title: Brain single cell 93

description: Brain single cell 93


title: NC-PKU-mix26-qia

status: Public on Sep 28 2023

type: SRA

city: Beijing

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

country: China

institute: Tsinghua University

description: small RNA-seq of  homo sapiens: healthy donor's plasma; Provided by Peking University First Affiliated Hospital.

library_source: transcriptomic

data_processing:
UMIs were extracted by umi_tools (version: 1.1.0) using regex: ^.+(?P<discard_1>AACTGTAGGCACCATCAAT)(?P<umi_1>.{{12}})(?P<discard_2>.+)
Adapters were removed by trim_galore (version 0.6.6) with parameters: --quality 30 --length 15 --trim-n --phred33
Reads were aligned  to reference by bowtie2 (version 2.3.5.1) with parameters: --norc --sensitive. Reads are aligned in the following sequnce: spikein_small, univec,  rRNA, miRNA, lncRNA, mRNA, piRNA, snoRNA, snRNA, srpRNA, tRNA, tucpRNA, Y_RNA, genome and circRNA. All reads unmapped in previous steps were mapped to the next reference.
Aligned reads were sorted by samtools (version 1.10)
Aligned reads were dedupliecated by umi_tools (version: 1.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: plasma

extract_protocol:
RNA was extracted from 0.2mL of plasma using miRNeasy Serum/Plasma Kit.
cell-free small RNA library was prepared using QIAseq miRNA Library Kit.

tag: gender

value: male

tag: age

tag: Stage

value: No stage (healthy donor)


title: Brain single cell 92

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Brain single cell 92

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
Fluorescent cells were sorted by FACS from Pdgfra-H2BGFP mice and Tagl-CREERT2;Ai14 mice as previously described (Vanlandewijck et al, 2018). Briefly, brain tissue from both males and females were mechanically and enzymatically digested and vascular fragments isolated using CD31 antibody coated Dynabeads and further digested into cell suspension.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

tag: tissue

value: brain

value: adult mice


title: Brain single cell 91

description: Brain single cell 91


title: hVCF-veh-557-cd4-

city: Providence

first: Sharon

last: Rounds

state: RI

address: 830 Chalkstone Avenue,, Building 35, Room 216

country: USA

institute: Brown University

description:
Human ventricular cardiac fibroblasts (hVCF)_Veh_rep1
hVCF-veh-557-cd4-_R1
Missing R2 raw file, no longer retrievable from the service provider.

data_processing:
The raw data was obtained in FASTQ format and sequence reads were trimmed to remove possible adapter sequences and poor quality nucleotides using Trimmomatic v.0.36. The trimmed reads were mapped to Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The unique gene hit counts were calculated using feature counts from Subread package v.1.5.2. And the gene hit counts were used for differential expression analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene hit counts

source_name: Human ventricular cardiac fibroblasts (hVCF) , Veh

growth_protocol: Primary hVCFs from 3 human donors (males and female) were cultured in FGMTM-3 Fibroblast Growth Medium-3 BulletKitTM (Cat# CC-4526), 0.1% gentamicin/ amphotericin-B (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) for 96h with or without IL-1B at a concentration of 10ng/mL before replacing the media with ImmunoCultTM –XF T-cell expansion media (Cat # 10981) supplemented with IL-1B or no treatment. ImmunoCultTM Human CD3/CD28 T-Cell Activator was added after 72h of culture in ImmunoCultTM –XF T-cell expansion media.

extract_protocol:
Total RNA was extracted from cardiac fibroblast cells using Qiagen RNeasy Mini Kit (Cat# 74134) isolation kit
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303) by Genewiz company. Initial sample QC analysis was performed followed by RNA library preparation with polyA selection and sequenced on illumina Hi Seq in 2 x 150 bp paired end configuration.

treatment_protocol: Cells were cultured in T-cell expansion media with T Cell Activator in the presence or absence of IL-1B (10ng/mL) for 14 days

tag: cell type

value: human ventricular cardiac fibroblast cells (hVCFs)

tag: donor info

value: hVCF (Lonza; Cat# CC-2904; Lot# 67771)

value: hVCF derived from explant during human heart transplant

tag: Sex

value: Female

tag: cells population

tag: treatment

value: untreated

tag: site

value: Human Ventricle


title: NC-PKU-mix25-qia


title: Brain single cell 89

description: Brain single cell 89


title: Brain single cell 90

description: Brain single cell 90


title: NC-PKU-mix24-qia


title: Brain single cell 96

description: Brain single cell 96


title: NC-PKU-mix23-qia


title: Brain single cell 85

description: Brain single cell 85


title: Brain single cell 87

description: Brain single cell 87


title: Brain single cell 83

description: Brain single cell 83


title: Brain single cell 95

description: Brain single cell 95


title: Brain single cell 82

description: Brain single cell 82


title: Brain single cell 81

description: Brain single cell 81


title: NC-PKU-mix22-qia


title: NK cells, IL18R1WT, day 2 post MCMV infection, biol rep 4

city: New York

first: Hyunu

last: Kim

state: NY

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.38) and aligned to the mm10 genome assembly using salmon (v.0.13.1).
Assembly: mm10
Supplementary files format and content: tsv file is tab delimited raw counts (1 count per pair of reads) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)

extract_protocol:
Total RNA was extracted from sorted NK cells using PicoPure RNA Isolation Kit (Thermo Fisher Scientific). After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2 ng total RNA with RNA integrity numbers ranging from 9 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification.
Subsequently, 3-10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE100 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 41 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 59% to 78%.

tag: genotype

value: WT

tag: infection

tag: replicate


title: NK cells, IL18R1WT, day 2 post MCMV infection, biol rep 3


title: NK cells, IL18R1WT, day 2 post MCMV infection, biol rep 2


title: hVCF-veh-282-cd4+

description:
Human ventricular cardiac fibroblasts (hVCF)_Veh_rep2
hVCF-veh-282-cd4_R2

value: hVCF (Lonza; Cat# CC-2904; Lot# 534282)


title: NK cells, IL18R1WT, noninfected, biol rep 5


title: Brain single cell 80

description: Brain single cell 80


title: NC-PKU-mix20-qia


title: Brain single cell 79

description: Brain single cell 79


title: NK cells, IL18R1WT, noninfected, biol rep 4


title: Brain single cell 77

description: Brain single cell 77


title: Brain single cell 88

description: Brain single cell 88


title: NC-PKU-mix15-qia

value: female


title: Brain single cell 84

description: Brain single cell 84


title: NC-PKU-mix21-qia


title: Brain single cell 75

description: Brain single cell 75


title: Brain single cell 73

description: Brain single cell 73


title: NK cells, IL18R1KO, day 2 post MCMV infection, biol rep 4


title: Brain single cell 74

description: Brain single cell 74


title: NK cells, IL18R1KO, day 2 post MCMV infection, biol rep 3


title: NC-PKU-9-qia


title: Brain single cell 76

description: Brain single cell 76


title: Brain single cell 72

description: Brain single cell 72


title: hVCF-veh-557-cd4+

description:
Human ventricular cardiac fibroblasts (hVCF)_Veh_rep1
hVCF-veh-557-cd4_R1

value: hVCF (Lonza; Cat# CC-2904; Lot#67771)


title: NC-PKU-mix0-qia


title: Brain single cell 71

description: Brain single cell 71


title: Brain single cell 69

description: Brain single cell 69


title: Brain single cell 70

description: Brain single cell 70


title: NC-PKU-14-qia


title: NK cells, IL18R1KO, day 2 post MCMV infection, biol rep 2


title: Brain single cell 67

description: Brain single cell 67


title: Brain single cell 68

description: Brain single cell 68


title: NK cells, IL18R1KO, noninfected, biol rep 4


title: Brain single cell 86

description: Brain single cell 86


title: NC-PKU-mix19-qia


title: Brain single cell 78

description: Brain single cell 78


title: Brain single cell 66

description: Brain single cell 66


title: Brain single cell 65

description: Brain single cell 65


title: NC-PKU-12-qia


title: NK cells, IL18R1KO, noninfected, biol rep 5


title: NK cells, IL18R1WT, noninfected, biol rep 3


title: NK cells, IL18R1KO, noninfected, biol rep 3


title: Brain single cell 64

description: Brain single cell 64


title: NC-PKU-11-qia


title: NC-PKU-10-qia


title: Brain single cell 61

description: Brain single cell 61


title: Brain single cell 62

description: Brain single cell 62


title: Brain single cell 63

description: Brain single cell 63


title: Brain single cell 60

description: Brain single cell 60


title: Brain single cell 59

description: Brain single cell 59


title: Brain single cell 58

description: Brain single cell 58


title: NC-PKU-13-qia


title: CRC-PKU-31-qia

description: small RNA-seq of  homo sapiens: colorectal cancer patient's plasma; Provided by Peking University First Affiliated Hospital.


title: CRC-PKU-32-qia


title: Brain single cell 57

description: Brain single cell 57


title: Brain single cell 56

description: Brain single cell 56


title: Brain single cell 55

description: Brain single cell 55


title: CRC-PKU-29-qia


title: Brain single cell 53

description: Brain single cell 53


title: Brain single cell 54

description: Brain single cell 54


title: Brain single cell 52

description: Brain single cell 52


title: Brain single cell 51

description: Brain single cell 51


title: NS1

city: Shanghai

first: Yashu

last: Li

address: No,1665, Kongjiang Road, Yangpu District

department: Department of Plastic Surgery

institute: Xinhua hospital, Shanghai Jiaotong University

data_processing:
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer.
Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged mus musculus pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Assembly: (miRBase) v22
Supplementary files format and content: tab-delimited text file included the raw tag counts of the mature miRNA for each Sample
Supplementary files format and content: tab-delimited text file included the normalized tag counts of the mature miRNA (tpm) for each Sample

source_name: skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) Size selection of ~150 bp PCR amplicons (corresponding to ~22nt miRNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina HiSeq sequencer following the manufacturer's instructions.

value: skin

tag: time

value: week 2 post operation

tag: group

value: normal scars formed in control group

value: wound edges on the lower back sutured in situ with no tension


title: NS3


title: HS1

value: hypertrophic scars generated in stretched group

value: wound edges on the upper back sutured to the rib cage with tension


title: NS2


title: HS3


title: CRC-PKU-28-qia

value: male


title: Brain single cell 50

description: Brain single cell 50

value: brain

value: adult mice


title: CRC-PKU-27-qia


title: Brain single cell 49

description: Brain single cell 49


title: Brain single cell 48

description: Brain single cell 48


title: WT9ewat

city: Shenyang

first: Wensu

last: Liu

state: Liaoning

address: 77 Puhe Road, Shenyang North New Area

institute: China Medical University

data_processing:
Quality control of the raw data was performed using FastQC software (v0.11.9)
Mapping was performed using STAR(v2.7.8)  with the default parameters. Reference genome annotation files were downloaded from NCBI (GRCm39)
The gene expression levels were quantified using featureCounts (v2.0.3) with raw counts. Gene expression levels were calculated using the transcripts per kilobase million (TPM) method that was used for further data processing.
Differential gene expression was assessed with DESeq2 (v1.32.0) using the raw count tables generated by featureCounts
Normalzation and Further analysis were performed using R and self-written codes
Assembly: GRCm39
Supplementary files format and content: .csv format indcluding the TPM values for all samples

source_name: subcutaneous fat

extract_protocol:
Total RNA of each sample was extracted by using RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
The transcriptome libraries were constructed by using NEBNext® Ultra RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations as described previously.

value: subcutaneous fat

value: normal+drug


title: WT9i

source_name: viceral fat

value: viceral fat


title: CRC-PKU-24-qia


title: Brain single cell 47

description: Brain single cell 47


title: WT99i

value: normal


title: CRC-PKU-23-qia


title: Brain single cell 46

description: Brain single cell 46


title: Brain single cell 45

description: Brain single cell 45


title: WT99ewat


title: CRC-PKU-30-qia


title: CRC-PKU-21-qia


title: HS2

value: WT


title: Brain single cell 44

description: Brain single cell 44


title: Brain single cell 43

description: Brain single cell 43


title: Brain single cell 41

description: Brain single cell 41


title: CRC-PKU-20-qia


title: Brain single cell 42

description: Brain single cell 42


title: Brain single cell 40

description: Brain single cell 40


title: Brain single cell 39

description: Brain single cell 39


title: CRC-PKU-19-qia


title: CRC-PKU-17-qia


title: WT98e


title: Brain single cell 38

description: Brain single cell 38


title: Brain single cell 36

description: Brain single cell 36


title: WT96e


title: CRC-PKU-16-qia


title: WT94i


title: Brain single cell 35

description: Brain single cell 35


title: Brain single cell 34

description: Brain single cell 34


title: CRC-PKU-15-qia


title: WT92i


title: CRC-PKU-14-qia


title: CRC-PKU-13-qia


title: Brain single cell 30

description: Brain single cell 30


title: WT92e


title: Brain single cell 31

description: Brain single cell 31


title: Brain single cell 33

description: Brain single cell 33


title: Brain single cell 32

description: Brain single cell 32


title: WT96i


title: Brain single cell 29

description: Brain single cell 29


title: STAD-PKU-9-pico

description: RNA-seq of homo sapiens: stomach cancer patient's plasma; Provided by Peking University First Affiliated Hospital; Constructed by SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian; Purpose: To explore novel plasma extracellular RNA biomarkers for cancer diagnosis

data_processing:
Adaptors and low-quality sequences in the raw sequencing data were trimmed using cutadapt version 2.3. Remeined reads were mapped to ERCC's spike-in sequences, NCBI's UniVec sequences and human rRNA sequences sequentially. GC oligos introduced in reverse transcription were trimmed off, after which reads shorter than 30 nt were discarded.
STAR (version 2.5.3a_modified) was used to map clean reads to the hg38 genome index built with the GENCODE v27 annotation
Duplicates in the aligned reads were removed using Picard Tools MarkDuplicates (version 2.20.0)
The count matrix was constructed using featureCounts11 v1.6.2 with the GENCODE v27 annotation, transcripts with uncertain coding potential annotation extracted from mitranscriptome, circular RNA annotation from circBase, Promoter, enhancer and repeat regions frm UCSC Genome Browser. Reads mapped to mitochondrial RNAs were excluded.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted from 1 mL of plasma using the Plasma/Serum Circulating RNA and Exosomal Purification kit (Norgen)
cell free RNA library is prepared using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian.


title: WT91e


title: WT98i


title: Brain single cell 27

description: Brain single cell 27


title: Brain single cell 28

description: Brain single cell 28


title: Brain single cell 25

description: Brain single cell 25


title: WT8ewat


title: Brain single cell 26

description: Brain single cell 26


title: Brain single cell 37

description: Brain single cell 37


title: STAD-PKU-7-pico


title: WT8i


title: STAD-PKU-8-pico


title: WT6i


title: Brain single cell 22

description: Brain single cell 22


title: Brain single cell 23

description: Brain single cell 23


title: Brain single cell 24

description: Brain single cell 24


title: Brain single cell 21

description: Brain single cell 21


title: STAD-PKU-6-pico


title: Brain single cell 20

description: Brain single cell 20


title: STAD-PKU-5-pico


title: WT5i


title: WT2i


title: Brain single cell 17

description: Brain single cell 17


title: Brain single cell 18

description: Brain single cell 18


title: WT2ewat


title: STAD-PKU-4-pico


title: Brain single cell 16

description: Brain single cell 16


title: STAD-PKU-3-pico


title: Brain single cell 15

description: Brain single cell 15


title: WT11ewat


title: STAD-PKU-38-pico


title: W5e


title: HFDbc62i

value: High-fat diet+drug


title: STAD-PKU-37-pico


title: Brain single cell 12

description: Brain single cell 12


title: Brain single cell 10

description: Brain single cell 10


title: STAD-PKU-36-pico

value: female


title: Brain single cell 14

description: Brain single cell 14


title: Brain single cell 13

description: Brain single cell 13


title: Brain single cell 11

description: Brain single cell 11


title: HFD62e


title: STAD-PKU-35-pico


title: Brain single cell 7

description: Brain single cell 7


title: Brain single cell 9

description: Brain single cell 9


title: Brain single cell 19

description: Brain single cell 19


title: Brain single cell 6

description: Brain single cell 6


title: Brain single cell 8

description: Brain single cell 8


title: HFD52e


title: STAD-PKU-34-pico


title: STAD-PKU-33-pico


title: Brain single cell 4

description: Brain single cell 4


title: Brain single cell 2

description: Brain single cell 2


title: Brain single cell 3

description: Brain single cell 3


title: STAD-PKU-32-pico


title: HFD27i


title: Brain single cell 1

description: Brain single cell 1


title: HFD26i


title: HFD26e


title: STAD-PKU-31-pico


title: STAD-PKU-30-pico


title: STAD-PKU-2-pico


title: HFD25i


title: Selaginella moellendorffii stem leaves csRNA-seq r2

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
csRNA-seq; nascent TSS mapping in S.moellendorffii cells; Experiment SD21
S.moellendorffii-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: csRNA-Seq

organism: Selaginella moellendorffii

source_name: stem & leaves

growth_protocol: A.thaliana Col-0 mature leaves were collected from plants grown as described (M. Wang et al. 2023), while A.thaliana Col-0 suspension cells were grown in 250-mL baffled flasks containing 50 mL of growth medium (3.2 g/L Gamborg’s B-5 medium, 3 mM MES, 3% [v/v] Suc, 1.1 mg L−1 2,4-dichlorophenoxyacetic acid). The cultures were maintained at 23°C under continuous light on a rotary shaker (160 rpm) and kindly provided as a frozen pellet by Dr. Ashley M. Brooks. Barley (Hordeum vulgare) RNA was isolated by Dr. Pete Hedley from embryonic tissue (including mesocotyl and seminal roots; EMB) isolated from grain tissues 4 days past germination (Mascher et al. 2017). Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light. Selaginella moellendorffii was purchased from Plant Delights Nursery and grown at the window under normal daylight for 1 week prior to isolating RNA from stems and leaves. C. reinhardtii, which was kindly provided by Dr. Will Ansari and Dr. Stephen Mayfield (UC San Diego), was grown to late logarithmic phase in TAP (Tris–acetate–phosphate) medium at 23°C under constant illumination of 5000 lux on a rotary shaker. Adult 2nd and 3rd leaves from Z. mays L. cultivar B73 was kindly provided by Dr. Lauri Smith (UC San Diego). Plants were grown in 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA. RNA from Z. mays L. cultivar B73 7d old shoot, root and leaves were grown in the Schmitz laboratory (University of Georgia) as described in (Ricci et al. 2019).

extract_protocol: csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles.  Total RNA-Seq Library Preparation  Strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Ribo-Zero Gold plant rRNA removal kit (Illumina, San Diego, CA). Samples were processed following the manufacturer’s instructions.

value: stem & leaves


title: Selaginella moellendorffii stem leaves csRNA-seq r1

description:
csRNA-seq; nascent TSS mapping in S.moellendorffii cells; Experiment SD1009
S.moellendorffii-10.tss.txt


title: HFD54i


title: STAD-PKU-29-pico


title: Brain single cell 5

description: Brain single cell 5


title: Hb27e


title: Selaginella moellendorffii stem leaves sRNA-seq r1

description:
sRNA-seq; small RNA mapping in S.moellendorffii cells; Experiment SD1070
S.moellendorffii-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.


title: Selaginella moellendorffii stem leaves 5GRO-seq r1

description:
5'GRO-seq; nascent TSS mapping in S.moellendorffii cells; Experiment SD180
S.moellendorffii-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: 5'GRO-seq


title: HFD25e


title: STAD-PKU-28-pico


title: T5_14d_1.Slide3.B1-1

type: other

city: Pittsburgh

first: Shuchang

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

hyb_protocol: Protocal provided and performed by resolve bioscience (https://your.resolve-biosciences.com/), with reference paper PMID: 35021063

data_processing: Gene count per cell were identified by QuPath

molecule: other

source_name: liver

growth_protocol: Mice were fed regular chow in standard caging and kept under a 12-hour light–dark cycle with no enrichment.

extract_protocol: Frozen livers were sectioned and sent on dry ice to resolve bioscience for further processing

treatment_protocol: were subjected to parialt hepatectomy (PH) in which 2/3 of the liver were removed.

value: 2 month


title: T5_14d_3.Slide3.D1

scan_protocol: Protocal provided and performed by resolve bioscience (https://your.resolve-biosciences.com/), with reference paper PMID: 35021063


title: T6_3m.Slide1.D2

label_protocol: Protocal provided and performed by resolve bioscience (https://your.resolve-biosciences.com/), with reference paper PMID: 35021063


title: T7_6m.Slide2.D2


title: H83i

value: High-fat diet


title: H83e


title: STAD-PKU-27-pico


title: T4_72h_2.Slide2.D1


title: T4_72h_1.Slide1.B1


title: T3_48h_2.Slide1.A1


title: T3_48h_1.Slide1.C2


title: Selaginella moellendorffii stem leaves GRO-seq r1

description:
GRO-seq; nascent transcriptome profiling in S.moellendorffii; Experiment SD385
S.moellendorffii-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: GRO-seq


title: T2_24h.Slide1.B2-2


title: STAD-PKU-25-pico


title: T2_24h.Slide1.B2-1


title: H51i


title: H82e


title: T1_0h_2.Slide2.A2


title: T5_14d_2.Slide3.C1


title: H50i


title: STAD-PKU-23-pico


title: H50e


title: STAD-PKU-22-pico


title: 7-doms_aPCA_output_bio_rep_2

city: Barcelona

first: Magdalena

last: Topolska

state: Barcelona

address: C/ del Dr. Aiguader, 88

department: Systems and Synthetic Biology

country: Spain

institute: Centre for Genomic Regulation

library_source: genomic

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Supplementary files format and content: Tabular format; contains the Dimsum fitness estimations and their corresponding errors
Library strategy: DNA-seq

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: For each of the two protein domains (GRB2-SH3 and PSD95-PDZ) and the pooled libraru (7-doms) for both the aPCA and bPCA  assays (abundancePCA and bindingPCA), each of the growth competitions was performed right after yeast transformation. After the first cycle of post-transformation plasmid selection, a second plasmid selection cycle (input) was performed by inoculating SC -URA/ADE at a starting OD600nm = 0.1 with the saturated culture. Cells were grown for 4 generations at 30ºC under constant agitation at 200 rpm. This allowed the pool of mutants to be amplified and enter the exponential growth phase. The competition cycle (output) was then started by inoculating cells from the input cycle into the competition media (SC -URA/ADE + 200 ug/mL Methotrexate) so that the starting OD600nm was 0.05. For that, the adequate volume of cells were collected, centrifuged at 3,000 rpm for 5 minutes and resuspended in the pre-warmed output media. Meanwhile, each input replicate culture was splitted in two and harvested by centrifugation for 5 min at 5,000g at 4ºC. Yeast cells were washed with water, pelleted and stored at -20ºC for later DNA extraction. After ~5 generations of competition cycle, each output replicate culture was splitted into two and harvested by centrifugation for 5 min at 5,000g at 4ºC, washed twice with water and pelleted to be stored at -20ºC

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 1 mL of DNA extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris-HCl pH8, 1mM EDTA pH8), frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 1 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.1 mL of NaOAc 3M and 2.2 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was allowed to dry overnight at RT. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (30 μL of QIAEX II beads). The samples were washed twice with PE buffer and eluted twice by 125 μL of 10 mM Tris-HCI buffer, pH 8.5 and then combined two elution. Finally, plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids.
We performed 2 consecutive PCR reactions for each sample. The first PCR (PCR1) is used to amplify the amplicons for sequencing, to add a part of the illumina sequencing adaptors to the amplicon and to increase nucleotide complexity for the sequencing reaction by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) is used to add the remainder of the illumina adaptor and to add demulitplexing indexes. All samples, except the GRB2-SH3 bPCA, were dual-indexed using differing barcode indexes both for the forward (5’ P5 Illumina adapter) and reverse oligos (3’ P7 Illumina adapter). The GRB2-SH3 bPCA library was single-indexed using a constant forward oligo  (3’ P7 Illumina adapter) and alternating reverse oligos (3’ P7 Illumina adapter). The amplicon library pools were run on a 2% agarose gel and were purified using QIAEX II Gel Extraction Kit (QIAGEN) and using 30uL of QIAEX II beads for each sample. The purified amplicons were subjected to Illumina 150bp paired-end NextSeq sequencing at the CRG Genomics Core Facility.

tag: protein domains

tag: assays

value: abundant PCA

tag: subtype

value: DNA amplicon


title: 7-doms_aPCA_output_bio_rep_1


title: 7-doms_aPCA_output_bio_rep_3


title: H23i


title: 7-doms_aPCA_input_bio_rep_3


title: STAD-PKU-21-pico

tag: gender

tag: age

tag: Stage


title: 7-doms_aPCA_input_bio_rep_1

tag: strain


title: 7-doms_aPCA_input_bio_rep_2


title: STAD-PKU-26-pico


title: H23e

tag: tissue


title: H22i


title: PSD95-PDZ3_bPCA_output_bio_rep_3

value: binding PCA


title: STAD-PKU-19-pico


title: PSD95-PDZ3_bPCA_output_bio_rep_2


title: PSD95-PDZ3_bPCA_input_bio_rep_3


title: PSD95-PDZ3_bPCA_input_bio_rep_2


title: H22e


title: STAD-PKU-24-pico


title: T1_0h_1.Slide1.A2


title: PSD95-PDZ3_bPCA_input_bio_rep_1


title: STAD-PKU-17-pico


title: Z2-KO3

first: Antonio

last: Postigo

state: BARCELONA

address: Casanova 143. Cellex 1B

institute: IDIBAPS/ICREA

description:
36h fasting
AP8668

data_processing:
RNA-seq reads were mapped against Homo sapiens reference genome with STAR (ENCODE parameters)
Genes were quantified with RSEM (default parameters)
Normalization and differential expression was performed with DESeq2
GO/KEGG enrichment analysis was performed with G:profiler
Genome_build: GRCm38
Supplementary_files_format_and_content: txt file containing RSEM expected counts

source_name: ZEB2 knock-out control 36h fasting - sample 3

growth_protocol: RNA from total muscle from mouse muscles

extract_protocol:
Total RNA was isolated using Trizol
0.5ug RNA was subjected to library synthesis using TruSeq® Stranded mRNA LT Sample Prep Kit

treatment_protocol: Muscle was dissected 36h after fasting

value: 36h fasting

tag: cell type

value: Total RNA from gastrocnemius muscle

value: ZEB2 flx/flx; HSACre (ZEB2-KO)


title: PSD95-PDZ3_aPCA_output_bio_rep_3


title: PSD95-PDZ3_aPCA_output_bio_rep_2


title: STAD-PKU-16-pico


title: Z2-KO2

description:
36h fasting
AP8667

source_name: ZEB2 knock-out control 36h fasting - sample 2


title: PSD95-PDZ3_aPCA_output_bio_rep_1


title: Z2-KO1

description:
36h fasting
AP8666

source_name: ZEB2 knock-out control 36h fasting - sample 1


title: STAD-PKU-15-pico


title: PSD95-PDZ3_aPCA_input_bio_rep_2


title: PSD95-PDZ3_aPCA_input_bio_rep_3


title: GRB2-SH3_bPCA_output_bio_rep_3


title: STAD-PKU-1-pico

value: male


title: GRB2-SH3_bPCA_output_bio_rep_2


title: Z2-C3

description:
36h fasting
AP8665

source_name: ZEB2 control 36h fasting - sample 3

value: ZEB2 flx/flx (control)


title: Z2-C2

description:
36h fasting
AP8664

source_name: ZEB2 control 36h fasting - sample 2


title: PSD95-PDZ3_aPCA_input_bio_rep_1


title: PSD95-PDZ3_bPCA_output_bio_rep_1


title: STAD-PKU-12-pico


title: STAD-PKU-18-pico


title: GRB2-SH3_bPCA_input_bio_rep_3


title: Z2-C1

description:
36h fasting
AP8663

source_name: ZEB2 control 36h fasting - sample 1


title: STAD-PKU-11-pico


title: Z1-KO3

description:
36h fasting
AP8662

source_name: ZEB1 knock-out control 36h fasting - sample 3

value: ZEB1 flx/flx; HSACre (ZEB1-KO)


title: GRB2-SH3_bPCA_input_bio_rep_2


title: GRB2-SH3_bPCA_input_bio_rep_1


title: GRB2-SH3_aPCA_output_bio_rep_3


title: STAD-PKU-10-pico


title: GRB2-SH3_aPCA_output_bio_rep_2


title: Z1-KO2

description:
36h fasting
AP8661

source_name: ZEB1 knock-out control 36h fasting - sample 2


title: NC-PKU-mix9-2-pico

description: RNA-seq of homo sapiens: healthy donor's plasma; Provided by Peking University First Affiliated Hospital; Constructed by SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian; Purpose: To explore novel plasma extracellular RNA biomarkers for cancer diagnosis

value: No stage (healthy donor)


title: GRB2-SH3_aPCA_output_bio_rep_1


title: STAD-PKU-13-pico


title: Z1-C3

description:
36h fasting
AP8659

source_name: ZEB1 control 36h fasting - sample 2

value: ZEB1 flx/flx (control)


title: GRB2-SH3_aPCA_input_bio_rep_1


title: GRB2-SH3_bPCA_output_bio_rep_1


title: NC-PKU-mix9-1-pico

source_name: plasma


title: Z1-KO1

description:
36h fasting
AP8660

source_name: ZEB1 knock-out control 36h fasting - sample 1


title: Physcomitrella patens plate culture sRNA-seq r2

description:
sRNA-seq; small RNA mapping in P.patens cells; Experiment SD578
P.patens-Gransden-10.tss.txt

organism: Physcomitrium patens

source_name: plate culture

value: plate culture


title: NC-PKU-mix8-2-pico


title: Zea mays leaf sRNA-seq r1

description:
sRNA-seq; small RNA mapping in Z.mays cells; Experiment SD938
Z.mays-leaf-10.tss.txt

organism: Zea mays

source_name: adult leaf

value: adult leaf


title: NC-PKU-mix8-4-pico


title: Z1-C2

description:
36h fasting
AP8658

source_name: ZEB1 control 36h fasting - sample 1


title: Physcomitrella patens plate culture sRNA-seq r1

description:
sRNA-seq; small RNA mapping in P.patens cells; Experiment SD726
P.patens-Gransden-10.tss.txt


title: Zea mays leaf csRNA-seq r3

description:
csRNA-seq; nascent TSS mapping in Z.mays cells; Experiment SD906
Z.mays-leaf-10.tss.txt


title: NC-PKU-mix8-3-pico


title: human CD4+  T cells_CD73+_biol rep 3

city: Essen

first: Hannah Sabeth

last: Sperber

state: NRW

address: Virchowstr. 171

department: Institute for transaltional HIV Research

country: Germany

institute: Essen University Hospital

description:
6-D3-CD73pos
raw_counts.csv
normalized_counts.csv
rlog_transformed_counts.csv

data_processing:
Paired-end sequencing was performed using the Illumina NovaSeq 6000 instrument to obtain a minimum of 20 million read pairs per sample with a read length of 2x150 bp.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Using DESeq2, a comparison of gene expression between samples was performed adjusting for the donor effect as confounding variable. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 (Benjamini-Hochberg method) and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: normalized counts for each sample
Supplementary files format and content: rlog transformed counts for each sample

source_name: Peripheral blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from three donors by Ficoll-Hypaque density gradient centrifugation (Corning) at 2000 rpm (~ 850 x g) at RT for 30 min, without brake. PBMCs were immediately processed to isolate CD4+ T cells by negative selection using the EasySep Human CD4+ T Cell Isolation Cocktail (StemCell Technologies) according to manufacturer’s protocol.

extract_protocol:
RNA preparation was conducted at Genewiz (USA).
library preparation was conducted at Genewiz (USA).

treatment_protocol: Freshly isolated CD4+ T cells from healthy blood donors were sorted based on their CD73 expression. To that purpose, cells were stained with APC anti-Human CD73 (1:50, Biolegend) diluted in PBS and incubated for 20 min at RT according to the manufacturer's protocol. Cells were washed and kept on ice. Fluorescence-activated cell sorting was performed using the MA900 Multi-Application Cell Sorter (Sony Biotechnologies). 3x10^6 CD73- and CD73+ CD4+ T cells were collected respectively, and stored as dry cell pellets at -80 °C until further processing.

tag: donor

value: Peripheral blood

value: blood-derived CD4+ T cells

tag: sorted cell type


title: human CD4+  T cells_CD73+_biol rep 1

description:
4-D1-CD73pos
raw_counts.csv
normalized_counts.csv
rlog_transformed_counts.csv


title: human CD4+  T cells_CD73+_biol rep 2

description:
5-D2-CD73pos
raw_counts.csv
normalized_counts.csv
rlog_transformed_counts.csv


title: NC-PKU-mix7-1-pico

value: female


title: human CD4+  T cells_CD73-_biol rep 2

description:
2-D2-CD73neg
raw_counts.csv
normalized_counts.csv
rlog_transformed_counts.csv


title: human CD4+  T cells_CD73-_biol rep 1

description:
1-D1-CD73neg
raw_counts.csv
normalized_counts.csv
rlog_transformed_counts.csv


title: GRB2-SH3_aPCA_input_bio_rep_2


title: NC-PKU-mix7-2-pico


title: Zea mays leaf csRNA-seq r2

tag: treatment


title: Zea mays leaf csRNA-seq r1

description:
csRNA-seq; nascent TSS mapping in Z.mays cells; Experiment SD760
Z.mays-leaf-10.tss.txt


title: GRB2-SH3_aPCA_input_bio_rep_3


title: cardiomyocyte, H3K4me3, CUT&RUN

city: nantes

first: Julien

last: Barc

address: 8 quai moncousu

country: France

institute: INSERM

data_processing:
Alignment with Bowtie2, with yeast spike-in factor
Filtering the hg19 blacklist regions with bedtools intersect -v -abam -b (from https://github.com/Boyle-Lab/Blacklist/tree/master/lists)
Sorting bams with samtools sort
Peak calling with MACS2 (--keep-dup all -g hs -q 0,01 –broad-cutoff 0,05)
Generating bigwigs files: bamCoverage --binSize 10 --smoothLength 30 –ignoreDuplicates
Assembly: Homo sapiens GRCH37
Supplementary files format and content: bw: bigWig. Indexed binary format. Dense continuous data displayed in Genome Browser
Library strategy: CUT&RUN

source_name: cardiomyocyte derived from human iPS cell

extract_protocol:
Cells were prepared using the CUT&RUN Assay Kit (CST, #86652).
CUT&RUN fragments were purified using Monarch PCR & DNA Cleanup Kit with oligonucleotide cleanup protocol (New England Biolabs, #T1030L). Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, #E7645L) complemented with NEBNext Multiplex Oligos for Illumina (New England Biolabs, #E6440L). End repair and A tailing were performed for 30 minutes at 20C and then 1 hour at 50C. DNA was cleaned using 0.9X Ampure XP Beads (Beckman Coulter, #A63881). Libraries were amplified using 13 cycles on the thermocycler and cleaned with 0.9X Ampure XP Beads (Beckman Coulter, #A63881). Libraires were validated using Agilent High Sensitivity D1000 ScreenTape.

tag: cut&run antibody


title: NC-PKU-mix6-6-pico


title: cardiomyocyte, CTCF, CUT&RUN

value: cardiomyocyte derived from human iPS cell

value: CTCF (CST, #3418T)


title: cardiomyocyte, pooled-libraries, ATAC-seq

data_processing:
Alignment with Bowtie2 -X 2000
Sorting bams and indexing with samtools
Peak calling with MACS2 (--keep-dup all -g hs -q 0,01 –broad-cutoff 0,05)
Generating bigwigs files: bamCoverage --binSize 10 --smoothLength 30 –ignoreDuplicates, with a scale factor computed by DESEQ2
Assembly: Homo sapiens GRCH37
Supplementary files format and content: bw: bigWig. Indexed binary format. Dense continuous data displayed in Genome Browser

extract_protocol:
DNA was tagmented using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina, #20034198) on permeablized cardiomyocytes (0.1% digitonin, Promega , #G9441) and then purified using DNA Clean and Concentrator (Zymo Research, #D4014).
Libraries were prepared using Nextera DNA Library Prep Kit (Illumina, #15028211) complemented with Nextera Index Kit (Illumina, #15055289). Libraries were amplified using 11 cycles on the thermocycler and cleaned with Ampure XP Beads (Beckman Coulter, #A63881). Libraires were validated using Agilent High Sensitivity D1000 ScreenTape.


title: cardiomyocyte, H3K27ac, CUT&RUN


title: LPS_CRISPRiB

city: Cambridge

last: Sun

state: MA

address: 455 Main St

department: EECS

institute: Whitehead Institute

description:
10x Genomics
iMGs.snRNAseq.Jan2023.counts.rds
iMGs.snRNAseq.Jan2023.metadata.rds

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPSC-induced microglia

extract_protocol:
sgRNAs were in vitro transcribed with sgRNA Precision Synthesis Kit (Thermo Fisher) delivered via lipofectamine. After 4 hours from sgRNA delivery, LPS was added to samples (LPS) and (CRISPRi). 12 hours later cells were harvested and processed.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Monocultures of iMGLs were treated with LPS (10 ng/mL) for 12 hours.

value: iPSC-induced microglia


title: NC-PKU-mix6-5-pico


title: LPS_CRISPRiA


title: cardiomyocyte, DC2555, ATAC-seq


title: Control2

description:
10x Genomics
iMGs.snRNAseq.May2022.counts.rds
iMGs.snRNAseq.May2022.metadata.rds

value: Ctrl


title: human CD4+  T cells_CD73-_biol rep 3

description:
3-D3-CD73neg
raw_counts.csv
normalized_counts.csv
rlog_transformed_counts.csv


title: cardiomyocyte, H3K4me1, CUT&RUN


title: LPS

value: LPS


title: NC-PKU-mix6-3-pico


title: AY5571

first: Cristina

last: Hernandez

address: Calle Natzaret 115-117

institute: Vall D'Hebron Institute of Oncology

data_processing:
The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x51bp, following the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 3.4.4).
RNA-seq reads were mapped against a combined reference genome of human (GRCh38) and mouse (GRCm39), using STAR aligner version 2.7.8a with ENCODE parameters. Annotated genes were quantified using a combined annotation of human GENCODE v42 and mouse GENCODE version M31, with software RSEM version 1.3.0 and default parameters. Subsequently, counts belonging to mouse genes were filtered out.
Differential expression analysis was performed independently for each cell line, using limma v3.6.1 R package. Counts were normalized with TMM and transformed with the ‘voom’ function into logCPM. The linear models were fitted with the voom-transformed counts adjusting for the sex covariate and constrasts were extracted. A gene set enrichment analysis (GSEA) was perfomed on the list of pre-ranked genes by the limma moderated t-statistic, with the R package fgsea v1.12 , against the Reactome database.
Assembly: gh38 and mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: ACUTE TX TUMOR #283

extract_protocol:
Tumors were disaggregated using the hard tissue homogenizing CK28-2 mL kit (#P000916-LYSKO-A, Bertin Technologies) following standard procedures in a Precellys® Evolution Homogeniser (Bertin Technologies). Total RNA from tumors was isolated using the RNeasey mini kit (#74104, Qiagen). Total RNA was quantified by Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and the RNA integrity was estimated by using RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent).
RNASeq libraries were prepared with KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Roche) following the manufacturer´s recommendations starting with 500 ng of total RNA as the input material. The library was quality controlled on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.

value: subcutaneous tumor

tag: cell line

value: Vehicle


title: AZ2481

source_name: ACUTE TX TUMOR #286


title: NC-PKU-mix6-4-pico

value: male


title: NC-PKU-mix8-1-pico


title: Control1


title: AZ2479

source_name: ACUTE TX TUMOR #282


title: LPS2


title: AZ2477

source_name: ACUTE TX TUMOR #278


title: AZ2476

source_name: ACUTE TX TUMOR #277


title: NC-PKU-mix6-1-pico


title: NC-PKU-mix6-2-pico


title: AZ2475

source_name: ACUTE TX TUMOR #275


title: LPS1


title: AZ2474

source_name: ACUTE TX TUMOR #273


title: NC-PKU-mix5-3-pico


title: cardiomyocyte, DC3001, ATAC-seq


title: AZ2471

source_name: ACUTE TX TUMOR #269


title: iMGLs, Treat96HrsB

data_processing:
Kallisto was ued for quantifying abundances of transcripts directly from fastq data. Gene expression level was represented by TPM (transcript per million) normalization for each sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: AICS-0090-391 iPSCs

growth_protocol: iPS-derived microglia-like cells (iMGLs) were differentiated following HPC differentiation kit (StemCell Technologies) and further patterned with IL34 and mCSF following established protocols.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEB PolyA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Pre-formed Amyloid Beta (1-42) fibrils (rPeptides) were added to monocultures and allowed to incubate up to 96 hours.

value: AICS-0090-391 iPSCs

tag: genotype

value: WT

value: Amyloid-beta

value: 96 hours


title: AZ2470

source_name: ACUTE TX TUMOR #268


title: iMGLs, Treat96HrsC

tag: time


title: NC-PKU-mix5-2-pico

source_name: plasma

value: No stage (healthy donor)


title: NC-PKU-mix5-1-pico


title: AZ2469

source_name: ACUTE TX TUMOR #266


title: iMGLs, Treat96HrsA


title: AZ2468

source_name: ACUTE TX TUMOR #264


title: iMGLs, Treat24HrsC

value: 24 hours


title: AZ2466

source_name: ACUTE TX TUMOR #261


title: AZ2465

source_name: ACUTE TX TUMOR #260


title: NC-PKU-mix4-2-pico


title: iMGLs, Treat24HrsB


title: NC-PKU-mix3-5-pico


title: AZ2463

source_name: ACUTE TX TUMOR #256

value: Jurkat


title: iMGLs, Treat24HrsA


title: AZ2462

source_name: ACUTE TX TUMOR #254


title: NC-PKU-mix3-4-pico


title: AZ2473

source_name: ACUTE TX TUMOR #272


title: AZ2460

source_name: ACUTE TX TUMOR #249


title: AZ2461

source_name: ACUTE TX TUMOR #251


title: AZ2472

source_name: ACUTE TX TUMOR #270


title: AZ2459

source_name: ACUTE TX TUMOR #246


title: NC-PKU-mix3-3-pico


title: AZ2458

source_name: ACUTE TX TUMOR #245


title: AZ2457

source_name: ACUTE TX TUMOR #243


title: NC-PKU-mix3-2-pico


title: NC-PKU-mix4-1-pico


title: AZ2478

source_name: ACUTE TX TUMOR #281


title: AZ2456

source_name: ACUTE TX TUMOR #242


title: NC-PKU-mix3-1-pico


title: AZ2467

source_name: ACUTE TX TUMOR #262


title: iMGLs, Treat4HrsA

source_name: AICS-0090-391 iPSCs

value: 4 hours


title: AZ2454

source_name: ACUTE TX TUMOR #239


title: AZ2455

source_name: ACUTE TX TUMOR #241


title: iMGLs, BaselineB

value: Control

value: 0 hour


title: AZ2464

source_name: ACUTE TX TUMOR #259


title: NC-PKU-mix30-pico

source_name: plasma


title: AZ2453

source_name: ACUTE TX TUMOR #238


title: AZ2452

source_name: ACUTE TX TUMOR #235


title: NC-PKU-mix29-pico


title: AZ2451

source_name: ACUTE TX TUMOR #233


title: iMGLs, BaselineA


title: iMGLs, Treat4HrsC


title: NC-PKU-mix28-pico


title: AZ2450

source_name: ACUTE TX TUMOR #232


title: AZ2449

source_name: ACUTE TX TUMOR #231


title: AZ2448

source_name: ACUTE TX TUMOR #229


title: NC-PKU-mix27-pico


title: TDIMI561_seq_2

city: Ann Arbor

first: Logan

middle: Alexander

last: Walker

state: MI

address: 109 Zina Pitcher Pl, Lab 3838 (loganaw)

department: Biophysics

institute: University of Michigan, Ann Arbor

data_processing:
Picard tools and samtools preprocessing of FASTQ.
RNA-SeQC and RSeQC quality control processing.
Bowtie2 alignment to contaminating sequences.
STAR alignment to the genome.
Quantification with featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: TSV-formatted count matrix files

source_name: AML Patient Tissue Sample_refset

extract_protocol:
Either trizol extraction, norgen column extraction, or both, as described in the manuscript. All extractions followed manufacturer instructions.
The Illumina TruSeq library preparation kit was used following manufacturer recommendation

value: AML Patient Tissue Sample

tag: groupid

value: refset


title: iMGLs, Treat4HrsB

value: iPSC-induced microglia


title: AZ2447

source_name: ACUTE TX TUMOR #228


title: iMGLs, BaselineC


title: TDIMI561_seq_1


title: AZ2446

source_name: ACUTE TX TUMOR #227


title: NC-PKU-mix26-pico


title: TDIMI558_seq_2


title: siNT Treg Donor 4

first: Franck

last: Rapaport

address: 350 Water Street

department: PMCB

institute: Sanofi

data_processing:
Read data were processed with Omicsoft Array Studio (Qiagen).  Illumina adaptors were trimmed using the bcl2fastq pipeline.
Raw data was reviewed using the “Raw Data QC” function within Array Studio.
Poor quality reads were filtered out using a Q score cutoff of 20.
Raw counts were then converted to FPKM using the “Report Gene/Transcript Counts” function in Array Studio.
Low counts were filtered then normalized using the 75th quantile.
A constant of 1 was added to all normalized FPKM data prior to a log2 transformation.
Assembly: Reads were mapped to the Human B38 Reference Genome using the Ensembl.R100 Gene Model.
Supplementary files format and content: 230825_SiRGS1.csv

source_name: PBMC

growth_protocol: 2x10^5 Tregs/mL were plated in Grex plates and supplemented with 500 IU of IL-2 and 100 ng/mL rapamycin

extract_protocol:
RNA was purified from isolated cells using the RNeasy Mini Kit (Qiagen, Cat. # 74104) with QIAshredder (Qiagen, Cat. #79654) homogenization according to the manufacturer’s instructions. Samples for RNA-seq underwent an additional purification using the RNase-free DNase set (Qiagen, Cat. #79254). RNA concentration and purity were assessed using NanoDrop 8000 (Thermo Scientific) and RNA-seq samples were also assessed using the Qubit™ 1X dsDNA HS Assay Kit (Invitrogen, Cat. # Q33230).
RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep Ligation kit (Illumina, Cat. #20040532) according to manufacturer’s recommendation

treatment_protocol: Tregs were either transfected with a non-targeting scrambled control (siNT) or a siRNA for RGS1 knockdown (siRGS1)

tag: individual

value: Donor 4

value: PBMC

value: Treg

value: scrambled control


title: siRGS1 Treg Donor 3

value: Donor 3

value: RGS1 knockdown


title: TDIMI560_seq_1


title: siNT Treg Donor 5

value: Donor 5


title: Trunk_10

city: Guangzhou

first: Zixin

last: Chen

state: Guangdong

address: No. 106, Zhongshan Second Road

department: Guangdong Cardiovascular Institute Medical Research Center

institute: Guangdong Provincial People's Hospital

data_processing:
FastQC software was used for raw fastq quanlity control. fastp software (v0.20.0) was used to trim adaptor and remove low quality reads.
After merge all the samples, Trinity software (v2.28.5) was used to assembl the transcriptome. The get_longest_isoform_seq_per_trinity_gene.pl script was used to get the longest unigenes.
After BUSCO (v5.3.0) evaluation with eukaryota_odb10 database, TransDecoder software (v5.5.0) was used to predict the longest ORFs.
The align_and_estimate_abundance.pl script (bowtie2 and RSEM) was ued to map and quanlify the expression of each unigene within each sample.
At last, unigene sequences were mapped to NR and swissprot database by diamond software (v1.2) for annotation.
Assembly: assembly by Trinity; unigene.fasta.gz
Supplementary files format and content: raw and normalize counts in excel format

organism: Dugesia japonica

source_name: Trunk

extract_protocol: 10-20 planarians were cut and separated into head, trunk, and tail, then mixed to extract total RNA, and then enriched mRNA by polyT for library construction

value: Trunk

tag: time point


title: TDIMI558_seq_1


title: siRGS1 Treg Donor 5


title: siNT Treg Donor 3


title: NC-PKU-mix25-pico

address: Shuangqing Road

institute: Tsinghua University

data_processing:
Adaptors and low-quality sequences in the raw sequencing data were trimmed using cutadapt version 2.3. Remeined reads were mapped to ERCC's spike-in sequences, NCBI's UniVec sequences and human rRNA sequences sequentially. GC oligos introduced in reverse transcription were trimmed off, after which reads shorter than 30 nt were discarded.
STAR (version 2.5.3a_modified) was used to map clean reads to the hg38 genome index built with the GENCODE v27 annotation
Duplicates in the aligned reads were removed using Picard Tools MarkDuplicates (version 2.20.0)
The count matrix was constructed using featureCounts11 v1.6.2 with the GENCODE v27 annotation, transcripts with uncertain coding potential annotation extracted from mitranscriptome, circular RNA annotation from circBase, Promoter, enhancer and repeat regions frm UCSC Genome Browser. Reads mapped to mitochondrial RNAs were excluded.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: male

value: No stage (healthy donor)


title: NC-PKU-mix24-pico


title: TDIMI557_seq_1


title: siRGS1 Treg Donor 2

value: Donor 2


title: NC-PKU-mix22-pico


title: NC-PKU-mix2-2-pico

value: female


title: Trunk_5


title: NC-PKU-mix21-pico


title: TDIMI556_seq_2


title: Trunk_3


title: TDIMI556_seq_1


title: NC-PKU-mix2-1-pico


title: siRGS1 Treg Donor 1

value: Donor 1


title: Trunk_1


title: siNT Treg Donor 1


title: TDIMI555_seq_2


title: Trunk_0


title: NC-PKU-mix20-pico


title: TDIMI555_seq_1


title: Trunk_7


title: Tail_10

source_name: Tail

value: Tail


title: Tail_7


title: NC-PKU-mix18-pico


title: TDIMI554_seq_1

value: AML Patient Tissue Sample


title: Patient sample

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

data_processing:
The library concentration was calculated using the Qubit 4.0 fluorometer and the libraries were pooled in an equimolar fashion. The single cell libraries were sequenced on an Illumina NovaSeq 6000 using a 2x150-bp approach to a final depth of 90 GB per library. The reads were demultiplexed according to the multiplexing index sequencing on Illumina’s BaseCloud platform.
Data PreprocessingPre-processing of Fastq data was conducted using CeleScope® (v.1.14.1; www.github.com/singleron-RD/CeleScope; Singleron Biotechnologies GmbH) to generate raw data, using default parameters. Low quality reads were removed. Sequences were mapped using STAR (https://github.com/alexdobin/STAR) and the human reference GRCh38 and genes were annotated using Ensembl 92. The reads were assigned to genes using featureCount (https://subread.sourceforge.net/) and the cell calling was performed by fitting a negative bimodal distribution and determining the threshold between empty wells and cell-associated wells to generate a count matrix file containing the number of Unique Molecular Identifier (UMI) for each gene within each cell. Downstream analysis was done in scanpy package implemented in Python software and Seurat library in R software. QC metrics, such as number of genes detected per cell (nFeature_RNA) and percentage of mitochondrial UMI (percent_mt) were extracted from the gene count matrix.  To remove non-viable cells, cells with high percentage of mitochondrial counts (>20%) were filtered out. To avoid doublets, the cells with a high number of detected genes (>6500) and high number of detected UMI (>30000) were removed. Cell debris characterized with a low number of detected genes (<200) were also removed from the data.
Clustering and Cell Type Annotations Data integration was conducted using Harmany via scanpy pipeline. A clustering analysis was conducted from the integrated 4 samples (control 1, control 2, disease and treated) using Scanpy. On the combined dataset, we computed the neighbourhood graph using the function scanpy.pp.neighbors with the option of n_neighbors = 10 and n_pcs = 10. We conducted unsupervised clustering of cells applying the leiden algorithm using the function scanpy.tl.leiden with resolution 1. Clusters were annotated based on the expression of known markers identified from several literatures. DA progenitors were annotated for their highly expressed markers such as NEUROG2, NHLH1 and SOX4. DA-0 was annotated based on the high expression of ERBB4 known to be expressed in DA neurons and low level of SYT1 a post-synaptic marker. DA-1/2 was annotated since it expressed a well-known DA neuronal marker NR4A2 as well as DCX and SYT1 among others. Meningeal cells were annotated based on the high expression of COL1A1, COL1A2, and LUM. Neural progenitors were annotated based on the expression of TOP2A, MKI67, and HMGB2. Cluster 2, 5, and 14 were annotated as Oligodendrocytes based on expression of RBFOX1. Astrocytes was annotated based on high expression of GFAP, AQP4, EDNRB and RFX4. Oligodendrocyte progenitors were annotated by the high-level expression of OLIG2. Cluster 7 was annotated as Radial glial cells which marked by high expression of FABP7. Glial progenitor was annotated since they expressed TOP2A, MKI67, and HMGB2 as well as FABP7. Ventral midbrain neurons (VMN) had gene markers that are close to but not identical as DA neurons and annotated based on celltypist using developing human brain models to find the closest cell type using logistic regression models to be ventral midbrain neurons. The gene expression for the cell cluster annotation was listed in Figure 5C. Control 1 (Detroit 551) and control 2 (CCD-1079Sk) were combined to make a control sample with further downstream analysis. Clustering and cell type annotations were kept the same with the cells for the control samples.
Assembly: human reference GRCh38
Supplementary files format and content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: human iPSC

growth_protocol: To manipulate the specification of neural progenitor cells, we split iPSCs at 70% confluence and seeded them onto Geltrex-coated plates in E8 medium. After 24 hours, we switched to a neural induction medium supplemented of 10 µM SB431542 (Tocris Bioscience, #1614), 10 µM N Acetyl L cysteine (NAC, Sigma-Aldrich, #A7250) and 2 µM AMPK inhibitor Compound C (EMD Millipore, #US1171261 1MG) to Chemically Defined Medium (CDM) containing 50% Iscove's Modified Dulbecco's Medium (IMDM, Thermo Fisher Scientific, #21980 065), 50% F12 Nutrient Mixture (Ham) liquid with GlutaMAX™, 5 mg/ml bovine serum albumin (BSA) Fraction V (Europa bioproducts ITD, #EQBAC62 1000), 1% (v/v) Lipid 100 X (Thermo Fisher Scientific, #11905 031), 450 μM 1 thioglycerol (Sigma-Aldrich, #M6145 25ML), 7 μg/ml insulin (Roche, #11376497001), and 15 mg/ml transferrin (Roche, #10652202001). Once cells reached the neural epithelial stage at day 5, we detached them using collagenase IV and then transferred them into non-treated culture dishes. From day 5 onwards, we maintained the neurospheres generated from CDM supplemented with FGF-8 (R&D Systems, #423-F8) for 7 days. From day 12, we switched to a medium containing Purmorphamine (PM, EMD Millipore, #540220-5MG) and FGF-8 for final patterning towards midbrain floor plate precursors. From day 19 onward, we embedded the hMOs in Matrigel Matrix and added Brain-derived neurotrophic factor (BDNF, PeproTech, # 450-02) and Glial cell line-derived neurotrophic factor (GDNF, PeproTech, #450-10) to the culture medium for final maturation up to four months.

extract_protocol:
To collect the organoids, they were removed from the culture medium and washed with 1x PBS (Invitrogen, #10010-23). The organoids were then finely cut into pieces of 1-2 mm using ophthalmic scissors. Next, the organoid pieces were digested in 2 ml of CellLive™ Tissue Dissociation Solution (Singleron Biotechnologies, #1190062) at 37°C for 15 minutes in a 15-ml centrifuge tube (Sarstedt, #62.5544.003), with continuous agitation on a thermal shaker. The degree of dissociation was periodically checked under a light microscope. Following digestion, the suspension was filtered through a 40-µm sterile strainer (Greiner#542040). The cells were then centrifuged at 350 x g for 5 minutes at 4°C, and the resulting cell pellets were resuspended in 1 ml of PBS. To assess cell viability and count, the cells were stained with a 0.4% w/v solution of Trypan Blue (Gibco, #15250-061). The cell number and viability were determined using a hemocytometer under a light microscope.
The single cell RNA-seq libraries were constructed using (GEXSCOPE™ Single Cell RNAseq Library Kit, Singleron Biotechnologies, cat no. 4161031) according to manufacturer´s instructions. Briefly, for each library, the concentration of the single-cell suspension was adjusted to 3x10^5 cells/ml with PBS and the suspension was loaded onto an SD microfluidic chip to capture 6000 cells. Paramagnetic beads conjugated to oligodT probes that carry a unique molecular identifier (UMI) and a barcode unique to each bead (from the same kit) were loaded, after which the cells were lysed. The beads bound to polyadenylated mRNA were extracted from the chip and reverse transcribed into cDNA at 42°C for 1.5 hours, and the cDNA amplified by PCR. The cDNA was then fragmented and ligated to indexed Illumina adapters. The fragment size distribution of the final amplified library was obtained on an Agilent Fragment Analyzer.
The library concentration was calculated using the Qubit 4.0 fluorometer and the libraries were pooled in an equimolar fashion. The single cell libraries were sequenced on an Illumina NovaSeq 6000 using a 2x150-bp approach to a final depth of 90 GB per library. The reads were demultiplexed according to the multiplexing index sequencing on Illumina’s BaseCloud platform.

value: IPSC derived midbrain organoid

value: POLG Disease

value: POLG mutation

value: control


title: TDIMI554_seq_2

value: refset


title: NC-PKU-mix19-pico

first: Zhi

last: Lu


title: siNT Treg Donor 2

value: PBMC

value: Treg

value: scrambled control


title: Tail_5


title: Patient sample with treatment

value: nicotinamide riboside


title: Control sample 2

value: wild type


title: NC-PKU-mix16-pico


title: NC-PKU-mix17-pico


title: TDIMI551_seq_2


title: Tail_3


title: Control sample 1


title: NC-PKU-mix15-pico


title: Tail_1


title: TDIMI551_seq_1


title: Tail_0


title: NC-PKU-mix1-3-pico

value: male


title: sample_41019081710228

city: Los Angeles

first: Matteo

last: Pellegrini

address: 405 Hilgard Avenue

institute: UCLA

description: Targeted Bisulfite Sequencing

data_processing:
The processing of bisulfite sequencing data was carried out using BSBolt (v1.5.0)
Demultiplexed FASTQ files were subjected to adapter removal using cutadapt (v4.1) and aligned to the GRCh38 reference genome using the BSBolt Align function.
PCR duplicates were removed using the samtools markdup function (v1.15) before calling methylation with BSBolt CallMethylation function.
Assembly: GRCh38
Supplementary files format and content: tab-delimeted text file includes methylation matrix for the 178 samples and 16,160 CpG sites

source_name: Buccal cells

extract_protocol:
DNA was extracted starting from 500µl following the protocol supplied by the manufacturer.
DNA libraries were prepared using the NEBNext UltraII library prep kit (New England Biolabs) and custom, pre-methylated Dual-Unique-Index adapters from Integrated DNA Technologies (IDT) were used for adapter ligation. Groups of 16 libraries, each carrying a different adapter, were pooled together, concentrated by drying with a SpeedVac system and used for targeted enrichment with custom made 5’-biotinylated oligos (IDT).

tag: Sex

value: F

value: Buccal cells


title: TDIMI549_seq_2


title: NC-PKU-mix1-2-pico

tag: gender

value: No stage (healthy donor)


title: sample_41019081710226

description: Targeted Bisulfite Sequencing

tag: age

value: M


title: TDIMI549_seq_1


title: TDIMI548_seq_2


title: Head_7

source_name: Head

value: Head


title: sample_41019081707201

description: Targeted Bisulfite Sequencing


title: TDIMI553_seq_1

value: AML Patient Tissue Sample


title: Head_5


title: Head_3


title: Head_10


title: sample_41019081710234

description: Targeted Bisulfite Sequencing


title: sample_41019081707188

description: Targeted Bisulfite Sequencing


title: sample_41019081707183

description: Targeted Bisulfite Sequencing


title: NC-PKU-mix1-1-pico

tag: Stage


title: Head_1


title: TDIMI546_seq_2


title: TDIMI548_seq_1


title: TDIMI546_seq_1


title: sample_41019081706802

description: Targeted Bisulfite Sequencing


title: NC-PKU-14-pico

value: female


title: NC-PKU-13-pico


title: NC-PKU-12-pico


title: Head_0


title: sample_41019081707198

description: Targeted Bisulfite Sequencing


title: sample_41019081706642

description: Targeted Bisulfite Sequencing


title: NC-PKU-11-pico


title: IVT

data_processing:
library strategy: m6A-REF-seq
FastQC software was used for raw fastq quanlity control. fastp software (v0.20.0) was used to trim adaptor and remove low quality reads.
According to the principles of single base m6A sequencing (ref: Zhang Z, Chen LQ, Zhao YL, Yang CG, Roundtree IA, Zhang Z, Ren J, Xie W, He C, Luo GZ. Single-base mapping of m6A by an antibody-independent method. Sci Adv. 2019 Jul 3;5(7):eaax0250), the m6A-REF-seq clean reads was mapped to the Trinity assembled transcriptome with hisat2 software (v2.4.2).
Using read coverage count (10) and decreasing ratio (0.1) as cutoffs, the m6A ratio was assined to each m6A site by REF - IVT.
Assembly: assembled with Trinity; unigene.fasta.gz
Supplementary files format and content: read count and m6A ratio in excel format

source_name: Intact

extract_protocol:
10-20 planarians were cut and separated into head, trunk, and tail, then mixed to extract total RNA, and then enriched mRNA by polyT for library construction
m6A-REF-seq

value: Intact

value: in vitro transcription (IVT) library without RNA modification as control


title: TDIMI545_seq_1


title: NC-PKU-10-pico

source_name: plasma

extract_protocol:
RNA was extracted from 1 mL of plasma using the Plasma/Serum Circulating RNA and Exosomal Purification kit (Norgen)
cell free RNA library is prepared using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian.


title: sample_41019081706613

description: Targeted Bisulfite Sequencing


title: NC-PKU-9-pico


title: sample_41019081706582

description: Targeted Bisulfite Sequencing


title: CRC-PKU-mix1-3-pico

description: RNA-seq of homo sapiens: colorectal cancer patient's plasma; Provided by Peking University First Affiliated Hospital; Constructed by SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian; Purpose: To explore novel plasma extracellular RNA biomarkers for cancer diagnosis


title: TDIMI544_seq_2


title: T10

value: Tail

value: MazF


title: T7


title: TDIMI544_seq_1

value: refset


title: sample_41019081706581

description: Targeted Bisulfite Sequencing


title: T3


title: TDIMI543_seq_2


title: sample_41019081706546

description: Targeted Bisulfite Sequencing


title: T5


title: TDIMI543_seq_1


title: CRC-PKU-mix1-2-pico


title: CRC-PKU-mix1-1-pico


title: CRC-PKU-9-pico


title: T1


title: T0


title: TDIMI542_seq_2


title: sample_41019081704278

description: Targeted Bisulfite Sequencing


title: CRC-PKU-8-pico


title: CRC-PKU-6-pico


title: TDIMI542_seq_1


title: sample_41019081704273

description: Targeted Bisulfite Sequencing


title: sample_41019081704252

description: Targeted Bisulfite Sequencing


title: TDIMI539_seq_2


title: M10

value: Trunk


title: M7


title: TDIMI539_seq_1


title: CRC-PKU-4-pico


title: sample_41019081704211

description: Targeted Bisulfite Sequencing


title: M5


title: TDIMI321_seq_2

source_name: AML Patient Tissue Sample_column_testset


title: sample_41019081704276

description: Targeted Bisulfite Sequencing


title: M3


title: CRC-PKU-41-pico


title: TDIMI321_seq_1


title: sample_41019081704169

description: Targeted Bisulfite Sequencing


title: CRC-PKU-40-pico


title: M0


title: TDIMI318_seq_1


title: sample_41019081704161

description: Targeted Bisulfite Sequencing


title: CRC-PKU-5-pico


title: sample_41019081704167

description: Targeted Bisulfite Sequencing


title: H10


title: CRC-PKU-39-pico


title: sample_41019081704160

description: Targeted Bisulfite Sequencing


title: CRC-PKU-38-pico


title: TDIMI317_seq_2


title: H7


title: TDIMI317_seq_1


title: sample_41019081704154

description: Targeted Bisulfite Sequencing


title: sample_41019081704172

description: Targeted Bisulfite Sequencing


title: CRC-PKU-37-pico


title: TDIMI316_seq_2


title: H5


title: sample_41019081704146

description: Targeted Bisulfite Sequencing


title: H3


title: TDIMI319_seq_1


title: CRC-PKU-3-pico


title: TDIMI316_seq_1


title: sample_41019081704141

description: Targeted Bisulfite Sequencing


title: H1


title: CRC-PKU-35-pico


title: sample_41019081704014

description: Targeted Bisulfite Sequencing


title: TDIMI313_seq_1


title: H0


title: sample_41019081703973

description: Targeted Bisulfite Sequencing


title: CRC-PKU-33-pico


title: TDIMI312_seq_1


title: Carica papaya young leaves total RNA-seq r1

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in C.papaya cells;
C.papaya-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.

organism: Carica papaya

source_name: young leaves

extract_protocol: csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles.  Total RNA-Seq Library Preparation  Strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Ribo-Zero Gold plant rRNA removal kit (Illumina, San Diego, CA). Samples were processed following the manufacturer’s instructions.

value: young leaves


title: Selaginella moellendorffii stem leaves total RNA-seq

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in S.moellendorffii leaf; Experiment SD921
S.moellendorffii-10.tss.txt

source_name: stem & leaves

value: stem & leaves


title: sample_41019081703964

description: Targeted Bisulfite Sequencing


title: CRC-PKU-32-pico


title: TDIMI311_seq_1


title: sample_41019081703967

description: Targeted Bisulfite Sequencing


title: CRC-PKU-31-pico


title: CRC-PKU-36-pico


title: TDIMI310_seq_1


title: sample_41019081703963

description: Targeted Bisulfite Sequencing


title: TDIMI315_seq_1


title: TDIMI309_seq_1


title: Chlamydomonas reinhardtii liquid culture total RNA-seq r3

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in C.reinhardtii leaf; Experiment SD830
C.reinhardtii-10.tss.txt

organism: Chlamydomonas reinhardtii

source_name: liquid culture

value: liquid culture


title: TDIMI545_seq_2


title: Chlamydomonas reinhardtii liquid culture total RNA-seq r1

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in C.reinhardtii leaf; Experiment SD541
C.reinhardtii-10.tss.txt


title: CRC-PKU-2-pico


title: sample_41019081703962

description: Targeted Bisulfite Sequencing


title: TDIMI308_seq_1


title: sample_41019081703958

description: Targeted Bisulfite Sequencing


title: Artemisinin inhibitory 24h 4

city: Worcester

first: Scarlet

last: Shell

state: Massachusetts

address: 60 Prescott St, WPI

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

description:
Artemisinin_inh_4
GEO_featureCounts_table.txt

data_processing:
Raw fastq files were demultiplexed using Cutadapt as in DOI 10.14806/ej.17.1.200.
Reads were aligned using BWA mem (DOI 10.1093/bioinformatics/btp324).
Reads aligned to genes were quantified using FeatureCounts (DOI 10.1093/bioinformatics/btt656).
Supplementary files format and content: GEO_featureCounts_table.txt is a tab-delimited text file that contains the output from running FeatureCounts on bam files generated from these fastq files. The FeatureCounts table can be used as input for DESeq2 for differential expression analysis.

organism: Mycobacterium tuberculosis

growth_protocol: Bacteria were grown in Middlebrook 7H9 supplemented with OADC, 0.2% glycerol, 0.05% Tween 80, and 24 μg/mL pantothenate (7H9) at 37 °C and 200 rpm. Bacteria were grown to mid-log phase, then diluted to OD 0.1 and treatments were applied.

extract_protocol:
5 ml of culture from the 24 hour time-points or 20 ml of culture from the 4 hour time-points was pelleted at 4 degrees, snap-frozen in liquid nitrogen, and stored at -80 until RNA extractions were performed. Pellets were resuspended in 1 ml Trizol or equivalent generic reagent, disrupted with a Fastprep 5G (MP Bio) using tubes pre-filled with 600 mg 100 um zirconium beads, molecular grade (OPS Diagnostics) for two cycles of 40 seconds each at 9 m/s. RNA was then extracted and purified with a Direct-Zol Kit (Zymo) including on-column DNase digestion.
rRNA was depleted using a set of biotinylated oligos designed as described in DOI 10.1128/mBio.00010-20. Paired-end Illumina sequencing libraries were constructed as described in DOI 10.1128/mBio.02012-21

treatment_protocol: Artemisinin and plant extracts were dissolved in DMSO. The concentrations of plant extracts indicated refer to the dry leaf mass used to make the extract, not the mass of the extract itself.

tag: strain

value: H37Rv deltaRD1 deltapanCD

value: 100 ug/mL artemisinin (1.33X MIC)


title: CRC-PKU-34-pico

city: Beijing

value: male


title: Artemisinin inhibitory 24h 3

description:
Artemisinin_inh_3
GEO_featureCounts_table.txt


title: CRC-PKU-29-pico


title: CRC-PKU-28-pico


title: Artemisinin inhibitory 24h 2

description:
Artemisinin_inh_2
GEO_featureCounts_table.txt


title: sample_41019081703951

description: Targeted Bisulfite Sequencing

value: F

value: Buccal cells


title: sample_41019081703943

description: Targeted Bisulfite Sequencing


title: CRC-PKU-27-pico


title: sample_41019081703939

description: Targeted Bisulfite Sequencing


title: Artemisinin inhibitory 24h 1

description:
Artemisinin_inh_1
GEO_featureCounts_table.txt


title: CRC-PKU-26-pico


title: Arteminsinin sub inhibitory 24h 4

description:
Artemisinin_sub_inh_4
GEO_featureCounts_table.txt

value: 37 ug/mL artemisinin (0.5X MIC)


title: sample_41019081703936

description: Targeted Bisulfite Sequencing


title: CRC-PKU-30-pico


title: TDIMI305_seq_1

tag: tissue

value: AML Patient Tissue Sample


title: TDIMI304_seq_1


title: CRC-PKU-25-pico

value: female


title: CRC-PKU-24-pico


title: sample_41019081703932

description: Targeted Bisulfite Sequencing

value: M

tag: cell type


title: TDIMI298_seq_2


title: sample_41019081703865

description: Targeted Bisulfite Sequencing


title: Arteminsinin sub inhibitory 24h 2

description:
Artemisinin_sub_inh_2
GEO_featureCounts_table.txt


title: TDIMI307_seq_1


title: Arteminsinin sub inhibitory 24h 3

description:
Artemisinin_sub_inh_3
GEO_featureCounts_table.txt


title: sample_41019081703849

description: Targeted Bisulfite Sequencing


title: TDIMI297_seq_1


title: CRC-PKU-22-pico


title: TDIMI306_seq_1


title: Arteminsinin sub inhibitory 24h 1

description:
Artemisinin_sub_inh_1
GEO_featureCounts_table.txt


title: TDIMI298_seq_1


title: Annua inhibitory 24h 4

description:
Annua_inh_4
GEO_featureCounts_table.txt

value: A. annua DCM extract from 4.5 mg leaf dry weight/mL (1X MIC)


title: TDIMI296_seq_2


title: CRC-PKU-19-pico


title: sample_41019081703829

description: Targeted Bisulfite Sequencing


title: CRC-PKU-23-pico


title: Annua sub inhibitory 24h 4

description:
Annua_sub_inh_4
GEO_featureCounts_table.txt

value: A. annua DCM extract from 2.25 mg leaf dry weight/mL (0.5X MIC)


title: CRC-PKU-20-pico


title: Annua inhibitory 24h 1

description:
Annua_inh_1
GEO_featureCounts_table.txt


title: sample_41019081703840

description: Targeted Bisulfite Sequencing


title: TDIMI294_seq_2


title: Annua sub inhibitory 24h 3

description:
Annua_sub_inh_3
GEO_featureCounts_table.txt


title: TDIMI296_seq_1


title: Annua inhibitory 24h 3

description:
Annua_inh_3
GEO_featureCounts_table.txt


title: CRC-PKU-21-pico


title: TDIMI291_seq_1


title: CRC-PKU-16-pico


title: TDIMI294_seq_1


title: sample_41019081703824

description: Targeted Bisulfite Sequencing


title: sample_41019081703821

description: Targeted Bisulfite Sequencing


title: CRC-PKU-17-pico


title: CRC-PKU-15-pico


title: CRC-PKU-18-pico


title: sample_41019081703825

description: Targeted Bisulfite Sequencing


title: Annua sub inhibitory 24h 1

description:
Annua_sub_inh_1
GEO_featureCounts_table.txt


title: Annua sub inhibitory 24h 2

description:
Annua_sub_inh_2
GEO_featureCounts_table.txt


title: TDIMI289_seq_1


title: TDIMI290_seq_1


title: sample_41019081703848

description: Targeted Bisulfite Sequencing


title: TDIMI295_seq_1


title: Annua inhibitory 24h 2

description:
Annua_inh_2
GEO_featureCounts_table.txt


title: sample_41019081703828

description: Targeted Bisulfite Sequencing


title: sample_41019081703820

description: Targeted Bisulfite Sequencing


title: Afra inhibitory 24h 4

description:
Afra_inh_4
GEO_featureCounts_table.txt

value: A. afra DCM extract from 2.5 mg leaf dry weight/mL (1X MIC)


title: sample_41019081703812

description: Targeted Bisulfite Sequencing


title: TDIMI288_seq_1


title: TDIMI283_seq_2


title: TDIMI285_seq_1


title: CRC-PKU-12-pico

description: RNA-seq of homo sapiens: colorectal cancer patient's plasma; Provided by Peking University First Affiliated Hospital; Constructed by SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian; Purpose: To explore novel plasma extracellular RNA biomarkers for cancer diagnosis


title: TDIMI287_seq_1


title: Afra inhibitory 24h 1

description:
Afra_inh_1
GEO_featureCounts_table.txt