title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1B6_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1C14_A

status: Public on Aug 30 2021

type: SRA

city: Bethesda

first: Augusto

last: Dulanto Chiang

state: Maryland

address: 9000 Rockville Pike

country: USA

institute: NIAID

library_source: transcriptomic

data_processing:
Adapters were trimmed using Trimmomatic
Reads were mapped to reference using BWA v0.7.17 using default parameters
Samtools v1.11 and Picard CollectRnaSeqMetrics (Picard tools v2.25.0) were used to obtain QC metrics.
Bam alignments from 10 resequenced libraries were merged using samtools. All Bam files and the PAO1 reference GFF file (Available from https://pseudomonas.com/downloads/pseudomonas/pgd_r_20_2/Pseudomonas_aeruginosa_PAO1_107/Pseudomonas_aeruginosa_PAO1_107.gff.gz , accessed 01/18/2021) were used to generate read counts for each sample with HTseq v0.11.4, using the htseq-count -s reverse -m union flags
Genome_build: GCA_000006765.1
Supplementary_files_format_and_content: htseq-count tabular format (.tsv)

molecule: total RNA

organism: Pseudomonas aeruginosa

source_name: Liquid culture (LB broth)

growth_protocol: Each isolate was streaked onto TSA with 5% Sheep Blood agar plates from glycerol stocks frozen at -80°C and incubated at 37°C for 20 hours. A quarter-loop of colonies was transferred and resuspended in fresh LB, in triplicate. Three biological replicates per isolate were included for the RNA-seq experiment. From these, 10mL liquid subcultures with a starting OD600 of 0.01 were grown in a vented 50mL tube at 37°C with shaking at 220 RPM for 12 hrs. At the mid-log growth phase (5 and 5.5 hours for the hypermutator and wild-type cells, respectively) 1.5mL of culture was mixed with 3mL of RNA-Protect Reagent (Qiagen, Germantown, MD, USA). Cell harvest was conducted as per the manufacturer’s instructions.

extract_protocol:
Total RNA was extracted with MagMAX Viral/Pathogen kit, modified to include a DNAse incubation step. One microgram of RNA underwent rRNA depletion with the NEBNext rRNA depletion kit for bacteria.
RNA-Seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® and NEBNext Multiplex Oligos for Illumina on an epMotion 5075 instrument.

treatment_protocol: Bacterial cultures were serially passaged on increasing concentrations of Ceftazidime-avibactam prior to whole-genome sequencing and RNA-seq.

tag: strain

tag: genotype

value: wild-type

tag: treatment

value: Ceftazidime/avibactam


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1A15_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1D16_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1A15_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1B6_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1A15_A


title: G1812_RNAseq_G1812_wounding_rep2

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

country: China

institute: Fudan University

data_processing:
Sequencing reads were cleaned with the Trim Galore, Trimmomatic, and Sickle programs.
The cleaned reads were mapped to WheatTu IGDBv1.0 using BWA for ChIP-seq and DNase-seq. HISAT2 for RNA-seq data. Bismark program for Bisulphite-seq.
For ChIP-seq and DNase-seq, MACS was used to identify read-enriched regions (peaks) with P value < 1e–10. The MAnorm package was used for the quantitative comparison of signals between samples with the following criteria: |M value| > 1 and P < 0.05.
For RNA-seq, featureCount program of the Subread package was used to determine the RNA-seq read density for the genes. The DEseq2 program was used for detecting differentially expressed genes based on the following criteria: |log2 fold-change| > 1 and P < 0.05.
For Bisulphite-seq, the extent of the cytosine methylation was determined with the bismark_methylation_extractor implemented in the Bismark program. Next, the methylation ratio of a cytosine was calculated as the number of mCs divided by the number of reads covering the position. Bases covered by fewer than three reads were considered low-confidence positions whose methylation ratios were not recorded.
Genome_build: IGDBv1.0
Supplementary_files_format_and_content: peak files and bigwig files
Supplementary_files_format_and_content: FPKM values for each sample

organism: Triticum urartu

source_name: seedling

growth_protocol: 16h light, 8h dark, 22°C

extract_protocol:
2.2 μg DNA extracted from the harvested seedlings were used to prepare ChIP-seq, DNase-seq and Bisulphite-seq. RNA was extracted using TRIzol and 2μg total RNA were used to prepare RNA-seq. Nuclei were extracted with H1B buffer(20 mM Tris-HCl, pH 8.0, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 40% glycerol, and 0.1% mercaptoethanol) for DNase-seq.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Regarding the cold and heat stress treatments, 7-day-old seedlings grown in soil were transferred to 4 °C for 5 hours, 40 °C for 7 hours, respectively. To assess the effects of drought, 7-day-old seedlings were cultivated in soil for another 2 weeks without watering. For the NaCl and ABA treatments, 7-day-old seedlings grown in soil were treated with 250 mM NaCl for 7 hours, 100 μm ABA for 2 weeks. For wounding stress, 7-day-old seedlings were injured on leaves by scissors and samples were taken 2.5 hours later.

tag: tissue

value: seedling

tag: accession

value: injured on leaves for 2.5 hours


title: G1812_RNAseq_G1812_heat_rep1

value: 40 °C for 7 hours


title: G1812_RNAseq_G1812_heat_rep2


title: G1812_ChIPseq_H3K4me3_ABA

library_source: genomic

data_processing:
Sequencing reads were cleaned with the Trim Galore, Trimmomatic, and Sickle programs.
The cleaned reads were mapped to WheatTu IGDBv1.0 using BWA.
MACS was used to identify read-enriched regions (peaks) with P value < 1e–10.
Genome_build: IGDBv1.0
Supplementary_files_format_and_content: peak files and bigwig files

molecule: genomic DNA

source_name: Triticum urartu seedling

extract_protocol:
For histone ChIP-seq assay, approximately 30 seedlings were pooled and ground to a powder. More than 10 ng ChIP DNA was used to prepare each sequencing sample. For TF ChIP-seq assay,  Tu plants grown on soil under 16 h light/ 8 h dark conditions for 2 weeks before protoplast isolation. Approximately, 30 ug pMD19-T plasmids containing p35S:3flag-AP2 DNA were transfected into leaf protoplasts using the PEG-mediated transfection method. After incubating the protoplasts at room temperature for 48 h under dark condition, the protoplasts were crosslinked with 1% formaldehyde in W5 solution for 10 min on ice and quenched with 32 ul 2 M glycine for 5 min. Protoplasts were collected by centrifuging at 600 g for 2 min at 4°C, wash with 500 ul W5 solution once and collected again. Protoplasts were lysed in 120 ul room temperature lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (wt/vol) SDS, 1 mM PMSF, 1× protease inhibitor cocktail) by vortex. Total lysates containing chromatin were subjected to sonication by Bioruptor until the chromatin was fragmented into 300bp-500bp.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For ABA treatments, 7-day-old seedlings grown in soil were treated with 100 μm ABA for 2 weeks.

tag: antibody

tag: antibody manufacturer

value: Abcam


title: G1812_ChIPseq_AP2-DREB-7

value: Flag

value: sigma


title: G1812_RNAseq_G1812_drought_rep2

value: cultivated in soil for 2 weeks without watering


title: G1812_RNAseq_G1812_wounding_rep1


title: G1812_RNAseq_G1812_CK_rep5


title: G1812_RNAseq_G1812_ABA_rep2

molecule: polyA RNA

value: 100 μm ABA for 2 weeks


title: G1812_RNAseq_G1812_drought_rep1


title: G1812_RNAseq_G1812_ABA_rep1


title: G1812_RNAseq_G1812_salt_rep1

value: NaCl for 7 hours


title: G1812_RNAseq_G1812_salt_rep2


title: G1812_RNAseq_G1812_CK_rep6


title: G1812_RNAseq_G1812_cold_rep2

value: 4 °C for 5 hours


title: G1812_RNAseq_G1812_CK_rep2


title: G1812_RNAseq_G1812_CK_rep1


title: G1812_RNAseq_G1812_CK_rep4


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1B6_B


title: G1812_DNaseseq_DHS_rep2


title: G1812_Bisulphiteseq_DNAmeth


title: G1812_RNAseq_G1812_CK_rep3


title: G1812_ChIPseq_H3K27me3_ABA

value: Upstate

tag: antibody catalog #


title: G1812_ChIPseq_H3K27me3


title: G1812_RNAseq_G1812_cold_rep1


title: G1812_ChIPseq_H3K4me3


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B4_B

value: mutSTn


title: SBP3

data_processing:
Library strategy: DAP-seq
Sequencing reads were cleaned with the fastp(version 0.20.0) and Trim Galore (version 0.4.4), which eliminated bases with low quality scores(< 25) and irregular GC contents, sequencing adapters, and short reads.
The remaining clean reads were mapped to the T. urartu genome with the Burrows–Wheeler Aligner(version 0.7.17-r1188).
The MACS(version 2.2.6) program was used to identify the read-enriched regions(peaks) based on the criteria: P < 1e−10. The peaks detected from samples introduced with Halo tag only were considered as non-specific bindings, and TF peaks overlapping with peaks detected from Halo samples were removed for subsequent analysis.
Genome_build: WheatTu IGDBv1.0
Supplementary_files_format_and_content: peak files and bigwig files

extract_protocol:
Genomic DNA was extracted from leaves using Plant DNAzol Reagent(invitrogen). RNA was extracted using TRIzol.
Genomic DNA was fragmented. And then end repaired using the End-It kit(Lucigen) and A-tailed using Klenow(3'-5' exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase(Promega). Full length TF was cloned into pIX-Halo vector. Halo-tagged TF was expressed in vitro using TNT SP6 Coupled Wheat Germ Extract System(Promega). Halo-TF was immobilized by Magne HaloTag Beads(Promega) and then incubated with the DNA library. TF specific binding DNA was eluted for 10 min at 98°C and amplified with indexed Illumina primer using Phanta Max Super-Fidelity DNA Polymerase(Vazyme). Meanwhile, to capture background DNA which captured by Halo, pIX-Halo vector without TF cloned was expressed and incubated with the DNA library as well. The PCR product was purified using VAHTS DNA Clean Beads(Vazyme).

tag: dap antibody

value: Halo (Promega-G7281)


title: NF-YC-1


title: G1812_ChIPseq_H3K9ac


title: WRKY14


title: NAC9


title: NAC27


title: NAC24


title: NAC22


title: NAC12


title: NAC10


title: NAC13


title: G1812_DNaseseq_DHS_rep1


title: NAC1


title: MYB32


title: MYB34


title: MYB36


title: MYB33


title: MYB30


title: MYB24


title: MYB21


title: NAC8


title: MYB22


title: MYB18


title: NAC23


title: MYB20


title: MYB2


title: MYB16


title: MYB14


title: MYB12


title: MYB6


title: HB-HD-ZIP-3


title: MYB15


title: GARP6


title: NAC11


title: LOB3


title: GARP-G2-1


title: LOB2


title: GARP2


title: GRAS2


title: MYB23


title: C3H-5


title: C2C2-5


title: C3H-2


title: C3H-1


title: C2C2-4


title: C2C2-3


title: Ctrl_3_Microarray

status: Public on Aug 31 2021

type: RNA

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

hyb_protocol: DNA targets were hybridized for 17h at 45°C on GeneChip Human Transcriptome Arrays 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip Expression Wash, Stain and Scan protocol (Affymetrix GeneChip Wash, Stain and Scan Kit, 900720).

scan_protocol: Subsequently, the GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: RMA normalization with Bioconductor package Oligo, filtering out non-main probes with Bioconductor package affycoretools, differential expression analysis with Bioconductor package limma.

label: biotin

organism: Homo sapiens

source_name: Jurkat cells (ATCC Clone E6-1, TIB152™)

label_protocol: The fragmented and biotinylated DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol (Affymetrix GeneChip® WT PLUS Reagent Kit, 902280) from 100 ng total RNA starting material and 5.5 µg cDNA intermediate product.

growth_protocol: Grown in RPMI + 10% FCS + Penicillin/Streptomycin, split every second day, feeding every day

extract_protocol: Cells were fixed by quickly releasing them into TRIzol. Cells were sheared with a needle and syringe. After chloroform extraction, 0.6ml RLT buffer was added to the aqueous supernatent. RNA was extracted with Quiagen Rneasy mini kit.

treatment_protocol: Jurkat cells were exposed to 15 minutes of hypergravity or to normal gravity

tag: gravity


title: bZIP8


title: C2C2-2


title: C2C2-1


title: LOB5


title: bZIP3


title: bZIP11


title: bHLH2


title: bHLH14


title: bZIP1


title: bHLH16


title: bHLH5


title: bHLH13


title: B3-10


title: bHLH12


title: AP2-14


title: Halo_rep2


title: AP2-15


title: Halo_rep3


title: Halo_rep1


title: ZFHD2


title: WRKY5


title: ZFHD1


title: bZIP5


title: WRKY8


title: bZIP4


title: WRKY20


title: WRKY21


title: WRKY16


title: WRKY30


title: WRKY19


title: bHLH7


title: WRKY13


title: WRKY18


title: WRKY15


title: WRKY12


title: WRKY11


title: WRKY10


title: NAC26


title: NAC4


title: NAC29


title: NAC2


title: NAC15


title: NAC18


title: NAC17


title: MYB31


title: NAC14


title: MYB19


title: MYB17


title: MYB13


title: MYB26


title: HSF1


title: MYB11


title: HB-HD-ZIP-2


title: HB-HD-ZIP-6


title: GARP5


title: C2H2-4


title: bZIP20


title: bZIP2


title: bZIP17


title: Trihelix1


title: bZIP10


title: bZIP7


title: AP2-RAV-26


title: AP2-ERF-23


title: bHLH10


title: AP2-ERF-13


title: AP2-DREB-8


title: MYB27


title: AP2-DREB-7


title: AP2-DREB-21


title: AP2-DREB-18


title: AP2-DREB-19


title: AP2-DREB-1


title: AGO3_plantlet

first: Antonin

last: Marchais

address: Universitatstrasse 2

department: Department of Biology

institute: ETHZ

description: small RNAs

data_processing:
Basecalls performed using HiSeq Control Soft. v. 2.0.12.0, RTA 1.17.21.3 and CASAVA 1.8 for Hiseq 2500 runs and using HiSeq Control Soft. v. 1.5.15.1, RTA 1.13.48.0 and CASAVA 1.8.2 for Hiseq 2000 runs.
sRNAseq reads were aligned to the TAIR10 genome assembly using ncPRO pipeline.
Genome_build: TAIR10
Supplementary_files_format_and_content: Sequence count for A. thaliana derived small RNAs

organism: Arabidopsis thaliana

source_name: AGO3 IP@FLAG

growth_protocol: Arabidopsis thaliana plants grown on soil underlong day light conditions for the siliques experiment and on MS plate under continuous light for the syringolin experiment

extract_protocol:
Total RNA was isolated with Trizol
Libraries construction was contracted out to Fasteris SA. At Fasteris SA, barcoded libraries were prepared such that four samples could be run per lane.
Libraries were prepared according to Illumina's instructions accompanying the sequencing Kit TruSeq™ SBS v5.

tag: ecotype

tag: genotype/variation

value: ago3-3 pAGO3-FHA-AGO3

tag: tissues

value: Plantlet

tag: ip reagent

value: EZview Red ANTI-FLAG M2 Affinity Gel from Sigma


title: AGO3_SylA_plantlet

description: small RNAs

source_name: AGO3 IP@FLAG Syringolin A

value: SyringolinA


title: Total_plantlet

description: small RNAs

source_name: Col0 Total


title: Total_SylA_plantlet

description: small RNAs

source_name: Col0 Total Syringolin A


title: T1

city: Shanghai

first: Quan

last: Wang

state: Shanghai

address: No.197 Ruijin 2nd Road, Shanghai, 200025, China

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Cochlea Modiolus

extract_protocol:
Cochlear modi  were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cochlea Modiolus

tag: cell type

value: spiral ganglion neuron

tag: group

value: degenerated


title: T3


title: bHLH11

value: seedling


title: T2


title: C3

value: control


title: C2


title: Intestinal Enteroid 68hr (Mm)

city: Cincinnati

first: Andrew

middle: E

last: Rosselot

state: OH

address: 231, Albert Sabin way

department: Department of Pharmacology and Systems Biology

institute: University of Cincinnati, College of Medicine

data_processing:
RNA-Seq data were pseudoaligned and quantified (transcript per million estimates) using a call to the software Kallisto within AltAnalyze version 2.1.4 and an Ensembl version 72 reference database.
Genome_build: mm10
Supplementary_files_format_and_content: exp.MIE_2020.txt
Supplementary_files_format_and_content: Mouse-enteroids_RAIN-24h_EMBO.xlsx

source_name: Intestinal Enteroid 68hr

growth_protocol: Mouse enteroids are derived from small intestinal tissue from C57B6 mice, added to 40µL of Matrigel (Corning) membrane matrix, suspended as a single 3D Matrigel dome within a 24-well plate and provided 400µL mouse enteroid media (Advanced DMEM/F-12 (Gibco), L-Glutamine (Gibco), Penicillin/Streptomycin (Gibco), N-2 (Gibco), B-27 (Gibco), 10mM HEPES solution (Millipore-Sigma), 50ng/mL recombinant murine EGF (Peprotech), and R-Spondin/Noggin conditioned media generated in-house. Enteroids were passaged every 4-7 days via a 27G syringe (BD). All samples were maintained in cell culture incubators set at 37°C and 5% CO2.

extract_protocol:
At each collection timepoint, cells were pelleted, suspended in 1mL TRI reagent (Molecular Research Center) and snap frozen in liquid N2. After completion of the time course, RNA was isolated via a RNeasy mini-kit column (Qiagen).
The cDNA synthesis and amplification were done as recommended by Clontech. cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents. Fragmented and tagged libraries were quantified using an agilent bio-analyzer, pooled and sequenced on an Illumina platform using the pair-end 100-bp sequencing strategy.

treatment_protocol: Samples were collected every two hours for 48-hours starting at 24-hours post circadian synchronization using dexamethasone.

value: Intestinal Enteroid

tag: passage

value: passaged every 4-7 days

tag: circadian clock


title: Intestinal Enteroid 64hr (Mm)

source_name: Intestinal Enteroid 64hr


title: Intestinal Enteroid 70hr (Mm)

source_name: Intestinal Enteroid 70hr


title: Intestinal Enteroid 66hr (Mm)

source_name: Intestinal Enteroid 66hr


title: C1

tag: strain


title: AP2-DREB-9


title: Intestinal Enteroid 62hr (Mm)

source_name: Intestinal Enteroid 62hr

tag: treatment


title: Intestinal Enteroid 60hr (Mm)

source_name: Intestinal Enteroid 60hr


title: Intestinal Enteroid 58hr (Mm)

source_name: Intestinal Enteroid 58hr


title: Intestinal Enteroid 56hr (Mm)

source_name: Intestinal Enteroid 56hr


title: Intestinal Enteroid 52hr (Mm)

source_name: Intestinal Enteroid 52hr


title: Intestinal Enteroid 50hr (Mm)

source_name: Intestinal Enteroid 50hr


title: Intestinal Enteroid 46hr (Mm)

source_name: Intestinal Enteroid 46hr


title: Intestinal Enteroid 42hr (Mm)

source_name: Intestinal Enteroid 42hr


title: Intestinal Enteroid 44hr (Mm)

source_name: Intestinal Enteroid 44hr


title: Intestinal Enteroid 48hr (Mm)

source_name: Intestinal Enteroid 48hr


title: Intestinal Enteroid 36hr (Mm)

source_name: Intestinal Enteroid 36hr


title: Intestinal Enteroid 40hr (Mm)

source_name: Intestinal Enteroid 40hr


title: Intestinal Enteroid 38hr (Mm)

source_name: Intestinal Enteroid 38hr


title: Intestinal Enteroid 32hr (Mm)

source_name: Intestinal Enteroid 32hr


title: Intestinal Enteroid 34hr (Mm)

source_name: Intestinal Enteroid 34hr


title: Intestinal Enteroid 28hr (Mm)

source_name: Intestinal Enteroid 28hr


title: Intestinal Enteroid 30hr (Mm)

source_name: Intestinal Enteroid 30hr


title: Intestinal Enteroid 26hr (Mm)

source_name: Intestinal Enteroid 26hr


title: Intestinal Enteroid 24hr (Mm)

source_name: Intestinal Enteroid 24hr


title: Intestinal Enteroid 54hr (Mm)

source_name: Intestinal Enteroid 54hr


title: 71405_RNA-seq Bhlhe40+/+ CCR6+ B cells d4 after immunization

city: Vienna

first: Maria

last: Fischer

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

data_processing:
Bulk RNA-seq: Sequence reads that passed the Illumina quality filtering were considered for alignment. Reads corresponding to mouse ribosomal RNAs (BK000964.1 and NR046144.1) were removed. The remaining reads were cut down to a read length of 44 bp and aligned to the mouse transcriptome (genome assembly version of July 2007 NCBI37/mm9) using TopHat version 1.4.1 (Trapnell et al, 2009). The calculation of RNA expression values was all based on the RefSeq database, which was downloaded from UCSC on January 10th, 2014. The annotation of immunoglobulin and T cell receptor genes was incorporated from the Ensembl release 67 (Cunningham et al, 2015). Genes with overlapping exons were flagged and double entries (i.e. exactly the same gene at two different genomic locations) were renamed. Genes with several transcripts were merged to consensus-genes consisting of a union of all underlying exons using the fuge software (I. Tamir, unpublished), which resulted in 25,726 gene models.  For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 (Anders et al, 2014) with the overlap resolution mode set to 'union'. The datasets were analyzed using the R package DESeq2 version 1.2.10 (Love et al, 74). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. Transcripts per million (TPM) were calculated from RNA-seq data, as described (Wagner et al, 2012).  GSEA was performed using the GSEA software from the Broad Institute (Subramanian et al, 2005). Genes were ranked on the basis of their change in expression (log2 fold values) as determined by the DESeq2 package and were compared to gene sets from the MSigDB or defined gene sets from literature or our data. GC B cell signature was used from Mabbott et al (Mabbott and Gray, 2014) with Bcl6 and Gcsam manually added to the signature. Early GC B cell signature was generated by pairwise comparison of our WT day 4 GC B and CCR6+ B cell datasets, using top 500 GC B cell-upregulated genes.
Genome_build: MM9 (MM10 for scRNA-seq)
Supplementary_files_format_and_content: text tab delim = TPM values in ASCII text format tab delimited

source_name: Splenic B cells

extract_protocol:
SMART-Seq v2 Cell protocoll Nextera XT
SMART-Seq v2 Cell protocoll Nextera XT

value: Splenic B cells

tag: genotype

tag: cell preparation

value: Ex vivo, FACS-sorted from spleens

tag: cell sorting strategy


title: 71407_RNA-seq Bhlhe40+/+ GC B cells d4 after immunization


title: 71403_RNA-seq Bhlhe40+/+ GC B cells d4 after immunization


title: 71404_RNA-seq Bhlhe40-/- GC B cells d4 after immunization


title: 71401_RNA-seq Bhlhe40+/+ CCR6+ B cells d4 after immunization


title: 71397_RNA-seq Bhlhe40+/+ CCR6+ B cells d4 after immunization


title: 58642_RNA-seq Bhlhe40-/- lymphoma from thymus  mouse 1

source_name: Thymus lymphoma B cells

extract_protocol:
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
NEBNext Ultra II

value: Thymus lymphoma B cells

value: Ex vivo, FACS-sorted from thymus lymphomas


title: 58643_RNA-seq Bhlhe40-/- lymphoma from lungs mouse 2

source_name: Lung lymphoma B cells

value: Lung lymphoma B cells

value: Ex vivo, FACS-sorted from lung lymphomas


title: 71400_RNA-seq Bhlhe40-/- GC B cells d4 after immunization


title: 58640_RNA-seq Bhlhe40-/- lymphoma from spleen mouse 1

source_name: Spleen lymphoma B cells

value: Spleen lymphoma B cells

value: Ex vivo, FACS-sorted from spleen lymphomas


title: 71398_RNA-seq Bhlhe40-/- CCR6+ B cells d4 after immunization


title: 58634_RNA-seq Bhlhe40-/- DZ GC B cells from mixed chimeras immunized with SRBC

value: CD19+CD95+GL7+CXCR4hiCD86lo CD45.2


title: 71402_RNA-seq Bhlhe40-/- CCR6+ B cells d4 after immunization


title: 71399_RNA-seq Bhlhe40+/+ GC B cells d4 after immunization


title: 58631_RNA-seq Bhlhe40-/- LZ GC B cells from mixed chimeras immunized with SRBC

value: CD19+CD95+GL7+CXCR4loCD86hi CD45.2


title: 58630_RNA-seq Bhlhe40-/- DZ GC B cells from mixed chimeras immunized with SRBC


title: 58635_RNA-seq  Bhlhe40-/- LZ GC B cells from mixed chimeras immunized with SRBC


title: 71406_RNA-seq Bhlhe40-/- CCR6+ B cells d4 after immunization


title: 58628_RNA-seq WT DZ GC B cells from mixed chimeras immunized with SRBC

value: CD19+CD95+GL7+CXCR4hiCD86lo CD45.1


title: reporter-PBS3

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
A bowtie2 index was built for the GRCm38 genome assembly using bowtie12 version 2.2.3. The RNA-seq reads of each of the 8 samples were mapped using Tophat13 version 2.0.9 supplied by Ensembl annotation file; GRCm38.78.gtf. Each sample's transcripts were assembled and their expression quantified using Cufflinks version 2.2.1 supplied by GRCm38.78.gtf. Normalization was performed via the median of the geometric means of fragment counts across all libraries.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized log2FPKM values are provided in a Supplementary Table 1.xlsx file.

source_name: primary motor neuron from CD1 mouse

growth_protocol: The pHSE-FLPo plasmid encoding FLPo (codon optimized Flippase) under the control of HS response element and the pFRT-RFP (reporter) and the pCAGIG (labeling all electroporated cells) constructs (2 µg/µl each) were transfered to into primary motor cortex (M1) by directional in utero electroporation at E (embryonic day) 15.

extract_protocol:
Intracellular contents were obtained from live single neurons in M1 of the mouse cortex at P (postnatal day) 30. The collected single-cell contents were expelled into a thin-walled RNA-free PCR tube (Eppendorf, NY), with 1% (final) IGEPAL CA-630 (Sigma-Aldrich, MO), and immediately frozen on dry ice for storage at −80°C until further processing.
The cDNA libraries were prepared using the SMARTer Ultra Low Input RNA Kit for Sequencing - v3 (TAKARA Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies) and Kapa Library Quantification Kit (Kapa Biosystems).
The libraries were pooled and diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol. The denatured libraries were diluted to 10 pM by pre-chilled hybridization buffer and loaded onto TruSeq SR v3 flow cells on an Illumina HiSeq 2500 (Illumina) and run for 51 cycles using a single-read recipe (TruSeq SBS Kit v3, Illumina) according to the manufacturer's instructions. Illumina CASAVA pipeline (released version 1.8, Illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter. Additional quality filtering used FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) to keep only reads that have at least 80% of bases with a quality score of 20 or more (conducted by fastq_quality_filter function) and reads left with > 10 bases after being trimmed with reads with a quality score of < 20 (conducted by fastq_quality_trimmer function).

treatment_protocol: Following electroporation, pregnant mice received intraperitoneal (i.p.) injections of 25% EtOH in PBS at 4.0 or 1.0 g/kg weight daily at E16 and E17. PBS alone was used as the control.

tag: reporter gene expression

value: pCAGIG (GFP) positive but RFP negative (didn't respond to heat shock)

tag: exposure in utelus

value: PBS

tag: time course

value: exposed to EtOH at E16-E17, neurons/RNA extracted at P30


title: reporter-PBS6


title: reporter-PBS5


title: reporter-PBS4


title: reporter-PBS1


title: reporter-PBS2


title: reporter+EtOH15

value: pCAGIG (GFP) and RFP (responded to heat shock) double positive

value: EtOH


title: 58632_RNA-seq  WT DZ GC B cells from mixed chimeras immunized with SRBC


title: 58633_RNA-seq WT LZ GC B cells from mixed chimeras immunized with SRBC

value: CD19+CD95+GL7+CXCR4loCD86hi CD45.1


title: reporter+EtOH14


title: reporter+EtOH13


title: reporter+EtOH8


title: reporter+EtOH7


title: reporter+EtOH9


title: reporter+EtOH11


title: reporter+EtOH3


title: 58629_RNA-seq WT LZ GC B cells from mixed chimeras immunized with SRBC

value: Splenic B cells


title: reporter+EtOH5


title: reporter+EtOH2


title: reporter-EtOH7


title: reporter+EtOH4


title: reporter+EtOH1


title: reporter-EtOH6


title: reporter-EtOH5


title: hiAM-2.52

city: Nijmegen

first: Rebecca

middle: Regina

last: Snabel

state: Gelderland

address: Geert Grooteplein 26-28

department: Molecular Developmental Biology

country: Netherlands

institute: RIMLS

description:
GRCh38.p13-counts.tsv
GRCh38.p13-CPM_log.tsv
LUMC-025-D12-1

data_processing:
Trimming of the reads and alignment was performed with seq2science (v0.4.0, https://doi.org/10.5281/zenodo.4451349).
Fastp (v0.20.1) trimmed the low quality 3’ ends and Salmon (v1.3.0) quant aligned the reads to the GRCh38.p13 genome from Ensembl, tximeta (v1.4.3) was used to generate the gene expression matrix.
The counts per million (CPM) were log1p-transformed.
Genome_build: GRCh38.p13 (Ensembl)
Supplementary_files_format_and_content: "metadata.tsv|" contains sample metadata, "GRCh38.p13-counts.tsv" contains the raw gene counts, "GRCh38.p13-CPM_log.tsv" contains the log1p-transformed counts per million.

source_name: human immortalized atrial myocyte

extract_protocol:
hiAMs RNA was extracted from proliferating and differentiated hiAMs seeded at a density of 10^5 cells/cm2 (10^6 cells per sample) using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. hESC-AMs RNA (10^6 cells per sample) using the NucleoSpin RNA kit (Macherey-Nagel) according to manufacturer’s instructions.
Libraries were generated from 200 ng RNA using the KAPA-RNA HyperPrep kit with RiboErase (Roche) to remove ribosomal RNA, according to manufacturer’s instructions. Library amplification was performed with 11 cycles.
Libraries were multiplexed and sequenced on NextSeq500 Illumina to generate 38bp PE reads.

value: human immortalized atrial myocyte

tag: monoclone

tag: timepoint

value: day 12 of differentiation


title: hiAM-2.38

description:
GRCh38.p13-counts.tsv
GRCh38.p13-CPM_log.tsv
LUMC-020-D12-2


title: reporter-EtOH4


title: reporter-EtOH1


title: hESC-AM3

description:
GRCh38.p13-counts.tsv
GRCh38.p13-CPM_log.tsv
LUMC-03-sortedD28-3

source_name: hESC-derived atrial myocyte

value: hESC-derived atrial myocyte

value: day 28 of differentiation


title: hESC-AM4

description:
GRCh38.p13-counts.tsv
GRCh38.p13-CPM_log.tsv
LUMC-04-sortedD28-4


title: hiAM-2.90

description:
GRCh38.p13-counts.tsv
GRCh38.p13-CPM_log.tsv
LUMC-036-D12-6


title: reporter+EtOH10


title: hESC-AM1

description:
GRCh38.p13-counts.tsv
GRCh38.p13-CPM_log.tsv
LUMC-01-sortedD28-1


title: reporter+EtOH12


title: reporter+EtOH6


title: reporter-EtOH2


title: TBP_ab_siEloA_0.5H-1

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Library strategy: CUT&Tag
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome hg38 with Bowtie2 aligner with parameters "--local --very-sensitive-local  --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700".
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files with merged replicates

growth_protocol: HCT116 cells were cultured under an atmosphere of 5% CO2 at 37 °C in McCoy’s 5A medium (Lonza) supplemented with 10% (v/v) fetal bovine serum (Invitrogen), 1% Penicillin-Streptomycin (Thermo Fisher Scientific), 1% GlutaMAX (Thermo Fisher Scientific) and 1% non-essential amino acids (Thermo Fisher Scientific).

extract_protocol:
Cells from one 10-cm dish containing ~8 × 106 HCT116 cells were transferred to a 1.5ml tube, and cell numbers were measured. Cells were cross-linked with 0.1% formaldehyde in phosphate-buffered saline for 2 min at room temperature before quenching with glycine to a final concentration of 0.125 M. Cells were resuspended in NE buffer, incubated on ice for 10 min, and nuclei were collected centrifugation at 600xg for 5 min. Cut&Tag assays were performed with up to 100,000 nuclei according to the method of Kaya-Okur et al. (2020). All libraries were sequenced on an Illumina NextSeq 500 according to the manufacturer’s instructions.
To amplify libraries as previously described in  Kaya-Okur et al. (2020), sample was mixed with 2 μL of a universal i5(10 μM) and a uniquely barcoded i7 primer((10 μM), using a different barcode for each sample. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cyclingconditions: 72 °C for 5 min (gapfilling); 98 °C for 30 s; 14 cycles of 98 °C for 10 sand 63 °C for 30 s;final extension at 72 °C for 1 min and hold at 8 °C. Post-PCR clean-up was performed by adding 1.3× volume of Ampure XP beads (BeckmanCounter), and libraries were incubated with beads for 15 min at RT, washed twicegently in 80% ethanol, and eluted in 30 μL 10 mM Tris pH 8.0.

treatment_protocol: HCT116 cells in 10 cm dishes (~2 × 106 cells per dish) were transfected with 10 nM siRNAs targeting human ELOA (ON-TARGET plus SMARTPool, L-005143-00, siRNA #1, J-005143-07-0002; or siRNA #3, J-005143-09-0002; Dharmacon), or with 10 nM siSTABLE Non-targeting siRNA #1 (D-001700-01; Dharmacon) using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen). siRNA sequences are listed in Table S1. siRNA containing media was removed after 6 hours. ~42 hours later cells were supplemented with thapsigargin in DMSO (final concentration of 300 nM), and cells were incubated a further 30, 60, or 120 min for CUT&Tag.

tag: antibody

value: anti-TBP, Proteintech cat#ab51841

tag: sirna

value: Elongin A (siELOA)

tag: time point


title: TBP_ab_NT_1H-1

value: control non-targeting siRNA


title: TBP_ab_NT_1H-2


title: TBP_ab_siEloA_0.5H-2


title: TBP_ab_NT_2H-2


title: TBP_ab_siEloA_0H-1


title: TBP_ab_siEloA_0H-2


title: TBP_ab_siEloA_2H-1


title: TBP_ab_siEloA_1H-2


title: hESC-AM2

description:
GRCh38.p13-counts.tsv
GRCh38.p13-CPM_log.tsv
LUMC-02-sortedD28-2

tag: cell type


title: TBP_ab_NT_0H-1


title: TBP_ab_siEloA_1H-1


title: TBP_ab_NT_2H-1


title: TBP_ab_NT_0.5H-1


title: CDK8_pt_siEloA_2H-2

value: anti-CDK8, Proteintech cat#22067-1-AP


title: CDK8_pt_siEloA_2H-1


title: TBP_ab_siEloA_2H-2


title: CDK8_pt_siEloA_0H-2


title: CDK8_pt_siEloA_1H-2


title: CDK8_pt_siEloA_1H-1


title: CDK8_pt_siEloA_0H-1


title: CDK8_pt_siEloA_0.5H-2


title: CDK8_pt_siEloA_0.5H-1


title: 58641_RNA-seq  Bhlhe40-/- lymphoma from liver  mouse 1

source_name: Liver lymphoma B cells

value: Liver lymphoma B cells

value: Ex vivo, FACS-sorted from liver lymphomas


title: CDK8_pt_NT_2H-1


title: TBP_ab_NT_0H-2


title: CDK8_pt_NT_2H-2


title: TBP_ab_NT_0.5H-2


title: CDK8_pt_NT_1H-2


title: CDK8_pt_NT_0.5H-1


title: CDK8_pt_NT_0H-1


title: ATF6_pt_siEloA_1H-2

value: anti-ATF6, Proteintech cat#24169-1-AP


title: CDK8_pt_NT_0H-2


title: ATF6_pt_siEloA_2H-1


title: ATF6_pt_siEloA_2H-2


title: CDK8_pt_NT_0.5H-2


title: CDK8_pt_NT_1H-1


title: ATF6_pt_siEloA_1H-1


title: ATF6_pt_siEloA_0.5H-2


title: ATF6_pt_NT_2H-2


title: ATF6_pt_siEloA_0H-2


title: ATF6_pt_siEloA_0.5H-1


title: ATF6_pt_NT_1H-2


title: ATF6_pt_NT_1H-1


title: ATF6_pt_NT_0H-2


title: ATF6_pt_NT_0.5H-2


title: ATF6_pt_NT_0H-1


title: MED15_pt_siEloA_2H-2

value: anti-MED15, Proteintech cat#11566-1-AP


title: MED15_pt_siEloA_2H-1


title: MED15_pt_siEloA_1H-2


title: ATF6_pt_NT_0.5H-1


title: MED15_pt_siEloA_0H-1


title: MED15_pt_siEloA_0H-2


title: MED15_pt_siEloA_1H-1


title: MED15_pt_siEloA_0.5H-1


title: MED15_pt_siEloA_0.5H-2


title: MED15_pt_NT_0H-2


title: MED15_pt_NT_1H-2


title: ATF6_pt_siEloA_0H-1


title: MED15_pt_NT_2H-1


title: ATF6_pt_NT_2H-1


title: MED15_pt_NT_0H-1


title: MED15_pt_NT_1H-1


title: MED15_pt_NT_2H-2


title: MED15_pt_NT_0.5H-1


title: MED15_pt_NT_0.5H-2


title: EloA_pt_siEloA_1H-1

value: anti-TCEB3, Proteintech cat#10502-1-AP


title: EloA_pt_siEloA_0H-2


title: EloA_pt_siEloA_2H-1


title: EloA_pt_siEloA_0.5H-1


title: EloA_pt_siEloA_0.5H-2


title: EloA_pt_NT_2H-2


title: EloA_pt_NT_1H-2


title: EloA_pt_siEloA_0H-1


title: EloA_pt_NT_2H-1


title: EloA_pt_NT_1H-1


title: EloA_pt_NT_0H-1


title: EloA_pt_NT_0H-2


title: MED1_siEloA_2H-2

value: anti-MED1, Sigma cat#17-10530


title: EloA_pt_siEloA_2H-2


title: MED1_siEloA_1H-2


title: EloA_pt_NT_0.5H-1


title: MED1_siEloA_2H-1


title: MED1_NT_2H-1


title: MED1_siEloA_1H-1


title: MED1_siEloA_0.5H-1


title: MED1_siEloA_0H-1


title: MED1_siEloA_0.5H-2


title: MED1_siEloA_0H-2


title: MED1_NT_2H-2


title: EloA_pt_siEloA_1H-2


title: MED1_NT_0.5H-1


title: MED1_NT_0H-2


title: MED1_NT_0.5H-2


title: MED1_NT_1H-1


title: MED1_NT_0H-1


title: MED1_NT_1H-2


title: EloA_pt_NT_0.5H-2


title: S2p_siEloA_2H-1

value: anti-Phospho-Rpb1 CTD (Ser2) E1Z3G, Cell Signaling cat#13499


title: S2p_siEloA_2H-2


title: S2p_siEloA_1H-2


title: S2p_siEloA_0H-2


title: S2p_siEloA_1H-1


title: S2p_siEloA_0.5H-2


title: S2p_NT_2H-1


title: S2p_NT_2H-2


title: S2p_NT_1H-2


title: S2p_NT_0.5H-1


title: S5p_siEloA_2H-2

value: anti-Phospho-Rpb1 CTD (Ser5) D9N5I, Cell Signaling cat#13523


title: S2p_siEloA_0.5H-1


title: S2p_NT_1H-1


title: S5p_siEloA_1H-1


title: S5p_siEloA_2H-1


title: S2p_NT_0H-1


title: S2p_NT_0H-2


title: S2p_NT_0.5H-2


title: S5p_siEloA_0.5H-1


title: S5p_siEloA_0H-1


title: S5p_siEloA_0H-2


title: S5p_NT_2H-2


title: S5p_NT_1H-2


title: S5p_NT_2H-1


title: S2p_siEloA_0H-1


title: S5p_NT_0H-1


title: S5p_NT_0.5H-1


title: S5p_NT_0.5H-2


title: S5p_siEloA_1H-2


title: S5p_NT_0H-2


title: S5p_NT_1H-1


title: S5p_siEloA_0.5H-2


title: pancreatic tumor 60

first: Wei

last: Guo

address: Yueyang road 320, Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description:
Basal
YX16341T

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 genome using Hisat2 v2.1.0.
Raw count for transcripts was calculated using HTseq v0.12.4.
Normalization of gene expression was performed by SizeFactors using DEseq v1.24.0 in R.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with gene expression for every gene and every sample.

source_name: pancreas

extract_protocol:
Frozen tumor tissues were aseptically sliced into appropriate sizes and placed in sterile tubes. Total RNA were extracted using AllPrep DNA/RNA Mini Kit(QIAGEN).
RNA samples were applied to library construction and whole transcriptome sequencing on the Illumina platform.

treatment_protocol: tumor samples were obtained from surgical specimens and immediately frozen at -80°C prior to nucleic acid extraction.

tag: tissue

value: Pancreas

tag: tissue type

value: Primary

tag: sample type

value: Frozen tumor


title: pancreatic tumor 58

description:
Basal
YX16327T


title: pancreatic tumor 47

description:
Basal
YX15214T


title: pancreatic tumor 45

description:
Basal
YX15187T


title: pancreatic tumor 62

description:
Classical
YX16347T


title: pancreatic tumor 50

description:
Basal
YX16068T


title: pancreatic tumor 61

description:
Hybrid
YX16343T


title: pancreatic tumor 55

description:
Basal
YX16094T


title: pancreatic tumor 59

description:
Classical
YX16335T


title: pancreatic tumor 52

description:
Hybrid
YX16075T


title: pancreatic tumor 51

description:
Basal
YX16070T


title: pancreatic tumor 57

description:
Basal
YX16295T


title: pancreatic tumor 53

description:
Basal
YX16079T


title: pancreatic tumor 49

description:
Basal
YX16011T


title: pancreatic tumor 48

description:
Hybrid
YX16009T


title: pancreatic tumor 54

description:
Basal
YX16087T


title: pancreatic tumor 44

description:
Basal
YX15166T


title: pancreatic tumor 42

description:
Basal
YX15047T


title: pancreatic tumor 43

description:
Basal
YX15106T


title: pancreatic tumor 41

description:
Classical
YX16236T


title: pancreatic tumor 38

description:
Classical
YX16222T


title: 22Rv1_Luteolin_48hr

city: Nagoya

first: Aya

last: Naiki-Ito

address: 1-Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Experimental Pathology and Tumor Biology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

description: miRNA

hyb_protocol: 250 ng of labeled RNA was used for hybridization with TaKaRa Hybridization Chamber at 32°C for 16 hours. After hybridization, the miRNA Oligo chips were washed sequential.

scan_protocol: The miRNA Oligo chips were scanned by 3D-gene Scanner 3000 (Toray)

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals

source_name: 22Rv1, treated luteolin, 48hr

label_protocol: 250 ng of total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: 22Rv1 cells were cultured in RPMI1640 medium.

extract_protocol: Total RNA was extracted from 22Rv1using ISOGEN (Nippon Gene) following manufacturer's instructions

treatment_protocol: 22Rv1 cells were treated  25 μM luteolin for 48 hours.

tag: cell line

value: luteolin, 48hr

value: Human prostate cancer cell line


title: pancreatic tumor 56

description:
Basal
YX16172T


title: pancreatic tumor 36

description:
Hybrid
YX16207T


title: pancreatic tumor 37

description:
Hybrid
YX16218T


title: pancreatic tumor 39

description:
Hybrid
YX16224T


title: pancreatic tumor 34

description:
Basal
YX16202T


title: pancreatic tumor 31

description:
Classical
YX16185T


title: pancreatic tumor 30

description:
Hybrid
YX16180T


title: pancreatic tumor 28

description:
Classical
YX16177T


title: pancreatic tumor 46

description:
Hybrid
YX15211T


title: pancreatic tumor 32

description:
Hybrid
YX16188T


title: pancreatic tumor 19

description:
Hybrid
YX16144T


title: pancreatic tumor 23

description:
Hybrid
YX16158T


title: pancreatic tumor 21

description:
Classical
YX16153T


title: pancreatic tumor 27

description:
Classical
YX16166T


title: pancreatic tumor 25

description:
Basal
YX16160T


title: pancreatic tumor 20

description:
Classical
YX16147T


title: pancreatic tumor 26

description:
Hybrid
YX16161T


title: pancreatic tumor 29

description:
Classical
YX16178T


title: pancreatic tumor 18

description:
Hybrid
YX16141T


title: pancreatic tumor 17

description:
Classical
YX16139T


title: pancreatic tumor 24

description:
Hybrid
YX16159T


title: pancreatic tumor 22

description:
Hybrid
YX16155T


title: pancreatic tumor 40

description:
Classical
YX16227T


title: pancreatic tumor 16

description:
Hybrid
YX16135T


title: pancreatic tumor 15

description:
Hybrid
YX16132T


title: pancreatic tumor 14

description:
Hybrid
YX16130T


title: pancreatic tumor 13

description:
Classical
YX16128T


title: pancreatic tumor 11

description:
Classical
YX16120T


title: pancreatic tumor 12

description:
Classical
YX16127T


title: pancreatic tumor 35

description:
Hybrid
YX16203T


title: 22Rv1_Control_48hr

description: miRNA

source_name: 22Rv1, nontreated, 48hr

tag: treatment

value: nontreated, 48hr


title: pancreatic tumor 33

description:
Hybrid
YX16194T


title: pancreatic tumor 10

description:
Classical
YX16119T


title: pancreatic tumor 8

description:
Classical
YX16112T


title: pancreatic tumor 7

description:
Classical
YX16062T


title: pancreatic tumor 5

description:
Classical
YX16041T


title: pancreatic tumor 6

description:
Classical
YX16057T


title: pancreatic tumor 4

description:
Hybrid
YX16036T


title: pancreatic tumor 1

description:
Classical
YX15261T


title: pancreatic tumor 2

description:
Classical
YX15263T


title: C442G_WT3_WCE

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Paired-end ChIP-seq libraries were sequenced on Illumina NextSeq500. Reads were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 20 -m 25), and mapped to mm10 genome (Gencode) using bowtie2  (parameters: --local, -X 2000). Uniquely mapped reads were extracted using samtools (-F 4, -f 0x2, -q 39). Narrow peaks were called using MACS2 compared to background input samples (WCE, whole cell extract) (parameters: --bw 300 -B -f --SPMR -keep-dup auto -q 0.05 BAMPE --nomodel).
Genome_build: mm10
Supplementary_files_format_and_content: Peaks detected by MACS2

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. mTEChi were sorted and Aire binding sites in the genome were determined by ChIPseq.
ChIPseq libraries were prepared for sequencing using a modified ChIPseq protocol (Blecher-Gonen et al., 2013, Bansal et al, 2017)

tag: strain

value: mTEChi

tag: age

value: 4-7 weeks

tag: genotype

value: Aire +/+


title: pancreatic tumor 3

description:
Hybrid
YX15271T


title: C442G_WT2_WCE


title: Aire_C313Y_WT_WCE_rep1

value: NOD X C57BL/6 F1


title: C442G_HET1_WCE

value: Aire +/C442G


title: C442G_HET3_ChIP


title: Aire_C313Y_WT_ChIP_rep1


title: C442G_HET1_ChIP


title: C442G_WT2_ChIP


title: C442G_WT3_ChIP


title: Aire_C313Y_WT_ChIP_rep2


title: Aire_C313Y_HET_WCE_rep2

value: Aire +/C313Y


title: Aire_C313Y_HET_WCE_rep1


title: pancreatic tumor 9

description:
Hybrid
YX16113T


title: Aire_C313Y_HET_ChIP_rep1


title: PSC_3W_Rep_4 [CJ10_21_sample_36_S36]

city: MANCHESTER

first: Alexander

last: Kononov

address: Oglesby Building, 555 Wilmslow Rd,

country: United Kingdom

institute: Cancer Research UK Manchester Institute

data_processing:
RNA-Seq reads were quality checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) software and trimming of bases was performed.
Raw sequencing reads were then aligned to the mouse genome assembly (GRCm38.75) in single-end mode using the STAR aligner with default parameters (Dobin, A., et al., STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 2013. 29(1): p. 15-21.)
Mapped data were converted to normalised read counts (expression) using featureCounts [5] and the Ensembl GTF annotation (Mus_musculus.GRCm38.75.gtf).
Differential expression (DE) was evaluated using the DESeq2 Bioconductor package
Genes with relative expression of Benjamini-Hochberg-adjusted p-value < 0.05, and Log2FoldChange > 1 were considered to be differentially expressed
Genome_build: mouse genome assembly (GRCm38.75)
Supplementary_files_format_and_content: raw counts

growth_protocol: Fibroblasts were cultured with/without tumour cells and/or macrophages for 72h and FACS-isolated based on mCherry expression

extract_protocol:
Isolated fibroblasts were immediately lysed in RLT buffer. RNA was extracted using QIAGEN Rneasy Plus Kit according to manufacturer's recommendation
QuantSeq 3’ mRNA-Seq Library Prep Kit

value: Pancreas stellate cells (PSCs)

tag: culture condition

value: Co-culture with tumour cells and macrophages (3W)


title: PSC_Mono_Rep_4 [CJ10_21_sample_34_S34]

value: Mono-culture


title: Aire_C313Y_HET_ChIP_rep2


title: PSC_3W_Rep_3 [CJ10_21_sample_33_S33]


title: PSC_2W_Rep_4 [CJ10_21_sample_35_S35]

value: Co-culture with tumour cells (2W)


title: PSC_2W_Rep_3 [CJ10_21_sample_32_S32]


title: Aire_C313Y_WT_WCE_rep2


title: PSC_3W_Rep_2 [CJ10_21_sample_30_S30]


title: C442G_HET3_WCE


title: PSC_Mono_Rep_2 [CJ10_21_sample_28_S28]


title: PSC_2W_Rep_2 [CJ10_21_sample_29_S29]


title: PSC_3W_Rep_1 [CJ10_21_sample_27_S27]


title: PSC_2W_Rep_1 [CJ10_21_sample_26_S26]


title: PSC_Mono_Rep_1 [CJ10_21_sample_25_S25]


title: Satellite Cells – NF-YA cKO, rep3

city: Modena

first: Carol

last: Imbriano

address: Via Campi 213/D

department: Life Sciences

country: Italy

institute: University of Modena and Reggio Emilia

data_processing:
Alignment performed with bowtie2 within rsem-calculate-expression against mm10 transcriptome.
Gene quantification performed with rsem-calculate-expression -p 8 --paired-end --bowtie2 --estimate-rspd --no-bam-output --append-names $R1 $R2 ref res/$sample
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing gene or isoforms expression as counts, TPM and FPKM for each sample.

source_name: Satellite Cells

extract_protocol:
RNA was extracted from cells by using Ripospin II mini Kit (GeneAll), according to the manufacturer’s protocol.
500ng of total RNA followed by Illumina TruSeq Stranded Total RNA preparation protocol.

treatment_protocol: Injected Tamoxifen at 20mg/ml in 5-7 weeks old mice

value: 5-7 weeks old mice

value: Satellite Cells

value: NF-YA cKO


title: Satellite Cells – NF-YA fl/fl, rep3

value: NF-YA fl/fl


title: Satellite Cells – NF-YA fl/fl, rep1


title: 313x_mTEChi_Mut_14

data_processing:
Data was processed using UTAP pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded over genes annotated in RefSeq release using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with the betaPrior set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts, normalized abundance measurements and DESeq2 analysis

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. mTEChi were sorted and RNA was extracted using Dynabeads. MARSseq protocol was used construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et. Al. 2014)
Bulk Mars-Seq (3' end-RNA-seq)

value: Aire C313X/C313X


title: Satellite Cells – NF-YA fl/fl, rep2


title: Satellite Cells – NF-YA cKO, rep1


title: Satellite Cells – NF-YA cKO, rep2


title: 313x_mTEChi_Mut_1


title: 313x_mTEChi_Het_8

value: Aire +/C313X


title: 313x_mTEChi_wt_7


title: PSC_Mono_Rep_3 [CJ10_21_sample_31_S31]


title: djc31 djc62_1

city: Planegg-Martinsried

first: Serena

last: Schwenkert

address: Grosshadernerstr. 2-4

department: Biology

country: Germany

institute: LMU

data_processing:
Galaxy platform
adaptors were removed with Trimmomatic (Bolger et al., 2014)
sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Arabidopsis genome (TAIR10) with the gapped-read mapper RNA Star.
Reads were counted with featureCounts (Liao et al., 2014) with the help of the gene annotation in Araport11 (www.araport.org/data/araport11).
Genome_build: TAIR10
Supplementary_files_format_and_content: xlsx file includes read count values for each sample

source_name: plants at the four-leaves stage

growth_protocol: Plants were grown on soil to the four-leaves stage

extract_protocol:
Total RNA from plants was isolated using Trizol (Invitrogen, Carlsbad, USA) and purified using Direct-zol™ RNA MiniPrep Plus columns (Zymo Research, Irvine, USA) according to the manufacturer’s instructions. RNA integrity and quality was assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
Illumina Tru-Seq
lncRNA-Seq

treatment_protocol: long day conditions (day: 16 h 100 μmol photons m-2 s-1, 21°C; night: 8 h dark, 16°C)

value: djc31 djc62 double mutant

tag: developmental  stage

value: four-leaves stage

value: plant


title: djc31 djc62_3


title: 313x_mTEChi_Het_3

value: mTEChi

value: 4-7 weeks


title: 313x_mTEChi_wt_6

value: Aire +/+


title: djc62_2

value: djc62 (SALK_050913) mutant


title: djc62_3


title: djc62_1


title: djc31_3

value: djc31 (SALK_034886) mutant


title: 313x_mTEChi_wt_2


title: djc31_2


title: Aire_C442G_mut_93

value: Aire C442G/C442G


title: djc31_1


title: Aire_C442G_mut_90


title: Col-0_2

value: wild type


title: Col-0_3


title: djc31 djc62_2


title: Aire_C442G_mut_92


title: 313x_mTEChi_Mut_10


title: Aire_C442G_mut_83


title: Aire_C442G_mut_80


title: Col-0_1


title: WT HFD_rep3

city: Seoul

first: Yoon

middle: Keun

last: Cho

address: 1, Gwanak-ro Bldg 20-417, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.38. (Trimmomatic option : ILLUMINACLIP:[TruSeq3-PE-2.fa]:2:30:10:5:true ,LEADING:3 , TRAILING:3 , SLIDINGWINDOW:4:15, MINLEN:36).
To estimate expression levels, the RNA-Seq reads were mapped to Mus musculus genome (mm10) using HISAT2 version 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie version 1.3.4d software in default options.
The read count data of filtered genes was normalized by RLE (Relative Log Expression) normalization with DESeq2. The nbinomWaldTest function in DESeq2 was used to test for differential expression. The output prints foldChange, p-value and FDR values which corrected by the Benjamin-Hochberg procedure. DEGs was determined by |fold change|>=2 and p-value <0.05. For DEGs, hierarchical clustering analysis was performed with complete linkage method and Euclidean distance as a measure of similarity.
Gene-enrichment analysis and KEGG pathway analysis for DEGs were also performed based on Gene Ontology (http://geneontology.org/) and KEGG pathway (https://www.genome.jp/kegg/) database respectively. All statistical analysis and visualization of differentially expressed genes was conducted using R.3.5.1 (www.r-project.org).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: GEO_processed excel file_Lee_HFD.txt: Tab-delimited text file includes abundance measurements.

source_name: gonadal white adipose tissue

growth_protocol: Mice were fed a NCD or HFD and were kept on a 12-h light/12-h dark cycle with free access to food and water at 22±1 °C.

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen) and processed as per manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit, according to the manufacturer.

treatment_protocol: Mice were fed a NCD or HFD for 8 weeks at the age of 6 weeks.

value: Wild-type

value: 8 weeks of HFD feeding

value: gonadal white adipose tissue


title: Aire_C442G_het_91

value: Aire +/C442G


title: Aire_C442G_het_85


title: Aire_C442G_het_87


title: retinal cells

city: Saint Louis

first: Joseph

middle: C.

last: Corbo

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program. Sample demultiplexing with the mkfastq function from Cell Ranger software(version 3.1.0, 10X Genomics). Sample alignment with the count function from Cell Ranger software (version 6.0.0, 10X Genomics). Paired end reads were mapped to the zebrafish genome (GRCz11) using Cell Ranger software (version 6.0.0, 10X Genomics). Mapped reads were quantified using the Cell Ranger software with a custom annotation (v432_dr_adult_eye.gtf, included as processed file). The GFP transcript sequence was added manually to the reference assembly as an extra chromosome.
Data were analyzed using the Seurat R package (v4.0.0). We retained all cells that expressed >500 genes, and we considered all genes expressed in at least five cells.  Cells with greater than 30% mitochondrial gene content or >40,000 unique molecular identifiers were removed from the analysis. For the remaining cells, a gene expression matrix was normalized to total cellular read counts using the Seurat SCTransform function. The 3,000 most variable genes, identified by the SCTransform function, were used for Principal Component Analysis. The top 30 principal components were selected for subsequent analysis. Graph-based clustering was performed to obtain a set of transcriptionally distinct clusters. At this point in the analysis, we deliberately set parameters to "over cluster" the data, to avoid combining distinct cell types and to identify sub-populations of low-quality cells for removal.
To retain high-quality photoreceptors and bipolar cells only, we subjected our data to multiple rounds of clustering, filtering, and selection. In the first round, we retained those clusters characterized either by the presence of one or more of the following opsin genes or phototransduction genes (rho, opn1sw1, opn1sw2, opn1mw1, opn1mw2, opn1mw3, opn1mw4, opn1lw1, opn1lw2, gnat1, or gnat2) or bipolar-specific genes (e.g., gnao1b , vsx1 , cabp2a, cabp5a and cabp5b) among the top 20 most differentially expressed genes as identified by the FindAllMarkers function in Seurat. We also removed clusters consisting of low-quality cells with low total gene counts (500-1,000 genes/cell) compared with high-quality photoreceptor clusters (1,000-3,000 genes/cell for rods and 1,000-4,000 genes/cell for cones). In the second round of clustering and selection, we removed clusters that showed co-expression of photoreceptor genes and Müller glial genes (icn, fxyd6l, mt2, rlbp1a, and glula). We also removed one cluster showing co-expression of photoreceptor and bipolar genes and with low total gene counts. In the final round of clustering and selection, we removed a rod subpopulation with low total gene counts and retained 2,186 high-quality cells.
Genome_build: GRCz11
Supplementary_files_format_and_content: The Gene transfer format (GTF) containing information about gene structure used for counting the transcripts in the data
Supplementary_files_format_and_content: Seurat object for scRNA-seq data

organism: Danio rerio

source_name: retinal cells

extract_protocol:
Retinas of five-month-old adult zebrafish were were harvested at around zeitgeber time 3 (ZT 3). The dissected retinas were dissociated with a papain dissociation solution, followed by further incubation with 10% FBS in DMEM and DNaseI. After the trituration, the samples were resuspended in sorting buffer (20 mM HEPES and 0.04% bovine serum albumin in Calcium- and magnesium-free HBSS, pH 7.4). Four retinas from two individuals were combined for Tg(rho:EGFP) fish, while six retinas from three individuals were combined for Tg(gnat2:EGFP) fish. The filtered samples were incubated in a solution of propidium iodide and Hoechst 33342. GFP-positive cells were isolated via fluorescence-activated cell sorting (FACS). Dead cells were then removed based on propidium iodide positivity. Intact rods and cones were then selected based on the presence of both blue (Hoechst 33342) and green fluorescence (GFP). About 35,000 viable, intact GFP-positive cells (PI-, GFP+, Hoechst+) and 1,500 GFP-negative cells (PI-, GFP-, Hoechst+) were collected from Tg(gnat2:EGFP) fish, while 10,000 GFP-viable, intact GFP-positive cells and 1,500 GFP-negative cells were collected from Tg(rho:EGFP) fish. These isolated cells were collected into the sorting buffer in one tube. Approximately 6,000 single cells were loaded into a 10X Chromium Single Cell Chip.
Single cell libraries were made with Chromium 3’ v3 platform following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: adult

tag: transgene


title: WT NCD_rep3

value: 8 weeks of NCD feeding


title: WT HFD_rep1


title: WT HFD_rep2


title: Aire_C442G_mut_84


title: Aire_C442G_het_81


title: Aire_C442G_het_82


title: Aire_C442G_wt_89


title: MPs_CT_1169 (small RNA)

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
AB Lifescope mapping versus hg19 human build.
Read counting versus mirbase v18 annotation reference.
Genome_build: hg19
Supplementary_files_format_and_content: Read count matrix [microRNA x sample]

source_name: Myogenic Progenitor cells derived from an healthy donor

growth_protocol: The growth culture medium was Ham’s F10 medium supplemented with 20% FBS, 10 mM Hepes, 10-6 M dexamethasone, 2.5 ng/mL basic fibroblast growth factor, 100 U/mL penicillin, and 100 mg/mL streptomycin. Myogenic and adipogenic differentiations were induced by switching to differentiation medium (DM): Ham’s F10/F12/low-glucose DMEM with 2mM glutamine (2v/1v/1v) supplemented with 1% horse serum (Gibco, Thermo Fisher Scientific, Villebon sur Yvette, France), 500 nM dexamethasone, 50 μM 1-methyl-3-isobutylmethyl xanthine (MIX), 7.5 μg/mL insulin, 7.5 μg/mL transferrin, 0.1 nM triiodothyronine, and 50 nM rosiglitazone (PPARγ agonist). Two days later, cells were placed in the same medium lacking MIX and dexamethasone. Fibrogenic differentiation was obtained with the above DM complemented with 1.5 ng/ml TGFβ1. This differentiation medium was replaced every 2 days and cells were collected after 2 or 5 days of differentiation to analyze fibrogenesis.

extract_protocol:
TRI-reagent (Euromedex, Souffelweyersheim, France)
SOLiD

treatment_protocol: Cells were treated or not with 5 ng/mL TGFβ1 for 48h

value: Myogenic Progenitor cells

tag: medium

value: Differentiation medium


title: WT NCD_rep2


title: Aire_C442G_wt_86


title: FAP_TGF_1169 (small RNA)

source_name: Fibro-Adipogenic muscle Progenitor cells derived from an healthy donor

value: Differentiation medium + TGFβ1


title: FAP_TGF_1019 (small RNA)

value: Fibro-Adipogenic muscle Progenitor cells


title: MPs_CT_1008 (small RNA)


title: MPs_CT_1019 (small RNA)


title: Aire_KO_436

value: mTEChi

value: Aire -/-


title: Aire_KO_431

value: 4-7 weeks


title: FAP_TGF_1008 (small RNA)


title: MP_TGF_1169 (small RNA)


title: MP_TGF_1008 (small RNA)


title: MP_TGF_1019 (small RNA)


title: Aire_KO_429


title: Aire_C442G_wt_88

value: Aire +/+


title: FAP_CT_1019 (small RNA)


title: FAP_CT_1008 (small RNA)


title: DMD_H (small RNA)

source_name: Muscle Duchenne Muscular Dystrophy donor biopsy

extract_protocol:
TRI-reagent (Euromedex, Souffelweyersheim, France)
SOLiD: NEB next small library prep set for SOLiD (New England Biolabs, Ipswich, MA, USA)

tag: disease state

value: muscle

tag: tissue source

value: paravertebral


title: Aire_wt_434


title: Aire_wt_438


title: WT NCD_rep1


title: DMD_F (small RNA)

value: Muscle Duchenne Muscular Dystrophy donor biopsy


title: DMD_G (small RNA)


title: DMD_A (small RNA)


title: DMD_D (small RNA)


title: Aire_wt_432


title: Aire_wt_430


title: DMD_E (small RNA)


title: DMD_C (small RNA)


title: DMD_B (small RNA)


title: Aire_het_439

value: Aire +/-


title: CT_1 (small RNA)

source_name: Muscle Healthy donor biopsy

value: Muscle Healthy donor biopsy

value: intervertebral


title: CT_3 (small RNA)

value: unknown


title: pupal neuron_shepkd_rep3

city: Buffalo

first: Dahong

state: Other

address: 955 Main Street

institute: SUNY Buffalo

data_processing:
Adapter sequences were trimmed from reads with cutadapt (v2.3; -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --minimum-length 18)
Reads were aligned to Flybase release dm6 reference with bowtie2 (v2.3.5; --very-sensitive, pair-end mode)
Reads were depleted for those aligned to mitochondria (egrep -v chrM) and for multi-mapped reads with samtools (v1.9)
Uniquely mapped reads were further depleted for PCR duplicates with picard (MarkDuplicates REMOVE_DUPLICATES=true)
ATAC-seq peak calling was performed with macs2 (v2.2.6; pair-end mode -f BAMPE)
differential accessibility was called with the R package DiffBind (edgeR, FDR<0.1 and lfc>0.3)
Genome build: dm6
Supplementary_files_format_and_content: bw files that are used for ATAC-seq quantification and visulization

organism: Drosophila melanogaster

source_name: pupal neurons

growth_protocol:
Fly stocks and crosses were grown on standard cornmeal-yeast-agarose medium at 25°C
BG3-c2 cells were cultured at 25°C in Schneider’s medium supplied with 10% FBS and 10 μg/mL insulin with no antibiotic.

extract_protocol:
4C-seq DNA was extract by phenol-chloroform after restriction digestion and ligation for PCR amplification.  DNA was extracted by phenol-chloroform after transposition for amplifying ATAC-seq libraries.
4C-seq and ATAC-seq libraries were generated according to published protocols VAN DE WERKEN et al. 2012, Methods Enzymol and CORCES et al. 2017, Nat Methods, respectively

treatment_protocol: Knockdown of shep is achieved through elav>shep-RNAi, Dcr, mCD8::GFP; control animals are elav>Dcr, mCD8::GFP. BG3 cells are treated with dsRNA targeting shep or GFP, as experimental or control groups.

value: FACS-isolated neurons

value: elav>Dcr-2, mCD8::GFP, shep-RNAi


title: Aire_het_435


title: FAP_CT_1169 (small RNA)


title: Aire_KO_428


title: Aire_het_437


title: pupal neuron_shepkd_rep1


title: pupal neuron_shepkd_rep2


title: CT_2 (small RNA)


title: pupal neuron_control_rep3

value: elav>Dcr-2, mCD8::GFP


title: pupal neuron_control_rep2


title: Aire_het_433


title: V303M_42_MUT

value: NOD

value: Aire V303M/V303M


title: V303M_53_MUT


title: pupal neuron_control_rep1


title: larval neuron_shepkd_rep1

source_name: larval neurons


title: larval neuron_control_rep3


title: V303M_40_MUT


title: larval neuron_shepkd_rep3


title: larval neuron_shepkd_rep2


title: V303M_54_HET

value: Aire +/V303M


title: Aire_het_440

value: mTEChi


title: V303M_50_HET


title: V303M_41_HET


title: V303M_51_WT


title: V303M_49_WT


title: V303M_47_WT


title: larval neuron_control_rep2


title: AireY86CmTEChiMUT9

value: Aire Y86C/Y86C


title: larval neuron_control_rep1


title: AireY86CmTEChiMUT5

value: 4-7 weeks


title: AireY86CmTEChiMUT4


title: Sample 67_ShM_DIF14_samp1

city: Genova

first: Kiril

last: Tuntevski

address: Via Morego 30

institute: Istituto Italiano di Tecnologia

data_processing:
Pair-ended reads were trimmed for adapters using Cutadapt.
Quality trimming was done with Seqtrim in MATLAB, sliding window 25 bp, maximum 2 base-pairs at a quaity of 26.
Quantification was performed using the Salmon suite on the NCBI mouse genome, release 67, with default parameters.
Genome_build: NCBI37/mm9 - release 67
Supplementary_files_format_and_content: Salmonoutput file (.sf)

source_name: Primary  adult neural stem cell

growth_protocol: Hippocampal NPCs were prepared and expanded as described previously (Babu et al., 2011; Pons-Espinal et al., 2019; Walker and Kempermann, 2014) and induction of spontaneous differentiation by growth factor removal was done as previously described (Pons-Espinal 2017, and Pons-Espinal, Gasperini et al 2019); viral induced-neuronal differentiation of aNPCs was done by transduction of a viral construct expressing Ascl1-ERT2 as previously described (Braun et al., 2013).

extract_protocol:
Total RNA was extracted from aNPCs (proliferating and differentiating conditions) with QIAzol protocol (Qiagen) according to the manufacturer’s instructions.
Primary adult hippocampal neural stem cells (aNSCs) transduced with a short hairpin scramble (Sh-Scramble, control), or with a Mili¬-targeted short hairpin (as demonstrated previously, ), were raised to confluence and allowed to spontaneously differentiate for 4, 7 or 14 days, by removal of FGF and EGF from the growth medium.

treatment_protocol: To constitutively knockdown MILI expression in vitro, aNPCs were infected at MOI=5 with a lentivirus encoding for shMILI (plKO.1, Sigma), or control lentivirus (SHC202, Sigma) both decorated with an eGFP reporter. GFP-positive cells were first selected by FACS after three passages, and then plated in proliferating or differentiating media, as previously described.

tag: strain background

value: Hippocampal adult neural stem cell (aNSC)

tag: differentiation day

tag: genotype/variation

value: ShortHairpinMILIkd

tag: flow cell


title: Sample 69_ShM_DIF14_samp2

tag: cell type


title: Sample 60_ShM_DIF4_samp3


title: Sample 66_ShM_DIF7_samp3


title: Sample 65_ShM_DIF7_samp3


title: Sample 62_ShM_DIF7_samp1


title: Sample 61_ShM_DIF7_samp1


title: Sample 68_ShM_DIF14_samp1


title: AireY86CmTEChiHET3

tag: tissue

value: Aire +/Y86C


title: Sample 64_ShM_DIF7_samp2


title: Sample 71_ShM_DIF14_samp3


title: Sample 72_ShM_DIF14_samp3


title: PTP-Meg2 wt3_P6: Meg2 wt retina biological rep 3

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

hyb_protocol: Probes were hybridised to the GeneChip MouseGene 1.0 ST arrays at 45°C for 16 hours. Hybridised arrays were then washed and stained on a Fluidics Station 450 using the Fluidics Station Program FS450_0007.

scan_protocol: Arrays were scanned on a GeneChip® Scanner 3000 7G

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with robust multiarray average algorithm (Affymetrix): RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

source_name: Meg2 wt retina

label_protocol: Samples for the GeneChip Mouse Gene 1.0 ST arrays were prepared and hybridized to the arrays according to the Ambion whole-transcript expression and the Affymetrix whole-transcript terminal labelling and control kit manuals. Briefly, for each sample, 300 ng of total RNA was reverse-transcribed into cDNA using a random hexamer oligonucleotide tagged with a T7 promoter sequence. After second strand synthesis, double-stranded cDNA was used as a template for amplification with T7 RNA polymerase to obtain antisense cRNA. Random hexamers were then used to reverse-transcribe the cRNA into single-stranded sense strand cDNA. The cDNA was then fragmented by uracil DNA glycosylase and apurinic/apyrimidic endonuclease 1. Fragment size was checked using the Agilent 2100 Bioanalyzer (fragment size between 50–200 bp). Fragmented sense cDNA was biotin-labelled !

growth_protocol: Mouse retinae dissected from P0 Meg2 knockout and wild-type mice (background strain: C57BL/6NTac)

extract_protocol: P0 mice were identified as wild-type or Meg2 knockout mutants by genotyping. Tissue samples were snap frozen in liquid N2. Both retinae of an animal were pooled. Total RNA was extracted from retinae of WT and Meg2 KO mice using the RNeasy mini kit (Qiagen). A DNase treatment was made during the isolation procedure.

treatment_protocol: not applicable

value: retina

value: Meg2 wild-type


title: Sample 59_ShM_DIF4_samp3


title: PTP-Meg2 wt2_P4: Meg2 wt retina biological rep 2


title: Sample 70_ShM_DIF14_samp2


title: PTP-Meg2 Ko2_P3: Meg2 ko retina biological rep 2

source_name: Meg2 ko retina

value: Meg2 knockout


title: Sample 58_ShM_DIF4_samp2


title: Sample 63_ShM_DIF7_samp2


title: AireY86CmTEChiHET10


title: Sample 56_ShM_DIF4_samp1


title: AireY86CmTEChiHET14


title: Sample 55_ShM_DIF4_samp1


title: Sample 57_ShM_DIF4_samp2


title: PTP-Meg2 Ko3_P5: Meg2 ko retina biological rep 3


title: PTP-Meg2 wt1_P2: Meg2 wt retina biological rep 1


title: Sample 54_ShM_DIF0_samp3


title: PTP-Meg2 Ko1_P1: Meg2 ko retina biological rep 1


title: AireY86CmTEChiWT3

value: Aire +/+


title: AireY86CWT2


title: Aire_C313Y_MUT3

value: Aire -/C313Y


title: Aire_C313Y_MUT2


title: BG3 cells - shepkd_rep3

data_processing:
Library strategy: 4C-seq
Reads were aligned to Flybase release dm6 reference with bowtie2
Metadata information; restriction enzymes, sequencing primers, reference genome ID, replicate information, viewpoint location and sorted bam file names was used to generate in-silico digested reference genome
Mapped reads were then counted using the ‘countFragmentOverlaps’ command in a strand specific manner
The counts from both the left and right fragment ends were combined using the ‘combineFragEnds’ command
z-scores were calculated for each of the potential peaks using the ‘getZScores’ command
Genome build: dm6
Supplementary_files_format_and_content: bw files that are used for quantification and visulization

source_name: BG3-c2 cells

value: Nervous system-derived cell cultures

value: shep dsRNA


title: Sample 51_ShM_DIF0_samp2


title: AireY86CmTEChiWT1


title: Sample 46_ShS_DIF14_samp2

value: ShortHairpinScramble


title: Sample 48_ShS_DIF14_samp3


title: Sample 53_ShM_DIF0_samp3


title: Sample 52_ShM_DIF0_samp2


title: Sample 49_ShM_DIF0_samp1


title: BG3 cells - shepkd_rep2


title: Sample 47_ShS_DIF14_samp3


title: larval brain_Shep_ChIP-seq

data_processing:
Adapter sequences were trimmed from reads with cutadapt (v2.3; -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --minimum-length 18)
Reads were aligned to Flybase release dm6 reference with bowtie2 (v2.3.5; --very-sensitive, pair-end mode)
Reads were depleted for those aligned to mitochondria (egrep -v chrM) and for multi-mapped reads with samtools (v1.9)
Uniquely mapped reads were further depleted for PCR duplicates with picard (MarkDuplicates REMOVE_DUPLICATES=true)
ChIP-seq peak calling was performed with macs2 (v2.2.6)
Genome_build: dm6
Supplementary_files_format_and_content: bw files that are used for visulization

source_name: larval brain

extract_protocol:
ChIP-seq and CUT&Tag libraries were extracted by phenol-chloroform and Ampure beads after PCR amplification, respectively.
ChIP-seq and CUT&Tag libraries were generated according to published protocols Matzat et al. PLOS Gen, 2012 and Hatice S Kaya-Okur, Steven Henikoff 2020. Bench top CUT&Tag. protocols.io,   respectively

value: larval brain

tag: chip antibody

value: anti-Shep (in-house as used in Matzat et al., PLOS Gen, 2012)


title: larval brain_Shep_input

tag: treatment

value: none (input)


title: Sample 45_ShS_DIF14_samp2


title: BG3 cells - shepkd_rep1


title: Sample 44_ShS_DIF14_samp1


title: Aire_C313Y_MUT1

tag: strain

value: NOD

value: mTEChi


title: 75C313Y_het

tag: age

value: 4-7 weeks

value: Aire +/C313Y


title: Sample 43_ShS_DIF14_samp1

value: Hippocampal adult neural stem cell (aNSC)


title: Sample 41_ShS_DIF7_samp3


title: Sample 40_ShS_DIF7_samp2


title: Sample 42_ShS_DIF7_samp3


title: BG3 cells - GFP_control_rep2

tag: genotype

value: GFP dsRNA


title: Sample 50_ShM_DIF0_samp1

value: ShortHairpinMILIkd


title: Sample 39_ShS_DIF7_samp2


title: BG3 cells - GFP_control_rep1


title: 50C313Y_het


title: Sample 37_ShS_DIF7_samp1


title: Sample 36_ShS_DIF4_samp3


title: Sample 35_ShS_DIF4_samp3


title: Sample 38_ShS_DIF7_samp1


title: BG3 cells - GFP_control_rep3


title: Sample 32_ShS_DIF4_samp1


title: Sample 31_ShS_DIF4_samp1


title: Sample 33_ShS_DIF4_samp2


title: 405aireko

value: Aire -/-


title: 404aireko


title: Sample 30_ShS_DIF0_samp3


title: Sample 29_ShS_DIF0_samp3


title: 402aireh

value: Aire+/-


title: Sample 27_ShS_DIF0_samp2


title: Sample 28_ShS_DIF0_samp2


title: 395aireh

value: Aire +/-


title: Sample 25_ShS_DIF0_samp1


title: 53C313Y_het


title: Organoid_day_158_rep3

city: Munich

first: Elisabeth B

last: Binder

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4213_S3

data_processing:
Raw reads were processed using FastQC, cutadap and aligned using the STAR aligner to GRCh38.
featureCounts was used to extract gene quantification, gencode v23.
The counts data were batch-corrected, normalized and analyzed and using the ImpulseDE2 framework.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv with raw gene counts per sample

growth_protocol: Brain organoids were grown using an unpatterend protocol (Lancaster et al 2014)

extract_protocol:
Organoids (following 17, 23, 40, 70, 120, 140, or 158 days in culture) were collected for bulk RNA extractions using the RNeasy Mini extraction kit (74104, Qiagen) according to the manufacturer’s instructions. RNA quality and concentrations were measured on an Agilent 2100 Bioanalyzer (Agilent). Three replicates were analyzed per time point, every sample containing 1-3 pooled organoids.
Sequencing libraries were prepared from a starting amount of 100ng total RNA using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (E7370L, New England Biolabs) using ribosomal depletion as a selection method. Libraries were sequenced paired-end on an Illumina HiSeq4000 system at the Helmholtz Zentrum Core Facility (Munich, DE). 5 libraries were pooled per lane for a total coverage of on average 50 M reads/library

treatment_protocol: Wild-type organoids

value: brain organoid

tag: age (in days)

tag: replicate


title: Organoid_day_140_rep3

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4219_S9


title: 73C313Y_het


title: Organoid_day_158_rep2

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4212_S2


title: Organoid_day_140_rep2

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4224_S14


title: Organoid_day_158_rep1

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4225_S15


title: Sample 34_ShS_DIF4_samp2


title: 406aireko


title: 392aireh


title: Organoid_day_120_rep3

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4211_S1


title: Organoid_day_140_rep1

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4218_S8


title: Aire_C313Y_Wildtype3

value: Aire +/+


title: Sample 24_WT_DIF14_samp3

value: WildType


title: Sample 20_WT_DIF14_samp1


title: Sample 22_WT_DIF14_samp2


title: Sample 21_WT_DIF14_samp2


title: Sample 19_WT_DIF14_samp1


title: Organoid_day_120_rep1

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4217_S7


title: Organoid_day_120_rep2

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4223_S13


title: Aire_C313Y_Wildtype2


title: Sample 18_WT_DIF7_samp3


title: Sample 26_ShS_DIF0_samp1

value: ShortHairpinScramble


title: Sample 16_WT_DIF7_samp2


title: Sample 17_WT_DIF7_samp3


title: 80C313Y_WT


title: Sample 15_WT_DIF7_samp2


title: 78C313Y_WT


title: Sample 12_WT_DIF4_samp3


title: Organoid_day_70_rep2

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4227_S17


title: Sample 13_WT_DIF7_samp1


title: Sample 14_WT_DIF7_samp1


title: Sample 23_WT_DIF14_samp3


title: 52C313Y_WT


title: Organoid_day_70_rep1

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4222_S12


title: Sample 11_WT_DIF4_samp3


title: Organoid_day_40_rep3

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4226_S16


title: Sample 10_WT_DIF4_samp2


title: Organoid_day_40_rep2

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4233_S23


title: Aire_C313Y_Wildtype1


title: Organoid_day_23_rep3

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4232_S22


title: Organoid_day_40_rep1

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4238_S28


title: Aire_C442G_WT_B6_2

description: nucleosome-free chromatin

data_processing:
Paired-end raw reads were trimmed using cutadapt (with the parameters -q 25 -m 30), and mapped to genome mm10 (Gencode) using bowtie2 (with the parameter --local).
Following alignment, mitochondrial genes are removed from the analysis, and duplicated reads were removed using picard-tools.
Nucleosome-free fragments at the length <120bp were selected from the remaining unique reads, and broad peaks were called using MACS2 (with the parameters --bw 120 -B -f BAMPE --SPMR –B --shift -50 --extsize 100 -keep-dup all -q 0.05).
Genome_build: mm10
Supplementary_files_format_and_content: Peaks detected by MACS2

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. mTEChi were sorted and chromaton accessible regions purified.
ATAcseq libraries were prepared for sequencing using using a modified ATACseq protocol (Buenrostro et al., 2016, Lara-Astiaso et al., 2014)


title: 45C313T_WT


title: Sample 8_WT_DIF4_samp1


title: Organoid_day_23_rep2

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4231_S21


title: Sample 9_WT_DIF4_samp2


title: Aire_C442G_HET_B6_2

description: nucleosome-free chromatin

value: Aire +/C442G


title: Aire_C442G_WT_B6_1

description: nucleosome-free chromatin


title: Sample 7_WT_DIF4_samp1


title: Organoid_day_70_rep3

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4228_S18


title: Aire_C313Y_WT2

description: nucleosome-free chromatin


title: Organoid_day_23_rep1

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4237_S27


title: Sample 4_WT_DIF0_samp2


title: Week 7, fish 1

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Arrays were scanned with GenePix® 4100A. Microarray Scanner.

data_processing: Images were processed using the standard procedures of the feature extraction. After removal of flagged spots lowess normalization was performed.

organism: Salmo salar

source_name: RBC from uninfected salmon

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol.

growth_protocol: Salmon post smolts were kept in tanks with sea water under standard conditions.

extract_protocol: RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with RNeasy mini kit (QIAGEN).

treatment_protocol: Challenge was performed by cohabitation with virus shedders. Peripheral blood from the caudal vein was collected in heparinized vacutainers and used for isolation of erythrocytes.

value: Red blood cells

value: Uninfected

tag: time point

value: Week 7

source_name: RBC from infected salmon

value: PRV infection


title: Sample 5_WT_DIF0_samp3


title: Aire_C442G_HET_B6_1

description: nucleosome-free chromatin

value: mTEChi

value: 4-7 weeks


title: Week 7, fish 2


title: Sample 6_WT_DIF0_samp3

value: Hippocampal adult neural stem cell (aNSC)


title: Week 7, fish 4


title: 47C313T_WT

value: NOD


title: Organoid_day_17_rep3

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4230_S20


title: Aire_C313Y_WT1

description: nucleosome-free chromatin


title: Organoid_day_17_rep1

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4229_S19


title: Sample 3_WT_DIF0_samp2


title: Aire_C313Y_Het3

description: nucleosome-free chromatin

value: Aire +/C313Y


title: Week 5, fish 3

value: Week 5


title: Organoid_day_17_rep2

description:
Bulk RNA sequencing (NEBNext - ribosomal depletion)
MUC4214_S4


title: Sample 2_WT_DIF0_samp1


title: SUIT2 100 U/mL IFNβ 24 hour 3

city: Los Angeles

first: Caius

middle: Gabriel

last: Radu

state: CA

address: 650 Charles E. Young Drive, South

department: Molecular and Medical Pharmacology

institute: University of California Los Angeles

data_processing:
Reads were aligned to Human hg38 genome with STAR 2.7.8a.
Ensembl Transcripts release 101 gtf was used for gene feature annotation to generate raw read counts per gene.
For normalization of read counts per gene,each gene read counts was added 1.0E-4 and normalizaed by TMM normalization performed in Partek Flow.
Genome_build: hg38
Supplementary_files_format_and_content: TMM normalization performed in Partek Flow

source_name: pancreas cancer cells

growth_protocol: Human SUIT2 pancreas cancer cells were seeded at 500,000 cells / well in 6 well plates in 2 mL of growth media for 24 hours before treatment.

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA kit (Machery-Nagel Cat# 740955).
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina HiSeq 3000 platform).

treatment_protocol: At the time of treatment, media was removed and replaced with fresh media supplmented with 100 U/mL human IFNβ.

tag: cell line

value: pancreas cancer cells

value: 100 U/mL human IFNβ for 24 hours


title: SUIT2 100 U/mL IFNβ 24 hour 2


title: Week 5, fish 5


title: Week 5, fish 6


title: SUIT2 100 U/mL IFNβ 24 hour 1


title: Sample 1_WT_DIF0_samp1


title: Week 5, fish 2


title: Aire_WT_B6_2

description: nucleosome-free chromatin


title: Week 7, fish 3


title: E026 PMA + Ionomycin R2

city: Doha

first: Nico

last: Marr

address: Education City

country: Qatar

institute: Hamad Bin Khalifa University

data_processing:
Raw RNA-seq reads were aligned with UCSC human genome assembly version hg38, with STAR aligner (Dobin et al., 2013).
HTseq-count (Anders et al., 2015) was used to count the reads mapping to each gene feature. Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq-count is used to get the count files, followed by DESeq2 package in R for normalization and log2 transformation.

source_name: PBMC

growth_protocol: PBMCs were isolated from buffy coat using Ficoll-Plaque density gradient. PBMCs were cultured in RPMI 1640+Glutamax

extract_protocol:
RNeasy mini kit (Qiagen): cDNA was prepared with the SMART-Seq RNA kit (Takara Bio) for low-input RNA and DNA library preparation and used the Nextera XT DNA Library Preparation Kit (Illumina) and the Nextera XT Index Kit v2 set A (Illumina), respectively
cDNA

treatment_protocol: stimulated for 2 h with IFNa/IFNb, PMA+Ionomycin, cGAMP and MDP. LyoVec were used as reagent control. RPMI is the unstimulated condition.

value: PBMC

tag: disease state

value: Healthy Control

value: PMA+Ionomycin

tag: timepoint


title: p53+/-;Tsc1fl/fl;Alb-Cre  tissue 2

city: Chongqing

first: Chuanming

last: Xie

state: Chongqing

address: 30 Gaotanyan Rd

department: Institute of Hepatobiliary Surgery

institute: Southwest Hospital

data_processing:
The sequencing data in the fastq files were first removed adapters using cutadapt.
Reads in fastq.gz format were mapped to the mm9 using STAR.
Mapped reads were assembled using StringTie.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: liver tissue of p53+/-;Tsc1fl/fl;Alb-Cre  mouse

growth_protocol: liver tissues islolated from each genotype mice monitored for up to 320 days

extract_protocol:
Total RNA was isolated using TRIzol method and then depleted the ribosomal RNA, tRNA, etc using a "ribo-depletion" kit (Epicentre). All samples were run onto the same gel using HiSeq Rapid 50 Cycle Single-Read and 4 samples multiplexed into each lane with total of three lanes.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 320 days

value: liver


title: Aire_WT_B6_1

description: nucleosome-free chromatin

value: Aire +/+


title: p53+/-;Tsc1fl/fl;Alb-Cre  tissue 1

source_name: liver tissue of p53+/-;Tsc1fl/fl;Alb-Cre mouse


title: p53+/-;Tsc1fl/fl;Alb-Cre  tissue 3


title: SUIT2 100 U/mL IFNβ 6 hour 3

value: 100 U/mL human IFNβ for 6 hours


title: E027 PMA + Ionomycin R2


title: SUIT2 100 U/mL IFNβ 6 hour 1


title: E027 IFNa-IFNb R2

value: IFNa-IFNb


title: SUIT2 100 U/mL IFNβ 6 hour 2


title: Aire_KO_B6_1

description: nucleosome-free chromatin

value: Aire -/-


title: Tsc1fl/fl;Alb-Cre  tissue 3

source_name: liver tissue of Tsc1fl/fl;Alb-Cre  mouse


title: Aire_KO_B6_2

description: nucleosome-free chromatin

value: mTEChi


title: E027 RPMI R2

value: RPMI


title: SUIT2 control treated 3

value: control treated


title: AC14 at T3 2

city: Cambridge

first: Jonathan

middle: Morris

last: Urbach

state: Massachusetts

address: 400 Technology Sq Rm 851

institute: Ragon Institute of MGH, MIT and Harvard

description:
AC Patient AC14 Time Point T3 2
A110X.S0062

data_processing:
Illumina sequencing run was deemultiplexed using bcl2fastq veersion 2.19.1.403.
Reads were then mappeed to the hg38 transcriptome using the RSEM pipeline version 1.3.0 with bowtie aligner version 1.2.2. Read counts were calculated as expected counts, and rounded to integer values for analysis with DESeq2, or used without rounding in edgeR.
Differential expression analysis was performed using DESeq2 version 1.26.0 using a model including the following terms: "~ Patient.Category + Batch + UGPS + Pct.Mitochondrial.Transcripts + Align.Rate + CD4.Count"
Prior to differential expression analysis, genes were filtered to have at least 5 expected counts in at least 10% of samples.
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: The expected counts matrix (GEO.EC.gz) includes counts for samples and genes listed by their respective ENSEMBL gene IDs and gene symbols, delimited by an underscore. The GEO.sample_metadata.gz file is complete sample metadata including QC evaluations in tab-separated format. A0173.A110X.T3.REST.PCvSC.dv2.rslt.tsv.gz is the DESeq2 result set as tab-separated values.

source_name: Sorted tetramer positive CD8+ lymphocytes

growth_protocol: Cryopreserved PBMCs were thawed and rested overnight in RPMI + 10% FBS.

extract_protocol:
Replicate populations of viable tetramer+ CD8+ T cells were sorted into RLT Plus lysis buffer supplemented with 1% betamercaptoethanol and frozen at -80°C. RNA was extracted using QIAGEN AllPrep kits.
Smartseq2 bulk protocol using oligo-dT primers to amplify cDNA from mRNA, followed by Illumina Nextera XT tagmentation and NextSeq 550 sequencing.

treatment_protocol: CD8 T cells were enriched by magnetic isolation then stained for peptide-HLA tetramer, anti-CD8 and viability dye and sorted by FACS at 4°C.

tag: patientid

value: AC

tag: Sex

value: M

tag: batch

tag: ugps


title: E026 IFNa-IFNb R2

tag: cell type


title: Aire_C313Y_Het2

description: nucleosome-free chromatin

tag: tissue

value: 4-7 weeks

value: Aire +/C313Y


title: AC14 at T3 1

description:
AC Patient AC14 Time Point T3 1
A110X.S0061

value: Sorted tetramer positive CD8+ lymphocytes


title: Tsc1fl/fl;Alb-Cre  tissue 1

source_name: liver tissue of Tsc1fl/fl;Alb-Cre mouse


title: SUIT2 control treated 2

value: pancreas cancer cells


title: AC14 at T1 2

description:
AC Patient AC14 Time Point T1 2
A110X.S0054


title: E025 IFNa-IFNb R2

value: PBMC

value: Healthy Control


title: E026 RPMI R2


title: p53+/- tissue 3

source_name: liver tissue of p53+/- mouse

value: 320 days


title: CUT&Tag_H3K27ac

last: Chen

data_processing:
Library strategy: CUT&TAG
Adapter sequences were trimmed from reads with cutadapt (v2.3; -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --minimum-length 18)
Reads were aligned to Flybase release dm6 reference with bowtie2 (v2.3.5; --very-sensitive, pair-end mode)
Reads were depleted for those aligned to mitochondria (egrep -v chrM) and for multi-mapped reads with samtools (v1.9)
Uniquely mapped reads were further depleted for PCR duplicates with picard (MarkDuplicates REMOVE_DUPLICATES=true)
CUT&Tag peak calling was performed with macs2 (v2.2.6; pair-end mode -f BAMPE)
Genome_build: dm6
Supplementary_files_format_and_content: bw files that are used for visulization

source_name: pupal brain

value: pupal brain

value: elav>Dcr-2, mCD8::GFP

tag: chip antibody

value: anti-H3K27ac (Abcam ab4729)


title: p53+/- tissue 2

value: liver


title: SUIT2 control treated 1

tag: treatment


title: E026 PMA + Ionomycin R1

value: PMA+Ionomycin


title: CUT&Tag_H3K27me3

source_name: pupal neurons

value: FACS-isolated neurons

value: anti-H3K27me3 (Cell Signaling Technology 9733)


title: p53+/- tissue 1


title: AC17 at T3 1

description:
AC Patient AC17 Time Point T3 1
A110X.S0046


title: AC14 at T1 1

description:
AC Patient AC14 Time Point T1 1
A110X.S0053


title: E026 IFNa-IFNb R1

value: IFNa-IFNb


title: E026 RPMI R1

value: RPMI


title: E025 PMA + Ionomycin R2


title: spinal motor neurons, SOD-4

city: Parkville

first: fatemeh

last: zanganeh

state: Victoria

address: 30 royal pde

country: Australia

institute: Florey

description:
E12_Transcriptomics_DeSeq2.CSV
E12_FeatureCount.txt
E12_S_R4

data_processing:
Align reads to mouse Genome and Output concordant aligned reads as fastq - HiSat2  (v 2.1.0) : hisat2  -x "UCSC_mm10"  --al-conc  "output"  --rna-strandness fr  --no-mixed --no-discordant. Output concordant aligned reads as BAM
Generate  read counts for each gene - Feature-count  (v 1.6.3) : Feature count -t 'exon' -g 'gene_id'
Differential Expression Analysis - DESeq2 (v1.12.4) : DESeq2  (test = "Wald")
Genome_build: Mus_musculus_UCSC_mm10
Supplementary_files_format_and_content: CSV file containing DESeq2 output

source_name: spinal cord

extract_protocol:
The spinal cord  were rapidly dissected from the embryo day 12.5. The isolated tissue was dissociated using Neural Tissue Dissociation Kit (Miltenyi Biotec). Motor neurons were sorted using FACS AriaTM Fusion Flow Cytometer (Becton Dickinson). The cells were directly collected in RLT lysis Buffer (Qiagen). Total RNA extracted using the RNeasy Mini Kit (Qiagen) including DNase treatment.
cDNA libraries were prepared using NeuGen Ovation® SoLo kit.

value: spinal motor neurons

tag: developmental stage

value: Embryonic day 12.5

value: SOD1G93A mouse model of amyotrophic lateral sclerosis


title: CUT&Tag_H3K4me1

value: anti-H3K4me1 (Abcam ab8895)


title: E027 PMA + Ionomycin R1


title: spinal motor neurons, SOD-3

description:
E12_Transcriptomics_DeSeq2.CSV
E12_FeatureCount.txt
E12_S_R3


title: Tsc1fl/fl;Alb-Cre  tissue 2

tag: age


title: LMN85-T

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCm38 reference GENCODE annotation (p6) using STAR (2.6.0c)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: Intestinal Tissue

growth_protocol: Villin-Cre mice were bred to Msh2 flox/flox mice to generate VCMsh2 mice. Mice were genotyped to confirm knock-in/knock-out status of Cre transgene and Msh2, respectively.

extract_protocol:
Total RNA for Library Preparation and Sequencing analysis was purified from microdissected VcMsh2 FFPE tumor and normal intestinal tissue using the RNAeasy Plus Kit (QIAGEN) that included a genomic DNA elimination step.
Coding RNA transcripts were enriched using mouse exome panel hybridization (Twist Biosciences).  Size, concentration, and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were generated using Illumina’s TruSeq RNA sample Prep Kit v3, following the manufacurer’s protocol.
Sequencing of 8–10 pM of each library was done on the NovaSeq sequencer as 75bp paired-end read runs.

treatment_protocol: Aspirin or Naproxen impregnated pelleted NWD1 (400 ppm Aspirin or 166 ppm Naproxen) at the age of weaning were given to mice assigned to those arms. Starting at the age of 6-8 weeks, mice enrolled in FSP vaccine alone and FSP vaccine plus NSAID arms were vaccinated subcutaneously in either left or right hind 4 times bi-weekly followed by 4 times monthly. Per shot, each mouse received 50 μg of each FSP combined with 20 μg of the adjuvant. Mice were monitored over their lifetime by RARC Veterinary Services and the investigator twice a week for the following signs to determine euthanasia; (1) weight loss (2) poor coat quality (3) hunched posture (4) pale limbs (anemia).

value: Intestinal Tissue

tag: tissue type

value: Tumor

tag: group

value: RV

value: FSP vaccine


title: LMN09-T

value: R

value: Western Diet


title: E027 IFNa-IFNb R1

value: PBMC

value: Healthy Control


title: spinal motor neurons, SOD-2

description:
E12_Transcriptomics_DeSeq2.CSV
E12_FeatureCount.txt
E12_S_R2

tag: genotype


title: LMN84-T

value: NV

value: Naproxen + FSP vaccine


title: AC17 at T2 2

description:
AC Patient AC17 Time Point T2 2
A110X.S0038

value: Sorted tetramer positive CD8+ lymphocytes

value: AC

tag: replicate

value: M


title: E025 RPMI R2

value: RPMI


title: spinal motor neurons, SOD-1

description:
E12_Transcriptomics_DeSeq2.CSV
E12_FeatureCount.txt
E12_S_R1

value: spinal motor neurons

value: Embryonic day 12.5