title: PDX MCL, PRMT53, 2 weeks in vivo

city: Columbus

first: Shelby

last: Sloan

state: OHIO

address: 410 W 12th Ave

institute: Ohio State University

data_processing:
DESeq2
Pairwise comparisons within each cell type for treatment vs control
Supplementary files format and content: tab-delimited text files

source_name: lymphoma

growth_protocol: PDX in vivo

extract_protocol:
Total RNA was extracted using the Total RNA Purification Kit (Norgen Cat#17200) and QIAshredder Columns (Qiagen Cat#79654). RNA integrity was interrogated using the Agilent 2100 Bioanalyzer.
TrueSeq stranded mRNA libraries were prepared with Poly-A selection Ribodepletion library prep

value: lymphoma

value: PDX AA MCL

value: Mantle Cell Lymphoma

value: MCL


title: Brain, WNV, 7 dpi, m6

status: Public on Sep 27 2023

type: SRA

city: Madrid

first: Miguel A.

last: Martín-Acebes

state: Madrid

address: Ctra. de La Coruña, km 7, 5

country: Spain

institute: INIA-CSIC

library_source: transcriptomic

data_processing:
Average base quality was determined by Fastqc
Sequence reads were trimmed using trimmomatic to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed sequence reads were mapped to mm10 using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1
Known genes and transcripts were assembled with StringTie based on reference genome model.  After assembly, abundance of gene/transcript was calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample.
Read count data was normalized with Relative Log Expression (RLE) method in DESeq2 R library. RLE normalized count was adopted for negative binomial Wald Test(nbinomWaldTest) in DESeq2.
Statistical analysis is performed using Fold Change, nbinomWaldTest using DESeq2 per comparison pair. Significant results are selected on conditions of |fc|>=2 & nbinomWaldTest raw p-value<0.05.
Assembly: mm10
Supplementary files format and content: processed_data_brain.xlsx represents counts, FPKMs, TPMs for all samples

molecule: total RNA

organism: Mus musculus

source_name: Brain

growth_protocol:
Experimental infections in mice were performed in the biosafety level 3 (BSL-3) facilities at Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CISA, INIA-CSIC)
Animals were kept with ad libitum access to food and water and were anesthetized under isoflurane and humanely sacrificed at 3, 7 and 10 days post-infection.

extract_protocol:
Total brain RNA was extracted from tissue samples using Ribopure following manufacturer's protocols
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol:
Mice were infected intraperitoneally (i.p.) with 10e4 plaque forming units (PFU) of WNV in 200 µL of Minimum Essential Medium Eagle (Corning) mock-infected animals were also inoculated i.p. with 200 µL of culture media
Mock-infected animals were also inoculated i.p. with 200 µL of culture media

tag: strain

tag: tissue

value: Brain

tag: genotype

value: WT

tag: infection

value: WNV

tag: time

value: Day 07


title: Hi-C_CK-p25_Step2Replicate3

city: Cambridge

first: Vishnu

last: Dileep

state: MA

address: 43 Vassar St

department: Brain and Cognitive Sciences

country: USA

institute: Massachusetts Institute of Technology

library_source: genomic

data_processing:
Hi-C experiments were analyzed using Homer and Juicer pipeline
For HOMER pipeline, Reads were trimmed for GATC sites and mapped using bowtie2. Mapped reads were analyzed using the makTagDirectory command in the Homer pipeline. Processed files (.hic) were created using the tagDir2hicFile.pl script in Homer.
In addition to homer pipeline, Juicer pipeline was used to create hic files for combined CK-p25 samples Con, Step 1, and Step 2 as described in Rao et al.,2014. In Brief, paired-end read pairs were aligned separately to the mouse genome (mm10) using BWA. Next, duplicates/invalid pairs were removed. Interaction matrices were generated at resolutions of 2.5Mb, 1Mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, and 5kb.
Assembly: mm10
Supplementary files format and content: Processed Hi-C data in an indexed binary format (.hic) that can be accessed using the Juicebox tool (https://aidenlab.org/juicebox/)

molecule: genomic DNA

source_name: Forebrain

extract_protocol:
In situ Hi-C was performed as previously described in Rao et al., 2014. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. P301S Tau mice and primary neuronal culture Hi-C were performed using FANS isolated nuclei with the Dovetail Hi-C kit (SKU: 21004) Illumina libraries were sequenced in 38 bp paired-end mode.
Library construction was performed using the custom protocol as described in Rao et al, 2014 or using the library preparation module in the Dovetail Hi-C kit (SKU: 21004)
Illumina libraries were sequenced in 38 bp paired-end mode

value: Forebrain

tag: cell type

value: Neuron

tag: treatment

value: 2 weeks induction (removal of doxycycline from diet)


title: Hi-C_CK-p25_Step1Replicate3


title: Brain, WNV, 7 dpi, m2


title: PDX MCL, PRMT52, 2 weeks in vivo

organism: Homo sapiens

tag: cell line


title: PDX MCL, PRMT51, 2 weeks in vivo


title: Brain, Mock, 7 dpi, m8

value: Mock


title: Hi-C_ETP_5uM48h_91374012

source_name: Primary culture

value: Primary culture

value: Etoposide


title: Brain, Mock, 7 dpi, m10


title: Hi-C_CK-p25_Step2Replicate1


title: Hi-C_CK-p25_Step1Repicate1


title: CN1030L1

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

data_processing:
Fastq files were mapped to the UCSC hg19 reference genome using STAR
gene-level counts were obtained from the alignment using featureCounts from the SubRead package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: iPSC-derived nerons

growth_protocol: Induced pluripotent stem cells (iPSCs) were generated from four subjects (two males and two females). Specifically, we performed iPSC reprogramming using peripheral blood mononuclear cells (PBMCs) and the CytoTune™-iPS 2.0 Sendai Reprogramming Kit (A16517, Thermo Fisher, USA) as described previously. All iPS cell lines showed normal karyotypes, and they all expressed pluripotency markers. Cell lines were regularly characterized and verified to be free from mycoplasma. We then generated iPSC-derived forebrain neurons as reported previously. Briefly, iPS cells were cultured on Matrigel with mTeSR1 Plus media (STEMCELL technology, MA, USA). We suspended 3-D iPSC aggregates in embryoid body (EB) medium, consisting of FGF-2-free iPS cell medium supplemented with 2 μM dorsomorphin (STEMCELL technology, MA, USA) and 2 μM A-83 (STEMCELL technology, MA, USA), in non-treated polystyrene plates for 6 days. EB Medium was renewed every day. After 6 days, we replaced EB medium by neural induction medium (NPC medium) consisting of DMEM/F12, 1x N2 supplement, 1x NEAA, 2 ug ml−1 heparin (Tocris Bioscience) and 2 μM cyclopamine (Tocris Bioscience). The floating EBs were then transferred to Matrigel-coated plates at day 7 to form neural tube-like rosettes. The attached rosettes were kept for 15 days with NPC medium change every other day. On day 22, we transferred the rosettes to low attachment plates in NPC medium containing 1x B27 (Thermo fisher). On day 24, neural progenitor spheres were dissociated and placed onto Matrigel-coated plates in neuron culture medium, consisting of Neurobasal medium supplemented with 1x glutamax, 1x B27, 0.2 mM L-Ascorbic Acid, and 0.5 mM cAMP (Sigma-Aldrich, St Louis, MO), 10 ng ml−1 BDNF and 10 ng ml−1 GDNF. Medium was replaced every three days during continuous culture

extract_protocol:
Total RNA was extracted using Trizol and the RNeasy mini kit (Qiagen, Valencia, CA, USA). The RNA integrity numbers (RIN) were above 9.5 for RNA samples.
RNA-seq experiments were conducted by GENEWIZ using an Illumina HiSeq 4000 with eight samples in each lane using 100bp paired end index reads

treatment_protocol: The naïve form of FGF21 (100 ng/mL, PeproTech, cat: 100-42) at physiologically relevant concentration was used to perform the proposed experiments. Additionally, the concentrations of the naïve form of FGF21 (Peprotech, cat#100-42) [17; 18] and PF-05231023 (MedChemExpress, cat: HY-113697)  were selected to fall within the range of blood concentrations for this drug observed during preclinical and clinical studies.

value: iPSC-derived nerons

value: 7 days treatment with drug renew daily


title: PDX MCL, IB2, 2 weeks in vivo

value: ibrutinib


title: Hi-C_CK-p25_Step1Replicate2


title: Brain, Mock, 7 dpi, m5


title: Hi-C_CK-p25_ConReplicate3


title: Brain, Mock, 7 dpi, m9


title: PDX MCL, IB1, 2 weeks in vivo

value: lymphoma


title: Brain, Mock, 7 dpi, m6


title: PDX MCL, VC2, 2 weeks in vivo

value: PDX AA MCL

value: Vehicle Control


title: PDX MCL, IB3, 2 weeks in vivo

value: Mantle Cell Lymphoma

value: MCL


title: CN1030F1


title: PDX MCL, VC3, 2 weeks in vivo


title: PDX MCL, VC1, 2 weeks in vivo


title: CN1030F2


title: Brain, Mock, 7 dpi, m3

value: Brain

value: WT


title: Brain, WNV, 3 dpi, m8

value: WNV

value: Day 03


title: Hi-C_CK-p25_ConReplicate2

value: Forebrain

value: Neuron


title: Brain, WNV, 3 dpi, m9


title: Hi-C_CK-p25_ConReplicate1

value: 2 weeks induction (removal of doxycycline from diet)


title: BLISS_CKp25_Step2_Replicate2

data_processing:
FASTQ files were demultiplexed based on sample barcodes
PCR duplicates were removed based on the UMI
Reads after removing PCR duplicates were mapped to mm10 genome build using Bowtie2
Mapped sam files were converted to bam files using samtools view and to bed files using bedtools bamtobed
Assembly: mm10
Supplementary files format and content: bed files with DNA double-strand break locations

extract_protocol:
BLISS was performed as previously described in Yan et al., 2017. Sorted neurons were attached to a MatTek 35 mm Dish | No. 1.0 Coverslip | 14 mm Glass Diameter | Poly-D-Lysine Coated (P35GC-1.0-14-C) by adding sorted cells to the center coverslip in 4% formaldehyde in PBS and spinning at 2000xg for 2 minutes. The attached nuclei were then end-repaired and A-tailed. Next BLISS adaptors were ligated overnight at 16°C. Excess BLISS adaptors were washed off and genomic DNA was isolated. Next DNA was sonicated to an average size of 500 bp and in-vitro transcribed. Transcribed RNA was isolated, and reverse transcribed to cDNA to prepare Illumina sequencing libraries.
Custom BLISS adaptors containing RA3 and RA5 sequences were amplified using RP1 and  selected RPI Illumina primers as described in the Illumina TruSeq Small RNA Library Preparation Kit.
Illumina libraries were sequenced in 75 bp single-end mode.

value: Neurons


title: OA_FLS1_UT

city: Atlanta

first: Sergio

last: Ramirez-Perez

state: Georgia

address: 615 Michael St NE

department: Orthopaedics

institute: Emory University

description: FLS_OA 1 - log2 total RPKM

data_processing:
NovaSeq 6000 Paired-end sequencing was used, PE150, Q30≥85%.
Sequenced reads were mapped to the homo sapiens GRCh37 genome assembly using DNASTAR software, normalization was performed by RPKM on ArrayStar software . We obtained xxx genes.
Assembly: GRCh37
Supplementary files format and content: Matrix table - delimited text files include normalized expression levels for each sample

source_name: FLS

extract_protocol:
Synovial fibriblats from RA and OA patients were cultured and RNA was harvested using Trizol reagent.
Human mRNA Sequencing (WOBI) was used to perform RNA sample QC. Poly A enrichment was implemented for mRNA library preparation. NovaSeq PE150 was used to generate 6 G raw data per sample.

value: FLS

value: Untreated

tag: diagnosis

value: Osteoarthritis


title: JBV_145-2

type: RNA

city: Gifu

first: Kazuki

last: Heishima

address: Yanagido 1-1

country: Japan

institute: Gifu University

description: Gene expression in JBV cells treated for 48hr with miR-145

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarray 8x60K Version 3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: JBV, 48hr, miR-145, replicate 2

label_protocol: Labeling was performed with Agilent Low input Amp Labeling Kit (Cat. #5190-2305, Agilent).

growth_protocol: RPMI1640 supplemented with 10%FBS

extract_protocol: After 2 washes with PBS, the cells were lysed with 400 µL of Homogenization Solution containing 4 µL of 1-Thioglycerol. Subsequently, 200μl of Lysis Buffer was added to 200 µL of 1-Thioglycerol/Homogenization Solution containing lysed cells. After vigorous vortex for 15 seconds, all 400 μL of the lysate was transferred to Maxwell RSC Cartridge. After 5 μL of the DNase I Solution had been added to the cartridge, the cartridge was applied to the Promega Maxwell RSC instrument, and total RNA was purified. The RNA integrities of the samples were checked by using Agilent 2100 Bioanalyzer (Agilent, CA, USA).

treatment_protocol: JBV cells were treated for 48 hours with control miRNA or miR-145.

tag: tumor type

value: Bladder cancer

tag: tissue/cell line

value: cell line


title: RA_FLS3_ST2825

description: RA_ST2 - log2 total RPKM

value: Rheumatoid arthritis


title: RA_FLS4_ST2825

description: RA_ST3 - log2 total RPKM


title: Brain, WNV, 3 dpi, m2


title: RA_FLS1_ST2825

description: RA_ST1 - log2 total RPKM


title: RA_FLS4_LPS_ST2825

description: LSP_ST-3 - log2 total RPKM

value: LPS + ST2825


title: RA_FLS3_LPS_ST2825

description: LPS_ST-2 - log2 total RPKM


title: Brain, WNV, 3 dpi, m1


title: JBV_145-1

source_name: JBV, 48hr, miR-145, replicate 1


title: JBV_C2

description: Gene expression in JBV cells treated for 48hr with control miRNA

source_name: JBV, 48hr, control miRNA, replicate 2


title: Brain, WNV, 3 dpi, m4


title: BLISS_CKp25_Step1_Replicate2


title: BLISS_CKp25_Con_Replicate1


title: BLISS_CKp25_Step1_Replicate1


title: JBV_C1

source_name: JBV, 48hr, control miRNA, replicate 1


title: Vitiligo 7

city: Chia-Yi

first: Hui

middle: Chun

last: Yu

address: No. 2, Min-Sheng Rd, Dalin Town

department: Medical research

country: Taiwan

institute: Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation

description: T cells isolation from Vitiligo patients PBMC

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing:
Scanned images are analyzed by Feature extraction10.7.3.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.
Raw signal data was normalized by quantile normalization for differential expressed genes discovering.

source_name: peripheral blood mononuclear cell

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

extract_protocol: Total RNA extraction was performed using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The extracted RNA was quantified by a ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) at OD260 nm and then qualitied by a Bioanalyzer 2100 (Agilent Technology, USA) using an RNA 6000 labchip kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Freshly drawn peripheral blood from healthy controls and vitiligo patinets. Leukocyte-enriched supernatants were separated using a Ficoll-Hypaque density gradient solution (specific gravity 1.077; Pharmacia Biotech, Uppsala, Sweden). The mononuclear cells were then aspirated from the interface, after centrifugation at 250 × g for 25 min. Finally, T cells were obtained using anti-human CD3-coated magnetic beads by the IMag Cell Separation System (BD Bioscience, Franklin Lakes, NJ, USA).

value: T cells

tag: gender

value: female

tag: subject status

value: Vitilogo patient


title: Tfeb TG 3

city: Los Angeles

first: Christine

last: Quach

state: CA

address: 1450 Biggy St NRT 5509

institute: University of Southern California

data_processing:
RNA-seq data analysis was done using Partek Flow v 10.0
Sequence reads were trimmed based on quality score (min quality score 20, min length 25)
Trimmed sequence reads were mapped using STAR 2.7.3a to both genome (mm10) and transcriptome (Gencode vM25)
Aligned sequence reads were quantified to Gencode vM25 using Partek E/M
Gene-level read counts were filtered to exclude low-expressed genes (exclude genes where maximum <=10) and normalized (add 1 then upper quartile normalization)
Differential expression analysis was done using Partek's Gene-Specfic Analysis (GSA) analysis
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw read counts for Atg5 samples
Supplementary files format and content: Tab-delimited text files include raw read counts for Tfeb samples

source_name: Lung

extract_protocol: RNA was harvested using RNeasy Mini Kit (Qiagen). 10ng of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Mice were administered Poly(I:C) intranasally for 3 consecutive days.

value: Lung

value: CD11c+ APCs

value: Pulmonary macrophages, monocytes, dendritic cells


title: Vitiligo 6


title: Control 4

description: T cells isolation from heathly controls  PBMC

value: heathly control


title: BLISS_CKp25_Con_Replicate2

value: Forebrain


title: Brain, Mock, 3 dpi, m7

value: Brain

value: WT

value: Mock

value: Day 03


title: Brain, Mock, 3 dpi, m8


title: F712 Oxycodone, low

city: La Jolla

first: Francesca

last: Telese

address: 9500 Gilman Drive

department: Psychiatry

institute: UCSD

description:
Single nucleus RNA transcripts from NAcc
933000320187083

library_source: transcriptomic single cell

data_processing:
library strategy: snRNA-seq (Mulitome GEX)
The FASTQ data were firstly aligned to the Rattus norvegicus mRatBN7.2/rn7 genome using the CellRanger arc 2.0.0 pipeline
Assembly: mRatBN7.2/rn7
Supplementary files format and content: filtered_feature_bc_matrix.h5

organism: Rattus norvegicus

source_name: Brain-Nucleus accumbens core (NAcc)

growth_protocol: The brain tissues were collected from rats sacrificed after 4 weeks of prolonged abstinence from oxycodone intravenous self-administration. The rats used in this study displayed a low addiction index-like behavior, which is calculated using several behavioral measures, as detailed in Carrete et al, 2021.

extract_protocol:
Brain tissue was extracted and snap-frozen (at −30°C). Cryosections of approximately 500 microns (Bregma 2.28-0.72 mm) were used to dissect the nucleus accumbens core punches on a −20°C frozen stage. Punches from three sections were combined for each rat.
using the Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog number 1000282) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide (10X Genomics)

value: Brain-Nucleus accumbens core (NAcc)

tag: Sex

value: F

value: heterogeneous stock

value: Oxycodone


title: RA_FLS3_LPS

description: RA_LPS_2 - log2 total RPKM

value: FLS

value: LPS

value: Rheumatoid arthritis


title: Tfeb TG 1


title: Control 2

value: T cells

value: female


title: Tfeb TG 2

value: Lung

value: CD11c+ APCs


title: RA_FLS1_LPS

description: RA_LPS_1 - log2 total RPKM


title: BLISS_CKp25_Step2_Replicate1

value: Neurons

value: 2 weeks induction (removal of doxycycline from diet)


title: RA_FLS1_LPS_ST2825

description: LPS_ST-1 - log2 total RPKM

value: LPS + ST2825


title: oBM1_hsc_CITEseq

city: Lund

first: Göran

last: Karlsson

state: Scania

address: Kilinkgatan 26 BMC B12

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

data_processing:
Library strategy: CITE-seq
Libraries were processed using Cellranger version 3.0.2 to generate the count matrices. The count matrices were demultiplexed into individual samples based on HTO UMIs. Cells that had minimum 50% reads from one of the HTO were assigned to that corresponding sample.
Genome_build: hg38
Supplementary_files_format_and_content: The count matrices were saved in MTX format along with Barcodes (TSV format file) and gene names (TSV format file). For each sample, for three files were zipped together and deposited in GEO

source_name: Aged Bone Marrow sample1

extract_protocol:
For CITE-seq; cell were stained with CITEseq antibodies, sorted and 10x genomics 3' RNA was performed.
Libaries were prepered according to 10x genomics 3’ V2 kit with the addition of CITEseq protocol. Libraries were sequenced on a Illumina Nextseq.

tag: population

value: FACS sorted

value: human hematopoietic stem cell (HSC)


title: Brain, Mock, 3 dpi, m9

value: Brain

value: WT

value: Mock

value: Day 03


title: Brain, Mock, 3 dpi, m3


title: RA_FLS4_UT

description: RA_UT3 - log2 total RPKM

value: Untreated


title: Vitiligo 4

value: Vitilogo patient


title: oBM2_hpc_CITEseq

source_name: Aged Bone Marrow sample2


title: Tfeb WT 2

value: Pulmonary macrophages, monocytes, dendritic cells

value: Tfeb flox/flox


title: Control 3

value: T cells

value: heathly control


title: Brain, Mock, 3 dpi, m6


title: F411 Oxycodone, low

description:
Single nucleus RNA transcripts from NAcc
933000320047485

value: Brain-Nucleus accumbens core (NAcc)

value: F

value: heterogeneous stock

value: Oxycodone


title: Brain, 2-DG, 6 dpi, m1

data_processing:
Average base quality was determined by Fastqc
Sequence reads were trimmed using trimmomatic to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed sequence reads were mapped to mm10 using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1
Known genes and transcripts were assembled with StringTie based on reference genome model.  After assembly, abundance of gene/transcript was calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample.
Read count data was normalized with Relative Log Expression (RLE) method in DESeq2 R library. RLE normalized count was adopted for negative binomial Wald Test(nbinomWaldTest) in DESeq2.
Statistical analysis is performed using Fold Change, nbinomWaldTest using DESeq2 per comparison pair. Significant results are selected on conditions of |fc|>=2 & nbinomWaldTest raw p-value<0.05.
Assembly: mm10
Supplementary files format and content: processed_data_drugs.xlsx represents counts, FPKMs, TPMs for all samples

growth_protocol:
Experimental infections in mice were performed in the biosafety level 3 (BSL-3) facilities at Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CISA, INIA-CSIC)
Animals were kept with ad libitum access to food and water and were anesthetized under isoflurane and humanely sacrificed at 6 days post-infection.

treatment_protocol:
Mice were infected intraperitoneally (i.p.) with 10e4 plaque forming units (PFU) of WNV in 200 µL of Minimum Essential Medium Eagle (Corning) and mock-infected animals were also inoculated i.p. with 200 µL of culture media
Drugs were intraperitoneally administered at a dose 200 mg/Kg for DCA or 500 mg/Kg in the case of 2-DG

value: WNV

value: Day 06


title: Tfeb WT 3

value: Lung

value: CD11c+ APCs


title: RA_FLS4_LPS

description: RA_LPS_3 - log2 total RPKM

value: FLS

value: LPS

value: Rheumatoid arthritis


title: Brain, Mock, 3 dpi, m1

value: Brain

value: WT

value: Mock

value: Day 03


title: yBM1_hsc_CITEseq

source_name: Young Bone Marrow sample1

value: FACS sorted

value: human hematopoietic stem cell (HSC)


title: Atg5 KO 2

value: Pulmonary macrophages, monocytes, dendritic cells


title: yBM2_hpc_CITEseq

source_name: Young Bone Marrow sample2


title: oBM1_hpc_CITEseq


title: Tfeb WT 1

value: Tfeb flox/flox


title: Brain, 2-DG, 6 dpi, m4


title: RA_FLS3_UT

description: RA_UT2 - log2 total RPKM

value: Untreated


title: yBM1_hpc_CITEseq


title: MS0183KK

city: New Haven

first: Matthew

last: Girgenti

address: 34 Park St

institute: Yale School of Medicine

library_source: genomic single cell

data_processing:
ArchR was used to cluster the data and annotate cell types
MACS2 was used to call peak in the seven cell types
bigWig files were generated in ArchR
Supplementary files format and content: bw

source_name: post mortem human brain

extract_protocol:
20-30 mg of pulverized tissue was added into 5 ml of ice-cold “lysis buffer”, Protector, protease inhibitors, TX-100 were added immediately before use. The suspension was transferred to Dounce tissue grinder (15ml volume, Wheaton #357544; autoclaved, RNAse free, ice-cold) and homogenized with loose and tight pestles, 30 cycles each, with constant pressure and without introduction of air. The homogenate was strained through 40-µm tube top cell strainer  pre-wetted with 1ml “isolation buffer”. Final 15 ml of solution was mixed by inverting the tube 10x and carefully pipetted into 2 ultracentrifuge tubes onto the “isolation buffer” cushion (5 ml) without disrupting the phases. The tubes were centrifuged at 30000 x g, for 60 min at 4 ˚C on the ultracentrifugeand rotor. Upon end of ultracentrifugation, the supernatant was carefully and completely removed and 100 ul of resuspension buffer Pellets were gently dissolved by pipetting 30x with 1ml pipette tip, pooled and filtered through 35-µm tube top cell strainer Finally, nuclei were counted on hemocytometer and diluted to 1 million/ml with “sample-run buffer”.
The nuclei samples were processed within for snATAC-seq with targeted nuclei recovery of 10,000 nuclei on microfluidic Chromium System (10x Genomics) by following the manufacturer’s protocol (10x Genomics, ATAC).
single nuclei ATAC-seq

value: post mortem human brain

tag: disease

value: normal control


title: yBM2_hsc_CITEseq


title: Brain, 2-DG, 6 dpi, m5

source_name: Brain

value: WNV

value: Day 06


title: MS0145YY

value: psychiatric diagnostic group PTSD


title: Atg5 WT 3

value: Lung

value: CD11c+ APCs

value: Atg5 flox/flox


title: Atg5 KO 3


title: CB3_hsc_CITEseq

source_name: Cord Blood sample3


title: MS0204LL

value: psychiatric diagnostic group MDD


title: RA_FLS1_UT

description: RA_UT1 - log2 total RPKM

value: FLS

value: Rheumatoid arthritis


title: Atg5 KO 1


title: MS0197YY


title: Brain, 2-DG, 6 dpi, m2

value: Brain

value: WT


title: CB2_hsc_CITEseq

source_name: Cord Blood sample2

value: FACS sorted

value: human hematopoietic stem cell (HSC)


title: Brain, 2-DG, 6 dpi, m3


title: Atg5 WT 2

value: Pulmonary macrophages, monocytes, dendritic cells


title: MS0097BB


title: Brain, DCA, 6 dpi, m2

value: DCA


title: Atg5 WT 1


title: cd4pos.WT.rep3

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

data_processing:
Consistent quality validation using FastQC v0.11.2 (Babraham Institute).
Raw reads were trimmed to remove adapters and bases with average quality score (Q; Phred33) of 20 using a 4-bp sliding window (SlidingWindow:4:20) with Trimmomatic v0.32 (Bolger et al., 2014).
Trimmed reads were aligned to the primary assembly of the GRCm38 mouse genome using STAR v2.4.1a removing alignments containing noncanonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical).
Aligned reads were assigned to genes in the GENCODE vM13 comprehensive gene annotation using featureCounts (v1.4.6-p4) with default settings.
Differential expression analysis was performed using DESeq2 (v1.22.0) running on R (v3.5.1).
Assembly: mm10
Supplementary files format and content: cd4pos.rnaseq.KO_v_WT.TPM.txt: Tab-delimited text file (single table) including TPM values, ENSEMBL IDs and gene symbols for all samples.

source_name: Inguinal lymph node

extract_protocol:
Single cell suspensions were obtained from iLNs of host mice (Tcra-/-), and fate-mapped (ZsGreen+) WT or KO cells were FACS-sorted. RNA was purified using the RNeasy Plus Micro Kit (Qiagen).
Library construction was performed at Duke Sequencing and Genomic Technologies Shared Resource facility using the Clontech SMARTer v3/v4 Ultralow Input RNA-seq Kit (Takara Biosciences).

treatment_protocol: EAE induction

value: Inguinal lymph node

tag: disease state

value: Day 7

value: Fate-mapped primary CD4+ T cell

value: Il17aCre/WT R26Zsgreen/WT

tag: congenic marker

value: Female


title: CB3_hpc_CITEseq


title: CB1_hsc_CITEseq

source_name: Cord Blood sample1


title: Brain, DCA, 6 dpi, m4

tag: strain

tag: tissue

value: WNV

value: Day 06


title: MS0095YY

value: post mortem human brain


title: MCF7 cells, epirubicin, 100 nM, rep3

city: Ottawa

first: Julie

last: St-Pierre

state: Ontario

address: 451 Smyth Rd

department: Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Ottawa

description:
Epi100_3
EpirubicinResistantCells_log2CPM.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (v0.38)
Trimmed sequence reads were mapped to GRCh38.p13 using STAR (v2.7.3a) (parameters- quantMode: GeneCounts sjdbOverhang: 100)
Read count extraction was performed using subread (v2.0.0)
Read normalization and statistics were performed with edgeR (v3.34.1)
Assembly: GRCh38.100
Supplementary files format and content: tab-delimited text files include log2 CPM values for each Sample

source_name: Breast adenocarcinoma

extract_protocol:
Five million cells were collected at passage and rinsed with ice-cold PBS before being snap-frozen on dry ice. Total RNA was extracted using PureLink RNA Mini Kit (ThermoFisher) and Purelink DNase Set according to manufacturer's instructions.
Paired-end libraries were made using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina and according to manufacturer's instructions.

value: Breast adenocarcinoma

value: epirubicin 100 nM


title: CB2_hpc_CITEseq


title: Brain, DCA, 6 dpi, m5

tag: genotype

tag: infection


title: MS0002II

value: normal control


title: Brain, DCA, 6 dpi, m1

value: Brain

tag: time


title: cd4pos.WT.rep2

tag: cell type


title: CB1_hpc_CITEseq

tag: treatment


title: MCF7 cells, epirubicin, 100 nM, rep2

description:
Epi100_2
EpirubicinResistantCells_log2CPM.txt

tag: cell line


title: yBM_CD11_on_yBM_hsc_scATAC-seq

description: Cut-sites of yBM_CD11A recounted on yBM_hsc peaks (see data processing step)

data_processing:
Barcode filtering: Post-sequencing nuclei were processed using the cellranger-atac pipeline (version 1.2.0), after alignment to the human genome (GRCh38) and barcode identification. Each barcode identified by Cellranger in the aligned reads are categorized into either cell associated barcodes or background barcodes. To perform this categorization, a sorted list of the total number of UMIs (Log2 transformed) associated with each barcode were created. Thereafter the minima in the gradient of this list were calculated using Numpy’s ‘gradient’ function. The minima in the first 100 and beyond 10000th elements are ignored because the expected number of cells were between that range. Cells were further removed if they had had either too high (log2 % > 4) or too low (log2 % < -3) percentage of reads from mitochondrial genes.
MACS2 peak calling: Only the fragments were recovered from the BAM by considering only those reads that aligned as proper pairs and with mapping quality (MAPQ score) higher than 20. Fragments associated with non-cell barcodes were discarded. The terminal ends of the fragments were saved thus recording all the cut sites in the BAM files. The chromosome-wise BED files of cut sites were merged from the replicates and only one cut site was recorded at a given genomic location. The sorted, replicate merged, chromosome-wise BED files were then used to identify regions of high accessibility (‘peaks’) using MACS2 software. For each population of cells the same parameters used in the MACS2 call were: ‘-s 150 --nomodel --shift -75 --extsize 150’; the genome size was set as chromosome size in each MACS2 call. Next, in order to create a cell-peak matrix of each population, the number of cut sites in each peak for each cell were recounted.
Additionally, the cut-sites of the samples for the peak regions of other samples were also counted. For example, the cut-sites from yBM CD38- (yBM_hsc )cells were taken and recounted in the yBM CD34+ (yBM_hpc)peaks to create a cell-peak matrix called 'yBM_hsc_on_yBM_hpc'
Genome_build: GRCh38
Supplementary_files_format_and_content: The count matrices were saved in MTX format along with Barcodes (TSV format file) and gene names (TSV format file). For each sample, for three files were zipped together and deposited in GEO. The cells from biological replicates for a population were merged together in the same MTX files and the replicate identity was saved in Barcode.

source_name: Young Bone Marrow

extract_protocol:
For scATAC-seq; Cells were sorted, nuclei isolated and 10x ATACseq was performed.
Libaries were prepered according to 10x genomics ATACseq kit. Libraries were sequenced on a Illumina NOVAseq.

tag: immunophenotype

value: Young Bone Marrow


title: Brain, Mock, 6 dpi, m5

value: WT

value: Uninfected

value: Mock


title: MCF7 cells, epirubicin, 50 nM, rep3

description:
E50_3
EpirubicinResistantCells_log2CPM.txt

value: epirubicin 50 nM


title: Brain, Mock, 6 dpi, m3


title: MCF7 cells, epirubicin, 100 nM, rep1

description:
Epi100_1
EpirubicinResistantCells_log2CPM.txt


title: Brain, Mock, 6 dpi, m6


title: yBM_CD11_on_yBM_hpc_scATAC-seq

description: Cut-sites of yBM_CD11A recounted on yBM_hpc peaks (see data processing step)

value: CD34+CD38-CD11A+ and CD34+

value: FACS sorted


title: cd4pos.Itga3.KO.rep2

value: Inguinal lymph node

value: Day 7

value: Fate-mapped primary CD4+ T cell

value: Itga3fl/fl Il17aCre/WT R26Zsgreen/WT


title: cd4pos.Itga3.KO.rep1

value: Female


title: cd4pos.Itga3.KO.rep3


title: yBM_CD35_on_yBM_hsc_scATAC-seq

description: Cut-sites of yBM_CD35 recounted on yBM_hsc peaks (see data processing step)


title: Brain, DCA, 6 dpi, m3

value: WNV

value: DCA

value: Day 06


title: MCF7 cells, epirubicin, 50 nM, rep1

description:
E50_1
EpirubicinResistantCells_log2CPM.txt

value: Breast adenocarcinoma


title: Brain, Mock, 6 dpi, m9

value: Brain


title: cd4pos.WT.rep1

value: Il17aCre/WT R26Zsgreen/WT


title: MCF7 cells, epirubicin, 50 nM, rep2

description:
E50_2
EpirubicinResistantCells_log2CPM.txt


title: MCF7 cells, epirubicin, 25 nM, rep2

description:
E25_2
EpirubicinResistantCells_log2CPM.txt

value: epirubicin 25 nM


title: TKO_iPC_48h_3

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

data_processing:
Samples were sequenced on NextSeq 500 and the 75bp single-end reads (fastqs) were generated from the raw BCLs using Illumina's bcl2fastq.
the raw fastq files were filtered by trimmomatic to remove the adaptor sequences and low- quality reads.
filtered reads were aligned to mouse genome (mm39) by STAR with default parameters.
raw counts were generated by featureCounts
raw counts were normalized and processed with DESeq2 in R.
Assembly: mm39
Supplementary files format and content: comma-separated values include normalized counts for each sample
Supplementary files format and content: comma-separated values include raw counts for each sample

source_name: B cell

growth_protocol: Follicular B cells isolated from mouse spleen were firstly cultured with NIH3T3 cell overexpressing CD40L and BAFF (referred as 40LB in the text) plus IL-4 on 100mm cell culture dish at density of 0.5million cells/dish. After 4-days culture, follicular B cells were induced into iGCB cells.The iGCB cells were then sorted and cultured with fresh prepared 40LB plus IL-21 for 24h, 48h (namely iPC 24h and iPC 48h). iGCB cells, iPC 24h and iPC 48h cells were sorted for RNA isolation.

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to manufacture's instruction

value: Spleen

value: B cells

value: miR-17-92 family TKO

value: cultured with 40LB cells plus IL-21


title: TKO_iPC_48h_2


title: MCF7 cells, epirubicin, 25 nM, rep3

description:
E25_3
EpirubicinResistantCells_log2CPM.txt


title: Brain, WNV, 3 dpi, m6

value: WT

value: Day 03


title: yBM_hpc_on_yBM_hsc_scATAC-seq

description: Cut-sites of yBM_hpc recounted on yBM_hsc peaks (see data processing step)

value: CD34+ and CD34+CD38-

value: FACS sorted

value: Young Bone Marrow


title: TKO_iPC_48h_1


title: WT-iPC_48h_2


title: MCF7 cells, epirubicin, 15 nM, rep3

description:
E15_3
EpirubicinResistantCells_log2CPM.txt

value: epirubicin 15 nM


title: yBM_CD11_scATAC-seq

description: 1 Biological replicate


title: WT-iPC_48h_3


title: MCF7 cells, epirubicin, 25 nM, rep1

description:
E25_1
EpirubicinResistantCells_log2CPM.txt


title: WT-iPC_48h_1


title: MCF7 cells, epirubicin, 15 nM, rep2

description:
E15_2
EpirubicinResistantCells_log2CPM.txt


title: Brain, Mock, 6 dpi, m8

value: Uninfected

value: Mock


title: iMPCs grown on aligned PCL electrospun substrate with Matrigel

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description:
10x Genomics
AP_MA

data_processing:
CellRanger v7.0.0 used for demultiplexing + read mapping + barcode assignment + UMI counting
Seurat v4.2.1 used for quality control + normalization + sample integration + dimensionality reduction + cell clustering
Monocle3 v1.2.9 used for trajectory analysis
Assembly: GRCm39 (GENCODE release M26)
Supplementary files format and content: Filtered feature-barcode count matrices from CellRanger

source_name: induced myogenic progenitors

extract_protocol:
We first detached the cells from the PCL scaffolds by treating them with 2mg/ml Dispase II for 20 mins at 37°C, followed by 0.25% Trypsin-EDTA for 10 mins. Scaffolds were then removed, and remaining cells were centrifugated for 5 mins at 300g. To separate iMPC clumps to single cells, 0.25% Trypsin-EDTA were again applied to the cell pellet for 5 mins and neutralized with iMPC medium.
The libraries were constructed using Single cell 3’ reagent kit v3.1 on 10x platform (10x Genomics, Pleasanton, CA).

value: induced myogenic progenitors

value: chemically reprogrammed myogenic cells from fibroblasts

value: Cultured in presence of F/R/C

tag: growth protocol

value: substrate with Matrigel


title: iMPCs grown on aligned PCL electrospun substrate without Matrigel

description:
10x Genomics
AP

value: substrate without Matrigel


title: TKO_iPC_24h_3

value: Spleen


title: yBM_hsc_scATAC-seq

description: 2 Biological replicates


title: yBM_hpc_scATAC-seq

description: 2 Biological replicates


title: MCF7 cells, epirubicin, 15 nM, rep1

description:
E15_1
EpirubicinResistantCells_log2CPM.txt

value: Breast adenocarcinoma


title: yBM_hsc_on_yBM_hpc_scATAC-seq

description: Cut-sites of yBM_hsc recounted on yBM_hpc peaks (see data processing step)

value: CD34+CD38- and CD34+


title: yBM_CD35_on_yBM_hpc_scATAC-seq

description: Cut-sites of yBM_CD35 recounted on yBM_hpc peaks (see data processing step)


title: TKO_iPC_24h_2

value: B cells

value: miR-17-92 family TKO

value: cultured with 40LB cells plus IL-21


title: MCF7 cells, epirubicin, 10 nM, rep3

description:
E10_3
EpirubicinResistantCells_log2CPM.txt

value: epirubicin 10 nM


title: TKO_iPC_24h_1


title: MCF7 cells, epirubicin, 10 nM, rep2

description:
E10_2
EpirubicinResistantCells_log2CPM.txt


title: MCF7 cells, epirubicin, 10 nM, rep1

description:
E10_1
EpirubicinResistantCells_log2CPM.txt


title: NM E. coli tRNAs control treatment (minus DMS) 30mers / 1:2 / 10 replicate 1

city: University Park

first: McCauley

middle: O'Brien

last: Meyer

email: mcobmeyer35@gmail.com, mxm1357@psu.edu

state: PA

address: 241 Chemistry Building

department: Biochemistry and Molecular Biology

institute: Penn State University

description:
Library 40
NM_30mers_12_10_merged_out.tar.gz

data_processing:
The adapters on the 3'-end of the reads were removed by cutadapt version 2.6 with Python version 3.6.13
ShapeMapper2 version 2.1.5 was used to align the reads to the sequences of the tRNA genes retrieved from the genomic tRNA database.
ShapeMapper2 version 2.1.5 was used to calculate the normalized DMS reactivity with the min-mutation-separation set to 1 for structure prediction and 0 for natural mutational profiling. The DMS reactivity was divided by the average DMS reacvtivity of the top 10% of the reactive nucleotides.
Then the correlation of the DMS reactivity between replicate experiments was evaulated by a custom R script available at https://github.com/MacMeyer1/Scripts-to-make-figures-for-tRNAs-in-peptide-rich-droplets
If the DMS reactivity between replicates was well correlated, the raw fastq files containing the reads were combined and ShapeMapper2 version 2.1.5 was used to again align the reads and calculate the normalized DMS reactivity.
Supplementary files format and content: Each processed file is a tar.gz directory containing the output of ShapeMapper2 version 2.1.5.
Library strategy: DMS-Map-Seq

organism: Escherichia coli

source_name: E. coli

extract_protocol:
Trizol extraction
To facilitate ligation onto the 3’-end of RNAs, the ligation adapter must be 5’-end adenylated. The adapter adenylation reaction was prepared as follows: water, 10 μM Mth RNA ligase (M2611A), 200 μM ATP, 20 μM of the ligation adapter (called 3' adapter in supplemental material excel sheet), and 1X 5’ DNA Adenylation reaction buffer (B2610S). The reaction was incubated at 65 °C for 1 h, after which, the enzyme was heat inactivated at 85 C for 5 min. We performed the RT primer ligation reaction as follows: 25% PEG 8000, 1X T4 RNA Ligase Reaction Buffer, 3 μM adenylated DNA oligonucleotide from the previous step, 4 μL of RNA recovered from a DMS experiment, and 200 U of T4 RNA Ligase 2 truncated (New England Biolabs). The reaction was incubated at 16 °C overnight, and the next day, the ligated product was fractionated alongside an unligated starting material lane on a 10% denaturing (8.3 M urea 1X TBE) polyacrylamide gel. The gel was stained with SYBR-GOLD and bands were visualized with UV light. The ligated band was excised, cut into ~1 mm x 1mm squares, and placed in a 1.7 mL tube with 450 μL of TEN-250 buffer and crush and soaked at 4 °C overnight. The ligated product was recovered by ethanol precipitation. The ligated products were reverse transcribed by marathon reverse transcriptase in the presence of Mn2+ ions to induce mutations at DMS modification sites and encourage readthrough.9,10; The ligated product and reverse transcription primer were renatured together at 90 °C for 1 min and then cooled to 4 °C for 10 min to hybridize them. The marathon reverse transcription reaction contained the following: 50 mM Tris-HCl (pH 8.3), 200 mM KCl, 5 mM dithiothreitol, 20% glycerol, 2 mM MnCl2, 250 μM of each dNTP, less than 500ng of ligated product, 250 nM of reverse transcription primer (called RT primer in supplemental material excel sheet) and 10-20 U of Marathon Reverse Transcriptase (Kerafast). The reaction was incubated at 42 °C for 1 h, then ~200 mM NaOH was added, and the reaction was heated to 95 °C for 5 min to denature the reverse transcriptase and degrade the RNA template. Then an equal volume of 2X formamide loading dye (0.025% w/v bromophenol blue, 90% formamide, 10 mM EDTA) was added and the sample was fractionated on a 10% denaturing (8.3 M urea 1X TBE) polyacrylamide gel. The gel was stained with SYBR-GOLD, bands were visualized under UV-light, the RT product band was excised, cut into ~1 mm x 1mm squares, placed in a 1.7 mL tube with TEN-250 buffer and crush and soaked at 4 °C overnight. The reverse transcription product was recovered by ethanol precipitation.  The single-stranded cDNA from the reverse transcription was circularized using CircLigase II. The reaction was prepared as follows: 1X Circligase reaction buffer (Lucigen), 2.5 mM MnCl2, 1 M betaine, single-stranded cDNA from the reverse transcription, and 3.3 U of CircLigase II (Lucigen). The reaction was incubated at 60 °C for 2 h. The circularized product was used in indexing PCR without further purification. The PCR was prepared as follows, 1X Phusion HF reaction buffer, 0.5 μM indexing primer, 0.5 μM reverse primer (called PCR reverse in supplemental material excel sheet), 200 μM of each dNTP, circularized DNA, and 0.5 U of Phusion HF DNA Polymerase. The thermocycler program was based on that from Yamagami et al.2 and was performed as follows: initial denaturation at 98 °C for 30 sec, denature at 98 °C for 10 sec, anneal at 60 °C for 10 sec, elongate at 72 °C for 5 sec, repeat steps 2-4 for 17 cycles before a final extension at 72 °C for 5 min. PCR products were fractionated on an 8% non-denaturing TBE polyacrylamide gel ran at 180 V for 90-120 min. The gel was stained with SYBR-GOLD, bands were visualized with UV light, the PCR product band was excised, cut into ~1 mm x 1mm squares, and placed in a 1.7 mL with TEN-250 buffer and crush and soaked at 4 °C overnight. The indexed library was recovered by Nucleospin Gel and PCR Clean-Up kit (Macherey-Nagel). Afterwards, the concentrations of each library were measured via a micro-volume UV-vis spectrophotometer (Denovix). Before the libraries were sequenced, they were evaluated for quality and appropriate length by the TapeStation system (Agilent). To determine the concentration of each library, qPCR was performed. Libraries were sequenced by Illumina NextSeq (150 nt single-end sequencing and High-output flow cells) with the standard Illumina primer.

value: control


title: WT-iPC_24h_2

value: WT


title: MCF7 cells, epirubicin, 5 nM, rep3

description:
E5_3
EpirubicinResistantCells_log2CPM.txt

value: epirubicin 5 nM


title: NM E. coli tRNAs DMS treated 30mers / 1:2 / 10 replicate 3

description:
Library 39
NM_30mers_12_10_merged_out.tar.gz

value: Dimethyl sulfate


title: yBM_CD35_scATAC-seq

description: 1 Biological replicate

value: FACS sorted

value: Young Bone Marrow


title: WT-iPC_24h_1


title: MCF7 cells, epirubicin, 5 nM, rep2

description:
E5_2
EpirubicinResistantCells_log2CPM.txt


title: NM E. coli tRNAs DMS treated 30mers / 1:2 / 10 replicate 2

description:
Library 38
NM_30mers_12_10_merged_out.tar.gz


title: Partial Responder sample of Tumor liver (Mouse 3)

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver containing metastases of CRC origin

extract_protocol:
Liver metastases were isolated and dissociated into single cells by physical (chopping the tissue into small pieces) and enzymatic (collagenase, Dispase II and DNAse) digestion followed by a filtering step using a 0.4mm cell strainer. No antibody staining was performed, single cells were resuspended in autoMACS running buffer containing 7AAD (BioLegend/ 420404) in a 1/50 dilution. Viable cells were sorted based by gating on single 7AAD negative cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1, 10x Genomics, ref. CG000204). Briefly, sorted cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: condition

value: Partial Responder


title: MCF7 cells, epirubicin, 5 nM, rep1

description:
E5_1
EpirubicinResistantCells_log2CPM.txt


title: TKO_iPC_0h_3

value: untreated

value: 0 h


title: TKO_iPC_0h_2


title: NM E. coli tRNAs DMS treated 30mers / 1:2 / 10 replicate 1

description:
Library 37
NM_30mers_12_10_merged_out.tar.gz


title: MCF7 cells, epirubicin, 1 nM, rep3

description:
E1_3
EpirubicinResistantCells_log2CPM.txt

value: epirubicin 1 nM


title: Control sample of Tumor liver (Mouse 3)

description: 10x Genomics

value: Liver containing metastases of CRC origin

value: Control


title: TKO_iPC_0h_1

value: Spleen


title: NM E. coli tRNAs control treatment (minus DMS) 10mers / 1:2 / 10 replicate 3

description:
Library 24
NM_10mers_12_10_merged_out.tar.gz


title: NM E. coli tRNAs control treatment (minus DMS) 30mers / 1:2 / 10 replicate 3

description:
Library 42
NM_30mers_12_10_merged_out.tar.gz


title: MCF7 cells, epirubicin, 1 nM, rep2

description:
E1_2
EpirubicinResistantCells_log2CPM.txt

value: Breast adenocarcinoma


title: Resistant sample of Tumor liver (Mouse 2)

description: 10x Genomics

value: Resistant


title: NM E. coli tRNAs control treatment (minus DMS) 10mers / 1:2 / 10 replicate 2

description:
Library 23
NM_10mers_12_10_merged_out.tar.gz


title: Partial Responder sample of Tumor liver (Mouse 2)

description: 10x Genomics


title: WT_iPC_0h_3

value: B cells


title: NM E. coli tRNAs control treatment (minus DMS) 30mers / 1:2 / 10 replicate 2

description:
Library 41
NM_30mers_12_10_merged_out.tar.gz


title: WT-iPC_24h_3

value: cultured with 40LB cells plus IL-21


title: WT_iPC_0h_2


title: Partial Responder sample of Tumor liver (Mouse 1)

description: 10x Genomics


title: MCF7 cells, epirubicin, 1 nM, rep1

description:
E1_1
EpirubicinResistantCells_log2CPM.txt


title: Control sample of Tumor liver (Mouse 2)

description: 10x Genomics


title: NM E. coli tRNAs control treatment (minus DMS) 10mers / 1: 1 / 0.5 replicate 3

description:
Library 21
NM_10mers_11_05_merged_out.tar.gz

value: control


title: WT_iPC_0h_1

value: WT


title: NM E. coli tRNAs control treatment (minus DMS) 10mers / 1:2 / 10 replicate 1

description:
Library 22
NM_10mers_12_10_merged_out.tar.gz


title: MCF7 cells, DMSO control for epirubicin, rep2

description:
CTREpi_2
EpirubicinResistantCells_log2CPM.txt


title: MCF7 cells, DMSO control for epirubicin, rep3

description:
CTREpi_3
EpirubicinResistantCells_log2CPM.txt


title: NM E. coli tRNAs control treatment (minus DMS) 10mers / 1: 1 / 0.5 replicate 2

description:
Library 20
NM_10mers_11_05_merged_out.tar.gz


title: NM E. coli tRNAs control treatment (minus DMS) 10mers / 1: 1 / 0.5 replicate 1

description:
Library 19
NM_10mers_11_05_merged_out.tar.gz


title: MCF7 cells, DMSO control for epirubicin, rep1

description:
CTREpi_1
EpirubicinResistantCells_log2CPM.txt


title: Naive, scRNAseq

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

description: 10x Genomics

data_processing:
Raw scRNA-seq reads of samples were processed individually according to 10x Genomics CellRanger software (cellranger-5.0.1) and mapped to the mm10 genome with default parameters.
Each sample was imported in to Seurat R package and merged. We filtered out cells with fewer than 400 detected expressed genes, or more than 3500 genes to prevent empty cells and doublets respectively. Genes that were expressed in less than 3 cells were filtered out.
Cells with over 10% of raw reads mapping to mitochondrial genes were filtered out. Mitochondrial genes were also removed from the gene expression matrix.
Assembly: mm10

source_name: One-centimeter spinal cord segment encompassing the matched non-injured area (T10) from adult GFAP-Cre:R26-tdT mice

extract_protocol:
One-centimeter segment encompassing the epicenter of the injury or matched non-injured area was harvested for tissue dissociation (including 18 cords in Naïve, 9 cords in Sham, and 8 cords in SCI1M group). After the mice were euthanized, transcardial perfusion with cold PBS was performed and cords were dissociated using a mixed digestion solution of papain, trypsin-EDTA, DNase I and L-cysteine in DMEM supplemented with BSA at 37°C under gentle shaking for 15 mins. After digestion solution was removed by centrifugation, cells were triturated with fire-polished glass Pasteur pipettes in fresh DMEM supplemented with 0.5% BSA. The supernatant containing cells were separated from the undissociated tissue at the bottom and stored at 4°C. The undissociated tissue was processed through above steps once more. Cell suspension were collected, passed through 70-µm strainer, and purified by density gradient centrifugation with 4% BSA-supplemented DMEM to eliminate remaining tissue clots and dead cells. To remove myelin, cells were then resuspended in a cold DPBS supplemented with 0.5% BSA containing Myelin Removal Beads II (Miltenyi Biotec; cat #130-096-733) following the manufacturer’s protocol. Next, tdT+/DAPI- cells for scRNA library preparation were collected by FACS using a BD FACS Aria II flow cytometer (BD Biosciences) with a 100 µm nozzle at 4°C. Samples were then washed in DMEM with 10% fetal bovine serum to reach the concentration at 400-1000 cells per ul. Cells from each sample were stained with Trypan Blue and cell viability was calculated on hemocytometer before loading on 10x Chromium.
Naïve, Sham and SCI1M samples were sequenced. Sample libraries were prepared by The University of Houston Sequencing and Editing Core (UH-SNEC) based on Chromium Single Cell 3’ Library and Gel Bead Kit instructions (v3-v3.1). All samples were indexed with Single Index Kit T Set A (10X Genomics; PN-1000213) or Chromium i7 Multiplex Kits (10X Genomics; PN-120262). Paired-end sequencing was performed using the NovaSeq 6000 (Sham and SCI1M) or NextSeq 500 (Naïve) sequencing instrument at recommended settings (R1: 28 cycles; i7 index: 8 cycles; i5 index: none; and R2: 91 cycles).

value: Astrocytes

tag: age

value: 4-6 months old


title: Resistant sample of Tumor liver (Mouse 1)

description: 10x Genomics


title: Control sample of Tumor liver (Mouse 1)

description: 10x Genomics


title: MCF7 cells, doxorubicin, 100 nM, rep3

description:
Dox100_3
DoxorubicinResistantCells_log2CPM.txt

value: doxorubicin 100 nM


title: NM E. coli tRNAs DMS treated 10mers / 1:2 / 10 replicate 3

description:
Library 18
NM_10mers_12_10_merged_out.tar.gz

value: Dimethyl sulfate


title: Htt Q111 NPC replicate 1

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

institute: University of Trento

data_processing:
Illumina Casava 1.8 software was used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence and low-quality nucleotides, then aligned and quantified against the mouse Gencode v23 transcriptome using STAR
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample

source_name: NPC

growth_protocol: The allelic series of heterozygous Hdh CAG knock-in mouse embryonic stem cell (mESC) lines, consisting of 4 alleles of different Htt CAG size (20, 50, 89 and 111 CAG) were kindly given by Dr. Marcy E. MacDonald (Massachussets General Hospital and Harvard Medical School, Boston, US). They were cultured in KnockOut DMEM (Gibco), supplemented with 15% of ES cell FBS (Gibco), 2 mM L-glutamine (Gibco), 100 U/ml Penicillin/Streptomycin (Gibco), 1% Non-essential Amino Acids (Gibco), 0.1 mm 2-mercaptoethanol (Sigma) and 1000 U/ml of leukemia inhibitory factor (LIF) (Voden), on plates coated with 0.1% gelatin (Millipore) and with a feeder layer of CF-1 IRR MEF (TebuBio). Differentiation of mESC to mNPC was performed as described in Conti et al., PLoS Biology 2005.  Both mESCs and mNPCs were incubated at 37°C and 5% CO2.

extract_protocol:
RNA was extracted from cell lines by using TRIzol reagent (Invitrogen) following manufacturer's instructions.
The RNA samples were subjected to DNAse I treatment (Ambion) according to manufacturer instructions . RNA library preparation was obtained using the standard Illumina protocols: Illumina NextSeq 500 according to manufacturer instructions and libraries were sequenced using paired-end, 75bp reads, obtaining approx. 60M reads/library.

treatment_protocol: Self-renewing mES cells were dissociated and plated onto 0.1% gelatin-coated tissue culture plastic at a density of 0.5–1.5  104/cm2 in N2B27 medium. N2B27 is a 1:1 mixture of DMEM/F-12 (Thermo Fisher Scientific) supplemented with N-2 supplement (Gibco) and Neurobasal medium (Thermo Fisher Scientific) complemented with B27 supplement (Thermo Fisher Scientific).The medium was renewed every other day. After 7 days, cells were detached using Accutase (Thermo Fisher Scientific) and plated on 3 µg/ml laminin-coated tissue culture dishes in NS expansion medium. Mouse neural progenitor cells were routinely passaged 1:2-1:4 every 3-5 days using Accutase and maintained in NS medium, composed by Euromed-N (Euroclone) supplemented with 1:1000 FGF (R&D) and EGF (Sigma), 1% N-2 Supplement (Gibco), 2 mM L-glutamine (Gibco) and 100 U/ml Penicillin/Streptomycin (Gibco) on laminin-coated plates (Sigma, 3.5 µg/ml).

value: NPC

value: Q111 Htt


title: Htt Q111 NPC replicate 2


title: MCF7 cells, doxorubicin, 100 nM, rep2

description:
Dox100_2
DoxorubicinResistantCells_log2CPM.txt


title: Htt Q92 NPC replicate 2

value: Q92 Htt


title: NM E. coli tRNAs DMS treated 10mers / 1:2 / 10 replicate 2

description:
Library 17
NM_10mers_12_10_merged_out.tar.gz


title: LenR_Len

city: Shatin

first: Karl Kam Hei

last: So

state: New Territories

address: 608A, Lo Kwee-Seong Integrated Biomedical Sciences Building, The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: 10X Chromium Next GEM 3’ v3 chemistry Single Cell kit

data_processing:
cellranger-5.0.1
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: polyA RNA

source_name: liver tumor

extract_protocol:
Tumors from mouse livers were harvested, cut into small pieces in ice-cold perfusion buffer (25mM HEPES pH7.4, 0.5mM EDTA in PBS) and transferred to gentleMACS C tube with four rounds of dissociation in digestion buffer with 0.5 mg/ml Collagenase IV and 0.1 mg/ml DNaseI (Roche) using gentleMACS dissociator. The cell suspensions were passed through 70 µm cell strainers prior to loading to percoll gradient mix to create the gradient. After centrifugation, the pellets were subjected to red blood cell lysis and resuspended in PBS supplemented with 2% FBS. Isolated cells were stained with anti-CD45-APC antibody for 45 minutes on ice. LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit was used for exclusion of dead cells. Isolated cells were analyzed and the live CD45+ subpopulation was sorted on a BD FACSAriaIII cell sorter
The sorted live CD45+ cells stored in ice-cold FACS buffer were processed according to manufacturer’s instructions by encapsulation into single cell gel beads and unique molecular identifier barcoding using the 10X Genomics Chromium Next GEM 3’ v3 chemistry Single Cell kit at The Beijing Genomics Institute. Libraries were prepared and sequenced on Illumina NovaSeq platform.

value: liver tumor

value: CD45+ immune cells

value: lenvatinib-resistant mouse HCC model

value: lenvatinib


title: LenR_Combo

value: lenvatinib and palbociclib


title: MCF7 cells, doxorubicin, 100 nM, rep1

description:
Dox100_1
DoxorubicinResistantCells_log2CPM.txt

value: Breast adenocarcinoma


title: Htt Q92 NPC replicate 1


title: NM E. coli tRNAs DMS treated 10mers / 1:2 / 10 replicate 1

description:
Library 16
NM_10mers_12_10_merged_out.tar.gz


title: Lexis_snRNA-seq_KO

first: Zhengyi

last: Zhang

address: Westwood

institute: UCLA

description: single-nucleus RNA sequencing

data_processing:
Sequencing data was package and analyzed using 10x Genomics Cell Ranger analysis tool. The R package Seurat (V4) was used to cluster the cells in the merged matrix (Hao et al., 2021).
Assembly: mm10
Supplementary files format and content: TSV; MTX: Matrix files

source_name: iWAT

extract_protocol:
We isolated the nuclei of iWAT from western diet fed male mice using a protocol slightly modified from recent publication (Sarvari et al., 2021; Van Hauwaert et al., 2021). Briefly, iWAT from 3 mice of Lexis-AdWT group or Lexis-AdWT group were isolated (without lymph node) pooled (according to group) and minced. 2 ml NIB buffer (250 mM Sucrose, 10 mM HEPES, 1.5 mM MgCl2, 10 mM KCl, 0.001% IGEPAL CA-630, 0.2 mM DTT, 0.5 U/µL RNase inhibitor) were added to 400 mg pooled iWAT, then homogenized with 2 ml glass dounce homogenizer. After filtering through 70 µm cell strainer, another 2 ml NIB was added to the filtered homogenate and centrifuged at 1000 g× 10 min× 4 °C. The lipid layer was aspirated, pellet was resuspended in the remaining supernatant and then transferred to a new pre-cooled 5 ml DNA low binding tube on ice and added 2 ml NIB. Nuclei were pelleted by centrifuging at 500 g × 10 min× 4 °C, resuspended in 100 µL NRB (1% BSA in PBS, 0.04 U/ µL RNase inhibitor) and filtered through a 40 µm tip strainer. 15,000 nuclei were taken out and resuspended in NRB as previous protocol described (Sarvari et al., 2021; Van Hauwaert et al., 2021).
We performed 10x Genomics single-nucleus RNA sequencing at USC Norris Molecular Genomics Core immediately after nuclei isolation. Single cell RNA sequencing was prepared using 10x Genomics 3' v3.1 (Cat number: 1000092) following manufacturer's protocol. Samples were parsed into single nuclei using 10x Genomics Chromium Controller and libraries were simultaneously prepared. Prepared single cell RNA sequencing libraries were sequenced on the Illumina Novaseq6000 platform at a read length of 28x90 and read depth of 50,000 reads/cell for 5000-7000 cells.
Prepared single cell RNA sequencing libraries were sequenced on the Illumina Novaseq6000 platform at a read length of 28x90 and read depth of 50,000 reads/cell for 5000-7000 cells.

treatment_protocol: Western diet

value: iWAT

value: Lexis KO

value: Western diet


title: MCF7 cells, doxorubicin, 50 nM, rep3

description:
D50_3
DoxorubicinResistantCells_log2CPM.txt

value: doxorubicin 50 nM


title: NM E. coli tRNAs DMS treated 10mers / 1: 1 / 0.5 replicate 3

description:
Library 15
NM_10mers_11_05_merged_out.tar.gz


title: Lexis_snRNA-seq_WT

description: single-nucleus RNA sequencing

value: Lexis WT


title: MCF7 cells, doxorubicin, 50 nM, rep2

description:
D50_2
DoxorubicinResistantCells_log2CPM.txt


title: Htt Q50 NPC replicate 1

value: Q50 Htt


title: Htt Q50 NPC replicate 2


title: MCF7 cells, doxorubicin, 50 nM, rep1

description:
D50_1
DoxorubicinResistantCells_log2CPM.txt


title: NM E. coli tRNAs DMS treated 10mers / 1: 1 / 0.5 replicate 2

description:
Library 14
NM_10mers_11_05_merged_out.tar.gz


title: Lexis_ChIRP_Rnase_O

description: Unbiased chromatin-affinity assay: Rnase control

data_processing:
The raw reads in Fastqsanger files obtained after sequencing were demultiplexed and converted to Fastq files by the UCLA BSCRC sequencing core. Raw reads in Fastq format were uniquely mapped to reference mouse genome (NCBI37/mm9) using Bowtie2 and SAM files were generated. SAM files were converted to BAM files and sorted by SAMtools . MACS2 was used for peak calling.
Assembly: mm9
Supplementary files format and content: BedGraph.gz: BedGraph
Library strategy: ChIRP-seq

extract_protocol:
Unbiased chromatin-affinity assay was performed according to the published protocol with modification (Mumbach et al., 2019).
A total of 100 million preadipocytes (pre-treated with GW1929 for 24 hours) were used for each replicate and 2 replicates were performed for each group. For negative control, RNase A and RNase H were added as the amount of 2 μg per million cells.
Libraries were paired-end sequenced by NovaSeq S4 with read lengths of 150bp

treatment_protocol: GW1929 for 24 hours

value: Preadipocyte

value: WT


title: NM E. coli tRNAs DMS treated 10mers / 1: 1 / 0.5 replicate 1

description:
Library 13
NM_10mers_11_05_merged_out.tar.gz

value: Dimethyl sulfate


title: MCF7 cells, doxorubicin, 25 nM, rep3

description:
D25_3
DoxorubicinResistantCells_log2CPM.txt

value: doxorubicin 25 nM


title: Lexis_ChIRP_O2

description: Unbiased chromatin-affinity assay


title: Htt Q20 NPC replicate 2

value: NPC

value: Q20 Htt


title: Lexis_ChIRP_Rnase_E


title: CT 3

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

country: China

institute: Sun Yat-sen University

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads of each sample were aligned to the reference genome of Lumnitzera littorea via hisat2 program
Gene counts were obtained using featureCounts.
Supplementary files format and content: One csv file containing raw count values for each sample

organism: Lumnitzera littorea

source_name: leaves, shoots and roots

growth_protocol: One-year-old seedlings of L. littorea with 5–6 true leaves and a height of 30 ± 2 cm were chosen as experimental materials, and grown at controlled climatic conditions: day/night photoperiod, 12/12 h; 50% relative humidity and 80% relative light intensity during the day; and 70% relative humidity and zero relative light intensity during the night.

extract_protocol:
Total RNAs was extracted from the leaves, shoots and roots of each plant using EASYspin Plus Complex Plant RNA Kit.
Illumina libraries were prepared following manufacturer’s instruction

treatment_protocol: The seedlings were divided into two groups: one group were grown under the temperature of 25°C day/23°C night (normal condition) for 48 h, while the other were grown under the temperature of 8°C day/5°C night (chilling stress).

value: leaves, shoots and roots

value: 1 year

value: wt

value: chilling stress


title: MCF7 cells, doxorubicin, 25 nM, rep2

description:
D25_2
DoxorubicinResistantCells_log2CPM.txt

value: Breast adenocarcinoma


title: Htt Q20 NPC replicate 1


title: CT 2


title: Htt WT NPC replicate 1

description: HttWTNPCa

value: wild type


title: Htt WT NPC replicate 2

description: HttWTNPCb


title: MCF7 cells, doxorubicin, 25 nM, rep1

description:
D25_1
DoxorubicinResistantCells_log2CPM.txt


title: CT 1


title: Lexis_ChIRP_O1

description: Unbiased chromatin-affinity assay


title: Lexis_ChIRP_E2

description: Unbiased chromatin-affinity assay


title: MCF7 cells, doxorubicin, 15 nM, rep3

description:
D15_3
DoxorubicinResistantCells_log2CPM.txt

value: doxorubicin 15 nM


title: CK 3

value: control


title: Htt KO NPC replicate 2

description: HttKONPCb

value: Htt knockout


title: CK 2


title: P3

city: Austin

first: Elle

last: Roberson

state: Texas

address: 2401 Speedway, PAT 216

department: Molecular Biosciences

institute: University of Texas at Austin

description: 3' TagSeq

data_processing:
Fastq datasets were initially processed to collapse duplicates based on TagSeq molecular barcodes Sequencing data quality, both before and after TagSeq pre-processing, was evaluated using the FastQC tool
Paired-end pseudo alignment was performed using kallisto (ver 0450) with the options --single-overhang -l 200 -s 50, against the mouse transcriptome (GENCODE M25 transcript sequences)
Downstream analysis of kallisto estimated counts was performed in R (ver 344)
The tximport package (v160) was used to roll up transcript-level counts into gene-level counts provided to the DESeq2 package (ver 1181)
Before DESeq2 analysis, count data matrices were filtered to remove genes with fewer than 1 read across all included samples
Assembly: GENCODE M25 transcriptome (transcript sequences and main gene annotation set)
Supplementary files format and content: Tab-delimited abundance.tsv text files provide kallisto per-transcript estimated counts and transcripts per million values for each sample

source_name: Uterus

extract_protocol:
Dissected uterine samples were collected in triplicate for each of the four stages Uterine tissue was  disrupted  using a Beadbug 6 Microtube Homogenizer (Sigma-Adlrich) and the lysate spun through a QIAshredder column (Qiagen) to fully homogenize Total RNA was isolated from each sample using RNeasy mini columns with DNase digestion
RNA integrity number (RIN) was measured using an Agilent Bioanalyzer and 100 ng of RNA was used for the TagSeq protocol The fragmentation/RT mix was prepared and added to each RNA sample, then heated to 95°C for 25 minutes on a Thermocycler and immediately put on ice for 2 minutes After cooling and addition of the template switching oligo and SmartScribe RT, the fragmented RNA reaction was incubated at 42°C for 1hr, 65°C for 15 min Next an AmPure bead clean-up was completed for the cDNA before it was amplified to incorporate the Illumina sequencing primer site, followed by another cleanup The remaining portions of the Illumina adapter (the i5 and i7 indices) were then added through an additional 4 cycles of PCR Final libraries were quantified with PicoGreen then pooled equally for size selection using the Blue Pippin from 355-550 bp
3' RNA-Seq

value: Uterus

value: Swiss Webster

tag: Sex

value: Female

value: Wild type

tag: estrous cycle stage

value: Proestrus


title: MCF7 cells, doxorubicin, 15 nM, rep2

description:
D15_2
DoxorubicinResistantCells_log2CPM.txt


title: Htt KO NPC replicate 1

description: HttKONPCa


title: CK 1


title: MCF7 cells, doxorubicin, 15 nM, rep1

description:
D15_1
DoxorubicinResistantCells_log2CPM.txt


title: MCF7 cells, doxorubicin, 10 nM, rep3

description:
D10_3
DoxorubicinResistantCells_log2CPM.txt

value: doxorubicin 10 nM


title: P1

description: 3' TagSeq


title: P2

description: 3' TagSeq


title: Htt Q111 mESC replicate 1

source_name: mESC

value: mESC

value: Q111 Htt


title: MCF7 cells, doxorubicin, 10 nM, rep2

description:
D10_2
DoxorubicinResistantCells_log2CPM.txt


title: Htt Q92 mESC replicate 2

value: Q92 Htt


title: MCF7 cells, doxorubicin, 10 nM, rep1

description:
D10_1
DoxorubicinResistantCells_log2CPM.txt


title: M7

description: 3' TagSeq

value: Metestrus


title: Htt Q92 mESC replicate 1


title: Lexis_ChIRP_E1

description: Unbiased chromatin-affinity assay

value: Preadipocyte

value: WT


title: MCF7 cells, doxorubicin, 5 nM, rep3

description:
D5_3
DoxorubicinResistantCells_log2CPM.txt

value: Breast adenocarcinoma

value: doxorubicin 5 nM


title: T3

city: Zhanjiang City

first: Ju

last: Zhimin

address: 1 Haida Road, Mazhang District

institute: Guangdong Ocean University

data_processing:
Trinity software (v2.4.0)
Raw sequences were filtered by removing adapter sequences and low-quality reads.
Clean reads were assembled de novo without a reference genome using the Trinity software (v2.4.0)
Reads count exctraction and normalization were performrd by Trinity software (v2.4.0)
Assembly: Transcript sequence obtained by Trinity splicing was used as reference sequence
Supplementary files format and content: gene_fpkm
Supplementary files format and content: Trinity.fasta

organism: Penaeus merguiensis

source_name: Hepatopancreas

extract_protocol:
RNA was extracted from hepatopancreas samples using TRIzol® reagent (Invitrogen, USA). RNA quantity and quality were assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). High-quality RNA samples were then purified and fragmented
RNA libraries for RNA seq were prepared by using Illumina HiSeqTM 2500 platform (Illumina, San Diego, CA, USA)

value: Hepatopancreas

value: 0.5 mg/L Cd Treatment 3 72 hours


title: C1

value: Control 1 72 hours


title: Htt Q50 mESC replicate 2

value: Q50 Htt


title: M6

description: 3' TagSeq

value: Uterus

value: Swiss Webster


title: T2

value: 0.5 mg/L Cd Treatment 2 72 hours


title: C2

value: Control 2 72 hours


title: E5

description: 3' TagSeq

value: Female

value: Wild type

value: Estrus


title: Htt Q50 mESC replicate 1

value: mESC


title: C3

value: Control 3 72 hours


title: T1

value: 0.5 mg/L Cd Treatment 1 72 hours


title: MCF7 cells, doxorubicin, 5 nM, rep1

description:
D5_1
DoxorubicinResistantCells_log2CPM.txt


title: Htt Q111 mESC replicate 2

value: Q111 Htt


title: E4

description: 3' TagSeq


title: Htt Q20 mESC replicate 2

value: Q20 Htt


title: E3

description: 3' TagSeq


title: MCF7 cells, doxorubicin, 1 nM, rep3

description:
D1_3
DoxorubicinResistantCells_log2CPM.txt

value: Breast adenocarcinoma

value: doxorubicin 1 nM


title: COS-7, siLONP2, biol rep 3

city: Montreal

first: Akihiro

last: Yamashita

address: 3801 University Ave

institute: McGill University

data_processing:
STAR version 2.7.1a
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35.
Trimmed sequence reads were aligned to the reference Chlorocebus sabaeus genome version ChlSab1.1 (gene annotation from Ensembl 104) or Homo sapiens genome version GRCh38 (gene annotation from Gencode version 37) using STAR version 2.7.1a.
Raw gene expression counts were obtained directly from STAR, and normalization and differential expression analysis were performed using DESeq2 version 1.30.1.
For comparison analyses between COS-7 and U2OS, gene identifiers were converted from C. sabaeus to H. sapiens using the R/Bioconductor package biomaRt (version 2.48.3).
Assembly: ChlSab1.1 and GRCh38
Supplementary files format and content: tab-delimited excel file includes normilised read counts for genes and differential expression analysis for each samples

organism: Chlorocebus aethiops

source_name: kidney

extract_protocol:
Total RNA was extracted from each cell using RNeasy Plus (QIAGEN) after 168 h siRNA transfection.
RNA libraries for RNA-seq were prepared using KAPA stranded RNA‐seq LibraryPrep Kit following manufacturer's protocols.

value: kidney

value: fibroblast-like cell

value: LONP2 knockdown


title: Htt Q20 mESC replicate 1


title: MCF7 cells, doxorubicin, 1 nM, rep2

description:
D1_2
DoxorubicinResistantCells_log2CPM.txt


title: COS-7, siLONP2, biol rep 2


title: D5

description: 3' TagSeq

value: Uterus

value: Diestrus


title: MCF7 cells, doxorubicin, 5 nM, rep2

description:
D5_2
DoxorubicinResistantCells_log2CPM.txt

value: doxorubicin 5 nM


title: MCF7 cells, DMSO control, rep3

description:
CTRDox_3
DoxorubicinResistantCells_log2CPM.txt


title: D4

description: 3' TagSeq

value: Swiss Webster


title: Htt WT mESC replicate 1

description: HttWTESCa

value: wild type


title: M5

description: 3' TagSeq

value: Female

value: Wild type

value: Metestrus


title: MCF7 cells, doxorubicin, 1 nM, rep1

description:
D1_1
DoxorubicinResistantCells_log2CPM.txt


title: COS-7, siNT, biol rep 3

value: WT


title: MCF7 cells, DMSO control, rep2

description:
CTRDox_2
DoxorubicinResistantCells_log2CPM.txt


title: Htt KO mESC replicate 1

description: HttKOESCa

value: mESC

value: Htt knockout


title: SCI1M, scRNAseq

description: 10x Genomics

source_name: One-centimeter spinal cord segment encompassing the epicenter of the injury (T10) area from adult GFAP-Cre:R26-tdT mice

value: Astrocytes

value: 4-6 months old


title: Sham, scRNAseq

description: 10x Genomics

source_name: One-centimeter spinal cord segment encompassing the epicenter of the laminectomy surgery (T10)  area from adult GFAP-Cre:R26-tdT mice


title: Htt KO mESC replicate 2

description: HttKOESCb


title: COS-7, siNT, biol rep 2


title: COS-7, siNT, biol rep 1


title: MCF7 cells, DMSO control, rep1

description:
CTRDox_1
DoxorubicinResistantCells_log2CPM.txt

source_name: Breast adenocarcinoma

value: Breast adenocarcinoma


title: COS-7, siLONP2, biol rep 1

value: kidney


title: Dana.ovary.1

status: Public on Sep 26 2023

city: Cambridge

first: Susanne

last: Bornelöv

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Removal of adators using Trim Galore! (v0.6.4, --stringency 6 -e 0.1).
Alignment to the reference genome using HiSeq2 (v2.2.0, -max-seeds 100 -q -k 1).
Converting to bigWig and scaling to cpm using bamCoverage from deeptools (v3.3.2, --binSize 1 --ignoreForNormalization chrM  --normalizeUsing CPM --exactScaling --skipNonCoveredRegions, and additionally --filterRNAstrand and --scaleFactor).
Supplementary files format and content: bigWig showing read coverage per position. File name indicate species, genome assembly, strand, and sample.

organism: Drosophila ananassae

source_name: ovary

growth_protocol: All Drosophila species were maintained at room temperature on species-specific food.

extract_protocol:
Ovaries from 10-20 flies were dissected in ice-cold PBS and total RNA was extracted using TRIzol.  Briefly, ovaries were lysed in TRIzol (Thermo Fisher Scientific), and RNA was phase separated using chloroform (Sigma-Aldrich).   Total RNA in the aqueous fraction was precipitated using 100% isopropanol, washed with 70% ethanol, and dissolved in nuclease free water (Invitrogen).  Ribosomal RNA was depleted using RiboPOOL (siTOOLs, Biotech) following the manufacturer's protocol. The indicated RiboZero libraries were prepared as previously described (Kneuss et al., 2019, PMID: 31416967).
RNA-seq libraries were produced using NEBNext Ultra Directional Library Prep Kit for Illumina, following the manufacturer’s instructions for rRNA depleted RNA.

value: ovary

tag: rrna depletion

value: RiboPOOL

tag: assembly


title: Dana.ovary.3


title: Dana.ovary.4


title: Dana.ovary.1 small-RNA-Seq

data_processing:
Trim Galore! (v0.6.4, --stringency 30 -e 0.1 -a TGCTTGGACTACATATGGTTGAGGGTTGTA --length 18 -q 0) was first run to remove an abundant rRNA sequence, followed by a second run (--stringency 5 -e 0.1 --length 18 --max_length 35 -q 0) to remove adapter sequences (specified using ‘-a’), and any flanking random nucleotides (‘--clip_R1’ and/or ‘--three_prime_clip_R1’ with appropriate arguments).
The processed reads were mapped to a miRNA hairpin database (miRBase release 22.1) using bowtie (v1.2.3, -S -n 2 -M 1 -p 20 --best --strata --nomaqround --chunkmbs 1024) with ‘--un’ and ‘--max’ to extract unmapped reads.
Reads not mapping to miRNAs were aligned to the respective reference genomes using bowtie (-S -n 2 -M 1 -p 20 --best --strata --nomaqround --chunkmbs 1024).
Multi-mapping reads were extracted into a separate BAM file using awk (MQ<10).
The BAM files were converted to bigWig using bamCoverage from deepTools (Ramírez et al., 2016) (v3.3.2, --binSize 1 --ignoreForNormalization chrM  --normalizeUsing CPM --exactScaling --skipNonCoveredRegions --minFragmentLength 23 --maxFragmentLength 30) and additionally ‘--filterRNAstrand’ to separate the two strands, ‘---scaleFactor’ to scale counts per million to reflect all mapped reads, and optionally ‘--minMappingQuality 50’ when extracting uniquely mapped reads.
Supplementary files format and content: bigWig showing read coverage per position. File name indicate species, genome assembly, strand, and sample.

extract_protocol:
Small RNAs were isolated using the TraPR Small RNA Isolation Kit (Lexogen) following the manufacturer's instructions. The soma-enrichment sRNA-seq libraries were generated for 13 species (2 replicates each) similar to published protocols (Akkouche et al., 2013; Chirn et al., 2015), with modifications.  In brief, 75-100 ovary pairs were dissected in ice-cold PBS.  Ovaries were dissociated for 18 minutes in 0.25% Trypsin (Sigma-Aldrich) at 25˚C, shaking at 800 rpm.  Dissociated tissue was pushed through a 40 µm nylon mesh (Greiner Bio-one) washed with equal volume Schneider 2 medium (Thermo Fisher Scientific) and then pelleted.  Cell count was quantified using the Luna-FL (Logos Biosystems).  Cells were pelleted and directly used as input for sRNA isolation using the TraPR Small RNA Isolation Kit (Lexogen).
sRNA libraries were generated using the Small RNA-Seq Library Prep Kit (Lexogen) with minor modifications.  Both primers A3 and A5 as well as the primer RTP were used at 0.5x.

tag: enrichment


title: Dfic.ovary_FC.1 small-RNA-Seq

organism: Drosophila ficusphila

value: somatic follicle cells


title: Dfic.ovary.1


title: Dana.ovary.2 small-RNA-Seq


title: Dana.ovary.2


title: Htt WT mESC replicate 2

description: HttWTESCb


title: Dfic.ovary.1 small-RNA-Seq


title: Dana.ovary_FC.1 small-RNA-Seq


title: Dfic.ovary_FC.2 small-RNA-Seq


title: Dana.ovary_FC.2 small-RNA-Seq


title: Dana.ovary.3 small-RNA-Seq


title: ATAC_dere_ovary_rep1

description: 8 ovaries

data_processing:
genome build/assembly: droEre1
The paired-end reads were trimmed of adapter sequences TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG and GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG using Cutadapt tool (v1.18; default parameters).
Burrows-Wheeler Aligner (BWA) (v0.7.17, bwa mem -M -t 4) was used to align the trimmed paired reads to each genome assembly.
Duplicates were marked using Picard tool (v2.9.0) (MarkDuplicates, validation stringency=lenient). SAMtools (v1.9) was used for indexing and filtering. The quality metrics for the aligned ATAC-seq reads were assessed using ataqv (v1.0.0)
The ATAC-seq peaks were called with MACS2 (v2.1.1.20160309) using --nomodel --shift -37 --extsize 73 parameters and FDR cut-off q ≤ 0.05
Conservation of ATAC-seq peaks were assessed by performing LiftOver (UCSC) or NCBI BLAST+ (2.14.0 release) of the ATAC-seq peak regions to find orthologous genomic regions in the other species and checking if they also have an ATAC-seq peak in that region.
Supplementary files format and content: RPKM-normalized bigWig files for each sample and RPKM-normalized bigWig files of merged biological replicates
Supplementary files format and content: narrowPeak files of ATAC-seq peaks from MACS2

organism: Drosophila erecta

extract_protocol:
The freshly dissected instact ovaries were directly lysed in ATAC-Resuspension Buffer (RSB, 10 mM Tris-HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2 in nuclease free water) containing 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin and washed out with cold ATAC-RSB containing 0.1% Tween-20.
The transposition reaction was performed with 25 μl 2x TD buffer from and 2.5 μl transposase (100nM final) from Illumina Tagment DNA Enzyme and Buffer Small Kit (Illumina 20034197), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O at 37°C for 30 minutes in a thermomixer with 1000 RPM mixing. Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) was used for a clean-up. The transposed fragments were amplified for 5 cycles [72 °C for 5 min, 98 °C for 30 s (98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min) × 5] using NEBNext 2x MasterMix and primer pairs of the universal primer Ad1 and the index primers Ad2. This was followed by qPCR amplification to determine additional cycle number. Amplified DNA was purified using Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and eluted in 20 μl H2O. AMPure XP beads (Beckman Coulter) were used for double-sided bead purification. 100-600 bp fragments were selected using Blue Pippin (Sage Science).

value: female


title: Dere.ovary.4 small-RNA-Seq


title: Dere.ovary.1 small-RNA-Seq


title: D3

description: 3' TagSeq

value: Uterus

tag: strain

value: Diestrus


title: Dere.ovary.6

tag: tissue


title: Dere.ovary.5


title: ATAC_dere_ovary_rep2

description: 20 ovaries

tag: genotype

value: wild type


title: Dere.ovary.3 small-RNA-Seq


title: Dere.ovary.2 small-RNA-Seq


title: Dere.ovary.6 small-RNA-Seq


title: Dere.ovary.7


title: Dere.ovary.2


title: Dere.ovary.4


title: Dfic.ovary.2 small-RNA-Seq


title: Dere.ovary.1


title: Dere.ovary.5 small-RNA-Seq


title: BL60_0h_DMSO_Replicate 1

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description: 2x50 cycle

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using STAR2
Raw read counts per gene were called with Htseq-Count
FPKM Normalization and median shift
Assembly: hg19
Supplementary files format and content: DLBCL_Prednisolone_RNAseq_FPKM_Normalized_Log2.txt.gz

source_name: cell line

growth_protocol: All cells were grown in advanced RPMI supplemented with 5% FBS with pen/strep and glutamine.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini kit.
Libraries were generated using TruSeq stranded mRNA library prep (illumina)

treatment_protocol: All cells were grown at 0.5 x 10^6 cells/ml and either treated in duplicates with vehicle (DMSO), prednisolone (25nm or 10µM) for 0h 6h and 24h.

value: cell line

value: human DLBCL cell line

value: Cas9 engineered


title: BL60_24h_Prednisolone_Replicate 1

description: 2x50 cycle


title: BL60_6h_Prednisolone_Replicate 1

description: 2x50 cycle


title: human_8C_EMB5

city: New York

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The developer version of the PacBio Iso-Seq3 pipeline (v.3.4.0) was used for preparing full-length non-chimeric (FLNC) reads from the raw sequencing data. First, subreads were intramolecular error-corrected and polished using the circular consensus sequencing (CCS) algorithm (v.5.0.0) to produce highly accurate (>Q10) CCS reads, each requiring a minimum of 1 complete polymerase pass. The polished CCS reads were then passed to the lima tool (v.2.0.0) to remove barcodes (if used), SMART-Seq primers and template-switching oligo sequences and orient the isoforms into the correct 5’ to 3’ direction. The refine command was then used to remove polyA tails and concatemers to generate full-length non-chimeric (FLNC) reads ready for downstream analysis. The FLNC reads per Sequel II SMRTcell were then mapped to the GRCh38 genome assembly using the splice-aware aligner, minimap2 (v2.17), with the following parameters: minimap2 -ax splice -uf --secondary=no -C5 --MD. Unmapped full-length reads, and reads with <50 MAPQ, were removed using sambamba (v0.5.6).  SAM files containing aligned PacBio FLNC reads were processed using TranscriptClean (v2.0.2). Uniquely mapped long- RNA-Seq reads were integrated to generate a novel isoform-resolved transcriptome using TALON (v5.0).
Genome_build: hg38
Supplementary_files_format_and_content: GTF file containing isoforms detected from PacBio RNA sequencing

source_name: embryo

extract_protocol:
Donated embryos were thawed using the Quinn's Advantage Thaw Kit (SAGE) following the manufacturer’s instructions. Single embryos were lysed to release mRNA, which was primed using a modified oligo-dT primer and reverse-transcribed using template switching technology to generate full-length cDNA using the SMART-Seq v4 Ultra Low Input RNA kit (Clontech, Takara; Cat# 634897), following the manufacturer’s instructions. The first-strand cDNA templates were then amplified using 14-16 cycles of LD-PCR and then purified using AMPure XP beads (Beckman Coulter).
Full-length cDNA was used as input for preparing SMRTbell libraries using the SMRTbell Express Template Preparation Kit v2.0 as recommended by the manufacturer (Pacific Biosciences). Samples with enough cDNA mass (> 100 ng) were prepped as individual libraries and those with little mass available (<100 ng) were pooled together for library prep. Briefly, the cDNA was treated with a DNA Damage Repair mix to repair nicked DNA, followed by an End Repair and A-tailing reaction to repair blunt ends and adenylate each template. Next, overhang SMRTbell adapters are ligated onto the ends of each template and purified with 0.6X AMPure PB beads to remove small fragments and excess reagents (Pacific Biosciences). The completed SMRTbell libraries were then annealed to sequencing primer v4 and bound to sequencing polymerase 2.0 before being sequenced using one SMRTcell 8M on the Sequel II system with a 24-hour movie.


title: Dere.ovary_FC.2 small-RNA-Seq


title: BL60_24h_Prednisolone_Replicate 2

description: 2x50 cycle


title: Dere.ovary_FC.1 small-RNA-Seq


title: Dere.ovary.3


title: human_merged_TD01673

value: merged


title: human_1C_EMB1


title: Dere.ovary.8


title: BL60_6h_Prednisolone_Replicate 2

description: 2x50 cycle


title: human_2C_EMB2


title: BL60_0h_DMSO_Replicate 2

description: 2x50 cycle


title: human_4C_EMB3


title: human_blastocyst_EMB6

value: blastocyst


title: human_1C_1


title: BE2

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

data_processing:
mapping of reads was done using: bowtie2  --local using P.aeruginosa PAO1 as template genome
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
Count values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Assembly: Pseudomonas aeruginosa PAO1 ASM676v1 genomic
Supplementary files format and content: Tab delimited text file

organism: Pseudomonas aeruginosa

source_name: Bacterial

growth_protocol: P.aeruginosa PAO1 were grown in CAMHB medium at 37 degees celcius. Cultures were aerated with shaking 220rpm.

extract_protocol:
Cell were lysed using glassbead and total RNA was isolated using TRIzol/chlorophorm extraction followed by ethanol and isopropanol precipitation
Standard library preparation protocol of BGI for Illumina RNA-Seq

treatment_protocol: Bacterial cells were grown in CAMHB untill reached OD600 =1 and BSS(16 μM) , eravacycline(0.5μM) or the combination was added to the treated culture. After 30 minutes, cells were collected for the RNA extraction. Subsequently cells were harvested by centrifugation at 10.000 x g for 1 minute, snap-frozen in liquid nitrogen and stored at -80°C prior to RNA isolation.

value: BSS and Eravacycline treatment 2


title: human_1C_4


title: BE1

value: BSS and Eravacycline treatment 1


title: human_4C_EMB4


title: swi6-delta mst2-delta set1-delta _9me3_IP_rep2_endogenous

city: Waltham

first: Melissa

last: Seman

address: 415 South St

institute: Brandeis University

data_processing:
sequences were trimmed with Trimmomatic, aligned with BWA, and normalized using bamCompare with subtraction of input and RPKM
Supplementary files format and content: bigwig files from bamCompare

organism: Schizosaccharomyces pombe

source_name: fission yeast

growth_protocol: YEA, grown to log phase at 32C

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cells were lysed with bead beating.
ChIP-seq libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. 1 ng of DNA was used as starting material.

value: swi6-delta mst2-delta set1-delta

tag: chip antibody

value: IP

value: fission yeast


title: human_morula_MOR

value: morula


title: BSS2

value: BSS treatment 2


title: swi6-delta set1-delta _9me3_IP_rep2_endogenous

value: swi6-delta set1-delta


title: swi6-delta mst2-delta _9me3_IP_rep2_endogenous

value: swi6-delta mst2-delta


title: E1

value: Eravacycline treatment 1


title: PA2

value: control 2


title: WT_9me3_input_rep1_endogenous

value: WT

value: input


title: BSS1

value: BSS treatment 1


title: swi6-delta _9me3_IP_rep2_endogenous


title: WT_9me3_IP_rep2_endogenous


title: swi6-delta mst2-delta _9me3_IP_rep1_endogenous


title: swi6-delta mst2-delta set1-delta _9me3_IP_rep1_endogenous


title: swi6-delta set1-delta _9me3_IP_rep1_endogenous


title: biol rep 3, S.aureus+ S. anginosus + tonsillar cells , test, 3h

city: Tromsø

middle: Merethe

last: Hanssen

address: Hansine Hansens veg 18

department: Medical Biology

country: Norway

institute: University of Tromsø

description: BR3.reads aligned against S. aureus from bacterial mix with host at 3h

data_processing:
RNA seq reads were generated from 12  samples in two runs of RNA-seq. The overall pipeline for RNA-seq data analysis included generating FASTQ-format files containing reads sequenced from an NGS platform, quality control and trimming, aligning reads to an annotated reference genome, and quantifying expression of genes.
Each library produced between 45 – 184 million reads, were pre-processed for quality check using FASTQC/0.11.9-Java-11. Filtering (removable of adaptor dimer reads) and trimming (removable of low-quality bases) was performed by Trimmomatic/0.39-Java-11. Then, only those sequences with a quality score Q > equal to 20 and a minimum of 55 nucleotide sequence lengths were retained in the dataset.
The final quality check was performed in the trimmed file. S. aureus TR145 strain was used as a reference genome for the mapping performed by Bowtie2/2.4.4-GCC-10.3.0. For all the samples, percentage of mapping efficacy was retrieved from Bowtie2 and sorted by Samtools/1.14-GCC-11.2.0.
Further, the gene count matrix for gene expression analysis was identified using the featureCounts program implemented in the SourceForge Subread package.
Differentially expressed genes analysis of the test group and the control group (each group has three biological replicates per conditions) was analyzed using the DESeq R package (1.38.0).
DEGs were calculated under log2|FoldChnage|(log2|FC|) > 2 and a false discovery rate (FDR) adjusted p (padj) < 0.05.
Supplementary files format and content: raw RNA seq reads generated after RNA sequencing for each Samples (total 12)
Supplementary files format and content: tab-delimited text files include count matrix complied after feature count tool for each Sample

organism: Staphylococcus aureus

source_name: HTEpiC- Human tonsils epithelial cells

growth_protocol: The bacterial strains grown to log phase OD600nm =0.8 -1.2 were diluted to OD600nm = 0.36 – 0.42 (corresponding to 0.6 - 1.2 x 108 CFU/ml) and seeded into wells with host cells at a Multiplicity of Infection (MOI) of 5.

extract_protocol:
After 1 and 3h post-infection, the media was aspirated, and the host cells were washed twice with fresh media to remove unbound bacteria. The host cells were then trypsinized and lysed with Triton-X. The released bacterial mix was then collected from three technical replicates and pooled together for RNA extraction. Plate enumeration, adhesion assay and cytotoxicity assay were also performed.
Total RNA extracted from three replicates of S. aureus cocultured with S. anginosus in the absence/presence of host cells collected at time points of 1 h and 3 h were processed for RNA-seq library preparation. The samples were sequenced on an Illumina 550 platform, with dual indexes, and paired-end mode. The final sequencing concentration was 1.8 pM.
Prior to RNA libraries for RNA-seq, depletion of bacterial rRNA was performed with the RiboCop rRNA depletion kit for Gram-Positive Bacteria (G+), according to the manufacturer’s protocol. In total 12 samples were processed for libraries construction using Lexogen’s CORALLTM Total RNA-Seq Kit with RiboCop following the manufacturer's protocols.

value: HTEpiC- Human tonsils epithelial cells

value: primary epithelial cell line

tag: time

value: bacterial mix with Host

tag: group


title: biol rep 3, S. aureus + S. anginosus, control, 3h

description: BR3.reads aligned against S. aureus from bacterial mix without host at 3h

tag: cell type

tag: treatment

value: bacterial mix without Host


title: biol rep 3, S.aureus+ S. anginosus + tonsillar cells , test, 1h

description: BR3.reads aligned against S. aureus from bacterial mix with host at 1h

tag: cell line


title: E2

value: Eravacycline treatment 2


title: swi6-delta _9me3_IP_rep1_endogenous


title: PA1

value: control 1


title: WT_9me3_IP_rep1_endogenous

value: IP


title: biol rep 3, S. aureus + S. anginosus, control, 1h

description: BR3.reads aligned against S. aureus from bacterial mix without host at 1h


title: swi6-delta set1-delta _9me2_input_rep2_endogenous

value: fission yeast


title: swi6-delta mst2-delta set1-delta _9me2_input_rep2_endogenous

value: swi6-delta mst2-delta set1-delta


title: swi6-delta _9me2rep2_9me3rep2_input_endogenous


title: biol rep 2, S. aureus + S. anginosus, control, 3h

description: BR2.reads aligned against S. aureus from bacterial mix without host at 3h


title: swi6-delta mst2-delta _9me2_input_rep2_endogenous


title: biol rep 2, S.aureus+ S. anginosus + tonsillar cells , test, 1h

description: BR2.reads aligned against S. aureus from bacterial mix with host at 1h


title: biol rep 2, S. aureus + S. anginosus, control, 1h

description: BR2.reads aligned against S. aureus from bacterial mix without host at 1h


title: WT_9me2_input_rep2_endogenous