title: Cbp3_W303 sel-mitoRP, rep2

city: Boston

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: Library name: Cbp3_W303_2

library_source: other

data_processing:
Reads were trimmed to remove ligated 3’ linker (CTGTAGGCACCATCAAT) with Cutadapt (Martin. EMBnet.journal, 2011. DOI:10.14806/ej.17.1.200). Reads without linker were discarded and the unique molecular identifier (UMI, consisting of 4 random nucleotides introduced at the 5’ end with the RT primer and 10 random nucleotides introduced at the 3’ end with the linker) was then extracted from remaining reads using a custom script. For all Aep1, Aep2, and the first two replicates of Cbs1 samples, synthetic COX2 RNA oligos of 40 and 33 nucleotides (UAACAACAUUCAUUAUGAAUGAUGUACCAACACCUUAUGC and UAACAACAUUCAUUAUGAAUGAUGUACCAACAC) were used as size markers in a separate gel lane during mitoribosome footprint size selection. The oligos contaminated some of the Aep1 and Aep2 samples that were run in adjacent lanes and were removed in silico using BBTools’ BBDuk (sourceforge.net/projects/bbmap/) with a k-mer length of 30.
Reads mapping to abundant non-coding RNAs (rRNA, tRNA) were filtered out after alignment using bowtie1 (Langmead et al. Genome Biology, 2009). Remaining reads were aligned to the S. cerevisiae genome assembly R64 (UCSC: sacCer3) using STAR 2.7.3 (Dobin et al. Bioinformatics, 2013). PCR duplicates were identified by their UMI and removed using a custom script.
Ribosome A site positions were determined using an offset from the 3’ end of each read, depending on its length: 37:[-15], 38:[-16], 39:[-17], 40:[-17], 41:[-17]. Shorter read lengths have ambiguous offsets and were omitted.
Unless otherwise noted, read counts at each A site position were summed across replicates (2 to 6 replicates for each sample) and normalized by total mitochondrial mRNA-mapping reads (rpm). Enrichment over total mitoribosomes was then calculated by summing rpm values in a sliding 9-nt window and dividing by the corresponding sum in the total (Mrps17) dataset.
A threshold was set so that if more than 3 positions had no coverage in either sample the enrichment value was set to 0. This was to avoid spurious signal due to low coverage.
Assembly: Saccharomyces cerevisiae  assembly R64 (UCSC: sacCer3) for S288C, and assembly ASM216351v1 for W303
Supplementary files format and content: Processed data files ending in *Mito_mRNA.noDups.Asite_37to41_P.rpm.bedGraph are rpm-normalized bedGraph files for each replicate. These have been A-site transformed and only use reads sized 37 to 41 nt.
Supplementary files format and content: Processed data files ending in *Mito_mRNA.noDups.Asite_37to41_PAll.rpm_Mrps17_normRollWin9_max3zeros_forIGV_nolog.bedGraph are made by summing the rpm values for each replicate of a sample then normalizing to the respective Mrps17 data, as described. Columns are 1) chromosome 2) Window-normalized A-site position - 1 3) Window-normalized A-site A-site position 4) Value (fold enrichement) 5) Log1p raw sample counts in window 6) Log1p raw norm sample counts in window
Supplementary files format and content: Only plus-strand data is included for all processed files
Library strategy: Ribo-seq

molecule: other

growth_protocol: Yeast were grown in YPGal (1% yeast extract, 2% peptone, 2% galactose), pH 5.0, until an OD600 of approximately 1.

extract_protocol:
Frozen cells with lysis buffer were  mechanically lysed using liquid nitrogen-chilled 50 mL canisters for six cycles of 3 min at 15 Hz using a Retsch MM301 mixer mill
Lysates were treated with RNase I and pelleted through a 24% sucrose cushion to isolate ribosomes, crosslinks were reversed, and protected RNA fragments were isolated using acid phenol chloroform. Gel-purified RNA was treated with PNK and ligated to a pre-adenylated adapter (CTGTAGGCACCATCAATNNNNNNNNNN) using T4 RNA ligase 2, K227Q, truncated. Superscript III was used for reverse transcription and circ ligase for circularization. Illumina adapters were introduced by 10-14 cycles of PCR.

treatment_protocol: 150 mL of culture was snap chilled prior to formaldehyde crosslinking by pouring the culture into a prechilled 500 mL centrifuge bottle filled with 50 grams of frozen, crushed ice cubes made from MilliQ water. The culture was quickly swirled in the centrifuge bottle and placed on ice. 10 mL of 16% formaldehyde was added to the chilled culture and the crosslinking proceeded for 1 hr on ice with swirling every 15 minutes. 11 mL of 2.5 M glycine was added to the culture to quench the crosslinking reaction.

value: MATa; leu2-3,112 trp1-1 ura3-1 ade2-1 his3-11,15 can1-100 nuc1::URA3 CBP3-3xFLAG::TRP1

value: sucrose cushion


title: Cbp3_W303 sel-mitoRP, rep3

status: Public on Jul 16 2025

type: SRA

department: Genetics

country: USA

description: Library name: Cbp3_W303_3

organism: Saccharomyces cerevisiae

tag: cell line

tag: strain

tag: genotype

tag: treatment


title: Cbp3_W303 sel-mitoRP, rep1

description: Library name: Cbp3_W303_1


title: TET2_LPS_rep1

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: T1_LPS

library_source: transcriptomic

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Assembly: hg38
Supplementary files format and content: .csv, salmon raw gene counts and median-ratios normalized gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: iMG (induced Microglia)

growth_protocol: iPSCs were differentiated into iMGLs

extract_protocol:
200,000 iMGLs were collected and RNA extraction was performed with the RNeasy mini kit (QIAGEN).
RNA sequencing libraries were prepared by Azenta Life Sciences using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions

treatment_protocol: NS/ LPS

value: iMG (induced Microglia)

tag: cell type

value: LPS-treated

value: TET2 delE3-11/WT


title: DNMT3A_LPS_rep3

description: Library name: D3_LPS

value: DNMT3A R882H/WT


title: DNMT3A_LPS_rep2

description: Library name: D2_LPS


title: Mrps17_W303 sel-mitoRP, rep2

description: Library name: Mrps17_W303_2

value: MATa; leu2-3,112 trp1-1 ura3-1 ade2-1 his3-11,15 can1-100 nuc1::URA3 MRPS17-3xFLAG::TRP1


title: smc2-8_Input_3hr_Rep1

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description: Library name: smc2-8_Input_3hr_Rep1

library_source: genomic

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009).Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis. 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) (for single-end data) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Assembly: SK1 (Yue et al., 2017)
Supplementary files format and content: bedGraph files

molecule: genomic DNA

source_name: Nucleus

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C, except for H7606 which was innoculated at OD600 = 0.8 in BYTA medium and grown for 20 hours at room temperature. H7797 was also grown in BYTA medium at room temperature for the 34C experiments. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)). Rapamycin was added at 0h where indicated.

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013). A second sonication step was added just before library prep where indicated using a Bioruptor Pico (Diagenode, NJ, USA) with the following settings: 30 secs ON and 30 secs OFF for 5 cycles.
ChIP samples were processed as described in Blitzblau et al., 2012. The quality of the libraries was assessed using the 2100 Bioanalyzer or 2200 Tapestation. Library concentrations were quantified using qPCR prior to pooling. Sequencing was performed on Illumina NextSeq 500 instruments at the NYU Biology Genomics Core.

treatment_protocol: For 34C experiments, strains were shaken in SPO medium at room temperature for 1 hour and shifted to 34 degrees Celsius for the remaining time.

tag: tissue

value: Nucleus

value: Meiosis Hour 3

value: WT


title: BIN67-CnR H3K4me3-2

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description: Library name: Sample5

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2
Assembly: hg38
Supplementary files format and content: CUT&RUN: peak file per sample
Supplementary files format and content: RNA-seq: txt count file for all samples
Library strategy: CUT&Run

growth_protocol: BIN-67 cells were maintained in RPMI supplemented with 10% FBS and 1%Penicillin/Streptomycin. This maintenance media was also the same media that DMSO, dTAGV-1 and dTAGV-1-NEG was diluted in.

extract_protocol:
For RNA-seq, RNA was extracted from 2-3 million cells using Trizol and the Direct-zol RNA mini prep kit by Zymo Research. For CUT&RUN, 500,000 cells were bound to ConA beads and processed following the Cell Signaling CUT&RUN kit protocol. For MYC and IgG three separate reactions, equivalent to 1.5 million cells, was pooled together during the DNA purification step before library generation. For H3K4me3, one reaction was sufficient to achieve signal.
For RNA-seq, libraries were made at Novogene using their standard methods with polyA-enrichment. For CUT&RUN, we made libraries of purified DNA fragments using the NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina.

treatment_protocol: All cells were treated with 500 nM dTAGV-1, 500 nM dTAGV-1-NEG, or matched DMSO control for 24 hr (RNA-seq). For CUT&RUN, no treatment was performed prior to collection.

tag: cut&run antibody

value: H3K4me3, included in Cell Signaling kit

value: Cell Line

tag: genetic modification

value: N-terminal HA-FKBPF36V dTAG module on MYC

value: No treatment


title: Mrps17 cbp3KO sel-mitoRP, rep2

description: Library name: Mrps17_Cbp3_2

value: mrps17::MRPS17-3XF cbp3delta::kanMX6 MATa GAL2 HAP1 MIP1[S] G1981A ura3delta0


title: Mrps17_W303 sel-mitoRP, rep1

description: Library name: Mrps17_W303_1


title: WT_LPS_rep3

description: Library name: N3_LPS

value: Isogenic WT


title: WT_Input_3hr_antiHop1_Rep1

description: Library name: WT_Input_3hr_Rep1


title: Mrps17 cbp3KO sel-mitoRP, rep1

description: Library name: Mrps17_Cbp3_1


title: DNMT3A_LPS_rep1

description: Library name: D1_LPS


title: BIN67-CnR MYC-1

description: Library name: Sample3

value: MYC, Cell Signaling, 13987


title: Mrx4 cbp3KO sel-mitoRP, rep3

description: Library name: Mrx4_Cbp3_3

value: mrps17::MRPS17-3XHA mrx4::MRX4-3XF cbp3delta::kanMX6 MATa GAL2 HAP1 MIP1[S] G1981A ura3delta0


title: Mrx4 cbp3KO sel-mitoRP, rep2

description: Library name: Mrx4_Cbp3_2

value: sucrose cushion


title: TET2_Control_rep3

description: Library name: T3_ctrl

value: iMG (induced Microglia)

value: No Stimulation (NS)


title: Mrx4 cbp3KO sel-mitoRP, rep1

description: Library name: Mrx4_Cbp3_1


title: Cbs1 mrx4KO sel-mitoRP, rep1

description: Library name: Cbs1_mrx4_1

value: mrps17::MRPS17-3XHA cbs1::CBS1-3XF mrx4delta::kanMX6 MATa GAL2 HAP1 MIP1[S] G1981A ura3delta0


title: WT_LPS_rep1

description: Library name: N1_LPS

value: LPS-treated


title: BIN67-CnR IgG-1

description: Library name: Sample1

value: Normal igG, Cell Signaling, 2729


title: TET2_Control_rep2

description: Library name: T2_ctrl

value: TET2 delE3-11/WT


title: Cbs1 mrx4KO sel-mitoRP, rep2

description: Library name: Cbs1_mrx4_2


title: Mrps17 mrx4KO sel-mitoRP, rep2

description: Library name: Mrps17_mrx4_2

value: mrps17::MRPS17-3XF mrx4delta::kanMX6 MATa GAL2 HAP1 MIP1[S] G1981A ura3delta0


title: TET2_Control_rep1

description: Library name: T1_ctrl


title: DNMT3A_Control_rep3

description: Library name: D3_ctrl

value: DNMT3A R882H/WT


title: Mrps17 mrx4KO sel-mitoRP, rep1

description: Library name: Mrps17_mrx4_1


title: DNMT3A_Control_rep2

description: Library name: D2_ctrl


title: DNMT3A_Control_rep1

description: Library name: D1_ctrl


title: Mrx4 sel-mitoRP, rep2

description: Library name: Mrx4_2

value: mrps17::MRPS17-3XHA mrx4::MRX4-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3delta0


title: WT_LPS_rep2

description: Library name: N2_LPS


title: WT_Control_rep2

description: Library name: N2_ctrl


title: WT_Control_rep3

description: Library name: N3_ctrl


title: WT_Control_rep1

description: Library name: N1_ctrl


title: Mrx4 sel-mitoRP, rep1

description: Library name: Mrx4_1


title: Hypothalamus,green 3 days,rep5

city: Rehovot

first: Joanna

last: Bartman

address: Hertzl 229

country: Israel

institute: The Hebrew University of Jerusalem

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2H5

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt.Remaining reads were mapped onto 3’ UTR regions (1000 bases) of the , GRCg6a genome according to Ensembl (release 105) annotations, using STAR .Counts for each gene were quantified using htseq-count .
Assembly: GRCg6a
Supplementary files format and content: Counts matrix for downstream analysis. Each row is a gene and each column is a sample

molecule: total RNA

organism: Gallus gallus

source_name: hypothalamus

extract_protocol:
RNA was extarcted from frozen hypothalamus tissues using tri reagent.
75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output.

value: hypothalamus

value: whole cell tissue lysate

value: green last 3 days illuminated incubation


title: HepG2, ORF_Flag_2

city: Guangzhou

first: Lei

last: Zhao

address: Xinzao Road

country: China

institute: Guangzhou Medical University

description:
Library name: ORF_Flag_2
Column name in All_sample_counts.xls: ORF_Flag_2

data_processing:
The adapter and low-quality reads were filtered out through cutadapt (version 1.11). Clean reads were mapped to the reference genomes by Hisat2 (version 2.1.0), allowing up to two mismatches. These genes were subjected to alignment against public protein databases; NR (RefSeq non-redundant proteins). Featurecount (v1.6.0) was used for transcript abundance estimation and normalization of expression values as FPKM (Fragments per kilobase of transcript per million fragments mapped). Differentially expressed genes were identified with edgeR with a filter threshold of FDR<0.05 and |log2FoldChange| > 1.
Assembly: GRCh38
Supplementary files format and content: xls files include raw counts for each Sample

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries constructed with the VAHTS universal V10 Library Prep Kit

value: Human hepatocellular carcinoma cells


title: Hypothalamus,green 3 days,rep6

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2H6


title: HepG2, ORF_Flag_1

description:
Library name: ORF_Flag_1
Column name in All_sample_counts.xls: ORF_Flag_1


title: Hypothalamus,green 3 days,rep1

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2H1


title: Cbs2 sel-mitoRP, rep4

description: Library name: Cbs2_4

value: mrps17::MRPS17-3XHA cbs2::CBS2-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3delta0


title: Hypothalamus,green,male,rep9

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2E9

value: green illuminated incubation


title: HepG2, ORF_Flag_3

description:
Library name: ORF_Flag_3
Column name in All_sample_counts.xls: ORF_Flag_3


title: HepG2, NC_3

description:
Library name: NC_3
Column name in All_sample_counts.xls: NC_3


title: HepG2, NC_2

description:
Library name: NC_2
Column name in All_sample_counts.xls: NC_2


title: Control HaCaT cells

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

country: Japan

institute: Yamaguchi university

description: Library name: HaCaT_no

data_processing:
FASTQ files produced by Illimina NovaSeq6000 were imported to CLC Genomics Workbench software (ver.22.0.1).
The 3' end of the sequenced read was trimmed by one nucleotide. Reads with more than 2 ambiguous nucleotides and reads with low quality scores were removed using CLC Genomics Workbench software (ver.22.0.1).
Trimmed sequence reads were mapped to GRCh37 release-75 using CLC genomics workbench with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.22.0.1).
Assembly: GRCh37
Supplementary files format and content: Csv files include RPKM and TPM values for each sample.

source_name: Immortalized human keratinocytes

extract_protocol:
Total RNA was isolated from the each sample using the RNeasy Mini Kit (Qiagen). Polyadenylated mRNA was purified using oligo dT beads included in the NEBNext Poly (A) mRNA Magnet Isolation Module (New England Biolabs, NEB). Purified mRNA was used for the construction of sequencing libraries using NEBNext Ultra II RNA library Prep kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB).
The purified mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences included in NEBNext Multiplex Oligos for Illumina were inserted to cDNA fragments with PCR amplification. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Tapestation 4200 D1000 (Agilent). The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina NovaSeq6000 DNA sequencer with 50 bp paired-end cycle sequencing kit (Illumina).

value: Immortalized human keratinocytes

value: untreated


title: Cbs2 sel-mitoRP, rep3

description: Library name: Cbs2_3

value: sucrose cushion


title: HaCaT cells treated with AGE

description: Library name: HaCaT_AGE

value: treated with AGE


title: Hypothalamus,green,male,rep2

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2E2


title: Cbs2 sel-mitoRP, rep1

description: Library name: Cbs2_1


title: Hypothalamus,green 3 days,rep7

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2H7


title: sumatriptan (0uM) treatment_3

city: Kawasaki

first: Tatsuto

last: Kageyama

state: Kanagawa

address: Life Innovation Center, 3-25-22 Tonomachi

institute: Kanagawa Institute of Industrial Science and Technology

description:
Library name: Sample8
Suma.txt
TV0149_06

data_processing:
Data processing were conducted using NovaSeq Control Software v1.7.5, Real Time Analysis (RTA) v3.4.4, bcl2fastq2 v2.20, and DRAGEN Bio-IT Platform v3.9.3
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes row counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: hair follicle

growth_protocol: Adult human DP cells were obtained from PromoCell (Heidelberg, Germany), passaged up to passage four with dermal papilla cell growth medium (DPCGM), and used for 2D culture.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen) from DP cells 100 μM 5-HT or 50 μM Sumatriptan succinate.
RNA library for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit

treatment_protocol: Dermal papilla cells (2 × 104 cells) were cultured in 0.5 mL DPCGM medium supplemented with/without 100 μM 5-HT or 50 μM Sumatriptan succinate. Gene expression in DP cells was assessed after 3 days of culture.

value: hair follicle

value: dermal papilla cells

value: sumatriptan (0uM)


title: sumatriptan (0uM) treatment_2

description:
Library name: Sample7
Suma.txt
TV0149_05


title: Hypothalamus,white,male,rep7

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2C7

value: white illuminated incubation


title: sumatriptan (0uM) treatment_1

description:
Library name: Sample6
Suma.txt
TV0149_04


title: Hypothalamus,white,male,rep6

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2C6


title: sumatriptan (50uM) treatment_2

description:
Library name: Sample4
Suma.txt
TV0149_02

value: sumatriptan (50uM)


title: Cbs1 sel-mitoRP, rep3

description: Library name: Cbs1_3

value: mrps17::MRPS17-3XHA cbs1::CBS1-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3delta0


title: sumatriptan (50uM) treatment_3

description:
Library name: Sample5
Suma.txt
TV0149_03


title: Cbs1 sel-mitoRP, rep4

description: Library name: Cbs1_4


title: Cbs1 sel-mitoRP, rep2

description: Library name: Cbs1_2


title: Hypothalamus,white,male,rep3

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2C3


title: 5HT (0uM) treatment_1

description:
Library name: Sample2
5HT.txt

value: 5HT (0uM)


title: sumatriptan (50uM) treatment_1

description:
Library name: Sample3
Suma.txt
TV0149_01


title: Hypothalamus,white,male,rep1

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2C1

value: hypothalamus


title: Mrx1 sel-mitoRP, rep3

description: Library name: Mrx1_3

data_processing:
*library strategy: selective mitoRibo-seq
Reads were trimmed to remove ligated 3’ linker (CTGTAGGCACCATCAAT) with Cutadapt (Martin. EMBnet.journal, 2011. DOI:10.14806/ej.17.1.200). Reads without linker were discarded and the unique molecular identifier (UMI, consisting of 4 random nucleotides introduced at the 5’ end with the RT primer and 10 random nucleotides introduced at the 3’ end with the linker) was then extracted from remaining reads using a custom script. For all Aep1, Aep2, and the first two replicates of Cbs1 samples, synthetic COX2 RNA oligos of 40 and 33 nucleotides (UAACAACAUUCAUUAUGAAUGAUGUACCAACACCUUAUGC and UAACAACAUUCAUUAUGAAUGAUGUACCAACAC) were used as size markers in a separate gel lane during mitoribosome footprint size selection. The oligos contaminated some of the Aep1 and Aep2 samples that were run in adjacent lanes and were removed in silico using BBTools’ BBDuk (sourceforge.net/projects/bbmap/) with a k-mer length of 30.
Reads mapping to abundant non-coding RNAs (rRNA, tRNA) were filtered out after alignment using bowtie1 (Langmead et al. Genome Biology, 2009). Remaining reads were aligned to the S. cerevisiae genome assembly R64 (UCSC: sacCer3) using STAR 2.7.3 (Dobin et al. Bioinformatics, 2013). PCR duplicates were identified by their UMI and removed using a custom script.
Ribosome A site positions were determined using an offset from the 3’ end of each read, depending on its length: 37:[-15], 38:[-16], 39:[-17], 40:[-17], 41:[-17]. Shorter read lengths have ambiguous offsets and were omitted.
Unless otherwise noted, read counts at each A site position were summed across replicates (2 to 6 replicates for each sample) and normalized by total mitochondrial mRNA-mapping reads (rpm). Enrichment over total mitoribosomes was then calculated by summing rpm values in a sliding 9-nt window and dividing by the corresponding sum in the total (Mrps17) dataset.
A threshold was set so that if more than 3 positions had no coverage in either sample the enrichment value was set to 0. This was to avoid spurious signal due to low coverage.
Assembly: Saccharomyces cerevisiae  assembly R64 (UCSC: sacCer3)
Supplementary files format and content: Processed data files ending in *Mito_mRNA.noDups.Asite_37to41_P.rpm.bedGraph are rpm-normalized bedGraph files for each replicate. These have been A-site transformed and only use reads sized 37 to 41 nt.
Supplementary files format and content: Processed data files ending in *Mito_mRNA.noDups.Asite_37to41_PAll.rpm_Mrps17_normRollWin9_max3zeros_forIGV_nolog.bedGraph are made by summing the rpm values for each replicate of a sample then normalizing to the respective Mrps17 data, as described. Columns are 1) chromosome 2) Window-normalized A-site position - 1 3) Window-normalized A-site A-site position 4) Value (fold enrichement) 5) Log1p raw sample counts in window 6) Log1p raw norm sample counts in window
Supplementary files format and content: Only plus-strand data is included for all processed files

value: mrps17::MRPS17-3XHA mrx4::MRX1-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: 5HT (100uM) treatment_1

description:
Library name: Sample1
5HT.txt


title: Cbs2 sel-mitoRP, rep2

description: Library name: Cbs2_2


title: Hypothalamus,green,male,rep7

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2E7

value: whole cell tissue lysate


title: Homo sapiens, THP-1 Cells, experiment Peri drug group

city: Shenzhen

first: Wenjie

last: Li

address: 3025 Shennan Middle Road

department: Department of Hematology

institute: Sun Yat-sen University

description:
Library name: THP-1-Peri
Column name gene_count.txt: THP-1-Peri_count

data_processing:
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: hg38
Supplementary files format and content: Tab separated table count values of genes for each sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: experiment


title: HepG2, NC_1

description:
Library name: NC_1
Column name in All_sample_counts.xls: NC_1

value: Human hepatocellular carcinoma cells


title: Homo sapiens, THP-1 Cells, control blank

description:
Library name: THP-1-DMSO
Column name gene_count.txt: THP-1-DMSO_count

value: Control blank


title: Homo sapiens, K562 Cells, control blank

description:
Library name: K562-DMSO
Column name gene_count.txt: K562-DMSO_count


title: Mrx1 sel-mitoRP, rep1

description: Library name: Mrx1_1


title: Hypothalamus,dark,male,rep6

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2A6

value: dark


title: Atp22 smt1KO sel-mitoRP, rep3

description: Library name: Atp22smt1d_3

value: mrps17::MRPS17-3XHA atp22::ATP22-3XF smt1{delta}::kanMX6 MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: white adipocyte + Control - Subject 4

city: Copenhagen

first: Søren

last: Nielsen

address: Blegdamsvej 9

department: 1The Centre for Physical Activity Research

country: Denmark

institute: Rigshospitalet

description: Library name: SHBG4_2

data_processing:
STAR aligner 2.7.9
Assembly: Ensembl 105
Supplementary files format and content: Counts data

source_name: Abdominal subcutaneous adipose tissue

growth_protocol: human ASPCs were maintained in proliferation media (DMEM/F-12 supplemented with 10% FBS, 1% PenStrep and 1 nM FGF-1). Adipocyte differentiation was induced two days after adipocyte progenitor cultures were 100% confluent by removal of FGF-1 from the media and addition of a differentiation cocktail consisting of DMEM/F12 containing 1% PS, 0.1 μM dexamethasone (Sigma– Aldrich), 100 nM insulin (Actrapid, Novo Nordisk or Humulin, Eli Lilly), 200 nM rosiglitazone (Sigma– Aldrich), 540 μM isobutylmethylxanthine (IBMX, Sigma–Aldrich), 2 nM T3 (Sigma–Aldrich) and 10 μg/ml transferrin (Sigma–Aldrich). After three days of differentiation, IBMX was removed from the cell culture media and cells were differentiated for an additional three days with the remaining differentiation compounds. Following this, rosiglitazone was removed from the media and cells were differentiated for an additional six days before the cells were considered fully differentiated.

extract_protocol:
RNA was harvested in TRIzol. RNA was isolated with the Qiagen RNeasy Micro kit using the "RNA Cleanup after lysis and homogenization with QIAzol lysis reagent".  250 ng total RNA were used for the construction of sequencing libraries.
Tecan Universal Plus Total RNA-seq library preparation kit

treatment_protocol: stimulation of adipocytes with purified human SHBG (Bio-Rad, Hercules, California, USA, Cat# PHP147) was done by adding SHBG to the media once, in relation to the last media change during differentiation (three days), in a concentration of 100 nM.

value: Abdominal subcutaneous adipose tissue

value: Primary cells differentiated from tissue-extracted progenitors

value: Adipocytes

value: control


title: white adipocyte + Control - Subject 3

description: Library name: SHBG3_2


title: Hypothalamus,dark,male,rep5

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2A5


title: white adipocyte + SHBG - Subject 3

description: Library name: SHBG3_1


title: Atp22 smt1KO sel-mitoRP, rep1

description: Library name: Atp22smt1d_1

value: sucrose cushion


title: white adipocyte + Control - Subject 1

description: Library name: SHBG1_2


title: white adipocyte + SHBG - Subject 4

description: Library name: SHBG4_1


title: Atp22 smt1KO sel-mitoRP, rep2

description: Library name: Atp22smt1d_2


title: Hypothalamus,dark,male,rep4

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2A4


title: Spike-specific memory B cells, Post Dose 3 Timepoint 6, BCR

city: Toronto

first: Tania

middle: H

last: Watts

state: Ontario

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

description:
Library name: Post dose 3_memory B cells_BCR
BCR sequencing

data_processing:
CITE-seq: FASTQ paired-end reads were processed using the cellranger count command from 10x Genomics’ Cell Ranger (v.8.0.0) and aligned against the human reference refdata-gex-GRCh38-2024-A. BCR-seq: FASTQ paired-end reads were processed using cellranger vdj command 10x Genomics’ Cell Ranger (v8.0.0) and aligned to the VDJ reference- vdj_GRCh38_alts_ensembl-7.1.0.
CITE-seq: Raw UMI count matrices were generated by the cellranger pipeline.
BCR-seq: filtered_contig.fasta and filtered_contig_annotations.csv outputted by cellranger were then used to assign V,D, and J genes using IgBlast as described here: https://immcantation.readthedocs.io/en/stable/getting_started/10x_tutorial.html#assign-v-d-and-j-genes-using-igblast. In brief, V(D)J contigs were processed using the Immcantation framework (v4.5.0). Contigs were aligned to the IMGT reference using IgBLAST (v4.5.0, installed in the Docker container “immcantation/suite”).
Assembly: refdata-gex-GRCh38-2024-A
Supplementary files format and content: CITE-seq GEX and HTO (libraries are combined in tsv and matrix files): Tab-separated values files and matrix files. Files are found in Supplementary Files
Supplementary files format and content: BCR-seq: Timepoint4_BCR_filtered_contig.fasta and Timepoint6_BCR_filtered_contig.fasta (fasta files contain assembled contigs),  Timepoint4_BCR_filtered_contig_annotations.csv and Timepoint6_BCR_filtered_contig_annotations.csv (csv files contain contig annotations), Timepoint4_BCR_igblast_db-pass.tsv and timepoint6_BCR_igblast_db-pass.tsv (post contig alignment using IgBlast, contains AIRR rearrangement data in tab-separated values files)
Supplementary files format and content: Timepoint4_feature_reference.csv contains feature reference information for Timepoint 4. Timepoint6_feature_reference.csv contains feature reference information for Timepoint 6.

source_name: blood

extract_protocol:
Spike-specific memory B cells (bound to Spike-PE tetramer) were sorted from the PBMCs of healthy controls (n=3), anti-TNF treated IBD patients (n=5) and anti-IL-12/23 treated IBD patients (n=4). Post dose 2 (Timepoint 4) and post dose 3 (Timepoint 6) samples were sorted and sequenced in two batches, by Timepoint. Single cells were encapsulated in Gel-Beads-in emulsions (GEMs) using a 10X Genomics Chromium X with the Chromium GEM-X Single Cell 5' Kit v3.
CITE-seq gene expression libraries (Single Cell 5' R2-only v3, 10X Genomics) and BCR V(D)J libraries (Single Cell V(D)J R2-only v3, 10X Genomics) were prepared as recommended by the 10X Genomics user guides.

value: blood

value: B cell

value: mixed samples (immunized)

tag: library type

value: BCR

tag: batch


title: white adipocyte + SHBG - Subject 2

description: Library name: SHBG2_1


title: white adipocyte + SHBG - Subject 1

description: Library name: SHBG1_1


title: Mrps17 smt1KO sel-mitoRP, rep3

description: Library name: Mrps17smt1d_3

value: mrps17::MRPS17-3XF smt1{delta}0 MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: Spike-specific memory B cells, Post Dose 3 Timepoint 6, HTO

description:
Library name: Post dose 3_memory B cells_HTO
Hashtag-derived oligonucleotide (HTO)

data_processing:
CITE-seq: FASTQ paired-end reads were processed using the cellranger count command from 10x Genomics’ Cell Ranger (v.8.0.0) and aligned against the human reference refdata-gex-GRCh38-2024-A. BCR-seq: FASTQ paired-end reads were processed using cellranger vdj command 10x Genomics’ Cell Ranger (v8.0.0) and aligned to the VDJ reference- vdj_GRCh38_alts_ensembl-7.1.0.
CITE-seq: Raw UMI count matrices were generated by the cellranger pipeline.
BCR-seq: filtered_contig.fasta and filtered_contig_annotations.csv outputted by cellranger were then used to assign V,D, and J genes using IgBlast as described here: https://immcantation.readthedocs.io/en/stable/getting_started/10x_tutorial.html#assign-v-d-and-j-genes-using-igblast. In brief, V(D)J contigs were processed using the Immcantation framework (v4.5.0). Contigs were aligned to the IMGT reference using IgBLAST (v4.5.0, installed in the Docker container “immcantation/suite”).
Assembly: refdata-gex-GRCh38-2024-A
Supplementary files format and content: CITE-seq GEX and HTO (libraries are combined in tsv and matrix files): Tab-separated values files and matrix files. Files are found in Supplementary Files
Supplementary files format and content: BCR-seq: Timepoint4_BCR_filtered_contig.fasta and Timepoint6_BCR_filtered_contig.fasta (fasta files contain assembled contigs),  Timepoint4_BCR_filtered_contig_annotations.csv and Timepoint6_BCR_filtered_contig_annotations.csv (csv files contain contig annotations), Timepoint4_BCR_igblast_db-pass.tsv and timepoint6_BCR_igblast_db-pass.tsv (post contig alignment using IgBlast, contains AIRR rearrangement data in tab-separated values files)
Supplementary files format and content: Timepoint4_feature_reference.csv contains feature reference information for Timepoint 4. Timepoint6_feature_reference.csv contains feature reference information for Timepoint 6.
Library strategy: CITE-seq

molecule: protein

value: HTO

tag: hto

value: TotalSeq_C_0251_anti-human_Hashtag_1 (healthy control #1), TotalSeq_C_0252_anti-human_Hashtag_2 (healthy control #2), TotalSeq_C_0253_anti-human_Hashtag_3 (healthy control #3), TotalSeq_C_0254_anti-human_Hashtag_4 (anti-IL-12/23 treated IBD patient #1), TotalSeq_C_0255_anti-human_Hashtag_5 (anti-IL-12/23 treated IBD patient #2), TotalSeq_C_0256_anti-human_Hashtag_6 (anti-IL-12/23 treated IBD patient #3), TotalSeq_C_0257_anti-human_Hashtag_7 (anti-IL-12/23 treated IBD patient #4), TotalSeq_C_0258_anti-human_Hashtag_8 (anti-TNF treated IBD patient #1), TotalSeq_C_0259_anti-human_Hashtag_9 (anti-TNF treated IBD patient #2), TotalSeq_C_0260_anti-human-Hashtag_10 (anti-TNF treated IBD patient #3), TotalSeq_C_0296_anti-human_Hashtag_11 (anti-TNF treated IBD patient #4)


title: Mrx1 sel-mitoRP, rep2

description: Library name: Mrx1_2

value: mrps17::MRPS17-3XHA mrx4::MRX1-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: Hypothalamus,dark,male,rep8

description:
Sequencing Libraries were prepared using Bulk MARS-Seq. 75 SR reads were sequenced on 4 lane(s) of an Illumina NextSeq High output. The output was ~15 million reads per sample.
H2A8

value: hypothalamus

value: whole cell tissue lysate


title: Mrps17 smt1KO sel-mitoRP, rep2

description: Library name: Mrps17smt1d_2


title: 888mel:IgSF11-/-_2

city: Fukushima

first: Yasuyuki

last: Kobayashi

state: Fukushima

address: Hikarigaoka 1

institute: Fukushima medical university

description: Library name: Sample 8

data_processing:
RNA sequencing was performed by Rhelixa, by using Illumina Nova Seq 6000. The raw data was mapped to human reference genome (GRCh38) by bowtie2. The index trimmed paired-ended 150 bp reads were aligned to the reference to generate bam files.
The mapped bam files were imported to SeqMonk software (Babraham Bioinformatics; https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) as paired ended RNA-Seq data.
Quantification was performed by using the default RNA-Seq quantitation pipeline.
P-value was calculated from the intensity difference and representative genes of showing significant change (P<0.05)
Assembly: GRCh38
Supplementary files format and content: Matrix table with gene expression ratio for every gene

source_name: Melanoma

growth_protocol: Dulbecco's Modified Eagle medium supplimented with 10% Fetal bovine serum and 1% penicillin streptomycin

extract_protocol:
Total RNA isolaton was performed using TRIzol reagent (Thermo Fisher) and its standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Melanoma

value: IgSF11 knockout


title: 888mel:IgSF11-/-_1

description: Library name: Sample 7


title: Spike-specific memory B cells, Post Dose 3 Timepoint 6, GEX

description:
Library name: Post dose 3_memory B cells_mRNA
polyA RNA

value: mRNA


title: 888mel_2

description: Library name: Sample 6

value: WT


title: 888mel_1

description: Library name: Sample 5


title: Homo sapiens, K562 Cells, experiment Peri drug group

description:
Library name: K562-Peri
Column name gene_count.txt: K562-Peri_count

value: experiment


title: A375:IgSF11_2

description: Library name: Sample 4

value: IgSF11 overexpression


title: Smt1 sel-mitoRP, rep2

description: Library name: Smt1_2

value: mrps17::MRPS17-3XHA smt1::SMT1-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0

value: sucrose cushion


title: A375:IgSF11_1

description: Library name: Sample 3


title: white adipocyte + Control - Subject 2

description: Library name: SHBG2_2

value: Abdominal subcutaneous adipose tissue

value: Primary cells differentiated from tissue-extracted progenitors

value: Adipocytes

value: control


title: A375_2

description: Library name: Sample 2


title: Spike-specific memory B cells, Post Dose 2 Timepoint 4,  HTO

description:
Library name: Post dose 2_memory B cells_HTO
Hashtag-derived oligonucleotide (HTO)

value: blood

value: B cell

value: mixed samples (immunized)

value: HTO

value: TotalSeq_C_0251_anti-human_Hashtag_1 (healthy control #1), TotalSeq_C_0252_anti-human_Hashtag_2 (healthy control #2), TotalSeq_C_0253_anti-human_Hashtag_3 (healthy control #3), TotalSeq_C_0254_anti-human_Hashtag_4 (anti-IL-12/23 treated IBD patient #1), TotalSeq_C_0255_anti-human_Hashtag_5 (anti-IL-12/23 treated IBD patient #2), TotalSeq_C_0256_anti-human_Hashtag_6 (anti-IL-12/23 treated IBD patient #3), TotalSeq_C_0257_anti-human_Hashtag_7 (anti-IL-12/23 treated IBD patient #4), TotalSeq_C_0258_anti-human_Hashtag_8 (anti-TNF treated IBD patient #1), TotalSeq_C_0259_anti-human_Hashtag_9 (anti-TNF treated IBD patient #2), TotalSeq_C_0260_anti-human-Hashtag_10 (anti-TNF treated IBD patient #3), TotalSeq_C_0296_anti-human_Hashtag_11 (anti-TNF treated IBD patient #4), TotalSeq_C_0262_anti-human_Hashtag_12 (anti-TNF treated IBD patient #5)


title: Smt1 sel-mitoRP, rep1

description: Library name: Smt1_1


title: A375_1

description: Library name: Sample 1

value: Melanoma


title: Pet111 sel-mitoRP, rep2

description: Library name: Pet111_2

value: mrps17::MRPS17-3XHA pet111::PET111-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: ResA_siNTC_2

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

description: Library name: Sample 11

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018).FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Assembly: hg38
Supplementary files format and content: The columns of the counts.txt files are: (1) ensemble gene name; (2) gene symbol; (3) sample read count

source_name: ResA

growth_protocol: PC3 cells were cultured in RPMI + 10% FBS. ResA cells were cultured in RPMI + 10% FBS + 10µM Enzalutamide.

extract_protocol:
RNA was extracted from harvested cells using the RNeasy Plus Mini Kit (Qiagen cat# 74034) according to the manufacturer’s protocol.
The libraries were barcoded, pooled, and sequenced using paired-end, 151 bp sequencing at the University of Michigan Advanced Genomics Core.

treatment_protocol: siNTC (Non-targeting control siRNA) or siCDK2 (siRNA targeting CDK2) were transfected usign Lipofectamine 3000 (Thermo Fisher Scientifc cat# L3000015).

value: ResA

value: siNTC


title: ResA_siNTC_1

description: Library name: Sample 10


title: Pet111 sel-mitoRP, rep1

description: Library name: Pet111_1


title: ResA_siCDK2_3

description: Library name: Sample 9


title: ResA_siNTC_3

description: Library name: Sample 12


title: Spike-specific memory B cells, Post Dose 2 Timepoint 4, GEX

description:
Library name: Post dose 2_memory B cells_mRNA
polyA RNA

value: mRNA


title: Mrps17 smt1KO sel-mitoRP, rep1

description: Library name: Mrps17smt1d_1

value: mrps17::MRPS17-3XF smt1{delta}0 MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: 11_CTR

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

description:
Library name: 11_CTR
mapped to HG38

data_processing:
Aligned: STAR,  Ref.genome: Homo_sapiens.GRCh38.dna.primary_assembly.fa (Ensembl),
quantification: featureCounts
Assembly: HG38
Supplementary files format and content: matrix with ENS number and samples in each one column

source_name: Primary activated CD4 cells from PBMC

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells,

extract_protocol:
Total RNA purification (Norgen, Ontario, Canada)
RNA-seq

treatment_protocol: culture activated with anti-CD3, 48h with or without Insulin, 10nM

value: Primary activated CD4 cells from PBMC

tag: person

value: CTRL


title: Spike-specific memory B cells, Post Dose 2 Timepoint 4, BCR

description:
Library name: Post dose 2_memory B cells_BCR
BCR sequencing

value: BCR


title: Aep2 sel-mitoRP, rep6

description: Library name: Aep2_6

value: mrps17::MRPS17-3XHA aep2::AEP2-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0

value: sucrose cushion


title: ResA_siCDK2_2

description: Library name: Sample 8


title: 10_INS

description:
Library name: 10_INS
mapped to HG38

value: Insulin 10nM


title: Aep2 sel-mitoRP, rep5

description: Library name: Aep2_5


title: ResA_siCDK2_1

description: Library name: Sample 7


title: PC3_siNTC_1

description: Library name: Sample 4


title: Aep2 sel-mitoRP, rep4

description: Library name: Aep2_4


title: PC3_siNTC_3

description: Library name: Sample 6


title: 10_CTR

description:
Library name: 10_CTR
mapped to HG38


title: PC3_siCDK2_3

description: Library name: Sample 3


title: PC3_siCDK2_2

description: Library name: Sample 2


title: Aep1 sel-mitoRP, rep4

description: Library name: Aep1_4

value: mrps17::MRPS17-3XHA aep1::AEP1-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: 08_CTR

description:
Library name: 08_CTR
mapped to HG38


title: 08_INS

description:
Library name: 08_INS
mapped to HG38


title: 243I,RPMI - FBS,RNA-seq

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

data_processing:
nf-core RNAseq pipeline version 3.10.1
Assembly: Refseq hg38 and NC_001802.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: PBMC

extract_protocol:
Zymo Quick DNA/RNA Microprep Kit
RNA libraries for RNA-seq were prepared using NuGen Universal RNA Seq Kit following the manufacturer's protocol, sequenced using SP200 flow cell and 100bp paired end.

value: PBMC

value: Monocyte Derived Macrophage

value: utx


title: 243J,RPMI - FBS,RNA-seq

value: DA


title: PC3_siCDK2_1

description: Library name: Sample 1


title: Aep1 sel-mitoRP, rep3

description: Library name: Aep1_3


title: 11_INS

description:
Library name: 11_INS
mapped to HG38


title: 07_INS

description:
Library name: 07_INS
mapped to HG38


title: Aep1 sel-mitoRP, rep2

description: Library name: Aep1_2


title: 243F,SFM,RNA-seq


title: 243G,DMEM - FBS,RNA-seq


title: 04_CTR

description:
Library name: 04_CTR
mapped to HG38


title: 243A,DMEM + FBS,RNA-seq


title: 03_INS

description:
Library name: 03_INS
mapped to HG38


title: 243H,DMEM - FBS,RNA-seq


title: 07_CTR

description:
Library name: 07_CTR
mapped to HG38


title: PC3_siNTC_2

description: Library name: Sample 5


title: Cbp1 sel-mitoRP, rep2

description: Library name: Cbp1_2

value: mrps17::MRPS17-3XHA cbp1::CBP1-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: 03_CTR

description:
Library name: 03_CTR
mapped to HG38


title: 243E,SFM,RNA-seq


title: 243D,RPMI + FBS,RNA-seq


title: Atp22 sel-mitoRP, rep1

description: Library name: Atp22_1

value: mrps17::MRPS17-3XHA atp22::ATP22-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: 04_INS

description:
Library name: 04_INS
mapped to HG38


title: 242G,DMEM - FBS,RNA-seq


title: 243B,DMEM + FBS,RNA-seq


title: Atp22 sel-mitoRP, rep3

description: Library name: Atp22_3


title: 242J,RPMI - FBS,RNA-seq


title: Atp22 sel-mitoRP, rep2

description: Library name: Atp22_2


title: Cbp1 sel-mitoRP, rep1

description: Library name: Cbp1_1


title: 243C,RPMI + FBS,RNA-seq


title: Aep3 sel-mitoRP, rep3

description: Library name: Aep3_3

value: mrps17::MRPS17-3XHA aep3::AEP3-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: 242I,RPMI - FBS,RNA-seq


title: Aep3 sel-mitoRP, rep2

description: Library name: Aep3_2


title: 242H,DMEM - FBS,RNA-seq


title: Sample 22, NP cells, cRGD + IGM3, Day 4

city: St. Louis

first: Nathaniel

last: Huebsch

state: MO

address: 1 Brookings Drive

department: Biomedical Egnineering

institute: Washington University in St.Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0. All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: Ensembl GRCh38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Nucleus Pulposus

growth_protocol: NP cells were enzymatically isolated from surgical waste tissue (exempt from IRB review, Washington University Institutional Review Board) as previously described in Gilchrist+, 2011, PLoS One (volume 6, no. 11). Briefly, tissue fractions were removed from surgical samples and digested for 4 h at 37°C and 5% CO2 in medium containing 0.4% type II collagenase.  and 2% pronase.  Cells were passed through a 70 μm cell strainer.  The isolated cells (P0) were plated in tissue culture flasks in Ham’s F12 medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S) until confluence. For co-culture experiments, primary human NP were seeded in the bottom wells of 24-well Transwell plates  with 0.4 μm permeable polyester membrane inserts. These cells were cultured at a density of 30,000 cells per well in F12 medium containing 10% FBS and 1% pencillin-streptomycin under hypoxic condition (37°C and 5% CO2 and 2% O2) for 24 h before co-culture with MSCs.

extract_protocol:
After 4 days, mRNA was extracted using the Rneasy mini kit with DNase I digestion (Qiagen). RNA quality was ensured to be greater than 8 using a Bioanalyzer (Agilent). Ds-cDNA was consructed using Clontech SMARTer Ultra Low RNA kit for Illumina Sequencing. cDNA was fragmented using a Covaris E220 sonicator. cDNA was blunt ended, an A base added to 3' ends, and then Illumina sequencing adapters ligated to the ends. Ligated fragments were amplified for 12 cycles and run on an Illumina NovaSeq reading 150 bases from both ends to a depth of 30 million reads per sample.
RNA libraries were prepared using SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol

treatment_protocol: Cells were on TCPS Transwell co-culture with MSC encapsulated in alginate, cRGD-alginate, or cRGD/IGM-3-alginate in medium containing no serum challenged with 1ng/mL IL-1β for 4 days

value: Nucleus Pulposus

value: nucleus pulposus cells

value: co-cultured with MSCs in cRGD + IGM3, IL-1B


title: Sample 20, NP cells, Alginate, Day 4

value: co-cultured with MSCs in alginate, IL-1B


title: 242F,SFM,RNA-seq


title: 242D,RPMI + FBS,RNA-seq


title: Sample 21, NP cells, cRGD, Day 4

value: co-cultured with MSCs in cRGD, IL-1B


title: 242E,SFM,RNA-seq


title: 242B,DMEM + FBS,RNA-seq


title: Aep3 sel-mitoRP, rep1

description: Library name: Aep3_1


title: 242C,RPMI + FBS,RNA-seq


title: 242A,DMEM + FBS,RNA-seq


title: Sample 19, NP cells, Day 4

value: TCPS monolayer, IL-1B


title: 224J,RPMI - FBS,RNA-seq


title: 224I,RPMI - FBS,RNA-seq


title: Pet309 sel-mitoRP, rep2

description: Library name: Pet309_2

value: mrps17::MRPS17-3XHA pet309::PET309-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: Sample 18, NP cells, cRGD + IGM3, Day 4


title: 224G,DMEM - FBS,RNA-seq


title: Pet309 sel-mitoRP, rep1

description: Library name: Pet309_1

value: sucrose cushion


title: 224H,DMEM - FBS,RNA-seq


title: Sample 17, NP cells,  cRGD, Day 4


title: 224E,SFM,RNA-seq


title: 224F,SFM,RNA-seq


title: Mrps17 sel-mitoRP, rep1

description: Library name: Mrps17_1

value: mrps17::MRPS17-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: Mrps17 sel-mitoRP, rep2

description: Library name: Mrps17_2


title: 224D,RPMI + FBS,RNA-seq


title: Sample 16, NP cells,  Alginate, Day 4


title: 221I,RPMI - FBS,RNA-seq


title: SCC2-FRB SMC4-PK9 + rapa resonicated anti-Rec8 rep2

description: AH9722B-788-813-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009).Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis.
3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) (for single-end data) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Axis sites (Red1 summits in wild type conditions) were identified using MACS2 narrow and -log10 qvalue of 20.
Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph
Supplementary_files_format_and_content: bed

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)). Rapamycin was added at 0h where indicated.

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013). A second sonication step was added just before library prep where indicated using a Bioruptor Pico (Diagenode, NJ, USA) with the following settings: 30 secs ON and 30 secs OFF for 5 cycles.
Library preparation was performed using Illumina TruSeq DNA Sample Prep Kits v1 but adaptors were used at 1:20 dilution. Amplified ChIP DNA between 300 and 500bp was gel purified on 1.8% agarose gel. Quality of all libraries was checked on 2200 Tapestation or Agilent 2100 Bioanalyzer. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 51 bp single-end or paired-end reads.

tag: meiotic time point

value: 3 hour

tag: antibody


title: Lymphocytes, LNs, Naive

first: Pablo

last: Penaloza-MacMaster

address: 3 Blackfan Circle

department: CVVR

institute: Beth Israel Deaconess Medical Center

description:
Library name: Naive
10x Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell RNA sequencing data from mouse samples were processed using the Cell Ranger (cloud analysis) pipeline developed by 10x Genomics. Raw base call (BCL) files were demultiplexed into FASTQ files using the cellranger mkfastq command, with sample sheet information specifying index assignment. If FASTQ files were already available, this step was skipped. Reads were aligned to the mouse reference genome (mm10) using the cellranger count pipeline with default parameters. The mm10 reference transcriptome provided by 10x Genomics (refdata-gex-mm10-2020-A) was used for alignment and gene annotation. During this process, Cell Ranger performed read alignment using STAR, filtered and corrected barcodes, quantified unique molecular identifiers (UMIs), and generated a gene-cell count matrix. The resulting filtered_feature_bc_matrix directory containing the gene-barcode count matrix was used for downstream analysis. Cell Ranger also provided quality control metrics and summary statistics in the web_summary.html file.
Assembly: Mouse mm10
Supplementary files format and content: Protein_barcodes.tsv.gz, Protein_features.tsv.gz, Ad5_barcodes.tsv.gz, Ad5_features.tsv.gz: Tab separated barcodes and features files
Supplementary files format and content: Naive_sample_filtered_feature_bc_matrix.h5, mRNA_sample_filtered_feature_bc_matrix.h5: HDF5 file
Supplementary files format and content: Protein_matrix.mtx.gz, Ad5_matrix.mtx.gz: MEX matrix file

organism: Mus musculus

source_name: Lymph nodes

extract_protocol:
C57BL/6 mice were immunized intramuscularly with each respective vaccine. At day 1 post-vaccination, lymph nodes from five mice were pooled and MACS-sorted with a CD45 MACS positive selection kit (STEMCELL) and used for single-cell sequencing.
Library was performed accodring to the manufacturer's instructions  (Chromium GEM-X Single Cell 5' Reagent Kits v3).

value: Lymph nodes

value: Lymphocytes

value: Immune cells

value: Control


title: Sample 13, NP cells, cRGD, Day 4


title: 224B,DMEM + FBS,RNA-seq

value: PBMC

value: Monocyte Derived Macrophage

value: DA


title: SCC2-FRB + rapa resonicated input rep2

description: AH9724I-793-820-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: SCC2-FRB + rapa resonicated input rep2


title: Lymphocytes, LNs, Protein

description:
Library name: Protein
10x Genomics

value: Protein vaccine


title: 224A,DMEM + FBS,RNA-seq

value: utx


title: Sample 14, NP cells,  cRGD + IGM3, Day 4

value: Nucleus Pulposus

value: nucleus pulposus cells

value: co-cultured with MSCs in cRGD + IGM3, IL-1B


title: 224C,RPMI + FBS,RNA-seq


title: SCC2-FRB + rapa resonicated anti-PK9 rep2


title: Sample 12, NP cells,  Alginate, Day 4

value: co-cultured with MSCs in alginate, IL-1B


title: 221G,DMEM - FBS,RNA-seq


title: Sample 15, NP cells, Day 4

value: TCPS monolayer, IL-1B


title: 221H,DMEM - FBS,RNA-seq


title: Sample 10, NP cells,  cRGD + IGM3, Day 4


title: Sample 11, NP cells, Day 4


title: Lymphocytes, LNs, mRNA

description:
Library name: mRNA
10x Genomics

value: mRNA vaccine


title: 221F,SFM,RNA-seq


title: 221E,SFM,RNA-seq


title: Sample 9, NP cells,  cRGD, Day 4

value: co-cultured with MSCs in cRGD, IL-1B


title: Lymphocytes, LNs, Ad5

description:
Library name: Ad5
10x Genomics

value: Ad5 vaccine


title: SCC2-FRB + rapa resonicated input rep1

source_name: SCC2-FRB + rapa resonicated input rep1

value: 3 hour


title: 221D,RPMI + FBS,RNA-seq


title: E16.5 Sox10-Cre 2 ; Eed Fl/Fl craniofacial tissue,  H3K27me3 Cut & Tag

city: San Francisco

first: Angelo

last: Pelonero

state: CA

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

description: Library name: KO_E165_R2 H3k27Me3

data_processing:
Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq
fastqs aligned to GRCm38 via nfcore cut and run v 3.2.2
Assembly: GRCm38
Supplementary files format and content: BigWig Coverage Tracks
Library strategy: CUT&Tag

source_name: craniofacial

extract_protocol:
Active Motif Cut & Tag Assay Kit -manufacturers protocol.
Active Motif Cut & Tag Assay Kit - standard i5 and i7 indexing

value: craniofacial

value: Sox10-Cre ; Eed Fl/Fl


title: SCC2-FRB + rapa resonicated anti-PK9 rep1


title: Sample 8, NP cells,  Alginate, Day 4


title: no FRB tag SMC4-PK9 + rapa resonicated anti-PK9 rep2

description: AH9723I-791-816-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph


source_name: SCC2-FRB SMC4-PK9 + rapa resonicated anti-Rec8 rep1 pair1


title: 221J,RPMI - FBS,RNA-seq


title: 221C,RPMI + FBS,RNA-seq


title: E16.5 Sox10-Cre 1 ; Eed Fl/Fl craniofacial tissue,  H3K27me3 Cut & Tag

description: Library name: KO_E165_R1 H3k27Me3


title: 221B,DMEM + FBS,RNA-seq


title: E16.5 Sox10-Cre 1 ; Eed WT/Fl craniofacial tissue  H3K27me3 Cut & Tag

description: Library name: WT_E165_R1 H3k27Me3

value: Sox10-Cre ; Eed WT/Fl


title: Sample 7, NP cells,  cRGD + IGM3, Day 4


title: no FRB tag SMC4-PK9 + rapa resonicated anti-PK9 rep1


title: E16.5 Sox10-Cre 2 ; Eed WT/Fl craniofacial tissue,  H3K27me3 Cut & Tag

description: Library name: WT_E165_R2 H3k27Me3


title: no FRB tag SMC4-PK9 + rapa resonicated input rep1


title: 221A,DMEM + FBS,RNA-seq

value: PBMC


title: Sample 4, NP cells, cRGD + IGM3, Day 4


title: E12.5 Sox10-Cre 2 ; Eed Fl/F craniofacial tissue,  H3K27me3 Cut & Tag

description: Library name: KO_E125_R3 H3k27Me3

value: Sox10-Cre ; Eed Fl/F


title: E12.5 Sox10-Cre 1 ; Eed Fl/F craniofacial tissue,  H3K27me3 Cut & Tag

description: Library name: KO_E125 H3k27Me3


title: 219J,RPMI - FBS,RNA-seq

value: Monocyte Derived Macrophage

value: DA


title: 219I,RPMI - FBS,RNA-seq

value: utx


title: SCC2-FRB SMC4-PK9 + rapa resonicated anti-PK9 rep1

description: AH9722I-789-814-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph


title: 219H,DMEM - FBS,RNA-seq


title: Sample 5, NP cells,  Alginate, Day 4

value: Nucleus Pulposus


title: E12.5 Sox10-Cre 2 ; Eed WT/Fl craniofacial tissue,  H3K27me3 Cut & Tag

description: Library name: WT_E125_R2 H3k27Me3


title: SCC2-FRB SMC4-PK9 + rapa resonicated anti-PK9 rep2


title: Sample 2, NP cells, Alginate, Day 4

value: nucleus pulposus cells


title: E12.5 Sox10-Cre 1 ; Eed WT/Fl craniofacial tissue, H3K27me3 Cut & Tag

description: Library name: WT_E125_R1 H3k27Me3


title: Sample 3, NP cells, cRGD, Day 4


title: SCC2-FRB SMC4-PK9 + rapa resonicated input rep2

description:
AH9722I-789-814-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph
AH9722B-788-813-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph


title: 219G,DMEM - FBS,RNA-seq


title: Sample 1, NP cells, Day 4,


title: SCC2-FRB SMC4-PK9 + rapa resonicated input rep1


title: no tag + rapa resonicated anti-PK9 rep2

description: AH6978I-775-799-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: no tag + rapa resonicated anti-PK9 rep2


title: no FRB tag SMC4-PK9 + rapa resonicated input rep2


title: Biological replicate #3 Astrocytes, transducted with lentivirus expressing FLAG-GADD45G

city: Dallas

first: tianjin

last: shen

state: Texas

address: 5323 Harry Hines Boulevard, Dallas, TX 75390

department: Molecular Biology

institute: UT Southwestern Medical Center

description: Library name: GADD45G-3-IP

data_processing:
Base-calling were performed using CASAVA v1.8 for Illumina output
CHIP-seq reads were trimmed from 3' end until the final base had a quality score > 40, using fastp v0.20.0, discarding the reads shorter than 50bp
CHIP-seq reads were aligned to the UCSC mm39 genome using BWA software (v0.7.12-r1039); alignments with mapping quality less than 13 were filtered out
Sample correlation and reads enrichment was calculated using the Deeptools (v3.5.1) plotCorrelation and plotEnrichment, respectively, with the bam files. Heatmaps of reads were generated from the bigwig files using the Deeptools computeMatrix followed by plotHeatmap.
The ChIP-seq peaks were called using MACS2 (v2.2.7.1), with a q-value threshold of 0.05. The distribution of peaks in various functional areas was calculated using ChIPseeker software.
Assembly: mm39
Supplementary files format and content: bigWig, narrowPeak

source_name: brain

growth_protocol: Primary WT astrocytes were cultured with serum-free C2 medium (DMEM:F12:Neurobasal (2:2:1), 1% N2 and 1% B27 (Invitrogen)) at 37 °C and 5% CO2 incubator.

extract_protocol:
After RNase A treatment, Proteinase K digestion and reverse cross-linking, immunoprecipitated DNA was purified and quantified for ChIP-seq.
Immunoprecipitated DNA for library preparations was provided to Novogene (CA, USA) with NEBNext® Ultra™ II DNA Library Prep Kit and Illumina PE150 sequencing. The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

treatment_protocol: Astrocytes were crosslinked with 1% methanol-free formaldehyde(Sigma Aldrich, F8775). After quenching and lysis, Chromatin was sheared for 15 minutes (sonication for 30 seconds followed by a 30 second pause, go and shear progress) using a Bioruptor at 4°C.

value: brain

value: astrocytes


title: Sample 6, NP cells,  cRGD, Day 4

value: co-cultured with MSCs in cRGD,IL-1B


title: 219F,SFM,RNA-seq


title: Biological replicate #2 Astrocytes, transducted with lentivirus expressing FLAG-GADD45G

description: Library name: GADD45G-2-IP


title: 219E,SFM,RNA-seq


title: Biological replicate #1 Astrocytes, transducted with lentivirus expressing FLAG-GADD45G

description: Library name: GADD45G-1-IP


title: no tag + rapa resonicated input rep2

first: Andreas

last: Hochwagen

institute: New York University

source_name: no tag + rapa resonicated input rep2


title: 219D,RPMI + FBS,RNA-seq


title: no tag + rapa resonicated anti-PK9 rep1

source_name: no tag + rapa resonicated anti-PK9 rep1


title: CTCF-GFP-AID mESC, CUT&Tag GFP Ab, CTCF, rep2

city: Zurich

last: Dimitriu

address: Winterthurerstrasse 190

country: Switzerland

institute: ETH Zurich

description: Library name: CTCF_CT_r2

data_processing:
Reads were trimmed with trim_galore. Aligned to mm10 using Bowtie2, filtered using SAMtools. Peaks were called by merging the bam files of thw two replicates first, then using MACS2 and a q-value of < 0.1.
Coverage tracks were generated from the filtered, deduplicated alignment files using bamCompare and a bin size of 20.
Peaks were annotated using ChIPseeker and GO analysis was performed using rGREAT.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: E14Tg2a AID-eGFP-CTCF

growth_protocol: mESCs were cultured on 0.2% gelatin-coated culture dishes in Knockout DMEM supplemented with 15% Fetal Bovine Serum (FBS) qualified for ES cells, 1X GlutaMax, 1X Penicillin/Streptomycin, 1X MEM Non-Essential Amino Acid, 100 μM β–Mercaptoethanol, and 1000 U/ml Leukemia inhibitory factor. Medium was changed daily and mESCs were passaged every 2 days

extract_protocol:
400,000 fresh mESCs were collected by treatment with StemPro Accutase at 37dC for 5 min and centrifugation at 600xg for 3 min and washed with Wash buffer, bound to conA beads and then incubated with either primary Ab, then secondary Ab, then pAG-Tn5 for CUT&Tag or nanobody-Tn5 for NanoTag. Tagmentation was performed at 37dC for 1 hr.
Libraries were prepared using the NEBNext PCR master mix and i5 and i7 indexes for CUT&Tag. Libraries were amplified with the amount of cycles determined by qPCR required to reach 1/3 of the maximuml fluorecence. Double-sided cleanup of libraries wwas performed using AMPUre XP beads. Libraries were quantified using Agilent High Sensitivity DNA Tapestation kit.

value: E14Tg2a AID-eGFP-CTCF

value: mouse embryonic stem cells

value: CTCF-eGFP-AID


title: no tag + rapa resonicated input rep1

city: New York

address: 1009 Silver Center 100 Washington Square East

source_name: no tag + rapa resonicated input rep1

value: 3 hour


title: 219C,RPMI + FBS,RNA-seq


title: Biological replicate #3 Astrocytes, transducted with lentivirus expressing FLAG

description: Library name: FLAG-3-IP

value: FLAG


title: CTCF-GFP-AID mESC, CUT&Tag GFP Ab, CTCF, rep1

description: Library name: CTCF_CT_r1


title: Nanog-Venus mESC, CUT&Tag GFP Ab, Nanog, rep1

description: Library name: Nanog_CT_r1

value: Nanog-Venus


title: Biological replicate #1 Astrocytes, transducted with lentivirus expressing FLAG

description: Library name: FLAG-1-IP


title: spo11-Y135F resonicated input rep2

description: AH8643I-170-765-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: spo11-Y135F resonicated input rep2


title: TAF3-GFP mESC, CUT&Tag GFP Ab, TAF3, rep2

description: Library name: TAF3-GFP_CT_r2


title: 219A,DMEM + FBS,RNA-seq


title: Brain, exosome treated LFD, biological replicate 4

city: Boston

first: Gerald

middle: V

last: Denis

address: 72 East Concord Street

institute: Boston University

data_processing:
Sequencing reads were processed using the nf-core rnaseq pipeline.
Reads were quality trimmed using Trimmomatic to remove adapters and low-quality bases.
Quality-checked reads were aligned to the mouse reference genome using STAR aligner.
Gene expression counts were generated using featureCounts based on the GRCm38/mm10 annotation.
Differential gene expression analysis was performed using DESeq2 to compare Control and Experimental groups.
Assembly: GRCm39/mm39 mouse reference genome.
Supplementary files format and content: Tab-delimited text files containing raw gene counts for each sample.

growth_protocol: Murine E0771 cells, used as a syngeneic TNBC model, were cultured in DMEM medium with 4.5 g/L glucose and L-glutamine, without sodium pyruvate, supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 10 μg/mL streptomycin (Corning). Cells were maintained at 37°C in 5% CO2

extract_protocol:
Total RNA was extracted from E0771 cells treated with HFD or LFD-derived exosomes using the RNeasy Plus Mini Kit (QIAGEN, Cat. No. 74136), following the manufacturer's protocol. RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
Libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit, as per the manufacturer's protocol. Final libraries were checked for quality using an Agilent Bioanalyzer and quantified using a Qubit fluorometer.

treatment_protocol: Cells were treated with exosomes isolated from HFD or LFD plasma on Day 0 and cultured for 72 hours until 70% confluency was reached.

value: Mammary adenocarcinoma cells

value: E0771-GFP (AAV)

value: LFD-plasma derived exosomes


title: SMC4-PK9 spo11-Y135F resonicated anti-PK9 rep2

description: AH8630I-168-763-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph


title: Biological replicate #2 Astrocytes, transducted with lentivirus expressing FLAG

description: Library name: FLAG-2-IP


title: TAF3-GFP mESC, CUT&Tag GFP Ab, TAF3, rep1

description: Library name: TAF3-GFP_CT_r1


title: Brain, exosome treated LFD, biological replicate 3


title: SMC4-PK9 spo11-Y135F resonicated input rep2


title: spo11-Y135F resonicated anti-PK9 rep2

source_name: spo11-Y135F resonicated anti-PK9 rep2


title: H727 cells, Pan-KRAS siRNA, 48 hrs, Biol Rep 2

city: Chapel Hill

first: Alessandro

last: Porrello

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
RNA-seq quantification with STAR/Salmon workflow.
Reads were mapped to GRCh38 using STAR 2.7.6a (parameters: --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM).
Quantification of transcripts (gene-level) was performed using Salmon 1.4.0, based on the human transcriptome defined by GENCODE, Release 36.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes Salmon-quantification of transcripts (gene-level) for each sample.

growth_protocol: H727 cells were maintained in RPMI1640 supplemented with 10% FBS in humidified atmosphere with 5% CO2 and 37C.

extract_protocol:
RNA was extracted using the Quick RNA Mini Prep kit (Zymo Research).
mRNAseq libraries were created from up to 1000 ng of total RNA using a TruSeq Stranded mRNA Library Prep Kit (Illumina 20020595) following the manufacturer’s protocol (Illumina 1000000040498). Libraries were created using a Hamilton NGS STAR automated liquid handler.

treatment_protocol: H727 cells were transfected with siRNAs at 20 nM with Lipofectamine RNAiMAX following manufacturer's protocol and RNA was collected after 48 hours.

value: lung cancer

value: KRAS knockdown

value: transfection, Pan-KRAS siRNA

tag: time

value: 48 hrs


title: TAF3-GFP mESC, CUT&Tag IgG Ab

description: Library name: IgG_CT

value: WT


title: WT mESC, NanoTag

description: Library name: WT_NT

data_processing:
Reads were trimmed with trim_galore. Aligned to mm10 using Bowtie2, filtered using SAMtools. Peaks were called by merging the bam files of thw two replicates first, then using MACS2 and a q-value of < 0.1.
Coverage tracks were generated from the filtered, deduplicated alignment files using bamCompare and a bin size of 20.
Peaks were annotated using ChIPseeker and GO analysis was performed using rGREAT.
Assembly: mm10
Supplementary files format and content: bigWig


title: In vitro, exosome treated LFD, technical replicate 5


title: rec8D SCC2-HA anti-Red1 rep2

description: AH8869B-381-771-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: rec8D SCC2-HA anti-Red1 rep2

value: anti-HA


title: H727 cells, Pan-KRAS siRNA, 48 hrs, Biol Rep 1


title: CTCF-GFP-AID mESC, NanoTag, CTCF, rep2

description: Library name: CTCF_NT_r2


title: rec8D SCC2-HA input rep2

source_name: rec8D SCC2-HA input rep2


title: H727 cells, EFTX-G12V siRNA, 48 hrs, Biol Rep 3

value: KRAS-G12V knockdown

value: transfection, EFTX-G12V siRNA


title: In vitro, exosome treated LFD, technical replicate 4


title: H727 cells, Pan-KRAS siRNA, 48 hrs, Biol Rep 3


title: Nanog-Venus mESC, CUT&Tag GFP Ab, Nanog, rep2

description: Library name: Nanog_CT_r2


title: 219B,DMEM + FBS,RNA-seq

source_name: PBMC

value: PBMC

value: Monocyte Derived Macrophage

value: DA


title: H727 cells, EFTX-G12V siRNA, 48 hrs, Biol Rep 2


title: Nanog-Venus mESC, NanoTag, Nanog, rep2

description: Library name: Nanog_NT_r2

value: mouse embryonic stem cells


title: In vitro, exosome treated LFD, technical replicate 3


title: In vitro, exosome treated LFD, technical replicate 2


title: SCC2-3HA spo11-Y135F anti-HA rep2

description: AH8868B-397-769-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: SCC2-3HA spo11-Y135F anti-HA rep2

value: 3 hour


title: H727 cells, EFTX-G12V siRNA, 48 hrs, Biol Rep 1


title: SCC2-3HA spo11-YF135F input rep2

source_name: SCC2-3HA spo11-YF135F input rep2


title: In vitro, exosome treated LFD, technical replicate 1


title: SCC2-3HA anti-HA rep2

description: AH8867B-379-767-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph

source_name: SCC2-3HA anti-HA rep2


title: TAF3-GFP mESC, NanoTag, TAF3, rep2

description: Library name: TAF3_NT_r2


title: Nanog-Venus mESC, NanoTag, Nanog, rep1

description: Library name: Nanog_NT_r1

value: Nanog-Venus


title: Brain, exosome treated HFD, biological replicate 5

value: Mammary adenocarcinoma cells

value: HFD-plasma derived exosomes


title: SCC2-3HA input rep2

source_name: SCC2-3HA input rep2


title: H727 cells, Neg Ctrl siRNA, 48 hrs, Biol Rep 2

value: transfection, negative control siRNA


title: H727 cells, Neg Ctrl siRNA, 48 hrs, Biol Rep 1

value: lung cancer


title: Brain, exosome treated HFD, biological replicate 4

value: E0771-GFP (AAV)


title: CTCF-GFP-AID mESC, NanoTag, CTCF, rep1

description: Library name: CTCF_NT_r1

value: E14Tg2a AID-eGFP-CTCF

value: CTCF-eGFP-AID


title: TAF3-GFP mESC, NanoTag, TAF3, rep1

description: Library name: TAF3_NT_r1


title: dgcn5_input

city: Chuncheon-si, Gangwon-do

first: Jueun

last: Kim

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
BedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Candida albicans SC5314 (PRJNA10701)
Supplementary files format and content: bigwig

organism: Candida albicans

source_name: yeast cell

growth_protocol: C. albicans were grown in YPD  media (1% yeast extracts, 2% peptone, 2% glucose) and harvested during the exponential growth phase, at an OD600 of 1.0 for yeast growth. To prepare hyphal status cells, C. albicans grown in YPD were harvested at OD600 of 0.9 and transferred to preheated YPD containing 10% FBS. Hyphal formation was induced by incubating cells at 37°C with shaking.

extract_protocol:
Cells were crosslinked using 1% formaldehyde for 5 minutes. Before sonication, the cells were treated with zymolyase to produce spheroplasts.
ChIP-seq libraries were prepared using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina (NEB, E6240, following the manufacturer’s instructions. 10 ng of ChIPed DNA was used as starting material.

value: yeast cell

tag: chip antibody

value: YPD


title: Aorta-derived cells, Rep 2, CMO multiplex. Groups: Ctrl2_4wks, ImP2_4wks, Ctrl2_8wks, ImP2_8wks.

city: Madrid

first: Diego

last: Mañanes

state: Madrid

address: C. de Melchor Fernández Almagro, 3

country: Spain

institute: Spanish National Center for Cardiovascular Research

description:
Library name: SC_Multiplex_CMO_Rep_2
CMO reads from multiplexed samples from 4 conditions (replicate 2): Ctrl2_4wks: pool of 3 ApoE-/- mice with no ImP treatment for 4 weeks; ImP2_4wks: pool of 3 ApoE-/- mice with ImP treatment for 4 weeks; Ctrl2_8wks: pool of 3 ApoE-/- mice with no ImP treatment for 8 weeks; ImP2_8wks: pool of 3 ApoE-/- mice with ImP treatment for 8 weeks.

data_processing:
Single-cell RNA-sequencing data were processed using the Cell Ranger (v6.1.2) default parameters and the mm10 (GRCm38.p6) mouse genome reference provided by 10x Genomics.
Results from RNA quantification were imported into R (v4.1.2) and analyzed using Seurat (v4.2.1). Cells were filtered to retain those with <7.5% mitochondrial RNA content, more than 200 genes and less than 6,000 genes, and with a number of unique molecular identifiers (UMIs) comprised between 1,000 and 50,000. Then, the remaining cells were demultiplexed using the cellhashR R package (v1.0.2) using htodemux, bff_cluster, gmm_demux, multiseq and dropletutils methods. The consensus classification was finally used for further analyses.
Counts were normalized for library size using Seurat’s default normalization parameters. RNA count was used as a source of unwanted variation and regressed using Seurat’s built-in regression models.
Assembly: mm10 (GRCm38.p6) mouse genome
Supplementary files format and content: matrix.mtx.gz files contain the raw read counts per gene per cell in the MTX format. A file is provided for every biological replicate.
Supplementary files format and content: features.tsv.gz files contain names of detected genes of the MTX files. A file is provided for every biological replicate.
Supplementary files format and content: barcodes.tsv.gz files contain cell barcodes of the MTX files. A file is provided for every biological replicate.

source_name: Aorta

growth_protocol: 12 to 16 weeks-old ApoE-/- mice house at the Spanish National Centre for Cardiovascular Disease (CNIC)

extract_protocol:
After treatment, mice were perfused with 10 mL of  PBS via cardiac puncture to remove blood contamination from vascular tissue. The aortas were kept in cold Dulbecco's Modified Eagle Medium (DMEM) to be digested. Perivascular fat was removed and the thoracic aorta with arch was opened longitudinally and cut into smaller pieces that were incubated for 30 min at 37ºC in a water bath in digestion buffer (Collagenase A (25 mg/ml), (Roche/Sigma #10103586001). Dispase II (25 mg/ml), (Roche/Sigma #04942078001), DNase I (250 μg/ml) (Roche/Sigma #10104159001) elastase (25 μg/ml) and Libersase TL (0.2 Wünsch units/ml, # 5401119001). After incubation time the digested tissue was mixed by pipetting, filtered through a 70 μm strainer and spinned at 400 x g 5 min at 4ºC. To obtain enough cell numbers, 3 aortae per condition were pooled. Each sample was labeled with a cell multiplexing oligo (CMO) using the CMO labeling for Single Cell RNA Sequencing Protocol from 10x Genomics. Cells labeled with CMOs were washed, labelled with SytoxGreen and Hoechst to ensure cell viability and live cells sorted with a FACs Aria cell sorter.
Samples were pooled and single-cell RNA-seq was performed following the Chromium Next GEM Single Cell 3’ v3.1 with feature barcode technology for cell multiplexing protocol (10x Genomics). Briefly, cells were first counted and checked their viability using the Countess 3 cell counter (Thermofisher). Next, cells were loaded onto a 10x Genomics chip of the Chromium Controller (10x Genomics).

treatment_protocol: ApoE-/- 8 weeks male mice were treated (or not) in the drinking water with ImP (400μg/mouse/day) for 4 or 8 weeks.

value: Aorta

tag: age

value: 12-16 weeks old

value: Aorta-derived cells

value: ApoE-/-

value: Treatment with ImP (400μg/mouse/day) in the drinking water for 4 or 8 weeks or no treatment


title: Brain, exosome treated HFD, biological replicate 2

tag: cell line


title: Brain, exosome treated HFD, biological replicate 3


title: Aorta-derived cells, Rep 1, CMO multiplex. Groups: Ctrl1_4wks, ImP1_4wks, Ctrl1_8wks, ImP1_8wks.

description:
Library name: SC_Multiplex_CMO_Rep_1
CMO reads from multiplexed samples from 4 conditions (replicate 1): Ctrl1_4wks: pool of 3 ApoE-/- mice with no ImP treatment for 4 weeks; ImP1_4wks: pool of 3 ApoE-/- mice with ImP treatment for 4 weeks; Ctrl1_8wks: pool of 3 ApoE-/- mice with no ImP treatment for 8 weeks; ImP1_8wks: pool of 3 ApoE-/- mice with ImP treatment for 8 weeks.


title: H441 cells, Pan-KRAS siRNA, 48 hrs, Biol Rep 3

growth_protocol: H441 cells were maintained in RPMI1640 supplemented with 10% FBS in humidified atmosphere with 5% CO2 and 37C.

treatment_protocol: H441 cells were transfected with siRNAs at 20 nM with Lipofectamine RNAiMAX following manufacturer's protocol and RNA was collected after 48 hours.

value: lung adenocarcinoma

value: KRAS knockdown

value: transfection, Pan-KRAS siRNA

value: 48 hrs


title: Aorta-derived cells, Rep 2, GEX multiplex. Groups: Ctrl2_4wks, ImP2_4wks, Ctrl2_8wks, ImP2_8wks.

description:
Library name: SC_Multiplex_GEX_Rep_2
Gene expression reads from multiplexed samples from 4 conditions (replicate 2): Ctrl2_4wks: pool of 3 ApoE-/- mice with no ImP treatment for 4 weeks; ImP2_4wks: pool of 3 ApoE-/- mice with ImP treatment for 4 weeks; Ctrl2_8wks: pool of 3 ApoE-/- mice with no ImP treatment for 8 weeks; ImP2_8wks: pool of 3 ApoE-/- mice with ImP treatment for 8 weeks.


title: Brain, exosome treated HFD, biological replicate 1

value: Mammary adenocarcinoma cells

value: HFD-plasma derived exosomes


title: dset1_input


title: H441 cells, Pan-KRAS siRNA, 48 hrs, Biol Rep 1


title: H727 cells, Neg Ctrl siRNA, 48 hrs, Biol Rep 3

value: lung cancer

value: WT

value: transfection, negative control siRNA


title: H441 cells, EFTX-G12V siRNA, 48 hrs, Biol Rep 3

value: KRAS-G12V knockdown

value: transfection, EFTX-G12V siRNA


title: S33

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

description:
Library name: KO4339-8-5_S33
counts_Jan_2023.csv.gz

data_processing:
Sequencing quality was assessed using Fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Next, the bioinformatic tool cutadap (Martin, 2011) was used to remove adapter sequences, trim low-quality bases, and filter short reads. Lastly, processed reads were mapped to the mouse reference genome (GRCm39) using STAR v2.6.1(Dobin et al., 2013) and reads that map onto each gene will be quantified using the featureCounts tool included in Subread software package (https://subread.sourceforge.net/). The generated count table was imported to R to perform differential gene expression (DEG) analysis using the DESeq2 package (Love, Huber, & Anders, 2014). Lowly expressed genes were filtered out, retaining genes with at least 15 counts in 14 or more samples to improve data robustness. Variance stabilizing transformation (VST) was applied to normalize the dataset for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: tsv

source_name: Brain

extract_protocol:
RNA was isolated from CD11b-positive microglial cells by using Direct-zol RNA Miniprep Plus (Product #: R2072; Zymo Research, USA) according to manufacturer’s instruction. The isolated RNA was immediately frozen at -80°C and sent to sequence
RNA-seq library preparation was performed using Poly(A) selection, where polyadenylated mRNA transcripts were selectively enriched and the sequencing was performed in the Illumina's NovaSeq platform with 30 million read pairs per sample.

treatment_protocol: WT and P2RY12 deficient littermate mice were subjected to an intraperitoneal (i.p.) injection of LPS (1 mg/kg)

value: Brain

value: Microglia

value: ko

value: lps

value: Total RNA


title: Aorta-derived cells, Rep 1, GEX multiplex. Groups: Ctrl1_4wks, ImP1_4wks, Ctrl1_8wks, ImP1_8wks.

description:
Library name: SC_Multiplex_GEX_Rep_1
Gene expression reads from multiplexed samples from 4 conditions (replicate 1): Ctrl1_4wks: pool of 3 ApoE-/- mice with no ImP treatment for 4 weeks; ImP1_4wks: pool of 3 ApoE-/- mice with ImP treatment for 4 weeks; Ctrl1_8wks: pool of 3 ApoE-/- mice with no ImP treatment for 8 weeks; ImP1_8wks: pool of 3 ApoE-/- mice with ImP treatment for 8 weeks.

value: Aorta

value: 12-16 weeks old

value: Aorta-derived cells

value: ApoE-/-

value: Treatment with ImP (400μg/mouse/day) in the drinking water for 4 or 8 weeks or no treatment


title: dset1_H3

value: yeast cell

value: YPD


title: WT_hypha_H3

value: clinical isolate

value: YPD supplemented with 10% serum, 37℃, 30 min


title: H441 cells, EFTX-G12V siRNA, 48 hrs, Biol Rep 2

value: lung adenocarcinoma

value: 48 hrs


title: S32

description:
Library name: KO4339-8-4_S32
counts_Jan_2023.csv.gz


title: WT_H3


title: H441 cells, EFTX-G12V siRNA, 48 hrs, Biol Rep 1

value: KRAS-G12V knockdown

value: transfection, EFTX-G12V siRNA


title: S31

description:
Library name: KO4339-8-3_S31
counts_Jan_2023.csv.gz

value: Brain

value: Microglia


title: H441 cells, Pan-KRAS siRNA, 48 hrs, Biol Rep 2

value: KRAS knockdown

value: transfection, Pan-KRAS siRNA


title: WT_input


title: dset1_hypha_3H_H3K4ac_rep2

value: acetyl H3K4

value: YPD supplemented with 10% serum, 37℃, 3 h


title: In vitro, exosome treated HFD, technical replicate 2

value: Mammary adenocarcinoma cells

value: E0771-GFP (AAV)

value: HFD-plasma derived exosomes


title: S30

description:
Library name: KO4339-8-2_S30
counts_Jan_2023.csv.gz

value: ko

value: lps

value: Total RNA


title: In vitro, exosome treated HFD, technical replicate 1


title: H441 cells, Neg Ctrl siRNA, 48 hrs, Biol Rep 2

value: WT

value: transfection, negative control siRNA


title: dset1_hypha_3H_H3K4ac_rep1

value: yeast cell


title: dset1_hypha_H3

value: YPD supplemented with 10% serum, 37℃, 30 min


title: Brain, control, biological replicate 3

value: No treatment


title: WT_hypha_3H_H3K4ac_rep2

value: clinical isolate


title: In vitro, exosome treated HFD, technical replicate 5


title: S29

description:
Library name: KO4339-7-5_S29
counts_Jan_2023.csv.gz

value: Brain

value: Microglia

value: ns


title: S28

description:
Library name: KO4339-7-4_S28
counts_Jan_2023.csv.gz


title: Brain, control, biological replicate 2


title: H441 cells, Neg Ctrl siRNA, 48 hrs, Biol Rep 1

value: lung adenocarcinoma

value: 48 hrs


title: WT_hypha_3H_H3K4ac_rep1

value: acetyl H3K4

value: YPD supplemented with 10% serum, 37℃, 3 h


title: In vitro, exosome treated HFD, technical replicate 3

value: Mammary adenocarcinoma cells

value: E0771-GFP (AAV)

value: HFD-plasma derived exosomes


title: In vitro, exosome treated HFD, technical replicate 4


title: PK10-46

city: St. Petersburg

first: JUNKO

last: SAWADA

address: 600 5th Street South

institute: Johns Hopkins All Children's Hispital

description: N/A,

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Pertek®Flow® was used for trimming, QC, alignment by STAR - 2.7.8a
Assembly: hg38_ensembl_release91_v2
Supplementary files format and content: Tab determined text file which include Normalized_counts from DESeq2

source_name: Tumor tisseue

extract_protocol:
Archived PDAC FFPE tumor samples were categorized as TLS-positive or TLS-negative based on H&E staining. Under a microscope, the tumor areas were marked using a marker on the bottom side of the H&E-stained slide glasses. The non-stained FFPE slides, which were serial sections of the H&E-stained sections, were used for tumor tissue collection. When scraping the non-stained FFPE tissues, the H&E-stained slide (with the marked tumor areas) was stacked beneath the non-stained FFPE slide. Using the markers visible through the stacked slides, only the tumor tissues were carefully scraped and collected from the non-stained FFPE sections. Total RNA was extracted from FFPE slides using Qiagen RNeasy FFPE kit following anufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Tumor tisseue


title: S26

description:
Library name: KO4339-7-2_S26
counts_Jan_2023.csv.gz

value: ko

value: Total RNA


title: dgcn5_hypha_H3K4ac

value: yeast cell


title: dset1_hypha_H3K4ac_rep2

value: YPD supplemented with 10% serum, 37℃, 30 min


title: PK19-12

description: TLS-rich


title: etr-30PFTα-4h-rep2

city: Shanghai

first: Lin

last: Li

address: 220 Handan Road

institute: Fudan university

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. (Reference: [1] Chen S ,  Zhou Y ,  Chen Y , et al. fastp : an ultra-fast all-in-one FASTQ preprocessor. 2018.)
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. (Reference: [2] Kim D, Langmead B, Salzberg S L. HISAT: a fast spliced aligner with low memory requirements[J]. Nature methods, 2015, 12(4): 357-360.)
The mapped reads of each sample were assembled by StringTie in a reference-based approach. (Reference: [3] Pertea M, Pertea G M, Antonescu C M, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads[J]. Nature biotechnology, 2015, 33(3): 290-295.)
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM[4] was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2[5] or DEGseq[6]. DEGs with |log2FC|≧1 and FDR＜ 0.05(DESeq2 ) or FDR ＜ 0.001(DEGseq) were considered to be significantly different expressed genes. (Reference: [4] Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011;12:323.)
In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value＜0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and Python scipy software, respectively. (Reference: [5] Love M I, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J]. Genome biology, 2014, 15(12): 550.[6] Wang L, Feng Z, Wang X, et al. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data[J]. Bioinformatics, 2009, 26(1): 136-138.)
Assembly: TAIR10 (ensemble_55)
Supplementary files format and content: XLS; Quantitative annotation results table of gene tpm expression

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: The Col-0/etr1-1 seedlings grown under white light for 6 hours, then turned to dark condition at 22°C for 4 days.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq X Plus sequencer (2 × 150bp read length).

treatment_protocol: 4-day-old dark-grown seedlings were transferred to 1/2 MS liquid medium complemented with 30 μM PFT-α, 10 μM ACC or 1‰ DMSO (v/v) for 4 h, and whole seedlings were collected.

value: whole seedlings

value: etr1-1 mutants

value: 30 uM PFT-{alpha} for 4 h


title: H441 cells, Neg Ctrl siRNA, 48 hrs, Biol Rep 3

value: WT

value: transfection, negative control siRNA


title: PK19-11

description: TLS-rich


title: S25

description:
Library name: KO4339-6-5_S25
counts_Jan_2023.csv.gz

value: Brain

value: Microglia

value: wt

value: lps


title: S24

description:
Library name: KO4339-6-4_S24
counts_Jan_2023.csv.gz


title: PK18-61

description: TLS-rich


title: etr-mock-4h-rep2

value: DMSO for 4 h


title: S27

description:
Library name: KO4339-7-3_S27
counts_Jan_2023.csv.gz

value: ns


title: dset1_hypha_H3K4ac_rep1

value: acetyl H3K4


title: etr-mock-4h-rep1


title: etr-30PFTα-4h-rep1


title: S23

description:
Library name: KO4339-6-3_S23
counts_Jan_2023.csv.gz


title: PK18-11

description: TLS-rich

value: Tumor tisseue


title: WT_hypha_H3K4ac_rep1

value: clinical isolate


title: S22

description:
Library name: KO4339-6-2_S22
counts_Jan_2023.csv.gz

value: Total RNA


title: Col-10ACC-4h-rep3

value: wildtype

value: 10 uM ACC for 4 h


title: PK18-25

description: TLS-rich