title: Repolarization: 2h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M1_M0_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B3_ad008

status: Public on Sep 17 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: DG

tag: Sex

value: male

tag: age

tag: strain


title: Repolarization: 1h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

city: Bellevue

first: Serena

last: Liu

state: Washington

department: Genome Sciences

institute: University of Washington

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M1_M2_2

library_source: transcriptomic

data_processing:
For bulk RNA-seq, demultiplexed reads were aligned to the mouse (mm10) reference genome using Tophat v2.0.14 with default settngs; aligned reads were quantified using Cuffquant v2.2.2, and a normalized gene expression matrix was generated using Cuffnorm v2.2.2.
For single-cell RNA-seq data, expression matrix files and BAM files were generated using cellranger (10X genomics) version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.
For bulk ATAC-seq, demultiplexed reads were aligned to the mouse (mm10) reference genome using Tophat v2.0.14 with default settings; PCR duplicates were removed using Samtools v1.9, and data from all alignment files were merged into a single file for peak calling using MACS v2.1.0 (parameters: --nomodel --keep-dup-all --extsize 200 --shift -100 -B --SPMR --call-summits) to generate a master list of peaks observed in the experiment. A peak count matrix was calculated by using Bedtools v2.28.0 to compute the intersection between each sample's aligned reads and the master list of peaks.
Genome_build: mm10
Supplementary_files_format_and_content: For bulk RNA-seq, an expression matrix (csv format) containing FPKM data for all conditions across all replicates is provided. For 10X single cell RNA-seq, three files are provided for each sample: 1) matrix files containing the UMI expression data, 2) tsv file containing gene metadata, 3) tsv file containng barcode (i.e. cell) metadata. For bulk ATAC-seq, a count matrix (tsv format) containing peak counts for all samples and replicates measured is provided.

molecule: total RNA

source_name: bone-marrow derived macrophages (BMDMs) from 6-10 week old C57BL/6J mice

growth_protocol: C57BL/6J (6-10 weeks) mice were killed by cervical dislocation, and bone marrow cells were harvested by flushing femure bones with RPMI-1640. Bone marrow cells were plated at a concentration of 6 x 10^6 cells per 3 cm petri dish, then cultured in a base media of RPMI-1640 with 20% horse serum, 100 U/mL penicillin, 100 μg/mL streptomycin, and 20 ng/mL macrohpage colony stimulating factor (MCSF).

extract_protocol:
For bulk RNA-seq, trizol followed by phenol extraction of bulk RNA. For single-cell RNA-seq, 10X Genomics single cell gene expression protocol following manufacturer recommendations. For bulk ATAC-seq, nuclei extraction and DNA tagmentation was performed as described in Buenrostro et al. (2013) "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position." Nature Methods 10, 1213-18.
For bulk RNA-seq, libraries were prepared using the Illumina TruSeq kit, following manufacturer recommendations. For single-cell RNA-seq, 10X Genomics single cell gene expression protocol following manufacturer recommendations. For bulk ATAC-seq, library prep was performed as described in Buenrostro et al. (2013) "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position." Nature Methods 10, 1213-18.

treatment_protocol: On day 7 of culture, cells were stimulated with 100 ng/mL LPS and 25 ng/mL interferon-γ (IFN-γ) or 25 ng/mL interleukin-4 (IL-4) to induce polarization to M1 or M2 states, respectively, or maintained in base media as a control (M0). For repolarization, BMDMs were primed with LPS + IFN-γ or IL-4 for 24h, washed with PBS, then either treated with the opposing stimulus, maintained in the original stimulus, or returned to base media. Samples were collected for bulk RNA-seq analysis 1h, 2h, 4h, 6h, 12h, and 24h post-treatment for polarization, and 1h, 2h, 4h, 6h, 12h, 24h, and 72h post-treatment for repolarization. Three biological replicates were collected for the full set of polarization and repolarization conditions. For single-cell RNA-seq, a single biological replicate was collected in which cells were harvested and cultured as described above for a subset of polarization conditions: 0h M0, 6h M0, 6h M1, 6h M2, 24h M0, 24h M1, 24h M2. For bulk ATAC-seq, cells were also harvested and cultured as described above for three biological replicates of the following conditions: 0h M0, 24h M1, 72h M1→M0.

tag: cell type

value: Bone-marrow derived macrophages (BMDMs)

tag: cytokines added

value: LPS + IFN-gamma, PBS wash, then IL-4


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B3_ad007


title: CS17_D_2

city: Edinburgh

first: Edie

last: Crosse

address: 5 Little France Road

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

description:
Total RNA (ribosome depleted)
CS17_Raw_Counts.txt

data_processing:
Adapter trimming Flexbar/2.5
Alignment STAR/2.5.1b
Gene counts with bedtools multicov, gtf = Homo_sapiens.GRCh38.86.gtf.gz
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: .txt, raw read count matrices are provided with ENSEMBL_ID row names, sample column names

organism: Homo sapiens

source_name: Embryo dorsal aorta

extract_protocol:
Human embryos embedded in OCT were sectioned in a caudal-to-rostral direction using a cryotome FSE cryostat (Thermo Scientific).  Sections were stained using a rapid Haematoxylin and Eosin staining protocol - 3 minutes (min) in 70% ethanol, 1 min H2O, 4 min Mayer’s Haematoxylin Solution (Sigma-Aldrich), 2 min tap H2O, 15 seconds Eosin Y (Sigma-Aldrich), 1 min 70% ethanol, 1 min 90% ethanol, 3 mins 100% ethanol. All H2O was treated with diethyl pyrocarbonate (DEPC) and all reagents were pre-cooled in ice except 100% ethanol which was room temperature. The laser capture microscope used was the PALM microbeam (Zeiss). The microscope and surrounding area were sprayed down with RNaseAWAY ® (Sigma-Aldrich). Sections were viewed and microdissected in brightfield using a 10X objective. The microdissected regions were collected into the caps of AdhesiveCap 500 opaque (Zeiss) 500µl PCR tubes. 15µl lysis buffer (0.2% Triton X-100 (Sigma-Aldrich), 2U/µl RNase inhibitor (Takara), Phosphate Buffer Solution (PBS, (Nichterwitz et al., 2016)) was added directly on top of the dissected tissue in the tube caps and the tubes closes in an inverted position. PicoPure RNA Isolation Kit was used to extract RNA for samples 1-12. Samples 13-30 were directly amplified from lysed material
SMARTer® Stranded Total RNA-Seq Kit v2 -Pico Input Mammalian kit (Takara) for samples 1-12, LCM-Seq (Picelli et al., 2014) for samples 13-30.

tag: embryo

tag: developmental stage

tag: tissue

value: dorsal aorta

tag: subdomain

value: Dorsal ([D])


title: CS17_DL_2

value: Dorsal-lateral ([DL])


title: Repolarization: 1h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M2_M1_2

value: IL-4, PBS wash, then LPS + IFN-gamma


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B4_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B3_ad004


title: Repolarization: 1h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M2_M0_2

value: IL-4, PBS wash, then none


title: CS17_VL_2

value: Ventro-lateral ([VL])


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B3_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B2_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B2_ad010


title: CS17_V_2

value: Ventral ([V])


title: Repolarization: 1h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M1_M2_0


title: Repolarization: 1h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M1_M2_1


title: Repolarization: 1h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M2_M0_1


title: CS17_D_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B2_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B2_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B11_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B2_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B11_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B2_ad006


title: CS17_V_1


title: Repolarization: 1h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M1_M0_0

value: LPS + IFN-gamma, PBS wash, then none


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B2_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B11_ad007


title: Repolarization: 1h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M1_M0_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B11_ad002


title: Polarization: 24h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_24h_M2_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B11_ad004


title: MKZ_Diff_Neg_12d

city: Villingen-Schwenningen

first: Lars

last: Kaiser

address: Jakob-Kienzle-Str. 17

department: Medical and Life Sciences

country: Germany

institute: University Furtwangen

data_processing:
Alignment using Bowtie
Identification of exon-exon splice junctions via TopHat
Cuffdiff for quantification of transcripts and differential expression
Genome_build: hg38
Supplementary_files_format_and_content: tsv files were generated using CuffDiff showing the differential expression of two populations

source_name: cell culture

extract_protocol:
NucleoSpin RNA XS Kit (Macheray-Nagel)
purification of poly-A containing mRNA, fragmentation, random primed cDNA synthesis and 50 bp single read by third-contractor

tag: culture time (days)

tag: lineage

value: Dendritic cells/Eosinophils


title: CS17_VL_1


title: Repolarization: 1h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M2_M0_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B11_ad001


title: NK_Diff_Neg_10d

value: Neutrophils/Dendritic cells


title: CS17_DL_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B10_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B11_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B11_ad012


title: Repolarization: 1h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M1_M0_1


title: Ery_Diff_Neg_6d

value: Erythrocytes/Neutrophils


title: Polarization: 24h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_24h_M2_0


title: CD34_native_0h

description: Processed data for this sample are included in all processed data files included in this series.

value: Myeloid Progenitor


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B10_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B10_ad001


title: Polarization: 24h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_24h_M1_2

value: LPS + IFN-gamma


title: JY304_60-min

city: New York

first: Jamie

last: Yang

state: NY

address: 1150 St. Nicholas Avenue

institute: Columbia University

description: rRNA depleted total RNA

data_processing:
Fastq files were clipped for adapter sequence and then trimmed to remove bases of low quality score
Reads were aligned to reference transcriptome of S. cerevisiae S288C using kallisto (Nature biotechnology 34: 525-527)
Genome_build: S. cerevisiae S288C (version R64-2-1)
Supplementary_files_format_and_content: tab-delimited text files include estimated gene counts and TPM for every sample

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast were grown in standard complete + glucose (sc+glu) media at 30℃ shaking at 220 rpm

extract_protocol:
RNA was isolated using the YeaStar RNA Kit (Zymo Research), treated with DNAse I, rRNA removed using Ribo-Zero rRNA Removal Kit (Illumina)
Samples were barcoded and prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: Yeast were grown to mid-log phase in sc+glu media at 30℃, washed, resuspended in deionized water, exposed to 2 min of ethanol stress, recovered in deionized water

tag: treatment

tag: background strain

tag: genotype


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B10_ad002

value: DG


title: JY304_30-min

description: rRNA depleted total RNA


title: Polarization: 24h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_24h_M1_1


title: Polarization: 24h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_24h_M2_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B1_ad012

value: male


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B1_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B1_ad010


title: JY304_15-min

description: rRNA depleted total RNA


title: Polarization: 24h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_24h_M0_2

value: Bone-marrow derived macrophages (BMDMs)


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B1_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B1_ad008


title: JY304_pre-stress

description: rRNA depleted total RNA

value: pre-stress


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B10_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B1_ad004


title: JY304_rich-media

description: rRNA depleted total RNA

value: rich-media


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A9_ad010


title: Polarization: 24h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_24h_M0_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A9_ad004


title: Polarization: 24h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_24h_M0_0


title: WT_60-min

description: rRNA depleted total RNA

value: wild-type


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A9_ad001


title: Polarization: 12h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_12h_M2_2


title: WT_30-min

description: rRNA depleted total RNA


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A9_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A9_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A8_ad012


title: WT_15-min

description: rRNA depleted total RNA


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A8_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A8_ad006


title: Polarization: 12h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_12h_M1_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B1_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A8_ad004


title: WT_rich-media

description: rRNA depleted total RNA


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A8_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B1_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A7_ad012


title: post_rep3

description: amplified deletion library barcodes

data_processing:
The unique 20-nucleotide TAG sequence for each gene deletion was isolated from each sequencing read based on universal primer sequences flanking the TAG sequence
Reads were aligned to reference file of all TAG sequences using bowtie2, default settings (Nature 9: 357-359)
DEseq2 (Genome Biology 15: 500) was used to determine gene deletions that were significantly enriched or depleted after stress exposure. Enrichment score was determined based on average fitness of the triplicates. Significance was determined by Benjamini-Hochberg adjusted p-value < 0.05.
Genome_build: reference file of TAG sequences
Supplementary_files_format_and_content: text files include abundance of each TAG sequence

extract_protocol:
DNA was isolated using the YeaStar Genomic DNA Kit (Zymo Research). Pooled deletion library barcodes, which consisted of a unique 20-nucleotide TAG sequence for each gene deletion, were amplified in parallel.
Illumina Truseq adapters were added to the amplified barcodes for sequencing.

treatment_protocol: Yeast were grown to mid-log phase in sc+glu media at 30℃, washed, resuspended in deionized water, exposed to 2 min of 24.5% ethanol stress, subjected to an outgrowth period in sc+glu media at 30℃ until early log phase. All pre-stress and post-stress samples performed in triplicates.

value: ethanol stress

value: S. cerevisiae knockout collection


title: Polarization: 12h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_12h_M1_0


title: Polarization: 12h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_12h_M1_1


title: Polarization: 12h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_12h_M2_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A7_ad004


title: Polarization: 12h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_12h_M2_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A7_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A8_ad007


title: WT_pre-stress

description: rRNA depleted total RNA


title: post_rep2

description: amplified deletion library barcodes


title: Polarization: 6h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_6h_M2_2


title: post_rep1

description: amplified deletion library barcodes


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A6_ad012


title: Polarization: 6h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_6h_M2_1


title: pre_rep3

description: amplified deletion library barcodes


title: Repolarization: 4h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M1_M0_1


title: Repolarization: 2h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M2_M1_2

value: IL-4, PBS wash, then LPS + IFN-gamma


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A6_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A6_ad010


title: pre_rep2

description: amplified deletion library barcodes


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A6_ad007


title: Polarization: 6h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_6h_M2_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A7_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A7_ad007


title: pre_rep1

description: amplified deletion library barcodes


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A6_ad006


title: Polarization: 6h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_6h_M1_0


title: Polarization: 6h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_6h_M1_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A6_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A7_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A6_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A6_ad001


title: Polarization: 4h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_4h_M2_1


title: Polarization: 4h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_4h_M2_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A5_ad012


title: Sheep_Nematode_Treated

city: CHENNAI

first: Florida

last: Tilton

state: Tamil Nadu

address: 7, Leo Muthu Street, Kalaimagal Nagar, Ekkaduthangal

country: India

institute: Biozone Research Technologies

description: processed data file: Both_Control_&_Treated_Sheep.txt

data_processing:
All the 150bp paired end raw reads (IlluminaNextSeq500) were quality checked for low quality bases and adapter sequences (Processing of raw reads). Quality check and processing was done using In-house perl scripts.
All processed reads were assembled into transcripts without any reference (De-novo) both samples independently using Trinity software (trinityrnaseq-r20140413p1).
Unigenes were generated after clustering the merged sequences from both Control and Treated samples using CD-HIT.
The reads for the samples were separately aligned to the corresponding unigene sequences and read count profiles were generated. DESeq "R" package was used for differential gene expression.
Genome_build: fasta files
Supplementary_files_format_and_content: Both_Control_&_Treated_Chick.txt: Tab-delimited text file with abundance measurements.
Supplementary_files_format_and_content: Both_Control_&_Treated_Sheep.txt: Tab-delimited text file with abundance measurements.

organism: Trichostrongylus colubriformis

source_name: Intestine

growth_protocol: Collection of parasites (Nematodes of Poultry): For the present study, the desired parasites are Ascaridia galli which parasitizes chicken. The intestines of freshly slaughtered fowls, were collected from local slaughterhouse and washed with normal saline solution. These intestines were then dissected and the nematodes were extracted. The average size of the nematode was found to be 5 cm. These parasitic worms, were used to test the anthelmintic activity with bryophyte extracts in vitro. The identification of nematodes was done in the department of Zoology, OUCW, Koti, Hyderabad by using Phase contrast microscope.

extract_protocol:
Preparations of Aqueous extract (Maceration method) Bryophyte, Pottia lanceolata samples were cleaned removing soil debris, by thorough washings with water. The active ingredient was extracted, using cold maceration method dried in shade, powdered using mortar and pestle. The crude aqueous extract was centrifuged, at 5,000 rpm for 5 minutes, using Remi centrifuge. The clear supernatant was used for the treatment and the precipitate was discarded. Piperazine citrate (glaxo smithkline) was used as the standard anthelmintic drug during the experimentation.
To study the gene expression pattern, the control and treated (bryophyte extract Pottia lanceolata) parasites were preserved in RNA later solution, and were subjected to RNA extraction and isolation using RNA mini easy kit. The Extraction was performed as per the protocol, provided by the manufacturer. Extracted RNA was subjected to quality and quantity check, prior to library construction. Library preparation was performed following NEB Next Ultra RNA Library Prep Kit (#E7490L). In brief, approximately 110-350 ng of Total RNA was used to isolate mRNA using Poly dT beads. mRNA was fragmented and converted to cDNA according to the protocol. cDNA was end repaired and purified using Ampure XP beads. Cleaned DNA was adapter ligated and purified using Ampure XP beads. These adapter ligated fragments were subjected to 12cycles of PCR using primers provided in the kit. The PCR products were purified using Ampure XP beads. Quantification and size distribution of the prepared library was determined using Qubit fluorometer (Table 1) and Agilent Tape station D1000 Kit (Agilent Technologies) according to the manufacturer’s instructions. The steps followed to generate the FastQ reads from Total RNA libraries are as follows: 1. The pooled/multiplexed libraries were put into the Illumina Hiseq Sequencer for sequencing which generated raw data in the bcl format. 2. Bcl files were De-multiplexed using sample wise Barcode information to get the sample specific sequences. 3. De-multiplexing resulted into raw reads in FastQ format, which was used for downstream analysis.

treatment_protocol: Anthelmintic activity assay was carried out as per the method of Ajaiyeoba et al., 2001. The assay was performed in vitro, using cestodes and nematodes of sheep and poultry. Test samples of the extract was prepared at the concentrations, 10, 20 and 50 mg/ml of bryophyte extract dissolved in distilled water. Six worms, each of chicken nematodes Ascaridia galli and sheep nematodes Trychostrongyles were placed in petri dish measuring 9 cm in diameter. Similarly cestode parasites Railletina tetragona, which parasitizes chicken and sheep cestode Moniezia expansa were placed in petri dishes and 25 ml of bryophyte extract was added to the petri dishes. Piperazine citrate of concentration 10mg/ml was prepared and used as reference standard and double distilled water was used as control. Extract solution and standard solution were freshly prepared, prior to experimentation. Observations were made and the time taken for paralysis was noted when no movement of any sort could be observed. Time of death of worms were recorded after ascertaining that worms neither moved when shaken vigorously nor when dipped in warm water. It was observed that at higher concentrations of bryophyte extract produced paralytic effect much earlier and the time taken for death was shorter for all types of worms. Aqueous extract of bryophyte exhibited anthelmintic activity in dose dependent manner showing maximum efficacy at 20 mg/ml concentration on cestodes and nematodes. However the plant extract exhibited more potent activity at lowest concentration 10mg/ml against Ascaridia galli. Anthelmintic activity of the extract was compared with standard drug piperazine citrate. These results suggest that Pottia lanceolata bryophyte extract exhibited significant anthelmintic activity when compared to Tortula subulata.

tag: host

value: Ovis aries

tag: host tissue

value: Intestine

value: Whole body

value: Pottia lanceolata bryophyte extract


title: Polarization: 4h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_4h_M1_2


title: RNA-seq_Whisker scl14-2, after transplantation, clone

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.9.3). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Rattus norvegicus (version Rnor 6.0) genome using STAR (v. 2.5.2b, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using R. norvegicus (Ensembl Rnor 6.0.87) gene annotation.
Genome_build: Rattus norvegicus (version Rnor 6.0)
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

organism: Rattus norvegicus

source_name: Whisker cells after transplantation into skin, subclone 14

growth_protocol: Various tissues were dissected from EFGP rats at PN57 (whisker), PN137 (thymus), PN200 (Vagina and trachea) and PN201 (Bladder). Tissues were harvested and kept in cold Hank’s Balanced Salt Solution (HBSS) complemented with 10% Fetal Bovine Serum (Thymus) or cold Dulbecco Modified Eagle's Medium (DMEM) supplemented with 10% Fetal Bovine Serum during dissection (other tissues). Thymic single lobes were placed in individual 35 mm size Petri dishes and washed in HBSS without Ca2+ and Mg2+ twice before being dissociated  in 0.05% trypsin solution containing 0.1% EDTA at 37°C . Other tissues  were mechanically minced before being dissociated in 0.05% trypsin solution containing 0.1% EDTA at 37°C with a gentle stirring. Skin grafts containing GFP-positive hair follicles were carefully dissected from the back of recipient nude mice and dissociated in 30 ml of 0.05% trypsin containing 0.1% EDTA at 37°C for 60 to 120 min.

extract_protocol:
Total RNA was prepared using the RNeasy Mini Kit (QIAGEN Inc.) and the RNase-Free DNase Set (Qiagen Inc).
RNA-seq libraries were prepared using 400 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Caliper Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA) using a Caliper-developed automated script.

treatment_protocol: Tissues and hair follicle cells were cultivated on a feeder layer of irradiated 3T3-J2 cells in a 3:1 DMEM F12 medium supplemented as described (Bonfanti et al., 2010). EGFP-positive cells were FACS-sorted for analysis.

value: constitutively express the Enhanced Green Fluorescent protein (EGPF) (green rat CZ-004'' SDTgN (act-EGFP)obsCZ-004)

value: Sprague-Dawley

value: Whisker


title: Sheep_Nematode_Control

value: Control


title: Polarization: 6h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_6h_M1_2

value: LPS + IFN-gamma


title: Polarization: 4h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_4h_M2_0


title: RNA-seq_Whisker Cl7-2, before transplantation, clone

source_name: Whisker cells before transplantation into skin, clone 7


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A5_ad010

tag: brain region

value: DG

value: male


title: A989_48_18TH

type: RNA

city: München

first: Michael

last: Quante

address: Ismaninger Str 22

department: II Medizinische Klinik

institute: Technische Universität München

description: Gene expression data from whole SCJ/cardia tissue

hyb_protocol: 3.8 µg of fragmented and labeled sscDNA were hybridized to an Affymetrix Mouse Gene 2.1 ST Array Plate. For hybridization, washing, staining and scanning an Affymetrix GeneTitan® system was used.

scan_protocol: Affymetrix GeneTitan® system

data_processing: Summarized probe set signals were calculated by using the RMA algorithm with the Affymetrix GeneChip Expression Console Software.

label: Biotin

source_name: SCJ/cardia tissue

label_protocol: 150 ng of total RNA were used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin

growth_protocol: Mice were maintained up to 12 months age in accordance with the German Animal Welfare and Ethical Guidelines of the Klinikum rechts der Isar, TUM, Munich, Germany.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and then underwent RNA Cleanup using Qiagen RNeasy mini with on-column DNAse digestion according to the manufacturer’s instructions.

treatment_protocol: See individual sample characteristics for details.

tag: facility

value: MRI

tag: diet

value: chow


title: A989_44_14TH_2


title: RNA-seq_Whisker scl14, after transplantation, clone


title: A989_46_16TH


title: RNA-seq_Whisker Cl7, before transplantation, clone


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A5_ad007

tag: Sex

tag: age

tag: strain


title: Polarization: 4h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_4h_M1_1

tag: cell type

value: Bone-marrow derived macrophages (BMDMs)

tag: cytokines added


title: RNA-seq_Vaginal cells RC-2, after transplantation, bulk

source_name: Vagina cells after transplantation into skin, bulk

tag: tissue

value: Vagina


title: A989_43_13TH


title: Polarization: 4h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_4h_M1_0


title: Polarization: 2h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_2h_M2_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A5_ad006


title: Polarization: 2h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_2h_M2_1


title: RNA-seq_Vaginal cells RC, after transplantation, bulk


title: A989_47_17TH


title: RNA-seq_Vaginal cells-2, before transplantation, bulk

source_name: Vagina cells before transplantation into skin, bulk


title: RNA-seq_Vaginal cells, before transplantation, bulk


title: Polarization: 2h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_2h_M2_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A5_ad004


title: A989_42_12TH_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A4_ad012


title: RNA-seq_Trachea Cells RC-2, after transplantation, bulk

source_name: Trachea cells after transplantation into skin, bulk

value: Trachea


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A5_ad002


title: Polarization: 2h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_2h_M1_2


title: A989_45_15TH


title: A989_39_9TH


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A4_ad010


title: Polarization: 2h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_2h_M1_1


title: A989_41_11TH


title: A989_40_10TH


title: RNA-seq_Trachea Cells RC, after transplantation, bulk


title: A989_38_8TH


title: RNA-seq_Trachea Cells-2, before transplantation, bulk

source_name: Trachea cells before transplantation into skin, bulk


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A4_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A4_ad008


title: Polarization: 1h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_1h_M2_2


title: Polarization: 2h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_2h_M1_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A5_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A4_ad004


title: RNA-seq_Thymus Cells RC-2, after transplantation, bulk

source_name: Thymic epithelial cells 4months after first transplatation into skin, bulk 907

value: Thymus


title: Polarization: 1h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_1h_M2_1


title: A989_37_7TH


title: A989_36_6TH


title: RNA-seq_Thymus Cells-2, before transplantation, bulk

source_name: Thymic epithelial cells 4months before transplantation, clone 9


title: Polarization: 1h M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_1h_M2_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A3_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A3_ad012


title: RNA-seq_Thymus Cells, before transplantation, bulk


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A3_ad008


title: Polarization: 1h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_1h_M1_2


title: Polarization: 1h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_1h_M1_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A4_ad001


title: A989_32_2TH_2


title: A989_35_5TH


title: A989_31_1TH


title: A989_33_3TH


title: Polarization: 1h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_1h_M1_0


title: RNA-seq_Trachea Cells, before transplantation, bulk


title: Polarization: 0h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_0h_M0_2


title: A989_34_4TH_2


title: A989_30_12NS

value: WT

value: Freising

value: HFD


title: RNA-seq_Thymus Cells RC, after transplantation, bulk


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A3_ad007


title: Polarization: 24h M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_24h_M1_0


title: RNA-seq_Dome cells RC, after transplantation, bulk

source_name: Bladder (dome) cells after transplantation into skin, bulk

value: Bladder (dome) cells


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A3_ad006


title: Polarization: 0h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_0h_M0_1


title: RNA-seq_Dome cells-2, before transplantation, bulk

source_name: Bladder (dome) cells before transplantation into skin, bulk

value: constitutively express the Enhanced Green Fluorescent protein (EGPF) (green rat CZ-004'' SDTgN (act-EGFP)obsCZ-004)


title: A989_28_10NS

description: Gene expression data from whole SCJ/cardia tissue


title: Polarization: 0h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
Pol_0h_M0_0


title: RNA-seq_Dome cells, before transplantation, bulk

value: Sprague-Dawley


title: 72h M1→M0-depolarized mouse BMDMs, bulk ATAC-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with LPS + IFN-γ to induce polarization into an M1 state for 24h, then washed with PBS and returned to base media for another 72h. Bulk ATAC-seq was collected for 0h M0, 24h M1, and 72h M1→M0 conditions in biological triplicate, according to the Buenrostro et al. (2013) protocol.
mph_m1polrp_count_mat.txt
M1-M0_72h_rep3

value: LPS + IFN-gamma, PBS wash, then none


title: RNA-seq_Dome cells RC-2, after transplantation, bulk


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A3_ad002

source_name: C57BL/6J Male P56 Mouse Brain


title: Shh_GFPPositive_E10.5Head_ATAC-seq

first: Robert

last: Hill

address: MRC Human Genetics Unit, Crewe Road South

institute: MRC Human Genetics Unit

description: Accessible DNA regions

data_processing:
Sequenced reads were trimmed for adapter sequence, mapped to mm9 whole genome using bowtie v2.3.
Unmapped reads and mitochondrial reads were removed. Subsequently duplicate reads were filtered using Picard REMOVE_DUPLICATES=TRUE.
Reads were then shifted by +4 bp for the positive strand and -5 bp for the negative strand.
Peaks were called usings MACS2 callpeak using -g mm -f BEDPE -B broad cutoff 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: broadPeaks cutoff 0.01 peak data

source_name: eGFP/Cre-Shh positive cell population from mouse head

extract_protocol:
Entire E10.5 day heads were dissected from an individual Shh GFP positive embryo. A single cell suspension was made by incubating the dissected head in a 1:5 trypsin:versene solution for 15 minutes. Cells were pelleted, washed in PBS and resuspended in PBS then sent for FAC sorting for GFP positive cells.
Resulting GFP positive cells were subject to the ATAC-seq protocol from Buenrostro et al. 2015. Following this protocol the samples was subject to an additional left and right size selection purification step using SPRI select beads (#B23318) at a 0.95x and 1.4x bead ratio.

tag: cell population

value: E10.5 Shh expressing population

value: eGFP/Cre-Shh mice


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A2_ad008

value: DG


title: A989_27_9NS


title: 72h M1→M0-depolarized mouse BMDMs, bulk ATAC-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with LPS + IFN-γ to induce polarization into an M1 state for 24h, then washed with PBS and returned to base media for another 72h. Bulk ATAC-seq was collected for 0h M0, 24h M1, and 72h M1→M0 conditions in biological triplicate, according to the Buenrostro et al. (2013) protocol.
mph_m1polrp_count_mat.txt
M1-M0_72h_rep1

source_name: bone-marrow derived macrophages (BMDMs) from 6-10 week old C57BL/6J mice


title: 72h M1→M0-depolarized mouse BMDMs, bulk ATAC-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with LPS + IFN-γ to induce polarization into an M1 state for 24h, then washed with PBS and returned to base media for another 72h. Bulk ATAC-seq was collected for 0h M0, 24h M1, and 72h M1→M0 conditions in biological triplicate, according to the Buenrostro et al. (2013) protocol.
mph_m1polrp_count_mat.txt
M1-M0_72h_rep2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A2_ad007

value: male


title: 24h M1-polarized mouse BMDMs, bulk ATAC-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with LPS + IFN-γ to induce polarization into an M1 state for 24h, then washed with PBS and returned to base media for another 72h. Bulk ATAC-seq was collected for 0h M0, 24h M1, and 72h M1→M0 conditions in biological triplicate, according to the Buenrostro et al. (2013) protocol.
mph_m1polrp_count_mat.txt
M1_24h_rep3

value: LPS + IFN-gamma


title: 24h M1-polarized mouse BMDMs, bulk ATAC-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with LPS + IFN-γ to induce polarization into an M1 state for 24h, then washed with PBS and returned to base media for another 72h. Bulk ATAC-seq was collected for 0h M0, 24h M1, and 72h M1→M0 conditions in biological triplicate, according to the Buenrostro et al. (2013) protocol.
mph_m1polrp_count_mat.txt
M1_24h_rep2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A2_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A2_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A2_ad004


title: A989_26_8NS

value: chow


title: 0h unpolarized mouse BMDMs, bulk ATAC-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with LPS + IFN-γ to induce polarization into an M1 state for 24h, then washed with PBS and returned to base media for another 72h. Bulk ATAC-seq was collected for 0h M0, 24h M1, and 72h M1→M0 conditions in biological triplicate, according to the Buenrostro et al. (2013) protocol.
mph_m1polrp_count_mat.txt
M0_0h_rep3

value: Bone-marrow derived macrophages (BMDMs)


title: 24h M1-polarized mouse BMDMs, bulk ATAC-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with LPS + IFN-γ to induce polarization into an M1 state for 24h, then washed with PBS and returned to base media for another 72h. Bulk ATAC-seq was collected for 0h M0, 24h M1, and 72h M1→M0 conditions in biological triplicate, according to the Buenrostro et al. (2013) protocol.
mph_m1polrp_count_mat.txt
M1_24h_rep1


title: A989_22_4NS_2


title: A989_24_6NS_2


title: A989_23_5NS


title: Quadriceps_24m_rep2

first: Xu

last: Wang

address: EPFL SV IBI-SV NCEM AI 1148 (Bâtiment AI) Station 15

department: School of Life Sciences

institute: École polytechnique fédérale de Lausanne

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner

data_processing: Microarray data was normalized with RMA-sketch method and analyzed using the Affymetrix Expression and Transcriptome analysis consoles.

label: biotin

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (Part Number 4411974) according to manufactures protocols, then 5500ng cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

growth_protocol: Female C57BL/6J mice were group housed and received standard chow (#2018, containing 18% protein, 50% carbohydrate and 6.0% fat; Harlan Laboratories, Madison, WI, USA).

extract_protocol: Tissues were frozen in liquid nitrogen for biochemical and molecular analyses. Total RNA was isolated using Trizol (Life Technologies) and purified using the RNeasy Mini Kit (Qiagen) in accordance with the manufacturer’s instructions. It was then assessed for degradation using an Advanced Analytical Agilent Fragment Analyzer.

treatment_protocol: After reaching the age of 24 (~6 month) or 103 weeks (~24 month), mice were sacrificed after overnight fasting.

value: female

value: 24 month

value: Quadriceps


title: A989_25_7NS

value: WT


title: Quadriceps_24m_rep3


title: A989_21_3NS_2

value: Freising


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A2_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A2_ad001


title: 0h unpolarized mouse BMDMs, bulk ATAC-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with LPS + IFN-γ to induce polarization into an M1 state for 24h, then washed with PBS and returned to base media for another 72h. Bulk ATAC-seq was collected for 0h M0, 24h M1, and 72h M1→M0 conditions in biological triplicate, according to the Buenrostro et al. (2013) protocol.
mph_m1polrp_count_mat.txt
M0_0h_rep2


title: Quadriceps_6m_rep3

value: 6 month


title: A989_19_1NS_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A12_ad006


title: Quadriceps_6m_rep2


title: 0h unpolarized mouse BMDMs, bulk ATAC-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with LPS + IFN-γ to induce polarization into an M1 state for 24h, then washed with PBS and returned to base media for another 72h. Bulk ATAC-seq was collected for 0h M0, 24h M1, and 72h M1→M0 conditions in biological triplicate, according to the Buenrostro et al. (2013) protocol.
mph_m1polrp_count_mat.txt
M0_0h_rep1


title: Quadriceps_6m_rep1


title: A989_20_2NS_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A2_ad002


title: 24h M2-polarized mouse BMDMs, 10X single-cell RNA-seq

description: Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization into either M1 or M2 states, with unpolarized (M0) as the control state. Single cell RNA-seq was performed using the 10X Genomics platform (library prep and final sequencing performed as outlined in the 10X documentation for their single-cell solution kit).


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A12_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A11_ad008


title: Liver_24m_rep3

value: liver


title: A989_18_12AN_2

value: MRI


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A11_ad012


title: Quadriceps_24m_rep1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A11_ad007


title: 24h M1-polarized mouse BMDMs, 10X single-cell RNA-seq


title: Liver_24m_rep2


title: 6h M2-polarized mouse BMDMs, 10X single-cell RNA-seq


title: 24h unpolarized mouse BMDMs, 10X single-cell RNA-seq


title: A989_16_10AN_2


title: Liver_24m_rep1


title: A989_17_11AN_2


title: A989_14_8AN_2


title: Liver_6m_rep3


title: Liver_6m_rep2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A11_ad006


title: 6h M1-polarized mouse BMDMs, 10X single-cell RNA-seq


title: Liver_6m_rep1


title: MB_6

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

state: PA

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. The fragments per kilobase per million mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: Homo Sapiens(GRCh37/hg19)
Supplementary_files_format_and_content: FPKM represents summary of gene expression level analysis by FPKM; DEG represents differential gene expression analysis

source_name: breast cancer cells

growth_protocol: The MCF-10A, MCF-7, SK-BR-3, and MDA-MB-231 cells were plated in 6-cm dish at a density of 5×105 cells/dish in triplicate and incubated overnight for attachment.

extract_protocol:
The cells were harvested by trypsin treatment and total RNA was extracted using the RNeasy mini kit (Qiagen, Germantown, MD).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with DMSO (final concentration- 0.01%) or 2 µM of WA for 16 hours prior to RNA isolation and RNA-Seq analysis.

tag: cell line name

value: Cells were treated with 2 uM of WA for 16 hours.


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A11_ad004


title: A989_13_7AN_2


title: A989_15_9AN_2


title: MB_5


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A11_ad002


title: A989_12_6AN

value: FXR


title: 0h unpolarized mouse BMDMs, 10X single-cell RNA-seq


title: 6h unpolarized mouse BMDMs, 10X single-cell RNA-seq


title: MB_4


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A11_ad001


title: MB_3

value: Cells were treated with vehicle (DMSO) for 16 hours.


title: A989_11_5AN_2


title: Esrrb_NT_3

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

data_processing:
RNA sequencing reads were aligned to the mouse genome mm10 with TopHat2 aligner with default input parameters. The number of reads that were mapped to each Ensembl gene (GRCm38) was counted using the Python package HTSeq. Principal component analysis and differential expression analysis was performed with raw counts using the R package DESeq2. Genes were considered as deregulated if |log2FC|> 1 and FDR < 0.01 using Benjamini-Hochberge multiple test adjustment
Genome_build: mm10
Supplementary_files_format_and_content: txt files include raw counts for each gene in each sample

source_name: ES cells grown in growth factor depleted matrigel

growth_protocol: ES cell lines were maintained in the presence of 2i/Lif (0.4 µM PD0325901, 3 µM CHIR99021 and 4 ng/ml Lif), on plastic dished coated with 0.2% gelatin and passaged at 1:6 ratio using 0.05% Trypsin-EDTA

extract_protocol:
To recover cells from matrigel, warmed mixture of accutase and trypsin (1:2) was applied to dissolve matrigel. After 30 mins at 37 ºC, the cells were washed for twice with PBS. The RNAeasy Mini Kit (Qiagen) was used to extract total RNA
1 ug of total RNA, with RIN (RNA integrity number) numbers above 7 (Agilent 2100 Bioanalyzer) were used. mRNA is enriched using NEBNext® Poly(A) mRNA Magnetic Isolation Module and cDNA library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit. Sequencing was performed on the NextSeq 500 system (75 cycles, high output, v2.5).

treatment_protocol: ES cells were resuspended in matrigel (2000 cells per 1 µl of matrigel) and plated on petri dishes. To solidify the hydrogel, the plate was placed for 2-3 min in a cell culture incubator at 37°C. After that, each well was filled with N2B27 medium supplemented with single or combination of inhibitors inhibitors – DMSO, 0.4 µM PD and 3 µM CHIR99021, 3 µM CHIR99021 or 12 ng/ml Fgf2 and 20 ng/ml Activin A cultured for 48h at 37°C and 5% CO2 atmosphere in air. Esrrb fl/fl ES cells expressing tamoxifen-inducible Cre were cultured without or in the presence of 4OHT for 1 day before 3D culture. Then, cells were resuspended in matrigel (2000 cells per 1 µl of matrigel) and plated on petri dishes. To solidify the hydrogel, the plate was placed for 2-3 min in a cell culture incubator at 37°C. After that, each well was filled with N2B27 medium supplemented with 3 µM CHIR99021 and cultured for 24 hours.

value: Mouse Embryonic stem cells

tag: passage

value: Acr-EGFP transgenic mice (Nakanishi et al., 1999)


title: A989_10_4AN_2


title: MB_2

tag: treatment


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A10_ad012

value: DG

value: male


title: Esrrb_NT_2


title: Esrrb_NT_1


title: A989_09_3AN_3

value: chow


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A10_ad008


title: A989_08_2AN_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A10_ad007


title: Esrrb_4OHT_3


title: SK_6


title: Esrrb_4OHT_2


title: SK_5


title: A989_07_1AN_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A10_ad006


title: Esrrb_4OHT_1


title: A989_06_6CM_2


title: 2i_3

source_name: E14 ES cells grown in growth factor depleted matrigel

value: strain 12910la


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A10_ad002


title: SK_3


title: SK_2


title: A989_03_3CM_2


title: SK_4


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A10_ad004


title: 2i_1


title: A989_05_5CM_2


title: SK_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A10_ad001


title: MB_1


title: 2i_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A10_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A1_ad012


title: FGF2_Activin_2


title: FGF2_Activin_3


title: S2 nbrKO

city: Vienna

first: Ivica

last: Sowemimo

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

description:
18-30 nt size selection for miRNA seq
126418

data_processing:
Basecalling performed using RTA 1.18.66.3
Adapters ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG") are removed with cutadapt (v1.2.1; parameter: -O 6 --discard-untrimmed -e 0.1).
Random 4mers are removed at 5' and 3' ends. Reads with length between 18-30nt were kept.
Putative contamination was filtered out by aligning to sequences of S2 viruses (derived from Genbank) with tailor (v1.1)
The reads were aligned with tailor (v1.1) with a minimal prefix match length of 18.
Counts were calculated with htseq-count (v0.9.1). The parameters were stranded=yes and  “intersection-nonempty”. A GTF containing the FlyBase r5.57 annotation supplemented with cisNATs and structured loci was used. The pre-miRNA annotation was split in two halves assigned to 5' and 3' of each miRNA region, respectively. Reads with multiple alignments were counted as their fraction to each location/feature. Feature types are summarized by following hierarchy (AS = antisense): mitochondrial mapping, rRNA, rRNA_AS, tRNA, tRNA_AS, pre_miRNA_5p3p, pre_miRNA_5p3p_AS, pre_miRNA, pre_miRNA_AS, transposable_element, transposable_element_AS, __no_feature, cisNATs, cisNATs_AS, structured_loci, structured_loci_AS, pseudogene, pseudogene_AS, ncRNA, ncRNA_AS, snoRNA, snoRNA_AS, snRNA, snRNA_AS, mRNA, mRNA_AS, intron, intron_AS.
RPM was calculated excluding reads matching to rRNA, rRNA_AS, tRNA, tRNA_AS.
Genome_build: Flybase r5.57
Supplementary_files_format_and_content: TSV file; count table

organism: Drosophila melanogaster

source_name: Drosophila Schneider (S2) cells

growth_protocol: Drosophila Schneider 2 (S2) cells were cultured in Schneider’s Drosophila Medium (Gibco) containing 10% FBS (Gibco), maintained at 25°C and passaged every 3 days

extract_protocol:
Total RNA was extracted from S2 cell culture collected in Trizol using a phenol-chloroform-based standard protocol, according to manufacturer's instructions.
Small RNA sequencing libraries were constructed from an input of 25ug total RNA. In-house protocol: size select 18-30nt RNA; deplete 2S rRNA; ligate 3p linker; size select ligation product; ligate 5p linker; size select ligation product; reverse transcription; qPCR library amplification. 3p and 5p adapters contain 4N at ligation interface (Jayaprakash et al, NAR, 2011)

treatment_protocol: Drosophila S2 cells were depleted of Nbr by CRISPR-Cas9 genome engineering (as previously described in Reichholf et al., Mol Cell, 2019); if indicated, S2-nbrKO cells were stably transfected with the indicated constructs;

value: nbrKO

tag: cell line

value: Schneider (S2) cells


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A1_ad008


title: FGF2_Activin_1


title: Nbr(wt) overexpression in S2 nbrKO

description:
18-30 nt size selection for miRNA seq
126417

tag: genotype

value: Act5C>Nbr(wt); nbrKO


title: M7_4


title: A989_01_1CM


title: NbrCTD overexpression in S2 nbrKO

description:
18-30 nt size selection for miRNA seq
126416

value: Act5C>NbrCTD; nbrKO


title: CH_3


title: M7_3


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A1_ad007


title: A989_04_4CM_2


title: M7_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A1_ad001


title: M7_2


title: DMSO_3


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A1_ad004


title: CH_2


title: A989_02_2CM_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A1_ad006


title: M7_6


title: M7_5


title: CH_1


title: 10A_6

source_name: normal mammary epithelial cells


title: CEMBA190627_10F_1_CEMBA190627_10F_2_A1_ad010


title: dissected Drosophila midbrain - rep6 - lane1

city: Oxford

first: Christoph

last: Treiber

address: Mansfield Rd

department: Centre for Neural Circuits and Behaviour

institute: University of Oxford

data_processing:
merged overlapping reads
created in-silico paired-end reads from contigs
aligned to masked Drosophila reference genome (Dmel 6.25)
converted bam to wig (Galaxy)
Genome_build: Dmel 6.25
Supplementary_files_format_and_content: wig

molecule: polyA RNA

source_name: dissected midbrain

extract_protocol:
RNeasy Mini kit, Qiagen, UK
TruSeq, Illumina, ~350nt long fragments, 250nt paired-end reads

value: midbrain


title: dissected Drosophila midbrain - rep6 - lane2


title: DMSO_2


title: DMSO_1


title: dissected Drosophila midbrain - rep5 - lane1


title: dissected Drosophila midbrain - rep4 - lane2


title: mmu_delGly_siSnrnp70_2

city: Okawa

first: Tadashi

last: Nakaya

state: Fukuoka

address: 137-1 Enokizu

department: School of Pharmacy at Fukuoka

country: Japan

institute: International University of Health and Welfare

description: NFLAG-delGly expression plus Snrnp70 KD2

data_processing:
Obtained reads were mapped to the mouse genome (mm10) using HISAT2 version 2.1.0. with following parameters; --phred33 --rna-strandness RF -t --no-unal -p 4.
For gene count, HTseq-count (version 0.11.2) was used.
The gene count results of all samples obtained as above were combined into single file.
Genome_build: mm10
Supplementary_files_format_and_content: A text file contains read counts for genes for eight samples.

source_name: Neurons

growth_protocol: Mouse embryonic stem cells (ES, E14Tg2A.4) were maintained in ES medium on gelatinized plates without feeder cells. Neuronal differentiation was performed as described previously (Wichterle et al., 2009). Cells were maintained into ADFNB+GDNF.

extract_protocol:
Total RNA was isolated from neurons using Trizol reagent (Thermo).
Total RNA prepared as above was submitted to Novogene Co., Inc to prepare library using Eukaryotic directional mRNAseq kit (Illumina).

treatment_protocol: NFLAG-delGly, shRNA for Luciferase or shRNA for Snrnp70 were expressed in ES cell derived neurons by lentivirus system and cells were treated with DOX to induce expression of the exogenous protein or shRNA along with Geneticin to select the cells infected with virus.

value: ES cell derived neurons


title: LPS-serum-injection

city: Guangzhou

first: Xinping

state: Guangdong

address: 1838 N. Guangzhou Ave

country: China

institute: Southern Medical University

description: stereotactic injection of LPS-serum

data_processing:
Demultiplexing of the bcl file into a FASTQ file was performed using bcl2fastq
generate the UMI count matrix with cellranger’s (version 2.2.0) ‘cellranger count’ function for each library
Genome_build: using mouse (mm10-1.2.0) genome reference sequences
Supplementary_files_format_and_content: a matrix include UMI count for each cell

source_name: whole brain

extract_protocol:
Cell suspension mixture of two brains randomly picked from each treatment, was generated using MACS Adult Brain Dissociation Kit (Miltenyi Biotec, USA) following the manufacturer’s instruction. Messenger RNA from approximately ∼7,000 cells, captured and lysed within nanoliter-sized gel beads in emulsion, was reverse transcribed and barcoded using polyA primers with unique molecular identifier sequences before being pooled, amplified, and used for library preparation.
Cells were then processed through the Chromium Single-cell 3’ v2 Library Kit (10× Genomics) by the Oebiotech (Shanghai, China). Briefly, 10,000 cells were loaded onto a single channel of the 10× Chromium Controller.

treatment_protocol: Intraperitoneal injection (IPI) of lipopolysaccharide (LPS) at a dosage of 150 ug/kg was done twice on post-natal day 45 and 46 to activate the immune system on 5 mice. The serum was taken from the immune activated mice on post-natal day 47. IPI of saline was done on 5 mice at the same time and the serum was taken from these mice as well. The intracerebroventricular injection (ICVI) of 15 ul of serum was performed on 8 adolescent mice using microinjection for each treatment. The mice were anesthetized using 0.01 ml/g of 0.75% pentobarbital sodium solution and perfusion was carried out to remove blood from the brain tissues. The whole brain was taken immediately after the mouse was executed.

value: whole brain

value: post natal day 54

value: LPS


title: 10A_4

value: Cells were treated with 2 uM of WA for 16 hours.


title: NbrCTD-GWp overexpression in S2 nbrKO

description:
18-30 nt size selection for miRNA seq
126415

value: Act5C>NbrCTD-GWp; nbrKO


title: SK-N-SH_32

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

department: Medical Faculty

institute: University Heidelberg

description: single-cell RNA-seq (MARS-seq)

data_processing:
Pool barcode, cell-specific tags and UMIs were extracted and reads with ambiguous plate/cell-specific tags were filtered
Sequenced reads were trimmed for adaptor sequence, and mapped to hg19 whole genome combined with ERCC spike-in pseudo-assembly using Bowtie2 v2.1.0  and the standard parameters “-m 1 -t --best --chunkmbs 64 –strata”
Sequence reads were filtered for reads mapping to a range of -1000 to +200 bp from a known transcription termination site
Genome_build: hg19
Supplementary_files_format_and_content: dgCMatrix object with counts as an RDS file R file

source_name: Neuroblastoma cell lines

growth_protocol: SK-N-SH cells were cultured in RPMI1640 medium supplemented with 10% fetal calf serum and 1% penicillin/streptomycin at 37°C and 5% CO2 and subcultured every 3-4 days.

extract_protocol:
Cells were harvested using versene and single-cells were sorted into 384-well plates.
Libraries were prepared as described previously (Jaitin et al., 2014)

treatment_protocol: Cells were not treated.

tag: type

value: cell line

value: SK-N-SH


title: 10A_3

value: Cells were treated with vehicle (DMSO) for 16 hours.


title: 10A_1


title: SK-N-SH_29

description: single-cell RNA-seq (MARS-seq)


title: dissected Drosophila midbrain - rep4 - lane1


title: dissected Drosophila midbrain - rep2 - lane2


title: dissected Drosophila midbrain - rep5 - lane2


title: mmu_delGly_siSnrnp70_1

description: NFLAG-delGly expression plus Snrnp70 KD1


title: SK-N-SH_31

description: single-cell RNA-seq (MARS-seq)


title: dissected Drosophila midbrain - rep3 - lane1


title: SK-N-SH_30

description: single-cell RNA-seq (MARS-seq)


title: dissected Drosophila midbrain - rep3 - lane2


title: SK-N-SH_28

description: single-cell RNA-seq (MARS-seq)


title: mmu_siSnrnp70_2

description: Snrnp70 KD2

value: Snrnp70 KD2


title: 10A_5


title: mmu_delGly_siLuc_1

description: NFLAG-delGly expression plus Luciferase KD


title: 10A_2


title: dissected Drosophila midbrain - rep2 - lane1


title: saline-serum-injection

description: stereotactic injection of saline-serum

value: saline


title: SK-N-SH_27

description: single-cell RNA-seq (MARS-seq)


title: C5

city: Berlin

first: Malte

last: Spielmann

address: Ihnestraße 63

institute: Max Planck Institute for Molecular Genetics

data_processing:
Cell Ranger v3 mkfastq
Cell Ranger v3 count
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw UMI count matrix, gene metdata and cell metadata

extract_protocol:
The left hemi-midbrain was removed. This midbrain block was then snap-frozen at -120°C and cryosectioned at ~15 μm thickness in the transverse plane. The resulting sections were stored at -80°C. Addapted 10x Genomics protocol for nuclei isolation was used to extract the nuclei. Sorted nuclei were processed using the Chromium Next GEM Single Cell 3’ Kit v3.1 to generate the cDNA libraries
The sample was prepared for sequencing using standard Illumina protocol and sequenced on Illumina NovaSeq 6000-S2

tag: disease state

value: Healthy control

tag: age at death

value: M

tag: pmi (h)

value: Midbrain

tag: molecule subtype

value: nuclear RNA


title: C4

tag: Sex


title: mmu_delGly_siLuc_2

value: NFLAG-delGly expression plus Luciferase KD


title: mmu_siLuc_2

description: Luciferase KD

value: Luciferase KD


title: dissected Drosophila midbrain - rep1 - lane1

value: midbrain


title: mmu_siSnrnp70_1

description: Snrnp70 KD1

value: ES cell derived neurons

value: Snrnp70 KD1


title: A989_29_11NS

description: Gene expression data from whole SCJ/cardia tissue

source_name: SCJ/cardia tissue

value: WT

tag: facility

value: Freising

tag: diet

value: HFD


title: SK-N-SH_26

description: single-cell RNA-seq (MARS-seq)

value: cell line


title: C3


title: mmu_siLuc_1

description: Luciferase KD

tag: cell type

tag: strain


title: dissected Drosophila midbrain - rep1 - lane2

tag: tissue


title: C6


title: C2


title: C1

value: F


title: U87_DPF3CM_3 RNA-seq

city: GuangZhou

first: liu

last: xincheng

address: zhongshan Road 74

institute: sysu

data_processing:
We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value,28S/18S and the fragment length distribution.
We use internal software SOAPnuke to filter reads
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression  level with RSEM
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: The cells were cultured according to the guideline of ATCC

extract_protocol:
Total RNA was isolated from cultured cell lines. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers ere used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced using Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U87 cells were treated with bulk control/combination of 0.5mM 8-cpt-cAMP and 1nM MS275  for 48 hours. Total RNA was extracted from 1×10^6 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent for RNA sequencing

tag: genotype/variation

value: U87 cells transfer plasmid containing DPF3 gene and treated with 0.5mM 8-cpt-cAMP and 1nM MS275 for 48hr.


title: SK-N-SH_25

description: single-cell RNA-seq (MARS-seq)

value: SK-N-SH


title: U87_DPF3CM_2 RNA-seq


title: SK-N-SH_23

description: single-cell RNA-seq (MARS-seq)


title: SK-N-SH_22

description: single-cell RNA-seq (MARS-seq)


title: U87_DPF3CM_1 RNA-seq


title: SK-N-SH_24

description: single-cell RNA-seq (MARS-seq)


title: IPD5

value: Idiopathic Parkinson's disease (IPD)


title: IPD4


title: SK-N-SH_21

description: single-cell RNA-seq (MARS-seq)


title: SK-N-SH_20

description: single-cell RNA-seq (MARS-seq)


title: U87_DPF3V_1 RNA-seq

value: U87 cells transfer plasmid containing DPF3 gene.


title: SK-N-SH_19

description: single-cell RNA-seq (MARS-seq)


title: IPD1


title: U87_NCCM_3 RNA-seq

value: Control

value: U87 cells transfer empty plasmid as a control and treated with 0.5mM 8-cpt-cAMP and 1nM MS275 for 48hr.