title: 1-fgfr3lof/lof

city: Paris

first: Emilie

last: Dambroise

address: 24 bd Montparnasse

country: France

institute: Institut Imagine

description:
Single-cell RNA-seq
mRNA

data_processing:
Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters.
Reads were aligned against the GRCz11-3.0.0 reference transcriptome.
The RNA data quality control and downstream analysis were performed using the Seurat R package (version 3.0.2) and the standard Seurat v3 integration workflow. We filtered cells that had (i) unique feature counts over 2000 or below 500, or (ii) more than 20% of mitochondrial counts. After data filtering, we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat (SC_fgfr3_Cranial-Vault-ZF_combined_samples).
We used the FindMarkers function to define marker of each cluster (Findmarkers_by_cluster.xlsx file).
We used the FindMarkers function to compute differentially expressed genes (DEGs) for each of the identity classes in the dataset (DEGS.xlsx file).
We subset cluster 4 from SC_fgfr3_Cranial-Vault-ZF_combined_samples matrix and performed new clustering (resolution 0.2) and we obtained SC_fgfr3_Cranial-Vault-ZF_Subset-Cluster4.
Genome_build: GRCz11-3.0.0
Supplementary_files_format_and_content: *-raw_feature_bc_matrix.h5
Supplementary_files_format_and_content: Findmarkers_by_cluster.xlsx
Supplementary_files_format_and_content: DEGS.xlsx

source_name: Cranial vault

extract_protocol:
The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs, the anterior parts of the frontal bones, and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. After a wash in PBS, cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer, and the cells were washed in a-MEM supplement with 10% FBS. Prior to flow cytometry, the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells, beads were used to select events larger than 3 µm. Hoechst-positive cells (cells with a nucleus) and Syber-green-negative cells (live cells) were sorted.
The scRNA-seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 (10x Genomics), according to the manufacturer’s instructions. Briefly, cells were counted, diluted at 1000 cells/µL in PBS+0.04% BSA, and 6500 cells were loaded in the 10x Chromium Controller to generate single-cell gel beads in an emulsion. After reverse transcription, the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 (Illumina) on paired end strands (read 1: 28bp; read 2: 91bp), with a mean read depth of 25000 reads per cell.

value: Cranial vault

tag: length

value: 9 mm


title: Embryos, wt_90_3

status: Public on May 18 2020

type: SRA

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

country: USA

institute: Washington University School of Medicine

library_source: transcriptomic

data_processing:
Raw reads were trimmed with cutadapt to remove low quality bases
Trimmed reads were aligned to danio rerio genome GRCz10 using STAR_2.5.4b with Ensembl v83 annotation
Aligned reads were quantified using featureCounts 1.6.3 from the subreads package
Genome_build: GRCz10
Supplementary_files_format_and_content: gene counts text file

molecule: total RNA

organism: Danio rerio

source_name: 50 pooled WT embryos at 90% epiboly

growth_protocol: Embryos obtained from natural mating were maintained at 28.5C until 90% epiboly stage

extract_protocol:
Embryos were lysed and total RNA isolated using Trizol, then cleaned up using a Qiagen Rneasy kit.
Samples were depleted of ribosomal RNA using the Illumina Ribo-Zero kit and libraries prepared using TruSeq stranded total RNA reagents.

tag: tissue

value: embryo

tag: genotype

value: WT


title: Donor1_Stim_Rep_1_TCR

city: San Francisco

first: Eric

last: Shifrut

state: CA

address: 513 Parnassus Ave, HSW 1033

institute: University of California, San Franscisco

description: Enrichment PCR of TCR KI

data_processing:
Fastq files from 10x gene expression library were processed with Cell Ranger, using default parameters.
Fastq files for TCR KI barcodes were matched to the reference barcodes in the pooled library.
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample, gene expression (GEX) tar file contains a named count matrix of genes by cells for all cells passing filter. For TCR KI barcode files, tsv files contain a two column table of the identified KI gene(s) for each cell barcode in

molecule: polyA RNA

organism: Homo sapiens

source_name: pan T cells

growth_protocol: CD3+ cells were stimulated, edited by electroporation two days later, and then grown in IL-2.

extract_protocol: ChromiumTM Single Cell 3’ v3 Protocol (CG000183)

treatment_protocol: TCR stimulus with or without TGFB ; In vivo TILs vs ex vivo input cells

value: T cells


title: WT-2011-3

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Quality trimming : cutadapt 1.15
Read mapping : READemption (0.4.3) and segemehl (0.2.0)
Coverage plot generation: READemption (0.4.3)
Genome_build: CP004140.1, EF437940.1
Supplementary_files_format_and_content: nucleotide wise coverage in wiggle format

organism: Sinorhizobium meliloti

growth_protocol: 50 ml-Erlenmeyer flasks were filled with 30 TY medium containing streptomycin (250 µg/ml).  For strains OE and EVC, Tc (10 µ/ml) was added . Cultures were grown at 30 °C and 140 r. p. m. to an OD600 nm of 0.5.

extract_protocol:
Total RNA  was extracted with 1 ml TRIzol (cell disruption was performed  in the cell suspension using glass beads in a shaking mill). Precipitated RNA was dissolved in cold ultrapure water and imediately subjected to additional hot-phenol purification. 10 µg RNA was treated with TURBO DNase and used for RNAseq.  RNA from three independent biological samples was pooled. Each pool was used for three independent cDNA libraries.
The total RNA samples were first fragmented using ultrasound (4 pulses of 30 sec at 4°C). Each sample was used for three independent cDNA synthesis. First, an oligonucleotide adapter was ligated to the 3' end of the

treatment_protocol: 15 ml culture was added to a 50 ml-tube filled with ice rocks an centrifuged at 6,000 g at 4 °C. The cell pellet was dissolved in 1 ml cold TY medium, transferred to an Eppendorf tube and centrifuged for 5 min and 6,000 r.p.m.at 4 °C. The pellet was used immediately for isolation of total RNA  .

tag: strain

tag: genoypte/variation

value: wild type

tag: sample type

value: Liquid culture


title: A12

city: NEW DELHI

first: Anurag

middle: Singh

last: Rathore

state: DELHI

address: Lab no. 356, Block III

department: Chemical Engineering

country: India

institute: Indian Institute of Technology

data_processing:
The raw data generated was checked for the quality using FastQC. Reads were pre processed to remove the adapter sequences and removal of the low quality bases (<q30). Pre-processing of the data is done with Cutadapt. The pre-processed high quality data was aligned to reference genome using Bowtie2. Bowtie with  default parameter was run to identify the alignment percentage.
Genome_build: Escherichia coli_BL21(DE3), GCF_000022665.1 assembly was downloaded from NCBI
Supplementary_files_format_and_content: HTSeq4 was used to estimate and calculate gene abundance. Absolute counts for each genes were  identified ,which were used in differential expression calculations. DESeq5 was used to calculate the differentially expressed genes using Microaerobic conditions (M10, M12, M14) as test and Aerobic conditions ( A10, A12, A14) as control. Genes were categorized into UP, Down and Neutrally regulated based on the log2fold change cutoff of 1 value.

organism: Escherichia coli BL21(DE3)

source_name: bacterial cell

growth_protocol: Aerobic (A) and Microaerobic (M) fermentation was carried out in E.coli BL21(DE3) and E.coli cells were grown in Kortz based media (containing 100g/l lactose) in bioreactor under strict oxygen control conditions to late log phase, cells were collected at different time points (10th,12th,14th hour) and proceeded for RNA isolation

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) using manufacturer’s instructions.
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® UltraTM Directional RNA Library Prep Kit (New England BioLabs, MA, USA) at Genotypic Technology Pvt. Ltd., Bangalore, India. ~2.5μg of total RNA was taken for rRNA depletion using Ribo-Zero rRNA Removal Kit (Bacteria). ~50 ng of Qubit quantified ribodepleted RNA was taken for fragmentation and priming. The fragmented and primed mRNA was further subjected to first strand synthesis in the presence of Actinomycin D (Gibco, life technologies, CA, USA) followed by second strand synthesis. The double stranded cDNA was purified using HighPrep PCR magnetic beads (Magbio Genomics Inc, USA). The purified cDNA was end-repaired, adenylated and ligated to Illumina multiplex barcode adapters as per NEBNext® UltraTM Directional RNA Library Prep Kit protocol.

tag: treatment

value: Aerobic (A) fermentation

tag: growth phase

value: late log phase cultures

tag: time point

value: 12th hour


title: 2-fgfr3+/+

description:
Single-cell RNA-seq
mRNA

tag: genotype/variation


title: M10

value: Microaerobic (M) fermentation

value: 10th hour


title: Embryos, wt_90_1


title: Embryos, wt_90_2


title: WT-2011-2


title: WT-2011-1


title: Ctl_S18

city: Bruxelles

first: Cedric

last: Blanpain

address: route de Lennik, 808

country: Belgium

institute: Université Libre De Bruxelles

library_source: genomic

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 HEADCROP:10 CROP:70 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60”.
ATAC-seq paired-end reads were then aligned to mouse genome Grcm38 using Bowtie2 (version 2.2.6) using options “-X 2000 --fr --very-sensitive --no-discordant --no-unal --no-mixed –non-deterministic”.
Mitochondrial reads, reads from unmapped or random contigs and reads with a mapping quality less than 20 were removed using samtools.
Duplicate reads were removed by Picard tools (http://broadinstitute.github.io/picard/).
Peak calling was performed on each individual sample by macs2 (version 2.1.0.20151222)  using options “-f BAMPE -g mm -q 0.05 --nomodel --call-summits -B –SPMR”. TDF files were generated with IGVtools from the treat_pileup.bdg
Peaks from the different subpopulations were merged for downstream analysis.
Reads counts of each merged peaks for each individual sample were calculated by HTSeq-count using options “-r pos -m intersection-nonempty”. These counts were normalized for one million of mapped reads in merged peaks and fold<
Peaks were associated to genes with GREAT software with the following association rules : “basal plus extension” with parameters : 5.0kb in proximal upstream, 1.0kb in proximal downstream and 100.0kb in distal.
Genome_build: Grcm38
Supplementary_files_format_and_content: tdf
Supplementary_files_format_and_content: peaks
Supplementary_files_format_and_content: counts

molecule: genomic DNA

organism: Mus musculus

source_name: Back skin  inetrfollicular epidermis

extract_protocol: Cells were centrifuged and cell pallets were resuspended in 100ul of lysis buffer (TrisHCl 10mM, NaCl 10mM, MgCl2 3mM, Igepal 0.1%) and centrifuged at 500g for 25 minutes at 4ºC. Supernatant was carefully discarded and nuclei were resuspended in 50ul of reaction buffer (Tn5 transposase 2.5ul, TD buffer 22.5ul, from Nextera DNA sample preparation kit, Illumina, and 25ul H20). The reaction was performed at 37ºC for 30min and was stopped by addition of 5ul of clean up buffer (NaCl 900mM, EDTA 300mM). DNA was purified using the MiniElute purification kit (QIAGEN) following manufacturer protocol. DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from200 to 800bp (BluePippin, Sage Sciences), following manufacturer ́s recommendations.


title: A10


title: M14

value: 14th hour


title: cardiac_wt_mouse_iso-seq

status: Public on May 17 2020

city: Washington

first: Prech

middle: Brian

last: Uapinyoying

state: District of Columbia

address: 111 Michigan Ave, NW

department: Genetic Medicine

institute: Children's National Medical Center

description:
mRNA
PacBio Isoform Sequencing (IsoSeq)
processed data files: excovator_exon-based_counts.xlsx, exphaser_transcript_structure_counts.xlsx, 686_genes_exon_ratios.pdf

data_processing:
Base-calling, generating ccs reads, IsoSeq method (ICE and Quiver) using SMRT analysis v.2.3.140936. Did not collapse redundant isoforms using ToFU. Demultiplexing samples and merging data from multiple smrtCells using custom scripts, https://github.com/puapinyoying/isoseq_manuscript_resources/tree/master/s1_scripts_for_processing_rawdata
Alignment performed using STAR_2.5.0am. 'STARlong --runThreadN 15 --genomeDir /data/references/gencode/mouse/mm10 --runMode alignReads --outSAMattributes NH HI NM MD --readNameSeparator space --outFilterMultimapScoreRange 1 --outFilterMismatchNmax 2000 --scoreGapNoncan -20 --scoreGapGCAG -4 --scoreGapATAC -8 --scoreDelOpen -1 --scoreDelBase -1 --scoreInsOpen -1 --scoreInsBase -1 --alignEndsType Local --seedSearchStartLmax 50 --seedPerReadNmax 100000 --seedPerWindowNmax 1000 --alignTranscriptsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 10000 --readFilesIn all_quivered_hq.100_30_0.99.fastq'
exCovator script for exon-based differential usage analysis. Example: 'python exCOVator.py --bam cardiac.bam edl.bam soleus.bam --gff mm10_686.gff --species mouse --release 85 -o 686_genes_exon_ratios'
exPhaser for transcript structure identification and quantification. Example: 'python exPhaser.py --bams bams/edl.bam bams/soleus.bam --gtf refs/2019-07-15_m22_refs/neb_mm10_chr_m22.gtf --bed neb/neb_122-152.bed --outputPrefix neb_122-152'
Genome_build: GENCODE primary mouse sequence and annotation (GRCm38) version M10 (Ensembl 85) released 2016-07-19.
Supplementary_files_format_and_content: Compiled multiple analysis output text files as sheets inside an Excel workbook for each of the two scripts.

source_name: Cardiac Muscle (apex only)

extract_protocol:
Muscle tissue was dissected, flash frozen in isopentane, and crushed on dry ice. Total RNA extracted using mirVana kit following protocol.
cDNAs were generated using barcoded primers using Clonetech SMARTer PCR cDNA Synthesis Kit (#634925) and size selected for 5-10kb using BluePippin prior to SMRT template generation and sequencing following PacBio IsoSeq protocol.

tag: age

value: 8 weeks

tag: gender

value: Male

value: Cardiac Muscle (apex only)


title: edl_wt_mouse_iso-seq

source_name: Extensor digitorum longus muscle (whole)


title: 2-fgfr3lof/lof

description:
Single-cell RNA-seq
mRNA


title: M12


title: psWAT_22h_mRNAseq_rep3

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

country: Qatar

institute: Sidra Medicine

description:
STF_rCountTable.txt
0700170141_S192_L007

data_processing:
Sample Fastq files were aligned to the mouse reference genome GRCm38.p5 v91 using TopHat/2.1.1
Mapped reads were filtered for unique mapping to the genome.  The number of unique reads mapping to each gene (GencodeM16 annotation) was counted with  HTSeq-count (0.9.1, -t exon and –m union)

source_name: psWAT

extract_protocol:
Organs (OB, BRN, CBL, BST, STM, LIV, and iBAT) were homogenized in Lysis RLT Buffer (Qiagen) supplemented with 1% β-mercaptoethanol (Sigma-Aldrich) using the OMNI tissue homogenizer (TH) (OMNI International). Homogenized organ lysates were then loaded onto the QIAshredder homogenizer spin columns (Qiagen) for further homogenization and elimination of insoluble debris. Total RNA was extracted using RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol. White-adipose tissues (pgWAT and psWAT) were homogenized in Qiazol (Qiagen) and RNA extracted with the Lipid RNeasy Lipid Tissue Mini Kit (Qiagen). mRNA was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina), with a selected insert size of 120–210 bp
mRNA was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina), with a selected insert size of 120–210 bp

tag: organ

value: psWAT

tag: fasting duration

value: twenty two

tag: animal


title: psWAT_18h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169961_S190_L007

value: eighteen


title: psWAT_18h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169901_S151_L005


title: psWAT_18h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170261_S150_L005


title: psWAT_22h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170081_S191_L007


title: 1-fgfr3+/+

description:
Single-cell RNA-seq
mRNA

value: Cranial vault

value: 9 mm


title: psWAT_22h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700213341_S152_L005


title: psWAT_2h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170171_S147_L005

value: two


title: psWAT_12h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170181_S189_L007

value: twelve


title: psWAT_8h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169951_S187_L007

value: eight


title: psWAT_12h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700213311_S149_L005


title: psWAT_2h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170121_S146_L005


title: psWAT_12h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700213271_S148_L005


title: psWAT_8h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170071_S188_L007


title: psWAT_8h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170011_S142_L004


title: soleus_wt_mouse_isoseq

source_name: Soleus muscle (whole)

value: Soleus muscle (whole)


title: psWAT_0h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170001_S144_L005

value: zero


title: pgWAT_22h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170471_S170_L006

source_name: pgWAT

value: pgWAT


title: pgWAT_22h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700213261_S171_L006


title: pgWAT_22h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170411_S169_L006


title: pgWAT_18h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170351_S168_L006


title: psWAT_2h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170061_S145_L005


title: psWAT_0h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169881_S183_L007


title: pgWAT_18h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170661_S166_L006


title: pgWAT_18h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170291_S167_L006


title: pgWAT_12h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700213221_S165_L006


title: pgWAT_12h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170581_S164_L006


title: psWAT_0h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169941_S143_L005


title: pgWAT_12h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170521_S161_L005


title: DME #1

city: Daejeon

first: Bong Ihn

last: Koh

address: 291 Daehakro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Dura mater endothelial cells (Dura mater ECs)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Dura mater

tag: cell type

value: endothelial cell (EC)


title: pgWAT_8h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170341_S196_L007


title: pgWAT_8h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170461_S160_L005


title: pgWAT_8h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170401_S159_L005


title: iBAT_22h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168881_S46_L003

source_name: iBAT

value: iBAT


title: pgWAT_0h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170391_S155_L005


title: pgWAT_2h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170511_S156_L005


title: pgWAT_0h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170331_S154_L005


title: pgWAT_2h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170451_S193_L007


title: pgWAT_2h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170571_S157_L005


title: iBAT_22h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700213301_S12_L001


title: iBAT_18h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168641_S29_L002


title: iBAT_18h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169001_S235_L008


title: iBAT_8h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168811_S234_L008


title: iBAT_12h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168961_S69_L004


title: iBAT_22h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700213251_S11_L001


title: iBAT_8h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168751_S233_L008


title: iBAT_2h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168861_S77_L005


title: iBAT_12h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168871_S81_L005


title: iBAT_8h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168691_S80_L005


title: iBAT_2h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168801_S88_L005


title: iBAT_0h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168741_S76_L005


title: iBAT_0h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168681_S232_L008


title: iBAT_0h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168621_S231_L008


title: LIV_22h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168011_S22_L002

source_name: Liver

value: Liver


title: LIV_22h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700167951_S21_L002


title: LIV_22h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700167891_S20_L002


title: pgWAT_0h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170271_S153_L005


title: LIV_18h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700167831_S19_L002


title: iBAT_18h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168701_S89_L005


title: LIV_18h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700167771_S18_L002


title: LIV_18h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168141_S17_L002


title: iBAT_12h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168921_S82_L005


title: iBAT_2h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168911_S67_L004


title: LIV_12h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168061_S15_L002


title: K562wt_NS

city: Bethesda

first: Lorinc

last: Pongor

state: MD

address: 37 Convent Dr,

department: DTB

institute: NIH

description:
Nascent-strand sequencing
K562wt_NS.bam.scaled.bw
K562_WT_top10percent.bed

data_processing:
Library strategy: DNA-seq
NS-seq data and published data: The obtained fastq files were aligned using the bwa aligner (version 0.7.17). Data deriving from human cell lines were aligned to the hg19 genome version, and mm10 genome version for mouse sequencing data. Aligned (unsorted) reads were sorted using samtools (version 1.8), followed by duplicate marking using picard-tools (version 2.9.2).
Replication timing data was processed using the dragen analysis pipeline (01.003.044.02.05.01.40152) by the sequencing facility using the hg19 genome version.
NS-seq data peak calling: NS-seq peaks were identified using MACS peak caller (version 2.1.1.20160309), using the –nomodel setting, and FDR set to 0.01 to filter low quality peaks. Both narrow and broad peaks were called. To remove low quality peaks, the top 10% of narrow peaks were intersected with the broad peaks to retrieve the highest scoring regions. Called peaks for each cell line and condition were sorted and merged using bedtools  (version 2.27.1).
Peak calling of published ATAC-seq data: Peaks were identified using MACS peak caller (version 2.1.1.20160309), using the –nomodel setting, and FDR set to 0.01 to filter low quality peaks. Called peaks for each cell line and condition were sorted and merged using bedtools (version 2.27.1).
Coverage track generation: Coverage tracks and peak quantifications were created with BAMscale. ATAC-seq data was processed using the default parameters. OK-seq data was processed with "--operation rfd" mode. ENDseq data was processed with the "--operation endseqr" mode. Replication timing data was processed with the "--operation reptime" mode.
Genome_build: Human: hg19, Mouse: mm10
Supplementary_files_format_and_content: bw (bigwig) files were generated with BAMscale, peak FPKM scores were generated using BAMscale, BED files were generated with MACS and bedtools

source_name: Nascent-strand sequencing

growth_protocol: Cancer cells were grown in RPMI medium.

extract_protocol:
NS-seq: DNA fractionation was performed using a 5-30% sucrose gradient to collect DNA fractions ranging from 0.5 to 2 kb. Five prime single-strand DNA ends were phosphorylated by T4 polynucleotide kinase (T4PK) (NEB, M0201S). After phenol/chloroform treatment to remove T4 PK, DNA was precipitated, resuspended and then treated with lambda-exonuclease (NEB, M0262S) to remove genomic DNA fragments that lacked the phosphorylated RNA primer. After RNAse treatment and DNA purification (Qiagen PCR purification kit, 28004), single stranded nascent strands were random-primed using the Klenow and DNA Prime Labeling System (Invitrogen, 18187013)
TruSeq_Pair_End_Seq_Sample_Prep

tag: cell line

value: bone marrow


title: K562_WT_G1

description:
K562_WT_AS.bam_vs_K562_WT_G1.bam.log2.bw
K562_reptime_segmentation_recolored.bed

source_name: G1 synchronized cells

extract_protocol:
Replication timing: To get the pure G1 phase cells, 1 × 108 K562 cells were washed twice with cold PBS and fractionated by elutriation at each of the following flow speeds: 15 × 2, 16 × 2, 17 × 2, 18 × 2 19 × 2, 20 × 2 ml/min. Each fraction was stained by DAPI in PBS and confirmed by FACS. Genomic DNA from G1 phase and asynchronized K562 cells was extracted simultaneously according to manufacturer’s instructions (Qiagen, 69506).
TruSeq_Pair_End_Seq_Sample_Prep

tag: cell phenotype

value: G1 synchronized cells


title: LIV_12h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168101_S16_L002


title: K562_WT_AS

source_name: Asynchronous cells

tag: tissue

value: Asynchronous cells


title: LIV_8h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700167821_S11_L001


title: LIV_8h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700167881_S12_L001


title: LIV_8h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700167941_S13_L002


title: LIV_2h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168051_S7_L001


title: CFBE RPF with RPL12 siRNA treatment

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

description: Ribosme protected

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-2: -v 2 --best --strata -m 1
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-2 the middle nucleotide of each read was taken.
Read counts were normalized by million mapped reads and transcript length for each nucleotide
Supplementary_files_format_and_content: normalized counts

source_name: CFBE RPF with RPL12 siRNA treatment

growth_protocol: Cystic Fibrosis Bronchial Epithelial cells were grown at 37°C to 80% confluency in Eagle's MEM, transfected with siRNA and recovered for 96 h.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA using the Ribo-Zero Gold rRNA Removal Kit (Illumina) and spiked with ERCC RNA Spike-In Mix(Thermo Fisher).
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009}

value: CFBE cells


title: LIV_12h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168001_S14_L002


title: CFBE RPF with scrambled siRNA treatment

description: Ribosme protected

source_name: CFBE RPF with scrambled siRNA treatment


title: CFBE RPF without siRNA treatment

description: Ribosme protected

source_name: CFBE RPF without siRNA treatment


title: LIV_2h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700167931_S5_L001


title: LIV_0h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700167871_S4_L001


title: LIV_2h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700167991_S6_L001


title: CFBE mRNA with RPL12 siRNA treatment, harringtonine chased for 90s


title: CFBE RPF with RPL12 siRNA treatment, harringtonine chased for 90s

description: Ribosme protected


title: LIV_0h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700167811_S3_L001


title: LIV_0h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700167751_S2_L001


title: STM_22h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168431_S65_L006

source_name: Stomach

value: Stomach

value: twenty two


title: STM_22h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168371_S64_L006


title: STM_18h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168251_S62_L006

value: eighteen


title: SIP15_6G

city: Geelong

first: Erica

last: Todd

address: Pigdons Rd

country: Australia

institute: Deakin University

data_processing:
will be provided later
Genome_build: NCBI Assembly: GCA_009762535.1, fNotCel1.pri

organism: Notolabrus celidotus

source_name: gonad

growth_protocol: Wild-caught fish were maintained in 400-litre recirculating seawater tank systems under a natural photoperiod. In each tank, a social group was established consisting of a dominant terminal-phase (TP) male and 4 to 6 initial-phase (IP) individuals.

extract_protocol:
Gonads were removed and immediately preserved in either RNAlater solution or flash frozen by submersion in isopentane on dry ice. RNA was extracted using Trizol reagent with column purification and DNase treatment.
Illumina TruSeq Stranded mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Following a 3-week acclimation period, initial-phase (IP) females were induced to change sex using aromatase inhibition (intramuscular fadrazole implants, 200 ug) or social manipulation (removal of dominant male). Animals were serially sampled in a time-series up to 92 days. Animals sampled on day 0 before manipulation and from non-manipulated tanks served as controls.

value: gonad

tag: sex change stage

value: will be provided later

tag: experiment


title: SIP15_16G


title: SIP15_8G


title: SIP15_9G


title: SIP15_7G


title: STM_18h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168191_S61_L006

tag: strain


title: SIP15_11G


title: STM_22h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168311_S63_L006


title: STM_18h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168561_S60_L006


title: STM_12h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168521_S59_L006

value: twelve


title: STM_12h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168481_S58_L006


title: STM_12h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168421_S57_L006


title: STM_8h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168361_S56_L006

value: eight


title: SI18_BF5G


title: SI18_BF3G


title: SI18_BF2G


title: STM_8h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168241_S54_L005


title: SI18_8G


title: SI18_7G


title: SI18_9G


title: STM_2h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168411_S50_L005

value: two


title: STM_2h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168471_S51_L005


title: SI18_5G


title: STM_2h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168351_S49_L005


title: SI18_M4G


title: STM_0h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168291_S48_L005

value: zero


title: STM_0h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168171_S46_L005


title: SI18_BF4G


title: BST_22h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170111_S141_L004

source_name: BrainStem

value: BrainStem


title: SI18_50G


title: SI18_49G


title: SI18_48G


title: BST_22h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170051_S140_L004


title: SI18_BF1G


title: SI18_51G


title: STM_8h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168301_S55_L005


title: BST_22h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169991_S139_L004


title: SI18_47G


title: BST_18h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169931_S138_L004


title: BST_18h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169871_S137_L004


title: SI18_44G


title: SI18_42G


title: BST_18h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170241_S136_L004


title: BST_12h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170201_S135_L004


title: SI18_40G


title: BST_12h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170161_S134_L004


title: BST_12h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170101_S133_L004


title: SI18_39G


title: SI18_52G


title: SI18_3G


title: STM_0h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168231_S47_L005


title: BST_8h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170041_S132_L004


title: SI18_37G


title: SI18_38G


title: SI18_45G


title: BST_8h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169921_S130_L004


title: BST_2h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700170031_S124_L004


title: BST_8h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169981_S131_L004


title: BST_2h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700170091_S125_L004


title: SI18_33G


title: SI18_34G


title: BST_0h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169971_S123_L004


title: SI18_35G


title: SI18_36G


title: BST_2h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700170151_S126_L004


title: SI18_41G


title: SI18_32G


title: BST_0h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169851_S121_L004


title: SI18_31G


title: CBL_22h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169721_S120_L003

source_name: Cerebellum

value: Cerebellum


title: SI18_30G


title: SI18_2G


title: CBL_22h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169661_S119_L003


title: SI18_28G


title: CBL_22h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169601_S118_L003


title: CBL_18h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169541_S117_L003


title: SI18_27G


title: CBL_18h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169481_S116_L003


title: SI18_25G


title: CBL_18h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169841_S115_L003


title: CBL_12h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169801_S114_L003


title: SI18_23G


title: SI18_24G


title: SI18_22G


title: BST_0h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169911_S122_L004


title: CBL_12h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169711_S112_L003


title: CBL_12h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169761_S113_L003


title: SI18_21G


title: CBL_8h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169651_S111_L003


title: CBL_8h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169531_S109_L003


title: SI18_16G


title: CBL_8h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169591_S110_L003


title: SI18_20G


title: SI18_18G


title: SI18_14G


title: SI18_29G


title: CBL_2h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169701_S104_L003


title: CBL_2h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169751_S105_L003


title: SI18_11G


title: SI18_10G


title: CBL_2h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169641_S103_L003


title: CBL_0h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169521_S101_L003


title: SI16_5G


title: CBL_0h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169581_S102_L003


title: BRN_22h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700213191_S62_L004

source_name: Brain

value: Brain


title: SI16_58G


title: SI16_57G


title: BRN_22h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700213421_S24_L002


title: SI16_53G


title: BRN_18h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700213381_S6_L001


title: SI16_49G


title: SI18_15G


title: BRN_22h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700213401_S61_L004


title: BRN_18h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700213361_S5_L001


title: BRN_12h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700213291_S3_L001


title: BRN_18h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700213331_S4_L001


title: SI16_4G


title: SI16_52G


title: Si16_3G


title: SI16_40G


title: SI16_45G


title: SI16_38G


title: BRN_8h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700213411_S22_L002


title: BRN_12h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700213241_S60_L004


title: BRN_2h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700213321_S58_L004


title: SI16_37G


title: SI16_36G


title: SI16_34G


title: BRN_8h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168781_S23_L002


title: BRN_8h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700213391_S59_L004


title: BRN_2h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168891_S20_L002


title: CBL_0h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169461_S100_L003


title: SI16_2G


title: SI16_29G


title: SI16_30G


title: BRN_0h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168711_S1_L001


title: BRN_2h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700213281_S57_L004


title: BRN_12h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700168941_S39_L003


title: SI16_28G


title: BRN_0h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700168591_S83_L005


title: BRN_0h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700168651_S38_L003


title: SI16_24G


title: SI16_26G


title: OB_22h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169241_S43_L004

source_name: OB

value: OB


title: SI16_23G


title: SI16_27G


title: OB_22h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169301_S44_L004


title: OB_18h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169061_S40_L004


title: OB_22h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169181_S42_L004


title: OB_18h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169121_S41_L004


title: SI16_1G


title: SI16_22G


title: SI16_21G


title: OB_12h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169341_S37_L004


title: OB_18h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169421_S39_L004


title: SI16_16G


title: OB_8h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169231_S35_L004


title: OB_12h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169381_S38_L004


title: OB_12h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169291_S36_L004


title: AI14A_6G


title: AI14A_8G


title: OB_8h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169171_S34_L003


title: AI14A_29G


title: OB_8h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169111_S33_L003


title: AI14A_27G


title: OB_2h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169331_S29_L003


title: AI14A_26G


title: OB_2h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169281_S28_L003


title: AI14A_25G


title: SI16_18G


title: OB_2h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169221_S27_L003


title: AI14A_24G


title: OB_0h_mRNAseq_rep3

description:
STF_rCountTable.txt
0700169161_S26_L003


title: AI14A_15G


title: AI14A_22G


title: AI14A_30G


title: OB_0h_mRNAseq_rep2

description:
STF_rCountTable.txt
0700169101_S25_L003


title: stimulated rep1

city: Munich

first: Nina

middle: Henriette

last: Uhlenhaut

state: Bavaria

address: Ingolstädter Landstraße 1,  Neuherberg

department: Molecular Endocrinology

institute: HelmholtzZentrum München - IDC

data_processing:
Mapping against mm10 mouse genome using bwa 7.12
Duplicate removal using samtools v2.4.0 and Downsampling
Peak calling with macs2 version 2.1.1 using Input (GSM3212800) as control
Create peak universe (broad and narrow)
Genome_build: mm10
Supplementary_files_format_and_content: narrowpeak and broadpeak files were produced using macs2 representing peaks

source_name: gastrocnemius

extract_protocol:
ChIP was performed as previously described (Mir et al., Methods Mol Biol 1966: 39-70, 2019) with minor modifications. Briefly, for each ChIP-seq sample  around 1g of frozen muscle tissue (pooled gastrocnemius muscles from 6 different mice) was homogenized, filtered through a 70µm cell strainer, and pellet fixed in 1% Formaldehyde. Nuclei were purified and chromatin sonicated to a 1-0.5 kb size by using Diagenode Bioruptor Plus. Sheared chromatin was then immunoprecipitated with anti-H3S10ph antibodies (Active Motif; Lot No:08308001), and ChIP DNA was then purified and sequenced.
Libraries from ChIP DNA were prepared by use of KAPA Hyperprep Kit (Kapa Biosystems, KK8504), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies) and used at a final concentration of 68 nM. Adapted ligated libraries were size selected (360-610 bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science, CDF2010). Libraries concentration was estimated by Real Time PCR, with KAPA Library Quantification Kit (Kapa Biosystems, KK4873). Quality of the libraries was evaluated by use of the Agilent High Sensitivity DNA Kit (Agilent) in a 2100 Bioanalyzer (Agilent).

treatment_protocol: 5 month old male C57BL/6 mice were maintained on 12:12 light:dark and standard chow diet. Mice were anesthetized by an intraperitoneal injection of xylazine (Xilor) (20 mg/Kg) and Zoletil (10 mg/Kg). Muscle lengthening was achieved by dorsal or plantar flexing of the foot at a velocity of 40 mm/s while the gastrocnemius muscle was stimulated at 100 Hz to induce a full eccentric tetanic contraction. The footplate was moved 200 ms after initiation of stimulation train, thus eccentric pull occurred during the isometric plateau of the tetanus. The range of movement during the pull was 30°, clearly inside physiological limits of movement for the foot. Total duration of tetanic stimulation was limited to 600 ms, assuring no sag of force. This protocol was repeated 50 times, waiting 30 seconds between each contraction. Immediately after stimulation, mice were sacrificed by cervical dislocation and muscles were collected and snap frozen in liquid nitrogen.

value: Stimulated 50 eccentric contractions

tag: chip antibody

value: H3S10ph (Active Motif; Lot No:08308001)


title: stimulated rep2

tag: treatment


title: unstimulated rep2

value: unstimulated contralateral


title: AI14A_23G


title: OB_0h_mRNAseq_rep1

description:
STF_rCountTable.txt
0700169041_S24_L003


title: AI14A_14G


title: AI14A_11G


title: AI14A_12G


title: Dendritic cells from IRE1 knock out mice treated with LPS, replicate 4

status: Public on May 16 2020

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against mm10 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM

source_name: dendritic cells

extract_protocol:
RNA was isolated using RNeasy MinElute kit (Qiagen) from LPS- or zymosan-stimulated murine bone marrow-derived DC.
All samples passed RNA quality control examined by Agilent Bioanalyzer 2100, and mRNA libraries were generated and sequenced at the Weill Cornell Epigenomics Core Facility

value: KO

value: LPS

tag: replicate


title: Dendritic cells from IRE1 knock out mice treated with LPS, replicate 2


title: unstimulated rep1


title: Dendritic cells from IRE1 knock out mice treated with LPS, replicate 1


title: Dendritic cells from IRE1 knock out mice treated with Zymosan, replicate 4

value: Zymosan


title: WT CD4 Treg-1

city: San Antonio

first: Nu

address: 7703 Floyd Curl

institute: UT Health San Antonio

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and reads with low quality nucleotide were removed, then mapped to mm10 whole genome using STAR.
Mapped regions can be classified as exons, introns, or intergenic regions.
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced was calculated
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Spleens were removed and processed to obtain lymphocytes. Post CD8 enrichment, cells were stained for required cell type and FACS sorted.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen

value: 3 month old WT mice


title: WT CD49lo-2


title: WT CD8 Treg


title: WT CD4 Treg-2


title: WT CD49lo-1


title: Dendritic cells from IRE1 knock out mice treated with Zymosan, replicate 3


title: Dendritic cells from IRE1 knock out mice treated with Zymosan, replicate 1


title: Dendritic cells from IRE1 knock out untreated mice, replicate 3

value: untreated


title: Dendritic cells from IRE1 knock out mice treated with Zymosan, replicate 2


title: Dendritic cells from IRE1 knock out untreated mice, replicate 4


title: Dendritic cells from IRE1 knock out untreated mice, replicate 2


title: Dendritic cells from IRE1 knock out untreated mice, replicate 1


title: Dendritic cells from IRE1 wild type mice treated with LPS, replicate 2

value: WT


title: Dendritic cells from IRE1 knock out mice treated with LPS, replicate 3


title: Dendritic cells from IRE1 wild type mice treated with LPS, replicate 1


title: Dendritic cells from IRE1 wild type mice treated with LPS, replicate 4


title: Dendritic cells from IRE1 wild type mice treated with LPS, replicate 3


title: Dendritic cells from IRE1 wild type untreated mice, replicate 3


title: Dendritic cells from IRE1 wild type untreated mice, replicate 2


title: Dendritic cells from IRE1 wild type mice treated with Zymosan, replicate 2


title: Dendritic cells from IRE1 wild type untreated mice, replicate 4


title: Dendritic cells from IRE1 wild type mice treated with Zymosan, replicate 1


title: Dendritic cells from IRE1 wild type mice treated with Zymosan, replicate 3


title: 151B

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Standard Illumina Infinium MethylationEPIC Kit protocols

scan_protocol: Illumina iScan System and iScan Control Software

data_processing:
Processed BeadChips were scanned on an Illumina HiScan and intensity values were imported into GenomeStudio (Illumina) for data quality assessment, color correction and background subtraction. A data matrix was then exported as beta values representing percent DNAm ranging from 0 to 1 (0=unmethylated and 1=methylated). Next, a probe filtering step removed SNP probes, polymorphic probes, cross hybridizing probes46, and probes with missing values or detection p values >1e16. After filtering, 794,811 probes remained within the autosomes, 17,4660 in the X chromosome, and 31 in the Y chromosome. Probes on the X and Y chromosomes for males, and X chromosomes for females were separated from the autosomes for the remainder of preprocessing and data analysis. Next, because the Illumina platform includes two probe types (Type I and II) with different distributions, data normalization was performed using beta mixture quantile method
beta mixture quantile normalized and batch corrected with combat betas

extract_protocol: (Oragene saliva collection) and Qiagen Blood and Tissue Kit

tag: batch

tag: Sex

value: Female


title: 30_T2

label_protocol: Standard Illumina Infinium MethylationEPIC Kit protocols

tag: age

value: Male


title: 24B


title: 43_T2


title: 106_Rep3


title: Dendritic cells from IRE1 wild type untreated mice, replicate 1


title: 24_T2_B


title: 121


title: 43


title: 18


title: 95_T2


title: 75_T2


title: Dendritic cells from IRE1 wild type mice treated with Zymosan, replicate 4


title: 95


title: 140_T2


title: 18_T2


title: 140


title: 33_T2


title: 180


title: 116_T2


title: 121_T2


title: 49


title: 75


title: 151_T2_B


title: 30


title: 155_T2


title: 116


title: 145_T2


title: 155


title: 94_T2


title: 28_T2


title: 145


title: 17_T2


title: 128


title: 50


title: 137


title: 137_T2


title: 17


title: 128_T2


title: 50_T2


title: 33


title: 67


title: 5_T2


title: 49_T2


title: 124


title: 28


title: 23_T2


title: 124_T2


title: 3_T2


title: 152


title: 67_T2


title: 3


title: 180_T2


title: 152_T2


title: 23


title: 5


title: 81_T2


title: 20_T2


title: 81


title: 94


title: 20


title: 90_T2


title: 19B


title: 90


title: 19_T2_B


title: 112_T2


title: 126_T2


title: 112


title: 126


title: 171


title: 47


title: 58_T2


title: 89


title: 97


title: 58


title: 134_T2


title: 106_Rep2


title: 134


title: 97_T2


title: 65_T2


title: 156_T2


title: 61


title: 127


title: 106_T2_Rep2


title: 171_T2


title: 127_T2


title: 16


title: 114


title: 16_T2


title: 65


title: 59_T2


title: 13_T2


title: 156


title: 13


title: 130


title: 59


title: 89_T2


title: 47_T2


title: 114_T2


title: 61_T2


title: 1


title: 64_T2


title: 159


title: 1_T2


title: 64


title: 104_T2


title: 104


title: 159_T2


title: 108


title: 69


title: 63


title: 48


title: 153


title: 54_T2


title: 63_T2


title: 69_T2


title: 48_T2


title: 130_T2


title: 35_T2


title: 35


title: 183_T2


title: 153_T2


title: 87


title: 32


title: 32_T2


title: 25_T2


title: 54


title: 108_T2


title: 25


title: 87_T2


title: 154


title: 154_T2


title: 160


title: 170


title: 160_T2


title: 125


title: 170_T2


title: 183


title: 147


title: 70


title: 125_T2


title: 12


title: 102_T2


title: 12_T2


title: 147_T2


title: 85_T2


title: 102


title: 72_T2


title: 72


title: 163_T2_B


title: 85


title: 15


title: 193_T2


title: 76


title: 76_T2


title: 115_T2


title: 115


title: 79


title: 193


title: 15_T2


title: 79_T2


title: 101_T2


title: 92


title: 70_T2


title: 163


title: 53_T2


title: 92_T2


title: 77


title: 101


title: shControl of X01

city: Seoul

first: Young Taek

last: Oh

address: 50 Irwon-dong, Gangnam-gu

institute: Samsung Medical Center

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: counts and FPKM

source_name: X01 GSC

growth_protocol: DMEM F/12 media

extract_protocol: Qiagen RNA mini kit

treatment_protocol: shRNA transfection

tag: knockdown

value: shControl


title: JZL184 of X01

data_processing:
none provided by the submitter
Genome_build: human genome 19 (hg19)
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

extract_protocol:
Qiagen RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cornig matrigel


title: shARS2 of X01


title: 53


title: 77_T2


title: 60


title: 68


title: SpenKO_Cl2_input_K4K27_Rep1

city: Stanford

first: Howard

middle: Y.

last: Chang

state: CALIFORNIA

address: 269 Campus Drive, CCSR 2130

institute: Stanford

data_processing:
Sequence were mapped to the mm9 genome build using Bowtie2. Duplicate reads were then removed using Picard Tools.
Peaks were called using MACS2 with a q-value cutoff of 0.01 with input as background. Peaks called from two technical replicates were compared by IDR package and further filtered by the Irreproducible Discovery Rate(<0.05), if differential peak  calling was applied. Broad peak calling for K9me3 was done by epic using merged bam file from two replicates.
Reproducible peaks from WT and KO conditions were merged and reads in these peaks were counted across all libraries. Differential peaks were called using reads counts from reproducible peaks with DESeq2(fold change >=2 and Padjust <0.01 ).
Bigwig files were generated from nonredundant bam files using bedtools for visualization.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using bedtools

source_name: cultured cell

growth_protocol: HATX WT and Spen KO clone 2 and clone 3 cell lines were gift of A. Wutz and are described in detail in Monfort et al., 2015.  mESCs were cultured in serum/lif conditions (Knockout DMEM (GIBCO 10829018), 1% Penicillin/streptomycin, 1% GlutaMax, 1%non-essential amino acids, beta-mercaptoethanol, Hyclone fetal bovine serum (Fisher SH3007103), and 0.01% LIF (ESGRO ESG1107).  Cells were cultured on 0.2% gelatin-covered plates and passaged every 2-3 days as needed.

extract_protocol:
Cells were then lysed (50mM HEPES-KOH, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10 minutes at 4’C.  Nuclei were lysed (100 mM Tris pH 8.0, 200mM NaCl, 1mM EDTA, 0.5 mM EGTA) for 10 minutes at room temperature.  Chromatin was resuspended in sonication buffer (10 mM Tris pH 8.0, 1mM EDTA, 0.1% SDS) and sonicated using a Covaris Ultrasonicator to an average length of 220 bp.
For all ChIPs, 5 million cells per replicate were incubated with 5 ug (Histone) or 7.5 ug (Oct4) antibody overnight at 4’C .  Antibody-bound chromatin was incubated with Protein G Dynabeads (Invitrogen, 10004D) for 4 hours at 4’C and eluted in Tris buffer (10mM Tris pH 8.0, 10mM EDTA, 1% SDS).  Crosslinks were reversed by incubation overnight at 65’C followed by treatment with 0.2 mg/mL proteinase K (Life Technologies, AM2548) and 0.2 mg/mL RNAse A (Qiagen).  DNA was purified using Qiagen Minelute Columns (Qiagen, 28006).  For library preparation, 4 ng ChIP DNA was incubated with transposase (Illumina, Fc-121-1030) for 10’ at 55’C.  DNA was then amplified using Nextera barcoding adapters and sequenced on an Illumina Nextseq (2x75 bp reads).

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 minutes at room temperature and subsequently quenched with 0.125M glycine.   Cells were then snap frozen and stored at -80’C.

value: mouse embryonic stem cells

value: mixed genomic background

tag: genotype/variation

value: SpenKO

tag: clone

value: Clone 2


title: SpenKO_Cl2_input_K4K27_Rep2


title: SpenKO_Cl2_ChIP_H3K4me3_Rep2

value: H3K4me3:Active Motif 39159


title: SpenKO_Cl2_ChIP_H3K4me3_Rep1


title: SpenKO_Cl2_ChIP_H3K27Ac_Rep1

value: H3K27Ac:Active Motif 39133


title: SpenKO_Cl2_ChIP_H3K27Ac_Rep2


title: 68_T2


title: 111


title: HATX_WT_input_K9_Rep2


title: HATX_WT_input_Oct4_Rep2


title: 100


title: 46_T2


title: 111_T2


title: HATX_WT_input_K4K27_Rep2


title: 60_T2


title: 100_T2


title: Vehicle of X01

value: Vehicle


title: HATX_WT_input_K9_Rep1


title: HATX_WT_input_Oct4_Rep1


title: HATX_WT_ChIP_H3K9me3_Rep1

value: H3K9me3:abcam AB8898


title: HATX_WT_input_K4K27_Rep1


title: HATX_WT_ChIP_H3K9me3_Rep2


title: 151_T2


title: 6


title: HATX_WT_ChIP_H3K4me3_Rep1


title: HATX_WT_ChIP_H3K4me3_Rep2


title: HATX_WT_ChIP_H3K27Ac_Rep2


title: 46


title: HATX_WT_ChIP_H3K27Ac_Rep1


title: 84


title: 136_T2


title: 29_T2


title: 84_T2


title: 36_T2_B


title: 123_T2


title: 29


title: V6.5_RRM_minusDox_invivo_irCLIP_FLAG_Rep1

data_processing:
The raw sequence were split by sample barcode and UMI sequence were extract and added to reads name using in house python script.
Adaptor sequence and polyA sequence were first trimmed using CutAdapt.  Trimmed reads were mapped to the same mouse genome build (mm9) using STAR.
PCR duplications were further removed using UMI tools. The coverage of the 5’ position were calculated using bedtools.
Genome locations with >=3 coverage were identified as RT stop causing by potential binding by SPEN.
To focus on the repeat elements, the trimmed sequences were mapped to the expressed repeat elements using STAR. PCR duplication were also removed using UMI tools. Technical replicates were merged for each experiment condition. The RT-stop were identified in the same way (coverage  > =3).
Genome_build: mm9

growth_protocol: mESCs were cultured in serum/lif conditions (Knockout DMEM (GIBCO 10829018), 1% Penicillin/streptomycin, 1% GlutaMax, 1%non-essential amino acids, beta-mercaptoethanol, Hyclone fetal bovine serum (Fisher SH3007103), and 0.01% LIF (ESGRO ESG1107).  Cells were cultured on 0.2% gelatin-covered plates and passaged every 2-3 days as needed.

extract_protocol:
nuclear RNA was isolated as previously described (Gagnon et al., 2014).
20 μg nuclear RNA was then fragmented (Ambion, AM8740), and incubated with 5 μg recombinant Spen RRMproteins (RRM2-4 WT or RRM2-4:RRM3 Mt) at 4C for 2 hours.  RNA-protein complexes were then transferred to a 3cm cell culture dish on ice and crosslinked (254nM UV-C) at 0.3J/cm2.  Following crosslinking, RNA-protein complexes were incubated with antibody-bound Protein A Dynabeads at 4C for 2 hours.  Following IP, beads were washed with IPP buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 0.05% NP-40, 5mM EDTA), low salt buffer (10 mM Tris-HCl pH7.4, 50 mM NaCl, 1mM EDTA, 0.1% NP-40), and high salt buffer (10 mM Tris-HCl pH7.4, 500 mM NaCl, 1 mM EDTA, 0.1% NP-40, 0.1%SDS).

treatment_protocol: For in vivo irCLIP experiments, V6.5 male mESCs, or HATX Spen KO Clone 2 mESCs were transduced with a lentivirus carrying Spen RRMs 2-4 with the SV40 nuclear localization signal, 2x HA tags, and 3x FLAG tag (“SpenRRM-FLAG”; pLVX-EF1a-SV40NLS-SpenRRM234-2xHA-3xFLAG-IRES-zsGreen).  Following transduction, GFP+ cells were FACS sorted and single colonies were picked.  Western blotting was used to confirm the expression of SpenRRM-FLAG at 37 kDa.  irCLIP was performed exactly as described (Zarnegar et al., 2016).

value: wildtype

value: in vivo

tag: clip-protein

value: transduced  SpenRRM-FLAG +anti-FLAG (Sigma Aldrich F3165)


title: V6.5_RRM_minusDox_invivo_irCLIP_FLAG_Rep2

tag: cell type


title: V6.5_RRM3Mt_minusDox_invitro_irCLIP_IgG_Rep2

value: transduced  SpenRRM-FLAG +anti-IgG antibody


title: 36


title: V6.5_RRM2-4_minusDox_invitro_irCLIP_IgG_Rep2


title: V6.5_RRM3Mt_minusDox_invitro_irCLIP_FLAG_Rep2


title: V6.5_RRM3Mt_minusDox_invitro_irCLIP_FLAG_Rep1


title: 123


title: V6.5_RRM3Mt_minusDox_invitro_irCLIP_IgG_Rep1


title: 136


title: 6_T2


title: 98_T2


title: V6.5_RRM2-4_minusDox_invitro_irCLIP_IgG_Rep1


title: V6.5_RRM2-4_minusDox_invitro_irCLIP_FLAG_Rep2


title: 98


title: 2_T2


title: 83


title: 107_T2


title: SpenKO_RRM_plusDox_invivo_irCLIP_FLAG_Rep2

value: mouse embryonic stem cells Spen KO Clone 2

value: Spen KO


title: 107

value: Female


title: V6.5_RRM_minusDox_invivo_irCLIP_IgG


title: SpenKO_RRM_minusDox_invivo_irCLIP_IgG


title: SpenKO_RRM_plusDox_invivo_irCLIP_FLAG_Rep1


title: SpenKO_RRM_minusDox_invivo_irCLIP_FLAG_Rep4


title: 2


title: 83_T2

value: Male


title: SpenKO_RRM_minusDox_invivo_irCLIP_FLAG_Rep3


title: SpenKO_RRM_minusDox_invivo_irCLIP_FLAG_Rep1

value: in vitro


title: 34_T2


title: 88


title: 132


title: SpenKO_RRM3Mt_plusDox_invitro_irCLIP_IgG_Rep1

value: RRM2-4:RRM3 Mt+anti-IgG antibody


title: SpenKO_RRM_minusDox_invivo_irCLIP_FLAG_Rep2

value: mixed genomic background


title: 132_T2


title: 56


title: 88_T2


title: SpenKO_RRM3Mt_plusDox_invitro_irCLIP_FLAG_Rep2

value: RRM2-4:RRM3 Mt +anti-FLAG (Sigma Aldrich F3165)


title: V6.5_RRM2-4_minusDox_invitro_irCLIP_FLAG_Rep1

value: mouse embryonic stem cells


title: SpenKO_RRM_plusDox_invivo_irCLIP_IgG

value: Clone 2


title: SpenKO_RRM3Mt_minusDox_invitro_irCLIP_FLAG_Rep2

value: mouse embryonic stem cells Spen KO Clone 3

value: Clone 3


title: SpenKO_RRM3Mt_minusDox_invitro_irCLIP_IgG_Rep1


title: 34


title: SpenKO_RRM3Mt_plusDox_invitro_irCLIP_FLAG_Rep1


title: 86


title: SpenKO_RRM2-4_plusDox_invitro_irCLIP_IgG_Rep1

value: RRM2-4 WT +anti-IgG antibody


title: SpenKO_RRM3Mt_minusDox_invitro_irCLIP_FLAG_Rep1


title: 56_T2


title: 113_T2


title: 37


title: SpenKO_RRM2-4_plusDox_invitro_irCLIP_FLAG_Rep2

value: RRM2-4 WT +anti-FLAG (Sigma Aldrich F3165)


title: SpenKO_RRM2-4_minusDox_invitro_irCLIP_IgG_Rep1


title: SpenKO_RRM2-4_plusDox_invitro_irCLIP_FLAG_Rep1


title: SpenKO_RRM2-4_minusDox_invitro_irCLIP_FLAG_Rep2


title: 113


title: 86_T2


title: 37_T2


title: 31_T2


title: SpenKO_Cl3_plusDox_ATAC

data_processing:
Basecalls performed on the sequence machince with BCL2FASTQ.
ATAC adapters and barcodes were trimmed using CutAdapt Software. Sequences were aligned to the mm9 genome using Bowtie2 software
Non-concordant reads  were filtered out
Peaks were called using Macs2 software with a no-shifting model - peaks were called separately for the X chromosome and the autosomes and then merged
Peaks were filtered using IDR software with a  cutoff of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using  bedtools

extract_protocol:
Nuclei were isolated using NP-40-containing buffer and subsequently transposed with adapter-loaded hyperactive Tn5 transposase (Illumina).
Following clean-up transposed fragments were directly amplified and barcoded using Nextera indexes

treatment_protocol: For Xist induction experiments(plusDox), mESCs were plated at a density of 75,000 cells/well in a 6-well plate.  24 hours after plating, cells were treated with 2ug/mL doxycycline for 48 hours

value: SpenKO


title: SpenKO_Cl2_plusDox_ATAC


title: 109


title: 106_T2_Rep1


title: SpenKO_Cl3_minusDox_ATAC


title: SpenKO_Cl2_minusDox_ATAC


title: 109_T2


title: HATX_WT_plusDox_ATAC

value: HATX WT


title: 106_Rep1


title: 96


title: 96_T2


title: HATX_WT_minusDox_ATAC


title: 55_T2


title: SpenKO_Cl2_RNAseq_R1

data_processing:
Basecalls performed on the sequence machince with BCL2FASTQ
RNA-seq reads were mapped to the mm9 genome using STAR
Following read alignment, reads were assigned to transcripts using FeatureCounts in R (RSubread).
Differential genes were called using DESeq2 (fold change >=2, Padjust<0.001).
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression were counted using FeatureCounts in R (RSubread). GTF file from gencode was used for feature assignment  (https://www.gencodegenes.org/mouse_releases/1.html).

extract_protocol:
RNA-seq library preparation was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2102).
In place of poly-A selection, we performed Ribosomal RNA depletion using the RiboMinus Eukaryote System v2 (Life Tech. A15026).

value: mouse embryonic stem cells Spen KO


title: 31


title: 55


title: HATX_WT_RNAseq_R2


title: SpenKO_Cl2_RNAseq_R2


title: 110


title: 110_T2


title: SpenKO_RRM2-4_minusDox_invitro_irCLIP_FLAG_Rep1

value: mouse embryonic stem cells Spen KO Clone 2


title: HATX_WT_RNAseq_R1


title: 138_T2


title: 138


title: 14


title: 42_T2


title: 14_T2


title: 120


title: 57_T2


title: MDA-MB-231 siLuc Rep2

city: Lyon

first: Peter

last: Mulligan

state: If applicable (USA / Canada)

address: 28 rue Laennec

institute: Inserm Research Unit 1052, Cancer Research Center of Lyon (CRCL)

data_processing:
Raw data were aligned on the human genome (hg38) with STAR v2.7.0f (Dobin et al., 2013) and default parameters. Read counts on each genes of the Gencode annotation v29 were produced by STAR. The analyses were performed using R (v 3.4.4) and illustrations produced with the ggplot2 (Wickham, H., 2016) and ggpubr packages. Starting from raw counts, we used the R package DESeq2 (Love et al, 2014) (v1.14) to perform the differential expression analyses. Each time the design was set as ~REP + TYPE, where REP refers to the replicate number (paired analysis) and TYPE to the treatment group. Differential expression was tested using the Wald test, and p-values were corrected with the Benjamini-Hochberg method.
Genome_build: hg38

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells (ATCC, HTB-26) were grown in DMEM GlutaMAX (Gibco, 10566016) supplemented with 10 % of FBS (Gibco, 10270-106), 1 % penicillin/streptomycin (Gibco, 15140122). Cells were grown at 37°C and 5% CO2 in a humidified incubator and passaged every 2 – 4 days by trypsinization. Cells were regularly tested for mycoplasma using a commercial kit (ATCC, 30-1012K), and cultures renewed from low passage stocks every two months or less.

extract_protocol:
RNA was extracted from sub-confluent cells using TRI-reagent (Sigma, T9424).
RNA libraries were prepared with the TruSeq Stranded Total-RNA kit (Illumina).

treatment_protocol: MDA-MB-231 cells were transfected with CDYL2 esiRNA (Sigma, EHU042511) or esiLuciferase (Sigma, EHUFLUC) using Interferin reagent (Polyplus, 409-10) according to the manufacturer's instructions. RNA was extracted 72h post-transfection.

value: Breast cancer

tag: transfection

value: Control


title: MDA-MB-231 siCDYL2 Rep1


title: MDA-MB-231 siCDYL2 Rep3


title: MCF7-CDYL2 Rep1

source_name: MCF7 cells

growth_protocol: MCF7 cells (ATCC, HTB-22) and their derivatives were grown in DMEM Low Glucose (Gibco, 31885-023) supplemented with 10 % of FBS (Gibco, 10270-106), 40 µg/mL of gentamicin (Gibco, 15710-049) and 0.6 µg/mL of insulin (NovoRapid, 3525909). Cells were grown at 37°C and 5% CO2 in a humidified incubator and passaged every 2 – 4 days by trypsinization. Sustained expression of ER-alpha in MCF7 was validated regularly by western blotting and immunofluorescence. Cells were regularly tested for mycoplasma using a commercial kit (ATCC, 30-1012K), and cultures renewed from low passage stocks every two months or less.

treatment_protocol: CDYL2 cDNA was cloned by PCR from an MCF7 cDNA library and inserted into the Gateway pENTR-D-TOPO vector (Invitrogen, K240020). Sequencing on both strands confirmed that the cDNA corresponded to a published CDYL2 sequence (Genbank, NM_152342.2). The cloned cDNA was then transferred into MSCV plasmid (Addgene # 41033) using LR Clonase (Invitrogen, 11791100), and the resulting expression construct validated by sequencing. MCF7 cells were then stably transduced with MSCV (Vector) or MSCV-CDYL2 retroviruses and selected for 14 days using 2 µg/mL puromycin (Sigma, P8833). Expression was confirmed by western blotting and immunofluorescence using CDYL2 antibody.

tag: transduction


title: MCF7-Vector Rep3

tag: tissue

value: MSCV


title: MCF7-CDYL2 Rep2


title: MCF7-Vector Rep1


title: MDA-MB-231 siLuc Rep1


title: 42

value: Male


title: MDA-MB-231 siLuc Rep3


title: MCF7-Vector Rep2


title: 22_T2


title: MDA-MB-231 siCDYL2 Rep2


title: 120_T2

value: Female


title: MCF7-CDYL2_Input

description: Input chromatin control

data_processing:
Pair end DNA sample libraries were sequenced using Illumina. Raw sequences were aligned to human genome hg19, using Bowtie 2.0  (Langmead and Salzberg, 2012) with paired-end parameters. Normalized and subtraction bigwig files were obtaining using deepTools (Ramírez et al., 2016). Analysis of ChIP-Seq data was in the galaxeast.fr instance. Significant peaks were called using MACS2 (Zhang et al., 2008, p. 2).
Genome_build: hg19

extract_protocol:
Cells were grown to sub-confluence in 15 cm tissue culture treated plates (Corning), cross-linked, washed and pelleted. The resulting cell pellets were pre-treated by incubating in lysis buffer A (Lysis Buffer 1 (50 mM HEPES pH 7.5; 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× protease inhibitors) for 10 minutes at 4°C, then lysis buffer B (10 mM Tris-HCl pH 8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1× protease Inhibitors) for 10 minutes at room temperature, as previously described (Lee et al., 2006). They were then lysed in buffer C (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1%; Na-Deoxycholate, 1× protease inhibitors) supplemented with 0.5% SDS, incubated on ice for 30 minutes with occasional vortexing, then sonicated on ice to an average fragment size of 150 bp using a sonicator (Branson, Digital Sonifier 450). The sonicated lysate was centrifuged at 12,000 r.p.m. in a benchtop centrifuge at 4°C, the supernatant diluted five times in buffer C, and 1 mL aliquots of this added to 50 µL of magnetic protein A beads (Invitrogen) pre-coated with 5 µg of anti-CDYL2 IgG (MyBiosource, MBS821304). These were incubated overnight at 4°C with rotation, then pelleted and washed with two sequential additions each of wash buffer 1 (0.1% SDS, 1%Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8, 150mM NaCl), wash buffer 2 (0.1% SDS, 1%Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8, 500mM NaCl), wash buffer 3 (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8), and TE buffer (10mM Tris-HCl, 1mM EDTA, pH 8.0, 50 mM NaCl). Chromatin was eluted by incubating for 30 minutes at 65°C  in elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA pH 8, 1% SDS) with frequent vortexing. Crosslinks were reversed by overnight incubation at 65°C, and eluates treated with RNAse A (Sigma) for 2h, followed by Proteinase K for 2h, then extracted using a classical Phenol-Chloroform/Ethanol precipitation protocol.
Pair end DNA sample libraries were prepared using the MicroPlex Library Preparation Kit v2 (Diagenode) according to the manufacturer’s instructions.

tag: tumor type

tag: vector

value: Input chromatin


title: MCF7-Vector _CDYL2 ChIP

description: CDYL2 ChIP seq


title: MCF7-CDYL2 Rep3


title: 45


title: MCF7-CDYL2_CDYL2 ChIP

description: CDYL2 ChIP seq


title: 45_T2


title: 57


title: 22


title: 201533620035_R07C01

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using iSCAN BeadArray reader

data_processing: R library minfi

label: Cy5, Cy3

source_name: Tissue Control CT12

label_protocol: Standard Illumina protocol

extract_protocol: DNA isolation using DNA QIAamp FFPE Tissue Kit

value: Tissue Control


title: 201533620035_R05C01

source_name: Tissue Control CT10


title: 201533620035_R06C01

source_name: Tissue Control CT11


title: 201533620035_R04C01

source_name: Tissue Control CT9


title: 201533620035_R03C01

source_name: Tissue Control CT8


title: DSS UA rep3

city: Hangzhou

first: Mingqian

last: Li

address: Gucui Road 234

country: China

institute: Tongde hospital of Zhejiang Province

data_processing:
The raw data of RNA-seq was inspected using FastQC and mapped to the reference genome (GRCm38).
The  FPKM of genes was calculated by hisat2 and cuffdiff

source_name: mouse colon

extract_protocol:
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: colon

tag: strain

value: DSS UA treated


title: DSS UA rep2


title: UA DSS rep2

value: UA DSS treated


title: UA DSS rep3


title: DSS UA rep1


title: DSS rep3

value: DSS treated


title: UA DSS rep1


title: 201533620035_R01C01

source_name: Tissue Control CT6


title: DSS rep1


title: 201533620035_R02C01

source_name: Tissue Control CT7


title: Con rep3

value: untreated


title: 201533620011_R07C01

source_name: Tissue Control CT4


title: 201533640024_R01C01

source_name: Tissue Control CT2


title: 201533620011_R06C01

source_name: Tissue Control CT3


title: 201533620011_R08C01

source_name: Tissue Control CT5


title: 201533640011_R07C01

source_name: Tissue Control CT1


title: Con rep2


title: Tumor specific T cells, KO2

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

data_processing:
Basecalls performed using bcl2fastq version 2.18
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using BWA (v0.7.15)
Ailgned sam files convert to bam by samtools, and extract mapped reads then remove duplicated mapped reads, use bedtools convert bam files to bed format.
peaks were called using SICER version 1.1 with the following setting: redundancy threshold (1), window size (200), gap size (400), FDR (0.05).
Use deeptools convert bam file to bigwig and plot the figure.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated and normalized using SICER

source_name: Tumor specific T cell

extract_protocol:
A total of 1 × 10e5 B16-F10 cells were injected subcutaneously into 6 to ~10-week-old female C57BL/6J mice (six mice per group). On day 21, mice were euthanized and subcutaneous tumors were digested with 1 mg/ml collagenase D supplemented with 10 U/ml DNase I. OVA-specific CD8+ TILs were sorted using a BD FACS Aria cell sorter, and gene profiling, ATAC-seq library construction and high-throughput sequencing were performed on approximately 50,000 sorted cells.
Libraries were prepared according to Vazyme's instructions accompanying the DNA Sample Kit (TD501). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq 4000 instrument following the manufacturer's protocols.

value: mouse T cell

tag: genotype

value: HPK1 knockout


title: Tumor specific T cells, WT2

value: wild type


title: DSS rep2

tag: treatment


title: 201557510028_R03C01

source_name: Adrenocortial tumor C41

value: Adrenocortial tumor


title: Tumor specific T cells, WT3


title: 201557510028_R02C01

source_name: Adrenocortial tumor C37


title: 201557510028_R04C01

source_name: Adrenocortial tumor C32


title: 201533610012_R04C01

source_name: Adrenocortial tumor C27


title: Tumor specific T cells, KO1


title: 201533610012_R07C01

source_name: Adrenocortial tumor C10


title: Tumor specific T cells, WT1


title: 201533610011_R08C01

source_name: Adrenocortial tumor C33


title: 201533610011_R06C01

source_name: Adrenocortial tumor C24


title: SpenKO_Cl2_input_Oct4_Rep1

source_name: cultured cell

value: mouse embryonic stem cells

value: mixed genomic background

value: SpenKO

value: Clone 2

tag: chip antibody


title: 201533610011_R07C01

source_name: Adrenocortial tumor C15


title: Con rep1

source_name: mouse colon


title: FYDN12-ABA-2

city: Shanghai

first: Liming

last: Luo

address: 800 Dongchuan RD. Minhang District

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Then, to getting a stable data from three biological repeats, we build up the expression matrix and a fitter was set that each gene in the same sample from three biological repeats should follow the rule that standard deviation of each gene must smaller than the mean of them. Then two matrix were generated from the fitted gene expression levels, the first matrix was build up by samples and gene expression levels, centralized it and generating the heatmap by using R package Pheatmap(3). Meanwhile, the second matrix was build up in the way that genes was separated into two groups by the ABA treatment or not for the ANOVA. Genes were considered differentially expressed when the adjusted P value (FDR) was ≤0.05 and the absolute fold change was ≥2
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana seedling

growth_protocol: 5-d-old WT, nrp1 nrp2, FyPP3DN and nrp1 nrp2 / FyPP3DN vertically grown seedling were treated under 5 μM ABA condition for 24h, meanwhile the control group grown without any treatment for 24h.

extract_protocol:
Total RNA was extracted from those seedling by using the Quick RNA Isolation Kit.
The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) or Ribo-Zero™ rRNA removal Kit (illumina). The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（by AxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: Treatment group: 5 μM ABA treated for 24 hour. Control group: growing under normal condition

value: seedling

value: 5-day-old + 24h treatment

tag: aba treatment

value: With ABA treatment

tag: background ecotype

value: Columbia 0

value: nrp1 nrp2 and FyPP3DN


title: FYDN12-ABA-1

tag: age


title: FYDN12-ABA-3


title: KO12-ABA-2

value: nrp1 nrp2


title: 201533610011_R05C01

source_name: Adrenocortial tumor C22


title: SpenKO_Cl2_input_K9_Rep2


title: KO12-ABA-1


title: 201557510049_R07C01

source_name: Adrenocortial tumor C28


title: 201533610012_R03C01

source_name: Adrenocortial tumor C19


title: 201557510049_R08C01

source_name: Adrenocortial tumor C13


title: 201557510049_R04C01

source_name: Adrenocortial tumor C16


title: 201533610012_R06C01

source_name: Adrenocortial tumor C38


title: SpenKO_Cl2_input_Oct4_Rep2


title: 201533610012_R02C01

source_name: Adrenocortial tumor C25


title: KO12-ABA-3


title: 201557510049_R05C01

source_name: Adrenocortial tumor C34


title: 201557510049_R02C01

source_name: Adrenocortial tumor C23


title: 201557510049_R01C01

source_name: Adrenocortial tumor C30


title: FYDN-ABA-2


title: SpenKO_Cl2_input_K9_Rep1


title: FYDN-ABA-1


title: WT-ABA-3

value: WT


title: SpenKO_Cl2_ChIP_H3K9me3_Rep2

value: H3K9me3:abcam AB8898


title: FYDN-ABA-3


title: SpenKO_Cl2_ChIP_H3K9me3_Rep1


title: 201557510031_R06C01

source_name: Adrenocortial tumor C36


title: 201557510031_R04C01

source_name: Adrenocortial tumor C20


title: 201557510031_R03C01

source_name: Adrenocortial tumor C9


title: HATX_WT_ChIP_Oct4_Rep2

source_name: cultured cell

value: Oct4:Santa Cruz sc-8629


title: 201533610011_R04C01

source_name: Adrenocortial tumor C3


title: WT-ABA-2


title: SpenKO_Cl2_ChIP_Oct4_Rep2


title: SpenKO_Cl2_ChIP_Oct4_Rep1


title: 201557510031_R02C01

source_name: Adrenocortial tumor C18


title: 201557510031_R01C01

source_name: Adrenocortial tumor C11


title: WT-ABA-1

source_name: Arabidopsis thaliana seedling


title: 201557510026_R08C01

source_name: Adrenocortial tumor C48


title: HATX_WT_ChIP_Oct4_Rep1


title: 201557510026_R05C01

source_name: Adrenocortial tumor C21


title: 201557510026_R03C01

source_name: Adrenocortial tumor C12


title: FYDN12-3

value: Without ABA treatment


title: wasp_infected_48hr_2_dropseq

city: Quechee

last: Steinbaugh

state: VT

address: PO Box 1520

institute: Acid Genomics

description:
Drop-seq blood sample 5: wasp infected 48 hr 2 (128 hr AEL)
dropseq-120hr-circulation-merged-expr-all-genes.txt
dropseq_sample_5

data_processing:
inDrops samples: Harvard inDrops v3 library format FASTQ files were processed using the bcbio-nextgen 1.0.6a0-d2b5b522 single-cell RNA-seq pipeline (https://github.com/bcbio/bcbio-nextgen).
Commands:  umis fastqtransform;   umis demultiplex_samples;   umis cb_filter;   umis cb_histogram;   rapmap quasiindex;   rapmap quasimap;   samtools index;   umis fasttagcount;   umis sparse
A sparse matrix of UMI de-duped reads-per-gene-per cell was generated as a gene x cell sparse matrix for all samples combined (tagcounts.mtx).
10x Chromium samples: FASTQ files were aligned with Cell Ranger v3.1.0 against the FlyBase reference genome using default settings.
Drop-seq samples: FASTQ files were processed using the standard pipeline described in Macosko et al., 2015.
Count matrices were filtered for low quality cells, inspecting a combination of genes per cell, UMI counts per cell, mitochondrial content per cell, transcriptome complexity per cell and other metrics.
Genome_build: Drosophila melanogaster, FlyBase release r6.27
Supplementary_files_format_and_content: Matrix Market Exchange Format (sparse matrix)

organism: Drosophila melanogaster

source_name: blood

growth_protocol: Precisely staged L3 larvae (96 hr after egg lay [AEL]) were used for the wounded experiments.

extract_protocol:
Larvae were bled and the hemocytes were were encapsulated at the Single Cell Core from ICCB-Longwood screening facility with inDrops (Zilionis et al., 2017), 10x Genomics, or Drop-seq technologies.
For inDrops samples: Reverse transcription and library preparation were done at the same facility as previously described (Zilionis et al., 2017). 10x cells were prepared following the manufacturer's protocol. All the Drop-seq and cDNA synthesis methods followed a previous study (Macosko et al., 2015).

treatment_protocol: 96 hr AEL larvae were either wounded with clean tungsten needle at the dorso-posterior side of each larva or left unwounded (for controls). For wasp infestations, 72 hr AEL Oregon R larvae were utilized.

value: wasp infected 48 hr (128 hr AEL)

value: blood

tag: technology

value: Drop-seq

tag: replicate


title: FYDN12-1


title: wasp_infected_48hr_3_dropseq

description:
Drop-seq blood sample 6: wasp infected 48 hr 3 (128 hr AEL)
dropseq-120hr-circulation-merged-expr-all-genes.txt
dropseq_sample_6


title: FYDN12-2


title: VDR ChIP-seq in human monocytic THP-1 cell line treated with 1:1 DMSO-ethanol (1hr, rep2)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

data_processing:
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v1.7 using default parameters
tag directory generation with homer makeTagDirectory using -checkGC parameter
bedgraph generation with homer makeUCSCfile using -fsize 1e50 -norm parameters
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

source_name: VDR ChIP-seq_THP-1_1:1 DMSO-ethanol_1hr

growth_protocol: The human monocytic cell line THP-1 was maintained in RPMI medium supplemented with 10% fetal calf serum, 1× Glutamax and 50 mg/l Gentamycin.

extract_protocol:
Cells were double crosslinked and lysed. Immunoprecipitation was carried out with an antibody for VDR (sc-13133). Protein antibody complexes were washed six times and eluted from Protein A coated paramagnetic beads. DNA was purified with the Qiagen Minelute kit.
Libraries were prepared with the TruSeq ChIP library systems (Illumina) according to the manufacturer protocol.

treatment_protocol: Control: 60 min prior to chromatin ChIP assay, THP-1 cells were maintained in phenol red-free RPMI supplemented with 10% charcoal stripped fetal calf serum and treated with 1:1 DMSO-ethanol. Calcitriol: 60 min prior to chromatin ChIP assay, THP-1 Cells were maintained in phenol red-free RPMI supplemented with 10% charcoal stripped fetal calf serum and treated with calcitriol (100nM, solved in 1:1 DMSO:ethanol).

tag: cell line

value: human monocytic cell line

value: 1:1 DMSO-ethanol (1hr)


title: VDR ChIP-seq in human monocytic THP-1 cell line treated with 100 nM calcitriol (D3) (1hr, rep2)

source_name: VDR ChIP-seq_THP-1_100 nM calcitriol (D3)_1hr

value: 100 nM calcitriol (1h)


title: VDR ChIP-seq in human monocytic THP-1 cell line treated with 100 nM calcitriol (D3) (1hr, rep1)

value: 100 nM calcitriol (1hr)


title: 201557510014_R08C01

source_name: Adrenocortial tumor C35

value: Adrenocortial tumor


title: 201557510014_R07C01

source_name: Adrenocortial tumor C31


title: wasp_infected_48hr_1_dropseq

description:
Drop-seq blood sample 4: wasp infected 48 hr 1 (128 hr AEL)
dropseq-120hr-circulation-merged-expr-all-genes.txt
dropseq_sample_4


title: KO12-2

value: seedling

value: 5-day-old + 24h treatment


title: wasp_infected_24hr_3_dropseq

description:
Drop-seq blood sample 3: wasp infected 24 hr 3 (96 hr AEL)
dropseq-96hr-circulation-merged-expr-all-genes.txt
dropseq_sample_3

value: wasp infected 24 hr (96 hr AEL)


title: KO12-1

value: Columbia 0


title: 201557510014_R03C01

source_name: Adrenocortial tumor C17


title: wasp_infected_24hr_2_dropseq

description:
Drop-seq blood sample 2: wasp infected 24 hr 2 (96 hr AEL)
dropseq-96hr-circulation-merged-expr-all-genes.txt
dropseq_sample_2


title: 201557510026_R07C01

source_name: Adrenocortial tumor C26


title: nRNAseq_5minLight15minRest3

city: Sai Kung

first: Yukinori

last: Hirano

address: Clear water bay

department: LIFS

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
The adaptors were trimmed via Trimommatic, followed by mapping to the Drosophila reference genome, dm6 from UCSC using STAR.
The reads with low mapping quality below 8 and the non-primary mapped reads were eliminated.
MACS was used for peak calling in ChIP-seq on Strand NGS software, using a default setting except for the following parameters; 10-4 as a P-value cutoff, and 3 as a enrichment factor.
The binding sites were determined when the peaks were overlapped in at least 2 out of 3 biological replicates.
For RNA-seq, the filtered reads were analyzed with HTSeq-count to obtain numbers of the reads mapped on exons, which was further analyzed on R using DESeq2
Genome_build: dm6
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include statistical results and fold enrichment comparing to naive samples

source_name: mushroom body

growth_protocol: Flies were raised under a 12 h:12 h, light:dark cycle, at 25℃ and 60% humidity.

extract_protocol:
Heads were collected and homogenized in crosslinking buffer. The nuclei were dissolved in extraction buffer, sonicated to dissociate the individual nuclei, and precipitated with ANTI-FLAG M2 Affinity Gel. The precipitates were rinsed 4 times in extraction buffer, with 5 min nutation at 4℃ between washes, and subjected to ChIP analysis or RNA extraction for RNA-seq.
The library for ChIP-seq was prepared by NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs inc. Ipswich, MA, USA), and that for nuclear RNA-seq was prepared by Oligo d(T)25 Magnetic Beads (New England Biolabs inc. Ipswich, MA, USA), and NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs inc. Ipswich, MA, USA), according to the manufacturer’s instructions.

treatment_protocol: Flies were subjected to optogenetic activation by expressing CsChrimson with red-light illumination.

tag: line

value: mushroom body

value: 5-min optogenetic activation followed by 15-min rest


title: nRNAseq_5minLight15minRest2


title: nRNAseq_5minLight15minRest1


title: 201533610012_R08C01

source_name: Adrenocortial tumor C5


title: wasp_infected_24hr_1_dropseq

description:
Drop-seq blood sample 1: wasp infected 24 hr 1 (96 hr AEL)
dropseq-96hr-circulation-merged-expr-all-genes.txt
dropseq_sample_1


title: FYDN-2


title: 201533610012_R05C01

source_name: Adrenocortial tumor C6


title: FYDN-3


title: FYDN-1


title: nRNAseq_5minLight10minRest3

value: 5-min optogenetic activation followed by 10-min rest


title: nRNAseq_5minLight10minRest2


title: KO12-3

value: nrp1 nrp2


title: unwounded_4_and_wounded_4_indrops_multiplexed

description:
inDrops blood sample 3: unwounded 4 (i5 index: GAGCCTTA; revcomp TAAGGCTC) and wounded 4 (i5 index: TTATGCGA; revcomp TCGCATAA)
indrops_sample_2

value: multiplexed:unwounded (uninjured) and wounded (injured)

value: inDrops


title: 201533610011_R02C01

source_name: Adrenocortial tumor C7


title: nRNAseq_5minLight10minRest1


title: VDR ChIP-seq in human monocytic THP-1 cell line treated with 1:1 DMSO-ethanol (1hr, rep1)

tag: cell type


title: 201533610012_R01C01

source_name: Adrenocortial tumor C29


title: WT-3

value: Without ABA treatment

value: WT


title: 201533610011_R01C01

source_name: Adrenocortial tumor C1


title: nRNAseq_5minLight5minRest3

value: 5-min optogenetic activation followed by 5-min rest


title: 201557510014_R06C01

source_name: Adrenocortial tumor C14


title: unwounded_3_and_wounded_3_indrops_multiplexed

description:
inDrops blood sample 2: unwounded 3 (i5 index: GAGCCTTA; revcomp TAAGGCTC) and wounded 3 (i5 index: CTATTAAG; revcomp CTTAATAG)
indrops_sample_1

value: blood


title: WT-2

source_name: Arabidopsis thaliana seedling


title: wounded_2_10x

description:
10x Chromium blood sample 4: wounded 2
10x_sample_4

value: wounded (injured)

value: 10x Chromium


title: wounded_1_10x

description:
10x Chromium blood sample 2: wounded 1
10x_sample_2


title: nRNAseq_5minLight5minRest2


title: WT-1


title: 201557510049_R06C01

source_name: Adrenocortial tumor C46

value: Adrenocortial tumor


title: PBMCs, Day_180

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v2.1.1 mkfastq pipline (10x Genomics) and bcl2fastq2 v 2.20.0 (Illumina)
Data qualty control, data filtering, cell barcode processing, UMI compression, 5' transcript alignment, and single-cell gene counting was performed using the CellRanger v2.1.1 count pipeline (10x Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv, mtx files generated by CellRanger v2.1.1

organism:
Homo sapiens
Dengue virus

source_name: Sorted PBMC

extract_protocol:
Single-cell RNAseq libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) and the Chromium Single Cell Analyzer (10x Genomics) according to the manufacture's protocol (User guide RevC)
Indexed sequencing libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) according to the manufacture's protocol (User guide RevC). In short, sequencing libraries were generated by  1) transcript fragmentation and end-repair, 2) post-fragmentation size-selection using SPRIselect beads, 3) Adaptor ligation and 4) sample index PCR and SPRIselect cleanup

treatment_protocol: Cryopreserved PBMCs were thawed and washed with RPMI media supplemented with 10% fetal calf serum prior to analysis. Populations of interest (CD3+CD19- T cells and CD3-CD19+ B cells) were isolated from the unfractionated PBMCs by flow cytometric sorting using a BD FACSAria Fusion instrument. Post-sort population purity was assessed prior to downstream analysis, and sorted T and B cells pooled together in for subsequent processing. Sorted cells were washed in PBS supplemented with 2% fetal calf serum prior to scRNAseq library generation

value: Pooled CD3+CD19- T cells and CD3-CD19+ B cells

tag: infection

value: DENV infection

tag: time

value: Fever day 180


title: nRNAseq_5minLight5minRest1

tag: tissue


title: 201557510049_R03C01

source_name: Adrenocortial tumor C8


title: PBMCs, Day_minus_1

value: Fever day -1


title: unwounded_1_10x

description:
10x Chromium blood sample 1: unwounded 1
10x_sample_1

source_name: blood

value: unwounded (uninjured)


title: 201557510031_R05C01

source_name: Adrenocortial tumor C42


title: nRNAseq_5minLight2

value: mushroom body

value: 5-min optogenetic activation


title: HIC099_eB

city: Columbus

first: Patrick

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

description: DNA - Hi-C DNA seq

data_processing:
HI-C Reads were processed using Juicer pipeline
Genome_build: mm9
Supplementary_files_format_and_content: hic files as produced by Juicer. The files are inter_30.hic.

extract_protocol:
5x10^6 formaldehyde-cross-linked cells were lysed on ice for 15 minutes with 250 μl of ice-cold Hi-C lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% Igepal CA630) containing protease inhibitors (Roche). Chromatin was digested using DpnII (100 U) at 37°C for 6 hours. The digested DNA ends were then filled and marked with biotin using Klenow, followed by ligation with T4 DNA ligase. After reversing the cross-links, DNA was fragmented using a Covaris E220 Evolution Sonicator followed by size-selection for 300-500bp using AMPure XP Beads (Beckman Coulter).
DNA end-repair was performed using NEBNext Ultra II DNA Library Prep Kit according to the manufacturer’s instructions using 1μg of the Hi-C DNA. Adaptor-ligated DNA was then selected for 300-400bp using AMPure XP beads and the biotinylated DNA fragments were pulled down using MyOne Streptavidin T1 beads (Life Technologies). The final Hi-C library was generated with 5 PCR cycles using the NEBNext Ultra II DNA Library Prep Kit and NEBNext Dual Index primers (NEB) for Illumina sequencing.
Paired end using NEBNext Ultra II DNA Library Prep Kit and NEBNext Dual Index primers (NEB)

tag: tissue source

value: cell line - 63-12 pre B cell

tag: protocol

value: Hi-C

tag: rnp

value: eBeta (eB)


title: unwounded_2_10x

description:
10x Chromium blood sample 3: unwounded 2
10x_sample_3


title: NKR cells, DENV1_infected_NS1pos_spike

description:
polyA RNA + DENV RNA
Spike" refers to the addition of a DENV-specific primer to the sequencing reaction in addition to an Oligo(dT) primer

organism:
Homo sapiens
Dengue virus 1 Nauru/West Pac/1974

source_name: Cell line

treatment_protocol: Cultured CEM.NKR.DC-SIGN cells were washed with RPMI media supplemented with 10% fetal calf serum prior to analysis. Populations of interest (total viable cells or surface DENV1 NS1 positive cells) were isolated by flow cytometric sorting using a BD FACSAria Fusion instrument. Post-sort population purity was assessed prior to downstream analysis. Sorted cells were washed in PBS supplemented with 2% fetal calf serum prior to scRNAseq library generation.

value: DENV1 infected sorted NS1 pos

tag: primer

value: Oligo(dT) + DENV specific


title: 201557510026_R06C01

source_name: Adrenocortial tumor C43


title: HIC100_Myc

description: DNA - Hi-C DNA seq

source_name: 63-12 RNP-Myc

value: Myc Promoter


title: NKR cells, DENV1_infected_NS1pos

value: Oligo(dT)


title: HIC097_eB

description: DNA - Hi-C DNA seq


title: nRNAseq_5minLight1

tag: treatment


title: HIC098_Myc

description: DNA - Hi-C DNA seq


title: 201557510026_R04C01

source_name: Adrenocortial tumor C4


title: HIC077_6312_rep2

description: DNA - Hi-C DNA seq


title: nRNAseq_naive2

source_name: mushroom body

value: naïve


title: 201557510026_R01C01

source_name: Adrenocortial tumor C39


title: 201557510014_R04C01

source_name: Adrenocortial tumor C40


title: NKR cells, DENV1_infected

value: DENV1 infected


title: nRNAseq_naive1


title: 201557510014_R02C01

source_name: Adrenocortial tumor C44

value: Adrenocortial tumor


title: input-1_DNA_combined

tag: chip antibody


title: HIC071_P5424_rep2

description: DNA - Hi-C DNA seq

value: cell line - p5424 thymocyte


title: 201557510031_R08C01

source_name: Adrenocortial tumor C45


title: 201557510014_R01C01

source_name: Adrenocortial tumor C47


title: CoRest-C_light3

value: anti-myc (2278, Cell Signaling Technology, lot 5)


title: HIC056_P5424_rep1

description: DNA - Hi-C DNA seq


title: PBMCs, Day_minus_2

value: Pooled CD3+CD19- T cells and CD3-CD19+ B cells

value: DENV infection

value: Fever day -2


title: nRNAseq_naive3

value: mushroom body


title: HIC072_DN_Thy_rep2

description: DNA - Hi-C DNA seq

source_name: Double Negative (DN) thymocyte

value: Thymus


title: CoRest-C_light2

value: 5-min optogenetic activation