title: S9CC47_R18_3h_in

city: Stanford

first: Sahin

last: Naqvi

state: CA California

address: 265 Campus Drive, Lokey Stem Cell Research Building/SIM1

institute: Stanford University

data_processing:
Truseq adapter sequences and low-quality bases (-Q 10) were trimmed from sequencing reads using skewer v0.2.2 and aligned to the human genome (hg38) using bowtie2 v2.4.1 with the following settings: --very-sensitive, --X 2000. Read mate pair information was corrected with samtools v1.10 fixmate, PCR duplicates were removed using samtools markdup, and mitochondrial reads and low mapping quality reads (-q 20) were removed using samtools view.  bigWig files for visualization were generated using deeptools v3.5.0 bamCoverage with the following settings: -bs 10 --normalizeUsing RPGC --samFlagInclude 64 --samFlagExclude 8 --extendReads.
Reads were counted over reproducible ATAC peak regions using bedtools
Assembly: hg38
Supplementary files format and content: V5, TWIST1, or TFAP2A ChIP-Seq read counts over reproducible ATAC peak regions
Supplementary files format and content: V5 ChIP-Seq bigWig coverage files

source_name: H9 hESC

growth_protocol: hESCs were differentiated to cranial neural crest cells (CNCCs) using a protocol described previously (Bajpai et al., 2010; Prescott et al., 2015). Briefly, hESCs were grown for 5-6 days until large colonies formed, then were disaggregated using collagenase IV and gentle pipetting. Clumps of ~200 hESCs were washed in PBS and transferred to a 10cm Petri dish in neural crest differentiation media (NDM). NDM: 1:1 ratio of DMEM-F12 and Neurobasal, 0.5x Gem21 NeuroPlex Supplement With Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF (PeproTech, 100-18B), 20ng/ml EGF (PeproTech, AF-100-15) and 5ug/ml bovine insulin (Gemini Bio-Products, 700-112P). After 7-8 days, neural crest emerged from neural spheres attached to the Petri dish, and after 11 days, neural crest cells were passaged onto fibronectin-coated 6-well plates (~1m cells/well) using accutase and fed with neural crest maintenance media (NMM). NMM: 1:1 ratio of DMEM-F12 and neurobasal, 0.5x Gem21 NeuroPlex Supplement with Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF, 20ng/ml bFGF EGF and 1mg/ml BSA (Gemini). After 2-3 days, neural crest cells were plated at ~1m cells/well of a 6-well plate and the following day cells were fed with neural crest long-term media. Long term media: neural crest maintenance media + 50pg/ml BMP2 (PeproTech, 120-02) + 3uM CHIR-99021 (Selleck Chemicals, S2924) (BCh media). After transition to BCh media, CNCCs at subsequent passages were plated at ~800,000 cells/well of a 6-well plate. CNCCs were then passaged twice to passage 4 where depletion experiments were performed

extract_protocol:
One fully confluent 10 cm plate of cells was cross-linked per ChIP experiment in 10 mL PBS with 1% methanol-free formaldehyde for 10 min and quenched with a final concentration of 0.125M glycine for 5 min with nutation. Cross-linked cells were scraped into tubes with 0.001% Triton X in PBS, washed with PBS without Triton, pelleted by centrifugation, flash-frozen in liquid nitrogen and stored at −80°C. Samples were defrosted on ice and resuspended in 5mL LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, with 1X cOmplete Protease Inhibitor Cocktail and PMSF) and rotated vertically for 10 min at 4°C. Samples were centrifuged for 5 min at 1350 x g at 4°C, and resuspended in 5mL LB2 (10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, with 1X cOmplete Protease Inhibitor Cocktail and optionally 1mM PMSF) and rotated vertically for 10 min at 4°C. Samples were centrifuged for 5 min at 1350 x g at 4°C, resuspended in 300 uL LB3 per sonicated sample, and incubated for 10 min on ice. Samples were sonicated in 1.5 mL Bioruptor Plus TPX microtubes (Diagenode, c30010010-50) on Bioruptor Plus for 10 cycles of 30sec ON/30sec OFF. Every 5 cycles, samples were lightly vortex and briefly centrifuged. Samples were diluted in additional LB3 to 1 mL, pelleted at 16,000 RCF for 10 min, and the supernatant was removed. Triton X-100 was added to 1%.
To check DNA size distribution and quantity, a 10 uL aliquot of sonicated chromatin from each sample was diluted to 100 uL in Elution Buffer (50 mM Tris, 10 mM EDTA, 1% SDS) with 0.0125 M NaCl and 0.2 mg/mL RNase A and incubated at 65C for 1 hour, followed by addition of Proteinase K to 0.2 mg/mL and an additional 1 hour of 65C incubation. DNA was purified using Zymo DNA Clean & Concentrator Kit with ChIP DNA Binding Buffer (Zymo, D5201-1-50) and size distribution and quantity was assessed by separation on a 1% agarose gel and Qubit HS DNA kit, respectively. Qubit measurements were used to normalize samples to the same DNA concentration.
Following normalization, the chromatin was divided for input (2%) and ChIP samples. A minimum of 25 ug DNA was used for histone ChIPs, and 50 ug for V5 ChIPs. 5 μg anti-H3K27ac (Active Motif, 39133) antibody or 10 μg anti-V5 (Abcam, ab9116 or ab15828), TWIST1 (Abcam, ab50887), or TFAP2A (Cell Signaling Technology, C83E10) antibody was added per ChIP sample, and incubated overnight at 4°C. Protein G Dynabeads (ThermoFisher) were first blocked with Block solution (0.5% BSA (w/v) in 1X PBS) and then added to cleared chromatin to bind antibody-bound chromatin for a 4-6 hour incubation. Chromatin-bound Dynabeads were washed at least 6 times with chilled RIPA wash buffer (50 mM HEPES-KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate), followed by a wash with chilled TE + 50 mM NaCl. Chromatin was eluted for 30 min in Elution Buffer (50 mM Tris, 10 mM EDTA, 1% SDS) at 65°C with frequent vortexing. The ChIP and input samples were then incubated at 65°C overnight to reverse cross-links (12-16 hours). Samples were diluted and sequentially digested with RNase A (0.2 mg/mL) for 2 hours at 37°C followed by Proteinase K (0.2 mg/mL) for 2 hours at 55°C for 2-4 hours to digest protein. ChIP and input samples were purified by Zymo DNA Clean & Concentrator Kit with ChIP DNA Binding Buffer.
Samples were quantified by Qubit dsDNA HS assay kit, and 10-50ng of ChIP DNA was used for library preparation with end repair, A-tailing, and adaptor ligation (NEB). Following USER enzyme treatment, libraries were cleaned up with one round of single-side AMPure XP bead clean-up, then amplified to add indices using NEBNext Ultra II Q5 Master Mix and NEBNext Multiplex Oligos for Illumina kit (NEB, E7335S) with 4-6 cycles (as determined by input amounts from NEB protocol). ChIP libraries were purified by two rounds of double-sided AMPure XP bead clean-up (0.5x then 0.4x initial sample volume of beads added) to remove large fragments and deplete adaptors. Library concentration and quality within ChIP or input groups was assessed by Qubit dsDNA HS assay kit and separation on a PAGE gel, and used to pool within ChIP or input groups. KAPA qPCR was used to pool across ChIP or input groups. Pooled libraries were sequenced using Novaseq 6000 platform (2x 150bp).

treatment_protocol: dTAGV-1 (Tocris, 6914) at a range of concentrations was added to BCh media, with an equivalent amount of DMSO as vehicle control, for the indicated times.

tag: differentiation batch

value: H9 hESC

value: hESC-derived P4 cranial neural crest cells (CNCCs)

tag: genotype

tag: treatment concentration (m)

tag: treatment time

tag: relative sox9 level

tag: antibody

value: input


title: SL03_052_KO_S

status: Public on Oct 23 2022

type: SRA

city: Morgantown

first: Christina

middle: M

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

country: USA

institute: DHHS/PHS/CDC/NIOSH

library_source: transcriptomic

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed for adaptor sequence low-quality using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:adapters/TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MENLEN:60
Sequences were mapped  to mm10 whole genome using Hisat2/2.1.0 with the following parameters: -q --downstream-transcriptome-assembly --dta-cufflinks --fr --no-mixed --time --non-deterministic --met-file
Aligned sequences were identified, sorted, and counted using Samtools/1.8 and HTSeq/0.11.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimted text file including raw counts in a matrix containing all samples

molecule: total RNA

organism: Mus musculus

growth_protocol: This study was conducted in an AAALAC approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the Institutional Animal Care and Use Committee. Heterozygous 129S-Slc26a4tm1Erg/AjgJ mice (Stock no: 018424) were purchased from the Jackson Laboratory (Bar Harbor, ME) and bred in our animal facility (NIOSH, Morgantown, WV). Progeny were genotyped to identify homozygous wildtype (Pds+/+), homozygous knockout (Pds-/-), and heterozygous (Pds+/-) mice. Approximately 3 months old male Pds+/+ and Pds‑/- were used in the study. Throughout the period of the study, the mice were housed in groups of < 5 mice/cage and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to 7913 NIH-31 diet (Envigo, Indianapolis, IN) and filtered tap water.

extract_protocol:
Total RNA, including miRNA and other small RNA molecules, was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc.; Valencia, CA) following the procedure provided by the manufacturer, including optional DNase treatment with RNase-Free DNase (Qiagen, Inc.; Valencia, CA).
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq® Stranded Total RNA Library Prep  (Illumina, Inc., San Diego, CA) following the  manufacturer's protocol.  Briefly, following depletion of  ribosomal RNA (rRNA), the RNA samples were purified, fragmented (68°C for 5 minutes), and primed for cDNA synthesis.  The denatured and cleaved RNA fragments were purified using a bead cleanup and reverse transcribed into first strand cDNA using reverse transcriptase and random primers.  While synthesizing the double stranded cDNA, dUPT was incorporated in place of dTTP followed by the addition of a single ‘A’ nucleotide to the 3 prime ends to facilitate proper adapter ligation to each sample. Indexing adapters provided in the library preparation kit were ligated to the ends of the ds cDNA.  After adapter ligation, the samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).

treatment_protocol: Exposures were performed in a whole-body inhalation chamber. There were 4 different exposure groups: wildtype mice exposed to air; wildtype mice exposed to silica (15mg/m3, 6hours/day, 4days Min-U-Sil5 silica); knockout mice exposed to air; knockout mice exposed to silica (15mg/m3, 6hours/day, 4days Min-U-Sil5 silica). There were 3 different post-exposure time points at which point the mice were euthanized and samples collected: 01 day, 03 months, and 09 months following exposure to air or silica.

tag: strain background

tag: slc26a4 genotype

value: homozygous knockout

tag: treatment

value: silica

tag: post-exposure timepoint

value: 03 months

tag: tissue

value: lung

tag: molecule type

value: total RNA including small RNAs


title: SL03_050_KO_S


title: SL03_049_KO_S


title: Metoprolol_3

city: Guangzhou

first: Jing

last: Tan

address: No.74 Zhongshan Rd II

department: Department of Biochemistry, Zhongshan Medical School

country: China

institute: Sun Yat-sen University

data_processing:
We used internal software SOAPnuke to filter reads, followed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read). After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format (see FASTQ Format in help page FASTQ Format).
We used HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step. For HISAT which is much faster, sensitive and high accuracy analysis software.
We mapped clean reads to reference using Bowtie2, v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: AllSamples.GeneExpression.FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: heart apex

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. We used Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value, 28S/18S and the fragment length distribution.
1) mRNA enrichment: Oligo dT Selection or rRNA depletion; 2) RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer; 3) End repair, add A tailing and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments; 4) PCR amplification: The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; 5) Denature and cyclization: Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase; 6) Sequencing on BGISEQ-500 platform.

treatment_protocol: 1-day-old neonatal mice that underwent apical resection were injected subcutaneously with anti-arrhythmic drugs (amiodarone, metoprolol, propranolol, lidocaine, ivabradine) or isoproterenol for seven consecutive days.

tag: age

value: post natal day 7

tag: strain

value: ICR

value: apical resection and metoprolol treatment

value: heart apex


title: SL03_038_KO_A

source_name: homozygous knockout_air_3 months_lung

value: air


title: S9CC47_R18_3h_V5

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: V5 (Abcam ab15828)


title: SL03_039_KO_A


title: Metoprolol_2


title: Metoprolol_1


title: SL03_036_KO_A


title: SL03_035_KO_A


title: SL03_034_KO_A


title: SL03_033_KO_A


title: S9CC47_R18_0h_V5


title: S9C13_R21_5nM_in


title: SL03_024_WT_S

value: homozygous wildtype


title: Amiodarone_2

value: apical resection and amiodarone treatment


title: SL03_023_WT_S


title: Amiodarone_3


title: SL03_021_WT_S


title: S9C13_R21_5nM_T1

value: TWIST1 (Abcam, ab50887)


title: Amiodarone_1


title: SL03_020_WT_S


title: S9C13_R21_5nM_AP

value: H9 hESC

value: TFAP2A (Cell Signaling Technology, C83E10)


title: SL03_022_WT_S


title: S9CC47_R18_0h_in

value: hESC-derived P4 cranial neural crest cells (CNCCs)

value: input


title: SL03_019_WT_S

value: silica


title: S9C13_R21_500nM_in


title: Isoprel_2

value: apical resection and isoproterenol treatment


title: S9C13_R21_500nM_T1


title: SL03_011_WT_A

source_name: homozygous wildtype_air_3 months_lung

value: 03 months

value: lung


title: SL03_010_WT_A

value: total RNA including small RNAs


title: SL03_012_WT_A


title: NS_3

value: post natal day 7

value: ICR

value: apical resection


title: Isoprel_1

value: heart apex


title: SL03_009_WT_A

value: air


title: SL03_008_WT_A

value: homozygous wildtype


title: SL03_007_WT_A


title: NS_2


title: Isoprel_3


title: SL00_213_KO_S

source_name: homozygous knockout_silica_1 day_lung

value: homozygous knockout

value: 01 day


title: SL00_214_KO_S


title: SL00_211_KO_S


title: SL00_212_KO_S


title: S9C13_R21_500nM_AP

value: H9 hESC


title: S9C13_R21_1p6nM_AP

value: TFAP2A (Cell Signaling Technology, C83E10)


title: S9C13_R21_1p6nM_T1

value: hESC-derived P4 cranial neural crest cells (CNCCs)

value: TWIST1 (Abcam, ab50887)


title: SL00_209_KO_S

value: silica


title: Double-KO rep3

city: Montpellier

first: Daniel

last: Fisher

address: 1919 Route de Mende

department: IGMM

country: France

institute: CNRS

data_processing:
Base calling was performed with ZebraCallV2 software  FastQC was used to perform quality control of the sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p6 genome using STAR_2.6.0c with default parameters.
Counts of the reads per genes were calculated in the mapping step with the STAR software using the The Ensembl mouse genome annotations (release 93).
Differential expression analysis were performed using an Ad hoc
Supplementary_files_format_and_content: Raw counts of reads per gene

source_name: intestinal organoids

growth_protocol: Mouse intestine epithelium and organoid sample preparation.  For intestine epithelium samples, a fragment of intestine was cut and flushed with PBS. It was incubated for 5-10 minutes in EDTA-containing buffer (500ml RPMI, 20mM Hepes, 1% Penicillin/Streptomycin (Sigma P4333), 12.5μg/ml DTT, 2mM EDTA pH 7.4 and 10% FBS) to allow easy detachment of the intestine epithelium. The intestinal tube was opened longitudinally and put over a horizontal plate to allow scrapping of the epithelial cells by trawling two needles in opposite directions over the tissue. Cells were recovered from the plate by wetting them with a small volume (200μl) of PBS. They were put into an Eppendorf tube where they were spun down to remove most of the PBS. Pellets were snap frozen and conserved at -80°C.

extract_protocol:
After 7 days of treatment with 600nM 4-Hydroxytamoxifen, organoids were lysed and RNA was extracted following the Trizol RNA isolation protocol (W.M. Keck Foundation Biotechnology Microarryay Resource Laboratory at Yale University) until the end of the phase-separation step. Total RNA cleanup with DNase digestion was performed by addition of 1.5 volumes of absolute ethanol on top of the aqueous phase obtained after the phase-separation and following the Qiagen RNeasy protocol (W.M. Keck Foundation Biotechnology Microarryay Resource Laboratory at Yale University). RNA integrity was analysed on Agilent 2100 bioanalyzer.
All conditions were prepared as biological triplicates and sent to BGI Tech Solutions (HongKong)- Co for library preparation and RNA sequencing. Purification of mRNA from total RNA was achieved using oligo(dT)-attached magnetic beads and then fragmented for random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis.

value: intestinal organoids

value: CDK8-/- and CDK19-/-


title: Double-KO rep2


title: S9C13_R21_0nM_in

value: input


title: S9C13_R21_0nM_T1


title: SL00_197_KO_A

source_name: homozygous knockout_air_1 day_lung

value: lung

value: total RNA including small RNAs


title: SL00_195_KO_A


title: SL00_196_KO_A


title: S9C13_R21_1p6nM_in


title: S9C13_R21_0nM_AP


title: S9C13_R18_5nM_in


title: CDK19-KO rep3


title: CDK19-KO rep2


title: Double-KO rep1


title: SL00_194_KO_A


title: SL00_184_WT_S

source_name: homozygous wildtype_silica_1 day_lung


title: SL00_183_WT_S


title: SL00_193_KO_A


title: CDK19-KO rep1


title: NS_1

value: post natal day 7

value: ICR


title: SL00_182_WT_S


title: SL00_180_WT_S


title: SL00_181_WT_S


title: S9C13_R18_5nM_AP


title: TCRs of GP33-specific CD8 T cells in LCMV-Clone13-infected mice at D28 p.i. [D28 LCMV Cl13 GP33 scTCR-seq]

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

library_source: transcriptomic single cell

data_processing:
processed with CellRanger 3.1 using the mm10 mouse genome indices from 10x Genomics
Assembly: mm10
Supplementary files format and content: CellRanger 3.1 output

source_name: spleen

extract_protocol:
Sorted GP33-specific CD8 T cells were processed according to 10X Genomics protocol guidelines to obtain single-cell cDNA libraries
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6 mice infected with 2x106 PFU/mouse of LCMV-Clone 13 28 days prior to euthanasia

value: spleen

value: T lymphocyte

value: 28 days post intra-peritoneal infection with LCMV-Clone13


title: SL00_210_KO_S

value: homozygous knockout


title: SL00_179_WT_S

value: homozygous wildtype

value: 01 day


title: CDK8-KO rep3


title: SL00_198_KO_A

value: air


title: SL00_172_WT_A

source_name: homozygous wildtype_air_1 day_lung


title: S9C13_R18_500nM_T1

value: H9 hESC

value: hESC-derived P4 cranial neural crest cells (CNCCs)


title: CDK8-KO rep2


title: S9C13_R18_5nM_T1

value: TWIST1 (Abcam, ab50887)


title: DH2

city: Xuzhou

first: Wei

last: Tang

address: Kunpeng Road num 78

institute: Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: PRJNA301667
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Ipomoea batatas

source_name: leaves and tuberous roots

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

value: leaves and tuberous roots

value: drought and heat


title: DH3


title: SL00_169_WT_A


title: SL00_171_WT_A


title: CDK8-KO rep1

value: intestinal organoids


title: DH1


title: DR3

value: drought


title: S9C13_R18_500nM_AP

value: TFAP2A (Cell Signaling Technology, C83E10)


title: S9C13_R18_500nM_in

value: input


title: WT rep1

value: wild type


title: S9C13_R18_1p6nM_in


title: S9C13_R18_1p6nM_AP


title: VentralMeso_St13_rep3

city: Evanston

first: Carole

last: LaBonne

address: 2205 Tech Dr

department: Molecular Biosciences

data_processing:
Read quality evaluated with FastQC
Mapped to X. laevis v9.2 genome downloaded from xenbase using STAR2.6.0
Assembly: X. laevis v9.2
Supplementary files format and content: single csv file of read count for all genes in each sample

organism: Xenopus laevis

source_name: animal cap

growth_protocol: population of animal caps were dissected at stage 8.5 and collected at respective stages

extract_protocol:
Animal caps were flash frozen in trizol. RNA was harvested using Trizol reagent extraction from Xenopus animal caps. 1ug total RNA was used for construction of sequencing libraries
Illumina TruSeq mRNA-Seq Library Prep Kit- standard protocols

treatment_protocol: see characteristic:treatment in Samples section above

value: 20 ng/uL BMP4/7

tag: developmental stage

tag: lineage

value: Ventral Mesoderm


title: SL00_168_WT_A

value: lung

value: total RNA including small RNAs


title: WT rep3

tag: genotype


title: VentralMeso_St13_rep2


title: DR1


title: SL00_167_WT_A

value: homozygous wildtype


title: S9C13_R18_0nM_in

tag: differentiation batch

tag: treatment concentration (m)


title: VentralMeso_St13_rep1


title: NK cells, Glutor, long-term, BC77 [A18-BC77-long-Glutor_S18]

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

country: Germany

institute: University Hospital Essen

data_processing:
Reads were processed with standard Illumina Basecalling
Trimmed with TrimGalore v0.6.0 and standard settings
Alignment was performed with hisat2 v2.2.1 to grch38 and standard settings
Raw counts were summed up with summarizeOverlaps from R-Package GenomicAlignments v1.8.4
Assembly: hg38
Supplementary files format and content: Csv file contains raw counts of sequencing reads

source_name: blood

growth_protocol: Human NK cells were isolated from PBMC from healthy donors with the Dynabeads® UntouchedTM Human NK Cell-Kit according to the manufacturer's instructions (Invitrogen). Isolated NK cells were seeded in 96-well round-bottom plates (Nunc) at a density of 1 – 1.5*Mio/ mL -1 with 30 Gy irradiated feeder cells (K562-mbIL15-41BBL) in medium at a ratio of 2:1 (NK cells:feeder cells) with 200 U/mL IL-2 and 100 ng/mL IL-21 and incubated at 37°C humidified 5% CO2. On day 8, NK cells were re-stimulated with fresh feeder cells at a ratio of 2:1 (NK cells:feeder cells). In the next weeks, NK cells were counted every 72h. If cell count was below 3xMio /ml a medium exchange was performed, if cell count was 3xMio /ml or higher cells were split to a density of 1.5 – 2 *Mio/ mL -1 supplemented with 100 U/mL IL-2. On day 14 recombinant 2.5 ng/mL IL-15 was added and  NK cells were analyzed on day 21 of culture.

extract_protocol:
RNA was isolated using Rneasy mini plus kit (Qiagen)
QuantSeq 3’ mRNA-Seq Library Prep Kit FWD

treatment_protocol: For long-term treatment with 100 nM Glutor, 100nM Glupin or 0.1% DMSO these substances were added to the culture at day zero and to the fresh medium added to the culture every 72. On day 21, cells were used for RNA isolation.

value: blood

tag: origin

value: buffy coat

value: primary human CD3-CD56+  NK cells

tag: time

value: 21 days

value: 100 nM Glutor


title: SL00_170_WT_A

tag: strain background

value: air

value: 01 day


title: HT2

value: leaves and tuberous roots

value: heat


title: HT3


title: WT rep2

value: intestinal organoids


title: S9C13_R18_0nM_AP

value: H9 hESC

value: hESC-derived P4 cranial neural crest cells (CNCCs)

tag: treatment time

tag: relative sox9 level

tag: antibody

value: TFAP2A (Cell Signaling Technology, C83E10)


title: DR2

tag: tissue

tag: treatment

value: drought


title: NK cells, DMSO, long term, BC77 [A16-BC77-long-DMSO_S16]

value: 0.1% DMSO


title: VentralMeso_St12_rep3

value: 20 ng/uL BMP4/7

value: Ventral Mesoderm


title: S9C13_R18_1p6nM_T1

value: TWIST1 (Abcam, ab50887)


title: VentralMeso_St12_rep2


title: HT1


title: NK cells, Glutor, long-term, BC74 [A15-BC74-long-Glutor_S15]

value: blood

value: buffy coat


title: C13R21_5nM_in

value: input


title: CK3


title: C13R21_5nM_V5

value: V5 (Abcam ab15828)


title: VentralMeso_St12_rep1


title: NK cells, Glupin, long term, BC74 [A14-BC74-long-Glupin_S14]

value: primary human CD3-CD56+  NK cells

value: 21 days

value: 100 nM Glupin


title: C13R21_500nM_in


title: CK2

value: leaves and tuberous roots


title: S9C13_R18_0nM_T1


title: NK cells, DMSO, long term, BC74 [A13-BC74-long-DMSO_S13]


title: NK cells, Glupin, long term, BC77 [A17-BC77-long-Glupin_S17]


title: NK cells, Glutor, long-term, BC72 [A12-BC72-long-Glutor_S12]

value: 100 nM Glutor


title: VentralMeso_St11_rep4


title: VentralMeso_St11_rep3


title: NK cells, Glupin, long term, BC72 [A11-BC72-long-Glupin_S11]


title: C13R21_1p6nM_in

value: H9 hESC


title: C13R21_0nM_in

value: hESC-derived P4 cranial neural crest cells (CNCCs)


title: VentralMeso_St11_rep2


title: SnxB 24h rep3

description: rRNA-depleted total RNA

data_processing:
Base calling was performed with ZebraCallV2 software  FastQC was used to perform quality control of the sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p6 genome using STAR_2.6.0c with default parameters.
Counts of the reads per genes were calculated in the mapping step with the STAR software using the The Ensembl mouse genome annotations (release 93).
Differential expression analysis were performed using an Ad hoc
Supplementary files format and content: Raw counts of reads per gene

value: intestine

tag: agent

value: Senexin B

tag: time point


title: VentralMeso_St11_rep1


title: SnxB 24h rep1

description: rRNA-depleted total RNA


title: SnxB 24h rep2

description: rRNA-depleted total RNA


title: VentralMeso_St10.5_rep3


title: NK cells, DMSO, long term, BC72 [A10-BC72-long-DMSO_S10]

value: 0.1% DMSO


title: NK cells, Glutor, long-term, BC67 [A9-BC67-long-Glutor_S9]


title: NK cells, Glupin, long term, BC67 [A8-BC67-long-Glupin_S8]


title: VentralMeso_St11_rep5

value: 20 ng/uL BMP4/7


title: C13R21_0nM_V5

tag: cell line


title: SnxB 16h rep3

description: rRNA-depleted total RNA


title: VentralMeso_St10.5_rep2

value: Ventral Mesoderm


title: VentralMeso_St10.5_rep1


title: SnxB 16h rep1

description: rRNA-depleted total RNA


title: C13R18_5nM_V5

tag: cell type


title: SnxB 16h rep2

description: rRNA-depleted total RNA


title: CK1


title: VentralMeso_St10_rep3

tag: developmental stage


title: C13R18_500nM_in


title: NK cells, Glupin, long term, BC66 [A5-BC66-long-Glupin_S5]


title: DMSO 24h rep2

description: rRNA-depleted total RNA

value: DMSO


title: NK cells, DMSO, long term, BC66 [A4-BC66-long-DMSO_S4]

value: blood


title: C13R18_500nM_V5


title: C13R18_1p6nM_in


title: DMSO 24h rep1

description: rRNA-depleted total RNA


title: VentralMeso_St10_rep1

tag: lineage


title: VentralMeso_St9_rep3


title: DMSO 16h rep3

description: rRNA-depleted total RNA


title: NK cells, Glutor, long-term, BC60 [A3-BC60-long-Glutor_S3]

value: buffy coat


title: DMSO 24h rep3

description: rRNA-depleted total RNA


title: VentralMeso_St10_rep2


title: VentralMeso_St9_rep2


title: NK cells, Glupin, long term, BC60 [A2-BC60-long-Glupin_S2]


title: VentralMeso_st9_rep1


title: DMSO 16h rep2

description: rRNA-depleted total RNA


title: C13R18_0nM_in

tag: genotype

value: input


title: NK cells, DMSO, long term, BC60 [A1-BC60-long-DMSO_S1]


title: C13R18_0nM_V5

tag: differentiation batch

value: V5 (Abcam ab15828)


title: DMSO 16h rep1

description: rRNA-depleted total RNA


title: control2, input

status: Public on Oct 22 2022

city: Shanghai

first: Jinhong

address: Yishan road 600,Xuhui district,Shanghai

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

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 hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-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
Assembly: 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.
Supplementary files format and content: hg38
Supplementary files format and content: Methylated_RNA_sites
Library strategy: MeRIP-seq

organism: Mus

source_name: liver

extract_protocol: input samples and m6A immunoprecipitated RNA samples were used to build up the RNA sequencing library following manufacturer’s instructions of NEBNext ® Ultra II Directional RNA Library Prep Kit

value: liver

tag: diet

value: HFD


title: control3, input


title: C13R18_1p6nM_V5

tag: treatment concentration (m)


title: treat2, input


title: control1, input


title: treat3, input


title: treat1, input


title: treat3

value: N6-methyladenosine (m6A)


title: control2


title: control3


title: tarsal joint_levofloxacin [Hindpaws_SpA.DBA1.Levo vs SpA.DBA1.control]

type: RNA

city: Chihuahua

first: Susana

middle: Aideé

last: González-Chávez

state: Chihuahua

address: Circuito Universitario Campus II

department: Facultad de Medicina

country: Mexico

institute: Universidad Autónoma de Chihuahua

description: RNA equimolar pools from six mice in each group were made.

hyb_protocol: Hybridization was performed using the M22K_01 (UNAM, Mexico City, Mexico) chip containing 23,232 genes from the mouse genome

scan_protocol: The scan and acquisition of the signal were developed using the ScanArray 4000 (Packard BioChips Technologies, Billerica, Massachusetts, USA).

data_processing: The analysis of the microarray scanning was done using GenArise Microarray Analysis Tool software (UNAM), and the lists of differentially expressed genes (DEGs) (Z-score ≥ 1.5 SD) were obtained

source_name: Tarsal joint, spontaneous arthritis, no levofloxacin, control

label_protocol: Reverse transcription-polymerase chain reaction (RT-PCR) was performed, and the resulting complementary DNA (cDNA) from SpA.DBA/1.Levo group was labeled with Cy5, while the cDNA from the SpA.DBA/1.control group was labeled with Cy3

growth_protocol: Mice with SpA, no treated

extract_protocol: Total RNA was purified using the RNeasy® Mini Kit (Qiagen, Hilden, Germany) extraction kit, following the manufacturer’s protocol

treatment_protocol: No treated

tag: strain

tag: gender

value: male

tag: arthritis model

value: spontaneous arthritis

value: Tarsal joint

source_name: Tarsal joint, spontaneous arthritis, levofloxacin

treatment_protocol: Levofloxacin


title: spine_levofloxacin [Spine_SpA.DBA1.Levo vs SpA.DBA1.control]

source_name: Spine, spontaneous arthritis, no levofloxacin, control

value: Spine

source_name: Spine, spontaneous arthritis, levofloxacin


title: treat1


title: Gut_levofloxacin [Gut_SpA.DBA1.Levo vs SpA.DBA1.control]

source_name: Gut, spontaneous arthritis, no levofloxacin, control

value: Gut

source_name: Gut, spontaneous arthritis, levofloxacin


title: control1


title: treat2


title: UoCB6_input

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

institute: University of Michigan Medical School

data_processing:
Paired-end reads were aligned to hg38 using BWA-ALN (v 0.7.17).
Bam files were filtered (samtools view) to retain only paired reads in a proper pair (flags: 0x1, 0x2), and to remove reads flagged as secondary alignments, not passing quality control, PCR or optical duplicates, and supplementary alignments (flags: 0x100, 0x200, 0x400, 0x800).
Reads were filtered to retain only read-pairs mapping to <=2 sites genome-wide (X0 tag <=2 for both reads).
Display files were generated with deeptools bamCoverage (options: "--binSize 25 --normalizeUsing CPM --extendReads")
Genome_build: hg38
Supplementary_files_format_and_content: bigwig (hg38 fragment coverage, normalized to fragments per million post-filtering)

source_name: UoCB6 cell line

growth_protocol: All cell lines were cultured in RPMI 1640 + Glutamax supplemented with 10% fetal calf serum, penicillin/streptomycin, nonessential amino acids, 1 mM sodium pyruvate, and 55 micromolar 2-mercaptoethanol

extract_protocol:
Five to twenty million cells were cross-linked in PBS + 1% formaldehyde for 10 minutes at room temperature (histone marks) or 37C (TFs), quenched with 1/20th volume of 2.5M glycine, washed twice in cold PBS with protease inhibitors, and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted at 3000g, and resuspended in cold SDS lysis buffer (0.3% SDS for H3K27ac and 1% SDS for TFs, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes. Nuclei were fragmented on a Q800R2 Sonifier (QSonica) as follows: three cycles of amplitude = 50, pulse times: 30s on / 30s off, total on time = 3:20 m, temperature = 80C (histone marks) or two cycles of amplitude = 70, pulse times: 45s on / 15s off, total on time = 8:50 m, temperature = 40C (TFs). Samples were diluted 1:3 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4°C overnight with 2-5 ug of antibody. Antibody-chromatin complexes were captured with protein G–conjugated beads, washed, and eluted. After reversal of cross-linking, RNase and proteinase K treatment were performed and DNA was purified with Ampure XP beads for library preparation. Input sample was prepared by the same approach without immunoprecipitation.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated (Quick T4 DNA ligase, NEB) to barcoded illumina adaptors (Single-Indexed Adapter Kit, KAPA, #KK8700). Each reaction was followed by clean-up with AMPure XP beads. Ligation products were amplified by PCR for 14-18 cycles with illumina indexing primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection.

treatment_protocol: DoxOn vector-transduced Reh cell populations were induced with 500 ng/ml doxycycline (dox) for 48 hours prior to harvest for H3K27ac or V5 ChIP-Seq

value: B-lymphoblastic leukemia cell line

tag: transgene

tag: drug treatment

tag: chip-seq antibody


title: SUDHL6_input

source_name: SUDHL6 cell line

value: Diffuse large B-cell lymphoma cell line


title: SUDHL4_input

source_name: SUDHL4 cell line


title: SUPB15_input

source_name: SUPB15 cell line


title: Reh_input

source_name: Reh cell line

value: Reh


title: SEM_input

source_name: SEM cell line

value: SEM


title: SUPB13_input

source_name: SUPB13 cell line


title: Pfeiffer_input

source_name: Pfeiffer cell line

value: Pfeiffer


title: RS411_input

source_name: RS411 cell line


title: KOPN8_input

source_name: KOPN8 cell line


title: NALM6_input

source_name: NALM6 cell line


title: OCILy3_input

source_name: OCILy3 cell line


title: AT2_input

source_name: AT2 cell line


title: MUTZ5_input

source_name: MUTZ5 cell line


title: MHHCALL3_input

source_name: MHHCALL3 cell line


title: SUPB15_H3K27ac

value: H3K27ac (Active Motif Cat #39133)


title: SUDHL6_H3K27ac


title: SUPB13_H3K27ac


title: SP49_H3K27ac

description: Reanalysis of GSM2571828

source_name: SP49 cell line

value: Mantle cell lymphoma cell line


title: SEM_H3K27ac


title: SUDHL4_H3K27ac


title: RS411_H3K27ac


title: C13R21_1p6nM_V5

source_name: H9 hESC

value: H9 hESC

value: hESC-derived P4 cranial neural crest cells (CNCCs)

tag: treatment

tag: treatment time

tag: relative sox9 level

tag: antibody


title: Pfeiffer_H3K27ac

tag: cell line

tag: cell type


title: Reh_H3K27ac


title: REH_ETV6R399C_r2_H3K27ac

source_name: REH cell line

value: doxycycline


title: REH_tBFP_r2_H3K27ac


title: REH_ETV6R399C_r1_H3K27ac


title: REH_ETV6WT_r2_H3K27ac


title: REH_ETV6WT_r1_H3K27ac


title: UoCB6_H3K27ac

source_name: UoCB6 cell line


title: embryos,ancestors exposed in high sugar diet,H3K9me3_2

city: hangzhou

first: JIE

last: YANG

state: ZheJiang

address: Yuhangtang Road No.388,Zhejiang Province, Zijingang Campus of Zhejiang University, nano building 560 room

department: science life institute

institute: ZheJiang Univeristy

data_processing:
Raw reads were cleaned using trim_galore. The reads were then aligned to the dm6 genome assembly using STAR v2.5.3a with the options “--alignIntronMax 1 --alignEndsType EndToEnd” as previously reporte.
The parameter “--outFilterMultimapNmax 1” was applied to include only the uniquely mapped reads.
Duplicate reads were then removed using MarkDuplicates from gatk package v.4.1.4.1. Replicate samples were merged using the samtools v1.10. For ChIP-seq, bigwig tracks were generate using bamCompare from deeptools 3.3.1 (parameters: --skipNAs --scaleFactorsMethod readCount --operation log2 --extendReads 200).
Negative values were set to zero. ChIP-seq profiles were created by computeMatrix and plotProfile in deeptools 3.3.1. IGV v.2.4.13 was used to visualize the bigwig tracks.
The difference peak of ChIP-seq data was found by using macs2 v2.2.6 with the options “bdgdiff”. The parameters is “--t1 --c1 --t2 --c2 --d1 --d2 --o-prefix” and others were default.
Assembly: using macs2 v2.2.6 and genomicRanges R package
Supplementary files format and content: Dm6

organism: Drosophila melanogaster

source_name: cycle 11 embryos

extract_protocol:
embryos were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor Pico (Diagenode).
ChIP-seq libraries were prepared  mRNA-Seq Sample Preparation Kit (Illumina) .

tag: tissue

value: cycle 11 embryos

value: W+VDRC

value: the flies' mother fed with high sugar diet  (contains 20percent sucrose)  from egg to adult


title: embryos,ancestors exposed in high sugar diet(H3K27me3,H3,H3K27ac,H3K9me2,H3K9me3)_2

tag: genotype

value: the flies' mother fed with normal food (contains 10percent sucrose) diet from egg to adult


title: AT1_input

source_name: AT1 cell line


title: embryos,ancestors exposed in high sugar diet(H3K27me3,H3,H3K27ac,H3K9me2,H3K9me3)_1


title: NALM6_H3K27ac


title: embryos,ancestors exposed in high sugar diet,H3_2


title: AT2_H3K27ac


title: MUTZ5_H3K27ac


title: embryos,ancestors exposed in high sugar diet,H3K27ac_2


title: embryos,ancestors exposed in high sugar diet,H3_1


title: C13R21_500nM_V5

tag: differentiation batch

value: V5 (Abcam ab15828)


title: AT1_H3K27ac


title: UoCB6_ETV6-ChIP-Seq

value: ETV6 (Santa Cruz, # sc-166835x)


title: KOPN8_H3K27ac


title: MHHCALL3_H3K27ac


title: embryos,ancestors exposed in high sugar diet,H3K9me3_1


title: SEM_ETV6-ChIP-Seq


title: embryos,control group,input(H3K27me3)_3


title: REH_tBFP_r1_H3K27ac


title: embryos,ancestors exposed in high sugar diet,H3K9me2_2


title: OCILy3_H3K27ac


title: embryos,ancestors exposed in high sugar diet,H3K9me2_1


title: embryos,ancestors exposed in high sugar diet,H3K27ac_1


title: Reh_ETV6-WT-V5_V5-ChIP-Seq

source_name: Reh cell line

value: V5 tag (ThermoFisher #R960-25)


title: HAL01_H3K27ac

source_name: HAL01 cell line

value: B-lymphoblastic leukemia cell line


title: embryos,ancestors exposed in high sugar diet,H3K27me3_1


title: embryos,control group,input(H3K27me3)_2


title: embryos,ancestors exposed in high sugar diet,H3K27me3_2


title: UoCB6_ERG-ChIP-Seq

value: ERG (Cell Signaling Technologies # 97249)


title: NALM6_ETV6-ChIP-Seq


title: embryos,control group,input(H3,H3K27ac,H3K9me2,H3K9me3)_1


title: SUPB13_ATAC-Seq

source_name: SUPB13 cell line

extract_protocol:
Nuclei were isolated from 50,000 cells for each sample using Nuclei EZ prep-Nuclei Isolation Kit (Sigma-Aldrich, USA). The transposition reaction mix (25μl of 2X TD buffer, 2.5μl of Tn5 transposase (Illumina, San Diego, CA, USA), 15ul of PBS and 7.5μl of nuclease free water) was added to nuclei and incubated at 37°C for 1hour in an orbital shaker at 300RPM. 50uL Qiagen buffer PB was added to each sample to stop the reaction and DNA was isolated with AMPure XP beads (Beckman Coulter).
15 cycles of PCR were performed with transposed DNA using the dual index primers and NEBNext PCR Master Mix, followed by AMPure XP purification.


title: embryos,control group,H3K9me3_1


title: embryos,control group,H3_1


title: embryos,control group,H3_2


title: UoCB6_ATAC-Seq


title: SUPB15_ATAC-Seq

source_name: SUPB15 cell line


title: embryos,control group,H3K27ac_2


title: embryos,control group,H3K9me2_2


title: SUDHL6_ATAC-Seq

source_name: SUDHL6 cell line

value: Diffuse large B-cell lymphoma cell line


title: SEM_ATAC-Seq

source_name: SEM cell line

value: SEM


title: SUDHL4_ATAC-Seq

source_name: SUDHL4 cell line


title: embryos,control group,H3K27ac_1


title: RS411_ATAC-Seq

source_name: RS411 cell line


title: Control mice rep4

city: Durham

last: Yang

state: NC

address: 303 Research Drive

department: Anesthesiology

institute: Duke University Medical Center

data_processing:
the FastQC tool was used followed by use of the Trimmomatic tool to clip away adaptor sequence that might be present (TruSeq3-PE.fa:2:30:10) and to remove both 5' nucleotide bias (HEADCROP:12) and low quality sequence (TRAILING:20, SLIDINGWINDOW:4:20, MINLEN:15).
Surviving read pairs per library were then mapped against the current instance of the mouse genome (GRCm38) using the "RNA-Seq" tool supported within the CLCbio Genomics Workbench (https://www.qiagenbioinformatics.com/) under default parameters.
Expression per known gene (GRCm38.83.gtf) was enumerated in TPM (Transcript Per Million) units. This expression was then imported into R and pedestalled by 2, Log2 transformed, filtered to remove genes not having at least one transformed value >1, and quantile normalized
For surviving genes, the Welch-modified t-test was applied under Benjamini-Hochberg false discovery rate multiple comparison correction condition to identify those having dysregulated expression between XBP1s-TG and control
Genome_build: GRCm38v68 version of the mouse genome
Supplementary_files_format_and_content: Excel file with normalized expression values.

source_name: hippocampus

extract_protocol:
Hippocampus were removed and snap frozen in liquid nitrogen. RNA was prepared using Trizol reagent (Invitrogen), treated with DNase, and purified with RNA Cleanup kit (Qiagen). The KAPA Stranded mRNA-Seq Kit (KapaBioSystems) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

tag: age

value: 2-month old

value: Control


title: embryos,control group,H3K9me3_2


title: Reh_ATAC-Seq

value: Reh


title: embryos,control group,H3K27me3_2


title: REC1_ATAC-Seq

source_name: REC1 cell line

value: Mantle cell lymphoma cell line


title: MUTZ5_ERG-ChIP-Seq

source_name: MUTZ5 cell line


title: embryos,control group,H3K27me3_1


title: OCILy7_ATAC-Seq

source_name: OCILy7 cell line


title: Control mice rep3


title: Control mice rep2


title: OCILy3_ATAC-Seq

source_name: OCILy3 cell line


title: Control mice rep1


title: OCILy1_ATAC-Seq

source_name: OCILy1 cell line


title: NK cells, Glutor, long-term, BC66 [A6-BC66-long-Glutor_S6]

source_name: blood

value: blood

tag: origin

value: buffy coat

value: primary human CD3-CD56+  NK cells

tag: time

value: 21 days

value: 100 nM Glutor


title: embryos,control group,H3K9me2_1

source_name: cycle 11 embryos

value: cycle 11 embryos

value: W+VDRC

value: the flies' mother fed with normal food (contains 10percent sucrose) diet from egg to adult


title: XBP1s-TG rep4

tag: strain


title: SP49_ATAC-Seq

source_name: SP49 cell line


title: C13R18_5nM_in

source_name: H9 hESC

value: H9 hESC

value: hESC-derived P4 cranial neural crest cells (CNCCs)

tag: treatment concentration (m)

value: input


title: XBP1s-TG rep3


title: NK cells, DMSO, long term, BC67 [A7-BC67-long-DMSO_S7]

value: 0.1% DMSO


title: MUTZ5_ATAC-Seq

value: B-lymphoblastic leukemia cell line

tag: transgene


title: XBP1s-TG rep2

value: hippocampus

value: 2-month old


title: Karpas422_ATAC-Seq

source_name: Karpas422 cell line

value: Diffuse large B-cell lymphoma cell line

tag: drug treatment


title: HAL01_ATAC-Seq

source_name: HAL01 cell line


title: NALM6_ATAC-Seq

source_name: NALM6 cell line


title: MHHCALL3_ATAC-Seq

source_name: MHHCALL3 cell line


title: Mino_ATAC-Seq

source_name: Mino cell line

value: Mino

value: Mantle cell lymphoma cell line


title: Pfeiffer_ATAC-Seq

source_name: Pfeiffer cell line

value: Pfeiffer


title: KOPN8_ATAC-Seq

source_name: KOPN8 cell line


title: Granta519_ATAC-Seq

source_name: Granta519 cell line


title: XBP1s-TG rep1

source_name: hippocampus


title: DoHH2_ATAC-Seq

source_name: DoHH2 cell line


title: JeKo1_ATAC-Seq

source_name: JeKo1 cell line


title: Reh_tBFP_r3_RNA-Seq

data_processing:
RNA-Seq quantification was performed with Salmon 0.11.3. A salmon index (-k 31) was generated from Ensembl release 75 transcripts.
Transcript-level expression was then quantified (salmon quant -l --incompatPrior --validateMappings) from paired-end RNA-Seq data.
Genome_build: hg38 / ENSEMBL 2014
Supplementary_files_format_and_content: Salmon transcript quantification files

source_name: Reh cell line

extract_protocol:
RNA was isolated via RNEasy columns with on-column DNAase digestion.
RNA-seq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina per manufacturer’s instructions

treatment_protocol: DoxOn vector-transduced Reh cell populations were induced with 500 ng/ml doxycycline (dox) for 48 hours prior to harvest for RNA-Seq

value: Reh

value: doxycycline


title: Reh_tBFP_r2_RNA-Seq


title: Reh_ETV6-WT-V5_r3_RNA-Seq


title: Reh_tBFP_r1_RNA-Seq


title: 414C2_d14_Total_cells

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

data_processing:
Cell-specific FASTQ files were generated by deconvolution of UMIs and cell barcodes using bcl2fastq 2.20.0.422 (Illumina)
Alignment to the human reference genome GRCh38 and UMI counting were conducted by Cell Ranger v3.1.0 pipeline (10×Genomics)
Genome_build: GRCh38-3.0.0 (downloaded from 10x Genomics)
Supplementary_files_format_and_content: tsv and mtx files were generated using Cell Ranger v3.1.0.

source_name: bone-lineage cells

growth_protocol: For the induction of 3D osteocytogenesis from iPS cells, we performed the bone-like nodules induction method (6×10^5 iPS cells were seeded) on pig type I collagen gel (Cellmatrix, Nitta gelatin) in a 12well plate.

extract_protocol:
cDNA was synsthesized directly from cells.
Dissociated cells were resuspended in PBS containing 1% BSA, immediately followed by a library preparation targeting single cells using the Chromium Single Cell 3’ Reagent Kit v3 (10×Genomics) and Chromium Controller (10×Genomics) according to the manufacturer’s instructions.

treatment_protocol: Whole cells：The induced cells with collagen gel were treated with 0.1% collagenase (Nitta gelatin) for 20 min at 37 °C with shaking and treated with TrypLE (Thermo) for 5 min at 37 °C with pipetting. Inside cells：The induced cells with collagen gel were treated with TrypLE for 5 min at 37 °C and removed the supernatant cells. The remained collagen gel with induced cells were treated with 0.1% collagenase for 20 min at 37 °C with shaking and pipetting.

value: human iPS cell-derived bone-lineage cells

tag: group

value: Whole cells


title: Mjan nucleoid Log8U MNase

city: Cardiff

first: Nicholas

middle: Anthony

last: Kent

address: Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

description: chromatin/nucleoid

data_processing:
Paired reads were trimmed to the 5’ 25 bases and aligned to an index created from NCBI RefSeq chromosome (NC_000909.1) using Bowtie v1.2.2  with command line flags: -v 2 --trim3 75 --maxins 1000 --fr -k 1 --sam.
SAM file data was sorted using SAMTools 1.9
Assembly: NCBI RefSeq chromosome NC_000909.1
Supplementary files format and content: Aligned read pairs were sorted according to “chromatin particle size” classes based on paired read end-to-end distance value +/- 10% starting at 30bp and incrementing in 15bp steps to capture variable histone dimer MNase protections of 30bp each. Frequency distributions of the mid-point positions between read pairs were calculated to define “chromatin particle positions” and lightly smoothed by taking a 3-bin moving average. Process was performed using SAM2PartN_sgr_full.plx and then reformatted from .sgr to .bedGraph. Code available at https://github.com/chromatin-kent/chromatin_tools
Supplementary files format and content: Processed data files describe data encompassing the most common MNase protected species (hypernucleosomes/slinkies/curly-fries)  in M. jannaschii which range from 90bp to 450bp in 30bp (histone dimer size) intervals. File names are in the form: chra_b_PartN_Sample_cbp_NC.bedGraph where: a=1 denotes data from the main Mjan chromosome (NC_000909.1); b=12 is a unique Kent lab identifier; N is the “chromatin particle size”/paired-read end-to-end distance (e.g. Part270 means that this file plots the frequency distribution of sequence read mid point positions from MNase-protected species of 270bp in length corresponding to hypernucleosomes consisting of 9 x 30bp-binding histone dimers); Sample describes the input type as in this metadata); c = 5 denotes that the frequency distribution is binned to 5bp chromosomal intervals; NC denotes that the chromosome ID string in the .bedGraph Column 0 is the Refseq NC_ designation (useful to know when you display in IGB or IGV). We recommend that you display this data in IGB using a reference GCF file such as  GCF_000091665.1_ASM9166v1_genomic.gff

organism: Methanocaldococcus jannaschii

source_name: clonal cell culture

growth_protocol: M. jannaschii DSM 2661 cells were grown in 100 l fermenters in minimal medium containing 0.3 mM K2HPO4, 0.4 mM KH2PO4, 3.6 mM KCl, 0.4 M NaCl, 10 mM NaHCO3, 2.5 mM CaCl2, 38 mM MgCl2, 22 mM NH4Cl, 31 µM Fe(NH4)2(SO4)2, 1 mM C6H9NO6, 1.2 µM MgSO4, 0.4 mM CuSO4, 0.3 µM MnSO4, 36 nM FeSO4, 36 nM CoSO4, 3.5 nM ZnSO4, 4 nM KAl(SO4)2, 16 nM H3BO3, 42 µM Na2SeO4, 0.3 nM Na2WO4, 11 µM NaMoO4, 44 µM (NH4)2Ni(SO4)2 and 2 mM Na2S supplied with H2:CO2 gas in a 4:1 ratio at 85 °C

extract_protocol:
0.2 g wet cells (wet weight) were resuspended in 5 ml PBS supplemented with EDTA-free protease inhibitor cocktail (Thermo Fisher) and centrifuged at 1,500 x g for 10 min at 4C to remove larger sulphide precipitates. These steps were repeated for a total of five washes. The final supernatant was then centrifuged at 14,000 x g for 10 min at 4C. The cell pellet was resuspended in 1.25 ml extraction buffer (25 mM HEPES pH 7.0, 15 mM MgCl2, 100 mM NaCl, 0.4 M sorbitol, 0.5% Triton X-100) supplemented with protease inhibitor and incubated at 4C for 30 min. Subsequently, 100 µl aliquots were centrifuged at 14,000 x g for 15 min at 4C and the supernatant was removed. The chromatin pellets were resuspended in 50 µl extraction buffer with protease inhibitor and subjected to MNase digestion. For the naked genomic DNA control, DNA was extracted from the resuspended chromatin pellets using the DNeasy blood and tissue kit (Qiagen) according to manufacturer’s bacteria protocol. 50 µl resuspended chromatin or 6 µg genomic DNA was digested with the indicated amounts of MNase (Thermo Fisher) in 100 µl MNase buffer (20 mM Tris-HCl pH 7.4, 25 mM NaCl, 5 mM CaCl2) at 37C for 30 min before the addition of 10 µl stop solution (2% SDS, 0.1 M EDTA, 0.1 M EGTA). DNA was purified using the QIAquick PCR purification kit (Qiagen) and eluted in 50 µl H2O.
MNase-seq adapter libraries were prepared using NEBNext reagents (New England Biolabs) according to manufacturer’s instructions, except that libraries were size selected on polyacrylamide gels to preserve the full size distribution of MNase digested fragments. DNA was sequenced in 100 nucleotide paired-end mode on an Illumina HiSeq 2000 using v3 TruSeq SBS reagents

value: clonal cell culture

value: Log phase

value: WT

tag: treatment

value: MNase digest 8 units/ml


title: Mjan gDNA MNase

description: genomic DNA

value: MNase digest


title: 414C2_d14_cells_in_gel

value: Cells migrated into gel matrix


title: Reh_ETV6-WT-V5_r2_RNA-Seq

value: B-lymphoblastic leukemia cell line


title: WS+HL+HS-Cleo biol rep3

city: Vila-real

first: Damián

last: Balfagón Sanmartín

state: Castellón

address: C/Polo Bernabé, Nº40, piso 3 puerta 7

country: Spain

institute: Universitat Jaume I

data_processing:
Paired-ends sequenced reads obtained from the Novaseq 6000 system were quality tested using FastQC v0.11.7 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), trimmed reads were mapped to reference genome with HISAT2 v2.1.0  (Kim, Langmead & Salzberg 2015) and transcript was assembled by StringTie v2.1.3b (Pertea et al. 2015, 2016) with aligned reads. Citrus sinensis (GCF_000317415.1_Csi_valencia_1.0) obtained from NCBI genome database (https://www.ncbi.nlm.nih.gov/genome) was used as genome of reference.
Assembly: GCF_000317415.1_Csi_valencia_1.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Citrus sinensis

source_name: Leaf

extract_protocol:
RNA extraction and purification was performed using Maxwell® 16 LEV plant RNA Purification Kit protocol and automated Maxwell® 16 MDx Instrument.
mRNA libraries were prepared using the Illumina TruSeq Stranded mRNA HT Library Prep Kit (Illumina, https://www.illumina.com/)

value: Leaf

value: Cleopatra mandarin (Citrus reshni Hort. Ex Tan.)

value: Water stress, high light and heat stress combiantion


title: Reh_ERG-ChIP-Seq

tag: chip-seq antibody

value: ERG (Cell Signaling Technologies # 97249)


title: WS+HS-Cleo biol rep3

value: Water stress and heat stress combination


title: WS+HL+HS-Cleo biol rep2


title: Reh_ETV6-R399C-V5_r3_RNA-Seq


title: WS+HS-Cleo biol rep2


title: Reh_ETV6-R399C-V5_r2_RNA-Seq


title: Reh_ETV6-WT-V5_r1_RNA-Seq


title: WS+HL+HS-Cleo biol rep1


title: Reh_ETV6-R399C-V5_r1_RNA-Seq


title: WS+HL-Cleo biol rep3

value: Water stress and high light combination


title: WS+HL-Cleo biol rep1


title: AT1_ATAC-Seq

source_name: AT1 cell line


title: IL-1α/TNFα/C1q, replicate 1

first: Chang

last: Liu

address: 1954 Hua Shan Road

department: School of Biomedical Engineering

institute: Shanghai Jiao Tong University

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China).
The genome-wide transcriptomic analysis was performed on a set of 4 separate experiments.
Differential expression analysis was identified using the DESeq (2012) R package functions estimate Size Factors and nbinom Test.
p value < 0.05 and fold change > 2 or fold change < 0.5 was set as the threshold for significantly differential expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Brain

extract_protocol:
Untreated astrocytes and Cocktail treated astrocytes were harvested, and total RNA was isolated using TRIzol (Invitrogen). RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Brain

value: Astrocytes


title: IL-1α/TNFα/C1q, replicate 2


title: IL-1α/TNFα/C1q, replicate 4


title: IL-1α/TNFα/C1q, replicate 3


title: AT2_ATAC-Seq

source_name: AT2 cell line


title: HL+HS-Cleo biol rep3

value: High light and heat stress combiantion


title: HL+HS-Cleo biol rep2


title: HL+HS-Cleo biol rep1


title: HS-Cleo biol rep3

value: Heat stress


title: No treatment, replicate 1

value: No treatment


title: No treatment, replicate 2


title: Mjan nucleiod Log3U MNase

description: chromatin/nucleoid

value: clonal cell culture

value: Log phase

value: MNase digest 3 units/ml


title: No treatment, replicate 4

value: WT


title: HL-Cleo biol rep3

value: High light


title: HS-Cleo biol rep1


title: KPCM 5

city: Omaha

first: Surinder

middle: K

last: Batra

address: 42 and Emile

institute: UNMC

data_processing:
RNA sequencing was be perform on RNA extracted from age-matched KPC and KPCM pancreatic tissues. The alignment was performed using HISAT2 using GRCm38 mouse genome index. The read assignment and normalization was done using featureCounts and DESeq2 R package respectively. The code used for these analysis is accessible on GitHub (rchirravurivenkata/KPCM-KPC-MUC16-KO-and-KPC-).
Assembly: GRCm38

source_name: Pancreas

growth_protocol: Role of MUC16 in the PDAC progression, tumor microenvironment, and metastasis in cooperation with KrasG12D and Trp53R172H mutations

extract_protocol:
mirVana™ miRNA Isolation Kit was used to isolate RNA. RNA quality was checked with an Agilent Bioanalyzer (Agilent Technologies, Inc.) and all of the RINs (RNA integrity numbers) were 10.
Library preparation was achieved using the Illumina TruSeq RNA Sample Preparation Kit

value: Pancreas

value: 25 weeks


title: KPCM 8


title: KPCM 6


title: HL-Cleo biol rep1

value: Leaf

value: Cleopatra mandarin (Citrus reshni Hort. Ex Tan.)


title: HL-Cleo biol rep2


title: KPCM 4


title: KPCM 9


title: WS-Cleo biol rep3

value: Water stress


title: WS-Cleo biol rep2


title: WS+HS-Cleo biol rep1

value: Water stress and heat stress combination


title: CT-Cleo biol rep 3

value: Control


title: HS-Cleo biol rep2


title: KPC 1


title: KPC 2


title: CT-Cleo biol rep 2


title: WS+HL-Cleo biol rep2

value: Water stress and high light combination


title: KPC 3


title: No treatment, replicate 3

value: Brain

value: Astrocytes


title: CT-Cleo biol rep 1


title: WS+HL+HS-Car biol rep1

value: Carrizo citrange (Poncirus trifoliata L. Raf. x Citrus sinensis L. Osb.)

value: Water stress, high light and heat stress combiantion


title: WS+HL+HS-Car biol rep3


title: WS-Cleo biol rep1


title: WS+HS-Car biol rep3


title: HD #48

city: Bethesda

first: Amanda

last: Henning

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
Illumina BaseSpace applications were used for data processing. Specifically, alignment and transcript quantification was performed using the RNA-Seq Alignment application (v2.0.2). This application utilizes the STAR aligner and Salmon for transcript quantification. These analyses were conducted using the default parameters.
Assembly: hg19
Supplementary files format and content: *.quant.sf is the transcript quantification output file from Salmon. There are plain-text, tab-separated files with a single header line.

source_name: Blood

extract_protocol:
B cells were isolated from frozen PBMC using the EasySep Human B cell Isolation kit (StemCell Tech), and RNA was isolated from B cells using the RNeasy Plus Micro kit (Qiagen).
Libraries were prepared using the TruSeq RNA Exome kit (Illumina) following manufacturer's protocol.

value: B cells

tag: diagnosis

value: Healthy Donor


title: HD #19


title: HD #44


title: HD #2


title: WS+HL+HS-Car biol rep2


title: WS+HS-Car biol rep2


title: WS+HS-Car biol rep1


title: HCV-BNHL #74

value: HCV-associated BNHL


title: HD #72


title: HCV-BNHL #30


title: HCV-BNHL #33


title: WS+HL-Car biol rep3


title: HD #67


title: HCV-BNHL #18


title: HCV-BNHL #4


title: HL+HS-Car biol rep3

value: High light and heat stress combiantion


title: WS+HL-Car biol rep2


title: HCV #73

value: HCV+


title: HL+HS-Car biol rep1


title: HL+HS-Car biol rep2


title: HCV #69


title: HCV #62


title: HS-Car biol rep3

value: Heat stress


title: HL-Car biol rep3

value: High light


title: HCV #46


title: HS-Car biol rep1

value: Leaf


title: HCV #42


title: BNHL #37

value: BNHL


title: HCV #41


title: HL-Car biol rep2


title: WS-Car biol rep2

value: Water stress


title: HCV-BNHL #14


title: HCV #43


title: WS+HL-Car biol rep1


title: WS-Car biol rep1


title: CT-Car biol rep 3


title: HCV #49


title: BNHL #32


title: CT-Car biol rep 1


title: HS-Car biol rep2


title: BNHL #10


title: HCV #47


title: BNHL #20


title: CT-Car biol rep 2


title: AN017_Day_18

city: Tabuk

first: Sael

last: Alatawi

address: Duba Road

country: Saudi Arabia

institute: University of Tabuk

data_processing:
The MAGeCK tool was used to determine sgRNAs that were significantly depleted at day 18 compared to day 0 representing those targeting genes that were essential for cell survival (hits)
Assembly: GeCKO v2
Supplementary files format and content: Comma-separated values file includes the raw count matrix values for each Sample

source_name: DLBCL

growth_protocol: Cell lines were established from single-cell suspensions of ATM-/-nu-/- lymphomas, cultured in RPMI containing 15% FCS, 1% pyruvate, 1% NEAA/β-mercaptoethanol (50uM) and 1% penicillin/streptomycin

extract_protocol:
Cells were cultured at optimal cell number to maintain ≥1000-fold coverage of the CRISPR sgRNA library. At day 0 and 18 (~14 doublings), DNA isolated from harvested viable cells was subjected to targeted deep sequencing of sgRNAs
Libraries were prepared using NextSeq HIGH 150 v2.5 kit  according to the manufacturer’s instructions.
NextSeq HIGH 150 v2.5 kit

value: DLBCL

value: B-cells

value: ATM -/-


title: BNHL #7


title: HL-Car biol rep1


title: AN017_Day_0


title: WS-Car biol rep3


title: BNHL #27


title: 50F2_Day_18


title: GCM1 KD1 EVT 3

city: London

first: Stephen

middle: J

last: Renaud

state: Ontario

address: 1151 Richmond Street

department: Anatomy and Cell Biology

country: Canada

institute: University of Western Ontario

data_processing:
Partek Flow was used for all analyses.
Sequenced reads were trimmed for adaptor sequences, masked for low-quality sequence,  then mapped to hg38 genome using STAR (2.7.3a).
Counts Per Million (CPM) + 1.0 were calculated using Partek Flow.
Genome_build: hg38 (release 102, ENSEMBL)
Supplementary_files_format_and_content: Matrix table with raw or nomalized gene counts for every gene and every sample.

source_name: Placenta

growth_protocol: Control or GCM1-deficient human trophoblasts were cultured in either cytotrophoblast or extarvillous trophoblast media.

extract_protocol:
RiboZol was used to extract RNA from cells. The aqueous layer was removed, diluted in 70% ethanol, placed on RNeasy columns, treated with DNase I, and RNA purified.
RNA libraries were prepared according to manufacturer's instructions using the NEBNEXT® Ultra™ Library Kit for Illumina®

treatment_protocol: Trophoblast stem cells were infected with lentivirus targeting GCM1 or a scrambled control. Cells were then cultured in cytotrophoblast or extravillous trophoblast media.

value: Placenta-derived trophoblasts

value: GCM1 knockdown extravillous trophoblast


title: GCM1 KD1 EVT 1


title: CTRL EVT 3

value: Wildtype extravillous trophoblast


title: GCM1 KD1 CT 3

value: GCM1 knockdown cytotrophoblast


title: CTRL EVT 1


title: CTRL EVT 2


title: 50F2_Day_0


title: GCM1 KD1 CT 2


title: GCM1 KD1 CT 1


title: GCM1 KD1 EVT 2


title: UAT-2019-F-1047

city: Barcelona

first: Alfonso

last: Parrilla

address: Paseo Vall Hebron (VHIR)

institute: Vall Hebron Research Institute (VHIR)

description: Xenograft SK-OV-3_EV_3

hyb_protocol: Standard Affymetrix protocol; Performed at UAT (VHIR)

data_processing:
Data was processed with Expression Console and Transcription Analysis Console (TAC)
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_S_Human
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: xenograft tumors generated with SK-OV-3 pIND_EV cells

label_protocol: Biotinylated

growth_protocol: Xenografts tumors grown in Nude Mice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (miRNeasy; Qiagen).

treatment_protocol: SK-OV-3 cells were implanted into Nude mice and developed tumors

tag: cell line source

value: Human Ovarian Cancer Cell Line

tag: cell line genotype/variation

value: pIND_EV (Empty vector)

tag: host strain

value: nude mouse

value: xenografts tumors


title: CTRL CT 2

tag: cell type

value: Wildtype cytotrophoblast


title: HAL01_input

source_name: HAL01 cell line

tag: cell line

value: B-lymphoblastic leukemia cell line


title: CTRL CT 1


title: UAT-2019-F-1048

description: Xenograft SK-OV-3_EV_4

scan_protocol: Standard Affymetrix protocol; Performed at UAT (VHIR)

tag: tissue


title: SEM_ERG-ChIP-Seq

source_name: SEM cell line

value: SEM

value: ERG (Cell Signaling Technologies # 97249)


title: 32542_slide4_D2

status: Public on Oct 21 2022

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: Probe-based spatial transcriptomics

hyb_protocol: Tissues were primed followed by overnight hybridization of all probes specific for the target genes. Samples were washed the next day to remove excess probes and fluorescently tagged in a two-step color development process.

scan_protocol: Samples were imaged on a Zeiss Celldiscoverer 7, using the 50x Plan Apochromat water immersion objective with an NA of 1.2 and the 0.5x magnification changer, resulting in a 25x final magnification. Standard CD7 LED excitation light source, filters, and dichroic mirrors were used together with customized emission filters optimized for detecting specific signals. Excitation time per image was 1000 ms for each channel (DAPI was 20 ms). A z-stack was taken at each region with a distance per z-slice according to the Nyquist-Shannon sampling theorem. The custom CD7 CMOS camera (Zeiss Axiocam Mono 712, 3.45 µm pixel size) was used.   For each region, a z-stack per fluorescent color (two colors) was imaged per imaging round. A total of 8 imaging rounds were done for each position, resulting in 16 z-stacks per region. The completely automated imaging process per round (including water immersion generation and precise relocation of regions to image in all three dimensions) was realized by a custom python script using the scripting API of the Zeiss ZEN software (Open application development).

data_processing: The algorithms for spot segmentation were written in Java and are based on the ImageJ library functionalities. Only the iterative closest point algorithm is written in C++ based on the libpointmatcher library (https://github.com/ethz-asl/libpointmatcher). As a first step all images were corrected for background fluorescence. A target value for the allowed number of maxima was determined based upon the area of the slice in µm² multiplied by the factor 0.5. This factor was empirically optimized. The brightest maxima per plane were determined, based upon an empirically optimized threshold.  The number and location of the respective maxima was stored. This procedure was done for every image slice independently. Maxima that did not have a neighboring maximum in an adjacent slice (called z-group) were excluded. The resulting maxima list was further filtered in an iterative loop by adjusting the allowed thresholds for (Babs-Bback) and (Bperi-Bback) to reach a feature target value (Babs: absolute brightness, Bback: local background, Bperi: background of periphery within 1 pixel). This feature target values were based upon the volume of the 3D-image. Only maxima still in a z-group of at least 2 after filtering were passing the filter step. Each z-group was counted as one hit. The members of the z-groups with the highest absolute brightness were used as features and written to a file. They resemble a 3D-point cloud. To align the raw data images from different imaging rounds, images had to be corrected. To do so the extracted feature point clouds were used to find the transformation matrices. For this purpose, an iterative closest point cloud algorithm was used to minimize the error between two point-clouds. The point clouds of each round were aligned to the point cloud of round one (reference point cloud). The corresponding point clouds were stored for downstream processes. Based upon the transformation matrices the corresponding images were processed by a rigid transformation using trilinear interpolation. The aligned images were used to create a profile for each pixel consisting of 16 values (16 images from two color channels in 8 imaging rounds). The pixel profiles were filtered for variance from zero normalized by total brightness of all pixels in the profile. Matched pixel profiles with the highest score were assigned as an ID to the pixel. Pixels with neighbors having the same ID were grouped. The pixel groups were filtered by group size, number of direct adjacent pixels in group, number of dimensions with size of two pixels. The local 3D-maxima of the groups were determined as potential final transcript locations. Maxima were filtered by number of maxima in the raw data images where a maximum was expected. Remaining maxima were further evaluated by the fit to the corresponding code. The remaining maxima were written to the results file and considered to resemble transcripts of the corresponding gene. The ratio of signals matching to codes used in the experiment and signals matching to codes not used in the experiment were used as estimation for specificity (false positives). Baysor  (v0.5.0) was used  for cell segmentation (Petukhov et al., 2021) that considered both transcript expression localization as well as DAPI images with a scale of 50 and standard deviation of 12.5%.

source_name: Liver

extract_protocol: Two biological replicates for each dose group were examined by placing 10 µm thick frozen liver sections in O.C.T compound (Sakura, Torrance, CA) in one of 8 designated custom slide regions.

treatment_protocol: Mice were orally gavaged with TCDD in sesame oil vehicle every 4 days for 28 days.

value: Charles Rivers Laboratories

tag: Sex

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Yes

tag: formula

tag: vendor

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: dose

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: 32542_slide4_C1

description: Probe-based spatial transcriptomics

tag: strain

value: Charles Rivers Laboratories

value: Male


title: 32542_slide4_B1

description: Probe-based spatial transcriptomics

value: day

value: degree celsius


title: 32542_slide4_A1

description: Probe-based spatial transcriptomics

value: percent

value: Innovive cage


title: UAT-2019-F-1044

description: Xenograft SK-OV-3_BORA_4

source_name: xenograft tumors generated with SK-OV-3 pIND_BORA cells

value: Human Ovarian Cancer Cell Line

value: pIND_BORA (BORA overexpressing vector)

value: nude mouse

value: xenografts tumors


title: 32542_slide4_B2

description: Probe-based spatial transcriptomics

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Yes

value: Accustandard


title: UAT-2019-F-1042

description: Xenograft SK-OV-3_BORA_2


title: UAT-2019-F-1046

description: Xenograft SK-OV-3_EV_2

value: pIND_EV (Empty vector)


title: 32542_slide5_D1_1

description: Probe-based spatial transcriptomics

value: Charles Rivers Laboratories

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: 32542_slide5_D1_2

description: Probe-based spatial transcriptomics

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage


title: 32542_slide5_D2

description: Probe-based spatial transcriptomics

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940


title: LOC1

city: San Miguel de Tucuman

first: Leonardo

last: Albarracin

address: Chacabuco 145

country: Argentina

institute: CERELA

description: Gene expression after 3 hours after the stimulation with the TLR4 agonist.

hyb_protocol: cRNA was synthesized.

scan_protocol: After scanning the slides using an Agilent microarray scanner, Dedicated software was used to quantify the fluorescent signal at each spot.

data_processing: Data normalization and expression analysis were performed with GeneSpring software version 13.1 (Agilent Technologies). Significant genes up and down regulated in test samples (those stimulated with LPS or L. plantarum plus LPS) with respect to control samples (without LPS stimulation) were identified. Genes with significant changes in transcript abundance were selected on the basis of two criteria: a t-test P value of less than 0.05, which was considered statistically significant, and a cutoff in transcript abundance of at least 2-fold. Statistical analysis was conducted with the Limma package from BioConductor in R software (version 3.2.5).Data normalization and expression analysis were performed with GeneSpring software version 13.1 (Agilent Technologies). Significant genes up and down regulated in test samples (those stimulated with LPS or L. plantarum plus LPS) with respect to control samples (without LPS stimulation) were identified. Genes with significant changes in transcript abundance were selected on the basis of two criteria: a t-test P value of less than 0.05, which was considered statistically significant, and a cutoff in transcript abundance of at least 2-fold. Statistical analysis was conducted with the Limma package from BioConductor in R software (version 3.2.5).

source_name: RAW macrophages

label_protocol: Label total RNA using Low Input Quick Amp Labeling Kit (Agilent) cRNA was synthesized.

extract_protocol: Total RNA was isolated from L. plnatarum-treated and control macrophages using RNeasy Mini Kit (Qiagen, Tokyo, Japan) and treated with DNase.

tag: cell

value: RAW macrophages

tag: treatment


title: LOC3


title: 32542_slide4_D1

description: Probe-based spatial transcriptomics

value: Harlan Teklad

value: Yes

value: Accustandard


title: 32542_slide5_A2

description: Probe-based spatial transcriptomics

value: Charles Rivers Laboratories

value: Room temperature

value: sesame oil


title: 32542_slide5_B1

description: Probe-based spatial transcriptomics

value: milliliter

value: oral gavage

value: microgram per kilogram


title: 32542_slide5_C1

description: Probe-based spatial transcriptomics

value: Male

value: day

value: Carbon dioxide euthanasia


title: 32542_slide5_B2

description: Probe-based spatial transcriptomics

value: degree celsius

value: percent

value: Innovive cage


title: mettl4-1_rep1

first: Wenhao

last: Xie

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

data_processing:
Raw RNA-seq paired-end reads were filtered to remove the adapters and reads length less than 20 bp and reads with low sequencing base quality score using Cutadapt (version 3.5) (Martin, 2011).The filter reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Hisat2 (version 2.2.1) (Kim et al., 2015). High mapping quality reads were obtained using SAMtools (version 1.13) (Li et al., 2009). The track files which fragments were normalized as fragments per bin(bin size = 10 bp) per million mapped fragments were obtained using bamCoverage tool in deepTools (version 3.5.1) (Ramirez et al., 2012) and viewed with IGV (version 2.11.2) (Thorvaldsdottir et al., 2013). FeatureCounts (version 2.0.1) was used to calculate the read number for each gene (Liao et al., 2014). DESeq2 (version 1.32.0) was used to identify differentially expressed genes (DEGs) (Love et al., 2014). Compared to the mutant and wild-type, genes that showed |log2foldchange| ≥ log2(1.5) and p value < 0.05 were considered to be DEGs. Gene ontology (GO) enrichment analysis was carried out with DAVID (Dennis et al., 2003) and ClusterProfiler(Yu et al., 2012). Different alternatively splicing genes between the mutant and the wild-type (threshold of |Δψ| > 0.1, pvalue < 0.05) were identified by rMATS (version 4.1.1) (Shen S, et al., 2014).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for each Sample.

organism: Arabidopsis thaliana

source_name: 14-day-old seddlings grown up under long-day condition (22°C and 16-h-light/10-h-dark)

growth_protocol: Plants were cultured on MS medium under long-day condition (22°C and 16-h-light/8-h-dark)  for 14 days.

extract_protocol:
Total RNA was extracted from seedlings using an RNAprep pure Plant Kit (Tiangen Biotech) under the guidance of manufacturer’s instructions.
Strand-specific RNA-seq library was constructed according to the KAPA stranded mRNA-seq Kit instructions(Illumina® Platforms, KR0960-v5.17; www.kapabiosystems.com).

value: seedling

tag: development stage

tag: genotype


title: UAT-2019-F-1043

description: Xenograft SK-OV-3_BORA_3

tag: cell line source

value: Human Ovarian Cancer Cell Line

tag: cell line genotype/variation

value: pIND_BORA (BORA overexpressing vector)

value: nude mouse

value: xenografts tumors


title: 32542_slide5_A1

description: Probe-based spatial transcriptomics

value: Charles Rivers Laboratories

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Yes

value: Accustandard


title: Col_rep2

source_name: 14-day-old seddlings grown up under long-day condition (22°C and 16-h-light/9-h-dark)

value: wild-type


title: UAT-2019-F-1041

description: Xenograft SK-OV-3_BORA_1

tag: cell type

tag: host strain


title: 32542_slide4_A2

description: Probe-based spatial transcriptomics

value: Male

value: day

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: mettl4-1_rep2

source_name: 14-day-old seddlings grown up under long-day condition (22°C and 16-h-light/11-h-dark)

tag: tissue

value: seedling


title: Col_rep1

source_name: 14-day-old seddlings grown up under long-day condition (22°C and 16-h-light/8-h-dark)


title: UAT-2019-F-1045

description: Xenograft SK-OV-3_EV_1

value: Human Ovarian Cancer Cell Line

value: pIND_EV (Empty vector)

value: nude mouse

value: xenografts tumors


title: 32542_slide5_C2

description: Probe-based spatial transcriptomics

value: Charles Rivers Laboratories

tag: Sex

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad


title: DP_IW+Th_2

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

institute: Kanazawa University

data_processing:
Illumina RTA software was used for base-calling.
Sequence reads were mapped to the zebrafish reference genome (GRCz11) using HiSAT2 (version 2.1.0).
Tags per million (TPM) were calculated using the Subread (ver. 1.6.4).
Assembly: GRCz11
Supplementary files format and content: Tags per million (TPM) values for each sample.

organism: Danio rerio

source_name: gata2a+ runx1+ cells co-cultured with ZKS cells in the presence of both IWR-1-endo and Thpo

extract_protocol:
Total RNAs were extracted from sorted cells using RNeasy Mini Kit (QIAGEN).
Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic-polycytidylic acid, and total RNA was extracted using RNeasy Mini Kit. Reverse transcription (RT) was performed using Super Script III (Thermo Fisher Scientific) and an RT primer, which contains oligo-dT, T7 promoter, and PCR target region sequences. After digestion of remaining RT primers by exonuclease I (Takara), a poly-A tail was added to the 3’ ends of the first-strand cDNAs using terminal transferase (Sigma). The second-strand DNA was then synthesized using MightyAmp DNA polymerase (Thermo Fisher Scientific) and a tagging primer, which contains oligo-dT and PCR target region sequences. PCR amplification was performed using a suppression primer, which allow to amplify small-size DNA that contains complementary sequences at both ends of the template DNA. The amplified double-strand cDNA was purified using QIAquick PCR Purification Kit (Qiagen). Library preparation was performed using Nextera XT DNA Library Preparation Kit (illumina).

value: Sorted from the kidney

tag: age

value: adult

value: wild type


title: DP_IW+Th_1

value: gata2a+ runx1+ cells co-cultured with ZKS cells in the presence of both IWR-1-endo and Thpo


title: DP_uncul_1

source_name: uncultured gata2a+ runx1+ cells

value: uncultured gata2a+ runx1+ cells


title: CTRL CT 3

value: Placenta-derived trophoblasts

value: Wildtype cytotrophoblast


title: LPS

value: RAW macrophages

value: LPS


title: DP_cocul_2

source_name: gata2a+ runx1+ cells co-cultured with ZKS cells


title: DP_uncul_2


title: Ac-LDL-hi-1

data_processing:
Illumina RTA software was used for base-calling.
Sequence reads were mapped to the zebrafish reference genome (GRCz11) using HiSAT2 (version 2.1.0).
Tags per million (TPM) were calculated using the Subread (ver. 1.6.4).
Genome_build: GRCz11
Supplementary_files_format_and_content: Tags per million (TPM) values for each sample.

source_name: sinusoids

extract_protocol:
Total RNAs were extracted from sorted cells using RNeasy Mini Kit (QIAGEN).
Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic-polycytidylic acid, and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription (RT) was performed using Super Script III (Thermo Fisher Scientific) and an RT primer containing oligo-dT, T7 promoter, and PCR target region sequences. After digestion of remaining RT primers by exonuclease I (Takara), a poly-A tail was added to the 3’ ends of the first-strand cDNAs using terminal transferase (Sigma). The second-strand DNA was synthesized using MightyAmp DNA polymerase (Thermo Fisher Scientific) and a tagging primer containing oligo-dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small-size DNA containing complementary sequences at both ends of the template DNA. The amplified double-strand cDNA was purified using QIAquick PCR Purification Kit (Qiagen). Library preparation was performed using the Nextera XT DNA Library Preparation Kit (illumina).

value: sinusoids


title: pdgfrb-1

source_name: pericytes

value: pericytes


title: pdgfrb-2


title: DP_cocul_1

value: gata2a+ runx1+ cells co-cultured with ZKS cells


title: Ac-LDL-hi-2


title: ZKS-1

source_name: ZKS cells

value: ZKS cells


title: FE1_Hydrazine_4hr plus 20hr washout_6mM_b

city: North Chicago

first: Rita

last: Ciurlionis

address: 1 North Waukegan Road

institute: Abbvie

data_processing:
Fastq files were generated and uploaded to OmicSoft ArrayStudio (Qiagen)
Standard Internal ArrayStudio Mouse RNASeq Pipeline was run:
Raw data QC, Filtering NGS files, Align to Mouse.B38 and GeneModel Ensembl.R78, Raw Data QC and Post Alignment QC, Optional summarize Fusion, Exon Junctions, and Mutations, Perform Quantification, log2FPKM_UQ, Log2TPM, Trim UTRs by data, Generate BAS files. No default Land ALV files.
Assembly: OSA4 was used for alignment to Mouse B6.0 reference genome and the GeneModel Ensemble.R83 Build
supplementary file data content: counts

extract_protocol:
Qiazol extraction followed by DNaseI treatment
1 μg of total RNA per sample was subjected to library synthesis using the Illumina TruSeq V2 Stranded mRNA Library Prep Kit.
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina dual indicess prior to 15 cycles of PCR. 1.3pM library pool was loaded on an Illumina HI OUTPUT flow cell and sequenced at 2 X75bp paired end on an Illumina NextSeq 500 instrument, approx 10 million reads per sample

tag: cell line

value: lung epithelial cells

value: 6 mM hydrazine

tag: time

value: 4hr plus 20 hr washout


title: FE1_Hydrazine_4hr plus 20hr washout_10mM_c

value: 10 mM hydrazine


title: FE1_Hydrazine_4hr plus 20hr washout_6mM_a


title: FE1_Hydrazine_4hr plus 20hr washout_10mM_b


title: 32542_slide4_C2

description: Probe-based spatial transcriptomics

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Yes

tag: formula

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: FE1_Hydrazine_4hr plus 20hr washout_6mM_c

value: lung epithelial cells

value: 6 mM hydrazine

value: 4hr plus 20 hr washout


title: ZKS-2

value: Sorted from the kidney

value: adult

value: wild type

value: ZKS cells


title: FE1_Hydrazine_4hr plus 20hr washout_4mM_a

value: 4 mM hydrazine


title: FE1_Hydrazine_4hr plus 20hr washout_4mM_b


title: FE1_Hydrazine_4hr plus 20hr washout_vehicle_c

value: 0 mM hydrazine


title: FE1_Hydrazine_4hr plus 20hr washout_vehicle_b


title: FE1_Hydrazine_4hr_10mM_b

value: 10 mM hydrazine

value: 4 hr


title: FE1_Hydrazine_4hr_10mM_c


title: FE1_Hydrazine_4hr plus 20hr washout_1mM_c

value: 1 mM hydrazine


title: FE1_Hydrazine_4hr plus 20hr washout_vehicle_a


title: FE1_Hydrazine_4hr_6mM_a


title: FE1_Hydrazine_4hr_6mM_b


title: FE1_Hydrazine_4hr_4mM_e


title: FE1_Hydrazine_4hr plus 20hr washout_10mM_a


title: FE1_Hydrazine_4hr_4mM_d


title: FE1_Hydrazine_4hr_4mM_c


title: FE1_Hydrazine_4hr_6mM_c


title: FE1_Hydrazine_4hr_4mM_a


title: FE1_Hydrazine_4hr_1mM_c


title: FE1_Hydrazine_4hr plus 20hr washout_4mM_c


title: FE1_Hydrazine_4hr plus 20hr washout_1mM_a


title: FE1_Hydrazine_4hr_1mM_a


title: FE1_Hydrazine_4hr_vehicle_b


title: FE1_Hydrazine_4hr_vehicle_c


title: FE1_Hydrazine_4hr_vehicle_a


title: mouse breast (no tumor)

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

institute: Stanford University

description: slice of mouse endogenous breast tissue (no tumor)

data_processing:
The libraries were then sequenced using NextSeq (Illumina), and Bcl files were demultiplexed.
Raw FASTQ files and histology images were processed by sample with the Space Ranger software, which uses STAR v.2.5.1b (Dobin et al., 2013) for genome alignment, against the Cell Ranger mm10 reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/ (Dobin et al., 2013).
To analyze the spatial distribution of cell types in Visium data, pairwise cell-cell neighbor interactions were quantified by extracting a feature matrix, f, of the probability of cell type representation in each Visium spot. An adjacency matrix, j, was then used to identify neighboring Visium spots within k=5 nearest neighbors. For each possible cell-cell pairing, a pairing score was calculated as the dot product of individual cell type vectors in f with the adjacency matrix (i.e. f1⋅j⋅f2) using AdjacencyScore in R (Govek et al., 2021). Scores were averaged at the group-level, then subtracted between groups to quantify the magnitude of differential cell pairings in early tumor vs. native breast tissue and late tumor vs. early tumor.
Assembly: mm10

source_name: breast

extract_protocol:
Mouse tissue was processed according to the Visual Spatial Protocol-Tissue Preparation Guide by 10X Genomics.
In brief, we flash froze tissue samples in OCT using a Thermo Scientific Thermo-Flask benchtop container filled three quarters with liquid nitrogen and a small, round, metal bowl with 1-inch height worth of isopentane. A pair of sturdy needle-drivers was used to maneuver the isopentane bowl in and out of the Thermo-Flask. The isopentane bowl was incubated in liquid nitrogen for about 10 minutes. Tissue was completely frozen in approximately one minute, wrapped in aluminum foil, stored immediately in a box containing dry ice, and transferred to a -80°C freezer. Tumor tissues were cryosectioned at -20 degrees onto gene expression slides.
RNA-seq: The samples were uniquely barcoded, pooled, and sequenced on HiSeq (Illumina). scRNA-seq: cDNA libraries were sequenced on a NextSeq 500 Illumina platform aiming for 50,000 reads per cell. scATAC-seq: cDNA libraries were sequenced on a NextSeq 500 Illumina platform. In total, we generated scATAC-seq profiles from 5,353 cells, which yielded on average 13.0 × 10^3 unique fragments mapping to the nuclear genome. Spatial transcriptomics: The libraries were then sequenced using NextSeq (Illumina).
The Gene Expression Slide & Reagent kit was followed per protocol, and used to produce sequencing libraries.

value: breast

value: unsorted (all cells)

value: black 6


title: mouse breast tumor late stage replicate 2

description: slice of mouse endogenous breast tumor harvested at late stage (replicate 2)


title: mouse breast tumor late stage replicate 1

description: slice of mouse endogenous breast tumor harvested at late stage (replicate 1)