title: BAY-598 4uM Round-05 (exp220)

description:
Library name: BAY-598 4uM_Round-05 (exp220)
sgRNAs PCR-amplified from genomic DNA

value: BAY-598 4uM


title: Ileum_CD_Noninflamed [I0262 ITDF00A Xenium337]

status: Public on Mar 13 2026

type: RNA

city: Chicago

first: Parambir

last: Dulai

state: IL

address: 259 E Erie St Ste 1600

country: USA

institute: Northwestern University

hyb_protocol: Xenium Human

scan_protocol: Xenium Human

data_processing: We performed cell quality control (QC) on CosMx multi-tissue, Xenium multi-tissue, Xenium colon-specific, CosMx 6K, and Xenium 5K data. For CosMx multi-tissue, we performed QC by removing the cells with fewer than 20 unique molecular identifiers (UMIs). For Xenium multi-tissue and Xenium colon-specific, we performed QC by removing the cells with fewer than 5 UMIs. For CosMx 6K and Xenium 5K data, we performed QC by excluding the cells with fewer than 50 UMIs. After QC, we normalized and transformed the raw datasets using log normalization (each cell’s gene counts are divided by its total counts, multiplied by 10,000, and log transformed). For CosMx 6K and Xenium 5K data, the top 3,000 highly variable genes were next identified. After further scaling the data, we performed principal component analysis on the normalized data and clustered the cells through a shared nearest neighbor approach.

label: Xenium Human Probe Set

molecule: total RNA

organism: Homo sapiens

source_name: human Ileum

label_protocol: Xenium Human

growth_protocol: Colonic biopsies were obtained with informed consent from healthy and IBD patients during routine screening. All procedures were approved by Northwestern University IRB committee (STU00214234) operating under the main biorepository IRB (STU00203172) at the Digestive Health Center. A standardized biopsy collection protocol was used, and biopsies were targeted for the most inflamed portion of each segment, and if no inflammation was present, they were taken from areas adjacent to where routine care biopsies were taken to most closely align with routine care histology assessments.

extract_protocol: Biopsies were immediately placed in formalin jars fixed and transferred to the Northwestern University Pathology Core for automated embedding, cataloging, and H&E imaging. Formalin-fixed, paraffin-embedded blocks were cut into sections on positively charged slides, and full block sections were used for all experiments.

tag: tissue

value: Ileum


title: GW501516 25uM Round-06 (exp285)

type: SRA

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

description:
Library name: GW501516 25uM_Round-06 (exp285)
sgRNAs PCR-amplified from genomic DNA

library_source: genomic

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
For each round (batch of simultaneously-run screens), read counts for all control samples (untreated, DMSO 0.1%-0.3% or ethanol 0.1%-0.3% treated) were summed together. Read counts for samples that were grown together for part of the 8 days of the screen were also summed together so that each sample represented in the processed data files is independent in terms of genetic drift.
Assembly: sgRNAs from the Extended knock-out (EKO) library (Bertomeu et al. 2017).
Supplementary files format and content: sgrna_read_counts_refseq_genes.txt : sgRNA read counts for controls and each independent screen  (sequenced sample experiment numbers are indicated in the colunm headers), targeted refSeq gene symbols (January 2016) and updated HGNC gene symbols (2020).
Supplementary files format and content: sgrna_read_counts_exons_and_hypothetical_genes.txt : sgRNA read counts for controls and each independent screen  (sequenced sample experiment numbers are indicated in the colunm headers), targeted exons (hg19 coordinates) and hypothetical genes (AceView or Gencode symbols).
Library strategy: CRISPR Screen

molecule: genomic DNA

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C. Media was changed every two days and cells diluted to 400,000 cells/ml.

extract_protocol:
genomic DNA extracted using the Gentra Puregene kit according to the manufacturer’s instructions (QIAGEN), and sgRNA sequences were PCR-amplified
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices followed by SPRI beads purification of sequencing-ready amplicons.

treatment_protocol: A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 8 days (see Bertomeu et al., 2017 for details). The pooled EKO library was split in different T-75 flasks, compounds added, and propagated for 8 days. Fresh media and compound was added at each cell passage. The untreated control sample with multiple collected time-points was grown in T-175 spinner flasks.

tag: cell line

tag: cell type

value: pre-B lymphoid cell line

tag: treatment

tag: batch


title: iPSC_MG_Slc37a2_mut2 (Slc37a2) timepoint 28 rep 1

city: Zurich

first: Izaskun

last: Mallona

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: Library name: 20220504.B-SLC-EX6C5_1_R1

library_source: transcriptomic

data_processing:
RNA-seq raw reads were processed using ARMOR (PMC6643886). Reads were aligned and counted against the human genome GRCh38 assembly and Gencode release 43 annotation using salmon v1.4.0 and STAR 2.7.7a.
Assembly: GRCh38
Supplementary files format and content: shiny_sce.rds
Supplementary files format and content: R (SingleCellExperiment) RDS file, to be read with `readRDS()` in base R. Even if these data are bulk RNA-seq, it makes use of the SingleCellExperiment class. It contains two SingleCellExperiment objects generated using the ARMOR RNA‑seq workflow: one at the transcript level and one at the gene level. The transcript‑level object (sce_tx) includes 111,002 transcripts across 13 samples, with assays for raw counts, transcript abundances, and effective lengths. Row metadata contains transcript and gene identifiers as well as gene symbols and names. Sample‑level metadata includes sample name, type, treatment group, batch, mutation status, and timepoint.  The gene‑level object (sce_gene) contains 20,337 genes across the same 13 samples, with assays for raw counts, abundances, effective lengths, and log‑CPM values computed via edgeR. Row metadata includes gene identifiers, associated transcript IDs, gene symbols and names, and differential expression statistics produced by ARMOR/edgeR for the experimental contrasts (mainly mutants vs WT). Sample metadata is identical to that of the transcript‑level object. All samples correspond to iPSC‑derived microglia, including wild‑type controls and mutant lines for Slc37a2 and TREM2, processed in this analysis in a single batch.

molecule: polyA RNA

extract_protocol:
Total RNA was extracted from mature iMGL (1*106 cells) using both the RNeasy Micro kit (Qiagen) or the Direct-zol RNA miniprep (Zymo Research), according to the manufacturers’ protocols. The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed.
The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Fragment Analyzer (Agilent, Santa Clara, California, USA).  The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.

tag: genotype

value: day 28


title: iPSC_MG_Slc37a2_mut1 (Slc37a2) timepoint 28 rep 2

description: Library name: 20220504.B-SLC-EX2B1_2_R1


title: Ileum_CD_Inflamed [I0294 ITDF00A Xenium337]


title: K. marxianus, Heat 39C, biorep2

city: Berkeley

first: Kaylee

middle: Elizabeth

last: Christensen

state: CA

address: Koshland Hall rm 321

department: Plant and Microbial Biology

institute: UC Berkeley

description: Library name: Km 39C 2

data_processing:
mapped to genome with TopHat with default parameters, input to Htseq for raw read counts
Assembly: custom pseudogenomes for our lab strains of K. marxianus Km31 and K. lactis yLB72
Supplementary files format and content: column 1 lists gene name, column 2 lists raw read count

organism: Kluyveromyces marxianus

source_name: yeast

growth_protocol: colonies from YPD plates picked into YPD for overnight growth, back-diluted to 0.05 OD in 50mL

extract_protocol:
Direct-Zol RNA MicroPrep RNA kit (Zymo Research)
mRNA enrichment with Poly (A) capture; RNA fragmentation with Covaris; cDNA reverse transcription; RNA library preparation done by Novogene, Inc.

treatment_protocol: grown at condition listed in 50mL back-diluted culture until reached 0.4-0.85 OD, 2OD units suspended in 1mL of RNAlater and stored at 4C for <48 hours

value: yeast

value: K. marxianus Km31


title: VE-822 40nM Round-06 (exp300)

description:
Library name: VE-822 40nM_Round-06 (exp300)
sgRNAs PCR-amplified from genomic DNA


title: K. marxianus, Heat 39C, biorep3

description: Library name: Km 39C 3


title: GCT_N_015

type: genomic

city: Utrecht

first: Leendert

last: Looijenga

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center

description: Tumor DNA from patient GCT_N_015 with TE

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to human Infinium Methylation 450K Beadchip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing:
minfi package in R environment (v4.4.2).
Average beta.

label: Cy3 and Cy5

source_name: Tumor DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the DNeasy Blood & Tissue Kit (69504, Qiagen)

tag: histology

value: TE

tag: Sex

value: Male

tag: location

value: Retroperitoneum

tag: age

tag: gct type

value: I

tag: material

value: Frozen

tag: disease state

value: Germ cell tumor

value: Tumor DNA


title: iPSC_MG_Slc37a2_mut1 (Slc37a2) timepoint 28 rep 1

description: Library name: 20220504.B-SLC-EX2B1_1_R1


title: iPSC_MG WT timepoint 28 rep 2

description: Library name: 20220504.B-WTC_2_R1

value: WT


title: iPSC_MG WT timepoint 28 rep 1

description: Library name: 20220504.B-WTC_1_R1


title: GCT_N_031

description: Tumor DNA from patient GCT_N_031 with TE

value: Female

value: Sacrum


title: Geldanamycin 0.015-0.025uM Round-07 (exp316)

description:
Library name: Geldanamycin 0.015-0.025uM_Round-07 (exp316)
sgRNAs PCR-amplified from genomic DNA

value: Geldanamycin 0.015uM, then 0.025uM


title: Trientine 500uM Round-08 (exp534)

description:
Library name: Trientine 500uM_Round-08 (exp534)
sgRNAs PCR-amplified from genomic DNA

value: Trientine 500uM


title: iPSC_MG WT timepoint 38 rep 3

description: Library name: 20220209.A-tw029_WT_3_R1

value: day 38


title: GCT_N_048

description: Tumor DNA from patient GCT_N_048 with TE


title: Salubrinal 20uM Round-07 (exp399)

description:
Library name: Salubrinal 20uM_Round-07 (exp399)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Salubrinal 20uM


title: iPSC_MG WT timepoint 38 rep 2

description: Library name: 20220209.A-tw029_WT_2_R1


title: K. marxianus, Control 28C, biorep3

description: Library name: Km 28C 3

value: yeast


title: GCT_N_023

description: Tumor DNA from patient GCT_N_023 with TE

value: Mediastinum


title: K. marxianus, Control 28C, biorep2

description: Library name: Km 28C 2

value: K. marxianus Km31


title: GCT_N_047

description: Tumor DNA from patient GCT_N_047 with TE

value: TE


title: GCT_N_025

description: Tumor DNA from patient GCT_N_025 with TE


title: K. marxianus, Control 28C, biorep1

description: Library name: Km 28C 1


title: iPSC_MG WT timepoint 34 rep 2

description: Library name: 20220209.A-av111_WT_002_R1

value: day 34


title: K. marxianus, Heat 39C, biorep1

description: Library name: Km 39C 1


title: GCT_N_021

description: Tumor DNA from patient GCT_N_021 with TE

value: I


title: SGC2043 10uM Round-03 (exp152)

description:
Library name: SGC2043 10uM_Round-03 (exp152)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: RS-1 10uM Round-08 (exp519)

description:
Library name: RS-1 10uM_Round-08 (exp519)
sgRNAs PCR-amplified from genomic DNA

value: RS-1 10uM


title: K. marxianus, MMS, biorep3

description: Library name: Km MMS 3


title: Spinner flask No treatment Day 2 Round-07 (exp601)

description:
Library name: SF No treatment D2_Round-07 (exp601)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: iPSC_MG WT timepoint 34 rep 1

description: Library name: 20220209.A-av111_WT_001_R1


title: Centrinone 500nM Round-07 (exp343)

description:
Library name: Centrinone 500nM_Round-07 (exp343)
sgRNAs PCR-amplified from genomic DNA

value: Centrinone 500nM


title: GRO_WT_hESC_RepSox_rep2

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: College of Future Technology

country: China

institute: Peking University

description: Library name: Sample 44

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7). Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) by STAR (v2.7.10a) or Bowtie2 (v2.4.5). The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawcounts and bigWig files for GRO-seq
Library strategy: GRO-Seq

molecule: nuclear RNA

growth_protocol: WIBR3 Human ESCs were grown in mTeSRTM (STEMCELL Technologies) on Matrigel-coated dish at 37°C under 5% CO2. V6.5 mouse ESCs were grown on gelatin-coated dish at 37°C under 5% CO2, in KnockOutTM DMEM (Gibco) supplemented with 15% FBS (Hyclone), nonessential amino acids, 2-mercaptoethanol, and 1,000 units/ml lymphocyte inhibitory factor.

extract_protocol:
For bulk RNA library construction, total RNA was extracted following the standard TRIzol protocol (invitrogen); For GRO-seq library construction, RNAs are hydrolyzed and purified using beads coated with antibodies to 5-bromo-2-deoxyuridine (BrdU).
RNA libraries for RNA-seq were prepared using AHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer’s protocols; RNA libraries for GRO-seq using AccuNext Small RNA-seq Library Kit for Illumina (Accurate Biology) following manufacturer’s protocols.

value: human embryonic stem cell

value: WT

value: 10 μM RepSox


title: K. marxianus, MMS, biorep2

description: Library name: Km MMS 2


title: GCT_N_060

description: Tumor DNA from patient GCT_N_060 with TE

value: Male

value: Testis

value: Frozen

value: Germ cell tumor

value: Tumor DNA


title: CAY10603 550nM Round-08 (exp467)

description:
Library name: CAY10603 550nM_Round-08 (exp467)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: iPSC_MG WT timepoint 34 rep 3

description: Library name: 20220209.A-av111_WT_003_R1


title: GRO_WT_hESC_RepSox_rep1

description: Library name: Sample 43


title: GCT_N_079

description: Tumor DNA from patient GCT_N_079 with GER

value: GER

value: CNS

value: Unknown

value: II

value: FFPE


title: DMSO 0.1% D8Spinner flask 2 Round-08 (exp541)

description:
Library name: Ctl DMSO 0.1_ D8_SF2_Round-08 (exp541)
sgRNAs PCR-amplified from genomic DNA

value: DMSO 0.1%


title: GCT_N_080

description: Tumor DNA from patient GCT_N_080 with TE

value: TE


title: GCT_N_064

description: Tumor DNA from patient GCT_N_064 with TE


title: K. marxianus, ethanol, biorep3

description: Library name: Km ethanol 3

value: yeast

value: K. marxianus Km31


title: GRO_WT_hESC_DMSO_rep2

description: Library name: Sample 42

value: human embryonic stem cell

value: WT

value: DMSO


title: K. marxianus, ethanol, biorep2

description: Library name: Km ethanol 2


title: GRO_WT_hESC_DMSO_rep1

description: Library name: Sample 41


title: Talazoparib 55.2nM Round-09 (exp625)

description:
Library name: Talazoparib 55.2nM_Round-09 (exp625)
sgRNAs PCR-amplified from genomic DNA

value: Talazoparib 55.2nM


title: K. marxianus, ethanol, biorep1

description: Library name: Km ethanol 1


title: K. marxianus, MMS, biorep1

description: Library name: Km MMS 1


title: GCT_N_065

description: Tumor DNA from patient GCT_N_065 with GER

value: Female


title: MIR302_Dif_D14_low_rep2

description: Library name: Sample 28

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7). Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) by STAR (v2.7.10a) or Bowtie2 (v2.4.5). The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawcounts and bigWig files for GRO-seq

value: cardiomyocyte differentiation


title: GCT_N_033

description: Tumor DNA from patient GCT_N_033 with TE

value: Retroperitoneum

value: I

value: Frozen

value: Germ cell tumor

value: Tumor DNA


title: K. marxianus, caffeine, biorep2

description: Library name: Km caffeine 2


title: K. marxianus, caffeine, biorep3

description: Library name: Km caffeine 3


title: GCT_N_305

description: Tumor DNA from patient GCT_N_305 with MIX

value: MIX

value: Sacrum


title: GCT_N_316

description: Tumor DNA from patient GCT_N_316 with MIX

value: Ovary


title: MIR302_Dif_D14_high_rep2

description: Library name: Sample 26


title: K. marxianus, caffeine, biorep1

description: Library name: Km caffeine 1


title: MIR302_Dif_D14_high_rep1

description: Library name: Sample 25


title: MIR302_Dif_D20_rep2

description: Library name: Sample 24


title: GCT_N_046

description: Tumor DNA from patient GCT_N_046 with YST

value: YST

value: Male

value: Mediastinum


title: MIR302_Dif_D14_low_rep1

description: Library name: Sample 27

value: human embryonic stem cell


title: Erlotinib 10uM Round-05 (exp216)

description:
Library name: Erlotinib 10uM_Round-05 (exp216)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Erlotinib 10uM


title: Meningeal mast cells, LCMV, rep 3

first: Qingqing

last: Li

address: Shuangqing Road, No. 30

department: Institute for Immunology and School of Basic Medical Sciences

institute: Tsinghua University

data_processing:
The sequencing data was filtered with SOAPnuke.
The clean reads were mapped to the reference genome using HISAT.
Bowtie2 was applied to align the clean reads to the gene set.
Expression level of gene was calculated by RSEM.
Differential expression analysis was performed using the DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include TPM values for each sample

organism: Mus musculus

source_name: Meningeal mast cells

extract_protocol:
Isolated cell samples were lysed using the Discover-sc WTA Kit V2.
Libraries were constructed using the Discover-sc WTA Kit V2.

value: Meningeal mast cells

tag: infection

value: LCMV


title: Thioridazine 5uM Round-08 (exp530)

description:
Library name: Thioridazine 5uM_Round-08 (exp530)
sgRNAs PCR-amplified from genomic DNA

value: Thioridazine 5uM


title: 4-Nitroquinoline N-oxide 500nM Round-08 (exp446)

description:
Library name: 4-Nitroquinoline N-oxide 500nM_Round-08 (exp446)
sgRNAs PCR-amplified from genomic DNA

value: 4-Nitroquinoline N-oxide 500nM


title: GCT_N_013

description: Tumor DNA from patient GCT_N_013 with MIX

value: Female

value: I


title: MIR302_Dif_D20_rep1

description: Library name: Sample 23

value: cardiomyocyte differentiation


title: GCT_N_304

description: Tumor DNA from patient GCT_N_304 with MIX

value: Frozen

value: Germ cell tumor

value: Tumor DNA


title: Meningeal mast cells, LCMV, rep 1


title: ALDA-1 10uM Round-06 (exp262)

description:
Library name: ALDA-1 10uM_Round-06 (exp262)
sgRNAs PCR-amplified from genomic DNA

value: ALDA-1 10uM


title: Momordin Ic 10uM Round-08 (exp506)

description:
Library name: Momordin Ic 10uM_Round-08 (exp506)
sgRNAs PCR-amplified from genomic DNA

value: Momordin Ic 10uM


title: Meningeal mast cells, LCMV, rep 2


title: Azithromycin 100uM Round-08 (exp452)

description:
Library name: Azithromycin 100uM_Round-08 (exp452)
sgRNAs PCR-amplified from genomic DNA

value: Azithromycin 100uM


title: (R)-(+)-1,1'-Binaphthyl-2,2'-diamine 8uM Round-03 (exp111)

description:
Library name: (R)-(+)-1,1_-Binaphthyl-2,2_-diamine 8uM_Round-03 (exp111)
Illumina HiSeq 2000,  sgRNAs PCR-amplified from genomic DNA


title: Meningeal mast cells, PBS, rep 3

value: No infection


title: Deguelin 150nM Round-05 (exp209)

description:
Library name: Deguelin 150nM_Round-05 (exp209)
sgRNAs PCR-amplified from genomic DNA

value: Deguelin 150nM


title: MIR302_Dif_D12_rep1

description: Library name: Sample 21

value: human embryonic stem cell


title: GCT_N_014

description: Tumor DNA from patient GCT_N_014 with MIX

value: MIX

value: Sacrum


title: ONC212 150nM Round-08 (exp513)

description:
Library name: ONC212 150nM_Round-08 (exp513)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: Meningeal mast cells, PBS, rep 2

value: Meningeal mast cells


title: GCT_N_012

description: Tumor DNA from patient GCT_N_012 with MIX

value: Male

value: Testis


title: Tunicamycin 0.04-0.075uM Round-07 (exp419)

description:
Library name: Tunicamycin 0.04-0.075uM_Round-07 (exp419)
sgRNAs PCR-amplified from genomic DNA

value: Tunicamycin 0.04uM, then 0.075uM


title: GCT_N_063

description: Tumor DNA from patient GCT_N_063 with YST

value: YST

value: I


title: Meningeal stromal cells, LCMV, rep 3

source_name: Meningeal stromal cells

growth_protocol: After euthanizing the mice, the dural meninges were harvested and subsequently digested using 1 mg/ml collagenase D (Roche) and 50 μg/ml DNase I (Roche). Following termination of digestion, the mixture was filtered using a 100 μm strainer. Magnetic beads for CD45 (Biolegend) staining were applied, and negative selection was employed to remove immune cells. Subsequently, after lysing erythrocytes with ACK,the stromal cells were cultured in DMEM medium (Corning) supplemented with 10% FBS and PS.

treatment_protocol: LCMV Armstrong was used to infect meningeal stromal cells at an MOI ratio of 2:1.

value: Meningeal stromal cells

value: wildtype

value: LCMV


title: GCT_N_136

description: Tumor DNA from patient GCT_N_136 with SE

value: SE

value: II

value: Frozen

value: Germ cell tumor

value: Tumor DNA


title: Spinner flask No treatment D3 Round-06 (exp595)

description:
Library name: SF No treatment D3_Round-06 (exp595)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: MIR302_Dif_D12_rep2

description: Library name: Sample 22

value: human embryonic stem cell

value: cardiomyocyte differentiation


title: GCT_N_130

description: Tumor DNA from patient GCT_N_130 with SE


title: MIR302_Dif_D5_rep2

description: Library name: Sample 20


title: MIR302_Dif_D0_rep1

description: Library name: Sample 17


title: GCT_N_036

description: Tumor DNA from patient GCT_N_036 with YST


title: MIR302_Dif_D0_rep2

description: Library name: Sample 18


title: GCT_N_029

description: Tumor DNA from patient GCT_N_029 with YST

value: Female

value: Ovary


title: MIR302_Dif_D5_rep1

description: Library name: Sample 19


title: Meningeal stromal cells, LCMV, rep 2


title: Tubacin 1.6uM Round-07 (exp416)

description:
Library name: Tubacin 1.6uM_Round-07 (exp416)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Tubacin 1.6uM


title: Tretinoin 8uM Round-07 (exp333)

description:
Library name: Tretinoin 8uM_Round-07 (exp333)
sgRNAs PCR-amplified from genomic DNA

value: Tretinoin 8uM


title: Meningeal stromal cells, PBS, rep 3

value: No infection


title: GCT_N_253

description: Tumor DNA from patient GCT_N_253 with SE

value: Male

value: Testis


title: Meningeal stromal cells, PBS, rep 2

value: Meningeal stromal cells

value: wildtype


title: Meningeal stromal cells, LCMV, rep 1

value: LCMV


title: Meningeal mast cells, PBS, rep 1

value: Meningeal mast cells


title: UM0125461 740nM Round-02 (exp84)

description:
Library name: UM0125461 740nM_Round-02 (exp84)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: GCT_N_045

description: Tumor DNA from patient GCT_N_045 with YST

value: YST

value: I

value: Frozen

value: Germ cell tumor


title: cfRNA_water6_NTC

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

description:
Library name: cfRNA_water6_NTC
Water control cfRNA (water6)

data_processing:
Reads were aligned to the human genome (GRCh38/hg38) using STAR, quantified with HTSeq, and processed as described in [Author et al., Year, DOI: 10.xxxx/xxxxx].
Unaligned and control reads were retained and deposited as raw FASTQ files.
Assembly: Human GRCh38 / hg38 (for cfDNA and cfRNA libraries).
Supplementary files format and content: Raw and processed data are provided as gzipped FASTQ and gene-count matrices, respectively.

source_name: water control

extract_protocol:
Not applicable. Participant plasma and water controls were processed in parallel using identical reagents and workflows.
Libraries were prepared using Illumina-compatible cfDNA and cfRNA library kits, following manufacturer protocols, and sequenced as paired-end 2 × 75 bp reads on Illumina NextSeq 500 (cfDNA) or NovaSeq 6000 (cfRNA). Full details are provided in [ https://doi.org/10.1101/2025.06.10.658831].

value: water control

value: cell-free RNA


title: Meningeal mast cells, PBS, rep 4


title: negative_control

city: Montreal

first: Peter

middle: M

last: Siegel

state: Quebec

address: 1160 Pine Ave. West

department: Rosalind and Morris Goodman Cancer Research Centre

institute: McGill University

description:
Library name: TMA1_025
negative control

data_processing:
Reads were trim (trimGalore," --stringency 4 --q 20 --dont_gzip --adapter AGATCGGAAGAGCACACGTCTGAACTCC -a2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTT"), the UMI were extracted (umiExtract," --bc-pattern=NNNNNNNNNNNNNN"), aligned to tag sequences (bowtie2," --end-to-end -L 4 --trim5 0 --trim3 0 --norc"), and deduplicated by UMIs (umiDedup," --edit-distance-threshold=3").
As in standard NanoString workflow, 1-5 probes were used to measure the expression of each target gene (n = 1,825) and 88 spike-in probes as negative controls.
The geometric mean of each target and negative control was calculated per ROI (region of interest). The limit of quantification (LOQ) was calculated, per ROI, as two standard deviations above the geometric mean of the negative controls.
Targets with no values across ROIs above the LOQ were excluded from the analysis.
Differential gene expression analysis between invasive and circumscribed conditions was performed for lung and breast samples using the DESeq2 R package (version 1.34.0). The Benjamini-Hochberg Procedure (pAdjustMethod = “BH”) was used to control for multiple testing (Benjamini & Hochberg, 1995). The geometric mean matrix was rounded so it could be used as input for DESeq2.
Assembly: GRCh38
Supplementary files format and content: *_DEG_by_DESeq2.csv: comma separated values with DESeq2 outputs (LFC, p-values, base mean, etc).
Supplementary files format and content: Step1_CTA_Initial_Dataset_Raw_counts_all.csv: has the raw counts per probe.
Supplementary files format and content: *png: segment profiling of the ROIs.
Library strategy: Spatial Transcriptomics

extract_protocol:
A tissue microarray (TMA) was constructed from formalin-fixed paraffin-embedded surgically resected metastatic tissue. Selected tissue blocks captured the interface between the metastatic  lesion and the adjacent tissue.
RNAs are marked with a Photoreleased GeoMx™ DSPDNA oligo tag with a barcode to identify gene target, and UMI. PCR with Unique Dual IndexingPrimers (i5 index x i7 index) toidentify Primers (i5 index x i7 index) to AOIs.


title: cfRNA_water5_NTC

description:
Library name: cfRNA_water5_NTC
Water control cfRNA (water5)


title: cfRNA_water2_NTC

description:
Library name: cfRNA_water2_NTC
Water control cfRNA (water2)


title: Meningeal stromal cells, PBS, rep 1


title: cfRNA_water3_NTC

description:
Library name: cfRNA_water3_NTC
Water control cfRNA (water3)


title: Adefovir 20uM Round-07 (exp332)

description:
Library name: Adefovir 20uM_Round-07 (exp332)
sgRNAs PCR-amplified from genomic DNA

value: Adefovir 20uM


title: C. rosea, stress, rep9, T19 (RH9T19)

city: Vienna

first: Hannes

middle: M.

last: Kramml

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

description: Library name: RH9T19

data_processing:
Sample preprocessing was conducted using fastp (v0.23.2) with following parameters: -q 30, -l 80, --detect_adapter_for_pe
STAR (v2.7.10b) and RSEM utilized read alignment and polyploid/allele-aware estimation of normalized transcripts per million (TPM) for each sample
Data matrices for downstream analyses were constructed and integrated via custom scripts in R (Clusia panomics database)
Assembly: CmuV2.3_predom, CmuV2.3_alt
Supplementary files format and content: tab-delimited file of TPM values for all samples combined per species
Supplementary files format and content: tab-delimited file includes raw counts, normalized counts, TPM, and FPKM values for each sample separately

organism: Clusia rosea

source_name: Leaf

extract_protocol:
Total RNA was extracted according to the protocol of Oliveira, R. R. et al. (2015) with an adapted extraction buffer (2.5 M NaCl, 2.5% PVP, 100 mM Tris, 25 mM EDTA, 2.5% -mercaptoethanol and 2% SDS). Purification was done using AMPure beads, mRNA enrichment and cDNA synthesis via NEB polyA kit.
Standard RNA library preparation was conducted for 150 bp paired-end Illumina sequencing on a NovaSeq S4 XP system.

value: Leaf

tag: condition

value: Stress

tag: time


title: Invasive Lung rep8

description:
Library name: TMA1_023
Invasive and PanCK

source_name: Lung

value: Lung


title: Invasive Breast rep7

description:
Library name: TMA1_024
Invasive and PanCK

source_name: Breast

value: Breast


title: snRNA-seq of Mus musculus: adult female heart tissue with Angiotensin II and BPF (biological_replicate_3)

first: Qingtao

last: Meng

address: No.10, West Tou Tiao, Youan Men Wai, Fengtai District

institute: capital Medical University

description:
Library name: D3_S1_L001
10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were processed with Cell Ranger software (v9.01, 10x Genomics), which aligned the cDNA to the mouse reference genome (mm10) and generated the gene barcode matrix.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: heart

growth_protocol: Female C57BL/6 germ-free mice (6–8 weeks old, 20–22 g) were procured from Empharmatech Co., Ltd (Nanjing, China). The mice received food and water in specific-pathogen-free (SPF) conditions.

extract_protocol:
The mouse heart was excised and rinsed with pre-chilled DPBS to remove residual blood cells. The tissues were then minced into approximately 1 mm3 pieces using sterile scissors and incubated on ice in 2 mL of ice cold Nuclei EZ Lysis Buffer (NUC-101, Sigma-Aldrich) to isolate nuclei. Subsequently, 2 mL of pre-chilled 4% BSA was added to dilute the lysate. The suspension was centrifuged at 300 × g for minutes at 4°C, and the supernatant was discarded. The nuclear pellet was resuspended in a mixture of 2 mL lysis buffer and 4% BSA, and incubated on ice for minutes. Cell debris was removed using debris removal solution ( 130090101, Miltenyi Biotec). The nuclear pellet was then resuspended and washed with 4 mL of the provided buffer, followed by incubation on ice for minutes. After centrifugation, the pellet was resuspended in nuclear resuspension buffer containing PBS supplemented with 2% BSA and 0.1% RNase inhibitor (N2615, Promega), followed by nuclei counting.
snRNA-Seq experiment was performed by BioMiao Biotechnology (Beijing) Co. Ltd. According to the protocol for the 10x Chromium Single Cell 3′ v4 Reagent Kit, the single cell suspension was loaded onto a 10x Chromium Chip for cDNA amplification and library construction. The libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: The BPF group received oral gavage of BPF (50 μg/kg) for two weeks prior to hypertension induction. Hypertension was induced by subcutaneous implantation of osmotic pumps (Alzet Model 2002, USA). Under isoflurane anesthesia, the pumps continuously delivered angiotensin II at a rate of 400 ng/kg/min (approximately 0.576 mg/kg/day) for 14 days. From the day of pump implantation, BPF-treated groups continued to receive their respective daily doses of BPF via oral gavage for an additional 14 days, while the control group received an equal volume of vehicle (corn oil). The total experimental duration was 28 days.

value: heart

value: 6-8 weeks old

value: female

value: Angiotensin II and BPF


title: cfRNA_water1_NTC

description:
Library name: cfRNA_water1_NTC
Water control cfRNA (water1)


title: Invasive Lung rep7

description:
Library name: TMA1_022
Invasive/NA and PanCK


title: cfRNA_water4_NTC

description:
Library name: cfRNA_water4_NTC
Water control cfRNA (water4)


title: snRNA-seq of Mus musculus: adult female heart tissue with Angiotensin II and BPF (biological_replicate_4)

description:
Library name: D4_S1_L001
10x Genomics


title: snRNA-seq of Mus musculus: adult female heart tissue with Angiotensin II and BPF (biological_replicate_2)

description:
Library name: D2_S1_L001
10x Genomics


title: Invasive Breast rep6

description:
Library name: TMA1_021
Invasive and PanCK


title: snRNA-seq of Mus musculus: adult female heart tissue with Angiotensin II and BPF (biological_replicate_5)

description:
Library name: D5_S1_L001
10x Genomics


title: C. rosea, stress, rep9, T13 (RH9T13)

description: Library name: RH9T13


title: C. rosea, stress, rep9, T08 (RH9T08)

description: Library name: RH9T08


title: cfRNA_NTC_8

description:
Library name: cfRNA_NTC_8
Non-template control cfRNA, run 8

source_name: NTC

value: NTC


title: snRNA-seq of Mus musculus: adult female heart tissue with Angiotensin II and BPF (biological_replicate_1)

description:
Library name: D1_S1_L001
10x Genomics


title: Invasive Breast rep5

description:
Library name: TMA1_019
Invasive and PanCK


title: cfRNA_NTC_5

description:
Library name: cfRNA_NTC_5
Non-template control cfRNA, run 5


title: THZ531 0.11-0.35uM Round-07 (exp412)

description:
Library name: THZ531 0.11-0.35uM_Round-07 (exp412)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: C. rosea, stress, rep9, T04 (RH9T04)

description: Library name: RH9T04


title: snRNA-seq of Mus musculus: adult female heart tissue with Angiotensin II (biological_replicate_5)

description:
Library name: C5_S1_L001
10x Genomics

value: Angiotensin II


title: snRNA-seq of Mus musculus: adult female heart tissue with Angiotensin II (biological_replicate_4)

description:
Library name: C4_S1_L001
10x Genomics


title: cfRNA_NTC_6

description:
Library name: cfRNA_NTC_6
Non-template control cfRNA, run 6


title: cfRNA_NTC_7

description:
Library name: cfRNA_NTC_7
Non-template control cfRNA, run 7


title: C. rosea, stress, rep5, T19 (RH5T19)

description: Library name: RH5T19


title: Invasive Lung rep6

description:
Library name: TMA1_020
Invasive and PanCK


title: C. rosea, stress, rep5, T13 (RH5T13)

description: Library name: RH5T13


title: cfRNA_NTC_4

description:
Library name: cfRNA_NTC_4
Non-template control cfRNA, run 4


title: cfRNA_NTC_3

description:
Library name: cfRNA_NTC_3
Non-template control cfRNA, run 3


title: Invasive Lung rep5

description:
Library name: TMA1_018
Invasive and PanCK


title: Invasive Lung rep4

description:
Library name: TMA1_017
Invasive and PanCK


title: snRNA-seq of Mus musculus: adult female heart tissue with Angiotensin II (biological_replicate_2)

description:
Library name: C2_S1_L001
10x Genomics


title: C. rosea, stress, rep5, T08 (RH5T08)

description: Library name: RH5T08


title: cfRNA_NTC_2

description:
Library name: cfRNA_NTC_2
Non-template control cfRNA, run 2


title: snRNA-seq of Mus musculus: adult female heart tissue with Angiotensin II (biological_replicate_3)

description:
Library name: C3_S1_L001
10x Genomics


title: C. rosea, stress, rep5, T04 (RH5T04)

description: Library name: RH5T04


title: C. rosea, stress, rep1, T19 (RH1T19)

description: Library name: RH1T19


title: Circumscribed Lung rep5

description:
Library name: TMA1_016
Circumscribed and PanCK


title: Invasive Lung rep3

description:
Library name: TMA1_015
Invasive and PanCK


title: Pcbp1/2-dKO

city: Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No. 600 Dunyu Road, Sandun Town, Xihu District

department: School of Life Sciences

institute: Westlake University

description:
Library name: Sample 2
10x Genomics

data_processing:
For initial processing and gene expression estimation, we used Cell Ranger (v.6.1.2). Each library was aligned to an indexed mm10 genome using Cell Ranger Count.
Assembly: Mouse mm10
Supplementary files format and content: bam files

source_name: bone marrow

extract_protocol:
Sorted cells were resuspended in PBS containing 0.4% FBS, and the concentration was adjusted to target approximately 10000 cells per sample.
Cells were loaded onto a Chromium Next GEM Chip G together with reverse transcription master mix and Single Cell 3' v3.1 Gel Beads to generate gel beads-in-emulsion (GEMs). Within each GEM, reverse transcription produced barcoded cDNA, which was subsequently amplified, fragmented, and subjected to adaptor ligation and sample index attachment. Final libraries were sequenced on an Illumina NovaSeq 6000 platform.

value: bone marrow

value: B lineage cells

value: Mb1-Cre+/- Pcbp1 fl/fl Pcbp2 fl/fl


title: cfRNA_NTC_1

description:
Library name: cfRNA_NTC_1
Non-template control cfRNA, run 1


title: Invasive Lung rep2

description:
Library name: TMA1_014
Invasive and PanCK


title: Invasive Breast rep4

description:
Library name: TMA1_013
Invasive and PanCK


title: C. rosea, stress, rep1, T08 (RH1T08)

description: Library name: RH1T08


title: cfRNA_100337_T3

description:
Library name: cfRNA_100337_T3
Plasma cfRNA 100337, T3

source_name: plasma

value: plasma


title: C. rosea, stress, rep1, T13 (RH1T13)

description: Library name: RH1T13


title: cfRNA_100337_T2

description:
Library name: cfRNA_100337_T2
Plasma cfRNA 100337, T2

value: cell-free RNA


title: WT

description:
Library name: sample1
10x Genomics

value: Mb1-Cre+/- Pcbp1 +/+ Pcbp2 +/+


title: cfRNA_100267_T3

description:
Library name: cfRNA_100267_T3
Plasma cfRNA 100267, T3


title: snRNA-seq of Mus musculus: adult female heart tissue with Angiotensin II (biological_replicate_1)

description:
Library name: C1_S1_L001
10x Genomics


title: Invasive Breast rep3

description:
Library name: TMA1_012
Invasive and PanCK


title: Circumscribed Lung rep4

description:
Library name: TMA1_011
Circumscribed


title: BMDM, IL-4+ 1mM CoA,48hrs, rep4,R1

city: Los Angeles

first: Anthony

last: Jones

address: 650 Charles E Young Dr. South, Room 23-305

department: Department of Molecular and Medical Pharmacology

institute: University of California, Los Angeles

description:
Library name: Sample 12
M

data_processing:
Gene expression quantification from the resulting fastqs was performed using Salmon v1.21.1 in mapping-based  mode. Reads were selectively aligned to the GENCODE vM25 mouse reference transcriptome with corrections for sequence-specific and GC content biases.
Assembly: mm10
Supplementary files format and content: Tab-delimited File with TPMs listed

source_name: Primary bone marrow-derived macrophages

growth_protocol: BMDMs are isolated and differentiated in  10% (v/v) conditioned medium from CMG-14-12 cells as a source of macrophage colony stimulate factor (M-CSF)

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit 500 according to the manufacturers’ protocol
RNA libraries were prepared with KAPA stranded mRNA-Seq kit. High throughput sequencing was performed on Illumina NovaSeq 6000 (paired end, 2x150bp) targeting 100 million reads per sample. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1. Gene expression quantification from the resulting fastqs was performed using Salmon v1.21.1 in mapping-based mode. Reads were selectively aligned to the GENCODE vM25 mouse reference transcriptome with corrections for sequence-specific and GC content biases.

treatment_protocol: On the 8th day of differentiation, BMDMs were incubated with the indicated treatment for the listed amount of time.

value: Primary bone marrow-derived macrophages

value: WT

value: IL-4 + 1mM CoA


title: BMDM, IL-4+ 1mM CoA,48hrs, rep3,R1

description:
Library name: Sample 11
L


title: C. rosea, control, rep8, T19 (RD8T19)

description: Library name: RD8T19

value: Leaf

value: Control


title: C. rosea, stress, rep1, T04 (RH1T04)

description: Library name: RH1T04

value: Stress


title: BMDM, IL-4+ 1mM CoA,48hrs, rep1,R1

description:
Library name: Sample 9
J


title: cfRNA_100337_T1

description:
Library name: cfRNA_100337_T1
Plasma cfRNA 100337, T1


title: BMDM, IL-4,48hrs, rep4,R1

description:
Library name: Sample 8
I


title: Circumscribed Lung rep3

description:
Library name: TMA1_010
Circumscribed and PanCK

value: Lung


title: cfRNA_100267_T2

description:
Library name: cfRNA_100267_T2
Plasma cfRNA 100267, T2


title: cfRNA_100257_T2

description:
Library name: cfRNA_100257_T2
Plasma cfRNA 100257, T2


title: C. rosea, control, rep7, T13 (RD7T13)

description: Library name: RD7T13


title: Circumscribed Breast rep1

description:
Library name: TMA1_007
Circumscribed and PanCK

value: Breast


title: Circumscribed Melanoma rep2

description:
Library name: TMA1_008
Circumscribed and MelA

source_name: Melanoma

value: Melanoma


title: cfRNA_100257_T1

description:
Library name: cfRNA_100257_T1
Plasma cfRNA 100257, T1


title: Invasive Lung rep1

description:
Library name: TMA1_009
Invasive and PanCK


title: cfRNA_100257_T3

description:
Library name: cfRNA_100257_T3
Plasma cfRNA 100257, T3


title: C. rosea, control, rep8, T04 (RD8T04)

description: Library name: RD8T04


title: Invasive Melanoma rep1

description:
Library name: TMA1_005
Invasive and MelA


title: C. rosea, control, rep8, T08 (RD8T08)

description: Library name: RD8T08


title: BMDM, IL-4,48hrs, rep2,R1

description:
Library name: Sample 6
G


title: Invasive Breast rep2

description:
Library name: TMA1_006
Invasive and PanCK


title: C. rosea, control, rep7, T19 (RD7T19)

description: Library name: RD7T19


title: C. rosea, control, rep8, T13 (RD8T13)

description: Library name: RD8T13


title: BMDM, IL-4,48hrs, rep1,R1

description:
Library name: Sample 5
F


title: C. rosea, control, rep7, T04 (RD7T04)

description: Library name: RD7T04


title: BMDM, NT,48hrs, rep4,R1

description:
Library name: Sample 4
E

value: No Treatment


title: BMDM, IL-4+ 1mM CoA,48hrs, rep2,R1

description:
Library name: Sample 10
K


title: cfRNA_100256_T3

description:
Library name: cfRNA_100256_T3
Plasma cfRNA 100256, T3


title: C. rosea, control, rep7, T08 (RD7T08)

description: Library name: RD7T08


title: BMDM, IL-4,48hrs, rep3,R1

description:
Library name: Sample 7
H


title: Invasive Breast rep1

description:
Library name: TMA1_004
Invasive and PanCK


title: cfRNA_100267_T1

description:
Library name: cfRNA_100267_T1
Plasma cfRNA 100267, T1


title: Circumscribed Lung rep2

description:
Library name: TMA1_003
Circumscribed and PanCK


title: cfRNA_100256_T1

description:
Library name: cfRNA_100256_T1
Plasma cfRNA 100256, T1


title: BMDM, NT,48hrs, rep3,R1

description:
Library name: Sample 3
D


title: BMDM, NT,48hrs, rep2,R1

description:
Library name: Sample 2
C


title: cfRNA_100256_T2

description:
Library name: cfRNA_100256_T2
Plasma cfRNA 100256, T2


title: C. rosea, control, rep6, T19 (RD6T19)

description: Library name: RD6T19


title: C. rosea, control, rep6, T08 (RD6T08)

description: Library name: RD6T08


title: C. rosea, control, rep6, T04 (RD6T04)

description: Library name: RD6T04


title: cfRNA_100248_T1

description:
Library name: cfRNA_100248_T1
Plasma cfRNA 100248, T1


title: cfRNA_100248_T3

description:
Library name: cfRNA_100248_T3
Plasma cfRNA 100248, T3


title: HIV LPS, Mouse 9

city: Bronx

first: Harris

last: Goldstein

state: NY

address: 1300 Morris Park Avenue

department: Pediatrics

institute: Albert Einstein College of Medicine

description: Library name: BQ15

data_processing:
Raw FASTQ files were checked for their quality using FastQC (V0.11.8).
Cutadapt (v2.0) was used to remove short or low-quality reads and adapters. Trimmed reads were then aligned to the mouse genome, mm10, using STAR aligner (v2.4.2) with default parameters
The alignment reults were then evaluated through Qualimap (v.2.2.2a) to confirm that all samples had consistent coverage, alignment rate, and no 5' or 3' bias.
The Ensembl gene model was used to count and summarize the uniquely mapped reads that overlap with known exons/features through feature Counts v1.5.0 post3.
The edge library was used in gene expression analysis to filter low expressed reads using CPM and normalize the samples using the TMM method for further analysis.
Voom was used to estimate the differential expression among the biological samples from monocytes isolated from 3 mice for each experimental condition. To lower Type 1 Error Rate and increased confidence, a p-value cutoff of 0.01 (p<0.01) was used to select the unique genes with a significant expression change of > 1.5-fold.
Assembly: mm10
Supplementary files format and content: Tab delimited text file of raw gene counts per samples (column)

source_name: Bone Marrow

extract_protocol:
CD11b monocytes were isolated from mouse bone marrow by immunomagnetic sorting using CD11b microbeads (Miltenyi Biotec). Monocytes were counted and lysed in Buffer RLT Plus. RNA was was extracted from the cell lysate using the RNeasy Micro Kit (QIAGEN) according to the manufacturer's instructions.
Bulk mRNA sequencing analysis using total RNA from each sample (~20 ng) was performed by Novogene (Durham, NC). Sequencing libraries were generated from the RNA (1 ug/sample) using the NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's protocol.

treatment_protocol: Mice were treated either with PBS or LPS (3 mg/kg, i.p.) for 24 hrs before their bone marrow was harvested for further analysis

value: Bone Marrow

value: CD11b+ monocytes

value: JRCCC

value: LPS


title: WT LPS, Mouse 11

description: Library name: BQ11

value: CCC


title: Circumscribed Melanoma rep1

description:
Library name: TMA1_002
Circumscribed and MelA


title: WT LPS Mouse 12

description: Library name: BQ12


title: cfRNA_100248_T2

description:
Library name: cfRNA_100248_T2
Plasma cfRNA 100248, T2

value: plasma

value: cell-free RNA


title: TLE4_KO_1

description: Library name: TLE4_KO_1

data_processing:
Reads were aligned using Bowtie2.2.5, with default parameters, to all RefSeq transcripts (retrieved in january 2016) for most samples, combined with ERCC spike-in sequences for samples represented in read_counts_ERCC_spike-in.txt and to Gencode (V23) transcripts for samples represented in read_counts2.txt. Alignments with fewer than 2 inserted or deleted bases and a maximum edit distance of 5 (i.e. the sum of inserted, deleted, or mismatched bases) were counted to generate read counts per transcript. For samples represented in read_counts1.txt, read counts for transcripts of the same gene wre summed to produce gene-specific read counts.
Assembly: RefSeq transcripts from January 2016 , ERCC spike-in sequences or Gencode V23 transcripts
Supplementary files format and content: All processed data files are tab-delimited text files with each row corresponding to genes, transcripts or ERCC spike-in RNAs and each column to a sample. All contain row and column headers.

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C. 1 million NALM-6 cells (unless otherwise noted) were collected from an exponentially growing culture (800,000 cells per mL).

extract_protocol:
Cell were centrifugated for 5 min at 2,300 x g at 4°C, resuspended in 1 mL TRIzol (Ambion, Life Technologies) and samples processed by the IRIC Genomic platform. In the case of PABIR1 knockout versus wild type cells, cell concentration was measured using a Beckman Z2 Coulter counter in triplicate. ERCC RNA loading control Spike-in mix (Ambion Ref. 4456740) was diluted 1:20 in water and 20 µL per mL spiked in Trizol prior to addition of 1 mL over each cell pellet. Total RNA was isolated using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
RNA was quantified using Qubit (Thermo Scientific) and quality was assessed with the 2100 Bioanalyzer (Agilent Technologies). Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche) using poly-A selection (Thermo Scientific).

treatment_protocol: Specified samples were treated with DMSO 0.1% or 5uM FK-506. Knockout populations were infected with lentivirus infection plus selection,

value: pre-B lymphoid cell line

value: TLE4 knockout

value: No treatment


title: C. rosea, control, rep6, T13 (RD6T13)

description: Library name: RD6T13

value: Leaf


title: Circumscribed Lung rep1

description:
Library name: TMA1_001
Circumscribed and PanCK


title: PBMCs, A.G.-ES-treated

city: Lanzhou

first: Ke

last: Zhou

state: Gansu

address: No. 1 Yingmen Village Gansu Agricultural University

institute: National Natural Science Foundation of China

description:
Library name: b1
Sequenced on GeneMind SURFSeq 5000

data_processing:
Sequencing data were demultiplexed and processed to generate a cell-by-gene UMI count matrix using cell barcodes and UMIs, followed by quality control, normalization, dimensionality reduction, clustering and cell-type annotation.
Assembly: Ovis aries (sheep)
Supplementary files format and content: Processed data are provided as gene-by-cell expression matrices (UMI counts) with accompanying cell-level metadata, including cell barcodes and sample annotations.

organism: Ovis aries

source_name: Peripheral blood

growth_protocol: Not applicable. PBMCs were freshly isolated and processed immediately without in vitro culture.

extract_protocol:
PBMCs were isolated from sheep peripheral blood using HISTOPAQUE 1083 density-gradient separation. The PBMC layer at the interface was collected and washed. Cell number and viability were assessed using a SeekMate Tinitan Fluorescence Cell Counter (SeekGene, M002C) with AO/PI reagent. Debris and dead cells were removed when necessary (Miltenyi, 130-109-398/130-090-101). Cells were resuspended at 1 × 10^6 cells/mL in RPMI 1640 supplemented with 2% FBS for downstream single-cell library preparation.
Single-cell RNA-seq libraries were prepared using the SeekOne DD Single Cell 3’ library preparation kit (SeekGene, K00202) on a SeekOne chip S3 according to the manufacturer’s instructions. Briefly, cells were loaded with reverse transcription reagents, and barcoded hydrogel beads and partitioning oil were used to generate droplets. Reverse transcription was performed to generate barcoded cDNA, followed by droplet breakage, cDNA purification and PCR amplification. Amplified cDNA was then fragmented, end-repaired, A-tailed and ligated to sequencing adapters, and indexed PCR was performed to generate 3’ libraries containing cell barcodes and unique molecular identifiers. Libraries were purified with VAHTS DNA Clean Beads (Vazyme, N411-01) and evaluated using Qubit (Thermo Fisher Scientific, Q33226) and a Bio-Fragment Analyzer (Bioptic, Qsep400).

treatment_protocol: Animals received no treatment or A.G.-ES acupoint embedding at bilateral ST36 prior to blood collection.

value: Peripheral blood

value: PBMCs


title: cfRNA_100217_T3

description:
Library name: cfRNA_100217_T3
Plasma cfRNA 100217, T3


title: cfRNA_100217_T2

description:
Library name: cfRNA_100217_T2
Plasma cfRNA 100217, T2


title: BMDM, NT,48hrs, rep1,R1

description:
Library name: Sample 1
B

value: Primary bone marrow-derived macrophages

value: WT


title: AAVS1

description: Library name: AAVS1

value: wild type


title: Azami_green

description: Library name: Azami_green


title: cfRNA_100217_T1

description:
Library name: cfRNA_100217_T1
Plasma cfRNA 100217, T1


title: cfRNA_100206_T2

description:
Library name: cfRNA_100206_T2
Plasma cfRNA 100206, T2


title: PBMCs, untreated

description:
Library name: a1
Sequenced on GeneMind SURFSeq 5000


title: TLE4_KO_2

description: Library name: TLE4_KO_2


title: K52Q-V5 trehalose biol rep 3

city: Boston

first: Renato

last: Santos

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Library name: k52q_tre3

data_processing:
Adapter sequences and low-quality bases were removed using Trim Galore v0.6.11 (Cutadapt v5.2) with parameters: --quality 20 --length 20 --stringency 3 --paired. All 12 samples retained 100% of read pairs after trimming
Trimmed reads were aligned to the Vibrio cholerae N16961 reference genome (NC_002505.1 and NC_002506.1) using HISAT2 v2.2.2 with parameters: --rna-strandness RF --no-spliced-alignment --no-unal --dta. BAM files were sorted and indexed using SAMtools v1.23. All samples achieved ≥97% overall alignment rate.
Read counting was performed using featureCounts v2.1.1 (Subread) with parameters: -t gene -g locus_tag -p --countReadPairs --fracOverlap 0.2 -s 2 (sense) and -s 1 (antisense). The annotation encompassed 3,612 gene features across both chromosomes.
Differential expression analysis was performed using DESeq2 in R. Design formula: ~condition (CRP_maltose, K52Q_maltose, CRP_trehalose, K52Q_trehalose). Pre-filtering: genes with ≥10 counts in at least 3 samples. Four pairwise contrasts were computed. DEGs were defined as |log2FC| > 1 and padj < 0.05 (Benjamini-Hochberg).
Quality assessment of raw and trimmed reads was performed with FastQC v0.12.1 and aggregated with MultiQC v1.33.
Assembly: Vibrio cholerae O1 biovar El Tor str. N16961: NC_002505.1 (Chromosome I) and NC_002506.1 (Chromosome II)
Supplementary files format and content: Tab-separated DESeq2 results tables containing log2 fold change, standard error, Wald statistic, p-value, and adjusted p-value for each pairwise contrast.

organism: Vibrio cholerae C6706

source_name: planktonic

growth_protocol: Vibrio cholerae C6706 strains carrying chromosomally integrated CRP-V5 or K52Q-V5 were grown overnight in LB medium at 27°C with shaking at 200 rpm. Overnight cultures were washed and resuspended in M9 minimal medium supplemented with 0.8% maltose or 0.8% trehalose as the sole carbon source, then cultivated for approximately 3 hours at 27°C with shaking at 200 rpm to mid-exponential phase

extract_protocol:
Direct-zol RNA Miniprep Plus Kit following manufacturer's instructions
Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10 bp unique dual indices (UDI). The kit employs dUTP incorporation during second-strand cDNA synthesis to confer strand specificity, producing RF-oriented paired-end reads. Sequencing was performed on an Illumina NovaSeq X Plus generating paired-end 150 bp reads. Demultiplexing, quality control, and adapter trimming were performed with bcl-convert v4.2.4

treatment_protocol: Not applicable. Genotype and carbon source conditions are described in the growth protocol

value: planktonic


title: HIV LPS, Mouse 8

description: Library name: BQ13

value: Bone Marrow


title: PFI-3 10uM Round-03 (exp144)

description:
Library name: PFI-3 10uM_Round-03 (exp144)
sgRNAs PCR-amplified from genomic DNA

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
For each round (batch of simultaneously-run screens), read counts for all control samples (untreated, DMSO 0.1%-0.3% or ethanol 0.1%-0.3% treated) were summed together. Read counts for samples that were grown together for part of the 8 days of the screen were also summed together so that each sample represented in the processed data files is independent in terms of genetic drift.
Assembly: sgRNAs from the Extended knock-out (EKO) library (Bertomeu et al. 2017).
Supplementary files format and content: sgrna_read_counts_refseq_genes.txt : sgRNA read counts for controls and each independent screen  (sequenced sample experiment numbers are indicated in the colunm headers), targeted refSeq gene symbols (January 2016) and updated HGNC gene symbols (2020).
Supplementary files format and content: sgrna_read_counts_exons_and_hypothetical_genes.txt : sgRNA read counts for controls and each independent screen  (sequenced sample experiment numbers are indicated in the colunm headers), targeted exons (hg19 coordinates) and hypothetical genes (AceView or Gencode symbols).
Library strategy: CRISPR Screen

value: PFI-3 10uM


title: HIV LPS, Mouse 7

description: Library name: BQ14

value: CD11b+ monocytes

value: JRCCC


title: K52Q-V5 trehalose biol rep 2

description: Library name: k52q_tre2


title: K52Q-V5 trehalose biol rep 1

description: Library name: k52q_tre1


title: HIV, Mouse 6

description: Library name: BQ6

value: PBS


title: Actinomycin D 10nM Round-00 (exp4)

description:
Library name: Actinomycin D 10nM_Round-00 (exp4)
sgRNAs PCR-amplified from genomic DNA

value: Actinomycin D 10nM


title: cfRNA_100206_T1

description:
Library name: cfRNA_100206_T1
Plasma cfRNA 100206, T1

value: plasma

value: cell-free RNA


title: HIV, Mouse 5

description: Library name: BQ4


title: cfRNA_100200_T3

description:
Library name: cfRNA_100200_T3
Plasma cfRNA 100200, T3


title: cfRNA_100306_T3

description:
Library name: cfRNA_100306_T3
Plasma cfRNA 100306, T3


title: CRP-V5 trehalose biol rep 3

description: Library name: crp_tre3


title: UNC1999 2uM Round-03 (exp155)

description:
Library name: UNC1999 2uM_Round-03 (exp155)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: UNC1999 2uM


title: Nifuroxazide 1uM Round-01 (exp51)

description:
Library name: Nifuroxazide 1uM_Round-01 (exp51)
sgRNAs PCR-amplified from genomic DNA

value: Nifuroxazide 1uM


title: cfRNA_100200_T2

description:
Library name: cfRNA_100200_T2
Plasma cfRNA 100200, T2


title: cfRNA_100206_T3

description:
Library name: cfRNA_100206_T3
Plasma cfRNA 100206, T3


title: WT LPS, Mouse 10

description: Library name: BQ10

value: CCC

value: LPS


title: WT, Mouse 1

description: Library name: BQ1


title: CRP-V5 trehalose biol rep 1

description: Library name: crp_tre1


title: NFN1 1uM Round-03 (exp100)

description:
Library name: NFN1 1uM_Round-03 (exp100)
sgRNAs PCR-amplified from genomic DNA

value: NFN1 1uM


title: WT, Mouse 2

description: Library name: BQ2


title: cfRNA_100200_T1

description:
Library name: cfRNA_100200_T1
Plasma cfRNA 100200, T1


title: K52Q-V5 maltose biol rep 3

description: Library name: k52q_mal3


title: cfRNA_100306_T2

description:
Library name: cfRNA_100306_T2
Plasma cfRNA 100306, T2


title: CRP-V5 trehalose biol rep 2

description: Library name: crp_tre2


title: K52Q-V5 maltose biol rep 1

description: Library name: k52q_mal1


title: HIV, Mouse 4

description: Library name: BQ5


title: WT, Mouse 3

description: Library name: BQ3


title: Rifampicin 10uM Round-00 (exp32)

description:
Library name: Rifampicin 10uM_Round-00 (exp32)
sgRNAs PCR-amplified from genomic DNA

value: Rifampicin 10uM


title: S06858

first: Katy

last: Trampel

state: Illinois

address: 303 East Superior Street

description:
Library name: S06858
Column Name in All Samples Counts.csv: S06858.genes

data_processing:
Expected counts were calculated using RSEM v.1.3.0.
Assembly: Assembly: GRCm39
Supplementary files format and content: csv file containing combined read counts
Supplementary files format and content: .bam files containing aligned sequences

source_name: Heart

extract_protocol:
Hearts were fixed in RNA later and shipped to Genewiz by Azenta Life Sciences for RNA sequencing. RNA libraries were prepared by Genewiz by Azenta Lifesciences.
Reads were aligned to the Mus musculus GRCm39 reference genome available on GENCODE using STAR aligner v.2.5.2, and BAM files were generated.

value: Heart

value: p38delta knockout

value: 30 mg/kg Doxorubicin


title: JQ1 10nM Round-03 (exp130)

description:
Library name: JQ1 10nM_Round-03 (exp130)
sgRNAs PCR-amplified from genomic DNA

extract_protocol:
genomic DNA extracted using the Gentra Puregene kit according to the manufacturer’s instructions (QIAGEN), and sgRNA sequences were PCR-amplified
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices followed by SPRI beads purification of sequencing-ready amplicons.

value: JQ1 10nM


title: CRP-V5 maltose biol rep 3

description: Library name: crp_mal3

value: planktonic


title: Ribavirin 10uM Round-01 (exp52)

description:
Library name: Ribavirin 10uM_Round-01 (exp52)
sgRNAs PCR-amplified from genomic DNA

value: Ribavirin 10uM


title: S06857

description:
Library name: S06857
Column Name in All Samples Counts.csv: S06857.genes


title: K52Q-V5 maltose biol rep 2

description: Library name: k52q_mal2


title: cfRNA_100261_T3

description:
Library name: cfRNA_100261_T3
Plasma cfRNA 100261, T3


title: CRP-V5 maltose biol rep 1

description: Library name: crp_mal1


title: TRAIL 50ng/mL Round-00 (exp36)

description:
Library name: TRAIL 50ng/mL_Round-00 (exp36)
sgRNAs PCR-amplified from genomic DNA

value: TRAIL 50ng/mL


title: cfRNA_100306_T1

description:
Library name: cfRNA_100306_T1
Plasma cfRNA 100306, T1


title: S06808

description:
Library name: S06808
Column Name in All Samples Counts.csv: S06808.genes


title: CRP-V5 maltose biol rep 2

description: Library name: crp_mal2


title: S06846

description:
Library name: S06846
Column Name in All Samples Counts.csv: S06846.genes


title: cfRNA_100255_T3

description:
Library name: cfRNA_100255_T3
Plasma cfRNA 100255, T3


title: Rotenone 2uM Round-00 (exp33)

description:
Library name: Rotenone 2uM_Round-00 (exp33)
sgRNAs PCR-amplified from genomic DNA

value: Rotenone 2uM


title: Spinner flask No treatment Day 0 Round-00 (exp0)

description:
Library name: SF No treatment D0_Round-00 (exp0)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: cfRNA_100261_T1

description:
Library name: cfRNA_100261_T1
Plasma cfRNA 100261, T1

value: plasma

value: cell-free RNA


title: (R)-(+)-1,1'-Binaphthyl-2,2'-diamine 10uM (S)-(-)-1,1'-Binaphthyl-2,2'-diamine 10uM Round-03 (exp93)

description:
Library name: (R)-(+)-1,1_-Binaphthyl-2,2_-diamine 10uM_(S)-(-)-1,1_-Binaphthyl-2,2_-diamine 10uM_Round-03 (exp93)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: DOXF5

description:
Library name: DOXF5
Column Name in All Samples Counts.csv: DOXF5.genes

value: WT


title: DOXF2

description:
Library name: DOXF2
Column Name in All Samples Counts.csv: DOXF2.genes


title: DOXF3

description:
Library name: DOXF3
Column Name in All Samples Counts.csv: DOXF3.genes


title: 2-Methoxyestradiol 200nM Round-01 (exp40)

description:
Library name: 2-Methoxyestradiol 200nM_Round-01 (exp40)
sgRNAs PCR-amplified from genomic DNA

value: 2-Methoxyestradiol 200nM


title: cfRNA_100261_T2

description:
Library name: cfRNA_100261_T2
Plasma cfRNA 100261, T2


title: cfRNA_100255_T2

description:
Library name: cfRNA_100255_T2
Plasma cfRNA 100255, T2


title: cfRNA_100255_T1

description:
Library name: cfRNA_100255_T1
Plasma cfRNA 100255, T1


title: DOXF4

description:
Library name: DOXF4
Column Name in All Samples Counts.csv: DOXF4.genes


title: S06807

description:
Library name: S06807
Column Name in All Samples Counts.csv: S06807.genes


title: cfRNA_100177_T2

description:
Library name: cfRNA_100177_T2
Plasma cfRNA100177, T2


title: SB203580 25uM Round-03 (exp149)

description:
Library name: SB203580 25uM_Round-03 (exp149)
sgRNAs PCR-amplified from genomic DNA


title: cfRNA_100177_T3

description:
Library name: cfRNA_100177_T3
Plasma cfRNA100177, T3


title: Isonicotinamide 500uM Round-03 (exp129)

description:
Library name: Isonicotinamide 500uM_Round-03 (exp129)
sgRNAs PCR-amplified from genomic DNA

value: Isonicotinamide 500uM


title: A-366 10uM Round-03 (exp115)

description:
Library name: A-366 10uM_Round-03 (exp115)
sgRNAs PCR-amplified from genomic DNA


title: A-196 10uM Round-03 (exp114)

description:
Library name: A-196 10uM_Round-03 (exp114)
sgRNAs PCR-amplified from genomic DNA


title: DOXF1

description:
Library name: DOXF1
Column Name in All Samples Counts.csv: DOXF1.genes


title: MPNST patient 8, sample 4

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: Gene expression estimates as RMA values on log2-scale

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip Human Transcriptome 2.0 Arrays (HTA 2.0) according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing:
Gene level expression values were estimated according to the robust multi-array average (RMA) approach implemented with the justRMA function in the R package affy and using custom CDF files from Brainarray (hta20_Hs_ENTREZG_25.0.0).
hta20_Hs_ENTREZG.cdf
hta20_Hs_ENTREZG_desc.txt

label: Biotin

source_name: Patient with advanced MPNSTs

label_protocol: 100 ng total RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from fresh frozen tumor tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

tag: patient

tag: tumor

value: MPNST

tag: sampling

value: Biopsy


title: MPNST patient 8, sample 3

value: Metastasis, back of head

value: Surgical specimen


title: Pimelic Diphenylamide 106 500nM Round-00 (exp27)

first: Micheal

last: Tyers

address: 555 University Avenue

description:
Library name: Pimelic Diphenylamide 106 500nM_Round-00 (exp27)
sgRNAs PCR-amplified from genomic DNA

tag: cell line

tag: cell type

value: Pimelic Diphenylamide 106 500nM


title: MPNST patient 7, sample 1


title: MPNST patient 5, sample 1


title: MPNST patient 8, sample 2

value: Metastasis, scalp


title: Spinner flask No treatment Day 4 Round-03 (exp575)

description:
Library name: SF No treatment D4_Round-03 (exp575)
sgRNAs PCR-amplified from genomic DNA

tag: treatment

tag: batch


title: IL-33 prime, rep 2

description: Library name: Sample4

data_processing:
Raw reads were quality-filtered using fastp (v0.20.0) to remove adaptor sequences, low-quality reads. Clean reads were aligned to the reference genome using BWA (v0.7.12), and reads mapping to mitochondrial or chloroplast DNA were discarded. Only uniquely mapped, properly paired reads with MAPQ ≥13, were retained for downstream analysis.
Peak calling was performed using MACS2 (v2.2.7.1). Peaks were normalized to a fixed width of 500 bp centered on the summit. Motif analysis was conducted using HOMER (v4.11). Genomic annotation and nearest gene identification were performed using ChIPseeker. Differentially accessible peaks between groups were identified by merging peaks with bedtools and comparing mean RPM values.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include RPM values for samples

source_name: Peritoneal cells derived mast cells

growth_protocol: The peritoneal lavage fluid was collected after euthanasia and cultured in RPMI 1640 medium (Sigma) supplemented with 10 ng/ml IL-3 (Sino Biological), 30 ng/ml SCF (Sino Biological), 10% FBS, Penicillin-Streptomycin. The medium was changed every 3-4 days, and after 10 days, flow cytometry was employed to determine the maturation rate of peritoneal cell-derived mast cells (>98%).

extract_protocol:
50,000 live PCMCs were lysed and processed to isolate nuclei, followed by transposition with Tn5 transposase at 37 °C for 30 minutes.
Equimolar adaptors were ligated, and libraries were amplified by PCR using the ATAC-seq_Novogene Kit (Novogene). Libraries were purified with AMPure beads and quantified using Qubit. Sequencing was performed on the Illumina NovaSeq platform generating 150bp paired-end reads.

treatment_protocol: PCMCs were primed with 200 ng/ml IL-33 (PeproTech) for 24 h, followed by ATAC sequencing analysis.

value: Peritoneal cells derived mast cells

value: IL-33 prime


title: cfRNA_100137_T3

description:
Library name: cfRNA_100137_T3
Plasma cfRNA 100137, T3

tag: tissue


title: cfRNA_100008_T3

description:
Library name: cfRNA_100008_T3
Plasma cfRNA 100008, T3


title: MPNST patient 8, sample 1

value: Metastasis, soft-tissue


title: cfRNA_100177_T1

description:
Library name: cfRNA_100177_T1
Plasma cfRNA100177, T1


title: IL-33 prime, rep 1

description: Library name: Sample3


title: MPNST patient 3, sample 2


title: cfRNA_100137_T1

description:
Library name: cfRNA_100137_T1
Plasma cfRNA 100137, T1


title: WT_mESC_UNC0638_48h_rep2

description: Library name: Sample 36

value: mouse embryonic stem cell

tag: genotype


title: cfRNA_100137_T2

description:
Library name: cfRNA_100137_T2
Plasma cfRNA 100137, T2


title: No prime, rep 1

description: Library name: Sample1

value: No prime


title: hPA, Donor 2, perturb-seq

city: Durham

first: Samuel

last: Reisman

state: NC

address: 1328 Campus Drive

institute: Duke University

description:
Library name: hPA, Donor 2, perturb-seq
10x Genomics

data_processing:
Demultiplexing and unique molecular identifier (UMI) count generation for each transcript and gRNA per cell barcode was performed using CellRanger v6.0.1 (10x Genomics). UMI counts tables were extracted and used for subsequent analyses in R using Seurat v4.1.0 and normalized with sctransform. High-quality cells across donors were aggregated for further analyses. gRNA assignment: gRNAs were assigned to cells using CLEANSER. Cells were then grouped for differential expression analysis using MAST based on gRNA assignments. A stringent threshold for gRNA-hit counts was applied to ensure all cells had received gRNA-hit, and all cells below the threshold were excluded from downstream analysis.
Assembly: hg38
Supplementary files format and content: .tsv feature, barcode, and matrix files

source_name: astrocyte

growth_protocol: Primary human astrocytes derived from the fetal cerebral cortex were purchased (Sciencell 1800) and routine cell culture was performed following the supplier’s protocol. Upon thawing, cells were seeded on plates coated with poly-D-lysine (PDL), and grown in Astrocyte Medium (Sciencell 1801) supplemented to 10% fetal bovine serum (Gibco) to encourage proliferation. Culture medium was replaced every two days until cultures reached 70% confluence, and subsequently every three days until cultures reached 95% confluence. To passage, cells were rinsed with PBS and dissociated using 0.025% trypsin. To eliminate residual potential progenitor cells and non-proliferative neuronal cells, astrocytes expanded for two passages. All experiments were initiated upon replating after the second passage reached confluence. Astrocytes were subjected to freeze/thaw cycles.

extract_protocol:
Paired screen gRNA library was delivered at MOI = 0.3 alongside gRNA-hit (MOI = 3) with Thy1.1 in place of the puromycin resistance cassette. Ten days after transduction, cells were collected for processing.
Cells were collected and gRNA and gene expression libraries were prepared using the 10X High-throughput kit with 5’ gRNA Direct Capture (10x Genomics) according to manufacturer protocol and sequenced on an Illumina Novaseq.

treatment_protocol: Primary human astrocytes were cultured as described above until the second passage reached confluence. Cells were then dissociated, counted, and transduced by plating at 9 x 10⁴ cells/cm² in fresh Astrocyte Medium containing packaged lentivirus encoding CRISPRa machinery, ORF, or shRNA. The day of transduction was designated as day 0. On day 1, medium was replaced with fresh astrocyte medium without lentivirus. Beginning on day 2, 1 µg/mL puromycin (Thermo Fisher) was added to all medium changes through day 6 to select for transduced cells. To support the survival of diverse neural cell states, culture medium was switched to a basal co-culture formulation on day 3 consisting of DMEM/F12 supplemented with 0.5% FBS, 1x N-2, 3.5 mM glucose, and 100 U/mL penicillin-streptomycin (all from Gibco). On day 8, the co-culture medium was supplemented with 20 ng/mL BDNF and 10 ng/mL NT-3 (Peprotech). Unless otherwise noted, all cell culture media was refreshed every 48 hours. Unless otherwise noted, cells were collected for analysis on day 10.

value: astrocyte

value: perturb-seq library

value: neronal reprogramming


title: Brain, WT, 7 months, Male, ZT6, rep2

city: La Jolla

first: Paula

last: Desplats

address: 9500 Gilman Dr. MTF346 MC0624

department: Department of Neuroscience and  Department of Pathology

institute: University California San Diego

description: Fresh frozen spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to a custom mm10 genome with the human APP transgene gene added.
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: Brain

extract_protocol:
Brain hemispheres collected and placed in OCT and then flash frozen in isopentane in liquid nitrogen. One hemibrain from each mouse was cryosectioned at -18°C sagittally to a thickness of 10 mm.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Brain

value: WT

value: 7 months

tag: Sex

value: Male

tag: zeitgeber time


title: No prime, rep 2

description: Library name: Sample2


title: cfRNA_100008_T2

description:
Library name: cfRNA_100008_T2
Plasma cfRNA 100008, T2

value: plasma

value: cell-free RNA


title: Nicotinamide Riboside 100uM Round-03 (exp139)

institute: The Hospital for Sick Children

description:
Library name: Nicotinamide Riboside 100uM_Round-03 (exp139)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Nicotinamide Riboside 100uM


title: cfRNA_100008_T1

description:
Library name: cfRNA_100008_T1
Plasma cfRNA 100008, T1


title: Brain, WT, 7 months, Male, ZT6, rep1

tag: age


title: MPNST patient 3, sample 4

value: MPNST

value: Surgical specimen1


title: Bortezomib 50nM Round-00 (exp7)

description:
Library name: Bortezomib 50nM_Round-00 (exp7)
sgRNAs PCR-amplified from genomic DNA

value: Bortezomib 50nM


title: MPNST patient 4, sample 1

value: Metastasis, liver

value: Biopsy


title: WT_mESC_DMSO_48h_rep2

description: Library name: Sample 34

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7). Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) by STAR (v2.7.10a) or Bowtie2 (v2.4.5). The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawcounts and bigWig files for GRO-seq

extract_protocol:
For bulk RNA library construction, total RNA was extracted following the standard TRIzol protocol (invitrogen); For GRO-seq library construction, RNAs are hydrolyzed and purified using beads coated with antibodies to 5-bromo-2-deoxyuridine (BrdU).
RNA libraries for RNA-seq were prepared using AHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer’s protocols; RNA libraries for GRO-seq using AccuNext Small RNA-seq Library Kit for Illumina (Accurate Biology) following manufacturer’s protocols.

value: mouse embryonic stem cell

value: DMSO


title: MPNST patient 3, sample 3


title: GSK-LSD1 10uM Round-03 (exp123)

description:
Library name: GSK-LSD1 10uM_Round-03 (exp123)
sgRNAs PCR-amplified from genomic DNA

value: GSK-LSD1 10uM


title: WT_mESC_UNC0638_48h_rep1

description: Library name: Sample 35


title: MPNST patient 6, sample 1

value: Metastasis


title: Rapamycin 10uM Round-00 (exp30)

description:
Library name: Rapamycin 10uM_Round-00 (exp30)
sgRNAs PCR-amplified from genomic DNA

value: Rapamycin 10uM


title: YM155 0.2nM Round-01 (exp61)

description:
Library name: YM155 0.2nM_Round-01 (exp61)
sgRNAs PCR-amplified from genomic DNA


title: Brain, WT, 7 months, Male, ZT18, rep1

value: Brain

value: WT


title: Brain, WT, 7 months, Male, ZT12, rep1

value: 7 months

value: Male


title: MPNST patient 1, sample 1

description: Gene expression estimates as RMA values on log2-scale

value: Surgical specimen


title: Rapamycin 1uM Round-00 (exp29)

description:
Library name: Rapamycin 1uM_Round-00 (exp29)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Rapamycin 1uM


title: KU-0063794 3.8uM Round-02 (exp71)

description:
Library name: KU-0063794 3.8uM_Round-02 (exp71)
sgRNAs PCR-amplified from genomic DNA


title: WT_mESC_UNC0638_7days_rep2

description: Library name: Sample 32


title: hPA, Donor 2, perturb-seq, CRISPR

description:
Library name: hPA, Donor 2, perturb-seq, CRISPR
10x Genomics

value: astrocyte

value: perturb-seq library

value: neronal reprogramming


title: hPA, Donor 1, perturb-seq

description:
Library name: hPA, Donor 1, perturb-seq
10x Genomics


title: Brain, WT, 7 months, Male, ZT0, rep2


title: Brain, WT, 7 months, Male, ZT12, rep2


title: MPNST patient 3, sample 1

value: Recurrence, MPNST


title: Spinner flask No treatment Day 2 Round-03 (exp574)

description:
Library name: SF No treatment D2_Round-03 (exp574)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: hPA, Donor 1, perturb-seq, CRISPR

description:
Library name: hPA, Donor 1, perturb-seq, CRISPR
10x Genomics


title: Brain, WT, 7 months, Male, ZT0, rep1


title: Nocodazole 100nM Round-03 (exp94)

description:
Library name: Nocodazole 100nM_Round-03 (exp94)
sgRNAs PCR-amplified from genomic DNA

value: Nocodazole 100nM


title: Brain, WT, 7 months, Male, ZT18, rep2


title: Rifampicin 1uM Round-00 (exp31)

description:
Library name: Rifampicin 1uM_Round-00 (exp31)
sgRNAs PCR-amplified from genomic DNA

value: Rifampicin 1uM


title: WT_mESC_DMSO_7days_rep1

description: Library name: Sample 29

value: mouse embryonic stem cell

value: DMSO


title: Docetaxel 2nM Round-01 (exp45)

description:
Library name: Docetaxel 2nM_Round-01 (exp45)
sgRNAs PCR-amplified from genomic DNA

value: Docetaxel 2nM


title: Metformin 40uM Round-03 (exp132)

description:
Library name: Metformin 40uM_Round-03 (exp132)
sgRNAs PCR-amplified from genomic DNA

value: Metformin 40uM


title: WT_mESC_DMSO_48h_rep1

description: Library name: Sample 33

value: WT


title: WT_mESC_UNC0638_7days_rep1

description: Library name: Sample 31


title: Brain, WT, 7 months, Female, ZT6, rep2

description: Fresh frozen spatial transcriptomics sequencing

value: Brain

value: 7 months

value: Female


title: REDDIT_mESC_Ctrl_rep2

description: Library name: Sample 14

value: mCherry-TAG-GFP


title: astrocyte, hPA, gRNA 194, Day10, rep 3

description:
Library name: Sample 15
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNA194_rep3

data_processing:
Raw FASTQ reads were trimmed with Trimmomatic v0.32 and aligned to the GRCh38 reference genome using the STAR RNA-seq aligner v2.4.1a. Gene-level counts were generated with featureCounts from the Subread package v1.4.6-p4, using Gencode v22 for transcript annotation
Assembly: hg38
Supplementary files format and content: csv file including raw counts for each sample

extract_protocol:
Total RNA was isolated using a Total RNA Purification Plus Kit or Total RNA Purification Plus Micro Kit (Norgen).
Total RNA was submitted to Azenta for standard RNA-seq with poly(A) selection and ERCC spike-in controls

value: gRNA 194


title: astrocyte, hPA, gRNA 113, Day10, rep 3

description:
Library name: Sample 9
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNA113_rep3

value: astrocyte

value: gRNA 113


title: WT_mESC_DMSO_7days_rep2

description: Library name: Sample 30


title: astrocyte, hPA, gRNA 194, Day10, rep 1

description:
Library name: Sample 13
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNA194_rep1

value: neronal reprogramming


title: astrocyte, hPA, gRNA 155, Day10, rep 3

description:
Library name: Sample 12
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNA155_rep3

value: gRNA 155


title: Brain, WT, 7 months, Female, ZT12, rep3


title: Etoposide 10uM Round-00 (exp20)

description:
Library name: Etoposide 10uM_Round-00 (exp20)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Etoposide 10uM


title: astrocyte, hPA, gRNA 113, Day10, rep 2

description:
Library name: Sample 8
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNA113_rep2


title: Brain, WT, 7 months, Female, ZT6, rep1


title: astrocyte, hPA, gRNA 194, Day10, rep 2

description:
Library name: Sample 14
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNA194_rep2


title: REDDIT_Lncenc1_rep1

description: Library name: Sample 15


title: 1-Methylnicotinamide chloride 1000uM Round-03 (exp113)

description:
Library name: 1-Methylnicotinamide chloride 1000uM_Round-03 (exp113)
sgRNAs PCR-amplified from genomic DNA

value: 1-Methylnicotinamide chloride 1000uM


title: Brain, WT, 7 months, Female, ZT18, rep1


title: astrocyte, hPA, gRNA 155, Day10, rep 1

description:
Library name: Sample 10
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNA155_rep1


title: GSK591 2.6uM Round-03 (exp128)

description:
Library name: GSK591 2.6uM_Round-03 (exp128)
sgRNAs PCR-amplified from genomic DNA


title: Brain, WT, 7 months, Female, ZT18, rep2


title: REDDIT_mESC_Ctrl_rep1

description: Library name: Sample 13

value: mouse embryonic stem cell


title: REDDIT_Lncenc1_rep2

description: Library name: Sample 16


title: astrocyte, hPA, gRNA 155, Day10, rep 2

description:
Library name: Sample 11
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNA155_rep2


title: astrocyte, hPA, gRNA 113, Day10, rep 1

description:
Library name: Sample 7
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNA113_rep1


title: Chloramphenicol 2uM Round-00 (exp12)

description:
Library name: Chloramphenicol 2uM_Round-00 (exp12)
sgRNAs PCR-amplified from genomic DNA

value: Chloramphenicol 2uM


title: Peritoneal mast cells, KI, rep 2

description: Library name: Sample5

data_processing:
The sequencing data was filtered with SOAPnuke.
The clean reads were mapped to the reference genome using HISAT.
Bowtie2 was applied to align the clean reads to the gene set.
Expression level of gene was calculated by RSEM.
Differential expression analysis was performed using the DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include TPM values for samples

source_name: Peritoneal mast cells

extract_protocol:
Isolated cell samples were lysed using the Discover-sc WTA Kit V2.
Libraries were constructed using the Discover-sc WTA Kit V2.

value: Peritoneal mast cells


title: Brain, WT, 7 months, Female, ZT0, rep2


title: Spinner flask No treatment Day 0 Round-01 (exp556)

description:
Library name: SF No treatment D0_Round-01 (exp556)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Brain, WT, 7 months, Female, ZT12, rep1

value: WT


title: Peritoneal mast cells, KI, rep 3

description: Library name: Sample6


title: Brain, WT, 7 months, Female, ZT12, rep2

value: Brain


title: astrocyte, hPA, non-targeting, Day10, rep 2

description:
Library name: Sample 5
Column name in FOXO4_gRNAs_RNAseq_counts.csv: NT_rep2

value: non-targeting


title: No treatment Round-01 (exp62)

description:
Library name: Ctl No treatment D8_Round-01 (exp62)
sgRNAs PCR-amplified from genomic DNA


title: astrocyte, hPA, non-targeting, Day10, rep 1

description:
Library name: Sample 4
Column name in FOXO4_gRNAs_RNAseq_counts.csv: NT_rep1


title: Spinner flask No treatment Day 4 Round-02 (exp566)

description:
Library name: SF No treatment D4_Round-02 (exp566)
sgRNAs PCR-amplified from genomic DNA


title: astrocyte, hPA, gRNA-hit, Day10, rep 3

description:
Library name: Sample 3
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNAhit_rep3

value: gRNA-hit


title: DMSO 0.1% Round-02 (exp91)

description:
Library name: Ctl DMSO 0.1_ D8_Round-02 (exp91)
sgRNAs PCR-amplified from genomic DNA

value: DMSO 0.1%


title: astrocyte, hPA, non-targeting, Day10, rep 3

description:
Library name: Sample 6
Column name in FOXO4_gRNAs_RNAseq_counts.csv: NT_rep3


title: Peritoneal mast cells, WT, rep 3

description: Library name: Sample3


title: Brain, WT, 14 months, Male, ZT6, rep1

description: Fresh frozen spatial transcriptomics sequencing

value: 14 months

value: Male


title: Peritoneal mast cells, WT, rep 2

description: Library name: Sample2


title: Brain, WT, 7 months, Female, ZT0, rep1

value: 7 months

value: Female


title: Carbonyl cyanide 3-chlorophenylhydrazone 1uM Round-00 (exp11)

description:
Library name: Carbonyl cyanide 3-chlorophenylhydrazone 1uM_Round-00 (exp11)
sgRNAs PCR-amplified from genomic DNA


title: astrocyte, hPA, gRNA-hit, Day10, rep 2

description:
Library name: Sample 2
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNAhit_rep2

value: astrocyte

value: neronal reprogramming


title: OICR-9429 10uM Round-03 (exp142)

description:
Library name: OICR-9429 10uM_Round-03 (exp142)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: GSK343 3uM Round-03 (exp124)

description:
Library name: GSK343 3uM_Round-03 (exp124)
sgRNAs PCR-amplified from genomic DNA

value: GSK343 3uM


title: Meningeal mast cells, KO, Day6, rep 2

description: Library name: Sample23

source_name: Meningeal mast cells

value: Meningeal mast cells

value: 6 days post infection


title: astrocyte, hPA, gRNA-hit, Day10, rep 1

description:
Library name: Sample 1
Column name in FOXO4_gRNAs_RNAseq_counts.csv: gRNAhit_rep1


title: Meningeal mast cells, KO, Day6, rep 3

description: Library name: Sample24


title: Brain, WT, 14 months, Male, ZT18, rep1


title: hPA, non-targeting, Day10, rep3

description:
Library name: Sample 6
Column name in gRNAhit_RNA-seq_counts.csv: NT_3


title: Peritoneal mast cells, KI, rep 1

description: Library name: Sample4

value: Peritoneal mast cells


title: Brain, WT, 14 months, Male, ZT12, rep2


title: Peritoneal mast cells, WT, rep 1

description: Library name: Sample1


title: Doxycycline 10uM Round-00 (exp18)

description:
Library name: Doxycycline 10uM_Round-00 (exp18)
sgRNAs PCR-amplified from genomic DNA

value: Doxycycline 10uM


title: Brain, WT, 14 months, Male, ZT18, rep2

value: WT


title: Meningeal mast cells, KO, Day6, rep 1

description: Library name: Sample22


title: Brain, WT, 14 months, Male, ZT6, rep2

value: Brain


title: hPA, non-targeting, Day10, rep1

description:
Library name: Sample 4
Column name in gRNAhit_RNA-seq_counts.csv: NT_1

value: non-targeting


title: 5-Fluorouracil 2uM Round-00 (exp1)

description:
Library name: 5-Fluorouracil 2uM_Round-00 (exp1)
sgRNAs PCR-amplified from genomic DNA

value: 5-Fluorouracil 2uM


title: hPA, non-targeting, Day10, rep2

description:
Library name: Sample 5
Column name in gRNAhit_RNA-seq_counts.csv: NT_2


title: Spinner flask No treatment Day 0 Round-03 (exp573)

description:
Library name: SF No treatment D0_Round-03 (exp573)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Meningeal mast cells, WT, Day6, rep 3

description: Library name: Sample21


title: Vinblastine 200nM Round-03 (exp108)

description:
Library name: Vinblastine 200nM_Round-03 (exp108)
sgRNAs PCR-amplified from genomic DNA

value: Vinblastine 200nM


title: Brain, WT, 14 months, Female, ZT6, rep2

value: 14 months


title: Meningeal mast cells, WT, Day6, rep 2

description: Library name: Sample20


title: HMS-I1 1uM Round-01 (exp46)

description:
Library name: HMS-I1 1uM_Round-01 (exp46)
sgRNAs PCR-amplified from genomic DNA

value: HMS-I1 1uM


title: Brain, WT, 14 months, Male, ZT12, rep1

value: Male


title: hPA, gRNA-hit, Day10, rep 3

description:
Library name: Sample 3
Column name in gRNAhit_RNA-seq_counts.csv: gRNAhit_3

value: astrocyte

value: gRNA-hit


title: Brain, WT, 14 months, Female, ZT6, rep1

value: Female


title: Meningeal mast cells, WT, Day6, rep 1

description: Library name: Sample19


title: Brain, WT, 14 months, Male, ZT0, rep1


title: hPA, gRNA-hit, Day10, rep 1

description:
Library name: Sample 1
Column name in gRNAhit_RNA-seq_counts.csv: gRNAhit_1

value: neronal reprogramming


title: Paclitaxel 2nM Round-01 (exp54)

description:
Library name: Paclitaxel 2nM_Round-01 (exp54)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Paclitaxel 2nM


title: Meningeal mast cells, KO, Day5, rep 3

description: Library name: Sample18

value: Meningeal mast cells

value: 5 days post infection


title: Prochlorperazine 5.2uM Round-02 (exp77)

description:
Library name: Prochlorperazine 5.2uM_Round-02 (exp77)
sgRNAs PCR-amplified from genomic DNA

value: Prochlorperazine 5.2uM


title: Brain, WT, 14 months, Female, ZT18, rep3

description: Fresh frozen spatial transcriptomics sequencing

value: Brain

value: WT


title: Hep G2 cells, TRIB3 sh2_Rep_03

city: Zhengzhou

first: QIang

last: Ji

state: Henan

address: Jinshui Rd

department: Translational Research Institute

institute: Henan People's Hospital

description:
Library name: TRIB3_sh2_3
Column name in FPKM_anno_TRIB3_knockdown.xls: sh2-3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.  The clean  reads were mapped to the GRCh38 using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCh38
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: Liver

growth_protocol: Hep G2 cells were maintained in DMEM high glucose supplemented with 10% fetal bovine serum (FBS) and antiviotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: For the TRIB3 knockdown experiment, Hep G2 cells were infected with lentivirus carrying either Control shRNA, TRIB3 sh1, or TRIB3 sh2. After 48 hours of infection, cells were selected with puromycin for another 48 hours.

value: Liver

value: Hep G2

value: tumor cells

value: lentivirus infected


title: Meningeal mast cells, KO, Day5, rep 2

description: Library name: Sample17


title: Cycloheximide 20nM Round-00 (exp14)

city: Toronto

description:
Library name: Cycloheximide 20nM_Round-00 (exp14)
sgRNAs PCR-amplified from genomic DNA

value: Cycloheximide 20nM


title: Brain, WT, 14 months, Female, ZT18, rep2

value: 14 months


title: hPA, gRNA-hit, Day10, rep 2

description:
Library name: Sample 2
Column name in gRNAhit_RNA-seq_counts.csv: gRNAhit_2

value: astrocyte


title: Spinner flask No treatment Day 6 Round-03 (exp576)

description:
Library name: SF No treatment D6_Round-03 (exp576)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Hep G2 cells, TRIB3 sh1_Rep_03

description:
Library name: TRIB3_sh1_3
Column name in FPKM_anno_TRIB3_knockdown.xls: sh1-3


title: SGC0649 7uM Round-03 (exp150)

description:
Library name: SGC0649 7uM_Round-03 (exp150)
sgRNAs PCR-amplified from genomic DNA

value: SGC0649 7uM


title: Meningeal mast cells, KO, Day5, rep 1

description: Library name: Sample16


title: Meningeal mast cells, WT, Day5, rep 2

description: Library name: Sample14


title: Hep G2 cells, TRIB3 sh2_Rep_01

description:
Library name: TRIB3_sh2_1
Column name in FPKM_anno_TRIB3_knockdown.xls: sh2-1


title: Hep G2 cells, TRIB3 sh2_Rep_02

description:
Library name: TRIB3_sh2_2
Column name in FPKM_anno_TRIB3_knockdown.xls: sh2-2


title: Lapatinib 5uM Round-01 (exp47)

description:
Library name: Lapatinib 5uM_Round-01 (exp47)
sgRNAs PCR-amplified from genomic DNA

value: Lapatinib 5uM


title: Meningeal mast cells, WT, Day5, rep 3

description: Library name: Sample15


title: Hep G2 cells, TRIB3 sh1_Rep_02

description:
Library name: TRIB3_sh1_2
Column name in FPKM_anno_TRIB3_knockdown.xls: sh1-2


title: Brain, WT, 14 months, Female, ZT12, rep1

value: Female


title: Brain, WT, 14 months, Female, ZT0, rep2


title: Wortmannin 5uM Round-00 (exp38)

description:
Library name: Wortmannin 5uM_Round-00 (exp38)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Wortmannin 5uM


title: Meningeal mast cells, KO, Day4, rep 3

description: Library name: Sample12

value: Meningeal mast cells

value: 4 days post infection


title: Spinner flask No treatment Day 8 Round-03 (exp157)

description:
Library name: SF No treatment D8_Round-03 (exp157)
sgRNAs PCR-amplified from genomic DNA


title: Meningeal mast cells, WT, Day5, rep 1

description: Library name: Sample13

value: 5 days post infection


title: Hep G2 cells, TRIB3 sh1_Rep_01

description:
Library name: TRIB3_sh1_1
Column name in FPKM_anno_TRIB3_knockdown.xls: sh1-1


title: Brain, WT, 14 months, Female, ZT12, rep2

value: Brain

value: WT


title: Meningeal mast cells, KO, Day4, rep 2

description: Library name: Sample11


title: Brain, WT, 14 months, Female, ZT18, rep1


title: Hep G2 cells, Ctrl_shRNA_Rep_03

description:
Library name: Ctrl_shRNA_3
Column name in FPKM_anno_TRIB3_knockdown.xls: Control3

value: Liver

value: Hep G2


title: Brain, WT, 14 months, Female, ZT0, rep1


title: Wortmannin 500nM Round-00 (exp37)

description:
Library name: Wortmannin 500nM_Round-00 (exp37)
sgRNAs PCR-amplified from genomic DNA

value: Wortmannin 500nM


title: Meningeal mast cells, KO, Day4, rep 1

description: Library name: Sample10


title: Brain, APP23, 7 months, Male, ZT6, rep1

value: 7 months

value: Male


title: Hep G2 cells, Ctrl_shRNA_Rep_02

description:
Library name: Ctrl_shRNA_2
Column name in FPKM_anno_TRIB3_knockdown.xls: Control2

value: tumor cells

value: lentivirus infected


title: Hep G2 cells, Ctrl_shRNA_Rep_01

description:
Library name: Ctrl_shRNA_1
Column name in FPKM_anno_TRIB3_knockdown.xls: Control1


title: Brain, APP23, 7 months, Male, ZT18, rep2

description: Fresh frozen spatial transcriptomics sequencing


title: Meningeal mast cells, WT, Day4, rep 2

description: Library name: Sample8


title: 1,1'-Binaphthyl-2,2'-diamine 2uM Round-00 (exp16)

description:
Library name: 1,1_-Binaphthyl-2,2_-diamine 2uM_Round-00 (exp16)
sgRNAs PCR-amplified from genomic DNA

value: 1,1'-Binaphthyl-2,2'-diamine 2uM


title: Meningeal mast cells, WT, Day4, rep 1

description: Library name: Sample7


title: Nocodazole 20nM Round-00 (exp23)

description:
Library name: Nocodazole 20nM_Round-00 (exp23)
sgRNAs PCR-amplified from genomic DNA

value: Nocodazole 20nM


title: Brain, APP23, 7 months, Male, ZT12, rep2


title: Brain, APP23, 7 months, Male, ZT18, rep1


title: Hep G2 cells, Glutamin deprivation_24hours_Rep_02

description:
Library name: Gln_Dep_24h_2
Column name in FPKM_anno_Gln_deprivation.xls: DE24-2

treatment_protocol: For the glutamine deprivation experiment, cells were seeded in 60 mm culture dishes. At 24 hours post-seeding, the culture medium was replaced with glutamine-free DMEM (supplemented with GlutaMAX™ as a glutamine substitute), and cells were cultured for an additional 12 or 24 hours.

value: Glutamine deprivation


title: Pterostilbene 16uM Round-02 (exp78)

description:
Library name: Pterostilbene 16uM_Round-02 (exp78)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Pterostilbene 16uM


title: Brain, APP23, 7 months, Male, ZT6, rep2


title: Meningeal mast cells, KO, NC, rep 3

description: Library name: Sample6

value: Meningeal mast cells

value: No infection


title: Meningeal mast cells, WT, Day4, rep 3

description: Library name: Sample9

value: 4 days post infection