title: RNA-Seq-II Retinal ganglion cells, GFP overexpression, replicate 2

city: Tampa

first: Xuewei

address: 4001 E Fletcher Ave, ALZ 339

department: Molecular Medicine

institute: University of South Florida

data_processing:
Raw FASTQ data were mapped to the mouse reference genome (GRCm38) using STAR aligner (version 2.7.0d) with default parameters.
The number of counts per gene was estimated using the “quantMode” command in STAR.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file including raw count for each library

source_name: Retinal ganglion cells

extract_protocol:
RNA was isolated from retinal ganglion cells using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific KIT0204) following the manufacture’s manual.
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Kit (Illumina).

treatment_protocol: AAV2-GFP or AAV2-Ezh2-Y726D was injected into the vitreous body and the optic nerve was crushed after two weeks. Three days after the optic nerve crush, retinal ganglion cells were enriched from dissociated retinal cells by fluorescence-activated cell sorting.

value: Retinal ganglion cells


title: RNA-Seq-II Retinal ganglion cells, GFP overexpression, replicate 3

status: Public on Dec 22 2023

type: SRA

last: Wang

state: FL

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: genotype


title: RNA-Seq-I Retinal ganglion cells, Ezh2 overexpression, replicate 1

treatment_protocol: AAV2-GFP or AAV2-Ezh2 was injected into the vitreous body and the optic nerve was crushed after two weeks. Three days after the optic nerve crush, retinal ganglion cells were enriched from dissociated retinal cells by fluorescence-activated cell sorting.


title: RNA-Seq-I Retinal ganglion cells, Ezh2 overexpression, replicate 2


title: RNA-Seq-II Retinal ganglion cells, Ezh2-Y726D overexpression, replicate 3


title: RNA-Seq-II Retinal ganglion cells, Ezh2-Y726D overexpression, replicate 2


title: THP-1, LPS+IFNα2, 3h

city: Shanghai

first: Guanxing

last: Zhai

state: Shanghai

address: 2901 Caolang Road, Shanghai

country: China

institute: Shanghai Public Health Clinical Center, Fudan University

data_processing:
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.
The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar.
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software8-9. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: hg38
Supplementary files format and content: Excel files include the FPKM values of for each sample.

organism: Homo sapiens

growth_protocol: THP-1 cells were cultured in RPMI1640 supplemented with 10%FBS+1%P/S, seeded in a 24-well plate, 1E5/well.

extract_protocol:
Total RNA was extracted using the RNAzol reagent (Molecular Research Center, OH, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: THP-1 treatment was divided into the following groups: Mock (Blank), LPS, LPS+TIF, LPS+IFNα2, and LPS+TFF2. After treatment with the above protein at 100 μM for 2 h, LPS (10 ng/ml) was stimulated for 1, 3, 6, 12, and 24 h.

tag: cell line

value: leukemia monocytic cell

value: WT

tag: treatment


title: THP-1, LPS+IFNα2, 24h


title: RNA-Seq-II Retinal ganglion cells, GFP overexpression, replicate 1


title: THP-1, LPS+TIF, 24h

value: LPS+TIF


title: RNA-Seq-I Retinal ganglion cells, GFP overexpression, replicate 2


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_119

city: Bethesda

first: Avindra

last: Nath

state: Maryland

address: 10 Center Drive

institute: NIH/NINDS

description:
Peripheral Blood Mononuclear Cells, HV, Baseline
Illuminasoftware bcl2fastq v.2.17

data_processing:
Illuminasoftware bcl2fastq v.2.17
RNA sequences were subjected to quality control  through FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Adapters were removed using Trimmomatic: https://github.com/timflutre/trimmomatic
Alignment to the human genome (GRCh38) using STAR
Gene expression levels were quantified using FeaturesCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene expression levels for each sample

source_name: Blood

extract_protocol:
RNA was extracted from PBMC’s of participants using miRNeasy Micro Kit (QIAGEN).
Dual index libraries were constructed with at least one unique index per each patient library using the TruSeq Stranded Total RNA HT Kit (Illumina).

tag: tissue

value: Blood

tag: Sex

value: Female


title: RNA-Seq-II Retinal ganglion cells, Ezh2-Y726D overexpression, replicate 1


title: RNA-Seq-I Retinal ganglion cells, GFP overexpression, replicate 1


title: RNA-Seq-I Retinal ganglion cells, Ezh2 overexpression, replicate 3


title: THP-1, LPS+IFNα2, 1h


title: THP-1, LPS+TIF, 12h


title: hESC, SNE (soluble nuclear extract), Day3, rep1 [D10-1_RRL21043-V]

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatics (version 0.36).
Trimmed sequence reads were mapped to hg38 (GENCODE v28) human genome using Hisat2 (v2.0.5) with parameter “--rna-strandness RF”.
The gatk was used to remove PCR duplicates from aligned BAM files.
Raw counts at the gene level were calculated with featureCounts (version 1.6.2). Isoform-level expression was quantified as transcripts per million reads (TPM) with Salmon (version 1.3.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: H1 hESC

growth_protocol: Human ESC line H1 were maintained in mTeSR1 (StemCell Technologies, 85850) on matrigel (Corning, 354277)-coated plates. hESCs were fed with fresh hESC medium daily.

extract_protocol:
definitive mesoderm cells differentiation protocol:
To initiate mesoderm differentiation, hESCs were plated onto matrigel-coated 6-well plates with 70% of cell confluence, and then these cells were cultured in IMDM medium (Gibco, 12440053) plus 10% FBS (Gibco, 10099141), 2 mM Glutamine (Gibco, 25030164), 50 μg/mL Ascorbic Acid (StemCell Technologies, 72132), 0.1 μM Monothioglycerol (Sigma, M6145), 10 ng/mL BMP4 (StemCell Technologies, 02524) for 1 day. And then cells were cultured 4 days in the above medium supplemented with bFGF (2.5 ng/mL, StemCell Technologies, 78003.1). Cells were fed with fresh medium daily.
subcellular isolation protocol:
Operations refer to Subcellular Protein Fractionation Kit’s (Thermo Fisher, 78840) instruction. We collected cells and added cytoplasmic extraction buffer in the tube. After incubating the tube at 4°C for 10 min and centrifuging at 500 × g for 5 min, we immediately transferred the supernatant (cytoplasmic extract). Then we added the membrane extraction buffer, incubated at 4℃ for 10 min and centrifuged at 3000 × g for 5 min, and transferred the supernatant (membrane extract). We further added the nuclear extraction buffer. After incubating at 4℃ for 30 min and centrifuging at 5000 × g for 5 min, we transferred the supernatant (soluble nuclear extract) fraction. Similarly, we added nuclear extraction buffer containing CaCl2 (5 mM) and micrococcal nuclease (300 units), incubated at room temperature for 15 min, centrifuged at 20,000 × g for 5 min, and transferred the supernatant (chromatin-bound nuclear extract) fraction. Finally, pellet extraction buffer was added in tube. After incubating at room temperature for 10 min and centrifuging at 20,000 × g for 5 min, we obtained the supernatant (i.e., the cytoskeletal extract). All of the buffers were supplemented with protease inhibitor and RNase inhibitor.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: H1 hESC

value: embryonic stem cells

value: mesoderm differentiation

tag: time

value: Day 3


title: RNA-Seq-I Retinal ganglion cells, GFP overexpression, replicate 3


title: THP-1, LPS+IFNα2, 6h


title: THP-1, LPS+TFF2, 1h


title: THP-1, LPS+TIF, 6h


title: THP-1, LPS, 24h

value: LPS


title: THP-1, LPS, 3h


title: 33586_WT_Ifnar1ASO1_300 ug_female

city: Carlsbad

first: Christine

middle: C

last: Hong

state: CA

address: 2855 Gazelle Ct

department: Neurology

institute: Ionis Pharmaceuticals

data_processing:
Libraries were sequenced as 75 bp fragments with a median depth of 4.2 million reads per sample on an Illumina NextSeq500.
Gene quantitation was performed with Salmon (v 0.7.2) and Ensembl build 81.
Assembly: 81
Supplementary files format and content: Plain-text, tab-separated file that include TPM and count values for each sample

source_name: Cortex

extract_protocol:
Tissue samples were homogenized in Trizol using FastPrep beads on a Precellys 24 homogenizer. RNA was isolated and DNase treated on an RNeasy 96-well plate (Qiagen).
Next generation sequencing libraries were generated using QuantSeq 3’ mRNA-Seq Library Prep FWD Kit (015.96, Lexogen) according to the manufacturer’s instructions.

value: Cortex

tag: strain background

value: mixed C57Bl/6 and Balb/c

value: female

value: Ifnar1ASO1_300 ug


title: THP-1, LPS+TIF, 1h


title: 33585_WT_ControlASO_500 ug_female

value: Ifnar1ASO1_500 ug


title: THP-1, LPS, 12h


title: THP-1, LPS, 6h


title: THP-1, LPS, 1h


title: THP-1, Blank, 6h

description: Blank

value: No tratment


title: 33587_WT_Vehicle_0 ug_male

value: male

value: Vehicle_0 ug


title: 33583_WT_Ifnar1ASO1_300 ug_female

value: WT


title: 33581_WT_Ifnar1ASO1_300 ug_male


title: 33578_WT_Ifnar1ASO2_500 ug_female


title: 33579_GIFN_Ifnar1ASO2_500 ug_male

value: GIFN


title: 33580_GIFN_Vehicle_0 ug_female


title: 33582_WT_Vehicle_0 ug_male


title: 33577_WT_ControlASO_500 ug_female


title: Semen, buccal swab, vasectomy male, sample 35

city: Los Angeles

first: Matteo

last: Pellegrini

address: 610 Charles E. Young Drive South

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

library_source: genomic

data_processing:
BSBolt (v1.5.0)
First, the GRCh38 human reference genome was indexed with the BSBolt Index command and the FASTQ files were aligned to the reference genome using the BSBolt Align command. Post-alignment processing including PCR duplicate removal was performed using SAMtools (v1.15).
Next, the BSBolt CallMethylation command was used to generate CGmap files before the methylation matrix aggregation. We only kept methylation sites above a minimum read depth coverage of 40.
Finally, we imputed the matrix with the BSBolt Impute command to fill in the missing values using the k-Nearest Neighbors (kNN) method.
Assembly: GRCh38 human reference genome
Supplementary files format and content: tab separated text format CGmap files describing the methylation status of observed cyotsines for each sample

molecule: genomic DNA

source_name: Semen, buccal swab

extract_protocol:
Prior to DNA extraction, buccal and semen swabs were incubated overnight at 50°C. DNA was extracted using reagents from DNA Genotek (Stittsville, Ontario, Canada).
500 ng of extracted DNA were used for TBSq library preparation. Fragmented DNA was subject to end repair, dA-tailing, and adapter ligation using the NEBNext Ultra II Library prep kit using custom pre-methylated adapters (IDT). Pools of 16 purified libraries were hybridized to the biotinylated probes according to the manufacturer’s protocol. Captured DNA was treated with bisulfite prior to PCR amplification using KAPA HiFi Uracil+ (Roche) with the following conditions: 2 min at 98°C; 14 cycles of 98°C for 20 sec, 60°C for 30 sec, 72°C for 30 sec; 72°C for 5 minutes; hold at 4°C. Library QC was performed using the Highnsitivity D1000 Assay on a 2200 Agilent TapeStation. Pools of 96 libraries were sequenced on a NovaSeq6000 (S1 lane) as paired-end 150 bases.

value: Semen, buccal swab

value: Human seminal fluids, human buccal swab


title: Semen, buccal swab, vasectomy male, sample 37


title: THP-1, LPS+TIF, 3h

value: leukemia monocytic cell

value: LPS+TIF


title: 33573_WT_ControlASO_500 ug_male


title: 33574_GIFN_Ifnar1ASO2_500 ug_male


title: Semen, buccal swab, vasectomy male, sample 34


title: Semen, buccal swab, vasectomy male, sample 33


title: Semen, buccal swab, vasectomy male, sample 36


title: 33572_GIFN_ControlASO_300 ug_female


title: Semen, buccal swab, vasectomy male, sample 31


title: 33571_GIFN_Ifnar1ASO1_300 ug_female


title: Semen, buccal swab, vasectomy male, sample 30


title: 33576_GIFN_ControlASO_300 ug_male


title: Semen, buccal swab, vasectomy male, sample 29


title: Semen, buccal swab, vasectomy male, sample 32


title: 33569_GIFN_Vehicle_0 ug_female


title: 33575_GIFN_Ifnar1ASO1_300 ug_male


title: 33568_WT_ControlASO_500 ug_female


title: 33584_GIFN_Ifnar1ASO1_300 ug_male


title: Semen, buccal swab, vasectomy male, sample 28


title: Semen, buccal swab, vasectomy male, sample 27


title: 33567_WT_ControlASO_500 ug_male


title: 33570_WT_ControlASO_500 ug_male


title: Semen, buccal swab, vasectomy male, sample 25


title: 33562_GIFN_Vehicle_0 ug_male


title: 33565_WT_Ifnar1ASO2_500 ug_female


title: Semen, buccal swab, vasectomy male, sample 21


title: Semen, buccal swab, vasectomy male, sample 22


title: Semen, buccal swab, vasectomy male, sample 24


title: 33564_WT_Ifnar1ASO2_500 ug_female


title: 33563_WT_Vehicle_0 ug_female


title: Semen, buccal swab, vasectomy male, sample 23


title: Semen, buccal swab, vasectomy male, sample 19


title: Semen, buccal swab, vasectomy male, sample 20


title: 33561_WT_Ifnar1ASO2_500 ug_female


title: Semen, buccal swab, vasectomy male, sample 16


title: 33566_WT_ControlASO_300 ug_female


title: Semen, buccal swab, vasectomy male, sample 13


title: Semen, buccal swab, vasectomy male, sample 14


title: 33559_GIFN_Ifnar1ASO2_500 ug_male


title: 33560_WT_ControlASO_300 ug_male


title: 33558_GIFN_ControlASO_300 ug_female


title: 33557_GIFN_Ifnar1ASO1_300 ug_male


title: Semen, buccal swab, vasectomy male, sample 18


title: 33555_GIFN_Vehicle_0 ug_male


title: Semen, buccal swab, vasectomy male, sample 15


title: 33556_WT_Ifnar1ASO1_300 ug_female


title: 33554_WT_Ifnar1ASO2_500 ug_male


title: Semen, buccal swab, vasectomy male, sample 26


title: 33553_GIFN_ControlASO_500 ug_female


title: Semen, buccal swab, vasectomy male, sample 17


title: 33552_GIFN_Vehicle_0 ug_male


title: 33551_WT_Vehicle_0 ug_female


title: Semen, buccal swab, vasectomy male, sample 9


title: Semen, buccal swab, vasectomy male, sample 12


title: 33550_GIFN_Vehicle_0 ug_male


title: Semen, buccal swab, vasectomy male, sample 10


title: 33549_GIFN_Ifnar1ASO2_500 ug_male


title: Semen, buccal swab, vasectomy male, sample 8


title: 33544_WT_Ifnar1ASO2_500 ug_male


title: 33547_WT_Ifnar1ASO1_300 ug_male


title: 33548_GIFN_Ifnar1ASO1_300 ug_female


title: 33543_GIFN_Ifnar1ASO2_500 ug_male


title: 33546_WT_Vehicle_0 ug_female


title: 33541_GIFN_ControlASO_300 ug_male


title: Semen, buccal swab, vasectomy male, sample 7


title: Semen, buccal swab, vasectomy male, sample 6


title: MT2-5

city: bethesda

first: David

last: Peeney

state: MD

address: 10 Center Drive, Building 10, 6B05

institute: NCI

data_processing:
Partek Flow
Read contaminants and low-quality reads (Phred score <20) were removed using Bowtie 2.
Trimmed reads were aligned to the mouse (mm10) genome using STAR and annotated to RefSeq transcripts using Partek’s expectation-maximization algorithm.
Counts were subjected to median ratio normalization prior to cluster analysis and differential expression analysis (DEseq2).
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain the median ratio normalized counts for all samples

molecule: polyA RNA

source_name: lung

growth_protocol: Mice were housed approximately 5 mice/cage, under a 12-hour light/dark cycle with access to Purina chow and water ad libitum. For early metastatic lungs; 1× 106 LL2-Luc cells in 100µL PBS/mouse were subcutaneously injected at the dorsal flank. For intratracheal instillation, 1× 106 LL2-Luc2 cells in 50µL PBS/mouse were intratracheally administered

extract_protocol:
Approximately 3mm3 tissue was minced in 500uL buffer RP1 (Machery Nagel) + 1% bME + 0.5% antifoam Y-30 using M-tubes (Miltenyi Biotech), homogenized using a GentleMACS disruptor on the “RNA” protocol (Miltenyi Biotech). The lysate was passed through a 20Ga needle at least 5 times to produce the stock lysate. For RNA extraction, 200uL stock lysate was mixed with 500uL buffer RLT (Qiagen) homogenized further using a Qiashredder (Qiagen). The flow through was mixed 600uL 70% EtOH and loaded into a RNeasy spin column (Qiagen), then processed according to the manufacturer’s instructions.
PolyA selection was used to enrich for mRNA and RNA sequencing was performed by Azenta Life Science.

treatment_protocol: Mice were treated daily with recombinant human TIMP2 at 200ug/kg/day via intraperitoneal injection.

tag: strain

value: lung

value: Lewis Lung Carcinoma

value: mutant Timp2

value: Tumor-free


title: Semen, buccal swab, vasectomy male, sample 5


title: Semen, buccal swab, vasectomy male, sample 2


title: Semen, buccal swab, vasectomy male, sample 4


title: Semen, buccal swab, vasectomy male, sample 3


title: MT2-4


title: 33545_WT_Vehicle_0 ug_male

value: Cortex

value: mixed C57Bl/6 and Balb/c


title: Semen, buccal swab, vasectomy male, sample 11


title: 33542_WT_ControlASO_300 ug_male

value: Ifnar1ASO1_300 ug


title: MT2-3


title: Semen, buccal swab, infertile male, sample 47


title: Semen, buccal swab, vasectomy male, sample 1


title: Semen, buccal swab, vasectomy male, sample 0


title: 33539_GIFN_ControlASO_300 ug_female

value: female


title: 33540_WT_Ifnar1ASO2_500 ug_male

value: Ifnar1ASO1_500 ug


title: 33536_WT_ControlASO_300 ug_female


title: MT2-2


title: Semen, buccal swab, infertile male, sample 45


title: Semen, buccal swab, infertile male, sample 41


title: Semen, buccal swab, infertile male, sample 40


title: WT-5

value: wt


title: Semen, buccal swab, infertile male, sample 34


title: Semen, buccal swab, infertile male, sample 37


title: Semen, buccal swab, infertile male, sample 44


title: 33537_GIFN_ControlASO_300 ug_male

value: male


title: Semen, buccal swab, infertile male, sample 36


title: Semen, buccal swab, infertile male, sample 43


title: Semen, buccal swab, infertile male, sample 46


title: Semen, buccal swab, infertile male, sample 42


title: Semen, buccal swab, infertile male, sample 39


title: Semen, buccal swab, infertile male, sample 38


title: 33538_WT_Vehicle_0 ug_male

value: WT

value: Vehicle_0 ug


title: 33533_WT_ControlASO_500 ug_female


title: WT-4


title: WT-3


title: 33534_GIFN_ControlASO_500 ug_male

value: GIFN


title: Semen, buccal swab, infertile male, sample 32

value: Semen, buccal swab

value: Human seminal fluids, human buccal swab


title: Semen, buccal swab, infertile male, sample 35


title: Semen, buccal swab, infertile male, sample 30


title: 33535_GIFN_Ifnar1ASO2_500 ug_male


title: MT2-1


title: Semen, buccal swab, infertile male, sample 31


title: WT-2


title: Semen, buccal swab, infertile male, sample 33


title: Semen, buccal swab, infertile male, sample 26


title: Semen, buccal swab, infertile male, sample 27


title: Semen, buccal swab, infertile male, sample 29


title: 33532_WT_ControlASO_300 ug_female


title: Semen, buccal swab, infertile male, sample 23


title: Semen, buccal swab, infertile male, sample 25


title: Semen, buccal swab, infertile male, sample 24


title: 33530_WT_ControlASO_500 ug_male


title: 33529_GIFN_ControlASO_500 ug_male


title: 33528_GIFN_ControlASO_300 ug_female


title: Semen, buccal swab, infertile male, sample 20


title: Semen, buccal swab, infertile male, sample 22


title: WT-1


title: Semen, buccal swab, infertile male, sample 19


title: MT2 + T2-5


title: MT2 + T2-4


title: MT2 + T2-3


title: Semen, buccal swab, infertile male, sample 18


title: MT2 + T2-2


title: Semen, buccal swab, infertile male, sample 17


title: 33531_GIFN_ControlASO_500 ug_male


title: 33526_WT_Ifnar1ASO1_300 ug_male


title: Semen, buccal swab, infertile male, sample 21


title: 33525_GIFN_Vehicle_0 ug_female


title: Semen, buccal swab, infertile male, sample 14


title: Semen, buccal swab, infertile male, sample 16


title: Semen, buccal swab, infertile male, sample 28


title: WT + T2-2


title: MT2 + T2-1


title: Semen, buccal swab, infertile male, sample 12


title: WT + T2-5


title: Semen, buccal swab, infertile male, sample 15


title: Semen, buccal swab, infertile male, sample 11


title: WT + T2-3


title: 33524_GIFN_ControlASO_500 ug_female


title: 33521_WT_Vehicle_0 ug_female


title: WT + T2-4


title: Patient_12

first: Jinchao

last: Jia

address: No. 197 Ruijin Second Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) 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 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12)
Differentially expressed genes (DEGs) with a fold change >2 and p value< 0.05 were determined using DEGseq analysis package
Assembly: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary files format and content: text files include read count values for each Sample

source_name: peripheral monocytes

growth_protocol: freshly isolated

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from patients with AOSD and HC using Lymphoprep (Serumwerk Bernburg AG) under sterile conditions following the manufacturer’s instructions. Monocytes were isolated with CD14 positive magnetic sorting (Miltenyi Biotec, Bergisch Gladbach, Germany).
Oligo(dT)-attached magnetic beads-purified mRNA was fragmented into pieces at appropriate temperature. cDNA was generated by random hexamer-primed reverse transcription. Afterwards, RNA Index Adapters and A-Tailing Mix were added to end repair. The cDNA fragments were amplified by polymerase chain reaction (PCR), and products were purified using Ampure XP Beads. The products were qualified on Agilent Technologies 2100 bioanalyzer. The double-strand PCR products were denatured and circularized by the splint oligo sequence to construct the final library. Then the single-strand circle DNA was formatted as the final library. The final library was amplified by phi29 to produce DNA nanoball (DNB) with more than 300 copies of one molecule. DNBs were loaded into patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Monocytes

tag: disease state

value: naïve AOSD


title: 33527_GIFN_ControlASO_500 ug_female


title: 33522_GIFN_Ifnar1ASO1_300 ug_male


title: Semen, buccal swab, infertile male, sample 13


title: Semen, buccal swab, infertile male, sample 10


title: WT + T2-1

value: lung

value: Lewis Lung Carcinoma


title: Patient_11


title: Semen, buccal swab, infertile male, sample 9


title: MT2 HBSS-4

value: mutant Timp2

value: HBSS Tumor Control


title: Semen, buccal swab, infertile male, sample 8


title: MT2 HBSS-3


title: MT2 HBSS-5


title: Patient_10


title: Semen, buccal swab, infertile male, sample 7


title: Semen, buccal swab, infertile male, sample 5


title: MT2 HBSS-1


title: 33520_WT_ControlASO_300 ug_male

value: Cortex

value: mixed C57Bl/6 and Balb/c


title: Patient_9


title: Semen, buccal swab, infertile male, sample 6


title: Patient_8


title: 33519_GIFN_ControlASO_300 ug_male

value: Ifnar1ASO1_300 ug


title: Patient_7


title: 33523_WT_ControlASO_300 ug_female

value: female


title: MT2 HBSS-2


title: Semen, buccal swab, infertile male, sample 4


title: 33517_WT_Vehicle_0 ug_male


title: Semen, buccal swab, infertile male, sample 3


title: WT HBSS-5

value: wt


title: Semen, buccal swab, infertile male, sample 2


title: 33516_GIFN_ControlASO_500 ug_male

value: male

value: Ifnar1ASO1_500 ug


title: 33514_WT_ControlASO_300 ug_male

value: WT


title: 33515_GIFN_Ifnar1ASO1_300 ug_female

value: GIFN


title: Semen, buccal swab, infertile male, sample 1

value: Semen, buccal swab


title: WT HBSS-2


title: Patient_6


title: Patient_4


title: WT HBSS-3


title: 33512_GIFN_ControlASO_500 ug_female


title: Patient_5


title: Patient_3


title: WT HBSS-1


title: 33518_GIFN_Ifnar1ASO1_300 ug_female


title: 33513_WT_Ifnar1ASO2_500 ug_female


title: 33511_WT_Ifnar1ASO2_500 ug_female


title: Early metastatic lungs (subcutaneous model) - HBSS control - 4


title: Early metastatic lungs (subcutaneous model) - HBSS control - 5


title: Patient_2


title: Patient_1


title: Control 2 Day 88, Replicate 2, scRNAseq

city: Portland

first: Lauren

last: Rylaarsdam

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Molecular & Medical Genetics

institute: Oregon Health & Science University

library_source: transcriptomic single cell

data_processing:
Sequencing was done using 100bp, paired-end reads with a targeted 300-400 million reads per sample. Raw data was demultiplexed and reads were aligned to GRCh38 using the CellRanger pipeline. Due to the number of years spanning this work, CellRanger v.3.0.2 was used to generate matrix files for C1, C3, CRISPR-R203W, and A1 day 40 samples; v4.0.0 was used to process the A2 day 40 sample, and v7.0.1 was used for all day 88 samples. Day 40 and 88 samples were analyzed independently. FASTQ files were received after completion of the project.
Assembly: GRCh38
Supplementary files format and content: Both FASTQ files and the matrix files generated by CellRanger are included in this dataset.

source_name: Cortical organoid (88 days of differentiation)

growth_protocol: Organoids were cultured according to the Pasca dorsal forebrain protocol (PMC5805137; PMC6597009). Day 88 samples were generated using the Stem Cell Technologies kit developed based on this protocol (Cat #08620).

extract_protocol:
Cells were dissociated from organoids using the Worthington Papain Dissociation System (LK003150). Steps were performed with sterile materials in a tissue culture hood. At day 40-42, two organoids between 3-4mm were selected per genotype. Just one day 88 organoid was used per sample due to limited availability of tissue. Organoids were pooled and washed with PBS + 0.2% BSA, then chopped into ~0.5mm pieces using a #10 blade. Organoids were incubated in a sterile-filtered 5 mL solution containing 20 U/mL papain in 1x EBSS, 0.46% sucrose, 26mM NaHCO3 (included in kit), 0.5mM EDTA (included in kit), and DNase (included in kit) equilibrated with 95%O2:5% CO2. Organoid pieces were incubated for 75 minutes on a 95 RPM orbital shaker in a 37ºC incubator and triturated using wide bore tips (Rainin, 30389218) every 30 minutes to help break up pieces. Following incubation, organoids were triturated one more time and transferred to a 15 mL conical vial. Cells were spun at 300 xg for 5 minutes. The pellet was resuspended in a 3 mL papain inhibitor solution containing 2 mg/mL ovomucoid inhibitor, 2 mg/mL albumin, 0.46% sucrose, and DNAse in 1x EBSS (all from Worthington, kit LK003150). This cell suspension was gently applied on top of a 5 mL solution of 10 mg/mL ovomucoid inhibitor, 10 mg/mL albumin, and 0.46% sucrose to create a density gradient. The gradient was spun at 70 xg for 6 minutes. The pellet was washed with 5 mL PBS + 0.2% BSA and spun again at 300 xg for 5 minutes. The pellet was resuspended in 130 µL PBS + 0.2% BSA and filtered to remove cell clumps (Bel-Art, H13680-0040), resulting in the final single-cell suspension.
The library prep was conducted by Northwestern’s Center for Genetic Medicine using the 10x Chromium library prep system (Single Cell 3' v3 chemistry; 10X Genomics).

treatment_protocol: PACS1(+/+) and PACS1(+/R203W) organoids were cultured in parallel. Additional treatments were not applied.

value: Heterogeneous neurons


title: 33510_WT_Ifnar1ASO2_500 ug_male


title: Early metastatic lungs (subcutaneous model) - HBSS control - 3


title: Semen, buccal swab, infertile male, sample 0

value: Human seminal fluids, human buccal swab


title: WT HBSS-4


title: Affected 1 Day 88, Replicate 1, scRNAseq

value: Cortical organoid (88 days of differentiation)


title: CRISPR R203W Day 88, Replicate 1, scRNAseq

description: Heterozygous PACS1 R203W variant introduced into the GM03651 background using CRISPR/Cas9

value: GM03651 (CRISPR)


title: Control 2 Day 88, Replicate 1, scRNAseq


title: Day 4, Replicate 3, CROP

city: San Francisco

first: Martin

last: Kampmann

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute of Neurodegenerative Disease

institute: University of California, San Francisco

description: CROPSeq sgRNAs

data_processing:
A kallisto index was generated from the human transcriptome using the ENSEMBL cDNA reference (GRcH38). Introns were annotated using the GRCh38 version 105 genome annotation. The default k-mer size (k=31) was used in generation of the index. The 10X sequences were then pseudo-aligned to this index using kallisto-bustools 95. The ‘lamanno’ workflow was specified, and the reads were mapped to both spliced and unspliced transcripts. After pseudo-alignment, barcodes were then corrected and filtered against the 10X-v3 cell barcode whitelist. Total gene level counts were calculated by aggregating both spliced/unspliced counts.
A kallisto index was generated for the sgRNA library with a k-mer size of 15. The sgRNA enrichment PCR sequences were then pseudo-aligned to this index using kallisto-bustools 95. After pseudo-alignment, barcodes were corrected and filtered against the 10X-v3 cell barcode whitelist. Cells were then assigned to guides using geomux (https://github.com/noamteyssier/geomux), which performs a hypergeometric test for each cell on its observed guide counts, then calculates a log2-odds ratio between the highest counts. Cells were assigned to their majority guide if their Benjamini-Hochberg corrected P-value was below 0.05, the log-odds ratio was above 1, and the total number of UMIs were greater than 5.
Assembly: Homo_sapiens.GRCh38.105
Supplementary files format and content: h5ad - gene spliced/unspliced abundances
Supplementary files format and content: h5ad - sgRNA abundance

source_name: brain

growth_protocol: Dorsal forebrain fate neural progenitor cells were generated from iPSCs through dual SMAD inhibition and WNT inhibition using small molecules (adapted from Qi et al., 201744). At day -1, iPSCs were plated on Matrigel coated plates at ~400k cells/cm2  in mTeSR plus medium (STEMCELL Technologies, Cat#100-0276). From day 0 to day 3, cells were fed with KSR medium (15% Knockout Serum Replacement  in Knockout DMEM, 1xGlutaMAX, 1xMEM-NEAA, 0.1mM BME)  containing small molecules 250nM LDN193189 (LDN) (Tocris, Cat No. 6053), 10uM SB431542 (SB) (Tocris, Cat#1614) and 5uM XAV939 (XAV) (Tocris, Cat#3748). At day 4, cells were cultured in ⅔ KSR + ⅓ N2 (DMEM/F12, 1x N2, 1x B27 -Vitamin A, 1x GlutaMAX, 1x MEM-NEAA) + LDN/SB/XAV, and at day 5 medium switched to ⅓ KSR + ⅔  N2 + LDN/SB/XAV. At day 6, cells were passaged with EDTA at 1:2 and cultured on Matrigel coated plates in NPC medium containing DMEM/F12, 1xN2, 1xB27 -Vitamin A, 1x GlutaMAX, 1x MEM-NEAA, 10ng/ml FGF2 (Peprotech, Cat#100-18B) and 10ng/ml EGF (Fisher Scientific, Cat# 236EG200) supplemented with 5uM XAV. At day 7, cells were fed with the same medium as day 6. At day 8, cells were passaged at 1:3 using Accutase (STEMCELL Technologies, Cat#07920) and cultured in NPC medium on Matrigel coated plates onwards.

extract_protocol:
We produced a pool of lentiviruses containing the CROP-seq sgRNA library and transduced NPC with relatively low titer of lentiviruses (10-20% transduction efficiency) to minimize multiple infections in which a cell receives more than one sgRNA. NPC cultures after puromycin selection were used for the CROP-seq experiment. At day 0, day 2 and day 4 of differentiation, cells were harvested using papain (Worthington, Cat#9001-73-4). Cells were prepared according to 10x Genomics general sample preparation protocol.At each time point, ~90k cells were loaded into 3 wells (~30k cells per well) of the Chromium Next GEM Chip G for GEM preparation. GEMs of each time point were stored in -20°C. Single cell library preps of all 9 samples from the three time points were conducted together according to the protocol provided for Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics, Cat#PN-1000121). Concentrations of libraries were measured using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat#5067-4626) on Bioanalyzer.
At each time point, ~90k cells were loaded into 3 wells (~30k cells per well) of the Chromium Next GEM Chip G for GEM preparation. GEMs of each time point were stored in -20°C. Single cell library preps of all 9 samples from the three time points were conducted together according to the protocol provided for Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics, Cat#PN-1000121). Concentrations of libraries were measured using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat#5067-4626) on Bioanalyzer. Briefly, three PCR reactions were performed followed by 1x SPRIselect beads (Fisher Scientific, Cat#NC0406407) cleanup after each PCR reaction. In PCR1, 15ng full-length cDNA from single cell RNA-seq library prep per sample was used as a template. In PCR2, 10ng post-cleanup PCR1 product was used as a template. In PCR3, 10ng post-cleanup PCR2 product was used as a template to add sample indices. All PCR reactions were conducted using KAPA Hotstart HiFi ReadMix (VWR, Cat#103568-584) with annealing temperature at 62°C (15 sec) and extension at 72°C (15 sec) for 18 cycles (PCR1) or 15 cycles (PCR2 and PCR3). Concentrations of post-PCR3 products were measured using Qubit dsDNA HS assay kit (Thermo Scientific, Cat#Q32854).
Samples of single cell RNA-seq libraries and enriched sgRNAs were pooled together at 5nM for sequencing on S2 and S4 flow cells of Illumina NovaSeq. Approximately 1 billion reads were generated per sample.

treatment_protocol: To establish individual hcASD gene knock-down NPC lines, NPCs with CRISPRi machinery were transduced with a lentiviral vector carrying a targeting sgRNA. Specifically, lentiviruses were produced in Lenti-X 293T cells (Takara Bio, Cat#632180) and lentivirus-containing supernatants were concentrated using Lenti-X concentrator (Takara Bio, Cat#631231). NPCs were transduced and selected using 4ug/ml puromycin (Fisher Scientific, Cat#5015328) to obtain greater than 90% transduced cells in culture. The transduction efficiency was evaluated by measuring BFP expression in the sgRNA lentiviral vector by flow cytometry. Knock down efficiency of a sgRNA was validated by qPCR. Specifically, we extracted total RNA from NPCs transduced with non-targeting control sgRNA and hcASD targeting sgRNA as described above. Samples were collected in triplicates for each condition. We then converted the total RNA into cDNA through reverse transcription. We used cDNA to measure the target gene expression using the double delta Ct method and calculated the log2FC of a target gene in hcASD gene knocked down cells compared to the control cells.

value: brain

value: neural progenitor cells

tag: differentiation day

value: CRISPRi


title: 33509_GIFN_Vehicle_0 ug_female

value: Cortex

value: Vehicle_0 ug


title: Early metastatic lungs (subcutaneous model) - HBSS control - 1

value: lung

value: Lewis Lung Carcinoma

value: HBSS Tumor Control


title: HC_10

value: Monocytes

value: healthy control


title: HC_7


title: Early metastatic lungs (subcutaneous model) - HBSS control - 2

value: wt


title: HC_9


title: 33508_WT_Ifnar1ASO1_300 ug_male

value: mixed C57Bl/6 and Balb/c

value: male

value: WT

value: Ifnar1ASO1_300 ug


title: Day 4, Replicate 1, CROP

description: CROPSeq sgRNAs


title: Early metastatic lungs (subcutaneous model) - rTIMP2 at day 7 - 4

value: Timp2 (day 7)


title: 33507_GIFN_Ifnar1ASO1_300 ug_female

value: female

value: GIFN


title: HC_5


title: Early metastatic lungs (subcutaneous model) - rTIMP2 at day 7 - 1


title: Early metastatic lungs (subcutaneous model) - rTIMP2 at day 7 - 3


title: HC_8


title: HC_6


title: Early metastatic lungs (subcutaneous model) - rTIMP2 at day 7 - 2


title: Day 4, Replicate 2, CROP

description: CROPSeq sgRNAs

value: brain

value: neural progenitor cells


title: Early metastatic lungs (subcutaneous model) - rTIMP2 at day 0 - 3

value: Timp2 (day 0)


title: HC_4


title: Day 4, Replicate 2, 10X

description: 10X Transcripts

value: CRISPRi


title: Early metastatic lungs (subcutaneous model) - rTIMP2 at day 0 - 5

value: lung


title: Day 2, Replicate 1, CROP

description: CROPSeq sgRNAs


title: HC_3


title: Day 2, Replicate 3, CROP

description: CROPSeq sgRNAs


title: Early metastatic lungs (subcutaneous model) - rTIMP2 at day 0 - 1

value: Lewis Lung Carcinoma


title: Day 2, Replicate 3, 10X

description: 10X Transcripts


title: Day 2, Replicate 2, CROP

description: CROPSeq sgRNAs


title: RRBS Retinal ganglion cells, Ezh2-Y726D overexpression, injured, replicate 3

data_processing:
Sequencing reads from bisulfite-treated classic RRBS libraries were identified using standard Illumina base calling software.
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore 0.6.4.
Alignment to the mouse reference genome (GRCm38) was performed using Bismark 0.19.0.
Methylated and unmethylated read totals for each CpG site were called using MethylDackel 0.5.0.
Assembly: GRCm38
Supplementary files format and content: Files containing DNA methylation tracks for each library

extract_protocol:
DNA was extracted from retinal ganglion cells using the Quick-DNA Microprep Plus Kit (Zymo Research D4074) following the manufacture’s manual.
RRBS library preparation and sequencing were done by Zymo Research. Briefly, 10 ng genomic DNA was digested with 30 units of MspI. Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor-ligated fragments ≥ 50 bp in size were recovered using the DNA Clean & Concentrator-5 Kit (Zymo Research D4003). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning Kit (Zymo Research D5030). Preparative-scale PCR was performed, and the product was purified with the DNA Clean & Concentrator-5 Kit (Zymo Research D4003).

treatment_protocol: AAV2-GFP, AAV2-Ezh2, or AAV2-Ezh2-Y726D was injected into the vitreous body and the optic nerve was crushed after two weeks. Uninjured groups only received AAV2 injection but did not undergo optic nerve crush. Three days after the optic nerve crush (injured groups) or 17 days after AAV2 injection (uninjured groups), retinal ganglion cells were enriched from dissociated retinal cells.

value: Retinal ganglion cells


title: HC_2

value: Monocytes


title: Day 2, Replicate 2, 10X

description: 10X Transcripts


title: Day 4, Replicate 1, 10X

description: 10X Transcripts


title: Early metastatic lungs (subcutaneous model) - rTIMP2 at day 0 - 4


title: RRBS Retinal ganglion cells, Ezh2-Y726D overexpression, injured, replicate 2


title: Early metastatic lungs (subcutaneous model) - rTIMP2 at day 0 - 2


title: Day 4, Replicate 3, 10X

description: 10X Transcripts


title: Affected 1 Day 40, Replicate 1, scRNAseq

source_name: Cortical organoid (40 days of differentiation)

value: Heterogeneous neurons


title: RRBS Retinal ganglion cells, Ezh2-Y726D overexpression, injured, replicate 1


title: Affected 2 Day 40, Replicate 1, scRNAseq

description: A2-1 and A2-2 were technical replicates combined for analysis

value: Cortical organoid (40 days of differentiation)


title: Serumal exosomes from healthy control 4

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

institute: The Affiliated Cancer Hospital of Nanjing Medical University

description:
Normal4
control-4

data_processing:
Basecalls performed using Solexa pipeline v1.8.
Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5',3'-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
The abundance of tRF & tiRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM).
Assembly: hg19
Supplementary files format and content: Normalized read counts using DESeq2 in the statistical program R after removing the tsRNAs that were expressed in low levels.

source_name: Serumal exosomes

extract_protocol:
The mixture containing serum and phosphate buffered saline (PBS) was centrifuged at 2000g for 30 minutes. Then the supernatant was sent to centrifuge at 12,000g for 45 minutes after removal of the pellet. Exosomes were pelleted by ultracentrifugation of the supernatant at 100,000g for 120 minutes. Trizol method was used to separate RNA from exosomes.
tRNA derived fragments (tRF & tiRNA) are heavily decorated by RNA modifications that interfere with small RNA-seq library construction. We do the following treatments before library preparation for total RNA samples: 3'-aminoacyl (charged) deacylation to 3'-OH for 3'adaptor ligation, 3'-cP (2',3'-cyclic phosphate) removal to 3'-OH for 3'adaptor ligation, 5'-OH (hydroxyl group) phosphorylation to 5'-P for 5'-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2101.
For standard small RNA sequencing on Illumina NextSeq instrument, the sequencing type is 50bp single read.

value: Serumal exosomes

tag: disease

value: Healthy control


title: RRBS Retinal ganglion cells, Ezh2 overexpression, injured, replicate 3


title: Serumal exosomes from healthy control 2

description:
Normal2
control-2


title: HC_1

value: healthy control


title: Serumal exosomes from healthy control 1

description:
Normal1
control-1


title: RRBS Retinal ganglion cells, Ezh2 overexpression, injured, replicate 2


title: Day 0, Replicate 3, CROP

description: CROPSeq sgRNAs


title: Day 2, Replicate 1, 10X

description: 10X Transcripts


title: Day 0, Replicate 2, CROP

description: CROPSeq sgRNAs


title: RRBS Retinal ganglion cells, Ezh2 overexpression, injured, replicate 1


title: Day 0, Replicate 1, CROP

description: CROPSeq sgRNAs


title: Control 3 Day 40, Replicate 1, scRNAseq


title: Control 1 Day 40, Replicate 1, scRNAseq


title: Serumal exosomes from healthy control 3

description:
Normal3
control-3


title: Day 0, Replicate 2, 10X

description: 10X Transcripts


title: RRBS Retinal ganglion cells, GFP overexpression, injured, replicate 2


title: B cells donor 3342 TP1, Hiseq ADT

city: San Antonio

first: Evelien

middle: M

last: Bunnik

state: TX

address: 7703 Floyd Curl Drive

department: MIMG

institute: UT Health San Antonio

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
3342_TP1_barcodes.tsv
3342_TP1_genes.tsv
3342_TP1_matrix.mtx
SeuratObj_Res_0.6.rds

library_source: other

data_processing:
From the single-cell RNA sequencing Seurat object, the antibody capture component (assay = ADT) was extracted. This antibody matrix was normalized using CLR normalization (Seurat method NormalizeData) and scaled using Seurat routine ScaleData.
CellRanger
Assembly: hg38
Supplementary files format and content: CellRanger output files: _barcodes.tsv, _genes.tsv, _matrix.mtx
Supplementary files format and content: Germline annotations for V-gene, D-gene, and J-gene segments, constant region assignments, CDR3 sequences, and clonotype assigments for heavy and light chains: _filtered_contig_annotations.csv
Supplementary files format and content: Change-O output files for productively rearranged antibody heavy chains: _VDJ_heavy_productive_germ-pass.tsv
Supplementary files format and content: Seurat object of gene expression and antibody-derived tag data: SeuratObj_Res_0.6.rds
Library strategy: CITE-seq

molecule: protein

source_name: PBMCs

extract_protocol:
Cryopreserved PBMCs were thawed, followed by isolation of B cells by negative magnetic selection. Naïve B cells (CD21+CD27-) and antigen-experienced B cells (all other B cells) were then isolated by fluorescence-activated cell sorting by first gating on live CD19+CD20+ cells, and subsequently on CD21 and CD27 expression. Antigen-experienced cells were mixed with a small proportion of naive B cells and then loaded onto the 10x Genomics controller.
Standard 10x Genomics instructions were followed for the construction of 5' gene expression, antibody-derived tag (ADT), and V(D)J sequencing libraries.

value: PBMCs

value: CD19+ CD20+ B cells

tag: adt

value: TotalSeq-C0005 anti-human CD80, TotalSeq-C0053 anti-human CD11c, TotalSeq-C0136 anti-human IgM, TotalSeq-C0140 anti-human CD183 (CXCR3), TotalSeq-C0154 anti-human CD27, TotalSeq-C0181 anti-human CD21, TotalSeq-C0375 anti-human IgG Fc, TotalSeq-C0577 anti-human CD73 (Ecto-5'-nucleotidase)


title: B cells donor 3342 TP2, Hiseq ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
3342_TP2_barcodes.tsv
3342_TP2_genes.tsv
3342_TP2_matrix.mtx
SeuratObj_Res_0.6.rds


title: Day 0, Replicate 3, 10X

description: 10X Transcripts


title: Serumal exosomes from breast cancer patient 2

description:
Tumor2
Ca002

value: Breast cancer


title: Serumal exosomes from breast cancer patient 4

description:
Tumor4
Ca004


title: Serumal exosomes from breast cancer patient 3

description:
Tumor3
Ca003


title: RRBS Retinal ganglion cells, GFP overexpression, injured, replicate 1


title: CRISPR R203W Day 40, Replicate 1, scRNAseq

value: GM03651 (CRISPR)


title: B cells donor 3342 TP2, Hiseq GEX

description:
RNA
GEX (5' RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
3342_TP2_barcodes.tsv
3342_TP2_genes.tsv
3342_TP2_matrix.mtx
SeuratObj_Res_0.6.rds

data_processing:
Sequencing reads were mapped to the human reference genome and assigned to individual cells of origin using cell-specific barcodes in CellRanger v3.1.0. Sequence data were then processed using Seurat v3.2.3, following their default pipeline. Low-quality cells with high (>2500) or low (<200) UMI counts were filtered from the samples. Prior to clustering and UMAP visualization, all IGH, IGK, and IGL transcripts were removed from the single cell gene expression data. Gene expression levels for each cell were normalized by total expression, multiplied by a scale factor (10,000), and log-transformed. Cells with >5% mitochondrial reads were excluded. The 2000 most variable genes based on their average expression and dispersion were used for principal component analysis to reduce the dimensionality of the data. Clustering was performed using the Louvain algorithm implemented in the FindClusters function of Seurat (algorithm = 1, resolution = 0.6, dims. use = 1:20).
CellRanger
Assembly: hg38
Supplementary files format and content: CellRanger output files: _barcodes.tsv, _genes.tsv, _matrix.mtx
Supplementary files format and content: Germline annotations for V-gene, D-gene, and J-gene segments, constant region assignments, CDR3 sequences, and clonotype assigments for heavy and light chains: _filtered_contig_annotations.csv
Supplementary files format and content: Change-O output files for productively rearranged antibody heavy chains: _VDJ_heavy_productive_germ-pass.tsv
Supplementary files format and content: Seurat object of gene expression and antibody-derived tag data: SeuratObj_Res_0.6.rds
Library strategy: CITE-seq


title: B cells donor 3342 TP2, VDJ

description:
V(D)J
V(D)J: read1 file contains cell barcode and UMI; read2 contains variable region reads
3342_TP2_filtered_contig_annotations.csv
3342_TP2_VDJ_heavy_productive_germ-pass.tsv

data_processing:
V(D)J sequencing data was processed using CellRanger vdj. Single-cell heavy chain variable region sequences were then analyzed using the Immcantation pipeline. The Immcantation package Change-O v0.4.4 was used to align lymphocyte receptor sequences to germline sequences for downstream analysis.
CellRanger
Assembly: hg38
Supplementary files format and content: CellRanger output files: _barcodes.tsv, _genes.tsv, _matrix.mtx
Supplementary files format and content: Germline annotations for V-gene, D-gene, and J-gene segments, constant region assignments, CDR3 sequences, and clonotype assigments for heavy and light chains: _filtered_contig_annotations.csv
Supplementary files format and content: Change-O output files for productively rearranged antibody heavy chains: _VDJ_heavy_productive_germ-pass.tsv
Supplementary files format and content: Seurat object of gene expression and antibody-derived tag data: SeuratObj_Res_0.6.rds
Library strategy: VDJ-seq


title: B cells donor 3342 TP1, Hiseq GEX

description:
RNA
GEX (5' RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
3342_TP1_barcodes.tsv
3342_TP1_genes.tsv
3342_TP1_matrix.mtx
SeuratObj_Res_0.6.rds


title: RRBS Retinal ganglion cells, Ezh2-Y726D overexpression, uninjured, replicate 3


title: B cells donor 3342 TP1, VDJ

description:
V(D)J
V(D)J: read1 file contains cell barcode and UMI; read2 contains variable region reads
3342_TP1_filtered_contig_annotations.csv
3342_TP1_VDJ_heavy_productive_germ-pass.tsv


title: Day 0, Replicate 1, 10X

description: 10X Transcripts

value: brain

value: neural progenitor cells


title: H58-t79-R

first: Xin

middle: Wei

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: *** Due to patient privacy concerns, patient data will be submitted to dbGaP. ***

data_processing:
After demultiplexing with bcl2fastq, reads were aligned, tagged, and counted with Cell Ranger (version 6.0.1). All samples yielded a high number of reads ranging from 100-500 million and with >95% Q30 bases in barcodes.
Raw gene counts were normalized to the same sequencing depth using Cell Ranger. The raw counts were used to construct a Seurat object, which kept all genes expressed in at least 0.1% of cells.
All cells with fewer than 500 detected genes or with at least 50% of their detected genes being mitochondrial were filtered out.
Log-normalization was run with a scale factor of 10,000 using Seurat (version 4.1.0).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver tumor

extract_protocol:
Single cells were then captured either directly or from cryopreserved cell stocks, following the protocol of the Chromium Next GEM Chip G Single Cell Kit (10x Genomics, PN-1000127).
The libraries were prepared with the Chromium Next GEM Single Cell 3’ Kit (10x Genomics, PN-1000269) following the kit instruction manuals. Libraries were then pooled and sequenced with Illumina HiSeq 4000/NovaSeq 6000 platforms, targeting sequencing depth of 50,000 raw reads per cell.

treatment_protocol: Tumor tissues were stored in a tissue storage buffer (Miltenyi Biotec, Catalog #130-100-008) immediately after surgical removal and were digested with a Tumor Dissociation Kit (Miltenyi Biotec, Catalog #130-095-929) in Tumor Dissociation C Tubes (Miltenyi Biotec, Catalog #130-093-237).

value: Liver tumor

tag: cancer type

value: Hepatocellular carcinoma

tag: age


title: RRBS Retinal ganglion cells, Ezh2-Y726D overexpression, uninjured, replicate 2


title: RRBS Retinal ganglion cells, GFP overexpression, injured, replicate 3


title: H77-t0


title: H73-t7


title: H58-t6


title: RRBS Retinal ganglion cells, Ezh2 overexpression, uninjured, replicate 3


title: H73-t0


title: Serumal exosomes from breast cancer patient 1

description:
Tumor1
Ca001


title: RRBS Retinal ganglion cells, Ezh2 overexpression, uninjured, replicate 2


title: H34-t97


title: H68-t19


title: RRBS Retinal ganglion cells, Ezh2 overexpression, uninjured, replicate 1


title: H68-t0


title: H34-t30


title: TYLMS cells, Scramble, 3

city: Fukuoka

first: Masaya

last: Kanahori

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Orthopaedic Surgery

country: Japan

institute: Kyushu University

data_processing:
RaNA-seq
Data were processed on a web browser using RaNA-seq (Prieto et al., 2020).
The FASTQ files are pre-processed with the Fastp tool (Chen et al., 2018), and expression quantification is performed with Salmon (Patro et al., 2017).
These reads are also normalized as TPM.
Assembly: hg38
Supplementary files format and content: raw counts, TPM for each Sample

growth_protocol: TYLMS-1 cells were cultured at 37 ℃ under 5% CO2 in a 1:1 mixture of Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) and Ham’s F-12 medium (Sigma-Aldrich) with 10% foetal bovine serum (FBS) (HyClone).

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using the Illumina Stranded-specific library preparation method (dUTP method).

treatment_protocol:
TYLMS-1 cells were treated to inhibit EPCAM signalling with 40 μM TAPI-1 (Selleck Chemicals) and 10 μM DAPT (Selleck Chemicals) when the cells reached approximately 60% confluence. The inhibitors were administered once at 0 h in all the cultures. The cells were collected 48 h after administation.
siRNA was transfected into TYLMS-1 cells when the cells reached approximately 60% confluence. For EPCAM knockdown, a Silencer Select Pre-Designed siRNA (s529200; s529201, Thermo Fisher Scientific) was transfected using Lipofectamine 3000 (Thermo Fisher Scientific), following the manufacturer's protocol. Control cells were transfected with Silencer Negative Control No.1 siRNA (AM4611, Thermo Fisher Scientific). The cells were collected 48 h after transfection.

value: human leiomyosarcoma cell line

value: Scramble


title: TYLMS cells, Scramble, 2


title: TYLMS cells, siEPCAM, 2

value: EPCAM knockdown


title: TYLMS cells, siEPCAM, 1


title: TYLMS cells, siEPCAM, 3


title: TYLMS cells, non-teatment, 3

value: DMSO only


title: TYLMS cells, Scramble, 1


title: TYLMS cells, non-teatment, 2


title: H34-t20


title: H58-t79-L


title: RRBS Retinal ganglion cells, GFP overexpression, uninjured, replicate 2

value: Retinal ganglion cells


title: RRBS Retinal ganglion cells, Ezh2-Y726D overexpression, uninjured, replicate 1


title: H49-t68


title: H34-t6


title: RRBS Retinal ganglion cells, GFP overexpression, uninjured, replicate 1


title: RRBS Retinal ganglion cells, GFP overexpression, uninjured, replicate 3


title: TYLMS cells, TAPI + DAPT, inhibitor 3

value: EPCAM inhibited


title: H49-t0


title: H58-t0


title: TYLMS cells, TAPI + DAPT, inhibitor 2


title: ATAC Retinal ganglion cells, Ezh2-Y726D overexpression, replicate 2

data_processing:
Adapters of Illumina reads were removed with Cutadapt.
Pair-end ATAC-seq reads were mapped to the mouse reference genome (GRCm38) using Bowtie2 with default parameters.
Qualified properly paired reads (MAPQ score > 10) were assessed by SAMTools.
Duplicate reads were removed with MarkDuplicates function in Picard.
MACS2 was used to call peak regions of each sample
multiBamSummary function in deepTools was used to calculate read counts for all samples.
Assembly: GRCm38
Supplementary files format and content: narrow.Peak

extract_protocol:
50,000 retinal ganglion cells were pelleted by centrifugation (500 g, 5 min, 4°C), washed with ice-cold PBS, pelleted again by centrifugation (500 g, 5 min, 4°C), and lysed in 50 μl ice-cold lysis buffer. Immediately after lysis, nuclei were pelleted by centrifugation (500 g, 10 min, 4°C), resuspended in 50 μl transposase reaction mix (Tagment DNA TDE1 Enzyme and Buffer Kits, Illumina 20034197) and incubated at 37°C for 30 min. After the transposition reaction, the product was purified with the DNA Clean & Concentrator-5 Kit (Zymo Research D4003).
20 μl tagmented DNA was PCR amplified with NEBNext High-Fidelity PCR Master mix (New England Biolabs M0541) and forward and reverse UDI primers. Amplification was first performed for 5 cycles, following which 5 μl of each partially amplified library was used to perform qPCR to determine the additional number of PCR cycles needed for each library. Final amplified libraries were purified using 1.1× Ampure XP bead purification (Beckman Coulter A63880).

treatment_protocol: AAV2-GFP, AAV-Ezh2, or AAV2-Ezh2-Y726D was injected into the vitreous body and the optic nerve was crushed after two weeks. Three days after the optic nerve crush, retinal ganglion cells were enriched from dissociated retinal cells by fluorescence-activated cell sorting.


title: H58-t36


title: ATAC Retinal ganglion cells, Ezh2-Y726D overexpression, replicate 1


title: H34-t0


title: H08-t0


title: H01-t99


title: H01-t86


title: ATAC Retinal ganglion cells, Ezh2 overexpression, replicate 3


title: TYLMS cells, non-teatment, 1


title: H01-t0


title: C46-t0

value: Intrahepatic cholangiocarcinoma


title: ATAC Retinal ganglion cells, Ezh2 overexpression, replicate 1


title: ATAC Retinal ganglion cells, GFP overexpression, replicate 3


title: C46-t7


title: WT HAP1 cells exposed to 0 nM trabectedin, biological replicateR3

city: Zurich

first: Shana

last: Sturla

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
*library strategy: genome-wide ligation of 3'-OH ends followed by sequencing (GLOE-Seq)
After demultiplexing of sequencing data, each sample was represented by two fastq.gz files, with the first file containing 101-nucleotide-long genomic reads (R1) and the second storing the respective 10-nucleotide long UMIs (R2). The quality of the R1 and R2 data was checked using FastQC/0.11.9 (Andrews, 2010). Low-quality and adaptor-containing reads were removed via trimmomatic/0.38 (Bolger et al., 2014), using the following parameters: for R1, SE ILLUMINACLIP:Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:101; for R2, SLIDINGWINDOW:4:15 MINLEN:10. Using a custom Python/3.7.4 script employing the module Biopython/1.79, we merged the R1 and R2 records that passed trimming, incorporating the 10-nucleotide-long R2 sequences in the name of respective R1 reads. These reads were mapped to human reference genome GRCh38 via bowtie2/2.3.5.1, using the pre-built bowtie2 (Langmead & Salzberg, 2012) index from https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip and default settings. Read duplicates were removed by the tool dedup of umi_tools/1.1.2 toolkit (Smith et al., 2017), grouping reads with the same R2 sequence stored in the read name (method=unique). samtools/1.12 (Li et al., 2009) were employed to remove unmapped reads, sort, index and generate statistics of bam files. bedtools2/2.29.2 (Quinlan & Hall, 2010) was used to covert bam files to bed files. Each read represented one unit of DNA-break signal, which we positioned at the nucleotide located immediately upstream of the 5’ end of the read. Since a GLOE-Seq read is the reverse complement of the DNA fragment captured in the protocol (Sriramachandran et al., 2020), the strand of the nucleotide bearing the signal was changed to the opposite to the one on which the respective read was mapped. In this way signal positioning, the original DNA break is on the 5’ side of the nucleotide bearing the signal. Using AWK and a custom Python/3.7.4 script with the modules numpy/1.21.5 and pandas/0.25.1, we implemented the described DNA-break-signal positioning, which resulted in the deposited sample-specific tsv-files. In these tsv-files, each line reflects one DNA break revealed by one mapped read. The tsv-files contain the following columns: 1) the chromosome, 2) the 0-based coordinate and 3) the strand of the nucleotide bearing the signal (this nucleotide is immediately downstream of the break), 4) MAPQ score of the read. All code: https://gitlab.ethz.ch/eth_toxlab/trabi-seq
Assembly: GRCh38
Supplementary files format and content: In the provided sample-specific tsv-files, each line reflects one DNA break revealed by one mapped read. The tsv-files contain the following columns: 1) the chromosome, 2) the 0-based coordinate and 3) the strand of the nucleotide bearing the signal (this nucleotide is immediately downstream of the break), 4) MAPQ score of the read.

growth_protocol: HAP1 cells were maintained in IMDM containing 4.5 g/L glucose with 10% fetal bovine serum, 1% penicillin-streptomycin, and GlutaMAXTM (Gibco) at 37°C with 5% CO2. U2OS WT, XPC-KO, CSB-KO and XPA-KO cells were maintained in McCoy’s 5a modified cell culture medium (Gibco) with 10% fetal bovine serum, 1% penicillin-streptomycin at 37°C with 5% CO2.

extract_protocol:
For the Nb.BsrDI treatment experiment, genomic DNA was extracted using the Monarch genomic DNA purification kit (T3010) from untreated U2OS wildtype cells after harvesting (5 min incubation with 0.25 % trypsin). For the experiments with cells, nuclei isolation followed the GLOE-seq protocol for mammalian cells (PMID: 32320643) with the following modification. Isolation of genomic DNA from mammalian cell culture: Agarose plugs were incubated with 6 mL of proteinase K solution and shaken at 170 rpm.
For the Nb.BsrDI treatment experiment, DNA library for Illumina sequencing was prepared according to GLOE-Seq protocol ‘Steps y23 – 28: Denaturation and ligation of 3’-OH termini (yeast)’ onwards (PMID: 32320643). For the experiments with cells, nuclei isolation and DNA library preparation for sequencing followed the GLOE-seq protocol for mammalian cells (PMID: 32320643) with the following modifications. Isolation of genomic DNA from mammalian cell culture: Agarose plugs were incubated with 6 mL of proteinase K solution and shaken at 170 rpm. Fragmentation and capture of biotinylated single-stranded DNA: DNA was sonicated with an average fragment length of 300 nucleotides with Qsonica for 5 min at 4 °C in cycles of 15 s ON and 5 s OFF with 20 % amplitude. DNA was purified twice with AMPure beads with elution in 50 μL dH2O. Streptavidin MyOne C1 dynabeads were resuspended after washing in 50 μL bind and wash buffer (2x) for a 1:1 beads to sample ratio. Second strand synthesis, end polishing and ligation of the distal adaptor: Reagents for second strand synthesis, end polishing and distal adaptor ligation were combined on ice and mixed by pipetting. For the distal adaptor either 3792-UMI or 3792-UMI.v2 (different indexes) were annealed with 3791. DNA was purified with AMPure beads and eluted in 30 μL of dH2O. qPCR: Before the final library amplification described in (Sriramachandran et al., 2020), qPCR with reaction conditions identical to the final PCR used for library amplification was done for quality control. Samples (1 μL) were diluted in deionized water (9.4 μL) and combined with 1x Q5 buffer, 0.2mM dNTPs, 0.1 μM i5 illumina indexing primer, 0.1 μM P7-short primer, 1x EvaGreen and 0.1 units of Q5 high-fidelity DNA polymerase. qPCR protocol included 120 s initial denaturation at 95 °C, 40 cycles of 15 s denaturation at 95 °C, 30 s annealing at 60 °C and 20 s extending at 72 °C, as well as 95 s final extension at 72 °C. Library amplification: The library was scaled up from 20 μL to 50 μL using entire samples. A customized P7-short primer compatible with the UMI-containing distal adaptors was used. Samples were purified with AMPure beads with a 1:1 bead to sample ratio. The DNA libraries were sequenced on an Illumina NovaSeq 6000 with a single-read protocol and the read length of 101 nucleotides (R1); additionally, 15 cycles were run on R2 to read UMI and custom indexes introduced by the oligos 3792-UMI or 3792-UMI.v2. For each sample, we deposited these R1 and R2 sequencies. Supplementary Table 1 of the manuscript (titled the same way) summarizes the reagents, enzymes, kits, oligonucleotides, and other materials used for GLOE-seq experiments.

treatment_protocol: For the Nb.BsrDI treatment experiment, genomic DNA was extracted using the Monarch genomic DNA purification kit (T3010) from untreated U2OS wildtype cells after harvesting (5 min incubation with 0.25 % trypsin). Existing breaks were blocked by incubating 5 μg DNA first with 10 units of T4 PNK per 4 ng DNA and 1x NEBuffer 2 for 30 min at 37 °C, and then with 250 μM ddNTP mix, 2 units of Therminator IX DNA polymerase and 1x ThermoPol buffer for 10 min at 60 °C. DNA was purified with ProNex size-purification system (NG2001, Promega) with 8:5 beads to sample ratio. DNA was incubated with 2.5 units of Nb.BsrDI and 1x CutSmart buffer for 90 min at 65 °C and then with 5 units antarctic phosphatase and 1x antarctic phosphatase buffer for 30 min at 37 °C, and purified as described above. In the experiments with cells, cells were grown up to 60-80 % confluency and incubated for 24 h with 1 mM palbociclib isethionate for G1 enrichment. Cells were then treated with 0.1 % DMSO, 20 nM or 50 nM trabectedin in combination with 1mM palbociclib isethionate for 2 h. Cells were washed with PBS and underwent a 2-h recovery in cell culture media without trabectedin in the presence of 1 mM palbociclib isethionate.

value: wild type

value: 0 nM trabectedin


title: WT HAP1 cells exposed to 0 nM trabectedin, biological replicateR2


title: WT HAP1 cells exposed to 0 nM trabectedin, biological replicateR1


title: Peripheral blood mononuclear cells healthy donor 5 [PB_HC5]

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

description:
CelSeq-2
barcodes.tsv

data_processing:
Failed reactions were identified by low levels of ERCC external RNA controls and excluded. Furthermore, a liveness threshold was calculated for each plate based on the wells with no cell added, in order to distinguish live cells from dead and/or apoptotic cells. This threshold was set to a minimum of 500 transcripts.
The percentage of transcripts mapping to the mitochondrial genome was calculated and cells with more mitochondrial‐encoded transcripts over nuclear ones were removed. Mitochondrial and ERCC transcripts were removed from the dataset, as well as cells with <1000 nuclear‐encoded transcripts or <500 genes. In addition, cells with >150.000 nuclear‐encoded transcripts were removed. Genes with low expression, that is either having less than 5 cells expressing the gene or less than two cells with less than two transcripts, were removed. A total of 105 cells, forming a distinct cluster of erythroid lineages, was identified based on high 515 levels of hemoglobin complex genes, and was removed. To improve cross‐sample comparisons, ambient mRNA contamination in individual cells was estimated and removed using DecontX. DecontX was run for all samples (batches) individually. Removal of cells with less than 1000 nuclear‐encoded transcripts was repeated on the decontaminated counts matrix outputted by DecontX.
All subsequent analyses were performed using R (version 4.0.2) and the package Seurat (version 3.2.2,RRID:SCR_007322) with default parameters unless stated otherwise. The SCTransform() function was used to normalize and scale the data, and to identify variable genes. To avoid clustering of cells based on specific cell processes, genes associated with sex (XIST, TSIX, and Y chromosome‐specific genes), cell cycle phase, dissociation stress (heat shock proteins; GO:0006986), and activity (ribosomal protein genes; GO:0022626), were removed as described before.
Assembly: hg38 Patch 10 human genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood mononuclear cells

extract_protocol:
Tumor material was collected in the operating room by Truecut biopsy (samples at diagnosis) or surgical resection (debulking procedure after induction chemotherapy). The Dutch samples were gently dissociated into single‐cells and sorted by flow cytometry for single‐cell RNA sequencing using the CEL‐Seq2 platform. In brief, preparation of the tumor pieces for single‐cell RNA sequencing was started within 4 hours after the surgery. The material was minced into pieces <1mm3 and dissolved by enzymatic digestion with collagenase I, II and IV (2.5 mg/mL) at 37°C with agitation for max. 1 hour. The samples were filtered through a 70 μm cell strainer and washed in DMEM. Cells were further separated into a single cell suspension with the NeuroCult dissociation kit according to the manufacturer's protocol (StemcellTM Technologies, cat#05707), washed and stained with DAPI and DRAQ5. Next to this unbiased strategy, some samples were additionally stained with antibodies to enrich for T cell populations (NB124, NB125 with CD3‐PE (Biolegend, cat#300308); NB124 with TCRγδ‐BV421 (Biolegend, cat#331217) or with GD2‐FITC (BD Biosciences, cat#563439) to enrich for tumor cells (000GGU, 000GXF, NB106, NB107, NB098, NB125, NB125, NB130, NB152). Single live cells were sorted into 384‐well plates containing 10 μl of mineral oil, 50 nl of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike‐Ins on a FACSJazz, FACSAria II or Sony SH800S machine and subsequently spun down, snap‐frozen on dry ice, and stored in ‐80⁰C to proceed with the total transcriptome amplification, library preparation and sequencing. Peripheral blood mononuclear cells (PBMC) from 5 healthy young adult donors (mean age 28) were isolated by Ficoll-Paque (VWR) density centrifugation and stained with fixable viability dye efluor506 (eBioscience, cat#65‐0866‐14), CD3‐PE (Biolegend, cat#300308) and CD56‐APC (Biolegend, cat#318310) antibodies. Subsequently, live CD3+ T cells and CD56+ NK cells were FACS sorted into 384‐well plates containing 10 μl of mineral oil, 50 nl of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike‐Ins on a Sony SH800S machine. The plates were spun down, snap‐frozen on dry ice, and stored in ‐80⁰C to proceed with the total transcriptome amplification, library preparation and sequencing.
All samples were processed for total transcriptome amplification, library preparation and sequencing into Illumina sequencing libraries as previously described70. Paired‐end 2x75 bp sequencing read length was used to sequence the prepared libraries using the Illumina NextSeq sequencer. Sharq preprocessing and QC pipeline were applied to process the single‐cell RNA‐seq data as described71. Read mapping was done using STAR version 2.6.1 (RRID:SCR_004463) on the hg38 Patch 10 human genome. Function featureCounts (RRID:SCR_012919) of the subread package (version 1.5.2) was used to assign reads based on GENCODE version 26 (RRID:SCR_014966).

value: Peripheral blood mononuclear cells

tag: tumor type

tag: tumor stage

value: female


title: Peripheral blood mononuclear cells healthy donor 4 [PB_HC4]

description:
CelSeq-2
barcodes.tsv


title: C26-t0


title: RNA-seq, LRPPRC KO+LSFC point mutant, rep 2

city: Boston

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were trimmed to remove ligated 3’ linker with trim galore
Reads were aligned to the GRCh38 human reference genome from GENCODE using BowTie2. Read counts were summed across genes using featureCounts.  Parameters: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. Differential expression analysis was then done using DEseq9
Assembly: hg38
Supplementary files format and content: DESeq2 output

growth_protocol: Cells were grown to 80% confluency in a 10 cm plate (two plates per sample) in DMEM (thermofisher) supplemented with 10% FBS (Gibco), 5 mL Antibiotic/Antimycotic (ThermoFisher), 100 ug/mL Uridine, 3 mM Sodium Formate.

extract_protocol:
Cells were collected by trypsinization and washed once with PBS before resuspending in one mL of Trizol (ThermoFisher Scientific). RNA was extracted following the Trizol manufacturer’s specifications.
Libraries were prepared by novogen using their lncRNA library preparation service

tag: cell type

value: LRPPRC KO + LSFC

value: untreated

tag: mouse spike-in%

tag: umi


title: ATAC Retinal ganglion cells, GFP overexpression, replicate 2

first: Xuewei

address: 4001 E Fletcher Ave, ALZ 339

institute: University of South Florida

tag: genotype


title: WT HAP1 cells exposed to 50 nM trabectedin, biological replicateR3

tag: cell line

tag: treatment

value: 50 nM trabectedin


title: RNA-seq, LRPPRC KO+LSFC point mutant, rep 1

data_processing:
Reads were trimmed to remove ligated 3’ linker with trim galore
Reads were aligned to the GRCh38 human reference genome from GENCODE using BowTie2. Read counts were summed across genes using featureCounts.  Parameters: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. Differential expression analysis was then done using DEseq8
Assembly: hg38
Supplementary files format and content: DESeq2 output


title: Peripheral blood mononuclear cells healthy donor 3 [PB_HC3]

description:
CelSeq-2
barcodes.tsv

tag: tissue

tag: Sex

value: male


title: WT HAP1 cells exposed to 50 nM trabectedin, biological replicateR2


title: TYLMS cells, TAPI + DAPT, inhibitor 1


title: RNA-seq, LRPPRC KO+LRPPRC WT, rep 2

data_processing:
Reads were trimmed to remove ligated 3’ linker with trim galore
Reads were aligned to the GRCh38 human reference genome from GENCODE using BowTie2. Read counts were summed across genes using featureCounts.  Parameters: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. Differential expression analysis was then done using DEseq7
Assembly: hg38
Supplementary files format and content: DESeq2 output

value: LRPPRC KO + LRPPRC WT


title: ATAC Retinal ganglion cells, GFP overexpression, replicate 1


title: ATAC Retinal ganglion cells, Ezh2 overexpression, replicate 2


title: RNA-seq, LRPPRC KO+LRPPRC WT, rep 1

data_processing:
Reads were trimmed to remove ligated 3’ linker with trim galore
Reads were aligned to the GRCh38 human reference genome from GENCODE using BowTie2. Read counts were summed across genes using featureCounts.  Parameters: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. Differential expression analysis was then done using DEseq6
Assembly: hg38
Supplementary files format and content: DESeq2 output


title: Peripheral blood mononuclear cells healthy donor 1 [PB_HC1]

description:
CelSeq-2
barcodes.tsv


title: Peripheral blood mononuclear cells healthy donor 2 [PB_HC2]

description:
CelSeq-2
barcodes.tsv


title: 3_FT_SA83926_SFO_sd_rep2

city: Pasadena

first: Tongtong

address: 1200 E California Blvd

institute: California Institute of Technology

description: 10x Genomics

data_processing:
Gene-cell matrices were generated by mapping sequencing reads to mm10 based mouse pre-mRNA reference transcriptome with Cell Ranger 6.1.2
Assembly: mm10
Supplementary files format and content: Processed data files are simple gene-cell matrices (genes as rows, cell indexes as columns).

source_name: Subfornical organ (SFO)

extract_protocol:
Animals were anaesthetized with isoflurane. Brains were extracted and dissected in NMDG-ACSF. Tissue was digested with papain in trehalose-HEPES-ACSFand triturated to generate single cell suspensions. For stimulus to cell-type mapping experiments, actinomycin-D was included in NMDG-ACSF and trehalose-HEPES-ACSF to block artificial induction of immediate early genes.
Sequencing libraries were constructed following 10x Genomics 3' v3.1 standard protocols.

value: Subfornical organ (SFO)

tag: strain

value: 7-8 weeks


title: WT HAP1 cells exposed to 50 nM trabectedin, biological replicateR1


title: 2_FT_SA215061_SFO_sd_rep1

description: 10x Genomics


title: C26-t5

value: Liver tumor


title: XPA knockout U2OS cells exposed to 0 nM trabectedin, biological replicateR3

value: XPA knockout


title: RNA-seq, LRPPRC KO, rep 2

data_processing:
Reads were trimmed to remove ligated 3’ linker with trim galore
Reads were aligned to the GRCh38 human reference genome from GENCODE using BowTie2. Read counts were summed across genes using featureCounts.  Parameters: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. Differential expression analysis was then done using DEseq5
Assembly: hg38
Supplementary files format and content: DESeq2 output

value: LRPPRC KO


title: Posttreatment NBL M259AAA_T, not paired, scRNAseq [M259AAA_T_scR_CEL-Seq2_5]

description:
CelSeq-2
barcodes.tsv

source_name: NBL tumor paravertebral lesion left

value: NBL tumor paravertebral lesion left

value: High-risk NBL

value: post-treatment

value: MYCN non-amplified


title: RNA-seq, LRPPRC KO, rep 1

data_processing:
Reads were trimmed to remove ligated 3’ linker with trim galore
Reads were aligned to the GRCh38 human reference genome from GENCODE using BowTie2. Read counts were summed across genes using featureCounts.  Parameters: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. Differential expression analysis was then done using DEseq4
Assembly: hg38
Supplementary files format and content: DESeq2 output


title: 1_FT_SA215060_SFO_sated

description: 10x Genomics


title: testis, H+H+Cd, rep2

city: Hefei

first: Yong-Wei

last: Xiong

state: Anhui

address: Hefei 230032, China

institute: Anhui Medical University

data_processing:
Then, the final quantification of library was conducted by qPCR.
After denaturing with 0.1 M NaOH, 8 pM single stranded DNA was amplified in situ at the NovaSeq S4 Reagent Kit.
The end of generated fragment was sequenced using Illumina NovaSeq 6000 sequencer for 150 cycles.
Next, quality control and statistical analysis (comparison rate, rRNA/mtRNA content and gene unbiasedness of the sequencing fragments) were conducted to determine whether the sequencing data could be used for subsequent analysis.
Finally, quantitative analysis of gene expression, differential expression gene screening and GO functional significant enrichment analysis were performed.
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes RPKM values for each sample

source_name: testis

extract_protocol:
Total RNA of mouse testes was extracted, and quality inspections were performed. The sequencing library was constructed with 2.0 μg total RNA from each sample.
The library from enriched RNA was constructed by KAPA Stranded RNA-Seq Library Prep Kit (Illumina) and inspected by Agilent 2100 Bioanalyzer.

value: testis

value: WT

value: High-fat diet and CdCl2 treatment


title: testis, H+H+Cd, rep3


title: Posttreatment NBL M259AAA_T, not paired, scRNAseq [M259AAA_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: RNA-seq, HEK-293T WT, rep 2

data_processing:
Reads were trimmed to remove ligated 3’ linker with trim galore
Reads were aligned to the GRCh38 human reference genome from GENCODE using BowTie2. Read counts were summed across genes using featureCounts.  Parameters: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. Differential expression analysis was then done using DEseq3
Assembly: hg38
Supplementary files format and content: DESeq2 output


title: Posttreatment NBL M259AAA_T, not paired, scRNAseq [M259AAA_T_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv


title: XPA knockout U2OS cells exposed to 0 nM trabectedin, biological replicateR1

value: 0 nM trabectedin


title: testis, H+H+Cd, rep1


title: XPA knockout U2OS cells exposed to 50 nM trabectedin, biological replicateR3


title: XPA knockout U2OS cells exposed to 50 nM trabectedin, biological replicateR2


title: Posttreatment NBL M259AAA_T, not paired, scRNAseq [M259AAA_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv


title: XPA knockout U2OS cells exposed to 50 nM trabectedin, biological replicateR1


title: RNA-seq, LRPPRC KO + LSFC point mutant, rep 2

description:
HEK_RNAseq2-3_featureCounts_CDSignore1stlast_multi_noDups.txt
HEK_RNAseq2-3_featureCounts_CDS_multi_noDups_mito_RPKSmt_noPseudo_ncRNA.txt
TElog_vs_rescue_fromRPKS.txt
RNA_seq_Mito2

data_processing:
Reads were trimmed to remove ligated 3’ linker (CTGTAGGCACCATCAAT) with Cutadapt. Reads without linker were discarded and the unique molecular identifier (UMI) was then extracted from remaining reads using a custom script. UMIs consisted of either 6 or 10 random nucleotides at the 3’ end ligated as part of the 3’ linker, and either 0 or 4 random nucleotides at the 5’ end. Trimmed reads were filtered after alignment using bowtie1 to human rRNA (allowing 1 internal and 1 5’ mismatch) and human tRNA (allowing 1 internal, 1 5’, and 3 3’ mismatches).  Remaining reads were aligned to the GRCh38 human reference genome from GENCODE using STAR 2.7.3. For mitoRP samples with mouse spike-ins, the M17 mouse reference genome from GENCODE was merged with the human genome. STAR mismatch parameters for mitoRP and cytoRP: --outFilterMismatchNoverReadLmax 0.07 and --outFilterMismatchNmax 3. STAR parameters for RNA-seq: default. PCR duplicates were identified by their UMI and removed using a custom script.
Read counts were summed across genes using Rsubread featureCounts. Parameters for mitoRP: readShiftType  = "upstream", readShiftSize = 14, read2pos = 3, allowMultiOverlap = TRUE, useMetaFeatures = TRUE, countMultiMappingReads = TRUE, strandSpecific = 1, GTF.featureType='CDS'. The GTF annotation file was modified to exclude the first 6 codons of all genes (which are variable depending on whether there is a 5’ UTR) and all overlapping regions. Paramters for cytoRP: readShiftType  = "downstream", readShiftSize = 17, read2pos = 5, allowMultiOverlap = TRUE, useMetaFeatures = TRUE, countMultiMappingReads = TRUE, strandSpecific = 1, GTF.featureType='CDS'. Parameters for RNA-seq: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. The GTF annotation file was modified to exclude overlapping regions in mitochondrial genes. Read counts were normalized to feature size and mouse mitochondrial mRNA-aligning spike-in count using a custom script.
Assembly: hg38
Supplementary files format and content: *_CDSignore1stlast_multi_noDups.txt files are tab-separated with a header showing sample names. They contain read counts for coding sequences across the genome. All aligned reads, after PCR duplicate removal, are included ('multi'), not just uniquely aligned ones.
Supplementary files format and content: *_multi_noDups_mito_RPKSmt_noPseudo_ncRNA.txt files are tab-separated with a header showing sample names. They  contain length- and spike-in normalized counts for mitochondrial mRNAs.
Supplementary files format and content: TElog_vs_rescue_fromRPKS.txt is tab-separated with a header showing sample names. It contains translation efficiency values for mitochondrial mRNAs normalized to the rescue cell line ('KOplWT') and log2-transformed

growth_protocol: Cells were grown in DMEM (Thermo), supplemented with 10% FBS (Thermo), in the absence of antibiotics to 75-80% confluency.

extract_protocol:
For mitoribosome profiling, growth medium was aspirated and cells were quickly rinsed once with ice-cold 1X PBS ph:7.4. Lysis was performed on ice in a glass homogenizer with a loose setting. We used 50 ml of lysis buffer for 106 cells. We used lauryl maltoside at 0.25% in combination with 50 mM NH4Cl, 20 mM MgCl2, 0.5 mM DTT, 10 mM Tris pH: 7.5 and 1X EDTA-free Protease inhibitor cocktail (Roche). For Cytoribosome profiling, cell cultures growth and lysis were performed as for mitoribosome profiling. We used lysis and buffer conditions described in Shalgi et al, 2013, for polysome profiling. For RNA-seq, some of the lysates prepared for mitoribosome profiling were reserved and  further treated with 90 ug/mL of Proteinase K and 0.5 % SDS at 42 0C for 20 minutes.
All libraries were prepared as described in Ingolia et al, 2012, with a few modifications. For mitoribosome profiling we did not rRNA deplete. For RNA-seq we included gel purified RNA sizes of 30-70 nucleotides. For all libraries we introduced randomized nucleotides to serve as a unique molecular identifier (UMI) to the linker ligation at 3’ (/5rApp/NNNNNNNNNNCTGTAGGCACCATCAAT/3ddC/) and the reverse transcription step at 5’(/5Phos/NNNNGATCGTCGGACTGTAGAACTCTGAACCTGTC/iSp18/CACTCA/iSp18/CAAGCAGAAGACGGCATACGAGATATTGATGGTGCCTACAG).

value: LRPPRC KO + LSFC

value: untreated


title: RNA-seq, HEK-293T WT, rep 1

data_processing:
Reads were trimmed to remove ligated 3’ linker with trim galore
Reads were aligned to the GRCh38 human reference genome from GENCODE using BowTie2. Read counts were summed across genes using featureCounts.  Parameters: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. Differential expression analysis was then done using DEseq2
Assembly: hg38
Supplementary files format and content: DESeq2 output


title: testis, H+Cd, rep3


title: Posttreatment NBL M259AAA_T, not paired, scRNAseq [M259AAA_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

source_name: NBL tumor left adrenal gland

value: NBL tumor left adrenal gland

value: Intermediate-risk NBL

value: male


title: testis, H+Cd, rep2


title: XPC knockout U2OS cells exposed to 0 nM trabectedin, biological replicateR3

value: XPC knockout


title: XPA knockout U2OS cells exposed to 0 nM trabectedin, biological replicateR2


title: Posttreatment NBL M241AAE_T, not paired, scRNAseq [M241AAE_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: mitoRP, LRPPRC KO + LSFC point mutant, rep 2

description:
HEK_hMitoRP2-3_featureCounts_allSizesAsite_CDSignore1stlast_multi_noDups.txt
HEK_hMitoRP2-3_featureCounts_allSizesAsite_CDSignore1stlast_multi_noDups_mito_RPKSmt_noPseudo_ncRNA.txt
TElog_vs_rescue_fromRPKS.txt
RP_Mito2

data_processing:
Reads were trimmed to remove ligated 3’ linker (CTGTAGGCACCATCAAT) with Cutadapt. Reads without linker were discarded and the unique molecular identifier (UMI) was then extracted from remaining reads using a custom script. UMIs consisted of either 6 or 10 random nucleotides at the 3’ end ligated as part of the 3’ linker, and either 0 or 4 random nucleotides at the 5’ end. Trimmed reads were filtered after alignment using bowtie1 to human rRNA (allowing 1 internal and 1 5’ mismatch) and human tRNA (allowing 1 internal, 1 5’, and 3 3’ mismatches).  Remaining reads were aligned to the GRCh38 human reference genome from GENCODE using STAR 2.7.3. For mitoRP samples with mouse spike-ins, the M17 mouse reference genome from GENCODE was merged with the human genome. STAR mismatch parameters for mitoRP and cytoRP: --outFilterMismatchNoverReadLmax 0.07 and --outFilterMismatchNmax 3. STAR parameters for RNA-seq: default. PCR duplicates were identified by their UMI and removed using a custom script.
Read counts were summed across genes using Rsubread featureCounts. Parameters for mitoRP: readShiftType  = "upstream", readShiftSize = 14, read2pos = 3, allowMultiOverlap = TRUE, useMetaFeatures = TRUE, countMultiMappingReads = TRUE, strandSpecific = 1, GTF.featureType='CDS'. The GTF annotation file was modified to exclude the first 6 codons of all genes (which are variable depending on whether there is a 5’ UTR) and all overlapping regions. Paramters for cytoRP: readShiftType  = "downstream", readShiftSize = 17, read2pos = 5, allowMultiOverlap = TRUE, useMetaFeatures = TRUE, countMultiMappingReads = TRUE, strandSpecific = 1, GTF.featureType='CDS'. Parameters for RNA-seq: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. The GTF annotation file was modified to exclude overlapping regions in mitochondrial genes. Read counts were normalized to feature size and mouse mitochondrial mRNA-aligning spike-in count using a custom script.
Assembly: hg38
Supplementary files format and content: *_CDSignore1stlast_multi_noDups.txt files are tab-separated with a header showing sample names. They contain read counts for coding sequences across the genome. All aligned reads, after PCR duplicate removal, are included ('multi'), not just uniquely aligned ones.
Supplementary files format and content: *_multi_noDups_mito_RPKSmt_noPseudo_ncRNA.txt files are tab-separated with a header showing sample names. They  contain length- and spike-in normalized counts for mitochondrial mRNAs.
Supplementary files format and content: TElog_vs_rescue_fromRPKS.txt is tab-separated with a header showing sample names. It contains translation efficiency values for mitochondrial mRNAs normalized to the rescue cell line ('KOplWT') and log2-transformed
Library strategy: Mitoribosome profiling


title: XPC knockout U2OS cells exposed to 0 nM trabectedin, biological replicateR2


title: testis, H+Cd, rep1


title: mitoRP, LRPPRC KO + LSFC point mutant, rep 1

description:
HEK_hMitoRP2-3_featureCounts_allSizesAsite_CDSignore1stlast_multi_noDups.txt
HEK_hMitoRP2-3_featureCounts_allSizesAsite_CDSignore1stlast_multi_noDups_mito_RPKSmt_noPseudo_ncRNA.txt
TElog_vs_rescue_fromRPKS.txt
RP_Mito1


title: XPC knockout U2OS cells exposed to 0 nM trabectedin, biological replicateR1


title: RNA-seq, LRPPRC KO + LSFC point mutant, rep 1

description:
HEK_RNAseq2-3_featureCounts_CDSignore1stlast_multi_noDups.txt
HEK_RNAseq2-3_featureCounts_CDS_multi_noDups_mito_RPKSmt_noPseudo_ncRNA.txt
TElog_vs_rescue_fromRPKS.txt
RNA_seq_Mito1


title: Posttreatment NBL M241AAE_T, not paired, scRNAseq [M241AAE_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: Posttreatment NBL M259AAA_T, not paired, scRNAseq [M259AAA_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: Paneth cells, ABX + TNF, replicate4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
checking read quality with fastqc v0.12.1 – no quality based preprocessing required
data were mapped with the STAR (2.7.10a) to the mouse reference genome/transcriptome (mm39/gencode v28) using default paremeters with following additions: --clip5pNbases 12 to remove a strong sequence bias at the 5’ end, --quantMode GeneCounts to obtain read counts per sample immediatly from STAR
per sample read couns were merged into a count matrix and further processed in R using the DESeq2 libary
Assembly: mm39
Supplementary files format and content: tab delimited text file with raw counts as obtained with STAR from each sample

source_name: small intestine

growth_protocol: mice were kept in an SPF animal house with ad libitum access to fooed and water

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit according to the manufacturers instructions. RNA was shipped to VIB nucleomics core for library preparation and seuencing
RNA-seq libraries were prepared using the illumina TruSeq Stranded mRNA kit using the manufacturers instructions

treatment_protocol: Mice were treated with broad spectrum antibiotics for 2 weeks and then treatd with PBS or  1µg/gTNF for 3 hours. The small intestine was extracted and panetch cells were purified using FACS (markers c-KIT and Cd24a). RNA was then axtracted from the purified Pcs

value: small intestine

value: Paneth cells (FACS purified)

tag: treatment 1

value: Antibiotics 2 weeks

tag: treatment 2

value: 3h TNF (1µg/g)


title: Astrocyte Allo-3

city: Tucson

first: Tian

last: Wang

state: AZ

address: 1230 N Cherry Avenue

department: Center for innovation in brain science

institute: Univeristy of Arizona

data_processing:
Transcripts were mapped to rat genome (ensemble release 95) using Salmon 0.14
Tximport V1.6.0 was used to generate a counts table
DESeq2 V1.18.1 was used to calculate normalized read counts for each gene and/or transcript and to perform expression analysis
Assembly: rat genome (ensemble release 95)
Supplementary files format and content: csv files of normalized count
Supplementary files format and content: csv files of VST-nomalized expression

organism: Rattus norvegicus

source_name: E18 Primary Astrocyte

extract_protocol:
RNA was purified using PureLink™ RNA Mini Kit (Invitrogen, 12183018A) following manufacturer’s instructions. Purelink™ DNase (Invitrogen, 12185010) was used to eliminate DNA contamination. Purified RNA was eluded in RNase-free, diH2O. RNA concentration and quality were checked by NanoDrop™ One.
RNA libraries for RNA-seq were prepared using the Stranded mRNA-Seq library prep kit following manufacturer's protocols.

value: E18 Primary Astrocyte

value: Allo treated


title: Posttreatment NBL M241AAE_T, not paired, scRNAseq [M241AAE_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

value: post-treatment

value: MYCN non-amplified


title: XPC knockout U2OS cells exposed to 50 nM trabectedin, biological replicateR2

value: 50 nM trabectedin


title: XPC knockout U2OS cells exposed to 50 nM trabectedin, biological replicateR3


title: Posttreatment NBL M241AAE_T, not paired, scRNAseq [M241AAE_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv


title: Paneth cells, ABX + TNF, replicate3

value: WT


title: Astrocyte Allo-2


title: Paneth cells, ABX + TNF, replicate1


title: Posttreatment NBL M732AAA_T, not paired, scRNAseq [M732AAA_T_scR_CEL-Seq2_6]

description:
CelSeq-2
barcodes.tsv

value: High-risk NBL


title: XPC knockout U2OS cells exposed to 50 nM trabectedin, biological replicateR1


title: Astrocyte Veh-3

value: Veh treated


title: Paneth cells, ABX + TNF, replicate2


title: Paneth cells, ABX + PBS, replicate4

value: 3h PBS


title: Posttreatment NBL M732AAA_T, not paired, scRNAseq [M732AAA_T_scR_CEL-Seq2_5]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland


title: Posttreatment NBL M732AAA_T, not paired, scRNAseq [M732AAA_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: Neuron Allo-2-2

source_name: E18 Primary Neuron

value: E18 Primary Neuron


title: CSB knockout U2OS cells exposed to 50 nM trabectedin, biological replicateR2

value: CSB knockout


title: Posttreatment NBL M732AAA_T, not paired, scRNAseq [M732AAA_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv

value: male


title: Paneth cells, ABX + PBS, replicate1

value: small intestine


title: Paneth cells, ABX + PBS, replicate2

value: Paneth cells (FACS purified)


title: Posttreatment NBL M732AAA_T, not paired, scRNAseq [M732AAA_T_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv


title: Neuron Allo-2-1


title: Paneth cells, ABX + PBS, replicate3

value: Antibiotics 2 weeks


title: Astrocyte Veh-1


title: Astrocyte Veh-2


title: Posttreatment NBL M732AAA_T, not paired, scRNAseq [M732AAA_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv


title: CSB knockout U2OS cells exposed to 0 nM trabectedin, biological replicateR2

value: 0 nM trabectedin


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_11]

description:
CelSeq-2
barcodes.tsv


title: Neuron Allo-1-2


title: Astrocyte Allo-1

value: E18 Primary Astrocyte


title: WT U2OS cells exposed to 0 nM trabectedin, biological replicateR2

value: wild type


title: E15_5_WT scRNA-seq

city: Shanghai

first: Ping

last: Lu

address: No 1630 Dongfang Road, Pudong New Area

institute: Shanghai Cancer Institute

data_processing:
Raw reads were processed to generate gene expression profiles using an internal pipeline
Cell type identification and clustering analysis were performed by Seurat program
the Seurat program (http://satijalab.org/seurat/, R package, v.3.0.1) was applied for analysis of RNA-Sequencing data. UMI count tables were loaded into R using read.table function
parameter resolution to 0.6 was set for FindClusters function to clustering analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated values files

source_name: E15.5 fetal pancreas

extract_protocol:
Pancreatic tissues of E13.5 and E15.5 embryos were collected, disassociated by TrypLE™ Express (ThermoFisher 12605010), labelled with EpCAM and then purified by flow cytometry.
Individual libraries were diluted to 4 nM and pooled for sequencing. At last, pools were sequenced on Illumina novaseq6000 with 150 bp paired end reads. Individual libraries were diluted to 4 nM and pooled for sequencing. At last, pools were sequenced on Illumina novaseq6000 with 150 bp paired end reads

value: E15.5 fetal pancreas

tag: strain background

value: Setd2 f/f; WT


title: Neuron Allo-1-1

value: Allo treated