title: Human heart (1D cDNA)

source_name: Human heart tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human heart were purchased from Clontech
50 ng of poly(A)+ RNA from human heart tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human heart


title: Limb cells, WT_285

status: Public on Oct 14 2022

type: SRA

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Raw sequencing reads was processed with Perl scripts to ensure the quality of data used in further analysis. We first removed the adaptor-polluted reads (reads containing more than 5 adapter-polluted bases) and the low-quality reads (reads with the number of phred Quality value less than 19 accounting for more than 15% of total bases). And then discarded reads with number of N bases accounting for more than 5 %. The obtained clean data was mapped to the mm10 genome release with bowtie2 using default parameters. Reads count for each gene in each sample was counted by HTSeq.
The reads were mapped to the mouse genome (mm10) using bowtie2.
The mapped reads for genes were counted via featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Limb cells, WT

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.

treatment_protocol: In general, embryonic experiments were performed on pooled sibling limbs of one litter (three to five limbs per pool). Embryos were genotyped and wild-type and Scx-/- mice were dissected and limbs were isolated. We finely chopped the tissue with small scissors in a drop of DMEM, and then digested the tissues in type I Collagenase 0.1% / Trypsin 0.05% (Life Technologies) diluted in low-glucose Dulbecco’s modified Eagle’s (L-DMEM) medium (Gibco) solution at 37°C for 10 min. Then, we let tissues to settle down and collected the supernatant in a fresh 50 ml tube, before adding 10-20% of fetal bovine serum to quench trypsin (on ice to stop collagenase). We repeated digestion steps for 4 times or more till all tissues are digested. The supernatants were then pooled. We filtered the pooled supernatants through 70μ cell filters (Falcon BD), and centrifuge for 10 min at 1600 rpm, before re-suspending the pellet in DMEM containing 2% serum, and kept cell suspension on ice until load on chip.

tag: age

tag: genotype

value: WT

tag: cell type

value: limb cells


title: Limb cells, WT_282


title: Limb cells, WT_283


title: No Stim Day 5

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

country: USA

institute: University of Arizona

library_source: transcriptomic single cell

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq
Then aligned against the mm9 (mouse) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis
Assembly: mm9 (mouse)

source_name: GFP+ murine cells from parabiomes, D5

growth_protocol: A GFP and non-GFP mouse were parabiomed. An excisional wound was created on the non-GFP mouse. E-stim treatment was applied daily until D5. Tissue was harvested for analysis.

extract_protocol:
Tissue was enzymatically digested, cells were collected and washed. These cellular suspensions were then submitted for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) at the Stanford Functional Genomics Facility (SFGF) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA).
cDNA was fragmented followed by end repair and A-tailing at 65°C for 30min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a HiSeq 4000 Illumina platform aiming for 50,000 reads per cell.

treatment_protocol: Mice wounds were treated daily with e-stimulation until D5, at which point the tissue was collected.

tag: passages

value: Freshly isolated and submitted

tag: tissue

value: skin

tag: treatment

value: no stimulation


title: Limb cells, WT_280


title: Limb cells, WT_281


title: GR1009

city: Taipei

first: Hsu-Feng

last: Chu

address: No.155, Sec.2, Linong Street

country: Taiwan

data_processing:
HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument for base calling
Cutadapt (v1.9.1) for quality control
Bowtie2 (v2.2.6) for mapping
HT-seq (v0.6.1) for calculation of fragments per kilobases per million reads (FPKM)
DESeq (v1.38.0) for differential analysis
Genome_build: GenBank ID: CP071000.1
Supplementary_files_format_and_content: Matrix table with gene annotations, counts, and FPKM

organism: Limosilactobacillus fermentum

source_name: bacteria culture

growth_protocol: The bacterial culture was struck out on MRS agar plate and incubated anaerobically at 37oC for 48 h. The bacterial cells were scraped from the agar plate and dissolved in designated buffer for further experiments.

extract_protocol:
Total RNA preparation was carried out using TRIzol Max Bacterial RNA Isolation Kit (Thermofisher, MA, USA) following manufacturer’s instructions.
The rRNA was then depleted from extracted RNA and the cDNA library was synthesized using random primers. The library was ligated with adaptors and filtered according to molecular weight

tag: strain


title: Limb cells, WT_27


title: Human brain - pons (1D cDNA)

city: Philadelphia

first: Yi

last: Xing

state: PA

address: 3501 Civic Center Blvd

department: Department of Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia

description:
processed data file:
30ClontechTissue_1D_cDNA_N2_R0_abundance.esp
30ClontechTissue_1D_cDNA_N2_R0_updated.gtf

data_processing:
Basecalling was performed in fast mode with Guppy (version 3.6.0) for all Nanopore sequencing data in this study (https://community.nanoporetech.com/downloads). Basecalling of direct RNA and cDNA libraries were done using config files rna_r9.4.1_70bps_fast.cfg and dna_r9.4.1_450bps_fast.cfg respectively.
Consensus sequences from multiple copies of cDNA found in each long read of an LRCA library were obtained by running SPIRIT (https://github.com/Xinglab/SPIRIT). In brief, nhmmer is first used to find splint sequences from each read with the parameter ‘-T 8 --max’. Sequences with similar lengths separated by each pair of neighboring splint sequences were considered as copies of cDNA. If three or more copies of cDNA were identified, their consensus was obtained using abPOA (https://github.com/Xinglab/abPOA).
Reads were then mapped to either the SIRVome or hg19 reference genome using minimap2 (v2.17) with parameters “-ax splice --splice-flank=no -w 4 -k 14” and either SIRV transcript annotations or GENCODE v34 annotations (https://www.gencodegenes.org/human/release_34lift37.html).
Alignment files (SAM format) were next processed by ESPRESSO (https://github.com/Xinglab/espresso) using default settings and either SIRV transcript annotations or GENCODE v34 annotations. Reads that either map to the mitochondrial genome or contain large continuous insertions (≥20 nt) in the raw alignment were filtered out by ESPRESSO.
Genome_build: hg19, SIRVome
Supplementary_files_format_and_content: .esp files are tab-delimited matrices generated by ESPRESSO that contain read count estimates for all identified isoforms (rows) across all samples (columns); .gtf files generated by ESPRESSO are in GTF format and provide genomic coordinates for all identified transcript isoforms and their corresponding exons

molecule: polyA RNA

organism: Homo sapiens

source_name: Human brain - pons tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain (pons) were purchased from Clontech
50 ng of poly(A)+ RNA from human brain - pons tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain - pons

tag: nanopore library type

value: 1D cDNA


title: Limb cells, WT_279


title: Limb cells, WT_278


title: Human brain - frontal lobe (1D cDNA)

source_name: Human brain - frontal lobe tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain (frontal lobe) were purchased from Clontech
50 ng of poly(A)+ RNA from human brain - frontal lobe tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain - frontal lobe


title: GR1008


title: Human brain - medulla oblongata (1D cDNA)

source_name: Human brain - medulla oblongata tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain (medulla oblongata) were purchased from Clontech
50 ng of poly(A)+ RNA from human brain - medulla oblongata tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain - medulla oblongata


title: Limb cells, WT_277


title: Tregs, FS-WT1

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: cells were isolated from steady state large intestine

data_processing:
Quality control was the first step for processing raw sequence reads by FastQC.
Then adapter sequences and poor-quality reads were removed.
Reads were mapped to Mouse Genome Assembly GRCm38 by STAR v2.5
Gene expression quantification was called by RSEM v1.2 with default parameters on GENCODE mouse M16 gene annotation file
Genome_build: mm10
Supplementary_files_format_and_content: csv, raw counts of sequencing reads from replicates samples with tracking ID, gene short name.

source_name: LI Tregs

extract_protocol:
Cells were lysed in Trizol (Invitrogen) and total RNA was extracted.
Library construction and sequencing was performed by BGI Genomics, BGI-Wuhan. RNA were treated with DNase I and purified with magnetic beads with Oligo (dT). RNA were mixed with the fragmentation buffer and were fragmented into short fragments. Then cDNA was synthesized using the mRNA fragments as templates. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments were connected with adapters. Suitable fragments were selected for the PCR amplification as templates. Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used for quantification and qualification of the sample library. 150bp paired sequencing was performed using Illumina HiSeqTM4000.

value: large intestine

value: LI Tregs


title: Limb cells, WT_274


title: tpst-1+PSY5 7d rep1

city: Nagoya

first: Yoshikatsu

last: Matsubayashi

state: Aichi

address: Chikusa

department: Graduate School of Science

country: Japan

institute: Nagoya University

data_processing:
RNA-seq data was mapped to Arabidopsis TAIR10 genome release using the bioinformatic pipeline of Illumina Base Space Sequence Hub.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Arabidopsis thaliana

source_name: Seedling

extract_protocol:
Total RNA was prepared from roots and shoots of the plants using an RNeasy kit (Qiagen).
Total RNA (1 µg) was used to prepare RNA-seq libraries, using a TruSeq RNA Sample Prep Kit v2 (MiniSeq) and NEBNext Ultra II RNA Library Prep Kit (NextSeq550) (Illumina) according to the manufacturer’s instructions.

value: Seedling

tag: developmental stage

value: 7 days

value: 1uM PSY5 treatment

tag: time


title: tpst-1+PSY5 7d rep2


title: Limb cells, WT_276


title: Limb cells, WT_275


title: Limb cells, WT_271


title: tpst-1+PSY5 24h rep3


title: Limb cells, WT_272


title: tpst-1+PSY5 7d rep3


title: Human brain - temporal lobe (1D cDNA)

source_name: Human brain - temporal lobe tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain (temporal lobe) were purchased from Clontech
50 ng of poly(A)+ RNA from human brain - temporal lobe tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain - temporal lobe


title: Limb cells, WT_273


title: Human brain - hippocampus (1D cDNA)

source_name: Human brain - hippocampus tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain (hippocampus) were purchased from Clontech
50 ng of poly(A)+ RNA from human brain - hippocampus tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain - hippocampus


title: Human brain - thalamus (1D cDNA)

source_name: Human brain - thalamus tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain (thalamus) were purchased from Clontech
50 ng of poly(A)+ RNA from human brain - thalamus tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain - thalamus


title: Limb cells, WT_270

value: WT


title: Limb cells, WT_26

value: limb cells


title: Limb cells, WT_269


title: Human brain - corpus callosum (1D cDNA)

source_name: Human brain - corpus callosum tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain (corpus callosum) were purchased from Clontech
50 ng of poly(A)+ RNA from human brain - corpus callosum tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain - corpus callosum


title: tpst-1+PSY5 24h rep1


title: Human kidney (1D cDNA)

source_name: Human kidney tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human kidney were purchased from Clontech
50 ng of poly(A)+ RNA from human kidney tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human kidney


title: Limb cells, WT_268


title: Human brain - caudate nucleus (1D cDNA)

source_name: Human brain - caudate nucleus tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain (caudate nucleus) were purchased from Clontech
50 ng of poly(A)+ RNA from human brain - caudate nucleus tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain - caudate nucleus


title: Limb cells, WT_267


title: Limb cells, WT_266


title: Limb cells, WT_265


title: tpst-1+PSY5 6h rep3


title: Human brain - cerebellum (1D cDNA)

source_name: Human brain - cerebellum tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain (cerebellum) were purchased from Clontech
50 ng of poly(A)+ RNA from human brain - cerebellum tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain - cerebellum


title: Limb cells, WT_264


title: tpst-1+PSY5 6h rep2


title: Limb cells, WT_262


title: Human spinal cord (1D cDNA)

source_name: Human spinal cord tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human spinal cord were purchased from Clontech
50 ng of poly(A)+ RNA from human spinal cord tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human spinal cord

value: 1D cDNA


title: Limb cells, WT_25


title: tpst-1+PSY5 6h rep1


title: tpst-1+PSY5 2h rep3


title: Limb cells, WT_259


title: tpst-1+PSY5 24h rep2


title: Limb cells, WT_257


title: Human brain (1D cDNA)

source_name: Human brain tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain were purchased from Clontech
50 ng of poly(A)+ RNA from human brain tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain


title: Human fetal brain (1D cDNA)

source_name: Human fetal brain tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human fetal brain were purchased from Clontech
50 ng of poly(A)+ RNA from human fetal brain tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human fetal brain


title: HEK293T-3 (direct RNA)

description:
processed data file:
HEK293T_Direct_RNA_SIRV_N2_R0_abundance.esp
HEK293T_Direct_RNA_SIRV_N2_R0_updated.gtf

source_name: HEK293T cells

growth_protocol: HEK293T cells were grown at 37°C in a humidified chamber with 5% CO2. Low passage HEK293T cells (ATCC, #CRL-3216) were maintained in DMEM (Gibco, #11-885-084) supplemented with 10% fetal bovine serum (FBS, Corning, #45000-734), 1% GlutaMAX (Gibco, #35050061), and 100 U/ml penicillin-streptomycin (Gibco, #15140122).

extract_protocol:
Total RNA from HEK293T cells were extracted using TRIzol reagent (Invitrogen, #15596018)
20 μg of total RNA extracted from HEK293T cells were subjected to poly(A)+ RNA selection using Dynabeads mRNA DIRECT purification kit (Invitrogen, #61011) following the manufacturer’s instructions. Approximately 500 ng of the resulting poly(A)+ RNA, along with 25 ng of SIRV-Set1-E2 RNA, were pooled in one tube as input for direct RNA library generation. The libraries were made by following the standard SQK-RNA002 protocol with the optional reverse transcription step included.

tag: cell line

value: direct RNA


title: Limb cells, WT_260

source_name: Limb cells, WT

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.


title: Human fetal spinal cord (1D cDNA)

source_name: Human fetal spinal cord tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human fetal spinal cord were purchased from Clontech
50 ng of poly(A)+ RNA from human fetal spinal cord tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human fetal spinal cord


title: tpst-1+PSY5 2h rep2

value: Seedling

value: 7 days


title: Limb cells, WT_261


title: Limb cells, WT_258


title: tpst-1+PSY5 2h rep1

value: 1uM PSY5 treatment


title: Limb cells, WT_256


title: Limb cells, WT_254


title: tpst-1+PSY5 0h rep2


title: Limb cells, WT_263


title: HEK293T-2 (direct RNA)


title: Limb cells, WT_253


title: Limb cells, WT_250


title: Limb cells, WT_252


title: Limb cells, WT_251


title: tpst-1+PSY5 0h rep1


title: Human brain - cerebral cortex (1D cDNA)

source_name: Human brain - cerebral cortex tissue

extract_protocol:
Poly(A)+ RNA (5 μg) from human brain (cerebral cortex) were purchased from Clontech
50 ng of poly(A)+ RNA from human brain - cerebral cortex tissue were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: Human brain - cerebral cortex


title: tpst/psyr123 Shoot rep4

data_processing:
RNA-seq data was mapped to Arabidopsis TAIR10 genome release using the bioinformatic pipeline of illumina Base Space Sequence Hub.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Shoot

extract_protocol:
Total RNA was prepared from roots and shoots of the plants using an RNeasy kit (Qiagen).
Total RNA (1 µg) was used to prepare RNA-seq libraries, using a TruSeq RNA Sample Prep Kit v2 (MiniSeq) and NEBNext Ultra II RNA Library Prep Kit (NextSeq550) (illumina) according to the manufacturer’s instructions.

value: Shoot


title: Limb cells, WT_249

value: WT


title: HEK293T-1 (1D cDNA)

description:
processed data file:
PC3E_GS689_HEK293T_1D_cDNA_N2_R0_abundance.esp
PC3E_GS689_HEK293T_1D_cDNA_N2_R0_updated.gtf

extract_protocol:
Total RNA from HEK293T cells were extracted using TRIzol reagent (Invitrogen, #15596018)
500 ng of total RNA extracted from HEK293T cells were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.


title: Limb cells, WT_255

value: limb cells


title: Limb cells, WT_248


title: HEK293T-1 (direct RNA)


title: tpst/psyr123 Shoot rep3


title: GS689-3 (LRCA)

description:
processed data file:
PC3E_GS689_LRCA_N2_R0_abundance.esp
PC3E_GS689_LRCA_N2_R0_updated.gtf

source_name: GS689 cells

growth_protocol: GS689 cells, which are metastatic variants of PC-3 cells, were isolated from a secondary metastatic liver tumor by in vivo passaging of PC-3 cells in SCID mice. GS689 cells were grown at 37°C in a humidified chamber with 5% CO2 and maintained in DMEM/F12 with 10% FBS, 1X nonessential amino acids (NEAA, Gibco, #11140050), and 400 μg/ml G418 (Gibco, #10131035).

extract_protocol:
Total RNA from GS689 cells were extracted using TRIzol reagent (Invitrogen, #15596018)
500 ng of total RNA extracted from GS689 cells were used as templates for cDNA synthesis following the R2C2 method with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. Additional RT oligos were digested using 1 μl of Exonuclease I at 37°C for 20 min and 80°C for 10 min. After reverse transcription, a UMI sequence was added to the 3’ end of cDNA by strand extension reaction using Phusion HiFi DNA polymerase (NEB, #M0530), a template oligo including 60 random bases of C, G, and T (B60), and a 3’ 3C-spacer. The reaction was performed by incubating at 95°C for 3 min, followed by 5 cycles of (98°C for 15 s, 67°C for 15 s, 72°C for 15 s) with a final extension at 72°C for 5 min. UMI-coded cDNA products were aliquoted into multiple tubes and PCR amplified using KAPA HiFi ReadyMix by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 15 s, 72°C for 4 min) with a final extension at 72°C for 5 min. PCR products were purified with 1X volume of SPRIselect beads. A ~100 bp dsDNA sequence was amplified from Lambda DNA as a DNA splint for circularization of cDNA. The PCR conditions of DNA splint were the same as that of cDNA except that 30-cycle PCR and 20 s of extension step in each cycle were executed. Equal amounts of cDNA and DNA splints (~200 ng) were used for Gibson Assembly reaction by incubating with 2X NEBuilder HiFi DNA Assembly Master Mix (NEB, #E2621) at 50°C for 60 min. Linear DNA was digested using a mixture of Exonuclease I and III (NEB, #0206) at 37°C for 4-12 hrs and 80°C for 15 min. A universal oligo that anneals to the PCR adapter sequence of circular dsDNA was used to initiate linear rolling circular amplification. The reaction was performed using 1 μl of Phi29 DNA polymerase at 30°C for 16 hrs and 65°C for 15 min. LRCA products were purified with 0.7X volume of SPRIselect beads. The second strand synthesis of LRCA-generated ssDNA products was performed using Phusion DNA polymerase and Taq DNA ligase (NEB, #M0208) by gap-filling and ligation reaction at 50°C for 60 min. dsDNA sequences were then sheared by g-TUBE (Covaris, #520079) to the desired size (around 8-10 kb) following the vendor’s instructions. Sheared DNA products were purified with 0.5X volume of SPRIselect beads and subjected to 1D library construction following the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.

value: LRCA


title: Limb cells, WT_246


title: Limb cells, WT_24


title: HEK293T-3 (1D cDNA)


title: Limb cells, WT_245


title: tpst-1+PSY5 0h rep3

source_name: Seedling

extract_protocol:
Total RNA was prepared from roots and shoots of the plants using an RNeasy kit (Qiagen).
Total RNA (1 µg) was used to prepare RNA-seq libraries, using a TruSeq RNA Sample Prep Kit v2 (MiniSeq) and NEBNext Ultra II RNA Library Prep Kit (NextSeq550) (Illumina) according to the manufacturer’s instructions.


title: tpst/psyr123 Shoot rep1


title: Limb cells, WT_244


title: GS689-3 (1D cDNA)

extract_protocol:
Total RNA from GS689 cells were extracted using TRIzol reagent (Invitrogen, #15596018)
500 ng of total RNA extracted from GS689 cells were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.


title: psyr123 Shoot rep4


title: GS689-2 (LRCA)


title: Limb cells, WT_241


title: HEK293T-2 (1D cDNA)


title: Limb cells, WT_243


title: psyr123 Shoot rep3


title: Limb cells, WT_247


title: tpst/psyr123 Shoot rep2


title: GS689-2 (1D cDNA)


title: Limb cells, WT_240


title: psyr123 Shoot rep2


title: Limb cells, WT_242


title: Limb cells, WT_237


title: Limb cells, WT_238


title: GS689-1 (LRCA)


title: GS689-1 (1D cDNA)


title: psyr123 Shoot rep1


title: Limb cells, WT_234


title: Limb cells, WT_233


title: tpst+PSY5 Shoot rep3


title: PC3E-3 (1D cDNA)

description:
processed data file:
PC3E_1D_cDNA_SIRV_N2_R0_abundance.esp
PC3E_1D_cDNA_SIRV_N2_R0_updated.gtf
PC3E_GS689_HEK293T_1D_cDNA_N2_R0_abundance.esp
PC3E_GS689_HEK293T_1D_cDNA_N2_R0_updated.gtf

source_name: PC3E cells

growth_protocol: PC3E cells were derived from the PC-3 cell line by sorting E-cadherin-positive cells, which exhibit epithelial characteristics. PC3E cells were grown at 37°C in a humidified chamber with 5% CO2 and maintained in DMEM/F12 with 10% FBS, 1X nonessential amino acids (NEAA, Gibco, #11140050), and 400 μg/ml G418 (Gibco, #10131035).

extract_protocol:
Total RNA from PC3E cells were extracted using TRIzol reagent (Invitrogen, #15596018)
200 ng of total RNA extracted from PC3E cells along with 100 pg of SIRV-Set1-E2 RNA were used as templates for cDNA synthesis following the SMART-seq2 protocol with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. PCR amplification of first-strand cDNA using KAPA HiFi ReadyMix (KAPA Biosystems, #KK2602) was performed by incubating at 95°C for 3 min, followed by 15 cycles of (98°C for 20 s, 67°C for 20 s, 72°C for 4min) with a final extension at 72°C for 5 min. PCR products were treated with Exonuclease I (NEB, #M0293) to remove unused primers and then purified using 0.8X volume of SPRIselect beads (Beckman Coulter, #B23318). 1D Nanopore libraries were then constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.


title: tpst+PSY5 Shoot rep4


title: PC3E-3 (LRCA)

description:
processed data file:
PC3E_LRCA_SIRV_N2_R0_abundance.esp
PC3E_LRCA_SIRV_N2_R0_updated.gtf
PC3E_GS689_LRCA_N2_R0_abundance.esp
PC3E_GS689_LRCA_N2_R0_updated.gtf

extract_protocol:
Total RNA from PC3E cells were extracted using TRIzol reagent (Invitrogen, #15596018)
200 ng of total RNA extracted from PC3E cells along with 100 pg of SIRV-Set1-E2 RNA were used as templates for cDNA synthesis following the R2C2 method with some modifications. The reverse transcription and template-switching reaction was performed by Maxima H minus reverse transcriptase (Thermo Scientific, #EP0751) under the following conditions: 42°C for 90 min, 85°C for 5 min. Additional RT oligos were digested using 1 μl of Exonuclease I at 37°C for 20 min and 80°C for 10 min. After reverse transcription, a UMI sequence was added to the 3’ end of cDNA by strand extension reaction using Phusion HiFi DNA polymerase (NEB, #M0530), a template oligo including 60 random bases of C, G, and T (B60), and a 3’ 3C-spacer. The reaction was performed by incubating at 95°C for 3 min, followed by 5 cycles of (98°C for 15 s, 67°C for 15 s, 72°C for 15 s) with a final extension at 72°C for 5 min. UMI-coded cDNA products were aliquoted into multiple tubes and PCR amplified using KAPA HiFi ReadyMix by incubating at 95°C for 3 min, followed by 13 cycles of (98°C for 20 s, 67°C for 15 s, 72°C for 4 min) with a final extension at 72°C for 5 min. PCR products were purified with 1X volume of SPRIselect beads. A ~100 bp dsDNA sequence was amplified from Lambda DNA as a DNA splint for circularization of cDNA. The PCR conditions of DNA splint were the same as that of cDNA except that 30-cycle PCR and 20 s of extension step in each cycle were executed. Equal amounts of cDNA and DNA splints (~200 ng) were used for Gibson Assembly reaction by incubating with 2X NEBuilder HiFi DNA Assembly Master Mix (NEB, #E2621) at 50°C for 60 min. Linear DNA was digested using a mixture of Exonuclease I and III (NEB, #0206) at 37°C for 4-12 hrs and 80°C for 15 min. A universal oligo that anneals to the PCR adapter sequence of circular dsDNA was used to initiate linear rolling circular amplification. The reaction was performed using 1 μl of Phi29 DNA polymerase at 30°C for 16 hrs and 65°C for 15 min. LRCA products were purified with 0.7X volume of SPRIselect beads. The second strand synthesis of LRCA-generated ssDNA products was performed using Phusion DNA polymerase and Taq DNA ligase (NEB, #M0208) by gap-filling and ligation reaction at 50°C for 60 min. dsDNA sequences were then sheared by g-TUBE (Covaris, #520079) to the desired size (around 8-10 kb) following the vendor’s instructions. Sheared DNA products were purified with 0.5X volume of SPRIselect beads and subjected to 1D library construction following the standard SQK-LSK109 protocol. cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 minutes and 65°C for 20 min. End-prepared cDNA were purified with 1X volume of AMPure XP beads and eluted in 60 μl of Nuclease-free water. Adapter ligation was then performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, the libraries were purified using 0.45X volume of AMPure XP beads and short fragment buffer (SFB) to enrich all fragments equally.


title: Limb cells, WT_235


title: Limb cells, WT_232


title: tpst+PSY5 Shoot rep2


title: Limb cells, WT_231


title: PC3E-2 (LRCA)


title: Limb cells, WT_239


title: Limb cells, WT_22


title: Limb cells, WT_23


title: Limb cells, WT_230


title: tpst-1 Shoot rep4


title: Limb cells, WT_229


title: Limb cells, WT_228


title: PC3E-1 (LRCA)


title: PC3E-2 (1D cDNA)


title: tpst-1 Shoot rep3


title: tpst+PSY5 Shoot rep1


title: Limb cells, WT_227


title: PC3E-1 (1D cDNA)


title: Limb cells, WT_236


title: Limb cells, WT_226


title: tpst-1 Shoot rep2


title: Limb cells, WT_225


title: Limb cells, WT_224


title: Limb cells, WT_223


title: Limb cells, WT_221


title: WT Shoot rep4

value: Wild type


title: Limb cells, WT_220


title: Limb cells, WT_222


title: WT Shoot rep3


title: Limb cells, WT_218


title: WT Shoot rep2


title: Limb cells, WT_217


title: Limb cells, WT_216


title: Limb cells, WT_215


title: WT Shoot rep1


title: Limb cells, WT_213


title: tpst-1 Shoot rep1


title: Limb cells, WT_21


title: Limb cells, WT_212


title: Limb cells, WT_214


title: Limb cells, WT_211


title: Limb cells, WT_20


title: Limb cells, WT_210


title: 4_ΔΔ_pH7.4_t240

city: Jena

first: Enrico

last: Garbe

address: Albert-Einstein-Straße 10

department: (Epi-)Genetics of Fungal Infections

country: Germany

institute: HKI Jena

data_processing:
Fastq files were assessed for sequence quality using FastQC (version 0.11.9) and a genome index from file C_albicans_SC5314_A22_current_chromosomes.fasta fom http://www.candidagenome.org/ was created with bowtie2 (version 2.4.2). Mapping of reads to the index was performed with bowtie2. Reads were counted and assigned to the corresponding genome using function featureCounts of R package Rsubread (version 2.2.6). Contrasts were calculated using R package DESeq2 (version 1.28.1). R version 4.0.4 was used.
Assembly: C_albicans_SC5314_A22_current_chromosomes.fasta
Supplementary files format and content: Raw.Counts.C.Albicans.Hyphae.csv, Comma seperated text file containing counts of all samples

organism: Candida albicans

source_name: Planktonic cells

growth_protocol: C. albicans were pre-grown overnight at 37°C in SD and used to set log-cultures in SD at OD600 0.3. Log-cultures were incubated at 37°C until OD600 of ~1 was reached. Cells were collected, washed with and resuspended in 1xYNB solution and used to set OD600 to 0.3 in the respective test medium and incubated at 37°C. Cells used for inoculation were also collected for t 0 min. After the indicated time test cultures were split and used for either metabolite or RNA extraction. All cultures were incubated in flasks with 180 pm shaking.

extract_protocol:
For total RNA isolation cells were resuspended in 440 µl AE buffer with 10% SDS and 440 µl of Acid-phenol:Chloroform with isoamyl alcohol (Ambion, Germany) was added. The suspension was thoroughly mixed and incubated for 5 min at 65°C, frozen at -20°C for 30 min and subsequently thawed at 65°C for 5 min. The phases were separated via 4 min centrifugation at 16000 g, the upper aqueous phase transferred and 1/10 of the volume sodium acetate (pH 5.3) and 1 volume of 2 propanol was added to precipitate the RNA for at least 30 min at -20°C. The supernatant was discarded after 10 min centrifugation at 12000 g, the RNA pellet washed twice with 80 % ethanol and finally solved in 300 µl nuclease free H2O. Quality and quantity of the RNA was assessed using 2100 Bioanalyzer (Agilent Technologies, California, USA) and Nanodrop (Thermo Fischer Scientific, Massachusetts, USA) measurements.
A total amount of 0.4 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA. Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA by mRNAusing poly-T oligo-attached magnetic beads. Fragmentation was carried out by Covaris sonication. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using dTTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality and quantity are assessed by Qubit and real-time PCR. Sequencing platform was Illumina Novaseq 6000 PE150.
Paired end RNA sequencing of cDNA fragments of preferentially 150~200 bp in length.

treatment_protocol: Cells were separated from test medium by centrifugation 2 min at 4000g and 4ºC. Cells were snap frozen in liquid nitrogen and stored at -80°C until further processing.

value: Strain

tag: genotype/variation

tag: media type

tag: time point

value: 240 min


title: Limb cells, WT_209


title: Limb cells, WT_219


title: 1_ΔΔ_pH7.4_t240


title: Limb cells, WT_208


title: 3_ΔΔ_pH7.4_t240


title: autophagy deficient LSEC at 2weeks of high fat diet, biological rep4

type: RNA

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: Gene expression data from LSEC from endothelial autophagy deficiet mice after 2 weeks of high fat diet

hyb_protocol: Following DNA fragmentation and labelling, 2ug of cDNA were hybridized for 16 hr at 45C on Mouse Clariom S Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Mouse Clariom S arrays were scanned using the Affymetrix GCS3000 scanner 7G

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

label: biotin

source_name: Mouse, Atg5lox/lox;VE-cadherin-Cre

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip™WT PLUS Reagent Kit Manual Target Preparation for GeneChip™Whole Transcript (WT)

growth_protocol: 8 weeks old mice were fed a high fat diet for 2 weeks

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were fed a high fat diet for 2 weeks

value: liver sinusoidal endothelial cells


title: Limb cells, WT_207


title: autophagy deficient LSEC at 2weeks of high fat diet, biological rep5


title: autophagy deficient LSEC at 2weeks of high fat diet, biological rep1


title: autophagy deficient LSEC at 2weeks of high fat diet, biological rep2


title: Limb cells, WT_206


title: wild type LSEC at 2weeks of high fat diet, biological rep6

description: Gene expression data from LSEC from wild type mice after 2 weeks of high fat diet

source_name: Mouse, Atg5lox/lox


title: autophagy deficient LSEC at 2weeks of high fat diet, biological rep3


title: wild type LSEC at 2weeks of high fat diet, biological rep3


title: 4_ΔΔ_pH7.4_t90

value: 90 min


title: Limb cells, WT_205


title: wild type LSEC at 2weeks of high fat diet, biological rep5


title: wild type LSEC at 2weeks of high fat diet, biological rep4


title: 2_ΔΔ_pH7.4_t240


title: Limb cells, WT_204


title: Limb cells, WT_202


title: Limb cells, WT_203


title: 2_ΔΔ_pH7.4_t90


title: 1_ΔΔ_pH7.4_t90


title: CM4, control, rep5

city: Yangzhou

first: Wang

last: Laidi

state: Jiangsu

address: East Wenhui Road

institute: Yangzhou University

data_processing:
Illumina NovaSeq 6000
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Clean data were mapped to the duck reference genome (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/GCF_015476345.1_ZJU1.0_genomic.fna.gz) by Hisat2 (version: 2.0.5).
mRNA levels was quantified by the value of fragments per kilobase of exon per million mapped reads (FPKM).
Assembly: ZJU1.0
Supplementary files format and content: tab-delimited text files include RPKM values for all Samples

organism: Anas platyrhynchos

source_name: breast muscle

extract_protocol:
RNA was extracted by a Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: breed

value: Runzhou white crest duck

value: breast muscle

tag: Sex

value: male

value: control group

value: ducks were fed by 2% duck oil

value: Day 28


title: CM5, control, rep5


title: PBMC, Sarcoidosis29

city: Chicago

first: Christian

last: Ascoli

state: IL

address: 840 S Wood Street, Room 920-N CSB

department: Division of Pulmonary, Critical Care, Sleep and Allergy

institute: University of Illinois at Chicago

data_processing:
Aligned and quantified using Salmon against Ensembl GRCh38.p12, indexed at transcript level
Adapters were removed using software Cutadapt and then checked with FastQC for quality. All sequences have Phred score > 30 and therefore passed the quality check.
Mapping-based index was built against the human reference genome (Ensembl GRCh38) at the transcript level using Salmon (command: salmon index).
Sequences were quantified into Salmon output file formats using Salmon (command: salmon quant) against the index built in the previous step.
Genome_build: GRCh38.cdna.all
Supplementary_files_format_and_content: ACCESS_mRNA_Count_Matrix_Rounded.txt; salmon tar archive.

source_name: PBMC

extract_protocol:
PBMCs were isolated from these samples via a standard Ficoll-hypaque density gradient. After PBMCs were obtained, RNA was isolated utilizing the guanidinium thiocyanate phenolchloroform  extraction method.
Transcriptomic libraries were prepared with the Illumina TruSeq Stranded mRNA Sample Preparation kit with a minimum input of 0.1ug of total RNA as directed by the manufacturer in accordance with the low sample protocol.

tag: finn lab id

tag: alternate id

tag: disease status

value: Sarcoidosis

tag: batch

tag: pair

tag: race/ethnicity

value: Caucasian

tag: gender

value: Female

tag: age group

tag: smoking history

value: Negative

tag: treatment at sample collection


title: wild type LSEC at 2weeks of high fat diet, biological rep2

tag: cell type


title: Limb cells, WT_200

tag: age

tag: genotype

value: WT

value: limb cells


title: 4_hgc1Δ_pH7.4_t240

tag: strain

tag: genotype/variation

tag: media type


title: wild type LSEC at 2weeks of high fat diet, biological rep1


title: CM3, control, rep5

tag: breed

tag: tissue

tag: Sex

tag: treatment

tag: time


title: CM2, control,rep5


title: 3_hgc1Δ_pH7.4_t240

tag: time point


title: Limb cells, WT_1


title: 3_ΔΔ_pH7.4_t90


title: Limb cells, WT_199


title: CM1, control, rep5


title: PBMC, Sarcoidosis27

tag: finn lab id

tag: alternate id

tag: disease status

tag: batch

tag: pair

tag: race/ethnicity

value: Male

value: Positive


title: 2_hgc1Δ_pH7.4_t240

value: Strain

value: 240 min


title: HM5, linseed oil, rep5

value: linseed oil group

value: ducks were fed by 2% linseed oil


title: PBMC, Sarcoidosis23

tag: gender

tag: age group

tag: smoking history

tag: treatment at sample collection


title: PBMC, Sarcoidosis25


title: 1_hgc1Δ_pH7.4_t240

tag: strain

tag: genotype/variation

tag: media type


title: Limb cells, WT_201

tag: age

tag: genotype

tag: cell type


title: Limb cells, WT_198


title: HM3, linseed oil, rep5

tag: breed

value: Runzhou white crest duck

tag: tissue

value: breast muscle

tag: Sex

tag: treatment

tag: time


title: 4_hgc1Δ_pH7.4_t90

tag: time point

value: 90 min


title: PBMC, Sarcoidosis22

tag: finn lab id

tag: alternate id

tag: disease status

tag: batch

tag: pair

tag: race/ethnicity


title: 3_hgc1Δ_pH7.4_t90

tag: strain

tag: genotype/variation


title: HM2, linseed oil, rep5

value: male


title: PBMC, Sarcoidosis21

tag: gender

tag: age group

tag: smoking history

tag: treatment at sample collection


title: 2_hgc1Δ_pH7.4_t90

tag: media type


title: HM1, linseed oil, rep5

tag: breed

tag: tissue

tag: Sex

value: Day 28


title: PBMC, Sarcoidosis18

value: Sarcoidosis


title: PBMC, Sarcoidosis28

value: Caucasian


title: Limb cells, WT_197

tag: age

tag: genotype

tag: cell type


title: Limb cells, WT_196


title: 1_hgc1Δ_pH7.4_t90

tag: time point


title: Limb cells, WT_195


title: PBMC, Sarcoidosis17

tag: finn lab id

tag: alternate id

tag: disease status

tag: batch

value: Female


title: CL5, control, rep5

source_name: liver

value: liver

tag: treatment

value: control group

value: ducks were fed by 2% duck oil

tag: time


title: Limb cells, WT_19

value: WT

value: limb cells


title: 4_WT_pH7.4_t240

tag: strain

value: Strain

tag: genotype/variation

value: wild type


title: Limb cells, WT_194


title: HM4, linseed oil, rep5

value: linseed oil group


title: CL3, control, rep5


title: PBMC, Sarcoidosis15

tag: pair

tag: race/ethnicity

tag: gender

tag: age group

tag: smoking history

value: Negative

tag: treatment at sample collection


title: CL4, control, rep5

tag: breed

value: Runzhou white crest duck

tag: tissue

tag: Sex


title: Limb cells, WT_193

tag: age

tag: genotype

tag: cell type


title: PBMC, Sarcoidosis13

tag: finn lab id

tag: alternate id

tag: disease status

tag: batch

value: Male

value: Positive


title: CL2, control, rep5

value: male

tag: treatment

tag: time


title: PBMC, Sarcoidosis12

tag: pair

tag: race/ethnicity


title: 2_WT_pH7.4_t240

tag: strain

tag: genotype/variation

tag: media type

tag: time point

value: 240 min


title: Limb cells, WT_191


title: Limb cells, WT_18


title: Limb cells, WT_190


title: HL5, linseed oil, rep5

tag: breed

tag: tissue

value: ducks were fed by 2% linseed oil

value: Day 28


title: Limb cells, WT_188

tag: age


title: 1_WT_pH7.4_t240


title: HL3, linseed oil, rep5

tag: Sex


title: Limb cells, WT_189

tag: genotype

tag: cell type


title: PBMC, Control28

tag: finn lab id

tag: alternate id

value: Control

value: Caucasian

tag: gender

tag: age group

tag: smoking history

tag: treatment at sample collection


title: 2_WT_pH7.4_t90

value: 90 min


title: 3_WT_pH7.4_t90


title: PBMC, Control29

tag: disease status

tag: batch

tag: pair

tag: race/ethnicity

value: Female


title: CL1, control, rep5

value: liver

tag: treatment

value: control group

value: ducks were fed by 2% duck oil

tag: time


title: 4_WT_pH7.4_t90

tag: strain

value: Strain

tag: genotype/variation

value: wild type

tag: media type

tag: time point


title: PBMC, Control25


title: HL2, linseed oil, rep5

tag: breed

tag: tissue

tag: Sex

value: linseed oil group


title: PBMC, Control27

tag: finn lab id

tag: alternate id

tag: gender


title: 1_WT_pH7.4_t90


title: 3_WT_pH7.4_t240


title: 3_ΔΔ_pH4_t240


title: PBMC, Sarcoidosis8

value: Sarcoidosis

tag: age group

tag: smoking history

tag: treatment at sample collection

value: Negative


title: PBMC, Sarcoidosis4

tag: disease status

tag: batch

tag: pair

value: Male


title: PBMC, Control23

tag: race/ethnicity

value: Positive


title: 4_ΔΔ_pH4_t240

tag: strain

value: 240 min


title: Limb cells, WT_186

tag: age

tag: genotype

value: WT

tag: cell type

value: limb cells


title: Limb cells, WT_192


title: Limb cells, WT_187


title: HL1, linseed oil, rep5

tag: breed

value: Runzhou white crest duck

value: male

tag: treatment

value: ducks were fed by 2% linseed oil

tag: time

value: Day 28


title: HL4, linseed oil, rep5

tag: tissue

value: liver

tag: Sex


title: Limb cells, WT_185


title: PBMC, Control21

tag: finn lab id

tag: alternate id

value: Control

value: Caucasian

tag: gender

value: Female


title: PBMC, Control22

tag: age group

tag: smoking history

tag: treatment at sample collection


title: 1_ΔΔ_pH4_t240

value: Strain

tag: genotype/variation

tag: media type

tag: time point


title: 2_ΔΔ_pH4_t240

tag: strain


title: Limb cells, WT_184

tag: age

tag: genotype


title: PBMC, Control18

tag: disease status

tag: batch

tag: pair

tag: race/ethnicity


title: Limb cells, WT_183

tag: cell type


title: Limb cells, WT_181


title: PBMC, Control17

tag: finn lab id


title: Limb cells, WT_182


title: 2_ΔΔ_pH4_t90

value: 90 min


title: 4_ΔΔ_pH4_t90


title: 3_ΔΔ_pH4_t90


title: PBMC, Control15

tag: alternate id


title: mRNA-Seq Old replicate 4

city: Beijing

first: Yehua

last: Li

address: shengmingkexueyuanlu7hao, changping

institute: NIBS

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR v2.6.1a with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: Old pituitary

growth_protocol: Wild-type C57BL/6 mice were housed at the animal center in the National Institute of Biological Sciences in a Specific Pathogen Free (SPF) facility within individually ventilated cages as well as the controlled temperature, humidity and light-dark cycle, and a regular rodent chow diet.

extract_protocol:
The isolated pituitary from young (2-3M) or old (18-24M) mouse was directly lysate in lysis buffer and RNA was extracted using RNAprep pure Cell/Bacteria Kit following the manufacturer’s instructions. Concentration of RNA was measured and the sample passed quality checks was used for RNA sequencing library preparation.
Libraries for mRNA abundance examination was prepared by using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

tag: growth phase

value: 18-24 month


title: mRNA-Seq Old replicate 3


title: Limb cells, WT_180


title: Limb cells, WT_17


title: mRNA-Seq Old replicate 2


title: PBMC, Control12

tag: gender

tag: age group

value: Negative


title: 1_ΔΔ_pH4_t90


title: PBMC, Control13

value: Male

tag: smoking history

tag: treatment at sample collection


title: mRNA-Seq Old replicate 1


title: Len_2

city: Seongnam-si

first: KyuBum

last: Kwack

address: 335, Pangyo-ro, Bundang-gu

department: Institute Department of Biomedical Science

country: South Korea

institute: College of Life Science, CHA University

description: Gene expression data from human NK cells activated with IL-2 and 1uM Len for 12 days

hyb_protocol: Turn Affymetrix® Hybridization Oven on, set the temperature to 45°C and set the RPM to 60. Turn the rotation on and allow the oven to preheat. Equilibrate the arrays to room. Prepare hybridization master mix and hybridization cocktatil(add the appropriate amount of Hybridization Master Mix to each fragmented and biotin-labeled ss-cDNA sample). Inject the appropriate amount of the specific sample into the array through one of the septa. Place the arrays into hybridization oven trays. Load the trays into the hybridization oven and incubate with rotation at 60 rpm for 16hr at 45℃. temperature immediately before use. Label the array with the name of the sample that will be hybridized. Register the sample and array information into AGCC. Prepare hybridization master mix and hybridization cocktatil(add the appropriate amount of Hybridization Master Mix to each fragmented and biotin-labeled ss-cDNA sample). Inject the appropriate amount of the specific sample into the array through one of the septa. Place the arrays into hybridization oven trays. Load the trays into the hybridization oven and incubate with rotation at 60 rpm for 16hr at 45℃.

scan_protocol: Image was acquired with Affymetrix GeneChip® Scanner 3000 7G and data extracted using by Affymetrix GeneChip® Command Console® Software (AGCC)

data_processing: After robust multi-array Average (RMA) normalization using Expression Console 1.4, differentially expressed gene (DEG) analysis was performed, involving fold change filtering and statistical filtering using R 3.1.3.

source_name: pNK cell_IL2+1uM Len_donor 2

label_protocol: In this procedure, the purified, sense-strand cDNA was fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that was covalently linked to biotin. 5.5 μg of singlestranded cDNA was required for fragmentation and labeling.

growth_protocol: Human PBMCs were isolated from 2 healthy donors and cultured with RPMI1640 media (Hyclone) supplemented with 10% FBS (Thermo Fisher Scientific), 50 μM β-mercaptoethanol (Sigma-Aldrich) and 1% penicillin/streptomycin (Thermo Fisher Scientific). PBMCs were treated with DMSO or 1μM lenalidomide plus 200U/ml IL-2 every 3 days. On day 12, NK cells were purified with NK cell isolation kit (Miltenyi Biotec) according to the manufacturer's instruction.

extract_protocol: Total RNA was extracted using mirVana™ miRNA Isolation Kit (ThermoFisher scientific) and processed for quality control of total RNA using ND-1000 spectrophotometer (Thermo Scientific), 2100 Expert Bioanalyzer (Agilent, Santa Clara, CA) and RNA 6000 Nano Kit (Agilent).

treatment_protocol: PBMCs were treated with 200unit/ml IL-2 and 1μM lenalidomide every 3 days. On day 12, NK cells were purified with NK cell isolation kit (Miltenyi Biotec) according to the manufacturer's instruction.

value: NK cell

tag: donor type

value: healthy donor

tag: treatment


title: 4_hgc1Δ_pH4_t240

tag: strain

tag: genotype/variation

tag: media type

tag: time point

value: 240 min


title: Limb cells, WT_179

tag: age

tag: genotype

value: WT

value: limb cells


title: 3_hgc1Δ_pH4_t240


title: Len_1

source_name: pNK cell_IL2+1uM Len_donor 1

value: activated with IL-2 and 1uM Len for 12 days


title: PBMC, Control8

value: ACCESS 13

tag: disease status

tag: batch

tag: pair

tag: race/ethnicity


title: Limb cells, WT_178

tag: cell type


title: PBMC, Control4

tag: finn lab id

tag: alternate id

tag: gender

value: Positive


title: Control_2

description: Gene expression data from human NK cells activated with IL-2 and DMSO for 12 days

source_name: pNK cell_IL2+DMSO_donor 2


title: mRNA-Seq Young replicate 4

source_name: Young pituitary

tag: growth phase

value: 2-3 month


title: 2_hgc1Δ_pH4_t240


title: Control_1

source_name: pNK cell_IL2+DMSO_donor 1

tag: donor type

value: activated with IL-2 and DMSO for 12 days


title: mRNA-Seq Young replicate 3


title: Limb cells, WT_177

source_name: Limb cells, WT


title: 1_hgc1Δ_pH4_t240


title: mRNA-Seq Young replicate 1


title: Limb cells, WT_175


title: Limb cells, WT_176


title: Limb cells, WT_173


title: Limb cells, WT_174


title: AXER-/- Medaka embryo heart, 5 dpf

city: Kyoto

first: Byungseok

last: Jin

state: Sakyo-ku

address: Kitashirakawa-oiwake

department: Biophysics

institute: Kyoto University

data_processing:
Read 1 reads were processed with fastp (version 0.21.0) (Chen et al., 2018) using the following parameters: --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31.
The trimmed reads were then mapped to the mouse reference sequences of Mus_musculus.GRCm38.cdna.all.fa, using BWA mem (version 0.7.17-r1188) (Li and Durbin, 2009) with default parameters.
Read count for each gene was calculated with salmon using -l IU, which specifies library type (version v0.12.0) (Patro et al., 2017).
Supplementary files format and content: Read count data for each Sample

organism: Oryzias latipes

source_name: heart

extract_protocol:
RNA was harvested by the acid quanidinium/phenol/chloroform method using Isogen (Nippon Gene, Tokyo, Japan). 20 ng of total RNA was used for the construction of sequencing libraries.
RNA-Seq were conducted according to Lasy-Seq ver. 1.1 protocol (https://sites.google.com/view/lasy-seq/).

tag: tissue

value: heart

tag: cell line

value: Japanese medaka HdrR

value: whole heart

value: AXER-/-


title: AXER+/+, ATF6(N/+) Medaka embryo heart, 5 dpf

description: RNA-Seq were conducted according to Lasy-Seq ver. 1.1 protocol (https://sites.google.com/view/lasy-seq/).


title: AXER-/-, ATF6(N/+) Medaka embryo heart, 5 dpf


title: AXER-/-, XBP1(S/+) Medaka embryo heart, 5 dpf


title: AXER+/+, XBP1(S/+) Medaka embryo heart, 5 dpf


title: TNFRv, subject 4 [K210TNFRv_S15]

city: Belvaux

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

data_processing:
The raw RNA-seq fastq files were quality-checked using the FastQC software and the data was pre-processed using the software package Rsubread (version 1.32.2).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values derived from Rsubread processing for each sample

source_name: gingiva

extract_protocol:
Total RNA was extracted using the QIAcube and the QIAcube standard RNeasy mini kit (Qiagen) using the DNase digestion protocol.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA library prep kit following manufacturer's protocols.

treatment_protocol: Cells seeded at a density of 2 x 106 cells in T25 flasks were stimulated with TNF-α or vehicle (KSFM, containing <0.1% ethanol) for 30 min (5 % CO2, 37 °C), washed twice with PBS and then incubated with RvD1n-3 DPA (0.1 nM) or vehicle (KSFM, containing <0.1% ethanol) for 5 h (5 % CO2, 37 °C).

value: gingiva

tag: subject id

value: subject 4

value: oral epithelial cells

tag: treatment

value: TNFRv


title: TNF, subject 4 [K210TNF_S14]

value: TNF


title: 2_hgc1Δ_pH4_t90

tag: strain

value: Strain

tag: genotype/variation

tag: media type

tag: time point

value: 90 min


title: vehicle control, subject 4 [K210vehiclectr_S13]

value: vehicle control


title: 1_hgc1Δ_pH4_t90


title: mRNA-Seq Young replicate 2

tag: genotype

value: WT


title: Limb cells, WT_172

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.

tag: age

value: limb cells


title: 4_hgc1Δ_pH4_t90


title: Limb cells, WT_170


title: RV, subject 4 [K210Rv_S16]

value: RV


title: RV, subject 3 [K38Rv_S12]

value: subject 3


title: 3_hgc1Δ_pH4_t90


title: Limb cells, WT_171


title: Limb cells, WT_16


title: TNFRv, subject 3 [K38TNFRv_S11]


title: TNF, subject 3 [K38TNF_2_S15]


title: Limb cells, WT_169


title: 3_WT_pH4_t240

value: wild type

value: 240 min


title: 2_WT_pH4_t240


title: 1_WT_pH4_t240


title: pDCs, IMQ_4

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: pDCs from IMQ mouse

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark).

growth_protocol: Spleen was dissociated into single-cell suspension by spleen dissociation kit (Mylteni biotec) according to the manufacturer’s instruction. From this suspension, we purified pDCs using plasmacytoid dendritic cell isolation kit (Myltenyi biotec) according to the manufacturer’s instruction.

extract_protocol: Total RNA was extracted from isolated pDCs by miRNeasy Micro Kit (Qiagen).

treatment_protocol: FVB/NJcl female mice were purchased from Clea (Tokyo, Japan). The skin on the right ear of the mice of 7-9 weeks of age were treated topically, 3 times weekly, with 1.25 mg of 5% Imiquimod (IMQ) cream (Mochida Pharmaceutical). Vaseline was used for control. Mice were sacrificed at 4 weeks.

value: spleen

value: splenic pDCs

value: IMQ

tag: disease state

value: IMQ-induced SLE mouse model


title: vehicle control, subject 3 [K38vehiclectr_S9]

value: gingiva

tag: cell type


title: Limb cells, WT_168


title: AXER+/+ Medaka embryo heart, 5 dpf

value: heart

value: Japanese medaka HdrR

value: whole heart

value: AXER+/+


title: 4_WT_pH4_t240

value: Strain


title: pDCs, IMQ_2


title: pDCs, IMQ_3


title: RV, subject 2 [K169Rv_S8]

value: subject 2

value: oral epithelial cells


title: 3_WT_pH4_t90

value: 90 min


title: TNFRv, subject 2 [K169TNFRv_S7]

value: TNFRv


title: Limb cells, WT_167

value: WT

value: limb cells


title: 2_WT_pH4_t90

value: wild type


title: TNF, subject 2 [K169TNF_S6]

value: TNF


title: 1_WT_pH4_t90


title: Limb cells, WT_166


title: Limb cells, WT_164


title: Limb cells, WT_165


title: pDCs, Control_4

source_name: pDCs from Control mouse

value: spleen

value: splenic pDCs

value: control


title: vehicle control, subject 2 [K169vehiclectr_S5]

value: gingiva

value: vehicle control


title: 4_ΔΔ_GlcNAc_t240

source_name: Planktonic cells

value: N-Acetylglucosamine

value: 240 min


title: pDCs, Control_3


title: Limb cells, WT_163


title: pDCs, IMQ_1

value: IMQ

value: IMQ-induced SLE mouse model


title: 2_ΔΔ_GlcNAc_t240

value: Strain


title: 3_ΔΔ_GlcNAc_t240


title: 4_WT_pH4_t90


title: TNFRv, subject 1 [K186TNFRv_S3]

value: subject 1

value: oral epithelial cells


title: 1_ΔΔ_GlcNAc_t240


title: Limb cells, WT_162


title: Limb cells, WT_161


title: pDCs, Control_1


title: Limb cells, WT_160


title: vehicle control, subject 1 [K186vehiclectr_S1]


title: 3_ΔΔ_GlcNAc_t90

value: 90 min


title: 4_ΔΔ_GlcNAc_t90


title: CZTRN01_3

city: Prague

first: Martin

last: Bezdicka

state: Czech Republic

address: V Uvalu 84

department: Department of Pediatrics

country: Czech Republic

institute: Second Faculty of Medicine and Motol University Hospital

data_processing:
Illumina BaseSpace Sequence Hub was used for basecalling.
Trimming using cutadapt.
Aligned against hg38 with the Gencode annotation release 38 (May 2021), performed along with gene counting by the STAR aligner with parameters mostly set as advised by the manufacturer of the Collibri library construction kit.
Gene counts provided by the STAR program.
The gene counts tables and the sample metadata were assembled into a DESeq2 DESeqDataSet object.
Assembly: hg38 with the Gencode annotation release 38 (May 2021).
Supplementary files format and content: raw gene counts per sample

source_name: Human podocytes with steroid-sensitive nephrotic syndrome serum CZTRN01

growth_protocol: The standard cultivation medium consisted of RPMI 1640 with 10 % FBS heat inactivated, 1 % insulin-transferrin-selenium (1 % penicillin-streptomycin only in undifferentiated state).

extract_protocol:
The cells were lysed and the RNA was harvested using Trizol reagent and the PureLink RNA Mini Kit.
Collibri™ 3´ mRNA Library Prep Kit (ThermoFisher Scientific, A38110096).

treatment_protocol: 10 %  human serum samples (from SSNS or SRNS patients) were incubated at 37°C in 5% CO2 for 72 hours in standard medium without FBS and ITS. There were three biological replicates for all samples.

value: Differentiated human immortalized podocytes

value: standard cultivation medium

tag: clinical group

value: steroid-sensitive

tag: replicates

value: biological replicate TRN01, technical replicate 3


title: Limb cells, WT_15

data_processing:
Raw sequencing reads was processed with Perl scripts to ensure the quality of data used in further analysis. We first removed the adaptor-polluted reads (reads containing more than 5 adapter-polluted bases) and the low-quality reads (reads with the number of phred Quality value less than 19 accounting for more than 15% of total bases). And then discarded reads with number of N bases accounting for more than 5 %. The obtained clean data was mapped to the mm10 genome release with bowtie2 using default parameters. Reads count for each gene in each sample was counted by HTSeq.
The reads were mapped to the mouse genome (mm10) using bowtie2.
The mapped reads for genes were counted via featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample

value: WT

value: limb cells


title: pDCs, Control_2

value: spleen

value: splenic pDCs

value: control


title: CZTRN01_2

value: biological replicate TRN01, technical replicate 2


title: CZTRN01_1

value: biological replicate TRN01, technical replicate 1


title: RV, subject 1 [K186Rv_S4]

value: gingiva

value: RV


title: 1_ΔΔ_GlcNAc_t90

value: Strain

value: N-Acetylglucosamine


title: Limb cells, WT_159


title: Limb cells, WT_158


title: Limb cells, WT_157


title: 2_ΔΔ_GlcNAc_t90


title: CZ14087_3

source_name: Human podocytes with steroid-sensitive nephrotic syndrome serum CZ14087

value: biological replicate 14087, technical replicate 3


title: 3_hgc1Δ_GlcNAc_t240

value: 240 min


title: 2_hgc1Δ_GlcNAc_t240


title: Limb cells, WT_155


title: CZ14087_2

value: Differentiated human immortalized podocytes

value: biological replicate 14087, technical replicate 2


title: TNF, subject 1 [K186TNF_S2]

value: subject 1

value: oral epithelial cells

value: TNF


title: Limb cells, WT_156

value: WT

value: limb cells


title: CZ14054_2

source_name: Human podocytes with steroid-sensitive nephrotic syndrome serum CZ14054

value: standard cultivation medium

value: steroid-sensitive

value: biological replicate 14054, technical replicate 2


title: 1_hgc1Δ_GlcNAc_t240


title: CZ14054_3

value: biological replicate 14054, technical replicate 3


title: Limb cells, WT_154


title: CZ14054_1

value: biological replicate 14054, technical replicate 1


title: 4_hgc1Δ_GlcNAc_t90

value: 90 min


title: CZ13702_3

source_name: Human podocytes with steroid-sensitive nephrotic syndrome serum CZ13702

value: biological replicate 13702, technical replicate 3


title: 3_hgc1Δ_GlcNAc_t90

value: Strain

value: N-Acetylglucosamine


title: 2_hgc1Δ_GlcNAc_t90


title: CZ13702_2

value: biological replicate 13702, technical replicate 2


title: Limb cells, WT_152


title: Limb cells, WT_151


title: 1_hgc1Δ_GlcNAc_t90


title: CZ13702_1

value: Differentiated human immortalized podocytes

value: biological replicate 13702, technical replicate 1


title: 4_WT_GlcNAc_t240

value: wild type

value: 240 min


title: Limb cells, WT_150


title: CZ13508_3

source_name: Human podocytes with steroid-sensitive nephrotic syndrome serum CZ13508

value: biological replicate 13508, technical replicate 3


title: Limb cells, WT_14

value: WT


title: CZ13508_2

value: biological replicate 13508, technical replicate 2


title: CZ12983_3

source_name: Human podocytes with steroid-sensitive nephrotic syndrome serum CZ12983

value: standard cultivation medium

value: biological replicate 12983, technical replicate 3


title: CZ13508_1

value: steroid-sensitive

value: biological replicate 13508, technical replicate 1


title: CZ12983_2

value: biological replicate 12983, technical replicate 2


title: 2_WT_GlcNAc_t240


title: 4_WT_GlcNAc_t90

value: 90 min


title: 4_hgc1Δ_GlcNAc_t240


title: Limb cells, WT_148

value: limb cells


title: CZ12655_3

source_name: Human podocytes with steroid-sensitive nephrotic syndrome serum CZ12655

value: biological replicate 12655, technical replicate 3


title: Limb cells, WT_146


title: 2_WT_GlcNAc_t90

value: Strain

value: N-Acetylglucosamine


title: Limb cells, WT_145


title: 1_WT_GlcNAc_t90


title: CZ12655_2

value: Differentiated human immortalized podocytes

value: biological replicate 12655, technical replicate 2


title: CZ12983_1

value: biological replicate 12983, technical replicate 1


title: Limb cells, WT_142


title: Limb cells, WT_147


title: 4_ΔΔ_SD-HS_t240

value: SD with 10% human serum

value: 240 min


title: CZ12655_1

value: biological replicate 12655, technical replicate 1


title: 3_WT_GlcNAc_t240

value: wild type


title: Limb cells, WT_153

value: WT


title: Limb cells, WT_143


title: 2_ΔΔ_SD-HS_t240


title: 3_ΔΔ_SD-HS_t240


title: Limb cells, WT_141


title: Limb cells, WT_149


title: 1_WT_GlcNAc_t240


title: Limb cells, WT_144


title: 1_ΔΔ_SD-HS_t240


title: Limb cells, WT_13


title: 4_ΔΔ_SD-HS_t90


title: CZ12212_2

source_name: Human podocytes with steroid-sensitive nephrotic syndrome serum CZ12212

value: standard cultivation medium

value: biological replicate 12212, technical replicate 2


title: CZ12212_1

value: steroid-sensitive

value: biological replicate 12212, technical replicate 1


title: Limb cells, WT_138


title: 2_ΔΔ_SD-HS_t90

value: 90 min


title: 3_ΔΔ_SD-HS_t90


title: CZ11915_2

source_name: Human podocytes with steroid-sensitive nephrotic syndrome serum CZ11915

value: biological replicate 11915, technical replicate 2


title: 3_WT_GlcNAc_t90


title: CZ11915_3

value: biological replicate 11915, technical replicate 3


title: patient 9, day3, scRNA-seq

city: Toronto

first: Adam

last: Gehring

state: ON

address: 101 College St

country: Canada

institute: UHN

description:
E5
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 and reference GRCh38-2020-A (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: GRCh38-2020-A
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: PBMC

extract_protocol:
PBMCs were cryopreserved until ready to create library. PBMCs were quickly thawed at 37degrees celcius, washed to remove freezing media, and resuspended in PBS + 0.1% low endotoxin BSA to confirm viability of cells was >80%.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).

tag: individual

value: patient 9

value: PBMC

value: Placebo

tag: timepoint


title: CZ11136_3

source_name: Human podocytes with steroid-resistant nephrotic syndrome serum CZ11136

value: Differentiated human immortalized podocytes

value: steroid-resistant

value: biological replicate 11136, technical replicate 1


title: Limb cells, WT_136

last: OUYANG

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

source_name: Limb cells, WT

value: limb cells


title: CZ12212_3

value: biological replicate 12212, technical replicate 3


title: CZ11915_1

value: biological replicate 11915, technical replicate 1


title: patient 9, day7, scRNA-seq

description:
E6
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: patient 9, day0, scRNA-seq

description:
E4
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: 4_hgc1Δ_SD-HS_t240

value: Strain

value: SD with 10% human serum

value: 240 min


title: CZ11136_2

value: standard cultivation medium


title: Limb cells, WT_135

value: WT


title: patient 8, day7, scRNA-seq

description:
E3
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: patient 8


title: Limb cells, WT_140


title: 3_hgc1Δ_SD-HS_t240


title: CZ11136_1


title: Limb cells, WT_134


title: Limb cells, WT_139


title: 2_hgc1Δ_SD-HS_t240


title: Limb cells, WT_133


title: Limb cells, WT_137


title: CZ9488_3

source_name: Human podocytes with steroid-resistant nephrotic syndrome serum CZ9488

value: biological replicate 9488, technical replicate 3


title: 1_hgc1Δ_SD-HS_t240


title: patient 8, day0, scRNA-seq

description:
E1
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: patient 8, day3, scRNA-seq

description:
E2
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: Limb cells, WT_132


title: 1_ΔΔ_SD-HS_t90

value: 90 min


title: CZ9488_1

value: biological replicate 9488, technical replicate 1


title: Limb cells, WT_131


title: patient 7, day7, scRNA-seq

description:
D6
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: patient 7

value: PBMC


title: patient 7, day3, scRNA-seq

description:
D5
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: Placebo


title: 3_hgc1Δ_SD-HS_t90


title: 4_hgc1Δ_SD-HS_t90


title: CZ9019_3

source_name: Human podocytes with steroid-resistant nephrotic syndrome serum CZ9019

value: Differentiated human immortalized podocytes

value: steroid-resistant

value: biological replicate 9019, technical replicate 3


title: 2_hgc1Δ_SD-HS_t90


title: patient 7, day0, scRNA-seq

description:
D4
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: Limb cells, WT_12

value: limb cells


title: Limb cells, WT_130


title: patient 6, day7, scRNA-seq

description:
D3
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: patient 6

value: PEG-IFN-lambda


title: 1_hgc1Δ_SD-HS_t90

value: Strain

value: SD with 10% human serum


title: CZ9019_2

value: standard cultivation medium

value: biological replicate 9019, technical replicate 2


title: CZ9019_1

value: biological replicate 9019, technical replicate 1


title: patient 6, day3, scRNA-seq

description:
D2
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: Limb cells, WT_129

value: WT


title: CZ5837_3

source_name: Human podocytes with steroid-resistant nephrotic syndrome serum CZ5837

value: biological replicate 5837, technical replicate 3


title: 4_WT_SD-HS_t240

value: wild type

value: 240 min


title: Limb cells, WT_128


title: 3_WT_SD-HS_t240


title: CZ9488_2

value: biological replicate 9488, technical replicate 2


title: CZ5837_2

value: biological replicate 5837, technical replicate 2


title: patient 5, day7, scRNA-seq

description:
C6
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: patient 5

value: PBMC


title: Limb cells, WT_127


title: 2_WT_SD-HS_t240


title: Limb cells, WT_126


title: 1_WT_SD-HS_t240


title: patient 5, day3, scRNA-seq

description:
C5
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: Limb cells, WT_125


title: patient 5, day0, scRNA-seq

description:
C4
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: 4_WT_SD-HS_t90

value: 90 min


title: patient 4, day7, scRNA-seq

description:
C3
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: patient 4


title: 3_WT_SD-HS_t90