10 μM RECTAS for 6 h  for 6 h

tag: derived tissue

value: leukemia

tag: cell line

value: WEHI3 leukemia cells


title: iMacrophage_5hmC_SEAL

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
Assembly: mm10
Library strategy: SEAL

growth_protocol: For iMacrophage transdifferentiation, 10 million C10 cells were induced to reprogram by the addition of 100 nM of β-estradiol (Sigma-Aldrich; Cat. #E8875) and grown with 10 ng/ml of IL-3 (Peprotech; Cat. #213-13), CSF-1 (Peprotech; Cat. #315-02) and 350 nM Ascorbic acid (Sigma-Aldrich; Cat. # A8960) and then collected on day 2.

extract_protocol: 5hmC-Seal was performed as previously described with modifications. Briefly, 80 μg genomic DNA was resuspended in TE buffer and sonicated to 200 bp fragments using a Covaris S220 sonicator. Fragmented DNA was precipitated by ethanol and sodium acetate and resuspended in TE buffer. The selective 5hmC chemical labeling was performed in 100 μl glucosylation buffer (50 mM HEPES buffer pH 8.0, 25 mM MgCl2) containing above fragmented DNA, β-GT (NEB, Cat. No. M0357), UDP-Azide-Glucose (Active Motif, Cat. No. 55020), and incubated at 37°C for 1.5 hr. After the reaction, DNA was cleaned up with QIAquick Nucleotide Removal Kit. The labeled DNA was eluted with ddH2O, after which 1mM DBCO-PEG4-Biotin (Click Chemistry Tools) was added and incubated at 37°C for 2 hours. Then, the biotin-labeled DNA was pulled down by C1 Streptavidin beads (ThermoFisher, Cat. No. 650-01) for 30 minutes at room temperature. The captured DNA fragments were processed for library construction as described in SAR-seq (above).  For 5fC-SEAL, we modified the previously described protocol, which reduces 5fC to 5hmC using NaBH452. We labeled the newly generated 5hmC (derived from 5fC reduction with NaBH4) with an azide-modified glucose as described above for 5hmC-Seal. In brief, 80 μg of fragmented i3Neurons genomic DNA was incubated in 100 μl glucosylation buffer (50 mM HEPES buffer pH 8.0, 25 mM MgCl2) containing unmodified UDP-Glucose (NEB, Cat No. M0357), and β-GT for 1.5 hours at 37°C. The labeled DNA was cleaned up with QIAquick Nucleotide Removal Kit. Then, an equal volume of freshly prepared NaBH4 (Aldrich, Cat. No. 213462) solution was added to the glucose-blocked DNA solution. The reaction mixture was vortexed and incubated in a Thermomixer for 15 minutes at room temperature. The chemical labeling and capture were performed as described above for 5hmC-SEAL.

tag: genotype


title: iMacrophage_WT_0h_RNA-seq_rep1


title: WEHI3_RECTAS_rep2


title: ATAC_CR_156

tag: cell type

value: Peripheral blood mononuclear cells

value: M


title: E14 NPC rep2

description: Wild type neural progenitor cells differentiated from ESC

value: WT


title: iMacrophage_ddT_S1ENDseq

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
bigwig files were made for positive (*.pos.bw) and negativ (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig
Assembly: hg19 for human, mm10 for mourse.
Library strategy: END-seq

extract_protocol:
For END-seq, live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing. For S1-END-seq, cells were collected and embedded in 1% agarose plugs, lysed and digested with Proteinase K (1 hour at 50°C, followed by 7 hours at 37°C), washed with TE buffer, and then treated with RNAse A for 1 hour at 37°C. Plugs were then washed in EB and equilibrated in S1 nuclease buffer (40 mM sodium acetate pH 5.2, 300 mM NaCl, 2 mM ZnSO4) for 30 minutes. 1.8 U of S1 nuclease was added to 100 µL of S1 nuclease buffer per plug and incubated on ice for 15 minutes to allow for the enzyme to diffuse into the plug. The reaction mix was then placed at 37°C for 20 minutes before addition of EDTA (10 mM final concentration) to terminate the reaction. Finally, plugs were processed through the standard END-seq protocol
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).

value: ddT, 20 hours prior to cell harvesting

value: 40 µM

tag: in-situ treatment

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37°C for 20 mins.


title: WEHI3_RECTAS_rep1


title: iMacrophage_ddG_S1ENDseq

value: ddG, 20 hours prior to cell harvesting


title: E14 NPC rep1


title: WEHI3_DMSO_rep3

value: Treatment with 0.1% DMSO  for 6 h


title: ATAC_CR_155

tag: gender


title: ATAC_CR_154


title: Auts2-/- ESC rep2

description: Auts2-/- mouse embyronic stem cells

value: ESC


title: ATAC_CR_153


title: Auts2-/- ESC rep1

description: Auts2-/- mouse embyronic stem cells


title: ATAC_CR_152


title: WEHI3_DMSO_rep2


title: WEHI3_DMSO_rep1


title: Pan02_RECTAS_rep3

source_name: Pan02 pancreatic adenocarcinoma cells

value: pancreatic adenocarcinoma

value: Pan02 pancreatic adenocarcinoma cells


title: iMacrophage_TDGKO_ddC_S1ENDseq

value: TDG-/-

value: Aphidicolin, 24 hours prior to cell harvesting; ddC, 20 hours prior to cell harvesting

value: 4 µM Aphidicolin; 40 µM ddC


title: Auts2-/- NPC rep1

value: NPC

value: untreated


title: E14 ESC rep1

description: Wild type mouse embyronic stem cells


title: Macrophage_WT_ddC_S1ENDseq


title: ATAC_CR_150


title: IN cytoplasm profiling replicate 2

city: Hsinchu

first: Joye

last: Li

address: 1001 University Road

country: Taiwan

institute: National Chiao Tung University

description: cytoplasmic RNA

data_processing:
The raw reads of fastq were preprocessed with the adapter trimmer PEAT (https://github.com/jhhung/PEAT)
Processed reads aligned with the ad hoc NTA aligner Tailor (https://github.com/jhhung/Tailor); We configured Tailor by setting the minimum sequence alignment length to 18 nt and maximum hit occurrence to at most 10 positions.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: Embryoid bodies

growth_protocol: ESCs were cultured and differentiated into spinal MNs/INs as previously described (Wichterle et al., 2002; Wichterle et al., 2009). Two dosages of SAG treatment (500 nM SAG for MNs; 5 nM for INs, respectively) in addition to RA were applied during the differentiation process. Cells were collected followed by the subcellular fractionation on day 7 for miRNA-seq.

extract_protocol:
Subcellular fractioned RNA were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols with TruSeq Small RNA Library Prep Kit-Set A.

tag: developmental stage

value: day 7

tag: biological replicates

value: replicate 2


title: iMacrophage_ddC_S1ENDseq

tag: treatment


title: Pan02_RECTAS_rep2

value: Treatment with 10 μM RECTAS for 6 h  for 6 h


title: ATAC_CR_148

value: Peripheral blood mononuclear cells

value: M


title: iMacrophage_NT_SAR-seq

description: EdU incorporated DNA

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
Assembly: hg19 for human, mm10 for mourse.
Library strategy: SAR-seq

growth_protocol: For neuronal differentiation, 20–25 million iPSCs were plated on day 0 onto a 15-cm plate in N2 medium (knockout Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium; Life Technologies Corporation, cat. no. 12660012) with N2 supplement (Life Technologies, cat. no. 17502048), 1× GlutaMAX (Thermofisher Scientific, cat. no. 35050061), 1× MEM nonessential amino acids (NEAA) (Thermofisher Scientific, cat. no. 11140050), 10 μM ROCK inhibitor (Y-27632; Selleckchem, cat. no. S1049), and 2 μg/ml doxycycline (Clontech, cat. no. 631311). N2 medium was changed once a day for two more days. On day 3, cells were replated onto freshly prepared dishes coated with freshly prepared poly-L-ornithine (PLO; 0.1 mg/ml; Sigma, cat. no. P3655-10MG). Pre-neuron cells were cultured in i3Neuron Culture Media: BrainPhys media (Stemcell Technologies, cat. no. 05790) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific, cat. no. A3582801), 10 ng ml−1 BDNF (PeproTech, cat. no. 450-02), 10 ng ml−1 NT-3 (PeproTech, cat. no. 450-03), 1 μg ml−1 mouse laminin (Sigma, cat. no. L2020-1MG), and 2 μg ml−1 doxycycline (Clontech, cat. no. 631311). i3Neurons were then fed by half media change on day 6 and then, collected on day 7. For the iMacrophage transdifferentiation, 10 million C10 cells were induced to reprogram by the addition of 100 nM of β-estradiol (Sigma-Aldrich; Cat. #E8875) and grown with 10 ng/ml of IL-3 (Peprotech; Cat. #213-13), CSF-1 (Peprotech; Cat. #315-02) and 350 nM Ascorbic acid (Sigma-Aldrich; Cat. # A8960) and then collected on day 2.

extract_protocol:
15 million i3Neuron or iMacrophages were incubated with 20 μM EdU for 18 hr. For i3Neurons, cells were harvested and washed with PBS and incubated with accutase for 5-10 minutes. Cells were then collected using a cell scrapper (Corning), pelleted at 200xg for 5 minutes and resuspended in cold 0.1% BSA in PBS. For iMacrophages, cells were washed, trypsinized and resuspended in cold 0.1% BSA in PBS. Cold methanol was then added dropwise into all samples during slow vortexing to 80% final concentration. Samples were stored at -20C until processed.
Cells were permeabilized on ice for 10 min and resuspended in 1 mL of Click-iT reaction solution for 2 hrs shaking at room temperature. Cells were then lysed with Proteinase K overnight at 37C. DNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) according to manufacturer’s instructions. DNA was sonicated to 150-200 bp fragments using a Covaris S220 sonicator. Biotin-EdU labeled DNA fragments were pulled down using MyOne Streptavidin C1 Beads (ThermoFisher #650-01) and incubated at 24C shaking in a ThermoMixer C at 800 rpm for 30 min. Dynabeads were washed 3x in W&B (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1 M NaCl, 0.1% Tween (freshly added)), 2x in EB (10 mM Tris-HCl pH 8.0), and 1x T4 DNA Ligase Buffer (NEB). Dynabeads were resuspended in end-repair reaction and incubated at 24C shaking at 800 rpm for 30 min. Dynabeads were washed 1x in 1X W&B, 2x EB, and 1x NEBuffer 2 (NEB) and resuspended in A-tailing reaction mix (NEB), followed by incubation at 37C shaking at 800 rpm for 30 min. Dynabeads were washed 1x in NEBuffer 2 and resuspended in ligation reaction mix (NEB), 5 nM annealed TruSeq truncated adapter and incubated at 25C shaking at 600 rpm for 20 min. Ligation reaction was stopped by adding 50 mM EDTA, and Dynabeads were washed 3x in 1X W&B, 3x EB. PCR amplified for 16 cycles with Kapa HiFI HotStart Ready Mix using TruSeq index adapters. PCR products were separated from DynaBeads and cleaned using AMPure Beads XP. library concentrations were calculated by KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems) and sequenced on Illumina NextSeq 550 (75 bp single read).   In the indicated experiments C/EBPα-induced macrophages were treated with the following compounds: Aphidicolin (APH; 4 μM) 4 hours before EdU incubation. PARPi (Olaparib; 5 μM) and ddC, ddA, ddG or ddT (40 µM) were added 20 hours prior to harvest. For i3Neurons, 40 µM of ddA, ddT, ddG or ddC chain-terminating nucleosides, 40 µM Ara-A and 20 µM Ara-C were added to cells for 18 hours prior to cell harvesting for SAR-seq experiments. 40 µM Gemcitabine was added to cells 2 hours prior to cell harvesting for SAR-seq experiments.

treatment_protocol: Neurons and iMacrophage cells were incubated with 20 uM EdU for 18 hours, unless otherwise noted.

value: WT

value: Aphidicolin, 24 hours prior to cell harvesting

value: 4 µM


title: iMacrophage_ddC_SAR-seq

description: EdU incorporated DNA


title: iMacrophage_ddC_PairedwithOthers_S1ENDseq

value: ddC, 20 hours prior to cell harvesting

value: 40 µM

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37°C for 20 mins.


title: MN cytoplasm profiling replicate 2

description: cytoplasmic RNA

tag: strain


title: ATAC_CR_147

tag: age


title: Pan02_DMSO_rep3

value: Treatment with 0.1% DMSO  for 6 h

value: pancreatic adenocarcinoma

value: Pan02 pancreatic adenocarcinoma cells


title: ATAC_CR_146


title: iMacrophage_PARPi_SAR-seq

description: EdU incorporated DNA

value: Aphidicolin, 24 hours prior to cell harvesting; Olaparib, 20 hours prior to cell harvesting

value: 5 µM

tag: harvested day


title: Pan02_DMSO_rep2


title: MN cytoplasm profiling replicate 1

description: cytoplasmic RNA

value: replicate 1


title: E14 ESC rep2

description: Wild type mouse embyronic stem cells

value: ESC

value: untreated


title: ATAC_CR_145


title: iMacrophage_ddA_S1ENDseq

value: ddA, 20 hours prior to cell harvesting

tag: dose


title: MC38_RECTAS_rep3

source_name: MC38 colorectal carcinoma cells

value: Treatment with 10 μM RECTAS for 6 h  for 6 h

value: coloretal carcinoma

value: MC38 colorectal carcinoma cells


title: Balb-C male mouse liver_Nafion BP2-6.0 [EPACorton_P01_B10]

city: Research Triangle Park

first: Christopher

last: Corton

address: 109 TW Alexander Dr.

institute: US-EPA

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample. Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user. The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Data normalization was not done
genome build: GRCm38.p5; GCF_000001635.25
Supplementary_files_format_and_content: counts

source_name: Balb-C male mouse liver_Nafion BP2-6.0

extract_protocol: The liver tissues (~50-100 mg) were preserved in RNAlater (Qiagen, Valencia, CA) and stored at -80°C until RNA extraction. Total RNA was extracted from tissue samples 2-6 months later with Trizol by polytron homogenization. The resultant RNA was further purified using the RNeasy Mini Kit (Qiagen), and RNA integrity was checked with Bioanalyzer RNAnanochip. Samples were submitted to BioSpyder for analysis using the mouse whole genome platform.

treatment_protocol: Balb-C male mice at 10-12 weeks of age were dosed by gavage for 7 consecutive days using 20-gauge stainless steel feeding needles. Doses of 0, 0.03, 0.3, 3.0, and 6.0 mg/kg-day were administered once daily in the afternoon. Control animals were administered an equal volume of deionized water. Four biological replicates consisting of individual animals were included in each dose group. RNA was isolated and gene expression was determined using the mouse TempO-Seq targeted RNA-Seq platform (BioSpyder, Inc; Carlsbad CA).

value: Balb-C

value: 10-12 weeks

tag: Sex

value: male

value: Nafion BP2

value: 6 mg/kg

tag: tissue

value: liver


title: Balb-C male mouse liver_Nafion BP2-6.0 [EPACorton_P01_B09]


title: ATAC_CR_144

value: Peripheral blood mononuclear cells

value: M


title: MC38_RECTAS_rep2


title: iMacrophage_WT_PARPi_SAR-seq

city: Shanghai

description: EdU incorporated DNA

value: WT

value: Aphidicolin, 24 hours prior to cell harvesting; Olaparib, 20 hours prior to cell harvesting


title: iMacrophage_TDGKO_PARPi_SAR-seq

description: EdU incorporated DNA

value: TDG-/-

value: 5 µM


title: Pan02_RECTAS_rep1

value: pancreatic adenocarcinoma

value: Pan02 pancreatic adenocarcinoma cells


title: IN cytoplasm profiling replicate 1

description: cytoplasmic RNA

value: day 7

value: replicate 1


title: Balb-C male mouse liver_Nafion BP2-6.0 [EPACorton_P01_B08]


title: ATAC_CR_143


title: MC38_RECTAS_rep1

value: Treatment with 10 μM RECTAS for 6 h  for 6 h

value: coloretal carcinoma

value: MC38 colorectal carcinoma cells


title: Tumor E8-2

data_processing:
Alignment-free quantification with salmon (1.5.2)
Normalization with DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv matrix of log2(TPM) (genes x samples)

source_name: C3-TAg Tumor 1339 derived parental cell line

extract_protocol:
Organoid/ECM gels were collected in 15 mL conical tubes, snap frozen and stored in -80 C freezer. For RNA extraction, the gels were thawed on ice and disintegrated in 500 uL Trizol by repeatedly passing the mixture through a 23G needle. RNA was then further purified using the RNeasy Kit (Qiagen, 74104) following the manufacturer's protocol.
TruSeq RNA library prep using manufacturer protocols

treatment_protocol: 1000 C3-TAg tumor organoids or 60,000-80,000 noninvasive cells were embedded in a 500 µl ECM mixture (2.4 mg/ml Collagen I and 2 mg/ml Matrigel or Cultrex) and plated on top of 500 uL base layer of ECM in 6 cm dishes and overlaid with growth media as listed above.

tag: majority phenotype

value: Non-invasive

tag: growth protocol

value: Cells were embedded in a mixture of collagen I and matrigel and overlaid with DMEM/F-12 media with 1% FBS, 1X ITS, 10 ng/ml FGFb, 1X non-essential amino acids. Cells were grown for 6 days.

value: Tumor


title: Balb-C male mouse liver_Nafion BP2-6.0 [EPACorton_P01_B07]

value: Balb-C

value: 10-12 weeks

value: male

value: Nafion BP2

value: 6 mg/kg

value: liver


title: ATAC_CR_142

value: Peripheral blood mononuclear cells

value: F


title: ATAC_CR_151


title: Tumor E8-1


title: MC38_DMSO_rep3

tag: condition

value: Treatment with 0.1% DMSO  for 6 h

tag: derived tissue


title: Tumor C6-2


title: ATAC_CR_141

value: M


title: Balb-C male mouse liver_Nafion BP2-3.0 [EPACorton_P01_B06]

source_name: Balb-C male mouse liver_Nafion BP2-3.0

value: 3 mg/kg


title: Pan02_DMSO_rep1

value: pancreatic adenocarcinoma

tag: cell line

value: Pan02 pancreatic adenocarcinoma cells


title: Balb-C male mouse liver_Nafion BP2-3.0 [EPACorton_P01_B05]


title: MC38_DMSO_rep2

value: coloretal carcinoma

value: MC38 colorectal carcinoma cells


title: Tumor C6-1

value: Non-invasive

value: Cells were embedded in a mixture of collagen I and matrigel and overlaid with DMEM/F-12 media with 1% FBS, 1X ITS, 10 ng/ml FGFb, 1X non-essential amino acids. Cells were grown for 6 days.


title: MC38_DMSO_rep1


title: Balb-C male mouse liver_Nafion BP2-3.0 [EPACorton_P01_B04]

value: Balb-C


title: ATAC_CR_139

tag: cell type


title: Tumor B6-2

value: Tumor


title: LLC_RECTAS_rep3

source_name: LLC lung carcinoma cells

value: Treatment with 10 μM RECTAS for 6 h  for 6 h

value: lung carcinoma

value: LLC lung carcinoma cells


title: ATAC_CR_138


title: Balb-C male mouse liver_Nafion BP2-3.0 [EPACorton_P01_B03]

value: 10-12 weeks

value: male

value: Nafion BP2

value: liver


title: LLC_RECTAS_rep2


title: Balb-C male mouse liver_Nafion BP2-0.3 [EPACorton_P01_B02]

source_name: Balb-C male mouse liver_Nafion BP2-0.3

value: 0.3 mg/kg


title: LLC_RECTAS_rep1


title: ATAC_CR_137

value: Peripheral blood mononuclear cells

value: F


title: Tumor B6-1


title: Tumor 1339-2

source_name: C3-TAg Tumor 1339

value: Invasive

value: Digested organoids were embedded in a mixture of collagen I and matrigel and overlaid with DMEM/F-12 media with 1X ITS, 10 ng/ml FGFb, 1X non-essential amino acids. Organoids were grown for 2 days.


title: Balb-C male mouse liver_Nafion BP2-0.3 [EPACorton_P01_A12]


title: ATAC_CR_136

value: M


title: Balb-C male mouse liver_Nafion BP2-0.3 [EPACorton_P01_A11]


title: ATAC_CR_135


title: Tumor 1332-2

source_name: C3-TAg Tumor 1132


title: LLC_DMSO_rep3

value: Treatment with 0.1% DMSO  for 6 h


title: Tumor 1339-1


title: Balb-C male mouse liver_Nafion BP2-0.3 [EPACorton_P01_A10]


title: LLC_DMSO_rep2


title: LLC_DMSO_rep1


title: ATAC_CR_140


title: Tumor 1153-2

source_name: C3-TAg Tumor 1153


title: ATAC_CR_134


title: Balb-C male mouse liver_Nafion BP2-0.03 [EPACorton_P01_A09]

source_name: Balb-C male mouse liver_Nafion BP2-0.03


title: Balb-C male mouse liver_Nafion BP2-0.03 [EPACorton_P01_A08]


title: EG7_RECTAS_rep2

source_name: EG7 lymphoma cells

value: lymphoma

value: EG7 lymphoma cells


title: EG7_RECTAS_rep3


title: ATAC_CR_132


title: Balb-C male mouse liver_Nafion BP2-0.03 [EPACorton_P01_A07]

value: Balb-C


title: ATAC_CR_133


title: ATAC_CR_131


title: EG7_RECTAS_rep1

value: Treatment with 10 μM RECTAS for 6 h  for 6 h


title: Balb-C male mouse liver_Nafion BP2-0.03 [EPACorton_P01_A06]


title: Tumor 1151-2

source_name: C3-TAg Tumor 1151

value: Tumor


title: ATAC_CR_130


title: EG7_DMSO_rep3


title: Balb-C male mouse liver_DMSO-0 [EPACorton_P01_A05]

source_name: Balb-C male mouse liver_DMSO-0

value: Control

value: 0 mg/kg


title: Tumor 1151-1


title: ATAC_CR_129

source_name: Peripheral blood mononuclear cells