title: Liver, stressed liver cancer, rep4

description: Sample 36

data_processing:
Illumina Casava1.7 software used for basecalling.
Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted ). Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality). Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The sequencing reads were mapped to the mm10 using STAR algorithm
Htseq-count algorithm was used to count reads mapped to each gene uniquely
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes counts values of each gene symbol for each sample

source_name: Liver

extract_protocol:
Total RNA of all liver cells was extracted using Trizol (Invitrogen) according to the manufacturer’s  instructions. Sequencing library was prepared from one microgram of total RNA
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA Sample Prep Kit following manufacturer's protocols

value: Liver

value: Epithelial cells

value: Male

value: HTVi of Akt/Nras/SBT and chronic stress

tag: time

value: Week 4


title: D920T211

status: Public on May 01 2026

type: SRA

city: Paris

first: Alessandro

last: Donada

address: 11 rue Pierre et Marie Curie, Batiment Curie, RDC, R12, UMR168 - Equipe Perie

country: France

institute: Institut Curie

description: Library name: Dataset_A_8

library_source: transcriptomic single cell

data_processing:
FASTQ files for each single cell were generated using bcl2fastq (version 2.20.0), with default parameters. The Read 1 contain the TSO (constant tag sequence and a UMI) followed by cDNA or only cDNA.  The Read 2 contain cDNA only. Index1 and index2 reads correspond to cell-specific barcode. The scRNA-SmartSeq3 pipeline v1.2.1 (https://doi.org/10.5281/zenodo.15056215) was used to generate UMI count tables from FASTQ files. Briefly, reads were aligned to the human genome (hg38) using STAR (version 2.7.8a) and assigned to genes using FeatureCounts (deeptools version 3.5.0). UMIs were extracted, deduplicated and counted for each gene using umiTools (version 1.1.1). Low-quality cells were filtered out based on a minimum of 500 genes detected and a percentage of mitochondrial RNA lower than 20. Families composed of only one cell were also removed. Counts were normalised using SCTransform function with default parameters from R Seurat package (version 4.3.0).  CITE-seq: Raw sequencing reads were processed using Cellranger v3.1.0. To obtain a reads/cell/gene count table, reads were mapped to the human GRCh38 reference genome. Cells with less than 1000 genes per cell and with a high percentage (> 30%) of mitochondrial genes were removed from downstream analyses. Following our filtering procedures, the average UMI count per cell was 4406. The median number of genes detected per cell was 1662, 2.2% mapped to mitochondrial genes. Data normalization and integration were performed using the default Seurat v4 approach FindIntegrationAnchors() followed by IntegrateData(), and differentially expressed genes were determined using a logistic regression in Seurat on the non-integrated data using the FindConservedMarkers() function. Pathway based analyses were performed using the enrichR package. Unsupervised clustering was performed on the significant variable genes using the 10 first PCA followed by the nonlinear dimensionality reduction technique UMAP. Annotation of the data was obtained by mapping published signatures using the AddModuleScore() method of Seurat.
Assembly: Human hg38
Supplementary files format and content: html/raw data QC for SMART-seq3
Supplementary files format and content: mtx and h5/matrix count for CITE-seq

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
SMART-seq3: Single cell distribution of individual cell families has been performed using the cellenONE platform (Cellenion). Briefly, we selected individual wells of 96-wells plates displaying at least four cells, harvested the entire well, centrifugated for 8’ at 300g and resuspended in 6 µL of PBS 1X (Sigma). Then, the whole volume was loaded into the machine, but due to the dead volume, effectively only 4 µL of this cell suspension could be redistributed. Individual cells were each sorted directly into single wells of 96-wells plates (90 cells per plate) at 4 °C, each well containing 3 µL of lysis buffer. The lysis buffer contains 0.03 µL Triton X100 (ThermoFisher Scientific), 0.0375 µL Recombinant RNAse Inhibitor (Takara Bio), 0.2 µL dNTP 10mM (ThermoFisher Scientific), 0.5 µL PEG 40% (Sigma), 0.04 µL SMARTseq3 oligo-dT 100 μM (/5BiosG/ACGAGCATCAGCAGCATACGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN; IDT) and ultrapure RNAse water (Invitrogen).  CITE-seq: Magnetic sorted CD34+ cells from umbilical cord blood were plated at a cell density of 1x105 cells/mL, using the same culture condition described for the condition Diff. Cells were harvested after 96 hours, counted with a haemocytometer, and resuspended in cold PBS 1X (ThermoFisher Scientific) containing 2% Bovine Serum Albumin (BSA, Euromedex) and 0.01% Tween 20 (Sigma), to a final concentration of 106 cells/mL. 100 µL of this cell suspension was incubated with a mix of previously prepared CITE-seq antibodies. Cells were incubated for 30 minutes at 4 °C, washed three times with the same solution used for the incubation and resuspended in 16.5 µL, at a final concentration of 1000 cells/mL.
SMART-seq3: Reverse transcription (RT) and the subsequent steps were performed accordingly to the SMART-seq3 technique40. Briefly, lysates in each well underwent RT (42 °C for 90 mins, 10 cycles at 50 °C 2 mins + 42 °C 2 mins, and finally 85 °C for 5 mins) on ice, in presence of template switch oligonucleotide at 100 µM (/5BiosG/AGAGACAGATTGCGCAATGNNNNNNNNrGrGrGIDT), 0.04 µL Maxima H minus reverse transcriptase (ThermoFisher Scientific), TRIS-HCl 1M PH 8.3 (Invitrogen), 0.12µL NaCl 1M (Invitrogen), 0.04 µL GTP 100mM (ThermoFisher Scientific), 0,32 µL DTT 100mM (ThermoFisher Scientific), 0.1 µL MgCl2 50mM (ThermoFisher Scientific) and 0.05 µL Recombinant RNAse Inhibitor (Takara Bio) and water. The following PCR step was performed immediately after, using the Kapa Hifi HotStart Ready Mix (Roche), and forward (100 µM TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATTGCGCAATG) and reverse (25 µM ACGAGCATCAGCAGCATACGA) primers (IDT technologies) for 25 cycles. After DNA purification using AMPure XP microbeads (ratio 0.8:1) (Beckman Coulter, A63881), the cDNA was tagmented in a final volume of 2 µL, using the Nextera XT DNA Library preparation kit (Illumina). The following library amplification was performed adding 1.5 µL of UDI primers and 2,5 µL of PCR mix including the Phusion High Fidelity DNA polymerase (ThermoFisher Scientific). After tagmentation, the different samples were pooled, purified using AMPure XP microbeads (ratio 0.9:1) and sequenced at 100-bp paired end on a high-output flow cell, using a NovaSeq SP, 800M reads (Illumina).  CITE-seq: Approximately 1.65x104 cells were loaded, to obtain a final yield of 1x104 recovered cells. Cells were processed accordingly to the Chromium Single Cell 3’ library v3.1 (10x Genomics). Libraries were sequenced using a Novaseq s1 (Illumina), allocating at least 20,000 reads per cell for the mRNA library, and 5,000 reads for the Antibody Derived Tags (ADT) library

tag: tissue

value: Blood

tag: cell type

value: Haematopoietic stem and progenitors


title: control_M1_fat

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

country: USA

institute: Washington University in St. Louis

description:
Library name: Fat_control_rep1
control_M1_fat

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the Ensembl release 101 primary assembly with STAR version 2.5.1a
Aligned reads were imported to Partek Flow software for downstream analysis
DEGs were identified with DESeq2 package implemented in Partek Flow
Assembly: Ensembl release 101
Supplementary files format and content: tab-delimited text file includes raw gene counts for each sample

organism: Mus musculus

source_name: white adipose tissue

growth_protocol: Tissues were stored in RNALater (Thermofisher) in 4 degree overnight and transferred to -20 degree until RNA extraction

extract_protocol:
RNA was extracted with the magnetic bead based MaxwellRSC 48 instrument using the Maxwell RSC simply RNA Tissue kit
For muscle, library was prepared according to manufacturer’s protocol with Clontech SMARTer method kit; for fat and hypothalamus, library was prepared with RiboErase method kit

value: white adipose tissue

tag: strain

tag: treatment

value: vehicle


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +24h doxycycline, replicate 3, sequencing run 2

city: Oxford

first: I-Jun

last: Lau

address: Old Rd

department: Botnar Research Centre

country: United Kingdom

institute: University of Oxford

description: Library name: 24HR_3-run-2

library_source: genomic

data_processing:
Capture-C analysis was performed using CapCruncher v0.2.0 (https://doi.org/10.5281/zenodo.6326102).
Assembly: mm10
Supplementary files format and content: Bigwigs generated as part of CapCruncher v0.2.0 (63) (https://doi.org/10.5281/zenodo.6326102).
Library strategy: Capture-C

molecule: genomic DNA

source_name: E14 (TOT2N variant) containing stable integration of TetR-MybTA constuct

extract_protocol:
Cells fixed with 2% formaldehyde and lysed on ice
The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for the generation of the 3C libraries was similar to other 3C-based methods. Briefly, cells were crosslinked with 2% formaldehyde, quenched with cold glycine, washed in phosphate buffered saline, resuspended in cold lysis buffer and snap frozen to -80. Cells were thawed on ice, pelleted and resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37 °C for 1h at 1400 rpm on a Thermomixer, followed by a further incubation of 1h after the addition of Triton X-100 (final concentration 1.67%). An overnight digestion was performed using DpnII (final concentration 500U/ml; 37 °C / 1400 rpm). The digested chromatin was ligated overnight using T4 DNA HC ligase (final concentration 10U/ml; 16 °C / 1400 rpm). The samples were de-crosslinked overnight with Proteinase K at 65 °C, followed by a 30 min incubation at 37 °C with RNase. A Phenol/Chloroform extraction was performed, followed by an ethanol precipitation and wash. Digestion efficiencies were assessed by gel electrophoresis and RT-PCR, which showed digestion efficiencies higher than 80%. The DNA contents of the DpnII 3C libraries were quantitated using a Qubit fluorometer. 2 ug DNA was adapter ligated using a strategy based on sonication combined with the NEBNext Ultra II DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resulting captured library was assessed using the Agilent ScreenTape system. The libraries were sequenced using the Illumina NextSeq (150bp paired end reads) platform.

tag: cell line

value: Doxycycline 1 µg/ml


title: D920T208

description: Library name: Dataset_A_7


title: 10mg_M5_fat

description:
Library name: Fat_10mg_rep4
10mg_M5_fat

value: 10mg/kg oxaliplatin


title: Liver, stressed liver cancer, rep3

city: Shanghai

first: Lu

last: Li

state: Shanghai

address: No. 650, Xinsongjiang Road, Songjiang District, Shanghai, China

department: Shanghai General Hospital

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: Sample 35

tag: genotype

value: WT

tag: Sex


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +24h doxycycline, replicate 3, sequencing run 1

description: Library name: 24HR_3-run-1

value: E14 (TOT2N variant) containing stable integration of TetR-MybTA constuct


title: Liver, stressed liver cancer, rep2

description: Sample 34


title: D920T207

description: Library name: Dataset_A_6


title: 10mg_M4_fat

description:
Library name: Fat_10mg_rep3
10mg_M4_fat


title: 10mg_M3_fat

description:
Library name: Fat_10mg_rep2
10mg_M3_fat


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +24h doxycycline, replicate 2, sequencing run 1

description: Library name: 24HR_2-run-1


title: D920T206

description: Library name: Dataset_A_5


title: 10mg_M2_fat

description:
Library name: Fat_10mg_rep1
10mg_M2_fat


title: Liver, liver cancer, rep4

description: Sample 32

value: HTVi of Akt/Nras/SBT


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +24h doxycycline, replicate 2, sequencing run 2

description: Library name: 24HR_2-run-2


title: Liver, stressed liver cancer, rep1

description: Sample 33


title: D920T205

description: Library name: Dataset_A_4


title: D920T204

description: Library name: Dataset_A_3


title: Liver, liver cancer, rep3

description: Sample 31


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +24h doxycycline, replicate 1, sequencing run 2

description: Library name: 24HR_1-run-2


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +24h doxcycline, replicate 1, sequencing run 1

description: Library name: 24HR_1-run-1


title: D920T202

description: Library name: Dataset_A_2


title: control_M2_Muscle

description:
Library name: Muscle_control_rep2
control_M2_Muscle

source_name: skeletal muscle

value: skeletal muscle


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +1h doxycycline, replicate 3, sequencing run 2

description: Library name: 1HR_3-run-2


title: control_M3_Muscle

description:
Library name: Muscle_control_rep3
control_M3_Muscle


title: Liver, liver cancer, rep2

description: Sample 30


title: BM-MSCs Hypoxia 2

city: Delhi

first: Sujata

last: Mohanty

state: Delhi

address: Ansari nagar

department: Stem Cell Facility

country: India

institute: AIIMS, New Delhi

description: Library name: CB2

data_processing:
The size selected and purified libraries were analyzed in 4200 Tape Station system (Agilent Technologies) using High sensitivity D1000 Screen tape as per manufacturer instructions
The sequenced raw reads often contain low quality reads with adapters, which will affect the quality of downstream analysis. To avoid this, raw reads containing ambiguous base (Ns), poly (A) tails and the reads lacking 3’ adapter were removed using Cutadapt v1.18. Finally, low quality bases were trimmed to get high quality reads using Trimmomatic v0.39 in single-end mode with quality cut-off of 20 wherever applicable.
The high-quality reads were mapped to the reference genome using bowtie v1.3.1 aligner with default parameters. Unmapped reads were discarded and reads mapped on genome were considered for downstream analysis.
SmallRNA sequencing data is known to include reads from other category of small non-coding RNAs such as tRNA, snoRNA, snRNA and piRNA ect. Sample-wise reads were mapped against the customized database of Rfam (Database built after removing miRNA and their precursor sequences from the Rfam) using Bowtie v1.3.1 aligner with default parameters. The unmapped against Rfam database were considered for downstream analysis
Reads which are not mapped to Rfam, were mapped to known repeat sequences i.e. Repbase (v22) using Bowtie v1.3.1 aligner with default parameters. Reads mapped on Repbase database were discarded and unmapped reads were considered for downstream analysis.
Reads having length less than 18 nts and greater than 30 nts were excluded from the analysis. The reads which have length between 18-30 bases were considered for miRNA identification.
Assembly: The high-quality reads were mapped to the reference genome using bowtie v1.3.1 aligner with default parameters. Unmapped reads were discarded and reads mapped on genome were considered for downstream analysis.
Supplementary files format and content: 1 PDF file-EGI_Final Report_Dr. Sujata Mohanty_GA243209_Small RNA Seq_17-10-2024.pdf containing all the processed data along with the respective graphs

source_name: umbilical cord

growth_protocol: standard cell culture treatment

extract_protocol:
Trizol chloroform extraction was performed and total RNA was isolated
The small RNA sequencing libraries were prepared from the received total RNA samples using illumina NEBNext® Multiplex Small RNA Library Prep Kit for Illumina (NEB) as per the manufacturer’s instruction. Briefly, approximately 1ug of RNA was processed for 3' adapter ligation followed by 5’ adaptor ligation. The adaptor ligated RNA samples were then converted to cDNA using reverse transcriptase followed by PCR amplification using common primer and indexed primer. The enriched library was then purified using Spin column followed by AMPureXP bead-based size selection.

treatment_protocol: hypoxia and normoxia

value: umbilical cord

value: primary MSCs

value: Stem Cell


title: control_M4_Muscle

description:
Library name: Muscle_control_rep4
control_M4_Muscle


title: D920T201

description: Library name: Dataset_A_1


title: Liver, late-stage HCC, rep3

description: Sample 28

value: Liver

value: Epithelial cells

value: HTVi of ΔN90-β-Catenin/c-Met/SBT

value: Week 8


title: Liver, liver cancer, rep1

description: Sample 29

value: Male

value: Week 4


title: control_M1_Muscle

description:
Library name: Muscle_control_rep1
control_M1_Muscle


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +1h doxycycline, replicate 2, sequencing run 2

description: Library name: 1HR_2-run-2


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +1h doxycycline, replicate 3, sequencing run 1

description: Library name: 1HR_3-run-1


title: Rifamycin O rep2

city: China

first: Jinlian

last: Wei

institute: ECUST

description:
Library name: Sample 5
drug_2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Assembly: GRCh38.p10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
K562 cells were removed, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: K562 cells were cultured in T25 culture flasks, and treated with DMSO or 30 μM Rifamycin O.

value: AML cells

value: Rifamycin O treatment


title: Rifamycin O rep3

description:
Library name: Sample 6
drug_3


title: Liver, late-stage HCC, rep1

description: Sample 26


title: Liver, late-stage HCC, rep2

description: Sample 27


title: 10mg_M4_muscle

description:
Library name: Muscle_10mg_rep4
10mg_M4_muscle


title: Rifamycin O rep1

description:
Library name: Sample 4
drug_1


title: 10mg_M5_muscle

description:
Library name: Muscle_10mg_rep5
10mg_M5_muscle

value: vehicle


title: 10mg_M3_muscle

description:
Library name: Muscle_10mg_rep3
10mg_M3_muscle

value: 10mg/kg oxaliplatin


title: 10mg_M2_muscle

description:
Library name: Muscle_10mg_rep2
10mg_M2_muscle


title: DMSO rep3

description:
Library name: Sample 3
control_3

value: WT

value: DMSO treatment


title: Liver, early-stage HCC, rep3

description: Sample 25


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +1h doxycycline, replicate 2, sequencing run 1

description: Library name: 1HR_2-run-1

value: E14 (TOT2N variant) containing stable integration of TetR-MybTA constuct

value: Doxycycline 1 µg/ml


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct, replicate 3, sequencing run 2

description: Library name: TA_3-run-2


title: Liver, early-stage HCC, rep2

description: Sample 24


title: Liver, early-stage HCC, rep1

description: Sample 23


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +1h doxycycline, replicate 1, sequencing run 1

description: Library name: 1HR_1-run-1


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct, replicate 3, sequencing run 1

description: Library name: TA_3-run-1


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct +1h doxycycline, replicate 1, sequencing run 2

description: Library name: 1HR_1-run-2


title: DMSO rep2

description:
Library name: Sample 2
control_2


title: 10mg_M1_muscle

description:
Library name: Muscle_10mg_rep1
10mg_M1_muscle

value: skeletal muscle


title: DMSO rep1

description:
Library name: Sample 1
control_1


title: D1408T79

description: Library name: Dataset_B_79

value: Blood

value: Haematopoietic stem and progenitors


title: RNA-seq of sinc-3

city: Changsha

first: Duan

last: peiyun

address: 139 Renmin Zhong Lu,

institute: The second xiangya hospital of central south university

description:
Library name: sinc-3
sinc-3

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Subsequently, approximately 48M clean reads per sample were preserved for further analysis. The clean reads were aligned to the reference genome via HISAT2.
The FPKM for each gene was calculated, and gene read counts were acquired through HTSeq-count. PCA analysis was undertaken using R (version 3.2.0) to assess the biological replication of samples. Differential expression analysis was executed employing DESeq2, with a q-value < 0.05 and fold change > 2 designated as the criteria for significantly differentially expressed genes (DEGs).
Hierarchical clustering analysis of DEGs was conducted using R (version 3.2.0) to elucidate the expression patterns of genes across various groups and samples.
Assembly: GRCh38
Supplementary files format and content: Processed data file is a gene expression matrix in tab-delimited text (.txt) format. Each row represents one gene, and each column corresponds to one sample (e.g., si1097-1, sinc-1, etc.). The values are FPKM (Fragments Per Kilobase of transcript per Million mapped reads), indicating normalized gene expression levels. The file includes both si1097-treated and control samples.

source_name: neural progenitor cells

growth_protocol: Neural progenitor cells were cultured under standard maintenance conditions.

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy Micro Kit according to the manufacturer’s protocol.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Cells were transfected with si1097 or control RNA sequences.

value: neural progenitor cells


title: Day-OPLN6

first: Hui

address: 800 Dongchuan Road

institute: SHSCI

data_processing:
snRNA-seq data was transformed from  FASTQ into matrix data utilizing Cellranger.
Assembly: mm10
Supplementary files format and content: RData file include gene count values for each sample
Supplementary files format and content: csv file include metadata for each sample

molecule: nuclear RNA

source_name: lymph node

extract_protocol:
The cell suspension is processed through the 10X Genomics Chromium system to form Gel Beads-in-emulsion (GEMs), which are then transferred to a PCR machine for reverse transcription.
10X Genomics 3’ RNA

value: lymph node


title: Day-3PLN4


title: Liver, healthy, rep2

description: Sample 21

value: Liver

value: Epithelial cells

value: Without treatment

value: Week 0


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct, replicate 2, sequencing run 1

description: Library name: TA_2-run-1


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct, replicate 2, sequencing run 2

description: Library name: TA_2-run-2


title: 3261

city: New York

first: yu

last: liu

state: NY

address: 1428 Madison Ave

institute: Mount Sinai

data_processing:
Raw 10× read processing and quality control Raw sequence reads were quality-checked using FastQC software. The CellRanger version 7.0 software suite from 10× Genomics was used to process, align and summarize unique molecular identifier (UMI) counts against the mouse GRCm38 assembly reference genome analysis set, obtained from https://www.10xgenomics.com. Filtered count matrices from CellRanger were imported into R for further processing. Low quality cells are filtered, such as cell for which a high percentage of UMIs originated from mitochondrial features (more than 20%) and cell with fewer than 200 expressed genes. Three methods (doubletfinder, scds and scDblFinder) are applied to detect doublets, doublets cells identified by at least two methods are filtered. Median absolute deviation method is used to derive a cutoff for the maximum number of genes in cell. After filtering, 34,417 cells are left, used for further analysis. The Seurat R package (version 5.0) is used to normalization, integration using harmony, and plotting. Slingshot is used for trajectory and psudotime analysis. Cellchat is used for cell-cell communication between macrophage and neurons.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: small bowel

extract_protocol:
Wild-type mice were anesthetized by isoflurane after which they were sacrificed by cervical dislocation. The GI tract was harvested with care to prevent nicking major blood vessels. The mesenteric fat was removed as much as possible. The small bowel contents were flushed out with ice-cold 1X PBS (which did not contain RNase inhibitor or Actinomycin D). After cleaning the tissue was transferred to a petri-dish containing ice-cold Opti-MEM (with 2uM Actinomycin D). The LM-MP tissue was peeled on a sterile 1 ml pipette and placed in sterile RNase free tubes containing maintenance media (composition given below) and kept on ice. After all the animals have been sacrificed and LM-MP isolated, using new single edged blade, the LM-MP was chopped into minute pieces. The chopped tissues were digested in 50ml conical tubes with digestion media (composition given below) for 35 mins at 37C with shaking. The tubes were then vortexed for 30 sec at the highest speed followed by trituration with 1ml pipette tips. Samples were centrifuged for 7mins at 200g at temperature of 4C. Supernatants were aspirated gently and re-suspended in 4-5ml of Maintenance Buffer. The re-suspended pellets were passed through a 100 micron cell sieve after which the eluents were triturated with fire polished glass pipettes. The samples were centrifuged for 7mins at 200g, the supernatants aspirated, and the pellets resuspended in 3-4ml of Maintenance Buffer followed by trituration with glass pipettes. The washing process was repeated once more tand the pellets finally re-suspended in 1ml Maintenance Buffer and filtered through 40micron cell sieve and submitted to Hopkins Single Cell Sequencing Core.
Upon submission, the quality of the samples (viability and cell count) was assessed with Trypan Blue and Cell Countess (Invitrogen). The library was made using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X genomics). The depth of reads was 20,000/cell and the sequencing was carried out by NovaSeq 6000 (Illumina).

value: small bowel

value: wt

tag: dob

tag: date experiment

value: M


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct, replicate 1, sequencing run 2

description: Library name: TA_1-run-2

source_name: E14 (TOT2N variant) containing stable integration of rTetR-MybTA constuct


title: RNA-seq of sinc-2

description:
Library name: sinc-2
sinc-2


title: RNA-seq of sinc-1

description:
Library name: sinc-1
sinc-1


title: 3267

value: F


title: Liver, healthy, rep1

description: Sample 20

value: WT

value: Male


title: RNA-seq of si1097-3

description:
Library name: si1097-3
si1097-3


title: Capture-C in E14 (TOT2N variant) cells with TetR-MybTA construct, replicate 1, sequencing run 1

description: Library name: TA_1-run-1

value: E14 (TOT2N variant) containing stable integration of rTetR-MybTA constuct


title: 3265


title: Liver, foot shock stress, rep4

description: Sample 19

value: Shock stress

value: Day 7


title: Liver, foot shock stress, rep2

description: Sample 17


title: Liver, foot shock stress, rep3

description: Sample 18


title: RNA-seq of si1097-2

description:
Library name: si1097-2
si1097-2


title: Hash Tag Oligos - APLP1 Control

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description:
MHC antibodies (cell surface markers to label single cells from individual mice)
HTO_APLP1_Counts.csv
Sample 5

data_processing:
Library strategy: CITE-seq
mapping with bowtie2 to the mm10 genome (local mode, paired)
compressing SAM to BAM (samtools)
sorting the BAM files by region (samtools)
Hash tag oligos (HTOs) very counted by regular expression using custom R scripts for every possible cell barcode.
genes counted with 10X Genomics cellranger for Sample 1 & 2, with custom R scripts for Samples 3 to 4 and with Bioconductor R assays(summarizeOverlaps(mm10_gns, reads,mode="Union")) for samples 7 to 14
immunoprecipitation samples were mapped with bowtie2 (end-to-end alignment)
Genome_build: Mus Musculus (mm 10)
Supplementary_files_format_and_content: gene count tables

source_name: Hash Tag Oligos

growth_protocol: Neural stem cells were isolated from the sub-ventricular zone of adult mice

extract_protocol:
10X genomics, oligo(dT) capturing (Hash tag oligos conjugated to anti-MHC1 and anti-CD45; HTO_1: 155803 TotalSeq™-A0302 anti-mouse Hashtag 2 Antibody BioLegend, HTO_2: 155805 TotalSeq™-A0303 anti-mouse Hashtag 3 Antibody BioLegend, HTO_3: 155807 TotalSeq™-A0304 anti-mouse Hashtag 4 Antibody BioLegend)
10X Genomics library preparation

treatment_protocol: cultured NSC were treated either with BMP4 for 3 days or EGF

value: Hash Tag Oligos

tag: nsc isolation

value: freshly isolated

value: no treatment

value: wildtype

tag: sequenced molecule

value: hash-tag-oligos


title: Female-Male, CD8+ T cells, day4, clone 13

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

country: Canada

institute: University of Manitoba

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, read alignment, and gene counting were performed using Cell Ranger v3
Using Seurat v4.3 in R, samples were filtered to contain cells with at least 100 reads, and features present in at least 10 cells
Cells were further filtered to those containing less than 6000 features and less than 5% mitochondrial reads
Activated naïve T cells were removed by filtering out clusters of naïve cells with higher expression of Cd44 and Cd62L
After above filtering steps, filtered samples were saved as sparse matrices in Market Exchange Format (MEX)
Assembly: mm10
Supplementary files format and content: Sparse matrices in Market Exchange Format (MEX), consisting of gzipped tsv files of barcodes and features, and gzipped matrix files

molecule: polyA RNA

source_name: CD8+ T cells

growth_protocol: primary murine CD8 T lymphocytes were used for scRNA-seq experiments

extract_protocol:
Murine splenocytes were harvested at 4, 7, 28, and 40 days after virus infection and processed into single cell suspensions of CD8 T lymphocytes. Following CD8 T cell isolation by magnetic bead based enrichment, naive and activated CD8 T lymphocytes harvested at different times post-infection were FACS sorted on a BD Aria III.  The purity of sorted cell populations was confirmed on the BD Aria III prior to downstream scRNA-seq cDNA library generation.
10x Genomics Next GEM Single Cell 3' v3.1 protocol, single-index

treatment_protocol: in vivo viral infections of LCMV-Armstrong and LCMV-clone 13 were performed in mice to generate activated CD8 T lymphocytes.  Non-infected naïve murine CD8 T lymphocytes were untreated.

value: CD8+ T cells

tag: age

value: 6-8 weeks old

tag: donor strain

tag: recipient strain

tag: donor sex

value: Female

tag: recipient sex

tag: infection strain

value: LCMV-clone 13

tag: days post_infection


title: 3260

tag: tissue

value: small bowel

value: wt


title: RNA-seq of si1097-1

description:
Library name: si1097-1
si1097-1

value: neural progenitor cells

tag: cell type


title: Liver, foot shock stress, rep1

description: Sample 16

value: Liver

value: Epithelial cells

value: WT

tag: treatment

tag: time


title: Hash Tag Oligos - APLP1-/-

description:
MHC antibodies (cell surface markers to label single cells from individual mice)
HTO_APLP1_Counts.csv
Sample 6

tag: genotype


title: NPM1 patient 10, diagnosis+relapse sample replicate 2 [Illumina NovaSeq 6000]

city: Napels

first: Wout

last: Megchelenbrink

address: Vico de Crecchio 7

department: Precision Medicine

country: Italy

institute: University of Campania "Luigi Vanvitelli”

description:
Library name: NPM1_10_rep2_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000

data_processing:
scRNA-seq data analysis. FASTQ files were aligned to the human GRCh38 reference using CellRanger v5.0 (10x Genomics). Pooled samples were demultiplexed into patients using germline SNPs and subsequently into DX vs RL samples using sample-specific HTOs. First, BAM generated by Cell Ranger were used as input for cellsnp-lite23 to count the REF and ALT occurrences per cell barcode across ~13 million known SNPs from gnomAD with minor allele frequency ≥ 0.01. Next, vireoSNP24 was used to assign cells to donors using the donor-matched WXS samples (DX timepoint) as a reference. Next, the hashtag count matrix was generated from a FASTQ file using CITE-seq-Count followed by DX vs RL demultiplexing with Seurat v5.025. Cells with fewer than 200 unique molecular identifiers (UMIs), more than 5,000 UMIs, or more than 15% mitochondrial reads were discarded.
Assembly: GRCh38 (v37)
Supplementary files format and content: R/Seurat object of the single cell RNA-seq data without batch correction. Raw and normalized counts can be extracted from the Seurat object.

source_name: bone marrow mononuclear cells

extract_protocol:
Cryopreserved AML samples were thawed at 37°C. Viable cells were enriched using an Annexin V MicroBead Kit (Miltenyi Biotec). After washing with cold PBS, cells were resuspended in 500 μl 0.5% PBA (0.5% BSA, 1 x PBS) with 0.2% human serum and incubated for 10 min on ice. After centrifugation and removal of the supernatant, cells were resuspended in 100 μl cold 0.5% PBA with 1 μl of unique cell hashing antibody (Biolegend, TotalSeq-A1-4) and incubated for 20 min on ice. Subsequently, cells were washed after spinning down and resuspended with an appropriate amount of 0.04% PBA (0.04% BSA, PBS) for the following procedures.
Libraries were processed using a GemCode Single-Cell instrument and a Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit (10x Genomics), according to the manufacturer’s instructions, until the cDNA amplification step. Hashtag oligo (HTO) primers were added during the cDNA amplification PCR, and cDNA was generated following the 10x Single Cell 3’ v2 protocol. Hashed cells were diluted to 1 million cells/ml and pooled together immediately before loading. Four samples (2 pairs) were pooled and loaded into one lane of a 10x Genomics Chromium Chip. Following PCR, 0.6X volume of SPRI beads were used to separate larger cDNA fragments (retained on beads) from cellular mRNA from the HTO-containing fraction (in supernatant). The cDNA fraction derived from cellular mRNA was processed according to the 10x Single Cell 3’ v2 protocol. An additional 1.4X volume of SPRI beads was added to the HTO fraction to obtain a final SPRI volume of 2X SPRI. After cleanup and final elution, a separate PCR program was set up to generate HTO libraries.

value: bone marrow mononuclear cells


title: Liver, social defeat stress, rep6

description: Sample 15

tag: Sex

value: Male

value: Social defeat stress

value: Day 10


title: WJ-MSCs Normoxia 2

description: Library name: CC2

source_name: bone marrow

value: bone marrow

tag: cell line

value: primary MSCs

value: Stem Cell


title: NPM1 patient 10, diagnosis+relapse sample replicate 1 [Illumina NovaSeq 6000]

description:
Library name: NPM1_10_rep1_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Female-Male, CD8+ T cells, day28, clone 13

description: 10x Genomics

value: CD8+ T cells


title: biofilm, CEA10, rep4

city: Hanover

first: Charles

last: Puerner

state: NH

address: 1 Rope Ferry Rd

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth College

description:
Library name: CEA10_BF5
column name in biofilm_vs_planktonic.txt is CEA10_BF5

data_processing:
trimming was performed with cutadapt v 2.4: nextseq-trim=20, minumum length = 1, quality cutoff = 20
Read mapping was performed with STAR v 2.7.2b: output type = BAM SortedByCoordinate, outFilterType = BySJout, genome = A1163 (v  FungiDB-52), gff file = AF293  (v FungiDB-52)
Read counting was performed with htseq-count v 0.11.2: format = BAM, stranded = no, order = pos
Assembly: FungiDB-52_AfumigatusAf293_Genome.fasta
Supplementary files format and content: tab-delimited text file included raw counts for each sample

organism: Aspergillus fumigatus

source_name: Mycelium (submerged Biofilm)

growth_protocol: 37 °C, 5% CO2, SCN media

extract_protocol:
Tissue was harvested in TRI reagent with bead beating, RNA was purified from the aqueous phase with Qiagen RNAeasy Plus Mini kit. DNA contamination was removed with the TURBO DNA-free kit (Ambion). 100 or 200 ng of RNA was used for library construction.
RNA libraries for RNAseq were prepared using the mRNA HyperPrep kit (Kapa Bioscience) following manufacturer’s instructions.

treatment_protocol: Hypoxia treated planktonic cultures were switched to 0.2% O2 + 5% CO2 for 30 minutes

value: Mycelium (submerged Biofilm)


title: biofilm, CEA10, rep3

description:
Library name: CEA10_BF4
column name in biofilm_vs_planktonic.txt is CEA10_BF4


title: Liver, social defeat stress, rep5

description: Sample 14


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 4 [Illumina NovaSeq 6000]

description:
Library name: NPM1_08_09_rep4_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Female-Male, CD8+ T cells, day7, clone 13

description: 10x Genomics

value: 6-8 weeks old

value: Female


title: Liver, social defeat stress, rep4

description: Sample 13


title: biofilm, CEA10, rep2

description:
Library name: CEA10_BF3
column name in biofilm_vs_planktonic.txt is CEA10_BF3


title: Female-Male, CD8+ T cells, day40, Armstrong

description: 10x Genomics

value: LCMV-Armstrong


title: biofilm, CEA10, rep1

description:
Library name: CEA10_BF2
column name in biofilm_vs_planktonic.txt is CEA10_BF2


title: Liver, healthy, rep3

description: Sample 22

value: Without treatment

value: Week 0


title: Female-Male, CD8+ T cells, day7, Armstrong

description: 10x Genomics


title: Female-Male, CD8+ T cells, day4, Armstrong

description: 10x Genomics


title: Liver, social defeat stress, rep3

description: Sample 12

value: Liver


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 3 [Illumina NovaSeq 6000]

description:
Library name: NPM1_08_09_rep3_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Liver, social defeat stress, rep1

description: Sample 10

value: Epithelial cells


title: biofilm, AF293, rep3

description:
Library name: AF293_BF4
column name in biofilm_vs_planktonic.txt is AF293_BF4


title: Male-Male, CD8+ T cells, day7, clone 13

description: 10x Genomics

value: LCMV-clone 13


title: biofilm, AF293, rep4

description:
Library name: AF293_BF5
column name in biofilm_vs_planktonic.txt is AF293_BF5


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 1 [Illumina NovaSeq 6000]

description:
Library name: NPM1_08_09_rep1_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000

value: bone marrow mononuclear cells


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 4 [Illumina NovaSeq 6000]

description:
Library name: NPM1_06_07_rep4_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Liver, social defeat stress, rep2

description: Sample 11

value: WT

value: Male


title: Male-Male, CD8+ T cells, day7, Armstrong

description: 10x Genomics


title: biofilm, AF293, rep2

description:
Library name: AF293_BF3
column name in biofilm_vs_planktonic.txt is AF293_BF3


title: Liver, restraint stress, rep4

description: Sample 8

value: Restraint stress

value: Day 16


title: biofilm, AF293, rep1

description:
Library name: AF293_BF2
column name in biofilm_vs_planktonic.txt is AF293_BF2


title: NPM1 patient 08+09, diagnosis+relapse sample replicate 2 [Illumina NovaSeq 6000]

description:
Library name: NPM1_08_09_rep2_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Liver, restraint stress, rep5

description: Sample 9


title: Male-Male, CD8+ T cells, day4, clone 13

description: 10x Genomics


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 1 [Illumina NovaSeq 6000]

description:
Library name: NPM1_06_07_rep1_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Liver, restraint stress, rep3

description: Sample 7


title: Liver, restraint stress, rep2

description: Sample 6


title: Male-Male, CD8+ T cells, naïve

description: 10x Genomics


title: Male-Male, CD8+ T cells, day4, Armstrong

description: 10x Genomics


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 2 [Illumina NovaSeq 6000]

description:
Library name: NPM1_06_07_rep2_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Female-Female, CD8+ T cells, day7, clone 13

description: 10x Genomics


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 4 [Illumina NovaSeq 6000]

description:
Library name: NPM1_04_05_rep4_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Liver, without stress, rep4

description: Sample 4

value: Without stress

value: Day 0


title: Female-Female, CD8+ T cells, day7, Armstrong

description: 10x Genomics

value: CD8+ T cells


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 3 [Illumina NovaSeq 6000]

description:
Library name: NPM1_04_05_rep3_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Liver, without stress, rep3

description: Sample 3


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 1 [Illumina NovaSeq 6000]

description:
Library name: NPM1_04_05_rep1_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Female-Female, CD8+ T cells, day4, clone 13

description: 10x Genomics


title: NPM1 patient 04+05, diagnosis+relapse sample replicate 2 [Illumina NovaSeq 6000]

description:
Library name: NPM1_04_05_rep2_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Liver, restraint stress, rep1

description: Sample 5


title: Neural Stem Cells - EGF

description:
long (100 bp paired-end) reads to capture 3'UTRs
Sample 2

data_processing:
mapping with bowtie2 to the mm10 genome (local mode, paired)
compressing SAM to BAM (samtools)
sorting the BAM files by region (samtools)
Hash tag oligos (HTOs) very counted by regular expression using custom R scripts for every possible cell barcode.
genes counted with 10X Genomics cellranger for Sample 1 & 2, with custom R scripts for Samples 3 to 4 and with Bioconductor R assays(summarizeOverlaps(mm10_gns, reads,mode="Union")) for samples 7 to 14
immunoprecipitation samples were mapped with bowtie2 (end-to-end alignment)
Genome_build: Mus Musculus (mm 10)
Supplementary_files_format_and_content: gene count tables

source_name: Neural Stem Cells

value: Neural Stem Cells

value: cultured

value: cultured with EGF for 3 days

value: wildtype

value: mRNA


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 2 [Illumina NovaSeq 6000]

description:
Library name: NPM1_02_03_rep2_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 3 [Illumina NovaSeq 6000]

description:
Library name: NPM1_02_03_rep3_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Neural Stem Cells - BMP4

description:
long (100 bp paired-end) reads to capture 3'UTRs
Sample 1

value: cultured with BMP4 for 3 days


title: WT motor neurons, P30 days, rep5

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

data_processing:
barcode and adapter removal: FASTX toolkit (v0.0.14) -- NaN
quality filtering: FastQC (v0.11.8) -- quality >20, leading/trailing 5, minlength 36
remove non-mRNAs: Bowtie2 -- rRNA, miRNA, tRNA, piRNA, snRNA, rmsk removal
RSEM: RSEM (v1.3.1) -- strand-specific, bowtie2, genome-bam
DESeq2: DESeq2(1.26.0)
Differential Expression Analysis: DEBrowser  1.24.0 -- To perform DE analysis DEBrowser interface used
RNA-Seq pipeline : DolphinNext Ver. 6 -- To execute data processing steps above for all the samples (https://dolphinnext.umassmed.edu/index.php?np=1&id=800)
Assembly: mm10
Supplementary files format and content: *gene_expression_expected_count.tsv:RSEM expected counts; *DE_Analysis.csv: DeSeq2 L2FC & adjusted p-values for comparisons. The read counts in this table are MRN normalized using deBrowser.

source_name: motor neurons

extract_protocol:
Mouse lumbar spinal cord motor neurons were collected by laser capture microdissection.
RNA was extracted using an PicoPure RNA Isolation Kit (ThermoFisher), including a DNAse digestion step.
Novogene Ultra-low RNA Input RNA sequencing services were used for RNASeq. For each sample, 2 ng of total RNA was used for the construction of sequencing libraries using Smart-Seq v4 Ultra Low Input RNA / cDNA library preps.

tag: tissue sample

value: lumbar spinal cord

value: motor neurons

value: P30 days


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 1 [Illumina NovaSeq 6000]

description:
Library name: NPM1_02_03_rep1_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000

value: bone marrow mononuclear cells


title: Siglec F_ 3 day_biologycal rep_2

type: RNA

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

description: Gene expression data from Siglec F+ alveolar macrophages in 3 day after liver resection

hyb_protocol: Samples were hybridized to the array at 45°C for 16 hours, followed by washing. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip™ Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 7g GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 7g

data_processing:
The data were analyzed with Transcriptome Analysis Console (TAC) Software  version 4.0.2 using Affymetrix default analysis settings and RMA algorithm
The data were analyzed with Transcriptome Analysis Console (TAC) Software  version 4.0.2 using Affymetrix default analysis settings and RMA algorithm

label: biotin

source_name: Siglec F+ alveolar macrophagesRNA

label_protocol:
Transcriptome analysis was performed using microarray Clariom™ S Assay, mouse (Applied Biosystems™). After RNA expraction reverse transcription using the WT Amplification Kit was performed to synthesize first-, second-strand cDNA, cRNA and ss-cDNA incubating at appropriate temperatures and purifying via magnetic beads. Then ss-cDNA was fragmented, labeled with biotin.
Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol:
Siglec F+ alveolar macrophages were collected, frozen, lysed in QIAZOL reagent for the following RNA extraction
Macrophages samples were collected, frozen, lysed in QIAZOL reagent for the following RNA extraction

extract_protocol:
Total RNA was isolated from  alveolar macrophages  using QIAZOL reagent according to standart protocol
Ordinary extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol:
Animals in which the liver was intact served as a control group. Animals with 70% liver resection was served as a comparison group.  The animals were removed from the experiment after 1 day (24 hours), 3 and 7 days. Alveolar macrophages from lungs were sorted with magnetic beads with anti-Siglec F antiboby in 1,3 and 7 days after liver resection and in control group
Macrophages samples were cellected on different time periods after cocultivation with Ito cells, CD146cells, HGF/cultivation with MCSF


title: WT motor neurons, P30 days, rep2

value: WT


title: WT motor neurons, P30 days, rep4


title: Siglec F_ 3 day_biologycal rep_3

value: Siglec F+ alveolar macrophages in 3 day after liver resection


title: NPM1 patient 01, relapse sample [Illumina NovaSeq 6000]

description:
Library name: NPM1_01_RL_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: ld-2

city: Chuncheon

first: Dong-Hoon

last: Jeong

state: Gangwon-do

address: Room #8306, Department of Life Science, 1 Hallymdaehak-gil

department: Dept. of Life Science

country: South Korea

institute: Hallym University

data_processing:
Processing of the small RNA sequencing data was performed using CLC Genomics Workbench version 11.0.1 (Qiagen, Germany).
Rice miRNAs registered in miRBase Release 22 were used for searching mature miRNA with a perfect match and for obtaining their expression values
The expression levels were normalized to TP5M (Transcripts per 5 million reads).
Differentially expressed mature miRNAs between wild type and ld mutants were called if the fold change difference was more than 2 or less than 2 and statistically significant with less than 0.01 of P-value using the EDGE test in a CLC Genomics.
Genome_build: Rice genome (MSU 7.0)
Supplementary_files_format_and_content: exel file with read count of rice miRNAs

organism: Oryza sativa

source_name: young panicle

growth_protocol: Japonica wild type and all mutant seeds were germinated and grown on 1/2 Murashige and Skoog (MS) media for 10 days, and subsequently transferred to soil. Rice plants were grown either in a greenhouse with a light/dark cycle of 14/10 h (30/20°C) or in an experimental field plot under natural environmental conditions in summer.

extract_protocol:
Total RNAs from young panicles of wild type, ld-1, and ld-2 were isolated using Trizol reagent (Invitrogen, USA) and 20 to 30-nt of small RNAs were purified by gel purification from a 15% denaturing PAGE gel.
Small RNA libraries were constructed using the NEXTFlex Small RNA-seq kit v3 (Bioo Scientific, USA) and sequenced on an Illumina MiSeq platform.

treatment_protocol: No treatment

tag: tag

value: ld-2 mutant


title: ld-1

value: ld-1 mutant


title: Siglec F_intact_biologycal rep_3

description: Gene expression data from Siglec F+ alveolar macrophages, intact liver


title: homozygous Sod1 knock out motor neurons, P30 days, rep4

value: homozygous Sod1 knock out


title: NPM1 patient 01, diagnosis sample [Illumina NovaSeq 6000]

description:
Library name: NPM1_01_DX_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Siglec F_7day_biologycal rep_2

description: Gene expression data from Siglec F+ alveolar macrophages in 7 day after liver resection


title: Siglec F_1day_biologycal rep_2

description: Gene expression data from Siglec F+ alveolar macrophages in 1 day after liver resection


title: NPM1 patient 02+03, diagnosis+relapse sample replicate 4 [Illumina NovaSeq 6000]

description:
Library name: NPM1_02_03_rep4_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: Siglec F_ 3 day_biologycal rep_1


title: Siglec F_intact_biologycal rep_1

value: Siglec F+ alveolar macrophages,  intact liver


title: Liver, without stress, rep2

description: Sample 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted ). Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality). Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The sequencing reads were mapped to the mm10 using STAR algorithm
Htseq-count algorithm was used to count reads mapped to each gene uniquely
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes counts values of each gene symbol for each sample

source_name: Liver

value: Liver

value: Epithelial cells

value: Male

value: Without stress

value: Day 0


title: Female-Female, CD8+ T cells, day4, Armstrong

description: 10x Genomics

value: CD8+ T cells

value: 6-8 weeks old

value: Female

value: LCMV-Armstrong


title: Siglec F_7day_biologycal rep_1

value: Siglec F+ alveolar macrophages in 7 day after liver resection


title: Liver, without stress, rep1

description: Sample 1


title: NPM1 patient 06+09, diagnosis sample,protein

description: Library name: NPM1_06_09_DX_scTapestri_protein

library_source: other

data_processing:
FASTQ files were processed using the Tapestri cloud pipeline v3 and aligned against the refererence genome GRCh37 (hg19). Libraries containing two patient samples were demultiplexed using homozygous SNPS (see manuscript). H5 files can be loaded into MissionBio Mosaic and cells belonging to a single patient can be subsetted using the file "scTapestri_90K_cell_barcodes_annotated.tsv" file for all barcodes. Samples were integrated in R/Seurat as described in the manuscript.
Assembly: GRCh37 (hg19)
Supplementary files format and content: The HDF5 files(h5) contain the raw SNV, CNV and ADT count matrices that were generated by the Tapestri pipeline (version 3). Each file contains  the ouput of a library with two multiplexed samples. These files can be analyzed e.g., in MissionBio Mosaic. The file "scTapestri_90K_cell_barcodes_annotated.tsv" contains meta data for each barcode, including the sample of origin and may be used to subset and/or filter cells from these matrices.
Supplementary files format and content: The file "scTapestri_90K_cell_barcodes_annotated.tsv" the meta data for each barcoded cell (BC).
Supplementary files format and content: The file "scTapestri_90K_cells_unfiltered.rds" contains the normalized antibody data for all profiled cells (unfiltered) in an integrated R/Seurat object.
Supplementary files format and content: The file "scTapestri_filtered_and_annotated_Seurat_object_list.rds" contains the filtered SNV, CNV and normalized antibody data in an integrated Seurat object list, where each item in the list corresponds to a patient.
Supplementary files format and content: The file "scTapestri_filtered_annotated_integrated.rds" contains the normalized antibody reads and dimensionality reductions for the filtered cells in an integrated R/Seurat object.

molecule: protein

extract_protocol:
Cryopreserved bone marrow mononuclear cells were thawed, washed with PBS, filtered through a 40-μm cell strainer, and counted using an automated cell counter. Approximately 140,000 viable cells were loaded onto the Tapestri V3 platform.
Single-cell DNA + protein sequencing was conducted using the Tapestri platform (MissionBio) with a customized amplicon panel based on sample-matched WXS data. 45 surface proteins were targeted using the “TotalSeq-D Heme Oncology” panel (Biolegend). Two donor samples with at least 3 “opposite” homozygous SNPs were multiplexed.

value: bone marrow mononuclear cells


title: Wild type

value: Wild-type


title: Female-Female, CD8+ T cells, naïve

description: 10x Genomics


title: homozygous Sod1 knock out motor neurons, P30 days, rep3

value: lumbar spinal cord

value: motor neurons

value: P30 days


title: NPM1 patient 06+09, diagnosis sample,DNA

description: Library name: NPM1_06_09_DX_scTapestri_DNA


title: Siglec F_1day_biologycal rep_3

value: Siglec F+ alveolar macrophages in 1 day after liver resection


title: homozygous Sod1 knock out motor neurons, P30 days, rep2

value: homozygous Sod1 knock out


title: homozygous Sod1 knock out motor neurons, P30 days, rep1


title: Siglec F_7day_biologycal rep_3


title: Sfp1-K655/657Q, 30min in glucose, rep2

city: Quebec city

first: Jacques

last: Cote

address: 9 McMahon Street

department: CHU de Québec-Université Laval Research Center

institute: Laval University

data_processing:
Reads were trimmed using fastp v0.23.2. Quality check was performed on raw and trimmed data to ensure the quality of the reads using FastQC v0.11.9 and MultiQC v1.12. The quantification was performed with Kallisto v0.48.0 against the Saccharomyces cerevisiae transcriptome (R64-1-1 downloaded from Ensembl release 109). The principal component analysis was completed with the FactoMineR v2.7 R package
Assembly: sacCer3
Supplementary files format and content: fastq

organism: Saccharomyces cerevisiae

source_name: LPY

growth_protocol: Yeast cells were grown in YPD overnight at 30 ˚C to the exponential phase. The next day, cells were collected by centrifugation and washed twice with water before resuspending in the media containing 2% raffinose as the single carbon source. Glucose was then added to the culture to a final 2% after raffinose incubation. Total RNA was extracted at 15min, 30min and 60min upon glucose addition.

extract_protocol:
Total RNA was extracted following the hot-phenol protocol. In brief, cell pellets were resuspended in 400 μL TES solution (10 mM Tris HCl, 10 mM EDTA, and 0.5% SDS). 400 μL acid phenol was added and then vortexed. The cell suspensions were incubated at 65 ˚ C for 30 minutes with occasional, brief vortexing. Top speed centrifuge was performed to separate the aqueous phase. The aqueous phase was transferred and 400 μL chloroform was added followed by another round of vortex and centrifuge. RNAs were precipitated with sodium acetate and 100% ethanol. Initial precipitated RNAs were washed with ice-cold 70% ethanol. RNA pellets were resuspended in 50 μL RNase-free H2O. Reverse transcription was performed following the 2X SYBR Green PCR Master Mix kits protocol.
NEBNext Ultra II Directional RNA library and NEBNext Poly(A) - dual index

value: LPY


title: PAH PASMC4 siDNM2

city: Kingston

first: Stephen

last: Archer

address: 94 Stuart Street

department: Department of Medicine

institute: Queen's University

description: Library name: PASMC4siDnm2_S18_R1_001

data_processing:
Sequence files were demultiplexed, and processed using fastqc and multiqc prior to trimming with BBDuk, aligned to the human GRCh genome with Star, and counts files created with HT-Seq Count. Differential analysis was performed using a pair-wise approach and implemented in DESeq2 package (v1.44) in R (v4.4.0)and they were included in the GO:BP (Gene Ontology Biological Process) analysis using gprofiler2(v.0.2.3)
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt

source_name: Small Pulmonary Artery

growth_protocol: 5 PAH PASMC Cell lines were cultured in Medium 231 supplemented with smooth muscle cell growth supplement (SMGS, Life Technologies, Carlsbad, CA, USA) under standard conditions (37°C, 5% CO₂).

extract_protocol:
Total RNA was isolated using RNeasy Kit (Qiagen) catalog#74104 following the manufacturer’s protocol.
Libraries for RNAseq analysis were constructed using the Lexogen 3’ kit according to manufacturers’protocols (Lexogen, Austria), and validated using Qubit 4 (Thermofisher Scientific). Successful libraries were pooled and diluted to an equimolar concentration resulting in a total pool of 4 nM. Dilution and denaturationwere performed according to Illumina protocols to result in a 2.2pM input (optimized for the Lexogen 3’ kit). Single-end sequencing of 75 cycles was performed on an Illumina Nextseq550 using a High Output v2 reagent cartridge with each sample having a minimum depth of 5 million reads.

treatment_protocol: The PAH PASMCs were grown to 60-80% confluence and transfected with 225 picomole of ctrl- siRNA or siDNM2 using the Lipofectamine® RNAiMAX Transfection Reagent (Life Technologies, Carlsbad, CA) for 48 hours before harvesting.

value: Small Pulmonary Artery

value: PASMC

value: PAH PASMC


title: NPM1 patient 03+05, replase sample,protein

description: Library name: NPM1_03_05_RL_scTapestri_protein


title: PAH PASMC4 Ctrl-siRNA

description: Library name: PASMC4NC1_S17_R1_001

value: Ctrl siRNA


title: PAH PASMC8 Ctrl-siRNA

description: Library name: PASMC8NC1_S13_R1_001


title: NPM1 patient 03+05, relapse sample,DNA

description: Library name: NPM1_03_05_RL_scTapestri_DNA


title: PAH PASMC8 siDNM2

description: Library name: PASMC8siDnm2_S14_R1_001


title: Sfp1-K655/657Q, 30min in glucose, rep1


title: NPM1 patient 03+05, diagnosis sample,protein

description: Library name: NPM1_03_05_DX_scTapestri_protein


title: homozygous Sod1 G85R motor neurons, P30 days, rep2

value: homozygous Sod1 G85R


title: Siglec F_intact_biologycal rep_2

value: Siglec F+ alveolar macrophages,  intact liver


title: Sfp1-K655/657R, 30min in glucose, rep2


title: Siglec F_1day_biologycal rep_1


title: Sfp1-K655/657R, 30min in glucose, rep1


title: homozygous Sod1 G85R motor neurons, P30 days, rep4


title: homozygous Sod1 G85R motor neurons, P30 days, rep3


title: PAH PASMC7 siDNM2

description: Library name: PASMC7siDnm2_S10_R1_001


title: NPM1 patient 03+05, diagnosis sample,DNA

description: Library name: NPM1_03_05_DX_scTapestri_DNA


title: Sfp1-wt, 30min in glucose, rep1


title: NPM1 patient 02+10, replase sample,protein

description: Library name: NPM1_02_10_RL_scTapestri_protein


title: PAH PASMC3 siDNM2

description: Library name: PASMC3siDnm2_S6_R1_001


title: homozygous Sod1 G85R motor neurons, P30 days, rep1


title: Sfp1-K655/657Q, 15min in glucose, rep1


title: PAH PASMC7 Ctrl-siRNA

description: Library name: PASMC7NC1_S9_R1_001


title: Sfp1-K655/657Q, 15min in glucose, rep2


title: WT motor neurons, P70 days, rep4

value: WT

value: P70 days


title: WT motor neurons, P70 days, rep5


title: NPM1 patient 02+10, relapse sample,DNA

description: Library name: NPM1_02_10_RL_scTapestri_DNA


title: Sfp1-wt, 30min in glucose, rep2


title: Sfp1-K655/657R, 15min in glucose, rep2


title: WT motor neurons, P70 days, rep2


title: PAH PASMC1 siDNM2

description: Library name: PASMC1siDnm2_S2_R1_001


title: NPM1 patient 02+10, diagnosis sample,protein

description: Library name: NPM1_02_10_DX_scTapestri_protein


title: NPM1 patient 02+10, diagnosis sample,DNA

description: Library name: NPM1_02_10_DX_scTapestri_DNA


title: WT motor neurons, P70 days, rep3


title: PAH PASMC1 Ctrl-siRNA

description: Library name: PASMC1NC1_S1_R1_001


title: Sfp1-K655/657R, 15min in glucose, rep1


title: NPM1 patient 01+08, replase sample,protein

description: Library name: NPM1_01_08_RL_scTapestri_protein


title: NPM1 patient 01+08, relapse sample,DNA

description: Library name: NPM1_01_08_RL_scTapestri_DNA


title: Sfp1-wt, 15min in glucose, rep2


title: PAH PASMC3 Ctrl-siRNA

description: Library name: PASMC3NC1_S5_R1_001


title: CN,RAD21_ICRF_ChIP_1

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description:
Library name: CN,RAD21_ICRF_ChIP_1
SPMR-normalized peak calling was performed with both Input replicates and ICRF replicates

data_processing:
Raw fastq.gz sequencing reads were analyzed for quality control using FastQC, trimmed using Trimmomatic, and aligned to the mm10 reference genome (GRCm38.p6 assembly) using BWA-MEM.
BAM files were marked and filtered for duplicate reads using Samtools.
Peaks were called using MACS3 from biological duplicates and pseudo-replicates where each ChIP sample was normalized to input DNA.
MACS3-generated bedGraph files were converted to bigWig files using Kent Utils for individual replicates and pooled replicates
Assembly: mm10
Supplementary files format and content: BigWig, generated from peak calling using both input replicates and condition replicates

source_name: Primary Cortical Neuron

growth_protocol: Dissociated cortical neurons from E16 Swiss-Webster mice (Charles River) were plated at a density of 5 million cells/plate in 10 cm plates. The plates were pre-coated with poly-D-lysine (0.5 mg/ml) overnight at 37°C, followed by washing twice with dH2O. Neurons were maintained in neurobasal media (GIBCO) supplemented with L-glutamine, penicillin/streptomycin, and B27. Cells were treated by adding drug directly to the culture media 30 minutes prior to collection

extract_protocol:
ChIP was performed for two biological replicates using a ChIP assay kit (MilliporeSigma) as described by the manufacturer. Briefly, DIV13 primary cortical neurons (~15M cells per replicate) were crosslinked with 1% formaldehyde for 10 minutes at 37°C, washed twice with ice-cold PBS, scraped, and resuspended in SDS lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, protease and phosphatase inhibitor cocktail). Cells were sonicated to shear DNA to 200-500 bp using a bioruptor (Diagenode; high power, 30 seconds on/30 seconds off for 40 cycles). Samples were then centrifuged at 13,000 RPM for 10 minutes at 4°C to remove cellular debris, and the supernatant was diluted up to 2 mL in ChIP dilution buffer (16.7 mM Tris-HCl pH 8, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS). Prior to immunoprecipitation, 1% of each sample transferred to a clean tube to be used for input normalization. Samples were then incubated with appropriate antibody overnight at 4°C followed by incubation with ChIP-grade protein A/G magnetic beads (Thermo) for 3 hours at 4°C. Antibody-conjugated beads were washed with low salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 150 mM NaCl), high salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 0.25 M LiCl), and twice with TE buffer (50 mM Tris-HCl pH 8, 1 mM EDTA) for 5 minutes each with agitation at room temperature. Immunoprecipitated protein-DNA complexes were eluted from the magnetic beads in 500 µl ChIP elution buffer (1% SDS, 0.1 M NaHCO3). DNA-protein crosslinks for immunoprecipitated samples and input DNA were reversed via incubation with an additional 20 mM NaCl for 4 hours at 37°C and residual protein was digested with Proteinase K (NEB) for 1 hour at 45°C. DNA was precipitated using phenol/chloroform isolation and ethanol precipitation, washed with 70% ethanol, and resuspended in 50 µl TE buffer.
Samples were prepared for sequencing using a paired-end library preparation kit compatible with Illumina sequencing instruments (KAPA biosciences) according to the manufacturer’s instructions. Following library amplification, DNA fragment size was assessed via Tapestation (Agilent) to ensure a final library size of 350-450 bp. DNA concentration was quantified by fluorometry (dsDNA high sensitivity Qubit assay, Thermo) to ensure equal DNA concentration for each replicate before replicates were pooled and sequenced on an Illumina NextSeq 500 instrument using V2.5 reagents to an average depth of 25-35 million reads per replicate.

treatment_protocol: DIV13 primary cortical neurons were bath stimulated with 100 micromolar ICRF-193 for 1 hour prior to collection or with 50 micromolar NMDA for 10 minutes followed by washout and recovery in drug-free media for 50 minutes prior to collection

value: Primary Cortical Neuron

tag: chip antibody

value: RAD21 (GeneTex, GTX106012)

value: ICRF


title: WT motor neurons, P70 days, rep1

value: lumbar spinal cord

tag: age


title: CN,RAD21_ICRF_ChIP_2

description:
Library name: CN,RAD21_ICRF_ChIP_2
SPMR-normalized peak calling was performed with both Input replicates and ICRF replicates


title: NPM1 patient 01+08, diagnosis sample,DNA

description: Library name: NPM1_01_08_DX_scTapestri_DNA

value: bone marrow mononuclear cells


title: homozygous Sod1 knock out motor neurons, P70 days, rep4

value: motor neurons


title: homozygous Sod1 knock out motor neurons, P70 days, rep3


title: Sfp1-K655/657Q, 2% raffinose, rep2


title: CN,RAD21_NMDA_ChIP_2

description:
Library name: CN,RAD21_NMDA_ChIP_2
SPMR-normalized peak calling was performed with both Input replicates and NMDA replicates

value: NMDA


title: Sfp1-wt, 15min in glucose, rep1


title: homozygous Sod1 knock out motor neurons, P70 days, rep2

value: homozygous Sod1 knock out


title: Sfp1-K655/657R, 2% raffinose, rep2

value: LPY


title: shLARS1_RNC

city: Guangzhou

first: Haining

last: Liu

address: Zhongshan road 2

institute: The first affiliated hospital of sun yat-sen university

description:
Library name: Sample4
Column name in raw_count.txt: shLARS1_rnc

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
Assembly: Hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: RBE

growth_protocol: RBE cells were  cultrued in RMPI 1640 medium. Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
Total RNA samples were isolated with Trizol following the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit,

treatment_protocol: LARS1 gene knockdown was mediated by short hairpin RNA.

value: RBE

value: Introhepatic cholangiocarcinoma cells


title: CN,RAD21_NMDA_ChIP_1

description:
Library name: CN,RAD21_NMDA_ChIP_1
SPMR-normalized peak calling was performed with both Input replicates and NMDA replicates


title: homozygous Sod1 knock out motor neurons, P70 days, rep1


title: CN,RAD21_CON_ChIP_2

description:
Library name: CN,RAD21_CON_ChIP_2
SPMR-normalized peak calling was performed with both Input replicates and CON replicates


title: CN,RAD21_CON_ChIP_1

description:
Library name: CN,RAD21_CON_ChIP_1
SPMR-normalized peak calling was performed with both Input replicates and CON replicates


title: NPM1 patient 01+08, diagnosis sample,protein

description: Library name: NPM1_01_08_DX_scTapestri_protein


title: Sfp1-K655/657R, 2% raffinose, rep1


title: shLARS1_Input

description:
Library name: Sample3
Column name in raw_count.txt: shLARS1_input


title: homozygous Sod1 G85R motor neurons, P70 days, rep3


title: homozygous Sod1 G85R motor neurons, P70 days, rep4


title: NC_RNC

description:
Library name: Sample2
Column name in raw_count.txt: NC_rnc


title: CN,RAD21_Input_2

description: Library name: CN,RAD21_Input_2


title: Sfp1-wt, 2% raffinose, rep2


title: homozygous Sod1 G85R motor neurons, P70 days, rep2


title: CN,RAD21_Input_1

description: Library name: CN,RAD21_Input_1


title: Sfp1-wt, 2% raffinose, rep1


title: NPM1 patient 06+07, diagnosis+relapse sample replicate 3 [Illumina NovaSeq 6000]

description:
Library name: NPM1_06_07_rep3_scRNA_Seq, NovaSeq 6000
Libraries were sequenced on an Illumina Nextseq 500 and resequenced on an Illumina NovaSeq6000


title: NC_Input

description:
Library name: Sample1
Column name in raw_count.txt: NC_input


title: Sfp1-K655/657Q, 2% glucose, rep2


title: homozygous Sod1 G85R motor neurons, P70 days, rep1


title: WT5 LaminA

city: Houston

first: Priyatansh

last: Gurha

state: Texas

address: 6770 Bertner Ave

department: School of Medicine

institute: UTHealth

description: Library name: WT5-LaminA-fastq

data_processing:
Peaks were called by Epic2
Diffbind was used for differential peak enrichment
Assembly: GRCM39
Supplementary files format and content: bed files for LAD peaks
Library strategy: CUT&Run

source_name: Cardiac

growth_protocol: Isolated CM

extract_protocol:
Cardiac myocyte were isolated using the langerdoff isolation method
Illumina library construction protocol

value: Cardiac

value: Cardiac myocyte

value: Wild type


title: WT5 IgG

description: Library name: WT5-IgG-fastq


title: Sfp1-K655/657R, 2% glucose, rep2


title: WT motor neurons, P120 days, rep6

value: P120 days


title: Sfp1-K655/657Q, 2% glucose, rep1


title: WT4 IgG

description: Library name: WT4-IgG-fastq


title: WT motor neurons, P120 days, rep4Repeat

value: WT


title: Sfp1-K655/657R, 2% glucose, rep1


title: 78-ON

city: HOUSTON

first: anil

middle: k

last: sood

state: TEXAS

address: 7777 knight road, unit 173

department: Gyn Oncology and Rep Medicine

institute: UT MD Anderson Cancer Center

description: Library name: 26630

data_processing:
Spatial transcriptomics data were processed using Seurat v5 in R 4.4.1. Data integration across samples was performed using RPCA. Dimensionality reduction, clustering, and UMAP visualization were based on the integrated data. Spots with low quality or marked for deletion were excluded. Differential expression analysis and module scoring were performed on filtered tumor spots across pre and post treament samples. AR gene expression was specifically evaluated across these groups.
Assembly: not provided
Supplementary files format and content: Matrix
Library strategy: Spatial Transcriptomics

source_name: Vagina

extract_protocol:
Tissue sections (10 μm) were mounted onto Visium Spatial Gene Expression slides (10x Genomics), fand stained with hematoxylin and eosin. Tissue permeabilization was performed according to the manufacturer's recommendations. RNA was captured in situ on the slide and reverse-transcribed to generate spatially barcoded cDNA
Libraries were prepared using the 10x Genomics Visium Spatial Gene Expression protocol, following the manufacturer’s instructions. Spatially barcoded cDNA was amplified and converted into sequencing-ready libraries. Libraries were sequenced on an Illumina Nova Seq 6000 platform.

value: Vagina

tag: response to_therapy

value: Complete response

tag: time point

value: ON


title: WT motor neurons, P120 days, rep5


title: Sfp1-wt, 2% glucose, rep2


title: 78-PRE

description: Library name: 26629

value: PRE


title: WT3 IgG

description: Library name: WT3-IgG-fastq


title: 59-PRE

description: Library name: 26615

source_name: Peritoneum

value: Peritoneum

value: Progressive disease


title: 59-ON

description: Library name: 26616


title: 61-PRE

description: Library name: 26617

value: Liver

value: Partial  response


title: 54-ON

description: Library name: 26612


title: IgG, Sfp1-Q mut, rapamycin, rep1

data_processing:
Raw reads were trimmed using fastp v0.20.1. Trimmed reads were aligned on the Saccharomyces cerevisiae genome (R64-1-1 - sacCer3) using bwa mem v0.7.17 and samtools v1.13. The macs2 v2.2.1 software was used to perform the peak calling and regions were annotated using the ChIPseeker package v1.30.3 in R v4.1.2. Raw signal tracks and normalized tracks (in reads per million, RPM) were produced from mapped reads using deepTool's bamCoverage tool v3.3.0 and bedtools genomecov tool v2.17.0, respectively. Tracks were converted to the bigwig format using bedGraphToBigWig v2.8 and signal tracks were visualized with IGV. For transcription factors, IgG negative control tracks were subtracted from normalized RPM tracks using deepTools 'bigwigCompare'. For histone marks, signal tracks were normalized to histone H3 levels. Cut&Run reads mapping were then divided into promoter groups of genes (RIBI, RIBI-like, RP genes and subcategories) for the generation of heat maps using ComplexHeatmap v2.10.0 and EnrichedHeatmap v1.24.0 packages. Box plots and associated Wilcoxon tests were computed using means of bins per gene and were produced using the ggboxplot and stat_compare_means functions, respectively, with the default settings of the ggpubr v0.5.0 package. Publicly available Htz1 ChIP-seq data in wild-type yeast were obtained from Gene Expression Omnibus (GEO) under accession code GSE54105. Following alignment and peak calling as previously described, intersection of Htz1 genomic regions with Sfp1 peaks was completed using Intervene v0.6.5.
Assembly: sacCer3
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

extract_protocol:
Chromatin was digested by Mnase treatment and DNA was purified with NEB Monarch PCR and DNA purification kit following the protocol. DNA was quantified by Qubit HS DNA kit.
NEBNext Ultra II DNA


title: 61-ON

description: Library name: 26618


title: WT2 LaminA

description: Library name: WT2-LaminA-fastq


title: WT motor neurons, P120 days, rep4

value: lumbar spinal cord

value: motor neurons


title: WT4 LaminA

description: Library name: WT4-LaminA-fastq


title: WT motor neurons, P120 days, rep3Repeat


title: WT3 LaminA

description: Library name: WT3-LaminA-fastq


title: Sfp1-wt, 2% glucose, rep1

value: LPY


title: WT motor neurons, P120 days, rep3


title: 54-PRE

description: Library name: 26611


title: WT motor neurons, P120 days, rep2


title: Eaf1, Sfp1-Q mut, rapamycin, rep2


title: WT motor neurons, P120 days, rep1


title: heterozygous TgSOD1 G93A motor neurons, P120 days, rep4

value: heterozygous TgSOD1 G93A


title: WT1 LaminA

description: Library name: WT1-LaminA-fastq

value: Cardiac


title: 52-ON

description: Library name: 26610

source_name: Pelvic peritoneum

value: Pelvic peritoneum


title: 67-ON

description: Library name: 26626

source_name: Pleura

value: Pleura

value: Stable disease


title: 67-PRE

description: Library name: 26625


title: Mouse podocyte USP40 siRNA#2 biol rep 3

city: Shinagawa-ku

first: Kunio

last: Kawanishi

state: Tokyo

address: 1-5-8 Hatanodai

country: Japan

institute: Showa Medical University

description:
Library name: USP40_si2_rep3
RNA extracted 48h after USP40 siRNA#2 transfection

data_processing:
High-quality reads were aligned to the Mus musculus reference genome (GRCm39). Gene-level read counts were generated from aligned reads. Principal component analysis (PCA) and hierarchical clustering were performed; Euclidean distance and average linkage were applied for clustering. Differential expression analysis was conducted using DESeq2 in R. Genes with adjusted p-value < 0.1 and |log2 fold change| > 0.3 were considered differentially expressed.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files containing gene-level raw read counts. Rows represent Ensembl gene identifiers and columns correspond to individual biological replicates. Differential expression result tables include log2 fold change, p-value, and adjusted p-value. Additional processed files include normalized count matrices used for PCA and heatmap visualization.

source_name: kidney

growth_protocol: Immortalized mouse podocyte cells were cultured under permissive conditions at 33°C in RPMI 1640 medium supplemented with 10% fetal bovine serum and interferon-γ. For differentiation, cells were shifted to 37°C without interferon-γ for 10–14 days prior to transfection experiments.

extract_protocol:
Total RNA was extracted and RNA quality was assessed using the Agilent RNA 6000 Nano kit (Cat#5067-1511) on a Bioanalyzer. One hundred nanograms of total RNA were evaluated for quality control, and 1250 ng of high-quality RNA were used for library preparation.
Poly(A)+ RNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat#E7490). Strand-specific libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat#E7770L). Libraries were amplified with 12 PCR cycles. Library size distribution was validated using the Agilent DNA 7500 kit (Cat#5067-1506). Each biological replicate corresponds to an independent RNA-seq library. Paired-end sequencing (2 × 36 bp) was performed on an Illumina NextSeq 500 using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles; Cat#20024906), generating two FASTQ files per sample (R1 and R2). Raw sequencing reads were adapter-trimmed and quality-filtered using CLC Genomics Workbench version 23.02.

treatment_protocol: Cells were transfected with Silencer Select siRNAs targeting USP40 (s105625: siRNA#1; s105626: siRNA#2) or Silencer Select Negative Control No.1 siRNA (4390843) using Lipofectamine RNAiMAX. Total RNA was isolated 48 hours after transfection.

value: kidney

value: immortalized mouse podocyte

value: podocyte

value: wild-type

tag: batch


title: Sfp1, Sfp1-wt, rapamycin, rep1


title: 66-PRE

description: Library name: 26623

value: PRE


title: heterozygous TgSOD1 G93A motor neurons, P120 days, rep2

value: P120 days


title: heterozygous TgSOD1 G93A motor neurons, P120 days, rep1


title: 66-ON

description: Library name: 26624

value: Peritoneum

value: ON


title: Mouse podocyte USP40 siRNA#1 biol rep 3

description:
Library name: USP40_si1_rep3
RNA extracted 48h after USP40 siRNA#1 transfection


title: Mouse podocyte USP40 siRNA#2 biol rep 1

description:
Library name: USP40_si2_rep1
RNA extracted 48h after USP40 siRNA#2 transfection


title: Sfp1, Sfp1-Q mut, rapamycin, rep1


title: heterozygous TgSOD1 G93A motor neurons, P120 days, rep3


title: Eaf1, Sfp1-Q mut, rapamycin, rep1


title: WT2 IgG

description: Library name: WT2-IgG-fastq

value: Cardiac myocyte

value: Wild type


title: IgG, Sfp1-wt, rapamycin, rep1


title: Eaf1, Sfp1-wt, rapamycin, rep1


title: 52-PRE

description: Library name: 26609

value: Partial  response


title: WT1 IgG

description: Library name: WT1-IgG-fastq


title: 69-ON

description: Library name: 26628


title: IgG, Sfp1-Q mut, 2% glucose, rep1

value: LPY


title: Mouse podocyte USP40 siRNA#1 biol rep 1

description:
Library name: USP40_si1_rep1
RNA extracted 48h after USP40 siRNA#1 transfection


title: Sfp1-K655/657Q, 2% raffinose, rep1


title: homozygous Sod1 knock out motor neurons, P120 days, rep2

value: lumbar spinal cord

value: motor neurons

value: homozygous Sod1 knock out


title: Eaf1, Sfp1-wt, rapamycin, rep2


title: Mouse podocyte control siRNA biol rep 3

description:
Library name: USP40_NC_rep3
RNA extracted 48h after control siRNA transfection

value: Silencer Select Negative Control No.1 siRNA (4390843)


title: 63-ON

description: Library name: 26620

value: Pelvic peritoneum

value: Stable disease


title: Eaf1, Sfp1-Q mut, 2% glucose, rep2


title: homozygous Sod1 G85R motor neurons, P120 days, rep4

value: homozygous Sod1 G85R


title: 69-PRE

description: Library name: 26627


title: Mouse podocyte control siRNA biol rep 1

description:
Library name: USP40_NC_rep1
RNA extracted 48h after control siRNA transfection

value: kidney

value: immortalized mouse podocyte

value: podocyte


title: Mouse podocyte control siRNA biol rep 2

description:
Library name: USP40_NC_rep2
RNA extracted 48h after control siRNA transfection

value: wild-type


title: homozygous Sod1 knock out motor neurons, P120 days, rep3

value: P120 days


title: Sfp1, Sfp1-Q mut, 2% glucose, rep1


title: 63-PRE

description: Library name: 26619

value: PRE


title: Mouse podocyte USP40 siRNA#2 biol rep 2

description:
Library name: USP40_si2_rep2
RNA extracted 48h after USP40 siRNA#2 transfection


title: homozygous Sod1 G85R motor neurons, P120 days, rep2


title: homozygous Sod1 G85R motor neurons, P120 days, rep3


title: Mouse podocyte USP40 siRNA#1 biol rep 2

description:
Library name: USP40_si1_rep2
RNA extracted 48h after USP40 siRNA#1 transfection


title: Eaf1, Sfp1-Q mut, 2% glucose, rep1


title: 50-PRE

description: Library name: 26607

source_name: Lung, NOS

value: Lung, NOS


title: Sfp1, Sfp1-wt, 2% glucose, rep1


title: IgG, Sfp1-wt, 2% glucose, rep1


title: 58-ON

description: Library name: 26614

value: Peritoneum

value: Complete response

value: ON


title: homozygous Sod1 knock out motor neurons, P120 days, rep1

value: lumbar spinal cord


title: 58-PRE

description: Library name: 26613


title: homozygous Sod1 G85R motor neurons, P120 days, rep1

value: motor neurons


title: Skin, inoculated with S. aureus-infected RAW 264.7 cells, 2 day, rep3

city: Xiamen

first: Bin

last: Fang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

description: Library name: Sample 6

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output
Low quality bases were trimmed by using trimmomatic (version: 0.38) (The options and parameters used to filter raw reads were: ILLUMINACLIP:MeRIP-PE.fa:2:30:10:1:true SLIDINGWINDOW:30:15 AVGQUAL:15 LEADING:15 TRAILING:15 HEADCROP:8 MINLEN:30
Clean reads were mapped to GRCm39(GenCode vM29) using hisat2 with default parameters.
The R package exomePeak was used to call peaks and detect differential peaks  from filtered alignment files. The annotation file used to annotate the peaks was downloaded from GenCode (vM29). Only peaks with p < 0.05 and foldchange >=1.5 were identified as being significantly differential peaks
Assembly: GRCh38
Supplementary files format and content: counts per gene, log2FoldChange

source_name: Epithelial tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,15596018) )
The MeRIP libraries using eluted RNA were constructed using SMARTer Stranded Total RNA-Seq Kit version 2 (Takara/Clontech) according to the manufacturer’s protocol.

value: Epithelial tissue

value: Macrophage


title: Skin, inoculated with S. aureus-infected RAW 264.7 cells, 2 day, rep2

description: Library name: Sample 5


title: Eaf1, Sfp1-wt, 2% glucose, rep2

value: LPY


title: 31-ON

description: Library name: 26598

value: Partial  response


title: Skin, inoculated with S. aureus-infected RAW 264.7 cells, 2 day, rep1

description: Library name: Sample 4


title: homozygous Sod1 knock out motor neurons, P120 days, rep4

value: homozygous Sod1 knock out


title: Eaf1, Sfp1-wt, 2% glucose, rep1


title: Skin, control, 2 day, rep3

description: Library name: Sample 3

value: control


title: IgG, Esa1-FRB, +rapa, rep1

value: SFP1-13myc FRB-Esa1 fpr1delta::HphMX tor1-1::URA3RPL13A-2*FKBP12::TRP1


title: 31-PRE

description: Library name: 26597

source_name: Inguinal lymph node

value: Inguinal lymph node


title: MC38_Gpr65

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

description: BD Rhapsody

data_processing:
Raw fastq-sequencing reads were loaded into BD Targeted Rhapsody Analysis Pipeline hosted by SevenBridgesGenomics and analyzed using version 1.9 of the pipeline.
Data were filtered as follows using Partek Flow version 10.0.20.1231: Cells with more than 10% mitochondrial genes and doublets/multiplets were excluded; a noise reduction filter was used to filter out features with an expression value of <1 in 99% of cells;
Data were normalized by calculating counts per million (CPM), adding 1 and log transforming to the base of 2
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every cell, gene and sample

source_name: MC38 tumors

extract_protocol:
At day 17 (B16), respectively at day 16 (MC38) single cell suspensions were prepared from excised whole tumors by tissue digestion using murine tumor dissociation kit and gentleMACS dissociator (Miltenyi Biotec). CD45+ cells were enriched by murine CD45 (TIL) MicroBeads (Miltenyi Biotec) using MACS technology. To enrich purity viable CD45+ cells were sorted using AriaII flow cytometer (BD Bioscience).
Capturing of single cells was performed using the BD Rhapsody system (BD Biosciences). For multiplexing samples, tumorinfiltrating CD45+ cells from WT and Gpr65-KO mice were labeled by sample tags against CD45 conjugated with unique oligos (B16_Gpr65 experiment: WT1=Sample tag (ST) 5; WT2=ST6; WT3=ST7, WT4=ST8; KO1=ST9; KO2=ST10; KO3=ST11; KO4=ST12); MC_38_Gpr65 experiment: WT1=ST7; WT3=ST9; KO1=ST10; KO2=ST11; KO3=ST12; Sequences of sample tags can be found under Doc ID 210970) and were loaded on BD Rhapsody cartridge. Capture of single RNA molecules on barcoded magnetic Oligo-dT- beads and cDNA synthesis was performed as described in the manual (Single cell capture and cDNA synthesis with the BD Rhapsody single-cell analysis system; Doc ID: 210966 Rev. 1.0). mRNA and Sample Tag Libraries were prepared following the manual (mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol; 23--21712-00). Upon purifyingWTA and Sample tag library, concentration of libraries was assessed by Qubit 2.0 using the DNA high sensitivity kit and average library size was determined on a bioanalyzer using a high-sensitivity DNA chip. Final sequencing library was prepared by dilution and pooling of mRNA and Sample tag library following the recommendations of the sequencing preparation sheet provided by BD. The libraries were sequenced on a HiSeq2500 (B16_Gpr65) using a HiSeq PE Rapid Cluster Kit v2 (PE-402-4002) and combining three HiSeq Rapid SBS Kits v2 (50 cycles). MC38_Gpr65 libraries were sequenced on Illumina's NovaSeq 6000 at Novogene (Cambridge, UK). For processing of the sequencing raw data BD targeted multiplex Rhapsody analysis pipeline version 1.5 was used. For visualization the software Partek Flow (Partek Inc.) has been used.

treatment_protocol: Gpr65-deficient and respective littermate control mice were injected s.c. either with 2x10^5 B16F10 melanoma or 1x10^6 MC38 colon adenocarcinoma cells. Tumor growth was measured using a caliper.

value: MC38 tumors

value: tumor-infiltrating CD45+ cells

value: WT and Gpr65-KO


title: 29-PRE

description: Library name: 26593

source_name: Peritoneum, NOS

value: Peritoneum, NOS

value: PRE


title: Skin, control, 2 day, rep1

description: Library name: Sample 1


title: Sfp1, Esa1-FRB, +rapa, rep2


title: Skin, control, 2 day, rep2

description: Library name: Sample 2


title: 29-ON

description: Library name: 26594


title: 18-ON

description: Library name: 26584

value: Progressive disease


title: IgG, Esa1-FRB, -rapa, rep1


title: Sfp1, Esa1-FRB, -rapa, rep2


title: Foxp3-GFP+ Treg, NOD Control, rep6

city: Bar Harbor

first: Dave

last: Serreze

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Library name: NOD_GFP_JF02884-6

data_processing:
bowtie2
edgeR
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include expected counts for each sample

source_name: Spleen

extract_protocol:
RNeasy Mini Kit
KAPA mRNA HyperPrep Kit

value: Spleen

value: Foxp3-GFP+ Treg

value: Control NOD


title: D30-2

city: Shanghai

first: Jiawen

last: Qian

address: 130 Dong'an Road

department: Immunology

institute: Fudan University

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
 MT% < 20%;
 Cell Gene Number < 10000;
 Cell Gene Number > 200.
PCA and tSNE/UMAP analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: tumor-bearing brain hemisphere

extract_protocol:
Tumor-bearing hemisphere were harvested, percoll gradient isolation of immune cells were conducted, CD45hi/loCD11b+ cells were sorted by FACS analysis, and RNA was harvested. Chromium Single Cell 3’V3.1 Reagent Kits (10X Genomics, Pleasanton, CA) was used for the construction of sequencing libraries.
RNA libraries were generated by 10xGenomics Single Cell 3' Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

tag: strain

value: tumor-bearing brain hemisphere

value: CD45hi/loCD11b+ cells

value: wild type

tag: disease state

value: GL261 glioma

value: GL261 glioma day 30


title: Foxp3-GFP+ Treg, NOD Control, rep5

description: Library name: NOD_GFP_JF02861-2


title: 18-PRE

description: Library name: 26583


title: N-1

description: 10x Genomics

source_name: normal brain hemisphere

value: normal brain hemisphere

value: Healthy control


title: Foxp3-GFP+ Treg, NOD Control, rep4

description: Library name: NOD_GFP_JF02857-8


title: Sfp1, Esa1-FRB, +rapa, rep1

value: SFP1-13myc FRB-Esa1 fpr1delta::HphMX tor1-1::URA3RPL13A-2*FKBP12::TRP1


title: N-2

description: 10x Genomics


title: D20-2

description: 10x Genomics

value: GL261 glioma day 20


title: D10-2

description: 10x Genomics

value: GL261 glioma day 10


title: 22-ON

description: Library name: 26586

value: Pelvic peritoneum

value: Partial  response

value: ON


title: D30-1

description: 10x Genomics


title: D20-1

description: 10x Genomics


title: Foxp3-GFP+ Treg, NOD Control, rep2

description: Library name: NOD_GFP_JF02836-37


title: 22-PRE

description: Library name: 26585

value: PRE


title: Foxp3-GFP+ Treg, NOD Control, rep3

description: Library name: NOD_GFP_JF02854-6

value: Spleen


title: IgG, Sfp1-FRB, +rapa, rep1


title: Sfp1, Esa1-FRB, -rapa, rep1


title: 16-ON

description: Library name: 26580

source_name: Retroperitoneum

value: Retroperitoneum


title: IgG, Sfp1-FRB, -rapa, rep1


title: YN 02m Hip Exp1 33898 20 Hi20

city: South San Francisco

first: Oliver

last: Hahn

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences, LLC

description: Unstranded mRNA-seq

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7, parameters: --paired --length 25). Trimmed sequences were aligned using STAR (v2.5.3a). Multi-mapped reads were filtered. Data visualization and analysis were performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: DESeq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Genome_build: GRCm38
Supplementary_files_format_and_content: OPLCB_counttable.txt: Tab-delimited text file including raw counts for each sample.

source_name: hippocampus

extract_protocol:
RNeasy Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

value: hippocampus

value: Male

value: Naive


title: Foxp3-GFP+ Treg, Nfkbid KO, rep5

description: Library name: NFKBID_KO_GFP_NA968-NFKBID_KO_GFP_NA944_pool

value: Foxp3-GFP+ Treg

value: NOD- Nfkbid-KO


title: Eaf1, Sfp1-FRB, +rapa, rep2


title: D10-1

description: 10x Genomics

value: tumor-bearing brain hemisphere

value: CD45hi/loCD11b+ cells

value: wild type

value: GL261 glioma


title: Foxp3-GFP+ Treg, NOD Control, rep1

description: Library name: NOD_GFP_JF02834-35

value: Control NOD


title: YN 02m Hip Exp1 33898 17 Hi17

description: Unstranded mRNA-seq


title: NPM1 patient 10, relapse sample

city: Napels

first: Wout

last: Megchelenbrink

address: Vico de Crecchio 7

institute: University of Campania "Luigi Vanvitelli”

description:
Library name: NPM1_10_RL_bulk_RNA_Seq
Counts are in column "P10_RL" in the processed data file

data_processing:
RNA-seq data were quantified using STAR-Fusion, using the Gencode GRCh38 (v37) reference genome, with parameters “--quantMode GeneCounts” and “--twopassMode Basic”. Gene counts were processed in R using DESeq2.
Assembly: GRCh38 (v37)
Supplementary files format and content: BulkRNAseq_STAR_CountTable.tsv contains the STAR-Fusion raw read counts (unnormalized) per gene per sample.

source_name: bone marrow mononuclear cells

extract_protocol:
Total RNA was extracted using a RNeasy RNA extraction kit (QIAGEN). A 300 ng/sample of total RNA was used as input for library preparation.
Libraries were prepared using a KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche), following the manufacturer’s instructions.

value: bone marrow mononuclear cells


title: YN 02m Hip Exp1 33898 14 Hi14

description: Unstranded mRNA-seq


title: YN 02m Hip Exp1 33898 12 Hi12

description: Unstranded mRNA-seq


title: Foxp3-GFP+ Treg, Nfkbid KO, rep2

description: Library name: NFKBID_KO_GFP_NA951-NFKBID_KO_GFP_NA940_pool


title: Foxp3-GFP+ Treg, Nfkbid KO, rep3

description: Library name: NFKBID_KO_GFP_NA960-NFKBID_KO_GFP_NA926_pool


title: Eaf1, Sfp1-FRB, +rapa, rep1


title: Eaf1, Sfp1-FRB, -rapa, rep2


title: 16-PRE

description: Library name: 26579


title: Eaf1, Sfp1-FRB, -rapa, rep1