title: Rep2_Lib45_c-47

source_name: cells, 3.89 h after swarm expansion, 6802 µm distance from the swarm center (= point of inoculation)

tag: cell type


title: Microbiota of adrenal gland from subject ACC5

status: Public on Sep 20 2023

type: SRA

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of human adrenal gland biopsy

library_source: genomic

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose
qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 275 --p-trunc-len-r 168 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x ~/GRCh38_noalt_as -U filtered_dna-sequences.fasta  -S bowtie2_SAM_output.txt -f -p 4
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads filtered_dna-sequences.qza --o-classification taxonomy.qza
R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: filtered_dna-sequences.fasta: text containing every processed ASV code and sequence retained after off-target reads decontamination
Supplementary files format and content: feature_table.csv: CSV text file containing the abundance table (after off-target reads decontamination)
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequences
Library strategy: paired-end (2x300) amplicon sequencing

molecule: genomic DNA

organism: Homo sapiens

source_name: Adrenal gland

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

tag: tissue

value: Adrenal gland

tag: gender

value: M

tag: age

tag: condition

value: ACC

tag: acc stage

value: I-II

tag: secretion

value: Cortisol

tag: fastq id

tag: sequencing batch


title: UK5_Calu3_GammaP1B_24h_3

city: San Francisco

first: Mehdi

last: Bouhaddou

state: CA

country: USA

institute: University of California San Francisco

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence using Trimmomatic.
Reads were mapped to Homo_sapiens ensembl_release-101 genome using HISAT2.
Counts of reads mapped to protein coding genes were extracted using featureCount and are reported.
Assembly: Not relevant
Supplementary files format and content: count values for each Sample

molecule: total RNA

source_name: epithelial lung cancer cells

extract_protocol:
Total RNA was extracted from 10^6 cells using the Qiagen RNeasy Kit after inactivating the virus post infection.
The chosen method of rRNA removal was rRNA depletion for mRNA and long noncoding species. RNA was primed with random hexamers for first-strand cDNA synthesis and then second-strand cDNA synthesis. All samples were sequenced on HiSeq 4000.

tag: sars-cov-2 voc

value: Gamma (P.1)

tag: collection time point

tag: additional conditions

tag: experiment group

tag: cell line


title: Microbiota of adrenal gland from subject ACC1


title: Microbiota of adrenal gland from subject ACC3


title: Rep2_Lib44_c-46

city: Basel

first: Kazuki

last: Nosho

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
Sequencing of the cDNA libraries was performed by MPGC (Cologne, Germany) or D-BSSE genomics facilty (Basel, Switzerland)
Sequence reads were trimmed for adaptor sequence/short sequence (<35 nt) using Trimmomatic v0.39
Trimmed sequence reads were mapped to B. subtilis NCIB3610 genome and plasmid (NCBI Accession number: NZ_CP020102 and NZ_CP020103) using HISAT2 v2.2.1 in single-end mode.
Reads mapped to all cetegory of genes (CDS, ncRNA, tmRNA, signal recognition particle RNA, ribonuclease P RNA, tRNA, rRNA) were counted using featureCounts v2.0.1 with fractional counting for multi-mapping and multi-overlapping reads (-OM --fraction) in a strand-specific manner (-s 2). Of those, reads mapped in tRNA and rRNA were removed and the remaining reads were used for the downstream analysis.
All genes for which there were at least 2 samples with a read count of at least 10 were used for the downstream analysis. Samples with remaining reads of < 1 million reads were excluded and the rest of the samples were used for normalization using edgeR (version 3.6.1) and transformed (log2).
Supplementary files format and content: comma-separated files include mapped read count data for each sample
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at expansion phase
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at lag and expansion phase

organism: Bacillus subtilis

source_name: cells, 3.89 h after swarm expansion, 4584 µm distance from the swarm center (= point of inoculation)

growth_protocol: Bacterial cells were spotted onto the center of a 9 cm petri dish filled with LB soft-agar (0.5% agar) medium and incubated at 30°C for swarm expansion.

extract_protocol:
RNA was isolated by the hot phenol method (Jahn et al, J Microbiol Methods, 2008) with some modifications. Prepared RNA was DNase-digested and cleaned up using RNACleanXP. Depletion of ribosomal RNA was performed using DIY method (Culviner et al, mBio, 2020). Integrity of the prepared RNA was tested using a TapeStation.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB, E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a TapeStation.

treatment_protocol: Cells that started swarm expansion were collected into the lysis buffer by our custom sampling robot. Cells before swarm expansion (lag phase) were collected by being suspened in the lysis buffer.

value: Bacteria

tag: genotype

value: WT chromosome; comI_Q12L in natual plasmid

tag: strain

tag: time after expansion (h)

tag: position (um)


title: Rep2_Lib42_c-43

source_name: cells, 3.59 h after swarm expansion, 11076 µm distance from the swarm center (= point of inoculation)

tag: cell type


title: Microbiota of adrenal gland from subject ACC6

tag: tissue

tag: gender

value: F

value: Androgens


title: Microbiota of adrenal gland from subject ACC2

tag: age

tag: condition


title: UK5_Calu3_GammaP1A_24h_2


title: Microbiota of adrenal gland from subject ACC12

tag: acc stage

tag: secretion


title: UK5_Calu3_GammaP1A_24h_3


title: Microbiota of adrenal gland from subject ACC11

tag: fastq id

tag: sequencing batch


title: UK5_Calu3_Delta2A_24h_1

tag: sars-cov-2 voc

tag: collection time point


title: Microbiota of adrenal gland from subject ACC13


title: Rep2_Lib43_c-45

source_name: cells, 3.89 h after swarm expansion, 2292 µm distance from the swarm center (= point of inoculation)


title: Microbiota of adrenal gland from subject ACC14


title: Microbiota of adrenal gland from subject ACC10


title: Rep2_Lib46_c-48

source_name: cells, 3.89 h after swarm expansion, 9021 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib40_c-41

source_name: cells, 3.59 h after swarm expansion, 6748 µm distance from the swarm center (= point of inoculation)


title: Microbiota of adrenal gland from subject ACC15


title: UK5_Calu3_GammaP1A_24h_1

tag: additional conditions

tag: experiment group


title: Rep2_Lib41_c-42

source_name: cells, 3.59 h after swarm expansion, 8912 µm distance from the swarm center (= point of inoculation)

tag: genotype


title: Microbiota of adrenal gland from subject ACC22


title: UK5_Calu3_Beta1_24h_3

tag: cell line


title: Microbiota of adrenal gland from subject ACC21

value: Aldhosterone


title: Rep2_Lib39_c-40

source_name: cells, 3.59 h after swarm expansion, 4585 µm distance from the swarm center (= point of inoculation)

tag: strain

tag: time after expansion (h)


title: UK5_Calu3_Beta1_24h_2


title: Microbiota of adrenal gland from subject H9

value: Healthy


title: Microbiota of adrenal gland from subject ACC9


title: UK5_Calu3_Beta1_24h_1


title: Rep2_Lib38_c-39

source_name: cells, 3.59 h after swarm expansion, 2293 µm distance from the swarm center (= point of inoculation)

tag: cell type

tag: position (um)


title: Microbiota of adrenal gland from subject H8

tag: tissue

tag: gender


title: UK5_Calu3_AlphaA_24h_3


title: Microbiota of adrenal gland from subject H7

tag: age

tag: condition


title: Microbiota of adrenal gland from subject H6

tag: acc stage

tag: secretion


title: Rep2_Lib36_c-37

source_name: cells, 3.27 h after swarm expansion, 9975 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib37_c-38

source_name: cells, 3.27 h after swarm expansion, 11359 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_AlphaA_24h_2


title: Microbiota of adrenal gland from subject ACC26

tag: fastq id

tag: sequencing batch


title: Microbiota of adrenal gland from subject H5


title: Microbiota of adrenal gland from subject ACC24


title: Rep2_Lib35_c-36

source_name: cells, 3.27 h after swarm expansion, 8592 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_IC19_24h_3

tag: sars-cov-2 voc

tag: collection time point


title: Microbiota of adrenal gland from subject ACC23


title: Microbiota of adrenal gland from subject ACC25


title: Rep2_Lib34_c-35

source_name: cells, 3.27 h after swarm expansion, 7207 µm distance from the swarm center (= point of inoculation)


title: Microbiota of adrenal gland from subject ACC8


title: Microbiota of adrenal gland from subject H1


title: Rep2_Lib32_c-33

source_name: cells, 3.27 h after swarm expansion, 4439 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_AlphaA_24h_1

tag: additional conditions

tag: experiment group


title: Microbiota of adrenal gland from subject H4


title: Microbiota of adrenal gland from subject H2


title: Rep2_Lib33_c-34

source_name: cells, 3.27 h after swarm expansion, 5824 µm distance from the swarm center (= point of inoculation)

tag: genotype


title: Rep2_Lib31_c-32

source_name: cells, 3.27 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)

tag: strain


title: Microbiota of adrenal gland from subject H3

source_name: Adrenal gland


title: UK5_Calu3_IC19_24h_2

source_name: epithelial lung cancer cells

tag: cell line


title: Microbiota of adrenal gland from subject ACC19


title: Microbiota of adrenal gland from subject ACC18


title: UK5_Calu3_IC19_24h_1


title: Rep2_Lib30_c-30

source_name: cells, 3.02 h after swarm expansion, 9170 µm distance from the swarm center (= point of inoculation)

tag: cell type

tag: time after expansion (h)


title: Microbiota of adrenal gland from subject ACC17

tag: tissue


title: UK5_Calu3_VIC_24h_3


title: Rep2_Lib29_c-29

source_name: cells, 3.02 h after swarm expansion, 7642 µm distance from the swarm center (= point of inoculation)

tag: position (um)


title: UK5_Calu3_VIC_24h_2


title: Microbiota of adrenal gland from subject ACC16

tag: gender

tag: age


title: UK5_Calu3_VIC_24h_1


title: UK5_Calu3_Mock_24h_3

value: Mock


title: Microbiota of adrenal gland from subject ACC7

tag: condition

tag: acc stage


title: UK5_Calu3_Mock_24h_1


title: UK5_Calu3_Mock_24h_2


title: Rep2_Lib26_c-26

source_name: cells, 3.02 h after swarm expansion, 3057 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_PolyIC_10h_3

value: Poly I:C stimulation


title: Rep2_Lib25_c-25

source_name: cells, 3.02 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib24_c-24

source_name: cells, 2.67 h after swarm expansion, 7638 µm distance from the swarm center (= point of inoculation)


title: Microbiota of adrenal gland from subject ACC20

tag: secretion

tag: fastq id


title: SNU182 input

city: Jinan

first: Tao

last: Su

state: Shandong

address: 440 Jiyan Rd

country: China

institute: Shandong Cancer Hospital and Institute

data_processing:
Trimming was used to cut off sequencing connectors and low-quality fragments of sequencing data
The data obtained after Trimming (clean reads) are analyzed again through FastQC for quality statistics
The clean data were mapping to reference genome (GRCh38)
The uniquely mapped reads were perfromed Peak calling
Generate BigWig file
Assembly: GRCh38
Supplementary files format and content: BigWig

source_name: liver

extract_protocol:
Such as the standard ChIP protocol, the DNA enriched by magnetic beads is eluted after washing, then decross-linked, and purified to obtain DNA
After detecting the size and concentration of DNA fragments, the DNA was sequenced by Illumina NovaSeq 6000

value: liver


title: SNU182 H3K27ac


title: Rep2_Lib23_c-23

source_name: cells, 2.67 h after swarm expansion, 6111 µm distance from the swarm center (= point of inoculation)


title: Huh7 input


title: SNU387 H3K27ac


title: SK-Hep-1 input


title: Rep2_Lib22_c-22

source_name: cells, 2.67 h after swarm expansion, 4584 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_PolyIC_10h_1

tag: sars-cov-2 voc


title: UK5_Calu3_AlphaAplusRux_10h_3

tag: collection time point


title: Huh7 H3K27ac


title: SK-Hep-1 H3K27ac


title: Rep2_Lib28_c-28

source_name: cells, 3.02 h after swarm expansion, 6114 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib21_c-21

source_name: cells, 2.67 h after swarm expansion, 3055 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib27_c-27

source_name: cells, 3.02 h after swarm expansion, 4585 µm distance from the swarm center (= point of inoculation)


title: SK-Hep-1 cells, m6A

data_processing:
Trimming was used to cut off sequencing connectors and low-quality fragments of sequencing data
The data obtained after Trimming (clean reads) are analyzed again through FastQC for quality statistics
The clean data were mapping to reference genome (GRCh38)
The uniquely mapped reads were perfromed Peak calling
Generate bedgraph file
Assembly: GRCh38
Supplementary files format and content: bedgraph

extract_protocol:
Such as the standard MeRIP protocol, the RNA enriched by magnetic beads
After detecting the quality and concentration of RNA, the RNA was sequenced by Illumina NovaSeq 6000


title: SK-Hep-1 cells, m6A_input


title: T47D cells, ESR1 Y537S-homozygous, R5020, rep 3

city: Chicago

first: Rosemary

middle: J

last: Huggins

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

description: T47D_DESeq2_results_and_norm_counts.xlsx

data_processing:
RNA-seq data were uploaded to the Galaxy platform and analyzed using the public server at usegalaxy.org
Sequencing files were mapped to the hg19 human reference genome using Bowtie2
Read counts per gene were generated from the aligned sequences using HTSeq-Count
DESeq2 was used to determine differentially expressed genes between each cell variant and between each treatment (Factor 1: Cell type (WT, Het, Hom), Factor 2: Treatment (Vehicle, R5020))
DESeq2 results were filtered to include only differentially expressed transcripts with both |log2(fold change)| > 1 and p-adj. < 0.05
Assembly: hg19
Supplementary files format and content: Tabular files of raw HTSeq-Counts for each sample
Supplementary files format and content: Spreadsheets of DESeq2 results and normalized counts comparing Y537S-Het v WT, Y537S-Hom v WT, and Y537S-Hom v Y537S-Het

growth_protocol: MCF7 cell variants were maintained in phenol red-free DMEM containing 5% FBS, 1% Pen/Strep, and 1% L-Glutamine. T47D ERα WT and ERα Y537S-het cell lines were maintained in phenol red-free RPMI media containing 10% FBS and 1% Pen/Strep. T47D Y537S-hom cells were maintained in phenol red-free MEM containing 10% CSS, 1% Pen/Strep, and 0.2 ug/uL puromycin for continuous selection. MCF7 cell variants were hormone-deprived in DMEM containing 10% CSS, and T47D cell variants were cultured in RPMI containing 10% CSS for 48 hours prior to experimentation.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus kit (#74104) according to the manufacturer's protocol. RNA concentrations were quantified by Nanodrop nucleic acid measurement.
RNA library preparation for sequencing was completed using the KAPA mRNA HyperPrep Kit (#KR1352) according to the manufacturer's protocol.

treatment_protocol: Cells were treated for 2 hours with vehicle or 10 nM R5020 for PR stimulation.

value: mammary epithelial adenocarcinoma

value: ESR1 Y537S-homozygous

tag: treatment

value: 10nM R5020 (PR-stimulated)


title: SNU387 input


title: UK5_Calu3_PolyIC_10h_2

tag: additional conditions

tag: experiment group


title: UK5_Calu3_Delta2AplusTPCA_10h_3


title: UK5_Calu3_AlphaAplusRux_10h_1


title: T47D cells, ESR1 Y537S-homozygous, R5020, rep 2

tag: genotype


title: Rep2_Lib19_c-19

source_name: cells, 2.37 h after swarm expansion, 6114 µm distance from the swarm center (= point of inoculation)

tag: strain


title: T47D cells, ESR1 Y537S-homozygous, hormone-deprived, rep 3

tag: cell line

tag: cell type

value: Vehicle (hormone-deprived)


title: T47D cells, ESR1 Y537S-homozygous, R5020, rep 1


title: T47D cells, ESR1 Y537S-homozygous, hormone-deprived, rep 1


title: Rep2_Lib17_c-17

source_name: cells, 2.37 h after swarm expansion, 3057 µm distance from the swarm center (= point of inoculation)

tag: time after expansion (h)


title: Rep2_Lib18_c-18

source_name: cells, 2.37 h after swarm expansion, 4585 µm distance from the swarm center (= point of inoculation)

tag: position (um)


title: UK5_Calu3_Delta2AplusTPCA_10h_2


title: UK5_Calu3_AlphaAplusRux_10h_2


title: T47D cells, ESR1 Y537S-homozygous, hormone-deprived, rep 2


title: T47D cells, ESR1 Y537S-heterozygous, R5020, rep 3

value: ESR1 Y537S-heterozygous


title: Rep2_Lib16_c-16

source_name: cells, 2.37 h after swarm expansion, 1529 µm distance from the swarm center (= point of inoculation)


title: T47D cells, ESR1 Y537S-heterozygous, R5020, rep 2


title: UK5_Calu3_Delta2AplusRux_10h_3


title: T47D cells, ESR1 Y537S-heterozygous, R5020, rep 1


title: T47D cells, ESR1 Y537S-heterozygous, hormone-deprived, rep 2


title: T47D cells, ESR1 WT, R5020, rep 3

value: ESR1 WT


title: Rep2_Lib15_c-15

source_name: cells, 2.07 h after swarm expansion, 4583 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_Delta2AplusRux_10h_2

source_name: epithelial lung cancer cells


title: T47D cells, ESR1 Y537S-heterozygous, hormone-deprived, rep 1


title: UK5_Calu3_AlphaWT_10h_3


title: Rep2_Lib13_c-13

source_name: cells, 2.07 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: T47D cells, ESR1 WT, hormone-deprived, rep 3


title: UK5_Calu3_Delta2AplusTPCA_10h_1


title: Rep2_Lib14_c-14

source_name: cells, 2.07 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: T47D cells, ESR1 WT, R5020, rep 1


title: UK5_Calu3_AlphaWT_10h_2


title: T47D cells, ESR1 WT, hormone-deprived, rep 2


title: Rep2_Lib12_c-12

source_name: cells, 1.77 h after swarm expansion, 4585 µm distance from the swarm center (= point of inoculation)


title: T47D cells, ESR1 Y537S-heterozygous, hormone-deprived, rep 3


title: Rep2_Lib11_c-11

source_name: cells, 1.77 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: T47D cells, ESR1 WT, hormone-deprived, rep 1


title: MCF7 cells, ESR1 Y537S-homozygous, R5020, rep 2

description: MCF7_DESeq2_results_and_norm_counts.xlsx


title: MCF7 cells, ESR1 Y537S-homozygous, R5020, rep 1


title: MCF7 cells, ESR1 Y537S-homozygous, hormone-deprived, rep 3


title: MCF7 cells, ESR1 Y537S-homozygous, hormone-deprived, rep 2


title: MCF7 cells, ESR1 Y537S-homozygous, R5020, rep 3


title: UK5_Calu3_AlphaWT_10h_1


title: UK5_Calu3_Delta2AplusRux_10h_1


title: T47D cells, ESR1 WT, R5020, rep 2


title: Rep2_Lib9_c-9

source_name: cells, 1.47 h after swarm expansion, 4583 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_AlphaOrf6KO_10h_2


title: Rep2_Lib7_c-7

source_name: cells, 1.47 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_AlphaOrf6KO_10h_1


title: MCF7 cells, ESR1 Y537S-homozygous, hormone-deprived, rep 1


title: MCF7 cells, ESR1 Y537S-heterozygous, R5020, rep 3


title: MCF7 cells, ESR1 Y537S-heterozygous, R5020, rep 2


title: MCF7 cells, ESR1 Y537S-heterozygous, hormone-deprived, rep 3


title: MCF7 cells, ESR1 Y537S-heterozygous, hormone-deprived, rep 2


title: UK5_Calu3_AlphaOrf9bKO_10h_2


title: Rep2_Lib5_c-5

source_name: cells, 1.17 h after swarm expansion, 1527 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib6_c-6

source_name: cells, 1.17 h after swarm expansion, 3055 µm distance from the swarm center (= point of inoculation)


title: MCF7 cells, ESR1 Y537S-heterozygous, R5020, rep 1


title: UK5_Calu3_AlphaOrf9bKO_10h_3


title: Rep2_Lib20_c-20

source_name: cells, 2.67 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib8_c-8

source_name: cells, 1.47 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_AlphaOrf9bKO_10h_1


title: Rep2_Lib3_c-3

source_name: cells, 0.87 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: MCF7 cells, ESR1 WT, R5020, rep 2


title: UK5_Calu3_AlphaOrf6KO_10h_3


title: UK5_Calu3_GammaP1B_10h_3


title: MCF7 cells, ESR1 WT, hormone-deprived, rep 3


title: MCF7 cells, ESR1 Y537S-heterozygous, hormone-deprived, rep 1


title: Rep2_Lib4_c-4

source_name: cells, 0.87 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib2_c-2

source_name: cells, 0.68 h after swarm expansion, 3057 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_GammaP1B_10h_2


title: Rep2_Lib1_c-1

source_name: cells, 0.68 h after swarm expansion, 1529 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_GammaP1B_10h_1


title: MCF7 cells, ESR1 WT, R5020, rep 3


title: MCF7 cells, ESR1 WT, hormone-deprived, rep 2


title: MCF7 cells, ESR1 WT, hormone-deprived, rep 1


title: Oscc, S2, IP

city: Shanghai

first: Jingwen

last: Yang

address: Zhizaoju Road No.639

institute: Shanghaijiaotong University

description:
Oscc2
Methylated_RNA_sites.circRNA.xlsx

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Clean reads of input libraries were aligned to reference genome (UCSC HG19) by STAR software
The CircRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4)
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps
These peaks overlapping with exons of circRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by source genes of differentially methylated circRNAs separately.
Assembly: HG19
Supplementary files format and content: Methyalted_RNA_sites.circRNA.xlsx；Contains methylation site information

source_name: tongue

extract_protocol:
Total RNA was extracted using Trizol reagent
m6A RNA immunoprecipitation was performed with the GenSeqTM m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).
MeRIP-Seq

tag: tissue

value: oral mucosal tissue

tag: group

value: SCC

tag: fraction

value: IP


title: Oscc, S3, IP

description:
Oscc3
Methylated_RNA_sites.circRNA.xlsx


title: UK5_Calu3_Delta2A_10h_3


title: Oscc, S1, IP

description:
Oscc1
Methylated_RNA_sites.circRNA.xlsx


title: Control, K3, IP

description:
Control3
Methylated_RNA_sites.circRNA.xlsx

value: LK


title: UK5_Calu3_Delta2A_10h_2


title: Control, K1, IP

description:
Control1
Methylated_RNA_sites.circRNA.xlsx


title: Control, K2, IP

description:
Control2
Methylated_RNA_sites.circRNA.xlsx


title: Rep1_Lib94_b-98

source_name: cells, 6.77 h after swarm expansion, 22666 µm distance from the swarm center (= point of inoculation)

value: Bacteria

value: WT chromosome; comI_Q12L in natual plasmid


title: Rep1_Lib95_b-99

source_name: cells, 6.77 h after swarm expansion, 26055 µm distance from the swarm center (= point of inoculation)


title: MCF7 cells, ESR1 WT, R5020, rep 1


title: UK5_Calu3_Delta2A_10h_1

source_name: epithelial lung cancer cells


title: Rep1_Lib93_b-97

source_name: cells, 6.77 h after swarm expansion, 19279 µm distance from the swarm center (= point of inoculation)


title: Oscc, S2, Input

description:
Oscc2
Methylated_RNA_sites.circRNA.xlsx

value: input


title: Oscc, S1, Input

description:
Oscc1
Methylated_RNA_sites.circRNA.xlsx


title: Control, K3, Input


title: Control, K2, Input


title: UK5_Calu3_GammaP1A_10h_3

value: Gamma (P.1)


title: UK5_Calu3_GammaP1A_10h_2


title: Control, K1, Input


title: Rep1_Lib92_b-96

source_name: cells, 6.77 h after swarm expansion, 15891 µm distance from the swarm center (= point of inoculation)


title: primary ATRT, ATRT60

city: Paris

first: Mamy

middle: Jean de Dieu

last: ANDRIANTERANAGNA

state: Ile de France

address: 26 rue d'Ulm

department: Centre de Recherche

country: France

institute: Institut Curie

data_processing:
Raw data were processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility, following standard analysis in the field and available at https://github.com/bioinfo-pf-curie/RNA-seq.
Sequencing adaptors were trimmed using TrimGalore!
read QC were performed using fastqc
read mapping on GRCh39/hg19 reference genonme were performed using STAR (version 2.5.3a) and the refFlat gene annotation downloaded from UCSC
duplicated reads were marked with picard and removed
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: a single tab-delimited text file include TPM values for each Sample

molecule: polyA RNA

source_name: primary ATRT

extract_protocol:
Total RNA was obtained from 10 fresh-frozen tumour samples using the Qiagen RNAeasy kit (Qiagen, Venlo, Netherlands), according to the manufacturer’s procedure.
Barcode Illumina compatible libraries were generated from 750 ng of total RNA for each sample using the TruSeq Stranded mRNA Library Preparation Kit (Illumina). Libraries were sequenced using the Illumina HiSeq 2500 platform.

tag: anatomic location

value: Cerebral Cortex

tag: age at_diagnosis

value: primary ATRT


title: Rep1_Lib91_b-95

source_name: cells, 6.77 h after swarm expansion, 12506 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_GammaP1A_10h_1


title: Rep1_Lib96_b-100

source_name: cells, 6.77 h after swarm expansion, 29443 µm distance from the swarm center (= point of inoculation)


title: Oscc, S3, Input

description:
Oscc3
Methylated_RNA_sites.circRNA.xlsx


title: UK5_Calu3_Beta1_10h_3


title: primary ATRT, ATRT45

value: Cranial Nerves


title: primary ATRT, ATRT38

value: Cerebellar Anterior Lobe


title: UK5_Calu3_Beta1_10h_2


title: Rep1_Lib89_b-93

source_name: cells, 6.77 h after swarm expansion, 5730 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib90_b-94

source_name: cells, 6.77 h after swarm expansion, 9118 µm distance from the swarm center (= point of inoculation)


title: primary ATRT, ATRT37

value: Intraventricular


title: UK5_Calu3_Beta1_10h_1


title: Rep1_Lib88_b-92

source_name: cells, 6.77 h after swarm expansion, 1910 µm distance from the swarm center (= point of inoculation)


title: primary ATRT, ATRT31


title: Rep1_Lib87_b-91

source_name: cells, 6.44 h after swarm expansion, 24432 µm distance from the swarm center (= point of inoculation)


title: primary ATRT, ATRT28

value: Spinal Cord


title: UK5_Calu3_AlphaA_10h_3


title: primary ATRT, ATRT01


title: Rep1_Lib86_b-89

source_name: cells, 6.44 h after swarm expansion, 16983 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_AlphaA_10h_2


title: Rep1_Lib84_b-87

source_name: cells, 6.44 h after swarm expansion, 9479 µm distance from the swarm center (= point of inoculation)


title: IC-032, DAPT, replicate 3

data_processing:
Raw data were processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility, following standard analysis in the field and available at https://github.com/bioinfo-pf-curie/RNA-seq.
Sequencing adaptors were trimmed using TrimGalore!
read QC were performed using fastqc
read mapping on GRCh39/hg19 reference genome were performed using STAR (version 2.5.3a) and the refFlat gene annotation downloaded from UCSC
duplicated reads were marked with picard and then removed
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: a single tab-delimited text file includes matrix of TPM values with sample in columns and genes on rows

growth_protocol: ATRT cell line CHLA-02-ATRT (#CRL-3020, ATCC) was cultured according to the manufacturer’s protocol. IC-032 cell line, established in Curie Institute from a supra-tentorial ATRT, was cultured in DMEM/F12 supplemented with 20 ng/mL FGF, 20 ng/mL EGF, and 1x B27 supplement (#15360284, Fisher Scientific).

extract_protocol:
RNAs were extracted using the Nucleospin II kit (Macherey-Nagel). The tumor cell content was visually estimated before RNA extractions.
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.,).
Libraries were sequenced using the illumina NovaSeq platforms in the 100 bp paired-end mode.

treatment_protocol: 3 independant samples of CHLA-02-ATRT and IC-032 cells were treated with DMSO or DAPT at 10 µM for 7 days.

value: ATRT cell lines

value: DAPT

tag: time

value: Day 7


title: IC-032, DMSO, replicate 3

value: DMSO


title: IC-032, DAPT, replicate 1


title: IC-032, DMSO, replicate 2


title: UK5_Calu3_IC19_10h_3

tag: sars-cov-2 voc


title: IC-032, DAPT, replicate 2


title: primary ATRT, ATRT49


title: primary ATRT, ATRT46

value: MCP/ICV


title: IC-032, DMSO, replicate 1


title: primary ATRT, ATRT36


title: CHLA-02, DAPT, replicate 3


title: UK5_Calu3_IC19_10h_2

tag: collection time point


title: CHLA-02, DAPT, replicate 2

tag: treatment


title: Rep1_Lib83_b-86

source_name: cells, 6.44 h after swarm expansion, 5731 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib82_b-85

source_name: cells, 6.44 h after swarm expansion, 1911 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_IC19_10h_1

tag: additional conditions


title: CHLA-02, DMSO, replicate 2


title: CHLA-02, DMSO, replicate 3


title: UK5_Calu3_VIC_10h_3

tag: experiment group


title: CHLA-02, DMSO, replicate 1

tag: genotype


title: Rep1_Lib80_b-83

source_name: cells, 6.13 h after swarm expansion, 19984 µm distance from the swarm center (= point of inoculation)

tag: strain


title: 11 PCW snRNAseq

city: Los Angeles

first: Stanislao

last: Travisano

address: 4650 Sunset Blvd

department: Cardiothoracic Surgery

institute: Children's Hospital Los Angeles

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: barcodes ,features and matrix files

source_name: Epicardial dissection

extract_protocol:
Samples were microdissected by peeling the epicardial/subepicardial layers from the ventricle and from the peritruncal region of the Aorta and of the Outflow tract and resuspended in cold DMEM + 0.02% BSA + 10% FBS. Epicardial preparation was first resuspended in WB (Wash Buffer) and then moved to a freshly prepare lysis buffer (LB).
Chromium Single Cell 3' Library & Gel Bead Kit v3 and Single Cell Multiome ATAC + Gene Expression Kit following the manufacturer's instructions

treatment_protocol: No treatment

value: Epicardial dissection

value: WT

tag: age

value: 11 PCW


title: UK5_Calu3_VIC_10h_2

tag: cell line


title: UK5_Calu3_AlphaA_10h_1


title: Rep1_Lib85_b-88

source_name: cells, 6.44 h after swarm expansion, 13230 µm distance from the swarm center (= point of inoculation)

tag: cell type

value: Bacteria

value: WT chromosome; comI_Q12L in natual plasmid

tag: time after expansion (h)


title: Rep1_Lib79_b-82

source_name: cells, 6.13 h after swarm expansion, 16421 µm distance from the swarm center (= point of inoculation)

tag: position (um)


title: 10 PCW snRNAseq

description: 10x Genomics

value: 10 PCW


title: UK5_Calu3_VIC_10h_1

source_name: epithelial lung cancer cells


title: A-YW9_viremic_scATAC-seq

city: New Haven

first: Yulong

last: Wei

state: CT

address: 295 Congress Avenue

department: Microbial Pathogenesis

institute: Yale University

description: scATAC-seq

library_source: genomic single cell

data_processing:
RTA3 was used for basecalling
Cellranger-Arc count (v2.0)
Seurat (v4.3.0)
Signac (v1.7)
MACS3 (v3.0.0)
HOMER (v4.11)
chromVAR (v1.18)
Assembly: hg38
Supplementary files format and content: scATAC-seq filtered_feature_bc_matrices from cellranger-arc, filtered
Supplementary files format and content: atac_cut_sites.bigwig; atac_fragments.tsv.gz; atac_peak_annotation.tsv; atac_peaks.bed; per_barcode_metrics.csv

source_name: memory CD4+ Tcells

extract_protocol:
Refer to Mimitou et al., Nature Biotechnology 2021 for nuclear DNA extraction in DOGMA-seq protocol.
ATAC libraries for RNA-seq were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Library construction kit following manufacturer's protocols.
scATAC-seq (from DOGMA-seq)

value: memory CD4+ Tcells

tag: disease state

value: viremia (≤ 48 days)

tag: group


title: A-HD1_uninfected_scATAC-seq

description: scATAC-seq

value: uninfected


title: UK5_Calu3_Mock_10h_3

value: Mock


title: A-YW10_viremic_scATAC-seq

description: scATAC-seq


title: Rep1_Lib78_b-81

source_name: cells, 6.13 h after swarm expansion, 12856 µm distance from the swarm center (= point of inoculation)


title: A-YW6_suppressed_scATAC-seq

description: scATAC-seq

value: virally suppressed (≥ 1 year)

value: Antiretroviral therapy


title: CHLA-02, DAPT, replicate 1

value: ATRT cell lines


title: UK5_Calu3_Mock_10h_2


title: A-YW8_viremic_scATAC-seq

description: scATAC-seq


title: Rep1_Lib77_b-80

source_name: cells, 6.13 h after swarm expansion, 9294 µm distance from the swarm center (= point of inoculation)


title: A-YW5_suppressed_scATAC-seq

description: scATAC-seq


title: UK5_Calu3_Mock_10h_1


title: Rep1_Lib81_b-84

source_name: cells, 6.13 h after swarm expansion, 23546 µm distance from the swarm center (= point of inoculation)


title: A-YW3_suppressed_scATAC-seq

description: scATAC-seq


title: A-YW4_suppressed_scATAC-seq

description: scATAC-seq


title: UK4_HAE_Delta_72h_2

source_name: primary human airway epithelial cells

value: Primary HAE


title: A-YW1_suppressed_scATAC-seq

description: scATAC-seq


title: A-YW2_suppressed_scATAC-seq

description: scATAC-seq


title: Rep1_Lib76_b-79

source_name: cells, 6.13 h after swarm expansion, 5731 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib75_b-78

source_name: cells, 6.13 h after swarm expansion, 1910 µm distance from the swarm center (= point of inoculation)


title: UK4_HAE_Delta_72h_3


title: Rep1_Lib74_b-77

source_name: cells, 5.80 h after swarm expansion, 22081 µm distance from the swarm center (= point of inoculation)


title: HD1_uninfected_scRNA-seq

description: scRNA-seq

library_source: transcriptomic single cell

data_processing:
RTA3 was used for basecalling
Cellranger count (v5.0.1)
Seurat (v4.3.0)
Harmony (v3.8)
fGSEA (v1.22)
WGCNA (v1.70)
Assembly: hg38
Supplementary files format and content: scRNA-seq filtered_feature_bc_matrices from cellranger

extract_protocol:
Refer to Mimitou et al., Nature Biotechnology 2021 for cellular RNA extraction in DOGMA-seq protocol.
RNA libraries for RNA-seq were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Library construction kit following manufacturer's protocols.
scRNA-seq (from DOGMA-seq)


title: YW10_viremic_scRNA-seq

description: scRNA-seq


title: YW9_viremic_scRNA-seq

description: scRNA-seq


title: YW6_suppressed_scRNA-seq

description: scRNA-seq


title: UK4_HAE_Gamma_72h_2

value: Gamma (P.1)


title: YW3_suppressed_scRNA-seq

description: scRNA-seq


title: YW2_suppressed_scRNA-seq

description: scRNA-seq


title: UK4_HAE_Beta_72h_3


title: UK4_HAE_Delta_72h_1


title: Rep1_Lib72_b-75

source_name: cells, 5.80 h after swarm expansion, 16246 µm distance from the swarm center (= point of inoculation)


title: C-YW10_viremic_feature_barcoding

description:
feature barcoding
Participant_Hashtags.txt
ADT_HTO_bc_sequences.txt

library_source: other

data_processing:
RTA3 was used for basecalling
Cellranger count (v5.0.1)
Seurat (v4.3.0)
DSB (v1.0.3)
Assembly: hg38
Supplementary files format and content: feature barcoding filtered_feature_bc_matrices from cellranger
Supplementary files format and content: Participant_Hashtags.txt; ADT_HTO_bc_sequences.txt

molecule: protein

extract_protocol:
Refer to Mimitou et al., Nature Biotechnology 2021 for surface protein capture in DOGMA-seq protocol.
ADT/HTO libraries for Feature Barcoding were prepared using Chromium  Single Cell 3' Feature Barcode  Library Kit following manufacturer's protocols.
Feature Barcoding (ADT/HTO, from DOGMA-seq)


title: YW5_suppressed_scRNA-seq

description: scRNA-seq


title: YW8_viremic_scRNA-seq

description: scRNA-seq


title: Rep1_Lib73_b-76

source_name: cells, 5.80 h after swarm expansion, 19163 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib71_b-74

source_name: cells, 5.80 h after swarm expansion, 13328 µm distance from the swarm center (= point of inoculation)


title: YW4_suppressed_scRNA-seq

description: scRNA-seq


title: UK4_HAE_Beta_72h_2


title: Rep1_Lib68_b-70

source_name: cells, 5.80 h after swarm expansion, 1529 µm distance from the swarm center (= point of inoculation)


title: C-YW9_viremic_feature_barcoding


title: C-YW8_viremic_feature_barcoding


title: Rep1_Lib67_b-69

source_name: cells, 5.51 h after swarm expansion, 19530 µm distance from the swarm center (= point of inoculation)


title: C-YW5_suppressed_feature_barcoding


title: Rep1_Lib70_b-72

source_name: cells, 5.80 h after swarm expansion, 7496 µm distance from the swarm center (= point of inoculation)


title: YW1_suppressed_scRNA-seq

description: scRNA-seq


title: Rep1_Lib69_b-71

source_name: cells, 5.80 h after swarm expansion, 4585 µm distance from the swarm center (= point of inoculation)


title: C-YW4_suppressed_feature_barcoding


title: UK4_HAE_Gamma_72h_1


title: UK4_HAE_Beta_72h_1


title: Rep1_Lib66_b-68

source_name: cells, 5.51 h after swarm expansion, 16538 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib65_b-67

source_name: cells, 5.51 h after swarm expansion, 13547 µm distance from the swarm center (= point of inoculation)


title: UK4_HAE_Gamma_72h_3


title: UK4_HAE_Alpha_72h_3


title: C-YW6_suppressed_feature_barcoding

source_name: memory CD4+ Tcells


title: C-YW3_suppressed_feature_barcoding


title: C-YW2_suppressed_feature_barcoding


title: UK4_HAE_Alpha_72h_2


title: C-HD1_uninfected_feature_barcoding


title: C-YW1_suppressed_feature_barcoding


title: OA11.Input

city: zhengzhou

first: yang

last: yu

state: henan province

address: jianshe road

department: Department of orthopedics

institute: the First Affiliated Hospital of Zhengzhou University

data_processing:
paired-end reads were harvested from the Illumina Novaseq 6000 sequencer, and Q30 was used for quality control. After 3’ adaptor-trimming and low-quality read removal via cutadapt software (v1.9.3), clean reads of all libraries were aligned to the reference genome (UCSC MM10) using the Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified using MACS software. Differentially methylated sites were identified by diffReps with a fold change threshold >2 and P-value <0.0001. The differentially expressed genes were identified using the DESeq2 R package with a P-value < 0.05 and fold change > 2 as the cutoff criteria.
Assembly: GRCh38/hg38

source_name: cartilage

extract_protocol:
Knee cartilage samples of medial condyles were collected from three patients who underwent knee arthroplasty due to advanced OA and three patients who underwent thigh amputation due to trauma. Fresh samples were immediately frozen in liquid nitrogen and stored at -80 ℃ for detection. The total RNA from each sample was extracted using TRIzol reagent (Invitrogen Corporation, Carlsbad, CA). The content of rRNA in the total RNA was reduced using the Ribo-Zero rRNA Removal Kit (Illumina, Inc., CA, USA). The concentration of total RNA was measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). RNA with an OD260/OD280 ratio range of 1.8–2.1 was marked as acceptable.
The m5C-IP-Seq service was provided by CloudSeq Inc. (Shanghai, China). Total RNA was subjected to immunoprecipitation with the GenSeq® m5C-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. RNA libraries for IP and input samples were then constructed with the GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using the Agilent 2100 bioanalyzer and then sequenced on a NovaSeq platform..
MeRIP-seq

tag: tissue

value: cartilage


title: Rep1_Lib64_b-66

source_name: cells, 5.51 h after swarm expansion, 10556 µm distance from the swarm center (= point of inoculation)


title: UK4_HAE_Alpha_72h_1


title: OA2.Input


title: OA.Input

description: OA


title: UK4_HAE_IC19_72h_3


title: Rep1_Lib63_b-65

source_name: cells, 5.51 h after swarm expansion, 7568 µm distance from the swarm center (= point of inoculation)


title: UK4_HAE_IC19_72h_2

source_name: primary human airway epithelial cells


title: N.Input

description: N


title: N2.Input


title: Rep1_Lib61_b-63

source_name: cells, 5.51 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib62_b-64

source_name: cells, 5.51 h after swarm expansion, 4584 µm distance from the swarm center (= point of inoculation)


title: UK4_HAE_IC19_72h_1


title: OA2.IP


title: OA11.IP


title: OA.IP

description: OA


title: N.IP

description: N


title: Rep1_Lib60_b-62

source_name: cells, 5.21 h after swarm expansion, 17472 µm distance from the swarm center (= point of inoculation)


title: IgG

city: Guangzhou

first: Rui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
Raw reads were cleaned using cutadapt and aligned to the hg19 genome using Bowtie2
PCR duplicates were removed using picard MarkDuplicates. Genome coverage files for UCSC genome browser were generated by deepTools
Peaks were called by MACS2 and annotated by annotatePeaks.pl in Homer
Visualization of the genomic regions was performed with IGV.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT& TAG

growth_protocol: The CUT&Tag was performed by Jiayin Biotechnology Ltd. (Shanghai, China)

extract_protocol:
Bead-bound cells were suspended by dig wash buffer with 1:50 dilution of anti-MLL1, RNAPII, YTHDC2 or H3K4me3 antibody incubated on a roating platform overnight at 4 °C.After removing primary antibodies, the corresponding secondary antibody was diluted 1:100 in dig wash buffer and cells were incubated for 60 min. Then cells were washed using dig wash buffer. A 1:100 dilution of pA-Tn5 adapter complex was prepared in dig-med buffer and incubated with cells for 1 h. Cells were washed with Dig-med buffer. Then cells were resuspended in tagmentation buffer (10mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
Sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end.

treatment_protocol: PANC-1 cells (1×106) were incubated with 10μL Concanavalin A coated magnetic beads (Bangs Laboratories) for 10 min.

value: Human PDAC cell lines

tag: chip antibody

value: IgG


title: UK4_HAE_VIC_72h_2


title: UK4_HAE_VIC_72h_3


title: Rep1_Lib59_b-61

source_name: cells, 5.21 h after swarm expansion, 15324 µm distance from the swarm center (= point of inoculation)


title: OS-NOES-3

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Reads were trimmed with trimmomatic, and QC was performed using FastQC.
Reads were mapped to the GRCh38 transcriptome using STAR and gene expression was quantified with RSEM.
Differential expression analysis was performed with DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited files containing estimated count and FPKM for each gene in every sample

source_name: OS myobundles, SpX21 flight, Day18

growth_protocol: Injectable hydrogel mixtures (3.3 mg/mL rat tail collagen I, and 22% (v/v) Matrigel) were combined with YA- and OS-derived CD56+ enriched myoblasts. The cell-laden hydrogels were injected into the PDMS chips to a final cell density of 15 and 20 million cells/mL for YA- and OS-derived cells, respectively. Cells were allowed to polymerize at 37°C for 60 min and seeding ports were sealed using polylactic acid (PLA, Makerbot, Brooklyn, NY) plugs. Chips were perfused with degassed Skeletal Muscle Growth media supplemented with 0.1 mg/ml Primocin (InvivoGen, San Diego, CA) at a constant flow rate of 1 mL/h at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using Quiagen kit. Illumina TruSeq RNA Sample Prep Kit (Cat#) was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Young- and old-derived skeletal muscle myobundles were exposed to microgravity for 10 days and matching ground control group

value: Skeletal muscle

value: Enriched CD56+ myoblasts

value: Wild type ( cell line)

tag: biorep

value: Exposed to microgravity (Non EStim)


title: UK4_HAE_VIC_72h_1

tag: sars-cov-2 voc


title: N11.Input


title: Rep1_Lib57_b-59

source_name: cells, 5.21 h after swarm expansion, 11028 µm distance from the swarm center (= point of inoculation)

value: Bacteria

value: WT chromosome; comI_Q12L in natual plasmid


title: OS-NOES-2


title: N11.IP


title: UK4_HAE_Mock_72h_3

tag: collection time point


title: Rep1_Lib56_b-58

source_name: cells, 5.21 h after swarm expansion, 8881 µm distance from the swarm center (= point of inoculation)


title: OS-NOES-1

tag: treatment


title: YA-NOES-3

source_name: YA myobundles, SpX21 flight, Day18


title: UK4_HAE_Mock_72h_2

tag: additional conditions


title: YA-NOES-2


title: YA-NOES-1


title: GC-OS-NOES-3

source_name: OS myobundles, ground control, Day18

value: Earth control (Non EStim)


title: UK4_Calu3_DeltaE_24h_3

source_name: epithelial lung cancer cells

tag: experiment group


title: UK4_HAE_Mock_72h_1


title: Rep1_Lib55_b-57

source_name: cells, 5.21 h after swarm expansion, 6733 µm distance from the swarm center (= point of inoculation)

tag: genotype


title: Rep1_Lib54_b-56

source_name: cells, 5.21 h after swarm expansion, 4584 µm distance from the swarm center (= point of inoculation)

tag: strain


title: GC-OS-NOES-2


title: GC-OS-NOES-1


title: Rep1_Lib53_b-55

source_name: cells, 5.21 h after swarm expansion, 2292 µm distance from the swarm center (= point of inoculation)


title: N2.IP

source_name: cartilage


title: GC-YA-NOES-3

source_name: YA myobundles, ground control, Day18


title: UK4_Calu3_DeltaE_24h_2


title: Rep1_Lib58_b-60

source_name: cells, 5.21 h after swarm expansion, 13176 µm distance from the swarm center (= point of inoculation)


title: GC-YA-NOES-2


title: GC-YA-NOES-1


title: UK4_Calu3_DeltaE_24h_1


title: UK4_Calu3_DeltaNSP12_24h_3


title: Rep1_Lib51_b-53

source_name: cells, 4.92 h after swarm expansion, 13336 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib52_b-54

source_name: cells, 4.92 h after swarm expansion, 15524 µm distance from the swarm center (= point of inoculation)


title: UK4_Calu3_DeltaNSP12_24h_2


title: D_1 PDX in mice, ICAM1-MMAE, Day42

city: ZHEJIANG

first: Bing

last: Zhu

state: 浙江

address: No.150 Dongfang street, Qiantang district, Hangzhou

institute: Institute of Basic Medicine and Cancer Chinese Academy of Sciences

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: subcutaneous tumor tissue

growth_protocol: Tumor tissues of PDX models were cut into 8 mm3 pieces and subcutaneously transplanted into the right dorsal flank of 4-6 weeks old female nude mice. After xenograft tumors were stably formed to 50-100 mm3, mice were intravenously injected with different drugs

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol:
Mice were randomly distributed in five groups, and dealt with different treatment of PBS, Gemcitabine, ICAM1 monoclonal antibody, ICAM1-MMAE or ICAM1-Dxd in an equivalent dosage of 5 mg/kg every 3 days via tail vein injection, with a total of 4 injections.
The tumor volumes were monitored for 6 weeks. At the endpoint, mice were euthanized and subcutaneous tumors were excised to perform RNA-seq analysis.

value: subcutaneous tumor tissue

tag: time

value: patient derived xenograft (PDX) of Cholangicarcinoma

value: ICAM1-MMAE, a dosage of 5 mg/kg every 3 days via tail vein injection, with a total of 4 injections


title: D_3 PDX in mice, ICAM1-MMAE, Day42


title: D_2 PDX in mice, ICAM1-MMAE, Day42


title: Rep1_Lib49_b-51

source_name: cells, 4.92 h after swarm expansion, 8959 µm distance from the swarm center (= point of inoculation)


title: UK4_Calu3_DeltaNSP12_24h_1

tag: cell line


title: C_2 PDX in mice, ICAM1-Dxd, Day42

tag: cell type

value: ICAM1-Dxd, a dosage of 5 mg/kg every 3 days via tail vein injection, with a total of 4 injections


title: Rep1_Lib50_b-52

source_name: cells, 4.92 h after swarm expansion, 11147 µm distance from the swarm center (= point of inoculation)

tag: time after expansion (h)


title: C_3 PDX in mice, ICAM1-Dxd, Day42


title: C_1 PDX in mice, ICAM1-Dxd, Day42


title: B_3 PDX in mice, ICAM1 mAb, Day42

value: ICAM1 mAb, a dosage of 5 mg/kg every 3 days via tail vein injection, with a total of 4 injections


title: B_1 PDX in mice, ICAM1 mAb, Day42


title: B_2 PDX in mice, ICAM1 mAb, Day42


title: UK4_Calu3_Gamma_24h_3


title: Rep1_Lib48_b-50

source_name: cells, 4.92 h after swarm expansion, 6771 µm distance from the swarm center (= point of inoculation)

tag: position (um)


title: A_2 PDX in mice, PBS, Day42

value: PBS, a dosage of 5 mg/kg every 3 days via tail vein injection, with a total of 4 injections


title: UK4_Calu3_Gamma_24h_1

value: Gamma (P.1)


title: Rep1_Lib47_b-49

source_name: cells, 4.92 h after swarm expansion, 4584 µm distance from the swarm center (= point of inoculation)


title: A_3 PDX in mice, PBS, Day42


title: Rep1_Lib46_b-48

source_name: cells, 4.92 h after swarm expansion, 2292 µm distance from the swarm center (= point of inoculation)


title: UK4_Calu3_Beta_24h_3


title: A_1 PDX in mice, PBS, Day42


title: MCF7-oeCON-3

city: shanghai

first: Yaqi

last: Qiu

state: shanghai

address: 上海市徐汇区宜山路600号上海市第六人民医院

institute: shanghaijiaotong university

description: control

data_processing:
CLC genomics workbench v 11.0.1
sequence reads were trimmed for adaptor sequence using CLC genomic benchwork (parameter Quality limit:0.05)
trimmed sequence reads were mapped to GRCh38.p13 using CLC genomic benchwork
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file include counts values for all samples.

source_name: breast

growth_protocol: MCF7 cells were cultured in MEM supplemented with 10% fetal calf serum, 10 µg/ml insulin, 100 U/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
Total RNA was extracted from cultured cells using RNAiso Plus (9108, Takara Bio, Shiga, Japan) according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocals.

treatment_protocol: We firstly established a stable cell line by transfection of CD44 cDNA into MCF7 cells which expresses low level of CD44 and then we used RNA-sequencing (RNA-seq) to compare mRNA expression profiles between the MCF7vector and MCF7CD44 cells.

value: breast

value: breat cancer cell

value: vector


title: MCF7-oeCON-2

address: 上海市徐汇区宜山路600号上海市第六人民医院

description: control


title: MCF7-oeCON-1

address: 上海市徐汇区宜山路600号上海市第六人民医院

description: control


title: UK4_Calu3_Beta_24h_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence using Trimmomatic.
Reads were mapped to Homo_sapiens ensembl_release-101 genome using HISAT2.
Counts of reads mapped to protein coding genes were extracted using featureCount and are reported.
Assembly: Not relevant
Supplementary files format and content: count values for each Sample

extract_protocol:
Total RNA was extracted from 10^6 cells using the Qiagen RNeasy Kit after inactivating the virus post infection.
The chosen method of rRNA removal was rRNA depletion for mRNA and long noncoding species. RNA was primed with random hexamers for first-strand cDNA synthesis and then second-strand cDNA synthesis. All samples were sequenced on HiSeq 4000.


title: Rep1_Lib45_b-47

data_processing:
Sequencing of the cDNA libraries was performed by MPGC (Cologne, Germany) or D-BSSE genomics facilty (Basel, Switzerland)
Sequence reads were trimmed for adaptor sequence/short sequence (<35 nt) using Trimmomatic v0.39
Trimmed sequence reads were mapped to B. subtilis NCIB3610 genome and plasmid (NCBI Accession number: NZ_CP020102 and NZ_CP020103) using HISAT2 v2.2.1 in single-end mode.
Reads mapped to all cetegory of genes (CDS, ncRNA, tmRNA, signal recognition particle RNA, ribonuclease P RNA, tRNA, rRNA) were counted using featureCounts v2.0.1 with fractional counting for multi-mapping and multi-overlapping reads (-OM --fraction) in a strand-specific manner (-s 2). Of those, reads mapped in tRNA and rRNA were removed and the remaining reads were used for the downstream analysis.
All genes for which there were at least 2 samples with a read count of at least 10 were used for the downstream analysis. Samples with remaining reads of < 1 million reads were excluded and the rest of the samples were used for normalization using edgeR (version 3.6.1) and transformed (log2).
Supplementary files format and content: comma-separated files include mapped read count data for each sample
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at expansion phase
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at lag and expansion phase

source_name: cells, 4.62 h after swarm expansion, 13236 µm distance from the swarm center (= point of inoculation)

extract_protocol:
RNA was isolated by the hot phenol method (Jahn et al, J Microbiol Methods, 2008) with some modifications. Prepared RNA was DNase-digested and cleaned up using RNACleanXP. Depletion of ribosomal RNA was performed using DIY method (Culviner et al, mBio, 2020). Integrity of the prepared RNA was tested using a TapeStation.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB, E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a TapeStation.


title: Rep1_Lib44_b-46

source_name: cells, 4.62 h after swarm expansion, 11047 µm distance from the swarm center (= point of inoculation)


title: MCF7-oeCD44-3

address: 上海市徐汇区宜山路600号上海市第六人民医院

description: CD44 overexpression

value: CD44 overexpression


title: MCF7-oeCD44-1

address: 上海市徐汇区宜山路600号上海市第六人民医院

description: CD44 overexpression


title: UK4_Calu3_Alpha_24h_3

source_name: epithelial lung cancer cells


title: Rep1_Lib43_b-45

source_name: cells, 4.62 h after swarm expansion, 8858 µm distance from the swarm center (= point of inoculation)


title: MCF7-oeCD44-2

address: 上海市徐汇区宜山路600号上海市第六人民医院

description: CD44 overexpression


title: Rep1_Lib42_b-43

source_name: cells, 4.62 h after swarm expansion, 4585 µm distance from the swarm center (= point of inoculation)


title: PER-403,72h,1uM taz [PER-403 S4]

city: boston

first: Chris

middle: A

last: French

state: MA

address: 75 francis st.

department: Pathology

institute: BWH

description: 1uM taz

data_processing:
Quality-controlled reads are aligned to the human genome (GRCh38/hg38) and to ERCC92 spike-in sequences using a splice-aware aligner (STAR89) with Ensembl. transcriptome annotations.
Differential expression (DE) analysis is performed using RUVSeq to identify unwanted variation followed by edgeR91 and/or DESeq2
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: DMEM supplemented with either 10% FBS (10-15) or 20% BGS (PER-403).

extract_protocol:
RNA was harvested using RNAeasy (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. ERCC92 spike-in RNA is added to normalize reads.
RNA libraries for RNA-seq were prepared using the Roche KAPA HyperPrep RNA RiboErase Kit following manufacturer's protocols.

value: NUT carcinoma cell line

value: 1uM taz

tag: time point


title: PER-403,72h,DMSO [PER-403 S8]

description: DMSO

value: DMSO


title: PER-403,96h,1uM taz [PER-403 S9]

description: 1uM taz


title: UK4_Calu3_Alpha_24h_2


title: UK4_Calu3_Alpha_24h_1


title: PER-403,72h,1uM taz [PER-403 S20]

description: 1uM taz


title: PER-403,72h,DMSO [PER-403 S24]

description: DMSO


title: Rep1_Lib40_b-41

source_name: cells, 4.07 h after swarm expansion, 12381 µm distance from the swarm center (= point of inoculation)

value: Bacteria


title: UK4_Calu3_IC19_24h_2


title: Rep1_Lib41_b-42

source_name: cells, 4.62 h after swarm expansion, 2292 µm distance from the swarm center (= point of inoculation)

value: WT chromosome; comI_Q12L in natual plasmid


title: PER-403,36h,1uM taz [PER-403 S17]

description: 1uM taz


title: Rep1_Lib39_b-40

source_name: cells, 4.07 h after swarm expansion, 10906 µm distance from the swarm center (= point of inoculation)


title: PER-403,144h,1uM taz [PER-403 S29]

description: 1uM taz


title: PER-403,144h,1uM taz [PER-403 S13]

description: 1uM taz


title: Rep1_Lib38_b-39

source_name: cells, 4.07 h after swarm expansion, 9412 µm distance from the swarm center (= point of inoculation)


title: UK4_Calu3_Beta_24h_1


title: 10-15,72h,1uM taz [S9]

description: 1uM taz


title: PER-403,36h,1uM taz [PER-403 S1]

description: 1uM taz


title: Rep1_Lib37_b-38

source_name: cells, 4.07 h after swarm expansion, 7932 µm distance from the swarm center (= point of inoculation)


title: 10-15,96h,1uM taz [S5]

description: 1uM taz


title: UK4_Calu3_VIC_24h_3


title: Rep1_Lib35_b-36

source_name: cells, 4.07 h after swarm expansion, 5521 µm distance from the swarm center (= point of inoculation)


title: 10-15,36h,1uM taz [S30]

description: 1uM taz


title: 10-15,72h,DMSO [S13]

description: DMSO


title: UK4_Calu3_VIC_24h_1


title: UK4_Calu3_VIC_24h_2


title: Rep1_Lib34_b-34

source_name: cells, 4.07 h after swarm expansion, 3819 µm distance from the swarm center (= point of inoculation)


title: 10-15,72h,1uM taz [S25]

description: 1uM taz


title: UK4_Calu3_IC19_24h_1


title: PER-403,96h,1uM taz [PER-403 S25]

description: 1uM taz


title: UK4_Calu3_Mock_24h_3

value: Mock


title: UK4_Calu3_Mock_24h_1


title: 10-15,144h,1uM taz [S1]

description: 1uM taz


title: 10-15,144h,1uM taz [S17]

description: 1uM taz


title: 10-15,72h,DMSO [S29]

description: DMSO


title: 10-15,36h,1uM taz [S14]

description: 1uM taz


title: UK4_Calu3_DeltaE_10h_3


title: 10-15,96h,1uM taz [S21]

description: 1uM taz


title: Rep1_Lib33_b-33

source_name: cells, 4.07 h after swarm expansion, 2292 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib32_b-32

source_name: cells, 4.07 h after swarm expansion, 764 µm distance from the swarm center (= point of inoculation)


title: vmid_ind-197216

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

data_processing:
Smart-seq3 read analysis was performed using zUMI v2.9.7, providing the expected barcodes file, using STAR 2.7.7a with additional STAR parameters "--limitOutSJcollapsed 50000000 --limitSjdbInsertNsj 2000000 --clip3pAdapterSeq CTGTCTCTTATACACATCT" and Homo sapiens Ensembl GRCh38 release 94 as a reference. zUMI generated inex UMI counts were used for downstream analyses.
Assembly: hg38
Supplementary files format and content: tab separated text includes zUMI intron exon UMI counts for each sample

source_name: Brain organoid

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen). cDNA synthesis was performed using 1µg of total RNA and Superscript II (Invitrogen) enzyme, following protocols provided by the manufacturer.
Smart-seq3
Illumina NovaSeq S4

value: Brain organoid

value: neural tissue

value: WT

tag: age

value: 60 day

tag: sample type

value: individual ventral midbrain organoid


title: Rep1_Lib36_b-37

source_name: cells, 4.07 h after swarm expansion, 6475 µm distance from the swarm center (= point of inoculation)


title: vmid_ind-197214

tag: tissue


title: Rep1_Lib31_b-31

source_name: cells, 3.72 h after swarm expansion, 9933 µm distance from the swarm center (= point of inoculation)


title: UK4_Calu3_DeltaNSP12_10h_3


title: UK4_Calu3_DeltaNSP12_10h_2


title: Ctx_ind-197206

value: individual cortical organoid


title: Str_ind-197209

value: individual striatal organoid


title: Ctx_ind-197207


title: UK4_Calu3_DeltaNSP12_10h_1


title: Ctx_ind-197205


title: Fusion_vmid-197204

value: ventral midbrain patterned part of an organoid assembloid


title: Rep1_Lib28_b-28

source_name: cells, 3.72 h after swarm expansion, 5348 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib25_b-25

source_name: cells, 3.72 h after swarm expansion, 764 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib27_b-27

source_name: cells, 3.72 h after swarm expansion, 3820 µm distance from the swarm center (= point of inoculation)


title: Fusion_Str-197194

value: striatal patterned part of an organoid assembloid


title: Fusion_Ctx-197196

value: cortex patterned part of an organoid assembloid


title: Rep1_Lib24_b-24

source_name: cells, 3.43 h after swarm expansion, 9166 µm distance from the swarm center (= point of inoculation)


title: Fusion_Ctx-197199


title: Rep1_Lib22_b-22

source_name: cells, 3.43 h after swarm expansion, 6111 µm distance from the swarm center (= point of inoculation)


title: Fusion_Str-197197


title: vmid_ind-197213


title: UK4_Calu3_Gamma_10h_1

source_name: epithelial lung cancer cells

value: Gamma (P.1)


title: UK4_Calu3_Beta_10h_2


title: Fusion_vmid-197195


title: UK4_Calu3_Gamma_10h_3


title: Pooled GEX library for 9 brain organoid tissues

data_processing:
scRNA-seq reads were processed using cellranger count v7.0.0 with default settings, using the prebuild 10X GRCh38 reference refdata-gex-GRCh38-2020-A and providing barcode information via feature-ref (provided as supplementary file).  Seurat v4.1.1 was used to perform dimensionality reduction, clustering, and visualization for the scRNA-seq data. Samples were demultiplexed using MULTIseqDemux (McGinnis et al., 2018). Stressed cells were removed using gruffi (Vertesy et al., 2022). Only cells with more than 1500 detected genes, UMI counts greater than 3000 and less than 10% mitochondrial content were retained for further analysis.
Assembly: hg38
Supplementary files format and content: Seurat object of filtered cell data stored in rds format

extract_protocol:
Fusions were separated by a scalpel.  Ventral Midbrain, striatal and cortical tissue were processed separately. Before dissociation, necrotic material from the core of the organoid was washed off in PBS-/-. Organoids were then transferred into a 1.5ml Eppendorf tube and all PBS was removed. 1ml of Trypsin-Accutase (1:10) (Trypsin: Thermo Fisher, Cat.# 15090046) plus DNAse (2ul/ml, TURBOTM DNase, Thermo AM2238) was added to the organoids and the tubes were transferred to a tube shaker at 37°C 700RPM. Tubes were flipped every 3-4 minutes until the tissue was dissolved, or for a maximum of 40min. After dissociation, 500µl of ice-cold PBS-/-were added on top. Eventually forming cloudy material on top of the solution can be removed with a pipet. Tubes were then spun down in a precooled (4°C) table centrifuge at 400rpm for 5min. Then, as much liquid as possible was removed without damaging the cell pellet. Resuspend pellets carefully in 400ul of PBS-/-and filtered through a 40µm cell strainer. Cells were then counted. Live cell count had to be above 80% and above a concentration of 200.000cells/ml, but not more than 2.7mio cells/ml. Samples were diluted down, where needed. Multiseq labeling using MULTI-seq Lipid-Modified Oligos was performed directly after counting following the manufacturer's protocol (Sigma-Aldrich, Cat.# LMO001). In brief, 40ul of anchor solution including barcode was mixed with the sample and incubated on ice for 5min. 40µl of co-anchor were then added and mixed and incubated on ice for 5min. The reaction was then topped up with 1ml of ice-cold PBS-/-containing 2% BSA, and mixed to bind residual anchor and co-anchor. Cells were spun down at 400-600RPM for 5min at 4°C. The supernatant was removed and cells were resuspended in 200µl PBS-/-with 2% BSA and supplemented with 0.8µg/ml DAPI. Cells were then FACS sorted for live cell sorting (DAPI-) in a FACS Aria III machine and a 70µm nozzle (approx. 1nl per cell) into a 1.5ml Eppendorf tube with 20µl of PBS-/-and 2% BSA.
Cells were dissociated into single cell suspension, labelled with MULTIseq lipid-modified oligos for multiplexing (McGinnis et al, 2019, DOI:10.1038/s41592-019-0433-8.) and sorted  equivalently for DAPI negative (intact) cells in a FACS sorter. Library was created according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).
Illumina NovaSeq S1


title: Rep1_Lib23_b-23

source_name: cells, 3.43 h after swarm expansion, 7638 µm distance from the swarm center (= point of inoculation)


title: RP87N

city: Kalyani

first: Partha

middle: P.

last: Majumder

state: West Bengal

country: India

institute: National Institute of Biomedical Genomics

data_processing:
Raw sequencing reads were converted to FASTQ files; data quality was assessed using FASTQC (https://qubeshub.org/resources/fastqc). Low quality reads and adapter sequences were removed. RNA-sequence data were processed in accord with the TCGA mRNA Analysis pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/).
Assembly: hg19 (NCBI 37)
Supplementary files format and content: TXT

source_name: biopsy of normal

extract_protocol:
total RNA was extracted using RNeasy kit (QIAGEN)
RNA sequencing libraries were generated using TruSeq RNA Library Prep Kit v2 (Illumina), following the manufacturer’s protocol

value: biopsy of normal

tag: patient id

tag: recurrence

value: NR

tag: survival

value: DIED

tag: Sex

value: Female

tag: tobacco

value: NO

tag: grade

value: PoorlyDifferentiated


title: UK4_Calu3_Beta_10h_3

tag: sars-cov-2 voc

tag: collection time point

tag: additional conditions

tag: experiment group


title: Fusion_vmid-197201

value: Brain organoid

tag: cell line

tag: cell type

tag: genotype


title: Fusion_vmid-197198

value: neural tissue


title: Rep1_Lib20_b-20

source_name: cells, 3.43 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)

value: Bacteria

value: WT chromosome; comI_Q12L in natual plasmid

tag: strain

tag: time after expansion (h)

tag: position (um)


title: Fusion_Str-197203

tag: tissue

value: WT

tag: age

value: 60 day

tag: sample type


title: Pooled LMO library for 9 brain organoid tissues

molecule: other

tag: treatment


title: Fusion_Ctx-197202


title: Fusion_Ctx-197193


title: Rep1_Lib26_b-26

source_name: cells, 3.72 h after swarm expansion, 2292 µm distance from the swarm center (= point of inoculation)


title: UK4_Calu3_Gamma_10h_2


title: RP84T

source_name: biopsy of tumor

value: biopsy of tumor

tag: patient id

tag: recurrence

value: R

tag: survival

tag: Sex

value: Male

value: ModeratelyDifferentiated


title: Str_ind-197212

value: individual striatal organoid


title: Str_ind-197211


title: UK4_Calu3_DeltaE_10h_2

tag: sars-cov-2 voc

tag: collection time point


title: Rep1_Lib17_b-17

source_name: cells, 3.23 h after swarm expansion, 4584 µm distance from the swarm center (= point of inoculation)


title: vmid_ind-197215

value: individual ventral midbrain organoid


title: Rep1_Lib30_b-30

source_name: cells, 3.72 h after swarm expansion, 8405 µm distance from the swarm center (= point of inoculation)


title: UK4_Calu3_DeltaE_10h_1

tag: additional conditions

tag: experiment group


title: RP87T

value: NR

tag: tobacco

tag: grade


title: Ctx_ind-197208

tag: cell line

tag: cell type

tag: genotype

value: individual cortical organoid


title: Rep1_Lib29_b-29

source_name: cells, 3.72 h after swarm expansion, 6877 µm distance from the swarm center (= point of inoculation)

tag: strain

tag: time after expansion (h)

tag: position (um)


title: UK4_Calu3_Beta_10h_1


title: UK4_Calu3_Alpha_10h_3


title: RP81N

tag: tissue

value: biopsy of normal

value: ALIVE

tag: age

value: YES


title: RP86T

tag: patient id

tag: recurrence


title: UK4_Calu3_IC19_10h_2


title: RP81M

source_name: biopsy of margin

value: biopsy of margin

tag: survival

tag: Sex


title: Rep1_Lib19_b-19

source_name: cells, 3.43 h after swarm expansion, 1529 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib18_b-18

source_name: cells, 3.23 h after swarm expansion, 6112 µm distance from the swarm center (= point of inoculation)


title: RP86M


title: RP84N

value: DIED

value: NO


title: Rep1_Lib21_b-21

source_name: cells, 3.43 h after swarm expansion, 4583 µm distance from the swarm center (= point of inoculation)

value: Bacteria

value: WT chromosome; comI_Q12L in natual plasmid


title: RP86N


title: UK4_Calu3_Alpha_10h_2

tag: sars-cov-2 voc

tag: collection time point


title: UK4_Calu3_Alpha_10h_1

tag: additional conditions

tag: experiment group


title: RP80T

tag: tobacco

tag: grade


title: UK4_Calu3_IC19_10h_3

tag: cell line


title: RP80N


title: RP81T


title: UK4_Calu3_VIC_10h_3


title: Rep1_Lib14_b-14

source_name: cells, 2.76 h after swarm expansion, 6112 µm distance from the swarm center (= point of inoculation)

tag: cell type

tag: genotype


title: Rep1_Lib16_b-16

source_name: cells, 3.23 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)

tag: strain

tag: time after expansion (h)


title: UK4_Calu3_IC19_10h_1


title: Rep1_Lib13_b-13

source_name: cells, 2.76 h after swarm expansion, 4584 µm distance from the swarm center (= point of inoculation)

tag: position (um)


title: Rep1_Lib15_b-15

source_name: cells, 3.23 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: RP84M

tag: tissue

tag: age


title: RP78T

tag: patient id

tag: recurrence

value: Female


title: RP80M

tag: survival

tag: Sex


title: UK4_Calu3_VIC_10h_1

source_name: epithelial lung cancer cells

tag: sars-cov-2 voc

tag: collection time point


title: Rep1_Lib12_b-12

source_name: cells, 2.76 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: RP78M


title: RP75N

source_name: biopsy of normal

value: WellDifferentiated


title: RP75T

value: biopsy of tumor


title: RP74T

value: Male


title: RP78N

value: ModeratelyDifferentiated


title: RP74M


title: RP74N


title: UK4_Calu3_Mock_10h_2

value: Mock

tag: additional conditions

tag: experiment group


title: Rep1_Lib11_b-11

source_name: cells, 2.76 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib10_b-10

source_name: cells, 2.46 h after swarm expansion, 4585 µm distance from the swarm center (= point of inoculation)


title: UK4_Calu3_Mock_10h_3


title: RP72N

tag: tobacco

tag: grade


title: RP72T

source_name: biopsy of tumor


title: UK4_Calu3_Mock_10h_1

tag: cell line


title: Rep1_Lib9_b-9

source_name: cells, 2.46 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)

tag: cell type

tag: genotype


title: RP71T


title: Rep1_Lib8_b-8

source_name: cells, 2.46 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)

tag: strain

tag: time after expansion (h)


title: RP72M

tag: tissue


title: YTHDC2 rep3

data_processing:
adaptors, low-quality bases and reads shorted than 17 nucleotides were trimmed by cutadapt
Sequence-based removal of PCR duplicates was discarded with samtools and picard
Reads were then mapped to human genome (hg19) with STAR
CLIP peaks were called using Piranha
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: After treatment with 4-thiouridine (200 µM) for 14 h, PANC-1 cells were subjected to UV crosslinking and lysed on ice.

extract_protocol:
After end repair using T4 PNK (NEB), the bead-antibody-RNA complexes were treated with proteinase K, and the bound RNA was purified by acidic phenol/chloroform extraction and ethanol precipitation.
For PAR-CLIP sequencing, the purified RNAs were utilized for library construction using the NEBNext small RNA library prep kit (E7330S) and sequenced on an Illumina HiSeq4000

treatment_protocol: Cell lysate was then sonicated, digested with DNase I and RNase I for 15 min at 37 °C and incubated with Dynabeads protein A/G (Millipore) conjugated with anti-CFL1/METTL3/YTHDC2 antibody overnight at 4 °C.

value: Human PDAC cell lines

tag: chip antibody


title: UK4_Calu3_Mock_24h_2


title: RP71M

tag: patient id

value: NR

tag: age


title: YTHDC2 rep2


title: UK4_Calu3_VIC_10h_2


title: RP70N

tag: recurrence

tag: survival


title: Rep1_Lib7_b-7

source_name: cells, 2.16 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)

tag: position (um)


title: Rep1_Lib6_b-6

source_name: cells, 2.16 h after swarm expansion, 1529 µm distance from the swarm center (= point of inoculation)


title: RP70M

source_name: biopsy of margin

tag: Sex


title: RP71N


title: RP68T

value: PoorlyDifferentiated


title: RP68N

value: biopsy of normal


title: RP68M


title: YTHDC2 rep1


title: Rep1_Lib5_b-5

source_name: cells, 1.86 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: METTL3 siCFL1_3


title: Rep1_Lib4_b-4

source_name: cells, 1.86 h after swarm expansion, 1529 µm distance from the swarm center (= point of inoculation)


title: RP66N

value: ALIVE


title: METTL3 siCFL1_1


title: METTL3 siCFL1_2


title: Rep1_Lib3_b-3

source_name: cells, 1.56 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: RP66M


title: RP65M


title: RP64T


title: RP65N


title: METTL3 rep2


title: Rep1_Lib2_b-2

source_name: cells, 1.56 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: Rep1_Lib1_b-1

source_name: cells, 1.26 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: RP70T

value: YES


title: RP64N


title: RP64M

value: biopsy of margin


title: METTL3 rep1


title: Nr3c1-Foxp3Cre_tumorTreg_3

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Six mRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using SMARTer ultra-low input RNA v4 -Nextera XT DNAand paired-end sequencing.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts (GENCODE_M21) using STAR.
The gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
Low count genes were filtered prior to CPM and quantile normalization using Limma voom followed by differential expression of genes analysis.
Assembly: mm10; GENCODE_M21
Supplementary files format and content: Comma-separated values (.csv) file containing a matrix of normalized expression produced in this study.

organism: Mus musculus

source_name: tumor

growth_protocol: Not applicable.

extract_protocol:
Solid tumors were mechanically isolated, digested with Liberase TL and DNase I, tumor cells depleted on a Percoll gradient, and infiltrating cells washed and stained with Blue Live/Dead dye and antibodies against CD45, CD4, CD25, and sorted on a BD FACSAria Fusion. Total RNA was extracted using Qiagen RNeasy mini kits.
The SMARTer Ultra Low Input RNA Kit was used to generate cDNA, which was then made into a sequencing ready library using the Nextera® XT DNA Sample Preparation Kit from Illumina. The final purified sequencing ready library was quantitated by qPCR before cluster generation and sequencing on Illumina NextSeq 2000 P2 run.

treatment_protocol: Not applicable.

value: tumor

value: B16.F10 melanoma

tag: treatment

value: LiberaseTL+DNaseI digestion, FACS sorting

tag: time

value: day 15 after tumor inoculation


title: RP62T

tag: tobacco

value: NO


title: RP62N

tag: grade


title: Nr3c1-Foxp3Cre_tumorTreg_2

tag: cell line


title: Nr3c1-Foxp3Cre_tumorTreg_1

tag: cell type


title: RP62M


title: RP65T

value: Female


title: Control_tumorTreg_3

tag: genotype


title: A rep 9

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 9

data_processing:
Isolated eccDNAs were mapped with Circle_Finder integrating the mm10 built of the mouse genome. The minNonOverlap between two split reads equaled to 10.  eccDNA sizes were assessed from mt-free DNAs, indicating that 100Kb is a cutoff for all short circles.
eccDNAs with a length greater than Lmax = 100Kb were filtered out. Clusters of circles within a distance smaller than Dmin = 10b were merged and summed up as split reads of the merged circles.  Split reads with less than two junction tags (JTmin = 2) were excluded.
Circle annotations were accomplished using bedtools intersect of the resulting eccDNA bed files, implementing a Genecodemm10.bed file with the gene coordinates.
To quantificy the produced per gene eccDNAs (PpGCs) we unified the circles based on genes, i.e., all the eccDNAs that carried the same gene or fragment of this gene were grouped together.  Unified eccDNAs were scaled by gene length, multiplying each Produced per Gene eccDNA i (PpGCi) by a scale factor LMax/Li,  where LMax is the length of the longest gene found in the dataset, and Li is the length of the gene i.
Data equalization was performed by the log2(PpGC+1) transform on of the quantified PpGCs. In-house software was used to merge the PpGCsresults into a single text file used in the downstream analysis in Matlab (MathWorks).  We performed quantile normalization to equalize the data and stabilized them through the log2 transform of the data plus one.  The heatmap of the most highly variable PpGCs, the hierarchical clustering dendrograms  (calculated using the unweighted pair group method with arithmetic mean and Euclidean distance measure),  and the PCAs were performed using in?home functions developed in Matlab (MathWorks).
Assembly: mm10
Supplementary files format and content: tab-delimited text file include log2 produced per gene eccDNAs (PpGCs) values for each sample

source_name: spinal cord

growth_protocol: The B6.Cg-Tg(SOD1*G93A)1Gur/J strain (stock # 004435, Jackson Laboratory, Bar Harbor, ME, USA) served to induce an ALS-like phenotype in Mus musculus. The ALS pathology is provoked by the constitutive overexpression of a human mutant superoxide dismutase1 gene (hSOD1G93A)  compromising the SOD1 capacity to neutralize superoxide anion radicals.  Motor symptoms in male mutants developed at ages between 18-21 weeks and were assessed according to a standardized,  investigator-neutral clinical score protocol.  Inclusion of males only required the manifestation of a severity score of 1 or 2 within the target age indicated.  Sex- and age-matched C57BL/6J mice served as controls.  Animals that did not timely develop a motor phenotype were excluded from the study.  Tissue extraction:  After score approval, animals were euthanized by an overdose of volatile isoflurane CP (CP Pharma, Burgdorf, Germany).  The spine was microscopically dissected from surrounding tissue, the vertebral column was opened and the myelon was exposed.  The spinal cord was excavated in toto, detached from meninges and transferred to ice-cold PBS.  The cervical segment was dissected from thoracic and lumbar parts, collected into Eppendorf tubes and immediately frozen at -80°C for further analysis.

extract_protocol:
Total DNA extracted from mouse cervical spinal cord was digested with exonuclease V (New England Biolabs) to remove linear DNA. 50,000 copies of the plasmid p4339, 20,000 copies of YGPM25009 and 10,000 copies of pBR322  were added as internal controls to 400ng of DNA per sample.  These DNA mixtures were incubated at 37C with 30IU exonuclease V (RecBCD), 1X NEBuffer 4, and 1mM ATP.  Every 24 hours, 30IU fresh exonuclease V and 1mM ATP was added to the reactions, which were incubated for 7 days in total.  After 7 days, exonuclease reactions were inactivated for 30 min at 70C and subjected to DNA clean-up  with Agencourt AMPure XP beads (BD) according to the manufacturer?s instructions.  Briefly, reactions were mixed with 1.8x beads solution and incubated at RT for 5 min to bind.  Supernatants were discarded, beads were washed twice with 80% ethanol and briefly evaporated.  DNA was eluted in 60microl of 10mM Tris-HCl, pH 8.  Removal of linear DNA was confirmed by PCR analysis of the presence of the Cox5b sequence in DNA before and after treatment.  15microl of exonuclease-digested DNA were subjected to rolling circle amplification using TruePrime RCA (4BaseBio) according to manufacturer's instructions.  Briefly, DNA was denatured for 3 min with buffer D and neutralized with buffer N.  Denatured DNA was mixed with enzyme 1, enzyme 2, dNTPs and reaction buffer and incubated at 30C for 48 hours.  Afterwards, reactions were inactivated for 10 min at 65C.
After DNA extraction from control and ALS samples, the phi29-polymerase amplified DNA strands were sheared into fragments of 200 bp and approx. 400(350bp) bp in size using a Covaris LE220 ultrasonicator (Covaris, Brighton, UK)  with operating parameters set as the following: 20s ultrasound, acoustic duty factor 25%, peak incident power 500W,  cycles per burst 500, 24 cycles.  Appropriate fragment size (200-500bp) was captured with the aid of AMPure XP beads (Agencourt, Beverly, USA).  Fragmented DNA was then incubated with Bacteriophage T4 DNA polymerase (ENZYMATICS, Beverly, USA)  for 30 min at 20C for trimming to obtain blunt ends devoid of 3'-overhangs or 5'-gaps, which were further 3?-adenlyated to create sticky ends.  These DNA fragments were ligated at both ends to T-tailed adapters and amplified via PCR according to the following step-wise procedures:  3 min at 95C followed by 8 cycles of 20 sec at 98C, 15 sec at 60C, 30 sec at 72C, 10 min at 72C for further elongation.  The obtained PCR products were purified via AMPure XP beads (Agencourt, Beverly).  The DNA library was sequenced on BGISEQ-500 by paired-end sequencing of 150bp intervals both from the forward and reverse strand,  with an average sequencing data of 138M reads per library, to provide high-quality alignment across all genomic regions.

treatment_protocol: After score approval, animals were euthanized by an overdose of volatile isoflurane CP (CP Pharma, Burgdorf, Germany). The spine was microscopically dissected from surrounding tissue, the vertebral column was opened and the myelon was exposed.  The spinal cord was excavated in toto, detached from meninges and transferred to ice-cold PBS.  The cervical segment was dissected from thoracic and lumbar parts, collected into Eppendorf tubes and immediately frozen at -80°C for further analysis.  DNA isolation : DNA extraction from individual cervical spinal cord samples of control and mutant animals was performed according  to kit-facilitated standard procedures (Nucleospin tissue DNA/RNA and Protein kit, Macherhey Nagel GmbH & Co KG, Germany).  Briefly, each tissue specimen was thawed and homogenized with a motorized pestle applying 25microl of proteinase k to the initial buffer system.  Each suspension was vortexed vigorously and the homogenate was kept at 56C overnight.  The next day, the samples were vortexed, supplemented by the indicated buffer solution and incubated at 70C for 10 min.  For DNA extraction, 210microl of ethanol were added to each sample suspension.  Solutions were poured on the nucleospin columns placed into the collection tubes and centrifuged at 11,000 x g for 1 min.  The flow-through was discarded and the columns were again centrifuged as aforementioned.  The extracted DNA was washed in 500 microl of appropriate buffer solution and centrifuged.  The flow-through was discarded and the column was centrifuged as before.  The washing step was repeated with an adequate buffer solution.  The flow-through was discarded and the empty column was centrifuged as before to dry the silica membrane,  then transferred to a sterile 1.5 ml Eppendorf tube.  The collected genomic DNA was eluted in 30 microl of appropriate pre-warmed buffer and incubated at RT for 2 min,  then centrifuged at 11,000 x g for 2 min.  The genomic DNA concentration of each sample was measured spectrophotometrically by NanoDrop systems.

value: spinal cord

tag: condition

value: ALS

tag: strain


title: CFL1 rep2


title: RP59T

tag: tissue

value: biopsy of tumor

value: R

value: Male


title: METTL3 rep3

value: Human PDAC cell lines

tag: chip antibody


title: CFL1 rep3


title: RP59N

tag: patient id

value: PoorlyDifferentiated


title: CFL1 rep1


title: RP66T

value: NR

tag: age

value: ModeratelyDifferentiated


title: Control_tumorTreg_2


title: RP59M

tag: recurrence

value: ALIVE


title: RP58T

tag: survival

value: YES


title: LPL9_Pre GEX

city: Duarte

first: Szymon

last: Szymura

address: 1500 E Duarte Rd

department: Toni Stephenson Lymphoma Center

institute: City of Hope

description: scRNA-seq

data_processing:
The alignments, demultiplexing, barcode processing and gene counting was performed using CellRanger software version 3.1.0
Assembly: hg19
Supplementary files format and content: Matrix files of gene counts

source_name: bone marrow

extract_protocol:
Snap frozen bone marrow samples were thawed in culture media, washed with wash buffer and loaded onto 10x Genomics Chromium Chip
Library preparation for gene expression was performed using 5' 10x Genomics Kit according to manufacturer's protocol

value: bone marrow

value: primary cells

value: bone marrow cells

tag: individual

value: Patient LPL9

value: Pre


title: LPL9_Post GEX

description: scRNA-seq

value: Post


title: A rep 7

description: replicate 7

value: spinal cord


title: A rep 6

description: replicate 6

value: ALS


title: LPL8_Pre_Post GEX

description:
scRNA-seq
LPL8_barcodes.tsv.gz
LPL8_features.tsv.gz
LPL8_matrix.mtx.gz
HTO_details_README.txt

value: Patient LPL8

value: Pre, Post