title: Ino80K929Rrep3

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to sacCer3 whole genome using bowtie v0.12.2 with parameters -q -p 5 -e 100 -y -a -m 10 --best --strata
gene count
Assembly: sacCer3
Supplementary files format and content: count

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells were grown in YPD until mid-log phase

extract_protocol: Libraries were prepared using the HTP KAPA kit

treatment_protocol: No treatment

value: yeast cells

value: treatment


title: PB019.TAACAGCC

status: Public on Dec 10 2022

type: SRA

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

country: USA

institute: Columbia University

library_source: transcriptomic

data_processing:
Low-input bulk RNA-seq: Reads were aligned to the mouse reference genome GRCm38 and transcriptome annotation (Gencode vM10) using the STAR aligner with parameters –sjdbOverhang 65 –twopassMode Basic after trimming poly(A)-tails from the 3’-ends. The aligned reads were demultiplexed using the well-identifying barcodes, correcting all single-nucleotide errors. All reads with the same well-identifying barcode, UMI, and gene mapping were collapsed to represent an individual transcript. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance one of another UMI with the same well-identifying barcode and gene. For each 96-well plate, after generating a final list of individual transcripts with unique combinations of well-identifying barcodes, UMIs, and gene mapping, we produced a molecular count matrix for downstream analysis.
Single-nucleus RNA-seq: snRNA-seq data were processed as described previously (Yuan et al., 2018) (code available at: https://github.com/simslab/DropSeqPipeline8). Reads were aligned to the mouse reference genome GRCm38 and transcriptome annotation (Gencode vM10) using the STAR aligner with parameters –sjdbOverhang 65 –twopassMode Basic after trimming poly(A)-tails from the 3’-ends. All reads that uniquely aligned to a given gene body (including introns) were kept for downstream filtering analysis, because a large fraction of nuclear transcripts are unspliced. The aligned reads were demultiplexed using the cell-identifying barcodes, correcting all single-nucleotide errors. All reads with the same cell-identifying barcode, UMI, and gene mapping were collapsed to represent an individual transcript. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance one of another UMI with the same cell-identifying barcode and gene. For each sample, after generating a final list of individual transcripts with unique combinations of cell-identifying barcodes, UMIs, and gene mapping, we produced a molecular count matrix for downstream analysis. We first performed unsupervised clustering on the count matrices using the PhenoGraph (Levine et al., 2015) implementation of Louvain community detection after selection of highly variable genes and construction of a k-nearest neighbors graph as described previously (Levitin et al., 2019). We identified 38 clusters (Supp. Fig. 4a), two of which showed statistically significant co-enrichment of dopamine neuron markers such as Th and Slc6a3 based on the binomial test for expression specificity (Shekhar et al., 2016). We identified six major cell types with sufficient coverage for downstream analysis as shown in the UMAP (Becht et al., 2018) embedding in Figure 3a. The assignment of PhenoGraph clusters into major cell type groupings was based on key marker genes significantly enriched in each cluster, as shown in Supp. Fig. 4b: Oligodendrocytes (Mal, Mag, Mog), Astrocytes (Gja1, Fgfr3, Atp1a2), Microglia (C1qb, Siglech, Csf1r), VGLUT2 neurons (Slc17a6, Cacna2d1, Ntng1), GABA neurons (Slc32a1, Gad1, Gad2), and DA neurons (Th, Slc6a3, En1, Slc10a4). Rare populations with insufficient cell numbers (e.g., mural cells, T cells) or ambiguous neuronal clusters possibly containing multiplets (e.g., Gad1+/Gad2+/Slc17a7+/Th+) were excluded from downstream analysis.
Assembly: GRCm38 / Gencode vM10
Supplementary files format and content: Tab-delimited text files containing count matrix for each cell or sample with sample or well-identifying barcode in the header.

molecule: total RNA

organism: Mus musculus

source_name: ventral midbrain

growth_protocol: DATIRES-Cre:Ifngr1fl experimental litters were bred from a cross of DATIRES-Cre/wt;Ifngr1fl/fl x DATwt/wt;Ifngr1fl/fl mice such that Cre+ mice (DATIRES-Cre/wt;Ifngr1fl/fl) could be compared to Cre- littermates with no modification of the Ifngr1 locus (DATwt/wt;Ifngr1fl/fl).

extract_protocol:
Nuclei were prepared from the ventral midbrain of mice at 48 hours after injection of saline or IFN-γ. Mice were sacrificed by cervical dislocation and brains were rapidly extracted and submerged in ice-cold phosphate-buffered saline (PBS). Brains were placed on an ice-cold brain matrix (Zivic Instruments) and separated into 0.5-1.0 mm sections using ice cold razor blades. Ventral midbrain tissue was dissected from slices between approximately -2.5 mm to -3.75 mm AP to Bregma. First, the cortex, hippocampi, and any hypothalamus or white matter ventral to the midbrain were removed. A single horizontal cut was made just dorsal to the rostral linear nucleus and all dorsal tissue was discarded. The remaining tissue containing the SN/VTA was flash frozen on liquid nitrogen and stored at -80°C.  Nuclei preparation and sorting were conducted as described by Krishnaswami et al. (2016) with only minor modifications. Frozen tissue was thawed in nuclear isolation medium 1 (NIM1: 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris, pH 8.0) supplemented with 1 mM DTT, 0.2 U/µL SUPERaseIN, 1x EDTA-free Protease Inhibitor Cocktail (Roche), and 0.1% Triton X-100. Tissue was homogenized on ice in a glass-glass dounce homogenizer with 30 gentle strokes of loose and tight clearance pestles. All subsequent purification steps were performed on ice or at 4oC unless otherwise specified. Lysates were spun at 500xg for 5 minutes, resuspended in NIM1 supplemented as above and also with 1% BSA, and passed through a 40µm cell strainer cap. Nuclei were centrifuged again at 500xg for 5 minutes and resuspended in staining buffer (PBS supplemented with 1% BSA, 5 mM MgCl2, 0.2 U/µL SUPERaseIN, 1 µg/mL propidium iodide, and 2 µg/mL mouse anti-NeuN AlexaFluor488). After 30 minutes incubation on ice, nuclei were centrifuged at 500xg for 5 minutes and resuspended in 0.5 mL of FACS buffer (PBS + 0.04% BSA, 0.2 U/µL SUPERaseIN, and 1 µg/mL propidium iodide) for sorting.    Nuclei sorting was conducted on a BD Influx (BD Biosciences) using a 100 μm nozzle at 11.1 psi. Single nuclei were gated first using FSC-H vs. FSC-A and then on propidium iodide fluorescence. NeuN/AlexaFluor488 fluorescence was used to establish NeuN- and NeuN+ gates on the single nuclei population. Nuclei were sorted directly into 96 well plates (for bulk nuclei RNA-seq with 96-well plate, pooled library construction) or into 1.5 mL Eppendorf tubes that had been previously coated with 0.1% BSA in PBS overnight at 37oC (for snRNA-seq).
Low-input bulk RNA-seq: The protocol for plate based, 3’ end unique molecular indicator (UMI)-based RNA sequencing of single cells has been described previously (Snyder et al., 2019) as well as modifications to accommodate ultra-low input samples (Hobson et al., 2022b). See Supplementary File 1 for sequences of all custom primers and oligonucleotides used in this protocol. For neuronal and glial nuclei analysis in Figure 1-2, 100 NeuN- or NeuN+ nuclei were sorted directly into the wells of a 96 well plate containing 3 µL of nuclease-free water containing 1 U/µL SUPERaseIN (sort volume ~3 µL for total volume of ~6 µL). After adding 1.5 µL of 10 µM barcoded RT primer (Integrated DNA Technologies), primer annealing was performed at 72°C for 3 minutes. Reverse transcription was performed by adding 7.5 µL RT mix to each well (2.81 µL of 40% polyethylene glycol 8000, 0.15 µL of 100 mM dNTPs, 3 µL of 5X Maxima H RT Buffer, 0.2 µL of 200 U/µL Maxima H Reverse Transcriptase (ThermoFisher), 0.2 µL of 20 U/µL SUPERaseIN, and 0.15 µL of 100 µM Template Switching Oligo (Integrated DNA Technologies), and 1 µL of nuclease free water). Reverse transcription was performed at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes, 42°C for 2 minutes, 75°C for 10 minutes, followed by a 4°C hold. Excess primers were removed by adding 2 µL of Exonuclease I mix (1.875U ExoI in water) to each well and incubating at 37°C for 30 minutes, 85°C for 15 minutes, 75°C for 30 seconds, 4°C hold. All wells were pooled into a single 15-ml falcon tubes and cDNA was purified and concentrated using Dynabeads™ MyOne™ Silane beads (ThermoFisher) according to the manufacturer’s instructions. The cDNA was split into duplicate reactions containing 25 µl cDNA, 25 µl 2x HIFI HotStart Ready Mix (Kapa Biosystems), and 0.2 M SMART PCR Primer. PCR was run as follows: 37°C for 30 minutes, 85°C for 15 minutes, 75°C for 30 seconds, 4°C hold. Duplicate reactions were combined and purified using 0.7 volumes AMPure XP beads (Beckman Coulter). The amplified cDNA was visualized on an Agilent 2100 Bioanalyzer and quantified using a Qubit II fluorometer (ThermoFisher). Single-nucleus RNA-seq: NeuN nuclear sorting was conducted as described above. Approximately 70% NeuN+ and 30% NeuN- single nuclei were sorted per sample. Sorted nuclei were placed on ice and immediately submitted to the Columbia Single Cell Analysis Core (Columbia Genome Center) for 10X Genomics Chromium Single Cell 3’ v3 library preparation according to the manufacturer's instructions.
low-input bulk RNA-seq (PLATE-seq) and single-nucleus RNA-seq

treatment_protocol: All surgical procedures were approved by the Institutional Animal Care and Use Committee and the Department of Comparative Medicine at New York State Psychiatric Institute. Mice were anesthetized with 4% isoflurane. Animals were transferred onto a Kopf Stereotaxic apparatus and maintained under isoflurane anesthesia (1–2%). After hair removal and sterilization of the scalp using chlorhexidine and ethanol, a midline incision was made. Bregma and Lambda coordinates were determined, and minor adjustments in head position were made to match the DV coordinates. Saline or IFN-γ was injected at AP –3.2, ML −0.9, and DV −4.4. A small hole was drilled into the skull and 400 nL of 0.9% saline or 0.9% saline + 100 ng/µL recombinant mouse IFN-γ (40 ng IFN-γ total) was injected through a pulled glass pipet using a Nanoject 2000 (Drummond Scientific; 8 pulses of 50 nL). At 5 minutes after injection, the glass pipet was slowly withdrawn over 5 min. After closing the skin with vicryl sutures, mice received 0.5 mL of 0.9% saline i.p. and were allowed to recover for >1 hour before being returned to their home cages.

tag: strain

tag: tissue

value: ventral midbrain

tag: cell type

value: NeuN+ nuclei

tag: genotype

value: wildtype

tag: treatment

value: IFNG

tag: time point

value: 48 hrs


title: Ino80K929Rrep2

country: China

tag: cell line


title: PB019.GGCTCAAA


title: tubal ectopic pregnancy rep3

city: Shanghai

first: Xiaoya

last: Zhao

state: -- None selected --

address: No. 910, Hengshan Rd

institute: School of Medicine, Shanghai Jiaotong University

data_processing:
Illumina Casava1.8 software used for basecalling.
removing  reads  containing  ploy-N, with  5’ adapter contaminants,  without  3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data.
The small RNA tags were mapped to reference sequence by Bowtie-0.12.9
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization   formula:   Normalized   expression   =   mapped   readcount/Total reads*1000000
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: villi

extract_protocol:
placental villi were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: villi

value: placenta

tag: gestational days


title: WTIno80rep3

value: Control


title: WTIno80rep2


title: WTIno80rep1


title: tubal ectopic pregnancy rep2


title: H2AZ4KRrep3


title: PB019.CAAGGGAT


title: PB019.CCTTTGGT


title: H2AZ4KRrep2


title: PB019.TGTAGTGG


title: PB019.CGTGTCTA


title: tubal ectopic pregnancy rep1


title: PB019.CAATCCGA


title: H2AZ4KRrep1


title: WTH2AZrep3

value: WT H2AZ


title: intrauterine pregnancy rep4


title: WTH2AZrep1


title: intrauterine pregnancy rep5


title: WTH2AZrep2


title: PB019.TTGGTACC

value: 24 hrs


title: tubal ectopic pregnancy rep4


title: intrauterine pregnancy rep3


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 30 days after grafting. -DVC3

city: qingdao

first: ji

last: piyu

address: changcheng road

institute: Qingdao Agricultural University

description: Pyrus communis L. × Pyrus bretschneideri R. and Pyrus ussuriensis maxim.

data_processing:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the   concentration, quality and integrity were determined using a NanoDrop spectrophotometer   (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample   preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA   was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was   carried out using divalent cations under elevated temperature in an Illumina proprietary   fragmentation buffer.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The gene expression level was calculated based on FPKM (Fragments Per Kilo bases per Million fragments).
Genome_build: Pyrus x bretschneideri (assembly Pbr_v1.0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Pyrus hybrid rootstock

source_name: stem

extract_protocol:
Total RNA was extracted and purified using the RNAprep Pure Plant Kit (Tiangen,Beijing, China). After RNA extraction purification and library construction, the samples were subjected to Paired-end (PE) sequencing based on Illumina sequencing platform using Next-Generation Sequencing (NGS).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stem

value: 30 days


title: intrauterine pregnancy rep2


title: Ino80K929Rrep1


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 30 days after grafting. -DVC2


title: intrauterine pregnancy rep1


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 9 days after grafting. -DSD3

value: 9 days


title: PB019.AGCTCTTG


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 30 days after grafting. -DVC1


title: PB019.CAGAATGG


title: PB019.AGCAGGAT


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 9 days after grafting. -DSD2


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 9 days after grafting. -DSD1


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 5 days after grafting. -DCF1

value: 5 days


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 5 days after grafting. -DCF3


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 5 days after grafting. -DCF2


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 1 day after grafting. -DSS3

value: 1 day


title: RKO cells transfected with siNC

first: Yuguo

last: Liu

address: 320 Yue Yang Road

department: Institute for Nutritional Sciences, SIBS

institute: Chinese Academy of Sciences

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH37 whole genome using bowtie MapSplice version 2.1.7.
The stat of mapped reads was list in MappingStatistic_RKO-SINC.xls andMappingStatistic_RKO-SIU2.xls
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: GRCH37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: control RKO cell

extract_protocol:
RKO cells treated with siNC or sihnRNPU.Then total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Lifetech protocol.

value: RKO

value: colorectal

value: control


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 30 days after grafting. -SVC3

description: Pyrus communis L. × Pyrus bretschneideri R.


title: Differentiated 2DF-derived iMACs, cell line K7 (rep 2)

city: Moscow

first: Irina

last: Lyadova

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

data_processing:
Trimming: CLC Genomics Workbench 20.0.4 (https://digitalinsights.qiagen.com) was used for read trimming with the following parameters: “quality scores - 0.005; trim ambiguous nucleotides – 2; remove 5’-terminal nucleotides – 1; remove 3’-terminal nucleotides – 1; discard reads below a length of 25”.
Read mapping: The high-quality reads were uniquely mapped using the CLC Genomics Workbench (length fraction = 1 and similarity fraction = 0.95) to the reference genome of H. sapiens.
Readcount obtaining: readcounts were calculated for each gene using CLC Genomics Workbench. Total number of reads mapped on a gene was used as a readcount for the gene.
Assembly: GRCh38
Supplementary files format and content: Raw gene readcounts for each sample.

extract_protocol:
For RNA isolation, the cells were homogenized using syringe and needle or a QIAshredder kit, and RNA was isolated using RNeasy Micro (<5x10^5 cells) or RNAeasy Mini (>5x105 cells) Kits.
RNA concentrations were measured using a Qubit™ RNA HS Assay Kit and RNA integrity number (RIN) was assessed using an RNA 6000 Pico Kit for Bioanalyzer. Only RNA samples with RIN > 8 were used for subsequent library preparation. PolyA RNA was isolated using a NEBNext Poly(A) mRNA Magnetic Isolation Module, containing magnetic Oligo d(T) beads. Transcriptome libraries were constructed using a NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions. Libraries were prepared with a starting amount of 150 ng and amplified with 15 PCR cycles. RNA was fragmented to the average size of 200nt by incubation at 94 °C for 10 min. Libraries were quantified with a Qubit dsDNA HS Kit and the size distribution was determined with a High Sensitivity DNA Kit for Bioanalyzer.

value: iPSC-derived macrophages

value: 2DF protocol of differentiation, CD14+ iMacs


title: Differentiated 2DF-derived iMACs, cell line K7 (rep 1)


title: PB019.GCAATTCC

value: ventral midbrain

value: NeuN+ nuclei

value: wildtype

value: IFNG


title: PB019.CTTGAGGA


title: RKO cells transfected with sihnRNPU

source_name: hnRNPU gene knockdown RKO cell

value: hnRNPU gene knockdown


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 1 day after grafting. -DSS1


title: PB019.GACTGTGT


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 30 days after grafting. -SVC2


title: Differentiated EBS-derived iMACs, cell line K7 (rep 1)

value: EBS protocol of differentiation, CD14+ iMacs


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 30 days after grafting. -SVC1


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 9 days after grafting. -SSD3


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 9 days after grafting. -SSD2


title: Differentiated 2DF-derived iMACs, cell line iMA (rep 4)

source_name: iMA

value: iMA


title: PB019.TCCTACCA

value: 24 hrs


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 5 days after grafting. -SCF3

value: stem


title: PB019.AGAAGCCA


title: Differentiated EBS-derived iMACs, cell line iMA (rep 4)


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 5 days after grafting. -SCF2


title: PB019.CTCTCTCA


title: The sample is the part of graft union of QAUP-1 on Qingzhen D1 are collected on 1 day after grafting. -DSS2


title: PB019.TGGGTTGT


title: Differentiated 2DF-derived iMACs, cell line iMA (rep 2)


title: PB019.GCACTAAG


title: Differentiated EBS-derived iMACs, cell line iMA (rep 2)


title: PB019.ATGCGCTT

value: 6 hrs


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 1 day after grafting. -SSS1


title: PB019.GTTGGAAC


title: PB019.AGGACTAC


title: ∆hexRK 3

city: Iowa City

first: Anthony

last: Pannullo

state: IA

address: 431 Newton Road

institute: University of Iowa

data_processing:
ProkSeq version 2.0
Adapter trimming and read QC done by FastQC (parameters were automatically detemrined through Prokseq v 2.0 pipeline)
Reads aligned to genome using Bowtie2 (parameters were automatically detemrined through Prokseq v 2.0 pipeline)
Differential expression counts done by FeatureCounts (parameters were automatically detemrined through Prokseq v 2.0 pipeline)
Differential Expression Statisical Analysis done by DESeq2 (parameters were automatically detemrined through Prokseq v 2.0 pipeline)
Assembly: FN545816.1
Supplementary files format and content: text files included DESeq2 analysis output comparing 3 biological replicates of WT R20291 to 3 biological replicates of ∆hexRK

organism: Clostridioides difficile

source_name: Bacterial Culture

growth_protocol: Overnight cultures were grown in TY then subcultured 1:100 in 100 mL of TY. Subcultures were grown to OD600 0.7-0.8

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA library prep was performed by using Illumina RiboZero Plus librabry preperation kit

treatment_protocol: Not applicable

value: Bacterial Culture

value: deltahexRK

value: Not applicable


title: ∆hexRK 2


title: WT R20291 2

value: WT


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 9 days after grafting.-SSD1

value: 9 days


title: WT R20291 3


title: 2DF-derived iMacs, cell line iMA (rep 2), day 10

value: iPSC-derived macrophages

value: 2DF protocol of differentiation, day 10


title: 2DF-derived iMacs, cell line iMA (rep 2), day 19

value: 2DF protocol of differentiation, day 19


title: WT R20291 1


title: PB019.GTCCTAGT

value: ventral midbrain

value: NeuN+ nuclei


title: ∆hexRK 1


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 5 days after grafting. -SCF1

value: 5 days


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 1 day after grafting. -SSS3

value: 1 day


title: The sample is the part of graft union of Qingzhen D1 on Qingzhen D1 are collected on 1 day after grafting. -SSS2


title: 2DF-derived iMacs, cell line iMA (rep 2), day 6

value: 2DF protocol of differentiation, day 6


title: Δgra-orf32 mutant, on ISP2 plates, 24 h 3

city: Guangzhou

first: Ming-Rong

last: Deng

state: Guangdong

address: No.100 Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Assembly: GCF_000830005.1_ASM83000v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Streptomyces vietnamensis

source_name: spores

growth_protocol: the mutant was cultivated on ISP2 and YEME plates at 30 °C for 24 h

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA purified from 1 μg of total RNA using rRNA-removing probes was used for the construction of sequencing libraries.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then USER Enzyme was used to degrade the second strand of cDNA containing U, In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: spores

value: in-frame deletion of gra-orf32

value: cultivated on ISP2 plates for 24 hours


title: Δgra-orf32 mutant, on YEME plates, 24 h 2

value: cultivated on YEME plates for 24 hours


title: Δgra-orf32 mutant, on YEME plates, 24 h 3


title: Δgra-orf32 mutant, on YEME plates, 24 h 1


title: Differentiated 2DF-derived iMACs, cell line iMA (rep 1)

value: iMA

value: 2DF protocol of differentiation, CD14+ iMacs


title: PB019.CGCCTTTT

value: wildtype

value: IFNG

value: 6 hrs


title: Δgra-orf32 mutant, on ISP2 plates, 24 h 2


title: EBS-derived iMacs, cell line iMA (rep 2), day 19

value: iPSC-derived macrophages

value: EBS protocol of differentiation, day 19


title: PB019.TACACCAG


title: 2DF-derived iMacs, cell line iMA (rep 2), day 0

value: 2DF protocol of differentiation, day 0


title: EBS-derived iMacs, cell line iMA (rep 2), day 10

value: EBS protocol of differentiation, day 10


title: Δgra-orf32 mutant, on ISP2 plates, 24 h 1


title: RNA-seq of ovary about GYR, rep3

city: Nanning City

first: Tian

last: Wu

address: Xixiangtang District, Nanning City, Guangxi Zhuang Autonomous Region

institute: Guangxi University

data_processing:
Illumina Casava1.7 software used for basecalling.
The high-quality sequences filtered by fastp were mapped to the mouse reference genome by Bowtie2 (v2.0.0.5) and Tophat (v2.0.0).
Then, the mapping readings were assembled and GTF files were generated by StringTie (v2.2.0). The GTF files were then merged into one file by Cuffmerge, from which the counts of each gene were extracted.
The library size (count) was calculated using cheepelev et al. 's protocol, Nucleic Acid Research, 2009. In short, the exons of all the isomers of a gene are combined into a meta-transcript. The number of declining reads in the exon of this meta-transcript is counted according to the meta-transcript size and the library size.
Assembly: GRCg6a
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Gallus gallus

source_name: ovary

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

tag: breed

value: GYR


title: PB019.GTCGATAG

value: ventral midbrain

value: NeuN+ nuclei


title: BMI Epididymis PacBio

city: Kunming

first: Jinlong

last: Huo

state: Yunnan

address: Jin-hei

department: Faculty of Animal Science and Technology

institute: Yunnan Agricultural University

description: Full-length RNA

data_processing:
PacBio long-reads bam files were processed using SMRT Link v9.0 followed by the IsoSeq v3 pipeline (https://github.com/PacificBiosciences/IsoSeq). IsoSeq long-reads processing steps include circular consensus sequence (CCS) generation using ccs, primer removal and demultiplexing using lima. The above workflow generates full-length non-chimeric (FLNC) reads and non-full-length reads based on the presence of 5′ and 3′ adapters and the presence of poly-A tails.
RNA-seq short reads were trimmed using cutadapt v3.0 by removing adapter sequences and low-quality bases. Trimmed reads were aligned to the Sus scrofa reference genome assembly Sscrofa11.1 using STAR and the featureCounts program from Subread package was used to quantify the RNA-seq datasets.
Genome_build: Sus Scrofa genome (assembly Sscrofa11.1, Breed: Duroc, https://www.ncbi.nlm.nih.gov/assembly/GCF_000003025.6/)
Supplementary_files_format_and_content: PacBio: Full-length non-chimeric (FLNC) reads in fasta format. RNAseq: featureCounts results of gene raw counts.

organism: Sus scrofa

source_name: BMI Epididymis

growth_protocol: BMI boars were raised at Yunnan Agricultural University and were harvested at the age of 12-month old.

extract_protocol:
Total RNA was extracted from five mixed testicles samples and five mixed epididymal samples using TRIzol (Thermo Fisher Scientific, Invitrogen, Catalog #15596018) following the protocol provided by the manufacturer. The RIN (RNA integrity number) value of RNA samples was determined by an Agilent 2100 Bioanalyzer and 1% agarose gel electrophoresis. The quality control step ensures that RIN values are above 7.5 and 28S/18S ratios are greater than or equal to 1.5. The purity and concentration of RNAs were detected with a Nanodrop microspectrophotometer (Thermo Fisher Scientific).
Oligo(dT) magnetic beads were used to enrich RNAs with poly-A tails and a SMARTer cDNA synthesis kit (Takara, Clontech, Catalog #634925) was used to generate full-length cDNA molecules. For Illumina RNAseq, the cDNA fragments were purified with a QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands, Catalog # 28106), followed by end repair, base addition, and ligation to sequencing adapters. The ligation products were further size selected by agarose gel electrophoresis and amplified by PCR.

treatment_protocol: No treatment prior to the sample collection.

value: Epididymis

value: Banna mini-pig inbred line (BMI)

tag: age

value: adult


title: EBS-derived iMacs, cell line iMA (rep 2), day 6

value: EBS protocol of differentiation, day 6


title: EBS-derived iMacs, cell line iMA (rep 2), day 0

value: iMA

value: EBS protocol of differentiation, day 0


title: PB019.CCTCTATC

value: wildtype


title: RNA-seq of ovary about Yaoshan, rep3

value: Yaoshan


title: PB019.CATCCTAG

value: IFNG

value: 6 hrs


title: PB019.GGTACTCA


title: iMacs, cell line iMA (rep 2), iPSC

value: iPSC-derived macrophages

value: EBS/2DF protocol of differentiation, iPSC (day -4)


title: BMI Testis PacBio

description: Full-length RNA

source_name: BMI Testis

value: Testis


title: RNA-seq of ovary about Yaoshan, rep2

value: ovary


title: PB019.GCTCATGA


title: RNA-seq of ovary about GYR, rep1

value: GYR


title: 2DF-derived iMacs, cell line iMA (rep 1), day 19

value: 2DF protocol of differentiation, day 19


title: PB019.ACTGAAGC

value: ventral midbrain

value: NeuN+ nuclei


title: CBMNC-ADT

city: Indianapolis

first: Jered

last: Myslinski

state: IN

address: 950 W Walnut Street

department: Nephrology and Hypertension

institute: Indiana University School of Medicine

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 !Sample_data_processing = (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; Seurat RDS files

source_name: endothelial

extract_protocol:
To collect HUVECs from human umbilical cord, Liberase solution was infused into the vessel to release ECs from the basement membrane. The solution containing digested ECs was flushed into tubes for EC recovery. To collect CBMNCs from human umbilical cord blood samples, Ficoll-Paque was added to the anti-coagulated blood (diluted in PBS) and cell separation was performed according to the manufacturer’s protocol. Both HUVECs and CBMNCs were magnetically sorted with CD34 beads and resuspended with DMEM/10%FBS.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 and v3 protocol, 10x Genomics).

value: endothelial

value: Freshly isolated and MACS sorted CBMNCs


title: HUVEC-ADT

description: 10X Genomics

value: Freshly isolated and MACS sorted HUVECs


title: wt1tbx18_2

city: Pittsburgh

first: guang

last: li

state: PA

address: 530 45th St. 8116 Rangos Research Center

institute: university of pittsburgh

description:
processed data file:
multiSeqBarcodes_to_samples.xlsx
wt1_metadata.csv; tbx18_metadata.csv;
wt1_filtered_feature_bc_matrix.rds; tbx18_filtered_feature_bc_matrix.rds;

data_processing:
Reads were processed using the Cell Ranger (version 3.1.0) count pipeline using the human reference genome GRCm38.p4, annotations from Ensembl (version 84) with the arguments --chemistry= SC3Pv3, --expect-cells=5,000, 10,000 and 25,000 , depending on the specific library. For MULTIseq fastq files, library_type was set to "Custom".
Sample demultiplexing was performed using the R package deMULTIplex (version 1.0.2) [https://github.com/chris-mcginnis-ucsf/MULTI-seq].
Quality control and filtering were performed using the R package scater [10.1093/bioinformatics/btw777] (v1.14.6). For each sample, cells with total library size >=2000, number of detected genes >=1000 and <= 8000, and <=30% percentage of mitochondrial reads were considered. Additionally doublets with the same MULTI-seq barcode were filtered using the scds R package [10.1093/bioinformatics/btz698] (v1.2.0) as described in Supplementary Note XYZ.1. For each sample, we created Seurat [REF] objects and processed with the standard Seurat workflow, involving normalization with "LogNormalize", followed by variable feature selection with "vst", and scaling. Individual sample Seurat objects were merged into a single Seurat object and the top principal components that cumulatively explain >80% of variance in the data were used for batch correction using Harmony.
The sample metadata, barcodes, counts matrices, and log-normalized counts are additionally provided as processed data files.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: rds, xlsx, and csv files.

source_name: MULTIseq pooled samples

extract_protocol:
Cardiac cells from emryonic and neonatal mouse hearts were dissociated with were sequencially incubated with 0.25% Trypsin/EDTA and a collagenase HBSS+/+ mixture before filtered through a 40 μm filter. The cells from each sample were stained with with a unique MULTI-seq barcode separately and pooled before library preparation.
The pooled cells were captured in 10X Chromium (10X Genomics, 120223) by following the single cell 3’ reagent kits v3 user guide. Briefly, cells were loaded into each chip well to be partitioned into gel beads in emulsion (GEMs) in the Chromium controller. We targeted for 25,000 cells in each chip well and profiled one well for the first batch experiment and two chip wells for the second experiment. The cells were then lysed and barcoded reverse transcribed in the GEMs. After breaking the GEMs and further cleanup and amplification, the cDNA was enzymatically fragmented and 3′ end fragments were selected for library preparation. After further processing including end repair, A-tailing, adaptor ligation, and PCR amplification, a string of sequences including sample index, UMI sequences, barcode sequences, and sequencing primer P5 and P7 were added to cDNA on both ends. The libraries were sequenced on HiSeq X Ten or Nova-seq platform.

value: two strains (CD1, C57BL/6)


title: CB-ECFC (Cord blood-endothelial colony forming cells)

description: 10X Genomics

value: CB-ECFC


title: RNA-seq of ovary about Yaoshan, rep1


title: PB019.GATGATCC

value: wildtype

value: Saline

value: 24 hrs


title: RNA-seq of ovary about GYR, rep2


title: PB019.AAGCAGGA


title: PB019.GCAACGTT

value: 72 hrs


title: Sample P5_P9

description:
processed data file:
multiSeqBarcodes_to_samples.xlsx
C57BL6_metadata.csv
C57BL6_filtered_feature_bc_matrix.rds

value: Cardiac cells from emryonic and neonatal mouse hearts


title: PB019.TCAACAGG


title: Sample E9.5_P3

description:
processed data file:
multiSeqBarcodes_to_samples.xlsx
CD1_metadata.csv
CD1_filtered_feature_bc_matrix.rds


title: HUVEC

description: 10X Genomics


title: wt1tbx18_1


title: Sample E18_P1


title: EBS-derived iMacs, cell line iMA (rep 1), day 19

value: iMA

value: iPSC-derived macrophages

value: EBS protocol of differentiation, day 19


title: U87_NC_3

city: Jining

first: Wei

last: Meng

address: 89 Guhuai Road

department: Affiliated Hospital of Jining Medical University

institute: Jining Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38.p13 human genome
Read count extraction and normalization were performed using RSEM software
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Glioblastoma

extract_protocol:
RNA was harvested using Rneasy mini plus kit (VZ6). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Normal control

value: Glioblastoma


title: EBS-derived iMacs, cell line iMA (rep 1), day 10

value: EBS protocol of differentiation, day 10


title: PB019.GGATGATC

value: ventral midbrain

value: NeuN+ nuclei


title: 2DF-derived iMacs, cell line iMA (rep 1), day 6

value: 2DF protocol of differentiation, day 6


title: EBS-derived iMacs, cell line iMA (rep 1), day 6

value: EBS protocol of differentiation, day 6


title: CBMNC

description: 10X Genomics

value: endothelial

value: Freshly isolated and MACS sorted CBMNCs


title: A20_2

city: Qingdao

first: Lianbin

last: Xu

address: No.700, Changcheng Road

department: College of Animal Science and Technology

data_processing:
Illumina Casava 1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Pancreatic beta cells

growth_protocol: 20×the standard arginine concentration in DEME medium

extract_protocol:
RNA was harvested using Trizol reagent from the MIN6 beta cells. Illumina NEBNext Ultra™ Directional RNA Library Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MIN6 pancreatic beta cells

value: high-arginine culture


title: 2DF-derived iMacs, cell line iMA (rep 1), day 0

value: 2DF protocol of differentiation, day 0


title: PB019.TGCACGTA

value: wildtype

value: Saline

value: 24 hrs


title: U87_KD_2

value: CHRM Knockdown


title: U87_NC_1


title: 2DF-derived iMacs, cell line iMA (rep 1), day 10

value: iMA

value: iPSC-derived macrophages

value: 2DF protocol of differentiation, day 10


title: A20_3


title: PB019.CGGCATAA


title: 2DF-derived iMacs, cell line iMA (rep 1), iPSC

value: 2DF protocol of differentiation, iPSC (day -4)


title: U87_NC_2

value: Normal control

value: Glioblastoma


title: EBS-derived iMacs, cell line iMA (rep 1), day 0

value: EBS protocol of differentiation, day 0


title: A20_1


title: A1_3

growth_protocol: 1×the standard arginine concentration in DEME medium

value: standard-arginine culture


title: EBS-derived iMacs, cell line iMA (rep 1), iPSC

value: EBS protocol of differentiation, iPSC (day -4)


title: U87_KD_1


title: PB019.TCTCGGAT

value: ventral midbrain

value: NeuN+ nuclei

value: 72 hrs


title: 2DF-derived iMacs, cell line K7, day 19

value: 2DF protocol of differentiation, day 19


title: PB019.AAGTGGTG

value: wildtype


title: A1_1

value: MIN6 pancreatic beta cells


title: U87_KD_3


title: HS578T 17PKO_DOX_48H_rep2

first: Kun

last: Huang

address: 410 W 10th street

institute: Indiana University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.7.9a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to GENCODE hg38 genes using featureCounts (from subread v2.0.1) with the following parameters: “-s2 –p –Q 10”.
Assembly: hg38
Supplementary files format and content: raw counts

source_name: Breast cancer

growth_protocol: HS578T cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from HS578T cells using TRIzol (Ambion) and the miRNeasy Mini kit (Qiagen).
The cDNA library was constructed using the KAPA RNA Hyper Prep Kit (Roche Corporate) and the quality was accessed by the Qubit and Agilent Bioanalyzer. The library pool was sequenced in 100b paired-end read format on NovaSeq 6000 (Illumina)

treatment_protocol: HS578T cells treated with control (DMSO) or doxorubicin (170nM for 17p-intact cells and 1μm for 17p-KO cells) for 48 h .

value: Breast cancer

value: Eukaryotic cells

value: one copy of chrom 17p knockout

value: Doxorubicin treated


title: HS578T 17PKO_DOX_48H_rep3


title: PB019.TACCTTGG

value: Saline


title: PB019.CTAGCTGT


title: 2DF-derived iMacs, cell line K7, day 10

value: iPSC-derived macrophages

value: 2DF protocol of differentiation, day 10


title: A1_2


title: PB019.TCGTCTAG


title: A01_2

growth_protocol: 0.1×the standard arginine concentration in DEME medium

value: low-arginine culture


title: 2DF-derived iMacs, cell line K7, iPSC

value: 2DF protocol of differentiation, iPSC (day -4)


title: A01_1


title: 2DF-derived iMacs, cell line K7, day 6

value: 2DF protocol of differentiation, day 6


title: HS578T CAS9_DOX_48H_rep3

value: WT


title: HS578T CAS9_DOX_48H_rep1


title: PB019.ATGCTGAG

value: ventral midbrain

value: 24 hrs


title: PB019.AGTCTTCG

value: NeuN+ nuclei


title: EBS-derived iMacs, cell line K7, day 19

value: EBS protocol of differentiation, day 19


title: Tel.Mar.M

city: Shenyang

first: Wang

middle: Ming

last: Lin

address: 120 Dongling Road

institute: shenyang agricultural university

data_processing:
Clean reads were mapped to the reference genome CHIR_2.0. The abundances of the miRNA sequencing reads were reported in TPM using the Bowtie (v.0.12.9) pipeline without mismatch.
mirdeep2(v.2.0.0.5) and srna-tools-cli softwares were used to predict the potential miRNA candidates.
The available software miREvo (v1.1) and mirdeep2 (v.2.0.0.5) were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps.
Assembly: Capra hircus CHIR_2.0
Supplementary files format and content: tab-delimited text files include TPM values for each miRNA in each sample
Supplementary files format and content: Matrix table with raw  gene counts for every gene and every sample

organism: Capra hircus

source_name: Secondary hair follicle

growth_protocol: Skin samples were taken from middle of the scapula , and the secondary hair follicles were separated from the skin with scalpel under dissecting microscope.

extract_protocol:
Total RNA was extracted from the secondary follicles using the RNAiso plus as the manufacturer’s instructions (Takara Biotechnology Dalian, Co. Ltd., China).
Total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
A total of 3 µg RNA per sample were used as the basis for small RNA library construction by sequencing company (Novogene, Beijing, China). The sRNA library was sequenced at Illumina HiSeq 2500 platform (Illumina, San Diego, CA, USA).

treatment_protocol: Temporarily stored in normal saline at 4 ° C for collected secondary hair follicles and than rapidly frozen in liquid nitrogen.

value: Liaoning cashmere goat

value: Secondary hair follicle

value: 1.5 years

value: Mar

tag: gender

value: male


title: HS578T 17PKO_DOX_48H_rep1

value: Breast cancer

value: Eukaryotic cells

value: one copy of chrom 17p knockout

value: Doxorubicin treated


title: HS578T 17PKO_DMSO_48H_rep3

value: untreated


title: EBS-derived iMacs, cell line K7, day 10

value: iPSC-derived macrophages

value: EBS protocol of differentiation, day 10


title: A01_3

value: MIN6 pancreatic beta cells

value: low-arginine culture


title: HS578T 17PKO_DMSO_48H_rep2


title: PB019.GCAGGTAA

source_name: ventral midbrain

value: ventral midbrain

value: wildtype

value: Saline

value: 48 hrs


title: EBS-derived iMacs, cell line K7, day 6

value: EBS protocol of differentiation, day 6


title: Tel.Feb.M

value: Liaoning cashmere goat

value: Secondary hair follicle

value: 1.5 years

value: Feb


title: Tel.Mar.F

value: Mar

value: female


title: HS578T CAS9_DOX_48H_rep2

value: Breast cancer

value: Eukaryotic cells

value: WT

value: Doxorubicin treated


title: HS578T 17PKO_DMSO_48H_rep1

value: one copy of chrom 17p knockout

value: untreated


title: PB019.ACCGTCAT

value: ventral midbrain

value: NeuN+ nuclei


title: 2DF-derived iMacs, cell line K7, day 0

value: iPSC-derived macrophages

value: 2DF protocol of differentiation, day 0


title: EBS-derived iMacs, cell line K7, iPSC

value: EBS protocol of differentiation, iPSC (day -4)


title: EBS-derived iMacs, cell line K7, day 0

value: EBS protocol of differentiation, day 0


title: Cat.Dec.M

value: Liaoning cashmere goat

value: Secondary hair follicle

value: Dec

value: male


title: Tel.Feb.F

value: 1.5 years

value: Feb

value: female


title: HS578T cas9_DMSO_48H_rep3

value: Breast cancer

value: Eukaryotic cells

value: WT


title: PB019.CACTTAGC

value: wildtype

value: Saline

value: 24 hrs


title: Col_Gln3

city: Taipei

first: Ming-Hsiun

last: Hsieh

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Low quality reads, which are shorter than 35 base pairs or have an error probability greater than 0.05, were filtered out.
Mapping reads to the Arabidopsis reference genome TAIR10 by using BLAT method.
Reverse R1 BAM file of each sample under SAMtools.
For each sample, pick up R1-reversed BAM file and R2 BAM file for reads per kilo-base-pair gene model per million mapped reads (RPKM) computation.
TMM normalization is applied to normalize all RPKM files.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text file include normalized RPKM values for each sample

organism: Arabidopsis thaliana

source_name: 12-day-old seedlings

growth_protocol: Arabidopsis seeds were surface sterilized and grown on 1/2 MS-modified basal salt mixture without N (M531, PhytoTechnology Laboratories) containing 0.05% (w/v) 2-(N-morpholine)-ethanesulfonic acid (MES), 0.5% (w/v) Suc, 0.8% (w/v) agar, adjusted to pH 5.7 with 1 N KOH, and supplemented with 5 mM NH4NO3 or 5 mM Gln. The plates were sealed with parafilm, kept at 4℃ for 2 days and then transferred to the growth room on a 16-h-light/8-h-dark cycle at 22°C for 12 days.

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Columbia (Col) ecotype

value: 12-day-old seedlings


title: Cat.Dec.F


title: PB019.GAGTCGAT

value: ventral midbrain

value: NeuN+ nuclei


title: PB019.CTCTGGTT

value: 48 hrs


title: Col_Gln2


title: HS578T cas9_DMSO_48H_rep1

value: untreated


title: HS578T cas9_DMSO_48H_rep2


title: PB019.CCACACTT


title: ToHa-IPE2-3

city: Sydney

first: Hani

middle: Jieun

last: Kim

address: The University of Sydney

country: Australia

institute: The University of Sydney

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retinal organoid

extract_protocol:
Organoids were dissociated and subset of cell suspension was stained with 0.4% Trypan Blue (Gibco) and assessed for viability and concentration using Countess II Automated Cell Counter (Invitrogen).  Single cell suspensions were passed through 40µm cell strainer (Corning) and concentration was adjusted to 1000 cells/µL. Suspension were loaded in single-cell-B Chip (10X Genomics) for target output of 10,000 cells per sample. Single-cell droplet capture was performed on the Chromium Controller (10X Genomics).
Library preparation was performed in accordance with the Single-Cell 3’ v3 protocol.

value: Retinal organoid

value: retinal


title: Cat.Nov.M

value: Liaoning cashmere goat

value: Secondary hair follicle

value: 1.5 years

value: Nov

value: male


title: PB019.GTAAACGG

first: Peter

last: Sims

address: 3960 Broadway, Lasker 203AC

data_processing:
Low-input bulk RNA-seq: Reads were aligned to the mouse reference genome GRCm38 and transcriptome annotation (Gencode vM10) using the STAR aligner with parameters –sjdbOverhang 65 –twopassMode Basic after trimming poly(A)-tails from the 3’-ends. The aligned reads were demultiplexed using the well-identifying barcodes, correcting all single-nucleotide errors. All reads with the same well-identifying barcode, UMI, and gene mapping were collapsed to represent an individual transcript. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance one of another UMI with the same well-identifying barcode and gene. For each 96-well plate, after generating a final list of individual transcripts with unique combinations of well-identifying barcodes, UMIs, and gene mapping, we produced a molecular count matrix for downstream analysis.
Single-nucleus RNA-seq: snRNA-seq data were processed as described previously (Yuan et al., 2018) (code available at: https://github.com/simslab/DropSeqPipeline8). Reads were aligned to the mouse reference genome GRCm38 and transcriptome annotation (Gencode vM10) using the STAR aligner with parameters –sjdbOverhang 65 –twopassMode Basic after trimming poly(A)-tails from the 3’-ends. All reads that uniquely aligned to a given gene body (including introns) were kept for downstream filtering analysis, because a large fraction of nuclear transcripts are unspliced. The aligned reads were demultiplexed using the cell-identifying barcodes, correcting all single-nucleotide errors. All reads with the same cell-identifying barcode, UMI, and gene mapping were collapsed to represent an individual transcript. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance one of another UMI with the same cell-identifying barcode and gene. For each sample, after generating a final list of individual transcripts with unique combinations of cell-identifying barcodes, UMIs, and gene mapping, we produced a molecular count matrix for downstream analysis. We first performed unsupervised clustering on the count matrices using the PhenoGraph (Levine et al., 2015) implementation of Louvain community detection after selection of highly variable genes and construction of a k-nearest neighbors graph as described previously (Levitin et al., 2019). We identified 38 clusters (Supp. Fig. 4a), two of which showed statistically significant co-enrichment of dopamine neuron markers such as Th and Slc6a3 based on the binomial test for expression specificity (Shekhar et al., 2016). We identified six major cell types with sufficient coverage for downstream analysis as shown in the UMAP (Becht et al., 2018) embedding in Figure 3a. The assignment of PhenoGraph clusters into major cell type groupings was based on key marker genes significantly enriched in each cluster, as shown in Supp. Fig. 4b: Oligodendrocytes (Mal, Mag, Mog), Astrocytes (Gja1, Fgfr3, Atp1a2), Microglia (C1qb, Siglech, Csf1r), VGLUT2 neurons (Slc17a6, Cacna2d1, Ntng1), GABA neurons (Slc32a1, Gad1, Gad2), and DA neurons (Th, Slc6a3, En1, Slc10a4). Rare populations with insufficient cell numbers (e.g., mural cells, T cells) or ambiguous neuronal clusters possibly containing multiplets (e.g., Gad1+/Gad2+/Slc17a7+/Th+) were excluded from downstream analysis.
Assembly: GRCm38 / Gencode vM10
Supplementary files format and content: Tab-delimited text files containing count matrix for each cell or sample with sample or well-identifying barcode in the header.

extract_protocol:
Nuclei were prepared from the ventral midbrain of mice at 48 hours after injection of saline or IFN-γ. Mice were sacrificed by cervical dislocation and brains were rapidly extracted and submerged in ice-cold phosphate-buffered saline (PBS). Brains were placed on an ice-cold brain matrix (Zivic Instruments) and separated into 0.5-1.0 mm sections using ice cold razor blades. Ventral midbrain tissue was dissected from slices between approximately -2.5 mm to -3.75 mm AP to Bregma. First, the cortex, hippocampi, and any hypothalamus or white matter ventral to the midbrain were removed. A single horizontal cut was made just dorsal to the rostral linear nucleus and all dorsal tissue was discarded. The remaining tissue containing the SN/VTA was flash frozen on liquid nitrogen and stored at -80°C.  Nuclei preparation and sorting were conducted as described by Krishnaswami et al. (2016) with only minor modifications. Frozen tissue was thawed in nuclear isolation medium 1 (NIM1: 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris, pH 8.0) supplemented with 1 mM DTT, 0.2 U/µL SUPERaseIN, 1x EDTA-free Protease Inhibitor Cocktail (Roche), and 0.1% Triton X-100. Tissue was homogenized on ice in a glass-glass dounce homogenizer with 30 gentle strokes of loose and tight clearance pestles. All subsequent purification steps were performed on ice or at 4oC unless otherwise specified. Lysates were spun at 500xg for 5 minutes, resuspended in NIM1 supplemented as above and also with 1% BSA, and passed through a 40µm cell strainer cap. Nuclei were centrifuged again at 500xg for 5 minutes and resuspended in staining buffer (PBS supplemented with 1% BSA, 5 mM MgCl2, 0.2 U/µL SUPERaseIN, 1 µg/mL propidium iodide, and 2 µg/mL mouse anti-NeuN AlexaFluor488). After 30 minutes incubation on ice, nuclei were centrifuged at 500xg for 5 minutes and resuspended in 0.5 mL of FACS buffer (PBS + 0.04% BSA, 0.2 U/µL SUPERaseIN, and 1 µg/mL propidium iodide) for sorting.    Nuclei sorting was conducted on a BD Influx (BD Biosciences) using a 100 μm nozzle at 11.1 psi. Single nuclei were gated first using FSC-H vs. FSC-A and then on propidium iodide fluorescence. NeuN/AlexaFluor488 fluorescence was used to establish NeuN- and NeuN+ gates on the single nuclei population. Nuclei were sorted directly into 96 well plates (for bulk nuclei RNA-seq with 96-well plate, pooled library construction) or into 1.5 mL Eppendorf tubes that had been previously coated with 0.1% BSA in PBS overnight at 37oC (for snRNA-seq).
Low-input bulk RNA-seq: The protocol for plate based, 3’ end unique molecular indicator (UMI)-based RNA sequencing of single cells has been described previously (Snyder et al., 2019) as well as modifications to accommodate ultra-low input samples (Hobson et al., 2022b). See Supplementary File 1 for sequences of all custom primers and oligonucleotides used in this protocol. For neuronal and glial nuclei analysis in Figure 1-2, 100 NeuN- or NeuN+ nuclei were sorted directly into the wells of a 96 well plate containing 3 µL of nuclease-free water containing 1 U/µL SUPERaseIN (sort volume ~3 µL for total volume of ~6 µL). After adding 1.5 µL of 10 µM barcoded RT primer (Integrated DNA Technologies), primer annealing was performed at 72°C for 3 minutes. Reverse transcription was performed by adding 7.5 µL RT mix to each well (2.81 µL of 40% polyethylene glycol 8000, 0.15 µL of 100 mM dNTPs, 3 µL of 5X Maxima H RT Buffer, 0.2 µL of 200 U/µL Maxima H Reverse Transcriptase (ThermoFisher), 0.2 µL of 20 U/µL SUPERaseIN, and 0.15 µL of 100 µM Template Switching Oligo (Integrated DNA Technologies), and 1 µL of nuclease free water). Reverse transcription was performed at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes, 42°C for 2 minutes, 75°C for 10 minutes, followed by a 4°C hold. Excess primers were removed by adding 2 µL of Exonuclease I mix (1.875U ExoI in water) to each well and incubating at 37°C for 30 minutes, 85°C for 15 minutes, 75°C for 30 seconds, 4°C hold. All wells were pooled into a single 15-ml falcon tubes and cDNA was purified and concentrated using Dynabeads™ MyOne™ Silane beads (ThermoFisher) according to the manufacturer’s instructions. The cDNA was split into duplicate reactions containing 25 µl cDNA, 25 µl 2x HIFI HotStart Ready Mix (Kapa Biosystems), and 0.2 M SMART PCR Primer. PCR was run as follows: 37°C for 30 minutes, 85°C for 15 minutes, 75°C for 30 seconds, 4°C hold. Duplicate reactions were combined and purified using 0.7 volumes AMPure XP beads (Beckman Coulter). The amplified cDNA was visualized on an Agilent 2100 Bioanalyzer and quantified using a Qubit II fluorometer (ThermoFisher). Single-nucleus RNA-seq: NeuN nuclear sorting was conducted as described above. Approximately 70% NeuN+ and 30% NeuN- single nuclei were sorted per sample. Sorted nuclei were placed on ice and immediately submitted to the Columbia Single Cell Analysis Core (Columbia Genome Center) for 10X Genomics Chromium Single Cell 3’ v3 library preparation according to the manufacturer's instructions.
low-input bulk RNA-seq (PLATE-seq) and single-nucleus RNA-seq


title: Col_Gln1


title: Col_NN2


title: JKCMRI2-ANAI-2

description: 10x Genomics

value: UCL UCLOOi017-A-1


title: PB019.TCGATGCA

value: wildtype


title: 2niPE2-ANAI-4

description: 10x Genomics


title: Col_NN3


title: PB019.TAAGGACG

value: Saline


title: Ana.Sep.M

value: Sep


title: Col_NN1

value: Columbia (Col) ecotype


title: Ana.Sep.F

value: female


title: scRNA_seq_Catagen

city: Lanzhou

first: qingbo

last: zheng

address: No.335, Jian 'gouyan, Xiaoxihu, Qilihe District, Lanzhou City, Gansu Province

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

description:
Skin tissue from scapula of yak during hair follicle catagen for single cell RNA sequencing
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Yak, LU_Bosgru_v3.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Bos grunniens

source_name: skin

extract_protocol:
Skin tissue was collected from the scapular anagen of healthy Tianzhu white yak about 2 years old. After cleaning and disinfection, the skin tissue was washed twice with PBS and 75 % ethanol, and cut into 0.5 × 0.2 cm strips. The skin tissue was digested with 0.25 % disperse enzyme in 37 ° C incubator for 2 hours, and the single hair follicle was pulled out. After digestion with 0.25 % trypsin for 0.5 hours, cells were observed under a microscope to see if they all fell off the hair shaft. After repeated blowing, the cells were filtered and centrifuged by 40 μm cell sieve, and the cells were resuspended by DMEM.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: skin

value: hair follicle

tag: developmental stage

value: catagen


title: Ana.May.F

value: May


title: Ana.May.M


title: PB019.CTTACACC

institute: Columbia University

value: ventral midbrain

value: NeuN+ nuclei

value: 24 hrs


title: PB019.GCTTAGAC

value: 48 hrs


title: 2niPE2-ANAI-3

description: 10x Genomics

value: Retinal organoid

value: retinal


title: scRNA_seq_Anagen

description:
Skin tissue from scapula of yak during hair follicle anagen for single cell RNA sequencing
10x Genomics

value: anagen


title: Kyse410_scramble_rep1

city: Luzhou

first: xu

last: liu

address: 25th Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

data_processing:
Illumina bcl2fastq 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRch37.p13 whole genome using HISAT2 (version 2.1.0) with default parameters
Read counts are aggregated at the gene level using HTseq(version 0.9.1) and then identified DEGs using R package DESeq2
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: text files include raw counts  for each Sample

source_name: human esophagus

extract_protocol:
Total RNA of stably infected cells was isolated with Trizol and the polyadenylated mRNAs were extracted using Dynabeads Oligo (dT) 25 beads
Three replicates were created for RNA-seq library construction using VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme Biotech), following the manufacturer’s instructions.

value: squamous cell carcinoma cells

tag: expression

value: scramble control


title: Kyse410_scramble_rep2


title: PB019.TTACTCGC

city: New York

value: wildtype

value: Saline


title: PB019.GTTAGCCT

value: 6 hrs


title: PB019.TAGAGGGT


title: Kyse410_shUHRF1_rep3


title: nuc2, snRNAseq

city: Planegg

first: Ines

last: Hellmann

address: Großhaderner Straße 2

department: Anthropology and Human Genomics, Faculty of Biology

country: Germany

institute: Ludwig-Maximilians-Universität München

description: 10x Genomics

data_processing:
The scRNA-seq and snRNA-seq data were processed using Cell Ranger 3.0.2 using as reference genome and annotation mm10 version 2020A for the scRNA-seq data and and a pre-mRNA version of mm10 2.1.0 as reference for snRNA-seq.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: HDF5 matrix files
Library strategy: snRNA-seq

source_name: Kidney

extract_protocol:
The RNALater reserved frozen tissue of 3 mice kidney quarters were thawed and transferred to one petri dish preloaded with 1 ml TST buffer containing 10 mM Tris, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20 (Roche, 11332465001) and 0.01% BSA (Sigma, B8667). It was minced with a razor blade for 10 minutes on ice. The homogenized tissue was then passed through a 40 µm cell strainer (VWR, 21008-949) into a 50 ml conical tube. One ml TST buffer was used to rinse the petri dish and collect the remaining tissue into the same tube. It was then mixed with 3 ml of ST buffer containing 10 mM Tris, 146 mM NaCl, 1 mM CaCl2 and 21 mM MgCl2 and spun down at 500g for 5 min at 4°C followed by supernatant removal. In the second experiment this washing step was repeated 2 more times. The pellet was resuspended in 100 µl ST buffer and passed through a 35 µm filter. The nuclei concentration was measured using the K2 Cellometer (Nexcelom Bioscience) with the AO nuclei stain (Nexcelom Bioscience, CS1-0108-5ML).
The cells or nuclei were loaded onto a 10x Chromium Next GEM G chip (10x Genomics, 1000120) aiming for recovery of 10,000 cells or nuclei. The RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent kit v3.1 (10x Genomics, 1000121) following vendor protocols. The libraries were pooled and sequenced on NovaSeq S1 100c flow cells (Illumina) with 28 bases for read1, 55 bases for read2 and 8 bases for index1 and aiming for 20,000 reads per cell.

value: Kidney

value: C57BL/6, CAST/EiJ and 129S1/SvImJ

value: Kidney cells


title: rep3, scRNAseq

description: 10x Genomics

data_processing:
The scRNA-seq and snRNA-seq data were processed using Cell Ranger 3.0.2 using as reference genome and annotation mm10 version 2020A for the scRNA-seq data and and a pre-mRNA version of mm10 2.1.0 as reference for snRNA-seq.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: HDF5 matrix files

extract_protocol:
One of each kidney sagittal quarter from three perfused mice of different strains C57BL/6, CAST/EiJ and 129S1/SvImJ were harvested into cold RPMI (Thermo Fisher Scientific, 11875093) with 2\% heat-inactivated Fetal Bovine Serum (Gibco, Thermo Fisher Scientific, 16140-071; FBS) and 1\% penicillin/streptomycin (Gibco, Thermo Fisher Scientific, 15140122). Each piece of the tissue was then minced for 2 minutes with a razor blade in 0.5 ml 1x liberase TH dissociation medium (10x concentrated solution from Millipore Sigma, 05401135001, reconstituted in DMEM/F12(Gibco, Thermo Fisher Scientific, 11320-033 in a petri dish on ice. The chopped tissue pieces were then pooled into one 1.5 ml Eppendorf tube and incubated in a thermomixer at 37°C for 1 hour at 600rpm with gentle pipetting for trituration every 10 minutes. The digestion mix was then transferred to a 15 ml conical tube and mixed with 10 ml 10\% FBS RPMI. After centrifugation in a swinging bucket rotor at 500g for 5 min at 4°C and supernatant removal, the pellet was resuspended in 1ml red blood cell lysing buffer (Sigma Aldrich, R7757). The suspension was spun down at 500g for 5 min at 4°C followed by supernatant removal. The pellet cleared of the red blood cell ring was then resuspended in 250 µl Accumax (Stemcell Technologies, 7921) and incubated at 37°C for 3 mins. The reaction was stopped by mixing with 5 ml 10\% FBS RPMI and spinning down at 500g for 5 min at 4°C followed by supernatant removal. The cell pellet was then resuspended in PBS with 0.4\% BSA (Sigma, B8667) and passed through a 30 µm filter (Sysmex, 04-004-2326). The cell suspension was then assessed for viability and concentration using the K2 Cellometer (Nexcelom Bioscience) with the AOPIcell stain (Nexcelom Bioscience, CS2-0106-5ML).
The cells or nuclei were loaded onto a 10x Chromium Next GEM G chip (10x Genomics, 1000120) aiming for recovery of 10,000 cells or nuclei. The RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent kit v3.1 (10x Genomics, 1000121) following vendor protocols. The libraries were pooled and sequenced on NovaSeq S1 100c flow cells (Illumina) with 28 bases for read1, 55 bases for read2 and 8 bases for index1 and aiming for 20,000 reads per cell.


title: Kyse410_shUHRF1_rep2


title: Kyse410_shUHRF1_rep1


title: Cat.Nov.F

value: Liaoning cashmere goat

value: Secondary hair follicle

value: 1.5 years

value: Nov

value: female


title: Kyse410_scramble_rep3


title: RNaseH-2

city: Beijing

first: li

last: kuan

address: zhongguancun

institute: Tsinghua University

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the genome of Oryza sativa Japonica Group (GCF_000005425.2 Build 4.0) using bowtie2 version 2.3.3.1.
Duplicated reads were removed by picard version 1.12
Read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC)) using deeptools version 3.1.2
Genome_build: Oryza sativa Japonica Group (GCF_000005425.2 Build 4.0)
Supplementary_files_format_and_content: Input-1-Watson: Watson strand of input-1 DNA; Input-1-Crick: Crick strand of input-1 DNA

molecule: genomic DNA

organism: Oryza sativa

source_name: RNaseH

extract_protocol:
Nuclei were isolated from rice, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases; the negative control was treated with RNase H (New England Biolabs) overnight. DRIP was performed as described in Xu et al., 2017 and Sun et al., 2013. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 ul Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonoicated to 150 bp fragments .
The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

tag: germplasm

tag: genotype/variation

value: Wild type

value: leaf

tag: antibody

value: S9.6 antibody

tag: pull-down

value: DNA:RNA hybrid


title: Input-1

source_name: Input


title: RNaseH-1


title: rep1, scRNAseq

description: 10x Genomics

tag: strain


title: nuc3, snRNAseq

description: 10x Genomics

tag: tissue


title: rep2, scRNAseq

description: 10x Genomics

tag: cell type


title: Input-2


title: TE10_scramble_rep3

value: squamous cell carcinoma cells


title: PB019.ATCTGACG

value: ventral midbrain

value: NeuN+ nuclei

tag: genotype

value: 24 hrs


title: PB019.AGTGAGAG

value: wildtype

tag: treatment

value: Saline

value: 6 hrs


title: Spike-2

source_name: Spike

value: spike


title: PB019.ACCAAGTC

tag: time point


title: PB016

value: IFNG

value: 48 hrs


title: Spike-1


title: TE10_scramble_rep2

tag: cell line

value: scramble control


title: Callus-2

source_name: Callus

value: callus


title: PB019.GTTCCCAA


title: TE10_scramble_rep1


title: PB019.GATATCGC


title: PB019.TTATCCCG


title: TE10_shUHRF1_rep3


title: PB015


title: PB013


title: Sample E10.5_P4

value: two strains (CD1, C57BL/6)

value: Cardiac cells from emryonic and neonatal mouse hearts


title: Callus-1

value: Wild type


title: PB019.TAGCGTCA


title: Sample P2_P9


title: TE10_shUHRF1_rep2


title: TE10_shUHRF1_rep1


title: PB019.ACTCCACT


title: Flagleaf-2

source_name: Flagleaf

value: flag leaf

value: S9.6 antibody


title: Flagleaf-1

value: DNA:RNA hybrid


title: Thymus.Nile_T173F

status: Public on Dec 09 2022

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

description: Biopsy - tissue

data_processing:
RSEM: Reads were mapped to the human genome using Bowtie 0.12.8 (Langmead et al. 2009) allowing up to 2-mismatches. The gene expression values are estimated by RSEM tool
CRSP: we used CRSP tool to estimate the gene expression values. The CRSP tool allows estimation of gene expression values from RNA-seq data for species lacking a sequenced genome or corresponding gene annotations.
Assembly: NaN
Supplementary files format and content: text and gene expression values

organism: Arvicanthis niloticus

growth_protocol: Nile grass rat biopsy samples

extract_protocol:
Total RNAs from 28 Nile grass rat vascular samples were isolated using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column DNase digestion (Qiagen #79254).
Illumina truSeq Protocol

value: Thymus

value: No treatment - healthy tissue


title: Trachea.Nile_T173F

description: Biopsy - tissue

value: Trachea


title: Uterus.Nile_T3F

description: Biopsy - tissue

value: Uterus


title: Stomach.Glandular.Nile_T3F

description: Biopsy - tissue

value: Stomach


title: Ovary.Nile_T3F

description: Biopsy - tissue

value: Ovary


title: Testis.Nile_T424

description: Biopsy - tissue

value: Testis


title: Stomach.NonGlandular.Nile_T3F

description: Biopsy - tissue


title: Spleen.Nile_T3F

description: Biopsy - tissue

value: Spleen


title: Ovary.Nile_T173F

description: Biopsy - tissue


title: Pancreas.Nile_T173F

description: Biopsy - tissue

value: Pancreas


title: Nerve.Sciatic.Nile_T426

description: Biopsy - tissue

value: Nerve


title: Nerve.Sciatic.Nile_T3F

description: Biopsy - tissue


title: Pancreas.Nile_T3F

description: Biopsy - tissue


title: Muscle.Skeletal.Nile_T426

description: Biopsy - tissue

value: Muscle


title: Liver.Lobe.Biggest.Nile_T3F

description: Biopsy - tissue

value: Liver


title: Kidney.RenalPelvis.Nile_T173F

description: Biopsy - tissue

value: Kidney


title: Muscle.Skeletal.Femur.Nile_T3F

description: Biopsy - tissue


title: Kidney.RenalPelvis.Nile_T426

description: Biopsy - tissue


title: Lung.Lobe.Left.Nile_T3F

description: Biopsy - tissue

value: Lung


title: Liver.Nile_T426

description: Biopsy - tissue


title: Kidney.Medulla.Nile_T3F

description: Biopsy - tissue


title: Kidney.Cortex.Nile_T3F

description: Biopsy - tissue


title: Kidney.Artery.Nile_T3F

description: Biopsy - tissue


title: Kidney.AdrenalGland.Nile_T173F

description: Biopsy - tissue


title: Intestine.Duodenum.Nile_T426

description: Biopsy - tissue

value: Intestine


title: Intestine.Jejunum.Nile_T3F

description: Biopsy - tissue


title: Intestine.Ileum.Nile_T3F

description: Biopsy - tissue


title: Intestine.Duodenum.Nile_T3F

description: Biopsy - tissue


title: Intestine.Colon.Nile_T3F

description: Biopsy - tissue


title: Intestine.Cecum.Nile_T173F

description: Biopsy - tissue


title: Heart.Atrium.Right.Nile_T3F

description: Biopsy - tissue

value: Heart


title: Eye.Retina.Nile_T426

description: Biopsy - tissue

value: Eye


title: Eye.Nerve.Optic.Nile_T3F

description: Biopsy - tissue


title: Heart.Ventricle.Right.Nile_T173F

description: Biopsy - tissue


title: Eye.RPE.Nile_T3F

description: Biopsy - tissue


title: Eye.Retina.Left.Nile_T3F

description: Biopsy - tissue


title: Esophagus.BarrettsEsophagusJunction.Nile_T3F

description: Biopsy - tissue

value: Esophagus


title: Eye.Midbrain.Middle.Nile_T3F

description: Biopsy - tissue

value: No treatment - healthy tissue


title: Eye.Retina.Right.Nile_T3F

description: Biopsy - tissue


title: Eye.HarderianGland.Nile_T3F

description: Biopsy - tissue


title: Brain.ThalamusAndHypothalamus.Middle.Nile_T3F

description: Biopsy - tissue

value: Brain


title: Brain.Rostral.Cortex.Middle.Nile_T3F

description: Biopsy - tissue


title: Brain.MedullaOblongata.Nile_T3F

description: Biopsy - tissue


title: Brain.ProximalSpinalCord.Nile_T3F

description: Biopsy - tissue


title: Brain.Hippocampus.Nile_T426

description: Biopsy - tissue


title: Brain.Pons.Nile_T3F

description: Biopsy - tissue


title: Brain.Hippocampus.Left.Nile_T3F

description: Biopsy - tissue


title: BoneMarrow.Nile_T3F

description: Biopsy - tissue

value: BoneMarrow


title: Brain.Cerebellum.Middle.Nile_T3F

description: Biopsy - tissue


title: Bone.Femur.Nile_T426

description: Biopsy - tissue

value: Bone


title: Brain.Caudal.Cortex.Left.Nile_T3F

description: Biopsy - tissue


title: Bladder.Nile_T173F

description: Biopsy - tissue

value: Bladder


title: Bone.Femur.Nile_T3F

description: Biopsy - tissue


title: Adipose.InguinalFat.Nile_T3F

description: Biopsy - tissue

value: Adipose


title: Adipose.Mesentery.Nile_T173F

description: Biopsy - tissue


title: Eye.Cornea.Nile_T3F

description: Biopsy - tissue


title: P7_NFs

city: Tianjin

first: xudong

address: Qixiangtai Road

institute: Tianjin medical university

description:
NFs_CAFs_RNAseq_FPKM.txt
P7.RNAseq.bigwig

data_processing:
Reads were aligned to the reference human genome assembly hg19 using hisat2 version 2.1.0 with default parameters. Assembling full-length transcripts and quantifications for each gene to generate Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) values were performed by StringTie v2.1.1. For GSVA analyses of RNA-seq data from 7 pairs of primary NFs and matched CAFs, FPKM values were log2-transformed. The analyses were carried out by R package gsva (method=‘ssgsea’) against MSigDB gene sets v7.3.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each Sample
Supplementary_files_format_and_content: Bigwig files for each patient were matched NFs-subtracted, which were generated by deeptools v3.5.1 bigwigCompare

source_name: primary fibroblasts

growth_protocol: Tumor tissues and corresponding para-tumoral non-malignant tissues were surgically removed from invasive breast cancer patients with axillary lymph node metastasis. Primary fibroblasts were maintained in Growth Medium in a humidified 5% CO2 environment at 37°C.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing by Beijing Genomics Institute (BGI).

value: normal fibroblasts

tag: patient


title: P3_CAFs

description:
NFs_CAFs_RNAseq_FPKM.txt
P3.RNAseq.bigwig

value: cancer associated fibroblasts


title: P3_NFs


title: P4_NFs

description:
NFs_CAFs_RNAseq_FPKM.txt
P4.RNAseq.bigwig


title: P2_CAFs

description:
NFs_CAFs_RNAseq_FPKM.txt
P2.RNAseq.bigwig


title: P2_NFs


title: P1_CAFs

description:
NFs_CAFs_RNAseq_FPKM.txt
P1.RNAseq.bigwig


title: P1_NFs


title: D2

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
Quality control of data was performed using FastQC package
Reads were aligned to Aspergillus nfumigatus (Af293) genome using hisat2 (version 2.1.0)
Differential gene expression testing was performed using DESeq2 (version 1.20.0)
Assembly: Genome: http://www.aspergillusgenome.org/download/sequence/A_fumigatus_Af293/current/A_fumigatus_Af293_version_s03-m05-r16_chromosomes.fasta.gz; Genome features file (GFF): http://www.aspergillusgenome.org/download/gff/A_fumigatus_Af293/A_fumigatus_Af293_version_s03-m05-r16_features_with_chromosome_sequences.gff.gz
Supplementary files format and content: Excel file containing the following collumns for each sample: Gene ID, Count, Transcript length, RPKM

organism: Aspergillus fumigatus

source_name: fungal mycelia

growth_protocol: Strains were maintained on Barratt’s minimal medium agar plates (Barratt et al. 1965) and conidia collected freshly from plates incubated at 37 °C for 6 d were used in all experiments. For submerged cultivation 100 ml aliquots of Barratt’s minimal broth supplemented with 5 g/l yeast extract (in 500 ml Erlenmeyer flasks) were inoculated with 50,000,000 conidia and were incubated for 16 h at 37 °C and at 3.7 Hz shaking frequency. Mycelia were separated by filtration, were washed and transferred into 100 ml fresh Barratt’s minimal broth containing 10 g/l glucose, 4 g/l casein peptone, 10 g/l glucose and 4 g/l casein peptone, or containing no carbon source. Cultures were further incubated at 37 °C and at 3.7 Hz shaking frequency for 4 h (glucose containing cultures) or for 24 h.

extract_protocol:
Total RNA was isolated from lyophilized mycelia using TRISOL reagent (Chomczynski 1993). RNA concentration and purity were determined using NanoDrop and capillary electrophoresis.
RNA-Seq libraries were prepared from total RNA using TruSeq RNA Sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: Exponentially phase mycelia were transferred in to fresh media containing 10 g/l glucose, 4 g/l casein peptone, 10 g/l glucose and 4 g/l casein peptone, or containing no carbon source.

value: fungal mycelia

tag: culturing condition

value: Glucose + peptone


title: D1


title: D3


title: Adipose.BrownFat.Nile_T3F

description: Biopsy - tissue


title: C3

value: Glucose


title: CVX26_C2D10

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

data_processing:
Encoding Sanger/Illumina 1.9 software used for basecalling.
Quality trimming is performed to remove adapter sequences and polyA tails.  Then trimmed reads were aligned to human genome GRCh38/hg38 (Genome Reference Consortium Human Build 38), INSDC Assembly GCA_000001405.28, Dec 2013) using STAR 2.6.1d and featureCounts v2.0.0 was used to generate the raw counts
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Fingerstick

extract_protocol:
RNA was extracted using the Tempus Spin RNA Isolation Kit (ThermoFisher), which was adapted for the handling of small blood volumes. Contaminating DNA was removed using the TurboDNAse kit (ThermoFisher), and RNA was quantitated on a Qubit instrument (ThermoFisher) and QCed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).
mRNA-sequencing was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (75 single-end)

tag: patientid

tag: timepoint

value: Not treated

value: BOOST

value: Peripheral blood


title: CVX26_C2D09


title: CVX26_C2D07


title: CVX26_C2D14


title: CVX26_C2D06


title: Adipose.AdrenalGland.Nile_T173F

description: Biopsy - tissue


title: CVX26_C2D08


title: C2


title: P7_CAFs

last: Wu


title: CVX26_C2D05


title: H37RV-infected M2-polarized BM derived macrophages (mouse C)

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

data_processing:
Adaptor sequences and low-quality score bases (Phred score < 20) were trimmed using Trim Galore (version 0.2.7)
reads were mapped to the mouse genome reference sequence (Ensembl GRCm38 release 81) using kallisto (v0.43.0)
protein coding genes were selected, and samples were normalized using the weighted trimmed mean of M-values algorithm (TMM), as implemented in the R package edgeR
reads were log2-transformed using voom, within the limma package [21], and low-expressed genes, defined as those showing median log2-transformed expression lower than 2 within all conditions (i.e. combination of cell-type and infection status) were filtered out
Assembly: Mus musculus GRCm38 release 81
Supplementary files format and content: tab-delimited text file includes read counts for each Sample

extract_protocol: RNA was extracted using Trizol (Invitrogen)

tag: sampleID

tag: infection

value: RV

tag: mouse

value: C


title: CVX26_C2D04


title: P4_CAFs


title: H37RV-infected M2-polarized BM derived macrophages (mouse D)

value: D


title: C1


title: CVX26_C2D02


title: CVX26_C2D01


title: B3

value: Peptone


title: Uninfected M2-polarized BM derived macrophages (mouse C)

value: NI


title: CVX25_C2D14


title: H37RV-infected M2-polarized BM derived macrophages (mouse B)

value: B


title: CVX25_C2D10


title: B2


title: CVX25_C2D09


title: Uninfected M2-polarized BM derived macrophages (mouse D)


title: CVX25_C2D07


title: Uninfected M2-polarized BM derived macrophages (mouse B)


title: Uninfected M2-polarized BM derived macrophages (mouse A)

value: A


title: CVX25_C2D08


title: CVX25_C2D05


title: CVX25_C2D03


title: B1


title: H37RV-infected M2-polarized BM derived macrophages (mouse A)


title: A3

value: Carbon-starved


title: CVX25_C2D06


title: H37RV-infected M1-polarized BM derived macrophages (mouse D)


title: A2


title: CVX25_C2D04


title: Uninfected M1-polarized BM derived macrophages (mouse D)


title: CVX21_C2D14


title: CVX25_C2D01


title: A1


title: CDCA_3

city: Nanjing

first: Yu

last: Pi

state: Jiangsu

address: NO. 1 Weigang, Nanjing Agricultural University

institute: Nanjing Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Transcripts Per Million reads (TPM) were calculated. In short, firstly, divide the read counts by the length of each gene in kilobases and get the reads per kilobase (RPK). Secondly, count up all the RPK values in a sample and divide this number by 1,000,000 and get the “per million” scaling factor. Finally, divide the RPK values by the “per million” scaling factor.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TMP values for each Sample of every genes with gene ID, gene name, and gene discription.

source_name: CDCA

extract_protocol:
After 24 hr treatments and collected the IPEC-J2 cells. The total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Porcine Small Intestinal Epithelial Cells

tag: treatments

value: treated with CDCA

tag: treatments time

value: 24 hr


title: CVX25_C2D02


title: CDCA_2


title: CVX21_C2D08


title: Uninfected M1-polarized BM derived macrophages (mouse C)


title: H37RV-infected M1-polarized BM derived macrophages (mouse C)


title: CVX21_C2D09


title: CVX21_C2D05


title: H37RV-infected M1-polarized BM derived macrophages (mouse B)


title: CON_3

source_name: CON

value: treated with PBS


title: CVX21_C2D03


title: CON_2


title: Uninfected M1-polarized BM derived macrophages (mouse B)


title: H37RV-infected M1-polarized BM derived macrophages (mouse A)


title: CON_1


title: CVX21_C2D02


title: CVX20_C2D14


title: CVX21_C2D01


title: CVX21_C2D10


title: H37RV-infected Alveolar macrophages (mouse C)

source_name: AM

value: AM


title: CVX20_C2D10


title: Intestine.Rectum.Nile_T173F

description: Biopsy - tissue

value: Intestine

value: No treatment - healthy tissue


title: CVX20_C2D06

value: Not treated

value: BOOST


title: CVX21_C2D07

value: Peripheral blood


title: Uninfected Alveolar macrophages (mouse C)

value: C


title: CVX20_C2D05


title: CDCA_1


title: CVX20_C2D07


title: CVX20_C2D04


title: H37RV-infected Alveolar macrophages (mouse B)

value: RV


title: CVX21_C2D06


title: CVX21_C2D04


title: CVX20_C2D03


title: Uninfected M1-polarized BM derived macrophages (mouse A)


title: Uninfected Alveolar macrophages (mouse B)


title: CVX20_C2D01


title: CVX20_C2D09


title: KOi2

type: RNA

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 5.5 μg of biotinylated cDNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix Clariom™ S (mouse) for 17 hours at 45°C. Steps for washing and staining were processed on the fluidics station 450 using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix; Santa Clara, CA).

scan_protocol: Image Analysis was performed on GCOS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA).

data_processing: Signal intensities (raw data) were log2 transformed and normalized using RMA summarization method.

label: biotin

source_name: alveolar macrophages

label_protocol: 2-10 ng of total RNA were used for biotin labelling according GeneChip® Pico Kit (Affymetrix).

extract_protocol: RNAeasy (Qiagen). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).

treatment_protocol: Female C57BL/6 wildtype mice (Envigo CRS GmbH - Rossdorf, Germany) and CD47-/- mice (JAX stock #003173; Jackson Laboratory - Bar Habor-Maine, USA) were anesthetized by ketamine (100 mg/kg body weight)/ xylazine (5 mg/kg body weight) and intranasally infected with 75 PFUs influenza virus A/PR/8/34 (25 µl). 3dpi isolation of murine alveolar macrophages was achieved by repeated BAL (5x 1ml PBS) and a subsequent sorting of the cells based on their autofluorescence via the BD FACSAria II to obtain an untouched aMФ population.

value: alveolar macrophages

tag: Sex

value: female

value: infected with influenza A


title: H37RV-infected Alveolar macrophages (mouse A)

tag: strain

value: A


title: KOi1


title: CVX19_C2D14

tag: tissue


title: CVX19_C2D10


title: Uninfected Alveolar macrophages (mouse A)

tag: cell type

value: NI


title: CVX19_C2D09


title: hippocampus, surgery, day 3, rep2

first: Yi

last: Sun

address: No.8 Gongti Nanlu, Chao-Yang District

institute: Beijing Chao-Yang hospital

data_processing:
Data was aligned using the HISAT2 program (Johns Hopkins University, Baltimore, MD, USA) with default parameters
The Python package HTseq (version 5.4.2) was used for quantification
R (version 5.2.0) was used for bioinformatics analysis
ClusterProfile (version 3.10) was used for Gene Ontology (GO) and network analysis.
Gene set enrichment analysis (GSEA) was performed using MSigDB (version 7.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: hippocampus

extract_protocol:
the mice were anesthesized and hippocampus were taken. Total RNA was extracted from the mouse hippocampus using Trizol (Tiangen, Beijing, China).
Complementary DNA was synthesized with DNA polymerase I and RNaseH. Products were purified by polymerase chain reaction to generate the sequencing  library and then quantified using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: hippocampus

tag: genotype

value: WT

value: surgery

tag: age

value: 12 months

tag: time

value: postoperative day3


title: CVX20_C2D02


title: CVX19_C2D03


title: CVX19_C2D02


title: CVX19_C2D04


title: CVX19_C2D05


title: CVX19_C2D01