title: RNA-seq young MPP3 rep1


title: 218177

status: Public on Dec 05 2020

type: SRA

city: Oxford

first: Lucy

last: Garner

address: Experimental Medicine, Level 5, John Radcliffe Hospital

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
BCL files were converted to FASTQ files using bcl2fastq (v2.20.0)
Reads were trimmed using Trimmomatic (v0.36)
Trimmed reads were aligned to GRCh38 using STAR (v2.5.3a; --outFilterMismatchNoverLmax 0.04 --outFilterType BySJout --outMultimapperOrder Random)
Alignments were filtered using Samtools v1.6 to retain only primary alignments and properly paired reads
Ensembl gene counts were generated using featureCounts (v1.6.0; -C -B -p)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw gene counts: Ensembl gene IDs and raw gene counts for all samples and genes

molecule: polyA RNA

organism: Homo sapiens

source_name: small intestine

extract_protocol:
Small intestinal biopsies were collected at the time of endoscopy and transported in R10 (RPMI-1640 [Lonza] + 10% FCS [Sigma-Aldrich] + 1% penicillin/streptomycin [Sigma-Aldrich]), before cryopreservation in freezing medium (10% DMSO [Sigma-Aldrich], 90% FCS [Sigma-Aldrich]). When required, samples were rapidly thawed in a 37°C water bath and washed in 20 ml R10 before tissue dissociation. Duodenal samples were incubated in R10 media with 1 mg/ml Collagenase D (Roche) and 100 μg/ml DNase (Thermo Fisher Scientific) for one hour in a shaking incubator at 37°C. Biopsies were then dissociated by vigorous agitation using a GentleMACS Dissociator (Miltenyi Biotec), then strained through a 70 μm filter. Cells were washed with R10 media. Mononuclear cells were isolated on a discontinuous 70% and 35% Percoll gradient (GE Healthcare) by centrifugation at 700 g for 20 minutes without brake. Mononuclear cells were collected from the interface and washed in R10. Single cells were index-sorted into 96-well plates with one cell per well in 2.3 μl lysis buffer (0.8% (vol/vol) Triton X-100 and 2 U/μL RNase inhibitor).
Smart-seq2 libraries were generated following the published protocol (S. Picelli et al., Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc. 9, 171–181 (2014)) with External RNA Controls Consortium RNA (1:100,000) added prior to sequencing.

tag: donor

tag: cell type

value: CD8+ T cell

tag: cd103 status

tag: disease state

value: intestinal transplant recipient


title: RNA-seq young MPP2 rep2

city: Minato-ku

first: Atsushi

last: Iwama

state: Tokyo

address: 4-6-1, Shirokanedai

department: Center for Stem Cell Biology and Regenerative Medicine

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
alignment:TopHat2 (version 2.0.13; with default parameters) and Bowtie2 (version 2.1.0) were used for alignment to the reference mouse genome (mm10 from the University of California, Santa Cruz Genome Browser;) with annotation data from iGenomes (Illumina)
Row count for each gene symbol are generated by StringTie
Data normalization:DESeq2
DESeq2 were used to perform statistical analysis for differentially expressed genes
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: 10 week multipotent progenitor 2s

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen)
Total RNA were subjected to reverse transcription and amplification with a SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech). After sonication with an ultrasonicator (Covaris), the libraries for RNA-seq were generated from fragmented DNA with 8 cycles of amplification using a NEB Next Ultra DNA Library Prep Kit (New England BioLabs). After the libraries were quantified using the Bioanalyzer (Agilent), samples were subjected to sequencing with Hiseq1500 (Illumina) and 61 cycles of the sequencing reactions were performed.

value: Murine bone marrow derived MPP2s

tag: surface markers

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48+ Flt3-

tag: age

tag: strain


title: 218122


title: 217189


title: 218120


title: 217110


title: 217108


title: 216193


title: RNA-seq young HSC rep1

source_name: 10 week hematopoietic stem cells

value: Murine bone marrow derived HSCs

value: IL-7- Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-


title: 216106


title: RNA-seq young MPP2 rep1


title: aged H3K4me3 HSC rep1

library_source: genomic

data_processing:
alignment:sequences were aligned to mouse genome sequences (mm10) with Bowtie2(default setting). Only uniquely mapped reads were retained for downstream analysis
We used macs2(ver2.2.6) to detect peak of histone modification with nomodel option
For H3K4me3, narrow peaks with a q-value cutoff of 0.05 was adopted. For H3K27me3, broad peaks with a q-value cutoff of 0.10 was adopted.
For visualization to make bigwig files,reads per million mapped read (RPM) values of the sequenced reads were calculated every 2,000-base pair bin with a shifting size of 200 base pairs using bed tools and normalized with the amount of ChIP DNA in the H3K27me3 analysis.
Genome_build: mm10

molecule: genomic DNA

source_name: 20 month hematopoietic stem cells

extract_protocol:
Cells were cross-linked with 0.5% formaldehyde at 37°C for 2 min, washed with PBS containing 2% FBS, lysed with ChIP buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM CaCl2, 0.5% NP40, and protease inhibitor cocktail)
Extracted samples were sonicated for 5 sec × 3 times (90 sec on ice) using a Bioruptor (Cosmo Bio). Cells were digested with micrococcal nuclease (MNase) (NEB) at 37°C for 40 min and treated with 10 mM EDTA to stop the reaction. After the addition of an equal volume of RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% NP40, 0.5% sodium deoxycholate, and 0.1% SDS), cells were resonicated for 5 sec × 10 times (300 sec on ice) using the Bioruptor. After centrifugation, the soluble chromatin fraction was immunoprecipitated at 4°C overnight with Dynabeads M-280 Sheep anti-Rabbit IgG conjugated with an anti-H3K27me3 (07-449, Millipore), anti-H2AK119ub1 (8240, Cell Signaling Technology),or anti-H3K4me3 (07-473, Millipore) antibody. Immunoprecipitates were washed with high salt ChIP buffer (500 mM NaCl) four times and TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA) twice. Bound chromatin and 25 μl of input DNA were suspended in 47.5 and 22.5 μl of elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, and 250 mM NaCl), respectively, and vortexed. After the addition of 5 μl of 5 M NaCl, the  solutions were incubated at 65°C for 4 hr and then treated with 25 μg/ml RNase A (Sigma-65 Aldrich) at 37°C for 30 min and 0.1 mg/ml proteinase K (Roche) at 50°C for 1 hr to reverse formaldehyde crosslinking. Eluted DNA was purified with a MinElutePCR Purification Kit (Qiagen).DNA libraries were prepared from input and ChIP DNA samples using a ThruPLEX DNA-seq Kit (Rubicon Genomics) according to the manufactures’instructions. DNA libraries were quantified using high sensitivity Chip on the Bioanalyzer (Agilent) and sequenced with Hiseq1500 (Illumina) according to the manufacturer’s instructions. Sixty-one cycles of sequencing reactions were performed.

tag: chip antibody

value: anti-H3K4me3 (07-473, Millipore)


title: aged H3K4me3 HSC rep2


title: 219132


title: young H3K4me3 HSC rep2


title: RNA-seq young MPP4 rep1

source_name: 10 week multipotent progenitor 4s

value: Murine bone marrow derived MPP4s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3+


title: 215179


title: RNA-seq young MPP1 rep2

source_name: 10 week multipotent progenitor 1s

value: Murine bone marrow derived MPP1s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48- Flt3-


title: 215181


title: 214169


title: 215118


title: aged H2AK119ub1 HSC rep2

value: anti-H2AK119ub1 (8240, Cell Signaling Technology)


title: RNA-seq young HSC rep2


title: aged H2AK119ub1 HSC rep1


title: 214130


title: RNA-seq young MPP1 rep1


title: 213157


title: young H2AK119ub1 HSC rep2


title: young H3K4me3 HSC rep1


title: 213155


title: young H2AK119ub1 HSC rep1


title: 213142


title: aged H3K27me3 HSC rep2

value: anti-H3K27me3 (07-449, Millipore)


title: 212154


title: 212145


title: young HSC input rep2


title: 212143


title: young H3K27me3 HSC rep2


title: 211133


title: young HSC input rep1


title: 211166


title: young H3K27me3 HSC rep1


title: 214167


title: 211131


title: 210178


title: aged CLP rep2

data_processing:
Sequences were aligned to mouse genome sequences (mm10) with Bowtie2(default setting) .
Mapped reads are subsampled with samtools to make numbers of reads same in all samples.
Macs2(ver2.2.6) was used to call peaks with nomodel, narrow peak option. With a q-value cutoff of 0.001
For visualization to make bigwig files,reads per million mapped read (RPM) values of the sequenced reads were calculated every 200-base pair bin with a shifting size of 100 base pairs using bed tools and normalized with the amount of ChIP DNA in the H3K27me3 analysis.
Genome_build: mm10

source_name: 20 month common lymphoid progenitor

extract_protocol:
Transposase reaction was performed using nuclei prepared from freshly sorted 20,000 cells of each fraction
Libraries were then generated using a NEBNext Ultra DNA Library Prep Kit (New England BioLabs, Beverly, MA, USA). Library DNA was size-selected (240 - 360 bps) with BluePippin (Sage Science, Beverly, MA, USA). Sequencing was performed using HiSeq1500 (Illumina) with a single-read sequencing length of 60 bp.

value: Murine bone marrow derived CLPs

value: IL-7+ Lin- Sca-1 low c-kit low


title: aged CLP rep1


title: 210119


title: 209190


title: aged MEP rep2

source_name: 20 month megakaryocyte-erythrocyte progenitors

value: Murine bone marrow derived MEPs

value: IL-7- Lin- Sca-1- c-kit+ FcgR- CD34-


title: 210121

value: CD8+ T cell


title: 209109

value: intestinal transplant recipient


title: aged MEP rep1


title: aged HSC input rep2


title: 208192


title: 208107


title: aged MPP4 rep2

source_name: 20 month multipotent progenitor 4s


title: aged GMP rep1

source_name: 20 month granulocyte-macrophage progenitors

value: Murine bone marrow derived GMPs

value: IL-7- Lin- Sca-1- c-kit+ FcgR+ CD34+


title: aged HSC input rep1

value: Murine bone marrow derived HSCs


title: 209107


title: 207180


title: aged MPP3 rep2

source_name: 20 month multipotent progenitor 3s

value: Murine bone marrow derived MPP3s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3-


title: aged MPP4 rep1

value: Murine bone marrow derived MPP4s


title: aged H3K27me3 HSC rep1

value: IL-7- Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-


title: 207178


title: 207119


title: aged MPP2 rep1

source_name: 20 month multipotent progenitor 2s

value: Murine bone marrow derived MPP2s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48+ Flt3-


title: 206168


title: aged MPP3 rep1


title: 206131


title: aged MPP1 rep1

source_name: 20 month multipotent progenitor 1s

value: Murine bone marrow derived MPP1s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48- Flt3-


title: aged MPP1 rep2


title: 205156


title: 205154


title: aged MPP2 rep2


title: aged HSC rep4


title: aged GMP rep2


title: 206166


title: aged HSC rep2


title: aged HSC rep1


title: 204144


title: 205143


title: aged HSC rep3


title: 204155


title: young CLP rep2

source_name: 10 week common lymphoid progenitor

value: Murine bone marrow derived CLPs


title: young CLP rep1

value: IL-7+ Lin- Sca-1 low c-kit low


title: 204142


title: 203167


title: young MEP rep2

source_name: 10 week megakaryocyte-erythrocyte progenitors

value: Murine bone marrow derived MEPs


title: 203132


title: 203130


title: young MEP rep1

value: IL-7- Lin- Sca-1- c-kit+ FcgR- CD34-


title: young GMP rep2

source_name: 10 week granulocyte-macrophage progenitors


title: 202179

value: CD8+ T cell


title: 202118

value: intestinal transplant recipient


title: young MPP4 rep1

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3+


title: 201191


title: young GMP rep1

value: Murine bone marrow derived GMPs

value: IL-7- Lin- Sca-1- c-kit+ FcgR+ CD34+


title: young MPP4 rep2


title: 202120


title: 201108


title: young MPP3 rep2

source_name: 10 week multipotent progenitor 3s

value: Murine bone marrow derived MPP3s


title: 201106

source_name: small intestine


title: young MPP2 rep1

source_name: 10 week multipotent progenitor 2s


title: S_T_2

city: London

first: Andreas

last: Schaefer

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCm38-release-89 transcriptome
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

source_name: AON R2

extract_protocol:
The minced tissue was gently homogenized in Nuclei PURE Lysis Buffer and 10% Triton X-100 using an ice-cold dounce and pestle, and filtered two times through a 40 μm cell strainer on ice. After centrifuging at 500 rpm for 5 min at 4 °C, the supernatant was aspirated and gently resuspended in 500 μl of cold buffer (1x of cold Hanks' Balanced Salt Solution HBSS, 1% nuclease-free BSA, RNasin Plus and 1/2000 DRAQ5). Fluorescence-activated nuclei sorting of single nuclei was performed using a BD FACSAriaTM III Cell Sorter  with a 70 μm nozzle at a sheath pressure of 70 psi. Total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit.
Libraries were prepared using the Next Single Cell / Low Input RNA Library Prep Kit (New England Biolabs). The quality and quantity of the final libraries was assessed with TapeStation D1000 Assay (Agilent Technologies) before sequencing with an Illumina HiSeq 4000.

treatment_protocol: A retrogradely transported Adeno Associated Virus (retroAAV-CAG-H2B-GFP) was injected stereotaxically into multiple sites of piriform cortex (PCx) and anterior olfactory nucleus (AON).

tag: tissue

value: anterior olfactory nucleus

tag: rna population

value: Nuclear mRNA

tag: developmental stage

value: adult


title: S_T_3

source_name: AON R3


title: young MPP2 rep2

value: Murine bone marrow derived MPP2s


title: young MPP1 rep1


title: S_M_2

source_name: PCx R2

value: piriform cortex


title: young MPP3 rep1

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3-


title: S_T_1

source_name: AON R1


title: young HSC rep3

source_name: 10 week hematopoietic stem cells

value: Murine bone marrow derived HSCs

value: IL-7- Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-


title: S_M_1

source_name: PCx R1


title: S_M_3

source_name: PCx R3


title: young HSC rep1


title: OBseqR3

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library
Read counting was done against the 10X mm10-3.0.0_premrna reference transcriptome with annotation for the GFP and tdT gene added.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Raw read count matrix for each sample in form of the Cell Ranger matrix, features and barcodes files.

source_name: olfactory bulb single-nuclei RNA-Seq

extract_protocol:
The minced tissue was gently homogenized in Nuclei PURE Lysis Buffer and 10% Triton X-100 using an ice-cold dounce and pestle, and filtered two times through a 40 μm cell strainer on ice. After centrifuging at 500 rpm for 5 min at 4 °C, the supernatant was aspirated and gently resuspended in 500 μl of cold buffer (1x of cold Hanks' Balanced Salt Solution HBSS, 1% nuclease-free BSA, RNasin Plus and 1/2000 DRAQ5). Fluorescence-activated nuclei sorting of single nuclei was performed using a BD FACSAriaTM III Cell Sorter  with a 70 μm nozzle at a sheath pressure of 70 psi.
Libraries were prepared using the Next Single Cell / Low Input RNA Library Prep Kit (New England Biolabs). The quality and quantity of the final libraries were assessed with TapeStation D5000 Assay (Agilent Technologies) before sequencing with an Illumina HiSeq 4000 using the 10X kit version Chromium Single Cell 3’ v3.

tag: Stage

value: olfactory bulb


title: OBseqR2


title: OBseqR1


title: S3 rep3

city: Shenyang

first: WEI

last: SUN

state: Liaoning

address: No.155 Nanjing Bei Street

country: China

institute: the First Hospital of China Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low  quality bases which will affect the following assembly and analysis. Thus, to get high quality  clean reads, reads were further filtered by fastp  (version 0.18.0)
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome  RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean  reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the  reference genome using HISAT2.2.4 with “-rna-strandness RF” and other parameters set as  a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a  reference-based approach. For each transcription region, a FPKM (fragment per kilobase of  transcript per million mapped reads) value was calculated to quantify its expression  abundance and variations, using StringTie software.
Genome_build: GRCh38.release 94
Supplementary_files_format_and_content: abundance measurements

source_name: transfected si-NEAT1_2 K1 cells

extract_protocol:
Thyroid cancer cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line background

tag: tissue source

value: Papillary Thyroid cancer

tag: genotype/variation


title: young MPP1 rep2

source_name: 10 week multipotent progenitor 1s

value: Murine bone marrow derived MPP1s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48- Flt3-


title: 18DAP WT embryo mRNA-seq Rep1

city: Beijing

first: Jincheng

last: Long

state: Beijing

address: Hai Dian district ,Yuanmingyuan Road.Beijing

department: National Maize improvement center

institute: China Agricultural University

data_processing:
For ChIP-seq,  low quality reads and potential adaptor sequence was removed using Trim_galore (https://github.com/FelixKrueger/TrimGalore). Clean reads were then mapped to the reference B73 genome (Jiao et.al 2017) (release AGPV4) with Bowtie2 (-no-unal -I 0 -X 800 -no-discordant). Mapped reads with MAPQ>=5 were retained. Potential PCR duplicates was removed by MarkDuplicates V2.17.10 from Picard tools (https://github.com/broadinstitute/picard).
ChIP-seq peaks were called using MACS2 (v 2.1.2) with the following setting:  -g 2.3e+9 -B -SPMR -q 0.01.
For mRNA-seq, low quality reads and adaptor sequence were trimmed using Trim_galore. Clean reads were subsequently mapped to maize reference genome (B73_RefGen_v4.43. gff3) with Tophat-2.0.10.  Expression level of genes was calculated in FPKM (fragment per kilobase per million) using Cufflinks-2.2.1 packages.
Genome_build: B73_RefGen_v4
Supplementary_files_format_and_content: peak text files, bedGraph, FPKM for RNA-seq

organism: Zea mays

source_name: Maize developing seed

growth_protocol: Maize plants were grown in the field at Beijing in the summer of 2017

extract_protocol:
Developing maize ears were harvested at 18 days after pollination (DAP). Maize embryo was then isolated from the kernel using scalpel. After washing 3 times with steriziled ddH2O (to remove endosperm contaminate),  collected embryo was directely put into the liquid nitrogen.
mRNA of WT 18 DAP embyo was first purified from the total RNA using  NEBNext Poly(A) mRNA Magnetic Isolation Module.Next,NEBNext® Ultra™ II RNA Library Prep Kit (New England BioLabs) was used to make the mRNA-seq library.

treatment_protocol: No special treatment to all of the biological materials.

value: developing embryo

tag: genotype

value: WT

value: 18 DAP


title: 18DAP WT embryo IgG ChIP-seq ChIP Rep2

description: IgG_ChIP-seq_WT_Rep2_treat_pileup.bdg.gz; IgG_ChIP-seq_WT_Rep2_control_lambda.bdg.gz

extract_protocol:
18 DAP embryo chromatin was isolated as previously described (Yang et a;.2016).Briefly, formaldehyde-fixed samples were ground to fine powder in liquid nitrogen. Nuclei pellets were suspended in a buffer containing 0.25 M sucrose, 10 mM Tris-HCl, pH 8, 10 mM MgCl2, 1% Triton X-100, 5 mM β-mercaptoethanol, 0.1 mM PMSF, and protease inhibitors (one mini tablet per milliliter; Roche). The suspensions were transferred to microfuge tubes and centrifuged at 12,000g for 10 min. The pellets were suspended in 1.7 M sucrose, 10 mM Tris-HCl, pH 8, 2 mM MgCl2, 0.15% Triton X-100, 5 mM β-mercaptoethanol, 0.1 mM PMSF, and protease inhibitors (one tablet in 30 mL solution; Roche), and centrifuged through a layer of the same buffer in microfuge tubes. The nuclear pellets were lysed in a buffer containing 50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS, and protease inhibitors (one tablet in 30 mL solution; Roche). The lysed nuclei were sonicated with a Bioruptor (UCD-200) in a water bath at 4°C for 12 cycles with 30s on and 30s off.Immunoprecipitation was performed using about 10 µg of chromatin, following a previously described protocol (Locatelli et al., 2009). Typically, 10 μL of affinity-purified antibody were used for immunoprecipitation. The precipitated DNA was dissolved in 50 μL 10 mM Tris-HCl, pH 7.5, 1 mM EDTA and treated with RNase (DNase-free).
Antibody pulled-down DNA was subject to regular DNA library preparation procedure with NEBNext Ultra II DNA library Prep Kit (New England BioLabs).

value: IgG


title: 18DAP WT embryo H3K9me2 ChIP-seq ChIP Rep2

description: H3K9me2_ChIP-seq_WT_Rep2_treat_pileup.bdg.gz; H3K9me2_ChIP-seq_WT_Rep2_control_lambda.bdg.gz

tag: chip antibody manufacturer

value: Abclonal Company (Cat #A2359)


title: 18DAP WT embryo H3K9me2 ChIP-seq ChIP Rep1

description: H3K9me2_ChIP-seq_WT_Rep1_treat_pileup.bdg.gz;H3K9me2_ChIP-seq_WT_Rep1_control_lambda.bdg.gz


title: young HSC rep4


title: N2 rep2

source_name: transfected NC K1 cells

value: NC


title: N1 rep1


title: S1 rep1


title: N3 rep3


title: Nitrate treatment rep 3

city: La Laguna

first: Jose

last: Gonzalez

address: School of Pharmacy

department: Dept. Microbiology

country: Spain

institute: University of La Laguna

data_processing:
HiSeq 2500 machine in High Output run mode using v4 chemistry
Instrument Control Software 2.2.58
Bioconductor DESeq
Supplementary_files_format_and_content: log FC and amino acid sequence

organism: Shewanella algae

source_name: Bacterial static cultures

growth_protocol: Shewanella algae static cultures in MB medium were supplemented with DMSO (35 mM), nitrate (35 mM), TMAO (35 mM) or non-supplemented.

extract_protocol:
RNA purification was performed with the Direct-Zol RNA Miniprep Plus kit. Residual genomic DNA was removed upon DNAse treatment with the Turbo DNA-free kit. rRNA was depleted from 550 ng of total RNA using Illumina Ribo-Zero rRNA removal kit. Sequencing libraries were prepared using Illumina TruSeq stranded total RNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CECT 5071


title: young HSC rep2


title: 18DAP WT embryo IgG ChIP-seq ChIP Rep1

description: IgG_ChIP-seq_WT_Rep1_treat_pileup.bdg.gz; IgG_ChIP-seq_WT_Rep1_control_lambda.bdg.gz


title: 18DAP WT embryo ZmAGO4 ChIP-seq input Rep2

value: none (input)


title: 18DAP WT embryo ZmAGO4 ChIP-seq input Rep1


title: 18DAP WT embryo H3K9me2 ChIP-seq input Rep1


title: S2 rep2


title: Nitrate treatment rep 1


title: 18DAP WT embryo mRNA-seq Rep2


title: Nitrate treatment rep 2


title: DMSO treatment rep 3


title: DMSO treatment rep 2


title: 18DAP zmddm1b embryo ZmDDM1B ChIP-seq input Rep2


title: 18DAP zmddm1b embryo ZmDDM1B ChIP-seq input Rep1


title: 18DAP WT embryo ZmAGO4 ChIP-seq ChIP Rep1

value: produced by this lab


title: 18DAP WT embryo H3K9me2 ChIP-seq input Rep2


title: 18DAP zmddm1b embryo ZmDDM1B ChIP-seq ChIP Rep2


title: DMSO treatment rep 1


title: Control experiment rep 3


title: 18DAP zmddm1b embryo ZmDDM1B ChIP-seq ChIP Rep1


title: 18DAP WT embryo ZmDDM1B ChIP-seq input Rep1


title: 18DAP WT embryo ZmAGO4 ChIP-seq ChIP Rep2


title: 18DAP WT embryo ZmDDM1B ChIP-seq input Rep2


title: Rbp53MYCNsclcOFFDOX_T4

city: Seattle

first: David

last: MacPherson

state: WA

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to mm9 using TopHat v2.0.8b. Counts were generated from Tophat alignments at the gene-level employing the "intersection-strict" overlap mode in HTSeq v0.6.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include counts genreated at the gene-level by HTSeq-count.

source_name: mouse SCLC tumor

extract_protocol:
Cells were lysed in TRIzol reagent with RNA isolated following manufacturers instructions.
RNA-seq libraries were prepared using theNEBNext Ultra RNA Library Prep Kit for Illumina (catalog E7530L). Briefly, 500 ng total RNA was used to isolate mRNA with the NEB Next Oligo dT Magnetic Isolation Module (catalog E7490L). The isolated mRNA undergoes fragmentation, priming, cDNA synthesis and end repair/dA-tail. Individual index primers for multiplexing were added during PCR library enrichment after adaptor ligation.

value: tumor

tag: tumor type

value: mouse SCLC

value: Rb;p53,TRE-MYCN, LSL-RTTA

tag: doxycycline status

value: 7 days OFF DOX


title: 18DAP WT embryo ZmDDM1B ChIP-seq ChIP Rep2


title: Emx-cre KO

city: New Haven

first: Nenad

last: Sestan

address: 333 Cedar Street, SHM C-316C

department: Neuroscience

institute: Yale University School of Medicine

description:
s7
processed data file:
mouseBrain.Han.Neuron2020.RPKM.txt
mouseBrain.Han.Neuron2020.count.txt

data_processing:
Sequencing data was quality controlled by FastQC
RNA-seq and Chip-seq reads were aligned to the mouse genome (NCBI37/mm9) using STAR (v2.4.0e) and Bowtie (0.12.5) respectively. For RNA-seq alignment, to improve the mapping quality of splice junction reads, mouse gene annotation retrieved from the GENCODE project (version M1) was additionally provided. Command line "--sjdbOverhang 74" was used to construct splice junction library. For Chip-seq alignment, we used the default parameters.
We used RSEQTools and SAMtools to calculate the gene expression. We used HTSeq (v0.6.1) to calculate the gene reads count values for each annotation entry. The gene RPKM values were calculated using in-house R script. We used MACS (version 2.0.9) to call peaks.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with gene counts and RPKM for every gene and every sample; Peak text file

source_name: P0 neocortex

growth_protocol: For the ChIP-Seq experiments,N2A cells were cultured in a 10cm dish and transfected with pCAG-V5 or pCAG-Fezf2-V5 plasmids. After 48 hours of transfection, cells were fixed and processed for chromatin isolation.

extract_protocol:
For knockout experiments, P0 neocortices were isolated and for over-expression studies, FAC sorting at P3 was performed. The samples were use for RNA isolation using Qiagen minElute RNAeasy Kit
Libraries were prepared with Illumina TruSeq mRNA preparation kit (Illumina RS-122-2101) from whole cortices,  NuGEN Ovation V2 system (NuGEN, 0510-32) for Fezf2 over-expressing, FAC sorted cells, and  for ChIP seq experiments using llumina TruSeq ChIP Libary Preparation Kit as per the manufacturer’s instructions. Libraries were quality-controlled by Tapestation/ Bioanalyzer analysis and sequenced on Illumina HiSeq 2000 platform at Yale Center for Genome Analysis (YCGA) to generate 75 bp single reads.  NuGEN Ovation V2 system (NuGEN, 0510-32)

treatment_protocol: For knockout experiments, Fezf2 floxed allele is deleted from the progenitors using Emx1-cre and for over expression experiments, in utero electroporations with Fezf2 or Gfp plasmids were performed at E16.5

tag: strain/cell type

value: Fezf2 knockout

value: Neocortex


title: Control experiment rep 2


title: 18DAP zmddm1a embryo ZmDDM1A ChIP-seq input Rep2


title: 18DAP zmddm1a embryo ZmDDM1A ChIP-seq input Rep1


title: S_aureus_USA300_biofilm_BHI_3

city: Sherbrooke

first: Pascale

middle: B.

last: Beauregard

state: Quebec

address: 2500 Boulevard de l'Université

department: Département de Biologie

country: Canada

institute: Université de Sherbrooke

description: Geneious_DEGs_S_aureus_USA300_Biofilm_vs_planktonic_in_BHI.txt

data_processing:
Trimming with BBDuk plug-in for Geneious Prime software version 2020.0.3. Kmer length : 27. Discarding short read (minimum 10 pb). Trimming low quality (both end, minimum 6).
Trimmed data were then aligned with Bowtie2 plug-in for Geneious Prime software version 2020.0.3 using an “end-to-end” alignment type, a “High Sensitivity / Medium” preset and using the  “do not trim option”, against the following reference chromosomes.
Expression quantification was performed with the build-in tool of Geneious Prime software version 2020.0.3, calculating RPKM, FPKM and TPM for each annotation on the reference sequence. Ambiguously mapped reads counted as partial matches.
Differentially expressed genes (DEGs) were assed with DESeq2 by combining the 3 biological replicates of each condition and comparing biofilm cultures vs planktonic cultures in either TSBg(s), BHIg(s) or both. Only the genes with an adjusted P-value ≤ 0.05 were retained for further analysis. DEGs were consider upregulated if they had a log2 fold change ≥ 2.0 and downregulated if they had a log2 fold change ≤ -2.0. For the transcriptomic study on media effect on genes expression, DEGs with a log2 fold change ≥ 2.0 are considered upregulated in BHIg(s) while DEGs with a log2 fold change ≤ 2.0 are considered upregulated in TSBg(s).
Genome_build: GenBank accession number GCA_000013425.1 (for S. aureus SH1000, a close descended of the ancestral strain NCTC 8325); GenBank accession number GCA_000017085.1 (for S. aureus USA300); GenBank accession number GCA_000742975.1 (for E. faecalis ATCC 29212) and GenBank accession number GCA_000007785.1 (for E. faecalis V583).
Supplementary_files_format_and_content: tab-delimited text files including Locus Tag, Gene name (if available), Description (if available), Minimum, Maximum, cds length, Direction, nucleotide sequence, Differential Expression Adjusted P-value, Differential Expression Log2 Ratio, Differential Expression Wald Statistic, Differential Expression Absolute Confidence and Differential Expression Base Mean.

organism: Staphylococcus aureus

source_name: Biofilm cells

growth_protocol: 200 µl of the appropriate biofilm inducing medium (TSBg(s) or BHIg(s)) is added in wells of a 48-wells culture plate and inoculated to an OD600 of 0.005 with the bacteria suspension. Planktonic cells are grown with agitation while biofilm cells are grown without agitation until RNA harvesting time (9h for S. aureus strains and 7h for E. faecalis strains)

extract_protocol:
Cells were suspended in 250 µl of fresh lysis buffer (45 mg/ml of lysozyme, 16 µl/ml of lysostaphin 5 mg/ml and 10 µl/ml of mutanolysin 5 U/µl in Tris-EDTA) and incubated for 1h at 37°C, while mixed by every 15 min. They were then transferred in O-Ring tubes with 25 to 50 mg of acid-washed beads and mixed with 3 volumes of TRI Reagent®, to be lysed mechanically with a FastPrep-24™ Classic (MP Biomedicals, Santa Anna, CA, USA) (speed of 4.5 m/sec, 2x 20s). Total RNA was extracted with the Direct-zol™ RNA Miniprep Plus kit (Zymo Research, Irvine, CA, USA) following the manufacturer instruction, including the DNAse I (New England Biolabs, Ipswich, MA, USA) treatment in the extraction column. RNA quantity and the integrity number (RIN) were evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). To remove ribosomal RNA (rRNA), samples were treated using a Pan-Prokaryote riboPOOL™ kit (siTOOLs Biotech Gmbh, Planegg, Germany) coupled with streptavidin magnetic beads (New England Biolabs, Ipswich, MA, USA). mRNA was eluted in 50 µl of nuclease-free water and then cleaned and concentrated using a Clean & Concentrator kit (Zymo Research, Irvine, CA, USA).
Libraries were prepared for RNA sequencing according to the instructions of the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New Englands Biolabs, Ipswich, MA, USA). RNA samples were fragmented 7 min instead to produce fragments superior to 100 pb. Instead of the adaptors provided with the kit, we used TruSeq compatible YIGA adaptors. Nucleic acid purification was performed using Mag-Bind® TotalPure NGS beads (Omega Bio-Tek Inc, Norcross, GA, USA) following the recommended ratio of the NEBNext® kit. Ligation products were subject to PCR amplification using a reverse primer containing a unique 8 bp index for each sample. Concentration of the libraries was measured using a Quant-iT™ PicoGreen™ dsDNA Assay Kit (Invitrogen, Carlsbad, CA, USA) and 1.13 ng of each sample were pool in 80 µl of nuclease-free water. Quantity and quality of the final mix were confirmed with an Agilent 2100 Bioanalyzer before submitting.

treatment_protocol: Planktonic cells (3 biological replicates) were washed with cold PBS and kept in RNA stabilization solution (25 mM sodium citrate, 10 mM EDTA, 47% ammonium sulphate, adjusted to pH 5.2), centrifuged, the supernatant discarded, and the pellet kept at -80°C until extraction. Biofilms (3 biological replicates) were washed with cold PBS and then suspended in RNA stabilization solution by scraping the bottom of the well until enough cells were harvested. Biofilms cells were then centrifuged, the supernatant discarded, and the pellet kept at -80°C until extraction

tag: rna harvesting time


title: 18DAP WT embryo ZmDDM1A ChIP-seq input Rep2


title: Rbp53MYCNsclcOFFDOX_T1


title: 18DAP zmddm1a embryo ZmDDM1A ChIP-seq ChIP Rep1


title: S_aureus_USA300_biofilm_BHI_1


title: 18DAP zmddm1a embryo ZmDDM1A ChIP-seq ChIP Rep2


title: 18DAP WT embryo ZmDDM1A ChIP-seq ChIP Rep2


title: Emx-cre WT

description:
s8
processed data file:
mouseBrain.Han.Neuron2020.RPKM.txt
mouseBrain.Han.Neuron2020.count.txt

value: Fezf2 Wildtype


title: Rbp53MYCNsclcONDOX_T7

value: ON DOX


title: S_aureus_USA300_biofilm_BHI_2

description:
Due to a mix-up in the index during submission process prior to sequencing, Ef_V583_Biofilm_BHI_3 should be treated as Sa_USA300_Biofilm_BHI_2 and vice-versa.
Geneious_DEGs_S_aureus_USA300_Biofilm_vs_planktonic_in_BHI.txt


title: S_aureus_USA300_biofilm_TSB_3

description: Geneious_DEGs_S_aureus_USA300_Biofilm_vs_planktonic_in_TSB.txt


title: Rbp53MYCNsclcONDOX_T6


title: 18DAP WT embryo ZmDDM1A ChIP-seq ChIP Rep1

value: developing embryo


title: S_aureus_USA300_biofilm_TSB_2

description:
Due to a mix-up in the index during submission process prior to sequencing, Ef_V583_Biofilm_TSB_3 should be treated as Sa_USA300_Biofilm_TSB_2 and vice-versa.
Geneious_DEGs_S_aureus_USA300_Biofilm_vs_planktonic_in_TSB.txt


title: Control experiment rep 1


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 48 hours post injection, rep D

city: Saint Paul

first: Amelia

middle: Ryan Isis

last: Lindsey

email: amlind@iu.edu, alindsey@umn.edu

state: MN

address: 1500 Gortner Ave

department: Department of Entomology

institute: University of Minnesota

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 48 hours post injection, replicate D

data_processing:
Following demultiplexing, reads were mapped to extracted reference transcripts of either the Drosophila melanogaster reference genome (release 6.16) (dos Santos et al., 2014) or the wMel strain Wolbachia genome (GenBank accession NC_002978.6 (Wu et al., 2004)) using the RSEM v. 1.3.0 (Li and Dewey, 2011) programs ‘rsem-prepare-reference’ and ‘rsem-calculate-expression’, employing the default Bowtie aligner (Langmead and Salzberg, 2012).
Transcript abundance was summarized and imported to R v. 3.3.1 ‘Bug in Your Hair’ (R Core Team, 2014) with tximport v. 1.2.0 (Soneson et al., 2015).
Expression values for each gene were normalized with a TMM normalization in EdgeR v. 3.16.5 (McCarthy et al., 2012; Robinson et al., 2010).
Genome_build: Drosophila melanogaster reference genome (release 6.16) (dos Santos et al., 2014)
Supplementary_files_format_and_content: Text file with TMM normalized expression values per gene found to be expressed in the dataset.

organism: Drosophila melanogaster

source_name: Pool of 5 adult virgin females

growth_protocol: Fly stocks were maintained on standard cornmeal-agar medium at 25 °C on a 24-hour light: dark cycle under density-controlled conditions.

extract_protocol:
RNA was extracted from pools of flash frozen flies using TRIzol™ Reagent (Invitrogen) following bead-beating, and according to manufacturer’s instructions. rRNAs and other uncapped RNA species were depleted from RNA samples using the Terminator™ 5´-Phosphate-Dependent Exonuclease (Lucigen).
cDNA libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs) following manufacturer’s recommendations, including a seven minute fragmentation time, 10 cycles of PCR amplification, and use of a specific barcode from the NEBNext® Multiplex Oligos for Illumina® Index Primers Set 1 or 2 (New England Biolabs). Quality and quantity of total RNA, depleted RNA, and final libraries was assessed using a TapeStation 2200 (Agilent).

treatment_protocol: We established in vivo systemic viral infections in adult Drosophila, using a block design with a time series. Flies with or without Wolbachia (W+/W-), were injected with either virus or saline (SINV+/SINV-), and collected at 6, 24, and 48 hours post-injection (hpi). For each unique condition of W-SINV-time, we generated four biological replicates (A-D), with each replicate consisting of a pool of five virgin females. Specific conditions for generating the fly infection conditions are as follows: five-day-old virgin female Drosophila were anesthetized with CO2 and injected with either: (a) 50 nl sterile PBS, or (b) 50 nl of freshly grown SINV (1010 PFU/mL in PBS) using a nanoinjector (Drummond Scientific). Pools of five flies (representing a single biological replicate) were injected in a randomized order across a five-hour time period, and capillary needles were changed between fly types (Wolbachia-colonized or not) and injection type (PBS or SINV) to avoid cross-contamination. Exact time of injection was recorded, and the pool of five females was placed in a vial containing standard cornmeal-agar medium supplemented with antibiotic-antimycotic (Corning) and a fresh Kimwipe. Subsequently. 6, 24, or 48 hpi flies were flash frozen in liquid nitrogen and stored at -80 °C until further processing.

tag: treatment

value: Wolbachia-colonized

value: Injected with sindbis virus

tag: timepoint

value: 48 hours post injection


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 48 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 48 hours post injection, replicate C


title: Rbp53MYCNsclcONDOX_T5


title: Rbp53MYCNsclcOFFDOX_T3


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 48 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 48 hours post injection, replicate B


title: Rbp53MYCNsclcOFFDOX_T2


title: 18DAP WT embryo ZmDDM1B ChIP-seq ChIP Rep1

tag: strain

value: WT

tag: age

value: 18 DAP


title: Rbp53MYCNsclcONDOX_T4

tag: tissue


title: S_aureus_USA300_planktonic_BHI_3

source_name: Planktonic cells


title: 18DAP WT embryo ZmDDM1A ChIP-seq input Rep1

tag: chip antibody


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 24 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 24 hours post injection, replicate C

value: 24 hours post injection


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 24 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 24 hours post injection, replicate D


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 48 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 48 hours post injection, replicate A


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 24 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 24 hours post injection, replicate B


title: S_aureus_USA300_biofilm_TSB_1


title: Rbp53MYCNsclcONDOX_T3


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 24 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 24 hours post injection, replicate A


title: S_aureus_USA300_planktonic_BHI_2


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 6 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 6 hours post injection, replicate D

value: 6 hours post injection


title: Rbp53MYCNsclcONDOX_T1


title: S_aureus_USA300_planktonic_BHI_1


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 6 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 6 hours post injection, replicate A


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 6 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 6 hours post injection, replicate B


title: Rbp53MycNcellsG9577offDox

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to mm9 using STAR v2.5.2a. Counts were generated from STAR alignments at the gene-level using featureCounts v1.6.0.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include counts genreated at the gene-level by featureCounts.

source_name: mouse SCLC derived cell line

value: SCLC derived cell line

value: OFF DOX for 4 days


title: S_aureus_USA300_planktonic_TSB_3


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 48 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 48 hours post injection, replicate D

value: Wolbachia-free


title: S_aureus_USA300_planktonic_TSB_2


title: Rbp53MycNcellsG9529offDox

value: mouse SCLC

value: Rb;p53,TRE-MYCN, LSL-RTTA


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 48 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 48 hours post injection, replicate B


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 48 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 48 hours post injection, replicate C


title: S_aureus_USA300_planktonic_TSB_1


title: Rbp53MycNcellsG9488offDox


title: S_aureus_SH1000_biofilm_BHI_3

description: Geneious_DEGs_S_aureus_SH1000_Biofilm_vs_planktonic_in_BHI.txt


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 48 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 48 hours post injection, replicate A


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 24 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 24 hours post injection, replicate D


title: Rbp53MycNcellsG9351offDox


title: S_aureus_SH1000_biofilm_BHI_2


title: Rbp53MYCNsclcONDOX_T2

value: tumor


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 24 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 24 hours post injection, replicate C


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 24 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 24 hours post injection, replicate B


title: Rbp53MycNcellsG9577onDox


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/SINV-injected), 6 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/SINV-injected), flash frozen 6 hours post injection, replicate C


title: Rbp53MycNcellsG4314offDox


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 24 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 24 hours post injection, replicate A


title: Rbp53MycNcellsG9529onDox


title: S_aureus_SH1000_biofilm_TSB_3

description: Geneious_DEGs_S_aureus_SH1000_Biofilm_vs_planktonic_in_TSB.txt


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 6 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 6 hours post injection, replicate B


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 6 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 6 hours post injection, replicate A


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 6 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 6 hours post injection, replicate C


title: CAG-Fezf2-E-V5

description:
FEZF2_E_V5
processed data file:
FEZF2A_peaks.txt
FEZF2E_peaks.txt

source_name: Neuroblastoma 2A cells

value: Neuroblastoma 2A cells

value: Fezf2-V5  over-expression


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/SINV-injected), 6 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/SINV-injected), flash frozen 6 hours post injection, replicate D


title: Rbp53MycNcellsG9488onDox

value: ON DOX


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 48 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 48 hours post injection, replicate D

value: Injected with phosphate buffered saline


title: S_aureus_SH1000_biofilm_TSB_2


title: CAG-Fezf2-A-V5

description:
FEZF2_A_V5
processed data file:
FEZF2A_peaks.txt
FEZF2E_peaks.txt

value: Fezf2-V5 over-expression


title: S_aureus_SH1000_biofilm_TSB_1


title: CAG-V5

description:
FEZF2_Input
processed data file:
FEZF2A_peaks.txt
FEZF2E_peaks.txt


title: Rbp53MycNcellsG9351onDox


title: Rbp53MycNcellsG4314onDox


title: S_aureus_SH1000_planktonic_BHI_2


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 48 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 48 hours post injection, replicate B

value: Wolbachia-colonized


title: S_aureus_SH1000_planktonic_BHI_3

description: Geneious_DEGs_S_aureus_SH1000_Biofilm_vs_planktonic_in_BHI.txt


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 48 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 48 hours post injection, replicate C

value: 48 hours post injection


title: Fezf2 + GFPRep 5

description:
Sample_KH12
processed data file:
mouseBrain.Han.Neuron2020.RPKM.txt
mouseBrain.Han.Neuron2020.count.txt

source_name: P3 neocortex

value: CD-1® IGS

value: Fezf2 over-expression

value: Neocortex


title: KONecOt3

city: Erlangen

first: Darja

last: Andreev

address: Glückstraße 6

department: Medicine 3

country: Germany

institute: Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen

description: genes.readcount.xls

data_processing:
Base Quality and Phred score relationship using the Illumina CASAVA software
The filtered reads were aligned to the Mus musculus genome (Mus_musculus.GRCm38) with HISAT2 (version 2.0.5).
HTSeq (version 0.6.1) was used to count the read numbers mapped of each gene, including known and novel genes.
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: xls raw counts as datamatrix

source_name: Osteoclasts

growth_protocol: Osteoclasts were differentiated in vitro from bone marrow derived monocytes (BMMs) in a concentration of 1x10^6 cells/ml in 48-well plates (500µl/well) in osteoclast medium composed of αMEM+GlutaMAX (Gibco) with 10 % FCS (Biochrom) and 1 % PS (Gibco), supplemented with 20 ng/ml M-CSF and 10 ng/ml RANKL (both from Peprotech) at 37°C, 5,5 % CO2. Medium was changed every 2 days.

extract_protocol:
At day 3 of osteoclast culture, RNA was harvested using peqGOLD TRIfast (Peqlab) according to the standard protocol.
NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) was used with 1 µg of total RNA for the construction of sequencing libraries. Clustering of the index-coded samples was completed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina), according to the manufacturer’s instructions. The library preparations were sequenced on an Illumina HiSeq platform and paired-end reads were generated.

treatment_protocol: At day 1 of culture, pre-osteoclasts were stimulated in a 1:2 ratio with either supernatant collected from viable osteocytes (control condition) or necrotic osteocytes (generated by serum starvation) for 24h.

tag: cell type

value: Osteoclasts differentiated from bone marrow derived monocytes

value: Mincle knockout

value: 1:2 ratio of supernatant from necrotic osteocytes for 24h


title: S_aureus_SH1000_biofilm_BHI_1


title: Fezf2 + GFP Rep4

description:
Sample_KH11
processed data file:
mouseBrain.Han.Neuron2020.RPKM.txt
mouseBrain.Han.Neuron2020.count.txt


title: S_aureus_SH1000_planktonic_BHI_1


title: KONecOt2

description: genes.readcount.xls


title: S_aureus_SH1000_planktonic_TSB_3


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 24 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 24 hours post injection, replicate D

value: 24 hours post injection


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 48 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 48 hours post injection, replicate A


title: GFP rep3

description:
Sample_KH9
processed data file:
mouseBrain.Han.Neuron2020.RPKM.txt
mouseBrain.Han.Neuron2020.count.txt

value: Gfp control


title: Fezf2 + GFP Rep3

description:
Sample_KH10
processed data file:
mouseBrain.Han.Neuron2020.RPKM.txt
mouseBrain.Han.Neuron2020.count.txt


title: S_aureus_SH1000_planktonic_TSB_2

description: Geneious_DEGs_S_aureus_SH1000_Biofilm_vs_planktonic_in_TSB.txt


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 24 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 24 hours post injection, replicate C


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 24 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 24 hours post injection, replicate B


title: CtNecOt3

description: genes.readcount.xls

value: C57BL/6 wildtype


title: KONecOt1

description: genes.readcount.xls


title: CtNecOt2

description: genes.readcount.xls


title: S_aureus_SH1000_planktonic_TSB_1


title: GFP Rep1

description:
Sample_KH7
processed data file:
mouseBrain.Han.Neuron2020.RPKM.txt
mouseBrain.Han.Neuron2020.count.txt


title: E_faecalis_29212_biofilm_BHI_3

description: Geneious_DEGs_E_faecalis_ATCC_29212_Biofilm_vs_planktonic_in_BHI.txt

organism: Enterococcus faecalis


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 6 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 6 hours post injection, replicate D

value: 6 hours post injection


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 24 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 24 hours post injection, replicate A


title: GFP rep2

description:
Sample_KH8
processed data file:
mouseBrain.Han.Neuron2020.RPKM.txt
mouseBrain.Han.Neuron2020.count.txt


title: E_faecalis_29212_biofilm_BHI_1


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 6 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 6 hours post injection, replicate C


title: KO3

description: genes.readcount.xls

value: 1:2 ratio of supernatant from viable osteocytes for 24h


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 6 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 6 hours post injection, replicate B


title: KO2

description: genes.readcount.xls


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-colonized/saline-injected), 6 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-colonized/saline-injected), flash frozen 6 hours post injection, replicate A


title: E_faecalis_29212_biofilm_BHI_2


title: E_faecalis_29212_biofilm_TSB_3

description: Geneious_DEGs_E_faecalis_ATCC_29212_Biofilm_vs_planktonic_in_TSB.txt


title: gAraRC_rep3

city: Qingdao

first: Guodong

last: Liu

state: Shandong

address: Binhai Road 72

department: State Key Laboratory of Microbial Technology

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and were trimmed for the bases from both the 3' end and 5' end when the base quality is below 3. We also slides a 4-base window from the 5' end and cuts reads when the mean quality falls below 18. Then, the reads that are shorter than 36 bp after trimming were filtered out.
Sequenced reads were aligned to the genome using hisat2 2.0.0-beta with default parameters for paired-end reads.
Raw counts of mapped reads on gene-level were quantificated using featureCounts v1.5.0-p1 with "-s 2" parameter specified for "reverse" stranded-specific library construction.
The measure FPKM (fragments per kilobase per million mapped fragments) was used to show the gene expression values. Deseq2 normailization was used latter to compare the gene expression levels between samples and perform statistical analysis.
Genome_build: Penicillium oxalicum 114-2 genomic sequence (NCBI accession: PRJNA60877)
Supplementary_files_format_and_content: One matrix table in text format including FPKM values for each genes.

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: All strains were first precultured in Vogel's medium with 2% glucose for 24 h, and then transferred to Vogel's medium without carbon source for 4 hours cultivation at 30 degrees C, 200 rpm.

extract_protocol:
Total RNA was prepared from the mycelia by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer's protocol.
mRNA libraries were prepared for sequencing using KAPA mRNA Capture Kit and KAPA Stranded RNA-Seq Kit according to the manufacturer's instructions.

treatment_protocol: Mycelia were filtered by filter paper.

tag: strain/genotype

value: mutant expressing the transcription factor mutant AraR(A731V)


title: CtNecOt1

description: genes.readcount.xls


title: KO1

description: genes.readcount.xls


title: Fezf2 + GFP rep1

description:
Sample_KH5
processed data file:
mouseBrain.Han.Neuron2020.RPKM.txt
mouseBrain.Han.Neuron2020.count.txt


title: gAraRC_rep2


title: E_faecalis_29212_biofilm_TSB_2


title: gAraRC_rep1


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 48 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 48 hours post injection, replicate D

value: Wolbachia-free


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 48 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 48 hours post injection, replicate C

value: Injected with phosphate buffered saline


title: gXlnRC_rep3

value: mutant expressing the transcription factor mutant XlnR(A871V)


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 48 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 48 hours post injection, replicate B


title: gXlnRC_rep2


title: E_faecalis_29212_planktonic_BHI_2


title: E_faecalis_29212_biofilm_TSB_1


title: Ct2

description: genes.readcount.xls


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 48 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 48 hours post injection, replicate A


title: E_faecalis_29212_planktonic_BHI_3


title: Ct1

description: genes.readcount.xls


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 24 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 24 hours post injection, replicate D


title: CD44+CD51-TNCs (3)

city: Bronx

first: Paul

last: Frenette

state: NY

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description: Table S1 Bulk RNA-Seq.xlsx

data_processing:
Gene lengths were obtained from the annotation file gencode.vM9.annotation.gtf. To determine the length of a gene, the combined length of non-overlapping exons was used. Raw values from the RNA-Seq data were converted to log2 RPKM values using the gene lengths in R, with the prior.count argument set to 1.
Genes with a CPM value > 0.1 in at least 25% of all 12 samples were retained, resulting in a total of 25,955 genes. Normalization factors were used to scale library sizes via the TMM method from edgeR (version 3.16.5). The “estimateDisp” function in edgeR was then used to estimate common, trended, and tagwise negative binomial dispersions. A negative binomial generalized log-linear model was fitted to the read counts for each gene and this model was used to test for differentially expressed genes between the CD44+ CD51– and CD51+ TNCs using a generalized linear model (GLM) likelihood ratio test. The fitting and tests were done using edgeR functions glmFit and glmLRT.
A gene was only tested for differential expression in this analysis if it had a CPM > 0.1 in at least 50% of samples. edgeR was used to calculate normalization factors to scale the library sizes using the TMM method.
The “estimateDisp” function in edgeR was used to estimate common, trended, and tagwise negative binomial dispersions. An exact test was used to find differentially expressed genes between CD44+ CD51– and CD51+ TNCs.
Genome_build: GRCm38.primary_assembly.genome.fa
Supplementary_files_format_and_content: Expression values (RPKM) for CD44+ CD51– TNCs and CD51+ TNCs.

source_name: Bone marrow

extract_protocol:
Bone marrow were enzymatically dissociated and cell populations were sorted into lysis buffer. RNA extraction was performed using RNeasy Plus Micro Kit (Qiagen) according to the manufacturer's protocol.
Librairies were prepared using Nextera XT DNA Library Preparation Kit

value: Digested bone marrow

tag: sorted cell


title: E_faecalis_29212_planktonic_BHI_1


title: gCXC_rep3

value: mutant expressing the chimeric transcription factor CXC


title: E_faecalis_29212_planktonic_TSB_3


title: CD51+TNCs (2)

description: Table S1 Bulk RNA-Seq.xlsx


title: gCXC_rep2


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 24 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 24 hours post injection, replicate B


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 24 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 24 hours post injection, replicate C


title: CD44+CD51-TNCs (2)

description: Table S1 Bulk RNA-Seq.xlsx


title: Fezf2 + GFP rep2

description:
Sample_KH6
processed data file:
mouseBrain.Han.Neuron2020.RPKM.txt
mouseBrain.Han.Neuron2020.count.txt

value: CD-1® IGS


title: CD51+TNCs (1)

description: Table S1 Bulk RNA-Seq.xlsx


title: E_faecalis_29212_planktonic_TSB_2


title: gCXC_rep1


title: WT_rep3

value: wild type 114-2


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 24 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 24 hours post injection, replicate A


title: Ct3

description: genes.readcount.xls


title: gXlnRC_rep1


title: CD51+TNCs (3)

description: Table S1 Bulk RNA-Seq.xlsx


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 6 hours post injection, rep D

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 6 hours post injection, replicate D


title: E_faecalis_V583_biofilm_BHI_2

description:
Due to a mix-up in the index during submission process prior to sequencing, Ef_V583_Biofilm_BHI_3 should be treated as Sa_USA300_Biofilm_BHI_2 and vice-versa.
Geneious_DEGs_E_faecalis_V583_Biofilm_vs_planktonic_in_BHI.txt


title: WT_rep2


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 6 hours post injection, rep C

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 6 hours post injection, replicate C


title: CD44+CD51-TNCs (1)

description: Table S1 Bulk RNA-Seq.xlsx


title: hCSCFD4

city: Bielefeld

first: Christian

last: Kaltschmidt

address: Universitätstraße 25

department: Department of Cell Biology

institute: University of Bielefeld

data_processing:
Mapping: Tophat, Version V2.0.9, Parameter: mismatch = 2
Quantification: HTseq, Version v0.6.1, Parameter: -m union
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: cardiac stem cells

extract_protocol:
RNA was harvested using Macherey Nagel RNA isolation Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary adult stem cells

tag: culture method

value: cultured in DMEM-F12 + 10% FCS + 5ng/ml FGF2 + 10ng/ml EGF


title: WT_rep1


title: E_faecalis_V583_biofilm_BHI_1

description: Geneious_DEGs_E_faecalis_V583_Biofilm_vs_planktonic_in_BHI.txt


title: hCSCFD2


title: E_faecalis_29212_planktonic_TSB_1


title: hCSCMD3


title: Resistant strain2/Ketoconazole

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Illumina casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.35 as default parameter, then mapped to Salmonella enterica serivar Typhimurium 14028s whole genome using bowtie v. 2.2.4 with parameters -t --very-sensitive
The mapped reads were counted by featureCounts (http://bioinf.wehi.edu.au/featureCounts/) and normalized as TMM value by using edgeR.
Genome_build: Malassezia restricta KCTC 27527
Supplementary_files_format_and_content: Excel file including TPM values and locus_tags for genes of M. restricta.

organism: Malassezia restricta

source_name: Clinical isolate

growth_protocol: M. restricta cells were cultured on LNA medium at 34°C for 3 days.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat#74104).
Illumina Stranded TruSeq Total RNA Sample Prep Kit (Cat#RS-122-2201) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cultured cells on control plate were collected and replated on LNA medium containing ketoconazole 0, 5 ug/mL and incubated for 6 h.

value: ketoconazole 0.5 ug/mL


title: Resistant strain1/Ketoconazole


title: Resistant strain2/no treatement


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 6 hours post injection, rep A

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 6 hours post injection, replicate A


title: Resistant strain1/no treatement


title: hCSCMD1


title: ITSCF278

source_name: inferior turbinate stem cells

value: cultured in DMEM-F12 + 10% human blood plasma + 40ng/ml FGF2 + 20ng/ml EGF + 1x B27


title: E_faecalis_V583_biofilm_TSB_2

description: Geneious_DEGs_E_faecalis_V583_Biofilm_vs_planktonic_in_TSB.txt


title: E_faecalis_V583_planktonic_BHI_3


title: Susceptible strain/Ketoconazole

description: REF-K


title: E_faecalis_V583_biofilm_TSB_1


title: E_faecalis_V583_planktonic_BHI_2


title: E_faecalis_V583_biofilm_BHI_3


title: ITSCF272


title: ITSCM257


title: Susceptible strain/no treatment

description: REF


title: E_faecalis_V583_planktonic_BHI_1


title: scATAC_CellLine_LowLoading

city: San Francisco

first: Michael

middle: Ryan

last: Corces

state: CA

address: 1650 Owens Street

department: Neurological Disease

institute: Gladstone Institute

description:
10x Genomics scATAC-seq performed on a mixture of cell lines loaded at a lower concentration to create doublets but not as many as the high concentration.
demuxlet_CellLineLow_mergedBAMs.best
CellLine_LowLoading.fragments.tsv.gz
CellLine_LowLoading-MotifMatrix-SE.rds
CellLine_LowLoading-PeakMatrix-SE.rds

data_processing:
Raw sequencing data was converted to FASTQ format using cellranger-atac mkfastq (10x Genomics, version 1.0.0)
Single-cell ATAC-seq reads were aligned to the hg19 reference genome (https://support.10xgenomics.com/single-cell-atac/software/downloads/latest) and quantified using cellranger-count (10x Genomics, version 1.0.0)
Genotypes used to perform demuxlet were determined as follows for each cell line: Bulk ATAC-seq FASTQ files were processed and aligned using PEPATAC (http://code.databio.org/PEPATAC/) as described previously. Peaks were identified using MACS2 and a union set of variable-width accessible regions was identified using bedtools merge (version 2.26.0). These accessible regions were genotyped across all samples using samtools mpileup (version 1.5) and Varscan mpileup2snp (version 2.4.3) with the following parameters “--min-coverage 5 --min-reads2 2 --min-var-freq 0.1 --strand-filter 1 --output-vcf 1”. All positions containing a single nucleotide variant were compiled into a master set and then each cell line was genotyped at those specific single-base locations using samtools mpileup. The allelic depth at each position was converted into a quaternary genotype (homozygous A, heterozygous AB, homozygous B, or insufficient data to generate a confident call). Then, for each cell line, inferred genotype probabilities were created based on those quaternary genotypes and a VCF file was created for input to demuxlet using recommended parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Processed scATAC-seq data is provided as an R SummarizedExperiment object. This object contains row and column metadata corresponding to the individual cells and peak regions of chromatin accessibility. This object also contains a sparse matrix representing Tn5 transposase insertion counts per peak region:
CellLine_HighLoading.fragments.tsv.gz:  fragments
CellLine_LowLoading.fragments.tsv.gz:  fragments
CellLine_LowLoading-MotifMatrix-SE.rds:  SummarizedExperiment RDS (R data file)
CellLine_LowLoading-PeakMatrix-SE.rds:  SummarizedExperiment RDS (R data file)
CellLine_HighLoading-MotifMatrix-SE.rds:  SummarizedExperiment RDS (R data file)
CellLine_HighLoading-PeakMatrix-SE.rds:  SummarizedExperiment RDS (R data file)
demuxlet_CellLineHigh_mergedBAMs.best:  demuxlet.best
demuxlet_CellLineLow_mergedBAMs.best:  demuxlet.best

source_name: Admixed Immortalized Cell Lines

extract_protocol:
Cultured cells were viably cryopreserved in aliquots of 100,000 cells using 100 ul of BAMBANKER freezing media (Wako Chemicals 302-14681) so that scATAC-seq could be performed on all cells at the same time. For each cell line, cells were thawed via the addition of 1 mL ice-cold resuspension buffer (RSB) [10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2] containing 0.1% Tween-20 (RSB-T). Cells were pelleted in a fixed-angle rotor at 300 RCF for 5 minutes at 4°C. The supernatant was removed, and the pellet was resuspended in 100 uL of ice-cold lysis buffer (RSB containing 0.1% Tween-20, 0.1% NP-40, and 0.01% digitonin) and incubated on ice for 3 minutes. To dilute lysis, 1 mL of chilled RSB-T was added to each tube and the cells were pelleted as before. The supernatant was removed and the pelleted nuclei were resuspended in Diluted Nuclei Buffer (10x Genomics). The nuclei stock concentration was determined for each cell line using Trypan Blue and a total of 5,000 nuclei from each cell line were pooled together and loaded into the 10x Genomics scATAC-seq (v1) transposition reaction.
scATAC-seq library preparation was performed as recommended by the manufacturer.

tag: cell line

value: all cell lines were mixed together

tag: source

value: variable

tag: growth media


title: Pool of five virgin female w[1118] D. melanogaster (Wolbachia-free/saline-injected), 6 hours post injection, rep B

description: Pool of five virgin female w[1118] Drosophila melanogaster (Wolbachia-free/saline-injected), flash frozen 6 hours post injection, replicate B

tag: genotype


title: E_faecalis_V583_planktonic_TSB_3


title: scATAC_CellLine_HighLoading

description:
10x Genomics scATAC-seq performed on a mixture of cell lines loaded at a high concentration to create many doublets.
demuxlet_CellLineHigh_mergedBAMs.best
CellLine_HighLoading.fragments.tsv.gz
CellLine_HighLoading-MotifMatrix-SE.rds
CellLine_HighLoading-PeakMatrix-SE.rds


title: E_faecalis_V583_biofilm_TSB_3

description:
Due to a mix-up in the index during submission process prior to sequencing, Ef_V583_Biofilm_TSB_3 should be treated as Sa_USA300_Biofilm_TSB_2 and vice-versa.
Geneious_DEGs_E_faecalis_V583_Biofilm_vs_planktonic_in_TSB.txt


title: E_faecalis_V583_planktonic_TSB_2


title: C1305 3uM 8h A549 replicate 1

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

description: DMSO control (8 hours)

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
STAR version 2.5.3b was used to align the FASTQ files to the reference genome with parameters --outReadsUnmapped Fastx, --outSAMtype BAM SortedByCoordinate, --outSAMattributes All
For biological replicates, HTSeq-count version 0.9.1 was used to estimate transcript abundances with paramters -r pos, -t exon, -I gene_id, -a 10, -s no, -f bam
For biological replicates, DESeq2 was used to normalize and calculate differentially expressed genes following their default protocol
For samples without biological replicates, Cufflinks version 2.2.1 was used to estimate transcript abundances with parameters --library-type fr-firststrand, -G, -L
For samples without biological replicates, Cuffdiff was used for differential expression using default paramters.
Genome_build: Gencode GRCh38 p7 Release 25
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample

source_name: human non-small lung carcinoma A549 cells (ATCC CCL-185)

growth_protocol: 16HBE14o- and cells were cultured in Minimum Essential Modified Eagle's Medium (Invitrogen) with 10% fetal bovine serum (FBS), while HTC 116 cells were cultured in McCoy's 5a Medium (Invitorgen) with 10% FBS and A549 cells were cultured in RPMI 1640 media, supplemented with 10% FBS in a humidified incubator at 37°C in 5% CO2. All experiments were conducted at a final confluence of 70-80%.

extract_protocol: Total RNA containing the small ncRNA fraction was isolated using miRNeasy kit (Qiagen, 217004)

treatment_protocol: Cells were exposed for 8h and 24h to C1305 at  3µM (IC50 at 24h)  and 10 µM concentrations, the controls were mantained with DMSO for 8 or 24 hours

value: human non-small lung carcinoma


title: C1305 10uM 8h A549

description: DMSO control (8 hours)


title: E_faecalis_V583_planktonic_TSB_1


title: C1305 3uM 8h A549 replicate 2

description: DMSO control (8 hours)


title: CaSki-NC

city: Chongqing

first: Min

last: He

address: Yixueyuan Road, Yuzhong District

department: Molecular Medicine and Cancer Research Center

institute: Chongqing Medical University

description: wild type CaSki cell

data_processing:
Illumina Novaseq™ 6000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat v2.0
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using edgeR.
Genome_build: hg38

source_name: DLEU2 negative control cell

growth_protocol: CaSki cells were maintained in RPMI 1640 medium supplemented with 10% FBS

extract_protocol:
Total RNA was isolated using RNA TRIzol Reagent (Invitrogen)
RNAseq library was prepared using Illumina Novaseq™ 6000 protocol, according to the manufacturer's instructions.

treatment_protocol: CaSki cells were transfected with si-DLEU2 or si-NC by Lipofectamine2000 Transfection Reagent

value: CaSki

value: cervical cancer cell

value: CaSki cells were transfected with si-NC by Lipofectamine2000 Transfection Reagent


title: LGE E12.5 IgG replicate 2

status: Public on Dec 04 2020

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: CUT&RUN

data_processing:
Library strategy: CUT&RUN
CUT&RUN reads were aligned to mouse genome, mm10, using STAR. Read pairs were connected with each other to form fragments, then split into two groups by fragment size, nucleosome free reads (<120bp) and nucleosomal reads (>150bp).
BigWig files were generated using nucleosome free fragments in read-per-million (RPM) scale after resizing fragments into 100bp to normalize fragment length bias between samples.
Genome_build: mm10
Supplementary_files_format_and_content: RPM-normalized bigwig file

source_name: Mouse E12.5 LGE

extract_protocol:
Samples were thawed at 37°C and washed in DMEM with 5% FBS. Cells were pooled and washed in DPBS with 0.04% BSA and protease inhibitor cocktail. After binding to Concavalin A beads, cells were divided into 6 samples of ~1x106 cells and duplicates were incubated with either the M2-FLAG antibody (Sigma) or an IgG control antibody. CUT&RUN was performed as previously described with the following exceptions (Skene and Henikoff 2017; Skene et al. 2018). A rabbit anti-mouse secondary antibody was used due to the low affinity of protein A for mouse IgG1 (M2-FLAG antibody). MNase digestion after the addition of CaCl2 was performed at 0°C for 45 minutes. After stopping MNase digestion, released DNA fragments were purified using the Nucleospin DNA cleanup kit.
Libraries were prepared using the NEBNext Ultra II DNA library prep kit for Illumina sequencers, and PCR products between ~150bp and 350bp were size selected using AMPure XP beads. Bar-coded libraries were sequenced on an Illumina NextSeq 550 sequencer at a depth of ~20 million paired-end 75bp reads.

treatment_protocol: CUT&RUN assays were performed on dissected LGE tissue from 65 homozygous Gsx22xFLAG E12.5 mouse embryos (6 litters). LGE tissue from each litter was pooled, dissociated by pipetting in 0.05% Trypsin-EDTA (Gibco), passed through a 40 µm cell strainer (Corning), step-frozen in CryoStor freezing media (STEMCELL Technologies), and stored at -80°C.

value: Outbred

value: Lateral ganglionic eminence (LGE)

tag: developmental stage

tag: antibody

value: mouse IgG


title: LGE E12.5 Gsx2/Flag replicate 2

description: CUT&RUN

value: M2 anti-FLAG


title: LGE E12.5 IgG replicate 1

description: CUT&RUN


title: ER-HOXA9 Non-treated Day 0 rep2

city: Boston

first: Barry

last: Zee

state: MA

address: 61 Binney Street

department: Newborn Medicine

institute: Boston Children's Hospital

description: labeled as BZ04 in featurecount

data_processing:
RTA2 software was used for basecalling and STAR (2.7.0f) was used to align data to mouse genome to generate BAM files
differential gene expression analysis was performed with deeptools (3.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Granulocyte-monocyte progenitor

growth_protocol: Cells were cultured in RPMI160 media with10% volume heat-inactivated FBS, 4mM glutamine, stem cell factor, and 0.5 micromolar beta-estradiol

extract_protocol:
Total RNA was purified with Trizol exraction of cells. PolyA RNA was enriched with magnetic beads
Libraries were prepared according to manufacturer's instructions

treatment_protocol: Cells were treated with DMSO or 200nM GSK-LSD1 plus 5uM mercaptopurine plus 5uM cerulenin for 3 days

value: Bone marrow

tag: agent


title: ER-HOXA9 Drug treated Day 3 rep2

description: labeled as BZ06 in featurecount

value: 200nM GSK-LSD1 plus 5uM mercaptopurine plus 5uM cerulenin


title: ER-HOXA9 Vehicle Day 3 rep2

description: labeled as BZ05 in featurecount

value: DMSO


title: ER-HOXA9 Vehicle Day 3 rep1

description: labeled as BZ02 in featurecount


title: LGE E12.5 Gsx2/Flag replicate 1

description: CUT&RUN


title: ER-HOXA9 Drug treated Day 3 rep1

description: labeled as BZ03 in featurecount


title: MiR-204-3p-m - input DNA

city: Guangzhou

first: Si-Jia

last: Liang

state: Guangdong

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Zhongshan School of Medicine, Sun Yat-Sen University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, using trim_galore version 0.6.4.
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3.
Duplicate reads are removed by Picard version 2.20.7.
Peaks were called using macs2 version 2.2.4.
Genome_build: hg38
Supplementary_files_format_and_content: Align files; peak text files;

source_name: Macrophages

growth_protocol: Human peripheral blood mononuclear cells were isolated from healthy volunteer donors by Percoll density gradient centrifugation, and were then differentiated into HMDMs in RPMI-1640 medium supplemented with 10% fetal calf serum, 1% HEPES, 1% penicillin/streptomycin, and 100 ng/ml of macrophage colony-stimulating factor.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the KAPA Hyper Prep Kit (Part# KK8502). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000following the manufacturer's protocols.

treatment_protocol: HMDMs were transfected with miRNA mimics negative control or miRNA-204-3p mimics for 24 h.

value: human monocyte-derived macrophages

tag: treatment

value: transfected with miR-204-5p mimics


title: ITSCM251

value: primary adult stem cells


title: MiR-204-3p-m - H3K4me3

value: transfected with miR-204-4p mimics


title: MiR-204-3p-m - H3K27ac

value: H3K27ac (abcam,ab4729)

value: transfected with miR-204-3p mimics


title: CaSki-siDLEU2

description: DLEU2 knockdown CaSki cell

source_name: DLEU2 knockdown CaSki cell

value: CaSki cells were transfected with si-DLEU2 by Lipofectamine2000 Transfection Reagent


title: NC-m - H3K27ac

value: transfected with mimics negative control


title: ER-HOXA9 Non-treated Day 0 rep1

description: labeled as BZ01 in featurecount


title: 0.1% DMSO vehicle, biological replicate 3

type: RNA

city: Tucson

first: Randy

middle: L

last: Bogan

state: Arizona

address: 1177 E. 4th St, Shantz Building Room 623

department: SACBS

institute: University of Arizona

hyb_protocol: Labeled target is fragmented at 95°C in the presence of high magnesium concentration. The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD, and CreX (Affymetrix) in hybridization buffer. Ten µg of target is hybridized for 16 hours at 45°C to the GeneChip Rhesus Macaque Genome Array (Affymetrix), followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: Affymetrix GeneChip Command Console (AGCC) v. 3.1.1

data_processing: Data are normalized across arrays using the robust multichip analysis (RMA) algorithim

label: biotin

organism: Macaca mulatta

source_name: Dispersed luteal cells from Day 12 CL

label_protocol: Ambion Message AMP Premier

growth_protocol: Cells were grown on fibronectin-coated plates for 24 hours in serum-free DMEM/F12 medium containing 10 mM HEPES, 100 U/ml penicillin, 100 µg/ml streptomycin, 10 mg/ml gentamicin, 3 mg/ml BSA, 20 mg/ml insulin, 5 µg/ml transferrin, 25 nM selenium, and 10 µg/ml aprotinin; and maintained at 37°C with 5% CO2 in air

extract_protocol: Trizol extraction with further purification over RNeasy spin columns (Qiagen)

treatment_protocol: Cells were treated for 24 hours immediately following isolation and plating

value: luteal

value: 12 days post LH-surge

tag: treated with

tag: treatment time

value: 24 hr


title: 0.1% DMSO vehicle, biological replicate 2


title: NC-m - input DNA


title: NC-m - H3K4me3


title: 1 µM T0901317, biological replicate 1


title: 0.1% DMSO vehicle, biological replicate 1


title: 1 µM T0901317, biological replicate 3


title: 1 µM T0901317, biological replicate 2


title: Fresh frozen metastatic tumor_26

type: genomic

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

hyb_protocol: Genome-wide copy number variation was measured by a 2-color microarray approach using Agilent SurePrint G3 ISCA Human Cancer CGH+SNP 180K x 4 arrays

scan_protocol: CytoCGH_0205_Oct12 protocol and Agilent G4900DA SureScan Microarray Scanner System

data_processing:
Probe fluorescence intensity data was extracted from scanned microarray images using Agilent Cytogenomics software Edition 2.5.8.1. GC Correction, Diploid Peak Centralization (normalization) and Aberration Detection Method 2 (quality control) algorithms were also applied using this software. Aggregate data (all 27 samples) were further analyzed using NEXUS Copy Number software (Biodiscovery) to identify recurring genomic aberrations.
Feature extraction files for each sample and data matrix contain the normalized log10 Cy5/Cy3 values for each probe, results of aggregate data analysis by NEXUS Copy Number software include frequency and chromosome region of common aberrations

source_name: Tumor

label_protocol: Cancer and reference DNA (500ng each) were labeled with fluorescent dyes, Cy5 and Cy3 respectively, using the SureTag Complete DNA Labeling Kit (Agilent Technologies)

extract_protocol: EZ1 Advanced workstation and DNA Tissue Kit (Qiagen, Germantown, MD).

value: lung cancer mestastatic brain tumor

tag: gender

value: M

tag: type

value: squamous

source_name: normal human reference DNA

tag: reference source

value: Agilent catalog number 5190-3796


title: Fresh frozen metastatic tumor_16

tag: tissue

value: F

value: small

value: Agilent catalog number 5190-3797


title: Fresh frozen metastatic tumor_22

value: adeno


title: Fresh frozen metastatic tumor_27

value: poorly-mod diff squamous


title: Fresh frozen metastatic tumor_14

value: poorly diff carcinoma


title: Fresh frozen metastatic tumor_18


title: Fresh frozen metastatic tumor_17

value: moderately diff adeno


title: Fresh frozen metastatic tumor_20

value: poorly diff adeno


title: Fresh frozen metastatic tumor_11


title: Fresh frozen metastatic tumor_21


title: Fresh frozen metastatic tumor_23


title: Fresh frozen metastatic tumor_7


title: RNA_seq_dd-UV-2

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

description: dd mutant without UVB treatment. Duplicate biological replicate 2

data_processing:
Bisulfite-seq reads were filtered using Trimmomatic and then aligned to the TAIR10 genome using BSMAP. For RNA-seq analysis, reads were filtered with Trimmomatic and then aligned to the TAIR10 genome using HISAT2. The alignments were then filtered with a bash code to keep the uniquely mapped reads. The quantification of gene expression was performed with Cufflinks.
Genome_build: TAIR10
Supplementary_files_format_and_content: methratio output files  were converted to bedGraph via custom awk scripts and bedGraph files were converted to BigWig files via the UCSC "bedGraphToBigWig" executable script

organism: Arabidopsis thaliana

source_name: RNA isolated from whole 10 day old seedlings and converted to cDNA through library preparation

growth_protocol: Plants were grown on 1/2X MS agar (0.7%) + 1% sucrose throughout treatment.  Treatment began on Day 1 after sowing with 1.5  mE of UV-B (315 nm) and 60 mE white light  and terminated on Day 10 of treatment when the plants were frozen in liquid nitrogen before mRNA or DNA extraction for sequencing.

extract_protocol:
RNA was extracted by PureLink RNA Mini Kit (Cat no. 12183018A. Invitrogen). DNA was extracted via the Qiagen Dneasy DNA extraction kit (catalog # 69104).
RNA-seq libraries were constructed using the illumina TruSeq Stranded mRNA LT kit (ref no15032612) following manufacterers' instructions. For bisulfite-sequencing libraries, the genomic DNA was fragmented to a mean size of 100-300 bp by sonication using a Covaris S220 focused-ultrasonicator (Covaris), followed by end-repair, 3’-end adenylation and methylated adaptor ligation using Illumina TruSeq DNA kit (Illumina). Then bisulﬁte conversion was performed using a Zymo EZ DNA Methyl-ation-Lightning kit (Zymo Research). The bisulfite-converted, adaptor-ligated DNA was enriched by PCR for 12-15 cycles using KAPA HiFi HotStart Uracil+ Kit  (KAPA Biosystems), purified with Agencourt beads (NuGen).

tag: ecotype

value: drm1-2 drm2-2 T-DNA mutations

value: whole seedling

value: dd mutant without UVB treatment.


title: RNA_seq_ddwUV-1

description: dd mutant with UVB treatment. duplicate biological replicate 1

value: dd mutant with UVB treatment.


title: Fresh frozen metastatic tumor_25


title: Fresh frozen metastatic tumor_15


title: Fresh frozen metastatic tumor_6


title: Fresh frozen metastatic tumor_12


title: Fresh frozen metastatic tumor_19


title: RNA_seq_ddwUV-2

description: dd mutant with UVB treatment. Duplicate biological replicate 2


title: Fresh frozen metastatic tumor_13


title: Fresh frozen metastatic tumor_10


title: Fresh frozen metastatic tumor_8

value: well diff adeno


title: RNA_seq_dd-UV-1

description: dd mutant without UVB treatment. Duplicate biological replicate 1


title: RNA_seq_ColwUV-1

description: Col-0 with UVB treatment. Duplicate biological replicate 1

value: wildtype

value: Col-0 with UVB treatment.


title: Fresh frozen metastatic tumor_24

value: lung cancer mestastatic brain tumor


title: Fresh frozen metastatic tumor_4

value: M

value: poorly diff squamous

value: Agilent catalog number 5190-3796


title: Fresh frozen metastatic tumor_5


title: Fresh frozen metastatic tumor_3


title: RNA_seq_Col-UV-2

description: Col-0 without UVB treatment. Duplicate biological replicate 2

value: Col-0 without UVB treatment.


title: BAT SVF 8w C57BL/6J WT

city: Neuherberg

first: Matthias

last: Heinig

address: Ingolstädter Landstrasse

institute: Helmholtz-Zentrum München

data_processing:
Pre-processing of sequencing results to generate transcript matrices was performed using the 10x genomics Cell Ranger pipeline with default settings (v2.1.1) and aligning to the GRC38 genome build and genome annotation release 94 from Ensembl.
Genome_build: GRCm38
Supplementary_files_format_and_content: QC filtered cell ranger output consists of gene by barcode (cell) count matrices in sparse matrix market format (mtx) and corresponding row and column annotation in *genes.tsv and *barcode.tsv files

source_name: Interscapular brown adipose tissue

extract_protocol:
Brown adipose tissues were isolated from interscapular area of three 8 week old, male WT C57BL/6 mice. BAT was minced and digested with 1mg/ml type-A collagenase (Gibco) in DMEM (Gibco) for 30 minutes at 37°C. The SVF was obtained by centrifugation and live cells were sorted using flow cytometry following dead cell exclusion using 7-AAD.
Single cell libraries were generated using the ChromiumTM Single cell 3'library and gel bead kit v2 (PN #120237) from 10x Genomics.

tag: strain

value: Stromal vascular fraction of brown adipose tissue

tag: age

value: post natal week 8

value: wild type


title: RNA_seq_Col-UV-1

description: Col-0 without UVB treatment. Duplicate biological replicate 1


title: RNA_seq_ColwUV-2

description: Col-0 with UVB treatment. Duplicate biological replicate 2


title: ER-HOXA9 Combo treated Day 2 rep2 [ATAC-Seq]

data_processing:
After investigating the quality of the raw data, sequencing adapters and low-quality bases were trimmed using Trimmomatic 0.38. Cleaned reads were then aligned to reference genome mm10 using bowtie2.
Aligned reads were filtered using samtools 1.9 to keep alignments that (1) have a minimum mapping quality of 30, (2) were aligned concordantly, and (3) were the primary called alignments. PCR or optical duplicates were marked using Picard 2.18.26 and removed. Prior to peak calling, reads mapping to mitochondria (mt) were called and filtered, and reads mapping to unplaced contigs were removed.
MACS2 2.1.2 was used for peak calling to identify open chromatin regions. For each pair-wise comparison, peaks from condition A and condition B were merged and peaks found in either condition were kept for downstream analyses. Reads falling beneath peaks were counted in all samples, and these counts were used for differential peak analyses using the R package Diffbind.
Genome_build: mm10
Supplementary_files_format_and_content: Differential peak analysis for each comparison of conditions and filtered peaks

extract_protocol:
After cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C and purified with Minelute PCR Purification Kit (Qiagen, Cat. #28004) to produce tagmented DNA samples.
Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries.

treatment_protocol: Cells were treated with DMSO or 200nM GSK-LSD1, 5uM mercaptopurine or 5uM cerulenin as single or triple combinations for 2 days

value: Bone marrow

value: Combo


title: ER-HOXA9 CER treated Day 2 rep2 [ATAC-Seq]

value: 5uM cerulenin


title: Fresh frozen metastatic tumor_9

value: adeno


title: Fresh frozen metastatic tumor_1

value: poorly diff adeno


title: ER-HOXA9 CER treated Day 2 rep1 [ATAC-Seq]


title: ER-HOXA9 Combo treated Day 2 rep1 [ATAC-Seq]


title: ER-HOXA9 6MP treated Day 2 rep2 [ATAC-Seq]

value: 5uM mercaptopurine


title: ER-HOXA9 LSD1i treated Day 2 rep2 [ATAC-Seq]

value: 200nM GSK-LSD1


title: ER-HOXA9 6MP treated Day 2 rep1 [ATAC-Seq]


title: ER-HOXA9 LSD1i treated Day 2 rep1 [ATAC-Seq]


title: ER-HOXA9 Veh treated Day 2 rep2 [ATAC-Seq]

value: DMSO


title: ER-HOXA9 Non-treated Day 0 rep2 [ATAC-Seq]


title: ER-HOXA9 Non-treated Day 0 rep1 [ATAC-Seq]


title: ER-HOXA9 Veh treated Day 2 rep1 [ATAC-Seq]


title: WT_Fs_003

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

data_processing:
Reads were aligned to the mouse genome assembly mm10.GRCm38.
Alignment was done with HISAT2 v2.1.0 with default parameters including splice sites obtained from gene annotations
Gene annotations from GENCODE vM17 were used for all analysis
Uniquely aligned reads were extracted using grep with parameters “-v 'NH:i:[2-9]'” and SAMtools v1.3.138, with parameters “view -h -F 4 -q 20 -b” and sorted and indexed using SAMtools.
Reads in genes were counted using Rsubread v1.28.1.
Differential gene expression between any pair of samples was assessed using DESeq2 v1.18.1, using default FDR adjustment of p-values for multiple hypothesis testing.
Genome_build: mm10.GRCm38.
Supplementary_files_format_and_content: csv with results of pairwise differential expression analysis and normalized read counts

source_name: CD44+ OT-I T cells from D6 LCMV-OVA infected host

growth_protocol: Recipient mice were fed ad libitum or fasted

extract_protocol:
Samples were double sorted into Trizol
RNA libraries were prepared for sequencing using SMARTer amplification (TAKARA) and standard Illumina protocols

treatment_protocol: Recipient mice were infected with LCMV- OVA and fasted for 24h on d5 post-infection beginning at 6pm

value: Spleen

value: WT

tag: host absorptive state

value: Fasted for 24h on D5 post-infection (Fs)


title: WT_Fs_001


title: WT_Fs_002


title: WT_AL_001

value: Fed Ad libitum (AL)


title: KO_Fs_002

value: FXR KO


title: WT_AL_002


title: WT_AL_003


title: Fresh frozen metastatic tumor_2

value: lung cancer mestastatic brain tumor

value: M

value: invasive squamous

value: Agilent catalog number 5190-3796


title: KO_Fs_001


title: KO_AL_003