title: B16F10 shRNA Ctrl replicat1

description: Library name: N1-CTRL


title: Patient 1 month after treatment with guideline based therapy_19

status: Public on Dec 08 2025

type: SRA

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

country: Japan

institute: Tsukuba university

description: Library name: 19_1

library_source: transcriptomic

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 20.0.0; Qiagen, Redwood City, CA).
Assembly: hg19
Supplementary files format and content: excel files include expression values of total counts, RPKM, TPM, and CPM for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood cells

extract_protocol:
Silica-membrane-based RNA isolation and purification in a spin-column format were performed using the PAXgene Blood RNA kit (Qiagen). Extracted RNA was globin-cleared using the Ambion GLOBINclear kit (Thermo Fisher, Waltham, MA). Then, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) and converted to an Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). CD19, CD56, CD123, and CD235a antibodies was used to obtain remaining eosinophils. Total RNA from eosinophils was extracted using TRIzol™ Reagent (Invitrogen). Then, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) and converted to an Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Whole blood cells


title: Dp16_placenta_euploid_Dam47_embryo6

type: RNA

city: Bethesda

first: Laura

middle: L

last: Baxter

state: MD

address: 35A Convent Drive

department: NHGRI

country: USA

institute: NIH

description: Gene expression data from mouse E18.5 placenta

hyb_protocol: Arrays were washed and stained using the GeneTitan Hybridization, Wash, and Stain kit with streptavidin-phycoerythrin protocol according to the manufacturer's instructions.           Arrays were scanned using the GeneTitan automated microarray system.

data_processing: Microarray data were analyzed using Transcriptome Analysis Console (TAC) software (version 4.0.0) (Thermo Fisher Scientific) using RMA normalization

label: biotin

organism: Mus musculus

source_name: Mouse E18.5 placenta

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate using Mouse Clariom S HT arrays (Cat. No. 902970, Thermo Fisher Scientific) and the GeneTitan automated microarray system.

growth_protocol: Mouse placentas were collected at E18.5 (late gestation), snap frozen, and stored at -80°C until RNA extraction.

extract_protocol: RNA was processed and hybridized on Mouse Clariom S HT 96-array plates (902970; ThermoFisher Scientific) using GeneChip WT Plus Reagent Kits following the manufacturer’s protocol (902281; ThermoFisher Scientific).

tag: genotype

value: EUP

tag: model

tag: Sex

value: Male


title: MU412C - Replicate 3_sRNA

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

description: Library name: MU412C_C_sRNA

data_processing:
Raw paired-end (PE)  and single-end reads from M. lusitanicus RNA-seq datasets were quality-checked using FastQC v0.11.9
Adapters were removed with Trim Galore! V.0.4.3.1
Reads with a Phred quality score (q) ≤32 and/or a total length < 20 nt were removed from the analysis
Assembly: Mucor lusitanicus (CBS 277.49) v2 (https://mycocosm.jgi.doe.gov/pages/search-for-genes.jsf?organism=Mucci2)
Supplementary files format and content: Spreadsheet including counts, log2FC, differential expression statistics and functional annotation for every gene

organism: Mucor lusitanicus

source_name: Spores

growth_protocol: MU636 and MU412 spores were co-incubated with J774A.1 murine macrophages at an MOI of 1.5:1 for 1 hour at 37 °C.

extract_protocol:
Total RNA was extracted using the mirVana kit (AM1561) and treated with DNase (Sigma, On-Column DNaseI treatment set)
NEBNext® Ultra™ Directional RNA Library Prep Kit

tag: tissue

value: Spores

tag: co-culture

value: Mutant strain (r3b2delta)


title: Dp16_placenta_euploid_Dam34_embryo4

scan_protocol: Arrays were scanned using the GeneTitan automated microarray system.


title: B16F10 shRNA OSGEP#2 replicat3

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

description: Library name: Clea6-TotalRNA

data_processing:
Quality check – FastQC v0.11.9
Trimming (RNA-seq) - Nfcore-rnaseq v.3.0 built in function (--clip_r1 1 \ --clip_r2 1 \ --three_prime_clip_r1 1 \ --three_prime_clip_r2 1 \ --trim_nextseq 10)
Trimming (Ribo-seq) – TrimGalore v.0.6.6 CutAdapt (Adaptor clipping (“TCTCCTTGCATAATCACCAACC”) and 5’ (NNNNT) and 3’ (NNNN) trimming (--cut 5 & --cut -4) with a minimum length required of 20nt)
Alignment - Nfcore-rnaseq – STAR v.3.0
Assembly: Mus musculus coding transcriptome for Ribo-seq (GRCm39) and Mus musculus genome for RNA-seq (GRCm38 - v41)
Supplementary files format and content: Raw counts in tab-delimated table

molecule: polyA RNA

source_name: Cell

growth_protocol: B16F10 were cultured in a humidified incubator at 37°C with 5% CO2, grown in Dulbecco’s modified Eagle’s medium (DMEM, LONZA) supplemented with 1% glutamine and 1% penicillin-streptomycin and 10% FBS (GIBCO)

extract_protocol:
B16F10 cells depleted or not for OSGEP were grown to confluence in a 10 cm dish and treated with 10 µg/mL cycloheximide for 5 minutes at 37ºC to arrest translation, followed by cell lysis and RNA digestion. Active ribosomes were then pulled down using a puromycin analog (RiboLace probe) and magnetic beads, with two pulldowns performed for each sample. RNA was subsequently extracted with the acid phenol-chloroform method, followed by size selection of 25-35 bp fragments in a 15% TBE-urea PAGE gel using Immagina’s PAGExt gel extraction system. RPFs were quantified with the Qubit™ microRNA Assay Kit before proceeding with the library preparation
RPF library preparation with LACEseq involved sequential 5’ phosphorylation, ligation, and circularization steps, with small RNA purification after each step using the RNA Clean & Concentrator™-5 kit from Zymo Research. Reverse transcription and an initial PCR amplification were then performed, followed by cleanup of the PCR product using AMPure XP beads. A second PCR amplification was carried out to incorporate unique dual indexes using Immagina’s iUDI Plate. Final cleanup of the indexed library was done using the NucleoSpin Gel and PCR Clean-Up kit followed by size selection in a 10% TBE PAGE gel with PAGExt gel extraction
Library quality and size was confirmed on a Bioanalyzer, and sequencing was conducted on a NovaSeq (Illumina) at the NGS platform of the GIGA Institute, with 70 million reads per sample.

value: Cell

tag: cell line

value: melanoma

value: KD OSGEP


title: Patient before treatment with guideline based therapy_19

description: Library name: 19_0


title: B16F10 shRNA Ctrl replicat3

description: Library name: Clea5-TotalRNA

value: WT


title: B16F10 shRNA OSGEP#1 replicat2

description: Library name: N2-O1

data_processing:
Raw reads were demultiplexed and adapter-trimmed using Illumina bcl2fastq conversion software v2.20. They were processed within our custom nextflow RNAseq pipeline inspired from nf-core/rnaseq. We used TrimGalore to trimm a single base at 5' and 3' ends of each read and to perform a quality based trimming after removing poly-G tails. Then, we did the STAR alignment and Salmon quantification
Assembly: Genome Reference reference genome fa and the annotations from Ensembl release genes
Supplementary files format and content: Raw counts from Salmon

extract_protocol:
Cells were washed three times with cold PBS and lysed in RIP buffer (150 mmol/L KCl, 25 mmol/L Tris pH 7.4, 5 mmol/L EDTA,0.5 mmol/L DTT, 0.5%NP40) supplemented with protease inhibitor for 30min at 4°C. Lysates were cleared by centrifugation at 10.000G for 15min at 4°C. 1mg of lysate were mixed with anti-FLAG anti-A/G protein conjugated magnetic beads (MedeChemExpress, #HY-K0207, #HY-K0202 respectively) according manufacturer’s instruction. Binding reaction was incubated on rotation overnight at 4°C. Beads were washed 4 times with RIP buffer and elution was completed with buffer elution A (0.15M glycine, pH3). After 10min, neutralization buffer (1M TrisHCl pH8.0) was added and followed by incubation with 10mg/mL of proteinase K (FischerScientific, #10103533) at 55°C for 1h. The RNA bound to FLAG-RIG was extracted using TRIzol protocol (Invitrogen)
Library preparation was performed using 10 ng of total RNA following the Illumina Stranded Total RNA Ligation with Ribo-Zero Plus protocol  (Illumina). The final library profiles were assessed using the QIAxcel Advanced System (Qiagen), and concentrations were measured by qPCR using the SYBR Fast KAPA Kit.Indexed Libraries were pooled in equimolar ratios, and the pooled library was sequenced on the NovaSeq 6000 platform using an S2 flow cell with paired-end 150 bp reads, with 50 Mi fragments sequenced per sample.


title: MU412C - Replicate 2_sRNA

description: Library name: MU412C_B_sRNA


title: Patient 1 month after treatment with guideline based therapy_18

description: Library name: 18_1


title: Dp16_placenta_trisomic_Dam34_embryo2

value: TS


title: B16F10 shRNA OSGEP#2 replicat1

description: Library name: N1-O2


title: MU412C - Replicate 1_sRNA

description: Library name: MU412C_A_sRNA


title: Dp16_placenta_trisomic_Dam34_embryo3

value: Female


title: Dp16_placenta_trisomic_Dam34_embryo6


title: Patient before treatment with guideline based therapy_18

description: Library name: 18_0


title: MU636M - Replicate 3

description: Library name: MU636M_C

source_name: Spores&Macrophages

value: J774A.1 murine macrophages

value: Wild-type strain


title: B16F10 shRNA OSGEP#2 replicat2

description: Library name: Clea4-TotalRNA


title: B16F10 shRNA Ctrl replicat2

description: Library name: Clea3-TotalRNA


title: Dp16_placenta_trisomic_Dam33_embryo7


title: Dp16_placenta_trisomic_Dam33_embryo6


title: Patient 1 month after treatment with guideline based therapy_17

description: Library name: 17_1


title: B16F10 shRNA OSGEP#2 replicat1

description: Library name: Clea2-TotalRNA


title: MU636M - Replicate 2

description: Library name: MU636M_B


title: Dp16_placenta_euploid_Dam34_embryo1


title: Patient before treatment with guideline based therapy_17

description: Library name: 17_0


title: MU636M - Replicate 1

description: Library name: MU636M_A


title: GOT1_30 MBq_(1×30_2w-fractions)_replicate 5

city: Gothenburg

first: Eva

last: Forssell-Aronsson

address: Gula Stråket 2B

country: Sweden

institute: University of Gothenburg

description: Test

data_processing:
Sham-treated samples were used as a control. We compared the relative expression in GOT1 tumor tissue between the controls and the treatment groups at the day of sacrificing the animals. For data analysis, we used Microsoft Excel to calculate fold-expression of the target genes based upon the the 2-∆∆Ct method (Livak and Schmittgen 2001). The relative expression compared to controls were analyzed by Welch T-test, and p<0.05 was considered significant. Target gene signals in all samples (test and controls) are normalized to geometric average of housekeeping genes provided in the same array, resulting in ∆Ct values, where ∆Ct=(Ct_Target-Ct_HKG). ∆Ct values for all test replicates were normalized against the average of corresponding control replicates, resulting in ∆∆Ct, where ∆∆Ct= ∆Ct_test replicate - average ∆Ct_control. 2^-∆∆CT values for each condition were considered as fold change expression of test samples compared to controls (untreated). Fold change is determined for target genes in all replicates of test samples as 2^-∆∆Ct where ∆∆Ct= ∆Ct_test replicate - average ∆Ct_control
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPLP0, GAPDH, ACTB.
Matrik non-normalized reports raw data Ct values for target and housekeeping genes in all control and test replicates.
Fold change worksheet reports 2^-∆∆Ct, calculated as indicated in the data processing

label: SYBR Green

source_name: GOT1, 30 MBq 177-Lu-octreotate (1×30, 2w-fractions), replicate 5

label_protocol: For each reaction, a final volume of 25 µl was used which contained 12.5 µl of RT2 SYBR Green Mastermix (QIAGEN, Valencia, USA), 11.5 µl of nuclease free water and 1 µl of cDNA (1.7 µg of total RNA). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with thermal profile starting by activation of HotStart DNA Taq polymerase at 95 °C for 10 min followed by 45 cycles of 95 °C for 15 sec and 65 °C for 1min. Analysis of RT-qPCR raw data (cycle numbers) was performed with the LightCycler 480 Soft Ware 1.5.1.

extract_protocol: According to the manufacturer's protocol, total RNA was extracted from frozen tumor tissue samples using the Allprep® DNA/RNA kit (QIAGEN, Valencia, USA). RNA purity, integrity and concentration were ascertained using the Nanodrop 1000 spectrometer (Thermo Scientific, Waltham, Massachusetts, USA), Tapestation electrophoresis system (Agilent Technologies, Palo Alto, CA, USA) and Qubit 3.0 fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts, USA). Reverse transcription was performed from 200 ng total RNA using the RT2 First Strand Kit (QIAGEN, Valencia, USA).

tag: host mouse strain

value: Balb/c NM

tag: tissue type

value: GOT1 xenograft

tag: treatment group

value: Lu-177-octreotate 30 MBq (1x30 2w-fractions)


title: GOT1_30 MBq_(1×30_2w-fractions)_replicate 4

description: Test

source_name: GOT1, 30 MBq 177-Lu-octreotate (1×30, 2w-fractions), replicate 4


title: B16F10 shRNA Ctrl replicat1

description: Library name: Clea1-TotalRNA


title: B16F10 shRNA OSGEP#2 replicat3 RPF

description: Library name: Clea-6-RPF

data_processing:
Quality check – FastQC v0.11.9
Trimming (RNA-seq) - Nfcore-rnaseq v.3.0 built in function (--clip_r1 1 \ --clip_r2 1 \ --three_prime_clip_r1 1 \ --three_prime_clip_r2 1 \ --trim_nextseq 10)
Trimming (Ribo-seq) – TrimGalore v.0.6.6 CutAdapt (Adaptor clipping (“TCTCCTTGCATAATCACCAACC”) and 5’ (NNNNT) and 3’ (NNNN) trimming (--cut 5 & --cut -4) with a minimum length required of 20nt)
Alignment - Nfcore-rnaseq – STAR v.3.0
Assembly: Mus musculus coding transcriptome for Ribo-seq (GRCm39) and Mus musculus genome for RNA-seq (GRCm38 - v41)
Supplementary files format and content: Raw counts in tab-delimated table
Library strategy: Ribo-Seq


title: Patient 1 month after treatment with guideline based therapy_16

description: Library name: 16_1


title: MU636C - Replicate 2

description: Library name: MU636C_B


title: MU636C - Replicate 3

description: Library name: MU636C_C


title: B16F10 shRNA Ctrl replicat3 RPF

description: Library name: Clea-5-RPF


title: B16F10 shRNA OSGEP#2 replicat2 RPF

description: Library name: Clea-4-RPF


title: MU412M- Replicate 3

description: Library name: MU412M_C


title: Patient before treatment with guideline based therapy_15

description: Library name: 15_0


title: MU636C - Replicate 1

description: Library name: MU636C_A


title: GOT1_30 MBq_(1×30_2w-fractions)_replicate 3

description: Test

source_name: GOT1, 30 MBq 177-Lu-octreotate (1×30, 2w-fractions), replicate 3


title: B16F10 shRNA Ctrl replicat2 RPF

description: Library name: Clea-3-RPF


title: GOT1_30 MBq_(1×30_2w-fractions)_replicate 1

description: Test

source_name: GOT1, 30 MBq 177-Lu-octreotate (1×30, 2w-fractions), replicate 1


title: B16F10 shRNA OSGEP#2 replicat1 RPF

description: Library name: Clea-2-RPF


title: GOT1_30 MBq_(1×30_2w-fractions)_replicate 2

description: Test

source_name: GOT1, 30 MBq 177-Lu-octreotate (1×30, 2w-fractions), replicate 2


title: Patient before treatment with guideline based therapy_14

description: Library name: 14_0


title: MU412M - Replicate 1

description: Library name: MU412M_A


title: MU412M - Replicate 2

description: Library name: MU412M_B


title: Patient 1 month after treatment with guideline based therapy_13

description: Library name: 13_1


title: Patient 1 month after treatment with guideline based therapy_14

description: Library name: 14_1


title: Dp16_placenta_euploid_Dam33_embryo5


title: GOT1_60 MBq_(1×60_2w-fractions)_replicate 4

description: Test

source_name: GOT1, 60 MBq 177-Lu-octreotate (1×60, 2w-fractions), replicate 4

value: Lu-177-octreotate 60 MBq (1x60 2w-fractions)


title: MU412C- Replicate 3

description: Library name: MU412C_C


title: GOT1_60 MBq_(1×60_2w-fractions)_replicate 5

description: Test

source_name: GOT1, 60 MBq 177-Lu-octreotate (1×60, 2w-fractions), replicate 5


title: Patient before treatment with guideline based therapy_16

description: Library name: 16_0

value: Whole blood cells


title: GOT1_60 MBq_(1×60_2w-fractions)_replicate 3

description: Test

source_name: GOT1, 60 MBq 177-Lu-octreotate (1×60, 2w-fractions), replicate 3


title: Patient 1 month after treatment with guideline based therapy_15

description: Library name: 15_1


title: Patient before treatment with guideline based therapy_13

description: Library name: 13_0


title: Patient 1 month after treatment with guideline based therapy_12

description: Library name: 12_1


title: DMSO,lung, scRNAseq

city: shanghai

first: wanqi

last: fang

address: jiangwan

country: China

institute: fudan

description:
Library name: Sample1
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger softw  v6.0.2.(http://support.10Xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38; mm10
Supplementary files format and content: matrix files

source_name: lung

extract_protocol:
Arter gavage,   lung  carcinoma  mouse tumors from STK-treated and DMSO-treated mice were dissected. Then the tumor were dissociated according to the manufacter‘s instruction (Miltenyi Biotec, CAS#130-096-730) and  tumor single cell suspension were acquired. DAPI (Sigma‒Aldrich, Cat# D9542) was used to identify live or dead cells. Cell surface maker CD45  staining was performed by adding appropriately conjugated fluores cent primary antibodies (Biolegend, CAS#147712) to the cells and incubating  at room temperature for 1 hour in the dark. After staining, CD45+Cell are sorted through Fluorescence activated cell sorting(FACS).
Library was performed according to the manufacter‘s instruction  (Chromium_Next_GEM_Single_Cell_5_v2_UserGuide_10Xgenomics_CG000331). Brifely, CD45+immune cells were resuspended in the master mix and loaded together with partition oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence,Uique Molecular Identifier(UMI) and 10X Barcode. The pooled barcoded cDNA was then cleaned up with silane Dynabeads, amplified by PCR and the appropriate sized fragments were selected with SPRlselect reagent for subsequent library contraction. During the library construction llumina R2 primer sequence, paired-end constructs with P5 and P7 sequence and a sample index were added.

value: lung

value: lung cell

tag: treatment

value: lung carcinoma from DMSO-treated

tag: batch


title: MU412C - Replicate 2

description: Library name: MU412C_B

value: Spores

value: Mutant strain (r3b2delta)


title: GOT1_60 MBq_(1×60_2w-fractions)_replicate 2

description: Test

source_name: GOT1, 60 MBq 177-Lu-octreotate (1×60, 2w-fractions), replicate 2


title: MU412C - Replicate 1

description: Library name: MU412C_A


title: GOT1_60 MBq_(1×60_2w-fractions)_replicate 1

description: Test

source_name: GOT1, 60 MBq 177-Lu-octreotate (1×60, 2w-fractions), replicate 1


title: STK,scRNAseq

description:
Library name: Sample2
10X Genomics

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger softw  v6.0.2.(http://support.10Xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38
Supplementary files format and content: mm10
Supplementary files format and content: matrix files

source_name: liver

extract_protocol:
Arter gavage,  hepatocellular carcinoma  mouse tumors from STK-treated and DMSO-treated mice were dissected. Then the tumor were dissociated according to the manufacter‘s instruction (Miltenyi Biotec, CAS#130-096-730) and  tumor single cell suspension were acquired. DAPI (Sigma‒Aldrich, Cat# D9542) was used to identify live or dead cells. Cell surface maker CD45  staining was performed by adding appropriately conjugated fluores cent primary antibodies (Biolegend, CAS#147712) to the cells and incubating  at room temperature for 1 hour in the dark. After staining, CD45+Cell are sorted through Fluorescence activated cell sorting(FACS).
Library was performed according to the manufacter‘s instruction  (Chromium_Next_GEM_Single_Cell_5_v2_UserGuide_10Xgenomics_CG000331). Brifely, CD45+immune cells were resuspended in the master mix and loaded together with partition oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence,Uique Molecular Identifier(UMI) and 10X Barcode. The pooled barcoded cDNA was then cleaned up with silane Dynabeads, amplified by PCR and the appropriate sized fragments were selected with SPRlselect reagent for subsequent library contraction. During the library construction llumina R2 primer sequence, paired-end constructs with P5 and P7 sequence and a sample index were added.

value: liver

value: liver cell

value: MYC-ON

value: hepatocellular carcinoma form STK-treated


title: DMSO,scRNAseq

description:
Library name: Sample1
10X Genomics

value: hepatocellular carcinoma form DMSO-treated


title: GOT1_60 MBq_(2×30_2w-fractions)_replicate 3

description: Test

source_name: GOT1, 60 MBq 177-Lu-octreotate (2×30, 2w-fractions), replicate 3

value: Lu-177-octreotate 60 MBq (2x30 2w-fractions)


title: Patient 1 month after treatment with guideline based therapy_11

description: Library name: 11_1

source_name: Whole blood cells


title: B16F10 shRNA Ctrl replicat1 RPF

description: Library name: Clea-1-RPF

value: Cell

value: melanoma

value: WT


title: Patient before treatment with guideline based therapy_12

description: Library name: 12_0


title: Patient before treatment with guideline based therapy_11

description: Library name: 11_0


title: X5403

first: Alex

last: DeCasien

address: 9000 Rockville Pike

department: LNG

institute: National Institute on Aging

description: Library name: P1D05-5403-PFC_S84

data_processing:
Prior to further RNA-seq data analysis, we filtered out genes that were very lowly or not detectably expressed in our samples. Specifically, we removed genes with an average CPM less than 10 in all donor species x batch groups, resulting in 11,450 genes across 32 samples.
Assembly: Mus musculus GRCm39 release 110
Supplementary files format and content: fastq

source_name: frontal cortex

extract_protocol:
MagMAX™ mirVana™ Total RNA Isolation Kit
Tag-based RNA-seq (TagSeq) on the NovaSeq 2000 SR100

treatment_protocol: microbiome inoculation

value: frontal cortex

value: Macaque

value: F


title: X188

description: Library name: P1B05-188-PFC_S82


title: X406

description: Library name: P1C05-406-PFC_S83


title: Patient 1 month after treatment with guideline based therapy_10

description: Library name: 10_1

value: Whole blood cells


title: Sample 5, 54 hour, replicate 3

city: Nanjing

first: Hao

last: Huang

address: Dongnandaxue Road

department: Department of Bioinformatics

institute: Southeast University

description:
Library name: S5H54R3
10x Genomics

data_processing:
Cell Ranger 5.0.1, the function count was used to align reads to the reference genome (mm10) with default parameters, and the R package Seurat v4.0 was applied for downstream analysis.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Eight-week-old male C57BL/6J mice  were anesthetized with 500 mg/kg tribromoethanol  and were killed by cervical dislocation. After the animals were sacrificed, brain tissues (hippocampus) were isolated, placed in 2 mL enzyme-free centrifuge tubes, and stored at 25 ̊C at constant temperature. Postmortem tissues were sampled at 0 h (snap frozen, H0), 24 h (H24), 36 h (H36), 48 h (H48), and 54 h (H54), followed by snap frozen in liquid nitrogen and stored at -80 ̊C until use. For the reliability of the data, we maintained the consistency of the environment for each sample and set up biological replicates of three mice per group.
Sorted nuclei were processed using the 10× Chromium Single Cell 3′ Library and Gel Bead Kit v3, nuclei were immediately loaded onto a Chromium Single Cell Processor for barcoding of RNA from single nuclei. The quality of cDNA was assessed using the Agilent× v3.1 to generate the cDNA libraries. The quality of cDNA was assessed using the Agilent 2100 Bioanalyzer System. Sequencing libraries were constructed according to the manufacturer’s instructions and then sequenced in a NovaSeq 6000 sequencing system.

value: hippocampus

tag: time


title: Sample 5, 54 hour, replicate 4

description:
Library name: S5H54R4
10x Genomics


title: Patient before treatment with guideline based therapy_10

description: Library name: 10_0


title: STK,lung, scRNAseq

description:
Library name: Sample2
10X Genomics

value: lung

value: lung cell

value: lung carcinoma from STK-treated


title: GOT1_60 MBq_(2×30_2w-fractions)_replicate 1

description: Test

source_name: GOT1, 60 MBq 177-Lu-octreotate (2×30, 2w-fractions), replicate 1

value: Balb/c NM

value: GOT1 xenograft


title: X5404

description: Library name: P1A05-5404-PFC_S81


title: X189

description: Library name: P1H04-189-PFC_S80


title: Patient 1 month after treatment with guideline based therapy_9

description: Library name: 9_1


title: GOT1_30 MBq_(2×15_2w-fractions)_replicate 5

description: Test

source_name: GOT1, 30 MBq 177-Lu-octreotate (2×15, 2w-fractions), replicate 5

value: Lu-177-octreotate 30 MBq (2x15 2w-fractions)


title: Sample 5, 54 hour, replicate 1

description:
Library name: S5H54R1
10x Genomics


title: Sample 4, 48 hour, replicate 3

description:
Library name: S4H48R3
10x Genomics


title: GOT1_30 MBq_(2×15_2w-fractions)_replicate 4

description: Test

source_name: GOT1, 30 MBq 177-Lu-octreotate (2×15, 2w-fractions), replicate 4


title: Patient before treatment with guideline based therapy_9

description: Library name: 9_0


title: GOT1_30 MBq_(2×15_2w-fractions)_replicate 3

description: Test

source_name: GOT1, 30 MBq 177-Lu-octreotate (2×15, 2w-fractions), replicate 3


title: X401

description: Library name: P1F04-401-PFC_S78


title: Sample 4, 48 hour, replicate 2

description:
Library name: S4H48R2
10x Genomics


title: Patient 1 month after treatment with guideline based therapy_8

description: Library name: 8_1


title: GOT1_30 MBq_(2×15_2w-fractions)_replicate 2

description: Test

source_name: GOT1, 30 MBq 177-Lu-octreotate (2×15, 2w-fractions), replicate 2


title: GOT1_60 MBq_(2×30_2w-fractions)_replicate 2

description: Test

source_name: GOT1, 60 MBq 177-Lu-octreotate (2×30, 2w-fractions), replicate 2


title: Sample 4, 48 hour, replicate 1

description:
Library name: S4H48R1
10x Genomics


title: X414

description: Library name: P1E04-414-PFC_S77

value: E


title: Patient before treatment with guideline based therapy_8

description: Library name: 8_0


title: GOT1_30 MBq_(2×15_2w-fractions)_replicate 1

description: Test

source_name: GOT1, 30 MBq 177-Lu-octreotate (2×15, 2w-fractions), replicate 1


title: Sample 5, 54 hour, replicate 2

description:
Library name: S5H54R2
10x Genomics


title: GOT1_120 MBq_(2×60_1w-fractions)_replicate 3

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (2×60, 1w-fractions), replicate 3

value: Lu-177-octreotate 120 MBq (2x60 1w-fractions)


title: Sample 3, 36 hour, replicate 3

description:
Library name: S3H36R3
10x Genomics


title: Patient 1 month after treatment with guideline based therapy_7

description: Library name: 7_1


title: X5192

description: Library name: P1D04-5192-PFC_S76


title: X5194

description: Library name: P1B04-5194-PFC_S74


title: Sample 3, 36 hour, replicate 1

description:
Library name: S3H36R1
10x Genomics


title: GOT1_120 MBq_(2×60_1w-fractions)_replicate 1

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (2×60, 1w-fractions), replicate 1


title: X5408

description: Library name: P1G04-5408-PFC_S79


title: X411

description: Library name: P1C04-411-PFC_S75


title: Sample 3, 36 hour, replicate 2

description:
Library name: S3H36R2
10x Genomics


title: X409

description: Library name: P1A04-409-PFC_S73


title: Sample 2, 24 hour, replicate 3

description:
Library name: S2H24R3
10x Genomics


title: Patient 1 month after treatment with guideline based therapy_6

description: Library name: 6_1


title: Patient before treatment with guideline based therapy_6

description: Library name: 6_0


title: X981

description: Library name: P1H03-981-PFC_S72

value: D


title: GOT1, saline, replicate 4

description: Control

source_name: GOT1, saline, replicate 4

value: 0.9% NaCl


title: GOT1, saline, replicate 3

description: Control

source_name: GOT1, saline, replicate 3


title: X132

description: Library name: P1G03-132-PFC_S71


title: Sample 2, 24 hour, replicate 1

description:
Library name: S2H24R1
10x Genomics


title: Patient before treatment with guideline based therapy_5

description: Library name: 5_0


title: X210

description: Library name: P1F03-210-PFC_S70


title: Patient 1 month after treatment with guideline based therapy_5

description: Library name: 5_1


title: Sample 1, 0 hour, replicate 3

description:
Library name: S1H0R3
10x Genomics


title: GOT1, saline, replicate 2

description: Control

source_name: GOT1, saline, replicate 2


title: Patient 1 month after treatment with guideline based therapy_4

description: Library name: 4_1


title: Patient before treatment with guideline based therapy_7

description: Library name: 7_0


title: GOT1, saline, replicate 1

description: Control

source_name: GOT1, saline, replicate 1


title: Sample 1, 0 hour, replicate 2

description:
Library name: S1H0R2
10x Genomics


title: Patient before treatment with guideline based therapy_4

description: Library name: 4_0


title: GOT1_120 MBq_(2×60_1w-fractions)_replicate 2

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (2×60, 1w-fractions), replicate 2


title: X984

description: Library name: P1D03-984-PFC_S68

value: C


title: GOT1_120 MBq_(1×120_1d-fractions)_replicate 3

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (1×120, 1d-fractions), replicate 3

value: Lu-177-octreotate 120 MBq (1x120 1d-fractions)


title: Patient 1 month after treatment with guideline based therapy_3

description: Library name: 3_1

source_name: Whole blood cells


title: X145

description: Library name: P1E03-145-PFC_S69

source_name: frontal cortex

value: frontal cortex


title: GOT1_120 MBq_(1×120_1d-fractions)_replicate 4

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (1×120, 1d-fractions), replicate 4


title: Patient before treatment with guideline based therapy_3

description: Library name: 3_0


title: X5140

description: Library name: P1B03-5140-PFC_S66


title: Patient 1 month after treatment with guideline based therapy_2

description: Library name: 2_1


title: Sample 2, 24 hour replicate 2

description:
Library name: S2H24R2
10x Genomics

source_name: hippocampus


title: GOT1_120 MBq_(1×120_1d-fractions)_replicate 2

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (1×120, 1d-fractions), replicate 2


title: CD8aa_from CD8ab_3

city: Singapore

first: Lukasz

last: Wojciech

address: 5 Science Drive 2 Blk MD4

country: Singapore

institute: Nus

description: Library name: CD8aa_6

data_processing:
The raw reads were aligned to the reference genome using Hisat2 v2.1.0
SeqMonk v1.46.0 data analyzer (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) was used to generate a raw reads expression matrix
Assembly: mm10
Supplementary files format and content: Tab-delimited file includes raw counts for each sample

source_name: small intestine

extract_protocol:
The RNA was isolated from sorted TCRβ CD8αα+, TCRβ CD8αβ+ and TCRβ CD4+ IEL. using RNAeasy isolation KIT
Synthesis of libraries was performed using MagMAXTM DNA Multi-Sample Ultra Kit

treatment_protocol: Adoptive transfer of T cell into Rag -/- lymphopenic host

value: small intestine

value: intraepithelial T lymphocyte

value: WT

tag: progeny

value: CD8ab progeny


title: GOT1_120 MBq_(1×120_1d-fractions)_replicate 1

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (1×120, 1d-fractions), replicate 1


title: X5136

description: Library name: P1A03-5136-PFC_S65


title: CD8aa_from CD8ab_1

description: Library name: CD8aa_4


title: X5141

description: Library name: P1C03-5141-PFC_S67


title: Patient before treatment with guideline based therapy_2

description: Library name: 2_0

value: Whole blood cells


title: GOT1_120 MBq_(2×60_1d-fractions)_replicate 5

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (2×60, 1d-fractions), replicate 5

value: Lu-177-octreotate 120 MBq (2x60 1d-fractions)


title: Patient 1 month after treatment with guideline based therapy_1

description: Library name: 1_1


title: CD8aa_from_CD4_3

description: Library name: CD8aa_3

value: CD4 progeny


title: CD8aa_from_CD4_2

description: Library name: CD8aa_2


title: GOT1_120 MBq_(2×60_1d-fractions)_replicate 4

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (2×60, 1d-fractions), replicate 4

value: Balb/c NM


title: Patient before treatment with guideline based therapy_1

description: Library name: 1_0


title: X552

description: Library name: P1G02-552-PFC_S63

value: Human

value: B


title: CD8aa_from_CD4_1

description: Library name: CD8aa_1


title: Sample 1, 0 hour, replicate 1

description:
Library name: S1H0R1
10x Genomics

value: hippocampus


title: X891

description: Library name: P1F02-891-PFC_S62


title: GOT1_120 MBq_(2×60_1d-fractions)_replicate 3

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (2×60, 1d-fractions), replicate 3

value: GOT1 xenograft


title: Hepa_scram3

description:
Library name: Sample45
Hepa_scram3

data_processing:
The raw sequencing data underwent a comprehensive bioinformatic analysis pipeline. Following initial quality control and adapter trimming, the high-quality reads were aligned to the reference genome using [Specify Software, e.g., HISAT2/STAR]. Subsequently, both known and novel transcripts were assembled and quantified, enabling the prediction of previously unannotated genes. Finally, differential gene expression analysis was performed between experimental conditions using [Specify Software, e.g., DESeq2/edgeR] to identify statistically significant transcriptional changes.
Assembly: GRCm38

source_name: Hepa1-6 cells

growth_protocol: The cell lines were seeded in 6-well plates and maintained under standard culture conditions to reach an appropriate confluence prior to subsequent experimental procedure.

extract_protocol:
Following the treatment period, total RNA was isolated from all cell samples using TRIzol reagent, strictly adhering to the manufacturer's recommended protocol to ensure high-quality RNA integrity.
Sequencing libraries were constructed, with the SMARTer kit employed for certain samples requiring specific adapter handling. High-throughput sequencing was then performed on the Illumina HiSeq platform using a paired-end sequencing strategy. Raw sequencing data underwent a rigorous quality control pipeline: adapter sequences and low-quality bases, which were predominantly concentrated at the 3' ends, were dynamically trimmed using Skewer.

treatment_protocol: For drug treatment studies, cells were exposed to the specified compounds for a duration of 48 hours. For genetic knockdown experiments, the respective knockdown cell lines were utilized and processed 24 hours post-seeding.

value: Hepa1-6 cells

value: liver cell line

value: scramble-knockdown


title: GOT1_120 MBq_(2×60_1d-fractions)_replicate 2

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (2×60, 1d-fractions), replicate 2


title: X892

description: Library name: P1E02-892-PFC_S61


title: Hepa_scram2

description:
Library name: Sample44
Hepa_scram2


title: X915

description: Library name: P1D02-915-PFC_S60


title: CD8aa_from CD8ab_2

description: Library name: CD8aa_5


title: CD8ab_IEL_3

description: Library name: CD8ab_3


title: GOT1_120 MBq_(2×60_1d-fractions)_replicate 1

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (2×60, 1d-fractions), replicate 1


title: CD8ab_IEL_2

description: Library name: CD8ab_2


title: GOT1_120 MBq_(3×40_1d-fractions)_replicate 4

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (3×40, 1d-fractions), replicate 4

value: Lu-177-octreotate 120 MBq (3x40 1d-fractions)


title: Hepa_scram1

description:
Library name: Sample43
Hepa_scram1


title: CD8ab_IEL_1

description: Library name: CD8ab_1


title: Hepa_sh3_3

description:
Library name: Sample42
Hepa_sh3_3


title: GOT1_120 MBq_(3×40_1d-fractions)_replicate 3

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (3×40, 1d-fractions), replicate 3


title: X916

description: Library name: P1H02-916-PFC_S64

value: frontal cortex


title: GOT1_120 MBq_(3×40_1d-fractions)_replicate 2

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (3×40, 1d-fractions), replicate 2


title: CD4_IEL_3

description: Library name: CD4_3

value: small intestine


title: X890

description: Library name: P1A02-890-PFC_S57


title: CD4_IEL_2

description: Library name: CD4_2

value: intraepithelial T lymphocyte


title: Hepa_sh3_1

description:
Library name: Sample40
Hepa_sh3_1


title: CD4_IEL_1

description: Library name: CD4_1

value: WT


title: X590

description: Library name: P1H01-590-PFC_S56

value: A


title: Hepa_sh2_3

description:
Library name: Sample39
Hepa_sh2_3


title: X921

description: Library name: P1G01-921-PFC_S55


title: S. sputigena treated Sample6

city: Richmond

first: Daniel

last: Miller

state: Virginia

address: 1101 E. Marshall St. Sanger Hall 5-009

institute: Virginia Commonwealth University

description:
Counts for 618 genes using total RNA harvested from TIGK cells
S6

hyb_protocol: nCounter

scan_protocol: nCounter

data_processing: Raw counts for each sample were normalized using the geometric mean of positive control genes within the Host Response Panel kit. Normalization, calculating differential expression and significance was performed by Rosalind.

source_name: Telomerase-immortalized gingival keratinocyte (TIGK)

growth_protocol: TIGKs were maintained in monolayer cultures at 37°C and 5% CO2 in DermaLife K serum-free complete medium (Lifeline Cell Technologies). GECs were grown to near confluency (~70-90% confluency) and were enumerated before use in the experiments described. S. sputigena was cultured in Tryptone-Yeast Extract-Gelatin-Volatile fatty acids-Serum (TYGVS) growth media under anaerobic conditions and were used in mid-log phase of growth. Bacteria cells were estimated based on optical density using the conversion of 1x10^9 cells per mL at 1.0 OD at 600 nm.

extract_protocol: After washing, cells were lysed with RLT buffer (Qiagen) and total RNA was purified using Trizol reagent.

treatment_protocol: TIGKs were cultured to near confluency in a 6-well tissue culture plate. Afterwards, cells remained naive or were challenged with 100 S. sputigena cells per TIGK cell for 4 hours. Three technical replicate samples were produced for each treatment, and the experiment was repeated in two experimental replicates for six samples per treatment.

value: TIGK

value: S. sputigena-treated


title: X919

description: Library name: P1C02-919-PFC_S59


title: X918

description: Library name: P1C01-918-PFC_S51


title: SE,rep2

city: Beijing

first: Zhao

last: Zhou

state: Beijing

address: No. 5 Yiheyuan road

institute: Peking University

data_processing:
Sequenced reads were trimmed by SOAPnuke (V2.1.0) ( –lowQual=20，–nRate=0.005，–qualRate=0.5)
then mapped to mm10 whole genome using HISAT2 (v2.1.0), and raw counts were calculated by FeatureCounts
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: primary peritoneal macrophages

growth_protocol: Primary pertoneal macrophages were maintain in DMEM supplemented with 10% fetal bovine serum in humidified atmosphere with % CO2 at 37 ℃.

extract_protocol:
Total RNA is extracted by Trizol reagent, then enriched with oligo-dT beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary macrophage


title: Hepa_sh2_1

description:
Library name: Sample37
Hepa_sh2_1


title: SE,rep1


title: S. sputigena treated Sample4

description:
Counts for 618 genes using total RNA harvested from TIGK cells
S4


title: X917

description: Library name: P1A01-917-PFC_S50

source_name: frontal cortex


title: X586

description: Library name: P1B02-586-PFC_S58


title: S. sputigena treated Sample5

description:
Counts for 618 genes using total RNA harvested from TIGK cells
S5


title: SA,rep3


title: Hepa_sh1_2

description:
Library name: Sample35
Hepa_sh1_2


title: S. sputigena treated Sample2

description:
Counts for 618 genes using total RNA harvested from TIGK cells
S2


title: Hepa_sh3_2

description:
Library name: Sample41
Hepa_sh3_2


title: SA,rep2


title: S. sputigena treated Sample1

description:
Counts for 618 genes using total RNA harvested from TIGK cells
S1


title: Hepa_sh1_1

description:
Library name: Sample34
Hepa_sh1_1


title: VENT_16

city: Santa Cruz

first: Hunter

last: Schweiger

state: California

address: 2300 Delaware

institute: UCSC Genomics Institute

description:
Library name: Sample 7
Pip-seq

data_processing:
Cells were excluded if they had mitochondrial content > 20%, unique gene counts below the 5th percentile, or total RNA counts > 50,000. SCTransform was applied with mitochondrial regression,ariable genes were selected (Lause et al., 2021; Choudhary and Satija, 2022). Dimensionality and 3,000 v reduction was performed using 40 principal components, followed by Leiden clustering at resolutions from 0.5 to 2. Clusters were visualized using UMAP (Becht et al., 2019}, and resolution selection was guided by marker gene expression. Cell types were annotated using the Allen Brain Atlas (Yao et al., 2021}), UCSC Cell Browser (Speir et al., 2021}, and the Arlotta developmental atlas (Di Bella et al., 2021). For reference mapping, dorsal forebrain datasets were integrated using Seurat’s standard workflow: log-normalization (scale factor 10,000), variable gene selection, data scaling, and PCA (30 components). Harmony was used for integration prior to label transfer via canonical correlation analysis (CCA)-based anchor identification (Hao et al., 2024). Neuronal cells were subset and dimensionality reduction was redone after reperforming SCTransform to rescale neuronal genes.
Assembly: GRCm39 mouse reference genome (GENCODE vM29 2022.04, Ensembl 106)
Supplementary files format and content: Processed data counts and metadata are in the .rds object format from Seurat

source_name: Ventral Forebrain organoid

extract_protocol:
Organoids were dissociated using the Worthington Papain Dissociation System (#LK003150) following manufacturer instructions. Libraries were prepared using the PIPseq T2 Single Cell RNA v4.0PLUS platform (Fluent #FBSSCRT28V4.05) or Illumina Single Cell 3' RNA Prep, T2 (Illumina #20135689), pooling 3,333 cells per genotype (10,000 total per library).
Sequencing was conducted on an AVITI PE75 Flowcell (Element Biosciences) at the UC Davis Technologies Core, generating approximately 900 million reads. Raw FASTQ files were processed using the PIPseeker pipeline (v3.3), with default parameters for alignment, transcript quantification, and cell calling against the GRCm39 mouse reference genome (GENCODE vM29 2022.04, Ensembl 106).

value: Ventral Forebrain organoid

value: Neurons


title: VENT_30

description:
Library name: Sample 6
Pip-seq


title: VENTRAL_D60_2

description:
Library name: Sample 5
Pip-seq


title: SE,rep3


title: Hepa_sh2_2

description:
Library name: Sample38
Hepa_sh2_2


title: SA,rep1


title: Hepa_lucif3

description:
Library name: Sample33
Hepa_lucif3

value: lucif-knockdown


title: GOT1_120 MBq_(3×40_1d-fractions)_replicate 1

description: Test

source_name: GOT1, 120 MBq 177-Lu-octreotate (3×40, 1d-fractions), replicate 1

value: Balb/c NM


title: Untreated Sample 6

description:
Counts for 618 genes using total RNA harvested from TIGK cells
N6

value: Untreated


title: SASAI_D30

description:
Library name: Sample 4
Pip-seq

source_name: Dorsal Forebrain organoid

value: Dorsal Forebrain organoid


title: WT,rep3


title: Hepa_lucif2

description:
Library name: Sample32
Hepa_lucif2

value: Hepa1-6 cells

value: liver cell line


title: DORSAL_D60_2

description:
Library name: Sample 3
Pip-seq


title: Untreated Sample 5

description:
Counts for 618 genes using total RNA harvested from TIGK cells
N5


title: S. sputigena treated Sample3

description:
Counts for 618 genes using total RNA harvested from TIGK cells
S3


title: Untreated Sample 4

description:
Counts for 618 genes using total RNA harvested from TIGK cells
N4


title: DORSAL_D30_2

description:
Library name: Sample 2
Pip-seq


title: CT26_sh3_3

description:
Library name: Sample30
CT26_sh3_3

source_name: CT26 cells

value: CT26 cells

value: colon carcinoma cell line


title: WT,rep1


title: Hepa_sh1_3

description:
Library name: Sample36
Hepa_sh1_3


title: Untreated Sample 3

description:
Counts for 618 genes using total RNA harvested from TIGK cells
N3


title: CL_F85

city: Solna

first: Jasper

last: Panten

address: Tomtebodavägen 23

institute: SciLifeLab

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1).
Assembly: GRCm39
Supplementary files format and content: comma delimited text file

growth_protocol: Cells were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in 2i-containing ESC media (DMEM, 15% FBS, 0.1 mM β-mercaptoethanol, 1,000 U/mL−1 leukaemia inhibitory factor (LIF), CHIR99021 (3 µM), and PD0325901 (1 µM)). NPC differentiation and subcloning was performed as previously described [Gendrel et al., 2014]. NPCs were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in NPC media (N2B27 media supplemented with with FGF2 (10 ng/mL) and EGF (10 ng/mL, both Peprotech)).

extract_protocol:
RNA was extracted from > 1M NPCs using the RNeasy kit and on-column DNAse digestion (Qiagen). RNA was quantified with Qubit RNA Broad Range assay (Invitrogen, Q10211).
RNA was sent to Novogene for RNA integrity and purity quality check followed by Eukaryotic strand-specific mRNA (with PolyA-enrichment) library preparation.
Libraries were then pooled and sequenced on an Illumina Novaseq 6000 platform for 2x150bp paired-end reads for 80 million reads total per sample.

treatment_protocol: All samples were generated from untreated cell lines.

tag: strain

value: 129/Sv x CAST/EiJ

value: neural progenitor cell

value: wild type

value: untreated

tag: experiment number


title: CT26_sh3_2

description:
Library name: Sample29
CT26_sh3_2


title: Untreated Sample 2

description:
Counts for 618 genes using total RNA harvested from TIGK cells
N2

value: TIGK


title: DORSAL_D16

description:
Library name: Sample 1
Pip-seq


title: LPM SPF 4

city: Melbourne

first: Lachlan

last: Dryburgh

state: Victoria

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

country: Australia

institute: The Peter Doherty Institute for Infection and Immunity

description: Library name: Large peritoneal macrophages from SPF mice, replicate 4

data_processing:
Aligned to GRCm39 with STAR (v2.7.8a).
Counts matrix of Ensembl annoatated genes (release 105) generated with subreads (v2.0.0) featureCounts.
Downstream analysis with R (v4.2.0) and limma (v4.54.1).
Assembly: GRCm39/Ensembl release 105
Supplementary files format and content: tab-seperated raw counts matrix with rows representing transcripts and columns representing samples

source_name: C57BL/6J specific pathogen free

growth_protocol: Peritoneal cells were isolated from C57BL/6J mice from Specific Pathogen Free or Germ Free conditions. After antibody staining, large peritoneal macrophages were isolated by fluorescence activated cell sorting.

extract_protocol:
RNA was isolated using the Qiagen Rneasy Micro kit. Macrophages were sorted directly into the lysis buffer and then RNA extracted as per the manufacturer's instructions.
The libraries were constructed using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero™ Plus, following the manufacturer's protocol.

treatment_protocol: C57BL/6J mice were raised in Specific Pathogen Free or Germ Free conditions.

value: Peritoneal cavity

value: large peritoneal macrophages

value: WT

value: Germ free


title: CL_F77


title: CT26_sh3_1

description:
Library name: Sample28
CT26_sh3_1


title: LPM SPF 3

description: Library name: Large peritoneal macrophages from SPF mice, replicate 3


title: Untreated Sample 1

description:
Counts for 618 genes using total RNA harvested from TIGK cells
N1


title: CL_F75


title: CT26_sh2_3

description:
Library name: Sample27
CT26_sh2_3


title: CT26_sh2_2

description:
Library name: Sample26
CT26_sh2_2


title: LPM SPF 2

description: Library name: Large peritoneal macrophages from SPF mice, replicate 2


title: CL_F74


title: Mp_WT

first: Mengfei

last: Song

address: 北京市海淀区颐和园路5号

institute: Peking university

description: Library name: Mp_WT

library_source: genomic

data_processing:
Adapter sequences and low-quality reads were removed by fastp.
Clean reads were mapped to MpTak1_V5.1 genome assembly of Marchantia polymorpha reference genome using bowtie2.
Raw interaction matrixes and ICE normalized matrixes were generated using HiC-Pro with default parameters.
Assembly: MpTak1_V5.1
Supplementary files format and content: Hi-C matrices in .hic format produced by juicer software

molecule: genomic DNA

organism: Marchantia polymorpha

source_name: total seedlings

growth_protocol: grown in at 25degreeC (12h light/12h dark)

extract_protocol:
Samples were cross-linked under vacuum infiltration for 30 min with 3% formaldehyde at 4℃ and quenched with 0.375 M final concentration glycine for 5 min. The cross-linked samples were subsequently lysed. Endogenous nuclease was inactivated with 0.3% SDS, then chromatin DNA were digested by 100U MboI (NEB), and marked with biotin-14-dCTP (Invitrogen) and then ligated by 50U T4 DNA ligase (NEB). After reversing cross-links, the ligated DNA was extracted through QIAamp DNA Mini Kit (Qiagen) according to manufacturers’ instructions. Purified DNA was sheared to 300- to 500-bp fragments and were further blunt-end repaired,
A-tailed and adaptor-added, followed by purification through biotin-streptavidin–mediated pull-down and PCR amplification. Finally, the Hi-C libraries were quantified and sequenced on the Illumina Nova-seq platform (San Diego, CA, USA). Two biological replicates were processed for each material

value: total seedlings

tag: developmental stage

value: 14-day-old seedlings

value: Cam1 ecotype


title: Hepa_lucif1

description:
Library name: Sample31
Hepa_lucif1

tag: cell type

value: lucif-knockdown


title: Mp-pll3-3

address: 北京市海淀区颐和园路5号

description: Library name: Mp-pll3-3

data_processing:
Illumina bcl-convert v3.7.5 software used for basecalling.
After removing reads with adapter sequences and low quality by fastp, the high-quality reads were mapped to the MpTak1_V5.1 genome assembly of Marchantia polymorpha with parameters “--dta --min-intronlen 50 --max-intronlen 6000”. Only unique mapping and MAPQ score > 20 reads were kept using SAMtools version 1.6 for subsequent analysis.
Assembly: MpTak1_V5.1
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA from 14-d-old WT and mutant seedlings grown in at 25°C (12h light/12h dark) were isolated using RNeasy Plant Mini Kits (Sigma). Three biological replicates for each sample were subjected to RNA-seq.
Poly (A) RNA from 1 μg total RNA was used to generate the cDNA library according to the TruSeq RNA Sample Prep Kit protocol. The library was then sequenced using a HiSeq Xten system (Illumina).

tag: genotype

value: pll3 mutant


title: LPM SPF 1

description: Library name: Large peritoneal macrophages from SPF mice, replicate 1


title: CL_F69


title: CT26_sh2_1

description:
Library name: Sample25
CT26_sh2_1


title: Mp-pll3-2

address: 北京市海淀区颐和园路5号

description: Library name: Mp-pll3-2


title: CL_F66


title: CL_F54


title: LPM Germ Free 4

description: Library name: Large peritoneal macrophages from germ free mice, replicate 4

source_name: C57BL/6J germ free


title: CT26_sh1_2

description:
Library name: Sample23
CT26_sh1_2


title: CL_F49


title: LPM Germ Free 3

description: Library name: Large peritoneal macrophages from germ free mice, replicate 3


title: Mp-pll2-3

address: 北京市海淀区颐和园路5号

description: Library name: Mp-pll2-3

value: pll2 mutant


title: LPM Germ Free 2

description: Library name: Large peritoneal macrophages from germ free mice, replicate 2


title: CT26_sh1_3

description:
Library name: Sample24
CT26_sh1_3

value: CT26 cells


title: Mp_pll2

address: 北京市海淀区颐和园路5号

description: Library name: Mp_pll2


title: CT26_sh1_1

description:
Library name: Sample22
CT26_sh1_1

value: colon carcinoma cell line


title: Mp-pll2-2

address: 北京市海淀区颐和园路5号

description: Library name: Mp-pll2-2


title: LPM Germ Free 1

description: Library name: Large peritoneal macrophages from germ free mice, replicate 1


title: CT26_lucif3

description:
Library name: Sample21
CT26_lucif3


title: CL_F47

value: 129/Sv x CAST/EiJ


title: Mp-pll2-1

address: 北京市海淀区颐和园路5号

description: Library name: Mp-pll2-1


title: CL_F42

value: neural progenitor cell


title: CT26_lucif2

description:
Library name: Sample20
CT26_lucif2


title: CL_F38

value: wild type


title: LPM_GF_4

description: Library name: Large peritoneal macrophages from GF mice, replicate 4

data_processing:
Paired-end reads aligned to GRCm39 using bwa-mem2 (v2.2.1).
Reads at Mr1 locus extracted and coverage calculated with SAMTools (v1.16.1).
Downstream analysis with R  (v4.2).
Assembly: GRCm39
Supplementary files format and content: tab seprated table of read counts, rows represent position in GRCm39 chromosome 1, columns represent samples.

source_name: C57BL/6J  germ free

growth_protocol: Tissues were isolated from C57BL/6J mice from Specific Pathogen Free or Germ Free conditions. After single cell suspensions were prepared from tissues and then antibody staining, the indicated cell types were isolated by fluorescence activated cell sorting.

extract_protocol:
The ATACseq protocol from Grandi et al (DOI: 10.1038/s41596-022-00692-9) was followed as described. Cells were sorted into PBS and processed as per Grandi et al using reagents described.
Libraries were prepared, amplified and quantitated as described in Grandi et al (DOI: 10.1038/s41596-022-00692-9).


title: Mp-pll1-2

address: 北京市海淀区颐和园路5号

description: Library name: Mp-pll1-2

value: pll1 mutant


title: CT26_lucif1

description:
Library name: Sample19
CT26_lucif1


title: LPM_GF_2

description: Library name: Large peritoneal macrophages from GF mice, replicate 2


title: CL_F37

value: untreated


title: Hepa_stk6

description:
Library name: Sample18
Hepa_stk6

source_name: Hepa1-6 cells

value: Hepa1-6 cells

value: liver cell line

value: cells with stk-treatment


title: Mp-pll3-1

address: 北京市海淀区颐和园路5号

description: Library name: Mp-pll3-1


title: LPM_GF_1

description: Library name: Large peritoneal macrophages from GF mice, replicate 1

value: large peritoneal macrophages


title: Mp-pll1-1

address: 北京市海淀区颐和园路5号

description: Library name: Mp-pll1-1

value: total seedlings


title: CL_F35


title: Hepa_stk4

description:
Library name: Sample16
Hepa_stk4

value: WT


title: LPM_SPF_4

source_name: C57BL/6J  specific pathogen free


title: Mp-WT-2

address: 北京市海淀区颐和园路5号

description: Library name: Mp-WT-2

value: 14-day-old seedlings

value: Cam1 ecotype


title: LPM_SPF_3


title: Hepa_stk3

description:
Library name: Sample15
Hepa_stk3


title: Mp-WT-3

address: 北京市海淀区颐和园路5号

description: Library name: Mp-WT-3


title: Hepa_stk5

description:
Library name: Sample17
Hepa_stk5


title: Mp-WT-1

address: 北京市海淀区颐和园路5号

description: Library name: Mp-WT-1


title: CL_F32


title: LPM_GF_3

description: Library name: Large peritoneal macrophages from GF mice, replicate 3


title: Mp-pll1-3

address: 北京市海淀区颐和园路5号

description: Library name: Mp-pll1-3


title: Hepa_stk2

description:
Library name: Sample14
Hepa_stk2


title: CL_F29


title: Kar4_WT_none_3

first: Hernan

middle: A

last: Lorenzi

state: Maryland

address: 8 Center Dr, Bldg 8A

department: National Institutes of Diabetes and Digestive and Kidney Diseas

institute: National Institutes of Health

description: Library name: 39279

data_processing:
Reads were aligned using bwa-mem (Li 2013) against the sacCer3 genome using default options. Aligned and sorted BAM files then had duplicates and non-uniquely mapped reads removed using Picard Tools MarkDuplicates (https://github.com/broadinstitute/picard) using default options (except VALIDATION_STRINGENCY=’LENIENT’) and samtools (v1.19.2 and htslib v1.19.1) (Bonfield et al. 2021; Danecek et al. 2021). BAM files were then further cleaned using samtools view -f 2 (read mapped in proper pair) and -q 30 (minimum mapping quality 30) options.
Assembly: sacCer3
Supplementary files format and content: Bigwig files for final aligned reads after cleaning/deduplication, depth-normalized

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to mid log-phase at 30 °C in YPD pH 3.5 (buffered with 85 mM succinic acid) and split into two portions.

extract_protocol:
Following bead beating and sonication, chromatin from TAP-tagged yeast strains was incubated overnight on IgG-conjugated magnetic Sepharose beads.
Libraries were prepared from immunoprecipitated DNA as described in the ChIP-exo 5.1 protocol (Rossi et al. 2018) pooled at equimolar concentration, and size selected by agarose gel excision (200-500bp). Sequencing was performed in-house on an Element Biosciences AVITI sequencer (2 x 75bp high output kit) to an average of 10M paired-end reads per sample, with data management, quality control, and processing through the PEGR automated workflow (Shao et al. 2022).

treatment_protocol: For the pheromone-treated samples, alpha factor (ABI Scientific; Sterling, VA) dissolved in methanol was added to the culture to 10 µg/ml (6 µM) final concentration. An equal volume of methanol (to 1% v/v final concentration) was added to control cells. Cells were then grown for an additional 90 minutes, at which point >95% had formed shmoos, and formaldehyde was added to a final concentration of 1% and incubated for 15 minutes at 30 °C with shaking. Crosslinking was stopped by the addition of 2.5 M glycine to a final concentration of 125 mM. Approximately 50 OD of crosslinked cells were harvested by centrifugation, washed twice with ST buffer (10 mM Tris-Cl pH 7.5, 100 mM NaCl) containing a protease inhibiter cocktail at 0.2% (cOmplete mini, EDTA-free, Roche), and cell pellets were flash frozen in liquid nitrogen. Samples were shipped to the Cornell BRC Epigenomics Facility for ChIP-exo processing and sequencing.

value: MATa his3D1 leu2D0 met15D0 ura3D0 KAR4::TAP-HIS3MX6


title: LPM_SPF_1


title: Hepa_stk1

description:
Library name: Sample13
Hepa_stk1


title: CL_F27


title: B_SPF_4

description: Library name: B cells from SPF mice, replicate 4

value: B lymphocytes


title: Kar4_WT_alpha_3

description: Library name: 39278


title: Hepa_dmso3

description:
Library name: Sample12
Hepa_dmso3

value: cells with dmso-treatment


title: CL_F26


title: CL_F25


title: Hepa_dmso2

description:
Library name: Sample11
Hepa_dmso2


title: Ste12_kar4∆_alpha_2

description: Library name: 39272

value: MATa his3D1 leu2D0 met15D0 ura3D0 STE12::TAP-HIS3MX6 kar4::KanMX


title: Ste12_kar4∆_none_2

description: Library name: 39273


title: CL_F24

value: 129/Sv x CAST/EiJ


title: Hepa_dmso1

description:
Library name: Sample10
Hepa_dmso1


title: LPM_SPF_2


title: B_SPF_2

description: Library name: B cells from SPF mice, replicate 2


title: Ste12_WT_none_2

description: Library name: 39271

value: MATa his3D1 leu2D0 met15D0 ura3D0 STE12::TAP-HIS3MX6


title: CL_F34

value: neural progenitor cell

value: wild type


title: CT26_stk6

description:
Library name: Sample9
CT26_stk6

value: CT26 cells

value: colon carcinoma cell line


title: CL_F23

value: untreated


title: E7.0_Ctrl, snRNAseq

first: Jingjing

last: He

state: 2 Sipailou

address: 2 Sipailou

department: School of Life Science and Technology

description: 10x Genomics

data_processing:
The barcoded processing and gene counting were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryo

extract_protocol:
To prepare single cells for snRNA-seq, embryos at E7.0 were dissected in cold sterile 1×PBS without Ca2+, Mg2+ under a stereo microscope. Embryos were staged based on their morphology. The Reichert?s membrane and ectoplacental cone were removed, and genotypic identification of embryos was carried out. Embryos were placed into a 1.5 ml microfuge tube and digested into single cells using TrypLETM Express (Thermo) at 37°C.
snRNA-seq was performed on single-cell suspensions using 10× Genomics.

value: Hand1 F/F or Hand1 F/+

value: embryo

tag: age


title: Ste12_WT_alpha_2

description: Library name: 39270


title: AM_SPF_3

description: Library name: Alveolar macrophages from SPF mice, replicate 3

value: alveolar macrophages


title: Kar4_WT_none_2

description: Library name: 36220


title: CT26_stk5

description:
Library name: Sample8
CT26_stk5

value: WT

value: cells with stk-treatment


title: AM_SPF_2

description: Library name: Alveolar macrophages from SPF mice, replicate 2


title: Kar4_WT_alpha_2

description: Library name: 36219


title: E7.0_Hand1 CKO, snRNAseq

description: 10x Genomics

value: Hand1 F/F; Mesp1 cre


title: E7.0, snATACseq

description: 10x Genomics

data_processing:
The alignment, filtering, barcode counting and counting of both ATAC and GEX molecules were made using the Cell Ranger ARC software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Distal colon

extract_protocol:
Embryos staged at E7.0 were collected and washed with cooled 0.5% BSA/PBS for twice. Sufficient embryos were pooled and then subjected to 200 uL TrypLE for cell dissociation for 10 min at 37°C with frequent gentle mixture. Single-cell suspension of embryos were then quenched and washed with 0.5% BSA/PBS, and finally filtered using 40 μm Flowmi cell strainer.
The acquired single cell suspension were then subjected to nuclei isolation, library preparation by following the manufacturer’s instruction. The library was sequenced on Novaseq 6000 platform with recommended sequencing depths and read lengths.
scMulti-omics

value: Goblet cells

value: Distal colon


title: AM_SPF_1

description: Library name: Alveolar macrophages from SPF mice, replicate 1


title: B_SPF_3

description: Library name: B cells from SPF mice, replicate 3

value: B lymphocytes


title: E7.0, snRNAseq

description: 10x Genomics

source_name: 8th section of the small intestine

value: 8th section of the small intestine


title: 919_Non UV

city: Seattle

first: Jie

last: An

state: WA

address: 750 Republican Street

institute: University of Washington

description: Library name: KE37

data_processing:
Reads were aligned to the mm10 genome. Doublets were removed using scDblFinder v1.12.0 with default settings. Seurat merge was used to combine the sample matrices into a single gene expression matrix.
Seurat 4.3.0 was used to process the expression matrix. Cells containing fewer than 200 UMI and/or >25% mitochondrial reads were removed. Gene expression was log normalized, scaled using Seurat.
Principal component analysis was used to reduce the dimensionality of the data, and then UMAP coordinates were computed and used to cluster the cells.
Clusters were labeled using a custom list of biomarker genes. Batch effect correction was performed using harmony v1.0, utilizing each individual donor as a batch
Assembly: Reads were aligned to the mm10 genome.
Supplementary files format and content: RDS withRDS objects

source_name: Skin

growth_protocol: Mice used in this study were 12-16 week old C57BL/6 (B6, wild type) females.

extract_protocol:
Nuclei isolation and fixation was performed by the Brotman Baty Institute at the University of Washington.
Single-nucleus combinatorial indexing RNA-seq (sci-RNA-seq3) was performed as described {Cao, et al 2019} and largely followed the optimized sci-RNA-seq3 protocol {Martin,et al 2023 }. In sci-RNA-seq3, three rounds of barcoding - introduced by reverse transcription, hairpin ligation, and indexed PCR reactions - tag transcripts with unique combinatorial indices that can be traced back to individual nuclei. The library was sequenced on an Illumina NovaSeq S4 flow cell at the University of Washington Northwest Genomics Center core sequencing facility.

treatment_protocol: Mice were anesthetized with isoflurane and a single dose of UVB (500 mJ/cm2) was delivered to the shaved whole back using FS40T12/UVB bulbs (National Biological Corporation). The narrow band UVB light energy (290-320 nm) at the dorsal surface was measured with Photolight IL1400A radiometer with a SEL240/UVB detector (International Light Technologies). Biopsies were taken at times 0 and 12 hrs (scRNAseq). All animal experiments were approved by the Institutional Animal Care and Use Committee of the University of Washington, Seattle.

value: Skin

value: Non-treated


title: Kar4_WT_none_1

description: Library name: 36212

value: MATa his3D1 leu2D0 met15D0 ura3D0 KAR4::TAP-HIS3MX6


title: CT26_stk2

description:
Library name: Sample5
CT26_stk2


title: Input_ChIP_2

data_processing:
Adapter sequences were removed from Fastq files using trim_galore (v0.6.6) with default parameters. After trimming, ChIP-seq reads were aligned to the mm10 mouse genome using Bowtie2 (v2.3.4.3) with ‘--no-mixed’ and ‘--no-discordant’ parameters. The aligned files were sorted and converted to BAM format using SAMtools (v1.9). BigWig files were subsequently generated using deepTools bamCoverage (v3.5.0), employing CPM normalization and ignoring duplicates. Peak calling was performed with MACS2 (v 2.2.7.1) with a significance threshold of p-value less than 1e-5.
Assembly: mm10
Supplementary files format and content: *.bw: bigWig files;*.narrowPeak: bed files

growth_protocol: Mouse E14 ESCs were differentiated into embryoid bodies (EBs) at a density of 75,000 cells/ml in 6 cm dishes for 48 h in serum-free media (DMEM (Hyclone, SH30243.01), DMEM/F12 (1:1) (Gibco, 11320-033), 0.05% BSA (Sigma, A1933), 1 × GlutaMax (Gibco, 35050-061), B27 supplement (Gibco, 12587010), N2 supplement (Gibco, 17502048), supplemented with 50 mg/ml ascorbic acid (Alfa Aesar, 50-81-7) and 4.5×10-4 M monothioglycerol). EBs were dissociated into single cells and re-aggregated as MES cells for 40 h at 50,000 cells/ml in the presence of 5 ng/mL human VEGF (Novoprotein, C083) and 10 ng/ml human Activin A (Peprotech, 96-120-14-10) and 0.3 ng/ml human BMP4 (R&D, 5020-BP-010). MES cells were dissociated and plated as a monolayer in gelatin-coated 12-well plate at 50,000 cells/ml in StemPro-34 (Gibco, 10639011) supplemented with 5 ng/mL VEGF (Novoprotein, C083), 10 ng/mL human basic FGF (Gibco, PMG0035) and 25 ng/mL FGF10 (R&D, 345-FG-250). CP cells were harvested after differentiation for 32 h.

extract_protocol:
5 × e6 cells were crosslinked with 1% formaldehyde for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. Fixed cells were incubated in 0.5 ml lysis buffer for 10 mins on ice. After adding 1 ml dilution buffer, chromatins were sonicated into 200-800 bp fragments using Bioruptor (Diagenode) and immunoprecipitated with protein A agarose beads and specific antibody at 4 ? for 12 h. Immunoprecipitates were washed with Wash Buffer I, Wash Buffer II, Wash Buffer III and TE, respectively. After the final wash, DNA was eluted and reverse-crosslinked at 65?°C for at least 6 h. DNA was then purified and used for PCR amplification or ChIP-seq library preparation. ChIP-seq libraries were prepared with VAHTS Universal DNA Library Prep Kit for sequencing.
The ChIP-seq libraries were prepared with VAHTS Universal DNA Library Prep Kit for Illumina V3

value: Mouse Embryonic stem cells


title: Kar4_WT_alpha_1

description: Library name: 36211


title: 918_Non UV

description: Library name: KE36

value: 12-16 week old C57BL/6 (B6, wild type) females


title: B_SPF_1

description: Library name: B cells from SPF mice, replicate 1


title: CT26_TK1

description:
Library name: Sample4
CT26_stk1

value: CT26 cells

value: colon carcinoma cell line


title: 917_Non UV

description: Library name: KE35


title: Ste12_kar4∆_none_1

description: Library name: 36206

value: MATa his3D1 leu2D0 met15D0 ura3D0 STE12::TAP-HIS3MX6 kar4::KanMX


title: CT26_dmso3

description:
Library name: Sample3
CT26_dmso3

value: cells with dmso-treatment


title: Input_ChIP_1


title: Ste12_kar4∆_alpha_1

description: Library name: 36205


title: 922_12hr_UV

description: Library name: KE34

value: UVR Radiation


title: Foxf1_HA_ChIP_Rep_2

tag: chip antibody

value: HA(Homemade)


title: CT26_stk4

description:
Library name: Sample7
CT26_stk4

value: WT

value: cells with stk-treatment


title: 921_12hr_UV

description: Library name: KE33

tag: tissue


title: CT26_dmso2

description:
Library name: Sample2
CT26_dmso2


title: Ste12_WT_none_1

description: Library name: 36204

value: MATa his3D1 leu2D0 met15D0 ura3D0 STE12::TAP-HIS3MX6


title: CT26_dmso1

description:
Library name: Sample1
CT26_dmso1


title: Foxf1_HA_ChIP_Rep_1


title: Ste12_WT_alpha_1

description: Library name: 36203


title: 920_12hr_UV

description: Library name: KE32


title: Hand1_HA_ChIP


title: SK-N-SH cells, RGS6e Reverse, rep1

status: Public on Dec 07 2025

city: Guangzhou

first: Zhongju

last: Wang

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

description: Library name: SK-N-SH-RGS6e-OE-1-

data_processing:
The raw sequencing data obtained from the Illumina platform, referred to as Raw Reads, undergoes data processing to generate high-quality sequences, known as Clean Reads. This processing involves the removal of low-quality sequences and the elimination of adapter contamination. The Clean Reads are then aligned to the hg19 reference genome using the STAR aligner with default parameters. Quantification is performed using FeatureCounts, resulting in the generation of Counts and FPKM values.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM or Count values.

source_name: SK-N-SH

growth_protocol: The SK-N-SH cells were cultured in MEM supplemented with 1%Pen-Strep, 1%NEAA and 10% FBS (FSP500, ExCell Bio) at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
Trizol reagent was used to extract total RNA.
Using magnetic beads coated with Oligo(dT), mRNA with polyA tails is enriched and purified from RNA samples. Fragmentation Buffer is then added to the purified mRNA to fragment it. The resulting RNA fragments serve as templates for the reverse transcription process, utilizing random primers to synthesize the first strand of cDNA. Subsequently, a 2nd Strand Marking Buffer and a 2nd Strand/End Repair Enzyme Mix are introduced to synthesize the second strand of cDNA. Following this, end repair is performed, an adenine base is added, and sequencing adapters are ligated. The target fragments are then recovered through magnetic bead selection and subjected to PCR amplification, thereby completing the entire library preparation process.

value: SK-N-SH

value: neuroblastoma


title: SK-N-SH cells, RGS6e Reverse, rep2

description: Library name: SK-N-SH-RGS6e-OE-2-


title: CT26_stk3

description:
Library name: Sample6
CT26_stk3


title: SK-N-SH cells, RGS6e Forward, rep1

description: Library name: SK-N-SH-RGS6e-OE-1


title: SK-N-SH cells, pcDNA3.1, rep 2

description: Library name: SK-N-SH-pcDNA3-1-2


title: SK-N-SH cells, RGS6e Forward, rep2

description: Library name: SK-N-SH-RGS6e-OE-2


title: sorted neurons, low gfp, mouse 376

city: Los Angeles

first: J Edward

last: van Veen

state: CA

address: 610 Charles E Young Dr

department: IBP

institute: University of California, Los Angeles

description: Library name: 376l

data_processing:
transcriptome assembly - kallisto 0.46.2
Assembly: GRCm39
Supplementary files format and content: tsv files containing gene level counts

source_name: brain

extract_protocol:
Total RNA isolation from cells in trozol follwed by rRNA depletion
Illlumina ultra low input

value: brain

value: neuron

value: vehicle


title: SK-N-SH cells, pcDNA3.1, rep1

description: Library name: SK-N-SH-pcDNA3-1-1


title: sorted neurons, low gfp, mouse 375

description: Library name: 375l

value: estradiol


title: sorted neurons, low gfp, mouse 367

description: Library name: 367l


title: Cla SDX cells bio3

city: Taipei

first: Ying-Chung Jimmy

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Life Science

country: Taiwan

institute: National Taiwan University

data_processing:
The data was processed using Cell Ranger v7.1.0 pipeline from 10x Genomics with the commands "cellranger mkref" and "cellranger count" to generate single-cell transcript abundance matrices named filtered_feature_bc_matrix.h5.
Assembly: Cunninghamia lanceolata (https://doi.org/10.1101/2022.10.25.513437)
Supplementary files format and content: hd5

organism: Cunninghamia lanceolata

source_name: SDX

growth_protocol: Around 6-month-old C. lanceolate plants, named Yang061 (National Fine Forest Varieties ID: China R-SC-CL-003-2018), were purchased from Fujian Yangkou State Owned Forest Farm and were raised to 2-year-old.

extract_protocol:
Tree stems were cut into 10-cm segments. Debarked stem segments were dipped into freshly prepared enzyme solution (20 mM MES, pH 5.7, 0.25 M mannitol, 20 mM KCl, 1.5% wt/vol cellulase R10, 0.4% wt/vol Macerozyme R10, 0.2% wt/vol Pectolyase Y23, 10 mM CaCl2, and 0.1% BSA) for ~2 h at room temperature. Enzyme-digested stem segments were transferred to MMG solution (4 mM MES, pH 5.7, 0.25 M mannitol and 15 mM MgCl2, room temperature) to release SDX protoplasts. The protoplasts were filtered with 70-μm nylon mesh, pelleted at 900g centrifugation for 3 min at room temperature, and resuspended in MMG solution. The isolated SDX protoplasts were observed using a fluorescence microscope.
Single-cell sequencing libraries of three biological replicates for C. lanceolate were generated using Chromium Single Cell 3’ Library and Gel Bead Kit v2 or v3 (10x Genomics) according to user manual. The number of cells loaded following to the instructions in the 10x Genomics manual aimed at minimizing the formation of doublets or multiplets.

value: SDX

tag: line

value: wild type


title: Cla SDX cells bio2


title: sorted neurons, low gfp, mouse 363

description: Library name: 363l


title: sorted neurons, high gfp, mouse 375

description: Library name: 375h


title: CT19 cortex snRNA-seq

city: Tokyo

first: Masaki

last: Nishioka

address: Bunkyo-ku Hongo 2-1-1

institute: Juntendo University

description:
Library name: CT19-FrC
10x Genomics 3' GEM dual index v3.1

data_processing:
Sequencing output files were processed with Cell Ranger (v7.0.0, 10x Genomics) using default parameters and the GRCh38-A reference genome to generate count data. All samples achieved a read depth exceeding 50,000 reads per nucleus, with a median depth of 74,000.
Assembly: GRCh38 (10x Genomics GRCh38-2020-A)
Supplementary files format and content: Tab-separated barcode and matrix files were generated in the 10x Genomics Cell Ranger format. The features.tsv.gz file was shared across all samples.

source_name: Frontal cortex (BA10)

extract_protocol:
Thalamic sections were prepared from the medial portion of the thalamic slab encompassing the mammillary body, and frontal cortex sections were prepared from the BA10 cortical slab. Section thickness ranged from 100–200 μm. Cell nuclei were isolated from ~50 mg of thalamic or frontal cortex tissue, with myelin removed by four-layer density-gradient centrifugation using OptiPrep (35%, 29%, 25%, and 0%) supplemented with RNase inhibitor. To minimize systematic bias due to experimental batches, two specimens (one from a bipolar disorder patient and one from a control subject) were processed in parallel from nuclei isolation through snRNA-seq library preparation. All procedures were performed by the same experimenter, who was blinded to disease status, to avoid inter-experimenter variability.
Nuclei isolated from the medial thalamus and frontal cortex were subjected to library preparation using the 10x Genomics Chromium Single Cell 3’ RNA v3.1 dual index protocol, following the manufacturer’s instructions (10x Genomics). The target recovery was 5,000 nuclei per sample, and libraries were amplified with 14 PCR cycles. Sequencing was performed on the Illumina NextSeq 2000 platform according to the protocols provided by Illumina and 10x Genomics. To minimize experimental bias, all library preparations were carried out by the same experimenter, with case–control pairs processed in parallel.

value: Frontal cortex (BA10)


title: CT20 cortex snRNA-seq

description:
Library name: CT20-FrC
10x Genomics 3' GEM dual index v3.1


title: sorted neurons, low gfp, mouse 365

description: Library name: 365l


title: sorted neurons, high gfp, mouse 376

description: Library name: 376h


title: sorted neurons, high gfp, mouse 367

description: Library name: 367h


title: sorted neurons, low gfp, mouse 359

description: Library name: 359l


title: CT17 cortex snRNA-seq

description:
Library name: CT17-FrC
10x Genomics 3' GEM dual index v3.1


title: sorted neurons, high gfp, mouse 363

description: Library name: 363h


title: sorted neurons, high gfp, mouse 365

description: Library name: 365h


title: CT16 cortex snRNA-seq

description:
Library name: CT16-FrC
10x Genomics 3' GEM dual index v3.1


title: sorted neurons, high gfp, mouse 359

description: Library name: 359h


title: Treat_iso15-5

city: Chongqing

first: Juan

address: No. 131 Yubei Road, Shapingba District

institute: Chongqing University

description:
Library name: Treat_iso15-5
Treat_iso15-5

data_processing:
Raw sequencing reads were filtered to remove low-quality reads and adapters. Clean reads were aligned to the human reference genome using Hisat2. Gene expression levels were quantified as FPKM. Differential expression analysis was performed to identify DEGs, followed by GSEA for pathway enrichment analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

source_name: cell

extract_protocol:
Total RNA was extracted from HCC cells using a commercial RNA extraction kit (Trizol reagent). RNA purity and integrity were verified by NanoDrop and agarose gel electrophoresis, respectively.
cDNA libraries were constructed from qualified total RNA. Briefly, mRNA was enriched using oligo(dT) beads, fragmented, and reverse-transcribed into cDNA. After end repair, adapter ligation, and PCR amplification, the libraries were quality-controlled and quantified before sequencing.

value: cell

tag: cell line

value: hepatocellular carcinoma cells


title: CT14 cortex snRNA-seq

description:
Library name: CT14-FrC
10x Genomics 3' GEM dual index v3.1


title: CT13 cortex snRNA-seq

description:
Library name: CT13-FrC
10x Genomics 3' GEM dual index v3.1


title: Treat_iso15-4

description:
Library name: Treat_iso15-4
Treat_iso15-4


title: Treat_iso15-3

description:
Library name: Treat_iso15-3
Treat_iso15-3


title: Treat_iso15-1

description:
Library name: Treat_iso15-1
Treat_iso15-1


title: CT12 cortex snRNA-seq

description:
Library name: CT12-FrC
10x Genomics 3' GEM dual index v3.1


title: CT09 cortex snRNA-seq

description:
Library name: CT09-FrC
10x Genomics 3' GEM dual index v3.1


title: CT10 cortex snRNA-seq

description:
Library name: CT10-FrC
10x Genomics 3' GEM dual index v3.1


title: Cla SDX cells bio1


title: CT11 cortex snRNA-seq

description:
Library name: CT11-FrC
10x Genomics 3' GEM dual index v3.1


title: Control_con-5

description:
Library name: Control_con-5
Control_con-5


title: CT08 cortex snRNA-seq

description:
Library name: CT08-FrC
10x Genomics 3' GEM dual index v3.1


title: Control_con-4

description:
Library name: Control_con-4
Control_con-4


title: CT05 cortex snRNA-seq

description:
Library name: CT05-FrC
10x Genomics 3' GEM dual index v3.1


title: CT15 cortex snRNA-seq

description:
Library name: CT15-FrC
10x Genomics 3' GEM dual index v3.1


title: Control_con-1

description:
Library name: Control_con-1
Control_con-1


title: Control_con-2

description:
Library name: Control_con-2
Control_con-2


title: CT07 cortex snRNA-seq

description:
Library name: CT07-FrC
10x Genomics 3' GEM dual index v3.1


title: CT04 cortex snRNA-seq

description:
Library name: CT04-FrC
10x Genomics 3' GEM dual index v3.1


title: CQ1_231

city: 南充市

first: ziru

last: zhou

state: 四川

address: 顺庆区涪江路234号

institute: 川北医学院

description: Library name: sample4

data_processing:
Sequencing data quality control、Reference genome alignment、Quantification、Differential analysis、Enrichment analysis、Alternative splicing analysis、Variant calling
Assembly: GRCh38
Supplementary files format and content: File 'gene_count.xls': Tab-delimited text file constituting the raw gene expression count matrix. Rows represent genes (with gene identifiers in the first column), and columns represent individual libraries/samples (e.g., CK1_231, CQ2_231). The values are the raw read counts aligned to each gene, serving as the primary data for differential expression analysis.

extract_protocol:
After 48 hours of PM2.5 exposure, total RNA was extracted using TRIzol reagent (Invitrogen, USA).
Libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions, and sequencing was ultimately performed on an Illumina NovaSeq 6000 platform.


title: CQ3_231

description: Library name: sample6


title: Treat_iso15-2

description:
Library name: Treat_iso15-2
Treat_iso15-2


title: CT02 cortex snRNA-seq

description:
Library name: CT02-FrC
10x Genomics 3' GEM dual index v3.1


title: CT03 cortex snRNA-seq

description:
Library name: CT03-FrC
10x Genomics 3' GEM dual index v3.1


title: CT01 cortex snRNA-seq

description:
Library name: CT01-FrC
10x Genomics 3' GEM dual index v3.1


title: CT18 cortex snRNA-seq

description:
Library name: CT18-FrC
10x Genomics 3' GEM dual index v3.1


title: BD21 cortex snRNA-seq

description:
Library name: BD21-FrC
10x Genomics 3' GEM dual index v3.1


title: BD19 cortex snRNA-seq

description:
Library name: BD19-FrC
10x Genomics 3' GEM dual index v3.1


title: CK1_231

description: Library name: sample1

value: Control


title: CK2_231

description: Library name: sample2


title: MCF-7_CQ2

description: Library name: sample5

data_processing:
Sequencing data quality control、Reference genome alignment、Quantification、Differential analysis、Enrichment analysis、Alternative splicing analysis、Variant calling
Assembly: GRCh38
Supplementary files format and content: File 'gene_count.xls': Tab-delimited text file constituting the raw gene expression count matrix. Rows represent genes (with gene identifiers in the first column), and columns represent individual libraries/samples (e.g., MCF7_CK1, MCF7_CQ2). The values are the raw read counts aligned to each gene, serving as the primary data for differential expression analysis.


title: BD18 cortex snRNA-seq

description:
Library name: BD18-FrC
10x Genomics 3' GEM dual index v3.1


title: BD17 cortex snRNA-seq

description:
Library name: BD17-FrC
10x Genomics 3' GEM dual index v3.1


title: CQ2_231

description: Library name: sample5


title: MCF-7_CQ1

description: Library name: sample4


title: BD20 cortex snRNA-seq

description:
Library name: BD20-FrC
10x Genomics 3' GEM dual index v3.1


title: BD16 cortex snRNA-seq

description:
Library name: BD16-FrC
10x Genomics 3' GEM dual index v3.1


title: CT06 cortex snRNA-seq

description:
Library name: CT06-FrC
10x Genomics 3' GEM dual index v3.1


title: Control_con-3

description:
Library name: Control_con-3
Control_con-3


title: BD15 cortex snRNA-seq

description:
Library name: BD15-FrC
10x Genomics 3' GEM dual index v3.1


title: MCF-7_CK3

description: Library name: sample3


title: WT,rep2

data_processing:
Sequenced reads were trimmed by SOAPnuke (V2.1.0) ( –lowQual=20，–nRate=0.005，–qualRate=0.5)
then mapped to mm10 whole genome using HISAT2 (v2.1.0), and raw counts were calculated by FeatureCounts
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: primary peritoneal macrophages

extract_protocol:
Total RNA is extracted by Trizol reagent, then enriched with oligo-dT beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary macrophage


title: MCF-7_CK2

description: Library name: sample2


title: C_J16_H

city: Montpellier

first: Eric

last: Rivals

address: 161 Rue Ada

department: Montpellier University and CNRS

country: France

institute: Laboratoire d'informatique, de robotique et de microélectronique de Montpellier

description:
Library name: C_J16_H_S54_R1_001
polysome profiling - replicate C - time D16

data_processing:
Transcriptome (cytosomal fraction) and translatome (polysomal fraction) libraries read quality were assessed using FastQC v0.11.9 (Babraham Institute, Cambridge, UK). Reads were filtered according to quality threshold Q35, and were trimmed of 10 bases at their start, using Cutadapt v3.2. With Cutadapt, we set the minimal length of trimmed reads at 50 nucleotides; all trimmed reads shorter than 50 were removed from the analysis. High quality reads were then aligned using STAR v2.7.9a, on the release 104 of the Homo sapiens reference genome GRCh38 primary_assembly, and annotated with the GRCh38.104 Ensembl annotation file. Quantification of mapped reads was performed using featureCounts from subread v2.0.1. Statistical differential analyses were performed between the different times of the kinetic. Day 0 (D0) was used as control and compared to others times of the kinetic (D1, D2, D7, D14 and D16) for each fraction, whether cytoplasmic and polysomal (> at 3 ribosomes on the RNA). Statistics used Wald test from DESeq2 R package v1.30.1 (Supplemental Tables 1, 2 and 3).
For each dataset, the read counts were filtered with a minimum of 1 count per million per biological sample after size factors estimation (Relative Log Expression normalization), and then dispersion was estimated (using DESeq2). P-value adjustment that corrects for multiple tests to lower the risk of false discovery was performed with the method of Benjamini and Hochberg. Genes with BH corrected p-values below 0.05 were kept. Then, results from these simple comparisons are used in a double comparison between fractions to categorize genes involved in transcription or translation or in both mechanisms, using Pandas v1.1.5. Gene identifications were performed with biodbnet dbtodb API. Functional annotations were performed with gProfileR v0.2.1 using a g:SCS threshold < at 0.05. GO terms were then classified according to their depths and levels using goatools v1.3.1. Differential transcripts were annotated from the databases with msigdb R package v1.2.0. Fisher p-value corrected by FDR were performed on results from the enrichment according to the probability of their presence in the human genome. The heatmap was performed using matplotlib v3.3.0, seaborn v0.11.2, pandas v1.1.5 and clustergrammer v2. PCA in 3 dimensions was performed with rgl R package.
Assembly: GRCh38 v104
Supplementary files format and content: tab-delimited text files include count values for each Sample.

molecule: cytoplasmic RNA

source_name: cell line

growth_protocol: The CRC cell line HCT-116 (ATCC CCL-247) was obtained from ATCC. This cell line was authenticated by PCR single-locus-technology (Eurofins, Ebersberg, Germany). CRC cells were maintained in Dulbecco Minimum Essential Medium— GlutaMax (Invitrogen) supplemented with 10% fetal bovine serum (FBS), penicillin (100U/mL) and streptomycin (100μg/mL) at 37 °C with 5% CO2. Cells were routinely tested against mycoplasma infection.

extract_protocol:
At each time point of the experiment (namely D0 (before adding 5-FU to medium), D1, D2, D7, D14 and D16), cells were treated for 10 min with emetin (Sigma) 25µg/ml, washed twice with PBS, and harvested by trypsination. Cytoplasmic lysates were prepared by incubation of cells for 10 min in hypotonic buffer (10 mM Tris-HCl pH 7.4, 0.5 mM MgCl2, 10 mM KCl, 1X CompleteTM EDTA free protease inhibitor (Roche) and 10 U/mL RNAseOutTM (Invitrogen)) followed by addition of 0.7 % NP-40. Swelling cells are lysed by shaking in Precellys Evolution tissue homogenizer (10s, 4500rpm). Nuclei were pelleted by centrifugation at 750 g for 5 min at 4°C, and mitochondria were pelleted by centrifugation at 12,000 g for 10 min at 4°C. The protein content of the cytosolic extract was measured by Bradford assay and samples containing 2mg protein were loaded over 15–50% sucrose gradients (poured using the Gradient Master (Serlabo Technologies)). After ultracentrifugation at 38,000rpm for 105 min at 4°C on a SW41 Beckman rotor, 18 fractions of 700µl each were collected from each gradient while 254nm absorbance profiles were generated using an ISCO UA-6 detector. RNA sampless were extracted from 150 µL of each polysomal fraction using TRIzolTM LS reagent (Invitrogen) following manufacturer’s instructions and suspended in RNAse-free water. A fraction of each sample was loaded on an agarose gel, to identify their RNA content, and polysomal fractions containing mRNA with more than three ribosomes were pooled.
RNA-seq libraries were prepared using the Universal Plus mRNA-seq kit (Tecan Trading AG, Switzerland) according to the manufacturer’s instructions. Briefly, polyadenylated RNAs were selected using oligo-dT magnetic beads. We fragmented the polyA+ RNAs using divalent cations at elevated temperature and reverse-transcribed them using random hexamers, reverse transcriptase and actinomycin D. Deoxy-TTP was replaced by dUTP during the second strand synthesis to prevent its amplification by PCR. We repaired the double-stranded cDNAs and we adenylated them at their 3' ends followed by a ligation to Tecan adaptors including UDIs. We submitted ligated cDNAs to a strand selection prior to a PCR amplification for 15 cycles and purified the PCR products using AMPure XP Beads (Beckman Coulter Genomics, Brea, CA, USA). The size distribution of the resulting libraries was monitored using a Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA) and the libraries were quantified using the KAPA Library quantification kit (Roche, Basel, Switzerland). Libraries were denatured with NaOH, neutralized with Tris-HCl, and diluted to 300 pM. We performed the clustering and sequencing on a NovaSeq 6000 (Illumina, San Diego, CA, USA) using the single-read 100nt protocol on an S2 flow cell, to generate 50 to 84 million sequences.

treatment_protocol: Cells were plated 48 h before 5-FU treatment. 5-FU was kindly provided by the Centre Léon Bérard (Lyon, FRANCE). The stock solution (ACCORD 50mg/ml) was diluted immediately before use in DMEM and added to cell culture medium. CRC cells were seeded at 10^6 cells/10cm dish. Forty-eight hours after seeding, HCT-116 were treated with 10μM 5-FU over 48h.

value: HCT-116 (ATCC CCL-247)

value: CRC cancerous colorectal cell

value: heavy fraction RNA at D16

value: C


title: CK3_231

description: Library name: sample3


title: BD12 cortex snRNA-seq

description:
Library name: BD12-FrC
10x Genomics 3' GEM dual index v3.1


title: MCF-7_CK1

description: Library name: sample1


title: BD14 cortex snRNA-seq

description:
Library name: BD14-FrC
10x Genomics 3' GEM dual index v3.1


title: C_J16_CYTO

description:
Library name: C_J16_CYTO_S42_R1_001
transcriptome - replicate C - time D16

value: cytoplasmic RNA at D16


title: BD11 cortex snRNA-seq

description:
Library name: BD11-FrC
10x Genomics 3' GEM dual index v3.1


title: C_J14_H

description:
Library name: C_J14_H_S53_R1_001
polysome profiling - replicate C - time D14

value: heavy fraction RNA at D14


title: BD10 cortex snRNA-seq

description:
Library name: BD10-FrC
10x Genomics 3' GEM dual index v3.1


title: MCF-7_CQ3

description: Library name: sample6


title: BD09 cortex snRNA-seq

description:
Library name: BD09-FrC
10x Genomics 3' GEM dual index v3.1


title: B_J16_CYTO

description:
Library name: BJ16_CYTO_S24_R1_001
transcriptome - replicate B - time D16

value: B


title: B_J14_H

description:
Library name: B_J14_H_S35_R1_001
polysome profiling - replicate B - time D14


title: BD07 cortex snRNA-seq

description:
Library name: BD07-FrC
10x Genomics 3' GEM dual index v3.1


title: BD08 cortex snRNA-seq

description:
Library name: BD08-FrC
10x Genomics 3' GEM dual index v3.1


title: BD06 cortex snRNA-seq

description:
Library name: BD06-FrC
10x Genomics 3' GEM dual index v3.1


title: A_J16_H

description:
Library name: AJ16_H_S18_R1_001
polysome profiling - replicate A - time D16

value: A


title: A_J14_H

description:
Library name: AJ14_H_S17_R1_001
polysome profiling - replicate A - time D14


title: BD05 cortex snRNA-seq

description:
Library name: BD05-FrC
10x Genomics 3' GEM dual index v3.1


title: B_J14_CYTO

description:
Library name: BJ14_CYTO_S23_R1_001
transcriptome - replicate B - time D14

value: cytoplasmic RNA at D14


title: BD04 cortex snRNA-seq

description:
Library name: BD04-FrC
10x Genomics 3' GEM dual index v3.1


title: BD02 cortex snRNA-seq

description:
Library name: BD02-FrC
10x Genomics 3' GEM dual index v3.1


title: A_J14_CYTO

description:
Library name: AJ14_CYTO_S5_R1_001
transcriptome - replicate A - time D14


title: C_J7_H

description:
Library name: C_J7_H_S52_R1_001
polysome profiling - replicate C - time D7

value: heavy fraction RNA at D7


title: BD01 cortex snRNA-seq

description:
Library name: BD01-FrC
10x Genomics 3' GEM dual index v3.1


title: C_J14_CYTO

description:
Library name: C_J14_CYTO_S41_R1_001
transcriptome - replicate C - time D14


title: CT20 thalamus snRNA-seq

description:
Library name: CT20-Tha
10x Genomics 3' GEM dual index v3.1

source_name: Medial thalamus

value: Medial thalamus


title: C_J2_H

description:
Library name: C_J2_H_S51_R1_001
polysome profiling - replicate C - time D2

value: heavy fraction RNA at D2


title: BD13 cortex snRNA-seq

description:
Library name: BD13-FrC
10x Genomics 3' GEM dual index v3.1

value: Frontal cortex (BA10)


title: CT17 thalamus snRNA-seq

description:
Library name: CT17-Tha
10x Genomics 3' GEM dual index v3.1


title: CT19 thalamus snRNA-seq

description:
Library name: CT19-Tha
10x Genomics 3' GEM dual index v3.1


title: CT18 thalamus snRNA-seq

description:
Library name: CT18-Tha
10x Genomics 3' GEM dual index v3.1


title: C_J1_CYTO

description:
Library name: C_J1_CYTO_S38_R1_001
transcriptome - replicate C - time D1

value: cytoplasmic RNA at D1


title: CT16 thalamus snRNA-seq

description:
Library name: CT16-Tha
10x Genomics 3' GEM dual index v3.1


title: C_J2_CYTO

description:
Library name: C_J2_CYTO_S39_R1_001
transcriptome - replicate C - time D2

value: cytoplasmic RNA at D2


title: CT15 thalamus snRNA-seq

description:
Library name: CT15-Tha
10x Genomics 3' GEM dual index v3.1


title: C_J1_H

description:
Library name: C_J1_H_S50_R1_001
polysome profiling - replicate C - time D1

value: heavy fraction RNA at D1


title: C_J7_CYTO

description:
Library name: C_J7_CYTO_S40_R1_001
transcriptome - replicate C - time D7

value: cytoplasmic RNA at D7


title: C_J0_H

description:
Library name: C_J0_H_S49_R1_001
polysome profiling - replicate C - time D0

value: HCT-116 (ATCC CCL-247)

value: heavy fraction RNA at D0


title: B_J16_H

description:
Library name: B_J16_H_S36_R1_001
polysome profiling - replicate B - time D16

value: CRC cancerous colorectal cell

value: heavy fraction RNA at D16


title: C_J0_CYTO

description:
Library name: C_J0_CYTO_S37_R1_001
transcriptome - replicate C - time D0

value: cytoplasmic RNA at D0

value: C


title: CT14 thalamus snRNA-seq

description:
Library name: CT14-Tha
10x Genomics 3' GEM dual index v3.1


title: B_J7_H

description:
Library name: B_J7_H_S34_R1_001
polysome profiling - replicate B - time D7

value: B


title: CT13 thalamus snRNA-seq

description:
Library name: CT13-Tha
10x Genomics 3' GEM dual index v3.1