title: B-cells from young, Rps15 wildtype mouse, biological replicate 1 (paired RNA-seq)

description:
Library name: WT1_AGGCAATG_GAACGAAG
Mice aged 3-6 months


title: Myometrium from fibroid patient (MyoF), patient MP348

status: Public on Jun 01 2025

type: genomic

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

country: USA

institute: Michigan State University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Raw idat files were processed into beta values in R  using the openSesame pipeline from Sesame (version  1.23.6). Beta values were then batch corrected using ChAMP (version 2.36.0)
Batch corrected beta values using ChAMP, following initial openSesame pipeline using Sesame.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: myometrium

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using colums from the Qiagen DNEasy Blood and Tissue kit

tag: tissue

value: myometrium

tag: race/ethnicity

value: AA

tag: age

tag: batch


title: Myometrium from fibroid patient (MyoF), patient MP355

value: C


title: Myometrium from fibroid patient (MyoF), patient MP346


title: [DDB_PD_002]_[HMP3397_fast_feed]_[Fed-batch]_[18h]_[R1]

type: SRA

city: Kgs. Lyngby

first: Felix

last: Beulig

address: Kemitorvet 220

country: Denmark

institute: Novo Nordisk Center for Biosustainability

library_source: transcriptomic

data_processing:
First, raw read trimming was performed using Trim Galore with default options, followed by FastQC on the trimmed reads. Next, reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using Bowtie. The read direction was inferred using RSeQC. Read counts were generated using featureCounts. All quality control metrics were compiled using MultiQC. Finally, the expression dataset was reported in units of log-transformed transcripts per million (log(TPM).
Assembly: Reference genome E. coli MG1655 (NC_000913.3)
Supplementary files format and content: Raw data files and comma-delimited text file reporting logtpm values for each sample

molecule: total RNA

organism: Escherichia coli

source_name: Escherichia coli cells

growth_protocol: Batch-to-fed-batch fermentation experiments were performed in 0.25 L Ambr® fermenters (Sartorius) with 2 different media compositions (“High Metal” and “Low Metal” medium)

extract_protocol:
All transcriptome samples were collected and prepared in biological duplicates, whereby either 2 ml of culture (low cell density culture, batch phase) or 0.5 ml of culture (high cell density culture, fed batch phase) was added to 6 ml of Qiagen RNA-protect Bacteria Reagent immediately after sample collection. This solution was then vortexed for 30 seconds, incubated at room temperature for 5 minutes, and then centrifuged. The supernatant was then removed and the cell pellet was stored at -80° C. The RNeasy Mini Kit (Qiagen) was used to extract and purify RNA from the cell pellets per vendor protocol, including on-columns DNase treatment for 30 minutes at room temperature. RNA was quantified using qubit fluorometer (Thermofisher) and integrity was assessed using fragment analyzer (Agilent Technologies).
Ribosomal RNA was removed using QIAseq FastSelect –5S/16S/23S kit (Qiagen). Sequencing libraries were prepared with the KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) and assessed using fragment analyzer (Agilent Technologies). The libraries were then subjected to paired end sequencing on Illumina Nextseq using Nextseq Mid Output kit (Illumina) with a read length of 150 bp.

treatment_protocol: The “Low Metal” batch media contained base medium (22 g L-1 D-(+)-glucose monohydrate, 7.6 g L-1 (NH4)2SO4, 15.7 g L-1 KH2PO4, 0.241 g L-1 MgSO4, 100 mg L-1 thiamine hydrochloride, 0.5 mL L-1 Antifoam 204), and 1 mL L-1 of trace metal solution (0.48 g L-1 CuSO4·5H2O, 0.54 mg L-1 CoCl·7H2O, 0.54 g L-1 ZnSO4·7H2O, 2 g L-1 CaCl2·2H2O, 41.8 g L-1 FeCl3·6H2O, 0.3 g L-1 MnSO4·H2O, 33.4 g L-1 Na2EDTA, 0.5 g L-1 Na2MoO4·2H2O). The “High Metal” batch media contained the same base medium, 3.5 mL L-1 trace metal solution and was additionally supplemented with 1.86 g L-1 citric acid monohydrate and 41.8 mg L-1 FeCl3·6H2O, 21.6 mg L-1 ZnSO4·5H2O). Initial batch fermentations were performed with base medium until complete glucose consumption, marked by a 50% decline in the rate of CO2 formation, triggering an automatic switch to fed-batch operation with continuous supply of the feed medium (550 g L-1 D-(+)-glucose monohydrate, 13.7 g L-1 MgSO4·7H2O)

tag: cell type

value: Escherichia coli cells

tag: strain


title: B-cells from young, Rps15-S138F homozygous mutant mouse, biological replicate 3 (paired RNA-seq)

city: Boston

first: Catherine

middle: J.

last: Wu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: Hom3_AAGTCCTC_GTACCACA
Mice aged 3-6 months

data_processing:
Adapters were removed using fastx_clipper from FASTX-Toolkit (Ribo-seq)
UMIs were removed using umi_tools (Ribo-seq)
Ribosomal RNA and tRNA were removed using Bowtie version 1.0.05 (Ribo-seq)
Transcriptomic alignment with STAR (v2.7.0a) (--alignIntronMin 20 --alignIntronMax 100000 --outFilterMismatchNmax 1 --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --twopassMode Basic)
Ribo-seq reads were further aligned to padded (± 20 nucleotides) canonical protein-coding ORFs using STAR (v2.7.0a) (-alignIntronMin 2 --alignIntronMax 1 --outFilterMismatchNmax ---scoreDelOpen -10000 --scoreInsOpen -10000 1 --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --twopassMode Basic)
RSEM (v1.2.31) was used for transcript and ORF expression quantitation.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited quantitation files show raw RPF or RNA transcript counts

molecule: polyA RNA

organism: Mus musculus

source_name: B-cells

extract_protocol:
Spleens or femurs of mice were mechanically dissociated into a single cell suspension. B-cells were negatively selected using the MACS Mouse B cell Isolation Kit (Miltenyi Biotec, #130-090-862). Total RNA was extracted with Qiagen RNAeasy kits.
200 ng per sample was used as input into an automated variant of the Illumina TruSeq Stranded mRNA Sample Preparation Kit (which preserves strand orientation of the RNA transcript). Oligo dT beads were used to enrich mRNA from the total RNA sample, followed by heat fragmentation and cDNA synthesis. The resultant 400 bp cDNA underwent dual-indexed library preparation, including ‘A’ base addition, adapter ligation using P7 adapters, and PCR enrichment using P5 adapters.

value: B-cells

tag: genotype


title: [DDB_PD_002]_[HMP3397_fast_feed]_[Fed-batch]_[18h]_[R2]


title: Myometrium from fibroid patient (MyoF), patient MP345


title: HNSCC_25_TUMOUR

type: protein

city: Brisbane

first: Arutha

last: Kulasinghe

state: QLD

address: 37 kent st

country: Australia

institute: University of Queensland

scan_protocol: The slides were incubated overnight with primary antibodies, which included module antibodies and morphology markers, excluding the nuclei stain. Following the incubation, post-fixation and nuclei staining were conducted to complete the staining process.

data_processing:
Quality control of the data was conducted based on previously established pipeline for spatial data (standR, Liu et al, Nucleic Acids Research. 2023) using the probe normalised protein (probeQC) counts. Low expressing proteins with less than 5 counts per sample in more than 90% of the samples were removed. Sample QC filters out low expression FOVs based on protein expression depth (> 100,000 per FOW) and nuclei count (> 100 cells per FOV). The filtered data is normalised using the "relative log expression” (RLE) scaling factor method. The normalised/scaled log2-transformed counts per million (logCPM) of the data is provided as inputs.
The "relative log expression” (RLE) normalised log2-transformed counts per million (logCPM) of the the QC filtered data is provided

molecule: protein

source_name: biopsy

label_protocol: FFPE tissue sections were prepared for GeoMX DSP profiling. Briefly, tissue sections were mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C.After baking, the slides underwent deparaffinization, rehydration, and antigen retrieval to prepare the tissue for staining.

extract_protocol: total protein

treatment_protocol: Samples were fixed in formalin and paraffin embedded (FFPE) for GeoMx processing

tag: Sex

value: M

tag: tissue location

value: Pharynx

tag: case

tag: tumor stage

value: UK

tag: deceased

value: Y

tag: tumor stage (general)


title: Myometrium from fibroid patient (MyoF), patient MP359


title: HNSCC_24_TUMOUR

value: early


title: B-cells from young, Rps15-S138F homozygous mutant mouse, biological replicate 1 (paired RNA-seq)

description:
Library name: Hom1_CAACTCCA_GCCTATGT
Mice aged 3-6 months


title: Myometrium from fibroid patient (MyoF), patient MP344


title: HNSCC_24_TME


title: [DDB_PD_002]_[HMP3397_slow_feed]_[Fed-batch]_[7h]_[R2]


title: HNSCC_23_TME


title: B-cells from young, Rps15-S138F heterozygous mutant mouse, biological replicate 3 (paired RNA-seq)

description:
Library name: Het3_ATGCCTAG_ACTGCTTG
Mice aged 3-6 months


title: Myometrium from fibroid patient (MyoF), patient MP342


title: [DDB_PD_002]_[HMP3397_slow_feed]_[Fed-batch]_[7h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient MP332


title: [DDB_PD_002]_[HMP3397_fast_feed]_[Fed-batch]_[3h]_[R1]


title: B-cells from young, Rps15-S138F heterozygous mutant mouse, biological replicate 1  (paired RNA-seq)

description:
Library name: Het1_GTCATCGT_TTGAGCTC
Mice aged 3-6 months


title: HNSCC_25_TME


title: B-cells from young, Rps15-S138F homozygous mutant mouse, biological replicate 4 (paired RNA-seq)

description:
Library name: Hom4_GTCGATTG_TAGTGGTG
Mice aged 3-6 months


title: HNSCC_23_TUMOUR


title: HNSCC_22_TUMOUR


title: [DDB_PD_002]_[HMP3397_fast_feed]_[Fed-batch]_[3h]_[R2]


title: B-cells from young, Rps15 wildtype mouse, biological replicate 3 (age-matched normal)

description:
Library name: CD19-Cre4_ATCACG
Mice aged 18-24 months


title: HNSCC_21_TME

value: N

value: Advanced


title: HNSCC_22_TME


title: [DDB_PD_002]_[HMP3397_slow_feed]_[Batch]_[0h]_[R2]


title: Myometrium from fibroid patient (MyoF), patient MP322

value: A


title: Myometrium from fibroid patient (MyoF), patient MP330


title: [DDB_PD_002]_[HMP3397_fast_feed]_[Batch]_[0h]_[R2]


title: Myometrium from fibroid patient (MyoF), patient MP323


title: HNSCC_21_TUMOUR


title: B-cells from young, Rps15 wildtype mouse, biological replicate 1 (age-matched normal)

description:
Library name: CD19-Cre2_CGATGT
Mice aged 18-24 months


title: B-cells from young, Rps15-S138F heterozygous mutant mouse, biological replicate 2 (paired RNA-seq)

description:
Library name: Het2_TTACCGAC_AGTACACG
Mice aged 3-6 months


title: Myometrium from fibroid patient (MyoF), patient MP321


title: Myometrium from fibroid patient (MyoF), patient MP319


title: B-cells from leukemic, Rps15-S138F heterozygous mutant mouse, biological replicate 2

description:
Library name: RPS15-CLL2_GGCTAC
Mice developed CLL-like disease 18-24 months


title: [DDB_PD_002]_[HMP3427_slow_feed]_[Fed-batch]_[86h]_[R1]


title: HNSCC_20_TUMOUR

value: Lip


title: B-cells from leukemic, Rps15-S138F heterozygous mutant mouse, biological replicate 3

description:
Library name: RPS15-CLL3_ATCACG
Mice developed CLL-like disease 18-24 months


title: HNSCC_19_TME


title: [DDB_PD_002]_[HMP3427_slow_feed]_[Fed-batch]_[53h]_[R2]


title: Myometrium from fibroid patient (MyoF), patient MP317


title: Myometrium from fibroid patient (MyoF), patient MP315


title: B-cells from leukemic, Rps15-S138F heterozygous mutant mouse, biological replicate 1

description:
Library name: RPS15-CLL1_TAGCTT
Mice developed CLL-like disease 18-24 months


title: [DDB_PD_002]_[HMP3427_fast_feed]_[Fed-batch]_[27h]_[R2]


title: B-cells from young, Rps15 wildtype mouse, biological replicate 2 (age-matched normal)

description:
Library name: CD19-Cre3_TGACCA
Mice aged 18-24 months


title: Myometrium from fibroid patient (MyoF), patient MP308


title: B-cells from old, Rps15 wildtype mouse, biological replicate 2

description:
Library name: WT1_S2
Mice aged 20-24 months


title: B-cells from old, Rps15 wildtype mouse, biological replicate 3

description:
Library name: WT1_S3
Mice aged 20-24 months


title: [DDB_PD_002]_[HMP3427_slow_feed]_[Fed-batch]_[53h]_[R1]


title: B-cells from old, Rps15 wildtype mouse, biological replicate 1

description:
Library name: WT1_S1
Mice aged 20-24 months


title: HNSCC_19_TUMOUR


title: HNSCC_18_TME


title: Myometrium from fibroid patient (MyoF), patient MP306

value: H


title: HNSCC_18_TUMOUR


title: B-cells from old, Rps15-S138F heterozygous mutant mouse, biological replicate 3

description:
Library name: Het3_S6
Mice aged 20-24 months


title: [DDB_PD_002]_[HMP3397_slow_feed]_[Batch]_[0h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient MP305


title: HNSCC_17_TME


title: B-cells from old, Rps15-S138F heterozygous mutant mouse, biological replicate 2

description:
Library name: Het2_S5
Mice aged 20-24 months


title: HNSCC_17_TUMOUR


title: Myometrium from fibroid patient (MyoF), patient MP162


title: Myometrium from fibroid patient (MyoF), patient MP313


title: B-cells from old, Rps15-S138F heterozygous mutant mouse, biological replicate 1

description:
Library name: Het1_S4
Mice aged 20-24 months


title: HNSCC_20_TME


title: B-cells from young, Rps15-S138F heterozygous mutant mouse, biological replicate 2

description:
Library name: GTGAAA_Het2
Mice aged 3-6 months


title: [DDB_PD_002]_[HMP3427_slow_feed]_[Fed-batch]_[7h]_[R1]


title: HNSCC_16_TUMOUR


title: [DDB_PD_002]_[HMP3427_fast_feed]_[Fed-batch]_[3h]_[R2]


title: 18881, Kidney, Healthy control, untreated

city: Oxford

first: Maria

last: Dermit

state: Oxfordshire

country: United Kingdom

institute: Novo nordisk research centre oxford

data_processing:
STAR v.2.7.0f
GRCm38 Mus musculus genome
96 Ensembl reference transcriptome
Assembly: 96 Ensembl reference transcriptome
Supplementary files format and content: text file with gene-level count values for each sample

source_name: Kidney

extract_protocol:
RNA was isolated using the NucleoSpin® kit (MACHEREY-NAGEL) and cDNA library was generated using a total of 10 ng-1 µg purified RNA from each sample using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
cDNA libraries were sequenced on a  using NextSeq 500/550 High Output Kit V2 (Illumina).

value: Kidney

tag: condition

value: Healthy control

tag: treatment

value: untreated


title: Myometrium from fibroid patient (MyoF), patient MP100

value: myometrium


title: 18880, Kidney, Healthy control, untreated


title: Myometrium from fibroid-free patient (MyoN), patient MP502

value: C


title: [DDB_PD_002]_[HMP3427_fast_feed]_[Fed-batch]_[18h]_[R2]

value: Escherichia coli cells


title: 18879, Kidney, Healthy control, untreated


title: Myometrium from fibroid-free patient (MyoN), patient MP516


title: HNSCC_15_TME


title: 18878, Kidney, Healthy control, untreated


title: [DDB_PD_002]_[HMP3427_fast_feed]_[Fed-batch]_[18h]_[R1]


title: [DDB_PD_002]_[HMP3427_fast_feed]_[Batch]_[0h]_[R1]


title: HNSCC_14_TME


title: Myometrium from fibroid-free patient (MyoN), patient MP497


title: Myometrium from fibroid-free patient (MyoN), patient MP499


title: [DDB_PD_002]_[HMP3427_slow_feed]_[Batch]_[0h]_[R1]


title: [DDB_PD_002]_[HMP3427_slow_feed]_[Batch]_[0h]_[R2]


title: HNSCC_16_TME


title: [DDB_PD_002]_[HMP3427_slow_feed]_[Fed-batch]_[86h]_[R2]


title: 18876, Kidney, MASH, Treatment 0194-0499

value: MASH

value: Treatment 0194-0499


title: HNSCC_13_TME

value: M


title: Myometrium from fibroid-free patient (MyoN), patient MP496


title: [DDB_PD_001]_[HMP3396]_[Fed-batch]_[72h]_[R2]


title: HNSCC_15_TUMOUR

value: UK


title: HNSCC_13_TUMOUR


title: 18875, Kidney, MASH, Treatment 0194-0499


title: [DDB_PD_001]_[HMP3396]_[Fed-batch]_[72h]_[R1]


title: Myometrium from fibroid-free patient (MyoN), patient MP495


title: HNSCC_12_TME


title: 18874, Kidney, MASH, Treatment 0194-0499


title: Myometrium from fibroid-free patient (MyoN), patient MP490


title: HNSCC_14_TUMOUR


title: HNSCC_12_TUMOUR


title: 18873, Kidney, MASH, Treatment 0194-0499


title: 18877, Kidney, MASH, Treatment 0194-0499


title: Myometrium from fibroid-free patient (MyoN), patient MP485

value: AA


title: [DDB_PD_002]_[HMP3427_fast_feed]_[Batch]_[0h]_[R2]


title: [DDB_PD_001]_[HMP3396]_[Batch]_[5h]_[R3]


title: 18872, Kidney, MASH, Treatment 0194-0499


title: Myometrium from fibroid-free patient (MyoN), patient MP500


title: HNSCC_11_TUMOUR

value: F

value: early


title: [DDB_PD_001]_[HMP3396]_[Batch]_[5h]_[R2]


title: Myometrium from fibroid-free patient (MyoN), patient MP479


title: 18870, Kidney, MASH, Treatment 0194-0499


title: [DDB_PD_001]_[HMP3396]_[Batch]_[5h]_[R1]


title: 18868, Kidney, MASH, Vehicle

value: Vehicle


title: Myometrium from fibroid-free patient (MyoN), patient MP473


title: Myometrium from fibroid-free patient (MyoN), patient MP478


title: HNSCC_10_TUMOUR


title: HNSCC_11_TME


title: [DDB_PD_001]_[HMP3396]_[Fed-batch]_[16h]_[R2]


title: Myometrium from fibroid-free patient (MyoN), patient MP484


title: 18867, Kidney, MASH, Vehicle


title: HNSCC_9_TUMOUR


title: 18866, Kidney, MASH, Vehicle


title: Myometrium from fibroid-free patient (MyoN), patient MP472


title: [DDB_PD_001]_[HMP3397]_[Fed-batch]_[72h]_[R2]


title: [DDB_PD_001]_[HMP3397]_[Fed-batch]_[72h]_[R1]


title: 18871, Kidney, MASH, Treatment 0194-0499


title: 18864, Kidney, MASH, Vehicle


title: [DDB_PD_002]_[HMP3427_fast_feed]_[Fed-batch]_[27h]_[R1]


title: HNSCC_9_TME


title: [DDB_PD_001]_[HMP3396]_[Fed-batch]_[16h]_[R1]


title: [DDB_PD_001]_[HMP3397]_[Fed-batch]_[16h]_[R2]


title: HNSCC_8_TME


title: HNSCC_10_TME


title: Myometrium from fibroid-free patient (MyoN), patient MP459


title: Myometrium from fibroid-free patient (MyoN), patient MP450


title: 18865, Kidney, MASH, Vehicle


title: 18863, Kidney, MASH, Vehicle


title: Myometrium from fibroid-free patient (MyoN), patient MP451


title: HNSCC_7_TME


title: Myometrium from fibroid-free patient (MyoN), patient MP408


title: Myometrium from fibroid-free patient (MyoN), patient MP452


title: HNSCC_7_TUMOUR


title: [DDB_PD_001]_[HMP3397]_[Batch]_[5h]_[R2]


title: HNSCC_6_TME

value: N


title: [DDB_PD_001]_[HMP3397]_[Batch]_[5h]_[R1]


title: [DDB_PD_001]_[HMP3397]_[Fed-batch]_[16h]_[R1]


title: 18862, Kidney, MASH, Vehicle


title: [DDB_PD_001]_[HMP3427]_[Fed-batch]_[72h]_[R2]


title: HNSCC_8_TUMOUR

value: Lip


title: [DDB_PD_001]_[HMP3427]_[Fed-batch]_[72h]_[R1]


title: ABX 5-FU [J701_AHJFM7BGX2_TAGGCATG-TCTTACGC_DZ-12]

city: Bronx

first: Dachuan

last: Zhang

state: NY

address: 1301 Morris Park Avenue, Price Center 113

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Sequencing reads were aligned to the mouse genome (mm10) using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a).
Aligned reads were then quantified to transcriptome (mm10; Ensembl Transcripts release 83) and normalized.
Differentially expressed genes were identified using Partek Flow.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each sample; fold change and p value for comparisons

source_name: HSC_ABX 5-FU

extract_protocol:
Total RNA from 2000 sorted HSCs was extracted using the RNeasy Plus Micro Kit (Qiagen) and assessed for quality using Aligent 2100 Bioanalyzer (Agilent Technologies).
Complementary DNA libraries were generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) and the Nextera XT DNA Sample preparation Kit (Illumina).

treatment_protocol: Mice were treated with broad-spectrum antibiotics (ampicillin, neomycin, metronidazole and vancomycin, ABX) in drinking water for 4-6 weeks, and then challenged with 5-fluorouracil (5-FU, 200mg/kg i.v.). Mice were analyzed under steady state, or at Day 12 following 5-FU challenge.

value: bone marrow

value: ABX

value: Hematopoietic stem cells (HSCs)


title: Myometrium from fibroid-free patient (MyoN), patient MP407


title: ABX 5-FU [J701_AHJFM7BGX2_GGACTCCT-AGAGGATA_DZ-11]


title: HNSCC_6_TUMOUR


title: HNSCC_5_TME


title: ABX 5-FU [J701_AHJFM7BGX2_TCCTGAGC-ATAGAGAG_DZ-10]


title: Myometrium from fibroid-free patient (MyoN), patient MP399


title: Myometrium from fibroid-free patient (MyoN), patient MP398


title: Myometrium from fibroid-free patient (MyoN), patient MP402


title: HNSCC_4_TME


title: HNSCC_5_TUMOUR


title: [DDB_PD_001]_[HMP3427]_[Batch]_[5h]_[R2]


title: Myometrium from fibroid-free patient (MyoN), patient MP397


title: ABX [J701_AHJFM7BGX2_CGTACTAG-TCTACTCT_DZ-08]

value: control


title: ABX [J701_AHJFM7BGX2_AGGCAGAA-TCTTACGC_DZ-09]


title: ABX [J701_AHJFM7BGX2_TAAGGCGA-TCTACTCT_DZ-07]


title: HNSCC_3_TME

value: Y


title: Myometrium from fibroid-free patient (MyoN), patient MP365

value: myometrium

value: C


title: Myometrium from fibroid-free patient (MyoN), patient MP363


title: Ctrl 5-FU [J701_AHJFM7BGX2_TAGGCATG-AGAGGATA_DZ-06]

source_name: HSC_Ctrl 5-FU


title: [DDB_PD_001]_[HMP3427]_[Batch]_[5h]_[R3]

value: Escherichia coli cells


title: HNSCC_4_TUMOUR


title: HNSCC_3_TUMOUR


title: Ec78_RepreRad_rep2

city: Shinjuku-ku

first: Aa

middle: Haeruman

last: Azam

state: Tokyo

address: Toyama 1-23-1

department: Research Center for Therapeutic Drugs and Vaccines Development

country: Japan

institute: The National Institute of Infectious Diseases

data_processing:
Sequencing quality was examined by FastQC v0.12.1 software
3' adapter was trimmed from raw reads by Trimmomatic v0.39
Trimmed reads were aligned to the genomic DNA of E. coli DH10B, plasmid pBAD-Ec78 (pLG008-plasmid), and plasmid pATc-Rad (pKLC83-orf75 (Rad)) using Bowtie 2 v2.5.3
Read counts were determined using featureCounts v2.0.6, and normalization along with detection of differentially expressed genes (DEGs) and RNas was carried out using TCC-GUI
Assembly: Genome of E.coliDH10B, plasmid pBAD-Ec78, plasmid pATc-Rad
Supplementary files format and content: unique read count file (XLSX format)

growth_protocol: The E.coliDH10B cells containing plasmid inducible retron (pBAD-Ec78) or negative control (pKLC23) and pKL83-Rad or the negative control (pKLC83) were diluted 1:100 in 10mL LB medium supplemented with antibiotics (20μg/mL chloramphenicol and 100μg/mL ampicillin).

extract_protocol:
After induction, bacteria were grown to an OD600of 1. Total RNA was extracted from cells using a miRNA isolation kit (QIAGEN, Catalog number #217004) according to the manufacturer’s recommendation.
RNA sequencing was performed utilizing Transcriptome Sequencing of the Macrogen Japan NGS service on the Novaseq6000 platform. The TruSeq Stranded Total RNA Library kit (for bacteria) (Illumina, San Diego, USA) was utilized subsequent to the removal of rRNA from the sample. The read length was 100 base pairs, and the sequencing run scale was set at 4 gigabytes per sample.

treatment_protocol: After 30min of growth at 37 °C with shaking at 250 rpm, expression of the retron and Rad were induced with 0.2%arabinose(final concentration) and 50 ng/mL ATc (final concentration), respectively.

value: early stationary (OD600 = 1)

value: treated with 0.2% arabinoese and 50 ng/ml Atc


title: Ec78_RepreRad_rep3


title: Ctrl 5-FU [J701_AHJFM7BGX2_TCCTGAGC-TCTACTCT_DZ-04]


title: [DDB_PD_001]_[HMP3427]_[Fed-batch]_[16h]_[R1]


title: Myometrium from fibroid-free patient (MyoN), patient MP361


title: HNSCC_2_TME

value: M

value: UK


title: Ec78_RepreRad_rep1


title: [DDB_PD_001]_[HMP3427]_[Batch]_[5h]_[R1]


title: HNSCC_2_TUMOUR


title: Ec78_InducRad_rep3


title: Myometrium from fibroid-free patient (MyoN), patient MP358


title: Ctrl 5-FU [J701_AHJFM7BGX2_GGACTCCT-TCTTACGC_DZ-05]


title: Myometrium from fibroid-free patient (MyoN), patient MP356


title: HNSCC_1_TUMOUR


title: Ctrl [J701_AHJFM7BGX2_TAAGGCGA-TCTTACGC_DZ-01]


title: Myometrium from fibroid-free patient (MyoN), patient MP362


title: MM337-M8-Vehicle

status: Public on May 27 2025

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
Gene expression estimates were computed as Transcript Per Million (TPM) values from paired-end FASTQ files using the software Kallisto in AltAnalyze version 2.1.0, using the human Ensembl version 72 transcriptome reference.
Assembly: hg19
Supplementary files format and content: TPM Expression values (tab delimited text file)

source_name: Skin

extract_protocol:
500 ng of total RNA was purified from tumor biopsies using Qiagen Rneasy Kit according to the manufacturer’s instructions.
The RNA-Seq libraries were prepared from the purified RNA by using TruSeq RNA Library Prep Kit v2 (Illumina) for gene expression analyses.
Paired-end RNA-Seq was performed with HiSeq (Illumina). An average of ~40 million paired-end reads.

value: Skin

value: Melanoma


title: MM-337-M2-Cobimetinib + Regorafenib

value: Cobimetinib + Regorafenib


title: MM505-M2-Vehicle

value: Vehicle


title: Spider early germ-band, snRNA-seq

status: Public on May 31 2025

city: Takatsuki

first: Yasuko

last: Akiyama-Oda

state: Osaka

address: Murasaki-cho 1-1

institute: JT Biohistory Research Hall

description:
Library name: Sample2
BD Rhapsody

library_source: transcriptomic single cell

data_processing:
We used BD Rhapsody WTA analysis pipeline on the Seven Bridges Genomics cloud platform.
After quality filter of read pairs, the cell barcode and the unique molecular index (UMI) were identified from R1 reads, and R2 reads were aligned to the STAR index created form the Paratsteatoda genome reference using STAR-2.5.2b. For the nucleus data, a modified gtf file was utilized to enable the counting of reads mapped to both introns and exons.
Following a UMI error correction step, a cell/gene count matrix, the final output of the pipeline,  was obtained.
Using the Seurat package (v.4.1.1), the count matrix was filtered by the number of unique genes and the total number of RNA molecules.
The count matrix was log-normalized.
Assembly: GCF_000365465.3_Ptep_3.0
Supplementary files format and content: Comma-separated text files that include the count matrix of the pipeline output.
Supplementary files format and content: Tab-separated text files that include the filtered count matrix.
Supplementary files format and content: Tab-separated text files that include the log-normalized count matrix.

organism: Parasteatoda tepidariorum

source_name: 20 whole embryos

growth_protocol: Embryos were incubated at 25 ˚C until they reached the appropriate stages.

extract_protocol:
Spider embryos were dechorionated with 100% commercial bleach, rinsed with distilled water, and transferred into CGBS-CMF (55 mM NaCl, 40 mM KCl, 10 mM Tricine, pH6.95) containing 0.01% BSA (for cells) or 0.5% BSA (for nuclei). The vitelline membrane was then manually removed with forceps. For cell dissociation, the devitellinized embryos were incubated in CGBS-CMF containing 1 mg/mL erastase for 5 minutes at room temperature. Subsequently, the cell suspension was filtered through 70-mm and 10-mm cell strainers (pluriStrainer-Mini) and collected in a 1.5-mL DNA LoBind Tube (Eppendorf). Finally, BSA was added to a final concentration of 1%. For nuclei isolation, the devitellinized embryos were centrifuged in a 1.5-mL LoBind tube (Eppendorf) and resuspended in 400 mL homogenization buffer (250 mM Sucrose, 10 mM Tris (pH 8.0), 25 mM KCl, 5 mM MgCl2, 0.1% Triton-X100, 0.1 mM DTT, 100 u/mL RNase Inhibitor (SUPERaseIn RNase Inhibitor: Invitrogen, AM2694), Protease Inhibitor at 1:100 dilution (Nacalai tesque, 25955-11)). The sample was then homogenized with a loose plastic pestle (fisher scientific) by 40 strokes. The nucleus sample was subsequently centrifuged and resuspended with CGBS-CMF-0.5% BSA-100 u/mL RNase Inhibitor solution, followed by filtration through the 40-mm cell strainer. This centrifugation and resuspension steps were repeated twice. Finally, 4 volumes of CellCover (Anacyte Laboratories) were added to both the cell and nucleus samples, which were then stored at 4 ˚C until further use.
The stored cells or nuclei were centrifuged and resuspended with the CGBS-CMF-based solution, and they were individualized using BD Rhapsody microwell-based platform, followed by library construction according to the manufacture’s instructions. Construction of the single-nucleus RNA-seq library was performed with some modifications; RNase Inhibitor was added to the Sample buffer, and Proteinase K was added to the Lysis buffer, and the lysis step was prolonged from 2 minutes to 5 minutes.

value: 20 whole embryos

value: all extracted nuclei

value: WT


title: Spider early germ-band, scRNA-seq

description:
Library name: Sample1
BD Rhapsody

source_name: 15 whole embryos

value: 15 whole embryos

value: all dissociated cells


title: Sorted T-cells from PBMC, Parse v2 VDJ/TCR, sample F5

city: Seattle

first: Anna

last: Elz

state: WA

address: 1201 Eastlake Ave E

institute: Fred Hutchinson Cancer Center

description:
Library name: parse_v2_tcr_F5
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data

data_processing:
Sequencing Depth and Downsampling: Sample sequencing was conducted to achieve a depth exceeding 25,000 reads per cell for WT libraries except for FLEX which targeted 10,000 reads per cell.  TCR libraries all targeted for 5000 reads per cell. When sequencing surpassed the targets, FASTQs were downsampled to 25,000 reads per cell for the WT libraries and 5000 reads per cells for TCR libraries using seqtk version 1.3 with random seed 100 (Li, 2012).
Generating count matrices: The software provided by each kit vendor was utilized to generate UMI count matrices from the downsampled FASTQs. Pipelines were run with default parameters unless otherwise specified. For the 10x kits, CellRanger version 8.0.0 with the multi subcommand was employed with the reference version refdata-gex-GRCh38-2024-A. Parse data was processed with splitpipe v1.2.1 using parse’s hg38_V1.1.3 reference. Fluent data was processed with PIPseeker version 3.3.0 with reference gex-reference-GRCh38-2022.04. For each sample, PIPseeker generates 5 outputs of varying sensitivity for calling cells from background. We selected the sensitivity levels on a per-sample basis informed by the knee plots and vendor guidelines. Scale data was processed through scaleRNA version 1.5 with default parameters, library structure version 1.1 and the prebuilt GRCH38 reference genome provided by Scale. FASTQs were generated at the library level by passing raw BCL folders into the first scaleRNA run. We then ran Scale’s bc_parser (distributed with the nextflow pipeline) with the `--demux` flag and options to output 2 read files and 2 index files for each sample. These were downsampled and ran with default parameters to produce the filtered expression matrix.
Assembly: GRCh38
Supplementary files format and content: The first set of processed files are pipeline outputs from downsampled data. For WT/GEX libraries, processed files include files needed to construct the counts matrix. Either h5 files, or matrix + barcode + feature files. For VDJ/TCR libraries, the processed data files have the final clone assemblies.
Supplementary files format and content: The second set of processed files are the Seurat RDS files for each kit, with all samples for that kit merged. The datasets were processed to remove low quality cells and low-abundance genes. Data was clustered at the kit level and annotated manually using reference mapping and key gene expression. See the manuscript for full details.

source_name: PBMC

extract_protocol:
Benchmark I:  3’ Whole transcriptome comparison Multiple donor leukopak frozen aliquots were purchased from Bloodworks Northwest.  PBMCs from two healthy donors F1 and F5, stored in liquid nitrogen were thawed at 37 degrees C., transferred into 10ml prewarmed thawing media (Gibco RPMI 1640 + 10% FBS) and centrifuged at 500 x g for 5 minutes at 4 degrees. Cells were washed in 10ml cold 1XPBS -MgCl and -CaCl (Gibco), followed by subsequent centrifugation at 500 x g for 5 minutes and the pellet resuspended in 10ml 1X PBS.  The CellacaMX (Revvity) live-dead assay was used to count AOPI stained cells. Viability was 83% and 88% respectively.  Each cell suspension was aliquoted for use in the 10X Genomics GEM-X and NextGEM assays in which the cell suspensions were loaded in replicate, with a targeted recovery of 20,000 and 10,000 cells, respectively.  The remaining cell suspensions were aliquoted out in technical replicates of 1 million cells and fixed using Parse’s Cell Fixation v3 User Manual (UM0027 v1.1), Fluent’s Demonstrated Protocol DSP-Methanol Fixation for Cells (FB0004708), and 10x Demonstrated Protocol Fixation of Cells and Nuclei for Chromium Fixed RNA Profiling (FLEX) (CG000478 Rev C). Separate aliquots of F1 and F5 donors were processed as above except with PBS 1% BSA for the final resuspension.  One set was fixed in technical replicates of 1 million cells following the Scale’s standard fixation kit protocol Rev. B.  The second set of aliquots was processed as above with PBS + 0.04% BSA and Promega RNase Inhibitor resuspension and no fixation for Fluent’s PIPseq V.  Benchmark II:  5’ WT, TCR single cell comparison Frozen PBMCs from four healthy donors (F1, F2, F4, and F5) of mixed sex (3 males, 1 female) and ethnicity (3 persons of Caucasian descent and 1 person of Asian descent) supplied by Bloodworks Northwest were processed in two batches one week apart (F1, F2 followed by F4, F5). Cells were thawed in a 37°C water bath before transfer to thawing media (Gibco RPMI 1640 + 10% FBS). Samples were then centrifuged at 400 x g for 10 minutes at 4°C. The supernatant was decanted, and the pellet resuspended in 10 mL of sorting media (cold Gibco 1X PBS + 1% BSA), followed by an additional centrifugation at 400 x g for 10 minutes. Each sample was next resuspended in 200 µL of stain media. Cells were stained to enrich for T-cells and to remove as many B-cells as possible. We stained the samples with human CD3, CD45, and CD19 (citation for antibodies). 7AAD was used to assess the in-flight viability of the cells during the sort. We sorted T cells using the Becton-Dickenson Symphony S6 cytometer. The final population was CD3+, CD45+, and CD19-. An aliquot of the sorted T-cells was stained with AOPI and assessed for viability and cell counts using the Nexcelom CellacaMX (Revvity).  Viabilities ranged from 88-90 % (F1 and F2) and 83-87% (F4 and F5).  An aliquot of the of each donor T-cells was utilized for 10x Genomics GEM-X 5′ v3 (CG000733 RevA) and NextGEM 5′ v2 (CG000331 RevE) assays, in which 20,000 and 10,000 cells were targeted for recovery, respectively. The remaining cell suspension, ~1.5 million cells, was fixed following Parse Evercode Cell Fixation v2 (UM0039 v2.3). Cells were frozen and later processed as directed by Evercode TCR Human WT + TCR v1 (UM0018).
Benchmark I:  3’ Whole transcriptome comparison 10x Genomics FLEX Fixed RNA profiling Per the 10x Genomics CG000527 Rev E protocol, fixed cells were incubated overnight with mRNA transcript probes targeting ~18K genes, with the left handle containing a sample specific barcode. Following probe hybridization, samples were counted and pooled equally before a series of washes to remove unbound probes.  After counting the pool, a volume targeting a recovery of 40,000 cells was combined with a master mix that contains enzymes that ligate and extend the probes during GEM incubation. This mixture was then loaded into the NEXT GEM Chip Q with gel beads and partitioning oil. Following microfluidic GEM generation on the ChromiumX, the GEMs were recovered and amplified to generate product to put into library preparation.  A portion of the amplified material was re-amplified with library specific P5 and P7 indices. 10x Genomics GEM-X 3’v4 and NextGEM v3.1 Following the 10X Genomics GEM-X 3’v4 (CG000731) and NextGEM v3.1 (CG000315) protocols, PBMCs from donor F1 and donor F5 were combined with a reverse transcript mastermix and loaded on to a microfluidic chip (Chromium GEM-X 3’ chip and NextGEM Chip G) along with partitioning oil and barcoded gel beads. Cells were partitioned into droplets containing gel beads using the ChromiumX instrument and subsequently underwent reverse transcription. The cDNA was recovered, cleaned, and amplified to create enough material for library preparation. To generate gene expression libraries, a portion of cDNA was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final amplification. Fluent Biosciences PIPseq v.4 Fixed cells were partitioned, and libraries generated using the PIPseq T20 3’ Single Cell RNA Kit v4.0PLUS User Guide (FB0002130 Rev 8.3). To target a recovery of 20,000 cells per sample, 8uls of a cell suspension at a concentration of approximately 5000 cells/ul were captured in emulsion with Particle-templated Instant Partitions (PIPs), followed by cell lysis and barcoding unique to each PIP. The emulsions were then broken, and the mRNA reverse transcribed to generate cDNA. cDNA was then amplified, isolated from the PIPs, fragmented, end repaired and A-tailed, adapter ligated, and indexed with unique P7 and P5 indices.  Fluent Biosciences PIPseq V Sample replicates of live cells (40,000 each) were loaded into PIPs for capture and barcoding as described in PIPseq V T20 3’ Single Cell RNA kit User Guide (FB0005261). To target a recovery of 20,000 cells per sample, 8ul of 5000 cells/ul were captured in emulsion with Particle-templated Instant Partitions (PIPs), followed by cell lysis and barcoding unique to each PIP. The emulsions were then broken, and the mRNA reverse transcribed to generate cDNA. cDNA was then amplified, isolated from the PIPs, fragmented, end repaired and A-tailed, adapter ligated, and indexed with unique P7 and P5 indices. Parse Evercode v3 Following the Parse protocol UMWT3300, fixed and permeabilized PBMCs were thawed, and counted using trypan blue and a hemocytometer, diluted and added to 12 wells per replicate of Plate 1 as directed by the sample loading table (48 wells total across all replicates). Following reverse transcription, cells were pooled and split an additional two times, the last of which added a barcode containing R2 and Biotin for magnetic bead enrichment Cells were pooled again, counted, and distributed into eight sublibraries each targeting under 12,500 cells where they were lysed and the biotin labelled cDNA recovered with binder beads. cDNA bound to the binder beads was washed and incubated with a template switch oligo to add a 5’ adapter to the cDNA. The cDNA was amplified and bead cleaned. A portion of this cleaned product was fragmented, adapter ligated and had p5 and p7 indices added in a final PCR. Scale Biosciences Following the Scale 1020796 Rev A protocol, fixed cells at a concentration of approximately 2000 cells/ul were added to 96 wells of barcode plate 1 and well IDs documented to map back cells to their sample of origin. The cells underwent reverse transcription and were then pooled by centrifugation into a funnel. Cells were washed and then split across a 384 well ligation plate where cells were barcoded. Cells were again pooled by centrifugation, washed, and counted to assess for recovery. The cell stock was diluted to approximately 460 cells/ul and 4uls loaded into each well of the final distribution plate, with the remainder saved at -80 degrees. In the final distribution plate, the cell membrane is broken down, cDNA is tagmented with a transposase, and the library specific P5 and P7 indexes added.  Benchmark II:  5’ WT, TCR single cell comparison 10X Genomics GEM-X 5’v3 and Next GEM 5’v2 Following the 10X Genomics GEM-X 5’v3 (CG000733) and NextGEM 5’v2 (CG000331) protocols, sorted T cells were added to a reverse transcription mastermix and loaded on to a microfluidic chip (Chromium GEM-X 5’ chip and NextGEM Chip K respectively) with partitioning oil and barcoded gel beads. Cells were partitioned into droplets containing gel beads (GEMS) and subsequently underwent reverse transcription.  The cDNA was recovered and cleaned before being amplified to create enough material for library preparation for gene expression and TCR. To generate TCR libraries, a small amount of cDNA underwent 2 rounds of PCR with a set of TCR specific primers. A portion of the PCR product was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final PCR. To generate gene expression libraries, a portion of cDNA was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final PCR.  Parse Evercode TCR Fixed and permeabilized T cells were thawed, counted using trpyan blue and a hemocytometer, following Parse protocol UMIT2300.  Each sample was diluted according to the sample loading table and recounted before dispensing into 12 wells per sample of Plate 1 (48 wells total). Following reverse transcription, cells were pooled and split an additional two times to add barcodes, the last pool and split also adding the R2 and biotin. Cells were pooled, counted, and distributed into eight sublibraries each targeting 12,500 cells. Cells were lysed and biotin labelled cDNA recovered with binder beads.  cDNA bound to the binder beads was washed and incubated with a template switch oligo to add a 5’ adapter to the cDNA. The cDNA was amplified and bead cleaned to be usable in TCR and whole transcriptome library preparation. Whole transcription libraries undergo library preparation as described in Evercode TCR Human WT + TCR v1 (UM0018), which utilized the Parse v2 WT chemistry. The TCR library is generated from a subset of the WT cDNA in a PCR reaction targeting the V(D)J segments of the CDR3 region of the T cell.

value: PBMC

value: Sorted T-cells

value: Parse Evercode v.2 TCR


title: Sorted T-cells from PBMC, Parse v2 GEX/WT, sample F2

description:
Library name: parse_v2_gex_F2
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data


title: Ctrl [J701_AHJFM7BGX2_AGGCAGAA-AGAGGATA_DZ-03]

value: bone marrow

value: control

value: Hematopoietic stem cells (HSCs)


title: Ec78_InducRad_rep2

value: early stationary (OD600 = 1)

value: treated with 0.2% arabinoese and 50 ng/ml Atc


title: MM505-M8-Cobimetinib + Regorafenib

value: Skin


title: Ctrl [J701_AHJFM7BGX2_CGTACTAG-ATAGAGAG_DZ-02]


title: HNSCC_1_TME

value: M

value: Lip

value: UK

value: early


title: Sorted T-cells from PBMC, Parse v2 GEX/WT, sample F1

description:
Library name: parse_v2_gex_F1
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data


title: NTHi_apf_5, 5 hours growth

city: Baltimore

first: Adonis

last: D'Mello

state: Maryland

address: Health Science Facility III, 670 W Baltimore St 3rd floor

institute: IGS- University of Maryland Baltimore

description:
Library name: hFlu_sup_371_206_S2_L001
NTHi_raw_counts.txt

data_processing:
FASTQ files were mapped to their respective genomes using HISAT for Homo sapiens and Bowtie2 for nontypeable NTHi 48P106H1 and Mcat 48P118B genomes (Accession numbers NTHi: CP020006, Mcat: CP158365).
Gene expression counts for all samples were estimated using HTseq
Supplementary files format and content: All files are tab-delimited raw HTSeq counts of gene expression for each species, Homo sapiens, Nontypable Haemophilus influenzae & Moraxella catarrhalis.
Assembly: GRCh38

organism: Haemophilus influenzae

source_name: Nontypeable Haemophilus influenzae

growth_protocol: Two days prior to the assay, NCI-H292 cells were grown to confluence in culture media, which contained RPMI 1640 medium (ATCC modification) and 10% heat inactivated fetal bovine serum (FBS). After 24 hours and when cells reached confluence, the culture media was replaced with base media (i.e., (RPMI 1640 medium) and no FBS. Low passage bacterial strains were grown on chocolate agar II plates and incubated overnight at 37C with 5% CO2. On the day of the assay, liquid bacteria cultures were started from a fresh overnight plate at OD600 ~0.1 and grown at 37C to OD600 ~0.4 to 0.5. NTHi was cultured in brain heart infusion (BHI) + 5% Fildes and Mcat was grown in -BHI broth. Bacteria were placed on ice, 6 ml of bacteria were centrifuged at 3,220 x g for 5 min, the pellet was washed with 6 mL D-PBS, pelleted again and suspended in in six mL base media (RPMI 1640).

extract_protocol:
RNA was extracted using a pre-lysis step, the Maxwell 16 LEV simplyRNA Tissue Kit (Cat# AS1280), and the Maxwell 16 Instrument (Promega) according to the manufacturer’s instructions. Briefly, the bacteria pellet was thawed and suspended in 200µL PBS with mutanolysin and proteinase K and incubated for 25 minutes at 37C.  We added 400µL homogenization solution containing 1-thioglycerol, vortexed the sample, put it on ice and added 400µL lysis buffer. Samples were vortexed and transferred to the maxwell LEV cartridge. After extraction, we added an extra DNAse treatment of the RNA with RNase-Free DNase (Qiagen #79254). RNA was purified using the Qiagen RNeasy Mini Elute Clean-up kit according to the manufacturer’s instructions. 1µg of purified RNA was sent to the Yale Center for Genome Analysis (YCGA) for sequencing.
The Kapa Biosystems rRNA depletion kit was used for ribosomal RNA reduction and samples were sequenced on the Illumina NovaSeq 6000 instrument using a 100bp paired-end read protocol and multiplexed with a target of 10 million reads per sample for bacteria supernatant experiments, 5 million reads for bacteria culture, 75 million reads for H292 cells, and 150M reads per sample for bacteria/cell line culture experiments.

treatment_protocol: For the media alone assays (wo), we added 4mL of base media into new TC flasks with 2mL washed bacteria (2ml of NTHi or 2ml Mcat or 1mL each for the mix). The flasks were incubated for 5 hours at 37ºC. For the in vitro cell culture assays, the base media was removed from the flasks containing confluent H292 cells and replaced with 4 mL fresh base media per flask, two mL of bacteria were added per flask, the samples were mixed by gentle pipetting and the flasks incubated for 5 hours at 37C with 5% CO2. The NTHi and Mcat supernatant flasks were prepared in a similar manner with minor modifications. Two mLs of Mcat were added to confluent H292 cells, after a 5-hour incubation at 37C with 5% CO2, the Mcat supernatant was removed and filtered through a 0.22µm syringe filter and kept on ice. For the assay, 1.5 mL of Mcat supernatant was added with 0.5 mL of 2X concentrated NTHi and the flasks were incubated for 5 hours at 37C with 5% CO2. Flasks containing infected H292 cells were fractioned into “apical fluid” (apf), containing free floating non-adhered/non-invaded bacteria, and adhered/invaded bacteria on or within H292 cells (cell). The fractions were transferred to RNAprotect (Qiagen, Valencia, CA). Samples were vortexed for 5 seconds, incubated for five minutes at room temperature and then centrifuged for 10 min at 5000 x g and 4°C. The supernatant was discarded, and the pellet frozen at -80°C until RNA extraction.

value: Nontypeable Haemophilus influenzae


title: NTHi_wo_1, 5 hours growth

description:
Library name: H_flu_wo_194_383_S85_L004
NTHi_raw_counts.txt


title: NTHi_wo_3, 5 hours growth

description:
Library name: hfluwoB_207_370_S94_L004
NTHi_raw_counts.txt


title: Ec78_InducRad_rep1


title: NTHi_apf_6, 5 hours growth

description:
Library name: hflusupB_230_347_S89_L004
NTHi_raw_counts.txt


title: NTHi_wo_2, 5 hours growth

description:
Library name: hFlu_wo_358_219_S8_L001
NTHi_raw_counts.txt


title: NTHi_Msup_apf_3, 5 hours growth

description:
Library name: C-HMSsup_279_298_S41
NTHi_raw_counts.txt


title: NTHi_Msup_apf_2, 5 hours growth

description:
Library name: B-HMSsup_225_352_S35
NTHi_raw_counts.txt


title: NTHi_apf_3, 5 hours growth

description:
Library name: C-Hflusup_213_364_S37
NTHi_raw_counts.txt


title: NTHi_apf_2, 5 hours growth

description:
Library name: B-Hflusup_232_345_S31
NTHi_raw_counts.txt


title: NTHi_Msup_apf_1, 5 hours growth

description:
Library name: A-HMSsup_261_316_S29
NTHi_raw_counts.txt


title: Sorted T-cells from PBMC, Parse v2 GEX/WT, sample F5

description:
Library name: parse_v2_gex_F5
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data


title: NTHi_apf_1, 5 hours growth

description:
Library name: A-Hflusup_268_309_S25
NTHi_raw_counts.txt


title: Uninf_cell_2, 5 hours growth

description:
Library name: H292_b_299_278_S11_L001
Host_raw_counts.txt

source_name: Lung

value: Lung

tag: cell line

value: Epithelial carcinoma

value: WT


title: Uninf_cell_1, 5 hours growth

description:
Library name: H292_a_311_266_S10_L001
Host_raw_counts.txt


title: Uninf_cell_3, 5 hours growth

description:
Library name: H292_c_382_195_S12_L001
Host_raw_counts.txt


title: NTHi_cell_6, 5 hours growth

description:
Library name: hflucellB_279_298_S90_L004
Host_raw_counts.txt
NTHi_raw_counts.txt

organism:
Haemophilus influenzae
Homo sapiens

value: Epithelial carcinoma, Nontypeable Haemophilus influenzae


title: NTHi_cell_5, 5 hours growth

description:
Library name: hFlu_cell_335_242_S5_L001
Host_raw_counts.txt
NTHi_raw_counts.txt


title: NTHi_cell_3, 5 hours growth

description:
Library name: C-Hflucel_201_376_S38
Host_raw_counts.txt
NTHi_raw_counts.txt


title: NTHi_Msup_cell_2, 5 hours growth

description:
Library name: B-HMScel_208_369_S36
Host_raw_counts.txt
NTHi_raw_counts.txt


title: NTHi_cell_2, 5 hours growth

description:
Library name: B-Hflucel_220_357_S32
Host_raw_counts.txt
NTHi_raw_counts.txt


title: NTHi_Msup_cell_3, 5 hours growth

description:
Library name: C-HMScel_267_310_S42
Host_raw_counts.txt
NTHi_raw_counts.txt


title: NTHi_Msup_cell_1, 5 hours growth

description:
Library name: A-HMScel_244_333_S30
Host_raw_counts.txt
NTHi_raw_counts.txt


title: Sorted T-cells from PBMC, Parse v2 VDJ/TCR, sample F4

description:
Library name: parse_v2_tcr_F4
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data

value: PBMC

value: Sorted T-cells


title: [DDB_PD_003]_[DDB7_WT]_[Batch]_[0h]_[R1]

value: Escherichia coli cells


title: NTHi_cell_4, 5 hours growth

description:
Library name: H_flu_cell_254_323_S82_L004
Host_raw_counts.txt
NTHi_raw_counts.txt


title: Mcat_wo_1, 5 hours growth

description:
Library name: m_cat_wo_206_371_S84_L004
Mcat_raw_counts.txt

organism: Moraxella catarrhalis

source_name: Moraxella catarrhalis

value: Moraxella catarrhalis


title: NTHi_cell_1, 5 hours growth

description:
Library name: A-Hflucel_285_292_S26
Host_raw_counts.txt
NTHi_raw_counts.txt


title: Mcat_apf_2, 5 hours growth

description:
Library name: mCat_sup_383_194_S1_L001
Mcat_raw_counts.txt


title: Mcat_apf_1, 5 hours growth

description:
Library name: m_cat_sup_278_299_S30_S78_L004
Mcat_raw_counts.txt


title: Mcat_apf_3, 5 hours growth

description:
Library name: mcatsupB_255_322_S87_L004
Mcat_raw_counts.txt


title: Mcat_cell_2, 5 hours growth

description:
Library name: mCat_cell_347_230_S4_L001
Host_raw_counts.txt

organism:
Moraxella catarrhalis
Homo sapiens

value: Epithelial carcinoma, Moraxella catarrhalis


title: Mcat_cell_3, 5 hours growth

description:
Library name: mcatcellB_219_358_S88_L004
Host_raw_counts.txt


title: Mix_wo_3, 5 hours growth

description:
Library name: mixwoB_195_382_S95_L004
NTHi_raw_counts.txt
Mcat_raw_counts.txt

organism:
Moraxella catarrhalis
Haemophilus influenzae

source_name: Nontypeable Haemophilus influenzae, Moraxella catarrhalis


title: Mix_wo_2, 5 hours growth

description:
Library name: Mix_wo_346_231_S9_L001
NTHi_raw_counts.txt
Mcat_raw_counts.txt

value: Nontypeable Haemophilus influenzae, Moraxella catarrhalis


title: Mix_apf_5, 5 hours growth

description:
Library name: Mix_sup_359_218_S3_L001
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: Mix_apf_3, 5 hours growth

description:
Library name: C-Mixsup_196_381_S39
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: Mcat_wo_2, 5 hours growth

description:
Library name: mCat_wo_370_207_S7_L001
Mcat_raw_counts.txt


title: Mix_apf_4, 5 hours growth

description:
Library name: mix_sup_231_346_S80_L004
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: Mix_apf_2, 5 hours growth

description:
Library name: B-Mixsup_249_328_S33
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: Mcat_wo_3, 5 hours growth

description:
Library name: mcatwoB_265_312_S93_L004
Mcat_raw_counts.txt


title: Mix_cell_3, 5 hours growth

description:
Library name: C-Mixcel_280_297_S40
Host_raw_counts.txt
NTHi_raw_counts.txt
Mcat_raw_counts.txt

organism:
Moraxella catarrhalis
Haemophilus influenzae
Homo sapiens

value: Epithelial carcinoma, Nontypeable Haemophilus influenzae, Moraxella catarrhalis


title: Mix_apf_1, 5 hours growth

description:
Library name: A-Mixsup_273_304_S27
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: Mix_cell_2, 5 hours growth

description:
Library name: B-Mixcel_237_340_S34
Host_raw_counts.txt
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: Mix_cell_5, 5 hours growth

description:
Library name: Mix_cell_323_254_S6_L001
Host_raw_counts.txt
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: Mix_cell_6, 5 hours growth

description:
Library name: mixcellB_267_310_S92_L004
Host_raw_counts.txt
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: Mix_cell_1, 5 hours growth

description:
Library name: A-Mixcel_256_321_S28
Host_raw_counts.txt
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: Mix_cell_4, 5 hours growth

description:
Library name: mix_cell_242_335_S83_L004
Host_raw_counts.txt
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: PDL012_slide2

type: other

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

description: M-Goliath-A1_slide2_xenium_output.tar.gz

hyb_protocol: A total of 343 unique genes were included in the analysis of this dataset. 246 genes came from an early version of the Xenium human lung base panel (PD_336) and 97 genes from a custom designed panel (CVEVZD). The custom panel was curated based on human lung single cell analysis data (Habermann et al. 2020), selecting for genes useful in cell type identification and/or with suspected involvement in IPF. Gene panel probe hybridization occurred overnight for 18 hours at 50°C (Bio-Rad DNA Engine Tetrad 2). Subsequent washes the next day removed unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) and followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched; autofluorescence is a known issue in lung tissue as well as a byproduct of formalin-fixation (Davis et al. 2014). Following PBS and PBS-T washes, DAPI was used to stain sample nuclei. Finalized slides were stored in PBS-T in the dark at 4°C for ≤5 days until being loaded onto the Xenium Analyzer instrument. Stepwise Xenium FFPE preparation guidelines and buffer recipes can be found in 10X Genomics Demonstrated Protocol CG000578.

scan_protocol: Xenium Analyzer is fully automated. The user marks regions for analysis by manually selecting sample location on an initial low-resolution image. After loading consumable reagents and slides, internal sample and liquid handling mechanics control experiment progression. Data collection occurs in cycles of fluorescently labeled probe binding, image acquisition, and probe stripping. Localized points of fluorescence intensity detected during the rounds of imaging are then defined as potential RNA puncta.

data_processing: Each gene on the panel has a unique fluorescence pattern across the image channels. Puncta that match a specific pattern are then decoded and labeled according to the gene ID. All image FOVs (4240 x 2960 pixels) and associated detected transcripts are computationally stitched together via the DAPI-stained image. The data in this paper was acquired on instrument software version 1.6.1.0 and analysis version xenium-1.6.0.8. Detailed instructions on instrument operation and consumable preparation can be found in 10X Genomics’ Demonstrated Protocol CG000582.

molecule: other

label_protocol: Deparaffinization and decrosslinking was performed to make subcellular RNA targets accessible (10X Genomics Demonstrated Protocol CG000580).

growth_protocol: A 5um section of each archived lung FFPE block was H&E stained and presented to a clinician who identified areas of interest. One core from each sample was manually punched out using a puncher from the “Quick-Ray Manual Tissue Microarrayer Full Set” and a custom square-shaped 3mm tip. A custom square recipient block mold was created, and paraffin wax (VWR 76548-194) was poured to mold empty core spaces for each core in a 3x6 sample layout with one empty core for orientation. Once complete, blocks are placed face down on a clean glass slide and briefly heated in a warm drawer (~60°C) to slightly melt the paraffin together and even the block face. TMA blocks were then cooled to room temperature overnight, removed from the slide, sealed, and stored at 4°C.

extract_protocol: Sectioning was performed at 5um on a Leica RM2135 with a water float temperature of 40°C. Sections were placed on Xenium slides (10X Genomics) and left to dry overnight. Slides were baked the next day at 42°C for 3 hours, then stored in a sealed dessicator at room temperature for a maximum of 10 days. Two adjacent sections were placed on Xenium slides to serve as technical replicates.

treatment_protocol: All protocol workstations and equipment were cleaned using RNase Away (RPI 147002) followed by 70% Isopropanol. All reagents, including water, were molecular grade nuclease-free.

value: 40 weeks

value: 0 weeks

value: Hypoxic-Ischemic Encephalopathy


title: PDL016_slide2

value: 35 weeks

value: 28 weeks

value: 63 weeks

value: ARB fetopathy (severe BPD)


title: Mcat_cell_1, 5 hours growth

description:
Library name: m_cat_cell_266_311_S81_L004
Host_raw_counts.txt

value: Lung


title: PDL013_slide2

value: 36 weeks

value: Encephalitis


title: PDL010_slide2

value: 34 weeks

value: 4 weeks

value: 38 weeks

value: Meningitis


title: Mix_wo_1, 5 hours growth

description:
Library name: mix_wo_277_300_S86_L004
NTHi_raw_counts.txt
Mcat_raw_counts.txt


title: PDL014_slide2

value: 29 weeks

value: CHAOS syndrome


title: PDL011_slide2

value: 35 ish weeks


title: Mix_apf_6, 5 hours growth

description:
Library name: mixsupB_218_359_S91_L004
NTHi_raw_counts.txt
Mcat_raw_counts.txt

value: Nontypeable Haemophilus influenzae, Moraxella catarrhalis


title: PDL007_slide2

value: 26 weeks

value: 2 weeks

value: Pulmonary Hypoplasia


title: PDL008_slide2

value: 27 weeks

value: 16 weeks

value: 43 weeks

value: BPD


title: Sorted T-cells from PBMC, NextGEM 5' VDJ/TCR, sample F4

description: Library name: nextgem_5p_tcr_F4

value: PBMC

value: Sorted T-cells

value: 10x Genomics' Chromium NextGEM 5′ v2


title: Sorted T-cells from PBMC, GEM-X 5' VDJ/TCR, sample F5

description: Library name: gemx_5p_tcr_F5

value: 10x Genomics' GEM-X 5′ v3


title: PDL005_slide2

value: 24 weeks

value: 0 weeks

value: Prematurity


title: PDL003_slide2

value: 21 weeks


title: PDL004_slide2

value: 23 weeks

value: 7 weeks

value: 30 weeks

value: Necrotizing enterocolitis


title: PDL017_slide2

value: 28 weeks

value: 30 years

value: BPD (explant of adult with BPD)


title: PDL001_slide2

value: 16 weeks

value: Not viable


title: PDL013_slide1

description: M-Goliath-B1_slide1_xenium_output.tar.gz

value: 36 weeks

value: Encephalitis


title: Sorted T-cells from PBMC, NextGEM 5' GEX/WT, sample F5

description: Library name: nextgem_5p_gex_F5

value: PBMC

value: Sorted T-cells

value: 10x Genomics' Chromium NextGEM 5′ v2


title: PDL012_slide1

value: 40 weeks

value: 0 weeks

value: Hypoxic-Ischemic Encephalopathy


title: Sorted T-cells from PBMC, NextGEM 5' VDJ/TCR, sample F5

description: Library name: nextgem_5p_tcr_F5


title: PDL002_slide2

value: 18 weeks


title: Sorted T-cells from PBMC, NextGEM 5' GEX/WT, sample F4

description: Library name: nextgem_5p_gex_F4


title: PDL011_slide1

value: 35 weeks

value: 35 ish weeks


title: PDL016_slide1

value: 63 weeks

value: ARB fetopathy (severe BPD)


title: Sorted T-cells from PBMC, GEM-X 5' GEX/WT, sample F5

description: Library name: gemx_5p_gex_F5

value: 10x Genomics' GEM-X 5′ v3


title: Sorted T-cells from PBMC, NextGEM 5' GEX/WT, sample F1

description: Library name: nextgem_5p_gex_F1


title: PDL010_slide1

value: 34 weeks

value: 4 weeks

value: 38 weeks

value: Meningitis


title: PDL007_slide1

value: 26 weeks

value: 2 weeks

value: 28 weeks

value: Pulmonary Hypoplasia


title: Sorted T-cells from PBMC, GEM-X 5' GEX/WT, sample F4

description: Library name: gemx_5p_gex_F4

value: PBMC

value: Sorted T-cells


title: Sorted T-cells from PBMC, GEM-X 5' GEX/WT, sample F1

description: Library name: gemx_5p_gex_F1


title: PDL004_slide1

value: 23 weeks

value: 7 weeks

value: 30 weeks

value: Necrotizing enterocolitis


title: PDL008_slide1

value: 27 weeks

value: 16 weeks

value: 43 weeks

value: BPD


title: Sorted T-cells from PBMC, GEM-X 5' VDJ/TCR, sample F4

description: Library name: gemx_5p_tcr_F4

value: 10x Genomics' GEM-X 5′ v3


title: PDL001_slide1

value: 0 weeks

value: Not viable


title: CISH-KO CAR-NK cells 3

status: Public on May 26 2025

city: Guangzhou

first: guozhu

last: xie

address: Shatainan Road No.1023-1063

country: China

institute: Southern Medical University

description: Library name: Sample 6

data_processing:
The raw gene expression matrix generated by processing raw sequencing data for each sample were using DNBelab_C4scRNA ( v2.1.1).
Assembly: Homo_sapiens_9606.10Xgenomic.refdata-gex-GRCh38-2020-A.v2005
Supplementary files format and content: Tab-separated values files and matrix files

source_name: NK cells

extract_protocol:
NK cells are resuspended in PBS. The cells are stained with 0.4% trypan blue to assess cell viability under microscopic observation. Cells with greater than 80% viability are qualified for library construction process.
Library construction is performed by using DNBelab C Series High-throughput Single-cell RNA Library Preparation Set V3.0 (MGI,China).

value: NK cells


title: CISH-KO CAR-NK cells 2

description: Library name: Sample 5


title: LV CAR-NK cells 3

description: Library name: Sample 3


title: LV CAR-NK cells 2

description: Library name: Sample 2


title: d5

status: Public on May 25 2025

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University

description: Library name: day5

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refse coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5
Library strategy: Spatial Transcriptomics

source_name: periosteum

extract_protocol:
Femurs were collected at different time points, fixed in 4% paraformaldehyde (PFA) overnight at 4°C, decalcified in Morse’s solution for 20 hours at room temperature, and subsequently processed for paraffin embedding and 6-μm longitudinal sectioning
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: periosteum


title: d15

description: Library name: day15


title: Plasma bulk cell-free RNA, group C patient 14

status: Public on May 24 2025

city: Stanford

first: Alireza

last: Raissadati

state: California

address: 269 Campus Drive

department: Cardiovascular Institute

institute: Stanford

description: Library name: C14

data_processing:
Raw sequencing reads were trimmed using TrimGalore (v.0.6.10) . Duplicate reads were removed based on unique molecular indices with umi-tools (v.1.1.4). Reads were mapped to the hg38 genome using Star (v.2.7.10) and v.45 of the gencode gene annotation files. Gene counts generated from all mapped reads using Featurecounts from the Rsubread R package (v.2.12.3).
Assembly: hg38
Supplementary files format and content: processed_counts_all.xlsx

source_name: Plasma

extract_protocol:
RNA was extracted from plasma using the Norgen cfRNA plasma isolation kit. 8ul of eluent was used for library preparation.
RNAseq libraries were prepared using the Takara SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit.

value: Plasma

tag: group

value: ICI-m with or without extracardiac irAE


title: Plasma bulk cell-free RNA, group C patient 13

description: Library name: C13

tag: tissue


title: Plasma bulk cell-free RNA, group C patient 10

description: Library name: C10


title: Plasma bulk cell-free RNA, group C patient 11

description: Library name: C11


title: d0

description: Library name: day0


title: LV CAR-NK cells 1

description: Library name: Sample 1


title: Plasma bulk cell-free RNA, group C patient 7

description: Library name: C7


title: Plasma bulk cell-free RNA, group C patient 5

description: Library name: C5


title: Plasma bulk cell-free RNA, group C patient 9

description: Library name: C9


title: Plasma bulk cell-free RNA, group C patient 4

description: Library name: C4


title: PDL003_slide1

value: 21 weeks

value: Prematurity


title: PDL014_slide1

value: 29 weeks

value: CHAOS syndrome


title: PDL002_slide1

value: 18 weeks


title: Plasma bulk cell-free RNA, group C patient 2

description: Library name: C2


title: Plasma bulk cell-free RNA, group C patient 6

description: Library name: C6


title: Plasma bulk cell-free RNA, group C patient 3

description: Library name: C3


title: Plasma bulk cell-free RNA, group C patient 8

description: Library name: C8


title: Plasma bulk cell-free RNA, group C patient 1

description: Library name: C1


title: CISH-KO CAR-NK cells 1

description: Library name: Sample 4


title: Plasma bulk cell-free RNA, group B patient 6

description: Library name: B6

value: ICI-treated cancer patients with extracardiac irAE only


title: Plasma bulk cell-free RNA, group B patient 7

description: Library name: B7


title: Plasma bulk cell-free RNA, group C patient 12

description: Library name: C12


title: Sorted T-cells from PBMC, Parse v2 GEX/WT, sample F4

description:
Library name: parse_v2_gex_F4
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data

value: PBMC

value: Sorted T-cells

value: Parse Evercode v.2 TCR


title: Plasma bulk cell-free RNA, group B patient 4

description: Library name: B4


title: Plasma bulk cell-free RNA, group B patient 3

description: Library name: B3


title: [DDB_PD_001]_[HMP3427]_[Fed-batch]_[16h]_[R2]

source_name: Escherichia coli cells

value: Escherichia coli cells


title: Plasma bulk cell-free RNA, group B patient 5

description: Library name: B5


title: Plasma bulk cell-free RNA, group B patient 2

description: Library name: B2


title: Plasma bulk cell-free RNA, group A patient 2

description: Library name: A2

value: ICI-treated cancer patients without irAE


title: Plasma bulk cell-free RNA, group A patient 4

description: Library name: A4


title: Plasma bulk cell-free RNA, group B patient 1

description: Library name: B1


title: Plasma bulk cell-free RNA, group A patient 3

description: Library name: A3


title: Plasma bulk cell-free RNA, group A patient 5

description: Library name: A5


title: Plasma bulk cell-free RNA, group A patient 1

description: Library name: A1


title: Endosperm 65, MuActive plant ND58-65

status: Public on May 09 2025

city: Athens

first: Brad

last: Nelms

state: Georgia

address: 120 East Green St

department: Genetics

institute: University of Georgia, Athens

description:
MuSeq2 Endosperm chip from MuActive plant ND58-65
Library name: E65

library_source: genomic

data_processing:
Processed file "MuSeq2 data for maize tissues.csv.gz" was generated by mapping the Mu sequencing reads to the W22 V2 genome using Bowtie2 and bam files were converted to txt files which were then imported into R. Sample txt files were filtered and combined into a large matrix, containing unique molecules detected per sample per genome location across all MuSeq2 samples in the dataset.
Processed file "'MuSeq2 data for maize tissues _ separated Left and Right transposon borders.tar'" was generated from "MuSeq2 data for maize tissues.csv.gz" by separating the molecules based on transposon border. Each row represents the chromosome, position, and direction for each molecule detected.
Assembly: W22 Version 2
Supplementary files format and content: To generate processed file "MuSeq2 data for maize tissues.csv.gz", Sequencing reads were mapped to the W22 V2 genome with Bowtie2. Reads were then converted to molecule counts using both the adapter ligation position and a unique molecular identifier (UMI) incorporated during adapter ligation. Molecule counts mapping to both sides of the transposon border were combined. The rownames in this file are listed as chromosome:position1,position2 where positions 1 and 2 are the first genomic coordinate immediately adjacent to the the left and right side of the transposon insertion (respectively).
Supplementary files format and content: Processed file "MuSeq2 data for maize tissues separated Left and Right transposon borders.tar” data was generated as an intermediate in calculating "MuSeq2 data for maize tissues.csv.gz". This contains two csv files with the molecule counts separated for left and right side of the transposon. The rownames are given as chromosome:position where the position is the genomic coordinate immediately adjacent to the transposon border.

organism: Zea mays

source_name: Endosperm

growth_protocol: All Mu-Active plants were first grown in vermiculite and transplanted 10-13 days after sowing to soil, where they were grown in maturity in a greenhouse. Mu-Inactive samples were grown in soil and grown for 10-13 days until the V2 stage before being harvested.

extract_protocol:
Leaf and root samples were extracted using a Qiagen Dneasy plant mini kit according to manufacturers instructions. DNA from Pollen and Endosperm samples were extracted using a modified CTAB DNA extraction protocol (see methods). All DNA samples were then sheared to a mean of 1000 bp using a Covaris E220 Evolution.
Libraries were constructed for all samples by first ligating a custom Museq Adapter, and then subsequent PCR reactions to selectively amplify genomic regions adjacent to Mu insertions. See Methods for details
A universal adapter was ligated onto the sheared DNA, then DNA fragments spanning the genome-transposon junction were amplified by PCR and sequenced using the MuSeq2 protocol.

value: Endosperm

value: W22 MuActive


title: KBM7 Dam-LMNB1/ChIC H3K27me3 (KIN8790.index21)

status: Public on May 17 2025

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: KIN8790.index21
kbm7_damchic_controls.h5ad.gz

data_processing:
Dam&ChIC data processing is largely based on the workflow and scripts described in Rooijers et al., 2019 and Markodimitraki et al., 2020 (available at: https://github.com/KindLab/scDamAndTools), but adapted to allow for computational separation of scDamID and sortChIC derived reads and further processing of sortChIC reads.
All reads are demultiplexed by comparing their sample barcode (e.g. single-cell barcode) located at the start of each read (R1 in case of paired-end sequenced libraries) conform to the read layout of 5′-[3 nt UMI][8 nt barcode]TC[gDNA]-3′ for scDamID and 5′-[3 nt UMI][8 nt barcode]WN[gDNA]-3′ for sortChIC reads, to a reference list of barcodes and zero mismatches between the observed barcode and reference are allowed. Sample barcodes and UMIs are trimmed off the reads to only retain gDNA sequences. The UMI sequences were appended to the read name for downstream processing. Per sample barcode, scDamID and sortChIC reads remain mixed at this point.
After preprocessing, the reads were aligned to a reference genome using bowtie2 (v. 2.4.1) with parameters: ‘‘--seed 42 --very-sensitive -N 1’’. Before alignment a ‘GA’ dinucleotide was prepended to the reads that has effectively been digested off scDamID fragments during DpnI gDNA digestion. For human samples, reads were aligned to reference genome hg19 (GRCh37) and mouse samples to mm10 (GRCm38). For allele-specific processing for X-chromosome inactivation experiments, data were aligned to reference genomes generated by imputing 129S1/SvImJ and CAST/EiJ single nucleotide polymorphisms obtained from the Sanger Mouse Genomes project (Keane et al., 2011) onto the mm10 reference genome. The reads were assigned to either genotype by aligning reads to both references. Reads that aligned with lower edit distance (SAM tag ‘NM’) or higher alignment score (SAM tag ‘AS’) in case of equal edit distance to one of the genotypes were assigned to that genotype. Reads aligning with equal edit distance and alignment score to both genotypes were considered of ‘ambiguous’ genotype. Reads that yielded an alignment with mapping quality (BAM field ‘MAPQ’) lower than 10 were discarded.
Following read alignment with ‘GA’ prepended dinucleotide, reads were considered scDamID in case of perfect alignment on genomic GATC motifs. Residual reads were considered sortChIC and their original sequences (i.e., without prepended GA dinucleotide) were realigned using hisat2 (v. 2.1.0) with parameters: ‘‘--seed 42 --no-spliced-alignment --mp '2,0' --sp '4,0'”. These sortChIC-considered reads were further pruned given MNase’s strong adenine or thymidine-nucleotide cut preference; only sortChIC reads were kept that lead with an ‘A’ or ‘T’ base. In addition, we observed that a larger fraction of sortChIC reads (i.e., that do not map on a genomic GATC motif) are ‘TC’-dinucleotide leading in Dam&ChIC libraries than in sortChIC libraries and hence decided to exclude TC-leading reads from Dam&ChIC-derived sortChIC libraries.
Assembly: GRCm38
Supplementary files format and content: H5AD

source_name: Blood

growth_protocol: Human haploid KBM7 cells were cultured in suspension in IMDM medium (10% FBS and 1% Pen/Strep). Human HT-1080 cells were cultured in DMEM medium (10% FBS and 1% Pen/Strep). Mouse F1 hybrid Cast/EiJ x 129SvJ embryonic stem cells (mESCs; a kind gift from the Joost Gribnau laboratory) were cultured on a monolayer of irradiated feeders (MEFs) in CM+/+ (G-MEM + 10% FBS, 1% Pen/Strep, 1× GlutaMAX (Gibco), 1× NEVitaminC, 1× sodium pyruvate, 0.1 mM 2-ME and 1000 U/ml ESGROmLIF (EMD Millipore, ESG1107))

extract_protocol:
double thymidine block: cells received 2 mM thymidine for 15 hours, followed by 9 hours of release, followed by a second thymidine block for 13 hours.
MN was activated thorugh 2mM CaCl2 for 30min at 4C at inactivated by EGTA addition. Cells were lysed (protK + NP40), fragments end-repaired (Klenow) and adenine methylated sites were cut (DpnI). Dam and ChIC fragemnts are ligated to blunt end adaptors containing a cell barcode and unique molecular identifier and a T7 promoter. After pooling DNA is amplified by in vitro transcription, before rundom hexamer based reverse transcription and final indexing PCR for sequencing.

treatment_protocol: Dam-POI induction: For Kbm7 cells 0.5 nM Shield-1 was added to stabilize the protein at the indicated timepoint. For mESCs 1mM IVitaminC was added 24h prior to induction, to ensure protein degradation.

value: Blood

value: chronic myelogenous leukemia


title: RLP_9mo_F_ATAC_rep2

status: Public on May 02 2025

city: LA JOLLA

first: Maria Luisa

last: Amaral

state: CA

address: 9500 GILMAN DR

institute: UCSD

description:
Library name: MM_1022_1_2
10X Multiome ATAC

data_processing:
Single-nucleus RNA-seq (snRNA-seq) data were generated using the 10X Genomics Multiome platform and processed with Cellranger-arc v2.0.2 to generate raw gene expression matrices. The data were aligned and quantified using the mouse reference genome (refdata-cellranger-arc-mm10-2020-A-2.0.0). Doublets were identified and removed using DoubletFinder from the Cell Ranger output for each sample65. Downstream analysis was performed using Seurat v5 in R. Individual samples were then merged into a single Seurat object. Quality control was applied to remove low-quality nuclei, filtering out cells with fewer than 500 or more than 6000 detected genes, and cells with >10% mitochondrial reads. Normalization was performed using the SCTransform (SCT) workflow, which models technical noise while preserving biological variation. Dimensionality reduction was carried out with PCA, and the top 30 components were used to compute a shared nearest neighbor (SNN) graph for clustering using the Leiden algorithm. UMAP was used for visualization. Following initial clustering, further manual filtering was applied to remove remaining doublets and low-quality subclusters. Specifically, subclusters containing >50% cells with low UMI counts or high doublet scores were excluded.
Assembly: mm10
Supplementary files format and content: These files are filtered_feature_bc_matrix.h5 files generated using the cellranger-arc count pipeline (v2.0.2, 10x Genomics). Each file corresponds to a single multiome sample and contains filtered gene expression and chromatin accessibility matrices. Filtering was performed automatically by Cell Ranger ARC based on quality metrics to retain high-confidence cells.

source_name: DR+LC+PAG+PCG (PAG/PCG)

extract_protocol:
All experimental procedures using live animals were performed at the Salk Institute, and were approved by the Animal Care and Use Committee (IACUC). The Salk Institute has approved Assurance from NIH Office of Protection from Research Risks (D16-00328). C57BL/6J male and female mice were purchased from the Jackson Laboratory at 7, 38 and 63 weeks of age and maintained in the Salk animal barrier facility on 12-h dark light cycles with food ad libitum until brain extraction (housing conditions: temperature of 21-23C, relative humidity of 61-63%). For synchronizing the estrous cycle in females ahead of brain extraction, females were exposed to male bedding for three days such that they would be in di-estrous at time of dissection. All animals were dissected between 1 and 5 pm to ensure similarity of circadian rhythm. Brains were extracted at 2, 9 or 18 months of age, sliced coronally at 600 µm and regions dissected in an ice-cold dissection buffer as previously described (Liu et al., Nature 2021) according to the Allen Brain Reference Atlas CCF (version 3)59 (CCFv3). Dissected tissue corresponding to the same region (across the anterior posterior axis) from each animal was collected across brain slabs and stored at -80C. For nuclei isolation, region pools from 3-14 animals were processed for each of 2?3 biological replicas per region. Comprehensive brain dissection metadata are provided in Supplementary Table 1. No statistical methods were used to predetermine sample sizes. We empirically determined the number of animals needed to obtain sufficient nuclei from each brain region to run single nuclei sequencing experiments. We use two to three biological replicas for all single-cell epigenomic experiments to achieve minimum reproducibility for large-scale projects. Blinding and randomization was not performed during handling of the tissue samples. Additionally, all dissected regions were previously digitally registered into CCFv3 using ITK-SNAP60 (v.4.0.0) at 25um resolution.
Nuclei were pelleted with a swinging bucket centrifuge (1000g, 10 min, 4°C; 5920R, Eppendorf). Nuclei pellets were resuspended in sort buffer (1% BSA, 2uM 7-AAD, 1x cOmplete EDTA?free protease inhibitor and 1U/uL RNasin in PBS) and stained 10 mins on ice. Nuclei were sorted, and 120,000 nuclei were collected in 90 uL of collection buffer (5% BSA and 5U/uL RNasin). Nuclei were centrifuged (500 × g for 5 min at 4°C), and resuspended in nuclei permeabilization buffer (1mM DTT (D9779, Sigma), 0.2% IGEPAL-CA630 (Sigma), 1X cOmplete EDTA-free protease inhibitor (05056489001, Roche) and 5% BSA (A7906, Sigma) in PBS) incubated on ice for 1 min. Added 900 uL wash buffer and and pelleted again (500g, 5 min, 4°C; 5920R, Eppendorf). The nuclei were resuspended in 10uL of 1X Nuclei Buffer and counted using a hemocytometer. A total of 18,000 nuclei were loaded per tagmentation reaction loaded onto a Chromium Controller (10x Genomics) for downstream 10X Multiome ATAC and gene expression workflows. Final library concentration was assessed by Qubit dsDNA HS Assay Kit (Invitrogen) and fragment size was checked using Tapestation High Sensitivity D1000 (Agilent) to ensure that proper fragment sizes. Libraries were sequenced using the NextSeq500 and a NovaSeq6000 (Illumina).

treatment_protocol: No treatment was applied to mice

value: DR+LC+PAG+PCG (PAG/PCG)

value: WT

value: female


title: RLP_9mo_F_ATAC_rep1

description:
Library name: MM_1043_1_2
10X Multiome ATAC


title: RLP_2mo_F_ATAC_rep1

description:
Library name: MM_985_1_2
10X Multiome ATAC


title: RLP_2mo_F_ATAC_rep2

description:
Library name: MM_1100_1_2
10X Multiome ATAC


title: lps_W3

status: Public on May 22 2025

city: Chongqing

first: Ye

last: shusen

address: No.1 Medical College Road, Yuzhong District, Chongqing

institute: Chongqing Medical University

description: Library name: Sample 3

data_processing:
5,000 activated CD4+ T cells (Live&Dead-CD3+CD4+CD44hi) from spleen of LPS challenged mice were lysed in 10 μl TCL buffer plus 1% 2-mercaptoethanol. Librar-ies were processed with SMARTSeq2 (15) with three biological replicates per condi-tion, and paired-end sequenced (150 bp×2) with a 75 cycle Nextseq 500 high output V2 kit.
Obtained RNA-seq reads were aligned to the mouse genome and transcrip-tome (GENCODE GRCm38 vM25, mm10) using Spliced Transcripts Alignment to a Reference (STAR) (version 2.7.5c) with ‘twopassMode Basic’, expression abundances were estimated using RSEM (version 1.3.3).
The count matrices output from gene results were processed with the R package (version 3.32.0) to ana-lyze differential gene expression with default parameters.
KEGG Enrichment was performed using custom script with clusterProfiler (version 3.16.1) and hi-erarchical file from ‘http://rest.kegg.jp’ and visualized using ggplot2 (version 3.3.3), GSEA was run with the official tool (GSEA version 4.2.1, MsigDB hallmark v7.3) and reploted in R.
Overall Expression (OE) was computed as previously de-scribed.
Assembly: GRCm39
Supplementary files format and content: This count matrix was generated using RSEM (version 1.3.3) to quantify gene expression levels from RNA-Seq data.
Supplementary files format and content: RSEM counts matrix

source_name: spleen

growth_protocol: no culture in vitro

extract_protocol:
Muring LPS model construction, and CD4+T cell of spleen was sorted
CD4+T cells were lysed in 10 μl TCL buffer plus 1% 2-mercaptoethanol,  Librar-ies were processed with SMARTSeq2.

treatment_protocol: LPS challenge

value: spleen

value: CD4+T cell

value: immune cell

value: LPS


title: lps_K1

description: Library name: Sample 4

value: DOCK2 KO


title: lps_K3

description: Library name: Sample 6


title: lps_W2

description: Library name: Sample 2


title: lps_W1

description: Library name: Sample 1


title: RLP_18mo_F_ATAC_rep1

description:
Library name: MM_1102_1_2
10X Multiome ATAC


title: RLP_18mo_F_ATAC_rep2

description:
Library name: MM_1076_1_2_3
10X Multiome ATAC


title: NAC_9mo_F_ATAC_rep2

description:
Library name: MM_1097_1_2
10X Multiome ATAC

source_name: Nucleus Accumbens (ACB)

value: Nucleus Accumbens (ACB)


title: NAC_9mo_F_ATAC_rep1

description:
Library name: QY_1587_1_2
10X Multiome ATAC


title: NAC_2mo_F_ATAC_rep2

description:
Library name: MM_993_1_2
10X Multiome ATAC


title: NAC_2mo_F_ATAC_rep1

description:
Library name: MM_949_1_2
10X Multiome ATAC


title: NAC_18mo_F_ATAC_rep1

description:
Library name: MM_1074_1_2
10X Multiome ATAC


title: HCP_9mo_F_ATAC_rep3

description:
Library name: EE_171_1_2
10X Multiome ATAC

source_name: Posterior hippocampus (PHC)

value: Posterior hippocampus (PHC)


title: lps_K2

description: Library name: Sample 5


title: HCP_9mo_F_ATAC_rep1

description:
Library name: QY_1585_1_2
10X Multiome ATAC


title: HCP_9mo_F_ATAC_rep2

description:
Library name: MM_1045_1_2
10X Multiome ATAC


title: HCP_2mo_F_ATAC_rep1

description:
Library name: MM_1041_1_2
10X Multiome ATAC


title: HCP_18mo_F_ATAC_rep2

description:
Library name: MM_1099_1_2
10X Multiome ATAC


title: HCA_9mo_F_ATAC_rep2

description:
Library name: MM_1020_1_2
10X Multiome ATAC

source_name: Anterior hippocampus (AHC)

value: Anterior hippocampus (AHC)


title: HCA_2mo_F_ATAC_rep1

description:
Library name: MM_1095_1_2
10X Multiome ATAC


title: HCP_18mo_F_ATAC_rep1

description:
Library name: MM_1028_1_2
10X Multiome ATAC


title: HCA_9mo_F_ATAC_rep1

description:
Library name: QY_1601_1_2
10X Multiome ATAC


title: HCA_18mo_F_ATAC_rep2

description:
Library name: MM_1075_1_2
10X Multiome ATAC


title: FC_2mo_F_ATAC_rep2

description:
Library name: QY_1593_1_2
10X Multiome ATAC

source_name: Frontal Cortex (FC)

value: Frontal Cortex (FC)


title: FC_9mo_F_ATAC_rep1

description:
Library name: QY_1605_1_2
10X Multiome RNA


title: FC_9mo_F_ATAC_rep2

description:
Library name: KA_35_1_2
10X Multiome ATAC


title: FC_2mo_F_ATAC_rep1

description:
Library name: MM_988_1_2_3
10X Multiome ATAC


title: ENT_9mo_F_ATAC_rep2

description:
Library name: QY_1618_1_2
10X Multiome ATAC

source_name: Entorhinal cortex (ENT)

value: Entorhinal cortex (ENT)


title: ENT_9mo_F_ATAC_rep3

description:
Library name: EE_172_1_2
10X Multiome ATAC


title: NAC_18mo_F_ATAC_rep2

description:
Library name: MM_1098_1_2
10X Multiome ATAC


title: FC_18mo_F_ATAC_rep1

description:
Library name: QY_1696_1_2
10X Multiome ATAC


title: ENT_9mo_F_ATAC_rep1

description:
Library name: MM_1101_1_2_3
10X Multiome ATAC


title: ENT_2mo_F_ATAC_rep2

description:
Library name: MM_1002_1_2
10X Multiome ATAC


title: FC_18mo_F_ATAC_rep2

description:
Library name: MM_1077_1_2
10X Multiome ATAC


title: ENT_18mo_F_ATAC_rep3

description:
Library name: EE_168_1_2
10X Multiome ATAC


title: HCP_2mo_F_ATAC_rep2

description:
Library name: MM_992_1_2
10X Multiome ATAC


title: ENT_18mo_F_ATAC_rep1

description:
Library name: MM_1030_1_2
10X Multiome ATAC


title: ENT_18mo_F_ATAC_rep2

description:
Library name: QY_1700_1_2
10X Multiome ATAC


title: CP_9mo_F_ATAC_rep3

description:
Library name: EE_170_1_2
10X Multiome ATAC

source_name: Caudate Putamen (CP)

value: Caudate Putamen (CP)


title: HCA_2mo_F_ATAC_rep2

description:
Library name: QY_1589_1_2
10X Multiome ATAC


title: CP_9mo_F_ATAC_rep1

description:
Library name: QY_1595_1_2
10X Multiome ATAC


title: HCA_18mo_F_ATAC_rep1

description:
Library name: MM_1034_1_2
10X Multiome ATAC


title: CP_18mo_F_ATAC_rep1

description:
Library name: MM_1103_1_2
10X Multiome ATAC


title: AMY_9mo_F_ATAC_rep2

description:
Library name: QY_1616_1_2
10X Multiome ATAC

source_name: Amygdala (AMY)

value: Amygdala (AMY)


title: CP_18mo_F_ATAC_rep2

description:
Library name: QY_1698_1_2
10X Multiome ATAC


title: AMY_9mo_F_ATAC_rep1

description:
Library name: QY_1599_1_2
10X Multiome ATAC


title: AMY_2mo_F_ATAC_rep3

description:
Library name: EE_169_1_2
10X Multiome ATAC


title: AMY_2mo_F_ATAC_rep2

description:
Library name: MM_1003_1_2
10X Multiome ATAC


title: AMY_2mo_F_ATAC_rep1

description:
Library name: MM_981_1_2_3_4
10X Multiome ATAC


title: AMY_18mo_F_ATAC_rep2

description:
Library name: QY_1702_1_2
10X Multiome ATAC


title: AMY_18mo_F_ATAC_rep3

description:
Library name: EE_167_1_2
10X Multiome ATAC


title: AMY_18mo_F_ATAC_rep1

description:
Library name: MM_1073_1_2
10X Multiome ATAC


title: NTHi_apf_4, 5 hours growth

description:
Library name: H_flu_sup_243_334_S79_L004
NTHi_raw_counts.txt

source_name: Nontypeable Haemophilus influenzae

value: Nontypeable Haemophilus influenzae


title: Cnt2

city: London

first: Silvia

last: Marino

address: Blizard Institute, 4 Newark Street

institute: Queen Mary University of London

description: FFPE Spatial transcriptome sequencing

data_processing:
*library strategy: Spatial transcriptomics
Raw sequencing data were processed using 10xGenomics Space Ranger pipeline to genrate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Rangers default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger default settings
Assembly: GRCh38
Supplementary files format and content: _aligned_fiducials.jpg: aligned fudicials of tissue image
Supplementary files format and content: _detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: _scalefactors_json.json: scale factors in json format
Supplementary files format and content: _spatial_enrichment.csv: table of Moran's I values for each feature
Supplementary files format and content: _tissue_hires_image.png: high resolution image of tissue
Supplementary files format and content: _tissue_lowres_image.png: low resolution image of tissue
Supplementary files format and content: _tissue_positions.csv: list of spatial barcodes and the coordinates specifying the tissue spot
Supplementary files format and content: _filtered_feature_bc_matrix.h5: feature barcode matrix

source_name: Brain

extract_protocol:
FFPE tissue samples were cut at 10μm with a microtome
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions

value: Brain

value: Control


title: Cnt11

description: FFPE Spatial transcriptome sequencing


title: RT13

description: FFPE Spatial transcriptome sequencing

value: Radiotherapy


title: CP_9mo_F_ATAC_rep2

description:
Library name: QY_1608_1_2_3
10X Multiome ATAC

value: WT

value: female


title: Cnt3

description: FFPE Spatial transcriptome sequencing


title: Cnt4

description: FFPE Spatial transcriptome sequencing


title: CP_2mo_F_ATAC_rep2

description:
Library name: MM_989_1_2_3
10X Multiome ATAC


title: RT14

description: FFPE Spatial transcriptome sequencing


title: RT8

description: FFPE Spatial transcriptome sequencing


title: RT9

description: FFPE Spatial transcriptome sequencing


title: Cnt8

description: FFPE Spatial transcriptome sequencing


title: RT6

description: FFPE Spatial transcriptome sequencing


title: RT10

description: FFPE Spatial transcriptome sequencing


title: RT4

description: FFPE Spatial transcriptome sequencing


title: RT2

description: FFPE Spatial transcriptome sequencing


title: RT3

description: FFPE Spatial transcriptome sequencing


title: CP_2mo_F_ATAC_rep1

description:
Library name: MM_946_1_2
10X Multiome ATAC


title: RT12

description: FFPE Spatial transcriptome sequencing


title: RT1

description: FFPE Spatial transcriptome sequencing


title: L5_NP_CTX_Glut.9mo

status: Public on Apr 30 2025

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: sample 38
read length: 151

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Supplementary files format and content: tab-delimited files (CONTACT files) describing the raw contact number between two genome regions . Columns are: 1. Strand1 (0 for forward, anything else for reverse), 2. Chromosome1, 3. Position1, 4. restriction site fragments, 5. Strand2 (0 for forward, anything else for reverse), 6.  Chromosome2, 7. Position2, 8. restriction site fragments, 9. the score imputed to this read
Library strategy: snm3C-seq

source_name: brain

extract_protocol:
Mouse brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

treatment_protocol: For all snm3C-seq samples, in-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

value: brain


title: L5_IT_CTX_Glut.9mo

description:
Library name: sample 35
read length: 151


title: L6_CT_CTX_Glut.18mo

description:
Library name: sample 39
read length: 151


title: L5_NP_CTX_Glut.8wk

description:
Library name: sample 37
read length: 151


title: L6_IT_CTX_Glut.18mo

description:
Library name: sample 42
read length: 151


title: L6_IT_CTX_Glut.8wk

description:
Library name: sample 43
read length: 151


title: L6_CT_CTX_Glut.8wk

description:
Library name: sample 40
read length: 151


title: L5_IT_CTX_Glut.8wk

description:
Library name: sample 34
read length: 151


title: L5_ET_CTX_Glut.9mo

description:
Library name: sample 32
read length: 151


title: L6_IT_CTX_Glut.9mo

description:
Library name: sample 44
read length: 151


title: L5_ET_CTX_Glut.8wk

description:
Library name: sample 31
read length: 151


title: L45_IT_CTX_Glut.9mo

description:
Library name: sample 29
read length: 151


title: L45_IT_CTX_Glut.8wk

description:
Library name: sample 28
read length: 151


title: L45_IT_CTX_Glut.18mo

description:
Library name: sample 27
read length: 151


title: L23_IT_PPP_Glut.18mo

description:
Library name: sample 24
read length: 151


title: L6_CT_CTX_Glut.9mo

description:
Library name: sample 41
read length: 151


title: L23_IT_PPP_Glut.9mo

description:
Library name: sample 26
read length: 151


title: L23_IT_ENT_Glut.8wk

description:
Library name: sample 22
read length: 151


title: L23_IT_ENT_Glut.18mo

description:
Library name: sample 21
read length: 151


title: L23_IT_ENT_Glut.9mo

description:
Library name: sample 23
read length: 151


title: L23_IT_CTX_Glut.9mo

description:
Library name: sample 20
read length: 151


title: L23_IT_CTX_Glut.8wk

description:
Library name: sample 19
read length: 151


title: DG_Glut.18mo

description:
Library name: sample 15
read length: 151


title: L5_NP_CTX_Glut.18mo

description:
Library name: sample 36
read length: 151


title: L23_IT_CTX_Glut.18mo

description:
Library name: sample 18
read length: 151


title: DG_Glut.9mo

description:
Library name: sample 17
read length: 151


title: DG_Glut.8wk

description:
Library name: sample 16
read length: 151


title: CEA-BST_Gaba.9mo

description:
Library name: sample 14
read length: 151


title: CA3_Glut.18mo

description:
Library name: sample 9
read length: 151


title: CA3_Glut.9mo

description:
Library name: sample 11
read length: 151


title: CEA-BST_Gaba.8wk

description:
Library name: sample 13
read length: 151


title: CEA-BST_Gaba.18mo

description:
Library name: sample 12
read length: 151


title: CA1-ProS_Glut.8wk

description:
Library name: sample 7
read length: 151


title: CA1-ProS_Glut.9mo

description:
Library name: sample 8
read length: 151


title: Astro-TE_NN.8wk

description:
Library name: sample 4
read length: 151


title: CA1-ProS_Glut.18mo

description:
Library name: sample 6
read length: 151


title: Astro-TE_NN.9mo

description:
Library name: sample 5
read length: 151


title: Astro-NT_NN.18mo

description:
Library name: sample 0
read length: 151


title: Astro-NT_NN.8wk

description:
Library name: sample 1
read length: 151