title: RA14 SFMC --

city: Dublin 2

first: Megan

middle: Mary

last: Hanlon

state: Dublin

address: Trinity biomedical sciences institute, trinity college dublin

department: School of Medicine

country: Ireland

institute: Molecular Rheumatology research group

data_processing:
Raw read quality was evaluated using FastQC before reads were trimmed for adaptors and sequence quality. Trimmed reads were aligned to human CRCh38.84 reference genome using STAR RNA-seq aligner.
Aligned reads were quantified for each gene. Aligned data were evaluated for quality using several quality metrics (e.g. mapping rate, coverage) and visually inspected for samples deviating from the population across multiple metrics and principal component analysis.
Assembly: Trimmed reads were aligned to human CRCh38.84 reference genome using STAR RNA-seq aligner
Supplementary files format and content: tab-delimited text files of TPM for each Sample

source_name: Primary human cells

growth_protocol: Synovial tissue biopsies obtained at the time of arthroscopy were mechanically and enzymatically digested using the GentleMacs dissociator and a soft tumour dissociation kit (Miltenyi Biotech, Germany), according to manufacturer’s instructions to yield a single cell suspension of synovial tissue cells. This single synovial cell suspension was then filtrated through a 70 μm cell strainer.

extract_protocol:
High quality RNA was isolated from RA CD206+CD163+ and CD206-CD163- synovial tissue and fluid using the RNAqueous total RNA isolation kit (BD Biosciences and the purity of RNA samples was assessed using a NanoDrop 2000 spectrophotometer (ThermoFisher).
RNA samples were reverse transcribed and sequence libraries were generated by Janssen Pharmaceutical, Spring House, PA, USA, using the NuGen Ovation Universal RNA-seq System. The resulting sequencing libraries were analysed using the Cali-per LabChip GX and quantified using KAPA qPCR.

treatment_protocol:
Synovial fluid was obtained from patients undergoing arthroscopy. SFMC were isolated by Ficoll-Metrizoate density gradient centrifugation. Fluid was diluted in a 1:1 ratio with PBS before layering over 15 mL of Lymphoprep (STEMCELL Technologies) and centrifuged at 1400 RPM for 25 min with the brake inactivated. The cloudy SFMC layer was removed at the density gradient interface.
CD206+CD163+ and CD206-CD163- macrophages were sorted from RA synovial tissue and fluid using the FACSAria fusion sorter.

value: Primary human cells

value: FACS sorted CD206-CD163- synovial fluid macrophages

tag: disease

value: Rheumatoid Arthritis


title: CUT&RUN E6.5 visceral endoderm, female, SMC3, rep2

status: Public on Sep 10 2024

type: SRA

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

country: China

institute: Tsinghua University

description: smc3 E6.5 VE female rep2

library_source: genomic

data_processing:
library strategy: CUT&RUN
Illumina Casava1.8 software was used for basecalling.
Sequencing reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then aligned to mm9 reference genome with random chromosome cleaned by Bowtie2 (version 2.3.4.1) under the parameters -t -q -N 1 -L 25 -X 700 --no-unal --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
Sequencing reads were assigned to two alleles with SNPsplit (v0.3.2) (Krueger and Andrews, 2016)
We normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome.
bigWig files were visualized withUCSC genome browser
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: visceral endoderm

extract_protocol:
Embryos were first resuspended in washing buffer (20mM HEPES-KOH pH 7.5, 150mM NaCl, 0.5mM spermidine and protease inhibitor) and then bound to the Concanavalin-coated magnetic beads (Polyscience, #86057) in binding buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM CaCl2 and 1mM MnCl2). The samples were incubated in antibody buffer (washing buffer plus 0.005%~0.01% digitonin and 2mM EDTA) with antibody diluted at ratio of 1:100 at 4°C on Thermomixer for 3 hrs at 300 rpm. Beads were then washed and incubated with protein A-MNase (pA-MNase) (to a final concentration of 400 to 700 ng/ml) at 4°C for 1-3 hrs on a thermomixer at 300 rpm. Targeted chromatin was digested for 30 min on ice after adding 2 ml of 100 mM CaCl2. The reaction was then terminated with 2× stop buffer (340mM NaCl, 20mM EDTA\, 4mM EGTA, 50μg/mL RNase A, 100μg/mL glycogen and 0.005%~0.01% digitonin). Samples were then incubated at 37°C for 20 min to release the targeted fragment.
CUT&RUN libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645S)  following manufacturer's protocols. The libraries were purified and size-elected with AMPure XP beads (Beckman Coulter, #A63881).

tag: cell type

value: visceral endoderm

tag: strain

value: C57BL/6N X PWK/PhJ

tag: chip antibody

value: SMC3 (Abcam, #ab9263)


title: RA12 SFMC ++

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: FACS sorted CD206+CD163+ synovial fluid macrophages

tag: treatment

tag: time


title: RA14 SFMC ++


title: CUT&RUN E6.5 visceral endoderm, female, SMC3, rep1

description: smc3 E6.5 VE female rep1


title: PB1_177_385 minimal replication no NS2 library #3

city: San Diego

first: Alistair

middle: Brian

last: Russell

state: CA

address: 9500 Gilman Dr,

department: Biological Sciences

country: USA

institute: University of California, San Diego

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays without NS2
noNEP_3.tsv

library_source: other

data_processing:
Data were processed with a custom pipeline available at https://github.com/Russell-laboratory/NS2_sequence_specificity
Assembly: A/WSN/1933
Supplementary files format and content: Either barcodes from length variant libraries, and their relative amounts (see GSE183442 for assignment of barcodes to variant identity), or nucleotide at sites as they would map to full-length PB1.
Supplementary files format and content: All processed files are in a tab-seperated value format.
Library strategy: amplicon sequencing

molecule: other

organism: Influenza A virus (A/WSN/1933(H1N1))

growth_protocol: Samples were from transfections of HEK293T cells grown in D10 media and transfected with indicated libraries and minimal IAV replication components with, or without, NS2. Plasmid libraries rescued from E. coli.

extract_protocol:
RNA was extracted using Monarch Total RNA Miniprep Kit from New England Biolabs (NEB #T2010)
Custom amplicon sequencing, or custom 5' RACE using Template Switching RT Enzyme Mix (New England Biolabs, #M0466)

treatment_protocol: Transfection using BioT.

value: minimal replication assay without NS2


title: RA10 SFMC --


title: RA10 SFMC ++


title: RA3 SFMC --

value: FACS sorted CD206-CD163- synovial tissue macrophages


title: CUT&RUN E6.5 epiblast, female, SMC3, rep2

description: smc3 E6.5 Epi female rep2

source_name: epiblast

value: epiblast


title: PB1_177_385 minimal replication no NS2 library #2

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays without NS2
noNEP_2.tsv


title: RA3 SFMC ++

value: FACS sorted CD206+CD163+ synovial tissue macrophages


title: RA10 BXN --


title: PB1_177_385 minimal replication no NS2 library #1

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays without NS2
noNEP_1.tsv


title: CUT&RUN E13.5 fibroblast, female, CTCF, rep1

description: ctcf E13.5 fibroblast female rep1

source_name: fibroblast

value: fibroblast

value: CTCF (Active motif, #61311)


title: RA10 BXN ++


title: RA9 BXN --


title: RA9 BXN ++


title: RACE PB1_177_385 mutation library #3

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library, sequence of ends for comparison with RNA 5' RACE data.
plas_3.tsv

source_name: plasmid

value: plasmid


title: RA8 BXN --


title: CUT&RUN E9.5 fibroblast, female, CTCF, rep1

description: ctcf E9.5 fibroblast female rep1


title: RA8 BXN ++


title: RA7 BXN--


title: RACE PB1_177_385 mutation library #2

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library, sequence of ends for comparison with RNA 5' RACE data.
plas_2.tsv


title: RA12 SFMC --


title: CUT&RUN E6.5 extraembryonic ectoderm, female, CTCF, rep1

description: ctcf E6.5 ExE female rep1

source_name: extraembryonic ectoderm

value: extraembryonic ectoderm


title: RACE PB1_177_385 mutation library #1

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library, sequence of ends for comparison with RNA 5' RACE data.
plas_1.tsv


title: PB1_177_385 mutation library #3

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library
plas_3.tsv


title: RA7 BXN ++


title: RA6 BXN ++


title: CUT&RUN E6.5 epiblast, female, CTCF, rep2

description: ctcf E6.5 Epi female rep2


title: CUT&RUN E6.5 epiblast, female, SMC3, rep1

description: smc3 E6.5 Epi female rep1


title: RA5 BXN --


title: RA6 BXN --


title: PB1_177_385 mutation library #1

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library
plas_1.tsv


title: CUT&RUN E6.5 visceral endoderm, female, CTCF, rep1

description: ctcf E6.5 VE female rep1


title: RA5 BXN ++


title: RA4 BXN --


title: PB1_177_385 mutation library #2

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library
plas_2.tsv


title: RA2 BXN --


title: RA4 BXN ++


title: CUT&RUN E6.5 epiblast, female, CTCF, rep1

description: ctcf E6.5 Epi female rep1


title: PB1 Barcode mininimal replication with NS2 library #3

description: Length-variant barcoded library as described in Mendes and Russell, 2021, subjected to IAV minimal replication assays with NS2

value: minimal replication assay with NS2


title: ChIP-seq E6.5 visceral endoderm, female, H3K27ac, rep1

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequencing reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then aligned to mm9 reference genome with random chromosome cleaned by Bowtie2 (version 2.3.4.1) under the parameters -t -q -N 1 -L 25 -X 700 --no-unal --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
Sequencing reads were assigned to two alleles with SNPsplit (v0.3.2) (Krueger and Andrews, 2016)
We normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome.
bigWig files were visualized withUCSC genome browser
Assembly: mm9
Supplementary files format and content: bigWig

extract_protocol:
STAR ChIP-seq was performed as previously described (Zhang et al., 2021; Zhang et al., 2016). Briefly, extraembryonic tissues were first lysed and then subjected to MNase digestion by incubating with MNase working buffer (50 mM Tris-HCl pH 8.0, 1 mM CaCl2 and 0.2% Triton X-100) containing diluted MNase (Sigma, #N3755-200UN) at 37 °C for exact 5 min. The reaction was terminated by stop buffer (110 mM Tris-HCl pH 8.0 and 55 mM EDTA). After adding cold 2× RIPA buffer (1.8% Triton X-100, 280 mM NaCl, 0.2% SDS, 0.2% sodium deoxycholate (DOC), 5 mM EGTA and proteinase inhibitor) and spinning at max speed in 4 °C for 10 min, the soluble chromatin containing supernatant was incubated with 1mg H3K27ac antibody (ActiveMotif, #39133) in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC, 1 mM EDTA and proteinase inhibitor) at 4°C overnight with rotation. Protein A/G dynabeads (Thermo Fisher Scientific) were used to bind the antibody at 4°C for 2 to 3 hours with rotation. The beads were then washed five times with RIPA buffer and once with LiCl buffer (10 mM Tris-HCl pH 8.0, 250mM LiCl, 1 mM EDTA, 0.5% NP-40 and 0.5% DOC). Beads bound chromatin were then digested with proteinase K (NEB, #P8107S) at 55°C for 90 min, followed by incubation at 72°C for 40 min to inactivate the proteinase K.
STAR ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645S)  following manufacturer's protocols. The libraries were purified and size-elected with AMPure XP beads (Beckman Coulter, #A63881).

value: H3K27ac (ActiveMotif, #39133)


title: ChIP-seq E6.5 extraembryonic ectoderm, female, H3K27ac, rep1


title: RA2 BXN ++

value: Primary human cells


title: RNA-seq E9.5 yolk sac, female, rep1

description: rna E9.5 yolk sac female rep1

data_processing:
Illumina Casava1.8 software was used for basecalling.
All reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then mapped to mm9 genome by HISAT2 (v.2.2.0) (Kim et al., 2019) under the parameters –dta --no-softclip.
The gene expression level was calculated by StringTie (v.2.1.1) (Pertea et al., 2015) using the refFlat database from the UCSC genome browser.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each stage of embryos with replicates merged.

source_name: Yolk sac

extract_protocol:
Embryos were lysed in lysis buffer (0.2% (vol/vol) Triton X-100 and 2 U/μl RNase inhibitor). The polyadenylated mRNAs were captured by the oligodT primers,
RNA-seq (Smart-seq2): mRNAs were subjected to the Smart-seq2 protocol as described previously (Picelli et al., 2014).

value: Yolk sac

tag: genotype

value: wild type


title: RA1 BXN --

value: Rheumatoid Arthritis


title: NCI-H1770 H3K27ac

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
ChIP-seq reads were aligned to the reference genome (hg38) using BWA 0.7.17. Reads with mapping quality < 10 were not counted, and reads aligned to the same position and strand were only counted once. H3K27ac peaks were called using HOMER12, with style ‘histone’ for variable length. Density signals were calculated by deeptools’s bamCoverage.
RNA-seq reads were mapped to the hg38 reference genome using STAR 2.7.10a (Ref. 17) and Ensembl release 99 annotations. Reads were counted with featureCounts, discarding reads with mapping quality < 10. Density signals were calculated by deeptools’s bamCoverage11 with BPM normalization.
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: NCI-H727, NCI-H1770 and NCI-H835 cell lines were acquired from ATCC. The cell lines were cultured in complete RPMI 1640 media (Gibco, Thermo Fisher Scientific, Massachusetts, USA) supplemented with 10% or 5% fetal bovine serum (FBS; HyClone, Utah, UK), 1% penicillin streptomycin (Diagnovum, Tilburg, Netherlands), 1% L-glutamine (Sartorius, Göttingen, Germany), 1% sodium pyruvate (Sartorius), and 1% non-essential amino acids (Diagnovum). LNET xenografts were established 5 days following the subcutaneous injection of 4*106 NCI-H727 cells to the back of athymic nude mouse (FOXN1NU NU/NU mouse).

extract_protocol:
2 mm tissue sample was homogenized in tri-reagent and RNA was extracted flowing the standard tri-reagent protocol. After precipitation RNA was resuspended in appropriate volume of Rnase free water supplemented with RNA inhibitors (New England Biolabs).
RNA-seq libraries were generated using the KAPA mRNA Hyperprep Kit according to the manufacturer's instructions. ChIP DNA was used to generate sequencing libraries using KAPA Hyper Prep Kit.

treatment_protocol: A51 treated cells were treated with 150nM BTX-A51.

value: Neuroendocrine


title: PB1 Barcode mininimal replication with NS2 library #1


title: T9 H3K27ac

source_name: Lung neuroendocrine tumor

tag: tissue

value: Lung neuroendocrine tumor


title: RNA-5-WAT17

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

data_processing:
Hisat2 for sequence alignment
Stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
Samtools tools for related file processing
Assembly: hg18
Supplementary files format and content: Tab-delimited txt file includes FPKM expression values for each sample

source_name: WAT

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using the RNeasy Mini Kit (Qiagen, Carlsbad, USA) according to the manufacturer’s instructions
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: WAT

value: White adipocyte


title: PB1 Barcode mininimal replication no NS2 library #3

description: Length-variant barcoded library as described in Mendes and Russell, 2021, subjected to IAV minimal replication assays without NS2

value: minimal replication assay without NS2


title: RNA-seq E6.5 extraembryonic ectoderm, female, rep2

description: rna E6.5 ExE female rep2

source_name: Extraembryonic ectoderm

value: Extraembryonic ectoderm

value: C57BL/6N X PWK/PhJ


title: RNA-5-WAT9


title: RNA-seq E6.5 extraembryonic ectoderm, female, rep1

description: rna E6.5 ExE female rep1


title: RNA-5-BAT16

source_name: BAT

value: BAT

value: Brown adipocyte


title: PB1 Barcode mininimal replication no NS2 library #2


title: RNA-seq E6.5 visceral endoderm, female, rep3

description: rna E6.5 VE female rep3

source_name: Visceral endoderm

value: Visceral endoderm


title: RNA-5-BAT9


title: RNA-seq E6.5 visceral endoderm, female, rep2

description: rna E6.5 VE female rep2


title: PB1 Barcode mininimal replication no NS2 library #1


title: islets, wildtype, rep5

city: Vancouver

first: Francis

middle: C

last: Lynn

state: BC

address: 950 28th Ave W

department: Surgery

country: Canada

institute: University of British Columbia

description:
36WT.counts
20160511_DESeq2_normalized_Med15.csv

data_processing:
ENSEMBL Mus musculus genome GRCm38p.4 fastq and gtf annotation file were used for alignments.
STAR v2.4.0.1was used to index the genome fastq files, align sample transcriptomes against the genome, and output as sorted by coordinate BAM files.
Counts were generated from BAM files with HTSeq against annotated genes from GRCm38p.4.
Differential gene analysis was performed between control and experimental samples using DESeq2, with an FPKM criteria of ≥5 in two or more samples, applying a Wald test on P values from genes passing filtering, and adjusted for multiple testing via Benjamini and Hochberg procedure.
Assembly: ENSEMBL Mus musculus genome GRCm38p.4
Supplementary files format and content: CSV text file includes log2FoldChange and normalized counts of all samples. Normalized counts were generated using DESeq2 (median of ratios).

source_name: Pancreatic islets

growth_protocol: Animals were housed under a 12-h light/dark cycle, fed ad libitum with standard chow diet (5010; Lab Diets)

extract_protocol:
TRIzol was used to isolate total RNA.
SMARTer Stranded RNA-seq Kit (Takara Bio USA 634839) was used for library construction.

treatment_protocol: Collagenase type XI in Hank's buffered saline solution (HBSS) at 900 units/mL was used to isolate mouse islets.

value: Pancreatic islets

tag: Sex

value: Male

value: Ins1Cre; Med15floxed

value: WT


title: islets, knockout, rep5

description:
34BWT.counts
20160511_DESeq2_normalized_Med15.csv

value: Med15 KO


title: RNA-5-WAT6


title: islets, wildtype, rep4

description:
34KO.counts
20160511_DESeq2_normalized_Med15.csv


title: RNA-seq E6.5 visceral endoderm, female, rep1

description: rna E6.5 VE female rep1

value: wild type


title: HA Barcode mininimal replication with NS2 library #2

value: minimal replication assay with NS2


title: islets, knockout, rep4

description:
31BKO.counts
20160511_DESeq2_normalized_Med15.csv


title: PB1 Barcode mininimal replication with NS2 library #2


title: islets, knockout, rep3

description:
19KO.counts
20160511_DESeq2_normalized_Med15.csv


title: RA1 BXN ++

value: Primary human cells

value: FACS sorted CD206+CD163+ synovial tissue macrophages

value: Rheumatoid Arthritis


title: RNA-seq Trophectoderm of E3.5 blastocyst, female, rep3

description: rna E3.5 TE female rep3

source_name: Trophectoderm

value: Trophectoderm


title: HA Barcode mininimal replication no NS2 library #3

value: minimal replication assay without NS2


title: islets, wildtype, rep3

description:
30BWT.counts
20160511_DESeq2_normalized_Med15.csv


title: HA Barcode mininimal replication with NS2 library #1


title: islets, wildtype, rep2

description:
13WT.counts
20160511_DESeq2_normalized_Med15.csv


title: islets, knockout, rep1

description:
12KO.counts
20160511_DESeq2_normalized_Med15.csv


title: HA Barcode mininimal replication with NS2 library #3


title: RNA-seq Trophectoderm of E3.5 blastocyst, female, rep2

description: rna E3.5 TE female rep2


title: RNA-seq E6.5 epiblast, female, rep1

description: rna E6.5 Epi female rep1

source_name: Epiblast

value: Epiblast


title: RNA-5-BAT13


title: HA Barcode mininimal replication no NS2 library #2


title: HA Barcode mininimal replication no NS2 library #1


title: Th9_ TOFA_3_H3K27Ac_H3K9me3_Input

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

country: Japan

institute: KAZUSA DNA Research Institute

data_processing:
For RNA-sequence, read sequences (75 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using STAR (version 2.7.9a).
Fragments per kilobase of transcripts for each gene were calculated using Subread (version 2.0.1, 13 ).
ATAC-seq ror ChIP-seq eads were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)  using Bowtie2.
Normalization was performed using RPGC method with Bamcoverage of Deeptools.
mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)
Assembly: Excel files include TPM values for each Sample
Supplementary files format and content: wig files were generated using "Deep tools".

source_name: Spleen

growth_protocol: See method in article

extract_protocol:
See method in article
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (LEXOGEN), ATAC-Seq (ACTIVE MOTIF), or NEBNext Ultra II DNA Library Prep with Sample Purification Beads (NEW ENGLAND BioLabs)  was used for library constraction according to the manufacturer's protocol.

treatment_protocol: See method in article

value: Spleen

value: CD4 T cell

value: Wild type

value: TOFA


title: RNA-seq Trophectoderm of E3.5 blastocyst, female, rep1

description: rna E3.5 TE female rep1

value: C57BL/6N X PWK/PhJ


title: Th9_ TOFA_2_H3K27Ac_H3K9me3_Input


title: RNA-seq Inner cell mass of E3.5 blastocyst, female, rep2

description: rna E3.5 ICM female rep2

source_name: Inner cell mass

value: Inner cell mass


title: Th9_ TOFA_1_H3K27Ac_H3K9me3_Input


title: Total RNA-seq of NC

city: Nantong

first: Zhan

last: Chen

state: Jiangsu

address: No. 666 Shengli Road

department: Urology Surgery

institute: The Second Affiliated Hospital of Nantong University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: ACHN cells

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: ACHN cells

value: NC

value: Negative Control ACHN cells


title: RNA-seq Inner cell mass of E3.5 blastocyst, female, rep1

description: rna E3.5 ICM female rep1

value: wild type


title: Th9_ Control_3_H3K27Ac_H3K9me3_Input

value: Vehicle


title: Th9_ Control_2_H3K27Ac_H3K9me3_Input


title: Total RNA-seq of ACHN_sh

value: KIAA1429 knockout ACHN cells


title: islets, knockout, rep2

description:
16KO.counts
20160511_DESeq2_normalized_Med15.csv

value: Pancreatic islets

value: Male

value: Ins1Cre; Med15floxed

value: Med15 KO


title: Th9_ Control_1_H3K27Ac_H3K9me3_Input


title: Th17_ TOFA_2_H3K9Ac_Input


title: RNA-seq Morula, female, rep3

description: rna morula female rep3

source_name: Morula embryo

value: Morula embryo


title: p glutamine 8h_6

city: Cologne

first: Bruna

last: Martins Garcia

address: Joseph-Stelzmann-Strasse 9B

country: Germany

institute: Max Planck Institute for Biology of Ageing

description: 174305 36

data_processing:
Quality check: FastQC 0.11.8
Strand determination: kallisto 0.46.1 & RSeQC 4.0.0
Mapping and quantification: kallisto 0.46.1
Batch effects removal: limma 3.54.0
Differential analysis: limma 3.54.0
Assembly: Ensembl Homo sapiens release 105
Supplementary files format and content: Excel table of gene expression

growth_protocol: U2OS cells were culture in DMEM 4.5 g/L glucose + 10% FBS + 1% P/S at 37C and 5% CO2

extract_protocol:
RNA were extract with Trizol reagent follwing the manufacturer instructions
Libraries were prepared using the Illumina® Stranded TruSeq® RNA sample preparation Kit and 500 ug of RNA

treatment_protocol: U2OS cells were culture in DEMEM 4.5 g/L glucose with or without 2 mM of glutamine, 1 mM aKG or 200 nM ISRIB

value: osteosarcoma

value: wild-type

value: glutamine 8h


title: Th17_ TOFA_1_H3K9Ac_Input

value: Spleen

value: CD4 T cell

value: Wild type

value: TOFA


title: RNA-seq Morula, female, rep2

description: rna morula female rep2

value: C57BL/6N X PWK/PhJ


title: Th17_ Control_2_H3K9Ac_Input


title: RNA-seq Morula, female, rep1

description: rna morula female rep1


title: p glutamine 8h_5

description: 174303 35


title: islets, wildtype, rep1

description:
9WT.counts
20160511_DESeq2_normalized_Med15.csv

value: WT


title: Th9_ TOFA_2_H3K9Ac_Input


title: CD11c-IL-33KO, RNA-seq 3

city: Philadelphia

first: Juan

middle: M.

last: Inclan-Rico

state: PA

address: 3800 Spruce St

department: Pathobiology

institute: University of Pennsylvania, School of Veterinary Medicine

data_processing:
FASTQ filese were checked with FASTQC v 0.11.9 (www.bioinformatics.babraham.ac.uk/projects) and sequence reads were trimmed for adaptor sequence with trimmomatic-0.39
Trimmed sequence reads were mapped to mm10 using  using Kallisto v 0.46.1 in Ubuntu 22.4 desktop
Raw counts with TPM values were processed with kallisto sleuth pipeline (https://scilifelab.github.io/courses/rnaseq/labs/kallisto)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include tpm values for each Sample

source_name: Abdominal skin biopsy from naive mice

extract_protocol:
Skin biopsies were homogenized and tissue RNA was isolated using the Qiagen RNAeasy plus kit (Qiagen). RNA integrity was measured with an Agilent RNA TapeStation, and concentration measured with the qubit fluorometer (Invitrogen).
RNA libraries for samples with RIN values greater than 7 were used for sequencing, and RNA was normalized to 500ng per sample.  Libraries were generated using the Illumina stranded mRNA prep kit (Illumina) and sequenced using an Illumina NextSeq 550 in a single-end 75-base pair (bp) read configuration, at a depth of at least 30 million reads per sample.

value: Abdominal skin biopsy from naive mice

tag: gender

value: male

value: CD11c cre x IL-33 fl/fl

tag: age

value: 8-10 week old


title: Th9_ TOFA_1_H3K9Ac_Input


title: RNA-seq 8-cell, female, rep2

description: rna 8cell female rep2

source_name: 8-cell embryo

value: 8-cell embryo

value: wild type


title: p aKG 8h_6

description: 174293 30

value: aKG 8h


title: CD11c-IL-33KO, RNA-seq 2


title: p glutamine 8h_4

description: 174301 34


title: RNA-seq 8-cell, female, rep3

description: rna 8cell female rep3


title: CD11c-IL-33KO, RNA-seq 1


title: Th9_ Control_2_H3K9Ac_Input

value: Vehicle


title: Th9_ Control_1_H3K9Ac_Input


title: RNA-seq 8-cell, female, rep1

description: rna 8cell female rep1


title: p aKG 8h_4

description: 174289 28

value: osteosarcoma


title: p aKG 8h_5

description: 174291 29

value: wild-type


title: Th9_ TOFA_2_H3K9me3

tag: antibody


title: MEF cells, PWK-Xi, SMC3, rep2

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequencing reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then aligned to mm9 reference genome with random chromosome cleaned by Bowtie2 (version 2.3.4.1) under the parameters -t -q -N 1 -L 25 -X 700 --no-unal --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
Sequencing reads were assigned to two alleles with SNPsplit (v0.3.2) (Krueger and Andrews, 2016)
We normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome.
bigWig files were visualized withUCSC genome browser
Assembly: mm9
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: immortal MEF

growth_protocol: Immortal MEF cells were cultured on 0.1% gelatin precoated dishes in DMEM (Gibco, Cat #11995-073) containing 10% NBCS (Gibco, #16010159), 0.1 mM β-mercaptoethanol (Sigma, #M6250) and 50ug/ml penicillin-streptomycin (Hyclone, #SV30010). Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were first resuspended in washing buffer (20mM HEPES-KOH pH 7.5, 150mM NaCl, 0.5mM spermidine and protease inhibitor) and then bound to the Concanavalin-coated magnetic beads (Polyscience, #86057) in binding buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM CaCl2 and 1mM MnCl2). The samples were incubated in antibody buffer (washing buffer plus 0.005%~0.01% digitonin and 2mM EDTA) with antibody diluted at ratio of 1:100 at 4°C on Thermomixer for 3 hrs at 300 rpm. Beads were then washed and incubated with protein A-MNase (pA-MNase) (to a final concentration of 400 to 700 ng/ml) at 4°C for 1-3 hrs on a thermomixer at 300 rpm. Targeted chromatin was digested for 30 min on ice after adding 2 ml of 100 mM CaCl2. The reaction was then terminated with 2× stop buffer (340mM NaCl, 20mM EDTA\, 4mM EGTA, 50μg/mL RNase A, 100μg/mL glycogen and 0.005%~0.01% digitonin). Samples were then incubated at 37°C for 20 min to release the targeted fragment.
CUT&RUN libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645S)  following manufacturer's protocols. The libraries were purified and size-elected with AMPure XP beads (Beckman Coulter, #A63881).

value: mouse embryonic fibroblast cells

value: immortal MEF

value: SMC3 (Abcam, #ab9263)


title: Control, RNA-seq 2

value: CD11c cre


title: Control, RNA-seq 1


title: Th17_ Control_1_H3K9Ac_Input

value: Spleen

value: CD4 T cell

value: Wild type


title: MEF cells, PWK-Xi, SMC3, rep1

value: C57BL/6N X PWK/PhJ


title: Th9_ Control_2_H3K9me3


title: Th9_ TOFA_1_H3K9me3

value: TOFA


title: MEF cells, B6-Xi, SMC3, rep1

value: PWK/PhJ X C57BL/6N


title: MEF cells, B6-Xi, SMC3, rep2


title: p glutamine 8h_3

description: 174257 12

value: glutamine 8h


title: Th9_ Control_1_H3K9me3


title: MEF cells, PWK-Xi, CTCF, rep2

value: CTCF (Active motif, #61311)


title: NP21009 CITEseq

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description:
10x Genomics
NP21009_barcodes.tsv.gz
NP21009_features.tsv.gz
NP21009_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using cell ranger, and gene counts were computed by aligning to the human genome GRCh38 and then analyzed using R4.4.1 with Seurat toolkit package 4.2.0
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: Nasal polyp

extract_protocol:
Nasal polyp and tonsil tissues were collected at surgery, placed in PBS-Tween with protease inhibitors, and processed in RPMI with 10% fetal bovine serum and 1% penicillin-streptomycin. They were fragmented, treated with DNase I and collagenase, dissociated, strained, and RBCs were depleted before preparing single-cell suspensions for flow cytometry, sorting, or 10x genomics, with cell viability confirmed by trypan blue staining.
Library was peformed according to the manufacter's instructions (single cell 3' v2 protocol, 10xGenomics). Single cell suspensions was mixed with the master mix and loaded together with partioning oil and gel beads into the chip to generate the GEM.

value: Nasal polyp

value: B lineage cells, and other cells

tag: library type

value: ADT

tag: adt

value: TotalSeq-B0050 anti-human CD19, TotalSeq-B0154 anti-human CD27, TotalSeq-B0389 anti-human CD38, TotalSeq-B0384 anti-human IgD, TotalSeq-B0911 anti-phycoerythrin


title: Th9_ TOFA_2_H3K27Ac


title: TN21006 CITEseq

description:
10x Genomics
TN21006_barcodes.tsv.gz
TN21006_features.tsv.gz
TN21006_matrix.mtx.gz

source_name: Tonsil

value: Tonsil


title: p glutamine 8h_2

description: 174255 11

value: osteosarcoma

value: wild-type


title: p glutamine 8h_1

description: 174253 10


title: MEF cells, PWK-Xi, CTCF, rep1

value: mouse embryonic fibroblast cells

value: immortal MEF


title: NP21040 scRNAseq

description:
10x Genomics
NP21040_barcodes.tsv.gz
NP21040_features.tsv.gz
NP21040_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using cell ranger, and gene counts were computed by aligning to the human genome GRCh38 and then analyzed using R4.4.1 with Seurat toolkit package 4.2.0
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

value: mRNA


title: Th9_ TOFA_1_H3K27Ac

value: Spleen

value: CD4 T cell


title: Control, RNA-seq 3

value: Abdominal skin biopsy from naive mice

value: male

value: CD11c cre

value: 8-10 week old


title: TN19056 CITEseq

description:
10x Genomics
TN19056_barcodes.tsv.gz
TN19056_features.tsv.gz
TN19056_matrix.mtx.gz


title: NP21040 CITEseq


title: p aKG 8h_2

description: 174243 5

value: aKG 8h


title: Th9_ Control_2_H3K27Ac

value: Wild type

value: Vehicle


title: NP21009 scRNAseq

value: Nasal polyp

value: B lineage cells, and other cells


title: p aKG 8h_3

description: 174245 6


title: m glutamine 8h_6

description: 174287 27

value: glutamine starvation 8h


title: p aKG 8h_1

description: 174241 4

value: osteosarcoma


title: Th17_ TOFA_2_H3K9Ac

value: TOFA


title: m glutamine 8h_4

description: 174283 25

value: wild-type


title: Th9_ Control_1_H3K27Ac


title: m glutamine 8h_5

description: 174285 26


title: MEF cells, PWK-Xi, H3K27ac, rep2

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequencing reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then aligned to mm9 reference genome with random chromosome cleaned by Bowtie2 (version 2.3.4.1) under the parameters -t -q -N 1 -L 25 -X 700 --no-unal --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
Sequencing reads were assigned to two alleles with SNPsplit (v0.3.2) (Krueger and Andrews, 2016)
We normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome.
bigWig files were visualized with UCSC genome browser
Assembly: mm9
Supplementary files format and content: bigWig

extract_protocol:
STAR ChIP-seq was performed as previously described (Zhang et al., 2021; Zhang et al., 2016). Briefly, cells were first lysed and then subjected to MNase digestion by incubating with MNase working buffer (50 mM Tris-HCl pH 8.0, 1 mM CaCl2 and 0.2% Triton X-100) containing diluted MNase (Sigma, #N3755-200UN) at 37 °C for exact 5 min. The reaction was terminated by stop buffer (110 mM Tris-HCl pH 8.0 and 55 mM EDTA). After adding cold 2× RIPA buffer (1.8% Triton X-100, 280 mM NaCl, 0.2% SDS, 0.2% sodium deoxycholate (DOC), 5 mM EGTA and proteinase inhibitor) and spinning at max speed in 4 °C for 10 min, the soluble chromatin containing supernatant was incubated with 1mg H3K27ac antibody (ActiveMotif, #39133) in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC, 1 mM EDTA and proteinase inhibitor) at 4°C overnight with rotation. Protein A/G dynabeads (Thermo Fisher Scientific) were used to bind the antibody at 4°C for 2 to 3 hours with rotation. The beads were then washed five times with RIPA buffer and once with LiCl buffer (10 mM Tris-HCl pH 8.0, 250mM LiCl, 1 mM EDTA, 0.5% NP-40 and 0.5% DOC). Beads bound chromatin were then digested with proteinase K (NEB, #P8107S) at 55°C for 90 min, followed by incubation at 72°C for 40 min to inactivate the proteinase K.
STAR ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645S)  following manufacturer's protocols. The libraries were purified and size-elected with AMPure XP beads (Beckman Coulter, #A63881).

value: mouse embryonic fibroblast cells

value: immortal MEF

value: C57BL/7N X PWK/PhJ

value: H3K27ac (ActiveMotif, #39133)


title: m glutamine 8h_3

description: 174239 3


title: MEF cells, B6-Xi, CTCF, rep1

value: PWK/PhJ X C57BL/6N

value: CTCF (Active motif, #61311)


title: MEF cells, PWK-Xi, H3K27ac, rep1

value: C57BL/6N X PWK/PhJ


title: TN21006 scRNAseq

value: Tonsil

value: mRNA


title: MEF cells, B6-Xi, CTCF, rep2


title: TN19056 scRNAseq


title: MEF cells, PWK-Xi, rep1 RNA-Seq

data_processing:
Illumina Casava1.8 software was used for basecalling.
All reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then mapped to mm9 genome by HISAT2 (v.2.2.0) (Kim et al., 2019) under the parameters –dta --no-softclip.
The gene expression level was calculated by StringTie (v.2.1.1) (Pertea et al., 2015) using the refFlat database from the UCSC genome browser.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each allele of MEF cells

extract_protocol:
Cells were lysed in lysis buffer (0.2% (vol/vol) Triton X-100 and 2 U/μl RNase inhibitor). The polyadenylated mRNAs were captured by the oligodT primers,
mRNAs were subjected to the Smart-seq2 protocol as described previously (Picelli et al., 2014).
RNA-seq (Smart-seq2)


title: AML_02_scRNAseq

city: New York

first: Maria

last: Sirenko

state: NY

address: 550 1st Avenue

institute: NYU Langone

description: 10X 5' v1 gene expression profiling of bone marrow mononuclear cells, lymphoid depleted.

data_processing:
cellranger version 5.0.1
seurat 4.3
Assembly: grch38-2020-A
Supplementary files format and content: counts matrix and metadata

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
bone marrow mononuclear cells flow sorted to enrich for myeloid and blast cells and remove dead cells
10X 5' V1 GEX

value: Bone marrow

value: diagnosis


title: MEF cells, B6-Xi, rep1 RNA-Seq


title: m glutamine 8h_1

description: 174234 1


title: Sox9iresGFP PND3  XX

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: 10X Genomics

data_processing:
All subsequent analyses were performed in R v.3.6.0 using the Seurat (v3) package.  Genes were considered to be ‘expressed’ if the estimated (log10) count was at least 0.1. Primary filtering was then performed by removing from consideration: cells expressing fewer than 50 genes and cells for which mitochondrial genes made up greater than 10% of all expressed genes.
All further analyses done using Seurat v4 R package. Genes were deemed “expressed” if their estimated (log10) count was at least 0.1. Initial filtering excluded cells expressing fewer than 50 genes and cells with mitochondrial gene expression greater than 3 standard deviations from the mean.
Assembly: mm10
Supplementary files format and content: tab delimited text containing raw counts

source_name: Pituitary

growth_protocol: Harvested from PND3 animal

extract_protocol:
Chromium Controller and Chromium10x 3 prime v2.0, Chromium Single Cell 30 Reagent Kits UserGuide (v3 Chemistry)
Chromium Next GEM Single Cell

value: Pituitary

value: F

value: Stem cell


title: Sox9iresGFP PND3  XY

description: 10X Genomics

value: M


title: anti-IFNAR rep3

city: Berkeley

first: Yeara

last: Jo

address: 485 Weill Hall

institute: University of California, Berkeley

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The sequencing reads were aligned to a mouse genome (mm10; Genome Reference Consortium GRCm38) using BWA with the following parameters: “bwa mem -M -k 32”. Low quality and unmapped reads were removed using samtools with the following parameters: “-F 0x70c -q 30”.
After the removal of duplicated reads, peaks for eachindividual replicate were identified using MACS2 with q value cutoff of 0.01.
Genome_build: Mm10 (GRCm38)
Supplementary_files_format_and_content: Excel xls files include peaks called by MACS2

extract_protocol:
Lin-c-Kitint/loFlt3+ cells (Lin includes B cells (CD19, B220), T cells (Thy1.2, CD3, CD4, and CD8), NK cells (NK1.1), red  blood cells (Ter119), granulocytes (Gr-1), and monocytes (CD11b)) were FACS-purified from bone marrow. Purified cells were resuspended in lysis buffer and spun down 600g for 30 min at 4°C. Nuclei pellet was resuspended into transposition reaction mixture containing Tn5 transposase from Nextera DNA Sample Prep Kit (Illumina) and incubated for 30 min with gentle shaking at 37°C.
ATAC-seq library was constructed by Nextera DNA Sample Prep Kit (Illumina). Following purification, we first amplified the full libraries for 5 cycles and the additional number of cycles needed for the remaining 45 μL reaction was determined as published in the original protocol (Buenrostro et al., 2013) . The libraries were purified using a Qiagen PCR cleanup kit in 20 μL. Libraries were amplified for a total of 10–12 cycles. The library was pooled and size-selected to range between 100bp and 600bp by using PippinHT (Sage Sciences). Samples were subsequently analyzed on a HiSeq 4000 instrument using a single read 100bp protocol.

treatment_protocol: 7 weeks old female C57Bl/6J mice were intravenously infected with 2x10^6 plaque forming units of lymphocytic choriomeningitis virus strain Clone-13. C57BL/6J mice were intraperitoneally (i.p.) injected with 500ug/mouse of neutralizing antibody (nAb) against IFNAR or anti-mouse IgG1 isotype control on days -1 and 0 post LCMV Cl13-infecteion. Mice were then treated with 250ug/mouse anti-IFNAR nAb or isotype control i.p. on days 2,4, and 6 post-LCMV Cl13 infection.

value: 7 weeks

value: female

value: 8 days post infection

tag: infection

value: LCMV Clone 13

value: anti-IFNAR neutralizing antibody


title: H1 hiN D14, LLPHwt/wt, RNAseq, rep3

city: Singapore

first: Teodorus Theo

last: Susanto

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Ribo-seq: Due to the short insert length, only analysis of Read 1 was necessary. cutadapt version 2.4 was used to trim 3′ adapter sequences from Read 1 with parameters “-j 0 -u 3 -a AGATCGGAAGAGCACAGTCTGAACTCCAGTCAC --discard-untrimmed -m 15”.
Ribo-seq: In-line barcodes were demultiplexed using fastx_barcode_splitter.pl (http://hannonlab.cshl.edu/fastx_toolkit/) with parameters “--eol”. Unique molecular identifiers and in-line barcodes were extracted using UMI-tools version 1.0.1 with parameters “extract --extract-method=string --bc-pattern=NNNNNCCCCC -–3prime”.
Ribo-seq: Reads were filtered by quality using fastq_quality_filter (http://hannonlab.cshl.edu/fastx_toolkit/) with parameters “-Q33 -q 20 -p 70 -z”.
Ribo-seq: To remove reads originating from rRNA, transfer RNA (tRNA), and small nuclear RNA (snRNA), reads aligning to these sequences using bowtie2 version 2.3.4.3 with parameters “-L 18” were discarded. PCR duplicates were then removed using UMI-tools.
Ribo-seq: Ribosome A site positions were determined by offsetting the distance of the 5’ end of each RFP read to canonical start sites in each length group and adding 4 nucleotides.
Ribo-seq: Reads aligning to the CDS were used for RFP libraries. Reads mapping to mitochondrial DNA genes were excluded from further analysis
RNA-seq: cutadapt version 2.4 was used to trim 3′ adapter sequences "AGATCGGAAGAGCACAGTCTGAACTCCAGTCAC" from Read 1 and trim 5' adapter sequences "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" from Read 2
RNA-seq: To remove reads originating from rRNA, transfer RNA (tRNA), and small nuclear RNA (snRNA), reads aligning to these sequences using bowtie2 version 2.3.4.3 with parameters “-L 18” were discarded. PCR duplicates were then removed using UMI-tools.
RNA-seq: Reads aligning to the entire transcript were used for RNA-seq libraries. Transcript abundance was quantified using Salmon v1.4.0 with parameters:  -t <gencode.v43.pc_transcripts.EnsemblCanonical.protein_coding.fa.gz> -l A. Reads mapping to mitochondrial DNA genes were excluded from further analysis
Transcripts with counts per million (CPM) >2 were retained for downstream analysis RFP and RNA-seq libraries were normalized separately by the trimmed mean of M-values method in edgeR.
Differential RFP and RNA-seq abundance and enrichment were analyzed using voom and limma. Multiple testing correction was performed using the Benjamini-Hochberg method.
Assembly: GENCODE release 43 (GRCh37) (gencode.v43.pc_transcripts.EnsemblCanonical.protein_coding)
Supplementary files format and content: tab-delimited text file that includes read counts for both RNAseq and Ribo-seq of LLPH+/+ and LLPHNterm/Nterm hiNs DIV 14
Supplementary files format and content: comma-separated file that contains translation efficiency of detected genes in LLPH+/+ and LLPHNterm/Nterm hiNs DIV 14

source_name: derived from H1-hESC

growth_protocol: LLPH+/+ and LLPHNterm/Nterm hiNs were grown until DIV 14 as mentioned in “Methods: Generation of human induced neurons (hiNs) from H1-hESC with Ngn2 overexpression (related to Figures 3C-3G and S4E-S4F)”, with modifications below. Glia was not added on day 5 and premature hiN cells were not detached and instead left growing on matrigel coated 6-well plate for the full 14 days. On day 5, media was fully replaced to Neurobasal (NB) zero + 2 µg/mL Doxycycline (Dox) + 4 µM Cytosine β-D-arabinofuranoside (AraC). On day 10, 50% of spent media was replaced with NB zero + 2 µg/mL Dox + 4 µM AraC.

extract_protocol:
Each cell pellet was lysed in 400 μL cold lysis buffer A (20 mM HEPES (Sigma Aldrich, H3375-100G), adjusted to pH 7.6 by KOH (Sigma Aldrich, 221473-500G) (HEPES-KOH), 15 mM magnesium acetate (Mg(OAc)2) (Sigma Aldrich, M5661-250G), 60 mM NH4Cl (Sigma Aldrich, A9434-500G), 1 mM dithiothreitol (DTT; Pierce, A39255), 100 µg/mL CHX , 1% Triton X-100 (Sigma Aldrich, T8787), 0.5% sodium deoxycholate (Sigma Aldrich, D6750),  8% glycerol (Sigma Aldrich, G9012-100ML), 20 U/mL TURBO DNase (Ambion, AM2238), 200 U/mL SUPERase·In™ RNase Inhibitor (Ambion, AM2696), 1× Halt™ Protease and Phosphatase Inhibitor (Thermo Scientific, 78443), in nuclease-free water (Invitrogen, 10977015)). Cells were then lysed by vortexing at high speed for 30 seconds and putting them back on ice for 30 seconds. This was repeated another two times for a total of 3 minutes. The samples were then incubated on ice for 30 minutes and vortexed briefly for 10 seconds every 10 minutes. The cytoplasmic fraction was enriched by centrifuging the lysates twice at 800 ×g for 5 minutes at 4 °C, then once at 8,000 ×g for 5 minutes at 4 °C, and finally once at 20,817 ×g for 5 minutes at 4 °C, with the supernatants being moved to fresh chilled tubes after each centrifugation.
Ribo-seq: Ribosome profiling libraries were prepared by generally following the published protocol of McGlincy and Ingolia with modifications below. Cytoplasmic lysate (~375 µg total RNA) was treated with 0.33 µg RNase A (Thermo Scientific, AM2271) and 200 U RNase T1 (Thermo Scientific, EN0541) for 30 min on rotator at room temperature. Digestion was stopped by adding 10 µL SUPERase·In™ RNase Inhibitor and transferring the samples on ice. Meanwhile, to isolate intact 80S ribosomes and ribosome footprints (RFPs), 10-50% linear sucrose gradients were made in 14x89 mm open-top polyallomer centrifuge tubes using a gradient maker (Biocomp, 108). Before layering the lysates onto the gradient, 200 μL sucrose gradient solution was removed from each centrifuge tube. Then, 200 μL cytoplasmic lysate containing 20 μg RNA was used for each RFP sample. The tubes were centrifuged using a SW 41 Ti swinging bucket rotor at 40,000 rpm for 2.5 hours at 4 °C. Fractions were collected for 30 seconds each using the Density Gradient Fraction System with a flow rate of 1.5 mL/minute). 80S were found in fraction 7 for hiN D14 LLPH+/+ rep 2 and LLPHNterm/Nterm rep 1, and fraction 6 and 7 for the other samples. A 3x volume of TRIzol LS (Thermo Fisher, 10296028) was added to these fractions. RFP samples were then extracted from TRIzol using the Direct-Zol Microprep Kit (Zymo, R2060) according to the manufacturer protocol. Subsequently, these samples were treated with TURBO DNase at 37 °C for 30 minutes according to the manufacturer protocol and cleaned up with Zymo RNA Clean & Concentrator Kit with some modifications to enrich for small RNAs (>17 nt, <200 nt). Adjusted binding buffer was prepared by mixing equal volumes of 100% ethanol and RNA binding buffer. Samples were first adjusted to 100 µL with nuclease free water. Then, 200 µL of adjusted binding buffer was added and mixed, followed by adding 450 µL of 100% ethanol and mixed. Samples were then processed with spin columns as per manufacturer protocol and eluted twice with 6 µL of nuclease free water each.
Ribo-seq: RFPs were denatured at 80°C for 90 seconds in denaturing sample loading buffer (10 mM EDTA and bromophenol blue (Fisher Scientific, MBX14107), in formamide (Promega, H5052)), then incubated on ice for 5 minutes before running on a 15% Tris-borate-EDTA-urea (TBE-urea) polyacrylamide gel. Fragments were size-selected using NI-800 and NI-801 (McGlincy, N.J., and Ingolia, N.T. (2017)) as 26–34 nt markers. Gel slices were freeze-thawed for at least 30 minutes at -80°C and 3 minutes at room temperature. They were then crushed by forcing the gel through a hole in a 0.5 mL tube pierced by a 20 gauge needle (Santa Cruz Biotechnology, sc-359535) by centrifuging at 15,000 ×g for 2 minutes. RNA were then extracted from the minced gel at room temperature overnight in 400 µL RNA extraction buffer (McGlincy, N.J., and Ingolia, N.T. (2017)) , then re-extracted with an additional 200 µL RNA extraction buffer for additional 3 hours, removing the minced gel by using 0.22 µm cellulose acetate centrifuge tube filters (Corning, 8160) and spinning at max speed for 2 minutes at room temperature. The combined 600 µL extraction was precipitated with 2 µL GlycoBlue (Thermo Fisher, AM9516) and 750 µL 100% isopropanol (Sigma Aldrich, PX1835-6) overnight at -80°C. Precipitated RFPs were pelleted at 21,000 ×g for 30 minutes at 4 °C, washed with ice-cold 80% ethanol in water, air dried at room temperature for 10 minutes, then dissolved in 4 µL of 10 mM Tris pH 8, dephosphorylated, and ligated to barcoded linkers as per the published protocol. RNA linkers were pre-adenylated beforehand using Mth RNA ligase (NEB, E2610S). Unreacted linker was deadenylated and digested as per the published protocol. The barcoded RFPs were then purified using Zymo Oligo Clean & Concentrator column (Zymo, D4060) according to the manufacturer’s protocol, and subsequently reverse-transcribed as per the published protocol. Template RNA was degraded by alkaline hydrolysis, and cDNA was purified using Zymo Oligo Clean & Concentrator column, denatured in sample loading buffer, and size selected on a 10% TBE-urea gel, as marked by NI-800 and NI-801 that had been processed in parallel with the samples. Gel slices were processed as described previously, and cDNA was extracted at room temperature overnight in 400 µL DNA extraction buffer (McGlincy, N.J., and Ingolia, N.T. (2017)), then re-extracted with an additional 200 µL DNA extraction buffer for 3 hours. The cDNA was pelleted, washed, and dried as described above, then resuspended in 15 µL 10 mM Tris pH 8. cDNA was circularized by adding 2 µL 10X CircLigase I buffer, 1 µL of 1 mM ATP, 1 µL of 50 mM MnCl2, and 1 µL of CircLigase I (Biosearch Technologies CL4111K) to the 15 µL of cDNA and incubating at 60°C for 12 hours, then 80°C for 10 minutes. Using 1 µL of circularized DNA template per 50 µL reaction, library construction to add indexing primers was performed as per the published protocol using a different reverse primer for each replicate. PCR products were purified using a Zymo DNA Clean & Concentrator column (Zymo, D4003). Size selection was performed on a 8% TBE-urea gel, with the lower bound marked by NI-803 (McGlincy, N.J., and Ingolia, N.T. (2017)) that had undergone library construction in parallel with the samples, and the upper bound at 170 nt as marked by O’Range 20 bp DNA ladder (Thermo, SM1323). Gel slices were extracted as described above. DNA was precipitated as described above, except using 1.25 µL of 20 µg/mL glycogen (Invitrogen, 10814-010) instead of GlycoBlue. The pellet was resuspended in 15 µL of 10 mM Tris pH 8. Library quality was analyzed on an Agilent 2100 Bioanalyzer (High-Sensitivity DNA) at the Stanford Protein and Nucleic Acid Facility. Library concentration was measured using Qubit dsDNA high sensitivity kit (Thermo Fisher, Q33231), and the RFP samples were then pooled in equal amounts.
RNA-seq: Ribosome profiling libraries were prepared by generally following the published protocol of McGlincy and Ingolia with modifications below. To isolate RNA input samples for RNA-seq, 10 µL of cytoplasmic lysate is transferred into 500 µL of cold TRIzol, mixed by pipetting, and stored at -80 °C for subsequent RNA extraction using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L). The remaining lysate (~375 µg total RNA) was processed for Ribo-seq library.
polyA-selected RNA samples were mixed together with RFP samples in 4:6 ratio. Libraries were sequenced by Novogene (Sacramento, CA) on a full lane Illumina NovaSeq X Plus with paired-end 150 bp reads.

treatment_protocol: hiNs were harvested using Accutase in the presence of 100 µg/mL cycloheximide (CHX) and lysed with lysis buffer B (20 mM Tris-HCl pH 7.5, 15 mM MgCl2, 150 mM NaCl, 1 mM DTT, 100 μg/mL CHX, 1% Triton X-100, 0.5% sodium deoxycholate, 8% glycerol, 20 U/mL TURBO DNase, 200 U/mL SUPERase InTM RNase inhibitor, 1x HaltTM protease and phosphatase inhibitor in nuclease-free water). Lysis was performed and the cytoplasmic fraction was enriched by serial centrifugation as described in “Methods: RAPIDASH for E14 mouse embryonic stem cells.”

value: derived from H1-hESC

value: human induced neurons (hiNs) days in vitro (DIV) 14

value: WT

value: Ngn2 overexpression


title: Th9_ TOFA_2_H3K9Ac

value: Spleen

value: CD4 T cell

value: Wild type

value: TOFA


title: Th17_ Control_1_H3K9Ac

value: Vehicle


title: MEF cells, B6-Xi, rep1 HiC

data_processing:
Illumina Casava1.8 software was used for basecalling.
Hi-C reads were processed using HiCPro 2.7.1b and replicates of same stage were pooled together
Cmpartment and TAD analysis were done with  cooltools (v0.3.2) (Venev et al., 2020)
Hi-C data was visulalized with Juicebox (v1.11.08) (Durand et al., 2016)
Assembly: mm9
Supplementary files format and content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Formaldehyde was then quenched with glycine for 10 min at RT.
sisHi-C libraries were produced as previously described (Du et al., 2017). Crosslinked embryos were washed with 1 × PBS and lysed in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min, the chromatin was solubilized with 0.5% SDS at 62 °C for 5 min. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP (Invitrogen, #19518018), the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, #65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Kapa HiFi PCR mix (Roche, #KK2602), and the products were purified and size-selected with AMPure XP beads (Beckman Coulter, #A63881).

value: immortal MEF

value: mouse embryonic fibroblast cells

value: PWK/PhJ X C57BL/6N

value: wild type


title: Th9_ TOFA_1_H3K9Ac


title: Th17_ TOFA_1_H3K9Ac


title: anti-IFNAR rep1

value: Bone marrow

value: 7 weeks

value: female


title: MEF cells, PWK-Xi, rep1 HiC

value: C57BL/6N X PWK/PhJ


title: Th9_ Control_2_H3K9Ac


title: Th17_ Control_2_H3K9Ac


title: isotype rep3

value: 8 days post infection

value: LCMV Clone 13

value: isotype control


title: Th9_ Control_1_H3K9Ac


title: ARPE-19_cino_24h 3

city: Shenzhen

first: Songbin

last: Wu

state: Guangdong

address: 89 Taoyuan Rd., Nanshan District,

department: Department of Pain Medicine

institute: Huazhong University of Science and Technology Union Shenzhen Hospital

description: cinobufagin treatment for 24 h

data_processing:
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GCF_000001405.39_GRCh38.p13

source_name: epithelial

growth_protocol: ARPE-19 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total cellular RNA was harvested using the Trizol method, and then 1 μg of total RNA was used to construct of sequencing libraries.
The final library was obtained by quantifying PCR yields by Qubit and pooling samples together to form single-stranded DNA circles (ssDNA circles) following the manufacturer's protocol.

treatment_protocol: ARPE-19 cells were cultured in 6-well plates the day prior to treatment, during which they were exposed to either cinobufagin (MCE, 320 nM) or DMSO for a duration of 24 hours.

value: epithelial

value: cell line

value: WT

value: cinobufagin


title: H1 hiN D14, LLPHwt/wt, RNAseq, rep1

value: derived from H1-hESC

value: human induced neurons (hiNs) days in vitro (DIV) 14

value: Ngn2 overexpression


title: m glutamine 8h_2

description: 174237 2

value: osteosarcoma

value: wild-type

value: glutamine starvation 8h


title: H1 hiN D14, LLPHNterm/Nterm, RNAseq, rep3

value: LLPHNterm/Nterm


title: H1 hiN D14, LLPHwt/wt, RNAseq, rep2


title: ARPE-19_cino_24h 1

description: cinobufagin treatment for 24 h


title: Th17_ TOFA_2_ATAC

value: Spleen

value: CD4 T cell

value: Wild type

value: TOFA


title: ARPE-19_DMSO_24h 3

description: DMSO treatment for 24 h

value: DMSO


title: isotype rep2

value: Bone marrow

value: 7 weeks

value: female

value: 8 days post infection

value: LCMV Clone 13

value: isotype control


title: ARPE-19_DMSO_24h 2

description: DMSO treatment for 24 h

value: epithelial

value: cell line

value: WT


title: isotype rep1


title: ARPE-19_cino_24h 2

description: cinobufagin treatment for 24 h

value: cinobufagin


title: anti-IFNAR rep2

value: anti-IFNAR neutralizing antibody


title: Th17_ Control_1_ATAC

value: Vehicle


title: Th17_ TOFA_1_ATAC

value: Spleen


title: bone marrow DC progenitors, Cl13 rep3 (RNA-seq)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Raw sequencing data were aligned to mouse genome mm10 (Genome  Reference Consortium GRCm38) by using Spliced Transcripts Alignment to a Reference  (STAR) aligner with the following parameters: “--outFilterType BySJout  --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --  outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20  --alignIntronMax 1000000 --alignMatesGapMax 1000000”.
Transcript data from STAR were analyzed using RSEM for gene and transcript level quantification
Genome_build: Mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text files include TPM (Transcripts Per Million) values for each sample

extract_protocol:
Lin-c-Kitint/loFlt3+ cells (Lin includes B cells (CD19, B220), T cells (Thy1.2, CD3, CD4, and CD8), NK cells (NK1.1), red  blood cells (Ter119), granulocytes (Gr-1), and monocytes (CD11b)) were FACS-purified from bone marrow and RNA was harvested using Qiagen Rneasy Micro Kit.
Illumina TruSeq RNA Library Prep Kit v2 was used with the whole available RNA for each sample to construct sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 7 weeks old female C57Bl/6J mice were intravenously infected with 2x10^6 plaque forming units of lymphocytic choriomeningitis virus strain Armstrong 53b or Clone-13 or left uninfected.

value: DC progenitors

value: LCMV Cl13 (chronic infection)


title: H1 hiN D14, LLPHNterm/Nterm, RNAseq, rep1

value: derived from H1-hESC

value: human induced neurons (hiNs) days in vitro (DIV) 14

value: LLPHNterm/Nterm

value: Ngn2 overexpression


title: Th17_ Control_2_ATAC

value: CD4 T cell

value: Wild type


title: H1 hiN D14, LLPHwt/wt, Ribo-seq, rep3

data_processing:
Ribo-seq: Due to the short insert length, only analysis of Read 1 was necessary. cutadapt version 2.4 was used to trim 3′ adapter sequences from Read 1 with parameters “-j 0 -u 3 -a AGATCGGAAGAGCACAGTCTGAACTCCAGTCAC --discard-untrimmed -m 15”.
Ribo-seq: In-line barcodes were demultiplexed using fastx_barcode_splitter.pl (http://hannonlab.cshl.edu/fastx_toolkit/) with parameters “--eol”. Unique molecular identifiers and in-line barcodes were extracted using UMI-tools version 1.0.1 with parameters “extract --extract-method=string --bc-pattern=NNNNNCCCCC -–3prime”.
Ribo-seq: Reads were filtered by quality using fastq_quality_filter (http://hannonlab.cshl.edu/fastx_toolkit/) with parameters “-Q33 -q 20 -p 70 -z”.
Ribo-seq: To remove reads originating from rRNA, transfer RNA (tRNA), and small nuclear RNA (snRNA), reads aligning to these sequences using bowtie2 version 2.3.4.3 with parameters “-L 18” were discarded. PCR duplicates were then removed using UMI-tools.
Ribo-seq: Ribosome A site positions were determined by offsetting the distance of the 5’ end of each RFP read to canonical start sites in each length group and adding 4 nucleotides.
Ribo-seq: Reads aligning to the CDS were used for RFP libraries. Reads mapping to mitochondrial DNA genes were excluded from further analysis
RNA-seq: cutadapt version 2.4 was used to trim 3′ adapter sequences "AGATCGGAAGAGCACAGTCTGAACTCCAGTCAC" from Read 1 and trim 5' adapter sequences "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" from Read 2
RNA-seq: To remove reads originating from rRNA, transfer RNA (tRNA), and small nuclear RNA (snRNA), reads aligning to these sequences using bowtie2 version 2.3.4.3 with parameters “-L 18” were discarded. PCR duplicates were then removed using UMI-tools.
RNA-seq: Reads aligning to the entire transcript were used for RNA-seq libraries. Transcript abundance was quantified using Salmon v1.4.0 with parameters:  -t <gencode.v43.pc_transcripts.EnsemblCanonical.protein_coding.fa.gz> -l A. Reads mapping to mitochondrial DNA genes were excluded from further analysis
Transcripts with counts per million (CPM) >2 were retained for downstream analysis RFP and RNA-seq libraries were normalized separately by the trimmed mean of M-values method in edgeR.
Differential RFP and RNA-seq abundance and enrichment were analyzed using voom and limma. Multiple testing correction was performed using the Benjamini-Hochberg method.
Assembly: GENCODE release 43 (GRCh37) (gencode.v43.pc_transcripts.EnsemblCanonical.protein_coding)
Supplementary files format and content: tab-delimited text file that includes read counts for both RNAseq and Ribo-seq of LLPH+/+ and LLPHNterm/Nterm hiNs DIV 14
Supplementary files format and content: comma-separated file that contains translation efficiency of detected genes in LLPH+/+ and LLPHNterm/Nterm hiNs DIV 14
Library strategy: Ribo-Seq


title: H1 hiN D14, LLPHwt/wt, Ribo-seq, rep2


title: bone marrow DC progenitors, Cl13 rep2 (RNA-seq)

value: Bone marrow

value: 7 weeks

value: female

value: 8 days post infection


title: Th9_ TOFA_2_ATAC

data_processing:
For RNA-sequence, read sequences (75 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using STAR (version 2.7.9a).
Fragments per kilobase of transcripts for each gene were calculated using Subread (version 2.0.1, 13 ).
ATAC-seq ror ChIP-seq eads were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)  using Bowtie2.
Normalization was performed using RPGC method with Bamcoverage of Deeptools.
mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)
Assembly: Excel files include TPM values for each Sample
Supplementary files format and content: wig files were generated using "Deep tools".

value: TOFA


title: bone marrow DC progenitors, Cl13 rep1 (RNA-seq)


title: Th9_ TOFA_1_ATAC


title: ARPE-19_DMSO_24h 1

description: DMSO treatment for 24 h

value: epithelial

value: cell line

value: WT

value: DMSO


title: 231siDCAF_Input

city: Guangzhou

first: Jianyou

last: Liao

address: Guangzhou

institute: Medical Research Center, Sun Yat-sen Memorial Hospital,  Sun Yat-sen University

data_processing:
ChIP-seq reads was generated using the DNBseq platform and obtained from BGI Genomics.
ChIP-seq reads was trimmed using SOAPnuke software and subsequently subjected to quality control using FastQC v0.11.6 before being utilized for further analysis.
ChIP-seq reads was aligned to the UCSC hg38 genome using Bowtie version 2.1.0 with default parameters.
To create ChIP-seq coverage plots,the mapped bam files were converted to bigWig file and visualized By IGV software.
Peaks were called using MACS2 with the signicance cut-off q-value<=0.01.
Assembly: hg38
Supplementary files format and content: bigWig,Peak

extract_protocol:
Nuclei were isolated from fixed MDA-MB-231 cells using 1% formaldehyde (10 minutes, RT) and quenched with 0.125 M glycine for 5 minutes. After centrifugation, the cells were resuspended in lysis buffer and subjected to sonication (Bioruptor, Diagenode) to yield 250-500 bp fragments
1.Sample QC:The corresponding sample quality control protocol will be selected depending upon sample types and product requirements. 2.End Repair, add “A”, Adaptor Ligation:After the reaction system and program are configured and set up, DNA fragments obtained from ChIP are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the DNAs.3.PCR:The PCR reaction system and program are configured and set up to amplify the product.4 .Library QC:The corresponding library quality control protocol will be selected depending upon product requirements.5. Circularization：Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.

value: Human triple negative breast cancer cell line

value: siDCAF


title: 231siNC_IP_RPA

value: siNC


title: bone marrow DC progenitors, Armstrong rep2 (RNA-seq)

value: DC progenitors

value: LCMV Armstrong 53b (acute infection)


title: bone marrow DC progenitors, Armstrong rep3 (RNA-seq)


title: H1 hiN D14, LLPHNterm/Nterm, Ribo-seq, rep3

value: derived from H1-hESC

value: human induced neurons (hiNs) days in vitro (DIV) 14

value: Ngn2 overexpression


title: Th9_ Control_2_ATAC

value: Spleen

value: CD4 T cell

value: Wild type

value: Vehicle


title: H1 hiN D14, LLPHNterm/Nterm, RNAseq, rep2

value: LLPHNterm/Nterm


title: R1149, oligo pools, after selection

first: Zhe

last: Zhang

address: Gaoke Innovation Center

department: Institute of Physical and Systems Biology

institute: Shenzhen Bay Laboratory

data_processing:
Paired-end fastq files from next-generation sequencing were merged by using PEAR. Both 5’ constant regions and 3’ constant regions of the assembled reads were trimmed by cutadapt. We used FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and vsearch to filter sequencing reads with low quality, and count the read number of identical sequences. The read numbers before and after selection were then summed up for each unique sequence. RNA-specific CODA Analysis was used for downstream analysis.
Assembly: N/A
Supplementary files format and content: The ra files contain tab-separated values in each line. The values from left to right are: number of mutations, mutated position, mutation type, read counts before selection, read counts after selection, relative enrichment ratio (fitness).
Library strategy: Tru-seq

organism: Escherichia coli

extract_protocol:
The assembled products were mixed with electrocompetent cells and transformed into electrocompetent cells in a 2-mm Gene Pulser cuvette (Bio-Rad, 165-2086) using an electroporation instrument (Bio-Rad, MicroPulser). The transformants were cultured on 20 mL LB for 1 h at 37 °C on a rotator with 220 rpm. After 1 h, the size of the constructed library was detected by the number of colonies after a gradient dilution on LB-agar plate (containing 100 μg/mL ampicillin). Then 100 μg/mL ampicillin was added to 20 mL LB and allowed to grow at 37 °C for 10 h and collected using centrifugation. The pellet was resuspended in LB medium containing 15% glycerol and stored at -80 °C for long term use. 10^7 clones from the mutated library were cultured and amplified. The corresponding plasmids were extracted. The BspQ I linearized vectors were transcribed to RNAs.
The purified RNA was reverse transcribed using ProtoScript® II Reverse Transcriptase (NEB, M0368L). The 20 μL reaction volume containing 4 µL 5 × ProtoScript II buffer, 2 μL 0.1 M DTT, 1 μL 10 mM dNTP, 0.2 μL RNase inhibitor (40 U/μL), 1 μL ProtoScript II RT (200 U/µL), 2 μL M13-RP and the RNA template. The reaction system was incubated at 42 °C for 1 h and then inactivated at 65 °C for 20 min. The cDNA product was stored at -20 °C for further use. A 10 μL cDNA product was utilized as the template for amplification (10 cycles) of the fragments with primers M13-FP/M13-RP. Then, the DNA sequence library was constructed using recycled fragments as the template with adaptor primers in PCR amplification reactions. The PCR products were purified by agarose gel electrophoresis with a Gel Extraction Kit (Omega, D2500-02).

treatment_protocol: The fragments of the mutated DNA library (from EP-PCR or Oligo pool) were amplified with primers M13-Plus-FP/M13-Plus-RP and the linearized pUC57-T7Q vector was amplified with primers AS-FP/AS-RP using PrimerSTAR HS DNA polymerase (Takara, R040A). The DNA fragments were loaded on the agarose-gel and the target bands were excised and recycled using a Gel Extraction Kit (Omega, D2500-02). DNA fragments and pUC57-T7Q vector were mixed with Exnase II in the reaction buffer on ice and the reaction system was incubated at 37 ℃ for 30 min (CloneExpress II One Step Cloning Kit, Vazyme, C112-02). The assembled products were purified with the RNA Clean & ConcentratorTM-5 (Zymo Research, R1016) and eluted with nuclease-free water.


title: bone marrow DC progenitors, Armstrong rep1 (RNA-seq)

value: Bone marrow

value: 7 weeks

value: female

value: 8 days post infection


title: H1 hiN D14, LLPHNterm/Nterm, Ribo-seq, rep2

value: WT


title: 231siDCAF_RPA

value: Human triple negative breast cancer cell line

value: siDCAF


title: H1 hiN D14, LLPHNterm/Nterm, Ribo-seq, rep1


title: Th9_ ACC3 KO_RNA

extract_protocol:
See method in article
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (LEXOGEN), ATAC-Seq (ACTIVE MOTIF), or NEBNext Ultra II DNA Library Prep with Sample Purification Beads (NEW ENGLAND BioLabs)  was used for library constraction according to the manufacturer's protocol.

value: ACC1 KO


title: Th9_ ACC2 KO_RNA


title: R1149, oligo pools, before selection


title: R1149, EP-PCR, after selection


title: H1 hiN D14, LLPHwt/wt, Ribo-seq, rep1


title: bone marrow DC progenitors, uninfected rep3 (RNA-seq)

value: DC progenitors

value: control

value: control (uninfected)


title: bone marrow DC progenitors, uninfected rep2 (RNA-seq)


title: Th9_ ACC1 KO_RNA


title: RAJI_MOCK_5(GEX)

first: Jean

last: Lim

address: 1468 Madison Ave

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing quality metrics were first assessed with FASTQC, and high sequencing quality was verified.
Sequencing reads were aligned to a combined human (GRCh38) and measles genome (IC323-eGFP) with the STAR aligner, and were sorted with SAMTools
Raw expression matrices were calculated with featureCounts.
Assembly: GRCh38, Genbank: MW401770
Supplementary files format and content: counts in .txt

source_name: RAJI-DCSIGNR

extract_protocol:
Cells were pelleted and resuspended in 500uL of Trizol. RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research).
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: RAJI-DCSIGNR cells were infected with measles virus (IC323-eGFP; pEMC-IC323eGFP) at an MOI=0.01 for 3 days, prior to seqeuencing.

value: RAJI-DCSIGNR

value: B Cell

value: mock


title: RAJI_MOCK_6(GEX)


title: R1116, oligo pools, after selection


title: R1149, EP-PCR, before selection


title: bone marrow DC progenitors, uninfected rep1 (RNA-seq)


title: 231siNC_Input

value: siNC


title: Th9_ Litter_3_RNA

value: Spleen

value: CD4 T cell

value: Wild type

value: Vehicle


title: RAJI_MOCK_4(GEX)


title: Th9_ Control_1_ATAC


title: R1116, oligo pools, before selection


title: bone marrow DC progenitors, Cl13 rep3 (ATAC-seq)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The sequencing reads were aligned to a mouse genome (mm10; Genome Reference Consortium GRCm38) using BWA with the following parameters: “bwa mem -M -k 32”. Low quality and unmapped reads were removed using samtools with the following parameters: “-F 0x70c -q 30”.
After the removal of duplicated reads, peaks for eachindividual replicate were identified using MACS2 with q value cutoff of 0.01.
Genome_build: Mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text files include TPM (Transcripts Per Million) values for each sample

value: Bone marrow

value: 7 weeks

value: female

value: LCMV Cl13 (chronic infection)


title: RAJI_measles_infected_3(GEX)

value: measles infected


title: bone marrow DC progenitors, Cl13 rep2 (ATAC-seq)

value: 8 days post infection


title: Th9_ Litter_1_RNA


title: RAJI_measles_infected_2(GEX)


title: bone marrow DC progenitors, Cl13 rep1 (ATAC-seq)

value: DC progenitors


title: R1116, EP-PCR, after selection


title: Th9_ TOFA_3_RNA

value: TOFA


title: bone marrow DC progenitors, Armstrong rep3 (ATAC-seq)

value: LCMV Armstrong 53b (acute infection)


title: R1116, EP-PCR, before selection


title: Th9_ Litter_2_RNA


title: RAJI_measles_infected_1(GEX)

value: RAJI-DCSIGNR


title: Th9_ TOFA_2_RNA


title: NP22077 CITEseq

description:
10x Genomics
NP22077_barcodes.tsv.gz
NP22077_features.tsv.gz
NP22077_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using cell ranger, and gene counts were computed by aligning to the human genome GRCh38 and then analyzed using R4.4.1 with Seurat toolkit package 4.2.0
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files
Library strategy: CITE-seq

value: Nasal polyp

value: B lineage cells, and other cells

value: ADT

value: TotalSeq-B0050 anti-human CD19, TotalSeq-B0154 anti-human CD27, TotalSeq-B0389 anti-human CD38, TotalSeq-B0384 anti-human IgD, TotalSeq-B0911 anti-phycoerythrin


title: bone marrow DC progenitors, Armstrong rep2 (ATAC-seq)


title: CPEB3, after selection


title: Th9_ TOFA_1_RNA

value: Spleen

value: CD4 T cell


title: NP22069 CITEseq

description:
10x Genomics
NP22069_barcodes.tsv.gz
NP22069_features.tsv.gz
NP22069_matrix.mtx.gz


title: bone marrow DC progenitors, Armstrong rep1 (ATAC-seq)


title: CPEB3, before selection


title: bone marrow DC progenitors, uninfected rep3 (ATAC-seq)

value: control

value: control (uninfected)


title: NP21010 CITEseq

description:
10x Genomics
NP21010_barcodes.tsv.gz
NP21010_features.tsv.gz
NP21010_matrix.mtx.gz


title: TN22072 CITEseq

description:
10x Genomics
TN22072_barcodes.tsv.gz
TN22072_features.tsv.gz
TN22072_matrix.mtx.gz

value: Tonsil


title: Th9_ Control_2_RNA

value: Wild type

value: Vehicle


title: bone marrow DC progenitors, uninfected rep2 (ATAC-seq)

value: Bone marrow

value: 7 weeks

value: female


title: Th9_ Control_1_RNA


title: Th9_ Control_3_RNA


title: 5TPY, after selection


title: TN22071 CITEseq

description:
10x Genomics
TN22071_barcodes.tsv.gz
TN22071_features.tsv.gz
TN22071_matrix.mtx.gz


title: 6LAS, before selection


title: bone marrow DC progenitors, uninfected rep1 (ATAC-seq)

value: DC progenitors


title: TN21055 CITEseq

description:
10x Genomics
TN21055_features.tsv.gz
TN21055_features.tsv.gz
TN21055_matrix.mtx.gz


title: 5TPY, before selection


title: Th17_TOFA_2_RNA

value: TOFA


title: mP525L_axonsJJn3

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

institute: University Medical Center Rostock

data_processing:
bcl2fastq: 2.17.1.14
alignment: Processed fastq files were aligned with the aligner GSNAP (v. 2017-11-15) to the human reference hg38 from Ensembl with the support of splice site detection which was done with the Ensembl annotation (gtf file) version 81
genecount: Fragments were assigned to Gene with featureCounts (v1.5.2) and Ensembl annotation (gtf file) version 81 was used to find gene regions
Assembly: hg38
Supplementary files format and content: bfx731.hg38.e81.txt.zip is a tab separated file with the output of featureCounts. Each columns is either describing characteristics of a gene (gene name, ensembl_id, strand, position, chromosom) or a sample. Each row list genes with the details of the gene and the counts per gene per sample.

source_name: Skin

growth_protocol: The generation of human NPCs and MNs was accomplished following the modifications protocol from Reinhardt et al. (2013) and described also in Naumann, Pall, et al., 2018(Reinhardt, Glatza et al. 2013, Naumann, Pal et al. 2018). In brief, colonies of iPSCs were collected and stem cell medium, containing 10 µM SB-431542, 1 µM Dorsomorphin, 3 µM CHIR 99021 and 0.5 µM pumorphamine (PMA), was added . After 2 days hESC medium was replaced with N2B27 consisting of the aforementioned factors and DMEM-F12/Neurobasal 50:50 with 1:200 N2 Supplement, 1:100 B27 lacking Vitamin A and 1% penicillin / streptomycin / glutamine. On day 4 150 µM ascorbic acid was added while Dorsomorphin and SB-431542 were withdrawn. 2 Days later the EBs were mechanically separated and replated on Matrigel coated dishes. For this purpose, Matrigel was diluted (1:100) in DMEM-F12 and kept on the dishes over night at room temperature. Possessing a ventralized and caudalized character the arising so called small molecule NPCs (smNPC) formed homogenous colonies during the course of further cultivation. It was necessary to split them at a ratio of 1:10–1:20 once a week using Accutase for 10 min at 37 °C. Final MN differentiation was induced by treatment with 1 µM PMA in N2B27 exclusively. After 2 days 1 µM retinoic acid (RA) was added. On day 9 another split step was performed to seed them on a desired cell culture system using microfluidic chambers. Neuronal maturation and axonal growth was stimulated with a gradient of trophic factors by adding 100 μl N2B27 with 500 μM dbcAMP to the proximal seeding site and 200 μl N2B27 with 500 μM dbcAMP, 10 ng/μl BNDF, 10 ng/μl GDNF and 100 ng/μl NGF to the distal exit site. The medium was replaced in this manner every third day. After 7 days, the first axons began spreading out at the exit site and cells were typically maintained for up to six weeks. Two-week-old microfluidic chambers with abundant outgrowth of axons were selected for RNA isolation and RNA-sequencing.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy columns including a column DNase digest. 10 ng of total RNA was used for the construction of sequencing libraries. mRNA was purified and exponentially amplified from total RNA using Takara Bio SMARTer-Seq (Takara Bio USA) according to the manufacturer’s instructions
RNA libraries for both soma and axon RNA-seq were prepared using SMARTer HV chemistry mRNA-Seq Library Prep Kit (Clontech/Takara Bio USA) and processed on an Illumina HiSeq 2500 platform according to the manufacturer’s instructions

treatment_protocol: not applicable

value: Skin

tag: iPSc source

value: Fibroblast

value: iPSC-derived spinal motor neurons

value: FUS-P525L eGFPhet (mutant)

value: Not applicable


title: NP22077 scRNAseq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using cell ranger, and gene counts were computed by aligning to the human genome GRCh38 and then analyzed using R4.4.1 with Seurat toolkit package 4.2.0
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

value: Nasal polyp

value: B lineage cells, and other cells

value: mRNA


title: mP525L_somaJJ_n3


title: 5E54, after selection


title: NP22069 scRNAseq


title: Th17_TOFA_1_RNA

value: Spleen

value: CD4 T cell


title: 5E54, before selection


title: wt_soma_JJ_n3

value: FUS-WT eGFPhet (isogenic control)


title: Th17_ Control_3_RNA

value: Wild type

value: Vehicle


title: 6LAS, after selection


title: Th17_ Control_2_RNA


title: TN22072 scRNAseq

value: Tonsil


title: MKO+DOX3

city: Jinan, Shandong

first: Lin

last: Xie

address: No.107, Wen Hua Xi Road

institute: Qilu Hospital of Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome GRCm39.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCm39.108
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: heart

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MKO mice and their littermates FLOXP mice were selected and randomly divided into four groups : FLOXP+NS, FLOXP+DOX, MKO+NS, MKO+DOX. The mice in the FLOXP+DOX and MKO+DOX groups were injected with an accumulative dose of 20 mg/kg doxorubicin (MCE, USA, cat# HY-15142) [5 mg/kg intraperitoneal (i.p.) injection at day 0, 7, 14, and 21], whereas an equivalent volume of normal saline was administered by intraperitoneal injection to the FLOXP+NS and MKO+NS groups.

value: heart

value: doxorubicin


title: MKO+DOX2


title: mP525L_axonsLM_2


title: Th17_ Control_1_RNA


title: TN22071 scRNAseq


title: Th17_TOFA_3_RNA

value: TOFA


title: TN21055 scRNAseq


title: MKO3

value: normal saline


title: wt_soma_LM_n2

value: Skin

value: Fibroblast


title: MKO+DOX1


title: wt_axons_LM_n2

value: iPSC-derived spinal motor neurons


title: mP525L_somaLM_2

value: FUS-P525L eGFPhet (mutant)

value: Not applicable


title: MKO2


title: Mouse_testis_spermatids_TENT5C_KO_19

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

description:
22_Mouse_19mutant_Testis
RNA isolated from testes obtained from Tent5c -/- mice

data_processing:
Obtained datasets were mapped to the mouse GRCm39 genome using STAR on default program settings. Read summarization was processed by featureCounts in the short-read mode (-p –O) including only features covered by at least 20% (–fracOverlapFeature 0.2). Differential expression analysis was preformed using DESeq2.
Assembly: GRCm39
Supplementary files format and content: DESeq2_table_long_spermatides_wt_and_Tent5c_mut.csv.gz: CSV file with differential expression analysis of elongated spermatides, WT vs TENT5C KO
Supplementary files format and content: DESeq2_table_round_spermatides_wt_and_Tent5c_mut.csv.gz: CSV file with differential expression analysis of round spermatides, WT vs TENT5C KO
Supplementary files format and content: DESeq2_table_round_long_spermatides_wt.csv.gz: : CSV file with differential expression analysis of WT spermatides, round vs elongated
Supplementary files format and content: DESeq2_table_testis_wt_and_Tent5c_mut.csv.gz: CSV file with differential expression analysis of whole testes sequencing, WT vs TENT5C KO

source_name: testis

extract_protocol:
For male germ cells isolation from testis, a protocol adapted from the work of Bastos et al. (2005)was used, as described in Brouze et al. (2024). Total RNA from testes and collected spermatides was isolated with TRI Reagent (Sigma) following manufacturer’s protocol. Tissues were homogenizedin TRI Reagent using glass Dounce homogenizer while collected cell pellets were suspended in TRI Reagent and lysed by pipetting. DNA traces from final RNA samples were removed using TURBO DNA free kit (Thermo Fisher Scientific) before further experiments.
rRNAs were removed from total DNA-free RNA samples with Ribo-Zero Gold rRNA-removal Kit (Illumina). rRNA-free samples were cleaned-up by 3M sodium acetate precitipation method. KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems) was used for sequencing libraries preparation, with random primers used for cDNA synthesis step. On each step of the procedure samples were cleaned-up using AMPure XP Reagent magnetic beads. Quality and fragment size distribution of the libraries was determined by electrophoresis on Agilent 2100 Bioanalyzer (Agilent Technologies Inc.).

value: testis

value: whole testes

value: Tent5c -/-


title: 20170406_WT_RS

description:
20170406_WT_RS
RNA isolated from round spermatides sorted out from testes obtained from Tent5c +/+ mice

value: round spermatids

value: WT


title: wt_axons_JJ_n3

value: FUS-WT eGFPhet (isogenic control)


title: mP525L_somaJJ_n1


title: MV-4-11 cells, 2 days, (R)-23a_200nM_rep2

first: Huahui

last: Guo

address: 190 Kaiyuan Avenue, Huangpu District, Guangzhou

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Sequence reads were trimmed for adaptor sequence using Trim Galore.
Fastp v0.21.0 was used to remove potential adapters and low-quality reads (parameter: fastp -w 10)
STAR v2.7.9a was applied to map the clean reads to both the human genome (GRCh38) and the ERCC spike-in sequences
Gene counts and the normalized expression value (TPM, transcripts per kilobase million) were computed by StringTie v2.1.4
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw gene counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: Peripheral blood

growth_protocol: MV-4-11 cells were maintained in IMDM medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was isolated from cell pallets using RNAiso Plus reagent (Takara) and 1 μg total RNA was used to generate cDNA with the PrimeScript™ RT Master Mix (Takara). RNA was quantified with NanoDrop followed by integrity evaluation via Agilent 5400 TapeStation analysis according to manufacturer's protocol.
RNA libraries for RNA-seq were prepared using mRNA-Seq library kit following manufacturer's protocol.

treatment_protocol: Cells were incubated for 2 days in the presence of DMSO or GSK032 (100 nM) or SAHA (100 nM) or combination of GSK032 and SAHA (COMBO, 100nM) or (R)-23a (100 nM or 200 nM) before performing RNA extraction.

value: Peripheral blood


title: MV-4-11 cells, 2 days, (R)-23a_200nM_rep1


title: MKO1


title: 20170406_WT_ES

description:
20170406_WT_ES
RNA isolated from long spermatides sorted out from testes obtained from Tent5c +/+ mice

value: long spermatids


title: MV-4-11 cells, 2 days, (R)-23a_100nM_rep2


title: 20170406_FamC_ES

description:
20170406_FamC_ES
RNA isolated from long spermatides sorted out from testes obtained from Tent5c -/- mice


title: wt_soma_JJ_n1


title: FLOXP+DOX3

value: heart


title: MV-4-11 cells, 2 days, (R)-23a_100nM_rep1


title: N1_WT-axons


title: FLOXP+DOX1

value: doxorubicin


title: axons_mP525L


title: MV-4-11 cells, 2 days, GSK032+SAHA_100nM_rep1


title: 20170223_WT_ES

description:
20170223_WT_ES
RNA isolated from long spermatides sorted out from testes obtained from Tent5c +/+ mice


title: 20170223_FamC_RS

description:
20170223_FamC_RS
RNA isolated from round spermatides sorted out from testes obtained from Tent5c -/- mice


title: FLOXP3


title: MV-4-11 cells, 2 days, SAHA_100nM_rep2


title: 20170223_WT_RS

description:
20170223_WT_RS
RNA isolated from round spermatides sorted out from testes obtained from Tent5c +/+ mice


title: NP21010 scRNAseq

extract_protocol:
Nasal polyp and tonsil tissues were collected at surgery, placed in PBS-Tween with protease inhibitors, and processed in RPMI with 10% fetal bovine serum and 1% penicillin-streptomycin. They were fragmented, treated with DNase I and collagenase, dissociated, strained, and RBCs were depleted before preparing single-cell suspensions for flow cytometry, sorting, or 10x genomics, with cell viability confirmed by trypan blue staining.
Library was peformed according to the manufacter's instructions (single cell 3' v2 protocol, 10xGenomics). Single cell suspensions was mixed with the master mix and loaded together with partioning oil and gel beads into the chip to generate the GEM.

value: Nasal polyp

value: B lineage cells, and other cells

value: mRNA


title: FLOXP1

value: normal saline


title: MV-4-11 cells, 2 days, SAHA_100nM_rep1


title: FLOXP2


title: 20170223_FamC_ES

description:
20170223_FamC_ES
RNA isolated from long spermatides sorted out from testes obtained from Tent5c -/- mice


title: 20170406_FamC_RS

description:
20170406_FamC_RS
RNA isolated from round spermatides sorted out from testes obtained from Tent5c -/- mice