title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid100-HBB-080

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid100-HBB-080_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B5-A5_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B5-A5.bw

value: CRISPR/Cas9, sgHBB, plasmid100-HBB-080


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid100-HBB-000

status: Public on Jul 15 2026

type: SRA

city: Zurich

first: Charles

middle: D

last: Yeh

state: ZH

address: Otto-stern-weg 7

department: D-BIOL

country: Switzerland

institute: ETH Zurich

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid100-HBB-000_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B3-A3_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B3-A3.bw

library_source: genomic

data_processing:
Illumina NGS adapter trimming (cutadapt)
DamID PCR adapter trimming (cutadapt)
filtering for known amplicon contaminants (if any) (cutadapt)
alignment to human genome (bowtie2)
alignment to Lambda phage genome (bowtie2)
count reads into GATC tiles of human genome (htseq-count)
spike-in correction, coverage-normalization (FPKM), background subtraction, and binning (analyzeRaPID)
Assembly: hg38
Supplementary files format and content: bigWig with RaPID-FPKM normalization at 5kbps and/or 25kbps binning
Library strategy: DamID-Seq

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

growth_protocol: RPMI 1640 base media supplemented to 10% with fetal bovine serum (tetracycline-screened), GlutaMAX, 1X PenStrep, 1ug/mL puromycin. Cells were cultured at +37C in 5%CO2 in log phase growth.

extract_protocol:
genomic DNA
RaPID-labelled fragments were enriched per the DamID PCR protocol with methylated Lambda gDNA spike-in.
Enriched DNA fragments (200-2000bps) were then sheared to 300-600bps.
NGS libraries were prepared using the NEBNext Ultra™ II DNA Library Prep Kit for Illumina.

treatment_protocol: pre-treatment with doxycycline (20-24h); DSB induction by CRISPR/Cas9 Nucleofection simultaneous with Shield1 treatment  wherein siRNA is used, pretreated at -2d prior to CRISPR/Cas9 Nucleofection and again simultaneously with CRISPR/Cas9 Nucleofection.

tag: tissue

value: blood

tag: cell line

tag: cell type

value: myelogenous leukemia

tag: treatment

value: CRISPR/Cas9, sgHBB, plasmid100-HBB-000

tag: batch


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid100-HBB-100

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid100-HBB-100_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B2-A2_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B2-A2.bw

value: CRISPR/Cas9, sgHBB, plasmid100-HBB-100


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid100-HBB-099

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid100-HBB-099_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B7-A7_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B7-A7.bw

value: CRISPR/Cas9, sgBFP, plasmid100-HBB-099


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid100-HBB-060

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid100-HBB-060_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B6-A6_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B6-A6.bw

value: CRISPR/Cas9, sgBFP, plasmid100-HBB-060


title: Patient-derived GSC, BT18, GFP, 1

city: Helsinki

first: Vasiliki

last: Gkini

address: Haartmaninkatu 8

department: HiLIFE/ Neuroscience Center

country: Finland

institute: University of Helsinki

description: Library name: BT18_P29_250512_GFP_S13

library_source: transcriptomic

data_processing:
RNA analysis up to raw gene counts was done using the Illumina Novaseq X on-board DRAGEN system (Illumina, San Diego, CA, USA; DRAGEN version 4.3.16, RNA app version 1.3.13; Reference GRCh38). Raw gene count data were processed in R (version 4.5.3) and were filtered to remove genes with counts per million (CPM) < 1 in fewer than 3 samples, TMM-normalized using edgeR (version 4.8.2), and log2-CPM expression values were obtained using voomWithQualityWeights from the limma package (version 3.66).
Supplementary files format and content: xlsx file with counts for each sample

molecule: total RNA

source_name: Patient-derived glioblastoma stem cells

growth_protocol: BT12, BT13 and BT18 cells were cultured in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham (11530566; Merk) supplemented with 2% B27 (11530536; Thermo Fisher Scientific), 1% glutamine, epidermal growth factor (EGF, 20 ng/ml; AF-100-15-500UG; PeproTech), and basic fibroblast growth factor (bFGF, 5 ng/ml; AF-100-18B-250UG; PeproTech). ZH305 were cultured in neurobasal medium supplemented with 2% B27, 1% glutamine, EGF (20 ng/ml), and bFGF (10 ng/ml). For passaging cells were dissociated with Accutase (25-058-CI; Corning)

extract_protocol:
Total RNA was isolated from lysed GFP-transduced cells using the NucleoSpin RNA plus kit (740984, Macherey-Nagel) according to the manufacturer’s instructions. To ensure that no residual DNA was left, the samples were digested with rDNAse using the NucleoSpin rDNAse set (740963, Macherey-Nagel) followed by a repurification of the RNA using the RNA Clean-up XS kit (740903, Macherey-Nagel). 200ng of total RNA was used for library construction.
Library preparation from 200 ng of total RNA was performed according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina Instruction Manual, Section 1 - Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA). The number of PCR cycles was 10 in the library amplification step. Libraries were barcoded with NEBNext® Multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA, USA).

value: Patient-derived glioblastoma stem cells

value: EGFP lentiviral transduction


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid100-HBB-095

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid100-HBB-095_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B8-A8_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B8-A8.bw

value: CRISPR/Cas9, sgBFP, plasmid100-HBB-095


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid100-HBB-080

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid100-HBB-080_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B5-A5_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B5-A5.bw

value: CRISPR/Cas9, sgBFP, plasmid100-HBB-080


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid100-HBB-000

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid100-HBB-000_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B3-A3_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B3-A3.bw

value: CRISPR/Cas9, sgBFP, plasmid100-HBB-000


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid100-HBB-100

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid100-HBB-100_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B2-A2_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B2-A2.bw

value: CRISPR/Cas9, sgBFP, plasmid100-HBB-100


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid100-HBB-090

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid100-HBB-090_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B4-A4_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B4-A4.bw

value: CRISPR/Cas9, sgBFP, plasmid100-HBB-090


title: K562-RaPID, sgHBB, 18h, rep6, 25kbps

description:
Library name: RaPIDseq_sgHBB_18h_rep6-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B1-A1_binned-25kbps.bw
C3R5X126_hg38_bkgrdSubtracted_B1-A1_binned-5kbps_raw.bw

value: CRISPR/Cas9, sgHBB


title: K562-RaPID, sgBFP, 18h, rep6, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep6-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B1-A1_binned-25kbps.bw
C3R5X126_hg38_bkgrdSubtracted_B1-A1_binned-5kbps_raw.bw

value: CRISPR/Cas9, sgBFP


title: K562-RaPID-BFP, sgBFP, 18h, rep1, 100kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep1-100kbps_C3R5X120
X120_gCY321_rBFP-A3-1-C5_Dox200_binned-100kbps.bw


title: K562-RaPID-BFP, sgNTC, 18h, rep1, 100kbps

description:
Library name: RaPIDseq_sgNTC_18h_rep1-100kbps_C3R5X120
X120_gCY321_rBFP-A3-1-C5_Dox200_binned-100kbps.bw

value: CRISPR/Cas9, sgCY930


title: K562-RaPID, sgCY1178, 18h, rep1, 100kbps

description:
Library name: RaPIDseq_sgCY1178_18h_rep1-100kbps_C3R5X120
X120_gCY1178_12A3_Dox80_hiRnp_binned-100kbps.bw

value: CRISPR/Cas9, sgCY1178


title: K562-RaPID, sgCY1177, 18h, rep1, 100kbps

description:
Library name: RaPIDseq_sgCY1177_18h_rep1-100kbps_C3R5X120
X120_gCY1177_12A3_Dox80_hiRnp_binned-100kbps.bw

value: blood

value: CRISPR/Cas9, sgCY1177


title: K562-RaPID, sgOR11H4-g1, 18h, rep1, 25kbps

description:
Library name: RaPIDseq_sgOR11H4-g1_18h_rep1-25kbps_C3R5X104
X86_gCY944_12A3_Dox100_binned-25kbps.bw

value: myelogenous leukemia

value: CRISPR/Cas9, sgOR11H4-g1


title: K562-RaPID, sgOR11H4-g3, 18h, rep1, 25kbps

description:
Library name: RaPIDseq_sgOR11H4-g3_18h_rep1-25kbps_C3R5X104
X86_gCY946_12A3_Dox100_binned-25kbps.bw

value: CRISPR/Cas9, sgOR11H4-g3


title: K562-RaPID, sgHBB, 18h, rep5, 25kbps

description:
Library name: RaPIDseq_sgHBB_18h_rep5-25kbps_C3R5X120
X120_gCY201_12A3_Dox80_nonStdRnpConc_binned-25kbps.bw
X120_gCY201_12A3_Dox80_nonStdRnpConc_binned-5kbps.bw


title: K562-RaPID, sgOR11H4-g2, 18h, rep1, 25kbps

description:
Library name: RaPIDseq_sgOR11H4-g2_18h_rep1-25kbps_C3R5X104
X86_gCY945_12A3_Dox100_binned-25kbps.bw

value: CRISPR/Cas9, sgOR11H4-g2


title: K562-RaPID, sgBFP, 18h, rep5, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep5-25kbps_C3R5X120
X120_gCY201_12A3_Dox80_nonStdRnpConc_binned-25kbps.bw
X120_gCY201_12A3_Dox80_nonStdRnpConc_binned-5kbps.bw
X120_gCY1177_12A3_Dox80_hiRnp_binned-100kbps.bw
X120_gCY1178_12A3_Dox80_hiRnp_binned-100kbps.bw


title: K562-RaPID, sgBFP, 18h, rep10, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep10-25kbps_C3R5X104
X86_gCY944_12A3_Dox100_binned-25kbps.bw
X86_gCY945_12A3_Dox100_binned-25kbps.bw
X86_gCY946_12A3_Dox100_binned-25kbps.bw


title: K562-RaPID, sgHBB, 18h, rep1, 25kbps, siDSS1

description:
Library name: RaPIDseq_sgHBB_siDSS1_18h_rep1-25kbps_LZX6
LZX6_R-E3_binned-25kbps.bw

value: CRISPR/Cas9, sgHBB, siDSS1


title: Growth restricted (FGR) 4

city: Ann Arbor

first: Ashley

last: Hesson

state: MI

address: 1500 E Medical Center Dr.

country: USA

institute: University of Michigan

description: Library name: SU-22-76027

data_processing:
RNA extraction, spatial transcriptomic library preparation and sequencing was performed by MedGenome, Inc. (Foster City, CA) using the Visium CytAssist platform (10x Genomics; Pleasanton, CA).
Initial processing and quality assessment was conducted in SpaceRanger (10xGenomics), with preliminary analyses and spot selection in Loupe Browser (10x Genomics Loupe Browser v8.0.0).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mat.gz: gene expression count data in Matrix Market Exchange Format
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.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: .tif: histology images
Supplementary files format and content: cytassist_image.tif: cytassist image
Library strategy: Spatial Transcriptomics

source_name: placenta

extract_protocol:
Paraffin scrolls were created of the selected areas and processed into Visium slides with a 6.5mm by 6.5mm capture area.
5,000 spots per capture area were acquired. Per sample, 90 million paired and 180 million total read per sample were processed.

treatment_protocol: No treatments were applied.

value: placenta

tag: condition

value: Growth restricted (FGR)


title: Well-grown (non FGR) 3

description: Library name: SU-21-55146

value: Well-grown (non FGR)


title: K562-RaPID, sgBFP, 18h, rep1, 25kbps, siDSS1

description:
Library name: RaPIDseq_sgBFP_siDSS1_18h_rep1-25kbps_LZX6
LZX6_R-E3_binned-25kbps.bw

value: CRISPR/Cas9, sgBFP, siDSS1


title: Well-grown (non FGR) 5

description: Library name: SU-23-27101


title: Growth restricted (FGR) 2

description: Library name: SU-19-33963


title: Growth restricted (FGR) 6

description: Library name: SU-23-86717.


title: Well-grown (non FGR) 1

description: Library name: SU-17-19302


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid12.5-HBB-099

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid12.5-HBB-099_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B7-A7_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B7-A7.bw

value: CRISPR/Cas9, sgHBB, plasmid12.5-HBB-099


title: c.elegans, BRE, Day17, rep1

city: Wuhan

first: Dan

middle: Yang

last: Wang

state: Hubei

address: No.1,Shizishan Street · Hongshan District

country: China

institute: Huazhong Agricultural University

data_processing:
Reads were assessed for quality with FastQC, filtered and trimmed with trimmomatic.
Trimmed sequence reads were mapped to the reference genome sequence using Hisat2 (version 2.0.5) and subsequently compressed and sorted using samtools (version 1.7).
Read counts were performed using featureCounts.
Assembly: cel235
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: C. elegans was grown on solid nematode growth media (NGM) plates seeded with OP50 bacteria at 20°C.

extract_protocol:
About 1000 worms were collected, washed in M9-buffer and extracted using the Ultrapure RNA Kit (Cowin Biotech). 1 μg of total RNA was submitted to the China National Gene Bank for library preparation and RNA sequencing using the DNBSEQ-T7 instrument.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Library Prep Set following manufacturer's protocols.

treatment_protocol: The synchronized L4 stage wild-type N2 worms were cultured on NGM containing E. coli OP50 for food, along with varied concentrations of BRE(0, 0.42, 1.04, or 1.67 mg/mL).

value: whole body

tag: genotype

value: WT (N2)

value: Black Rice Extract diet for 17 days after L4 larvae stage

tag: time

value: Day 17

tag: diet

value: BRE


title: c.elegans, BRE, Day17, rep3


title: c.elegans, BRE, Day17, rep2


title: c.elegans, BRE, Day15, rep3

value: Black Rice Extract diet for 15 days after L4 larvae stage

value: Day 15


title: c.elegans, BRE, Day15, rep1


title: c.elegans, BRE, Day15, rep2


title: c.elegans, BRE, Day11, rep2

value: Black Rice Extract diet for 11 days after L4 larvae stage

value: Day 11


title: c.elegans, BRE, Day11, rep3


title: c.elegans, BRE, Day11, rep1


title: c.elegans, BRE, Day6, rep2

value: Black Rice Extract diet for 6 days after L4 larvae stage

value: Day 6


title: c.elegans, BRE, Day6, rep1


title: c.elegans, Control, Day17, rep1

value: OP50 diet for 17 days after L4 larvae stage


title: c.elegans, Control, Day15, rep3

value: OP50 diet for 15 days after L4 larvae stage


title: c.elegans, Control, Day15, rep2


title: c.elegans, Control, Day17, rep2


title: c.elegans, Control, Day15, rep1


title: c.elegans, Control, Day17, rep3


title: c.elegans, Control, Day11, rep2

value: OP50 diet for 11 days after L4 larvae stage


title: c.elegans, Control, Day6, rep2

value: OP50 diet for 6 days after L4 larvae stage


title: c.elegans, Control, Day6, rep1


title: c.elegans, Control, Day6, rep3


title: c.elegans, Control, Day11, rep3


title: c.elegans, Control, Day1, rep3

value: OP50 diet for 1 day after L4 larvae stage

value: Day 1


title: c.elegans, Control, Day1, rep1

value: whole body


title: single B. thetaiotaomicron cells at MEP from well G12

city: Wurzburg

first: Elise

last: Bornet

address: Josef-Schneider Strasse 2

country: Germany

institute: Helmholtz Insitute

description: Library name: G12

library_source: transcriptomic single cell

data_processing:
Sequence reads were trimmed for Nextera adapter and MATQ-Seq primers using bbmap. bbduk.sh -Xmx10g t=20
Trimmed reads were then mapped to the reference genome using bowtie2 version 2.3.4.1. bowtie2 -p 30
features were assigned using featureCounts.
Read counts extraction was performed using feature counts version 2.0.1
Assembly: GCF_000011065.1
Supplementary files format and content: tab delimited text file contains raw counts for each sample

organism: Bacteroides thetaiotaomicron

growth_protocol: B. thetaiotaomicron cells were grown in tryptone yeast glucose (TYG) media to mid-exponential phase (OD2), anaerobiaclly at 37 degrees.

extract_protocol:
MATQ-Seq and ribosomal RNA depletion with DASH. A single cell was sorted per well of a 96 well plate. Cells were lysed using mechanical sonication. cDNA librairies were obtained using the MATQ-Seq reverse transcription protocol. Ribosomal cDNA was depleted from the cDNA librairies using DASH, optimized for bacteroides thetaiotaomicron.
Library were constructed using the Nextera XT kit from Illumina

treatment_protocol: Fixed in 50% RNAlater

value: WT

value: Fixed in 50% RNAlater


title: single B. thetaiotaomicron cells at MEP from well C12

description: Library name: C12


title: single B. thetaiotaomicron cells at MEP from well H12

description: Library name: H12


title: single B. thetaiotaomicron cells at MEP from well A12

description: Library name: A12


title: single B. thetaiotaomicron cells at MEP from well F11

description: Library name: F11


title: single B. thetaiotaomicron cells at MEP from well D11

description: Library name: D11


title: single B. thetaiotaomicron cells at MEP from well G11

description: Library name: G11


title: single B. thetaiotaomicron cells at MEP from well E12

description: Library name: E12


title: single B. thetaiotaomicron cells at MEP from well H11

description: Library name: H11


title: single B. thetaiotaomicron cells at MEP from well E11

description: Library name: E11


title: single B. thetaiotaomicron cells at MEP from well G10

description: Library name: G10


title: single B. thetaiotaomicron cells at MEP from well H10

description: Library name: H10


title: single B. thetaiotaomicron cells at MEP from well E10

description: Library name: E10


title: single B. thetaiotaomicron cells at MEP from well A10

description: Library name: A10


title: single B. thetaiotaomicron cells at MEP from well D10

description: Library name: D10


title: single B. thetaiotaomicron cells at MEP from well C10

description: Library name: C10


title: single B. thetaiotaomicron cells at MEP from well B10

description: Library name: B10


title: single B. thetaiotaomicron cells at MEP from well G9

description: Library name: G9


title: single B. thetaiotaomicron cells at MEP from well F9

description: Library name: F9


title: single B. thetaiotaomicron cells at MEP from well E9

description: Library name: E9


title: single B. thetaiotaomicron cells at MEP from well C9

description: Library name: C9


title: single B. thetaiotaomicron cells at MEP from well A9

description: Library name: A9


title: single B. thetaiotaomicron cells at MEP from well H8

description: Library name: H8


title: single B. thetaiotaomicron cells at MEP from well G8

description: Library name: G8


title: single B. thetaiotaomicron cells at MEP from well F8

description: Library name: F8


title: single B. thetaiotaomicron cells at MEP from well E8

description: Library name: E8


title: single B. thetaiotaomicron cells at MEP from well D8

description: Library name: D8


title: E. coli Δrnb Δrnr Δfbp, 4 min, rep6

status: Public on Jul 16 2026

city: Taipei

first: Sue

last: Lin-Chao

address: 128 Academia Road, Section 2, Nankang,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Library name: d3-4min-6

data_processing:
Paired-end raw sequencing reads were aligned to the Escherichia coli reference genome and transcriptome (GCF_000005845.2; ASM584v2) using STAR (v 2.7.11b)
Transcript abundance for 4,731 genes, including 92 exogenous ERCC spike-in RNAs, was then estimated by RSEM (v1.3.3)
Read-count-per-gene measurements were normalized across all samples using the ERCC spike-in RNAs according to the method described by Potts et al. Normalization factors (k values) were calculated from the sample at time 0 using the 24 most abundant ERCC spike-in RNAs (top 6 abundances from each A, B, C, and D group).
The geometric average of these k values served as the library normalization factor. Finally, normalized read counts were obtained by dividing the raw read counts for each sample by its corresponding library normalization factor.
Assembly: Escherichia coli (GCF_000005845.2; ASM584v2)
Supplementary files format and content: tab-deliminated text file includes log10-transformed and ERCC-normalized gene expression for each sample

organism: Escherichia coli

source_name: bacteria

growth_protocol: To study the effects of fbp deletion on the RNA half-life of PNPase-essential strains, E. coli MG1655 Δrnb Δrnr, and MG1655 Δrnb Δrnr Δfbp were cultured in 2 L flasks containing 400 mL of M9 supplemented with 0.2 % glucose and 0.4 % CAA at 37 ºC and 200 rpm.

extract_protocol:
Following rifampicin treatment, RNA was isolated as previously described [S. Lin-Chao, S. N. Cohen, The rate of processing and degradation of antisense RNAI regulates the replication of ColE1-type plasmids in vivo. Cell 65, 1233–1242 (1991)]
RNA quality was determined using an Agilent 5200 Fragment Analyzer and only samples with an RNA Quality Number of 8.0 or higher were used for subsequent steps. Before rRNA depletion, ERCC ExFold RNA Spike-In Mix (Thermo Fisher Scientific, Cat. No. 4456739) was added to each sample. In brief, 2 µg of total RNA was combined with 4 µL of a 1:100 dilution of the ERCC RNA spike-in in a final volume of 50 µL. Ribosomal RNA was depleted using the RiboMinus Bacteria 2.0 Transcriptome Isolation Kit (Thermo Fisher Scientific, Cat. No. A47335) following manufacturer's instructions. Next, cDNA synthesis and library preparation were performed using KAPA mRNA HyperPrep Kit (Roche, Cat. No. KK8581) following the manufacturer's protocol. Briefly, rRNA-depleted samples were fragmented into 200–300 bp fragments, and cDNA was synthesized and A-tailed. Then, Illumina TruSeq RNA UD Index V2 dual indexed adapters (IDT, Cat. No. 20042114) were ligated to the A-tailed cDNA and amplified by 12 PCR cycles. Library concentration was measured using a Qubit dsDNA HS Assay Kit (Invitrogen, Cat. No. Q32854) on a Qubit 3.0 Fluorometer (Invitrogen, Cat. No. Q32866). Final library quantification was performed with a qPCR-based method using the KAPA Library Quantification Kit (Roche, Cat. No. KK4824) on a BioRad CFX Opus 96 real-time PCR machine. The strand-specific RNA-sequencing libraries were pooled and sequenced on an Illumina NovaSeq X Plus sequencer with paired-end, 150 cycle reads, with an average of 5 million reads per sample.

treatment_protocol: When OD460 reached approximately 0.450 rifampicin (Sigma, Cat. No. R3501) was added to the cultures to a final concentration of 0.5 mg/mL and aliquots were withdrawn after different time points, a time point zero was used as a control before treatment.

value: bacteria

tag: strain

value: deletion-rnb deletion-rnr deletion-fbp

value: rifampicin

value: 4 min


title: DSP-1012550011232-E-A06

city: Osong-eup, Heungdeok-gu

first: WANG

last: FENG

state: Cheongju-si, Chungcheongbuk-do

address: Osongsaengmyeong ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea

country: South Korea

institute: chungbun national university

description:
Library name: ROI_005_Albumin
FFPE samples from 24-week-old mice on NCD and FFD diets liver tissues

data_processing:
Morphology markers: Albumin and Nuclear stain morphology markers Segment ROI (Alb)
Differential Expression Analysis: Differentially expressed genes (DEGs) were identified based on read counts. TMM+CPM normalization was applied using EdgeR within the R/Bioconductor framework, ensuring accurate expression level comparisons.
Assembly: The mouse genome assembly GRCm38
Supplementary files format and content: Processed data file is in format of text file containing ID, Gene Symbol, NCD/FFD Group
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Liver

extract_protocol:
Sequencing Saturation is a measure of sequencing depth for a sample [1 – % Unique reads]. Below 50% the counts become less reliable. Sensitivity for low expressing genes is depressed with lower sequencing saturation.  We use Q3 normalization as we find it consistently outperforms other methods like Negative Probe, which can over-normalize small regions and Housekeeper Normalization, which is susceptible to inconsistency in experiments investigating disparate sample types that often have different expression levels.
Using a patented DNA barcoding technology, synthetic DNA oligonucleotide barcodes are attached to antibodies for protein detection, and In Situ Probes for mRNA detection via a UV photocleavable linker. A single tissue section is labeled with a cocktail of these probes and 4 fluorescently labeled morphology markers. Regions of interest for molecular profiling are selected based on the fluorescent images, and UV light illuminates each region independent, which releases the barcodes from that region for subsequent counting. Molecular counts for each target in the panel can then be mapped back to distinct regions of interest and comparisons made within and between samples. The workflow is simple with many aspects of it automated in the system.  Staining can be done on an Autostainer, or manually on the bench.  The system first scans the fluorescence, and ROI selection is done right through the software.  Once ROIs are selected, the system goes through and picks from each region one at a time.  As barcodes are released, a microcapillary system sips up the tags, and dispenses them into a 96 well microtiter plate.  Those barcodes can then be read out on our nCounter platform, or an Illumina sequencer.

value: Liver

value: FFD


title: DSP-1012550011232-E-A07

description:
Library name: ROI_006_Albumin
FFPE samples from 24-week-old mice on NCD and FFD diets liver tissues


title: single B. thetaiotaomicron cells at MEP from well C8

description: Library name: C8


title: single B. thetaiotaomicron cells at MEP from well B8

description: Library name: B8


title: single B. thetaiotaomicron cells at MEP from well H7

description: Library name: H7


title: single B. thetaiotaomicron cells at MEP from well A8

description: Library name: A8


title: single B. thetaiotaomicron cells at MEP from well G7

description: Library name: G7


title: single B. thetaiotaomicron cells at MEP from well D7

description: Library name: D7


title: single B. thetaiotaomicron cells at MEP from well E7

description: Library name: E7


title: single B. thetaiotaomicron cells at MEP from well A7

description: Library name: A7


title: single B. thetaiotaomicron cells at MEP from well G6

description: Library name: G6


title: single B. thetaiotaomicron cells at MEP from well F6

description: Library name: F6


title: single B. thetaiotaomicron cells at MEP from well D6

description: Library name: D6


title: single B. thetaiotaomicron cells at MEP from well C6

description: Library name: C6


title: WT iBMDMs, 4hr time point, CV-Cglr3+, biological replicate 3

status: Public on Jul 17 2026

city: Boston

first: Stephanie

last: Ragland

state: MA

address: 1 Blackfan Circle

department: Gastroenterology

institute: Boston Children's Hospital

description: Library name: 68

data_processing:
Galaxy Server
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: iBMDMs

extract_protocol:
RNA was extraced from infected iBMDMs using 300 μL lysis buffer with 1% BME, followed by isolation with the Thermo Fisher Scientific PureLink kit (#12183025). RNA  was treated with Turbo DNase (Thermo #AM190) according to manufacturer's instructions. Illumina RNA-sequencing was performed by Azenta/Genewiz.
NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module

value: iBMDMs

value: macrophage

value: same batch for all


title: single B. thetaiotaomicron cells at MEP from well B6

description: Library name: B6


title: single B. thetaiotaomicron cells at MEP from well E6

description: Library name: E6


title: single B. thetaiotaomicron cells at MEP from well A6

description: Library name: A6


title: single B. thetaiotaomicron cells at MEP from well H5

description: Library name: H5


title: single B. thetaiotaomicron cells at MEP from well E5

description: Library name: E5


title: single B. thetaiotaomicron cells at MEP from well D5

description: Library name: D5


title: single B. thetaiotaomicron cells at MEP from well C5

description: Library name: C5


title: single B. thetaiotaomicron cells at MEP from well B5

description: Library name: B5


title: single B. thetaiotaomicron cells at MEP from well A5

description: Library name: A5


title: ASyS2

city: Pittsburgh

first: Alyxzandria

last: Gaydosik

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

description:
Library name: 24852
BC006

library_source: other

data_processing:
Using CellRanger 9.0, FASTQ files were aligned to 10X Genomics reference refdata-gex-GRCh38-2020-A and for fixed FLEX samples the probe set Chromium_Human_Transcriptome_Probe_Set_v1.0.1 was downloaded from 10X Genomics' website and utilized; fixed FLEX samples were also concurrently demultiplexed by probe barcode utilizing cellranger multi.  The resulting feature (in this case, genes) barcode matrices were generated as Hierarchical Data Format (HDF5 or H5) files.
Output Hierarchical Data Format (HDF5 or H5) gene barcode files were processed in R version 4.5.0 using the Seurat package (version 5.2.0)
Assembly: human GRCh38, 10X Genomics refdata-gex-GRCh38-2020-A
Supplementary files format and content: Hierarchical Data Format (HDF5 or H5) containing gene barcode matrices per sample

molecule: other

source_name: muscle

extract_protocol:
For fixed FLEX samples, each samples' FFPE block was cut into several scrolls and prepared into single cell suspensions following 10X Genomics' CG000632 Demonstrated Protocol.  Specifically, the gentleMACS Octo Dissociator for Isolation of Nuclei from FFPE Tissue Sections protocol was employed.  Briefly, scrolls were placed into the gentleMACS C tube and deparaffinized with xylene and rehydrated with graded ethanol washes (100% ethanol, 70% ethanol, 50% ethanol, 100% water), before resuspension in PBS.  Tissue was then dissociated with Liberase TH and the Miltenyi Octo Dissociator.  Nuclei were subsequently filtered through a 30 micron filters and counted with propidium iodided before proceeding to Chromium Fixed RNA Profiling protocols – Probe Hybridization.
Library construction was performed following the manufacturer’s (10X Genomics) official protocols.  For FFPE samples, the FLEX protocol was utilized and, once cell suspensions were generated from FFPE scrolls for each sample, the protocol Chromium Fixed RNA Profiling – Multiplexed Samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673) was utilized to hybridize individual probe barcodes per sample.  Once a probe barcode was associated per sample, library construction proceeded following User Guide CG000527 Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples.  Briefly, post-hybridization, the 16 samples containing different probe barcodes were pooled together and unbound probes were washed off.  The samples were then mixed with a Master Mix and loaded into Chromium Chip Q along with gel beads and partitioning oil.  The chip is then loaded into the Chromium X Series instrument to generate the Gel Beads-in-emulsion (GEMs) which are subsequently incubated, amplified, size-selected, indexed, and quantified.  The libraries are standard llumina paired-end constructs, beginning with P5 and ending with P7. The final library includes 16 bp 10x GEM Barcodes (10x Barcode) encoded at the start of TruSeq Read 1 (Read 1T). Finally, the sample index sequences are incorporated as the i5 and i7 index reads.

value: muscle

tag: sample group

value: ASyS


title: single B. thetaiotaomicron cells at MEP from well G4

description: Library name: G4


title: single B. thetaiotaomicron cells at MEP from well F4

description: Library name: F4


title: single B. thetaiotaomicron cells at MEP from well E4

description: Library name: E4


title: Control polyA-enriched RNA input 2

city: Chicago

first: Caraline

last: Sepich

state: Illinois

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

data_processing:
Read1 files from both sequencing experiments were merged using the Linux command cat and then quality checked using FastQC v0.11.5 .
Then, analysis was performed using a pipeline constructed by modifying the framework used by Zhou et al (PMID:PMID: 31548705). Unique molecular identifiers (UMIs) were extracted using UMI-tools. Adapters were trimmed using BBDuk from BBTools version 38.84.
Reads were mapped to the human genome hg38 using hisat2 v2.1.0.
Assembly: hg38
Supplementary files format and content: 240609_m3C_M8KD_mRNA_sites_GEO.csv is a csv file containing a list of putative m3C sites on RNA from the polyA-enriched RNA sequencing experiment. Information is given on the site location, mutation rate in each sample, and coverage for each sample. Calculations were done regarding demethylation rates and changes between control and METTL8 knockdown conditions. Sites were filtered to those in the control libraries with a mutation rate cutoff of 20% and demethylation rate of at least 10%. Information is also included regarding annotations.
Supplementary files format and content: 240609_m3C_M8KD_caRNA_sites_GEO.csv is a csv file containing a list of putative m3C sites on RNA from the chromatin-associated RNA sequencing experiment. Information is given on the site location, mutation rate in each sample, and coverage for each sample. Calculations were done regarding demethylation rates and changes between control and METTL8 knockdown conditions. Sites were filtered to those in the control libraries with a mutation rate cutoff of 20% and demethylation rate of at least 10%. Information is also included regarding annotations.

molecule: polyA RNA

source_name: HeLa

growth_protocol: Hela cells and derived stable clones were maintained in RPMI supplemented with 10% FBS as previously described.32 For lentivirus production, lentiviral construct TRCN0000236515 and SHC002 (pLKO.1-derived plasmid with target sequence GATCGCCGCTTACAAGTTAAT for METTL8 and CAACAAGATGAAGAGCACCAA as control) together with pCMV-dR8.2 dvpr and pCMV-VSVG were co-transfected into 293TN cells (System Biosciences). Viruses were concentrated using PEG-it Virus precipitation solution (System Biosciences) and used for infecting cells in the presence of TransDux (System Biosciences). Pools of stable transfectants were selected with 2ug/ml puromycin.

extract_protocol:
Total RNA was isolated from HeLa cells using Trizol (Invitrogen) according to the manufacturer’s instructions. Polyadenylated RNA was isolated from total RNA using the Dynabeads mRNA Direct kit (Life Technologies) as per manufacturer instructions. Chromatin-associated RNA was purified as previously described by Liu et al (PMID: 31949099) Small RNA was isolated from total RNA using the RNA Clean and Concentrator kit (Zymo) according to the manufacturer protocol for purification of small and large RNAs into separate fractions, saving the small RNA fraction.
Each RNA sample was fragmented, 3' end repaired, ligated to a 3' adaptor, treated with 5'-exonuclease anddeadenylase, and combined with spike-in probes containing m3C. Then, samples were split into 3 parts: 1 part to be treated withAlkBto demethylate m3C sites, and 2 other untreated technical replicates. Each part then underwent reverse transcription withProtoscriptII, RNase H treatment, linker ligation, PCR, and library purification.

value: HeLa

value: Control (Control shRNA)


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, untreated, biological replicate 2

description: Library name: 57

value: untreated


title: single B. thetaiotaomicron cells at MEP from well C4

description: Library name: C4


title: single B. thetaiotaomicron cells at MEP from well B4

description: Library name: B4


title: single B. thetaiotaomicron cells at MEP from well A4

description: Library name: A4


title: single B. thetaiotaomicron cells at MEP from well H3

description: Library name: H3


title: DM2

description:
Library name: 11624
BC005

value: DM


title: WT, rimeporide, replicate 1 [HSA-000036441]

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

data_processing:
Data was processed using nf-core/rnaseq v3.11.2 (doi:https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewelset al., 2020) using Gencode M31 gene annotations. Because the QuantSeq data only captures 3' tags from transcripts, the following custom parameters were supplied: extra_star_align_args: '--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA' and extra_salmon_quant_args: '--noLengthCorrection'.
Assembly: GRCm39
Supplementary files format and content: File raw_and_normalized_counts.xlsx is a Microsoft Excel file with four worksheets: 1. sample information, 2. gene information, 3. raw count table, 4. normalized count table (log2 counts per million).

source_name: brain

growth_protocol: For isolation of primary microglia, brains of neonatal mice (P1-P3) were removed and the cerebral cortices and hippocampus were harvested. Isolated tissues were diced into a fine slurry, suspended in 50mL cold HBSS, and centrifuged at 200xg for 3 minutes. Then, the pelleted tissue was resuspended in warm 0.25% Trypsin-EDTA (Gibco; Cat# 25200056), mixed by inversion, and incubated at 37C for 20 minutes with agitation (100rpm). After 20 minutes, the enzymatic digestion was stopped by adding primary microglia culture medium [DMEM/F12 (Gibco; Cat# 11-330-057), 10% HyClone FBS (Cytiva; Cat# SH30080.03), 1X GlutaMax (Gibco; Cat# 35050061), and penicillin-streptomycin (Gibco; Cat# 15140122)] supplemented with DNase-I (Sigma-Aldrich; Cat# 5025) at 625U/mL culture medium. Dissociated tissue was mixed by inversion 10-12 times and triturated until a homogenous, single-cell suspension was observed. Cells were pelleted by centrifugation at 200xg for 7 minutes, supernatant was removed, and the cells were resuspended in primary microglia culture medium. Cells were filtered through a 70mm strainer to create a single-cell suspension and counted. Poly-D-lysine (Sigma-Aldrich; Cat# P6407)-coated T-75 vented culture flasks were washed twice with PBS and primary microglia were seeded at a density of 6 million cells/flask. After 3 days, the medium was replaced with fresh primary microglia culture medium. Subsequently, half-media changes were performed every other day until the mixed glial culture reached a confluency of 90% (10-14 days). Microglia were then detached from the mixed glial flask using a heated orbital shaker for 2 hours at 240rpm at 37C and 5% CO2. The microglial suspension was centrifuged at 200xg for 8 minutes, resuspended in conditioned medium, counted, and seeded for experiments in 50% conditioned medium with 50% fresh medium. The original mixed glial culture flasks were replenished with fresh medium and maintained in culture with half-media changes every other day. Primary microglia were similarly harvested every 6-8 days for a total duration of 3 weeks. Isolated primary microglia were seeded at assay-dependent concentrations onto poly-D-lysine-coated plates in 50% conditioned medium from the mixed glial culture flask with 50% fresh primary microglia culture medium [DMEM/F12 (Gibco; Cat# 11-330-057), 10% HyClone FBS (Cytiva; Cat# SH30080.03), 1X GlutaMax (Gibco; Cat# 35050061), and penicillin-streptomycin (Gibco; Cat# 15140122)]. After 24 hours, seeded microglia were washed twice with PBS to remove debris, cultured in 50% fresh medium and 50% conditioned medium (collected from mixed glial culture flasks and centrifuged at 1000xg for 3 minutes to remove cellular debris), and used for experiments.

extract_protocol:
RNA was harvested from cells using the RNeasy Micro Kit (Qiagen), following the manufacturer’s protocol. RNA integrity (RIN) and concentration were measured by High Sensitivity RNA Screen Tape Analysis (Agilent) on a 4200 TapeStation System (Agilent). Libraries were generated using the QuantSeq 3’ mRNA-seq Library Prep Kit FWB for Illumina (Lexogen A01173) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Library quantity and quality were assessed with TapeStation High Sensitivity D1000 Screen Tape (Agilent 5067-5592) using High Sensitivity D1000 reagents (Agilent 5067-5593). Libraries were pooled in equimolar ratios and sent to SeqMatic for sequencing on a NovaSeq S1 (75bp, single-end reads).
Libraries were generated using the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Library quantity and quality were assessed with TapeStation High Sensitivity D1000 ScreenTape (Agilent 5067-5592) using High Sensitivity D1000 reagents (Agilent 5067-5593).

treatment_protocol: Cells were treated with 2uM rimeporide or equal percentage of DMSO (vehicle) for 72h prior to RNA extraction.

value: brain

tag: replicate

value: primary microglia

value: WT

value: rimeporide

tag: treatment dose

value: 2 uM

tag: treatment duration

value: 72 hours

tag: rin


title: WT, DMSO, replicate 2 [HSA-000036434]

value: DMSO

value: 0 uM


title: single B. thetaiotaomicron cells at MEP from well F3

description: Library name: F3

value: Fixed in 50% RNAlater


title: single B. thetaiotaomicron cells at MEP from well D3

description: Library name: D3


title: single B. thetaiotaomicron cells at MEP from well E3

description: Library name: E3


title: single B. thetaiotaomicron cells at MEP from well C3

description: Library name: C3


title: single B. thetaiotaomicron cells at MEP from well B3

description: Library name: B3


title: single B. thetaiotaomicron cells at MEP from well A3

description: Library name: A3


title: single B. thetaiotaomicron cells at MEP from well H2

description: Library name: H2


title: single B. thetaiotaomicron cells at MEP from well G5

description: Library name: G5


title: single B. thetaiotaomicron cells at MEP from well G2

description: Library name: G2


title: single B. thetaiotaomicron cells at MEP from well F5

description: Library name: F5


title: c.elegans, BRE, Day6, rep3

value: whole body

value: WT (N2)

value: Black Rice Extract diet for 6 days after L4 larvae stage

value: Day 6

value: BRE


title: single B. thetaiotaomicron cells at MEP from well F2

description: Library name: F2


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, CV-Cglr2+, biological replicate 2

description: Library name: 56

value: iBMDMs

value: macrophage

value: same batch for all


title: single B. thetaiotaomicron cells at MEP from well E2

description: Library name: E2


title: single B. thetaiotaomicron cells at MEP from well D2

description: Library name: D2


title: single B. thetaiotaomicron cells at MEP from well C2

description: Library name: C2


title: single B. thetaiotaomicron cells at MEP from well H1

description: Library name: H1


title: single B. thetaiotaomicron cells at MEP from well G1

description: Library name: G1


title: c.elegans, Control, Day11, rep1

value: OP50 diet for 11 days after L4 larvae stage

value: Day 11


title: single B. thetaiotaomicron cells at MEP from well F1

description: Library name: F1

value: WT


title: 100 B. thetaiotaomicron cells from well C1

description: Library name: C1


title: positive control, 50pg of hot phenol extracted RNA from B. thetaiotaomicron at MEP

description: Library name: B1


title: c.elegans, Control, Day1, rep2

value: OP50 diet for 1 day after L4 larvae stage

value: Day 1


title: negative control

description: Library name: NC


title: P9_R2_DNA

city: Seoul

first: HAN SAI

last: LEE

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea

institute: Seoul National University Seoul Metropolitan Government Boramae Medical Center

description: Library name: SAMPLES92

data_processing:
Raw sequencing reads from WGS and WTS were processed for quality control using FastQC (v. 0.11.9). Adapter trimming and quality filtering were conducted with Trimmomatic (v. 0.39).
For WGS data preprocessing, reads were aligned to the human reference genome (GRCh38) using BWA-MEM (v. 0.7.17). Duplicate reads were marked with Picard (v. 2.23.3). Post-alignment processing included duplicate marking with MarkDuplicates, base quality score recalibration with BaseRecalibrator and ApplyBQSR, and pileup generation using samtools mpileup, GetPileupSummaries, and CollectSequencingArtifactMetrics, following GATK best practices. WGS data quality was assessed using multiple metrics including sequencing depth (≥30×), mapping quality  (≥60), base quality scores (≥Q30), and coverage uniformity. Samples with <80% alignment rate or excessive duplicate rates (>30%) were excluded from downstream analysis.
For WTS data preprocessing, reads were aligned to GRCh38 using STAR (v. 2.7.5a). Gene expression quantification was calculated with RSEM (v. 1.3.3.)
Assembly: GRCh38
Supplementary files format and content: Anonymized_TPM_2026-01-16.xlsx: Normalized gene expression matrix in Excel format. The file contains quantification of transcript abundance measured in TPM. Rows represent gene identifiers (Ensembl ID), and columns represent anonymized sample IDs corresponding to the study metadata.
Supplementary files format and content: Anonymized_Variants_2026-01-16.xlsx: The file containing somatic variants identified from WGS data. These files include variant calls for nuclear DNA.
Supplementary files format and content: Anonymized_Variants_mitochondria_2026-01-16.xlsx: The file containing somatic variants identified from WGS data. These files include variant calls for mitochondrial DNA.
Supplementary files format and content: Anonymized_Metadata_2026-01-16.csv: The file containing de-identified clinical data of samples that were used for this study

source_name: Thyroid

extract_protocol:
gDNA and total RNA were extracted from fresh-frozen tissue samples using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. For DNA, quality and quantity were assessed using a Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and an Agilent 2100 Bioanalyzer. For RNA, concentration was calculated by Quant-IT RiboGreen (Invitrogen, Carlsbad, CA, USA), and quality control was performed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 7 required for inclusion. Additionally, the DV200 value (% of RNA fragments >200 bp) was determined for RNA samples by running them on a TapeStation RNA screentape (Agilent Technologies, Santa Clara, CA, USA).
For WGS, a total of 100 ng of gDNA was sheared using adaptive focused acoustic technology (Covaris, Woburn, MA, USA). The sequencing libraries were then prepared according to the manufacturer’s instructions of the TruSeq Nano DNA High Throughput Library Prep Kit (Illumina, San Diego, CA, USA). This process involved end-repairing the fragmented DNA to create blunt-ended molecules, followed by the addition of a single ‘A’ base and ligation of TruSeq DNA UD Indexing adapters. The products were then purified and enriched with PCR. For WTS, a total of 100 ng of total RNA was used for library construction with the Agilent SureSelectXT RNA Direct Library Preparation Kit. Briefly, the total RNA was fragmented using divalent cations under elevated temperature. These cleaved fragments were copied into first-strand cDNA using random primers, followed by second-strand cDNA synthesis. These cDNA fragments then underwent an end-repair process, the addition of a single ‘A’ base, and ligation of adapters, followed by PCR enrichment. For the capture of human exonic regions, 250 ng of the cDNA library was mixed with hybridization buffers, blocking mixes, RNase block, and the Agilent SureSelect XT Human All Exon capture library. Hybridization was conducted at 65°C for 24 hours. The captured library was then washed and subjected to a second round of PCR amplification.

value: Thyroid


title: P9_R1_DNA

description: Library name: SAMPLES90


title: P9_R3_DNA

description: Library name: SAMPLES91


title: P9_LN2_DNA

description: Library name: SAMPLES88


title: single B. thetaiotaomicron cells at MEP from well F12

description: Library name: F12


title: P9_LN3_DNA

description: Library name: SAMPLES89


title: P8_PC_DNA

description: Library name: SAMPLES85


title: P8_LN1_DNA

description: Library name: SAMPLES84


title: P9_Normal_DNA

description: Library name: SAMPLES86


title: P8_LN2_DNA

description: Library name: SAMPLES83


title: P8_Normal_DNA

description: Library name: SAMPLES82


title: P7_PC1_DNA

description: Library name: SAMPLES80


title: P7_PC3_DNA

description: Library name: SAMPLES79


title: P7_PC2_DNA

description: Library name: SAMPLES78


title: P7_Normal_DNA

description: Library name: SAMPLES77


title: P6_PC2_DNA

description: Library name: SAMPLES76


title: P6_PC3_DNA

description: Library name: SAMPLES75


title: P6_PC1_DNA

description: Library name: SAMPLES74


title: P6_LN1_DNA

description: Library name: SAMPLES73


title: P6_LN2_DNA

description: Library name: SAMPLES72


title: P6_Normal_DNA

description: Library name: SAMPLES71


title: P5_PC_DNA

description: Library name: SAMPLES70


title: P5_LN2_DNA

description: Library name: SAMPLES68


title: P5_LN3_DNA

description: Library name: SAMPLES69


title: P5_LN1_DNA

description: Library name: SAMPLES67


title: P5_Normal_DNA

description: Library name: SAMPLES66


title: P4_PC1_DNA

description: Library name: SAMPLES65


title: P4_PC2_DNA

description: Library name: SAMPLES64


title: P4_LN2_DNA

description: Library name: SAMPLES62


title: P4_LN1_DNA

description: Library name: SAMPLES63


title: P4_Normal_DNA

description: Library name: SAMPLES61


title: P3_PC1_DNA

description: Library name: SAMPLES60


title: P3_PC2_DNA

description: Library name: SAMPLES59


title: P3_LN_DNA

description: Library name: SAMPLES58


title: P3_Normal_DNA

description: Library name: SAMPLES57


title: P2_R1_DNA

description: Library name: SAMPLES55


title: P2_R4_DNA

description: Library name: SAMPLES56


title: P2_R3_DNA

description: Library name: SAMPLES54


title: P1_R3_DNA

description: Library name: SAMPLES50


title: P2_Normal_DNA

description: Library name: SAMPLES52


title: P1_R4_DNA

description: Library name: SAMPLES51


title: P1_R2_DNA

description: Library name: SAMPLES49


title: P1_R1_DNA

description: Library name: SAMPLES48


title: P9_R2_RNA

description: Library name: SAMPLES46


title: P1_Normal_DNA

description: Library name: SAMPLES47


title: P9_R3_RNA

description: Library name: SAMPLES45


title: P9_LN2_RNA

description: Library name: SAMPLES42


title: P8_PC_RNA

description: Library name: SAMPLES39


title: P9_Normal_RNA

description: Library name: SAMPLES40


title: P8_LN1_RNA

description: Library name: SAMPLES38


title: P8_Normal_RNA

description: Library name: SAMPLES36


title: P7_PC1_RNA

description: Library name: SAMPLES34


title: P7_LN_RNA

description: Library name: SAMPLES35


title: P7_PC3_RNA

description: Library name: SAMPLES33


title: P7_PC2_RNA

description: Library name: SAMPLES32


title: P7_Normal_RNA

description: Library name: SAMPLES31


title: P6_PC3_RNA

description: Library name: SAMPLES29


title: P6_LN1_RNA

description: Library name: SAMPLES27


title: P6_LN2_RNA

description: Library name: SAMPLES26


title: P6_Normal_RNA

description: Library name: SAMPLES25


title: P5_PC_RNA

description: Library name: SAMPLES24


title: P5_LN3_RNA

description: Library name: SAMPLES23


title: P5_Normal_RNA

description: Library name: SAMPLES20


title: P4_PC1_RNA

description: Library name: SAMPLES19


title: P4_PC2_RNA

description: Library name: SAMPLES18


title: P4_LN2_RNA

description: Library name: SAMPLES16


title: P4_LN1_RNA

description: Library name: SAMPLES17


title: P4_Normal_RNA

description: Library name: SAMPLES15


title: P3_PC1_RNA

description: Library name: SAMPLES14


title: P3_PC2_RNA

description: Library name: SAMPLES13


title: P3_LN_RNA

description: Library name: SAMPLES12


title: P3_Normal_RNA

description: Library name: SAMPLES11


title: P2_R4_RNA

description: Library name: SAMPLES10


title: P2_R1_RNA

description: Library name: SAMPLES9


title: P6_PC1_RNA

description: Library name: SAMPLES28


title: P2_Normal_RNA

description: Library name: SAMPLES6


title: P2_R3_RNA

description: Library name: SAMPLES8


title: P1_R4_RNA

description: Library name: SAMPLES5


title: P1_R3_RNA

description: Library name: SAMPLES4


title: P1_R2_RNA

description: Library name: SAMPLES3


title: P1_R1_RNA

description: Library name: SAMPLES2


title: P1_Normal_RNA

description: Library name: SAMPLES1


title: R8LUN_2

city: San Juan

first: Hector

last: Franco

state: Puerto Rico

address: 2nd Floor Centro Medico- Office #275

institute: University of Puerto Rico Comprehensive Cancer Center

description: Library name: Sample 32

data_processing:
Sequencing reads were quality filtered and adapter trimmed prior to alignment.
Trimmed reads were aligned to the human reference genome using a splice-aware aligner.
Gene-level read counts were generated from aligned reads using an annotation-based counting approach.
Assembly: hg38
Supplementary files format and content: CSV files contain gene-level raw read counts for each RNA-seq sample.
Supplementary files format and content: BCMetastasis_All_Samples_and_Clinical_Data.xlsx Clinical data file
Supplementary files format and content: differential_expression_Breast.csv  - (normal vs met)
Supplementary files format and content: differential_expression_Liver.csv  - (normal vs met)
Supplementary files format and content: differential_expression_Lung.csv  - (normal vs met)
Supplementary files format and content: Peaks2Gene_Met_Liver_Lung_Cancer_Links_MET_only_peaks.rds - peak to gene file
Supplementary files format and content: RNA_counts_Met_plus_GTEX.csv - CSV files contain gene-level raw read counts for each RNA-seq sample plus counts from GTEX dataset

source_name: lung

growth_protocol: Human tumor samples were obtained from autopsies and processed according to institutional protocols. Samples were flash frozen and stored at −80 °C until nucleic acid extraction.

extract_protocol:
RNA was extracted from frozen tumor samples using the Qiagen RNeasy Mini Kit (Qiagen, 74104) following the manufacturer’s protocol.  RNA quality and concentration were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA using a poly(A)-selected library preparation kit according to the manufacturer’s protocol.

treatment_protocol: No in vitro treatment was applied. Samples represent primary and metastatic tumor tissues collected at the time of surgery.

value: lung

value: lung metastatic tumor cells


title: R8LUN_1

description: Library name: Sample 31


title: R8LIV_2

description: Library name: Sample 30

source_name: liver

value: liver

value: liver metastatic tumor cells


title: R8LIV_1

description: Library name: Sample 29


title: R8BR_2

description: Library name: Sample 28

source_name: breast

value: breast

value: breast primary tumor cells


title: P9_LN1_DNA

description: Library name: SAMPLES87


title: R8BR_1

description: Library name: Sample 27


title: R49LUN_2

description: Library name: Sample 26


title: R49LUN_1

description: Library name: Sample 25


title: P7_LN_DNA

description: Library name: SAMPLES81


title: R49LIV_1

description: Library name: Sample 23


title: R49LIV_2

description: Library name: Sample 24


title: P2_R2_RNA

description: Library name: SAMPLES7


title: R49BR_3

description: Library name: Sample 22


title: R49BR_2

description: Library name: Sample 21


title: R49BR_1

description: Library name: Sample 20


title: R39LIV_2

description: Library name: Sample 19


title: R39LIV_1

description: Library name: Sample 18


title: R39BR_1

description: Library name: Sample 17


title: R36LUN_2

description: Library name: Sample 16


title: R36LUN_1

description: Library name: Sample 15


title: R36LIV_2

description: Library name: Sample 14


title: P2_R2_DNA

description: Library name: SAMPLES53


title: R33LUN_2

description: Library name: Sample 12


title: R36LIV_1

description: Library name: Sample 13


title: R33LUN_1

description: Library name: Sample 11


title: R33LIV_2

description: Library name: Sample 10


title: P9_R1_RNA

description: Library name: SAMPLES44


title: R33LIV_1

description: Library name: Sample 9


title: R23LUN_2

description: Library name: Sample 8


title: P9_LN3_RNA

description: Library name: SAMPLES43


title: P9_LN1_RNA

description: Library name: SAMPLES41


title: P8_LN2_RNA

description: Library name: SAMPLES37


title: R23LUN_1

description: Library name: Sample 7


title: R23LIV_1

description: Library name: Sample 5


title: R23LIV_2

description: Library name: Sample 6


title: R18LUN_2

description: Library name: Sample 4


title: R18LUN_1

description: Library name: Sample 3


title: R18LIV_2

description: Library name: Sample 2


title: R18LIV_1

description: Library name: Sample 1


title: N3

first: wenjun

last: shao

address: 237 Luoyu Road, Wuchang District

department: Hubei Key Laboratory of Stomatology

institute: School & Hospital of Stomatology, Wuhan University

description:
Library name: sample 6
control, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes fpkm for each sample

source_name: cell culture

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: cell culture

value: wt

value: control


title: N2

description:
Library name: sample 5
control, replicate biosample 2


title: single B. thetaiotaomicron cells at MEP from well B12

description: Library name: B12

value: Fixed in 50% RNAlater


title: P6_PC2_RNA

description: Library name: SAMPLES30


title: shIFT883

description:
Library name: sample 3
IFT88 knockdown, replicate biosample 3

value: knockdown

value: IFT88 knockdown


title: shIFT882

description:
Library name: sample 2
IFT88 knockdown, replicate biosample 2


title: shIFT881

description:
Library name: sample 1
IFT88 knockdown, replicate biosample 1


title: Static_Culture_Gel_3_resub

first: Shuchang

last: Liu

address: 203 Lothrop Street

description:
Library name: Sample 9
Static_Culture_Gel_3_resub

data_processing:
Low quality reads were filtered by Trimmomatic.
Surviving reads were aligned to human reference genome using STAR aligner.
Assembly: hg38
Supplementary files format and content: *STAR.ReadsPerGene.out.tab

source_name: Chondrocytes

extract_protocol:
Chondrocytes from static, rotary, or rotary + Kaempferol (KMP) hydrogels were lysed in QIAzol reagent (Qiagen). RNA was quantified (Qubit RNA BR Assay Kit, Thermo Fisher) and integrity assessed (Fragment Analyzer, Agilent).
Libraries were prepared with the KAPA mRNA HyperPrep Kit (Roche) using 500 ng RNA per sample, validated, pooled, and sequenced (Illumina NovaSeq6000, 50 million 100-bp paired-end reads/sample).

value: Chondrocytes


title: N1

description:
Library name: sample 4
control, replicate biosample 1


title: Static_Culture_Gel_2_resub

description:
Library name: Sample 8
Static_Culture_Gel_2_resub


title: Static_Culture_Gel_1_resub

description:
Library name: Sample 7
Static_Culture_Gel_1_resub


title: Rotary_Culture_Gel_Plus_Kaempferol3

description:
Library name: Sample 6
Rotary_Culture_Gel_Plus_Kaempferol3


title: Rotary_Culture_Gel_Plus_Kaempferol2

description:
Library name: Sample 5
Rotary_Culture_Gel_Plus_Kaempferol2


title: Leukemia cells-Piezo1cko_rep3

first: Haojian

last: Zhang

address: Donghu Rd.

institute: Wuhan University

description: Library name: KO-3

data_processing:
All raw sequencing data were preprocessed using fastp (V 0.20.1).
Then the preprocessed data were aligned to GRCm38 transcripts database by hisat2 (V 2.2.1).
The reads were quantified with featureCounts (V 2.0.1).
DESeq2 (V 1.28.1) was employed for data normalization and differential expression analysis of RNA-seq counts between WT and Piezo1cko LSCs.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalzied reads each Sample

source_name: bone marrow

extract_protocol:
Bone marrow cells were extracted from 8 to 10 weeks old Piezo1cko and wild-type (WT) AML mice.LSCs were sorted from WT and Piezo1cko BM leukemia cells.Total RNA were extracted with Trizol and mRNA were isolated with Oligo dT beads.
The RNA-seq library was prepared using our customized protocol based on Smart-seq2 as previously described. In brief, reverse transcription (RT) of total RNA were reverse transcribed with VN-anchored oligo-dT primer and TSO, the resulting full-length cDNA is preamplified with the ISPCR primer. Pre-amplified cDNA was fragmented by Tn5 enzyme, followed by library generation using TruePrep DNA Library Prep Kit V2 for illumine kit (Vazyme, Cat#TD501) and were pair-end sequenced on Illumina HiSeq X Ten sequencing platform.

value: bone marrow

value: Leukemia cells


title: Leukemia cells-Piezo1cko_rep2

description: Library name: KO-2


title: Rotary_Culture_Gel_Plus_Kaempferol1

description:
Library name: Sample 4
Rotary_Culture_Gel_Plus_Kaempferol1


title: Rotary_Culture_Gel_3_resub

description:
Library name: Sample 3
Rotary_Culture_Gel_3_resub


title: single B. thetaiotaomicron cells at MEP from well H9

description: Library name: H9

value: WT


title: Leukemia cells-Piezo1cko_rep1

description: Library name: KO-1


title: Rotary_Culture_Gel_2_resub

description:
Library name: Sample 2
Rotary_Culture_Gel_2_resub


title: Leukemia cells-WT_rep2

description: Library name: WT-2


title: PB06441-001 MM CD38 12 months

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: PB06441-001
H5 file contains RNA expression matrix

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), 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 Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed 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 analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000, RNA UMIs/cells between 1500 and 750000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Supplementary files format and content: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

source_name: Blood

extract_protocol:
PBMCs were removed from liquid nitrogen and rapidly 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 chromium 3′ single cell gene expression assay with Cell Hashing. 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 platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare (BMC Bioinformatics 2022, doi: 10.1186/s12859-022-04620-2) to generate sample-specific output files.

value: Blood

value: PBMC

tag: subject id

tag: birth year

tag: Sex

value: Male

tag: race

value: Caucasian

tag: days since_first_visit

tag: visit

value: MM CD38 12 months

tag: batch id

tag: sample bridging_control

value: FALSE


title: Rotary_Culture_Gel_1_resub

description:
Library name: Sample 1
Rotary_Culture_Gel_1_resub

tag: tissue

tag: treatment


title: Leukemia cells-WT_rep3

description: Library name: WT-3

tag: cell line

tag: cell type


title: Leukemia cells-WT_rep1

description: Library name: WT-1


title: PB06434-001 MM CD38 9 months

description:
Library name: PB06434-001
H5 file contains RNA expression matrix

value: MM CD38 9 months


title: P5_LN2_RNA

description: Library name: SAMPLES22

value: Thyroid


title: mES_diSP

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description:
Library name: Sample10
10x Genomics

data_processing:
10x library equencing was performed on Illumina HiSeq X. Sequencing data were analyzed using Illumina bcl2fastq software (version 2.20.0) and converted to FASTQ format files. Subsequently, alignment was performed using the cellranger count function of Cell Ranger Single Cell software (version 9.0.0, 10x Genomics) with using STAR aligner 2.7.2a. The GRCm38 mouse reference genome, mm10 r102  was used.
Assembly: GRCm38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Mouse embryonic stem cell

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.

value: Mouse embryonic stem cell


title: PB06432-001 MM CD38 18 months

description:
Library name: PB06432-001
H5 file contains RNA expression matrix

value: MM CD38 18 months


title: mES_iNP

description:
Library name: Sample9
10x Genomics


title: PB06428-001 MM CD38 12 months

description:
Library name: PB06428-001
H5 file contains RNA expression matrix

value: Female


title: P5_LN1_RNA

description: Library name: SAMPLES21


title: PB05134-001 MM CD38 9 months

description:
Library name: PB05134-001
H5 file contains RNA expression matrix


title: MK P0

description:
Library name: Sample7
10x Genomics

source_name: Mouse Kidney

value: Mouse Kidney


title: MK P7

description:
Library name: Sample8
10x Genomics


title: PB05144-001 MM CD38 6 months

description:
Library name: PB05144-001
H5 file contains RNA expression matrix

value: MM CD38 6 months


title: single B. thetaiotaomicron cells at MEP from well B9

description: Library name: B9

tag: genotype

value: Fixed in 50% RNAlater

tag: batch


title: PB05131-001 MM CD38 Progression

description:
Library name: PB05131-001
H5 file contains RNA expression matrix

value: MM CD38 Progression


title: MEK E15.5

description:
Library name: Sample6
10x Genomics


title: mCD_Nfat5_KO

description:
Library name: Sample5
10x Genomics

source_name: Mouse embryonic kidney

value: Mouse embryonic kidney


title: PB05122-001 MM CD38 4 months

description:
Library name: PB05122-001
H5 file contains RNA expression matrix

value: MM CD38 4 months


title: mCD_WT

description:
Library name: Sample4
10x Genomics


title: PB05121-001 MM CD38 Progression

description:
Library name: PB05121-001
H5 file contains RNA expression matrix

value: Blood


title: PB05118-001 MM CD38 6 months

description:
Library name: PB05118-001
H5 file contains RNA expression matrix

value: PBMC


title: mCD_Osm

description:
Library name: Sample2
10x Genomics


title: mouse 750 VA

description:
Library name: Sample3
10x Genomics


title: PB05117-001 MM CD38 8 weeks

description:
Library name: PB05117-001
H5 file contains RNA expression matrix

value: Male

value: MM CD38 8 weeks


title: mCD_Control

description:
Library name: Sample1
10x Genomics


title: PB05115-001 MM CD38 6 weeks

description:
Library name: PB05115-001
H5 file contains RNA expression matrix

value: Caucasian

value: MM CD38 6 weeks


title: PB04846-001 MM CD38 4 weeks

description:
Library name: PB04846-001
H5 file contains RNA expression matrix

value: MM CD38 4 weeks

value: FALSE


title: W23 tassel, 2 cm, rep 1

city: Davis

first: Blake

last: Meyers

state: CA

address: 451 Health Sciences Drive

department: Department of Plant Sciences

institute: UC  Davis Genome Center

description:
Library name: tas_2_r1
W23 tassel, 2 cm, rep 1

data_processing:
Mathioni et al, Current Protocols, 2017
Assembly: https://mpss.meyerslab.ucdavis.edu/public-dbs
Supplementary files format and content: tab-delimited file in which each line contains a unique  sequence and the number of times that sequence appears in the library

organism: Zea mays

source_name: tassel 2.0 cm

extract_protocol: Mathioni et al, Current Protocols, 2017

value: tassel 2.0 cm

value: cv W23


title: PB04844-002 MM CD38 Pre-treatment

description:
Library name: PB04844-002
H5 file contains RNA expression matrix

value: Female

value: Asian

value: MM CD38 Pre-treatment


title: W23 tassel, 2 cm, rep 2

description:
Library name: tas_2_r2
W23 tassel, 2 cm, rep 2


title: W23 tassel, 1.5 cm, rep 2

description:
Library name: tas_1_5_r2
W23 tassel, 1.5 cm, rep 2

source_name: tassel 1.0 cm

value: tassel 1.0 cm


title: PB04843-001 MM CD38 12 months

description:
Library name: PB04843-001
H5 file contains RNA expression matrix

value: MM CD38 12 months


title: PB04841-002 MM CD38 Pre-treatment

description:
Library name: PB04841-002
H5 file contains RNA expression matrix


title: W23 tassel, 1 cm, rep 1

description:
Library name: tas_1_r1
W23 tassel, 1 cm, rep 1

source_name: tassel 1.5 cm

value: tassel 1.5 cm


title: W23 tassel, 1 cm, rep 2

description:
Library name: tas_1_r2
W23 tassel, 1 cm, rep 2


title: PB04839-001 MM CD38 2 weeks

description:
Library name: PB04839-001
H5 file contains RNA expression matrix

value: MM CD38 2 weeks


title: W23 tassel, 1.5 cm, rep 1

description:
Library name: tas_1_5_r1
W23 tassel, 1.5 cm, rep 1


title: PB04834-001 MM CD38 4 months

description:
Library name: PB04834-001
H5 file contains RNA expression matrix

value: Blood

value: MM CD38 4 months


title: PB04830-002 MM CD38 9 months

description:
Library name: PB04830-002
H5 file contains RNA expression matrix

value: PBMC

value: Male

value: MM CD38 9 months


title: PB04827-002 MM CD38 12 months

description:
Library name: PB04827-002
H5 file contains RNA expression matrix

value: Caucasian


title: W23 tassel, 0.5 cm, rep 2

description:
Library name: tas_0_5_r2
W23 tassel, 0.5 cm, rep 2

source_name: tassel 0.5 cm

value: tassel 0.5 cm


title: W23 tassel, 0.5 cm, rep 1

description:
Library name: tas_0_5_r1
W23 tassel, 0.5 cm, rep 1


title: Azucena,R4

city: Aberdeen

first: Elaina

last: Collie-Duguid

address: 23 St Machar Drive

country: United Kingdom

institute: University of Aberdeen

data_processing:
Processed in Illumina Basespace (4.1.0)
Reads trimmed with Illumina Basespace app FASTQ Toolkit (2.0.0) to remove reads with phred score <20 and length <20nt and to remove adapter sequences
Aligned to IRGSP-1.0 Oryza sativa genome using HISAT2 aligner
Differential expression analysis using edgeR (3.36.0)
Assembly: IRGSP-1.0
Supplementary files format and content: matrix txt file containing counts for every sample: matrix column names listed in A33-A52.

organism: Oryza sativa

source_name: root

extract_protocol:
RNA was extracted using TriReagent and chloroform.  1µg of RNA was used to construct each library.
Sequencing libraries were prepared using the TruSeq stranded total RNA with Ribo-zero (RS-122-2301) following the low sample protocol.

value: root

tag: batch rep

value: Azucena


title: PB04690-002 MM CD38 6 months

description:
Library name: PB04690-002
H5 file contains RNA expression matrix

value: MM CD38 6 months

value: FALSE


title: PB04687-002 MM CD38 9 months

description:
Library name: PB04687-002
H5 file contains RNA expression matrix

value: Female


title: PB04688-002 MM CD38 9 months

description:
Library name: PB04688-002
H5 file contains RNA expression matrix

value: Asian


title: Azucena,R2


title: Bala,R4

value: Bala


title: PB02776-002 MM CD38 6 months

description:
Library name: PB02776-002
H5 file contains RNA expression matrix


title: PB04678-002 MM CD38 8 weeks

description:
Library name: PB04678-002
H5 file contains RNA expression matrix

value: MM CD38 8 weeks


title: Azucena,R3


title: Bala,R3


title: PB02774-002 MM CD38 4 weeks

description:
Library name: PB02774-002
H5 file contains RNA expression matrix

value: MM CD38 4 weeks


title: Azucena,R1


title: Bala,R2


title: single B. thetaiotaomicron cells at MEP from well F7

description: Library name: F7

value: WT

value: Fixed in 50% RNAlater


title: PB02769-002 MM CD38 4 months

description:
Library name: PB02769-002
H5 file contains RNA expression matrix

value: Blood

value: MM CD38 4 months


title: Bala,R1


title: PB02761-002 MM CD38 2 weeks

description:
Library name: PB02761-002
H5 file contains RNA expression matrix

value: PBMC

value: MM CD38 2 weeks


title: ModdaiKaruppan,R4

value: ModdaiKaruppan


title: PB02760-002 MM CD38 6 months

description:
Library name: PB02760-002
H5 file contains RNA expression matrix

value: Caucasian


title: single B. thetaiotaomicron cells at MEP from well B7

description: Library name: B7


title: single B. thetaiotaomicron cells at MEP from well C7

description: Library name: C7


title: ModdaiKaruppan,R3

value: root


title: ModdaiKaruppan,R1


title: PB02755-002 MM CD38 8 weeks

description:
Library name: PB02755-002
H5 file contains RNA expression matrix

value: Male


title: Sarali,R4

value: Sarali


title: PB02749-002 MM CD38 4 weeks

description:
Library name: PB02749-002
H5 file contains RNA expression matrix

value: FALSE


title: PB02751-001 MM CD38 6 weeks

description:
Library name: PB02751-001
H5 file contains RNA expression matrix

value: MM CD38 6 weeks


title: NiyanWee,R4

value: NiyanWee


title: NiyanWee,R3


title: PB02744-002 MM CD38 4 months

description:
Library name: PB02744-002
H5 file contains RNA expression matrix


title: NiyanWee,R2


title: PB02743-002 MM CD38 4 weeks

description:
Library name: PB02743-002
H5 file contains RNA expression matrix

value: Female

value: Other


title: PB02742-002 MM CD38 6 weeks

description:
Library name: PB02742-002
H5 file contains RNA expression matrix


title: 558M_PBMC_TCR

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

description:
Library name: 558M_PBMC_TCR
FFPE

data_processing:
Sequencing reads were aligned to the mouse reference transcriptome (mm10) using the Cell Ranger multi pipeline (10x Genomics, v9.0.0) with default parameters. This pipeline enables the joint processing of gene expression and TCR V(D)J profiling data from the same cellular libraries, allowing for the simultaneous quantification of transcriptomic profiles and immune receptor sequences.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 -> scRNA data
Supplementary files format and content: filtered_contig_annotations.csv -> immuno profiling results
Library strategy: TCR-seq

source_name: PBMC

extract_protocol:
Single-cell suspensions from each heart tissue and matched PBMC sample were loaded into separate wells of a Chromium Next GEM Chip N (10X Genomics, Cat# 2000418) to generate gel beads-in-emulsion (GEMs), each containing uniquely barcoded beads for downstream single-cell capture and indexing. Cell concentration was adjusted to approximately 700-2,000 cells/µL to target recovery of up to 20,000 cells per sample. Sequencing libraries for 5’ gene expression and T cell receptor (TCR) V(D)J profiling were prepared using the Chromium Next GEM Single Cell 5' HT Reagent Kits v2 (10X Genomics, Cat# 1000356), the Mouse Chromium Single Cell V(D)J Amplification Kits (10X Genomics, Cat#1000254) and the Library Construction Kit (10X Genomics, Cat# 1000190) according to the manufacturer’s instructions.
All libraries were sequenced on the Illumina NovaSeq 6000 system using paired-end reads with dual indexing 26 cycles for Read 1, 10 cycles for i7 Index, 10 cycles for i5 Index, and 90 cycles for Read 2), targeting 400 million reads per gene expression library and 100 million reads per TCR amplification library.


title: 558M_Heart_TCR

description:
Library name: 558M_Heart_TCR
FFPE


title: PB02727-003 MM CD38 Pre-treatment

description:
Library name: PB02727-003
H5 file contains RNA expression matrix

value: MM CD38 Pre-treatment


title: 558M_PBMC_scRNA

description:
Library name: 558M_PBMC_GE
FFPE

data_processing:
Sequencing reads were aligned to the mouse reference transcriptome (mm10) using the Cell Ranger multi pipeline (10x Genomics, v9.0.0) with default parameters. This pipeline enables the joint processing of gene expression and TCR V(D)J profiling data from the same cellular libraries, allowing for the simultaneous quantification of transcriptomic profiles and immune receptor sequences.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 -> scRNA data
Supplementary files format and content: filtered_contig_annotations.csv -> immuno profiling results


title: PB02723-002 MM CD38 9 months

description:
Library name: PB02723-002
H5 file contains RNA expression matrix

value: MM CD38 9 months


title: 558M_Heart_scRNA

description:
Library name: 558M_Heart_GE
FFPE

source_name: Heart

value: Heart


title: PB02722-002 MM CD38 4 weeks

description:
Library name: PB02722-002
H5 file contains RNA expression matrix

value: Blood

value: MM CD38 4 weeks


title: PB02721-002 MM CD38 2 weeks

description:
Library name: PB02721-002
H5 file contains RNA expression matrix

value: PBMC


title: Multiome, retina, ATAC

first: Oriol

last: Fornes

address: 1 DNA Way

institute: Genentech

description:
Library name: LIB6223751
ATAC component of joint single-nucleus multiome profiling

library_source: genomic single cell

data_processing:
Joint alignment of single-nucleus RNA-seq and single-nucleus ATAC-seq reads was performed using Cell Ranger ARC (version 2.0.0).
Assembly: GRCm38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

source_name: retina

extract_protocol:
Eight retinas from 11- and 93-week-old C57BL/6 mice (4 per age group) were rapidly dissected from enucleated eyes in cold PBS, immediately snap-frozen on dry ice, and stored at -80°C. Snap-frozen retinal tissue was transferred into a glass Dounce homogenizer containing 500 µL chilled 0.1× lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.01% Tween-20, 0.01% Nonidet P40 Substitute, 0.001% digitonin, 1% BSA, 1 mM DTT, 1× RNase inhibitor in nuclease-free water) and immediately homogenized. Homogenates were incubated on ice for 5 minutes, gently triturated using a wide-bore pipette tip, and incubated on ice for an additional 10 minutes. Following lysis, 500 µL of chilled wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 1% BSA, 1 mM DTT, 1× RNase inhibitor in nuclease-free water) was added, and the samples were mixed gently. Nuclei suspensions were sequentially filtered through 70 µm and 40 µm Flowmi cell strainers to remove debris and aggregates, centrifuged at 500 × g for 5 minutes at 4°C, washed twice with chilled wash buffer, and resuspended in chilled diluted nuclei buffer (1× Nuclei Buffer with 1 mM DTT and 1× RNase inhibitor).
Single-nucleus ATAC and gene expression libraries were constructed jointly using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to the manufacturer’s protocols. Ten thousand nuclei were targeted for library preparation. Nuclei suspensions were loaded using the Chromium Next GEM Chip J Single Cell Kit (10X Genomics). The resulting libraries were sequenced on an Illumina NovaSeq 6000 platform targeting a depth of 25,000 read pairs per nucleus.

value: retina

tag: library type

value: ATAC


title: PB02718-003 MM CD38 2 weeks

description:
Library name: PB02718-003
H5 file contains RNA expression matrix

value: Caucasian

value: MM CD38 2 weeks


title: brain, 20M, GSK, rep4

city: Shanghai

first: Kai

last: Yang

address: 197 Ruijin 2nd Road, Shanghai, 200025, China

department: Shanghai Institute of Traumatology and Orthopedics

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: GSK_brain_rep4

data_processing:
For scRNA-seq: Raw sequencing reads were processed using the Cell Ranger count pipeline (10x Genomics). High-quality reads were aligned to the mm10 mouse reference genome to generate the definitive feature-barcode matrices.
For CUT&Tag: Raw sequencing reads were quality-trimmed, and the high-quality adapter-trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie2. Downstream peak calling, motif analysis, and signal visualization were performed utilizing MACS2, HOMER, and deepTools, respectively.
Assembly: Mouse mm10
Supplementary files format and content: For scRNA-seq: Processed single-cell data are provided as tab-separated values (.tsv) files and market exchange matrix (.mtx) files containing the finalized feature-barcode expression matrices.
Supplementary files format and content: For CUT&Tag: Processed chromatin-binding profiles are provided as bigWig (.bw) files containing normalized genome-wide track intensities.

source_name: Endosteal/Cortical bone

growth_protocol: IDG-SW3 osteolineage cells were cultured and differentiated in osteogenic induction medium at 37°C in a humidified atmosphere containing 5% CO2 according to established standard protocols.

extract_protocol:
For single-cell RNA sequencing (scRNA-seq), the single-cell suspension was immediately loaded onto the Chromium Controller (10x Genomics) for automated droplet generation and single-cell barcoding.
For bulk RNA-seq, sequencing libraries were constructed using the NEBNext Ultra™ II RNA Library Prep Kit (NEB) following the manufacturer's protocol. For scRNA-seq, sequencing libraries were constructed using the Chromium Single Cell 5' Reagent Kit (10x Genomics) following the manufacturer's protocol. For CUT&Tag profiling, sequencing libraries were generated using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) in accordance with the manufacturer's instructions.

treatment_protocol: For CUT&Tag profiling, differentiating IDG-SW3 cells were treated with 10 μM Nutlin-3 for 4 hours to induce intracellular p53 stabilization prior to harvest.

value: Endosteal/Cortical bone

tag: strain

value: Male

tag: developmental stage

value: 20 months

value: WT

value: GSK (GSK@SDSSD@Lipo)


title: PB02717-002 MM CD38 8 weeks

description:
Library name: PB02717-002
H5 file contains RNA expression matrix

tag: subject id

tag: birth year

value: MM CD38 8 weeks

value: FALSE


title: PB02714-002 MM CD38 2 weeks

description:
Library name: PB02714-002
H5 file contains RNA expression matrix

tag: Sex

value: Female

tag: race

value: Asian


title: brain, 20M, GSK, rep3

description: Library name: GSK_brain_rep3


title: brain, 20M, GSK, rep2

description: Library name: GSK_brain_rep2


title: PB02700-003 MM CD38 Pre-treatment

description:
Library name: PB02700-003
H5 file contains RNA expression matrix

tag: days since_first_visit

tag: visit

value: MM CD38 Pre-treatment


title: brain, 20M, GSK, rep1

description: Library name: GSK_brain_rep1


title: PB02758-002 MM CD38 12 months

description:
Library name: PB02758-002
H5 file contains RNA expression matrix

value: Blood

value: MM CD38 12 months

tag: batch id

tag: sample bridging_control


title: PB02759-003 MM CD38 Pre-treatment

description:
Library name: PB02759-003
H5 file contains RNA expression matrix

tag: tissue

value: PBMC


title: Sarali,R2

value: root

value: Sarali


title: ModdaiKaruppan,R2

value: ModdaiKaruppan


title: brain, 20M, Vehicle, rep3

description: Library name: Veh_brain_rep3

tag: treatment

value: Vehicle (SDSSD@Lipo)


title: PB02748-002 MM CD38 8 weeks

description:
Library name: PB02748-002
H5 file contains RNA expression matrix

tag: cell type

value: Caucasian


title: PB02685-003 MM CD38 Pre-treatment

description:
Library name: PB02685-003
H5 file contains RNA expression matrix


title: brain, 20M, Vehicle, rep2

description: Library name: Veh_brain_rep2

value: Endosteal/Cortical bone

value: Male

tag: genotype


title: brain, 20M, Vehicle, rep1

description: Library name: Veh_brain_rep1

value: 20 months

value: WT


title: PB02093-02 MM CD38 6 months

description:
Library name: PB02093-02
H5 file contains RNA expression matrix

value: MM CD38 6 months


title: bone, 20M, GSK, rep3

description: Library name: GSK_bone_rep3

value: GSK (GSK@SDSSD@Lipo)


title: PB02089-04 MM CD38 Pre-treatment

description:
Library name: PB02089-04
H5 file contains RNA expression matrix

value: FALSE


title: bone, 20M, GSK, rep2

description: Library name: GSK_bone_rep2


title: PB02074-02 MM CD38 4 months

description:
Library name: PB02074-02
H5 file contains RNA expression matrix

value: MM CD38 4 months


title: bone, 20M, GSK, rep1

description: Library name: GSK_bone_rep1


title: PB02058-02 MM CD38 8 weeks

description:
Library name: PB02058-02
H5 file contains RNA expression matrix

value: MM CD38 8 weeks


title: bone, 20M, Vehicle, rep3

description: Library name: Veh_bone_rep3


title: bone, 20M, Vehicle, rep2

description: Library name: Veh_bone_rep2


title: PB02046-02 MM CD38 4 weeks

description:
Library name: PB02046-02
H5 file contains RNA expression matrix

value: Blood

value: MM CD38 4 weeks


title: PB01363-02 MM CD38 2 weeks

description:
Library name: PB01363-02
H5 file contains RNA expression matrix

value: PBMC

value: MM CD38 2 weeks


title: PB01362-03 MM CD38 Pre-treatment

description:
Library name: PB01362-03
H5 file contains RNA expression matrix

value: MM CD38 Pre-treatment


title: KO mice, Hemin 38hrs, Liver, mice#4

city: Lexington

first: Jianyao

last: Xue

state: Kentucky

address: 625 S Limestone APT 223

institute: University of Kentucky

description:
Library name: Samples 18
Liver4

data_processing:
(1) Data quality control: filtering reads containing adapter or with low quality; (2) Statistics analysis of data production of quality; (3) Mapping reads to reference genome (STAR); (4) Gene expression quantification (HTseq); (5) Differential expression analysis (DEseq2/edgeR). pair-end reads were 150-base-pair ones, output is 9G. NovaSeq 6000 Illumina platform was used Supplementary files format and content: fpkm Supplementary files format and content: readcount
Assembly: (1) Data quality control: filtering reads containing adapter or with low quality; (2) Statistics analysis of data production of quality; (3) Mapping reads to reference genome (STAR); (4) Gene expression quantification (HTseq); (5) Differential expression analysis (DEseq2/edgeR). pair-end reads were 150-base-pair ones, output is 9G. NovaSeq 6000 Illumina platform was used Supplementary files format and content: fpkm Supplementary files format and content: readcount
Supplementary files format and content: txt format. Gene id, followed by normalized gene counts WT mice n=3, KO mice n=3, log2 fold change, p value, adjusted p value, gene informations.

source_name: Liver

extract_protocol:
Total RNA was isolated by using RNeasy mini kit from Qiagen Total RNA was sent to Novogen for library constructiont, >= 100ng, A260/280 = 1.8-2.2
(1) Data quality control: filtering reads containing adapter or with low quality; (2) Statistics analysis of data production of quality; (3) Mapping reads to reference genome (STAR); (4) Gene expression quantification (HTseq); (5) Differential expression analysis (DEseq2/edgeR). pair-end reads were 150-base-pair ones, output is 9G. NovaSeq 6000 Illumina platform was used Supplementary files format and content: fpkm Supplementary files format and content: readcount

value: Liver

value: AlbCreSR-Bifl/fl

value: Hemin 38hrs


title: PB06443-001 MM Post Transplant 60 Days

description:
Library name: PB06443-001
H5 file contains RNA expression matrix

value: Caucasian

value: MM Post Transplant 60 Days


title: PB06442-001 MM Post Transplant 2 year

description:
Library name: PB06442-001
H5 file contains RNA expression matrix

value: Female

value: MM Post Transplant 2 year


title: WT mice, Hemin 38hrs, Liver, mice#6

description:
Library name: Samples 15
Liver6

value: SR-Bifl/fl


title: PB06440-001 Flu Year 2 Day 90

description:
Library name: PB06440-001
H5 file contains RNA expression matrix

value: Male

value: Flu Year 2 Day 90


title: PB06438-001 MM End Induction 1st Draw

description:
Library name: PB06438-001
H5 file contains RNA expression matrix

value: MM End Induction 1st Draw

value: FALSE


title: WT mice, Hemin 38hrs, Liver, mice#5

description:
Library name: Samples 14
Liver5


title: WT mice, Hemin 38hrs, Liver, mice#1

description:
Library name: Samples 13
Liver1


title: PB06437-002 Flu Year 1 Day 90

description:
Library name: PB06437-002
H5 file contains RNA expression matrix

value: Blood

value: African American

value: Flu Year 1 Day 90


title: KO mice, Hemin 38hrs, Kidney, mice#4

description:
Library name: Samples 12
Kidney4

source_name: Kidney

value: Kidney


title: PB06431-002 Flu Year 1 Day 7

description:
Library name: PB06431-002
H5 file contains RNA expression matrix

value: PBMC

value: Other

value: Flu Year 1 Day 7


title: KO mice, Hemin 38hrs, Kidney, mice#3

description:
Library name: Samples 11
Kidney3

value: AlbCreSR-Bifl/fl

value: Hemin 38hrs


title: PB06429-001 MM Post Induction 2-Cycles

description:
Library name: PB06429-001
H5 file contains RNA expression matrix

value: Caucasian

value: MM Post Induction 2-Cycles


title: PB02048-02 MM CD38 6 weeks

description:
Library name: PB02048-02
H5 file contains RNA expression matrix

value: MM CD38 6 weeks


title: bone, 20M, Vehicle, rep1

description: Library name: Veh_bone_rep1

value: Endosteal/Cortical bone

value: 20 months

value: WT

value: Vehicle (SDSSD@Lipo)


title: KO mice, Hemin 38hrs, Kidney, mice#2

description:
Library name: Samples 10
Kidney2


title: PB05147-001 MM End Induction 1st Draw

description:
Library name: PB05147-001
H5 file contains RNA expression matrix

value: Male

value: MM End Induction 1st Draw

value: FALSE


title: WT mice, Hemin 38hrs, Kidney, mice#6

description:
Library name: Samples 9
Kidney6

value: SR-Bifl/fl


title: PB05138-001 MM Post Transplant 90 Days

description:
Library name: PB05138-001
H5 file contains RNA expression matrix

value: Blood

value: MM Post Transplant 90 Days


title: KO mice, Hemin 38hrs, Liver, mice#3

description:
Library name: Samples 17
Liver3

value: Liver


title: KO mice, Hemin 38hrs, Liver, mice#2

description:
Library name: Samples 16
Liver2


title: WT mice, Hemin 38hrs, Kidney, mice#5

description:
Library name: Samples 8
Kidney5

value: Kidney


title: WT mice, Hemin 38hrs, Kidney, mice#1

description:
Library name: Samples 7
Kidney1


title: PB05130-002 MM Pre-Treatment

description:
Library name: PB05130-002
H5 file contains RNA expression matrix

value: PBMC

value: MM Pre-Treatment


title: PB05133-001 Flu Year 1 Day 0

description:
Library name: PB05133-001
H5 file contains RNA expression matrix

value: Caucasian

value: Flu Year 1 Day 0


title: KO mice, Hemin 38hrs, Lung, mice#4

description:
Library name: Samples 6
Lung4

source_name: Lung

value: Lung

value: AlbCreSR-Bifl/fl

value: Hemin 38hrs


title: PB05128-001 Flu Year 1 Stand-Alone

description:
Library name: PB05128-001
H5 file contains RNA expression matrix

value: African American

value: Flu Year 1 Stand-Alone


title: KO mice, Hemin 38hrs, Lung, mice#3

description:
Library name: Samples 5
Lung3


title: PB05127-001 Flu Year 1 Stand-Alone

description:
Library name: PB05127-001
H5 file contains RNA expression matrix

value: Male


title: KO mice, Hemin 38hrs, Lung, mice#2

description:
Library name: Samples 4
Lung2


title: PB05124-001 MM Post Transplant 60 Days

description:
Library name: PB05124-001
H5 file contains RNA expression matrix

value: MM Post Transplant 60 Days


title: PB02753-002 MM CD38 4 months

description:
Library name: PB02753-002
H5 file contains RNA expression matrix

value: Female

value: Asian

value: MM CD38 4 months

value: FALSE


title: WT mice, Hemin 38hrs, Lung, mice#6

description:
Library name: Samples 3
Lung6

value: SR-Bifl/fl


title: Sarali,R3

value: root

value: Sarali


title: PB02754-002 MM CD38 4 months

description:
Library name: PB02754-002
H5 file contains RNA expression matrix

value: Blood

value: PBMC


title: PB05116-002 MM Post Induction 2-Cycles

description:
Library name: PB05116-002
H5 file contains RNA expression matrix

value: Caucasian

value: MM Post Induction 2-Cycles


title: Sarali,R1


title: WT mice, Hemin 38hrs, Lung, mice#5

description:
Library name: Samples 2
Lung5

value: Lung


title: PB04848-001 MM Post Transplant 2 year

description:
Library name: PB04848-001
H5 file contains RNA expression matrix

value: Other

value: MM Post Transplant 2 year


title: WT mice, Hemin 38hrs, Lung, mice#1

description:
Library name: Samples 1
Lung1

value: Hemin 38hrs


title: PB04847-001 MM End Induction 1st Draw

description:
Library name: PB04847-001
H5 file contains RNA expression matrix

value: Male

value: MM End Induction 1st Draw


title: PB02731-002 MM CD38 6 weeks

description:
Library name: PB02731-002
H5 file contains RNA expression matrix

value: Female

value: MM CD38 6 weeks


title: S34KO_12hr_TGF_4

city: Thiruvananthapuram

first: Karthik

last: Chandiran

state: Kerala

address: 3103, School of Biology, Indian Institute of Science Education and Research - Thiruvananthapuram, Maruthamala P.O., Vithura, Kerala 695551

department: Biology

country: India

institute: IISER-Thiruvananthapuram

description: Library name: Sample-31

data_processing:
Sickle was used to perform quality control and trim the sequences when necessary with a minimum QC score of 25 and basepair length of 45 after trimming
Trimmed sequences were aligned to mm10 genome assembly using Hisat2
Using samtools aligned sequences were sorted and converted to BAM files
Assembly: mm39
Supplementary files format and content: counts

source_name: spleen, lymph node

extract_protocol:
Total RNA was extracted using Rneasy mini plus kit (Qiagen)
RNA libraries for RNAseq were created using Illumina TruSeq Stranded mRNA library preparation kit. Illumina MiSeq Nano v2 Reagent kit for pooling check

value: spleen, lymph node

tag: cell line

value: primary cells

value: CD8 T


title: NiyanWee,R1

value: root

tag: batch rep

value: NiyanWee


title: PB04845-001 MM Post Induction 2-Cycles

description:
Library name: PB04845-001
H5 file contains RNA expression matrix

source_name: Blood

value: Blood

value: African American

value: FALSE