title: Par1_ECko_Saline_Input_3

source_name: Liver

value: Liver


title: LiaS-Q146A-A

status: Public on Jun 10 2024

type: SRA

city: Houston

first: Anthony

last: Flores

state: TX

address: 6431 Fannin St., MSB 3.130

country: USA

institute: UTHSC/McGovern Medical School

library_source: transcriptomic

data_processing:
Base calls onboard Illumina HiSeq
Raw data files processed using CLC Genomics Workbench v23
Reads mapped to reference genome MGAS10870 (CP067090.1)
RPKM/TPM calculated using CLC Genomics Workbench v23
Assembly: MGAS10870 (CP067090.1)
Supplementary files format and content: Spreadsheet, normalized read counts

molecule: total RNA

organism: Streptococcus pyogenes

source_name: mutant

growth_protocol: GAS cells were grown in rich medium (Todd-Hewitt, 0.2% yeast extract) to an OD of 0.5 (mid-exponential phase)

extract_protocol:
Cells collected in RNA protect and total RNA extracted using Qiagen RNeasy protocol adapted for GAS as described in Methods
Libraries constructed using Illumina ScriptSeq Complete v3

treatment_protocol: No treatment

tag: strain

value: mutant

tag: replicate

value: A

tag: growth condition

value: in vitro


title: LiaS-R135G-X

value: X


title: Par1_EChet_Saline_Input_3

city: Oklahoma City

first: Rahul

last: Rajala

state: Oklahoma

address: 825 NE 13th Street

department: Cardiovascular Biology

institute: Oklahoma Medical Research Foundation

data_processing:
Fastq generation was performed using Illumina’s CASAVA-1.8.2 software
Alignment of raw sequences using HISAT2 and independently by SALMON
Differential gene expression performed by DESEQ2 and edgeR
Assembly: HISAT2 (Mus_musculus.GRCm39.dna.primary_assembly) /SALMON (Mus_musculus.GRCm39.107.transcripts.fa.salmon)
Supplementary files format and content: Collated HISAT2 data given as (CountsFile.csv), Collated SALMON data given as (TPMValues.csv)

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
RNA (before/after TRAP) was isolated using the Qiagen RNeasy kit. SMARTer Ultra Low Input kit (Clontech) was used for RNA conversion (5 ng for tissue lysate, 10 ng for EC-TRAP samples).
cDNA samples were sheared using the Covaris E220 Focused Ultra-sonicator which was followed by Quant-iT PicoGreen quantification (Thermo Fisher Scientific, catalog number P11496). A total of 5 ng cDNA per sample was used for library preparation based on the KAPA Hyper Prep method (KAPA Biosystems, catalog number KK8504). Following NEXTflex adapter ligation (BIOO Scientific, catalog number 514104), libraries were size-selected based on a double bead purification prior to amplification.

treatment_protocol: Tissues were flash-frozen in liquid nitrogen following a cycloheximide perfusion and mechanically dissociated

tag: tissue

tag: genotype

tag: treatment

value: Saline


title: LiaS-R135G-Y

value: Y


title: Par1_EChet_APAP_Input_3

value: APAP


title: Par1_EChet_APAP_Input_2


title: Par1_ECko_APAP_Bead_1

source_name: Liver EC

value: Liver EC


title: Par1_ECko_APAP_Input_3


title: Par1_ECko_APAP_Input_2


title: RNA-Seq of mus musculus:Embryo 3

city: Changchun

first: Zhengyang

last: Jin

state: Jilin

address: No. 1163 Xinmin Street

country: China

institute: Jilin University

description:
Well-ST-seq_10_4
Well-ST-seq_10 resolution

data_processing:
*library strategy: Well-ST-seq
The filtered data was mapped to the mouse genome (mm10 mouse) using SpaceRanger V1.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Embryo

extract_protocol:
Tissue was permeabilized with tissue permeabilizing enzyme for 12 minutes
RNA libraries for RNA-seq were prepared using Kapa HIFI HotStart ReadyMix PCR Kit following manufacturer's protocols.

value: Embryo

tag: age

tag: Sex

value: Female


title: Par1_ECko_Saline_Bead_3


title: LiaS-R135G-W

value: W


title: N3944_delta-dim5_polyA-mRNA-seq_third-rep

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

description: matrix column names: column1 = Neurospora crassa gene name; column2 = gene count value

data_processing:
Raw fastq files were mapped to the nc14 genome using HiSat2 (72), and gene count files were generated with htseq-count (73). Differential Expression analysis between strains was performed with DESeq2 (74) in R/Rstudio (75, 76), selecting significantly changed genes as those with expression log2 > 3.0 or log2 < -3.0 and an adjusted p-value < 0.001; bed files for display on IGV were generated from the DESeq2 output gene lists in Microsoft Excel, and volcano plots of log2 fold change vs. adjusted p-value were generated in R/R studio.
Assembly: Assembly: nc14_genome-seq-name.fasta (version 14; Rodriguez et al., [Pubmed ID: 35244156]), or the NKL2 genome generated here (deleted of the LGIIK9het25 constitutiive heterochromatic region).
Supplementary files format and content: htseq-count files are two column files with the first column being the gene name (specific to Neurospora crassa; NCU#), the second column being the count value of that gene

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC.

extract_protocol:
Cultures were harvested by vacuum filtration, placed in 2.0mL screw-top tubes, and 300µL of acid washed glass beads suspended in dH2O (150-212µm, Sigma Aldrich cat# G1145-10G), 350µL Acid Phenol:chloroform (5:1; ThermoFisher cat# AM9720), and 350µL NETS (300mM NaCl, 1mM EDTA, 10mM Tris pH 7.5, 0.2% SDS) were added. Samples were vortexed for 10 minutes at maximum speed and centrifuged at 4oC for 5 minutes at 13k rpm. The aqueous layer was transferred to two tubes (~250µL each), 650µL of cold 100% EtOH was added, and RNA was precipitated on ice for 10 minutes and pelleted by microcentrifugation at 4oC for 10 minutes at 13k rpm. The pellet was washed with cold 70% EtOH (made with DECP-treated dH2O), the supernatant was removed, and pellets were allowed to air dry for 15 minutes and resuspended in 50µL DEPC-treated dH2O. Insoluble material was removed by centrifugation, and the initial RNA concentration was measured by Nanodrop. Total RNA (10µg) was resuspended in 50µL of DEPC-treated dH2O. Total RNA cleanup was performed by the Zymo RNA clean and concentrator kit (Zymo Research cat# R1013), per the manufacturer’s protocol; the 15µL elution was divided into 4µL for Qubit concentration (RNA HS assay kit; ThermoFisher Scientific, cat# Q32852) and TapeStation (Agilent) quality control analysis, while the remaining 11µL was stored at -80oC. Only total RNA samples with high rRNA:mRNA ratios were used for library construction.
Polyadenylated messenger RNA (polyA mRNA) was selected with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs [NEB], cat# E7490L) and polyA mRNA sequencing libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat# E7760L and E7765L) per the manufacturer’s protocols; quadruplicate polyA mRNA-seq replicate libraries were constructed for each strain. All polyA mRNA-seq libraries were Illumina sequenced at the GC3F on a NovaSeq 6000 as SR118 reads.

treatment_protocol: Cultures were harvested by filtration and washed with 1xPBS prior to the RNA isolation protocol

value: mycelia

tag: cell type

value: asexual fungal hyphae

value: mat x; {delta}dim-5::bar+


title: Par1_EChet_APAP_Bead_1


title: N3944_delta-dim5_polyA-mRNA-seq_fourth-rep


title: N3944_delta-dim5_polyA-mRNA-seq_first-rep


title: agb1-3_NaCl 4h_rep3

type: RNA

city: Taipei

first: Yueh

last: Cho

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression after 4hr in Arabidopsis agb1-3 root

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Arabidopsis Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: root

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the TRI reagent (Invitrogen AM9738) following the manufacturer's recommendations. The DNase digestion (Qiagen) were used to remove genomic contamination. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The Arabidopsis wild-type and agb1-3 mutant seeds were sown on half-strength MS agar plates and grown under a 16 h/8 h light-dark cycle at 22 °C with a light intensity of 150 µmol m^-2 s^-1 for 7 days. The roots were detached from seedlings that had been immersed in 150 mM NaCl/MS liquid media for 0 or 4 hours.

value: root

value: NaCl 4h


title: Par1_ECko_Saline_Bead_2


title: NKL2_LGIIK9het25-deletion_polyA-mRNA-seq_third-rep

value: mat A; {delta}LGIIK9het25::hph


title: N3944_delta-dim5_polyA-mRNA-seq_second-rep


title: Par1_EChet_Saline_Bead_2


title: NKL2_LGIIK9het25-deletion_polyA-mRNA-seq_fourth-rep


title: NKL2_LGIIK9het25-deletion_polyA-mRNA-seq_second-rep


title: WT_N150_polyA-mRNA-seq_second-rep

value: mat A


title: agb1-3_NaCl 4h_rep2


title: NKL2_LGIIK9het25-deletion_polyA-mRNA-seq_first-rep


title: Par1_EChet_Saline_Bead_1


title: WT_N150_polyA-mRNA-seq_first-rep


title: WT_N150_polyA-mRNA-seq_fourth-rep


title: agb1-3_NaCl 0h_rep2

description: Gene expression after 0hr in Arabidopsis agb1-3 root

value: NaCl 0h


title: WT_N150_polyA-mRNA-seq_third-rep


title: Par1_ECko_Saline_Bead_1


title: agb1-3_NaCl 0h_rep3


title: Col-0_NaCl 4h_rep3

description: Gene expression after 4hr in Arabidopsis wild-type root


title: agb1-3_NaCl 4h_rep1


title: WT_N150_H3K27me2-3_rep1

library_source: genomic

data_processing:
Raw ChIP-seq data files, as fastq files, were mapped to version 14 of the Neurospora crassa genome (nc14) [Rodriguez et al., 2022 [Pubmed ID: ] with bowtie2 (version 2.4.2), and output sam files were converted to sorted bam files using samtools (version 1.14), which were used by Deeptools (version 3.5.0) to produce bigwig files with 25 basepair bin resolution, normalized by Reads per Kilobase Per Million Reads (RPKM), for display on the Integrative Genomics Viewer (IGV)
Assembly: Assembly: nc14_genome-seq-name.fasta (version 14; Rodriguez et al., [Pubmed ID: 35244156]), or the NKL2 genome generated here (deleted of the LGIIK9het25 constitutiive heterochromatic region).
Supplementary files format and content: the bigwig files are generated by Deeptools; briefly, these files divide the genome into bins and the number (count) of sequencing reads per bin is reported for each bin; the bigwig file format is a single column with the enrichment per bin displayed, and the seven headers indicate the chromosome and bin size.
Supplementary files format and content: the bedgraph files are generated by Deeptools; briefly, these files divide the genome into bins and the number (count) of sequencing reads per bin is reported for each bin; the bedgraph file format is a four column file, with the first column being the chromosome, second column being the bin start, third column being the bin stop, and fourth column being the bin enrichment

molecule: genomic DNA

extract_protocol:
Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication, which simultaneously sheared chromatin, using a Bioruptor Pico (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 1uL) and samples were nutated overnight at 4oC. The next day, equilibrated protein A/G magnetic agarose beads (Pierce/Thermo Scientific; cat # PI78609) was added to bind the antibody, incubated for 2 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC. Samples (IP and input) were decrosslinked at 65oC overnight. The next day, samples were RNaseA treated for two hours at 50oC, then proteinase K treated for 2 hours at 50oC, the DNA was extracted with phenol:chloroform:IAA (25:24:1), and DNA was precipitated with ethanol, sodium acetate, and glycogen, and allowed to precipitate overnight at -80oC. The next day, samples were precipitated by centrifugation, washed, dried in a Speedvac and resuspended in 30uL TE. ChIP DNA was quantified with a Qubit 3.0 using the HS method.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries. Each library was prepared using the NEB Next Ultra II Library Preparation Kit (New England Biolabs, #E7645L) with the adapters from the NEBNext® Multiplex Oligos for Illumina®(Index Primers Set 1 [E7335L] or 2 [E7500L]) according to the manufacturer’s instructions, except that final libraries were only PCR-amplified using eight cycles for amplification.

treatment_protocol: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 15 min in 0.5% formaldehyde at room temperature, with shaking at 100 rpm, and then quenched with 0.125M glycine for histone modification ChIP.

value: overnight growth (16hrs) in 1xVogels+1.5% sucrose

tag: chip-seq antibody

value: Active Motif anti-H3K27me2me3 (cat# 39535)


title: Par1_ECko_Saline_Input_2

value: Liver

value: Saline


title: Par1_ECko_APAP_Input_1

value: APAP


title: Par1_EChet_APAP_Input_1


title: Par1_EChet_Saline_Input_2


title: NKL2_LGIIK9het25-deletion_H3K9me3_rep2

value: Active Motif anti-H3K9me3 (cat# 39161)


title: Col-0_NaCl 4h_rep2


title: NKL2_LGIIK9het25-deletion_H3K9me3_rep1


title: Col-0_NaCl 4h_rep1


title: B3_CD05_C/C_Clone2

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

data_processing:
Raw fastq files (pair-end) were mapped to concatenated reference from human (GRCh38) and mouse (GRCm39) by Salmon (v0.11.3)
Counts were collected from the output of each Salmon.
Assembly: hunan GRCh38 and mouse GRCm39
Supplementary files format and content: FASTQ
Supplementary files format and content: tab-delimited text included raw counts per sample

organism:
Homo sapiens
Mus musculus

source_name: iPS-derived glutamatergic neuron and primary mouse astrocyte

growth_protocol: The hiPSCs were maintained in mTeSRPlus (StemCell #100-0276) with primocin (Invitrogen #ant-pm-1) on tissue culture plates coated with matrigel (Fisher Scientific #08-774-552) or geltrex (Fisher Scientific #A1413202) throughout the mutagenesis process. Mouse astrocyte were maitained in DMEM (Thermofisher: 10569010) with  FBS (Thermofisher: A5209501) and primocin The Institutional Review Board (IRB) of NorthShore University HealthSystem approved study.

extract_protocol:
Total RNA was extracted using Qiagen RNEasy mini spin columns and the concentrations verified by NanoDrop
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.Sequencing was performed on NovaX with 2x150 bp paired read

treatment_protocol: Reverse transfection was used for SNP editing. gRNAs were cloned to CROPseq-Guide-Puro vector (Addgene #86708) [Datlinger P, nature method, 2017]. Vector pSpCas9(BB)-2A-Puro (Addgene #62988) was used to express Cas9 [Ran FA,  nature protocol, 2013]. Vector pSUPERIOR.puro-shp53 (Addgene #38035) was used during the transfection to transiently inhibit p53 and increase editing efficiency [Ihry RJ, nature method, 2018]. In day 1, iPSC was accutased (07920, StemCell) into single cell, then centrifuged, and placed in a 15ml centrifuge tube at 4-6 × 105/1.8ml with 10 μM ROCK inhibitor (1254/1, R&D Systems). Lipofectamine stem reagent (STEM00001, Thermofisher) was used for transfections. In preparation stage, DNA including pSpCas9(BB)-2A-Puro (0.5 μl from 1 μl/ug stock), CROPseq-Guide-Puro vector (1 μl from 1μl/ug stock) pSUPERIOR.puro-shp53 vector (1 μl from 1μl/ug stock) and ssODNs (6 μl from 100uM stock) was mixed into 100 μl Opti-MEM media (31985062, Thermofisher) in 1.5ml tube; another 1.5 ml tube was filled with 8 μl Lipofectamine stem reagent and 100 μl Opti-MEM media. Two 1.5 ml tubes were combined and incubated for 10 minutes, then added in to iPSC single cell suspension, gently mixed well and plated into one well of 6 well plate. After 16 hours post transfection, all medium was carefully refreshed with 0.25 ug/ml puromycin and 10 μM ROCK inhibitor. After 48 hours post transfection, medium was refreshed with same reagents. After 72 hours post transfection, all puromycin was removed, and the cells were covered new medium with 5 μM ROCK inhibitor. In the next 2-3 day, half medium was refreshed without ROCK inhibitor in order to gradually reduce the ROCK inhibitor in the culture system. Once the cell colonies were formed and looked health, ROCK inhibitor was completely removed by refreshing the entire medium. After around 14 days post-transfection, colonies were individually picked into 96-well plates. DNA from a small fraction of cells in each colony was then extracted (QE09050, Epicentre) and used Sanger sequencing. Subcloning with low density (2-5000 cells/6 cm dish) was carried out if the colony was not pure. Following successful editing, three genomic positions of gRNA off-targets were selected based on their highest rankings and analyzed using Sanger sequencing

tag: cell line

value: human neuron/mouse astrocyte


title: B4_CD05_C/C_Clone2

value: iPS-derived glutamatergic neuron and primary mouse astrocyte


title: B9_CD05_T/T_Clone2


title: B10_CD05_T/T_Clone2


title: Par1_EChet_Saline_Input_1


title: B2_CD05_C/C_Clone1


title: Low-dose infected day 3 Hamster 3

city: Heidelberg

first: Stefan

last: Peidli

state: BW

address: Meyerhofstraße 1

department: Genome Biology

country: Germany

institute: European Molecular Biology Laboratory

library_source: transcriptomic single cell

data_processing:
Alignment, demultiplexing, UMI quantification, and cell-barcode selection (basic filtering) was done with cellranger v6.1.1 (10X Genomics).
Cells with less than 250 genes expressed were filtered out. After cell type identification, we filtered each cell type using the respective median UMI count as lower threshold prior to final cell type annotation.
Annotation and filtering of doublets using scrublet (v9.2.3).
Count normalization using scanpy.pp.normlize_total from scanpy (v1.9.1).
Log1p transform using scanpy.pp.log1p from scanpy (v1.9.1).
Assembly: doi:10.1093/gbe/evac100 (PMID: 35778793)
Supplementary files format and content: AnnData formatted sparse count matrix as AnnData (v0.8.0) .h5 files with all samples merged and processed.
Supplementary files format and content: Cellranger formatted sparse count matrices as .h5 file per sample.

organism: Phodopus roborovskii

source_name: lung

extract_protocol:
Established cell isolation protocols were modified to comply with BSL3 facility regulations. For single cell isolation, the caudal lobes of the right lung were stored in 1× PBS, 0.5% BSA containing 2 µg/ml actinomycin D. The lobes were dissociated mechanically and enzymatically. Tissue was first disrupted with forceps for 2 minutes in specific digestion medium (3.4 mg/mL collagenase Cls II (Merck), 1 mg/mL DNase I (PanReac AppliChem) in 2 mL Dispase medium per lung lobe (Corning), 50 caseinolytic units/mL) and then enzymatically digested at 37°C and 5% CO2 for 30 minutes. The cell suspension was further dissociated by pipetting, and filtered through 70 µm cell strainers. The suspensions were centrifuged at 350 g for 6 minutes at 4 °C, and the pellets were subjected to erythrocyte lysis by resuspension in appropriate buffer (BioLegend). The reaction was stopped by washing with PBS/BSA buffer and the cells were centrifuged. Cells were resuspended in low BSA buffer (1 × PBS, 0.04% BSA) and then filtered through 40 µm FloMi filters (Merck). Cell number and viability were determined microscopically using trypan blue.
Sequencing libraries were generated using the 3’ Chromium Next GEM Single Cell 3’ Reagent kit (10x Genomics) according to the manufacturer’s instructions, and sequenced on a NovaSeq 6000 device (Illumina).

treatment_protocol: 10- to 12-week-old male and female Syrian and Roborovski hamsters were infected intranasally with 1x10^4 or 1x10^5 plaque-forming units (pfu) SARS-CoV-2 (variant B1, isolate BetaCoV/Germany/BavPat1/2020) under anesthesia as previously described (PMID:34320400). To prevent any prolonged suffering, the hamsters were clinically examined twice daily. Animals with body weight loss >15% for more than 48 hours were euthanized according to the animal use protocol. For Roborovski hamsters, naive animals (n = 3) and animals at 2, and 3 days post infection (n = 3 each) were randomly selected. Euthanasia was performed by cervical dislocation and exsanguination under anesthesia as previously described (PMID:32698441). Among other materials, all lung lobes were collected for subsequent analyses. Specifically, the left lobe was used for histopathology, the right caudal lobe for single-cell analysis, the right cranial lobe for virological measurements, and the right middle lobe for bulk RNA and proteomic analysis as described (PMID:34381043).

value: lung

tag: infection

value: SARS-CoV-2 Variant B.1

tag: virus dose

tag: time

value: 3 dpi


title: B1_CD05_C/C_Clone1


title: B8_CD05_T/T_Clone2


title: B7_CD05_T/T_Clone1


title: Par4_ECko_APAP_Bead_3

value: Liver EC


title: A8_CD07_T/T_clone 2


title: Par4_EChet_APAP_Bead_3


title: A7_CD07_T/T_clone 2


title: High-dose infected day 3 Hamster 3


title: Col-0_NaCl 0h_rep2

description: Gene expression after 0hr in Arabidopsis wild-type root

value: root


title: Col-0_NaCl 0h_rep3


title: Col-0_NaCl 0h_rep1


title: Par1_ECko_Saline_Input_1


title: agb1-3_NaCl 0h_rep1


title: Low-dose infected day 3 Hamster 2


title: B5_CD05_C/C_Clone2


title: B6_CD05_T/T_Clone1


title: A4_CD07_C/C_clone 2


title: Par4_ECko_APAP_Bead_2


title: A2_CD07_C/C_clone 1


title: Low-dose infected day 2 Hamster 3

value: 2 dpi


title: HEL_AFF4KD_Pol ll

city: Shang Hai

first: Zimei

last: Yang

address: Dongchuan road 800

institute: Shang Hai Jiaotong University

data_processing:
For ChIP-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Assembly: hg38
Supplementary files format and content: BigWig files contains normalized read count (CPM, in 50-bp bins)

organism: Homo sapiens

source_name: HEL

growth_protocol: Human cells HEL and THP1 were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

extract_protocol: Normally, cells were fixed with 0.4%  (v/v) formaldehyde at room temperature for 10 min. To improve the ChIP efficiency, double  fixation was used. For double fixation with EGS (Thermo, cat. no. 21565) and formaldehyde, cells  were fixed initially with 1.5 mM EGS at room temperature for 30 min, and subsequently with 0.4%  formaldehyde at room temperature for 10 min. For double fixation with DMA (Thermo, cat. no.  20660) and formaldehyde, cells were fixed initially with 25 mM DMA at room temperature for 1 hr,  and subsequently with 0.4% formaldehyde at room temperature for 10 min. For sonication, fixed  cells were washed twice with PBS and resuspended in ice-cold RIPA-0.3 buffer (10 mM Tris-HCl,  1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% NaDOC, and 0.3 M NaCl, pH 7.4) supplemented  with Protease Inhibitor Cocktail (Millipore, cat. no. 535140) at a concentration of 40 million  cells/ml; genomic DNA was disrupted to a size range of 100 to 500 bp. For immunoprecipitation,  on day 1, antibodies were diluted in RIPA-0.3 and bound to Dynabeads protein A (Thermo, cat.  no. 10002D) by incubating at 4°C for 3 hrs. Afterwards, the bead-antibody complexes were  washed twice with RIPA-0.3 and then incubated with sonicated chromatin at 4°C overnight. On  day 2, after 2 washes with RIPA-0.5, 1 wash with RIPA-0.3, 1 wash with RIPA-0, 2 washes with  LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 0.25 M LiCl, 0.25% NP-40, and 0.25% NaDOC, pH  7.4), and 2 washes with TE buffer, bound protein-DNA complexes were resuspended in elution  buffer (10 mM Tris-HCl, 1mM EDTA, 0.2 M NaCl, and 1% SDS, pH 7.4) supplemented with 10  µg/ml RNase A for both elution and RNA digestion, and incubated at 55°C for 1 hr. Then  2 Proteinase K was added to a final concentration of 200 µg/ml, and after 30 min incubation the  temperature was increased to 65°C for crosslink reversal. After incubation for 4 to 6 hrs, DNA  was purified by ChIP DNA Clean & Concentrator (Zymo Research, cat. no. D5205).ChIP-seq libraries were constructed with 2-10 ng immunoprecipitated DNA. After end-repair, A_x0002_tailing, and barcode ligation, barcoded DNA was amplified by 16- to 18-cycle PCR.

value: HEL

value: Human erythroblast

value: Pol ll (Santa, SC-47701)


title: HEL_Ctrl_Pol ll

value: Ctrl


title: A6_CD07_T/T_clone 1


title: A5_CD07_T/T_clone 1


title: A1_CD07_C/C_clone 1


title: High-dose infected day 3 Hamster 2


title: HEL_AFF4KD_Pol ll (Ser-2p)

value: Pol II (Ser-2p) (Millipore, 04-1571)


title: Low-dose infected day 3 Hamster 1


title: Low-dose infected day 2 Hamster 1


title: Par4_EChet_APAP_Bead_2


title: Par4_EChet_APAP_Input_3

value: Liver


title: HEL_AFF4KD_PRO-seq

description: cell transducted by AF9 shRNA

library_source: other

data_processing:
The default parameters of fastp are used to control the quality of the raw data. Then, bowtie2 was used for data mapping (reference genome was hg38). Filter out MAPQ < 30 reads using samtools and convert bam files to bigwig files using bamCoverage.
Assembly: hg38
Supplementary files format and content: BigWig files contains normalized read count
Library strategy: PRO-seq

molecule: other

growth_protocol: Human cells HEL were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

extract_protocol:
Nascent RNA was extracted using Trizol and precipitated in 75% ethanol.
Extracted nascent RNA was fragmented by base hydrolysis in 0.2 N NaOH on ice for 10~12 min, and neutralized by adding 1× volume of 1 M Tris-HCl pH 6.8. For PRO-cap, the fragmentation step was omitted. Excessive salt and residual NTPs were removed by using P-30 column (Bio-rad). Fragmented nascent RNA was bound to 30 µl of Streptavidin M-280 magnetic beads (Invitrogen) following the manufacturer’s instructions. The beads were washed once in high salt (2 M NaCl, 50 mM TrisHCl pH 7.4, 0.5% Triton X-100), once in medium salt (300 mM NaCl, 10 mM Tris-HCl pH 7.4, 0.1% Triton X-100), and once in low salt (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100). Bound RNA was extracted from the bead using Trizol (Invitrogen) in two consecutive extractions, and the RNA fractions were pooled, followed by ethanol precipitation. For the first ligation reaction, fragmented nascent RNA was redissolved in H2O and incubated with 10 pmol of reverse 3’ RNA adaptor and T4 RNA ligase I (NEB) under manufacturer’s condition for 6hr at 20˚C. For PRO-cap, the standard 3’ RNA adaptor (Illumina) was used. Ligated RNA was enriched with biotin-labeled products by another round of Streptavidin bead binding and extraction. To repair 5’ ends, the RNA products were treated with Tobacco Acid Pyrophosphatase (TAP, Epicentre) and Polynucleotide Kinase (PNK, NEB). Each reaction was followed by an ethanol precipitation step. For PRO-cap, PNK treatment step was omitted, and Antarctic phosphatase (AP, NEB) was used to treat the RNA preparation prior to TAP treatment to enrich for 5’ capped RNA. Since these procedures repair 5’ ends after the 3’ ligation, selfcircularized products were not expected during the first ligation step. 5’ repaired RNA was ligated to reverse 5’ RNA adaptor (5'-rCrUrGrArArCrArArGrCrArGrArArGrArCrGrGrCrArUrArCrGrA-3' or 5'-rCrCrUrUrGrGrCrArCrCrCrGrArGrArArUrUrCrCrA-3’ for using TruSeq barcodes (Illumina)). Standard 5’ RNA adaptors were used for PRO-cap. Ligated RNA products were further enriched for biotin-labels by the third round of streptavidin bead binding and extraction. Adaptor ligated nascent RNA was reverse transcribed using 25 pmol RT primer (5’-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA3’(GX2 primer, Illumina) or 5’- AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3’ for TRU-seq barcodes (RP1 primer, Illumina). Standard Illumina RT primers were used for PRO-cap. A portion of the RT product was removed and used for trial amplifications to determine the optimal number of PCR cycles. For the final amplification, 12.5 pmol of GX1 primer (Illumina) or RPI-index primers (for TRU-seq barcodes, Illumina) was added to the RT product with Phusion polymerase (NEB) under standard PCR condition. Excess RT primer served as one primer of the pair used for the PCR. The product was amplified 12~18 cycles and PAGE purified before being analyzed by Illumina’s GenomeAnalyzer 2 or HiSeq 2000 machines.

tag: antibody


title: A3_CD07_C/C_clone 2


title: HEL_Ctrl_Pol ll (Ser-2p)


title: Par4_ECko_Saline_Bead_3

value: Saline


title: Par4_EChet_Saline_Input_3


title: Par4_EChet_Saline_Bead_3


title: p300_PGE2

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
All ChIP-Seq datasets were aligned to UCSC build version hg19 of the human genome using Bowtie2 (version 2.2.1; Langmead et al., 2012)with the following parameters: -end-to-end, -N0, -L20. We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak-finding algorithm to identify regions of ChIP-Seq peaks, with a q-value threshold of enrichment of 0.05 and false discovery rate of < 0.01 for all datasets. The genome-wide occupancy profile figures were generated by deeptools (Ramirez et al., 2016) using the reference-point mode and the scale-regions mode. The genomic distribution of peaks was plotted using the ChIPSeeker R package, annotatePeak to assign peaks to a genomic annotation, which includes whether a peak is in the TSS, Exon, 5’UTR, 3’ UTR, Intronic or Intergenic. The genomeannotation is from the R-bioconductor annotation packages. Heat maps of the ChIP-Seq binding were generated using the input normalized results of the MACS peak calling output. The outputted bedGraph files were converted to BigWig files. Those files were then processed using computeMatrix and plotHeatmap tools within the deeptools 3.0 package. Enhancers were assigned to genes using GREAT to the nearest genes within 15kb of peaks.
Peaks were called using MACS 2.0 with the following setting: q-value 0.05
Assembly: hg19
Supplementary files format and content: bedGraph pileup from MACS 2.0 output

source_name: Hematopoietic stem and progenitor cells

growth_protocol: 16,16-dimethyl prostaglandin E2 was purchased reconstituted in DMSO from Cayman Chemicals (cat. #14750), aliquoted and stored in -80°C until use. Cells were counted, collected and resuspended in StemSpan medium with 2% PenStrep (CD34+ Cells) or RPMI with 1% Penicillin-Streptomycin, but in the absence of additional cytokines or growth factors. Cells were treated with dmPGE2 (Cayman chemicals) or DMSO (vehicle control) for 2 hours.

extract_protocol: ChIP-Seq libraries were prepared using the following protocol. End repair of immunoprecipitated DNA was performed using the End-It End-Repair kit (Epicentre, ER81050) and incubating the samples at 25°C for 45 min. End-repaired DNA was purified using AMPure XP Beads (1.8X of the reaction volume) (Agencourt AMPure XP – PCR purification Beads, BeckmanCoulter, A63881) and separating beads using DynaMag-96 Side Skirted Magnet (Life Technologies, 12027). A-tails were added to the end-repaired DNA using NEB Klenow Fragment Enzyme (3’-5’ exo, M0212L), 1X NEB buffer 2 and 0.2mM dATP (Invitrogen, 18252-015) and by incubating the reaction mix at 37μC for 30 min. A-tailed DNA was cleaned up using AMPure beads (1.8X of reaction volume). Subsequently, cleaned up A-tailed DNA went through Adaptor ligation reaction using Quick Ligation Kit (NEB, M2200L) following manufacturer’s protocol. Adaptor-ligated DNA was first cleaned up using AMPure beads (1.8X of reaction volume), eluted in 100μl and then size-selected using AMPure beads (0.9X of the final supernatant volume, 90μl). Adaptor-ligated DNA fragments of proper size were enriched with PCR reaction using Fusion High-Fidelity PCR Master Mix kit (NEB, M0531S) and specific index primers supplied in NEBNext Multiplex Oligo Kit for Illumina (Index Primer Set 1, NEB, E7335L). Conditions for PCR used are as follows: 98°C, 30 sec; [98°C, 10 sec; 65°C, 30 sec; 72°C, 30 sec] X 15 to 18 cycles; 72°C, 5 min; hold at 4°C. PCR enriched fragments were cleaned up using AMPure beads (1X of reaction volume). Libraries were eluted in 20μl elution buffer. All the libraries went through quality control analysis using an Agilent Bioanalyzer and subjected to next-generation sequencing using Illumina Hiseq 2500 platform.

treatment_protocol: 20 million cells were crosslinked by the addition of 1/10 volume 11% fresh formaldehyde for 10 min at room temperature. The crosslinking was quenched by the addition of 1/20 volume 2.5M glycine for 5 minutes. Cells were washed twice with ice-cold PBS. Cells were lysed in 10mL of Lysis buffer 1 (50mM HEPES-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, plus protease and phosphatase inhibitors) for 10 min at 4°C. After centrifugation, cells were resuspended in 10 mL of Lysis buffer 2 (10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, plus protease and phosphatase inhibitors) for 10 min at room temperature. Cells were pelleted and resuspended in 3mL of sonication buffer (10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.05% N-lauroylsarcosine, plus protease and phosphatase Inhibitors) and sonicated in a Bioruptor sonicator for 36 cycles of 30 sec each followed by a 1min resting interval. Samples were centrifuged for 10min at 18,000g and 1% Triton-X was added to the supernatant. Prior to the immunoprecipitation, 50mL of protein G beads (Invitrogen 100-04D) for each reaction were washed twice with PBS, 0.5% BSA twice. Finally, the beads were resuspended in 250μL of PBS, 0.5% BSA and 5μg of each antibody. Beads were rotated for at least 6 hours at 4°C and then washed twice with PBS with 0.5% BSA. Cell lysates were added to the beads and incubated at 4°C overnight. Beads were washed 1x with (20mM Tris-HCl. pH 8, 150mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), 1x with (20mM Tris-HCl, pH 8, 500mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), 1x with (10mM Tris-HCl, pH 8, 250nM LiCl, 2mM EDTA, 1% NP4-0) and 1x with TE and finally resuspended in 200μL elution buffer (50mM Tris-Hcl, pH 8.0, 10mM EDTA, 0.5%–1% SDS). 50μL of cell lysates prior to addition to the beads was kept as input. Crosslinking was reversed by incubating samples at 65C for at least 6 hours. Afterwards the cells were treated with RNase and proteinase K and the DNA was extracted by Phenol/Chloroform extraction.

tag: tag

value: mobilised peripheral blood CD34+ cells


title: Low-dose infected day 2 Hamster 2


title: Par4_ECko_APAP_Input_3

value: APAP


title: High-dose infected day 2 Hamster 3


title: p300_DMSO


title: H2A.Zac_PGE2


title: High-dose infected day 3 Hamster 1


title: H2A.Zac_DMSO


title: Par4_ECko_APAP_Input_2


title: Naive Hamster 3

value: naive

value: 0 dpi


title: H3K27me3_PGE2


title: Par4_EChet_APAP_Input_2


title: Naive Hamster 2

value: lung


title: GATA2_PGE2


title: H3K4me1_DMSO


title: High-dose infected day 2 Hamster 1

value: SARS-CoV-2 Variant B.1


title: H3K27me3_DMSO


title: GATA2_DMSO


title: H3K4me1_PGE2


title: B4

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

description:
Raw_3.csv
Normalized_3.csv

data_processing:
Low-quality reads were removed by fastp with default parameters
Remaining clean reads were align to the Homo sapiens (human) genome assembly GRCh38 (hg38)/Mus musculus (house mouse) genome assembly GRCm39 (mm39) according to the corresponding species by Hisat2 with default parameters
Raw gene counts were generated by featurecount and then normalized by DEseq2
Assembly: hg38 or mm39
Supplementary files format and content: Matrix table with raw gene counts
Supplementary files format and content: Matrix table with normalized gene counts

source_name: monocyte-derived microglia

growth_protocol: For sample 1-12, mice were breed in cages before collection of tissue. For Sample 13 - 14, the monocyte-derived microglia were maintain in RPMI1640 medium, supplemented with 1 % P/S, 0.1 μg/ml IL-34 and 0.01 μg/ml GM-CSF

extract_protocol:
Total RNA from cultured MDMi and mouse cortex samples was extracted using TRIzol Reagent (Invitrogen, 15596026) according to the instruction.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: For sample 1-6, they were treated with SM03 (anti-human CD22 antibody) or IgG1 isotype 21 days before sacrifce. Antibodies were intravenously adminstrated once a week. For sample 7-12, mice were intracerebroventricularly injected with PBS or 9 μg mouse soluble CD22. Mouse cortice were collected 3 days after administration. For sample 13-20, cells were treated with 10 μg/mL sCD22 for 24 hours. Cells were then collected for RNA.

value: monocyte-derived microglia


title: Naive Hamster 1


title: High-dose infected day 2 Hamster 2


title: Par4_EChet_Saline_Bead_2

value: Liver EC


title: Par4_ECko_Saline_Bead_2


title: pCREB_DMSO


title: pCREB_PGE2


title: B3

description:
Raw_3.csv
Normalized_3.csv


title: Par4_ECko_Saline_Bead_1


title: H2A.Z_PGE2


title: RNA021706

city: Gent

first: Ramiro

last: Martinez

state: Flaanders

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: UGENT-OncoRNAlab

data_processing:
Deduplication: Clumpify used for deduplication.
Adaptor Trimming and Quality Filtering: Performed using Cutadapt with a quality threshold of 20 for both ends and a minimum length setting of 20. PolyA Trimming: Additional PolyA tail trimming was conducted using Cutadapt.
Software: STAR aligner Alignment Parameters: Two-pass mode, maximum allowed mismatches, minimum and maximum intron sizes specified. Specific parameters include out FilterMismatchNmax 999, outFilterMismatchNoverReadLmax 0.04, alignIntronMin 20, alignIntronMax 1000000, and alignMatesGapMax 1000000.E69 Gene Annotation File: Utilized GTF file from RNAatlas
Read Distribution Analysis: Samtools used for generating indexed stats and filtering BAM files to distinguish between uniquely mapped and multimapped reads. Region-Specific Analysis: Reads mapped to exons, introns, and intergenic regions analyzed using defined bed files.
Kallisto used for transcript-level quantification. Settings include strandedness and specific kallisto index. HTSeq-count employed for gene-level read counting, adjusted for reverse strand specificity.
Assembly: Reference Genome: Human genome (hg38)
Supplementary files format and content: tab delimited text file included raw counts for each sample
Supplementary files format and content: tab delimited text file included tpm for each sample (transcript level)

growth_protocol: MALME-3M was cultured in Iscove's Modified Dulbecco's Medium (IMDM; Thermo Fisher Scientific, Cat. #12440-053) supplemented with 20% fetal bovine serum (FBS; Merck Life Science, Cat. #F0804-500ML) and 100 U/mL penicillin and 100 ug/mL streptomycin (1%, PS). SK-MEL-5 cells were cultured in Eagle's Minimum Essential Medium (MEM; GIBCO. #12599049) supplemented with 10% FBS, 1 mM sodium pyruvate (Thermo Fisher Scientific, Cat. #11360070), 1% PS and 1% L-Glutamine. All cell lines were incubated at 37°C in a 5% CO₂ humidified environment. Cells were passaged every 3 days or when reaching 80-90% confluence. Cells were tested every months for mycoplasma contamination and were authenticated every 6 months by STR genotyping.

extract_protocol:
RNA was extracted using the miniRNAeasy kit (Qiagen, Cat# 217604) according to manufacturer’s instructions.
RNA libraries were prepared using Pico V3 fallowing manufacturer's recommendation
RNAseq - NovaSeq SP 200 cycles kit. We did 2 x 100 cycles

treatment_protocol: IFN-γ treatment: 24-hour exposure. Concentration for MALME-3M was 200ng/mL and for SK-MEL-5 was 150ng/mL

value: Melanoma

value: WT

value: IFN


title: B2

description:
Raw_3.csv
Normalized_3.csv


title: RNA021705


title: RNA021704


title: Par4_ECko_Saline_Input_3


title: B1

description:
Raw_3.csv
Normalized_3.csv


title: H3.3_PGE2


title: Par4_EChet_Saline_Bead_1


title: A4

description:
Raw_3.csv
Normalized_3.csv

value: PBS


title: Par4_EChet_APAP_Bead_1


title: A3

description:
Raw_3.csv
Normalized_3.csv


title: H3.3_DMSO


title: A2

description:
Raw_3.csv
Normalized_3.csv


title: Par4_ECko_APAP_Bead_1


title: H2A.Z_DMSO


title: RNA021701


title: RNA021702


title: Par4_ECko_Saline_Input_2


title: Par4_ECko_Saline_Input_1


title: H3K27ac_PGE2


title: A1

description:
Raw_3.csv
Normalized_3.csv


title: H3K27ac_DMSO


title: Par4_EChet_Saline_Input_2


title: Par4_ECko_APAP_Input_1


title: RNA021700


title: ATAC_dmPGE2_2h

data_processing:
All human ATAC-Seq datasets were aligned to build version NCBI37/HG19 of the human genome using Bowtie2 (version 2.2.1)  (Langmead et al., 2012) with the following parameters: --end-to-end, -N0, -L20. We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak finding algorithm to identify regions of ATAC-Seq peaks, with the following parameter --nomodel --shift -100 --extsize 200. A q-value threshold of enrichment of 0.05 was used for all datasets.
Assembly: hg19
Supplementary files format and content: bed file of called peaks

growth_protocol: Human CD34+ hematopoietic stem and progenitor cells (HSPCs), isolated from peripheral blood of granulocyte colony-stimulating factor (G-CSF) mobilized healthy volunteers, were purchased from the Fred Hutchinson Cancer Research Center. The cells were maintained in suspension culture as previously described by Trompouki et al., 2011.

extract_protocol:
5X104 CD34+ cells at specific differentiation stage tested were harvested by spinning at 500 x g for 5 min, 4° C. Cells were washed once with 50 uL of cold 1X PBS and spinned down at 500 x g for 5 min, 4° C. After discarding supernatant, cells were lysed using 50 uL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360) and spinned down immediately at 500 x g for 10 mins, 4 deg C. Then the cells were precipitated and kept on ice and subsequently resuspended in 25 uL 2X TD Buffer (Illumina Nextera kit), 2.5 uL Transposase enzyme (Illumina Nextera kit, 15028252) and 22.5 uL Nuclease-free water in a total of 50 uL reaction. Transposase reaction was continued for 1 hr at 37° C. Immediately following the reaction, DNA was purified using Qiagen MinElute PCR purification kit (28004) in a final volume of 10 uL.
Libraries were purified according to Illumina protocol using the transposed DNA, NEB PCR master mix, Sybr green, universal and library-specific Nextera index primers. First round of PCR cycles was performed with the following cycles: 72° C, 5 min; 98° C, 30 sec; [98°C, 10 sec; 63 °C, 30 sec; 72 °C, 1 min] X 5 cycles; hold at 4°C. Reactions were kept on ice and using a 5 uL reaction aliquot, appropriate number of additional cycles required for further amplification were determined in a side qPCR reaction with the following procedure: 98 °C , 30 sec; [98 °C, 10 sec; 63 °C, 30 sec; 72 °C, 1 min] X 20 cycles; hold at 4 °C. Upon determining the additional number of PCR cycles required further for each sample, library amplification was conducted using the following conditions: 98°C, 30 sec; [98°C,10 sec; 63°C, 30 sec; 72 °C, 1 min] X appropriate number of cycles; hold at 4°C. Libraries prepared went through quality control analysis using an Agilent Bioanalyzer. Samples with appropriate nucleosomal laddering profiles were selected for next generation sequencing using Illumina Hiseq 2500 platform

treatment_protocol: 16,16-dimethyl prostaglandin E2 was purchased reconstituted in DMSO from Cayman Chemicals (cat. #14750), aliquoted and stored in -80°C until use. Cells were counted, collected and resuspended in StemSpan medium with 2% PenStrep (CD34+ Cells) or RPMI with 1% Penicillin-Streptomycin, but in the absence of additional cytokines or growth factors. Cells were treated with dmPGE2 (Cayman chemicals) or DMSO (vehicle control) for 2 hours.


title: ATAC_DMSO_2h


title: RNA021699


title: RNA021698


title: Par4_EChet_Saline_Input_1


title: RNA021697


title: Par4_EChet_APAP_Input_1


title: RNA021703


title: MethylC-seq_B_stricta

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Bisulfite-seq: Methylpy (Schultz et al., 2015) with Cutadapt v1.9 and Bowtie 2.2.4.
Assembly: Bstricta_278_v1
Supplementary files format and content: compressed tab-separated text files in allc format. "allc" stands for all cytosine (C). Each row in an allc file corresponds to one cytosine in the genome. An allc file contain 7 mandatory columns and no header (https://github.com/yupenghe/methylpy#output-format).

organism: Boechera stricta

source_name: leaf

growth_protocol: Plants were grown at 23C under 15 hours of day light condition.

extract_protocol:
genomic DNA was isolated from leaf tissues using the DNeasy Plant Mini Kit (Qiagen)
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al., 2015). Briefly, genomic DNA was sonicated to around 200 bp using a Covaris S-series focused ultrasonicator, and end-repaired with an End-It DNA end-repair kit (Epicentre). The end-repaired DNA was subjected to A-tailing using Klenow 3′–5′ exo− (NEB) and ligated to methylated adapters using T4 DNA ligase (NEB). The ligated DNA was treated with sodium bisulfite reagent using the EZ DNA methylation-Gold kit and amplified using KAPA HiFi uracil + Readymix Polymerase. RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina) following the manufacturer’s instructions with limited modifications.

value: leaf


title: RMA-Qa1KO Tumor MHCIImin macrophages

city: Leiden

first: Sjoerd

middle: H

last: van der Burg

address: Albinusdreef 2

department: Medical Oncology

country: Netherlands

institute: LUMC

description: 10X Genomics

data_processing:
Fastq files were generated using Cell Ranger mkfastq (10x Genomics).
Fastq files were analyzed with the 10x Genomics Cell Ranger software v7.0.0 and the mouse mm10 reference using default settings.
Assembly: mouse mm10 reference
Supplementary files format and content: Tab-separated values files and matrix files

source_name: RMA-Qa1KO Tumor

extract_protocol:
For single cell RNA sequencing (scRNAseq) mice bearing RMA-Qa1b-/- tumors were treated with therapeutic vaccination when tumors reached a size of 10-50mm3. At time of regression, tumors were harvested and processed into single cell suspensions. From single cell suspensions MHCII+ and MHCII- macrophages (Live, CD45+, CD11b+, F4/80+) were sorted using the BD Aria cell sorter and collected at a purity >90%.
Single cell gene expression libraries were generated on the 10x Genomics Chromium X platform using the Chromium Next GEM Single Cell 3’ Library & Gel Bead Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit (10x Genomics) according to the manufacturer’s protocol.

value: RMA-Qa1KO Tumor

value: MHC-II- macrophage

value: Therapeutic vaccination


title: WT-H37Rv

city: London

first: Gerald

last: Larrouy-Maumus

address: South Kensington Campus

country: United Kingdom

institute: Imperial College London

data_processing:
SNPs called from reads using Galaxy. SNP overlap between samples assessed.
Assembly: Not applicable.
Supplementary files format and content: Excel file (xls) containing SNPs called for each sample and summary of overlapping SNPs.

organism: Mycobacterium tuberculosis H37Rv

source_name: bacterial cell

growth_protocol: The mycobacteria strains were cultured in 7H9 medium supplemented with 0.5 g/l Fraction V (bovine serum albumin), 0.05% tyloxapol, 0.2% dextrose, 0.2% glycerol, and 10 mM NaCl.

extract_protocol:
Prior to DNA extraction, Mtb was heat-killed at 98°C for 2 hours. Lipase and lysozyme were added to a final concentration of 2 mg/ mL. 5 μL of DNase free RNase (Boehringer Mannheim) were added to the preparation and incubated at 37°C overnight. The cells were then frozen in an ethanol/ dry ice bath and incubated at 75°C for 10 minutes. After cooling to room temperature, 20 % SDS were added to a final concentration of 0.5 mg/ mL and incubated at 50°C for one hour. DNA was extracted with phenol:chloroform, by adding equal volumes of both, mixing by inversion, and centrifuging at 13,000 x g for 5 minutes. DNA was precipitated by adding 1/50 volume of 5M NaCl and 2.5 volumes of 100 % ethanol and stored at -20°C overnight. The suspension was centrifugated at 15,000 x g for 5 minutes and washed twice with 70% ethanol. After airdrying the pellets for 5 mins, the DNA was resuspended in fresh 10 mM Tris -HCl pH 8.0 + 1 mM EDTA buffer and stored at 4 °C.
Library prep done with the NEB ultra II FS kit.

value: bacterial cell


title: 2-2-KO-Rv3728

value: Rv3728 KO


title: Brain,mRNA,Hydrogel1

city: Wuhan

first: Huayu

last: Kang

state: Hubei

address: Jiefang Avenue 1095,Qiaokou District

institute: Tongji Medical College, Huazhong University of Science & Technology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38/Rnor_6.0 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38/Rnor_6.0
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS™ Stranded mRNA-seq Library Prep Kit for Illumina®Library Prep Kit following manufacturer's protocols.

value: Brain

tag: sample group

value: BCCAO rats transplanted with BMSC-loaded hydrogel during EMS treatment

tag: time point

value: 7 days post EMS treatment


title: Brain,mRNA,Hydrogel2


title: RNA021696


title: RMA-Qa1KO Tumor MHCIIpos macrophages

description: 10X Genomics

value: MHC-II+ macrophage


title: 1-1-KO-Rv3728


title: 1-2-KO-Rv3728


title: Brain,mRNA,con3

value: bilateral common carotid artery occlusion (BCCAO) rats treated with EMS


title: Brain,mRNA,Hydrogel3


title: 0628-NC2

city: Nanjing

first: Jiawen

last: Cui

state: Jiangsu

address: TongJiaXiang #24

institute: China Pharmaceutical University

data_processing:
The generated clean reads were aligned to reference genome using orientation mode in HISAT2 software (http://daehwankimlab.github.io/hisat2/). Reads mapped to each gene were quantified using Feature Counts, with the subsequent calculation of the FPKM for every gene based on gene length and the mapped read count. Differential gene expression analysis was conducted using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html). Genes showing differential expression with | log2FC | > 1 and Padj < 0.05 were deemed significant. To elucidate the functional differences among samples and understand the enrichment of differentially expressed genes, GO enrichment analysis was performed. The cluster Profiler R package was employed for this GO functional enrichment.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes Fragments Per Kilobase per Million (FPKM).

extract_protocol:
Total RNA from H1975 cells treated with Almonertinib, EGF and EGFR-knockdown was isolated using the TRIzol® Reagent as prescribed by manufacturer (Magen).
Paired-end sequencing libraries were established utilizing the ABclonal mRNA-seq Lib Prep Kit (ABclonal, China). From 1 μg of total RNA, mRNA was enriched using oligo (dT) magnetic beads.

value: non-small cell lung cancer

value: siNC


title: 0628-NC3


title: Brain,mRNA,con2


title: Molar, Notum KO wild type, E16.5, biol rep1

city: Seodaemun-gu

first: Sung-Won

state: Seoul

address: Yonsei-ro 50,

department: Department of Oral Biology

country: South Korea

institute: Yonsei University College of Dentistry

data_processing:
Raw data (raw reads) of fastq format were first processed through Novogene in-house Perl scripts. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N, and low-quality reads from raw data. At the same time, Q20, Q30, and GC content of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Index of the reference genome (mm10) was built 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. The FPKM of each gene was calculated based on the length of the gene and read count mapped to the gene.
Assembly: mm10
Supplementary files format and content: Comma Separated Values File include fpkm values for each sample

source_name: Molar

extract_protocol:
Maxillary and mandibular molar tooth germs were dissected from Notum+/+and Notum-/- littermate mouse embryos at E14.5 and E16.5. Total RNA was extracted with TRIZOL® (Invitrogen) RNA extraction method. The RNA quality was assessed using RNA ScreenTape® (Agilent Technologies, Germany).
RNA Library Preparation and Sequencing was performed by Novogene, China. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was prepared, followed by the end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platform.

value: Molar

value: Wild type


title: Brain,mRNA,con1


title: Molar, Notum KO wild type, E16.5, biol rep2


title: 0628-NC1


title: 3 DPG Seedling Shoot, Cycloheximide_EPFL6_rep3

city: Philadelphia

first: Aman

middle: Yebio

last: Husbands

state: PA

address: 103B Caroline Lynch Bldg, 433 S University Ave

department: Biology

institute: The University of Pennsylvania

description:
T3CT3_S12
EPFL6_counts.txt

data_processing:
Reads were aligned using STAR 2.7.6a intron size was set to 1000nt
Reads were counted using featureCounts 2.0.0 at the meta feature (gene) level, chimeric reads and multimapping reads were filtered out
Genes without at least one count in all three replicates of a single condition were removed
Read counts were normalized using DESeq2_1.26.0 with a pairwise comparison design between all genotypes
Assembly: TAIR10.1 (Genome) Araport 11 (Reference)
Supplementary files format and content: Processed data file is a matrix containing the DESeq2 normalized counts for each sample. Each row is a gene (AGI) and each column is a sample.

source_name: 3 DPG Seedling Shoot

growth_protocol: Plants were grown under an 18h light/ 6 hour dark cycle (long day) at 21°C on modified Murashige and Skoog (MS) medium plates with 1% (w/v) sucrose added. Seeds were stratified for 2 days at 4°C before germination.

extract_protocol:
Samples were collected at 3 days post germination. Total RNA was extracted using a commercial kit
TruSeq mRNA kit from Illumina (Poly A enrichment)

treatment_protocol: For treatment, 10 seedlings were transferred per biological replicate into 1 ml of liquid MS medium. Seedlings in liquid medium were treated with 8.7μl of the 10μM EPFL6 solution or an equal volume of the treatment buffer. For cycloheximide treatments, seedlings in liquid medium were pretreated with 10μM cycloheximide for 10 minutes before EPFL6 or mock was added. 3 Replicates were performed for each condition

value: 3 DPG Seedling Shoot

value: clv3 epfl1 epfl2 epfl4 epfl6

value: 10uM Cycloheximide + 10uM EPFL6


title: 0628-siEGFR3

value: siEGFR


title: neonatalSN, OMM12_96_59

city: Turin

first: Chiara

last: Cicconetti

state: (TO)

address: Via Nizza, 52

department: Dept. of Life Sciences and Systems Biol

country: Italy

institute: University of Turin

data_processing:
After quality controls with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), raw reads were aligned to the mouse reference genome (UCSC mm10/GRCm38) using STAR 2.7.1a (Dobin et al., 2013) (with parameters –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04). Gene expression levels were quantified with featureCounts v1.6.3 (Liao et al., 2014) (options: -t exon -g gene_name) using GENCODE M23 annotation. Multi-mapped reads were excluded from quantification. Gene expression counts were next analysed using the edgeR package (Robinson et al., 2010). After low expressed genes filtration (1 count per million (CPM) in less than 3 samples), normalisation factors were calculated using the trimmed-mean of M-values (TMM) method (implemented in the calcNormFactors function).
Assembly: mm10/GRCm38
Supplementary files format and content: Tab-delimited text file of normalized read counts per gene/samples.

source_name: Sciatic nerves

growth_protocol: Neonatal (P8-14) and young adult (63-76 days old) germ-free (GF), gnotobiotic (colonized with Oligo-Mouse Microbiota12, OMM12) and SPF C57BL6/JZtm (complex microbiota) mice were obtained from the Central Animal Facility (Hannover Medical School, Hannover, Germany). Breeding and maintenance of GF and gnotobiotic mice was performed in plastic film isolators (Metall+Plastik GmbH, Radolfzell-Stahringen, Germany) located in a room with a controlled environment (20–22 °C, 50–55 % humidity) and 12-hour light/dark cycles. GF and gnotobiotic mice received pelleted 50 kGy gamma-irradiated feed (V1124-927, Ssniff Spezialdiäten GmbH, Germany) and autoclaved water ad libitum. SPF mice were housed in individually ventilated cages (XJ Edge, Allentown) in a room with a controlled environment (20–22 °C, 50–55 % humidity) and 12 h light/dark cycles. SPF mice received pelleted 50 kGy gamma-irradiated feed (1314 breeding diet for mice and rats, Altromin) and chlorinated water ad libitum. Routine microbiological monitoring according to FELASA recommendations (Mähler et al., 2014) and recommendations for maintaining gnotobiotic colonies (Nicklas et a., 2015) did not reveal any evidence of infection with common murine pathogens in SPF animals or contaminants in GF and gnotobiotic animals.   In total, this study included tissue sampling from 42 adult and 41 neonatal animals. The animals were sacrificed by decapitation (adults ones after inducing anaesthesia in CO2 atmosphere). All procedures were performed in accordance with the German Animal Welfare Legislation and the principles of the Basel Declaration and recommendations of Directive 2010/63/EU, they were approved by the local Institutional Animal Care and Research Advisory Committee and registered with the animal care committee of Lower-Saxony, Germany.

extract_protocol:
Neonatal and adult DRG and sciatic nerve total RNA was isolated using TRIzol reagent (Life Technology) and processed according to manufacturer's instructions.
Neonatal and adult DRG and sciatic nerve total RNA was isolated using TRIzol reagent (Life Technology) and processed according to manufacturer's instructions. Quality of the extracted RNAs was assessed using the RNA 6000 Nano Kit on Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Sequencing of pooled dorsal root ganglia and peripheral nerves collected from young adult CGM, GF and OMM12 mice was performed on the Illumina NextSeq 500 platform. Sequencing of pooled dorsal root ganglia and peripheral nerves collected from neonatal CGM, GF and OMM12 mice was performed on the Illumina NextSeq 1000 platform.

value: Sciatic nerves

tag: strain

tag: condition

value: Oligo-mouse microbiota

tag: developmental stage

value: Neonatal (P8-14)


title: Molar, Notum KO wild type, E14.5, biol rep2

tag: tissue

tag: genotype


title: neonatalSN, OMM12_96_58


title: 2-1-KO-Rv3728

value: bacterial cell

value: Rv3728 KO


title: Molar, Notum KO wild type, E14.5, biol rep1

tag: age


title: 0628-siEGFR2

tag: treatment


title: RNA021695

tag: cell type

value: Melanoma

value: WT


title: neonatalSN, GF_96_67

value: Germ free


title: Molar, Notum KO homozygous, E16.5, biol  rep1

value: Notum knockout homozygous


title: neonatalSN, GF_96_66


title: neonatalSN, OMM12_96_60


title: Molar, Notum KO homozygous, E16.5, biol rep2


title: 3 DPG Seedling Shoot, Cycloheximide_EPFL6_rep1

description:
T3CT1_S10
EPFL6_counts.txt


title: 0628-siEGFR1

value: non-small cell lung cancer


title: neonatalSN, GF_96_65


title: 0628-EGF3

value: EGF


title: Molar, Notum KO homozygous, E14.5, biol rep2

value: Molar


title: 0628-EGF2


title: neonatalSN, CGM_96_74

value: Complex microbiota


title: 3 DPG Seedling Shoot, Cycloheximide_rep2

description:
T3CM2_S8
EPFL6_counts.txt

value: 3 DPG Seedling Shoot

value: 10uM Cycloheximide


title: 3 DPG Seedling Shoot, Cycloheximide_rep1

description:
T3CM1_S7
EPFL6_counts.txt

value: clv3 epfl1 epfl2 epfl4 epfl6


title: Molar, Notum KO homozygous, E14.5, biol rep1


title: neonatalSN, CGM_96_73


title: muscle_PMK WT-66522.15

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

data_processing:
RNA-seq reads were trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20) and reads mapping to abundant sequences included in the iGenomes Ensembl GRCm38 bundle (mouse rDNA, mouse mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCm38/mm10 assembly obtained from Mus musculus Ensembl release 94. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting for QuantSeq experiments (-s 1).
Assembly: mm10
Supplementary files format and content: per gene read counts
Supplementary files format and content: tab separated file format

source_name: skeletal muscle/quadriceps

growth_protocol: Control (Gpcpd1 Flox/Flox Mck Cre negative; PMK WT) and MckCre-Gpcpd1 (Gpcpd1 Flox/Flox MckCre positive; PMK KO) mice were fed chow diet and maintained at standrad housing conditions

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit-FWD (cat #15, Lexogen, Vienna, Austria) using 1 μg of RNA per library, following manufacturer’s instructions.  11 cycles of library amplification were performed with indices from the first two columns of the i7 Index Plate for QuantSeq/SENSE with Illumina adapters 7001–7096 (cat #044, Lexogen). Libraries were eluted in 22 μL of the Elution Buffer, and double stranded DNA concentration was quantified by the KAPA Library Quantification Kit. The molar concentration of cDNA molecules was calculated from the double stranded DNA concentration and the region average size (determined by analyzing each sample on an Agilent 2200 Tapestation instrument (cat#5067–5584 and cat#5067–5585, Agilent, Santa Clara, CA)). Aliquots containing an equal number of nmoles of cDNA molecules from each library were pooled to a concentration of 10 nM of cDNA. The final pool was purified once more (to remove any free primers to prevent index-hopping) by adding 0.9x volumes of PB and proceeding from Step 30 onwards in the QuantSeq User Guide protocol. The library was eluted in 22 μL of the kit’s Elution Buffer.

treatment_protocol: Skeletal muscle (quadriceps) was surgicaly removed from terminally sacrificed 3 months old mice and frozen in LN2.

value: skeletal muscle/quadriceps

value: Control


title: 3 DPG Seedling Shoot, Cycloheximide_EPFL6_rep2

description:
T3CT2_S11
EPFL6_counts.txt

value: 10uM Cycloheximide + 10uM EPFL6


title: 0628-A3

value: Almonertinib


title: 3 DPG Seedling Shoot, EPLF6_rep3

description:
T3T3_S6
EPFL6_counts.txt

value: 10uM EPFL6


title: 0628-A2


title: 3 DPG Seedling Shoot, Cycloheximide_rep3

description:
T3CM3_S9
EPFL6_counts.txt


title: muscle_PMK WT-66523.16


title: 3 DPG Seedling Shoot, EPLF6_rep1

description:
T3T1_S4
EPFL6_counts.txt


title: 0628-A1


title: neonatalDRG, OMM12_96_82

source_name: Dorsal root ganglia

value: Dorsal root ganglia

value: Oligo-mouse microbiota

value: Neonatal (P8-14)


title: muscle_PMK KO-66519.12

value: MckCre Gpcpd1


title: 3 DPG Seedling Shoot, Mock_rep2

description:
T3M2_S2
EPFL6_counts.txt

value: Mock


title: muscle_PMK KO-66521.14


title: 3 DPG Seedling Shoot, Mock_rep1

description:
T3M1_S1
EPFL6_counts.txt


title: muscle_PMK KO-66520.13


title: 3 DPG Seedling Shoot, Mock_rep3

description:
T3M3_S3
EPFL6_counts.txt


title: neonatalDRG, OMM12_96_78


title: 0628-Control3

value: non-small cell lung cancer

value: control


title: 0628-Control1


title: 3 DPG Seedling Shoot, EPLF6_rep2

description:
T3T2_S5
EPFL6_counts.txt


title: muscle_PMK WT-66516.9


title: 0628-EGF1

value: EGF


title: 0628-Control2


title: neonatalDRG, GF_96_87

value: Germ free


title: neonatalDRG, GF_96_86


title: muscle_PMK KO-66518.11


title: neonatalSN, CGM_96_72

value: Sciatic nerves

value: Complex microbiota


title: muscle_PMK WT-66517.10


title: neonatalDRG, OMM12_96_80


title: Adjacent normal tissue2

city: shanghai

first: xindong

last: wei

address: 1200 Cailun Road, Shanghai

institute: shanghai university of Chinese medicine

data_processing:
The raw image data obtained from Illumina sequencing is converted into sequence data in FASTQ format by Base Calling.
Clean-data was obtained using Fastp software according to the steps below: 1)Remove the splice sequences in the reads, and remove the reads that do not have inserted fragments due to splice self-linkage and other reasons; 2) Trim off the low-quality (quality value less than 20) bases at the end of the sequence (3' end), if there is still quality value less than 10 in the remaining sequence, then the whole sequence will be eliminated, otherwise it will be retained; 3) Remove the reads containing more than 10% N ratio; 4) discard sequences with length less than 20bp after adapter and quality trimming.
The sequencing reads were compared to th reference genome using Bowtie2 using the improved BWT algorithm on the Hisat2.2.1 software.
CricRNAs identified by CIRI2 software which utilizes the BWA-MEM algorithm for sequence comparison to find back-spliced junction reads and detects circRNAs based on the junction reads of GT-AG signals.
Assembly: hg38/GRCh38
Supplementary files format and content: tab-delimited text file includes RPM for each Sample

source_name: LIVER

extract_protocol:
Total RNA was extracted from tissue samples by TRIzol reangent, and the concentration and purity of the extracted RNA was examined using Nanodrop 2000. 5ug of total RNA was used for construction of sequnencing libraries.
RNA libraries for RNA-Seq were prepared using TruSeqTM Stranded Total RNA Library Prep Kit following manufacturer's protocols after removing rRNA by Ribo-Zero Magnetic Kit and mRNA by RNase R.

value: LIVER

tag: individual

value: HCC patient 2


title: Adjacent normal tissue5

value: HCC patient 5


title: neonatalDRG, CGM_96_93


title: 2713-GF2

data_processing:
The generated clean reads were aligned to reference genome using orientation mode in HISAT2 software (http://daehwankimlab.github.io/hisat2/). Reads mapped to each gene were quantified using Feature Counts, with the subsequent calculation of the FPKM for every gene based on gene length and the mapped read count. Differential gene expression analysis was conducted using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html). Genes showing differential expression with | log2FC | > 1 and Padj < 0.05 were deemed significant. To elucidate the functional differences among samples and understand the enrichment of differentially expressed genes, GO enrichment analysis was performed. The cluster Profiler R package was employed for this GO functional enrichment.
Assembly: Ensembl_release109
Supplementary files format and content: Tab-delimited text files includes Fragments Per Kilobase per Million (FPKM).

tag: cell line


title: R_BM_Ly6G

city: Hachioji

first: Yoshihiro

last: Hayashi

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

description:
R_Ly6G
CountsTable_RH.txt

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
FASTQ files were processed in the AltAnalyze (version 2.1.3)
Transcript per million estimates were calculated in AltAnalyze through a built-in call to Kallisto for read pseudoalignment and transcript quantification (Ensembl 72, mm10)
Assembly: mm10
Supplementary files format and content: raw counts with genes in rows and samples in columns

source_name: Bone marrow

extract_protocol:
Bone marrow cells were harvested from individual mice. HSCPs were purified using EasySep Mice CD117 positive selection kit and mutant clone was FACS sorted. Ly6G+ mutant myeloid BM cells were FACS sorted. The total RNA was isorated using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: RUNX1 mutant


title: neonatalDRG, GF_96_85


title: 2713-NC2

value: siNC


title: Ctrl_BM_Ly6G

description:
WT_Ly6G
CountsTable_RH.txt

value: Control


title: neonatalDRG, CGM_96_95

value: Dorsal root ganglia


title: Adjacent normal tissue3

value: HCC patient 3


title: 2713-GF1


title: RH_BM_Ly6G

description:
RH_Ly6G
CountsTable_RH.txt

value: RUNX1 mutant with HMGA2-OE


title: 2713-NC1


title: Hepatocellular carcinoma4

source_name: HCC

value: HCC

value: HCC patient 4


title: 2713-GF3

value: non-small cell lung cancer


title: neonatalDRG, CGM_96_94

value: Neonatal (P8-14)


title: HMGA2_BM_Ly6G

description:
HMGA2_Ly6G
CountsTable_RH.txt


title: Hepatocellular carcinoma3


title: NPHS2Cre:Epac1fl/fl_NTS_Day11_3

city: Toulouse

first: Maximin

last: Détrait

address: 1 avenue Jean Poulhès- BP 84225

country: France

institute: INSERM I2MC

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences were trimmed or removed with fastp tool, with default parameters.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including expected counts and TPM

extract_protocol:
After euthanasia, kidneys from (day4) or (day11) were collected and embedded in matrix (O.C.T.) and snap-frozen in liquid nitrogen. Glomeruli were isolated from 10 µM cryosections by laser microdissection (Arcturus XT, Exilon), collected on Cupules CapSure® Macro LCM (Excilone, LCM 0211) and RNA was isolated with PicoPure® RNA isolation kit (Excilone).
RNA library preparation were realized following manufacturer’s recommendations (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from LEXOGEN).

treatment_protocol: Passive glomerulonephritis (GN) was induced in conditional knockdown 3-month-old female mice with specific Epac1 deletion in podocytes (NPHS2Cre: Epac1fl/fl) and in the littermate (Epac1fl/fl), by 2 consecutive days’ intravenous injection of decomplemented nephrotoxic serum (NTS; 18,5 µl/gBW), prepared as previously described (Mesnard et al., 2009; Salant and Cybulsky, 1988), while the control mice were injected with PBS. The mice were euthanatized at the early stage (day4) or later/established stage (day 11) of the GN.

tag: Sex

value: Female

value: NTS for 11 days

value: glomerulonephritis (late)


title: Hepatocellular carcinoma5


title: RISP_Het_treatment_Naïve_ageGroup_Adult_13

city: Chicago

first: Rogan

middle: A

last: Grant

address: 303 E Superior St, Simpson Querrey Biomedical Research Center 5-522

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

data_processing:
FASTQ files were generated using bcl2fastq 2.20 (Illumina) for NextSeq500 output or bcl-convert 4.0.3 (Illumina) for NextSeq2000 output using default parameters. To facilitate reproducible analysis, samples were processed using the publicly available nf-core/RNA-seq pipeline version 3.9 implemented in Nextflow 22.04.5.5708 using Singularity 3.8.1 with the minimal command nextflow run nf-core/rnaseq \ -r ‘3.9’ \ -profile nu_genomics \--additional_fasta ‘transgenes.fa’ \ --star_index false \ --three_prime_clip_r2 3 \ --genome ‘GRCm38’ for SMARTer-seq samples. For NEBnext samples, 3’ clipping was not performed. Briefly, lane-level reads were trimmed using trimGalore! 0.6.7 and aligned to the hybrid genome described above using STAR 2.6.1d. Gene-level assignment was then performed using salmon 1.5.2.
Assembly: GRCm38
Supplementary files format and content: Gzipped csv of raw counts from STAR/Salmon

extract_protocol:
For FACS of microglia for RNAseq and microglial enumeration, single cell suspension from whole brain were initially incubated in 1:50 Anti-mouse CD16/32 (biolegend 101302, clone 93) and, subsequently, stained with the following antibodies: 1:100 Anti-Mouse CD45.2-PacBlue (ebioscience 48-0454-82, clone 104) and 1:200 Anti-mouse CD11b(Mac-1)-APC (ebioscience, 50-0112-80, clone M1/70) in 200µL final volume of FACS Buffer. Viability was assessed with addition of DAPI 3 minutes before collection on flow cytometer (Fisher, D1306 0.1µg/mL final concentration). Immediately after sorting microglia were centrifuged at 500xg for 10 minutes at 4°C then resuspended in 350µL RLT plus buffer (Qiagen) and stored at -80°C until nucleic acid purification with the AllPrep DNA/RNA micro kit (Qiagen) for downstream analysis.
RNA quality and quantity were assessed using TapeStation 4200 High Sensitivity RNA tapes (Agilent), and RNA-seq libraries were prepared from 5-10ng of total RNA using the SMARTer Stranded Total RNA-seq Kit v2 (Takara Bio). For analysis of allele status, libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB E7370L). Library QC was then performed using TapeStation 4200 High Sensitivity DNA tapes (Agilent). Dual-indexed libraries were pooled and sequenced on a NextSeq 500 instrument (Illumina) for untreated RISP-/- and wild-type, age-matched animals, or a NextSeq2000 instrument for all other samples (Illumina) 75 or 100 cycles, respectively, single-end, to an average sequencing depth of 27.5 million reads per sample.

value: Brain

value: Microglia

value: RISP Het

value: Naive

tag: age group

value: Adult


title: RISP_KO_treatment_Naïve_ageGroup_Adult_13

value: RISP KO


title: RISP_Het_treatment_Naïve_ageGroup_Old_03

value: Old


title: Adjacent normal tissue1

value: LIVER

value: HCC patient 1


title: RISP_Het_treatment_Naïve_ageGroup_Old_02


title: RISP_Het_treatment_Naïve_ageGroup_Adult_12


title: Adjacent normal tissue4


title: Epac1fl/fl_NTS_Day11_4


title: NPHS2Cre:Epac1fl/fl_NTS_Day11_4


title: Hepatocellular carcinoma1


title: hUCMSC,mRNA,OE2

source_name: hUCMSC

value: hUCMSC

value: Human umbilical cord-derived mesenchymal stem cells

value: transferred with has-mir-183 vector and has-mir-96 vector


title: ChIP-Seq_GapR-HA(High)_hTERT-RPE1

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

description: Illumina HiSeq 4000 and Illumina NovaSeq 6000

data_processing:
Base calling: NovaSeqControl Software v1.8.0, RTA v3 ; HiSeq Control Software v2.2.68, RTA v1.18.66 ; bcl2fastq v2.20.0
Alignment: BWA (v0.7.17) was used to align FASTQ files on GRCh38.p13 reference genome (downloaded from ENCODE) augmented with Gluc_episomal DNA sequence.
Alignment conversion and sorting: the alignment produced by BWA were converted into BAM format and sorted with samtool (v1.10)
Peak calling was done with MACS2 (v2.2.7.1) callpeak using parameters --format BAM --gsize hs --SPMR --keep-dup 1 --qvalue 0.05 --nomodel --extsize 1000.
GapR peak filtering: the GapR peaks found by MACS2 were filtered to exclude: 1) peaks whose fold-enrichment is below 1.5; 2) peaks in telomeric region chr5:9277-12488; 3) peaks in centromeric region chr4:49709342-49712626; 3) peaks in episomal promoter regionchr6:73520103-73522066
GapR peaks were further annotated with ENCODE v41 genes located within a 10kb distance of them; and manually curated.
Assembly: hg38
Supplementary files format and content: bed.gz format, raw data alignment

growth_protocol: ChIP analysis was performed using chromatin extracted from about 5 × 10^6 HA-tagged GapR-expressing hTERT-RPE1 cells (Low expression = single lentiviral transduction ; High expression = double  lentiviral transductions) with cultured in a 10- cm diameter dish.

extract_protocol:
PBS, cells were resuspended and lysed for 10 min at 4°C in 1 mL Cell Lysis Buffer (20 mM Tris-HCl (pH 8.0), 85 mM KCl, 0.5% NP-40) supplemented with EDTA-free protease inhibitor cocktail (Roche, 4693132001). The nuclei were recovered by centrifugation at 500 g for 5 min at 4°C and washed once in the same buffer. Nuclei were resuspended in 500 μL Nuclei Lysis Buffer (10 mM Tris-HCl (pH 7.5), 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, protease inhibitor cocktail) and incubated for 10 min at 4°C. Chromatin was fragmented by sonication 3 × 10 s at 60% duty cycle, with 30 sec on wet-ice between sonication cycles, using a microtip-equipped SLPe sonifier (Branson Ultrasonics ™ Sonifier™, Brookfield, USA). The sonicated samples were centrifuged at 16,000 g for 10 min. The supernatants (500 µL) were collected and diluted with 1500 μl ChIP Dilution Buffer (0.01% SDS, 1.2 mM EDTA, 1.1% Triton X-100, 16.7 mM Tris-HCl (pH 8), 167 mM NaCl) supplemented with protease inhibitors and mixed with 50 μL Dynabeads™ Protein G (Invitrogen, 10009D) coupled with 3 μg anti-HA antibody (Invitrogen, MA5-27915). After overnight incubation at 4°C on a rotating wheel, the beads were washed twice with 1 mL Cell Lysis Buffer, twice with high-salt buffer (50 mM HEPES-KOH (pH 7.5), 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), once with LiCl buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 250 mM LiCl, 1% NP-40, and 1% sodium deoxycholate) and once with TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). To elute immunoprecipitated chromatin fragments, beads were incubated for 10 min at 65°C in 400 μL freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3). DNA crosslinks were reversed by overnight incubation at 65°C with 0.6M NaCl and 80 μg proteinase K (Eurobio Scientific, GEXPRK01-I5). Samples were extracted once with Phenol – chloroform – isoamyl alcohol (Sigma, 77617), once with chloroform (Reactolab SA, P02410E16), ethanol precipitated and then resuspended in water.
ChIP-enriched DNA were used to prepare libraries and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications. Library molarity and quality were assessed with the Qubit (Thermofisher Scientific) and Tapestation (Agilent Technologies - DNA High sensitivity chip). Libraries were sequenced on a HiSeq 4000 and a NovaSeq 6000 Illumina sequencers for SR100 reads.

treatment_protocol: Cells were harvested with trypsin-EDTA and collected by low-speed centrifugation 500 g for 5min. Cells were rinsed once with PBS, resuspended in DMEM and fixed with 1% formaldehyde (Sigma 47608) for 10 min at RT before quenching with 330 mM glycine 5min at RT and then incubated 15min on ice, and washed two further times with ice-cold PBS.

value: immortalized human retina pigment epithelial cells

value: WT GapR-HA(High) overexpressing cell

tag: chip antibody

value: Anti-HA (Invitrogen, MA-27915)


title: hUCMSC,mRNA,OE1


title: RISP_KO_treatment_Naïve_ageGroup_Adult_12


title: hUCMSC,mRNA,OE3


title: hUCMSC,mRNA,NC1

value: transferred with NC vector


title: Hepatocellular carcinoma2

value: HCC

value: HCC patient 2


title: RISP_Het_treatment_Naïve_ageGroup_Old_01

value: Brain

value: Microglia


title: hUCMSC,mRNA,NC2


title: NPHS2Cre:Epac1fl/fl_NTS_Day11_1

value: Female

value: NTS for 11 days

value: glomerulonephritis (late)


title: ChIP-Seq_GapR-HA(Low)_hTERT-RPE1

value: WT GapR-HA(Low) overexpressing cell


title: NPHS2Cre:Epac1fl/fl_NTS_Day11_2


title: RISP_Het_treatment_Naïve_ageGroup_Adult_04

value: RISP Het

value: Naive

value: Adult


title: Epac1fl/fl_NTS_Day11_2


title: ChIP-Seq_noHA(control)_hTERT-RPE1

value: WT


title: RISP_Het_treatment_Naïve_ageGroup_Adult_03


title: Epac1fl/fl_NTS_Day11_3


title: shSLC39A1-2-3

city: ShenZhen

first: Rui

state: Guangdong

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

data_processing:
The data generated from Illumina (or BGI) platform were used for bioinformatics analysis. All of the analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology.
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) 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.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include FPKM for each Sample

extract_protocol:
Total RNA was extracted from the  MHCC97H cells using TRIzol® Reagent according themanufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter_x0002_ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system.

value: HCC cell


title: hUCMSC,mRNA,NC3

value: hUCMSC

value: Human umbilical cord-derived mesenchymal stem cells


title: Epac1fl/fl_NTS_Day11_1


title: shSLC39A1-2-2


title: Disomes_Giro10

city: Wako-shi

first: Tilman

last: Schneider-Poetsch

email: tilman@cal.berkeley.edu, tsp@riken.jp

state: Saitam

address: 2-1 Hirosawa

department: Center for Sustainable Resource Science

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: Human Genome hg38
Supplementary files format and content: Text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts. Transcript names are based on UCSC nomenclature
Library strategy: Ribosome profiling

source_name: HEK293T flp-In

growth_protocol: HEK294T flip in cells grown in DMSO with 10% FBS and antibiotics at 37 deg C under 5% CO2

extract_protocol:
Cells were collected in lysis buffer, cleared of debris and lysates were snap frozen with liquid nitrogen and stored at -80 deg C
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification. For RNA-Seq, Poly(A) selection and cDNA synthesis were performed using Illumina Stranded mRNA Prep, Ligation (Illumina) and subsequent steps were performed by TruSeq Stranded Total RNA Library Prep Gold (Illumina).

treatment_protocol: Cells were treated with DMSO solvent or indicated concentration of girolline for 2 hrs

value: wild type

value: HEK293T flp-In

value: 10 µM girolline

tag: sample type

value: Disomes


title: RISP_Het_treatment_Naïve_ageGroup_Adult_02

value: Brain


title: NPHS2Cre:Epac1fl/fl_NTS_Day4_4

value: NTS for 4 days

value: glomerulonephritis (early)


title: Disomes_Giro1

value: 1 µM girolline


title: NPHS2Cre:Epac1fl/fl_NTS_Day4_2

value: Female


title: Disomes_DMSO2

value: DMSO


title: RISP_WT_treatment_Naïve_ageGroup_Adult_05

value: Microglia

value: RISP WT


title: shSLC39A1-2-1


title: shSLC39A1-1-2


title: Disomes_DMSO1


title: RISP_KO_treatment_Naïve_ageGroup_Adult_05

value: RISP KO

value: Naive

value: Adult


title: NPHS2Cre:Epac1fl/fl_NTS_Day4_3


title: 2713-NC3

value: non-small cell lung cancer

value: siNC


title: shSLC39A1-1-1

value: HCC cell


title: RISP_WT_treatment_PLX3397 Repopulation_ageGroup_Adult_04

value: PLX3397 Repopulation


title: NPHS2Cre:Epac1fl/fl_NTS_Day4_1


title: Monosomes_Giro10

value: wild type

value: HEK293T flp-In

value: 10 µM girolline

value: Monosomes


title: RISP_WT_treatment_PLX3397 Repopulation_ageGroup_Adult_03

value: Brain


title: Epac1fl/fl_NTS_Day4_2

value: NTS for 4 days

value: glomerulonephritis (early)


title: shCtrl-3


title: Monosomes_Giro1

value: 1 µM girolline


title: Monosomes_DMSO2

value: DMSO


title: Epac1fl/fl_NTS_Day4_3

value: Female


title: shCtrl-2


title: RISP_WT_treatment_PLX3397 Repopulation_ageGroup_Adult_02

value: Microglia

value: RISP WT


title: shCtrl-1


title: Monosomes_DMSO1


title: RISP_WT_treatment_PLX3397 Repopulation_ageGroup_Adult_01

value: Adult


title: Epac1fl/fl_NTS_Day4_1


title: RISP_Het_treatment_Naïve_ageGroup_Adult_01

value: RISP Het

value: Naive


title: NPHS2Cre:Epac1fl/fl_PBS_3

value: PBS

value: control


title: shSLC39A1-1-3

value: HCC cell


title: RNA_Giro10

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: Human Genome hg38
Supplementary files format and content: Text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts. Transcript names are based on UCSC nomenclature

value: wild type

value: HEK293T flp-In


title: sample3_3_ICH_32h

city: Jining

first: Daojing

address: 89 Guhuai Road

department: Department of neurology

institute: Affiliated Hospital of Jining Medical University

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: perihematomal edema tissue of post-intracerebral hemorrhage

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: immune cell

value: microglia, neutrophil


title: RNA_Giro1


title: NPHS2Cre:Epac1fl/fl_PBS_2


title: sample3_2_ICH_28h

value: perihematomal edema tissue of post-intracerebral hemorrhage


title: RISP_KO_treatment_PLX3397 Repopulation_ageGroup_Adult_04

value: Brain

value: RISP KO

value: PLX3397 Repopulation


title: NPHS2Cre:Epac1fl/fl_PBS_1

value: Female


title: RISP_KO_treatment_PLX3397 Repopulation_ageGroup_Adult_03

value: Microglia


title: RNA_DMSO2

value: DMSO


title: RISP_KO_treatment_PLX3397 Repopulation_ageGroup_Adult_02

value: Adult


title: sample3_1_ICH_26h


title: Epac1fl/fl_PBS_3


title: CD34plusPGE2_2h_No99

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
Quality control of RNA-Seq datasets was performed by FastQC and Cutadapt to remove adaptor sequences and low-quality regions. The high-quality reads were aligned to UCSC hg19 for human using Tophat 2.0.11 without novel splicing form calls.
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcript.
Assembly: hg19
Supplementary files format and content: excel files include RPKM values for each sample

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
Treated CD34+ and U937 cells were washed with PBS, then total RNA was extracted with the RNeasy mini plus kit from Qiagen.
5μg of RNA was subjected to ribosomal and mitochondrial RNA depletion using the RiboZero Gold kit (Human/Mouse/Rat, Epicentre #MRZG12324) according to manufacturer's instructions. The ribo-zero treated RNA was used to create multiplexed RNA-Seq libraries using the NEBNext Ultra RNA Library Prep Kit (Illumina E7530) according to the manufacturer’s instructions. Briefly 500pg of ribozero treated RNA was fragmented and used to produce cDNA libraries using the NEBnext Ultra RNA library prep kit (NEB, E7530S) according to the manufacturer’s protocol. Purified double-stranded cDNA underwent end-repair and dA-tailing reactions following manufacturer’s reagents and reaction conditions. The obtained DNAs were used for Adaptor Ligation using adaptors and enzymes provided in NEBNext Multiplex Oligos for Illumina (NEB #E7335) and following recommended reaction conditions. Eluted DNA was enriched with PCR reaction using Fusion High-Fidelity PCR Master Mix kit (NEB, M0531S) and specific index primers supplied in NEBNext Multiplex Oligo Kit for Illumina (Index Primer Set 1, NEB, E7335L). Conditions for PCR used are as follows: 98°C, 30 sec; [98°C, 10 sec; 65°C, 30 sec; 72°C, 30 sec] X 15 cycles; 72°C, 5 min; hold at 4°C. PCR reaction mix was purified using Agencourt AMPure XP beads (1X of reaction volume). Libraries were eluted in 20μl elution buffer. All the libraries went through quality control analysis using an Agilent Bioanalyzer and subjected to next-generation sequencing using Illumina Hiseq 2500 platform.

tag: tag

value: mobilised peripheral blood CD34+ cells


title: RISP_KO_treatment_PLX3397 Repopulation_ageGroup_Adult_01


title: Epac1fl/fl_PBS_2


title: sample2_3_ICH_12h

last: Li


title: RISP_Het_treatment_PLX3397 Repopulation_ageGroup_Adult_04

value: RISP Het


title: RNA_DMSO1


title: sample2_2_ICH_12h


title: sample2_1_ICH_12h


title: Epac1fl/fl_PBS_1

value: PBS


title: RISP_Het_treatment_PLX3397 Repopulation_ageGroup_Adult_03


title: T3_STR

city: 郑州市

first: 凯欣

last: 李

state: 河南省

address: 郑州市高新区金梭路

institute: CTQTC

data_processing:
Dr.tom platform for data analysis (https://biosys.bgi.com/#/report/login)
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Six brain regions of adult C57 mice at 6-7 weeks were extracted from PFc, VTA, Nac, STR, SN and HP
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

value: brain

tag: brain region

value: STR

value: KI


title: sample1_3_ICH_2h


title: CD34plusPGE2_2h_No72


title: T2_STR


title: sample1_2_ICH_3h


title: CD34plusDMSO_2h_No99


title: RISP_Het_treatment_PLX3397 Repopulation_ageGroup_Adult_02


title: RISP_Het_treatment_PLX3397 Repopulation_ageGroup_Adult_01


title: T1_STR


title: CD34plusDMSO_2h_No72


title: RISP_WT_treatment_PLX3397 Depletion_ageGroup_Adult_04

value: RISP WT

value: PLX3397 Depletion


title: sample1_1_ICH_2h

value: immune cell

value: microglia, neutrophil


title: T2_VTA

value: VTA


title: T3_VTA


title: CD34plusDMSO_2h_No20170829


title: PLC/PRF/5 cells, CircUCK2-SiRNA_3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2 2 . FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: hg38/GRCh38
Supplementary files format and content: Xlsx file includes FPKM for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, Chi


title: CD34plus-PGE2_2h


title: RISP_WT_treatment_PLX3397 Depletion_ageGroup_Adult_02

value: Brain


title: CD34plus-DMSO_2h


title: RISP_WT_treatment_PLX3397 Depletion_ageGroup_Adult_03


title: T1_VTA


title: PLC/PRF/5 cells, CircUCK2-SiRNA_1


title: CD34plusPGE2_2h_No20170829


title: RISP_KO_treatment_PLX3397 Depletion_ageGroup_Adult_02

value: RISP KO


title: PLC/PRF/5 cells, NC_SiRNA_3


title: T3_SN

value: SN


title: AS1


title: T2_SN


title: AS2


title: RISP_KO_treatment_PLX3397 Depletion_ageGroup_Adult_01

value: Microglia


title: PLC/PRF/5 cells, NC_SiRNA_2