title: WT_PR8-5


title: NKTs, wild-type, sample 2

status: Public on May 01 2023

type: SRA

city: HOUSTON

first: Leonid

last: Metelitsa

state: TX

address: 3639 Skyline Dr1102 Bates Ave., Ste. 1570

department: Pediatrics

country: USA

institute: BAYLOR COLLEGE OF MEDICINE/Texas Children's Hospital

library_source: transcriptomic

data_processing:
QC by FastQC (version 0.11.2)
Mapping and alignment by HISAT2 software (v2.1.0)
transcripts assembly by StringTie software (v1.3.5)
Generates raw read counts by prepDE.py (under stringtie software)
extracts coding genes by custom python scripts
Assembly: GRCh38.p13 assembly
Supplementary files format and content: gtf files including FPKM and TPM matrices for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: Peripheral blood of healthy donors was purchased from Gulf Coast Regional Blood Center. PBMCs were isolated from buffy coats by density gradient centrifugation. NKTs were purified using anti-iNKT microbeads (Miltenyi Biotec), and the negative PBMC fraction was irradiated (40 Gy) and aliquoted. Enriched NKTs were stimulated with an aliquot of autologous PBMCs pulsed with αGalCer (100 ng/mL; Kyowa Hakko Kirin). The culture was supplemented every other day with recombinant IL2 and IL21 (NCI, 200U/mL and CellGenix, 10ng/mL, respectively) in complete RPMI (RPMI 1640, 10% heat-inactivated FBS, 2 mM GlutaMAX-1). NKTs were expanded for 6 to 7 days and transduced with retroviral particles encoding the GFP.BTG1 or GFP.FFLuc construct in RetroNectin-coated plates (Takara Bio) for 48 hours then washed, replated, and cultured for continued expansion. NKT number was determined by trypan blue (Life Technologies) counting. At day 14 after NKT isolation, transduced NKTs were FACS sorted according to GFP expression.

extract_protocol:
RNA was harvested using the Rneasy Mini Plus kit.
RNA libraries were generated through polyA capture and reverse transcription of cDNA. Illumina PE150 technology was employed to sequence the sample (Novogene).

tag: tissue

value: Peripheral blood

tag: cell line

value: Primary human NKTs

tag: cell type

value: NKTs

tag: genotype

value: WT


title: ipRGC, P1, rep109

city: Baltimore

first: Alex

last: Kolodkin

state: Maryland

address: 725 N Wolfe St

department: Neuroscience

institute: Johns Hopkins University School of Medicine

description:
SmartSeq2
P1_108

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 version 2.1.0.
The resulting SAM files were converted to BAM files using SAMtools version 1.9.
Transcript abundance was estimated using Cuffquant and normalization was performed using Cuffnorm in Cufflinks version 2.2.1.
All analyses were performed using Seurat in R version 3.6.2.
Assembly: mm10
Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell
Supplementary files format and content: Cuffnorm matrix containing annotations for each gene
Supplementary files format and content: Cuffnorm matrix containing annotations for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Retina

extract_protocol:
Retinas were dissected in cold Hibernate A medium lacking Ca2+, Mg2+, and phenol red (BrainBits). Retinas were then dissociated in papain (Worthington Biochemical, LS003126), 5.5 mM Cysteine-HCl, and 1.1 mM EDTA dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) for seven minutes at 37°C. Cell suspension was passed through a 40 μm cell strainer (Falcon, 352340) and incubated for 30 minutes on ice with Brilliant Violet (BV)-421 anti-mouse CD90.2 antibody (BioLegend, 105341, 1:300), which binds to RGCs and provides an additional selection marker during FACS. The cells were then centrifuged and resuspended in 0.4% bovine serum albumin dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red). Cells were again centrifuged and resuspended in 2000 U/ml DNase I (New England Biolabs, M0303S) in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) prior to cell sorting. Individual GFP+, BV-421+ cells were sorted into a lysis solution consisting of 3500 U/ml RNase inhibitor (New England Biolabs, M0314S), 140 U/ml DNase I, and 0.17% v/v Triton X-100 in water using a MoFlo Legacy cell sorter (Beckman Coulter).
Single-cell DNA libraries were prepared according to the Smart-seq2 protocol (Picelli et al., Nature Protocols, 2014) and sequenced using an Illumina NextSeq 500 sequencer (75 bp paired-end reads, 400 million total reads).

value: Retina

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+

tag: age


title: E11.5, vMB, snapCREST, biol rep 3,CREST_sc, library 2

city: Shanghai

first: Yuejun

last: Chen

state: Shanghai

address: 320 Yue Yang Road

country: China

institute: CAS Center for Excellence in Brain Science and Intelligence Technology

data_processing:
Cellranger (7.0.0) was used to process scRNA-seq datasets. LinTind (https://bioconductor.org/packages/devel/bioc/html/LinTInd.html) was used to recover CREST barcodes for individual cells from bulk (identified by UMIs) or scRNA-seq (identified by 10X cell barcodes [CBs]) datasets.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ventral midbrain

extract_protocol:
Tissues, organoids and cultured cells were dissociated using papain (Worthington), Accutase (Gibco) or Trypsin-EDTA accordingly, and then pipetted into single-cell suspensions in collection medium [Neurobasal Medium, supplemented with 5% FBS]. Cells were filtered (Falcon 5mL Round Bottom Polyst) and then sorted by FACS to collect EGFP+/BFP+ cells for genomic DNA extraction (Vazyme) for bulk amplification or for single-cell RNA sequencing (10x Chromium System V3 or V3.1).
Single-cell RNA sequencing library were performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). CREST barcode libraries were amplified from the single-cell cDNA libraries generated in step 2.3 of the 10X Chromium single cell 3’ protocol with two rounds of PCR. Briefly, CREST_sc_1st_F and CREST_sc_1st_R primers were first used to enrich CREST barcodes tagged with 10X cell barcodes and UMIs. PCR products were purified using a 2-step bead purification process (0.5x then 1.1x) and then used as templates for a second round of PCR to attach sequencing adaptors and indices with CREST_sc_2nd_F and CREST_sc_2nd_R1/2 primers. The second-round PCR products (single-cell CREST libraries) were purified using a gel purification kit (Vazyme) and DNA of the targeted size collected.  For bulk amplification of CREST barcodes, both V1 and V2 CREST barcodes were enriched together from genomic DNA using three rounds of PCR amplification. Specifically, UMI-indexing PCR was first performed to identify CREST DNA from individual cells using the CREST_bulk_1st_F primer (containing 39 bp of partial Illumina sequencing adaptor, 12 bp of random UMI, and 20 bp of BFP binding sequence [10 bp upstream from CREST barcode]). Up to 500 ng of gDNA was used as template for UMI-indexing PCR for each library (for samples yielding less than 500 ng of gDNA, entire volumes were used as templates). The indexed CREST barcodes were purified using 1.6x VAHTS DNA Clean Beads (Vazyme) and amplified via a second round of PCR (using primers REST_bulk_2nd_F and CREST_bulk_2nd_R). Amplified CREST barcodes were selected and purified using a 2-step bead purification process (0.55x, then 1.45x) according to the manufacturer’s recommendations (Vazyme). Finally, sequencing adaptors and sample indices were attached to each library via a third round of PCR (using primers CREST_bulk_3rd_F and CREST_bulk_3rd_R1-8 [containing 8 bp indices]). PCR products were purified using 1.6x VAHTS DNA Clean Beads.

value: ventral midbrain

tag: treatment

value: FACS sort, EGFP+/BFP+ cells


title: ipRGC, P1, rep114

description:
SmartSeq2
P1_113


title: NKTs, wild-type, sample 1


title: ipRGC, P1, rep108

description:
SmartSeq2
P1_107


title: E11.5, vMB, snapCREST, biol rep 3,CREST_sc, library 1


title: E15.5, vMB, snapCREST, biol rep 1a,CREST_sc, library 3


title: ipRGC, P1, rep107

description:
SmartSeq2
P1_106


title: RNA_D4_40K_rep2

city: Beijing

first: Wenxue

last: Zhao

address: Yiheyuan Road

institute: Peking University

data_processing:
The raw sequences were cleaned using TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to human reference genome hg19 by STAR (v2.7.1a) with default parameter. All mapped bam files were converted to bigwig using bedtools (v2.24.0) (Quinlan, 2014). for visualization in IGV. High quality mapped reads were quantified using htseq -count (v0.11.3) (Anders et al., 2015). Differentially expressed genes were analyzed by DEseq2 (Love et al., 2014).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Total RNA was extracted from cultured LX-2 cells with 10,000,000 cells in each sample.
RNA sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina® (NEB England BioLabs). RNA-seq paired-end reads were sequenced on the Illumina NovaSeq 6000 platform.

value: liver

value: hepatic stellate cell line

value: wild type

value: cultured on stiff matrix for 4 days


title: NKTs, wild-type, sample 5


title: E11.5, vMB, snapCREST, biol rep 2,CREST_sc, library 3


title: RNA_D4_40K_rep1


title: WT_PR8-3

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

data_processing:
Adapters were trimmed using Trimmomatic-0.39
reads were aligned to mm10 genome using STAR2.7.1a
reads were summarized at the gene-level using featureCounts-1.4.6
gene expression was quantified using Cufflinks v2.2.1
Differential expression analysis was done using DESeq2v1.24
Genome_build: mm10
Supplementary_files_format_and_content: depth-normalized read counts and FPKM

source_name: Lung

extract_protocol: Single cells were produced from whole lungs from PR8-infected mice. The single cells were then enriched for monocytes using Miltenyi Biotech's monocyte sorting kit. Briefly, single cells were incubated with antibodies against non-monocyte markers and subsequently incuabted with beads that bind the primary antibodies. Using LS columns, the non-monocyte cells were captured and retained within the column while the unbound monocytes eluted through and were collected for RNA-sequencing. The purity and viability of the monocytes was assessed via flow cytometry post-sorting.

value: Monocyte

value: lung


title: WT_PR8-2


title: ipRGC, P1, rep106

description:
SmartSeq2
P1_105


title: RNA_D4_2K_rep2

value: cultured on soft matrix for 4 days


title: ipRGC, P1, rep105

description:
SmartSeq2
P1_104


title: WT_PR8-1


title: E11.5, vMB, snapCREST, biol rep 2,CREST_sc, library 2


title: E11.5, vMB, snapCREST, biol rep 2,CREST_sc, library 1


title: ipRGC, P1, rep110

description:
SmartSeq2
P1_109


title: IFNg_K0-4

value: IFN-g KO


title: RNA_D4_2K_rep1


title: Day7, organoid, pandaCREST, biol rep 3,CREST_sc, library 3

value: DIV Day7


title: IFNg_K0-3


title: ipRGC, P1, rep103

description:
SmartSeq2
P1_102


title: WT_PR8-4


title: ipRGC, P1, rep104

description:
SmartSeq2
P1_103


title: Day7, organoid, pandaCREST, biol rep 3,CREST_sc, library 2


title: IFNg_K0-2


title: RNA_D2_40K_rep1

value: cultured on stiff matrix for 2 days


title: Day7, organoid, pandaCREST, biol rep 3,CREST_sc, library 1


title: IFNg_K0-1


title: ipRGC, P1, rep102

description:
SmartSeq2
P1_101


title: RNA_D2_2K_rep2

value: cultured on soft matrix for 2 days


title: ipRGC, P1, rep101

description:
SmartSeq2
P1_100


title: 20 Days NO Treatment rep3

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to human genome using HISAT2
Reads counts for each gene
Assembly: maize B73 reference genome
Supplementary files format and content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts

organism: Zea mays

source_name: root

growth_protocol: Seed of the maize inbred line B73 was surface sterilized with Cl2 gas in fume hood for 6 h. After imbibing in aerated 1 mM CaCl2 overnight, seeds were placed on moistened filter paper in petri dishes to germinate in dark at 28 - 30 °C for 2 - 3 d. After germination, seeds were sown in 6-inch round pots filled with 860 g of calcined clay (Diamond Pro Calcined Clay Drying Agent). The pots with calcined clay were autoclaved for 3 times before planting. All transplanting procedures were performed in a laminar flow hood to prevent introduction of bacteria. To try to maintain a sterile environment, each pot was covered and sealed with a 6-inch sterile transparent plastic saucer. Plants were grown in the greenhouse with a 16/8 h dark/light cycle at 21/18 °C (day/night).

extract_protocol:
Total RNAs containing small RNAs were extracted using TRI Reagent (RT 111, Molecular Research Center), and then purified using a quick-RNA microprep kit (R1050, Zymoresearch).
standard library construction protocols for mRNAs and microRNAs.

treatment_protocol: Ten bacterial strains were selected in this study, including Arthrobacter, Chryseobacterium, Flavobacterium, Microbacterium, Pedobacter, Pseudomonas, Duganella, Shewanella, Acinetobacter and Bacillus (Table 1). The bacterial strains were streaked onto R2A agar and grown at room temperature for 2-3 d. A single colony from each strain was picked and inoculated in 5 ml of YPD medium. Liquid cultures of the bacteria were grown with agitation at 28 °C overnight. The overnight culture was then transferred into 50 ml of fresh YPD and incubated at 28 °C with agitation overnight. The OD600nm values were measured using a SPECTRONIC ® 20 GENESYSTM spectrophotometer. The liquid cultures were centrifuged, and the pellets were re-suspended in 25 - 50 ml (depending on OD600nm of each bacterium) of 10% YPD medium to equalize individual bacteria concentration to an OD600nm of 0.5. Equal volumes of each bacterial suspension were pooled together to obtain the bacterial synthetic community that was added to the plant roots.

tag: time point

value: 20 Days

tag: group

value: NO Treatment

tag: replicate

value: root


title: RNA_D2_2K_rep1


title: Day7, organoid, pandaCREST, biol rep 2,CREST_sc, library 2


title: pJun-TCP-rep2

library_source: genomic

data_processing:
library strategy: Cut&Tag
TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to cut adapters, and then trimmed reads were aligned to the human genome (hg19) using Bowtie2. Reads were sorted and converted to BAM format and duplicates were marked using Picard (https://broadinstitute.github.io/picard/). After normalizing the samples to the same sequencing depth, deepTools2 (v 3.3.1) software was used to plot the heat maps to show signals around peak regions with default parameters.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak, broadPeak

molecule: genomic DNA

extract_protocol:
Target genomic DNA was extracted using the NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit (NovoProtein, N259-YH01).
The CUT&Tag assay was performed using the NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit (NovoProtein, N259-YH01). 10,000 cells were washed twice with 1.5 mL of wash buffer and then mixed with activated concanavalin A beads. After successive incubations with the primary antibody (RT, 2h) and secondary antibody (RT, 1.5 h), the cells were washed and incubated with pAG-Tn5 for 1.5 h. Then, tagmentation buffer was added to activate tagmentation for 1 h. The tagment DNA fragments were purified using tagment DNA extract beads and washed by 80% ethanol. Then, the libraries were sequenced using the Illumina NovaSeq 6000 platform.

tag: antibody

value: p-Jun


title: pJun-TCP-rep1


title: 20 Days NO Treatment rep2


title: RNA_D2_40K_rep2


title: E11.5, vMB, pandaCREST, biol rep 3,CREST_sc, library 3

value: ventral midbrain


title: ipRGC, P1, rep99

description:
SmartSeq2
P1_98

value: Retina

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P1, rep97

description:
SmartSeq2
P1_96


title: Day7, organoid, pandaCREST, biol rep 2,CREST_sc, library 1

value: FACS sort, EGFP+/BFP+ cells


title: 20 Days NO Treatment rep1


title: ipRGC, P1, rep98

description:
SmartSeq2
P1_97


title: 14 Days NO Treatment rep3

value: 14 Days


title: ipRGC, P5, rep144

description:
SmartSeq2
P5_143


title: pJun-2K-rep1

value: hepatic stellate cell line

value: wild type


title: 14 Days NO Treatment rep2


title: E11.5, vMB, pandaCREST, biol rep 3,CREST_sc, library 2


title: H3K4me3_40K_rep2


title: E11.5, vMB, pandaCREST, biol rep 3,CREST_sc, library 1


title: ipRGC, P5, rep143

description:
SmartSeq2
P5_142


title: E11.5, vMB, pandaCREST, biol rep 2,CREST_sc, library 3


title: ipRGC, P1, rep100

description:
SmartSeq2
P1_99


title: H3K4me3_40K_rep1


title: Day7, organoid, pandaCREST, biol rep 2,CREST_sc, library 3


title: 7 Days NO Treatment rep3

value: 7 Days


title: E11.5, vMB, pandaCREST, biol rep 2,CREST_sc, library 2


title: ipRGC, P5, rep142

description:
SmartSeq2
P5_141


title: ipRGC, P5, rep141

description:
SmartSeq2
P5_140


title: pJun-2K-rep2


title: E11.5, vMB, pandaCREST, biol rep 2,CREST_sc, library 1


title: ipRGC, P5, rep139

description:
SmartSeq2
P5_138


title: 14 Days NO Treatment rep1


title: 20 Days Treatment rep3

value: Treatment


title: 7 Days NO Treatment rep1


title: P14, En1-MB, EGFP-postive, CREST_bulk

description:
En1_CREST_bulk_additional_v1_QC.rds
En1_CREST_bulk_additional_v2_QC.rds

data_processing:
library strategy: UMI-tagged bulk-seq
Cellranger (7.0.0) was used to process scRNA-seq datasets. LinTind (https://bioconductor.org/packages/devel/bioc/html/LinTInd.html) was used to recover CREST barcodes for individual cells from bulk (identified by UMIs) or scRNA-seq (identified by 10X cell barcodes [CBs]) datasets.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: midbrain and hindbrain

value: midbrain and hindbrain


title: H3K27me3_40K_rep2

value: cultured on stiff matrix for 2 days


title: 20 Days Treatment rep2


title: ipRGC, P5, rep140

description:
SmartSeq2
P5_139


title: E8, En1-MB, EGFP-postive, CREST_bulk


title: H3K27me3_40K_rep1


title: H3K4me3_2K_rep2

value: cultured on soft matrix for 2 days


title: 20 Days Treatment rep1

value: 20 Days


title: H3K27me3_2K_rep2


title: E8.5, En1-MB, EGFP-postive, CREST_bulk


title: ipRGC, P5, rep136

description:
SmartSeq2
P5_135


title: H3K27me3_2K_rep1


title: 7 Days NO Treatment rep2

value: NO Treatment


title: ipRGC, P5, rep138

description:
SmartSeq2
P5_137


title: 14 Days Treatment rep3

value: root


title: ipRGC, P5, rep137

description:
SmartSeq2
P5_136


title: E8.5, En1-MB, EGFP-negtive, CREST_bulk

value: FACS sort, EGFP-/BFP+ cells


title: ipRGC, P5, rep135

description:
SmartSeq2
P5_134


title: Adult, control, CREST_V2_bulk, biol rep 2

value: unsorted

value: Adult


title: 14 Days Treatment rep2


title: H3K27ac_40K


title: H3K4me3_2K_rep1


title: P14, En1-MB, EGFP-negtive, CREST_bulk


title: ipRGC, P5, rep134

description:
SmartSeq2
P5_133

value: Retina

value: ipRGC


title: H3K27ac_2K


title: ipRGC, P5, rep133

description:
SmartSeq2
P5_132

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: Adult, control, CREST_V2_bulk, biol rep 1


title: ATAC_D4_40K_rep2

data_processing:
The raw sequences were cleaned using TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to human reference genome hg19 by bowtie2 (v.2.4.1) with default parameter. All mapped bam files were converted to bigwig using bedtools (v2.24.0) (Quinlan, 2014). for visualization in IGV. PCR duplicates were removed using Picard (https://broadinstitute.github.io/picard/). Peaks were called using Macs2 with a relaxed q-value threshold of 0.05.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak

extract_protocol:
Each sample containes 100,000 cells and the cell pellet was collected using moderately cold lysis buffer.
The samples were centrifuged with 500 g, 4°C for 5 min. The cell pellet was resuspended with moderately cold lysis buffer, and library construction used the TruePrep DNA Library Prep Kit V2 for Illumina (TD502) (Vazyme Biotech Co., Ltd). DNA libraries were produced after 12 cycles of PCR amplification using the TruePrep library prep kit. After purification, the paired-end sequencing was performed on the Illumina Novaseq 6000 platform.

value: liver

value: cultured on stiff matrix for 4 days


title: 7 Days Treatment rep3


title: Adult, control, CREST_V1_bulk, biol rep 2

value: CREST-sgRNAs


title: ipRGC, P5, rep132

description:
SmartSeq2
P5_131


title: Adult, control, CREST_V1_bulk, biol rep 1


title: 7 Days Treatment rep2

value: 7 Days


title: ATAC_D4_2K_rep2

value: hepatic stellate cell line

value: wild type

value: cultured on soft matrix for 4 days


title: 7 Days Treatment rep1

value: Treatment


title: ATAC_D4_2K_rep1


title: 96h NO Treatment rep3


title: ipRGC, P5, rep131

description:
SmartSeq2
P5_130


title: ipRGC, P5, rep130

description:
SmartSeq2
P5_129


title: Day7, organoid, pandaCREST, biol rep 3, scRNAseq

description:
10x Genomics
Organoid_seurat_final.rds

source_name: organoid

value: organoid

value: FACS sort, EGFP+/BFP+ cells

value: DIV Day7


title: ATAC_D2_40K_rep2

value: cultured on stiff matrix for 2 days


title: E15.5, vMB, En1-Ai9, normal ref, scRNAseq

description:
10x Genomics
E15_seurat_final.rds

value: ventral midbrain

value: FACS sort, tdT+ cells


title: E11.5, vMB, pandaCREST, biol rep 3, scRNAseq

description:
10x Genomics
E11_seurat_final.rds


title: ipRGC, P5, rep129

description:
SmartSeq2
P5_128

value: Retina


title: ipRGC, P5, rep128

description:
SmartSeq2
P5_127

value: ipRGC


title: 96h NO Treatment rep1

value: NO Treatment

value: root


title: 14 Days Treatment rep1

value: 14 Days


title: 96h Treatment rep3


title: E15.5, vMB, snapCREST, biol rep 3, scRNAseq

description:
10x Genomics
E15_seurat_final.rds


title: ATAC_D2_2K_rep2

value: liver

value: cultured on soft matrix for 2 days


title: ATAC_D4_40K_rep1

value: hepatic stellate cell line

value: cultured on stiff matrix for 4 days


title: ipRGC, P5, rep127

description:
SmartSeq2
P5_126

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: E11.5, vMB, snapCREST, biol rep 3, scRNAseq

description:
10x Genomics
E11_seurat_final.rds


title: 96h Treatment rep2

value: Treatment


title: ATAC_D2_2K_rep1

value: wild type


title: ipRGC, P5, rep126

description:
SmartSeq2
P5_125


title: 96h Treatment rep1


title: Day7, organoid, pandaCREST, biol rep 2, scRNAseq

description:
10x Genomics
Organoid_seurat_final.rds

value: organoid

value: FACS sort, EGFP+/BFP+ cells


title: HS578T; CROPseq scRNAseq

city: La Jolla

first: Brenton

last: Munson

state: CA

address: 9500 Gilman Drive, MC 0688

department: Bioengineering

institute: University of California San Diego

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files, comma-separated values of cell barcode and gene perturbation

source_name: Breast; Mammary gland

extract_protocol:
After transduction, cells were grown for 7 days, then processed via 10X Genomics 3’ Single Cell mRNA Capture Kit v3 according to the manufacturers protocols. Unused cDNA from the library prep was used to amplify the CRISPR sgRNA sequences to improve cell annotation. In a 50 μL reaction, 20 μL of cDNA was mixed with 2.5 μL of the CROP-Seq_Guide_Amp primer(10μM), 2.5 μL of the NEB_Universal primer (1 0μM) (Supplemental File 1), and 25 μL of Kapa HiFi HotStart ReadyMix.
After amplifying and purifying the sgRNA libraries via a Qiagen PCR purification column, the libraries were then indexed for Illumina sequencing via an NEBNext multiplexed indexing oligo kit. 1 μL of the purified step 1 PCR amplicon as template (the sgRNA library) was added with 2.5 μL of each indexing primer per 50 μL Kapa HiFi reaction, and run for 6-8 cycles with an annealing temperature of 65 °C and an extension time of 45 seconds. The final sgRNA sequencing libraries were then purified using AmpureXP magnetic beads (Beckman A63881) at a 1.6:1 beads to DNA ratio.

treatment_protocol: A library of sgRNAs targeting all cyclin-dependent kinases and select associated epigentic factors were was screened in each cell line. To transduce the cells, lentivirus was mixed with the necessary volume of cell culture media containing 8 μg/mL polybrene. The virus-containing media was added to the cells at 30% confluency, and let incubate overnight. The following day, the virus/polybrene containing media was removed and replaced with fresh media. 48 hours after transduction, the cells were changed into puromycin (2 μg/mL) containing media. Cells were then grown as normal in media containing puromycin.

value: Triple Negative Breast Cancer

value: Breast; Mammary gland


title: E11.5, vMB, pandaCREST, biol rep 2, scRNAseq

description:
10x Genomics
E11_seurat_final.rds

value: ventral midbrain


title: 48h NO Treatment rep3


title: ATAC_D2_40K_rep1

value: cultured on stiff matrix for 2 days


title: ipRGC, P5, rep124

description:
SmartSeq2
P5_123

value: Retina

value: ipRGC


title: MDAMB431; CROPseq scRNAseq

description: 10X Genomics


title: ipRGC, P5, rep125

description:
SmartSeq2
P5_124


title: ipRGC, P5, rep123

description:
SmartSeq2
P5_122


title: 48h NO Treatment rep2

value: NO Treatment

value: root


title: E11.5, vMB, snapCREST, biol rep 2, scRNAseq

description:
10x Genomics
E11_seurat_final.rds


title: HL-60, circMLLT1e2

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

data_processing:
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.1 (Martin, 2011), setting minimum-length option to 20, error-rate 0.2 and overlap 5.
The resulting FASTQ files for total RNAseq respectively were analysed and quality checked using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were mapped against the human reference genome (hg19) using the Bowtie2 alignment algorithm (Langmead et al., 2012), allowing maximum 10 alignments to report per read. The outout SAM file compressed to a binary format (BAM) and sorted by queryname with SAMtools.
Post-alignment steps and peak-calling is done using genrich program (https://github.com/jsh58/Genrich). Peak files are compared for common or different genomic regions using BED tools.
Alignments and peaks were visualised and interrogated using the Integrative Genomics Viewer v2.3.80 (Thorvaldsdóttir et al., 2013).
Assembly: hg19

growth_protocol: HL-60 cells stably expressing transgenic constructs were cultivated in RPMI1640 medium with 10% FBS at 37oC with 5% carbon dioxide

extract_protocol:
HL-60 cells in logarithmic growth phase were counted and 100,000 live cells were used for the ATAC-Seq kit protocol (Active Motif)
Performed as per manufacturer's instructions

value: cell line

tag: kit

value: Active Motif ATAC-Seq kit


title: 48h Treatment rep3


title: MDAMB468; CROPseq scRNAseq

description: 10X Genomics


title: OPG,muscle.den5

first: Mingming

address: No.28 Fuxing Road

institute: Chinese PLA general hospital

data_processing:
Sequencing reads were mapped to the mouse genome reference build mm10 using STAR aligner.
Transcripts per million and DEGs were calculated using RSEM and ebseq packages.

source_name: muscle

extract_protocol:
Total RNA from GAS muscle samples was extracted from the sham and den groups using the TRIzol reagent.
The RNA-Sequencing library was constructed in a non-strand-specific manner

treatment_protocol: sham and denervation

value: muscle

value: denervation


title: 48h NO Treatment rep1


title: HL-60, circMLLe9-10


title: ipRGC, P5, rep122

description:
SmartSeq2
P5_121

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P5, rep121

description:
SmartSeq2
P5_120


title: E15.5, vMB, snapCREST, biol rep 2, scRNAseq

description:
10x Genomics
E15_seurat_final.rds


title: 48h Treatment rep2

value: Treatment


title: HL-60, pMIG (EV)


title: OPG,muscle.den4


title: OPG,muscle.den3


title: 48h Treatment rep1


title: OPG,muscle.den2


title: 24h NO Treatment rep3


title: ipRGC, P5, rep120

description:
SmartSeq2
P5_119


title: 96h NO Treatment rep2


title: ipRGC, P5, rep118

description:
SmartSeq2
P5_117


title: 24h NO Treatment rep2


title: OPG,muscle.den1


title: OPG,muscle,sham5

value: sham


title: C1_Rep03

city: Madison

first: Ryan

last: Behrens

address: 555 Science Dr

institute: University of Wisconsin-Madison

description:
c1.3
GEO_behr_wt-c1.txt

data_processing:
Sequence reads were mapped to hg38 (human genome assembly) using HISAT2 (version 2.0.5)
Annotated feature count tables were prepared using the htseq-count tool within HTSeq (version 0.6.0)
Differential gene expression analyses were performed using DESeq2 (version 1.26.0) from which normalized counts were determined and fold-change/statistics were calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited text file ('norm_counts') includes normalized read counts generated by DESeq2 for all samples
Supplementary files format and content: tab-delimited text files ('wt-c1' or 'wt-c2') includes DESeq2 results output

source_name: Jurkat (E6-1) derived

growth_protocol: Jurkat cell lines (WT, C1, and C2) were maintained in RPMI-1640 supplemented with FBS (10%), L-glutamine, and penicillin/streptomycin antibiotics. Culture supernatants tested negative for mycoplasma contamination

extract_protocol:
Total RNA extracts were prepared using the RNeasy Plus Mini kit (Qiagen) with genomic DNA (gDNA) elimination columns according to the manufacturer's instructions. 1µg of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-seq were generated using TruSeq® stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: 1.5E6 cells were plated in 10mL supplemented RPMI.  48 hours post-plating, cells were pelleted (400xG, 5 min @ 4C) and washed in chilled PBS.  Follwing wash, cell pellets were stored @ -80C.

value: Jurkat (E6-1) derived

value: T lymphocyte cell line

value: CCNT1.Y261 (MUT)


title: ipRGC, P5, rep117

description:
SmartSeq2
P5_116


title: C2_Rep01

description:
c2.1
GEO_behr_wt-c2.txt


title: ipRGC, P5, rep116

description:
SmartSeq2
P5_115


title: C2_Rep02

description:
c2.2
GEO_behr_wt-c2.txt


title: 24h NO Treatment rep1


title: OPG,muscle,sham3


title: ipRGC, P5, rep115

description:
SmartSeq2
P5_114


title: 24h Treatment rep3


title: 24h Treatment rep2


title: C1_Rep02

description:
c1.2
GEO_behr_wt-c1.txt


title: OPG,muscle,sham4


title: ipRGC, P5, rep114

description:
SmartSeq2
P5_113


title: C1_Rep01

description:
c1.1
GEO_behr_wt-c1.txt


title: ipRGC, P5, rep119

description:
SmartSeq2
P5_118


title: C2_Rep03

description:
c2.3
GEO_behr_wt-c2.txt


title: OPG,muscle,sham2


title: WT_Rep03

description:
wt.3
GEO_behr_wt-c1.txt
GEO_behr_wt-c2.txt

source_name: Jurkat (E6-1)

value: Jurkat (E6-1)

value: CCNT1.C261 (WT)


title: 24h Treatment rep1


title: ipRGC, P5, rep113

description:
SmartSeq2
P5_112


title: OPG,muscle,sham1


title: 12h NO Treatment rep1


title: WT,muscle,den4


title: WT,muscle,den5


title: ipRGC, P5, rep111

description:
SmartSeq2
P5_110


title: ipRGC, P5, rep109

description:
SmartSeq2
P5_108


title: ipRGC, P5, rep112

description:
SmartSeq2
P5_111


title: Senescent Ecs 2

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

country: Japan

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

data_processing:
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
The data was analyzed using the iPathwayGuide (ADVAITA).
The csCluster command of cummerbund was used to perform K-means clustering.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human umbilical vein endothelial cells

growth_protocol: Cells were regularly cultured in the CO2 incubator for cells at 37 °C under 5% CO2 levels.

extract_protocol:
RNAs were isolated from the cells using TRIzol, and then purified using NucleoSpin RNA clean-up kit (Macherey-Nagel #U0955)
Library was prepared using TruSeq RNA Exome (Illumina #20020189)

treatment_protocol:
HUVECs were cultured in HuMedia-EG2 medium (Kurabo #KE-2150S), and regularly passaged at 1:4 ratio when reached sub-confluent. Cells were passaged until they did not show obvious proliferation with enlarged and flattened morphology (usually passage 18-20). Cellular senescence was confirmed by enhanced senescence-associated β-GAL activity; reduced proliferation; increased expression of senescence-associated genes such as p16 and p21; accumulated DNA damage assessed by immunocytochemistry for γH2AX. P3 HUVECs were regularly used as young early passage ECs.
For virus infection, 1 x 10e5 cells were plated on 12-well plate, and incubated with SARS-CoV-2 (at MOI 1 or 50) or influenza A (at MOI 1) for 1 hour with gentle rotation, followed by changing medium with fresh growth one. RNAs were extracted from the cells 72 hours after the infection.

value: Human umbilical vein endothelial cells

value: endothelial cells

value: Control


title: WT,muscle,den2


title: 12h NO Treatment rep2

value: NO Treatment


title: WT_Rep01

description:
wt.1
GEO_behr_wt-c1.txt
GEO_behr_wt-c2.txt


title: WT,muscle,den3


title: ipRGC, P5, rep110

description:
SmartSeq2
P5_109

value: Retina

value: ipRGC


title: WT_Rep02

description:
wt.2
GEO_behr_wt-c1.txt
GEO_behr_wt-c2.txt


title: Senescent Ecs 3


title: 12h Treatment rep3

value: root


title: Senescent Ecs 1


title: ipRGC, P5, rep108

description:
SmartSeq2
P5_107


title: 12h Treatment rep2


title: WT,muscle,sham4

value: muscle


title: Young Ecs 3


title: 12h Treatment rep1


title: Young Ecs 2


title: 12h NO Treatment rep3


title: ipRGC, P5, rep106

description:
SmartSeq2
P5_105


title: ipRGC, P5, rep107

description:
SmartSeq2
P5_106


title: 6h NO Treatment rep3


title: WT,muscle,sham5


title: Senescent ECs infected with SARS-CoV-2 at 72 hpi 3

value: SARS-CoV-2 infection


title: WT,muscle,sham2


title: ipRGC, P5, rep104

description:
SmartSeq2
P5_103

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: 6h NO Treatment rep1


title: 6h NO Treatment rep2


title: WT,muscle,sham3


title: Senescent ECs infected with SARS-CoV-2 at 72 hpi 2


title: Young Ecs 1


title: WT,muscle,den1

value: denervation


title: WT,muscle,sham1

value: sham


title: Young ECs infected with SARS-CoV-2 at 72 hpi 3


title: 6h Treatment rep3

value: Treatment


title: R72_2

first: Yifeng

last: Wang

state: China

address: Feitai region Dongda road

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%.
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.5).
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung tissue cells

extract_protocol:
extracted from lung tissue using Trizol
mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads, mRNA molecules were fragmented into small pieces using fragmentation reagent after reaction a certain period in proper temperture. First-strand cDNA was generated using random hexamer-primed reverse transcription,followed by a second-strand cDNA synthesis.

value: lung

tag: strain

tag: Sex

value: female

value: 8 weeks

value: treated with yersinia pestis strain 201 for 72h


title: 6h Treatment rep1


title: ipRGC, P5, rep103

description:
SmartSeq2
P5_102


title: 6h Treatment rep2


title: Senescent ECs infected with SARS-CoV-2 at 72 hpi 1

value: Human umbilical vein endothelial cells


title: R72_1


title: ipRGC, P5, rep101

description:
SmartSeq2
P5_100


title: ipRGC, P5, rep102

description:
SmartSeq2
P5_101


title: Young ECs infected with SARS-CoV-2 at 72 hpi 1

value: endothelial cells


title: 3h NO Treatment rep3


title: Young ECs infected with SARS-CoV-2 at 72 hpi 2


title: ipRGC, P5, rep100

description:
SmartSeq2
P5_99


title: ipRGC, P5, rep105

description:
SmartSeq2
P5_104


title: R48_3

value: treated with yersinia pestis strain 201 for 48h


title: 3h NO Treatment rep2

value: NO Treatment


title: 3h NO Treatment rep1


title: ipRGC, P5, rep98

description:
SmartSeq2
P5_97

value: Retina


title: Cerebrospinal fluid, Normal N, Input

first: Lixin

last: Ma

address: Haidian District

department: Neurosurgery

institute: Sanbo Brain Hospital

data_processing:
Briefly,  raw data were generated after sequencing,  image analysis, base calling and quality filtering on Illumina NovaSeq 6000 sequencer.
Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.3) software, high quality clean reads were generated. Then these clean reads were aligned to Human reference genome  (HG19) using bowtie2  software  (v2.2.4) with default parameters.
Peak calling was performed with MACS software (v2.0). Differentially methylated regions were identified by diffReps software (v1.55.4).The methylated regions were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Assembly: hg19
Supplementary files format and content: Excel format, ChIP-enriched Peaks

source_name: cerebrospinal fluid

extract_protocol:
Genomic DNA was isolated using phenol–chloroform, precipitated with ethanol and sonicated to 100–500 bp using Bioruptor (Diagenode). Sonicated DNA was end repaired, A tailed, and ligated to adapters by using NEBNext® Ultra™ DNA Library Prep Kit (NEB). Then, MeDIP was performed with a monoclonal antibody against 5-methylcytosine by following the standard manufacturer’s protocol (Active Motif).
MeDIP DNA libraries were quantified using Quant-iT PicoGreen dsDNA Kits (Life Technologies), and subjected to high-throughput 150 base paired-end sequencing on Illumina sequencer according to the manufacturer’s recommended protocol.

value: cerebrospinal fluid

tag: disease state

value: control

value: no

tag: molecule type

value: ctDNA

tag: ip antibody


title: ipRGC, P5, rep97

description:
SmartSeq2
P5_96

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: R48_2


title: Cerebrospinal fluid, Normal N, IP

value: monoclonal antibody against 5-methylcytosine


title: 3h Treatment rep2

value: Treatment

value: root


title: Cerebrospinal fluid, Glioblastoma G1, Input

value: female

value: glioblastoma


title: 3h Treatment rep1


title: R72_4

value: lung

value: 8 weeks

value: treated with yersinia pestis strain 201 for 72h


title: 3h Treatment rep3


title: Cerebrospinal fluid, Glioblastoma G4, IP


title: 1h NO Treatment rep3


title: Cerebrospinal fluid, Glioblastoma G3, IP

value: male


title: R24_3

value: treated with yersinia pestis strain 201 for 24h


title: R24_2


title: ipRGC, P1, rep96

description:
SmartSeq2
P1_95

value: Retina


title: Cerebrospinal fluid, Glioblastoma G2, IP

value: cerebrospinal fluid


title: R24_4


title: ipRGC, P1, rep94

description:
SmartSeq2
P1_93


title: ipRGC, P1, rep93

description:
SmartSeq2
P1_92


title: ipRGC, P5, rep99

description:
SmartSeq2
P5_98


title: R0_3

value: untreated


title: 1h NO Treatment rep2

value: NO Treatment


title: Cerebrospinal fluid, Glioblastoma G1, IP

value: no

value: ctDNA


title: 1h NO Treatment rep1


title: R48_1

value: treated with yersinia pestis strain 201 for 48h


title: ipRGC, P1, rep92

description:
SmartSeq2
P1_91

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P1, rep91

description:
SmartSeq2
P1_90


title: R0_2


title: 1h Treatment rep3

value: Treatment

value: root


title: ipRGC, P1, rep90

description:
SmartSeq2
P1_89


title: ipRGC, P1, rep95

description:
SmartSeq2
P1_94


title: Tissue, Normal N

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the human reference genome (HG19) with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
Assembly: hg19
Supplementary files format and content: Excel format, raw counts, normalized counts

source_name: normal tissue

extract_protocol:
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads.

value: female

value: normal tissue

value: control


title: Tissue, Glioblastoma  T3

source_name: tumor tissue

value: tumor tissue

value: glioblastoma


title: R0_1

value: lung

value: 8 weeks


title: Tissue, Glioblastoma  T4


title: 1h Treatment rep2


title: Myonuclear OV 7 [P18702_107]

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

description:
P18702_107
Experiment 4

data_processing:
Raw counts from RNA-sequencing were used as inputs into R (Version 4.1.0) or Partek Flow.
Alignment was performed using STAR with mmu39. After filtering low-expressed genes, DESeq2 (Version 1.34.0) was used for normalization and differential analyses of RNA-sequencing data to identify differentially expressed genes (DEGs) with pairwise comparisons.
After filtering low-expressed genes, DESeq2 (Version 1.34.0) was used for normalization and differential analyses of RNA-sequencing data to identify differentially expressed genes (DEGs) with pairwise comparisons.
Assembly: mm10
Supplementary files format and content: *_counts.txt: Tab-delimited text files include count values for each Sample.

source_name: Plantaris (skeletal muscle)

growth_protocol: Synergist ablation overload of the plantaris muscle or doxycycline-induced Myc expression.

extract_protocol:
The aqueous phase was transferred to a new tube and further processed on columns using the Direct-zol Kit (Zymo Research, Irvine, CA, USA).
PolyA for HSA-Myc and C57BL6, and ribosome depletion for HSA-GFP (low-input).

treatment_protocol: Sham/Overload or Doxycycline.

value: Plantaris (skeletal muscle)

value: HSA-GFP

value: Synergist Ablation Overload


title: 1h Treatment rep1


title: Myonuclear Sham 6 [P18702_106]

description:
P18702_106
Experiment 4

value: Sham Surgery


title: Tissue, Glioblastoma  T1

value: no


title: ipRGC, P1, rep88

description:
SmartSeq2
P1_87

data_processing:
FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 version 2.1.0.
The resulting SAM files were converted to BAM files using SAMtools version 1.9.
Transcript abundance was estimated using Cuffquant and normalization was performed using Cuffnorm in Cufflinks version 2.2.1.
All analyses were performed using Seurat in R version 3.6.2.
Assembly: mm10
Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell
Supplementary files format and content: Cuffnorm matrix containing annotations for each gene
Supplementary files format and content: Cuffnorm matrix containing annotations for each sample

source_name: Retina

value: Retina


title: ipRGC, P1, rep87

description:
SmartSeq2
P1_86

value: ipRGC


title: Myonuclear Sham 2 [P18702_104]

description:
P18702_104
Experiment 4


title: 30 min NO Treatment rep3

value: 30 min

value: NO Treatment


title: 30 min NO Treatment rep1

value: root


title: ipRGC, P1, rep86

description:
SmartSeq2
P1_85

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: Tissue, Glioblastoma  T2

value: male


title: Myonuclear OV 5 [P18702_105]

description:
P18702_105
Experiment 4


title: ipRGC, P1, rep85

description:
SmartSeq2
P1_84


title: Myonuclear OV 2 [P18702_102]

description:
P18702_102
Experiment 4


title: Patient 5 [pre_5B]

city: Halle

first: Edith

last: Willscher

state: Deutschland

address: Ernst-Grube-Straße 40

department: Internal Medicine IV

country: Germany

institute: Martin Luther University of Halle-Wittenberg

description: transcriptome of in vitro expanded MSC

data_processing:
Raw data was quality controlled for GC content and filtered to remove adapter contamination or reads with low quality (base quality less than 20). Clean reads were mapped to reference genome GRCh38 with HISAT2 and transcript abundance was estimated by read counts as FPKM value. HTSeq software was used to analyze the gene expression levels using union mode. Differential expression and all downstream analysis was performed in Rstudio using package DeSeq2.
Assembly: GRCh38
Supplementary files format and content: log normalized raw read counts per gene

source_name: bone marrow

growth_protocol:
MSC were isolated from the bone marrow, then separated by centrifugation using Ficoll (anprotech) density gradients
Cells were suspended in growth medium and plated at an initial seeding density of 1–2.5x10^5 cells/cm2; non-adherent cells were discarded after 18-24h. MSC-growth medium was composed of DMEM (low glucose, GlutamaX™, pyruvate; Gibco) supplemented with 10% human platelet lysate (HPL) and heparin (500IE/100ml; Sigma). Media was exchanged every 2 to 3 days. Cells were passaged with 0.05% trypsin/ 0.022% EDTA (Sigma) when colony-forming unit fibroblasts (CFU-F) were present and had reached 50% confluence within the colonies. Cells were then replated at 200cells/cm2 either immediately or after cryopreservation in liquid nitrogen. Cultures were grown at 37°C in a humidified atmosphere of 5% CO2/ 95% air.

extract_protocol:
Total RNA of 1-1.5x10^6 MSC per culture was extracted using TRIzol reagent (Invitrogen) according to manufacturer´s instructions.
cDNA was synthesized and amplified with the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio). After amplification the samples were cleaned using magnetic beads. Sequencing was performed (Novogene) and16.8 million reads were obtained per samples with single/paired end sequencing.

value: bone marrow

tag: timepoint

value: pre allogenic stem cell transplantation

value: MSC derived

tag: subject id

value: Patient 5


title: Myonuclear OV 3 [P18702_103]

description:
P18702_103
Experiment 4

tag: tissue


title: Myonuclear Sham1 [P18702_101]

description:
P18702_101
Experiment 4


title: 30 min Treatment rep3

value: Treatment


title: ipRGC, P1, rep84

description:
SmartSeq2
P1_83

extract_protocol:
Retinas were dissected in cold Hibernate A medium lacking Ca2+, Mg2+, and phenol red (BrainBits). Retinas were then dissociated in papain (Worthington Biochemical, LS003126), 5.5 mM Cysteine-HCl, and 1.1 mM EDTA dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) for seven minutes at 37°C. Cell suspension was passed through a 40 μm cell strainer (Falcon, 352340) and incubated for 30 minutes on ice with Brilliant Violet (BV)-421 anti-mouse CD90.2 antibody (BioLegend, 105341, 1:300), which binds to RGCs and provides an additional selection marker during FACS. The cells were then centrifuged and resuspended in 0.4% bovine serum albumin dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red). Cells were again centrifuged and resuspended in 2000 U/ml DNase I (New England Biolabs, M0303S) in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) prior to cell sorting. Individual GFP+, BV-421+ cells were sorted into a lysis solution consisting of 3500 U/ml RNase inhibitor (New England Biolabs, M0314S), 140 U/ml DNase I, and 0.17% v/v Triton X-100 in water using a MoFlo Legacy cell sorter (Beckman Coulter).
Single-cell DNA libraries were prepared according to the Smart-seq2 protocol (Picelli et al., Nature Protocols, 2014) and sequenced using an Illumina NextSeq 500 sequencer (75 bp paired-end reads, 400 million total reads).

tag: cell type


title: ipRGC, P1, rep89

description:
SmartSeq2
P1_88

tag: genotype


title: Patient 4 [pre_4B]

description: transcriptome of in vitro expanded MSC

value: Patient 4


title: Patient 5 [pre_5A]

description: transcriptome of in vitro expanded MSC


title: ipRGC, P1, rep83

description:
SmartSeq2
P1_82

tag: age


title: 30 min Treatment rep2


title: Patient 4 [pre_4A]

description: transcriptome of in vitro expanded MSC


title: 30 min NO Treatment rep2


title: Sham RNA 72h OV [TOTSHAM3]

description:
TOTSHAM3
Experiment 1

value: Plantaris (skeletal muscle)

tag: treatment


title: 0h NO Treatment rep3

tag: time point


title: 0h NO Treatment rep2

tag: group


title: Sham RNA 72h OV [TOTSHAM2]

description:
TOTSHAM2
Experiment 1


title: Patient 3 [pre_3B]

description: transcriptome of in vitro expanded MSC

value: Patient 3


title: Total RNA 72h OV [TOTOVLD3]

description:
TOTOVLD3
Experiment 1

value: Synergist Ablation Overload


title: Patient 3 [pre_3A]

description: transcriptome of in vitro expanded MSC


title: Patient 2 [pre_2B]

description: transcriptome of in vitro expanded MSC

value: Patient 2


title: ipRGC, P1, rep81

description:
SmartSeq2
P1_80

value: Retina


title: Patient 2 [pre_2A]

description: transcriptome of in vitro expanded MSC


title: ipRGC, P1, rep79

description:
SmartSeq2
P1_78

value: ipRGC


title: Total RNA 72h OV [TOTOVLD2]

description:
TOTOVLD2
Experiment 1


title: wild-type (Tagged), BioRep3

city: Pittsburgh

first: Karen

last: Arndt

state: PA

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

description:
Klactis_rRNA-blacklisted_RawCountMatrix.txt
Scereviciae_Antisense_mRNA_RawCountMatrix.txt
Scereviciae_Sense_mRNA_RawCountMatrix.txt
Scereviciae_Unstranded_mRNA_RawCountMatrix.txt

data_processing:
Using STAR (v2.7.5a) aligner, all reads were first aligned to the K. lactis (spike in) genome (Ensembl ASM251v1). The following parameters were used: --outFilterMultimapNmax 2, --outFilterMismatchNmax 1, --outMultimapperOrder Random, --quantMode GeneCounts, --seedSearchStartLmaxOverLread 0.5, --winAnchorMultimapNmax 15, --alignIntronMax 1000. Sense-mapping counts were estimated using featureCounts and used to construct K. lactis raw count matrix as input into DEseq2. Features corresponding to K. lactis rRNA were filtered out to mitigate variations due to variable rRNA depletion efficiency among samples.
Reads that did not map to K. lactis were designated for alignment to the S. cerevisiae S288C genome (Ensembl R64-1-1). The following parameters were used: --outFilterMultimapNmax 2, --outFilterMismatchNmax 1, --outMultimapperOrder Random, --quantMode GeneCounts, --seedSearchStartLmaxOverLread 0.5, --winAnchorMultimapNmax 15, --alignIntronMax 800. Sense, antisense or unstranded counts were estimated using featurCounts. Features other than protein-coding genes (mRNAs) were filtered out to create S. cerevisiae raw counut matrices.
S. cerevisiae counts were normalized using sample-specific size factors estimated in DEseq2 based on K. lactis (spike in) sense counts.
Differential expression analysis of the S. cerevisiae spike-in corrected counts was done using DESeq2.
Assembly: sacCer3 for S. cerevisiae, and ASM251v1 for K. lactis
Supplementary files format and content: tab-delimited text files showing raw (un-normalized) feature (gene) counts. Both "library name” and “title” fields from the SAMPLES section above were concatenated for each sample and used as identifiers for the column names in the provided matrices. The first row "geneID" in each matrix represents feature names.

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: S. cerevisiae or K. lactis cells were grown in YPD and harvested at log phase (OD600 = 0.8–1.0) and were mixed in a 9:1 ratio, respectively, according to the OD600 measurements.

extract_protocol:
Total RNA was extracted from the spiked-in cell mixture using hot acid phenol. The quality of extracted RNA was assessed by gel electrophoresis (1% TBE gel), and concentrations were determined by Qubit RNA HS kit (Invitrogen). DNase treatment of the RNA samples was done on-column using RNase-Free DNase Set (QIAGEN) followed by rRNA-depletion using S. cerevisiae riboPOOLs probes (siTOOLs Biotech).
Sequencing libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB #E7760) coupled with AMPure XP bead purification (Beckman Coulter) with 18-22 ng of rRNA-depleted RNA as an input. Library quality and fragment distribution were assessed on an Agilent fragment analyzer.

value: yeast cell

value: MATa his3{delta}200 lys2-128{delta} ura3-52 trp1{delta}63 3xHA-RTF1 RAD6-13xMYC::KanMX

tag: spike in species

value: Kluyveromyces lactis

tag: spike in type

value: cell

tag: spike-in to sample ratio


title: wild-type (Tagged), BioRep2

tag: strain


title: Patient 1 [pre_1B]

description: transcriptome of in vitro expanded MSC

value: Patient 1


title: 30 min Treatment rep1

value: 30 min

tag: replicate

value: root


title: ipRGC, P1, rep78

description:
SmartSeq2
P1_77

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P1, rep82

description:
SmartSeq2
P1_81


title: Total RNA 72h OV [TOTOVLD1]

description:
TOTOVLD1
Experiment 1


title: Patient 1 [pre_1A]

description: transcriptome of in vitro expanded MSC

value: bone marrow

value: pre allogenic stem cell transplantation

value: MSC derived


title: wild-type (Tagged), BioRep1


title: ipRGC, P1, rep80

description:
SmartSeq2
P1_79


title: 0h NO Treatment rep1

value: NO Treatment


title: ipRGC, P1, rep77

description:
SmartSeq2
P1_76


title: Sham RNA 72h OV [TOTSHAM1]

description:
TOTSHAM1
Experiment 1

value: Plantaris (skeletal muscle)

value: Sham Surgery


title: wild-type (Untagged), BioRep3

value: MATa his3{delta}200 lys2-128{delta} ura3-52 trp1{delta}63


title: ipRGC, P1, rep76

description:
SmartSeq2
P1_75

value: Retina


title: Patient 5 [post_5B]

description: transcriptome of in vitro expanded MSC

value: post allogenic stem cell transplantation

value: Patient 5


title: Non-EU Sham [NEUSHAM1]

description:
NEUSHAM1
Experimetn 3


title: wild-type (Untagged), BioRep1

value: yeast cell


title: Patient 5 [post_5A]

description: transcriptome of in vitro expanded MSC


title: ipRGC, P1, rep75

description:
SmartSeq2
P1_74

value: ipRGC


title: Patient 4 [post_4B]

description: transcriptome of in vitro expanded MSC

value: Patient 4


title: Non-EU 72h OV [NEUOVLD2]

description:
NEUOVLD2
Experiment 3

value: Synergist Ablation Overload


title: Patient 4 [post_4A]

description: transcriptome of in vitro expanded MSC


title: rtf1-108-110AAA, BioRep3

value: MATa his3{delta}200 lys2-128{delta} ura3-52 trp1{delta}63 3HA-rtf1-108-110AAA RAD6-13xMYC::KanMX

value: Kluyveromyces lactis

value: cell


title: Non-EU 72h OV [NEUOVLD3]

description:
NEUOVLD3
Experiment 3


title: ipRGC, P1, rep74

description:
SmartSeq2
P1_73

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: Non-EU Sham [NEUSHAM2]

description:
NEUSHAM2
Experiment 3


title: Patient 3 [post_3B]

description: transcriptome of in vitro expanded MSC

value: bone marrow

value: Patient 3


title: Non-EU 72h OV [NEUOVLD1]

description:
NEUOVLD1
Experiment 3


title: ipRGC, P1, rep73

description:
SmartSeq2
P1_72


title: rtf1-108-110AAA, BioRep1


title: ipRGC, P1, rep72

description:
SmartSeq2
P1_71


title: wild-type (Untagged), BioRep2


title: EU Sham [EUSHAM1]

description:
EUSHAM1
Experiment 2


title: EU Sham [EUSHAM2]

description:
EUSHAM2
Experiment 2


title: Patient 2 [post_2B]

description: transcriptome of in vitro expanded MSC

value: MSC derived

value: Patient 2


title: Patient 3 [post_3A]

description: transcriptome of in vitro expanded MSC


title: ipRGC, P1, rep71

description:
SmartSeq2
P1_70


title: EU 72h OV [EUOVLD2]

description:
EUOVLD2
Experiment 2

value: Plantaris (skeletal muscle)


title: ipRGC, P1, rep70

description:
SmartSeq2
P1_69


title: EU 72h OV [EUOVLD3]

description:
EUOVLD3
Experiment 2


title: Patient 2 [post_2A]

description: transcriptome of in vitro expanded MSC


title: rad6D (Tagged), BioRep2

value: MATa his3{delta}200 lys2-128{delta} ura3-52 trp1{delta}63 3xHA-RTF1 rad6{delta}::KanMX


title: rad6D (Tagged), BioRep3


title: ipRGC, P1, rep68

description:
SmartSeq2
P1_67

value: Retina


title: ipRGC, P1, rep69

description:
SmartSeq2
P1_68


title: rad6D (Tagged), BioRep1


title: rad6D (Untagged), BioRep3

value: MATa his3{delta}200 lys2-128{delta} ura3-52 trp1{delta}63 rad6{delta}::KanMX


title: rtf1-108-110AAA, BioRep2


title: Patient 1 [post_1B]

description: transcriptome of in vitro expanded MSC

value: post allogenic stem cell transplantation

value: Patient 1


title: Dox Myc [MYC_THREE_PLANT]

description:
MYC_THREE_PLANT
Experiment 5

value: HSA-Myc

value: Doxycycline


title: ipRGC, P1, rep67

description:
SmartSeq2
P1_66

value: ipRGC


title: Dox Myc [MYC_TWO_PLANT]

description:
MYC_TWO_PLANT
Experiment 5


title: ST9

city: Nanjing

first: Binghua

last: Li

state: Jiangsu

address: Zhongshan road 321, Nanjing, Jiangsu, China

department: Department of Hepatobiliary Surgery

institute: the Affiliated Drum Tower Hospital, Medical School of Nanjing University

data_processing:
Sequence data were removed from adaptors and low-quality reads using the Cutadapt. The sequence quality was verified using FastQC. The cleaned sequence data were aligned to the human reference genome (GRCh38, which is called hg38 at UCSC) by HISAT2. SAMtools was used to convert between the formats, sort and index the alignment output. The read count program called featureCounts was used to quantify reads to genes.
Assembly: hg38
Supplementary files format and content: Transcripts per million (TPM) values for each sample

source_name: Tumor

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511), high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Tumor

value: hepatocellular carcinoma


title: ST8


title: Dox Myc [MYC_ONE_PLANT]

description:
MYC_ONE_PLANT
Experiment 5


title: ipRGC, P1, rep66

description:
SmartSeq2
P1_65


title: ipRGC, P1, rep64

description:
SmartSeq2
P1_63


title: Dox Control [CON_TWO_PLANT]

description:
CON_TWO_PLANT
Experiment 5


title: ST6


title: EU 72h OV [EUOVLD1]

description:
EUOVLD1
Experiment 2

value: Synergist Ablation Overload


title: rad6D (Untagged), BioRep1

value: yeast cell

value: Kluyveromyces lactis

value: cell


title: Dox Myc [MYC_FOUR_PLANT]

description:
MYC_FOUR_PLANT
Experiment 5


title: rad6-R6Q, BioRep2

value: MATa his3{delta}200 lys2-128{delta} ura3-52 trp1{delta}63 3xHA-RTF1 rad6-R6Q-13xMyc::KanMX


title: rad6-R6Q, BioRep3


title: ST7


title: ST5


title: rad6-R6Q, BioRep1


title: rad6D (Untagged), BioRep2


title: ipRGC, P1, rep63

description:
SmartSeq2
P1_62

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: rad6-R6A,M10A, BioRep3

value: MATa his3{delta}200 lys2-128{delta} ura3-52 trp1{delta}63 3xHA-RTF1 rad6-R6A,M10A-13xMyc::KanMX


title: ipRGC, P1, rep62

description:
SmartSeq2
P1_61


title: Dox Control [CON_THREE_PLANT]

description:
CON_THREE_PLANT
Experiment 5

value: Plantaris (skeletal muscle)


title: rad6-R6A,M10A, BioRep2


title: ipRGC, P1, rep61

description:
SmartSeq2
P1_60

value: Retina


title: ipRGC, P1, rep59

description:
SmartSeq2
P1_58


title: Left ventricle, DOCA-salt HTO

city: Nashville

first: Charles

middle: Duncan

last: Smart

address: 2201 West End Ave

department: Molecular Physiology and Biophysics

institute: Vanderbilt University

description:
Cardiac immune cells from DOCA-salt treated mice; four biological replicates
doca.salt barcodes
doca.salt features.tsv.gz
doca.salt matrix.mtz.gz

library_source: other

data_processing:
Alignment, filtering, barcode and UMI detection performed using default parameters in 10X CellRanger
Normalization of RNA assay using Seurat v4 with default settings
Normalization of ADT assay using Seurat v4 with "CLR" method
Normalization of hashtag (HTO) assay using Seurat v4 with "CLR" method
Assembly: mm10
Supplementary files format and content: Data processed using CellRanger to create features, barcodes, matrix files

molecule: protein

source_name: Heart

extract_protocol:
Left ventricular tissue was perfused with PBS.Tissue was minced with fine scissors into small pieces and digested with Liberase TM for 30 minutes at 37 degrees C. Immune cells were then enriched for using magnetic beads toward CD45 (Miltenyi). Resulting samples were then stained with hashtags and extracellular antibodies. Finally samples were ashed and experimental groups pooled. Cells were then sorted for live single CD45+ cells and loaded onto the 10X controller.
Libraries were prepared according to manufacturer's instructions for 10X Chromium Single Cell 5' Reagent Kit v2 with the 5' Feature Barcode Library Kit by the Vanderbilt Technologies for Advanced Genomics core targeting 20,000 cells/lane and sequenced on a NovaSeq 6000 targeting 50,000 reads per cell

value: Heart

tag: cell line

value: tissue

value: Immune

value: DOCA-salt


title: ipRGC, P1, rep65

first: Alex

address: 725 N Wolfe St

institute: Johns Hopkins University School of Medicine

description:
SmartSeq2
P1_64


title: ipRGC, P1, rep60

description:
SmartSeq2
P1_59


title: Left ventricle, DOCA-salt GEX


title: ST2


title: ipRGC, P1, rep58

description:
SmartSeq2
P1_57


title: ST1


title: ST12


title: Left ventricle, Sham HTO

description:
Cardiac immune cells from sham controls; four biological replicates
sham barcodes.tsv.gz
sham features.tsv.gz
sham matrix.mtx.gz

value: Sham


title: ST11


title: Dox Control [CON_ONE_PLANT]

description:
CON_ONE_PLANT
Experiment 5

value: HSA-Myc

value: Doxycycline


title: ST4

value: Tumor

value: hepatocellular carcinoma


title: Left ventricle, Sham GEX


title: H2B-K123R, BioRep3

value: yeast cell

value: MATa his3{delta}200 lys2-128{delta} ura3-52 trp1{delta}63 HTA1-htb1K123R HTA2-htb2-K123R


title: H2B-K123R, BioRep2

value: Kluyveromyces lactis

value: cell


title: H2B-K123R, BioRep1


title: ipRGC, P1, rep55

description:
SmartSeq2
P1_54

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: SP9

source_name: Nontumor

value: Nontumor

value: liver


title: ipRGC, P1, rep56

description:
SmartSeq2
P1_55

value: Retina


title: e. coli, 50 µM MgSO4, rep1

city: Sherbrooke

first: Eric

last: Massé

state: QC

address: 3201, Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

data_processing:
Raw reads were checked for quality by FastQC software (version 0.11.9)
Adapter and linker sequences were removes from the reads using the Cutadapt (Version 3.7)
Low-quality reads with quality score less than 20 and reads shorter than 16 nucleotides were discarded using Trimmomatic (Version 0.38).
 The remaining reads were then mapped to the E. coli genome MG1655 (NC_000913.3) using Bowtie2 (Version 2.4.2). Reads for each gene were counted using FeatureCounts from Subread package  (Version 2.0.1).
Differential expression were identified and calculated using edgeR package (Version 3.32.1). Genes with a log2 fold change > 1 and a false discovery rate (FDR) < 0.05 were considered as significant. Low and high Mg2+ Ribo-seq data types had both two biological replicates.
Assembly: Escherichia coli K12 mg1655
Supplementary files format and content: featureCountsResults.csv
Supplementary files format and content: edgerResults.csv

organism: Escherichia coli K-12

source_name: strain mg1655

growth_protocol: MG86 strain was grown in M63 glucose containing 20 µM or 50 µM MgSO4 at 37°C to late exponential phase.

extract_protocol:
Ribosome profiling was done according to an adaptation of the method described in  Ingolia et al. 2012 (Ingolia et al. 2012). Briefly, MG86 (ΔpmgtA :: placUV5) strain was grown in M63 minimal medium (0.2% glucose) containing 20µM MgSO4 or 50µM MgSO4   (high Mg2+ condition) at 37°C until late exponential phase. Chloramphenicol (100 mg/mL) was added for 2 min at 37°C.  Cells were chilled on ice for 5 min and centrifuged at 2900 x g for 20 min at 4°C for harvest.  The resulting cell pellet was washed using 10 ml RP buffer (10 mM MgCl2, 100mM NH2Cl, 20 mM Tris pH 8.0) with 1mM chloramphenicol and centrifuged again at 2900 x g for 10 min at 4°C. The pellet was freeze using liquid nitrogen.  The cells were resuspended in 2 ml of RP buffer with 1mM chloramphenicol, 100 U/mL DNase I and 0.05 U/µL Superase-in and lysed using a French Press (430 psi, six times).  Lysate was then cleared by centrifugation (17000 x g, 30 min, 4°C).  Lysate (500 µL, 25 units Abs260nm) was digested using 1500 U MNase, with 5 mM CaCl2, rotated at 1400 x g for 60 min at 25°C.  The digestion was stopped with 6 mM EGTA, then transferred to sucrose cushion and centrifuge at 35 000 rpm at 4°C for 2 h 30.  The purification and analyse were then performed as previously described (Ingolia et al. 2012).
RNA-size selection and generation of the cDNA libraries was performed as described (Ingolia and al. , 2012)

value: strain mg1655

value: [delta]pmgtA ::placUV5

value: 50 uM MgSO4


title: rad6-R6A,M10A, BioRep1

value: MATa his3{delta}200 lys2-128{delta} ura3-52 trp1{delta}63 3xHA-RTF1 rad6-R6A,M10A-13xMyc::KanMX


title: immune cells of melanoma from Irg1-/- mice

city: Shang Hai

first: LEILEI

last: CHEN

address: Dongan Road 131#

institute: Fudan University

description: BD Rhapsody

data_processing:
Basecalls performed using CASAVA version 1.8.
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter.
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
* MT% < 10%;
* Cell Gene Number < 10000;
* Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include counts for each cell. barcodes.tsv, features.tsv, matrix.mtx files.

source_name: melanoma

growth_protocol: Cells were cultured at 37℃ in DMEM, supplemented with 10% FBS. B16-F10 cells were resuspended in PBS at 1x10^7 cells/mL and 2x10^5 cells were subcutaneously injected into the right flank of C57BL/6 mice on Day 0.

extract_protocol:
Ten days after inoculation, tumors were harvested and 100 mm3 of each tumor was collected. Tumor tissues from three mice of the same group were randomly combined into one mixed sample, and then tissues were digested and went through 70 μm filters to achieve single-cell suspensions. After treatment with red blood cell lysis buffer for 5 minutes at room temperature, all samples were washed and re-suspended in flow cytometry buffer (PBS/0.5% albumin/2 Mm EDTA). In the end, Cd45+ immune cells (n = 6000 per sample) were sorted by flow cytometry and subjected to single-cell RNA sequencing.
BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by Illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: melanoma

value: CD45+ tumor immune cells


title: immune cells of melanoma from Irg1+/+ mice

description: BD Rhapsody


title: e. coli, 50 µM MgSO4, rep2


title: ST3

value: Tumor


title: ST10

value: hepatocellular carcinoma


title: ipRGC, P1, rep53

last: Kolodkin

description:
SmartSeq2
P1_52


title: ipRGC, P1, rep54

description:
SmartSeq2
P1_53


title: ipRGC, P1, rep57

description:
SmartSeq2
P1_56


title: SP8


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 3, library 7

first: Yuejun

last: Chen

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Brain Science and Intelligence Technology

description:
Nkx2_1_CREST_bulk_v1_QC_blacklist_filtered.rds
Nkx2_1_CREST_bulk_v2_QC_blacklist_filtered.rds

data_processing:
Cellranger (4.0.0) was used to process scRNA-seq datasets. LinTind (https://bioconductor.org/packages/devel/bioc/html/LinTInd.html) was used to recover CREST barcodes for individual cells from bulk (identified by UMIs) or scRNA-seq (identified by 10X cell barcodes [CBs]) datasets.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: UMI-tagged bulk-seq

source_name: cortex

extract_protocol:
Tissues, organoids and cultured cells were dissociated using papain (Worthington), Accutase (Gibco) or Trypsin-EDTA accordingly, and then pipetted into single-cell suspensions in collection medium [Neurobasal Medium, supplemented with 5% FBS]. Cells were filtered (Falcon 5mL Round Bottom Polyst) and then sorted by FACS to collect EGFP+/BFP+ cells for genomic DNA extraction (Vazyme) for bulk amplification or for single-cell RNA sequencing (10x Chromium System V3 or V3.1).
Single-cell RNA sequencing library were performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). CREST barcode libraries were amplified from the single-cell cDNA libraries generated in step 2.3 of the 10X Chromium single cell 3’ protocol with two rounds of PCR. Briefly, CREST_sc_1st_F and CREST_sc_1st_R primers were first used to enrich CREST barcodes tagged with 10X cell barcodes and UMIs. PCR products were purified using a 2-step bead purification process (0.5x then 1.1x) and then used as templates for a second round of PCR to attach sequencing adaptors and indices with CREST_sc_2nd_F and CREST_sc_2nd_R1/2 primers. The second-round PCR products (single-cell CREST libraries) were purified using a gel purification kit (Vazyme) and DNA of the targeted size collected.  For bulk amplification of CREST barcodes, both V1 and V2 CREST barcodes were enriched together from genomic DNA using three rounds of PCR amplification. Specifically, UMI-indexing PCR was first performed to identify CREST DNA from individual cells using the CREST_bulk_1st_F primer (containing 39 bp of partial Illumina sequencing adaptor, 12 bp of random UMI, and 20 bp of BFP binding sequence [10 bp upstream from CREST barcode]). Up to 500 ng of gDNA was used as template for UMI-indexing PCR for each library (for samples yielding less than 500 ng of gDNA, entire volumes were used as templates). The indexed CREST barcodes were purified using 1.6x VAHTS DNA Clean Beads (Vazyme) and amplified via a second round of PCR (using primers REST_bulk_2nd_F and CREST_bulk_2nd_R). Amplified CREST barcodes were selected and purified using a 2-step bead purification process (0.55x, then 1.45x) according to the manufacturer’s recommendations (Vazyme). Finally, sequencing adaptors and sample indices were attached to each library via a third round of PCR (using primers CREST_bulk_3rd_F and CREST_bulk_3rd_R1-8 [containing 8 bp indices]). PCR products were purified using 1.6x VAHTS DNA Clean Beads.

value: cortex

value: FACS sort, EGFP+/BFP+ cells


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 3, library 8


title: SP7


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 3, library 6


title: ipRGC, P1, rep51

description:
SmartSeq2
P1_50


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 3, library 5


title: ipRGC, P1, rep52

description:
SmartSeq2
P1_51


title: SP5


title: HGSOC030_WES

city: Seongnam-si

first: Je-Gun

last: Joung

address: 335, Pangyo-ro, Bundang-gu

country: South Korea

institute: CHA University

description: Whole exome-seq S030T

data_processing:
For whole exome sequencing, sequenced reads were aligned to the reference human genome (GRCh37) using the Burrows-Wheeler Aligner (BWA). After pre-processing using the Genome Analysis Toolkit (GATK), variants were called by Mutect2.
An RNA sequencing library was prepared by cDNA amplification, end-repair, 3’ end adenylation, adapter ligation, and amplification. Library quality and quantity were measured using the Bioanalyzer and Qubit.
Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).
Reads from the FASTQ files were mapped to the hg19 human reference genome, using STAR alignment tool. Raw read counts mapped to genes were measured using the BAM format file by RSEM.
Assembly: hg19
Supplementary files format and content: Excel file include TPM (Transcripts Per Million) normalized expression values for samples
Library strategy: Whole Exome Sequencing (WES)

source_name: ovarian tumor

extract_protocol:
Tumor DNA and 27 RNA were extracted from tumor tissues using ALLPrep DNA/RNA mini kit
Whole transcriptome sequencing was performed using the library constructed with 500 ng genomic RNA from each sample. The library construct was performed using a Truseq RNA sample preparation v2 kit (Illumina, USA). Whole-exome sequencing was carried out using 200 ng genomic DNA per sample, which was sheared using Covaris S220 (Covaris, MA, USA). A paired-end sequencing library was constructed using SureSelect XT Human All Exon v5 and a SureSelect XT reagent kit, HSQ (Agilent Technologies, Santa Clara, CA, USA)

tag: desease state

value: platinum-resistant recurrent ovarian cancer

value: ovarian tumor


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 3, library 4


title: SP6


title: HGSOC029_WES

description: Whole exome-seq S029T


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 3, library 3


title: ipRGC, p1, rep50

city: Baltimore

description:
SmartSeq2
P1_49

value: ipRGC


title: HGSOC028_WES

description: Whole exome-seq S028T


title: SP4


title: ipRGC, P1, rep49

description:
SmartSeq2
P1_48

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 3, library 2

city: Shanghai


title: ipRGC, P5, rep95

description:
SmartSeq2
P5_94


title: HGSOC027_WES

description: Whole exome-seq S027T


title: HGSOC025_WES

description: Whole exome-seq S025T


title: e. coli, 20 µM MgSO4, rep2

value: 20 uM MgSO4


title: SP3

value: Nontumor

value: liver


title: ipRGC, P5, rep94

description:
SmartSeq2
P5_93

value: Retina


title: SP1


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 2, library 8


title: ipRGC, P5, rep93

description:
SmartSeq2
P5_92


title: HGSOC023_WES

description: Whole exome-seq S023T


title: HGSOC024_WES

description: Whole exome-seq S024T


title: ipRGC, P5, rep96

description:
SmartSeq2
P5_95


title: HGSOC026_WES

description: Whole exome-seq S026T


title: SP11


title: HGSOC022_WES

description: Whole exome-seq S022T


title: ipRGC, P5, rep92

description:
SmartSeq2
P5_91


title: ipRGC, P5, rep91

description:
SmartSeq2
P5_90


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 3, library 1


title: e. coli, 20 µM MgSO4, rep1

value: strain mg1655

value: [delta]pmgtA ::placUV5


title: SP2


title: SP12


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 2, library 7


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 2, library 5


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 2, library 6


title: SP10


title: HGSOC021_WES

description: Whole exome-seq S021T


title: PT8


title: ipRGC, P5, rep90

description:
SmartSeq2
P5_89


title: PT6


title: HGSOC020_WES

description: Whole exome-seq S020T


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 2, library 4


title: ipRGC, P5, rep89

description:
SmartSeq2
P5_88


title: PT5


title: HGSOC019_WES

description: Whole exome-seq S019T


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 1, library 8


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 2, library 2


title: PT7


title: HGSOC018_WES

description: Whole exome-seq S018T


title: ipRGC, P5, rep88

description:
SmartSeq2
P5_87


title: PT3


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 2, library 3


title: HGSOC017_WES

description: Whole exome-seq S017T


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 2, library 1


title: ipRGC, P5, rep87

description:
SmartSeq2
P5_86


title: PT4


title: ipRGC, P5, rep86

description:
SmartSeq2
P5_85


title: HGSOC014_WES

description: Whole exome-seq S014T


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 1, library 5


title: PT1


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 1, library 7


title: ipRGC, P5, rep85

description:
SmartSeq2
P5_84


title: PT2


title: ipRGC, P5, rep84

description:
SmartSeq2
P5_83


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 1, library 6


title: HGSOC012_WES

description: Whole exome-seq S012T


title: HGSOC010_WES

description: Whole exome-seq S010T


title: HGSOC015_WES

description: Whole exome-seq S015T


title: ipRGC, P5, rep83

description:
SmartSeq2
P5_82


title: PT19


title: ipRGC, P5, rep82

description:
SmartSeq2
P5_81


title: HGSOC016_WES

description: Whole exome-seq S016T


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 1, library 4


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 1, library 3


title: ipRGC, P5, rep81

description:
SmartSeq2
P5_80


title: PT18


title: HGSOC009_WES

description: Whole exome-seq S009T


title: PT16


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 1, library 1


title: HGSOC011_WES

description: Whole exome-seq S011T


title: PT15


title: HGSOC013_WES

description: Whole exome-seq S013T


title: PT17


title: PT14


title: P0, Nkx2.1-CTX, CREST_bulk, biol rep 1, library 2


title: ipRGC, P5, rep79

description:
SmartSeq2
P5_78


title: ipRGC, P5, rep80

description:
SmartSeq2
P5_79


title: P0, En1-MB, CREST_bulk

source_name: midbrain

value: midbrain


title: E15.5, En1-MB, CREST_bulk, biol rep 3, library 2


title: ipRGC, P5, rep78

description:
SmartSeq2
P5_77


title: HGSOC007_WES

description: Whole exome-seq S007T


title: ipRGC, P5, rep77

description:
SmartSeq2
P5_76


title: HGSOC006_WES

description: Whole exome-seq S006T


title: PT11


title: ipRGC, P5, rep76

description:
SmartSeq2
P5_75


title: CT9


title: E15.5, En1-MB, CREST_bulk, biol rep 3, library 1


title: ipRGC, P5, rep75

description:
SmartSeq2
P5_74


title: HGSOC005_WES

description: Whole exome-seq S005T


title: ipRGC, P5, rep74

description:
SmartSeq2
P5_73


title: PT10


title: HGSOC008_WES

description: Whole exome-seq S008T


title: CT8


title: E15.5, En1-MB, CREST_bulk, biol rep 2, library 2


title: E15.5, En1-MB, CREST_bulk, biol rep 1, library 2


title: ipRGC, P5, rep72

description:
SmartSeq2
P5_71


title: ipRGC, P5, rep73

description:
SmartSeq2
P5_72


title: HGSOC003_WES

description: Whole exome-seq S003T


title: CT7


title: E15.5, En1-MB, CREST_bulk, biol rep 1, library 1


title: HGSOC002_WES

description: Whole exome-seq S002T


title: CT6


title: E12.5, En1-MB, CREST_bulk


title: ipRGC, P5, rep71

description:
SmartSeq2
P5_70


title: E10.5, En1-MB, CREST_bulk, biol rep 2


title: ipRGC, P5, rep70

description:
SmartSeq2
P5_69


title: HGSOC030_RNAseq

description: RNA-seq S030T

data_processing:
An RNA sequencing library was prepared by cDNA amplification, end-repair, 3’ end adenylation, adapter ligation, and amplification. Library quality and quantity were measured using the Bioanalyzer and Qubit.
Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).
Reads from the FASTQ files were mapped to the hg19 human reference genome, using STAR alignment tool. Raw read counts mapped to genes were measured using the BAM format file by RSEM.
Excel file include TPM (Transcripts Per Million) normalized expression values for samples
An RNA sequencing library was prepared by cDNA amplification, end-repair, 3’ end adenylation, adapter ligation, and amplification. Library quality and quantity were measured using the Bioanalyzer and Qubit.
Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).
Reads from the FASTQ files were mapped to the hg19 human reference genome, using STAR alignment tool. Raw read counts mapped to genes were measured using the BAM format file by RSEM.
Assembly: hg19
Supplementary files format and content: Excel file include TPM (Transcripts Per Million) normalized expression values for samples


title: ipRGC, P5, rep69

description:
SmartSeq2
P5_68


title: CT4


title: CT5


title: HGSOC004_WES

description: Whole exome-seq S004T


title: HGSOC029_RNAseq

description: RNA-seq S029T


title: E10.5, En1-MB, CREST_bulk, biol rep 1


title: E15.5, En1-MB, CREST_bulk, biol rep 2, library 1


title: E9.5, En1-MB, CREST_bulk

source_name: midbrain and hindbrain

value: midbrain and hindbrain


title: CT3


title: ipRGC, P5, rep67

description:
SmartSeq2
P5_66


title: CT2


title: HGSOC027_RNAseq

description: RNA-seq S027T


title: HGSOC001_WES

description: Whole exome-seq S001T


title: Day12, MEF, CREST_bulk

source_name: embryonic  fibroblasts

value: embryonic  fibroblasts

value: Lentivirus-Cre infection, FACS sort, EGFP+/BFP+ cells


title: ipRGC, P5, rep66

description:
SmartSeq2
P5_65


title: HGSOC026_RNAseq

description: RNA-seq S026T


title: CT13

value: Tumor

value: hepatocellular carcinoma


title: Day9.5, MEF, CREST_bulk


title: ipRGC, P5, rep65

description:
SmartSeq2
P5_64


title: CT1


title: Day7.5, MEF, CREST_bulk


title: HGSOC025_RNAseq

description: RNA-seq S025T


title: CT12


title: ipRGC, P5, rep63

description:
SmartSeq2
P5_62


title: CT11


title: HGSOC024_RNAseq

description: RNA-seq S024T


title: HGSOC023_RNAseq

description: RNA-seq S023T


title: Day5.5, MEF, CREST_bulk


title: ipRGC, P5, rep64

description:
SmartSeq2
P5_63


title: ipRGC, P5, rep68

description:
SmartSeq2
P5_67


title: CT10


title: HGSOC028_RNAseq

description: RNA-seq S028T


title: HGSOC022_RNAseq

description: RNA-seq S022T


title: Day5, MEF, CREST_bulk


title: Day4.5, MEF, CREST_bulk


title: ipRGC, P5, rep62

description:
SmartSeq2
P5_61


title: HGSOC021_RNAseq

description: RNA-seq S021T


title: CP9


title: ipRGC, P5, rep61

description:
SmartSeq2
P5_60


title: CP8


title: Day4, MEF, CREST_bulk


title: HGSOC020_RNAseq

description: RNA-seq S020T


title: ipRGC, P5, rep60

description:
SmartSeq2
P5_59


title: CP7


title: Day3, MEF, CREST_bulk


title: Day3.5, MEF, CREST_bulk


title: CP6


title: HGSOC019_RNAseq

description: RNA-seq S019T


title: HGSOC018_RNAseq

description: RNA-seq S018T


title: ipRGC, P5, rep58

description:
SmartSeq2
P5_57


title: Day2.5, MEF, CREST_bulk


title: HGSOC017_RNAseq

description: RNA-seq S017T


title: Day2, MEF, CREST_bulk


title: CP4


title: HGSOC016_RNAseq

description: RNA-seq S016T


title: CP5


title: Patient 1 [post_1A]

description: transcriptome of in vitro expanded MSC

value: bone marrow

value: post allogenic stem cell transplantation

value: MSC derived

value: Patient 1


title: ipRGC, P5, rep56

description:
SmartSeq2
P5_55

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: Day1.5, MEF, CREST_bulk


title: HGSOC014_RNAseq

description: RNA-seq S014T

value: platinum-resistant recurrent ovarian cancer

value: ovarian tumor


title: Day7, organoid, pandaCREST, biol rep 1,CREST_sc, library 3

data_processing:
Cellranger (4.0.0) was used to process scRNA-seq datasets. LinTind (https://bioconductor.org/packages/devel/bioc/html/LinTInd.html) was used to recover CREST barcodes for individual cells from bulk (identified by UMIs) or scRNA-seq (identified by 10X cell barcodes [CBs]) datasets.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: organoid

value: organoid

value: FACS sort, EGFP+/BFP+ cells

value: DIV Day7


title: ipRGC, P5, rep57

description:
SmartSeq2
P5_56

value: Retina


title: ipRGC, P5, rep55

description:
SmartSeq2
P5_54


title: ipRGC, P5, rep54

description:
SmartSeq2
P5_53


title: Day1, MEF, CREST_bulk


title: CP3

value: Nontumor

value: liver


title: CP1


title: ipRGC, P5, rep52

description:
SmartSeq2
P5_51


title: CP13


title: CP2


title: ipRGC, P5, rep59

description:
SmartSeq2
P5_58


title: ipRGC, P5, rep51

description:
SmartSeq2
P5_50


title: ipRGC, P5, rep53

description:
SmartSeq2
P5_52


title: E11.5, vMB, pandaCREST, biol rep 1,CREST_sc, library 3

source_name: ventral midbrain

value: ventral midbrain


title: HGSOC013_RNAseq

description: RNA-seq S013T


title: Day7, organoid, pandaCREST, biol rep 1,CREST_sc, library 2


title: Day7, organoid, pandaCREST, biol rep 1,CREST_sc, library 1


title: HGSOC015_RNAseq

description: RNA-seq S015T


title: CP12


title: HGSOC009_RNAseq

description: RNA-seq S009T


title: CP10


title: CP11


title: Gr2-YZ014-Nude-no4

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

data_processing:
Basecalling using bcl2fastq 2.19
Cell Ranger pipeline (10x Genomics, Cellranger count v3) with default parameters  and a combined GrCh38/Rnor6 reference genome
Seurat (v 4 and R version 4.0.1) was applied to the scRNA-data for downstream analysis of matrix files.
Assembly: GrCH38/Rnor6

source_name: Striatal graft of dopamine progenitors, 6 months old

growth_protocol: RC17 hESCs (Roslin Cells) were cultured at 37 °C and 5% CO2 and used for all transplantation experiments. Regional patterning of hESCs toward a ventral midbrain (VM) fate was performed via dual SMAD inhibition to induce neuralization, GSK3 inhibitor-mediated caudalization, and SHH-mediated ventralization. Lentiviral barcoded VM cells were transplanted into striatal brain region of Parkinsonism rat, including Sprague-Dawley rat (n=6) as well as athymic nude rats (n=6). Lesion of the nigrostriatal pathway in rats was induced by unilateral injection of 6-hydroxydopamine into the right medial forebrain bundle (MFB).

extract_protocol:
Grafted VM patterned hESCs cells were dissected from rat striatum (n = 6 for VM intrastriatal grafts at 3 month post-transplantation, n = 6 for hESC intrastriatal grafts at 6 month post-transplantation) and transferred to a glass douncer containing 1 ml of nuclei lysis buffer (consisted of sucrose, CaCl2, MgAc, EDTA, Tril-HCl, DTT, Triton X-100, RNase inhibitor and RNase-free water) on ice. Tissue was completely minced and homogenized to nuclei suspension by sample grinding with Dounce homogenizers with 10 strokes with loose pestle and then 10 strokes with tight pestle. The nuclei suspension was filtered by loading through a 35-µm-diameter filter and followed by centrifuging for 10 min at 900g and 4 °C.
According to 10X protocols.

tag: culture condition

value: 6 months in vivo


title: E11.5, vMB, pandaCREST, biol rep 1,CREST_sc, library 2


title: Gr2-YZ014-Nude-no3


title: ipRGC, P1, rep48

description:
SmartSeq2
P1_47


title: HGSOC007_RNAseq

description: RNA-seq S007T


title: ipRGC, P1, rep46

description:
SmartSeq2
P1_45


title: HGSOC010_RNAseq

description: RNA-seq S010T


title: ipRGC, P5, rep49

description:
SmartSeq2
P5_48


title: E11.5, vMB, pandaCREST, biol rep 1,CREST_sc, library 1


title: HGSOC011_RNAseq

description: RNA-seq S011T


title: HGSOC008_RNAseq

description: RNA-seq S008T


title: E15.5, vMB, snapCREST, biol rep 1,CREST_sc, TaqPlusMaster


title: E15.5, vMB, snapCREST, biol rep 1,CREST_sc, AceTaq


title: E15.5, vMB, snapCREST, biol rep 1,CREST_sc, TaqPlus


title: HGSOC005_RNAseq

description: RNA-seq S005T


title: HGSOC012_RNAseq

description: RNA-seq S012T


title: ipRGC, P1, rep47

description:
SmartSeq2
P1_46


title: Gr1-YZ014-Nude-no15


title: HGSOC004_RNAseq

description: RNA-seq S004T


title: Gr2-YZ014-Nude-no1


title: HGSOC006_RNAseq

description: RNA-seq S006T


title: ipRGC, P5, rep50

description:
SmartSeq2
P5_49


title: Gr1-YZ014-Nude-no6


title: HGSOC003_RNAseq

description: RNA-seq S003T


title: G2-YZ013-SD-no4

source_name: Striatal graft of dopamine progenitors, 3 months old

value: 3 months in vivo


title: Gr1-YZ014-Nude-no12


title: G2-YZ013-SD-no6


title: NO92N

city: Guangzhou

first: Yujing

last: He

state: guangdong

address: No.1023-1063 South Shatai Road, Baiyun District, Guangzhou City, Guangdong Province

department: thoracic

institute: nanfang hospital

data_processing:
The original image data file obtained by high-throughput sequencing is converted into the original data of sequencing sequence (Raw) through CASAVA base calling analysis Data), the results are stored in FASTQ (abbreviated as fq) file format, which contains sequence information of sequencing data and its corresponding sequencing quality information
Quality Score or Q-score is obtained based on the Phred mass value formula, an integer mapping is used to determine the probability of base calling errors
AT and GC separation was checked in the distribution of base types
Based on the sequencing characteristics of the Illumina platform, datas from dual end sequencing were used and taken Q30 with an average proportion of over 85%
Sequencing align Clean Reads with the reference genome was used Hisat2 to obtain positional information on the reference genome or gene, as well as sequence characteristic information unique to the sequencing sample
The quality of transcriptome library is assessed by evaluating the randomness of mRNA fragmentation, the dispersion of inserted fragment length, and the adequacy of library capacity and mapped Data
Gene expression quantification was used with network flow algorithms and optional denovo assembly to assemble complex datasets into transcripts. FPKM (Fragments Per Kilobase of script per Million fragments mapped) was an indicator to measure transcript or gene expression levels
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: esophageal squamous carcinoma

extract_protocol:
Total RNA was harvested using Tiangen DP411, CLB+Adlai RN40, CTAB+Adlai RN40, Tiangen DP762-T1C reagent kit/TRIzol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared following Soexa TruSeq RNA protocols.

value: esophageal squamous carcinoma

value: Cisplatin sensitive


title: E11.5, vMB, snapCREST, biol rep 1,CREST_sc, library 2


title: E11.5, vMB, snapCREST, biol rep 1,CREST_sc, library 3


title: E11.5, vMB, snapCREST, biol rep 1,CREST_sc, library 1


title: BC-G2-YZ013-ratSD8-Nuc1


title: G1-YZ013-SD-no12


title: G1-YZ013-SD-no13


title: ipRGC, P1, rep40

description:
SmartSeq2
P1_39

source_name: Retina


title: ipRGC, P1, rep45

description:
SmartSeq2
P1_44


title: ipRGC, P1, rep43

description:
SmartSeq2
P1_42


title: Day7, organoid, pandaCREST, biol rep 1, scRNAseq

description: 10x Genomics


title: E11.5, vMB, pandaCREST, biol rep 1, scRNAseq

description: 10x Genomics


title: E11.5, vMB, snapCREST, biol rep 1, scRNAseq

description: 10x Genomics


title: ipRGC, P1, rep37

description:
SmartSeq2
P1_36


title: RPM

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

data_processing:
The preprocessing steps such as generation and demultiplexing of FASTQ files from the raw sequencing reads (bclfastq, v2.20), aligning to UCSC mm10 transcriptome, and generating raw count matrices were conducted using Cell Ranger (v6.0.1) (10x Genomics) with default parameters. Cumulus software v1.5.0 (Bo, L. et al 2020) was used to combine expression matrices and to remove cell doublets by Scrublet v0.2.1 (Wolock, S.L. et al 2019). The pipelines were run in Terra Cloud Platform (http://app.terra.bio). We performed downstream analysis using the R software package Seurat v3.2.2 (Butler et al., 2018). Low-quality cells with less than 500 genes detected and all genes expressed in less than 10 cells were filtered out, leaving 26,543 cells and 20,094 genes for further analysis.
Assembly: mm10

source_name: retina

growth_protocol: All mice were housed under a standard 12-hour light (≤150 lux)/12-hour dark cycle and bred using standard procedures.

extract_protocol:
Eyes were enucleated for retinal tissue isolation. After removing the anterior chamber and lens, the retina was dissected from the posterior eye cup. Then, the retinal cells were dissociated using the Papain Dissociation System (#LK003153, Worthington Biochemical) following the manufacturer's instructions.
Libraries were pooled and sequenced on Illumina NovaSeq6000 with ~500 million reads per library.

treatment_protocol: Light damage was induced in photosensitive Abca4-/-Rdh8-/- mice by exposure to white light delivered at 10,000 lux (150-W spiral lamp, Commercial Electric, Cleveland, OH) for 30 min. Mice were dark-adapted 24 hr prior to photobleaching, and pupils were dilated with 1% ophthalmic tropicamide 30 min prior to light exposure. 2 mg/kg BAY 60-7550, rolipram, or BC11-38 were administered in DMSO vehicle by intraperitoneal injection 30 min prior to light exposure.

tag: age (weeks)

value: 1 day post-bleach, 2 mg/kg Rolipram


title: HGSOC002_RNAseq

description: RNA-seq S002T


title: ipRGC, P1, rep41

description:
SmartSeq2
P1_40


title: ipRGC, P1, rep44

description:
SmartSeq2
P1_43


title: 2-RC17-LvLib1-2-BC-Vmcells-G1

source_name: Midbrain progenitors, day 18

value: 18 days in vitro


title: E15.5, vMB, snapCREST, biol rep 1, scRNAseq

description: 10x Genomics


title: 1D

value: 1 day post-bleach, DMSO vehicle


title: ipRGC, P1, rep38

description:
SmartSeq2
P1_37

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: NO79AG

value: Cisplatin resistant


title: NO108


title: ipRGC, P1, rep39

description:
SmartSeq2
P1_38


title: NB

value: non-bleached, DMSO vehicle


title: ipRGC, P1, rep35

description:
SmartSeq2
P1_34


title: 1-RC17-LvLib1-2-BC-Vmcells-G1


title: BC-G1-YZ013-ratSD15-Nuc1


title: NO106shiguanca


title: BC11

value: 1 day post-bleach, 2 mg/kg BC11-38


title: NO96shiguanN


title: hTERT-RPE1 p53+/A276P, treated with nutlin-3a

first: Fred

last: Bunz

address: 1550 Orleans Street

department: Radiation Oncology

institute: Johns Hopkins University

data_processing:
Geneious Prime Version 2020.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk
Trimmed sequence reads were mapped to Hg38 using the Geneious RNA mapper (parameters-maximum gaps per read 10%, maximum 20% mismatches, minimum overlap identity 80%)
Read count extraction and normalization were performed using Geneious Prime.
Assembly: GRCh38
Supplementary files format and content: tab-delimited excel files include raw read counts, raw transcript counts, RPKM and TPM values for each Sample

growth_protocol: hTERT-RPE1cells were maintained in DMEM/F12 supplemented with 6% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using the Monarch total RNA miniprep kit (NEB). 500 ng of total RNA was used for polyA selection prior to the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were untreated (control) or treated with the p53 activator nutlin-3a (10 µM) for 8 hours prior to harvest..

value: hTERT-immortalized retinal pigment epithelial cells

value: 10 microM nutlin-3a

tag: time

value: 8 h