title: Stage 9 pou5f3.3, sox3 MO rep E1

status: Public on Sep 13 2022

first: Miler

middle: T

last: Lee

address: 4249 Fifth Ave

department: Biological Sciences

description:
s9_pou_sox_mo_e_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

data_processing:
Reads were mapped to the X. laevis v9.2 genome using HISAT2 v2.2.1 (--no-discordant)
Mapped reads were assigned to gene exons (Xenbase v9.2 models) using featureCounts v2.0.1 in reversely-stranded paired-end mode with default parameters, or introns with --minOverlap 10 on a custom non-repeat non-exonic annotation based on Xenbase models
Assembly: X. laevis v9.2
Supplementary files format and content: CSV exon and intron raw and normalized read counts

organism: Xenopus laevis

source_name: Whole embryos

extract_protocol:
Two embryos per sample were snap frozen and homogenized in 500ul of TRIzol Reagent (Invitrogen #15596026) followed by 100ul of chloroform. Tubes were spun at 18,000 x g at 4C for 15 minutes, the aqueous phase was transferred to a fresh tube with 340 ul of isopropanol and 1 ul of GlycoBlue (Invitrogen #AM9515), then precipitated at -20C overnight. Precipitated RNA was washed with cold 75% ethanol and resuspended in 50ul of nuclease-free water. Concentration was determined by NanoDrop.
rRNA depletion was performed as per Phelps et al NAR 2021: 1ul of antisense nuclear rRNA oligos and 1ul of antisense mitochondrial rRNA oligos (final concentration 0.1 uM per oligo) were combined with 1ug of total RNA in a 10ul buffered reaction volume (100mM Tris-HCl  pH 7.4, 200mM NaCl, 10mM DTT), heated at 95C for 2 minutes and cooled to 22C at a rate of 0.1C/s in a thermocycler. Next, 10U of thermostable RNaseH (NEB #M0523S) and 2uL of provided 10X RNaseH buffer were added and volume brought to 20uL with nuclease-free water. The reaction was incubated at 65C for 5 or 30 minutes, then 5U of TURBO DNase (Invitrogen #AM2238) and 5uL of provided 10x buffer was added, volume brought to 50uL with nuclease-free water and incubated at 37C for 30 minutes. The reaction was purified and size selected to >200 nts using Zymo RNA Clean and Concentrator-5 (Zymo #R1013) according to manufacturer’s protocol, eluting in 10uL of nuclease-free water. The WT Stage 5 sample was also depleted of mitochondrial COX2 and COX3 mRNA as part of Phelps et al NAR 2021. Strand-specific RNA-seq libraries were constructed using NEB Ultra II RNA-seq library kit (NEB #E7765) according to manufacturer’s protocol with fragmentation in first-strand buffer at 94C for 15 minutes. Following first and second strand synthesis, DNA was purified with 1.8X AmpureXP beads (Beckman #A63880), end repaired, then ligated to sequencing adaptors diluted 1:5. Ligated DNA was purified with 0.9X AmpureXP beads and PCR amplified for 8 cycles, then purified again with 0.9X AmpureXP beads. Libraries were verified by Qubit dsDNA high sensitivity (Invitrogen #Q32851) and Fragment Analyzer prior to multiplexed sequencing at the Health Sciences Sequencing Core at Children’s Hospital of Pittsburgh.

treatment_protocol: Dejellied embryos were incubated in MR/3 (33 mM NaCl, 0.6 mM KCl, 0.67 mM CaCl2, 0.33 mM MgCl2, 1.67 mM HEPES, pH 7.8) at 23C and collected at their respective NF stages based on morphology. All stage 9 embryos were collected halfway through the stage, at 8 hours post fertilization. Triptolide samples were bathed in 20 uM triptolide in DMSO at stage 1 and cycloheximide samples were bathed in 500 ug/mL cycloheximide in DMSO at stage 8; both were collected when batch-matched, untreated embryos reached stage 9. Equivalent volumes of DMSO were used to treat control samples. Morpholino treated embryos were injected at stage 1 with pou5f3.2, pou5f3.3, sox3, and/or GFP control morpholino.

value: Whole embryos

tag: strain

value: WT

value: 40ng pou5f3.3 + 40ng sox3 morpholino


title: Stage 9 GFP MO rep E1

type: SRA

city: Pittsburgh

state: PA

country: USA

institute: University of Pittsburgh

description:
s9_gfp_mo_e_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

tag: developmental stage

tag: treatment

value: 80ng GFP morpholino


title: s-E15.5-WT-8B

status: Public on Nov 03 2022

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Small RNA-seq reads were trimmed using fastx 0.0.14 and cutadapt 1.8.3:  zcat ${FILE}.fastq.gz | fastx_trimmer -f 5 -i - -o ${FILE}.tmp.fastq  cutadapt --format="fastq" --front=GTTCAGAGTTCTACAGTCCGACGATCNNNN --adapter=NNNNTGGAATTCTCGGGTGCCAAGG --error-rate=0.075 --times=2 --overlap=14 --minimum-length=12 --max-n=0.1 --output="${FILE}.fastq" --trim-n --match-read-wildcards ${FILE}.tmp.fastq
Trimmed reads were mapped to mouse (mm10) genome using STAR 2.7.3a with following parameters:  STAR --readFilesIn ${FILE}.fastq.gz --genomeDir ${GENOME_INDEX} --runThreadN 12 --genomeLoad NoSharedMemory --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix ${FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 99999  --outFilterMismatchNoverLmax 0.1 --outFilterMatchNminOverLread 0.66 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.29.2 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE} -bg -split > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: mm10
Supplementary_files_format_and_content: coverage genome browser tracks files:  - .bigWig format  - generated in a non-stranded mode.   - not normalized for library size

organism: Mus musculus

source_name: mouse E15.5 embryos

extract_protocol:
Embryos were homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by Qiazol-chloroform extraction and ethanol precipitation method.
Small RNA libraries were constructed using Nextflex Small RNA-seq kit v3 for Illumina (Perkin Elmer) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15 cycles were used for PCR amplification and NextFlex beads were used for size selection.

treatment_protocol: E15.5 embryos were removed from the uterus and washed in PBS. The yolk sac was taken for genotyping and embryos were transferred into RNAlater (Thermo Fisher Scientific)

value: Dicer wt/wt

tag: age

value: embryo

tag: fraction

value: small RNA

tag: replicate


title: s-E15.5-XHOM-4

value: Dicer X/X


title: s-E15.5-XHOM-10B-r2


title: s-E15.5-WT-1


title: Stage 9 CHX GFP MO rep D2

description:
s9_chx_gfp_mo_d_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: cycloheximide, 80ng GFP morpholino


title: Stage 9 CHX pou5f3.3, sox3 MO rep C1

description:
s9_chx_pou_sox_mo_c_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: cycloheximide, 40ng pou5f3.3 + 40ng sox3 morpholino


title: Stage 9 CHX sox3 MO rep C2

description:
s9_chx_sox_mo_c_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: cycloheximide, 40ng sox3 + 40ng GFP morpholino


title: Stage 9 CHX GFP MO rep D1

description:
s9_chx_gfp_mo_d_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 CHX pou5f3.3, sox3 MO rep C2

description:
s9_chx_pou_sox_mo_c_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 CHX pou5f3.3 MO rep C2

description:
s9_chx_pou_mo_c_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: cycloheximide, 40ng pou5f3.3 + 40ng GFP morpholino


title: Stage 9 CHX GFP MO rep C2

description:
s9_chx_gfp_mo_c_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 triptolide rep A2

description:
s9_trip_a_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: triptolide


title: Stage 9 DMSO rep A1

description:
s9_dmso_a_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: DMSO


title: Stage 9 triptolide rep A1

description:
s9_trip_a_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 DMSO rep A2

description:
s9_dmso_a_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 CHX pou5f3.3 MO rep C1

description:
s9_chx_pou_mo_c_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 rep A2

description:
s9_a_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 rep E1

description:
s9_e_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: s-E15.5-WT-6


title: Stage 9 rep A1

description:
s9_a_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 CHX pou5f3.3, sox3 MO high concen rep D1

description:
s9_chx_pou_sox_mo_high_d_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: cycloheximide, 55ng pou5f3.3 + 75ng sox3 morpholino


title: Stage 7

description:
s7_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 8

description:
Previously submitted as GSM4629159
s8_GSM4629159
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 5 (COX2, COX3 deplete) rep 2

description:
Previously submitted as GSM4813825
s5_GSM4813825
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 no antibody rep 2

library_source: genomic

data_processing:
Reads were mapped to the X. laevis v10.1 genome using bowtie2 2.4.2 (--no-mixed --no-discordant), discarding reads on the mitochondrial chromosome. High quality (MAPQ>=30) were retained for analysis, allowing at most 1 fragment per unique coordinate
Paired reads were joined and converted to bigWigs normalized to total number of retained fragments per million, using bedtools v2.30.0 genomecov and wigToBigWig
Assembly: X. laevis v10.1
Supplementary files format and content: bigWig files of coverage pooled across replicates
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol:
CUT&RUN procedure was based on Hainer et al Cell 2019 and Skene et. al. Nature Protocols 2019. 12 embryos per sample were collected, devitellinized in 1mg/mL pronase, dissolved in MR/3, and cells were dissociated in 1 mL of NP2.0 buffer (Briggs et al Science 2018) with gentle agitation. Dissociated cells were lysed in NE buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 500M spermidine, 0.1% Triton X-100, 20% glycerol) with gentle pipetting with a clipped P1000, and the lysate was centrifuged at 600xg in 4C for 3 min. The free nuclei were then bound to 300 L of activated concanavalin A beads at RT for 10mins. Nuclei were blocked for 5 min at RT then incubated in 1:100 dilution of primary antibody for 2 hr at 4C, washed, incubated in a 1:200 dilution of pA/G MNase for 1 hr at 4C, and washed again. The bound MNase was activated with 2 mM CaCl2 and allowed to digest for 30 mins, then stopped using 2x STOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 g/mL RNase A, 40 g/mL glycogen). Nuclei were incubated at 37C for 20 min followed by centrifuging for 5 min at 16,000xg, drawing off the DNA fragments with the supernatant. The extracted fragments were treated with SDS and proteinase K at 70C for 10 min followed by phenol chloroform extraction. Purified DNA was resuspended in 50 L of water and verified by Qubit dsDNA high sensitivity and Fragment Analyzer.
Sequencing libraries were built using the NEB Next Ultra II library build kit (E7645S) and size selected on an agarose gel to 150-600 bp. Libraries were multiplexed and sequenced paired-end at the Health Sciences Sequencing Core at Children’s Hospital of Pittsburgh.

treatment_protocol: For transcription factor CUT&RUN, WT embryos were injected at Stage 1 with 400 pg of N-terminal V5 tagged pou5f3.3.L or sox3.S mRNA.

tag: antibody


title: Stage 10.5 H3K27ac

value: ActiveMotif #39135


title: Stage 8 Pou5f3.3 no antibody

value: Injected with 400 pg V5-pou5f3.3 mRNA


title: Stage 9 CHX sox3 MO rep C1

description:
s9_chx_sox_mo_c_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: Whole embryos


title: Stage 8 Sox3 no antibody

value: WT

value: Injected with 400 pg V5-sox3 mRNA


title: Stage 8 Sox3 V5

value: Invitrogen #R960-25


title: Stage 9 CHX GFP MO rep C1

description:
s9_chx_gfp_mo_c_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 H3K27ac rep 1


title: Stage 9 H3K4me3 rep 1

value: Millipore #05-745R


title: Stage 9 H3K27ac rep 2


title: Stage 9 H3K4me3 rep 2


title: Stage 8 H3K27ac rep 2


title: Stage 8 no antibody


title: Stage 9 animal cap ATAC rep 2

description:
s9_pool_open_hq_v10.1.bw
s9_open_v10.1.narrowPeak

data_processing:
Reads were mapped to the X. laevis v10.1 genome using bowtie2 2.4.2 (--no-mixed --no-discordant -X2000), discarding reads on the mitochondrial chromosome. High quality (MAPQ>=30) sub-nucleosomal sized fragments (<=130 bp) were retained for analysis, allowing at most 1 fragment per unique coordinate
bigWigs were pooled across replicates and normalized to total number of retained fragments per million, using bedtools v2.30.0 genomecov and wigToBigWig. MACS 2.2.7.1 was used to call peaks on open fragments
Assembly: X. laevis v10.1
Supplementary files format and content: bigWig files of open chromatin coverage pooled across replicates, narrowPeak file of MACS peaks of open chromatin

source_name: animal cap

extract_protocol:
ATAC procedure was based on Esmaeili et al Dev Biol 2020. Dejellied embryos were incubated in MR/3 (33 mM NaCl, 0.6 mM KCl, 0.67 mM CaCl2, 0.33 mM MgCl2, 1.67 mM HEPES, pH 7.8) at 23C until desired NF stage and then devitellinized with 1 mg/mL pronase. Ectodermal explants (animal caps) were dissected using watch-maker forceps in 0.7x MR. Two caps were used per transposition reaction. Caps were washed in ice cold PBS and centrifuged at 500xg in 4C for 5mins twice. Caps were washed again and lysed in 50 µl of RSB buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630) with a clipped P200 pipet. The lysate was pelleted at 500xg in 4C for 10 min and resuspended in in 47.5 µl TD buffer (10 mM Tris pH 7.6, 5 mM MgCl2, 10% dimethylformamide) and 2.5 µl of 3 µM Tn5 transposome (Addgene #112112). Nuclei were transposed with gentle shaking for 1 hr at 37C before adding 2.5 µl proteinase K and incubating overnight at 37C.
Transposed DNA was purified using EconoSpin Micro columns (Epoch) and amplified using 25 µM indexed Nextera primers with Thermo Phusion Flash master mix for 12 cycles. The amplified library was column cleaned and verified by Qubit dsDNA high sensitivity and Fragment Analyzer and sequenced multiplexed paired end at the Health Sciences Sequencing Core at Children’s Hospital of Pittsburgh. For reps 1 and 2, after initial sequencing, libraries were subsequently size selected on an agarose gel to enrich for 150-250 and 250-600 bp fragments and resequenced pooled. For reps 3 and 4, libraries were only size selected for 150-250 bp.

value: animal cap


title: Stage 8 H3K4me3


title: Stage 8 H3K27ac rep 1


title: Stage 6

description:
s6_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 5 (COX2, COX3 deplete) rep 1

description:
s5_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 8 animal cap ATAC rep 2 size selected


title: Stage 8 animal cap ATAC rep 1 size selected


title: Stage 9 animal cap ATAC rep 1 size selected


title: Stage 9 CHX rep B2

description:
s9_chx_b_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv

value: cycloheximide


title: Stage 9 no antibody rep 1


title: Stage 9 animal cap ATAC rep 1


title: Stage 9 CHX pou5f3.3, sox3 MO high concen rep D2

description:
s9_chx_pou_sox_mo_high_d_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 8 Pou5f3.3 V5


title: Stage 9 DMSO rep B1

description:
s9_dmso_b_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Stage 9 CHX rep B1

description:
s9_chx_b_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Fat_044A

status: Public on Sep 08 2022

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

country: Japan

institute: Faculty of Medicine, Shimane University

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts derived with Subread:featureCount 1.46.p5.  CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCh38.76
Supplementary files format and content: The counts per million (CPM) reads were log-transformed (attached processed data file) and used to evaluate the effects of SC and ILT treatments in skeletal muscle and subcutaneous adipose tissue.

organism: Homo sapiens

source_name: Subcutaneous adipose tissue

growth_protocol: RNA was isolated from frozen skeletal muscle and subcutaneous adipose tissue samples obtained from people with obesity and type 2 diabetes before and after standard care (SC) and intensive lifestyle therapy (ILT) treatments.

extract_protocol:
Total RNA was isolated from frozen skeletal muscle and subcutaneous adipose tissue samples by using TRIzol Reagent (#15596018; Invitrogen) and RNeasy mini kit (Qiagen, Valencia, CA), respectively, in combination with an RNase-free DNase Set (Qiagen)
TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA)

tag: sample type

value: Before

value: ILT


title: Stage 9 DMSO rep B2

description:
s9_dmso_b_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Fat_043A

value: SC


title: Fat_040B

value: After


title: Stage 9 animal cap ATAC rep 2 size selected


title: Fat_040A


title: Fat_039B


title: Fat_033B


title: Fat_032B


title: Fat_032A


title: Fat_030B


title: Fat_026B


title: Fat_026A


title: Stage 8 animal cap ATAC rep 2


title: Fat_033A


title: Fat_025A


title: Fat_029B


title: Fat_021B


title: Fat_043B


title: Fat_039A


title: Fat_019B


title: Stage 9 triptolide rep B1

description:
s9_trip_b_1
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Fat_018A


title: Stage 8 animal cap ATAC rep 1


title: Fat_030A


title: Fat_013A


title: Fat_018B


title: Fat_013B


title: Fat_008A


title: Fat_008B


title: Fat_025B


title: Fat_004A


title: Fat_021A


title: Fat_019A


title: Fat_003A


title: Fat_029A


title: Fat_044B


title: Stage 9 triptolide rep B2

description:
s9_trip_b_2
Phelps23_exon_counts.csv
Phelps23_intron_counts.csv
Phelps23_exon_tpm.csv
Phelps23_intron_rpkm.csv


title: Muscle_044B

source_name: Skeletal muscle


title: Muscle_043A


title: Muscle_039B


title: Fat_003B


title: Muscle_043B


title: Muscle_039A


title: Muscle_040A


title: Fat_004B


title: Muscle_033A


title: Muscle_030A


title: Muscle_029A


title: Muscle_026A


title: Muscle_030B


title: Muscle_025B


title: Muscle_021B


title: Muscle_033B


title: Muscle_029B


title: Muscle_025A


title: Muscle_021A


title: Muscle_044A


title: Muscle_008A


title: Muscle_008B


title: Muscle_013A


title: Muscle_026B


title: Muscle_040B


title: Muscle_003A


title: Muscle_003B


title: Muscle_013B


title: Muscle_004A


title: Muscle_004B


title: MERFISH_10

status: Public on Apr 26 2022

type: RNA

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: Transcripts were selected for their specificity to cell types, or enrichment for microglia states.

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Encoded MERFISH images of RNA spots were de-multiplexed using MERlin https://github.com/emanuega/MERlin), using the codebook provided by Vizgen.  This pipeline outputs a table with the coordinates and identity of all detected transcripts. Decoded data were used to generate binary mosaics of the tissue in which transcripts represented a single pixel. Microglia were segmented using methods similar to those described by Favuzzi et al. Images of binary DAPI-identified nuclei were used to segment all other cell types. Counts tables were produced by summing the number of each transcript inside the area of segmented cells (Mg and DAPI-identified nuclei). Mg- and DAPI-segmentation counts were combined by concatenating their respective counts tables.

growth_protocol: Standard mouse housing conditions

extract_protocol: Brains were flash frozen in LN, then mounted in OCT. 10 micron-thick sections were mounted on pre-treated coverslips, fixed with 4% PFA, washed with PBS, then stored in ethanol. Coverslips were then processed via manufacturer's protocol.

treatment_protocol: Cx3cr1-GFP heterozgous mice were used to genetically label microglia. Genotypes were obtained through standard breeding.

value: Cx3cr1 GFP tg/+

value: S1 cortex


title: MERFISH_9


title: MERFISH_8


title: MERFISH_7


title: MERFISH_6


title: MERFISH_5


title: MERFISH_4


title: MERFISH_3


title: Case_5

status: Public on May 01 2022

type: genomic

city: Bethesda

first: Drew

last: Pratt

state: Maryland

address: 10 Center Drive, Building 10, Room 2S235

department: Laboratory of Pathology

institute: National Institutes of Health

description: Tumor

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: R package meffil v1.3.1

label: Cy5 and Cy3

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was bisulfite-converted with the EZ DNA Methylation Kitm (Zymo Research D5001)

value: M

tag: os_status (0=alive, 1=deceased)

tag: material

value: FFPE


title: MERFISH_1


title: Case_9

description: Tumor

value: Frozen


title: Case_4

description: Tumor

value: F


title: Case_8

description: Tumor


title: Case_7

description: Tumor


title: Genomic DNA from myxopapillary ependymoma 106

status: Public on Apr 25 2022

city: Hamburg

first: Michael

last: Bockmayr

address: Martinistr. 52

department: Pediatric Hematology and Oncology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing: Statistical analysis was performed using the minfi package version 1.30.0 with the statistical programming language R version 3.6.0

source_name: myxopapillary ependymoma 106

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

tag: mpe subtype

value: A

tag: histology

value: tanycytic


title: Genomic DNA from myxopapillary ependymoma 117

source_name: myxopapillary ependymoma 117

tag: Sex

value: male

tag: localization

value: lumbar

tag: resection

value: GTR

value: myxoid


title: Case_3

description: Tumor


title: Case_2

description: Tumor


title: Genomic DNA from myxopapillary ependymoma 104

source_name: myxopapillary ependymoma 104

value: female

tag: pfs [years]

tag: pfs status

value: NED

value: lumbosacral


title: Genomic DNA from myxopapillary ependymoma 105

source_name: myxopapillary ependymoma 105

value: B


title: Genomic DNA from myxopapillary ependymoma 103

source_name: myxopapillary ependymoma 103


title: Patient_12

status: Public on Aug 22 2022

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

hyb_protocol: Sodium bisulfite treated gDNA was amplified and enzymatically fragmented before hybridization to the microarray. After washing and staining, the microarray was scanned using the iScan device (Illumina).

scan_protocol: Infinium MethylationEPIC microarray platform

data_processing: Raw red/green channel *.idat files were imported into R using the RnBeads packages for initial quality  control, data normalization (SWAN) and extraction of β-values representing the percentage of  methylation for each CpG site on the microarray. SNP-enriched, cross-reactive, non-CpG  and sex chromosome specific probes were removed from further analyses. Unreliable  measurements were determined using the Greedycut algorithm implemented in RnBeads and  probes of highest impurity were iteratively removed from the dataset. Differential methylation  was calculated using limma and RnBead´s rank cutoff. The top 1000 differentially methylated  CpG sites were used for further analyses.

label: Cy3, Cy5

source_name: oligodendroglioma

label_protocol: 500ng of gDNA was sodium bisulfite converted using the EpiTect Fast DNA Bisulfite Kit (Qiagen, Germantown, MD, USA), processed using the Infinium HD FFPE DNA Restore Kit (Illumina, San Diego, CA, USA) and processed for microarray hybridization using Infinium MethylationEPIC Kit.

extract_protocol: Genomic DNA (gDNA) was extracted using the Maxwell FFPE Plus Kit (Promega, Madison, Wisconsin, USA).

tag: tissue

value: oligodendroglioma

tag: patient outcome

value: Benefit


title: Genomic DNA from myxopapillary ependymoma 102

source_name: myxopapillary ependymoma 102


title: Genomic DNA from myxopapillary ependymoma 107

source_name: myxopapillary ependymoma 107

value: relapsed


title: Genomic DNA from myxopapillary ependymoma 101

source_name: myxopapillary ependymoma 101


title: Genomic DNA from myxopapillary ependymoma 100

source_name: myxopapillary ependymoma 100

value: papillary


title: Patient_21


title: Patient_3


title: Genomic DNA from myxopapillary ependymoma 93

source_name: myxopapillary ependymoma 93

value: FFPE


title: Patient_15


title: Patient_7


title: Bap1 cKO rep2

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
The adapter sequences and the ends of the reads less than Phred quality score 20 were removed and simultaneously the reads shorter than 50 bp were removed by using cutadapt v.2.8. Filtered reads were mapped to the reference genomes using the aligner STAR v.2.7.1a.
Gene expression estimation was conducted by RSEM v.1.3.1.
To normalize sequencing depth among samples, FPKM and TPM values were calculated. Differentially expressed genes were identified using the R package called TCC v.1.26.0 based on the estimated read counts.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files including RPKM values for each sample

molecule: polyA RNA

source_name: endosteal mesenchymal stromal cells

extract_protocol:
Total RNA from control (n = 3) and Bap1 cKO (n = 3) endosteal MSCs were extracted using TRIzol reagent (Molecular Research Center) according to the manufacturer’s instructions.
The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina). These cDNA libraries were qualified with the Agilent 2100 BioAnalyzer (Agilent) and quantified with the KAPA library quantification kit (Kapa Biosystems) according to the manufacturer’s library protocol.

tag: strain

tag: genotype

value: Bap1 cKO (Prx1-cre;Bap1fl/fl)


title: Genomic DNA from myxopapillary ependymoma 92

source_name: myxopapillary ependymoma 92

tag: age


title: Patient_6


title: Bap1 cKO rep1


title: Patient_14


title: Genomic DNA from myxopapillary ependymoma 99

source_name: myxopapillary ependymoma 99


title: Bap1 WT rep3

value: Wild Type (Bap1fl/fl)


title: MERFISH_2

value: Cx3cr1 GFP tg/+

value: S1 cortex


title: Genomic DNA from myxopapillary ependymoma 90

source_name: myxopapillary ependymoma 90

value: male


title: Patient_11


title: Bap1 WT rep2


title: Genomic DNA from myxopapillary ependymoma 89

source_name: myxopapillary ependymoma 89

value: lumbar

value: tanycytic


title: Patient_2


title: Patient_5


title: Bap1 WT rep1


title: Genomic DNA from myxopapillary ependymoma 88

source_name: myxopapillary ependymoma 88

value: GTR


title: Patient_17


title: Patient_10


title: Genomic DNA from myxopapillary ependymoma 87

source_name: myxopapillary ependymoma 87

value: female

value: myxoid


title: Genomic DNA from myxopapillary ependymoma 85

source_name: myxopapillary ependymoma 85

value: NED


title: Genomic DNA from myxopapillary ependymoma 84

source_name: myxopapillary ependymoma 84

value: B


title: Genomic DNA from myxopapillary ependymoma 82

source_name: myxopapillary ependymoma 82


title: Genomic DNA from myxopapillary ependymoma 81

source_name: myxopapillary ependymoma 81

value: A

value: STR


title: Patient_18

source_name: oligodendroglioma

value: oligodendroglioma


title: Patient_9

value: Benefit


title: Patient_4


title: Genomic DNA from myxopapillary ependymoma 79

source_name: myxopapillary ependymoma 79

value: FFPE


title: Genomic DNA from myxopapillary ependymoma 78

source_name: myxopapillary ependymoma 78

value: lumbosacral


title: Genomic DNA from myxopapillary ependymoma 77

source_name: myxopapillary ependymoma 77


title: Genomic DNA from myxopapillary ependymoma 76

source_name: myxopapillary ependymoma 76

value: thoracic

value: papillary


title: Patient_1


title: Genomic DNA from myxopapillary ependymoma 72

source_name: myxopapillary ependymoma 72


title: Patient_20


title: Genomic DNA from myxopapillary ependymoma 68

source_name: myxopapillary ependymoma 68


title: Genomic DNA from myxopapillary ependymoma 75

source_name: myxopapillary ependymoma 75


title: Genomic DNA from myxopapillary ependymoma 73

source_name: myxopapillary ependymoma 73


title: Genomic DNA from myxopapillary ependymoma 71

source_name: myxopapillary ependymoma 71


title: Patient_16


title: Genomic DNA from myxopapillary ependymoma 70

source_name: myxopapillary ependymoma 70


title: Genomic DNA from myxopapillary ependymoma 69

source_name: myxopapillary ependymoma 69


title: Genomic DNA from myxopapillary ependymoma 63

source_name: myxopapillary ependymoma 63


title: Patient_13


title: Patient_19


title: Genomic DNA from myxopapillary ependymoma 61

source_name: myxopapillary ependymoma 61


title: Genomic DNA from myxopapillary ependymoma 62

source_name: myxopapillary ependymoma 62


title: Genomic DNA from myxopapillary ependymoma 60

source_name: myxopapillary ependymoma 60

value: sacral


title: Genomic DNA from myxopapillary ependymoma 50

source_name: myxopapillary ependymoma 50

value: male


title: Genomic DNA from myxopapillary ependymoma 49

source_name: myxopapillary ependymoma 49


title: Genomic DNA from myxopapillary ependymoma 47

source_name: myxopapillary ependymoma 47

value: lumbar


title: Genomic DNA from myxopapillary ependymoma 46

source_name: myxopapillary ependymoma 46

value: tanycytic


title: Genomic DNA from myxopapillary ependymoma 45

source_name: myxopapillary ependymoma 45


title: Genomic DNA from myxopapillary ependymoma 43

source_name: myxopapillary ependymoma 43

value: Frozen


title: Genomic DNA from myxopapillary ependymoma 42

source_name: myxopapillary ependymoma 42


title: Genomic DNA from myxopapillary ependymoma 185

source_name: myxopapillary ependymoma 185


title: Genomic DNA from myxopapillary ependymoma 41

source_name: myxopapillary ependymoma 41

value: female


title: Genomic DNA from myxopapillary ependymoma 183

source_name: myxopapillary ependymoma 183


title: Genomic DNA from myxopapillary ependymoma 38

source_name: myxopapillary ependymoma 38


title: Genomic DNA from myxopapillary ependymoma 91

source_name: myxopapillary ependymoma 91

value: myxoid


title: Genomic DNA from myxopapillary ependymoma 37

source_name: myxopapillary ependymoma 37

value: relapsed


title: Genomic DNA from myxopapillary ependymoma 40

source_name: myxopapillary ependymoma 40

value: B

value: NED


title: Genomic DNA from myxopapillary ependymoma 35

source_name: myxopapillary ependymoma 35


title: Genomic DNA from myxopapillary ependymoma 39

source_name: myxopapillary ependymoma 39


title: Genomic DNA from myxopapillary ependymoma 44

source_name: myxopapillary ependymoma 44

value: A


title: Patient_8

source_name: oligodendroglioma

value: oligodendroglioma


title: Genomic DNA from myxopapillary ependymoma 182

source_name: myxopapillary ependymoma 182


title: Genomic DNA from myxopapillary ependymoma 98

source_name: myxopapillary ependymoma 98

value: STR


title: Genomic DNA from myxopapillary ependymoma 180

source_name: myxopapillary ependymoma 180


title: Genomic DNA from myxopapillary ependymoma 33

source_name: myxopapillary ependymoma 33

value: FFPE

value: thoracolumbar


title: Genomic DNA from myxopapillary ependymoma 181

source_name: myxopapillary ependymoma 181


title: Genomic DNA from myxopapillary ependymoma 179

source_name: myxopapillary ependymoma 179


title: Genomic DNA from myxopapillary ependymoma 178

source_name: myxopapillary ependymoma 178


title: Genomic DNA from myxopapillary ependymoma 184

source_name: myxopapillary ependymoma 184


title: Bap1 cKO rep3

source_name: endosteal mesenchymal stromal cells

value: Bap1 cKO (Prx1-cre;Bap1fl/fl)


title: Genomic DNA from myxopapillary ependymoma 31

source_name: myxopapillary ependymoma 31

value: GTR


title: Genomic DNA from myxopapillary ependymoma 177

source_name: myxopapillary ependymoma 177


title: Genomic DNA from myxopapillary ependymoma 29

source_name: myxopapillary ependymoma 29


title: Genomic DNA from myxopapillary ependymoma 176

source_name: myxopapillary ependymoma 176


title: Genomic DNA from myxopapillary ependymoma 175

source_name: myxopapillary ependymoma 175


title: Genomic DNA from myxopapillary ependymoma 36

source_name: myxopapillary ependymoma 36

value: cerebral

value: papillary


title: Genomic DNA from myxopapillary ependymoma 173

source_name: myxopapillary ependymoma 173


title: Genomic DNA from myxopapillary ependymoma 172

source_name: myxopapillary ependymoma 172


title: Genomic DNA from myxopapillary ependymoma 27

source_name: myxopapillary ependymoma 27

value: male

value: lumbar


title: Genomic DNA from myxopapillary ependymoma 26

source_name: myxopapillary ependymoma 26

value: tanycytic


title: Genomic DNA from myxopapillary ependymoma 171

source_name: myxopapillary ependymoma 171

value: Frozen


title: Genomic DNA from myxopapillary ependymoma 174

source_name: myxopapillary ependymoma 174


title: Genomic DNA from myxopapillary ependymoma 25

source_name: myxopapillary ependymoma 25

value: female

value: lumbosacral

value: myxoid


title: Genomic DNA from myxopapillary ependymoma 24

source_name: myxopapillary ependymoma 24

value: B

value: NED


title: Genomic DNA from myxopapillary ependymoma 169

source_name: myxopapillary ependymoma 169


title: Genomic DNA from myxopapillary ependymoma 22

source_name: myxopapillary ependymoma 22


title: Genomic DNA from myxopapillary ependymoma 167

source_name: myxopapillary ependymoma 167


title: Genomic DNA from myxopapillary ependymoma 170

source_name: myxopapillary ependymoma 170


title: Genomic DNA from myxopapillary ependymoma 166

source_name: myxopapillary ependymoma 166


title: Genomic DNA from myxopapillary ependymoma 168

source_name: myxopapillary ependymoma 168


title: Genomic DNA from myxopapillary ependymoma 165

source_name: myxopapillary ependymoma 165


title: Genomic DNA from myxopapillary ependymoma 164

source_name: myxopapillary ependymoma 164

value: A


title: Genomic DNA from myxopapillary ependymoma 86

source_name: myxopapillary ependymoma 86


title: Genomic DNA from myxopapillary ependymoma 19

source_name: myxopapillary ependymoma 19

value: relapsed


title: Genomic DNA from myxopapillary ependymoma 30

source_name: myxopapillary ependymoma 30

value: FFPE


title: Genomic DNA from myxopapillary ependymoma 17

source_name: myxopapillary ependymoma 17


title: Genomic DNA from myxopapillary ependymoma 15

source_name: myxopapillary ependymoma 15


title: Genomic DNA from myxopapillary ependymoma 162

source_name: myxopapillary ependymoma 162


title: Genomic DNA from myxopapillary ependymoma 161

source_name: myxopapillary ependymoma 161


title: Genomic DNA from myxopapillary ependymoma 160

source_name: myxopapillary ependymoma 160


title: Genomic DNA from myxopapillary ependymoma 13

source_name: myxopapillary ependymoma 13


title: Genomic DNA from myxopapillary ependymoma 20

source_name: myxopapillary ependymoma 20


title: Genomic DNA from myxopapillary ependymoma 21

source_name: myxopapillary ependymoma 21

value: thoracolumbar


title: Genomic DNA from myxopapillary ependymoma 11

source_name: myxopapillary ependymoma 11

value: STR


title: Genomic DNA from myxopapillary ependymoma 9

source_name: myxopapillary ependymoma 9

value: GTR


title: Genomic DNA from myxopapillary ependymoma 12

source_name: myxopapillary ependymoma 12


title: Genomic DNA from myxopapillary ependymoma 97

source_name: myxopapillary ependymoma 97


title: Genomic DNA from myxopapillary ependymoma 10

source_name: myxopapillary ependymoma 10


title: Genomic DNA from myxopapillary ependymoma 96

source_name: myxopapillary ependymoma 96


title: Genomic DNA from myxopapillary ependymoma 94

source_name: myxopapillary ependymoma 94

value: thoracic


title: Genomic DNA from myxopapillary ependymoma 95

source_name: myxopapillary ependymoma 95


title: Genomic DNA from myxopapillary ependymoma 8

source_name: myxopapillary ependymoma 8


title: Genomic DNA from myxopapillary ependymoma 7

source_name: myxopapillary ependymoma 7


title: Genomic DNA from myxopapillary ependymoma 59

source_name: myxopapillary ependymoma 59


title: Genomic DNA from myxopapillary ependymoma 18

source_name: myxopapillary ependymoma 18


title: Genomic DNA from myxopapillary ependymoma 5

source_name: myxopapillary ependymoma 5


title: Genomic DNA from myxopapillary ependymoma 6

source_name: myxopapillary ependymoma 6


title: Genomic DNA from myxopapillary ependymoma 58

source_name: myxopapillary ependymoma 58


title: Genomic DNA from myxopapillary ependymoma 4

source_name: myxopapillary ependymoma 4

value: papillary


title: Genomic DNA from myxopapillary ependymoma 16

source_name: myxopapillary ependymoma 16

value: male


title: Genomic DNA from myxopapillary ependymoma 163

source_name: myxopapillary ependymoma 163


title: Genomic DNA from myxopapillary ependymoma 3

source_name: myxopapillary ependymoma 3


title: Genomic DNA from myxopapillary ependymoma 1

source_name: myxopapillary ependymoma 1

value: lumbar


title: Genomic DNA from myxopapillary ependymoma 2

source_name: myxopapillary ependymoma 2


title: Genomic DNA from myxopapillary ependymoma 14

source_name: myxopapillary ependymoma 14


title: WT_LPS4hr

status: Public on Apr 24 2022

city: Los Angeles

first: Katherine

middle: M

last: Sheu

state: CA

address: 611 Charles E Young Dr E

institute: UCLA

data_processing:
Raw fastq files were aligned to mm10 using bwa following the ENCODE ATAC-seq pipeline. Two versions of bigwig files were generated by the fold enrichment of signal over expected background, and a p-value track representing statistical significance.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: macrophage

extract_protocol: Used the protocol from Buenrostro et al, 2015

tag: cell type

value: myeloid-progenitor-derived-macrophage

tag: treatment

value: LPS

tag: time point

value: WT


title: Genomic DNA from myxopapillary ependymoma 159

source_name: myxopapillary ependymoma 159


title: WT_LPS0hr

value: untreated


title: 4KO_4hr

tag: strain background

tag: genotype/variation

value: Rel-/-Tnf-/-Nfkbie-/-Nfkbia-/-

value: bone-marrow-derived-macrophage (BMDM)


title: X_8

status: Public on Mar 31 2022

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description:
X_8
Bulk RNA-seq
counts.csv

data_processing:
Bulk RNA-seq was aligned using the STAR software, and counted using featureCounts.
Single-nuclei RNA-seq was aligned using the CellRanger software (10x).
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: counts.csv: Counts data for bulk RNA-seq.
Supplementary_files_format_and_content: HM*.csv: Counts for single-nuclei RNA-seq.

source_name: Skeletal muscle

extract_protocol:
Bulk RNA-seq: Muscle biopsies were homogenized using a mortar and pestle with liquid nitrogen. RNA was extracted from the powdered samples using the RNeasy Fibrous Tissue Mini Kit (Qiagen) and the QIAcube automatic processor (Qiagen). Integrity and concentration of the RNA were assessed using the Tapestation 4200 (Agilent Technologies), with the cut-off for acceptable integrity being an RNA integrity number (RIN) >7.
Batch-tag-seq libraries were then produced from the RNA and run on the HiSeq 4000 by the DNA Technologies Core at U.C. Davis.
Single-nuclei RNA-seq: Nuclei were isolated from the biopsies using the Singulator instrument (S2 Genomics). The instrument was primed with cold nuclei isolation and storage buffers (S2 Genomics) and the biopsy was loaded into the cartridge and covered with the 19.7 mm grinding cap. The “Nuclei_All_Tissues” protocol was used to isolate nuclei, after which the nuclei were centrifuged for 5 minutes and resuspended in buffer. The nuclei were counted using a Countess II Automated Cell Counter (Invitrogen), centrifuged again for 5 minutes and resuspended at the proper concentration for use in the Chromium Single Cell 5’ Library and Gel Bead Kit v1 (10X Genomics).
Samples were processed using the Chromium Single Cell A Chip Kit and Chromium Controller (10X Genomics). Quality control was performed on the Tapestation 4200 (Agilent Technologies). Libraries were sequenced in one lane of a NovaSeqS4 by the U.C. Davis Genomics Core.

tag: group

value: Old Healthy

value: Skeletal muscle

tag: 6 min walk test (m/s)

tag: biodex (kg)

tag: time up and go (s)

tag: sppb

tag: grip strength (kg)

tag: leg press (kg)


title: X_81

description:
X_81
Bulk RNA-seq
counts.csv

value: Sarcopenia

tag: tissue


title: X_80

description:
X_80
Bulk RNA-seq
counts.csv


title: 4KO_0hr

value: none; untreated


title: X_7

description:
X_7
Bulk RNA-seq
counts.csv


title: responder_rep4

status: Public on Apr 07 2022

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: BALF derived from responders

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000 systems, with 101 bp single-end reads obtained.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: BALF derived from responders

extract_protocol:
RNA was extracted from BALF cells stored in RNAlater. An miRNeasy Mini Kit (Qiagen) was utilized for total RNA extraction.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio). An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina) according to the SMARTer Kit instructions.

tag: cell line

value: bronchoalveolar lavage fluid


title: X_75

description:
X_75
Bulk RNA-seq
counts.csv


title: X_78

description:
X_78
Bulk RNA-seq
counts.csv


title: X_74

description:
X_74
Bulk RNA-seq
counts.csv


title: X_76

description:
X_76
Bulk RNA-seq
counts.csv


title: X_72

description:
X_72
Bulk RNA-seq
counts.csv


title: X_71

description:
X_71
Bulk RNA-seq
counts.csv


title: X_70

description:
X_70
Bulk RNA-seq
counts.csv

value: UNCLASSIFIED


title: X_6

description:
X_6
Bulk RNA-seq
counts.csv


title: X_77

description:
X_77
Bulk RNA-seq
counts.csv


title: X_67

description:
X_67
Bulk RNA-seq
counts.csv

value: Young Healthy


title: X_68

description:
X_68
Bulk RNA-seq
counts.csv


title: Genomic DNA from myxopapillary ependymoma 74

source_name: myxopapillary ependymoma 74

tag: Sex

value: female

tag: mpe subtype

value: B

tag: material

value: FFPE

tag: pfs [years]

tag: pfs status

value: NED

tag: localization

tag: resection

value: GTR


title: X_66

description:
X_66
Bulk RNA-seq
counts.csv

tag: age


title: Genomic DNA from myxopapillary ependymoma 80

source_name: myxopapillary ependymoma 80

value: male

tag: histology

value: myxoid


title: X_9

description:
X_9
Bulk RNA-seq
counts.csv

tag: group

tag: 6 min walk test (m/s)


title: X_61

description:
X_61
Bulk RNA-seq
counts.csv

tag: biodex (kg)

tag: time up and go (s)


title: X_62

description:
X_62
Bulk RNA-seq
counts.csv

tag: sppb

tag: grip strength (kg)


title: X_63

description:
X_63
Bulk RNA-seq
counts.csv

tag: tissue

tag: leg press (kg)


title: X_73

description:
X_73
Bulk RNA-seq
counts.csv


title: X_65

description:
X_65
Bulk RNA-seq
counts.csv


title: X_64

description:
X_64
Bulk RNA-seq
counts.csv


title: X_79

description:
X_79
Bulk RNA-seq
counts.csv


title: X_59

description:
X_59
Bulk RNA-seq
counts.csv


title: X_60

description:
X_60
Bulk RNA-seq
counts.csv


title: X_57

description:
X_57
Bulk RNA-seq
counts.csv


title: X_58

description:
X_58
Bulk RNA-seq
counts.csv


title: X_56

description:
X_56
Bulk RNA-seq
counts.csv


title: X_54

description:
X_54
Bulk RNA-seq
counts.csv


title: X_51

description:
X_51
Bulk RNA-seq
counts.csv


title: X_52

description:
X_52
Bulk RNA-seq
counts.csv


title: X_47

description:
X_47
Bulk RNA-seq
counts.csv


title: X_50

description:
X_50
Bulk RNA-seq
counts.csv


title: X_49

description:
X_49
Bulk RNA-seq
counts.csv


title: X_53

description:
X_53
Bulk RNA-seq
counts.csv


title: X_4

description:
X_4
Bulk RNA-seq
counts.csv


title: X_45

description:
X_45
Bulk RNA-seq
counts.csv


title: X_41

description:
X_41
Bulk RNA-seq
counts.csv


title: X_40

description:
X_40
Bulk RNA-seq
counts.csv


title: X_33

description:
X_33
Bulk RNA-seq
counts.csv


title: X_43

description:
X_43
Bulk RNA-seq
counts.csv


title: X_3

description:
X_3
Bulk RNA-seq
counts.csv


title: X_32

description:
X_32
Bulk RNA-seq
counts.csv


title: X_46

description:
X_46
Bulk RNA-seq
counts.csv


title: X_38

description:
X_38
Bulk RNA-seq
counts.csv


title: X_44

description:
X_44
Bulk RNA-seq
counts.csv


title: X_42

description:
X_42
Bulk RNA-seq
counts.csv


title: X_37

description:
X_37
Bulk RNA-seq
counts.csv


title: X_39

description:
X_39
Bulk RNA-seq
counts.csv


title: X_29

description:
X_29
Bulk RNA-seq
counts.csv


title: X_30

description:
X_30
Bulk RNA-seq
counts.csv


title: X_27

description:
X_27
Bulk RNA-seq
counts.csv


title: X_26

description:
X_26
Bulk RNA-seq
counts.csv


title: X_25

description:
X_25
Bulk RNA-seq
counts.csv


title: X_55

description:
X_55
Bulk RNA-seq
counts.csv


title: X_22

description:
X_22
Bulk RNA-seq
counts.csv


title: X_20

description:
X_20
Bulk RNA-seq
counts.csv


title: X_23

description:
X_23
Bulk RNA-seq
counts.csv


title: X_35

description:
X_35
Bulk RNA-seq
counts.csv


title: X_21

description:
X_21
Bulk RNA-seq
counts.csv


title: X_48

description:
X_48
Bulk RNA-seq
counts.csv


title: X_24

description:
X_24
Bulk RNA-seq
counts.csv


title: X_2

description:
X_2
Bulk RNA-seq
counts.csv


title: X_17

description:
X_17
Bulk RNA-seq
counts.csv


title: X_16

description:
X_16
Bulk RNA-seq
counts.csv


title: X_19

description:
X_19
Bulk RNA-seq
counts.csv


title: X_18

description:
X_18
Bulk RNA-seq
counts.csv


title: X_14

description:
X_14
Bulk RNA-seq
counts.csv


title: X_15

description:
X_15
Bulk RNA-seq
counts.csv


title: X_10

description:
X_10
Bulk RNA-seq
counts.csv


title: X_13

description:
X_13
Bulk RNA-seq
counts.csv


title: X_1

description:
X_1
Bulk RNA-seq
counts.csv


title: OldHM23

description:
HM23
Single-nuclei RNA-seq

value: Old


title: YouHM21

description:
HM21
Single-nuclei RNA-seq

value: Young


title: OldHM11

description:
HM11
Single-nuclei RNA-seq


title: YouHM13

description:
HM13
Single-nuclei RNA-seq


title: OldHM15

description:
HM15
Single-nuclei RNA-seq


title: OldHM9

description:
HM9
Single-nuclei RNA-seq


title: OldHM12

description:
HM12
Single-nuclei RNA-seq


title: YouHM10

description:
HM10
Single-nuclei RNA-seq


title: YouHM8

description:
HM8
Single-nuclei RNA-seq


title: X_34

description:
X_34
Bulk RNA-seq
counts.csv


title: OldHM7

description:
HM7
Single-nuclei RNA-seq


title: OldHM2

description:
HM2
Single-nuclei RNA-seq


title: OldHM3

description:
HM3
Single-nuclei RNA-seq


title: OldHM4

description:
HM4
Single-nuclei RNA-seq


title: X_5

description:
X_5
Bulk RNA-seq
counts.csv


title: YouHM5

description:
HM5
Single-nuclei RNA-seq


title: X_11

description:
X_11
Bulk RNA-seq
counts.csv


title: YouHM22

description:
HM22
Single-nuclei RNA-seq


title: 971PSQ333 [Subcutaneous adipose tissue]

status: Public on Oct 01 2021

description:
Baseline
971PSQ333

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts derived with Subread:featureCount 1.46.p5.  RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCh38.76
Supplementary_files_format_and_content: The counts per million (CPM) reads were log-transformed (attached processed data file) and used to select genes that were significantly (P<0.005) positively and negatively associated with AT pO2 by using Pearson’s correlation.

source_name: Subcutaneous adipose tissue

growth_protocol: RNA was isolated from frozen subcutaneous adipose tissue samples obtained from people who were metabolically-healthy lean (MHL), metabolically-healthy obese (MHO), and metabolically-unhealthy obese (MUO).

extract_protocol:
RNA was harvested using Qiazol Reagent with Rneasy Mini Kit (Qiagen).
TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA)

tag: tag

value: Ob-NAFLD


title: 973PSQ354 [Subcutaneous adipose tissue]

description:
Baseline
973PSQ354


title: 980PSQ441 [Subcutaneous adipose tissue]

description:
Baseline
980PSQ441


title: 276PE028 [Subcutaneous adipose tissue]

description:
Baseline
276PE028


title: 270PE004 [Subcutaneous adipose tissue]

description:
Baseline
270PE004


title: 978PSQ405 [Subcutaneous adipose tissue]

description:
Baseline
978PSQ405


title: 551PE041 [Subcutaneous adipose tissue]

description:
Baseline
551PE041


title: 968PSQ297 [Subcutaneous adipose tissue]

description:
Baseline
968PSQ297


title: 970PSQ326 [Subcutaneous adipose tissue]

description:
Baseline
970PSQ326


title: 974PSQ360 [Subcutaneous adipose tissue]

description:
Baseline
974PSQ360


title: 967PSQ294 [Subcutaneous adipose tissue]

description:
Baseline
967PSQ294


title: 558PSQ255 [Subcutaneous adipose tissue]

description:
Baseline
558PSQ255


title: OldHM6

description:
HM6
Single-nuclei RNA-seq


title: 563PE040 [Subcutaneous adipose tissue]

description:
Baseline
563PE040


title: 271PE006 [Subcutaneous adipose tissue]

description:
Baseline
271PE006


title: 556PSQ251 [Subcutaneous adipose tissue]

description:
Baseline
556PSQ251


title: 273PE009 [Subcutaneous adipose tissue]

description:
Baseline
273PE009


title: OldHM1

description:
HM1
Single-nuclei RNA-seq


title: 269PSQ199 [Subcutaneous adipose tissue]

description:
Baseline
269PSQ199


title: 264PSQ070 [Subcutaneous adipose tissue]

description:
Baseline
264PSQ070


title: 964PSQ007 [Subcutaneous adipose tissue]

description:
Baseline
964PSQ007


title: 962PSQ428 [Subcutaneous adipose tissue]

description:
Baseline
962PSQ428

value: Ob-NL


title: 266PSQ137 [Subcutaneous adipose tissue]

description:
Baseline
266PSQ137


title: 961PSQ426 [Subcutaneous adipose tissue]

description:
Baseline
961PSQ426


title: 975PSQ366 [Subcutaneous adipose tissue]

description:
Baseline
975PSQ366


title: 963PSQ472 [Subcutaneous adipose tissue]

description:
Baseline
963PSQ472


title: 959PSQ340 [Subcutaneous adipose tissue]

description:
Baseline
959PSQ340


title: 966PSQ266 [Subcutaneous adipose tissue]

description:
Baseline
966PSQ266


title: 958PSQ332 [Subcutaneous adipose tissue]

description:
Baseline
958PSQ332


title: 560PSQ267 [Subcutaneous adipose tissue]

description:
Baseline
560PSQ267


title: 957PSQ291 [Subcutaneous adipose tissue]

description:
Baseline
957PSQ291


title: 258PSQ168 [Subcutaneous adipose tissue]

description:
Baseline
258PSQ168


title: 253PSQ127 [Subcutaneous adipose tissue]

description:
Baseline
253PSQ127


title: 256PSQ161 [Subcutaneous adipose tissue]

description:
Baseline
256PSQ161


title: 257PSQ162 [Subcutaneous adipose tissue]

description:
Baseline
257PSQ162


title: 248PSQ089 [Subcutaneous adipose tissue]

description:
Baseline
248PSQ089


title: 559PSQ256 [Subcutaneous adipose tissue]

description:
Baseline
559PSQ256


title: 564PSQ170 [Subcutaneous adipose tissue]

description:
Baseline
564PSQ170


title: 252PSQ120 [Subcutaneous adipose tissue]

description:
Baseline
252PSQ120


title: 244PSQ034 [Subcutaneous adipose tissue]

description:
Baseline
244PSQ034


title: 268PSQ191 [Subcutaneous adipose tissue]

description:
Baseline
268PSQ191


title: 251PSQ115 [Subcutaneous adipose tissue]

description:
Baseline
251PSQ115


title: 242PSQ027 [Subcutaneous adipose tissue]

description:
Baseline
242PSQ027


title: 239PSQ019 [Subcutaneous adipose tissue]

description:
Baseline
239PSQ019


title: 240PSQ023 [Subcutaneous adipose tissue]

description:
Baseline
240PSQ023


title: 567PSQ271 [Subcutaneous adipose tissue]

description:
Baseline
567PSQ271

value: Lean-NL


title: 954PSQ454 [Subcutaneous adipose tissue]

description:
Baseline
954PSQ454


title: 566PSQ236 [Subcutaneous adipose tissue]

description:
Baseline
566PSQ236


title: 237PSQ013 [Subcutaneous adipose tissue]

description:
Baseline
237PSQ013


title: 952PSQ252 [Subcutaneous adipose tissue]

description:
Baseline
952PSQ252


title: 555PSQ250 [Subcutaneous adipose tissue]

description:
Baseline
555PSQ250


title: 234PSQ204 [Subcutaneous adipose tissue]

description:
Baseline
234PSQ204


title: 232PSQ147 [Subcutaneous adipose tissue]

description:
Baseline
232PSQ147


title: 230PSQ128 [Subcutaneous adipose tissue]

description:
Baseline
230PSQ128


title: 255PSQ146 [Subcutaneous adipose tissue]

description:
Baseline
255PSQ146


title: 552PSQ064 [Subcutaneous adipose tissue]

description:
Baseline
552PSQ064


title: 194PSQ116 [Subcutaneous adipose tissue]

description:
Baseline
194PSQ116


title: MUO_563PE040

tag: time point

value: Baseline

tag: condition

value: MUO

value: Subcutaneous adipose tissue


title: MUO_275PE012


title: 229PSQ073 [Subcutaneous adipose tissue]

description:
Baseline
229PSQ073


title: MUO_276PE028


title: MUO_270PE004


title: MUO_274PE011


title: MUO_273PE009


title: MUO_551PE041


title: MUO_973PSQ354


title: MUO_975PSQ366


title: MUO_271PE006


title: MUO_980PSQ441


title: MUO_970PSQ326


title: MUO_968PSQ297


title: MUO_971PSQ333


title: MUO_272PE007


title: MUO_556PSQ251


title: MUO_562PSQ286


title: MUO_972PSQ343


title: MUO_981PSQ469


title: MUO_558PSQ255


title: MUO_553PSQ185


title: MUO_266PSQ137


title: 233PSQ150 [Subcutaneous adipose tissue]

description:
Baseline
233PSQ150


title: MUO_268PSQ191


title: MUO_964PSQ007


title: MUO_260PSQ001


title: MUO_265PSQ086


title: MHO_959PSQ340

value: MHO


title: MHO_958PSQ332


title: MHO_559PSQ256


title: MHO_957PSQ291


title: MHO_257PSQ162


title: MHO_258PSQ168


title: MHO_256PSQ161


title: MUO_269PSQ199


title: MHO_564PSQ170


title: MHO_253PSQ127


title: MHO_255PSQ146


title: MHO_254PSQ139


title: MHO_259PSQ194


title: MHO_252PSQ120


title: MHO_249PSQ100


title: MHO_248PSQ089


title: MHO_247PSQ072


title: MHO_245PSQ042


title: MHO_244PSQ034


title: MHO_240PSQ023


title: MHO_246PSQ052


title: MHL_954PSQ454

value: MHL


title: MHO_235BPSQ004


title: MHO_237PSQ013


title: MHO_236PSQ005


title: MHL_561PSQ285


title: MHL_567PSQ271


title: MHL_952PSQ252


title: MHL_555PSQ250


title: MHL_233PSQ150


title: MHL_234PSQ204


title: MHL_232PSQ147


title: MHL_229PSQ073


title: MHL_230PSQ128


title: MHL_566PSQ236


title: MHO_251PSQ115


title: MHO_243PSQ031


title: MHL_194PSQ116


title: MHL_231PSQ141


title: MHL_552PSQ064


title: mock-1

status: Public on Sep 10 2021

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

description:
morrison_count_matrix.tsv.gz
morrison_metadata.tsv.gz

data_processing:
Single-cell RNA-seq libraries were processed using the 10X Genomics cellranger software (5.0.1). Analysis was performed using the R package Seurat (4.0.0). Cell type identification was performed with clustifyr (1.0.0) using references built from published data.
Supplementary_files_format_and_content: Cellranger output files

source_name: Lymph node

growth_protocol: Mice were housed and bred at the University of Colorado School of Medicine under specific pathogen-free conditions and were distributed randomly into groups containing approximately even division of sexes for experiments. WT male mice were purchased commercially and were age matched and distributed randomly across groups. Mice 4 weeks of age were used in all experiments. All mouse experiments were performed under animal biosafety level 2 or 3 conditions, as appropriate.

extract_protocol:
At 24 hpi the draining popliteal lymph node from mock- or CHIKV-inoculated mice were pooled into individual replicates (3 replicates; LNs from 5 mice pooled per replicate). Lymph nodes were mechanically homogenized using a 22G needle in Click’s medium (Irvine Scientific, 9195) supplemented with 5 mg/mL liberase DL (Roche, 05401160001) and 2.5 mg/mL DNase (Roche 10104159001) for 1 h at 37C. After incubation, digested tissues were clarified by passing through a 100 μm cell strainer. Cell suspensions were enriched for CD45- cells by labeling cells with PE-conjugated anti-mouse CD45 (30-F11), CD140A (APA5), and Ter119 (Ter119) monoclonal antibodies and subsequent depletion of PE-labeled cells using Miltenyi anti-PE microbeads (130-048-801) and Miltenyi MACS LS (130-042-401) columns according to the manufacturer’s instructions with the following modifications: (1) we used 25% of the recommended volume of anti-PE microbeads and (2) we subjected the CD45- enriched cell fraction to a second MACS LS column. All cell suspensions post-column enrichment were enumerated using a hemocytometer. Cell fractions throughout the procedure were analyzed for PE-labeled cell depletion and enrichment of CD45- cells by flow cytometry.
Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128)

treatment_protocol: WT C57BL/6 mice were mock-inoculated (n = 3) or inoculated with 10e3 PFU of CHIKV (n = 3) in the left rear footpad.

value: Lymph node

tag: strain

tag: genotype

value: WT

tag: inoculation

value: mock

tag: time

value: 24 hpi


title: mock-3

institute: University of Colorado School of Medicine


title: mock-2


title: chikv-1

value: chikv


title: chikv-3


title: chikv-2


title: Human Ependymoma Tissue [EPEND319]

status: Public on Aug 25 2021

city: Nottingham

first: Timothy

middle: A

last: Ritzmann

address: Coates Road

department: Children's Brain Tumour Research Centre

country: United Kingdom

institute: University of Nottingham

hyb_protocol: Illumina Protocol

scan_protocol: Illumina Protocol

data_processing: Bioconductor (version 3.3) package minifi (version 1.18) using function preprocessIllumina. Data filtered for SNPs, sex chromosomes and probes with detection p-value>0.01.

label: biotin/dnp

source_name: Human Ependymoma Tissue

label_protocol: Illumina Protocol

extract_protocol: DNA extracted from formalin fixed, paraffin embedded material using the Qiagen ALLprep kit as per protocol.

value: Ependymoma

tag: methylation class

value: PFB

tag: classifier score

tag: who grade

value: II

tag: tumour location

value: PF

tag: event free survival

tag: overall survival

tag: survival status

value: A

tag: recurrence

value: No

tag: 1q gain

value: no gain

tag: resection status

value: CSR


title: Human Ependymoma Tissue [EPEND173]

tag: tissue

value: PFA

value: III

value: ISR


title: Human Ependymoma Tissue [EPEND320]

value: D

value: Yes


title: Human Ependymoma Tissue [EPEND037]

value: gain


title: Human Ependymoma Tissue [EPEND020]


title: Human Ependymoma Tissue [EPEND097]


title: Human Ependymoma Tissue [EPEND207]


title: Human Ependymoma Tissue [EPEND382]

value: RELA

value: ST


title: Human Ependymoma Tissue [EPEND224]


title: Human Ependymoma Tissue [EPEND203]


title: Human Ependymoma Tissue [EPEND316]


title: Human Ependymoma Tissue [EPEND182]


title: Human Ependymoma Tissue [EPEND205]


title: Human Ependymoma Tissue [EPEND039]


title: RB 51

status: Public on Aug 11 2021

data_processing:
Human. B38 was used for alignment reference.
Ensembl.R86 (57992 gene IDs) was used for anlysis of RNA-Seq data.
Genome_build: Ensembl.R86 (57992 gene IDs) was used for anlysis of RNA-Seq data.
Supplementary_files_format_and_content: The fragments per kilobase million reads upper quartile (FPKM-UQ) values were calculated and used for further gene expression analyses

source_name: Liver

extract_protocol:
RNA was harvested using Trizol Reagent (Invitrogen).
Truseq-total RNA (Ribozero depletion)

value: Liver

tag: Sex

value: Female

tag: diagnosis

value: obese


title: RB 44

value: Male


title: RB 52


title: RB 43


title: Human Ependymoma Tissue [EPEND029]

value: Ependymoma


title: RB 33


title: Human Ependymoma Tissue [EPEND036]

value: II

value: PF


title: RB 31


title: Human Ependymoma Tissue [EPEND110]

value: A

value: No

value: no gain


title: Human Ependymoma Tissue [EPEND223]

value: PFB


title: RB 37


title: RB 30


title: Human Ependymoma Tissue [EPEND280]

value: III

value: ISR


title: Human Ependymoma Tissue [EPEND305]

value: PFA

value: D

value: Yes


title: RB 21


title: Human Ependymoma Tissue [EPEND311]


title: Human Ependymoma Tissue [EPEND304]

value: RELA

value: ST


title: Human Ependymoma Tissue [EPEND209]


title: RB 20

value: Liver

value: Female


title: Human Ependymoma Tissue [EPEND306]

value: CSR


title: Human Ependymoma Tissue [EPEND181]

value: Ependymoma


title: RB 23

value: obese


title: Human Ependymoma Tissue [EPEND312]

value: II

value: PF

value: gain


title: RB 18


title: Human Ependymoma Tissue [EPEND019]


title: RB 14

value: Male


title: RB 9


title: RB 19


title: RB 40


title: sample.6_ANKO3

status: Public on Jul 01 2021

description: 6.CGAACTTGAG-TTATGGTGGT.H7M5YDSXY_CGAACTTGAG-TTATGGTGGT_S47_L003

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultiplexer written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

source_name: Subcutaneous WAT_ANKO

growth_protocol: ANKO mice were generated by using adiponectin-Cre transgenic mice and Nampt flox mice.

extract_protocol:
Subcutaneous white adipose tissue samples were removed, flash frozen by liquid nitrogen, and RNA was harvested using Qiazol Reagent with Rneasy Mini Kit (Qiagen).
Ribo-Zero Gold kit

treatment_protocol: Mice were kept at room temperature under a normal regular-chow fed condition.

tag: strain background

tag: genotype/variation

value: ANKO (adipocyte specific Nampt knockout)

value: Subcutaneous white adipose tissue (WAT)


title: Human Ependymoma Tissue [EPEND113]

value: PFB

value: A

value: No

value: no gain


title: RB 17


title: sample.4_ANKO1

description: 4.CATAGTCACA-ACGAGGACCA.H7M5YDSXY_CATAGTCACA-ACGAGGACCA_S28_L003


title: RB 16


title: sample.3_flox/flox3

description: 3.CAGCATGAGC-TTACCGATTC.H7M5YDSXY_CAGCATGAGC-TTACCGATTC_S26_L003

source_name: Subcutaneous WAT_control

value: flox/flox (control)


title: sample.1_flox/flox1

description: 1.AATCATCTGG-GAACCACAGG.H7M5YDSXY_AATCATCTGG-GAACCACAGG_S6_L003


title: sample.2_flox/flox2

description: 2.AGGTCCATTC-TCAATGAGGT.H7M5YDSXY_AGGTCCATTC-TCAATGAGGT_S20_L003


title: sample.5_ANKO2

description: 5.TCGCTTGCAC-ATCAGTCCTA.H7M5YDSXY_TCGCTTGCAC-ATCAGTCCTA_S64_L003


title: RB 41


title: Human Ependymoma Tissue [EPEND201]

value: YAP

value: ST


title: E15.5

status: Public on Jun 17 2021

city: Oxford

first: Steve

last: Twigg

address: John Radcliffe Hospital

institute: University of Oxford

description: E15.5 alone

data_processing:
Quality control of raw reads was performed with FastQC version 0.11.7, fastq_screen version 0.7.0 and multiqc (Ewels et al., 2016) version 0.9. Samples were counted individually and aggregated with cellranger (10X Genomics) version 2.1.1. All other parameters were set to their default values.
Data analysis was performed with Seurat (Stuart et al., 2019) version 3.2.0. The aggregate gene/barcode matrix (`raw_gene_bc_matrices_mex`) was loaded using `CreateSeuratObject` and `Read10X` with `min.cells = 10, min.genes = 200`. Cells were filtered to exclude cells with fewer than 1000 UMIs, fewer than 1000 genes, more than 7.5% mitochondrial content (calculated as the fraction of reads assigned to a gene on the chromosome `MT`), and more 3% Hbb/Hba centent (to remove red blood cells, and cells with high contamination for red blood cell specific genes). Filtered cells were normalized with SCTransform, and cell cycle scoring and regression was performed for each dataset with the default list of human cell-cycle genes (converted to mouse gene symbols). Datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat. In brief, an object list including both datasets was created, 3000 features were selected using the SelectIntegrationFeatures following by PrepSCTIntegration, anchors were identified using FindIntegrationAnchors, and the data was integrated using IntegrateData.
Dimensionality reduction was performed using the first 30 principal components (PCs) with UMAP (McInnes et al., 2018) (`min_dist = 0.5, n_neighbors = 50`). Clustering was performed with `FindClusters` and `resolution=1`. Cluster marker genes were identified with `FindAllMarkers` using parameters `min.pct  = 0.2, logfc.threshold = 0.5, max.cells.per.ident = 1000, min.cells.gene = 5`. Secondary dimensionality reduction and clustering of the osteogenic and mesenchymal subset was performed as above, after subsetting for cluster numbers 0, 1, 2, 4, 5, 7, and 9.
Genome_build: mm10
Supplementary_files_format_and_content: The matrix, genes are barcode files for the E15.5 and E17.5 datasets are respectively: E15_matrix.mtx,  E15_barcodes.tsv, E15_features.tsv, and E17_matrix.mtx, E17_barcodes.tsv, E17_genes.tsv.
Supplementary_files_format_and_content: composite_full_clusters.rds - this is an R object of the Bioconductor class ExpressionSet. It can be imported into R with `readRDS`. It contains the gene counts, sample metadata, and feature metadata of the full E15.5-E17.5 composite datset.
Supplementary_files_format_and_content: composite_mesenchyme_bone_subset.rds - this contains the gene counts, sample metadata, and feature metadata of the osteogenic-mesenchyme subset of E15.5-E17.5 composite datset.
Supplementary_files_format_and_content: the 'E15_17_composite_data' and 'E15_17_composite_metadata' files contain respectively, the Seurat SCT expression data (3000 genes x 12,170 cells) and metadata from the osteogenic-mesenchyme subset.

source_name: wildtype_coronal suture

extract_protocol:
E15.5 and E17.5 embryos were isolated, and the skin, the brain, and some of the meningeal layers were peeled away, leaving the bony skull. For E15.5 embryos the coronal suture was dissected away from the skull cap using microdissection scissors, and 10 coronal sutures were rinsed in PBS and enzymatically dissociated with a final concentration of 3 mg/mL of Collagenase II (Worthington) and 4 units/mL of Dispase (COMPANY) in DMEM/F12 (company) for 45 min. For E17.5 embryos coronal sutures were dissected out in ice cold PBS using a scalpel blade, isolating a strip containing the overlapping frontal and parietal bone fronts (which appears opaque compared to adjacent regions) and avoiding the most apical and basal aspects of the suture. Isolated sutural strips from embryos from two litters in 3 batches (batch 1, 10 sutures from litter 1; batch 2 and 3, 3 sutures each from litter 2) were cut into small fragments in HBBS and digested using Collagenase IV (Worthington, USA; final concentration in HBBS of 2 mg/mL) for 30 min. Dissociation was terminated with 2% Fetal Bovine Serum and cells were passed through a 0.35 µM filter (E15.5) or Pluri-strainer Mini 70 µm (E17.5; pluriSelect Life Science, Germany). For E15.5 sample preparation, dead cells were removed using the Dead Cell Removal kit (Miltenyi Biotec 130-090-101) and cells counts were determined with a hemocytometer. The three batches of E17.5 dissociated cells were separately sorted by FACs to remove debris, cell doublets and likely dead cells (BD FACSAria Fusion; 100 µM nozzle) prior to library preparation.
Transcriptome libraries  for single cells were captured using 10X genomics Chromium Single Cell 3’ Library and Gel Bead Kit v2 following manufacturer’s guidelines. Sequencing for E15.5 coronal sutures was performed with Illumina’s HiSeq 3000/4000 PE Cluster Kit at the Children’s Hospital Los Angeles’ Molecular Genomics Core, and for E17.5 cells, PE sequencing was run on an Illumina HiSeq 4000 at the Oxford Genomics Centre Wellcome Centre for Human Genetics, Oxford achieving an average of  ~150,000 mean reads per cell for E15.5 and ~92,000 mean reads per cell for E17.5.
scRNAseq

tag: strain

value: Coronal suture

tag: developmental stage


title: RB 45

value: Liver

value: Female


title: Human Ependymoma Tissue [EPEND313]

value: Ependymoma

tag: methylation class

value: RELA

value: III

value: CSR


title: 15688X7 RO091 CCSP-Cre RPMA

status: Public on May 22 2021

city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

description: Bulk RNA Sequencing

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 94.
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCounts output files combined into a single tab-delimited matrix

source_name: RPMA GEMM

extract_protocol:
RNeasy Mini Kit (Qiagen) with the standard protocol
Illumina TruSeq Stranded Total RNA Library Ribo-Zero Gold Prep kit

tag: genotype

value: RPMA tumor


title: 15688X8 RO090 SPC-Cre RPMA

description: Bulk RNA Sequencing


title: 15688X6 RO082 CCSP-Cre RPMA

description: Bulk RNA Sequencing


title: 15688X5 RO075 CMV-Cre RPMA

description: Bulk RNA Sequencing


title: 15688X4 RO074 CMV-Cre RPMA

description: Bulk RNA Sequencing


title: 15688X3 RO085 CGRP-Cre RPMA

description: Bulk RNA Sequencing


title: Human Ependymoma Tissue [EPEND169]

value: PFA

tag: classifier score

tag: who grade

value: PF

value: D

value: Yes


title: 15688X1 RO037 CGRP-Cre RPMA Het

description: Bulk RNA Sequencing


title: 14034X10 ASCL1 ChIP RPM2 (PB499)

data_processing:
Reads were aligned to the mm10 build of the mouse genome with bowtie using the following parameters: -m 1 -t --best -q -S -l 32 -e 80 -n 2.
Peaks were called with MACS2 using a p value cutoff of 1e-10 and the mfold parameter bounded between 15 and 100.
For visualization, MACS2 produced bedgraphs with the –B and –SPMR options.
Genome_build: mm10

source_name: SCLC lung tumor cells

growth_protocol: Lung tumor growth initiated in Rb1fl/fl;p53fl/fl;MycT58ALSL/LSL mice following intratracheal administration of Ad-CGRP-Cre

extract_protocol:
Individual lung tumors from mice were micro-dissected, flash frozen and stored at -80°C until ChIP. Tumors were prepared for ChIP by pulverizing frozen tumors into a fine powder.
Samples were resuspended in PBS and DNA was crosslinked in 1% formaldehyde. Fixation was terminated by adding glycine.
Chromatin was sheared using a Diagenode Bioruptor and mouse tumor chromatin was immunoprecipitated with respective antibodies.
The immunoprecipitated chromatin was purified with the Zymo ChIP DNA Clean and Concentrator kit.
Libraries were prerpared using a NEBBext ChIP-Seq Library kit and sequenced on an Illumina HiSeq 2500 (single-end 50 bp reads with a min of 35 million reads per sample).

treatment_protocol: Untreated tumors

value: SCLC lung tumor cells

tag: antibody

value: anti-ASCL1 (BD Pharmingen cat#BD556604)


title: 15739X1 RPR2 CGRP

description:
RPR2_CGRP tumor
Single-cell RNA seq

data_processing:
The RPR2 sample was demultiplexed with 10x cellranger mkfastq version 3.1.0 to create fastq files with the I1 sample index, R1 cell barcode+UMI and R2 sequence.
Reads were aligned to the mouse genome (refdata-cellranger-mm10-3.0.0 from 10X Genomics with  EGFP+Cas9 added) and count barcodes and UMIs were generated using cellranger count 3.1.0 with expected-cells set to 8000 per library
Genome_build: mm10 with EGFP+Cas9
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MEX format from cellranger count.

source_name: RPR2 GEMM tumor

growth_protocol: Tumors initated with adenoviral-Cre via intranasal or intratracheal infection into lungs and harvested at various time points decided by microCT imaging

extract_protocol:
Enzymatic/mechanical digestion into single cell suspension then immediate sequencing
10X Chromium Single Cell Gene Expression Solution with 3’ chemistry, version 3 (for RPMA and RPM samples). 10X Chromium Single Cell Gene Expression Solution with 3’ chemistry, version 2 (for RPR2 sample).
Targeted cell recovery of 8k cells (for RPM, RPR2, and RPMA_CMV samples) and 3.4k cells (for RPMA_CGRP). 10x gel beads and reverse transcription reagents were added to cell suspensions and loaded to chromium single cell controller to form gel-bead-in emulsions (GEMs). From GEMs, cDNA was generated from barcoded mRNA and subsequent A tailing, end repair, adaptor ligation, sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D1000 ScreenTape on Agilent tech 2200 tapestation system and quantified KAPA Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000 w 2x150 paired end seq aiming for 200 million reads per sample.

treatment_protocol: No treatment

tag: ID

tag: mouse genotype

value: Rb1 fl/fl;Trp53 fl/fl;Rbl2 fl/fl


title: 14034X11 NEUROD1 ChIP RPM3 (PB502)

value: anti-NEUROD1 (Santa Cruz Biotechnologycat#sc-108)


title: 18538X2 RPMA CGRP

description:
RPMA_CGRP tumor
Single-cell RNA seq

source_name: RPMA GEMM tumor

value: Rb1 fl/fl;Trp53 fl/fl;H11b-MycT58ALSL/LSL;Ascl1 fl/fl


title: 18571X2 RPM CGRP

description:
RPM_early CGRP tumor
Single-cell RNA seq

source_name: RPM-CAS9 GEMM tumor


title: 18602X1 RPMA CMV

description:
RPMA_CMV tumor
Single-cell RNA seq


title: Human Ependymoma Tissue [EPEND298]

value: PFB

value: II

tag: tumour location

tag: event free survival

tag: overall survival

tag: survival status

tag: recurrence

value: no gain

value: ISR


title: Human Ependymoma Tissue [EPEND163]

tag: tissue

value: Ependymoma

tag: 1q gain

tag: resection status


title: 410_IFNg_ATAC

status: Public on May 10 2021

data_processing:
Raw fastq files were aligned to hg38 using bowtie2 following the ENCODE ATAC-seq pipeline. Two versions of bigwig files were generated by the fold enrichment of signal over expected background, and a p-value track representing statistical significance.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: Human melanoma cells

extract_protocol: Used the protocol from Corces et al., 2017

tag: cell type

value: Human melanoma cell line

tag: treatment

value: treated with IFNg for 2-5 weeks

tag: cell line


title: 370_IFNg_ATAC


title: 370_d0_ATAC

value: Untreated


title: 410_TNF_ATAC

value: treated with TNF for three days


title: 14034X9 ASCL1 ChIP RPM1 (PB490)

tag: genotype


title: 410_d0_ATAC


title: 381_IFNg_ATAC


title: 370_TNF_ATAC


title: 14034X12 NEUROD1 ChIP RPM4 (PB503)


title: Human Ependymoma Tissue [EPEND350]

tag: methylation class

value: PFA

tag: classifier score

value: III

value: PF

value: gain


title: 3998MEL_IFNg_ATAC


title: 257A2_d0_ATAC


title: 381_TNF_ATAC


title: 3998MEL_d0_ATAC


title: 3998MEL_TNF_ATAC


title: 399_d0_ATAC


title: 381_d0_ATAC


title: 308_TNF_ATAC


title: 399_IFNg_ATAC


title: 257A2_IFNg_ATAC


title: 257A2_TNF_ATAC


title: 308_d0_ATAC


title: 308_IFNg_ATAC


title: NMN_89C_Insulin_S12

status: Public on May 01 2021

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts derived with Subread:featureCount 1.46.p5.  RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCh38.76
Supplementary_files_format_and_content: Gene counts data were attached.

source_name: Quadriceps muscle tissue

growth_protocol: Quadriceps muscle tissue was obtained during the basal period and during the hyperinsulinemic-euglycemic clamp procedure (insulin infusion).

extract_protocol:
Total RNA was isolated from frozen quardiceps skeletal muscle samples by using TRIzol Reagent (#15596018; Invitrogen) in combination with a RNase-free DNase Set (Qiagen).
TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA)

tag: agent

value: NMN

tag: time point

value: After

tag: group

value: Insuin infusion


title: 262_d0_ATAC


title: 262_IFNg_ATAC


title: Human Ependymoma Tissue [EPEND297]

tag: who grade

tag: tumour location

value: A

value: No


title: NMN_89C_Basal_S38

value: Basal


title: NMN_89A_Insulin_S93

value: Before


title: 399_TNF_ATAC


title: NMN_89A_Basal_S32


title: NMN_85A_Insulin_S78


title: NMN_85C_Insulin_S83


title: NMN_85A_Basal_S77


title: NMN_7C_Insulin_S3

value: Placebo


title: NMN_7C_Basal_S42


title: NMN_7A_Insulin_S27


title: NMN_85C_Basal_S86


title: NMN_77C_Basal_S55


title: NMN_77C_Insulin_S47


title: NMN_77A_Insulin_S87


title: NMN_72A_Insulin_S30


title: NMN_77A_Basal_S20


title: 262_TNF_ATAC


title: NMN_72A_Basal_S31


title: NMN_72C_Insulin_S26


title: NMN_70C_Basal_S74


title: NMN_7A_Basal_S66


title: NMN_70A_Basal_S25


title: NMN_70C_Insulin_S43


title: NMN_70A_Insulin_S62


title: NMN_68A_Insulin_S73


title: NMN_68C_Insulin_S80


title: NMN_68A_Basal_S89


title: NMN_65A_Insulin_S65


title: NMN_65C_Insulin_S9


title: NMN_65A_Basal_S70


title: NMN_62C_Insulin_S94


title: NMN_72C_Basal_S23


title: NMN_62C_Basal_S60


title: NMN_62A_Insulin_S10


title: NMN_65C_Basal_S35


title: NMN_46C_Basal_S82


title: NMN_57A_Insulin_S63


title: NMN_57C_Basal_S21


title: NMN_57A_Basal_S19


title: NMN_46A_Basal_S88


title: NMN_46A_Insulin_S56


title: NMN_46C_Insulin_S8


title: NMN_62A_Basal_S50


title: NMN_45A_Basal_S1


title: NMN_40C_Insulin_S41


title: NMN_45C_Insulin_S61


title: NMN_68C_Basal_S36


title: NMN_45C_Basal_S64


title: NMN_37C_Basal_S67


title: NMN_37A_Insulin_S57


title: NMN_33C_Insulin_S79


title: NMN_33A_Insulin_S34


title: NMN_33C_Basal_S92


title: NMN_57C_Insulin_S4


title: NMN_33A_Basal_S22


title: NMN_32C_Basal_S90


title: NMN_45A_Insulin_S71


title: NMN_32C_Insulin_S33


title: NMN_32A_Insulin_S40


title: NMN_31C_Basal_S28


title: NMN_32A_Basal_S37


title: NMN_31A_Insulin_S59


title: NMN_28A_Insulin_S17


title: NMN_28C_Basal_S69


title: NMN_40C_Basal_S2


title: NMN_18C_Insulin_S6


title: NMN_18A_Insulin_S75


title: NMN_37A_Basal_S16


title: NMN_40A_Insulin_S84


title: NMN_16C_Insulin_S58


title: NMN_40A_Basal_S46


title: NMN_18C_Basal_S54


title: NMN_37C_Insulin_S5


title: NMN_18A_Basal_S7


title: NMN_16A_Basal_S29


title: NMN_15C_Insulin_S45


title: NMN_16A_Insulin_S72


title: NMN_15A_Insulin_S76


title: NMN_28C_Insulin_S52


title: NMN_31A_Basal_S51


title: NMN_31C_Insulin_S24


title: NMN_15A_Basal_S11


title: NMN_12C_Insulin_S53


title: NMN_12C_Basal_S13


title: NMN_12A_Insulin_S39


title: NMN_28A_Basal_S14


title: NMN_16C_Basal_S85


title: NMN_11C_Insulin_S44


title: NMN_12A_Basal_S49


title: NMN_11A_Basal_S91


title: NMN_11A_Insulin_S48


title: NMN_15C_Basal_S81


title: NMN_11C_Basal_S15


title: P32

status: Public on Apr 21 2021

hyb_protocol: Sodium bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned using Illumina´s Iscan

data_processing: Illumina IScan Control Software 3.4.8.0

source_name: Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from tissue samples using Maxwell RSC FFPE Plus DNA Kit according to standard instructions

tag: phenotype

value: Non-responder


title: P22


title: P24


title: P27


title: P10


title: P17


title: P30


title: P18


title: P11


title: P34

value: Responder


title: P9


title: P8


title: P14


title: P26


title: P23


title: P25


title: P33


title: P21


title: P19


title: VATR_SAT_3

status: Public on Apr 01 2021

description:
sample.18
Under a high-fat diet condition
VATR_all.gene_counts.txt

data_processing:
Basecalling with Illumina RTA 1.9.
Demultiplexing with Illumina bcl2fastq2.
Fastq files were combined and aligned with STAR 2.5.1a.
Gene counts derived with Subread:featureCount 1.46.p5. RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCm38.76
Supplementary_files_format_and_content: VATR_all.gene_counts.txt: Gene counts in tab-delimited text format.

source_name: Subcutaneous white adipose tissue, VAT removal

growth_protocol: C57BL/6J male mice (#000664) were purchased from the Jackson Laboratory. All mice were housed in a barrier facility with 12-h light/12-h dark cycles and were allowed free access to a regular-chow diet and water. At 8-9 months of age, mice were assigned to sham operation and VAT removal operation groups (described below).

extract_protocol:
Subcutaneous white adipose tissue and liver samples were removed, flash frozen by liquid nitrogen, and RNA was harvested using Qiazol Reagent with RNeasy Mini Kit (Qiagen) and Trizol (Invitrogen).
RiboErase

treatment_protocol: After the abdominal cavity was opened, epididymal visceral fat pads were removed. Sham operation consisted of abdominal incision without fat pads removal. All mice were fed with a high-fat diet after surgery procedure.

tag: strain

tag: Sex

value: Male

tag: age

value: Adult

value: Subcutaneous white adipose tissue

value: VAT-R

tag: condition

value: High-fat diet


title: VATR_SAT_5

description:
sample.20
Under a high-fat diet condition
VATR_all.gene_counts.txt

tag: tissue


title: P28


title: VATR_SAT_2

description:
sample.17
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: P20


title: P13


title: P31


title: VATR_SAT_1

description:
sample.16
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: P12


title: P35


title: Sham_SAT_5

description:
sample.15
Under a high-fat diet condition
VATR_all.gene_counts.txt

source_name: Subcutaneous white adipose tissue, sham surgery

value: Sham


title: Sham_SAT_3

description:
sample.13
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: P6


title: Sham_SAT_2

description:
sample.12
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: Sham_SAT_1

description:
sample.11
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: P29


title: VATR_Liver_5

description:
sample.10
Under a high-fat diet condition
VATR_all.gene_counts.txt

source_name: Liver, VAT removal

value: Liver


title: VATR_Liver_4

description:
sample.9
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: VATR_Liver_2

description:
sample.7
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: VATR_Liver_1

description:
sample.6
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: VATR_Liver_3

description:
sample.8
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: Sham_Liver_3

description:
sample.3
Under a high-fat diet condition
VATR_all.gene_counts.txt

source_name: Liver, sham surgery


title: Sham_Liver_2

description:
sample.2
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: PF-SE33_2

status: Public on Mar 22 2021

city: Berlin

first: Felix

last: Thierfelder

address: Charitépl. 1

institute: Charite

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip and Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
using R (version 4.0.2)  minfi_1.36.0 package
arrays from different plattforms were combined using combineArrays function; beta values were normalized using minfi PreprocessFunnorm function; detection p-values was calculated using detectionP function; for methylated and unmethylated signals preprocess, Illumina function was used for normalization

label: cy3, cy5

source_name: infratentorial

extract_protocol: genomic DNA was extracted and purified from FFPE tumor samples using Tissue DNA Purification Kit (Promega) according to the manufacturer´s protocol

tag: gender

value: m

tag: subtype

value: mixed, distinct


title: Sham_Liver_1

description:
sample.1
Under a high-fat diet condition
VATR_all.gene_counts.txt

tag: treatment


title: PF-SE50


title: PF-SE49


title: Sham_Liver_5

description:
sample.5
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: P16


title: PF-SE47


title: P15


title: PF-SE48


title: PF-SE46


title: PF-SE45


title: P7


title: PF-SE42


title: PF-SE40


title: PF-SE41


title: PF-SE39


title: PF-SE38


title: Sham_Liver_4

description:
sample.4
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: PF-SE36

value: f


title: PF-SE43


title: PF-SE34

value: mixed, diffuse


title: VATR_SAT_4

description:
sample.19
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: P5


title: PF-SE28


title: PF-SE21


title: PF-SE27


title: PF-SE16


title: PF-SE15


title: PF-SE30


title: PF-SE18


title: PF-SE14

value: pure SE


title: PF-SE32


title: PF-SE20


title: PF-SE29


title: PF-SE13


title: PF-SE12


title: PF-SE26


title: PF-SE25


title: PF-SE23


title: PF-SE22


title: PF-SE19


title: PF-SE11


title: PF-SE33


title: PF-SE37


title: PF-SE24


title: PF-SE17


title: PF-SE31


title: PF-SE10


title: PF-SE9


title: PF-SE5


title: PF-SE4


title: Sham_SAT_4

description:
sample.14
Under a high-fat diet condition
VATR_all.gene_counts.txt


title: PF-SE3


title: PF-SE7


title: P2


title: PF-SE8


title: PF-SE6


title: PF-SE35


title: Batch 3 bulk RNAseq SHD5

status: Public on Feb 10 2021

city: New Haven

first: Andrew

last: Martins

state: Connecticut

address: 100 College Street Rm 1155

department: Immunobiology

institute: Yale School of Medicine

description:
For each sample, a sample of 100,000 cells was processed in Trizol using the miRNAeasy micro kit (Qiagen, Germantown, MD; catalogue number 217084) and standard RNA sequencing libraries were generated using Illumina Truseq library (Illuimna, San Diego, CA; 20020595) preparation kits. Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The sequencing reads were adapter and quality trimmed and then aligned to the human genome using the splice-aware STAR aligner and SNP calls were generated using the previously published protocol: Nucleic Acids Research, Volume 47, Issue 21, 02 December 2019, Page e136. These SNP calls were then used along with the demuxlet software (https://github.com/statgen/demuxlet) to demultiplex the single cell multimodal RNAseq data (see supplemental demux.best files). Counts per gene were generated using htseq count (version 0.9.1) and the UCSC hg19 genome annotation.
B2_B3_bulkRNAseq_countmtx.csv

data_processing:
fastq generation: Illumina bcl2fastq 2.20
mapping, CellRanger 3.1.0 (10x Genomics)
sample demultiplexing: popscle demuxlet (https://github.com/statgen/popscle)
secondary analysis: Seurat 3.1.0 (R package)
T cell receptor VDJ analysis: CellRanger 3.1.0
One anonymized donor (SDH8) was excluded from further analysis, as we discovered an extremely expanded B phenotype consistent lymphoma in this sample. An additional leukopack-derived PBMC sample (CHI014, anonymized and without demographic information)  was used in each experimental batch as a technical control, but not used in later comparisons. Samples HDVO_bc and HDML_bc in Batch 2 were used as a test of cyropreserving buffy coat samples, and were not used in the furtehr analysis.
Genome_build: hg19 (cellranger version 1.2.0, https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#hg19_1.2.0)
Supplementary_files_format_and_content: CellRanger count matrices in h5 data format; T cell clonal analysis, comma seperated values

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Frozen PBMC samples were thawed, recovered and washed using RPMI media with 10% FBS and 10mg/mL DNase I (STEMCELL 07470). Samples from different donors were pooled evenly before staining; single cells can be demultiplexed in silico using individual specific single nucleotide polymorphism (SNP) information during data analysis (see below; demultiplexing for each lane is provided in the *demux.best supplemental files). Multiple cell pools were prepared, such that cells from the same individual but different timepoints would be in different pools. PBMC pools were Fc blocked (Human TruStain FcX, BioLegend 422302) and stained with Totalseq-C human ‘hashtag’ antibodies (BioLegend), washed with staining buffer (2% BSA in PBS). This round of hashtag staining allows the different pools to be identified in the analysis, which when combined with the SNP-based demultiplexing, allows full identification of each sample. A fraction of the combined cells was used for sorting total B, T, CD14+ monocyte and CD14- innate cell populations (batch 1) or non-naïve T and B cells (batches 2 and 3). Separately for the unsorted and sorted cell fractions, hashtagged PBMC pools were combined and cells were stained with a cocktail of TotalSeq-C human lyophilized panel (BioLegend) of 192 surface proteins. Then, cells were washed three times, resuspended in PBS, and counted before proceeding immediately to the single cell partition step. Flow cytometry sorting to enrich certain cell populations was performed as follows: Pooled PBMC samples from different donors were washed with PBS and incubated with Zombie Red Fixable viability dye (1:1000 in PBS, BioLgend) for 20 minutes at 4°C protected from light. Then cells were washed with flow staining buffer (10% FBS in PBS) and Fc blocked (Human TruStain FcX, BioLegend) for 15 minutes on ice. For experimental batches 2 and 3, the non-naïve B- and T- cell populations were sorted. The fluorescence-labeled antibody cocktail against human CD45(APC/Cyanine7, BioLegend 368516), CD3(AF488, BioLegend 344810), CD19(APC, BioLegend 363006), CCR7(BV786, BioLegend 353230), CD95(BV650, BioLgend 305642), IgD(PerCP-Cy5.5, BioLegend 348208) and CD27(PE/Cyanine7, BioLegend 356412) were added at the end of blocking, and incubated for 20 minutes at 4°C in the dark. Cells were washed and sorted on a BD Aria sorter in Biosafety Level 3 (BSL3) lab (BD Biosciences). Non-naïve B cell population was gated by CD45+CD19+IgD- or CD27+ and non-naïve T cell population was gated by CD45+CD3+CCR7low or CD95+. Sorted cells were CITE-seq stained, washed three times, resuspended in PBS and counted before proceeding to the single cell partition step. For experimental batch 1, total B, T, CD14+ monocyte and CD14- innate cell populations were sorted and pooled with unsorted PBMCs by ratio 1:1:1:1:1 to balance the number of each population captured in the final pool for CITE-seq assay. The fluorescence-labeled antibody cocktail against human CD14(BV421, BioLegend 325628), CD3(AF488, BioLegend 344810), CD45(PE/Cyanine7, BioLegend 393408), CD19(APC, BioLegend 363006) and Totalseq-C human hashtag antibodies(BioLegend) were added at the end of blocking, and incubated for 20 minutes at 4°C in the dark. Cells were washed and sorted on a BD Aria sorter in Biosafety Level 3 (BSL3) lab (BD Biosciences). B cell population was gated by CD45+CD19+CD3-; T cell population was gated by CD45+CD3+CD19-; monocyte population was gated by CD45+CD3-CD19-CD14+; other myeloid cells were gated by CD45+CD3-CD19-CD14-. Sorted 4 populations and unsorted PBMCs were pooled evenly. Then the final pool was CITE-seq stained, washed three times, resuspended in PBS and counted before proceeding to the single cell partition step.
PBMC samples were mixed with the reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using 10x 5’ Chromium Single Cell Immune Profiling Next GEM v1.1 chemistry (10x Genomics, Pleasanton, CA). The RT step was conducted in the Veriti Thermo Cycler (ThermoFisher Scientific, Waltham, MA). Single cell gene expression, cell surface protein, and T cell receptor (TCR) libraries were prepared as instructed by 10x Genomics user guides (https://www.10xgenomics.com/resources/user-guides/). All libraries were quality controlled using Bioanalyzer (Agilent, Santa Clara, CA) and quantified using Qubit Fluorometric (ThermoFisher). 10x Genomics 5’ Single cell gene expression, cell surface protein tag, TCR and BCR libraries were pooled and sequenced on Illumina NovaSeq platform (Illumina, San Diego, CA) using the sequencing parameters recommended by the 10x Genomics 5’ v1.1 user guide. Sequencing saturation of the libraries ranged from approximately 60-80% for the cDNA and 20-40% for the surface protein tag libraries.

tag: unsorted or sorted t/b cells

value: Unsorted

tag: timepoint

value: Healthy Control

tag: molecule

value: mRNA


title: Batch 3 bulk RNAseq HGR0000392_T0

value: Timepoint 0


title: Batch 3 bulk RNAseq SHD6


title: SS

status: Public on Feb 18 2021

data_processing:
Cell Ranger 4.0 was used to align reads to mm10.
Data was processed using Cell Ranger count to obtain a counts matrix.
Genome_build: mm10
Supplementary_files_format_and_content: bam files; tsv and mtx files from CellRanger filtered counts output

source_name: Bone-marrow derived macrophage

growth_protocol: Differentiate bone-marrow monocytes for 7 days with BMDM differentiation media consisting of IMDM with 30% L929 supernatant, 10% FBS. Cells were replated to treatment dishes on day 5.

extract_protocol:
At 8hrs cells were washed once with PBS, and lifted into suspension by incubating with Accutase for 5mins at 37C. Cells were labeled with TotalSeqB hashtag antibodies and pooled for 10x capture and sequencing.
Chromium Single Cell 3’ GEX Version 3.1 for RNA library, and Chromium Single Cell 3ʹ Feature Barcode Library Kit for tag libraries.

treatment_protocol: Wildtype (WT) and Sjogren’s Syndrome (SS) cells were stimulated with 10ng/ml TNF, or 100ng/ml LPS, or 50ug/ml pIC for 8 hours.  For both WT and SS samples, these three conditions, plus a no stimulus control, are identified by the TotalSeqB barcodes LPS: CTTTGTCTTTGTGAG TNF: TATGCTGCCACGGTA; PIC: GAGTCTGCCAGTATC; None: TATAGAACGCCAGGC

value: Pooled TNF, LPS, pIC, None

tag: celltype

value: macrophage


title: P3

value: Responder


title: Batch 3 bulk RNAseq HGR0000430_T1

value: Timepoint 1


title: PF-SE1


title: Batch 3 bulk RNAseq HGR0000392_T3

value: Timepoint 3


title: Batch 3 bulk RNAseq SHD3


title: Batch 3 bulk RNAseq HGR0000429_T2

value: Timepoint 2


title: Batch 3 bulk RNAseq HGR0000429_T1


title: WT


title: Batch 3 bulk RNAseq HGR0000142_T0


title: Batch 3 bulk RNAseq SHD1


title: P1

value: Non-responder


title: Batch 3 bulk RNAseq HGR0000135_T1


title: Batch 3 bulk RNAseq HGR0000135_T0


title: P4


title: Batch 3 bulk RNAseq HGR0000134_T0


title: Batch 3 bulk RNAseq HGR0000102_T0


title: Batch 3 bulk RNAseq HGR0000102_T1


title: Batch 3 bulk RNAseq HGR0000134_T1


title: Batch 3 bulk RNAseq HGR0000101_T1


title: Batch 3 bulk RNAseq HGR0000101_T0


title: Batch 3 bulk RNAseq HGR0000101_T3


title: Batch 3 bulk RNAseq HGR0000051_T3


title: Batch 3 bulk RNAseq HGR0000051_T1


title: Batch 3 bulk RNAseq HGR0000051_T0


title: Batch 2 bulk RNAseq SHD4


title: Batch 2 bulk RNAseq SHD8

value: Healthy Control (excluded due to abnormal lymphoma-like B cells found upon analysis)


title: Batch 2 bulk RNAseq SHD7


title: Batch 3 bulk RNAseq CHI014_B3

value: Technical Control