title: PB03515-001 flex scRNA-seq

description:
SRR30204374, SRR30204373, SRR30204372, SRR30204371, SRR30204370, SRR30204369, SRR30204368, SRR30204367, SRR30204365, SRR30204364, SRR30204291, SRR30204290, SRR30204289, SRR30204288, SRR30204287, SRR30204286, SRR30204285, SRR30204284, SRR30204282, SRR30204281, SRR30204280, SRR30204279, SRR30204278, SRR30204277
10x Flex ligation probe-based sequencing


title: Trigeminal ganglion_Replicate 5

status: Public on Sep 12 2025

type: SRA

city: New Haven

first: Sviatoslav

middle: N

last: Bagriantsev

state: Connecticut

address: 333 Cedar St

department: Cellular and Molecular Physiology

country: USA

institute: Yale University

description:
Library name: TG_5
Column names: RawCounts_TG_5 and TPM_TG_5

library_source: transcriptomic

data_processing:
Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA) software. Primary analysis is performed using Illumina's CASAVA 1.8.2 software suite.
Raw sequencing reads were trimmed and filtered using Trimmomatic v0.39 with default parameters.
Filtered reads were aligned to the reference genome of a closely related species, Paramormyrops kingsleyae (PKINGS_0.1; NCBI, accessed June 2021), using STAR v2.7.7a with default parameters
Aligned reads were quantified using featureCounts (Subread v2.0.1) with strandedness set to 0.
Raw read counts were then normalized to Transcripts Per Million (TPM) in R.
Assembly: The reference genome is GCF_002872115.1 (PKINGS_0.1), from a closely related species, Paramormyrops kingsleyae (NCBI, accessed June 2021).
Supplementary files format and content: The processed data file in CSV format contains raw read counts and TPM values for six replicates each of trigeminal ganglion, brain, and spinal cord, covering all protein-coding genes annotated in the reference genome.

molecule: total RNA

organism: Gnathonemus petersii

source_name: Trigeminal ganglion

extract_protocol:
Total RNA was extracted separately from trigeminal ganglia, brains (cerebella), and spinal cords from 6 individual fish using TRIzol reagent (Invitrogen, cat. no. 15596026), following the manufacturer’s instructions. RNA concentration and integrity number (RIN) were assessed by Agilent 2100 Bioanalyzer (Agilent, cat. no. G2946CA). RNA concentrations for all samples were in the range of 5.2–146.1 ng/µl and RIN values were in the range of 7.9–9.5.
Libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs, cat. no. E6420L).

tag: tissue

value: Trigeminal ganglion


title: Medial olivocochlear neuron MOC06

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description:
Library name: MOC06
Column name in RawCountFile.txt= MOC06

data_processing:
RNA-seq libraries were prepared using Nextera DNA Library Preparation kits (Illumina) and sequenced on an Illumina MiSeq in 75 bp paired end configuration. FASTQ files were extracted using bcl2fastq and the reads were mapped to the mouse genome (GRCm38.vM11) using the STAR v2.5.2 aligner.
Read counts are generated during mapping with the quantMode utility of the STAR aligner, producing a‘RAWCOUNTFILE’. We also generated normalized counts per gene (CPM, or counts per million reads).  DGE analyses were performed using the R packages DESeq2, EdgeR and Limma-Voom.
Assembly: mm10 (GRCm38.vM11)
Supplementary files format and content: Tab-delimited file with raw counts per sample
Supplementary files format and content: Tab-delimited file with normalized (CPM) counts per sample.

organism: Mus musculus

source_name: medial olivocochlear neuron

growth_protocol: Transgenic mice, acute brainstem slices

extract_protocol:
cytoplasm aspiration, cDNA library generation with SmartSEQ2
Nextera DNA Library Preparation kits (Illumina)

tag: cell type

value: medial olivocochlear neuron

tag: genotype

value: wild-type

tag: treatment

value: RNA-seq after patch clamp


title: Siberian Hamster, DMH, 16wk SD, Rep 1

city: Glasgow

first: Calum

last: Stewart

address: Jarrett Building, University of Glasgow

country: United Kingdom

institute: University of Glasgow

description:
DMH244
DMHExpressedGenesTranscripts.CSV

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25 reads)
Minimap2 used to align reads to Mus musculus genome (GCRm39)
Transcript expression levels generated  using Salmon
Assembly: GRCmm39
Supplementary files format and content: Transcript expression levels generated  using Salmon

molecule: polyA RNA

organism: Phodopus sungorus

extract_protocol:
RNA was extracted using the Qiagen RNEasy plus mini-kit
RNA Libraries were constructed using the PCR_cDNA sequencing barcoding kit (SQK-PCB109, Oxford Nanopore) as per manufacturers instructions


title: PB03511-001 flex scRNA-seq

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
SRR30239487, SRR30239486, SRR30239484, SRR30239438, SRR30239437, SRR30239435, SRR30239479, SRR30239478, SRR30239477, SRR30239476, SRR30239475, SRR30239474, SRR30239473, SRR30239472, SRR30239447, SRR30239446, SRR30239444, SRR30239443, SRR30239442, SRR30239441, SRR30239440, SRR30239439, SRR30239436, SRR30239416
10x Flex ligation probe-based sequencing

library_source: other

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the  Fixed RNA Profiling capability (version 7.0.0, released May 17, 2022), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For all initial analyses, we used a Python single-cell data analysis package – Scanpy (v1.9.6). High quality cells were selected based on the following cutoffs: <4.5% mitochondria reads, number of genes detected between 500 and 5000, RNA UMIs/cells less than 12000 and number of reads less than 30000. Doublets were detected and filtered out with the Scrublet package accessed through scanpy.external.pp.scrublet call and the doublet filtration threshold was set at less than 0.2
After QC filtering, all remaining cells were clustered using a workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; natural log transformation using scanpy.pp.log1p; dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'; nearest neighbor distance matrix and neighborhood graph computed using scanpy.pp.neighbors with the parameters n_neighbors=50, use_rep='X_pca', n_pcs=30;
Assembly: GRCh38/hg38
Supplementary files format and content: h5 files

molecule: other

organism: Homo sapiens

source_name: Blood

extract_protocol:
PBMCs were removed from liquid nitrogen and immediately thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca. After adding 30 mL cold AIM V media, cells were re-pelleted and resuspended to the appropriate concentrations for scRNAseq.
scRNAseq libraries were generated using a modified 10x genomics flex single cell gene expression assay. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq 6000 or X platform.

value: Blood

value: PBMC

tag: subject id

tag: age at_enrollment

tag: Sex

value: Female

tag: race

value: Asian

tag: cmv status

value: Negative

tag: batch id

tag: sample bridging_control

value: FALSE

tag: pooled sample_id

tag: probe barcode_id


title: Siberian Hamster, DMH, 12wk SD, Rep 1

description:
DMH277
DMHExpressedGenesTranscripts.CSV


title: Trigeminal ganglion_Replicate 4

description:
Library name: TG_4
Column names: RawCounts_TG_4 and TPM_TG_4


title: Medial olivocochlear neuron MOC05

description:
Library name: MOC05
Column name in RawCountFile.txt= MOC05


title: Siberian Hamster, DMH, 8wk SD, Rep 1

description:
DMH305
DMHExpressedGenesTranscripts.CSV


title: PB03487-001 flex scRNA-seq

description:
SRR30204234, SRR30204233, SRR30204232, SRR30204231, SRR30204339, SRR30204338, SRR30204337, SRR30204336, SRR30204335, SRR30204334, SRR30204332, SRR30204331, SRR30204330, SRR30204329, SRR30204328, SRR30204327, SRR30204326, SRR30204325, SRR30204324, SRR30204323, SRR30204321, SRR30204320, SRR30204319, SRR30204318
10x Flex ligation probe-based sequencing

value: Caucasian

value: Positive


title: Medial olivocochlear neuron MOC04

description:
Library name: MOC04
Column name in RawCountFile.txt= MOC04


title: Siberian Hamster, DMH, 4wk SD, Rep 1

description:
DMH356
DMHExpressedGenesTranscripts.CSV


title: Trigeminal ganglion_Replicate 2

description:
Library name: TG_2
Column names: RawCounts_TG_2 and TPM_TG_2


title: Medial olivocochlear neuron MOC03

description:
Library name: MOC03
Column name in RawCountFile.txt= MOC03


title: Siberian Hamster, DMH, 24wk SD, Rep 1

description:
DMH178
DMHExpressedGenesTranscripts.CSV


title: Trigeminal ganglion_Replicate 1

description:
Library name: TG_1
Column names: RawCounts_TG_1 and TPM_TG_1


title: Siberian Hamster, DMH, LD, Rep 1

description:
DMH417
DMHExpressedGenesTranscripts.CSV


title: PB03485-001 flex scRNA-seq

description:
SRR30239415, SRR30239414, SRR30239432, SRR30239431, SRR30239430, SRR30239429, SRR30239428, SRR30239427, SRR30239426, SRR30239425, SRR30239424, SRR30239423, SRR30239421, SRR30239419, SRR30239418, SRR30239417, SRR30239470, SRR30239469, SRR30239468, SRR30239467, SRR30239466, SRR30239465, SRR30239412, SRR30239411
10x Flex ligation probe-based sequencing


title: Medial olivocochlear neuron MOC02

description:
Library name: MOC02
Column name in RawCountFile.txt= MOC02


title: Siberian Hamster, MBH, 32wk SD, Rep 6

description:
MBH113
MBHExpressedGenesTranscripts.CSV


title: PB03483-001 flex scRNA-seq

description:
SRR30239537, SRR30239518, SRR30239519, SRR30239520, SRR30239502, SRR30239501, SRR30239517, SRR30239516, SRR30239515, SRR30239514, SRR30239512, SRR30239511, SRR30239510, SRR30239509, SRR30239508, SRR30239507, SRR30239506, SRR30239485, SRR30239483, SRR30239482, SRR30239480, SRR30239500, SRR30239499, SRR30239498
10x Flex ligation probe-based sequencing


title: dRBSdATG, xylA, NusG-myc, replicate 2

city: Seoul

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

library_source: genomic

data_processing:
The quality of the sequence reads obtained from ChIP-exo was checked by FastQC (version 0.11.8).
The sequence reads were aligned to the reference genome using bowtie (version 1.2.2) with the following options to generate SAM output files: -X 5000 -n 2 -p 3 -3 9 -S. For the raw data generated from NovaSeq 6000, the bowtie options were as follows: -X 5000 -n 2 -p 3 -3 69 -S.
For Bowtie alignment, we updated the reference genome by applying innate mutations in our lab strain. Strains for the lacZ-related experiment are lack of lacY and lacA gene, which, however, does not affect lacZ expression. prepared multiple variants of the reference genome in advance by updating some of the sequences on the genome, such as dRBSdATG and modified UTR, to properly map the sequence reads generated from different genotype samples.
In the xylA samples, the aligned reads were manually normalized by dividing 10^9 × (reads on the xylAB operon and its upstream region) into total reads aligned to genome. The reads from the other gene samples, galE, galP, lacZ, and rhaB, were also normalized respectively in accordance with their operon sequences.
Assembly: NC_000913.3
Supplementary files format and content: gff, normalized counts of sequencing reads around the target region

molecule: genomic DNA

organism: Escherichia coli

source_name: bacterial cell

extract_protocol:
E. coli cells induced for 4 hours with proper inducer were cross-linked by 1% formaldehyde at room temperature for 30 min. The cross-linked cells were harvested and lysed, followed by sonication for DNA fragmentation. If necessary, cells were treated with 50 μg/mL bicyclomycin (BCM) for 30 minutes or 150 μg/mL rifampicin for 15 minutes prior to harvest.
The sheared DNA was immunoprecipitated by proper antibodies (anti-RNAP β or c-Myc). After binding to chromatin beads, immunoprecipitated DNA was end-repaired, dA-tailed, and ligated with the first adapter using the KAPA HyperPrep Kit (KAPA Biosystems). Adapter-ligated DNA samples were then nick-repaired and exonuclease-treated. The DNA samples were eluted from the beads by reversing protein-DNA crosslinking at 65 °C. Primer extension and second adapter ligation were performed in sequence. Finally, the DNA samples were enriched by PCR, using KAPA HotStart ReadMix in HyperPrep Kit (KAPA Biosystems). DNAs after each reaction were purified and size-selected using either AMPure XP beads (Beckman Coulter, Brea, CA, USA) or Zymo DNA Clean & Concentrator (Zymo, Irvine, CA, USA).

value: bacterial cell

tag: strain

tag: substrain

tag: chip antibody

value: c-Myc Antibody (9E10) (Santa Cruz Biotech, #sc-40)

value: Deletion of RBS & start codon of xylA; 8-myc-tagged NusG

value: 0.4% D-xylose induction for 4 hours


title: Medial olivocochlear neuron MOC01

description:
Library name: MOC01
Column name in RawCountFile.txt= MOC01


title: xylA, BCM-treated, replicate 2

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)

value: WT

value: 0.4% D-xylose induction for 4 hours; 50 μg/mL BCM treatment for 30 min


title: Siberian Hamster, MBH, 28wk SD, Rep 6

description:
MBH172
MBHExpressedGenesTranscripts.CSV


title: Lateral olivocochlear neuron LOC18

description:
Library name: LOC18
Column name in RawCountFile.txt= LOC18

source_name: Lateral olivocochlear neuron

value: Lateral olivocochlear neuron

value: wild-type


title: PB03490-001 flex scRNA-seq

description:
SRR30239410, SRR30239409, SRR30239408, SRR30239407, SRR30239406, SRR30239405, SRR30239404, SRR30239403, SRR30239420, SRR30239401, SRR30239400, SRR30239471, SRR30239451, SRR30239450, SRR30239449, SRR30239448, SRR30239464, SRR30239463, SRR30239461, SRR30239460, SRR30239459, SRR30239458, SRR30239457, SRR30239456
10x Flex ligation probe-based sequencing

value: Blood

value: Hispanic or Latino origin


title: PB03477-001 flex scRNA-seq

description:
SRR30204393, SRR30204392, SRR30204391, SRR30204390, SRR30204389, SRR30204388, SRR30204363, SRR30204362, SRR30204361, SRR30204360, SRR30204358, SRR30204357, SRR30204356, SRR30204355, SRR30204354, SRR30204353, SRR30204352, SRR30204351, SRR30204350, SRR30204349, SRR30204347, SRR30204346, SRR30204345, SRR30204344
10x Flex ligation probe-based sequencing

value: PBMC

value: Male


title: Siberian Hamster, MBH, 24wk SD, Rep 6

description:
MBH188
MBHExpressedGenesTranscripts.CSV


title: xylA, rifampicin-treated


title: Lateral olivocochlear neuron LOC17

description:
Library name: LOC17
Column name in RawCountFile.txt= LOC17

value: RNA-seq after patch clamp


title: PB03482-001 flex scRNA-seq

value: Female

value: American Indian

value: Negative

value: FALSE


title: PB03475-001 flex scRNA-seq

description:
SRR30204394, SRR30204359, SRR30204348, SRR30204343, SRR30204341, SRR30204340, SRR30204255, SRR30204253, SRR30204252, SRR30204251, SRR30204250, SRR30204249, SRR30204248, SRR30204247, SRR30204245, SRR30204244, SRR30204243, SRR30204242, SRR30204241, SRR30204240, SRR30204239, SRR30204238, SRR30204237, SRR30204236
10x Flex ligation probe-based sequencing

value: Caucasian

value: Positive


title: Siberian Hamster, MBH, 20wk SD, Rep 6

description:
MBH217
MBHExpressedGenesTranscripts.CSV


title: xylA, UTR 300bp, replicate 2

value: bacterial cell

value: xylA with UTR 300 bp

value: 0.4% D-xylose induction for 4 hours


title: Trigeminal ganglion_Replicate 3

description:
Library name: TG_3
Column names: RawCounts_TG_3 and TPM_TG_3

value: Trigeminal ganglion


title: PB03471-001 flex scRNA-seq

description:
SRR30239487, SRR30239486, SRR30239484, SRR30239438, SRR30239437, SRR30239435, SRR30239479, SRR30239478, SRR30239477, SRR30239476, SRR30239475, SRR30239474, SRR30239473, SRR30239472, SRR30239447, SRR30239446, SRR30239444, SRR30239443, SRR30239442, SRR30239441, SRR30239440, SRR30239439, SRR30239436, SRR30239416
10x Flex ligation probe-based sequencing


title: Siberian Hamster, MBH, 16wk SD, Rep 6

description:
MBH265
MBHExpressedGenesTranscripts.CSV


title: PB03468-001 flex scRNA-seq


title: Lateral olivocochlear neuron LOC15

description:
Library name: LOC15
Column name in RawCountFile.txt= LOC15

value: Lateral olivocochlear neuron


title: PB03455-001 flex scRNA-seq


title: xylA, UTR 200bp, replicate 2

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)

value: xylA with UTR 200 bp


title: Siberian Hamster, MBH, 8wk SD, Rep 6

description:
MBH397
MBHExpressedGenesTranscripts.CSV


title: Lateral olivocochlear neuron LOC14

description:
Library name: LOC14
Column name in RawCountFile.txt= LOC14

value: wild-type


title: Lateral olivocochlear neuron LOC13

description:
Library name: LOC13
Column name in RawCountFile.txt= LOC13


title: PB03451-001 flex scRNA-seq

value: Blood

value: PBMC


title: Siberian Hamster, MBH, 4wk SD, Rep 6

description:
MBH314
MBHExpressedGenesTranscripts.CSV


title: xylA, UTR 100bp, replicate 2

value: xylA with UTR 100 bp


title: Lateral olivocochlear neuron LOC12

description:
Library name: LOC12
Column name in RawCountFile.txt= LOC12

value: RNA-seq after patch clamp


title: Siberian Hamster, MBH, LD, Rep 6

description:
MBH141
MBHExpressedGenesTranscripts.CSV


title: xylA, UTR 100bp, replicate 1


title: PB03450-001 flex scRNA-seq

description:
SRR30204234, SRR30204233, SRR30204232, SRR30204231, SRR30204339, SRR30204338, SRR30204337, SRR30204336, SRR30204335, SRR30204334, SRR30204332, SRR30204331, SRR30204330, SRR30204329, SRR30204328, SRR30204327, SRR30204326, SRR30204325, SRR30204324, SRR30204323, SRR30204321, SRR30204320, SRR30204319, SRR30204318
10x Flex ligation probe-based sequencing

value: Male


title: PB03447-001 flex scRNA-seq

value: Female

value: Hispanic or Latino origin

value: Negative


title: Siberian Hamster, MBH, 32wk SD, Rep 5

description:
MBH152
MBHExpressedGenesTranscripts.CSV


title: xylA, UTR 54bp, replicate 2

value: xylA with UTR 54 bp


title: Lateral olivocochlear neuron LOC10

description:
Library name: LOC10
Column name in RawCountFile.txt= LOC10


title: Siberian Hamster, MBH, 28wk SD, Rep 5

description:
MBH163
MBHExpressedGenesTranscripts.CSV


title: xylA, UTR 300bp, replicate 1

value: bacterial cell


title: Lateral olivocochlear neuron LOC11

description:
Library name: LOC11
Column name in RawCountFile.txt= LOC11


title: xylA, UTR 54bp, replicate 1


title: PB03440-001 flex scRNA-seq

description:
SRR30239415, SRR30239414, SRR30239432, SRR30239431, SRR30239430, SRR30239429, SRR30239428, SRR30239427, SRR30239426, SRR30239425, SRR30239424, SRR30239423, SRR30239421, SRR30239419, SRR30239418, SRR30239417, SRR30239470, SRR30239469, SRR30239468, SRR30239467, SRR30239466, SRR30239465, SRR30239412, SRR30239411
10x Flex ligation probe-based sequencing

value: Caucasian

value: FALSE


title: PB03436-001 flex scRNA-seq

description:
SRR30239543, SRR30239542, SRR30239492, SRR30239434, SRR30239445, SRR30239433, SRR30239422, SRR30239413, SRR30239402, SRR30239462, SRR30239541, SRR30239525, SRR30239536, SRR30239513, SRR30239481, SRR30239497, SRR30239496, SRR30239495, SRR30239494, SRR30239493, SRR30239491, SRR30239490, SRR30239489, SRR30239488
10x Flex ligation probe-based sequencing


title: Lateral olivocochlear neuron LOC09

description:
Library name: LOC09
Column name in RawCountFile.txt= LOC09


title: Lateral olivocochlear neuron LOC16

description:
Library name: LOC16
Column name in RawCountFile.txt= LOC16


title: rhaB, replicate 2

value: WT

value: 0.2% L-rhamnose induction for 4 hours


title: xylA, UTR 200bp, replicate 1

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)

value: 0.4% D-xylose induction for 4 hours


title: Lateral olivocochlear neuron LOC08

description:
Library name: LOC08
Column name in RawCountFile.txt= LOC08

value: Lateral olivocochlear neuron

value: wild-type


title: Siberian Hamster, MBH, 20wk SD, Rep 5

description:
MBH216
MBHExpressedGenesTranscripts.CSV


title: PB03434-001 flex scRNA-seq

description:
SRR30204276, SRR30204275, SRR30204274, SRR30204273, SRR30204271, SRR30204270, SRR30204269, SRR30204268, SRR30204411, SRR30204410, SRR30204409, SRR30204408, SRR30204407, SRR30204406, SRR30204404, SRR30204403, SRR30204402, SRR30204401, SRR30204400, SRR30204399, SRR30204398, SRR30204397, SRR30204396, SRR30204395
10x Flex ligation probe-based sequencing

value: Blood

value: PBMC

value: Positive


title: Siberian Hamster, MBH, 12wk SD, Rep 6

description:
MBH280
MBHExpressedGenesTranscripts.CSV


title: Lateral olivocochlear neuron LOC07

description:
Library name: LOC07
Column name in RawCountFile.txt= LOC07

value: RNA-seq after patch clamp


title: PB03433-001 flex scRNA-seq

value: Female

value: Asian


title: lacZ, replicate 2

value: Deletion of lacY and lacA

value: 1 mM IPTG induction for 4 hours


title: Siberian Hamster, MBH, 16wk SD, Rep 5

description:
MBH283
MBHExpressedGenesTranscripts.CSV


title: Lateral olivocochlear neuron LOC06

description:
Library name: LOC06
Column name in RawCountFile.txt= LOC06


title: PB03429-001 flex scRNA-seq

value: Male

value: Negative


title: Siberian Hamster, MBH, 12wk SD, Rep 5

description:
MBH278
MBHExpressedGenesTranscripts.CSV


title: lacZ, replicate 1

value: bacterial cell


title: Lateral olivocochlear neuron LOC05

description:
Library name: LOC05
Column name in RawCountFile.txt= LOC05


title: Siberian Hamster, MBH, 8wk SD, Rep 5

description:
MBH306
MBHExpressedGenesTranscripts.CSV


title: gal, replicate 2

value: WT

value: 0.2% D-galactose induction for 4 hours


title: PB03423-001 flex scRNA-seq

value: FALSE


title: Lateral olivocochlear neuron LOC04

description:
Library name: LOC04
Column name in RawCountFile.txt= LOC04


title: PB03435-001 flex scRNA-seq

value: Caucasian


title: Siberian Hamster, MBH, 4wk SD, Rep 5

description:
MBH352
MBHExpressedGenesTranscripts.CSV


title: PB03422-001 flex scRNA-seq


title: Lateral olivocochlear neuron LOC03

description:
Library name: LOC03
Column name in RawCountFile.txt= LOC03

value: Lateral olivocochlear neuron


title: Siberian Hamster, MBH, 24wk SD, Rep 5

description:
MBH180
MBHExpressedGenesTranscripts.CSV


title: Siberian Hamster, MBH, LD, Rep 5

description:
MBH238
MBHExpressedGenesTranscripts.CSV


title: gal, replicate 1

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)


title: Lateral olivocochlear neuron LOC02

description:
Library name: LOC02
Column name in RawCountFile.txt= LOC02

value: wild-type


title: Siberian Hamster, MBH, 32wk SD, Rep 4

description:
MBH153
MBHExpressedGenesTranscripts.CSV


title: xylA, replicate 1

value: 0.4% D-xylose induction for 4 hours


title: PB03414-001 flex scRNA-seq

description:
SRR30239455, SRR30239454, SRR30239453, SRR30239452, SRR30239540, SRR30239538, SRR30239539, SRR30239521, SRR30239522, SRR30239523, SRR30239524, SRR30239503, SRR30239504, SRR30239505, SRR30239526, SRR30239527, SRR30239528, SRR30239529, SRR30239530, SRR30239531, SRR30239532, SRR30239533, SRR30239534, SRR30239535
10x Flex ligation probe-based sequencing

value: Blood

value: PBMC

value: Positive


title: Lateral olivocochlear neuron LOC01

description:
Library name: LOC01
Column name in RawCountFile.txt= LOC01

value: RNA-seq after patch clamp


title: rhaB, replicate 1

value: 0.2% L-rhamnose induction for 4 hours


title: dRBSdATG, xylA, rifampicin-treated

value: Deletion of RBS & start codon of xylA


title: recruited sNAM after injury, rep 3

city: Freiburg

first: Julia

last: Kolter

address: Breisacher Str. 115b

country: Germany

institute: University of Freiburg

data_processing:
The resulting .bcl files were converted into .fastq files with the bcl2fastq v2.18 software.
Trimmed (Cutadapt) raw reads were aligned to the mm10 murine reference genome with STAR (Version 2.7.2b)
Data was quantified with feature counts (Liao et al., 2014).
Differential expression analysis between groups was performed with DESeq2 (version 1.24.0) (Love et al., 2014) in R (version 3.6.1) (R Core Team 2015).
Assembly: mm10
Supplementary files format and content: tab-limited text file including normalized counts for each sample

source_name: ear skin

extract_protocol:
CD11b+ CD64+ Lin- macrophages were sorted from left ear (injury) and right ear (homeostasis) for interstitial macrophages (GFP-/Tomato-), resident nerve-associated macrophages (GFP+/Tomato+) and recruited nerve-associated macrophages after injury (GFP+/Tomato-) by FACS. RNA was extracted using the RNAmicro Kit Plus (Qiagen). The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 250 pg total-RNA. Double stranded cDNA was amplified by LD PCR (13 cycles) and purified via magnetic bead clean-up.
Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA)

treatment_protocol: CX3CR1-creERT2/gfp R26-tdT/+ mice were induced with Tamoxifen, and 3 weeks later, left ears were punched. Skin was extracted after 10d.

value: Cxcr1creERT2/gfp R26tdT/+

value: ear skin

value: macrophage

value: tamoxifen + punch

tag: reporter

value: GFP+/Tomato-


title: Siberian Hamster, MBH, 28wk SD, Rep 4

description:
MBH162
MBHExpressedGenesTranscripts.CSV


title: Siberian Hamster, MBH, 24wk SD, Rep 4

description:
MBH196
MBHExpressedGenesTranscripts.CSV


title: PB03416-001 flex scRNA-seq

description:
SRR30204374, SRR30204373, SRR30204372, SRR30204371, SRR30204370, SRR30204369, SRR30204368, SRR30204367, SRR30204365, SRR30204364, SRR30204291, SRR30204290, SRR30204289, SRR30204288, SRR30204287, SRR30204286, SRR30204285, SRR30204284, SRR30204282, SRR30204281, SRR30204280, SRR30204279, SRR30204278, SRR30204277
10x Flex ligation probe-based sequencing

tag: tissue

value: Female

value: FALSE


title: recruited sNAM after injury, rep 2

tag: cell type


title: dRBSdATG, xylA, UTR 300bp, replicate 2

value: bacterial cell

tag: genotype

value: Deletion of RBS & start codon of xylA with UTR 300 bp


title: xylA, replicate 2

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)

value: WT

tag: treatment


title: dRBSdATG, xylA, UTR 300bp, replicate 1

value: 0.4% D-xylose induction for 4 hours


title: PB03406-001 flex scRNA-seq

description:
SRR30204393, SRR30204392, SRR30204391, SRR30204390, SRR30204389, SRR30204388, SRR30204363, SRR30204362, SRR30204361, SRR30204360, SRR30204358, SRR30204357, SRR30204356, SRR30204355, SRR30204354, SRR30204353, SRR30204352, SRR30204351, SRR30204350, SRR30204349, SRR30204347, SRR30204346, SRR30204345, SRR30204344
10x Flex ligation probe-based sequencing

value: Blood

value: PBMC

tag: subject id

value: Male

value: Hispanic or Latino origin

value: Negative


title: PB03410-001 flex scRNA-seq

description:
SRR30204394, SRR30204359, SRR30204348, SRR30204343, SRR30204341, SRR30204340, SRR30204255, SRR30204253, SRR30204252, SRR30204251, SRR30204250, SRR30204249, SRR30204248, SRR30204247, SRR30204245, SRR30204244, SRR30204243, SRR30204242, SRR30204241, SRR30204240, SRR30204239, SRR30204238, SRR30204237, SRR30204236
10x Flex ligation probe-based sequencing

tag: age at_enrollment

value: Caucasian

value: Positive


title: dRBSdATG, xylA, UTR 200bp, replicate 2

value: Deletion of RBS & start codon of xylA with UTR 200 bp


title: PB03404-001 flex scRNA-seq

description:
SRR30204317, SRR30204316, SRR30204315, SRR30204314, SRR30204313, SRR30204312, SRR30204310, SRR30204309, SRR30204308, SRR30204307, SRR30204306, SRR30204305, SRR30204304, SRR30204303, SRR30204302, SRR30204301, SRR30204299, SRR30204298, SRR30204297, SRR30204296, SRR30204295, SRR30204294, SRR30204293, SRR30204292
10x Flex ligation probe-based sequencing

tag: Sex

value: Asian


title: sNAM after injury, rep 3

value: Cxcr1creERT2/gfp R26tdT/+

value: ear skin

value: macrophage

value: tamoxifen + punch

value: GFP+/Tomato+


title: Siberian Hamster, MBH, 16wk SD, Rep 4

description:
MBH255
MBHExpressedGenesTranscripts.CSV


title: Siberian Hamster, MBH, 12wk SD, Rep 4

description:
MBH289
MBHExpressedGenesTranscripts.CSV


title: sNAM after injury, rep 2


title: PB03398-001 flex scRNA-seq

tag: race

value: FALSE


title: Siberian Hamster, MBH, 8wk SD, Rep 4

description:
MBH398
MBHExpressedGenesTranscripts.CSV


title: dRBSdATG, xylA, UTR 100bp, replicate 2

value: bacterial cell

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)

value: Deletion of RBS & start codon of xylA with UTR 100 bp


title: sNAM after injury, rep 1


title: PB03390-001 flex scRNA-seq

value: Blood

value: PBMC

value: Female

tag: cmv status


title: PB03384-001 flex scRNA-seq

description:
SRR30239537, SRR30239518, SRR30239519, SRR30239520, SRR30239502, SRR30239501, SRR30239517, SRR30239516, SRR30239515, SRR30239514, SRR30239512, SRR30239511, SRR30239510, SRR30239509, SRR30239508, SRR30239507, SRR30239506, SRR30239485, SRR30239483, SRR30239482, SRR30239480, SRR30239500, SRR30239499, SRR30239498
10x Flex ligation probe-based sequencing

value: Hispanic or Latino origin

value: Negative

tag: batch id


title: Siberian Hamster, MBH, 4wk SD, Rep 4

description:
MBH351
MBHExpressedGenesTranscripts.CSV


title: PB03395-001 flex scRNA-seq

value: Male

value: Positive

tag: sample bridging_control


title: sNAM, rep 3

value: tamoxifen

value: GFP-/Tomato-


title: dRBSdATG, xylA, UTR 200bp, replicate 1

value: Deletion of RBS & start codon of xylA with UTR 200 bp

value: 0.4% D-xylose induction for 4 hours


title: dRBSdATG, xylA, UTR 100bp, replicate 1


title: PB03344-001 flex scRNA-seq

value: Caucasian

tag: pooled sample_id


title: Siberian Hamster, MBH, 20wk SD, Rep 4

description:
MBH231
MBHExpressedGenesTranscripts.CSV


title: sNAM, rep 2

value: Cxcr1creERT2/gfp R26tdT/+

value: ear skin

value: macrophage


title: dRBSdATG, xylA, UTR 54bp, replicate 2

value: bacterial cell

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)

value: Deletion of RBS & start codon of xylA with UTR 54 bp


title: recruited sNAM after injury, rep 1

value: tamoxifen + punch

value: GFP+/Tomato-


title: dRBSdATG, xylA, UTR 54bp, replicate 1


title: sNAM, rep 1


title: Siberian Hamster, MBH, 28wk SD, Rep 3

description:
MBH165
MBHExpressedGenesTranscripts.CSV


title: dRBSdATG, rhaB, replicate 2

value: Deletion of RBS & start codon of rhaB

value: 0.2% L-rhamnose induction for 4 hours


title: PB03339-001 flex scRNA-seq

value: Blood

value: PBMC

value: Female

value: FALSE

tag: probe barcode_id


title: Siberian Hamster, MBH, 24wk SD, Rep 3

description:
MBH187
MBHExpressedGenesTranscripts.CSV


title: interstitial macrophages after injury, rep 2

value: GFP+/Tomato+


title: PB03334-001 flex scRNA-seq

value: Male

value: Positive


title: PB03335-001 flex scRNA-seq

value: Caucasian

value: Negative


title: dRBSdATG, rhaB, replicate 1

tag: strain


title: interstitial macrophages after injury, rep 1

value: Cxcr1creERT2/gfp R26tdT/+

value: ear skin

value: macrophage


title: dRBSdATG, lacZ, replicate 2

value: bacterial cell

tag: substrain

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)

value: Deletion of RBS & start codon of lacZ; deletion of lacY and lacA

value: 1 mM IPTG induction for 4 hours


title: PB03328-001 flex scRNA-seq

value: Hispanic or Latino origin


title: Siberian Hamster, MBH, 20wk SD, Rep 3

description:
MBH226
MBHExpressedGenesTranscripts.CSV


title: Siberian Hamster, MBH, 16wk SD, Rep 3

description:
MBH251
MBHExpressedGenesTranscripts.CSV


title: dRBSdATG, lacZ, replicate 1

tag: chip antibody


title: interstitial macrophages, rep 3

value: tamoxifen

tag: reporter

value: GFP-/Tomato-


title: Siberian Hamster, MBH, 12wk SD, Rep 3

description:
MBH276
MBHExpressedGenesTranscripts.CSV


title: dRBSdATG, galP, replicate 2

value: Deletion of RBS & start codon of galP

value: 0.2% D-galactose induction for 4 hours


title: PB03327-001 flex scRNA-seq

tag: tissue

value: Blood

value: PBMC

value: Female

value: FALSE


title: Siberian Hamster, MBH, LD, Rep 4

description:
MBH247
MBHExpressedGenesTranscripts.CSV

tag: cell type


title: PB03314-001 flex scRNA-seq

value: Positive


title: interstitial macrophages, rep 2

tag: genotype

value: Cxcr1creERT2/gfp R26tdT/+


title: interstitial macrophages after injury, rep 3

value: ear skin

tag: treatment

value: tamoxifen + punch

value: GFP+/Tomato+


title: dRBSdATG, galP, replicate 1

value: bacterial cell

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)


title: Siberian Hamster, MBH, 8wk SD, Rep 3

description:
MBH399
MBHExpressedGenesTranscripts.CSV


title: interstitial macrophages, rep 1

value: macrophage


title: Siberian Hamster, MBH, 32wk SD, Rep 3

description:
MBH160
MBHExpressedGenesTranscripts.CSV


title: dRBSdATG, galE, replicate 2

value: Deletion of RBS & start codon of galE


title: PB03309-001 flex scRNA-seq

tag: subject id

value: Caucasian


title: WT3_control [9]

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

description: Monocytes treated with M-CSF

data_processing:
alignment with STAR_2.5.3a (--outFilterMismatchNmax 10)
counting reads with featureCounts
Differential Gene Expression with LIMMA
Genome_build: mm10 GRCm38; basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: count data

source_name: Myeloid cells

extract_protocol:
Total RNA was extracted using RNA spin columns (PureLink RNA Mini Kit, Ambion). RNA quantification was carried out using Qubit Fluorimetric Quantification (Life Technologies) and 500ng of RNA were used to prepare the library.
TruSeq Stranded mRNA (Illumina)
RNA-Seq;NextSeq 500;SE;1x75;Nextera Index

tag: individual

value: Bone Marrow-derived monocytes

value: Vehicle

tag: condition


title: PB03308-001 flex scRNA-seq

description:
SRR30204234, SRR30204233, SRR30204232, SRR30204231, SRR30204339, SRR30204338, SRR30204337, SRR30204336, SRR30204335, SRR30204334, SRR30204332, SRR30204331, SRR30204330, SRR30204329, SRR30204328, SRR30204327, SRR30204326, SRR30204325, SRR30204324, SRR30204323, SRR30204321, SRR30204320, SRR30204319, SRR30204318
10x Flex ligation probe-based sequencing

tag: age at_enrollment

tag: Sex

value: Male

tag: race

value: African American


title: Siberian Hamster, MBH, 4wk SD, Rep 3

description:
MBH332
MBHExpressedGenesTranscripts.CSV


title: Siberian Hamster, MBH, LD, Rep 3

description:
MBH248
MBHExpressedGenesTranscripts.CSV


title: dRBSdATG, galE, replicate 1

value: 0.2% D-galactose induction for 4 hours


title: WT2_PFM037_TNF [8]

description: Monocytes treated with M-CSF +PFM037 +TNF


title: PB03297-001 flex scRNA-seq

description:
SRR30239415, SRR30239414, SRR30239432, SRR30239431, SRR30239430, SRR30239429, SRR30239428, SRR30239427, SRR30239426, SRR30239425, SRR30239424, SRR30239423, SRR30239421, SRR30239419, SRR30239418, SRR30239417, SRR30239470, SRR30239469, SRR30239468, SRR30239467, SRR30239466, SRR30239465, SRR30239412, SRR30239411
10x Flex ligation probe-based sequencing

value: Blood

value: PBMC

value: Female

tag: cmv status

tag: batch id

tag: sample bridging_control


title: Siberian Hamster, MBH, 32wk SD, Rep 2

description:
MBH149
MBHExpressedGenesTranscripts.CSV


title: WT2_TNF [7]

description: Monocytes treated with M-CSF +TNF

value: TNF


title: dRBSdATG, xylA, replicate 2

tag: strain

value: Deletion of RBS & start codon of xylA

value: 0.4% D-xylose induction for 4 hours


title: PB03287-001 flex scRNA-seq

value: Negative

value: FALSE

tag: pooled sample_id

tag: probe barcode_id


title: Siberian Hamster, MBH, 28wk SD, Rep 2

description:
MBH174
MBHExpressedGenesTranscripts.CSV


title: dRBSdATG, xylA, replicate 1

value: bacterial cell

tag: substrain

tag: chip antibody

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)


title: Siberian Hamster, MBH, 24wk SD, Rep 2

description:
MBH181
MBHExpressedGenesTranscripts.CSV

tag: cell type


title: CD8+ DCs_tumor

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: RNA Seq- CD8 DCs

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to Ensembl GRCz11 whole genome using STAR 3.0
Transcript abundance were calculated with Htseq-count
Assembly: GRCz11
Supplementary files format and content: raw count files

organism: Danio rerio

source_name: CD8 dendritic cells

growth_protocol: Melanoma tumors were extracted from 6wpf zebrafish, mesh and the cells were made into single cell suspension

extract_protocol:
Cell sorting
Illumina XT library prep kit, according to protocol

tag: tissue

value: Melanoma

value: Myeloid cells

tag: egfp status

value: EGFP+


title: WT2_control [5]

description: Monocytes treated with M-CSF

value: Bone Marrow-derived monocytes

tag: treatment

value: Vehicle


title: WT2_PFM037 [6]

description: Monocytes treated with M-CSF +PFM037

tag: individual


title: Siberian Hamster, MBH, 20wk SD, Rep 2

description:
MBH214
MBHExpressedGenesTranscripts.CSV


title: WT1_PFM037_TNF [4]

tag: condition


title: Siberian Hamster, MBH, 16wk SD, Rep 2

description:
MBH252
MBHExpressedGenesTranscripts.CSV


title: PB03285-001 flex scRNA-seq

description:
SRR30239487, SRR30239486, SRR30239484, SRR30239438, SRR30239437, SRR30239435, SRR30239479, SRR30239478, SRR30239477, SRR30239476, SRR30239475, SRR30239474, SRR30239473, SRR30239472, SRR30239447, SRR30239446, SRR30239444, SRR30239443, SRR30239442, SRR30239441, SRR30239440, SRR30239439, SRR30239436, SRR30239416
10x Flex ligation probe-based sequencing

tag: subject id

tag: age at_enrollment

value: Male

value: Hispanic or Latino origin


title: zfCD8/lck_thymus_T_1.5m

description: RNA Seq CD8 T cells

source_name: CD8 T cells

growth_protocol: Thymi were extracted from 6wpf zebrafish, mesh and the cells were made into single cell suspension

treatment_protocol: No treatment

value: Thymus

value: lymphocytes


title: PB03303-001 flex scRNA-seq

description:
SRR30239543, SRR30239542, SRR30239492, SRR30239434, SRR30239445, SRR30239433, SRR30239422, SRR30239413, SRR30239402, SRR30239462, SRR30239541, SRR30239525, SRR30239536, SRR30239513, SRR30239481, SRR30239497, SRR30239496, SRR30239495, SRR30239494, SRR30239493, SRR30239491, SRR30239490, SRR30239489, SRR30239488
10x Flex ligation probe-based sequencing

value: Blood

value: PBMC

tag: Sex

value: Female

tag: race

value: Caucasian

value: Positive


title: PB03282-001 flex scRNA-seq

tag: cmv status

value: Negative

tag: batch id

value: FALSE


title: Mfrn1, scRNAseq

city: Pittsburgh

first: Yvette

last: Yien

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
demultiplexing, barcoded processing, gene counting and aggregation were carried out using CellRanger.
Assembly: GRCZ11
Supplementary files format and content: tab separated values and matrix files.

source_name: whole embryo, homogenized

extract_protocol:
10, 3-dpf zebrafish embryos from WT and mfrn mutant fish were were homogenized in 300 µL PBS containing 10% FBS and through a 70 µm cell strainer.
10x genomics, 3' protocol; manufacturer's instructions.

value: whole embryo, homogenized

tag: genotype

value: MFRN1 (Mfrn1 mutant)


title: WT1_PFM037 [2]

description: Monocytes treated with M-CSF +PFM037


title: WT, scRNAseq

description: 10x genomics

value: Wild-type (WT)


title: Siberian Hamster, MBH, 8wk SD, Rep 2

description:
MBH310
MBHExpressedGenesTranscripts.CSV


title: Siberian Hamster, MBH, 12wk SD, Rep 2

description:
MBH292
MBHExpressedGenesTranscripts.CSV


title: PB03267-001 flex scRNA-seq

description:
SRR30204276, SRR30204275, SRR30204274, SRR30204273, SRR30204271, SRR30204270, SRR30204269, SRR30204268, SRR30204411, SRR30204410, SRR30204409, SRR30204408, SRR30204407, SRR30204406, SRR30204404, SRR30204403, SRR30204402, SRR30204401, SRR30204400, SRR30204399, SRR30204398, SRR30204397, SRR30204396, SRR30204395
10x Flex ligation probe-based sequencing

tag: sample bridging_control

tag: pooled sample_id


title: KO4

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

institute: City of Hope

description:
Library name: Sample 8
Bulk RNAseq raw counts

data_processing:
Partek Flow build version 12.8.0
Sequence reads were aligned to GRCm39/mm39 using STAR v2.7.8a with validation of quality through prealignment and postalignment quality assurance (QA)/quality control (QC) using Partek Flow
Aligned reads were subject to quantify to mm39 using the Parteck E/M algorithm then annote using Ensembl Transcripts replease 114 and fitlered genes by excluding counts less than 10  and include only protein coding genes across all samples.
Filtered reads were normalized and performed differential expression analysis comparing KO vs WT using DESeq2
Assembly: GRCm39/mm39
Supplementary files format and content: A tab-delimited text file including raw counts for all samples.

source_name: Spleen

growth_protocol: RPMI 1640 medium (Corning Inc.) containing 2 mM l-glutamine, 50 µM β-mercaptoethanol, penicillin (100 U/ml), streptomycin (100 mg/ml), and 10% FBS (Corning Inc.)

extract_protocol:
RNA extraction with the RNeasy Mini Kit (QIAGEN)，1.0 ug of total RNA was used for the constrction of sequecing libraries.
RNA  libraries for RNA-seq were prepared using with kapa RNA hyperprep kit with riboerase kit  following manufacture's protocols.

treatment_protocol: TGF-β,hamster anti-CD3 , hamster anti-CD28 ,anti-IFNγ and anti-IL-4 treatment for 36 h

value: Spleen

tag: cell line

value: iTreg cell

value: T cell

value: TDRD3 knokout


title: Siberian Hamster, MBH, 4wk SD, Rep 2

description:
MBH333
MBHExpressedGenesTranscripts.CSV


title: WT1_TNF [3]

description: Monocytes treated with M-CSF +TNF

value: Bone Marrow-derived monocytes

value: TNF


title: WT4_PFM037_TNF [16]


title: PB03187-001 flex scRNA-seq

value: Male

value: African American

tag: probe barcode_id


title: PB03184-001 flex scRNA-seq

value: Blood

tag: cell type

value: PBMC


title: WT4_TNF [15]

description: Monocytes treated with M-CSF +TNF


title: PB03275-001 flex scRNA-seq

tag: tissue

value: Hispanic or Latino origin


title: Siberian Hamster, MBH, LD, Rep 2

description:
MBH205
MBHExpressedGenesTranscripts.CSV


title: KO2

description:
Library name: Sample 6
Bulk RNAseq raw counts

value: TGF-β,hamster anti-CD3 , hamster anti-CD28 ,anti-IFNγ and anti-IL-4 treatment


title: WT4_PFM037 [14]

description: Monocytes treated with M-CSF +PFM037


title: PB03286-001 flex scRNA-seq

value: Negative


title: Siberian Hamster, MBH, 32wk SD, Rep 1

description:
MBH161
MBHExpressedGenesTranscripts.CSV


title: KO1

description:
Library name: Sample 5
Bulk RNAseq raw counts


title: KO3

description:
Library name: Sample 7
Bulk RNAseq raw counts


title: PB03171-001 flex scRNA-seq

description:
SRR30239455, SRR30239454, SRR30239453, SRR30239452, SRR30239540, SRR30239538, SRR30239539, SRR30239521, SRR30239522, SRR30239523, SRR30239524, SRR30239503, SRR30239504, SRR30239505, SRR30239526, SRR30239527, SRR30239528, SRR30239529, SRR30239530, SRR30239531, SRR30239532, SRR30239533, SRR30239534, SRR30239535
10x Flex ligation probe-based sequencing

value: Caucasian

value: FALSE


title: WT4_control [13]

description: Monocytes treated with M-CSF

value: Vehicle


title: PB03166-001 flex scRNA-seq

value: Female

value: Positive


title: WT4

description:
Library name: Sample 4
Bulk RNAseq raw counts

value: Spleen

value: iTreg cell

value: WT


title: Siberian Hamster, MBH, 28wk SD, Rep 1

description:
MBH175
MBHExpressedGenesTranscripts.CSV


title: WT3_PFM037_TNF [12]

value: Bone Marrow-derived monocytes


title: Siberian Hamster, MBH, 24wk SD, Rep 1

description:
MBH178
MBHExpressedGenesTranscripts.CSV


title: WT3

description:
Library name: Sample 3
Bulk RNAseq raw counts

value: T cell


title: WT3_TNF [11]

description: Monocytes treated with M-CSF +TNF

value: TNF


title: PB03152-001 flex scRNA-seq


title: Siberian Hamster, MBH, 20wk SD, Rep 1

description:
MBH213
MBHExpressedGenesTranscripts.CSV


title: WT2

description:
Library name: Sample 2
Bulk RNAseq raw counts


title: WT3_PFM037 [10]

description: Monocytes treated with M-CSF +PFM037


title: Siberian Hamster, MBH, 16wk SD, Rep 1

description:
MBH244
MBHExpressedGenesTranscripts.CSV


title: WT1

description:
Library name: Sample 1
Bulk RNAseq raw counts


title: WT1_control [1]

description: Monocytes treated with M-CSF

value: Wild type (WT) 1


title: PB03203-003 flex scRNA-seq

value: Blood

value: American Indian


title: PB03146-001 flex scRNA-seq

description:
SRR30204394, SRR30204359, SRR30204348, SRR30204343, SRR30204341, SRR30204340, SRR30204255, SRR30204253, SRR30204252, SRR30204251, SRR30204250, SRR30204249, SRR30204248, SRR30204247, SRR30204245, SRR30204244, SRR30204243, SRR30204242, SRR30204241, SRR30204240, SRR30204239, SRR30204238, SRR30204237, SRR30204236
10x Flex ligation probe-based sequencing

value: PBMC


title: Siberian Hamster, MBH, 12wk SD, Rep 1

description:
MBH277
MBHExpressedGenesTranscripts.CSV


title: Siberian Hamster, MBH, 8wk SD, Rep 1

description:
MBH305
MBHExpressedGenesTranscripts.CSV


title: 601b

first: Jennifer

last: Davis

state: WA

address: 850 Republican St, Brotman #343

department: Lab Medicine and Pathology

institute: University of Washington

description: Library name: 127.043b

data_processing:
Cleaned reads were aligned to the reference genome (GRCm38/mm10) using STAR. Doublets were identified using scrublet and subsequently filtered out. Further analysis and quality filtering was performed using the Seurat package in R.
Assembly: GRCm38/mm10
Supplementary files format and content: Matrices with sample-specific cell annotations, qc stats, gene annotations, and umi counts

molecule: nuclear RNA

source_name: Cardiac ventricle

extract_protocol:
For single nucleus RNA sequencing (snRNAseq), whole heart samples were prepared using the sci-RNA-seq3 combinatorial indexing method as described previously with the following modifications. Briefly, 2 hearts from each condition were snap frozen in liquid nitrogen. Nuclei were isolated from frozen tissues by grinding the frozen tissue with a mortar and pestle, lysing the powdered tissue in hypotonic lysis buffer B, and dissociating the tissue in a gentleMACS M tube run on the “Protein 001” program followed by 50 strokes in a Dounce homogenizer with a type A/loose pestle. Lysates were subsequently filtered through a 40μm filter and centrifuged at 500xg for 5 minutes at 4°C. The nuclear pellet was then resuspended in 0.3M SPBSTM and filtered through a 20μm filter. The nuclei were subsequently fixed in methanol/DSP for 5 minutes at room temperature. The fixed nuclei were subsequently rehydrated with 0.3M SPBSTM, spun down at 500xg for 5 minutes at 4°C, and resuspended in 0.3M SPBSTM. The fixed nuclei were then aliquoted, snap frozen, and stored at -80°C until sequencing.
Libraries were constructed using the sci-RNA-seq3 combinatorial indexing method as described previously. Sequencing was performed at the Northwest Genomics Center on a Novaseq 6000 flow cell.

value: Cardiac ventricle

tag: batch


title: 601

description: Library name: 127.043


title: Nanos-Upd L Fraction 4 Replicate 2-PE

city: Baltimore

first: Daniel

last: Ringwalt

address: 3400N Charles St

department: Biology

institute: Johns Hopkins University

description: Library name: Sample 8

data_processing:
Reads were aligned to dm6 using Bowtie 2 (version 2.4.5). For PE (paired-end) indicated samples only, reads were filtered for proper pairs (SAM flag 2).
The template (the long single-end read or the alignment of the mates) was categorized using the midpoint base pair into bins of size 1 kb and step 1 kb.
Each pileup series is divided by a normalization factor: The total count of fragments itself divided by one million, and then the entry is further divided by the bin's width in kb. This yields FPKM quantification.
The timing enrichment is estimated on each bin also including one adjacent bin in each direction of the reference (if present). Thus, FPKM is effectively taken over 3 kb windows.
Assembly: dm6
Supplementary files format and content: CSV: Chromosome (dm6), start and end sliding window coordinates using BED file format semantics, and each series pileup of fragments divided by a normalization factor.

organism: Drosophila melanogaster

source_name: testis tumor

growth_protocol: Fly crosses were maintained on standard molasses media at 25C.

extract_protocol:
Whole tumor testes of the appropriate genotype were dissected in Schneider's media to obtain 100-200 pairs. The dissected testes were incubated for 15 minutes in media containing 100mM BrdU. After removing the media, nuclei were isolated by resuspending testes in 1mL homogenization buffer. Testis tissues were dounce homogenized with 20 strokes with loose pestle (A), followed by 40 strokes with tight pestle (B), before pipetting gently ~20 times with a wide bore tip. Nuclei were filtered through at 40uM cell strainer, then 10uM cell strainer into a fresh tube. The homozenization buffer was removed after pelleting nuclei. The pelleted nuclei were resuspended in resuspension buffer containing propidium iodide and incubated on ice for 30 minutes before proceeded to the cell sorter.  Nuclei were sorted on a MoFlo XDP cell sorter by gating for GSP+ nuclei and dividing S-phase nuclei into 4 equal fractions corresponding to early, early-mid, late-mid, or late replicating nuclei. Following the sort, DNA was purified from the nuclei. The purified DNA was next sonicated into ~200bp fragments, before initiating library preparion.
The NEB DNA Ultra II library prep kit for Illumina was incorporated into the Repli-seq protocol.  The first two steps of the NEBNext Ultra II DNA Library Prep Kit (End Prep and Adapter Ligation) were performed according to the manufacturer's instructions. The adapter-ligated DNA fragments were cleaned using the Zymo Research DNA Clean & Concentrator-5 kit. Next,  BrdU-containing DNA was immunoprecipitated, which enriches for DNA that was actively replicating at a specific stage in S-phase. The immunoprecipitated DNA was purified using a DNA Clean & Concentrator-5 kit from Zymo Research. Efficiency of the BrdU-immunoprecipitation was calculated using qPCR of the sample DNA compared against a serial dilution of known DNA concentrations. This method determined the number of PCR cycles required for library amplification. PCR amplification of the DNA fragments was performed following the NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: Whole dissected tumor testes were incubated with BrdU for 15 minutes at room temperature.

value: testis tumor

value: y[1] w[1118] P{hs70FLP} ; P{w[+mC]=GAL4::VP16-nanos.UTR} / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

value: GSC-like


title: Siberian Hamster, MBH, 4wk SD, Rep 1

description:
MBH356
MBHExpressedGenesTranscripts.CSV


title: s4

description:
Sult2B1b 4 Ly6C high CD11c+ MHC-II+
Ly6C high CD11c+ MHC-II+ FACS-sorted from Sult2B1b-LLC 4

data_processing:
alignment with STAR_2.5.3a (--outFilterMismatchNmax 10)
counting reads with featureCounts
Differential Gene Expression with LIMMA
Genome_build: mm10 GRCm38
basic annotation mm10 GRCm38 M13 Gencode
Supplementary_files_format_and_content: xls with count data

source_name: myeloid cells

growth_protocol: Ly6Chigh CD11c+ MHC-II+ and Ly6C low cells were FACS-sorted from 10-day established Mock- or SULT2B1b-LLC tumors

extract_protocol:
Total RNA was extracted using RNA spin columns (PureLink RNA Mini Kit, Ambion). RNA quantification was carried out using Qubit Fluorimetric Quantification (Life Technologies) and 500ng of RNA were used to prepare the library.
SMART-Seq v4 Ultra Low Input RNA (TaKaRa)
RNA-Seq;NextSeq 500;SE;1x75;Nextera Index;

value: Sult2B1b 4 Ly6C high CD11c+ MHC-II+


title: SULT2B1b_LLC_2

description:
Sult2B1b 2 Ly6C high CD11c+ MHC-II+
Ly6C high CD11c+ MHC-II+ FACS-sorted from Sult2B1b-LLC 2

value: Sult2B1b 2 Ly6C high CD11c+ MHC-II+


title: MJD1389b

description: Library name: 127.042b


title: PB03180-001 flex scRNA-seq

value: Male

value: Positive

value: FALSE


title: Siberian Hamster, MBH, LD, Rep 1

description:
MBH417
MBHExpressedGenesTranscripts.CSV


title: PB03199-003 flex scRNA-seq

value: Female

value: Asian


title: SULT2B1b_LLC_1

description:
Sult2B1b 1 Ly6C high CD11c+ MHC-II+
Ly6C high CD11c+ MHC-II+ FACS-sorted from Sult2B1b-LLC 1

value: Sult2B1b 1 Ly6C high CD11c+ MHC-II+


title: Nanos-Upd ML Fraction 3 Replicate 2-PE

description: Library name: Sample 7


title: Nanos-Upd EM Fraction 2 Replicate 2-PE

description: Library name: Sample 6


title: PB03195-001 flex scRNA-seq

value: Caucasian

value: Negative


title: Nanos-Upd E Fraction 1 Replicate 2-PE

description: Library name: Sample 5


title: 10 day old seedling, Atplh3_NaCl_R2

city: Gautam Buddha Nagar

first: Rohini

last: Garg

state: UP

address: Shiv Nadar University, NH - 91, Tehsil Dadri

country: India

institute: Shiv Nadar University

data_processing:
The FASTQ files obtained from RNA-seq were pre-processed using NGS QC Toolkit (v2.3.3) to remove adapters and low-quality reads.
Filtered high-quality reads were mapped on the Arabidopsis thaliana genome using HISAT2.
The mapped reads were aligned into transcripts using StringTie followed by identification of DEGs using Cuffdiff.
FPKM for each sample is reported in processed file
Assembly: Arabidopsis thaliana genome (TAIR10)
Supplementary files format and content: Excel file containing fpkm values of all genes in all the samples across all combinations (WT_control Vs Atplh1_control; WT_control Vs Atplh2_control; WT_control Vs Atplh3_control; WT_control Vs WT_ABA;  Atplh1_control Vs Atplh1_ABA;   Atplh2_control Vs Atplh2_ABA;  Atplh3_control Vs Atplh3_ABA;  WT_control Vs WT_NaCl; Atplh1_control Vs Atplh1_NaCl; Atplh2_control Vs Atplh2_NaCl; Atplh3_control Vs Atplh3_NaCl)

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis thaliana wild type (Col 0) and mutants (Atplh1, Atplh2, Atplh3 ) seedlings were grown in growth chamber for 10 days in MS media with and without ABA, NaCl

extract_protocol:
Total RNA was isolated using TRIzol. The extracted RNA samples were quantified using Qubit 2.0 Fluorometer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5 day old seedlings were grown in MS media with and without ABA, NaCl for  another 5 days. 10 day old seedlings were harvested from wild type and mutant under control and treatment conditions.

value: whole seedling

tag: age

value: 10 day old seedling

tag: treatment

value: NaCl


title: MJD1389

description: Library name: 127.042

value: Cardiac ventricle


title: 10 day old seedling, Atplh3_NaCl_R3


title: MJD1387b

description: Library name: 127.041b

value: WT


title: PB03173-001 flex scRNA-seq

description:
SRR30239415, SRR30239414, SRR30239432, SRR30239431, SRR30239430, SRR30239429, SRR30239428, SRR30239427, SRR30239426, SRR30239425, SRR30239424, SRR30239423, SRR30239421, SRR30239419, SRR30239418, SRR30239417, SRR30239470, SRR30239469, SRR30239468, SRR30239467, SRR30239466, SRR30239465, SRR30239412, SRR30239411
10x Flex ligation probe-based sequencing

value: Blood

value: PBMC

value: African American


title: S2L

description:
Sult2B1b 2 Ly6C low
Ly6C low cells FACS-sorted from Sult2B1b-LLC 2

tag: condition

value: Sult2B1b 2  Ly6C low


title: MJD1387

description: Library name: 127.041


title: 10 day old seedling, Atplh3_NaCl_R1


title: S4L

description:
Sult2B1b 4 Ly6C low
Ly6C low cells FACS-sorted from Sult2B1b-LLC 4

value: Sult2B1b 4  Ly6C low


title: Siberian Hamster, Pituitary, 28wk SD, Rep 6

description:
Pit172
PitExpressedGenesTranscripts.CSV

source_name: Pituitary Dissection

value: Pituitary Dissection


title: s3

description:
Sult2B1b 3 Ly6C high CD11c+ MHC-II+
Ly6C high CD11c+ MHC-II+ FACS-sorted from Sult2B1b-LLC 3

value: Sult2B1b 3 Ly6C high CD11c+ MHC-II+


title: S3L

description:
Sult2B1b 3  Ly6C low
Ly6C low cells FACS-sorted from Sult2B1b-LLC 3

value: Sult2B1b 3 Ly6C low


title: Siberian Hamster, Pituitary, 24wk SD, Rep 6

description:
Pit188
PitExpressedGenesTranscripts.CSV


title: 10 day old seedling, Atplh3_ABA_R3

value: ABA


title: MJD1388

description: Library name: 127.040


title: Mock_LLC_4

description:
Mock 4 Ly6C high CD11c+ MHC-II+
Ly6C high CD11c+ MHC-II+ FACS-sorted from Mock-LLC 4

value: Mock-LLC

value: Mock 4 Ly6C high CD11c+ MHC-II+


title: Siberian Hamster, Pituitary, 20wk SD, Rep 6

description:
Pit217
PitExpressedGenesTranscripts.CSV


title: Mock_LLC_3

description:
Mock 3 Ly6C high CD11c+ MHC-II+
Ly6C high CD11c+ MHC-II+ FACS-sorted from Mock-LLC 3

value: Mock 3 Ly6C high CD11c+ MHC-II+


title: Siberian Hamster, Pituitary, 16wk SD, Rep 6

description:
Pit265
PitExpressedGenesTranscripts.CSV


title: MDJ1395b

description: Library name: 127.039b


title: 10 day old seedling, Atplh3_ABA_R1

value: whole seedling


title: Mock_LLC_2

description:
Mock 2 Ly6C high CD11c+ MHC-II+
Ly6C high CD11c+ MHC-II+ FACS-sorted from Mock-LLC 2

value: Mock 2 Ly6C high CD11c+ MHC-II+


title: 10 day old seedling, Atplh3_control_R3

value: 10 day old seedling

value: control


title: MJD1395

description: Library name: 127.039

value: Cardiac ventricle


title: MJD1392b

description: Library name: 127.038b


title: Siberian Hamster, Pituitary, 12wk SD, Rep 6

description:
Pit280
PitExpressedGenesTranscripts.CSV


title: M4L

description:
Mock 4 Ly6C low
Ly6C low cells FACS-sorted from Mock-LLC 4

value: Mock 4 Ly6C low


title: Siberian Hamster, Pituitary, 32wk SD, Rep 6

description:
Pit113
PitExpressedGenesTranscripts.CSV


title: 10 day old seedling, Atplh3_control_R2


title: Siberian Hamster, Pituitary, 8wk SD, Rep 6

description:
Pit397
PitExpressedGenesTranscripts.CSV


title: MJD1388b

description: Library name: 127.040b


title: 10 day old seedling, Atplh3_control_R1


title: M3L

description:
Mock 3 Ly6C low
Ly6C low cells FACS-sorted from Mock-LLC 3

value: Mock 3 Ly6C low


title: 10 day old seedling, Atplh3_ABA_R2


title: Siberian Hamster, Pituitary, 4wk SD, Rep 6

description:
Pit314
PitExpressedGenesTranscripts.CSV


title: Mouse 2, TTR>NICD-CAG>tdT HDTVi 3-weeks

city: Philadelphia

first: Abhinav

last: Illendula

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description:
Library name: Reprogramming_Sample_2
10X Genomics

data_processing:
Raw sequencing data files were first processed using the Cell Ranger v5.0 pipeline from 10x Genomics using default parameters. Reads were mapped to the GRCm39 reference modified to include the tdTomato sequence, and the resultant data were then processed using the Seurat V4.3 package in R.
Cells which did not meet QC criteria (n_feature count between 400-7000 and <15% mitochondrial genes) were filtered out prior to downstream analysis.
Assembly: GRCm39
Supplementary files format and content: Matrix h5

source_name: Liver

extract_protocol:
Three weeks after HDTVi, the abdominal  vena cava was cannulated with the thoracic  vena cava clamped. The portal vein was snipped and 20 mL HBSS -/- buffer was perfused. Then, HBSS +/+ with 4 mg/mL Liberase was perfused until the liver was digested to acheive a single-cell suspension. Cells were washed with HBSS -/- and incubated with EpCAM fluorophore-conjugated antibody and DAPI. Cells were sorted on FACSymphony S6 into DMEM supplemented with 10% FBS.
Manufacturers instructions were followed to partition cells into Gel Beads-in-emulsions (GEMs) together with unique 10X barcodes using the Chromium Controller. cDNA libraries were produced from GEMs to generate a barcoded single cell library for each mouse. Sequencing data were obtained using the Illumina NovaSeq 6000 platform.

treatment_protocol: TTR>NICD-CAG>tdT PiggyBac transposon HDTVi

value: Liver

value: male

value: 8 weeks pre-injection

value: TTR>NICD-CAG>tdT HDTVi 3-weeks


title: 10 day old seedling, Atplh2_NaCl_R3

value: NaCl


title: M2L

description:
Mock 2 Ly6C low
Ly6C low cells FACS-sorted from Mock-LLC 2

value: Mock 2 Ly6C low


title: 10 day old seedling, Atplh2_NaCl_R2


title: Mouse 1, TTR>NICD-CAG>tdT HDTVi 3-weeks

description:
Library name: Reprogramming_Sample_1
10X Genomics


title: Siberian Hamster, Pituitary, LD, Rep 6

description:
Pit141
PitExpressedGenesTranscripts.CSV

value: Pituitary Dissection


title: M1L

description:
Mock 1 Ly6C low
Ly6C low cells FACS-sorted from Mock-LLC 1

value: Mock-LLC

value: Mock 1 Ly6C low


title: Heart, running 16 weeks, myocardial infarction

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: 10x Genomics

data_processing:
CellRanger v7.1 used for demultiplexing + read mapping + barcode assignment + UMI counting
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files and matrix market files

source_name: Heart

extract_protocol:
Two (baseline) and four (infarct) mouse hearts from male and female mice were pooled together per group for further processing. Cardiac ventricles were collected, snap frozen in liquid-N2 and stored at -80°C until further processing. Hearts were allowed to sit on ice in a petri dish for 5 min, before mincing them with surgical blades (Fine Science Tools, #10020-00) into a paste-like mash. The minced sample was moved to a 15 ml Dounce homogenizer together with 5 ml of ice-cold lysis buffer (NaCl 146 mM, Tris-HCl 10 mM, CaCl2 1 mM, MgCl2 21 mM, 0.5% CHAPS, 0.1% BSA, SUPERnase InTM RNase inhibitor 20 U/ml [AM2696, ThermoFisher Scientific]) and left to lyse for another 5 min on ice. Then, 9 ml of wash buffer (2% BSA in PBS with 20 U/ml SUPERnase InTM RNase inhibitor) was added and the pestle A was lowered 10 times to homogenize the tissue. The resulting suspension was filtered first through 70 µm strainer, then through 40 µm strainer  and subsequently transferred to a clean 15 ml centrifuge tube. Following a centrifugation (450 g for 5 minutes at 4°C), the supernatant was removed, and the pellet was washed with 10 ml of wash buffer and centrifuged again. After the supernatant was removed, the nuclei-containing pellet was transferred to a 5 ml round bottom FACS tube and stained with Hoechst 34580 (Thermo Fisher Scientific, #H21486) in PBS for 5 minutes. Hoechst+ nuclei were sorted (85 µm nozzle, 4-way purity sorting mode) using a BD FACSAria III into the wash buffer. and immediately loaded into the 10x Genomics Chromium instrument.
Nuclei obtained using FACS were suspended in wash buffer targeting the required a concentration of 1,000 cells/μl and loaded onto the 10x Genomics Chromium controller (Next GEM Chip G, #2000177). Samples were loaded into 4 wells, corresponding to one well per experimental group (sedentary, running, sedentary-infarct, running-infarct). Libraries were generated following 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 Dual Index (CG000315 Rev E). Quality control of cDNA and final libraries was done using 4200 TapeStation System (Agilent) and D5000 High Sensitivity ScreenTape and Reagents. Libraries were sequenced on the Illumina Novaseq 6000 system.

value: Heart

value: running 16 weeks - myocardial infarction

tag: genetic background

value: WT


title: Siberian Hamster, Pituitary, 32wk SD, Rep 5

description:
Pit152
PitExpressedGenesTranscripts.CSV


title: NCI-H1693, PRT3789, 48 hr, ATAC-seq, rep3

city: Wilmington

first: Michael

last: Hulse

state: DE

address: 175 Innovation Blvd

institute: Prelude Therapeutics

description:
Library name: sample_3789_50nM_3_48_hr_ATAC
Column name in PLX115780_assay_data.csv:sample_3789_50nM_3_48_hr_ATAC

data_processing:
FASTQ files were processed using the nf-core/atacseq pipeline (v2.0)
Adapter sequences were removed with Trim Galore.
Reads were aligned with Bowtie2 to GRCh38 (NCBI, p.14, release 110) and duplicates were marked and removed from all samples with picard.
Peaks were called with macs2 (peak mode: narrow) using a p-value threshold of 0.00001 and an effective genome size of 2,940,000,000.
Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER.
Peak counts were generated using featureCounts.
Downsteam analysis was performed using Pluto Bio (https://pluto.bio).
Assembly: GRCh38 (NCBI, p.14, release 110)
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample
Supplementary files format and content: bigWig

growth_protocol: NCI-H1693 cells (SMARCA4-deficient NSCLC line) were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37°C in a humidified atmosphere with 5% CO₂. Cells were seeded to achieve ~70–80% confluence at the time of treatment.

extract_protocol:
After 48 h treatment, viable cells were harvested, cryopreserved, and shipped on dry ice to GENEWIZ (now Azenta Life Sciences) for ATAC-seq library preparation. Nuclei were isolated from thawed cells and processed using the Omni-ATAC protocol for tagmentation and library generation.
Isolated nuclei were tagmented with Tn5 transposase to integrate sequencing adapters into open chromatin regions. Tagmented DNA was purified, PCR amplified, and libraries were quantified and quality-checked by Bioanalyzer. Libraries were sequenced on an Illumina platform to generate 2 × 150 bp paired-end reads.

tag: time point

value: 48 hr


title: 10 day old seedling, Atplh2_NaCl_R1

value: whole seedling

value: 10 day old seedling


title: Mock_LLC_1

description:
Mock 1 Ly6C high CD11c+ MHC-II+
Ly6C high CD11c+ MHC-II+ FACS-sorted from Mock-LLC 1

value: Mock 1 Ly6C high CD11c+ MHC-II+


title: Heart, running 16 weeks

description: 10x Genomics

value: running 16 weeks


title: Heart, sedentary, myocardial infarction

description: 10x Genomics

value: sedentary - myocardial infarction


title: NCI-H1693, PRT3789, 48 hr, ATAC-seq, rep2

description:
Library name: sample_3789_50nM_2_48_hr_ATAC
Column name in PLX115780_assay_data.csv:sample_3789_50nM_2_48_hr_ATAC


title: MJD1392

description: Library name: 127.038

value: Cardiac ventricle


title: Siberian Hamster, Pituitary, 24wk SD, Rep 5

description:
Pit180
PitExpressedGenesTranscripts.CSV


title: 10 day old seedling, Atplh2_ABA_R2

value: ABA


title: Siberian Hamster, Pituitary, 20wk SD, Rep 5

description:
Pit216
PitExpressedGenesTranscripts.CSV


title: NCI-H1693, DMSO, 48 hr, ATAC-seq, rep3

description:
Library name: DMSO_3_48_hr_ATAC
Column name in PLX115780_assay_data.csv:DMSO_3_48_hr_ATAC

value: DMSO


title: Siberian Hamster, Pituitary, 16wk SD, Rep 5

description:
Pit283
PitExpressedGenesTranscripts.CSV


title: Heart, sedentary

description: 10x Genomics

value: sedentary


title: Tumor2_D1

city: Warsaw

first: Karol

last: Jacek

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

description:
Fresh frozen Spatial transcriptome sequencing
F88_02

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 : counts matrix
Supplementary files format and content: aligned_fiducials.jpg.gz:  aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz:  image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz:  scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz:  hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz:  low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz:  list of spatial barcodes and the coordinates specifying spots

source_name: brain, GL261

growth_protocol: Ten weeks old male mice (C57BL/6J) had hole drilled at following coordinates : 1 mm anterior and 2 mm lateral from bregma.  GL261 tdT++luc++ cells (80,000 in 1 ?l of DMEM)  were stereotactically injected with a Hamilton syringe to the right striatum 3 mm deep from the surface of the brain.

extract_protocol:
At day 21 the mice were anesthetized and sacrified. The brains were removed and snap-frozen in tissue freezing medium on dry ice.
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction

value: brain, GL261

tag: strain background

value: 1x 80,000 GL261 cells injection


title: NCI-H1693, DMSO, 48 hr, ATAC-seq, rep2

description:
Library name: DMSO_2_48_hr_ATAC
Column name in PLX115780_assay_data.csv: DMSO_2_48_hr_ATAC


title: Siberian Hamster, Pituitary, 12wk SD, Rep 5

description:
Pit278
PitExpressedGenesTranscripts.CSV

value: Pituitary Dissection


title: 10 day old seedling, Atplh2_control_R2

value: control


title: Tumor1_C1

description:
Fresh frozen Spatial transcriptome sequencing
F88_01


title: Siberian Hamster, Pituitary, 8wk SD, Rep 5

description:
Pit306
PitExpressedGenesTranscripts.CSV


title: 10 day old seedling, Atplh2_ABA_R3


title: Siberian Hamster, Pituitary, LD, Rep 5

description:
Pit238
PitExpressedGenesTranscripts.CSV


title: 10 day old seedling, Atplh1_NaCl_R3

value: NaCl


title: BMDM+TGF, rep 3

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Trimmed raw reads were aligned to mm10 using STAR (version 2.7.3).
Differential expression analysis between groups was performed with DESeq2 (version 1.24.0) (Love et al., 2014) in R (version 3.6.1) (R Core Team 2015).
Assembly: mm10
Supplementary files format and content: tab-limited text file including normalized counts for each sample

source_name: bone marrow

growth_protocol: BMDMs were differentiated from bone marrow with 50ng/ml MCSF.

extract_protocol:
Macrophages were sorted based on CD11b and CD64 expression. RNA was extracted using the RNAmicro Kit Plus (Qiagen).
Libraries were prepared using 10 ng RNA and the SMART-Seq Stranded Kit (Takara).

treatment_protocol: After 5d, BMDMs were either cultured alone, with DRG neurons or 0.02ng/ml TGF-b.

value: bone marrow

value: bone marrow-derived macrophages

value: 0.02ng/ml TGF-b

tag: time


title: NCI-H1693, PRT3789, 72 hr, rep3

description:
Library name: sample_3789_50nM_3_72_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:sample_3789_50nM_3_72_hr_cell_pellet_for_RNA

data_processing:
FASTQ files were processed using the nf-core/rnaseq pipeline (v3.17.0) (auto strandedness).
Adapter sequences were removed with Trim Galore.
Reads were aligned with STAR to GRCh38 (NCBI, p.14, release 110) and quantified to gene counts using RSEM.
Downsteam analysis was performed using Pluto Bio (https://pluto.bio).
Assembly: GRCh38 (NCBI, p.14, release 110)
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

extract_protocol:
At each time point, cells were washed with PBS and harvested as pellets. Pellets were flash-frozen in liquid nitrogen and shipped on dry ice to GENEWIZ (now Azenta Life Sciences) for RNA extraction using the Qiagen RNeasy Plus Kit (Qiagen, Cat# 74136) according to the manufacturer’s protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer.
RNA samples with RNA Integrity Number (RIN) ≥ 8 were used for library preparation. mRNA was enriched using oligo(dT) beads and converted to cDNA using random hexamer priming. Strand-specific libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit, including end repair, A-tailing, adapter ligation, and PCR amplification. Libraries were quantified, pooled, and sequenced on an Illumina platform to produce 2 × 150 bp paired-end reads.

value: 72 hr


title: BMDM+TGF, rep 1


title: Sham2_B1

description:
Fresh frozen Spatial transcriptome sequencing
F87_02

source_name: brain

value: brain

value: 1x PBS injection


title: NCI-H1693, PRT3789, 48 hr, ATAC-seq, rep1

description:
Library name: sample_3789_50nM_1_48_hr_ATAC
Column name in PLX115780_assay_data.csv:sample_3789_50nM_1_48_hr_ATAC

value: 48 hr


title: Siberian Hamster, Pituitary, 28wk SD, Rep 5

description:
Pit163
PitExpressedGenesTranscripts.CSV

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25 reads)
Minimap2 used to align reads to Mus musculus genome (GCRm39)
Transcript expression levels generated  using Salmon
Assembly: GRCmm39
Supplementary files format and content: Transcript expression levels generated  using Salmon

extract_protocol:
RNA was extracted using the Qiagen RNEasy plus mini-kit
RNA Libraries were constructed using the PCR_cDNA sequencing barcoding kit (SQK-PCB109, Oxford Nanopore) as per manufacturers instructions


title: NCI-H1693, DMSO, 72 hr, rep2

description:
Library name: DMSO_2_72_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:DMSO_2_72_hr_cell_pellet_for_RNA


title: NCI-H1693, PRT3789, 72 hr, rep1

description:
Library name: sample_3789_50nM_1_72_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:sample_3789_50nM_1_72_hr_cell_pellet_for_RNA


title: 10 day old seedling, Atplh2_ABA_R1

value: whole seedling

value: 10 day old seedling


title: 10 day old seedling, Atplh1_NaCl_R1


title: 10 day old seedling, Atplh2_control_R1


title: 10 day old seedling, Atplh1_NaCl_R2


title: Siberian Hamster, Pituitary, 4wk SD, Rep 5

description:
Pit352
PitExpressedGenesTranscripts.CSV


title: 10 day old seedling, Atplh1_ABA_R3

value: ABA


title: NCI-H1693, DMSO, 72 hr, rep3

description:
Library name: DMSO_3_72_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:DMSO_3_72_hr_cell_pellet_for_RNA

value: DMSO


title: Sham1_A1

description:
Fresh frozen Spatial transcriptome sequencing
F87_01


title: Siberian Hamster, Pituitary, 32wk SD, Rep 4

description:
Pit153
PitExpressedGenesTranscripts.CSV


title: 10 day old seedling, Atplh2_control_R3


title: BMDM+TGF, rep 2


title: NCI-H1693, DMSO, 72 hr, rep1

description:
Library name: DMSO_1_72_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:DMSO_1_72_hr_cell_pellet_for_RNA


title: NCI-H1693, PRT3789, 48 hr, rep3

description:
Library name: sample_3789_50nM_3_48_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:sample_3789_50nM_3_48_hr_cell_pellet_for_RNA


title: Siberian Hamster, Pituitary, 28wk SD, Rep 4

description:
Pit162
PitExpressedGenesTranscripts.CSV


title: 10 day old seedling, Atplh1_ABA_R2


title: Siberian Hamster, Pituitary, 20wk SD, Rep 4

description:
Pit231
PitExpressedGenesTranscripts.CSV


title: BMDM from coculture with DRG, rep 2

value: co-culture with DRG neurons


title: NCI-H1693, PRT3789, 72 hr, rep2

description:
Library name: sample_3789_50nM_2_72_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:sample_3789_50nM_2_72_hr_cell_pellet_for_RNA


title: NCI-H1693, PRT3789, 48 hr, rep2

description:
Library name: sample_3789_50nM_2_48_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:sample_3789_50nM_2_48_hr_cell_pellet_for_RNA


title: BMDM from coculture with DRG, rep 3


title: 10 day old seedling, Atplh1_control_R3


title: Siberian Hamster, Pituitary, 16wk SD, Rep 4

description:
Pit255
PitExpressedGenesTranscripts.CSV


title: BMDM from coculture with DRG, rep 1


title: BMDM, rep 3

value: monoculture


title: 10 day old seedling, Atplh1_control_R2


title: NCI-H1693, DMSO, 48 hr, rep3

description:
Library name: DMSO_3_48_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:DMSO_3_48_hr_cell_pellet_for_RNA


title: BMDM, rep 2


title: Siberian Hamster, Pituitary, 8wk SD, Rep 4

description:
Pit398
PitExpressedGenesTranscripts.CSV


title: BMDM, rep 1


title: Siberian Hamster, Pituitary, 12wk SD, Rep 4

description:
Pit289
PitExpressedGenesTranscripts.CSV


title: NCI-H1693, PRT3789, 48 hr, rep1

description:
Library name: sample_3789_50nM_1_48_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:sample_3789_50nM_1_48_hr_cell_pellet_for_RNA


title: 10 day old seedling, WT_NaCl_R3

value: Wild type:Col 0


title: NCI-H1693, DMSO, 48 hr, rep2

description:
Library name: DMSO_2_48_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:DMSO_2_48_hr_cell_pellet_for_RNA


title: Siberian Hamster, Pituitary, 24wk SD, Rep 4

description:
Pit196
PitExpressedGenesTranscripts.CSV

value: Pituitary Dissection


title: miR30a_KO_O2_F5_24544

first: Krithika

last: Lingappan

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Sequenced reads were trimmed for adaptor sequence using TrimGalore
Reads were mapped to the UCSC mouse reference genome mm10 using STAR
featureCounts was used to evaluate gene expression level as read counts
Assembly: mm10 GRCm38.101
Supplementary files format and content: tab-delimited text file include read counts for each sample

growth_protocol: Neonatal mice were used for this project.

extract_protocol:
Lungs were harvested on PND 21, flash frozen in liquid nitrogen, and RNA was extracted using the Zymo Direct-zol RNA kit followed by quality control of the extracted RNA samples
RNA libraries were prepared using the NEBNext Ultra II Directional RNA-Seq Sample Preparation with rRNA Depletion

treatment_protocol: miR-30a -/- neonatal mice were exposed to hyperoxia [95% FiO2, postnatal day (PND) 1-5] or room air before being euthanized on PND 21.

tag: strain

value: Lung

value: Postnatal day 21

value: hyperoxia

tag: Sex

value: female


title: NCI-H1693, DMSO, 48 hr, rep1

description:
Library name: DMSO_1_48_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:DMSO_1_48_hr_cell_pellet_for_RNA


title: 10 day old seedling, WT_NaCl_R2

tag: genotype

value: NaCl


title: Siberian Hamster, Pituitary, LD, Rep 4

description:
Pit247
PitExpressedGenesTranscripts.CSV


title: Siberian Hamster, Pituitary, 32wk SD, Rep 3

description:
Pit160
PitExpressedGenesTranscripts.CSV


title: 10 day old seedling, WT_NaCl_R1


title: miR30a_KO_O2_F2_24541


title: NCI-H1693, PRT3789, 6 hr, rep2

description:
Library name: sample_3789_50nM_2_6_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:sample_3789_50nM_2_6_hr_cell_pellet_for_RNA

value: 6 hr


title: Siberian Hamster, Pituitary, 28wk SD, Rep 3

description:
Pit165
PitExpressedGenesTranscripts.CSV


title: Siberian Hamster, Pituitary, 4wk SD, Rep 4

description:
Pit351
PitExpressedGenesTranscripts.CSV


title: miR30a_KO_O2_M3_24536

value: male


title: NCI-H1693, DMSO, 6 hr, rep3

description:
Library name: DMSO_3_6_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:DMSO_3_6_hr_cell_pellet_for_RNA


title: Siberian Hamster, Pituitary, 24wk SD, Rep 3

description:
Pit187
PitExpressedGenesTranscripts.CSV


title: miR30a_KO_O2_M2_24535


title: NCI-H1693, PRT3789, 6 hr, rep3

description:
Library name: sample_3789_50nM_3_6_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:sample_3789_50nM_3_6_hr_cell_pellet_for_RNA


title: 10 day old seedling, WT_ABA_R2


title: 10 day old seedling, WT_ABA_R1


title: Siberian Hamster, Pituitary, 20wk SD, Rep 3

description:
Pit226
PitExpressedGenesTranscripts.CSV


title: miR30a_KO_O2_M1_24534


title: NCI-H1693, PRT3789, 6 hr, rep1

description:
Library name: sample_3789_50nM_1_6_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:sample_3789_50nM_1_6_hr_cell_pellet_for_RNA


title: 10 day old seedling, Atplh1_ABA_R1


title: Siberian Hamster, Pituitary, 12wk SD, Rep 3

description:
Pit276
PitExpressedGenesTranscripts.CSV


title: NCI-H1693, DMSO, 6 hr, rep1

description:
Library name: DMSO_1_6_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv: DMSO_1_6_hr_cell_pellet_for_RNA


title: Siberian Hamster, Pituitary, 16wk SD, Rep 3

description:
Pit251
PitExpressedGenesTranscripts.CSV


title: miR30a_KO_O2_F4_24543


title: 10 day old seedling, WT_control_R3

value: control


title: 10 day old seedling, WT_control_R2


title: NCI-H1693, DMSO, 6 hr, rep2

description:
Library name: DMSO_2_6_hr_cell_pellet_for_RNA
Column name in PLX108809_assay_data.csv:DMSO_2_6_hr_cell_pellet_for_RNA


title: miR30a_KO_RA_F5_24532

value: room air


title: miR30a_KO_RA_F6_24533


title: sh1_3

city: Shanghai

first: Xintian

last: Zhang

address: 639 Zhi Zao Ju Road

country: China

institute: Shanghai Jiao Tong University

data_processing:
Raw data (raw reads) were processed using Trimmomatic.The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM and read counts value of each transcript was calculated using bowtie2 and eXpress.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: intestine

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’ s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: intestine

value: human CRC cells

value: stably infected with lentivirus carrying TRIM21 shRNA


title: Siberian Hamster, Pituitary, 8wk SD, Rep 3

first: Calum

last: Stewart

address: Jarrett Building, University of Glasgow

institute: University of Glasgow

description:
Pit399
PitExpressedGenesTranscripts.CSV


title: miR30a_KO_RA_F2_24529


title: Siberian Hamster, Pituitary, 4wk SD, Rep 3

description:
Pit332
PitExpressedGenesTranscripts.CSV


title: sh1_2


title: 10 day old seedling, WT_ABA_R3

value: whole seedling

value: 10 day old seedling

value: ABA


title: Cardiac fibroblasts, +serum media, Day7wTGFb Biol Rep2

city: Pamplona

first: Laura

last: Pilar Aguado Alvaro

address: Av. de Pío XII, 55

country: Spain

institute: Center for Applied Medical Research (CIMA)- University of Navarra

description: Primary Cas9 cardiac fibroblasts were grown on serum-containing media for 7 days and  stimulated with TGFb for 24 hours

data_processing:
Sequencing reads in FASTQ format  were processed with Cutadapt (v2.10), trimming adapters and filtering based on quality.
Alignment to the mm10 mouse reference genome was conducted using STAR (v2.7.3a), employing default parameters for optimal mapping
Gene expression quantification and matrix generation were conducted using featureCounts, a component of the Rsubread package (v2.0.1)
Gene annotations were based on GENCODE gene symbols
Pre-analysis filtering for genes with adequate counts was performed using filterByExpr from the edgeR package (v3.32.1)
Subsequent data transformation, normalization, and differential gene expression analysis were carried out with the DESeq2 package (v1.30.0) in R
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized values for each sample

growth_protocol: Cardiac fibroblasts were isolated from Cas9-mice and seeded either on serum-free media (DMEM KO + 20% knockout serum replacement (KSR) (Gibco) + 1% non-essential amino acids (NEAA) (Gibco) + 100 μM beta-mercaptoethanol (Gibco) + 1% P/S + 1% L-Glutamine) or on serum-containing media (DMEM + 10% fetal bovine serum (FBS) + 1% P/S + 1% L-Glutamine)

extract_protocol:
Poly-A RNA was extracted with Dynabeads Oligo dT (Ambion)
PCR amplification with NPM PCR Master Mix (Illumina) using P5NEXTPT5 primer and i7 indexed primers

treatment_protocol: Primary Cas9 cardiac fibroblasts were treated or not with pro-fibrotic cytokine TGFb (2.5 ng/ml)

value: Heart

tag: media

value: +serum media

value: Fibroblast

value: TGFb


title: Siberian Hamster, Pituitary, LD, Rep 3

description:
Pit248
PitExpressedGenesTranscripts.CSV

value: Pituitary Dissection


title: Cardiac fibroblasts, +serum media, Day7woTGFb Biol Rep2

description: Primary Cas9 cardiac fibroblasts were grown on serum-containing media for 7 days without fibrotic stimulation with TGFb

value: Unstimulated


title: miR30a_KO_RA_M4_24525

value: Lung

value: Postnatal day 21


title: Cardiac fibroblasts, serum-free media, Day7wTGFb Biol Rep2

description: Primary Cas9 cardiac fibroblasts were grown on serum-free media for 7 days and  stimulated with TGFb for 24 hours

value: serum-free media


title: Siberian Hamster, Pituitary, 32wk SD, Rep 2

description:
Pit149
PitExpressedGenesTranscripts.CSV


title: Siberian Hamster, Pituitary, 28wk SD, Rep 2

description:
Pit174
PitExpressedGenesTranscripts.CSV


title: shNC_2

value: stably infected with lentivirus carrying control shRNA


title: miR30a_KO_RA_M1_24522

value: room air

value: male


title: Cardiac fibroblasts, serum-free media, Day7woTGFb Biol Rep2

description: Primary Cas9 cardiac fibroblasts were grown on serum-free media for 7 days without fibrotic stimulation with TGFb


title: shNC_1

value: intestine

value: human CRC cells


title: Siberian Hamster, Pituitary, 24wk SD, Rep 2

description:
Pit181
PitExpressedGenesTranscripts.CSV


title: Cardiac fibroblasts, +serum media, Day7wTGFb Biol Rep1


title: zf lck+ cells

description: ATAC Seq lck cells

data_processing:
All ATAC-Seq datasets were aligned to build version danRer7 of the zebrafish genome using Bowtie2 (version 2.2.1)  (Langmead et al., 2012) with the following parameters: --end-to-end, -N0, -L20. We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak finding algorithm to identify regions of ATAC-Seq peaks, with the following parameter --nomodel --shift -100 --extsize 200. A q-value threshold of enrichment of 0.05 was used for all datasets.
Assembly: danRer7
Supplementary files format and content: narrowPeak file of called peaks

source_name: lck lymphoctes

extract_protocol:
Cell sorting
Illumina XT library prep kit, according to protocol

value: Thymus

value: lck lymphoctes

tag: egfp status

value: EGFP+


title: Wh7_7D_2

city: Nangang

first: Kreeti

last: Kajal

state: Taipei City

address: R337, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan

country: Taiwan

description: Library name: Wh7_7D_2

data_processing:
TRimmomatic v0.36 was used for adaptor clipping and sequence quality trimming with a sliding-window approach. HISAT2 was used for transcriptome alignment.
Differential expression analysis was performed using StringTie (StringTie v2.1.4) and DEseq (DEseqv1.39.0) or DEseq2 (DEseq2v1.28.1) via an in-house pipeline from Welgene Biotech.
Assembly: RNA reads were aligned to the reference genome Release 6 plus ISO1 MT NCBI RefSeq ID GCF_000001215.4
Supplementary files format and content: PRJNA1264666_rawcount.txt, tab-delimited text files, raw count of all samples
Supplementary files format and content: PRJNA1264666_DeSeq2_results.txt, tab-delimited text files, result od DESeq2 analysis.

source_name: Gut

extract_protocol:
Fly guts were dissected and frozen by dipping in liquid nitrogen, then stored at -80°C until use. Total RNA was extracted using a standard Trizol (Novel-Gene) extraction protocol. In brief, 20-30 frozen guts were homogenized in 200 μl of Triazol, followed protocol. In brief, 20-30 frozen guts were homogenized in 200 μl of Triazol, followed by a phase separation step with 200 μl 1-bromo-3-chloropropane (Sigma-Aldrich). RNA was precipitated using 500 μl isopropanol. The pellet was washed with 75% ethanol twice and re-suspended in 40 μl RNAse-free water. RNA-seq was performed according to the standard Illumina protocol (Welgene, Taiwan). In brief, RNA was quantified.
Then, library preparation was carried out by SureSelect XT HS2 mRNA Library Preparation kit (Agilent), followed by AMPure XP beads (Beckman Coulter, USA) for size selection.

value: Gut


title: Siberian Hamster, Pituitary, 20wk SD, Rep 2

city: Glasgow

description:
Pit214
PitExpressedGenesTranscripts.CSV


title: Cardiac fibroblasts, +serum media, Day7woTGFb Biol Rep1

value: Heart

value: +serum media


title: 10 day old seedling, WT_control_R1

value: whole seedling

value: 10 day old seedling

value: Wild type:Col 0

value: control


title: Siberian Hamster, Pituitary, 16wk SD, Rep 2

description:
Pit252
PitExpressedGenesTranscripts.CSV

value: Pituitary Dissection


title: sh1_1

tag: cell line

value: stably infected with lentivirus carrying TRIM21 shRNA


title: WT_7D_2

institute: Institute of Cellular and Organismic Biology

description: Library name: WT_7D_2

value: yw


title: Siberian Hamster, Pituitary, 12wk SD, Rep 2

description:
Pit292
PitExpressedGenesTranscripts.CSV


title: Cardiac fibroblasts, serum-free media, Day7wTGFb Biol Rep1

value: serum-free media

value: Fibroblast

value: TGFb


title: Plasma exosomal miRNA, Dengue with warning sign, patient 55

type: RNA

city: Kubang Kerian, Kota Bharu

first: Gokulakannan

last: Venkatesan

state: Kelantan

address: Kampus Kesihatan Universiti Sains Malaysia, Jalan Raja Perempuan Zainab 2, Kubang Kerian, 16150 Kota Bharu, Kelantan

department: School of Dental Sciences

country: Malaysia

institute: Universiti Sains Malaysia

description: miRNA expression analysis in plasma exosome of dengue without warning sign.

hyb_protocol: 1.65 µg of Cy3-labeled cRNA in hybridization buffer was hybridized onto the Agilent Human miRNA Microarray (release/version) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, United States) according to the manufacturer’s protocol. Arrays were hybridized in an Agilent hybridization oven at 55°C for 20 hours with rotation at 20 rpm.

scan_protocol: After hybridization, microarrays were washed using the Agilent Gene Expression Wash Buffers according to the manufacturer’s instructions. Arrays were scanned using the Agilent Microarray Scanner System (Agilent Technologies, United States) at 5 µm resolution, using default one-color settings.

data_processing: GeneSpring GX software (Agilent Technologies, United States) was used for data analysis. The differential expression was determined using the moderated t-test with Benjamin-Hochberg multiple testing corrections. The cut-off for significantly expressed miRNAs were fixed to a probability value of less than 5% (p<0.05), and the fold change was set to be greater than 2.0 (FC > 2).

source_name: Human plasma exosomes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Approximately two to three millilitres of left over peripheral venous blood in an ethylenediaminetetraacetic acid tube was used to isolate plasma.  The blood was centrifuged at 2,000 X g for 15 minutes and 12,000 X g for 45 minutes at 4◦C for plasma isolation. Exosomes were isolated at 110,000 x g at 4o C for two hours from the isolated plasma. The total RNA was extracted using miRNeasy micro kit (Qiagen, United States) according to manufacturer’s protocol, and quantified using NanoDrop (Thermo Fisher Scientific, United States). The quality of total RNA and the presence of miRNAs were confirmed using RNA 6000 Pico chip and small RNA chip (Agilent Technologies, United States), respectively.

value: Plasma

tag: gender

value: Female


title: Plasma exosomal miRNA, Dengue with warning sign, patient 48


title: miR30a_KO_RA_M5_24526

value: Lung

value: Postnatal day 21

value: room air

value: male


title: shNC_3

value: intestine

tag: cell type

value: human CRC cells

value: stably infected with lentivirus carrying control shRNA


title: Plasma exosomal miRNA, Dengue with warning sign, patient 30

tag: tissue


title: Siberian Hamster, Pituitary, 8wk SD, Rep 2

description:
Pit310
PitExpressedGenesTranscripts.CSV


title: ATAC Biol rep 2; KO, CD101+ TEX

city: Melbourne

first: Lachlan

last: Dryburgh

state: Victoria

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

country: Australia

institute: The Peter Doherty Institute for Infection and Immunity

description: Sample 16 KO CD101+ TEX

data_processing:
Alignment by BWA-mem2, to GRCm39.
Alignments sorted with SAMTools and peak called MACS2.
Peaks merged with Homer and counts matrix generated with FeatureCounts.
Peaks with log2 counts-per-million < 1 in all samples were filtered.
Assembly: GRCm39
Supplementary files format and content: Tab delimitted table of raw counts of filtered genes.
Supplementary files format and content: Rows represent MACS2 called peaks and columns samples.

extract_protocol:
Cells were lysed using cold ATAC buffer (10 mM Tris–HCl pH 7.5, 10 mM NaCl and 3 mM MgCl2 in UltraPure DNase/RNase-free distilled water (Thermo Fisher Scientific)) comprising NP40 (Millipore-Sigma, 0.1 %), Tween-20 (Millipore-Sigma, 0.1 %) and digitonin (Promega, 0.01 %) for 3 min. Nuclei were pelleted at 500 g for 10 min 4 °C and resuspended in Transposition Mix (Tagment DNA buffer and Tn5 Tagment DNA TDE1 Enzyme from Illumina, PBS, UltraPure DNase/RNase-free distilled water, 0.001 % digitonin, 0.1 % Tween-20). Enzymatic transposition of DNA was achieved by incubation at 37 °C for 30 min at 1000 rpm. DNA was purified using the DNA Clean and Concentrator-5 Kit (Zymo Research).
Fragments were barcoded in a PCR reaction with unique Adapter sequences using the NEBNext Ultra II Q5 2x Master Mix (New England Biolabs). Library concengtrations were quantified using the NEBNext Libary Quant Master Mix Kit (New England Biolabs) by qPCR. Individual samples were further amplified to obtain unified library concentrations.

value: Spleen

value: CD8 T Lymphocytes


title: TrafficJam-Upd H3K9me3 IP Replicate 2

description: Library name: Sample 28

data_processing:
Reads were aligned to dm6 using Bowtie 2 (version 2.4.5), and filtered for proper pairs (SAM flag 2), MAPQ at least 20, and mated fragment length between 100 and 200 bp.
Fragments were called as putative nucleosome locations, using the single bp midpoint between the two proper pairs as the location estimate.
Pileup data frames were created to identify monosome density, as the count of nucleosome locations in a 40 bp window with 20 bp sliding step (50% overlap).
Each pileup series is divided by a normalization factor: A fragment count subsetted to the 2L, 2R, 3L, 3R, and 4 (autosomes) smoothed to 1 kb window and then taking the genome-wide median.
Assembly: dm6
Supplementary files format and content: CSV: Chromosome (dm6), start and end sliding window coordinates using BED file format semantics, and each series pileup of fragments divided by a normalization factor.

extract_protocol:
Tesis tumors were dissected in sterile Schnieder's media supplemented with 10% fetal bovine serum (FBS). Testis tissue was digested to completion in TrypLE supplemented with 2mg/mL collagenase by incubating with intermittent agitation at 37C. Digested tissue was filtered first through at 40um filter, then a 10um filter before pelleting cells by centrifugation at 1,200rpm. After removing the supernatant, cells were resuspended in Schnieder's media + FBS and fixed in 1% formaldehyde for 5 minutes followed by quencing the reaction with glycine for an addition 5 minutes. Fixed cells were pelleted and washed with cold PBS before starting the chromatin immunocleavage (ChIC) protocol.  For a single ChIC sample, the anti-GFP + Protein A (PA)-MNase complex was prepared and incubated with fixed cells, allowing the complex to bind to chromatin. A series of washes removed excess PA-MNase-GFP complex. Chromatin from the targeted cell type was then digested by activation of the MNase enzyme. The soluble chromatin was separated from insoluble chromatin by centrifugation. A small portion of the solubilized chromatin was set aside to function as input and the remainder of the chromatin used to perform immunoprecipitation.  Immunoprecipitation for a specific histone modification was performed overnight. The next day, protein-bound beads were washed in a series of low salt washes. The DNA was eluted from beads and processed alongside the input samples to reverse the crosslinks. The DNA from both samples was then purified using the Qiagen MinElute Cleanup Kit before proceeding with library preparation.
Purified DNA from the Input and Immunoprecipitation samples were prepared for sequencing following the instructions included in the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB#7645).

value: testis tumor

value: w[1118]; traffic Jam - GAL4 / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

tag: chromatin type

value: CySC-like chromatin

tag: chip antibody

value: H3K9me3, Diagenode #C15410056

tag: batch


title: ATAC Biol rep 2; KO, CX3CR1+ TEX

description: Sample 15 KO CX3CR1+ TEX

tag: treatment


title: Wh7_7D_1

description: Library name: Wh7_7D_1

value: Gut


title: Siberian Hamster, Pituitary, 4wk SD, Rep 2

description:
Pit333
PitExpressedGenesTranscripts.CSV

value: Pituitary Dissection