title: time-restricted feeding, C, 8PM

description:
Canton-S, Female
TRF_C_8PM


title: IFCa3

status: Public on Jan 19 2023

type: SRA

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

library_source: genomic

data_processing:
Fastq files were aligned using Bismark v0.20.1 in PBAT mode against the GRCm38 genome where SNP positions between C57B6 and CBA were N masked using the SNPSplit_genome_preparation script.
Bismark BAM files were split into reads deriving from C57B6, CBA or Undefined BAM files using SNPsplit v0.4
Methylation calls were extracted from the split BAM files using the bismark methylation extractor with default parameters
Assembly: GRCm38
Supplementary files format and content: CpG methylation counts in Bismark coverage file format

molecule: genomic DNA

organism: Mus musculus

source_name: mouse blastocyst

extract_protocol:
Blastocysts were individually collected and lysed in 10 μl of RLT buffer
DNA was purified using solid phase reversible immobilization (SPRI) beads and converted with bisulphite reagent using EZ DNA Methylation-Gold kit (ZYMO Research, D5005). DNA was eluted in EB buffer and individual blastocyst PBAT libraries were prepared as outlined below. First-strand synthesis was performed using Klenow exo-tagged (New England Biolabs) and a biotinylated oligo I (5-[Btn]CTACACGACGCTCTTCCGATCTNNNNNNNNN-3), followed by Exo-I treatment (New England Biolabs) and SPRI purification. Purified DNA was incubated with Dynabeads Strepatavidin M-280 beads (ThermoFisher Scientific) to capture biotinylated DNA and second strand synthesis was carried out using reverse oligo II (5’-TGCTGAACCGCTCTTCCGATCTNNNNNNNNN 3’). Libraries were amplified using indexed iPCRTag reverse primers (54) with KAPA HiFi (Kapa Biosystem) DNA polymerase for 15 PCR cycles and purified using SPRI beads (Agencourt Ampure XP bead). Libraries were quantitated and quality control was checked using Agilent High Sensitivity DNA kit and KAPA Illumina Library Quantifcation Kit for Illumina (KAPA Biosystems)
Bisulfite-Seq (PBAT)

tag: tissue

value: mouse blastocyst

tag: oocyte collection_method

value: In vitro follicule culture oocyte maturation derived from adult mouse

tag: treatment


title: time-restricted feeding, C, 4PM

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute for Biological Studies

description:
Canton-S, Female
TRF_C_4PM

library_source: transcriptomic

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the mm10 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: indirect flight muscle

growth_protocol: All flies were kept at 22 °C, 50% humidity in a 12 h light/12 h dark (LD) cycle

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen)
Libraries were pooled and sequenced using an Illumina HiSeq 2500 with 50-bp single-read chemistry

treatment_protocol: ALF and TRF flies were subjected to vials with assigned diet at zeitgeber time zero (ZT0) 9AM (lights on), and were switched to either a food media vial (for ALF) or a 1.1% agar vial (for TRF) at 9 PM (lights off).

value: indirect flight muscle

tag: Sex

value: Female

tag: strain

value: Canton-S

tag: genotype

value: wild type

tag: diet

value: normal

value: time-restricted feeding

tag: time


title: IFCa4


title: IFCa2


title: time-restricted feeding, C, 8AM

description:
Canton-S, Female
TRF_C_8AM


title: time-restricted feeding, C, 4AM

description:
Canton-S, Female
TRF_C_4AM


title: SOp4

value: superovulation of prepubertal mouse


title: time-restricted feeding, C, 12PM

description:
Canton-S, Female
TRF_C_12PM


title: SOp2


title: SOp1


title: ad libitum feeding, SK2, 8PM

description:
Sphingosine kinase 2, Female
ALF_SK2_8PM

value: Sphingosine kinase 2

value: ad libitum feeding


title: SOp3


title: SOa4

value: superovulation of adult mouse


title: SOa3


title: time-restricted feeding, HF, 12PM

description:
Canton-S+HFD, Female
TRF_HF_12PM

value: HFD


title: ad libitum feeding, SK2, 8AM

description:
Sphingosine kinase 2, Female
ALF_SK2_8AM


title: time-restricted feeding, C, 12AM

description:
Canton-S, Female
TRF_C_12AM


title: NO4

value: natural ovulation


title: ad libitum feeding, SK2, 4AM

description:
Sphingosine kinase 2, Female
ALF_SK2_4AM


title: SOa1


title: ad libitum feeding, SK2, 12PM

description:
Sphingosine kinase 2, Female
ALF_SK2_12PM


title: ad libitum feeding, SK2, 4PM

description:
Sphingosine kinase 2, Female
ALF_SK2_4PM


title: SOa2


title: ad libitum feeding, HF, 8PM

description:
Canton-S+HFD, Female
ALF_HF_8PM


title: ad libitum feeding, SK2, 12AM

description:
Sphingosine kinase 2, Female
ALF_SK2_12AM


title: ad libitum feeding, HF, 8AM

description:
Canton-S+HFD, Female
ALF_HF_8AM


title: NO3


title: IFCa1


title: NO2


title: NO1


title: ad libitum feeding, HF, 12PM

description:
Canton-S+HFD, Female
ALF_HF_12PM


title: ad libitum feeding, HF, 4PM

description:
Canton-S+HFD, Female
ALF_HF_4PM


title: ad libitum feeding, HF, 4AM

description:
Canton-S+HFD, Female
ALF_HF_4AM


title: 9RUN_m

city: Stockholm

first: Leonidas

middle: S

last: Lundell

state: Stockholm

address: Von Eulers Väg 4a

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institute

data_processing:
star/2.7.2b STAR --outReadsUnmapped Fastx --outSAMstrandField intronMotif--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate
subread/1.6.2 featureCounts -p -B -C -T $threads -t exon -g gene_id
limma_3.48.3 filterByExpr.DGEList(dataDGE, design = model.matrix(~0 + group + sex), min.count = 15)
Assembly: mm 10, release 99
Supplementary files format and content: processed.data.csv contains cpm after filtering by expression with cutoff at 10 counts along with HUGO symbol, ensmbl, and entrezID

source_name: Murine inguinal white adipose tissue from exercised animals sampled at ZT3

extract_protocol:
Inguinal adipose tissue was used for RNA extraction. Tissues were homogenized using TissueLyser (Qiagen) in 1 mL TRIzol (Sigma-Aldrich). Chloroform was added, samples were mixed, subjected to centrifugation, and the aqueous phase was transferred to a new tube. Thereafter, 1:1 70% ethanol was added, and the total volume was loaded on silica-membrane columns. RNA extraction was performed using a commercially available kit (Rneasy lipid tissue kit, Qiagen). DNase treatment was performed. RNA concentration and purity were assessed by absorbance at 260 and 280 nm using NanoDrop One (Thermo Fisher Scientific, Waltham, MA).
Aliquots of RNA (1000 ng) were analyzed using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina) as described (ref). Ribosomal RNA was removed from the sample using 35 μl of rRNA removal beads (Illumina) on a magnetic plate followed by cleanup of the ribosomal-depleted RNA with 193 μl of Agencourt RNAClean XP beads (Beckman Coulter), 70% ethanol wash, and elution into 10 μl elution buffer (Illumina). The RNA sample was fragmented for 4 min at 94°C in Elute, Prime, Fragment High Mix (Illumina) and then subjected to first-strand cDNA synthesis with 1 μl of Superscript III reverse transcriptase (Life Technologies) per sample using a thermocycler programmed to 25°C for 10 min, 50°C for 15 min, and 70°C for 15 min. Second-strand cDNA was synthesized by addition of Second-Strand Marking Master Mix, and samples were incubated at 16°C for 60 min. Samples were subjected to another bead cleanup before A-tailing and ligation of adapters as per kit instructions (Illumina). Following a third bead cleanup, samples were enriched for DNA fragments by amplification using the Illumina polymerase chain reaction (PCR) Primer Cocktail and PCR Master Mix, subjected to 98°C for 30 min, followed by a predefined cycle (98°C for 10 s, 60°C for 30 s, and 72°C for 30 s) that was repeated 3 to 15 times, on the basis of each individual sample, and finally incubated for 5 min at 72°C. Samples were cleaned and validated for DNA concentration using the Qubit dsDNA HS assay kit (Invitrogen) and for base pair size and purity using the Agilent High Sensitivity DNA chip and Bioanalyzer instrument.
38-bp paired-end sequencing on a NextSeq500

value: inguinal white adipose tissue

value: male

tag: sampling time

tag: exercise

value: RUN


title: 8SED_e

source_name: Murine inguinal white adipose tissue from sedentary animals sampled at ZT15

value: SED


title: ad libitum feeding, HF, 12AM

description:
Canton-S+HFD, Female
ALF_HF_12AM


title: 7Run_e

source_name: Murine inguinal white adipose tissue from exercised animals sampled at ZT15


title: ad libitum feeding, C, 8PM

description:
Canton-S, Female
ALF_C_8PM


title: ad libitum feeding, C, 4PM

description:
Canton-S, Female
ALF_C_4PM


title: 6SED_e


title: 4SED_m

source_name: Murine inguinal white adipose tissue from sedentary animals sampled at ZT3


title: 5Run_e


title: ad libitum feeding, C, 8AM

description:
Canton-S, Female
ALF_C_8AM


title: ad libitum feeding, C, 4AM

description:
Canton-S, Female
ALF_C_4AM


title: Rat_WKYxBN_Epiblast_rep4 [WxB_EB4]

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

country: Japan

institute: Nara Medical University

description:
WGBS (rPBAT)
rat_epiblast_maternal_rep1-3_x1.bw
rat_epiblast_maternal_rep1-3_x5.bw
rat_epiblast_paternal_rep1-3_x1.bw
rat_epiblast_paternal_rep1-3_x5.bw
rat_epiblast_total_rep1-3_x1.bw
rat_epiblast_total_rep1-3_x5.bw

data_processing:
>Sequencing reads were trimmed using Trimmomatic (v0.32) and the following parameters: SLIDINGWINDOW:3:10 MINLEN:36 ILLUMINACLIP:TruSeq2-3-PE.fa:2:30:10.
>Read pairs that survived trimming were aligned to diploid rat or mouse pseudogenomes using MEA and Bismark.
>Duplicate reads were removed and the number of methylated and unmethylated reads overlapping each CpG of the rat or mouse genome was reported. This resulted in total (allele-agnostic), maternal- and paternal-specific CpG report files.
>Replicates and reciprocal crosses were merged for visualization and analyses.
>CpGs covered by at least 5 (total) or 1 (maternal or paternal) sequencing reads were assessed for methylation levels and genome-wide tracks were sunsequently generated for visualization.
Genome_build: rn6
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for each sample

organism: Rattus norvegicus

source_name: epiblast

extract_protocol:
Genomic DNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s protocols.
One hundred nanograms of genomic DNA from JF1 (female) and C57BL/6 (male) mouse hybrids were prepared for Methyl-seq (Illumina) library construction. Twenty nanograms of genomic DNA from the other mouse and rat hybrid crosses were prepared for rPBAT or tPBAT library construction.

treatment_protocol: E8.5 F1 hybrid rat embryos were isolated from reciprocally crossing BN/CrlCrlj (BN rat) and WKY/NCrlCrlj (WKY rat) strains. E7.25 F1 hybrid mouse embryos were isolated from reciprocally crossing C57BL/6N and JF1/Ms strains. For both rat and mouse embryos, the ectoplacental cone (EPC) was dissected from the rest of the embryo before removing the visceral endoderm. Finally, the epiblast (EB) was dissected from the extraembryonic ectoderm (ExE). Each ExE lysate was used for rapid genetic sex determination by direct PCR amplification of the Y chromosome gene using specific primers for mouse Zfy and rat Sry. Only female EBs and EPCs were subjected to whole genome bisulphite sequencing.

value: F1 hybrid resulting from female WKY and male BN rats

tag: age

value: embryonic days 8.5

tag: cell type

value: epiblast

value: female


title: Rat_WKYxBN_EPC_rep3

data_processing:
>Reads were trimmed using Trimmomatic (v0.32) to remove 2 nucleotides of the 5’ end of read 2
>Sequencing reads were further trimmed using Trimmomatic (v0.32) and the following parameters: SLIDINGWINDOW:3:10 MINLEN:36 ILLUMINACLIP:TruSeq2-3-PE.fa:2:30:10.
>Read pairs that survived trimming were aligned to genome build mm10 or rn6 using STAR (v2.4.0.i) and PCR duplicate reads were flagged using Picard MarkDuplicates (v1.92).
>Library quality was assessed using samtools flagstat (v1.1) and Picard CollectRNASeqMetrics.
>Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using samtools parameters: samtools view -bh -q 255 -F 1540.
>NCBI RefSeq mouse transcript annotations (n=106,520 isoforms, 35,977 genes) were downloaded from the UCSC Table Browser (last updated 2017-11-16). NCBI RefSeq rat transcript annotations (n=69,194 isoforms, 30,871 transcripts) were downloaded from the UCSC Table Browser (last updated 2018-03-09).
>Gene expression values were calculated by averaging read coverage over exons using VisRseq (v0.9.12) and normalized to the total number of aligned reads and transcript length in kilobases (RPKM).
>Genome browser compatible normalized bigWigs were generated using bedtools genomecov (v2.22.1).
Genome_build: rn6
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for each sample

source_name: EPC

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s protocols.
One nanogram of embryonic total RNA was reverse transcribed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio) according to the manufacturer's protocol.

treatment_protocol: E8.5 F1 hybrid rat embryos were isolated from reciprocally crossing BN/CrlCrlj (BN rat) and WKY/NCrlCrlj (WKY rat) strains as well as between strains BN/CrlCrlj and F334/NSlc (F344/N rat). E7.25  F1 hybrid mouse embryos were isolated from reciprocally crossing C57BL/6N and JF1/Ms strains. For both rat and mouse embryos, the ectoplacental cone (EPC) was dissected from the rest of the embryo before removing the visceral endoderm. Finally, the epiblast (EB) was dissected from the extraembryonic ectoderm (ExE). Each ExE lysate was used for rapid genetic sex determination by direct PCR amplification of the Y chromosome gene using specific primers for mouse Zfy and rat Sry. Only female EBs and EPCs were subjected to strand-specific RNA-sequencing.

value: wild type

value: EPC


title: ad libitum feeding, C, 12PM

description:
Canton-S, Female
ALF_C_12PM

value: indirect flight muscle

value: Female

value: Canton-S

value: normal


title: 3RUN_m


title: ad libitum feeding, C, 12AM

description:
Canton-S, Female
ALF_C_12AM

value: ad libitum feeding


title: Rat_WKYxBN_EPC_rep2


title: Rat_WKYxBN_EPC_rep4 [WxB_EPC4]

description:
WGBS (rPBAT)
rat_ectoplacentalcone_maternal_rep1-3_x1.bw
rat_ectoplacentalcone_maternal_rep1-3_x5.bw
rat_ectoplacentalcone_paternal_rep1-3_x1.bw
rat_ectoplacentalcone_paternal_rep1-3_x5.bw
rat_ectoplacentalcone_total_rep1-3_x1.bw
rat_ectoplacentalcone_total_rep1-3_x5.bw


title: Rat_WKYxBN_Epiblast_rep3 [WxB_EB3]


title: 24SED_e


title: 23Run_e


title: Rat_WKYxBN_Epiblast_rep3


title: Rat_WKYxBN_Epiblast_rep2


title: A549sgTSC2_TRAIL_1

city: Amsterdam

first: Joleen

last: Traets

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Read mapping was performed using STAR (2.7.3a)
Read counts per gene were quantified using HTSeq (0.12.4)
Read counts were normalised using DEseq2 (1.30.0)
Assembly: human GRCh38
Supplementary files format and content: Raw counts and fastq files

organism: Homo sapiens

growth_protocol: Cells were cultured with DMEM supplemented with 10% FBS and pen/strep in 5% CO2 incubator at 37 degree

extract_protocol:
RNA was extracted using RLT buffer (Qiagen, 79216)
Librararies were prepared for sequencing using standard Illumina protocols

treatment_protocol: D10 melanoma and A549 lung cancer cell lines expressing sgCtrl or sgTSC2 were seeded in 10cm tissue culture dishes for 48h. Tumor cells were challenged with T cell or TRAIL (D10: 10ng/ml; A549: 100ng/ml) overnight. Supernatant containing cell debris and T cells was discarded and pure viable tumor cells were sorted by FACSAria Fusion Cell Sorters.

tag: cell line

value: TRAIL


title: A549sgCTRL_TRAIL_2

value: sgCTRL


title: Rat_WKYxBN_Epiblast_rep1


title: 22SED_e

value: inguinal white adipose tissue


title: cells; 8h phosphate starved with cycloheximide; biol_rep3

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts
Supplementary files format and content: DESeq output file

molecule: polyA RNA

organism: Schizosaccharomyces pombe

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA Seq

tag: growth phase

value: 8 h phopshate starved culture

tag: growth medium

value: ePMGT(-PO4) medium

value: h-

value: 100 µg/ml cycloheximide


title: cells; 8h phosphate starved with cycloheximide; biol_rep2


title: 21Run_e

value: male

value: RUN


title: Rat_WKYxBN_EPC_rep3 [WxB_EPC3]

value: F1 hybrid resulting from female WKY and male BN rats

value: embryonic days 8.5

value: female


title: A549sgCTRL_TRAIL_1


title: 2SED_m

value: SED


title: cells; 8h phosphate starved with cycloheximide; biol_rep1


title: Rat_BNxWKY_EPC_rep3

value: F1 hybrid resulting from female BN and male WKY rats

value: wild type

value: EPC


title: A549sgTSC2_T cell_2

value: T cell


title: Rat_BNxWKY_EPC_rep2


title: A549sgTSC2_TRAIL_2

value: TRAIL


title: cells; 4h phosphate starved with cycloheximide; biol_rep3

value: 4 h phopshate starved culture


title: A549sgTSC2_T cell_1


title: Rat_WKYxBN_EPC_rep1


title: Rat_BNxWKY_Epiblast_rep3

value: epiblast


title: cells; 4h phosphate starved with cycloheximide; biol_rep2


title: 19RUN_m

value: inguinal white adipose tissue


title: A549sgCTRL_T cell_2

value: sgCTRL


title: Rat_BNxWKY_EPC_rep1


title: A549sgCTRL_T cell_1


title: Rat_BNxWKY_Epiblast_rep2


title: 18SED_m


title: cells; 2h phosphate starved with cycloheximide; biol_rep3

value: 2 h phopshate starved culture

value: ePMGT(-PO4) medium

value: h-


title: D10sgTSC2_TRAIL_2


title: 17RUN_m

value: male

value: RUN


title: Rat_BNxWKY_Epiblast_rep1

value: embryonic days 8.5


title: 16SED_e


title: cells; 2h phosphate starved with cycloheximide; biol_rep2

value: 100 µg/ml cycloheximide


title: D10sgTSC2_TRAIL_1


title: Rat_F344xBN_EPC_rep3

value: F1 hybrid resulting from female F344/N and male BN rats

value: female


title: cells; 2h phosphate starved with cycloheximide; biol_rep1


title: 1RUN_m


title: 15Run_e


title: 20SED_m

value: SED


title: Rat_F344xBN_EPC_rep2

value: wild type

value: EPC


title: D10sgCTRL_TRAIL_2

value: TRAIL


title: cells; 8h phosphate starved; biol_rep2

value: 8 h phopshate starved culture

value: no drug


title: 13Run_e

value: inguinal white adipose tissue


title: cells; 8h phosphate starved; biol_rep3


title: Rat_F344xBN_EPC_rep1


title: 14SED_e


title: D10sgCTRL_TRAIL_1

value: sgCTRL


title: cells; 4h phosphate starved with cycloheximide; biol_rep1

value: 4 h phopshate starved culture


title: D10sgTSC2_T cell_2

value: T cell


title: 12SED_m


title: 11RUN_m


title: Rat_F344xBN_Epiblast_rep2

value: epiblast


title: cells; 8h phosphate starved; biol_rep1

value: ePMGT(-PO4) medium

value: h-


title: Rat_F344xBN_Epiblast_rep3

value: embryonic days 8.5


title: cells; 4h phosphate starved; biol_rep3


title: D10sgTSC2_T cell_1


title: D10sgCTRL_T cell_2


title: Rat_BNxF344_EPC_rep2

value: F1 hybrid resulting from female BN and male F344/N rats


title: D10sgCTRL_T cell_1


title: Rat_F344xBN_Epiblast_rep1

value: F1 hybrid resulting from female F344/N and male BN rats


title: MPRA_P28-RNA28

city: Boston

first: Pingzhu

last: Zhou

state: MA

address: 320 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description:
MPRA pool RNA
P300-MPRA-counts.txt
Amplicon-seq

data_processing:
Trimmomatic was used to trim the 3' end of the read by quality score, removing bases <28.
Adapters were removed from the 5' read ends, and forward and reverse reads were aligned to mm10 using Bowtie2.
Concordantly aligned reads for each enhancer were counted using Bedtools.
assembly: mm10
P300-MPRA.txt: tab delimited text file containing the raw number of reads for each enhancer at each timepoint.

source_name: P28 ventricles

growth_protocol: In vivo maturation

extract_protocol:
Ventricles were collected at P28. RNA was extracted by Trizol and purified by Zymo RNA Clean and Concentrator column with DNAse digestion.
RNA reverse transcribed with Oligo-dT, MPRA reporter transcripts were selectively amplfied, and NGS adapters added during two rounds of PCR.

value: wildtype

value: postnatal day 28

tag: type

value: MPRA RNA

value: P300-MPRA library


title: cells; 4h phosphate starved; biol_rep1


title: 10SED_m

value: male

value: SED


title: cells; 2h phosphate starved; biol_rep3

value: 2 h phopshate starved culture

value: no drug


title: Tbx21-/E (biol rep 4)

city: Freiburg

first: Vincent

last: Schipperges

address: Breisacher Str. 153

department: Institut für Medizinische Bioinformatik und Systemmedizin

country: Germany

institute: Universitätsklinikum Freiburg

data_processing:
The raw RNA sequencing files were pre-processed using Trimmomatic, clipping adapters removing reads with low base quality (< 20)
The trimmed reads were then aligned using STAR with the GRCm38 mouse reference genome from Ensembl
Normalization and differential gene expression analysis was performed with the R/Bioconductor package DESeq2 separately for each of the six pairwise comparisons between the four groups.
Assembly: mm10
Supplementary files format and content: tab-delimited text files, reads per gene

source_name: spleen

extract_protocol:
RNA was extracted by using RNeasy Micro Kit (Quiagen; Hilden, Germany) and treated with DNase I to eliminate possible genomic DNA contamination. Quantity and Purity were measured with High Sensitivity RNA ScreenTape (Agilent; Santa Clara, CA, USA).
cDNA synthesis, amplification and library preparation were performed with NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs Gmbh; Frankfurt, Germany)

treatment_protocol: From spleens of SMARTA TCR tg Tbx21+/+, Tbx21+/-, Tbx21+/E and Tbx21-/E mice on a CD90.1 (Thy1.1) background SMARTA CD4+ T cells were isolated by Dynabeads Untouched Mouse CD4 Cells Kit (Invitrogen, ThermoFisher Scientific; Waltham, MA, US) with a purity of > 97%. For each genotype 2x104 SMARTA (CD90.1+) CD4+ T cells were intravenously injected into five C57BL/6 recipient mice on a CD90.2 background. One day later mice were infected intravenously with 200 plaques forming units LCMV (WE). On day eight after infection spleens were harvested and SMARTA (CD90.1+) CD4+ T cells isolated by FACS for RNA extraction.

value: spleen

value: primary

value: SMARTA CD4+ T cells

value: LCMV infection


title: Rat_BNxF344_Epiblast_rep2

value: wild type

value: epiblast

value: female


title: Tbx21-/E (biol rep 3)


title: MPRA_P28-RNA26


title: MPRA_P28-RNA27


title: cells; 2h phosphate starved; biol_rep2

value: ePMGT(-PO4) medium

value: h-


title: H3K36me3_rep2

data_processing:
>Sequencing reads were trimmed using Trimmomatic (v0.32) and the following parameters: SLIDINGWINDOW:3:10 MINLEN:20 ILLUMINACLIP:TruSeq2_SE.fa:2:30:10.
>Reads that survived trimming were aligned to genome build mm10 or rn6 using Bowtie2 (2.2.3) and PCR duplicate reads were flagged using Picard MarkDuplicates (v1.92).
>Library quality was assessed using samtools flagstat (v1.1).
>Uniquely aligned, non-PCR-duplicate reads were used for bigwig creation using deeptools bamCoverage (v3.3.0) and parameters: --binSize 0,50,200 --smoothLength 0,100,2000 minMappingQuality 10 --normalizeUsing CPM –ignoreDuplicates --ignoreForNormalization chrX chrM chrY --outFileFormat bigwig
Genome_build: rn6
Supplementary_files_format_and_content: bigwig files for each sample

source_name: GV stage oocyte

extract_protocol:
Oocytes were incubated with rabbit anti-H3K27me3 antibody, rabbit anti-H3K4me3 antibody, or rabbit anti-H3K36me3 in a wash buffer (20 mM HEPES (pH7.5), 150 mM NaCl, 0.5 mM Spermidine, complete EDTA-free protease inhibitor cocktail, 0.02% Digitonin) containing 2 mM EDTA at 4C on a plastic dish overnight. After the oocytes were washed twice by the wash buffer on a plastic dish, they were incubated with Protein A-MNase (500 ng/ml) provided by the Steven Henikoff Lab at 4C for 3 hrs on a plastic dish. After washing twice, the oocytes were transferred into a 1.5 ml tube containing pre-activated BioMag Plus Concanavalin A (ConA) beads. The sequential step of the antibody incubation followed by the ConA binding prevents loss of oocytes during wash steps. After the oocytes were bound to ConA beads and the buffer was replaced to the wash buffer, CaCl2 was added at a final concentration of 2 mM to activate the MNase. After 20 min of digestion on ice, the digestion reaction was stopped and DNA fragments were recovered.
CUT&RUN libraries were prepared as previously described (Inoue et al., Genes Dev., 2018). PCR amplification was performed for 11-15 cycles.

treatment_protocol: GV stage rat oocytes were collected from ovary of 3-4 wk old BrlHan:WIST (Clea Japan) rats 48-50 h after administration of PMSG. Briefly, cumulus-oocyte complexes were collected in PB1 with 200 µM IBMX (Sigma), and subsequently incubated in the presence of 5-10 µg/ml cytochalasin B for 5-10 min to loosen the connection between cumulus cells and oocytes. Then, the cumulus cells were mechanically removed by repeated pipetting using a glass capillary, and the zona pellucida were removed by brief incubation in acidic Tyrode’s solution.

value: Wild type

value: GV stage oocyte

tag: chip antibody


title: Rat_BNxF344_Epiblast_rep1

value: F1 hybrid resulting from female BN and male F344/N rats

value: embryonic days 8.5


title: Tbx21-/E (biol rep 2)

tag: tissue


title: cells; 2h phosphate starved; biol_rep1


title: cells; phosphate rich; biol_rep3

value: log phase culture

value: YES medium


title: Tbx21-/E (biol rep 1)


title: Tbx21+/- (biol rep 4)


title: MPRA_P28-RNA25

value: wildtype

value: postnatal day 28

value: MPRA RNA

value: P300-MPRA library


title: cells; 4h phosphate starved; biol_rep2

value: 4 h phopshate starved culture

value: no drug


title: cells; phosphate rich; biol_rep2


title: H3K27me3_rep2


title: MPRA_P28-RNA23


title: MPRA_P28-RNA24


title: Tbx21+/- (biol rep 3)

value: spleen

value: primary

value: SMARTA CD4+ T cells

value: LCMV infection


title: MPRA_P28-RNA22


title: Rat_BNxF344_EPC_rep1

value: wild type

value: EPC

value: female


title: Tbx21+/- (biol rep 2)


title: MPRA_P28-RNA21


title: H3K36me3_rep1

value: Wild type

value: GV stage oocyte


title: H3K27me3_rep1


title: cells; phosphate rich; biol_rep1

value: log phase culture

value: h-


title: MPRA_P28-RNA20

value: wildtype


title: maf1_48h

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts

source_name: cultures

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

value: h+ maf1[delta]::natMX

tag: lab strain number

tag: growth conditions

value: 48 h phopshate starved culture, ePMGT(-PO4) medium

tag: developmental stage

value: Quiescence in -PO4


title: MPRA_P28-RNA19

value: postnatal day 28

value: MPRA RNA

tag: treatment

value: P300-MPRA library


title: Tbx21+/E (biol rep 4)

value: spleen

value: primary

tag: genotype


title: maf1_24h

value: 24 h phosphate starved culture, ePMGT(-PO4) medium


title: H3K4me3_rep1

tag: strain

value: H3K4me3 (Active Motif, #39159)


title: MPRA_P28-RNA18


title: Subject 266, CD8+ T cells, expanded with IL-4 + IL-15

city: Pittsburgh

first: Daniella

last: Schwartz

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing:
Novaseq6000 was used for 50-cycle single-end read sequencings, which were processed with bcl2fastq 2.17.1 to generate FastQ files.
Reads were processed using the ccbr pipeliner tool (github), which utilized cutadapt for trimming and STAR 2.7.0 to map to the human transcriptome (hg19)
gene expression values (fragments per kilobase exon per million mapped reads [fpkm]) were calculated and normalized with RSEM 1.3.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: CD8+ T cells

growth_protocol: PBMCs from were thawed and incubated with media containing overlapping peptide libraries containing SARS-CoV-2 structural proteins for spike, membrane, envelope, and nucleocapsid (A&A Peptide, San Diego, CA, USA). Pulsed PBMCs were plated in 96-well plates at 200,000 cells/well in media with one of six cytokine conditions. Cells were split on day 7 of culture and supplemented with additional media and cytokines

extract_protocol:
Total RNA was extracted from 10,000–50,000 cells using phenol:choloroform, and mRNA sequencing libraries were generated from all sorted cells
RNA libraries for RNA-seq were prepared using NEBNext Ultra II mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Culture conditions were: IL-4 (400 IU/mL) + IL-7 (10 ng/mL), IL-7 (10 ng/mL) + IL-15 (5 ng/mL), IL-4 (400 IU/mL) + IL-15 (5 ng/mL), IL-6 (100 ng/mL) + IL-15 (5 ng/mL), IL-15 alone (5 ng/mL), or no cytokines (R&D Systems, Minneapolis, MN, USA).
On day 10, expanded VSTs from 4 donors were re-stimulated with SARS-CoV-2 pepmixes encompassing spike, nucleocapsid, membrane, and envelope with CD28/CD89d (BD Biosciences) and incubated for 4 h. Cell viability was assessed using Live-Dead-near-infrared (IR). Cells were surface stained with fluorophore-conjugated antibodies against CD8-BV605, CD8-BV421, CD19-FITC, CD16-FITC, and CD14-FITC (Biolegend) and then sorted for CD8+ and CD8+ cells. Cells were not stained with CD3+ antibodies to prevent non-specific cell activation. Cells were then frozen and preserved in Trizol (Invitrogen, Waltham, MA, USA).

value: CD8+ T cells


title: Subject 266, CD8+ T cells, expanded with IL-15 + IL-6


title: Tbx21+/E (biol rep 2)

value: SMARTA CD4+ T cells

value: LCMV infection


title: Tbx21+/E (biol rep 1)


title: maf1_36h

value: 36 h phosphate starved culture, ePMGT(-PO4) medium


title: Subject 266, CD8+ T cells, expanded with IL-15 + IL-7


title: Tbx21+/E (biol rep 3)


title: MPRA_P28-RNA16


title: maf1_4h

value: 4 h phosphate starved culture, ePMGT(-PO4) medium

value: limited growth in -PO4


title: Tbx21+/+ (biol rep 4)


title: MPRA_P28-RNA15

value: wildtype


title: maf1_0h

growth_protocol: log phase cultures, 30ºC, YES medium

value: h+ maf1[delta]::natMX

value: log phase culture, YES medium

value: vegetative growth


title: Tbx21+/- (biol rep 1)


title: maf1_8h

value: 8 h phosphate starved culture, ePMGT(-PO4) medium


title: MPRA_P28-RNA14

value: postnatal day 28

value: MPRA RNA


title: Tbx21+/+ (biol rep 3)

value: spleen


title: H3K4me3_rep2

value: Wild type

value: GV stage oocyte


title: WT_48h

value: h-

value: 48 h phosphate starved culture, ePMGT(-PO4) medium

value: Quiescence in -PO4


title: Tbx21+/+ (biol rep 2)

value: primary

value: SMARTA CD4+ T cells

value: LCMV infection


title: Subject 266, CD8+ T cells, expanded without exogenous cytokines

value: CD8+ T cells

value: vehicle control


title: MPRA_P28-RNA13

value: wildtype

value: P300-MPRA library


title: Tbx21+/+ (biol rep 1)


title: WT_36h

value: 36 h phosphate starved culture, ePMGT(-PO4) medium


title: Subject 273, CD8+ T cells, expanded with IL-4 + IL-15


title: maf1_12h

value: h+ maf1[delta]::natMX

value: 12 h phosphate starved culture, ePMGT(-PO4) medium

value: limited growth in -PO4


title: WT_24h

value: 24 h phosphate starved culture, ePMGT(-PO4) medium


title: MPRA_P28-RNA12

value: postnatal day 28

value: MPRA RNA


title: MPRA_P28-RNA11


title: Purified Cardiomyocyte-P42_rep3

data_processing:
Sequenced reads aligned to mm10 reference by Juicer
Paired reads were binned to .cool file by Cooler
Biological replicates were combined to single .cool file by Cooler
Compartment, loop and TAD insulation score were calculated by Cooltools; TAD splits were defined by TADsplimer
Genome_build: mm10
Supplementary_files_format_and_content: .cool file containing raw and balanced Hi-C contact matrix
Supplementary_files_format_and_content: Plain txt files include compartment scores

source_name: Heart

extract_protocol:
For each biological replicate, 2M purified cardiomyocytes were fixed in PBS supplemented with 1% formaldehyde for 10 min at RT and then quenched with 125 mM glycine for 5 min at RT. Nuclei were isolated by treating with a hypotonic buffer (10 mM Tris-HCl, pH 8.0, 10 mM KCl, 1 mM MgCl2, 0.2% Igepal CA630) on ice for 10 min. Pelleted nuclei were permeabilized using 0.5% SDS and incubated for 10 min at 62 °C. Chromatin was digested using the 4-base cutter restriction enzyme MboI (200 units, NEB) at 37 °C overnight. After inactivation of MboI for 20 min at 62 °C, single stranded overhangs were filled with biotinylated-14-dATP (Life Technologies) and dCTP, dGTP, and dTTP using Klenow DNA polymerase (40 units, NEB) for 90 min at 37 °C. DNA was then ligated for 4 h at 16 °C using T4 DNA ligase (2,000 units, NEB). Reverse crosslinking was performed by incubating at 55 °C with proteinase K for 30 min and then 68 °C overnight. Purified DNA was sonicated using an ultra sonicator to 300-700 bp small fragments. After size selection and purification using SPRI beads (Beckman Coulter), biotinylated DNA was isolated using Dynabeads MyOne T1 Streptavidin beads (Life Technologies).
Sequencing libraries were prepared on magnetic beads and final PCR amplification was carried out for 6 cycles. Size distribution of bead-purified libraries was checked using a High Sensitivity D1000 ScreenTape on a Tapestation (Agilent) and quantified using Qubit (Life Technologies). Libraries were sequenced on Hiseq 4000 (100 bp PE, Illumina)

treatment_protocol: For E12.5, E16.5, P0, and P7 CMs, ventricular apexes were dissociated using the Neonatal mouse cardiomyocyte isolation kit (Cellutron Life Technologies) and purified using the mouse neonatal cardiomyocyte isolation kit (Miltenyi). P14, P28, and P42 CMs were dissociated and purified from ventricular apexes by Langendorf collagenase perfusion followed by differential sedimentation

value: Heart

value: Cardiomyocyte


title: WT_12h

value: h-


title: Subject 266, CD8+ T cells, expanded with IL-15


title: Subject 273, CD8+ T cells, expanded with IL-15 + IL-7


title: WT_8h

value: 8 h phosphate starved culture, ePMGT(-PO4) medium


title: Subject 266, CD8+ T cells, expanded with IL-4 + IL-7


title: Subject 273, CD8+ T cells, expanded with IL-15


title: Purified Cardiomyocyte-P42_rep2


title: MPRA_P28-RNA10


title: MPRA_P28-RNA17


title: MPRA_P28-RNA8


title: Subject 273, CD8+ T cells, expanded with IL-4 + IL-7


title: MPRA_P28-RNA9


title: WT_4h

value: 4 h phosphate starved culture, ePMGT(-PO4) medium


title: Subject 273, CD8+ T cells, expanded without exogenous cytokines


title: Purified Cardiomyocyte-P0_rep2


title: MPRA_P28-RNA7


title: Purified Cardiomyocyte-P0_rep3


title: Subject 273, CD8+ T cells, expanded with IL-15 + IL-6


title: C636 cells, EV-infected, 2 dpi, rep2

city: Hong Kong

first: Xudong

last: Liu

address: Tat Chee Avenue Kowloon Tong

country: China

institute: City University of Hong Kong

data_processing:
Raw data were trimmed using Trimmomstic 0.39.
Trimmed reads were aligned to viral genomes and Aedes albopictus C6/36 genome (GenBank assembly accession: GCA_001876365.2) using TopHat 2.1.1.
Aligned transcripts were quantified via HTSeq 0.11.3.
Assembly: GenBank assembly accession: GCA_001876365.2
Supplementary files format and content: Tab-delimited text files include gene count values for each Sample

organism: Aedes albopictus

source_name: Larva

growth_protocol: C636 cells were maintained at 28 °C with 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS), 1% tryptose phosphate broth, 2 mM L-glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Invitrogen, Waltham, MA, USA) when each virus reached the highest titer, that is, 1 dpi for E/C, 2 dpi for E/V, and 3 dpi for EILV. The total RNA of mock-infected cells was isolated at 1 dpi.
PolyA+ transcripts were enriched and subjected to library preparation.

treatment_protocol: C636 cells were seeded in 6-well plates at a density of 5*10^5 cells/well and infected with EILV, E/C, or E/V at MOI 0.1 or mock-infected in triplicates.

value: Larva

value: Insect cell line

value: WT

value: EV-infected


title: Subject 282, CD8+ T cells, expanded with IL-4 + IL-15

value: CD8+ T cells


title: MPRA_P28-RNA6

value: wildtype

value: P300-MPRA library


title: Subject 282, CD8+ T cells, expanded with IL-15 + IL-6


title: Purified Cardiomyocyte-E12.5_rep3


title: MPRA_P28-RNA5


title: Purified Cardiomyocyte-P42_rep1


title: C636 cells, EC-infected, 1 dpi, rep3

value: EC-infected


title: Purified Cardiomyocyte-E12.5_rep2


title: Subject 282, CD8+ T cells, expanded with IL-15 + IL-7


title: MPRA_P28-RNA4


title: MPRA_P28-RNA3


title: Subject 282, CD8+ T cells, expanded with IL-15


title: Purified Cardiomyocyte-E12.5_rep1


title: Subject 282, CD8+ T cells, expanded with IL-4 + IL-7


title: C636 cells, EC-infected, 1 dpi, rep1


title: C636 cells, EC-infected, 1 dpi, rep2


title: Subject 282, CD8+ T cells, expanded without exogenous cytokines

value: vehicle control


title: WT_0h

value: log phase culture, YES medium

value: vegetative growth


title: WT3 ATAC

first: Fleur

last: Peters

address: Meibergdreef 9

institute: Amsterdam UMC (AMC)

data_processing:
ATACseq: Sequencing reads were trimmed and aligned to the GRCm38v93 reference genome using HISAT2 v2.1.0. Pre-processing of the data was done using the ENCODE pipeline (https://www.encodeproject.org/atac-seq/) followed by peak-calling with MACS2 v2.2.7.1 (bandwidth=300, p-value cut-off=0.01).
RNAseq: Sequencing reads were trimmed and aligned to the GRCm38v93 reference genome using STAR v2.5.4. Count matrices were created with HTSeq v0.6.11.0
Genome_build: mm10: GRCm38v93
Supplementary_files_format_and_content: Raw count files and peak files

source_name: Splenic CD8+ T cells

extract_protocol:
Total RNA was extracted with the Qiagen Micro kit and for ATAC seq, the omni-atac protocol was used with the Illumina transposase kit
NEBNext low input kit for RNAseq and NEBNext high fidelity master mix using barcoded primer for the ATAC libraries

value: Splenic CD8+ T cells

tag: condition

value: wild-type

tag: library prep

value: Omni-ATAC protocol


title: C636 cells, EV-infected, 2 dpi, rep3


title: WT1 ATAC


title: Purified Cardiomyocyte-P0_rep1

value: Heart

value: Cardiomyocyte


title: WT2 ATAC


title: MPRA_P28-RNA1

value: postnatal day 28

value: MPRA RNA


title: Subject 295, CD8+ T cells, expanded with IL-4 + IL-15


title: C636 cells, EILV-infected, 3 dpi, rep3

value: Larva

value: Insect cell line

value: EILV-infected


title: MPRA_P7-RNA28

source_name: P7 ventricles

extract_protocol:
Ventricles were collected at P7. RNA was extracted by Trizol and purified by Zymo RNA Clean and Concentrator column with DNAse digestion.
RNA reverse transcribed with Oligo-dT, MPRA reporter transcripts were selectively amplfied, and NGS adapters added during two rounds of PCR.

value: postnatal day 7


title: MPRA_P7-RNA27

value: wildtype


title: CLL4 ATAC

value: CLL


title: C636 cells, EILV-infected, 3 dpi, rep1

value: WT


title: C636 cells, EV-infected, 2 dpi, rep1

value: EV-infected


title: CLL3 ATAC


title: Subject 295, CD8+ T cells, expanded with IL-15 + IL-6

value: CD8+ T cells


title: Subject 295, CD8+ T cells, expanded with IL-15 + IL-7


title: C636 cells, mock-infected, 1 dpi, rep3

value: Mock-infected


title: Subject 295, CD8+ T cells, expanded with IL-15


title: C636 cells, mock-infected, 1 dpi, rep2


title: CLL2 ATAC

value: Splenic CD8+ T cells


title: MPRA_P28-RNA2

value: P300-MPRA library


title: MPRA_P7-RNA26


title: MPRA_P7-RNA25


title: CLL1 ATAC

value: Omni-ATAC protocol


title: MPRA_P7-RNA24


title: Two_wt_sti

city: shanghai

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

institute: Zhejiang University

description: Bone marrow cells from and wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with CCR7L for 12 h and then subjected to RNA seq.

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute  using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome GRCm38.p4 (mm10).
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM).

source_name: mouse BMDC

extract_protocol:
BMDC were stimulated with or without  CCR7L for 12 h and  collected for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

treatment_protocol: Bone marrow cells from Extl1-dificient  and wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with or without  CCR7L for 12 h and then subjected to RNA seq.

value: mouse BMDC

value: wild type


title: Subject 295, CD8+ T cells, expanded without exogenous cytokines

value: vehicle control


title: Subject 295, CD8+ T cells, expanded with IL-4 + IL-7


title: MPRA_P7-RNA22

value: MPRA RNA


title: C636 cells, mock-infected, 1 dpi, rep1

value: Larva


title: MPRA_DNA2

description:
AAV genomic DNA MPRA pool
P300-MPRA-counts.txt
Amplicon-seq

organism: Adeno-associated virus 9

source_name: uninjected AAV

extract_protocol:
Viral DNA was released from the capsid by Proteinase-K digestion.
MRPA enhancer DNA was selectively amplfied, and NGS adapters added during two rounds of PCR.

value: Control DNA


title: Subject 266, CD4+ T cells, expanded with IL-4 + IL-15

source_name: CD4+ T cells

treatment_protocol:
Culture conditions were: IL-4 (400 IU/mL) + IL-7 (10 ng/mL), IL-7 (10 ng/mL) + IL-15 (5 ng/mL), IL-4 (400 IU/mL) + IL-15 (5 ng/mL), IL-6 (100 ng/mL) + IL-15 (5 ng/mL), IL-15 alone (5 ng/mL), or no cytokines (R&D Systems, Minneapolis, MN, USA).
On day 10, expanded VSTs from 4 donors were re-stimulated with SARS-CoV-2 pepmixes encompassing spike, nucleocapsid, membrane, and envelope with CD28/CD49d (BD Biosciences) and incubated for 4 h. Cell viability was assessed using Live-Dead-near-infrared (IR). Cells were surface stained with fluorophore-conjugated antibodies against CD4-BV605, CD8-BV421, CD19-FITC, CD16-FITC, and CD14-FITC (Biolegend) and then sorted for CD4+ and CD8+ cells. Cells were not stained with CD3+ antibodies to prevent non-specific cell activation. Cells were then frozen and preserved in Trizol (Invitrogen, Waltham, MA, USA).

value: CD4+ T cells


title: MPRA_DNA3


title: MPRA_P7-RNA23

value: postnatal day 7


title: Two_wt_ctrl

description: Bone marrow cells from  wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated without CCR7L for 12 h and then subjected to RNA seq.


title: Two_ko_sti

description: Bone marrow cells from Extl1-dificient mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with CCR7L for 12 h and then subjected to RNA seq.


title: Subject 266, CD4+ T cells, expanded with IL-15 + IL-6


title: C636 cells, EILV-infected, 3 dpi, rep2

value: Insect cell line

value: EILV-infected


title: MPRA_P7-RNA21

value: wildtype


title: Subject 266, CD4+ T cells, expanded with IL-15 + IL-7


title: Two_ko_ctrl

description: Bone marrow cells from Extl1-dificient mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated without CCR7L for 12 h and then subjected to RNA seq.


title: MPRA_DNA1


title: One_wt_sti


title: NR-MRPA_DNA3

description:
AAV genomic DNA MPRA pool
NR-MPRA-counts.txt
Amplicon-seq

data_processing:
Overlapping paired-end reads were merged with PEAR (Paired-End reAd mergeR)
Merged reads were trimmed down to their central 30bp using Trimmomatic.
A Python script was used to count the number of reads containing the central 20bp of each enhancer.
assembly: mm10
NR-MPRA.txt: tab delimited text file containing the raw number of reads for each enhancer.


title: MPRA_P7-RNA20


title: One_wt_ctrl


title: NR-MRPA_DNA2


title: NR-MRPA_DNA1


title: Subject 266, CD4+ T cells, expanded with IL-4 + IL-7


title: Subject 266, CD4+ T cells, expanded without exogenous cytokines


title: One_ko_ctrl


title: Subject 273, CD4+ T cells, expanded with IL-4 + IL-15


title: MPRA_P7-RNA18


title: 2tr

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome GRCm38.p4 (mm10).
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM).

extract_protocol:
BMDC were stimulated with or without CCR7 ligand CCL19 and CCL21 for 12 h and collected for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

treatment_protocol: Bone marrow cells from  wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with or without CCR7 ligand CCL19 and CCL21 for 12 h

value: BMDC were stimulated with CCR7 ligand CCL19 and CCL21 for 12 h


title: Subject 266, CD4+ T cells, expanded with IL-15


title: Subject 273, CD4+ T cells, expanded with IL-15 + IL-7


title: MPRA_P7-RNA14


title: Subject 273, CD4+ T cells, expanded with IL-15 + IL-6


title: MPRA_P7-RNA16


title: MPRA_P7-RNA17


title: Subject 273, CD4+ T cells, expanded with IL-15


title: One_ko_sti


title: MPRA_P7-RNA13


title: 3un

value: BMDC were stimulated without CCR7 ligand CCL19 and CCL21 for 12 h


title: Subject 273, CD4+ T cells, expanded with IL-4 + IL-7


title: MPRA_P7-RNA11


title: Subject 273, CD4+ T cells, expanded without exogenous cytokines


title: MPRA_P7-RNA19


title: 2un


title: MPRA_P7-RNA12


title: 1un


title: Subject 282, CD4+ T cells, expanded with IL-4 + IL-15


title: MPRA_P7-RNA10


title: Muscle WT 2months Rep4

city: padova

first: Maria

last: Pennuto

state: Padova

address: via ugo bassi 58b

country: Italy

institute: University of Padua

data_processing:
Trascripts were quantify using Salmon (v1.9.0) in paired-end mode
Gene counts were obtained with tximport R package using mouse ENSEMBL102 gene to transcript map
Assembly: GRCm38; transcript annotation Ensembl-102
Supplementary files format and content: Tar of Salmon quantification directory

source_name: skeletal muscle (quadriceps)

extract_protocol:
Total RNA was extracted from the samples using TRIZOL, following manufacturer's protocol.
cDNA libraries were prepared with TruSeq Stranded mRNA (Illumina), according to the manufacturer's protocol.

value: skeletal muscle (quadriceps)

tag: disease state

value: control

value: WT

value: 2 Months-old


title: Muscle WT 2months Rep2

tag: age


title: MPRA_P7-RNA15

value: P300-MPRA library


title: 3tr

tag: cell type

value: mouse BMDC

value: wild type


title: Subject 282, CD4+ T cells, expanded with IL-15 + IL-6


title: MPRA_P7-RNA9

value: MPRA RNA


title: 1tr


title: Rat_WKYxBN_EPC_rep2 [WxB_EPC2]

extract_protocol:
Genomic DNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s protocols.
One hundred nanograms of genomic DNA from JF1 (female) and C57BL/6 (male) mouse hybrids were prepared for Methyl-seq (Illumina) library construction. Twenty nanograms of genomic DNA from the other mouse and rat hybrid crosses were prepared for rPBAT or tPBAT library construction.

value: F1 hybrid resulting from female WKY and male BN rats

value: embryonic days 8.5

value: EPC

tag: Sex

value: female


title: Rat_WKYxBN_EPC_rep1 [WxB_EPC1]


title: Muscle WT 1month Rep4

value: 1 Month-old


title: MPRA_P7-RNA8

value: postnatal day 7


title: Subject 282, CD4+ T cells, expanded with IL-15 + IL-7

value: CD4+ T cells


title: Muscle WT 2months Rep3


title: MPRA_P7-RNA7

value: wildtype


title: Rat_BNxWKY_EPC_rep3 [BxW_EPC3]

description:
WGBS (tPBAT)
rat_ectoplacentalcone_maternal_rep1-3_x1.bw
rat_ectoplacentalcone_maternal_rep1-3_x5.bw
rat_ectoplacentalcone_paternal_rep1-3_x1.bw
rat_ectoplacentalcone_paternal_rep1-3_x5.bw
rat_ectoplacentalcone_total_rep1-3_x1.bw
rat_ectoplacentalcone_total_rep1-3_x5.bw

value: F1 hybrid resulting from female BN and male WKY rats


title: Subject 282, CD4+ T cells, expanded with IL-4 + IL-7


title: Rat_BNxWKY_EPC_rep2 [BxW_EPC2]


title: Subject 282, CD4+ T cells, expanded with IL-15


title: Muscle WT 1month Rep1

value: skeletal muscle (quadriceps)


title: Muscle WT 1month Rep2

value: control


title: MPRA_P7-RNA6


title: MPRA_P7-RNA5


title: Muscle AR100Q 2months Rep3

value: SBMA


title: Subject 282, CD4+ T cells, expanded without exogenous cytokines

value: vehicle control


title: Rat_WKYxBN_Epiblast_rep2 [WxB_EB2]

value: epiblast


title: MPRA_P7-RNA4

value: P300-MPRA library


title: Muscle AR100Q 2months Rep2

value: 2 Months-old


title: Rat_WKYxBN_Epiblast_rep1 [WxB_EB1]

value: wild type


title: MPRA_P7-RNA3

value: MPRA RNA


title: Subject 295, CD4+ T cells, expanded with IL-15 + IL-6


title: Muscle WT 2months Rep1

value: WT


title: Muscle WT 1month Rep3


title: Rat_BNxWKY_Epiblast_rep3 [BxW_EB3]

description:
WGBS (tPBAT)
rat_epiblast_maternal_rep1-3_x1.bw
rat_epiblast_maternal_rep1-3_x5.bw
rat_epiblast_paternal_rep1-3_x1.bw
rat_epiblast_paternal_rep1-3_x5.bw
rat_epiblast_total_rep1-3_x1.bw
rat_epiblast_total_rep1-3_x5.bw

value: embryonic days 8.5


title: Subject 295, CD4+ T cells, expanded with IL-15 + IL-7


title: Muscle AR100Q 2months Rep1


title: MPRA_P7-RNA2


title: Rat_BNxWKY_Epiblast_rep2 [BxW_EB2]

value: female


title: Muscle AR100Q 1month Rep4

value: 1 Month-old


title: Subject 295, CD4+ T cells, expanded with IL-15


title: Rat_BNxWKY_EPC_rep1 [BxW_EPC1]

value: EPC


title: Rat_BNxWKY_Epiblast_rep1 [BxW_EB1]


title: MPRA_P7-RNA1

value: postnatal day 7


title: Muscle AR100Q 1month Rep3


title: Muscle AR100Q 1month Rep1


title: Subject 295, CD4+ T cells, expanded with IL-4 + IL-7

value: CD4+ T cells


title: Subject 295, CD4+ T cells, expanded without exogenous cytokines


title: Muscle AR100Q 1month Rep2


title: Subject 295, CD4+ T cells, expanded with IL-4 + IL-15


title: MPRA_P0-RNA12

source_name: P0 ventricles

extract_protocol:
Ventricles were collected at P0. RNA was extracted by Trizol and purified by Zymo RNA Clean and Concentrator column with DNAse digestion.
RNA reverse transcribed with Oligo-dT, MPRA reporter transcripts were selectively amplfied, and NGS adapters added during two rounds of PCR.

value: wildtype

value: postnatal day 0


title: MPRA_P0-RNA10


title: MPRA_P0-RNA11


title: BaF3-T315I treated with JOA_2

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

description: FPKM-BaF3-T315I cell line.xls

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38(Homo sapiens) and (mm10)mus musculus
Supplementary files format and content: FPKM value

source_name: BaF3-T315I cell line treated with JOA 2

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: incubating with JOA for 48 h

tag: cell line

tag: agent

value: 2 uM JOA


title: Patient 5, healthy, scRNAseq

city: Lund

first: David

last: Gomez Jimenez

state: Skane

address: Scheelevägen 2

department: Immunotechnology

institute: Lund University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Pre-processing of scRNA-seq was performed using Cell Ranger (v6.0). This pipeline included sample de-multiplexing, barcode processing, and 3’ gene counting. Reads were aligned to the GRCh38 transcriptome (v. 2020-A) and single cells within each sample were merged using the aggregate function in Cell Ranger. A total of 11,663 single cells with an average of 92,500 raw reads per cell were further analyzed in R (v4.0.3) and R studio (v1.4.1103) using the Seurat package (v4.0.1)
Assembly: GRCh38
Supplementary files format and content: H5 files containing single cell transcriptomes after CellRanger filtering (STAR pipeline default settings).

source_name: Paired healthy tonsil

extract_protocol:
Samples were cut into small fragments in RPMI 1640 medium (Thermo Fisher Scientific, Bremen, Germany) supplemented with 0.1mg/mL gentamycin (Sigma-Aldrich, St Louis, MO). The tissue fragments were enzymatically digested with Collagenase IV (Sigma-Aldrich) (2.0 mg/mL) and DNase I (Sigma Aldrich) (200 Kunits/mL) for 20 minutes at 37°C. Cells were filtered using a 70 μm cell strainer (BD Biosciences, San Jose, CA). For scRNA-seq, CD45+ CD13+ HLA-DR+ myeloid cells were isolated using FACSAria IIu (BD Biosciences) by cell sorting into FACS tubes containing 3ml of fetal calf serum (FCS) (Life Technologies, Carlsbad, CA). Sorted myeloid cells were washed twice and resuspended in 45 μL of PBS supplemented with 0.04% w/v bovine serum albumin (BSA). Cells were stained with Fixable viability stain 620 (BD Biosciences) to assess cell viability. Cells were washed and non-specific binding was blocked with ChromPure mouse IgG whole molecule (Jackson ImmunoResearch, West Grove, PA) for 15 minutes at room temperature. Cells were immediately stained with the appropriate antibody panel for 20 min at 4°C, washed, and sorted on a FACSAria IIu instrument (BD Biosciences).
The scRNA-seq libraries were prepared according to the user guide manual (CG000204) provided by 10X Genomics’ Chromium Single Cell 3’Reagent Kit (v3.1) (10X Genomics, Pleasanton, CA). Briefly, sorted cellular suspensions of myeloid cells were loaded on a Single Cell chip to encapsulate single cells using the 10X Chromium controller. Encapsulated cells were then subjected to in-drop lysis and reverse transcription reactions. The emulsion droplets were disrupted, and barcoded cDNA was purified using silene magnetic dynabeads (Thermo Fisher Scientific, Waltham, MA), followed by 12-14 cycles of PCR amplification using a C1000 Touch™ Thermal Cycler with 96–Deep Well Reaction Module (#1851197, Bio-Rad. Hercules, CA). The amplified cDNA was purified with the SPRIselect reagent kit (Beckman coulter, Brea, CA) and subjected to enzymatic fragmentation, end repair, A-tailing, size selection with SPRIselect, adaptor ligation, post-ligation cleanup with SPRIselect, and sample index PCR followed by cleanup with SPRIselect. Library size and quality were assessed with High Sensitivity D1000 ScreenTape using a 4200 TapeStation System (G2991BA, Agilent, Santa Clara, CA). The cDNA libraries were sequenced on NovaSeq 6000 System (R1 – 28, i7 8, R2 – 91 cycles, Illumina, San Diego, CA).

value: Myeloid antigen presenting cells

value: Paired healthy tonsil

value: Male

tag: patient number

tag: tumor stage

value: Healthy


title: BaF3-T315I treated with JOA_1

description: FPKM-BaF3-T315I cell line.xls

source_name: BaF3-T315I cell line treated with JOA 1


title: MPRA_P0-RNA9

tag: type

value: P300-MPRA library


title: Patient 5, cancer, scRNAseq

description: 10x Genomics

source_name: Tonsillar cancer

tag: tissue

value: Tonsillar cancer

value: II


title: Patient 4, cancer, scRNAseq

description: 10x Genomics


title: BaF3-T315I treated with control_2

description: FPKM-BaF3-T315I cell line.xls

source_name: BaF3-T315I cell line treated with control 2

treatment_protocol: incubating with control for 48 h

value: Control


title: Patient 3, cancer, scRNAseq

description: 10x Genomics


title: MPRA_P0-RNA7

value: MPRA RNA


title: BaF3-T315I treated with control_1

description: FPKM-BaF3-T315I cell line.xls

source_name: BaF3-T315I cell line treated with control 1


title: MPRA_P0-RNA6


title: MPRA_P0-RNA8


title: Patient 2, cancer, scRNAseq

description: 10x Genomics

value: I


title: Ahrr wt2

city: St. Louis

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

data_processing:
The cellranger (v3.1.0) function was used to align to align reads and generate gene–cell expression matrices using the mm10 reference genome. We filtered out low-quality cells from the dataset if the number of UMI was fewer than 1000 or genes detected was fewer than 500. Cells with low complexity (< 0.8), as defined by the fraction of genes over UMI, were filtered out. We also excluded those cells with a high percentage of mitochondrion reads (>20%). In addition, all genes that were not detected in at least 10 of all the single cells were discarded. Data analyses were performed using the R software package Seurat (http://satijalab.org/seurat/)56. Data were scaled and transformed and variable genes identified using the SCTransform function57, and linear regression was performed to remove unwanted variation due to cell quality (% mitochondrial reads. Data from both genotypes were then integrated using the top 3000 variable features and principal component analysis was performed using these variable genes, and the first 40 principal components (PCs) were used to perform UMAP to embed the dataset into two dimensions. Next, the first 40 PCs were used to construct a shared nearest-neighbor graph (SNN; FindNeighbors) and this SNN was used to cluster the dataset (FindClusters (resolution = 0.4)) using a graph-based modularity-optimization algorithm of the Louvain method for community detection. Despite sorting on CD3+ cells, minor clusters of contaminating B cells and myeloid cells were identified and removed for downstream analysis. After filtering out contaminating cell types, PCA, UMAP, and clustering analysis were redone using the same parameters as above. Cellular identity was determined by finding DE genes for each cluster using Seurat’s implementation of the Wilcoxon rank-sum test (FindMarkers) and comparing those markers to known cell type-specific genes from previous datasets. Differential gene analysis comparing IEL from different genotypes was performed using the R package MAST 58.
Assembly: mm10
Supplementary files format and content: .h5 cellranger output, filtered expression matrices

source_name: CD3+ siIEL

extract_protocol:
IEL and LPLs were isolated from small intestinal epithelium and lamina propria respectively. Small intestines were flushed with HBSS to remove the fecal content. Peyer’s patches were removed followed by longitudinal opening and cut into 1cm pieces. Then, the pieces were washed by gently agitating for 20 minutes followed by vertexing. The flow through was collected and the cycle repeated once again. The flow through was subjected to DTT treatment and Percoll 40-70% gradient separation for isolation of IEL. For LPL isolation, the pieces were rinsed properly with HBSS and then proceeded to digestion with complete RPMI supplemented with collagenase-IV. The undigested tissue chunks were removed by passing through 100-micron mess and then the digests were subjected to 40%-70% Percoll gradient centrifugation for isolation of LPL.
WT and Ahrr–/– IEL (CD45+, CD3+, CD19–) were sorted using BD FACS ARIA-II. Sorted cells were sequenced using the10X Genomics Single Cell 3’ v3 platform.

value: Ahrr WT

value: CD3+ small intestinal IEL


title: Patient 1, cancer, scRNAseq

description: 10x Genomics

value: Female


title: MPRA_P0-RNA5


title: SI-NET-seq primary fibroblast IV.3 (F1) R2

city: Innsbruck

first: Univ.-Prof. Dr. Andreas

last: Mayer

address: Innrain 80/82

department: Institute for Genomics and RNomics

country: Austria

institute: Biocenter, Medical University Innsbruck

description: 12 nt random molecular barcodes

data_processing:
library strategy: SI-NET-seq
Data processing of SI-NET-seq data sets was performed similar as described in Arnold et al., 2021.
Pre-processing: The ten 5’ end nucleotides corresponding to the molecular barcode, are trimmed from the reads, but remain associated with the read using a custom python script.
Mapping: Reads are aligned using the STAR aligner (v2.5.3a) (Dobin et al., 2013) with the following parameters : -clip3pAdapterSeq ATCTCGTATGCCGTCTTCTGCTTG -clip3pAdapterMMp 0.21 -clip3pAfterAdapterNbases 1 -outFilterMultimapNmax 1 -outSJfilterOverhangMin 3 1 1 1- outSJfilterDistToOtherSJmin 0 0 0 0 -alignIntronMin 11 -alignEndsType EndToEnd. The reference genome consisted of a joined reference genome which we assembled from human (GRCh38.p12) and mouse (GRCm38.p6) reference genomes. The alignment was performed with the GENCODE annotation v28.
Filtering: We removed putative contaminations such as reverse transcription mispriming events (barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read), PCR duplicates (reads that align to the same genomic position and contain identical barcode) and splicing intermediates (exact single bp 3’ ends of introns and exons) identified by GENCODE annotation v28.
RNA POL II Occupancy: We extracted the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, using a custom python script. Reads mapping to the mouse genome were seperated from human observations.
Masking: In silico masking of loci from abundant non-nascentRNA species as described in the respective publication.
Assembly: Human (hg38/GRCh38) and the spiked-in mouse (mm10/GRCm38)
Supplementary files format and content: bigWig files: raw Pol II occupancy profiles.

source_name: primary fibroblast

growth_protocol: Patient fibroblast cell lines were cultured in DMEM containing 10% FBS (PAN FBS Supreme), 5% penicillin-streptomycin. Murine NIH 3T3 cells that were used as spike ins were grown in DMEM containing 10% FBS (Bovine Calf Serum, iron-fortified, Sigma), 5% penicillin-streptomycin. Fibroblast cell lines were counted and re-seeded at 3,5 x 106 cells/T175 flask twice a week. NIH 3T3 cells were diluted to 4 x 106 cells/T175 flask every two days.

extract_protocol:
Nascent RNA was extracted as described by Arnold et al., 2021.
Libraries were constructed as described by Arnold et al., 2021 with the following modification: For reverse transcription of nascent RNAs the SuperScript IV Reverse Transcriptase (ThermoFisher) was used.

treatment_protocol: No treatments were performed.

tag: proband

value: IV.1 (F1) = heterozygous knockdown for TAPT1

tag: molecule

value: nascentRNA


title: MPRA_P0-RNA4

value: wildtype

value: postnatal day 0

tag: treatment


title: Ahrr ko2

tag: genotype

value: Ahrr KO


title: SI-NET-seq primary fibroblast IV.3 (F1) R1

description: 11 nt random molecular barcodes


title: SCC25_RE_plasma_rep3

type: RNA

city: Greifswald

first: Julia

last: Berner

address: Felix-Hausdorff-Straße 2

institute: Leibniz Institute for Plasma Science and Technology

description: Gene expression 7 days after the eighth plasma exposure.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851C)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um).

data_processing: The scanned images were analyzed with GeneSpring14.9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  For further analysis, signal intensities were normalized to house keeping gene ACTB (A_23_P135769), samples were filtered by flags (at least all samples have acceptable values) and significantly different expressed genes determined by moderate t-test showing at least a fold change of 5 over the control.

source_name: head and neck cancer cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNA purification (Bio&Sell, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000C Spectrophotometer.

extract_protocol: RNA was isolated from cell pellets using a RNA isolation kit (Bio & Sell, Germany) according to the manufacturer's protocol. RNA concentrations and purity of each sample were determined using a spectrophotometer (NanoDrop 2000C; Thermo Fisher Scientific).

treatment_protocol: Head and neck cancer cells were exposed to gas plasma once or weekly in eight treatment cycles.

tag: gas plasma treatement cycles


title: MPRA_P0-RNA3

data_processing:
Trimmomatic was used to trim the 3' end of the read by quality score, removing bases <28.
Adapters were removed from the 5' read ends, and forward and reverse reads were aligned to mm10 using Bowtie2.
Concordantly aligned reads for each enhancer were counted using Bedtools.
assembly: mm10
P300-MPRA.txt: tab delimited text file containing the raw number of reads for each enhancer at each timepoint.


title: Ahrr ko1


title: Unaffected peripheral

city: NEWCASTLE

first: Megan

middle: Saphana Rose

last: Hasoon

address: Newcastle University

institute: Newcastle University

description:
RPE_peripheral_meta.csv
RPE_peripheral_embeddings.csv
RPE_peripheral_counts.csv

data_processing:
The sequencing data was aligned to human reference genome (GRCh38) using CellRanger Version 3.0.1.
The following filtering thresholds were applied to the data: minimum counts per cell of  2000, minimum genes per cell of 500 and maximum percentage mitochondria of 20%
The DoubletFinder R package was used to find and remove doublets.
Seurat was used to normalise the data and the first 2000 highly variable genes, identified through vst selection were chosen for the clustering analysis.
The gene expression values were then scaled and the number of counts, number of genes and percentage of mitochondria reads per cell were regressed.
A PCA dimension reduction was applied using the selected highly variable genes.
This was followed by Harmony batch correction where batch was set to sample ID. We then constructed a shared nearest-neighbour graph using the first 10 components of the harmony embeddings
The data was clustered using a resolution of 0.6.
Assembly: GRCh38
Supplementary files format and content: csv file of meta data, csv file of umap embeddings and matrix of raw gene counts for each cell

source_name: retinal pigment epithelium

extract_protocol:
Adult and fetal human donor eyes were donated for research following informed consent by family members and in accordance with the Declaration of Helsinki. All adult human tissue was provided by NHS Blood and Transplant Tissue and Eye Services or the Newcastle and Sunderland NHS Trust following ethical approval (18/YH/04/20). The human fetal material was provided by the Joint MRC/Wellcome Trust (MR/R006237/1) Human Developmental Biology Resource  under ethics permission 08/H0906/21+5 issued by the NorthEast-Newcastle and North Tyneside 1 Research Ethics Committee. All donor information is reported in Table S1. Five  eyes from adult donor tissues and four samples from 12-21 PCW terminations were used for scRNA-Seq. All donor eyes were received in the laboratory within 24h post-mortem and the eye globe was further dissected in Hank's Balanced Salt Solution (HBSS) immediately after collecting tissue. Two further eye samples from one intermediate AMD patient and one unaffected subject were obtained through exenteration procedures performed at RVI, Newcastle (Table S1). To acquire foveal and peripheral RPE and choroid from these, a 7 mm macular-centred punch and a 7mm peripheral trephine from the inferotemporal region were used, as shown in Figure S5. The neural retina was separated from the underlying RPE and choroid.
The excised RPE was dissociated to single cells using a multi tissue dissociation kit (Miltenyi Biotec). Dissociation time varied from 15 to 45 minutes depending on the age of the tissue and a gentleMACS Dissociator (Miltenyi Biotec) was used to aid dissociation of the adult tissue. Cell count and viability were monitored using a Tali Image-Based Cytometer and Viability Kit (Thermo Fisher Scientific).
For scRNA-Seq, cells were captured, and libraries generated using the Chromium Single Cell 3′ Library & Gel Bead Kit, version 3 (10x Genomics). scRNA-Seq libraries were sequenced to 50,000 reads per cell on an Illumina NovaSeq 6000.

tag: Stage

tag: condition

value: unaffected

tag: region

value: peripheral


title: SCC25_WT_plasma_rep4

description: Gene expression 7 days after a single plasma exposure.


title: SCC25_RE_plasma_rep2


title: SCC25_RE_plasma_rep4


title: SCC25_RE_plasma_rep1


title: SCC25_WT_plasma_rep1


title: MPRA_P0-RNA2

tag: age


title: Unaffected macula

description:
RPE_fovea_meta.csv
RPE_fovea_embeddings.csv
RPE_fovea_counts.csv

value: fovea


title: SCC25_WT_plasma_rep3


title: MPRA_P0-RNA1

value: P300-MPRA library


title: SCC25_WT_plasma_rep2


title: Ahrr wt1

tag: cell type


title: NR-MRPA_RNA13

description:
MPRA pool RNA
NR-MPRA-counts.txt
Amplicon-seq

value: postnatal day 7

value: NR-MPRA library


title: AMD peripheral

value: AMD


title: Adult - donor 2

description:
RPE_adult_meta.csv
RPE_adult_embeddings.csv
RPE_adult_counts.csv

value: adult


title: AMD macula


title: SCC25_WT_ctrl_rep2

description: Gene expression before plasma exposure in untreated WT cells


title: NR-MRPA_RNA14

value: MPRA RNA


title: NR-MRPA_RNA12


title: A431_RE_plasma_rep4


title: SCC25_WT_ctrl_rep1


title: Adult - donor 5


title: Adult - donor 3


title: A431_RE_plasma_rep3


title: A431_RE_plasma_rep2


title: A431_RE_plasma_rep1


title: A431_WT_plasma_rep4


title: 21 PCW

description:
RPE_PCW_meta.csv
RPE_PCW_embeddings.csv
RPE_PCW_counts.csv


title: NR-MRPA_RNA8


title: A431_WT_plasma_rep3


title: Adult - donor 4


title: NR-MRPA_RNA9


title: Adult - donor 1


title: NR-MRPA_RNA11


title: 20 PCW


title: NR-MRPA_RNA7


title: NR-MRPA_RNA6


title: NR-MRPA_RNA4


title: NR-MRPA_RNA5


title: K562 treated with JOA_2

description: FPKM-K562 cell line.xls

source_name: K562 cell line treated with JOA 2

value: 2 uM JOA


title: NR-MRPA_RNA3

source_name: P7 ventricles


title: A431_WT_plasma_rep1


title: NR-MRPA_RNA2


title: 12PCW


title: A431_WT_ctrl_rep2


title: A431_WT_plasma_rep2


title: NR-MRPA_RNA10


title: K562 treated with JOA_1

description: FPKM-K562 cell line.xls

source_name: K562 cell line treated with JOA 1


title: K562 treated with control_2

description: FPKM-K562 cell line.xls

source_name: K562 cell line treated with control 2

value: Control


title: NR-MRPA_RNA1


title: C118

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from human leukocytes

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering none NA.

source_name: leukocytes, whole blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: A total of 0.5 - 1.5 mL of whole blood were used for white blood cells (WBC) RNA extraction using the QIAamp RNA Blood Mini kit (Qiagen).

treatment_protocol: Whole blood samples were collected during hospitalization (average of 14 days after symptoms) or from volunteers (average of 9 days after symptoms). Whole blood was collected in an EDTA-containing tube as storage in maximum 6 hours for RNA extraction and plasma separation.

tag: gender

value: Male

tag: age (yr)

tag: group

value: Mild

tag: comorbidity

value: No


title: C044

description: Gene expression from human leukocytes


title: A431_WT_ctrl_rep1

tag: cell line


title: K562 treated with control_1

description: FPKM-K562 cell line.xls

source_name: K562 cell line treated with control 1

tag: agent


title: P42_CM_p300_RNA-seq_rep3

data_processing:
For RNA-seq data, reads mapped to mm10 genome using STAR.
Sam converted to BAM using Samtools
For RNA-seq data, reads counts for all genes were done by HTSeq-count.
Genome_build: mm10
Supplementary_files_format_and_content: text files containing raw reads count of all genes in all replicates

source_name: Heart

extract_protocol: For E12.5, E16.5, P0, and P7 CMs, ventricular apexes were dissociated using the Neonatal mouse cardiomyocyte isolation kit (Cellutron Life Technologies) and purified using the mouse neonatal cardiomyocyte isolation kit (Miltenyi). P14, P28, and P42 CMs were dissociated and purified from ventricular apexes by Langendorf collagenase perfusion followed by differential sedimentation. Purified cardiomyocytes were used with three biological replicates per group for RNA-seq. RNA was purified using the Purelink RNA mini kit (Life Technologies). Ribosomal RNA was depleted using Ribo-Zero rRNA removal kits (Epicentre). RNA-seq libraries were prepared using ScriptSeq v2 library kit (Epicentre). Libraries were sequenced using an Illumina NextSeq500 with single end 75   bp reads. At least 50 M reads were obtained for each biological replicate.

tag: strain

tag: tissue

value: ventricle cardiomyocytes

tag: developmental stage


title: C148

description: Gene expression from human leukocytes

value: Female


title: 16PCW


title: CLL10 RNA

source_name: Splenic CD8+ T cells

value: Splenic CD8+ T cells

value: CLL

tag: library prep

value: NEBNext Low input RNA library prep


title: P42_CM_p300_RNA-seq_rep1


title: P42_CM_p300_RNA-seq_rep2


title: CLL8 RNA


title: CLL7 RNA


title: SI-NET-seq primary fibroblast V.1 (F1) R2

description: 10 nt random molecular barcodes

data_processing:
Library strategy: SI-NET-seq
Data processing of SI-NET-seq data sets was performed similar as described in Arnold et al., 2021.
Pre-processing: The ten 5’ end nucleotides corresponding to the molecular barcode, are trimmed from the reads, but remain associated with the read using a custom python script.
Mapping: Reads are aligned using the STAR aligner (v2.5.3a) (Dobin et al., 2013) with the following parameters : -clip3pAdapterSeq ATCTCGTATGCCGTCTTCTGCTTG -clip3pAdapterMMp 0.21 -clip3pAfterAdapterNbases 1 -outFilterMultimapNmax 1 -outSJfilterOverhangMin 3 1 1 1- outSJfilterDistToOtherSJmin 0 0 0 0 -alignIntronMin 11 -alignEndsType EndToEnd. The reference genome consisted of a joined reference genome which we assembled from human (GRCh38.p12) and mouse (GRCm38.p6) reference genomes. The alignment was performed with the GENCODE annotation v28.
Filtering: We removed putative contaminations such as reverse transcription mispriming events (barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read), PCR duplicates (reads that align to the same genomic position and contain identical barcode) and splicing intermediates (exact single bp 3’ ends of introns and exons) identified by GENCODE annotation v28.
RNA POL II Occupancy: We extracted the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, using a custom python script. Reads mapping to the mouse genome were seperated from human observations.
Masking: In silico masking of loci from abundant non-nascentRNA species as described in the respective publication.
Genome_build: Human (hg38/GRCh38) and the spiked-in mouse (mm10/GRCm38)
Supplementary_files_format_and_content: bigWig files: raw Pol II occupancy profiles.

tag: proband

value: V.1 (F1) = homozygous knockout for TAPT1

tag: molecule

value: nascentRNA


title: SI-NET-seq primary fibroblast V.5 (F1) R1

description: 10 nt random molecular barcodes

value: V.5 (F1) = homozygous knockout for TAPT1


title: SI-NET-seq primary fibroblast WT2 R2

description: 10 nt random molecular barcodes


title: CLL9 RNA


title: WT5 RNA

value: wild-type


title: C072

description: Gene expression from human leukocytes

value: Systemic Arterial Hypertension


title: P14_CM_p300_RNA-seq_rep3


title: SI-NET-seq primary fibroblast WT2 R1

description: 10 nt random molecular barcodes


title: C048

description: Gene expression from human leukocytes


title: C149

description: Gene expression from human leukocytes


title: SI-NET-seq primary fibroblast V.1 (F1) R1

description: 10 nt random molecular barcodes


title: WT4 RNA


title: C071

description: Gene expression from human leukocytes


title: RNA-seq primary fibroblast WT2

data_processing:
Mapping: Reads are aligned using the STAR aligner (v2.5.3a) (Dobin et al., 2013) with the default parameters to the human GRCh38.p12 reference genome. The alignment was performed with the GENCODE annotation v28.
Quantification: Transcript abundance of the annotated genes from GENCODE v2852 using HTSeq v0.11.453 in 'union' mode.
Genome_build: Human (hg38/GRCh38)
Supplementary_files_format_and_content: bigWig files: transcript coverage of uniquely mapped reads.

source_name: primary cutaneous fibroblasts

growth_protocol: Primary patient-derived Fibroblast cells were cultured at 5% CO2 and 37°C in high glucose DMEM (HyClone) supplemented with 10% fetal bovine serum (FBS) (HyClone), 1X penicillin/streptomycin (Thermo Fisher Scientific) and 2 mM L-glutamine (Biological Industries)

extract_protocol:
RNA from primary dermal fibroblasts was extracted using the RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing according to standard manufacturer's protocols

treatment_protocol: No treatment


title: P14_CM_p300_RNA-seq_rep2


title: WT2 RNA

extract_protocol:
Total RNA was extracted with the Qiagen Micro kit and for ATAC seq, the omni-atac protocol was used with the Illumina transposase kit
NEBNext low input kit for RNAseq and NEBNext high fidelity master mix using barcoded primer for the ATAC libraries


title: P14_CM_p300_RNA-seq_rep1


title: SI-NET-seq primary fibroblast V.5 (F1) R2

description: 10 nt random molecular barcodes


title: WT1 RNA


title: RNA-seq primary fibroblast WT1


title: C152

description: Gene expression from human leukocytes


title: KO [scRNA-seq]

city: Shanghai

first: Juan

state: Shanghai

address: 800 Xiangyin Road

institute: Institute of Immunology, Second Military Medical University

description: scRNA-seq analysis of the lymph node cells from wild-type and Extl1-deficient mice post inflammatory challenge with DNFB for 2 days

data_processing:
Sequencing depth was normalized by using CellRanger (version v3.1.0).
We used Seurat package (version 3.0)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Cells defined as macrophage, monocyte, dendritic cells, natural killer cells, T cells and B cells.
Genome_build: mm10;hsa
Supplementary_files_format_and_content: cell barcode, gene, gene-barcode counts files

source_name: lymph node cells

extract_protocol:
Draining lymph node cells were collected and single cells were harvested.
Single-cell RNA sequence library were prepared by using version 1 Chromium Single-Cell 3’ Library, Gel Bead & Mutiplex Kit (10x Genomics)

treatment_protocol: Wild-type and Extl1-deficient micemice challenged with DNFB for 2 days.

value: lymph node cells

tag: strain background

tag: genotype

tag: treatment

value: 2 days after DNFB challenge


title: C129

description: Gene expression from human leukocytes

value: Severe

value: Obesity; Diabetes mellitus


title: P7_CM_p300_RNA-seq_rep3


title: RNA-seq primary fibroblasts V.1 (F1)


title: C108

description: Gene expression from human leukocytes


title: P7_CM_p300_RNA-seq_rep1


title: RNA-seq primary fibroblasts IV.3 (F1)

value: IV.3 (F1) = Heterozygous for TAPT1 knockout allele


title: P7_CM_p300_RNA-seq_rep2


title: C122

description: Gene expression from human leukocytes

value: Male

value: Mild

value: Cardiopathy


title: CO3.1_3

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
Week-4 mature astrocytes
CO3@1@diff@4@S60@CAACAATG@CCGTGAAG

data_processing:
Sequencing: Sequence-libraries of each sample were equimolarly pooled and sequenced on Illumina NovaSeq 6000 (S1 flowcell 100 cycles kit v1.5, 100 bp Single Read (100-8-8-0)) at the VIB Nucleomics Core (www.nucleomics.be).
Preprocessing: Low-quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.40.0 (Morgan et al., 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead et al., 2012).
Mapping: The preprocessed reads were aligned with STAR aligner v2.5.2b to the reference genome of Homo sapiens (GRCh38) (Dobin et al., 2013). Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al., 2009).
Counting: The number of reads in the alignments that overlap with gene features was counted with featureCounts 1.5.3 (Liao et al., 2014). Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id. We removed genes for which all samples had less than 1 count-per-million. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor (Risso et al., 2011).
Differential gene expression: With the EdgeR 3.24.3 package of Bioconductor, a negative binomial generalized linear model (GLM) was fitted against the normalized counts (Robinson et al., 2007). We did not use the normalized counts directly but worked with offsets. Differential expression was tested for with a GLM likelihood ratio test, also implemented in the EdgeR package. The resulting p-values were corrected for multiple testing with Benjamini-Hochberg to control the false discovery rate (Benjamini et al., 1995).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Astrocytes

extract_protocol:
Total RNA was isolated using RNeasy® Mini Kit (Qiagen, Hilden, Germany, Cat N° 74104) according to the manufacturer’s instructions. RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-8000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent).
Per sample, an amount of 1µg of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: # 1000000040498 v00 October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first-strand cDNA and subsequently converted into double-stranded cDNA in a second-strand cDNA synthesis reaction using DNA Polymerase I and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library.

value: hiPSC-derived astrocytes

value: FUS P525P (isogenic control)

tag: replicate

value: Replicate 3


title: Mouse-Hippocampus-WT-RIP-YTHDF2-rep1

city: Shenzhen

first: Mengru

last: Zhuang

state: Guangdong

address: 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the  reference genome using BWA mem (v 0.7.12)
The MACS2 (version 2.1.0) peak calling  software was used to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Homer (Heinz et al., 2010) was used to detect the denovo sequence motif and the matched known motifs.
Peak related genes can be confirmed by PeakAnnotator
Genome_build: GRCm38

source_name: Hippocampus

extract_protocol:
Hippocampus tissus was lysated with lysis buffer in  EZ-Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore), then processed following the manuscript. RNA was harvested using Trizol reagent.
The library was constructed by Novogene Corporation (Beijing, China) following their manual.

value: Hippocampus

tag: age

value: post natal day 40


title: P0_CM_p300_RNA-seq_rep2

address: 320 Longwood Ave

institute: Boston Children's Hospital

value: ventricle cardiomyocytes


title: CO3.1_2

description:
Week-4 mature astrocytes
CO3@1@diff@2@S59@GGTGAACC@TCCAACGC

tag: cell type

value: Replicate 2


title: Mouse-Hippocampus-WT-RIP-Input-rep2


title: CO3.1_1

description:
Week-4 mature astrocytes
CO3@1@diff@1@S58@AACAGGTT@CTTGGTAT

value: Replicate 1


title: Mouse-Hippocampus-WT-RIP-YTHDF2-rep2


title: P0_CM_p300_RNA-seq_rep1


title: Mouse-Hippocampus-WT-RIP-Input-rep1


title: RNA-seq primary fibroblast V.5 (F1)

value: V.5 (F1) = homozygous knockout for TAPT1


title: CO2.2_3

description:
Week-4 mature astrocytes
CO2@2@diff4@S54@GAATGAGA@AATGCCTC

value: FUS R521R (isogenic control)


title: C077

description: Gene expression from human leukocytes

tag: gender

tag: age (yr)

value: Obesity; Systemic Arterial Hypertension; Diabetes mellitus


title: C092

description: Gene expression from human leukocytes

tag: group

value: Severe

tag: comorbidity

value: Systemic Arterial Hypertension; Diabetes mellitus


title: E16.5_CM_p300_RNA-seq_rep3


title: C080

description: Gene expression from human leukocytes

value: Female

value: Obesity


title: C003

description: Gene expression from human leukocytes

value: Male

value: Systemic Arterial Hypertension; Cardiopathy


title: Ctrl-rep3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38

source_name: Hippocampus dentate gyrus

extract_protocol:
Total RNA was extracted from DG deficient in YTHDF2 and the negative control DG by Trizol.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Hippocampus dentate gyrus granule cell

value: Hippocampus dentate gyrus


title: WT [scRNA-seq]

value: lymph node cells

value: wild-type

value: 2 days after DNFB challenge


title: C110

description: Gene expression from human leukocytes


title: CO2.2_2

description:
Week-4 mature astrocytes
CO2@2@diff2@S53@AGGCAGAG@GGCATTCT

value: hiPSC-derived astrocytes


title: CO2.2_1

description:
Week-4 mature astrocytes
CO2@2@diff1@S52@TGGTGGCA@TTACAGGA


title: Ctrl-rep2

value: post natal day 40


title: Ctrl-rep1


title: E16.5_CM_p300_RNA-seq_rep2

value: ventricle cardiomyocytes


title: P0_CM_p300_RNA-seq_rep3


title: E16.5_CM_p300_RNA-seq_rep1


title: Group3.1_3

description:
Week-4 mature astrocytes
3@1@diff@3@S63@ATGGCATG@GGTACCTT

value: FUS P525L

value: Replicate 3


title: E12.5_CM_p300_RNA-seq_rep2


title: Group3.1_1

description:
Week-4 mature astrocytes
3@1@diff@1@S61@AAGATACT@ATGTAAGT

value: Replicate 1


title: E12.5_CM_p300_RNA-seq_rep1


title: E12.5_CM_p300_RNA-seq_rep3


title: cKO-rep1


title: Group2.2_3

description:
Week-4 mature astrocytes
2@2@diff@6@S57@ACCTTGGC@ATGAGGCC

value: FUS R521H


title: Group3.1_2

description:
Week-4 mature astrocytes
3@1@diff@2@S62@GGAGCGTC@GCACGGAC

value: Replicate 2


title: P42_CM_p300_bioChIP-seq_rep2

data_processing:
For ChIP-seq data, reads mapped to mm10 reference genome using Bowtie.
Sam converted to BAM using Samtools
For ChIP-seq data, Peak calling was done by MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file of chip-seq signal

extract_protocol:
E12.5 to P42 heart ventricles were harvested, homogenized, and crosslinked in 1% formaldehyde in PBS for 10 minutes at room temperature and subsequently quenched with 125 mM glycine for 5 min.
Chromatin was fragmented using a microtip sonicator (Qsonica, S-3000) at 30% amplitude for 8 minutes. Biotinylated P300 and bound chromatin was pulled down by incubation with streptavidin beads (ThermoFisher Scientific, 11206D). Bead-bound chromatin was resuspended in SDS elution buffer (50 mM Tris–HCl pH 8,10 mM EDTA, 1% SDS) and incubated overnight at 65 °C to reverse crosslinking. After RNAse A and Proteinase K treatment, ChIP DNA was purified using Qiagen MinElute columns.
Libraries were constructed using the KAPA HyperPrep ChIP-seq library preparation kit (Roche, cat# 07962347001).


title: C103

description: Gene expression from human leukocytes

value: Female

value: Severe


title: Mouse_JF1xC57BL/6_EPC_rep1 [JxC_EPC1]

city: Kashihara

first: Hisato

last: Kobayashi

address: 840 Shijo-Cho

institute: Nara Medical University

description:
WGBS (Illumina's TruSeq DNA Methylation Kit)
mouse_ectoplacentalcone_maternal_rep1-3_x1.bw
mouse_ectoplacentalcone_maternal_rep1-3_x5.bw
mouse_ectoplacentalcone_paternal_rep1-3_x1.bw
mouse_ectoplacentalcone_paternal_rep1-3_x5.bw

data_processing:
>Sequencing reads were trimmed using Trimmomatic (v0.32) and the following parameters: SLIDINGWINDOW:3:10 MINLEN:36 ILLUMINACLIP:TruSeq2-3-PE.fa:2:30:10.
>Read pairs that survived trimming were aligned to diploid rat or mouse pseudogenomes using MEA and Bismark.
>Duplicate reads were removed and the number of methylated and unmethylated reads overlapping each CpG of the rat or mouse genome was reported. This resulted in total (allele-agnostic), maternal- and paternal-specific CpG report files.
>Replicates and reciprocal crosses were merged for visualization and analyses.
>CpGs covered by at least 5 (total) or 1 (maternal or paternal) sequencing reads were assessed for methylation levels and genome-wide tracks were sunsequently generated for visualization.
Genome_build: rn6
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for each sample

source_name: EPC

extract_protocol:
Genomic DNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s protocols.
One hundred nanograms of genomic DNA from JF1 (female) and C57BL/6 (male) mouse hybrids were prepared for Methyl-seq (Illumina) library construction. Twenty nanograms of genomic DNA from the other mouse and rat hybrid crosses were prepared for rPBAT or tPBAT library construction.

treatment_protocol: E8.5 F1 hybrid rat embryos were isolated from reciprocally crossing BN/CrlCrlj (BN rat) and WKY/NCrlCrlj (WKY rat) strains. E7.25 F1 hybrid mouse embryos were isolated from reciprocally crossing C57BL/6N and JF1/Ms strains. For both rat and mouse embryos, the ectoplacental cone (EPC) was dissected from the rest of the embryo before removing the visceral endoderm. Finally, the epiblast (EB) was dissected from the extraembryonic ectoderm (ExE). Each ExE lysate was used for rapid genetic sex determination by direct PCR amplification of the Y chromosome gene using specific primers for mouse Zfy and rat Sry. Only female EBs and EPCs were subjected to whole genome bisulphite sequencing.

value: F1 hybrid resulting from female JF1/Ms and male C57BL/6N mice

value: embryonic days 7.25

value: wild type

value: EPC

tag: Sex

value: female


title: Group2.2_2

description:
Week-4 mature astrocytes
2@2@diff@5@S56@GTTCCAAT@GCAGAATT


title: P28_CM_p300_bioChIP-seq_rep2

city: Boston

first: Pingzhu

last: Zhou

tag: strain


title: KO2--LPS2

description: Bone marrow cells from Extl1-dificient  mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with  LPS for 12 h and then subjected to RNA seq.

data_processing:
cDNA library construction and sequencing were performed by Shanghai Biotechnology Corporation using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome GRCm38.p4 (mm10).
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: GRCm38.p4 (mm10)
Supplementary_files_format_and_content: FPKM, counts

source_name: mouse BMDC_KO_LPS

extract_protocol:
BMDC were stimulated with or without  LPS for 12 h and  collected for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by Shanghai Biotechnology Corporation using Illumina HiSeq platform.

treatment_protocol: Bone marrow cells from Extl1-dificient  and wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with or without  LPS for 12 h and then subjected to RNA seq.

value: bone-marrow derived DC (BMDC)

value: LPS for 12 h


title: Group2.2_1

description:
Week-4 mature astrocytes
2@2@diff@4@S55@GCAATGCA@AACGTTCC

value: hiPSC-derived astrocytes