title: KA10_SF_time_OP4_Control

description: Library name: KA10_SF_OP4


title: CTRL__UT CTRL_UT_2

status: Public on Jul 30 2026

type: SRA

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

country: USA

institute: NIH

description:
Library name: CTRL_UT_2
dr_ciliopathy_treatments_cts.csv.gz

library_source: transcriptomic

data_processing:
fastp fastq trimming
decoy aware salmon index
salmon quant --index  --libType A --seqBias --gcBias             --validateMappings
tximport into R (4.4)
gencode.v47.primary_assembly.annotation.gtf.gz
Assembly: GRCh38.primary_assembly.genome.fa.gz
Supplementary files format and content: counts, csv

molecule: polyA RNA

organism: Homo sapiens

source_name: RPE

growth_protocol: All human samples were collected under an IRB-approved protocol at NEI (protocol #11-E1- 0245). Cells isolated from donor tissue were reprogrammed using Sendai virus-mediated delivery (CytoTune, LifeTechnologies) of the four Yamanaka factors (c-MYC, KLF4, OCT4, SOX2) following the manufacturer's recommendations. For differentiation, iPSCs were seeded onto vitronectin (ThermoFisher) coated T75 flasks followed by guided protocol. Triphasic developmentally guided protocol to generate retinal pigment epithelium from induced pluripotent stem cells, Sharma et. al. 2022

extract_protocol:
RNA was isolated from RPE monolayer 5 weeks post-seeding on transwells, using RNA extraction kit, Macherey&Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were collected after 5 weeks of maturation on transwell inserts. Samples were either untreated or treated after 4days of seeding with Pioglitazone and 6days of seeding with Galunisetib.

tag: tissue

value: RPE

tag: cell line

value: CTRL

tag: cell type

value: iRPE

tag: treatment

value: UT


title: KA10_SF_time_OP10_Control

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: Library name: KA10_SF_OP10

data_processing:
Differential analysis for comparisons between iPAAG treated and operated untreated controls was computed using Limma (Linear modeling and empirical Bayes) Voom (Mean–variance modeling) method (limma v3.62.2) longitudinal analysis with baseline (week 2 operated joints) with TMM normalization and duplicate Correlation() (block = patient) to estimate within-patient correlation
Fastp v0.23.2 was used to trim adapters and low-quality reads, STAR version 2.7.10b was used for alignment to Equus caballus EquCab3.0, annotated with Ensembl 113 and feature counts Version 2.0.1 was used to quantify reads.
Assembly: Equus caballus EquCab3.0
Supplementary files format and content: voom_logCPM_normalized_SF.csv

molecule: total RNA

organism: Equus caballus

source_name: synovial fluid

growth_protocol: Synovial fluid samples (≥ 3 mL) were obtained at baseline (pre surgery) and every two weeks throughout study duration until end term (0, 2, 4, 6, 8, 10). To obtain synovial fluid samples, horses were sedated, and joints were aseptically prepared in routine fashion as described for treatment administration. Synovial fluid samples were collected under sterile conditions during routine arthrocentesis. Approximately 3 to 7 mL of synovial fluid were placed in a 15 mL conical tube and placed on ice for transport to the laboratory for processing.

extract_protocol:
The fluid was digested with 0.3 mg/mL hyaluronidase (Sigma, St. Louis, MO, USA) by incubation in a bead bath for 15 minutes at 37 ºC. Next the sample was centrifuged at 750 x g for 10 minutes at 8 ºC. The remaining cell pellet was washed with PBS and centrifuged at 500 x g for 10 minutes at 8 ºC. The cell pellet was resuspended in about 1 to 2 mL of PBS and transferred into a 2 mL microcentrifuge tube. The sample was then centrifuged for 500 x g for 15 minutes. The supernatant was discarded, and the cells were lysed in RLT buffer (Qiagen, Germantown, MD, USA) with 1% ß-Mercaptoethanol (BME; EMD Millipore Corp, Billerica, MA, USA) and stored at -80 ºC until RNA extraction.
Library preparation was conducted on synovial fluid samples using the SMARTer® Stranded Total RNA-Seq Kit -Pico input (Takara Bio USA, Inc.)

treatment_protocol: Treatment – Horses (n=8/group) were randomly assigned to receive either intra-articular 2.5% injectable polyacrylamide hydrogel (Arthramid®, Contura Vet, Franklin, TN, USA) injection (2 mL) or phosphate buffered saline (2 mL) injection. Briefly, horses were sedated with detomidine hydrochloride 0.01 mg/kg and butorphanol tartrate 0.01 mg/kg intravenously. The previously operated middle carpal joint was aseptically prepared in routine fashion and injected intra-articularly at day 14 of the study.

value: synovial fluid

value: SF cells


title: CTRL__UT CTRL_UT_1

description:
Library name: CTRL_UT_1
dr_ciliopathy_treatments_cts.csv.gz


title: KA10_SF_time_OP2_Control

description: Library name: KA10_SF_OP2


title: KA10_SF_time_OP0_Control

description: Library name: KA10_SF_OP0


title: CTRL__PIO CTRL_PIO_2

description:
Library name: CTRL_PIO_2
dr_ciliopathy_treatments_cts.csv.gz

value: PIO


title: KA09_SF_time_OP8_Control

description: Library name: KA09_SF_OP8


title: CTRL__PIO CTRL_PIO_1

description:
Library name: CTRL_PIO_1
dr_ciliopathy_treatments_cts.csv.gz


title: KA09_SF_time_OP6_Control

description: Library name: KA09_SF_OP6


title: CTRL__GAL CTRL_GAL_2

description:
Library name: CTRL_GAL_2
dr_ciliopathy_treatments_cts.csv.gz

value: GAL


title: KA14_SF_time_OP0_iPAAG

description: Library name: KA14_SF_OP0


title: CTRL__GAL CTRL_GAL_3

description:
Library name: CTRL_GAL_3
dr_ciliopathy_treatments_cts.csv.gz


title: KA09_SF_time_OP2_Control

description: Library name: KA09_SF_OP2


title: CTRL__GAL CTRL_GAL_1

description:
Library name: CTRL_GAL_1
dr_ciliopathy_treatments_cts.csv.gz


title: KA09_SF_time_OP0_Control

description: Library name: KA09_SF_OP0


title: CEP290__UT CEP290_UT_3

description:
Library name: CEP290_UT_3
dr_ciliopathy_treatments_cts.csv.gz


title: CEP290__UT CEP290_UT_2

description:
Library name: CEP290_UT_2
dr_ciliopathy_treatments_cts.csv.gz


title: KA08_SF_time_OP8_iPAAG

description: Library name: KA08_SF_OP8


title: CEP290__UT CEP290_UT_1

description:
Library name: CEP290_UT_1
dr_ciliopathy_treatments_cts.csv.gz


title: KA08_SF_time_OP6_iPAAG

description: Library name: KA08_SF_OP6


title: CEP290__PIO CEP290_PIO_3

description:
Library name: CEP290_PIO_3
dr_ciliopathy_treatments_cts.csv.gz


title: KA08_SF_time_OP4_iPAAG

description: Library name: KA08_SF_OP4


title: CEP290__PIO CEP290_PIO_2

description:
Library name: CEP290_PIO_2
dr_ciliopathy_treatments_cts.csv.gz


title: CEP290__PIO CEP290_PIO_1

description:
Library name: CEP290_PIO_1
dr_ciliopathy_treatments_cts.csv.gz


title: HEK293T Xenograft mitochondrion isolation biol rep 3

status: Public on Jul 31 2026

city: Shanghai

first: Jiapeng

last: Liu

address: Yueyang Road 320

department: SIBCB

country: China

institute: CEMCS, CAS

description:
Library name: Sample 16
Ribosomal RNA Depletion

library_source: other

data_processing:
Quantification of gene expression level. Reference genome and gene model annotation files (v44) were downloaded from genome website directly. Index of the reference genome was built using STAR-2.7.9a and paired-end clean reads were aligned to the reference genome using STAR-2.7.9a.
FeatureCounts was used to count the read numbers mapped to each gene.
Differential expression analysis. Differential expression analysis of two groups (two biological replicates per condition) was performed using the DESeq2 R package (1.42.0).
Assembly: GRCh38

molecule: other

source_name: HEK293T Xenograft

extract_protocol:
RNA was harvested using VeZol Reagent (R411, Vazyme).
RNA libraries for RNA-seq were prepared using Ribo-MagOff rRNA Depletion Kit (N420, Vazyme) and VAHTS Universal V10 RNA-seq Library Prep Kit (NR616, Vazyme) fllowing manufacturer's protocols.

treatment_protocol: PRADA metabolic labeling in living cells. Cells stably expressing the indicated PRADA construct were grown to approximately 90% confluency. Cells were then incubated in fresh media containing 100 µM s4U for 5 hrs at 37°C. The media were then replaced with fresh media containing 0.5 mM alkyne phenol and 100 µM s4U for another 30 minutes. To initiate PRADA labeling, a final concentration of 10 mM D-amino acid was added for 30 minutes. The cells were then rinsed with quench solution three times to terminate the labeling reaction. Cells omitting D-amino acid treatment were used as the unlabeled control group. PRADA labeling in mice. 1 × 10^7 HEK-PRADA stable cells in 100 μL PBS were subcutaneously implanted into the hind leg regions of B-NDG mouse. Tumour sizes were measured with calliper and tumour volumes were calculated according to the standard formula (length × width × Height × π/6). For s4U metabolic labeling, s4U was dissolved in 2 mL saline solution and injected intraperitoneally at a dose of 430 mg/kg body weight. 5 hours after injection, tumor-bearing B-NDG mice were anesthetized and intratumorally injected with 1 mL saline solution containing 30 mM alkyne phenol, 100 mM D-Ala, and 100 mM D-Phe. The solution was prepared using non-contact ultrasound-assisted dissolution (<45°C). After 30 minutes, another 1 mL of the solution was injected. After an additional 30 min, the mice were euthanized, and the tissues were collected for subsequent experiments. Mice receiving only 30 mM alkyne phenol in saline solution were used as unlabeled negative controls.

value: HEK293T Xenograft

value: a stable clone derivative of the human embryonic kidney (HEK) 293 cell line

tag: genotype


title: KA08_SF_time_OP10_iPAAG

description: Library name: KA08_SF_OP10


title: KA08_SF_time_OP0_iPAAG

description: Library name: KA08_SF_OP0


title: Exp_2_CB839

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: Library name: Exp_2_CB839

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the GENCODE v27 reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: RPKM normalized expression values for all ENTREZ genes

organism: Mus musculus

source_name: Germinal Center B cell

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
RNA-seq libraries were generated at the Vanderbilt Vantage Genomics Core using the Tecan Ovation kit.

treatment_protocol: All cells were cultured with anti-CD40, BAFF, IL-4, and IL-5 for 3 days in the presence or absence of CB-839 (a GLS1 inhibitor) and UK-5099 (an MPC inhibitor).

value: Germinal Center B cell

tag: strain

tag: batch


title: CEP290__GAL CEP290_GAL_2

description:
Library name: CEP290_GAL_2
dr_ciliopathy_treatments_cts.csv.gz


title: KA07_SF_time_OP8_iPAAG

description: Library name: KA07_SF_OP8


title: KA07_SF_time_OP6_iPAAG

description: Library name: KA07_SF_OP6


title: BBS__UT BBS_UT_3

description:
Library name: BBS_UT_3
dr_ciliopathy_treatments_cts.csv.gz


title: KA07_SF_time_OP4_iPAAG

description: Library name: KA07_SF_OP4


title: BBS__UT BBS_UT_2

description:
Library name: BBS_UT_2
dr_ciliopathy_treatments_cts.csv.gz


title: KA07_SF_time_OP2_iPAAG

description: Library name: KA07_SF_OP2


title: BBS__UT BBS_UT_1

description:
Library name: BBS_UT_1
dr_ciliopathy_treatments_cts.csv.gz


title: Nanostring of human3

type: RNA

city: Beijing

first: Junping

last: Zhang

state: Beijing

address: No. 50, Yikesong Road, District Haidian, Beijing

institute: Sanbo Brain Hospital Capital Medical University

description: LongBenifit

hyb_protocol: hybridization of 100 ng RNA to a version of the NanoString PanCancer code set for reading on the nCounter platform

scan_protocol: nCounter

data_processing: nSolver Analysis software, IO 360 Data Analysis Service

label: brain glioma

source_name: SD/PD

label_protocol: As little as 10 ng with nCounter RNA Low Input Kit and Panel specific primer pools (sold separately)

extract_protocol: The tumor tissue was divided into two parts. MagMAX FFPE RNA Ultra Kit (item No. A31881 ThermoFisher) was used to extract RNA from the tumor tissue, and the RNA was inspected according to relevant quality inspection standards. After the quality inspection was qualified, the RNA sequencing library was constructed

tag: gender

value: male


title: KA07_SF_time_OP10_iPAAG

description: Library name: KA07_SF_OP10


title: Splenic CD8+ T cells, anti-CD3/CD28 activated, 24-hours, Dusp2 conditional knockout, mouse 2

city: Rochester

first: Emilia

middle: R

last: Dellacecca

state: MN

address: 200 First Street SW, Kellen Building 02-102

department: Immunology

institute: Mayo Clinic

description: Library name: 116C_A

data_processing:
Raw RNA sequencing paired-end reads were processed through Mayo RNA-Seq bioinformatics pipeline, MAP-Rseq (v3.1.5) to align to genome build mm39.
Variants were called using the RVBoost module from MAPR-seq.
Gene and exon expression quantification were performed using the Subread package to obtain both raw and normalized (FPKM) reads.
FASTQC, MultiQC, and RSEQC tools were used for comprehensive quality control assessment of the aliqned reads.
Assembly: mm39
Supplementary files format and content: Tab-delimited text file including raw counts and FPKM for each sample

source_name: Spleen

growth_protocol: CD8+ T cells were maintained in RPMI 1640 + 10% fetal bovine serum, 20 mM HEPES buffer, and 1X penicillin/streptomycin at 37 degrees Celsius with 5% CO2.

extract_protocol:
Total RNA was isolated with TRIzol Reagent (Invitrogen), prior to inclusion in spin-column based isolation (Zymo Research). 100 ng of total RNA was used for construction of cDNA libraies.
Libraries were prepared with Illumina Stranded mRNA Prep kit following manufacturer's instructions. The concentration and size distribution of the completed libraries were determined with the Agilent TapeStation's D1000 ScreenTape and Qubit fluorometry.

treatment_protocol: CD8+ T cells were activated with anti-CD3/CD28 beads (Gibco) for 24-hours, rested cells were maintained under the same conditions without addition of beads.

value: Spleen

value: CD8+ T cells

value: Activated with anti-CD3/CD28

tag: Sex

value: Male


title: BBS__PIO BBS_PIO_3

description:
Library name: BBS_PIO_3
dr_ciliopathy_treatments_cts.csv.gz


title: BBS__PIO BBS_PIO_2

description:
Library name: BBS_PIO_2
dr_ciliopathy_treatments_cts.csv.gz


title: WT.GCB.1

description: Library name: WT.GCB.1

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: Wild type

value: SRBC immunization


title: SJOS030605_X2

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
Library name: SJOS030605_X2
10X Genomics 3’ RNA kit

library_source: transcriptomic single cell

data_processing:
Aligning and transcript counting were performed using 10x Genomics Cell Ranger version 7
Assembly: Hg38 for patient samples. Combined Hg38 and mm10 for PDX samples
Supplementary files format and content: processed data reflect cell ranger output from the filter_bc_matrix folder, including feature names, cell barcode IDs, and expression count matrix (unnormalized)

source_name: OS

extract_protocol:
cells or nuclei were extracting using protocols described in Slyper et al Nat Medicine 2020 (https://doi.org/10.1038/s41591-020-0844-1)
Libraries were generating using the 10x Genomics 3' gene expression kits version 3.1

value: OS

tag: group

value: O-PDX

tag: method

value: nucleus

tag: sjid

tag: age

value: female

tag: primary site

value: Femur

tag: sample site

value: Chest wall

tag: timepoint

value: recurrence

tag: sample

value: primary

tag: treatment status

value: treated


title: SJOS063833_X1

description:
Library name: SJOS063833_X1
10X Genomics 3’ RNA kit

tag: tissue

value: Lung

value: diagnostic

value: metastasis


title: BBS__PIO BBS_PIO_1

description:
Library name: BBS_PIO_1
dr_ciliopathy_treatments_cts.csv.gz

value: RPE

tag: cell line

tag: cell type

value: iRPE

value: PIO


title: KA06_SF_time_OP6_iPAAG

description: Library name: KA06_SF_OP6

value: synovial fluid

value: SF cells


title: BBS__GAL BBS_GAL_3

description:
Library name: BBS_GAL_3
dr_ciliopathy_treatments_cts.csv.gz

tag: treatment

value: GAL


title: KA06_SF_time_OP4_iPAAG

description: Library name: KA06_SF_OP4


title: BBS__GAL BBS_GAL_2

description:
Library name: BBS_GAL_2
dr_ciliopathy_treatments_cts.csv.gz


title: KA06_SF_time_OP2_iPAAG

description: Library name: KA06_SF_OP2


title: KA06_SF_time_OP10_iPAAG

description: Library name: KA06_SF_OP10


title: BBS__GAL BBS_GAL_1

description:
Library name: BBS_GAL_1
dr_ciliopathy_treatments_cts.csv.gz


title: BBS1B DR45

description:
Library name: DR45
dr_ciliopathy_cts.csv.gz

tag: genotype

value: Bardet-Biedl-Syndrome

value: Untreated


title: BBS1B DR44

description:
Library name: DR44
dr_ciliopathy_cts.csv.gz


title: KA05_SF_time_OP6_iPAAG

description: Library name: KA05_SF_OP6


title: CTRL MS19H DR39

description:
Library name: DR39
dr_ciliopathy_cts.csv.gz

value: Healthy Control


title: KA06_SF_time_OP0_iPAAG

description: Library name: KA06_SF_OP0


title: KA05_SF_time_OP4_iPAAG

description: Library name: KA05_SF_OP4


title: KA05_SF_time_OP10_iPAAG

description: Library name: KA05_SF_OP10


title: KA05_SF_time_OP0_iPAAG

description: Library name: KA05_SF_OP0


title: BBS16 DR35

description:
Library name: DR35
dr_ciliopathy_cts.csv.gz


title: KA03_SF_time_OP8_iPAAG

description: Library name: KA03_SF_OP8


title: BBS16 DR34

description:
Library name: DR34
dr_ciliopathy_cts.csv.gz


title: LCA5 DR30

description:
Library name: DR30
dr_ciliopathy_cts.csv.gz

value: Leber's Congenital Amaurosis


title: KA03_SF_time_OP6_iPAAG

description: Library name: KA03_SF_OP6


title: LCA5 DR29

description:
Library name: DR29
dr_ciliopathy_cts.csv.gz


title: KA03_SF_time_OP10_iPAAG

description: Library name: KA03_SF_OP10


title: LCA5 DR28

description:
Library name: DR28
dr_ciliopathy_cts.csv.gz


title: KA03_SF_time_OP0_iPAAG

description: Library name: KA03_SF_OP0


title: BBS10A DR24_2

description:
Library name: DR24_2
dr_ciliopathy_cts.csv.gz


title: KA02_SF_time_OP8_Control

description: Library name: KA02_SF_OP8


title: BBS10A DR23_2

description:
Library name: DR23_2
dr_ciliopathy_cts.csv.gz


title: KA02_SF_time_OP6_Control

description: Library name: KA02_SF_OP6


title: BBS10A DR22_2

description:
Library name: DR22_2
dr_ciliopathy_cts.csv.gz


title: KA02_SF_time_OP4_Control

description: Library name: KA02_SF_OP4


title: CTRL D3C DR18_2

description:
Library name: DR18_2
dr_ciliopathy_cts.csv.gz


title: KA02_SF_time_OP2_Control

description: Library name: KA02_SF_OP2


title: CEP290__GAL CEP290_GAL_1

description:
Library name: CEP290_GAL_1
dr_ciliopathy_treatments_cts.csv.gz


title: CTRL D3C DR17_2

description:
Library name: DR17_2
dr_ciliopathy_cts.csv.gz


title: KA02_SF_time_OP10_Control

description: Library name: KA02_SF_OP10


title: CTRL D3C DR16_2

description:
Library name: DR16_2
dr_ciliopathy_cts.csv.gz


title: KA07_SF_time_OP0_iPAAG

description: Library name: KA07_SF_OP0


title: KA02_SF_time_OP0_Control

description: Library name: KA02_SF_OP0


title: KA06_SF_time_OP8_iPAAG

description: Library name: KA06_SF_OP8


title: PRPF31 DR15_2

description:
Library name: DR15_2
dr_ciliopathy_cts.csv.gz

value: Autosomal dominant retinitis pigmentosa


title: KA01_SF_time_OP8_Control

description: Library name: KA01_SF_OP8


title: PRPF31 DR14_2

description:
Library name: DR14_2
dr_ciliopathy_cts.csv.gz


title: KA01_SF_time_OP6_Control

description: Library name: KA01_SF_OP6


title: PRPF31 DR13_2

description:
Library name: DR13_2
dr_ciliopathy_cts.csv.gz


title: KA01_SF_time_OP4_Control

description: Library name: KA01_SF_OP4


title: BBS1B DR43

description:
Library name: DR43
dr_ciliopathy_cts.csv.gz


title: KA05_SF_time_OP8_iPAAG

description: Library name: KA05_SF_OP8


title: BBS1A DR12_2

description:
Library name: DR12_2
dr_ciliopathy_cts.csv.gz


title: CTRL MS19H DR38

description:
Library name: DR38
dr_ciliopathy_cts.csv.gz


title: KA05_SF_time_OP2_iPAAG

description: Library name: KA05_SF_OP2


title: KA01_SF_time_OP2_Control

description: Library name: KA01_SF_OP2


title: BBS1A DR11_2

description:
Library name: DR11_2
dr_ciliopathy_cts.csv.gz


title: CTRL MS19H DR37

description:
Library name: DR37
dr_ciliopathy_cts.csv.gz


title: WT, P0, rep1

city: New York

first: YIYING

last: ZHANG

state: New York

address: 1150 St. Nicholas Ave

department: Pediatrics

institute: Columbia University

description: Library name: RG301

data_processing:
fastq files were aligned to the mouse reference genome GRCm39 using HISAT2 in Galaxy Version 21.01
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Assembly: mouse reference genome GRCm39
Supplementary files format and content: tab-delimited text file containing raw integer gene-level counts of all samples

source_name: pituitary

growth_protocol: Pituitaries were collected and flash-frozen in liquid nitrogen and stored at -80oC before RNA extraction

extract_protocol:
RNA was isolated using Total RNA Purification Plus Micro Kit  (Norgen Biotek) and processed as per manufacturer’s instructions.
libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit Gold (Illumina) with Ribo-Zero Plus rRNA Depletion Kit  according to the manufacturer’s instructions.

treatment_protocol: no treatment

value: pituitary

value: male

value: wild-type


title: SJWT046157_D1

description:
Library name: SJWT046157_D1
10X Genomics 3’ RNA kit

source_name: WT

value: WT

value: Patient

value: nucleus

value: kidney

value: primary

value: untreated


title: KA01_SF_time_OP10_Control

description: Library name: KA01_SF_OP10

value: synovial fluid


title: BBS1A DR10_2

description:
Library name: DR10_2
dr_ciliopathy_cts.csv.gz

value: RPE

value: iRPE


title: CEP290 DR09_2

description:
Library name: DR09_2
dr_ciliopathy_cts.csv.gz

value: Joubert Syndrome


title: synovium_time_10wk_iPAAG_KA17

description: Library name: sample32

data_processing:
demultiplexed FASTQ reads generated from CU Genomics Core were analyzed using the Alpine High-Performance Computing Resource at the University of Colorado Boulder. Fastp v0.23.2 was used to trim adapters and low-quality reads
STAR version 2.7.10b was used for alignment to Equus caballus EquCab3.0, annotated with Ensembl 113 and feature counts Version 2.0.1 was used to quantify reads
Differential analysis for comparisons between iPAAG treated and operated untreated controls was computed using Limma (Linear modeling and empirical Bayes) Voom (Mean–variance modeling) method (limma v3.62.2) longitudinal analysis with baseline (week 2 operated joints) with TMM normalization and duplicate Correlation() (block = patient) to estimate within-patient correlation
Assembly: Equus caballus EquCab3.0
Supplementary files format and content: Counts_ProNozero_Synovium.csv

source_name: synovium

extract_protocol:
Synovial biopsies (approximately 2 mm x 10 mm samples) were obtained arthroscopically using ferris-smith rongeurs at time of surgical model induction at baseline prior to osteochondral fragment induction and at end-term week 10 immediately postmortem. Tissue samples were placed in complete media with Dulbecco’s Modified Eagle’s Medium (DMEM; Corning, catalogue #10-014-CM) with Fetal Bovine Serum (FBS; PEAK SERUM, Wellington, CO, USA). The tissue was washed with PBS and minced into 1mm pieces in a 6 well plate Type 2 collagenase (ThermoFisher, Waltham, MA, USA) in Hank’s Balanced Salt Solution (HBSS; Corning, Durham, NC, USA) which was used at 0.4 U/mL. Tissue digestion was conducted in a CO2 incubator at 37 ºC for 60 minutes. Samples were agitated every 20 minutes with a pipette. Following digestion, the digested homogenate was passed through a strainer then transferred to a 15 mL conical and centrifuged at 526 x g for 5 min. Pelleted cells were washed twice with PBS then transferred to microcentrifuge tube. The microcentrifuge tube with the sample was spun at 100 x g for 15 minutes at 8 ºC to remove dead cells. The supernatant was discarded, and the cells were lysed in RLT buffer (Qiagen, catalogue # 79216) with 1% ß-Mercaptoethanol (BME; EMD Millipore Corp, Billerica, MA, USA) and stored at -80 ºC until RNA extraction.
Library preparation for synovium was conducted with Tecan/Nugen Universal Plus mRNA-seq Poly A prep kit .

treatment_protocol: Osteoarthritis was induced in one randomly assigned middle carpal joint as previously described. Briefly, an 8 mm osteochondral fragment was created on the distal aspect of the radial carpal bone at the level of the synovial plica and allowed to remain adhered to the joint capsule. The gap around the fragment was expanded to 15 mm using a motorized arthroscopic burr (Arthrex, Munich, Germany). The fragment and bone debris were not lavaged from the joint as described.18,19 Arthroscopy was performed on the contralateral middle carpal joint as sham-operation and to confirm the lack of any significant osteoarthritis lesions. Arthroscopic portals were closed with 2-0 nylon suture in simple interrupted pattern. Carpi were bandaged in routine manner with bandages changed every 3 to 5 days for 14 days when sutures were removed.

value: synovium

value: iPAAG


title: KA01_SF_time_OP0_Control

description: Library name: KA01_SF_OP0

value: SF cells


title: BBS16 DR36

description:
Library name: DR36
dr_ciliopathy_cts.csv.gz

value: Bardet-Biedl-Syndrome

value: Untreated


title: synovium_time0_iPAAG_KA17

description: Library name: sample31


title: CEP290 DR08_2

description:
Library name: DR08_2
dr_ciliopathy_cts.csv.gz


title: CEP290 DR07_2

description:
Library name: DR07_2
dr_ciliopathy_cts.csv.gz


title: synovium_time_10wk_Control_KA16

description: Library name: sample30

value: Control


title: Lap2alpha KO dermal fibroblast, rep 3

city: Vienna

first: Roland

last: Foisner

address: Dr.-Bohr-Gasse 9

country: Austria

institute: Max Perutz Labs, Medical University of Vienna

description:
Library name: RNAseq.Lap2alphaKO.Rep3
Illumina NextSeq 550

data_processing:
Raw reads were mapped to the reference mouse genome assembly Mus musculus using STAR v2.7.10b with default settings using the mouse genome annotation GRCm38.102 from ENSEMBL
The gene counts were calculated using Rsubread v2.8.2.
Assembly: GRCm38
Supplementary files format and content: The number of counts for each sample for the genes with a minimum total of 1 mapped read across all 6 replicates. Gene IDs are ENSEMBL gene IDs.

source_name: mouse dermal fibroblast

growth_protocol: DMEM supplemented with 10% fetal calf serum, 100 U/ml penicillin and 100 μg/ml streptomycin; cultured at 37°C and 5% CO2

extract_protocol:
Total RNA was extracted with the RNAeasy® mini kit from Qiagen
Libraries were prepared by the Next Generation Sequencing facility at the Vienna Biocenter Core Facilities, Vienna, Austria, starting with polyA enrichment using the NEBNext® Poly(A) mRNA Magnetic Isolation Module, followed by the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina®.

value: mouse dermal fibroblast

value: Lap2alpha KO


title: MYO7A DR06_2

description:
Library name: DR06_2
dr_ciliopathy_cts.csv.gz

value: Usher Syndrome


title: synovium_time0_Control_KA16

description: Library name: sample29


title: Lap2alpha KO dermal fibroblast, rep 2

description:
Library name: RNAseq.Lap2alphaKO.Rep2
Illumina NextSeq 550


title: MYO7A DR05_2

description:
Library name: DR05_2
dr_ciliopathy_cts.csv.gz


title: Wildtype dermal fibroblast, rep 3

description:
Library name: RNAseq.WT.Rep3
Illumina NextSeq 550

value: WT


title: Lap2alpha KO dermal fibroblast, rep 1

description:
Library name: RNAseq.Lap2alphaKO.Rep1
Illumina NextSeq 550


title: synovium_time_10wk_Control_KA15

description: Library name: sample28


title: MYO7A DR04_2

description:
Library name: DR04_2
dr_ciliopathy_cts.csv.gz


title: Wildtype dermal fibroblast, rep 2

description:
Library name: RNAseq.WT.Rep2
Illumina NextSeq 550


title: synovium_time0_Control_KA15

description: Library name: sample27


title: Wildtype dermal fibroblast, rep 1

description:
Library name: RNAseq.WT.Rep1
Illumina NextSeq 550


title: BBS10B DR03_2

description:
Library name: DR03_2
dr_ciliopathy_cts.csv.gz


title: Lap2alpha KO dermal fibroblast, rep 3

description:
Library name: ATACseq.Lap2alphaKO.Rep3
Illumina NextSeq 550

library_source: genomic

data_processing:
Reads were mapped to the reference mouse genome using bowtie2 v2.5.1 with the setting --very-sensitive
ATACseq peaks were called with Genrich using 3 replicates of each WT and KO with the settings -j -y -r -e MT -q 0.01
Signal track files of the mapped reads were generated using bamCoverage from deepTools v3.5.1 using RPKM normalization method
Assembly: GRCm38
Supplementary files format and content: narrowPeak files contain the peaks called for either WT or KO samples using all replicates for each sample together, therefore there is only 1 peak file for each 3 replicate set.
Supplementary files format and content: Bigwig files contain the RPKM-normalized signal tracks of each replicate, generated using the bam (mapping) files using bamCoverage from deepTools.

molecule: genomic DNA

extract_protocol:
Nuclei were prepared by gentle lysis, followed immediately by chromatin transposition using Tn5 transposase.
Libraries were prepared by the Next Generation Sequencing facility at the Vienna Biocenter Core Facilities, Vienna, Austria, starting with nuclei isolation, followed by tagmentation using Tn5 transposase  and library amplification with KAPA HiFi HotStart ReadyMix.  Post-amplification cleanup used AMPure XP beads, with final quantification performed via qPCR and fragment analysis. Post-amplification cleanup used AMPure XP beads, with final quantification performed via qPCR and fragment analysis.


title: BBS10B DR02_2

description:
Library name: DR02_2
dr_ciliopathy_cts.csv.gz


title: synovium_time_10wk_iPAAG_KA14

description: Library name: sample26


title: Lap2alpha KO dermal fibroblast, rep 2

description:
Library name: ATACseq.Lap2alphaKO.Rep2
Illumina NextSeq 550


title: Lap2alpha KO dermal fibroblast, rep 1

description:
Library name: ATACseq.Lap2alphaKO.Rep1
Illumina NextSeq 550


title: Wildtype dermal fibroblast, rep 3

description:
Library name: ATACseq.WT.Rep3
Illumina NextSeq 550


title: BBS10B DR01_2

description:
Library name: DR01_2
dr_ciliopathy_cts.csv.gz


title: Wildtype dermal fibroblast, rep 2

description:
Library name: ATACseq.WT.Rep2
Illumina NextSeq 550


title: synovium_time_10wk_Control_KA13

description: Library name: sample24


title: PEO_4_3

city: North Chicago

first: Weihang

last: Chai

state: Illinois

address: 3333 N Green Bay Rd, IRP 257

department: Center for Genetic Diseases

institute: Rosalind Franklin University of Medicine and Sciences, Chicago Medical School

description: Library name: Sample 9

data_processing:
HISAT2 v2.2.1 Raw data underwent QC to remove low-quality reads, reads with excessive “N”, and adapters to produce high-quality reads.
Trimmed sequence reads were mapped to GRCh38 (hg38) using HISAT2 v2.2.1 (or STAR) with default parameters.
Assembly: GRCh38
Gene expression levels were normalized as FPKM (fragments per kilobase of transcript sequence per million mapped reads) values to determine the transcript abundance in each sample.
Supplementary files format and content: xls file contains gene count and FPKM values for each sample

growth_protocol: PEO1 cell lines were cultured in RPMI 1640 medium supplemented with 10% FBS

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol
Poly(A)+ RNA enrichment, sequencing library preparation and quantification were performed by Novogene (Sacramento, CA)

treatment_protocol: PEO1 cell used in this study are not treated with anything. Olaparib-resistant PEO1-R cells were established from the parental PEO1 line through intermittent, incremental in vitro exposure to Olaparib. The drug concentration was gradually increased from 0.5 to 20 µM over a six-month period. At each concentration, cells were treated with Olaparib for 48 hours, after which the medium was replaced with drug-free complete medium. The cells were then allowed to recover and proliferate until reaching approximately 80-90% confluence. Once stable growth was maintained for at least one to two passages at each concentration, the olaparib dose was doubled, and the treatment cycle was repeated until the final concentration was achieved.

value: ovarian adenocarcinoma cells

value: BRCA2 mutant, TP53 mutant

value: No Treatment used for this study


title: synovium_time0_iPAAG_KA14

description: Library name: sample25


title: PEO_4_2

description: Library name: Sample 8


title: CD4_T_Cells_Neonate_Cesarean_Section_2

city: Cuernavaca

first: LInda

middle: AImara

last: Kempis

state: Morelos

address: Avenida Universidad 1001

department: CIDC

country: Mexico

institute: UAEM

description:
Library name: Basal_Cesarean_Term_2
Cesarean_Section_2

data_processing:
The quality of the data was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).  Adapters and low-quality sequences were trimmed or discarded using Trimmomatic. Quality check using FastQC was performed again on the trimmed sequences.
Reads were aligned to the human reference genome GRCh38/hg38 to generate the Binary Alignment Map (BAM) files with STAR (v2.4.2a).
Adaptors and low quality reads were cut using Trimmomatic version 0.39 with the following parameters: “ILLUMINACLIP:Truseq3-SE:2:30:10 TRAILING:3 MINLEN:40”9. The reads were aligned against reference transcriptome GRCh38/hg38, using the STAR 2.4.2ª software with the following parameters: “runMode alignReads -outSAMtype BAM SortedByCoordinate -outFilterMultimapNmax 1”10. The BAM (Binary Aligment Map) files generated by alignment were visualized in regions of interest with IGV. Read counting per gene was obtained using the software HTSeq-count. To identify differentially expressed genes, we used the DESeq2 package in R (Bioconductor).
DESeq2 (v1.50.2) was used to screen differentially expressed genes and normalization of the count data.
Assembly: hg38
Supplementary files format and content: counts_sizefactor_normalized.txt
Supplementary files format and content: raw_data_with_zeros_unnormalized.txt

source_name: Cord Blood

extract_protocol:
Total RNA from CD4+ T cells was extracted using TRIZOL® Reagent, following the manufacturer’s protocol.
RNA-seq libraries were constructed at the Transcriptomic & Genomic Platform Marseille Luminy (Aix-Marseille University, TAGC) using the TruSeq RNA Library Prep Kit v2 (Illumina; California, USA). Libraries were paired end sequenced on an Illumina NextSeq 500 sequencer.

treatment_protocol: CD4+T cells were cultured in RPMI 1640 medium supplemented with 2 mM glutamine, commercial antibiotics (50 U/mL penicillin,50lg/mL streptomycin) and 5% fetal coalf serum. Cells were activated with 1µg/mL anti-CD3 (OKT3; TONBO Bio-sciences) and 1µg/mL anti-CD28 (CD28.2;TONBO Biosciences) , cross-linked with 1ug/mL goat anti-mouse (Polyclonal,Bioss) and incubated for 6 h under 5% CO2 at 37°C

value: Cord Blood

value: Male

value: Neonatal CD4+ T cell

tag: sample group

tag: batch


title: synovium_time0_Control_KA13

description: Library name: sample23


title: Wildtype dermal fibroblast, rep 1

description:
Library name: ATACseq.WT.Rep1
Illumina NextSeq 550


title: CD4_T_Cells_Neonate_Cesarean_Section_4

description:
Library name: Basal_Cesarean_Term_4
Cesarean_Section_4


title: CD4_T_Cells_Neonate_Cesarean_Section_3

description:
Library name: Basal_Cesarean_Term_3
Cesarean_Section_3


title: synovium_time_10wk_iPAAG_KA12

description: Library name: sample22


title: CD4_T_Cells_Neonate_Cesarean_Section_1

description:
Library name: Basal_Cesarean_Term_1
Cesarean_Section_1


title: synovium_time0_iPAAG_KA12

description: Library name: sample21


title: CD4_T_Cells_Neonate_Natural_Birth_3

description:
Library name: Basal_Natural_Birth_Term_3
Natural_Birth_3


title: PEO_1_R_3

description: Library name: Sample 6


title: CD4_T_Cells_Neonate_Natural_Birth_2

description:
Library name: Basal_Natural_Birth_Term_2
Natural_Birth_2


title: CD4_T_Cells_Neonate_Preterm_4

description:
Library name: Basal_Cesarean_Preterm_4
Preterm_4

value: Female


title: PEO_1_R_2

description: Library name: Sample 5


title: CD4_T_Cells_Neonate_Preterm_3

description:
Library name: Basal_Cesarean_Preterm_3
Preterm_3


title: synovium_time_10wk_Control_KA11

description: Library name: sample20

value: synovium


title: synovium_time0_Control_KA11

description: Library name: sample19


title: CD4_T_Cells_Neonate_Preterm_2

description:
Library name: Basal_Cesarean_Preterm_2
Preterm_2


title: PEO_1_R_1

description: Library name: Sample 4


title: CD4_T_Cells_Neonate_Preterm_1

description:
Library name: Basal_Cesarean_Preterm_1
Preterm_1


title: E19_P, pNeuroD cell population, PBS treatment, rep 2

city: Paris

first: Tabitha

last: Rücker

address: 25, rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Adapter trimming was performed with cutadapt v. 3.1 (parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA x.fastq). Trimmed sequences were aligned using RNA STAR aligner (v. 2.7.8a) against the GRCm38/mm10 reference. For Gap-aware read counting featureCounts (v. 2.0.1) was applied.
Read counts were normalized by rlog transformation with DESeq2 and subjected to downstream analyses.
Assembly: mm10
Supplementary files format and content: comma-separated value file includes raw counts for each sample (countTable_RNAseq.csv).
Supplementary files format and content: comma-separated value file includes normalized counts of each sample (rld_transformed_counts.csv).

source_name: cerebral cortex

extract_protocol:
Total RNA was extracted from frozen aliquots of 10,000 sorted cells using the RNeasy® Micro Kit (Qiagen, #74004).
From total RNA cDNA was synthesized, PolyA enriched and amplified using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories, # 634891). cDNA was then further processed with the Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1096).

value: cerebral cortex

value: neuronal cells

tag: transgene constructs

value: pNeuroD-eGFP/pCAG-tDimer

value: 19 days old embryo (E19)

value: PBS

tag: harvest mode


title: CD4_T_Cells_Neonate_Natural_Birth_1

description:
Library name: Basal_Natural_Birth_Term_1
Natural_Birth_1


title: Fertile control 9

city: Valencia

first: Ana

last: Corachán

state: València

address: Avenida Fernando Abril Martorell, 106, torreA, Planta 7

country: Spain

institute: IVIRMA Global Research Alliance, IVI Foundation, IIS La Fe

description: Library name: D9_S7

data_processing:
Sequencing data was processed and statistically analyzed in R (v4.5.1) using packages from Bioconductor (v3.21).Raw FASTQ files were processed to remove adapters and clean the sequences using the following programs: FastQC (Andrews, 2010), BBduk (Bushnell et al., 2017), Subread (Liao et al., 2013, 2019), MultiQC (Ewels et al., 2016), and edgeR  (Robinson et al., 2009).
miRNAs present in the samples were mapped against the human genome (GRCh38) using the Subread aligner and annotated with the miRBase database
After read mapping and quantification with the featureCounts function from the Rsubread package (v2.22.1), all samples had more than 1 million reads successfully assigned to annotated miRNAs, which was set as the minimum threshold for inclusion in the analysis. miRNAs with zero counts across all samples were removed.
Read counts for these miRNAs were then normalized using the Trimmed Mean of M-values (TMM) method (Ritchie et al., 2015) and expressed as counts per million (CPM), as implemented in the edgeR package (v4.6.3).
Assembly: GRCh38 using the Subread aligner and annotated with the miRBase database
Supplementary files format and content: counts_plasma.txt; microRNA counts for all samples included in the study

source_name: plasma

extract_protocol:
Total RNA including small RNA extraction was performed from 200 µL of plasma using miRNeasy Serum/Plasma Advanced kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol.
Libraries were prepared from total RNA using NEXTFLEX® Small RNA-Seq Kit v4 with Unique Dual Indices (UDIs) (Revvity Inc., Massachusetts, USA) following manufacturer’s instructions. The quality control and concentration of the libraries were verified using the Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) with high-sensitivity DNA chips. Subsequently, an equimolar pool of each library was prepared for sequencing on the NextSeq 550 NGS platform (Illumina, San Diego, CA, USA) using single-read sequencing with 50 cycles (1×50 bp).

value: plasma

tag: disease stage

value: non-disease


title: PEO_1_3

description: Library name: Sample 3


title: synovium_time_10wk_Control_KA10

description: Library name: sample18

value: Control


title: Fertile control 8

description: Library name: D8_S21


title: synovium_time0_Control_KA10

description: Library name: sample17


title: Fertile control 7

description: Library name: D7_S16


title: Fertile control 6

description: Library name: D6_S11


title: PEO_1_2

description: Library name: Sample 2


title: KA03_SF_time_OP2_iPAAG

description: Library name: KA03_SF_OP2

value: synovial fluid

value: SF cells


title: synovium_time_10wk_Control_KA09

description: Library name: sample16


title: PEO_4_1

description: Library name: Sample 7

value: ovarian adenocarcinoma cells

value: BRCA2 mutant, TP53 mutant


title: Fertile control 5

description: Library name: D5_S12


title: synovium_time0_Control_KA09

description: Library name: sample15


title: PEO_1_1

description: Library name: Sample 1

value: No Treatment used for this study


title: Fertile control 3

description: Library name: D3_S3


title: synovium_time_10wk_iPAAG_KA08

description: Library name: sample14

value: iPAAG


title: Fertile control 10

description: Library name: D10_S13


title: ATAC-Seq, IGF2BP3 Knockout, Replicate 2

city: Hershey

first: Irina

last: Elcheva

state: PA

address: 500 University Drive

department: Department of Pediatrics

institute: Penn State College of Medicine

description: Library name: ATAC_IGF2BP3_KO_Rep2

data_processing:
ATAC-seq reads were trimmed using fastp v0.24.1 (default settings) and aligned to the GRCh38 genome using BWA-MEM v0.7.17. Peaks were called with MACS2 v3.0.0 using parameters "-g hs -f BAMPE". Peaks from all samples were merged using BEDTools merge v2.30.0, and read counts over merged peak regions were obtained using BEDTools multicov.
Assembly: GRCh38
Supplementary files format and content: bed files containing combined peaks

source_name: embryonic kidney

growth_protocol: HEK293T cells were growing in DMEM basal media with L-Glutamine, 4.5g/L Glucose and Sodium Pyruvate (Corning 10-013CV), 1% of penicillin-streptomycin

extract_protocol:
The ATAC-seq protocol was based on the Buenrostro et al.[ Nature Methods volume 10, pages1213–1218 (2013)], with the following modifications: (1) Adjusted lysis step and transposition buffer based on Omni-ATAC protocol [Corces MR ey al.,  Nature methods 14: 959 (2017)] which can yield larger number of peaks (~2x) and reduced mitochondrial reads by ~20%; (2) Magnetic bead DNA purification instead of column purification.
ATAC-seq libraries were prepared following the Buenrostro et al. protocol with modifications. An adjusted lysis step and Omni-ATAC–based transposition buffer were used to increase peak yield and reduce mitochondrial reads. For each reaction, 100,000 cells were processed using 5 µL of Tn5 transposase (Illumina Tagment DNA Enzyme and Buffer Kit). Following transposition, libraries were purified using AMPure XP magnetic beads instead of column purification. Libraries were then PCR-amplified and indexed with unique dual-index primers according to the manufacturer’s guidelines.

treatment_protocol: There was no special treatment of HEK293T cells in addition to IGF2BP1, 2, 3 genes knockouts. The gene knockouts were performed using transient transfection of HEK293T cells with non-integrating plasmids co-expressing three sgRNAs targeting IGF2BP1, 2, or 3, and GFP (Santa Cruze, CA). Single GFP-positive cells were sorted and depositied into individual wells of 96-well plate. Colonies were assessed for endogenous expression of IGF2BP proteins compared to CRISPR/Cas9 non-tareting control produced in parallel with IGF2BP-KO using sgRNA non-targeting any mammalian gene (SantaCruz, CA). One clone of each gene knockout was used for ATAC-seq and RNA-seq analysis.

value: embryonic kidney

value: Human embryonic kidney 293 T cells

value: IGF2BP3 gene knockout

value: no treatment

value: batch 3


title: ATAC-Seq, IGF2BP3 Knockout, Replicate 1

description: Library name: ATAC_IGF2BP3_KO_Rep1

value: batch 2


title: synovium_time0_iPAAG_KA08

description: Library name: sample13

value: synovium


title: Fertile control 4

description: Library name: D4_S18


title: Fertile control 1

description: Library name: D1_S6


title: Fertile control 2

description: Library name: D2_S9


title: Infertile control 9

description: Library name: C9_S30


title: ATAC-Seq, IGF2BP2 Knockout, Replicate 2

description: Library name: ATAC_IGF2BP2_KO_Rep2

value: IGF2BP2 gene knockout


title: Infertile control 8

description: Library name: C8_S1

value: plasma


title: synovium_time_10wk_iPAAG_KA07

description: Library name: sample12


title: Infertile control 7

description: Library name: C7_S5

value: non-disease


title: ATAC-Seq, IGF2BP2 Knockout, Replicate 1

description: Library name: ATAC_IGF2BP2_KO_Rep1


title: Infertile control 6

description: Library name: C6_S8


title: synovium_time0_iPAAG_KA07

description: Library name: sample11


title: Infertile control 5

description: Library name: C5_S15


title: Infertile control 4

description: Library name: C4_S23


title: synovium_time_10wk_iPAAG_KA06

description: Library name: sample10


title: ATAC-Seq, IGF2BP1 Knockout, Replicate 3

description: Library name: ATAC_IGF2BP1_KO_Rep3

value: IGF2BP1 gene knockout


title: Infertile control 2

description: Library name: C2_S19


title: ATAC-Seq, IGF2BP1 Knockout, Replicate 2

description: Library name: ATAC_IGF2BP1_KO_Rep2


title: synovium_time0_iPAAG_KA06

description: Library name: sample9


title: Infertile control 1

description: Library name: C1_S4


title: Adenomyosis 9

description: Library name: A9_S17

value: disease


title: ATAC-Seq, CRISPR Control, Replicate 2

description: Library name: ATAC_CRISPR_CTRL_Rep2

value: WT (CRISPRCas9 non-targeting control)


title: Adenomyosis 8

description: Library name: A8_S20


title: synovium_time0_iPAAG_KA05

description: Library name: sample7


title: Adenomyosis 7

description: Library name: A7_S27


title: ATAC-Seq, CRISPR Control, Replicate 1

description: Library name: ATAC_CRISPR_CTRL_Rep1


title: synovium_time_10wk_iPAAG_KA03

description: Library name: sample6


title: Adenomyosis 6

description: Library name: A6_S2


title: Adenomyosis 4

description: Library name: A4_S14


title: Total RNA-Seq, IGF2BP3 Knockout, Replicate 2

description: Library name: TotalRNA_IGF2BP3_KO_Rep2

data_processing:
RNA-seq reads were aligned to GRCh38 using STAR, and gene-level read counts were quantified using featureCounts. Differential expression analysis was performed using DESeq2 v1.44.0.
Assembly: GRCh38
Supplementary files format and content: matrix format txt files containing Read counts and FPKM values

extract_protocol:
Subcellular RNA from nuclear and cytoplasmic compartments of HEK293T cells with CRIPSR/Cas9-mediated IGF2BPs-KO and non-targeting control was isolated using the RNA subcellular isolation kit (Active Motif, Carlsbad, CA). Total RNA was extracted using Active Motif kit as well. All isolated RNA samples underwent DNase I treatment with DNA-free DNA Removal Kit (Invitrogen, Carlsbad, CA).
RNA-seq libraries were prepared from 200 ng total RNA using the Illumina Stranded mRNA Prep, Ligation kit with polyA selection, followed by fragmentation, cDNA synthesis, end repair, adaptor ligation with unique dual indexes (IDT for Illumina RNA UD Indexes Set A), and PCR amplification. Libraries were sequenced on Illumina NovaSeq 6000 generating paired-end 50 bp reads.

value: batch 4


title: Adenomyosis 5

description: Library name: A5_S22


title: synovium_time0_iPAAG_KA03

description: Library name: sample5


title: Adenomyosis 3

description: Library name: A3_S26


title: Total RNA-Seq, IGF2BP3 Knockout, Replicate 1

description: Library name: TotalRNA_IGF2BP3_KO_Rep1


title: Adenomyosis 1

description: Library name: A1_S28


title: Adenomyosis 10

description: Library name: A10_S24


title: Total RNA-Seq, IGF2BP2 Knockout, Replicate 2

description: Library name: TotalRNA_IGF2BP2_KO_Rep2


title: Adenomyosis 2

description: Library name: A2_S10


title: synovium_time_10wk_iPAAG_KA05

description: Library name: sample8


title: synovium_time0_Control_KA02

description: Library name: sample3

value: Control


title: Total RNA-Seq, IGF2BP2 Knockout, Replicate 1

description: Library name: TotalRNA_IGF2BP2_KO_Rep1


title: synovium_time_10wk_Control_KA02

description: Library name: sample4


title: MycCaP tumor, Combination

city: Chicago

first: ping

last: xie

state: IL

address: 300 E Superior St, Tarry 4-726

institute: Northwestern University Feinberg School of Medicine, Chicago , Illinois, US

description: Library name: PX1-4

data_processing:
The raw data were processed using the Space Ranger.
The downstream analysis was performed on Bioturing.
Assembly: mm39
Supplementary files format and content: csv files include LSMean values for each sample

source_name: prostate cancer

growth_protocol: MycCaP tumors were subcutaneously inoculated on FVB background male mice, and treated with vehicle, olaparib, a-CD73 or combination from day 7 post tumor inoculation, and harvested at day 25 post tranlsation.

extract_protocol:
The frozen tissue were mounted on 10x visium slides, and capturing RNA onto spatially barcoded spots.
10x visium V1

treatment_protocol: Treated with vehicle, olaparib (daily), a-CD73 (biweekly), or combination from Day 7 post tumor inoculation for 15 days

value: prostate cancer

value: MycCaP

value: Epithelial cells

value: wild type

value: Combination


title: Infertile control 3

description: Library name: C3_S29


title: synovium_time_10wk_Control_KA01

description: Library name: sample2


title: MycCaP tumor, Olaparib

description: Library name: PX1-2

value: Olaparib


title: MycCaP tumor, a-CD73

description: Library name: PX1-3


title: Total RNA-Seq, IGF2BP1 Knockout, Replicate 2

description: Library name: TotalRNA_IGF2BP1_KO_Rep2

value: embryonic kidney

value: Human embryonic kidney 293 T cells

value: no treatment


title: synovium_time0_Control_KA01

description: Library name: sample1

value: synovium


title: MycCaP tumor, Vehicle

description: Library name: PX1-1

value: Veh


title: Total RNA-Seq, IGF2BP1 Knockout, Replicate 1

description: Library name: TotalRNA_IGF2BP1_KO_Rep1

value: batch 1


title: CTRL__UT CTRL_UT_3

description:
Library name: CTRL_UT_3
dr_ciliopathy_treatments_cts.csv.gz

data_processing:
fastp fastq trimming
decoy aware salmon index
salmon quant --index  --libType A --seqBias --gcBias             --validateMappings
tximport into R (4.4)
gencode.v47.primary_assembly.annotation.gtf.gz
Assembly: GRCh38.primary_assembly.genome.fa.gz
Supplementary files format and content: counts, csv

extract_protocol:
RNA was isolated from RPE monolayer 5 weeks post-seeding on transwells, using RNA extraction kit, Macherey&Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: RPE

value: CTRL

value: iRPE

value: UT


title: Human iPSC line iP149-1, low-coverage whole-genome sequencing coverage

city: Novisibirsk

first: Veniamin

last: Fishman

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences

description:
Library name: iP149-1_WGS
Quantitative whole-genome sequencing coverage track used to refine the Xq25 duplication breakpoints.

data_processing:
Reads were aligned to the GRCh38/hg38 human genome.
Genome-wide quantitative coverage was calculated from the aligned reads and stored as a bigWig track.
The coverage track was inspected in Integrative Genomics Viewer to characterize the Xq25 duplication.
WGS raw reads are intentionally not included in this processed-only GEO submission.
Assembly: GRCh38/hg38
Supplementary files format and content: The bigWig contains quantitative genome-wide read-coverage values for the iP149-1 human iPSC line.
Supplementary files format and content: Uncompressed binary bigWig track.

growth_protocol: Human iPSCs were maintained in mTeSR1 medium on Matrigel-coated dishes at 37 degrees C with 5% CO2 and passaged using TrypLE at a 1:5 split ratio.

extract_protocol:
Genomic DNA was extracted from iP149-1 cells.
A whole-genome library was prepared using the VAHTS Universal DNA Library Prep Kit for Illumina according to the manufacturer's instructions and sequenced as paired-end reads.

treatment_protocol: No experimental treatment was applied for the low-coverage WGS analysis.

value: induced pluripotent stem cell

value: Patient-derived iPSC line carrying a tandem Xq25 duplication encompassing STAG2


title: CD122+ cells - Donor 112 - Pre-treatment

city: Seattle

first: Laura

last: Cooeny

state: WA

address: 1201 9th Ave

department: University of Michigan

institute: Immune Tolerance Network

description:
Library name: lib57771_AAAF23WHV
Donor ID: 112; Sample name: Sub_112_D1; Study day: D1 (Pre-treatment); barcode suffix -7 in aggregated matrix P381-1_aggr_noNorm_raw_feature_bc_matrix.h5

data_processing:
Base-calling and demultiplexing were performed using Cell Ranger (10x Genomics, v4.0.0) mkfastq to generate per-library FASTQ files.
Reads were aligned to the reference genome, and cell barcodes, UMIs, and gene-level counts were processed using Cell Ranger count (v4.0.0).
Cell Ranger aggr (v4.0.0) was used to aggregate the 8 libraries (lib56699, lib56700, lib56701, lib56702, lib57769, lib57770, lib57771, lib57772) without depth normalization into a single raw feature-barcode matrix; libraries are distinguished by the GEM well barcode suffix (-1 through -8, respectively, matching the order above).
Assembly: GRCh38.91
Supplementary files format and content: HDF5-format raw feature-barcode matrix (P381-1_aggr_noNorm_raw_feature_bc_matrix.h5) containing unfiltered gene-level UMI counts (58,302 features x cell barcodes) for all 8 libraries, aggregated without depth normalization via Cell Ranger aggr. Libraries are distinguished by the barcode GEM-well suffix (-1 through -8), corresponding to lib56699, lib56700, lib56701, lib56702, lib57769, lib57770, lib57771, lib57772, respectively.
Supplementary files format and content: Comma-separated file (<libId>_metrics_summary.csv) containing Cell Ranger per-library QC metrics, including estimated cell count, mean reads per cell, median genes per cell, total reads, valid barcode rate, sequencing saturation, Q30 base rates, genome/transcriptome mapping rates, fraction reads in cells, total genes detected, and median UMI counts per cell.

source_name: peripheral blood mononuclear cells (PBMC)

extract_protocol:
CD122+ non-myeloid cells were FACS-sorted directly from thawed PBMC into single-cell suspension. Cells were loaded onto the 10x Genomics Chromium Controller for partitioning into Gel Bead-in-Emulsions (GEMs), where cells were lysed and mRNA reverse-transcribed to barcoded cDNA using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1, Dual Index (BRI Genomics Core protocol: next_gem_single_cell_3_prime_v3_1_dual_index_10x_genomics).
Barcoded cDNA was amplified and used to construct sequencing-ready libraries using the Chromium Next GEM Single Cell 3' Gene Expression Library Construction Kit v3.1, Dual Index (BRI Genomics Core protocol: next_gem_single_cell_3_prime_v3_1_dual_index_10x_genomics_gex_lib_prep). Paired-end sequencing of pooled libraries was run on a NextSeq 2000 (Illumina).

treatment_protocol: Subjects in the Pandion PT-101 Phase 1a IL-2 mutein trial who received the 10mg IL-2 mutein dose (Cohort 3) were sampled at pre-treatment baseline and Day 8 post-dose. CD122+ non-myeloid cells (including NK cells, ILCs, and CD122+ T cells) were sorted from PBMC at each timepoint for single-cell RNA-seq.

value: CD122+ cells

value: 10mg mutein


title: CD122+ cells - Donor 112 - Day 8 post-dose

description:
Library name: lib57772_AAAF23WHV
Donor ID: 112; Sample name: Sub_112_D8; Study day: D8 (Day 8 post-dose); barcode suffix -8 in aggregated matrix P381-1_aggr_noNorm_raw_feature_bc_matrix.h5

value: peripheral blood mononuclear cells (PBMC)


title: Total RNA-Seq, CRISPR Control, Replicate 4

description: Library name: TotalRNA_CRISPR_CTRL_Rep4

value: WT (CRISPRCas9 non-targeting control)

value: batch 4


title: CD122+ cells - Donor 116 - Day 8 post-dose

description:
Library name: lib57770_AAAF23WHV
Donor ID: 116; Sample name: Sub_116_D8; Study day: D8 (Day 8 post-dose); barcode suffix -6 in aggregated matrix P381-1_aggr_noNorm_raw_feature_bc_matrix.h5


title: CD122+ cells - Donor 116 - Pre-treatment

description:
Library name: lib57769_AAAF23WHV
Donor ID: 116; Sample name: Sub_116_D1; Study day: D1 (Pre-treatment); barcode suffix -5 in aggregated matrix P381-1_aggr_noNorm_raw_feature_bc_matrix.h5


title: CRISPR/Cas9-edited human iPSC clone 146-1-2v6, RNA-seq coverage

description:
Library name: 146-1-2v6_RNAseq
Stranded oligo-dT RNA-seq; quantitative CPM-normalized 1-bp coverage track. Parent line: iP146-1.

data_processing:
Reads were aligned to the GRCh38/hg38 human genome with STAR version 2.5.2b.
Coordinate-sorted BAM files were produced with samtools.
Genome-wide coverage was calculated from each BAM with deepTools bamCoverage using 1-bp bins and CPM normalization.
No smoothing was applied; coverage values are stored as native bigWig binary tracks.
RNA-seq raw reads are intentionally not included in this processed-only GEO submission; targeted NGS and PCR-genotyping raw data are in SRA BioProject PRJNA1499378.
Assembly: GRCh38/hg38
Supplementary files format and content: Each bigWig contains genome-wide per-base read coverage normalized to counts per million mapped reads for one human iPSC clone.
Supplementary files format and content: Files are uncompressed binary bigWig tracks, one file per sample.

extract_protocol:
Total RNA was extracted from each iPSC clone and polyadenylated RNA was selected by an oligo-dT-based stranded workflow.
Stranded oligo-dT RNA-seq libraries were prepared and sequenced as paired-end reads on an Illumina platform.

treatment_protocol: Cells were electroporated with 1 microgram pSpCas9(BB)-2A-Puro carrying the relevant STAG2 guide RNA, selected with 1 microgram/ml puromycin for 2 days, clonally isolated 10 days after electroporation, and expanded.

value: CRISPR/Cas9-edited clone derived from iP146-1

value: CRISPR/Cas9 genome editing with pSpCas9(BB)-2A-Puro followed by clonal expansion


title: CD122+ cells - Donor 123 - Day 8 post-dose

description:
Library name: lib56702_AAAF2CLHV
Donor ID: 123; Sample name: D_Sub_123_D8; Study day: D8 (Day 8 post-dose); barcode suffix -4 in aggregated matrix P381-1_aggr_noNorm_raw_feature_bc_matrix.h5


title: Total RNA-Seq, CRISPR Control, Replicate 3

description: Library name: TotalRNA_CRISPR_CTRL_Rep3

value: embryonic kidney

value: Human embryonic kidney 293 T cells

value: no treatment

value: batch 3


title: CRISPR/Cas9-edited human iPSC clone 146-1-5v1, RNA-seq coverage

description:
Library name: 146-1-5v1_RNAseq
Stranded oligo-dT RNA-seq; quantitative CPM-normalized 1-bp coverage track. Parent line: iP146-1.


title: CD122+ cells - Donor 114 - Day 8 post-dose

description:
Library name: lib56700_AAAF2CLHV
Donor ID: 114; Sample name: B_Sub114_D8; Study day: D8 (Day 8 post-dose); barcode suffix -2 in aggregated matrix P381-1_aggr_noNorm_raw_feature_bc_matrix.h5


title: CRISPR/Cas9-edited human iPSC clone 149-4-7v6, RNA-seq coverage

description:
Library name: 149-4-7v6_RNAseq
Stranded oligo-dT RNA-seq; quantitative CPM-normalized 1-bp coverage track. Parent line: iP149-4.

value: CRISPR/Cas9-edited clone derived from iP149-4


title: Total RNA-Seq, CRISPR Control, Replicate 2

description: Library name: TotalRNA_CRISPR_CTRL_Rep2

value: batch 2


title: CD122+ cells - Donor 114 - Pre-treatment

description:
Library name: lib56699_AAAF2CLHV
Donor ID: 114; Sample name: A_Sub114_D1; Study day: D1 (Pre-treatment); barcode suffix -1 in aggregated matrix P381-1_aggr_noNorm_raw_feature_bc_matrix.h5


title: Treg (CD127-CD25+) - Donor 199 - Day 29

description:
Library name: lib59198_AAAFM27HV
Donor ID: 199; Study day: D29

data_processing:
Adapter and quality trimming of raw reads was performed using FastqMcf (ea-utils).
Read quality was assessed using FastQC (v0.11.3).
Alignment metrics, duplication rates, and RNA-seq QC metrics (ribosomal/intronic/UTR/coding base composition, 5'/3' bias) were computed using Picard tools (v1.134; CollectRnaSeqMetrics, MarkDuplicates) and Samtools (v1.2).
Base-calling and demultiplexing were performed automatically on BaseSpace (Illumina) to generate FASTQ files.
Reads were aligned to the reference genome using STAR (v2.4.2a); gene-level read counts were generated using HTSeq-count (v0.4.1) in 'intersection (nonempty)' mode with a minimum alignment quality of 20.
Assembly: GRCh38, Ensembl release 91
Supplementary files format and content: Comma-separated file (combined_counts_GEO_submission.csv) containing gene-level raw read counts, with Ensembl gene IDs as rows and library names (matching "library name" column in SAMPLES section) as columns.

source_name: PBMC

extract_protocol:
PBMCs were thawed and immediately immunolabeled and FACS-sorted for sequencing. Dead cells were excluded from all sorts by staining with the Fixable Viability Dye eFluor™ 780 (eBioscience). For bulk RNA-seq, 250–500 CD4+CD127loCD25+ Tregs were sorted directly into lysis buffer, and cDNA was prepared using the SMART-Seq Ultra Low Input RNA Kit for Sequencing (Takara Bio).
RNA-seq libraries were constructed using the NexteraXT DNA Library Preparation Kit (Illumina) with half the recommended volumes and reagents. Paired-end sequencing of pooled libraries was run on a NextSeq 2000 (Illumina) with 59-base reads and a target depth of 5 million reads per sample.

treatment_protocol: Healthy adult volunteers in the Phase 1a single ascending dose trial received a single dose of Placebo, 1mg, 3.5mg, 5mg, or 10mg IL-2 mutein MK-6194/PT-101 subcutaneously. PBMC samples were collected at pre-treatment baseline (-10) and on study days 1 (prior to the dose, which occurred on day 1), 8, 15, and 29 and cryopreserved. For details on the clinical trial, see Scheid, et al., Safety, pharmacokinetics, and pharmacodynamics of MK-6194, an IL-2 mutein designed to selectively activate regulatory T cells: single ascending dose and multiple ascending dose trial data, ImmunoHorizons, Volume 9, Issue 5, May 2025, vlaf005, https://doi.org/10.1093/immhor/vlaf005.

value: PBMC

value: 3.5mg mutein


title: CD122+ cells - Donor 123 - Pre-treatment

description:
Library name: lib56701_AAAF2CLHV
Donor ID: 123; Sample name: C_Sub_123_D1; Study day: D1 (Pre-treatment); barcode suffix -3 in aggregated matrix P381-1_aggr_noNorm_raw_feature_bc_matrix.h5


title: Total RNA-Seq, CRISPR Control, Replicate 1

description: Library name: TotalRNA_CRISPR_CTRL_Rep1

value: batch 1


title: Treg (CD127-CD25+) - Donor 199 - Day 8

description:
Library name: lib59194_AAAFM27HV
Donor ID: 199; Study day: D8


title: Treg (CD127-CD25+) - Donor 199 - Day 15

description:
Library name: lib59196_AAAFM27HV
Donor ID: 199; Study day: D15


title: CRISPR/Cas9-edited human iPSC clone 149-1-6v1, RNA-seq coverage

description:
Library name: 149-1-6v1_RNAseq
Stranded oligo-dT RNA-seq; quantitative CPM-normalized 1-bp coverage track. Parent line: iP149-1.

value: induced pluripotent stem cell

value: CRISPR/Cas9-edited clone derived from iP149-1


title: Nuclear RNA-Seq, IGF2BP3 Knockout, Replicate 2

description: Library name: NuclearRNA_IGF2BP3_KO_Rep2

molecule: nuclear RNA

value: IGF2BP3 gene knockout


title: Infertile control 10

description: Library name: C10_S25

value: plasma

value: non-disease


title: Treg (CD127-CD25+) - Donor 199 - Day 1

description:
Library name: lib59192_AAAFM27HV
Donor ID: 199; Study day: D1


title: ATAC-Seq, IGF2BP1 Knockout, Replicate 1

description: Library name: ATAC_IGF2BP1_KO_Rep1

value: IGF2BP1 gene knockout


title: Treg (CD127-CD25+) - Donor 181 - Day 29

description:
Library name: lib59190_AAAFM27HV
Donor ID: 181; Study day: D29

value: Placebo


title: Treg (CD127-CD25+) - Donor 181 - Day 15

description:
Library name: lib59188_AAAFM27HV
Donor ID: 181; Study day: D15


title: Nuclear RNA-Seq, IGF2BP3 Knockout, Replicate 1

description: Library name: NuclearRNA_IGF2BP3_KO_Rep1


title: CRISPR/Cas9-edited human iPSC clone 149-1-20v6, RNA-seq coverage

description:
Library name: 149-1-20v6_RNAseq
Stranded oligo-dT RNA-seq; quantitative CPM-normalized 1-bp coverage track. Parent line: iP149-1.

value: CRISPR/Cas9 genome editing with pSpCas9(BB)-2A-Puro followed by clonal expansion


title: KA09_SF_time_OP10_Control

description: Library name: KA09_SF_OP10

data_processing:
Differential analysis for comparisons between iPAAG treated and operated untreated controls was computed using Limma (Linear modeling and empirical Bayes) Voom (Mean–variance modeling) method (limma v3.62.2) longitudinal analysis with baseline (week 2 operated joints) with TMM normalization and duplicate Correlation() (block = patient) to estimate within-patient correlation
Fastp v0.23.2 was used to trim adapters and low-quality reads, STAR version 2.7.10b was used for alignment to Equus caballus EquCab3.0, annotated with Ensembl 113 and feature counts Version 2.0.1 was used to quantify reads.
Assembly: Equus caballus EquCab3.0
Supplementary files format and content: voom_logCPM_normalized_SF.csv

source_name: synovial fluid

extract_protocol:
The fluid was digested with 0.3 mg/mL hyaluronidase (Sigma, St. Louis, MO, USA) by incubation in a bead bath for 15 minutes at 37 ºC. Next the sample was centrifuged at 750 x g for 10 minutes at 8 ºC. The remaining cell pellet was washed with PBS and centrifuged at 500 x g for 10 minutes at 8 ºC. The cell pellet was resuspended in about 1 to 2 mL of PBS and transferred into a 2 mL microcentrifuge tube. The sample was then centrifuged for 500 x g for 15 minutes. The supernatant was discarded, and the cells were lysed in RLT buffer (Qiagen, Germantown, MD, USA) with 1% ß-Mercaptoethanol (BME; EMD Millipore Corp, Billerica, MA, USA) and stored at -80 ºC until RNA extraction.
Library preparation was conducted on synovial fluid samples using the SMARTer® Stranded Total RNA-Seq Kit -Pico input (Takara Bio USA, Inc.)

value: synovial fluid

value: SF cells


title: Nuclear RNA-Seq, IGF2BP2 Knockout, Replicate 2

description: Library name: NuclearRNA_IGF2BP2_KO_Rep2

value: embryonic kidney

value: Human embryonic kidney 293 T cells

value: IGF2BP2 gene knockout

value: no treatment

value: batch 4


title: Treg (CD127-CD25+) - Donor 181 - Day 8

description:
Library name: lib59186_AAAFM27HV
Donor ID: 181; Study day: D8

value: PBMC


title: Treg (CD127-CD25+) - Donor 179 - Day 29

description:
Library name: lib59182_AAAFM27HV
Donor ID: 179; Study day: D29

value: 3.5mg mutein


title: Nuclear RNA-Seq, IGF2BP2 Knockout, Replicate 1

description: Library name: NuclearRNA_IGF2BP2_KO_Rep1

value: batch 3


title: CRISPR/Cas9-edited human iPSC clone 149-4-3v1, RNA-seq coverage

description:
Library name: 149-4-3v1_RNAseq
Stranded oligo-dT RNA-seq; quantitative CPM-normalized 1-bp coverage track. Parent line: iP149-4.

value: induced pluripotent stem cell

value: CRISPR/Cas9-edited clone derived from iP149-4


title: NE-4C cells, WT, not treated, biorep 3

city: Boulder

first: Anneke

middle: Dixie

last: Kakebeen

state: Colorado

address: A1B43 MCDB Main Office, 1945 Colorado Ave

department: Molecular Cellular and Developmental Biology

institute: university of colorado boulder

description:
Library name: WT_NO_3
column name in scaled_counts.tsv: WT_NO3

data_processing:
Nextflow Core: RNASeq (https://nf-co.re/rnaseq/3.14.0/) was used to trim, align, and quantify reads. Input was FASTQ files and a data sheet, Output produced was "salmon.merged.gene_counts_scaled" which is the equivalent of rawcounts.tsv
nextflow run nf-core/rnaseq --input NF_samplesheet.csv --outdir NF_OUT -w WORK/ --save_trimmed  --fasta BUILD_INDEX/Mus_musculus.GRCm39.dna.primary_assembly.fa --gtf BUILD_INDEX/Mus_musculus.GRCm39.109.gtf -profile singularity
Raw_counts.tsv was read into R and postprocessed using DESeq2
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa; Mus_musculus.GRCm39.109.gtf
Supplementary files format and content: tab separated values include raw counts for each Sample

growth_protocol: NE-4C cells were originally derived from E9 mouse embryonic brain (Schlett and Madarász, 1997). Our stocks were purchased from ATCC (CRL-2925). Cells were grown at 37oC and 5% CO2 conditions in MEM (Gibco 41090101) supplemented with 10% FBS, 1xMEM nonessential amino acids (Gibco 11140050), 1xGlutaMax (Gibco 35050061), and 1% penicillin-streptomycin (Gibco 15070063). The NE-4C cell line was routinely tested in the lab for mycoplasma contamination.

extract_protocol:
WT and knockout cells were collected by trypsinization from three independent passages and frozen as cell pellets. The “NO” condition (not induced) were collected without perturbations. The “RA” condition (retinoic acid induced) were treated for 24 hours with RA followed by basal media until collection at 3 days post induction. Total RNA was then extracted from cell pellets using Zymo kit R1054
Libraries were prepared  by The University of Colorado, Anschutz Shared Genomics Core (RRID: SCR_021984) using the Universal Plus™ mRNA-Seq library preparation kit with NuQuant

treatment_protocol: NE-4C neuronal differentiation was induced by addition of 1µM all-trans retinoic acid (RA) (Sigma-Aldrich # 302-79-4) for 24 hours followed by incubation in growth media (Varga et al., 2008).

value: nerual progenitor cells

value: WT

value: 0 days


title: CRISPR/Cas9-edited human iPSC clone 146-7-3v1, RNA-seq coverage

description:
Library name: 146-7-3v1_RNAseq
Stranded oligo-dT RNA-seq; quantitative CPM-normalized 1-bp coverage track. Parent line: iP146-7.

value: CRISPR/Cas9-edited clone derived from iP146-7


title: Nuclear RNA-Seq, IGF2BP1 Knockout, Replicate 2

description: Library name: NuclearRNA_IGF2BP1_KO_Rep2

value: IGF2BP1 gene knockout

value: batch 2


title: NE-4C cells, WT, not treated, biorep 2

description:
Library name: WT_NO_2
column name in scaled_counts.tsv: WT_NO2


title: NE-4C cells, WT, not treated, biorep 1

description:
Library name: WT_NO_1
column name in scaled_counts.tsv: WT_NO1


title: Treg (CD127-CD25+) - Donor 179 - Day 8

description:
Library name: lib59178_AAAFM27HV
Donor ID: 179; Study day: D8


title: NE-4C cells, WT, RA treated, biorep 3

description:
Library name: WT_RA_3
column name in scaled_counts.tsv: WT_RA3

value: RA

value: 3 days post induction


title: CRISPR/Cas9-edited human iPSC clone 149-4-4v1, RNA-seq coverage

description:
Library name: 149-4-4v1_RNAseq
Stranded oligo-dT RNA-seq; quantitative CPM-normalized 1-bp coverage track. Parent line: iP149-4.

value: CRISPR/Cas9 genome editing with pSpCas9(BB)-2A-Puro followed by clonal expansion


title: Treg (CD127-CD25+) - Donor 179 - Day 15

description:
Library name: lib59180_AAAFM27HV
Donor ID: 179; Study day: D15


title: Nuclear RNA-Seq, CRISPR Control, Replicate 4

description: Library name: NuclearRNA_CRISPR_CTRL_Rep4

value: embryonic kidney

value: Human embryonic kidney 293 T cells

value: WT (CRISPRCas9 non-targeting control)


title: Treg (CD127-CD25+) - Donor 179 - Day 1

description:
Library name: lib59176_AAAFM27HV
Donor ID: 179; Study day: D1

value: PBMC


title: PBMCs, patient 3, set 2, scRNAseq

city: Munich

first: Johanna

last: Klughammer

address: Feodor Lynen Str 25

country: Germany

institute: Gene Center LMU

description:
Library name: P3_sample_set_2
10x Genomics, hashed and geneticicall demultiplexed

data_processing:
Raw data processing was performed using the cellranger v7.1.0 multi pipeline (setting expect-cells = 20000 and include-introns = True).
Cells were demultiplexed using an in-house hashtag demultiplexer and genetically with CellSNP-lite (v1.2.2) and Vireo (v0.5.8). Sample-doublets were identified and subsequently removed using our hashtag demultiplexer, Vireo (v0.5.8).
Assembly: GRCh38
Supplementary files format and content: .h5 files containing sample-demultiplexed count matrix including cell and gene IDs.

source_name: Blood

extract_protocol:
Frozen PBMCs of 3 patients and 5 controls were processed following our protocol for Sample-Multiplexed, FACS-Preprocessing of PBMCs with Rare Cell Type enrichment (https://dx.doi.org/10.17504/protocols.io.j8nlk82m5l5r/v1). In brief, samples were thawed, washed, stained with PE anti-human CD123, APC anti-human CD303, and TotalSeq™-C antibody hashtags (BioLegend) before sample pooling. Pool 1 consisted of patients 1 and 2, and controls sc Co3, sc Co4, and sc Co5 and three more samples not relevant to this study, and pool 2 consisted of patient 3 and controls sc Co1 and sc Co2 and five more samples not relevant to this study. Pools were cleared of dead cells and enriched for pDCs using the BD FACSAria™ III Cell Sorter.  During sorting, monocytes were filtered out for pool 1, while they were retained for pool2.
33,000 live cells were loaded onto two lanes each (referred to as set1 and set2) of the Chip G of the Chromium Next GEM Single Cell 5' v2 (Dual Index) Kit (10x Genomics). GEX libraries were constructed according to the kit instructions. Libraries were sequenced on a P3 Flow Cell on an Illumina NextSeq 1000 machine.

value: Blood

value: A507Pfs*25 de novo


title: Nuclear RNA-Seq, CRISPR Control, Replicate 3

description: Library name: NuclearRNA_CRISPR_CTRL_Rep3

value: no treatment

value: batch 3


title: Treg (CD127-CD25+) - Donor 184 - Day 29

description:
Library name: lib59174_AAAFM27HV
Donor ID: 184; Study day: D29

value: 3.5mg mutein


title: CRISPR/Cas9-edited human iPSC clone 146-1-2v1, RNA-seq coverage

description:
Library name: 146-1-2v1_RNAseq
Stranded oligo-dT RNA-seq; quantitative CPM-normalized 1-bp coverage track. Parent line: iP146-1.

value: induced pluripotent stem cell

value: CRISPR/Cas9-edited clone derived from iP146-1


title: PBMCs, patient 3, set 1, scRNAseq

description:
Library name: P3_sample_set_1
10x Genomics, hashed and geneticicall demultiplexed


title: NE-4C cells, WT, RA treated, biorep 2

description:
Library name: WT_RA_2
column name in scaled_counts.tsv: WT_RA2

value: nerual progenitor cells

value: WT


title: Nuclear RNA-Seq, IGF2BP1 Knockout, Replicate 1

description: Library name: NuclearRNA_IGF2BP1_KO_Rep1

value: IGF2BP1 gene knockout

value: batch 1


title: NE-4C cells, WT, RA treated, biorep 1

description:
Library name: WT_RA_1
column name in scaled_counts.tsv: WT_RA1

value: RA

value: 3 days post induction


title: CRISPR/Cas9-edited human iPSC clone 149-4-1v6, RNA-seq coverage

description:
Library name: 149-4-1v6_RNAseq
Stranded oligo-dT RNA-seq; quantitative CPM-normalized 1-bp coverage track. Parent line: iP149-4.

value: CRISPR/Cas9-edited clone derived from iP149-4

value: CRISPR/Cas9 genome editing with pSpCas9(BB)-2A-Puro followed by clonal expansion


title: Nuclear RNA-Seq, CRISPR Control, Replicate 2

description: Library name: NuclearRNA_CRISPR_CTRL_Rep2

value: embryonic kidney

value: Human embryonic kidney 293 T cells

value: WT (CRISPRCas9 non-targeting control)

value: batch 2


title: Treg (CD127-CD25+) - Donor 184 - Day 15

description:
Library name: lib59172_AAAFM27HV
Donor ID: 184; Study day: D15

value: PBMC


title: PBMCs, patient 2, set 2, scRNAseq

description:
Library name: P2_sample_set_2
10x Genomics, hashed and geneticicall demultiplexed

value: Blood

value: R198* Heterozygous


title: NE-4C cells, Faf2 KO, not treated, biorep 3

description:
Library name: KO_NO_3
column name in scaled_counts.tsv: KO_NO3

value: FAF2 KO

value: 0 days


title: Nuclear RNA-Seq, CRISPR Control, Replicate 1

description: Library name: NuclearRNA_CRISPR_CTRL_Rep1

value: no treatment


title: PBMCs, patient 2, set 1, scRNAseq

description:
Library name: P2_sample_set_1
10x Genomics, hashed and geneticicall demultiplexed


title: Treg (CD127-CD25+) - Donor 184 - Day 8

description:
Library name: lib59170_AAAFM27HV
Donor ID: 184; Study day: D8

value: 3.5mg mutein


title: Cytoplasmic RNA-Seq, IGF2BP3 Knockout, Replicate 4

description: Library name: CytoplasmicRNA_IGF2BP3_KO_Rep4

molecule: cytoplasmic RNA

value: IGF2BP3 gene knockout

value: batch 5


title: NE-4C cells, Faf2 KO, not treated, biorep 2

description:
Library name: KO_NO_2
column name in scaled_counts.tsv: KO_NO2

value: nerual progenitor cells


title: NE-4C cells, Faf2 KO, not treated, biorep 1

description:
Library name: KO_NO_1
column name in scaled_counts.tsv: KO_NO1


title: Treg (CD127-CD25+) - Donor 184 - Day 1

description:
Library name: lib59168_AAAFM27HV
Donor ID: 184; Study day: D1


title: PBMCs, patient 1, set 1, scRNAseq

description:
Library name: P1_sample_set_1
10x Genomics, hashed and geneticicall demultiplexed


title: PBMCs, patient 1, set 2, scRNAseq

description:
Library name: P1_sample_set_2
10x Genomics, hashed and geneticicall demultiplexed


title: Treg (CD127-CD25+) - Donor 015 - Day 29

description:
Library name: lib59158_AAAFM27HV
Donor ID: 015; Study day: D29

value: 1mg mutein


title: Cytoplasmic RNA-Seq, IGF2BP3 Knockout, Replicate 3

description: Library name: CytoplasmicRNA_IGF2BP3_KO_Rep3


title: Treg (CD127-CD25+) - Donor 181 - Day 1

description:
Library name: lib59184_AAAFM27HV
Donor ID: 181; Study day: D1

value: Placebo


title: NE-4C cells, Faf2 KO, RA treated, biorep 3

description:
Library name: KO_RA_3
column name in scaled_counts.tsv: KO_RA3

value: RA

value: 3 days post induction


title: Cytoplasmic RNA-Seq, IGF2BP3 Knockout, Replicate 2

description: Library name: CytoplasmicRNA_IGF2BP3_KO_Rep2

value: embryonic kidney

value: Human embryonic kidney 293 T cells

value: batch 4


title: Treg (CD127-CD25+) - Donor 015 - Day 15

description:
Library name: lib59156_AAAFM27HV
Donor ID: 015; Study day: D15

value: PBMC


title: PBMCs, control 5, set 2, scRNAseq

description:
Library name: scCo5_sample_set_2
10x Genomics, hashed and geneticicall demultiplexed

value: Blood

value: control


title: NE-4C cells, Faf2 KO, RA treated, biorep 2

description:
Library name: KO_RA_2
column name in scaled_counts.tsv: KO_RA2

value: FAF2 KO


title: Cytoplasmic RNA-Seq, IGF2BP3 Knockout, Replicate 1

description: Library name: CytoplasmicRNA_IGF2BP3_KO_Rep1

value: batch 3


title: Treg (CD127-CD25+) - Donor 015 - Day 1

description:
Library name: lib59154_AAAFM27HV
Donor ID: 015; Study day: D1


title: NE-4C cells, Faf2 KO, RA treated, biorep 1

description:
Library name: KO_RA_1
column name in scaled_counts.tsv: KO_RA1


title: PBMCs, control 5, set 1, scRNAseq

description:
Library name: scCo5_sample_set_1
10x Genomics, hashed and geneticicall demultiplexed


title: PBMCs, control 4, set 2, scRNAseq

description:
Library name: scCo4_sample_set_2
10x Genomics, hashed and geneticicall demultiplexed


title: Cytoplasmic RNA-Seq, IGF2BP2 Knockout, Replicate 1

description: Library name: CytoplasmicRNA_IGF2BP2_KO_Rep1

value: IGF2BP2 gene knockout

value: no treatment


title: Treg (CD127-CD25+) - Donor 001 - Day 15

description:
Library name: lib59152_AAAFM27HV
Donor ID: 001; Study day: D15


title: Cytoplasmic RNA-Seq, IGF2BP2 Knockout, Replicate 2

description: Library name: CytoplasmicRNA_IGF2BP2_KO_Rep2


title: Treg (CD127-CD25+) - Donor 001 - Day 8

description:
Library name: lib59150_AAAFM27HV
Donor ID: 001; Study day: D8


title: PBMCs, control 4, set 1, scRNAseq

description:
Library name: scCo4_sample_set_1
10x Genomics, hashed and geneticicall demultiplexed


title: Masster muscle, KPC, rep 3

city: Gainesville

first: Andrew

last: Judge

state: FL

address: 1275 Center Drive, Biomedical Sciences Building RM J303

institute: University of Florida

description: Library name: KPCMasseter-4

data_processing:
Raw reads were assessed using FastQC (v0.12.1) and trimmed using Fastp (v0.23.4). Processed reads were aligned to the mouse reference genome (mm10) using STAR (v2.7.11b) with splice-aware mapping. Gene-level expression was quantified using Salmon (v1.10.3) in selective alignment mode against a decoy-aware transcriptome index, and transcript-level estimates were summarized to gene-level counts using tximport (v1.26.0).
Assembly: mm10
Supplementary files format and content: xlsx file contains counts for each sample

source_name: Masseter muscle

extract_protocol:
Total RNA was isolated from muscles using TRIzol reagent (Invitrogen) followed by chloroform extraction, isopropanol precipitation, and DNase treatment. RNA integrity was assessed using an Agilent TapeStation 4200.
Poly(A)-selected libraries were prepared from 250 ng RNA using the Illumina mRNA Prep kit and sequenced on an Illumina NovaSeq X Series instrument (2 × 150 bp) to a minimum depth of 40 million reads per sample at the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR) core facility.

treatment_protocol: An orthotopic pancreatic cancer mouse model was used to induce cachexia. Murine KPC FC1245 pancreatic cancer cells, derived from tumors of a KPC (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx-1-Cre) mouse, were generously gifted by Dr. David Tuveson (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY). Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in 5% CO₂. KPC pancreatic cancer cells (1.5 × 10⁵ cells; passage 10) diluted in 50 μL sterile saline (KPC group; n = 8) or 50 μL sterile saline alone (Sham group; n = 8) were orthotopically injected into the tail of the mouse pancreas. All animals received perioperative analgesia consisting of Meloxicam (15 mg/kg, subcutaneous) administered immediately prior to surgery and every 24 hours for 72 hours, as well as Ethiqa-XR (3.25 mg/kg, subcutaneous) administered once prior to surgery.

value: Masseter muscle

value: KPC tumor-bearing


title: Masseter muscle, KPC rep 2

description: Library name: KPCMasseter-3


title: Cytoplasmic RNA-Seq, IGF2BP1 Knockout, Replicate 2

description: Library name: CytoplasmicRNA_IGF2BP1_KO_Rep2

value: IGF2BP1 gene knockout

value: batch 2


title: Treg (CD127-CD25+) - Donor 001 - Day 1

description:
Library name: lib59148_AAAFM27HV
Donor ID: 001; Study day: D1

value: Placebo


title: Masseter muscle, KPC, rep 1

description: Library name: KPCMasseter-1


title: PBMCs, control 3, set 2, scRNAseq

description:
Library name: scCo3_sample_set_2
10x Genomics, hashed and geneticicall demultiplexed


title: Cytoplasmic RNA-Seq, IGF2BP1 Knockout, Replicate 1

description: Library name: CytoplasmicRNA_IGF2BP1_KO_Rep1

value: batch 1


title: PBMCs, control 3, set 1, scRNAseq

description:
Library name: scCo3_sample_set_1
10x Genomics, hashed and geneticicall demultiplexed


title: Masster muscle, Sham/Control, rep 4

description: Library name: ShamMasseter-4

value: Non-tumor bearing


title: Cytoplasmic RNA-Seq, CRISPR Control, Replicate 4

description: Library name: CytoplasmicRNA_CRISPR_CTRL_Rep4

value: embryonic kidney

value: WT (CRISPRCas9 non-targeting control)


title: Treg (CD127-CD25+) - Donor 233 - Day 29

description:
Library name: lib59146_AAAFM27HV
Donor ID: 233; Study day: D29

value: 5mg mutein


title: Masster muscle, Sham/Control, rep 3

description: Library name: ShamMasseter-3


title: Treg (CD127-CD25+) - Donor 233 - Day 15

description:
Library name: lib59144_AAAFM27HV
Donor ID: 233; Study day: D15

value: PBMC


title: PBMCs, control 2, set 2, scRNAseq

description:
Library name: scCo2_sample_set_2
10x Genomics, hashed and geneticicall demultiplexed

value: Blood


title: Treg (CD127-CD25+) - Donor 233 - Day 8

description:
Library name: lib59142_AAAFM27HV
Donor ID: 233; Study day: D8


title: PBMCs, control 2, set 1, scRNAseq

description:
Library name: scCo2_sample_set_1
10x Genomics, hashed and geneticicall demultiplexed

value: control


title: Masseter muscle, Sham/Control, rep 2

description: Library name: ShamMasseter-2


title: Cytoplasmic RNA-Seq, CRISPR Control, Replicate 3

description: Library name: CytoplasmicRNA_CRISPR_CTRL_Rep3

value: Human embryonic kidney 293 T cells


title: Cytoplasmic RNA-Seq, CRISPR Control, Replicate 2

description: Library name: CytoplasmicRNA_CRISPR_CTRL_Rep2


title: Treg (CD127-CD25+) - Donor 233 - Day 1

description:
Library name: lib59140_AAAFM27HV
Donor ID: 233; Study day: D1


title: PBMCs, control 1, set 2, scRNAseq

description:
Library name: scCo1_sample_set_2
10x Genomics, hashed and geneticicall demultiplexed


title: Masseter muscle, Sham/Control, rep 1

description: Library name: ShamMasseter-1


title: Treg (CD127-CD25+) - Donor 119 - Day 29

description:
Library name: lib59138_AAAFM27HV
Donor ID: 119; Study day: D29


title: Cytoplasmic RNA-Seq, CRISPR Control, Replicate 1

description: Library name: CytoplasmicRNA_CRISPR_CTRL_Rep1


title: PBMCs, control 1, set 1, scRNAseq

description:
Library name: scCo1_sample_set_1
10x Genomics, hashed and geneticicall demultiplexed


title: Obese-9

city: Nanjing

first: Jiashuo

last: Li

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

description: Library name: Obese-9

data_processing:
The raw bisulfite sequencing reads were trimmed to remove adaptors and low-quality bases by using trim_galore (v0.6.10) (parameters: -q 20 --phred33 --length 30 --stringency 3 --paired --clip_R1 10 --clip_R2 10). Next, Bismark (v0.24.2) was used to map clean reads to GRCm38/GRCh38 with single-end alignment mode (parameters: --non_directional --bowtie2 --bam --single_end). PCR duplicates were removed using deduplicate_bismark with default parameters. And only the high-quality reads (MAPQ > 10) were retained for further analysis. DNA methylation level estimation. The DNA methylation level of each cytosine site in the reference genome sequence was calculated as the percentage of reads supporting C (methylated). Unless otherwise specified, the DNA methylation level of CpG sites in a given sample or region refers to the average methylation level across that sample or region. Owing to the low number of input cells, CpG sites with read depths ≥1 were included for methylation analysis. For DNA methylation pattern profiling, the whole genome was divided into consecutive 20-kb windows, and the average methylation level within each bin was calculated. Principal component analysis (PCA) of methylation data was performed using methylKit (v1.30.0). Differentially methylated regions (DMRs) calling. Differential methylation analysis was performed using metilene (v0.2.6) with default parameters, and differentially methylated regions (DMRs) were annotated using ChIPseeker (v1.36.0).
Assembly: GRCh38,GRCm39
Supplementary files format and content: BigWig including CG sites methylation values for each sample
Library strategy: EM-seq

source_name: oocyte

extract_protocol:
Collect 15 mouse oocytes/one human oocyte for cell lysis.
Whole-genome bisulfite sequencing (WGBS) was performed on mouse oocytes using 15 oocytes as input, whereas Enzymatic Methyl-seq (EM-seq) was applied to human oocytes starting from a single cell due to its high efficiency with minimal input. Library preparation and sequencing: Mouse metaphase II (MII) oocytes (n = 15 per replicate, two biological replicates per group) were used for WGBS. Briefly, cells were lysed in buffer (10 mM Tris-HCl, pH 7.4, 2% SDS), and genomic DNA was extracted and digested with proteinase K. Purified DNA was subjected to bisulfite conversion using the EZ DNA Methylation-Gold Kit (ZYMO, D5008), followed by purification with Agencourt AMPure XP beads (Beckman). The converted DNA was end-repaired and dA-tailed, then ligated to Illumina sequencing adapters. Libraries were amplified for 13 cycles using Illumina universal PCR primer and indexed primers. For human samples, individual oocytes were lysed and genomic DNA were fragmented to ~ 300 bp using a DNA fragmentation device (Shanghai Jingxin, DNA Fragmentation Model 26A). Libraries were constructed using the NEBNext® Enzymatic Methyl-seq kit (NEB, E7120 L) and the Unique Dual Index Primer pairs (NEB, E7140L). Unmethylated lambda phage DNA and CpG-methylated plasmid pUC19 DNA were included as negative and positive controls. For single-oocyte libraries, amplification was performed for 18 cycles. Libraries were purified using the DNA Clean & Concentrator-5 kit (ZYMO, D4013). Finally, equimolar amounts of libraries were pooled and subjected to paired-end sequencing on an Illumina NovaSeq 6000 platform.

value: oocyte


title: Treg (CD127-CD25+) - Donor 119 - Day 15

description:
Library name: lib59136_AAAFM27HV
Donor ID: 119; Study day: D15


title: LAM 20, Visium

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Sample 20

data_processing:
Visium and Visium HD spatial transcriptomics data were generated using the 10x Genomics Visium V4 Slide – FFPE v2 platform and processed using Space Ranger v2.1.1 and v3.1.2 with the 10x built in human reference (GRCh38-2020- A) and the Visium Human Transcriptome Probe Set v2.0.
10X Genomics Xenium was used to perform Xenium in situ expression analysis.
Assembly: GRCh38
Supplementary files format and content: LAM18.tar.gz: 10x Visium HD Space Ranger output folder
Supplementary files format and content: LAM19.tar.gz: 10x Xenium Space Ranger output folder
Supplementary files format and content: LAM20.tar.gz: 10x Visium Space Ranger output folder
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Tissue was collected by The National Disease Research Interchange (NDRI) from 4 donors with lymphangioleiomyomatosis lungs. Samples ≤ 0.5 cm2 were cut from the locations outlined above, which were fixed for 24 h in 10% neutral buffered formalin and processed into wax (FFPE). H&E staining was used to determine the morphology of tissue blocks before proceeding with ST.
10x Visium and Xenium ST experiments were performed by the Advanced Genomics Core at the University of Michigan according to the manufacturer’s protocol. 10x Visium HD experiment were prepared from FFPE blocks for 10x Visium HD analysis by the Integrated Pathology Research Facility (CCHMC) according to the Visium HD FFPE Tissue Preparation Handbook (10x Genomics, CG000684, Rev A).

value: Lung


title: Digastric muscle, KPC rep 2

description: Library name: KPCdigastric-3

source_name: Digastric muscle

value: Digastric muscle


title: Digastric muscle, KPC, rep 3

description: Library name: KPCdigastric-4


title: Obese-8

description: Library name: Obese-8


title: LAM 19, Xenium

description: Library name: Sample 19


title: Treg (CD127-CD25+) - Donor 119 - Day 8

description:
Library name: lib59134_AAAFM27HV
Donor ID: 119; Study day: D8


title: Digastric muscle, KPC, rep 1

description: Library name: KPCdigastric-2


title: Treg (CD127-CD25+) - Donor 119 - Day 1

description:
Library name: lib59132_AAAFM27HV
Donor ID: 119; Study day: D1


title: LAM 18, Visium HD

description: Library name: Sample 18


title: Digastric muscle, Sham/Control, rep 3

description: Library name: Shamdigastric-4


title: Obese-7

description: Library name: Obese-7


title: Obese-6

description: Library name: Obese-6


title: Digastric muscle, Sham/Control, rep 2

description: Library name: Shamdigastric3


title: SR30-OE-L3,0dpi

first: Dong

last: Yan

state: Jiangsu

address: NO.1 Weigang

institute: Nanjing Agricultural University

data_processing:
These RNA-seq libraries were sequenced using Illumina Nova in paired-end mode with a read length of 150 bp (Berry Genomics, Beijing, China). The RNA-seq reads with low quality were removed using trimmomatic (v0.39). Then, the remaining reads were aligned to the ITAG4.0 tomato genome (https://solgenomics.net/) using Hisat2 v2.2.1 with default parameters. Reads mapping to multiple locations were discarded and only uniquely mapped reads were retained for subsequent analysis.
Assembly: Tomato genome version SL4.0 and Annotation ITAG4.0
Supplementary files format and content: excel file includes TPM values for each samples

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: tomato (Solanum lycopersicum) plants were grown in the greenhouse for 8-12 weeks under 14 h at 24°C and 10 h at 22°C.

extract_protocol:
Eight-week-old tomato leaves were used for RNA sequencing. Total RNA was extracted using the Invitrogen PureLink RNA Mini Kit (catalog no.12183018A, USA)
RNA libraries for RNA seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Berry Genomics, Beijing, China)

value: leaf

value: overexpression of SR30


title: Treg (CD127-CD25+) - Donor 023 - Day 29

description:
Library name: lib59130_AAAFM27HV
Donor ID: 023; Study day: D29

value: 1mg mutein


title: Obese-5

description: Library name: Obese-5


title: Digastric muscle, Sham/Control, rep 1

description: Library name: Shamdigastric-2


title: Treg (CD127-CD25+) - Donor 023 - Day 15

description:
Library name: lib59128_AAAFM27HV
Donor ID: 023; Study day: D15


title: SR30-OE-L2,0dpi


title: Obese-4

description: Library name: Obese-4


title: SR30-OE-L1,0dpi


title: Treg (CD127-CD25+) - Donor 023 - Day 1

description:
Library name: lib59124_AAAFM27HV
Donor ID: 023; Study day: D1


title: H3K27me3 coverage on THC -treated spheroids at 3 days-post treatment, replicate 2

city: Madrid

first: Leonardo

last: Beccari

address: Nicolas Cabrera 1

institute: Centro de Biología Molecular Severo Ochoa (CSIC)

description: Library name: THC_3d_H3K27me3_rep2

data_processing:
CUT&Tag sequencing reads were processed using a custom workflow in Galaxy (https://usegalaxy.eu). Adapter trimming and quality filtering were performed with Cutadapt (Galaxy version 5.2), and reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.5.4) with the --very-sensitive option. Alignments were sorted using Picard SortSam (version 3.1.1.0), and further filtering was performed with SAMtools (version 1.8) to retain properly mapped reads. For H3K27me3 samples, genome-wide coverage tracks were generated using deepTools bamCoverage with CPM normalization (10 bp bins) and converted to BigWig files for visualization. Peaks were called per replicate using MACS3 in broad peak mode (--broad, q-value < 0.05), using paired-end mode (BAMPE) and retaining duplicates (--keep-dup all). For H3K4me3 samples, coverage tracks were generated using bedtools genomecov with scaling factors calculated using the ChIPseqSpikeInFree framework (Hongjian J et al 2020) and converted to BigWig format. Peaks were called using MACS3 in narrow peak mode (q-value < 0.05, --keep-dup all). Reproducible peaks were identified using the IDR framework.
Assembly: mm10
Supplementary files format and content: coverage files are providaded as bigwig, MACS3 callpeak results as provided as narrowPêak (H3K4me3) or .broadPeak (H3K27me3( files
Library strategy: CUT&Tag

source_name: tumoroids

extract_protocol:
CUT&Tag was performed using the Active Motif protocol (Active Motif #53160), following the manufacturer’s specifications. Briefly, spheroids per sample were dissociated using Accutase, and 500,000 cells per sample were immobilized on concanavalin A-coated magnetic beads. Cells were sequentially incubated with 2 µg of primary antibodies against H3K4me3 (Sigma 17-614) or H3K27me3 (Abcam ab6002) overnight at 4°C with gentle rocking, followed by incubation with a-rabbit (H3K4me3) or a-mouse (H3K27me3) secondary antibodies  to enhance signal detection. Bead-bound cells were then incubated with a protein A–Tn5 transposase fusion protein preloaded with sequencing adapters. After targeted tagmentation (60 min at 37°C), DNA fragments were released by proteinase K digestion and purified using column-based cleanup for library preparation.
Libraries were prepared using KAPA polymerase (Roche, KK2612) and single-index barcoded primers  as described in Buenrostro J et al 2025 . Library amplification cycles were determined by qPCR (CT + 2 for each sample). Libraries were purified using SPRI beads (CleanNA, # CNGS-0050), and quality was assessed by fluorometric quantification and fragment size analysis. Sequencing was performed on an Illumina NovaSeq X platform using 150 bp paired-end reads.

value: tumoroids

value: PyMT derived organoids

value: breast cancer

value: WT

value: THC

tag: antibody


title: WT-L3,0dpi


title: H3K27me3 coverage on THC -treated spheroids at 3 days-post treatment, replicate 1

description: Library name: THC_3d_H3K27me3_rep1


title: Obese-3

description: Library name: Obese-3


title: Obese-2

description: Library name: Obese-2


title: Treg (CD127-CD25+) - Donor 012 - Day 29

description:
Library name: lib59123_AAAFM27HV
Donor ID: 012; Study day: D29


title: WT-L2,0 dpi


title: H3K27me3 coverage on SR2 -treated spheroids at 3 days-post treatment, replicate 2

description: Library name: SR2_3d_H3K27me3_rep2


title: Treg (CD127-CD25+) - Donor 012 - Day 15

description:
Library name: lib59121_AAAFM27HV
Donor ID: 012; Study day: D15


title: WT-L1,0 dpi


title: H3K27me3 coverage on SR2 -treated spheroids at 3 days-post treatment, replicate 1

description: Library name: SR2_3d_H3K27me3_rep1


title: Lean-13

description: Library name: Lean-13


title: Treg (CD127-CD25+) - Donor 012 - Day 8

description:
Library name: lib59119_AAAFM27HV
Donor ID: 012; Study day: D8