title: C1q_treated_lung

city: Noda

first: Tatsuro

last: Ogawa

address: 2641, Yamasaki

country: Japan

institute: Tokyo University of Science

data_processing:
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) were processed as follows. Adapter trimming of sequencing data was performed using cutadapt 2.10. Filtered reads were chunked into 16 parts for parallel processing by using Seqkit 0.14.0. Filtered cell barcode reads were annotated by Python script provided by BD Biosciences with minor modification for compatibility to Python 3.7. Reference RNA sequences were built by concatenating cDNA and ncRNA fasta files of the Ensembl database (build GRCm38 release-101). Associated cDNA reads were mapped to reference RNA using bowtie2-2.4.2 by the following parameters: -p 2 --very-sensitive-local -N 1 -norc -seed 656565 -reorder. Then, cell barcode information of each read was added to the bowtie2-mapped BAM files by the python script and pysam 0.15.4 (https://github.com/pysam-developers/pysam), and read counts of each gene in each cell barcode were counted using mawk. Resultant count data was converted to a single-cell gene-expression matrix file by using R-3.6.3. The inflection point of the knee-plot (total read count versus the rank of the read count) was detected using DropletUtils package in R-3.6.3. Cells of which total read count was over inflection point were considered as valid cells.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw tag-count values for each sample

source_name: lung

extract_protocol:
Murine lungs were isolated from C1q-administrated WT mice. Lungs were minced into 0.5 mm2 with a razor blade and digested with Liberase solution [RPMI-1640 (Nacalai Tesque) supplemented with 10% FBS (MP Bio Japan), 10 mM HEPES pH7.2-7.4 (Cytiva (Global Life Sciences Technologies Japan)), 0.25 mg/ml Liberase TM (Roche), and 2 kU/mL DNase I (Merck)] at 37 ºC for 60 minutes. Cell suspensions were washed and resuspended with 25% Percoll PLUS (Cytiva). After under layered 65% Percoll PLUS, cell suspensions were centrifuged at 20ºC for 1,000 ×g for 20 minutes, and the middle layer was collected. Resultant cell suspensions were washed and resuspended with 1000 μL of preparation medium [RPMI-1640 supplemented with 5% FBS and 10 mM HEPES]. Each single-cell suspension cell concentration was counted using Flow-count fluorospheres (Beckman Coulter) and a Gallios flow cytometer (Beckman Coulter).Cells were stained with 2.5 μg/ml of Totalseq anti-mouse Hashtag-A antibodies (BioLegend) at 4ºC for 30 minutes and washed thrice with Cell Staining Buffer (BioLegend) and pooled.
Pooled single-cell suspensions were subjected to a BD Rhapsody system with BD Rhapsody Targeted & Abseq Reagent kit (BD Biosciences) following the manufacture’s instructions. 20000 cells were subjected to the BD Rhapsody workflow. After reverse transcription, Exonuclease I treatment of the resultant BD Rhapsody beads was performed at 37ºC for 60 minutes with 1,200 rpm on a Thermomixer C with Thermotop. Resultant beads were immediately chilled on ice; the supernatant was removed and washed with 1 mL of WTA wash buffer [10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM EDTA, and 0.05% Tween-20], 200 μL of BD Rhapsody lysis buffer (for inactivation of enzyme), once with 1 ml of WTA wash buffer, twice with 500 μL of WTA wash buffer, resuspended with 200 μL of Beads resuspension buffer. During the washing step, beads-containing DNA LoBind tubes (Eppendorf Japan) were replaced twice. Exonuclease I-treated BD Rhapsody beads were subjected to TAS- Seq workflow for cDNA and/or hashtag library amplification (Shichino S., bioRxiv, 2021). 150 ng of amplified cDNA libraries was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina. Ligated products were purified by AmPure XP beads and 9 cycles of Barcoding PCR were performed. Resultant products were purified twice by double size selection with 0.5× → 0.3× (final 0.8×) AmPure XP beads and eluted with 30 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system with appropriate dilutions. Resultant libraries and barcoded hashtag libraries were quantified using the KAPA Library Quantification Kit. Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer.

treatment_protocol: WT mice were intratracheally administered with C1q (20 µg/mouse) and harvested lungs at day 0, 1, and 3.

value: WT

value: lung

tag: date

value: Day 0, 1, and 3


title: APP1-2_hippo_CD11c_pos_11_2_S11

status: Public on Mar 31 2024

type: SRA

city: Groningen

first: Takuya

last: Oshima

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences of Cells & Systems

country: Netherlands

institute: University Medical Center Groningen

library_source: transcriptomic single cell

data_processing:
Raw reads were demultiplexed with UMI-tools (v0.5.3).
A cell barcode whitelist with the known barcodes was used to filter the reads.
Reads were aligned with HISAT2 (v2.1.0) to the Ensembl genome Mus musculus (GRCm38, mm10) using default parameters.
Quantification was done with featureCounts (v1.6.0) using the flag -primary.
The unique molecules per gene and per cell were quantified using the UMI-tools function count.
Assembly: mouse GRCm38 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Microglia were isolated using a mechanical protocol with a Tissue Grinder Potter-Elvehjem at 4°C as previously described (Galatro et al., 2017). Microglia were sorted by gating the DAPIneg DRAQ5pos CD11bhigh CD45int CD11cneg/pos cells with FACS. Microglia were collected in 384-well PCR plates containing cell lysis buffer.
Sequencing libraries were generated based on the Smart-seq2 protocol as previously described (Alsema et al., 2020).
DNA sequencing was performed using a Illumina NextSeq 500 system at a final concentration of 2 pM with a 7% spike in PhiX DNA.

tag: tissue

value: brain

tag: Sex

value: male

tag: age

value: 6 month old

tag: genotype

value: wt

tag: region

value: hippocampus

tag: cell type

value: microglia

value: positive


title: 24272-normal-tissue

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
fastq files were generated with bcl2fastq(v2.0)
Sequence reads were trimmed for adaptor sequence and low-quality sequence(Q30) and mapped to GRCh38/hg38 (parameters- --outFilterMismatchNoverReadLmax 0.04,) with STAR v2.7
featureCounts was used to summerize raw counts(subread v1.6)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Homo sapiens

source_name: breast

extract_protocol:
RNA was harvested using RNeasy midi Kit(Qiagen).
RNA libraries for mRNA-seq were prepared using QIAseq Stranded mRNA Select Kit and QIAseq Stranded RNA Library Kit

value: breast

value: normal

tag: er

tag: pr

tag: treatment type

tag: menopause status


title: mouse_C1qvivo_7

data_processing:
Adapter trimming and quality filtering of sequencing data were performed using cutadapt v2.1.0. Filtered reads were mapped to GRCm38 Refseq RNA using Bowtie2-2.4.2 with the following parameters: -p 2 -L 16 --very-sensitive-local -N 1 -nofw -seed 656565 -reorder. Tag numbers of each gene were quantified as the expression level of each gene.
Between-sample normalization was performed against raw count data using Microsoft R open 3.5.1 (https://cran.r-project.org/) and TCC package (EEE-E method). Genes for which adjusted P < 0.05, fold change ≥ 2, and maximum expression ≥ 100 were identified as statistically significant differentially expressed genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw tag-count values for each sample

extract_protocol:
Lungs were isolated from control or C1q-administrated mice and minced into 0.5 mm2 with a razor blade and digested with Liberase solution [RPMI-1640 (Nacalai Tesque) supplemented with 10% FBS (MP Bio Japan, Tokyo, Japan), 10 mM HEPES pH7.2-7.4 (Cytiva (Global Life Sciences Technologies Japan)), 0.25 mg/ml Liberase TM (Roche), and 2 kU/mL DNase I (Merck)] at 37 ºC for 60 minutes. Cell suspensions were washed and resuspended with 25% Percoll PLUS (Cytiva). After under layered 65% Percoll PLUS, cell suspensions were centrifuged at 20ºC for 1,000 ×g for 20 minutes, and the middle layer was collected. Resultant cell suspensions were washed and resuspended with 1000 μL of preparation medium [RPMI-1640 supplemented with 5% FBS and 10 mM HEPES].
Transcriptome libraries were prepared on cell lysate resolved in lysis buffer. PolyA RNAs were isolated using Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) conjugated with biotin-3’ WTA-EcoP-dT25 according to the previous report with some modifications (GSE110711). To perform reverse transcription, beads were then suspended in 10 μL of RT mix [5× Superscript IV buffer (Thermo Fisher Scientific), 1 mM dNTP (Roche), 5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma), 6 mM MgCl2, 1 U/μL RNaseIn Plus Rnase Inhibitor (Promega), 10 U/μL Superscript IV (Thermo Fisher Scientific)], and incubated for 5 min at 35ºC, 30 min at 42ºC, and immediately cooled on ice. Beads were washed once with B&W-T buffer [5 mM Tris-HCl (pH 8.0) (Nippon Gene), 1 M NaCl (Merck), 1 mM EDTA (Nippon Gene) and 0.05% Tween-20 (Merck)], and once with Tris-HCl (pH 8.0). To digest free-primer, beads were then suspended in 10 μL of Exo I mix [10× Exo I buffer (New England Biolabs), 2 U/μL Exonuclease I (New England Biolabs)], and incubated for 30 min at 37ºC and immediately cooled on ice. Beads were washed twice with B&W-T buffer, and once with Tris-HCl (pH 8.0). To add polyC tail, beads were then suspended in 10 μL of polyC tailing mix [10× Thermopol buffer (New England Biolabs), 2 mM dCTP (Roche), 0.1 mM ddCTP (GE Healthcare), 1 mM CoCl2 (Roche), RNaseH (Invitrogen), 15 U/ul TdT enzyme (Roche)], and incubated for 30 min at 37ºC and immediately cooled on ice. Beads were washed once with B&W-T buffer, and once with Tris-HCl (pH 8.0). To synthesis 2nd strand, beads were then suspended in 10 μL of 2nd strand mix [1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems), 0.4 μM of primer (illumina-i7-9G)], and the thermal cycling was performed as following condition: for 3 min at 95°C, 20 sec at 98°C, 16 cycles of 1 min at 47°C and 2 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. To amplify the total cDNA, 10 μL of beads containing cDNA was added with 15 μL of first PCR mix [0.32 μM of primer (illumina-i7), 0.48 μM of primer (NH2-3’ WTA), and 1x KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed as following condition: for 3 min at 95°C, 12 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The first PCR products were purified by AmPure XP beads (Beckman-Coulter) at a 0.6:1 ratio of reagents to sample and eluted with 25 μL of nuclease-free water. 6.3uL of purified first PCR product was mixed with the 8.7 μL of second PCR mix [0.4 μM of primers (illumina-i7, NH2-3’ WTA), and 1× KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed as following condition: for 3 min at 95°C, 5 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The second PCR products were purified by AmPure XP beads at a 0.6:1 ratio of reagent to sample and eluted with 15 μL of 10 mM Tris-HCl (pH 8.0). 100 ng of the whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) with some modifications. The thermal cycling was performed as following condition: for 7 min at 32ºC, 30 min at 65ºC, and hold at 4ºC. Then, 1.25 μL of 1.5 μM illumine adapter was used for adapter ligation. Ligated products were purified by double size selection with 0.4× → 0.7× (final 1.1×) AmPure XP beads and eluted with 10 μL of nuclease-free water. The barcoding PCR was performed with 22.5 uL of barcoding mix [7.5 μL of the resulted eluates, 1 μM primers (ILMN_[UDI]_i5 and ILMN_[UDI]_i7), and 1× NEBNext Ultra II Q5 (New England Biolabs)], and the thermal cycling was performed as following condition: for 30 sec at 98°C, 9 cycles of 10 sec at 98°C and 75 sec at 65°C, followed by 5 min at 65°C, and hold at 4°C. Resultant products were purified twice by double size selection with 0.5× → 0.8 × (final 1.3×) AmPure XP beads and eluted with 12 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system (Shimazu) with appropriate dilutions. Final transcriptome libraries, whose lengths were around 300 base pairs, were quantified using the KAPA Library Quantification Kit (KAPA Biosystems). Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer (Illumina).

treatment_protocol: WT mice were intratracheally administered with C1q (20 µg/mouse) and lungs were harvested at day 3.

tag: strain

tag: treatment

value: C1q (20 ug/mouse)

value: Day 3


title: APP1-2_hippo_CD11c_pos_11_1_S11


title: mouse_C1qvivo_6


title: mouse_C1qvivo_5


title: 24246-tumor-tissue

value: tumor


title: KO_Day7_ORY_rep2

city: philadelphia

first: Ting

last: Zhao

address: 415 curie blvd

institute: University of Pennsylvannia

data_processing:
Raw sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina).
Adaptors were trimmed using Trimmomatic v0.32 software
Trimmed sequence reads were mapped to mouse reference genome GRCm38 using STAR v2.5.2a
Only uniquely mapped reads were quantified at the gene level and summarized to gene counts using STAR-quantMode (GeneCounts), with multimapping and chimeric alignments discarded.
Assembly: GRCm38
Supplementary files format and content: excel file including raw count of all genes for all the samples

source_name: dentate gyrus

growth_protocol: Adult NSCs were derived from the dentate gyrus of 7~8-week-old Hopx-CreERT2::Setd1afl/fl::H2B-GFP mice and cultured in the proliferation medium containing Neurobasal medium, 20 ng/ml FGF2, 20 ng/ml EGF, 2% B27, Glutamax, and  Penicillin/Streptomycin, on culture dishes precoated with poly-D-lysine.

extract_protocol:
RNA was extracted using TRIZOL (Invitrogen) and the kit of Zymo RNA Clean & Concentrator™-5. 300ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared based on SMART-seq2 method.

treatment_protocol: To induce quiescence, cells were plated into the proliferation medium at a density of 35,000-65,000 cells/cm2, and, after 16 h, fresh quiescence medium was added without EGF and with 20 ng/ml BMP4 and 20 ng/ml FGF2. Quiescent NPC cultures were infected with lentivirus expressing GFP (WT) or Cre-GFP (Setd1a KO). WT and Setd1a KO cultures were treated with DMSO (control) or ORY-1001.

value: dentate gyrus

value: Neural progenitor cells (NPCs)

value: KO

tag: time

value: Day 7

value: BMP4/FGF2; Lenti-Cre-GFP; ORY-1001


title: Control3

city: Hyderabad

first: Lava

middle: Kumar

last: Surarapu

state: Telangana

address: NIAB, Gowlidoddi, Gachiboli, Hyderabad, Telangana

country: India

institute: National Institute of Animal Biotechnology

data_processing:
FastQC (v0.11.9) was used to analyze the raw reads base quality and adapter content. Fastp (v0.12.4) was used to trim the adapter and low-quality bases
After trimming, reads were aligned to total transcripts of Mus musculus (GRCm39, Ensemble release 106 - Apr 2022) using Salmon (v0.12.0)
Transcript levels were imported into gene-level counts using Tximport (v1.22.0), and differential gene expression was done using DESeq2 (v1.34.0)
DE genes were used for Gene Ontology and KEGG enrichment using the R package cluster profile (v4.4.2) and plotted using enrichplot (v1.14.2)
Assembly: total transcripts of Mus musculus (GRCm39, Ensembl release 106 - Apr 2022)

source_name: Testes

extract_protocol:
Whole testes RNA was isolated using the TRIZOL method (Invitrogen) and purified using a Nucleospin Purification kit (Quiagen)
llumina RNA library preparation kit; NovaSeq6000 S4 reagent kitVl.5

value: Testes

value: Control


title: Control2


title: KO_Day7_ORY_rep1


title: KO_Day7_DMSO_rep4

value: BMP4/FGF2; Lenti-Cre-GFP; DMSO


title: lesional skin2 CAGE [Fads_Ix17.1R]

city: Saga

first: Satoshi

last: Nunomura

address: 5-1-1 Nabeshima

department: Department of Biomolecular Sciences

institute: Saga Medical School

data_processing:
Illumina RTA (Real Time Analysis) software was used for basecalling.
Sequenced reads were mapped to mm9 whole genome using BWA without changing any parameters.
Unmapped reads are then mapped to mm9 whole genome using HiSAT2 with the parameters set as defualt,   to map the reads that covers at least a part of exon2 as well as exon1.
Assembly: mm9
Supplementary files format and content: A tab-delimited text file includes RPKM values for all samples

source_name: skin

extract_protocol:
Total RNA was isolated using RNeasy Mini kit (#74104, Qiagen, Hilden, Germany). Quality of total RNA was assessed by Agilent bioanalyzer to ensure that RNA integrity number is over 7.0, and A260/280 and A260/230 ratios are over 1.8.
Five micrograms of total RNAs were used for synthesis of the cDNA   using a Library Preparation kit (DNAFORM, Japan)

value: post natal day 28

value: skin


title: 24217-tumor-tissue


title: lesional skin1 CAGE [Fads_Ix17.1L]


title: mouse_C1qvivo_2

value: WT

value: lung

value: Saline


title: KO_Day7_ORY_rep4


title: 24217-normal-tissue

value: breast

value: normal


title: KO_Day7_DMSO_rep3


title: KO_Day7_ORY_rep3


title: lesional skin4 CAGE [Fads_Ix17.2R]


title: 24106-tumor-tissue

value: Positive

value: Negative

value: No

value: Post


title: E4BP4 Transgenic

city: Ube

first: Akihiko

last: Taguchi

state: Yamaguchi

address: 1-1-1 minamikogushi

institute: Yamaguchi University

description:
TG_genematrix
ColonCD45singleCell

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline v5.0.0(0x Genomics) to generate FASTQ files and aligned to mm10 genome to gene expression count.
The data analysis was perfomed using Seurat software version 4.0
Genome_build: mm10

source_name: CD45+ cells in colon lamina propria

growth_protocol: Chow: normal diet and randomly fed, temprature: 22℃±1℃, Light-dark cycle: 12-hour light and 12-hour dark (lights on at AM8 and lights off at PM8)

extract_protocol:
Single cell suspensions from colonic lamina propria were prepared, and Live CD45+ cells were isolated using a FACSAria III Cell Sorter (BD Biosciences).  Approximately 10,000 single cells were loaded and treated using a Chromium Controller and Chromium Next GEM Single Cell 5’ Gel Bead Kit v1.1 (10x Genomics).
Sequencing libraries were generated using Next GEM Single Cell 5’ Library Kit v1.1 (10x Genomics) according to manufacturer's instructions.

treatment_protocol: Colitis was induced by adding DSS (MW 36,000–50,000, MP Biomedicals) to the drinking water for 7 days, followed by a 7-day recovery period with the drinking water without DSS and then sacrifice on day14. DSS water was prepared to a concentration of 2.0% in filtered drinking water.

value: E4BP4 Transgenic

tag: gating strategy

value: Live CD45+


title: KO_Day7_DMSO_rep2

value: dentate gyrus

value: Neural progenitor cells (NPCs)

value: KO

value: Day 7


title: mouse_C1qvivo_1

value: Day 3


title: Wild Type

description:
WT_genematrix
ColonCD45singleCell

value: Wild Type


title: MIR100HG knocking down A549 cells 3

city: Deyang

first: Hao

last: Zhang

state: Sichuan

address: No. 173 Taishan North Road

department: Department of Reproductive and Genetic Diseases

country: China

institute: Deyang People’s Hospital

data_processing:
Adapter sequences were removed from the original sequencing data and low-quality sequences were filtered
Clean data were aligned to reference genome by Hisat 2 software and transcripts were assembled by Stringtie software.
DEseq2 and EdgeR analysis were used to screen out differentially expressed genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: A549 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/ml streptomycin and 100 U/ml penicillin and incubated in 5% CO2 incubator at 37°C.

extract_protocol:
Total RNA was extracted from A549 cells using TRNzol Universal total RNA extraction kit.
The library was constructed using Tn5 DNA Library Prep Kit for Illumina according to manufacturers’ instructions.

treatment_protocol: A549 cells were transiently transfected with ASO-h-MIR100HG_003 or ASO Negative Control #1.

tag: cell line

value: lung cancer

value: MIR100HG knocking down


title: 24246-normal-tissue


title: mouse_C1qvitro_47

source_name: lung fibroblast

growth_protocol: Isolated fibroblasts from lungs were cultured in a 10-cm culture dish in DMEM supplemented with 10% FBS and 10 mM HEPES for 12 hours. Nonadherent cells were removed from the culture. Fibroblasts were passaged to a 24 well-plate and cultured in DMEM supplemented with 10% FBS and 10 mM HEPES.

extract_protocol:
Murine lungs were isolated from WT mouse. Lungs were minced into 0.5 mm2 with a razor blade and digested with Liberase solution [RPMI-1640 (Nacalai Tesque) supplemented with 10% FBS (MP Bio Japan, Tokyo, Japan), 10 mM HEPES pH7.2-7.4 (Cytiva (Global Life Sciences Technologies Japan)), 0.25 mg/ml Liberase TM (Roche), and 2 kU/mL DNase I (Merck)] at 37 ºC for 60 minutes. Cell suspensions were washed and resuspended with 25% Percoll PLUS (Cytiva). After under layered 65% Percoll PLUS, cell suspensions were centrifuged at 20ºC for 1,000 ×g for 20 minutes, and the middle layer was collected. Resultant cell suspensions were then depleted of lineage+ (CD31+, CD45+, EpCAM+, CD146+ and Ter119+) cells by negative selection with an AutoMACS cell separator (Miltenyi Biotech).
Transcriptome libraries were prepared on cell lysate resolved in lysis buffer. PolyA RNAs were isolated using Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) conjugated with biotin-3’ WTA-EcoP-dT25 according to the previous report with some modifications (GSE110711). To perform reverse transcription, beads were then suspended in 10 μL of RT mix [5× Superscript IV buffer (Thermo Fisher Scientific), 1 mM dNTP (Roche), 5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma), 6 mM MgCl2, 1 U/μL RNaseIn Plus Rnase Inhibitor (Promega), 10 U/μL Superscript IV (Thermo Fisher Scientific)], and incubated for 5 min at 35ºC, 30 min at 42ºC, and immediately cooled on ice. Beads were washed once with B&W-T buffer [5 mM Tris-HCl (pH 8.0) (Nippon Gene), 1 M NaCl (Merck), 1 mM EDTA (Nippon Gene) and 0.05% Tween-20 (Merck)], and once with Tris-HCl (pH 8.0). To digest free-primer, beads were then suspended in 10 μL of Exo I mix [10× Exo I buffer (New England Biolabs), 2 U/μL Exonuclease I (New England Biolabs)], and incubated for 30 min at 37ºC and immediately cooled on ice. Beads were washed twice with B&W-T buffer, and once with Tris-HCl (pH 8.0). To add polyC tail, beads were then suspended in 10 μL of polyC tailing mix [10× Thermopol buffer (New England Biolabs), 2 mM dCTP (Roche), 0.1 mM ddCTP (GE Healthcare), 1 mM CoCl2 (Roche), RNaseH (Invitrogen), 15 U/ul TdT enzyme (Roche)], and incubated for 30 min at 37ºC and immediately cooled on ice. Beads were washed once with B&W-T buffer, and once with Tris-HCl (pH 8.0). To synthesis 2nd strand, beads were then suspended in 10 μL of 2nd strand mix [1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington), 0.4 μM of primer (illumina-i7-9G)], and the thermal cycling was performed as following condition: for 3 min at 95°C, 20 sec at 98°C, 16 cycles of 1 min at 47°C and 2 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. To amplify the total cDNA, 10 μL of beads containing cDNA was added with 15 μL of first PCR mix [0.32 μM of primer (illumina-i7), 0.48 μM of primer (NH2-3’ WTA), and 1x KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed as following condition: for 3 min at 95°C, 12 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The first PCR products were purified by AmPure XP beads (Beckman-Coulter) at a 0.6:1 ratio of reagents to sample and eluted with 25 μL of nuclease-free water. 6.3uL of purified first PCR product was mixed with the 8.7 μL of second PCR mix [0.4 μM of primers (illumina-i7, NH2-3’ WTA), and 1× KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed as following condition: for 3 min at 95°C, 5 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The second PCR products were purified by AmPure XP beads at a 0.6:1 ratio of reagent to sample and eluted with 15 μL of 10 mM Tris-HCl (pH 8.0). 100 ng of the whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) with some modifications. The thermal cycling was performed as following condition: for 7 min at 32ºC, 30 min at 65ºC, and hold at 4ºC. Then, 1.25 μL of 1.5 μM illumine adapter was used for adapter ligation. Ligated products were purified by double size selection with 0.4× → 0.7× (final 1.1×) AmPure XP beads and eluted with 10 μL of nuclease-free water. The barcoding PCR was performed with 22.5 uL of barcoding mix [7.5 μL of the resulted eluates, 1 μM primers (ILMN_[UDI]_i5 and ILMN_[UDI]_i7), and 1× NEBNext Ultra II Q5 (New England Biolabs)], and the thermal cycling was performed as following condition: for 30 sec at 98°C, 9 cycles of 10 sec at 98°C and 75 sec at 65°C, followed by 5 min at 65°C, and hold at 4°C. Resultant products were purified twice by double size selection with 0.5× → 0.8 × (final 1.3×) AmPure XP beads and eluted with 12 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system (Shimazu) with appropriate dilutions. Final transcriptome libraries, whose lengths were around 300 base pairs, were quantified using the KAPA Library Quantification Kit (KAPA Biosystems). Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer (Illumina).

treatment_protocol: Cultured fibroblasts in 24 well-plate were serum starved for 24h and treated with C1q (1, 10, and 100 µg/ml) for 2, 24, 48, and 72h.

value: WT

value: lung

value: lineage (CD45, CD31, EpCAM, CD146 and Ter119) negative fibroblast


title: KO_Day7_DMSO_rep1

value: BMP4/FGF2; Lenti-Cre-GFP; DMSO


title: 24094-tumor-tissue

value: breast

value: tumor

value: Positive

value: Negative

value: Pre


title: mouse_C1qvitro_46


title: MIR100HG knocking down A549 cells 2


title: WT_Day7_ORY_rep4

value: dentate gyrus

value: BMP4/FGF2; Lenti-GFP; ORY-1001


title: mouse_C1qvivo_3

value: Saline


title: WT_Day7_ORY_rep3

value: Neural progenitor cells (NPCs)

value: Day 7


title: lesional skin3 CAGE [Fads_Ix17.2L]

value: post natal day 28

value: skin


title: 24094-normal-tissue

value: normal

value: No


title: MIR100HG knocking down A549 cells 1

value: lung

value: lung cancer

value: MIR100HG knocking down


title: mouse_C1qvitro_48

value: WT

value: lineage (CD45, CD31, EpCAM, CD146 and Ter119) negative fibroblast


title: 24106-normal-tissue

value: breast

value: Positive

value: Post


title: WT_Day7_ORY_rep2

value: dentate gyrus


title: mouse_C1qvitro_43

value: C1q (10 ug/ml)


title: negative control A549 cells 2

value: negative control


title: 23974-tumor-tissue

value: tumor


title: negative control A549 cells 3


title: WT_Day7_DMSO_rep4

value: Neural progenitor cells (NPCs)

value: Day 7

value: BMP4/FGF2; Lenti-GFP; DMSO


title: WT_Day7_ORY_rep1

value: BMP4/FGF2; Lenti-GFP; ORY-1001


title: 19185-tumor-tissue


title: 23974-normal-tissue

value: normal


title: WT_Day7_DMSO_rep3


title: mouse_C1qvitro_42

value: lung

value: C1q (1 ug/ml)


title: 23147-tumor-tissue


title: 23147-normal-tissue


title: negative control A549 cells 1

value: lung cancer


title: mouse_C1qvitro_36

value: WT


title: WT_Day7_DMSO_rep2


title: mouse_C1qvitro_40

value: lineage (CD45, CD31, EpCAM, CD146 and Ter119) negative fibroblast


title: mouse_C1qvitro_41


title: 19185-normal-tissue

value: breast


title: WT_Day7_DMSO_rep1


title: mouse_C1qvitro_45


title: mouse_C1qvitro_44


title: 19177-tumor-tissue


title: 19177-normal-tissue


title: MIR,passage 18, rep 3

city: Seoul

first: Tak-il

last: Jeon

address: 120 Neungdong-ro

department: Department of Stem Cell and Regenerative Biotechnology

country: South Korea

institute: Konkuk University

data_processing:
Adapter and low quality reads (<Q20) were removed using FASTX_Trimmer and BBMap.
n the trimmed reads were mapped to the reference genome using TopHat.
Gene expression levels were estimated using FPKM values by Cufflinks.
Assembly: hg19
Supplementary files format and content: The FPKM values were normalized based on Quantile normalization method using EdgeR within R.

source_name: mesenchymal stem cells

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen).
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit (NEW ENGLAND BioLabs, Inc., UK).

value: mesenchymal stem cells

value: MiR


title: WT_Day9_rep4

value: dentate gyrus

value: Day 9

value: BMP4/FGF2; Lenti-GFP


title: mouse_C1qvitro_35


title: WT_Day9_rep3


title: WT_Day9_rep2


title: mouse_C1qvitro_34


title: mouse_C1qvitro_33

value: C1q (10 ug/ml)


title: WT_Day9_rep1

value: Neural progenitor cells (NPCs)


title: mouse_C1qvitro_32


title: MIR,passage 18, rep 2


title: MIR,passage 18, rep 1


title: mouse_C1qvitro_31


title: KO_Day9_rep4

value: KO

value: BMP4/FGF2; Lenti-Cre-GFP


title: Control,passage 18, rep 3

value: Con


title: KO_Day9_rep3


title: Control,passage 18, rep 2


title: mouse_C1qvitro_30


title: KO_Day9_rep2


title: Rat alveolar macrophages, 24hr, Control for LPS, replicate 4

type: RNA

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression after 24hr in rat alveolar macrophages as vehicle cotrol

hyb_protocol: Each labeled cRNA probe was used separately for hybridization to a 4×44 K Whole Rat Genome Microarray (G2519F#14879; Agilent Technologies) at 65 °C for 17 h.

scan_protocol: Hybridized microarray slides were washed according to the manufacturer’s instructions and scanned with a DNA Microarray Scanner (Agilent) at 5 μm resolution.

data_processing: The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 12.0.3.1.

organism: Rattus norvegicus

label_protocol: Cyanine-3-labeled cRNA was prepared from RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 spectrophotometer.

growth_protocol: Rat alveolar macrophage cells (NR8383) obtained the American Type Culture Collection were cultured at 37 °C in 75-cm2 cell culture flasks in F-12K with 10 % (v/v) heat-inactivated fetal bovine serum (FBS) in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit (Qiagen, Japan) following the manufacturer’s instructions. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., US), and sample qualities were monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies, US).

treatment_protocol: The F-12K + FBS medium was removed by centrifugation, and cell cultures were then treated with working solutions of six types of CNFs (CNF1, CNF2, CNF3, CNF4, CNF5, or CNF6) and MCC. These cultures were subsequently seeded into individual wells of a 6-well plate and incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2. At this point, the cell concentrations were approximately 3.0 x 10^5 cells/mL.

tag: cell

value: Rat alveolar macrophages  (NR8385)

value: Vehicle control for LPS


title: Control,passage 18, rep 1


title: mouse_C1qvitro_29

value: lung

value: C1q (1 ug/ml)


title: KO_Day9_rep1


title: mouse_C1qvitro_28

value: WT


title: Rat alveolar macrophages, 24hr, LPS, replicate 4

description: Gene expression after 24hr in CNF6-exposed rat alveolar macrophages

value: Rat alveolar macrophages  (NR8384)

value: LPS


title: IMR90, p400-, replicate 2, RNA-seq mutants

city: Parma

first: Giorgio

last: Dieci

address: Parco Area delle Scienze 23/A

department: Deparment of Life Sciences

country: Italy

institute: University of Parma

data_processing:
Libraries were sequenced using Illumina HiSeq 4000 (dl1500, mock, dl312) or Illumina NovaSeq (dl1500_mut, mock_mut, RB-_mut, p300-_mut, p400-_mut) to obtain 100 or 150 bp-long reads, respectively.
RNA-seq reads were aligned to the GRCh38 human reference genome using STAR. Only uniquely mapped reads were considered for downstream analyses and subjected to counting with the featureCounts tool of the SubRead Python package.
Alus identified by the pipeline were subsequently filtered for an expression coverage of at least 1000 nt, corresponding to 5 paired-end reads of length 100 nt. The union of these Alus from all the samples in the experiment, considered only once, constitute the single, comprehensive list of expression-positive Alus. To be considered as expressed in a sample, each of the Alus in the comprehensive list needs to have more than 0 read counts in it.
Differentially expressed Alu sequences were identified using the DESeq2 package. Alu sequences with a log2 fold-change ≥ 0.5 or ≤ -0.5 and an adjusted p-value < 0.05 were deemed as differentially expressed.
Assembly: hg38
Assembly: AC_000008.1 (Human adenovirus 5)
Supplementary files format and content: bigWig (samples *.CM.bw are mapped to the hg38 human genome, whereas samples *_CPM.bw are mapped to the AC_000008.1 Adenovirus5 genome)

source_name: Lung

growth_protocol: IMR90 primary human fetal lung fibroblasts were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin at 37ºC in 5% CO2.

extract_protocol:
24 hours post-infection, cells were lysed with Trizol and total RNA was extracted using the Direct-zol RNA MiniPrep Plus (Zymo research). Eluted RNA was treated with DNase (Invitrogen).
Total RNA (1 μg) from dl1500, dl312 and mock infections was processed using a Ribo-Zero rRNA Removal Kit (Epicentre) to remove rRNA. Total RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA library Preparation kit. For the Adenovirus5 mutants experiment, total RNA (1 μg) from wt e1a (dl1500), e1a_RB-b-, e1a_p300-b-, e1a_p400-b- and mock infections was processed using the RiboCop rRNA Depletion Kit (Lexogen), and total RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA library Preparation kit.

treatment_protocol: Low passage IMR90 lung fibroblasts were grown to confluence in 60 mm dishes and incubated two more days without changing the medium to arrest cells in G1/0. On the day of infection, the medium was collected (conditioned medium) and confluent cells were incubated with mock or with the indicated Ad5-based vectors for 1 hr in PBS. At the end of the infection, cells were washed and transferred back to conditioned medium. The infections were performed at multiplicity of infection (MOI) 40 for dl1500 and dl312, 160 MOI for e1a_RB-b-, 60 MOI for e1a_p300-b- and 6 MOI for e1a_p400-b-, in order to achieve comparable amounts of wt and mutant e1a protein expression as assayed by Western blotting.

value: Lung

value: IMR90 human primary lung fetal fibroblasts

value: Contact-inhibited IMR90

value: p400 binding mutant-infected


title: WT_Day6_rep4

value: dentate gyrus

value: Day 6

value: BMP4/FGF2; Lenti-GFP


title: mouse_C1qvitro_24

value: lineage (CD45, CD31, EpCAM, CD146 and Ter119) negative fibroblast


title: IMR90, p400-, replicate 1, RNA-seq mutants


title: WT_Day6_rep3

value: Neural progenitor cells (NPCs)


title: mouse_C1qvitro_23


title: mouse_C1qvitro_22


title: IMR90, p300-, replicate 2, RNA-seq mutants

value: p300 binding mutant-infected


title: WT_Day6_rep2


title: IMR90, p300-, replicate 1, RNA-seq mutants


title: WT_Day6_rep1


title: mouse_C1qvitro_21

value: C1q (10 ug/ml)


title: IMR90, RB-, replicate 2, RNA-seq mutants

value: RB binding mutant-infected


title: mouse_C1qvitro_20

value: lung


title: KO_Day6_rep4

value: KO

value: BMP4/FGF2; Lenti-Cre-GFP


title: KO_Day6_rep3


title: Rat alveolar macrophages, 24hr, MCC, replicate 4

value: Rat alveolar macrophages  (NR8384)

value: MCC


title: IMR90, mock, replicate 2, RNA-seq mutants

value: Lung

value: WT

value: Mock-infected


title: KO_Day6_rep2


title: IMR90, RB-, replicate 1, RNA-seq mutants

value: IMR90 human primary lung fetal fibroblasts

value: Contact-inhibited IMR90


title: Rat alveolar macrophages, 24hr, CNF6, 4 replicates

description:
Gene expression after 24hr in CNF6-exposed rat alveolar macrophages
CF030_06

hyb_protocol: Each labeled cRNA probe was used separately for hybridization to a 4~44 K Whole Rat Genome Microarray (G2519F#14879; Agilent Technologies) at 65 ‹C for 17 h.

scan_protocol: Hybridized microarray slides were washed according to the manufacturerfs instructions and scanned with a DNA Microarray Scanner (Agilent) at 5 ƒÊm resolution.

label_protocol: Cyanine-3-labeled cRNA was prepared from RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturerfs instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 spectrophotometer.

growth_protocol: Rat alveolar macrophage cells (NR8383) obtained the American Type Culture Collection were cultured at 37 ‹C in 75-cm2 cell culture flasks in F-12K with 10 % (v/v) heat-inactivated fetal bovine serum (FBS) in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit (Qiagen, Japan) following the manufacturerfs instructions. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., US), and sample qualities were monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies, US).

treatment_protocol: F-12K + FBS medium was removed by centrifugation. Cell cultures were replaced with six kinds of the CNFs working solutions (CNF1, CNF2, CNF3, CNF4, CNF5, or CNF6), respectively. The cultures were seeded into each well of a 6-well plate and grown for 24 hours at 37 ?C in a humidified incubator with 5% CO2. Cell concentrations at this point were approximately 3.0 x 10^5 cells/mL.


title: mouse_C1qvitro_18

value: C1q (1 ug/ml)


title: Rat alveolar macrophages, 24hr, CNF1, 4 replicates

description:
Gene expression after 24hr in CNF1-exposed rat alveolar macrophages
CF030_01


title: Rat alveolar macrophages, 24hr, Control for CNF2 and CNF4, 4 replicates

description:
Gene expression after 24hr in rat alveolar macrophages as vehicle cotrol
CF030_002

value: Rat alveolar macrophages  (NR8383)

value: Vehicle control for CNF2 and CNF4


title: Rat alveolar macrophages, 24hr, CNF5, 4 replicates

description:
Gene expression after 24hr in CNF5-exposed rat alveolar macrophages
CF030_05


title: KO_Day6_rep1

value: dentate gyrus

value: Neural progenitor cells (NPCs)

value: Day 6


title: IMR90, mock, replicate 1, RNA-seq mutants


title: Rat alveolar macrophages, 24hr, CNF3, 4 replicates

description:
Gene expression after 24hr in CNF3-exposed rat alveolar macrophages
CF030_03


title: mouse_C1qvitro_17

value: lineage (CD45, CD31, EpCAM, CD146 and Ter119) negative fibroblast


title: Rat alveolar macrophages, 24hr, Control for CNF1 and CNF3, 4 replicates

description:
Gene expression after 24hr in rat alveolar macrophages as vehicle cotrol
CF030_001

value: Vehicle control for CNF1 and CNF3


title: mouse_C1qvitro_19

value: lung

value: C1q (10 ug/ml)


title: WT_Day5_rep4

value: Day 5

value: BMP4/FGF2; Lenti-GFP


title: IMR90, dl1500, replicate 2, RNA-seq mutants

value: Lung


title: mouse_C1qvitro_16

value: WT


title: Rat alveolar macrophages, 24hr, Control for MCC, replicate 4

value: Rat alveolar macrophages  (NR8384)

value: Vehicle control for MCC


title: Rat alveolar macrophages, 24hr, Control for CNF5 and CNF6, 4 replicates

description:
Gene expression after 24hr in rat alveolar macrophages as vehicle cotrol
CF030_003

value: Vehicle control for CNF5 and CNF6


title: Rat alveolar macrophages, 24hr, CNF2, 4 replicates

description:
Gene expression after 24hr in CNF2-exposed rat alveolar macrophages
CF030_02


title: WT_Day5_rep3


title: IMR90, dl1500, replicate 1, RNA-seq mutants

value: IMR90 human primary lung fetal fibroblasts

value: Contact-inhibited IMR90


title: C2C12 cells with Stat1 siRNA in GM24h, biological rep1

city: Hong Kong

first: Xianwei

last: Chen

address: Clearwater bay, Kowloon

institute: Hong Kong University of Science and Techanology

description: Gene expression data from C2C12 cells transfected with Stat1 siRNA and harvested at GM24h.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 h at 45C on Affymetrix GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: C2C12 cells were maintained in growth medium (GM) (Dulbecco’s modified Eagle’s medium supplemented with 20% fetal bovine serum, 100 Units/ml penicillin, and 100 μg/ml streptomycin) and differentiation was induced with differentiation medium (DM) (Dulbecco’s modified Eagle’s medium supplemented with 2% horse serum, 100 Units/ml penicillin, and 100 μg/ml streptomycin).

extract_protocol: Total RNA was extracted using the TRIzol Reagent (Invitrogen) following the manufacturer’s instructions.

treatment_protocol: C2C12 cells at indicated stage were harvested for total RNA extraction.

value: C2C12 cells


title: mouse_C1qvitro_12


title: Rat alveolar macrophages, 24hr, CNF4, 4 replicates

description:
Gene expression after 24hr in CNF4-exposed rat alveolar macrophages
CF030_04


title: C2C12 cells with Stat1 siRNA in DM12h, biological rep2

description: Gene expression data from C2C12 cells transfected with Stat1 siRNA and harvested at DM12h.


title: C2C12 cells with Stat1 siRNA in GM24h, biological rep2

source_name: C2C12 cells transfected with Stat1 siRNA and harvested at GM24h


title: C2C12 cells with Stat1 siRNA in DM12h, biological rep1

source_name: C2C12 cells transfected with Stat1 siRNA and harvested at DM12h


title: C2C12 cells with Jak1 siRNA in GM24h, biological rep2

description: Gene expression data from C2C12 cells transfected with Jak1 siRNA and harvested at GM24h.


title: C2C12 cells with Jak1 siRNA in GM24h, biological rep1

source_name: C2C12 cells transfected with Jak1 siRNA and harvested at GM24h


title: EDM_H12-Colon p14

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

data_processing:
Low quality sequences were trimmed or removed with Trimmomatic; STAR (version 2.6.0a) was used to align reads on reference genome (human genome hsGRCh38_94 ); The resulting transcriptome-aligned sequences were used for expression quantification by using RSEM (version 1.3.3) with “–forward-prob 0 ” option.
Genome_build: GRCm38 Ensembl 94
Supplementary_files_format_and_content: tab-delimited text files include log2(TPM) if TPM > 1 else TPM - 1 values for each Sample.

source_name: Colon

growth_protocol: Healthy and CD organoids were embedded in matrigel and cultured for 7 days using WNT, R-Spondin, Noggin conditioned media. EDMs were made by digesting organoids enzymatically and mechanically into single cells and seeded onto transwell inserts.

extract_protocol:
Cell recovery was used to extract the organoids from the matrigel domes. Organoids and EDMs were lysed with RNA lysis buffer following the manufacturer's instructions for the Zymo Research Quick-RNA MicroPrep Kit.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Organoids were allowed to proliferate for 7 days. EDMs differentiated for 48h.

tag: group

value: EDM

tag: behavior at diagnosis

value: Healthy


title: WT_Day5_rep2

tag: tissue

value: dentate gyrus

value: Neural progenitor cells (NPCs)


title: EDM_H14-Colon


title: C2C12 cells with Jak1 siRNA in DM12h, biological rep2

description: Gene expression data from C2C12 cells transfected with Jak1 siRNA and harvested at DM12h.


title: WT_Day5_rep1


title: mouse_C1qvitro_11

value: lineage (CD45, CD31, EpCAM, CD146 and Ter119) negative fibroblast


title: EDM_CD58-LC

value: penetrating


title: KO_Day5_rep4

value: KO

value: BMP4/FGF2; Lenti-Cre-GFP


title: mouse_C1qvitro_10

value: lung


title: mouse_C1qvitro_9

value: C1q (10 ug/ml)


title: EDM_CD42-R p7


title: EDM_CD32-LC p12


title: mouse_C1qvitro_8

value: WT


title: mouse_C1qvitro_7


title: mouse_C1qvitro_6

value: C1q (1 ug/ml)


title: C2C12 cells with Jak1 siRNA in DM12h, biological rep1

source_name: C2C12 cells transfected with Jak1 siRNA and harvested at DM12h


title: EDM_CD59-R

value: NSNP


title: C2C12 cells with GFP siRNA in GM24h, biological rep1

description: Gene expression data from C2C12 cells transfected with GFP siRNA and harvested at GM24h.


title: KO_Day5_rep3

value: Day 5


title: T4_Dox_Pos_Replicate1_scRNAseq

city: Utrecht

first: Peter

last: Haughton

address: Heidelberglaan 100

department: Pathology

institute: UMCU

data_processing:
Single cell RNA sequence data was de-multiplexed to FASTQ and aligned to the human reference genome (GRCh38 (hg38))
The single cell RNA-seq dataset was processed, explored and visualised using Cellenics® community instance (https://scp.biomage.net/) hosted by Biomage (https://biomage.net/). Briefly, cells with low quality reads, as determined by both high ERCC spike-in percentage and transcript number, and high mitochondrial reads (>5%) were removed, and mRNA expression data were normalized. To integrate data, “Harmony” was applied.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
HNSCC PDO matrices were digested and single cells were isolated using tyrpsin. Cells were FACS sorted into 384-well plates (Muraro et al, 2016).
Preparation of single-cell libraries was performed using the CEL-Seq2 protocol (Muraro et al. 2016; Hashimshony et al., 2016)

value: HNSCC patient derived organoid

value: Doxycyline Positive


title: C2C12 cells with GFP siRNA in GM24h, biological rep2

source_name: C2C12 cells transfected with GFP siRNA and harvested at GM24h

value: C2C12 cells


title: KO_Day4_rep4

value: Day 4


title: KO_Day5_rep2


title: C2C12 cells with GFP siRNA in DM12h, biological rep2

description: Gene expression data from C2C12 cells transfected with GFP siRNA and harvested at DM12h.


title: T4_Dox_Pos_Replicate2_scRNAseq


title: T4_Dox_Neg_Replicate2_scRNAseq

value: Doxycyline Negative


title: KO_Day4_rep3

value: dentate gyrus


title: mouse_C1qvitro_4


title: C2C12 cells with GFP siRNA in DM12h, biological rep1

source_name: C2C12 cells transfected with GFP siRNA and harvested at DM12h


title: KO_Day4_rep2

value: Neural progenitor cells (NPCs)


title: H14_S90_L003

value: ORG

value: Healthy


title: EDM_CD21-LC p11

value: EDM


title: H19_S95_L003


title: scATAC-seq for patient 2

city: Nanjing

first: zhang

last: zhang chenyang

address: 163 Xianlin Avenue

institute: Nanjing University

description: 10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: genomic DNA

extract_protocol:
scRNA-seq and scATAC-seq data generated in this study were performed on the 10× Chromium platform using single-cell 3’ V3.1 (scRNA-seq) or V1.1 (scATAC-seq) according to the manufacturer’s protocols including sample preparation, library preparation and instrument and sequencing settings. All libraries were sequenced on the NextSeq 500 platform (Illumina) with paired-end sequencing and dual indexing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: skin

tag: age

tag: Sex

value: male

value: No


title: T4_Dox_Neg_Replicate1_scRNAseq


title: KO_Day4_rep1

tag: genotype

value: KO

value: BMP4/FGF2; Lenti-Cre-GFP


title: mouse_C1qvitro_3

value: WT

value: lung

tag: cell type

value: lineage (CD45, CD31, EpCAM, CD146 and Ter119) negative fibroblast

value: untreatment


title: mouse_C1qvitro_5

value: C1q (1 ug/ml)


title: EDM_CD24-RC p10

value: Stricturing


title: KO_Day5_rep1

value: Day 5


title: scATAC-seq for patient 1

description: 10x Genomics


title: org_CD62-R p3

value: Penetrating


title: mouse_C1qvitro_2


title: WT_Day4_rep4

value: dentate gyrus

value: Neural progenitor cells (NPCs)

value: Day 4

value: BMP4/FGF2; Lenti-GFP


title: mouse_C1qvitro_1


title: org_CD58-LC p4

value: ORG


title: psoriasis skin tissue from the patient 3

description: 10x Genomics

value: skin

value: male


title: WT_Day4_rep3


title: org_CD42-R p11


title: psoriasis skin tissue from the patient 2

description: 10x Genomics

value: No


title: WT_Day4_rep2


title: psoriasis skin tissue from the patient 1

description: 10x Genomics


title: WT_Day4_rep1


title: normal skin tissue from the patient 3 A

description: 10x Genomics


title: IgG_CUTandRUN

library_source: genomic

data_processing:
Raw sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina).
Adaptors were trimmed using Trimmomatic v0.32 software
Trimeed sequence reads were uniquely  mapped to mouse reference genome mm10 using Bowtie2 v2.1.0
Low mapping quality reads were filtered by SAMtools v0.1.18
Peak calling was performed using MACS2 v2.2.8
Assembly: mm10
Supplementary files format and content: txt file including Setd1 peaks
Library strategy: CUT&RUN

extract_protocol:
Material was prepared using a CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, SKU: 14-1048) following manufactuer's protocols
Library was constructed following manufactuer's protocols (EpiCypher, SKU: 14-1048)

treatment_protocol: To induce quiescence, cells were plated into the proliferation medium at a density of 35,000-65,000 cells/cm2, and, after 16 h, fresh quiescence medium was added without EGF and with 20 ng/ml BMP4 and 20 ng/ml FGF2.

tag: antibody

value: Rabbit IgG CUT&RUN Negative Control Antibody (EpiCypher, SKU:13-0042)


title: org_CD32-LC p7

value: Penetrating; Perianal


title: Setd1a_CUTandRUN_rep2

value: Setd1a (Abcam, Ab70378)

value: WT


title: normal skin tissue from the patient 3 B

description: 10x Genomics


title: org_CD63-LC p4


title: normal skin tissue from the patient 2

description: 10x Genomics


title: normal skin tissue from the patient 1

description: 10x Genomics


title: org_CD52-R p5


title: Setd1a_CUTandRUN_rep1


title: RNA-Seq E4BP4_TG_Rep3

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the mm10 reference genome and displayed using UCSC annotated genes using STAR version 2.7.5a with default parameters.
Alingment files were transformed into "Tag Directory" using Homer version 4.11.1  “makeTagDirectory", then differantial expression alaysis (DeSeq2) was perfomed using Homer　“getDiffExpression.pl"
TPM files were created using Homer "analyzeRepeats.pl" and specifying "-count exons -tpm" .
Assembly: mm10
Supplementary files format and content: DeSeq2 analysis were performed using HOMER.
Supplementary files format and content: TPM files were generated using HOMER.

growth_protocol: RAW264.7 cells were cultured as a monolayer in 25 mM glucose Dulbecco’s modified Eagle’s medium (Sigma-Aldrich) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (FUJUFILM Wako) at 37 °C under 5% CO2. The RAW264.7 cells used in experiments were at fewer than 15 passages.

extract_protocol:
Total RNA of RAW264.7 cells was extracted using  a Quick-RNA Microprep Kit (ZYMO RESEARCH). Polyadenylated mRNA was separated from 200 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were generated using NEBNext Ultra 2 RNA LibraryPrep kit for Illumina (New England Biolabs) according to manufacturer's instructions. Library concentrations were assessed by a Bioanalyzer (Agilent) .

value: E4BP4 expressed

value: TG (E4BP4 expressed)

value: Basal condition


title: MIR,passage 7, rep 3

value: mesenchymal stem cells

value: MiR


title: org_CD50-R p6

value: Stricturing


title: MIR,passage 7, rep 2


title: org_CD24-RC p9


title: org_ CD35-LC P6

value: NSNP; Perianal


title: HepG2_siTCF7L2

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

institute: The University of Tokyo

description: Gene expression in HepG2 cells treated with TCF7L2 siRNA

hyb_protocol: 600 ng of Cy3-labeled RNA was hybridized at 65⁰C for 17 hours.

scan_protocol: The signals were detected by using the DNA microarray scanner (Agilent Technologies).

data_processing: The scanned images were extracted with Feature Extraction software (Version 10.7.3.1; Agilent Technologies) using default parameters.

source_name: HepG2 cells, TCF7L2 siRNA, rep1

label_protocol: 200 μg of total RNA were amplified and labeled using the Low Input QuickAmp Labeling kit (Agilent Technologies) according to the manufacturer’s protocols.

growth_protocol: HepG2 cells were grown in EMEM supplemented with 10% FBS (Biosera) and antibiotic/antimycotic solution (Fujifilm Wako Pure Chemical).

extract_protocol: RNA was extracted from the cells using RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: The cells were transfected with siRNAs using Lipofectamine RNAiMAX (Thermo Fisher Scientific) for 48 hours.

value: Liver

value: Hepatoblastoma

value: TCF7L2 siRNA


title: HepG2_siTCFs + siLEF1

description: Gene expression in HepG2 cells treated with TCF7, TCF7L1, TCF7L2, and LEF1 siRNAs

source_name: HepG2 cells, TCFs and LEF1 siRNAs, rep1

value: TCF7, TCF7L1, TCF7L2, and LEF1 siRNAs


title: org_CD27-R-NI p4

value: ORG


title: HepG2_siTCF7L1

description: Gene expression in HepG2 cells treated with TCF7L1 siRNA

source_name: HepG2 cells, TCF7L1 siRNA, rep1

value: TCF7L1 siRNA


title: HepG2_siTCF7

description: Gene expression in HepG2 cells treated with TCF7 siRNA

source_name: HepG2 cells, TCF7 siRNA, rep1

value: TCF7 siRNA


title: RNA-Seq E4BP4_TG_Rep1


title: HepG2_siβ-catenin-10

description: Gene expression in HepG2 cells treated with β-catenin-10 siRNA

source_name: HepG2 cells, β-catenin-10 siRNA, rep1

value: β-catenin-10 siRNA


title: HepG2_siβ-catenin-9

description: Gene expression in HepG2 cells treated with β-catenin-9 siRNA

source_name: HepG2 cells, β-catenin-9 siRNA, rep1

value: β-catenin-9 siRNA


title: HepG2_siLEF1

description: Gene expression in HepG2 cells treated with LEF1 siRNA

source_name: HepG2 cells, LEF1 siRNA, rep1

value: LEF1 siRNA


title: RNA-Seq CTRL_Rep2

value: macrophage

value: Control (mCherry expressed)


title: HepG2_siCtrl

description: Gene expression in HepG2 cells treated with control siRNA

source_name: HepG2 cells, Control siRNA, rep1

value: control siRNA


title: org_CD11-LC p10


title: ATAC-Seq E4BP4_TG_ATACRep3

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the mm10 reference genome and displayed using UCSC annotated genes using bowtie2 version 2.2.6 with default parameters.
Alingment files were transformed into "Tag Directory" using Homer version 4.11.1  “makeTagDirectory".
Assembly: mm10
Supplementary files format and content: Bedgraph were generated using HOMER.

extract_protocol:
Thirty thousand RAW264.7 cells each expressing E4BP4 or mCherry with lentivirus were used in the experiment.　Each cell was subjected to tagmentation Reaction and Purification using an ATAC-Seq Kit Manual Kit (Active Motif) according to the manufacturer's instructions.
Sequencing libraries were generated using ATAC-Seq LibraryPrep kit for Illumina (Active Motif) according to manufacturer's instructions. Library concentrations were assessed by a Bioanalyzer (Agilent) .

value: E4BP4 expressed

value: TG (E4BP4 expressed)

value: Basal condition


title: org_CD19-LC p9

value: Stricturing


title: RNA-Seq CTRL_Rep3


title: EP,passage 7, rep 3

source_name: mesenchymal stem cells

value: mesenchymal stem cells

value: WT

value: EP


title: org_CD20-LC p7


title: MIR,passage 7, rep 1

value: MiR


title: Control,passage 7, rep 2

value: Con


title: Control,passage 7, rep 1


title: EP,passage 7, rep 2


title: RNA-Seq CTRL_Rep1


title: RNA-Seq E4BP4_TG_Rep2


title: EP,passage 7, rep 1


title: org_CD60-LC p6

value: ORG


title: org_CD47-LC p8


title: org_CD30-LC p7

value: NSNP


title: Drosophila melanogaster apodeme cells 12 [apodeme-12]

city: Seattle

first: Jay

middle: Z

last: Parrish

state: WA

address: 3747 W Stevens Way NE

institute: University of Washington

data_processing:
Reads were demultiplexed with CASAVA (Illumina) and read quality was assessed using FastQC and MultiQC. Reads containing adapters were removed using Cutadapt version 2.4 and reads were mapped to the D. melanogaster transcriptome, FlyBase genome release 6.29, using Kallisto version 0.46.0 with default parameters.
Assembly: FlyBase genome release 6.29
Supplementary files format and content: FASTQ

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: epidermal cells

growth_protocol: Larvae were reared at 25 C under 12 h light / dark cycle on standard cornmeal/molassess media and isolated for dissection at 96 h after egg laying.

extract_protocol:
Larvae with cytoplasmic GFP expressed in different epidermal subsets were microdissected and dissociated in collagenase type I (Fisher 17-100-017) into single cell suspensions, largely as previously described, with the addition of 1% BSA to the dissociation mix. After dissociation, cells were transferred to a new 35 mm petri dish with 1 mL 50% Schneider’s media, 50% PBS supplemented with 1% BSA. Under a fluorescent stereoscope, individual fluorescent cells were manually aspirated with a glass pipette into PBS with 0.5% BSA, and then serially transferred until isolated without any additional cellular debris present. Ten cells per sample were aspirated together, transferred to a mini-well containing 3ul lysis solution (0.2 % Triton X-100 in water with 2 U / µL RNAse Inhibitor), lysed by pipetting up and down several times, transferred to a microtube, and stored at -80º C. For the picked cells, 2.3 µL of lysis solution was used as input for library preparation.
RNA-Seq libraries were prepared from the picked cells following the Smart-Seq2 protocol for full length transcriptomes. To minimize batch effects, primers, enzymes, and buffers were all used from the same lots for all libraries. Libraries were multiplexed, pooled, and purified using AMPure XP beads, quality was checked on an Agilent TapeStation, and libraries were sequenced as 51-bp single end reads on a HiSeq4000 at the UCSF Center for Advanced Technology.

treatment_protocol: Epidermal cells were isolated from control (GMR38F11-GAL4, UAS-2xEGFP/+) or miR-14 mutant (miR-14-delta1/miR-14-delta1; GMR38F11-GAL4, UAS-2xEGFP/+) larvae

value: epidermal cells

value: apodeme cells


title: ATAC-Seq CTRL_ATACRep1


title: Healthy_donor_8

city: Stanford

first: Mauro

last: Lago Docampo

address: 269 Campus Dr.

institute: Stanford University

data_processing:
FastQC v0.11.5
cutadapt v2.3
bowtie 1.2.2
Rsubread_1.32.4
DESeq2_1.22.2
Assembly: hg19
Supplementary files format and content: counts.csv; includes all processed counts used for DESeq2 analysis
Supplementary files format and content: coldata.csv; includes sample and conditions used for DESeq2.  Three samples were removed for the DE analysis (RSB102-10,  RSB102-11,RSB102-20) as they came out as outliers; however, all the data have been provided for the sake of transparency, in case GEO users want to use them anyway.

source_name: Plasma

extract_protocol:
Qiagen miRNEasy Advanced Serum/Plasma kit
RealSeq Biosciences Illumina Small RNA-like kit
Illumina NextSeq 500 v2 High-Output - SR 75 Cycle

treatment_protocol: 15.000 xg centrifugation to clean cell rests from plasma, then straight to the extraction kit with the supernatant

value: Plasma

tag: disease state

value: Healthy donor

tag: fraction

value: small RNA


title: Healthy_donor_7


title: Healthy_donor_9


title: RAW_E4BP4_rep2

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the mm10 reference genome and displayed using UCSC annotated genes using bowtie2 version 2.2.6 with default parameters.
Visualization in the Integrative Genomics Viewer (IGV): Alingment files were transformed into "Tag Directory" using Homer  version 4.11.1  “makeTagDirectory", and then rep1 and rep2 were merged. Bedgraph files were created using Homer "makeUCSCfile" and specifying "-norm 1e7" for normalization to 10 million reads.
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files were generated using HOMER.

extract_protocol:
RAW264.7 cells (54 million) were fixed for 30 minutes with 2 mM disuccinimidyl glutarate (DSG) and for 10 minutes with 1% formaldehyde. Nuclei were then isolated in buffer containing 1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and protease inhibitors and sonicated using a Bioruptor (COSMO BIO) to shear chromatin to 200-1000 bp fragments. Protein-DNA complexes were incubated with two kinds of antibodies against E4BP4 (sc-28203; Santa Cruz Biotechnology and 11773-1-AP; Proteintech) and immunoprecipitated with IgG paramagnetic beads (Invitrogen). Eluted chromatin was isolated using MinElute PCR Purification Kit (QIAGEN).
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions. Library concentrations were assessed by both a Bioanalyzer (Agilent) and NEBNext Library Quant Kit for Illumina (New England Biolabs).

tag: chip antibody

value: E4BP4 antibodies


title: org_H14-Colon p13

value: Healthy


title: DNA mehtylation of human stomach without HP innfection (G1_O3)

type: genomic

first: Harumi

last: Yamada

address: 2-4-41 Ebara Shinagawa-ku

department: Department of Epigenomics

institute: Hoshi University

hyb_protocol: Standard Illumina Protocol

scan_protocol: The array was scanned with an iScan System

data_processing: The data were analyzed using GenomeStudio Methylation Module Software.

label: Cy5 and Cy3

source_name: stomach

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted by standard phenol/chloroform method, and was quantified using a Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).

value: Gastric antrum

tag: hp infection

value: no


title: Control,passage 7, rep 3

tag: treatment


title: org_CD26-LC p8


title: ATAC-Seq E4BP4_TG_ATACRep2

value: E4BP4 expressed

value: TG (E4BP4 expressed)

value: Basal condition


title: org_CD59-R p4


title: org_H4 Colon p35


title: Muscle, Chow diet, female, rep1

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

data_processing:
Following sequencing and demultiplexing, reads were trimmed for adapters and filtered based on quality score using Fastp
High quality reads were aligned to the rat genome (rn6)using STAR (ver 2.7.6a)
resulting read alignments file for each sample was imported in Seqmonk (ver 1.48.1)
raw counts matrix of all genes was imported into DESeq2 (DESeq2 version 1.30.1) in R (ver 4.1)
Assembly: Rn 6
Supplementary files format and content: raw counts matrix of all genes in al samples

source_name: Gastronemius

extract_protocol:
gastrocnemius tissue (50-100 mg) was homogenized in 1 mL of Trizol using the Bead Mill 24 . Total RNA was isolated using a combination of TRI reagent  and RNeasy-mini columns, including on-column deoxyribonuclease digestion.
cDNA libraries for mRNA-sequencing were prepared using polyA-mRNA from individual RNA samples using Illumina TruSeq reagents

value: Gastronemius

tag: strain

value: Wistar

value: Female

value: Chow


title: DNA mehtylation of human stomach without HP innfection (G1_O2)


title: DNA mehtylation of human stomach without HP innfection (G1_O4)


title: RAW_input_rep2

value: input


title: Drosophila melanogaster apodeme cells 9 [apodeme-9]

value: epidermal cells


title: Drosophila melanogaster apodeme cells 8 [apodeme-8]

value: apodeme cells


title: ATAC-Seq E4BP4_TG_ATACRep1


title: Healthy_donor_5

value: Plasma


title: ATAC-Seq CTRL_ATACRep3

value: macrophage

value: Control (mCherry expressed)


title: Healthy_donor_10

value: Healthy donor

value: small RNA


title: Drosophila melanogaster apodeme cells 7 [apodeme-7]


title: org_CD28-R p8

source_name: Colon

value: ORG

value: NSNP


title: Drosophila melanogaster apodeme cells 11 [apodeme-11]


title: ATAC-Seq CTRL_ATACRep2


title: Healthy_donor_4


title: Drosophila melanogaster apodeme cells 6 [apodeme-6]


title: DNA mehtylation of human stomach without HP innfection (G1_O1)

value: Gastric antrum

value: no


title: DNA mehtylation of human stomach without HP innfection (G1_Y3)


title: M0 RAW264.7 cells replicate3 [re-analysis]

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the mm10 reference genome and displayed using UCSC annotated genes using STAR version 2.7.5a with default parameters.
Alingment files were transformed into "Tag Directory" using Homer version 4.11.1  “makeTagDirectory", then differantial expression alaysis (DeSeq2) was perfomed using Homer　“getDiffExpression.pl"
TPM files were created using Homer "analyzeRepeats.pl" and specifying "-count exons -tpm" .
Genome_build: mm10
Supplementary_files_format_and_content: DeSeq2 analysis were performed using HOMER.
Supplementary_files_format_and_content: TPM files were generated using HOMER.

source_name: M0 RAW264.7 cells

growth_protocol: RAW264.7 cells, which were generated as CTRL RAW264.7 cells using plasmid encoding the Cas9 nuclease without gRNA sequence for comparison to E4BP4 knockout RAW264.7 cells, were cultured as a monolayer in 25 mM glucose Dulbecco’s modified Eagle’s medium (Sigma-Aldrich) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (FUJUFILM Wako) at 37 °C under 5% CO2. The RAW264.7 cells used in experiments were at fewer than 15 passages.

extract_protocol:
Total RNA of RAW264.7 cells was extracted using  a Quick-RNA Microprep Kit (ZYMO RESEARCH). Polyadenylated mRNA was separated from 200 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were generated using NEBNext Ultra RNA LibraryPrep kit for Illumina (New England Biolabs) according to manufacturer's instructions. Library concentrations were assessed by both a Bioanalyzer (Agilent) and NEBNext Library Quant Kit for Illumina (New England Biolabs).

treatment_protocol: RAW264.7 cells were polarized toward the M2 phenotype with 10 ng/ml IIL-4 (PeproTech)  or without IL-4 as M0 condition.


title: Drosophila melanogaster apodeme cells 10 [apodeme-10]


title: org_CD21-LC P6


title: shScr-H

city: Tianjin

first: xudong

last: Wu

address: Qixiangtai Road

institute: Tianjin medical university

description: shScr

data_processing:
For m6A-seq data, clean reads were aligned to human reference genome (hg19) using Hisat2 version 2.1.0.
Peak calling and annotation were performed using R package exomePeak and ChIPseeker respectively.
Bigwig files were generated by deepTools V2.4.0
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file for each Sample

growth_protocol: All cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) and maintained at 37 °C with 5% CO2, but hypoxia experiments were performed inhypoxic incubator with 5% CO2 and 1% O2.

extract_protocol:
RNA was harvested using Trizol reagent.
Libraries were prepared according to SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 635005; Takara/Clontech, Japan).
library strategy: m6A-seq

value: glioblastoma cell line

value: Hypoxia


title: M0 RAW264.7 cells replicate2 [re-analysis]


title: WT-H

description: WT


title: Drosophila melanogaster apodeme cells 4 [apodeme-4]


title: M2-polarized RAW264.7 cells replicate3

source_name: M2-polarized RAW264.7 cells


title: WT-N

description: WT

value: Normoxia


title: DNA mehtylation of human stomach without HP innfection (G1_Y4)


title: Healthy_donor_6


title: Drosophila melanogaster apodeme cells 3 [apodeme-3]


title: 3_Tg

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Human pancreatic islets  RNA-seq by Illumina Novaseq6000

data_processing:
Reads were aligned to the human transcriptome (Ensembl version 94) using kallisto.
Transcript counts were converted to gene counts using tximport.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file contains read counts.

source_name: pancreatic islets

extract_protocol:
Total RNA was extated from human pancreatic islets using RNA Micro Kit (QIAGEN 74004).
RNA libraries were prepared using SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian.

value: pancreatic islets

value: TREATED

tag: replicate

value: Male


title: Drosophila melanogaster apodeme cells 2 [apodeme-2]

value: epidermal cells


title: M2-polarized RAW264.7 cells replicate1

tag: cell line


title: RAW_input_rep1

value: input


title: Healthy_donor_2

value: Plasma


title: input

description: input


title: PAH_8

value: Pulmonary Arterial Hypertension


title: DNA mehtylation of human stomach without HP innfection (G1_Y2)


title: PAH_7


title: M2-polarized RAW264.7 cells replicate2


title: shALKBH5-H


title: RAW_E4BP4_rep1

value: E4BP4 antibodies


title: 3_control

value: UNTREATED


title: Healthy_donor_3

value: Healthy donor

value: small RNA


title: Drosophila melanogaster apodeme cells 5 [apodeme-5]

value: apodeme cells


title: Drosophila melanogaster broad epidermal cells 12 [r38-12]

value: broad epidermal cells


title: DNA mehtylation of human stomach without HP innfection (G1_Y1)

value: Gastric antrum

value: no


title: M0 RAW264.7 cells replicate1

treatment_protocol: RAW264.7 cells were polarized toward the M1 phenotype with 100 ng/ml LPS (Sigma-Aldrich) and 50 ng/ml IFN-γ (PeproTech)  or without them as M0 condition.


title: Drosophila melanogaster broad epidermal cells 13 [r38-13]


title: PAH_5


title: Healthy_donor_1


title: M0 RAW264.7 cells replicate1 [re-analysis]


title: Drosophila melanogaster broad epidermal cells 10 [r38-10]


title: PAH_4


title: 1_control


title: 16_8_Tg

value: CTRL


title: PAH_10


title: PAH_9


title: 2_2_Tg

value: Female


title: PAH_3


title: Drosophila melanogaster apodeme cells 1 [apodeme-1]


title: PAH_6


title: 1_Tg

value: pancreatic islets


title: PAH_2


title: M0 RAW264.7 cells replicate3


title: 4_Tg

value: TREATED


title: 2_control


title: M0 RAW264.7 cells replicate2


title: PAH_25


title: 7_control

value: Male


title: M1-polarized RAW264.7 cells replicate3

source_name: M1-polarized RAW264.7 cells


title: PAH_23


title: M1-polarized RAW264.7 cells replicate2


title: M1-polarized RAW264.7 cells replicate1


title: Drosophila melanogaster broad epidermal cells 9 [r38-9]

value: epidermal cells


title: Drosophila melanogaster broad epidermal cells 11 [r38-11]


title: PAH_1


title: Drosophila melanogaster broad epidermal cells 3 [r38-3]


title: 6_Tg


title: Control RAW264.7 cells replicate3

source_name: Control RAW264.7 cells

tag: genotype/variation

value: Control


title: E4BP4 knockout RAW264.7 cells replicate1

source_name: E4BP4 knockout RAW264.7 cells

value: E4BP4 knockout


title: Drosophila melanogaster broad epidermal cells 7 [r38-7]


title: Drosophila melanogaster broad epidermal cells 2 [r38-2]


title: E4BP4 knockout RAW264.7 cells replicate3


title: Control RAW264.7 cells replicate1


title: Drosophila melanogaster broad epidermal cells 6 [r38-6]


title: 15_8_control


title: E4BP4 Transgenic replicate3 [TG_ColonMac_rep3]

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the mm10 reference genome and displayed using UCSC annotated genes using STAR version 2.7.5awith default parameters.
Alingment files were transformed into "Tag Directory" using Homer version 4.11.1  “makeTagDirectory", then differantial expression alaysis (DeSeq2) was perfomed using Homer　“getDiffExpression.pl"
TPM files were created using Homer "analyzeRepeats.pl" and specifying "-count exons -tpm" .
Genome_build: mm10
Supplementary_files_format_and_content: DeSeq2 analysis were performed using HOMER.
Supplementary_files_format_and_content: TPM files were generated using HOMER.

extract_protocol:
Single cell suspensions from colonic lamina propria were prepared, and colon macrophages were isolated using a FACSAria III Cell Sorter (BD Biosciences). Total RNA was extracted using a Direct-zol RNA Microprep Kit (ZYMO RESEARCH). Polyadenylated mRNA was separated from 20 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were generated using NEBNext Ultra RNA LibraryPrep kit for Illumina (New England Biolabs) according to manufacturer's instructions. Library concentrations were assessed by both a Bioanalyzer (Agilent) and NEBNext Library Quant Kit for Illumina (New England Biolabs).

value: Macrophage specific E4BP6 transgenic

tag: tissue/cell type

value: Colon macrophage


title: Drosophila melanogaster broad epidermal cells 5 [r38-5]


title: Control RAW264.7 cells replicate2


title: PAH_24

value: Plasma

value: Pulmonary Arterial Hypertension


title: PAH_20

value: small RNA


title: 7_Tg


title: Drosophila melanogaster broad epidermal cells 4 [r38-4]


title: U87 shScr-H

data_processing:
RNA-seq analysis was completed by BGI company(Shenzhen,China).
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each Sample
Supplementary_files_format_and_content: bigwig file for each Sample

source_name: U87 shScr Hypoxia

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEBNext Ultra RNA library Prep Kit for Illumina.

value: glioblastoma cell line

value: shScr

value: hypoxia


title: PAH_19


title: E4BP4 Transgenic replicate2 [TG_ColonMac_rep2]

value: Macrophage specific E4BP5 transgenic


title: 6_control

value: CTRL

value: UNTREATED


title: 4Y-3

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

description: yak

data_processing:
Pychopper was used to identify full-length sequences in valid sequencing data and NanoFilt was used to filter the full-length sequence.
Minimap2 was used to align the filtered full-length sequence with the reference gene and quickly construct a non-redundant transcript set.
The gffcompare was used to compare transcripts with known transcripts in the genome.
The alternative splicing types of each sample were obtained by suppa2.
Use Tofu (version: 13.0.0; parameter: default) alignment and search for fusion transcripts. Using MISA software for SSR prediction. The transcription factors were identified using the animal transcription factor database animalTFDB. TAPAS combined with the reference sequence of RefSeq database to identify APA.
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample.
Supplementary files format and content: Tab-delimited text files include DESeq2 results.
Supplementary files format and content: FASTA files

organism: Bos grunniens

source_name: testis

growth_protocol: Five groups of 6-month-old (6M), 18-month-old (18M), 30-month-old (30M), 4-year-old (4Y) male yaks and 4-year-old adult male cattle-yak (TES) were selected from the same cooperative in Xiahe County (N34°51'50', E102°26'9') in Gannan Tibetan Autonomous Prefecture for castration.

extract_protocol:
Total RNA was extracted from each testicular sample using TRIzol reagent. RNA quality was assessed using Nanodrop-2000 and 1% agarose gel electrophoresis.
Qualified RNA was used to prepare 1μg total RNA for cDNA library construction by cDNA-PCR sequencing kit. The cDNA library was sequenced on PromethION sequencer (Oxford Nanopore Technologies, Oxford, UK). These testing processes were conducted according to the protocol of the manufacturer.

treatment_protocol: The testicular tissue was washed with PBS and quickly placed in a freezer tube, immediately stored in liquid nitrogen.

value: testis

value: male

value: four years


title: Drosophila melanogaster mir14 mutation 7 [mir14-7]

value: epidermal cells

value: mir14 mutation


title: Drosophila melanogaster broad epidermal cells 8 [r38-8]

value: broad epidermal cells


title: E4BP4 Transgenic replicate1 [TG_ColonMac_rep1]

first: Akihiko

last: Taguchi

address: 1-1-1 minamikogushi

institute: Yamaguchi University

value: Macrophage specific E4BP4 transgenic


title: 4Y-2

description: yak


title: E4BP4 knockout RAW264.7 cells replicate2

value: E4BP4 knockout


title: PAH_22

value: Plasma


title: Wild Type replicate3 [WT_ColonMac_rep3]

value: Wild type

value: Colon macrophage


title: Drosophila melanogaster mir14 mutation 6 [mir14-6]


title: U87 shALKBH5-H

source_name: U87 shALKBH5 Hypoxia

value: glioblastoma cell line


title: 4_control

value: pancreatic islets

value: Male


title: Wild Type replicate2 [WT_ColonMac_rep2]


title: Drosophila melanogaster mir14 mutation 5 [mir14-5]


title: Drosophila melanogaster broad epidermal cells 1 [r38-1]


title: 30m-3

description: yak

value: thirty months


title: 4Y-1

description: yak


title: PAH_15

value: Pulmonary Arterial Hypertension

value: small RNA


title: PAH_21


title: Drosophila melanogaster mir14 mutation 3 [mir14-3]


title: Drosophila melanogaster mir14 mutation 8 [mir14-8]


title: Wild_Type_M2_BMDM_rep2

extract_protocol:
Bone marrow cells were harvested from femurs and tibias of WT mice. Differentiation into BMDMs was treated with 20 ng/ml recombinant macrophage colony-stimulating factor (M-CSF, PeproTech) and maintained in culture for 7 days. 4 hours after treatment with IL-4 (M2-BMDM) or without IL-4 (M0-BMDM), cells were harvested for total RNA extraction using a Direct-zol RNA Microprep Kit (ZYMO RESEARCH). Polyadenylated mRNA was separated from 100 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were generated using NEBNext Ultra RNA LibraryPrep kit for Illumina (New England Biolabs) according to manufacturer's instructions. Library concentrations were assessed by both a Bioanalyzer (Agilent) and NEBNext Library Quant Kit for Illumina (New England Biolabs).

treatment_protocol: BMDMs were polarized toward the M2 phenotype with 10 ng/ml IL-4 and 20 ng/ml M-CSF or received media containing 20 ng/ml M-CSF as M0 condition.


title: Drosophila melanogaster mir14 mutation 2 [mir14-2]


title: PAH_17


title: Wild Type replicate1 [WT_ColonMac_rep1]


title: Drosophila melanogaster mir14 mutation 1 [mir14-1]


title: Drosophila melanogaster mir14 mutation 4 [mir14-4]


title: Wild_Type_M2_BMDM_rep3


title: PAH_14


title: 30m-2

description: yak

value: testis


title: PAH_11


title: Drosophila melanogaster epidermal cells 8 [epi-8]

value: WT


title: PAH_16


title: Wild_Type_M0_BMDM_rep2


title: PAH_12


title: Wild_Type_M2_BMDM_rep1


title: 18m-2

description: yak

value: male

value: eighteen months


title: 6m-3

description: yak

value: six months


title: 30m-1

description: yak


title: PAH_18


title: PAH_13


title: 18m-1

description: yak


title: dCas9_Neg_exp2

city: Kyoto

first: Mitsuru

last: Sasaki-Honda

address: Shogoin, Sakyoku

department: Dept. of Clinical Application

institute: CiRA

data_processing:
Next seq 500 (Illuminia, CA) in the paired-end mode with 144 bp : 8 bp : 8 bp : 8 bp for R1:l1:l2:R2.
the sequenced reads of R1 were trimmed to remove adaptors and low-quality bases using Cutadapt with ‘-m 20 --nextseq-trim=20’ option.
The 8bp sequences of R2 were transferred as unique molecular identifiers (UMIs) to each corresponding strand name in R1 reads using UMI-tools extract function.
Then R1 reads were mapped to the reference human genome GRCh38, which downloaded from the NCBI RefSeq, using STAR
Dedupication was conducted using UMI-tools dedup function. After dedupication, HTSeq was used to calculate gene read counts, and the counted data were normalized by DEseq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: differentiated muscle cells

growth_protocol: Cells are maintained as PSC on an iMatrix-511 pre-coated dish in StemFit AK02N medium  .

extract_protocol:
Total RNA was obtained from sorted cells using the ReliaPrep RNA Cell Miniprep System (Promega). RNA quality was evaluated using a NanoDrop 2000 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer System (Agilent) with an RNA Pico Kit (Agilent, CA) according to the manufacture’s instruction.
5 ng of total RNA was used with the SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (TAKARA, Japan), according to the manufacture’s instruction.

treatment_protocol: Myogenic differentiation was induced by 1 ug/mL doxycycline to activate tetracycline inducible MyoD gene.

value: differentiated muscle cells

value: FSHD2 donor 1 iPSC

value: differentiated iPSC

value: Neg


title: 6m-2

description: yak


title: Drosophila melanogaster epidermal cells 5 [epi-5]

value: epidermal cells


title: 18m-3

description: yak


title: dCas9_KAL_tEP3_exp1


title: E12.5, wt, right lung, #3

city: University Park

first: Aimin

last: Liu

state: Pennsylvania

address: 201 Life Sciences Building

department: Biology

institute: The Pennsylvania State University

data_processing:
FastQC reports were generated and the data quality was inspected (trimming and adaptor removal were done by BGI Genomics before data delivery)
Data was mapped to the mouse refence genome (GRCM38 build) using hisat2.
The number of reads mapping to the annotated genes were obtained using featureCounts in the unstranded and paired mode (-p -s 0 parameters).
Assembly: GRCm38
Supplementary files format and content: gene counts for all 12 samples

source_name: lung

growth_protocol: embryos were produced by natural breeding between male and female mice carrying an Intu knockout allele

extract_protocol:
RNA was extracted from freshly dissected lungs using a NucleoSpin RNA miniprep kit (Macherey-Nagel). cDNA was synthesized using qScript cDNA SuperMix (Quanta Biosciences).
library was constructed by BGI genomics

value: lung

tag: strain background

value: wild type


title: Wild_Type_M0_BMDM_rep3

city: Ube


title: 6m-1

description: yak

tag: tissue


title: dCas9_KAL_tEP3_exp2


title: Wild_Type_M0_BMDM_rep1


title: Drosophila melanogaster epidermal cells 7 [epi-7]


title: Drosophila melanogaster epidermal cells 6 [epi-6]


title: Drosophila melanogaster epidermal cells 3 [epi-3]


title: WT,IP

city: Shanghai

first: Di

last: You

address: Meilong Road 130

institute: East China University of Science & Technology

data_processing:
The obtained DNA library  was  sequenced on Illumina sequencing platform.
Low quality bases were trimmed by using Trimmomatic(version: 0.36). Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data. It works with FASTQ or gzipp'ed FASTQ. With 'simple' trimming, each adapter sequence is tested against the reads, and if a sufficiently accurate match is detected, the read is clipped appropriately.
Clean reads were mapped to Arabidopsis thaliana(ENSEMBLE) using Bowtie2 (version:2.3.4.3) with default parameters. The alignment file(SAM) was transformed to BAM file and was filtered by the following criteria: (1) only keep unique aligned reads; (2) remove reads with low MAPQ(<30).
The MACS2 (version: 2.1.2) was used to identify transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with a control sample with the increase of specificity.
The peaks were annotated by ChIPseeker (version: 2.16.0), an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes. Comparison of ChIP peak profiles and annotation are also supported.
Assembly: Saccharopolyspora erythraea NRRL 2338(NCBI,ASM6288v1)
Supplementary files format and content: bigWig, Peak

organism: Saccharopolyspora erythraea

source_name: WT,IP

growth_protocol: TSB medium

extract_protocol:
Collected the cultured cells in centrifuge tube and then washed with 1X PBS buffer. After centrifugation and removing the supernatant, 1% formaldehyde in PBS buffer was used to cross-link DNA and proteins for about 10min at 37 ℃.
After that, 0.125 M of glycine was used to stop the crosslinking reaction. the cells were washed with precooled PBS with 0.5% bovine serum and by PBS supplemented with protease inhibitor compound (PIC). The cells were collected by centrifugation at 850 rpm for 3 min after each wash. The cells were resuspended in 200 μl ice-cold lyses buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 7.5 plus PIC) and then thawed on ice for 10 min to allow cell lyses. The cell lysate was sonicated using Bioruptor Pico to generate chromatin fragments of size range from 100 to 800 bp. One-tenth of the sonicated chromatin sample was separated for input control. The remaining chromatin was immunoprecipitated in ChIP dilution buffer (1% Triton, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 7.5) with 4 μg of antibody that has been pre-incubated with protein A/G magnetic beads (Invitrogen; 10003D). The immunoprecipitation reaction was incubated overnight at 4 °C and the beads were washed twice with each of the following buffers at 4 °C: RIPA buffer (10 mM Tris, 1 mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 0.1% Triton X-100); RIPA buffer plus 0.3 M NaCl; LiCl buffer (0.25 M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and TE buffer. The captured DNA and input control sample were reverse cross-linked by eluting the beads with elution buffer (1% SDS, 0.1 M NaHCO3) at 65 °C for 2 h, respectively. The eluted DNA was purified by phenol-chloroform extraction and precipitated with ethanol and glycogen. The obtained DNA was subjected to library preparation and sequenced on Illumina sequencing platform.


title: E12.5, wt, left lung, #3

tag: age


title: E12.5, wt, right lung, #2


title: dCas9_Neg_exp1


title: E12.5, wt, right lung, #1


title: Drosophila melanogaster epidermal cells 2 [epi-2]

source_name: epidermal cells


title: Drosophila melanogaster epidermal cells 4 [epi-4]


title: Drosophila melanogaster epidermal cells 1 [epi-1]


title: Mouse primary neuron, input

city: shanghai

first: Dong

last: Jian

address: 393 Middle Huaxia  Road

institute: shanghaitech university

data_processing:
The ChIP-seq data of ATRX were aligned to the mouse genome (release 109) using the Bowtie (1.3.0). SAM files were sorted and filtered using samtools (1.9)
Peak-calling performed with MACS (1.4.2) was run independently for each BAM files to detect genomic regions enriched for multiple overlapping DNA fragments (peaks) that were considered to be putative binding sites.
Peaks for further analyses were filtered using the same p value cutoff (5 ⅹ 10-2) by comparing the peaks obtained from the samples with those from the control samples.
Target genes were considered by at least one peak within 3 kb from the transcription start site (TSS)
Heat maps for showing the peaks within 3 kb from the TSS were visualized using the CHIPseeker package (1.26.2), GO terms analysis was generated using the clusterProfiler package (3.18.1).
Assembly: release 109
Supplementary files format and content: narrowPeak (except for Input group)

source_name: Mouse primary neuron

growth_protocol: Mouse primary neurons were isolated from C57BL6/J mice at E15.5-17.5. The cultured neurons were maintained in Neurobasal A media (Gibco), supplemented with B27, 2 mM glutamine, and 2% fetal bovine serum (Gibco).

extract_protocol:
The samples for ChIP analysis were extracted using SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 91820s) with antibodies against ATRX (Abcam ab97508). Input DNA was used to control for background.
DNA samples in input and IP groups were pair-end sequenced on Illumina Hi-Seq2500 platform.

treatment_protocol: Mouse primary neurons were infected by lentivirus at DVI5.

value: Mouse primary neuron


title: E12.5, wt, left lung, #2


title: Mouse primary neuron (DIV14), MICAL1-M1, ATRX,ChIP

value: ATRX antibody


title: Mouse primary neuron (DIV7), mCherry, ATRX,ChIP


title: Mouse primary neuron (DIV14), mcherry, ATRX,ChIP


title: OdisA,Input

source_name: OdisA,Input

value: disA overexpression


title: E12.5, wt, left lung, #1


title: Mouse primary neuron (DIV14), TBC1D3, ATRX,ChIP


title: E12.5, IntuKO, right lung, #1

value: Intu knockout


title: control_3

first: LIFANG

last: WANG

address: 393 Middle Huaxia Road

institute: SHANGHAITECH

library_source: other

data_processing:
The sequencing data was initially assessed for quality using the software FASTQ, followed by alignment of each miRNA sequencing dataset independently to the reference genome using HiSAT2. Transcriptome from each RNA-sequencing dataset was then extracted using the StringTie software. Differential miRNA cluster analysis was performed to compare miRNA expression of control and myrf-1(ju1121) mutant using DESeq2. Data normalization was done using the TPMnmethod, and the profiling differences between control and myrf-1(ju1121) mutant were compared using “Fold Change” (FC). A P-value was assigned to each gene and adjusted using the Benjamini and Hochberg method. Genes with P_adj < 0.05 were considered differentially expressed.
Assembly: WBcel235/ce11
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM for each sample

molecule: other

organism: Caenorhabditis elegans

source_name: the whole worm

extract_protocol:
To isolate myrf-1 mutants, late L1 stage worms were selected based on size and lack of pharyngeal GFP (a balancer mIn1 marker) using Biosorter. Over 10,000 worms were collected for each sample for further experimentation. Total RNA was extracted and assessed for quality and quantity using Nanodrop and Agilent 2100, respectively. Samples with a total quantity of 3-5 μg and high quality (RIN > 10) were selected for miRNA library construction.
The miRNA libraries were established and sequenced by Novogene Technology Co., Ltd. (Beijing, China).

value: the whole worm

value: BLW53 [Phlh-8-GFP(ayIs6)]

value: control


title: mutant_3

value: BLW1555 [myrf-1(ju1121)/ mIn1; Phlh-8-GFP(ayIs6)]

value: myrf-1 dysfunction mutant


title: AtPIN5-BY2_DMSO_1315

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

description: Novogene

data_processing:
reads were quality filterred by rcorrector and trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Nicotiana tabacum v1 Edwards 2017 (https://solgenomics.net/ftp/genomes/Nicotiana_tabacum/edwards_et_al_2017/)
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Nicotiana tabacum

source_name: suspension cell culture

growth_protocol: Tobacco cell line BY-2 (Nicotiana tabacum L. cv. Bright Yellow 2) was maintained in liquid Murashige and Skoog (MS) medium (3% sucrose (w/v), 4.3 g/l MS salts, 100 mg/l myo-inositol, 1mg/l thiamin, 0.2 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D), and 200 mg/l KH2PO4; pH 5.8), in the dark, at 27°C, under continuous shaking (150 rpm; orbital diameter 30 mm) and sub-cultured every 7 days.

extract_protocol:
protocol from Plant Total RNA Mini Kit, QIAGEN
performed by sequencing service company (Institute of Applied Biotechnologies or Novogene)

treatment_protocol: AtPIN5 expression was induced by 1 µM β-estradiol (diluted in DMSO) added at the beginning of the subculture interval. DMSO-treated cells used as a non-induced control.

tag: cultivar

value: Bright Yellow 2

tag: biological replicates

value: suspension cell culture

value: DMSO

tag: treatment time


title: AtPIN5-BY2_EST_1590

description: IAB

tag: cell type

value: EST


title: AtPIN5-BY2_EST_1588

description: IAB


title: E12.5, IntuKO, right lung, #2

tag: genotype


title: Testes,Srsf1-3, P10

city: Beijing

first: Wenlong

last: Lei

state: 北京

address: 北京市朝阳区北辰西路1号院5号

institute: 中国科学院

data_processing:
The adapter sequences and poly(A) tails at the 3′ end of raw reads were removed using Cutadapt (v.1.15) with two parameters: -f fastq -q 30,0 -a ATCTCGTATGCCGTCTTCTGCTT -m 18 --max-n 0.25 --trim-n., and -f fastq -a A{15} -m 18 -n 2.
Clean reads were first aligned to mouse pre-rRNA using Bowtie, and the remaining unmapped reads were then aligned to the mouse (mm9) reference genome.
For LACE-seq data mapping, two mismatches were allowed (Bowtie parameters: -v 2 -m 10 --best -strata; -v 2 -k 10 --best -strata).
Peaks were identified by Piranha with parameters: -s -b 20 -p 0.01. peaks without IgG signal were selected for further usage.
For motif analysis, LACE-seq peaks/clusters were first extended 30 nt to 5′ upstream, and overrepresented hexamers in the extended sequences were identified . The consensus motifs were generated from the top-10 enriched hexamers using WebLogo.
Assembly: mm9
Supplementary files format and content: bigWig, narrowPeak
Library strategy: LACE-seq

source_name: testes

extract_protocol:
Testes were resuspended in PBS and manually picked under a microscope using needles.
The LACE-seq library was single-end sequenced using Illumina HiSeq 2500 at Novogene. The step-by-step protocol for LACE-seq is provided at Nature Protocol Exchange.

value: testes

value: WT


title: mutant_1


title: mutant_2


title: Testes,IgG-1, P10

address: 北京市朝阳区北辰西路1号院5号


title: E12.5, IntuKO, left lung, #3

value: lung


title: control_2


title: OdisA,IP

source_name: OdisA,IP


title: WT,Input

source_name: WT,Input

value: wild type


title: E12.5, IntuKO, left lung, #2


title: AtPIN5-BY2_EST_1304

description: Novogene


title: control_1


title: E12.5, IntuKO, right lung, #3


title: Testes,Srsf1-2, P10

address: 北京市朝阳区北辰西路1号院5号


title: Testes,Srsf1-1, P10

address: 北京市朝阳区北辰西路1号院5号


title: E12.5, IntuKO, left lung, #1


title: AtPIN5-BY2_DMSO_1303

description: Novogene


title: AtPIN5-BY2_DMSO_1313

description: Novogene