title: 20221005_Unstimulated PBMCs, ADT-derived cDNA

first: Sophie

last: Gray-Gaillard

address: 429 E. 29th Street, room 314

institute: NYU School of Medicine

description: 10x Genomics

data_processing:
Cellranger software v7 (10X Genomics) was used to align FASTQ files to the human genome (GRCh38 ensemble) and to perform protein expression evaluation. Seurat v4.3.0 was used to process single cell libraries and integrate all the exCITE-seq modalities. scDblFinder quantified doublets, and scRepertoire was used to process TCR libraries.
Assembly: GRCh38 ensemble
Supplementary files format and content: barcodes.tsv.gz, matrix.mtx.gz, features.tsv.gz, filtered_contig_annotations.csv, matrix.mtx.gz

source_name: Peripheral blood mononuclear cells

extract_protocol:
Cells were processed for expanded cellular indexing of transcriptomes and epitopes by sequencing (exCITE-seq) using Chromium Next GEM Single Cell 5’ HT Kit v2. Cells were pooled and loaded onto Chromium HT Chips and run on a Chromium controller (10X Genomics).
Gene expression, V(D)J, and surface protein expression libraries were made using the 5’ Feature Barcode Kit, Chromium Single Cell V(D)J Amplification Kit, and Chromium Next GEM Single Cell 5’ Library Kit (10X Genomics) as recommended by the manufacturer.
exCITE-seq

treatment_protocol: Following written informed consent, peripheral blood was drawn by standard phlebotomy longitudinally from 24 adults (12 vaccine-primed and 12 infection-primed) in observational studies in accordance with NYU Institutional Review Board protocols (s18-02035 and s18-02037). Blood draws occurred eight months after second vaccination (“pre-booster”) and approximately one month post third vaccination (“post-booster”). Peripheral blood mononuclear cells (PBMC) were isolated from CPT vacutainers (BD Biosciences) within four hours of the blood draw and cryopreserved in liquid nitrogen. Briefly, cryopreserved PBMCs were thawed and rested overnight at 37°C. The next day, cells were stimulated with 15-mer peptide pools encompassing the SARS-CoV-2 Spike protein (S1, S, and S+ PepTivators, Miltenyi). Sterile water was used for the unstimulated controls. After stimulation for 20 hours at 37°C , cells were stained with antibodies against CD69 and CD137 conjugated to PE-Dazzle 594 and PE, respectively (Biolegend), for 30 minutes at room temperature in the dark, followed by magnetic bead enrichment using the EasySep Human PE Positive Selection Kit (STEMCELL Technologies).

value: Peripheral blood mononuclear cells

tag: library type

value: ADT

tag: antibodies/tags

value: TotalSeq-C0258 anti-human Hashtag 8 Antibody,TotalSeq-C0259 anti-human Hashtag 9 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody, TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0260 anti-human Hashtag 10 Antibody, TotalSeq-C0262 anti-human Hashtag 12 Antibody


title: 20221005_Unstimulated PBMCs,  mRNA-derived cDNA

status: Public on Mar 15 2024

type: SRA

city: New York

middle: L

state: New York

country: USA

description: 10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: mRNA


title: 20221005_Stimulated PBMCs, lane 5,  TCR-derived cDNA

description: 10x Genomics

value: TCR


title: Veh28

first: Cathy

last: Mendelsohn

state: NY

address: 1130 St. Nicholas Ave

department: Urology

institute: Columbia University Medical Center

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2.
To create ATAC-seq coverage plots, the locations of the mapped ATAC-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: basal bladder cancer urothelial cells

extract_protocol:
Cells (3.0× 105) were lysed in RSB containing NP40, Digitonin, and Tween-20.
DNA was incubated with transposition reaction mix containing PBS, 1%Digitonin, Tween-20, andTransposase(llumina). ATAC-seq libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 100-600bp in length using HighPrep™ PCR Clean-up beads from MagBio. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: treatment

value: 5 days vehicle treated bladder tumor tissue

tag: cell line

value: tissue

tag: tissue

value: basal bladder cancer urothelial cells


title: Veh69


title: Kuramochi siUCHL1 n3

city: Indianapolis

first: Sumegha

last: Mitra

state: IN

address: C547 Walther Hall (R3), 980 W Walnut Street

institute: Indiana University

library_source: transcriptomic

data_processing:
The raw RNA-seq reads were cleaned using Trimmomatic version 0.33 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the human genome reference, GRCh38 using tophat2 (version 2.0.0) (Kim et al. 2013).
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes from gencode v.25 using htseq-count tool (version 0.11.1) . Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s reverse -m union)
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files with counts of reads aligned to exon regions of each annotated gene

source_name: serous adenocarcinoma

growth_protocol: cells were cultured in 10% DMEM medium

extract_protocol:
RNA was isolated using miRNeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with control or UCHL1 siRNA using TransIT X2

value: High-grade serous ovarian cancer

value: UCHL1 siRNA

tag: tp53 mutation

value: D281Y (endogenous)


title: pa14.2pnacl.250umbrd1401.1

city: Cambridge

first: Thulasi

last: Warrier

state: MA

address: 415 Main Street

department: IDMP

institute: Broad Institute

description: replicate 1

data_processing:
BWA to align reads to reference and read counts generated using custom scripts.
DESeq2 (1.28.1) package in R was used to obtain fold changes in gene expression across multiple conditions
Assembly: NC_0088463.1 (UCBPP-PA14)
Supplementary files format and content: comma separated file with counts for each sample for each gene

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: Pseudomonas aeruginosa UCBPP-PA14

growth_protocol: Bacterial cultures were inoculated from glycerol stocks, grown overnight with appropriate selection antibiotics at 37ºC with shaking and sub-cultured at 37ºC with shaking until log-phase growth. Cultures were diluted to an OD600nm of 0.2-0.4.

extract_protocol:
At the end of the incubation period, samples were mixed with 30uL of 3X RNAgem Blue Buffer (Zygem, Charlottesville VA), and chemically lysed by incubation in a thermocycler at 75°C for 10 minutes. Total RNA was then extracted using the Direct-zol kit (Zymo Research, Irvin CA), and RNA quality and quantity were analyzed using the RNA ScreenTape with the 2200 TapeStation (Agilent, Santa Clara CA).
RNA-Seq libraries were prepared using the RNA TagSeq protocol previously described (Shishkin, A. et al. Nature methods. 2015. https://doi.org/10.1038/nmeth.3313)

treatment_protocol: LB medium with appropriate drugs such as BRD1401 or inducers such as arabinose was prepared at 2X final concentration and dispensed into 384 well plates. Diluted bacterial suspensions were added on top to achieve a final bacterial density of 0.1-0.2 OD600nm and incubated at 37ºC for 90 minutes. Three biological replicates were included.

tag: genotype

value: Pseudomonas aeruginosa UCBPP-PA14

value: 2percent NaCl + 250 microM BRD1401


title: Cas9-g2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description:
CAST-seq derived amplicons from gDNA
2 replicates

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the D-CAST pipeline with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: matrix table of translocation sites detected with D-CAST pipeline. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.

source_name: CAST-seq on sample treated with Cas9 nuclease

growth_protocol: Primary RDEB and JEB keratinocytes were cultivated in CNT-PRIME medium supplemented with 50 mg/mL primocin (invivoGen) and maintained at 37°C and 5% carbon dioxide in a humidified incubator.

extract_protocol:
Genomic DNA was extracted using the ReliaPrep™ Blood gDNA Miniprep System kit (Promega) according to the manufacturer’s protocol
Library construction was essentially performed as described by Turchiano et. al (Cell Stem Cell, 2021). Briefly, gDNA was fragmented by enzymatic digestion using the NEBNext® Ultra™ II FS DNA Library Prep (NEB) to obtain average fragment lengths of 350 bp. The DNA was end repaired and a protruding 3’-A nucleotide was added according to the manufacturer’s instructions  in order to enable the ligation of a linker sequence with a protruding 3’-T. After linker ligation, fragments were purified using the QIAquick PCR Purification Kit (NEB). The region of interest (on-target site) was amplified in two rounds of PCR using Q5® Hot Start High-Fidelity DNA Polymerase (NEB). PCR conditions were: 20 cycles at 95°C for 15 s, 63°C (first reaction) or 68°C (second reaction) for 20 s, 72°C for 20 s. The first reaction was performed with primers complementary to the linker sequence and to a sequence in close proximity to the on-target site (bait primer). Two decoy primers were introduced to reduce full-length amplification of the fragments which contain the on-target sequence without a chromosomal aberration event. The second PCR utilized nested primers to reduce the amount of mis-amplified fragments and to introduce a binding platform for barcoding primers. DNA fragments from the second PCR were purified using the QIAquick® PCR purification kit (Qiagen) and barcoded.
Third PCR introduced the barcoded Illumina adapter for sequencing (NEBNext® Multiplex Oligos for Illumina; Index Primers Sets 1-4). Sequencing was outsourced to service NGS provider Genewiz (part of Azenta Life Sciences) where it was performed on a Illumina NovaSeq6000 device collecting 2x150 bp paired-end reads.

treatment_protocol: Electroporation of RNPs into keratinocytes was performed using the Neon transfection system (Thermo Fisher Scientific) under the following conditions: 1,400 Volt, 20 ms, 2 pulses. 250,000 cells were treated with Alt-R™ SpCas9 Nuclease V3 or Alt-R™ SpCas9 D10A Nickase V3 (IDT) together with the gRNA (IDT) at a ratio of 4:1 (3µg + 750ng).

value: Patient-derived keratinocytes

value: RDEB223, homozygous c.425A>G


title: 20221005_Stimulated PBMCs, lane 5, mRNA-derived cDNA

description: 10x Genomics


title: pao1.2pnacl.250umbrd1401.2

description: replicate 2


title: embryo, 98h, rep1

city: Knoxville

first: Jianbin

last: Wang

state: TN

address: 1311 Cumberland Avenue

department: Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

data_processing:
Only read 1 (R1) files were processed. Reads containing two sequential telomeric repeats (TTAGGCTTAGGC or GCCTAAGCCTAA) were filtered from the data using an in-house Perl script
Reads were mapped to the appropriate genome with Bowtie2 (local alignment) and processed with SAMtools
For samples treated with restriction enzyme BEDTools intersect was used to remove reads mapped to restriction sites
The 5’-end position of each read was mapped, separated by strand, and normalized to ten million genome-mapped reads using BEDtools genomecov
The mapping results were converted to bigWig format using bedGraphToBigWig
To analyze new telomere addition during PDE developmental stages, END-seq reads containing two consecutive telomere repeats (filtered in step 1) were converted to the G-rich strand (TTAGGC).
Reads were mapped to the genome with Bowtie2 end-to-end alignment
Mapped reads were false-positive telomeric reads. Unmapped reads were trimmed with fastx_clipper “-v -n -l 25 -a TTAGGCTTAGGC” parameters.
Trimmed reads were mapped to the genome with bowtie2 (local alignment) and processed as described above except except the 3’-positions (the sites where new telomeres are added) rather than 5’-positions were obtained with BEDTools genomecov
Assembly: Ascaris suum ASM1343314v1, Parascaris univalens (Pu_v2)
Supplementary files format and content: bigWig file containing the 5' end of reads on the forward strand
Supplementary files format and content: bigWig file containing the 5' end of reads on the reverse strand
Supplementary files format and content: bigWig file with the 3' end of reads on the forward strand which contained two telomeric repeats (TTAGGCTTAGGC)
Supplementary files format and content: bigWig file with the 3' end of reads on the reverse strand which contained two telomeric repeats (TTAGGCTTAGGC)
Library strategy: END-seq

organism: Ascaris suum

source_name: Embryo

extract_protocol:
Ascaris females were collected, and the fertilized embryos (0hr, 1-cell before prenuclear fusion) were harvested and processed as previously described (Wang et al. 2011, Wang et al. 2014). Ascaris 0hr samples were incubated at 30°C with constant shaking for the desired time (from 50hr to 98hr). For all molecular experiments, the eggshells were first de-coated with bleach treatment (0.4 M KOH, 2% sodium hypochlorite) for 1.5 hours at 30°C. Parascaris samples were collected as described (Simmons et al. 2023, Wang et al. 2017). Parascaris eggs were prepared similarly to Ascaris, except the incubation was carried out at 37°C and the embryonation time was shorter (10-14hr).
An adapted END-seq protocol was used (Canela et al. 2016, Wong et al. 2021). Embryos were embedded in agarose plugs. Some plugs were treated with the restriction enzymes as internal controls. Plugs were treated with exonuclease VII and exonuclease T. Blunt ends were A-tailed and capped with END-seq adaptor 1 (Canela et al. 2016). Plugs were melted and DNA was sheared to 200-300 bp with a Covaris M220 focused ultrasonicator. DNA fragments containing END-seq adaptor 1 were isolated with Dynabeads MyOne Streptavidin C1. END-seq adaptor 2 was ligated to the sheared ends of the A-tailed DNA fragments. The hairpins within the adaptors were digested with USER, and the DNA was amplified with Illumina TruSeq primers and barcodes. The following modifications were made to the END-seq protocol to capture break ends with different features. For the direct capture method, we excluded the exonuclease VII and exonuclease T treatments. For the all-END protocol, the plugs were treated with T4 polymerase (with dNTPs).

value: Embryo

tag: developmental stage


title: embryo, 92h, rep2


title: Kuramochi siUCHL1 n1


title: pao1.2pnacl.250umbrd1401.1

description: replicate 1


title: embryo, 86h, rep2


title: 20221005_Stimulated PBMCs, lane 4,  TCR-derived cDNA

description: 10x Genomics


title: embryo, 92h, rep1


title: bep_hypo.2pnacl.125umbrd1401.3

description: replicate 3

value: oprL-hypomorph

value: 2percent NaCl + 125 microM BRD1401


title: bep_hypo.2pnacl.125umbrd1401.2

description: replicate 2


title: 20221005_Stimulated PBMCs, lane 4,  ADT-derived cDNA

description: 10x Genomics

value: Peripheral blood mononuclear cells

value: ADT


title: embryo, 86h, rep1


title: Kuramochi siCTL n1

value: control siRNA


title: pao1.2pnacl.250umbrd1401.3

description: replicate 3


title: 20221005_Stimulated PBMCs, lane 4, mRNA-derived cDNA

description: 10x Genomics

value: mRNA


title: bep_hypo.2pnacl.125umbrd1401.1

description: replicate 1


title: 20221005_Stimulated PBMCs, lane 3,  TCR-derived cDNA

description: 10x Genomics

value: TCR


title: bbx28-5_SS_rep3

city: CABA

first: Javier

last: Botto

state: BUENOS AIRES

address: AV SAN MARTIN 4453

department: FAC AGRONOMIA UBA

country: Argentina

institute: IFEVA

description: Arabidopsis thaliana

data_processing:
Data quality was assessed with FastQC
Reads were mapped to the A. thaliana TAIR10 (v. 45) genome with HISAT and BAM files were sorted with SAMtools
Counts per gene were obtained with Htseq.
Only these genes with CPM > 0.8 in at least three samples were retained for further analysis. Count genes were normalized to library length with edgeR package in R
Assembly: Arabidopsis thaliana TAIR10 (v. 45)
Supplementary files format and content: Raw_HTseq_output.txt: tab-delimited text file include counts for each gene in each sample based on HtseqCount
Supplementary files format and content: Filtered_normalized_counts.txt:  tab-delimited text file include normalized counts for each gene in each sample after filtering low expressed genes (CPM < 0.8) and normalizing counts with edgeR

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: Col-0 and bbx28-5 seeds were sown in clear plastic boxes on 0.8% agar/water and incubated in darkness at 4ºC. After four days, imbibed seeds were exposed to a white light pulse for 5 hours and kept in darkness for 14 h at 22ºC to induce germination. Then, the boxes were transferred to a short-day photoperiod (10h/14h) at 22ºC and maintained for two days in white light conditions to ensure complete de-etiolation. The third day, the boxes were transferred to the simulated shade or mantained in white light for four hours.

extract_protocol:
RNA was extracted using the Spectrum™ Plant Total RNA Kit. 1 µg of total RNA was used for library preparation.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 (ref. RS-122-2101/2) according to the manufacturer's protocol.

treatment_protocol: White light treatment consisted in a mixture of fluorescent and incandescent lamps (photosynthetically active radiation = 90 μmol m−2 s−1, red = 9.13 μmol m−2 s−1, blue = 8.1 μmol m−2 s−1, far-red = 8.3 μmol m−2 s−1). Simulated shade (photosynthetically active radiation = 20 μmol m−2 s−1, red = 0.8 μmol m−2 s−1, blue = 1.3 μmol m−2 s−1, far-red = 5.5 μmol m−2 s−1) treatment was provided by the same light sources in combination with a green acetate filter (#089; LEE Filters, http://www.leefilters.com).

value: Whole seedlings

tag: ecotype

value: Columbia

value: Simulated shade


title: pa14.2pnacl.3

description: replicate 3

value: 2percent NaCl + 0.5percent DMSO


title: 20221005_Stimulated PBMCs, lane 5,  ADT-derived cDNA

description: 10x Genomics

value: TotalSeq-C0258 anti-human Hashtag 8 Antibody,TotalSeq-C0259 anti-human Hashtag 9 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody, TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0260 anti-human Hashtag 10 Antibody, TotalSeq-C0262 anti-human Hashtag 12 Antibody


title: embryo, 80h, rep1


title: 20221005_Stimulated PBMCs, lane 3,  ADT-derived cDNA

description: 10x Genomics


title: bbx28-5_SS_rep2

description: Arabidopsis thaliana


title: embryo, 74h, rep2


title: Kuramochi siUCHL1 n2

value: High-grade serous ovarian cancer

value: UCHL1 siRNA

value: D281Y (endogenous)


title: pa14.2pnacl.2

description: replicate 2

value: Pseudomonas aeruginosa UCBPP-PA14


title: 20221005_Stimulated PBMCs, lane 3, mRNA-derived cDNA

description: 10x Genomics


title: pa14.2pnacl.1

description: replicate 1


title: embryo, 74h, rep1

value: Embryo


title: Kuramochi siCTL n3


title: Col-0_SS_rep3

description: Arabidopsis thaliana


title: 20221005_Stimulated PBMCs, lane 2,  TCR-derived cDNA

description: 10x Genomics


title: pao1.2pnacl.3

description: replicate 3


title: embryo, 70h, rep2

value: FseI


title: Col-0_SS_rep2

description: Arabidopsis thaliana


title: Kuramochi siCTL n2


title: 20221005_Stimulated PBMCs, lane 2,  ADT-derived cDNA

description: 10x Genomics


title: pao1.2pnacl.2

description: replicate 2


title: embryo, 80h, rep2


title: Col-0_SS_rep1

description: Arabidopsis thaliana


title: 20221005_Stimulated PBMCs, lane 2, mRNA-derived cDNA

description: 10x Genomics


title: bbx28-5_WL_rep3

description: Arabidopsis thaliana

value: White light


title: 20221005_Stimulated PBMCs, lane 1,  TCR-derived cDNA

description: 10x Genomics

value: Peripheral blood mononuclear cells


title: pao1.2pnacl.1

description: replicate 1


title: bep_hypo.2pnacl.2

description: replicate 2

value: oprL-hypomorph


title: embryo, 62h, rep2


title: bbx28-5_WL_rep2

description: Arabidopsis thaliana


title: bep_hypo.2pnacl.3

description: replicate 3


title: embryo, 65h, rep3

value: AsiSI


title: bbx28-5_SS_rep1

description: Arabidopsis thaliana


title: embryo, 62h, rep1


title: bep_hypo.2pnacl.1

description: replicate 1


title: 20221005_Stimulated PBMCs, lane 1,  ADT-derived cDNA

description: 10x Genomics

value: ADT


title: embryo, 58h, rep4


title: Col-0_WL_rep3

description: Arabidopsis thaliana


title: 20221005_Stimulated PBMCs, lane 1, mRNA-derived cDNA

description: 10x Genomics

value: mRNA


title: embryo, 58h, rep2


title: Col-0_WL_rep2

description: Arabidopsis thaliana

value: Whole seedlings


title: L4_CK1441;CK1943-4

city: Seattle

first: Nicole

last: Liachko

state: WA

address: 1660 Columbian Way S.

department: GRECC

institute: VA Puget Sound Health Care System

data_processing:
Sequencing was outsourced to University of Washington Northwest Genomics Center. Samples were sequenced with a target sequencing depth of 50-60 million reads per sample using NovaSeq S2 platform (Illumina) to generate 150bp paired end reads. NWGC provided us with paired .fastq files separated by each barcoded sample with the illumina adaptors trimmed.
paired .fastq files were aligned to the Caenorhabditis elegans.WBcel235 transcriptome using RNA-Star (default parameters) on Galaxy to produce sample .bam and .bai files
For differential expression analysis, reads were mapped and counted using salmon (default settings). Resulting files were imported and analyzed using DESeq2 on Galaxy.
Assembly: Ensemble C elegans genome WBcel235
Supplementary files format and content: .sf (salmon) transcript quantification

organism: Caenorhabditis elegans

source_name: whole body lysate

growth_protocol: C. elegans worms were grown on NGM agar plates at 20°C

extract_protocol:
RNA was extracted from L2 and L4 snap-frozen C. elegans pellets using TRIzol Reagent (Thermo Fisher Scientific, Inc.) per manufacturer’s protocol. RNA was resuspended in 50 µL sterile water and concentration was assessed using NanoPhotometer® NP80 spectrophotometer (Implen GmbH).
1000ng of RNA isolated from age synchronized L2 and L4 C. elegans was used for RNA sequencing library prep using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina) as per manufacturer’s protocol. RNA libraries from each sample were individually barcoded and pooled in batches of 16 stage-matched samples (L2 or L4 stage). Library quality was assessed using a Bioanalyzer (Agilent 2100) prior to sequencing

value: whole body lysate

tag: Stage


title: 20220401_Unstimulated PBMCs, ADT-derived cDNA

description: 10x Genomics

value: TotalSeq-C0258 anti-human Hashtag 8 Antibody,TotalSeq-C0259 anti-human Hashtag 9 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody, TotalSeq-C0255 anti-human Hashtag 5 Antibody


title: 20220401_Unstimulated PBMCs,  mRNA-derived cDNA

description: 10x Genomics


title: Col-0_WL_rep1

description: Arabidopsis thaliana

value: Columbia


title: embryo, 58h, rep1


title: L4_CK1943-4


title: 20220401_Stimulated PBMCs, lane 3,  TCR-derived cDNA

description: 10x Genomics

value: TCR


title: embryo, 70h, rep1


title: embryo, 54h, rep5


title: L4_CK1441-4


title: bsg-208-3_S11

city: Minneapolis

first: DeWayne

last: Townsend

state: Minnesota

address: 2231 6th Street SE

department: Integrative Biology and Physiology

institute: University of Minnesota

data_processing:
fastq files were aligned to version 1.109 of Mus musculus C57Bl-6NJ mouse reference genome GRCm39 using HISTAT2
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm from the subread package.
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by the DESeq2 package
Assembly: version 109 of mouse strain C57bl-6NJ reference genome GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for all samples.

source_name: Heart

growth_protocol: Mice were 4 months of age.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: Hearts were extracted following isoflurane OD/ cervical dislocation and flash frozen.

tag: background strain

value: bsg

tag: Sex

value: male


title: embryo, 54h, rep4


title: bsg-207-3_S7

value: female


title: bbx28-5_WL_rep1

description: Arabidopsis thaliana


title: L4_N2-4


title: bsg-207-2_S3


title: 20220401_Stimulated PBMCs, lane 2,  TCR-derived cDNA

description: 10x Genomics


title: L4_CK1441;CK1943-3


title: embryo, 54h, rep2


title: 20220401_Stimulated PBMCs, lane 3, mRNA-derived cDNA

description: 10x Genomics


title: L4_CK1943-3


title: embryo, 54h, rep1


title: bsg-206-1_S4


title: L4_CK1441-3


title: 20220401_Stimulated PBMCs, lane 2,  ADT-derived cDNA

description: 10x Genomics


title: embryo, 53h


title: bsg-205-2_S15


title: embryo, 52h, rep3


title: 20220401_Stimulated PBMCs, lane 1,  TCR-derived cDNA

description: 10x Genomics


title: embryo, 52h, rep2


title: L4_CK1441;CK1943-2


title: 20220401_Stimulated PBMCs, lane 2, mRNA-derived cDNA

description: 10x Genomics


title: 20220401_Stimulated PBMCs, lane 1,  ADT-derived cDNA

description: 10x Genomics


title: bsg-204-6_S2


title: embryo, 52h, rep1


title: L4_CK1943-2


title: 20220401_Stimulated PBMCs, lane 1, mRNA-derived cDNA

description: 10x Genomics


title: bsg-207-1_S8


title: 20220208_Unstimulated PBMCs, ADT-derived cDNA

description: 10x Genomics


title: embryo, 50h, rep4


title: bsg-204-5_S5


title: 20220401_Stimulated PBMCs, lane 3,  ADT-derived cDNA

description: 10x Genomics


title: bsg-204-4_S9


title: L4_N2-2


title: embryo, 50h, rep2


title: C06-112-4_S6

value: wild-type


title: L4_N2-3


title: C06-111-1_S16


title: 20220208_Stimulated PBMCs, lane 3,  ADT-derived cDNA

description: 10x Genomics


title: C06-112-1_S14


title: L4_CK1441-1


title: L4_CK1441;CK1943-1


title: embryo, 50h, rep1

value: Embryo


title: L4_N2-1


title: L4_CK1943-1


title: 20220208_Stimulated PBMCs, lane 3, mRNA-derived cDNA

description: 10x Genomics


title: bsg-205-1_S18


title: 20220208_Stimulated PBMCs, lane 3,  TCR-derived cDNA

description: 10x Genomics


title: C06-110-1_S1


title: L2_CK41/43_4


title: C06-109-2_S13


title: 20220208_Stimulated PBMCs, lane 2,  TCR-derived cDNA

description: 10x Genomics


title: 20220208_Stimulated PBMCs, lane 2,  ADT-derived cDNA

description: 10x Genomics


title: L2_CK43_4


title: embryo, 50h, rep5


title: 20220208_Unstimulated PBMCs,  mRNA-derived cDNA

description: 10x Genomics


title: L2_CK41_4


title: C06-109-1_S19


title: 20220208_Stimulated PBMCs, lane 1,  TCR-derived cDNA

description: 10x Genomics


title: C06-108-1_S12


title: 20220208_Stimulated PBMCs, lane 1,  ADT-derived cDNA

description: 10x Genomics


title: L2_N2_4


title: P14 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 3

city: Xiamen

first: Jinhang

last: He

state: Fujian

address: No.4221, South Xiang'an Road

country: China

institute: Xiamen University

data_processing:
Sequence reads were trimmed and adaptor removed by using fastp.
Cleanned sequence reads were mapped to GRcm38 Genome by using Hisat2
Raw count were calculated by using featurecounts
Assembly: GRcm38
Supplementary files format and content: tab-delimited txt files include raw count values for each Sample

extract_protocol:
The P14-T cell and OT1-T cell were sorted and stored in RNA Later Solution (Thermo Fisher Scientific) for a maximum of 24 h at 4 °C. Lung tissue was homogenized using TissueLyser II (Qiagen, Hilden, Germany) and RNA extraction was performed according to the manufacturer’s instructions (QIAamp Viral RNA Mini Kit (Qiagen)).
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.


title: Blood, cRBD3 immunization, rep3 [mRNA-seq]

city: 昆明市

first: 然

last: 安

state: 云南省

address: 茭菱路935号医学生物学研究所

department: Institute of Medical Biology

institute: Peking Union Medical College

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were mapped to the reference genome of Mus_musculus from Mus_musculus.GRCm38 using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text file includes rpkm values for each sample.

source_name: Whole blood

extract_protocol:
Total RNAs were extracted from blood using TRIzol Reagent (Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al. (DOI:10.1006/abio.1987.9999). 2 μg total RNAs were used for the construction of sequencing libraries.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: Whole blood

value: cRBD3 immunized

tag: strain

value: Balb/c


title: P14 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 2


title: L4_CK1441-2


title: L2_CK41/43_3


title: 20211216_Unstimulated PBMCs, ADT-derived cDNA

description: 10x Genomics

value: Peripheral blood mononuclear cells

value: TotalSeq-C0258 anti-human Hashtag 8 Antibody,TotalSeq-C0259 anti-human Hashtag 9 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody


title: 20220208_Stimulated PBMCs, lane 1, mRNA-derived cDNA

description: 10x Genomics


title: L2_CK43_3


title: Blood, cRBD3 immunization, rep1 [mRNA-seq]

address: 茭菱路935号医学生物学研究所


title: OT1 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 3


title: 20211216_Unstimulated PBMCs,  mRNA-derived cDNA

description: 10x Genomics


title: Blood, cRBD2 immunization, rep3 [mRNA-seq]

address: 茭菱路935号医学生物学研究所

value: cRBD2 immunized


title: Blood, cRBD3 immunization, rep2 [mRNA-seq]

address: 茭菱路935号医学生物学研究所


title: 20211216_Stimulated PBMCs, lane 1,  TCR-derived cDNA

description: 10x Genomics


title: OT1 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 2


title: L2_N2_3


title: L2_CK41/43_2


title: OT1 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 1


title: 20220208_Stimulated PBMCs, lane 2, mRNA-derived cDNA

description: 10x Genomics

value: mRNA


title: 20211216_Stimulated PBMCs, lane 1,  ADT-derived cDNA

description: 10x Genomics

value: ADT


title: Blood, cRBD2 immunization, rep1 [mRNA-seq]

address: 茭菱路935号医学生物学研究所


title: L2_CK43_2

value: whole body lysate


title: Blood, Cntrol, rep3 [mRNA-seq]

address: 茭菱路935号医学生物学研究所

value: untreated


title: 20211216_Stimulated PBMCs, lane 1, mRNA-derived cDNA

description: 10x Genomics


title: P14 T cells sorted from B16-OVA tumor treated with PBS, Replicate 3


title: L2_CK41_2


title: P14 T cells sorted from B16-OVA tumor treated with PBS, Replicate 2


title: 20211122_Unstimulated PBMCs, ADT-derived cDNA

description: 10x Genomics

value: TotalSeq-C0258 anti-human Hashtag 8 Antibody,TotalSeq-C0259 anti-human Hashtag 9 Antibody


title: P14 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 1


title: Blood, Cntrol, rep2 [mRNA-seq]

address: 茭菱路935号医学生物学研究所


title: 20211122_Unstimulated PBMCs,  mRNA-derived cDNA

description: 10x Genomics


title: L2_N2_2


title: P14 T cells sorted from B16-OVA tumor treated with PBS, Replicate 1


title: Blood, cRBD2 immunization, rep2 [mRNA-seq]

address: 茭菱路935号医学生物学研究所


title: L2_CK41_3


title: 20211122_Stimulated PBMCs, lane 1,  TCR-derived cDNA

description: 10x Genomics

value: TCR


title: OT1 T cells sorted from B16-OVA tumor treated with PBS, Replicate 2


title: Blood, Cntrol, rep1 [mRNA-seq]

address: 茭菱路935号医学生物学研究所


title: 20211122_Stimulated PBMCs, lane 1,  ADT-derived cDNA

description: 10x Genomics


title: L2_CK43_1


title: OT1 T cells sorted from B16-OVA tumor treated with PBS, Replicate 3


title: Blood, cRBD1 immunization, rep3 [mRNA-seq]

address: 茭菱路935号医学生物学研究所

value: cRBD1 immunized


title: L2_CK41_1


title: Blood, cRBD1 immunization, rep2 [mRNA-seq]

address: 茭菱路935号医学生物学研究所


title: 20211122_Stimulated PBMCs, lane 1, mRNA-derived cDNA

description: 10x Genomics


title: OT1 T cells sorted from B16-OVA tumor treated with PBS, Replicate 1


title: L2_N2_1


title: Blood, cRBD1 immunization, rep1 [mRNA-seq]

address: 茭菱路935号医学生物学研究所


title: Kudo3D_KPT_4

status: Public on Mar 14 2024

city: Bethesda

first: Kei

last: Kudo

state: MD

address: 9000 Rockville Pike

institute: NIH

description: NAS Order ID: CS034542

data_processing:
The samples have 118 to 137 million pass filter reads with more than 95% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR v2.7.0f aligner.
The gene expression quantification analysis was performed for all samples using STAR/RSEM tools. Both the normalized count and the raw count are provided as part of the data delivery.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Expercted count and  TPM and FPKM values for each Sample
Supplementary files format and content: Matrix table with expected gene counts for every gene and every sample

source_name: Ovarian cancer

growth_protocol: CP80 cells were maintained in RPMI1640 with 1% KnockOut serum replacement and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
mRNA was extracted from 3D-cultured CP80 using the RNeasyTM Plus Mini Kit.
8 mRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using Illumina Stranded mRNA Ligation Kit and paired-end sequencing.

treatment_protocol: CP80 cells were treated with vehicle or KPT-9274 1000 nM for 24h.

value: Ovarian cancer

value: Epithelial


title: Gly_SS

city: Tianjin

first: Feiyu

last: Fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

description: NBRC0988 cells grown overnight were inoculated into 100 ml of liquid Yeast Extract Peptone Dextrose (YEPD) medium with an initial inoculation OD600 of 0.1. These cells were then cultured for 15 hours at 30°C and 250 rpm. Subsequently, the cells were collected by centrifugation at 6,000g for 5 minutes. After being washed twice with phosphate-buffered saline (PBS), the cells were inoculated into fresh 100 mL of YEP medium containing 2% w/v glycerol. Following additional flask culturing for 5 hours at 30°C and 250 rpm, the yeast cells were collected by centrifugation for total RNA isolation and the construction of an Illumina RNA-seq library. Total RNA from the sample was isolated using TRIzol reagent (Invitrogen, Grand Island, USA) and subsequently utilized for high-throughput RNA sequencing. The 150-nt paired-end strand-specific RNA-seq library (SS_lib_type RF) was commercially generated at Novogene Biotechnology Co. Ltd (Tianjin, China) using the Illumina novaseq 6000 platform (Illumina, San Diego, USA).

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cyberlindnera jadinii NBRC0988 genome using HISAT 2 (v2.2.1)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated
Detailed parameters for reads mapping: hisat2 -p 8 -x CJ --rna-strandness RF --max-intronlen 1000 --no-mixed --no-discordant -1 SSGly_1.clean.fq.gz -2 SSGly_2.clean.fq.gz -S SSGly.sam
Assembly: Cyberlindnera jadinii NBRC0988 (Accession numbers： BAEL01000001-BAEL01001163 and DG000065-DG000077)
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample .

organism: Cyberlindnera jadinii NBRC 0988

source_name: Yeast cells

growth_protocol: NBRC0988 cells grown overnight were inoculated into 100 ml liquid Yeast Extract Peptone Dextrose (YEPD) medium with the initial inoculation amount of OD600= 0.1, and cultured for 15 hours to the logarithmic growth phase (OD600= 2-3).

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
150-nt paired-end strand-specific RNA-seq libraries (SS_lib_type RF)

treatment_protocol: The cells were collected by centrifugation at 6,000g for 5 minutes. After washing twice with phosphate buffer saline (PBS), they were inoculated into new 100 mL YEP medium containing 2% w/v glycerol. After flask culturing at 30°C and 250 rpm for an additional 5 hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction.

value: Yeast cells


title: Kudo3D_KPT_3

description: NAS Order ID: CS034542


title: Kudo3D_KPT_2

description: NAS Order ID: CS034542


title: Kudo3D_KPT_1

description: NAS Order ID: CS034542


title: Kudo3D_4

description: NAS Order ID: CS034542

value: No treatment


title: Kudo3D_2

description: NAS Order ID: CS034542


title: Kudo3D_3

description: NAS Order ID: CS034542


title: Kudo3D_1

description: NAS Order ID: CS034542


title: L2_CK41/43_1


title: VCaP_RNA_A485_DHT_rep1

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER. DMSO-EtOH vehicle control rep1 and rep2 were used for Dex-treated samples, and rep3 and rep4 were used for DHT-treated samples.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

molecule: polyA RNA

source_name: VCaP

growth_protocol: 22Rv1 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin, 1 µg/ml streptomycin and 2 mM L-glutamine. VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
The isolation of RNA was conducted using NEB Monarch Total RNA Miniprep Kit following manufacturer’s protocol.
NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: 22Rv1 and VCaP cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of treatments. 22Rv1 and VCaP cells were treated with vehicle (DMSO) or 1 µM A485 for 24 h and vehicle (EtOH), 100 nM of dihydrotestosterone (DHT), or 100 nM of Dexamethasone (Dex) for the last 18 h before the start of RNA extraction.

value: Vertebral Cancer of the Prostate

value: VCaP

tag: enz treatment

tag: inhibitor treatment

tag: hormone treatment

value: dihydrotestosterone, 100 nM


title: VCaP_RNA_A485_DHT_rep2


title: VCaP_RNA_A485_EtOH_rep3


title: VCaP_RNA_A485_EtOH_rep4


title: 22Rv1_RNA_A485_DHT_rep2

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line


title: VCaP_RNA_DMSO_EtOH_rep3


title: 22Rv1_RNA_A485_EtOH_rep4


title: VCaP_RNA_DMSO_EtOH_rep4


title: VCaP_RNA_DMSO_DHT_rep1


title: 22Rv1_RNA_A485_EtOH_rep3


title: 22Rv1_RNA_DMSO_DHT_rep1


title: 22Rv1_RNA_DMSO_DHT_rep2


title: 22Rv1_RNA_DMSO_EtOH_rep3


title: 22Rv1_RNA_DMSO_EtOH_rep4


title: VCaP_EP300_ENZ3w_Dex_rep2

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Corresponding input sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

extract_protocol:
For ChIP-seq, after 1% formaldehyde crosslinking, cells were harvested, chromatin was sonicated to 100-300 bp fragments, and protein-DNA complexes were isolated with specified antibody.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit according to instructions.

treatment_protocol: 22Rv1 and VCaP cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of treatments. 22Rv1 and VCaP cells were treated with vehicle (DMSO) or 1 µM A485 for 24 h and vehicle (EtOH), 100 nM of dihydrotestosterone (DHT), or 100 nM of Dexamethasone (Dex) for the last 1 h before the start of ChIPs.

value: 3 weeks

value: dexamethasone, 100 nM

tag: chip antibody

value: EP300 (Santa Cruz, sc-585)


title: VCaP_input_A485_rep1


title: VCaP_input_ENZ3w_DMSO_rep1


title: VCaP_EP300_ENZ3w_Dex_rep1


title: VCaP_EP300_ENZ3w_EtOH_rep1


title: VCaP_EP300_Dex_rep2


title: VCaP_RNA_DMSO_DHT_rep2


title: VCaP_EP300_EtOH_rep2


title: VCaP_GR_ENZ3w_A485_Dex_rep4

value: GR (Cell Signaling, 12041)


title: VCaP_EP300_Dex_rep1


title: VCaP_GR_ENZ3w_A485_Dex_rep3


title: VCaP_GR_ENZ3w_DMSO_Dex_rep3


title: VCaP_GR_ENZ3w_A485_Dex_rep2


title: VCaP_GR_ENZ3w_DMSO_Dex_rep4


title: VCaP_GR_ENZ3w_A485_Dex_rep1


title: 22Rv1_RNA_A485_DHT_rep1


title: VCaP_EP300_EtOH_rep1


title: VCaP_GR_A485_Dex_rep3


title: VCaP_GR_A485_Dex_rep4


title: VCaP_input_ENZ3w_A485_rep1


title: VCaP_GR_DMSO_Dex_rep4


title: VCaP_GR_ENZ3w_DMSO_Dex_rep2


title: VCaP_GR_A485_Dex_rep2


title: VCaP_input_DMSO_rep1


title: VCaP_EP300_ENZ3w_EtOH_rep2


title: VCaP_GR_DMSO_Dex_rep2


title: VCaP_GR_DMSO_Dex_rep1


title: VCaP_GR_A485_Dex_rep1


title: VCaP_AR_A485_DHT_rep2

value: AR (rabbit antiserum; Karvonen et al. 1997)


title: VCaP_AR_DMSO_DHT_rep2


title: 22Rv1_input_ENZ3w_A485_rep1


title: VCaP_AR_DMSO_DHT_rep1


title: 22Rv1_input_ENZ3w_DMSO_rep1


title: 22Rv1_input_A485_rep2


title: 22Rv1_input_DMSO_rep1


title: 22Rv1_EP300_ENZ3w_Dex_rep1


title: 22Rv1_EP300_ENZ3w_EtOH_rep2


title: 22Rv1_EP300_ENZ3w_Dex_rep2


title: 22Rv1_EP300_Dex_rep2


title: 22Rv1_EP300_ENZ3w_EtOH_rep1


title: 22Rv1_EP300_EtOH_rep2


title: VCaP_GR_ENZ3w_DMSO_Dex_rep1


title: 22Rv1_EP300_Dex_rep1


title: 22Rv1_FOXA1_ENZ3w_A485_Dex_rep2

value: FOXA1 (Abcam, ab23738)


title: 22Rv1_FOXA1_ENZ3w_A485_Dex_rep1


title: 22Rv1_EP300_EtOH_rep1


title: VCaP_GR_DMSO_Dex_rep3


title: 22Rv1_FOXA1_ENZ3w_A485_EtOH_rep1


title: 22Rv1_FOXA1_ENZ3w_DMSO_Dex_rep2


title: 22Rv1_FOXA1_ENZ3w_A485_EtOH_rep2


title: 22Rv1_FOXA1_ENZ3w_DMSO_Dex_rep1


title: 22Rv1_FOXA1_ENZ3w_DMSO_EtOH_rep2


title: 22Rv1_FOXA1_ENZ3w_DMSO_EtOH_rep1


title: 22Rv1_FOXA1_A485_Dex_rep1


title: 22Rv1_FOXA1_A485_Dex_rep2


title: 22Rv1_FOXA1_A485_EtOH_rep1


title: 22Rv1_FOXA1_DMSO_Dex_rep2


title: 22Rv1_FOXA1_A485_EtOH_rep2


title: 22Rv1_FOXA1_DMSO_Dex_rep1


title: 22Rv1_FOXA1_DMSO_EtOH_rep1


title: 22Rv1_H3K27ac_ENZ3w_A485_Dex_rep2

value: H3K27ac (Active Motif, 39133)


title: 22Rv1_FOXA1_DMSO_EtOH_rep2


title: 22Rv1_H3K27ac_ENZ3w_A485_Dex_rep1


title: 22Rv1_H3K27ac_ENZ3w_A485_EtOH_rep2


title: 22Rv1_H3K27ac_ENZ3w_A485_EtOH_rep1


title: 22Rv1_H3K27ac_ENZ3w_DMSO_Dex_rep1


title: 22Rv1_H3K27ac_ENZ3w_DMSO_Dex_rep2


title: 22Rv1_H3K27ac_A485_Dex_rep2


title: 22Rv1_H3K27ac_A485_Dex_rep1


title: 22Rv1_H3K27ac_ENZ3w_DMSO_EtOH_rep2


title: 22Rv1_H3K27ac_ENZ3w_DMSO_EtOH_rep1


title: 22Rv1_H3K27ac_A485_EtOH_rep1


title: 22Rv1_H3K27ac_DMSO_Dex_rep1


title: 22Rv1_H3K27ac_DMSO_Dex_rep2


title: 22Rv1_H3K27ac_DMSO_EtOH_rep2


title: 22Rv1_AR_A485_DHT_rep1


title: 22Rv1_AR_A485_DHT_rep2


title: 22Rv1_AR_DMSO_DHT_rep2


title: 22Rv1_H3K27ac_DMSO_EtOH_rep1


title: VCaP_AR_A485_DHT_rep1


title: VCaP_ATAC_ENZ3w_A485_EtOH_rep2

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Transposase treated naked DNA sample was used as the control sample (GSE214757).
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

extract_protocol:
For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Tn5 Transposase loaded with sequencing adapters.
ATAC-seq libraries were prepared with loaded Diagenode Tagmentase (#C01070012) according to instructions.

treatment_protocol: 22Rv1 and VCaP cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of treatments. 22Rv1 and VCaP cells were treated with vehicle (DMSO) or 1 µM A485 for 24 h and with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) for the last 1 h before the start of nuclei extraction.


title: VCaP_ATAC_ENZ3w_A485_Dex_rep2


title: VCaP_ATAC_ENZ3w_A485_Dex_rep1


title: 22Rv1_AR_DMSO_DHT_rep1


title: VCaP_ATAC_ENZ3w_A485_EtOH_rep1


title: VCaP_ATAC_ENZ3w_DMSO_Dex_rep2


title: VCaP_ATAC_ENZ3w_DMSO_Dex_rep1


title: VCaP_ATAC_ENZ3w_DMSO_EtOH_rep1


title: VCaP_ATAC_ENZ3w_DMSO_EtOH_rep2


title: VCaP_ATAC_A485_EtOH_rep2


title: VCaP_ATAC_DMSO_Dex_rep2


title: 22Rv1_H3K27ac_A485_EtOH_rep2


title: VCaP_ATAC_A485_Dex_rep1


title: VCaP_ATAC_A485_EtOH_rep1


title: Sample 4, Non-Immunized

city: Irvine

first: Lbachir

last: BenMohamed

state: California

address: 843 Health Sciences Road, Hewitt Hall, 2nd Floor

institute: University of California Irvine

data_processing:
Trimmed sequencing reads were mapped to Cavpor3.0 and feature count data was generated using htSeq.
Assembly: Cavpor3.0
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text file includes RPKM values for each sample.

organism: Cavia porcellus

source_name: PBMC

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 1.5ug of total RNA was used for building sequencing libraries.
RNA libraries for RNA-Seq were prepared using TruSeq Ribo-Zero Total RNA Library preparation Kit following manufacturer's protocols.

value: PBMC

value: Non-Immunized


title: Sample 2, Immunized

value: Immunized


title: VCaP_ATAC_DMSO_EtOH_rep1


title: VCaP_ATAC_DMSO_EtOH_rep2


title: VCaP_ATAC_DMSO_Dex_rep1


title: Sample 3, Non-Immunized


title: BMDM WT 2.0h TNFa

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

data_processing:
Samples were demultiplexed, trimmed, and mapped to the NCBI37/mm9 genome using Hisat2.
After alignment, samples were processed into BAM files using Samtools.
Read counts were extracted using SeqMonk. Normalized read counts (RPKMs) were generated by normalizing for sequencing depth (per million reads) and gene length (kilobases).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample.

molecule: nuclear RNA

source_name: BMDM

growth_protocol: Bone marrow was extracted from the hip, femur, tibia, and fibula of wild-type (C57/B16) or Nfkb1-/-, Blc3-/-, Nfkbiz-/-, Nfkbid-/- mice. Cells were differentiated for 6 days in cell culture using 8% M-CSF prior to stimulation.

extract_protocol:
Cellular fractionation was used to isolate nuclei and extract chromatin as previously described (Bhatt et al., Cell 2012).  Chromatin was resuspended in TRIzol and RNA was purified using Rneasy Columns (Qiagen). ~100ng of chromatin-associated RNA was used for library construction.
RNA-seq libraries were constructed using the Illumina Stranded TruSeq Kit, adapted from the manufacturer's instructions.

value: BMDM

value: Wild type

value: 2.0h TNFa


title: BMDM WT 6.0h TNFa

value: 6.0h TNFa


title: YoungOT1_Tum_Tterm_replicate7_ATACseq

city: Boston

first: Alex Chang-Yu

last: Chen

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

description:
YoungOT1_Tum_Tterm_7
NormCountsATAC_Intrinsic.txt

data_processing:
Raw fastq files were downloaded from Illumina BaseSpace and merged across lanes
Quality trimming and primer removal in raw fastq files were done with Trimmomatric (v.0.36) using the following parameters: LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:30 CROP:35.
Trimmed reads were aligned to mm10 with Bowtie2 (v.2.2.9) using a maximum insert size of 1,000.
Aligned bams were sorted, duplicates marked (Picard v.2.8.0) , and reads mapping to the blacklist region removed.
Peak-calling using MACS (v.2.1.1) was performed on merged bam files (Samtools v. 1.3.1) from biological replicates using a q-value threshold of 0.001. Consensus peaks from all biological conditions were merged to create a single peak universe. Cut sites were extracted from each biological replicate and the number of cuts in each peak region was quantified to generate a raw counts matrix.
Normalization and differential expression were performed using DESeq2 (v 1.28.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including DESeq2 normalized counts

source_name: B16-OVA Tumor

extract_protocol:
DNA was purified using a QIAgen MinElute Reaction Cleanup kit
Post-PCR bead cleanup was done using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt), and library quality was verified using Tapestation analysis.

value: CD8+ T cells

tag: cell subset

value: Tterm

tag: cell state

value: terminally exhausted

value: B16-OVA Tumor

tag: age

value: 10-12 weeks old

tag: sequencing batch

value: Batch 6


title: YoungOT1_Tum_Tterm_replicate6_ATACseq

description:
YoungOT1_Tum_Tterm_6
NormCountsATAC_Intrinsic.txt

tag: cell type

tag: tissue


title: AgedOT1_Tum_Tterm_replicate6_ATACseq

description:
AgedOT1_Tum_Tterm_6
NormCountsATAC_Intrinsic.txt

value: 64-68 weeks old

tag: genotype


title: AgedOT1_Tum_Tprog_replicate2_ATACseq

description:
AgedOT1_Tum_Tprog_2
NormCountsATAC_Intrinsic.txt

value: Tprog

value: progenitor exhausted


title: BMDM WT 1.0h TNFa

tag: treatment

value: 1.0h TNFa


title: CD40treatment_CD8T_youngTME_scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Gzipped files include 10x format single cell gene expression matrices, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Supplementary files format and content: tab-delimited text file including log normalized counts for each cell generated using Seurat in R

extract_protocol:
Live tumor-infiltrating CD8+ T cells (or OT-1 CD8+ T cells) and/or intratumoral CD45+ cells were sorted from tumors on day 15 after tumor inoculation by BD FACSSymphony S6 Sorter (BD).  Sorted cells were pooled into groups (five biological replicates per group) with independent mice being labeled with TotalSeq-B Hashtags (Biolegend). Cells were counted and loaded onto the Chromium Controller (10X Genomics) for a target recovery of 10,000 single cells per run.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: Endogenous CD8+ T cells


title: Endogenous_CD45cells_youngTME_scRNAseq

description: 10x Genomics

value: CD45+ T cells


title: Endogenous_CD45cells_agedTME_scRNAseq

description: 10x Genomics


title: VCaP_ATAC_A485_Dex_rep2

value: Vertebral Cancer of the Prostate

tag: cell line

value: VCaP

value: dexamethasone, 100 nM


title: Young_Endo_Tprog_replicate4_ATACseq

description:
Young_Endo_Tprog_4
NormCountsATAC_Endo.txt

value: Batch 1 & 2

value: Wild type


title: BMDM WT 0.5h TNFa

value: BMDM

value: 0.5h TNFa


title: BMDM WT 0.0h TNFa

value: Unstimulated


title: BMDM pre-treat ERKi, stim Lipid A 60m

value: pretreatment ERKi, 60m Lipid A


title: AgedOT1_Tum_Tprog_replicate1_ATACseq

description:
AgedOT1_Tum_Tprog_1
NormCountsATAC_Intrinsic.txt

value: CD8+ T cells

value: B16-OVA Tumor


title: BMDM pre-treat ERKi, stim Lipid A 30m

value: pretreatment ERKi, 30m Lipid A


title: BMDM pre-treat ERKi, stim Lipid A 0m

value: pretreatment ERKi, 0m Lipid A


title: BMDM pre-treat ERKi, stim Lipid A 15m

value: pretreatment ERKi, 15m Lipid A


title: Young_Endo_Tprog_replicate3_ATACseq

description:
Young_Endo_Tprog_3
NormCountsATAC_Endo.txt

value: Tprog

value: progenitor exhausted

value: 10-12 weeks old


title: Young_Endo_Tterm_replicate5_ATACseq

description:
Young_Endo_Tterm_5
NormCountsATAC_Endo.txt

value: Tterm

value: terminally exhausted


title: Sample 1, Immunized

value: PBMC

value: Immunized


title: Young_Endo_Tterm_replicate3_ATACseq

description:
Young_Endo_Tterm_3
NormCountsATAC_Endo.txt

value: Batch 1 & 2

value: Wild type


title: BMDM pre-treat DSMO, stim Lipid A 60m

value: BMDM

value: pretreatment DMSO, 60m Lipid A


title: Aged_Endo_Tprog_replicate3_ATACseq

description:
Aged_Endo_Tprog_3
NormCountsATAC_Endo.txt

value: 64-68 weeks old


title: Aged_Endo_Tprog_replicate2_ATACseq

description:
Aged_Endo_Tprog_2
NormCountsATAC_Endo.txt

value: CD8+ T cells


title: BMDM pre-treat DSMO, stim Lipid A 30m

value: pretreatment DMSO, 30m Lipid A


title: CD40treatment_CD8T_agedTME_scRNAseq

description: 10x Genomics

value: Endogenous CD8+ T cells

value: B16-OVA Tumor


title: BMDM pre-treat DSMO, stim Lipid A 0m

value: pretreatment DMSO, 0m Lipid A


title: Young_Endo_Tprog_replicate2_ATACseq

description:
Young_Endo_Tprog_2
NormCountsATAC_Endo.txt

value: Tprog


title: BMDM IkBz OE 0.0h

value: Unstimulated


title: BMDM IkBz OE TNFa 2.0h

value: 2.0h TNFa


title: BMDM Control TNFa 2.0h


title: Aged_Endo_Tterm_replicate2_ATACseq

description:
Aged_Endo_Tterm_2
NormCountsATAC_Endo.txt

value: Tterm


title: Young_Endo_Tterm_replicate1_ATACseq

description:
Young_Endo_Tterm_1
NormCountsATAC_Endo.txt

value: terminally exhausted

value: 10-12 weeks old


title: Aged_Endo_Tadys_replicate2_ATACseq

description:
Aged_Endo_Tadys_2
NormCountsATAC_Endo.txt

value: Tadys

value: age-associated dysfunctional


title: Young_Endo_Tprog_replicate1_ATACseq

description:
Young_Endo_Tprog_1
NormCountsATAC_Endo.txt

value: progenitor exhausted

value: Batch 1 & 2

value: Wild type


title: Aged_Endo_Tprog_replicate1_ATACseq

description:
Aged_Endo_Tprog_1
NormCountsATAC_Endo.txt

value: 64-68 weeks old


title: Young_Endo_Tterm_replicate2_ATACseq

description:
Young_Endo_Tterm_2
NormCountsATAC_Endo.txt

value: CD8+ T cells


title: BMDM Control 0.0h

value: BMDM


title: Aged_Endo_Tterm_replicate1_ATACseq

description:
Aged_Endo_Tterm_1
NormCountsATAC_Endo.txt


title: Young_Endo_Tterm_replicate4_ATACseq

description:
Young_Endo_Tterm_4
NormCountsATAC_Endo.txt


title: J2 BMDM Nfkb1-/-, Nfkb2-/- 2.0h R1

source_name: J2 BMDM

value: J2 BMDM

value: 2.0h Lipid A


title: Aged_Endo_Tadys_replicate1_ATACseq

description:
Aged_Endo_Tadys_1
NormCountsATAC_Endo.txt

value: B16-OVA Tumor


title: J2 BMDM Nfkb1-/-, Nfkb2-/- 0.0h R1


title: BMDM pre-treat DSMO, stim Lipid A 15m

value: pretreatment DMSO, 15m Lipid A


title: J2 BMDM Nfkb1-/- 0.0h

value: Unstimulated


title: XHT_F3

city: Guiyang

first: yue

middle: yue

last: Jin

address: Jiaxiu South Road, Huaxi District

department: College of agriculture

institute: Guizhou University

data_processing:
The image data of sequenced fragments measured by high-throughput sequencers are converted into sequence data (reads) by CASAVA base recognition, and the file format is fastq. All subsequent analyses are based on clean data for high quality analysis.
Sequence comparisons were made to reference genomes, and reference genomes and gene model annotation files were downloaded directly from the genome website. Using HISTA2 v2.05, searches of the reference genome were constructed and paired-end clean reads were compared to the reference genome using HISTA2 v2.05.
Differential expression analysis between the two comparison combinations (two biological replicates per group) was performed using DESeq2 software (1.20.0)
Benjamini and Hochberg's method was used to adjust the resulting p-values to control for discovery rates.
Assembly: http://39.100.233.196:82/download_genome/Brassica_Genome_data/Rapsa_Xiang_V1.0/
Supplementary files format and content: mRNA_gene.FPKM.xlsx

organism: Raphanus sativus

source_name: Leaves after  flowering

extract_protocol:
E.Z.N.A.™ Plant RNA Kit Protocol I (Standard Protocol).1. After plant leaves are ground in liquid nitrogen, collect ≤100mg of plant sample into a centrifuge tube, add 500µl of RB Buffer/10µl of β-mercaptoethanol, and vortex immediately to mix. 2. Place a gDNA Filter column into a 2ml collection tube, transfer the mixture to the gDNA Filter column, and centrifuge the sample for 5min at room temperature 14,000xg. 3. Transfer the filtrate to a new 1.5mL tube, add 0.5 times the volume of anhydrous ethanol, vortex at high speed for 20s to mix, and if precipitate precipitates, aspirate with a lance 10-15 times. 4. Place the HiBind® RNA Mini Binding Column into a 2 ml collection tube, transfer 700 μl of the mixture from step 3 to the HiBind® RNA Mini Binding Column, and centrifuge for 1 min at room temperature 12,000xg. Repeat step 4 until all of the mixture has been transferred to the column. 6. Place the HiBind® RNA Mini Binding Column into the same 2 ml collection tube, add 400 µl of RWF Wash Buffer, and centrifuge at room temperature for 30 s at 10,000 x g. Discard the filtrate. 7. Place the HiBind® RNA Mini Binding Column into the same 2 ml collection tube, add 400 µl of RWF Wash Buffer, and centrifuge at room temperature for 30 s. Dispose of the filtrate. 8. Add 500µl of RWF Wash BufferII (diluted with anhydrous ethanol in advance) to the same 2ml collection tube, centrifuge at 10,000xg for 30s at room temperature and discard the filtrate. 8. Repeat step 7. 9. Place the HiBind® RNA Mini Binding Columns into the same 2ml collection tube and centrifuge for 2min at room temperature at maximal speed, shake off the HiBind® RNA Mini Binding Columns and then centrifuge for 2min at room temperature. Drain the HiBind® RNA Mini binding column matrix; 10. Place the HiBind® RNA Mini binding column into the same 2 ml collection tube and centrifuge for 2 min at room temperature at maximum speed.10. Place the HiBind® RNA Mini Binding Column in a new 1.5 ml tube and add 50-100 µl of DEPC Water to the center of the HiBind® RNA Mini Binding Column membrane, leave at room temperature for 2 min, centrifuge at 10,000 x g for 1 min to elute the RNA; Note: The following may help to increase the amount of RNA produced.  Preheat DEPC Water at 65°C and let stand at room temperature for 5min before use; increase the volume of eluent;Perform a second elution with fresh DEPC Water (increases yield but results in lower concentration), add DEPC Water from the first elution back into the column for a second elution (increases elution concentration but does not increase yield much). Add DEPC Water from the first elution back into the column for a second elution (increases elution concentration but does not increase yield much)
The kit used for library construction is NEBNext@ UltraTm Directional RNA Library Prep Kit for lllumina®.Strand-specific library construction: Reverse transcription synthesizes the first strand of cDNA in the same way as NEB's normal library construction method, with the exception that when synthesizing the second strand, dTTP is replaced by dUTP in the dNTPs, followed by the same process of cDNA end repair, addition of A-tail, joining of sequencing junctions, and length selection, and then the second strand of the J-containing cDNA is degraded by USER enzyme before PCR amplification and library acquisition.

value: leaves

value: leaf pulp cell

tag: condition

value: after flowering


title: Aged_Endo_Tterm_replicate3_ATACseq

description:
Aged_Endo_Tterm_3
NormCountsATAC_Endo.txt

value: Tterm

value: terminally exhausted


title: BMDM IkBz OE Lipid A 2.0h


title: XHT_F1


title: J2 BMDM WT 0.0h


title: J2 BMDM Nfkb1-/- 2.0h


title: Hela

city: La Jolla

first: Heidi

last: Cook-Andersen

state: CA

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

data_processing:
Raw fast5 files were basecalled with Guppy (version 6.0.6) following parameters: --config dna_r9.4.1_450bps_hac.cfg --fast5_out --trim_strategy none --records_per_fastq 0 --device cuda:all:100% --recursive. and full length reads with all adapter sequences (from the CRTA, PCR primers, and sequencing adapter) were filtered by Pychopper (version 2.5.0) following parameters: -k PCS110. Only full-length reads with a minimum basecalling Q-value score of 9 and all adapter sequences were retained for further analysis. Reads were mapped to the GRCm38 mouse transcriptome with minimap (version 2.17) using the following parameters: -a -x map-ont. Reads per transcript were quantified with Salmon (version 0.14.1) using the following parameters: salmon quant -l A --noErrorModel. Read counts were normalized with ERCC standards by dividing read counts for each gene by the mean read count amongst ERCCs. Differential expression analysis was performed with DESeq2 (version 1.34.0).
Assembly: GRCm38
Supplementary files format and content: CountData.tsv file is a tab-delimited text file that contains normalized read counts exported from DESeq2 for each sample. Tail_lengths.tsv files contain measured poly(A) tail lengths for all genes or polyadenylated standards.

source_name: Hela

growth_protocol: Mouse oocytes were isolated from C57B6J female mice. For GV oocytes, 4-week old females were stimulated by intraperitoneal injection of 5 IU pregnant mare serum gonadotropin (PMSG; Lee BioSolutions, 493-10), ovaries were harvested 48 hours after PMSG injection, and denuded oocytes collected after brief digestion with trypsin (Fisher Scientific, 25200056), collagenase (Sigma-Aldrich, C9407), and DNAse in M2 media (Sigma-Aldrich, M7167). For MII oocytes, mice were injected with 5 IU HCG (Sigma-Aldrich, C1063) 48 hours after PMSG induction and ovulated MII oocytes collected from the ampulla 15 hours post-HCG and cumulus cells by brief hyaluronidase (Sigma-Aldrich, H4272) digestion per standard protocol. Mouse embryos were isolated from B6D2F1/J female mice mated with C57B6J males of known fertility at the time of hCG injection. 1-cell, early 2-cell, and late 2-cell embryos were collected at 27-28, 30-32, and 46-48 hrs post-HCG.

extract_protocol:
For each stage and replicate, total RNA was isolated from ~400 oocytes or embryos with Trizol reagent (Fisher Scientific, 15-596-018), followed by ethanol precipitation and RNA Clean & Concentrator-5 kit (Zymo Research, R1014) as per manufacturer’s protocol. RNA was eluted in 7 ul nuclease-free water and used immediately for Nanopore PCR-cDNA sequencing library prep. cDNA standards with the following sequences were obtained from IDT:  pA_cDNA_standard_10: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTACCAACGGCGACGAATAGTAGTTTACTTCCTCCCTGCGGGCCCCTCCTGAAGTGCCACCTATACGGCTTGTTGAAGCCGATTAGTACAATAGATTTATTCAACCCCAAAGGTCTACACTCCCGGCTTACTCTTAGCTGATATGTCGCGCAATATCAGCACCAACAGAAA  pA_cDNA_standard_40: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGGCAAAGAGACAATTATAGCGGCTAGGAACGCAACTAGTTATAACGAACGGCCTCGAATAGTAGAAAATATCCCTCCTCCGGGCACCTCCTGAAATGCCACATATTCGGGTTATTGGCAATATCAGCACCAACAGAAA  pA_cDNA_standard_50: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGAGAGCCAGCAACAATTGCAAATGTCAGATCAAAGTAATATTAGCAAACAATAAGTCCCTAACTAGTTGTGACCTTTTGTAAAGTGAATTTCATTATATATGCTGTGCAATATCAGCACCAACAGAAA   pA_cDNA_standard_70 :  CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCAACGGGGAGCCGAGATTATTGAGTGATCACCAGTAGCTGTACTATTATATAAGCTATTAAAGATTGATCAAAGTAAACATACCGCGCAATATCAGCACCAACAGAAA  pA_cDNA_standard_100: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCCAAGCGAAAACGGGTGCGTGGACTAGCGAGGAGCAAACGAAAATTCTTGGCCTGCGCAATATCAGCACCAACAGAAA  pA_cDNA_standard_130: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGGAGGCAATTCTATAAGAATGCATACGCAATATCAGCACCAACAGAAA   pA_cDNA_standard_150: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGAGCACGCAATATCAGCACCAACAGAAA
Approximately 400 oocytes or embryos per biological replicate per stage were used per sequencing run. An identical amount of ERCC spike-in standards51 per cell was added to samples at the beginning of RNA extraction. Nanopore PCR-cDNA sequencing (PCS) was performed with an early access cDNA-PCR Sequencing Kit (PCS-110) as per manufacturer’s protocol (Fig. S1A). This kit is most similar to the currently available cDNA-PCR Sequencing Kit (PCS-111). Briefly, ligation of Nanopore’s proprietary cDNA-RT adapter (CRTA) to the 3’ end of polyadenylated mRNAs enriched for transcripts with a minimum polyA tail length of 10 nt. Following enzymatic digestion of the adapter, RT with strand switching was performed, followed by selection of full-length transcripts by PCR amplification for 18 cycles. Sequencing adapters are then attached, followed by loading of the library onto a R9.4.1 flow cell (FLO-MIN106D) and sequenced in a Minion sequencing device with Minknow software (version 22.05.5). Libraries comprised of polyadenylated cDNA standards were prepared by PCR amplification using the following barcoded PCR primers from the Nanopore PCR-cDNA Barcoding Kit (SQK-PCB109), followed by attachment of sequencing adapters from the PCS-110 kit and sequencing on the Minion as per the PCS-110 protocol: pA_cDNA_standard_10: BC01, pA_cDNA_standard_40: BC02, pA_cDNA_standard_50: BC03, pA_cDNA_standard_70: BC04, pA_cDNA_standard_100: BC05, pA_cDNA_standard_130: BC06, and pA_cDNA_standard_150: BC07.

value: Hela


title: J2 BMDM Nfkb1-/-, Nfkb2-/- 2.0h R2


title: mRNA 6.0h TNFa

value: 6.0h TNFa


title: XHT_VG2

source_name: Leaves before  vernalization

value: before vernalization


title: mRNA 2.0h TNFa

value: Wild type

value: 2.0h TNFa


title: mRNA 1.0h TNFa

value: 1.0h TNFa


title: J2 BMDM Nfkb1-/-, Nfkb2-/- 0.0h R2


title: XHT_VG1


title: 619 WW Mutant, scRNAseq

first: Alain

last: Domissy

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using the Cell Ranger version 6.0.0  (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Comma-separated values files

source_name: Liver

extract_protocol:
Splenocytes from LCMV-cl13 or mock infected animals were isolated at designated time points. After red blood cell lysis and filtering through 70M filter, splenocytes were resuspended in T stimulation media (RPMI containing 10% FBS, 1% of each of the following Penicillin/Streptomycin, HEPES, Sodium Pyruvate, L-Glutamine, Non Essential Amino Acids, and 55M 2-Mercaptoethanol). 2x106 splenocytes were plated into 96-U bottom wells in the presence or absence of 5g/mL GP61-80 peptide (CD4 T cells) or 2mg/mL GP3361-80 (CD8 T cell) for 1 hour at 37C. After 1 hour incubation with peptide, Brefeldin A (0.4g/mL) was added and incubated for an additional 4 hours at 37C. Following stimulation and incubation, cell were spun down, washed with HBSS, and proceeded to extracellular and intracellular staining.
Library was performed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, the splenocytes were re-suspended in the master mix and loaded together with partitionog oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retro-transcripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane Dynabeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction.

value: Liver

value: Jurkat

value: sorted CD45+ tumor infiltrating cells

value: 619 WW Mutant


title: mRNA 6.0h LipidA

value: BMDM

value: 6.0h LipidA


title: XHT_VG3

value: leaves


title: Wild Type, scRNAseq

description: 10x Genomics

value: Wild Type


title: Gills,  Station C, biol rep 2

city: Cologne

first: Camilo

last: Escobar Sierra

state: NRW

address: Zülpicher Strasse 47b

department: Institute of Zoology

institute: University of Cologne

data_processing:
Quality improvement via an adaptor and low-quality reads filtering using TRIMMOMATIC, with a threshold of phred + 33 quality score of at least 25 for all bases, and a minimum length of 50 bp for all reads kept for downstream analyses
TRINITY v2.9.1 was used to create a de novo assembly using the nine pairs of clean sequences.
The reads of the raw nine paired sequences were aligned to the de novo transcriptome using SALMON
BUSCO v5.2.2 was used to assess transcriptome assembly completeness by searching against the actinopterygii_odb10 (Creation date: 2021-02-19) dataset.
The expression matrix was generated and the low expressions transcripts (minimum expression of 1.0) were filtered using TRINITY v2.9.1, the expression levels were normalized as transcripts per million transcripts (TPM). Identification of likely protein-coding regions in transcripts was performed with TRANSDECODER v5.5.0.
The filtered transcriptome sequencing reads were aligned to protein, signal peptides, and transmembrane domains using the tools, DIAMOND v2.0.8 [49], SIGNALP 6.0 [50], TMHMM v2.0 [51], and, HMMER v3.3.2 [52]. The de novo transcriptome was then functionally annotated using the tool TRINOTATE v3.2.2 [45].
Before the differential gene expression analysis, the SALMON tool was used to align the clean reads of the three sites to the filtered transcriptome and the mapping rate was calculated. The mapping tables were merged according to the stations and using TMM [53] normalization. Differential expression analysis with three biological replicates of the two stations with higher chloride (A and C) were compared to the reference condition (Station B) using the DESeq2 [54] package, the fold change cut-off was set at >2, and the FDR≤0.05.
Assembly: denovo assembly trinity TRINITY v2.9.1 with all biological replicates
Supplementary files format and content: tab-delimited text file with annotated TMM counts for each sample output of deseq2

organism: Gasterosteus aculeatus

source_name: Gills

extract_protocol:
RNA was extracted using an RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
Illumina Tru-Seq™ RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) was applied in generating sequencing libraries following the manufacturer’s protocol

value: Gills

value: 32  mg/L Chloride


title: XHT_F2

value: leaf pulp cell

value: after flowering


title: Gills,  Station A, biol rep 3

value: 26.378 mg/L Chloride


title: mRNA 0.5h LipidA

value: 0.5h LipidA


title: mRNA 1.0h LipidA

value: Wild type

value: 1.0h LipidA


title: Gills,  Station C, biol rep 1


title: Gills,  Station A, biol rep 2


title: mRNA 0.0h

value: Unstimulated


title: BMDM Nfkb1-WT 6.0h R3

value: 6.0h Lipid A


title: Gills,  Station A, biol rep 1


title: BMDM Nfkb1-WT 2.0h R3

value: 2.0h Lipid A


title: Gills,  Station B, biol rep 3

value: 12.912 mg/L Chloride


title: BMDM Nfkb1-WT 1.0h R3

value: 1.0h Lipid A


title: Gills,  Station B, biol rep 2


title: BMDM Nfkb1-WT 0.5h R3

value: BMDM

value: 0.5h Lipid A


title: Gills,  Station B, biol rep 1


title: BMDM Nfkb1-/- 6.0h R3


title: BMDM Nfkb1-/- 2.0h R3


title: Gills,  Station C, biol rep 3


title: BMDM Nfkb1-WT 0.0h R3


title: BMDM Nfkb1-/- 1.0h R3


title: Muscle, Mustn1-WT, rep1

city: Stockholm

first: Paulo

middle: R.

last: Jannig

address: Solnavägen 9

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description:
W1
normalized_counts_deseq2.csv
raw_counts_featureCounts.txt
mustn1_het_vs_mustn1_wt_deseq2.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.7.3a with extra arguments --outFilterMismatchNmax 33 --alignEndsType Local --alignSJoverhangMin 8 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --seedSearchStartLmax 12
Reads aligning to gene exons (Mus_musculus.GRCm38.94.gtf) were counted using featureCounts v2.0.3 program from Subread package, summarized at gene level.
Differential gene expression at FDR level 0.05 was obtained using DESeq2 R package, genes with total raw counts less then 10 across all samples were excluded from analysis
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw read counts for all samples
Supplementary files format and content: tab-delimited text files includes differetial gene expression analysis output from DESeq2

extract_protocol:
Total RNA was extracted from soleus muscles using TRI reagent (Sigma-Aldrich ref. T9424) according to the manufacturer's instructions. RNA was further purified using a Direct-zol RNA Miniprep kit (Zymo Research) including on-column DNAse I treatment. RNA quality was assessed using a 2100 Bioanalyzer system (Agilent Technologies) with an RNA integrity number (RIN) greater than 8 as a threshold.
Samples were purified by poly-A enrichment before library creation using Illumina TruSeq Stranded mRNA,

value: male

value: Wildtype


title: Muscle, Mustn1-WT, rep3

description:
W3
normalized_counts_deseq2.csv
raw_counts_featureCounts.txt
mustn1_het_vs_mustn1_wt_deseq2.txt


title: J2 BMDM WT 2.0h

value: J2 BMDM


title: Muscle, Mustn1-WT, rep2

description:
W2
normalized_counts_deseq2.csv
raw_counts_featureCounts.txt
mustn1_het_vs_mustn1_wt_deseq2.txt


title: BMDM Nfkb1-/- 0.5h R3


title: Muscle, Mustn1-Het, rep3

description:
H3
normalized_counts_deseq2.csv
raw_counts_featureCounts.txt
mustn1_het_vs_mustn1_wt_deseq2.txt


title: Muscle, Mustn1-Het, rep2

description:
H2
normalized_counts_deseq2.csv
raw_counts_featureCounts.txt
mustn1_het_vs_mustn1_wt_deseq2.txt


title: BMDM Nfkb1-/- 0.0h R3


title: mRNA 2.0h LipidA

value: 2.0h LipidA


title: Muscle, Mustn1-Het, rep1

description:
H1
normalized_counts_deseq2.csv
raw_counts_featureCounts.txt
mustn1_het_vs_mustn1_wt_deseq2.txt


title: BMDM Nfkb1-WT 6.0h R2


title: BMDM Nfkb1-WT 1.0h R2


title: BMDM Nfkb1-WT 0.5h R2


title: mRNA 0.5h TNFa

value: 0.5h TNFa


title: BMDM Nfkb1-/- 6.0h R2


title: BMDM Nfkb1-/- 2.0h R2


title: BMDM Nfkb1-/- 1.0h R2


title: BMDM Nfkb1-WT 0.0h R2


title: BMDM Nfkb1-/- 0.5h R2


title: BMDM Nfkb1-/- 0.0h R2


title: VCaP_RNA_ENZ3w_A485_Dex_rep1

value: Vertebral Cancer of the Prostate

value: VCaP

value: 3 weeks

value: dexamethasone, 100 nM


title: BMDM Nfkb1-WT 6.0h R1

value: Wild type


title: BMDM Nfkb1-WT 0.5h R1


title: BMDM Nfkb1-WT 1.0h R1


title: VCaP_RNA_ENZ3w_A485_EtOH_rep1


title: BMDM Nfkb1-WT 0.0h R1

value: Unstimulated


title: BMDM Nfkb1-WT 2.0h R2


title: BMDM Nfkb1-/- 0.5h R1


title: VCaP_RNA_ENZ3w_DMSO_EtOH_rep1


title: BMDM Nfkb1-WT 2.0h R1


title: VCaP_RNA_ENZ3w_DMSO_EtOH_rep2


title: VCaP_RNA_ENZ3w_DMSO_Dex_rep1


title: RDY73 cells, IAA, repB

city: Oklahoma City

first: John

middle: B

last: Ridenour

state: OK

address: 825 NE 13th St.

department: Cell Cycle and Cancer Biology Research Program

institute: Oklahoma Medical Research Foundation

data_processing:
Demultiplexed, paired-end 150 bp reads were preprocessed using fastp (version 0.23.2) to extract UMIs and bbduk from the BBMap package (version 36.99) to trim adapter sequences and polyA tails. Forward reads were processed using SLAM-DUNK (version 0.4.3), i.e., reads were aligned against the S. cerevisiae genome (version R64-3-1) or the spike-in Schizosaccharomyces pombe genome (version ASM294v2) using NextGenMap (version 0.5.5) and SNPs were called using VarScan 2 (version 2.4.5). Total read counts were defined as all reads remaining after filtering in SLAM-DUNK. A conversion per read threshold of ≥ 1 or ≥ 2 T>C conversions was used to define T>C read counts based on subsequent analysis.
Assembly: S. cerevisiae strain S288C version R64-3-1 (RefSeq Assembly GCF_000146045.2); S. pombe strain 972h- version ASM294v2 (RefSeq Assembly GCF_000002945.1)
Supplementary files format and content: Raw read count tables are provided in tab-separated values format (.tsv). *_scer_onetcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 1 T>C conversions for S. cerevisiae and *_scer_twotcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 2 T>C conversions for S. cerevisiae. *_spom_onetcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 1 T>C conversions for S. pombe and *_spom_twotcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 2 T>C conversions for S. pombe.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae cells were grown in YPD medium (10 g/l yeast extract, 20 g/l peptone, 20 g/l glucose, 20 mg/ml adenine sulfate) at 30°C with shaking at 220 rpm.

extract_protocol: RNA purification and DNase I treatment were performed using a Quick-RNA Fungal/Bacterial Miniprep kit and DNase I set (Zymo Research) following the manufacturer  s recommendations with minor modifications. Reagents (RNA lysis buffer, RNA wash buffer, RNA prep buffer, 100% ethanol, and nuclease-free water) were supplemented with DTT to maintain reducing conditions. Samples were protected from light when possible.

treatment_protocol: Saccharomyces cerevisiae cells were grown to an OD600 of ~0.45. Cultures were treated with 1 mM IAA freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 25 min. Immediately after IAA treatment, cultures were treated with 5 mM 4tU freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 4 min. Immediately after 4tU treatment, each culture was decanted into cold 100% methanol on dry ice. The resulting slurry was centrifuged at 3,000 g and 4°C to pellet the cells. Cells were resuspended in DNA/RNA shield (Zymo Research), flash frozen on dry ice, and stored at  -80°C. The final OD600 of the cultures was ~0.7. All experiments were performed in biological triplicate.

value: Saccharomyces cerevisiae

value: plus IAA, plus 4tU


title: RDY73 cells, IAA, repC


title: BMDM Nfkb1-/- 1.0h R1


title: RDY73 cells, DMSO, repC

value: minus IAA, plus 4tU


title: RDY73 cells, IAA, repA


title: VCaP_RNA_ENZ3w_A485_Dex_rep2


title: BMDM Nfkbiz-WT 2.0h R2

value: 2.0h Lipid A


title: VCaP_RNA_A485_Dex_rep2


title: RDY73 cells, DMSO, repB


title: BMDM Nfkbiz-WT 6.0h R2

value: BMDM

value: 6.0h Lipid A


title: BMDM Nfkb1-/- 0.0h R1


title: BMDM Nfkbiz-WT 1.0h R2

value: 1.0h Lipid A


title: VCaP_RNA_A485_Dex_rep1


title: VCaP_RNA_ENZ3w_A485_EtOH_rep2


title: VCaP_RNA_ENZ3w_DMSO_Dex_rep2


title: BMDM Nfkbiz-WT 0.5h R2

value: 0.5h Lipid A


title: RDY73 cells, DMSO, repA


title: BMDM Nfkbiz-/- 2.0h R2

value: Nfkbiz-/-


title: BMDM Control Lipid A 2.0h


title: RDY73 cells, control, repC

value: minus IAA, minus 4tU


title: BMDM Nfkbiz-WT 0.0h R2


title: VCaP_RNA_A485_EtOH_rep2


title: BMDM Nfkb1-/- 6.0h R1


title: BMDM Nfkbiz-/- 6.0h R2


title: BMDM Nfkbiz-/- 1.0h R2


title: RDY73 cells, control, repB


title: BMDM Nfkbiz-WT 6.0h R1


title: VCaP_RNA_DMSO_Dex_rep1


title: BMDM Nfkbiz-/- 0.5h R2


title: RDY73 cells, control, repA


title: BMDM Nfkbiz-WT 2.0h R1


title: RDY234 cells, IAA, repC

value: pGPD1-OsTIR1::HIS3 BDF2-3XV5-mAID-kanMX BDF1-3XV5-mAID-URA3 pBDF1-BDF1::TRP1


title: VCaP_RNA_DMSO_Dex_rep2

value: Vertebral Cancer of the Prostate


title: RDY234 cells, IAA, repB


title: VCaP_RNA_A485_EtOH_rep1

value: VCaP


title: BMDM Nfkbiz-WT 0.5h R1


title: VCaP_RNA_DMSO_EtOH_rep1


title: BMDM Nfkbiz-WT 1.0h R1


title: BMDM Nfkbiz-WT 0.0h R1


title: BMDM Nfkbiz-/- 6.0h R1


title: BMDM Nfkbiz-/- 2.0h R1


title: VCaP_RNA_DMSO_EtOH_rep2


title: 22Rv1_RNA_ENZ3w_A485_Dex_rep2

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

value: 3 weeks


title: BMDM Nfkbiz-/- 1.0h R1


title: RDY234 cells, IAA, repA


title: BMDM Nfkb1-/- 2.0h R1


title: BMDM Nfkbiz-/- 0.5h R1


title: 22Rv1_RNA_ENZ3w_A485_Dex_rep1

value: dexamethasone, 100 nM


title: RDY234 cells, DMSO, repC


title: BMDM Nfkbid-WT 6.0h R3

value: Wild type


title: 22Rv1_RNA_ENZ3w_A485_EtOH_rep2


title: BMDM Nfkbid-WT 2.0h R3


title: RDY234 cells, DMSO, repB

value: Saccharomyces cerevisiae


title: BMDM Nfkbid-WT 1.0h R3


title: RDY234 cells, DMSO, repA


title: 22Rv1_RNA_ENZ3w_A485_EtOH_rep1


title: BMDM Nfkbid-/- 6.0h R3

value: Nfkbid-/-


title: BMDM Nfkbid-WT 0.5h R3


title: 22Rv1_RNA_ENZ3w_DMSO_Dex_rep2


title: RDY234 cells, control, repC


title: BMDM Nfkbid-WT 0.0h R3

value: Unstimulated


title: RDY234 cells, control, repB


title: BMDM Nfkbid-/- 2.0h R3

value: 2.0h Lipid A


title: BMDM Nfkbid-/- 1.0h R3

value: BMDM


title: BMDM Nfkbid-/- 0.5h R3


title: BMDM Nfkbid-/- 0.0h R3


title: 22Rv1_RNA_ENZ3w_DMSO_EtOH_rep2


title: 29_SCF_Tet2

city: Cambridge

first: Fabiana

last: Duarte

state: Massachusetts

address: 7 Divinity Avenue

department: HSCRB

institute: Harvard University

data_processing:
Raw sequencing reads were trimmed using custom python scripts to remove adapter sequences.
The reads were aligned to mm10 genome using Bowtie2 (Langmead et al. 2012) with maximum fragment length set to 2 kb, and all other default settings (bowtie2 -X2000 --rg-id).
Mitochondrial, discordant and low quality reads were removed using SAMtools (Li et al. 2009) (samtools view -b -q 30 -f 0x2).
Duplicate sequences were removed using the picard toolkit (http:// broadinstitute.github.io/picard/).
Assembly: mm10
Supplementary files format and content: Counts file is a tab-delimited file of reads in peaks across samples in sparse matrix format. Row names for peaks can be pulled from .bed peak file (that is also provided with the scATAC-seq data).

source_name: Mouse bone marrow

growth_protocol: Immortalization of murine BM cells with HoxB8-ER was done as previously described with the following modifications. Filtered BM cells were layered over Ficoll-Plaque-Plus (GE Healthcare Biosciences), and centrifuged at 400 x g for 25 min at RT without break to enrich for mononuclear cells. Cells were incubated in a 6-well tissue culture plate for 48 hours at 37C with 5% CO2 prior to the retroviral transduction in RPMI (RPMI-1640, Corning) with 10% 2 mM L-glutamine, and 100U penicillin/streptomycin (all from Thermo Fisher), supplemented with 20 ng/ml stem cell factor (SCF), 10 ng/ml interleukin-3 (IL-3), and 10 ng/ml interleukin-6 (IL-6). Non-adherent cells were harvested and 500,000 cells were plated onto a 12-well tissue culture plate (Corning) coated with 10 mg/ml human fibronectin (Sigma). 1 ml of ecotropic retrovirus encoding MSCVneo-HA-ER-Hoxb8 was applied in the presence of 8 mg/ml polybrene and spinoculation was performed at 1000 x g for 60 min at RT. After transduction cells were maintained in RPMI supplemented with 0.5 uM beta-estradiol (Sigma, E2758) and conditioned media containing approximately 100 ng/ml SCF for the generation of neutrophil-biased cells or GM-CSF 10 ng/ml (Peprotech) for the generation of macrophage progenitors. Antibiotic selection was performed by adding G418 at 1 mg/ml final concentration until untransduced control cells were not viable (usually ~7 days). After selection, cells were FACS sorted into 96 well plates with culture media for the generation of single cell clones. For generation of Tet2 KO lines, each clone was transduced with integrase-defective lentiviral vector encoding for Cre recombinase or GFP as control at a Multiplicity of Infection (MOI) of 200.

extract_protocol:
Cells were washed twice with 1x PBS, counted, and resuspended to a concentration of 0.5 x 10^6 cells/mL.
2 μL of cells in 1x PBS (1,000 cells) were mixed with 2 μL of barcoded Tn5, 5 μL 2x Illumina Tagment DNA Buffer (TD), 0.1 μL 10% NP40 (final concentration 0.1%) and 0.9 μL H2O in a 96 well plate. Each well contained a different sample and Tn5 barcode. Cells were mixed and agitated on a ThermoMixer (Eppendorf) for 30 min at 37C. All the wells were pooled together on ice to prevent cross-contamination between Tn5 barcodes. Tagmented DNA was purified using a MinElute PCR Purification Kit (Qiagen), then minimally amplified for sequencing as previously described. Final libraries were purified using the MinElute PCR Purification Kit (Qiagen), and sequenced on a NextSeq 550 (150 cycles), using the following parameters: Read 1 92 cycles, i7 index read 8 cycles, and Read 2 66 cycles, 50% of PhiX Sequencing Control. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad).

value: Mouse bone marrow

tag: clone

value: SCF

value: Tet2 KO


title: 29_SCF_Control

value: Control


title: RDY234 cells, control, repA

value: minus IAA, minus 4tU


title: BMDM Nfkbid-WT 6.0h R2

value: 6.0h Lipid A


title: BMDM Nfkbid-WT 1.0h R2

value: 1.0h Lipid A


title: BMDM Nfkbid-WT 0.5h R2

value: 0.5h Lipid A


title: BMDM Nfkbiz-/- 0.0h R1

value: Nfkbiz-/-


title: BMDM Nfkbid-WT 2.0h R2


title: 22Rv1_RNA_ENZ3w_DMSO_EtOH_rep1

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

value: 3 weeks


title: 28_SCF_Tet2


title: BMDM Nfkbid-WT 0.0h R2

value: Wild type


title: BMDM Nfkbid-/- 6.0h R2


title: 28_SCF_Control


title: 27_SCF_Tet2


title: 22Rv1_RNA_ENZ3w_DMSO_Dex_rep1

value: dexamethasone, 100 nM


title: 22Rv1_RNA_A485_EtOH_rep1


title: BMDM Nfkbid-/- 0.0h R2

value: Nfkbid-/-


title: 27_SCF_Control


title: BMDM Nfkbid-WT 2.0h R1


title: BMDM Nfkbid-/- 0.5h R2


title: BMDM Nfkbid-WT 6.0h R1


title: 22Rv1_RNA_DMSO_Dex_rep1


title: 26_SCF_Tet2


title: BMDM Nfkbid-WT 0.5h R1


title: 22Rv1_RNA_A485_Dex_rep2


title: BMDM Nfkbid-WT 0.0h R1

value: Unstimulated


title: 26_SCF_Control


title: 22Rv1_RNA_DMSO_EtOH_rep2


title: BMDM Nfkbid-/- 6.0h R1


title: BMDM Nfkbid-/- 2.0h R1

value: 2.0h Lipid A


title: BMDM Nfkbid-WT 1.0h R1

value: BMDM


title: 22Rv1_RNA_A485_Dex_rep1


title: 25_SCF_Tet2

value: Mouse bone marrow


title: BMDM Nfkbid-/- 2.0h R2


title: 25_SCF_Control

value: SCF


title: BMDM Nfkbid-/- 1.0h R1


title: 22Rv1_RNA_A485_EtOH_rep2


title: BMDM Nfkbid-/- 0.0h R1


title: 24_SCF_Tet2

value: Tet2 KO


title: BMDM Bcl3-WT 2.0h R2


title: 22Rv1_RNA_DMSO_Dex_rep2


title: 22Rv1_input_A485_rep1


title: BMDM Bcl3-WT 6.0h R2


title: BMDM Bcl3-WT 1.0h R2


title: 22Rv1_GR_ENZ3w_A485_Dex_rep2

value: GR (Cell Signaling, 12041)


title: 23_SCF_Tet2


title: BMDM Bcl3-WT 0.0h R2


title: BMDM Bcl3-WT 0.5h R2


title: BMDM Nfkbid-/- 1.0h R2


title: BMDM Bcl3-/- 2.0h R2


title: 22Rv1_RNA_DMSO_EtOH_rep1


title: BMDM Bcl3-/- 6.0h R2


title: 22_SCF_Tet2

value: GMCSF


title: 23_SCF_Control

value: Control


title: 22Rv1_GR_ENZ3w_DMSO_Dex_rep2


title: BMDM Bcl3-/- 1.0h R2

value: 1.0h Lipid A


title: BMDM Bcl3-WT 6.0h R1

value: 6.0h Lipid A


title: 22Rv1_input_ENZ3w_A485_rep2


title: BMDM Bcl3-/- 0.0h R2


title: BMDM Bcl3-/- 0.5h R2

value: 0.5h Lipid A


title: BMDM Nfkbid-/- 0.5h R1


title: 22_SCF_Control


title: BMDM Bcl3-WT 2.0h R1


title: 22Rv1_GR_A485_Dex_rep2

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line


title: 24_SCF_Control


title: 22Rv1_GR_ENZ3w_A485_Dex_rep1

value: 3 weeks


title: BMDM Bcl3-WT 1.0h R1

value: Wild type


title: 22Rv1_GR_A485_Dex_rep1

value: dexamethasone, 100 nM


title: 21_SCF_Tet2


title: 21_SCF_Control


title: 22Rv1_GR_ENZ3w_DMSO_Dex_rep1


title: BMDM Bcl3-WT 0.0h R1


title: BMDM Bcl3-WT 0.5h R1


title: BMDM Bcl3-/- 6.0h R1


title: 22Rv1_GR_DMSO_Dex_rep1


title: 20_SCF_Tet2


title: 22Rv1_GR_DMSO_Dex_rep2


title: BMDM Bcl3-/- 2.0h R1


title: BMDM Bcl3-/- 0.5h R1


title: BMDM Bcl3-/- 0.0h R1


title: BMDM Bcl3-/- 1.0h R1


title: 22Rv1_ATAC_ENZ3w_A485_Dex_rep2


title: Oxa_9_02143AAC_TTGGCA

city: Barcelona

first: Genís

last: Camprecios

state: Catalonia

address: Rosselló 153

department: Hepatic Hemodynamics

country: Spain

institute: IDIBAPS

data_processing:
Sequence reads were quality-checked with FASTQC and trimmed for adaptor sequence/low-quality sequence using trim-galore
Trimmed reads were mapped to human genome Rnor_release92 using STAR-2.7.9a
Read count quantification was performed with featureCounts from subRead 2.0.3
Assembly: Rnor_release92
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Rattus norvegicus

extract_protocol:
Trizol and further purification with Qiagen Rneasy Mini kit with DNAseI on-column digestion
TruSeq stranded mRNA Library Prep (Illumina)

value: Liver

value: Sprague Dawley

value: Selfox


title: 19_GMCSF_Tet2


title: Oxa_7_02141AAC_TAAGAT


title: 20_SCF_Control


title: 22Rv1_ATAC_ENZ3w_A485_Dex_rep1


title: Oxa_6_02140AAC_CCGGTT


title: 18_SCF_Tet2


title: 22Rv1_ATAC_ENZ3w_A485_EtOH_rep2


title: 19_GMCSF_Control


title: Oxa_4_02138AAC_ATCTTG


title: 18_SCF_Control


title: Oxa_3_02137AAC_TGGCGG


title: Oxa_5_02139AAC_GCTCCA


title: Oxa_8_02142AAC_ACTTAC


title: 22Rv1_ATAC_ENZ3w_A485_EtOH_rep1


title: 22Rv1_ATAC_ENZ3w_DMSO_Dex_rep2


title: 17_SCF_Tet2


title: 22Rv1_ATAC_ENZ3w_DMSO_Dex_rep1


title: Oxa_10_02144AAC_GACCGT


title: Oxa_1_02135AAC_CGTTGG


title: 17_SCF_Control


title: Oxa_2_02136AAC_TTCTGG


title: LPS_6_02150AAC_ATAATT

value: LPS


title: LPS_5_02149AAC_TAAGAA


title: LPS_4_02148AAC_AATCCG


title: 16_SCF_Tet2

value: Mouse bone marrow


title: 22Rv1_ATAC_ENZ3w_DMSO_EtOH_rep1


title: 16_SCF_Control

value: SCF


title: LPS_3_02147AAC_AGGCCA


title: LPS_7_02151AAC_AACTTA


title: 22Rv1_ATAC_A485_Dex_rep2


title: 15_SCF_Tet2

value: Tet2 KO


title: LPS_1_02145AAC_CCGTTG


title: CT55_02157AAC_GGAGCC

value: None -Control


title: 22Rv1_ATAC_A485_Dex_rep1


title: 14_SCF_Tet2


title: CT46_02154AAC_GCCATT


title: CT52_02156AAC_GTCAAC


title: CT41_02153AAC_CCTAAC


title: 15_SCF_Control


title: CT49_02155AAC_CAGGAC


title: LPS_2_02146AAC_GCAACT


title: 14_SCF_Control


title: 22Rv1_ATAC_ENZ3w_DMSO_EtOH_rep2


title: CT40_02152AAC_CGTAGA


title: 22Rv1_ATAC_A485_EtOH_rep1


title: 22Rv1_ATAC_A485_EtOH_rep2


title: BMDM Nfkbiz-/- 0.0h R2

value: BMDM

value: Nfkbiz-/-

value: Unstimulated


title: 13_SCF_Tet2


title: 22Rv1_ATAC_DMSO_Dex_rep2


title: Lung biopsy, primary tumor site, for molecular profiling NGS

city: Irving

first: Phoenix

last: Holmes

state: Texas

address: 750 W John Carpenter Fwy Suite 800

institute: Caris Life Sciences

data_processing:
Trim adaptors and filter out low quality reads from fastq.gz files.
Call Salmon (v0.12.0) quant command to quantify gene expression based on trimmed fastq files. Then Salmon output file quant.sf is converted to isoform level Transcripts Per Kilobase Million(TPM)
Use BBMap to do dedup, then repeat above step to get TPM from deduped fastq files.
Reference Transcriptome is the Homo_sapiens.GRCh37.67 from ensemble.org.
Assembly: hg19
Supplementary files format and content: .csv file containing TPM data

source_name: Lung biopsy, Rt lower lobe

extract_protocol:
Qiagen RNEasy extract protocol from Nuclear Fast Red stained tissue
Custom cDNA Conversion Module - SureSelect Strand-Specific RNA Library Preparation Kit for Illumina

value: Lung biopsy, Rt lower lobe

value: carcinoma with choriocarcinoma features


title: 22Rv1_ATAC_DMSO_Dex_rep1

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line


title: 12_SCF_Tet2


title: 22Rv1_ATAC_DMSO_EtOH_rep1


title: BT549, siCtrl, rep2

city: Guangzhou

first: jiahui

last: zhang

state: Guangdong

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

data_processing:
Sequencing raw reads were preprocessed by filtering out ribosomal RNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Hisat2 (v.2.0.4) was used to map the cleaned reads to the human GRCh37 reference genome with two mismatches.
After genome mapping, StringTie (v.1.3.0) was run with a reference annotation to generate fragments per kilobase of transcript per million mapped reads (FPKM) for known gene models
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

growth_protocol: HS578T and BT549 were maintained in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from cell lines by using Trizol reagent
RNA libraries were prepared using KAPA Stranded RNA-Seq Library Prep Kit according to the manufacturer's protocol.

treatment_protocol: Cells were transfected with POU4F1 siRNA or control siRNA.

value: Basal-like breast cancer cell line

value: WT


title: BT549, siPOU4F1-1 rep1

value: POU4F1 knockdown


title: BT549, siCtrl, rep1


title: HS578T, siPOU4F1-2 rep2


title: BT549, siPOU4F1-1 rep2


title: 12_SCF_Control

value: Control


title: HS578T, siPOU4F1-2 rep1