title: Killifish - eye - adult

city: Baton Rouge

first: Patricia

last: Schneider

state: Louisiana

address: LSU 131 Life Sciences Building

department: Biological Sciences

institute: Louisiana State University

description:
Library name: A1_Fh_eye
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequences were aligned to the Fundulus heteroclitus reference genome to generate gene expression counts using Space Ranger’s default settings (version 3.1.3).
Gene Expression level of RefSeq coding genes were quantified using Spacer Ranger's default settings - version 3.1.3.
The data analysis was made in the Loupe browser software - version 8.1.2.
Assembly: GCF_011125445.2
Supplementary files format and content: A1_Fh_eye.tif: tissue image
Supplementary files format and content: A1_Fh_eye_barcodes.tsv.gz: list of spatial barcodes.
Supplementary files format and content: A1_Aa_head_features.tsv.gz: list of genes.
Supplementary files format and content: A1_Fh_eye_features.tsv.gz: gene expression count data in Matrix Market Exchange Format.
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

organism: Fundulus heteroclitus

source_name: eye

extract_protocol:
Fresh frozen head and eye were OCT embedded, and 10µm frozen sections were cut with cryostat (Leica).
Spatial transcriptome sequencing libraries were prepared with the 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to the manufacturer's instructions.

value: eye

tag: batch


title: HP_PB_2

status: Public on Apr 08 2026

type: SRA

city: Guangzhou

first: shuyi

last: kuang

state: Guangdong

address: ShaTai southern load

country: China

institute: Southern Medical Univercity

description: Library name: Sample5

library_source: transcriptomic

data_processing:
The R package DESeq2 (1.44.0) was used for diferential analysis of the count data and R package clusterProfiler (4.12.6) was used to perform different genes enrichment analysis.
Assembly: GRCh38.p13
Supplementary files format and content: csv files include FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Cells were extracted for RNA by Trizol reagent and subsequently sequenced using the DNBSEQ platform
RNA libraries were prepared for sequencing using standard DNBSEQ platform protocols

tag: tissue

value: Peripheral blood

tag: cell type

value: peripheral PMN-MDSCs

tag: treatment

value: Healthy pregancy group


title: HP_PB_3

description: Library name: Sample6


title: HP_PB_1

description: Library name: Sample4

value: Peripheral PMN-MDSCs


title: Donor 2, untreated, sample collection Day1

city: San Francisco

first: Pascal

last: Devant

address: 1650 Owens Street

country: USA

institute: Gladstone Institutes

description: Library name: Count_9NTD-D1-d2.counts

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Assembly: GRCh38
Supplementary files format and content: processed data format:csv, processed data content: raw counts

growth_protocol: Primary human monocytes were isolated from fresh peripheral blood Leukopaks (STEMCELL Technologies) with institutional review board-approved informed written consent. Leukopaks were washed twice with EasySep buffer (sterile PBS pH 7.4, 2% FCS, 1 mM EDTA pH 8.0) before isolation of monocytes using the Human Monocyte Enrichment kit without CD16 depletion (STEMCELL Technologies; 100-1525) according to manufacturer’s instruction. Briefly, PBMCs were diluted to 100x106 cells/ml in EasySep buffer, mixed with 100 µl of antibody cocktail per 100 million cells and incubated at RT for 5-10 mins. Magnetic beads were added and following 3 min of incubation at RT, tubes containing cells were placed in a magnetic field for 10 mins. Unbound cells (pure monocyte fraction) were removed, washed one more time with EasySep buffer. Cells were then counted and resuspended in Immunocult SF Macrophage media (STEMCELL technology; 10961) at a density of 1x106 cells/ml and seeded in TC-treated 6-well plate ( 3x106 cells per well). For macrophage differentiation, media was supplemented with 20 ng/ml of M-CSF (Peprotech; 300-25). Media was replenished every 24-72 h by adding at least one half volume of fresh media and cytokines. All tissue culture was performed under sterile conditions and cells were cultured in temperature-controlled incubators at 37°C and 5% CO2.

extract_protocol:
RNA extraction, library preparation, and next-generation sequencing was performed by GENEWIZ Inc. Total RNA was extracted from frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200(Agilent technologies, Palo Alto, CA, USA). ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 ° C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’e ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Freshly isolated monocytes subjected to Cas9EDV-mediated gene editing (50 ul of concentrated EDV per well) or nucleofection with Cas9-RNP targeting the AAVS1 locus, following by culture in M-CSF-containing media. Cells were harvested on Day 1 or Day 7 post isolation. Cells were detached using Accutase, washed twice with DPBS, pelleted by centrifugation.

value: monocyte-derived macrophages

tag: donor

value: Donor 2

value: untreated, sample collection Day1


title: AMA2_EVT

description: Library name: Sample2

source_name: Placenta

value: Placenta

value: Extravillus trophoblasts

value: Advanced pregancy group


title: Donor 1, Cas9EDV Day 0, sample collection Day7

description: Library name: Count_6EDV-AAV-D7-d1.counts

value: Donor 1

value: Cas9EDV Day 0, sample collection Day7


title: AMA1_EVT

description: Library name: Sample1


title: Donor 1, untreated, sample collection Day7

description: Library name: Count_4NTD-D7-d1.counts

value: untreated, sample collection Day7


title: Donor 1, Cas9EDV Day 4, sample collection Day7

description: Library name: Count_7EDV-AAV-D47-d1.counts

value: Cas9EDV Day 4, sample collection Day7


title: AMA3_EVT

description: Library name: Sample3


title: Donor 1, Cas9EDV Day 0, sample collection Day1

description: Library name: Count_3EDV-AAV-D1-d1.counts

value: Cas9EDV Day 0, sample collection Day1


title: brain organoids

city: Melbourne

first: Maria Rosaria

last: Nucera

state: VICTORIA

address: 50, Flemington road

department: Paediatrics

country: Australia

institute: University of Melbourne

description:
Library name: brain_organoids
organoid model
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the SAW pipeline
Images in format .czi were converted into .ipr and .tar format using ImageStudio software.
Assembly: mm10 for mouse tissue and GRCh38 for human organoids
Supplementary files format and content: file.gef : output of SAW pipeline
Supplementary files format and content: anndata.h5ad : output of SAW pipeline
Supplementary files format and content: image.ipr : image converted using ImageStudio, input of SAW pipeline
Supplementary files format and content: image.tar : image converted using ImageStudio, input of SAW pipeline
Library strategy: Spatial Transcriptomics

source_name: brain organoid

extract_protocol:
Samples were prepared and processed using the STOmics Transcriptomics kit (STOmics Cat# 111KT114) in accordance with manufacturer’s instructions (BGI Stereo-seq Transcriptomics set for Chip-on-a-slide user manual version B) with slight variations.
The cDNA purification and library preparation of each sample was constructed using the STOmics library preparation kit (STOmics Cat# 111KL114) in accordance with manufacturer’s instructions (BGI STOmics Stereo-seq Transcriptomics set for Chip-on-a-slide user manual version B).

treatment_protocol: the tissues are fresh frozen

value: brain organoid

tag: time

value: 1 month


title: CTRL-IgG-1.fq.gz

city: Hengyang

first: Hongye

last: Yan

state: Hunan

address: 69 Chuanshan Road

institute: The First Affiliated Hospital of University of South China

data_processing:
RNA-seq reads were filtered to get clean reads using FastQ (v0.20.0).
The clean reads were aligned to the human genome GRCh38.p13 using STAR (v2.7.9a)
Read counts were quantified by RSEM (1.3.3)
Differential gene expression analysis was done using DEseq2 package (v1.38.3)
P value was adjusted using the Benjamini–Hochberg method
Assembly: hg38
Supplementary files format and content: csv, gene expression for all samples

source_name: Forebrain Organoid

growth_protocol: Human forebrain organoids were cultured in media reported in published protocols

extract_protocol:
Qiagen miRNeasy Mini Kit was used to extract total RNA
Sequencing libraries were prepared for RNA-seq using standard DNBseq protocols

treatment_protocol: Anti-NMDAR1 IgG antibody (final concentration is 10 μg/mL) was added to the organoid culture media. 24 hours post anti-NMDAR1 IgG antibody exposure, total RNA was extracted.

value: Forebrain Organoid

tag: cell line

value: Human induced pluripotent stem cells


title: Donor 1, nucleofection Day 0, sample collection Day1

description: Library name: Count_2Nuc-AAV-D1-d1.counts

value: Peripheral blood


title: Donor 1, nucleofection Day 0, sample collection Day7

description: Library name: Count_5Nuc-AAV-D7-d1.counts


title: CTRL-IgG-3.fq.gz


title: Donor 2, Cas9-RNP nucleofection, stimulated with LPS + Interferon gamma

description: Library name: D2Nucstim

treatment_protocol: Freshly isolated monocytes subjected to Cas9EDV-mediated gene editing (50 ul of concentrated EDV per well) or nucleofection with Cas9-RNP targeting the AAVS1 locus, following by culture in M-CSF-containing media for 6 days . Cells were then stimulared with 100 ng/ml of LPS and 25 ng/ml of interferon gamma, or left untreated, and cells were collected for RNAseq 24h later. Cells detached using Accutase, washed twice with DPBS, pelleted by centrifugation.


title: Donor 2, Cas9-RNP nucleofection, no additional stimulation

description: Library name: D2Nuc


title: CTRL-IgG-4.fq.gz


title: CTRL-IgG-2.fq.gz


title: AntiNMDAR1-IgG-2.fq.gz


title: Donor 1, untreated, sample collection Day1

description: Library name: Count_1NTD-D1-d1.counts


title: Donor 2, no Cas9, stimulated with LPS + Interferon gamma

description: Library name: D2NTDstim


title: Donor 2, no Cas9, no additional stimulation

description: Library name: D2NTD

value: no Cas9, no additional stimulation


title: delta polA, 30C, 3

city: Amherst

first: Peter

last: Chien

state: MA

address: 240 Thatcher Rd, Life Science Laboratories Room N325

department: Biochemistry and Molecular Biology

institute: University of Massachusetts Amherst

description: Library name: dpolA_30C_3

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (Illumina)
Read quality control and filtering performed using fastq
Reads aligned to reference genome with bwa-mem
Read quantification performed with rsubread
Principal component analysis (PCA) and differential expression analysis are performed using DESeq2
Full pipeline can be found at https://github.com/baldikacti/chienlab-rnaseq/tree/v0.1.0
Assembly: NC_011916
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Caulobacter vibrioides NA1000

source_name: delta polA

growth_protocol: Cells were grown overnight in PYE medium (2g/L peptone, 1g/L yeast extract, 1 mM MgSO4, and 0.5 mM CaCl2) with aeration at 30°C. In the morning, cells were back-diluted to 0.1 OD600, and subsequently plated in a 96-well plate in triplicates (200µl/well) where each replicate was plated to 9 different wells each to get enough final volume

extract_protocol:
Cells were pelletted at 8000g for 2 minutes, and pellets snap-frozen in liquid nitrogen. Frozen pellets sent to SeqCenter, LLC for RNA isolation, library preparation, and sequencing.
Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded TotalRNA Prep Ligation with Ribo-Zero Plus kit with custom primers for depleting Caulobacter rRNA. Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads.

treatment_protocol: Cells were grown in the plate reader until the mid-log phase at 30°C (Control) or 39°C (Heat stress).

value: delta polA

value: Bacteria

tag: genotype

value: PolA knockout


title: AntiNMDAR1-IgG-1.fq.gz


title: delta polA, 30C, 1

description: Library name: dpolA_30C_1


title: AntiNMDAR1-IgG-3.fq.gz


title: Donor 2, EDV treated, no additional stimulation

description: Library name: D2EDV

value: monocyte-derived macrophages

value: Donor 2

value: EDV treated, no additional stimulation


title: Donor 2, EDV treated, stimulated with LPS + Interferon gamma

description: Library name: D2EDVstim


title: delta clpB, 30C, 1

description: Library name: dclpb_30C_1

source_name: delta clpB

value: delta clpB

value: ClpB knockout


title: Donor 1, Cas9-RNP nucleofection, no additional stimulation

description: Library name: D1Nuc

value: Donor 1


title: Donor 1, Cas9-RNP nucleofection, stimulated with LPS + Interferon gamma

description: Library name: D1Nucstim


title: Donor 1, EDV treated, stimulated with LPS + Interferon gamma

description: Library name: D1EDVstim


title: delta clpB, 30C, 2

description: Library name: dclpb_30C_2


title: delta clpB, 39C, 3

description: Library name: dclpb_39c_3

value: heat-stress (39C)


title: WT, 30C, 2

description: Library name: wt_30C_2

source_name: WT

value: WT


title: Donor 1, no Cas9, no additional stimulation

description: Library name: D1NTD


title: WT, 30C, 3

description: Library name: wt_30C_3


title: Donor 1, no Cas9, stimulated with LPS + Interferon gamma

description: Library name: D1NTDstim


title: WT, 30C, 1

description: Library name: wt_30C_1


title: delta clpB, 39C, 1

description: Library name: dclpb_39c_1


title: WT, 39C, 1

description: Library name: wt_39C_1


title: WT, 39C, 3

description: Library name: wt_39C_3


title: G62_siH1_A

city: Boston

first: Marco

last: Mineo

address: 60 Fenwood Rd, BTM 8016N

institute: Brigham and Women's Hospital

description: Library name: Sample 3

data_processing:
Trimmomatic program was used to remove adapter sequences and bases with base quality lower than three from the ends. Also, using sliding window method, bases of reads that did not qualify for window size 4, and mean quality 15 were trimmed. Afterward, reads with lengths shorter than 36bp were dropped to produce trimmed data.
Trimmed reads were aligned to the human genome from the UCSC hg38 using HISAT2.
Assembly: UCSC hg38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: Brain

growth_protocol: G62 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested from cells using TRIzol (Thermo Fisher Scientific Cat#15596026). 1 ug total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA kit following manufacturer's protocol.

value: Brain

value: glioblastoma


title: G62_siNC_A

description: Library name: Sample 1


title: Hi-C - Anableps ventral retina, biol rep2

description: Library name: Aa_retina_V3

library_source: genomic

data_processing:
Hi-C analysis was performed using HOMER v5.1 (Heinz et al., 2010) with an Arima-specific in silico–digested Anableps genome. Adapters were removed using the homerTools trim script (5' trimming), and reads were aligned independently to the Anableps genome using Bowtie2 v2.4.4. After alignment, we generated a paired-end tag directory for each replicate using makeTagDirectory with the parameters -tbp 1 and -removePEbg. Loops and TADs were identified using findTADsAndLoops.pl with a 3 kb resolution and an FDR threshold of 0.05. All loops and TADs were merged per condition using merge2Dbed, after which we quantified loops and TADs across all replicates and conditions. Differentially enriched loops and TADs were identified using getDiffExpression.pl with simpleNorm and edgeR parameters. Finally, we generated the hic file using tagDir2hicFile.pl with Juicer auto parameters. The loops were visualized in the Integrative Genomics viewer v2.14.1 software and the TADs in the genome browser website.
Assembly: GCA_014839685.1
Supplementary files format and content: tab-delimited text file includingAa_differentially_enriched_loops

molecule: genomic DNA

organism: Anableps anableps

source_name: Ventral retina

extract_protocol:
Hi-C was performed on freshly bisected dorsal and ventral retina tissue of Anableps anableps (two dorsal and two ventral biological replicas) using the Arima-HiC+ Kit (Arima Genomics, Cat. No. A510008, Carlsbad, CA, USA), following the manufacturer’s protocol. Briefly, tissues were crosslinked with formaldehyde and digested with a restriction enzyme cocktail provided in the kit. Proximity ligation was performed to join spatially proximal DNA fragments, followed by purification and fragmentation of the ligated DNA. Biotinylated fragments were enriched and processed for library preparation using the Arima Library Prep Module (Arima Genomics, Cat. No. A303011, Carlsbad, CA, USA).
Libraries were sequenced on the NovaSeq 6000 (Novogene Corporation Inc., Sacramento, CA, USA) using 150bp paired-end reads, yielding approximately 600 million read pairs per sample.

value: Ventral retina


title: delta clpB, 39C, 2

description: Library name: dclpb_39c_2


title: G62_siH1_B

description: Library name: Sample 4


title: WT, 39C, 2

description: Library name: wt_39C_2


title: Hi-C - Anableps ventral retina, biol rep1

description: Library name: Aa_retina_V2


title: Donor 1, EDV treated, no additional stimulation

description: Library name: D1EDV


title: G62_siNC_B

description: Library name: Sample 2


title: Hi-C - Anableps dorsal retina, biol rep2

description: Library name: Aa_retina_D3

source_name: Dorsal retina

value: Dorsal retina


title: U87H1KO_3

description: Library name: Sample 6

growth_protocol: U87 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested from cells using TRIzol (Thermo Fisher Scientific Cat#15596026). 1 ug total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA LT Sample Prep kit following manufacturer's protocol.


title: Hi-C - Anableps dorsal retina, biol rep1

description: Library name: Aa_retina_D2


title: U87H1KO_2

description: Library name: Sample 5


title: CIPHER-seq_PBMC_stimulated

city: Miami

first: Avni

last: Bhalgat

state: FL

address: 1580 NW 10th Ave, Room 746

institute: University of Miami

description: Library name: CIPHER-seq_stimulated

library_source: other

data_processing:
CellRanger Multi v9.0.1 pipeline; probe-based multiplexing, using the following probe IDs: BC001-Ustim_CalTag, BC002-Stim-CalTag, BC003-Unstim_ProteinTech, BC004-Stim_ProteinTech
Downstream data processing performed using Seurat R-based package.
Assembly: GRCh38 2024-A
Supplementary files format and content: Counts per sample stored in CellRanger H5 files
Library strategy: CITE-seq

molecule: other

source_name: PBMC

extract_protocol: Samples prepared using the 10X Cell Surface and Intracellular Protien Labeling for GEM-x Flex Gene Expression (Protocol: CG000781) labeling assay

treatment_protocol: PBMCs were resuspended at 1×10⁶ cells/mL in complete RPMI-1640 (10% heat-inactivated fetal bovine serum, 1% penicillin/streptomycin, 2 mM L-glutamine). For stimulated conditions, cells were treated with phorbol 12-myristate 13-acetate (PMA, 50 ng/mL) and ionomycin (1 µg/mL) for 4 h at 37 °C, 5% CO₂. Brefeldin A (5 µg/mL) was added during the final 3 h to block protein secretion and retain cytokines intracellularly. Unstimulated controls were incubated in parallel in the same medium without PMA/ionomycin but with brefeldin A added for the final 3 h to match handling. At the end of incubation, cells were washed twice in cold PBS + 0.04% BSA and counted before fixation.

value: PBMC

value: PMA/Ionomycin stimulation followed by Brefaldin A inhibition


title: CIPHER-seq_PBMC_unstimulated

description: Library name: CIPHER-seq_unstimulated

value: Brefaldin A inhibition


title: Proteintech_PBMC_stimulated

description: Library name: Proteintech_stimulated


title: delta clpB, 30C, 3

description: Library name: dclpb_30C_3

value: Bacteria


title: Proteintech_PBMC_unstimulated

description: Library name: Proteintech_unstimulated


title: U87H1KO_1

description: Library name: Sample 4


title: Anableps ventral retina, biolrep3

description: Library name: VRAA3

data_processing:
High quality sequencing reads were mapped to Anableps anableps Genome Asselmby GCA_014839685.1 using STAR V2.7.10b. Read count extraction was performed using featureCounts v2.0.6. Read count normalization and DGE analysis were performed using DEseq2.
Assembly: GCA_014839685.1
Supplementary files format and content: tab-delimited text file including raw counts for each sample

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen_ThermoFIsher).
mRNA enriched librraies were preparaed and sequenced at Novogene (https://www.novogene.com/us-en). Briefly, for each sample, 1 µg RNA was used to generated RNA sequencing librarires using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB,USA), follwing the manufacturee's recommendation.


title: Anableps ventral retina, biolrep1

description: Library name: VRAA1


title: Anableps dorsal retina, biolrep3

description: Library name: DRAA4


title: Anableps ventral retina, biolrep2

description: Library name: VRAA2


title: U87ctrl_3

description: Library name: Sample 3


title: U87ctrl_2

description: Library name: Sample 2


title: Anableps dorsal retina, biolrep1

description: Library name: DRAA2


title: MG10_Post_RNAseq

city: Shanghai

first: Sushan

last: Luo

state: Shanghai

address: 12 Wulumuqi Rd (M), Jing'An, Shanghai

institute: Huashan Hospital

description:
Library name: MG10_post
Peripheral blood sample collected from a patient with myasthenia gravis after 4 weekly infusions of efgartigimod (10 mg/kg). This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.

data_processing:
Raw RNA-seq data (FASTQ) underwent quality assessment using FastQC (v0.11.9). Reads were aligned to the human reference genome (GRCh38, Ensembl annotation) using HISAT2 (v2.2.1), and gene-level counts were generated with featureCounts (Subread v2.0.3). Differential expression analysis was performed in R (v4.5.2) using DESeq2 (v1.40.2) under a paired design. P-values were adjusted using the Benjamini–Hochberg method, with FDR < 0.05 considered statistically significant.PCA was conducted on variance-stabilized expression values to evaluate global transcriptomic structure. Pre-ranked gene set enrichment analysis (GSEA) was performed using clusterProfiler (v4.8.0) based on log2 fold change (log2FC) ranking against Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathway databases, with multiple-testing correction applied.
Assembly: GRCh38, Ensembl annotation
Supplementary files format and content: gene_counts.txt, sample_metadata.tsv

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from the samples using Trizol reagent (Invitrogen, USA).
RNA integrity was assessed prior to sequencing, and only samples meeting predefined quality criteria were included (OE Biotech Co., Ltd., Shanghai, China).

value: peripheral blood


title: Anableps dorsal retina, biolrep2

description: Library name: DRAA3


title: Anableps ventral retina, biol rep4

description: Library name: Aa_V5

data_processing:
Adapter sequences were removed from the reads using NGmerge (version 0.3) (Gaspar, 2018). The trimmed reads were aligned to theTetraodon reference genome (tetNig2) using Bowtie2 (version 2.2.5). Alignments were output as a BAM file, which was indexed using Samtools (version 1.18) (Li et al., 2009). The fragment size distribution graph was created using the ATACseqQC package (version 1.24.0) (Ou et al., 2018) in RStudio (version 4.3.1). The trimmed reads were name-sorted using Samtools (version 1.18) (Li et al., 2009) and further processed with Genrich (version 0.6.1) to call narrow peaks using the parameters -j -y -r -v -m -e -a -f, to remove duplicate reads, multimapped reads, and reads mapped to mitochondrial chromosomes. Downstream analysis of the ATAC-seq data was performed using DiffBind.
Assembly: GCA_014839685.1
Supplementary files format and content: tab-delimited text file including differential chromatin accessibility peaks identified from ATAC-seq data

extract_protocol:
ATAC-seq libraries were prepared following the Active Motif ATAC seq protocol, which is based on a combination of the Buenrostro et al., 2013 and the Corces et al., 2017. Dorsal and ventral retinas were dissected and subsequently used for nuclei extraction.
All ATAC-seq libraries were performed from 50,000 cells and were amplified within 10 total PCR cycles. After PCR amplification, the libraries were purified with magnetic beads following the manufacturer’s protocol. Libraries were sequenced by Novogene Corporation Inc. The sequencing was performed using Nova-seq Paired-end 150.


title: MG08_Post_RNAseq

description:
Library name: MG08_post
Peripheral blood sample collected from a patient with myasthenia gravis after 4 weekly infusions of efgartigimod (10 mg/kg). This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: MG09_Pre_RNAseq

description:
Library name: MG09_pre
Peripheral blood sample collected from a patient with myasthenia gravis before efgartigimod treatment. This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.

value: before efgartigimod treatment


title: MG09_Post_RNAseq

description:
Library name: MG09_post
Peripheral blood sample collected from a patient with myasthenia gravis after 4 weekly infusions of efgartigimod (10 mg/kg). This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: Anableps ventral retina, biol rep2

description: Library name: Aa_V2


title: U87ctrl_1

description: Library name: Sample 1


title: Anableps ventral retina, biol rep1

description: Library name: Aa_V1


title: Anableps dorsal retina, biol rep4

description: Library name: Aa_D5


title: WT_Kidney_3 (scRNA-seq)

city: Chicago

first: Navdeep

middle: S.

last: Chandel

state: IL

address: 303 E. Superior Street

department: Department of Medicine & Biochemistry and Molecular Genetics

institute: Northwestern University

description: Library name: NC-25-7

library_source: transcriptomic single cell

data_processing:
Data were processed using the Cell Ranger 8.0.1 pipeline (10x Genomics) with intronic reads disabled using the nf-core/scrnaseq 4.0.0 pipeline. Reads were aligned to the 10x Genomics 2020-A reference genome (GRCm38, GENCODE vM23/Ensembl98). Putative heterotypic doublets were then flagged for removal using scrublet 3.0.0 with manual thresholding of doublet scores, before removal using custom scripts in R 4.4.0. Cell calling was performed using the cellranger pipeline. Thresholding of Initial filtering and preprocessing was performed using Seurat 5.3.0, followed by integration using SCVI within SCVItools 1.3.3, and re-imported into Seurat for all clustering, dimensional reduction, and all downstream high-level analysis using inbuilt Seurat functions and custom scripts in R. Normalization was performed using SCTransform 0.4.1, and clustering was performed using the Leiden algorithm. Default parameters were used unless otherwise specified.
Assembly: GRCm38, GENCODE vM23/Ensembl98
Supplementary files format and content: Raw counts from cellranger and associated metadata in .mtx and .csv formats, respectively

organism: Mus musculus

source_name: Kidney

extract_protocol:
After mice (P11) were euthanized, they were perfused via the left ventricle with ice-cold Hanks’ balanced salt solution (HBSS) to remove blood, and the kidneys were harvested and minced with a sterile razor blade into small pieces (< 1 mm diameter). The tissue was digested in HBSS containing Liberase TM (0.30 mg/mL) (Roche, catalog no. 291963), Hyaluronidase (10 μg/mL) (Sigma, catalog no. H4272), and DNase1 (20 μg/mL) for 40 minutes at 37 °C on a shaker (300 rpm, Eppendorf Thermomixer 5355). The suspension was centrifuged at 300 × g for 5 min at 4 °C, and the supernatant was discarded. The cells were washed twice with 2 mL cold PBS (ThermoFisher, catalog no. 14190250) and pelleted. The pellets were resuspended in 5 mL of 0.25% Trypsin with DNase1 (20 μg/mL) and incubated for 15 min at 37 °C on a shaker for further digestion. Trypsin was inactivated with 2 mL 10% FBS in PBS after digestion, followed by centrifugation at 300 × g for 5 min at 4 °C. Cell pellets were washed once again with 10% FBS, followed by resuspending the cell pellets in ice-cold PBS supplemented with 0.01% BSA. The cell suspension was filtered sequentially through 70 μm and 40 μm strainers, pelleted, and resuspended in 0.01% BSA. Cell number and viability were analyzed using the Nexcelom Cellometer Auto2000 with the acridine orange (AO) and propidium iodide (PI) fluorescent staining method. All resuspensions used wide-bore tips.
Libraries were then generated using the 10X Genomics Universal 3’ V4 kit, according to the manufacturer’s instructions, using a 10X Genomics Chromium X Controller.

value: Kidney

value: Wild-Type


title: L2HGDH_OE_Kidney_4 (scRNA-seq)

description: Library name: NC-25-6

value: L2HGDH-Overexpressing (homozygous)


title: MG08_Pre_RNAseq

description:
Library name: MG08_pre
Peripheral blood sample collected from a patient with myasthenia gravis before efgartigimod treatment. This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: MG10_Pre_RNAseq

description:
Library name: MG10_pre
Peripheral blood sample collected from a patient with myasthenia gravis before efgartigimod treatment. This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: L2HGDH_OE_Kidney_3 (scRNA-seq)

description: Library name: NC-25-4


title: WT_Kidney_1 (scRNA-seq)

description: Library name: NC-25-3


title: WT_Kidney_2 (scRNA-seq)

description: Library name: NC-25-5


title: MG07_Pre_RNAseq

description:
Library name: MG07_pre
Peripheral blood sample collected from a patient with myasthenia gravis before efgartigimod treatment. This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: MG07_Post_RNAseq

description:
Library name: MG07_post
Peripheral blood sample collected from a patient with myasthenia gravis after 4 weekly infusions of efgartigimod (10 mg/kg). This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: Anableps dorsal retina, biol rep3

description: Library name: Aa_D4


title: CRISPRi-cenIR rep1

city: Iowa City

first: Craig

last: Ellermeier

state: IA

address: 431 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

description: Library name: CenIR-1

data_processing:
Fastq files were trimmed and filtered using a combination of Trimmomatic and FastQC
Alignment, normalization, and differential expression were analyzed with LaserGene v18.1.0.426
Annotation was imported from NCBI with additional information obtained from proGenomes v2.1.
All subsequent analysis was performed in Excel.
Assembly: AM180355
Supplementary files format and content: Comma separated values (csv) file contains linear rlog reads, log2 fold change and adjusted P-value

organism: Clostridioides difficile

source_name: Bacterial

growth_protocol: All cultures were grown in tryptone-yeast extract broth with 1% NaCl at 37C under anaerobic conditions

extract_protocol:
Cultures were fixed by mixing with an equal volume of cells with ice-cold 1:1 ethanol:acetone. Cells were lysed with a FastPrep-24 homogenizer and RNA was extracted with the Qiagen RNeasy kit. All samples had a RIN of 9.4 or higher (Agilent Bioanalyzer).
Illumina Stranded RNA library preparation paired with RiboZero Plus  was prepared per manufacturer's specifications.

value: Bacterial

value: sgRNA-cenI

value: 1% xylose, 13h


title: CRISPRi-cenIR rep2

description: Library name: CenIR-2


title: Negative control rep1

description: Library name: Con-1

value: sgRNA-neg


title: Anableps dorsal retina, biol rep2

description: Library name: Aa_D3

value: WT


title: Anableps dorsal retina, biol rep1

description: Library name: Aa_D1


title: L2HGDH_OE_Kidney_2 (scRNA-seq)

description: Library name: NC-25-2


title: Negative control rep2

description: Library name: Con-2


title: MG06_Post_RNAseq

description:
Library name: MG06_post
Peripheral blood sample collected from a patient with myasthenia gravis after 4 weekly infusions of efgartigimod (10 mg/kg). This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: ATRA-3

city: hohhot

first: yadong

last: gao

address: hohhot

institute: Inner Mongolia University

description:
Library name: sample6
Capra hircus secondary hair follicle dermal papilla cells treated with all-trans retinoic acid (ATRA) to investigate transcriptional changes induced by ATRA treatment.

data_processing:
Raw sequencing reads were filtered to remove adapters, poly-N sequences, and low-quality reads to obtain clean reads;Clean reads were aligned to the Capra hircus reference genome using HISAT2.;Gene expression levels were quantified as FPKM values using featureCounts.;Differential expression analysis between groups was performed using DESeq2.
Assembly: Capra hircus reference genome from NCBI.
Supplementary files format and content: Expression values were calculated as raw read counts.

organism: Capra hircus

source_name: skin

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent according to the manufacturer’s instructions. RNA quality and integrity were assessed using agarose gel electrophoresis and an Agilent 2100 Bioanalyzer.
RNA-seq libraries were constructed using a poly(A) mRNA enrichment method. mRNA was fragmented and reverse transcribed into cDNA, followed by end repair, adaptor ligation, and PCR amplification to generate sequencing libraries.

value: skin

value: primary culture

value: wild type

value: all-trans retinoic acid (ATRA) treatment


title: MG06_Pre_RNAseq

description:
Library name: MG06_pre
Peripheral blood sample collected from a patient with myasthenia gravis before efgartigimod treatment. This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: MG05_Post_RNAseq

description:
Library name: MG05_post
Peripheral blood sample collected from a patient with myasthenia gravis after 4 weekly infusions of efgartigimod (10 mg/kg). This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: Donor 6, untreated

description: Library name: ntd_d6

data_processing:
RNA-seq reads were aligned by Plasmidsaurus to a human reference genome using STAR aligner (v2.7.11) and BAM files were provided for downstream analysis. Gene-level read counts were quantified using featureCounts (Rsubread) . Differential expression analysis was performed using DESeq2.
Assembly: GRCh38, GENCODE48
Supplementary files format and content: processed data format:csv, processed data content: raw counts

extract_protocol:
Cells were resuspended in DNA/RNA Shield (Zymo Research) and sent for bulk RNAseq by Plasmidsaurus.
plasmidsaurus library preparation - conversion of mRNA into complementary DNA via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.

treatment_protocol: On Day 4 post isoolation, 50 ul of concentrated eVLPs were mixed with 2 ml of pre-warmed SF macrophage media supplemented with M-CSF. Media was aspirated from cells and eVLP-containing media was added followed by spinfection at 1250 g and 32°C for 1 h. Cells were incubated overnight before swapping media and returning to routine culture. Assesment of gene expression was performed 6 days post eVLP treatment.

value: Peripheral blood

value: Monocyte-derived macrophages

value: Donor 6

value: untreated


title: Donor 6, treated with A20/TNFAIP3-targeting Cas9-eVLP

description: Library name: a20_d6


title: ATRA-2

description:
Library name: sample5
Capra hircus secondary hair follicle dermal papilla cells treated with all-trans retinoic acid (ATRA) to investigate transcriptional changes induced by ATRA treatment.


title: Donor 5, treated with A20/TNFAIP3-targeting Cas9-eVLP

description: Library name: a20_d5

value: Donor 5


title: MG05_Pre_RNAseq

description:
Library name: MG05_pre
Peripheral blood sample collected from a patient with myasthenia gravis before efgartigimod treatment. This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.

value: peripheral blood

value: before efgartigimod treatment


title: Donor 5, treated with AAVS1-targeting Cas9-eVLP

description: Library name: aavs_d5

value: treated with AAVS1-targeting Cas9-eVLP


title: NC-3

description:
Library name: sample3
Capra hircus secondary hair follicle dermal papilla cells cultured under standard conditions without ATRA treatment and used as the control group for RNA sequencing analysis.

value: Control


title: Donor 6, treated with AAVS1-targeting Cas9-eVLP

description: Library name: aavs_d6


title: MG04_Pre_RNAseq

description:
Library name: MG04_pre
Peripheral blood sample collected from a patient with myasthenia gravis before efgartigimod treatment. This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: MG04_Post_RNAseq

description:
Library name: MG04_post
Peripheral blood sample collected from a patient with myasthenia gravis after 4 weekly infusions of efgartigimod (10 mg/kg). This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: Donor 4, treated with AAVS1-targeting Cas9-eVLP

description: Library name: aavs_d4

value: Donor 4


title: ATRA-1

description:
Library name: sample4
Capra hircus secondary hair follicle dermal papilla cells treated with all-trans retinoic acid (ATRA) to investigate transcriptional changes induced by ATRA treatment.


title: Donor 4, treated with A20/TNFAIP3-targeting Cas9-eVLP

description: Library name: a20_d4


title: Donor 5, untreated

description: Library name: ntd_d5


title: MG03_Post_RNAseq

description:
Library name: MG03_post
Peripheral blood sample collected from a patient with myasthenia gravis after 4 weekly infusions of efgartigimod (10 mg/kg). This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: NC-2

description:
Library name: sample2
Capra hircus secondary hair follicle dermal papilla cells cultured under standard conditions without ATRA treatment and used as the control group for RNA sequencing analysis.


title: Donor 4, untreated

description: Library name: ntd_d4


title: Donor 3, treated with AAVS1-targeting Cas9-eVLP

description: Library name: aavs_d3

value: Donor 3


title: MG03_Pre_RNAseq

description:
Library name: MG03_pre
Peripheral blood sample collected from a patient with myasthenia gravis before efgartigimod treatment. This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: NC-1

description:
Library name: sample1
Capra hircus secondary hair follicle dermal papilla cells cultured under standard conditions without ATRA treatment and used as the control group for RNA sequencing analysis.


title: Donor 3, treated with A20/TNFAIP3-targeting Cas9-eVLP

description: Library name: a20_d3


title: Donor 3, untreated

description: Library name: ntd_d3


title: S1 Ctx, WS 03

city: Cleveland

first: Daehoon

last: Lee

state: OH

address: 10900 Euclid Ave.

institute: Case Western Reserve University

data_processing:
https://biosys.bgi.com/
volcano plots of gene expression profiles generated by VolcaNoseR (https://goedhart.shinyapps.io/VolcaNoseR)
Gene Ontology (GO) enrichment analysis performed by ShinyGO database (http://bioinformatics.sdstate.edu/go)
Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed by Gene set enrichment analysis (GSEA) expression profiles in the online public database by WebGestalt (http://www.webgestalt.org)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary somatosensory cortex

extract_protocol:
Total RNAs were extracted from the S1 cortex without or with WS (90 min after the last stimulation) using the RNA 6000 Nano Kit (Agilent, Santa Clara, CA) and according to the manufactural protocol. RNA Integrity Number (RIN) was accessed for every sample, and the samples were considered qualified with RIN > 2. These Bulk RNA-seq samples were then subjected to RNA-seq analyses.
RNA libraries for RNA-seq were prepared using the DNBseq™ platform Prep Kit following the manufacturer's protocols

value: primary somatosensory cortex

value: neuron, astrocyte, endotheial cells, oligodendrocyte, pericyte, microglia

tag: strain

tag: age

value: Postnatal 21days

value: whisker stimulation


title: S1 Ctx, WS 02

value: WT


title: Donor 2, treated with A20/TNFAIP3-targeting Cas9-eVLP

description: Library name: a20_d2

value: Donor 2


title: S1 Ctx, WS 01


title: Donor 2, treated with AAVS1-targeting Cas9-eVLP

description: Library name: aavs_d2

value: Peripheral blood


title: MG02_Pre_RNAseq

description:
Library name: MG02_pre
Peripheral blood sample collected from a patient with myasthenia gravis before efgartigimod treatment. This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: Donor 1, treated with A20/TNFAIP3-targeting Cas9-eVLP

description: Library name: a20_d1

value: Monocyte-derived macrophages

value: Donor 1


title: Donor 2, untreated

description: Library name: ntd_d2

value: untreated


title: Donor4 human monocyte-derived macrophages treated with CD14-targeting eVLP sgRNA1

description: Library name: D4_CD14g1

data_processing:
RNA-seq reads were aligned by Plasmidsaurus to a human reference genome using STAR aligner (v2.7.11) and BAM files were provided for downstream analysis. Gene-level read counts were quantified using featureCounts (Rsubread) with GENCODE v44 annotations. Differential expression analysis was performed using DESeq2. Genes with fewer than 10 total counts across samples were excluded. Log2 fold changes were shrunk using the apeglm method, and adjusted p-values were calculated using the Benjamini–Hochberg false discovery rate procedure. For visualization of selected markers (CD14, CD45, and CD81), shrunk Log2 fold changes were extracted for each condition relative to non-targeting control samples
Assembly: GRCh38, GENCODE48
Supplementary files format and content: processed data format:csv, processed data content: raw counts

growth_protocol: Primary human monocytes were isolated from fresh peripheral blood Leukopaks (STEMCELL Technologies) with institutional review board-approved informed written consent. Leukopaks were washed twice with EasySep buffer (sterile PBS pH 7.4, 2% FCS, 1 mM EDTA pH 8.0) before isolation of monocytes using the Human Monocyte Enrichment kit without CD16 depletion (STEMCELL Technologies; 100-1525) according to manufacturer’s instruction. Briefly, PBMCs were diluted to 100x106 cells/ml in EasySep buffer, mixed with 100 µl of antibody cocktail per 100 million cells and incubated at RT for 5-10 mins. Magnetic beads were added and following 3 min of incubation at RT, tubes containing cells were placed in a magnetic field for 10 mins. Unbound cells (pure monocyte fraction) were removed, washed one more time with EasySep buffer. Cells were then counted and resuspended in Immunocult SF Macrophage media (STEMCELL technology; 10961) supplemented with differentiation cytokines (exact cytokines used are outlined below) at a density of 1x106 cells/ml and seeded in TC-treated 24-well plate (for most experiments; 0.5x106 cells per well) or 12-well plates (for pooled screens; 2.5x106 cells per well). For macrophage differentiation, media was supplemented with 20 ng/ml of M-CSF (Peprotech; 300-25). Media was replenished every 24-72 h by adding at least one half volume of fresh media and cytokines. All tissue culture was performed under sterile conditions and cells were cultured in temperature-controlled incubators at 37°C and 5% CO2.

treatment_protocol: 25 ul of concentrated eVLPs were mixed with 500 µl of pre-warmed SF macrophage media supplemented with M-CSF. Media was aspirated from cells and eVLP-containing media was added followed by spinfection at 1250 g and 32°C for 1 h. Cells were incubated overnight before swapping media and returning to routine culture. Assesment of gene expression was performed after 8 days for CRISPRoff-eVLPs


title: S1 Ctx, NW control 02


title: Donor4 human monocyte-derived macrophages treated with CD45-targeting eVLP sgRNA1

description: Library name: D4_CD45g1


title: Donor4 human monocyte-derived macrophages treated with CD45-targeting eVLP sgRNA2

description: Library name: D4_CD45g2


title: Donor 1, treated with AAVS1-targeting Cas9-eVLP

description: Library name: aavs_d1


title: MG02_Post_RNAseq

description:
Library name: MG02_post
Peripheral blood sample collected from a patient with myasthenia gravis after 4 weekly infusions of efgartigimod (10 mg/kg). This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: Donor 1, untreated

description: Library name: ntd_d1


title: MG01_Post_RNAseq

description:
Library name: MG01_post
Peripheral blood sample collected from a patient with myasthenia gravis after 4 weekly infusions of efgartigimod (10 mg/kg). This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.


title: L2HGDH_OE_Kidney_1 (scRNA-seq)

description: Library name: NC-25-1

value: Kidney

value: L2HGDH-Overexpressing (homozygous)


title: Donor4 human monocyte-derived macrophages treated with CD14-targeting eVLP sgRNA2

description: Library name: D4_CD14g2


title: MG01_Pre_RNAseq

description:
Library name: MG01_pre
Peripheral blood sample collected from a patient with myasthenia gravis before efgartigimod treatment. This sample is part of a paired longitudinal bulk RNA-seq study. Raw sequencing data have been deposited in NGDC under accession subHRA027638.

value: peripheral blood

value: before efgartigimod treatment


title: MOLM14_EVI1_OE3

city: Dalian

first: Jinsong

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description: Library name: Sample 12

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 27, GRCh38).
The Gene abundances are given as Reads Per Kilobase per Million mapped reads (RPKM) with “cuffnorm” command using the Cufflinks package.
Assembly: hg38
Supplementary files format and content: Excel file include RPKM values for each Sample …

extract_protocol:
Total RNA of small intestine cells from mouse were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

value: EVI1 overexpression


title: S1 Ctx, NW control 01


title: S1 Ctx, NW control 03


title: Donor4 human monocyte-derived macrophages treated with non-target eVLP

description: Library name: D4_NT


title: Donor4 human monocyte-derived macrophages treated with CD81-targeting eVLP

description: Library name: D4_CD81


title: MOLM14_EVI1_OE1

description: Library name: Sample 10


title: Donor4 untreated human monocyte-derived macrophages

description: Library name: D4_untreated


title: MOLM14_EVI1_OE2

description: Library name: Sample 11


title: Donor3 human monocyte-derived macrophages treated with CD45-targeting eVLP sgRNA1

description: Library name: D3_CD45g1


title: RORgt CUT&Tag of Th17 cells: Wild-type

city: shenzhen

first: huang

last: peiming

address: xinhu

institute: Sun Yat-sen University

description: Library name: WT_RoRrt

data_processing:
Quality Control: Raw reads were quality-filtered to remove low-quality data and adapters.
Assembly: Mus musculus
Supplementary files format and content: BigWig files (.bw) providing normalized coverage depth across the genome for visualization;A matrix file containing raw counts and normalized values for all genes.
Library strategy: CUT&Tag

source_name: Spleen

extract_protocol:
Total RNA was extracted from in vitro differentiated Th17 cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. (RNA-seq);In vitro differentiated Th17 cells were crosslinked to fix protein-DNA interactions. Cell lysis, chromatin fragmentation, immunoprecipitation, and subsequent ChIP-DNA extraction and purification were performed using a ChIP assay kit from Cell Signaling Technology (CST) strictly following the manufacturer's instructions. (Chip-seq); Intact nuclei were isolated from fresh in vitro differentiated Th17 cells. Simultaneous chromatin fragmentation and adapter ligation (tagmentation), followed by DNA extraction and purification, were carried out using an ATAC-seq kit from Vazyme according to the manufacturer's protocol. (ATAC-seq); Fresh in vitro differentiated Th17 cells were harvested and bound to Concanavalin A (ConA) magnetic beads. Permeabilization, antibody incubation, targeted DNA cleavage by transposome, and final DNA extraction were performed using a CUT&Tag kit from Vazyme according to the manufacturer's instructions. (CUT&Tag-seq).
RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit; For ATAC-seq and CUT&Tag-seq: Sequencing libraries were generated simultaneously during the tagmentation step and subsequently amplified by PCR using the respective Vazyme kits, following the manufacturer's instructions; For ChIP-seq: Sequencing libraries were constructed using Illumina TruSeq  according to the manufacturer's protocols.

value: Spleen

value: Th17 cells

value: Th17-polarizing conditions


title: Donor3 human monocyte-derived macrophages treated with CD45-targeting eVLP sgRNA2

description: Library name: D3_CD45g2

source_name: Peripheral blood


title: ATAC-seq of Th17 cells: Wild-type

description: Library name: WT-2A

data_processing:
Quality Control: Raw reads were quality-filtered to remove low-quality data and adapters.
Assembly: Mus musculus
Supplementary files format and content: BigWig files (.bw) providing normalized coverage depth across the genome for visualization;A matrix file containing raw counts and normalized values for all genes.


title: Donor3 human monocyte-derived macrophages treated with CD14-targeting eVLP sgRNA2

description: Library name: D3_CD14g2


title: Donor3 human monocyte-derived macrophages treated with CD14-targeting eVLP sgRNA1

description: Library name: D3_CD14g1


title: Donor3 human monocyte-derived macrophages treated with CD81-targeting eVLP

description: Library name: D3_CD81


title: RORgt CUT&Tag of Th17 cells: HO

description: Library name: HO_RoRrt


title: H3K4me3 ChIP-seq of Th17 cells: KO

description: Library name: KO_H3K4me3


title: Donor3 untreated human monocyte-derived macrophages

description: Library name: D3_untreated


title: ATAC-seq of Th17 cells: KO

description: Library name: KO-2A


title: Chaf1b ChIP-seq of Th17 cells: Wild-type

description: Library name: WT_chaf1b_p


title: MOLM14_control_rep3

description: Library name: Sample 9

value: wild type


title: K562_EVI1_OE3

description: Library name: Sample 6


title: MOLM14_control_rep2

description: Library name: Sample 8


title: MOLM14_control_rep1

description: Library name: Sample 7


title: Donor2 human monocyte-derived macrophages treated with CD14-targeting eVLP sgRNA2

description: Library name: D2_CD14g2


title: Donor2 human monocyte-derived macrophages treated with CD45-targeting eVLP sgRNA2

description: Library name: D2_CD45g2


title: Donor3 human monocyte-derived macrophages treated with non-target eVLP

description: Library name: D3_NT


title: H3K4me3 ChIP-seq of Th17 cells: Wild-type

description: Library name: WT_H3K4me3


title: Donor2 human monocyte-derived macrophages treated with CD14-targeting eVLP sgRNA1

description: Library name: D2_CD14g1


title: Donor2 human monocyte-derived macrophages treated with CD81-targeting eVLP

description: Library name: D2_CD81


title: Donor2 untreated human monocyte-derived macrophages

description: Library name: D2_untreated


title: Donor1 human monocyte-derived macrophages treated with CD14-targeting eVLP sgRNA2

description: Library name: D1_CD14g2


title: RNA-seq of Th17 cells: KO, biological replicate 2

description: Library name: KO2


title: Donor1 human monocyte-derived macrophages treated with CD45-targeting eVLP sgRNA1

description: Library name: D1_CD45g1


title: RNA-seq of Th17 cells: Wild-type, biological replicate 3

description: Library name: WT3


title: K562_EVI1_OE2

description: Library name: Sample 5


title: Donor1 human monocyte-derived macrophages treated with CD14-targeting eVLP sgRNA1

description: Library name: D1_CD14g1


title: Donor2 human monocyte-derived macrophages treated with CD45-targeting eVLP sgRNA1

description: Library name: D2_CD45g1


title: Donor1 human monocyte-derived macrophages treated with CD45-targeting eVLP sgRNA2

description: Library name: D1_CD45g2


title: RNA-seq of Th17 cells: KO, biological replicate 3

description: Library name: KO3


title: Donor2 human monocyte-derived macrophages treated with non-target eVLP

description: Library name: D2_NT


title: K562_Control_rep2

description: Library name: Sample 2


title: K562_Control_rep3

description: Library name: Sample 3


title: RNA-seq of Th17 cells: KO, biological replicate 1

description: Library name: KO1


title: K562_Control_rep1

description: Library name: Sample 1


title: K562_EVI1_OE1

description: Library name: Sample 4


title: Donor1 untreated human monocyte-derived macrophages

description: Library name: D1_untreated


title: Donor1 human monocyte-derived macrophages treated with CD81-targeting eVLP

description: Library name: D1_CD81


title: Donor1 human monocyte-derived macrophages treated with non-target eVLP

description: Library name: D1_NT


title: RNA-seq of Th17 cells: Wild-type, biological replicate 1

description: Library name: WT1


title: DC-12

city: Tianjin

first: Chen

last: Wenlong

state: 天津市

address: No. 23 Pingjiang Road, Hexi District

institute: 天津医科大学第二医院

description: Library name: simple12

data_processing:
Raw sequencing reads were subjected to quality control to remove low-quality reads and adapter sequences.
Clean reads were aligned to the human reference genome using standard alignment pipelines
Gene expression levels were quantified and normalized using appropriate bioinformatics tools.
Differential expression analysis was performed using DESeq2 with thresholds of Q < 0.05 and |log₂FC| > 1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include normalized gene expression values (e.g., counts/TPM) for each sample.

source_name: breast

growth_protocol: MDA-MB-231-ADR breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin in a humidified atmosphere with 5% CO₂ at 37°C.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA quality and quantity were assessed prior to library preparation.
RNA libraries were prepared using a standard mRNA-seq library preparation kit following the manufacturer’s protocol. Briefly, mRNA was enriched, fragmented, reverse transcribed into cDNA, followed by end repair, adapter ligation, and PCR amplification.

treatment_protocol: Cells were divided into four groups: control (Ctrl), TAZ, DOX, and TAZ+DOX. For TAZ and TAZ+DOX groups, cells were pretreated with 10 μM tazemetostat (TAZ) for 72 h prior to DOX exposure. DOX was then added and cells were incubated for an additional 48 h.

value: breast

value: breast cancer cells


title: RNA-seq of Th17 cells: Wild-type, biological replicate 2

description: Library name: WT2


title: HeLa_siEPHB2_si2_rep3

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

description: Library name: sample9

data_processing:
All libraries were sequenced on the Illumina NovaSeq 6000 instrument, and 150 bp paired-end reads were generated.
reads were mapped to the human GRCh38 reference genome using HISAT2 (version 2.0.4) with two mismatches
After genome mapping, StringTie (version 1.3.0) was run with a reference annotation to generate FPKM values for known gene models.
Differentially expressed genes were identified using edgeR. The significance threshold was set as false discovery rate (FDR) ≤ 0.05 and fold-change ≥ 2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include reads count for each Sample

source_name: an immortalized human cell line derived from the cervical cancer tumor

extract_protocol:
Total RNA was isolated from sample using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following the manufacturer’s instructions. Briefly, poly(A)-containing mRNA was purified using poly-T oligo-attached magnetic beads. Purified libraries were quantified using Qubit® 2.0 Fluorometer and validated using an Agilent 2100 Bioanalyzer to confirm insert size and molar concentration. Cluster generation was performed by cBot with the library diluted to 10 pM.

value: hela

value: siEPHB2 2

value: siEPHB2 (siRNA 2)


title: DC-11

description: Library name: simple11

value: WT


title: HeLa_siEPHB2_si2_rep2

description: Library name: sample8

value: an immortalized human cell line derived from the cervical cancer tumor


title: DC-10

description: Library name: simple10


title: DC-8

description: Library name: simple8


title: DC-6

description: Library name: simple6


title: mRNA E18.5 lung Lpar4 -197/Y pup 1

city: Cambridge

first: Daniel

last: Lin

address: 455 Main Street

institute: Whitehead Institute

description: Library name: Lpar4_Lung_L69_5_KO_M

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Gene counts were analyzed with DESeq2 v1.38.3 without use of the lfcShrink function.
Assembly: GRCm39v114
Supplementary files format and content: raw gene counts for all samples

source_name: Lung

extract_protocol:
Embryos were collected at E18.5 and dissected tissue was flash frozen in liquid nitrogen. Frozen tissue was transferred to a 50 mL conical tube, 1–2 mL of TRI Reagent was added, and the tissue was homogenized using a TissueRuptor and disposable probes (Qiagen). Following resuspension and/or homogenization, samples were phase separated with 100 μL 1-bromo-3-chloropropane (Sigma).
cDNA was prepared from total RNA using a poly(dT)VN primer. Following second strand synthesis, tagmentation, library indexing, and amplification, libraries were sequenced on the Illumina NovaSeq X Plus platform.

value: Lung

value: Lpar4 hemizygous trigger site mutant


title: DC-7

description: Library name: simple7


title: mRNA E18.5 lung Lpar4 -197/Y pup 2

description: Library name: Lpar4_Lung_L69_6_KO_M


title: HeLa_siEPHB2_si1_rep3

description: Library name: sample6

value: siEPHB2 1

value: siEPHB2 (siRNA 1)


title: mRNA E18.5 lung Lpar4 WT pup 1

description: Library name: Lpar4_Lung_L69_8_WT_M

value: Lpar4 WT


title: mRNA E18.5 lung Lpar4 WT pup 2

description: Library name: Lpar4_Lung_L69_10_WT_M


title: DC-4

description: Library name: simple4


title: HeLa_siEPHB2_si2_rep1

description: Library name: sample7


title: HeLa_siEPHB2_si1_rep1

description: Library name: sample4


title: mRNA E18.5 lung Lpar4 -197/Y pup 4

description: Library name: Lpar4_Lung_L50_2_KO_M


title: HeLa_siEPHB2_si1_rep2

description: Library name: sample5


title: DC-5

description: Library name: simple5


title: DC-3

description: Library name: simple3


title: HeLa_siCtrl_rep3

description: Library name: sample3

value: control


title: DC-9

description: Library name: simple9


title: LS174T cells, GucyCAR CM, rep3

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

description: Library name: LS174T-5F9-CM-D7981-4-21-3

data_processing:
Sequence reads were trimed for adapter sequence/low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR.
Gene- and isoform-level quantification from mapped reads using RSEM.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes gene counts for each sample.
Supplementary files format and content: Tab-delimited text file includes isoform counts for each sample.

growth_protocol: cell were grown in 10% FBS in MEM medium and passaged when reached 70% confluence.

extract_protocol:
Zymo research direct-zol RNA kit
PolyA selection was performed using Illumina NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: cell were treated with conditioned media from cancer cells co-cultured with control or GucyCART cells for 48hrs

value: Colorectal

value: GucyCAR CM


title: DC-2

description: Library name: simple2


title: LS174T cells, GucyCAR CM, rep2

description: Library name: LS174T-5F9-CM-D7981-4-21-2


title: mRNA E18.5 lung Lpar4 WT pup 4

description: Library name: Lpar4_Lung_L50_6_WT_M


title: DC-1

description: Library name: simple1


title: LS174T cells, GucyCAR CM, rep1

description: Library name: LS174T-5F9-CM-D7981-4-21-1


title: LS174T cells, control, rep2

description: Library name: LS174T-CD19-CM-D7981-4-21-2

value: Control


title: mRNA E18.5 lung Lpar4 -197/Y pup 3

description: Library name: Lpar4_Lung_L45_2_KO_M


title: mRNA E18.5 lung Lpar4 WT pup 3

description: Library name: Lpar4_Lung_L50_5_WT_M


title: WHIM30CR_109241, Basal-like triple-negative breast cancer patient-derived xenograft

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

description:
Library name: WHIM30CR_109241
RNA-Seq

data_processing:
Quality was assessed using FastQC v0.11.9
CutAdapt v4.1 removed adapters and low-quality base pairs
Alignment was done using STAR v2.7.11a using the command line options: “--outSAMtype BAM Unsorted --outSAMorder Paired --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outFilterMultimapNmax 1
Read counts and log2 TPM values were obtained with Salmon v0.8.2 “quant” algorithm using the “IU” library type
Assembly: GRCh38 (human) and GRcm38 (mouse)
Supplementary files format and content: the processed data file is a .tsv file containing gene counts for all submitted samples

source_name: PDX mammary tumor

growth_protocol: PDX tumors were grown orthotopically in NSG mice for 8 weeks.

extract_protocol:
Qiagen RNeasy kit
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

treatment_protocol: Carboplatin Resistant:  Mice with PDXs were grown and treated three times spaced out every 4 days with 40mg/kg of carboplatin. Once the tumors regrew they were passaged to new recipient mice and then treated with another set of carboplatin. This proceeded until the tumors no longer responded to carboplatin; at this point they were termed carboplatin-resistant.

value: PDX mammary tumor

value: Carboplatin Resistant

tag: tumor type

value: TNBC

value: Carboplatin


title: mRNA E18.5 heart Lpar4 -197/Y pup 4

description: Library name: Lpar4_Heart_L50_2_KO_M

source_name: Heart

value: Heart


title: LS174T cells, control, rep3

description: Library name: LS174T-CD19-CM-D7981-4-21-3


title: P13 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 02)

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Library name: P13_C3_D1_02

data_processing:
FASTQ files were processed using 10x Genomics Cell Ranger v7.1 to generate gene-by-cell UMI count matrices. Reads were aligned to the human reference genome GRCh38/hg38 build and GRCh38-2020-A and UMI counts were summarized per gene per cell barcode Cell Ranger output matrices (HDF5 format) were generated for each library; per-library summary metrics were exported.
Assembly: GRCh38-2020-A
Supplementary files format and content: Processed data are provided on the GEO Series record as (i) p11044_h5.tar.gz, a tar.gz archive containing per-library 10x Genomics gene expression UMI count matrices in HDF5 (.h5) format and per-library metrics summary CSV files, and (ii) p11044x.rda, an R/Seurat object containing the processed scRNA-seq dataset used in downstream analyses.
Supplementary files format and content: Each GSM corresponds to one 10x library; the matching matrix file is located within the tarball at p11044_h5/h5/<library_name>.h5 (library names match the “library name” field in the SAMPLES table). Raw FASTQ files are available via controlled access in dbGaP (phs004414.v1.p1).

source_name: tumor biopsy

extract_protocol:
Tumor biopsy tissue was dissociated using Collagenase IV (Sigma, Cat No. C5138-500MG) to generate a viable single-cell suspension. The suspension was quenched with ice-cold HBSS, and cells were washed 2x in PBS with BSA. Cells were processed according to standard 10x Genomics sample preparation procedures prior to droplet-based single-cell library preparation.
Single-cell 5’ gene expression libraries were prepared using the 10x Genomics Chromium platform according to the manufacturer’s protocol. 10x kit/chemistry v2.1 targeting 10,000 cells.  Libraries were sequenced on an Illumina platform using paired-end sequencing with index read (R1/R2/I1).

treatment_protocol: Participants received palbociclib in combination with the PD-1 inhibitor INCMGA00012 per the NCT04438824 phase II clinical trial protocol. Tumor biopsies were obtained at protocol-specified on-treatment timepoints (as indicated per sample).

value: tumor biopsy

value: palbociclib + INCMGA00012


title: WHIM30_109164, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: WHIM30_109164
RNA-Seq

value: PDX

value: Untreated


title: LS174T cells, control, rep1

description: Library name: LS174T-CD19-CM-D7981-4-21-1


title: WHIM30CR_109239, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: WHIM30CR_109239
RNA-Seq


title: P13 tumor biopsy scRNA-seq, C1D14 - palbociclib alone (rep 01)

description: Library name: P13_C1_D14_01

value: palbociclib


title: P13 tumor biopsy scRNA-seq, C1D14 - palbociclib alone (rep 02)

description: Library name: P13_C1_D14_02


title: WHIM30_108961, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: WHIM30_108961
RNA-Seq


title: P13 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 01)

description: Library name: P13_C3_D1_01


title: mRNA E18.5 heart Lpar4 -197/Y pup 3

description: Library name: Lpar4_Heart_L45_2_KO_M

value: Lpar4 hemizygous trigger site mutant


title: HeLa_siCtrl_rep1

description: Library name: sample1

value: an immortalized human cell line derived from the cervical cancer tumor

value: hela

value: WT


title: BCM-7482CR_110324, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-7482CR_110324
RNA-Seq


title: HeLa_siCtrl_rep2

description: Library name: sample2

value: control


title: BCM-7482CR_110326, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-7482CR_110326
RNA-Seq


title: BCM-7482CR_110323, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-7482CR_110323
RNA-Seq


title: BCM-7482_110317, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-7482_110317
RNA-Seq


title: mRNA E18.5 heart Lpar4 WT pup 3

description: Library name: Lpar4_Heart_L50_5_WT_M

value: Lpar4 WT


title: P12 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 02)

description: Library name: P12_C3_D1_02


title: mRNA E18.5 heart Lpar4 -197/Y pup 2

description: Library name: Lpar4_Heart_L69_6_KO_M


title: mRNA E18.5 heart Lpar4 WT pup 4

description: Library name: Lpar4_Heart_L50_6_WT_M


title: P12 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 01)

description: Library name: P12_C3_D1_01


title: BCM-7482_110316, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-7482_110316
RNA-Seq


title: mRNA E18.5 heart Lpar4 WT pup 2

description: Library name: Lpar4_Heart_L69_10_WT_M


title: BCM-3887CR_110347, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-3887CR_110347
RNA-Seq


title: BCM-3887_110319, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-3887_110319
RNA-Seq


title: mRNA E18.5 heart Lpar4 -197/Y pup 1

description: Library name: Lpar4_Heart_L69_5_KO_M


title: BCM-3887_110320, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-3887_110320
RNA-Seq


title: BCM-7482_110315, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-7482_110315
RNA-Seq


title: BCM-3887_110318, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-3887_110318
RNA-Seq


title: P12 tumor biopsy scRNA-seq, C1D14 - palbociclib alone (rep 02)

description: Library name: P12_C1_D14_02


title: P11 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 02)

description: Library name: P11_C3_D1_02


title: P12 tumor biopsy scRNA-seq, C1D14 - palbociclib alone (rep 01)

description: Library name: P12_C1_D14_01


title: BCM-3887CR_110175, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-3887CR_110175
RNA-Seq


title: BCM-2147CR_109121, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-2147CR_109121
RNA-Seq


title: BCM-2147CR_109136, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-2147CR_109136
RNA-Seq


title: mRNA E18.5 heart Lpar4 WT pup 1

description: Library name: Lpar4_Heart_L69_8_WT_M


title: BCM-2147CR_109178, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-2147CR_109178
RNA-Seq


title: mRNA E18.5 lung Atp6v1g1 hom pup 4

description: Library name: Atp6v1g1_Lung_L66_2_KO_F

value: Lung

value: Atp6v1g1 homozygous trigger site mutant


title: BCM-2147_109076, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-2147_109076
RNA-Seq

value: PDX mammary tumor


title: P11 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 01)

description: Library name: P11_C3_D1_01


title: BCM-3887CR_110350, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-3887CR_110350
RNA-Seq

value: Carboplatin Resistant

value: TNBC


title: mRNA E18.5 lung Atp6v1g1 hom pup 3

description: Library name: Atp6v1g1_Lung_L55_6_KO_M


title: P08 tumor biopsy scRNA-seq, C1D14 - palbociclib alone (rep 02)

description: Library name: P08_C1_D14_02


title: P08 tumor biopsy scRNA-seq, C1D14 - palbociclib alone (rep 01)

description: Library name: P08_C1_D14_01


title: BCM-2147_109073, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-2147_109073
RNA-Seq


title: BCM-2147_109176, Basal-like triple-negative breast cancer patient-derived xenograft

description:
Library name: BCM-2147_109176
RNA-Seq


title: mRNA E18.5 lung Atp6v1g1 WT pup 4

description: Library name: Atp6v1g1_Lung_L66_3_WT_F

value: Atp6v1g1 WT


title: mRNA E18.5 lung Atp6v1g1 WT pup 3

description: Library name: Atp6v1g1_Lung_L55_4_WT_M


title: RIP GSC387 shCONT input

city: Chapel Hill

first: DONGHAI

last: WANG

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

description: Library name: Sample6

data_processing:
Sequencing reads were aligned to the human reference genome (UCSC hg38) using Bowtie v1.1.2. For visualization, read coverage was normalized to counts per million (CPM) using deepTools and displayed in IGV. Correlation with RR-ChIP sequencing data was calculated using RR-ChIP peaks in R.
Assembly: hg38
Supplementary files format and content: Bigwig

molecule: nuclear RNA

source_name: GBM tissue

extract_protocol:
Ten million GSC cells were harvested and washed with ice-cold PBS. Cells were lysed on ice, and nuclear pellets were resuspended in glycerol buffer with RNase inhibitor, followed by addition of 2× NUN buffer and incubation. Chromatin pellets were collected by centrifugation, washed, and dissolved in TRIzol at 65 °C. RNA was extracted per manufacturer’s protocol, then incubated with Oligo(dT)25 beads to remove free mRNA and treated with DNase I. Purified RNA was obtained using VAHTS RNA Clean Beads. For ac4C RIP, chromatin-associated ac4C-modified RNA was enriched using the EpiQuik MeRIP Kit and ac4C antibody.
The resulting RNA was subjected to ribosomal RNA depletion using the NEBNext rRNA Depletion Kit v2 (NEB, #E7400S), and libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: GBM tissue

value: Glioblastoma stem cell

value: shCONT


title: RIP GSC387 shNAT10

description: Library name: Sample4


title: RIP GSC23 shNAT10

description: Library name: Sample3


title: RIP GSC387 shCONT

description: Library name: Sample2


title: GSC387 H3K27ac shNAT10 input

description: Library name: Sample8

data_processing:
Raw ChIP-Seq reads were aligned to the human reference genome (hg38) using Bowtie with default parameters. Read coverage was calculated using deepTools and normalized to counts per million (CPM). Heatmaps and metagene profiles were generated using the computeMatrix function in deepTools.
Assembly: hg38
Supplementary files format and content: Bigwig

extract_protocol:
GSC cells with NAT10 knockdown were crosslinked with 1% paraformaldehyde for 10 minutes and quenched with glycine for 5 minutes. After cell lysis, fixed chromatin was sonicated to generate DNA fragments ranging from 200 to 600 bp using a Diagenode Bioruptor Plus. DNA fragments were immunoprecipitated using H3K27ac antibodies (8173T, Cell signaling technology) and Protein A/G magnetic beads (16-663, Sigma).
Between 1–10 ng of immunoprecipitated DNA was used for library preparation with the NEBNext Ultra DNA Library Prep Kit for Illumina sequencing.


title: RIP GSC23 shCONT input

description: Library name: Sample5


title: P07 tumor biopsy scRNA-seq, C1D14 - palbociclib alone (rep 01)

description: Library name: P07_C1_D14_01

value: tumor biopsy


title: mRNA E18.5 lung Atp6v1g1 WT pup 2

description: Library name: Atp6v1g1_Lung_L32_3_WT_M


title: mRNA E18.5 lung Atp6v1g1 hom pup 2

description: Library name: Atp6v1g1_Lung_L32_9_KO_M


title: P06 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 01)

description: Library name: P06_C3_D1_01

value: palbociclib + INCMGA00012


title: GSC23 H3K27ac shNAT10 input

description: Library name: Sample6


title: GSC387 H3K27ac shCONT input

description: Library name: Sample7


title: mRNA E18.5 lung Atp6v1g1 WT pup 1

description: Library name: Atp6v1g1_Lung_L32_2_WT_F


title: RIP GSC23 shCONT

description: Library name: Sample1


title: mRNA E18.5 lung Atp6v1g1 hom pup 1

description: Library name: Atp6v1g1_Lung_L32_1_KO_F


title: GSC387 H3K27ac shNAT10 IP

description: Library name: Sample4


title: P03 tumor biopsy scRNA-seq, C1D14 - palbociclib alone (rep 02)

description: Library name: P03_C1_D14_02

value: palbociclib


title: GSC23 H3K27ac shNAT10 IP

description: Library name: Sample2


title: GSC23 H3K27ac shCONT input

description: Library name: Sample5


title: P03 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 02)

description: Library name: P03_C3_D1_02


title: P03 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 01)

description: Library name: P03_C3_D1_01


title: GSC23 H3K27ac shCONT IP

description: Library name: Sample1


title: P07 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 01)

description: Library name: P07_C3_D1_01


title: P05 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 01)

description: Library name: P05_C3_D1_01


title: mRNA E18.5 heart Atp6v1g1 hom pup 4

description: Library name: Atp6v1g1_Heart_L66_2_KO_F

value: Heart


title: mRNA E18.5 heart Atp6v1g1 WT pup 4

description: Library name: Atp6v1g1_Heart_L66_3_WT_F


title: GSC387 H3K27ac shCONT IP

description: Library name: Sample3


title: RA MΦs, GM-CSF 3

first: Shiva

last: Shahrara

address: 840 S. Wood St

institute: University of Illinois Chicago

description: Library name: Sample 6

data_processing:
Sequence reads were mapped to the human genome (GRCh38) reference using STAR aligner (2.7.10b). Raw read counts per gene were then generated by HT-Seq Count (2.0.5). Normalization occurred by calculating the Fragments per kilobase per million mapped reads (FPKM) and TPM (transcripts per kilobase million) values for each gene to correct for sequencing depth and gene length via StringTie (2.2.1).
Assembly: human genome (GRCh38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: RA PBMCs

extract_protocol:
RNA was isolated from cell samples using QIAzol and Chloroform phase separation and purified using RNeasy Mini Kit (Qiagen LLC, Germantown, MD). Isolated RNA sample quality was assessed BioAnalyzer Pico RNA Assay (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 (ThermoFisher, Massachusetts, USA).
Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 500bp with an insert size of about 350bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for [40] M PE reads per sample (20M in each direction).

treatment_protocol: Cells were stimulated with 100 ng/mL GM-CSF for 12 hrs.

value: RA PBMCs

value: macrophages

value: GM-CSF 3


title: P03 tumor biopsy scRNA-seq, C1D14 - palbociclib alone (rep 01)

description: Library name: P03_C1_D14_01


title: RA MΦs, PBS 3

description: Library name: Sample 3

value: PBS 3


title: P02 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 02)

description: Library name: P02_C3_D1_02


title: P02 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 01)

description: Library name: P02_C3_D1_01


title: mRNA E18.5 heart Atp6v1g1 WT pup 3

description: Library name: Atp6v1g1_Heart_L55_4_WT_M


title: RA MΦs, GM-CSF 2

description: Library name: Sample 5

value: GM-CSF 2


title: RA MΦs, PBS 2

description: Library name: Sample 2

value: PBS 2


title: mRNA E18.5 heart Atp6v1g1 WT pup 2

description: Library name: Atp6v1g1_Heart_L32_3_WT_M


title: Donor4, low CD80 expression bin

city: San Francisco

first: Pascal

last: Devant

address: 1650 Owens Street

institute: Gladstone Institutes

description:
Library name: CD80_D4_Low
processed data file column name: D4_low
CD80_TF_all_donors.count.txt

data_processing:
Sequencing reads were demultiplexed using BCL Convert (v4.2.7) and aligned to the sgRNA reference library using the count function in MAGeCK (v0.5.9.5), generating a table of sgRNA read counts for each sample
Assembly: GRCh38
Supplementary files format and content: raw counts
Library strategy: CRISPR Screen

growth_protocol: Primary human monocytes were isolated from fresh peripheral blood Leukopaks (STEMCELL Technologies) with institutional review board-approved informed written consent. Leukopaks were washed twice with EasySep buffer (sterile PBS pH 7.4, 2% FCS, 1 mM EDTA pH 8.0) before isolation of monocytes using the Human Monocyte Enrichment kit without CD16 depletion (STEMCELL Technologies; 100-1525) according to manufacturer’s instruction. Briefly, PBMCs were diluted to 100x106 cells/ml in EasySep buffer, mixed with 100 µl of antibody cocktail per 100 million cells and incubated at RT for 5-10 mins. Magnetic beads were added and following 3 min of incubation at RT, tubes containing cells were placed in a magnetic field for 10 mins. Unbound cells (pure monocyte fraction) were removed, washed one more time with EasySep buffer. Cells were then counted and resuspended in Immunocult SF Macrophage media (STEMCELL technology; 10961) supplemented with differentiation cytokines (exact cytokines used are outlined below) at a density of 1x106 cells/ml and seeded in TC-treated 24-well plate (for most experiments; 0.5x10^6 cells per well) or 12-well plates (for pooled screens; 2.5x106 cells per well). For macrophage differentiation, media was supplemented with 20 ng/ml of M-CSF (Peprotech; 300-25). Media was replenished every 24-72 h by adding at least one half volume of fresh media and cytokines. All tissue culture was performed under sterile conditions and cells were cultured in temperature-controlled incubators at 37°C and 5% CO2.

extract_protocol:
Sorted cells were pelleted and resuspended at up to 5x10^6 cells per 400 µl of lysis buffer (1% SDS, 50 mM Tris, pH 8, 10 mM EDTA). The remaining protocol reflects additives/procedures performed per each 400 µl reaction. 16 µl of NaCl (5M; Fisher Scientific; AM9760G) was added, and the sample was incubated on a heat block overnight at 66°C. The next morning, 8 µl of RNAse A (10mg/ml; Thermo Fisher; FEREN0531) was added, and the sample was vortexed briefly, and incubated at 37°C for 1 hour. Next, after 8 µl of Proteinase K (20mg/ml; ThermoFisher; AM2548) was added, the sample was vortexed briefly and incubated at 55°C for 1 hour. Homemade phase lock tubes were prepared for each sample by spinning 200 µl sterilized high vacuum grease gel (DuPont; B0857KKVR8) to the bottom of a 1.5 ml tube at 20,000 g for 1 minute and then 400 µl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1; Fisher Scientific; 15-593-031) was added to each tube. 400 µl of the sample was then added to the phase lock tube and the tube was shaken vigorously. The sample was centrifuged at maximum speed at room temperature for 5 minutes. The aqueous phase was transferred to a low-binding eppendorf tube (Eppendorf, Cat #022431021) and then 40 µl of Sodium Acetate (3M; VWR; 46-033-CI), 1µl GlycoBlue (Invitrogen; AM9515), and 600µl of room temperature isopropanol (Fisher Scientific; 32727-0010) was added. The sample was then vortexed and stored at -80°C for 30 minutes or until the sample had frozen solid. Next the sample was centrifuged at maximum speed at 4°C for 30 minutes, the pellet was washed with fresh 70% room temperature Ethanol, and allowed to air dry for 15 minutes. Pellets were then resuspended in Zymo DNA elution buffer (Zymo; D3004-4-10), and placed on the heat block at 65°C for 1 hour to completely dissolve the genomic DNA.
The sgRNA cassette was amplified and barcoded from the genomic DNA as initially described by Joung et al82. Up to 2.5 µg of genomic DNA were added to each 50 µL reaction, which included 25 µL of NEBNext Ultra II Q5 master mix (NEB; M0544L), 1.25 µL of the 10 µM forward primer and 1.25 µL of the 10 µM reverse primer, and H2O to 50 uL. Due to differences in sgRNA scaffold in the respective plasmid backbone, different reverse primer sets were used for CD80 and TNF screens. The following PCR cycling conditions were used: 98°C for 3 minutes, followed by 23 cycles at 98°C for 10 seconds, 63°C for 10 seconds, and 72°C for 25 seconds, and ending with 2 minutes at 72°C. Amplicons were purified using SPRIselect beads following manufacturer’s protocols (Beckman). The concentration of each sample was then measured using the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific, Cat #Q32854).

treatment_protocol: Pooled TNF screen: Primary monocytes from two healthy donors were isolated as described, and 360x106 cells from each donor were plated in 12-well plates (2.5x10^6 cells in 2 ml of media per well) in SF macrophage media + 20 ng/ml M-CSF. Additional culture media was either added or changed every 48 hours. 3 days after isolation, monocyte-derived macrophages were transduced with a sgRNA library packaged in a Vpx-containing lentiviral vector with a GFP marker at a pre-defined dose (7.5 ul of concentrated virus in 1 ml of media per well), resulting in ~65% and 90% transduction rate for either of the donors, respectively. 24 h after lentiviral transduction, the macrophages were treated with eVLP particles containing a scrambled/non-target sgRNA (50 ul of concentrated eVLP in 1 ml of media per well) and subsequently cultured in media with M-CSF as described above for another 5 days. Macrophages were stimulated with 50 ng/ml of ultrapure LPS isotype O:55 (Enzo) in the presence of GolgiPlug reagent for 5 h. Cells were then detached with Accutase for 30 min at 37°C, washed once with EasySep buffer and stained with Ghostdye Violet450 at 1:1000 dilution in EasySep buffer for 30 min on ice. Cells were then fixed using the CytoFix/Cytoperm kit (200 ul of Cytofix solution per 1 million cells) and stained with a APC-labeled human TNF-alpha. Cells were washed once with Perm/Wash buffer and resuspended at 20x10^6 cells/ml in EasySep buffer. Cell sorting was performed on a FACSARIA cell sorter at the UCSF Parnassus Flow Cytometry Core facility. We gated the population of single cells, which are GFP positive (transduced with lentivirus) and Ghostdye negative (viable) population and sorted the top and bottom 20% of TNF-alpha expressing cells. At least 12 million cells were sorted into each bin ensuring sufficient coverage. Pooled CD80 screen: Primary monocytes from four healthy donors were isolated as described, and 360x106 cells from each donor were plated in 12-well plates (2.5x10^6 cells in 2 ml of media per well) in SF macrophage media + 20 ng/ml M-CSF. Additional culture media was either added or changed every 48 hours. 3 or 4 days after isolation, monocyte-derived macrophages were transduced with the transcription factor and immunomodulator sgRNA library packaged in a Vpx-containing lentiviral vector with a GFP marker at a pre-defined dose (15 uL of  100x concentrated virus in 1 ml of media per well), resulting in at least ~70% transduction rate. 24 h after lentiviral transduction, the macrophages were treated with eVLP particles containing a scrambled/non-target sgRNA (35 ul of concentrated eVLP in 1 ml of media per well for Donor 1 and 2, 50 ul for Donor 3 and 4) and subsequently cultured in media with M-CSF as described above for another 5 days. Cells were then detached with Accutase for 30 min at 37°C, washed once with EasySep buffer and stained with Ghostdye Violet450 (1:1000) and APC anti-CD80 (Biolegend; 2 ul of antibody per 1 million cells) in EasySep buffer for 30 min on ice. Cells were washed once with Easysep buffer and resuspended at 20x106 cells/ml in EasySep buffer. Cell sorting was performed on a FACSARIA cell sorter at the UCSF Parnassus Flow Cytometry Core facility. We gated on single cells, which are GFP positive (transduced with lentivirus) and Ghostdye negative (viable) and sorted the top and bottom 20% of CD80 expressing cells. At least 10 million cells were sorted into each bin ensuring sufficient coverage.

value: Peripheral blood

value: monocyte-derived macrophages

tag: sample group

value: low CD80 expression bin


title: mRNA E18.5 heart Atp6v1g1 hom pup 1

description: Library name: Atp6v1g1_Heart_L32_1_KO_F

value: Atp6v1g1 homozygous trigger site mutant


title: mRNA E18.5 heart Atp6v1g1 hom pup 2

description: Library name: Atp6v1g1_Heart_L32_9_KO_M


title: P01 tumor biopsy scRNA-seq, C3D1 - palbociclib alone + IO (rep 01)

description: Library name: P01_C3_D1_01


title: Donor2, high CD80 expression bin

description:
Library name: CD80_D2_high
processed data file column name: D2_high
CD80_TF_all_donors.count.txt

value: high CD80 expression bin


title: Myeloid-library plasmid

description:
Library name: Myeloid_library
processed data file column name: Myeloid_library
Myeloid_lib.count.txt

source_name: monocyte-derived macrophages


title: mRNA E18.5 lung Lrrc58 WT pup 4

description: Library name: Lrrc58_Lung_L4_6_WT_F

value: Lung

value: Lrrc58 WT


title: Donor3, high CD80 expression bin

description:
Library name: CD80_D3_high
processed data file column name: D3_high
CD80_TF_all_donors.count.txt


title: Donor4, high CD80 expression bin

description:
Library name: CD80_D4_high
processed data file column name: D4_high
CD80_TF_all_donors.count.txt


title: Donor3, low CD80 expression bin

description:
Library name: CD80_D3_Low
processed data file column name: D3_low
CD80_TF_all_donors.count.txt


title: Donor2, low CD80 expression bin

description:
Library name: CD80_D2_Low
processed data file column name: D2_low
CD80_TF_all_donors.count.txt


title: MPNST_sample5

first: Lingling

last: Ge

address: Ninth people's hospital

institute: Shanghai Jiao Tong University

description: Library name: MPNST_sample5

data_processing:
We employed droplet-based scRNA-seq using the Chromium Single Cell 5’ solution from 10x Genomics to integrate transcriptome data from 9 PNF and 5 MPNST samples. Raw datasets were loaded using the Seurat (v5.0.1) in R.
Assembly: Huamn
Supplementary files format and content: barcodes, features, and matrix files
Supplementary files format and content: barcodes, features, and matrix files

source_name: tumor

extract_protocol:
Immediately following surgical excision, the tissue specimens were meticulously cleaned using Dulbecco’s Phosphate-Buffered Saline (DPBS) in a triple-wash protocol. Following this, the tissues were finely minced into fragments measuring 1 to 2 mm3. These tissue pieces were then subjected to enzymatic dissociation in a 37°C water bath for 45 minutes, with continuous agitation to enhance the process. The dissociation medium consisted of Collagenase I (Invitrogen, Carlsbad, CA, USA) and Dispase (Thermo Fisher Scientific, Waltham, MA, USA). Following digestion, a 40 μm sterile filter (Corning, NY, USA) was utilized to separate the dissociated cells from debris and other impurities. The filtered cell suspension was centrifuged at 1,000 rpm at 4°C for 10 minutes. After centrifugation, the cell pellets were gently resuspended in 1 mL of calcium- and magnesium-free PBS. The resuspended cells were adjusted to a concentration of 1,000-1,500 cells/μL, with a viability threshold exceeding 80% for subsequent sequencing analyses.
Single-cell gene expression libraries were constructed following the manufacturer’s guidelines, and single-cell RNA sequencing (scRNA-seq) was carried out on a NovaSeq 6000 sequencing platform.

value: tumor


title: MPNST_sample4

description: Library name: MPNST_sample4


title: TF-library plasmid

description:
Library name: TF_library
processed data file column name: sample1
sample1.count.txt


title: mRNA E18.5 heart Atp6v1g1 hom pup 3

description: Library name: Atp6v1g1_Heart_L55_6_KO_M


title: Donor1, high CD80 expression bin

description:
Library name: CD80_D1_high
processed data file column name: D1_high
CD80_TF_all_donors.count.txt


title: mRNA E18.5 heart Atp6v1g1 WT pup 1

description: Library name: Atp6v1g1_Heart_L32_2_WT_F

value: Atp6v1g1 WT


title: MPNST_sample3

description: Library name: MPNST_sample3


title: Donor1, low CD80 expression bin

description:
Library name: CD80_D1_Low
processed data file column name: D1_low
CD80_TF_all_donors.count.txt


title: Donor2, low TNF expression bin

description:
Library name: TNF_D2_Low
processed data file column name: D2_Low
TNF.count.txt

value: low TNF expression bin


title: MPNST_sample2

description: Library name: MPNST_sample2


title: Donor2, high TNF expression bin

description:
Library name: TNF_D2_high
processed data file column name: D2_High
TNF.count.txt

value: high TNF expression bin


title: mRNA E18.5 lung Lrrc58 hom pup 3

description: Library name: Lrrc58_Lung_L2_7_KO_F

value: Lrrc58 homozygous trigger site mutant


title: mRNA E18.5 lung Lrrc58 WT pup 3

description: Library name: Lrrc58_Lung_L2_5_WT_F


title: MPNST_sample1

description: Library name: MPNST_sample1


title: mRNA E18.5 lung Lrrc58 hom pup 4

description: Library name: Lrrc58_Lung_L4_4_KO_F