title: BM_SCA-1_pDCs_KO4_1.fq.gz

description: Library name: Sample_8

data_processing:
RNA sequencing was performed using the Illumina HiSeq2500 platform at the Beijing Genomics Institute (BGI, China). Differentially expressed genes were selected based on a P value < 0.05 and a fold change > 1.5.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: fpkm_count_matrix.xlsx
Supplementary files format and content: fpkm_count_matrix.xlsx

extract_protocol:
For RNA-seq analysis, 2×106 pDCs or Sca-1+ pDCs were sorted from BM of WT and cKO mice. BM pDCs were centrifuged at 1750 rpm for 5 min at 4°C to remove the supernatant. After resuspending in 1 mL of pre-cooled PBS, the cells were centrifuged again and the supernatant was discarded. To lyse the pDCs, 1 mL of TRNzol RNA extraction reagent was added, and the cells were thoroughly disrupted.
RNA for libraries for RNA-seq were prepared using  polyA_selected

value: Slc44a5 cKO


title: human 31 years old female

status: Public on Jul 15 2026

type: SRA

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description:
Library name: Sample14
10x Genomics

library_source: transcriptomic

data_processing:
10x library equencing was performed on Illumina HiSeq X. Sequencing data were analyzed using Illumina bcl2fastq software (version 2.20.0) and converted to FASTQ format files. Subsequently, alignment was performed using the cellranger count function of Cell Ranger Single Cell software (version 9.0.0, 10x Genomics) with using STAR aligner 2.7.2a. The GRCm38 mouse reference genome, mm10 r102  was used.
Assembly: GRCm38
Supplementary files format and content: Tab-separated value files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: human kidney tissue cells

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.

tag: tissue

value: human kidney tissue cells


title: BM_SCA-1_pDCs_KO3_1.fq.gz

city: Beijing

first: Ruiqun

last: Chen

address: Tsinghua University,Hai Dian, Beijing

country: China

institute: Tsinghua University

description: Library name: Sample_7

organism: Mus musculus

source_name: Bone marrow

value: Bone marrow

tag: cell line

value: pDCs

tag: cell type

value: Plasmacytoid dendritic cells

tag: genotype

value: Slc44a4 cKO

tag: treatment

value: No


title: DSP-1001660014867-Y-A11

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

country: USA

institute: UT Southwestern Medical Center

description: Library name: Sample 155

library_source: other

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw_dcc.tar:  raw read counts in DCC of tar
Supplementary files format and content: Protein_Q3_normalized_expression_matrix.txt  :  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format

molecule: protein

extract_protocol:
FFPE tissues were parafilm embedded, 5 µM sections were cut with cryostat
Spatial transcritpome sequencing libraries were prepared with Nanostring GeoMx DSP NGS library preparation kit according to manufacturer's instruction

tag: panel (wta_+ipa)

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

value: PF

tag: scan name

tag: roi

tag: segment


title: human iPS VA

description:
Library name: Sample11
10x Genomics

source_name: human induced pluripotent stem cell

value: human induced pluripotent stem cell


title: BM_SCA-1_pDCs_KO2_1.fq.gz

description: Library name: Sample_6

value: Slc44a3 cKO


title: human iPS VA FSK OSM

description:
Library name: Sample12
10x Genomics


title: DSP-1001660014867-Y-A10

description: Library name: Sample 154

value: IA


title: BM_SCA-1_pDCs_KO1_1.fq.gz

description: Library name: Sample_5

value: Slc44a2 cKO


title: HTR-8/Svneo, Mal-Sh-2

city: Xuzhou

first: Yunlong

last: Si

state: --- Select One ---

address: Jiangsu Key Laboratory of Brain Disease and Bioinformation

institute: Xuzhou medical university

description: Library name: Sample 5

data_processing:
Disembarkation data quality control
Matching genome
Differential RNA identification
Functional enrichment analysis
Assembly: Homo_sapiens.GRCh38.107
Supplementary files format and content: Excel file includes raw counts for each samples

extract_protocol:
Total RNA extraction
Pre-processing - Library building


title: HTR-8/Svneo, Mal-Sh-Con-3

description: Library name: Sample 3


title: DSP-1001660014867-Y-A09

description: Library name: Sample 153


title: HTR-8/Svneo, Mal-Sh-1

description: Library name: Sample 4


title: BM_SCA-1_pDCs_WT4_1.fq.gz

description: Library name: Sample_4

value: WT


title: DSP-1001660014867-Y-A08

description: Library name: Sample 152


title: HTR-8/Svneo, Mal-Sh-Con-2

description: Library name: Sample 2


title: HTR-8/SVneo, Mal-Sh-Con-1

description: Library name: Sample 1


title: IL15S5i 3

city: Montreal

first: Helene

last: Decaluwe

state: QC

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Sainte Justine

description:
Library name: Sample 15
Day 7 of in vitro culture

data_processing:
The raw gene count matrices were generated using HTSeq (v0.13.5) in non-stranded mode.
Raw counts were filtered to remove low-expressed transcripts.
Assembly: RNA-seq FASTQ files were aligned and mapped to the mouse genome (GENCODE 31/Ensembl v97 GRCm38/mm10) using the STAR aligner (v2.7) with 2-pass mapping mode and a re-generated genome index.
Supplementary files format and content: Matrix_STAT5i.xlsx

molecule: polyA RNA

source_name: Spleen

growth_protocol: P14+ CD8+ T cells were co-cultured with dendritic cells (1:1) isolated from B6 mice using EasySepTM Mouse CD11c Positive Selection Kit II (Stemcell, MA, USA) with a high dose of gp33 peptide (100 ng/ml, Cat#RP20257, Genscript) in complete RPMI.

extract_protocol:
At day 7, RNA was isolated from naïve or expanded CD8+ T cells using miRNeasy Mini Kit (QIAGEN). Poly-A mRNA enrichment was conducted using Dynabeads Oligo(dT) (ThermoFisher).
Library preparation was carried out with the KAPA RNA Hyperprep Kit (Roche).

treatment_protocol: At days 2, 4, and 6, P14 CD8+ T cells were numbered, normalized, and re-cultured in complete RPMI with a lower dose of gp33 peptide (1 ng/ml) either alone or in combination with IL-2 (100ng/ml; Cat#212-12, PeproTech) or IL-15 (200ng/ml; Cat#210-15, PeproTech). STAT5 inhibitor (STAT5i; 100 μM; Cat#573108; Millipore Sigma) was added on days 4 and 6.

value: Spleen

value: CD8 T cells

value: C57BL/6J CD45.2+ P14+ TCR transgenic specific for the gp33-41 epitope of the LCMV virus

value: GP33 peptide + IL-15 + STAT5i


title: BM_SCA-1_pDCs_WT3_1.fq.gz

description: Library name: Sample_3


title: H644C,3P7,replicate 3

city: Guangzhou

first: Huanpeng

state: Guangdong

address: Guangzhou International Bio-Island, Guangzhou, Guangdong, China

institute: Guangzhou National Laboratory

description:
Library name: Sample 6
Column name in All-gene.tpm.anno.xlsx: tpm_H644C

data_processing:
Data filtering: Raw data obtained from sequencing were filtered using the SOAPnuke software (v1.4.0)  to remove: (1) reads containing adapters (adapter contamination); (2) reads with unknown bases (N) exceeding 5% of the read length; (3) low‑quality reads (reads with more than 20% of bases having a quality value below 15). After filtration, clean data were obtained.
Alignment to reference genome: The resulting clean data were aligned to the reference genome sequence using the HISAT software (v2.1.0) .
Alignment to reference gene sequences: The clean data were aligned to the reference gene sequences using the Bowtie2 software (v2.2.5) , and then the RSEM software package (v1.2.8)  was used to calculate gene expression levels for each sample.
Assembly: GRCm38
Supplementary files format and content: All-gene.tpm.anno xlsx file includes tpm for each Sample.

source_name: Primary cells

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2. A total of 1 µg RNA per sample was used for sequencing library construction.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized double strand cDNA is subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and PE 150 bases reads are generated on BGISEQ-500 platform.

treatment_protocol: 3P7-CAR‑T and Ctrl-CAR‑T cells were co-cultured with MC38-Trop2 tumor cells for 48 hours without cytokine supplementation, after which CAR-T cells were sorted by flow cytometry. CAR-T cells were positively selected and subjected to transcription sequencing.

value: CD3 T cells

tag: age

value: 8 weeks old

tag: strain


title: DSP-1001660014867-Y-B10

description: Library name: Sample 166

value: Desmin


title: BM_SCA-1_pDCs_WT2_1.fq.gz

description: Library name: Sample_2

value: Bone marrow

value: pDCs

value: Plasmacytoid dendritic cells


title: IL15S5i 2

description:
Library name: Sample 14
Day 7 of in vitro culture


title: DSP-1001660014867-Y-A06

description: Library name: Sample 150

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: IL15S5i 1

description:
Library name: Sample 13
Day 7 of in vitro culture


title: DSP-1001660014867-Y-B05

description: Library name: Sample 161

value: PF


title: BM_SCA-1_pDCs_WT1_1.fq.gz

description: Library name: Sample_1

value: No


title: IL15 3

description:
Library name: Sample 12
Day 7 of in vitro culture

value: GP33 peptide + IL-15


title: BMPDC_WT3_1.fq.gz

description: Library name: Sample_3

data_processing:
RNA sequencing was performed using the Illumina HiSeq2500 platform at the Beijing Genomics Institute (BGI, China). Differentially expressed genes were selected based on a P value < 0.05 and a fold change > 1.5.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: fpkm_count_matrix2.xlsx

extract_protocol:
For RNA-seq analysis, 2×106 pDCs or BM pDCs were sorted from BM of WT and cKO mice. BM pDCs were centrifuged at 1750 rpm for 5 min at 4°C to remove the supernatant. After resuspending in 1 mL of pre-cooled PBS, the cells were centrifuged again and the supernatant was discarded. To lyse the pDCs, 1 mL of TRNzol RNA extraction reagent was added, and the cells were thoroughly disrupted.
RNA for libraries for RNA-seq were prepared using  polyA_selected


title: DSP-1001660014867-Y-A05

description: Library name: Sample 149

value: IA


title: IL15 2

description:
Library name: Sample 11
Day 7 of in vitro culture


title: P7_medulla_1

description:
Library name: Sample15
10x Genomics

source_name: Mouse Kidney

value: Mouse Kidney


title: P7_medulla_2

description:
Library name: Sample16
10x Genomics


title: IL15 1

description:
Library name: Sample 10
Day 7 of in vitro culture


title: primary hepatocyte, WT, vehicle, rep3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description: Library name: WT_VEH-3

data_processing:
Reads were quality checked with fastQC and preprocessed (adapter removal) with TRIMMOMATIC v0.34 (ILLUMINACLIP & MINLEN filters)
Reads were mapped to the mm39 reference genome with STAR (2.7.10b) and the gencode M30 and read counts were obtained using featurecounts
Differnatial gene expression was determined using DESeq2
Assembly: mm39
Supplementary files format and content: tab delimited count matrix with the raw counts per sample

source_name: liver

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
Library preparation was done using the illumina truseq stranded library kit and sequenced on an element AVITI instrument  according the the manufacturer's instructions

treatment_protocol: Primary hepatocytes were treated with either DMS verhicle or MJ041.

value: liver

value: primary hepatocyte

value: WT

value: DMSO vehicle


title: DSP-1001660014867-Y-A04

description: Library name: Sample 148


title: primary hepatocyte, WT, vehicle, rep2

description: Library name: WT_VEH-2


title: IL2S5i 3

description:
Library name: Sample 9
Day 7 of in vitro culture

value: Spleen

value: CD8 T cells

value: C57BL/6J CD45.2+ P14+ TCR transgenic specific for the gp33-41 epitope of the LCMV virus

value: GP33 peptide + IL-2 + STAT5i


title: IL2S5i 2

description:
Library name: Sample 8
Day 7 of in vitro culture


title: DSP-1001660014867-Y-A12

description: Library name: Sample 156


title: DSP-1001660014867-Y-A03

description: Library name: Sample 147


title: IL2S5i 1

description:
Library name: Sample 7
Day 7 of in vitro culture


title: primary hepatocyte, WT, vehicle, rep1

description: Library name: WT_VEH-1


title: DSP-1001660014867-Y-A02

description: Library name: Sample 146


title: IL2 3

description:
Library name: Sample 6
Day 7 of in vitro culture

value: GP33 peptide + IL-2


title: IL2 2

description:
Library name: Sample 5
Day 7 of in vitro culture


title: IL2 1

description:
Library name: Sample 4
Day 7 of in vitro culture


title: primary hepatocyte, WT, MJ041, rep3

description: Library name: WT_MJ041-3


title: Naive 3

description:
Library name: Sample 3
Day 7 of in vitro culture

value: Naive


title: DSP-1001660014603-Y-H12

description: Library name: Sample 145


title: HTR-8/Svneo, Mal-Sh-3

description: Library name: Sample 6


title: Naive 2

description:
Library name: Sample 2
Day 7 of in vitro culture


title: primary hepatocyte, WT, MJ041, rep2

description: Library name: WT_MJ041-2


title: DSP-1001660014603-Y-H11

description: Library name: Sample 144


title: Naive 1

description:
Library name: Sample 1
Day 7 of in vitro culture


title: primary hepatocyte, WT, MJ041, rep1

description: Library name: WT_MJ041-1


title: Dam-Lamin B1 (SCD007.index32)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: SCD007.index32
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz

library_source: genomic

data_processing:
Data generated by the scDam&T-seq protocol was largely processed following the workflow and scripts described in {Markodimitraki 2020}. Scripts and a workflow description are also available on www.github.com/KindLab/scDamAndTools.
All reads are demultiplexed based on the barcode present at the start of R1 using a reference list of barcodes. The reference barcodes contain both DamID-specific and CEL-seq2-specific barcodes and zero mismatches between the observed barcode and reference are allowed. The UMI information, also present at the start of R1, is appended to the read name.
DamID reads are aligned using bowtie2 (v. 2.3.3.1){Langmead 2012} with the following parameters: ‘‘--seed 42 --very- sensitive -N 1.’’ The mm10 reference genome is used for alignment. The resulting alignments are then converted to UMI-unique GATC counts by matching each alignment to known strand-specific GATC positions in the reference genome. Any reads that do not align to a known GATC position or have a mapping quality smaller than 10 are removed. Up to 2 unique UMIs are allowed for single-cell samples to account for the number of alleles. Finally, counts are binned at the desired resolution, generally 100 Kb.
CEL-seq2 reads are aligned using tophat2 (v. 2.1.1){Kim 2013} with the following parameters: ‘‘--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200.’’ The mm10 reference genome and the GRCm38 (v. 89) transcript models are used. Alignments are subsequently converted to transcript counts per gene with custom scripts that assign reads to genes similar to HTSeq’s79 htseq-count with mode ‘‘intersection_strict.’’
Assembly: GRCm38
Supplementary files format and content: H5AD

molecule: genomic DNA

source_name: brain

growth_protocol: C57BL/6J mice were obtained from the Jackson laboratories (strain 000664), bred in-house and used for all experiments. All mice were raised with their mothers up to 4 weeks of age, maintained in 12 hour light-dark cycles at 22 ± 1 °C and fed without restriction (standard laboratory chow, Special Diet Services (SDS), CRM (E)).

extract_protocol:
Mothers were sacrificed at E16.5 (48 hours after IUE) and whole brains from the pups were collected for immunostainings in ice-cold Leibovitz’s L-15 medium (Gibco, 11415064), washed in PBS and fixed by immersion in 4% paraformaldehyde (PFA, Sigma, 30525-89-4) in PBS at 4 °C overnight.
The scDam&T-seq processing was largely performed as previously described in {Markodimitraki 2020}, but reaction volumes of all mixes were equimolarly halved (0.5x) to reduce overall processing costs. As such, the added volumes per well were 50 nl CEL-seq2 primer (before sorting, with 5 µl mineral oil), 50 nl lysis mix, 75 nl reverse transcriptase mix, 925 nl second strand mix, 250 nl proteinase K mix, 150 nl DpnI mix, 50 nl of DamID adapter (1 µM concentration, 25 nM final during ligation) and 450 nl scDam&T T4 ligase mix. The overall composition of the mixes remains unaltered and the incubation times and temperatures are as described.

treatment_protocol: For the Dam-Lamin B1 injections, a DNA solution was prepared containing the EF1α-mRuby2-P2A-HA-miniAID-Dam-LaminB1 construct at either 0.5 μg/μl or 2.0 μg/μl and the GFP construct at 0.4 μg/μl.

value: brain

value: neural


title: DSP-1001660014603-Y-H10

description: Library name: Sample 143

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: Dam-Lamin B1 (KIN12927.index23)

description:
Library name: KIN12927.index23
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: primary hepatocyte, KO, vehicle, rep3

description: Library name: KO_VEH-3

value: Hnf4a KO


title: DSP-1001660014603-Y-H09

description: Library name: Sample 142

value: Desmin


title: Dam-Lamin B1 (KIN12927.index22)

description:
Library name: KIN12927.index22
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: DSP-1001660014867-C-A05

description: Library name: Sample 149

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw read counts in DCC
Supplementary files format and content: RNA_Q3_normalied_expression_matrix.txt  :  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format

value: IA


title: Dam-Lamin B1 (KIN12927.index21)

description:
Library name: KIN12927.index21
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: Dam-Lamin B1 (KIN12927.index20)

description:
Library name: KIN12927.index20
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: Dam-Lamin B1 (KIN12927.index19)

description:
Library name: KIN12927.index19
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: DSP-1001660014603-D-H09

description: Library name: Sample 142


title: DSP-1001660014603-Y-H08

description: Library name: Sample 141


title: DSP-1001660014867-C-A04

description: Library name: Sample 148


title: primary hepatocyte, KO, vehicle, rep2

description: Library name: KO_VEH-2


title: primary hepatocyte, KO, vehicle, rep1

description: Library name: KO_VEH-1


title: Dam-Lamin B1 (KIN12927.index18)

description:
Library name: KIN12927.index18
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: DSP-1001660014603-Y-H07

description: Library name: Sample 140

source_name: Lupus 2

value: Lupus 2

value: CF

value: DESMIN


title: Dam-Lamin B1 (KIN12927.index16)

description:
Library name: KIN12927.index16
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: primary hepatocyte, KO, MJ041, rep3

description: Library name: KO_MJ041-3

value: liver

value: primary hepatocyte


title: Dam-Lamin B1 (KIN12927.index14)

description:
Library name: KIN12927.index14
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: DSP-1001660014603-Y-H06

description: Library name: Sample 139


title: DSP-1001660014867-Y-A07

description: Library name: Sample 151


title: Dam-Lamin B1 (KIN12927.index13)

description:
Library name: KIN12927.index13
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: primary hepatocyte, KO, MJ041, rep2

description: Library name: KO_MJ041-2


title: Dam-Lamin B1 (KIN12785.index34)

description:
Library name: KIN12785.index34
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: DSP-1001660014603-Y-H05

description: Library name: Sample 138


title: primary hepatocyte, KO, MJ041, rep1

description: Library name: KO_MJ041-1


title: DSP-1001660014603-Y-H04

description: Library name: Sample 137


title: MeCP2-Dam126 (KIN10808.index47)

description:
Library name: KIN10808.index47
singlecell_mecp2_mouse_cortex.h5ad.gz

tag: sample group


title: Dam-Lamin B1 (KIN12785.index33)

description:
Library name: KIN12785.index33
singlecell_lads_perturb_mecp2_mouse_cortex.h5ad.gz


title: MeCP2-Dam126 (KIN10808.index46)

description:
Library name: KIN10808.index46
singlecell_mecp2_mouse_cortex.h5ad.gz


title: MeCP2-Dam126 (KIN10808.index45)

description:
Library name: KIN10808.index45
singlecell_mecp2_mouse_cortex.h5ad.gz


title: BY4P; fly whole body;Lsp2[B14];2-3 day;Polysome-Seq;rep3

city: changsha

first: cai

last: zixin

email: 964530737@qq.com, cangjie@hnu.edu.cn

state: 湖南Hunan

address: yuelu district tianma road

institute: Hunan university

description:
Library name: BY4P
Polysome-seq
raw_counts_Samples3.csv

data_processing:
We first performed quality control and adapter trimming on the raw sequencing reads using fastp (v0.23.2). Reads were then mapped to species-specific rRNA using Bowtie2 (v2.3.4.1) to remove ribosomal RNA contaminants. Clean reads were aligned to the Drosophila melanogaster (BDGP6.46) reference genome (ensembl.org/Drosophila_melanogaster/Info/Index) by STAR (v2.2.1). Uniquely mapped reads were summarized to Drosophila_melanogaster.BDGP6.46.110.chr.gtf annotated genes using featureCounts (v1.6.0). The resulting raw gene expression matrix was then imported into the R (v4.2.0) environment for further processing and analysis.
Assembly: BDGP6.46
Supplementary files format and content: csv file includes raw counts for each Sample

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
Whole female flies were ground in liquid nitrogen. A portion of the powdered tissue was reserved for total RNA extraction, while the remaining material was lysed and subjected to 10–45% sucrose density gradient centrifugation. Monosome and polysome fractions were collected after gradient fractionation. Total RNA and RNA from the monosome and polysome fractions were separately isolated using TRIzol reagent (Invitrogen, #15596026).
Poly(A)+ RNA was enriched from 2 μg of total RNA, monosome-bound RNA, or polysome-bound RNA using VAHTS mRNA Capture Beads (Vazyme, #N401). The enriched RNA was fragmented and subjected to end repair, adaptor ligation, and PCR amplification using the VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme, #NR604). Following library quality control and quantification, the libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads.

value: whole body

tag: time

value: 2-3 day

tag: batch

value: BY*P


title: MeCP2-Dam126 (KIN10808.index44)

description:
Library name: KIN10808.index44
singlecell_mecp2_mouse_cortex.h5ad.gz


title: BY2P; fly whole body;Lsp2[B14];2-3 day;Polysome-Seq;rep2

description:
Library name: BY2P
Polysome-seq
raw_counts_Samples3.csv


title: MeCP2-Dam126 (VER10654.index32)

description:
Library name: VER10654.index32
singlecell_mecp2_mouse_cortex.h5ad.gz


title: DSP-1001660014603-Y-H03

description: Library name: Sample 136


title: DSP-1001660014603-Y-H02

description: Library name: Sample 135


title: BY1P; fly whole body;Lsp2[B14];2-3 day;Polysome-Seq;rep1

description:
Library name: BYIP
Polysome-seq
raw_counts_Samples3.csv


title: MeCP2-Dam126 (VER10654.index21)

description:
Library name: VER10654.index21
singlecell_mecp2_mouse_cortex.h5ad.gz


title: Dam126 (KIN9826.index14)

description:
Library name: KIN9826.index14
singlecell_lads_mouse_cortex.h5ad.gz


title: DSP-1001660014603-Y-H01

description: Library name: Sample 134


title: Dam126 (KIN9826.index13)

description:
Library name: KIN9826.index13
singlecell_lads_mouse_cortex.h5ad.gz


title: BY4M; fly whole body;Lsp2[B14];2-3 day;Monosome-Seq;rep3

description:
Library name: BY4M
Monosome-seq
raw_counts_Samples3.csv

value: BY*M


title: Dam126 (KIN9826.index12)

description:
Library name: KIN9826.index12
singlecell_lads_mouse_cortex.h5ad.gz


title: DSP-1001660014603-Y-G12

description: Library name: Sample 133


title: BY2M; fly whole body;Lsp2[B14];2-3 day;Monosome-Seq;rep2

description:
Library name: BY2M
Monosome-seq
raw_counts_Samples3.csv


title: Dam-Lamin B1 (KIN9826.index11)

description:
Library name: KIN9826.index11
singlecell_lads_mouse_cortex.h5ad.gz

value: Dam-Lamin B1


title: Dam126 (KIN8164.index46)

description:
Library name: KIN8164.index46
singlecell_lads_mouse_cortex.h5ad.gz


title: DSP-1001660014603-Y-G11

description: Library name: Sample 132


title: Dam126 (KIN8164.index45)

description:
Library name: KIN8164.index45
singlecell_lads_mouse_cortex.h5ad.gz


title: PMs, KO2, VSV 4h

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

description: Library name: KO2

data_processing:
We first apply Stringtie (version: 1.3.0) to count the number of Fragments for each gene after Hisat2 alignment.
Then the TMM (trimmed mean of M values) method was used to standardize the expression levels across various samples.
We then use Perl script to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped fragments) value for each gene.
Apply edgeR for differential gene analysis, obtain p-value, and perform multiple hypothesis testing correction. By controlling the FDR (False Discovery Rate) to determine the threshold of p-value, the corrected p-value is q-value. At the same time, we calculate the differential expression multiple, which is Fold change
Genes that exhibit a fold change in expression level larger than 2.0 and a q-value less than 0.05 are referred to as differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

source_name: macrophages

growth_protocol: PMs were generated from mice in DMEM medium with 10% FBS.

extract_protocol:
Total RNA was extracted using MJzol animal RNA Extraction Kit (MagBeads) (Cat#T102096) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Library construction was perfromed following the steps of mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, adding A at the 3 'end, connecting connectors, enrichment, using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme), AHTS® mRNA Capure Beads (Human/Mouse/Rat) (Vazyme), VAHTS DNA Clean Beads (Vazyme), Qubit™ dsDNA HS Assay Kit (Invitrogen) and Agilent High Sensitivity DNA Kit (Aligent).

treatment_protocol: WT and Rbm25 deficient PMs were infected with vesicular stomatitis virus for 4 hours

value: macrophages

value: PMs

value: Mouse peritoneal macrophages

value: VSV for 4 hours


title: DSP-1001660014603-D-G07

description: Library name: Sample 128

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

value: PF


title: DSP-1001660014603-Y-G10

description: Library name: Sample 131


title: Sham_2 single-cell RNA-seq library

city: Manhasset

first: Hai

last: Huang

state: NY

address: 350 community drive

department: Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

description: Library name: liver_SedSham_rep2

data_processing:
Raw reads were assessed for quality using FastQC
Adapter trimming was performed using Trimmomatic
Reads were aligned to the mouse reference genome (mm10) using STAR
Gene counts were quantified using featureCounts
Downstream analysis including normalization and clustering was performed using Seurat (v4.4)
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed data files include gene-by-sample count matrices in CSV format

growth_protocol: Mice were maintained under SPF conditions with a 12-hour light/dark cycle and free access to food and water.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: CD45+ immune cells

value: wild-type (WT C57BL/6)

value: sham operation


title: BY1M; fly whole body;Lsp2[B14];2-3 day;Monosome-Seq;rep1

description:
Library name: BYIM
Monosome-seq
raw_counts_Samples3.csv


title: Dam126 (KIN7729.index27)

description:
Library name: KIN7729.index27
singlecell_lads_mouse_cortex.h5ad.gz

value: brain

value: neural


title: Dam126 / Dam-H3K9ac (KIN7437.index01)

description:
Library name: KIN7437.index01
singlecell_lads_mouse_cortex.h5ad.gz

value: Dam126 / Dam-H3K9ac


title: DSP-1001660014603-D-G08

description: Library name: Sample 129

value: Lupus 2


title: Dam-Lamin B1 (KIN7167.index03)

description:
Library name: KIN7167.index03
singlecell_lads_mouse_cortex.h5ad.gz


title: BY4R; fly whole body;Lsp2[B14];2-3 day;RNA-Seq;rep3

description:
Library name: BY4R
RNA-seq
raw_counts_Samples3.csv

value: whole body

value: 2-3 day

value: BY*R


title: Dam-Lamin B1 (KIN7167.index02)

description:
Library name: KIN7167.index02
singlecell_lads_mouse_cortex.h5ad.gz

value: Dam-Lamin B1


title: Dam-Lamin B1 (KIN7058.index43)

description:
Library name: KIN7058.index43
singlecell_lads_mouse_cortex.h5ad.gz


title: Dam-Lamin B1 (KIN6777.index34)

description:
Library name: KIN6777.index34
singlecell_lads_mouse_cortex.h5ad.gz


title: AY4P; fly whole body;Lsp2[A10];2-3 day;Polysome-Seq;rep3

description:
Library name: AY4P
Polysome-seq
raw_counts_Samples3.csv

value: AY*P


title: AY2P; fly whole body;Lsp2[A10];2-3 day;Polysome-Seq;rep2

description:
Library name: AY2P
Polysome-seq
raw_counts_Samples3.csv


title: Dam-Lamin B1 (KIN6777.index33)

description:
Library name: KIN6777.index33
singlecell_lads_mouse_cortex.h5ad.gz


title: DSP-1001660014603-Y-G06

description: Library name: Sample 127


title: Dam-Lamin B1 (KIN6777.index32)

description:
Library name: KIN6777.index32
singlecell_lads_mouse_cortex.h5ad.gz


title: DSP-1001660014603-Y-G07

description: Library name: Sample 128

value: DESMIN


title: Dam-Lamin B1 (KIN4223.index09)

description:
Library name: KIN4223.index09
singlecell_lads_mouse_cortex.h5ad.gz


title: AY1P; fly whole body;Lsp2[A10];2-3 day;Polysome-Seq;rep1

description:
Library name: AYIP
Polysome-seq
raw_counts_Samples3.csv


title: DSP-1001660014603-Y-G05

description: Library name: Sample 126


title: DSP-1001660014603-Y-G04

description: Library name: Sample 125


title: Dam-Lamin B1 (KIN3845.index01)

description:
Library name: KIN3845.index01
singlecell_lads_mouse_cortex.h5ad.gz


title: Dam-Lamin B1 (KIN2752.index35)

description:
Library name: KIN2752.index35
singlecell_lads_mouse_cortex.h5ad.gz


title: AY4M; fly whole body;Lsp2[A10];2-3 day;Monosome-Seq;rep3

description:
Library name: AY4M
Monosome-seq
raw_counts_Samples3.csv

value: AY*M


title: Dam-Lamin B1 (KIN2752.index34)

description:
Library name: KIN2752.index34
singlecell_lads_mouse_cortex.h5ad.gz


title: Dam-Lamin B1 (KIN2752.index33)

description:
Library name: KIN2752.index33
singlecell_lads_mouse_cortex.h5ad.gz


title: AY2M; fly whole body;Lsp2[A10];2-3 day;Monosome-Seq;rep2

description:
Library name: AY2M
Monosome-seq
raw_counts_Samples3.csv


title: DSP-1001660014603-Y-G02

description: Library name: Sample 123


title: AY1M; fly whole body;Lsp2[A10];2-3 day;Monosome-Seq;rep1

description:
Library name: AYIM
Monosome-seq
raw_counts_Samples3.csv


title: DSP-1001660014603-Y-G01

description: Library name: Sample 122


description:
Library name: Dam-LMNB1-Forelimb_Plate18_mpimg_L21679_RPI10
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

data_processing:
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID procesing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
CELseq alignment: CELseq R2 reads are aligned using GRCm38 (v. 89) transcript models and hisat2 (v. 2.1.0) with the following paramters: : “--mp 2,0 --sp 4,0”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
Assembly: mm10
Supplementary files format and content: RNA count table: count table containing UMI-unique transcript counts per gene for all single-cell samples; DamID count table: count table containing UMI-unique GATC counts per 20-kb interval for all single-cell samples; sample annotations: table containing detailed sample information for all single-cell samples; sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. DamID and CELseq barcodes follow a 3-NNNN-3-NNNN format, where "N" positions indicate the barcode-specific sequence,  the "3" indicates positions of a 3nt UMI sequence.

source_name: Forelimb

growth_protocol: scDam&T data collection was performed in transgenic C2 ESCs and mice carrying an inducible Dam-LMNB1 transgene. For mice, Dam-LMNB1 animals were bred with CAG-CreER mice to facilitate induction and, for mutant analyses, also with Sox9-Kcnj2 ΔCTCF mice. All mouse lines were maintained in a C57Bl.6/J background. For ESCs, a CreERT2 coding sequence was incorporated into the Dam-LMNB1 transgene to facilitate induction. Mouse G4 ESCs (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid) or C2 ESCs (Cellosurus) were grown as described previously on a mitomycin-inactivated CD1 mouse embryonic fibroblast feeder monolayer on gelatinised dishes at 37°C, 7.5% CO2. All ESCs were cultured in ESC medium containing knockout DMEM with 4,5 mg/ml glucose and sodium pyruvate supplemented with 15% FCS , 10 mM Glutamine, 1x penicillin/streptomycin , 1x non-essential amino acids, 1x nucleosides, 0.1 mM beta-Mercaptoethanol and 1000 U/ml LIF.

extract_protocol:
Embryos were isolated from the uteri of pregnant mothers between 8.5 and 13.5 days after the plug date. Embryos were dissected on ice in HBBS (for 8.5-day embryos) or PBS (for 9.5-13.5-day embryos), and staged based on morphology, size, and/or somite number.Samples were processed to create single cell suspensions differently depending on stage. Whole E8.5 embryos were pooled by precise somite number and transferred for tissue dissociation in 200 μl TrypLE Express (Gibco,12604013; Gibco) at 37 °C and triturated by pipetting at 10-20 minutes intervals for a total of 40 minutes. By contrast, tissues from E9.5 to E13.5 embryos were microdissected and pooled as needed. Tissues were then dissociated with Trypsin-EDTA (Thermo Fisher, 25300096; Thermo Fisher) and trituration by pipetting at 37°C at 2-3 minute intervals until no visible clumps remained (~5-15 minutes). Digestion was immediately halted by addition of 10% FCS/PBS. Following disassociation, all samples were cleared of  cell clumps by filtration (40 μm, Flowmi Cell Strainer, Scienceware) and then pelleted by centrifugation at 300 g for 5 minutes at 4°C. Cells were resuspended in FACS buffer [10%FCS/PBS, 10μM ROCK inhibitor (M1817; AbMole), 1μg/ml DAPI (D9542; Sigma-Aldrich)] in preparation for single-cell sorting.
The scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457).

treatment_protocol: Tamoxifen injection was used to trigger Dam-LMNB1 expression in mice via Cre-ERT2 mediated recombination. For ESCs induction, 1 uM of 4-OHT (Sigma, SML1666) was added to the media 7 hours prior to harvesting the cells.

tag: technique

value: scDam&T-seq

value: Forelimb

tag: Stage

value: tamoxifen induction

tag: plate

tag: subtypes

value: genomic DNA; mRNA


description:
Library name: Dam-LMNB1-Forelimb_Plate17_mpimg_L21679_RPI9
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

tag: tissue


title: AY4R; fly whole body;Lsp2[A10];2-3 day;RNA-Seq;rep3

description:
Library name: AY4R
RNA-seq
raw_counts_Samples3.csv

value: AY*R


title: DSP-1001660014603-Y-F12

description: Library name: Sample 121

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

value: PF


description:
Library name: Dam-LMNB1-Intestine_Plate44_mpimg_L20695_RPI2
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Intestine

value: Intestine


title: PMs, KO1, VSV 4h

description: Library name: KO1

value: macrophages

tag: cell line

value: PMs

tag: cell type

value: Mouse peritoneal macrophages

value: VSV for 4 hours


title: DSP-1001660014603-D-G02

description: Library name: Sample 123

value: Lupus 2

tag: treatment


title: DSP-1001660014603-D-F11

description: Library name: Sample 120

tag: panel (wta_+ipa)

value: IA


description:
Library name: Dam-LMNB1-Hindlimbs_Plate41_mpimg_L20695_RPI1
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Hindlimb

value: Hindlimb

tag: genotype


title: AY2R; fly whole body;Lsp2[A10];2-3 day;RNA-Seq;rep2

description:
Library name: AY2R
RNA-seq
raw_counts_Samples3.csv

value: whole body

value: 2-3 day


description:
Library name: Dam-LMNB1-Kidney_Plate42_mpimg_L20695_RPI6
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Kidney

value: scDam&T-seq

value: Kidney


description:
Library name: Dam-LMNB1-Hindlimbs_Plate21_mpimg_L20695_RPI5
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: tamoxifen induction


description:
Library name: Dam-LMNB1-Hindlimbs_Plate27_25_KIN4836_RPI5
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: genomic DNA; mRNA


description:
Library name: Dam-LMNB1-Hindlimbs_Plate25_27_KIN4836_RPI4
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: AY1R; fly whole body;Lsp2[A10];2-3 day;RNA-Seq;rep1

description:
Library name: AYIR
RNA-seq
raw_counts_Samples3.csv

value: AY*R


title: DSP-1001660014603-Y-F10

description: Library name: Sample 119

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

tag: scan name

tag: roi


description:
Library name: Dam-LMNB1-Hindlimbs_Plate24_KIN4612_RPI10
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-Y-F09

description: Library name: Sample 118

tag: segment


title: ThB2P;fly whole body;Thor[2];Lsp2[B14];polysome-Seq;rep2

description:
Library name: ThB2P
Polysome-seq

value: 15 day

value: ThB*P


description:
Library name: Dam-LMNB1-Hindlimbs_Plate13_KIN4612_RPI9
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-Y-G03

description: Library name: Sample 124

value: PF

value: DESMIN


title: DSP-1001660014603-Y-F08

description: Library name: Sample 117


title: CD122 low 2

description:
Library name: Sample 5
Day 21 post-infection

data_processing:
Reads were trimmed using Cutadapt.
The raw gene count matrices were generated using HTSeq (v0.6.1p1) in non-stranded mode.
Raw counts were filtered to remove low-expressed transcripts.
Assembly: RNA-seq FASTQ files were aligned and mapped to the mouse genome (GENCODE M6/Ensembl v81 GRCm38) using the STAR aligner (v2.4.2) with 2-pass mapping mode and a re-generated genome index.
Supplementary files format and content: counts

growth_protocol: CD45.1+ C57BL/6 recipient mice were housed under specific pathogen-free conditions at the CHU Sainte-Justine Research Center. Congenically distinct P14 TCR-transgenic CD8+ T cells specific for the LCMV gp33-41 epitope were used for adoptive co-transfer experiments.

extract_protocol:
Total RNA was extracted from FACS-sorted CD8+ Tetramer+ CD11a+ IL2Rβhi and IL2Rβlo T cells using a TRIzol-based protocol. Cells were sorted directly into TRIzol, lysed for 5 min at room temperature, followed by chloroform phase separation, isopropanol precipitation, ethanol washing, air drying, and resuspension of RNA in RNase-free water.
RNA libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer's instructions. Poly(A)+ RNA was enriched prior to library preparation.

treatment_protocol: Recipient mice received an adoptive co-transfer of 5,000 P14 IL2Rβ+/+ CD8+ T cells and 5,000 P14 IL2Rβ-/- CD8+ T cells one day before intravenous infection with 2 × 10^6 PFU of LCMV Clone 13. At day 21 post-infection, splenic virus-specific CD8+ Tetramer+ CD11a+ T cells were sorted according to IL2Rβ/CD122 surface expression into IL2Rβhi and IL2Rβlo populations for RNA sequencing.

value: Spleen

value: CD8 T cells

value: C57BL/6J CD45.2+ P14+ TCR transgenic specific for the gp33-41 epitope of the LCMV virus

value: Infected mice with LCMV-cl 13


title: ThB1P;fly whole body;Thor[2];Lsp2[B14];polysome-Seq;rep1

description:
Library name: ThB1P
Polysome-seq


title: CD122 high 3

description:
Library name: Sample 3
Day 21 post-infection


title: ThB3M;fly whole body;Thor[2];Lsp2[B14];monosome-Seq;rep3

description:
Library name: ThB3M
Monosome-seq

value: ThB*M


title: CD122 high 2

description:
Library name: Sample 2
Day 21 post-infection


title: PB01337-01 MM Post Transplant 60 Days

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: PB01337-01
H5 file contains RNA expression matrix

library_source: transcriptomic single cell

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000, RNA UMIs/cells between 1500 and 750000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Supplementary files format and content: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

source_name: Blood

extract_protocol:
PBMCs were removed from liquid nitrogen and rapidly thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca. After adding 30 mL cold AIM V media, cells were re-pelleted and resuspended to the appropriate concentrations for scRNAseq.
scRNAseq libraries were generated using a modified 10x genomics chromium 3′ single cell gene expression assay with Cell Hashing. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare (BMC Bioinformatics 2022, doi: 10.1186/s12859-022-04620-2) to generate sample-specific output files.

value: Blood

value: PBMC

tag: subject id

tag: birth year

tag: Sex

value: Male

tag: race

value: Other

tag: days since_first_visit

tag: visit

value: MM Post Transplant 60 Days

tag: batch id

tag: sample bridging_control

value: FALSE


title: DSP-1001660014603-Y-F06

description: Library name: Sample 115

tag: tissue

value: Lupus 2

value: IA


title: CD122 low 1

description:
Library name: Sample 4
Day 21 post-infection


title: ThB2M;fly whole body;Thor[2];Lsp2[B14];monosome-Seq;rep2

description:
Library name: ThB2M
Monosome-seq

value: whole body

tag: time

value: 15 day

tag: batch


title: Pou2f3 KO Infected- PR8 - Day 22 nonimmune

city: Philadelphia

first: Andrew

last: Vaughan

state: PA

address: 3800 Spruce Street

institute: University of Pennsylvania

description:
Library name: Sample 4
Raw Fastq File

data_processing:
Data processing was  performed using Cellranger (v.3.1.0).
Cellranger mkfastq was used to generate demultiplexed FASTQ files from the raw sequencing data.
Cellranger count was used to align sequencing reads to the mouse reference genome (GRCm38) and generate single-cell gene barcode matrices.
Post-processing and secondary analysis were performed using the Seurat package (v.4.4.1).
Assembly: GRCm38
Supplementary files format and content: RDS

source_name: Lung

growth_protocol: Harvested from living mice

extract_protocol:
Lungs were harvested from mice and single-cell suspensions were prepared. Briefly, lungs were perfused with ice cold PBS via the left atrium, lobes were separated and collected in ice cold Dulbecco’s Modified Eagle Medium (DMEM; Thermo Fisher Scientific) +10% fetal bovine serum (FBS; Thermo Fisher Scientific).  Once all mice were harvested, the lobes were placed in 1.5 mL of digestive media (DMEM with 0.15 mg/ml of Liberase TM (Roche # 5401119001),  0.014 mg/mL of DNase I (Sigma Aldrich # D4527-20KU) and 0.20 mg/mL of Dispase II (Sigma Aldrich D4693-1G), cut into small pieces and placed at 37°C to shake for 40-mins. The samples where then passed through a 16-G needle three times and placed back shaking at 37°C for 15-mins. The samples were then passed through a 18-G needle three times and filtered through a 70 µm strainer. The filters were washed with DMEM+10% FBS. Red blood cells were then lysed for 3-mins (Thermo Fisher Scientific #A1049201) and cells were manually counted using a hemacytometer. Whole-lung single-cell suspensions were then used for subsequent experiments
Single-cell RNA-Seq was performed using the Chromium System (10x Genomics) and the Chromium Single Cell 3’ Reagent Kits v2 (10x Genomics) at the Children’s Hospital of Philadelphia Center for Applied Genomics.

treatment_protocol: All viral infections utilized influenza strain A/H1N1/PR/8 obtained from Dr. Carolina Lopez. For influenza infection at the University of Pennsylvania, virus was administered intranasally. Mice ranging between 15 and 20 g in weight were infected with 30 tissue culture infectious dose (TCID) 50 units of PR8, mice weighing between 20 and 25 g were given 40 TCID50 units, and mice ranging between 25 and 30 g in weight were given 50 TCID50 units. For aeroallergen experiments, mice were first sensitized with 40 µg of Alternaria alternata extract intranasally. They were then challenged with 6 doses of A. alternata intranasally (20 µg) to induce allergen sensitivity as previously described. Control mice received Phosphate-Buffered Saline (PBS).

value: Lung

tag: cell type

value: CD45- Non immune cells

value: KO

tag: treatment


title: DSP-1001660014603-Y-F05

description: Library name: Sample 114

tag: panel (wta_+ipa)

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: CTRL1

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

institute: University of Liège

description: Library name: SV1-CTRL1

data_processing:
Fastq files were processed through nf-core/rnaseq pipeline (v1.4.2) with STAR/Salmon combination for mapping and quantification
Assembly: GRCm38 – Ensembl Release 97
Supplementary files format and content: Tab-delimited table with raw counts

source_name: Cortex

extract_protocol:
RNeasy® Plus Mini Kit, 74134, Qiagen
Stranded cDNA libraries were prepared with a NEBNext Ultra II directional RNA library prep kit (E7760, New England Biolabs), according to the manufacturer’s instructions.

treatment_protocol: Cortices from P3 NexCre/+;Cdk7lox/lox;R26EYFP/+ (Cdk7 KO)  and NexCre/+ ;Cdk7+/+ ;R26EYFP/+ (Ctrl) mouse pups were microdissected in ice-cold DPBS-glucose. They were dissociated using a gentleMACS™ instrument with a postnatal neuron dissociation kit (130-094-802, Miltenyi Biotec). The dissociated samples were filtered through a 70 µm strainer rinsed with DPBS containing 0.5% BSA, centrifuged at 300×g for 10 min at room temperature, and the supernatant discarded. The cell pellets were resuspended in 300 µL of phenol red-free HBSS and transferred into 5 mL tubes. Cortical neurons were sorted based on EYFP expression using a FACSAria™ III flow cytometer, harvested in HBSS supplemented with 10% FBS, and centrifuged at 300× g for 7 min at 4°C.  Cell pellets were finally lysed in RLT buffer (from RNeasy® Plus Mini Kit, 74134, Qiagen) completed with 1% 2-mercaptoethanol, and samples were stored at -80°C before RNA extraction.

value: Cortex

value: Cortical projection neurons

tag: genotype

value: NexCre/+;Cdk7+/+, R26EYFP/+


title: DSP-1001660014603-D-F04

description: Library name: Sample 113

tag: scan name

tag: roi


title: Pou2f3 KO uninfected - PBS - Day 22 nonimmune

description:
Library name: Sample 2
Raw Fastq File

value: HET

value: PBS


title: Pou2f3 HET Infected - PR8 - Day 22 nonimmune

description:
Library name: Sample 3
Raw Fastq File


title: DSP-1001660014603-D-F05

description: Library name: Sample 114

tag: segment


title: ThB3R;fly whole body;Thor[2];Lsp2[B14];RNA-Seq;rep3

description:
Library name: ThB3R
RNA-seq

value: ThB*R


title: Pou2f3 HET uninfected - PBS - Day 22 nonimmune

description:
Library name: Sample 1
Raw Fastq File


title: Pou2f3 KO Infected- PR8 - Day 22

description:
Library name: Sample 4
Raw Fastq File

growth_protocol: Harvest from living mice

value: CD45+ immune cells


title: DSP-1001660014603-Y-F04

description: Library name: Sample 113


title: Pou2f3 HET Infected - PR8 - Day 22

description:
Library name: Sample 3
Raw Fastq File


title: Pou2f3 KO uninfected - PBS - Day 22

description:
Library name: Sample 2
Raw Fastq File


title: DSP-1001660014603-Y-F02

description: Library name: Sample 111

source_name: Lupus 1

value: Lupus 1

value: PF


title: Pou2f3 HET uninfected - PBS - Day 22

description:
Library name: Sample 1
Raw Fastq File


title: ThB1R;fly whole body;Thor[2];Lsp2[B14];RNA-Seq;rep1

description:
Library name: ThB1R
RNA-seq


title: DSP-1001660014603-Y-F01

description: Library name: Sample 110

value: DESMIN


title: PT22_Tamoxifen_24_day_Rep1

city: Ann Arbor

first: Jeffrey

middle: A

last: Beamish

state: MI

address: 1500 E. Medical Center Drive, SPC 5364

department: Department of Internal Medicine, Division of Nephrology

institute: University of Michigan

description: Library name: PT22_Tamoxifen_24_day_Rep1

data_processing:
ATAC-seq libraries were sequenced on an Illumina HiSeq 2500 (125-nucleotide read length, paired end), trimmed, and aligned to the GRCm38/mm10 mouse using Bowtie2.
Assembly: GRCm38
Supplementary files format and content: bigWig files

growth_protocol: Modified PT-22 cells were cultured in DMEM supplemented with 3% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Samples were washed with PBS and nuclei were prepared using the NE-PER Nuclear and Cytoplasmic Extraction Reagents Kit (Invitrogen).
Nuclei were resuspended in 50 μl of 1× TD buffer, then incubated with 2–2.5 μl Tn5 enzyme for 30 min at 37 ⁰C (DNA Library Preparation Kit, Nextera). Samples were immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB). qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter).

treatment_protocol: Cells were treated with 1 uM 4-hydroxytamoxifen 2 d to deplete PAX8 or with vehicle. Samples were collected at 0, 3, 24 d.

value: Kidney

tag: cell line

value: Proximal tubule

value: 4-hydroxytamoxifen (1 uM)

tag: replicate


title: DSP-1001660014603-Y-E12

description: Library name: Sample 109

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw_dcc.tar:  raw read counts in DCC of tar
Supplementary files format and content: Protein_Q3_normalized_expression_matrix.txt  :  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format


title: ThA3P;fly whole body;Thor[2];Lsp2[A10];polysome-Seq;rep3

description:
Library name: ThA3P
Polysome-seq

value: whole body

value: 15 day

value: ThA*P


title: PT22_Tamoxifen_3_day_Rep1

description: Library name: PT22_Tamoxifen_3_day_Rep1


title: ThA2P;fly whole body;Thor[2];Lsp2[A10];polysome-Seq;rep2

description:
Library name: ThA2P
Polysome-seq


title: DSP-1001660014603-Y-E11

description: Library name: Sample 108

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: PT22_Ctrl_Rep2

description: Library name: PT22_Ctrl_Rep2


title: ThA1P;fly whole body;Thor[2];Lsp2[A10];polysome-Seq;rep1

description:
Library name: ThA1P
Polysome-seq


title: DSP-1001660014603-Y-E10

description: Library name: Sample 107


title: CRIC-seq PARN IP rep1

first: NAIJING

last: HU

address: No.11 Xizhimen South Street, Xicheng District

institute: Peking University People's Hospital

description:
Library name: Sample 3
Replicates were merged for processing

data_processing:
The raw reads files with fastq format are converted by Illumina bcl2fastq (v2.16).
The raw data from CRIC-seq libraries were processed with the RICpipe program (v1.0) for trimming and alignment to the mouse reference genome (mm10 version). The resulting alignments from STAR and bwa were then performed to RICpipe analysis for chimeric read extraction.
Assembly: mm10
Supplementary files format and content: Genome-wide CRIC-seq signal in bigwig format

growth_protocol: The primary B cells were cultured in RPMI1640 medium supplemented with 10% FBS and 100U of Penicillin-Streptomycin in 5% CO2 incubator at 37℃.

extract_protocol:
The spleen was isolated from 8-week old mice and disrupted in PBS  containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer. The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacture’s protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
The procedure was adopted as previously described (Ye et al., 2023)

treatment_protocol: Primary B cells were activated by LPS (5ug/ml, Sigma, Catalog #L3024) for 3 days.

value: Spleen

tag: strain

value: B cells

value: Wild type

value: LPS treatement

tag: antibody

value: anti-PARN


title: ThA3M;fly whole body;Thor[2];Lsp2[A10];monosome-Seq;rep3

description:
Library name: ThA3M
Monosome-seq

value: ThA*M


title: CRIC-seq IgG IP rep2

description:
Library name: Sample 2
Replicates were merged for processing

value: anti-IgG


title: DSP-1001660014603-Y-E09

description: Library name: Sample 106

extract_protocol:
FFPE tissues were parafilm embedded, 5 µM sections were cut with cryostat
Spatial transcritpome sequencing libraries were prepared with Nanostring GeoMx DSP NGS library preparation kit according to manufacturer's instruction

value: Lupus 1


title: CRIC-seq IgG IP rep1

description:
Library name: Sample 1
Replicates were merged for processing


title: ThA2M;fly whole body;Thor[2];Lsp2[A10];monosome-Seq;rep2

description:
Library name: ThA2M
Monosome-seq


title: CLIP-seq PARN LPS rep2

description:
Library name: Sample 6
Replicates were merged for processing

data_processing:
The raw reads files with fastq format are converted by Illumina bcl2fastq (v2.16).
After the sequencing of CLIP-seq libraries, raw data were trimmed using Trimmomatic software (v0.36) and aligned to mouse reference genome (mm10 version) using bowtie2 (v2.3.4.3).
Assembly: mm10
Supplementary files format and content: Genome-wide CLIP-seq signal in bigwig format

extract_protocol:
The spleen was isolated from 8-week old mice and disrupted in PBS  containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer  . The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacture’s protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
CLIP-seq was performed as previously described (Xue et al., 2009). Briefly, the isolated B cells were irradiated at 400mJ/cm2 with 254nm UV light. The crosslinked cells were lysed and 15ug of PARN (Abcam, Catalog # ab125185) specific antibody was applied to pull-down protein-RNA complexes. After micrococcal nuclease treatment, 3’RNA linker ligation and 5’end 32P labeling, the immunoprecipitated complexes were fractionated on 10% NuPAGE bis-tris gel and transferred to nitrocellulose membrane. The auto-radiographed PARN smear bands were cut and treated with Proteinase K to extract respective RNA by phenol and chloroform. The isolated RNA was then added a 5’ RNA linker and reverse transcribed by superscript reverse transcriptase III (life technologies, catalog# 18080-051). The PCR products were sequenced with illumina Hiseq 2500 platform.


title: DSP-1001660014603-Y-E08

description: Library name: Sample 105

value: PF


title: ThA1M;fly whole body;Thor[2];Lsp2[A10];monosome-Seq;rep1

description:
Library name: ThA1M
Monosome-seq


title: CLIP-seq PARN LPS rep1

description:
Library name: Sample 5
Replicates were merged for processing


title: CLIP-seq PARN rep2

description:
Library name: Sample 4
Replicates were merged for processing

value: No treatment


title: CLIP-seq PARN rep1


title: DSP-1001660014603-Y-E07

description: Library name: Sample 104

value: DESMIN


title: ThA3R;fly whole body;Thor[2];Lsp2[A10];RNA-Seq;rep3

description:
Library name: ThA3R
RNA-seq

value: ThA*R


title: CLIP-seq IgG rep2


title: CLIP-seq IgG rep1


title: 2P-seq PARN CKO rep2

data_processing:
The raw reads files with fastq format are converted by Illumina bcl2fastq (v2.16).
After sequencing the 2P-seq libraries, the raw data were processed by the PASfinder program (https://github.com/duzc-Repos/PASfinder), which performed adapter trimming, alignment to the mouse genome, and identification of alternative polyadenylation sites.
Assembly: mm10
Supplementary files format and content: Genome-wide 2P-seq signal in bigwig format

extract_protocol:
The spleen was isolated from 8-week old mice and disrupted in PBS  containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer. The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacture’s protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
2P-seq protocol was conducted according to previous study (Spies et al., 2013).

value: PARN knockout


title: DSP-1001660014603-Y-E05

description: Library name: Sample 102


title: DSP-1001660014603-Y-E04

description: Library name: Sample 101


title: 2P-seq shCtrl rep1

value: WT


title: B3P;fly whole body;Lsp2[B14];polysome-Seq;rep3

description:
Library name: B3P
Polysome-seq

value: whole body

value: 15 day

value: B*P


title: RNA-seq PARN CKO rep2

data_processing:
The raw reads files with fastq format are converted by Illumina bcl2fastq (v2.16).
After the sequencing of RNA-seq libraries, raw data were trimmed using Trimmomatic software.
Assembly: mm10
Supplementary files format and content: Genome-wide RNA-seq signal in bigwig format

extract_protocol:
The spleen was isolated from 8-week old mice and disrupted in PBS  containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer. The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacture’s protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
Total RNA of B cells was extracted by Trizol. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, a transcriptome sequencing library was established. Utilizing a TruSeq PE Cluster kit v3-cBot-HS (Illumina) on a cBot Cluster Generation System, index-coded samples were clustered in strict accordance with the manufacturer’s guidelines. Upon completion of the clustering process, the library preparations were subjected to sequencing on the Illumina NovaSeq platform, generating 150 bp paired-end reads. Rigorous quality control measures were implemented post-sequencing to ensure that downstream analyses were performed exclusively on pristine, high-quality data.

value: Spleen


title: DSP-1001660014603-Y-E03

description: Library name: Sample 100

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: RNA-seq PARN CKO rep1

value: B cells


title: B2P;fly whole body;Lsp2[B14];polysome-Seq;rep2

description:
Library name: B2P
Polysome-seq


title: RNA-seq shCtrl rep2

value: LPS treatement


title: B1P;fly whole body;Lsp2[B14];polysome-Seq;rep1

description:
Library name: B1P
Polysome-seq


title: Tumor from patient NB85 at diagnosis

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

description: Library name: NB85

data_processing:
quality control was carrried out with FastQC v0.11.8 and MultiQC v1.10
reads were mapped to GRCh38 and gene level counts were ouptut using STAR v2.7.10b with annotation from GENCODE (v38)
Read counts were imported into R v4.2.2 and normalised with DESeq2 v1.38.3
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt.gz: gzipped tab-delimited text file of raw (unnormalized) gene-level counts for all samples
Supplementary files format and content: normalized_counts.txt.gz: gzipped tab-delimited text file of normalized gene-level counts for all samples

source_name: neuroblastoma

extract_protocol:
RNA extraction was carried out using the QIAzol (QIAGEN, USA) (n=7) procedure or the AllPrep DNA/RNA Mini Kits (QIAGEN, USA) (n=11), according to manufacturer’s instructions
Libraries were prepared using the Illumina Stranded mRNA Library Prep Kit (Illumina)

value: neuroblastoma

value: neuroblastoma tumor cells

tag: age (days)

tag: Sex

value: female

tag: outcome

value: Alive

tag: event-free survival_(days)

tag: overall survival_(days)

tag: adrenergic or_mesenchymal_signature

value: ADRN

tag: death


title: DSP-1001660014603-Y-E01

description: Library name: Sample 98

tag: tissue

value: Lupus 1

tag: treatment

value: PF


title: Tumor from patient NB82 at diagnosis

description: Library name: NB82

tag: cell type


title: B3M;fly whole body;Lsp2[B14];monosome-Seq;rep3

description:
Library name: B3M
Monosome-seq

tag: genotype

tag: time

tag: batch

value: B*M


title: Tumor from patient NB74 at diagnosis

description: Library name: NB74

value: male

value: Died of Disease

value: MES


title: DSP-1001660014603-Y-D12

description: Library name: Sample 97

tag: panel (wta_+ipa)

tag: scan name

tag: roi

tag: segment

value: DESMIN


title: Tumor from patient NB71 at diagnosis

description: Library name: NB71

tag: age (days)


title: B2M;fly whole body;Lsp2[B14];monosome-Seq;rep2

description:
Library name: B2M
Monosome-seq

value: whole body

value: 15 day


title: Tumor from patient NB68 at diagnosis

description: Library name: NB68

tag: Sex


title: DSP-1001660014603-Y-D11

description: Library name: Sample 96

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: DSP-1001660014603-Y-E06

description: Library name: Sample 103


title: ThA2R;fly whole body;Thor[2];Lsp2[A10];RNA-Seq;rep2

description:
Library name: ThA2R
RNA-seq

value: ThA*R


title: 2P-seq shCtrl rep2

source_name: Spleen

value: Spleen

tag: strain

value: B cells

value: WT

value: LPS treatement


title: ThA1R;fly whole body;Thor[2];Lsp2[A10];RNA-Seq;rep1

description:
Library name: ThA1R
RNA-seq


title: 2P-seq PARN CKO rep1

value: PARN knockout


title: B1M;fly whole body;Lsp2[B14];monosome-Seq;rep1

description:
Library name: B1M
Monosome-seq


title: Tumor from patient NB63 at diagnosis

description: Library name: NB63

value: neuroblastoma

value: neuroblastoma tumor cells

value: female

tag: outcome

value: Alive

tag: event-free survival_(days)


title: Tumor from patient NB62 at diagnosis

description: Library name: NB62

tag: overall survival_(days)

tag: adrenergic or_mesenchymal_signature

value: ADRN


title: DSP-1001660014603-Y-D10

description: Library name: Sample 95

tag: tissue

value: Lupus 1

value: PF


title: Tumor from patient NB61 at diagnosis

description: Library name: NB61

value: male

tag: death


title: B3R;fly whole body;Lsp2[B14];RNA-Seq;rep3

description:
Library name: B3R
RNA-seq

value: whole body

tag: treatment

value: B*R


title: Tumor from patient NB60 at diagnosis

description: Library name: NB60

tag: cell type

value: MES


title: DSP-1001660014603-Y-D09

description: Library name: Sample 94

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: Tumor from patient NB58 at diagnosis

description: Library name: NB58

value: Died of Disease


title: B2R;fly whole body;Lsp2[B14];RNA-Seq;rep2

description:
Library name: B2R
RNA-seq

tag: genotype

tag: time

value: 15 day


title: Tumor from patient NB53 at diagnosis

description: Library name: NB53


title: DSP-1001660014603-Y-D08

description: Library name: Sample 93

tag: panel (wta_+ipa)

value: DESMIN


title: Tumor from patient NB46 at diagnosis

description: Library name: NB46


title: B1R;fly whole body;Lsp2[B14];RNA-Seq;rep1

description:
Library name: B1R
RNA-seq

tag: batch


title: DSP-1001660014603-Y-E02

description: Library name: Sample 99

tag: scan name

tag: roi


title: Tumor from patient NB45 at diagnosis

description: Library name: NB45

tag: age (days)


title: DSP-1001660014603-Y-D07

description: Library name: Sample 92

tag: segment


title: Tumor from patient NB43 at diagnosis

description: Library name: NB43

tag: Sex


title: Tumor from patient NB41 at diagnosis

description: Library name: NB41

tag: outcome


title: A3P;fly whole body;Lsp2[A10];polysome-Seq;rep3

description:
Library name: A3P
Polysome-seq

value: A*P


title: RNA-seq shCtrl rep1

value: Spleen

tag: cell line

value: B cells

value: WT

value: LPS treatement


title: DSP-1001660014603-Y-D06

description: Library name: Sample 91

value: IA


title: Tumor from patient NB38 at diagnosis

description: Library name: NB38

value: neuroblastoma

value: neuroblastoma tumor cells

value: Alive

tag: event-free survival_(days)

tag: overall survival_(days)

value: ADRN


title: A2P;fly whole body;Lsp2[A10];polysome-Seq;rep2

description:
Library name: A2P
Polysome-seq

tag: tissue

value: whole body


title: Tumor from patient NB18 at diagnosis

description: Library name: NB18

value: female

tag: adrenergic or_mesenchymal_signature

tag: death


title: DSP-1001660014603-Y-D05

description: Library name: Sample 90

value: Lupus 1

tag: treatment


title: Tumor from patient NB07 at diagnosis

description: Library name: NB07

tag: cell type

value: male

value: MES


title: A1P;fly whole body;Lsp2[A10];polysome-Seq;rep1

description:
Library name: A1P
Polysome-seq

tag: genotype

tag: time

value: 15 day


title: FAM13A KO D15 (GFP+ and GFP- fractions)

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: Library name: WA_WR_0818_4

data_processing:
The sample was processed using the standard Cellranger v.2 pipeline
Reads were mapped to GRCh38 with TdTomato reporter
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38 with TdTomato reporter
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5 format

source_name: iPSC-derived D15 cells from FAM13A KO

extract_protocol:
10X Chromium system
A hashtag oligo (HTO) library and a 3' gene expression library were constructed scRNA-seq

value: iPSC-derived D15 cells from FAM13A KO

tag: library type

value: mRNA


title: DSP-1001660014603-Y-D04

description: Library name: Sample 89

tag: panel (wta_+ipa)

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

tag: scan name


title: FAM13A WT D15 (GFP+ and GFP- fractions)

description: Library name: WA_WR_0818_3

source_name: iPSC-derived D15 cells from FAM13A WT

value: iPSC-derived D15 cells from FAM13A WT


title: A3M;fly whole body;Lsp2[A10];monosome-Seq;rep3

description:
Library name: A3M
Monosome-seq

tag: batch

value: A*M


title: DSP-1001660014603-Y-D03

description: Library name: Sample 88

value: CONTROL

tag: roi

tag: segment

value: DESMIN


title: FAM13A KO D0 (Biolegend Hashtag 1) and D6 (Biolegend Hashtag 2)

description: Library name: WA_WR_0818_2_HTO

data_processing:
The sample was processed using the standard Cellranger v.2 pipeline
Reads were mapped to GRCh38 with TdTomato reporter
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38 with TdTomato reporter
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5 format
Library strategy: CITE-seq

source_name: iPSC-derived D0 and D6 cells from FAM13A KO

value: HTO

tag: hto


title: A2M;fly whole body;Lsp2[A10];monosome-Seq;rep2

description:
Library name: A2M
Monosome-seq

data_processing:
We first performed quality control and adapter trimming on the raw sequencing reads using fastp (v0.23.2). Reads were then mapped to species-specific rRNA using Bowtie2 (v2.3.4.1) to remove ribosomal RNA contaminants. Clean reads were aligned to the Drosophila melanogaster (BDGP6.46) reference genome (ensembl.org/Drosophila_melanogaster/Info/Index) by STAR (v2.2.1). Uniquely mapped reads were summarized to Drosophila_melanogaster.BDGP6.46.110.chr.gtf annotated genes using featureCounts (v1.6.0). The resulting raw gene expression matrix was then imported into the R (v4.2.0) environment for further processing and analysis.
Assembly: BDGP6.46
Supplementary files format and content: csv file includes raw counts for each Sample


title: FAM13A WT D0 (Biolegend Hashtag 1) and D6 (Biolegend Hashtag 2)

description: Library name: WA_WR_0818_1_HTO

source_name: iPSC-derived D0 and D6 cells from FAM13A WT


title: FAM13A KO D0 and D6 GEX

description: Library name: WA_WR_0818_2

value: iPSC-derived D0 and D6 cells from FAM13A KO


title: DSP-1001660014603-Y-D02

description: Library name: Sample 87


title: FAM13A WT D0 and D6 GEX

description: Library name: WA_WR_0818_1

value: iPSC-derived D0 and D6 cells from FAM13A WT


title: A1M;fly whole body;Lsp2[A10];monosome-Seq;rep1

description:
Library name: A1M
Monosome-seq


title: DSP-1001660014603-Y-D01

description: Library name: Sample 86


title: HUVEC_ESD_4

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: Library name: OU35

data_processing:
Data were analysed using the Lexogen's proprietary sequence analysis platform. Trimming using Bbduk and quality control with FASTQC.
Assembly: HGhg38
Supplementary files format and content: raw counts; .tsv
Supplementary files format and content: normalized data; tsv

source_name: HUVEC

extract_protocol:
Qiagen RNeasy micro kit with DNase treatment
Libraries were prepared according to Lexogen's instructions accompanying the Kit (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina)

tag: cell line

value: HUVEC

value: ESD 4


title: A3R;fly whole body;Lsp2[A10];RNA-Seq;rep3

description:
Library name: A3R
RNA-seq

source_name: whole body

extract_protocol:
Whole female flies were ground in liquid nitrogen. A portion of the powdered tissue was reserved for total RNA extraction, while the remaining material was lysed and subjected to 10–45% sucrose density gradient centrifugation. Monosome and polysome fractions were collected after gradient fractionation. Total RNA and RNA from the monosome and polysome fractions were separately isolated using TRIzol reagent (Invitrogen, #15596026).
Poly(A)+ RNA was enriched from 2 μg of total RNA, monosome-bound RNA, or polysome-bound RNA using VAHTS mRNA Capture Beads (Vazyme, #N401). The enriched RNA was fragmented and subjected to end repair, adaptor ligation, and PCR amplification using the VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme, #NR604). Following library quality control and quantification, the libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads.

value: whole body

value: A*R


title: HUVEC_ESD_3

description: Library name: OU34

value: ESD 3


title: DSP-1001660014603-Y-C12

first: Chengsong

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: Sample 85


title: HUVEC_ESD_2

description: Library name: OU33

value: ESD 2


title: A2R;fly whole body;Lsp2[A10];RNA-Seq;rep2

description:
Library name: A2R
RNA-seq

value: 15 day


title: HUVEC_ESD_1

description: Library name: OU32

value: ESD 1


title: DSP-1001660014603-Y-C11

description: Library name: Sample 84


title: HUVEC_ESA_5

description: Library name: OU31

value: ESA 5


title: A1R;fly whole body;Lsp2[A10];RNA-Seq;rep1

description:
Library name: A1R
RNA-seq


title: HUVEC_ESA_4

description: Library name: OU30

value: ESA 4


title: DSP-1001660014603-Y-C10

description: Library name: Sample 83

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: HUVEC_ESA_3

description: Library name: OU29

value: ESA 3


title: W2P;fly whole body;Lpp[TS]>w1118;polysome-Seq;rep2

description:
Library name: W2P
Polysome-seq

value: W*P


title: HUVEC_ESA_2

description: Library name: OU28

value: ESA 2


title: DSP-1001660014603-Y-C09

description: Library name: Sample 82

value: CONTROL

value: DESMIN


title: W1P;fly whole body;Lpp[TS]>w1118;polysome-Seq;rep1

description:
Library name: W1P
Polysome-seq


title: HUVEC_ESA_1

description: Library name: OU27

value: ESA 1


title: HUVEC_NT_5

description: Library name: OU26

value: HUVEC

value: NT 5


title: DSP-1001660014603-Y-C08

description: Library name: Sample 81


title: HUVEC_NT_4

description: Library name: OU25

value: NT 4


title: HUVEC_NT_3

description: Library name: OU24

value: NT 3


title: W2M;fly whole body;Lpp[TS]>w1118;monosome-Seq;rep2

description:
Library name: W2M
Monosome-seq

value: whole body

value: W*M


title: DSP-1001660014603-Y-C07

description: Library name: Sample 80


title: HUVEC_NT_1

description: Library name: OU22

value: NT 1


title: HUVEC_NT_2

description: Library name: OU23

value: NT 2


title: W1M;fly whole body;Lpp[TS]>w1118;monosome-Seq;rep1

description:
Library name: W1M
Monosome-seq

value: 15 day


title: DSP-1001660014603-Y-C06

description: Library name: Sample 79


title: HUVEC_C4+mim29_5

description: Library name: OU21


title: Dam-Lamin B1 (KIN7167.index04)

description:
Library name: KIN7167.index04
singlecell_lads_mouse_cortex.h5ad.gz

data_processing:
Data generated by the scDam&T-seq protocol was largely processed following the workflow and scripts described in {Markodimitraki 2020}. Scripts and a workflow description are also available on www.github.com/KindLab/scDamAndTools.
All reads are demultiplexed based on the barcode present at the start of R1 using a reference list of barcodes. The reference barcodes contain both DamID-specific and CEL-seq2-specific barcodes and zero mismatches between the observed barcode and reference are allowed. The UMI information, also present at the start of R1, is appended to the read name.
DamID reads are aligned using bowtie2 (v. 2.3.3.1){Langmead 2012} with the following parameters: ‘‘--seed 42 --very- sensitive -N 1.’’ The mm10 reference genome is used for alignment. The resulting alignments are then converted to UMI-unique GATC counts by matching each alignment to known strand-specific GATC positions in the reference genome. Any reads that do not align to a known GATC position or have a mapping quality smaller than 10 are removed. Up to 2 unique UMIs are allowed for single-cell samples to account for the number of alleles. Finally, counts are binned at the desired resolution, generally 100 Kb.
CEL-seq2 reads are aligned using tophat2 (v. 2.1.1){Kim 2013} with the following parameters: ‘‘--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200.’’ The mm10 reference genome and the GRCm38 (v. 89) transcript models are used. Alignments are subsequently converted to transcript counts per gene with custom scripts that assign reads to genes similar to HTSeq’s79 htseq-count with mode ‘‘intersection_strict.’’
Assembly: GRCm38
Supplementary files format and content: H5AD

source_name: brain

extract_protocol:
Mothers were sacrificed at E16.5 (48 hours after IUE) and whole brains from the pups were collected for immunostainings in ice-cold Leibovitz’s L-15 medium (Gibco, 11415064), washed in PBS and fixed by immersion in 4% paraformaldehyde (PFA, Sigma, 30525-89-4) in PBS at 4 °C overnight.
The scDam&T-seq processing was largely performed as previously described in {Markodimitraki 2020}, but reaction volumes of all mixes were equimolarly halved (0.5x) to reduce overall processing costs. As such, the added volumes per well were 50 nl CEL-seq2 primer (before sorting, with 5 µl mineral oil), 50 nl lysis mix, 75 nl reverse transcriptase mix, 925 nl second strand mix, 250 nl proteinase K mix, 150 nl DpnI mix, 50 nl of DamID adapter (1 µM concentration, 25 nM final during ligation) and 450 nl scDam&T T4 ligase mix. The overall composition of the mixes remains unaltered and the incubation times and temperatures are as described.

value: brain

value: neural

tag: sample group

value: Dam-Lamin B1


title: W2R;fly whole body;Lpp[TS]>w1118;RNA-Seq;rep2

description:
Library name: W2R
RNA-seq

value: W*R


title: HUVEC_C4+mim29_4

description: Library name: OU20


title: DSP-1001660014603-Y-C05

description: Library name: Sample 78

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: HUVEC_C4+mim29_3

description: Library name: OU19


title: W1R;fly whole body;Lpp[TS]>w1118;RNA-Seq;rep1

description:
Library name: W1R
RNA-seq


title: HUVEC_C4+mim29_2

description: Library name: OU18


title: DSP-1001660014603-Y-C04

description: Library name: Sample 77

value: CONTROL


title: HUVEC_C4_5

description: Library name: OU16


title: R2P;fly whole body;Lpp[TS]>Rheb;polysome-Seq;rep2

description:
Library name: R2P
Polysome-seq

value: Lpp[TS]>Rheb

value: R*P


title: HUVEC_C4+mim29_1

description: Library name: OU17

value: HUVEC


title: DSP-1001660014603-Y-C03

description: Library name: Sample 76

value: DESMIN


title: R1P;fly whole body;Lpp[TS]>Rheb;polysome-Seq;rep1

description:
Library name: R1P
Polysome-seq


title: HUVEC_C4_4

description: Library name: OU15


description:
Library name: Dam-LMNB1-Forelimb_Plate34_mpimg_L21679_RPI11
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

data_processing:
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID procesing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
CELseq alignment: CELseq R2 reads are aligned using GRCm38 (v. 89) transcript models and hisat2 (v. 2.1.0) with the following paramters: : “--mp 2,0 --sp 4,0”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
Assembly: mm10
Supplementary files format and content: RNA count table: count table containing UMI-unique transcript counts per gene for all single-cell samples; DamID count table: count table containing UMI-unique GATC counts per 20-kb interval for all single-cell samples; sample annotations: table containing detailed sample information for all single-cell samples; sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. DamID and CELseq barcodes follow a 3-NNNN-3-NNNN format, where "N" positions indicate the barcode-specific sequence,  the "3" indicates positions of a 3nt UMI sequence.

source_name: Forelimb

tag: technique

value: scDam&T-seq

value: Forelimb

tag: Stage

value: tamoxifen induction

tag: plate

tag: subtypes

value: genomic DNA; mRNA


title: HUVEC_C4_3

description: Library name: OU14

tag: treatment


title: HUVEC_C4_2

description: Library name: OU13


title: DSP-1001660014603-Y-C02

description: Library name: Sample 75

tag: tissue


title: R2M;fly whole body;Lpp[TS]>Rheb;monosome-Seq;rep2

description:
Library name: R2M
Monosome-seq

value: whole body

tag: genotype

value: R*M


title: HUVEC_C4_1

description: Library name: OU12


title: DSP-1001660014603-Y-C01

description: Library name: Sample 74


title: HUVEC_mim29_5

description: Library name: OU11

value: mim29 5


title: HUVEC_mim29_4

description: Library name: OU10

value: mim29 4


title: R1M;fly whole body;Lpp[TS]>Rheb;monosome-Seq;rep1

description:
Library name: R1M
Monosome-seq

tag: time

value: 15 day


title: HUVEC_mim29_3

description: Library name: OU09

value: mim29 3


title: DSP-1001660014603-Y-B12

description: Library name: Sample 73


title: HUVEC_mim29_2

description: Library name: OU08

value: mim29 2


title: R2R;fly whole body;Lpp[TS]>Rheb;RNA-Seq;rep2

description:
Library name: R2R
RNA-seq

value: R*R


title: ThB3P;fly whole body;Thor[2];Lsp2[B14];polysome-Seq;rep3

description:
Library name: ThB3P
Polysome-seq

value: ThB*P


title: HUVEC_mim29_1

description: Library name: OU07

value: mim29 1


title: DSP-1001660014603-Y-B11

description: Library name: Sample 72

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

value: CONTROL


title: R1R;fly whole body;Lpp[TS]>Rheb;RNA-Seq;rep1

description:
Library name: R1R
RNA-seq

value: Lpp[TS]>Rheb


title: HUVEC_SCR_5

description: Library name: OU06

value: HUVEC

value: SCR 5


title: DSP-1001660014603-Y-B10

description: Library name: Sample 71


title: HUVEC_SCR_4

description: Library name: OU05

value: SCR 4


title: CD122 high 1

description:
Library name: Sample 1
Day 21 post-infection

data_processing:
Reads were trimmed using Cutadapt.
The raw gene count matrices were generated using HTSeq (v0.6.1p1) in non-stranded mode.
Raw counts were filtered to remove low-expressed transcripts.
Assembly: RNA-seq FASTQ files were aligned and mapped to the mouse genome (GENCODE M6/Ensembl v81 GRCm38) using the STAR aligner (v2.4.2) with 2-pass mapping mode and a re-generated genome index.
Supplementary files format and content: counts

value: Spleen

tag: cell type

value: CD8 T cells

value: C57BL/6J CD45.2+ P14+ TCR transgenic specific for the gp33-41 epitope of the LCMV virus

value: Infected mice with LCMV-cl 13


title: L2P;fly whole body;Lpp[TS]>Lsp2;polysome-Seq;rep2

description:
Library name: L2P
Polysome-seq

value: whole body

value: L*P


title: HUVEC_SCR_3

description: Library name: OU04

value: SCR 3


title: DSP-1001660014603-Y-B09

description: Library name: Sample 70

tag: panel (wta_+ipa)

value: DESMIN


title: HUVEC_SCR_2

description: Library name: OU03

value: SCR 2


title: L1P;fly whole body;Lpp[TS]>Lsp2;polysome-Seq;rep1

description:
Library name: L1P
Polysome-seq

value: 15 day


title: HUVEC_SCR_1

description: Library name: OU02

value: SCR 1


title: DSP-1001660014603-Y-B08

description: Library name: Sample 69

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

tag: scan name


title: S20,CD14_control, rep 5

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

description: Library name: Sample 20

data_processing:
The clean reads were aligned to reference genome by HISAT2. Sam filles were sorted as bam files and indexed by samtools.
The transcript count (number of reads per gene) were extract using stingTie (v1.3.5)  in default setting.
The transcript count in gene level data was further normalized and used to identify the differentially expressed genes by DEseq2 tool.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes normalized count for each Sample.

source_name: blood

extract_protocol:
RNA extracted by using the RNeasy Mini Kit (Qiagen). The quality and quantity of purified RNA was estimated on Nanodrop 1000 Spectrophotometer (ThermoFisher).
RNA libraries were prepared using the NEBNext Ultra II Non-Directional RNA Library Kit with PolyA selection (New England BioLabs).

value: blood

value: monocyte

value: control


title: L2M;fly whole body;Lpp[TS]>Lsp2;monosome-Seq;rep2

description:
Library name: L2M
Monosome-seq

tag: batch

value: L*M


title: S19,CD14_control, rep 4

description: Library name: Sample 19


title: DSP-1001660014603-Y-B07

city: Dallas

last: Zhu

description: Library name: Sample 68

value: CONTROL

tag: roi


title: S18,CD14_control, rep 3

description: Library name: Sample 18


title: L1M;fly whole body;Lpp[TS]>Lsp2;monosome-Seq;rep1

description:
Library name: L1M
Monosome-seq


title: DSP-1001660014603-Y-B06

description: Library name: Sample 67

tag: segment


title: S16,CD14_control, rep 1

description: Library name: Sample 16


title: L2R;fly whole body;Lpp[TS]>Lsp2;RNA-Seq;rep2

description:
Library name: L2R
RNA-seq

value: L*R


title: S17,CD14_control, rep 2

description: Library name: Sample 17


title: DSP-1001660014603-Y-B05

description: Library name: Sample 66


title: S15,CD14_CVID, rep 5

description: Library name: Sample 15

value: CVID patient


title: S14,CD14_CVID, rep 4

description: Library name: Sample 14


title: L1R;fly whole body;Lpp[TS]>Lsp2;RNA-Seq;rep1

description:
Library name: L1R
RNA-seq


title: S13,CD14_CVID, rep 3

description: Library name: Sample 13


title: S12,CD14_CVID, rep 2

description: Library name: Sample 12


title: Fibroblast_Intracellular_miRNA_rep3

city: Nantong

first: jiahui

last: he

state: Jiangsu

address: 江苏省南通市崇川区启秀路19号

department: 神经再生重点实验室

institute: Nantong University

description:
Library name: SAMPLES6
Column name in miRNA_expression_quantification.txt: Fibroblast_Intracellular_miRNA_rep3

data_processing:
Raw sequencing reads were generated via Illumina sequencing platform. Adapter sequences were removed using cutadapt. Reads shorter than 15 nt or longer than 41 nt were discarded. Quality filtering was performed using fastx_toolkit (v0.0.13) to retain reads with Q20 ≥ 80%, and NGS QC Toolkit (v2.3.2) was used to remove reads containing ambiguous ‘N’ bases, yielding clean reads. Clean reads were aligned to the Rfam (v10.0) database using blastn to filter out rRNA, tRNA, snRNA, snoRNA, and other non-coding RNA; repeat sequences were further removed using RepeatMasker. Remaining reads were mapped to the miRBase database to identify known miRNAs. miRDeep2 was used to predict novel miRNAs, and RNAfold was applied to predict secondary structures. miRNA expression levels were calculated as raw read counts and normalized to TPM (Transcripts Per Million). Differentially expressed miRNAs were identified using the DEG algorithm in R with a threshold of p < 0.05. Target genes were predicted using miRanda with parameters S ≥ 150, ΔG ≤ −30 kcal/mol, and strict 5' seed pairing. GO and KEGG enrichment analyses were performed using R based on hypergeometric distribution.
Assembly: Rnor_6.0
Supplementary files format and content: counts_anno.txt: Tab-delimited matrix of raw miRNA read counts with full gene annotation.
Supplementary files format and content: TPM_anno.txt: Tab-delimited matrix of TPM-normalized miRNA expression values across all samples.

organism: Rattus norvegicus

source_name: peripheral nerve, sciatic nerve

extract_protocol:
Total RNA was extracted from exosomes and intracellular fractions of rat peripheral nerve fibroblasts using a miRNA isolation kit. RNA quantity was determined using NanoDrop 2000, and RNA quality was verified by Agilent 2100 Bioanalyzer. One microgram of qualified total RNA was used for small RNA library preparation.
Total RNA was extracted and quantified using the NanoDrop 2000 spectrophotometer. RNA quality was verified using the Agilent 2100 Bioanalyzer. For each sample, 1 μg of total RNA was used for small RNA library preparation. The 3' adapter was first ligated to RNA using T4 RNA Ligase 2 (Deletion Mutant), followed by ligation of the 5' adapter using T4 RNA Ligase. Adapter-ligated RNA was reverse-transcribed into cDNA using SuperScript II Reverse Transcriptase. PCR amplification was then performed with the following conditions: 98°C for 30 s; 15 cycles of 98°C for 10 s, 60°C for 30 s, 72°C for 15 s; and a final extension at 72°C for 10 min. PCR products were separated by gel electrophoresis, and cDNA fragments of 147 nt and 157 nt were excised and purified. Library quality was assessed using the Agilent 2100 Bioanalyzer with a High Sensitivity DNA Chip.

value: peripheral nerve, sciatic nerve

value: nerve-derived fibroblast

value: wild type

value: untreated


title: DSP-1001660014603-Y-B04

description: Library name: Sample 65


title: S11,CD14_CVID, rep 1

description: Library name: Sample 11


title: DSP-1001660014603-Y-B03

description: Library name: Sample 64


title: S10,CD3_control, rep 5

description: Library name: Sample 10

value: T-cell


title: Fibroblast_Intracellular_miRNA_rep2

address: 江苏省南通市崇川区启秀路19号

description:
Library name: SAMPLES5
Column name in miRNA_expression_quantification.txt: Fibroblast_Intracellular_miRNA_rep2


title: S09,CD3_control, rep 4

description: Library name: Sample 9


title: DSP-1001660014603-Y-B02

description: Library name: Sample 63


title: S08,CD3_control, rep 3

description: Library name: Sample 8


title: Fibroblast_Intracellular_miRNA_rep1

address: 江苏省南通市崇川区启秀路19号

description:
Library name: SAMPLES4
Column name in miRNA_expression_quantification.txt: Fibroblast_Intracellular_miRNA_rep1