title: Saline, replicate2, scRNAseq

description: 10x Genomics

value: hippocampus

value: 18 weeks old

value: Saline, equal volume to methamphetamine for 29days, intraperitoneal injection


title: ATAC-Seq J12

status: Public on Sep 30 2025

type: SRA

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

country: USA

institute: Mayo Clinic

description: Library name: J12

library_source: genomic

data_processing:
Paired end reads were aligned using BWA
Reads were filtered to uniquely mapping read pairs
Peaks were called using MACS2 (q<0.01)
Assembly: hg38
Supplementary files format and content: peak files (narrowPeak)

molecule: genomic DNA

organism: Homo sapiens

source_name: jejunum

growth_protocol: Enteroids were cultured in Expansion Medium (EM, Advanced DMEM/F12, 1x B-27 supplement, 1 mM N-acetylcysteine, 50 ng/mL EGF, 500 nM A83-01, 10 µM SB 202190, 100 µg/mL Primocin, 50% v/v Wnt3A conditioned media, 15% v/v Rspondin-1 conditioned media, 10% v/v Noggin conditioned media).

extract_protocol:
Enteroid monolayers were washed with PBS and treated with Accutase at 25 °C for approximately 20 min to detach cells. The single cell suspension was collected in a low-binding microcentrifuge tube, washed, counted, and ~50,000 cells were resuspended in 100 µL Anti-Freezing Buffer (Advanced DMEM/F12, 10% v/v FBS, 10% DMSO) and stored at -80 °C prior to DNA extraction. After thawing, nuclei were extracted...
Cryopreserved cells were thawed, washed with PBS, and prepared following the Omni-ATAC approach (Corces MR et al, Nat Methods 2017, 14:959). Libraries were purified by AMPure XP magnetic beads with double size selection (0.55x and 1.35x), and size distribution determined by High Sensitivity NGS Fragment analysis kit.

treatment_protocol: Eneroids were plated on permeable tissue culture supports, cultured in EM until confluent, and then induced to differentiate for 5 d in Differentiation Medium (DM, same formulation as EM but lacking Wnt3A, Rspondin-1, A83-01, and SB 2020190).

tag: tissue

value: jejunum

tag: cell line

value: intestinal organoid (enteroid)

tag: cell type

value: intestinal epithelia

tag: genotype

value: obese


title: 299_SMARTER_F_63

city: Ulm

first: Emil

last: Chteinberg

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University Medical Center

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)

library_source: transcriptomic

data_processing:
FASTQ Files using Illumina BaseSpace BCL to FASTQ software version 2.2.0 and Illumina Local Run Manager Software version 2.0.0.
FASTQ Files were analyzed with HTG EdgeSeq Parser software version 5.5 to generate raw counts for a total of 298 genes.
Assembly: Assembly: GRCh38.p13
Supplementary files format and content: raw counts
Supplementary files format and content: log2(Count per million+1)

molecule: total RNA

source_name: Diffuse large B-ell lymphoma

extract_protocol:
Three hundred sixty DLBCLs tissues were processed. Using 5 ¬µm unstained FFPE sections. The optimal amounts of tissue for each HTG EdgeSeq panB Lymphoma assay. The sample preparation as performed according to the manufacturer’s instructions.
Probe_captured FFPE samples for EdgeSeq panB Lymphoma assay were amplified¨ and indexed via polymerase chain reaction (PCR) using the master mix (OneTaq HotStart 2X MasterMix in GC Buffer (New England Biolabs Inc., Ipswich, MA, USA), and indexing primers according to manufacturer’s instructions. The following library cleanup was performed using AMPure XP beads according to manufacturer’s instructions
Targeted mRNA Sequencing using HTG EdgeSeq Pan B_Cell Lymphoma Panel assay

value: Diffuse large B-ell lymphoma

tag: tissue-fixation

value: FFPE

tag: Sex

value: F

tag: age


title: Saline, replicate1, scRNAseq

city: Guangzhou

first: Hai

last: Qiu

state: Guangdong province

address: 1023 Satai South Road, Jingxi Street

department: Institute of forensic medicine

country: China

institute: southern medical university

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data was precessed by Fastp firstly (Chen, Zhou et al. 2018) to trim primer sequence and low quality bases.
Processing  sample demultiplexing, barcode processing, single cell 3' gene counting and aggretion, generating feature-barcode matrices by Cell Ranger v7.0(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

organism: Mus musculus

source_name: hippocampus

extract_protocol:
After harvested from mice,hippocampal tissues were washed in ice-cold RPMI1640 and dissociated using Tissue Dissociation Reagent A (Seekone K01301-30) from SeekGene as instructions. DNase Ⅰ (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Solarbio R1010) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albumin.
Single-cell RNA-Seq libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics Catalog No.1000268). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then loaded to the sample well in Chromium Next GEM Chip G. Subsequently Gel Beads and Partitioning Oil were dispensed into corresponding wells separately in chip. After emulsion droplet generation reverse transcription were performed at 53℃for 45 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Bar code and Unique Molecular Index. The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on illumina NovaSeq 6000 with PE150 read length or DNBSEQ-T7 platform with PE150 read length.

value: male

value: widetype

tag: treatment

value: Saline, equal volume to methamphetamine for 28days, intraperitoneal injection


title: ATAC-Seq J17

description: Library name: J17


title: ATAC-Seq J4

description: Library name: J4

value: obese, hyperabsorptive


title: ATAC-Seq J21

description: Library name: J21


title: Tcell_I3C2

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

description: 10x genomics

data_processing:
Sequencing reads were aligned to the mouse transcriptome using the Cell Ranger suite with default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
Cellular suspension (3000 cells) was loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer’s protocol. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v3.1 Reagent Kit (10X Genomics) according to manufacturer’s protocol.
Indexed libraries were equimolarly pooled and sequenced on an Illumina NovaSeq 6000 using paired-end 26x91bp as sequencing mode.

value: tumor

value: T cells

value: I3C diet


title: 299_RICOVER_60_M_62

value: M


title: ATAC-Seq J23

description: Library name: J23

value: lean


title: ATAC-Seq J2

description: Library name: J2


title: Tcell_I3C1

description: 10x genomics


title: 297_SMARTER_F_68


title: ATAC-Seq J1

description: Library name: J1


title: 297_MegaCHOEP_III_F_33


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr +Dox Replicate 2

city: Cincinnati

first: Brian

last: Gebelein

state: OH

address: 3333 Burnet Avenue, MLC 7007

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: EFBG0034
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Dox_48hr_Rep2

data_processing:
Quality-controlled FASTQ files were trimmed using Sickle/v1
Trimmed sequences were mapped using STAR version 2.7.9 to the hg38 genome with the transgenic regions added as an additional chromosome
Read count matrix was generated using reverse-strand calling to exons in Subread version 2.0.3
Counts were normalized using median of ratios method in DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file including the raw counts for each sample
Supplementary files format and content: tab-delimited text file containing the DESeq2-normalized counts for all samples

molecule: polyA RNA

growth_protocol: H9 hESC cultures were maintained in Essential 8 Flex Media in 5% CO2 environment at 37C

extract_protocol:
Monolayers were lysed using mirVana miRNA protocol and 500ng of total RNA was used for Poly-A selection and library preparation
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer protocols

treatment_protocol:
H9 hESC cultures were differentiated in Essential 6 Media supplemented with: (3 days) LDN193189, SB431542, XAV939; (3 days) LDN193189, SB431542; (4-6 days) IWP2, Activin A
Dox-induced cultures were treated with 100ng/mL doxycycline supplemented in standard differentiation media for 12-hours starting at Day 10

value: human embryonic stem cell

value: TRE3G-2xFLAG GSX2 WT

value: LGE-like differentiation

value: 100ng/mL Dox


title: ATAC-Seq J11

description: Library name: J11

value: jejunum

value: intestinal organoid (enteroid)

value: intestinal epithelia


title: Macro_I3C2

description: 10x genomics


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr -Dox Replicate 2

description:
Library name: EFBG0030
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: NoDox_48hr_Rep2


title: Tcell_control2

description: 10x genomics

value: AhR-poor diet


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr +Dox Replicate 3

description:
Library name: EFBG0035
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Dox_48hr_Rep3


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr +Dox Replicate 2

description:
Library name: EFBG0026
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Dox_24hr_Rep2


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr +Dox Replicate 1

description:
Library name: EFBG0033
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Dox_48hr_Rep1


title: 295_MegaCHOEP_III_M_36

value: Diffuse large B-ell lymphoma

value: FFPE


title: 294_MegaCHOEP_III_M_50


title: Macro_I3C1

description: 10x genomics


title: 290_SMARTER_F_66

value: F


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr +Dox Replicate 3

description:
Library name: EFBG0027
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Dox_24hr_Rep3


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr -Dox Replicate 1

description:
Library name: EFBG0029
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: NoDox_48hr_Rep1


title: Macro_control2

description: 10x genomics


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr +Dox Replicate 1

description:
Library name: EFBG0025
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Dox_24hr_Rep1


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr -Dox Replicate 3

description:
Library name: EFBG0023
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: NoDox_24hr_Rep3


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr -Dox Replicate 2

description:
Library name: EFBG0022
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: NoDox_24hr_Rep2


title: 290_RICOVER_60_F_65


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr -Dox Replicate 1

description:
Library name: EFBG0021
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: NoDox_24hr_Rep1


title: Macro_control1

description: 10x genomics


title: aorta, StingKO, AngII

city: Houston

first: Yanming

last: Li

state: TX

address: One Baylor Plaza

department: Michael E. DeBakey Department of Surgery

institute: Baylor College of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thoracic aorta

extract_protocol:
Samples of thoracic aorta were harvested from  mice (n=3) and were pooled in Hanks’ Balanced Salt Solution (HBSS, #14175095, Thermo Fisher Scientific, Waltham, MA) with 10% fetal bovine serum. Extra-aortic tissues, such as periaortic fat, were removed, and the aortic tissues were cut into small pieces and incubated with enzyme cocktail in HBSS containing Ca2+/Mg2+ (#14025092, Thermo Fisher) for 60 minutes at 37 °C. The cell suspension was filtered through a 40-μm cell strainer (CLS431750-50EA, Sigma-Aldrich), centrifuged at 350 g for 5 minutes, and resuspended by using cold HBSS (#14175095) with fetal bovine serum (5% vol/vol). Cells were stained with 4′, 6-diamidino-2-phenylindole (DAPI) and were sorted to select viable cells (≥95% viability) by using flow cytometry (FACS Aria III, BD Biosciences, Franklin Lakes, NJ).
Single-cell suspensions were dispensed separately onto the Chromium Controller (10x Genomics, Pleasanton, CA) with a target of 10,000 cells/sample. The scRNA-seq library was constructed by using the Chromium Single-Cell 3′ v3 Reagent Kit (10x Genomics). Cells were mixed with barcoded primer-linked gel beads. Each cell was barcoded with a unique index, and every transcript within a single cell was barcoded with a unique molecular identifier (UMI). cDNAs were pooled, truncated, and amplified to generate cDNA libraries that were sequenced using a Next Generation sequencer NovaSeq 6000 (Illumina, Inc., San Diego, CA) in a pair-end fashion to obtain more than 80,000 reads per cell.

treatment_protocol: To understand the role of STING in aorta, we performed single cell RNAseq of thoracic aortic tissues from wild type mice, AngII infused wild type mice, Sting KO mice, AngII infused Sting KO mice, and AngII infusion was applied for 7 days.

value: thoracic aorta

value: aortic cells

value: Sting-KO

value: high fat diet 5 weeks + AngII infusion 7 days


title: 29_DENSER_M_76

value: M


title: Tcell_control1

description: 10x genomics

value: tumor

value: T cells


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr +Dox Replicate 1

description:
Library name: EFBG0017
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Dox_12hr_Rep1

value: human embryonic stem cell

value: TRE3G-2xFLAG GSX2 WT


title: aorta, StingKO, Saline

description: 10x Genomics

value: normal diet + saline


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr -Dox Replicate 3

description:
Library name: EFBG0031
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: NoDox_48hr_Rep3

value: LGE-like differentiation


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr -Dox Replicate 3

description:
Library name: EFBG0015
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: NoDox_12hr_Rep3


title: aorta, WT, AngII

description: 10x Genomics

value: WT


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr -Dox Replicate 2

description:
Library name: EFBG0014
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: NoDox_12hr_Rep2


title: 290_MegaCHOEP_III_M_57


title: H9 TRE3G 2xFLAG-GSX2 WT Day 10 Replicate 3

description:
Library name: EFBG0011
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Day10_Rep3


title: aorta, WT, Saline

description: 10x Genomics


title: 289_MegaCHOEP_III_M_52

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)


title: 287_SMARTER_F_68


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr -Dox Replicate 1

description:
Library name: EFBG0013
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: NoDox_12hr_Rep1


title: H9 TRE3G 2xFLAG-GSX2 WT Day 10 Replicate 2

description:
Library name: EFBG0010
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Day10_Rep2


title: H9 TRE3G 2xFLAG-GSX2 WT Day 10 Replicate 1

description:
Library name: EFBG0009
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Day10_Rep1


title: 287_MegaCHOEP_III_F_42


title: Rescue_ RPUSD1_KO1_ctrl

city: Oxford

first: Linzhen

last: Kong

address: University of Oxford Old Road Campus Research Building

department: Nuffield Department of Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

description: Library name: sample20

library_source: other

data_processing:
Raw sequencing reads were processed by Cutadapt (v.4.9) to remove low-quality bases (-q 20) and short reads (-m 18), as well as to trim adaptors. 6mer unique molecular identifiers (UMIs) were extracted by UMI-tools extract (v.1.0.1) and used for deduplication. Paired reads were then merged into single reads using fastp (v.0.23.2)
Cleaned reads were first mapped to synthetic spike-ins and rRNA references using bowtie2 (v.2.4.4). The unaligned reads were subsequently mapped to tRNA references. High-confidence human tRNA sequences (hg38) were downloaded from GtRNAdb. Only non-redundant tRNA sequences were kept and appended with a “3’-CCA” end.
The aligned reads were then filtered and sorted using SAMtools (v.1.16.1). For synthetic spike-ins and rRNAs, only reads with MAPQ ≥ 10 were kept. For tRNAs, only reads with MAPQ ≥ 1 were kept. Deduplication was performed using UMI-tools dedup (v.1.0.1). Finally, mutations were counted by SAMtools mpileup (v.1.16.1) and cpup (v.0.1.0) (https://github.com/y9c/cpup)
Assembly: hg38
Supplementary files format and content: Excel table showing the mapping statistics and  Ψ list in HCT116 tRNAs

molecule: other

growth_protocol: HCT116 (ATCC, CCL-247) cells were cultured in McCoy’s 5A (Modified) Medium (Gibco) supplemented with 10% (v/v) FBS (Gibco) and 1% penicillin/streptomycin (Gibco) at 37 °C with 5% CO2

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and Direct-zol RNA Miniprep Plus (Zymo Research) according to the manufacturer’s protocol. Ribo– RNA was isolated using RiboMinus Eukaryote System v2 (Invitrogen) according to the manufacturer’s protocol. PolyA+ RNA was isolated by two rounds of polyA-tailed selection using Dynabeads mRNA DIRECT Purification Kit (Invitrogen) according to the manufacturer’s protocol. To remove genomic DNA contamination, RNA was then treated with Turbo DNase and purified by Zymo-IC Column with RNA binding buffer.
50–100 ng ribo– or polyA+ RNA was fragmented by NEBNext Magnesium RNA Fragmentation Module at 94 °C for 4 min according to the manufacturer’s protocol and purified by Zymo-IC Column with RNA binding buffer. The fragmented RNA was mixed with 5 μl 10× T4 PNK reaction buffer (NEB), 5 μl T4 PNK (NEB), and 2.5 μl SUPERase•In RNase Inhibitor (Invitrogen) in a 50 µL final solution and incubated at 37 °C for 1 h. The 3’-repaired RNA was purified by Zymo-IC Column with RNA binding buffer and eluted with 10 μl nuclease-free H2O. The eluted RNA was then mixed with 1 μl synthetic 30mer spike-ins (2%) and 1 μl of 20 μM RNA adapter (5’-/5rApp/AGATCGGAAGAGCGTCGTG/3SpC3/-3’), incubated at 70 °C for 2 min and immediately placed on ice. Next, 2.5 μl 10× T4 RNA Ligase reaction buffer (NEB), 1 μl SUPERase•In RNase Inhibitor, 7.5 μl 50% PEG 8000 (NEB), and 2 μl T4 RNA Ligase 2, truncated KQ (NEB) were added to the mixture and the reaction was incubated at 25 °C for 2 h followed by 16 °C for 14 h. To digest excess adapters, the solution was further diluted to 47 μl with nuclease-free H2O and treated with 2 μl 5’-Deadenylase (NEB) at 30 °C for 1 h followed by adding 1 μl RecJf (NEB) and incubating at 37 °C for 1 h. The 3’-ligated RNA was purified by Zymo-IC Column with RNA binding buffer and eluted with 10 μl nuclease-free H2O. A 7 μl aliquot was subjected to BACS library construction, while the rest 3 μl was saved as control sample and diluted to 12.5 μl with nuclease-free H2O. For BACS, 1 M 2-bromoacrylamide (Enamine) was prepared by dissolving the solid in DMSO. 7 μl 3’-ligated RNA was added into a 20 μl solution containing 250 mM 2-bromoacrylamide and 625 mM phosphate buffer (pH 8.5) and incubated at 85 °C for 30 min. The treated RNA was double purified by Micro Bio-Spin P-6 Tris Column (Bio-Rad) and Zymo-IC Column with RNA binding buffer and finally eluted with 12.5 μl nuclease-free H2O. Both treated and control RNA samples were mixed with 1 μl of 2 μM RT primer (5’-ACACGACGCTCTTCCGATCT-3’) and 1 μl of 10 mM dNTP mix (NEB), incubated at 70 °C for 2 min and immediately placed on ice. Next, 4 μl 5× Maxima H– RT buffer (Thermo), 0.5 μl RiboLock RNase Inhibitor (Thermo), and 1 μl Maxima H– Reverse Transcriptase (Thermo) were added to the mixture and the reaction was incubated at 50 °C for 1 h. To digest excess RT primers, the solution was treated with 1 μl Exo I (NEB) and incubated at 37 °C for 30 min followed by adding 1 μl of 0.5 M EDTA (Sigma) to quench the reaction. To hydrolyze the RNA, 2.5 µl of 1 M NaOH (Sigma) was added and the solution was then incubated at 70 °C for 12 min followed by adding 2.5 µl of 1 M HCl (Sigma) to neutralize NaOH. The cDNA was finally purified with Dynabeads MyOne Silane (Invitrogen) and eluted with 13 µl nuclease-free H2O. The eluted cDNA was then mixed with 2 µl of 25 μM cDNA adapter (5’-/5Phos/NNNNNNAGATCGGAAGAGCACACGTCTG/3SpC3/-3’), incubated at 70 °C for 2 min and immediately placed on ice. Next, 5 μl 10× T4 RNA Ligase reaction buffer, 25 μl 50% PEG 8000, 0.5 μl of 100 mM ATP (NEB), 3.5 μl DMSO (Thermo), and 1 μl T4 RNA Ligase 1, high concentration (NEB) were added to the mixture and the reaction was incubated at 25 °C for 16 h. The ligated cDNA was purified with Dynabeads MyOne Silane and eluted with 15 µl nuclease-free H2O. The eluted DNA was amplified with NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) and NEBNext Ultra II Q5 Master Mix for 10 cycles according to the manufacturer’s protocol. The PCR products were purified with 0.8× AMPure XP beads and quantified with Qubit dsDNA HS Assay Kit (Thermo) according to the manufacturer’s protocol. BACS and control libraries were sequenced on NextSeq 2000 (60 bp paired end) with no PhiX added.

value: control


title: Rescue_ RPUSD1_KO1_BACS

description: Library name: sample19

value: bacs


title: Rescue WT_ RPUSD1_KO1_ctrl

description: Library name: sample18


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr +Dox Replicate 3

description:
Library name: EFBG0019
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Dox_12hr_Rep3

value: 100ng/mL Dox


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr +Dox Replicate 2

description:
Library name: EFBG0018
Column name in counts_All_Samples.txt and normalized_counts_All_samples.txt: Dox_12hr_Rep2


title: 286_SMARTER_F_70

value: Diffuse large B-ell lymphoma

value: FFPE


title: 284_SMARTER_M_62


title: extracellular vesicles, postnatal day 7 mouse testis EVs (PND7) treated, biol rep 1

city: Shenzh

first: Tingting

last: ZHENG

state: Guangdong

address: Bulan Road

institute: Shenzhen Third People's Hospital

description: Library name: PND7, biol rep 1

data_processing:
After eliminating the low-quality reads, clean reads were mapped to reference genome and to other sRNA databases using Bowtie2 and cmsearch. Classification of sRNA follows the priority rule: MiRbase> pirnabank> snoRNA(human/plant)> Rfam> other sRNA to ensure a unique map of each entry. Novel miRNAs and piRNAs were predicted using miRDeep2 and Piano, respectively.
Assembly: 2020-A Mouse reference, mm10 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: text files include raw counts of each sample

source_name: extracellular vesicles isolated from postnatal day 7 mouse testis

extract_protocol:
Each preparation of PND7 testis EVs was isolated from ten PND7 C57/BL6 male mice. The tunica albuginea was removed using forceps to release the seminiferous tubules. The decapsulated testes were digested by 1ml Accumax (Thermo) per 20 mg tissue at room temperature for 1 hour. Tissues were gently pipetted up and down 20 times to maximize the cell yield followed by filtering through a 40 μM strainer. The digestion was stopped by the addition of 1 volume of PBS and the cells were pelleted by centrifugation at 300g 10 min. The supernatant of the single-cell suspension was collected and the EVs were isolated using exoEasy Maxi Kit (Qiagen, 76064) according to the manufacturer’s instructions. The EV preparation was further concentrated by ultracentrifugation (Hitachi CS-150GXII Micro UITRAcentrifuge) at 100,000g for 90 min at 4°C. The EV pellet was resuspended in 20 μl PBS and stored at -80℃ for further analysis.
treat EVs with proteinase K, PMSF and RNase A.RNA was extracted using miRNeasy Mini Kit.


title: 289_SMARTER_F_64

value: F


title: Empty vector_ RPUSD1_ KO1_ctrl

description: Library name: sample16


title: Empty vector_ RPUSD1_ KO1_BACS

description: Library name: sample15


title: heart, wt, rep 2, Day9

city: Hangzhou

first: Jiayin

last: Zhang

state: Zhejiang

address: Center for Genetic Medicine, Zhejiang University School of Medicine

institute: Zhejiang University

data_processing:
BGISEQ system were used for RNA-sequencing.
Raw sequencing reads were aligned to the musculus reference genome (GRCm38.p6) using HISAT.
Assembly: Genome assembly GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

source_name: heart

growth_protocol: Heart tissue of C57BL/6J mice at day 9 after birth.

extract_protocol:
Total RNA was extracted using Trizol following the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard DNBSEQ transcriptome protocols

value: heart

tag: time

value: day 9 after birth


title: heart, wt, rep 3, Day9


title: shTRUB2_2 HeLa_BACS

description: Library name: sample13

source_name: HeLa

value: HeLa


title: 281_MegaCHOEP_III_F_38


title: shTRUB2_2 HeLa_ctrl

description: Library name: sample14


title: shTRUB2_1 HeLa_ctrl

description: Library name: sample12


title: sh_NT_Ctrl_1 HeLa_ctrl

description: Library name: sample10


title: heart, wt, rep 1, Day9


title: shTRUB2_1 HeLa_BACS

description: Library name: sample11


title: extracellular vesicles, postnatal day 7 mouse testis EVs (PND7) treated, biol rep 2

description: Library name: PND7, biol rep 2

value: extracellular vesicles isolated from postnatal day 7 mouse testis


title: 278_SMARTER_M_70

value: M


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by placebo maintenance therapy, Sample 2

city: Philadelphia

first: John

middle: C

last: McVey

state: Pennsylvania

address: 3400 Spruce st

institute: University of Pennsylvania

description:
Library name: Sample 11
S22GC

data_processing:
DESeq2 (v1.32.0) was used for gene expression normalization and differential gene expression analysis across groups.
Assembly: Reads were mapped to the GRCm38/mm10 genome using the Base-Space Suite (Illumina).
Supplementary files format and content: CSV file including raw counts from every sample
Supplementary files format and content: CSV file including raw counts per sample

source_name: Tumor

growth_protocol: 1x106 cells were implanted subcutaneously into the flank of each mouse. Sex-matched eight- to twelve-week-old mice were block randomized in an unblinded manner.

extract_protocol:
Total RNA extracted using the RNeasy FFPE kit (Qiagen) from multiple 5μm serial sections cut from FFPE tissues
3' mRNA-seq libraries were generated from100 ng of DNase I–treated total RNA using the QuantSeq FWD Library Preparation Kit (Hexogen) according to the manufacturer’s directions.

treatment_protocol: Gemcitabine (120 mg/kg) suspended in PBS and cisplatin (4 mg/kg) suspended in 0.9% sodium chloride were administered by intra-peritoneal (i.p.) injection weekly. Olaparib (50 mg/kg) suspended in 4% DMSO, 30% PEG300 and 66% ddH2O was administered daily by i.p. injection.

value: Tumor

value: KPCB.c1 tumor cell line

value: Pancreatic cancer

value: Placebo maintenance

tag: batch

value: Day of death


title: extracellular vesicles, postnatal day 7 mouse testis EVs (PND7) treated, biol rep 3

description: Library name: PND7, biol rep 3


title: Ycko, replicate 2, HiC

first: Xiaoling

last: Wang

address: No. 195, West Dongfeng Road

institute: Guangzhou Medical University

data_processing:
The raw data was aligned to the mouse mm10 genomes and processed into allValidPairs files using Hic-Pro (v3.0.0). During this process, low-quality, single-and multiple-alignment reads were discarded. Subsequently, reads were assigned to DpnII restriction fragments, well-aligned reads were filtered to construct the Hi-C contact matrices. Validated contact pairs were normalized with KR normalization and saved as .hic files.
Assembly: mm10
Supplementary files format and content: .Hic

source_name: the spleen and lymphoid nodes

extract_protocol:
Treg cells isolated from the spleen and lymphoid nodes
Hi-C sequencing libraries were were used for Hi-C library construction using the EpiTect Hi-C kit (Qiagen, 59971), following the manufacturer’s protocols.

value: the spleen and lymphoid nodes

value: Treg cells from the spleen and lymph nodes

value: CtcfcKo


title: shTRUB2_1 HCT116 _BACS

description: Library name: sample5

value: bacs


title: shTRUB2_2 HCT116 _BACS

description: Library name: sample7


title: Yctr, replicate 2, HiC

value: CtrlCre


title: Rescue WT_ RPUSD1_KO1_BACS

description: Library name: sample17


title: sh_NT_Ctrl_1 HeLa_BACS

description: Library name: sample9


title: 283_MegaCHOEP_III_F_34

value: Diffuse large B-ell lymphoma

value: FFPE


title: shTRUB2_1 HCT116 _ctrl

description: Library name: sample6

value: control


title: 270_RICOVER_60_M_61


title: 270_SMARTER_M_73


title: Sh_NT_Ctrl_2 HCT116 _BACS

description: Library name: sample3


title: P0 Kidney LPD replicate 2

city: Clayton

first: Kieran

last: Short

address: 19 Innovation Walk

country: Australia

institute: Monash University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For E14.5 data, samples were sequenced with a paired-end single index configuration by Illumina NextSeq 2000. Cell Ranger version 5.0 (10x Genomics) was used to map raw data to references of gex-mm10-2020-A.
For the P0 snRNAseq data - 10X Genomics Cell Ranger 3 was used to process the NPD_19-5_19-8, NPD_24-3_24_2, LPD_5_4_5-2 and LPD_014-6_014 samples as above, with the exception of mapping using pre-mRNA transcripts based on mm10.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: E19.5 mouse kidney

extract_protocol:
For the E14.5 samples - two groups of kidneys five E14.5 kidneys, from 2 different females, per diet were pooled together and processed to obtain single-cell suspension. Approximately 10k single cells (per sample) were emulsified with Single Cell 3’ V3 beads (10X Genomics) and libraries generated on a 10X Chromium instrument. For the P0 samples - one snap frozen male and one snap frozen female kidney were placed in a cold Kimble dounce homogeniser and gentle nuclear extraction was performed using a nuclear lysis buffer (Sigma) dosed with RNAse inhibitors while grinding the kidneys. After homogenisation, nuclei were pelleted at 300 x g for 3 minutes, supernatant aspirated and resuspended in phosphate buffered saline containing RNAse inhibitors, centrifuged once more, aspirated, resuspended in PBS containing RNAseq inhibitor. Nuclei were stained with DAPI and flow sorted to enrich nuclei and remove any remaining particulates. Nuclei were finally processed by emulsion with 10X Genomics 3' V3 beads, and library generation on a 10X chromium instrument.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, kidney cells or nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Female and Males CD1 or C57BL6 mice were placed on low protein diet (6-8%) or Normal protein (20%) diet for 3 weeks before mating and maintaned on diet on diet during gestation. At E14.5 the embryos were dissected and the embryonic kidneys processed for single-cell RNA sequencing and E19.5 or P0 kidneys were dissected, snap frozen, and processed for single-nuclear RNA sequencing.

value: E19.5 mouse kidney

value: pooled male and female

tag: strain

value: WT

value: 8% Low Protein Diet


title: sh_NT_Ctrl_1 HCT116 _BACS

description: Library name: sample1


title: Yctr, replicate 1, HiC


title: sh_NT_Ctrl_1 HCT116 _ctrl

description: Library name: sample2


title: PUS7L_KO2_BACS

description: Library name: sample37


title: 27_DENSER_M_67

value: M


title: 277_MegaCHOEP_III_F_51

value: F


title: 269_SMARTER_M_62


title: PUS7L_KO2_CTRL

description: Library name: sample38


title: P0 Kidney NPD replicate 2

description: 10X Genomics

value: 20% Normal Protein Diet


title: shTRUB2_2 HCT116 _ctrl

description: Library name: sample8


title: P0 Kidney LPD replicate 1

description: 10X Genomics


title: 266_SMARTER_F_80


title: PUS7L_KO1_BACS

description: Library name: sample35


title: PUS7L_KO1_CTRL

description: Library name: sample36


title: 271_SMARTER_M_64


title: PUS3_KO2_CTRL

description: Library name: sample34


title: Ycko, replicate 1, HiC


title: PUS3_KO1_CTRL

description: Library name: sample32


title: Sh_NT_Ctrl_2 HCT116 _ctrl

description: Library name: sample4


title: PUS10_KO1_CTRL

description: Library name: sample28


title: PUS10_KO1_BACS

description: Library name: sample27


title: PUS3_KO2_BACS

description: Library name: sample33


title: PUS3_KO1_BACS

description: Library name: sample31


title: 265_SMARTER_F_61


title: RPUSD4_KO2_BACS

description: Library name: sample25


title: RPUSD4_KO1_CTRL

description: Library name: sample24


title: PUS10_KO2_BACS

description: Library name: sample29


title: 266_RICOVER_60_M_65


title: RPUSD3_KO2_CTRL

description: Library name: sample22


title: PUS10_KO2_CTRL

description: Library name: sample30


title: 264_SMARTER_F_70


title: 260_MegaCHOEP_III_M_51


title: 257_SMARTER_F_67


title: 261_SMARTER_F_76


title: P0 Kidney NPD replicate 1

description: 10X Genomics


title: Testis_DEHP_rep1

type: RNA

city: Yichang

first: Guoqing

last: Fu

address: 8 University Road

institute: China Three Gorges University

description: Gene expression after rats orally administrated 1000 mg/kg/day DEHP for 28 days in testis

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized onto Arraystar Rat piRNA Array in Agilent’s SureHyb Hybridization Chambers according to the manufacturer’s standard protocols (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 μm, Dye channel is set to Green and Green PMT is set to 10%-100%).

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent，version 11.0.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: testis, 28 day, DEHP,  replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: a)Cryopulverization of tissue using the Biopulverizer．①Place the BioPulverizer™ in a shallow container and cool thoroughly with either liquid nitrogen.　②Place prefrozen tissue in the well of the mortar.  ④Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS).　⑤Empty the powdered contents for subsequent homogenization or extraction procedures.  b)Homogenization using the Mini-Bead-Beater-16  ①Fill the 2 ml screw-cap microtube one-half full with 1.0mm beads. Then add TRIzol and tissue, being sure to fill the microtube almost to the top. Exclude as much air from the microtube as possible. Use screw-cap microtubes with integral o-ring seals in order to eliminate aerosol formation during the homogenization. Be sure there are no beads on the threads of the microtubes when screwing down the cap. 　②Insert 1 to 16 microtubes into the holder. Distribute them symmetrically as you would do with a centrifuge. Screw in the black plastic chamber cap until it is in contact with the tops of the microtube caps. Tighten the lid by hand so the vials are firmly held in place. Do not overtighten.　③Set the timer depending on the type of sample. Start the machine.

value: testis

tag: gender

value: male

value: DEHP


title: 258_SMARTER_F_70


title: Testis_DEHP_rep3

source_name: testis, 28 day, DEHP,  replicate 3


title: RPUSD4_KO1_BACS

description: Library name: sample23


title: 258_RICOVER_60_F_68


title: Testis_control_rep2

description: Gene expression after rats orally administrated corn oil for 28 days in testis

source_name: testis, 28 day, Control, replicate 2

value: corn oil (control)


title: RPUSD3_KO1_CTRL

description: Library name: sample20


title: 255_SMARTER_M_76


title: RPUSD3_KO1_BACS

description: Library name: sample19


title: 254_SMARTER_M_69


title: RPUSD1_KO2_CTRL

description: Library name: sample14


title: RPUSD2_KO2_CTRL

description: Library name: sample18


title: RPUSD4_KO2_CTRL

description: Library name: sample26


title: S21-6569

city: Seoul

first: Seo

middle: Young

last: Lee

state: Goyang-si,Gyeonggi-do

address: Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National Cancer Center

description: Gene expression profiling using NanoString nCounter

hyb_protocol: Hybridization reactions were set up with RNA samples and probe sets from the NanoString Metabolic Pathways Panel and incubated at 65 °C for 16–20 hours following the manufacturer’s instructions.

scan_protocol: After hybridization, samples were processed on the nCounter Prep Station for purification and immobilization of probe–target complexes. Digital counting of barcoded probes was performed using the NanoString nCounter Digital Analyzer at the manufacturer’s recommended resolution.

data_processing: Raw RCC files generated by the nCounter Digital Analyzer were imported into NanoString nSolver Analysis Software and normalized using the default positive control and housekeeping gene normalization procedures. Further downstream analyses, including clustering, GSVA, and survival analysis, were conducted in R using packages such as ggplot2 and pheatmap.

source_name: Adenocarcinoma

label_protocol: For NanoString assays, RNA samples were hybridized directly with reporter probes and capture probes provided in the NanoString Metabolic Pathways Panel. No enzymatic labeling or amplification steps were required, as the NanoString system uses color-coded probe pairs for direct digital detection.

extract_protocol: Total RNA was extracted from archival tumor tissue and whole blood samples collected prior to anti–PD-(L)1 treatment. RNA isolation was performed according to the manufacturer’s standard protocol for the NanoString Metabolic Pathways Panel (NanoString Technologies), ensuring RNA integrity suitable for hybridization.

value: Adenocarcinoma

tag: suvmax

tag: egfr mutation

tag: alk fusion

tag: metformin taken

value: No

tag: response

value: NR


title: Testis_control_rep1

source_name: testis, 28 day, Control, replicate 1

tag: tissue


title: S21-4306

source_name: Other

value: Other

value: R


title: S21-5882


title: PUSL1_KO2_CTRL

description: Library name: sample10

tag: cell line

value: control


title: Testis_DEHP_rep2

source_name: testis, 28 day, DEHP,  replicate 2


title: RPUSD2_KO1_CTRL

description: Library name: sample16


title: 249_SMARTER_F_68

source_name: Diffuse large B-ell lymphoma

tag: cell type

value: Diffuse large B-ell lymphoma

value: FFPE


title: RPUSD2_KO1_BACS

description: Library name: sample15

value: bacs


title: S21-4402

source_name: Squamous cell carcinoma

value: Squamous cell carcinoma


title: RPUSD3_KO2_BACS

description: Library name: sample21


title: PUSL1_KO1_BACS

description: Library name: sample7


title: Testis_control_rep3

source_name: testis, 28 day, Control, replicate 3


title: RPUSD1_KO2_BACS

description: Library name: sample13


title: RPUSD1_KO1_CTRL

description: Library name: sample12


title: RPUSD2_KO2_BACS

description: Library name: sample17


title: HCT1116_WT_CTRL

description: Library name: sample2


title: S21-3075

value: Yes


title: S21-15942


title: 252_SMARTER_M_62

value: M


title: 246_SMARTER_F_64

value: F


title: PUSL1_KO1_CTRL

description: Library name: sample8


title: 244_SMARTER_M_64


title: WT for SGT1ami time 24h rep 3

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

country: Spain

institute: Centre for Research in Agrigenomics

description: Library name: W24_6

data_processing:
Raw reads were processed for quality control and adapter removal using Trimmomatic  and aligned to the tomato reference genome (ITAG4.0; https://solgenomics.net/organism/Solanum_lycopersicum/genome) using STAR  within the Galaxy  server (www.usegalaxy.org). Read counts were obtained with feature Counts, and differential gene expression analysis was performed using DESeq2  in RStudio. Genes were considered differentially expressed if they exhibited an absolute log₂ fold-change (FC) ≥ 1 to WT plants (adjusted P ≤ 0.05, Wald’s test).
Assembly: tomato reference genome (ITAG4.0; https://solgenomics.net/organism/Solanum_lycopersicum/genome)
Supplementary files format and content: txt file containing normalised counts extracted with DESeq2

organism: Solanum lycopersicum

source_name: Leaves

growth_protocol: Tomato (S. lycopersicum cv. Micro-Tom) plants were grown in pots containing a substrate mixture of peat (Klasmann TS2), perlite, and vermiculite (3:1:1) under controlled environmental conditions. The growth chamber was set to a 16-h photoperiod (light intensity: 200 μmol m⁻² s⁻¹) and an 8-h dark period, with a day/night temperature of 25/22°C.

extract_protocol:
Total RNA was extracted from tomato leaves using the Maxwell® RSV Plant RNA Kit and the Maxwell® 16 Instrument (Promega), following the manufacturer’s instructions.
RNA-Seq libraries were generated and sequenced by BGI (Shenzhen, China) using DNBSEQ technology.

treatment_protocol: One-month-old were either kept under standard conditons or transferred to a growth chamber  at 4°C. Leaf samples (third and fourth leaves) were collected at time points 0h, 3h and 24h from both control and cold-treated plants. Experiments were conducted independently for each of the lines (SGT2ox and SGT1ami with the corresponding wild-type). Experiments were carried out in biologically independent triplicates.

value: Leaves

tag: genotype

value: WT


title: RPUSD1_KO1_BACS

description: Library name: sample11


title: PUSL1_KO2_BACS

description: Library name: sample9


title: WT for SGT1ami time 3h rep 1

description: Library name: W3_4

value: 3 h


title: 243_MegaCHOEP_III_F_58

tag: tissue-fixation


title: 253_SMARTER_M_65

tag: Sex


title: WT for SGT1ami time 24h rep 2

description: Library name: W24_5


title: WT for SGT1ami time 24h rep 1

description: Library name: W24_4


title: 242_SMARTER_M_68

tag: age


title: S21-15231


title: 246_MegaCHOEP_III_F_50


title: WT for SGT1ami time 3h rep 3

description: Library name: W3_6


title: HCT1116_WT_BACS

description: Library name: sample1

tag: treatment


title: S20-27996


title: S20-244B


title: WT for SGT1ami time 0h rep 2

description: Library name: W0_5

tag: time

value: 0 h


title: WT for SGT1ami time 3h rep 2

description: Library name: W3_5


title: S20-23179


title: S20-2877-Frol

value: Adenocarcinoma


title: WT for SGT1ami time 0h rep 1

description: Library name: W0_4


title: WT for SGT1ami time 0h rep 3

description: Library name: W0_6


title: 238_SMARTER_M_71


title: 24_MegaCHOEP_III_M_45


title: SGT1ami time 3h rep 2

description: Library name: S6_3_2


title: SGT1ami time 3h rep 3

description: Library name: S6_3_3


title: 238_MegaCHOEP_III_M_54


title: SGT1ami time 24h rep 2

description: Library name: S6_24_2


title: SGT1ami time 3h rep 1

description: Library name: S6_3_1


title: SGT1ami time 24h rep 3

description: Library name: S6_24_3


title: S20-21684

value: No


title: S20-20691


title: S20-18994-2

value: NR


title: 238_RICOVER_60_M_76


title: SGT1ami time 24h rep 1

description: Library name: S6_24_1


title: 234_SMARTER_M_66


title: S20-17653

value: Other


title: 234_MegaCHOEP_III_F_23


title: SGT1ami time 0h rep 3

description: Library name: S6_0_3


title: 233_SMARTER_M_65


title: SGT1ami time 0h rep 1

description: Library name: S6_0_1


title: WT for SGT2ox time 3h rep 1

description: Library name: W3_1


title: SGT1ami time 0h rep 2

description: Library name: S6_0_2


title: S20-11599


title: WT for SGT2ox time 24h rep 2

description: Library name: W24_2


title: WT for SGT2ox time 3h rep 3

description: Library name: W3_3


title: S20-13058


title: WT for SGT2ox time 3h rep 2

description: Library name: W3_2


title: WT for SGT2ox time 24h rep 3

description: Library name: W24_3


title: 233_MegaCHOEP_III_M_56


title: S20-11214


title: WT for SGT2ox time 0h rep 3

description: Library name: W0_3


title: S20-10708

value: R


title: S19-9942-2


title: 231_MegaCHOEP_III_M_52


title: WT for SGT2ox time 0h rep 2

description: Library name: W0_2


title: WT for SGT2ox time 24h rep 1

description: Library name: W24_1


title: 231_SMARTER_F_65


title: WT for SGT2ox time 0h rep 1

description: Library name: W0_1


title: SGT2ox time 3h rep 2

description: Library name: S13_2


title: SGT2ox time 3h rep 1

description: Library name: S13_1


title: S19-9942-1


title: S19-9426-3


title: SGT2ox time 24h rep 3

description: Library name: S124_3


title: SGT2ox time 3h rep 3

description: Library name: S13_3


title: SGT2ox time 0h rep 1

description: Library name: S10_1


title: S19-28078


title: Corneal Myofibroblast Medium curvature

city: Salt Lake City

first: Minju

last: Kim

state: Utah

department: Mechanical Engineering

institute: The University of Utah

description:
Library name: Sample 11
Human corneal myofibroblasts cultured on medium curvature-controlled chip at Day 9.

data_processing:
Raw sequencing reads were quality-checked using FastQC.
Reads were trimmed to remove adapters and low-quality bases using Trimmomatic.
High-quality reads were aligned to the human reference genome (GRCh38/hg38) using STAR aligner.
Gene-level counts were quantified using featureCounts.
Differential expression analysis was performed with DESeq2 (R package) using default parameters.
Assembly: GRCh38 / hg38
Supplementary files format and content: Tab-delimited text file (gene_count.txt) includes raw read counts for each gene across all samples.
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Corneal stroma

growth_protocol: Primary human corneal keratocytes (HCK; ScienCell, #6520) were cultured in Fibroblast Medium (#2301) supplemented with 2% FBS, 1% fibroblast growth supplement, and 1% penicillin–streptomycin on poly-L-lysine–coated flasks. Quiescent keratocytes, fibroblasts, and myofibroblasts were derived by modulating medium conditions (serum-free DMEM/F12 for keratocytes, 10% FBS + bFGF for fibroblasts, and 10% FBS + TGF-β for myofibroblasts). Cells were pre-cultured for 3 days under flat conditions, after which curvature was applied, and maintained at 37 °C, 5% CO₂ with medium changes every other day.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) followed by purification with RNeasy Mini Kit (Qiagen), according to the manufacturers’ instructions. RNA integrity was confirmed with an Agilent 5400 Bioanalyzer.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England BioLabs) with poly(A) mRNA enrichment.

treatment_protocol: Cells were exposed to curvature-controlled environments: flat (control), low curvature, medium curvature, and high curvature conditions. No additional chemical treatments were applied.

value: Corneal stroma

value: HK cell

value: Primary Keratocyte

value: wild type

value: Medium curvature

tag: batch


title: Corneal Myofibroblast Flat

description:
Library name: Sample 9
Human corneal myofibroblasts cultured on flat at Day 9.

value: Flat


title: 231_RICOVER_60_M_63

value: Diffuse large B-ell lymphoma

value: FFPE

value: M


title: Corneal Fibroblast High curvature

description:
Library name: Sample 8
Human corneal fibroblasts cultured on high curvature-controlled chip at Day 9.

value: High curvature


title: 230_SMARTER_F_77

value: F


title: S19-305

value: Squamous cell carcinoma


title: Corneal Fibroblast Low curvature

description:
Library name: Sample 6
Human corneal fibroblasts cultured on low curvature-controlled chip at Day 9.

value: Low curvature


title: Corneal Myofibroblast Low curvature

description:
Library name: Sample 10
Human corneal myofibroblasts cultured on low curvature-controlled chip at Day 9.


title: S19-869

value: No


title: SGT2ox time 24h rep 2

description: Library name: S124_2

value: Leaves


title: S19-25981

value: Adenocarcinoma


title: 229_SMARTER_M_76


title: SGT2ox time 24h rep 1

description: Library name: S124_1


title: SGT2ox time 0h rep 3

description: Library name: S10_3

value: 0 h


title: 221_SMARTER_F_62


title: S19-6055

value: R


title: Corneal Keratocyte Flat

description:
Library name: Sample 1
Human corneal keratocytes cultured on flat at Day 9.

value: Corneal stroma

value: HK cell


title: 229_MegaCHOEP_III_F_51


title: S19-25067


title: SGT2ox time 0h rep 2

description: Library name: S10_2


title: Corneal Myofibroblast High curvature

description:
Library name: Sample 12
Human corneal myofibroblasts cultured on high curvature-controlled chip at Day 9.

value: Primary Keratocyte

value: wild type


title: 227_SMARTER_F_68


title: 226_MegaCHOEP_III_F_56


title: S19-27943

value: Yes


title: S21-16565

value: Other

value: NR


title: 217_SMARTER_M_71

value: Diffuse large B-ell lymphoma

value: FFPE

value: M


title: OPTN KO - biol rep 3

city: San Francisco

first: Julie

last: Smeyers

state: CA

address: 1651 4th street

department: IND

institute: UCSF

description:
Library name: OPTN 3
OPTN_KO3

data_processing:
Raw data (raw reads) of fastq format were firstly processed throughin-house perl scripts. In this step, clean data (clean reads) were obtainedbyremoving reads containing adapter, reads containing ploy-N and lowqualityreads from raw data. At the same time, Q20, Q30 and GC content thecleandata were calculated. All the downstream analyses were based on thecleandata with high quality.
Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean 1 reads were aligned to the referencegenome using Hisat2 v2.0.5. We selected Hisat2 [2] as the mapping tool for that Hisat2 can generate a database of splice junctions based on the genemodel annotation file and thus a better mapping result than other non-splice mappingtools.
featureCounts [3] v1.5.0-p3 was used to count the reads numbers mappedto each gene. And then FPKM of each gene was calculated based onthelength of the gene and reads count mapped to this gene. FPKM, expectednumber of Fragments Per Kilobase of transcript sequence per Millions basepairs sequenced, considers the effect of sequencing depth and gene lengthfor the reads count at the same time, and is currently the most commonly usedmethod for estimating gene expression levels.
(For DESeq2 [4] with biological replicates) Differential expression [5] analysisof two conditions/groups (two biological replicates per condition) wasperformed using the DESeq2Rpackage (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expressiondatausing a model based on the negative binomial distribution. The resultingP-values were adjusted using the Benjamini and Hochberg's approachfor controlling the false discovery rate . Genes with an adjusted P-value<=0.05found by DESeq2 were assigned as differentially expressed. (For edgeR[6] without biological replicates) Prior to differential gene expressionanalysis, for each sequenced library, the read counts were adjusted by edgeRprogram package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeRRpackage (3.22.5). The P values were adjusted using the Benjamini &Hochberg method. Corrected P-value of 0.05 and absolute foldchangeof 2were set as the threshold for significantly differential expression.
Assembly: GRCh37
Supplementary files format and content: excel table

source_name: KOLF2.1 J

growth_protocol: Stem cells were cultured in StemFlex Medium on Geltrex-coated tissue cell culture plates at 37ºC in 5% CO2. ROCK inhibitor was added to media at the time of passaging and removed the next day.

extract_protocol:
Each sample consisted of 4 million cells, with RNA extracted from four independent passages. The RNA was harvested using the RNeasy Plus Mini Kit (Qiagen) and the concentration for each hiPSC sample was standardized to 500 ng/µL.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.The library was checked with Qubit and real-time PCR for quantificationand bioanalyzer for size distribution detection. Quantified libraries will bepooled and sequenced on Illumina platforms, according to effective libraryconcentration and data amount.

value: KOLF2.1 J

value: human stem cells

value: OPTN KO

value: no treatment


title: 225_SMARTER_F_68

value: F


title: TBK1 E696K SNV/WT - biol rep 4

description:
Library name: TBK1 Het 4
TBK1_Het4

value: TBK1 E696K SNV/WT


title: S19-23303

value: No


title: 225_MegaCHOEP_III_F_28


title: Corneal Fibroblast Medium curvature

description:
Library name: Sample 7
Human corneal fibroblasts cultured on medium curvature-controlled chip at Day 9.

value: Corneal stroma

value: Medium curvature


title: 216_RICOVER_60_M_69

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)


title: S19-26000

value: Adenocarcinoma

value: R


title: Corneal Fibroblast Flat

description:
Library name: Sample 5
Human corneal fibroblasts cultured on flat at Day 9.

value: HK cell

value: Primary Keratocyte

value: wild type

value: Flat


title: Corneal Keratocyte High curvature

description:
Library name: Sample 4
Human corneal keratocytes cultured on high curvature-controlled chip at Day 9.

value: High curvature


title: 215_SMARTER_F_72

value: Diffuse large B-ell lymphoma

value: FFPE


title: 216_SMARTER_F_62


title: TBK1 E696K SNV/WT - biol rep 1

description:
Library name: TBK1 Het 1
TBK1_Het1

value: KOLF2.1 J

value: human stem cells


title: TBK1 E696K SNV/SNV - biol rep 3

description:
Library name: TBK1 Hom 3
TBK1_Hom3

value: TBK1 E696K SNV/SNV

value: no treatment


title: Corneal Keratocyte Medium curvature

description:
Library name: Sample 3
Human corneal keratocytes cultured on medium curvature-controlled chip at Day 9.


title: Corneal Keratocyte Low curvature

description:
Library name: Sample 2
Human corneal keratocytes cultured on low curvature-controlled chip at Day 9.

value: Low curvature


title: TBK1 E696K SNV/SNV - biol rep 1

description:
Library name: TBK1 Hom 1
TBK1_Hom1


title: 214_MegaCHOEP_III_M_51

value: M


title: S19-18106

value: Squamous cell carcinoma

value: Yes

value: NR


title: S19-17991

value: Adenocarcinoma

value: R


title: S19-23488

value: No


title: TBK1 KO (B)- biol rep 3

description:
Library name: TBK1 KO B 3
TBK1_KOb3

value: TBK1 KO


title: TBK1 KO (B) - biol rep 2

description:
Library name: TBK1 KO B 2
TBK1_KOb2


title: OPTN KO - biol rep 4

description:
Library name: OPTN 4
OPTN_KO4

value: OPTN KO


title: 218_SMARTER_F_73

value: F


title: 222_SMARTER_M_67

value: Diffuse large B-ell lymphoma


title: S19-16742

value: Other


title: TBK1 KO (A)- biol rep 4

description:
Library name: TBK1 KO A 4
TBK1_KOa4

value: KOLF2.1 J


title: OPTN KO - biol rep 2

description:
Library name: OPTN 2
OPTN_KO2

value: human stem cells


title: OPTN KO - biol rep 1

description:
Library name: OPTN 1
OPTN_KO1


title: TBK1 KO (A) - biol rep 2

description:
Library name: TBK1 KO A 2
TBK1_KOa2


title: TBK1 E696K SNV/WT - biol rep 3

description:
Library name: TBK1 Het 3
TBK1_Het3

value: TBK1 E696K SNV/WT


title: Control - biol rep 4

description:
Library name: ctrl_4
Ctrl_4

value: Control

value: no treatment


title: S19-23075


title: TBK1 E696K SNV/WT - biol rep 2

description:
Library name: TBK1 Het 2
TBK1_Het2


title: S19-23210


title: TBK1 E696K SNV/SNV - biol rep 4

description:
Library name: TBK1 Hom 4
TBK1_Hom4

value: TBK1 E696K SNV/SNV


title: S19-20161


title: 203_SMARTER_F_64

value: FFPE


title: Control - biol rep 1

description:
Library name: ctrl_1
Ctrl_1


title: 214_SMARTER_F_75


title: S19-12296-A


title: TBK1 E696K SNV/SNV - biol rep 2

description:
Library name: TBK1 Hom 2
TBK1_Hom2


title: iNeurons - TBK1 KO (A)- biol rep 4

description: Library name: N23

growth_protocol: Stem cells were cultured in StemFlex Medium on Geltrex-coated tissue cell culture plates at 37ºC in 5% CO2. ROCK inhibitor was added to media at the time of passaging and removed the next day. Human iPSCs were differentiated into neurons by viral transduction using a lentiviral vector carrying doxycycline inducible NGN2 (Neurogenin 2) and cells maintained in neuronal media till D21

extract_protocol:
Each sample consisted of 4 million cells, with RNA extracted from four independent passages. The RNA was harvested using the RNeasy Plus Mini Kit (Qiagen) and the concentration for each hiPSC sample was standardized to 500 ng/µL.For differentiated iNeurons, RNA was harvested at D21 using the RNeasy Micro Kit (Qiagen) and RNA met a minimum concentration threshold of 150 ng/µL. .
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.The library was checked with Qubit and real-time PCR for quantificationand bioanalyzer for size distribution detection. Quantified libraries will bepooled and sequenced on Illumina platforms, according to effective libraryconcentration and data amount.

value: iNeurons


title: TBK1 KO (B)- biol rep 4

description:
Library name: TBK1 KO B 4
TBK1_KOb4


title: 21_DENSER_M_74

extract_protocol:
Three hundred sixty DLBCLs tissues were processed. Using 5 ¬µm unstained FFPE sections. The optimal amounts of tissue for each HTG EdgeSeq panB Lymphoma assay. The sample preparation as performed according to the manufacturer’s instructions.
Probe_captured FFPE samples for EdgeSeq panB Lymphoma assay were amplified¨ and indexed via polymerase chain reaction (PCR) using the master mix (OneTaq HotStart 2X MasterMix in GC Buffer (New England Biolabs Inc., Ipswich, MA, USA), and indexing primers according to manufacturer’s instructions. The following library cleanup was performed using AMPure XP beads according to manufacturer’s instructions
Targeted mRNA Sequencing using HTG EdgeSeq Pan B_Cell Lymphoma Panel assay

value: M


title: S19-17760

value: Squamous cell carcinoma

value: Yes

value: NR


title: S18-9537

value: Adenocarcinoma

value: No


title: TBK1 KO (B)- biol rep 1

description:
Library name: TBK1 KO B 1
TBK1_KOb1

value: TBK1 KO


title: 209_SMARTER_M_79

value: Diffuse large B-ell lymphoma


title: S18-8494


title: iNeurons - Control - biol rep 4

description: Library name: N19


title: iNeurons - TBK1 KO (B)- biol rep 3

description: Library name: N18


title: 199_SMARTER_M_78


title: iNeurons - TBK1 KO (A)- biol rep 3

description: Library name: N17


title: TBK1 KO (A)- biol rep 3

description:
Library name: TBK1 KO A 3
TBK1_KOa3


title: S19-14368


title: S18-7673


title: TBK1 KO (A)- biol rep 1

description:
Library name: TBK1 KO A 1
TBK1_KOa1


title: 204_SMARTER_F_65

value: F


title: S19-12296-B

value: R


title: iNeurons - Control - biol rep 3

description: Library name: N13

value: KOLF2.1 J


title: Control - biol rep 2

description:
Library name: ctrl_2
Ctrl_2

value: human stem cells


title: iNeurons - TBK1 KO (B)- biol rep 4

description: Library name: N24


title: 193_SMARTER_M_80


title: 200_SMARTER_F_67


title: S19-11770-3


title: iNeurons - TBK1 E696K SNV/SNV - biol rep 2

description: Library name: N10


title: 192_SMARTER_F_68


title: S18-347


title: 206_SMARTER_F_74


title: iNeurons - Control - biol rep 2

description: Library name: N7

value: Control


title: iNeurons - TBK1 E696K SNV/SNV - biol rep 4

description: Library name: N22

value: no treatment


title: 194_MegaCHOEP_III_F_52


title: 200_MegaCHOEP_III_M_21


title: iNeurons - TBK1 E696K SNV/WT - biol rep 4

description: Library name: N21

value: TBK1 E696K SNV/WT


title: iNeurons - OPTN KO - biol rep 4

description: Library name: N20

value: OPTN KO


title: 2_DENSER_M_71

value: FFPE


title: iNeurons - TBK1 E696K SNV/SNV - biol rep 3

description: Library name: N16

value: iNeurons

value: TBK1 E696K SNV/SNV


title: S18-7867

value: Squamous cell carcinoma


title: 195_MegaCHOEP_III_M_55

value: M


title: iNeurons - TBK1 KO (A)- biol rep 1

description: Library name: N5


title: iNeurons - TBK1 E696K SNV/SNV - biol rep 1

description: Library name: N4


title: S18-30027

value: Adenocarcinoma

value: NR


title: iNeurons - TBK1 E696K SNV/WT - biol rep 3

description: Library name: N15


title: S18-29608

value: No


title: iNeurons - OPTN KO - biol rep 3

description: Library name: N14


title: S18-30225


title: S18-4901


title: iNeurons - TBK1 KO (B)- biol rep 2

description: Library name: N12

value: TBK1 KO


title: iNeurons - TBK1 E696K SNV/WT - biol rep 2

description: Library name: N9


title: S18-30308


title: MCF10A_H1047R_3

city: London

first: George

last: Poulogiannis

address: 237 Fulham Road

department: Cell and Molecular Biology

institute: The Institute of Cancer Research

description:
Library name: Sample 15
RawCounts_MCF10A.csv

data_processing:
Raw FASTQ files were quality-checked using FastQC and aligned to the hg38 human reference genome using the STAR aligner with default parameters. Gene expression levels were quantified by extracting raw counts with featureCounts, using the GENCODE annotation as a reference. The resulting count matrix was used for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: Raw counts of MCF7 isogenic cell lines.
Supplementary files format and content: Raw counts of MCF10A isogenic cell lines.

source_name: Normal Breast

growth_protocol: Isogenic PI3K WT and their respective MUT (E545K and H1047R) MCF10A cells were cultured in DMEM/F-12 supplemented with 5% horse serum, 20 ng/ml epidermal growth factor (EGF), 100 ng/ml cholera toxin, 0.5 mg/ml hydrocortisone, 10 µg/mL insulin, 100 IU/mL penicillin and 100 μg/mL streptomycin. (PEST). MCF7 cells were maintained in DMEM supplemented with 10% FBS, 100 IU/mL penicillin and 100 μg/mL streptomycin. Media was replaced every two-three days with fresh media and the cells were trypsinized upon reaching 80% confluency.

extract_protocol:
Two million cells were seeded in 10 mm Petri dishes two days prior to RNA extraction. Total RNA was extracted using the RNeasy Kit for RNA Purification (Qiagen) following the manufacturer’s protocol. RNA quality was assessed using the Agilent TapeStation system, which provides RNA Integrity Number (RIN) scores to evaluate sample integrity. Only RNA samples with RIN ≥ 7 were used for downstream RNA sequencing to ensure high-quality transcriptomic data. RNA concentration was measured using the NanoDrop spectrophotometer, ensuring adequate yield for library preparation. Only samples with A260/A280 ratios between 1.8 and 2.1 were used to maintain RNA purity.
RNA-seq libraries were prepared using the NEBNextUltra II Directional RNA Library Prep Kit for Illumina with 1000 ng of input material. Sequencing was performed on the NovaSeq X Plus platform to generate high-depth transcriptomic data.

value: Normal Breast

value: Breast epithelial cell

value: PIK3CA MUT


title: 192_MegaCHOEP_III_M_33

first: Emil

last: Chteinberg

institute: Ulm University Medical Center

data_processing:
FASTQ Files using Illumina BaseSpace BCL to FASTQ software version 2.2.0 and Illumina Local Run Manager Software version 2.0.0.
FASTQ Files were analyzed with HTG EdgeSeq Parser software version 5.5 to generate raw counts for a total of 298 genes.
Assembly: Assembly: GRCh38.p13
Supplementary files format and content: raw counts
Supplementary files format and content: log2(Count per million+1)

value: Diffuse large B-ell lymphoma


title: iNeurons - OPTN KO - biol rep 2

description: Library name: N8

value: KOLF2.1 J


title: S18-25096-1


title: S18-24428

value: Other


title: 19_DENSER_F_69

value: F


title: 191_SMARTER_M_74


title: 183_SMARTER_F_67


title: 181_SMARTER_M_66


title: S18-16496

value: R


title: MCF10A_WT_2

description:
Library name: Sample 8
RawCounts_MCF10A.csv

value: PIK3CA WT


title: iNeurons - TBK1 KO (A)- biol rep 2

description: Library name: N11

value: iNeurons

value: no treatment


title: MCF7_MUT_2

description:
Library name: Sample 5
RawCounts_MCF7.csv

source_name: Breast cancer

value: Breast cancer

value: Cancer cell


title: iNeurons - TBK1 E696K SNV/WT - biol rep 1

description: Library name: N3

value: TBK1 E696K SNV/WT


title: iNeurons - TBK1 KO (B)- biol rep 1

description: Library name: N6


title: iNeurons - OPTN KO - biol rep 1

description: Library name: N2

value: OPTN KO


title: MCF7_WT_3

description:
Library name: Sample 3
RawCounts_MCF7.csv


title: S18-25140

description: Gene expression profiling using NanoString nCounter

value: Squamous cell carcinoma

value: Yes

value: NR


title: MCF7_WT_2

description:
Library name: Sample 2
RawCounts_MCF7.csv


title: S17-26452-1

value: Adenocarcinoma

value: No


title: 188_SMARTER_M_72

value: Diffuse large B-ell lymphoma

value: FFPE

value: M


title: HEK293T_random_cyto_2

city: Boulder

first: Mika

last: Nevo

state: Colorado

address: 2315 Walnut St

institute: CU Boulder

description:
Library name: 22017FL-22-01-18_S18
Cytoplasm

data_processing:
nf-core rnaseq v3.9 was used to process data
DESeq2 was used to perform differential expression analysis
Assembly: hg38, mm10
Supplementary files format and content: raw counts
Supplementary files format and content: differential expresion output from DESeq2

extract_protocol:
For P-body-seq, RNA was isolated from P-body and cytoplasmic fractions using the miRNeasy Micro Kit (QIAGEN).
For polyA RNA samples, cDNA libraries were constructed using the V4 ultra + Nextera XT kit for Illumina (Takara Bio). For P-body-seq for total RNA samples, libraries were prepared using Snap seq protocol.
Libraries were sequenced with paired-end 150-bp reads.


title: HEK293T_random_cyto_1

description:
Library name: 22017FL-22-01-17_S17
Cytoplasm


title: S17-23489-2


title: 163_RICOVER_60_F_68

city: Ulm

address: Albert-Einstein-Allee 11

value: F


title: 184_SMARTER_M_76


title: MCF10A_H1047R_2

description:
Library name: Sample 14
RawCounts_MCF10A.csv

value: Normal Breast

value: Breast epithelial cell

value: PIK3CA MUT


title: MCF10A_H1047R_1

description:
Library name: Sample 13
RawCounts_MCF10A.csv


title: d20_neurons_cyto_2

description:
Library name: 22017FL-22-01-26_S26
Cytoplasm


title: MCF10A_E545K_3

description:
Library name: Sample 12
RawCounts_MCF10A.csv


title: MCF10A_E545K_2

description:
Library name: Sample 11
RawCounts_MCF10A.csv


title: MCF10A_E545K_1

description:
Library name: Sample 10
RawCounts_MCF10A.csv


title: MCF10A_WT_3

description:
Library name: Sample 9
RawCounts_MCF10A.csv

value: PIK3CA WT


title: 176_SMARTER_M_72

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)


title: d20_neurons_pbody_2

description:
Library name: 22017FL-22-01-24_S24
Pbody


title: iNeurons - Control - biol rep 1

description: Library name: N1

value: KOLF2.1 J

value: iNeurons

value: Control

value: no treatment


title: liver_bud_prog_cyto_2

description:
Library name: 22017FL-22-01-30_S30
Cytoplasm


title: 16_DENSER_M_67


title: S17-20694

value: R


title: S18-1420


title: MCF10A_WT_1

description:
Library name: Sample 7
RawCounts_MCF10A.csv


title: S17-22569


title: liver_bud_prog_cyto_1

description:
Library name: 22017FL-22-01-29_S29
Cytoplasm


title: 160_SMARTER_M_66


title: 172_SMARTER_M_72


title: 157_SMARTER_M_68


title: MCF7_MUT_3

description:
Library name: Sample 6
RawCounts_MCF7.csv

value: Breast cancer

value: Cancer cell


title: 170_SMARTER_M_74


title: S17-27231

description: Gene expression profiling using NanoString nCounter

value: Other

value: Yes


title: liver_bud_prog_pbody_1

description:
Library name: 22017FL-22-01-27_S27
Pbody


title: S18-22339

value: Squamous cell carcinoma

value: No

value: NR


title: 17_DENSER_M_73

value: Diffuse large B-ell lymphoma

value: FFPE

value: M


title: S17-16283

value: Adenocarcinoma


title: 169_SMARTER_F_71

value: F


title: MCF7_WT_1

description:
Library name: Sample 1
RawCounts_MCF7.csv

value: PIK3CA WT


title: MCF7_MUT_1

description:
Library name: Sample 4
RawCounts_MCF7.csv

value: PIK3CA MUT


title: 166_MegaCHOEP_III_F_46


title: HEK293T_random_pbody_2

description:
Library name: 22017FL-22-01-16_S16
Pbody


title: S15-13510


title: ΔvanAB ΔsisA-D pBVMCS6-SisA 15´Vanillate-R2

city: Würzburg

first: Manuel

last: Velasco Gomariz

address: Josef-Schneider-Straße 2/D15

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

data_processing:
Pipeline for RNAseq analysis CLC Genomics Workbench 22.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics Workbench 22.0.2 (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to NC_011916.1 using CLC Genomics Workbench 22.0.2 (parameters-mismatch cost:2 insertion cost:3 deletion cost:3 lenght fraction: 0.8 similarity fraction: 0.8 strand specific:rev)
Read count extraction and normalization were performed using CLC genomic workbench
Assembly: NCBI Reference Sequence: NC_011916.1
Supplementary files format and content: xlsx file including TPM from each sample

organism: Caulobacter vibrioides CB15

source_name: bacterial cells

growth_protocol: Growth in M2G-Medium (M2 medium supplementd with 0.2% glucose), 200 rpm shaking, 30 °C until OD 0.3

extract_protocol:
RNA extraction using the SV Total RNA Isolation System Protocol from Promega (Z3100) including DNAse treatment, rRNAdepletion and mRNA purification
RNA libraries for RNAseq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®  following manufacturer´s protocol

treatment_protocol: 500 µM Vanillate, 15´

tag: strain

value: delta_vanAB delta_sisA-D pBVMCS6-SisA

value: bacterial cells

value: 500 microM Vanilalte


title: d20_neurons_cyto_1

description:
Library name: 22017FL-22-01-25_S25
Cytoplasm


title: S17-23257


title: ΔvanAB ΔsisA-D pBVMCS6-EV 15´Vanillate-R3

value: delta_vanAB delta_sisA-D pBVMCS6-EV


title: 150_SMARTER_M_77


title: ΔvanAB pBVMCS6-SisA 15´Vanillate-R3

value: delta_vanAB pBVMCS6-SisA


title: ΔvanAB ΔsisA-D pBVMCS6-EV 15´Vanillate-R1


title: HEK293T_random_pbody_1

description:
Library name: 22017FL-22-01-15_S15
Pbody


title: S17-26323


title: d20_neurons_pbody_1

description:
Library name: 22017FL-22-01-23_S23
Pbody


title: 150_RICOVER_60_F_65


title: S15-11468-28

value: R


title: ΔvanAB pBVMCS6-SisA 15´Vanillate-R2


title: 1499_RICOVER_noRTh_F_77


title: lysR2 knockout mutant-1

city: Shanghai

first: Jinjin

address: 800 Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

description:
Library name: Sample1
A2

data_processing:
Data processing was performed on the Majorbio Cloud Platform. After quality control (removal of low-quality reads and adapters), clean reads were mapped to the reference genome using Bowtie2. Gene expression was quantified with RSEM, and differential expression analysis was conducted using DESeq2/edgeR.
Assembly: The reference genome was the Streptomyces auratus strain CIBA Tu 96 (DSM 41897) linear chromosome, 8,422,644 bp in length, assembled in this study from PacBio RSII and Illumina sequencing data (as detailed in the final report dated 2020-12-24). The assembly process involved HGAP software for primary assembly followed by polishing with Illumina data, resulting in a final consensus concordance of 99.8950%.
Supplementary files format and content: CSV file (Exp_RSEM_TPM_20250624_101122.csv) contains RSEM-generated TPM expression values for all genes across the four samples, quantified against the Streptomyces auratus CIBA Tu 96 (DSM 41897) genome.

organism: Streptomyces auratus

extract_protocol:
RNA samples were extracted using RNAprep Pure Cell/Bacteria Kit manufacturer (DP430, TIANGEN) and digested with DNase I (Thermo, America).
RNA-seq libraries were constructed from the total RNA using the TruSeq™ Stranded Total RNA Library Prep Kit.

value: CIBA Tu 96 ( DSM 41897)

value: lysR2 knockout


title: 157_MegaCHOEP_III_F_40


title: E1_P_SS_R10

city: Baltimore

first: Atul

last: Daiwile

state: MD

address: 251 Bayview Blvd,

department: MNRB

institute: NIDA

description: Library name: Sample 72

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts were added to the table
Assembly: Rattus norvegicus Rnor6.0
Supplementary files format and content: tab-delimited text file includes raw counts fro each sample

source_name: Prefrontal Cortex

extract_protocol:
RNA was extracted using the protocol from RNeasy Mini Handbook (Qiagen)
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on two flowcell lanes. After clustering, the flowcells were loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol:
Rats were randomly segregated into two groups of saline (n = 6) or METH (0.1 mg/kg /infusion) (n = 18). On each training day, rats were trained to lever press on a fixed-ratio-1 (FR1) schedule for three 3-h daily sessions (total 9 h/d) with 30 min off intervals in between each session to intravenously self-administer (SA) METH for 20 days.
Subsequently, all METH SA rats were given the opportunity to earn METH accompanied by a concurrent delivery of a 0.5-s foot-shock through the grid floor at 50% of the reinforced lever-presses. We set the initial footshock at 0.18 mA and increased the foot-shock intensity by 0.06 mA up to a final current of 0.36 mA (with a total of 9 punishment days). After 9 days of foot-shock we identified two phenotypes. Some rats continued to take METH in presence of aversive stimuli (foot-shock 0.18 to 0.36mA) we termed those rats shock-resistant (SR), whereas some rats decrease their reinforced lever responding and we called them shock-sensitive (SS)

value: Prefrontal Cortex

value: Neural tissue

value: WT

value: METH Shock Sensitive


title: ΔvanAB pBVMCS6-EV 15´Vanillate-R2

value: delta_vanAB pBVMCS6-EV


title: 1492_RICOVER_noRTh_F_62

value: Diffuse large B-ell lymphoma

value: FFPE


title: ΔvanAB pBVMCS6-EV 15´Vanillate-R1


title: ΔvanAB ΔsisA-D pBVMCS6-CrfA 15´Vanillate-R3

value: delta_vanAB delta_sisA-D pBVMCS6-CrfA


title: S17-20166

value: Adenocarcinoma

value: No

value: NR


title: ΔvanAB ΔsisA-D pBVMCS6-CrfA 15´Vanillate-R2

value: bacterial cells

value: 500 microM Vanilalte


title: 1491_RICOVER_noRTh_M_80

value: M


title: 153_SMARTER_F_67

value: F


title: ΔvanAB ΔsisA-D pBVMCS6-CrfA 15´Vanillate-R1


title: liver_bud_prog_pbody_2

description:
Library name: 22017FL-22-01-28_S28
Pbody


title: 1488_RICOVER_noRTh_F_76


title: ΔvanAB ΔsisA-D pBVMCS6-SisA 15´Vanillate-R3

value: delta_vanAB delta_sisA-D pBVMCS6-SisA


title: 151_SMARTER_F_67


title: Mouse 457

city: Chicago

first: Blake

last: Gill

state: Illinois

address: 300 e superior st

department: Surgery

institute: Northwestern University

description: Total mRNA was analyzed using NS_MM_HOSTRESPONSE_V1.0+PLS_UF_ATKINSON_C10586

data_processing: nCounter nSolver 4.0. instructions can be found here: https://university.nanostring.com/nsolver-40-analysis-software-user-manual/894752 and Advanced Analysis 2.0. instruction per manufacturer: https://university.nanostring.com/advanced-analysis-20-user-manual/894772

label: nCounter Hybridization Probe

source_name: Left lung

label_protocol: mRNA was labeled with hybridization probes in the NanoString nCounter Mouse Host Response Codeset as well as the additional custom plus panel. All nCounter protocols were done so according to the manufacturer's protocols/manuals.

extract_protocol: mRNA was extracted with Qiagen Fibrous Tissue RNeasy mini kit.

value: Normal

value: left lung (Normal)


title: S16-26936-2

value: Squamous cell carcinoma

value: R


title: Mouse 413

value: 6hr Control

value: orthotopically transplanted allogeneic lung


title: ΔvanAB ΔsisA-D pBVMCS6-SisA 15´Vanillate-R1


title: 151_MegaCHOEP_III_F_29

value: Diffuse large B-ell lymphoma


title: Mouse 411


title: WT-2

description:
Library name: Sample4
WT4

value: CIBA Tu 96 ( DSM 41897)

value: WT


title: ΔvanAB ΔsisA-D pBVMCS6-EV 15´Vanillate-R2

value: delta_vanAB delta_sisA-D pBVMCS6-EV


title: E1_P_SR_R09

description: Library name: Sample 66

value: Prefrontal Cortex

value: Neural tissue

value: METH Shock Resistant


title: Mouse 408

value: 24hr Control


title: WT-1

description:
Library name: Sample3
A1

value: bacterial cells


title: ΔvanAB pBVMCS6-CrfA 15´Vanillate-R3

value: delta_vanAB pBVMCS6-CrfA

value: 500 microM Vanilalte


title: lysR2 knockout mutant-2

description:
Library name: Sample2
R2

value: lysR2 knockout


title: ΔvanAB pBVMCS6-SisA 15´Vanillate-R1

value: delta_vanAB pBVMCS6-SisA


title: ΔvanAB pBVMCS6-CrfA 15´Vanillate-R2


title: 1496_RICOVER_noRTh_F_79

value: FFPE

value: F


title: ΔvanAB pBVMCS6-CrfA 15´Vanillate-R1


title: 148_SMARTER_M_68

value: M


title: E1_P_SR_L10

description: Library name: Sample 64


title: ΔvanAB pBVMCS6-EV 15´Vanillate-R3

value: delta_vanAB pBVMCS6-EV


title: Mouse 392

value: 6hr Control

value: orthotopically transplanted allogeneic lung


title: E1_P_SS_R08

description: Library name: Sample 71

value: WT

value: METH Shock Sensitive


title: BMK240614-CC048-ZX01-0101

city: Jishou

first: Gui-Sheng

last: Li

address: 120 Renmin South Street

institute: Jishou University

description:
Library name: Unknown_CC048-004X0001
fresh frozon spatial transcriptomics

data_processing:
The package Seurat v5 provided tools in normalizing data, identifying clusters, and determining marker genes. The threshold for the marker gene was |log2FC| ≥ 0.5 and false discovery rate < 0.05. Spot clustering was visualized using BSTViewer V1.42 (BioMarker)
Assembly: GCA_020310875.1
Supplementary files format and content: BMK240614-CC048-004X0001-01-20240419-DA27BN18F5-B2-HE.txt, section photo digital version
Supplementary files format and content: barcodes.tsv.gz, for the level 7 resolution of spot-gene matrix
Supplementary files format and content: barcodes_cluster.tsv.gz, for the level 7 resolution of spot-gene matrix
Supplementary files format and content: barcodes_pos.tsv.gz, for the level 7 resolution of spot-gene matrix
Supplementary files format and content: barcodes_read.tsv.gz, for the level 7 resolution of spot-gene matrix
Supplementary files format and content: CR3.All_spots_counts.xls, Seurat processed level 7 resolution of spot-gene matrix
Supplementary files format and content: features.tsv.gz, for the level 7 resolution of spot-gene matrix
Supplementary files format and content: matrix.mtx.gz, for the level 7 resolution of spot-gene matrix
Supplementary files format and content: BMK240614-CC048-004X0001-01-20240419-DA27BN18F5-B2-HE.tif, section photo pixel version
Library strategy: Spatial Transcriptomics

organism: Ceratopteris richardii

source_name: shoot tips

extract_protocol:
RNA was trapped by poly(T)VN to the spot array, namely BMKMANU S1000 platform (BioMarker, Beijing)
Double-strand cDNA was synthesized to incorporate the spatial barcode and the unique molecular index (UMI), and furthermore the sample index. The fragmented DNA was obtained via enzymatic digestion

value: shoot tips


title: C12 - sgp130Fc Transgenic (C57BL/6) Liver, age 14 Months

city: Jerusalem

first: Jonathan

middle: H.

last: Axelrod

state: n

address: Ein Kerem

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah Hebrew University Hospital

description: Library name: C12_SL31SL39

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adapter trimming: trim_galore (uses cutadapt version 1.10)
Mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: HTseq-count version 0.6.1
Normalization and differential expression analysis: DESeq2 R package version 1.18.1
Assembly: The reference genome used in the analysis was downloaded from Ensembl (Mouse GRCm38.p6). Counting was performed using an annotation file downloaded from gencode (release M19) and alignment was performed using Tophat2 software.
Supplementary files format and content: processed data files forma: cvs. Content: Columns of with normalized counts grouped per condition. Note: WT-replica1 (C7_BL47BL51) and SGP-replica2 C11_SL29SL30) appeared to be exceptional from their group (i.e. exceptionally large variance) and thus were excluded fron the processed data analysis.

source_name: liver

growth_protocol: Male mice were housed under SPF conditions maintained at a temperature of ~23°C in a 12-hour light-dark cycle in Tecniplast Conventional cages with Teklad Laboratory Grade Sani-Chips bedding, and received sterile commercial rodent chow (Teklad Global 2918) and water ad libitum.

extract_protocol:
RNA was prepared from frozen liver samples (~50 mg) by homogenization in Trizol Reagent (Ambion) using a high-speed homogenizer (TissueLyser, Qiagen).
RNA libraries for RNA-seq were prepared using the CEL-Seq sample preparation protocol (PE: 15 (CEL-Seq barcode and UMI), 50 (data read) and barcode read) and sequenced on an Illumina HiSeq 2500.

treatment_protocol: Mice were grown to the age of 6 months or 14 months and sacrificed following xylosine ketamine anesthesia. Liver tissue samples were removed and snap-frozen in liquid nitrogen prior to RNA extraction.

value: liver

tag: gender

value: male

value: 14 Months

value: sgp130Fc transgenic


title: C -10 sgp130Fc Transgenic (C57BL/6) Liver, age 14 Months

description: Library name: C10_SL25SL26


title: Mouse 405

value: 24hr Control


title: E1_P_SS_R03

description: Library name: Sample 70

value: Prefrontal Cortex

value: Neural tissue


title: 1489_RICOVER_noRTh_M_75

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)

value: Diffuse large B-ell lymphoma


title: C6 - sgp130Fc Transgenic (C57BL/6) Liver, age 6 Months

description: Library name: C6_L207L126

value: 6 Months


title: C11 - sgp130Fc Transgenic (C57BL/6) Liver, age 14 Months

description: Library name: C11_SL29SL30


title: Mouse 458

value: Normal

value: left lung (Normal)


title: Mouse 456


title: Mouse 418


title: Mouse 459


title: E1_P_CT_R12

description: Library name: Sample 60

value: Control


title: 1487_RICOVER_noRTh_M_78

value: FFPE

value: M


title: C4 - sgp130Fc Transgenic (C57BL/6) Liver, age 6 Months

description: Library name: C4_L15L37


title: E1_P_SS_R02

description: Library name: Sample 69

value: WT


title: E1_P_SS_L03

description: Library name: Sample 67

value: METH Shock Sensitive


title: E1_P_SS_L04

description: Library name: Sample 68


title: 1486_RICOVER_noRTh_M_63


title: E1_P_SR_R07

description: Library name: Sample 65

value: METH Shock Resistant


title: E1_P_CT_R06

description: Library name: Sample 58


title: C1 - WT (C57BL/6) Control Liver, age 6 Months

description: Library name: C1_L303L58

value: liver


title: 1483_RICOVER_noRTh_M_74


title: Mouse 407

value: orthotopically transplanted allogeneic lung


title: 1475_RICOVER_noRTh_F_67

value: F


title: Mouse 409


title: CD14pos_PDL1pos_neutrophils_replicate_03

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

description:
Library name: DP_03
S12_DP_3

data_processing:
FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina). Reads were further processed with RTA v1.18.66.3. FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina). Sequencing reads were further processed as follows: Illumina adapters were trimmed and low-quality reads removed with Cutadapt v4.9 (10.14806/ej.17.1.200) (overlap = 7bp, minimum read length = 30bp). Quality control of the processed reads was done with fastQC. RSEM v1.3.1 was used to quantify expression levels against the mouse genome reference GRCm38  (default options). The count data were processed and normalized using limma v3.46 and edgeR v3.32.1, which were also used to perform pairwise differential expression analyses. To identify genes whose expression significantly varies across conditions, we applied a Likelihood Ratio Test (LRT) using DESeq2 v1.30.1, allowing the detection of global effects of a factor without the need to specify individual contrasts. The resulting significant genes were then clustered using the k-means algorithm from the stats package v4.0.3.
Sequenced reads were trimmed using cutadapt
Reads were quantified using RSEM
Assembly: GRCm38.84
Supplementary files format and content: raw counts matrix
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Neutrophils

extract_protocol:
RNA from isolated mouse neutrophils was extracted using RNAeasy micro kit (Quiagen ®). RNA quality was checked using capillary electrophoresis (Agilent). Samples were submitted for whole RNA next generation sequencing in the Genomics Unit of CNIC. 200 ng of total RNA was used to generate barcoded RNA sequencing libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Libraries were sequenced with HiSeq2500 (Illumina) to generate 50-nucleotide single reads, with a minimum of eight million reads per sample.
RNA integrity was assessed using Agilent Bioanalyzer 2100, with RNA integrity numbers (RIN) between 9.8 and 10.0. RNA samples were processed by Novogene (Munich, Germany) for library preparation and sequencing, and all samples passed the quality control criteria. Strand-specific libraries were generated based on Novogene´s standard protocol. Samples were sequenced on an Illumina platform to produce 150 bp pairwise reads (PE150) per sample.

treatment_protocol: Neutrophills were collected from the lungs of control, flu-infected or cancer bearing mice by FACS-sorting as Ly6G+CD11b+ cells and the described combination of markers associated to each sample

value: Neutrophils


title: CD14pos_PDL1pos_neutrophils_replicate_01

description:
Library name: DP_01
S10_DP_1


title: C8 - WT (C57BL/6) Control Liver, age 14 Months

description: Library name: C8_BL50BL49

value: male

value: 14 Months


title: 1469_RICOVER_noRTh_F_61


title: E1_P_SR_L08

description: Library name: Sample 63

value: Prefrontal Cortex

value: Neural tissue


title: 1478_RICOVER_noRTh_M_76

value: Diffuse large B-ell lymphoma


title: E1_P_CT_L12

description: Library name: Sample 56


title: 1454_RICOVER_noRTh_F_77


title: E1_P_SR_L02

description: Library name: Sample 61


title: C7 - WT (C57BL/6) Control Liver, age 14 Months

description: Library name: C7_BL47BL51


title: C9 - WT (C57BL/6) Control Liver, age 14 Months

description: Library name: C9_BL48BL52


title: 1468_RICOVER_noRTh_M_80


title: E1_P_SR_L05

description: Library name: Sample 62


title: C5 - sgp130Fc Transgenic (C57BL/6) Liver, age 6 Months

description: Library name: C5_L221L62

value: 6 Months

value: sgp130Fc transgenic


title: CD14neg_PDL1pos_neutrophils_replicate_02

description:
Library name: PDL1HI_02
S8_PDL1HI_2


title: 1459_RICOVER_noRTh_F_75


title: C2 - WT (C57BL/6) Control Liver, age 6 Months

description: Library name: C2_L233L240


title: 1452_RICOVER_noRTh_F_67


title: C3 - WT (C57BL/6) Control Liver, age 6 Months

description: Library name: C3_L201L310


title: E1_P_CT_R05

description: Library name: Sample 57

value: Control


title: CD14neg_PDL1pos_neutrophils_replicate_01

description:
Library name: PDL1HI_01
S7_PDL1HI_1


title: CD14neg_PDL1pos_neutrophils_replicate_03

description:
Library name: PDL1HI_03
S9_PDL1HI_3


title: 1448_RICOVER_noRTh_M_70

value: FFPE


title: E1_P_CT_L11

description: Library name: Sample 55


title: E1_P_CT_R11

description: Library name: Sample 59


title: E1_N_SS_R10

description: Library name: Sample 54

source_name: Nuclues Accumbens

value: Nuclues Accumbens


title: CD14pos_PDL1neg_neutrophils_replicate_01

description:
Library name: CD14+_01
S4_CD14pos_1


title: CD14pos_PDL1neg_neutrophils_replicate_02

description:
Library name: CD14+_02
S5_CD14pos_2


title: CD14pos_PDL1neg_neutrophils_replicate_03

description:
Library name: CD14+_03
S6_CD14pos_3


title: 1445_RICOVER_noRTh_M_80

value: M


title: Double_Negative_CD14neg_PDL1neg_neutrophils_replicate_01

description:
Library name: DN_01
S1_DN_01


title: 144_MegaCHOEP_III_F_49


title: E1_N_SS_R03

description: Library name: Sample 52

value: WT

value: METH Shock Sensitive


title: JunB-KO_JunB_OVEREXPRESSED_GMCSF_replicate_03

description:
Library name: JB_JB_GM_03
S24_JB_JB_GM_03

source_name: HoxB8-Derived Neutrophils

extract_protocol:
RNA from HoxB8-derived neutrophils was extracted using RNAeasy micro kit (Quiagen ®). RNA quality was checked using capillary electrophoresis (Agilent). Samples were submitted for whole RNA next generation sequencing in the Genomics Unit of CNIC. 200 ng of total RNA was used to generate barcoded RNA sequencing libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Libraries were sequenced with HiSeq2500 (Illumina) to generate 50-nucleotide single reads, with a minimum of eight million reads per sample.
RNA integrity was assessed using Agilent Bioanalyzer 2100, with RNA integrity numbers (RIN) between 9.8 and 10.0. RNA samples were processed by Novogene (Munich, Germany) for library preparation and sequencing, and all samples passed the quality control criteria. Strand-specific libraries were generated based on Novogene´s standard protocol. Samples were sequenced on an Illumina platform to produce 150 bp pairwise reads (PE150) per sample.

treatment_protocol: Culture of HoxB8 cells. For the flow cytometry and bulk RNA sequencing experiments, HoxB8 progenitors at day 3.5 of differentiation were seeded in 96-well plates at a density of 50,000 cells per well. Cells were cultured in complete DMEM medium (vehicle) or treated with GM-CSF (10ng/ml) for 48h, following the same conditions described for primary bone marrow neutrophil cultures. Vehicle or GM-CSF treated cells were collected at 48h after treatment for the analysis.

value: HoxB8-Derived Neutrophils

value: GM-CSF


title: 1442_RICOVER_noRTh_F_68

value: F


title: E1_N_SS_R08

description: Library name: Sample 53


title: 1438_RICOVER_noRTh_F_62


title: JunB-KO_JunB_OVEREXPRESSED_GMCSF_replicate_01

description:
Library name: JB_JB_GM_01
S22_JB_JB_GM_01


title: Double_Negative_CD14neg_PDL1neg_neutrophils_replicate_02

description:
Library name: DN_02
S2_DN_02

value: Neutrophils


title: JunB-KO_JunB_OVEREXPRESSED_vehicle_replicate_03

description:
Library name: JB_JB_VEH_03
S21_JB_JB_VEH_03

value: Vehicle


title: 1443_RICOVER_noRTh_M_73


title: 1437_RICOVER_noRTh_F_76


title: JunB-KO_JunB_OVEREXPRESSED_GMCSF_replicate_02

description:
Library name: JB_JB_GM_02
S23_JB_JB_GM_02


title: E1_N_SS_R02

description: Library name: Sample 51


title: JunB-KO_JunB_OVEREXPRESSED_vehicle_replicate_02

description:
Library name: JB_JB_VEH_02
S20_JB_JB_VEH_02


title: JunB-KO_JunB_OVEREXPRESSED_vehicle_replicate_01

description:
Library name: JB_JB_VEH_01
S19_JB_JB_VEH_01


title: E1_N_SS_L04

description: Library name: Sample 50


title: 1435_RICOVER_noRTh_F_72


title: JunB-KO_control_GMCSF_replicate_02

description:
Library name: JB_C_GM_02
S17_JB_C_GM_02

value: JunB-KO


title: E1_N_SS_L03

description: Library name: Sample 49


title: 1434_RICOVER_noRTh_F_70


title: JunB-KO_control_GMCSF_replicate_01

description:
Library name: JB_C_GM_01
S16_JB_C_GM_01


title: JunB-KO_control_GMCSF_replicate_03

description:
Library name: JB_C_GM_03
S18_JB_C_GM_03


title: JunB-KO_control_vehicle_replicate_03

description:
Library name: JB_C_VEH_03
S15_JB_C_VEH_03


title: 1432_RICOVER_noRTh_F_61


title: CD14pos_PDL1pos_neutrophils_replicate_02

description:
Library name: DP_02
S11_DP_2


title: JunB-KO_control_vehicle_replicate_02

description:
Library name: JB_C_VEH_02
S14_JB_C_VEH_02


title: E1_N_SR_R09

description: Library name: Sample 48

value: METH Shock Resistant


title: 1427_RICOVER_noRTh_M_72


title: Wild_type_JunB_OVEREXPRESSED_GMCSF_replicate_03

description:
Library name: WT_JB_GM_03
S12_WT_JB_GM_03


title: JunB-KO_control_vehicle_replicate_01

description:
Library name: JB_C_VEH_01
S13_JB_C_VEH_01


title: 1425_RICOVER_noRTh_F_69


title: Wild_type_JunB_OVEREXPRESSED_GMCSF_replicate_01

description:
Library name: WT_JB_GM_01
S10_WT_JB_GM_01


title: Wild_type_JunB_OVEREXPRESSED_GMCSF_replicate_02

description:
Library name: WT_JB_GM_02
S11_WT_JB_GM_02


title: E1_N_SR_L08

description: Library name: Sample 45

value: Neural tissue


title: E1_N_SR_L10

description: Library name: Sample 46


title: 1421_RICOVER_noRTh_M_61

value: Diffuse large B-ell lymphoma


title: Wild_type_JunB_OVEREXPRESSED_vehicle_replicate_02

description:
Library name: WT_JB_VEH_02
S8_WT_JB_VEH_02


title: Wild_type_JunB_OVEREXPRESSED_vehicle_replicate_01

description:
Library name: WT_JB_VEH_01
S7_WT_JB_VEH_01