title: Hela, sodium fluoroacetate treatment, rep1

value: sodium fluoroacetate treatment


title: day 0 - replicate 1 AS-367945-LR-45389

status: Public on Oct 02 2023

type: SRA

city: Heidelberg

first: Moritz

last: Jakab

address: Im Neuenheimer Feld

country: Germany

institute: German Cancer Research Center

description: day 0 - replicate 1

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was demultiplexed and fastq files were generated using using bcl2fastq software (Illumina, v2.20.0.422).
FASTQ files were mapped to the mouse reference genome using salmon (v0.7.2) and count matrices were constructed with tximport (v1.18.0)
Assembly: GRCm38
Supplementary files format and content: count matrices - CSV file includes raw counts for each sample
Supplementary files format and content: annotation sheets - CSV file inculding metadata for respective count matrix

molecule: polyA RNA

organism: Mus musculus

source_name: lung

extract_protocol:
Single cells were sorted directly into 96 well-plates containing 1 µl of lysis buffer per well, centrifuged and snap frozen in liquid nitrogen.
ScRNAseq libraries of tumour cell subpopulations and endothelial cells were constructed using a modified SMART-Seq2 protocol

tag: tissue

value: lung

tag: cell type

value: endothelial cells

tag: genotype

value: WT

tag: treatment

value: uninjected control animals


title: day 0 - replicate 1 AS-367943-LR-45389

description: day 0 - replicate 1


title: K562/ADR,  probe enrichment, Adriamycin treatment, rep2

city: Wuhan

first: Ziang

last: Lu

address: Wuhan University, No.299, Bayi Road, Wuchang District

country: China

institute: Wuhan University

library_source: transcriptomic

data_processing:
Raw reads were processed to remove adapters and low-quality bases with Trim Galore (v0.6.7).
Reads were first mapped to human rRNA sequences with bowtie2 (v2.2.5). Coverage near 18S modified sites were analyzed with deeptools bamCompare (v3.5.1).
Unmapped reads were next mapped to human genome (hg38) with STAR (v2.7.0d).
Peak calling and differential analysis were processed with exomepeak (v2.16.0).
Assembly: hg38
Supplementary files format and content: bigwig, normalized align result
Supplementary files format and content: bed, peaks and differential peaks result

molecule: total RNA

organism: Homo sapiens

growth_protocol: HeLa, HEK293T and MDA-MB-231 cells were maintained at 37 ℃ in DMEM (Procell, PM150210) medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin under 5% CO2. K562 and K562/ADR cells were maintained at 37 ℃ in RPMI-1640 (Procell, PM150110) medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin under 5% CO2.

extract_protocol:
Cellular total RNA was isolated according to the TRIzol reagent manufacturer’s protocol, followed by isopropanol precipitation.
The libraries were prepared with a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: For sodium fluoroacetate treatment, cells were grown to 80% confluence in the 10-cm plastic dishes, then incubated with 10 mM sodium fluoroacetate (self-synthesized) for 6 h. RNAs containing Fac4C (10 μg in 10 μl nuclease-free water) and 2 μl probes (40 mM in DMF, self-synthesized) were performed in 40 μl reaction buffer containing 4 μl Tris buffer (1 M in nuclease-free water, pH 8.5) with TCEP (50 mM). DBCO-S-S-biotin (Click Chemistry Tools, A112-10) or DBCO-Cy5 was added into the system for click reaction to a final concentration of 20 mM and incubated at 37 °C for 2 h.  For Nat10 inhibition, when HeLa cells were grown to 80% confluence, 50 μM Nat10 inhibitor (Remodelin, MedChemExpress, HY-16706) was added into the cells and maintained for 16  h at 37 ℃ followed by fluoroacetate treatment. For Adriamycin treatment, cells were grown to 80% confluence in the 10-cm plastic dishes, then incubated with 0.25 μM Adriamycin (Aladdin, A183027) for 24 h.

tag: cell line

tag: enrichment method

value: probe

value: Adriamycin treatment


title: day 0 - replicate 1 AS-367941-LR-45389

description: day 0 - replicate 1


title: Brain, Alzheimer’s Disease, sample 14

city: Philadelphia

first: Edward

last: Lee

state: PA

address: 613A Stellar Chance Laboratories; 422 Curie Blvd

country: USA

institute: University of Pennsylvania

description:
10x Genomics
AdsnRNAseq_GEO.h5ad
Microglia_GEO.h5ad
Astrocytes_GEO.h5ad

data_processing:
Reads, including intronic reads, were aligned to the hg38 genome sequence (GRCh38.p12) using CellRanger (v.3.0.2)
Nuclei were filtered to remove likely doublets and poor quality data. Nuclei were kept if (i) the number of expressed genes is between 200 and 4000 and (ii) mitochondrial gene UMI proportion is less than 5%. Genes expressed in less than ten cells were removed from further analysis.
Nuclei were clustered based on 2000 highly variable genes using DESC, an unsupervised deep-embedding algorithm for iterative single-cell clustering. Nuclei were clustered to 15 different resolutions and annotated based on known marker genes for microglia, endothelial cells, excitatory neurons, inhibitory neurons, astrocytes, oligodendrocytes, and oligodendrocyte progenitor cells. Nuclei with consistent cell type annotations across clustering resolutions were kept for downstream analysis.
Microglia and astrocytes were subset and further clustered to identify microglia and astrocyte subpopulations
Assembly: hg38
Supplementary files format and content: AdsnRNAseq_GEO.h5ad: AnnData containing nuclei read count matrix, nuclei annotations, and sample metadata for full dataset
Supplementary files format and content: Microglia_GEO.h5ad: AnnData containing nuclei read count matrix, nuclei annotations, and sample metadata for microglia
Supplementary files format and content: Astrocytes_GEO.h5ad: AnnData containing nuclei read count and CarDEC-denoised gene expression matrices, nuclei annotations, and sample metadata for astrocytes

molecule: nuclear RNA

source_name: dorsolateral prefrontal cortex

extract_protocol:
Frozen middle frontal neocortex brain tissue was transferred to a pre-chilled dounce homogenizer. Homogenization buffer consisted of 0.25 M sucrose in TKM buffer (50 mM Tris–HCl, pH 7.5, 25 mM KCl, 14 mM MgCl2, and 0.4 U/uL RNAse inhibitor and was added to the dounce homogenizer, at a ratio of 2 mL buffer per 125 mg of tissue. The homogenate was mixed with 2.3 M sucrose + TKM solution to generate a 1.6 M sucrose solution in a chilled ultracentrifuge tube pre-filled with 3 mL cushion buffer (1.8 M sucrose in TKM) and spun at 100,000×g for 45 min at 4 °C in a swinging bucket rotor (Sw-41Ti rotor on an XPN-80 ultracentrifuge). After ultracentrifugation, the myelin layer was removed, the supernatant aspirated and discarded, and the remaining pellet was re-suspended in 1X PBS and RNAsin Plus RNAse inhibitor.
Library construction was performed by the Center for Applied Genomics Sequencing Core at the Children’s Hospital of Philadelphia in accordance with manufacturer’s (10x Genomics) instructions.

value: dorsolateral prefrontal cortex

tag: apoe genotype

tag: trem2 genotype

tag: amyloid tau_(at)_pathology_score

value: A+T+


title: Brain, Alzheimer’s Disease, sample 13


title: K562/ADR,  probe enrichment, Adriamycin treatment, rep1


title: Brain, Alzheimer’s Disease, sample 12


title: K562/ADR,  no enrichment, Adriamycin treatment, rep2


title: day 0 - replicate 1 AS-367937-LR-45389

description: day 0 - replicate 1


title: Brain, Alzheimer’s Disease, sample 10


title: K562/ADR,  no enrichment, Adriamycin treatment, rep1


title: NIH-3T3,macroH2A1, Meta,input

city: Shanghai

first: Bi

middle: shan

last: Ye

state: Shanghai

address: Minhang district Dongchuan Road NO.800

department: School of Biomedical Engineering

institute: Shanghai JiaoTong University

library_source: genomic

data_processing:
The TrimGalore tool was used to perform quality control and adapter trimming on the reads, merely retaining the bases with a quality score above 20 for subsequent analysis with parameters: "-q 20 --stringency 1 --length 20 -e 0.1 --paired ".
Sequence reads were aligned to the mouse genome 38 (UCSC, mm10) using Bowtie2 tool with parameters: -q-X1000--very-sensitive -k1--no-mixed-p8-1-2. Samtools was used to remove reads that mapped to blacklist regions, unknown chromosome segments, unmapped reads and mitochondrial regions, and the remaining data were de-duplicated and one of the PCR duplicates was retained as a basic template and concerted to BAM format.The parameters of deduplication used were: markdup-r-t5. The BAM file index was built using the index option of Samtools.
Histone domains were generated by using R package normr using function “regimeR”, paired-end parameters: “countConfigPairedEnd (binsize = 1000, mapq = 30, midpoint=TRUE,tlenFilter = c(100, 300))” was used with “models = 3, Fdr = 0.1”.
Enriched bins were merged within big domains with software BedTools. The exportR option was used to export the macroH2A1-enriched regions and the normalization results in bed (genome region file) and BigWig (genome browser display file) formats.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: DMEM, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
After synchronization in metaphase, NIH-3T3 cells were collected and centrifuged at 1000rpm for 5 min. Cells were then washed with PBS and pelleted at 1000rpm for 5 min. The cells pellet was resuspended in 5ml 75mM KCl for 30 min at 37℃ and was centrifuged at 600×g for 5min at 4°C. The supernatant was removed and the cells pellet was resuspended in 5ml of PA buffer (15mM Tris-HCl pH 7.5, 0.5mM EGTA,2mM EDTA, 80mM KCl, 20mM NaCl, 0.5mM spermidine, 0.2mM spermine, and digitonin) and incubated on ice for 10min. The mixture was transferred to a Dounce homogenizer, and the chromosomes were released by 15-20 strokes before being centrifuged at 190×g for 5min at 4°C. The pellet was resuspended in 4-5ml of PA buffer and transferred to the Dounce homogenizer again. The remaining chromosomes were released by 10-15 strokes before being centrifuged at 190×g for 5min at 4°C. Both supernatants were carefully collected and filtered by 10μm and 5μm filter membranes. After centrifugation at 1750rpm for 10 min at 4°C, the chromosome pellet was resuspended in 1ml MNase buffer (15mM Tris-HCl pH 7.5, 0.5mM EGTA,2mM EDTA, 80mM KCl, 20mM NaCl, 0.5mM spermidine, 0.2mM spermine, 35mM CaCl2, 35mM Tris-HCl pH8.0, 10μg/ml BSA, 1mM PMSF and 1mM protein inhibitor cocktail). Micrococcal nuclease was added to 3μl and chromosomes were digested at 4 °C for 12h. The reaction was stopped by the addition of EGTA to 20mM. In G1/S phase, after synchronization treatment, NIH-3T3 cells were washed twice with icecold PBS. Cells were then pelleted at 1000rpm for 5 min at 4°C. The cells pellet was resuspended in 500μl of MNase buffer (15mM Tris-HCl pH 7.5, 0.5mM EGTA,2mM EDTA, 80mM KCl, 20mM NaCl, 0.5mM spermidine, 0.2mM spermine, 35mM CaCl2, 35mM Tris-HCl pH8.0, 10μg/ml BSA, 1mM PMSF, 1mM protein inhibitor cocktail and 0.5% NP-40). Micrococcal nuclease was added to 2μl and incubated at 4℃ for 12h. The reaction was stopped by adding EDTA to 20mM. Both the digested nuclear extract was centrifuged at 10,000g for 7 min at 4°C. The supernatant containing mono-nucleosomes was pre-cleared by incubation with protein A+G magnetic beads (Millipore, Cat.16-663x) for 2h and incubated overnight with antibodies to macroH2A1. Antibody-bound complex was isolated on protein A+G magnetic beads and DNA from antibody-bound and input DNA was purified by ethanol precipitation.
ChIP-seq libraries were prepared from 5-10ng of DNA per sample using the NEBNext Library Preparation Kit. Libraries were amplified using 13-15 cycles on the thermocycler. Post amplification libraries were size selected at 300bp in length using AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: To synchronize NIH-3T3 cells at G1/S phase, cells were first cultured with starvation treatment (DMEM with 0.5% FBS and 1% Pen/Strep) for 48h. Then, NIH-3T3 cells were washed and grown for 18h in fresh medium with 1% APH (10μg/ml) before they were collected. To synchronize NIH-3T3 cells at metaphase, cells were treated with colchicine (100ng/ml) for 12h before collection.

value: Mouse Embryonic Cells

tag: chip antibody


title: day 0 - replicate 1 AS-367933-LR-45389

description: day 0 - replicate 1


title: K562/ADR,  probe enrichment, no Adriamycin treatment, rep2


title: day 0 - replicate 1 AS-367935-LR-45389

description: day 0 - replicate 1


title: Brain, Alzheimer’s Disease, sample 9


title: Brain, Alzheimer’s Disease, sample 8


title: Hela, sodium fluoroacetate treatment, rep2

data_processing:
Raw reads were processed to remove adapters and low-quality bases with Trim Galore (v0.6.7).
Reads were first mapped to human rRNA sequences with bowtie2 (v2.2.5). Coverage near 18S modified sites were analyzed with deeptools bamCompare (v3.5.1).
Unmapped reads were next mapped to human genome (hg38) with STAR (v2.7.0d).
Peak calling and differential analysis were processed with exomepeak (v2.16.0).
Assembly: hg38
Supplementary files format and content: bigwig, normalized align result

source_name: Hela

value: Hela


title: day 0 - replicate 1 AS-367931-LR-45389

description: day 0 - replicate 1


title: NIH-3T3,macroH2A1, Meta, rep1

value: macroH2A1(Abcam,#ab37264 )


title: NIH-3T3,macroH2A1, Meta, rep2


title: NIH-3T3,macroH2A1, G1/S,input


title: K562/ADR,  no enrichment, no Adriamycin treatment, rep2


title: day 0 - replicate 1 AS-367929-LR-45389

description: day 0 - replicate 1


title: Brain, Pathology Aging, sample 6

value: A+T-


title: K562/ADR,  no enrichment, no Adriamycin treatment, rep1


title: K562/ADR,  probe enrichment, no Adriamycin treatment, rep1


title: day 0 - replicate 1 AS-367939-LR-45389

description: day 0 - replicate 1


title: Brain, Alzheimer’s Disease, sample 11


title: NIH-3T3,macroH2A1, G1/S, rep2


title: K562,  probe enrichment, Adriamycin treatment, rep2


title: NIH-3T3,macroH2A1, G1/S, rep1


title: day 0 - replicate 1 AS-367927-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-367925-LR-45389

description: day 0 - replicate 1


title: K562,  probe enrichment, Adriamycin treatment, rep1


title: Brain, Pathology Aging, sample 4


title: day 0 - replicate 1 AS-367923-LR-45389

description: day 0 - replicate 1


title: Brain, Pathology Aging, sample 3


title: K562,  no enrichment, Adriamycin treatment, rep1


title: day 0 - replicate 1 AS-367921-LR-45389

description: day 0 - replicate 1


title: 4T1 cells, Hypomethylated cells treated with SKL2001, rep5

description:
Hypo_SKL_5
VST_transformed_counts
DESeq2_results

data_processing:
Raw sequencing data was demultiplexed and fastq files were generated using using bcl2fastq software (Illumina, v2.20.0.422).
FASTQ files were mapped to the mouse reference genome using STAR aligner in htseq-count mode. Count matrices were constructed with DESeq2.
Assembly: GRCm38
Supplementary files format and content: Xlsx file includes VST transformed counts for each sample
Supplementary files format and content: Xlsx file contains results of differential gene expression analysis using DESeq2

source_name: cell line

extract_protocol:
RNA was extracted using the GenElute™ Total RNA Purification Kit (Sigma Adlrich) according to the manufacturer’s instruction. Total RNA was used for library preparation.
Poly(A) RNA was purified using oligo-dT-beads. Sequencing libraries were generated using the Illumina TruSeq mRNA stranded Kit following the manufacturer's instructions.

value: Murine breast cancer cells

tag: time

value: over-night

value: SKL2001 + decitabine


title: Brain, Pathology Aging, sample 7


title: 4T1 cells, Hypomethylated cells treated with SKL2001, rep4

description:
Hypo_SKL_4
VST_transformed_counts
DESeq2_results


title: 4T1 cells, Hypomethylated cells treated with SKL2001, rep3

description:
Hypo_SKL_3
VST_transformed_counts
DESeq2_results


title: Brain, Normal, sample 2

value: A-T-


title: K562,  probe enrichment, no Adriamycin treatment, rep2


title: day 0 - replicate 1 AS-367919-LR-45389

description: day 0 - replicate 1


title: 4T1 cells, Hypomethylated cells treated with SKL2001, rep2

description:
Hypo_SKL_2
VST_transformed_counts
DESeq2_results


title: K562,  probe enrichment, no Adriamycin treatment, rep1


title: Brain, Pathology Aging, sample 5


title: PAPgamma siRNA rep4

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

country: France

institute: UMR9002 CNRS-UM

data_processing:
CutAdapt to cut adapters
FASTQC for quality control
STAR_PE for alignment of reads on reference genome
samtools index to index bam files
HTSEQ_count_stranded to count reads on genes for differential expression analysis
extract_stranded_bam_PE to sort out forward and reverse reads
samtools_strd_index to index strand specific bam files
bamCoverage_RPGC to convert bam to bigwig
bamCoverage_strd_RPGC to convert stranded bam in bigwig
profmat_stranded_tss_gb to get wuantification matrix around TSS and scaled gene body for stranded bigwig
Assembly: hg38
Supplementary files format and content: bigwig files

source_name: HeLa

extract_protocol:
RNA was harvested using Trizol
RNA libraries for RNA-seq were prepared by Novogene
RNA-seq stranded paired-end, rRNA removal

treatment_protocol: siRNA (30nM) was transfected in HeLa cells using Interferin

value: HeLa

value: PAPgamma siRNA

value: Day 3


title: K562,  no enrichment, no Adriamycin treatment, rep2


title: 4T1 cells, Ctrl treated with SKL2001, rep3

description:
Ctrl_SKL_3
VST_transformed_counts
DESeq2_results

value: WT


title: 4T1 cells, Ctrl treated with SKL2001, rep2

description:
Ctrl_SKL_2
VST_transformed_counts
DESeq2_results


title: PAPgamma siRNA rep3


title: day 0 - replicate 1 AS-367911-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells

value: uninjected control animals


title: MDA-MB-231, no enrichment, rep2


title: K562,  no enrichment, Adriamycin treatment, rep2

value: Adriamycin treatment


title: PAPgamma siRNA rep2


title: PAPgamma siRNA rep1


title: day 0 - replicate 1 AS-367913-LR-45389

description: day 0 - replicate 1


title: 4T1 cells, Ctrl treated with SKL2001, rep1

description:
Ctrl_SKL_1
VST_transformed_counts
DESeq2_results


title: MDA-MB-231, no enrichment, rep1


title: day 0 - replicate 1 AS-367909-LR-45389

description: day 0 - replicate 1


title: Control siRNA rep4

value: Control siRNA


title: Brain, Normal, sample 1

value: dorsolateral prefrontal cortex


title: MDA-MB-231, antibody enrichment, rep2

value: antibody


title: AB2846

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: SPIDseq

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: meta_for_ncbi2.txt

source_name: C57/b6 PA-GFP

growth_protocol: Tumor cells (5×105 EO771-tdTomato cells) were suspended in PBS and mixed 1:1 with Matrigel (BD Biosciences, 354230). A total of 100 µL of cell mixture was injected into the right inguinal mammary glands of 8-week-old female PA-GFP C57BL/6 mice. Tumors were resected 3 weeks following the injection, and CT imaging of lungs was performed once a week until metastases appeared. Mice were anesthetized and lung perfusion was performed. Photoactivation and imaging were performed as described previously. Following perfusion and dissection of the intact lungs, lung lobes were separated (at this stage metastatic sites were often seen by eye as distinct red dots). Tissues were viewed in the microscope to identify metastases or validate the lack of tdTomato signal in distal normal, relapse-free, or Pre-MET tissues. Because we attempted to characterize metastasis as early as possible after their first detection, in some cases only one metastatic lesion was found and therefore we were able to only label either the core or the invasive margin.

extract_protocol:
Lung tissues or primary EO771 tumors underwent mechanical and enzymatic digestion for 15 min at 37°C (gentleMACSTM C tube, Miltenyi Biotec Inc., San Diego, CA; 0.1mg/ml DNase type I (Roche), and 1mg/ml Collagenase IV (Worthington) in RPMI-1640). Lungs were dissociated with the m_lung program, and tumors with the h_tumor program. Cells were then filtered through a 100µm cell strainer, washed with cold PBS, and centrifuged (5 min, 4°C, 300g). Following tissue digestion, cells were washed and resuspended in cold FACS buffer (0.5% BSA and 2 mM EDTA in PBS), and incubated with fluorophore conjugated antibodies (CD31-PE/Cy7, Biolegend 102417 ; CD45-APC/Cy7, Biolegend 103115). Following the staining cells were filtered through a 70-µm strainer. Before sorting, cells were stained with DAPI to exclude dead/dying cells. Cell sorting was performed using a BD FACSAria Fusion flow cytometer (BD Biosciences), gating for CD31-CD45+ cells, or when isolating photoactivated cells for CD31-GFP+ (after exclusion of dead cells and doublets).
3' end mRNA libraries were prepared for sequencing using SPID-seq.

tag: strain

value: C57/b6 PA-GFP

tag: mouse id

value: NO

tag: sorted cells_(gating)

tag: area

value: MET

tag: sample type

value: Primary tumor

tag: status

value: Primary


title: Control siRNA rep3


title: day 0 - replicate 1 AS-367907-LR-45389

description: day 0 - replicate 1

tag: tissue


title: 4T1 cells, Ctrl treated with SKL2001, rep4

description:
Ctrl_SKL_4
VST_transformed_counts
DESeq2_results

tag: cell type

value: Murine breast cancer cells

value: over-night


title: day 0 - replicate 1 AS-367915-LR-45389

description: day 0 - replicate 1

tag: genotype


title: day 0 - replicate 1 AS-367917-LR-45389

description: day 0 - replicate 1

tag: treatment


title: MDA-MB-231, antibody enrichment, rep1

tag: cell line


title: day 0 - replicate 1 AS-367905-LR-45389

description: day 0 - replicate 1


title: Control siRNA rep2

value: HeLa


title: AB2845

description: SPIDseq


title: AB2844

description: SPIDseq


title: K562,  no enrichment, no Adriamycin treatment, rep1

tag: enrichment method


title: Control siRNA rep1

value: Day 3


title: MDA-MB-231, probe enrichment, rep2

value: probe


title: day 0 - replicate 1 AS-367903-LR-45389

description: day 0 - replicate 1

value: lung

value: WT


title: AB2843

description: SPIDseq

value: BC #9


title: day 0 - replicate 1 AS-367901-LR-45389

description: day 0 - replicate 1

value: endothelial cells

value: uninjected control animals


title: Hela, no enrichment, rep2

value: Hela


title: MDA-MB-231, probe enrichment, rep1


title: AB2842

description: SPIDseq


title: day 0 - replicate 1 AS-367899-LR-45389

description: day 0 - replicate 1


title: AB2841

description: SPIDseq


title: MCF7 Fulvestrant pre-treated GR ChIP + dex rep 3

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

description: For those ones we did not use macs3, just the bam files to look at the enrichment in previously identified peaks.

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads).
For ChIP sequencing reads were aligned to the Human Reference Genome (hg38) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed. Peaks were called MACS peak caller version 3 (Zhang Y et al. Genome Biol 2008;9(9):R137). MACS3 was run with the default parameters.
Assembly: Hg38
Supplementary files format and content: peaks.bed

growth_protocol: DMEM + 10% FCS + 1% Pen/Strep, cultured at 5% CO2 and 37 °C.

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP)-seq was performed as previously described (Schmidt, D. et al. Methods 48, 240–248 (2009).In brief, cells were fixed in 1% formaldehyde for 10 min and quenched with 0.125M glycine. Nuclear lysates were extracted as previously described and sonicated for 13 cycles (30 sec on/30 sec off) using the Bioruptor® Pico (B01060001, Diagenode). ). Per ChIP, 50 µL of magnetic Protein A beads (10008D, Thermo Fisher Sci-entific) beads were conjugated to 7.5µL of GR antibody, or 5µg of ER antibody.
Immunoprecipitated DNA was processed for library preparation usin KAPA library preparation kit, KK8234, Roche.

treatment_protocol: Cells were left untreated or treated with 100nM Dexamethasone for 2 hours (with and without pre-treatment with Fulvestrant of 26 hours in total).

value: Breast Cancer Cells

value: 100nM Fulvestrant and 100nM Dexamethasone

tag: time point

value: 26h Fulvestrant + last 2h Dexamethasone

value: GR (12041, Cell Signaling Technology)


title: day 0 - replicate 1 AS-367897-LR-45389

description: day 0 - replicate 1


title: Hela, no enrichment, rep1


title: AB2840

description: SPIDseq

value: C57/b6 PA-GFP

value: NO

value: MET

value: Primary tumor


title: day 0 - replicate 1 AS-367895-LR-45389

description: day 0 - replicate 1


title: AB2806

description: SPIDseq

value: No-MET

value: Whole lungs

value: Relapse-free


title: Hela, antibody enrichment, rep2

value: antibody


title: MCF7 (mixed) input

value: WT

value: Vehicle

value: Input Sample


title: Hela, antibody enrichment, rep1


title: AB2805

description: SPIDseq

value: Lung section


title: day 0 - replicate 1 AS-367891-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells

value: uninjected control animals


title: MCF7 ER ChIP rep 3 + dex

value: Breast Cancer Cells

value: 100nM Dexamethasone


title: MCF7 ER ChIP rep 3 - dex


title: Hela, probe, NAT10 inhibition, rep1

value: Hela

value: probe

value: NAT10 inhibition


title: Hela, probe, NAT10 inhibition, rep2


title: day 0 - replicate 1 AS-367893-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-367889-LR-45389

description: day 0 - replicate 1


title: MCF7 ER ChIP rep 2 + dex


title: Hela, probe enrichment, no NAT10 inhibition, rep2


title: AB2804

description: SPIDseq

value: C57/b6 PA-GFP

value: NO

value: MET


title: AB2800

description: SPIDseq


title: day 0 - replicate 1 AS-367887-LR-45389

description: day 0 - replicate 1


title: MCF7 Fulvestrant pre-treated GR ChIP + dex rep 2

value: 100nM Fulvestrant and 100nM Dexamethasone

value: 26h Fulvestrant + last 2h Dexamethasone

value: GR (12041, Cell Signaling Technology)


title: day 0 - replicate 1 AS-367885-LR-45389

description: day 0 - replicate 1

value: WT


title: MCF7 ER ChIP rep 2 - dex

value: Vehicle


title: AB2799

description: SPIDseq

value: Lung section


title: AB2798

description: SPIDseq

value: No-MET

value: Distal normal tissue


title: MCF7 ER ChIP rep 1 + dex


title: HEK293T, no enrichment, rep2


title: day 0 - replicate 1 AS-367883-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells

value: uninjected control animals


title: MCF7 Fulvestrant pre-treated GR ChIP + dex rep 1

value: Breast Cancer Cells


title: MCF7 ER ChIP rep 1 - dex


title: AB2797

description: SPIDseq


title: HEK293T, no  enrichment, rep1


title: MCF7 GR ChIP rep 3 - dex

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads).
For ChIP sequencing reads were aligned to the Human Reference Genome (hg38) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed. Peaks were called MACS peak caller version 3 (Zhang Y et al. Genome Biol 2008;9(9):R137). MACS3 was run with the default parameters.
Assembly: Hg38
Supplementary files format and content: peaks.bed file should be empty as no peaks were called.


title: AB2796

description: SPIDseq

value: PA

value: MET Core


title: AB2795

description: SPIDseq

value: C57/b6 PA-GFP

value: ADJ

value: MET Invasive margin


title: day 0 - replicate 1 AS-367879-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-367877-LR-45389

description: day 0 - replicate 1


title: AB2794

description: SPIDseq

value: MET


title: MCF7 GR ChIP rep 2 + dex

value: 100nM Dexamethasone


title: MCF7 GR ChIP rep 3 + dex

value: GR (12041, Cell Signaling Technology)


title: HEK293T, antibody enrichment, rep1

value: antibody


title: Hela, probe enrichment, no NAT10 inhibition, rep1

value: Hela

value: probe


title: MCF7 GR ChIP rep 1 + dex

value: WT


title: day 0 - replicate 1 AS-367875-LR-45389

description: day 0 - replicate 1


title: MCF7 GR ChIP rep 2 - dex

value: Vehicle


title: HEK293T, probe enrichment, rep1


title: HEK293T, probe enrichment, rep2


title: AB2791

description: SPIDseq

value: NO

value: Lung section


title: day 0 - replicate 1 AS-367871-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells

value: uninjected control animals


title: AB2793

description: SPIDseq

value: PA

value: MET Core


title: MCF7 GR ChIP rep 1 - dex

value: Breast Cancer Cells


title: AB2792

description: SPIDseq

value: C57/b6 PA-GFP


title: day 0 - replicate 1 AS-367873-LR-45389

description: day 0 - replicate 1


title: HEL cell, shTMIGD2_biol rep 3

city: bronx

first: Hao

last: Wang

state: NY

address: 1300 morris park ave, Forch 405

institute: Albert Einstein College of Medicine

description: shRNA knockdown

data_processing:
RNA-seq reads from both the TMIGD2 knockdown HEL cells were aligned to the human genome (hg38) using the program STAR (version 2.6.1b)
HTSeq (version 0.6.1) was then used to count the number of RNA-seq fragments in each gene in the refSeq annotation (downloaded from the UCSC genome browser in 11/2019)
DESeq2 (version 3.11) was utilized to perform differential expression analysis and principal component analysis (PCA) on genes that had an average read count >= 1 in either of the two compared sample groups
Assembly: hg38
Supplementary files format and content: cvs
Supplementary files format and content: output from edgeR

source_name: HEL

growth_protocol: HEL cells were cultured in RPMI supplemented with 10% FBS and 1% penicillin & streptomycin.

extract_protocol:
Total RNA was isolated from the shCtrl and shTMIGD2 HEL cells with RNeasy Plus Mini Kit (QIAGEN) following the manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra II directional RNA workflow with Poly (A) mRNA enrichment for Illumina sequencing by Admera Health.

value: HEL

value: Erythroleukemia


title: day 0 - replicate 1 AS-367881-LR-45389

description: day 0 - replicate 1


title: HEK293T, antibody enrichment, rep2


title: Wildtype RNA-seq replicate 3

city: New York

first: Jitong

last: Cai

address: 435 E 30th street

department: NYU Langone Health

institute: NYU Langone Health

data_processing:
NEBNext Ultra II directional mRNA was quantified at the transcript-level by Salmon v1.6.0, aligning to known transcripts as well as those identified in the long-read sequencing. When observing mature mRNA transcripts, reads were aligned against a database of transcripts with and without introns. Salmon was run with sequence and position bias modelling enabled.
Differential gene expression analysis was performed in DESeq2.
Assembly: S288C
Supplementary files format and content: tab-delimited txt file contains a list of differential expression genes and related statistics
Supplementary files format and content: tab-delimited txt file contains the raw read count for each gene quantified by Salmon v1.6.0

organism: Saccharomyces cerevisiae

source_name: yeast cell

extract_protocol:
Total RNA was extracted from 50mL flash-frozen cell pellets grown to mid-log (OD600 ~0.65-0.85) using MasterPure yeast RNA purification kit (Lucigen Cat# MPY03100) including a DNaseI treatment step. RNA (diluted 1:10) quality and concentration were measured by Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Nano Kit (Cat# 5067-1511) and Qubit RNA High Sensitivity Kit (Thermo Fisher Cat# Q32852), respectively.
NEBNext Poly(A) mRNA magnetic isolation module (NEB Cat# E7490) was used to enrich poly(A) mRNA from 500 ng total RNA with 5 uL 1:500 diluted ERCC RNA Spike-In control mix (Thermo Fisher Cat# 4456740) in 50 uL. The NEBNext Ultra II directional RNA library prep kit for Illumina with sample purification beads (NEB Cat# E7765) was used to prepare stranded mRNA sequencing libraries from the poly(A) RNA. Libraries were amplified for 11 cycles with i7 index primers (NEB Cat# E7500S). Libraries were individually cleaned-up with 0.9 volumes of sample purification beads and concentration and size distributions were measured by Qubit dsDNA high sensitivity kit and by Agilent 2100 Bioanalyzer with the Agilent High Sensitivity DNA kit (Cat# 5067-4626). Equimolar amounts were combined of all samples, cleaned-up on 0.9 volumes of sample purification beads, and submitted for 150 bp paired end sequencing on the NextSeq 500 (Illumina) at the EMBL Genomics Core.

tag: parent strain

value: wildtype strain YZY597 as control

value: yeast cell


title: HEL cell, shTMIGD2_biol rep 1

description: shRNA knockdown


title: day 0 - replicate 1 AS-367867-LR-45389

description: day 0 - replicate 1


title: AB2789

description: SPIDseq

value: No-MET

value: Distal normal tissue


title: HEL cell, shCtrl_biol rep 3

description: shRNA knockdown

value: shCtrl


title: day 0 - replicate 1 AS-367865-LR-45389

description: day 0 - replicate 1

value: WT


title: HEL cell, shCtrl_biol rep 2

description: shRNA knockdown


title: Wildtype RNA-seq replicate 1


title: AB2787

description: SPIDseq

value: NO

value: Whole lungs

value: Relapse-free


title: Syn6.5 RNA-seq replicate 3

value: consolidation strain YZY463 with Syn6.5


title: AB2786

description: SPIDseq

value: BC #8

value: MET

value: Primary tumor

value: Primary


title: HEL cell, shTMIGD2_biol rep 2

description: shRNA knockdown


title: day 0 - replicate 1 AS-367863-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells

value: uninjected control animals


title: AB2785

description: SPIDseq

value: C57/b6 PA-GFP


title: day 0 - replicate 1 AS-367859-LR-45389

description: day 0 - replicate 1


title: HEL cell, shCtrl_biol rep 1

description: shRNA knockdown

value: HEL

value: Erythroleukemia


title: day 0 - replicate 1 AS-367861-LR-45389

description: day 0 - replicate 1


title: Syn6.5 RNA-seq replicate 2

value: yeast cell


title: day 0 - replicate 1 AS-367869-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-367857-LR-45389

description: day 0 - replicate 1


title: AB2784

description: SPIDseq

value: Lung section


title: Day6-YPPP, CD11c+I-AI-Eint cells day6_Mac_YPPP_2

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

country: Japan

institute: Kanazawa Medical University Hospital

data_processing:
The fastq fieles were generated using bcl2fastq software.
Sequenced reads were mapped to hg38 using HISAT2 (v2.1.0) with default parameter.
Reads Per Kilobase of exon per Megabase of library size (RPKM)  and Transcripts per Million (TPM) were calcurated by StringTie (v1.3.4d) with default parameter.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: GM-CSF Bone marrow culture

growth_protocol: Bone marrow cells from femur of C57BL/6 mice were cultured with 25 ng/ml GM-CSF and DMSO or YPPP.

extract_protocol:
Total RNA of the dendritic cells were extracted with AllPrep DNA/RNA kit (QIAGEN) according to manufacturer instructions.
The libraries were constructed using  NEB Next Ultra II Directional RNA Library Prep Kit according to manufacturer instructions.

treatment_protocol: DMSO or YPPP added to the dish of bone marrow culture at day 0.

value: Bone marrrow derived macrophages

tag: cell subset

value: YPPP for 6 days

tag: library type


title: Day6-YPPP, CD11c+I-AI-Eint cells day6_Mac_YPPP_1

value: NEB Next Ultra II Directional RNA Library Prep Kit


title: Day6-DMSO, CD11c+I-AI-Eint cells day6_Mac_2

value: DMSO for 6 days


title: AB2783

description: SPIDseq

value: NO


title: Syn6.5 RNA-seq replicate 1

value: consolidation strain YZY463 with Syn6.5


title: AB2790

description: SPIDseq

value: No-MET

value: Distal normal tissue


title: fin4-SAR 3

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned with the Cutadapt package (v3.4)  for trimming adaptors and low-quality bases with a quality phred-like score <20. Reads <75 pbs were excluded from RNA-seq analysis.
The genome of Arabidopsis thaliana (version TAIR10) from the database of ENSEMBL was used as the reference sequences for RNA-seq analysis. The cleaned reads of each sample were mapped to the reference genome by using the STAR package (Spliced Transcripts Alignment to a Reference, v2.7.9a)
Mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2), samtools, and scripts developed in house  to remove potential PCR duplicates and count uniquely mapped reads for gene expression analysis.
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

organism: Arabidopsis thaliana

source_name: lower leaves

extract_protocol:
RNA extraction is performed with RNeasy MiniElute Cleanup Kit (Qiagen, catalog # 74204) with on column DNAase I  (Qiagen; catalog # 79254) were followed. RNA samples were measured by the QUBIT fluorescent method (Invit.rogen) and Agilent Bioanalyzer.
An amount of 250 ng of high quality of total RNA with RIN of 7 or higher was used for library construction using the reagents provided in the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490) and the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Briefly, 200 ng of total RNA was used for mRNA isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490). Then the poly A enriched RNA was fragmented in NEBNext First Strand Synthesis Buffer via incubation at 94 °C for the desired time. This step was followed by first-strand cDNA synthesis using reverse transcriptase and random hexamer primer.  Synthesis of ds cDNA is done using the 2nd strand master mix provided in the kit, followed by end-repair and dA-tailing.  At this point, Illumina adaptors are ligated to the sample.  Finally, library was amplified, and followed by purification with AMPure beads (Beckman Coulter, catalog # A63881).  The library size and mass were assessed by analysis in the Agilent TapeStation using a High Sensitivity DNA1000 Screen Tape.  Typically, a 250-900 library peak is observed with the highest peak at ~420 bp. Barcoded libraries were pooled equimolarly for sequencing simultaneously for NavaSeq 6000 S4 2x150 cycles run

treatment_protocol: Three lower leaves on each four-week-old Arabidopsis plant were infiltrated with 1 mM MgCl2 (Mock) or Pseudomonas syringae pv. maculicola ES4326 (OD600 = 0.002 (SAR). After two days, one upper leaf on each plant was collected for total RNA extraction.

value: lower leaves


title: day 0 - replicate 1 AS-367855-LR-45389

description: day 0 - replicate 1

value: lung

value: WT


title: Wildtype RNA-seq replicate 2

value: wildtype strain YZY597 as control


title: fin4-SAR 2


title: AB2731

description: SPIDseq

value: C57/b6 PA-GFP

value: MET


title: Day6-DMSO, CD11c+I-AI-Eint cells day6_Mac_1


title: AB2721

description: SPIDseq

value: PA

value: MET Core


title: Day3-YPPP, CD11c+I-AI-Eint cells day3_Mac_YPPP_2

value: YPPP for 3 days


title: fin4-SAR 1


title: day 0 - replicate 1 AS-367851-LR-45389

description: day 0 - replicate 1

value: endothelial cells

value: uninjected control animals


title: Day3-YPPP, CD11c+I-AI-Eint cells day3_Mac_YPPP_1

value: Bone marrrow derived macrophages

value: NEB Next Ultra II Directional RNA Library Prep Kit


title: fin4-Mock 3


title: day 0 - replicate 1 AS-367849-LR-45389

description: day 0 - replicate 1


title: AB2720

description: SPIDseq

value: NO

value: Lung section


title: AB2719

description: SPIDseq


title: Day3-DMSO, CD11c+I-AI-Eint cells day3_Mac_2

value: DMSO for 3 days


title: fin4-Mock 2


title: day 0 - replicate 1 AS-367847-LR-45389

description: day 0 - replicate 1


title: AB2717

description: SPIDseq


title: Day3-DMSO, CD11c+I-AI-Eint cells day3_Mac_1


title: AB2716

description: SPIDseq


title: day 0 - replicate 1 AS-367845-LR-45389

description: day 0 - replicate 1


title: fin4-Mock 1


title: WT-SAR 3


title: Day6-YPPP, CD11c+I-AI-Ehigh cells day6_YPPP

value: Bone marrrow derived dendritic cells

value: YPPP for 6 days


title: WT-SAR 2

value: lower leaves


title: WT-SAR 1


title: Day6-DMSO, CD11c+I-AI-Ehigh cells day6_2

value: DMSO for 6 days


title: day 0 - replicate 1 AS-367839-LR-45389

description: day 0 - replicate 1

value: lung

value: WT


title: AB2710

description: SPIDseq

value: C57/b6 PA-GFP

value: MET


title: WT-Mock 3


title: AB2713

description: SPIDseq

value: No-MET

value: Distal normal tissue


title: AB2709

description: SPIDseq


title: day 0 - replicate 1 AS-367853-LR-45389

description: day 0 - replicate 1

value: endothelial cells


title: Day6-DMSO, CD11c+I-AI-Ehigh cells day6

description:
Day6-DMSO, CD11c+I-AI-Ehigh cells
day6


title: day 0 - replicate 1 AS-367837-LR-45389

description: day 0 - replicate 1

value: uninjected control animals


title: AB2708

description: SPIDseq


title: WT-Mock 2


title: WT-Mock 1


title: Day3-YPPP, CD11c+I-AI-Ehigh cells day3_YPPP_2

value: YPPP for 3 days


title: Day6-YPPP, CD11c+I-AI-Ehigh cells day6_YPPP_2

value: NEB Next Ultra II Directional RNA Library Prep Kit


title: AB2703

description: SPIDseq

value: ADJ

value: PA

value: MET Invasive margin


title: day 0 - replicate 1 AS-367843-LR-45389

description: day 0 - replicate 1


title: UKE1 cell 4OH tamoxifen treatment 3

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: In vitro cell culture

data_processing:
The quality control checks of raw sequencing data was performed using fastqc.
The alignment of processed reads against the GRCm38, Mus musculus, reference genome were performed using HISAT2.
The aligned sam files were sorted and converted to bam format using SAMtools, the transcript-based expression was quantified using featurecounts.
the normalisation and diffeerntial expression analysis was performed using DESeq2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: normalized expression level matrix (CPM)

source_name: UKE1 cell 4OH tamoxifen

growth_protocol: HEL cells were cultured in phenol red-free RPMI-1640 medium supplemented with 10% Charcoal Stripped fetal bovine serum and antibiotics. UKE-1 cells were cultured in phenol red-free IMDM medium supplemented with 10% Charcoal Stripped fetal bovine serum , antibiotics (penicillin, 100 I.U./ml; streptomycin, 100 µg/ml), 10% heat-inactivated horse serum (HS) and 1 μM hydrocortisone

extract_protocol:
RNA was isolated by Trizol Reagent, then clean-up by RNeasy Mini Column.
The libraries were prepared from 500ng total RNA with the NEB Ultra II directional RNA seq kit, with a PolyA selection, and ERCC spike ins.

treatment_protocol: Cells in treatment group were either treatded with 4-hydroxytamoxifen or vehicle control for 4 hours

value: 4OH tamoxifen, with HS

tag: replicate

value: replicate 3

tag: group

value: treatment


title: day 0 - replicate 1 AS-367835-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-367833-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-367841-LR-45389

description: day 0 - replicate 1


title: Day3-DMSO, CD11c+I-AI-Ehigh cells day3_2

value: Bone marrrow derived dendritic cells

value: DMSO for 3 days


title: day 0 - replicate 1 AS-367831-LR-45389

description: day 0 - replicate 1

value: lung

value: WT


title: UKE1 cell 4OH tamoxifen treatment 2

description: In vitro cell culture

value: replicate 2


title: AB2702

description: SPIDseq

tag: strain

value: C57/b6 PA-GFP

tag: mouse id

value: MET


title: day 0 - replicate 1 AS-367829-LR-45389

description: day 0 - replicate 1

value: endothelial cells


title: Day3-DMSO, CD11c+I-AI-Ehigh cells day3

description:
Day3-DMSO, CD11c+I-AI-Ehigh cells
day3


title: AB2699

description: SPIDseq

value: NO

tag: sorted cells_(gating)

tag: area

value: No-MET

value: Lung section

value: Distal normal tissue


title: UKE1 cell 4OH tamoxifen treatment 1

description: In vitro cell culture

value: replicate 1


title: day 0 - replicate 1 AS-367827-LR-45389

description: day 0 - replicate 1

value: uninjected control animals


title: Lineage (-) day0_2

description:
Lineage (-)
day0_2

source_name: Bone marrow

value: Lineage negative cells

value: NEB Next Ultra II Directional RNA Library Prep Kit


title: AB2698

description: SPIDseq

tag: sample type

tag: status


title: AB2697

description: SPIDseq

value: ADJ

value: PA

value: MET Invasive margin


title: UKE1 without HS 4OH tamoxifen treatment 3

description: In vitro cell culture

source_name: UKE1 without HS 4OH tamoxifen

value: 4OH tamoxifen, without HS

value: replicate 3

value: treatment


title: Lineage (-) day0

description:
Lineage (-)
day0

tag: cell type


title: day 0 - replicate 1 AS-367825-LR-45389

description: day 0 - replicate 1

tag: tissue

value: lung

tag: genotype

value: WT


title: AB2696

description: SPIDseq

value: C57/b6 PA-GFP

value: MET

value: MET Core


title: Day3-YPPP, CD11c+I-AI-Ehigh cells day3_YPPP

value: Bone marrrow derived dendritic cells

tag: treatment

value: YPPP for 3 days


title: AB2682

description: SPIDseq


title: UKE1 without HS 4OH tamoxifen treatment 2

description: In vitro cell culture

tag: cell line

value: replicate 2


title: day 0 - replicate 1 AS-367823-LR-45389

description: day 0 - replicate 1

value: endothelial cells

value: uninjected control animals


title: day 0 - replicate 1 AS-367821-LR-45389

description: day 0 - replicate 1


title: UKE1 without HS 4OH tamoxifen treatment 1

description: In vitro cell culture

value: replicate 1


title: AB2681

description: SPIDseq


title: AB2694

description: SPIDseq

value: NO

value: No-MET

value: Lung section

value: Distal normal tissue


title: AB2691

description: SPIDseq


title: HEL 4OH tamoxifen treatment 3

description: In vitro cell culture

source_name: HEL 4OH tamoxifen

value: HEL

value: 4OH tamoxifen

value: replicate 3


title: AB2678

description: SPIDseq


title: day 0 - replicate 1 AS-367819-LR-45389

description: day 0 - replicate 1

value: lung

value: WT


title: AB2677

description: SPIDseq

value: C57/b6 PA-GFP

value: MET


title: AB2599

description: SPIDseq


title: AB2690

description: SPIDseq


title: day 0 - replicate 1 AS-367817-LR-45389

description: day 0 - replicate 1


title: HEL 4OH tamoxifen treatment 2

description: In vitro cell culture

value: treatment


title: AB2687

description: SPIDseq

value: PA

value: MET Core


title: UKE1 cell control 3

description: In vitro cell culture

source_name: UKE1 cell

value: with HS

value: control


title: AB2598

description: SPIDseq


title: UKE1 cell control 2

description: In vitro cell culture

value: replicate 2


title: day 0 - replicate 1 AS-367813-LR-45389

description: day 0 - replicate 1

value: endothelial cells

value: uninjected control animals


title: AB2685

description: SPIDseq

value: ADJ

value: MET Invasive margin


title: day 0 - replicate 1 AS-367811-LR-45389

description: day 0 - replicate 1


title: AB2595

description: SPIDseq

value: NO

value: Lung section


title: AB2686

description: SPIDseq


title: UKE1 cell control 1

description: In vitro cell culture

value: replicate 1


title: AB2684

description: SPIDseq


title: day 0 - replicate 1 AS-367809-LR-45389

description: day 0 - replicate 1

value: lung


title: AB2594

description: SPIDseq


title: UKE1 without HS control 3

description: In vitro cell culture

source_name: UKE1 without HS

value: without HS

value: replicate 3


title: AB2683

description: SPIDseq

value: C57/b6 PA-GFP

value: MET


title: AB2593

description: SPIDseq

value: PA


title: day 0 - replicate 1 AS-367807-LR-45389

description: day 0 - replicate 1

value: WT


title: day 0 - replicate 1 AS-367815-LR-45389

description: day 0 - replicate 1


title: UKE1 without HS control 2

description: In vitro cell culture


title: HEL 4OH tamoxifen treatment 1

description: In vitro cell culture

value: HEL

value: 4OH tamoxifen

value: treatment


title: Cortex AH, replicate 1, Multiome (ATAC)

city: Lausanne

first: Flavia

last: Marzetta

address: Quartier Sorge - Batiment Genopode

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: 10x Genomics

library_source: genomic single cell

data_processing:
Cell Ranger ARC 2.0
Multiome FASTQ files were processed with the cellranger-arc count (v2.0.0, 10x Genomics) from the Cell Ranger Multiome pipeline with the default settings on the Mus musculus reference (refdata-cellranger-arc-mm10-2020-A-2.0.0).
3' RNA FASTQ files were processed with the cellranger count (v6.0.0, 10x Genomics) from the Single Cell Gene Expression pipeline on the Mus musculus reference (refdata-gex-mm10-2020-A), specifying the expected number of cells equal to 10'000 and retaining intron mapping reads in the analysis.
Assembly: mm10
Supplementary files format and content: 10X CellRanger hdf5 format files (containing tab-separated values files and matrix files) and ATAC fragments files

source_name: Cortex

growth_protocol: C57BL6N mice fed high fat diet (HFD) for 7 weeks and injected with streptozotocin (STZ)

extract_protocol: Chromium Next GEM Single Cell Multiome

treatment_protocol: Injected 1x with insulin (AH) or injected 12x with insulin during 4 weeks in fed conditions (RH)

tag: phenotype

value: diabetic (HFD+STZ)

tag: Sex

value: male

tag: age

value: 18 week old

value: Cortex

value: Brain cells

value: AH


title: AB2592

description: SPIDseq

value: MET Core


title: day 0 - replicate 1 AS-367805-LR-45389

description: day 0 - replicate 1

source_name: lung

value: lung

value: endothelial cells

value: uninjected control animals


title: UKE1 without HS control 1

description: In vitro cell culture

value: without HS

value: replicate 1

value: control


title: Cortex RH, replicate 1, Multiome (ATAC)

description: 10x Genomics

value: WT

value: RH


title: day 0 - replicate 1 AS-367803-LR-45389

description: day 0 - replicate 1


title: Hypothalamus AH, replicate 2, Multiome (ATAC)

description: 10x Genomics

source_name: Hypothalamus

value: Hypothalamus


title: AB2588

description: SPIDseq

value: C57/b6 PA-GFP

value: NO

value: MET

value: Lung section


title: HEL control 3

description: In vitro cell culture

value: HEL

value: replicate 3


title: AB2586

description: SPIDseq

value: No-MET

value: Distal normal tissue


title: HEL control 2

description: In vitro cell culture

value: replicate 2


title: day 0 - replicate 1 AS-367799-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells


title: AB2585

description: SPIDseq


title: Hypothalamus AH, replicate 1, Multiome (ATAC)

description: 10x Genomics

value: diabetic (HFD+STZ)

value: male

value: 18 week old

value: Brain cells

value: AH


title: AB2533

description: SPIDseq


title: day 0 - replicate 1 AS-367797-LR-45389

description: day 0 - replicate 1

value: WT

value: uninjected control animals


title: HEL control 1

description: In vitro cell culture

value: replicate 1

value: control


title: Cortex AH, replicate 2, RNA

description: 10x Genomics

data_processing:
Cell Ranger count 6.0
Multiome FASTQ files were processed with the cellranger-arc count (v2.0.0, 10x Genomics) from the Cell Ranger Multiome pipeline with the default settings on the Mus musculus reference (refdata-cellranger-arc-mm10-2020-A-2.0.0).
3' RNA FASTQ files were processed with the cellranger count (v6.0.0, 10x Genomics) from the Single Cell Gene Expression pipeline on the Mus musculus reference (refdata-gex-mm10-2020-A), specifying the expected number of cells equal to 10'000 and retaining intron mapping reads in the analysis.
Assembly: mm10
Supplementary files format and content: 10X CellRanger hdf5 format files (containing tab-separated values files and matrix files) and ATAC fragments files

extract_protocol: Chromium Single Cell 3ʹ reagents v3.1

value: Cortex


title: Hypothalamus RH, replicate 1, Multiome (ATAC)

description: 10x Genomics

value: Hypothalamus

value: RH


title: day 0 - replicate 1 AS-367795-LR-45389

description: day 0 - replicate 1

data_processing:
Raw sequencing data was demultiplexed and fastq files were generated using using bcl2fastq software (Illumina, v2.20.0.422).
FASTQ files were mapped to the mouse reference genome using salmon (v0.7.2) and count matrices were constructed with tximport (v1.18.0)
Assembly: GRCm38
Supplementary files format and content: count matrices - CSV file includes raw counts for each sample
Supplementary files format and content: annotation sheets - CSV file inculding metadata for respective count matrix


title: Cortex RH, replicate 2, RNA

description: 10x Genomics


title: AB2532

description: SPIDseq

value: C57/b6 PA-GFP

value: NO

value: No-MET

value: Lung section


title: Cortex AH, replicate 1, Multiome (RNA)

description: 10x Genomics


title: AB2529

description: SPIDseq

value: Whole lungs

value: Relapse-free


title: Cortex RH, replicate 1, Multiome (RNA)

description: 10x Genomics

value: diabetic (HFD+STZ)

value: male


title: WT BMDMs rep3

city: Montreal

first: André

last: Veillette

state: QC

address: 110 Des Pins Ouest Rm1065

department: Molecular Oncology

country: Canada

institute: IRCM

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the reference mouse genome version GRCm38 using STAR version 2.5.1b
Raw counts for each feature from GRCm38 ENSEMBL v93 annotation file were extracted using FeatureCounts v1.6.0
DESeq2 version 1.22.2 was used to normalize gene readcounts and compute differential expression between conditions
Assembly: GRCm38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow derived macrophages were generated by growing freshly isolated bone marrow cells for 7 days in medium supplemented with 30% (vol/vol) L929. cell-conditioned medium, as a source of colony-stimulating factor-1.

extract_protocol:
RNA was isolated from wild-type and SIRPa KO BMDMs using the RNeasy Plus Mini Kit (Cat# 74134, Qiagen), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment.

value: bone marrow cells

value: 8 weeks


title: AB2528

description: SPIDseq


title: WT BMDMs rep2

value: WT


title: day 0 - replicate 1 AS-367801-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells

value: uninjected control animals


title: Hypothalamus AH, replicate 2, Multiome (RNA)

description: 10x Genomics

value: 18 week old

value: Brain cells

value: AH


title: AB2527

description: SPIDseq

value: C57/b6 PA-GFP

value: MET

value: PA

value: MET Core


title: day 0 - replicate 1 AS-367789-LR-45389

description: day 0 - replicate 1


title: WT BMDMs rep1


title: Hypothalamus RH, replicate 2, Multiome (ATAC)

description: 10x Genomics

value: Hypothalamus

value: RH


title: Hypothalamus RH, replicate 2, Multiome (RNA)

description: 10x Genomics

value: diabetic (HFD+STZ)


title: day 0 - replicate 1 AS-367787-LR-45389

description: day 0 - replicate 1


title: SIRPa KO BMDMs rep3

value: SIRPa KO


title: AB2525

description: SPIDseq

value: NO

value: Lung section


title: day 0 - replicate 1 AS-367785-LR-45389

description: day 0 - replicate 1

value: WT


title: AB2524

description: SPIDseq

value: No-MET

value: Distal normal tissue


title: SIRPa KO BMDMs rep2

value: bone marrow cells

value: 8 weeks


title: Hypothalamus RH, replicate 1, Multiome (RNA)

description: 10x Genomics

value: male

value: 18 week old

value: Brain cells


title: day 0 - replicate 1 AS-367783-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells

value: uninjected control animals


title: AB2523

description: SPIDseq

value: C57/b6 PA-GFP


title: SIRPa KO BMDMs rep1


title: day 0 - replicate 1 AS-367781-LR-45389

description: day 0 - replicate 1


title: day 0 - replicate 1 AS-367793-LR-45389

description: day 0 - replicate 1


title: AB2522

description: SPIDseq

value: ADJ

value: PA

value: MET Invasive margin


title: proliferative metastatic 4T1 - replicate 3

data_processing:
Raw sequencing data were demultiplexed and FASTQ files were generated using bcl2fastq software (Illumina, v2.20.0.422). FASTQ files were trimmed using Trimgalore (v0.6.6) and mapped to the GRCm39 mouse reference genome using Bismark (v0.22.3). Forward and reverse strands were collapsed and methylation sites were called in Bismark. Differentially methylated regions were determined with the R package bsseq using default parameters (v1.26.0). For this, biological replicates were summed and methylation fractions for annotated genomic regions between the two conditions were compared. Regulatory elements, promoters and gene bodies were annotated with annotation sheets downloaded from Ensembl database (release 105).
Assembly: GRCm39

source_name: Lung

extract_protocol:
Genomic DNA was extracted using the NucleoSpin tissue mini kit for DNA from cells and tissue (Macherey-Nagel).
WGBS libraries were prepared using the xGenTM Methyl-Seq DNA Library Prep Kit (IDT) with partially modified steps in bead clean-up/size selection (see methods section for details).

value: Lung

value: Sorted metastatic 4T1

value: Breast cancer

value: intravenous injection


title: day 0 - replicate 1 AS-367791-LR-45389

description: day 0 - replicate 1

extract_protocol:
Single cells were sorted directly into 96 well-plates containing 1 µl of lysis buffer per well, centrifuged and snap frozen in liquid nitrogen.
ScRNAseq libraries of tumour cell subpopulations and endothelial cells were constructed using a modified SMART-Seq2 protocol

value: WT


title: day 0 - replicate 1 AS-367779-LR-45389

description: day 0 - replicate 1


title: Late_NaHS_treatment, rep3

city: Chengdu

first: Arman Ali

last: Shah

state: Sichuan

address: Wangjiang road 29, Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu

institute: Sichuan University

description:
Yeast
Late (after 72 hours inoculation)
Late_control_vs_late_NaHS_treatment.txt

data_processing:
Illumina NovaSeq 6000 sequencer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to R64-1-1 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: R64-1-1
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: Saccharomyces cerevisiae strain BY4742

growth_protocol: Yeast cells were grown in synthetic dextrose complete (SDC) according to Longo et al., 2007.

extract_protocol:
The total RNA was extracted using TRIzol Reagent according to the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara, China).
RNA-seq transcriptome library was prepared using TruSeq RNA sample preparation Kit from Illumina (San Diego, CA). Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer. The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle software with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using TopHat software.

treatment_protocol: Early (before 72 hours inoculation) or Late (after 72 hours inoculation) NaHS treatments.

value: NaHS

tag: time of treatment

value: More than 72 hr after inoculation


title: AB2520

description: SPIDseq

source_name: C57/b6 PA-GFP

value: MET

value: MET Core


title: proliferative metastatic 4T1 - replicate 2


title: AB2519

description: SPIDseq


title: Late_NaHS_treatment, rep2


title: Late_control, rep3

description:
Yeast
Late without Treatment
Late_control_vs_late_NaHS_treatment.txt

value: Control


title: Hypothalamus AH, replicate 1, Multiome (RNA)

description: 10x Genomics

value: diabetic (HFD+STZ)

value: male

value: 18 week old

value: Hypothalamus

value: Brain cells

value: AH


title: AB2516

description: SPIDseq

value: C57/b6 PA-GFP

value: NO

value: Lung section


title: day 0 - replicate 1 AS-367775-LR-45389

description: day 0 - replicate 1

value: lung

value: endothelial cells

value: uninjected control animals


title: Late_NaHS_treatment, rep1

value: NaHS


title: proliferative metastatic 4T1 - replicate 1

value: Lung

value: Sorted metastatic 4T1

value: Breast cancer

value: intravenous injection


title: day 0 - replicate 1 AS-367777-LR-45389

description: day 0 - replicate 1

value: WT


title: TPM1KO HPC 4

first: Christopher

last: Thom

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Raw data were aligned using STAR (v2.7.10) and featureCounts were output.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file contains feature counts.
Supplementary files format and content: Each processed data file contains WT vs TPM1KO cells at a given time point.

source_name: iPSC/iPSC-derived cells

extract_protocol:
Bulk RNA was isolated from iPSCs after feeder-free passage (day 0) and iPSC-derived cells, including mesoderm (day 2 cultures), FACS-sorted KDR+CD31+ endothelial cells (day 4), or non-adherent HPCs (day 8-9), using a PureLink RNA Micro kit (Invitrogen) according the manufacturer’s instructions.
CHOPWT14 and CHOP14 TPM1KO iPSC, endothelium, and HPCs libraries were prepared using a Takara Total RNA with ribosomal depletion kit. All other sample libraries were prepared using an Illumina TruSeq stranded kit.

value: iPSC/iPSC-derived cells


title: Late_control, rep2

value: Control

value: More than 72 hr after inoculation


title: latent metastatic 4T1 - replicate 4


title: TPM1KO HPC 3


title: AB2515

description: SPIDseq

value: MET


title: AB2514

description: SPIDseq


title: latent metastatic 4T1 - replicate 3


title: proliferative metastatic 4T1 - replicate 4


title: Late_control, rep1


title: TPM1KO HPC 2


title: Early_NaHS_treatment, rep3

description:
Yeast
Early (before 72 hours inoculation)
Early_control_vs_Early_NaHS_treatment.txt

value: Less than 72 hr after inoculation


title: latent metastatic 4T1 - replicate 1


title: AB2510

description: SPIDseq

value: C57/b6 PA-GFP

value: No-MET

value: Distal normal tissue


title: TPM1KO HPC 1


title: Early_NaHS_treatment, rep2


title: D20R injected labeled EC - replicate 6

data_processing:
Raw sequencing data was demultiplexed and fastq files were generated using using bcl2fastq software (Illumina, v2.20.0.422).
FASTQ files were mapped to the mouse reference genome using salmon (v0.7.2) and count matrices were constructed with tximport (v1.18.0)
Assembly: GRCm38
Supplementary files format and content: CSV file includes raw counts for each sample
Supplementary files format and content: Xlsx file contains metadata

extract_protocol:
RNA was extracted using Arcturus PicoPur Kit (Thermo Fisher Scientific). Total RNA was used for construction of sequencing libraries.
Poly(A) RNA was transcribed to full-length cDNA and amplified using the SMART-Seq2 protocol. Sequencing libraries were prepared using NEBNext® UltraTM II FS DNA library preparation kit (New England Biolabs) according the manufacturer’s protocol with DNA input below 100 ng.

value: Sorted cells

value: Lung endothelial cells

tag: time

value: day 3.5

value: intravenous D20R injection


title: AB2509

description: SPIDseq

value: ADJ

value: PA

value: MET Invasive margin


title: D20R injected labeled EC - replicate 5

value: Lung


title: Early_NaHS_treatment, rep1

value: NaHS


title: AB2508

description: SPIDseq


title: WT HPC 4

value: iPSC/iPSC-derived cells

value: WT


title: WT HPC 3


title: Early_control, rep3

description:
Yeast
Early without Treatment
Early_control_vs_Early_NaHS_treatment.txt

value: Control


title: D20R injected labeled EC - replicate 3


title: Early_control, rep2


title: D20R injected labeled EC - replicate 4


title: Early_control, rep1


title: AB2504

description: SPIDseq

value: NO

value: MET

value: Lung section


title: WT HPC 1


title: AB2507

description: SPIDseq

value: C57/b6 PA-GFP

value: MET Core


title: AB2511

description: SPIDseq

value: No-MET

value: Distal normal tissue


title: TPM1KO D4 4

tag: time point


title: D20R injected labeled EC - replicate 1

value: Sorted cells

value: Lung endothelial cells

value: day 3.5


title: latent metastatic 4T1 - replicate 2

value: Sorted metastatic 4T1

value: Breast cancer

value: intravenous injection


title: NTC_Liver_GalNAc_M_4

city: Worcester

first: Samuel

last: Hildebrand

state: MA

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: University of Massachusetts Medical School

data_processing:
FASTQ files were mapped to the mouse genome using STAR v2.7.6e with default settings. Custom .gtf files were used for each Alzheimer's mouse model.
Transcripts were quantified using RSEM v1.3.3 using default settings.
Libraries were normalized and differential expression analysis was performed using DESeq2 v1.22.2 with apeglm shrinkage and alpha=0.05
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts data from DESeq2 are provided as .csv files. Metadata files for DESeq2 analysis are provided as .csv files.

source_name: Liver

growth_protocol: Mice were fed on a normal chow diet

extract_protocol:
RNA was extracted using the NEB Monarch Total RNA Miniprep Kit (T2010S) with the protocol to purify long as well as short RNAs
Sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep kit (Illumina cat# 20020595) according to the manufacterers protocol. Briefly, PolyA RNA was purified with oligo-dT beads. This RNA was fragmented and first and second strand cDNA was synthesized. 3' cDNA ends were adenylated, adapters were ligated, and the library PCR was performed. library quality was checked using a Bioanalyzer High Sensitivity DNA kit (Agilent cat# 5067-4626). Libraries were purified from adapter dimers by gel extraction. Final libraries were quantified using the KAPA Library Quantification kit (Roche cat# 07960140001) according to the manufacterer's protocol.

treatment_protocol: Mice were injected with either a non-targeting control siRNA or a mouse Apoe targeting siRNA

value: Liver

value: NTC

tag: collection time post-treatment

value: 2 Months

tag: injection

value: Subcutaneous

tag: scaffold/conjugate

value: GalNAc

tag: strain


title: AB2496

description: SPIDseq

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: meta_for_ncbi2.txt

tag: mouse id

value: NO

tag: sorted cells_(gating)

tag: area

tag: sample type


title: NTC_Liver_GalNAc_M_3

tag: tissue


title: AB2495

description: SPIDseq

value: Lung section

tag: status


title: TPM1KO D4 2

tag: cell type

value: iPSC/iPSC-derived cells

tag: genotype


title: NTC_Liver_GalNAc_M_2

tag: treatment


title: 4T1 injected labeled EC - replicate 6

first: Moritz

last: Jakab

address: Im Neuenheimer Feld

institute: German Cancer Research Center

value: Lung

tag: cell line

value: WT

value: intravenous 4T1 injection


title: WT HPC 2


title: 4T1 injected labeled EC - replicate 4

value: Sorted cells


title: NTC_Liver_GalNAc_M_1


title: TPM1KO D4 1


title: AB2493

description: SPIDseq

value: C57/b6 PA-GFP

value: MET

value: PA

value: MET Core


title: WT D4 4


title: D20R injected labeled EC - replicate 2

value: Lung endothelial cells

value: day 3.5

value: intravenous D20R injection


title: 4T1 injected labeled EC - replicate 3


title: ApoEsiRNA_Liver_GalNAc_M_4

value: Liver

value: Apoe siRNA

value: 2 Months


title: WT D4 3


title: AB2503

description: SPIDseq

value: NO


title: AB2488

description: SPIDseq

value: No-MET

value: Lung section

value: Distal normal tissue


title: AB2491

description: SPIDseq


title: TPM1KO D4 3

value: iPSC/iPSC-derived cells


title: WT D4 2

value: WT


title: AB2487

description: SPIDseq


title: ApoEsiRNA_Liver_GalNAc_M_2

value: Subcutaneous

value: GalNAc


title: ApoEsiRNA_Liver_GalNAc_M_1


title: WT D4 1


title: 4T1 injected labeled EC - replicate 5

value: Lung

value: Sorted cells

value: intravenous 4T1 injection


title: AB2486

description: SPIDseq

value: C57/b6 PA-GFP

value: MET

value: PA

value: MET Core


title: D20R injected unlabeled EC - replicate 6

value: Lung endothelial cells

value: day 3.5

value: intravenous D20R injection


title: 4T1 injected labeled EC - replicate 1


title: 2AD_Liver_ApoEsiRNA_3

value: Liver

value: Apoe siRNA

value: 2 Months

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: D20R injected unlabeled EC - replicate 5

value: WT


title: AB2494

description: SPIDseq


title: TPM1KO D2 4

value: iPSC/iPSC-derived cells


title: AB2485

description: SPIDseq


title: TPM1KO D2 3


title: 4T1 injected labeled EC - replicate 2

value: Lung


title: TPM1KO D2 2


title: 2AD_Liver_ApoEsiRNA_2


title: 2AD_Liver_ApoEsiRNA_1


title: D20R injected unlabeled EC - replicate 4

value: Sorted cells


title: D20R injected unlabeled EC - replicate 3


title: AB2481

description: SPIDseq

value: NO

value: Lung section


title: ApoEsiRNA_Liver_GalNAc_M_3

value: Subcutaneous

value: GalNAc


title: TPM1KO D2 1


title: AB2480

description: SPIDseq

value: C57/b6 PA-GFP

value: MET


title: D20R injected unlabeled EC - replicate 2

value: Lung endothelial cells

value: day 3.5


title: 2AD_Liver_NTC_4

value: Liver

value: NTC


title: AB2479

description: SPIDseq

value: No-MET

value: Distal normal tissue


title: D20R injected unlabeled EC - replicate 1

value: intravenous D20R injection


title: 2AD_Liver_NTC_3

value: 2 Months

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: 2AD_Liver_NTC_1


title: AB2377

description: SPIDseq

value: NON-MET

value: ADJ

value: PA

value: MET Invasive margin


title: 4T1 injected unlabeled EC - replicate 4

value: Lung

value: Sorted cells

value: WT

value: intravenous 4T1 injection


title: AB2372

description: SPIDseq

value: C57/b6 PA-GFP

value: NO

value: Whole lungs

value: Relapse-free


title: 2AD_Liver_NTC_2

value: Liver

value: NTC


title: WT D2 3

value: iPSC/iPSC-derived cells


title: WT D2 1


title: WT D2 2


title: 4T1 injected unlabeled EC - replicate 6

value: Lung endothelial cells

value: day 3.5


title: 2AD_NTC_Cortex_F_11

source_name: Brain (Cortex)

value: Brain (Cortex)

value: 2 Months

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: AB2376

description: SPIDseq

value: No-MET


title: TPM1KO D0 5


title: 2AD_NTC_Cortex_F_8


title: AB2370

description: SPIDseq

value: NON-MET

value: ADJ

value: PA

value: MET Invasive margin


title: 4T1 injected unlabeled EC - replicate 3

value: Lung

value: Sorted cells

value: WT

value: intravenous 4T1 injection


title: 2AD_NTC_Cortex_F_10

value: NTC


title: TPM1KO D0 3

value: iPSC/iPSC-derived cells


title: TPM1KO D0 4


title: 2AD_NTC_Cortex_F_7


title: AB2371

description: SPIDseq

value: C57/b6 PA-GFP


title: 2AD_NTC_Cortex_F_6


title: 4T1 injected unlabeled EC - replicate 1

value: Lung endothelial cells

value: day 3.5


title: 4T1 injected unlabeled EC - replicate 2


title: AB2367

description: SPIDseq

value: NO

value: Lung section

value: Distal normal tissue


title: TPM1KO D0 2


title: WT D2 4


title: 4T1 injected unlabeled EC - replicate 5


title: AB2373

description: SPIDseq

value: No-MET

value: Whole lungs

value: Relapse-free


title: LPS treated total EC - replicate 6

value: day 1

value: intraperitoneal LPS injection


title: AB2364

description: SPIDseq


title: WT D0 5


title: 2AD_NTC_Cortex_F_5

value: Brain (Cortex)

value: 2 Months

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: LPS treated total EC - replicate 5

value: Lung

value: Sorted cells

value: WT


title: LPS treated total EC - replicate 3

value: Lung endothelial cells


title: WT D0 3

value: iPSC/iPSC-derived cells


title: AB2363

description: SPIDseq

value: C57/b6 PA-GFP

value: NO


title: 2AD_NTC_Cortex_F_3

value: NTC


title: 2AD_NTC_Cortex_F_4


title: AB2362

description: SPIDseq

value: MET

value: PA

value: MET Core


title: LPS treated total EC - replicate 4

value: day 1


title: AB2361

description: SPIDseq


title: 2AD_NTC_Cortex_M_2


title: 2AD_ApoEsiRNA_Cortex_F_8

value: Apoe siRNA


title: AB2360

description: SPIDseq


title: LPS treated total EC - replicate 1

value: intraperitoneal LPS injection


title: WT D0 2


title: 2AD_ApoEsiRNA_Cortex_F_7

value: Brain (Cortex)

value: 2 Months


title: LPS treated total EC - replicate 2


title: AB2340

description: SPIDseq

value: PreMET

value: Whole lungs

value: Pre-MET


title: PBS treated total EC - replicate 6

value: Lung

value: Sorted cells

value: WT

value: day 3.5

value: intravenous PBS injection


title: AB2336

description: SPIDseq

value: C57/b6 PA-GFP

value: BC #8

value: NO


title: PBS treated total EC - replicate 5

value: Lung endothelial cells


title: HEK293 Oleic Acid + FAC Rep 3

city: W 120 St

first: Brent

middle: R

last: Stockwell

state: New york

department: Biology

institute: Columbia University

description:
BM012
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt

data_processing:
Libraries are then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.
Genome center uses RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human:GRCh38.p12) using kallisto (0.46.1) with bootstrapping and follow on DGE analysis with Sleuth (version 0.30.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text file of est kallisto counts for all samples by gene
Supplementary files format and content: tab-delimited text file of est kallisto counts for all samples by transcript

extract_protocol:
Total RNA was extracted from cells using the AllPrep DNA/RNA Isolation Kit (Qiagen). Quality was assessed with Bioanalyzer (RIN for all samples = 10) and 2-3 ug per sample were submitted to the genome center for library construction.
Core uses poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry

value: Embryonic Kidney

value: Oleic Acid + FAC


title: 2AD_ApoEsiRNA_Cortex_F_6

value: Apoe siRNA

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: WT D0 4

value: iPSC/iPSC-derived cells


title: 2AD_ApoEsiRNA_Cortex_F_5

value: Brain (Cortex)

value: 2 Months


title: AB2332

description: SPIDseq

extract_protocol:
Lung tissues or primary EO771 tumors underwent mechanical and enzymatic digestion for 15 min at 37°C (gentleMACSTM C tube, Miltenyi Biotec Inc., San Diego, CA; 0.1mg/ml DNase type I (Roche), and 1mg/ml Collagenase IV (Worthington) in RPMI-1640). Lungs were dissociated with the m_lung program, and tumors with the h_tumor program. Cells were then filtered through a 100µm cell strainer, washed with cold PBS, and centrifuged (5 min, 4°C, 300g). Following tissue digestion, cells were washed and resuspended in cold FACS buffer (0.5% BSA and 2 mM EDTA in PBS), and incubated with fluorophore conjugated antibodies (CD31-PE/Cy7, Biolegend 102417 ; CD45-APC/Cy7, Biolegend 103115). Following the staining cells were filtered through a 70-µm strainer. Before sorting, cells were stained with DAPI to exclude dead/dying cells. Cell sorting was performed using a BD FACSAria Fusion flow cytometer (BD Biosciences), gating for CD31-CD45+ cells, or when isolating photoactivated cells for CD31-GFP+ (after exclusion of dead cells and doublets).
3' end mRNA libraries were prepared for sequencing using SPID-seq.

value: BC #7

value: No-MET

value: Whole lungs

value: Relapse-free


title: 2AD_ApoEsiRNA_Cortex_F_4


title: PBS treated total EC - replicate 3

city: Heidelberg

value: Lung

value: Sorted cells

value: WT

value: day 3.5

value: intravenous PBS injection


title: HEK293 Oleic Acid + FAC Rep 2

description:
BM008
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt

value: Embryonic Kidney


title: 2AD_ApoEsiRNA_Cortex_F_3


title: AB2202

description: SPIDseq

value: C57/b6 PA-GFP

value: BC #2

value: NO

value: Normal


title: AB2203

description: SPIDseq

value: BC #3


title: PBS treated total EC - replicate 2

value: Lung endothelial cells


title: AB2328

description: SPIDseq

value: BC #6


title: HEK293 Oleic Acid Rep 2

description:
BM006
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt

value: Oleic Acid


title: HEK293 FAC Rep 3

description:
BM011
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt

value: FAC


title: HEK293 FAC Rep 2

description:
BM007
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt


title: 2AD_ApoEsiRNA_Cortex_F_2

value: Brain (Cortex)

value: Apoe siRNA

value: 2 Months

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: PBS treated total EC - replicate 1

value: Lung

value: Sorted cells

value: WT

value: day 3.5


title: HIVE scRNA-seq CYR61 rep4

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

description: HIVE scRNA-seq CYR61 rep4

data_processing:
Data was processed by tool beenet analyze function (version 1.1): $BEENET analyze --sample-name=$sample --ref=$refDir --num-barcodes=5000 --out=$outPath $data1 $data2 (https://download.honeycomb.bio/)
Assembly: mm10 (beenet reference: 20210714-mm10.104)
Supplementary files format and content: Transcript Count Matrix generated by beenet (version 1.1)

source_name: bone marrow

extract_protocol:
Cells were removed from culture plate with accutase and processed using HIVE platform (https://download.honeycomb.bio/)
RNA libraries were prepared for sequencing using standard HIVE scRNA-seq protocols (https://honeycomb.bio/)
HIVE single-cell RNA-Seq ( https://honeycomb.bio/)

treatment_protocol: bone marrow was isolated from hind limbs of mice and cultured for 3 days with M-CSF. Cells were then treated for 24 hours with or without 4ug/mL Cyr61.

tag: gender

value: male

tag: age

value: 10 weeks

tag: agent


title: AB2200

description: SPIDseq

value: C57/b6 PA-GFP

value: BC #1

value: NO

value: Normal

value: Whole lungs


title: AB2197

description: SPIDseq

value: BC #3


title: HEK293 Control Rep2

description:
BM005
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt

value: Embryonic Kidney

value: Vehicle


title: HEK293 Oleic Acid Rep 3

description:
BM010
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt

value: Oleic Acid


title: HEK293 Oleic Acid + FAC Rep 1

description:
BM004
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt

value: Oleic Acid + FAC


title: 2AD_ApoEsiRNA_Cortex_F_1

value: Brain (Cortex)

value: Apoe siRNA

tag: collection time post-treatment

value: 2 Months

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: 5AD_ApoEsiRNA_2Months_M_F10

tag: injection


title: AB2196

description: SPIDseq


title: 5AD_ApoEsiRNA_2Months_M_F9

tag: scaffold/conjugate


title: HEK293 FAC Rep 1

description:
BM003
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt

value: FAC


title: HEK293 Oleic Acid Rep 1

description:
BM002
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt


title: PBS treated total EC - replicate 4

value: Lung

value: Sorted cells

value: Lung endothelial cells

value: WT

tag: time

value: day 3.5

value: intravenous PBS injection


title: HEK293 Control Rep1

description:
BM001
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt


title: HIVE scRNA-seq CYR61 rep3

description: HIVE scRNA-seq CYR61 rep3

tag: strain

value: male

value: 10 weeks


title: HEK293 Control Rep3

description:
BM009
est_counts_genes_kallisto.txt
est_counts_transcipts_kallisto.txt

value: Embryonic Kidney

value: Vehicle


title: 5AD_ApoEsiRNA_2Months_M_F4


title: AB2193

description: SPIDseq

value: C57/b6 PA-GFP

tag: mouse id

value: BC #1

value: NO

tag: sorted cells_(gating)

value: Normal

value: Whole lungs


title: AB2152

description: SPIDseq

tag: area

value: No-MET

tag: sample type

value: Relapse-free


title: HIVE scRNA-seq CYR61 rep2

description: HIVE scRNA-seq CYR61 rep2


title: 5AD_ApoEsiRNA_2Months_M_F8

tag: tissue

value: Brain (Cortex)

value: Apoe siRNA

value: 2 Months

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: HIVE scRNA-seq CTRL rep2

description: HIVE scRNA-seq CTRL rep2

value: control


title: HIVE scRNA-seq CYR61 rep1

description: HIVE scRNA-seq CYR61 rep1

value: male


title: 10X scRNA-seq KO rep2

description: 10X scRNA-seq KO rep2

data_processing:
Data was processed by cellranger count function with default parameter setting (version 3.1.0)
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix generated by cellranger (version 3.1.0)

source_name: liver

extract_protocol:
livers were removed and stored in FBS containing 10% DMSO. Tissue was thawed, digested using Gibco liver digent media on Miltenyi GentleMACS and put through a Miltenyi dead cell removal column. Cells were run through 10X Chromium platform and recovered for sequqncing using standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 12 weeks NASH diet (Tsuchida et al., 2018)

value: Cyr61 KO

value: 24 weeks


title: 5AD_ApoEsiRNA_2Months_M_F7


title: 5AD_ApoEsiRNA_2Months_M_F1


title: HIVE scRNA-seq CTRL rep4

description: HIVE scRNA-seq CTRL rep4

value: 10 weeks


title: AB2192

description: SPIDseq

value: C57/b6 PA-GFP

tag: status


title: C. parvum-infected cells, replicate 3 [cp_24_R3_T1]

city: St. Louis

first: L.

middle: David

last: Sibley

state: MO

address: 425 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

data_processing:
Raw reads from fastq files were mapped to the human reference transcriptome (Ensembl; Homo sapiens version 86) using Kallisto, version 0.46.0. All subsequent analyses were carried out using the statistical computing environment, R version 4.0.4 in RStudio version 2022.07.2 and Bioconductor, version 3.12
Transcript-level counts and abundance data were imported into R and summarized to gene level using the TxImport package. Data was normalized using the TMM method in EdgeR. Differentially expressed genes (FC>2 and FDR<.05) were identified on filtered-normalized, not batch-corrected gene expression matrix by linear modeling and Bayesian statistics using the Limma packageon.
Assembly: Ensembl; Homo sapiens version 86, GRCh38 Release 97
Supplementary files format and content: Tab-delimited text raw data includes raw gene counts summarized by tximport package
Supplementary files format and content: Filtered and normalized data file format and content: Tab-delimited text filtered normalized data includes gene expression for each sample after normalization with EdgeR package (TMM method).
Supplementary files format and content: Study design: Comma-separated values file with study design

source_name: Primary intestinal stem cells, differentiated

extract_protocol:
Cells were homogenized using a QiaShredder column (QIAGEN) and total RNA was purified using an RNeasy Mini kit (QIAGEN), then RNA libraries were prepared using standard Illumina techniques
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.

tag: cell type

value: epithelial intestinal cells (hALI)

tag: genotype

value: WT

value: C. parvum-infected cells


title: AB2189

description: SPIDseq

value: BC #2

value: NO

value: Normal

value: Whole lungs


title: Non-infected cells, replicate 2 [ni_24_R2_T1]

tag: cell line

value: Primary intestinal stem cells, differentiated

tag: treatment

value: Non-infected cells


title: 5AD_ApoEsiRNA_2Months_M_F5

value: Brain (Cortex)

value: Apoe siRNA

value: 2 Months

value: Bilateral Intracerebroventricular


title: AB2130

description: SPIDseq

value: BC #8

value: PreMET

value: Pre-MET


title: HIVE scRNA-seq CTRL rep3

description: HIVE scRNA-seq CTRL rep3

tag: gender

value: male

tag: age

value: 10 weeks

value: control


title: AB2188

description: SPIDseq

value: C57/b6 PA-GFP


title: HIVE scRNA-seq CTRL rep1

description: HIVE scRNA-seq CTRL rep1

tag: agent


title: C. hominis-infected cells, replicate 3 [ch_24_R3]

value: epithelial intestinal cells (hALI)

value: WT

value: C. hominis-infected cells


title: AB2151

description: SPIDseq

value: NO

value: No-MET

value: Whole lungs

value: Relapse-free


title: 10X scRNA-seq CTRL rep2

description: 10X scRNA-seq CTRL rep2

value: Control

value: 24 weeks


title: 5AD_ApoEsiRNA_2Months_M_F3

value: Brain (Cortex)

value: Apoe siRNA

tag: collection time post-treatment

value: 2 Months

tag: injection

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: Non-infected cells, replicate 3 [ni_24_R3_T1]

value: Primary intestinal stem cells, differentiated

value: Non-infected cells

tag: time


title: 10X scRNA-seq CTRL rep1

description: 10X scRNA-seq CTRL rep1

tag: strain

value: male


title: C. parvum-infected cells, replicate 2 [cp_24_R2_T1]

value: epithelial intestinal cells (hALI)

value: C. parvum-infected cells


title: 5AD_ApoEsiRNA_2Months_M_F2

tag: scaffold/conjugate


title: 5AD_NTC_2Months_M_E8

value: NTC


title: 5AD_NTC_2Months_M_E10


title: AB2131

description: SPIDseq

value: C57/b6 PA-GFP

tag: mouse id

value: BC #8

value: NO

tag: sorted cells_(gating)

value: PreMET

value: Pre-MET


title: Non-infected cells, replicate 1 [ni_24_R1_T1]

value: WT


title: 10X scRNA-seq KO rep1

description: 10X scRNA-seq KO rep1

value: Cyr61 KO

value: 24 weeks


title: C. hominis-infected cells, replicate 1 [ch_24_R1]

value: C. hominis-infected cells


title: C. parvum-infected cells, replicate 1 [cp_24_R1_T1]


title: Non-infected cells, replicate 3 [ni_24_R3]


title: AB2126

description: SPIDseq

tag: area

tag: sample type

value: Whole lungs


title: AB2129

description: SPIDseq

value: BC #9

tag: status


title: AB2128

description: SPIDseq


title: 5AD_NTC_2Months_M_E9

tag: tissue

value: Brain (Cortex)

value: 2 Months

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: C. hominis-infected cells, replicate 2 [ch_24_R2]

value: Primary intestinal stem cells, differentiated

tag: cell type

value: epithelial intestinal cells (hALI)

tag: genotype


title: Bulk RNAseq Cyr61 KO rep3

description: Bulk RNAseq Cyr61 KO rep3

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to human reference hg38 by STAR aligner (version 2.6.1a)
Gene count quantification by STAR aligner (option: --quantMode GeneCounts) (version 2.6.1a)
Assembly: mm10
Supplementary files format and content: Gene count quantification by STAR aligner (option: --quantMode GeneCounts) (version 2.6.1a)

extract_protocol:
livers were removed and flash frozen in liquid nitrogen. RNA was extracted with Nebnext II directional library prep kit and 1ug was used per library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Male


title: AB2127

description: SPIDseq

value: C57/b6 PA-GFP


title: 5AD_NTC_2Months_M_E5

tag: treatment

value: NTC


title: Non-infected cells, replicate 1 [ni_24_R1]

tag: cell line

value: Non-infected cells


title: Bulk RNAseq CTRL rep2

description: Bulk RNAseq CTRL rep2

tag: gender

tag: age

value: Control


title: Bulk RNAseq Cyr61 KO rep2

description: Bulk RNAseq Cyr61 KO rep2


title: AB2121

description: SPIDseq

value: BC #7

value: No-MET

value: Relapse-free


title: Bulk RNAseq Cyr61 KO rep1

description: Bulk RNAseq Cyr61 KO rep1

value: 24 weeks


title: AB2122

description: SPIDseq

value: Whole lungs


title: AB2123

description: SPIDseq


title: 5AD_NTC_2Months_M_E4

tag: collection time post-treatment


title: Bulk RNAseq CTRL rep3

description: Bulk RNAseq CTRL rep3


title: 5AD_NTC_2Months_M_E3

tag: injection


title: Bulk RNAseq CTRL rep1

description: Bulk RNAseq CTRL rep1


title: AB2120

description: SPIDseq


title: TREAT_HIGH_3

city: Shijiazhuang

first: chu

last: chen

state: Hebei

address: 361 Zhongshan East Road

department: Department of Toxicology

institute: Hebei medical university

data_processing:
Illumina Casava1.8 software used for basecalling.
First, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
Then aligned reads of samples to the reference genome using Hisat2 package.
The mapped reads of each sample were assembled using StringTie, and all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 and CIRI were used to  identified circRNAs.
Genome_build: mus musculus ensembl release-96
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Male mice, prefrontal cortex of the brain

growth_protocol: The mice normal eating and drinking. Male, C57BL/6 mice, at 5 weeks old, weight 17 ± 2 g. Before experiment, the animals were fed in the experimental room for 3 days to habituate to the environment of the laboratory. An ambient condition with temperature of 25 ± 2 ℃, relative humidity of 50 ± 2%, and photoperiod of 12 h was maintained throughout the study.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ Magnetic Gold Kit (Illumina, San Diego, USA).Then the left RNA was fragmented into pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, USA).

treatment_protocol: The PS NPs via oral gavage once per day and for 6 months.  The mice were treated with water in control group.

value: gavage 50 mg/kg body weight PS NPs

value: prefrontal cortex of the brain


title: Non-infected cells, replicate 2 [ni_24_R2]

value: WT

tag: time


title: 5AD_NTC_2Months_M_E6

value: Brain (Cortex)

value: 2 Months

value: Bilateral Intracerebroventricular

tag: strain


title: 5AD_NTC_2Months_M_E2

tag: scaffold/conjugate

value: Divalent siRNA


title: 5AD_NTC_2Months_M_E1


title: neonatal melanocyte (African-American males) cells, MelasolvTM treated, rep2

city: Yongin-si

first: Kyu-Han

last: Kim

state: Gyeonggi-do

address: 1920 Yonggu-daero, Giheung-gu, Gyeonggi-do, South Korea, AMOREPACIFIC Corp., R&D unit, BioScience Lab

country: South Korea

institute: AMOREPACIFIC Copr.

description:
1me-2_Read_Count
Human primary melanocytes
Chemical treated

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Triommomatic.
Trimmed sequence reads were mapped to human genome reference (UCSC hg19) using HISAT2 and BOWTIE2.
Read counts were quantified using STRINGTie.
Assembly: hg19
Supplementary files format and content: processed_data.txt: Tab-delimited text file including read counts for each Sample.

source_name: neonatal foreskin

growth_protocol: Human epidermal melanocytes derived from neonatal foreskin of moderately pigmented donors (African American males) were cultured in humidified atmosphere with 5% CO2 and supplemented with human melanocyte growth supplement.

extract_protocol:
Total RNA was extracted using the TRIzol reagent.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Melanocyte cells of passage between 2 and 5 were treated with 10ug/ml MelasolvTM for 1 day.

value: neonatal foreskin

value: cultured dermal melanocytes

tag: Sex

value: male

tag: population

value: African-American

value: Melasolv treated for 1 day


title: neonatal melanocyte (African-American males) cells, MelasolvTM treated, rep3

description:
1me-3_Read_Count
Human primary melanocytes
Chemical treated


title: AB2118

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

institute: Weizmann Institute of Science

description: SPIDseq

value: C57/b6 PA-GFP

tag: mouse id

value: BC #7

tag: sorted cells_(gating)

tag: area


title: neonatal melanocyte (African-American males) cells, MelasolvTM treated, rep1

description:
1me-1_Read_Count
Human primary melanocytes
Chemical treated

tag: tissue


title: 5AD_ApoEsiRNA_2Months_F_D10

value: Apoe siRNA


title: AB2117

description: SPIDseq

value: No-MET

tag: sample type

tag: status

value: Relapse-free


title: TREAT_HIGH_2

tag: treatment

value: gavage 50 mg/kg body weight PS NPs


title: neonatal melanocyte (African-American males) cells, untreated, rep3

description:
1C-3_Read_Count
Human primary melanocytes

tag: cell type

value: Untreated


title: TREAT_HIGH_1

value: prefrontal cortex of the brain


title: neonatal melanocyte (African-American males) cells, untreated, rep2

description:
1C-2_Read_Count
Human primary melanocytes


title: 5AD_ApoEsiRNA_2Months_F_D9

value: Brain (Cortex)


title: AB2116

description: SPIDseq

value: BC #6

value: NO

value: Whole lungs


title: neonatal melanocyte (African-American males) cells, untreated, rep1

description:
1C-1_Read_Count
Human primary melanocytes

value: neonatal foreskin


title: 5AD_ApoEsiRNA_2Months_F_D8

value: 2 Months

value: Bilateral Intracerebroventricular

value: Divalent siRNA


title: 5AD_ApoEsiRNA_2Months_F_D7


title: CON_2

value: gavage 0 mg/kg body weight PS NPs


title: CON_1


title: 5AD_ApoEsiRNA_2Months_F_D6


title: siHNRNPU D28 [P21001_121]

city: Solna

first: Kristiina

last: Tammimies

address: Visiongatan 4

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institutet

data_processing:
fastq files were aligned to version GRCh37/hg19 of human reference genome, using Star aligner.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Assembly: GRCh37/hg19 of human reference genome
Supplementary files format and content: tab-delimited text files include sequence counts per gene for each Sample

source_name: iPSCs-derived NES cells differentiated for 28 days

growth_protocol: Patient-derived and previously established NES cells were seeded on 20 µg/ml poly-L-ornithine, and 1 µg/ml laminin precoated plastic surfaces in DMEM/F12 + Glutamax medium supplemented with 0.05X B-27, 1X N-2, 10 ng/ml bFGF , 10 ng/ml EGF and 10 U/ml penicillin/streptomycin, replacing media every day. Upon starting the differentiation, cells were changed to medium with an increased 0.5X B-27 concentration without bFGF and EGF.

extract_protocol:
Cells were lysed in TRIzol reagent (Invitrogen), and RNA isolated with ReliaPrep RNA Cell Miniprep kit (Promega Z6012)
Libraries were prepared using the TruSeq Stranded Total RNA Kit with Ribo-Zero Gold, except for siNTC-D28 and siHNRNPU-D28 libraries prepared with Illumina TruSeq Stranded mRNA kit due to low RNA yields. All libraries were sequenced on the NovaSeq6000 platform with a 2x151 setup using NovaSeqXp workflow in S4 mode flowcell.

value: 0.5 microM siHNRNPU (Dharmacon E-013501-00-0010)


title: 5AD_NTC_2Months_F_D4

value: NTC


title: siNTC D28 [P21001_120]

value: 0.5 microM siNTC (Dharmacon D-001950-01-20)


title: siNTC D28 [P21001_112]


title: AB2029

description: SPIDseq

value: C57/b6 PA-GFP

value: BC #7

value: No-MET


title: AB2113

description: SPIDseq

value: Relapse-free


title: 5AD_NTC_2Months_F_D3


title: siHNRNPU D28 [P21001_119]


title: 5AD_NTC_2Months_F_D5


title: siHNRNPU D28 [P21001_113]


title: AB2028

description: SPIDseq


title: 5AD_NTC_2Months_F_D2


title: AB2027

description: SPIDseq


title: AB2026

description: SPIDseq


title: siNTC D28 [P21001_110]


title: AB2115

description: SPIDseq


title: 5AD_NTC_2Months_F_D1


title: siNTC D28 [P21001_118]


title: AB2023

description: SPIDseq


title: CON_3

value: prefrontal cortex of the brain