title: vIL6_THP1_r219_2

data_processing:
RNA-Seq data was analyzed using a STAR-HTSeq pipeline. Raw sequence reads (FASTQ format) were mapped with STAR to the reference human genome assembly (GRCh38/hg38, GENCODE release 36) and human herpesvirus 8 strain JSC-1 clone BAC16, complete genome (GQ994935.1), and gene-level read counts were quantified with HTSeq (htseq-count).
Processed data are gene-level read counts generated from the output of STAR alignment and quantified with HTSeq (htseq-count) for each sample.
Assembly: GRCh38/hg38 + Human herpesvirus 8 strain JSC-1 clone BAC16, complete genome (GQ994935.1)
Supplementary files format and content: Individual files in tab-separated text format. Each file contains Ensembl ID (column 1), gene name (column 2), and gene-level counts (column 3) for each gene.

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Kit (Zymo Research, Irvine, CA, USA)
Indexed, stranded mRNA-seq libraries were prepared from total RNA (100 ng) using the KAPA Stranded mRNA-Seq (Roche) according to the manufacturer’s standard protocol.

treatment_protocol: THP-1 and vIL-6/THP-1 cells were either mock-infected or infected with r219.KSHV for 72 hours.

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

value: r219.KSHV infection


title: vIL6_THP1_r219_3

status: Public on Aug 08 2023

type: SRA

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

country: USA

institute: UC Davis School of Medicine

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

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.

tag: cell line

tag: cell type

value: monocyte

tag: treatment


title: ALCL, biopsy, realpsed, 02 [REC_bio2]

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: ALCL biopsy

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).

tag: tissue

value: ALCL biopsy

tag: followup

value: REL

tag: patient id

tag: batch

tag: Sex

value: M

tag: rin


title: vIL6_THP1_r219_1


title: ALCL, biopsy, realpsed, 01 [REC_bio1]

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


title: sc-Patch-seq,Red only,Regenerating CSMN4

city: Los Angeles

first: Hugo

middle: Jae Mun

last: Kim

address: 4760 Templeton St, Unit 3113

department: Neuroscience

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

description:
Patch-seq
NoRegen_CSMN_004

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

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.

value: Cortical Spinal Motor Neuron

value: Brain

tag: strain

value: PTEN SOCS3 tdTomato

tag: age

value: 22 weeks old


title: ALCL, plasma S-EVs, complete remission, 14 [CR_exo14]

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

source_name: plasma small extracellular vesicles

value: plasma small extracellular vesicles

value: NR


title: vIL6_THP1_3

value: mock infection


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

description:
Patch-seq
Regen_CSMN_120


title: HCT116 cells, WT + siGL biol rep 1

city: DALLAS

first: David

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Rd

department: Pharmacology

institute: UT Southwestern Medical Center

data_processing:
Followed nf-core/smrnaseq workflow with Illumina mirTrace protocol and minimum trimmed length of 17 nt. DESeq2 package was used for differential analysis.
Assembly: /project/MRL/MRL_Core/shared/analysis_MRL/references/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa
Supplementary files format and content: Alignment files (bam)

source_name: Large intestine; Colon

growth_protocol: HCT116, colorectal cancer, cells were maintained in McCoy's 5A Media supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Trizol whole cell RNA extraction
Illumina TruSeq Small RNA library preparation kits with 1ug of total RNA
Illumina small-RNA-Seq with 3'adapter TGGAATTCTCGGGTGCCAAGG

value: Large intestine; Colon

value: epithelial

tag: genotype

value: WT siGL

tag: disease state

value: Carcinoma; Colorectal


title: HCT116 cells, WT + siGL biol rep 2


title: ALCL, plasma S-EVs, complete remission, 13 [CR_exo13]

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


title: vIL6_THP1_2

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


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

description:
Patch-seq
Regen_CSMN_119


title: ALCL, plasma S-EVs, complete remission, 12 [CR_exo12]

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


title: vIL6_THP1_1


title: HCT116 cells, WT + siTNRC6C biol rep 2

value: WT siTNRC6C


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

description:
Patch-seq
Regen_CSMN_118


title: sc-Patch-seq,Red only,Regenerating CSMN1

description:
Patch-seq
NoRegen_CSMN_001


title: LoS_r219_3

value: monocyte

value: No treatment

value: r219.KSHV infection


title: ALCL, plasma S-EVs, complete remission, 11 [CR_exo11]

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

value: M


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

description:
Patch-seq
Regen_CSMN_117

value: Cortical Spinal Motor Neuron


title: HCT116 cells, WT + siTNRC6C biol rep 1


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

description:
Patch-seq
Regen_CSMN_122

value: Brain


title: HCT116 cells, WT + siGL biol rep 3


title: ALCL, plasma S-EVs, complete remission, 10 [CR_exo10]

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

value: F


title: LoS_r219_2


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

description:
Patch-seq
Regen_CSMN_116

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: LoS_r219_1


title: HCT116 cells, DROSHA KO biol rep 3

value: DROSHA-/-


title: HCT116 cells, DROSHA KO biol rep 2


title: ALCL, plasma S-EVs, complete remission, 09 [CR_exo9]

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

value: plasma small extracellular vesicles

value: NR


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

description:
Patch-seq
Regen_CSMN_115


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

description:
Patch-seq
Regen_CSMN_121


title: LoS_3

value: mock infection


title: ALCL, plasma S-EVs, complete remission, 08 [CR_exo8]

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


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

description:
Patch-seq
Regen_CSMN_114


title: HCT116 cells, DROSHA KO biol rep 1

value: Large intestine; Colon

value: epithelial


title: HCT116 cells, WT + siTNRC6C biol rep 3

value: Carcinoma; Colorectal


title: ALCL, plasma S-EVs, complete remission, 07 [CR_exo7]

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


title: HCT116 cells, TNRC6A/B KO + siGL biol rep 3

value: TNRC6A-/-, TNRC6B-/-, siGL


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

description:
Patch-seq
Regen_CSMN_113


title: LoS_1

value: monocyte


title: LoS_2

value: No treatment


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

description:
Patch-seq
Regen_CSMN_112


title: ALCL, plasma S-EVs, complete remission, 05 [CR_exo5]

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


title: ALCL, plasma S-EVs, complete remission, 06 [CR_exo6]

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


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

description:
Patch-seq
Regen_CSMN_111


title: HCT116 cells, TNRC6A/B KO + siGL biol rep 1


title: Meningioma in Sporadic patient [Sporadic.14]

city: Bunkyo-ku

first: Satoru

last: Miyawaki

state: Tokyo

country: Japan

institute: The University of Tokyo

data_processing:
Trimmomatic was used for removing adaptor sequence and low-quality sequence.
HISAT2 was used for read alignment.
StringTie was used for expression count.
All transcripts with a variance of FPKM values across the samples of less than one were excluded.
Assembly: NCBI38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: tumor

extract_protocol:
miRNeasy Mini Kit (Qiagen, Tokyo, Japan)
a TruSeq Stranded mRNA Library Prep (Illumina)
The libraries were constructed using 400 ng of total RNA, polyA+ RNA isolation, cDNA synthesis, end repair, A-base attachment and ligation of Illumina's (San Diego, CA, USA) indexed adapters were performed. The quality of the libraries was assessed using an Agilent 2100 Bioanalyzer.

value: tumor

tag: group

value: Meningioma in Sporadic patient

value: Female


title: Meningioma in Sporadic patient [Sporadic.13]

value: Male


title: HCT116 cells, TNRC6A/B KO + siGL biol rep 2


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

description:
Patch-seq
Regen_CSMN_110

value: Cortical Spinal Motor Neuron

value: Brain


title: HCT116 cells, TNRC6A/B KO + siTNRC6C biol rep 3

value: TNRC6A-/-, TNRC6B-/-, siTNRC6C


title: ALCL, plasma S-EVs, complete remission, 04 [CR_exo4]

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

value: M


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

description:
Patch-seq
Regen_CSMN_109

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: HCT116 cells, TNRC6A/B KO + siTNRC6C biol rep 2


title: Meningioma in Sporadic patient [Sporadic.11]


title: ALCL, plasma S-EVs, complete remission, 03 [CR_exo3]

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

value: plasma small extracellular vesicles

value: NR


title: ALCL, plasma S-EVs, complete remission, 02 [CR_exo2]

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


title: Meningioma in Sporadic patient [Sporadic.10]


title: ALCL, plasma S-EVs, complete remission, 01 [CR_exo1]

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


title: ALCL, biopsy, complete remission, 14 [CR_bio14]

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

value: ALCL biopsy


title: Meningioma in Sporadic patient [Sporadic.8]


title: HCT116 cells, TNRC6A/B KO biol rep 3

value: Large intestine; Colon

value: epithelial

value: TNRC6A-/-, TNRC6B-/-

value: Carcinoma; Colorectal


title: HCT116 cells, TNRC6A/B KO + siTNRC6C biol rep 1


title: HCT116 cells, TNRC6A/B KO biol rep 2


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

description:
Patch-seq
Regen_CSMN_106


title: ALCL, biopsy, complete remission, 13 [CR_bio13]

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


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

description:
Patch-seq
Regen_CSMN_105


title: ALCL, biopsy, complete remission, 12 [CR_bio12]

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


title: HCT116 cells, AGO1/2/3 KO biol rep 3


title: Meningioma in Sporadic patient [Sporadic.12]

value: tumor


title: ALCL, biopsy, complete remission, 11 [CR_bio11]

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


title: Meningioma in Sporadic patient [Sporadic.6]

value: Meningioma in Sporadic patient


title: Meningioma in Sporadic patient [Sporadic.5]


title: HCT116 cells, AGO1/2/3 KO biol rep 2


title: Meningioma in Sporadic patient [Sporadic.7]

value: Female


title: HCT116 cells, AGO1/2/3 KO biol rep 1


title: Meningioma in Sporadic patient [Sporadic.4]


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

description:
Patch-seq
Regen_CSMN_108


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

description:
Patch-seq
Regen_CSMN_102


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

description:
Patch-seq
Regen_CSMN_107


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

description:
Patch-seq
Regen_CSMN_101


title: ALCL, biopsy, complete remission, 08 [CR_bio8]

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

value: F


title: Meningioma in Sporadic patient [Sporadic.3]


title: Meningioma in Sporadic patient [Sporadic.9]


title: Meningioma in Sporadic patient [Sporadic.2]


title: ALCL, biopsy, complete remission, 10 [CR_bio10]

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


title: HCT116 cells, TNRC6A/B KO biol rep 1


title: HCT116 cells, AGO1/2 KO biol rep 2


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

description:
Patch-seq
Regen_CSMN_099

value: Cortical Spinal Motor Neuron


title: ALCL, biopsy, complete remission, 07 [CR_bio7]

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


title: HCT116 cells, AGO1/2 KO biol rep 1


title: HCT116 cells, AGO1/2 KO biol rep 3


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

description:
Patch-seq
Regen_CSMN_104

value: Brain


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

description:
Patch-seq
Regen_CSMN_103


title: ALCL, biopsy, complete remission, 06 [CR_bio6]

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


title: Meningioma in Sporadic patient [Sporadic]


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

description:
Patch-seq
Regen_CSMN_098


title: HCT116 cells, AGO2 KO biol rep 3


title: ALCL, biopsy, complete remission, 05 [CR_bio5]

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


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

description:
Patch-seq
Regen_CSMN_097


title: ALCL, biopsy, complete remission, 09 [CR_bio9]

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


title: HCT116 cells, AGO2 KO biol rep 2


title: Meningioma in NF2 patient [NF2.12]

value: Meningioma in NF2 patient


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

description:
Patch-seq
Regen_CSMN_096


title: ALCL, biopsy, complete remission, 04 [CR_bio4]

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

value: M


title: HCT116 cells, AGO2 KO biol rep 1


title: ALCL, biopsy, complete remission, 03 [CR_bio3]

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


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

description:
Patch-seq
Regen_CSMN_100

value: PTEN SOCS3 tdTomato


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

description:
Patch-seq
Regen_CSMN_095

value: 22 weeks old


title: HCT116 cells, AGO1 KO biol rep 3


title: ALCL, biopsy, complete remission, 02 [CR_bio2]

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


title: Meningioma in Sporadic patient [Sporadic.1]

value: Male


title: Meningioma in NF2 patient [NF2.10]


title: HCT116 cells, AGO1 KO biol rep 2


title: HCT116 cells, AGO1 KO biol rep 1


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

description:
Patch-seq
Regen_CSMN_094


title: Meningioma in NF2 patient [NF2.11]


title: ALCL, biopsy, complete remission, 01 [CR_bio1]

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

value: NR


title: Meningioma in NF2 patient [NF2.9]


title: Donor 3 Vor

city: Chapel Hill

first: Edward

middle: Patrick

last: Browne

state: NC

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

data_processing:
sequencing quality reports generated with fastQC v 0.11. Sequencing adapters were trimmed from 3’ ends of reads using cutadapt v2.9. FASTX toolkit v0.0.14 was used to identify high-quality reads with options -q 20 -p 90.
Reads were aligned to the GRCh38 human genome using STAR v2.7.7a with options: --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --outFilterMismatchNmax 2 --alignIntronMax 1000000 --alignIntronMin 20 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --outSAMtype BAM Unsorted --outFilterType BySJout --outFilterScoreMin 1 --outFilterMultimapNmax 1
Expression of genes was quantified from the GENCODE v38 comprehensive gene annotation set restricted to reference chromosomes (gencode.v38.annotation.gtf.gz) using htseq-count v0.6.17 with options -f bam -r name -s no -a 10 -t exon -i gene_id -m intersection-nonempty.
Differential expression testing was accomplished in R using DESeq2 v1.34.0
A custom HIV reference genome containing the HIV-dGFP/Thy1.2 sequence was constructed using STAR v2.7.7a using the genomeGenerate command. RNAseq reads were then aligned to the HIV genome using STAR v2.7.7a with the option --genomeSAindexNbases 5 to account for the small reference genome size.
Assembly: GRCh38
Supplementary files format and content: Raw gene count matrix from all 6 samples generated by htseq
Supplementary files format and content: Differentially expressed genes in Vorinostat treated samples with summary statistics of fold-enrichment and p-values relative to DMSO control. Generated in DESEQ2

source_name: isolated CD4 T cells from peripheral blood

growth_protocol: Cells grown in RPMI supplemented with 10% FCS, L-Glutamine, HEPES, PenStrep, and Sodium Pyruvate. Media supplemented with 100U/mL recombinant IL2 and 1ng/mL recombinant IL7

extract_protocol:
RNA was extracted from 10^5 CD4 T cells using the RNeasy kit (Qiagen #)
cDNA synthesis was accomplished using the SMART-HTv4 (Takara, #634888) involving cDNA synthesis and cDNA amplification (7 cycles) using a template-switching oligo. Illumina sequencing libraries were prepared using the Illumina Nextera XT kit (Illumina #FC-131-1024) involving tagmentation and indexing PCR of cDNA.
The six libraries were constructed using a dual-index strategy and pooled at an equimolar ratio

treatment_protocol: Media containing 500nM Vorinostat or 1:1000 DMSO was replenished three times weekly for 21 days.

tag: drug treatment

value: Vorinostat 500nM


title: Meningioma in NF2 patient [NF2.13]


title: HCT116 cells, WT biol rep 3

value: Large intestine; Colon

value: WT


title: Meningioma in NF2 patient [NF2.8]


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

description:
Patch-seq
Regen_CSMN_091


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

description:
Patch-seq
Regen_CSMN_092


title: HCT116 cells, WT biol rep 2

value: epithelial


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

description:
Patch-seq
Regen_CSMN_090


title: HCT116 cells, WT biol rep 1

value: Carcinoma; Colorectal


title: Meningioma in NF2 patient [NF2.7]

value: tumor


title: Meningioma in NF2 patient [NF2.6]


title: Donor 1 Vor

value: isolated CD4 T cells from peripheral blood


title: Donor 3 DMSO


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

description:
Patch-seq
Regen_CSMN_089


title: HCT116 cells, PAN_WT biol rep 3

address: 6001 Forest Park Road

institute: UT-Southwestern Medical Center at Dallas

data_processing:
Briefly, raw sequencing reads were adapter-trimmed (cutadapt 1.16) and then mapped to hg38 using bowtie-1.1.2. miRNA annotation and quantification was carried out with miRge 2.0 using default settings.
Assembly: GRCh38

extract_protocol:
Trizol whole cell RNA extraction was used for non-immunoprecipitation experiments. Whole cell extract was used for immunoprecipitation experiments with different antibodies.
Illumina TruSeq Small RNA library preparation kits with 1ug of total RNA or immunoprecipitated RNA

tag: antibody


title: Meningioma in NF2 patient [NF2.5]

value: Female


title: Donor 2 DMSO


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

description:
Patch-seq
Regen_CSMN_088


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

description:
Patch-seq
Regen_CSMN_093


title: Donor 1 DMSO


title: Meningioma in NF2 patient [NF2.4]


title: Meningioma in NF2 patient [NF2.3]


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

description:
Patch-seq
Regen_CSMN_086


title: Meningioma in NF2 patient [NF2.2]


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

description:
Patch-seq
Regen_CSMN_087


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

description:
Patch-seq
Regen_CSMN_085


title: HCT116 cells, PAN_WT biol rep 1


title: HCT116 cells, PAN_3KO biol rep 3


title: HCT116 cells, PAN_WT biol rep 2


title: Donor 2 Vor


title: Meningioma in NF2 patient [NF2.1]


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

description:
Patch-seq
Regen_CSMN_084


title: HCT116 cells, PAN_3KO biol rep 1


title: Meningioma in NF2 patient [NF2]


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

description:
Patch-seq
Regen_CSMN_083


title: HCT116 cells, PAN_3KO biol rep 2


title: healthy human brain, IgG

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

library_source: genomic

data_processing:
library strategy: CUT&RUN
Raw reads were trimmed using Trimmomatic (0.39). Further barcode trimming was performed using the Kseq trimmer. Trimmed reads were aligned to the human genome (hg19) using the BWA aligner
Assembly: hg19
Supplementary files format and content: Aligned deduplicated and normalized bigwig files

molecule: genomic DNA

source_name: human brain

extract_protocol:
Frozen human brain tissue was thawed on ice and minced sharply into <1mm pieces. Next, 500 μl of chilled Nuclei EZ Lysis Buffer (Millipore Sigma, NUC-101, no. N3408) was added, and tissue was homogenized 10–20 times in a Dounce homogenizer. The homogenate was transferred to a 1.5-ml Eppendorf tube, and 1 ml of chilled Nuclei EZ Lysis Buffer was added. The homogenate was mixed gently with a wide-bore pipette and incubated for 5 min on ice. The homogenate was then filtered through a 70-μm mesh strainer and centrifuged at 500g for 5 min at 4 °C. Supernatant was removed, and nuclei were resuspended in 1.5 ml of Nuclei EZ Lysis Buffer and incubated for 5 min on ice. Nuclei were centrifuged at 500g for 5 min at 4 °C. After carefully removing the supernatant (pellet might be loose), nuclei were washed in wash buffer (1× PBS, 1.0% BSA and 0.2 U μl−1 of RNase Inhibitor). Nuclei were then centrifuged and resuspended in 1.4 ml of wash buffer for two additional washes. Nuclei were then filtered through a 40-μm mesh strainer. Intact nuclei were counted after counterstaining with Trypan blue in a standard cell counter.
The CUT&RUN Library Prep was performed using the Illumina NovaSeq 6000 Sequencing System at the University of Kansas Medical Center – Genomics Core (Kansas City, KS). Fragmented input and immunoprecipitated chromatin (5ng) was used to initiate the TruSeq ChIP Sample Prep Kit library preparation protocol with modifications for CUT&RUN sample input (Illumina Cat# IP-202-1012).

value: human brain

tag: chip antibody

value: IgG

value: healthy


title: HCT116 cells, PAN_2KO biol rep 3

tag: cell line


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

description:
Patch-seq
Regen_CSMN_081

tag: cell type

value: Cortical Spinal Motor Neuron

value: Brain


title: HCT116 cells, PAN_2KO biol rep 2


title: HCT116 cells, PAN_2KO biol rep 1


title: Alzheimer’s Disease, IgG

value: Alzheimer's Disease


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

description:
Patch-seq
Regen_CSMN_082

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: HCT116 cells, IN_WT biol rep 3


title: Alzheimer’s Disease, antibody gH2AX, biol rep 3


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

description:
Patch-seq
Regen_CSMN_078


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

description:
Patch-seq
Regen_CSMN_080


title: HCT116 cells, IN_WT biol rep 1


title: CKD-e-3

city: 重庆

first: 浩然

last: 肖

state: other

address: 重庆市沙坪坝区高滩岩正街30号

country: China

institute: 学校

data_processing:
R package DESeq2 v1.28.1
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with |log2 (Fold Change) | > 1 & q value < 0.05 were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed gene sets were implemented by the top G (http://www.bioconductor.org/packages/release/bioc/html/topGO.html) and KOBAS(61)package, respectively.

organism: Rattus norvegicus

source_name: Aorta

growth_protocol: CKD rats performed a two-step subtotal nephrectomy (5/6 Nx) and a right single nephrectomy  one week after the left subtotal nephrectomy.

extract_protocol:
Calcification was accelerated by feeding the rats with a high-phosphorus diet (1.2% Pi) throughout the study.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Rats in ANCR/E7 group were treated with 10 mg/kg ANCR/E7-EXO through the tail vein every 5 days. The control group was treated with the same volume of normal saline for 13 weeks.

value: Aorta

tag: treatment

value: engineered exosomes


title: Alzheimer’s Disease, antibody gH2AX, biol rep 1

tag: tissue


title: Alzheimer’s Disease, antibody gH2AX, biol rep 2


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

description:
Patch-seq
Regen_CSMN_079


title: HCT116 cells, IN_WT biol rep 2

value: Large intestine; Colon


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

description:
Patch-seq
Regen_CSMN_076


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

description:
Patch-seq
Regen_CSMN_077


title: CKD-e-2

address: 重庆市沙坪坝区高滩岩正街30号


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

description:
Patch-seq
Regen_CSMN_075


title: HCT116 cells, IN_A2KO biol rep 3


title: HCT116 cells, IN_A2KO biol rep 1


title: healthy human brain, antibody gH2AX, biol rep 1


title: healthy human brain, antibody gH2AX, biol rep 2


title: CKD-e-1

address: 重庆市沙坪坝区高滩岩正街30号


title: HCT116 cells, IN_A2KO biol rep 2


title: CKD-C-3

address: 重庆市沙坪坝区高滩岩正街30号

value: saline


title: healthy human brain, antibody gH2AX, biol rep 3


title: 1263R-CV_S88

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 29 using STAR (v2.6.1d) and RSEM (v1.3.1).
Briefly, 100bp paired-end reads were trimmed and aligned to the GENCODE reference transcriptome using STAR and reads were quantified using HT-Seq. Gene counts were generated for each sample and collated into a singular matrix.
Assembly: GrCh38, GENCODE release 29
Supplementary files format and content: "Pheno.csv" contains sample metadata, "counts.csv" contains raw counts, "SummaryStats.csv" contains the number and percentages of reads mapped for each sample

molecule: polyA RNA

source_name: Colon Organoid

growth_protocol: Normal 3D colon organoids included in the study were developed from biopsies of proximal or distal colon using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates. Organoids were split five days prior to stem cell enrichment and nine days prior to harvest. Colon organoids were grown in complex medium for a period of five days, re-plenishing fresh media on day three. On day five, media was aspirated and 500µL/well of the CV media (10ml complex media; 10µL 5 mM CHIR99021 (Stemcell Technologies: 72054); 100µL 100 mM Valproic Acid (Stemcell Technologies: 72292)) was added to each well, as previously [12]. Following this, organoids were grown for four additional days.

extract_protocol:
For RNA isolation, media was gently removed and 300μl RNA lysis Solution RA1 + 6μl TCEP (Machery-Nagel; Cat No: 740902.50) was added to each well. The lysate was collected in a 1.5ml Eppendorf tube. Each tube was vortexed vigorously and placed on ice. Further steps were carried out according to manufacturer’s protocol of the Machel-Nagel RNA XS kit. RNA was checked for quality using the Agilent 4200 Tapestation. Samples with RIN > =8.5 were considered for library preparation and sequencing using the Illumina NovoSeq
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II). Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103).  All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area are failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized.  Successful libraries are normalized to 10nM for submission to sequencing.
Libraries were multiplexed and sequenced on Illumina Novaseq6000 to generate 100bp PE reads.

value: right colon

value: stem cell enriched colon organoid

tag: ancestry

value: African American

tag: smoking

value: Never


title: 1270R-CV_S83

value: Female

value: European American


title: CKD-C-2

address: 重庆市沙坪坝区高滩岩正街30号


title: HCT116 cells, IN_A1KO biol rep 3

value: epithelial

value: Carcinoma; Colorectal


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

description:
Patch-seq
Regen_CSMN_074

value: Cortical Spinal Motor Neuron


title: 1252R-CV_S60

value: Former/Current


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

description:
Patch-seq
Regen_CSMN_071

value: Brain


title: 1246R-CV_S48


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

description:
Patch-seq
Regen_CSMN_073

value: PTEN SOCS3 tdTomato


title: 1268R-CV_S72


title: HCT116 cells, IN_A1KO biol rep 2


title: CterTg_Il1b3_S12

city: Chicago

first: Valentin

last: David

state: Illinois

address: 320 E Superior Street

department: Medicine

institute: Northwestern University

data_processing:
StrandNGS 4.0 was used for alignment and differential expression
Sequenced reads were trimmed for adaptor sequence,  masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Strand NGS 4.0
Assembly: mm10
Annotation: UCSC Transcripts (2018.02.25)
Reads were filtered using the Filter by Read Metrics filter with the following parameters: Quality threshold >= 20; N's allowed in read <= 0; Number of multiple matches allowed <= 1; Removed non-primary multiply mapped reads; Removed reads that are failing vendor's QC.
Strand specific reads: false
Max EM Iterations: 1000
Convergence criterion for EM: 0.001
Normalization Type = Deseq
Threshold for normalization = 1
Baseline type =  median of all samples
Supplementary files format and content: Matrix table with raw and normalized gene counts for every gene and every sample and differential group expression

source_name: CterTg mice injected with 250 ng/g IL-1B 6 hours prior to collection

extract_protocol:
We isolated total RNA from  bone using TRI reagent (Waltham, MA, USA) and purified RNA using RNeasy kit (Qiagen, Germantown, MD, USA) and submitted 1 µg of total RNA for sequencing.
Libraries were prepared according to Illumina's instructions, i.e, total RNA library for each individual sample was prepared using the TruSeq Total RNA-Seq Library Preparation Kit (Illumina, San Diego, CA), and the bar-coded cDNA libraries were sequenced for 150 bp pair end reads using Illumina HiSeq 4000.

value: Liver

value: 6 week-old mice

value: CterTg


title: HE, mRNA-derived cDNA

city: Philadelphia

first: Ken

last: Cadwell

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania Perelman School of Medicine

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

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Bone Marrow

extract_protocol:
BM hematopoietic cells were harvested from 4 mock-treated and 4 CA colonized mice. After RBCs were lysed,  cells from individual mouse were Hash-tagged and counted and checked for viability using a hematocytometer. Cells from each mouse were equally pooled and 25,000 cells were loaded into a Chromium Controller (10X Genomics).
Library was prepared using Chromium Single Cell 3 3ʹ CellPlex Kit Set A (10x Genomics PN-1000261) according to manufacturer’s protocol and counted using a Bio-Rad TC20 automated cell counter. Single cells were then encapsulated into emulsion droplets using Chromium Controller (10x Genomics). scRNA-seq and cell multiplexing libraries were constructed using Chromium Single Cell 3′ v3.1 Reagent Kit and 3’ Feature Barcode Kit (PN-1000268 & 1000262 respectively) according to the manufacturer’s protocol.
CITE-seq library: Amplified cDNA was evaluated on a Agilent BioAnalyzer 2100 using a High Sensitivity DNA Kit (Agilent Technologies) and final libraries on a Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies) E1 well of the Dual Index Kit TT Set A 5’-TTATTCGAGG-3’  primer as i7 primer and a 5’-AGCAGGACAG-3 as 5i  primer(Illumina).
HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with the Dual Index Kit NN Set A with F4 well 5’-AACACCTCTC-3’ primer as i7 primer (Illumina) with  5’-TCATACAATC-3’  as the i5 primer.
Following the final bead purification, individual libraries were diluted to 2nM and pooled for sequencing. Pools were sequenced with 100 cycle run kits (28bp Read1, 8bp Index1 and 91bp Read2) on the NovaSeq 6000 Sequencing System (Illumina)

treatment_protocol: PBS or CA

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: mRNA


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

description:
Patch-seq
Regen_CSMN_070

value: 22 weeks old


title: CterTg_Il1b2_S11

value: injected with 250 ng/g IL-1B 6 hours prior to collection


title: HCT116 cells, IN_A1KO biol rep 1

value: Large intestine; Colon


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

description:
Patch-seq
Regen_CSMN_072


title: HCT116 cells, IN_3KO biol rep 3


title: HCT116 cells, IN_3KO biol rep 2


title: 1239R-CV_S37

value: right colon

value: stem cell enriched colon organoid

value: Male

value: Never


title: CterTg_Il1b1_S10


title: 1229R-CV_S8

value: Female

value: African American


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

description:
Patch-seq
Regen_CSMN_068

value: Cortical Spinal Motor Neuron

value: Brain


title: HCT116 cells, IN_2KO biol rep 3

value: epithelial

value: Carcinoma; Colorectal


title: HCT116 cells,IN_3KO biol rep 1


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

description:
Patch-seq
Regen_CSMN_069

value: PTEN SOCS3 tdTomato


title: CKD-C-1

address: 重庆市沙坪坝区高滩岩正街30号

value: Aorta

value: saline


title: WT_Il1b3_S9

source_name: WT mice injected with 250 ng/g IL-1B 6 hours prior to collection

value: Liver

value: 6 week-old mice

value: WT


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

description:
Patch-seq
Regen_CSMN_067

value: 22 weeks old


title: HCT116 cells, IN_2KO biol rep 2

value: Large intestine; Colon


title: 1148R-CV_S20

value: right colon

value: stem cell enriched colon organoid

value: Former/Current


title: WT_Il1b2_S8

value: injected with 250 ng/g IL-1B 6 hours prior to collection


title: HE, HTO-derived cDNA

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

library_source: other

molecule: protein

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: HTO

value: Anti CD45 + Anti MHC classI :WT_PBS_1/TotalSeq-A0305 ; WT_PBS_2/TotalSeq-A0306 ; WT_PBS_3/TotalSeq-A0307 ; WT_PBS_4/TotalSeq-A0308 ;WT_CA_5/TotalSeq-A0309; WT_CA_6/TotalSeq-A0310; WT_CA_7/TotalSeq-A0311; WT_CA_8/TotalSeq-A0312


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

description:
Patch-seq
Regen_CSMN_066

value: Cortical Spinal Motor Neuron

value: Brain


title: HCT116 cells, IN_2KO biol rep 1

value: epithelial

value: Carcinoma; Colorectal


title: HCT116 cells, TNRC6B KO biol rep 3


title: WT_Il1b1_S7

value: Liver


title: 1121R-CV_S15

value: Female

value: European American

value: Never


title: CterTg_Ctr3_S6

source_name: CterTg mice injected with saline 6 hours prior to collection

value: 6 week-old mice

value: CterTg


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

description:
Patch-seq
Regen_CSMN_064

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: HCT116 cells,TNRC6B KO biol rep 2

value: Large intestine; Colon


title: CterTg_Ctr2_S5

value: injected with saline 6 hours prior to collection


title: 1112R-CV_S53

value: right colon

value: stem cell enriched colon organoid

value: African American


title: 1099R-CV_S3


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

description:
Patch-seq
Regen_CSMN_063

value: Cortical Spinal Motor Neuron


title: HCT116 cells, TNRC6B KO biol rep 1


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

description:
Patch-seq
Regen_CSMN_062

value: Brain


title: CterTg_Ctr1_S4


title: 1096R-CV_S42

value: Male


title: 1081R-CV_S30


title: HCT116 cells, TNRC6A/B KO biol rep 3

value: epithelial

value: TNRC6A-/-, TNRC6B-/-

value: Carcinoma; Colorectal


title: 1176R-CV_S25

value: European American


title: WT_Ctr3_S3

source_name: WT mice injected with saline 6 hours prior to collection

value: Liver

value: WT


title: HCT116 cells, TNRC6A/B KO biol rep 2


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

description:
Patch-seq
Regen_CSMN_061


title: 1055R-CV_S65

value: Female

value: Never


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

description:
Patch-seq
Regen_CSMN_060

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: WT_Ctr2_S2

value: 6 week-old mice

value: injected with saline 6 hours prior to collection


title: D503 GEX library 16

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

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: mRNA

tag: antibodies/tags


title: WT_Ctr1_S1


title: HCT116 cells, TNRC6A/B KO biol rep 1

value: Large intestine; Colon


title: HCT116 cells, TNRC6A KO biol rep 3


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

description:
Patch-seq
Regen_CSMN_059

value: Cortical Spinal Motor Neuron

value: Brain


title: D503 GEX library 15


title: HCT116 cells, TNRC6A KO biol rep 2

value: epithelial


title: HCT116 cells, TNRC6A KO biol rep 1

value: Carcinoma; Colorectal


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

description:
Patch-seq
Regen_CSMN_057


title: ECs_Mac_Intact_Replicate_2

first: Connor

last: Lantz

state: IL

address: 303 E. Chicago Ave. Ward 4-075

data_processing:
Adapters were trimmed from reads using cutadapt
Trimmed reads were aligned using STAR
Gene counting was performed using htseq-count
Differential expression was performed using DESeq2
Assembly: mm10

source_name: Colon Laina Propria

extract_protocol:
ECs were FACS-sorted from digested, LPS-stimulated colon mucosa with and without macrophage depletion by gating on CD45-/Live1-/CD31+ cells. Total mRNA was extracted from sorted ECs using RNeasy Plus Mini Kit (Qiagen), followed by quantification with Qubit and RIN quality assessment by 2100 Agilent Bioanalyzer (Agilent Technologies, Santa Clara. CA).
Low-input total cDNA library construction and Illumina sequencing: RNA-seq was conducted at the NUSeq Core Facility using a Illumina HiSeq 4000 NGS System (Illumina, San Diego, CA) to generate 50 bp reads with 300 million paired-end reads and 25 million reads per sample.

value: Colon Laina Propria


title: D503 GEX library 14


title: D503 GEX library 13


title: HCT116 cells, 3148_WT biol rep 3


title: ECs_Mac_Depleted_Replicate_3

value: Macrophage-depletion


title: D503 GEX library 12


title: D503 GEX library 10


title: D503 GEX library 11


title: HCT116 cells, 3148_WT biol rep 1

value: WT


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

description:
Patch-seq
Regen_CSMN_054


title: HCT116 cells, 3148_WT biol rep 2


title: ECs_Mac_Depleted_Replicate_2


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

description:
Patch-seq
Regen_CSMN_053


title: HCT116 cells, 3148_A2KO biol rep 3


title: D503 GEX library 9


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

description:
Patch-seq
Regen_CSMN_052


title: ECs_Mac_Depleted_Replicate_1


title: D503 GEX library 8


title: HCT116 cells, 3148_A2KO biol rep 2


title: GMP-st3

city: Beijing

first: Tianxiao

last: Xu

address: 52 Fucheng Road, Haidian District, Beijing

institute: Peking University Cancer Hospital

data_processing:
An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production. Then the cDNA production was checked by Qubit® 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2kbp. Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation. After library preparation, PerkinElmer LabChip® GX Touch and Step OnePlusTM Real-Time PCR System were introduced for library quality inspection. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing. DEGseq was used for differential gene expression (DEGs) analysis between two groups with three biological replicates (fold change≥2). The P-value was adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 were considered differentially expressed.
Genome_build: mm9

source_name: bone marrow

extract_protocol: The single-cell samples were collected in tubes with lysis component and ribonuclease inhibitor, then the amplification was carried out by the Smart-Seq2 method.

value: STING agonist treatment


title: ECs_Mac_Intact_Replicate_3


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

description:
Patch-seq
Regen_CSMN_058


title: ECs_Mac_Intact_Replicate_1


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

description:
Patch-seq
Regen_CSMN_051


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

description:
Patch-seq
Regen_CSMN_056


title: HCT116 cells, 3148_A2KO biol rep 1


title: GMP-st1


title: D503 GEX library 7


title: HCT116 cells, 2A7_WT biol rep 3


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

description:
Patch-seq
Regen_CSMN_055


title: GMP-nc3

value: control


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

description:
Patch-seq
Regen_CSMN_049

value: PTEN SOCS3 tdTomato


title: D503 GEX library 6


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

description:
Patch-seq
Regen_CSMN_050

value: 22 weeks old


title: GMP-nc2


title: HCT116 cells, 2A7_WT biol rep 2


title: HCT116 cells, 2A7_WT biol rep 1


title: D503 GEX library 5


title: D503 GEX library 4


title: GMP-nc1


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

description:
Patch-seq
Regen_CSMN_048


title: GMP-st2


title: LSK-st3


title: HCT116 cells, 2A7_A1KO biol rep 3


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

description:
Patch-seq
Regen_CSMN_046


title: HCT116 cells, 2A7_A1KO biol rep 2


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

description:
Patch-seq
Regen_CSMN_047


title: D503 GEX library 3


title: LSK-st2


title: D503 GEX library 2


title: D503 GEX library 1


title: HCT116 cells, 2A7_A1KO biol rep 1


title: LSK-st1


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

description:
Patch-seq
Regen_CSMN_045


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

description:
Patch-seq
Regen_CSMN_044


title: D496 GEX library 16


title: LSK-nc3


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

description:
Patch-seq
Regen_CSMN_043


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

description:
Patch-seq
Regen_CSMN_042


title: Sample 18, mRNA derived cDNA

city: Lebanon

first: Min Kyung

last: Lee

state: NH

address: 1 Medical Center Dr

institute: Dartmouth College

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Sample18_barcodes.tsv
Sample18_genes.tsv
Sample18_matrix.mtx

library_source: transcriptomic single cell

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings and aligning to the hg38 premRNA genome build
Assembly: hg38 premrna
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Brain tissue

extract_protocol:
Nuclei from fresh frozen tissues were isolated following the Nuclei Pure Prep nuclei isolation kit (Sigma-Aldrich, Catalog ID: NUC201) with some modifications. To summarize, ~10mg of tissue were washed with PBS to remove extraneous OCT the samples were frozen in. The tissue was homogenized with both wide and narrow pestles submerged in 2.5mL of the lysis buffer in a Dounce homogenizer. The lysate mixed with 4.5mL 1.8M sucrose cushion were gently layered on top of the 2.5mL of 1.8M sucrose cushion in Beckman ultracentrifuge tubes. Samples were centrifuged for 45 min at 13,000 RPM at 4°C in an ultracentrifuge. Samples were multiplexed with lipid-tagged oligonucleotides following the MULTI-seq protocol19. Nuclei were resuspended in 1% BSA PBS and filtered with 70um and 40um Flowmi filters.
Library was performed according to the manufacter’s instructions (single cell 3’ protocol, 10x Genomics). Cellular mRNA and hashtag oligonucleotides were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ protocol (10x Genomics) and with specific primers amplifying the HTO-derived tags.

value: Brain tissue

tag: library


title: Sample 5, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Sample5_barcodes.tsv
Sample5_genes.tsv
Sample5_matrix.mtx


title: LSK-nc2

tag: strain


title: D496 GEX library 14


title: LSK-nc1


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

description:
Patch-seq
Regen_CSMN_041

source_name: Brain

tag: age


title: Sample 1, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Sample1_barcodes.tsv
Sample1_genes.tsv
Sample1_matrix.mtx


title: D496 GEX library 13


title: Pool 22, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool22_barcodes.tsv
Pool22_genes.tsv
Pool22_matrix.mtx

value: HTO


title: wt_LP6_S52456

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 and 3.3.52 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.3 and 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam 1.17 (http://wtsi-npg.github.io/illumina2bam/) and custom programmes based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.5.2b and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.9 package DESeq2 1.24.0, running under R 3.6.
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: sorted macrophages

extract_protocol:
Colon lamina propria macrophages (Cd45+, Ly6G-, SiglecF-, Cd24-, Cd11c+/-, Cd103-, Cd11b+, Ly6C-, Cd64+, MHCII+) and Cd44+ epithelial cells (Cd45-, EpCAM+, Cd44+) from Tsc2fl/fl and Tsc2Lyz2-cre mice were isolated as per manufacturer’s instructions (MACS Miltenyi Biotec, 130-097-410) and FACS sorted at the FACS Core Unit of the Children’s Cancer Research Institute (CCRI) of Vienna.
For the generation of full-length cDNA, the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) was used.
The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina).
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 50 bp single-read chemistry.

value: colon

tag: genotype

value: Tsc2fl/fl Lyz2+/+

tag: Sex

value: male


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

description:
Patch-seq
Regen_CSMN_040


title: D496 GEX library 12

value: various

value: mononuclear cells (MNCs)

value: mRNA


title: wt_LP4_S52454

value: female


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

description:
Patch-seq
Regen_CSMN_039

value: Cortical Spinal Motor Neuron

value: Brain


title: Pool 22, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool22_barcodes.tsv
Pool22_genes.tsv
Pool22_matrix.mtx


title: D496 GEX library 10


title: wt_LP2_S52452


title: wt_EC7_S52442

source_name: sorted epithelial cells

value: EpCam+, CD44 high


title: D496 GEX library 15


title: D496 GEX library 11


title: Sample 3, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Sample3_barcodes.tsv
Sample3_genes.tsv
Sample3_matrix.mtx


title: Pool 21, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool21_barcodes.tsv
Pool21_genes.tsv
Pool21_matrix.mtx


title: Pool 21, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool21_barcodes.tsv
Pool21_genes.tsv
Pool21_matrix.mtx


title: D496 GEX library 9


title: D496 GEX library 8


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

description:
Patch-seq
Regen_CSMN_036


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

description:
Patch-seq
Regen_CSMN_035


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

description:
Patch-seq
Regen_CSMN_037


title: Pool 20, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool20_barcodes.tsv
Pool20_genes.tsv
Pool20_matrix.mtx


title: wt_EC4_S52450


title: wt_EC2_S52448


title: Pool 19, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool19_barcodes.tsv
Pool19_genes.tsv
Pool19_matrix.mtx


title: Pool 20, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool20_barcodes.tsv
Pool20_genes.tsv
Pool20_matrix.mtx


title: D496 GEX library 5


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

description:
Patch-seq
Regen_CSMN_034


title: D496 GEX library 6


title: Pool 18, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool18_barcodes.tsv
Pool18_genes.tsv
Pool18_matrix.mtx


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

description:
Patch-seq
Regen_CSMN_033


title: Pool 19, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool19_barcodes.tsv
Pool19_genes.tsv
Pool19_matrix.mtx


title: D496 GEX library 3


title: cre_LP8_S52458

value: Tsc2fl/fl Lyz2cre/+


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

description:
Patch-seq
Regen_CSMN_038


title: cre_LP10_S52446


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

description:
Patch-seq
Regen_CSMN_031


title: D496 GEX library 4


title: cre_EC9_S52433


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

description:
Patch-seq
Regen_CSMN_032


title: D496 GEX library 2


title: cre_EC8_S52443


title: wt_EC6_S52440


title: Pool 15, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool15_barcodes.tsv
Pool15_genes.tsv
Pool15_matrix.mtx


title: Pool 15, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool15_barcodes.tsv
Pool15_genes.tsv
Pool15_matrix.mtx


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

description:
Patch-seq
Regen_CSMN_030


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

description:
Patch-seq
Regen_CSMN_029


title: D496 GEX library 1

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


title: D496 GEX library 7

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


title: cre_EC5_S52438


title: cre_EC10_S52434


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

description:
Patch-seq
Regen_CSMN_028


title: cre_LP9_S52444


title: Pool 13, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool13_barcodes.tsv
Pool13_genes.tsv
Pool13_matrix.mtx


title: Pool 18, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool18_barcodes.tsv
Pool18_genes.tsv
Pool18_matrix.mtx


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

description:
Patch-seq
Regen_CSMN_026


title: Pancreatic differentiation 2D

city: Indianapolis

last: Arkenberg

state: IN

address: 980 W Walnut St

department: Otolaryngology - Head and Neck Surgery

institute: Indiana University School of Medicine

description: 10x Genomics

data_processing:
Raw data was processed using the Cell Ranger pipeline. Cell ranger mkfastq was used to generate fastq files from demultiplex raw base sequence calls.
Fastq files were aligned to human reference genome GRCh38 with RNAseq aligner STAR. Following, aligned reads were traced back to individual cells and gene expression was quantified based on the unique molecular indices( UMIs).
The filtered gene-barcode matrices were used for downstream analysis.
Assembly: GRCh38/hg38

growth_protocol: For 2D samples, Cellartis hiPSC12 cell line (ChiPSC12, Takara) were cultured on vitronectin (VTN)-coated tissue plates in Essential 8TM (E8, Gibco) medium.The media was supplemented with 10 µM ROCK inhibitor, Y-27632 (E8Y, Adipogen) for the first 24 hours following thawing or passaging to prevent anoikis. Differentiation was conducted in a 6-well plate using a commercial pancreatic progenitor differentiation kit (STEMCELL Technologies) without modification. For 3D differentiation, cells were encapsulated in  gelatin-based hydrogels consisting of 5 wt% gelatin-norbornene (GelNB)  with 0.6 wt% PEG4SH and 2 mM LAP. Encapsulated cells were grown for 4 days in E8Y media prior to differentiation using the pancreatic progenitor differentiation kit.

extract_protocol:
For 2D samples, differentiated cells were dissociated using TrypLE Select (Gibco) for 10 minutes. For 3D samples, cell laden hydrogels were treated with 1 hour Type 1 collagenase treatment (50 U/mL), and cells were dissociated with TrypLE Select for 15 minutes. Following, the cells were washed to remove debris and filtered with 40 µm strainer. Cells were washed three additional times with DPBS with 2%BSA (1000 rpm x 3 minutes).
Approximately, 10,000 single cells were recovered, and cDNA libraries were generated utilizing the v3.1 Next GEM Single Cell 3’ reagent kit and a Chromium single cell system (10x Genomics) and sequenced on a NovaSeq 6000 sequencer (Illumina) at the Center for Medical Genomics at Indiana University School of Medicine.

value: induced pluripotent stem cell

value: Pancreatic progenitor differentiation


title: tomato_24h_sh_2

city: Cold Spring Harbor

first: Ullas

middle: V.

last: Pedmale

address: 1 Bungtown RD

department: Pedmale

institute: Cold Spring Harbor Laboratory

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to either TAIR10 os ITAG4.1 whole genome using star v2.7.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated with cufflinks v2.1.1.

organism: Solanum lycopersicum

source_name: shaded root 24h

growth_protocol: Arabidopsis seedlings were grown in half-strength MS agar plates under constant white light for 5 days and subsequently kept in unshaded conditions or transfered to shade for the indicated time. Roots were harvested and immediately frozen in liquid nitrogen for RNA extraction. Tomato seedlings were grown in white light for 7 days under the same conditions and treatments described for Arabidopsis.

extract_protocol:
Arabidopsis total RNA was extracted with trizol-chloroform protocol. Tomato total RNA was extracted with a Promega ReliaPrep RNA miniprep System following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype/cultivar

value: root

value: shaded 24h


title: Pancreatic differentiation 3D GelNB

description: 10x Genomics


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

description:
Patch-seq
Regen_CSMN_027

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.

value: PTEN SOCS3 tdTomato

value: 22 weeks old


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

description:
Patch-seq
Regen_CSMN_025


title: tomato_24h_sh_1


title: Pool 12, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool12_barcodes.tsv
Pool12_genes.tsv
Pool12_matrix.mtx

value: Brain tissue


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

description:
Patch-seq
Regen_CSMN_024


title: tomato_12h_sh_2

source_name: shaded root 12h

value: shaded 12h


title: LEN05

city: Tsu city

first: Naoto

last: Fujiwara

state: Mie

address: 2-174 Edobashi

institute: Mie University

description: After lenvatinib treatment

data_processing:
Raw cDNA reads are aligned to the reference genome (hg19) using the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the gene levels. The count data were normalized using “Relative Log Expression” normalization (RLE) implemented in the DESeq2 R package. Poor-quality transcriptome profiles were determined based on inter-sample correlation <0.7 and excluded from the subsequent analyses.
Assembly: hg19
Supplementary files format and content: .gct file format (tab-delimited text) including normalized gene expression levels normalized within 15 tissues (LEN.gct).

source_name: Liver

extract_protocol:
Total RNA was extracted from human frozen HCC tissues by ISOGEN (NIPPON GENE).
RNA-seq library was prepared with the TruSeq Stranded mRNA Library Prep (Illumina) following manufacturer’s protocol. PolyA-tail-based RNA-seq.

value: Liver

tag: disease state

value: HCC

value: Lenvatinib


title: Pool 12, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool12_barcodes.tsv
Pool12_genes.tsv
Pool12_matrix.mtx

value: HTO


title: LEN03

description: After lenvatinib treatment


title: tomato_12h_sh_1


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

last: Kim

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

description:
Patch-seq
Regen_CSMN_023


title: Pool 13, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool13_barcodes.tsv
Pool13_genes.tsv
Pool13_matrix.mtx


title: Pool 11, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool11_barcodes.tsv
Pool11_genes.tsv
Pool11_matrix.mtx

value: mRNA


title: Pool 10, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool10_barcodes.tsv
Pool10_genes.tsv
Pool10_matrix.mtx


title: Pool 10, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool10_barcodes.tsv
Pool10_genes.tsv
Pool10_matrix.mtx


title: tomato_6h_sh_1

source_name: shaded root 6h

value: shaded 6h


title: tomato_6h_sh_2


title: CTR11

description: No preceding  treatment

value: Control


title: tomato_3h_sh_2

source_name: shaded root 3h

value: shaded 3h


title: LEN06

description: After lenvatinib treatment


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

description:
Patch-seq
Regen_CSMN_022

value: Cortical Spinal Motor Neuron

value: Brain


title: tomato_24h_wl_1

source_name: unshaded root 24h

value: unshaded 24h


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

description:
Patch-seq
Regen_CSMN_017


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

description:
Patch-seq
Regen_CSMN_019


title: CTR06

description: No preceding  treatment


title: Pool 9, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool9_barcodes.tsv
Pool9_genes.tsv
Pool9_matrix.mtx


title: CTR09

description: No preceding  treatment


title: tomato_12h_wl_2

source_name: unshaded root 12h

value: root

value: unshaded 12h


title: Pool 9, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool9_barcodes.tsv
Pool9_genes.tsv
Pool9_matrix.mtx


title: tomato_24h_wl_2


title: CTR10

description: No preceding  treatment


title: LEN02

description: After lenvatinib treatment


title: Pool 11, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool11_barcodes.tsv
Pool11_genes.tsv
Pool11_matrix.mtx


title: tomato_3h_sh_1


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

description:
Patch-seq
Regen_CSMN_016

value: PTEN SOCS3 tdTomato


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

description:
Patch-seq
Regen_CSMN_018

value: 22 weeks old


title: CTR08

description: No preceding  treatment


title: Pool 6, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool6_barcodes.tsv
Pool6_genes.tsv
Pool6_matrix.mtx

value: Brain tissue


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

description:
Patch-seq
Regen_CSMN_021


title: LEN01

description: After lenvatinib treatment


title: Pool 5, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool5_barcodes.tsv
Pool5_genes.tsv
Pool5_matrix.mtx


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

description:
Patch-seq
Regen_CSMN_020


title: tomato_12h_wl_1


title: CTR05

description: No preceding  treatment


title: CTR04

description: No preceding  treatment


title: Pool 5, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool5_barcodes.tsv
Pool5_genes.tsv
Pool5_matrix.mtx


title: Pool 4, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool4_barcodes.tsv
Pool4_genes.tsv
Pool4_matrix.mtx


title: CTR03

description: No preceding  treatment


title: tomato_6h_wl_1

source_name: unshaded root 6h

value: unshaded 6h


title: tomato_6h_wl_2


title: Pool 6, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool6_barcodes.tsv
Pool6_genes.tsv
Pool6_matrix.mtx


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

description:
Patch-seq
Regen_CSMN_014


title: CTR01

description: No preceding  treatment

value: Liver


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

description:
Patch-seq
Regen_CSMN_012


title: tomato_3h_wl_2

source_name: unshaded root 3h

value: unshaded 3h


title: Pool 3, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool3_barcodes.tsv
Pool3_genes.tsv
Pool3_matrix.mtx


title: CTR02

description: No preceding  treatment

value: HCC


title: Pool 4, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool4_barcodes.tsv
Pool4_genes.tsv
Pool4_matrix.mtx


title: Pool 3, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool3_barcodes.tsv
Pool3_genes.tsv
Pool3_matrix.mtx


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

description:
Patch-seq
Regen_CSMN_013


title: tomato_3h_wl_1


title: 4C Macaca fascicularis pDC Mock Patient1 Batch7

city: Lyon

first: Xavier

last: Grand

address: 46 allée d'Italie

country: France

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.

organism: Macaca fascicularis

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: sc-Patch-seq,Green,Red,Regenerating CSMN15

city: Los Angeles

first: Hugo

address: 4760 Templeton St, Unit 3113

description:
Patch-seq
Regen_CSMN_015


title: Pool 2, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool2_barcodes.tsv
Pool2_genes.tsv
Pool2_matrix.mtx

value: HTO


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

description:
Patch-seq
Regen_CSMN_010


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

description:
Patch-seq
Regen_CSMN_011


title: 44C Macaca fascicularis pDC Mock Patient6 Batch8


title: Colon, Delta, rep1

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Grch38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
Colonic biopsies were obtained from consented ulcerative colitis (UC) patients with Mayo endoscopic scores of 2-3 during routine screening. All procedures including biopsy collections and tissue processing were approval by the Northwestern University Institutional Review Board protocols (IRB). Biopsies were collected into DMEM media tubes, immediately transported to the lab, minced and digested by Liberase TH (0.1 WU/mL Sigma #5401135001) and DNase I (0.5U/mL, Roche #10104159001) in HBSS using 3 rounds of 10 min incubations (30 minutes total) at 37°C at 800rpm. The resulting cell suspensions were washed and passed through a 40mm strainer to ensure single cell separation. Following digest, cell viability was determined by Cellometer Auto 2000 Cell Viability Counter (Nexcelom Bioscience) at the NUseq Core. Prior to single-cell RNA sequencing, cell concentration was adjusted to by >100mL at 400 cells/ml) and cell viability of >70%.
10X Chromium 3' scRNA-seq; Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, single cells from colon biopsies 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.

value: Colon

value: Ulcerative colitis

value: Mayo endoscopic score 2-3


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

description:
Patch-seq
Regen_CSMN_009

value: Cortical Spinal Motor Neuron

value: Brain


title: Pool 2, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool2_barcodes.tsv
Pool2_genes.tsv
Pool2_matrix.mtx

value: mRNA


title: Colon, Beta, rep1

description: 10x Genomics


title: 36C Macaca fascicularis pDC Mock Patient5 Batch7


title: Pool 1, HTO derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Pool1_barcodes.tsv
Pool1_genes.tsv
Pool1_matrix.mtx


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

description:
Patch-seq
Regen_CSMN_008

value: PTEN SOCS3 tdTomato


title: 28C Macaca fascicularis pDC Mock Patient4 Batch8


title: Colon, Gamma, rep1

description: 10x Genomics


title: Pool 1, mRNA derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Pool1_barcodes.tsv
Pool1_genes.tsv
Pool1_matrix.mtx


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

description:
Patch-seq
Regen_CSMN_007

value: 22 weeks old


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

description:
Patch-seq
Regen_CSMN_006


title: W1_hiRPCp3_1056_N3

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

institute: CNRS-Universite Paris Sud

data_processing:
Image analysis and base calling is performed using the Illumina Real Time Analysis (3.4.4) software with default parameters.
Pass-filtered reads were mapped using STAR 2.7.3a
Count table of the gene features was obtained using FeatureCounts
Statistics and Differential expression analysis done with EdgeR
Pathways analysis representation done with the package GOPlot
Assembly: Ensembl genome assembly GRCh38 (release 98)
Supplementary files format and content: Tab-delimited text files of the raw counts

source_name: Retinal Progenitors

extract_protocol:
Total RNAs were extracted using the NucleoSpin RNA XS kit according to the manufacturer’s protocol. RNA yields and quality were determined using a NanoDrop ND-1000 Spectrophotometer and an Agilent 2100 Bioanalyzer.
RNA-seq libraries were constructed from 1 µg of total RNAs using the NEB Next Ultra II Directional RNA (New England Biolabs) and paired-end sequencing of 100 bases length was performed on a Novaseq system (Illumina).

value: Retinal Progenitors

tag: cell line

value: retinal cells

tag: time

value: Week 1

value: RPCM


title: H3K4me2 memory Th2 CD4+ T cell, resting (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 bowtie 2 using default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization.
HOMER was used to identify enriched regions ('peak calling') using findPeaks with -region -size 1000 -minDist 2500 options
Assembly: hg38
Supplementary files format and content: BedGraph genome-wide normalized signal profiles

source_name: peripheral blood

extract_protocol:
From PBMCs, untouched CD4+ T cells were isolated using the human CD4+ T Cell Isolation Kit (Miltenyi Biotec) according to manufacturer’s instructions, followed by fluorescence-activated cell sorting (FACS; using a FACSAria III, BD Biosciences) to isolate resting naive CD4+ T cells (live single CD4+ CD127+ CD25neg CD45RA+ cells), Th1 cells (live single CD4+ CD127+ CD25neg CD45RAneg CCR6neg CXCR3+ CXCR5neg CCR4- cells), Th17 cells (live single CD4+ CD127+ CD25neg CD45RAneg CCR6+ CXCR3neg CXCR5neg CCR4neg cells) and Th2 cells (live single CD4+ CD127+ CD25neg CD45RAneg CCR6neg CXCR3neg CXCR5neg CCR4+ cells).
Nextera DNA library construction (as described in Schmidl et al. Nature Methods 2015).

value: peripheral blood

tag: cell type

value: memory T cell

tag: chip antibody

value: H3K4me2 (ab32356, Abcam)


title: 12C Macaca fascicularis pDC Mock Patient2 Batch8

tag: tissue

value: PBMCs

value: pDC

tag: treatment

value: Mock


title: H3K4me2 memory Th2 CD4+ T cell, resting (rep2)


title: W1_hiRPCp3_1055_N2


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

description:
Patch-seq
Regen_CSMN_005


title: 8C Macaca fascicularis pDC HBV Patient1 Batch7

value: HBV


title: 20C Macaca fascicularis pDC Mock Patient3 Batch7


title: Colon, Alpha, rep1

description: 10x Genomics

value: Colon

value: Ulcerative colitis

value: Mayo endoscopic score 2-3


title: sc-Patch-seq,Green,Red,Regenerating CSMN4

description:
Patch-seq
Regen_CSMN_004

value: Cortical Spinal Motor Neuron

value: Brain


title: H3K4me2 memory Th2 CD4+ T cell, resting (rep1)


title: W1_hiRPCp3_1050_N3


title: H3K4me2 memory Th17 CD4+ T cell, resting (rep3)


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

description:
Patch-seq
Regen_CSMN_003

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: W1_hiRPCp3_1049_N2

value: Retinal Progenitors

value: retinal cells


title: 40C Macaca fascicularis pDC HBV Patient5 Batch7


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

description:
Patch-seq
Regen_CSMN_065


title: 48C Macaca fascicularis pDC HBV Patient6 Batch8


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

description:
Patch-seq
Regen_CSMN_002


title: H3K4me2 memory Th17 CD4+ T cell, resting (rep2)


title: W1_hiRPCp3_1048_N1

value: Week 1

value: RPCM


title: 24C Macaca fascicularis pDC HBV Patient3 Batch7


title: sc-Patch-seq,Green,Red,Regenerating CSMN1

description:
Patch-seq
Regen_CSMN_001


title: W1_hiRPCp3_1054_N1


title: H3K4me2 memory Th17 CD4+ T cell, resting (rep1)

value: peripheral blood

value: memory T cell


title: W1_hiRPCp2_1047_N3


title: 43C Macaca fascicularis mDC Mock Patient6 Batch6

value: PBMCs

value: mDC


title: 16C Macaca fascicularis pDC HBV Patient2 Batch8

value: pDC


title: BCAS, WT, day14

city: Kyoto

first: Kazuki

last: Nagayasu

address: 46-29 Yoshidashimoadachicho, Sakyo

department: Graduate School of Pharmaceutical Sciences

institute: Kyoto University

data_processing:
The reads were mapped to the genome sequence using HISAT2.
Gene expression was calculated using featureCounts of the Subread package.
Gene expression was further normalized using edgeR.
Assembly: mm10
Supplementary files format and content: 220222_normalized_exp.csv

source_name: Corpus callosum

extract_protocol:
At day 7, 10, or 14 after operation, corpus callosum was dissected from whole brain and snap frozen in liquid N2. Total RNA was isolated using ISOGEN reagent.
RNA libraries were prepared for sequencing using standard Novaseq6000 protocols

value: Corpus callosum

value: BCAS, day14

value: Wild type


title: H3K4me2 memory Th1 CD4+ T cell, resting (rep2)

value: H3K4me2 (ab32356, Abcam)


title: H3K4me2 memory Th1 CD4+ T cell, resting (rep1)


title: H3K4me2 naive CD4+ T cell, resting (rep3)

value: naive T cell


title: 3C Macaca fascicularis mDC Mock Patient1 Batch5

value: Mock


title: 35C Macaca fascicularis mDC Mock Patient5 Batch5


title: W1_hiRPCp2_1046_N2


title: Sham, WT, day14

value: Sham, day14


title: Sham, TRPA1-KO, day14

value: Trpa1 -/-


title: BCAS, TRPA1-KO, day14


title: W1_hiRPCp0_992_N2

value: Retinal Progenitors


title: W1_hiRPCp2_1045_N1

value: retinal cells


title: H3K4me2 naive CD4+ T cell, resting (rep1)


title: W1_hiRPCp0_993_N3

value: Week 1


title: BCAS, TRPA1-KO, day10

value: BCAS, day10


title: W1_hiRPCp0_991_N1

value: RPCM


title: 27C Macaca fascicularis mDC Mock Patient4 Batch6


title: 19C Macaca fascicularis mDC Mock Patient3 Batch5


title: BCAS, WT, day10


title: W6_ROs_1094_N3

source_name: Retinal Organoids

value: Retinal Organoids

value: Week 6

value: ProNM


title: Ref-1_S10

city: Houston

first: Weiyi

last: Peng

address: 3455 Cullen Blvd., Suite 342

department: Department of Biology and Biochemistry

institute: University of Houston

data_processing:
The MAGeCK (v0.5.9.4) count module was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “-l human_sgrna_sequences_A.library --control-sgrna human_sgrna_sequences_A.library.negctrl --norm-method control --sample-label C-1,C-2,C-3,control1,control2,control3,Ref-1 -n COVID-19_CRISPR_210212.count --fastq files.fq”. MAGeCK test module was then applied with parameters “-k COVID-19_CRISPR_210212.count.txt -c control1,control2,control3 -t C-1,C-2,C-3 --norm-method control --keep-tmp -n COVID-19_CRISPR_210212_C_control --control-sgrna human_sgrna_sequences_A.library.negctrl --gene-lfc-method secondbest”, to identify the genes that showed a  significant differential selection (|log2(fold-change)| ≥ 0.5 and p < 0.05) between the control and SARS-CoV-2 infection groups.
Assembly: hg38
Supplementary files format and content: txt
Library strategy: PCR amplicon of gRNA fragments

source_name: Lung

growth_protocol: A549 and related derived cell lines were obtained from the American Type Culture Collection (ATCC, Bethesda, MD). All cell lines and their genetically modified cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heated-inactivated fetal bovine serum (FBS; #S11150, R&D System, Minneapolis, MN) and 100μg/ml of Normocin (ant-nr-1, InvivoGen, San Diego, CA). The A549-hACE2 cells that stably express human ACE2 were generated previously and grown in the culture medium supplemented with 10 μg/mL Blasticidin (#A1113903; ThermoFisher, Waltham, MA). Cells were grown at 37 °C with 5% CO2. All cell lines were authenticated by short tandem repeat fingerprinting or the expression of tagged markers used for genetic modification. The mycoplasma detection kit (#13100-01, SouthernBiotech, Birmingham, AL) was used to routinely monitor for mycoplasma contamination of cultured cells. The maximum length of time of in vitro cell culture between thawing and use in the described experiments was two weeks.

extract_protocol:
Genomic DNA from all cell samples was extracted by using TRIzol (#15596026; ThermoFisher) according to the manufacturer’s protocol.
DNA fragments containing gRNA sequences were amplified and barcoded with adaptation by nested polymerase chain reaction (PCR) as previously described. The quality and concentration of all PCR products were determined by the Qubit ssDNA high sensitivity assay kit (#Q10212; ThermoFisher) and the bioanalyzer High Sensitivity DNA Kit (#5067-4626 2100; Agilent, Santa Clara, CA) respectively. Samples were then sequenced by Illumina Next-Generation Sequencing (NSG) at the MD Anderson Cancer Center Advanced Technology Genomics Core.

treatment_protocol: The optimized human genome-wide knockout (KO) CRISPR Library (H1) consisting of 92,817 gRNAs targeting 18,436 genes (5 gRNAs for each gene) was purchased from Addgene (Pooled library #1000000132) and used to generate lentivirus as described above. 1.5×108 of A549-AC cells were transduced with pooled library lentivirus at low multiplicity of infection (MOI; ~0.15-0.2) to ensure that each cell would receive only one gRNA as previously described. 48 hours after transduction, cells were cultured with growth medium in present of 1mg/ml puromycin to select transduced cells. 72 hours after puromycin selection, 30 million of cells were collected and used as the reference sample. 7 days post puromycin selection, pooled gRNA-expressing A549-AC cells were re-seeded in T175 cell culture flasks (10 million/flask). The next day, for the group receiving virus infection, SARS-CoV-2 virus was used to infect 2×108 of pooled A549-AC cells at MOI =5 for 48 hours. Pooled A549-AC cells cultured in the same assay medium were collected and served as the control group. 48 hours post SARS-CoV-2 infection, non-adhesive cells were removed by repeated wash using pre-warmed PBS. Adherent cells were harvested by using 0.25% Trypsin-EDTA (#15050065, ThermoFisher) and washed three time using PBS. Three replicated samples were collected for each group.

value: Lung

value: cell line

value: Reference (Early timepoint)


title: BCAS, TRPA1-KO, day7

value: Corpus callosum

value: BCAS, day7


title: W6_ROs_1093_N2


title: BCAS, WT, day7

value: Wild type


title: W6_ROs_1092_N1


title: 7C Macaca fascicularis mDC HBV Patient1 Batch5

value: PBMCs

value: mDC

value: HBV


title: 47C Macaca fascicularis mDC HBV Patient6 Batch6


title: control2_S2

value: Mock


title: C-3_S9

value: SARS-CoV-2 WA1 infection


title: 39C Macaca fascicularis mDC HBV Patient5 Batch5


title: shUsp7#2-3

city: Hangzhou

first: Chao

last: Liu

state: State...

address: Zhejiang University

institute: Zhejiang University

data_processing:
The FASTQ data were trimmed with fastp.
mapped to mouse genome mm10 via HISAT2 to generate count files.
Assembly: mm10
Supplementary files format and content: count

source_name: mouse embryonic stem cell

growth_protocol: Mouse embryonic stem cells E14 were cultured on 0.1% gelatin (Yeasen, Shanghai, China)-coated plates in Dulbecco’s Modification of Eagel’s Medium with 4.5g/L glucose(10-013-CVR; USA, Corning), supplemented with 15% fetal bovin serum (FBS, Cat:10099; Gibco, Australia), GlutaMAX (35050-61; Gibco, USA), MEM non-essential amino acids (11140-050, Gibco, USA), penicillin/streptomycin (Gibco), 0.1mM β-mercaptoethanol (M3148; Sigma), and 1000U/ml leukemia inhibitory factor (LIF, Millipore).

extract_protocol:
RNA was extracted by RNAiso Plus (Takara, 9109) following the manufacturer’s instruction.
RNA-seq library preparation and sequencing were performed by Novogene in Tianjin, China

treatment_protocol: Cells were transfected with lentivrius with short hair RNA for Usp7 or negtive control

tag: cell stype

value: mouse embryonic stem cell

value: Usp7 delepted


title: shUsp7#2-2


title: W4_ROs_1086_N5

value: retinal cells

value: Week 4


title: 23C Macaca fascicularis mDC HBV Patient3 Batch5


title: H3K4me2 naive CD4+ T cell, resting (rep2)

value: peripheral blood

value: naive T cell

value: H3K4me2 (ab32356, Abcam)


title: W4_ROs_1087_N6

value: Retinal Organoids

value: ProNM


title: W4_ROs_1085_N4


title: control1_S1

value: Lung

value: cell line


title: C-2_S8


title: shUsp7#2-1


title: 15C Macaca fascicularis mDC HBV Patient2 Batch6


title: C-1_S7


title: shCtrl-3

value: negtive conctrol


title: W4_ROs_1084_N3


title: 9C Macaca fascicularis LT Mock Patient2 Batch2

value: PBMCs

value: LT


title: 11C Macaca fascicularis mDC Mock Patient2 Batch6

value: mDC


title: shCtrl-2


title: control3_S3

value: Mock


title: W4_ROs_1083_N2


title: shCtrl-1


title: CSENaringenin5

city: Guangzhou 510275

first: Weiyang

last: Fan

address: School of Life Sciences, Sun Yat-sen University, No. 135 Xingang West Road, Guangzhou

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GRCm39 (mmu10)
Supplementary files format and content: excel,expression profiles

source_name: Small RNA of EVs from MH-S cells

growth_protocol: Mouse alveolar macrophage (MH-S, CRL-2019 from ATCC) cell lines were maintained in RPMI 1640, 0.05 mM 2-mercaptoethanol, GlutaMAX™ supplemented base medium. The base media were supplemented with penicillin-streptomycin (100 U/mL and 100 μg/mL, respectively) and 10% EV-depleted fetal bovine serum (i.e., FBS was ultracentrifuged at 100,000 g for 12 h, and then the supernatants were filtered by 0.1 µm sterile membrane to remove particle and EVs) for continuous maintenance of cultures.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: MH-S cells were divided into four groups, depending on the different treatments with or without 2.5% CSE, or 100 μM naringenin (Sigma-Aldrich, Missouri, USA) for 24 h.

value: MH-S cells

value: 24 hours

tag: source

value: extracellular vesicles (EVs)

value: EVs from 2.5% CSE and 100 μM naringenin co-treated MH-S cells


title: 41C Macaca fascicularis LT Mock Patient6 Batch2


title: CSENaringenin4