title: sc-Patch-seq,Red only,Regenerating CSMN144

description:
Patch-seq
NoRegen_CSMN_144


title: sc-Patch-seq,Red only,Regenerating CSMN139

status: Public on Aug 08 2023

type: SRA

city: Los Angeles

first: Hugo

middle: Jae Mun

last: Kim

state: CA

address: 4760 Templeton St, Unit 3113

department: Neuroscience

country: USA

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

description:
Patch-seq
NoRegen_CSMN_139

library_source: transcriptomic

data_processing:
The demultiplexing, barcoded processing, gene counting and STAR aligner was used to align the sample.
Assembly: mm22
Supplementary files format and content: Tap delimited expression table and phenotype table

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
The mice are sacrificed under perfusion of sucrose cutting solution, bubbling. The brain was sliced in 200-300um by viubratome, bubbling with CO2/O2. Tissue were recovered in the recovery chamber, bubbling. Using Patch Clamp approach, I generated giga-seal and extract the cell contents to the ppet. Then I freeze the cell in liquid nitrogen until the library prep
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
We amplified RNA using modified aRNA protocol for 2 cycles, followed by illumina Truseq mRNA prep.

treatment_protocol: At 8 weeks, I injected AAV-retro-cre to spinal cord, after 4 weeks, I apply spinal cord Injury, dorsal hemisection above the injection site. After 6 weeks, I injected AAV-retro-GFP to the 500um below the injury.  site.

tag: cell type

value: Cortical Spinal Motor Neuron

tag: tissue

value: Brain

tag: strain

value: PTEN SOCS3 tdTomato

tag: age

value: 22 weeks old


title: PC3 cells, expressing HA-METTL1

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
Sequencing reads were demultiplexed based on library specific barcodes, quality filtered (mean sequence quality >30) and trimmed (removing barcodes, PCR and sequencing adapters) using Flexbar (v.3.5.0 ) as described in Busch et al (2019).
Next, reads were processed with nf-core iCLIP 1.0.0 analysis pipeline:
Second round of trimming using Cutdapt (v3.0.0),
Sequences were pre-aligned with Bowtie2 (v2.4.2) against tRNA and rRNA sequences. The remaining unaligned reads were mapped against the reference genome sequence (GRCh38, NCBI) using STAR (v2.6.1d)
Potential PCR duplicates are removed based on their position and UMI sequences using UMI-tools (v1.1.1)
Reads counts were estimated by simple overlap with tRNA and rRNA sequences and reference genome annotation GRCH38 (NCBI) and subsequentlty normalized against library size and transcript length.
Assembly: GRCH38
Supplementary files format and content: lncRNA_RPM.csv (normalized read counts lncRNAs)
Supplementary files format and content: miRNA_RPM.csv (normalized read counts miRNAs)
Supplementary files format and content: premapping_smRNA_RPM.csv (normalized read counts smallRNAs)
Supplementary files format and content: protein_coding_RPM.csv (normalized read counts protein-coding RNAs)
Supplementary files format and content: tRNA_RPM.csv (normalized read counts tRNAs)
Supplementary files format and content: snoRNA_RPM.csv (normalized read counts snoRNAs)

organism: Homo sapiens

source_name: Prostate

growth_protocol: PC3 cells were cultured in DMEM with L-Glutamine and pyruvate (Gibco) supplemented with 10% FBS (Gibco) and 1% Penicillin/streptomycin, a humidified atmosphere at 37°C and 5% CO2. Cell cultures were tested for mycoplasma monthly and maintained mycoplasma-free.

extract_protocol:
Cells were cross-linked at 365 nm (150 mJ/cm2) inStratalinker 2400and then lysed with CLIP Lysis buffer (50 mM Tris-HCl pH7.4, 100 mM NaCl, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate in the presence of protease inhibitors) and passed 7-8 times through a 27G needle. For RNA digestion, two dilutions of RNase I (ThermoFisher Scientific, EN0602) were prepared in PBS (high: 1/50, and low: 1/250). 10mL of each dilution and 2mL of TurboDNase (ThermoFisher Scientific, AM2238) were added to 1 ml of each cell lysate (corresponding to ~1mg of protein) and incubated for 3 min at 37 ºC, and then placed on ice for > 3 min. For HA-METLL1 immunoprecipitation 30 µl of Pierce anti-HA magnetic beads (ThermoFisher Scientific, #88836) were used.
RNA 3’ ends were dephosphorylated usingPNK (NEB, M0201L) and FastAP Alkaline phosphatase (ThermoFisher Scientific, EF0654). Next, the 3’ pre-adenylated adapters L3-IR-App were ligated withT4 RNA Ligase (NEB, M0437M). Adaptors were removed and RNAs were treated withRecJfendonuclease (NEB, M0264S). RNA-protein complexes were run on a NuPAGE4-12% Bis-Tris gel(ThermoFisher Scientific, #NP0322BOX)and transferred onto a nitrocellulose membrane. RNA-bound complexes between 75 and 130 KDa were cut out from the membrane, andtreated with proteinase K. After phenol extraction,RNAs were reverse-transcribed withSuperscript IV (ThermoFisher Scientific, #18091050), and cDNA was circularized withCircLigase II (Biosearch Technologies, #CL9021K).PCR was performed with P3/P5 Solexa primers for 22 cycles, and the appropriate size of products were confirmed by gel electrophoresis.   Sequencing of the libraries was performed on a HiSeq X instrument following standard manufacturer’s procedures, with single-read, 151-bases read profile.
PAR-CLIP

treatment_protocol: For PAR-CLIP purposes cells were grown in 6-thioguanine (6SG) (Sigma-Aldrich) for 24 hours before cross-linking.

value: Prostate

tag: cell line

value: prostate cancer epithelial cell

tag: genotype

tag: rip antibody

value: anti-HA


title: PN96_Cortical_NEAT1ko-clone2_day19_rep2

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

country: China

institute: Peking University

data_processing:
Fastq data were quality-checked by FastQC (version 0.11.9). 150bp paired-end reads with adapters were trimmed by TrimGalore (v0.6.7) and cutadapt (v4.1).
Trimmed reads from each sample were mapped to the human genome (hg38) using STAR (v2.7.10a) with parameters outFilterMismatchNoverLmax=0.1 and outFilterMultimapNmax=1.
Gene read counts were quantified against the GENCODE v40 gene annotation using Subread featureCounts (v2.0.1).
Differentially expressed genes (DEGs) were identified by DESeq2 (v1.36.0) in R software (v4.2.0), where gene raw counts were inputted.
Assembly: GRCh38
Supplementary files format and content: Excel file includes TPM values for each sample and DESeq2 results of NEAT1 knockout versus control samples for hESC and four types of organoids.

molecule: polyA RNA

source_name: cortical organoids derived from human embryonic stem cells

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Magen) and reverse transcribed into cDNA using the HiScript II 1st Strand cDNA Synthesis Kit (Vazyme) following the manufacturer’s instruction.
RNA-Seq libraries were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer’s instructions. Briefly, total RNA was purified twice using poly-T oligo-attached magnetic beads before the synthesis of double-stranded (ds) cDNA. The ds-cDNA was ligated to adaptors (Vazyme) and sequenced by Illumina (Novogene).

tag: treatment

tag: time

value: day 19


title: Lung organoid, RDV-48hr

city: Fremont

first: Shannon

last: Choi

state: California

address: 44126 Paseo Padre Parkway

institute: Stanford School of Medicine

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification
After demultiplexing, sequence data was checked for overall quality and yield. Then, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL along with the SARS-CoV-2 Wuhan strain reference using the STAR aligner v.2.5.2b. The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed.
The Wald test was used to generate p-values and log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison.
Assembly: Homo sapiens GRCh38 reference genome available on ENSEMBL along with the SARS-CoV-2 Wuhan strain reference using the STAR aligner v.2.5.2b
Supplementary files format and content: CSV file of differential gene expression

source_name: Lung Organoid

extract_protocol:
DNA/RNA Shield (Zymo Research) TRIzol (Thermo Fisher Scientific), incubating for 30 min at RT and decontaminated out of the BSL3 facility. RNA was purified using an RNA Clean & Concentrator-25 kit (Zymo Research) per manufacturer instructions.
Ultra-low input RNA sequencing library was prepared by using SMART-Seq HT kit for full-length cDNA synthesis and amplification (Takara, San Jose, CA, USA), and Illumina Nextera XT (Illumina, San Diego, CA, USA) library was used for sequencing library preparation

value: Lung Organoid

value: SARS-CoV-2 + RDV - 48 hours


title: sc-Patch-seq,Red only,Regenerating CSMN142

description:
Patch-seq
NoRegen_CSMN_142


title: Lung organoid, SARS, Day 14, Rep2

value: SARS-CoV-2 - RDV - 14 days


title: PC3 cells, Control

value: empty vector


title: sc-Patch-seq,Red only,Regenerating CSMN141

description:
Patch-seq
NoRegen_CSMN_141


title: D503 HTO library 13

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

data_processing:
scRNA-seq reads were analyzed by pseudoalignment using kallisto v0.46.2 (GRCh38 with Gencode v24 annotation) and bustools v0.40.0. CITE-seq and hashtag barcodes were demultiplexed and extracted using DropSeqPipeline8 (https://github.com/simslab/DropSeqPipeline8). Hashtags were demultiplexed by CLR normalization, k-means clustering, and statistical identification of singlets by fitting a negative binomial model as described in Stoeckius et al, Genome Biology, 2018.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with cell-identifying barcodes, hashtags, and count matrix

source_name: various

extract_protocol:
Mononuclear cells (MNCs) were isolated from organ donor tissues from two subjects (D496 and D503) as described in Dominguez-Conde et al, Science, 2022.  A detailed protocol for each tissue site appears in the supplementary materials. For the FAC-sorted sample corresponding to PDC100-PDC101, we obtained peripheral blood from  a consenting, healthy volunteer (35  year-old male) by venous puncture. Peripheral blood mononuclear cells (PBMCs) were isolated using RosetteSep Granulocyte Depletion Cocktail (StemCell Technologies), following manufacturer’s protocols for density gradient centrifugation. Briefly, samples were incubated with the cocktail at 20°C for 10 minutes, diluted 1:1 with FACS buffer (DPBS 10% FBS 2mM EDTA), then layered over Ficoll-Plaque in SepMate PBMC isolation tubes (StemCell Technologies). Samples were centrifuged at 1200 x g for 10 minutes at 20°C, and PBMC layers were isolated according to instructions. Samples were washed (400 x g for 10 minutes) with FACS buffer. For further erythrocyte removal, pellets were resuspended in ACK lysis buffer (Gibco) incubated for 2 minutes at 37°C and washed with FACS buffer.  PBMCs were stained with Zombie NIR Fixable Viability dye (Biolegend) for 30 minutes. Samples were kept at 4°C in the dark. Cells were washed thrice with FACS buffer, resuspended in TrueStain FcX and TrueStain Monocyte Blocker (Biolegend) and incubated for 10 minutes. Cells were incubated with the FACS antibody cocktail for 30 minutes, then washed thrice with FACS buffer. Cells were incubated in TrueStain FcX (Biolegend) for 10 minutes, then stained using a custom Total Seq-A Universal Human Panel (Biolegend) for 30 minutes, according to manufacturer instructions. Samples were washed thrice with FACS buffer. Cells were sorted using a FACS Aria III (BD Biosciences). Seven T cell memory populations (CD4+ Naive, CD4+ TCM, CD4+ TEM,  CD8+ Naive, CD8+ TCM, CD8+ TEM,  CD8+ TEMRA), and monocytes were sorted into sterile, heat inactivated FBS. All sorts were high purity, with mean purity 94.4% (ranging from 97.1% to 91.8%).
For the organ donor tissues (D496 and D503), each single-cell suspension was hashtagged to allow pooling of samples for loading on the 10x Genomics Chromium instrument. Approximately 1M MNCs per tissue were transferred to 4 mL flow cytometry tubes. Cells were centrifuged at 400 x g for 5 minutes at 4C, supernatant removed, and re-suspended in PBS containing 5% (v/v) FBS and 2 mM EDTA. Cells were treated with Trustain FcX (Biolegend, 422302) and FcR Blocking Reagent (Miltenyi, 130-059-901) to reduce background labeling and incubated at 4C for 10 minutes. Each hashtag was spun at 14,000 x g for 10 minutes, and 1 uL of hashtag was added to each tube. The samples were incubated at 4C for 30 minutes, and subsequently centrifuged at 400 x g for 5 minutes at 4C and washed three times with PBS containing 5% (v/v) FBS and 2 mM EDTA. 200,000 cells from each sample was added to a single 4 mL flow cytometry tube. This tube was centrifuged at 400 x g for 5 minutes at 4C and re-suspended in PBS containing 5% (v/v) FBS and 2 mM EDTA. For each donor, the hashtagged cells were pooled and stained with the TotalSeq-A Human Universal Cocktail panel according to the manufacturer's instructions (Biolegend) and loaded across 16 channels of the 10x Genomics Chromium instrument for library construction using the 10x Genomics Single Cell 3' Solution (v3.1 1000121) according to the manufacturer's instructions with the manufacturer's recommended modifications for compatibility with the TotalSeqA cell hashing and CITE-seq reagents (Biolegend).
For the FACS-sorted PBMCs (PDC100-101), samples were counted, diluted to the appropriate volume, and loaded across two lanes of a 10x Genoimcs NextGEM chip. cDNA synthesis and amplification was performed using the 10x Genomics NextGEM 3' Kit v3.1 with the manufacturer's recommended modifications for compatibility with the TotalSeqA cell hashing and CITE-seq reagents (Biolegend). In this experiment, the hashtags correspond to FAC-sorted immune cell subsets (HTO1: Naive CD4 T cells, HTO2: Central Memory CD4 T cells, HTO3: Effector Memory CD4  T cells, HTO4: Naive CD8 T cells, HTO5: Central Memory CD8 T cells, HTO6: Effector Memory CD8 T cells, HTO7: CD8 TEMRA, HTO8: Monocytes).
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: various

value: mononuclear cells (MNCs)

tag: library type

value: HTO

tag: antibodies/tags


title: FACS GEX library 1

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

source_name: blood

value: blood

value: T cells and monocytes

value: mRNA


title: sc-Patch-seq,Red only,Regenerating CSMN138

description:
Patch-seq
NoRegen_CSMN_138

value: Cortical Spinal Motor Neuron

value: Brain


title: Lung organoid, RDV, Day 14, Rep2

value: SARS-CoV-2 + RDV - 14 days


title: sc-Patch-seq,Red only,Regenerating CSMN140

description:
Patch-seq
NoRegen_CSMN_140

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: sc-Patch-seq,Red only,Regenerating CSMN137

description:
Patch-seq
NoRegen_CSMN_137


title: Lung organoid, SARS-48hr

value: SARS-CoV-2 - RDV - 48 hours


title: sc-Patch-seq,Red only,Regenerating CSMN136

description:
Patch-seq
NoRegen_CSMN_136


title: D503 HTO library 15


title: PN96_Cortical_CTR_day19_rep2

value: cortical organoids derived from human embryonic stem cells

value: CTR

value: day 19


title: Lung organoid, RDV, Day 10, Rep2

value: Lung Organoid

value: SARS-CoV-2 + RDV - 10 days


title: sc-Patch-seq,Red only,Regenerating CSMN135

description:
Patch-seq
NoRegen_CSMN_135


title: D503 HTO library 10

value: various


title: PN96_Cortical_NEAT1ko-clone2_day19_rep1


title: PN96_Cortical_NEAT1ko-clone1_day19_rep2


title: D503 HTO library 9

value: mononuclear cells (MNCs)


title: sc-Patch-seq,Red only,Regenerating CSMN134

description:
Patch-seq
NoRegen_CSMN_134


title: Lung organoid, SARS, Day 7, Rep2

value: SARS-CoV-2 - RDV - 7 days


title: D503 HTO library 6

value: HTO


title: PN96_Cortical_CTR_day19_rep1


title: D503 HTO library 5


title: PN96_Nephron_CTR_day13_rep1

source_name: nephron organoids derived from human embryonic stem cells

value: day 13


title: Lung organoid, RDV, Day 7, Rep2

value: SARS-CoV-2 + RDV - 7 days


title: D503 HTO library 4


title: D503 HTO library 8


title: Lung organoid, SARS, Day 10, Rep2

value: SARS-CoV-2 - RDV - 10 days


title: sc-Patch-seq,Red only,Regenerating CSMN131

description:
Patch-seq
NoRegen_CSMN_131

value: Cortical Spinal Motor Neuron

value: Brain


title: PN96_hESC_NEAT1ko-clone1_rep2

source_name: human embryonic stem cells

value: human embryonic stem cells

value: day 0


title: D503 HTO library 7


title: PN96_Cortical_NEAT1ko-clone1_day19_rep1


title: D503 HTO library 2


title: PN96_hESC_NEAT1ko-clone2_rep2


title: sc-Patch-seq,Red only,Regenerating CSMN130

description:
Patch-seq
NoRegen_CSMN_130

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: PN96_hESC_CTR_rep2

value: CTR


title: sc-Patch-seq,Red only,Regenerating CSMN129

description:
Patch-seq
NoRegen_CSMN_129


title: Lung organoid, mock, Day 14, Rep1

value: Mock - 14 days


title: sc-Patch-seq,Red only,Regenerating CSMN128

description:
Patch-seq
NoRegen_CSMN_128


title: PN96_hESC_CTR_rep1


title: D503 ADT library 16

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

value: ADT

value: TotalSeq-A Human Universal Cocktail


title: PN96_hESC_NEAT1ko-clone1_rep1


title: PN96_hESC_NEAT1ko-clone2_rep1


title: sc-Patch-seq,Red only,Regenerating CSMN133

description:
Patch-seq
NoRegen_CSMN_133


title: sc-Patch-seq,Red only,Regenerating CSMN127

description:
Patch-seq
NoRegen_CSMN_127


title: Lung organoid, SARS, Day 3, Rep2

value: Lung Organoid

value: SARS-CoV-2 - RDV - 3 days


title: sc-Patch-seq,Red only,Regenerating CSMN132

description:
Patch-seq
NoRegen_CSMN_132


title: Lung organoid, SARS, Day 7, Rep1

value: SARS-CoV-2 - 7 days


title: D503 HTO library 3

value: various

value: mononuclear cells (MNCs)

value: HTO


title: Lung organoid, RDV, Day 3, Rep2

value: SARS-CoV-2 + RDV - 3 days


title: PN96_Hepatic_WT_day21_rep2

source_name: hepatic organoids derived from human embryonic stem cells

value: WT

value: day 21


title: D503 ADT library 13


title: sc-Patch-seq,Red only,Regenerating CSMN125

description:
Patch-seq
NoRegen_CSMN_125

value: Cortical Spinal Motor Neuron

value: Brain


title: D503 HTO library 1


title: Lung organoid, SARS, Day 14, Rep1

value: SARS-CoV-2 - 14 days


title: Lung organoid, SARS, Day 10, Rep1

value: SARS-CoV-2 - 10 days


title: sc-Patch-seq,Red only,Regenerating CSMN124

description:
Patch-seq
NoRegen_CSMN_124

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: sc-Patch-seq,Red only,Regenerating CSMN123

description:
Patch-seq
NoRegen_CSMN_123


title: D503 ADT library 15

value: ADT


title: Lung organoid, mock, Day 10, Rep1

value: Mock - 10 days


title: PN96_Lung_WT_day20_rep2

source_name: lung organoids derived from human embryonic stem cells

value: day 20


title: Chip_Hepatic_WT_day17_rep2

value: hepatic organoids derived from human embryonic stem cells

value: Chip

value: day 17


title: D503 ADT library 10

value: various

value: mononuclear cells (MNCs)

value: TotalSeq-A Human Universal Cocktail


title: D503 ADT library 14


title: PN96_Lung_WT_day20_rep1

value: lung organoids derived from human embryonic stem cells

value: WT


title: sc-Patch-seq,Red only,Regenerating CSMN122

description:
Patch-seq
NoRegen_CSMN_122

value: Cortical Spinal Motor Neuron


title: sc-Patch-seq,Red only,Regenerating CSMN126

description:
Patch-seq
NoRegen_CSMN_126

value: Brain


title: D503 ADT library 9


title: sc-Patch-seq,Red only,Regenerating CSMN121

description:
Patch-seq
NoRegen_CSMN_121


title: D503 ADT library 12


title: Lung organoid, SARS, Day 3, Rep1

value: Lung Organoid

value: SARS-CoV-2 - 3 days


title: D503 ADT library 8


title: PN96_Hepatic_WT_day21_rep1

value: day 21


title: Lung organoid, mock, Day 7, Rep1

value: Mock - 7 days


title: D503 ADT library 11

value: ADT


title: D503 ADT library 7


title: Lung organoid, mock, Day 3, Rep1

value: Mock - 3 days


title: PN96_Hepatic_WT_day17_rep2


title: Chip_Hepatic_WT_day17_rep1


title: PN96_Nephron_WT_day7_rep1

value: nephron organoids derived from human embryonic stem cells

value: day 7


title: WT2

city: Miaoli County

first: Paul

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

data_processing:
On-instrument base-calling with Illumina HiSeq 2500 BclToFastq v2.18.
Adaptor sequences were removed from raw sequences, and the quality of reads was examined by FastQC software. Low-quality regions were trimmed (Phred quality score of <20).
Gene expression level of read counts and TPM were calculated using CLC Genomics Workbench 21.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include TPM and read counts for each Sample

source_name: Cardiomyocyte

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (Qiagen, 74106). RNA quality and quantifications were inspected using an Agilent 2100 Bioanalyzer.
The mRNA sequencing libraries were prepared using a Truseq Stranded mRNA kit (Illumina), and 2x150 bp paired-read sequencing was performed using an Illumina HiSeq instrument

tag: cell lines

value: hESCs-CM

value: wild type


title: KO1


title: sc-Patch-seq,Red only,Regenerating CSMN120

description:
Patch-seq
NoRegen_CSMN_120

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: SKOV3, olaparib day7, recover day7

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

description: SKOV3 PGCC_R7

data_processing:
fastq files were preprocessed using fastp software to remove low quality reads
clean fastq files were mapped to human transcriptome (hg38) using salmon v0.14.1 to generate counts and TPM for each transcript
raw counts and TPM for each transcript were aggregated by gene symbols to generate a gene expression TPM table
Assembly: hg38
Supplementary files format and content: tab delimited txt file of TPM gene expression table

source_name: ovary

growth_protocol: Ovarian cancer cell lines and organoids were cultured in recommended culture media (MEM or McCoy 5A) supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit following the manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated with olaparib for 3-7 days, and recovered in regular medium for 3-14 days

value: ovary

value: 50uM olaparib

value: 7 days recover 7 days


title: PN96_Hepatic_WT_day17_rep1

value: hepatic organoids derived from human embryonic stem cells

value: WT

value: day 17


title: D503 ADT library 6

value: various

value: mononuclear cells (MNCs)

value: TotalSeq-A Human Universal Cocktail


title: WT1


title: sc-Patch-seq,Red only,Regenerating CSMN117

description:
Patch-seq
NoRegen_CSMN_117

value: Cortical Spinal Motor Neuron

value: Brain


title: PN96_Nephron_WT_day7_rep2

value: nephron organoids derived from human embryonic stem cells


title: sc-Patch-seq,Red only,Regenerating CSMN118

description:
Patch-seq
NoRegen_CSMN_118


title: SKOV3, olaparib day7

description: SKOV3 PGCC_D7

value: 7 days


title: Chip_Cortical_WT_day54_rep2

value: cortical organoids derived from human embryonic stem cells

value: Chip

value: day 54


title: D503 ADT library 5

value: ADT


title: KO2

value: hESCs-CM


title: Chip_Cortical_WT_day54_rep1


title: D503 ADT library 4


title: D503 ADT library 3


title: SKOV3, olaparib day3

description: SKOV3 PGCC_D3

value: ovary

value: 50uM olaparib

value: 3 days


title: sc-Patch-seq,Red only,Regenerating CSMN116

description:
Patch-seq
NoRegen_CSMN_116

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: PN96_Cortical_WT_day53_rep2

value: WT

value: day 53


title: SKOV3, DMSO day3

description: SKOV3 NC_D3

value: DMSO


title: sc-Patch-seq,Red only,Regenerating CSMN115

description:
Patch-seq
NoRegen_CSMN_115

value: Cortical Spinal Motor Neuron


title: D503 ADT library 2

value: various

value: mononuclear cells (MNCs)

value: TotalSeq-A Human Universal Cocktail


title: PN96_Cortical_WT_day53_rep1

value: cortical organoids derived from human embryonic stem cells


title: OVCA432, olaparib day3, recover day7

description: OVCA432 PGCC_R7

value: 400uM olaparib

value: 3 days recover 7 days


title: sc-Patch-seq,Red only,Regenerating CSMN119

description:
Patch-seq
NoRegen_CSMN_119

value: Brain


title: D503 ADT library 1

value: ADT


title: SPIN_Cortical_WT_day60_rep2

value: SPIN

value: day 60


title: sc-Patch-seq,Red only,Regenerating CSMN113

description:
Patch-seq
NoRegen_CSMN_113


title: OVCA432, olaparib day3

description: OVCA432 PGCC_D3

value: ovary

value: 3 days


title: SPIN_Cortical_WT_day60_rep1


title: OVCA432, DMSO, day3

description: OVCA432 NC_D3


title: sc-Patch-seq,Red only,Regenerating CSMN111

description:
Patch-seq
NoRegen_CSMN_111

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: D496 HTO library 16

value: HTO


title: Organoid 3008, olaparib day7, recover day14

description: ORG 3008 PGCC_R14

value: 5uM olaparib

value: 7 days recover 14 days


title: D496 HTO library 14

value: various


title: D496 HTO library 15

value: mononuclear cells (MNCs)


title: WTG-IP for acRIP-seq

city: Shanghai

first: Pin

last: Dong

address: No. 650, New Songjiang Road, Shanghai

institute: Shanghai General Hospital, Shangahi Jiao Tong University School of Medicine

data_processing:
acRIP-seq data processing Cutadapt (v2.5) was used to trim adapters and filter for sequences, remaining reads were then aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. ac4C peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Differential ac4C peak were identified using exomePeak R package under parameters: “PEAK_CUTOFF_PVALUE=NA,PEAK_CUTOFF_FDR=0.05,FRAGMENT_LENGTH=200” . GO and KEGG analysis were performed using clusterprofile R package (v3.6.0). ac4C-RNA-related genomic features were visualized using Guitar R package (v1.16.0). Identified ac4C peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 12 -rna”.
RNA-seq data processing Cutadapt (v2.5) was used to trim adapters and filter for sequences. Reads were aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: hg38
Supplementary files format and content: peak files
Supplementary files format and content: sig_diff_peak files

source_name: cell line

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852).
100μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The reaction was stopped by adding 10X EDTA (0.5M EDTA). Acetylated RNA immunoprecipitation was performed using EpiTM ac4C immunoprecipitation kit (Epibiotek, R1815). Briefly, the fragmented RNA was incubated with Anti-N4-acetylcytidine (ac4C) antibody (abcam, ab252215) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The ac4C-enriched RNA was purified by Zymo RNA clean and concentrator-25 kit (Zymo Research, R1017). The library was prepared by EpiTM mini longRNA-seq kit (Epibiotek, E1802). Both the input samples without IP and the ac4C IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

value: cell line

value: FaDu

value: shNC


title: WTG-Input for acRIP-seq


title: sc-Patch-seq,Red only,Regenerating CSMN109

description:
Patch-seq
NoRegen_CSMN_109

value: Cortical Spinal Motor Neuron


title: sc-Patch-seq,Red only,Regenerating CSMN110

description:
Patch-seq
NoRegen_CSMN_110

value: Brain


title: Organoid 3008, olaparib day7

description: ORG 3008 PGCC_D7

value: 7 days


title: KOG-Input for acRIP-seq


title: KOG-IP for acRIP-seq


title: Organoid 3008, olaparib day3

description: ORG 3008 PGCC_D3


title: D496 HTO library 13


title: sc-Patch-seq,Red only,Regenerating CSMN114

description:
Patch-seq
NoRegen_CSMN_114


title: D496 HTO library 12


title: sc-Patch-seq,Red only,Regenerating CSMN107

description:
Patch-seq
NoRegen_CSMN_107


title: Organoid 3008, DMSO day3

description: ORG 3008 NC_D3

value: DMSO


title: D496 HTO library 11


title: Organoid 2445, olaparib day7, recover day14

description: ORG 2445 PGCC_R14

value: 2uM olaparib


title: sc-Patch-seq,Red only,Regenerating CSMN112

description:
Patch-seq
NoRegen_CSMN_112


title: D496 HTO library 10


title: sc-Patch-seq,Red only,Regenerating CSMN108

description:
Patch-seq
NoRegen_CSMN_108


title: sc-Patch-seq,Red only,Regenerating CSMN106

description:
Patch-seq
NoRegen_CSMN_106


title: MS Non-responder 5 Baseline

city: Madrid

first: Alicia

last: Sanchez

address: Joaquín Rodrigo, 2 Majadahonda

institute: Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana

data_processing:
Quality control of the raw sequencing reads was performed with FastQC v.0.11.9.
Adapter sequences were trimmed with cutadapt v2.10.
Trimmed reads were quantified with Salmon v.1.3.0 and summarized to the gene level with tximeta v.1.6.3
Assembly: Salmon was used in selective alignment mode with the entire human genome as a decoy sequence.
Supplementary files format and content: tab-delimited excel file includes raw counts for each sample

source_name: Cells

extract_protocol:
Total RNA from PBMCs was extracted using the Maxwell 16 LEV simply RNA Cells kit (Promega Biotech Ibérica) on the Maxwell 16 instrument, according to the manufacturer’s instructions.
Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina’s recommendations. Briefly, poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA went through an end repair process, addition of a single “A” base to the 3’ end and ligation to the adapters. Finally, the products were purified and enriched with PCR to create the indexed final double stranded DNA library. The quality and quantity of the libraries were analysed in tapeStation 4200, using the High Sensitivity assay (Agilent Technologies

value: Cells

value: Primary

value: Peripheral blood mononuclear cells


title: D496 HTO library 9


title: MS Non-responder 4 12 months


title: sc-Patch-seq,Red only,Regenerating CSMN105

description:
Patch-seq
NoRegen_CSMN_105

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: MS Non-responder 4 Baseline


title: sc-Patch-seq,Red only,Regenerating CSMN104

description:
Patch-seq
NoRegen_CSMN_104


title: MS Non-responder 5 12 months


title: D496 HTO library 7

value: HTO


title: MS Non-responder 3 12 months


title: D496 HTO library 8


title: Organoid 2445, olaparib day3

description: ORG 2445 PGCC_D3

value: ovary

value: 3 days


title: MS Non-responder 2 12 months


title: D496 HTO library 6

value: various

value: mononuclear cells (MNCs)


title: MS Non-responder 3 Baseline


title: Organoid 2445, DMSO day3

description: ORG 2445 NC_D3


title: sc-Patch-seq,Red only,Regenerating CSMN102

description:
Patch-seq
NoRegen_CSMN_102


title: sc-Patch-seq,Red only,Regenerating CSMN103

description:
Patch-seq
NoRegen_CSMN_103


title: Organoid 2414, olaparib day7, recover day14

description: ORG 2414 PGCC_R14

value: 50uM olaparib

value: 7 days recover 14 days


title: sc-Patch-seq,Red only,Regenerating CSMN101

description:
Patch-seq
NoRegen_CSMN_101

value: Cortical Spinal Motor Neuron


title: Organoid 2414, olaparib day7

description: ORG 2414 PGCC_D7


title: D496 HTO library 5


title: MS Non-responder 2 Baseline


title: Organoid 2414, olaparib day3

description: ORG 2414 PGCC_D3


title: D496 HTO library 4


title: MS Non-responder 1 12 months


title: D496 HTO library 3


title: Organoid 2445, olaparib day7

description: ORG 2445 PGCC_D7


title: sc-Patch-seq,Red only,Regenerating CSMN99

description:
Patch-seq
NoRegen_CSMN_099

value: Brain


title: sc-Patch-seq,Red only,Regenerating CSMN100

description:
Patch-seq
NoRegen_CSMN_100


title: D496 HTO library 2


title: MCF7, olaparib day7, recover day7

description: MCF7 PGCC_R7

value: 7 days recover 7 days


title: MS Non-responder 1 Baseline


title: sc-Patch-seq,Red only,Regenerating CSMN98

description:
Patch-seq
NoRegen_CSMN_098


title: D496 HTO library 1


title: MS Responder 5 12 months


title: D496 ADT library 16

value: ADT

value: TotalSeq-A Human Universal Cocktail


title: MCF7, olaparib day7

description: MCF7 PGCC_D7

value: 7 days


title: MS Responder 5 Baseline

value: Cells

value: Primary


title: MCF7, olaparib day3

description: MCF7 PGCC_D3


title: D496 ADT library 15


title: MCF7, DMSO day3

description: MCF7 NC_D3

value: DMSO


title: sc-Patch-seq,Red only,Regenerating CSMN95

description:
Patch-seq
NoRegen_CSMN_095

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: sc-Patch-seq,Red only,Regenerating CSMN96

description:
Patch-seq
NoRegen_CSMN_096


title: MS Responder 4 Baseline

value: Peripheral blood mononuclear cells


title: Hey, olaparib day7, recover day7

description: Hey PGCC_R7

value: ovary

value: Hey


title: MS Responder 3 12 months


title: sc-Patch-seq,Red only,Regenerating CSMN94

description:
Patch-seq
NoRegen_CSMN_094


title: OVCA432, olaparib day3, recover day3

description: OVCA432 PGCC_R3

value: 400uM olaparib

value: 3 days recover 3 days


title: Organoid 2414, DMSO day3

description: ORG 2414 NC_D3

value: 3 days


title: Hey, olaparib day7

description: Hey PGCC_D7

value: 50uM olaparib


title: sc-Patch-seq,Red only,Regenerating CSMN93

description:
Patch-seq
NoRegen_CSMN_093

value: Cortical Spinal Motor Neuron

value: Brain


title: D496 ADT library 12

value: various

value: mononuclear cells (MNCs)

value: ADT


title: D496 ADT library 13

value: TotalSeq-A Human Universal Cocktail


title: MS Responder 3 Baseline

value: Cells

value: Primary


title: Hey, olaparib day3

description: Hey PGCC_D3


title: sc-Patch-seq,Red only,Regenerating CSMN92

description:
Patch-seq
NoRegen_CSMN_092

value: PTEN SOCS3 tdTomato


title: D496 ADT library 11


title: MS Responder 2 12 months


title: Hey, DMSO day3

description: Hey NC_D3

value: DMSO


title: sc-Patch-seq,Red only,Regenerating CSMN97

description:
Patch-seq
NoRegen_CSMN_097

value: 22 weeks old


title: sc-Patch-seq,Red only,Regenerating CSMN91

description:
Patch-seq
NoRegen_CSMN_091


title: MS Responder 4 12 months

value: Peripheral blood mononuclear cells


title: sc-Patch-seq,Red only,Regenerating CSMN90

description:
Patch-seq
NoRegen_CSMN_090


title: D496 ADT library 14


title: D496 ADT library 10


title: MS Responder 2 Baseline


title: shMLX_1

city: Shenzhen

first: Xin

state: Guangdong

address: 1068, Xueyuan Road

department: Institute of Synthetic Biology

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

data_processing:
Alignment was done using STAR (2.6.0).
Feature counting was performed using HTSeq (0.11.2).
Differential gene analysis and counts normalization were done using DEseq2 (1.24.0).
Assembly: hg38
Supplementary files format and content: Text files containing gene counts matrix.

growth_protocol: 143B cells were maintained in DMEM medium supplemented with 10% FBS and 1%  Penicillin and Streptomycin.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN, 74106) according to the user's manual.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® following manufacturer.

treatment_protocol: Sequences specific for knocking down MLX were designed and cloned into pLKO puro lentiviral vectors. 143B  cells were infected with the obtained lentivirus to knock down MLX.

value: osteosarcoma cell line

value: MLX knockdown

value: shMLX


title: MS Responder 1 12 months


title: sc-Patch-seq,Red only,Regenerating CSMN89

description:
Patch-seq
NoRegen_CSMN_089


title: MS Responder 1 Baseline


title: Healthy donor 10


title: shControl_1

value: Control

value: shControl


title: shMLX_2


title: sc-Patch-seq,Red only,Regenerating CSMN87

description:
Patch-seq
NoRegen_CSMN_087

value: Cortical Spinal Motor Neuron


title: sc-Patch-seq,Red only,Regenerating CSMN88

description:
Patch-seq
NoRegen_CSMN_088

value: Brain


title: shControl_2


title: D496 ADT library 6

value: various


title: memory Th2 CD4+ T cell, stimulated (rep3)

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Reads were aligned using HISAT2 v2.0.4. (RNA-seq) with default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization
RPKM generation, sample scaling and statistical analysis were performed using HOMER and its implementation of the R package DESeq2.
Assembly: hg38
Supplementary files format and content: RPKM expression values

source_name: peripheral blood

growth_protocol: T-cell culture medium consisted of RPMI 1640 (Gibco), 10% FCS (HyClone), 55 μM 2-mercaptoethanol (Sigma), 2 mML-alanyl-L-glutamine (GlutaMAX; Gibco), 1 mM sodium pyruvate (Gibco), 0.1 mM non-essential amino acids (Gibco), penicillin/streptomycin (Gibco), 10 mM HEPES (Gibco), 50 Units/mL rhIL2 (R&D).

extract_protocol:
RNA was extracted from ~50,000 resting (ex vivo) or in vitro activated naive CD4+ T cells and memory Th2 cells using the RNeasy Micro kit (Qiagen) according to manufacturer’s instructions.
RNA-Seq: Smart-seq2 library construction (as described in Picelli et al. Nature Methods (2013))

treatment_protocol: Freshly isolated T cells were activated in vitro at 1x106 cells/mL in 200 µL T-cell culture medium in round bottom 96-well culture plates using Human T-Activator CD3/CD28 Dynabeads (Thermo Fisher) in a 1:1 bead-to-cell ratio at 37°C 5% CO2 for 24 hours.

value: peripheral blood

value: memory Th2 CD4+ T cell

value: 24h anti-CD3/CD28 beads in vitro


title: D496 ADT library 7

value: mononuclear cells (MNCs)

value: ADT

value: TotalSeq-A Human Universal Cocktail


title: D496 ADT library 8


title: sc-Patch-seq,Red only,Regenerating CSMN86

description:
Patch-seq
NoRegen_CSMN_086

value: PTEN SOCS3 tdTomato


title: Healthy donor 8

value: Cells

value: Primary


title: D496 ADT library 5


title: memory Th2 CD4+ T cell, stimulated (rep2)


title: sc-Patch-seq,Red only,Regenerating CSMN85

description:
Patch-seq
NoRegen_CSMN_085

value: 22 weeks old


title: D496 ADT library 4


title: memory Th2 CD4+ T cell, stimulated (rep1)


title: D496 ADT library 9


title: sc-Patch-seq,Red only,Regenerating CSMN84

description:
Patch-seq
NoRegen_CSMN_084


title: D496 ADT library 3


title: memory Th2 CD4+ T cell, resting (rep3)


title: sc-Patch-seq,Red only,Regenerating CSMN83

description:
Patch-seq
NoRegen_CSMN_083


title: D496 ADT library 2


title: memory Th2 CD4+ T cell, resting (rep2)


title: sc-Patch-seq,Red only,Regenerating CSMN82

description:
Patch-seq
NoRegen_CSMN_082


title: Healthy donor 5

value: Peripheral blood mononuclear cells


title: Healthy donor 9


title: Healthy donor 4


title: memory Th2 CD4+ T cell, resting (rep1)


title: Healthy donor 3


title: naive CD4+ T cell, stimulated (rep3)

value: naive CD4+ T cell


title: FLVCR1 KO + FLVCR1 cDNA Choline Replete 2

first: Kivanc

last: Birsoy

address: 1230 York Avenue, The Rockefeller University  Box 225 Tim Kenny/Kivanc Birsoy

institute: The Rockefeller University

data_processing:
RNAseq results are generated by the NGSpipeR package.
Reads were aligned to the reference genome using Salmon kmer counting software.
Genome Sequence - Fasta = Bsgenom.Hsapiens.UCSC.hg38.fa
Gene Modelts - GTF = TxDb.Hsapiens.UCSC.hg38.knownGene.gtf.gz
ID to Symbol Mapping = or.Hs.eg_ID2Symbol.txt
ID to GO mapping = org.Hs.eg_GOAnno.txt
Assembly: Hsapiens.UCSC.hg38
Supplementary files format and content: .sf for each sample

source_name: HeLa

growth_protocol: Cells grown in standard RPMI with 10% FBS and seeded in 6 well plates for RNAseq.

extract_protocol:
Cells were harvested and RNA was isolated using a Qiagen RNeasy Mini Kit (Cat #74104) following manufacturer guidelines. 400ng total RNA was used for library construction.
TruSeq_stranded_mRNA_LT_kit Cat #20020594

treatment_protocol: After seeding cells the prior day in standard RPMI with 10% FBS, cells were washed twice with PBS and then treated with Cells were seeded in choline depleted media (Choline Free RPMI +10% dialyzed FBS) or choline replete media (Choline Free RPMI +3mg/L Choline Chloride +10% dialyzed FBS) and given fresh media the next day and RNA collected after 24 hours.

value: HeLa

value: FLVCR1 KO +FLVCR1 cDNA

value: Choline Free RPMI +3mg/L Choline Chloride + 10% dialyzed FBS


title: naive CD4+ T cell, stimulated (rep2)


title: Helathy donor 2


title: FLVCR1 KO + FLVCR1 cDNA Choline Replete 3


title: Healthy donor 1


title: sc-Patch-seq,Red only,Regenerating CSMN80

description:
Patch-seq
NoRegen_CSMN_080

value: Cortical Spinal Motor Neuron

value: Brain


title: Healthy donor 7


title: sc-Patch-seq,Red only,Regenerating CSMN78

description:
Patch-seq
NoRegen_CSMN_078


title: naive CD4+ T cell, stimulated (rep1)

value: peripheral blood


title: FLVCR1 KO + FLVCR1 cDNA Choline Replete 1


title: naive CD4+ T cell, resting (rep3)


title: FLVCR1 KO + FLVCR1 cDNA Choline Depleted 3

value: Choline Free RPMI + 10% dialyzed FBS


title: sc-Patch-seq,Red only,Regenerating CSMN77

description:
Patch-seq
NoRegen_CSMN_077


title: siSirt6 Human donor 6 siRNA Sirt6 (72 hours)

city: Philadelphia

first: John

middle: Andrew

last: Collins

state: PA

address: 1015 Walnut Street, Curtis Building, Suite 505

institute: Thomas Jefferson University

data_processing:
Overall quality of the next-generation sequencing data was evaluated using in-house perl scripts. Clean reads were obtained following removal of reads containing adapters, reads containing ploy-N and low-quality reads from raw data. Reads were mapped against the reference genome Homo Sapiens (GRCh38/hg38)and gene model annotation files were downloaded from genome website directly (http://ftp.ensembl.org/pub/).
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Parameters for mismatches were 2-6max and min penalties for mismatch; lower qual = lower penalty <2,6>.  of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach to control the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). Corrected P-value of 0.05 and absolute fold change of 2 were set as the threshold for significantly differential expression.
RNA expression was normalized by median and pareto scaled prior to multivariate analysis. All principal component analysis (PCA) and heat map analysis was conducted using MetaboAnalyst 4.0
Ingenuity Pathway Analysis (IPA, Ingenuity Systems, Redwood City, California, US), was used to analyze the RNASeq data for canonical pathways, upstream regulators, and disease and function analysis using the list of differentially expressed genes (log2FC cutoff of ±2 and FDR<0.05).
Supplementary files format and content: Tab delimited text file (.xls) including fkpm values for each sample

source_name: Primary isolated human chondrocytes

growth_protocol: Primary human chondrocytes cultured in monolayer at high density in DMEM supplemented with 10% Fetal Bovine Serum (FBS) and antibiotics

extract_protocol:
Total RNA from cells was extracted using the NucleoSpin RNA mini kit for RNA purification (Macherey-Nagel) according to manufacturer’s instructions.
Library preparation, RNA-sequencing, and initial data analysis was carried out by Novogene (see Suppl Materials and Methods for details)

treatment_protocol: Chondrocytes were nucleofected with siRNA to Sirt6 or an empty vector control (AMAXA nucleofection method) for 72 hours

value: Primary isolated human chondrocytes

value: 72 hours


title: Healthy donor 6


title: FLVCR1 KO + FLVCR1 cDNA Choline Depleted 2


title: siCtrl Human donor 6 empty vector control (72 hours)

value: siCtrl


title: sc-Patch-seq,Red only,Regenerating CSMN76

description:
Patch-seq
NoRegen_CSMN_076

source_name: Brain


title: D496 ADT library 1

value: various

value: mononuclear cells (MNCs)

value: ADT

value: TotalSeq-A Human Universal Cocktail


title: naive CD4+ T cell, resting (rep2)


title: sc-Patch-seq,Red only,Regenerating CSMN81

description:
Patch-seq
NoRegen_CSMN_081

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: FLVCR1 KO + FLVCR1 cDNA Choline Depleted 1


title: siSirt6 Human donor 5 siRNA Sirt6 (72 hours)


title: sc-Patch-seq,Red only,Regenerating CSMN75

description:
Patch-seq
NoRegen_CSMN_075


title: siCtrl Human donor 5 empty vector control (72 hours)


title: FLVCR1 KO + Empty Vector Choline Replete 3

value: FLVCR1 KO + Empty Vector


title: naive CD4+ T cell, resting (rep1)

value: naive CD4+ T cell


title: sc-Patch-seq,Red only,Regenerating CSMN79

description:
Patch-seq
NoRegen_CSMN_079


title: HPAC cells espressing shTRIM21#2 replicate 3

first: Ashenafi

last: Bulle

state: Missouri

address: 660 S Euclid Ave

department: Molecular Oncology

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCm38.76
Supplementary files format and content: Gene counts in tab-delimitted text format

source_name: HPAC

growth_protocol: HPAC cells were cultured in DMEM/10% FBS, 1% Pen/Strep.

extract_protocol:
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HPAC

value: Pancreatic cancer cells

value: Trim21 knockdown#2


title: sc-Patch-seq,Red only,Regenerating CSMN74

description:
Patch-seq
NoRegen_CSMN_074

value: Cortical Spinal Motor Neuron

value: Brain


title: sc-Patch-seq,Red only,Regenerating CSMN73

description:
Patch-seq
NoRegen_CSMN_073


title: HPAC cells espressing shTRIM21#2  replicate 2


title: siSirt6 Human donor 4 siRNA Sirt6 (72 hours)


title: siCtrl Human donor 4 empty vector control (72 hours)


title: HPAC cells espressing shTRIM21#2 replicate 1


title: FLVCR1 KO + Empty Vector Choline Replete 1

value: HeLa

value: Choline Free RPMI +3mg/L Choline Chloride + 10% dialyzed FBS


title: sc-Patch-seq,Red only,Regenerating CSMN72

description:
Patch-seq
NoRegen_CSMN_072


title: FLVCR1 KO + Empty Vector Choline Replete 2


title: sc-Patch-seq,Red only,Regenerating CSMN71

description:
Patch-seq
NoRegen_CSMN_071


title: siCtrl Human donor 3 empty vector control (72 hours)

value: Primary isolated human chondrocytes

value: 72 hours


title: FLVCR1 KO + Empty Vector Choline Depleted 3

value: Choline Free RPMI + 10% dialyzed FBS


title: HPAC cells espressing shTRIM21#1 replicate 3

value: Trim21 knockdown#1


title: FLVCR1 KO + Empty Vector Choline Depleted 2


title: sc-Patch-seq,Red only,Regenerating CSMN70

description:
Patch-seq
NoRegen_CSMN_070


title: HPAC cells espressing shTRIM21#1 replicate 2


title: HPAC cells espressing shTRIM21#1 replicate 1


title: siSirt6 Human donor 2 siRNA Sirt6 (72 hours)


title: siCtrl Human donor 2 empty vector control (72 hours)

value: siCtrl


title: FLVCR1 KO + Empty Vector Choline Depleted 1


title: Eye, CSC-NR

city: Seoul

first: Junyeop

last: Lee

address: 88, Olympic-ro 43gil, Sonpa-gu

department: Ophthalmology

country: South Korea

institute: Asan Medical Center, Seoul

data_processing:
PCR was performed for library amplification and libraries were carried out clean-up using QIAquick PCR Purification Kit (Qiagen, Inc, German) and AMPure XP beads (Beckmancoulter, Inc., USA).
The yield and size distribution of the small RNA libraries were assessed by the Agilent 2100 Bioanalyzer instrument for the High-sensitivity DNA Assay (Agilent Technologies, Inc., USA).
High-throughput sequences were produced by NextSeq500 system as way of single-end 75 sequencing (Illumina, SanDiego, CA., USA).
Assembly: hsa (miRDB)
Supplementary files format and content: Quantile normalization between samples in .xlsx file

source_name: Eye

extract_protocol:
Exosomal RNA was isolated by using ExoLutE® Exosome Isolation Kits (Rosetta, Seoul, Korea), following the manufacturer’s instructions.
The construction of library was performed using NEBNext Multiplex Small RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.
small RNA libraries

value: Eye

tag: condition

value: CSC-NR

tag: anti-vegf treatment

value: non-responder

tag: sample type

value: aqueous humor-derived exosomes


title: Eye, CSC-R

value: CSC-R

value: responder


title: sc-Patch-seq,Red only,Regenerating CSMN67

description:
Patch-seq
NoRegen_CSMN_067

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: siCtrl Human donor 1 empty vector control (72 hours)


title: siSirt6 Human donor 1 siRNA Sirt6 (72 hours)


title: sc-Patch-seq,Red only,Regenerating CSMN66

description:
Patch-seq
NoRegen_CSMN_066

value: Cortical Spinal Motor Neuron


title: siSirt6 Human donor31 siRNA Sirt6 (72 hours)


title: TSA treated human islets_rep_3

city: Lille

first: Frederik

last: Oger

address: Faculté de Médecine - Pôle Recherche - 2eme etage - 1 place de Verdun

country: France

institute: Université de Lille

description: RNA polyA

data_processing:
The demultiplexing of sequence data (from BCL files generated by Illumina sequencing systems to standard FASTQ file formats) was performed using bcl2fastq Conversion Software (Illumina; version 2.19.1).
Trimming of residuals adapters and low-quality reads was performed using Cutadapt software (version 1.7.1).
Sequence reads from FASTQ files were mapped to the mouse genome (mm10) or human genome (Hg38) using STAR Aligner (version 2.5.2b). On average, 38M reads were generated per sample, and 93.5 % +/- 0.9% of them were accurately mapped.
The counting of the different genes and isoforms was performed using RSEM (version 1.3). Finally, differential expression was performed using DESeq2 package
Assembly: mm10 (mouse) and Hg38 (human)
Supplementary files format and content: Tab-delimited text files include TPM and FPKM values for each sample

source_name: Human pancreatic islets

growth_protocol: Human pancreatic tissue was harvested from human, non-diabetic, adult donors. Isolation and pancreatic islet culture were performed as previously described (Kerr-Conte J, Transplation, 2010)

extract_protocol:
Total RNA was extracted from EndoCβH1, Min6, mouse pancreatic islets and human pancreatic islets using RNeasy Plus mini kit (Qiagen, 74136) according to the manufacturer’s instructions. Total RNA sample concentrations were determined using a Nanodrop spectrophotometer (Implen). RNA quality was verified using RNA 6000 nanochips (Agilent, 5067-1511) on the Agilent 2100 bioanalyzer (Agilent, G2939A). 500 ng of purified RNA with RNA integrity number (RIN) ≥8 was subsequently used for library preparation
500 ng of purified RNA with RNA integrity number (RIN) ≥8 was subsequently used for library preparation with the TrueSeq Stranded mRNA library Prep (Illumina, 20020594) and sequenced in paired end 2x75 on the NextSeq device.
Libraries were prepared with the TruSeq Stranded mRNA library Prep (Illumina, #20020594) and sequenced on the Illumina NextSeq500 system using a paired-end 2×75 bp protocol.

treatment_protocol: EndoCβH1, Min6, mouse pancreatic islets and human pancreatic islets were treated either with DMSO (0.1%) or TSA (0.5µM) for 16h.

value: Ex vivo human pancreatic islets


title: 4H Homo sapiens pDC Mock Patient1 Batch7

city: Lyon

first: Xavier

last: Grand

address: 46 allée d'Italie

institute: INSERM U1052, UCBL1, ENS de Lyon

data_processing:
Raw reads were quantified using the quasi-mapping-based mode of Salmon.
The references used were the Genome Reference Consortium Human Build 38 (hg38, Genbank accession GCA_000001405.15),
for the Human analysis and Macaca_fasicularis_5.0 (Genbank accession GCA_000364345.1) for the Monkey analysis.
Raw counts were processed using package DESeq2 in R/Bioconductor.
Assembly: hg38, GCA_000001405.15 and Macaca_fasicularis_5.0, GCA_000364345.1
Supplementary files format and content: Tab-delimited csv file containing normalized counts for Homo sapiens samples,
Supplementary files format and content: another tab-delimited csv file containg normalized counts for Macaca fascicularis samples.

source_name: PBMCs

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from human donors (n=6) and Mauritius cynomolgus macaques (n=6) using ficoll-plaque PLUS.

extract_protocol:
PBMCs were immediately sorted into pDC, mDC, T and B cell populations by FACS, collected and lysed using Trizol. RNA extraction was performed using Phasemaker Tubes Complete System.
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

treatment_protocol: For each condition, 15x10^6 PBMCs were incubated 2 h at 37°C with 5% CO2 in RPMI-1640 culture medium with or without HBV (MOI 100).

value: PBMCs

value: pDC

value: Mock

tag: patient

tag: batch


title: MEC1 SF3B1 K700E rep 3 H3B-8800

city: Barcelona

first: Estefania

last: Mancini

state: Barcelona

address: C/ Dr. Aiguader, 88

department: GENE REGULATION, STEM CELLS AND CANCER

institute: Centre for Genomic Regulation

description:
6 raw data files correspond to 3 paired-end technical replicates
mut_h3b_15b

data_processing:
Illumina universal adapters sequences were removed from the RNA-Seq reads with Cutadapt version 2.4 discarding all reads with length shorter than 15.
Splicing analyses of RNA-Seq data were performed using the toolset vast-tools v.2.5.1
Genome_build: hg38
Supplementary_files_format_and_content: This table consists of one row per alternative splicing (AS) event, each with six columns with basic information about the AS event and two columns for each of the N samples combined: (i) the inclusion level, using the Percent Spliced-In (PSI) metric, and (ii) a comma-separated array of five scores indicating the reliability of the PSI measure, as well as the normalized count of reads supporting inclusion and exclusion. Information about each score and the exact definitions for each AS event type can be found in https://github.com/vastgroup/vast-tools#combine-output-format.

source_name: Chronic lymphocytic leukemia

growth_protocol: MEC1 (DSMZ: ACC497) cell lines were cultured at 500.000 cells/ml in Iscove's modified Dulbecco's medium (IMDM) GlutaMAXTM medium (GIBCO 31980-022) supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) penicillin-streptomycin (GIBCO 15140122), in a humidified atmosphere at 37 °C containing 5% carbon dioxide.

extract_protocol:
RNA extraction was carried out using RNeasy Mini kit (Quiagen, 74104)
Libraries were prepared using the TruSeq stranded mRNA Library Prep (96 samples ref. 20020595 or 48 samples ref. 20020594) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing. Briefly, 1000-500 ng of total RNA were used for poly(A)-mRNA selection using poly-T oligo attached magnetic beads using two rounds of purification. During the second elution of the poly-A RNA, the RNA was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis. Then, the cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and random primers. The addition of Actinomycin D to the First Stand Synthesis Act D mix (FSA) prevents spurious DNA-dependent synthesis, while allowing RNA-dependent synthesis, improving strand specificity. After that, second strand cDNA was synthesized, removing the RNA template and synthesizing a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA using DNA Polymerase I and RNase H. These cDNA fragments, then had the addition of a single 'A' base to the 3’ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation. A corresponding single T nucleotide on the 3’ end of the adapter provides a complementary overhang for ligating the adapter to the fragments ensuring a low rate of chimera (concatenated template) formation. Subsequent ligation of the multiple indexing adapter to the ends of the ds cDNA. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends and to amplify the amount of DNA in the library. The PCR was performed with a PCR Primer Cocktail that anneals to the ends of the adapters. Final libraries were analyzed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (ref: 5067-1504 or ref: DNF-473, Agilent) to estimate the quantity and validate the size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (REF. 07960204001, Roche) prior to the amplification with Illumina’s cBot. Libraries were sequenced 2 * 125 bp on Illumina's HiSeq2500

treatment_protocol: 4 million cells (1 million/ml) were treated with 75nM H3B-8800 or DMSO (control) for 6 hours

value: MEC 1 ACC497 (DMSZ)

value: SF3B1 MUT c.2098A>G and c.2106G>A


title: TSA treated human islets_rep_2

description: RNA polyA

tag: cell type


title: sc-Patch-seq,Red only,Regenerating CSMN64

first: Hugo

last: Kim

address: 4760 Templeton St, Unit 3113

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

description:
Patch-seq
NoRegen_CSMN_064

data_processing:
The demultiplexing, barcoded processing, gene counting and STAR aligner was used to align the sample.
Assembly: mm22
Supplementary files format and content: Tap delimited expression table and phenotype table

extract_protocol:
The mice are sacrificed under perfusion of sucrose cutting solution, bubbling. The brain was sliced in 200-300um by viubratome, bubbling with CO2/O2. Tissue were recovered in the recovery chamber, bubbling. Using Patch Clamp approach, I generated giga-seal and extract the cell contents to the ppet. Then I freeze the cell in liquid nitrogen until the library prep
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
We amplified RNA using modified aRNA protocol for 2 cycles, followed by illumina Truseq mRNA prep.

tag: tissue

value: Brain


title: MEC1 SF3B1 K700E rep 2 H3B-8800

description:
6 raw data files correspond to 3 paired-end technical replicates
mut_h3b_38


title: sc-Patch-seq,Red only,Regenerating CSMN63

description:
Patch-seq
NoRegen_CSMN_063

tag: strain


title: 28H Homo sapiens pDC Mock Patient4 Batch8


title: MEC1 SF3B1 WT rep 3 H3B-8800

description:
6 raw data files correspond to 3 paired-end technical replicates
wt_h3b_34b

value: SF3B1 WT c.2106G>A


title: MEC1 SF3B1 K700E rep 1 H3B-8800

description:
6 raw data files correspond to 3 paired-end technical replicates
mut_h3b_41


title: sc-Patch-seq,Red only,Regenerating CSMN69

description:
Patch-seq
NoRegen_CSMN_069

tag: age


title: sc-Patch-seq,Red only,Regenerating CSMN62

description:
Patch-seq
NoRegen_CSMN_062


title: 36H Homo sapiens pDC Mock Patient5 Batch7


title: DMSO treated human islets_rep_2

description: RNA polyA


title: 12H Homo sapiens pDC Mock Patient2 Batch8


title: Eye, Control

value: Eye

value: control


title: MEC1 SF3B1 WT rep 2 H3B-8800

description:
6 raw data files correspond to 3 paired-end technical replicates
wt_h3b_b

tag: cell line

value: SF3B1 WT


title: sc-Patch-seq,Red only,Regenerating CSMN61

description:
Patch-seq
NoRegen_CSMN_061


title: sc-Patch-seq,Red only,Regenerating CSMN68

description:
Patch-seq
NoRegen_CSMN_068


title: 8H Homo sapiens pDC HBV Patient1 Batch7

value: HBV


title: DMSO treated human islets_rep_1

description: RNA polyA


title: sc-Patch-seq,Red only,Regenerating CSMN60

description:
Patch-seq
NoRegen_CSMN_060


title: sc-Patch-seq,Red only,Regenerating CSMN65

description:
Patch-seq
NoRegen_CSMN_065


title: 44H Homo sapiens pDC Mock Patient6 Batch8


title: 48H Homo sapiens pDC HBV Patient6 Batch8


title: MEC1 SF3B1 WT rep 1 H3B-8800

description:
6 raw data files correspond to 3 paired-end technical replicates
wt_h3b_a

tag: genotype


title: MEC1 SF3B1 K700E rep3

description:
6 raw data files correspond to 3 paired-end technical replicates
mut_dmso_15b

value: Control (DMSO)


title: TSA treated human islets_rep_1

description: RNA polyA


title: MEC1 SF3B1 K700E rep2

description:
6 raw data files correspond to 3 paired-end technical replicates
mut_dmso_38


title: TSA treated EndoCβH1 cells_rep_2

description: RNA polyA

growth_protocol: EndoCβH1 were cultured according the supplier's recommandations.

value: Human beta cell model - EndoCbetaH1


title: DMSO treated human islets_rep_3

description: RNA polyA


title: 32H Homo sapiens pDC HBV Patient4 Batch8


title: sc-Patch-seq,Red only,Regenerating CSMN59

description:
Patch-seq
NoRegen_CSMN_059

value: PTEN SOCS3 tdTomato


title: TSA treated EndoCβH1 cells_rep_1

description: RNA polyA


title: sc-Patch-seq,Red only,Regenerating CSMN57

description:
Patch-seq
NoRegen_CSMN_057

value: 22 weeks old


title: 24H Homo sapiens pDC HBV Patient3 Batch7


title: sc-Patch-seq,Red only,Regenerating CSMN56

description:
Patch-seq
NoRegen_CSMN_056

value: Cortical Spinal Motor Neuron


title: MEC1 SF3B1 WT rep 3

description:
6 raw data files correspond to 3 paired-end technical replicates
wt_dmso_34b


title: MEC1 SF3B1 K700E rep1

description:
6 raw data files correspond to 3 paired-end technical replicates
mut_dmso_41


title: 40H Homo sapiens pDC HBV Patient5 Batch7


title: DMSO treated EndoCβH1 cells_rep_3

description: RNA polyA


title: DMSO treated EndoCβH1 cells_rep_2

description: RNA polyA


title: sc-Patch-seq,Red only,Regenerating CSMN55

description:
Patch-seq
NoRegen_CSMN_055


title: 16H Homo sapiens pDC HBV Patient2 Batch8


title: DMSO treated EndoCβH1 cells_rep_1

description: RNA polyA


title: MEC1 SF3B1 WT rep 2

description:
6 raw data files correspond to 3 paired-end technical replicates
wt_dmso_b


title: 43H Homo sapiens mDC Mock Patient6 Batch6

value: mDC


title: MEC1 SF3B1 WT rep 1

description:
6 raw data files correspond to 3 paired-end technical replicates
wt_dmso_a


title: sc-Patch-seq,Red only,Regenerating CSMN54

description:
Patch-seq
NoRegen_CSMN_054


title: 3H Homo sapiens mDC Mock Patient1 Batch5

value: PBMCs


title: sc-Patch-seq,Red only,Regenerating CSMN53

description:
Patch-seq
NoRegen_CSMN_053


title: vIL6pos_CTCF_2

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

library_source: genomic

data_processing:
library strategy: CUT&RUN
Base calling and quality scoring were performed using bcl2fastq v2.17 for Novaseq 6000 output.
CUT&RUN reads were processed with fastp and aligned to the GRCh38 (hg38) human reference genome assembly with Bowtie2.
Hypergeometric Optimization of Motif EnRichment (HOMER) v4.11 was used for peak detection were annotated utilizing the defalt parameters described in the developer’s manual. The default settings with a minimum FDR (q-value) cut-off of 0.05 were used.
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data are in bigWig format.

molecule: genomic DNA

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium supplemented with 1% FBS, 2 mM L-glutamine, and antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin) in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were washed with PBS and wash buffer (20mM HEPES-KOH pH7.5, 150mM NaCl, 0.5mM spermidine (Sigma, S2626) and proteinase inhibitor (Roche). After removing wash buffer, cells were captured on magnetic ConA beads (Polysciences), in presence of CaCl2. Beads/cells complexes were washed with digitonin wash buffer (0.02% digitonin, 20mM HEPES-KOH pH7.5, 150mM NaCl, 0.5mM spermidine and 1x proteinase inhibitor) three times, and incubated with specific antibodies in 250 mL volume. After incubation, unbound antibody was washed by digitonin wash buffer 3 times. Beads were then incubated with the recombinant pAG-MNase, in 250μl digitonin wash buffer (1.0 mg/mL final concentration) for an hour at 4°C with rotation. Unbound pAG-MNase was removed by washing with digitonin wash buffer 3 times. Pre-chilled 2 mM CaCl2 containing digitonin wash buffer (200 mL) was added to beads and incubate on ice for 30 min. The pAG-MNase digestion was halted by the addition of 200μl 2× STOP solution (340mM NaCl, 20mM EDTA, 4mM EGTA, 50μg/ml RNase A, 50 mg/ml Glycogens). The beads were incubated/shaked at 37°C for 10min in tube shaker at 500 rpm to release digested DNA fragments from the insoluble nuclear chromatin. The supernatant was collected after centrifuge (16,000 x g for 5 min at 4°C) and place on magnetic stand. DNA was extracted using the NucleoSpin & PCR kit (Takara Bio, Kusatsu, Shiga, Japan).
Sequencing libraries were prepared from 3 ng of CUT&RUN DNA with the Kapa HyperPrep Kit (Roche) according to the manufacturer’s standard protocol. Libraries were multiplex sequenced (2 x 150bp, paired-end) on an Illumina NovaSeq 6000 sequencing system.

value: monocyte

tag: priming treatment

value: vIL-6 (100 ng/ml), continuous for 2 weeks

value: vIL-6 (100 ng/ml), 30 minutes

tag: cut&run antibody

value: CTCF


title: TSA treated EndoCβH1 cells_rep_3

description: RNA polyA

tag: treatment


title: 35H Homo sapiens mDC Mock Patient5 Batch5

value: Mock


title: HCT116 cells, SLAM_nolabeling_rep2

city: Berlin

first: Lorenzo

last: Calviello

address: Robert-Rössle-Straße 10, MDC, Haus 89

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

data_processing:
For Ribo-seq and RNA-seq, reads were stripped of their adapter, collapsed, and UMI sequences were removed. Clean reads were then mapped to rRNA, tRNA, snoRNA and miRNA sequences using bowtie2 using sequences retrieved from UCSC browser and aligning reads were discarded. Remaining reads were mapped to the genome and transcriptome using STAR v2.7.9a supplied with the GENCODE v32 GTF file. STAR parameters were: --outFilterMismatchNmax 3 --outFilterMultimapNmax 50 --chimScoreSeparation 10 --chimScoreMin 20 --chimSegmentMin 15 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignSJoverhangMin 500 --outSAMmultNmax 1 --outMultimapperOrder Random
For SLAM-seq, reads were mapped to the genome and transcriptome using same RNA-seq parameters, except for --outFilterMismatchNmax 10. Reads containing T>C mutations were extracted from the BAM file using GenomicAlignment and GenomicFiles Bioconductor packages.
Assembly: hg38
Supplementary files format and content: normalized bigwig tracks for Ribo-seq and RNA-seq, reads harboring T>C conversions for SLAM-seq
Library strategy: SLAM-seq

growth_protocol: HCT116 cells with inducible degradation of DDX3X were plated in 15cm plates at 20% confluency (~3.5x10 6 cells/plate). 48 hours post plating, when the cells were at ~ 70% confluency, the media was changed and fresh media with 500 M IAA or DMSO was added to cells. Cells were harvested at 0, 4, 8, 16, 24, and 48 hours post IAA addition.

extract_protocol:
For Ribo-seq and RNA-seq, Direct-zol kit (Zymo Research) was used to extract RNA. For SLAM-seq we used TRIzol (Ambion), following the SLAM-seq kit (SLAMseq Kinetics Kit – Catabolic Kinetics Module, Lexogen).
QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen for SLAM-seq, TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina) for RNA-seq and a modified Ribo-seq protocol (see manuscript).


title: sc-Patch-seq,Red only,Regenerating CSMN52

city: Los Angeles

description:
Patch-seq
NoRegen_CSMN_052

value: Brain


title: sc-Patch-seq,Red only,Regenerating CSMN58

description:
Patch-seq
NoRegen_CSMN_058


title: vIL6pos_CTCF_1


title: HCT116 cells, SLAM_nolabeling_rep1


title: vIL6neg_CTCF_2

value: No treatment


title: HCT116 cells, SLAM_DMSO_8h_rep2


title: sc-Patch-seq,Red only,Regenerating CSMN51

description:
Patch-seq
NoRegen_CSMN_051


title: vIL6neg_CTCF_1


title: 19H Homo sapiens mDC Mock Patient3 Batch5


title: HCT116 cells, SLAM_DMSO_8h_rep1


title: sc-Patch-seq,Red only,Regenerating CSMN50

description:
Patch-seq
NoRegen_CSMN_050


title: THP-1_vIL-6_polII_2

value: RNA polymerase II (Millipore, clone CTD4H8)


title: 11H Homo sapiens mDC Mock Patient2 Batch6


title: sc-Patch-seq,Red only,Regenerating CSMN49

description:
Patch-seq
NoRegen_CSMN_049


title: 7H Homo sapiens mDC HBV Patient1 Batch5


title: THP-1_vIL-6_polII_1


title: HCT116 cells, SLAM_DMSO_0h_rep1


title: sc-Patch-seq,Red only,Regenerating CSMN48

description:
Patch-seq
NoRegen_CSMN_048


title: THP-1_vIL-6_K27Ac_2

value: H3K27ac (CST, clone D5E4)


title: 47H Homo sapiens mDC HBV Patient6 Batch6

value: HBV


title: 39H Homo sapiens mDC HBV Patient5 Batch5


title: HCT116 cells, SLAM_Degron_8h_rep2


title: sc-Patch-seq,Red only,Regenerating CSMN47

description:
Patch-seq
NoRegen_CSMN_047


title: sc-Patch-seq,Red only,Regenerating CSMN46

description:
Patch-seq
NoRegen_CSMN_046


title: HCT116 cells, SLAM_Degron_8h_rep1


title: 27H Homo sapiens mDC Mock Patient4 Batch6


title: THP-1_vIL-6_K27Ac_1


title: 31H Homo sapiens mDC HBV Patient4 Batch6


title: sc-Patch-seq,Red only,Regenerating CSMN45

description:
Patch-seq
NoRegen_CSMN_045


title: THP-1_vIL-6_K4me3_2

value: H3K4me3 (CST, clone C42D8)


title: THP-1_vIL-6_K4me3_1


title: HCT116 cells, SLAM_Degron_0h_rep2


title: 23H Homo sapiens mDC HBV Patient3 Batch5


title: HCT116 cells, SLAM_Degron_0h_rep1


title: 15H Homo sapiens mDC HBV Patient2 Batch6


title: HCT116 cells, SLAM_DMSO_0h_rep2


title: sc-Patch-seq,Red only,Regenerating CSMN44

description:
Patch-seq
NoRegen_CSMN_044


title: THP-1_vIL-6_BRD4_2

value: BRD4 (CST, E2A7X)


title: HCT116 cells, RNA_DMSO_rep2

data_processing:
For Ribo-seq and RNA-seq, reads were stripped of their adapter, collapsed, and UMI sequences were removed. Clean reads were then mapped to rRNA, tRNA, snoRNA and miRNA sequences using bowtie2 using sequences retrieved from UCSC browser and aligning reads were discarded. Remaining reads were mapped to the genome and transcriptome using STAR v2.7.9a supplied with the GENCODE v32 GTF file. STAR parameters were: --outFilterMismatchNmax 3 --outFilterMultimapNmax 50 --chimScoreSeparation 10 --chimScoreMin 20 --chimSegmentMin 15 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignSJoverhangMin 500 --outSAMmultNmax 1 --outMultimapperOrder Random
For SLAM-seq, reads were mapped to the genome and transcriptome using same RNA-seq parameters, except for --outFilterMismatchNmax 10. Reads containing T>C mutations were extracted from the BAM file using GenomicAlignment and GenomicFiles Bioconductor packages.
Assembly: hg38
Supplementary files format and content: normalized bigwig tracks for Ribo-seq and RNA-seq, reads harboring T>C conversions for SLAM-seq


title: sc-Patch-seq,Red only,Regenerating CSMN43

description:
Patch-seq
NoRegen_CSMN_043

value: PTEN SOCS3 tdTomato


title: THP-1_vIL-6_BRD4_1


title: 9H Homo sapiens LT Mock Patient2 Batch2

value: LT


title: HCT116 cells, Ribo_DMSO_rep2

data_processing:
For Ribo-seq and RNA-seq, reads were stripped of their adapter, collapsed, and UMI sequences were removed. Clean reads were then mapped to rRNA, tRNA, snoRNA and miRNA sequences using bowtie2 using sequences retrieved from UCSC browser and aligning reads were discarded. Remaining reads were mapped to the genome and transcriptome using STAR v2.7.9a supplied with the GENCODE v32 GTF file. STAR parameters were: --outFilterMismatchNmax 3 --outFilterMultimapNmax 50 --chimScoreSeparation 10 --chimScoreMin 20 --chimSegmentMin 15 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignSJoverhangMin 500 --outSAMmultNmax 1 --outMultimapperOrder Random
For SLAM-seq, reads were mapped to the genome and transcriptome using same RNA-seq parameters, except for --outFilterMismatchNmax 10. Reads containing T>C mutations were extracted from the BAM file using GenomicAlignment and GenomicFiles Bioconductor packages.
Assembly: hg38
Supplementary files format and content: normalized bigwig tracks for Ribo-seq and RNA-seq, reads harboring T>C conversions for SLAM-seq
Library strategy: Ribo-seq


title: THP-1_No_polII_2


title: 41H Homo sapiens LT Mock Patient6 Batch2


title: sc-Patch-seq,Red only,Regenerating CSMN42

description:
Patch-seq
NoRegen_CSMN_042

value: Cortical Spinal Motor Neuron

value: 22 weeks old


title: HCT116 cells, RNA_DMSO_rep1


title: sc-Patch-seq,Red only,Regenerating CSMN41

description:
Patch-seq
NoRegen_CSMN_041


title: THP-1_No_polII_1


title: HCT116 cells, Ribo_DMSO_rep1


title: 33H Homo sapiens LT Mock Patient5 Batch1

value: PBMCs


title: 25H Homo sapiens LT Mock Patient4 Batch2


title: sc-Patch-seq,Red only,Regenerating CSMN40

description:
Patch-seq
NoRegen_CSMN_040


title: THP-1_No_K27Ac_2

value: monocyte


title: 1H Homo sapiens LT Mock Patient1 Batch1


title: sc-Patch-seq,Red only,Regenerating CSMN39

description:
Patch-seq
NoRegen_CSMN_039


title: HCT116 cells, RNA_08h_rep2


title: HCT116 cells, Ribo_08h_rep2


title: 17H Homo sapiens LT Mock Patient3 Batch1


title: THP-1_No_K4me3_2


title: HCT116 cells, RNA_08h_rep1


title: sc-Patch-seq,Red only,Regenerating CSMN38

description:
Patch-seq
NoRegen_CSMN_038


title: 5H Homo sapiens LT HBV Patient1 Batch1


title: THP-1_No_K4me3_1


title: HCT116 cells, Ribo_08h_rep1


title: THP-1_No_BRD4_2


title: 45H Homo sapiens LT HBV Patient6 Batch2


title: sc-Patch-seq,Red only,Regenerating CSMN37

description:
Patch-seq
NoRegen_CSMN_037


title: sc-Patch-seq,Red only,Regenerating CSMN36

description:
Patch-seq
NoRegen_CSMN_036


title: HCT116 cells, RNA_04h_rep2


title: sc-Patch-seq,Red only,Regenerating CSMN34

description:
Patch-seq
NoRegen_CSMN_034


title: 37H Homo sapiens LT HBV Patient5 Batch1


title: 29H Homo sapiens LT HBV Patient4 Batch2


title: HCT116 cells, Ribo_04h_rep2


title: sc-Patch-seq,Red only,Regenerating CSMN33

description:
Patch-seq
NoRegen_CSMN_033


title: 21H Homo sapiens LT HBV Patient3 Batch1


title: HCT116 cells, RNA_04h_rep1


title: vIL6_LPS3

data_processing:
SLAM-Seq datasets were analyzed using the T>C conversion-aware SLAM-DUNK (Digital Unmasking of Nucleotide conversion-containing k-mers) pipeline utilizing the default parameters (DOI: 10.1038/nmeth.4435, DOI: 10.1186/s12859-019-2849-7). Briefly, nucleotide conversion-aware read mapping of adapter- and poly(A)-trimmed sequences to the human GRCh38/hg38 reference genome assembly was performed with NextGenMap (DOI:10.1093/bioinformatics/btt468). Alignments were filtered for those with a minimum identity of 95% and minimum of 50% of the read bases mapped. For multi-mappers, ambiguous reads and non-3' UTR alignments were discarded, while one read was randomly selected from multimappers aligned to the same 3’ UTR. SNP calling (coverage cut-off of 10X and variant fraction cut-off of 0.8) with VarScan2 (DOI: 10.1101/gr.129684.111) was performed in order to mask actual T>C SNPs. Non-SNP T>C conversion events were then counted and the fraction of labeled transcripts determined. All output is contained in tcount files.
Assembly: GRCh38/hg38
Supplementary files format and content: The processed data is contained in the tcount file, which is the central output of slamdunk. These contain all results, conversion rates, and other statistics for each UTR. Tcount files are comma-separated text files containing one line entry per annotated 3’ UTR. Each entry contains the following columns:  chromosome, start, end, name, length, strand, conversionRate, readsCPM, Tcontent, coverageOnTs, conversionsOnTs, readCount, tcReadCount, and multimapCount.
Library strategy: SLAM-seq

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Kit (Zymo Research, Irvine, CA, USA)
Total RNA was isolated from cells following incubation with 4-Thiouridine (s4U; 300 uM). Subsequently, the 4-thiol groups in the s4Uracil-labeled transcripts were alkylated with iodoacetamide (IAA). QuantSeq 3’ mRNA-Seq (FWD) (Lexogen, Inc.) Illumina-compatible, indexed sequencing libraries were then prepared from the alkylated RNA samples (100 ng) according to the manufacturer’s protocol for oligo(dT)-primed first strand cDNA synthesis, random-primed second strand synthesis, and library amplification.

treatment_protocol: THP-1 and vIL-6/THP-1 cells were treated with either vehicle control, viral IL-6 (vIL-6), human IL-6 (hIL-6), transforming growth factor-B (TGF-B), or lipopolysaccharide (LPS). Additionally, sequential treatments of vIL-6 -> vIL-6 restimulation,  vIL-6 -> hIL-6 stimulation, and vIL-6 -> TGF-B stimulation were performed. Subsequently, the cells were incubated for an additional 1 hour in the presence of 4-Thiouridine (s4U; 300 uM) in order to label nascent transcripts. Following treatment, the cells were harvested for isolation of total RNA (containing s4Uracil-labeled transcripts) and followed by library preparation and next-generation sequencing (NGS).

value: vIL6 (100ng/ml, 2 weeks), then LPS (100 ng/ml, 6 hrs)

tag: labeling treatment

value: 4-Thiouridine (s4U; 300 uM) for 1 hour


title: HCT116 cells, Ribo_04h_rep1


title: THP-1_No_K27Ac_1

value: vIL-6 (100 ng/ml), 30 minutes


title: vIL6_LPS2


title: sc-Patch-seq,Red only,Regenerating CSMN32

description:
Patch-seq
NoRegen_CSMN_032


title: vIL6_LPS1


title: HCT116 cells, RNA_48h_rep2


title: sc-Patch-seq,Red only,Regenerating CSMN31

description:
Patch-seq
NoRegen_CSMN_031


title: 42H Homo sapiens LB Mock Patient6 Batch4

value: LB

value: Mock


title: 13H Homo sapiens LT HBV Patient2 Batch2


title: HCT116 cells, Ribo_48h_rep2


title: VIL6+3

value: vIL6 (100ng/ml, 2 weeks), then DMSO


title: sc-Patch-seq,Red only,Regenerating CSMN30

description:
Patch-seq
NoRegen_CSMN_030

value: Brain


title: sc-Patch-seq,Red only,Regenerating CSMN35

description:
Patch-seq
NoRegen_CSMN_035


title: 34H Homo sapiens LB Mock Patient5 Batch3


title: HCT116 cells, RNA_48h_rep1


title: VIL6+2


title: sc-Patch-seq,Red only,Regenerating CSMN29

description:
Patch-seq
NoRegen_CSMN_029


title: HCT116 cells, Ribo_48h_rep1


title: THP-1_No_BRD4_1

value: No treatment


title: VIL6+1


title: 26H Homo sapiens LB Mock Patient4 Batch4


title: vIL6-3

value: DMSO


title: sc-Patch-seq,Red only,Regenerating CSMN27

description:
Patch-seq
NoRegen_CSMN_027


title: sc-Patch-seq,Red only,Regenerating CSMN28

description:
Patch-seq
NoRegen_CSMN_028


title: 10H Homo sapiens LB Mock Patient2 Batch4


title: sc-Patch-seq,Red only,Regenerating CSMN26

description:
Patch-seq
NoRegen_CSMN_026


title: vIL6-2


title: 6H Homo sapiens LB HBV Patient1 Batch3

value: HBV


title: HCT116 cells, Ribo_24h_rep2


title: sc-Patch-seq,Red only,Regenerating CSMN25

description:
Patch-seq
NoRegen_CSMN_025


title: HCT116 cells, RNA_24h_rep1


title: vIL6-1


title: 46H Homo sapiens LB HBV Patient6 Batch4


title: LPS3

value: LPS (100 ng/ml), 6 hrs)


title: HCT116 cells, Ribo_24h_rep1


title: 38H Homo sapiens LB HBV Patient5 Batch3


title: HCT116 cells, RNA_16h_rep2


title: LPS2


title: sc-Patch-seq,Red only,Regenerating CSMN24

description:
Patch-seq
NoRegen_CSMN_024

value: PTEN SOCS3 tdTomato


title: 2H Homo sapiens LB Mock Patient1 Batch3


title: sc-Patch-seq,Red only,Regenerating CSMN23

description:
Patch-seq
NoRegen_CSMN_023


title: 30H Homo sapiens LB HBV Patient4 Batch4


title: 22H Homo sapiens LB HBV Patient3 Batch3


title: LPS1


title: sc-Patch-seq,Red only,Regenerating CSMN21

description:
Patch-seq
NoRegen_CSMN_021


title: HCT116 cells, RNA_16h_rep1


title: sc-Patch-seq,Red only,Regenerating CSMN22

description:
Patch-seq
NoRegen_CSMN_022


title: vIL-6_-rest_then_TGFb_restimulate_3

value: vIL6 (100ng/ml, 2 weeks), cytokine withdrawal (24 hrs), TGFb (100ng/ml, 30 minutes)


title: HCT116 cells, RNA_24h_rep2


title: vIL-6_-rest_then_TGFb_restimulate_2


title: 14H Homo sapiens LB HBV Patient2 Batch4


title: sc-Patch-seq,Red only,Regenerating CSMN20

description:
Patch-seq
NoRegen_CSMN_020

value: Cortical Spinal Motor Neuron


title: HCT116 cells, Ribo_16h_rep1


title: A549 cells, normoxia, TGFβ treatment, Day15, β-gal high, biol rep 3

city: Charlestown

first: Shyamala

last: Maheswaran

state: MA

address: 149 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Paired end reads were trimmed for quality using Trimmomatic (0.30) and aligned to the human genome (GRCh38) using TopHat2.
Raw gene read counts were calculated using HTSeq. Normalized counts were generated using DESeq2
Assembly: hg38
Supplementary files format and content: Comma separated table of full gene level transcriptome DESeq2 normalized counts

source_name: Lung

growth_protocol: Human lung cancer cell line, A549 was grown in Dulbeccco’s modified medium (DMEM).

extract_protocol:
RNA was isolated using RNeasy Mini kit (Qiagen) .
According to the manufacturer’s protocol, amplified cDNA was then generated using the SMARTer Ultra Ultra-Low-input RNA kit, version 4 (Clontech Laboratory) followed by Nextera® XT DNA Library Preparation kit (Illumina) for sample barcoding and fragmentation.

treatment_protocol: To induce senescence, A549 was treated with 5ng/ml TGFß under either normoxia (21% O2) or hypoxia (4% O2).

value: Lung

tag: stress

value: normoxia

value: TGFβ

tag: time


title: sc-Patch-seq,Red only,Regenerating CSMN19

description:
Patch-seq
NoRegen_CSMN_019

value: 22 weeks old


title: sc-Patch-seq,Red only,Regenerating CSMN18

description:
Patch-seq
NoRegen_CSMN_018


title: A549 cells, normoxia, TGFβ treatment, Day15, β-gal high, biol rep 1


title: vIL-6_-rest_then_TGFb_restimulate_1

value: monocyte

value: 4-Thiouridine (s4U; 300 uM) for 1 hour


title: A549 cells, normoxia, TGFβ treatment, Day15, β-gal high, biol rep 2


title: vIL-6_-rest_then_hIL-6_restimulate_3

value: vIL6 (100ng/ml, 2 weeks), cytokine withdrawal (24 hrs), hIL6 (100ng/ml, 30 minutes)


title: S-Evs, SUPM2 [SUPM2]

city: Padova

first: Stefania

last: Bortoluzzi

state: PD

address: Via U.Bassi 58/ B

department: Molecular Medicine

country: Italy

institute: University of Padova

description:
raw_data.txt.gz
normalized_data.txt.gz

data_processing:
Small RNAs were identified and quantified with miR&moRe2 v0.2.3
DESeq2 v1.24.0 was used to normalize read count data
Assembly: hg38
Supplementary files format and content: semicolon-delimited text files include raw read counts
Supplementary files format and content: semicolon-delimited text files include normalised read counts
Supplementary files format and content: semicolon-delimited text files include information of  the small RNAs newly predicted with respect to miRBase v22.1 annotation (sRNA name, miRNA precursor, strand, genomic position, nucleotide sequence, average normalised read counts)

source_name: Human cell line small extracellular vesicles

growth_protocol: Human ALCL cell lines Karpas 299 and SUP-M2 were maintained in RPMI 1640 medium (ThermoFisher Scientific, Waltham, MA), containing 15% heat-inactivated fetal bovine serum (FBS) (ThermoFisher Scientific), 2 mmol/l glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin (Merck Life Science, Darmstadt, Germany).

extract_protocol:
Circulating S-EVs RNA was obtained from 0.5 mL plasma by using the exoRNeasy Midi kit (Qiagen, Hilden, Germany), following the manufacturer’s instructions. Total RNA from ALCL primary tumors was obtained using Trizol reagent (ThermoFisher Scientific) according to the manufacturer’s protocol. Cultured cells were processed for RNA isolation using the total RNA Purification Kit (Norgen Biotek Corp., Thorold, Canada) as per the manufacturer’s protocol.
Small RNA-seq libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced single-end on an Illumina HiSeq 4000 platform (Illumina, San Diego, CA).


title: S-Evs, SUDHL1 [SUDHL1]

description:
raw_data.txt.gz
normalized_data.txt.gz

value: Human cell line small extracellular vesicles


title: S-Evs, SR786 [SR786]

description:
raw_data.txt.gz
normalized_data.txt.gz


title: vIL-6_-rest_then_hIL-6_restimulate_2


title: sc-Patch-seq,Red only,Regenerating CSMN16

description:
Patch-seq
NoRegen_CSMN_016


title: S-Evs, MAC2A [MAC2A]

description:
raw_data.txt.gz
normalized_data.txt.gz


title: vIL-6_-rest_then_hIL-6_restimulate_1


title: HCT116 cells, Ribo_16h_rep2


title: A549 cells, normoxia, TGFβ treatment, Day0, biol rep 2


title: vIL-6_-rest_then_vIL-6_restimulate_3

value: vIL6 (100ng/ml, 2 weeks), cytokine withdrawal (24 hrs), vIL6 (100ng/ml, 30 minutes)


title: A549 cells, normoxia, TGFβ treatment, Day0, biol rep 3


title: A549 cells, normoxia, TGFβ treatment, Day0, biol rep 1


title: Healthy donor, plasma S-EVs, 04 [CTR4]

description:
raw_data.txt.gz
normalized_data.txt.gz

source_name: plasma small extracellular vesicles

value: plasma small extracellular vesicles

tag: patient id


title: vIL-6_-rest_then_vIL-6_restimulate_2


title: A549 cells, hypoxia, TGFβ treatment, Day15, β-gal high, biol rep 3

value: hypoxia


title: Healthy donor, plasma S-EVs, 21 [CTR21]

description:
raw_data.txt.gz
normalized_data.txt.gz


title: sc-Patch-seq,Red only,Regenerating CSMN13

description:
Patch-seq
NoRegen_CSMN_013

value: Brain


title: vIL-6_-rest_then_vIL-6_restimulate_1


title: A549 cells, hypoxia, TGFβ treatment, Day15, β-gal high, biol rep 2


title: sc-Patch-seq,Red only,Regenerating CSMN17

description:
Patch-seq
NoRegen_CSMN_017


title: Healthy donor, plasma S-EVs, 16 [CTR16]

description:
raw_data.txt.gz
normalized_data.txt.gz


title: sc-Patch-seq,Red only,Regenerating CSMN12

description:
Patch-seq
NoRegen_CSMN_012


title: A549 cells, hypoxia, TGFβ treatment, Day15, β-gal high, biol rep 1


title: TGFb_2

value: TGFb (100ng/ml, 30 minutes)


title: sc-Patch-seq,Red only,Regenerating CSMN11

description:
Patch-seq
NoRegen_CSMN_011


title: Healthy donor, plasma S-EVs, 12 [CTR12]

description:
raw_data.txt.gz
normalized_data.txt.gz


title: TGFb_1


title: Healthy donor, plasma S-EVs, 11 [CTR11]

description:
raw_data.txt.gz
normalized_data.txt.gz


title: sc-Patch-seq,Red only,Regenerating CSMN15

description:
Patch-seq
NoRegen_CSMN_015


title: S-Evs, Karpas299 [Karpas299]

description:
raw_data.txt.gz
normalized_data.txt.gz

value: Karpas 299


title: TGFb_3


title: sc-Patch-seq,Red only,Regenerating CSMN9

description:
Patch-seq
NoRegen_CSMN_009

value: PTEN SOCS3 tdTomato


title: A549 cells, hypoxia, TGFβ treatment, Day0, biol rep 2


title: A549 cells, hypoxia, TGFβ treatment, Day0, biol rep 1


title: hIL-6_3

value: hIL6 (100ng/ml, 30 minutes)


title: sc-Patch-seq,Red only,Regenerating CSMN14

description:
Patch-seq
NoRegen_CSMN_014

value: Cortical Spinal Motor Neuron


title: sc-Patch-seq,Red only,Regenerating CSMN8

description:
Patch-seq
NoRegen_CSMN_008


title: ALCL, plasma S-EVs, relapsed, 05 [REC_exo5]

description:
raw_data.txt.gz
normalized_data.txt.gz

tag: followup

value: REL

tag: Sex

value: F


title: YAP5SA

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

library_source: transcriptomic single cell

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCh38 supplemented with sequences for tdTomato reporter and lentiviral BFP
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: iPSC-derived iAT2s transduced with YAP5SA lentivirus

growth_protocol: SPC2B2 iPSCs were differentiated into iAT2 cells and then transduced with lentivirus as a single cell suspension for 4 hours in polybrene. Cells were replated into 3D matrigel and grown in iAT2 media (CK + DCI) for 7 days.

extract_protocol:
Cells were dissociated to a single cell suspension using 0.05% trypsin and sorted for live cells using DRAQ7.
Single cells were captured for sequencing library preparation using a 10X Chromium (10X Genomics, Pleasanton, CA) instrument at the BUMC Single Cell Core. Single-cell RNA-seq libraries were prepared according to the Single Cell 3’ v2 Reagent Kits User Guide (10X Genomics). Sequence libraries were constructed using the Chromium Single-Cell 3’ Library Kit (10X Genomics). Sequencing libraries were loaded on a NextSeq500 (Illumina) to obtain a sequencing depth of~50K reads per cell. 3445 cells from WT YAP, 2539 cells from YAP5SA were captured and sequenced.

tag: lentivirus


title: hIL-6_1


title: sc-Patch-seq,Red only,Regenerating CSMN10

description:
Patch-seq
NoRegen_CSMN_010


title: ALCL, plasma S-EVs, relapsed, 06 [REC_exo6]

description:
raw_data.txt.gz
normalized_data.txt.gz

tag: batch


title: ALCL, plasma S-EVs, relapsed, 04 [REC_exo4]

description:
raw_data.txt.gz
normalized_data.txt.gz


title: hIL-6_2

tag: cell type


title: sc-Patch-seq,Red only,Regenerating CSMN7

description:
Patch-seq
NoRegen_CSMN_007

tag: tissue


title: ALCL, plasma S-EVs, relapsed, 03 [REC_exo3]

description:
raw_data.txt.gz
normalized_data.txt.gz

value: M


title: vIL-6_3

value: vIL6 (100ng/ml, 30 minutes)


title: A549 cells, hypoxia, TGFβ treatment, Day0, biol rep 3

value: Lung

value: TGFβ


title: sc-Patch-seq,Red only,Regenerating CSMN6

description:
Patch-seq
NoRegen_CSMN_006

tag: strain

value: 22 weeks old


title: vIL-6_2

value: monocyte

value: 4-Thiouridine (s4U; 300 uM) for 1 hour


title: sc-Patch-seq,Red only,Regenerating CSMN5

description:
Patch-seq
NoRegen_CSMN_005

tag: age


title: ALCL, plasma S-EVs, relapsed, 02 [REC_exo2]

description:
raw_data.txt.gz
normalized_data.txt.gz

value: plasma small extracellular vesicles


title: YAP5SA in CK+DCI

source_name: iPSC-derived iAT2s transduced with YAP5SA lentivirus grown in CKDCI medium in 3D

growth_protocol: SPC2B2 iPSCs were differentiated into iAT2 cells and either maintained in CKDCI medium, transduced with YAP5SA lentivirus, or grown in LDCI medium for 9 days.

extract_protocol:
Cells were dissociated to single cell using 0.05% trypsin and sorted for live cells using DRAQ7.
Single cells were captured for sequencing library preparation using a 10X Chromium (10X Genomics, Pleasanton, CA) instrument at the BUMC Single Cell Core. Single-cell RNA-seq libraries were prepared according to the Single Cell 3’ v2 Reagent Kits User Guide (10X Genomics). Sequence libraries were constructed using the Chromium Single-Cell 3’ Library Kit (10X Genomics). Sequencing libraries were loaded on a NextSeq500 (Illumina) to obtain a sequencing depth of~50K reads per cell. 623 iAT2s in CKDCI, 1212 cells from the YAP5SA in CKDCI condition and 1539 iAT1s in LDCI were captured and sequenced.

tag: media

value: CK DCI


title: ALCL, plasma S-EVs, relapsed, 01 [REC_exo1]

description:
raw_data.txt.gz
normalized_data.txt.gz


title: vIL-6_1

tag: cell line


title: ALCL, biopsy, realpsed, 06 [REC_bio6]

description:
raw_data.txt.gz
normalized_data.txt.gz

source_name: ALCL biopsy

value: ALCL biopsy

tag: rin


title: Control_3

value: DMSO


title: sc-Patch-seq,Red only,Regenerating CSMN3

description:
Patch-seq
NoRegen_CSMN_003

value: Brain


title: iAT1 ALI p1

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCh38 supplemented with sequences for GFP and tdTomato reporters
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: iPSC-derived iAT1 at ALI p1

growth_protocol: BU3 NGAT iPSCs were differentiated into iAT2s grown in 3D matrigel. They were then either maintained in iAT2 media (CKDCI) or differentiated into iAT1s in 3D (LDCI media). iAT2s were passaged as single cells and plated into 6.5mm transwell inserts in LDCI for p0 ALIs and iAT1s differentiated in 3D LDCI were passaged at single cells plated onto 6.5mm transwell inserts in LDCI for p1.

extract_protocol:
Cells were dissociated to single cell using 0.05% trypsin for 3D samples and Accutase for ALI samples. Each were sorted for live cells using DRAQ7.
Single cells were captured for sequencing library preparation using a 10X Chromium (10X Genomics, Pleasanton, CA) instrument at the BUMC Single Cell Core. Single-cell RNA-seq libraries were prepared according to the Single Cell 3’ v2 Reagent Kits User Guide (10X Genomics). Sequence libraries were constructed using the Chromium Single-Cell 3’ Library Kit (10X Genomics). Sequencing libraries were loaded on a NextSeq500 (Illumina) to obtain a sequencing depth of~50K reads per cell. 685 cells from CKDCI 3D, 1340 cells from LDCI 3D, 643 cells from LDCI ALI p0, and 1093 cells from LDCI ALI p1 were captured and sequenced.

value: LDCI

tag: culture

value: ALI


title: sc-Patch-seq,Red only,Regenerating CSMN2

description:
Patch-seq
NoRegen_CSMN_002

value: Cortical Spinal Motor Neuron

value: PTEN SOCS3 tdTomato


title: ALCL, biopsy, realpsed, 05 [REC_bio5]

description:
raw_data.txt.gz
normalized_data.txt.gz

value: REL

value: F


title: Control_2

tag: treatment


title: iAT1 ALI p0

source_name: iPSC-derived iAT1s at ALI p0


title: ALCL, biopsy, realpsed, 04 [REC_bio4]

description:
raw_data.txt.gz
normalized_data.txt.gz


title: Control_1

tag: labeling treatment


title: iAT1 3D

source_name: iPSC-derived iAT1s in 3D


title: WT-YAP

source_name: iPSC-derived iAT2s transduced with WTYAP lentivirus


title: ALCL, biopsy, realpsed, 03 [REC_bio3]

description:
raw_data.txt.gz
normalized_data.txt.gz

value: M


title: sc-Patch-seq,Green,Red,Regenerating CSMN123

description:
Patch-seq
Regen_CSMN_123


title: iAT2 3D

source_name: iPSC-derived iAT2s in 3D

value: CKDCI