title: Fibroblast_EV_miRNA_rep3

address: 江苏省南通市崇川区启秀路19号

description:
Library name: SAMPLES3
Column name in miRNA_expression_quantification.txt: Fibroblast_EV_miRNA_rep3


title: S07,CD3_control, rep 2

status: Public on Jul 15 2026

type: SRA

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

description: Library name: Sample 7

library_source: transcriptomic

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.

molecule: total RNA

organism: Homo sapiens

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).

tag: tissue

value: blood

tag: cell type

value: T-cell

tag: genotype

value: control


title: S05,CD3_CVID, rep 5

description: Library name: Sample 5

value: CVID patient


title: S06,CD3_control, rep 1

description: Library name: Sample 6


title: DSP-1001660014603-Y-B01

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 62

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

tag: treatment

value: CONTROL

tag: scan name

tag: roi

tag: segment

value: DESMIN


title: S04,CD3_CVID, rep 4

description: Library name: Sample 4


title: DSP-1001660014603-Y-A12

description: Library name: Sample 61


title: S03,CD3_CVID, rep 3

description: Library name: Sample 3


title: Fibroblast_EV_miRNA_rep2

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

country: China

institute: Nantong University

description:
Library name: SAMPLES2
Column name in miRNA_expression_quantification.txt: Fibroblast_EV_miRNA_rep2

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

tag: batch


title: DSP-1001660014603-Y-A11

description: Library name: Sample 60


title: S02,CD3_CVID, rep 2

description: Library name: Sample 2


title: Fibroblast_EV_miRNA_rep1

address: 江苏省南通市崇川区启秀路19号

description:
Library name: SAMPLES1
Column name in miRNA_expression_quantification.txt: Fibroblast_EV_miRNA_rep1


title: DSP-1001660014603-Y-A10

description: Library name: Sample 59


title: S01,CD3_CVID, rep 1

description: Library name: Sample 1


title: Mixed, barcode-transduced primary murine CD8 T cells, variable IL-2, in vitro, barcode library

city: Denver

first: Kole

middle: R

last: DeGolier

state: Colorado

address: 1400 Jackson St

department: Immunology and Genomic Medicine

institute: National Jewish Health

description:
Library name: 2025.KRD012bc
10X Genomics with custom retroviral barcoding

library_source: genomic

data_processing:
scATAC-seq files were demultiplexed using cellranger-atac mkfastq
Demultiplexed data was processed using the cellranger-atac pipeline.
Peaks were called and .bam files were generated using the ArchR pipeline (https://www.archrproject.com/bookdown/index.html).
Assembly: GRCmm10, GRChg38
Supplementary files format and content: .bam files containing peaksets called on single murine data experiment (2025.KRD012) or compiled human data experiments (KRD024, KRD029, KRD039, KRD040).

molecule: genomic DNA

organism: Mus musculus

source_name: Splenic T cells

growth_protocol:
In Vitro, Murine Cells: Mouse CAR T cells were cultured in cRPMI as described above. CD8+ T cells were isolated from 10-16 week old C57BL/6 mouse splenocytes using the MojoSort Mouse CD8 T Cell Isolation Kit (BioLegend, Cat No. 480035). On day 0, T cells were activated with 1µg/mL anti-CD3 and 1µg/mL anti-CD28 overnight. Cells were transduced on day 1 by centrifugation at 2000xg for 90 minutes at 37°C with fresh gammaretrovirus and 10ug/mL polybrene, followed by removal of retrovirus and polybrene after the spin and replacement with fresh media containing the specified amount of IL-2, either 10IU/mL or 100IU/mL (National Cancer Institute). Transduction was repeated on the following day (day 2), and then cells were removed from anti-CD3/anti-CD28 stimulation and plated at 1x106 cells/mL in fresh media containing IL-2. On day 3 and 4, cells were replated at 1x106 cells/mL in fresh media containing IL-2. For the “swap” condition, IL-2 concentration was changed from 100IU/mL to 10IU/mL. Cells were FACS sorted (Lymphocytes > Singlets > Live > CD8+ > mThy1.1+) and captured for scATAC-seq on day 5, 16 hours after the IL-2 “swap” (or media replacement for the “high” and “low” IL-2 conditions).
In Vitro, Human Cells: CD3+ human T cells were cultured in Human T Cell Expansion Media (hTCEM), consisting of AIM-V (Gibco, Cat No 12055-091) supplemented with 5% FBS and 10mM HEPES (Gibco, 15630-080). On day 0, T cells were thawed and activated with Dynabeads Human T cell Expander CD3/CD28 (Gibco, Cat No. 11141D) at a 3:1 bead:cell ratio at 1x106 cells/mL, in hTCEM supplemented with 40IU/mL IL-2 and cultured for 48 hours. On day 2, T cells were counted and transduced at 2x106 cells per well in a 6 well plate, with 10µg/mL Protamine Sulfate (Millipore-Sigma, Cat No. P4020-1G), spinning at 1000xg for 2.5 hours at 32°C. On day 3, T cells were transduced again with fresh virus. On day 4, beads were removed, and cells were plated in fresh hTCEM supplemented with 100IU/mL IL-2 at 0.5x106 cells/mL. On day 6, cells were replated at 0.5x106 cells/mL with fresh hTCEM and 100IU/mL IL-2, and a small aliquot was taken to check transduction efficiency. On day 8, cells were counted with a small aliquot taken for FACS sorting (Lymphocytes > Singlets > Live > CD4+ or CD8+ > mThy1.1+) and scATAC-seq capture (‘Pretransfer’ timepoint), with the rest cryopreserved in Freeze Media as described above.

extract_protocol:
After sorting, cells were pooled, washed once in cold PBS and then lysed in Lysis Buffer (Nuclease-Free H2O with 10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin) for the following times: 5 mins (cell lines), 3 mins (in vitro primary cells), 3 mins 45 seconds (ex vivo primary cells). Cells were then resuspended in 1X Nuclei Buffer and analyzed for nuclei count and lysis efficiency via 0.4% Trypan Blue staining on the Countess 3 (ThermoFisher), with >95% lysis efficiency typical. Cells were then diluted to ≤2.4x106 cells/mL for capture of ~8000 nuclei in a single 10X capture well, following manufacturer protocols for Chromium Next GEM Single Cell ATAC Reagent Kits v2 (10X Genomics, User Guide CG000496). Two modifications were required to this protocol for barcode enrichment, as described previously19: first, 1.32µL of 50µM spike-in barcode enrichment oligo was added to the GEM reaction master mix (step 2.1a in 10X protocol); second, the PCR following GEM generation was increased from 12 to 15 cycles (step 2.5a in 10X protocol). Libraries were prepared per manufacturer specifications and analyzed using the TapeStation (Agilent) and Qubit Fluorometer (ThermoFisher).
Final scATAC and barcode libraries were pooled to 10nM concentration for sequencing. Final concentrations for individual libraries in the pool were calculated to achieve a target sequencing depth of 40,000 reads/nuclei (scATAC library) and 1,000 reads/nuclei (barcode library).

treatment_protocol: In Vivo, Human Cells: NOD-Scid-Gamma (‘NSG’, NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ; Strain #: 005557, Jackson Laboratories) were obtained commercially and then bred in-house. For xenograft studies, between 4 and 9 male or female NSG mice (up to 20 weeks of age, same gender in a single experiment) received 1x106 NALM6-CD22Lo leukemia on day -3, followed by 1x106 CAR+ cells (pooled equally from all six CAR conditions) on day 0. Leukemia burden was monitored before CAR injection (day -1), on day 4, and on day 7 before marrow harvest, using the Xenogen In Vivo Imaging System (IVIS) Spectrum (Caliper Life Sciences) after intraperitoneal injection with D-Luciferin Potassium Salt (Revvity, Cat No. 122799A-5). Total flux (photons/s) was measured for each mouse using Living Image software (Revvity, v4.8.2). On day 7, bone marrow was harvested, filtered through a 70µm strainer, and red blood cells were lysed using ACK Lysing Buffer. Cells were then filtered again, and human cells were enriched using MojoSort Mouse CD45 Nanobead (BioLegend, Cat No. 480028) depletion of mouse bone marrow. Cells were stained and FACS sorted (Lymphocytes > Singlets > Live > CD45+/GFP- > CD4+ or CD8+ > mThy1.1+) for scATAC-seq capture (‘ex vivo’ timepoint). Xenograft animal studies were conducted at University of Colorado Anschutz Medical Campus in accordance with an animal protocol approved by the Institutional Animal Care and Use Committee (IACUC, Protocol 751).

value: Splenic T cells

value: CD8 T cell

value: WT

value: Barcoded CAR transduction


title: Mixed, barcode-transduced primary murine CD8 T cells, variable IL-2, in vitro, scATAC library

description:
Library name: 2025.KRD012
10X Genomics with custom retroviral barcoding

library_source: genomic single cell


title: Whole brain RNA-seq mouse 2225 PAP-1

city: NEW HAVEN

first: UPASNA

last: SRIVASTAVA

state: CT

address: 300 George Street , Department of Neurology, Yale School of medicine

department: Neurology

institute: YALE University

description:
Library name: 23238XR-07-12
Mouse ID: 2225; strain: not specified; RIN: 7.8

data_processing:
Reads were aligned to the Mus musculus reference genome (GRCm38/mm10) using STAR version 2.7.11a.
Gene-level counts were generated using STAR --quantMode GeneCounts.
Raw counts were imported into R version 4.3.2.
Differential expression analysis was performed using DESeq2 version 1.40.2.
Adjusted P values were calculated using the Benjamini-Hochberg method; genes with adjusted P<0.05 and |log2FC|>=0.25 were considered differentially expressed.
Assembly: GRCm38 (mm10)
Supplementary files format and content: CSV file containing raw STAR gene counts. Rows represent genes and columns represent biological samples.

source_name: Whole brain

growth_protocol: 5xFAD mice were maintained according to institutional animal care guidelines. Strain: not specified.

extract_protocol:
Total RNA was extracted from whole-brain tissue. RNA concentration was measured using the Qubit RNA High Sensitivity Assay and RNA integrity was assessed using the Agilent TapeStation. RIN values ranged from 7.8 to 8.9.
RNA sequencing libraries were prepared by Admera Health from total RNA.

treatment_protocol: Animals received Control, PBS, PAP-1 or ShK-223 treatments.

value: Whole brain

tag: mouse id

tag: strain

value: not specified

tag: rin

value: B


title: DSP-1001660014603-Y-A09

description: Library name: Sample 58


title: S524_40_choroidea_CrePos_PLX5622

city: Hamburg

first: Andreas

last: Neueder

address: Falkenried 94

department: Center for Molecular Neurobiology (ZMNH)

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Library name: S524_40_T35_23_20C_S40

data_processing:
FastQ files were quality checked with FastQC v0.11.5. All files passed QC. The reads were pseudo aligned against Ensembl mus musculus GRCm39 release vM29 and quantified using salmon v1.10.1. Counts were imported using tximport v1.24.0 into DESeq2 v1.36.0 and a intercept matrix was used to generate the normalised counts expression matrix (S524_normalized_counts.tsv)
Assembly: Ensembl mus musculus GRCm39 release vM29
Supplementary files format and content: S524_normalized_counts.tsv This file contains the normalised count matrix.

molecule: polyA RNA

source_name: choroidea

extract_protocol:
Total RNA was extracted from mouse retina and mouse choroid tissue stabilized in RNAlater buffer according to the “Purification of total RNA from animal and human tissue” protocol of the RNeasy Micro Kit (QIAGEN, Hilden, Germany). In brief, the tissue sample was stored in RNAlater and shipped at 2-8 °C. After centrifuging for 5 minutes at 5,000 x g, the RNAlater was removed and the sample was disrupted and homogenized in 350 µl RLT buffer containing 1% beta-mercaptoethanol with Precellys CK14 ceramic beads (1 cycle of 15 seconds at 5500 rpm) using a Precellys 24 Homogenisator (Bertin Corp., Rockville, MD, USA). Next the sample was centrifuged for 2 min at full speed and 350 µl of the cleared supernatant was transferred to a new tube. One volume of 70 % ethanol was added and the sample was applied to a RNeasy MinElute spin column followed by an on-column DNase digestion and several wash steps. Finally total RNA was eluted in 14 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip reagent set (Agilent, Palo Alto, CA, USA).
Library preparation and RNAseq were carried out as described in the Illumina “Stranded mRNA Prep Ligation” Reference Guide, the Illumina NextSeq 2000 Sequencing System Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA). In brief, 200 ng of total RNA was used for purifying the poly-A containing mRNA molecules using oligo(dT) magnetic beads. Following purification, the mRNA was fragmented to an average insert size of 200-400 bases using divalent cations under elevated temperature (94°C for 8 minutes). Next, the cleaved RNA fragments were reverse transcribed into first strand complementary DNA (cDNA) using reverse transcriptase and random hexamer primers. Thereby Actinomycin D was added to allow RNA-dependent synthesis and to improve strand specificity by preventing spurious DNA-dependent synthesis. Blunt-ended second strand cDNA was synthesized using DNA Polymerase I, RNase H and dUTP nucleotides. The incorporation of dUTP, in place of dTTP, quenches the second strand during the later PCR amplification, because the polymerase does not incorporate past this nucleotide. The resulting cDNA fragments were adenylated at the 3' ends and the pre-index anchors were ligated. Finally DNA libraries were created were created using a 13 cycles PCR to selectively amplify the anchor-ligated DNA fragments and to add the unique dual indexing (i7 and I5) adapters. The libraries were bead purified twice and quantified using the KAPA Library Quantification Kit. Equimolar amounts of each library were sequenced on an Illumina NextSeq 2000 instrument controlled by the NextSeq 2000 Control Software (NCS) v1.5.0.42699, using one 50 cycles P3 Flow Cell with the dual index, single-read (SR) run parameters. Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.10.30. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.

treatment_protocol: To induce choroidal neovascularization, mice were anaesthetized by intraperitoneal administration of ketamine hydrochloride  and xylazine. Pupillary dilatation was achieved by applying  tropicamide and phenylephrine hydrochloride. Six laser spots (150 mW, 100 μm and 100 ms) were applied to each eye using a frequency-doubled Nd:YAG-Laser. To induce microglia depletion mice were fed using a PLX5622 (Plexxikon Inc., Berkeley, California, USA) containing diet.

value: choroidea

value: CrePos


title: Whole brain RNA-seq mouse 2222 PAP-1

description:
Library name: 23238XR-07-11
Mouse ID: 2222; strain: not specified; RIN: 8.9

value: C


title: S524_39_choroidea_CrePos_PLX5622

description: Library name: S524_39_T35_23_19C_S39


title: DSP-1001660014603-Y-A08

description: Library name: Sample 57

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


title: S524_38_choroidea_CrePos_PLX5622

description: Library name: S524_38_T35_23_18C_S38


title: Whole brain RNA-seq mouse 2219 PAP-1

description:
Library name: 23238XR-07-10
Mouse ID: 2219; strain: not specified; RIN: 8.1


title: S524_36_choroidea_CrePos_PLX5622

description: Library name: S524_36_T35_23_16C_S36


title: Whole brain RNA-seq mouse 2210 ShK-223

description:
Library name: 23238XR-07-09
Mouse ID: 2210; strain: not specified; RIN: 8.6

value: CH


title: DSP-1001660014603-Y-A07

description: Library name: Sample 56

value: CONTROL

value: DESMIN


title: DSP-1001660014603-Y-A06

description: Library name: Sample 55


title: S524_37_choroidea_CrePos_PLX5622

description: Library name: S524_37_T35_23_17C_S37


title: S524_34_choroidea_CreNeg_PLX5622

description: Library name: S524_34_T35_23_14C_S34

value: CreNeg


title: S524_35_choroidea_CreNeg_PLX5622

description: Library name: S524_35_T35_23_15C_S35


title: S524_33_choroidea_CreNeg_PLX5622

description: Library name: S524_33_T35_23_13C_S33


title: DSP-1001660014603-Y-A05

description: Library name: Sample 54


title: Whole brain RNA-seq mouse 2208 ShK-223

description:
Library name: 23238XR-07-08
Mouse ID: 2208; strain: not specified; RIN: 8.3


title: S524_32_choroidea_CreNeg_PLX5622

description: Library name: S524_32_T35_23_12C_S32


title: Whole brain RNA-seq mouse 2207 ShK-223

description:
Library name: 23238XR-07-07
Mouse ID: 2207; strain: not specified; RIN: 8.0


title: S524_30_choroidea_CrePos_control

description: Library name: S524_30_T35_23_10C_S30

value: control


title: S524_31_choroidea_CreNeg_PLX5622

description: Library name: S524_31_T35_23_11C_S31


title: DSP-1001660014603-Y-A04

description: Library name: Sample 53


title: Whole brain RNA-seq mouse 2200 PBS

description:
Library name: 23238XR-07-06
Mouse ID: 2200; strain: not specified; RIN: 8.3

value: PBS


title: S524_28_choroidea_CrePos_control

description: Library name: S524_28_T35_23_08C_S28


title: DSP-1001660014603-Y-A03

description: Library name: Sample 52


title: S524_29_choroidea_CrePos_control

description: Library name: S524_29_T35_23_09C_S29


title: Whole brain RNA-seq mouse 2197 PBS

description:
Library name: 23238XR-07-05
Mouse ID: 2197; strain: not specified; RIN: 8.4


title: DSP-1001660014603-Y-A02

description: Library name: Sample 51


title: S524_27_choroidea_CrePos_control

description: Library name: S524_27_T35_23_07C_S27


title: S524_26_choroidea_CrePos_control

description: Library name: S524_26_T35_23_06C_S26


title: Whole brain RNA-seq mouse 2195 PBS

description:
Library name: 23238XR-07-04
Mouse ID: 2195; strain: not specified; RIN: 8.3


title: S524_24_choroidea_CreNeg_control

description: Library name: S524_24_T35_23_04C_S24


title: Whole brain RNA-seq mouse 2173 Control

description:
Library name: 23238XR-07-03
Mouse ID: 2173; strain: not specified; RIN: 8.1

value: Control


title: S524_23_choroidea_CreNeg_control

description: Library name: S524_23_T35_23_03C_S23


title: S524_25_choroidea_CreNeg_control

description: Library name: S524_25_T35_23_05C_S25


title: DSP-1001660014456-Z-E02

description: Library name: Sample 49

value: CF


title: DSP-1001660014456-Z-E03

description: Library name: Sample 50

value: Desmin


title: S524_22_choroidea_CreNeg_control

description: Library name: S524_22_T35_23_02C_S22


title: Whole brain RNA-seq mouse 2172 Control

description:
Library name: 23238XR-07-02
Mouse ID: 2172; strain: not specified; RIN: 8.6


title: S524_21_choroidea_CreNeg_control

description: Library name: S524_21_T35_23_01C_S21


title: S524_20_retina_CrePos_PLX5622

description: Library name: S524_20_T35_23_20R_S20

source_name: retina

value: retina


title: DSP-1001660014456-Z-E01

description: Library name: Sample 48


title: Whole brain RNA-seq mouse 2171 Control

description:
Library name: 23238XR-07-01
Mouse ID: 2171; strain: not specified; RIN: 8.0

value: Whole brain


title: S524_19_retina_CrePos_PLX5622

description: Library name: S524_19_T35_23_19R_S19


title: DSP-1001660014456-Z-D12

description: Library name: Sample 47


title: S524_18_retina_CrePos_PLX5622

description: Library name: S524_18_T35_23_18R_S18


title: DSP-1001660014456-Z-D11

description: Library name: Sample 46


title: S524_16_retina_CrePos_PLX5622

description: Library name: S524_16_T35_23_16R_S16


title: Bone

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: Bone

library_source: transcriptomic single cell

data_processing:
The sequencing data was first pre-processed using the 10X Genomics software Cell Ranger v10.0.0
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone

extract_protocol:
Femurs and tibias were dissected from Cxcl12-Cre;ZsGreen mice of 24-week-old. The proximal and distal metaphyses of the femurs and tibias were excised, and the diaphyseal bone tissues were immersed in Hank's balanced salt solution (HBSS). The collected tissues were enzymatically dissociated by incubation at 37 ºC for 60 min in HBSS containing 0.2% Collagenase and 0.2% Dispase. The isolated cell suspension was filtered through a 70 μm cell strainer, followed by red blood cell lysis using RBC Lysis Buffer. After washing with HBSS, the cell suspension was adjusted to 1.0 × 10⁷ cells/ml in HBSS. ZsGreen-positive cells were isolated using a BD FACSAria™ III cell sorter, and the sorted cells were resuspended in HBSS to a final concentration of 1.0 × 10⁷ cells/ml.
The sorted cell suspension was processed using the 10x Chromium X system with Chromium GEM-X Single Cell 5’ v3 reagents, according to the manufacturer’s instructions. Subsequently, reverse transcription for first-strand cDNA synthesis was performed within the GEMs to generate a single-cell library with individually barcoded cDNAs for each cell. The single-cell library was sequenced using NovaSeq X Plus.

value: Bone

value: Bone cells

value: Cxcl12-Cre;ZsGrren mice

tag: age

value: 24 weeks old

tag: Sex

value: male


title: S524_17_retina_CrePos_PLX5622

description: Library name: S524_17_T35_23_17R_S17

value: CrePos


title: S524_14_retina_CreNeg_PLX5622

description: Library name: S524_14_T35_23_14R_S14


title: S524_15_retina_CreNeg_PLX5622

description: Library name: S524_15_T35_23_15R_S15


title: DSP-1001660014456-Z-D10

description: Library name: Sample 45

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


title: Mouse testis FMRP RIP sample

city: changsha

first: tan

last: yueqiu

address: Xiangya School of Medicine, Kaifu District, Changsha, Hunan Province, China.

institute: central south of university

description:
Library name: IP1_FM_T
FMRP RNA immunoprecipitation sample from mouse testicular material. Column or sample name in processed table: IP1_FM_T.

data_processing:
Raw reads were quality-filtered and adapter-trimmed before downstream analysis.
Clean reads were aligned to the mouse reference genome GRCm38/mm10 using STAR, and aligned reads were sorted by genomic coordinates.
Gene-level counts and FMRP RIP/Input enrichment values were generated and provided in FMRP_RIPseq_gene_counts_and_enrichment.txt.gz.
Normalized genome coverage tracks were generated as bigWig files for the input and FMRP RIP samples.
Assembly: GRCm38/mm10
Supplementary files format and content: FMRP_RIPseq_gene_counts_and_enrichment.txt.gz: tab-delimited text file containing gene-level count and enrichment information for FMRP RIP-seq compared with input.
Supplementary files format and content: Input_T.bw and IP1_FM_T.bw: bigWig files containing normalized genome coverage tracks for the input and FMRP RIP samples.

source_name: testis

growth_protocol: Adult male mice were maintained under standard laboratory conditions. Testicular material was collected for RNA immunoprecipitation sequencing.

extract_protocol:
RNA was extracted from input and FMRP immunoprecipitated fractions after RNA immunoprecipitation. RNase-free conditions were maintained during sample preparation.
Sequencing libraries were prepared from RNA recovered from input and FMRP RIP fractions using a standard RNA-seq library preparation workflow and sequenced as paired-end reads.

treatment_protocol: Testicular lysates were prepared under RNA-preserving conditions. An aliquot was retained as input control, and FMRP-containing RNA-protein complexes were enriched by RNA immunoprecipitation using an anti-FMRP antibody.

value: testis

value: wild type

value: anti-FMRP RNA immunoprecipitation


title: Mouse testis input sample for FMRP RIP-seq

description:
Library name: Input_T
Input RNA sample collected prior to FMRP RNA immunoprecipitation. Column or sample name in processed table: Input_T.

value: input control for FMRP RIP-seq


title: DSP-1001660014456-Z-D09

description: Library name: Sample 44


title: S524_12_retina_CreNeg_PLX5622

description: Library name: S524_12_T35_23_12R_S12

value: CreNeg


title: S524_13_retina_CreNeg_PLX5622

description: Library name: S524_13_T35_23_13R_S13


title: DSP-1001660014456-Z-D08

description: Library name: Sample 43


title: S524_10_retina_CrePos_control

description: Library name: S524_10_T35_23_10R_S10

value: control


title: S524_11_retina_CreNeg_PLX5622

description: Library name: S524_11_T35_23_11R_S11


title: ES-treated no injury 3

city: Boston

first: Menglu

state: MA

address: 20 Staniford st

institute: Schepens Eye Research Institute, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School

description: Library name: Sample ES_no_injury_3

data_processing:
FastQC was used for quality control, Salmon 1.10.2 was used for counts and alignment, and DESeq2 was used for count normalization and statistical comparisons.
Assembly: GCRm39
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Trigeminal Ganglion

extract_protocol:
Total RNA from trigeminal ganglia tissue was extracted using Quick RNA miniprep kit (Zymo Research, Santa Cruze, CA). Messenger RNA was purified, and quality was evaluated using an Agilent Bioanalyzer, and only samples with RNA Integrity Number (RIN) >7 was used for RNA sequencing.
RNA-seq libraries were prepared by Novogene (Sacramento, CA, USA) using poly(A) enrichment and sequenced on an Illumina NovaSeqX Plus platform to generate 150 bp paired-end reads at a depth of 30 million reads per sample.

value: Trigeminal Ganglion

value: ES+no injury


title: DSP-1001660014456-Z-D07

description: Library name: Sample 42

value: CF


title: S524_09_retina_CrePos_control

description: Library name: S524_09_T35_23_09R_S09

value: retina


title: ES-treated no injury 2

description: Library name: Sample ES_no_injury_2


title: S524_08_retina_CrePos_control

description: Library name: S524_08_T35_23_08R_S08


title: ES-treated no injury 1

description: Library name: Sample ES_no_injury_1


title: S524_07_retina_CrePos_control

description: Library name: S524_07_T35_23_07R_S07


title: DSP-1001660014456-Z-D06

description: Library name: Sample 41

value: Desmin


title: ES-treated keratectomy injury 3

description: Library name: Sample ES_3

value: ES+keratectomy injury


title: S524_05_retina_CreNeg_control

description: Library name: S524_05_T35_23_05R_S05


title: S524_06_retina_CrePos_control

description: Library name: S524_06_T35_23_06R_S06


title: S524_04_retina_CreNeg_control

description: Library name: S524_04_T35_23_04R_S04


title: DSP-1001660014456-Z-D05

description: Library name: Sample 40


title: S524_03_retina_CreNeg_control

description: Library name: S524_03_T35_23_03R_S03


title: ES-treated keratectomy injury 2

description: Library name: Sample ES_2


title: DSP-1001660014456-Z-D04

description: Library name: Sample 39

value: PF


title: S524_02_retina_CreNeg_control

description: Library name: S524_02_T35_23_02R_S02


title: ES-treated keratectomy injury 1

description: Library name: Sample ES_1


title: S524_01_retina_CreNeg_control

description: Library name: S524_01_T35_23_01R_S01


title: DSP-1001660014456-Z-D03

description: Library name: Sample 38


title: CARimNKDinuNKTR

city: Valhalla

first: Wen

last: Luo

state: New York

address: 15 Dana Road

institute: New York Medical College

description: Library name: Sample 1

data_processing:
Reads were subsequently processed using the 10xGenomics Cell Ranger analytical pipeline (v6.0.1). An average of 22,740 human cells and 20,599 mouse cells were sequenced, with 4,701 postnormalization mean reads per cell. Data was further analyzed using Seurat v5 in R and filtered to remove dead cells (percent of mitochondrial reads > 20%) and doublets using cutoffs nCount_RNA < 25000, nFeature_RNA > 200 & < 5000.
Assembly: All samples were aligned to the human and mouse combined reference genome. Cells were assigned as human (or mouse) cells if greater than 75% of reads/Unique Molecular Identifiers (UMI) were aligned to human (or mouse) genome. Separated human and mouse cells were analyzed independently. Cell type assignment was performed using the singleR package.
Supplementary files format and content: Tab separated values files

source_name: Tumor

growth_protocol: A673-luc cells were implanted into the tibia (2x105 cells/site) of 4-6-weeks old female/male NSG mice (005557, Jackson Laboratory).

extract_protocol:
Tumors were dissociated using the human Tumor Dissociation Kit (130-095-929, Miltenyi Biotec) with the gentleMACS Octo Dissociator with heater according to the manufacturer’s instructions. Cell suspension was passed through a 70 mm Cell Strainer (431751, Corning, Corning, NY) and red blood cells were removed from the cell suspension using RBC Lysis Buffer (420301, BioLegend, San Diego, CA, USA). Dead cells were removed using the Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) according to the manufacturer’s instructions.
Viable cell suspensions were loaded into the Chromium Controller (10xGenomics, Pleasanton, CA, USA) to generate gel beads-in-emulsion (GEM) with each GEM containing a single cell as well as barcoded oligonucleotides. Next, the GEMs were placed in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scientific, Wilmington, DE, USA), and reverse transcription was performed in each GEM (GEMRT). After the reaction, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10X Genomics, Pleasanton, CA, USA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN, USA). Amplified full-length cDNAs from polyadenylated mRNA were then used to generate 3′ Gene Expression library (Chromium GEM-X Single Cell 3′ Reagent Kits v4) following the manufacturer’s instructions (10x Genomics, Pleasanton, CA, USA).

treatment_protocol: After validation of tumor engraftment by Xenogen In Vivo Imaging System (IVIS), PBS or NK/imNK or CAR-NK/imNK were injected (0.5-1x107 cells/animal, i.v., once a week for 6 weeks) together with or without NKTR-255 (0.3 mg/kg, i.v., once every two weeks) (generously provided by Nektar Therapeutics, San Francisco, CA) and/or dinutuximab (15 μg/animal, i.p. twice a week for 6 weeks) (generously provided by United Therapeutics, Silver Spring, MD).

value: Tumor

tag: cell line

value: Ewing sarcoma

value: WT

value: CARimNKDinuNKTR


title: keratectomy injury 3

description: Library name: Sample injury_3

value: Keratectomy injury


title: Control

description: Library name: Sample 2

value: Control


title: DSP-1001660014456-Z-D02

description: Library name: Sample 37

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


title: Retinal organoid, USH1C-1, rep3

city: Mainz

first: Kerstin

last: Nagel-Wolfrum

address: Hanns-Dieter-Hüsch-Weg 17

institute: Johannes Gutenberg University Mainz

description: Library name: Sample 7

data_processing:
Sequence quality of FastQ files was assessed via FastQC (v0.11.9). The samples were demultiplexed and analyzed using the 10X Genomics Cell Ranger software (v7.0.1; pipeline: multi). Reads were then mapped against reference genome GRCh38 (ensembl98, refdata-gex-GRCh38-2020-A) and counts were quantified using the probe set (Chromium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A) provided by 10X Genomics with default parameters. As the samples were multiplexed with other project data, sample-specific fastq files related to this manuscript were generated from the aligned BAM files using the cellranger bamtofastq pipeline (https://github.com/10XGenomics/bamtofastq). Downstream analysis was performed in a Conda environment (v24.7.1) using R (v4.3.3).
Quality control of cells and downstream analyses were conducted using the Seurat package (v5.1.0). Cells with mitochondrial gene expression levels three standard deviations above or below the median for each sample were removed. Cells whose numbers of detected transcripts were three standard deviations above or below the median per sample were excluded. Based on these quality control thresholds, 4.2% of cells were removed. Following, normalization was done using the SCTransform function (v2) of Seurat package (v0.4.1). Samples were integrated using IntegrateData and FindIntegrationAnchors function with CCA as a reduction method.
Assembly: GRCh38
Supplementary files format and content: Per-molecule information in HDF5 format

source_name: Retinal organoid

extract_protocol:
ROs were washed twice with 1 ml pre-warmed Hank’s Balanced Salt Solution (HBSS) (Thermo Fisher Scientific). For dissociation, ROs were incubated with 300 µl activated papain solution containing 8 U papain (CellSystems) and 48 µl activator consisting of 1.1 µM EDTA (Sigma-Aldrich), 5.5 mM L-cysteine (Fisher Scientific), 0.07 mM 2-mercaptoethanol (Thermo Fisher Scientific) and H2O for 40 min at 37 °C, 5% CO2. Tubes were gently inverted every 10 min and dissociation was stopped by placing the tubes on ice and adding 300 µl stop solution per RO containing DMEM/F12 + GlutaMAX, 10% FBS and 20 U/ml DNase (Sigma-Aldrich). After centrifuging at 200 × g and 4 °C for 30 s, ROs were washed with 1 ml DMEM/F12 + GlutaMAX, 10% FBS. Mechanical dissociation was performed by gently pipetting 20 times in 300 µl DMEM/F12 + GlutaMAX, 10% FBS until no clumps were visible anymore.
Fixation of single cells was performed by using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics) according to the manufacturer’s instructions. For probe hybridization and barcoding, we followed the guidelines (CG000527) of the Chromium Fixed RNA Profiling Reagent Kits, Human Transcriptome (10X Genomics). Between 284,000 and 824,000 cells per sample were used for hybridization to probe sets BC001-BC007. On average, 15,300 cells per sample were pooled for subsequent gel bead in emulsion (GEM) generation and gene expression library preparation. Library sequencing was performed in the NextSeq 2000 sequencer (Illumina), on a P3 100 flow cell, with 28 cycles for Read 1 and 90 cycles for Read 2, at the Genomics Core Facility, Institute of Molecular Biology, Mainz.

value: Retinal organoid

tag: time

value: week 35

value: male


title: Retinal organoid, USH1C-1, rep2

description: Library name: Sample 6


title: DSP-1001660014456-Z-D01

description: Library name: Sample 36


title: Retinal organoid, USH1C-1, rep1

description: Library name: Sample 5


title: keratectomy injury 2

description: Library name: Sample injury_2

value: Trigeminal Ganglion


title: keratectomy injury 1

description: Library name: Sample injury_1


title: Retinal organoid, healthy-1, rep4

description: Library name: Sample 4


title: DSP-1001660014456-Z-C12

description: Library name: Sample 35


title: Retinal organoid, healthy-1, rep3

description: Library name: Sample 3


title: non-treated control 3

description: Library name: Sample control_3

value: No treatment


title: Retinal organoid, healthy-1, rep2

description: Library name: Sample 2


title: DSP-1001660014456-Z-C11

description: Library name: Sample 34


title: Retinal organoid, healthy-1, rep1

description: Library name: Sample 1


title: non-treated control 2

description: Library name: Sample control_2


title: UC-96

first: Minyi

last: Lee

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University Chobanian & Avedisian School of Medicine

description: Library name: UC-96

data_processing:
Demultiplexing and creation of FASTQ files were automatically performed using the Illumina BaseSpace platform with default parameters.
Reads were aligned to the Genome Reference Consortium human build 38 (GRCh38) using STAR v2.6.0c.
Both gene and transcript level counts were calculated using RSEM v1.3.1 with annotation from Ensembl build 107.
Genes were filtered for analysis based on counts per million (CPM) reads mapped across all samples. Genes with CPM counts greater than 1 in more than 10% of the total number of patients were used in subsequent analyses. CPM was calculated using the calcNormFactors and cpm functions from the edgeR package (version 4.4.1).
Assembly: hg38
Supplementary files format and content: counts.tsv: tab-separated values (TSV) file containing 5737 x 120 matrix of "expected_count" values computed by RSEM

source_name: Nasal brushing

extract_protocol:
Total RNA was isolated from nasal brushings using the miRNeasy Mini Kit (Qiagen, Valencia, CA).
Libraries were generated using the Illumina TruSeq RNA Exome kit.

value: Nasal brushing

tag: subject id

tag: median tin

tag: cancer status

value: Benign

tag: gender

tag: smoking status

value: CURRENT

tag: sequencing batch


title: UC-94

description: Library name: UC-94

tag: tissue

value: female

value: FORMER


title: DSP-1001660014456-Z-C10

description: Library name: Sample 33

tag: panel (wta_+ipa)

tag: treatment

value: PF

tag: scan name

tag: roi

value: Desmin


title: non-treated control 1

description: Library name: Sample control_1

tag: genotype


title: UC-154

description: Library name: UC-154

value: Metastatic


title: DSP-1001660014456-Z-C09

description: Library name: Sample 32

tag: segment


title: UC-152

description: Library name: UC-152

tag: age

value: NEVER


title: UC-138

description: Library name: UC-138


title: DSP-1001660014456-Z-C08

description: Library name: Sample 31


title: UC-125

description: Library name: UC-125


title: EMT6 cells, DMSO

city: Jinan

first: Wenhao

last: Li

address: Wenhua Xi Road No. 107

institute: Qilu Hospital of Shandong University

description: Library name: Sample 3

data_processing:
Reads were trimmed to remove adaptor sequences using the Cutadapt software to obtain high–quality reads in FASTQ format.
Bowtie2 software was used to align the high–quality reads to the mouse mm10 genome.
DeepTools v2.0.7 was used to map the read density distribution in the ±3 kb regions around the transcription start site (TSS) of each gene.
A sliding window method was used to statistically analyze read abundance across the whole genome.
ATAC–seq–enriched picks were identified using MACS2 v2.1.1.
Assembly: mm10
Supplementary files format and content: bigwig, sample peaks

growth_protocol: EMT6 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were centrifuged, washed once with cold PBS, and resuspended in cold lysis buffer. After removal of the supernatant, the cell nuclei were resuspended in the transposition reaction system containing Tn5 Transposase, and the DNA were purified after incubation at 37℃ for 30 minutes.
The PCR reaction mixture was prepared with the purified DNA, and PCR amplification was performed. The final DNA libraries were sequenced on an Illumina NovaSeq X plus platform (Tsingke Biotech) after the DNA purification.

treatment_protocol: EMT6 cells were infected with lentivirus and selected by puromycin for stably expressing shCtrl or shKdm3b. EMT6 cells were treated with DMSO or P3FI-90 (10 μM) for 24 h.

tag: cell type

value: mouse mammary gland epithelial cancer cell

value: DMSO


title: UC-123

description: Library name: UC-123


title: DSP-1001660014456-Z-C07

description: Library name: Sample 30

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


title: UC-121

description: Library name: UC-121

value: Cancer


title: EMT6 cells, shKdm3b

description: Library name: Sample 2

tag: cell line

value: Kdm3b knockdown


title: UC-119

description: Library name: UC-119

value: male


title: DSP-1001660014456-Z-C06

description: Library name: Sample 29


title: UC-118

description: Library name: UC-118


title: EMT6 cells, shCtrl

description: Library name: Sample 1

value: shCtrl


title: UC-114

description: Library name: UC-114


title: DSP-1001660014456-Z-C05

description: Library name: Sample 28

value: IA


title: UC-108

description: Library name: UC-108

value: Nasal brushing


title: UC-60

description: Library name: UC-60

value: Benign


title: E14 TKO AEBP2 Short rescue Day4 RNA rep4

city: Seoul

first: Yingying

state: Seoul

address: 103 Daehak-ro

department: Department of Biomedical Sciences

country: South Korea

institute: Seoul National University

description: Library name: E14_TKO_AEBP2_Short_rescue_Day4_RNA_rep4

data_processing:
CUTnTag: Adaptor sequences were trimmed using Cutadapt, and the filtered reads were aligned to the mouse reference genome (mm10) with Bowtie2 using default parameters. Duplicate reads were identified and removed with Samtools markdup. Reads that failed to align to the mouse genome were subsequently mapped to the Drosophila genome (dm6), and the number of Drosophila-mapped reads was used to calculate the spike-in normalization factor.  ChIP-seq: and Libraries were prepared with NEB DNA library prep kit (NEB, E7645L) following the manufacturer’s protocol. Libraries were validated using the Tapestation HS D5000 screen tape.  RNA-seq: Adapter sequences were trimmed using Trimmomatic and reads were aligned to the hg38 reference genome using HISAT2. Transcript assembly was performed with StringTie for downstream analysis. Differential gene expression analysis was carried out using DESeq2 with p-value < 0.05 and log2 |fold change| > 1.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x antibiotics/antimycotics, 1x MEM non-Essential Amino Acids, 10mM 2-Mercaptoethanol, Leukemia inhibitory Factor, 1mM MEK1/2 inhibitor (PD0325901), 3mM GSK3 inhibitor (CHIR99021). Cells were cultured at 37°C at 5% CO2.

extract_protocol:
CUTnTag: CUT&Tag was carried out following the Epicypher protocol.  ChIP-seq: 3 x 106 cells were harvested and fixed sequentially with 2mM disuccinimidyl glutarate (DSG; Thermo Fisher, 20593) for 35 minutes followed by 1% formaldehyde for 10 minutes at room temperature. Crosslinking was quenched with 0.125M glycine, and nuclei were isolated in NE buffer and extracted nuclei were then resuspended 1% SDS lysis buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS) and sonicated by Covaris S220 sonicator (Power 175 W, Duty 10%, 200 cycles per burst) for 430 seconds to generate DNA fragments of approximately 200bp. Sheared chromatin was diluted in ChIP dilution buffer (16.7 mM Tris-HCl, pH 8.0, 0.01% SDS, 1.1% Triton X-100, 16.7 mM NaCl, 1.2 mM EDTA) and clarified by centrifugation at 13,000 rpm for 15 minutes at 4 °C. Chromatin was incubated overnight at 4 °C with Dynabeads protein A pre-bound to 2.4mg target antibody. 1 µg of Drosophila chromatin (Active Motif, #53083) and 0.1 µg of anti-Drosophila H2A.X antibody (Active Motif, #61686) were added per reaction to perform spike-in normalization. The next day, Dynabeads were washed three times with buffer A (140mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 10mM Tris-HCl pH 8), twice with buffer B (300mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 1% Triton X-100, 0.2% SDS, 0.1% sodium deoxycholate, 10mM Tris-HCl pH 8) and once with buffer C (250 mM LiCl, 10mM Tris-HCl pH 8, 1mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate). RNA was removed by treatment with RNAse A at 37 °C for 30 minutes and crosslinks were reversed overnight at 65 °C in the presence of Proteinase K and SDS treatment. Eluted DNAs were size selected using SPRIselect beads (Beckman B23319).  RNA-seq: cells were resuspended in 1 ml of Trizol (ThermoFisher, 15596026) and incubated for 5 minutes at room temperature. Then, 0.2 ml of Chloroform (Sigma, C2432) was added and the solution was vortexed vigorously. The mixture was centrifuged at 13,000 rpm for 15 minutes at 4°C, and the upper phase was transferred to a fresh tube. RNA was precipitated using isopropanol (Duksan, 857) and washed with ice-cold 70% ethanol (Sigma, E7023). The precipitated RNA was dissolved in DEPC-treated water (Invitrogen, AM9915G).
CUTnTag: The eluted DNA was amplified using 2x PCR master mix (Epicypher, 15-1018) with i5 and barcoded i7 primers. Subsequently, library DNA was purified with SPRIselect beads (Beckman B23319) ).  ChIP-seq: and Libraries were prepared with NEB DNA library prep kit (NEB, E7645L) following the manufacturer’s protocol. Libraries were validated using the Tapestation HS D5000 screen tape.  RNA-seq: Library preparation was performed using TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit (Illumina, RS-122-2301).

value: Mouse embryonic stem cell

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-short rescue


title: DSP-1001660014456-Z-C04

description: Library name: Sample 27


title: UC-333

description: Library name: UC-333

value: female

value: FORMER


title: E14 TKO AEBP2 Short rescue Day4 RNA rep3

description: Library name: E14_TKO_AEBP2_Short_rescue_Day4_RNA_rep3


title: UC-330

description: Library name: UC-330


title: UC-319

description: Library name: UC-319

value: CURRENT


title: DSP-1001660014456-Z-C03

description: Library name: Sample 26


title: UC-267

description: Library name: UC-267

value: Metastatic


title: E14 TKO AEBP2 Long rescue Day4 RNA rep4

description: Library name: E14_TKO_AEBP2_Long_rescue_Day4_RNA_rep4

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-long rescue


title: DSP-1001660014456-Z-C02

description: Library name: Sample 25


title: E14 TKO AEBP2 Long rescue Day4 RNA rep3

description: Library name: E14_TKO_AEBP2_Long_rescue_Day4_RNA_rep3


title: UC-228

description: Library name: UC-228


title: UC-221

description: Library name: UC-221


title: DSP-1001660014456-Z-C01

description: Library name: Sample 24


title: UC-177

description: Library name: UC-177

value: NEVER


title: E14 TKO Day4 RNA rep4

description: Library name: E14_TKO_Day4_RNA_rep4

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- (triple knockout)


title: UC-149

description: Library name: UC-149


title: DSP-1001660014456-Z-B12

description: Library name: Sample 23

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


title: UC-146

description: Library name: UC-146

value: Cancer


title: E14 TKO Day4 RNA rep3

description: Library name: E14_TKO_Day4_RNA_rep3


title: UC-134

description: Library name: UC-134


title: E14 WT Day4 RNA rep4

description: Library name: E14_WT_Day4_RNA_rep4

value: Wild type


title: DSP-1001660014456-Z-B11

description: Library name: Sample 22


title: UC-130

description: Library name: UC-130

value: male


title: UC-342

description: Library name: UC-342


title: DSP-1001660014456-Z-B10

description: Library name: Sample 21

value: PF

value: Desmin


title: UC-340

description: Library name: UC-340

value: Nasal brushing


title: E14 WT Day4 RNA rep3

description: Library name: E14_WT_Day4_RNA_rep3


title: UC-337

description: Library name: UC-337


title: DSP-1001660014456-Z-B09

description: Library name: Sample 20


title: UC-306

description: Library name: UC-306


title: E14 TKO AEBP2 Short rescue Day0 RNA rep3

description: Library name: E14_TKO_AEBP2_Short_rescue_Day0_RNA_rep3


title: UC-3

description: Library name: UC-3

value: Benign


title: DSP-1001660014456-Z-B08

description: Library name: Sample 19


title: UC-283

description: Library name: UC-283


title: E14 TKO AEBP2 Long rescue Day0 RNA rep3

description: Library name: E14_TKO_AEBP2_Long_rescue_Day0_RNA_rep3

value: Mouse embryonic stem cell


title: UC-282

description: Library name: UC-282


title: UC-194

description: Library name: UC-194


title: UC-226

description: Library name: UC-226


title: E14 TKO Day0 RNA rep3

description: Library name: E14_TKO_Day0_RNA_rep3


title: DSP-1001660014456-Z-B07

description: Library name: Sample 18

value: IA


title: UC-139

description: Library name: UC-139

value: female


title: E14 WT Day0 RNA rep3

description: Library name: E14_WT_Day0_RNA_rep3


title: UC-111

description: Library name: UC-111


title: DSP-1001660014456-Z-B06

description: Library name: Sample 17


title: DSP-1001660014456-Z-B05

description: Library name: Sample 16

value: CF


title: UC-105

description: Library name: UC-105

value: FORMER


title: E14 TKO AEBP2 Short rescue ChIP IgG rep1

description: Library name: E14_TKO_AEBP2_Short_rescue_ChIP_IgG_rep1

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-short rescue


title: UC-327

description: Library name: UC-327

value: Metastatic


title: UC-325

description: Library name: UC-325

value: NEVER


title: DSP-1001660014456-Z-B04

description: Library name: Sample 15


title: E14 TKO AEBP2 Long rescue ChIP IgG rep1

description: Library name: E14_TKO_AEBP2_Long_rescue_ChIP_IgG_rep1

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-long rescue


title: UC-313

description: Library name: UC-313


title: UC-311

description: Library name: UC-311


title: DSP-1001660014456-Z-B03

description: Library name: Sample 14

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


title: UC-310

description: Library name: UC-310

value: Cancer


title: E14 TKO ChIP IgG rep2

description: Library name: E14_TKO_ChIP_IgG_rep2

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- (triple knockout)


title: UC-308

description: Library name: UC-308


title: DSP-1001660014456-Z-B01

description: Library name: Sample 12


title: E14 WT ChIP IgG rep1

description: Library name: E14_WT_ChIP_IgG_rep1

value: Wild type


title: UC-293

description: Library name: UC-293


title: E14 TKO AEBP2 Short rescue ChIP SUZ12 rep2

description: Library name: E14_TKO_AEBP2_Short_rescue_ChIP_SUZ12_rep2


title: DSP-1001660014456-Z-A12

description: Library name: Sample 11


title: UC-280

description: Library name: UC-280


title: UC-288

description: Library name: UC-288

value: male


title: UC-274

description: Library name: UC-274


title: E14 TKO AEBP2 Short rescue ChIP SUZ12 rep1

description: Library name: E14_TKO_AEBP2_Short_rescue_ChIP_SUZ12_rep1


title: UC-266

description: Library name: UC-266


title: UC-263

description: Library name: UC-263


title: DSP-1001660014456-Z-A11

description: Library name: Sample 10

value: Desmin


title: E14 TKO AEBP2 Long rescue ChIP SUZ12 rep2

description: Library name: E14_TKO_AEBP2_Long_rescue_ChIP_SUZ12_rep2


title: UC-257

description: Library name: UC-257

value: Nasal brushing


title: E14 TKO AEBP2 Long rescue ChIP SUZ12 rep1

description: Library name: E14_TKO_AEBP2_Long_rescue_ChIP_SUZ12_rep1


title: UC-255

description: Library name: UC-255

value: Benign


title: DSP-1001660014456-Z-A10

description: Library name: Sample 9


title: UC-253

description: Library name: UC-253


title: DSP-1001660014456-Z-A09

description: Library name: Sample 8


title: UC-251

description: Library name: UC-251

value: CURRENT


title: UC-249

description: Library name: UC-249


title: E14 TKO ChIP SUZ12 rep2

description: Library name: E14_TKO_ChIP_SUZ12_rep2

value: Mouse embryonic stem cell


title: DSP-1001660014456-Z-A08

description: Library name: Sample 7


title: UC-246

description: Library name: UC-246


title: UC-244

description: Library name: UC-244

value: female


title: E14 TKO ChIP SUZ12 rep1

description: Library name: E14_TKO_ChIP_SUZ12_rep1


title: UC-242

description: Library name: UC-242


title: DSP-1001660014456-Z-A07

description: Library name: Sample 6

value: PF


title: UC-240

description: Library name: UC-240

value: FORMER


title: E14 WT ChIP SUZ12 rep2

description: Library name: E14_WT_ChIP_SUZ12_rep2


title: UC-238

description: Library name: UC-238


title: UC-236

description: Library name: UC-236


title: DSP-1001660014456-Z-A06

description: Library name: Sample 5


title: DSP-1001660014456-Z-B02

description: Library name: Sample 13

value: CF


title: E14 WT ChIP SUZ12 rep1

description: Library name: E14_WT_ChIP_SUZ12_rep1


title: UC-234

description: Library name: UC-234


title: DSP-1001660014456-Z-A05

description: Library name: Sample 4


title: E14 TKO AEBP2 Short rescue Day4 CUTnTag H3K27me3 rep2

description: Library name: E14_TKO_AEBP2_Short_rescue_Day4_CUTnTag_H3K27me3_rep2

data_processing:
CUTnTag: Adaptor sequences were trimmed using Cutadapt, and the filtered reads were aligned to the mouse reference genome (mm10) with Bowtie2 using default parameters. Duplicate reads were identified and removed with Samtools markdup. Reads that failed to align to the mouse genome were subsequently mapped to the Drosophila genome (dm6), and the number of Drosophila-mapped reads was used to calculate the spike-in normalization factor.  ChIP-seq: and Libraries were prepared with NEB DNA library prep kit (NEB, E7645L) following the manufacturer’s protocol. Libraries were validated using the Tapestation HS D5000 screen tape.  RNA-seq: Adapter sequences were trimmed using Trimmomatic and reads were aligned to the hg38 reference genome using HISAT2. Transcript assembly was performed with StringTie for downstream analysis. Differential gene expression analysis was carried out using DESeq2 with p-value < 0.05 and log2 |fold change| > 1.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-short rescue


title: UC-230

description: Library name: UC-230

value: Metastatic


title: UC-224

description: Library name: UC-224

value: NEVER


title: DSP-1001660014456-Z-A04

description: Library name: Sample 3

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


title: E14 TKO AEBP2 Short rescue Day4 CUTnTag H3K27me3 rep1

description: Library name: E14_TKO_AEBP2_Short_rescue_Day4_CUTnTag_H3K27me3_rep1


title: UC-215

description: Library name: UC-215


title: DSP-1001660014456-Z-A03

description: Library name: Sample 2


title: UC-213

description: Library name: UC-213


title: E14 TKO AEBP2 Long rescue Day4 CUTnTag H3K27me3 rep2

description: Library name: E14_TKO_AEBP2_Long_rescue_Day4_CUTnTag_H3K27me3_rep2

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-long rescue


title: UC-212

description: Library name: UC-212

value: Not Collected


title: DSP-1001660014456-Z-A02

description: Library name: Sample 1


title: UC-210

description: Library name: UC-210

value: Cancer


title: E14 TKO AEBP2 Long rescue Day4 CUTnTag H3K27me3 rep1

description: Library name: E14_TKO_AEBP2_Long_rescue_Day4_CUTnTag_H3K27me3_rep1


title: UC-208

description: Library name: UC-208


title: HUVEC shScramble vehicle treated 48h n3

first: Maximiliano

last: Arce

address: Dag Hammarskolds väg 20

country: Sweden

institute: Uppsala University

description: Library name: Sample 12

data_processing:
The quality control and adapter sequences were trimmed using Trim Galore (version: 0.6.7) with stringency of 3 base pair. Then trimmed paired-end reads were mapped to the human reference genome (GRCh38) using STAR aligner (version: 2.7.10a). The mapped reads were assigned to their target genes as expression values using “featureCounts” function in subread (version 2.0.2).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: umbilical cord

growth_protocol: HUVECs were grown in MV2 media (PromoCell) in collagen I coated plates until they reached 100% confluency

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen)
Sequencing libraries were prepared from 500ng total RNA. Paired-end 150bp read length, NovaSeq 6000 system, SP flowcell and v1.5 sequencing chemistry. using the TruSeq stranded mRNA library preparation kit (cat# 20020595, Illumina Inc.) including polyA selection. Unique dual indexes (cat# 20022371, Illumina Inc.) were used. The library preparation was performed according to the manufacturers’ protocol (#1000000040498)

treatment_protocol: Dabrafenib was added into MV2 full media at a final concentration of 5µM. DMSO was used as a vehicle.

value: umbilical cord

value: HUVEC

value: venous endothelial cell

value: WT

value: DMSO

tag: batch


title: EMT6 cells, P3FI-90

description: Library name: Sample 4

value: mouse mammary gland epithelial cancer cell


title: UC-203

description: Library name: UC-203

value: Nasal brushing

tag: subject id

value: Benign

value: male


title: E14 TKO Day4 CUTnTag H3K27me3 rep2

description: Library name: E14_TKO_Day4_CUTnTag_H3K27me3_rep2

value: Mouse embryonic stem cell

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- (triple knockout)


title: UC-201

description: Library name: UC-201

tag: median tin

value: female


title: UC-200

description: Library name: UC-200

tag: cancer status

value: FORMER


title: HUVEC shScramble vehicle treated 48h n2

description: Library name: Sample 11


title: UC-191

description: Library name: UC-191

value: Metastatic

tag: gender

value: NEVER


title: E14 TKO Day4 CUTnTag H3K27me3 rep1

description: Library name: E14_TKO_Day4_CUTnTag_H3K27me3_rep1


title: HUVEC shScramble vehicle treated 48h n1

description: Library name: Sample 10


title: UC-189

description: Library name: UC-189

tag: smoking status


title: UC-188

description: Library name: UC-188

tag: sequencing batch


title: E14 WT Day4 CUTnTag H3K27me3 rep2

description: Library name: E14_WT_Day4_CUTnTag_H3K27me3_rep2

value: Wild type


title: HUVEC shScramble dabrafenib treated 48h n3

description: Library name: Sample 9

tag: tissue

value: dabrafenib


title: UC-185

description: Library name: UC-185


title: E14 WT Day4 CUTnTag H3K27me3 rep1

description: Library name: E14_WT_Day4_CUTnTag_H3K27me3_rep1


title: UC-183

description: Library name: UC-183

value: Cancer


title: UC-181

description: Library name: UC-181


title: UC-179

description: Library name: UC-179


title: HUVEC shScramble dabrafenib treated 48h n2

description: Library name: Sample 8

value: umbilical cord

value: HUVEC


title: E14 TKO AEBP2 Short rescue CUTnTag H3K4me3 rep2

description: Library name: E14_TKO_AEBP2_Short_rescue_CUTnTag_H3K4me3_rep2

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-short rescue


title: UC-175

description: Library name: UC-175


title: HUVEC shScramble dabrafenib treated 48h n1

description: Library name: Sample 7

value: venous endothelial cell

value: WT


title: E14 TKO AEBP2 Short rescue CUTnTag H3K4me3 rep1

description: Library name: E14_TKO_AEBP2_Short_rescue_CUTnTag_H3K4me3_rep1


title: UC-172

description: Library name: UC-172

value: Nasal brushing


title: HUVEC shCCM3 vehicle treated 48h n3

description: Library name: Sample 6

value: CCM3 knockdown

value: DMSO


title: UC-170

description: Library name: UC-170

value: male


title: UC-168

description: Library name: UC-168


title: E14 TKO AEBP2 Long rescue CUTnTag H3K4me3 rep2

description: Library name: E14_TKO_AEBP2_Long_rescue_CUTnTag_H3K4me3_rep2

value: Mouse embryonic stem cell

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-long rescue


title: UC-166

description: Library name: UC-166

value: Benign


title: HUVEC shCCM3 vehicle treated 48h n2

description: Library name: Sample 5


title: UC-164

description: Library name: UC-164

value: FORMER


title: E14 TKO AEBP2 Long rescue CUTnTag H3K4me3 rep1

description: Library name: E14_TKO_AEBP2_Long_rescue_CUTnTag_H3K4me3_rep1


title: UC-162

description: Library name: UC-162

value: female

value: NEVER


title: HUVEC shCCM3 vehicle treated 48h n1

description: Library name: Sample 4


title: E14 TKO CUTnTag H3K4me3 rep2

description: Library name: E14_TKO_CUTnTag_H3K4me3_rep2

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- (triple knockout)


title: treat7D

city: 重庆

first: cc

last: z

address: 沙坪坝区高滩岩正街30号

institute: 陆军军医大学

description: Library name: Sample9

data_processing:
The raw gene expression matrix generated from each sample were aggregated using CellRanger(v5.0.1) provided on the 10x genomics website.
Downstream analysis was done using the R package Seurat (v 3.2.0);
Quality control was applied to cells based on number of detected genes and proportion of mitochondrial reads per cell
Assembly: ftp://ftp.ensembl.org/pub/release-102/fasta/rattus_norvegicus/
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus

source_name: bile duct

extract_protocol:
Bile duct samples were rinsed twice with Dulbecco's modified Eagle’s medium (DMEM) (Gibco, Grand Island, NY, USA) and cut into 1 mm3 pieces. Next, 5 mL of a mixed digestion enzyme solution (0.03% collagenase type I (Gibco), 0.05% collagenase type IV (Gibco), 0.05% dispase, 0.01% DNase I) was added, and the tissues were incubated at 37°C for 50-70 minutes. The reaction was stopped with DMEM containing 10% fetal bovine serum (FBS) (Gibco) and the sample was filtered through a 40 µm nylon mesh cell strainer. The precipitate was centrifuged at 350 x g for 5 minutes, and washed twice with DMEM containing 10% FBS. The cells were lysed with red Puregene RBC Lysis Solution (Qiagen, Duesseldorf, Germany) for 5 minutes at room temperature, and then dead cells and debris were removed with a Miltenyi Biotec Dead Cell Removal Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). The live cell rate was assessed using trypan blue staining, with a minimum requirement of 85%.
The 10x Genomics Chromium is based on GemCode technology and allows high-throughput single-cell 3' mRNA quantitative analysis in which describes intercellular heterogeneity. The cell suspension is stained with 0.4% trypan blue to assess cell viability under microscopic observation. Cells with greater than 80% viability are qualified for library construction process. Prepared single-cell suspension is then partitioned into GEMs (Gel Beads in Emulsions) in the automated Chromium Controller, and then mRNAs are reverse transcribed into cDNAs. The GEMs is broken and purified for a fixed period of time. A certain amount of cDNA amplified products is taken and subjected to fragmentation, end repair and addition of “A” base at the 3'-end of each strand. After that, the products are purified. The cDNAs are subjected to adaptor ligation and purified. The cDNA with adaptor is amplified via PCR and the products are subjected to library quality control. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: bile duct


title: HUVEC shCCM3 dabrafenib treated 48h n3

description: Library name: Sample 3

value: umbilical cord

value: dabrafenib


title: UC-90

description: Library name: UC-90

value: Metastatic


title: E14 TKO CUTnTag H3K4me3 rep1

description: Library name: E14_TKO_CUTnTag_H3K4me3_rep1


title: treat3D

address: 沙坪坝区高滩岩正街30号

description: Library name: Sample8


title: UC-85

description: Library name: UC-85

value: Cancer


title: HUVEC shCCM3 dabrafenib treated 48h n2

description: Library name: Sample 2

value: HUVEC

value: venous endothelial cell


title: E14 WT CUTnTag H3K4me3 rep2

description: Library name: E14_WT_CUTnTag_H3K4me3_rep2

value: Wild type


title: treat1D

address: 沙坪坝区高滩岩正街30号

description: Library name: Sample7


title: HUVEC shCCM3 dabrafenib treated 48h n1

description: Library name: Sample 1

value: CCM3 knockdown


title: UC-38

description: Library name: UC-38

value: Nasal brushing


title: E14 WT CUTnTag H3K4me3 rep1

description: Library name: E14_WT_CUTnTag_H3K4me3_rep1

value: Mouse embryonic stem cell


title: UC-30

description: Library name: UC-30


title: ctrl7D

address: 沙坪坝区高滩岩正街30号

description: Library name: Sample6


title: TRI-LC21 Cell line, rep3

city: Chengdu

first: Hao

address: Xinchuan road

institute: Sichuan university

description: Library name: TRI-LC21-3

data_processing:
Raw sequencing reads were subjected to quality control and aligned to the human reference genome using standard RNA-seq analysis pipelines. Gene expression levels were quantified and normalized. Differential expression analysis was performed between TRI-LC21 and BEAS-2B samples to identify significantly upregulated and downregulated genes. Gene set enrichment analysis (GSEA) was conducted to identify pathways associated with transcriptional changes.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from TRI-LC21 and BEAS-2B cells using standard RNA extraction procedures according to the manufacturer’s instructions.
RNA-seq libraries were prepared using standard protocols provided by the sequencing service provider (Novogene). Briefly, mRNA was enriched, fragmented, and reverse-transcribed into cDNA, followed by adapter ligation and PCR amplification to generate sequencing libraries.


title: ELKO_rep3

city: Chongqing

first: Hongsheng

last: Zhang

address: 1 Youyi Road, Yuzhong District

institute: Chongqing Medical University

description: Library name: ELKO3

data_processing:
The raw data were downloaded in FASTQ format. Quality control of the raw sequencing data was performed using FastQC (v0.11.9). Trimmomatic (v0.39) was used for trimming sequences to remove low-quality bases, adapter sequences, and repetitive sequences. The parameters used were PE, -threads 50, TruSeq3-PE-2. fa: 2:30:10:2, LEADING:3, TRAILING:3, MINLEN:36, HEADCROP:15. HISAT2 (v2.2.1) was used to align the sequencing data to the mouse reference genome (GRCm38), generating output in BAM format. The BAM files were sorted using samtools (v1.16.1). Gene quantification was performed using featureCounts (v2.0.3) with the parameters -p, --countReadPairs, -T 32, -s 0, -t exon, -g gene_name. Differential gene expression analysis was conducted using DESeq2 (v1.38.3). KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway and Gene Set Enrichment Analysis (GSEA) were performed using the richR (v0.0.34) package.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include rlogTransformed values for each Sample.

source_name: thalamus

extract_protocol:
RNA was harvested using trizol (Abclonal).
The extracted RNA was quantified, with concentration > 50 ng/µL, total RNA > 500 ng, and OD260/280 > 1.8. Samples meeting these criteria were used for library preparation and sequencing.

value: thalamus

value: ELKO


title: UC-28

description: Library name: UC-28

value: male

value: FORMER


title: ELKO_rep2

description: Library name: ELKO2


title: ctrl3D

address: 沙坪坝区高滩岩正街30号

description: Library name: Sample5


title: TRI-LC21 Cell line, rep2

description: Library name: TRI-LC21-2


title: ctrl1D

address: 沙坪坝区高滩岩正街30号

description: Library name: Sample4


title: TRI-LC21 Cell line, rep1

description: Library name: TRI-LC21-1


title: UC-24

description: Library name: UC-24

value: female


title: ELKO_rep1

description: Library name: ELKO1


title: sham3

address: 沙坪坝区高滩岩正街30号

description: Library name: Sample3


title: BEAS-2B Cell line, rep3

description: Library name: BEAS-2B-3


title: UC-160

description: Library name: UC-160

value: NEVER


title: EL_rep3

description: Library name: EL3

value: EL


title: sham2

address: 沙坪坝区高滩岩正街30号

description: Library name: Sample2

value: bile duct


title: UC-156

description: Library name: UC-156

value: Benign


title: BEAS-2B Cell line, rep2

description: Library name: BEAS-2B-2


title: EL_rep2

description: Library name: EL2


title: BEAS-2B Cell line, rep1

description: Library name: BEAS-2B-1


title: UC-147

description: Library name: UC-147

value: Metastatic


title: sham1

address: 沙坪坝区高滩岩正街30号

description: Library name: Sample1


title: EL_rep1

description: Library name: EL1


title: KMS-34-DMSO-Day7-Rep2

city: San Diego

first: Bo

last: Hu

address: 10300 Campus Point Dr

institute: Bristol Myers Squibb

description: Library name: KMS-34-DMSO-Day7-Rep2-RNAseq

data_processing:
Adapter sequences and low-quality bases were removed from paired-end RNA-seq FASTQ files using cutadapt
Trimmed paired-end reads were aligned using STAR v2.6.0c to the GRCh38 reference genome with ERCC spike-in sequences, using gene annotation from Ensembl release 91
STAR was run to generate coordinate-sorted genomic BAM files, as well as transcriptome alignments and gene-level counts
Duplicate reads were marked using Picard MarkDuplicates. Duplicate reads were flagged in the BAM file but not removed
Gene-level read counts were generated from aligned reads using featureCounts with GENCODE gene annotation
Assembly: hg38
Supplementary files format and content: TSV of gene counts

source_name: Bone marrow

growth_protocol: Cell lines were maintained in standard mammalian aseptic cell culture conditions at 37 °C and 5% CO2. All cell lines used in this study were cultured in RPMI 1640 supplemented with 10% heat-inactivated Fetal Bovine Serum (Gibco) and 10U/ml penicillin, 10ug/mL streptamycin

extract_protocol:
Purified total RNA from 2 million cells was sent to Azenta for Poly(A) RNA library preparation, with ERCC spike-in, using the Illumina Stranded mRNA Preparation protocol. Total RNA yield and quality was assessed using Qubit™ RNA HS Assay Kit (Q32855, ThermoFisher) and TapeStation High Sensitivity RNA ScreenTape (5067-5579, Agilent)
NGS libraries were pooled in equal quantity and sequenced at the Azenta NextGen DNA sequencing core using the NovaSeq 6000 (Illumina) to produce 20 million paired-end reads (50x50 bases) per each RNA-Seq library

treatment_protocol: Drug treatments or DMSO vehicle were administered to exponentially growing cells in fresh media at indicated concentrations. Cells were washed and diluted in fresh media containing compounds every 3-4 days over which the number of doublings were calculated from cell counts measured using Vi-CELL XR (Beckmann Coulter, CA).

value: Bone marrow

value: Multiple myeloma

value: DMSO

tag: time point


title: UC-141

description: Library name: UC-141


title: octuple-3

city: Liaocheng

first: Lu-shen

address: Hunan street

institute: Liaocheng University

description: Library name: Sample 12

data_processing:
Raw reads of fastq format  were processed using fastp1 and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq25. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Assembly: Araport11
Supplementary files format and content: Tab-delimited text files containing raw counts of RNA-seq reads per gene and per sample.

organism: Arabidopsis thaliana

source_name: Aerial parts of seedlings

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

value: Aerial parts of seedlings


title: 5ELKO_rep4

description: Library name: 5ELKO4


title: KMS-34-DMSO-Day7-Rep1

description: Library name: KMS-34-DMSO-Day7-Rep1-RNAseq

tag: treatment


title: UC-135

description: Library name: UC-135


title: octuple-2

description: Library name: Sample 11


title: 5ELKO_rep3

description: Library name: 5ELKO3


title: KMS-34-DMSO-Day14-Rep2

description: Library name: KMS-34-DMSO-Day14-Rep2-RNAseq


title: UC-109

description: Library name: UC-109

value: CURRENT


title: octuple-1

description: Library name: Sample 10


title: 5ELKO_rep2

description: Library name: 5ELKO2


title: quintuple-3

description: Library name: Sample 9


title: UC-91

description: Library name: UC-91

value: Nasal brushing


title: KMS-34-DMSO-Day14-Rep1

description: Library name: KMS-34-DMSO-Day14-Rep1-RNAseq


title: 5ELKO_rep1

description: Library name: 5ELKO1


title: quintuple-2

description: Library name: Sample 8


title: KMS-34-1uM-Day7-Rep2

description: Library name: KMS-34-1uM-Day7-Rep2-RNAseq


title: 5EL_rep5

description: Library name: 5EL5


title: UC-80

description: Library name: UC-80


title: KMS-34-1uM-Day7-Rep1

description: Library name: KMS-34-1uM-Day7-Rep1-RNAseq


title: quintuple-1

description: Library name: Sample 7


title: UC-82

description: Library name: UC-82

value: Cancer


title: 5EL_rep4

description: Library name: 5EL4

value: thalamus


title: triple-3

description: Library name: Sample 6


title: KMS-34-1uM-Day14-Rep2

description: Library name: KMS-34-1uM-Day14-Rep2-RNAseq


title: UC-78

description: Library name: UC-78


title: 5EL_rep3

description: Library name: 5EL3


title: triple-2

description: Library name: Sample 5


title: KMS-34-1uM-Day14-Rep1

description: Library name: KMS-34-1uM-Day14-Rep1-RNAseq


title: UC-64

description: Library name: UC-64


title: KMS-34-100nM-Day7-Rep2

description: Library name: KMS-34-100nM-Day7-Rep2-RNAseq


title: 5EL_rep2

description: Library name: 5EL2


title: UC-62

description: Library name: UC-62


title: triple-1

description: Library name: Sample 4


title: 5EL_rep1

description: Library name: 5EL1


title: WT-3

description: Library name: Sample 3

value: WT


title: UC-58

description: Library name: UC-58

value: male


title: KMS-34-100nM-Day7-Rep1

description: Library name: KMS-34-100nM-Day7-Rep1-RNAseq


title: G93ALAG3KO_140d_spinalcord_3

city: Minato-ku

first: Yuta

last: Morisaki

state: Tokyo

address: 1-5-30, Shibakoen

department: Faculty of Pharmacy

institute: Keio University

description: Library name: G93ALAG3KO_140d_spinalcord_3

data_processing:
Raw sequencing data were processed using Trim Galore (version 0.6.7) for quality control and adapter trimming. Transcript abundance was quantified using Salmon (version 1.9.0) against the mouse reference transcriptome (GRCm39). Count matrices were generated using tximport in R (version 4.2.1).
Assembly: GRCm39
Supplementary files format and content: Raw count data

source_name: spinal cord

extract_protocol:
RNA extraction from FACS-sorted cells using SMART-seq mRNA HT LP Kit
Using the SMART-seq mRNA HT LP Kit (Takara Bio), prepare a cDNA library from each sample.

value: spinal cord


title: WT-2

description: Library name: Sample 2


title: UC-54

description: Library name: UC-54

value: female

value: FORMER


title: KMS-34-100nM-Day14-Rep2

description: Library name: KMS-34-100nM-Day14-Rep2-RNAseq


title: G93ALAG3KO_140d_spinalcord_2

description: Library name: G93ALAG3KO_140d_spinalcord_2


title: UC-52

description: Library name: UC-52


title: WT-1

description: Library name: Sample 1


title: KMS-34-100nM-Day14-Rep1

description: Library name: KMS-34-100nM-Day14-Rep1-RNAseq


title: G93ALAG3KO_140d_spinalcord_1

description: Library name: G93ALAG3KO_140d_spinalcord_1


title: r1_ABA3

city: Hong Kong

first: Shumin

last: LIANG

address: 224 Waterloo Road, Kowloon Tong, HK

department: Biology

institute: Hong Kong Baptist University

description: Library name: r1_A3

data_processing:
After sequencing, raw read were subjected to quality control and trimmed by using fastqc (v0.11.8) to get high-quality reads.
High-quality reads were mapped to the Arabidopsis genome (TAIR10) using hisat2 (v2.2.1).
Calculated the read counts of each gene with FeatureCounts (included in Subread v2.0.8 software) to generate the count matrix for expression analysis.
Assembly: TAIR10(Assembly: GCA_000001735.1)
Supplementary files format and content: format:txt; content:raw counts for each sample

source_name: 5-day-old seedlings

growth_protocol: To grow seedlings on solid media, surface-sterilized seeds were placed on half-strength Murashige and Skoog (MS) Basal Salts (M524, Sigma-Aldrich) containing 1% (w/v) sucrose (15503-022, Invitrogen) and 1% agar (A1296, Sigma-Aldrich), with a pH of 5.8 adjusted by 1 M KOH.The plates with seeds were stratified in the dark at 4 ºC for three days and then placed in a growth chamber (Percival Scientific) at 22 ºC with 60% humidity and a light intensity of 125 mol m-2 sec-1 under a 16-h light/8-h dark photoperiod for 5 days.

extract_protocol:
Total RNA were extracted using TRIzol reagent (15596026, ThermoFisher) following the manufacturer's instruction.
The mRNA libraries (poly A enrichment) were prepared by Novogene Incorporation (Beijing, China) using reagents for Illumina.

treatment_protocol: The 5-day-old seedlings in plates were then transferred to MS liquid medium with or without 50 μM ABA (962169,Sigma-Aldrich) for 3 hours, and then sampling with liquid nitrogen.

value: 5-day-old seedlings

value: ABA


title: DSP-1001660014603-Y-G09

city: Dallas

first: Chengsong

last: Zhu

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: Sample 130

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

source_name: Lupus 2

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 2

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

value: DESMIN


title: BY2R; fly whole body;Lsp2[B14];2-3 day;RNA-Seq;rep2

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: BY2R
RNA-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: genotype

tag: time

value: 2-3 day

value: BY*R


title: BY1R; fly whole body;Lsp2[B14];2-3 day;RNA-Seq;rep1

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


title: Dam-Lamin B1 (KIN7167.index01)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: KIN7167.index01
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

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

tag: sample group

value: Dam-Lamin B1


title: DSP-1001660014603-Y-G08

description: Library name: Sample 129

tag: roi

tag: segment


title: UC-50

description: Library name: UC-50

value: Nasal brushing

value: Cancer

tag: age


title: KMS-11-DMSO-Day7-Rep2

description: Library name: KMS-11-DMSO-Day7-Rep2-RNAseq

value: Bone marrow

tag: cell line

tag: cell type

value: Multiple myeloma

value: DMSO


title: G93A_140d_spinalcord_3

description: Library name: G93A_140d_spinalcord_3

value: spinal cord


title: r1_ABA2

description: Library name: r1_A2

value: 5-day-old seedlings

value: ABA


title: UC-48

description: Library name: UC-48

tag: subject id

tag: median tin

tag: cancer status

value: male

value: FORMER


title: KMS-11-DMSO-Day7-Rep1

description: Library name: KMS-11-DMSO-Day7-Rep1-RNAseq


title: G93A_140d_spinalcord_2

description: Library name: G93A_140d_spinalcord_2


title: UC-45

description: Library name: UC-45

value: Benign

tag: gender

value: female

tag: smoking status

value: CURRENT

tag: sequencing batch


title: r1_ABA1

description: Library name: r1_A1

tag: tissue

tag: treatment


title: KMS-11-DMSO-Day14-Rep2

description: Library name: KMS-11-DMSO-Day14-Rep2-RNAseq

tag: time point


title: G93A_140d_spinalcord_1

description: Library name: G93A_140d_spinalcord_1


title: Nd_ABA3

description: Library name: Nd_A3

tag: genotype


title: UC-9

description: Library name: UC-9


title: Nd_ABA2

description: Library name: Nd_A2


title: KMS-11-DMSO-Day14-Rep1

description: Library name: KMS-11-DMSO-Day14-Rep1-RNAseq


title: UC-8

description: Library name: UC-8


title: KMS-11-1uM-Day7-Rep2

description: Library name: KMS-11-1uM-Day7-Rep2-RNAseq


title: P140_G93AKO_3

description: Library name: P140_G93AKO_3

source_name: microglia

value: microglia


title: P140_G93AKO_2

description: Library name: P140_G93AKO_2


title: KMS-11-1uM-Day7-Rep1

description: Library name: KMS-11-1uM-Day7-Rep1-RNAseq


title: Nd_ABA1

description: Library name: Nd_A1


title: UC-43

description: Library name: UC-43

value: NEVER


title: Cd_ABA3

description: Library name: Cd_A3


title: P140_G93AKO_1

description: Library name: P140_G93AKO_1


title: KMS-11-1uM-Day14-Rep2

description: Library name: KMS-11-1uM-Day14-Rep2-RNAseq


title: UC-42

description: Library name: UC-42


title: P120_G93AKO_3

description: Library name: P120_G93AKO_3


title: Dam-Lamin B1 (KIN6777.index31)

description:
Library name: KIN6777.index31
singlecell_lads_mouse_cortex.h5ad.gz

value: brain

value: neural


title: DSP-1001660014603-Y-F11

description: Library name: Sample 120

value: Lupus 2

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: IA

tag: scan name


description:
Library name: Dam-LMNB1-Forelimb_Plate23_mpimg_L21679_RPI29
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: batch

tag: subtypes

value: genomic DNA; mRNA