title: Infected, 10d, biol rep 3

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

state: Madrid

address: Campus de Montegancedo, Autovia M-40 (km 38)

institute: CBGP (UPM-INIA/CSIC)

data_processing:
Novogene Novogene Co., LTD Genomics Service (Cambridge, UK)
Original image data files from the Illumina platform were transformed to sequenced reads by CASAVA base recognition.
Sequence reads were trimmed for the adaptor sequence/low-quality reads were deleted using a Novogene in-house script (quality parameter limit: 0.05)
Trimmed sequence reads were mapped against the TAIR10 Arabidopsis genome using Tophat v2.0.12 (mismatch = 2).
Read count extraction and normalization was performed using HTSeq v0.6.3 (–m union parameter).
Assembly: TAIR10 Arabidopsis genome
Supplementary files format and content: tab-delimited text file includes read count values for each sample.

source_name: Roots

growth_protocol: Seedlings were grown vertically for seven days on 0.5x MS medium. Then, they were transferred to solidified Plant Nutrition Medium. Root tissue was harvested after two and teen days of co-cultivation, respectively.

extract_protocol:
DNA-free total RNA was extracted by employing the phenol/chloroform method described by Oñate-Sánchez & Vicente-Carbajosa, 2008, BMC Res. Notes.
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations.

treatment_protocol: Each seedling was either mock-infected by associating a 5 mm Ø medium plug extracted from sterile AP plates (control) or from AP plates harbouring a 1‐week‐old S. indica mycelium (co-cultivation).

value: Roots

value: S. indica infected

value: 10 days co-cultivation


title: GlucoBAT [Muscle-V2_14]

status: Public on Sep 04 2023

type: SRA

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

library_source: transcriptomic

data_processing:
fastp v0.20 used for read trimming
STAR v2.7.4a used for read mapping
Rsubread v2.2.4 used for gene expression quantification
R package edgeR v3..34 used for differential gene expression analysis
R package clusterProfiler v4.0 used for gene set enrichment analysis
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Muscle (M. vastus lateralis)

extract_protocol:
RNA was harvested using Trizol reagent
Smartseq II was applied to generate full length cDNA, Illumina DNA Prep Kit was used for the construction of sequencing libraries

tag: tissue

value: Muscle (M. vastus lateralis)

tag: subject

tag: treatment

value: Placebo

tag: day of_visit


title: DSHN-4-D4_08

type: RNA

city: Urbana

first: Erik

last: Nelson

state: IL

address: 523 Burrill, 407 South Goodwin Ave

country: USA

institute: University of Illinois at Urbana-Champaign

hyb_protocol: Hybridization reaction was set up based on the NanoString manuals. We calculated required amounts of RNA samples based on DV200, mix with the NanoString reporter CodeSet, hybridization buffer and Capture ProbeSet. The hybridization master mix was incubated at 65C for 20 hours and then loaded to the cartridge to run the assay.

scan_protocol: NanoString nCounter Sprint Profiler was used to examine RNA targets in samples; Mouse Myeloid Innate Immunity V2 was selected.

data_processing: nSolver Analysis Software 4.0 was the software used for data analysis; data was analyzed according to the user manual

organism: Mus musculus

source_name: Dendritic cells isolated from lungs

extract_protocol: Pooled lung samples were processed immediately for dissociation using Lung Dissociation Kit from Miltenyi Biotec (130-095-927). Dendritic cells were isolated from each pooled sample using CD11b (130-126-725) and   CD11c (130-125-835) beads from Miltenyi Biotec. RNA was isolated using Qiagen RNeasy Mini Kit

treatment_protocol: 24 mice were separated evenly into two treatment groups (placebo vs. DSHN). 10 days post-grafting was allowed for metastasis to occur before treatments. Dosage was 10mg/kg/mouse, and mice were treated daily for 7 days. Lungs were collected and 3 lungs from the same treatment group were pooled to be one sample.

tag: cancer cell grafted

value: 4T1 grafted

value: DSHN

tag: dosage

tag: treatment frequency

value: Daily for 7 days


title: Control U266 cell line sample 1

city: Lille

first: Lama

last: Hasan Bou Issa

address: 1 Rue du Professeur Calmette

country: France

institute: Canther

data_processing:
We used Bcbio_nextgen to process the RNA data
cutadapt was used to trim adapters
trimmed reads were aligned to Human reference genome (GRCh37) with tophat2
Assembly: GRCh37
Supplementary files format and content: tsv format
Supplementary files format and content: transcript information

growth_protocol: Cells were cultures in 90% RPMI-1640 + 10% FBS+ 1% penicilin/streptomycin

extract_protocol:
Total RNA was isolated from U266/Control and U266/MYC cells using RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
A starting amount of 500 ng of RNA was used to prepare poly-A enriched, single barcoded libraries using the NEBNext® Ultra™ RNA Library Prep Kit. Quality control of the libraries was evaluated by Bioanalyzer analysis with High Sensitivity chips. Sequencing was performed on a HiSeq 4000 ,

tag: cell line

tag: cell type

value: myeloma; plasmacytoma

value: control


title: DSHN-3-D3_07


title: GlucoBAT [Muscle-V2_13]

value: Prednisone


title: Infected, 10d, biol rep 2

country: Spain

molecule: polyA RNA

organism: Arabidopsis thaliana

tag: ecotype

tag: time


title: KO_1

data_processing:
Raw reads were mapped to indexed GRCm39/mm39 using STAR aligner.
FeatureCounts from Subread package was used for summarizing mapped read counts at the gene level
The output file from featureCounts were further processed using R pachages including filtering (cpm>=1 & gene should be detected across all replicates in one group) and normalized followed by differentially expressed gene analysis.
Assembly: GRCm39/mm39
Supplementary files format and content: Tab delimited text file containing raw read counts that successfully assigned to target genome for each sample
Supplementary files format and content: Tab delimited text file containing a summary of successfully assigned to target genome for each sample

source_name: Mammary tumor

growth_protocol: Tumors were collected once the tumor volumn reached 2000mm^3

extract_protocol:
Tumors were frozen in -80 until RNA isolation
Frozen tumor mass were dissociated using homogenizer
RNA was isolated using PureLink RNA Mini Kit from Invitrogen
At leat 3ug of total RNA was used for the construction of sequencing libraries
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand.

value: Mammary tumor

tag: model

value: MMTV-PyMT

tag: genotype

value: SHP KO


title: KO_4


title: DSHN-2-D2_06


title: Infected, 10d, biol rep 1


title: Control U266 cell line sample 2


title: Ctrl, 10d, biol rep 3

value: Control


title: Ctrl, 10d, biol rep 2


title: DSHN-1-D1_05


title: DMSO-4 -P4_04

value: DMSO


title: GlucoBAT [Muscle-V2_11]


title: GlucoBAT [Muscle-V2_12]


title: Infected, 2d, biol rep 3

value: 2 days co-cultivation


title: Ctrl, 10d, biol rep 1

value: Roots


title: Infected, 2d, biol rep 1

value: S. indica infected


title: DMSO-3 -P3_03


title: Ctrl, 2d, biol rep 3


title: DMSO-2 -P2_02


title: GlucoBAT [BAT-V5_9]

source_name: scBAT

value: scBAT


title: GlucoBAT [BAT-V5_8]


title: GlucoBAT [Muscle-V2_10]

value: Muscle (M. vastus lateralis)


title: DMSO-1 -P1_01


title: 2022_MM1+CO MC11-2

city: Busan

first: LEE

middle: SEONG

last: HYUK

address: Haeyang-ro

department: Department of Marine Biotechnology

country: South Korea

institute: Korea Institute of Ocean Science and Technology

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.32 as default parameter, then mapped to mm8 whole genome using bowtie v 2.2.4 with parameters -t --very-sensitive
Differential expression profiles indicated by FPKM value.
Assembly: PRJNA59043 (2013-06-10)
Supplementary files format and content: Excel file includes differential expression profiles and locus tags for genes of T. onnurineus NA1

organism: Thermococcus onnurineus NA1

source_name: bacterial cell

extract_protocol:
After cell harvest, RNA samples were prepared using TRIzol reagent. Genomic DNA was eliminated by DNaseI treatment.
To remove rRNA in total RNA, Ribo-Zero rRNA Removal Kits (Human/Mouse/Rat) (MRZH-11124, Epicentre, USA) was used. Nugen (2019 samples) or Truseq (2022 samples) total RNA Sample Prep Kit was used with 1 ug of rRNA depleted RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: condition

tag: growth phase

value: exponential phase

value: bacterial cell


title: 2022_MM1+CO MC11-1


title: GlucoBAT [BAT-V5_7]


title: 2019_MM1+CO MC11


title: Ctrl, 2d, biol rep 1


title: GlucoBAT [BAT-V5_5]

value: Placebo


title: 2022_MM1+CO WT-1

value: WT


title: GlucoBAT [BAT-V5_3]


title: 2019_MM1+CO WT


title: GlucoBAT [BAT-V5_16]


title: GlucoBAT [BAT-V5_4]


title: Quartet_methy_850K_SNT_NIST_3_20191026

type: genomic

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw idat files were processed using R package ChAMP v2.20.1. Next, samples with a proportion of failed probes (probe detection p-value > 0.01) above 0.1 were discarded. Finally, the Meth and Unmeth signals were used to calculate M values and β values. In this process, the offset was set to 100 and the beta threshold to 0.001.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from B lymphocyte

label_protocol: Standard Illumina Protocol

growth_protocol: Immortalized lymphoblastoid cell lines were established by Epstein-Barr virus (EBV). Peripheral blood mononuclear cells were isolated using a lymphocyte separation solution (Ficoll). Naïve B cells were sorted by EasySep Human naïve B Cell Enrichment Kit (STEMCELL, Catalog#19254), and infected by Epstein-Barr virus (EBV) by centrifugation at 2000 rpm for 1 hour. After incubation, the successfully infected and immortalized cells were propagated in culture medium. The Quartet LCLs were cultured in RPMI 1640 with 2 mM L-glutamine, 10%  heat-inactivated FBS (fetal bovine serum), and 1% PS (penicillin/streptomycin) at 37 °C with 5% CO2. The cells were passaged every 72 hours at a 1:4 split ratio.

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: To obtain the first batch of DNA reference materials (Lot NO 20160806), 2 x109 cells were harvested simultaneously for each cell line. Specifically, the cellsgrew in suspension and were centrifuged at 300 g for 5 mins to obtain celpellets. The cell pellets were then washed twice with cold PBS. The DNA reference materials were purified using the DNA with Blood &Cell Culture DNA Maxi Kit (Qiagen, Germany) according to the manufacturer'sinstructions, divided into 1000 aliquots for each of the Quartet members, andthen labeled as Quartet DNA D5 20160806, Quartet DNA D6 2016080641Quartet DNA F7 20160806, and Quartet DNA M8 20160806. A single viacontains approximate 10 ug of genomic DNA (220 ng/uL, 50 uL) in TE buffer(10 mM TRIS, pH 8.0, 1 mM EDTA, pH 8.0).The DNA integrity and long-term stability were evaluated by Agilent 2200TapeStation system (Agilent Technologies, USA). Concentrations weredetermined by NanoDrop ND-2000 spectrophotometer (Thermo FisherScientific,USA).

value: NIST

tag: Sex

value: Female

tag: disease state

value: normal

value: immortalized B-lymphoblastoid cell lines


title: Ctrl, 2d, biol rep 2

tag: tissue


title: Quartet_methy_850K_SNT_NIST_2_20191026


title: GlucoBAT [BAT-V5_6]

tag: subject

value: Prednisone


title: GlucoBAT [BAT-V5_14]

tag: treatment


title: GlucoBAT [BAT-V5_15]

tag: day of_visit


title: HHUA_shBHLHE40_rep2

city: Fukuoka City

first: Kazuo

last: Asanoma

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: HHUA BHLHE40 knockdown

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: cultured in DMEM containing 1.0 g/L glucose with 10% FBS

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: origin

value: endometrial cancer cells

value: HHUA cells


title: HHUA_shBHLHE40_rep3


title: HHUA_shCtrl_rep1

source_name: HHUA control


title: Quartet_methy_850K_SNT_M8_3_20191026


title: GlucoBAT [BAT-V5_13]


title: HHUA_shBHLHE40_rep1


title: Quartet_methy_850K_SNT_M8_2_20191026


title: HHUA_shCtrl_rep2


title: GlucoBAT [BAT-V5_12]


title: GlucoBAT [BAT-V5_10]


title: 2022_MM1+CO WT-2


title: Quartet_methy_850K_SNT_M8_1_20191026


title: Quartet_methy_850K_SNT_M8_2_20190517


title: GlucoBAT [BAT-V5_1]


title: Quartet_methy_850K_SNT_M8_1_20190517


title: GlucoBAT [BAT-V2_8]


title: HHUA_shCtrl_rep3


title: Quartet_methy_850K_SNT_LCL8_3_20191026


title: Quartet_methy_850K_SNT_LCL8_1_20191026


title: Quartet_methy_850K_SNT_NIST_1_20191026


title: Quartet_methy_850K_SNT_LCL7_3_20191026

value: Male


title: GlucoBAT [BAT-V2_9]


title: GlucoBAT [BAT-V5_11]


title: GlucoBAT [BAT-V2_6]


title: Quartet_methy_850K_SNT_LCL7_2_20191026


title: GlucoBAT [BAT-V2_5]


title: Quartet_methy_850K_SNT_M8_3_20190517


title: GlucoBAT [BAT-V2_4]


title: Quartet_methy_850K_SNT_LCL6_3_20191026


title: GlucoBAT [BAT-V2_3]


title: Quartet_methy_850K_SNT_LCL7_1_20191026


title: Infected, 2d, biol rep 2

value: 2 days co-cultivation


title: Quartet_methy_850K_SNT_LCL6_1_20191026


title: GlucoBAT [BAT-V2_14]


title: GlucoBAT [BAT-V2_15]


title: Quartet_methy_850K_SNT_LCL5_3_20191026


title: GlucoBAT [BAT-V2_13]


title: Quartet_methy_850K_SNT_F7_3_20191026


title: Quartet_methy_850K_SNT_LCL8_2_20191026


title: GlucoBAT [BAT-V2_7]


title: Quartet_methy_850K_SNT_LCL5_1_20191026


title: Quartet_methy_850K_SNT_F7_3_20190517


title: GlucoBAT [BAT-V2_10]


title: Quartet_methy_850K_SNT_LCL5_2_20191026


title: GlucoBAT [BAT-V2_12]


title: Quartet_methy_850K_SNT_F7_2_20191026


title: P024

city: Uppsala

first: Gustav

last: Arvidsson

state: Uppsala

address: Husargatan 3

department: Department of Medical Sciences

country: Sweden

institute: Uppsala Universitet

library_source: transcriptomic single cell

data_processing:
The wrapper function cellranger mkfastq was used to demultiplex samples that were pooled on a illumina NoveSeq 6000 lane and generate fastq files.
Fastq files for the gene expression libraries were aligned to the human reference genome GRCh38 using the prebuilt index “refdata-gex-GRCh38-2020-A” generating a unique molecular identifier (UMI) count matrix for each sample by means of the cell ranger count wrapper function with default settings (5.0.1, 10X Genomics, Pleasanton, California, USA).
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files and matrix files from cellranger count

source_name: Peripheral Blood

extract_protocol:
PBMCs were fractionated from whole peripheral blood samples applying Ficoll-Hypaque density-gradient centrifugation. B cells were isolated from PBMCs by negative selection using a B Cell Isolation Kit II (Miltenyi Biotec, Bergisch Gladbach), where non-B cells were labeled with biotinylated antibodies and subsequently magnetically labeled anti-biotin MACS MicroBeads for depletion using an LD column and magnetic bead separator.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1, 10x Genomics, protocol rev D) aiming to capture 4000–8000 cells per chromium chip lane. Following integrity assessment of the finished libraries by TapeStation, the libraries were sequenced using a NovaSeq 6000 instrument (paired-end sequenced 97 + 26 base pairs, Illumina Inc), aiming for a read depth of 50 000 reads per cell for the GEX libraries and 5 000 reads per cell for the VDJ libraries.

value: Peripheral Blood

tag: patient diagnosis

value: Primary Sjogren’s syndrome (pSS)

value: B cells

tag: group

value: SSAB


title: Quartet_methy_850K_SNT_F7_1_20191026

tag: cell line


title: Quartet_methy_850K_SNT_F7_1_20190517

tag: cell type


title: GlucoBAT [BAT-V2_16]

value: scBAT


title: P022

value: SSA+


title: P023


title: Quartet_methy_850K_SNT_LCL6_2_20191026


title: P021


title: P019


title: Quartet_methy_850K_SNT_D6_2_20191026


title: Quartet_methy_850K_SNT_D6_2_20190517


title: GlucoBAT [BAT-V2_11]


title: P017


title: Quartet_methy_850K_SNT_D6_1_20191026


title: P018


title: P016


title: P015

value: SSA-


title: Quartet_methy_850K_SNT_D5_3_20191026


title: Quartet_methy_850K_SNT_D6_1_20190517


title: P013


title: P014


title: Quartet_methy_850K_SNT_D5_3_20190517


title: Quartet_methy_850K_SNT_F7_2_20190517


title: P012


title: GlucoBAT [BAT-V2_1]

value: Placebo


title: P011


title: P010


title: Quartet_methy_850K_SNT_D6_3_20191026


title: Quartet_methy_850K_SNT_D5_2_20190517


title: Quartet_methy_850K_SNT_D6_3_20190517


title: P020


title: Quartet_methy_850K_SNT_BLD8_3_20191026


title: Quartet_methy_850K_SNT_D5_1_20190517


title: P008b


title: P009


title: Quartet_methy_850K_SNT_BLD8_2_20191026


title: P008a


title: Quartet_methy_850K_SNT_BLD7_3_20191026


title: P007a


title: Quartet_methy_850K_SNT_BLD7_2_20191026


title: Quartet_methy_850K_SNT_D5_2_20191026


title: MEF

city: Seoul

first: Kinarm

last: Ko

address: 120, Neungdong-ro, Gwangjin-gu

institute: Konkuk University

description: control

data_processing: miRNA microarray data were normalized by logarithmic transformation

label: SYBR Green

source_name: Mouse embryonic fibroblast

label_protocol: Mouse miRNome Sanger miRBase micro RNA Profiling Set ( Sytem Biosciences, USA) following the Manufacturer’s instructions. Using 10pg-10ug total RNA, tag all small RNAs with poly-A tails, anneal an oligo-dT adaptor, and generate first-strand cDNA through reverse transcription. Quantitative real-time PCR were performed with 40 cycles at 50 oC for 2minutes, 95 oC for 10minutes, 95 oC for 15 seconds and 60 oC for 1minutes.

extract_protocol: Using RNeasy and miRNeasy Mini Kits (Qiagen, Germany) following the supplier's instructions. Catalog number #RA670A-1

value: Fibroblast


title: Quartet_methy_850K_SNT_BLD6_2_20191026

value: Female


title: P005


title: Quartet_methy_850K_SNT_BLD7_1_20191026

value: normal


title: Quartet_methy_850K_SNT_BLD6_3_20191026

value: immortalized B-lymphoblastoid cell lines


title: Quartet_methy_850K_SNT_D5_1_20191026


title: P004


title: P003


title: P002


title: P001


title: C004

value: healthy

value: CTRL


title: M07e_DMSO_IgG_rep2

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

library_source: genomic

data_processing:
Sequencing reads were mapped to the human hg38 genome build using Bowtie2.
Regions of enrichment (peaks) were identified using SEACRv1.4 in stringent mode and IgG control normalization.
CBFA2T3-GLIS2 (C/G) peaks were identified by intersection of the high confidence peaks from CBFA2T3 and GLIS2 from C/G transduced cord blood samples using Bedtools intersect.
Motif enrichment and peak annotations were completed using Homerversion 4.11 with hg38 promoter sets.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: bed, peak calls from SEACR
Library strategy: Cut&Run

source_name: Blood

growth_protocol: Cells were grown as described in PMID: 36136600, 500K cells were used for all CUT&RUN samples

extract_protocol:
Fresh CB samples were processed with red blood cell lysis buffer, enriched for CD34+ cells using CliniMACS CD34 MicroBeads (Miltenyi Biotec, 130-017-501), and frozen down for the future use. On the day of sort, CD34+ cells from multiple pooled CB samples (8 units each) were thawed and stained with the following antibodies: CD45RA-APC-Cyanine7, CD38-PECy7 (Invitrogen), CD34-PerCP, CD90-BV421, EPCR-BV786, Lineage cocktail (CD3, 14, 16,19,20,56)-FITC (BD Biosciences) and DAPI (to exclude dead cells)
Cut&Run data were generated from human umbilical cord blood samples transduced with CBFA2T3-GLIS2 or GFP control

treatment_protocol: The M07e cell line was seeded at 1x106 cells/ml and cultured in RPMI (Gibco) +10%FBS +1X Glutamax (Gibco) + 10ng/ml IL-3 (STEMCELL Technologies). The WSU-AML cell line was also seeded at 1x106 cells/ml, cultured in RPMI (Gibco) +10%FBS +1X Glutamax (Gibco). Both cell lines were treated with FHD-186 or BRM-014 for 48 hours. FHD-286 was added at 1nM, 10 nM, and 100 nM. BRM-014 was added at 10 nM, 100 nM, and 1000 nM. A DMSO control group was included with each drug treatment. For the CUT&RUN experiments, the M07e line was treated with 100 nM FHD-286 for 24 hours, while the WSU-AML line was treated with 10 nM FHD-286 for 24 hours.

value: Blood

value: leukemia

tag: antibody

value: IgG


title: WSU-AML_DMSO_IgG_rep2

value: WSU-AML


title: Quartet_methy_850K_SNT_BLD8_1_20191026


title: M07e_DMSO_IgG_rep1


title: Quartet_methy_850K_SNT_BLD5_1_20191026


title: WSU-AML_DMSO_IgG_rep1


title: C003

value: Peripheral Blood


title: P006

value: Primary Sjogren’s syndrome (pSS)

value: B cells


title: P007b


title: Quartet_methy_850K_ENG_M8_3_20190517


title: C002


title: ESC

description: control

source_name: Mouse embryonic stem cell

value: Embryonic stem cell


title: NSC

description: test

source_name: Mouse fetal forebrain-derived neural stem cell

value: Neural stem cell


title: C001


title: control2

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

institute: Kanazawa Medical University Hospital

data_processing:
The fastq files were generated using MinKNOW software.
Sequenced reads were mapped to hg38 using Minimap2 (version 2.18) with default parameter.
The quantification and identification of transcripts were analyzed by FLAIR (v1.5.0) with default parameter.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include the counts of transcripts for each Sample
Supplementary files format and content: Matrix table with raw transcript counts for every sample

source_name: PBMC

extract_protocol:
Total RNA of the peripheral blood mononuclear cells and human iPSCs were extracted with TRIzol reagent (Thermo Fisher Scientific) according to manufacturer instructions.
The full-length double-stranded cDNA generated by SMARTer method was captured using TSC1 and TSC2 probe and then the captured double-stranded cDNA was ligated adapter for Nanopore long-read sequencing using the ligation sequencing kit(SQK-LSK109).

value: PBMC

tag: disease

value: control

tag: library type

value: SMARTer


title: TS178_HT_TSC

value: Tuberous sclerosis complex


title: Quartet_methy_850K_ENG_M8_1_20190517

value: Female

value: normal


title: Quartet_methy_850K_SNT_BLD6_1_20191026

value: immortalized B-lymphoblastoid cell lines


title: Quartet_methy_850K_ENG_F7_3_20190517

value: Male


title: control1


title: Quartet_methy_850K_SNT_BLD5_2_20191026


title: ZNF808-KO, S4, 3

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

country: United Kingdom

institute: University of Exeter Medical School

data_processing:
Stranded paired end 150bp RNA-seq reads were aligned to the hg19 genome using STAR and quantified against Gencode v36 release liftover to hg19 by RSEM using the RSEM-STAR pipeline, with additional options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --paired-end”. RSEM estimated read counts per sample were rounded.
Assembly: hg19
Supplementary files format and content: tab delimited file with raw counts for each gene

growth_protocol: Human embryonic stem cells (hESC) (WA01/H1 line, Wicell) were cultured on Matrigel-coated plates (BD Biosciences) in Essential 8 (E8) medium (Life technologies, A1517001) and passaged using EDTA. To carry out the differentiation experiments, hPSC were dissociated using EDTA, then seeded on new Matrigel-coated plates in E8 medium supplemented with 10 µM Rho-Associated kinase inhibitor (ROCKi, catalog no. Y-27632; Selleckchem catalog no. S1049) at a density of 0.21 million cells cm-1. After 24 h, the differentiation was started by washing the cells with PBS, then changing the medium to D0 medium. The differentiation was carried out using our optimized seven-stage protocol as previously described in doi:10.1038/s41587-022-01219-z.

extract_protocol: RNA extraction and library preparation for stranded polyA+ RNA-seq libaries was performed by NovoGene Co Ltd.

value: human embryonic stem cells (hESC)

tag: Stage

tag: genotype

tag: replicate


title: miR-eCLIP miR181-enriched with miR181a/b-1-KO sample3

city: Gießen

first: Andreas

last: Krueger

address: Schubertstr. 81

country: Germany

institute: Justus Liebig University

data_processing:
*library strategy: miR-eCLIP
Data was processed with racoon_clip processing pipeline (v0.0.5). The following steps are included in racoon_clip:
Quality filter: Sequencing reads from chimeric eCLIP were filtered for a Phred score >= 10 inside the unique molecular identifier (UMI) at positions 1-10 of each read
Adapter & UMI trimming: 3’ adapters (Illumina Universal Adapter, Illumina Multiplexing Adapter, and eCLIP adapters 1-20) were trimmed with FLEXBAR (version 3.5.0) 53 using two cycles (--adapter-trim-end RIGHT --adapter-error-rate 0.1 --adapter-min-overlap 1 --adapter-cycles 2). At the same time, UMIs were trimmed from the 5’ end of the reads and stored in the read names (--umi-tags, --barcode-trim-end LTAIL). Reads that were shorter than 15 nt after trimming were discarded (--min-read-length 15).
miR alignment: To separate regular eCLIP reads from chimeric reads generated through ligation of a miRNA and a corresponding mRNA fragment, the read starts were aligned to miRNA sequences from MiRBase 54. For this, filtered and trimmed reads were shortened to the first 24 nt with fastx_trimmer -l 24 (from FASTX-Toolkit, version 0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/). The read starts were then aligned to the matrue miR sequences from MiRBase (accessed 10.10.2022, based on the mm10 genome assembly) with bowtie2 (version 2.4.5, 55 with the following settings: --local -D 20 -R 3 -L 10 -i S,1,0.50 -k 20 --trim5 2, after creating an index of the miR genome assembly with bowtie2-build. The resulting alignment file was split intro read starts from chimeric and regular eCLIP reads using samtools view -f 0 (aligned) and samtools view -f 4 (unaligned), respectively (SAMtools version 1.11, 56. Then, the read names of the unaligned read starts were used to extract the complete regular eCLIP reads from the quality filtered and trimmed fastq files using seqkit grep -n (SeqKit version 2.3.1, 57) which were then sorted with seqkit sort -n. The read starts of chimeric reads were split by the position of their miRNA mapping start (positions 1-4, column 4 in sam file) using awk (mawk 1.3.3). Then, the respective reads were extracted from the quality filtered and trimmed fastq files according to the miRNA mapping start position with seqkit grep -n. Moreover, the names of the miRNA (column 3 of sam file) were extracted using awk and added to the beginning of the read names in the fastq files using seqkit replace -p ‘(.+)’ -r “{{kv}}”. For each miRNA mapping start position, the reads in the fastq files were trimmed by miRNA mapping start plus 21 nt from the 5’ end. Thus, the trimmed reads contained the mRNA portion of the chimeric reads, such that their 5’ position corresponded to the position of the UV crosslink. After trimming, the fastq files of the chimeric reads with miRNA start position 1-4 were merged again using cat. Reads with miRNA mapping starts at later positions were discarded.
Mapping:Regular eCLIP reads and trimmed chimeric reads were aligned to the mouse genome (version GRCm38.p6) using GENCODE gene annotation version M23, CHR with STAR (version 2.7.10, . In short, the genome was indexed with STAR –runMode genomeGenerate. Then, the regular and chimeric eCLIP reads of each sample were individually aligned to the genome with STAR –runMode alignReads (--sjdbOverhang 139, --outFilterMismatchNoverReadLmax 0.04, --outFilterMismatchNmax 999, -- outFilterMultimapNmax 1, --alignEndsType "Extend5pOfRead1", --outReadsUnmapped: "Fastx", --outSJfilterReads "Unique"). Obtained bam files were indexed with samtools index.
Duplicate removal:  umi_tools dedup --extract-umi-method read_id --method unique (UMI-tools version 1.1.1, 60).
Assembly: GRChm38.p6
Supplementary files format and content: bigWig (crosslink event per position): The deduplicated bam files of regular and trimmed chimeric eCLIP reads were converted into bed files using bedtools bamtobed (version 2.30.0) . The reads were the shifted by 1 nt upstream with bedtools shift -m 1 -p -1 because the UV crosslink sites should be positioned 1 nt upstream of the eCLIP read starts. The bed files were split into plus and minus strand, and the reads were then reduced to 1-nt crosslink events using awk. To allow for visualization, the bed files of 1 nt events were converted to bigWig files using bedGraphToBigWig (ucsc-bedgraphtobigwig version 377).
Supplementary files format and content: bed (chimeric reads): the miRNA name was extracted from the read name using awk. The bed files were split into plus and minus strand, and the reads were then reduced to 1-nt crosslink events using awk.

source_name: thymocytes

extract_protocol:
Total thymocytes were extracted from thymy using 70µm strainers.  Isolated cells were then crosslinked using a using 254nm UV-C Mercury bulb in the (Analytik Jena CL-1000M). Cells were frozen and sent to Eclipse Bioinnovations (San Diego, 92121 CA, USA).
Library construction was performed by Eclise Bioinnovations. No modifications were made to the published eCLIP methodology for this experiment. 20ug of total RNA was used per sample.
Sequencing was performed as PE150 on the NextSeq platform.

treatment_protocol: Mice were grown to 6 weeks of age under SPF conditions.

value: thymocytes

tag: treatment/ip


title: miR-eCLIP miR181-enriched with miR181a/b-1-KO sample1


title: miR-eCLIP miR181-enriched  sample3


title: Quartet_methy_850K_ENG_D6_3_20190517

tag: Sex

tag: disease state


title: Quartet_methy_850K_ENG_F7_1_20190517


title: ZNF808-KO, S2, 3


title: miR-eCLIP miR181-enriched  sample2


title: Quartet_methy_850K_ENG_F7_2_20190517


title: miR-eCLIP miR181-enriched with miR181a/b-1-KO sample2


title: Quartet_methy_850K_SNT_BLD5_3_20191026


title: WT-H1, S3, 3

value: WT


title: Quartet_methy_850K_ENG_D6_1_20190517


title: Quartet_methy_850K_ENG_M8_2_20190517


title: miR-eCLIP miR181-enriched sample1


title: Quartet_methy_850K_ENG_D6_2_20190517


title: miR-eCLIP_InputControl_Ago2IP_miR181KO_s3

value: input


title: ZNF808-KO, S3, 3


title: Quartet_methy_850K_ENG_D5_3_20190517


title: WT-H1, S2, 3


title: WT-H1, S4, 3


title: WT_7PM_biol rep 6

city: College Statioon

first: Vinaya

last: Shetty

state: TX

address: Heep Center, 2475 TAMU, 370 Olsen Blvd

department: Entomology

institute: Texas A&M University

data_processing:
The resulting sequences were evaluated for quality using FastQC (version 0.11.9.). Paired end adaptors were trimmed using TrimGalore v.0.6.6.
The Ae. aegypti genome sequence (version: AaegL5_2) from Vectorbase was used for mapping and alignments by HISAT2 (version 2.2.1). Raw read indexing and sorting alignments were performed using SAMtools (version 1.11) and count files were generated using HTseq (version 0.11.3).
Assembly: The Ae. aegypti genome sequence (version: AaegL5_2) from Vectorbase was used for mapping and alignments by HISAT2 (version 2.2.1).
Supplementary files format and content: Raw read indexing and sorting alignments were performed using SAMtools (version 1.11) and count files were generated using HTseq (version 0.11.3).
Supplementary files format and content: count files were generated using HTseq (version 0.11.3).

organism: Aedes aegypti

source_name: Whole body

extract_protocol:
Total RNA was isolated from each sample using miRNeasy (Qiagen) columns using the protocol provided by Qiagen.
Messenger RNA was enriched from about 1 μg of total RNA using the Poly-A enrichment method and cDNA libraries were prepared using an Illumina TruSeq RNA Library kit (Illumina).

tag: tissue

value: Whole body

value: female

value: Wildtype

tag: zitgeber time_point


title: miR-eCLIP_InputControl_Ago2IP_miR181KO_s2


title: Quartet_methy_850K_ENG_D5_2_20190517


title: WT-H1, S1, 3


title: WT_7PM_biol rep 5

tag: treatment


title: ZNF808-KO, S0, 3


title: miR-eCLIP_InputControl_Ago2IP_miR181KO_s1


title: Quartet_methy_850K_ENG_D5_1_20190517


title: WT-H1, S0, 3


title: miR-eCLIP_InputControl_Ago2IP_s3


title: WT_7PM_biol rep 4


title: Quartet_methy_850K_BIO_NIST_3_20170314

value: NIST


title: WT_7PM_biol rep 3


title: ZNF808-KO, S1, 3


title: Quartet_methy_850K_BIO_NIST_2_20170314


title: WT-H1, S4, 2


title: WT_7PM_biol rep 2


title: miR-eCLIP_InputControl_Ago2IP_s1


title: Quartet_methy_850K_BIO_LCL8_3_20170314


title: ZNF808-KO, S4, 2


title: ZNF808-KO, S3, 2


title: WT_7PM_biol rep 1


title: Quartet_methy_850K_BIO_NIST_1_20170314


title: CycKO_7PM_biol rep 6

value: Cycle gene knockout


title: miR-eCLIP Ago2IP with miR181a/b-1-KO sample2


title: miR-eCLIP Ago2IP with miR181a/b-1-KO sample3


title: CycKO_7PM_biol rep 5


title: WT-H1, S3, 2


title: Quartet_methy_850K_BIO_LCL8_2_20170314


title: ZNF808-KO, S2, 2


title: miR-eCLIP Ago2IP with miR181a/b-1-KO sample1


title: Quartet_methy_850K_BIO_LCL8_1_20170314


title: Quartet_methy_850K_BIO_LCL7_3_20170314


title: WT-H1, S2, 2


title: CycKO_7PM_biol rep 3


title: miR-eCLIP Ago2IP sample3


title: miR-eCLIP_InputControl_Ago2IP_s2


title: ZNF808-KO, S1, 2


title: Quartet_methy_850K_BIO_LCL7_2_20170314


title: CycKO_7PM_biol rep 2


title: miR-eCLIP Ago2IP sample2


title: Quartet_methy_850K_BIO_LCL7_1_20170314


title: WT-H1, S1, 2


title: miR-eCLIP Ago2IP sample1


title: WT-H1, S0, 2


title: WT_3PM_biol rep 6


title: Quartet_methy_850K_BIO_LCL6_3_20170314


title: Quartet_methy_850K_BIO_LCL6_2_20170314


title: WT_3PM_biol rep 5


title: ZNF808-KO, S0, 2


title: MM134 cells, 10 nM E2, 100 nM Dex, biol rep 2

city: Dallas

first: Baylee

middle: A

last: Porter

address: 5323 Harry Hines Blvd.

department: Internal Medicine

institute: UT Southwestern Medical Center

data_processing:
Raw data from the sequencer were demultiplexed and converted to fastq files using bcl2fastq (v2.17, Illumina)
The fastq files were checked for quality using fastqc (v0.11.2) and fastq_ screen (v0.4.4)
Fastq files were mapped to the human hg19 reference genome (from iGenomes) using STAR
Read counts were then generated using featureCounts
Assembly: human hg19

source_name: Breast; Mammary Gland

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
TruSeq Stranded mRNA library prep kit (Illumina) was used to generate the mRNA libraries

treatment_protocol: 100 nM Dexamethasone (Sigma), 10 nM E2 (Sigma), 0.1% ETOH, or 100 nM Dexamethasone plus 10 nM E2 in charcol stipped-FBS for 6 hours.

value: Breast; Mammary Gland

value: Breast cancer cell line

value: Wild type

value: 10 nM E2, 100 nM Dex


title: MM134 cells, 10 nM E2, 100 nM Dex, biol rep 1


title: ZNF808-KO, S4, 1


title: WT_3PM_biol rep 4


title: Quartet_methy_850K_BIO_LCL6_1_20170314

value: Female


title: WT-H1, S4, 1


title: CycKO_7PM_biol rep 4


title: MM134 cells, 100 nM Dex, biol rep 1

value: 100 nM Dex


title: CycKO_7PM_biol rep 1


title: WT_3PM_biol rep 3


title: MM134 cells, 100 nM Dex, biol rep 2


title: Quartet_methy_850K_BIO_LCL5_2_20170314

value: normal

value: immortalized B-lymphoblastoid cell lines


title: ZNF808-KO, S3, 1

value: human embryonic stem cells (hESC)


title: MM134 cells, 10 nM E2, biol rep 2

value: 10 nM E2


title: WT_3PM_biol rep 2


title: WT-H1, S3, 1

value: WT


title: MM134 cells, 10 nM E2, biol rep 1


title: Quartet_methy_850K_BIO_LCL5_1_20170314


title: WT_3PM_biol rep 1


title: ZNF808-KO, S2, 1


title: Quartet_methy_ILM_850K_SNT_M8_CGZ302_7002083


title: MM134 cells, Vehicle (ETOH), biol rep 2

value: Vehicle (100% ETOH)


title: CycKO_3PM_biol rep 6

value: Whole body


title: Quartet_methy_ILM_850K_SNT_F7_CGZ302_6993619

value: Male


title: WT-H1, S2, 1


title: MM134 cells, Vehicle (ETOH), biol rep 1


title: ZNF808-KO, S1, 1


title: SUM44-GR-GFP cells, 10 nM E2 plus 100 nM Dex, biol rep 2

treatment_protocol: 100 nM Dexamethasone (Sigma), 10 nM E2 (Sigma), 100% ETOH, or 100 nM Dexamethasone plus 10 nM E2 in charcol stipped-FBS for 6 hours.

value: GR-GFP


title: CycKO_3PM_biol rep 4

value: female


title: CycKO_3PM_biol rep 5

value: Cycle gene knockout


title: WT-H1, S1, 1


title: Quartet_methy_ILM_850K_SNT_M8_CGZ302_7000912


title: CycKO_3PM_biol rep 3


title: Quartet_methy_850K_BIO_LCL5_3_20170314


title: Quartet_methy_ILM_850K_SNT_F7_CGZ302_7000913


title: Quartet_methy_ILM_850K_SNT_D5_CGZ302_7002084


title: SUM44-GR-GFP cells, 10 nM E2 plus 100 nM Dex, biol rep 1

value: Breast; Mammary Gland


title: CycKO_3PM_biol rep 2


title: SUM44-GR-GFP cells, 100 nM Dex, biol rep 2

value: Breast cancer cell line


title: WT-H1, S0, 1


title: SUM44-GR-GFP cells, 100 nM Dex, biol rep 1


title: Quartet_methy_ILM_850K_SNT_F7_CGZ301_6993478


title: CycKO_3PM_biol rep 1


title: SUM44-GR-GFP cells, 10 nM E2, biol rep 2


title: H1, S4, input

data_processing:
Reads from each library were mapped on hg19 using Bowtie2 version 2.4.4 with the ‘very-sensitive-local’ setting. Mapped reads were compressed in BAM files and indexed using SAMtools version 1.1841. We used MACS2 2.2.7.1 to call peaks using the corresponding input datasets as background controls
Assembly: hg19
Supplementary files format and content: broadPeak Files

extract_protocol: Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® following to the manufacturer’s instructions.

tag: chip antibody


title: ZNF808-KO, S0, 1


title: H1, ZNF808KO, S4, input


title: WT_11AM_biol rep 6

value: Wildtype


title: Quartet_methy_ILM_850K_SNT_D6_CGZ301_6991154


title: Quartet_methy_ILM_850K_SNT_F7_CGZ302_7001074


title: SUM44-GR-GFP cells, 10 nM E2, biol rep 1


title: H1, ZNF808KO, S3, input


title: SUM44-GR-GFP cells, Vehicle (100% ETOH), biol rep 2


title: WT_11AM_biol rep 4


title: Quartet_methy_ILM_850K_SNT_M8_CGZ302_6993611


title: H1, S3, input


title: WT_11AM_biol rep 5


title: Quartet_methy_ILM_850K_SNT_F7_CGZ302_6993635


title: WT_11AM_biol rep 3


title: DS_CV_3: Down's syndrome chorionic villi DS_CV

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

institute: Cardiff University

data_processing:
FastQ files that contained high quality RNA sequencing reads were aligned to the 'GRCh38/hg38' genome build using HISAT2
DESeq2 was used to identify significant differential expression between samples
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file including per sample: Ensembl gene ID, total counts

source_name: Chorionic villi

growth_protocol: Both cells types (CV and DS-CV) were grown on standard culture medium consisting of HG-DMEM supplemented with 10% FBS, 1% L-glutamine and 1% of antimicotic/antibiotics

extract_protocol:
Cells were trypsinized, washed with PBS and total RNA extraction was performed using total RNA Purification Plus Kit (Norgen). RNA concentration and integrity were assessed using the RNA 6000 Nano Kit (Agilent Technologies).
cDNA libraries were prepared using the TruSeq stranded mRNA kit (Illumina)

value: Down's Syndrome

value: Chorionic villi

value: Mesenchymal stem cells (MSCs)


title: Quartet_methy_ILM_850K_SNT_F7_CGZ301_6991155

value: normal


title: WT_11AM_biol rep 2


title: Quartet_methy_ILM_850K_SNT_D6_CGZ302_8685692

value: Female

value: immortalized B-lymphoblastoid cell lines


title: H1, S2, input

value: human embryonic stem cells (hESC)


title: H1, ZNF808KO, S2, input


title: WT_11AM_biol rep 1


title: H1, ZNF808KO, S1, input


title: DS_CV_1: Down's syndrome chorionic villi DS_CV


title: Quartet_methy_ILM_850K_SNT_D6_CGZ302_7001075


title: CycKO_11AM_biol rep 6


title: H1, S1, input

value: WT


title: CV_2: Chorionic villi CV

value: Control


title: H1, ZNF808KO, S0, input


title: Quartet_methy_ILM_850K_SNT_D6_CGZ302_7002125


title: CV_3: Chorionic villi CV


title: CycKO_11AM_biol rep 4

value: Whole body


title: Quartet_methy_ILM_850K_SNT_D5_CGZ301_6993518


title: CycKO_11AM_biol rep 5


title: Quartet_methy_ILM_850K_SNT_M8_CGZ302_6993559


title: H1, S0, input


title: SUM44-GR-GFP cells, Vehicle (100% ETOH), biol rep 1

value: Vehicle (100% ETOH)


title: H1, ZNF808KO, S4, H3K27ac

value: Histone H3K27ac antibody (mAb) - Catalog number 39685, Active Motif


title: Quartet_methy_ILM_850K_SNT_F7_CGZ302_7002162

value: Male


title: CV_1: Chorionic villi CV


title: CycKO_11AM_biol rep 2

value: female

value: Cycle gene knockout


title: CycKO_11AM_biol rep 3


title: Control06

city: Sacramento

first: JAEHWAN

last: KIM

state: CA

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

data_processing:
CellRanger version 3.1 (10X Genomics) pipelines were used for demultiplexing base calls into Fastq, filtering, barcode counting and filtering, UMI counting and alignment with reference human genome GRCh38.
The quality control, normalization, linear regression of number of UMIs and scaling were performed using Seurat (v4.0).
Seurat R package (version 4.0, https://satijalab.org/seurat/) was used for the single-cell data integration. We first merged single-cell data of samples with the common sequencer and the identical reagent kit version. To harmonize merged groups into a single dataset without batch effects, correspondences between cells in three merged datasets were identified by the FIndIntegrationAnchors function, and used for data integration with the IntegratedData function in Seurat R package.
Principal component analysis and graph-based clustering analysis were performed with Seurat R package (version 4.0, https://satijalab.org/seurat/). Sixty principal components (PCs) were selected for Uniform Manifold Approximation and Projection (UMAP) for Dimension Reduction. With a resolution of 0.8, cells were clustered by the FindClusters function. Then, differentially expressed genes of each cluster compared to all other cells were found by the FindAllMarkers function. Differentially expressed genes between psoriasis and control within each cluster were found by the FindMarkers function. The average gene expression of psoriasis vs. control cells within a cluster was calculated by the AverageExpression function.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcode table, gene table and gene expression matrix files generated by Cell Ranger version 3.1.

source_name: Control skin from a healthy volunteer

extract_protocol:
6 mm punch skin biopsy tissues from human skin were bisected, and one of the two bisected skin tissues was incubated in culture medium for harvesting emigrating cells. Harvested skin tissue was immediately placed in 0.2% Dispase II (Sigma-Aldrich) and incubated in a humidified incubator at 37 Celsius and 5% CO2 for 3 hours. Then, epidermis and dermis were separated with forceps and sliced into small pieces with #10 blade scalpels. Epidermis and dermis were separately cultured in RPMI-1640 medium with L-glutamine (Cytiva) supplemented with 10% human albumin serum (Sigma-Aldrich) and without any enzyme or antibiotic agent in a humidified incubator at 37 Celsius and 5% CO2. Nonplastic adherent cells that had emigrated out of epidermis and dermis were harvested after 48 hours. The harvested cells from epidermis and dermis were filtered through a 40-µm cell strainer (Corning) and stored on ice.
The 10x Genomics Chromium Single Cell 3′ Reagents Kit user guide (https://support.10xgenomics.com/single-cell-gene-expression/library-prep) was used to prepare the single cell suspension. The appropriate volume of each sample was diluted to recover 10,000 cells. Subsequently, the single cell suspension, Gel Beads and oils were added to the 10x Genomics single-cell chip. After droplet generation, samples were transferred into PCR tubes and we performed reverse transcription using a ProFlex PCR Thermocycler System (Applied Biosystems). After reverse transcription, cDNA was recovered using a recovery agent, provided by 10x Genomics, followed by silane DynaBead clean-up as outlined in the user guide.

tag: study protocol

tag: jkr-0937 group

tag: time point

value: Baseline

tag: visit

value: Visit 2

tag: lesion

tag: psoriasis area-and-severity index

tag: biopsy collection date


title: H1, S4, H3K27ac

tag: cell line

tag: cell type

tag: Stage


title: Quartet_methy_ILM_850K_SNT_D6_CGZ301_6993558


title: Control05


title: H1, ZNF808KO, S3, H3K27ac

tag: genotype


title: DS_CV_2: Down's syndrome chorionic villi DS_CV

value: Down's Syndrome


title: Quartet_methy_ILM_850K_SNT_M8_CGZ302_6993638

tag: Sex


title: CycKO_11AM_biol rep 1


title: Control04


title: H1, S3, H3K27ac


title: Control03


title: WT_7AM_biol rep 6

value: Wildtype


title: H1, ZNF808KO, S2, H3K27ac


title: Quartet_methy_ILM_850K_SNT_D5_CGZ302_7002144

tag: disease state


title: WT_7AM_biol rep 5

tag: tissue


title: Quartet_methy_ILM_850K_SNT_M8_CGZ301_6993606


title: Quartet_methy_ILM_850K_SNT_M8_CGZ301_8685885


title: Control02


title: WT_7AM_biol rep 4

tag: zitgeber time_point


title: H1, S2, H3K27ac


title: WT_7AM_biol rep 3

tag: treatment


title: H1, ZNF808KO, S1, H3K27ac

tag: chip antibody


title: Psoriasis10_preTx_LS

source_name: Psoriasis lesional skin before secukinumab treatment

tag: study protocol

value: Visit 8


title: Quartet_methy_ILM_850K_SNT_D6_CGZ302_7002126

value: normal


title: Quartet_methy_ILM_850K_SNT_D5_CGZ302_6993598

value: Female


title: WT_7AM_biol rep 2


title: H1, S1, H3K27ac


title: Psoriasis09_preTx_LS

tag: jkr-0937 group


title: WT_7AM_biol rep 1


title: Quartet_methy_ILM_850K_SNT_F7_CGZ301_6993663

value: immortalized B-lymphoblastoid cell lines


title: Quartet_methy_ILM_850K_SNT_D5_CGZ302_6993599


title: H1, ZNF808KO, S0, H3K27ac

value: human embryonic stem cells (hESC)


title: H1, S0, H3K27ac

value: WT


title: CycKO_7AM_biol rep 5


title: CycKO_7AM_biol rep 6


title: Quartet_methy_ILM_850K_SNT_D6_CGZ301_6993648


title: CycKO_7AM_biol rep 4


title: H1, ZNF808KO, S4, H3K9me3

value: Histone H3K9me3 antibody (pAb) - Catalog number 39161, Active Motif


title: H1, S4, H3K9me3


title: Psoriasis08_postTx_week24_LS

source_name: Psoriasis lesional skin 24 weeks after secukinumab treatment

tag: time point

value: Visit 14


title: Psoriasis07_preTx_NL_02

source_name: Psoriasis nonlesional skin before secukinumab treatment

tag: visit


title: H1, ZNF808KO, S3, H3K9me3


title: Quartet_methy_ILM_850K_SNT_D5_CGZ301_8685798

source_name: genomic DNA from B lymphocyte


title: Control01

tag: lesion

value: Control


title: Quartet_methy_ILM_850K_SNT_D6_CGZ301_6993526


title: CycKO_7AM_biol rep 2

value: Whole body


title: H1, S3, H3K9me3


title: CycKO_7AM_biol rep 3


title: Quartet_methy_ILM_850K_SNT_F7_CGZ301_6993607

value: Male


title: H1, S2, H3K9me3


title: Psoriasis07_postTx_week48_LS

source_name: Psoriasis lesional skin 48 weeks after secukinumab treatment

value: Visit 17

tag: psoriasis area-and-severity index


title: CycKO_7AM_biol rep 1

value: female

value: Cycle gene knockout


title: wild-type strain 518, replicate 3

city: Puebla

first: Patricia

last: Sanchez-Alonso

state: Puebla

address: Av. San Claudio y 24 Sur, Col. San Manuel

department: Centro de Investigaciones en Ciencias Microbiologicas

country: Mexico

institute: Instituto de Ciencias, Benemerita Universidad Autonoma de Puebla

description:
WT-518_vs_ter1-02_Intersect.txt
WT-518_vs_ter1-24_Intersect.txt

data_processing:
Basecalls were performed using bcl2fastq2 v2.18
FastQC v.0.11.9: To check quality reports
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.36 (TruSeq3-PE-2.fa:2:30:10:1:true SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 AVGQUAL:30 MINLEN:25)
Trimmed sequence reads were mapped to Ustilago_maydis.Umaydis521_2.0. and quantified using Trinity v2.11.0 pipeline ($TRINITY_DIR/util/align_and_estimate_abundance.pl –seqType fq --samples_file samples.txt --est_method RSEM --aln_method bowtie2)
Read count extraction and normalization were performed using Trinity v2.11.0 pipeline ($TRINITY_DIR/util/abundance_estimates_to_matrix.pl --est_method RSEM)
Differential expression analysis was performed using the IDEAMEX online platform (http://www.uusmb.unam.mx/ideamex/) (parameters- logFC ≥ 2, FDR ≤ 0.01, CPM = 1)
Trinotate v3.2.2 : To make Annotation
Assembly: Reference sequence: https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi/release-56/fasta/ustilago_maydis/cds/Ustilago_maydis.Umaydis521_2.0.cds.all.fa
Supplementary files format and content: *_Intersect.txt: Tab-delimited text file with the following columns: logarithm base 2 of fold Change (logFC), logCoutPerMillon (logCPM), Pvalue, False Discovery Rate (FDR), columns for each sample with raw counts, results of Differential Expression, and Regulation. columns with normalized counts for each sample, results of differential expression, and regulation.

organism: Mycosarcoma maydis

extract_protocol:
Total RNA extraction from haploid cells of Ustilago maydis was performed as previously described Sanpedro-Luna et al., 2023
RNA libraries for RNA-seq were prepared using TruSeq RNA sample prep Kit v2 LT following manufacturer's protocols.

value: haploid cells


title: H1, ZNF808KO, S2, H3K9me3


title: Quartet_methy_ILM_850K_SNT_M8_CGZ301_6993519


title: Psoriasis08_postTx_week12_LS

source_name: Psoriasis lesional skin 12 weeks after secukinumab treatment

tag: biopsy collection date


title: wild-type strain 518, replicate 2

tag: cell line


title: Quartet_methy_ILM_850K_SNT_D5_CGZ302_6993639

tag: cell type


title: H1, ZNF808KO, S1, H3K9me3

tag: Stage


title: wild-type strain 518, replicate 1

tag: genotype


title: Psoriasis06_preTx_LS

value: Baseline

value: Visit 2


title: Psoriasis07_postTx_week12_LS


title: Psoriasis08_preTx_LS


title: Quartet_methy_ILM_850K_SNT_F7_CGZ302_7002143

tag: Sex


title: Psoriasis05_preTx_LS


title: mutant ter1 negative, strain ter1-24, replicate 3

description:
WT-518_vs_ter1-24_Intersect.txt
ter1-02_vs_ter1-24_Intersect.txt

value: ter1 knockdown

value: a2b2, ter1::hph


title: H1, ZNF808KO, S0, H3K9me3


title: Psoriasis05_postTx_week12_LS

value: Visit 8


title: mutant ter1 negative, strain ter1-24, replicate 2


title: H1, S0, H3K9me3


title: Psoriasis07_preTx_LS


title: Quartet_methy_ILM_850K_SNT_D6_CGZ302_6993610

value: Female

tag: disease state

value: normal

value: immortalized B-lymphoblastoid cell lines


title: Psoriasis04_preTx_LS


title: mutant ter1 negative, strain ter1-24, replicate 1

tag: tissue


title: Psoriasis04_postTx_week12_LS


title: Quartet_methy_ILM_850K_SNT_D5_CGZ301_8685714


title: Quartet_methy_ILM_850K_SNT_M8_CGZ302_7002161


title: mutant ter1 negative, strain ter1-02, replicate 3

description:
WT-518_vs_ter1-02_Intersect.txt
ter1-02_vs_ter1-24_Intersect.txt


title: Control08


title: Quartet_methy_ILM_850K_SNT_D5_CGZ301_6993527


title: Control09


title: Psoriasis02_preTx_LS


title: mutant ter1 negative, strain ter1-02, replicate 1


title: mutant ter1 negative, strain ter1-02, replicate 2


title: Control07


title: H1, S1, H3K9me3

value: human embryonic stem cells (hESC)

value: WT

value: Histone H3K9me3 antibody (pAb) - Catalog number 39161, Active Motif


title: Psoriasis01_preTx_LS


title: Quartet_methy_ILM_850K_SNT_M8_CGZ301_8685799


title: PumKO1 biological rep2

status: Public on Sep 03 2023

city: Minneapolis

first: Aaron

middle: C

last: Goldstrohm

state: MN

address: 321 Church Street S.E.

department: Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

data_processing:
sequencing adapters were trimmed and unique molecular identifiers (UMIs) annotated using fastp (version 0.14.1)
reads were aligned to the UCSC dm6 genome using hisat2 (version 2.1.0).
The alignments were then deduplicated using UMI-tools (version 1.0.1) and differential expression was analyzed using DEseq2 (1.23.110) and featureCounts (Rsubreads 1.30.9).
Assembly: dm6

organism: Drosophila melanogaster

source_name: cell line

growth_protocol: DL1 cells were grown in SDM media

extract_protocol:
RNA was purified using the Maxwell RSC simply RNA tissue extraction kit (Promega) with on-bead DNase I digestion. The RNA concentration was determined using a NanoDrop spectrophotometer. RNA samples were submitted for Agilent Tapestation analysis and RNA integrity number (RIN) values were 8.7-10. Total RNA was poly(A) selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolab).
We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. We then amplified the cDNA for 21 cycles with Universal primer and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 75 base-pair reads on a Nextseq 550 (Illumina).

treatment_protocol: For RNAi experiments, cells (3 million cells in 1 mL of serum free SDM per well of a 6-well dish) were bathed with 20 µg of dsRNA corresponding to either Pum, Not1, Pop2, or LacZ non-targeting control for 60 minutes. Then 2 mL of SDM containing 5% heat-inactivated FBS was added to each well. After 48 hours, the cells were harvested by centrifugation and suspended in 2 mL Phosphate Buffered Saline (PBS). RNA was purified from 1.5 mL of the cells, and the remaining 0.5 mL was reserved for western blot analysis.

value: cell line

value: Pumilio knockout


title: PumKO1 biological rep3


title: WT biological rep3

value: wild type


title: PumKO1 biological rep1


title: Control10

value: Control


title: Pop2RNAi biological rep3

value: RNAi


title: Pop2RNAi biological rep1


title: Pop2RNAi biological rep2


title: Quartet_methy_ILM_850K_SNT_D5_CGZ302_6993618


title: Not1RNAi biological rep2


title: Psoriasis03_preTx_LS


title: PumRNAi biological rep2


title: PumRNAi biological rep3


title: PumKO2 biological rep3


title: LacZRNAi biological rep3


title: LacZRNAi biological rep1


title: PumKO2 biological rep1


title: LacZRNAi biological rep2


title: WT biological rep2


title: Colon tissue from mice treated with PD 2

city: Louisville

first: Fangyi

last: Xu

state: Kentucky

address: 505 S Hancock street

department: BCC cancer center

institute: University of Louisville

description: Mice tissue (n=4) were dissected and pooled

hyb_protocol: Samples were hybridization to Applied Biosystem’s GeneChip™ miRNA 4.0 Array (Thermo Fisher Scientific, Waltham, MA) at 48°C for 18 hours.

scan_protocol: Affymetrix GeneChip® 7G scanner

data_processing: Data were analyzed using Transcription Analysis Software TAC (ThermoFisher, Waltham, MA).

label: Biotin

source_name: Colon tissue from mice treated with PD

label_protocol: RNA was labeled using Applied Biosystem’s FlashTag™ Biotin HSR RNA Labeling Kits (Thermo Fisher Scientific, Waltham, MA)

growth_protocol: Mouse colon dissected from 8-week-old mouse

extract_protocol: Samples were homogenerlized using Fastprep 24 Homogenizer (MP) in Qiazol lysis buffer. miRNA (500 ng) were extracted using the miRNeasy mini kit.

treatment_protocol: Each group of mice (n=8) were respectively fed with Trp depleted diet (TrpD, 0% tryptophan, w/w) or a paired diet (PD, 1.2% tryptophan, w/w).

value: colon

tag: age

tag: strain

value: paired diet (PD, 1.2% tryptophan, w/w)

tag: molecule

value: miRNA


title: Colon tissue from mice treated with PD 1

tag: treatment


title: Colon tissue from mice treated with TrpD 2

value: Trp depleted diet (TrpD, 0% tryptophan, w/w)


title: BMDM cells, untreated BMDM cells, 12 h, biol rep 3

city: Livermore

first: Cody

middle: Scott

last: Madsen

state: California

address: 4000 East Avenue Bldg 411

department: Biosciences and Biotechnology Division

institute: Lawrence Livermore National Lab

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0
RNA-seq data was analyzed using FastQC (v0.11.7), GNU parallel (20180422), Trimmomatic (0.39), STAR (2.6.0c) and featureCounts to generate the count table for all treatments and time points
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file for raw counts including all samples and time points

source_name: Bone marrow

growth_protocol: NA. Bone marrow derived macrophages were simply maintained in culture after extraction

extract_protocol:
Total RNA that was extracted by a Qiagen RNeasy kit (Qiagen, cat#74104) with RNase-free DNase Set (Qiagen, cat#79254) for NGS library preparation and sequencing
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit with IDT for Illumina TruSeq Unique Dual Index adapters following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays

treatment_protocol: Bone marrow derived macrophages were maintained at 37°C and 5% CO2 in DMEM (ThermoFisher, MA, USA), supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin and 100 U/mL recombinant macrophage colony-stimulating factor (M-CSF). BMDMs were maintained in these conditions for 7 days before being seeded at 5x104 into 96-well plates or 7x105-1x106 in 6-well plates and allowed to adhere overnight without penicillin-streptomycin

value: Bone marrow

value: Bone marrow derived macrophages

value: macrophage

value: untreated BMDM cells

tag: time


title: Not1RNAi biological rep3


title: BMDM cells, untreated BMDM cells, 24 h, biol rep 2


title: BMDM cells, untreated BMDM cells, 24 h, biol rep 1


title: Small intestine from mice treated with TrpD [HZ_B6_TrpD_SI_Tis_2]

description:
Mice tissue (n=4) were dissected and pooled
HZ_B6_TrpD_SI_Tis_2

growth_protocol: Mouse SI and colon dissected from 8-week-old mouse

value: Small intestine

tag: molecule subtype


title: Small intestine from mice treated with PD [HZ_B6_PD_SI_Tis_1]

description:
Mice tissue (n=4) were dissected and pooled
HZ_B6_PD_SI_Tis_1


title: Not1RNAi biological rep1


title: PumRNAi biological rep1


title: BMDM cells, Stat-1Klf6 with mannose, 12 h, biol rep 3

value: Stat-1Klf6 strain with mannose


title: Small intestine from mice treated with PD [HZ_B6_PD_SI_Tis_2]

description:
Mice tissue (n=4) were dissected and pooled
HZ_B6_PD_SI_Tis_2


title: Small intestine from mice treated with TrpD [HZ_B6_TrpD_SI_Tis_1]

description:
Mice tissue (n=4) were dissected and pooled
HZ_B6_TrpD_SI_Tis_1


title: WT biological rep1


title: Colon tissue from mice treated with TrpD 1


title: BMDM cells, Stat-1Klf6 with mannose, 12 h, biol rep 1

value: WT


title: BMDM cells, Stat-1Klf6 without mannose, 12 h, biol rep 3

value: Stat-1Klf6 strain without mannose


title: BMDM cells, Stat-1Klf6 with mannose, 12 h, biol rep 2


title: BMDM cells, Stat-1Klf6 with mannose, 24 h, biol rep 1


title: BMDM cells, untreated BMDM cells, 24 h, biol rep 3


title: BMDM cells, Stat-1Klf6 without mannose, 12 h, biol rep 2


title: BMDM cells, untreated BMDM cells, 12 h, biol rep 2


title: BMDM cells, Stat-1Klf6 without mannose, 12 h, biol rep 1


title: BMDM cells, extracellular bacteria control, 24 h, biol rep 3

value: LLO strain without IPTG


title: BMDM cells, untreated BMDM cells, 12 h, biol rep 1


title: PumKO2 biological rep2

value: cell line

value: Pumilio knockout


title: BMDM cells, extracellular bacteria control, 12 h, biol rep 2


title: BMDM cells, extracellular bacteria control, 24 h, biol rep 1


title: BMDM cells, extracellular bacteria control, 12 h, biol rep 1


title: BMDM cells, extracellular bacteria control, 12 h, biol rep 3


title: BMDM cells, extracellular bacteria control, 24 h, biol rep 2


title: BMDM cells, mannose sugar positive control, 12 h, biol rep 3

value: D-mannose


title: BMDM cells, Stat-1Klf6 with mannose, 24 h, biol rep 2


title: Psoriasis07_preTx_LS_02

tag: study protocol

tag: jkr-0937 group

tag: time point

tag: visit

value: Visit 8


title: BMDM cells, mannose sugar positive control, 24 h, biol rep 2

tag: cell line


title: Naringenin4 (C4)

city: guangzhou

first: jiashuo

last: zhang

address: 135 Xingang West Road, Guangzhou

institute: Sun Yat-sen University

description: Rat trachea was digested by 0.25% pancreatin at 4℃ for 24h, and then centrifuged to obtain rat airway epithelial cells

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: ftp://ftp.ensembl.org/pub/release-101/fasta/rattus_norvegicus/dna/
Supplementary files format and content: excel,expression profiles

organism: Rattus norvegicus

source_name: mRNA from airway epithelium cells

growth_protocol: The airway epithelium cells  were collected in PneumaCult-Ex plus (Stemcell, BC, Canada) and spread onto 12-well inserts of transwell plates (JET, Guangzhou, China). At about 80%-95% confluency, the rat airway epithelial cells were initiated by removing the PneumaCult-Ex plus from inserts leaving the apical surface exposed to air, and changing the PneumaCult-Ex plus to PneumaCult-ALI (Stemcell, BC, Canada). The cells were maintained at 37℃ with 5% CO2 for 3-4 weeks and the medium was replaced three times per week.

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: The airway epithelium cells were divided into three groups, depending on the different treatments with or without 10% CSE, or 100 μM naringenin for 24 h.

tag: cell type

value: airway epithelium cells

value: the airway epithelium cells were co-treated with 10% CSE and 100uM naringenin after naringenin pretreated for 4h;


title: BMDM cells, mannose sugar positive control, 12 h, biol rep 2


title: BMDM cells, Stat-1Klf6 without mannose, 24 h, biol rep 2


title: Naringenin5 (C5)


title: BMDM cells, Stat-1Klf6 without mannose, 24 h, biol rep 3


title: Naringenin1 (C1)


title: CSE5 (B5)

value: the airway epithelium cells were treated with 10% CSE for 24h;


title: BMDM cells, mannose sugar positive control, 12 h, biol rep 1


title: BMDM cells, Stat-1Klf6 with mannose, 24 h, biol rep 3


title: Naringenin3 (C3)


title: BMDM cells, mannose sugar positive control, 24 h, biol rep 1


title: BMDM cells, LPS interferon pro-inflammatory positive control, 24 h, biol rep 3


title: BMDM cells, LPS interferon pro-inflammatory positive control, 12 h, biol rep 3


title: CSE4 (B4)


title: N4

city: Shanghai

first: Chu-Ting

last: Yu

address: No. 168, Changhai Road

institute: Changhai Hospital

description: 2x100 paired-end sequence reads

data_processing:
To prepare for RNA sequencing, mirVana miRNA Isolation Kit (Ambion) was used to isolate total RNA, following the manufacturer's protocol.
The quality and quantity of the RNA analytes were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and only samples with a RNA Integrity Number (RIN) ≥ 7 were selected for downstream analysis.
The sequencing libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold following the manufacturer's instructions.
The libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or another platform) generating 150 bp/125bp paired-end reads.
After obtaining paired-end reads, clean reads were aligned to the hg38 genome with HISAT2 (version 2.2.0) and sorted with samtools (version 1.9).
Mapped reads were visualized with the Integrative Genomics Viewer (IGV).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: paracancerous

extract_protocol:
RNA was harvested using mirVana miRNA Isolation Kit (Ambion). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

tag: patient

value: patient 4

value: paracancerous


title: N3

description: 2x100 paired-end sequence reads

value: patient 3


title: BMDM cells, mannose sugar positive control, 24 h, biol rep 3

value: Bone marrow

value: Bone marrow derived macrophages

value: macrophage

tag: genotype


title: CSE3 (B3)


title: BMDM cells, LPS interferon pro-inflammatory positive control, 12 h, biol rep 1


title: Naringenin2 (C2)


title: BMDM cells, LPS interferon pro-inflammatory positive control, 12 h, biol rep 2


title: BMDM cells, LPS interferon pro-inflammatory positive control, 24 h, biol rep 1


title: N1

description: 2x100 paired-end sequence reads

value: patient 1


title: T4

description: 2x100 paired-end sequence reads

source_name: esophageal squamous cell carcinoma

value: esophageal squamous cell carcinoma


title: N2

description: 2x100 paired-end sequence reads

value: patient 2


title: CSE2 (B2)


title: CSE1 (B1)


title: BMDM cells, LPS pro-inflammatory positive control, 24 h, biol rep 3

value: WT

value: LPS


title: BMDM cells, LPS pro-inflammatory positive control, 24 h, biol rep 2


title: BMDM cells, LPS interferon pro-inflammatory positive control, 24 h, biol rep 2


title: BMDM cells, LPS pro-inflammatory positive control, 24 h, biol rep 1


title: Normal5 (A5)

value: the airway epithelium cells  received no treatment


title: T3

description: 2x100 paired-end sequence reads


title: BMDM cells, LPS pro-inflammatory positive control, 12 h, biol rep 1


title: BMDM cells, control LLO strain with mannose, 24 h, biol rep 3

value: LLO strain with mannose


title: Normal4 (A4)


title: T2

description: 2x100 paired-end sequence reads


title: Normal3 (A3)


title: T1

description: 2x100 paired-end sequence reads


title: BMDM cells, control LLO strain with mannose, 24 h, biol rep 2


title: BMDM cells, control LLO strain with mannose, 12 h, biol rep 2


title: BMDM cells, LPS pro-inflammatory positive control, 12 h, biol rep 3


title: BMDM cells, control LLO strain with mannose, 24 h, biol rep 1


title: BMDM cells, control LLO strain with mannose, 12 h, biol rep 1


title: Normal1 (A1)


title: Normal_Stomach.4

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: WT stomach

growth_protocol: 8- to 12-week-old WT C57BL/6 mice were starved for two hours prior to the procedure. Mice were anesthetized with isoflurane and the surgical site (epigastrium) scrubbed with a povidone-iodine scrub (Betadine) and rinsed with 70% alcohol. After opening the peritoneal cavity, the stomach was mobilized and opened up in the area of the forestomach. Afterwards the inside of the stomach was rinsed with saline to remove any residual food. Subsequently, the plasmid mix (50ul; see specifications below) was injected into the epithelial compartment in the corpus/antrum region using a 30-gauge syringe and tweezer electrodes were tightly placed around the injection bubble. Two pulses of electrical current (75V) given for 35-milisecond lengths at 500-milisecond intervals were then applied using an in vivo electroporator (NepaGene NEPA21 Type II Electroporator). After electroporation, the stomach was closed with absorbable sutures and the peritoneal cavity was rinsed with 0.5 mL of prewarmed saline. The peritoneal cavity was sutured, and the skin closed with skin staples. The mice were kept at 37°C until awoke, and post-surgery pain management was done with injections of buprenorphine and/or meloxicam for the 3 following days. Tumor formation was assessed by palpation or ultrasound imaging, and mice were sacrificed following early tumor development or at endpoint. Genome editing in EPO-GEMM tumors was confirmed by Sanger sequencing, and RNA collected from whole stomach tissue.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

value: Whole tissue

value: non-treated


title: BMDM cells, control LLO strain without mannose, 12 h, biol rep 3

value: LLO strain without mannose


title: 50nM SM04690 Gruop6-3

city: Guangzhou

first: Wu

last: Runze

address: SUN YAT-SEN UNIVERSITY

institute: SUN YAT-SEN UNIVERSITY

description: 50nM SM04690

data_processing:
Sequencing data were analyzed with our in-house pipeline (Fu et al. 2011, 2015)
Sequencing reads were mapped to the human hg19 reference genomes, and internal priming was filtered.
poly(A) sites were defined for each sample by clustering the unique mapped reads, and then, the poly(A) sites were merged together across samples.
Assembly: hg19
Supplementary files format and content: Wiggle Track format files containing a graphical trace on a genome

source_name: RKO

growth_protocol: Cells were maintained in DMEM or 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were harvested and total RNA was extracted with TRIzol
1 ug total RNA was used to prepare the IVT-SAPAS library according to the previous report (Fu et al., 2015). The quality of the library was evaluated with a Qsep400 Advance.

treatment_protocol: Cells cells were transiently transfected with plasmids carrying Myc tagged CLK2(Myc-CLK2) or carrying PEGFP tagged CPSF6/CPSF6_6SA or corresponding shRNA.In the drug treatment experiment, RKO cells were treated with corresponding concentrations of SM04690 (0nM(DMSO), 25nM, 50nM) for 6 hours and collected

value: RKO

value: 50nM SM04690 6h treatment


title: Normal_Stomach.2


title: BMDM cells, LPS pro-inflammatory positive control, 12 h, biol rep 2


title: 25nM SM04690 Gruop6-2

description: 25nM SM04690

value: 25nM SM04690 6h treatment


title: MPMsh2.6

source_name: MYC;sgp53;sgMsh2 gastric EPO-GEMM tumor


title: BMDM cells, control LLO strain without mannose, 24 h, biol rep 2


title: Normal_Stomach.1


title: MPMsh2.5


title: BMDM cells, control LLO strain without mannose, 24 h, biol rep 1


title: shCLK2+shCPSF6 Gruop5-4

value: CLK2+CPSF6  knockdown


title: BMDM cells, control LLO strain without mannose, 12 h, biol rep 2

value: Bone marrow


title: 0nM SM04690 Gruop6-1

description: 0nM SM04690

value: NC DMSO 6h treatment


title: BMDM cells, control LLO strain with mannose, 12 h, biol rep 3

value: Bone marrow derived macrophages

value: macrophage


title: BMDM cells, control LLO strain without mannose, 12 h, biol rep 1


title: Normal2 (A2)

value: airway epithelium cells


title: shCPSF6 Gruop5-3

value: CPSF6  knockdown


title: BMDM cells, control LLO strain without mannose, 24 h, biol rep 3

value: WT


title: MPMsh2.3


title: LA-4

city: Hefei

first: manman

last: Wang

address: 103 Meishan Road

institute: Anhui University of Chinese Medicine

description: Osteogenic differentiation for 14 days

data_processing:
The raw paired-end fastq reads underwent filtering by TrimGalore to eliminate adapters and low-quality bases, which was accomplished through the utilization of the Cutadapt tool.
The resulting clean reads were then aligned to the hg19 human genome using HISAT2, followed by reference-guided transcriptome assembly and gene expression quantification utilizing StringTie.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene_count values for each Sample

source_name: Human bone marrow mesenchymal stem cells

growth_protocol: The hBMSCs were expanded no more than passage 8 in growth medium (GM) containing Dulbecco’s modified Eagle’s medium-low glucose (DMEM-LG; Invitrogen, USA) supplemented with 10% (v/v) fetal bovine serum (FBS; Invitrogen, USA) and 1% (v/v) penicillin/streptomycin (P/S; Invitrogen, USA).

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424)
High-quality RNA samples were used to construct a sequencing library.

treatment_protocol: To induce osteogenic differentiation, cells were cultured in osteogenic medium (OM) composed of DMEM-LG supplemented with 5% FBS, 1% P/S, 10 mM β-glycerophosphate, 50 µg ml-1 ascorbic acid, and 10 nM dexamethasone (Sigma-Aldrich, USA).

tag: replicate

value: bio rep 4

tag: agent

value: LA

value: 14 days


title: Normal_Stomach.3

value: Whole tissue


title: shCLK2 Gruop5-2

value: CLK2  knockdown


title: BMDM cells, Klf4Gata3 with mannose, 24 h, biol rep 3

tag: tissue

value: Klf4Gata3 strain with mannose


title: BMDM cells, Klf4Gata3 with mannose, 12 h, biol rep 3


title: MPMsh2.2

value: non-treated


title: LA-2

description: Osteogenic differentiation for 14 days

value: bio rep 2

value: Human bone marrow mesenchymal stem cells


title: MPMsh2.1


title: GFP-CPSF6 Gruop4-2

value: GFP-CPSF6 overexpression


title: BMDM cells, Klf4Gata3 with mannose, 24 h, biol rep 2

value: Bone marrow


title: LA-1

description: Osteogenic differentiation for 14 days

value: bio rep 1


title: shNTC Gruop5-1

description: shNTC

value: RKO

value: NC


title: GFP Gruop4-1

description: GFP


title: 3HB-4

description: Osteogenic differentiation for 14 days


title: MApc.5

source_name: MYC;sgApc gastric EPO-GEMM tumor


title: MApc.6


title: LA-3

description: Osteogenic differentiation for 14 days

value: bio rep 3


title: BMDM cells, Klf4Gata3 with mannose, 12 h, biol rep 2

value: Bone marrow derived macrophages

value: macrophage


title: MYC-CLK2+GFP_15RA Gruop3-4

value: MYC-CLK2+GFP_15RA overexpression


title: BMDM cells, Klf4Gata3 with mannose, 24 h, biol rep 1

value: WT


title: 3HB-3

description: Osteogenic differentiation for 14 days

value: 14 days


title: MApc.4

value: Whole tissue


title: BMDM cells, Klf4Gata3 with mannose, 12 h, biol rep 1


title: MYC+CPSF6_15RA Gruop3-3

value: MYC+GFP-CPSF6_15RA overexpression


title: 3HB-2

description: Osteogenic differentiation for 14 days


title: MApc.3


title: GFP-CPSF6_15RA Gruop4-3

value: GFP-CPSF6_15RA overexpression


title: BMDM cells, Klf4Gata3 without mannose, 24 h, biol rep 3

value: Klf4Gata3 strain without mannose


title: 3HB-1

description: Osteogenic differentiation for 14 days


title: MApc.2

value: non-treated


title: BMDM cells, Klf4Gata3 without mannose, 12 h, biol rep 3


title: MApc.1


title: Myc+GFP Gruop3-1

description: Myc+GFP


title: BMDM cells, Klf4Gata3 without mannose, 24 h, biol rep 2


title: RKO_IVTSAPAS Gruop2-3

value: Cancer


title: MP.9

source_name: MYC;sgp53 gastric EPO-GEMM tumor


title: Control-4

description: Osteogenic differentiation for 14 days

value: bio rep 4

value: Human bone marrow mesenchymal stem cells

value: vehicle


title: Control-3

description: Osteogenic differentiation for 14 days


title: MPMsh2.4


title: NCM460_IVTSAPAS Gruop2-1

value: Normal


title: BMDM cells, Klf4Gata3 without mannose, 12 h, biol rep 2

value: Bone marrow


title: BMDM cells, Klf4Gata3 without mannose, 24 h, biol rep 1


title: MP.8


title: SW480_IVTSAPAS Gruop2-2


title: MP.7


title: Control-1

description: Osteogenic differentiation for 14 days

value: bio rep 1


title: Control-2

description: Osteogenic differentiation for 14 days

value: bio rep 2


title: Jurkat T cells incubated with FLU, 4 hrs 3

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

data_processing:
Subread (1.6.3) was used for aligning reads to the Ensembl human genome (GRCh38) .
The featureCounts function of Subread was used to quantify reads using the Homo_sapiens.GRCh38.84.gtf.
Assembly: GRCh38
Supplementary files format and content: featureCounts.txt is a tab-delimited text file which includes read counts for each sample

source_name: Jurkat T cells

growth_protocol: Jurkat T cells grown to confluence in 100 mm plates in complete medium .

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, cat. 74004) with minor modification.
RNA samples were submitted to the UNSW Ramaciotti Centre for Genomics for TruSeq Stranded mRNA-seq preparation and sequencing by NextSeq 6000 to produce 75 bp single end reads.

treatment_protocol: The Jurkat T cells were incubated with 10 µM FLU or vehicle for 4 h

value: Jurkat T cells

value: T cells

value: Flubendazole

value: 4 hrs


title: Myc-CLK2+GFP-CPSF6 Gruop1-6

value: Myc-CLK2+GFP-CPSF6 overexpression


title: BMDM cells, anti-inflammatory positive control, 24 h, biol rep 3

value: Bone marrow derived macrophages

value: macrophage

value: WT


title: BMDM cells, Klf4Gata3 without mannose, 12 h, biol rep 1

value: Klf4Gata3 strain without mannose


title: Myc-CLK2+CPSF6_Mut1 Gruop1-5

value: Myc-CLK2+GFP-CPSF6_Mut1 overexpression


title: Myc-CLK2+GFP Gruop3-2

value: Myc-CLK2  overexpression


title: MP.6

value: Whole tissue

value: non-treated


title: BMDM cells, anti-inflammatory positive control, 12 h, biol rep 3


title: MP.5


title: Jurkat T cells incubated with FLU, 4 hrs 2


title: Myc-CLK2+GFP Gruop1-4

value: Myc-CLK2 overexpression


title: MP.4


title: BMDM cells, anti-inflammatory positive control, 24 h, biol rep 2

value: Bone marrow


title: Jurkat T cells incubated with vehicle, 4 hrs 3

value: vehicle


title: Jurkat T cells incubated with vehicle, 4 hrs 2


title: MP.3


title: MP.1


title: BMDM cells, anti-inflammatory positive control, 12 h, biol rep 2


title: Jurkat T cells incubated with vehicle, 4 hrs 1


title: BMDM cells, anti-inflammatory positive control, 24 h, biol rep 1


title: Myc+GFP-CPSF6_Mut1 Gruop1-2

value: GFP-CPSF6_Mut1 overexpression


title: NIP RNA-seq Rep1

status: Public on Sep 02 2023

city: Nanjing

first: Mengqi

last: Li

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argricultural University

data_processing:
Quality filtering and adapter trimming were done using fastp.
MH-seq: Clean data from NIP and 93-11 were mapped to MSU7.0 and pseudo reference genome, respectively, by using Bowtie2.Only uniquely mapped reads were retained for the downstream analyses.
MH-seq: MHS peaks were identified using MACS2 software with the following parameters: macs2 callpeak -f BAMPE -g 3.8e+8 -q 0.01 --nomodel.
RNAseq: Clean data from NIP and 93-11 were mapped to MSU7.0 and pseudo reference genome, respectively, by using Hisat2.FPKM of each sample was calculated by using StringTie . The differentially expressed genes (DEGs) were compared by using DESeq2
Genome_build: MSU7.0
Supplementary_files_format_and_content: bigWig file were generated using deepTools
Supplementary_files_format_and_content: bed files were generated using MACS2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa Japonica Group

source_name: seedlings

growth_protocol: Uniformly germinated seeds of Nipponbare (Oryza sativa ssp. japonica) and 93-11 (Oryza sativa ssp. indica) were grown in the nutrient soil in a greenhouse with 28-30 °C and a 14 h/10 h light-dark cycle. Two-week-old seedlings from each variety were collected

extract_protocol:
RNA-seq: Two-week-old seedlings were collected from each variety were round into a fine powder in liquid nitrogen and immediately kept at -80 ℃ for RNA sequencing.
RNA-seq: Total RNA was extracted from ground powder using TRIzol. Total RNA was treated with DNaseI for completely removing contamination of genomic DNA. mRNA was enriched from DNaseI-treated RNA for library preparation and sequenced.

tag: cultivar

value: Nipponbare

value: seedlings

value: biological replicate1

tag: age

value: two weeks

tag: growth temperature

value: 28-30 degrees C and a 14 h/10 h light-dark cycle


title: MP.2

tag: treatment


title: NIP RNA-seq Rep2

value: biological replicate2


title: Myc+GFP Gruop1-1

description: Myc+GFP

value: NC


title: HiC_tetoP2.Gng8tTA.r2

first: Elizaveta

last: Bashkirova

state: NY

address: 3227 Broadway

department: Biochemistry

institute: Columbia University

data_processing:
HiC data was aligned with the distiller pipeline (https://github.com/mirnylab/distiller-nf). We filtered out unmapped reads and reads with a mapping quality below q30.
genome_build/assembly: mm10
supplementary_files_format_and_content: For HiC ".cool" contact matixes were generated with cooler.

source_name: tetoOlfr17 expressing cells from the olfactory epithelium

growth_protocol: Used adult >6 weeks mice

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2019
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2019

treatment_protocol: Papain dissociated single cells were fixed with 1% formaldehyde, qunched with glycine and FAC-sorted to isolate GFP+ cells. Isolatd cells were then used for Hi-C

value: tetoOlfr17*/+; Gng8-tTA*/+


title: NIP MH-seq Rep2

extract_protocol:
MH-seq: Two-week-old seedlings from each variety were collected for cross-linking using 1% formaldehyde in HEPES buffer pH=8.0 (20 mM HEPES, 1 mM EDTA, 100 mM NaCl and 1mM PMSF). The cross-linked samples were ground into a fine powder in liquid nitrogen for the preparation of nuclei and chromatin for the downstream experiments.
MH-seq: Nuclei isolation and purification was conducted as previously described (Zhang and Jiang 2018). The nuclei pellet was re-suspended using 1.0 ml of MNase digestion buffer, and equally divided into 200 μl each aliquot. The aliquoted nuclei were trimmed at 37 ℃ for 10 min using a series of MNase. After stopping enzymatic digestion using 0.5 M EDTA (pH 8.0), each MNase cleaved nuclei were reversely cross-linked at 65 ℃ overnight. After removal of RNA and protein contamination using sequential treatment with RNase A at 37 ℃ for 30 min and proteinase K at 55 ℃ for 2 h. DNA was precipitated using cold ethanol after phenol/chloroform purification. The DNA pellet was dissolved using 20 μl EB (10 mM Tris-HCl, pH 8.0). After running 12% PAGE in 1xTBE buffer, 40-100 bp small sized DNA fragments were recovered from the purified DNA for MNase hypersensitive sequencing (MH-seq) library preparation. MH-seq library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S).


title: HiC.tetoP2.Gng8tTA.r1

value: tetoOlfr17 expressing cells from the olfactory epithelium


title: RNA_tetoP2_Gng8tTA_r2

data_processing:
Adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550).
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. Unmapped reads and reads with a mapping quality below q30 were filtered out with Samtools.
BigWig files were generated using HOMER
genome_build/assembly: mm10
supplementary_files_format_and_content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

extract_protocol:
Cells were lysed in Trizol (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
RNA-seq libraries were prepared using the TruSeq RNA Library Prep Kit

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP + cells were isolated with FAC-sorting


title: RNA_tetoP2_Gng8tTA_r1


title: nchip_Z5_Ngn1GFPbright_tk79_r2

data_processing:
Adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). Reads were trimmed to 50bp before aligning.
Native ChIP-seq libraries were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000). Read 2 was poor quality, so the libraries were aligned single end with read 1 only. Unmapped reads and reads with a mapping quality below q30 were filtered out with Samtools.
BigWig files were generated using HOMER
genome_build/assembly: mm10
supplementary_files_format_and_content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: immature olfactory sensory neurons (iOSN)

growth_protocol: used young pups < P6

extract_protocol:
Cells were lysed to extract nuclei , nuclei were digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K79me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium ("zone4-5" anatomical region) was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP + (bright) cells were isolated with FAC-sorting


title: nchip_Z5_NfiABXko_K5CreER_INP_tk9_r2

data_processing:
Adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550).
Native ChIP-seq libraries were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000). Unmapped reads and reads with a mapping quality below q30 were filtered out with Samtools.
BigWig files were generated using HOMER
genome_build/assembly: mm10
supplementary_files_format_and_content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: tdTomato +(dim) cells from the regenerating olfactory epithelium: immediate neuronal progenitors (INP)

growth_protocol: Adult mice were injected 3x IP with tamoxifen (24 hours apart), 10 days following the first injection olfactory epithelium was ablated with an IP injection of methimazole. Then olfactory epithelium was regenerated for 8 days.

extract_protocol:
Cells were lysed to extract nuclei , nuclei were digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K9me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium ("zone4-5" anatomical region) was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then tomato + (dim) cells were isolated with FAC-sorting

value: tdTomato +(dim) cells from the regenerating olfactory epithelium:immediate neuronal progenitors (INP)

value: NfiAfl/fl; NfiBfl/fl; NfiXfl/fl; K5CreER*/+; Rosa-CAG-tdtomfl/fl


title: nchip_Z5_wt_K5CreER_INP_tk9_r1

value: K5CreER*/+; Rosa-CAG-tdtomfl/fl


title: NIP MH-seq Rep1


title: BMDM cells, anti-inflammatory positive control, 12 h, biol rep 1

value: Bone marrow derived macrophages

value: macrophage

value: WT

tag: time


title: nchip_Z5_NfiABXko_K5CreER_INP_tk9_r1


title: nchip_Z5_wt_K5CreER_INP_tk9_r2


title: nchip.Z5_OMPgfp_tk79_r3

source_name: mature olfactory sensory neurons (mOSN)

growth_protocol: Used adult >8 weeks mice

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium ("zone4-5" anatomical region) was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP + cells were isolated with FAC-sorting

value: mature olfactory sensory neurons (mOSN)


title: nchip_Z2_OMPgfp_tk79_r3

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium ("zone2-3" anatomical region) was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP + cells were isolated with FAC-sorting


title: nchip_Olfr1507_tk9_r2

source_name: Olfr1507 expressing mature olfactory sensory neurons (mOSN)


title: nchip_Olfr1507_tk79_r2

value: Olfr1507 expressing mature olfactory sensory neurons (mOSN)


title: RNA_Z5_wt_K5CreER_INP_r3

data_processing:
Adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). Reads were trimmed to 50bp before aligning.
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. Unmapped reads and reads with a mapping quality below q30 were filtered out with Samtools.
BigWig files were generated using HOMER
genome_build/assembly: mm10
supplementary_files_format_and_content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

extract_protocol:
Cells were lysed in Trizol (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
RNA-seq libraries were prepared using Ovation RNA-Seq System 1-16 for Model Organisms (Nugen 0348)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium ("zone4-5" anatomical region) was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then tdTomato + (dim) cells were isolated with FAC-sorting


title: RNA_Z5_wt_K5CreER_INP_r1


title: RNA_Z5_NfiABXko_K5CreER_INP_r3


title: RNA_Z5_NfiABXko_K5CreER_INP_r2


title: RNA_Z5_NfiABXhet_K5CreER_OMPgfp_r2

growth_protocol: Adult mice were injected 3x IP with tamoxifen (24 hours apart), 10 days following the first injection olfactory epithelium was ablated with an IP injection of methimazole. Then olfactory epithelium was regenerated for 40 days.

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium ("zone4-5" anatomical region) was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+, tdTomato + (dim) cells were isolated with FAC-sorting

value: NfiAfl/+; NfiBfl/+; NfiXfl/+; K5CreER*/+; OMPgfp*/+; Rosa-CAG-tdtomfl/fl


title: RNA_Z5_NfiABXko_K5CreER_INP_r1


title: RNA_Z5_wt_K5CreER_OMPgfp_r4


title: RNA_Z5_NfiABXhet_K5CreER_OMPgfp_r1