title: Undifferentiated  P19  cell exosomal RNA sample #2


title: LGG-91

status: Public on Feb 27 2023

type: genomic

city: Gothenburg

first: Helena

last: Carén

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC beadchips using standard Illumina protocols.

scan_protocol: Standard Illumina protocol

data_processing: Raw methylation data were processed on the HumanMethylation450 BeadChip with the R package wateRmelon and normalized with dasen using the statistical software R.

label: Cy5 and Cy8

molecule: genomic DNA

organism: Homo sapiens

source_name: Lower-grade glioma_91

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted using the QIAamp DNA FFPE tissue Kit  (Qiagen) according to the manufacturer's instructions except lysis with Proteinase K was performed overnight.

treatment_protocol: Tissue specimen were formalin-fixed and paraffin-embedded.

tag: genotype

value: IDH mutant

tag: tissue brain tumor

value: Lower-grade glioma


title: NAS_4  FIB_1  STH_2 patient 27

type: SRA

city: Indianapolis

first: Nick

last: Powell

state: United States

address: 950 W. Walnut St.

country: USA

institute: IUSM

library_source: transcriptomic

data_processing:
Raw data QC was performed, including base composition quality, fragment size, mapping read count, 3’ bias, read count mapping breakdown, adapter/phiX content, heterologous organism contamination, and sex/ethnicity prediction concordance. Greater than 100 million reads were obtained per sample and reads were mapped to a reference human transcriptome. The ratio between the highest and lowest total mapped reads per sample was 4.2, indicating good read depth consistency across samples. Each sample (or library) was assessed in 4 or 5 replicates (assays). Data correlation of replicates from the same sample were checked. One replicate from all 434 assays was excluded due to low correlation. Replicates were aggregated into one measurement value per sample per gene. There were 93 unique patients in the final cohort with both phenotype information and RNA-seq data.
Assembly: reads were mapped to a human transcriptome, GRCh37
Supplementary files format and content: NAFLD_RNA_counts.csv contains comma separated values of aggregated read counts per gene per sample

molecule: total RNA

source_name: Liver

extract_protocol:
BioChain Broad Range Total RNA isolation kit
Illumina HT Truseq Stranded kit

tag: tissue

value: Liver

tag: nas

tag: fibrosis

tag: steatohep


title: LGG-89

label: Cy5 and Cy6

source_name: Lower-grade glioma_89


title: NAS_2  FIB_0  STH_0 patient 29


title: LGG-88

label: Cy5 and Cy5

source_name: Lower-grade glioma_88


title: NAS_5  FIB_1  STH_2 patient 26


title: NAS_2  FIB_1  STH_0 patient 25


title: NAS_6  FIB_1  STH_2 patient 24


title: NAS_4  FIB_3  STH_2 patient 23


title: NAS_5  FIB_1  STH_2 patient 22


title: NAS_5  FIB_1  STH_2 patient 21


title: GFP negative HSPCs, scRNAseq

city: Paris

first: Jason

last: Cosgrove

address: 11 Rue Pierre et Marie Curie, Institut Curie, Batiment Curie, RDC12

country: France

institute: INSTITUT CURIE

description:
GFP negative HSPCs, scRNAseq
figure2_cellranger.tar.gz

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

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Lin- Sca1+ cKit+ HSPCs were purified from the bone marrow of DRAG mice by fluorescence-activated cell sorting. Cells were then processed as per the manufactureres guidelines (single cell 3’ v2-v3 protocol, 10x Genomics)
Library was performed according to the manufacter’s instructions (single cell 3’ v2-v3 protocol, 10x Genomics).

value: Bone Marrow

tag: cell type

value: HSPC

value: DRAG


title: 18 months, replicate 1, scRNAseq

description:
18 months, replicate 1, scRNAseq
18_months_m1_cellranger.tar.gz


title: 18 months, replicate 2, scRNAseq

description:
18 months, replicate 2, scRNAseq
18_months_m2_cellranger.tar.gz


title: 12 months, replicate 1, scRNAseq

description:
12 months, replicate 1, scRNAseq
12_months_cellranger.tar.gz


title: GFP positive HSPCs, scRNAseq

description:
GFP positive HSPCs, scRNAseq
figure2_cellranger.tar.gz


title: NAS_5  FIB_NA  STH_2 patient 19


title: 12 months, replicate 2, scRNAseq

description:
12 months, replicate 2, scRNAseq
12_months_cellranger.tar.gz


title: 6 months, replicate 2, scRNAseq

description:
6 months, replicate 2, scRNAseq
6_months_cellranger.tar.gz


title: LGG-80

label: Cy5 and Cy3

source_name: Lower-grade glioma_80


title: NAS_0  FIB_NA  STH_NA patient 20


title: 6 months, replicate 1, scRNAseq

description:
6 months, replicate 1, scRNAseq
6_months_cellranger.tar.gz


title: LGG-83

source_name: Lower-grade glioma_83


title: LGG-86

label: Cy5 and Cy4

source_name: Lower-grade glioma_86


title: 797mouse, tail, genomic DNA

city: Bunkyo-ku

first: Hiroshi

last: Asahara

state: Tokyo

address: 1-5-45 Yushima

department: Department of Systems BioMedicine

country: Japan

institute: Institute of Science Tokyo

library_source: genomic

data_processing:
library strategy: Amplicon-seq
fastq
cutadapt
fastx tool kit
CRISPresso2
Assembly: mm10
Supplementary files format and content: alleles and alignments to the specified reference for a subsequence around the sgRNA

source_name: tail

extract_protocol:
Mouse tail tips were lysed by buffer containing 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 10 mM EDTA, 0.1% sodium dodecyl sulfate and 2U/mL Proteinase K (161-28701; Wako, Osaka, Japan) at 55°C overnight. An equal volume of phenol/chloroform/isoamyl alcohol (311-90151; Nippon Gene, Tokyo, Japan) was added to the dissolved genomic DNA solution, mixed by vortexing, centrifuged at 20,400 ×g for 15 min. The supernatant containing genomic DNA was collected and precipitated with ethanol. The precipitated genomic DNA was dissolved in distilled water.
The genomic DNA was extracted from mouse tails and amplified using PCR with primers specific for genomic region of Tyrosinase. The following primers were used: 5’-GTGCACCATCTGGGACCTCAG-3’ and 5’-GACATAGACTGAGCTGATAG-3’. The sequencing libraries were generated by using NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer’s instruction.

treatment_protocol: Tg mice were treated with 75 mg tamoxifen/kg body weight through breast milk.

value: tail

value: cross of LSL (loxP-stop-loxP)-Cas9 mice with CAG-CreER mice

tag: Sex

value: male

tag: treatment

value: tamoxifen


title: LGG-77

source_name: Lower-grade glioma_77


title: NAS_5  FIB_1  STH_2 patient 17


title: LGG-76

source_name: Lower-grade glioma_76


title: LGG-75

source_name: Lower-grade glioma_75


title: NAS_2  FIB_4  STH_1 patient 18


title: LGG-65

source_name: Lower-grade glioma_65


title: 785mouse, tail, genomic DNA


title: LGG-71

source_name: Lower-grade glioma_71


title: NAS_4  FIB_1  STH_2 patient 14


title: NAS_3  FIB_2  STH_2 patient 16


title: 779mouse, tail, genomic DNA


title: LGG-64

source_name: Lower-grade glioma_64


title: LGG-78

source_name: Lower-grade glioma_78


title: NAS_4  FIB_0  STH_0 patient 12


title: LGG-57

source_name: Lower-grade glioma_57


title: m950_02wpi

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

description:
WGS985
Frequency table NRG mice.xlsx

data_processing:
The obtained reads were analyzed using the previously published VirVarSeq analysis pipeline (Verbist 2015 Bioinformatics, PMID: 25178459) with a set fixed quality value of 30 to call variation at the codon level. This package is available at http://sourceforge.net/projects/virtools/?source=directory. All samples had minimum coverage of 4,000 reads per position over the entire ORF. Variant calling frequency tables from VirVarSeq from samples of relevance were merged and filtered in R.
Assembly: NrHV-A: MF113386, NrHV-B: ON758386, RHV-rn1: KX905133
Supplementary files format and content: Frequency table NRG mice.xlsx lists viral substitutions as observed in NRG mice. For NRG mice where variation was less, substitutions with frequency of >20% in at least one sample were included in the processed data file.
Supplementary files format and content: Frequency table Rats.xlsx lists viral substitutions as observed in rats. For rats where variation was greater, positions with a combined frequency of one or several mutations >50% in at least two rats were kept. Individual substitutions with minimal contribution (<20%) at such position were not included.

source_name: Serum

extract_protocol:
Viral RNA was extracted using TRIzol, followed by standard on-column purification procedure. The wole ORF was reverse transcribed to generate viral cDNA. Samples were pre-incubated at 65ºC for 5 min prior to the reaction. RT was carried out at 50ºC for 2 h in the presence of RNase inhibitors using 0.1 μM primer TS-O-00319 (GCTTCCTGGAGCGGGCTAGATACTG). Amplification of the complete ORF was performed using Q5 High-Fidelity Hot start DNA Polymerase (NEB), including high GC Enhancer, and the primer pair TS-O-00318 (CCAAGCCCCAATGCCGTCCGGCACCGCTGCCCTTTTCGG) and TS-O-00361 (AGGTGAAGGGGGCATCGATG). Amplified DNA was purified using DNA Clean & Concentrator (Zymo Research).
Libraries were constructed using the NebNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs), using dual indices. cDNA input: 25ng, adapter ligation, bead-based size selection (AMPure XP beads; 200-350 bp), PCR enrichment using i7/i5 index primer set. Enriched libraries were washed twice using AMPure XP beads for complete depletion of residual adapter.
Libraries were sequenced paried-end on a Illumina Miseq using 500 PE V2 kit (Illumina).

treatment_protocol: Mice and rats were infected by intrahepatic inoculation of 10 µg in vitro-transcribed viral genomic RNA.

tag: strain

value: NOD-Rag1null IL2r null (NRG)

tag: immunodeficient

value: YES

value: Serum

tag: virus

value: NrHV-B(SLIS)

tag: molecule subtype

value: viral RNA


title: LGG-62

source_name: Lower-grade glioma_62


title: m949_02wpi

description:
WGS984
Frequency table NRG mice.xlsx


title: m968_02wpi

description:
WGS980
Frequency table NRG mice.xlsx

value: NrHV-B(L)


title: LGG-66

source_name: Lower-grade glioma_66


title: LGG-61

source_name: Lower-grade glioma_61


title: LGG-60

source_name: Lower-grade glioma_60


title: NAS_5  FIB_3  STH_2 patient 13

source_name: Liver


title: NAS_3  FIB_3  STH_2 patient 10


title: m972_02wpi

description:
WGS983
Frequency table NRG mice.xlsx

value: NrHV-B(SL)


title: NAS_3  FIB_1  STH_1 patient 9


title: m970_02wpi

description:
WGS982
Frequency table NRG mice.xlsx


title: LGG-55

source_name: Lower-grade glioma_55

value: IDH mutant


title: LGG-84

source_name: Lower-grade glioma_84

value: Lower-grade glioma


title: m966_02wpi

description:
WGS979
Frequency table NRG mice.xlsx


title: LGG-63

source_name: Lower-grade glioma_63


title: m964_02wpi

description:
WGS977
Frequency table NRG mice.xlsx

value: NrHV-B(S)


title: LGG-58

source_name: Lower-grade glioma_58


title: NAS_5  FIB_4  STH_2 patient 8

value: Liver


title: m963_02wpi

description:
WGS978
Frequency table NRG mice.xlsx


title: NAS_7  FIB_1  STH_2 patient 11


title: m967_02wpi

description:
WGS981
Frequency table NRG mice.xlsx


title: NAS_2  FIB_1  STH_1 patient 6


title: LGG-51

source_name: Lower-grade glioma_51


title: LGG-43

source_name: Lower-grade glioma_43


title: NAS_3  FIB_1  STH_2 patient 7


title: m959_02wpi

description:
WGS974
Frequency table NRG mice.xlsx

value: NrHV-B


title: NAS_3  FIB_2  STH_2 patient 5


title: NAS_4  FIB_NA  STH_NA patient 4


title: NAS_4  FIB_0  STH_1 patient 3


title: m957_02wpi

description:
WGS972
Frequency table NRG mice.xlsx


title: m975_02wpi

description:
WGS971
Frequency table NRG mice.xlsx

value: NrHV-A


title: m974_02wpi

description:
WGS970
Frequency table NRG mice.xlsx


title: m958_02wpi

description:
WGS973
Frequency table NRG mice.xlsx


title: m973_02wpi

description:
WGS969
Frequency table NRG mice.xlsx


title: Rat hippocampus - sdG27_fst_control_rep_3

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

country: Russia

institute: National Research Center «Kurchatov Institute»

data_processing:
Trimming was perfromed using Adapter Removal v2, using defaul parameters
Alignment on Rnor6.0 genome assembly  was performed using STAR and RSEM
SVA batch correction was applied to different batches to compensate for batch effects. Repeated sequences of sdG10_fst_20_m, sdG21_fst_control and sdG27_fst_control were combined due to lower number of reads obtained.
differential expression was obtained using limma voom protocol, using TMM and CPM normalizations
Genome_build: Rnor6.0
Supplementary_files_format_and_content: Processed count files  were obtained using RSEM.

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
Total RNA isolation was conducted using a Direct-Zol RNA Mini-Prep Kit (ZymoResearch) according to the manufacturer's recommendations. The concentration of total RNA isolated was measured using a Quant-iT RNA BR Assay Kit and a Qubit fluorimeter (Invitrogen). RNA quality was monitored using an Experion automated electrophoresis system (Bio-Rad Laboratories). The RNA quality index was higher than 8.5 in all samples.
Poly-a fraction of RNA was extracted from total RNA for RNA-seq. Sequencing libraries were prepared using NEBNext® mRNA Library Perp Reagent Set (NEB, USA). Sequencing was performed using HiSeq1500 (Illumina, USA), obtaining no less then 15 mln. reads of 50 length per library.

treatment_protocol: FST 20 m group were decapitated 20 minutes after FST presentation. FST 24 h group were decapitated 24 hours after FST presentation. Control group did not undergo FST.

value: hippocampus

value: Sprague Dawley

tag: batch

value: Control


title: LGG-42

source_name: Lower-grade glioma_42


title: NAS_6  FIB_1  STH_2 patient 2


title: SM Patient 073

city: Solna

first: Joakim

middle: S

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

institute: Karolinska Institutet

description:
10X_021_073
Filtered counts matrix from cellranger count

data_processing:
Cellranger Pipeline 6.0.1 (cellranger mkfastq)
Cellranger Pipeline 6.0.1 (cellranger count)
Combined file contains batch corrected (Harmony) counts merging the 3 datasets. Please refer to article methods for specfics
Fully processed file (Combined_10X_filematrix.h5ad) is a combined anndata object containing batch-corrected and merged samples (036, 073, and 089), annotated
Assembly: GRCh38
Supplementary files format and content: 10X Genomics .h5 and anndata h5ad files

molecule: polyA RNA

source_name: Human Bone Marrow

extract_protocol:
Further processing of MNC population (GEM generation, barcoding, cleanup, cDNA amplification) were done using reagents and protocol from 10x Genomics Chromium Single Cell 3' Reagent kit v3
Library construction was done using protocol and reagents from 10x Genomics Chromium Single Cell 3' Reagent kit v3

value: Human Bone Marrow

tag: cell population

value: Mononuclear cells (MNCs) from human bone marrow enriched using Ficoll separation mixed with FACS-isolated CD117+ FCɛR1+ cells (mast cells)

tag: disease

value: Systemic Mastocytosis


title: LGG-52

source_name: Lower-grade glioma_52


title: LGG-50

source_name: Lower-grade glioma_50


title: NAS_3  FIB_0  STH_1 patient 1


title: SM Patient 036

description:
10X_021_036
Filtered counts matrix from cellranger count


title: 4C_MNX1vp

city: Heidelberg

first: Christoph

last: Plass

address: Im Neueneimer Feld 280

department: Division of Cancer Epigenomics

country: Germany

institute: DKFZ (German Cancer Research Center)

description: 4C-seq using using a 5’ part of MNX1 as viewpoint (chr7:156800248-156802091;hg19)

data_processing:
4C-fastq single read data was processed using the pipe4C platform as described (PMID: 31351925).
Reads were aligned using bowtie2, version 2.3.5.1. (PMID: 22388286) and samtools 1.5 (https://github.com/samtools/samtools/releases/tag/1.5).
Final processing was done under R3.6.2 using the pipe4C script with default parameters. Reads mapped to the 4C fragment end library were normalized according to the default normalizeFactor 1000000. 3′-ends of sequences were trimmed using a sliding window (size 21) as soon as 2 out of 5 nucleotides had a quality encoding less than the default Q-score. The quality cutoff and trimlength were 0, the minimum amount of reads was 1000. NonBlind and mapUnique were set to FALSE.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig (bw)
Library strategy: 4C-seq

growth_protocol: GDM-1 cells were grown in RPMI 1640 supplemented with 20% fetal bovine serum.

extract_protocol:
Circular chromosome conformation capture (4C) was done essentially as described (PMID: 22961246) using two million cells and two rounds of restriction digestion with either BglII and NlaIII, or with NlaIII and Csp6I, depending on the viewpoint, each time followed by ligation.
First PCR 98°C for 30 sec, 10 cycles with 98°C for 15 sec, 61°C, 60°C or 54°C depending on the viewpoint for 20 sec with 0.5°C touch-down per cycle, 72°C for 2 min, then 30 or 25 cycles with 98°C for 15 sec, 56°C, 55°C or 49°C, depending on the viewpoint  for 20 sec, 72°C for 2 min, finally followed by 72°C for 1 min. Second PCR with 95°C, 3 min (initial melting) and 95°C, 20 sec, 62°C, 15 sec, 72°C, 40 sec (8 cycles).
4C sequencing libraries were generated in two PCR steps. In the first step, the  second ligation products, inverse primers and Q5 high fidelity enzyme were used. Libraries were generated in the second step with DNA from the first step essentially according to (PMID: 29224141) under real-time conditions.

tag: cell line

value: leukemic


title: Rat hippocampus - sdG10_fst_20_m_rep_3

value: forced swimming test - 20 min after


title: Rat hippocampus - sdG27_fst_control_rep_2


title: Rat hippocampus - sdG21_fst_control_rep_2


title: SM Patient 089

description:
10X_021_089
Filtered counts matrix from cellranger count


title: Rat hippocampus - sdG21_fst_control_rep_3


title: LGG-37

source_name: Lower-grade glioma_37

tag: genotype


title: Rat hippocampus - sdG27_fst_control_rep_1

value: Batch 3


title: Rat hippocampus - sdG10_fst_20_m_rep_2


title: GDM1_ATACseq

data_processing:
TrimGalore v. 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) was deployed together with Cutadapt v. 1.14 (https://cutadapt.readthedocs.io/en/stable/) using the non-default parameters “--paired”, “--nextera”, “--length_1 35”, and “--length_2 35” to perform adapter and quality trimming.
Bowtie2 v. 2.2.6 (PMID: 22388286) was used with the “--very-sensitive” flag and a maximum insertion length of 2500 bp to map trimmed reads against the GRCh37/hg19 reference genome.
Aligned reads belonging to the same lane-multiplexed library were combined using SAMtools merge v. 1.5 (https://github.com/samtools/samtools/releases/tag/1.5).  PCR duplicates were removed by means of Picard MarkDuplicates v. 2.17.4 (https://broadinstitute.github.io/picard/).
Discordant mappings and alignments with a Phred score below 20 were removed using SAMtools view.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig (bw)

extract_protocol:
Cell permeabilization of native cells and tagmentation reaction with a Tn5 transposome for "Assay for transposase-accessible chromatin by sequencing (ATAC-seq)" according to Corces et al. (PMID: 28846090). Tagmented DNA was purified with HighPrep beads (Biozym) after guanidinium-mediated inactivation of the transposome according to Weichenhan et al. (PMID: 29224141).
Libraries were prepared according to Weichenhan et al. (PMID: 29224141). Briefly, tagmented DNA was amplified by PCR under real-time conditions using a universal Illumina forward and a barcoded reverse primer and the NEBNext High Fidelity 2x PCR Master-Mix (NEB), and amplfication was monitored by inspecting real time the amplification curves. DNA was HighPrep bead-purified, Qubit (Invitrogen) quantitated and sized by TapeStation (Agilent) profiling.


title: UPMD1

type: RNA

city: Genoa

first: Adriana

middle: Agnese

last: Amaro

address: Largo Rosanna Benzi 10

department: Molecular Pathology

country: Italy

institute: IRCCS Ospedale Policlinico SAN MARTINO - IST - NATIONAL CANCER RESEARCH INSTITUTE

description: Gene expression data from uveal melanoma cells untreated

hyb_protocol: Following IVT , the RNA biotinylated were hybridized for 16 hr at 45°C on Affymetrix GeneChip™ HG-U133+ PM Array Strip in GeneAtlas Hybridization Station. GeneChips were washed and stained using  GeneAtlas™ Hybridization, Wash, and Stain Kit for 3' IVT Arrays.

scan_protocol: GeneChip were finally scanned using GeneAtlas Scanner.

data_processing: Affymetrix® Transcriptome Analysis Console (TAC) Software.  Data were preprocessed following the RMA procedure using quantile normalization

label: biotin

label_protocol: 500 ng of total of RNA was biotin labeled using the 3′ IVT Express Kit (Affymetrix) for array strips

growth_protocol: uveal melanoma cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 100 U/ml penicillin/streptomycin

extract_protocol: Total RNA was extracted using Rneasy Plus mini kit (Qiagen) following the manufacturers protocol. RNA quantity and quality were determined using a Nanodrop-1000 spectrophotometer (Nanodrop Technology) and Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment

value: uveal melanoma cell

value: GNA11 mutated cells


title: LGG-35

source_name: Lower-grade glioma_35

value: IDH mutant

tag: tissue brain tumor


title: Rat hippocampus - sdG21_fst_control_rep_1

tag: tissue


title: LGG-38

source_name: Lower-grade glioma_38

value: Lower-grade glioma


title: UPMD2


title: Rat hippocampus - sdG10_fst_20_m_rep_1


title: LGG-30

source_name: Lower-grade glioma_30


title: LGG-26

source_name: Lower-grade glioma_26


title: LGG-34

source_name: Lower-grade glioma_34


title: LGG-29

source_name: Lower-grade glioma_29


title: Rat hippocampus - sdG7_fst_20_m

value: Batch 2


title: UPMM2

value: GNAQ mutated cells


title: LGG-33

source_name: Lower-grade glioma_33


title: LGG-25

source_name: Lower-grade glioma_25


title: LGG-21

source_name: Lower-grade glioma_21


title: UPMM3


title: MEL290

value: wild type for Galfa proteins cells


title: LGG-27

source_name: Lower-grade glioma_27


title: Rat hippocampus - sdG25_fst_control


title: Rat hippocampus - sdG17_fst_24_h

value: forced swimming test - 24 hrs after


title: LGG-19

source_name: Lower-grade glioma_19


title: NAS_5  FIB_3  STH_2 patient 15

source_name: Liver

value: Liver

tag: nas


title: UPMM1


title: Rat hippocampus - sdG5_fst_20_m

source_name: hippocampus

value: hippocampus

value: Sprague Dawley


title: LGG-22

source_name: Lower-grade glioma_22


title: Rat hippocampus - sdG15_fst_24_h


title: LGG-36

source_name: Lower-grade glioma_36


title: Rat hippocampus - sdG14_fst_24_h


title: Sperm, FCD339C3

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

data_processing:
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome and get methylation calls with bsmap-2.6
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing information for each sample: chrBase, chr, base, strand, coverage, FreqC (methylation), FreqT

source_name: Sperm

extract_protocol:
Frozen sperm/isolated spermatogonia were thawed on ice and genomic DNA isolation was performed using Qiagen DNeasy Blood & Tissue Kits (Qiagen, Germany) according to the manufacturer’s guide, with modifications. For sperm samples, sperm was incubated overnight at 37oC in a buffer containing EDTA, Tris , sarkosyl , dithiothreitol (DTT) and proteinase K (Invitrogen, Canada). The following day, Buffer AL was added to the buffer, and incubated at 70oC for 10min and the manufacturer’s guide was continued.
Reduced representation bisulfite sequencing (RRBS) libraries were prepared according to previously published protocols using gel-free technique (Boyle, P. Genome Biol., 2012).  Briefly, ~500ng of  DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing.  Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplification.

treatment_protocol: Eight-week old F0 BALB/c females  were randomly sorted onto one of four folate defined diets (Harlan Teklad, USA) at least four weeks before mating: folic acid control (FCD; 2mg/kg diet) with the recommended daily intake of folic acid (35), 7-fold folic acid deficient (7FD, 0.3mg/kg diet), 10-fold folic acid supplemented (10FS, 20mg/kg diet) or 20-fold folic acid supplemented (20FS, 40mg/kg diet). The diets were supplemented with 1% succinylsulfathiazole to inhibit de novo synthesis of folate by gut flora. Following four weeks of maintenance on these defined diets, females were mated with ten-week old BALB/c males fed with regular 18% protein rodent chow diets (Harlen Teklad, USA). The F0 females were maintained on their respective diets throughout mating, gestation and lactation. Resultant F1 male pups were weaned at postnatal day (PND) 20 onto the same maternal folate defined diets, respectively. At 18 weeks of age, F1 males were mated with 10-week old BALB/c females fed regular mouse chow and were maintained on this diet throughout mating, gestation and lactation. Subsequent F2 male pups were weaned and maintained on regular rodent chow until 18 weeks of age, then were mated with 10-week old female BALB/c fed with regular rodent chow to produce unexposed F3 litters. Upon successful generation of the following generation of males, F1, F2 and F3 male mice were sacrificed at PND ~200.  Mature spermatozoa from paired cauda epididymides were collected  and kept frozen at -80oC until use.  Separate eight-week-old BALB/c F0 females were fed similar folic acid defined diets from 4 weeks prior to breeding with Oct4-GFP +/- regular rodent chow fed BALB/c males. Females were maintained on diets throughout gestation and lactation. F1 Oct4-GFP +/- males were sacrificed at PND 6 for spermatogonia isolation via fluorescent activated cell sorting and were kept frozen at -80oC until use.

value: Sperm

value: BALB/c

tag: diet

value: FCD

tag: generation


title: Rat hippocampus - sdG12_fst_20_m


title: LGG-12

source_name: Lower-grade glioma_12


title: Rat hippocampus - Slo_G6_II_fst_20_m

value: Batch 1


title: Sperm, FCD322C4

tag: cell type


title: LGG-11

source_name: Lower-grade glioma_11


title: MEL285


title: LGG-8

source_name: Lower-grade glioma_8


title: OMM1


title: 293T_10_hMCIDAS

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

hyb_protocol: cDNA was hybridized to the Genechip Primeview Human Array (Affymetrix, catalog # 901837) for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G using default parameters. Affymetrix GeneChip Command Console software (AGCC) was used to acquire GeneChip images and generate .CEL files for analysis.

data_processing: Arrays were processed in Bioconductor, using RMA background correction, quantile normalization and RMA summarization.

source_name: FLAG-MCIDAS

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2). Amplification was performed for 16 cycles. 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: HEK293T cells (Agilent) were grown in DMEM with 10% FBS and Pen/strep.

extract_protocol: RNA was extracted using Trizol and purified using the PureLink RNA mini kit.

treatment_protocol: Cells were transfected with the indicated vector using PEI.

tag: genotype/variation

value: hMCIDAS

tag: scan date

tag: scan time

tag: scan batch


title: Sperm, 7FD337CE4

tag: strain


title: Sperm, FCD319C


title: Sperm, FCD334AF1


title: Rat hippocampus - Slo_G24_II_fst_control

tag: treatment

value: Control


title: 293T_9_hMCIDAS


title: Sperm, 7FD314A


title: LGG-7

source_name: Lower-grade glioma_7


title: Rat hippocampus - Slo_G22_II_fst_control

tag: batch


title: Sperm, 7FD313B1


title: LGG-5

source_name: Lower-grade glioma_5


title: Rat hippocampus - Slo_G19_II_fst_24_h


title: 293T_6_hGemc1


title: 293T_5_hGemc1


title: 293T_4_FLAG-empty

source_name: FLAG vector control

value: FLAG-empty


title: Rat hippocampus - Slo_G18_II_fst_24_h


title: Sperm, 20FS346BE2


title: 293T_3_FLAG-empty


title: LGG-4

source_name: Lower-grade glioma_4


title: Control, replicate 2, scRNAseq

city: Beijing

first: Yuanyuan

last: Liu

address: Medical School of Chinese People's Liberation Army, 100039 Beijing, China.

country: China

description: 10x Genomics

library_source: transcriptomic single cell

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

source_name: 8th section of the small intestine

extract_protocol:
Sterile PBS on ice was used to preserve skin tissue samples immediately after dissection. The samples were subsequently cleaned by PBS twice and cut into pieces sized 2-4 mm. Then tissues were processed following the instructions of the dissociation kit (Multi Tissue Dissociation Kit 1, Miltenyi Biotec, 130-110-201) to complete the dissociation. The single-cell suspension was passed through 70 and 40 μm cell strainers and centrifuged for 10 min, 500 × g at 4 °C. The red blood cell (RBC) lysis solution (130-094-183, Miltenyi Biotec) and Dead Cell Removal Kit (130-090-10, MiltenyiBiotec)were successively added to remove erythrocytes or dead cells. The process resulted in highly viable, typically ≥85%, single-cell suspensions. For immediate single-cell capture, the cells were resuspended in 0.04% Ultra-Pure BSA in PBS (Thermo Fisher Scientific) and concentration was adjusted to ≥106 cells/ml.
The utilization of microdroplets in conjunction with barcoded primer beads enabled the capture of individual cells through the implementation of a droplet-based ultra-high throughput system for parallel gene expression detection. The Chromium Next GEM Single Cell 3ʹ Kit v3.1, developed by 10x Genomics (Part Number 1000268), was employed in the creation of gene expression (GEX) libraries. The generation of gel bead-in-emulsions, as well as the reverse transcription (RT) of the single-cell suspensions, was accomplished through the utilization of the 10x Genomics Single cell chip (Chromium Next GEM Chip G Single Cell Kit, Part Number 1000120, and an additional Dual Index Kit TT Set A, Part Number 1000215) run on the Chromium Controller (Part Number 110211) developed by 10x Genomics. The generated cDNA was amplified in order to produce GEX libraries after the RT step, subsequently quantified through the use of Qubit 3.0 fluorometer (Life Technologies, Part Number 15387293) and assessed through the utilization of HS DNA chips (Agilent Technologies, Part Number 5067-4627) in combination with the 2100 Bioanalyzer (Agilent Technologies, Part Number G2939BA). The Novaseq 6000, developed by Illumina, was employed for massively parallel sequencing.

value: Skin cells

value: 8th section of the small intestine

tag: age

value: 6 weeks old


title: Control, replicate 1, scRNAseq

institute: Medical School of Chinese People's Liberation Army

description: 10x Genomics


title: hucMSC-Exo, replicate 2, scRNAseq

description: 10x Genomics

source_name: Distal colon

value: Distal colon


title: Sperm, 20FS341AE1


title: Sperm, 7FD308G1


title: Rat hippocampus - Slo_G13_II_fst_24_h


title: LGG-2

source_name: Lower-grade glioma_2

value: IDH mutant

value: Lower-grade glioma


title: LGG-3

source_name: Lower-grade glioma_3


title: hucMSC-Exo, replicate 1, scRNAseq

description: 10x Genomics


title: Rat hippocampus - Slo_G2_II_fst_20_m

value: forced swimming test - 20 min after


title: Rat hippocampus - Slo_G1_II_fst_20_m


title: Ccr2-/- laser ADT

city: Chicago

first: Jeremy

middle: Arin

last: Lavine

state: Illinois

address: McGaw M343

department: Ophthalmology

institute: Northwestern University

library_source: other

data_processing:
Data was demultiplexed and counted using Cell Ranger version 6.0.0
Cell Ranger output was analyzed using Seurat version 4.1.1

molecule: protein

source_name: eye

extract_protocol: 10X Genomics Kit 3' v3, 10X genomics Library Construction kit

value: eye

tag: library type

value: ADT

value: laser


title: Wiltype laser ADT

value: C57BL/6J Wildtype


title: Sperm, 20FS305B

value: Sperm

value: BALB/c


title: Sperm, 20FS320B1


title: Rat hippocampus - Slo_G28_II_fst_control

source_name: hippocampus

value: hippocampus

value: Sprague Dawley

value: Batch 1


title: Sperm, 20FS329AG1


title: Sperm, 10FS350AC1


title: Ccr2-/- no laser ADT

value: sham


title: LGG-13

source_name: Lower-grade glioma_13


title: BAT, WT, Room temperature, rep2

city: Suwon

first: Eun-Ji

last: Park

address: 2066 Seobu-ro

country: South Korea

institute: Sungkyunkwan University

data_processing:
Transcriptomic sequencing was performed on a Novaseq platform. An initial sequence-level quality assessment was performed using FastQC. RNA-Seq reads were then mapped to the human mm10 reference genome using Tophat (v2.0.13). Assembly, quantification and differential expression analysis were performed using Cuffdiff (v2.2.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values

source_name: Brown adipose tissue

extract_protocol:
Total RNA was isolated from adipose tissues using QIAzol Lysis Reagent as manufacturer's instruction.  5ug of total RNA was used for the construction of sequencing libraries.
RNA-Seq libraries were prepared with a TruSeq Stranded mRNA Library Prep kit (Illumina) using purified RNAs isolated from BAT of Ssu72 WT and aKO mice

value: Brown adipose tissue

tag: Sex

value: male

value: ssu72 WT


title: BAT, SSU72 aKO, Room temperature, rep1

tag: genotype

value: ssu72 aKO


title: BAT, SSU72 aKO, Room temperature, rep2


title: BAT, SSU72 aKO, Room temperature, rep3


title: LGG-17

source_name: Lower-grade glioma_17

value: IDH mutant

tag: tissue brain tumor


title: BAT, WT, Room temperature, rep3

tag: tissue


title: U1 AMO-repeat 1 wdr33iCLIP-seq

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

institute: sysu

data_processing:
reads were mapped to human genome (hg19) allowing up to two  mismatches using Bowtie2 with the settings ‘bowtie2 -p 28 -N 1 -k 1’. The 5ʹ  end of the read maps was considered the crosslinking site.
The bioinformatics analysis for reads filtering and clustering were performed essentially as previously described (Lackford et al., 2014; Yao et al., 2012.)
Genome_build: hg19
Supplementary_files_format_and_content: Read coverage tracks are generated in the tdf format from the genome-mapped bam file.

source_name: Hela cells

growth_protocol: Hela cells were grown in DMEM +10% FBS medium

extract_protocol:
RNAs were purified with antibody targeting wdr33(Bethyl)
wdr33iCLIP-seq(s) were carried out using the standard iCLIP-seq protocol (König J et al. 2010)
iCLIP-seq

treatment_protocol: Control and U1 AMO were transfected into HeLa cells,after 12 hour.

value: U1 AMO


title: control AMO-repeat 2 wdr33iCLIP-seq

value: control


title: Widltype no laser ADT

value: eye


title: BAT, WT, Room temperature, rep1


title: Sperm, 10FS336F1

source_name: Sperm


title: control AMO-repeat 1 wdr33iCLIP-seq


title: wdr33 ChIP in U1 AMO sample repeat 2

data_processing:
ChIP-seq data  processing and analysis were performed according to the ENCODE ChIP-seq pipeline (https://www.encodeproject.org/data-standards/chip-seq/)
Genome_build: hg38
Supplementary_files_format_and_content: Read coverage tracks are generated in the BigWig (bw) format from the genome-mapped bam file.

source_name: wdr33 ChIP in U1 AMO sample repeat 2

extract_protocol:
ChIP-seqs were carried out using standard protocol
library were prepared using ChIP-seq preparation kit (Vazyme)

treatment_protocol: control and U1 AMOs were transfected into HeLa cells.

tag: cell line

value: HeLa

tag: transfection


title: CCN3 injected ventricles 3

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Alignment and gene-level quantification: Salmon version 1.4.0 was used to quasi-map reads to the transcriptome and quantify the abundance of each transcript. The transcriptome was first indexed using the decoy-aware method in Salmon with the entire genome file “GCF_000001635.27_GRCm39_genomic.fna.gz” as the decoy sequence. Then quasi-mapping was performed to map reads to transcriptome with additional arguments --seqBias and --gcBias to correct sequence-specific and GC content biases, --numBootstraps=30 to compute bootstrap transcript abundance estimates and --validateMappings to help improve the accuracy of mappings. Gene-level counts were then estimated based on transcript-level counts using the “bias corrected counts without an offset” method from the tximport package.
Normalization: When comparing expression levels, the numbers of reads per gene need to be normalized not only because of the differences in total number of reads, but because there could be differences in RNA composition such that the total number of reads would not be expected to be the same. The TMM (trimmed mean of M values) normalization in the edgeR package uses the assumption of most genes do not change to calculate a normalization factor for each sample to adjust for such biases in RNA composition. In this dataset, TMM normalization factors fluctuates between 0.94 and 1.03. A TMM value below 1 means the total library size is larger than it should be, and a TMM value above 1 means the total libary size is smaller than it should be. Again, there is no obvious consistent difference between treatments and they are all very close to 1.
Filter: While the NCBI GRCm39 Annotation 109 gene models have a total of 39,253 genes, many of these might not have detectable expression in these samples. Therefore, we set the detection threshold at 0.5 cpm (counts per million) in at least 3 sample (based on smallest replicate size), which resulted in 23,344 genes being filtered out, leaving 15,909 genes to be analyzed for differential expression that contain 99.91% of the reads. After filtering, TMM normalization was performed again and normalized log2-based count per million values (logCPM) were calculated using edgeR’s cpm() function with prior.count = 2 to help stabilize fold-changes of extremely low expression genes.
Remove Unwanted Variation Analysis: RUV factor of 2 was used to avoid over-fitting the model
Assembly: GCF_000001635.27_GRCm39_rna.fna.gz from NCBI
Supplementary files format and content: Comma seperated value (.csv) files of gene expression and counts per million
Supplementary files format and content: .html file of clustering after RUV removal

source_name: Cardiac Ventricle

extract_protocol:
Left ventricles were collected at 4 days post injury. Trizol phenol/chloroform extractions were utilized to attain total RNA.
The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche) . Read 1 aligns to the ANTISENSE strand.
The libraries were pooled; quantitated by qPCR and sequenced on one SP lane for 101 cycles from one end of the fragments on a NovaSeq 6000 with V1.5 sequencing kits. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).

treatment_protocol: Recombinant human CCN3 at a concentration of 6 µg/kg or PBS was administered by intraperitoneal injection daily for four days following surgical MI.

value: Cardiac Ventricle


title: CCN3 injected ventricles 2


title: Sperm, 10FS328BC

tag: diet

tag: generation


title: Ccr2-/- laser GEX

tag: cell type

value: mRNA

value: laser


title: Ccr2-/- no laser GEX


title: wdr33 ChIP in U1 AMO sample repeat 1

source_name: wdr33 ChIP in U1 AMO sample repeat 1


title: Widltype no laser GEX

value: C57BL/6J Wildtype


title: Sperm, 10FS343B1

value: Sperm

value: BALB/c


title: Sperm, 10FS317E2


title: wdr33 ChIP in control sample repeat 2

source_name: wdr33 ChIP in control sample repeat 2


title: Wiltype laser GEX


title: PBS injected control ventricles 3

value: PBS


title: Sperm, FCD245B

value: FCD


title: wdr33 ChIP in control sample repeat 1

source_name: wdr33 ChIP in control sample repeat 1


title: CCN3 injected ventricles 1


title: Young7

city: Shijiazhuang

first: Mengnan

last: Li

state: Hebei

address: No.238 Tianshan Street

institute: National Key Laboratory of Collateral Disease Research and Innovative Chinese Medicine

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adapter contamination, low quality bases and undetermined bases.
Reads that passed quality control were mapped to reference genome using Bismark
After alignment, reads were further deduplicated using samtool. For each cytosine site (or guanine corresponding to a cytosine on the opposite strand) in the reference genome sequence, the DNA methylation level was determined by the ratio of the number of reads supporting C (methylated) to that of total reads (methylated and unmethylated) using per scripts in house and MethPipe
Assembly: GRCm38.101
Supplementary files format and content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: Liver

extract_protocol:
Total DNA was extracted using QIAamp Fast DNA Tissue Kit (Qiagen, Dusseldorf, Germany) following the manufacturer's procedure. The quantity of DNA was measured by reading A260/280 ratios by spectrophotometer. When A260/280 ratios located range 1.8 to 2.0, DNA was available.
Whole genome bisulfite sequencing libraries were constructed using the Acegen Bisulfite-Seq Library Prep Kit (Acegen, Cat. No. AG0311) according to the manufacturer’s protocol. Briefly, 1 μg of genomic DNA spiked with 1 ng unmethylated Lambda DNA was fragmented by sonication to a mean size of approximately 200-500 bp, then end-repaired, 5'-phosphorylated, 3'-dA-tailed and ligated to 5-methylcytosine-modiﬁed adapters. After bisulﬁte treatment, the DNA was ampliﬁed with 10 cycles of PCR using Illumina 8-bp dual index primers.

value: Liver

value: without any treatment


title: PBS injected control ventricles 2


title: fip1 ChIP in U1 AMO sample repeat 2

source_name: fip1 ChIP in U1 AMO sample repeat 2


title: U1 AMO-repeat 2 wdr33iCLIP-seq


title: Sperm, FCD239C


title: Sperm, FCD234CF


title: Young6

value: male


title: fip1 ChIP in U1 AMO sample repeat 1

source_name: fip1 ChIP in U1 AMO sample repeat 1


title: Sperm, FCD223A


title: PBS injected control ventricles 1


title: NK cells, WT, rabbit IgG antibody

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
QC using FastQC
Alignment to mm10 using Bowtie2
Filtering and conversion using Samtools, Bedtools
Peak calling using SEACR
Assembly: mm10
Supplementary files format and content: BigWig files containing normalized peaks from CUT&Tag
Library strategy: CUT&Tag

source_name: spleen

extract_protocol:
Nuclei were isolated with cold nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine in 1X protease inhibitor buffer) and incubated with activated  concanavalin A (ConA) coated magnetic beads (EpiCypher) in PCR strip tubes at room temperature for 10 minutes. A 1:100 dilution of primary antibody in antibody buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1X Protease inhibitor cocktail; 0.05% Digitonin, 2 mM EDTA, 0.1% BSA) was added and nuclei were incubated with primary antibodies overnight at 4C. The next day, the strip tubes were incubated on a magnetic tube holder and supernatants were discarded. An appropriate secondary antibody was added diluted 1:100 in Dig-Wash (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1X Protease inhibitor cocktail; 0.05% Digitonin) and nuclei were incubated for 1 hour at room temperature. Nuclei were washed four times in Dig-Wash and then incubated with a 1:20 dilution of pAG-Tn5 adapter complex (EpiCypher) in Dig-300 buffer (1x Protease inhibitor cocktail, 20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine) for 1 hour at room temperature. To stop tagmentation, 25 uL Dig-300 buffer with 10 uL 1 M MgCl, 7.5 uL 0.5 M EDTA, 2.5 uL 10% SDS, and 5 uL 10 mg/mL proteinase K was added to each reaction and incubated at 55 degrees for 1 hour. DNA was extracted by phenol:chloroform:isoamyl alcohol separation. DNA was barcoded and amplified using the following conditions: a PCR mix of 25 uL NEBNext 2X mix, 2 uL each of barcoded forward and reverse 10 uM primers, and 21 uL of extracted DNA was amplified at: 58C for 5 min, 72C for 5 min, 98C for 45 sec, 16x 98C for 15 sec followed by 63C for 10 sec, 72C for 1 min. Amplified DNA libraries were purified by adding 1.3x volume of KAPA pure SPRI beads (Roche) to each sample and incubated for 10 minutes at room temperature. Samples were placed on a magned and unbound liquid was removed. Beads were rinsed twice with 80% ethanol, and DNA was eluted with 25 uL TE buffer. All individually i7-barcoded libraries were mixed at equal molar proportions for sequencing on an Illumina NovaSeq 6000 sequencer.
Libraries were constructed by tagmentation through pAG-Tn5 transposase and PCR amplification and barcoding.

value: spleen

value: isolated NK cells

value: WT


title: Sperm, 7FD237CF


title: Sperm, FCD202B


title: Young4


title: Young5


title: NK cells, UTX NKD, biol rep 1

value: UTX NKD


title: fip1 ChIP in control sample repeat 2

source_name: fip1 ChIP in control sample repeat 2

value: control


title: fip1 ChIP in control sample repeat 1

source_name: fip1 ChIP in control sample repeat 1

value: HeLa


title: NK cells, UTX NKD, biol rep 2


title: Sperm, 7FD226F


title: Young3


title: cpsf30 ChIP in U1 AMO sample repeat 2

source_name: cpsf30 ChIP in U1 AMO sample repeat 2

value: U1 AMO


title: Young2


title: cpsf30 ChIP in U1 AMO sample repeat 1

source_name: cpsf30 ChIP in U1 AMO sample repeat 1


title: Young1


title: cpsf30 ChIP in control sample repeat 2

source_name: cpsf30 ChIP in control sample repeat 2


title: NK cells, WT, biol rep 2


title: NK cells, WT, biol rep 3


title: Sperm, 7FD214A


title: NK cells, WT, biol rep 1


title: BZH7

value: treated with BZBS suspension daily (dissolved in 0.5% sodium carboxymethylcellulose) by oral gavage (2g/kg/d)


title: BZH6


title: Sperm, 7FD208G


title: cpsf160 ChIP in U1 AMO sample repeat 2

source_name: cpsf160 ChIP in U1 AMO sample repeat 2


title: BZH5


title: cpsf30 ChIP in control sample repeat 1

source_name: cpsf30 ChIP in control sample repeat 1


title: Sperm, 20FS246BE

source_name: Sperm


title: Sperm, 20FS248BE


title: Sperm, FCD345B1


title: MLL-ENL ∆YEATS (aa372-559) 1

city: Ann Arbor

first: Andrew

last: Muntean

state: MI

address: 1150 W. Medical Center Dr.

department: Department of Pathology

institute: University of Michigan

description: mRNA (polyA-enriched)

data_processing:
The reads were trimmed using Cutadapt v2.3, and quality control of the data was evaluated using FastQC v0.11.8 and Fastq Screen.
Reads were mapped to the reference genome GRCm38/mm10 (ENSEMBL) using STAR v2.7.8a.
Gene count estimates were generated using RSEM v1.3.3, and alignment options followed ENCODE standards for RNA-seq.
Assembly: GRCm38/mm10
Supplementary files format and content: single tab-delimited text file including RPKM values for each sample
Supplementary files format and content: single tab-delimited text file including annotated expected gene count for each sample

source_name: Lineage- bone marrow

growth_protocol: Both MLL-ENL and MLL-ENL ∆YEATS cells were maintained in IMEM supplemented with 15% stem cemm fetal bovine serum (scFBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using Lexogen Poly(A) Selection Kit and Swift RNA Library Kit per manufacturer's instructions

value: Lineage- bone marrow

value: MLL-ENL {delta}YEATS (aa372-559)

value: Transformed HSPCs

value: MLL-ENL with ENL aa(372-559)


title: MLL-ENL 2

description: mRNA (polyA-enriched)

value: MLL-ENL

value: MLL-ENL fusion


title: cpsf160 ChIP in U1 AMO sample repeat 1

source_name: cpsf160 ChIP in U1 AMO sample repeat 1


title: Sperm, 20FS241AE

value: Sperm

value: BALB/c


title: BZH4

value: Liver

value: male


title: Sperm, 20FS229CE


title: cpsf160 ChIP in control sample repeat 2

source_name: cpsf160 ChIP in control sample repeat 2


title: MLL-ENL 1

description: mRNA (polyA-enriched)


title: Sperm, 20FS220B


title: cpsf160 ChIP in control sample repeat 1

source_name: cpsf160 ChIP in control sample repeat 1


title: cpsf100 ChIP in U1 AMO sample repeat 2

source_name: cpsf100 ChIP in U1 AMO sample repeat 2


title: BZH1

source_name: Liver


title: Sperm, 10FS250AB


title: BZH3


title: MLL-ENL ∆YEATS (aa372-559) 2

description: mRNA (polyA-enriched)


title: Ros1-KO_caput epi_rep3

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

institute: Nagoya University

data_processing:
NovaSeq6000 (Illumina) using 101 bp single-ended mode
sequence reads were mapped onto mouse reference genome (mm10) using TopHat ver. 2.1.1
Fragments Per Kilobase of exon per Million mapped reads (RPKM) values for each gene were calculated using Cufflinks ver. 2.2.1
Assembly: mm10
Supplementary files format and content: A Microsoft Excel file including FPKM values for each Sample

source_name: caput epididymis

extract_protocol:
RNA was harvested using TRIzol (Invitrogen).
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA sample prep kit (Illumina) following manufacturer's protocols.

value: caput epididymis


title: Aged7

value: treated daily with saline only (oral gavage)


title: BZH2


title: Aged6


title: Sperm, 10FS228C


title: Ros1-KO_caput epi_rep2


title: cpsf100 ChIP in U1 AMO sample repeat 1

source_name: cpsf100 ChIP in U1 AMO sample repeat 1


title: Aged5


title: cpsf100 ChIP in control sample repeat 1

source_name: cpsf100 ChIP in control sample repeat 1


title: Ros1-KO_caput epi_rep1


title: cpsf100 ChIP in control sample repeat 2

source_name: cpsf100 ChIP in control sample repeat 2


title: input for U1 AMO sample (cpsf100,cpsf160,cpsf30,fip1, wdr33)


title: Sperm, 10FS217C


title: Sperm, FCD145B

value: FCD


title: Aged3


title: Sperm, FCD139C


title: Aged4


title: input for control sample (cpsf100,cpsf160,cpsf30,fip1, wdr33)

value: control


title: Aged2


title: Nicole-KO_caput epi_rep1

value: Nicole-/-


title: Nicole-KO_caput epi_rep2


title: Sperm, 10FS243B


title: ser5 ChIP in U1 AMO sample repeat 2

source_name: ser5 ChIP in U1 AMO sample repeat 2

value: HeLa

value: U1 AMO


title: Sperm, FCD131AF


title: Sperm, 10FS219C


title: Nicole-Het_caput epi_rep3

value: Nicole+/-


title: Sperm, FCD123A


title: Nicole-Het_caput epi_rep2


title: ser5 ChIP in control sample repeat 2

source_name: ser5 ChIP in control sample repeat 2


title: RNA-seq Day 1.5 WT replicate 7A

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D2-WT-7A

data_processing:
RNA-seq libraries followed by sequencing using Illumina HiSeq 4000 platform (single end, 50bp). ATAC-seq libraries were sequenced on an Illumina HiSeq 4000 platform (paired end, 100bp).
RNA-seq reads were mapped with HISAT2 (version 2.2.1)  to the mouse genome (mm10).  The counts for each gene were obtained by HtSeq.
ATAC-seq fastq files were trimmed to remove low-quality reads and adapters using Cutadapt (version 2.3). The reads were aligned to the reference mouse genome (mm10) with bowtie2 (version 2.2.9). Peak calling was performed with MACS2 (version 2.1.1). The peaks from all samples were merged into a single bed file, peaks from different samples that were closer than 10bp were merged into a single peak. HTseq (version 0.9.1) was used to count the number of reads that overlap each peak per sample.
Genome_build: mm10
Supplementary_files_format_and_content: csv files with number of reads mapped to the each gene or peak

source_name: Spleen

growth_protocol: Mice were bred at UCLA in accordance with the guidelines of the institutional Animal Care and Use Committee (IACUC). The following mouse strains were used in this study: C57BL/6 (CD45.2) (Jackson Labs, #000664), B6.SJL (CD45.1) (Jackson Labs, #002114), Klra8-/- (Ly49H-deficient), Rosa26ERT2Cre, Ncr1Cre, Utxfl/fl, UTX demethylase dead (UTXDMD) which harbors two point mutations at H1146A and E1148A. UTX is located on the X chromosome and escapes inactivation, it is expressed from 2 chromosomal copies in females but only one in males. Thus, to control for the number of UTX copies, experiments were conducted using 6-8 week old age-matched female UTXNKD and WT littermates in accordance with approved institutional protocols. Mixed bone marrow chimeric (mBMC) mice were generated by depleting host CD45.1xCD45.2 mice by intraperitoneal (i.p.) injection of busulfan (1mg/mL) at 20mg/kg for 3 consecutive days, which were then reconstituted 24 hours later with various mixtures of bone marrow cells from WT (CD45.1) and knockout (CD45.2) donor mice.

extract_protocol:
Mouse spleens, livers, lungs, lymph nodes, and blood were harvested and prepared into single cell suspensions as described previously11. Splenic single cell suspensions were lysed in red blood cell lysis buffer and resuspended in EasySep™ buffer (Stemcell). To avoid depleting Ly6C+ NK cells we developed a custom antibody cocktail as follows:  splenocytes were labeled with 10 μg per spleen of biotin conjugated antibodies against CD3 (17A2), CD19 (6D5), CD8 (53-6.7), CD88 (20/70), Ly6G (1A8), SiglecF (S17007L), TCRβ (H57-597), CD20 (SA275A11), CD172a (P84) and magnetically depleted from total splenocyte suspensions with the use of anti-biotin coupled magnetic beads (Biolegend).
RNA was isolated from the cells using RNeasy Mini kit (Qiagen) and used to generate RNA-seq libraries followed by sequencing using Illumina HiSeq 4000 platform (single end, 50bp). The reads were mapped with HISAT2 (version 2.2.1)  to the mouse genome (mm10).  The counts for each gene were obtained by HtSeq (Simon Anders, Paul Theodor Pyl, Wolfgang Huber HTSeq — A Python framework to work with high-throughput sequencing data Bioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638). Differential expression analyses were carried out using DESeq257  (version 1.24.0) with default parameters. Genes with adjusted p value <0.05 were considered significantly differentially expressed. Sequencing depth normalized counts were used to plot the expression values for individual genes. For ATAC-Seq, 50,000 cells per sample were lysed to collect nuclei and treated with Tn5 transposase (Illumina) for 30 minutes at 37°C with gentle agitation. The DNA was isolated with DNA Clean & Concentrator Kit (Zymo) and PCR amplified and barcoded with NEBNext High-Fidelity PCR Mix (New England Biolabs) and unique dual indexes (Illumina). The ATAC-Seq library amplification was confirmed by real-time PCR, and additional barcoding PCR cycles were added as necessary while avoiding overamplification. Amplified ATAC-Seq libraries were purified with DNA Clean & Concentrator Kit (Zymo). The purified libraries were quantified with Kapa Library Quant Kit (KAPA Biosystems) and quality assessed on 4200 TapeStation System (Agilent). The libraries were pooled based on molar concentrations and sequenced on an Illumina HiSeq 4000 platform (paired end, 100bp).

treatment_protocol: MCMV (Smith) was serially passaged through BALB/c hosts three times, and then salivary gland viral stocks were prepared with a dounce homogenizer for dissociating the salivary glands of infected mice 3 weeks after infection. Experimental mice in studies were infected with MCMV by i.p. injection of 7.5 x 103 plaque-forming units (PFU) in 0.5 mL of PBS. Mice were monitored and weighed daily and sacrificed when body weight dropped over 20% from initial weight.

value: NK cell

value: WT

tag: infection

value: MCMV

tag: time

value: Day 1.5


title: RNA-seq Day 1.5 WT replicate 8A

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D2-WT-8A


title: Nicole-Het_caput epi_rep1


title: Sperm, 7FD137CF


title: Sperm, FCD102G


title: ser5 ChIP in control sample repeat 1

source_name: ser5 ChIP in control sample repeat 1


title: ser2 ChIP in U1 AMO sample repeat 2

source_name: ser2 ChIP in U1 AMO sample repeat 2


title: Nicole-KO_caput epi_rep3


title: RNA-seq Day 1.5 WT replicate 5A

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D2-WT-5A


title: RNA-seq Day 1.5 KO replicate 8B

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D2-KO-8B

value: UTX KO


title: Sperm, 7FD114A

value: Sperm


title: ser2 ChIP in control sample repeat 2

source_name: ser2 ChIP in control sample repeat 2


title: RNA-seq Day 1.5 KO replicate 6B

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D2-KO-6B


title: ser2 ChIP in U1 AMO sample repeat 1

source_name: ser2 ChIP in U1 AMO sample repeat 1


title: Sperm, 7FD126E

source_name: Sperm

value: BALB/c


title: ser5 ChIP in U1 AMO sample repeat 1

source_name: ser5 ChIP in U1 AMO sample repeat 1


title: Yapfl/fl;Wwtr1fl/+;PostnMCM myofibroblast depletion cells [Yap]

data_processing:
Libraries were sequenced at the Roy J. Carver Biotechnology Center at the University of Illinois, Urbana Champaign on a NovaSeq 6000 using one S4 lane with 2X150nt reads.
Samples were demultiplexed using Cell Ranger v6.1.1.
The UMI counts per gene for all called cells were read into R and analyzed using Seurat. Genes were filtered out if they did not have at least 1 UMI in at least 20 cells, leaving 16,855 genes. Initial quality control involved performing sctranform normalization, principal components analysis, shared nearest neighbor cluster calling, and Uniform Manifold Approximation and Projection (UMAP) dimension reduction.
Marker genes per cluster were found by recursively comparing each cluster’s cells against all other clusters combined using a Wilcoxon Rank Sum test. . Within each cluster, gene expression differences between Yapfl/flWwtr1fl/+;PostnMCM and PostnMCM cells were tested also using a Wilcoxon Rank Sum test. The cells that expressed Postn were overwhelmingly in one cluster, so this one cluster was run by itself through the Seurat pipeline to find sub-clusters of cells.
Sub-cluster marker genes and within-subcluster of Yapfl/flWwtr1fl/+;PostnMCM and PostnMCM DEGs were calculated as before.
Assembly: A custom reference was made using NCBI’s GRCm39 genome and Annotation Release 109, along with Cloning vector pEGFP-1 (GenBank: U55761.1) and SA-betageo synthetic construct (full details of modifications in Supplemental R file).
Supplementary files format and content: Comma seperated value (.csv) file of gene expression for clusters with enough cells to compare and fibroblast subclusters.
Supplementary files format and content: RData file of filtered dataset

source_name: Cardiac Ventricle

extract_protocol:
Hearts were collected at 6 days post injury and intersitial cells were dissociated from ventricles by Langendorff perfusion. Viable cells were collected by fluorescence-activated cell sorting.
Single cell capture, cDNA synthesis, barcoding, and library preparation was performed using the 10x Chromium system using V3.1 chemistry.

treatment_protocol: A diet of 0.4 g/kg tamoxifen citrate chow (Envigo) was provided ad libitum starting immediately after MI and continued for 6 days.

value: Cardiac Ventricle

value: Interstitial cells

value: Tamoxifen


title: RNA-seq Day 1.5 KO replicate 5B

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D2-KO-5B


title: pcf11 ChIP in U1 AMO sample repeat 2

source_name: pcf11 ChIP in U1 AMO sample repeat 2


title: KO9aa_Rep2

city: Madison

first: Emery

middle: H

last: Bresnick

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

description: 9aa-Ins-expressing mutant

data_processing:
RNA-seq fragments were aligned by STAR (version 2.5.2b) to the mouse genome (mm10) with GENCODE basic gene annotations (version M22)
Gene expression levels were quantified by RSEM (version 1.3.0)
Assembly: mm10
Supplementary files format and content: TSV: RSEM quantification results at the gene level

source_name: Fetal liver

growth_protocol: Cells were cultured in expansion media containing β-estradiol

extract_protocol:
Qiagen RNeasy Micro Kit (74004)
RNA libraries were prepared through Illumina TruSeq Stranded Total RNA (rRNA reduction) protocol

treatment_protocol: Cells were incubated with retroviruses for 3 d and washed and resuspended in PBS with 2% FBS prior to FACS isolation.

value: Hematopoietic progenitors

value: Infected with 9aa-Ins vector


title: ser2 ChIP in control sample repeat 1

source_name: ser2 ChIP in control sample repeat 1

value: control


title: KO9aa_Rep3

description: 9aa-Ins-expressing mutant


title: Sperm, 20FS142G


title: Sperm, 20FS146F


title: KO9aa_Rep4

description: 9aa-Ins-expressing mutant


title: Aged1

source_name: Liver

value: Liver

value: male

value: treated daily with saline only (oral gavage)


title: RNA-seq Day 0 WT replicate 4A

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D0-WT-4A

value: Day 0


title: pcf11 ChIP in U1 AMO sample repeat 1

source_name: pcf11 ChIP in U1 AMO sample repeat 1

value: HeLa

value: U1 AMO


title: RNA-seq Day 0 WT replicate 3A

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D0-WT-3A

value: NK cell

value: WT


title: Sperm, 20FS129CE


title: KO9aa_Rep1

description: 9aa-Ins-expressing mutant


title: RNA-seq Day 0 WT replicate 1A

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D0-WT-1A


title: pcf11 ChIP in control sample repeat 2

source_name: pcf11 ChIP in control sample repeat 2


title: KOWG_Rep4

description: GATA2-expressing mutant

value: Infected with GATA2 vector


title: PostnMCM control cells [RGFP]

value: PostnMCM


title: pcf11 ChIP in control sample repeat 1

source_name: pcf11 ChIP in control sample repeat 1


title: RNA-seq Day 0 KO replicate 4B

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D0-KO-4B

value: UTX KO


title: KOWG_Rep2

description: GATA2-expressing mutant


title: KOWG_Rep3

description: GATA2-expressing mutant


title: cstf77 ChIP in U1 AMO sample repeat 2

source_name: cstf77 ChIP in U1 AMO sample repeat 2


title: Sperm, 20FS1020B

value: Sperm

value: BALB/c


title: Sperm, 20FS105B


title: RNA-seq Day 0 KO replicate 3B

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D0-KO-3B


title: Sperm, 7FD108G


title: cstf77 ChIP in U1 AMO sample repeat 1

source_name: cstf77 ChIP in U1 AMO sample repeat 1


title: Sperm, 10FS143B


title: RNA-seq Day 0 KO replicate 1B

description:
RNAseq_raw_counts_GEO.csv.gz
RNA-D0-KO-1B

source_name: Spleen


title: Sperm, 10FS128BC


title: KOWG_Rep1

description: GATA2-expressing mutant


title: cstf77 ChIP in control sample repeat 2

source_name: cstf77 ChIP in control sample repeat 2


title: cstf77 ChIP in control sample repeat 1

source_name: cstf77 ChIP in control sample repeat 1


title: Sperm, 10FS127E


title: Sperm, 10FS119C


title: ATAC Day 1.5 WT replicate 6

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D2-WT6

value: MCMV

value: Day 1.5


title: WTEmp_Rep3

description: wild type

value: Hematopoietic progenitors

value: Infected with empty vector


title: ATAC Day 1.5 WT replicate 4

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D2-WT4


title: CFIm68 ChIP in U1 AMO sample repeat 2

source_name: CFIm68 ChIP in U1 AMO sample repeat 2


title: CFIm68 ChIP in U1 AMO sample repeat 1

source_name: CFIm68 ChIP in U1 AMO sample repeat 1


title: WTEmp_Rep1

description: wild type


title: Sperm, 10FS117A

source_name: Sperm


title: ATAC Day 1.5 KO replicate 6

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D2-KO6


title: Spermatogonia, FCD127G_spg

source_name: Spermatogonia

value: Spermatogonia

value: FCD


title: CFIm68 ChIP in control sample repeat 2

source_name: CFIm68 ChIP in control sample repeat 2

value: control


title: ATAC Day 1.5 KO replicate 5

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D2-KO5


title: KOEmp_Rep4

description: mutant


title: Spermatogonia, FCD123BC_spg


title: CFIm68 ChIP in control sample repeat 1

source_name: CFIm68 ChIP in control sample repeat 1


title: Spermatogonia, FCD121AF_spg


title: input for U1 AMO sample (68, cstf77, pcf11, ser2, ser5) repeat 2


title: ATAC Day 0 WT replicate 3

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D0-WT3

value: Day 0


title: ATAC Day 1.5 KO replicate 4

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D2-KO4


title: KOEmp_Rep3

description: mutant

source_name: Fetal liver


title: KOEmp_Rep2

description: mutant


title: WTEmp_Rep4

description: wild type


title: Spermatogonia, FCD116BE2_spg


title: ATAC Day 0 WT replicate 2

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D0-WT2


title: input for U1 AMO sample (68, cstf77, pcf11, ser2, ser5) repeat 1

value: HeLa


title: ATAC Day 1.5 WT replicate 5

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D2-WT5


title: KOEmp_Rep1

description: mutant


title: input for control sample (68, cstf77, pcf11, ser2, ser5) repeat 2


title: Spermatogonia, 7FD125A_spg


title: WTEmp_Rep2

description: wild type


title: Rag1Cre-NFATc1-fl/fl_rep3

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v21.0.5 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome. Expression value=TPM
Genome_build: GRCm38
Supplementary_files_format_and_content: txt

source_name: gd thymocytes

growth_protocol: gd thymocyte selection was carried out TCRγ/δ+ T Cell Isolation Kit (Miltenyi Biotec) according to the manufacturer’s protocol

extract_protocol:
RNA preparation was carried out using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s protocol
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Nano chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 200 ng total RNA (RIN>8) using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. 11 cycles were run for final amplification of libraries. All quality controls were done using Invitrogen’s Qubit HS assay and average library size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.

value: gammadelta thymocytes

value: Rag1cre-Nfatc1-fl/fl (KO)


title: Rag1Cre-NFATc1-fl/fl_rep2


title: Spermatogonia, 7FD112BE3_spg


title: ATAC Day 0 KO replicate 3

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D0-KO3

value: NK cell


title: Rag1Cre-NFATc1-fl/fl_rep1


title: U1 mRNA-seq

data_processing:
Reads were trimmed, mapped using standard protocol(Novogene)
Genome_build: hg38
Supplementary_files_format_and_content: Read coverage tracks are generated in the tdf format from the genome-mapped bam file.

source_name: HeLa cell

extract_protocol:
Ribosome-associated RNAs were purified with sucrose-gradient
library were prepared using illumina small RNA sequencing kit

treatment_protocol: Control and U1 AMO were transfected into Hela cells, cells were harvested at 12 hour time point upon transfection.

value: U1 AMO


title: ATAC Day 0 KO replicate 2

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D0-KO2


title: Spermatogonia, 7FD112BE1_spg

data_processing:
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome and get methylation calls with bsmap-2.6
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing information for each sample: chrBase, chr, base, strand, coverage, FreqC (methylation), FreqT

extract_protocol:
Frozen sperm/isolated spermatogonia were thawed on ice and genomic DNA isolation was performed using Qiagen DNeasy Blood & Tissue Kits (Qiagen, Germany) according to the manufacturer’s guide, with modifications. For sperm samples, sperm was incubated overnight at 37oC in a buffer containing EDTA, Tris , sarkosyl , dithiothreitol (DTT) and proteinase K (Invitrogen, Canada). The following day, Buffer AL was added to the buffer, and incubated at 70oC for 10min and the manufacturer’s guide was continued.
Reduced representation bisulfite sequencing (RRBS) libraries were prepared according to previously published protocols using gel-free technique (Boyle, P. Genome Biol., 2012).  Briefly, ~500ng of  DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing.  Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplification.


title: NFATc1-fl/fl_rep3

value: Nfatc1-fl/fl (WT)


title: control mRNA-seq


title: ATAC Day 0 KO replicate 1

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D0-KO1

value: UTX KO


title: U1 Ribo-seq

data_processing:
Library strategy: Ribo-Seq
Reads were trimmed, mapped using standard protocol(Novogene)
Genome_build: hg38
Supplementary_files_format_and_content: Read coverage tracks are generated in the tdf format from the genome-mapped bam file.


title: Spermatogonia, 7FD110AB_spg


title: Spermatogonia, 7FD102BE2_spg


title: input for control sample (68, cstf77, pcf11, ser2, ser5) repeat 1


title: NFATc1-fl/fl_rep1


title: ATAC Day 0 WT replicate 1

description:
ATAC_raw_counts_GEO.csv.gz
ATAC-D0-WT1

value: WT


title: E12 adrenal gland XY Rep1 [170816_AG]

city: Genève

first: Serge

last: Nef

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

data_processing:
Demultiplexing using Cell Ranger mkfastq v2.1
Alignment, annotation and counting were performed with Cell Ranger count v2.1
Genome_build: GRCm38.p5 (mm10); Gencode vM15 annotation
Supplementary_files_format_and_content: sparse matrix of UMI count

source_name: E12 adrenal gland XY

extract_protocol:
Tissues were enzymatically dissociated. Viable single cells, from all samples except E12.5 ovaries and testis, were enriched by FACSorting. 3000 to 7000 single cells were loaded on a 10x Chromium instrument (10x Genomics).
Single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol.

value: Nr5a1 Tg

tag: sex chromosomes

value: XY

tag: developmental age

value: adrenal gland

tag: replicate


title: E12 adrenal gland XY Rep2 [180425_AG]


title: E12 testis XY Rep2 [170816_T]

source_name: E12 testis XY

value: testis


title: Spermatogonia, FCD116BE1_spg

tag: strain

value: BALB/c


title: U1 AMO-cytoplasm PAS-seq - repeat 2

description: 3'-seq kit (lexogen) was used to prepare 3'-seq library, and sequenced using PE150 strategy (novaseq）

data_processing:
Library strategy: PAS-seq
read 1 sequences were reverse complemented and mapped to human genome (hg38) allowing up to two  mismatches using Bowtie2 with the settings ‘bowtie2 -p 28 -N 1 -k 1’. The 3ʹ  end of the read maps was considered a poly(A) junction.
The bioinformatics analysis for reads filtering and clustering, internal priming removal, poly(A) site   identification and subsequent mRNA alternative polyadenylation (APA) analysis , were performed essentially as previously described (Lackford et al., 2014; Yao et al., 2012.)
Genome_build: hg38
Supplementary_files_format_and_content: Read coverage tracks are generated in the BigWig (bw) format from the genome-mapped bam file.

source_name: Hela cells

extract_protocol:
cytoplasmic fractions were isolated and RNAs were subsequently purified by Trizol reagent.
library were prepared using 3'-seq kit (lexogen, 016.024)

tag: treatment


title: E12 testis XY Rep1 [170724_T]


title: U1 AMO-cytoplasm PAS-seq - repeat 1


title: Spermatogonia, 20FS121A_spg

value: Spermatogonia


title: r08_40wpi

city: Copenhagen N

first: Troels

last: Scheel

address: Blegdamsvej 3

institute: University of Copenhagen

description:
RW-208-W
Frequency table Rats.xlsx

data_processing:
The obtained reads were analyzed using the previously published VirVarSeq analysis pipeline (Verbist 2015 Bioinformatics, PMID: 25178459) with a set fixed quality value of 30 to call variation at the codon level. This package is available at http://sourceforge.net/projects/virtools/?source=directory. All samples had minimum coverage of 4,000 reads per position over the entire ORF. Variant calling frequency tables from VirVarSeq from samples of relevance were merged and filtered in R.
Assembly: NrHV-A: MF113386, NrHV-B: ON758386, RHV-rn1: KX905133
Supplementary files format and content: Frequency table NRG mice.xlsx lists viral substitutions as observed in NRG mice. For NRG mice where variation was less, substitutions with frequency of >20% in at least one sample were included in the processed data file.
Supplementary files format and content: Frequency table Rats.xlsx lists viral substitutions as observed in rats. For rats where variation was greater, positions with a combined frequency of one or several mutations >50% in at least two rats were kept. Individual substitutions with minimal contribution (<20%) at such position were not included.

source_name: Serum

extract_protocol:
Viral RNA was extracted using TRIzol, followed by standard on-column purification procedure. The wole ORF was reverse transcribed to generate viral cDNA. Samples were pre-incubated at 65ºC for 5 min prior to the reaction. RT was carried out at 50ºC for 2 h in the presence of RNase inhibitors using 0.1 μM primer TS-O-00319 (GCTTCCTGGAGCGGGCTAGATACTG). Amplification of the complete ORF was performed using Q5 High-Fidelity Hot start DNA Polymerase (NEB), including high GC Enhancer, and the primer pair TS-O-00318 (CCAAGCCCCAATGCCGTCCGGCACCGCTGCCCTTTTCGG) and TS-O-00361 (AGGTGAAGGGGGCATCGATG). Amplified DNA was purified using DNA Clean & Concentrator (Zymo Research).
Libraries were constructed using the NebNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs), using dual indices. cDNA input: 25ng, adapter ligation, bead-based size selection (AMPure XP beads; 200-350 bp), PCR enrichment using i7/i5 index primer set. Enriched libraries were washed twice using AMPure XP beads for complete depletion of residual adapter.
Libraries were sequenced paried-end on a Illumina Miseq using 500 PE V2 kit (Illumina).

value: Lewis rat

tag: immunodeficient

value: NO

value: Serum

tag: virus

value: NrHV-B(SLIS)

tag: molecule subtype

value: viral RNA


title: r08_46wpi

description:
RW-212-G
Frequency table Rats.xlsx


title: r08_27wpi

description:
RW-212-F
Frequency table Rats.xlsx


title: E11 urogenital ridge XY Rep2 [170823_AGP]

source_name: E11 urogenital ridge XY

tag: genotype

value: urogenital ridge


title: control AMO-cytoplasm PAS-seq - repeat 2

value: HeLa

value: Control AMO


title: E11 urogenital ridge XY Rep1 [170814_AGP]

tag: tissue


title: control AMO-cytoplasm PAS-seq - repeat 1


title: control Ribo-seq

tag: cell line

value: control


title: Spermatogonia, 20FS111C1_spg


title: Spermatogonia, 20FS114AF1_spg


title: r08_08wpi

description:
MIB37-19
Frequency table Rats.xlsx


title: E10 urogenital ridge XY Rep2 [170830_AGP]

source_name: E10 urogenital ridge XY


title: Spermatogonia, 20FS126G2_spg


title: U1 AMO-repeat 1 CstF64 iCLIP-seq

data_processing:
reads were mapped to human genome (hg19) allowing up to two  mismatches using Bowtie2 with the settings ‘bowtie2 -p 28 -N 1 -k 1’. The 5ʹ  end of the read maps was considered the crosslinking site.
The bioinformatics analysis for reads filtering and clustering were performed essentially as previously described (Lackford et al., 2014; Yao et al., 2012.)
Genome_build: hg19
Supplementary_files_format_and_content: Read coverage tracks are generated in the tdf format from the genome-mapped bam file.

extract_protocol:
RNAs were purified with antibody targeting CstF64 (Bethyl)
CstF64 iCLIP-seq(s) were carried out using the standard iCLIP-seq protocol (König J et al. 2010)

tag: antibody

value: CstF64 antibody (Bethyl Laboratories)

value: U1 AMO


title: E10 urogenital ridge XY Rep1 [170828_AGP]

value: Nr5a1 Tg


title: r07_46wpi

description:
RW-212-E
Frequency table Rats.xlsx


title: r07_40wpi

description:
RW-208-V
Frequency table Rats.xlsx


title: Spermatogonia, 20FS114AF2_spg

tag: diet


title: E9 posterior trunk XY Rep2 [190408_AGP]

source_name: E9 posterior trunk XY

value: XY

value: posterior trunk


title: Spermatogonia, 10FS122BF1_spg

tag: generation


title: E9 posterior trunk XY Rep1 [190401_AGP]


title: r07_27wpi

description:
RW-212-D
Frequency table Rats.xlsx


title: control AMO-repeat 2 CstF64 iCLIP-seq

tag: cell type


title: control AMO-repeat 1 CstF64 iCLIP-seq


title: Spermatogonia, 10FS121E_spg


title: E12 ovary XX Rep2 [170816_O]

source_name: E12 ovary XX

value: XX

value: ovary


title: r07_08wpi

description:
MIB37-18
Frequency table Rats.xlsx


title: Spermatogonia, 10FS109AC_spg

value: Spermatogonia

value: BALB/c


title: Hela cells si-FUS-2

data_processing:
read 1 sequences were reverse complemented and mapped to human genome (hg38) allowing up to two  mismatches using Bowtie2 with the settings ‘bowtie2 -p 28 -N 1 -k 1’. The 3ʹ  end of the read maps was considered a poly(A) junction.
The bioinformatics analysis for reads filtering and clustering, internal priming removal, poly(A) site   identification and subsequent mRNA alternative polyadenylation (APA) analysis , were performed essentially as previously described (Lackford et al., 2014; Yao et al., 2012.)
Genome_build: hg38
Supplementary_files_format_and_content: Read coverage tracks are generated in the BigWig (bw) format from the genome-mapped bam file.

extract_protocol:
total RNAs were extracted using Trizol reagent
library were prepared using 3'-seq kit (lexogen, 016.024)

treatment_protocol: siRNAs targeting control and FUS protein were transfected into HeLa cells. cells were harvested upon 3 days upon transfection

value: tumor cell line

value: transfected with siFUS


title: Hela cells si-FUS-1


title: r08_01wpi

description:
MIB37-6
Frequency table Rats.xlsx

value: Lewis rat

value: NO

value: Serum

value: NrHV-B(SLIS)


title: U1 AMO-repeat 2 CstF64 iCLIP-seq

value: HeLa


title: Spermatogonia, 10FS126G1_spg


title: r07_01wpi

description:
RW-212-C
Frequency table Rats.xlsx

value: viral RNA


title: NFATc1-fl/fl_rep2

value: gammadelta thymocytes

value: Nfatc1-fl/fl (WT)


title: NC1Bio-_rep3

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v12.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome. Expression value=RPKM.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt

source_name: CD4-CD8- double negative thymocytes

growth_protocol: DN thymocyte selection was carried out using MACS magnetic separation with anti-CD4 (L3T4) and anti-CD8 (Ly-2) microbeads (Miltenyi Biotec) according to the manufacturer’s protocol

extract_protocol:
RNA preparation was carried out using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s protocol
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 50 ng total RNA (RIN>8) using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. Final PCr was performed with 13 cycles. All quality controls were done using Invitrogen’s Qubit HS assay and average library size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.

value: CD4-CD8- double negative thymocytes

value: NFATc1 overexpression


title: Hela cells si-control-2

value: transfected with control


title: r10_45wpi

description:
RW-212-J
Frequency table Rats.xlsx

value: NrHV-B


title: NC1Bio-_rep2


title: E11 urogenital ridge XX Rep2 [170823_AGP]

source_name: E11 urogenital ridge XX

value: Nr5a1 Tg

value: XX

value: urogenital ridge


title: Hela cells si-control-1

value: tumor cell line


title: Spermatogonia, 10FS122BF2_spg

value: Spermatogonia

value: BALB/c


title: NC1Bio-_rep1


title: E11 urogenital ridge XX Rep1 [170814_AGP]


title: Hela cells-si-U170K-2

data_processing:
read 1 sequences were reverse complemented and mapped to human genome (hg38) allowing up to two  mismatches using Bowtie2 with the settings ‘bowtie2 -p 28 -N 1 -k 1’. The 3ʹ 753 end of the read maps was considered a poly(A) junction.
The bioinformatics analysis for reads filtering and clustering, internal priming removal, poly(A) site   identification and subsequent mRNA alternative polyadenylation (APA) analysis , were performed essentially as previously described (Lackford et al., 2014; Yao et al., 2012.
Genome_build: hg38
Supplementary_files_format_and_content: Read coverage tracks are generated in the BigWig (bw) format from the genome-mapped bam file.

treatment_protocol: siRNAs targeting control and U1 specific proteins were transfected into HeLa cells. cells were harvested upon 3 days upon transfection

tag: transfection


title: E10 urogenital ridge XX Rep2 [170830_AGP]

source_name: E10 urogenital ridge XX


title: r10_22wpi

description:
RW-212-I
Frequency table Rats.xlsx

value: Lewis rat

value: NO


title: BirA-_rep3

value: WT


title: E10 urogenital ridge XX Rep1 [170828_AGP]


title: Hela cells-si-U170K-1


title: Hela cells-si-U1C-2


title: BirA-_rep2


title: E9 posterior trunk XX Rep2 [190408_AGP]

source_name: E9 posterior trunk XX

value: posterior trunk


title: r10_08wpi

description:
MIB37-21
Frequency table Rats.xlsx

value: Serum

value: viral RNA


title: r10_01wpi

description:
MIB37-8
Frequency table Rats.xlsx


title: E12 ovary XX Rep1 [170724_O]

value: ovary


title: Hela cells-si-U1C-1


title: r04_46wpi

description:
RW-212-B
Frequency table Rats.xlsx


title: NFATc1/A stimulated

data_processing:
59 bp sequence reads  that passed the Illumina quality filtering were aligned to the mouse genome assembly version of July 2007 (NCB I37/mm9), using the Map with Bowtie for Illumina (version 1.1.2) with the following parameters: Bowtie settings to use=full; Skip the first n reads (-s)=0; Only align the first n reads (-u)= -1; Trim n bases from high-quality (left) end of each read before alignment (-5)= 0; Trim n bases from low-quality (right) end of each read before alignment (-3)= 0; Maximum number of mismatches permitted in the seed (-n)= 2; Maximum permitted total of quality values at mismatched read positions (-e)= 70; Seed length (-l)= 35; Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)= Round to nearest 10; Number of mismatches for SOAP-like alignment policy (-v)= -1; Whether or not to try as hard as possible to find valid alignments when they exist (-y)= Do not try hard; Report up to n valid alignments per read (-k)= 1; Whether or not to report all valid alignments per read (-a)= Do not report all valid alignments; Suppress all alignments for a read if more than n reportable alignments exist (-m)= -1; Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)= False; Write all reads that could not be aligned to a file (--un)= False; Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)= doBest; Maximum number of backtracks permitted when aligning a read (--maxbts)= 800; Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)= do not use strata option; Override the offrate of the index to n (-o)= -1; Seed for pseudo-random number generator (--seed)= -1; Suppress the header in the output SAM file= False; Job Resource Parameters= no;
Peak calling was done using MACS on Galaxy (MACS version 2.1.1.) with default parameters, a genome size of 2,700,000,000 bp (mm9) and the reads from Rosa26BirA Cntrl+ IP as control sample: # Command line: callpeak --name MACS2 -t /galaxy-repl/main/files/024/721/dataset_24721846.dat -c /galaxy-repl/main/files/024/721/dataset_24721845.dat --format=BAM --gsize 2150570000 --bw 300 --mfold 5 50 --bdg --qvalue
Genome_build: mm9
Supplementary_files_format_and_content: Aligned reads (bigwig)
Supplementary_files_format_and_content: Peak calling MACS (bed)

source_name: isolated thymocytes in vitro stimulated with TPA and ionomycin for 4 hours

growth_protocol: single cell suspension of freshly isolated thymocytes

extract_protocol:
Chromatin from 1x107 fixed thymocytes was prepared using a lysis buffer containing 1% SDS and sonicated by a Vibra-Cell VCX 130 before precipitation of biotinylated protein/DNA conplexes by streptavidin beads
Sequencing libraries were prepared using 3ng decrosslinked and purified DNA employing the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® according to the manual (no size selection and 13 cycles of final PCR). All quality controls were done using Invitrogen’s Qubit HS assay and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay. Barcoded libraries were onboard clustered usingHiSeq® Rapid SR Cluster Kit v2 using 8pM and 50bps were sequenced on the Illumina HiSeq2500 using HiSeq® Rapid SBS Kit v2 (50 Cycle). The raw output data of the HiSeq was preprocessed according to the Illumina standard protocol

treatment_protocol: 4h stimulation by TPA (5 ng/ml) and ionomycin (0.5 microM)

value: thymocytes


title: r04_40wpi

description:
RW-208-S
Frequency table Rats.xlsx


title: Arabidopsis thaliana Root Nuclei_3

city: New York

first: Bruno

last: Guillotin

state: NY

address: 12 Waverly Place, Floor 6

department: Biology

institute: NYU-Biology-CGSB

description:
10x Genomics 3' RNA seq V3
Arabidopsis_Cells_Nuclei_Seurat_Obj.RData
Arabidopsis_Cells_Nuclei_expression_Matrix_raw_counts.RData
Arabidopsis_Cells_Nuclei_expression_Matrix_Norm_counts.RData

data_processing:
Cell Ranger 5.0.1 (10x Genomics) to generate gene-cell matrices. Gene reads were aligned to the Arabidopsis TAIR10.38, Maize B73 v4, Sorghum bicolor v3 and Setaria viridis v2 reference genomes.
Replicates (see Supplementary Table 1) were integrated and cells mapped using the Seurat package v4.0 66 as follows: first, genes with counts in fewer than three cells were excluded from the analysis and their counts were removed. Second, low-quality cells were removed using threshold variable depending on the library quality (see supplementary Table 1). Clustering of cells or nuclei separately were done by log-normalized raw counts and the 2000 most variable genes were identified for each replicate using the “vst” method in Seurat. Next, we used the FindIntegrationAnchors function to identify anchors between the three datasets, using 20 dimensions. A new profile with an integrated expression matrix containing cells from all replicates was produced with the IntegrateData function. For dimensionality reduction, the integrated expression matrix was scaled (linear transformed) using the ScaleData function, and Principal Component analysis (PCA) performed. The top 30 principal components were selected. Cells or nuclei were clustered using a K-nearest neighbor (KNN) graph, which is based on the Euclidean distance in PCA space. The FindNeighbors and FindClusters function with a resolution of 0.5. was applied. Next, non-linear dimensional reduction was performed using the UMAP algorithm with the top 30 PCs.
For the co-clustering of cells and nuclei, either dataset were treated similarly, all replicates were integrated at once using the seurat 'SCT' approach. First raw reads were normalized using the SCTransform function, then SelectIntegrationFeatures was used to identify anchors between the datasets, using 3000 features.
For multiple species clustering, all orthologous genes names from were replaced by their corresponding maize ID in sorghum and setaria raw features.tsv.gz files (Gene conversion in Supplementary Table 1). Anchors are combined using PrepSCTIntegration and selected using FindIntegrationAnchors. For clustering of maize, sorghum and setaria together, all species were considered equally using the FindIntegrationAnchors function. Finally, a Principal Component analysis (PCA) is performed using the first 100 principal components and a non-linear dimensional reduction was performed using the UMAP algorithm with the top 100 PCs.
Supplementary files format and content: Processed data include, R Seurat Objects of integrated datasets, expression matrices normalized and raw count extracted from the Seurat objects, and a metadata containing the cell identities, genes or UMI per cell.

organism: Arabidopsis thaliana

source_name: root meristem

growth_protocol: Arabidopsis seeds were imbibed for 48h at 4°C before being surface sterilized and placed on a nylon mesh (110um) and agar plates-1/2 × Murashige and Skoog salts (Sigma M5524), 0.5% sucrose, 0.8% Agar (Sigma A1296). Plant were transferred vertically in growth chambers set to 23°C and a 16 h light/8 h dark cycle (400 μmol m−2 s−1). Root tips were collected 7 days after transfer, cut with a feather scalpel at 150um from the tip and directly transferred to either the protoplast solution at room temperature or the nuclei lysis buffer at 4°C. Maize, Sorghum seeds were sterilized using bleach (1.5% active chloride) and 0.001% tween 20 for 20mins then 4% chloramine T for 20mins. Setaria seed germination was induced by incubation in 4% liquid smoke (Colgin, Authentic Natural Hickory) at 29°C for 24h.Then setaria seeds were sterilized using bleach (1.5% active chloride) and 0.001% tween 20 for 20mins. All seeds were placed between two layers of brown paper (Anchor Paper&Cie., 38# regular), rolled and covered with aluminum foil to prevent roots from exposure to direct light. Rolls were placed in a bucket of tap water at 28/24°C at 16 h light/8 h dark cycle (250 μmol m−2 s−1) for 7 days (15days for Setaria) before harvesting the root tips. Primary and seminal root tips were cut using a fine scalpel at 0.5 cm form the tip for Maize and Sorghum, 0.2cm from the tip for Setaria and transferred either to the pre-incubation solution for single cell or to the nuclei lysis buffer.

extract_protocol:
Root tip were incubated in a enzymatic solution to digest cell walls and produce protoplasts, or in lysis buffer for nuclei extraction. Protoplasts or nuclei were filtered using a cell strainer and used as input for the 10x Chromium Single Cell 3' kit
Libraries were prepared using Chromium Single Cell 3' Reagent Kit V2 and V3 protocol

value: Nuclei

value: root meristem

tag: age

value: 10 days old


title: Arabidopsis thaliana Root Nuclei_2


title: Cntrl +

value: isolated thymocytes in vitro stimulated with TPA and ionomycin for 4 hours


title: r10_35wpi

description:
RW-208-X
Frequency table Rats.xlsx

value: NrHV-B


title: r04_27wpi

description:
MIB53-18
Frequency table Rats.xlsx


title: NFATc1/A unstimulated

source_name: freshly isolated thymocytes

value: freshly isolated thymocytes


title: Hela cells-si-control-2

value: control


title: Arabidopsis thaliana Root Nuclei_1


title: Hela cells-si-U1A-2


title: r04_08wpi

description:
MIB37-15
Frequency table Rats.xlsx


title: E9 posterior trunk XX Rep1 [190401_AGP]

value: Nr5a1 Tg

tag: sex chromosomes

value: XX


title: Hela cells-si-control-1


title: RNA-Seq of Huh7 cells treated with 100ug/ml GO-Rg3-DOX-rep3 [P19760_127_S43]

city: Goteborg

first: Shadi

last: Rahimi

address: Kemivägen 10

department: Department of Biology and Biological Engineering

institute: Chalmers University of Technology

data_processing:
The raw reads were processed with the NGI RNAseq Pipeline (https://github.com/SciLifeLab/NGI-RNAseq). The GRCh37 reference genome was used to map the reads (https://support.illumina.com/sequencing/sequencing_software/igenome.html), and the percentage of uniquely mapped reads was between 79.7–83.6%. Raw read counts were calculated with feature Counts. In total 448,620,449 reads were uniquely mapped on the reference genomes. Samples contained between 8,598,597 to 14,340,446 unique reads.
Genome_build: GRCh37
Supplementary_files_format_and_content: txt file including raw gene counts

source_name: Tretaed Huh7 cells with 100ug/ml GO-Rg3-DOX

growth_protocol: Cells were seeded onto 6-well plates at a density of 4 × 105 cells per well and cultured for 24 h before treatment with GO, GO-Rg3-GO-Rg3-DOX, and DOX for 6 h.

extract_protocol:
Total RNA extraction was performed through RNeasy Mini Kit (Qiagen), and the quality examination was performed by Bioanalyzer (Agilent) through Agilent RNA 6000 Nano Kit.
Library was prepared through Illumina TruSeq Stranded mRNA.

value: Hepatocarcinoma cells

value: 100 ug/ml GO-Rg3-DOX


title: RNA-Seq of Huh7 cells treated with 100ug/ml GO-Rg3-DOX-rep1 [P19760_125_S41]


title: Arabidopsis thaliana Root Cell_6

description:
10x Genomics 3' RNA seq V2
Arabidopsis_Cells_Nuclei_Seurat_Obj.RData
Arabidopsis_Cells_Nuclei_expression_Matrix_raw_counts.RData
Arabidopsis_Cells_Nuclei_expression_Matrix_Norm_counts.RData

value: Protoplast


title: BirA-_rep1

value: CD4-CD8- double negative thymocytes

value: WT


title: FGK_6_30min [DE86NGSUKBR107556]

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

institute: University Hospital Bonn

data_processing:
Alignment with STAR against the mm10 reference genome
quantification of gene counts via Partek's E/M algorithm
normalized as Counts per million (CPM)
Flooring
Genome_build: mm10
Supplementary_files_format_and_content: normalized as Counts per million (CPM)

source_name: primary cDC1/APC_FGK_30min

growth_protocol: In vitro generation of bone marrow-derived DCs using Flt3 ligand followed by sort of cDC1

extract_protocol:
TRIzol - Direct-zolTM RNA MicroPrep kit (Zymo Research)
performed by the NGS Core Facility University Hospital Bonn according to the maufacturers' user guide for the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (https://www.lexogen.com/quantseq-3mrna-sequencing/#quantseqdownloads/)
1x 50bp single reads, 10mio reads deep per sample, Illumina HiSeq2500

treatment_protocol: In vitro stimulation of cDC1 with IFN-⍺A in the presence or the absence of anti-CD40 monoclonal antibody (FGK45.5).

tag: strain background

value: Bone-marrow

value: primary cDC1/APC


title: Arabidopsis thaliana Root Cell_5


title: FGK_4_15min [DE76NGSUKBR107542]

source_name: primary cDC1/APC_FGK_15min


title: RNA-Seq of Huh7 cells treated with 400ug/ml GO-Rg3-rep2 [P19760_118_S39]

source_name: Tretaed Huh7 cells with 400ug/ml GO-Rg3

value: 400 ug/ml GO-Rg3


title: r04_01wpi

department: Institute for Immunology and Microbiology

description:
MIB37-2
Frequency table Rats.xlsx

value: Lewis rat

value: NO

value: Serum

value: viral RNA


title: RNA-Seq of Huh7 cells treated with 100ug/ml GO-Rg3-DOX-rep2 [P19760_126_S42]


title: IFN_FGK_4_30min [DE92NGSUKBR107545]

source_name: primary cDC1/APC_IFN_FGK_30min


title: thaliana Root Cell_2

value: root meristem

value: 10 days old


title: Arabidopsis thaliana RootCell_3


title: r03_22wpi

description:
MIB53-17
Frequency table Rats.xlsx

source_name: Serum

value: NrHV-B


title: IFN_FGK_5_15min [DE81NGSUKBR107549]

source_name: primary cDC1/APC_IFN_FGK_15min


title: r03_08wpi

description:
MIB37-14
Frequency table Rats.xlsx


title: r03_45wpi

description:
RW-212-A
Frequency table Rats.xlsx


title: Unstim_6_240min [DE97NGSUKBR107552]

source_name: primary cDC1/APC_Unstim_240min


title: IFN_6_240min [DE70NGSUKBR107553]

source_name: primary cDC1/APC_IFN_240min


title: Unstim_5_240min [DE65NGSUKBR107546]


title: Hela cells-si-U1A-1

source_name: Hela cells


title: r03_01wpi

description:
MIB37-1
Frequency table Rats.xlsx


title: Arabidopsis thaliana Root Cell_1


title: N16 NRK-49F cells, pH6

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

data_processing:
Read alignment (HISAT2 2.1.0)
Read counting (featureCounts - 2.0.0)
Annotation with biomaRt and Ensembl 99
Assembly: rn6
Supplementary files format and content: .csv file including annotation raw counts (output of featureCounts) for each sample

growth_protocol: NRK-52E and NRK-49F were cultivated with DMEM medium (5% FCS, 1.5g/L NaHCO3), at 37°C, 5% CO2. For co-culture conditions, NRK-49F were directly sed in wells of 6-well plates, while NRK-52E were grown on permeable filter inserts that were embed onto the 6-well plates with the NRK-49F.

extract_protocol:
Total RNA was isolated with BluZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
polyA enrichment (performed by Novogene Europe)

treatment_protocol: Cells were synchronized for 24h with medium without FCS. The incubation with pH 7.4 or 6.0 was then started and was maintained for 48h

value: Fibroblast


title: Arabidopsis thaliana RootCell_4