title: Dial-up scRNA-seq, breast tissue sample WT-C (Gray et al. 2022).

description: Library name: Gray_2022_WT_C

source_name: breast

extract_protocol:
Dial-up transcript enrichment from single-cell WTA libraries was performed using a two-step PCR strategy. Target-specific primers for p16, p15, p14, and ANRIL were combined with a CA-SMART reverse primer to selectively amplify transcripts of interest while retaining cell barcodes and UMIs from the Seq-Well protocol. Amplified products underwent bead cleanup, followed by biotin pull-down (Dynabeads™ kilobaseBINDER™ Kit, Thermo 60101) to enrich the targeted transcripts, which were then eluted for downstream processing. See Methods section of the paper for further details
Dial-up transcripts were subjected to a second PCR to add Illumina sequencing adapters (P5, P7), dual indices (i5, i7), and sequencing primer binding sites. Amplified libraries were purified with a 0.9X bead cleanup and eluted in 1X TE. Final libraries were sequenced on an Illumina NextSeq 500 using a 75-cycle kit with custom read 1 and custom i5 primers (20 cycles read 1 for cell barcode + UMI, 56 cycles read 2 for transcript sequence, and 2 × 8-bp index reads). See Methods section of the paper for further details

value: breast

value: WT


title: 8051_Avonex_intermed_16

status: Public on Jun 23 2026

type: protein

city: Silver Spring

first: Lakshmi Manasa

middle: Sakuntala

last: Chekka

state: Maryland

address: 10903 New Hampshire Avenue

department: DARS, CDER

country: USA

institute: U.S. FDA

hyb_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

data_processing:
https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.
Read out is relative flourescent units (RFU) which is directly proportional to the amount of target protein in the initial sample, as informed by a standard curve generate for each protein-SOMAmer pair. Raw RFU is normalized as described in the data processing step above.

label: 5’ fluorophore, photocleavable linker, and biotin

molecule: protein

organism: Homo sapiens

source_name: EDTA plasma

growth_protocol: EDTA Plasma from healthy subjects was collected and stored at -80 degrees centigrade.

extract_protocol: EDTA plasma from whole blood

treatment_protocol: Subjects were randomized between IFNβ-1a (15 µg) and pegIFNβ-1a (62.5 µg).

tag: drug group

tag: delivery

value: IM

tag: dose

value: 15 μg

tag: timepoint


title: PT6F, CaOx, FLIGHT, FEMALE, replicate 4

type: SRA

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Library name: S_40

library_source: transcriptomic

data_processing:
FASTQ files were aligned to the Gencode GRCh38 v45 genome using HiSat2 and coordinate sorted using samtools
Counts/gene were summarized using the Bioconductor Rsubread package, using the Ensembl GRCh38 release 97 data.
Assembly: Ensembl GRCh38 release 97
Supplementary files format and content: Text file with genes in rows and samples in columns

molecule: total RNA

source_name: Primary PTEC cell culture

growth_protocol: In brief, proximal tubule epithelial cells were isolated from whole human donor kidneys (not suitable for transplantation) obtained from Novabiosis (Durham, NC), cryopreserved, and commercially shipped on dry ice to Kennedy Space Center (KSC) where they were cultured and seeded onto 10-15 triplex (TSC) devices per donor to achieve ≥8 fully confluent TSCs per donor. The TSC devices were maintained within the pneumatic Kidney Chip Perfusion Platform system (KCPP) at a flow rate of 1 mL min-1. The integration and operation of the KCPP has been described previously.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004) and converted to cDNA with 20 the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, 634891).
Sequencing libraries were constructed using the SMARTer ThruPlex DNA-Seq Kit (Takara, R400676) and sequenced on a NovaSeq 6000 instrument (Illumina, San Diego, CA).

treatment_protocol: Cultures were incubated for 3-7 days in a standard laboratory incubator prior to transfer to KCPP. Kidney MPS devices were subjected to 1g (control) or microgravity conditions (CRS-22, KSC launch 17:29 UTC, 06/03/21 and ISSNL docking at 09:09 UTC, 06/05/21) for 7 days before media exchange to control (unsupplemented media) or treatment media containing either 1000 µg ml-1 COM crystals or 1000 µg ml-1 COM crystals + 250 µm KCit (potassium citrate tribasic monohydrate, Sigma, St. Louis, MO). The cassettes containing control or treatment media were inverted 4 times to evenly distribute COM microcrystals prior to initiating flow. Exposure to COM crystals and KCit in the ground-based laboratories at KSC or at the ISSNL was performed as previously described12. Upon completion of the test phase, the KCPP was flushed with RNAlater at a flow rate of 10 mL min-1 for 2 h before being placed in ultracold stowage (ISSNL) or -80o C freezer (KSC). ISSNL samples were returned to earth (undocking at 14:45 UTC, 08/08/21) and shipped to the laboratory at UW.

tag: tissue

value: Primary PTEC cell culture

tag: cell type

value: PTEC

tag: gravity

value: microgravity

tag: treatment

value: 1 ng/ml Calcium Oxalate


title: 8051_Avonex_intermed_32

scan_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).


title: Dial-up scRNA-seq, breast tissue sample WT-A (Gray et al. 2022).

city: Cambridge

first: Neva

middle: Cherniavsky

last: Durand

state: MA

address: 75 Ames St

institute: Broad Institute

description: Library name: Gray_2022_Human-WT-1

library_source: transcriptomic single cell

data_processing:
Demultiplexed fastqs were aligned with STAR solo
Assembly: hg38
Supplementary files format and content: Raw STAR solo outputs: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

tag: genotype


title: PT6F, Control, FLIGHT, FEMALE, replicate 6

description: Library name: S_39

value: Control


title: 8051_Avonex_intermed_8

label_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).


title: Dial-up scRNA-seq, breast tissue sample WT-D (Gray et al. 2022).

description: Library name: Gray_2022_WT-D


title: Dial-up scRNA-seq, breast tissue sample BRCA2-A (Gray et al. 2022).

description: Library name: Gray_2022_Human-B2-1

value: BRCA-2 mtuant


title: 8051_Avonex_intermed_96


title: Dial-up scRNA-seq, breast tissue sample BRCA2-E (Gray et al. 2022).

description: Library name: Gray_2022_BRCA2-E


title: 8051_Avonex_intermed_3


title: PT6F, Control, FLIGHT, FEMALE, replicate 5

description: Library name: S_38


title: 8051_Avonex_intermed_0


title: Dial-up scRNA-seq, breast tissue sample BRCA2-D (Gray et al. 2022).

description: Library name: Gray_2022_BRCA2-D


title: 8048_Avonex_intermed_144


title: Dial-up scRNA-seq, breast tissue sample BRCA2-B (Gray et al. 2022).

description: Library name: Gray_2022_BRCA2-B


title: PT6F, Control, FLIGHT, FEMALE, replicate 4

description: Library name: S_37


title: PT7M, KCit, FLIGHT, MALE, replicate 3

description: Library name: S_36

value: 1 ng/ml Calcium Oxalate + 250 µM Potassium Citrate


title: Dial-up scRNA-seq, breast tissue sample BRCA1-D (Gray et al. 2022).

description: Library name: Gray_2022_BRCA1-D

value: BRCA-1 mtuant


title: Dial-up scRNA-seq, breast tissue sample BRCA1-C (Gray et al. 2022).

description: Library name: Gray_2022_BRCA1-C


title: 8048_Avonex_intermed_120


title: Dial-up scRNA-seq, breast tissue sample BRCA1-H (Gray et al. 2022).

description: Library name: Gray_2022_BRCA1-H


title: Dial-up scRNA-seq, WI-38 fibroblasts, PDL 50 (Chan et al. 2022)

description: Library name: Chan_2022_PDL_50

tag: cell line

value: fibroblast


title: Dial-up scRNA-seq, WI-38 fibroblasts, PDL 46 (Chan et al. 2022)

description: Library name: Chan_2022_PDL_46


title: PT7M, KCit, FLIGHT, MALE, replicate 2

description: Library name: S_35


title: 8048_Avonex_intermed_96


title: Dial-up scRNA-seq, WI-38 fibroblasts, PDL 37 (Chan et al. 2022)

description: Library name: Chan_2022_PDL_37


title: Dial-up scRNA-seq, WI-38 fibroblasts, PDL 33 (Chan et al. 2022)

description: Library name: Chan_2022_PDL_33


title: PT7M, KCit, FLIGHT, MALE, replicate 1

description: Library name: S_34


title: 8048_Avonex_intermed_72


title: 8048_Avonex_intermed_48


title: Dial-up scRNA-seq, WI-38 fibroblasts, PDL 29 (Chan et al. 2022)

description: Library name: Chan_2022_PDL_29


title: Dial-up scRNA-seq, WI-38 fibroblasts, PDL 25 (Chan et al. 2022)

description: Library name: Chan_2022_PDL_25


title: Region capture micro-C, WI-38 fibroblasts, PDL 57 Rep 2

description: Library name: microC_WI-38_PDL57_Rep2

library_source: genomic

data_processing:
Paired end reads were aligned to the UCSC hg38 genome using Juicer (default setting, version 2.0). Deduplicated paired reads were converted to contact matrices (.hic format file) using juicer_tools with pre at base pair delimited resolutions of 2.5 Mb, 1 Mb, 500 kb, 250 kb, 100 kb, 50 kb, 25 kb, 10 kb, 5 kb, 2 kb, 1 kb, 500 bp, 200 bp, 100 bp, 50 bp, 20 bp, and 10 bp. All contact matrices used for further analysis were VC-normalized with Juicer.
Assembly: hg38
Supplementary files format and content: Contact matrix hic file of combined replicates; loops in bedpe file

molecule: genomic DNA

extract_protocol:
Region Capture Micro-C (RCMC)  RCMC was performed as described (Kim et al. 2024; Goel et al. 2023) with minor modifications. Briefly, cells were double crosslinked with DSG and formaldehyde, nuclei were isolated, and chromatin was digested with MNase to predominantly mono- and di-nucleosome fragments. DNA ends were repaired, biotin-labeled, and proximity ligated. Crosslinks were reversed, DNA was purified, size-selected for dinucleosomes, and biotinylated ligation products were enriched using streptavidin beads. Illumina libraries were prepared with the NEBNext Ultra II kit, amplified, and purified.
For capture, 80-mer probes tiling the ~2.3 Mb CDKN2A locus were designed and synthesized (Twist Bioscience). Libraries were hybridized to probes, captured with streptavidin beads, PCR amplified, and sequenced (Illumina NextSeq500/550, paired-end 2×38 bp).


title: PT6F, KCit, FLIGHT, FEMALE, replicate 2

description: Library name: S_32


title: PT6F, KCit, FLIGHT, FEMALE, replicate 3

description: Library name: S_33


title: Region capture micro-C, WI-38 fibroblasts, PDL 57 Rep 1

description: Library name: microC_WI-38_PDL57_Rep1


title: Region capture micro-C, WI-38 fibroblasts, PDL 53.5 Rep 1

description: Library name: microC_WI-38_PDL53_Rep1


title: 8048_Avonex_intermed_32


title: PT6F, KCit, FLIGHT, FEMALE, replicate 1

description: Library name: S_31


title: Region capture micro-C, WI-38 fibroblasts, PDL 48 Rep 2

description: Library name: microC_WI-38_PDL48_Rep2


title: Region capture micro-C, WI-38 fibroblasts, PDL 33 Rep2

description: Library name: microC_WI-38_PDL33_Rep2


title: 8048_Avonex_intermed_16


title: Region capture micro-C, WI-38 fibroblasts, PDL 33 Rep1

description: Library name: microC_WI-38_PDL33_Rep1


title: 8048_Avonex_intermed_8


title: PT5F, KCit, FLIGHT, FEMALE, replicate 3

description: Library name: S_30


title: WI-38 fibroblasts, PDL54, whole cell extract

description: Library name: WCE_WI-38_PDL54

data_processing:
The CTCF and H3K27ac ChIP-seq datasets were processed via the ENCODE uniform pipeline (Hitz et al. 2023). Libraries produced from the same ChIP (technical replicates) were merged.
Assembly: hg38
Supplementary files format and content: Bigwig coverage tracks

extract_protocol:
Chromatin was prepared following ENCODE ChIP-seq guidelines, available here: https://www.encodeproject.org/documents/be2a0f12-af38-430c8f2d-57953baab5f5/@@download/attachment/Epigenomics_Alternative_Mag_Bead_ChIP_Protocol_v1.1_exp.pdf
Experiments were performed to ENCODE standards. The antibody to H3K27ac used was a polyclonal from Active Motif: part number is 39133, lot number 31814008. The antibody to CTCF used was a polyclonal antibody from Diagenode: part number is C15410210, lot number is A2359-00234P. All commercial histone antibodies were validated by at least two independent experiments. Histone mark antibody standards are available at the ENCODE portal: https://www.encodeproject.org/documents/4bb40778-387a-47c4-ab24-cebe64ead5ae/@@download/attachment/ENCODE_Approved_Oct_2016_Histone_and_Chromatin_associated_Proteins_Antibody_Characterization_Guidelines.pdf    The quality of the ChIP-seq data was determined using the read depth, NRF, two PCR bottlenecking coefficients (PBC1 and PBC2), replicate concordance (i.e., IDR), and FRiP. https://www.encodeproject.org/documents/4bb40778-387a-47c4-ab24-cebe64ead5ae/@@download/attachment/ENCODE_Approved_Oct_2016_Histone_and_Chromatin_associated_Proteins_Antibody_Characterization_Guidelines.pdf


title: 8048_Avonex_intermed_3


title: Region capture micro-C, WI-38 fibroblasts, PDL 21 Rep2

description: Library name: microC_WI-38_PDL21_Rep2


title: Region capture micro-C, WI-38 fibroblasts, PDL 21 Rep1

description: Library name: microC_WI-38_PDL21_Rep1


title: PT5F, KCit, FLIGHT, FEMALE, replicate 2

description: Library name: S_29


title: PT5F, KCit, FLIGHT, FEMALE, replicate 1

description: Library name: S_28


title: WI-38 fibroblasts, PDL33, whole cell extract, biological replicate

description: Library name: WCE_WI-38_PDL33_Rep2


title: WI-38 fibroblasts, PDL33, whole cell extract

description: Library name: WCE_WI-38_PDL33_Rep1


title: PT7M, CaOx, FLIGHT, MALE, replicate 3

description: Library name: S_27


title: WI-38 fibroblasts, PDL54, H3K27ac ChIP

description: Library name: H3K27ac_WI-38_PDL54

tag: chip antibody


title: 8048_Avonex_intermed_0


title: 8046_Avonex_intermed_144


title: WI-38 fibroblasts, PDL33, H3K27ac ChIP, biological replicate

description: Library name: H3K27ac_WI-38_PDL33_Rep2


title: 8046_Avonex_intermed_120


title: PT7M, CaOx, FLIGHT, MALE, replicate 2

description: Library name: S_26


title: WI-38 fibroblasts, PDL33, H3K27ac ChIP

description: Library name: H3K27ac_WI-38_PDL33_Rep1


title: WI-38 fibroblasts, PDL54, CTCF ChIP

description: Library name: CTCF_WI-38_PDL54

value: CTCF


title: WI-38 fibroblasts, PDL33, CTCF ChIP, biological replicate

description: Library name: CTCF_WI-38_PDL33_Rep2


title: WI-38 fibroblasts, PDL33, CTCF ChIP

description: Library name: CTCF_WI-38_PDL33_Rep1


title: PT6F, CaOx, FLIGHT, FEMALE, replicate 3

description: Library name: S_24


title: PT7M, CaOx, FLIGHT, MALE, replicate 1

description: Library name: S_25


title: 8046_Avonex_intermed_96


title: 8046_Avonex_intermed_72


title: Con_TON10

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level  3

department: Department of Pathology

country: Singapore

institute: National University Health System, Singapore

description: Library name: Con_TON10

data_processing:
Raw data quality was assessed with FastQC (v0.12.1)
Raw sequencing reads were mapped to the human reference genome (hg38) using bwa (v0.7.17). The alignment output was streamed directly to SAMtools (v1.20) for conversion from SAM to BAM format.
BAM files were then sorted by genomic coordinates using samtools
Genome-wide methylated regions and beta value were identified and generated using QSEA (v1.30.0).
The methylation regions were annotated with ChIPseeker (v1.38.0)
Assembly: hg38
Supplementary files format and content: csv format, Matrix of beta value of samples and annotation of the methylated regions.
Supplementary files format and content: csv format, Matrix of beta value of samples and annotation of the methylated regions.

source_name: Tonsil

growth_protocol: The Extranodal NK/T-cell Lymphoma cell lines included in this study were cultured in their respective culture media supplemented with appropriate additives and antibiotics, and maintained in a humidified incubator at 37°C with 5% CO2. Cells were then harvested and processed into formalin-fixed paraffin-embedded (FFPE) cell blocks for subsequent DNA extraction.

extract_protocol:
Total nucleic acids DNA were extracted from FFPE tissue sections using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen™), according to the manufacturer’s instructions. DNA concentration was measured by Qubit fluorometric quantification using the Qubit™ 1X dsDNA High Sensitivity (HS) Assay Kit (REF Q33230). DNA integrity and fragmentation were assessed using an Agilent 2100 Bioanalyzer with the High Sensitivity DNA reagents.
After immunoprecipitation, captured DNA was purified using the iPure Kit v2 (Diagenode). Libraries were amplified and indexed using NEBNext® Multiplex Oligos for Illumina® and the KAPA HyperPrep Kit, followed by purification and size selection with AMPure XP beads. Sequencing was performed as 150 bp paired-end reads on an Illumina HiSeq platform.

value: Tonsil

value: Not applicable

tag: batch


title: Con_TON9

description: Library name: Con_TON9


title: PT6F, CaOx, FLIGHT, FEMALE, replicate 2

description: Library name: S_23


title: Con_TON8

description: Library name: Con_TON8


title: 8046_Avonex_intermed_48


title: Con_TON7

description: Library name: Con_TON7


title: Con_TON6

description: Library name: Con_TON6


title: PT6F, CaOx, FLIGHT, FEMALE, replicate 1

description: Library name: S_22


title: 8046_Avonex_intermed_32


title: PT5F, CaOx, FLIGHT, FEMALE, replicate 3

description: Library name: S_21


title: Con_TON5

description: Library name: Con_TON5


title: Con_TON4

description: Library name: Con_TON4


title: Con_TON3

description: Library name: Con_TON3


title: PT5F, CaOx, FLIGHT, FEMALE, replicate 2

description: Library name: S_20


title: Con_TON2

description: Library name: Con_TON2


title: Con_TON1

description: Library name: Con_TON1


title: 8046_Avonex_intermed_8


title: 8046_Avonex_intermed_3


title: Con_NAS6

description: Library name: Con_NAS6

source_name: Nasal

value: Nasal


title: PT5F, CaOx, FLIGHT, FEMALE, replicate 1

description: Library name: S_19


title: Con_NAS5

description: Library name: Con_NAS5


title: Con_NAS4

description: Library name: Con_NAS4


title: PT7M, Control, FLIGHT, MALE, replicate 3

description: Library name: S_18


title: 8046_Avonex_intermed_0


title: PT7M, Control, FLIGHT, MALE, replicate 2

description: Library name: S_17


title: Con_NAS3

description: Library name: Con_NAS3


title: 8043_Avonex_intermed_144


title: Con_NAS2

description: Library name: Con_NAS2


title: PT7M, Control, FLIGHT, MALE, replicate 1

description: Library name: S_16


title: Con_NKC5

description: Library name: Con_NKC5

source_name: NK cell

value: NK cell


title: 8043_Avonex_intermed_120


title: Con_NKC3

description: Library name: Con_NKC3


title: Con_NKC4

description: Library name: Con_NKC4


title: Con_NKC2

description: Library name: Con_NKC2


title: PT6F, Control, FLIGHT, FEMALE, replicate 3

description: Library name: S_15


title: 8043_Avonex_intermed_96


title: 8046_Avonex_intermed_16


title: Con_NKC1

description: Library name: Con_NKC1


title: PT6F, Control, FLIGHT, FEMALE, replicate 2

description: Library name: S_14


title: Con_TC5

description: Library name: Con_TC5

source_name: T cell

value: T cell


title: 8043_Avonex_intermed_72

value: IM


title: 8043_Avonex_intermed_48

value: 15 μg


title: Con_TC4

description: Library name: Con_TC4


title: Con_TC2

description: Library name: Con_TC2


title: Con_TC3

description: Library name: Con_TC3


title: PT6F, Control, FLIGHT, FEMALE, replicate 1

description: Library name: S_13

value: Primary PTEC cell culture


title: 8043_Avonex_intermed_32


title: PT5F, Control, FLIGHT, FEMALE, replicate 2

description: Library name: EVT_4B

value: PTEC


title: PT5F, Control, FLIGHT, FEMALE, replicate 3

description: Library name: S_12

value: microgravity


title: Con_TC1

description: Library name: Con_TC1


title: Con_LN2

description: Library name: Con_LN2

source_name: Lymphnode

value: Lymphnode


title: Con_LN1

description: Library name: Con_LN1

value: Control


title: 8043_Avonex_intermed_16


title: Con_NAS1

description: Library name: Con_NAS1


title: PT5F, Control, FLIGHT, FEMALE, replicate 1

description: Library name: EVT_4A


title: 8043_Avonex_intermed_3


title: 8043_Avonex_intermed_8


title: ENKTL_CL2

description: Library name: ENKTL_CL2

source_name: ENKTL cell line

value: ENKTL cell line

value: ENKTL


title: PT10M, KCit, FLIGHT, MALE, replicate 3

description: Library name: EVT_3C

value: 1 ng/ml Calcium Oxalate + 250 µM Potassium Citrate


title: 8043_Avonex_intermed_0


title: ENKTL_CL3

description: Library name: ENKTL_CL3


title: PT10M, KCit, FLIGHT, MALE, replicate 2

description: Library name: EVT_3B


title: ENKTL_CL4

description: Library name: ENKTL_CL4

value: NKYS


title: ENKTL_SG20

description: Library name: ENKTL_SG20

source_name: ENKTL


title: PT10M, KCit, FLIGHT, MALE, replicate 1

description: Library name: EVT_3A


title: ENKTL_TW11

description: Library name: ENKTL_TW11


title: 8041_Pleg_intermed_312

value: SC


title: ENKTL_CL1

description: Library name: ENKTL_CL1


title: ENKTL_SG19B

description: Library name: ENKTL_SG19B


title: PT10M, CaOx, FLIGHT, MALE, replicate 3

description: Library name: EVT_2C

value: 1 ng/ml Calcium Oxalate


title: ENKTL_CL5

description: Library name: ENKTL_CL5


title: 8041_Pleg_intermed_216


title: ENKTL_SG19A

description: Library name: ENKTL_SG19A

value: Not applicable


title: 8041_Pleg_intermed_144


title: ENKTL_SG18

description: Library name: ENKTL_SG18


title: ENKTL_SG17

description: Library name: ENKTL_SG17


title: PT10M, CaOx, FLIGHT, MALE, replicate 1

description: Library name: EVT_2A


title: ENKTL_SG16

description: Library name: ENKTL_SG16


title: ENKTL_SG15

description: Library name: ENKTL_SG15


title: 8041_Pleg_intermed_120


title: PT10M, CaOx, FLIGHT, MALE, replicate 2

description: Library name: EVT_2B


title: ENKTL_SG14

description: Library name: ENKTL_SG14


title: PT10M, Control, FLIGHT, MALE, replicate 3

description: Library name: EVT_1C


title: ENKTL_SG13

description: Library name: ENKTL_SG13


title: 8041_Pleg_intermed_96


title: ENKTL_SG12

description: Library name: ENKTL_SG12


title: PT10M, Control, FLIGHT, MALE, replicate 2

description: Library name: EVT_1B


title: ENKTL_SG11B

description: Library name: ENKTL_SG11B


title: 8041_Pleg_intermed_72


title: PT10M, Control, FLIGHT, MALE, replicate 1

description: Library name: EVT_1A


title: ENKTL_SG11A

description: Library name: ENKTL_SG11A


title: ENKTL_TW10

description: Library name: ENKTL_TW10


title: ENKTL_TW9

description: Library name: ENKTL_TW9


title: ENKTL_TW8

description: Library name: ENKTL_TW8


title: 8041_Pleg_intermed_48


title: ADJIII-0169

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

description: Library name: ADJIII-0169

data_processing:
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.8a), with the annotation of known genes from gencode v37.
Gene expression was quantified using Salmon (1.4.0) and the annotation of protein coding genes from gencode v37.
Assembly: human genome GRCh38
Supplementary files format and content: rds file with 3 matrix, abudance, counts and length, with one patient per row

source_name: Cutaneous melanoma

extract_protocol:
RNA extractions were sequenced on the CLB platform, on an Illumina NovaSeq machine with a paired-end protocol  (64M reads).
Libraries were prepared with the RNAexome FFPE kit from Illumina.

value: Cutaneous melanoma


title: 8041_Pleg_intermed_32


title: ADJIII-0168

description: Library name: ADJIII-0168


title: ENKTL_TW7

description: Library name: ENKTL_TW7


title: ENKTL_TW6

description: Library name: ENKTL_TW6


title: 8041_Pleg_intermed_16


title: ENKTL_TW5

description: Library name: ENKTL_TW5


title: ADJIII-0161

description: Library name: ADJIII-0161


title: ENKTL_TW4

description: Library name: ENKTL_TW4


title: ENKTL_TW3

description: Library name: ENKTL_TW3


title: 8041_Pleg_intermed_8


title: ADJIII-0159

description: Library name: ADJIII-0159


title: ENKTL_TW2

description: Library name: ENKTL_TW2


title: 8041_Pleg_intermed_3


title: ENKTL_TW1

description: Library name: ENKTL_TW1


title: ADJIII-0157

description: Library name: ADJIII-0157


title: ENKTL_JP3

description: Library name: ENKTL_JP3


title: 8041_Pleg_intermed_0


title: ENKTL_JP2

description: Library name: ENKTL_JP2


title: ENKTL_JP1

description: Library name: ENKTL_JP1


title: ADJIII-0152

description: Library name: ADJIII-0152


title: 8035_Pleg_intermed_312


title: ENKTL_SG10

description: Library name: ENKTL_SG10


title: ADJIII-0150

description: Library name: ADJIII-0150


title: ENKTL_SG9

description: Library name: ENKTL_SG9


title: 8035_Pleg_intermed_216


title: ENKTL_SG8

description: Library name: ENKTL_SG8


title: ADJIII-0149

description: Library name: ADJIII-0149


title: 8035_Pleg_intermed_144


title: ENKTL_SG6B

description: Library name: ENKTL_SG6B


title: ADJIII-0144

description: Library name: ADJIII-0144


title: ENKTL_SG7

description: Library name: ENKTL_SG7


title: ENKTL_SG6A

description: Library name: ENKTL_SG6A


title: 8035_Pleg_intermed_120


title: ENKTL_SG5

description: Library name: ENKTL_SG5


title: ADJIII-0142

description: Library name: ADJIII-0142


title: ENKTL_SG4

description: Library name: ENKTL_SG4


title: 8035_Pleg_intermed_96


title: ENKTL_SG3

description: Library name: ENKTL_SG3


title: ADJIII-0140

description: Library name: ADJIII-0140


title: ENKTL_SG2

description: Library name: ENKTL_SG2


title: 8035_Pleg_intermed_72


title: 8035_Pleg_intermed_48


title: ADJIII-0139

description: Library name: ADJIII-0139


title: ENKTL_SG1

description: Library name: ENKTL_SG1


title: ENKTL_US5

description: Library name: ENKTL_US5


title: ADJIII-0137

description: Library name: ADJIII-0137


title: ENKTL_US4B

description: Library name: ENKTL_US4B


title: 8035_Pleg_intermed_32


title: ENKTL_US3

description: Library name: ENKTL_US3


title: ENKTL_US4A

description: Library name: ENKTL_US4A


title: ENKTL_US2

description: Library name: ENKTL_US2


title: ADJIII-0133

description: Library name: ADJIII-0133


title: ENKTL_US1

description: Library name: ENKTL_US1


title: 8035_Pleg_intermed_16


title: ADJIII-0127

description: Library name: ADJIII-0127


title: nTNKL_TW1

description: Library name: nTNKL_TW1

source_name: nodal-TNKL

value: nodal-TNKL


title: 8035_Pleg_intermed_8


title: 8035_Pleg_intermed_3


title: nTNKL_JP8

description: Library name: nTNKL_JP8


title: nTNKL_JP6

description: Library name: nTNKL_JP6


title: ADJIII-0121

description: Library name: ADJIII-0121


title: nTNKL_JP5

description: Library name: nTNKL_JP5


title: nTNKL_JP7

description: Library name: nTNKL_JP7


title: ADJIII-0124

description: Library name: ADJIII-0124


title: nTNKL_JP4

description: Library name: nTNKL_JP4


title: 8035_Pleg_intermed_0


title: nTNKL_JP3

description: Library name: nTNKL_JP3


title: ADJIII-0115

description: Library name: ADJIII-0115


title: ADJIII-0101

description: Library name: ADJIII-0101


title: nTNKL_JP2

description: Library name: nTNKL_JP2


title: nTNKL_KR1

description: Library name: nTNKL_KR1


title: 8033_Avonex_intermed_144


title: 8033_Avonex_intermed_120


title: ADJIII-0096

description: Library name: ADJIII-0096


title: nTNKL_JP1

description: Library name: nTNKL_JP1


title: nTNKL_SG2

description: Library name: nTNKL_SG2


title: 8033_Avonex_intermed_96


title: nTNKL_SG1

description: Library name: nTNKL_SG1


title: ADJIII-0095

description: Library name: ADJIII-0095


title: 8030_Avonex_low_96

treatment_protocol: Subjects were randomized between IFNβ-1a (7.5 µg) and pegIFNβ-1a (31.25 µg).


title: RPE/choroid tissue, Retinal_fibrosis_Col1_YFP_pos

city: Schlieren

first: Said

last: Aktas

state: Zurich

address: Wagistr 10

country: Switzerland

institute: Roche Innovation Center Zurich

description: Library name: Sample5

data_processing:
Sequencing data was processed using Cellranger and mapped to the mouse genome (mm10). The secondary analysis starting from raw counts was performed with the Scanpy package (version 1.9.6) (Wolf et al., 2018). Quality control measures included filtering out cells with high mitochondrial gene expression, cells with less than 200 or more than 10,000 expressed genes, and genes expressed in less than 3 cells. The processed data were normalized per total cell counts and log1p-transformed. Highly variable genes (n=4000) were selected for downstream analyses. Principal Component Analysis (PCA), t-Distributed Stochastic Neighbor Embedding (tSNE), and Uniform Manifold Approximation and Projection (UMAP) were employed for dimensionality reduction.
Assembly: mm10
Supplementary files format and content: mtx

organism: Mus musculus

source_name: Choroid

growth_protocol: C57Bl/6J mice and Col1a1-YFP mice (B6.Cg-Tg(Col1a1*3.6-Topaz)2Rowe/J, Strain 017466) mice were sourced from Jackson Laboratory and bred on-site. Col1a1-YFP mice were kept as a hemizygous line.

extract_protocol:
Mouse eyes were collected in 5% FBS in PBS and dissected to remove the cornea and lens. The retina and RPE/choroid were collected in digestion buffer (HBSS supplemented with 5% FBS, 10 mM HEPES, 1.5 mg/ml Collagenase and 0.1 mg/ml DNase I). Samples were digested for 40 min at 37°C, passed through a 70 um cell strainer, centrifuged for 5 min at 1,000 rpm and resuspended in 0.04% BSA in PBS. For scRNA seq analysis, cells were stained with PI and DRAQ5 and gated for PI negative, DRAQ5 positive and YFP positive/YFP negative cells and sorted on the BD FACSAria Fusion flow cytometer.
scRNA seq was performed using the 10X Genomics Chromium Single Cell 3ʹ v3 platform. YFP+ve and YFP-ve cells sorted from RPE/choroid tissue were resuspended in 0.04% BSA in PBS and loaded onto the Chromium controller. Chromium Single Cell 3’ v 3 reagents were used for library preparation according to the manufacturer’s protocol.

treatment_protocol: Mouse pupils were dilated with 1% tropicamide and 2.5% phenylephrine and anesthetized with ketamine/medetomidine (100/0.25 mg/kg). LiCNV was carried out using the Micron IV platform (532 nm, 300 mW, 100 ms, 50 um spot size, 3-4 spots per eye) in 8-12 week old Col1a1-YFP mice. In mice receiving the two stage LiCNV model, 7 days after the initial LiCNV, mice received a second set of laser burns (532 nm, 250 mW, 100 ms, 50 um spot size, 3-8 spots per eye) directly over the initial lesions.

value: Choroid


title: Sorted T CD4 AIM+ cells, LC11757, Long COVID

city: Santiago

first: Adolfo

middle: Alexis

last: Rojas-Hidalgo

address: OLIVOS 1007

country: Chile

institute: Universidad de Chile

description:
Library name: LC11757-AIM
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)

data_processing:
Initial data processing used CellRanger v7.1.0 (10x Genomics) for demultiplexing and alignment to human reference genome GRCh38.
Assembly: GRCh38
Supplementary files format and content: Expression matrix files of single-cell RNA sequencing experiments in HDF5 format (.h5)

source_name: PBMCs

extract_protocol:
Whole blood was collected from participants in heparin or EDTA-coated tubes, with processing initiated within four hours of collection. PBMCs were isolated from heparin tubes using Ficoll gradient separation and cryopreserved in cell freezing medium (90% heat-inactivated fetal bovine serum with 10% DMSO) until further use. CD4+ T cells were evaluated using an activation-induced marker (AIM) assay. Briefly, cryopreserved PBMCs were thawed, washed and cultured for 24 hours at 37°C and 5% CO2 with SARS-CoV-2 MPs containing spike and non-spike epitopes (1μg/mL), DMSO (negative control), or staphylococcal enterotoxin B (1μg/mL, positive control). Cells were pre-incubated with anti-human CD40 blocking antibody (0.5μg/mL) for 15 minutes prior to stimulation. Following stimulation, cells were stained with fluorochrome-conjugated antibodies, and CD16 and analyzed on a FACSAria IIu cell sorter (BD Biosciences). CD4+ T cells were classified into naïve (CCR7+CD45RA+), central memory (CCR7+CD45RA−), effector memory (CCR7−CD45RA−), and terminally differentiated effector memory (CCR7−CD45RA+) subsets. AIM+ cells were identified as OX40+41BB+. Three populations (naive, total memory, and AIM+) were sorted for subsequent single-cell RNA sequencing, with viability confirmed before experiments.
For sorted cells, indexed V(D)J, 5' Feature Barcode, and GEX libraries were prepared using the Chromium Next GEM Single Cell 5' v2 Dual Index kit with Feature Barcoding (10x Genomics). Pools of cells of the same subtype from five to seven individuals were obtained following the Cell Multiplexing Oligo Labeling protocol. Libraries were sequenced on Illumina NovaSeq platform.

value: PBMCs

value: T-cell

tag: age

tag: Sex

value: female

tag: severity

value: Moderate


title: RPE/choroid tissue, Retinal_fibrosis_Col1_YFP_neg

description: Library name: Sample4


title: RPE/choroid tissue, Retinal_wound_Col1_YFP_pos

description: Library name: Sample3


title: 8033_Avonex_intermed_48

value: IM

value: 15 μg


title: RPE/choroid tissue, Retinal_wound_Col1_YFP_neg

description: Library name: Sample2


title: 8033_Avonex_intermed_32


title: ADJIII-0087

description: Library name: ADJIII-0087


title: ADJIII-0089

description: Library name: ADJIII-0089


title: RPE/choroid tissue, Healthy

description: Library name: Sample1

value: Untreated


title: tumor cellr, Low glucose MYC overexpression, replicate 1

city: Wuhan

first: Wenlong

last: Jia

address: 1095 Jiefang Avenue

country: China

institute: Tongji Hospital

description: Library name: lowMYC

data_processing:
Raw sequencing reads were subjected to quality control and adapter trimming. Clean reads were aligned to the Homo sapiens reference genome GRCh38/hg38 using Bowtie2.
Duplicate or low-quality reads were removed, and genome-wide MYC-enriched regions were identified using a peak-calling algorithm. Peak files were generated separately for each biological sample.
Normalized MYC occupancy signal tracks were generated for genome-browser visualization. Genome-wide signal profiles and MYC-binding regions were visualized using Integrative Genomics Viewer.
Comparative analyses were performed to identify changes in MYC chromatin occupancy among high-glucose, low-glucose, and low-glucose plus MYC-overexpression conditions, with particular attention to the promoter and transcription start site regions of SLC1A5.
Assembly: Homo sapiens GRCh38/hg38
Supplementary files format and content: Processed data include BED or narrowPeak files containing MYC-enriched chromatin regions identified for each sample and normalized bigWig files showing genome-wide MYC occupancy profiles. Differential binding tables comparing the indicated glucose and MYC-expression conditions are also provided, where applicable.
Library strategy: CUT&Tag

source_name: liver tumor

growth_protocol: Human hepatocellular carcinoma cells were maintained under standard culture conditions at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Cells were collected and incubated with concanavalin A–coated magnetic beads. Cell membranes were permeabilized, and bead-bound cells were incubated with an anti-MYC primary antibody overnight at 4°C, followed by incubation with a secondary antibody. After washing, the cells were incubated with a protein A–Tn5 transposase fusion complex for antibody-guided chromatin tagmentation.
CUT&Tag libraries were constructed using the Hyperactive Universal CUT&Tag Assay Kit (Vazyme Biotech, TD904) according to the manufacturer’s protocol. Tagmented DNA was purified and PCR-amplified to generate sequencing libraries. Libraries were subjected to paired-end high-throughput sequencing on the SURFSeq 5000 platform.

treatment_protocol: Cells were cultured under plasma-level high-glucose, tumor-relevant low-glucose, or tumor-relevant low-glucose conditions with MYC overexpression before CUT&Tag profiling. CUT&Tag was performed using an antibody against MYC to assess glucose- and MYC-dependent changes in chromatin occupancy.

value: liver tumor

value: Tumor cells

value: MHCC97H cultured in low glucose MYC overexpression, MYC binding


title: ADJIII-0086

description: Library name: ADJIII-0086


title: tumor cellr, Low glucose, replicate 1

description: Library name: Low

value: MHCC97H cultured in low glucose, MYC binding


title: 8033_Avonex_intermed_16


title: ADJIII-0085

description: Library name: ADJIII-0085


title: tumor cellr, IGG, replicate 1

description: Library name: IGG

value: MHCC97H cultured in high glucose, IGG binding


title: LM3 cultured in low glucose, replicate 1

description: Library name: LM3L

data_processing:
Raw sequencing reads were quality controlled. Reads from human LM3 samples were aligned to the Homo sapiens reference genome GRCh38/hg38, whereas reads from mouse tumor-cell samples were aligned to the Mus musculus reference genome GRCm38/mm10, using Bowtie2.
Genome-wide accessible chromatin regions were identified using MACS2. Peak files were generated separately for each biological sample.
Normalized chromatin-accessibility signal tracks were generated for genome-browser visualization. ATAC-seq accessibility profiles were visualized using Integrative Genomics Viewer.
Assembly: For human LM3 samples: Homo sapiens GRCh38/hg38  For mouse tumor-cell samples: Mus musculus GRCm38/mm10
Supplementary files format and content: Processed data include BED or narrowPeak files containing accessible chromatin regions identified for each sample and normalized bigWig signal files showing genome-wide ATAC-seq accessibility profiles. Differentially accessible region tables comparing high- versus low-glucose LM3 cells and control-diet versus caloric restriction–derived mouse tumor cells are also provided, where applicable.

growth_protocol: Human LM3 hepatocellular carcinoma cells were maintained in culture under standard conditions. For the in vivo arm, male C57BL/6J mice were housed under specific-pathogen-free conditions with controlled temperature, humidity, and a 12-hour light/dark cycle. GFP-labeled tumor cells were implanted into mice to establish tumor-bearing models. Mice were assigned to either a control diet or a caloric restriction (CR) diet.

extract_protocol:
For LM3 samples, cultured cells were collected, washed with ice-cold phosphate-buffered saline, and lysed in cold lysis buffer to release nuclei. For mouse tumor samples, sorted GFP-positive tumor cells were washed with ice-cold phosphate-buffered saline and lysed in cold lysis buffer to release nuclei. Approximately 50,000 cells were used for each sample. Nuclei were collected by centrifugation and subjected to Tn5 transposase-mediated tagmentation.
ATAC-seq libraries were constructed using a Tn5 transposase-based library preparation kit (Vazyme Biotech, TD711). Isolated nuclei were incubated with the transposition reaction mixture at 37°C for 30 minutes. Tagmented DNA was purified, PCR-amplified, and subjected to high-throughput sequencing on an Illumina platform.

treatment_protocol: For the in vitro arm, LM3 cells were cultured under plasma-level high-glucose or tumor-relevant low-glucose conditions before collection for bulk ATAC-seq. For the in vivo arm, tumor-bearing mice were maintained on a control diet or subjected to caloric restriction. At the designated experimental endpoint, tumors were collected and dissociated into single-cell suspensions. Live GFP-positive tumor cells were isolated by fluorescence-activated cell sorting and immediately processed for bulk ATAC-seq.

value: LM3 cultured in low glucose


title: 8033_Avonex_intermed_8


title: 8033_Avonex_intermed_3


title: Whole blood, crystalloid, TAU-01, T3

city: Edinburgh

first: John

last: Cafferkey

address: Queens Medical Research Institute, Little France Campus

country: United Kingdom

institute: University of Edinburgh

description: Library name: TAU-01_T3

data_processing:
Adapter and quality trimming with Trimmomatic (Illumina/NEBNext adapters: R1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; R2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
Transcript quantification with Salmon v1.2.0 against the GENCODE release 43 transcriptome (GRCh38).
Transcript-level estimates imported and summarised to gene level with tximport; differential expression with DESeq2 (R 4.3.1, Bioconductor 3.18).
Assembly: GRCh38; GENCODE release 43.
Supplementary files format and content: Tab-delimited text. GEO_processed_gene_counts.tsv.gz = raw gene-level counts (rows=Ensembl gene ID + symbol, columns=samples). GEO_processed_gene_TPM.tsv = gene-level TPM.

source_name: Whole blood

growth_protocol: Not applicable, human samples

extract_protocol:
Whole blood collected into Tempus Blood RNA Tubes (Thermo Fisher #4342792). Total RNA extracted with the MagMAX for Stabilised Blood Tubes RNA Isolation Kit (Thermo Fisher #4451894). RNA integrity assessed on an Agilent Fragment Analyser (#5300, Standard Sensitivity RNA Analysis Kit DNF-471-0500; mean RQN 3.9); RNA and DNA quantified by Qubit (RNA broad-range #Q10210; dsDNA HS #Q32854). Samples with >20% DNA contamination were excluded; 69 of 76 samples proceeded to library preparation.
Libraries prepared from 250 ng total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) with the NEBNext Globin & rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E7550X). Stranded (dUTP second-strand) protocol; 11 cycles of PCR; barcoded with NEBNext Multiplex Oligos for Illumina Unique Dual Index Primer Pairs (NEB #E6442L).

treatment_protocol: Participants randomised within the ABC Sepsis trial to 5% human albumin solution or crystalloid for resuscitation. Whole blood collected into RNA-stabilising Tempus tubes at T1 (baseline), T2 and T3.

value: Whole blood

value: crystalloid


title: LM3 cultured in high glucose, replicate 1

description: Library name: LM3H

value: LM3 cultured in high glucose


title: 8033_Avonex_intermed_0


title: ADJIII-0083

description: Library name: ADJIII-0083

value: Cutaneous melanoma


title: ADJIII-0079

description: Library name: ADJIII-0079


title: Whole blood, crystalloid, TAU-01, T1

description: Library name: TAU-01_T1


title: Whole blood, crystalloid, RIE-19, T3

description: Library name: RIE-19_T3


title: ADJIII-0075

description: Library name: ADJIII-0075


title: 8031_Pleg_intermed_312

value: SC


title: Whole blood, crystalloid, RIE-19, T2

description: Library name: RIE-19_T2


title: Whole blood, crystalloid, RIE-19, T1

description: Library name: RIE-19_T1


title: Whole blood, crystalloid, RIE-18, T3

description: Library name: RIE-18_T3


title: 8031_Pleg_intermed_216


title: Whole blood, crystalloid, RIE-18, T2

description: Library name: RIE-18_T2


title: ADJIII-0073

description: Library name: ADJIII-0073


title: 8031_Pleg_intermed_144


title: ADJIII-0072

description: Library name: ADJIII-0072


title: Whole blood, crystalloid, RIE-18, T1

description: Library name: RIE-18_T1


title: Whole blood, crystalloid, RIE-16, T3

description: Library name: RIE-16_T3


title: ADJIII-0069

description: Library name: ADJIII-0069


title: Whole blood, crystalloid, RIE-16, T2

description: Library name: RIE-16_T2


title: 8027_Avonex_low_72


title: 8031_Pleg_intermed_120


title: Sorted T CD4 naive cells, LC11757, Long COVID

description:
Library name: LC11757-Naive
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)

value: PBMCs

value: T-cell


title: Whole blood, crystalloid, RIE-16, T1

description: Library name: RIE-16_T1


title: 8031_Pleg_intermed_96


title: Whole blood, crystalloid, RIE-15, T3

description: Library name: RIE-15_T3


title: Whole blood, crystalloid, RIE-15, T2

description: Library name: RIE-15_T2


title: ADJIII-0063

description: Library name: ADJIII-0063


title: Whole blood, crystalloid, RIE-15, T1

description: Library name: RIE-15_T1


title: 8031_Pleg_intermed_72


title: Whole blood, crystalloid, RIE-14, T3

description: Library name: RIE-14_T3


title: Whole blood, crystalloid, RIE-14, T2

description: Library name: RIE-14_T2


title: 8031_Pleg_intermed_48


title: ADJIII-0061

description: Library name: ADJIII-0061


title: ADJIII-0057

description: Library name: ADJIII-0057


title: 8031_Pleg_intermed_32


title: Whole blood, crystalloid, RIE-14, T1

description: Library name: RIE-14_T1


title: Whole blood, crystalloid, RIE-12, T3

description: Library name: RIE-12_T3


title: ADJIII-0054

description: Library name: ADJIII-0054


title: Whole blood, crystalloid, RIE-12, T2

description: Library name: RIE-12_T2


title: 8031_Pleg_intermed_16


title: Whole blood, crystalloid, RIE-10, T2

description: Library name: RIE-10_T2


title: Whole blood, crystalloid, RIE-12, T1

description: Library name: RIE-12_T1


title: Whole blood, crystalloid, RIE-10, T1

description: Library name: RIE-10_T1


title: Whole blood, crystalloid, RIE-08, T3

description: Library name: RIE-08_T3


title: ADJIII-0053

description: Library name: ADJIII-0053


title: 8031_Pleg_intermed_0


title: Whole blood, crystalloid, RIE-04, T3

description: Library name: RIE-04_T3


title: ADJIII-0041

description: Library name: ADJIII-0041


title: Whole blood, crystalloid, RIE-08, T1

description: Library name: RIE-08_T1


title: Whole blood, crystalloid, RIE-01, T3

description: Library name: RIE-01_T3


title: 8029_Pleg_intermed_312


title: Whole blood, crystalloid, RIE-01, T2

description: Library name: RIE-01_T2


title: 8029_Pleg_intermed_216


title: Whole blood, albumin, RIE-20, T3

description: Library name: RIE-20_T3

value: albumin


title: 8029_Pleg_intermed_144


title: Whole blood, albumin, RIE-20, T2

description: Library name: RIE-20_T2


title: ADJIII-0037

description: Library name: ADJIII-0037


title: 8029_Pleg_intermed_120


title: ADJIII-0025

description: Library name: ADJIII-0025


title: Whole blood, albumin, RIE-13, T2

description: Library name: RIE-13_T2


title: 8029_Pleg_intermed_72


title: 8031_Pleg_intermed_3


title: Whole blood, crystalloid, RIE-08, T2

description: Library name: RIE-08_T2


title: ADJIII-0047

description: Library name: ADJIII-0047


title: ADJIII-0040

description: Library name: ADJIII-0040


title: 8029_Pleg_intermed_48


title: Whole blood, albumin, RIE-11, T2

description: Library name: RIE-11_T2


title: ADJIII-0023

description: Library name: ADJIII-0023


title: Whole blood, albumin, RIE-13, T1

description: Library name: RIE-13_T1


title: ADJIII-0038

description: Library name: ADJIII-0038


title: Whole blood, albumin, RIE-20, T1

description: Library name: RIE-20_T1


title: Whole blood, albumin, RIE-17, T3

description: Library name: RIE-17_T3


title: Whole blood, albumin, RIE-11, T1

description: Library name: RIE-11_T1


title: Whole blood, albumin, RIE-17, T2

description: Library name: RIE-17_T2


title: ADJIII-0034

description: Library name: ADJIII-0034


title: ADJIII-0022

description: Library name: ADJIII-0022


title: Whole blood, albumin, RIE-09, T2

description: Library name: RIE-09_T2


title: 8029_Pleg_intermed_96


title: Whole blood, albumin, RIE-17, T1

description: Library name: RIE-17_T1


title: Whole blood, albumin, RIE-09, T3

description: Library name: RIE-09_T3


title: Whole blood, albumin, RIE-09, T1

description: Library name: RIE-09_T1


title: 8029_Pleg_intermed_16


title: ADJIII-0019

description: Library name: ADJIII-0019


title: 8029_Pleg_intermed_8


title: Whole blood, albumin, RIE-07, T1

description: Library name: RIE-07_T1


title: ADJIII-0018

description: Library name: ADJIII-0018


title: Whole blood, albumin, RIE-06, T3

description: Library name: RIE-06_T3


title: 8029_Pleg_intermed_3


title: Whole blood, albumin, RIE-06, T2

description: Library name: RIE-06_T2


title: Whole blood, albumin, RIE-05, T3

description: Library name: RIE-05_T3


title: Whole blood, albumin, RIE-05, T2

description: Library name: RIE-05_T2


title: 8022_Avonex_intermed_144

value: IM


title: ADJIII-0015

description: Library name: ADJIII-0015


title: Whole blood, albumin, RIE-05, T1

description: Library name: RIE-05_T1


title: W12_PBMC_G1_VDJ

status: Public on Jun 24 2026

city: La Jolla

first: Patrick

last: Madden

state: CA

address: 9420 Athena Circle

department: Center for Vaccine Innovation

institute: La Jolla Institute for Immunology

description:
Library name: W12_PBMC_G1_VDJ
VDJ 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: BCR-Seq

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
N332-GT5 epitope-specific B cells were isolated from peripheral blood samples collected from rhesus macaques immunized with N332-GT5 and subsequent heterologous boost immunizations. Probes for each boost immunogen were included in flow cytometry staining for each respective Group, allowing determination of the proportion of N332-GT5 epitope-specific cells cross-binding the boost immunogen (N332-GT5++KO– Boost++). Thawed cells were incubated with both N332-GT5 KO and Boost KO probes for twenty minutes at 4°C. Following that, cells were sequentially incubated with the combined Booster WT probes for fifteen minutes at 4°C and then with the combined N332-GT5 WT probes for thirty minutes at 4°C. A master mix of surface staining antibodies was added next, with 2 μg per 5 million cells of anti-human Total-Seq-C hashtag antibodies (Biolegend) following the surface staining, and incubated for thirty minutes at 4°C. Cells were then washed twice and prepared for sorting on BD FACSymphony S6 (BD Biosciences). Epitope-specific B cells were sorted at all time points.Once sorted, epitope-specific PBMC and LN FNA B cells were washed with PBS and loaded onto a Chromium chip and controller following the manufacturers protocol (10X Genomics).  Indexed V(D)J, Feature Barcode, and Gene Expression libraries were prepared following the 10X Genomics protocol with the Feature Barcoding Kit (10X Genomics) and sequenced on a NovaSeq 6000 (Illumina).
Libraries were constructed according to the manufacturer's protocol using the Chromium Next GEM Single Cell 5’ Reagent Kit v3.

value: PBMC

value: B cells

value: Protein immunized


title: 8022_Avonex_intermed_120

value: 15 μg


title: Whole blood, albumin, RIE-03, T2

description: Library name: RIE-03_T2


title: Whole blood, albumin, RIE-03, T3

description: Library name: RIE-03_T3


title: ADJIII-0011

description: Library name: ADJIII-0011


title: 8033_Avonex_intermed_72


title: Whole blood, albumin, RIE-03, T1

description: Library name: RIE-03_T1


title: 8022_Avonex_intermed_96


title: Whole blood, albumin, RIE-02, T3

description: Library name: RIE-02_T3


title: ADJIII-0010

description: Library name: ADJIII-0010


title: Whole blood, albumin, RIE-02, T2

description: Library name: RIE-02_T2


title: 8022_Avonex_intermed_72


title: Whole blood, albumin, RIE-02, T1

description: Library name: RIE-02_T1


title: 8029_Pleg_intermed_32


title: ADJIII-0021

description: Library name: ADJIII-0021


title: Whole blood, albumin, RAH-05, T3

description: Library name: RAH-05_T3


title: 8022_Avonex_intermed_48


title: ADJIII-0009

description: Library name: ADJIII-0009


title: Whole blood, albumin, RAH-05, T2

description: Library name: RAH-05_T2


title: ADJIII-0003

description: Library name: ADJIII-0003


title: Whole blood, albumin, RIE-07, T3

description: Library name: RIE-07_T3


title: Whole blood, albumin, RAH-05, T1

description: Library name: RAH-05_T1


title: Whole blood, albumin, RIE-07, T2

description: Library name: RIE-07_T2


title: Whole blood, albumin, RAH-04, T2

description: Library name: RAH-04_T2


title: ADJIII-0067

description: Library name: ADJIII-0067


title: ADJIII-0017

description: Library name: ADJIII-0017


title: Whole blood, albumin, RAH-04, T1

description: Library name: RAH-04_T1


title: 8022_Avonex_intermed_16


title: 7M

description: Library name: 7M

data_processing:
cellranger v7.1.0 , algo "multi" avec référence génome refdata-gex-GRCh38-2020-A et probeset Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A.csv
Assembly: genome refdata-gex-GRCh38-2020-A
Supplementary files format and content: matrix h5, raw and filtered, one per patient

source_name: Cutaneous melanoma metastasis

extract_protocol:
snPATHOseq protocol (Wang et al 2024, https://doi.org/10.1038/s42003-024-07043-2) from FFPE tissue.
Next GEM Flex protocol

value: Cutaneous melanoma metastasis


title: 8022_Avonex_intermed_32

source_name: EDTA plasma


title: Whole blood, albumin, RIE-13, T3

description: Library name: RIE-13_T3


title: Whole blood, albumin, RAH-03, T3

description: Library name: RAH-03_T3


title: Whole blood, albumin, RAH-03, T1

description: Library name: RAH-03_T1


title: 4M

description: Library name: 4M


title: 8029_Pleg_intermed_0


title: Whole blood, albumin, RIE-06, T1

description: Library name: RIE-06_T1


title: Whole blood, albumin, RAH-02, T3

description: Library name: RAH-02_T3


title: 8022_Avonex_intermed_8


title: ADJIII-0133

description: Library name: ADJIII-0133

data_processing:
spaceranger v3.0.0, algo "count" avec référence génome refdata-gex-GRCh38-2020-A et probeset Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv
Assembly: genome refdata-gex-GRCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
Briefly, five micron FFPE section were placed on histological slides (TOMO), deparafinized, stained with hematoxylin and eosin by the Research Pathology Platform at CRCL. After imaging, 6.5 x 6.5 mm areas were selected in the tissue section for each patient. After destaining and decrosslinking steps, human Visium probes were hybridized on the samples, ligated and transferred on the Visium capture slides using the CytAssist instrument (10X Genomics)
Libraries were then prepared and sequenced on a NovaSeq 6000 sequencer (Illumina) targeting 50,000 reads/spot.


title: Whole blood, albumin, RAH-02, T2

description: Library name: RAH-02_T2


title: 8031_Pleg_intermed_8


title: 8022_Avonex_intermed_3


title: 8022_Avonex_intermed_0


title: 16JB_Post_260330_invitro3hr

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

description:
Library name: Sample 22
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
16_Post

data_processing:
Transcript abundance was determined from FASTQ files using Salmon (v1.8.0) and the Ensembl reference transcript sequences. Transcript per million (TPM) values and gene level counts were calculated using the tximport R Bioconductor package (v1.22.0). Differential gene expression analysis was performed with the DESeq2 R Bioconductor package (v 1.44.0) .
Assembly: hg38
Supplementary files format and content: raw counts from DESeq2

source_name: HprAD - Human Subcutaneous Preadipocyte

extract_protocol:
RNA was harvested using the trizol-chloroform technique followed by the Qiagen Rneasy micro kit.
100ng of total RNA was used to generate RNA-Seq libraries using Illumina stranded mRNA kit (Catalog#: 20040534), following the manufactures protocol.   Libraries prepared with unique dual indexes were pooled at equal molar ratios.

treatment_protocol: In vitro adipocytes were collected 3 hours following incubation with plasma collected either in the resting (no exercise) state, or with plasma collected immediately following sprint-interval exercise or moderate-intensity exercise.

value: HprAD - Human Subcutaneous Preadipocyte

value: Adipocyte

value: MIE Plasma

tag: time

value: Post


title: Whole blood, albumin, RAH-02, T1

description: Library name: RAH-02_T1

value: Whole blood


title: 13EP_Post_260330_invitro3hr

description:
Library name: Sample 21
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
13_Post


title: ADJIII-0048

description: Library name: ADJIII-0048


title: ADJIII-0013

description: Library name: ADJIII-0013


title: ADJIII-0022

description: Library name: ADJIII-0022


title: 5AF_Post_260330_invitro3hr

description:
Library name: Sample 20
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
05_Post


title: ADJIII-0013

description: Library name: ADJIII-0013


title: Whole blood, crystalloid, RIE-04, T1

description: Library name: RIE-04_T1

value: crystalloid


title: 3JS_Post_260330_invitro3hr

description:
Library name: Sample 19
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
03_Post


title: 8020_Pleg_intermed_216


title: ADJIII-0019

description: Library name: ADJIII-0019

value: Cutaneous melanoma


title: 8020_Pleg_intermed_312

value: SC


title: Whole blood, crystalloid, RIE-01, T1

description: Library name: RIE-01_T1


title: 16JB_Pre_260330_invitro3hr

description:
Library name: Sample 17
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
16_Pre

value: Pre


title: 2ML_Post_260330_invitro3hr

description:
Library name: Sample 18
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
02_Post


title: PDX376_1018_20_AZD9833_41R

city: Barcelona

first: Alba

last: Mas Malavila

address: Saturnino Calleja 11-13

country: Spain

institute: VHIO

description:
Library name: 260
260 is a replicate of a sample treated with camizestrant from PDX376
2023-07-12_hg38_PDX376_deseq2_normalized_counts.txt

data_processing:
Raw reads were mapped to the human reference genome (Gencode, release 38) and counted at the gene level using STAR version 2.55.3a and parameters '--outSAMunmapped None --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts'.
Differential expression analysis was performed in the R (version 4.0.0)/ Bioconductor environment, using the DESeq2 package version 1.28.1
Assembly: RNA-seq reads were mapped against the human reference genome (Gencode 38) with STAR 2.5.3a using ENCODE parameters.
Supplementary files format and content: DESeq2 normalized counts in txt format

source_name: Breast cancer Patient Derived Xenograft

extract_protocol:
RNeasy Mini Kit (#74106, Qiagen)
KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche)

value: Breast cancer Patient Derived Xenograft

tag: condition

value: Treated

value: Camizestrant

tag: sensitivity

value: Sensitive


title: 13EP_Pre_260330_invitro3hr

description:
Library name: Sample 16
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
13_Pre


title: 8020_Pleg_intermed_144

data_processing:
https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.
Read out is relative flourescent units (RFU) which is directly proportional to the amount of target protein in the initial sample, as informed by a standard curve generate for each protein-SOMAmer pair. Raw RFU is normalized as described in the data processing step above.

tag: drug group

tag: delivery


title: 5AF_Pre_260330_invitro3hr

description:
Library name: Sample 15
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
05_Pre


title: 3JS_Pre_260330_invitro3hr

description:
Library name: Sample 14
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
03_Pre


title: 8020_Pleg_intermed_120

tag: dose

tag: timepoint


title: 8020_Pleg_intermed_96


title: PDX376_1018_20_RAD_13R

description:
Library name: 82
82 is a replicate of a sample treated with EP0062 from PDX376
2023-07-12_hg38_PDX376_deseq2_normalized_counts.txt

tag: tissue


title: 15RP_Post_260330_invitro3hr

description:
Library name: Sample 11
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
15_Post

tag: cell type

value: SIE Plasma


title: PDX376_1018_20_RAD_12R

description:
Library name: 36
36 is a replicate of a sample treated with EP0062 from PDX376
2023-07-12_hg38_PDX376_deseq2_normalized_counts.txt

tag: treatment


title: 10EC_Post_260330_invitro3hr

description:
Library name: Sample 10
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
10_Post


title: 8020_Pleg_intermed_72


title: PDX376_1018_20_Control_2R

description:
Library name: 81
81 is a replicate of a control sample from PDX376
2023-07-12_hg38_PDX376_deseq2_normalized_counts.txt

value: Control


title: 8020_Pleg_intermed_48


title: 8PF_Post_260330_invitro3hr

description:
Library name: Sample 9
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
08_Post


title: 4JA_Post_260330_invitro3hr

description:
Library name: Sample 8
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
04_Post


title: 1CB_Post_260330_invitro3hr

description:
Library name: Sample 7
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
01_Post


title: 8020_Pleg_intermed_32


title: PDX376_1018_20_Control_2L

description:
Library name: 34
34 is a replicate of a control sample from PDX376
2023-07-12_hg38_PDX376_deseq2_normalized_counts.txt


title: 17AA_Pre_260330_invitro3hr

description:
Library name: Sample 6
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
17_Pre


title: 15RP_Pre_260330_invitro3hr

description:
Library name: Sample 5
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
15_Pre


title: PDX512_1064_20_AZD9833_43R

description:
Library name: 257
257 is a replicate of a sample treated with camizestrant from PDX512
2023-07-18_hg38_PDX512_9_samples_deseq2_normalized_counts.txt


title: 8020_Pleg_intermed_16


title: 8PF_Pre_260330_invitro3hr

description:
Library name: Sample 3
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
08_Pre


title: PDX512_1064_20_AZD9833_44R

description:
Library name: 512_Z2
512_Z2 is a replicate of a sample treated with camizestrant from PDX512
2023-07-18_hg38_PDX512_9_samples_deseq2_normalized_counts.txt


title: 1CB_Pre_260330_invitro3hr

description:
Library name: Sample 2
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
01_Pre


title: 8020_Pleg_intermed_8


title: 4JA_Pre_260330_invitro3hr

description:
Library name: Sample 1
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
04_Pre


title: 8020_Pleg_intermed_3


title: scVDJ-Seq (TCR) of PBMC from year 9.3 patient#21

city: Philadelphia

first: Zhixuan

last: Zheng

state: Pennsylvania

address: 4258 chestnut st.

institute: Perelman School of Medicine at the University of Pennsylvania

description:
Library name: year 9.3 patient#21_VDJ
Single-cell 5′ TCR V(D)J library generated using 10x Genomics Chromium GEM-X v3 kit, sequenced on Illumina NextSeq 2000

library_source: other

data_processing:
Demultiplexing was performed using Illumina bcl2fastq v2.20. Filtered gene-barcode matrices were generated using Cell Ranger v8.0.1 (10x Genomics) with GRCh38 +CAR reference. Processed data were analyzed in Seurat v5.2.1 for QC, normalization, PCA/UMAP, clustering, and DEG analysis; TCR clonotypes were assigned using scRepertoire v2.5.1. Batch correction and functional enrichment were performed with Harmony v1.2.3, clusterProfiler v4.16.0, and ReactomePA v1.52.0.
Assembly: Homo sapiens GRCh38 (Ensembl 108) +  CAR sequence
Supplementary files format and content: Processed data include Seurat objects (.rds) containing normalized gene expression matrices, metadata, clustering assignments, and UMAP embeddings. TCR clonotype annotations are provided as filtered_contig_annotations.csv derived from Cell Ranger V(D)J analysis.

molecule: other

source_name: Peripheral blood

growth_protocol: FACS-purified PBMCs or CAR T cells were washed twice with PBS + 0.04% BSA and resuspended prior to 10x Genomics Chromium loading.

extract_protocol:
Single cells were encapsulated and lysed in 10x Genomics Chromium GEMs; mRNA was captured with oligo-dT beads for 5′ cDNA synthesis.
Gene-expression and TCR V(D)J libraries were prepared using Chromium GEM-X Single Cell 5′ Kit v3 (10x Genomics) and sequenced on Illumina NextSeq 2000.

treatment_protocol: Samples were collected at indicated clinical time points (peak and year 9.3 post CAR-T infusion) without in vitro treatment.

value: Peripheral blood

value: T cell


title: PDX512_1064_20_RAD_15R

description:
Library name: 256
256 is a replicate of a sample treated with EP0062 from PDX512
2023-07-18_hg38_PDX512_9_samples_deseq2_normalized_counts.txt


title: scRNA-Seq (5′) of PBMC from year 9.3 patient#21

description:
Library name: year 9.3 patient#21_GE
Single-cell 5′ RNA-seq library generated using 10x Genomics Chromium GEM-X v3 kit, sequenced on Illumina NextSeq 2000

value: Peripheral blood mononuclear cell


title: PDX512_1064_20_AZD9833_44L

description:
Library name: 512_Z1
512_Z1 is a replicate of a sample treated with camizestrant from PDX512
2023-07-18_hg38_PDX512_9_samples_deseq2_normalized_counts.txt


title: scVDJ-Seq (TCR) of PBMC from peak patient#21

description:
Library name: peak patient#21_VDJ
Single-cell 5′ TCR V(D)J library generated using 10x Genomics Chromium GEM-X v3 kit, sequenced on Illumina NextSeq 2000


title: 8020_Pleg_intermed_0

extract_protocol: EDTA plasma from whole blood


title: 8PF_Pre_250305_invitro12hr

description: Library name: Sample 40

treatment_protocol: Human abdominal subcutaneous adipose tissue was collected 7-10 days before, or 3-hours following, a graded exercise test on a treadmill. In vitro adipocytes were collected 12-hours following incubation with plasma collected either in the resting (no exercise) state, or with plasma collected immediately following sprint-interval exercise or moderate-intensity exercise.

value: HprAD - Human Subcutaneous Preadipocyte

value: Adipocyte


title: 8016_Avonex_intermed_144

value: IM

value: 15 μg


title: PDX512_1064_20_RAD_16R

description:
Library name: 512_R2
512_R2 is a replicate of a sample treated with EP0062 from PDX512
2023-07-18_hg38_PDX512_9_samples_deseq2_normalized_counts.txt


title: 8PF_pos_0_250305_invitro12hr

description: Library name: Sample 39


title: PDX512_1064_20_RAD_16L

description:
Library name: 512_R1
512_R1 is a replicate of a sample treated with EP0062 from PDX512
2023-07-18_hg38_PDX512_9_samples_deseq2_normalized_counts.txt


title: 8016_Avonex_intermed_120


title: 7SL_Pre_250305_invitro12hr

description: Library name: Sample 38

value: MIE Plasma


title: 7SL_pos_0_250305_invitro12hr

description: Library name: Sample 37


title: 8016_Avonex_intermed_96


title: PDX512_1064_20_Control_5R

description:
Library name: 512_C2
512_C2 is a replicate of a control sample from PDX512
2023-07-18_hg38_PDX512_9_samples_deseq2_normalized_counts.txt


title: 5AF_pos_0_250305_invitro12hr

description: Library name: Sample 35


title: 4JA_Pre_250305_invitro12hr

description: Library name: Sample 34


title: 8016_Avonex_intermed_72


title: PDX512_1064_20_Control_5L

description:
Library name: 512_C1
512_C1 is a replicate of a control sample from PDX512
2023-07-18_hg38_PDX512_9_samples_deseq2_normalized_counts.txt


title: 3JS_pos_0_250305_invitro12hr

description: Library name: Sample 31


title: PDX423_1002_20_AZD9833_41L

description:
Library name: 258
258 is a replicate of a sample treated with camizestrant from PDX423
2023-07-12_hg38_PDX423_deseq2_normalized_counts.txt

value: Resistant


title: 2ML_pos_0_250305_invitro12hr

description: Library name: Sample 29


title: PDX423_1002_20_AZD9833_42R

description:
Library name: 423_Z2
423_Z2 is a replicate of a sample treated with camizestrant from PDX423
2023-07-12_hg38_PDX423_deseq2_normalized_counts.txt


title: 17AA_pos_0_250305_invitro12hr

description: Library name: Sample 27


title: 17AA_Pre_250305_invitro12hr

description: Library name: Sample 28


title: 16JB_Pre_250305_invitro12hr

description: Library name: Sample 26


title: 8016_Avonex_intermed_32


title: 8016_Avonex_intermed_8


title: 15RP_Pre_250305_invitro12hr

description: Library name: Sample 24


title: 15RP_pos_0_250305_invitro12hr

description: Library name: Sample 23


title: PDX423_1002_20_RAD_16R

description:
Library name: 423_R2
423_R2 is a replicate of a sample treated with EP0062 from PDX423
2023-07-12_hg38_PDX423_deseq2_normalized_counts.txt


title: 13EP_Pre_250305_invitro12hr

description: Library name: Sample 22


title: 8016_Avonex_intermed_0


title: PDX423_1002_20_RAD_16L

description:
Library name: 423_R1
423_R1 is a replicate of a sample treated with EP0062 from PDX423
2023-07-12_hg38_PDX423_deseq2_normalized_counts.txt


title: 10EC_Pre_250305_invitro12hr

description: Library name: Sample 20


title: 8012_Pleg_intermed_312

value: SC


title: PDX512_1064_20_Control_4L

description:
Library name: 255
255 is a replicate of a control sample from PDX512
2023-07-18_hg38_PDX512_9_samples_deseq2_normalized_counts.txt


title: PDX423_1002_20_Control_2L

description:
Library name: 86
86 is a replicate of a control sample from PDX423
2023-07-12_hg38_PDX423_deseq2_normalized_counts.txt


title: 16_Post_240911_adipose

description: Library name: Sample 18

source_name: Adipose tissue

value: Adipose tissue

value: Heterogenous

value: Treadmill exercise


title: 2ML_Pre_250305_invitro12hr

description: Library name: Sample 30


title: 8012_Pleg_intermed_216


title: 15_Post_240911_adipose

description: Library name: Sample 17


title: PDX423_1002_20_Control_3R

description:
Library name: 423_C2
423_C2 is a replicate of a control sample from PDX423
2023-07-12_hg38_PDX423_deseq2_normalized_counts.txt

value: Breast cancer Patient Derived Xenograft


title: PDX423_1002_20_AZD9833_42L

description:
Library name: 423_Z1
423_Z1 is a replicate of a sample treated with camizestrant from PDX423
2023-07-12_hg38_PDX423_deseq2_normalized_counts.txt

value: Treated

value: Camizestrant


title: 13_Post_240911_adipose

description: Library name: Sample 16


title: 8012_Pleg_intermed_144


title: PDX423_1002_20_RAD_12L

description:
Library name: 87
87 is a replicate of a sample treated with EP0062 from PDX423
2023-07-12_hg38_PDX423_deseq2_normalized_counts.txt

value: Sensitive


title: 11_Post_240911_adipose

description: Library name: Sample 15


title: 8016_Avonex_intermed_3


title: 08_Post_240911_adipose

description: Library name: Sample 14


title: PDX423_1002_20_Control_3L

description:
Library name: 423_C1
423_C1 is a replicate of a control sample from PDX423
2023-07-12_hg38_PDX423_deseq2_normalized_counts.txt

value: Control


title: 04_Post_240911_adipose

description: Library name: Sample 13


title: PDX433.3_1375_22_RAD_Palbo_31R

description:
Library name: 276
276 is a replicate of a sample treated with EP0062 and palbociclib from PDX433.3
2023-07-12_hg38_PDX433.3_deseq2_normalized_counts.txt


title: 03_Post_240911_adipose

description: Library name: Sample 12


title: 8012_Pleg_intermed_96


title: 02_Post_240911_adipose

description: Library name: Sample 11


title: 8012_Pleg_intermed_72


title: 16_Pre_240911_adipose

description: Library name: Sample 9


title: PDX433.3_1375_22_Palbo_21L

description:
Library name: 273
273 is a replicate of a sample treated with palbociclib from PDX433.3
2023-07-12_hg38_PDX433.3_deseq2_normalized_counts.txt

value: Palbociclib


title: PDX433.3_1375_22_Palbo_21R

description:
Library name: 274
274 is a replicate of a sample treated with palbociclib from PDX433.3
2023-07-12_hg38_PDX433.3_deseq2_normalized_counts.txt


title: 13_Pre_240911_adipose

description: Library name: Sample 7


title: 11_Pre_240911_adipose

description: Library name: Sample 6


title: PDX376_1018_20_AZD9833_41L

description:
Library name: 259
259 is a replicate of a sample treated with camizestrant from PDX376
2023-07-12_hg38_PDX376_deseq2_normalized_counts.txt


title: 17AA_Post_260330_invitro3hr

description:
Library name: Sample 12
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
17_Post

value: SIE Plasma

value: Post


title: 2ML_Pre_260330_invitro3hr

description:
Library name: Sample 13
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
02_Pre

value: HprAD - Human Subcutaneous Preadipocyte

value: Adipocyte

value: Pre


title: 8012_Pleg_intermed_32


title: 08_Pre_240911_adipose

description: Library name: Sample 5


title: 8012_Pleg_intermed_120


title: PDX433.3_1375_22_RAD_11L

description:
Library name: 202
202 is a replicate of a sample treated with EP0062 from PDX433.3
2023-07-12_hg38_PDX433.3_deseq2_normalized_counts.txt


title: 10EC_Pre_260330_invitro3hr

description:
Library name: Sample 4
rawCounts_RNAseq_AdipMediaSwap_3hr.csv
10_Pre


title: 04_Pre_240911_adipose

description: Library name: Sample 4


title: 8012_Pleg_intermed_16


title: PDX433.3_1375_22_RAD_Palbo_31L

description:
Library name: 275
275 is a replicate of a sample treated with EP0062 and palbociclib from PDX433.3
2023-07-12_hg38_PDX433.3_deseq2_normalized_counts.txt


title: 03_Pre_240911_adipose

description: Library name: Sample 3


title: PDX433.3_1375_22_RAD_11R

description:
Library name: 203
203 is a replicate of a sample treated with EP0062 from PDX433.3
2023-07-12_hg38_PDX433.3_deseq2_normalized_counts.txt


title: 02_Pre_240911_adipose

description: Library name: Sample 2


title: scRNA-Seq (5′) of PBMC from peak patient#21

description:
Library name: peak patient#21 GE
Single-cell 5′ RNA-seq library generated using 10x Genomics Chromium GEM-X v3 kit, sequenced on Illumina NextSeq 2000

value: Peripheral blood

value: Peripheral blood mononuclear cell


title: 8012_Pleg_intermed_8

value: SC


title: 01_Post_240911_adipose

description: Library name: Sample 10

value: Adipose tissue


title: 01_Pre_240911_adipose

description: Library name: Sample 1

value: Heterogenous


title: PDX433.3_1375_22_Control_1R

description:
Library name: 201
201 is a replicate of a control sample from PDX433.3
2023-07-12_hg38_PDX433.3_deseq2_normalized_counts.txt


title: 15_Pre_240911_adipose

description: Library name: Sample 8

value: Treadmill exercise


title: LIMD1 KO C20

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

description: Library name: SAEC_LIMD1_KO_C20

data_processing:
Reads in the RNA-seq libraries contain a 10 nucleotide UMI at the 5’ end of each read, which was pruned from 5’ ends of R1 read sequences using umi_tools (v1.0.1). Next, 3’-adapters were trimmed from reads using cutadapt (v2.7), discarding reads less than 18 nucleotides remaining. Next, reads were mapped to a database of species-specific repetitive elements, from RepBase 18.05 using STAR (v2.7.6a) using the following parameter: --outFilterMultimapNmax 30. Reads that did not align to the repeats database were then mapped to the human genome (hg38) using STAR (v2.7.6a). PCR duplicates were removed using umi_tools (v1.0.0) by utilizing UMI sequences from the read names and mapping positions. Gene counts per sample were obtained using previously described pipelines for quantifying region-level coverage from eCLIP data [PMID: 32728246] as well as transcript information from GENCODE (V29). Differential expression analysis was performed using the R package DESeq2 (v 1.34.0) [PMID: 25516281].
Assembly: hg38
Supplementary files format and content: csv files containing unnormalised  raw gene counts

source_name: hSAEC

growth_protocol: SAEC cells were cultured at 37C at 5% CO2 and maintained in SAEC basal growth medium (with supplements) (antibiotic free).

extract_protocol:
1.25 m hSAECs were seeded in 15 cm dishes (1 per CRISPR clone, 3 clones per group) and grown for 7 days (media changed thrice) until ~80% confluent and counted (10m cells). Cells were spun down (300 g, 3 mins), supernatant removed, and washed with cold PBS. Cell pellets were flash frozen in liquid Nitrogen and stored at -80 °C and sent to EclipseBio for processing and analysis. Total RNA was isolated using the miRNeasy Mini Kit (Qiagen, 217084) and poly(A) RNA was isolated using Dynabeads Oligo (dT)25 (Thermo Fisher, 61005). RNA integrity and purity was measured using the Agilent 4200 TapeStation. To prepare RNA-sequencing libraries, 50 ng of poly(A) selected RNA was heat fragmented in 2X FastAP buffer and then treated with FastAP Thermosensitive Alkaline Phosphatase (Thermo Fisher, EF0654) and T4 Polynucleotide Kinase (NEB, M0201). An RNA adapter was then ligated to the 3′-ends of the mRNA fragments (T4 RNA Ligase, NEB), after which RNA was column purified (Zymo, R1016) and reverse transcribed with SuperScript III Reverse Transcriptase (Invitrogen, 18080085), then treated with ExoSAP-IT™ PCR Product Cleanup Reagent (ThermoFisher, 78202.4X.1.ML) to remove excess oligonucleotides. A 5’ Illumina DNA adapter (InvRand3Tr3) was ligated to the 3′-end of cDNA fragments with T4 RNA Ligase 1 (ssRNA Ligase) (NEB, #M0437M). After on-bead cleanup (Dynabeads MyOne Silane, Thermo Fisher, 37002D), qPCR was performed on an aliquot of each sample to identify the proper number of PCR cycles. The remainder of the sample was PCR amplified with barcoded Illumina compatible primers (Q5 polymerase, NEB, #M0491) and size selected using AMPure XP beads (Beckman Coulter, A63880). Libraries were quantified using Agilent TapeStation and sequenced on the Illumina NovaSeq platform.
To prepare RNA-sequencing libraries, 50 ng of poly(A) selected RNA was heat fragmented in 2X FastAP buffer and then treated with FastAP Thermosensitive Alkaline Phosphatase (Thermo Fisher, EF0654) and T4 Polynucleotide Kinase (NEB, M0201). An RNA adapter was then ligated to the 3′-ends of the mRNA fragments (T4 RNA Ligase, NEB), after which RNA was column purified (Zymo, R1016) and reverse transcribed with SuperScript III Reverse Transcriptase (Invitrogen, 18080085), then treated with ExoSAP-IT™ PCR Product Cleanup Reagent (ThermoFisher, 78202.4X.1.ML) to remove excess oligonucleotides. A 5’ Illumina DNA adapter (InvRand3Tr3) was ligated to the 3′-end of cDNA fragments with T4 RNA Ligase 1 (ssRNA Ligase) (NEB, #M0437M). After on-bead cleanup (Dynabeads MyOne Silane, Thermo Fisher, 37002D), qPCR was performed on an aliquot of each sample to identify the proper number of PCR cycles. The remainder of the sample was PCR amplified with barcoded Illumina compatible primers (Q5 polymerase, NEB, #M0491) and size selected using AMPure XP beads (Beckman Coulter, A63880). Libraries were quantified using Agilent TapeStation and sequenced on the Illumina NovaSeq platform.

treatment_protocol: Early passage WT SAECs were edited using the Dharmacon Edit-R CRISPR–Cas9 platform comprising EGFP–Cas9 mRNA, Edit-R tracrRNA, and a predesigned crRNA targeting exon 1 of LIMD1 (guide #3; 5′-CCGAGTTTGAGGAAACTCGC-3′) or a non-targeting synthetic sgRNA negative control.

value: hSAEC

tag: genotype

value: LIMD1 KO


title: 8012_Pleg_intermed_3


title: LIMD1 KO C2

description: Library name: SAEC_LIMD1_KO_C2

tag: cell line


title: PDX433.3_1375_22_Control_1L

description:
Library name: 200
200 is a replicate of a control sample from PDX433.3
2023-07-12_hg38_PDX433.3_deseq2_normalized_counts.txt

value: Breast cancer Patient Derived Xenograft


title: 5AF_Pre_250305_invitro12hr

description: Library name: Sample 36

value: MIE Plasma


title: 8012_Pleg_intermed_0


title: LIMD1 KO C10

description: Library name: SAEC_LIMD1_KO_C10


title: 8012_Pleg_intermed_48


title: 4JA_pos_0_250305_invitro12hr

description: Library name: Sample 33


title: LIMD1 Het C8

description: Library name: SAEC_LIMD1_Het_C8

value: LIMD1 Het


title: PDX476.1_982_20_AZD9833_41R

description:
Library name: 268
268 is a replicate of a sample treated with camizestrant from PDX476.1
2023-07-12_hg38_PDX476.1_deseq2_normalized_counts.txt

value: Treated

value: Camizestrant

value: Sensitive


title: LIMD1 Het C6

description: Library name: SAEC_LIMD1_Het_C6


title: 8016_Avonex_intermed_48

value: IM

value: 15 μg


title: 8008_Avonex_intermed_144


title: 3JS_Pre_250305_invitro12hr

description: Library name: Sample 32

value: HprAD - Human Subcutaneous Preadipocyte

value: Adipocyte


title: LIMD1 Het C11

description: Library name: SAEC_LIMD1_Het_C11


title: 8008_Avonex_intermed_120


title: Cas9 control C4

description: Library name: SAEC_Cas_C4

value: Cas9 control


title: PDX476.1_982_20_AZD9833_41L

description:
Library name: 267
267 is a replicate of a sample treated with camizestrant from PDX476.1
2023-07-12_hg38_PDX476.1_deseq2_normalized_counts.txt


title: PDX476.1_982_20_RAD_11R

description:
Library name: 11
11 is a replicate of a sample treated with EP0062 from PDX476.1
2023-07-12_hg38_PDX476.1_deseq2_normalized_counts.txt

value: Resistant


title: 8016_Avonex_intermed_16


title: Cas9 control C2

description: Library name: SAEC_Cas_C2


title: 8008_Avonex_intermed_96


title: Cas9 control C3

description: Library name: SAEC_Cas_C3


title: PDX476.1_982_20_RAD_11L

description:
Library name: 10
10 is a replicate of a sample treated with EP0062 from PDX476.1
2023-07-12_hg38_PDX476.1_deseq2_normalized_counts.txt


title: LIMD1 KO C2 technical replicate 2 (IP)

description: Library name: IP_LIMD1KO_C2_tr2

data_processing:
Initial processing and analysis was performed by Eclipsebio (https://eclipsebio.com/) with a proprietary analysis pipeline v1 developed from several published eCLIP publications: [10.1101/2022.02.13.480296]; [PMID 27018577]; [PMID 28766298]. The original bioinformatic pipelines are available (https://github.com/yeolab/eclip; https://github.com/YeoLab/chim-eCLIP). Briefly, UMIs were pruned from read sequences using umi_tools (v1.1.1). Next, 3' adapters were trimmed from reads using cutadapt (v3.2). Reads were then mapped to a custom database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the genome (UCSC version GRCh38/hg38) using STAR (v2.7.7a). PCR duplicates were removed using umi_tools (v1.1.1). AGO2 eCLIP peaks were identified within eCLIP samples using the peak caller CLIPper (v2.0.1) (55). For each peak, IP versus input fold enrichments and p-values were calculated. miRNAs from miRBase (v22.1) were "reverse mapped" to any reads that did not map to repetitive elements or the genome using bowtie (v1.2.3). The miRNA portion of each read was then trimmed, and the remainder of the read was mapped to the genome using STAR (v2.7.7a). PCR duplicates were resolved using umi_tools (v1.1.1), and miRNA target clusters were identified using CLIPper (v2.0.1). Each cluster was annotated with the names of miRNAs responsible for that target. Peaks were annotated using transcript information from GENCODE release 41 (GRCh38.p13) with the following priority hierarchy to define the final annotation of overlapping features: protein coding transcript (CDS, UTRs, intron), followed by non-coding transcripts (exon, intron). AGO2 clusters identified in the IP sample were then normalized against a paired input sample, with AGO2 peaks defined as a cluster with log2 fold enrichment ≥ 3 and p-value ≤ 0.001. Reproducible peaks were identified using IDR (Irreproducible Discovery Rate) analysis. Reproducible chimeric AGO2:miRNA-target peaks peaks were identified by filtering for peaks where each replicate contained at least three chimeric reads with miRNAs of the same miRNA seed family overlapping the peak. From here, AGO2- and chimeric peak data, stratified by genomic coordinate, gene, feature (RNA region), enrichment/chimeric read count per peak, and differences (fold change and p-values) between samples were further analysed using conventional methods (Microsoft Excel and GraphPad Prism v9.5.1). Further details on chimeric miR-eCLIP analysis can be obtained upon request.
Assembly: hg38
Supplementary files format and content: bigWig files
Library strategy: iCLIP

extract_protocol:
2 x 1.25m cells per replicate (n=4) per sample group were seeded per 15 cm dish and grown to ~80% confluence (2 x 10m cells each) before UV-crosslinking on ice at 254 nm (400 mJ/cm²). Cells were scraped, pelleted at 300 g, flash-frozen in liquid nitrogen, and stored at –80 °C. Pellets were lysed in cold eCLIP buffer containing protease and RNase inhibitors, then sonicated on a QSonica Q800R (75% amplitude, 30 s on/off for 10 cycles). Lysates were adjusted to fragment RNA with RNase I according to sample RIN, clarified by centrifugation, and aliquoted to yield 20 µg RNA per IP.
For miR-eCLIP experiments, the standard eCLIP protocol [PMID 27018577] was modified to enable chimeric ligation of miRNA and mRNA pairs associated with AGO2 according to bioRxiv preprint by Manakov et al, 2022 [10.1101/2022.02.13.480296]. AGO2 immunoprecipitation was carried out overnight at 4 °C with AGO2 antibody (Santa-Cruz, sc-53521)–coated magnetic beads (M280 Sheep Anti-Mouse IgG Dynabeads, Thermo Fisher 11202D), which were then washed under stringent high-salt and no-salt conditions. Beads were sequentially treated with PSP and PNK enzymes to repair RNA ends, and chimeric miRNA–mRNA ligation was performed on-bead using T4 RNA ligase. After additional washes, 3′ RNA adapters were ligated on-bead and RNA was released by proteinase K digestion. Matched Input RNA samples were processed in parallel: column cleanup, PSP/PNK end repair, and 3′ adapter ligation. Both IP and Input RNAs were reverse-transcribed using a chimera-specific primer, and the resulting cDNA underwent end repair by nuclease treatment and mild alkaline hydrolysis with bead-based cleanup. Overnight ligation of a single-stranded cDNA adapter was followed by PCR amplification using Illumina i7/i5 index primers, with cycle numbers determined by qPCR. Final libraries were purified with AMPure XP beads, quality-checked on an Agilent TapeStation, pooled equimolarly, and sequenced single-end (100 bp) on an Illumina platform, targeting ~50 million reads per IP sample and ~40 million reads per Input sample. Further details on chimeric miR-eCLIP protocol can be obtained upon request.

value: IP AGO2


title: 8008_Avonex_intermed_72


title: LIMD1 KO C2 technical replicate 1 (IP)

description: Library name: IP_LIMD1_KO_C2_tr1


title: LIMD1 KO C20 (IP)

description: Library name: IP_LIMD1KO_C20


title: PDX476.1_982_20_Control_1R

description:
Library name: 9
9 is a replicate of a control sample from PDX476.1
2023-07-12_hg38_PDX476.1_deseq2_normalized_counts.txt

value: Control


title: LIMD1 KO C10 (IP)

description: Library name: IP_LIMD1_KO_C10


title: 8008_Avonex_intermed_48


title: PDX476.1_982_20_Control_1L

description:
Library name: 8
8 is a replicate of a control sample from PDX476.1
2023-07-12_hg38_PDX476.1_deseq2_normalized_counts.txt


title: 8008_Avonex_intermed_32


title: LIMD1 Het C6 technical replicate 2 (IP)

description: Library name: IP_LIMD1het_C6_tr2


title: LIMD1 Het C11 (IP)

description: Library name: IP_LIMD1het_C11


title: 8008_Avonex_intermed_16


title: PDX479_975_20_RAD_Palbo_51R

description:
Library name: 287
287 is a replicate of a sample treated with EP0062 and palbociclib from PDX479
2023-07-12_hg38_PDX479_deseq2_normalized_counts.txt


title: Cas9 control C4 technical replicate 1 (IP)

description: Library name: IP_Cas_C4_tr1


title: PDX479_975_20_RAD_Palbo_51L

description:
Library name: 286
286 is a replicate of a sample treated with EP0062 and palbociclib from PDX479
2023-07-12_hg38_PDX479_deseq2_normalized_counts.txt


title: Cas9 control C2 (IP)

description: Library name: IP_Cas_C2


title: Cas9 control C4 technical replicate 2 (IP)

description: Library name: IP_Cas9_C4_tr2


title: 8008_Avonex_intermed_8


title: PDX479_975_20_Palbo_41R

description:
Library name: 285
285 is a replicate of a sample treated with palbociclib from PDX479
2023-07-12_hg38_PDX479_deseq2_normalized_counts.txt

value: Palbociclib


title: Cas9 control C3 (IP)

description: Library name: IP_Cas9_C3

value: hSAEC


title: LIMD1 KO C2 technical replicate 2 (input)

description: Library name: input_LIMD1KO_C2_tr2

value: LIMD1 KO


title: 8008_Avonex_intermed_0


title: PDX479_975_20_Palbo_41L

description:
Library name: 284
284 is a replicate of a sample treated with palbociclib from PDX479
2023-07-12_hg38_PDX479_deseq2_normalized_counts.txt

value: Breast cancer Patient Derived Xenograft


title: LIMD1 KO C2 technical replicate 1 (input)

description: Library name: input_LIMD1_KO_C2_tr1


title: PDX479_1332_22_AZD9833_21L

description:
Library name: 265
265 is a replicate of a sample treated with camizestrant from PDX479
2023-07-12_hg38_PDX479_deseq2_normalized_counts.txt


title: LIMD1 KO C10 (input)

description: Library name: input_LIMD1_KO_C10


title: PDX479_1332_22_AZD9833_21R

description:
Library name: 266
266 is a replicate of a sample treated with camizestrant from PDX479
2023-07-12_hg38_PDX479_deseq2_normalized_counts.txt


title: LIMD1 Het C8 (input)

description: Library name: input_LIMD1_Het_C8


title: LIMD1 KO C20 (input)

description: Library name: input_LIMD1KO_C20


title: 8007_Pleg_intermed_216

value: SC


title: LIMD1 Het C6 technical replicate 2 (input)

description: Library name: input_LIMD1het_C6_tr2

value: LIMD1 Het


title: LIMD1 Het C6 technical replicate 1 (input)

description: Library name: input_LIMD1_Het_C6_tr1


title: PDX479_1332_22_RAD_11R

description:
Library name: 264
264 is a replicate of a sample treated with EP0062 from PDX479
2023-07-12_hg38_PDX479_deseq2_normalized_counts.txt

value: Treated


title: LIMD1 Het C11 (input)

description: Library name: input_LIMD1het_C11


title: PDX479_1332_22_RAD_11L

description:
Library name: 263
263 is a replicate of a sample treated with EP0062 from PDX479
2023-07-12_hg38_PDX479_deseq2_normalized_counts.txt


title: Cas9 control C4 technical replicate 1 (input)

description: Library name: input_Cas_C4_tr1


title: 8007_Pleg_intermed_120


title: Cas9 control C4 technical replicate 2 (input)

description: Library name: input_Cas9_C4_tr2


title: PDX479_1332_22_Control_1R

description:
Library name: 262
262 is a replicate of a control sample from PDX479
2023-07-12_hg38_PDX479_deseq2_normalized_counts.txt


title: 8007_Pleg_intermed_96


title: siYthdf3

city: nantong

first: Xia

last: Jin

address: No. 399, Shiji Avenue, Chongchuan District, Nantong, Jiangsu, China

institute: Affiliated Maternity and Child Health Care Hospital of Nantong University

description:
Library name: Sample2
siYthdf3

data_processing:
Raw sequencing data was first filtered by fastp (v0.23.2), low-quality reads were discarded and the reads with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.The sequences were used for standard mRNA-seq analysis. They were mapped to the reference genome using STAR software (version 2.7.6a). Reads mapped to the exon regions of each gene and reads mapped to each trascript were counted by featureCounts respectively (Subread-1.5.1; Bioconductor) and then expression was calculated. Differentially expressed genes and differentially expressed transcripts between groups were identified using the edgeR package (version 3.40.2), and a p-value cutoff of 0.05 and a fold-change cutoff of 2 were used. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a p-value cutoff of 0.05 to determine a statistically significant enrichment. Alternative splicing events were detected by using rMATS (v4.1.2) with a p-value cutoff of 0.05 and an absolute value of Δψ of 0.1. After alignment, the reads are assembled de novo using the StringTie(v2.1.4) software. New transcripts were then obtained by discarding the reads whose class code is ‘=’.  Gene Set Enrichment Analysis (GSEA) was performed using the GSEA software with the GO and KEGG background datasets from the MSigDB database. Protein-protein interaction network of differentially expressed genes was analyzed using the STRING database. Transcription factors were annotated with two databases. For plants, the plantTFdb database was used. For animals, the animalTFdb database was used. Individual SNP and InDel were detected using bcftools (v1.17), and filtered using the filter module of bcftools. Filtered SNPs and InDels were annotated using the Variant Effect Predictor (VEP, v106.1) software. Time-series transcriptome data was clustered using the R package Mfuzz (v2.58.0) to delineate the groups of genes with similar expression patterns.
Assembly: Ensembl_mRatBN7_2_113
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: E18 cortical rat neurons

extract_protocol:
RNA was harvested using Trizol regent. 1 ug of total RNA was used forthe construction of sequencing libraries
For library preparation, the total RNA was used as input for RNA sequencing library preparation utilizing the KCTM Digital mRNA Library Prep Kit (Seqhealth Tech. Co., Ltd., Wuhan, China),according to the manufacturer's instructions. The kit eliminates duplication bias and errors in PCR and sequencing steps, by using unique molecular identifier (UID) of 12 random bases to label the cDNA molecules. The library preparation included the enrichment of PCR productscorresponding to fragments ranging from 200 to 500 base pairs. The enriched libraries were quantified and sequenced on a DNBSEQ-T7 platform (MGI) using the PE150 sequencing mode to generate paired-end reads.

value: E18 cortical rat neurons


title: PDX479_1332_22_Control_1L

description:
Library name: 261
261 is a replicate of a control sample from PDX479
2023-07-12_hg38_PDX479_deseq2_normalized_counts.txt


title: 8007_Pleg_intermed_72


title: siNC

description:
Library name: Sample1
siNC


title: ume6_Lactate_R3

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description: Library name: dume6_F_Lactate_R3

data_processing:
Processing is automated using the Tail-Tools pipeline, version 1.9 (https://github.com/Monash-RNA-Systems-Biology-Laboratory/tail-tools), and proceeds as follows: Reads are stripped of trailing poly(A) sequences. Reads are aligned using the STAR aligner. Any multi-mapping reads are assigned to one location at random. Counts per gene are produced with UMI deduplication. The UMI sequence can be found at the end of the read names in the FASTQ files. UMIs where the reads had an observed poly(A) tail of length at least 13 are also counted, and the average tail length from these UMIs is calculated. As 3'UTR annotations are not always accurate, reads up to 400 bases down-strand of a gene but not proceeding into another gene on the same strand are counted towards that gene.
Assembly: Candida auris B8441, downloaded 22 June 2020 from candidagenome.org.
Supplementary files format and content: CSV file containing counts of UMIs, counts of UMIs with a tail, and average tail lengths associated with each gene.

organism: Candidozyma auris

source_name: Candida auris cells

growth_protocol: Wild type and 3 transcription factor mutants grown in media containing either glucose or lactate as a carbon source. After 2 days growth on YP+2% Glucose and YP+2% Lactate plates at 30°C, cells were harvested directly from plates, washed in ice-cold ddH2O and pellets were stored at -80°C prior to RNA extraction.

extract_protocol:
Hot Phenol method: 1 ug of DNase treated Total RNA was used as library input.
Beilharz Lab Pooled PAT Seq  method

value: Candida auris cells

value: 470140  background

value: Grown in Lactate media


title: PDX244_988_20_RAD_Palbo_52R

description:
Library name: 272
272 is a replicate of a sample treated with EP0062 and palbociclib from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt

value: Sensitive


title: 8007_Pleg_intermed_48


title: ume6_Lactate_R2

description: Library name: dume6_F_Lactate_R2


title: ume6_Lactate_R1

description: Library name: dume6_F_Lactate_R1


title: PDX244_988_20_RAD_Palbo_52L

description:
Library name: 271
271 is a replicate of a sample treated with EP0062 and palbociclib from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt


title: irf1_Lactate_R3

description: Library name: dirf1_F_Lactate_R3


title: PDX244_988_20_Palbo_41R

description:
Library name: 288
288 is a replicate of a sample treated with palbociclib from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt


title: irf1_Lactate_R2

description: Library name: dirf1_F_Lactate_R2


title: irf1_Lactate_R1

description: Library name: dirf1_F_Lactate_R1


title: 8007_Pleg_intermed_16


title: brg1_Lactate_R3

description: Library name: dbrg1_F_Lactate_R3


title: 8007_Pleg_intermed_8


title: brg1_Lactate_R2

description: Library name: dbrg1_F_Lactate_R2


title: PDX244_988_20_AZD9833_72L

description:
Library name: 254
254 is a replicate of a sample treated with camizestrant from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt

value: Camizestrant


title: brg1_Lactate_R1

description: Library name: dbrg1_F_Lactate_R1


title: Wild_Type_Lactate_R3

description: Library name: 470140_F_Lactate_R3


title: 8007_Pleg_intermed_3


title: Wild_Type_Lactate_R2

description: Library name: 470140_F_Lactate_R2


title: PDX244_988_20_AZD9833_73R

description:
Library name: 244_Z2
244_Z2 is a replicate of a sample treated with camizestrant from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt


title: Wild_Type_Lactate_R1

description: Library name: 470140_F_Lactate_R1


title: 8007_Pleg_intermed_0


title: ume6_Glucose_R2

description: Library name: dume6_F_Glucose_R2

value: Grown in Glucose media