title: TAZ.T0.br2

description:
TAZ knockout screened in DMEM (minimal) + 10% FBS
Moffat_1425


title: maize crown root, inoculum CWR_G_W, Well_watered, plantID_779

status: Public on May 28 2025

type: SRA

city: Lawrence

first: Maggie

middle: R

last: Wagner

state: KS

address: 1200 Sunnyside Avenue

country: USA

institute: University of Kansas

description:
Library name: plantID_779
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

library_source: transcriptomic

data_processing:
UMIs were removed from all sequences and added to the read headers using UMI-tools. Next, cutadapt version 4.2 was used to remove the first four bases of each read, remove poly-A tails (if present), remove spurious poly-G runs using the --nextseq-trim=10 parameter, and remove adapter sequences. Reads that were <10 bp long or that aligned to maize rRNA gene sequences were removed; the remaining reads were aligned to the maize reference genome B73 RefGen_v550 using HISAT2 version 2.2.1. Aligned reads were converted to BAM format, sorted, and indexed using samtools version 1.9. We then used UMI-tools to de-duplicate reads that both shared a UMI and had identical mapping coordinates. Finally, we used the FeatureCounts function of the subread package version 2.0.5 with the maize genome annotation version Zm00001eb.1 and parameters -O --fraction -M --primary -g ID -t gene to generate a table of gene expression estimates.
Assembly: maize reference genome B73 RefGen_v5
Supplementary files format and content: tab-delimited FeatureCounts output (transcript counts per sample/library)

molecule: polyA RNA

organism: Zea mays

source_name: crown root

growth_protocol: growth chamber; multiple microbiome treatments; drought or well-watered

extract_protocol:
Macherey-Nagel NucleoSpin RNA Plant kit + Invitrogen DNA-Free kit
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

treatment_protocol: flash frozen

tag: tissue

value: crown root

tag: plant id

tag: inoculum type

value: live

tag: inoculum origin

value: CWR

tag: inoculum conditioning_host

value: gamagrass

tag: inoculum conditioning_water

tag: genotype

tag: testphase water_treatment


title: maize crown root, inoculum CWR_G_D, Well_watered, plantID_770

description:
Library name: plantID_770
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: plateA_day6

city: Cambridge

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

library_source: genomic

data_processing:
Data was processed following recommended guidelines for scNMT data (https://felixkrueger.github.io/Bismark/bismark/library_types/), as such all files were treated as single-end
Trim Galore (version 0.6.2) was used to trim reads, to remove the first 6 bp from their 5' end, and for auto-detection of adapter and poor quality from their 3' end
Bismark (version 0.22.1) was used to align DNA reads to the bisulfite converted GRCh38 genome (with the flag --non_directional specified), deduplicate reads, and finally perform methylation calling.
To reduce unwanted biases from the data (as discussed here: https://felixkrueger.github.io/Bismark/bismark/methylation_extraction/#optional-nome-seq-or-scnmt-seq) the bismark.cov.gz files were passed to the coverage2cytosine module of bismark (with the flag --nome-seq specified)
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files for each processed cell are provided and each genomic layer (CpG methylation or GpC accessibility), these are files are tab separated and contain DNA methylation data with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

molecule: genomic DNA

organism: Homo sapiens

source_name: Embryo

growth_protocol: Supernumerary blastocysts, cryopreserved at D5 or D6, were thawed using commercial kits specified by the clinic from which they were donated. Embryos were cultured in N2B27 medium (made in house) under mineral oil (Sage, #ART-4008) in a humidified incubator at 37oC, 7% CO2 and 5% O2. The zona pellucida surrounding the blastocyst was removed by short incubation in Tyrode Acid solution (Sigma, #T1788) prior to incubation in anti-human antibody (Sigma, H8765) diluted 1:4 in N2B27, for 1 hour at 37oC, 7% CO2 and 5% O2. The embryos were then rinsed in N2B27 and placed in N2B27 containing 2:5 non-heat inactivated rat serum (prepared in house) for 45 minutes.46 As outer cells became swollen and lysed, the whole blastocyst was transferred to N2B27 for 1 hour prior to manual removal of the degraded outer cells by pipetting using appropriately sized capillaries. For specific experiments, 50 μM Cycloheximide (Sigma, 4859), 1 μM Actinomycin D (ToCris, #1229) or 10 μM MG132 (ToCris, #1748) were added during immunosurgery to block protein translation, RNA transcription and protein degradation respectively. Following IS, ICMs were incubated in Accutase (Biolegend, 423201) on a warming pad for 10 mins. ICMs were dissociated into single cells using glass capillaries and transferred to a 96-well plate.

extract_protocol:
AMPure XP
Embryos from embryonic days 5-6 were collected in Corujo-Simon et al. in which scRNA-seq was performed using the RNA half of the scNMT-seq method. In this study we used the gDNA from the same cells to generate DNA methylation and chromatin accessibility data using the published scNMT-seq protocol (52). Briefly, genomic DNA was purified using AMPure XP beads then bisulfite converted with the Zymo EZ-96 DNA Methylation-Direct MagPrep kit. Sequencing libraries were then prepared from bisulfite converted fragments via random primed synthesis using oligos containing Illumina primer sequences, followed by indexing PCR.

value: Embryo


title: SG16374548_253949447555_2_4_0846-006-900_hr24

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

hyb_protocol: cRNA was hybridized to a human genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing:
Agilent Feature Extraction Software (v 10.7) was used for background subtraction and GeneSpring v.10.1 (Agilent Technologies, Inc., CA) software was used to conduct the preliminary data filtration and statistical analysis.
processed_data: Logratio (test/reference)

molecule: total RNA

source_name: Whole Blood

label_protocol: Total RNA (200-2000ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol: Total RNA was isolated using the PAXgene Blood RNA kit (Qiagen, Valencia, CA) following manufacturer directions

treatment_protocol: treatment protocol is not applicable

tag: age

tag: gender

value: Male

value: Alive

tag: timepoint

source_name: Agilent's Universal Human Reference RNA

tag: reference

value: Agilent's Universal Human Reference RNA


title: SG14244409_253949423794_1_1  0839-014-900 hr 120


title: TAZ.T19C.br2

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

description:
TAZ knockout screened in DMEM (minimal) + 10% FBS
Moffat_1428

data_processing:
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Assembly: TKOv3 sgRNA library
Supplementary files format and content: tab-delimited read count matrix
Library strategy: CRISPRseq

source_name: haematopoeitic

growth_protocol: Cells were cultured in IMDM media supplemented with 10% FBS and 1% Penicillin/Streptomycin and serially passaged for up to 18 days (propagated in biological triplicates).  Aliquots were pelleted at indicated timepoints for gDNA extraction and quantification by next-generation sequencing.

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer’s instructions
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.

value: haematopoeitic

tag: cell line

tag: cell type

value: chronic myelogenous leukemia-derived

value: TAZ 4bp deletion(HAP1)   (HZGHC004024c008)

tag: treatment

value: TKOv3 (lentiCRISPRv2)


title: SG14244409_253949423789_2_2  0839-013-900 hr 108


title: TAZ.T19C.br1

description:
TAZ knockout screened in DMEM (minimal) + 10% FBS
Moffat_716

value: TAZ 5bp deletion (HAP1)   (HZGHC004024c009)


title: SG14244409_253949423790_2_4 0839-012-900 hr 96


title: maize crown root, inoculum WEL_G_D, Well_watered, plantID_768

description:
Library name: plantID_768
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: WEL


title: TAZ.T19B.br1

description:
TAZ knockout screened in DMEM (minimal) + 10% FBS
Moffat_715


title: SG14244409_253949423789_1_1 0839-011-900 hr 84


title: SG14244409_253949423789_1_3  0839-010-900 hr 72


title: maize crown root, inoculum TRI_N_W, Well_watered, plantID_767

description:
Library name: plantID_767
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: TRI


title: TAZ.T19A.br1

description:
TAZ knockout screened in DMEM (minimal) + 10% FBS
Moffat_714


title: maize crown root, inoculum SVR_G_D, Well_watered, plantID_772

description:
Library name: plantID_772
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: SVR


title: SG14244409_253949423789_2_3  0839-009-900 hr 60


title: maize crown root, inoculum CWR_N_D, Well_watered, plantID_762

description:
Library name: plantID_762
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949423793_2_4 0839-008-900 hr 48


title: TAZ.T0.br1

description:
TAZ knockout screened in DMEM (minimal) + 10% FBS
Moffat_713


title: SG14244409_253949423789_2_1  0839-007-900 hr 36


title: maize crown root, inoculum WEL_G_W, Well_watered, plantID_760

description:
Library name: plantID_760
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949423790_2_2 0839-005-900 hr 12


title: SG14244409_253949423790_1_3 0839-015-900 hr 132


title: ABHD18.TAZ.T15C

description:
ABHD18/TAZ double-knockout screened in IMDM + 10% FBS
GIN_9758

value: ABHD18/TAZ 2bp deletion + 45bp deletion (HAP1)


title: SG14244409_253949423790_1_4 0839-003-900 hr 4


title: maize crown root, inoculum SVR_G_W, Well_watered, plantID_769

description:
Library name: plantID_769
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root


title: SG14244409_253949423793_2_3 0839-002-900 hr 2


title: ABHD18.TAZ.T15B

description:
ABHD18/TAZ double-knockout screened in IMDM + 10% FBS
GIN_9757


title: SG14244409_253949422266_2_1 0838-012-900

value: Deceased


title: ABHD18.TAZ.T15A

description:
ABHD18/TAZ double-knockout screened in IMDM + 10% FBS
GIN_9756


title: maize crown root, inoculum CWR_G_W, Well_watered, plantID_754

description:
Library name: plantID_754
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live

value: CWR


title: SG14244409_253949422266_1_3 0838-010-900


title: SG14244409_253949422266_1_2 0838-009-900


title: ABHD18.TAZ.T0

description:
ABHD18/TAZ double-knockout screened in IMDM + 10% FBS
GIN_9746


title: SG14244409_253949422280_2_4 0838-007-900


title: maize crown root, inoculum TRI_N_W, Well_watered, plantID_751

description:
Library name: plantID_751
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422280_2_3 0838-006-900


title: ABHD18.T11C

description:
ABHD18 knockout screened in IMDM + 10% FBS
GIN_8453

value: ABHD18 45bp deletion + 120bp deletion (HAP1)


title: ABHD18.T11B

description:
ABHD18 knockout screened in IMDM + 10% FBS
GIN_8452


title: SG14244409_253949422280_2_1 0838-003-900

value: Male


title: maize crown root, inoculum SVR_N_W, Well_watered, plantID_749

description:
Library name: plantID_749
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422266_1_1 0838-002-900


title: ABHD18.T11A

description:
ABHD18 knockout screened in IMDM + 10% FBS
GIN_8451


title: SG14244409_253949423793_2_1 0832-020-900 d21

value: Alive


title: maize crown root, inoculum Mock, Well_watered, plantID_759

description:
Library name: plantID_759
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: mock


title: maize crown root, inoculum CWR_G_W, Well_watered, plantID_748

description:
Library name: plantID_748
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: gamagrass


title: SG14244409_253949422280_1_2 0838-001-900

value: Agilent's Universal Human Reference RNA


title: SG14244409_253949423787_2_1 0832-019-900 d14


title: maize crown root, inoculum SVR_N_D, Well_watered, plantID_757

description:
Library name: plantID_757
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: ABHD18.T0

description:
ABHD18 knockout screened in IMDM + 10% FBS
GIN_8444

value: haematopoeitic

value: chronic myelogenous leukemia-derived


title: SG14244409_253949423787_2_3 0832-018-900 hr 168


title: maize crown root, inoculum SVR_N_D, Well_watered, plantID_747

description:
Library name: plantID_747
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422266_1_4 0838-011-900


title: RDH12_AD_12

city: LONDON

first: Mariya

last: Moosajee

address: 1 Midland Rd

institute: The Francis Crick Institute

data_processing:
Raw reads were quality and adapter trimmed using cutadapt (version 3.4) before alignment.
Reads were mapped and subsequent gene-level counted using RSEM 1.3.1 and STAR 2.7.10a against the human genome GRCh38 using annotation release 95, both from Ensembl.
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.38.3) within the R programming environment (version 4.2.2).
Assembly: GRCh38
Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.

source_name: Organoid

extract_protocol:
RNA was isolated, quantified and cDNA generated from two pooled organoids at day 303 week 44 (Qiagen, UK).
cDNA libraries were sequenced on a HiSeq 2500 with paired-end reads of 150 bp using Illumina Stranded Total RNA with Ribo-Zero Plus (Illumina, UK)

value: Organoid

value: RDH12-AD mutant


title: maize crown root, inoculum SVR_N_D, Well_watered, plantID_744

description:
Library name: plantID_744
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949423788_1_1 0832-016-900 hr 144


title: RDH12_AD_11


title: maize crown root, inoculum Mock, Well_watered, plantID_750

description:
Library name: plantID_750
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422280_2_2 0838-004-900


title: SG14244409_253949423793_2_2 0832-015-900 hr 132


title: SG14244409_253949423788_2_2 0832-013-900 hr 108


title: RDH12_AD_10


title: maize crown root, inoculum TRI_N_D, Well_watered, plantID_742

description:
Library name: plantID_742
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: TRI


title: maize crown root, inoculum TRI_G_D, Well_watered, plantID_741

description:
Library name: plantID_741
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949423788_1_3 0832-012-900 hr 96


title: SG14244409_253949423787_1_2 0832-011-900 hr 84


title: maize crown root, inoculum WEL_N_W, Well_watered, plantID_740

description:
Library name: plantID_740
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: WEL


title: RDH12_AD_9


title: SG14244409_253949423788_2_3 0832-010-900 hr 72


title: SG14244409_253949423787_1_4 0832-008-900 hr 48


title: maize crown root, inoculum WEL_G_D, Well_watered, plantID_737

description:
Library name: plantID_737
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949423793_1_4 0832-009-900 hr 60


title: SG14244409_253949423787_2_4 0832-017-900 hr 156


title: RDH12_AD_7


title: SG14244409_253949423787_1_3 0832-007-900 hr 36


title: maize crown root, inoculum SVR_N_W, Well_watered, plantID_735

description:
Library name: plantID_735
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: SVR


title: SG14244409_253949423788_1_4 0832-004-900 hr 8


title: SG14244409_253949423787_2_2 0832-005-900 hr 12


title: RDH12_AD_6


title: RDH12_AD_8


title: maize crown root, inoculum TRI_G_D, Well_watered, plantID_734

description:
Library name: plantID_734
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root


title: SG14244409_253949423788_2_1 0832-003-900 hr 4


title: RDH12_AD_5


title: SG14244409_253949423787_1_1 0832-001-900 hr 0


title: maize crown root, inoculum SVR_N_D, Well_watered, plantID_732

description:
Library name: plantID_732
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949423788_1_2 0832-014-900 hr 120


title: SG14244409_253949422272_2_2 0829-005-900


title: RDH12_AD_4


title: SG14244409_253949422272_2_1 0829-004-900


title: maize crown root, inoculum Mock, Well_watered, plantID_730

description:
Library name: plantID_730
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422272_1_4 0829-003-900


title: RDH12_AD_3


title: maize crown root, inoculum TRI_G_W, Well_watered, plantID_729

description:
Library name: plantID_729
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422272_1_3 0829-002-900


title: SG14244409_253949422272_1_2 0829-001-900


title: RDH12_AD_2


title: SG14244409_253949422278_2_4 0828-001-900

value: Deceased


title: RDH12_AD_1


title: SG14244409_253949422279_2_4 0826-020-900


title: maize crown root, inoculum CWR_G_D, Well_watered, plantID_728

description:
Library name: plantID_728
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live


title: maize crown root, inoculum WEL_N_D, Well_watered, plantID_727

description:
Library name: plantID_727
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422278_2_3 0826-018-900


title: SG14244409_253949422278_2_2 0826-017-900


title: maize crown root, inoculum WEL_N_D, Well_watered, plantID_726

description:
Library name: plantID_726
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422279_2_2 0826-015-900


title: SG14244409_253949422278_2_1 0826-016-900


title: maize crown root, inoculum SVR_N_W, Well_watered, plantID_725

description:
Library name: plantID_725
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422279_2_1 0826-014-900


title: WT_7

value: WT


title: WT_6


title: maize crown root, inoculum TRI_G_D, Well_watered, plantID_724

description:
Library name: plantID_724
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422277_2_4 0826-012-900


title: SG14244409_253949422279_1_4 0826-013-900


title: SG14244409_253949422279_1_3 0826-010-900


title: maize crown root, inoculum CWR_N_W, Well_watered, plantID_722

description:
Library name: plantID_722
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: CWR


title: WT_5


title: WT_4


title: SG14244409_253949422278_1_2 0826-009-900

value: Male


title: SG14244409_253949422278_1_3 0826-007-900

value: Alive


title: maize crown root, inoculum TRI_N_W, Well_watered, plantID_720

description:
Library name: plantID_720
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422279_2_3 0826-019-900


title: SG14244409_253949422279_1_2 0826-008-900


title: maize crown root, inoculum TRI_G_D, Well_watered, plantID_718

description:
Library name: plantID_718
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: WT_3


title: WT_8


title: WT_1


title: SG14244409_253949422276_1_4 0825-020-900


title: SG14244409_253949422278_1_4 0826-005-900


title: maize crown root, inoculum WEL_G_W, Well_watered, plantID_716

description:
Library name: plantID_716
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: WT_2


title: SG14244409_253949422277_2_1 0826-003-900


title: IP_M3Sh1_Nig2

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

data_processing:
For all sequencing data, the raw reads were subject to quality check using FastQC.Adapter and poor-quality sequences were removed using Trimmomatic (version 0.39) with default settings.
For the analysis of m6A-RIP-sequencing data, only uniquely mapped were selected by samtools for downstream analysis. m6A peaks enriched in immunoprecipitation over corresponding input samples were identified by MACS2 (version 2.1.0.20150731).
The effective genome size was calculated by the reference annotation. Significant (FDR-adjusted p < 0.05, |fold change between IP and input | ≥ 2, and a minimum peak read count of 10 across replicates and conditions) peaks were considered.
To identify high confident or consensus m6A peaks, peaks were intersected in a pair-wise fashion among two replicates using the BedTools package with a setting of ‘-f 0.5’.
bigWig files were generated using Bamcoverage.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: m6A-IP-Seq

growth_protocol: 5 μg of DNAse-treated total RNA were fragmented to approximately 200 bp of length. 500 ng of RNA was stored as input control at -80 C.

extract_protocol:
RNA was quantified using the Agilent 2100 Bioanalyzer on an RNA 6000 Pico Bioanalyzer chip (Agilent).
For deep sequencing analysis, library preparation was performed using the SMARTER Stranded Total RNA Seq kit v2-Pico Input Mammalian kit (Takara Bio), following the manufacturer’s instructions. The libraries were amplified for 16 cycles (IP) or 12 cycles (input) of PCR.  Library size and distribution were checked using the Agilent 2100 Bioanalyzer using the Agilent High-sensitivity DNA Kit (Agilent). Libraries were then sequenced using HiSeq2500 (Illumina) by Novogen (China), and a minimum of 20 million paired-end reads were obtained per sample.

treatment_protocol:
Fragmented RNA was subjected to two rounds of immunoprecipitation using Dynabeads Protein A/G (Invitrogen) and 5 μg of anti-m6A (Merck) antibody by incubation for 2 hours at 4C in a rotating platform. After washing, m6A-enriched RNA was eluted from the beads by adding 200 µl of RLT buffer from the RNeasy Mini Kit (Qiagen) and incubating for 2 minutes at room temperature.
Magnetic separation rack was used to separate beads from m6A-RNA. The supernatant was collected in a new tube, and 100% ethanol was added. The mixture was transferred to an RNeasy Mini Elute column (Qiagen) and centrifuged and washed with 500 μL of RPE buffer (Qiagen), then with 80% ethanol. The m6A enriched RNA was eluted with nuclease-free water.

value: macrophages

tag: m6a treatment_antibody

value: Merck

tag: agent

value: Nigericin and METTL3-deletion

tag: fraction

value: IP


title: maize crown root, inoculum SVR_N_W, Well_watered, plantID_715

description:
Library name: plantID_715
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: tissue

tag: plant id


title: SG14244409_253949422279_1_1 0826-004-900

value: Agilent's Universal Human Reference RNA


title: SG14244409_253949422277_2_2 0826-001-900


title: maize crown root, inoculum CWR_N_W, Well_watered, plantID_712

description:
Library name: plantID_712
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: inoculum type

tag: inoculum origin


title: SG14244409_253949422265_2_3 0825-017-900


title: SG14244409_253949422265_2_4 0825-016-900


title: IP_Ath_Nig2

value: Nigericin


title: SG14244409_253949422276_2_3 0825-018-900


title: IP_M3Sh1_Nig1


title: SG14244409_253949422278_1_1 0826-002-900


title: maize crown root, inoculum WEL_G_D, Well_watered, plantID_713

description:
Library name: plantID_713
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: inoculum conditioning_host

value: gamagrass

tag: inoculum conditioning_water


title: IP_Ath_Nig1


title: maize crown root, inoculum WEL_N_D, Well_watered, plantID_711

description:
Library name: plantID_711
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: genotype

tag: testphase water_treatment


title: SG14244409_253949422277_1_4 0825-014-900

tag: age

tag: gender


title: maize crown root, inoculum Mock, Well_watered, plantID_710

description:
Library name: plantID_710
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: mock


title: SG14244409_253949422265_1_1 0825-013-900

tag: timepoint

tag: reference


title: SG14244409_253949422276_1_2 0825-012-900


title: IP_Ath_DMSO2

tag: cell line

tag: cell type

value: DMSO


title: SG14244409_253949422277_2_3 0826-006-900


title: SG14244409_253949422265_1_2 0825-019-900


title: maize crown root, inoculum CWR_G_W, Well_watered, plantID_709

description:
Library name: plantID_709
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422277_1_3 0825-010-900


title: SG14244409_253949423790_1_2 0839-004-900 hr 8


title: SG14244409_253949422276_2_2 0825-015-900


title: INP_M3Sh1_Nig2

tag: m6a treatment_antibody

value: Input


title: IP_Ath_DMSO1

tag: agent


title: SG14244409_253949422265_1_3 0825-009-900


title: maize crown root, inoculum WEL_N_W, Well_watered, plantID_708

description:
Library name: plantID_708
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root

value: WEL


title: maize crown root, inoculum TRI_N_W, Well_watered, plantID_707

description:
Library name: plantID_707
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live

value: TRI


title: SG14244409_253949422276_2_1 0825-011-900


title: SG14244409_253949422265_2_2 0825-007-900


title: SG14244409_253949422265_1_4 0825-006-900


title: INP_M3Sh1_Nig1

tag: fraction


title: SG14244409_253949422265_2_1 0825-008-900


title: SG14244409_253949422276_1_1 0825-004-900


title: maize crown root, inoculum SVR_G_W, Well_watered, plantID_704

description:
Library name: plantID_704
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: tissue

value: SVR


title: SG14244409_253949422276_1_3 0825-003-900

value: Male


title: maize crown root, inoculum TRI_G_W, Well_watered, plantID_706

description:
Library name: plantID_706
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: plant id


title: SG14244409_253949422277_1_1 0825-005-900

value: Alive


title: SG14244409_253949422277_1_2 0825-002-900


title: maize crown root, inoculum SVR_G_W, Well_watered, plantID_703

description:
Library name: plantID_703
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: inoculum type


title: INP_Ath_Nig1

value: macrophages


title: INP_Ath_Nig2


title: SG16374548_253949447607_2_3_824-016-900_hr144


title: maize crown root, inoculum CWR_G_D, Well_watered, plantID_702

description:
Library name: plantID_702
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: inoculum origin

value: CWR


title: INP_Ath_DMSO2


title: SG16374548_253949447607_2_2_824-013-900_hr108


title: SG14244409_253949422276_2_4 0825-001-900


title: INP_Ath_DMSO1


title: SG16374548_253949447607_2_1_824-011-900_hr84


title: maize crown root, inoculum WEL_G_D, Well_watered, plantID_701

description:
Library name: plantID_701
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: inoculum conditioning_host


title: M3sh1 Nig2

data_processing:
mRNA-sequencing was performed for each biological duplicates of samples by Novogene (China). For all sequencing data, the raw reads were subject to quality check using FastQC.
Adapter and poor-quality sequences were removed using Trimmomatic (version 0.39) with default settings
Pair-end clean reads were then mapped to the human reference genome hg38 (EN-SEMBL 86 release, GRCm38) using STAR (version 2.5.2a)
Read counts for reads overlapping genomic regions were quantified with FeatureCounts from the Subread package. Differentially expressed genes were determined using the R package DESeq2 with reads per kilo base per million (RPKM)>1, a Benjamini-Hochberg (BH)-adjusted P < 0.05 and an absolute value of a fold change > 2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized count values for each Sample

growth_protocol: To activate the NLRP3 inflammasome, cells were primed with 500 ng/mL LPS (E. coli O111:B4, Sigma) for 3 hours at 37C, 5% CO2, and then stimulated with 20 μM Nigericin (Enzo Life Sciences) at 37C, 5% CO2 for 60 to 90 minutes (aiming to observe more than 50% pyroptosis under the microscope).

extract_protocol:
RNA-Seq RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using the TruSeq® Stranded Library Preparation Kit (Illumina), according to the manufacturers’ instructions

treatment_protocol:
Cell culture supernatants and cell lysates were collected for cytokine, lactate dehydrogenase (LDH), Caspase-1 Glo assays (Promega), pro-caspase-1/p20 western blot analyses and RNA extraction.
In general, experiments were performed by seeding 50 – 100 x 103 cells in 100 μL of culture media in 96 well plates, except for experiments to collect RNA and protein that were scaled up to 6 well plates containing 1-1.5 x 106 cells in 2 mL of media.

tag: treatment

value: treatment with METTL3-deleption, LPS and Nigericin


title: SG16374548_253949447539_2_4_824-005-900_hr12


title: SG16374548_253949447539_2_3_824-001-900_hr0


title: SG16374548_253949447607_1_4_824-008-900_hr48


title: maize crown root, inoculum CWR_N_W, Well_watered, plantID_700

description:
Library name: plantID_700
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: inoculum conditioning_water

tag: genotype


title: maize crown root, inoculum SVR_G_W, Well_watered, plantID_699

description:
Library name: plantID_699
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: testphase water_treatment


title: SG14244409_253949422264_2_4 0823-001-900

tag: age

tag: gender

value: Deceased


title: Ath Nig2

value: treatment with LPS and Nigericin


title: SG14244409_253949422264_2_1 0822-006-900

value: Female

tag: timepoint

tag: reference

value: Agilent's Universal Human Reference RNA


title: SG14244409_253949422264_2_3 0822-008-900


title: maize crown root, inoculum WEL_N_W, Well_watered, plantID_698

description:
Library name: plantID_698
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: Ath Nig1

tag: cell line

tag: cell type


title: maize crown root, inoculum WEL_G_W, Well_watered, plantID_697

description:
Library name: plantID_697
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: gamagrass


title: M3sh1 Nig1


title: Ath DMSO2

value: treatment with lipopolysaccharide (LPS)


title: SG14244409_253949422264_1_4 0822-005-900


title: SG14244409_253949422264_1_1 0822-002-900


title: maize crown root, inoculum WEL_G_W, Well_watered, plantID_696

description:
Library name: plantID_696
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949422264_1_3 0822-004-900


title: SG14244409_253949422264_1_2 0822-003-900


title: maize crown root, inoculum Mock, Drought, plantID_689

description:
Library name: plantID_689
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: mock

value: Drought


title: SG14244409_253949422264_2_2 0822-007-900


title: maize crown root, inoculum CWR_N_W, Well_watered, plantID_693

description:
Library name: plantID_693
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root


title: SG14244409_253949423793_1_3 0809-009-900 hr 72


title: SG14244409_253949423786_2_4 0809-008-900 hr 48


title: Ath DMSO1


title: SG14244409_253949422280_1_1 0822-001-900


title: SG14244409_253949423786_2_3 0809-007-900 hr 36


title: SG14244409_253949423786_2_2 0809-006-900 hr 24


title: SG14244409_253949423786_2_1 0809-005-900 hr 12


title: maize crown root, inoculum CWR_N_D, Drought, plantID_686

description:
Library name: plantID_686
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live


title: BMDM, KO, MDP-treated, biol rep 3

city: Singapore

first: Yuan

last: Qiao

address: 21 Nanyang Link, CBC 04-40

country: Singapore

institute: NTU

description:
Library name: Sample6_3
Column name in gene_count.txt and gene_fpkm.txt : KO_MDP03

data_processing:
Data processing were provided by Novogene Services on Illumina Novaseqplatform. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.
Raw reads of fastq files after cleanup were processed through fastq software followed by mapping using Hisat2 v2.0.5. with default parameters.
Quantification of gene expression level was conducted by featureCounts v1.5.0-p3 with default parameters.
Differential expression analysis was conducted by DESeq2Rpackage (1.20.0), with parameters set as |log2(FoldChange)| >= 1 & padj <= 0.05.
Enrichment analysis was conducted by clusterProfiler v3.8.1, with parameters set as padj < 0.05 for GO and KEGG enrichment analysis.
Assembly: GRCm39
Supplementary files format and content: A txt file including raw read values for each sample.
Supplementary files format and content: A txt file including FPKM values for each sample.

organism: Mus musculus

source_name: Bone marrow derived macrophages

extract_protocol:
RNA was extracted using Monarch Total RNA Miniprep kit (NEB). More than 500 ng RNA / sample was used for sequencing library construction.
Directional mRNA library preparation (poly A enrichment) was contructed by Novogene Services after quanlity control test by Agilent 2100.

value: Bone marrow derived macrophages

value: TLR4 knockout

value: MDP


title: SG14244409_253949423786_1_3 0809-003-900 hr 4

value: Male

value: Alive


title: maize crown root, inoculum CWR_G_D, Drought, plantID_673

description:
Library name: plantID_673
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: CWR


title: maize crown root, inoculum WEL_G_W, Drought, plantID_675

description:
Library name: plantID_675
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: WEL


title: BMDM, KO, MDP-treated, biol rep 2

description:
Library name: Sample6_2
Column name in gene_count.txt and gene_fpkm.txt : KO_MDP02


title: BMDM, KO, MDP-treated, biol rep 1

description:
Library name: Sample6_1
Column name in gene_count.txt and gene_fpkm.txt : KO_MDP01


title: SG14244409_253949423786_1_1 0809-001-900 hr 0


title: SG16374548_253949448308_2_2_0806-001-900_0hr-baseline


title: SG14244409_253949423786_1_2 0809-002-900 hr 2


title: BMDM, KO, GM-treated, biol rep 1

description:
Library name: Sample5_1
Column name in gene_count.txt and gene_fpkm.txt : KO_GM01

value: GM


title: maize crown root, inoculum Mock, Drought, plantID_672

description:
Library name: plantID_672
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: maize crown root, inoculum TRI_G_W, Drought, plantID_666

description:
Library name: plantID_666
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: TRI


title: BMDM, KO, GM-treated, biol rep 3

description:
Library name: Sample5_3
Column name in gene_count.txt and gene_fpkm.txt : KO_GM03


title: BMDM, KO, GM-treated, biol rep 2

description:
Library name: Sample5_2
Column name in gene_count.txt and gene_fpkm.txt : KO_GM02


title: maize crown root, inoculum WEL_G_D, Drought, plantID_663

description:
Library name: plantID_663
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949423786_1_4 0809-004-900 hr 8


title: endometrioid_endometrial_carcinoma_sample_9

city: Rio de Janeiro

first: Pedro

last: Nicolau Neto

state: RJ

address: 37 Andre Cavalcanti Street

department: PCM

country: Brazil

institute: INCA

description: RMA expression value derived from TAC software; core-gene analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Genetic Program of INCA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Expression console software (Affymetrix) for background correction and normalization.

label: biotin

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: not applicable

extract_protocol: RNA was isolated from endometrioid endometrial carcinoma surgical fragment with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: not applicable

value: Yes

value: I


title: maize crown root, inoculum TRI_N_W, Drought, plantID_681

description:
Library name: plantID_681
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: BMDM, KO, Water-treated, biol rep 3

description:
Library name: Sample4_3
Column name in gene_count.txt and gene_fpkm.txt : KO_UT03

value: Water


title: maize crown root, inoculum WEL_N_D, Drought, plantID_658

description:
Library name: plantID_658
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: BMDM, KO, Water-treated, biol rep 2

description:
Library name: Sample4_2
Column name in gene_count.txt and gene_fpkm.txt : KO_UT02


title: endometrioid_endometrial_carcinoma_sample_10

value: No


title: maize crown root, inoculum SVR_G_D, Drought, plantID_657

description:
Library name: plantID_657
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: SVR

value: gamagrass


title: endometrioid_endometrial_carcinoma_sample_5


title: maize crown root, inoculum WEL_N_D, Drought, plantID_664

description:
Library name: plantID_664
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root

value: Drought


title: Liver, AAV8-PPARaDISS, western diet + pemafibrate

city: Lille

first: Doriane

last: Henry

state: Haut de France

address: 1 Rue du Pr. Calmette

country: France

institute: INSERM UMR 1011

description:
Library name: DISS_WD_P
10X Genomics

library_source: transcriptomic single cell

data_processing:
After sequencing quality control, CellRanger v7.0.1 (10X Genomics, USA) was used to align reads to the mouse reference genome (mm10-2020-A reference obtained from 10X Genomics) and generate the counts matrix. The Seurat v.5 R package (Satija Lab) was used for further analysis of the raw counts.
Assembly: mm10-2020-A
Supplementary files format and content: RDS files, Matrix files and MetaData files

source_name: Liver

extract_protocol:
To isolate nuclei, frozen livers from 3 mice randomly selected in each group were diced in NP40 lysis buffer (IGEPAL® I3021, Sigma-Aldrich, USA), dounce homogenized, and incubated on ice for 5 minutes. The homogenate was filtered using a 70-µm cell strainer and then a 40-µm cell strainer, and centrifuged for 5 minutes at 500 x g at 4°C. The supernatant was removed and the nuclei pellets were resuspended in wash buffer (1% bovine serum albumin, 0.2U/µL RNAse inhibitor) and marked with Nuclear Pore Complex HTOs (Biolegend) to identify individual mice from each pool prior to FACS-purification using the dye SYTOX™ AADvanced™ (ThermoFischer, USA) to remove debris. Following collection, nuclei integrity was visually verified with Trypan blue staining and nuclei were counted.
Nuclei from individual mice were pooled at equal ratio prior to encapsulation. Encapsulation was performed using the 10X Chromium Controller using 3’ GEMs kits v3.1 with groups run in separate lanes. Libraries were sequenced targeting ~25k reads/nuclei.

value: Liver

value: Ldlr-/- Ppara-/-

tag: infection

value: western diet + pemafibrate

tag: Sex

value: female


title: endometrioid_endometrial_carcinoma_sample_4


title: Liver, AAV8-PPARaDISS, western diet

description:
Library name: DISS_WD
10X Genomics

tag: tissue

value: western diet


title: BMDM, KO, Water-treated, biol rep 1

description:
Library name: Sample4_1
Column name in gene_count.txt and gene_fpkm.txt: KO_UT01

value: Bone marrow derived macrophages

value: TLR4 knockout


title: endometrioid_endometrial_carcinoma_sample_7


title: UOK342-TEAD1-rep2_S19

city: Baltimore

first: Danfeng

last: Cai

address: 615 N Wolfe St

institute: Johns Hopkins Bloomberg School of Public Health

description: Library name: UOK342-TEAD1-rep2_S19

data_processing:
ChIP-seq data were processed using the following pipeline. Raw sequencing reads in FASTQ format were quality-checked using FastQC. Reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.5.3). The resulting BAM files were used to generate coverage tracks (bigWig format) using bamCoverage from the deepTools suite, without additional normalization.
Assembly: hg38
Supplementary files format and content: .bigwig file

source_name: kidney

extract_protocol:
The cells, washed in ice-cold PBS, were then lysed in cell lysis buffer, with subsequent nutation at 4°C. Cells were treated by dounce homogenization on ice, followed by centrifuge at 500 x g for 10min. The supernatant was discarded, and the pellets was resuspended using nuclear lysis buffer. Nuclear lysates were then sheared by Covaris E220 to achieve average chromatin length of 300-400 bp.
DNA was purified with ChIP DNA Clean & ConcentratorTM (ZYMO research, D5205) and library preparation was performed using NEBNext® Multiplex Oligos for Illumima®

value: kidney

value: patient-derived cell line

tag: antibody


title: UOK342-YAP1-rep2_S20

description: Library name: UOK342-YAP1-rep2_S20


title: UOK342-TEAD1-rep1_S7

description: Library name: UOK342-TEAD1-rep1_S7


title: UOK342-YAP1-rep1_S11

description: Library name: UOK342-YAP1-rep1_S11


title: endometrioid_endometrial_carcinoma_sample_6

value: Yes


title: BMDM, WT, MDP-treated, biol rep 3

description:
Library name: Sample3_3
Column name in gene_count.txt and gene_fpkm.txt : WT_MDP03

value: wildtype

value: MDP


title: endometrioid_endometrial_carcinoma_sample_2

value: I


title: Liver, AAV8-PPARaWT, western diet + pemafibrate

description:
Library name: WT_WD_P
10X Genomics


title: endometrioid_endometrial_carcinoma_sample_8

value: No


title: endometrioid_endometrial_carcinoma_sample_3


title: endometrioid_endometrial_carcinoma_sample_1


title: UOK342-H3K9me3-rep2_S21

description: Library name: UOK342-H3K9me3-rep2_S21


title: BMDM, WT, MDP-treated, biol rep 2

description:
Library name: Sample3_2
Column name in gene_count.txt and gene_fpkm.txt : WT_MDP02


title: maize crown root, inoculum TRI_G_D, Drought, plantID_654

description:
Library name: plantID_654
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: plant id

tag: inoculum type

value: live

value: TRI

value: gamagrass


title: UOK342-H3K9me3-rep1_S12

description: Library name: UOK342-H3K9me3-rep1_S12


title: Liver, AAV8-PPARaWT, western diet

description:
Library name: WT_WD
10X Genomics

value: Liver


title: maize crown root, inoculum SVR_N_W, Drought, plantID_653

description:
Library name: plantID_653
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root

tag: inoculum origin

value: SVR

tag: inoculum conditioning_host

value: Drought


title: BMDM, WT, MDP-treated, biol rep 1

description:
Library name: Sample3_1
Column name in gene_count.txt and gene_fpkm.txt : WT_MDP01

tag: treatment


title: Liver, AAV8-GFP, western diet + pemafibrate

description:
Library name: GFP_WD_P
10X Genomics

tag: genotype

value: Ldlr-/- Ppara-/-

value: western diet + pemafibrate

value: female


title: UOK342-H3K27ac-rep2_S13

description: Library name: UOK342-H3K27ac-rep2_S13

value: kidney


title: maize crown root, inoculum WEL_G_D, Drought, plantID_656

description:
Library name: plantID_656
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: WEL

tag: inoculum conditioning_water

tag: testphase water_treatment


title: UOK342-H3K27ac-rep1_S3

description: Library name: UOK342-H3K27ac-rep1_S3

value: patient-derived cell line


title: Liver, AAV8-GFP, western diet

description:
Library name: GFP_WD
10X Genomics

value: western diet


title: su008 Post Tumor 4

city: Stanford

first: Yonglu

last: Che

state: CA

address: 269 Campus Dr

department: Dermatology

institute: Stanford University

description:
Xenium Transcript Counts
FFPE-derived human patient tissue specimens analyzed using 10x Xenium in situ

hyb_protocol: See 10x Xenium manual for details

scan_protocol: See 10x Xenium manual for details

data_processing:
See 10x Xenium manual and associated manuscript for details
Data files: Transcript counts, cell boundary coordinates, nucleus coordinates, H&E images.

label: Nucleotide probes

source_name: PD-1 inhibitor treated tumor

label_protocol: Complimentary sequence nucleotide probes per manufactuer's specifications

growth_protocol: Human patient specimens preserved in FFPE

extract_protocol: Sectioning into 5µm sections onto Xenium slides

treatment_protocol: PD-1 inhibitor

tag: condition

value: su008 Post Tumor 4


title: BMDM, WT, GM-treated, biol rep 1

description:
Library name: Sample2_1
Column name in gene_count.txt and gene_fpkm.txt : WT_GM01

value: Bone marrow derived macrophages

value: wildtype

value: GM


title: maize crown root, inoculum TRI_N_W, Drought, plantID_646

description:
Library name: plantID_646
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live

value: TRI


title: su008 Post Tumor 3

value: su008 Post Tumor 3


title: maize crown root, inoculum SVR_G_D, Drought, plantID_650

description:
Library name: plantID_650
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root

value: gamagrass


title: BMDM, WT, GM-treated, biol rep 3

description:
Library name: Sample2_3
Column name in gene_count.txt and gene_fpkm.txt : WT_GM03


title: UOK122-YAP1-rep1_S9

description: Library name: UOK122-YAP1-rep1_S9


title: UOK342-IgG-rep1_S31

description: Library name: UOK342-IgG-rep1_S31

value: IgG


title: maize crown root, inoculum TRI_G_W, Drought, plantID_640

description:
Library name: plantID_640
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: Drought


title: UOK122-TEAD1-rep2_S16

description: Library name: UOK122-TEAD1-rep2_S16


title: su008 Post Tumor 2

value: su008 Post Tumor 2


title: BMDM, WT, Water-treated, biol rep 2

description:
Library name: Sample1_2
Column name in gene_count.txt and gene_fpkm.txt : WT_UT02

value: Water


title: su008 Post Tumor 1

value: su008 Post Tumor 1


title: maize crown root, inoculum WEL_N_D, Drought, plantID_649

description:
Library name: plantID_649
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: WEL


title: BMDM, WT, Water-treated, biol rep 3

description:
Library name: Sample1_3
Column name in gene_count.txt and gene_fpkm.txt : WT_UT03


title: maize crown root, inoculum CWR_G_W, Drought, plantID_638

description:
Library name: plantID_638
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: CWR


title: maize crown root, inoculum SVR_G_W, Drought, plantID_636

description:
Library name: plantID_636
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: SVR


title: su007 Pre Tumor 1

source_name: Treat-naive tumor

value: su007 Pre Tumor 1


title: UOK122-H3K9me3-rep2_S18

description: Library name: UOK122-H3K9me3-rep2_S18

value: kidney

value: patient-derived cell line


title: su002 Post Tumor 1

value: su002 Post Tumor 1


title: maize crown root, inoculum TRI_N_D, Drought, plantID_635

description:
Library name: plantID_635
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live


title: UOK122-H3K9me3-rep1_S10

description: Library name: UOK122-H3K9me3-rep1_S10


title: BMDM, WT, GM-treated, biol rep 2

description:
Library name: Sample2_2
Column name in gene_count.txt and gene_fpkm.txt : WT_GM02

value: Bone marrow derived macrophages

value: wildtype

value: GM


title: maize crown root, inoculum WEL_N_W, Drought, plantID_633

description:
Library name: plantID_633
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root


title: UOK122-YAP1-rep2_S17

description: Library name: UOK122-YAP1-rep2_S17


title: su002 Pre Tumor 2

value: su002 Pre Tumor 2


title: UOK122-H3K27ac-rep2_S25

description: Library name: UOK122-H3K27ac-rep2_S25


title: maize crown root, inoculum SVR_N_W, Drought, plantID_632

description:
Library name: plantID_632
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: Drought


title: UOK122-TEAD1-rep1_S6

description: Library name: UOK122-TEAD1-rep1_S6


title: su005 Post Node 1

source_name: PD-1 inhibitor treated tumor-draining lymph node

value: su005 Post Node 1


title: maize crown root, inoculum TRI_N_W, Drought, plantID_627

description:
Library name: plantID_627
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: TRI


title: CD45.2_Irg1KO3

city: detroit

first: Shailendra

last: Giri

state: MI

address: 2799 W grand boul

department: Neurology Research

institute: henry ford hospital

description: Library name: IRG1-KO-CD45-2.3

data_processing:
Paired-end sequencing (150 bp) was performed with an Illumina NovaSeq 6000 via NOVOGENE INC. We performed QC with FastQC and aligned 150 bp paired_x0002_end reads to GRCm38-mm10, with 89%-94% alignment rates via the STAR aligner. The STAR aligner was subsequently utilized for count calling for each sample. For differential expression analysis, we employed the limma-Voom package in R, with a padj cutoff of 0.1 and logFC of 0.58 (FC=1.5) was set. The threshold for filtering out genes with low expression was set to 0.5 CPM in at least 80% of the samples. For count normalization, we used the trimmed mean of M values (TMM) method. Finally, R was used to generate the plots for visualization.
Assembly: MM10
Supplementary files format and content: tab delimited

source_name: spinal cord+brain

extract_protocol:
Qiagen RNeasy Mini Kit
The samples with a high RIN of more than 7.28 were selected for library preparation for RNA_x0002_seq. PolyA-enriched RNA libraries were prepared and barcoded for multiplexing according to Illumina recommendations.

treatment_protocol: Chimera was generated via the use of 50:50 CD45.1 (Wt) and CD45.2 (Irg1 KO) BMs utilizing Bulsulfan method. After 6 weeks, chimeric mice (CD45.2 Irg1 KO: CD45.1 Wt) were immunized with MOG35-55. At the peak of disease, the mice were sacrificed, the brain/spinal cords were harvested, and single-cell suspensions were prepared via the Percoll density‒gradient method.  CD45.1 and CD45.2 cells were gated and FACS-sorted. The sorted populations were rerun on a BD FACSAria™ III to check the purity of the sorted population. RNA-seq was performed on CD45.1- and CD45.2-sorted cells from 5 independent animals.

value: spinal cord+brain

tag: strain

value: male

value: Irg1 KO


title: CD45.2_Irg1KO1

description: Library name: IRG1-KO-CD45-2.1


title: CD45.2_Irg1KO2

description: Library name: IRG1-KO-CD45-2.2


title: CD45.1_WT4

description: Library name: IRG1-KO-CD45-1.4

value: WT


title: UOK121-YAP1-rep1_S15

description: Library name: UOK121-YAP1-rep1_S15


title: UOK122-H3K27ac-rep1_S2

description: Library name: UOK122-H3K27ac-rep1_S2


title: maize crown root, inoculum CWR_G_D, Drought, plantID_628

description:
Library name: plantID_628
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: CWR

value: gamagrass


title: su005 Post Node 2

description:
Xenium Transcript Counts
FFPE-derived human patient tissue specimens analyzed using 10x Xenium in situ

value: su005 Post Node 2


title: UOK121-YAP1-rep2_S26

description: Library name: UOK121-YAP1-rep2_S26

value: kidney

value: patient-derived cell line


title: su005 Post Tumor 3

value: su005 Post Tumor 3


title: CD45.2_Irg1KO4

description: Library name: IRG1-KO-CD45-2.4


title: UOK121-TEAD1-rep2_S27

description: Library name: UOK121-TEAD1-rep2_S27


title: su005 Post Tumor 2

value: su005 Post Tumor 2


title: CD45.1_WT2

description: Library name: IRG1-KO-CD45-1.2


title: maize crown root, inoculum SVR_N_D, Drought, plantID_623

description:
Library name: plantID_623
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live

value: SVR


title: BMDM, WT, Water-treated, biol rep 1

description:
Library name: Sample1_1
Column name in gene_count.txt and gene_fpkm.txt : WT_UT01

value: Bone marrow derived macrophages

value: wildtype

value: Water


title: su006 Pre Tumor 1

value: su006 Pre Tumor 1


title: UOK121-TEAD1-rep1_S5

description: Library name: UOK121-TEAD1-rep1_S5


title: maize crown root, inoculum CWR_N_D, Drought, plantID_622

description:
Library name: plantID_622
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root

value: Drought


title: su002 Pre Tumor 1

value: su002 Pre Tumor 1


title: CD45.1_WT1

description: Library name: IRG1-KO-CD45-1.1

value: spinal cord+brain

value: male

value: WT


title: UOK121-H3K9me3-rep2_S29

description: Library name: UOK121-H3K9me3-rep2_S29


title: maize crown root, inoculum CWR_N_W, Drought, plantID_621

description:
Library name: plantID_621
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: CWR


title: su007 Post Tumor 1

value: su007 Post Tumor 1


title: brain,Adult,rep1

city: Wuhan

first: Hu

last: Zheng

state: Hubei

address: shizishan street No.1

department: College of Veterinary Medicine

country: China

institute: Huazhong Agricultural University

description: Library name: Adult

data_processing:
Raw data were processed using the BD Rhapsody™ Whole Transcriptome Analysis (WTA) pipeline (v1.11)
Assembly: mm10
Supplementary files format and content: Comma-separated values cell-gene matrix files

source_name: brain

extract_protocol:
Single-cell suspensions were collected from prefrontal cortex of c57bl/6 mouse brains. The tissues were digested with 3mg protease XXIII and 30U/ml papin, and single cells were suspended with 0.5% BSA.
Single-cell mRNA library was performed by the BD Rhapsody Single-Cell Analysis System (BD Biosciences, USA). Firstly，single-cell suspension in BSA was loaded into a BD Rhapsody cartridge with >200,000 microwells. Secondly, single-cell mRNA was captured by magnetic beads with barcoded capture oligos.Then, magnetic beads were collected for cDNA synthesis and library construction following the BD Rhapsody single cell 3’ whole transcriptome amplification (WTA) workflow. Finally, the libraries were sequenced on Illumina NovaSeq 6000 (Illumina, USA) with 300-bp reads (150-bp paired-end reads).

value: brain


title: UOK121-H3K9me3-rep1_S23

description: Library name: UOK121-H3K9me3-rep1_S23

value: kidney

value: patient-derived cell line


title: CD45.1_WT3

description: Library name: IRG1-KO-CD45-1.3


title: maize crown root, inoculum WEL_N_W, Drought, plantID_620

description:
Library name: plantID_620
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live

value: WEL


title: maize crown root, inoculum WEL_G_D, Drought, plantID_626

description:
Library name: plantID_626
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: gamagrass


title: UOK121-H3K7ac-rep1_S1

description: Library name: UOK121-H3K7ac-rep1_S1


title: brain,P4,rep1

description: Library name: P4


title: brain,P1,rep1

description: Library name: P1


title: su001 Post Node 1  rep 2

description:
Xenium Transcript Counts
transcripts file and parquet file available on GSMnnn
FFPE-derived human patient tissue specimens analyzed using 10x Xenium in situ

value: su001 Post Node 1  rep 2


title: maize crown root, inoculum TRI_N_D, Drought, plantID_615

description:
Library name: plantID_615
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: TRI


title: UOK121-1perinput-rep1_S30

description: Library name: UOK121-1perinput-rep1_S30

value: input


title: su001 Pre Tumor 2  rep 2

value: su001 Pre Tumor 2  rep 2


title: brain,P10,rep1

description: Library name: P10


title: su001 Pre Tumor 1  rep 2

value: su001 Pre Tumor 1  rep 2


title: maize crown root, inoculum TRI_N_D, Drought, plantID_608

description:
Library name: plantID_608
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root

value: Drought


title: HK2-YAP1-rep2_S32

description: Library name: HK2-YAP1-rep2_S32

source_name: kidney; Cortex; Proximal tubule

value: kidney; Cortex; Proximal tubule


title: maize crown root, inoculum CWR_G_W, Drought, plantID_609

description:
Library name: plantID_609
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: HK2-YAP1-rep1_S22

description: Library name: HK2-YAP1-rep1_S22


title: su001 Post Peri 1  rep 2

source_name: PD-1 inhibitor treated perilesional skin

value: su001 Post Peri 1  rep 2


title: Kupffer cells, wild type mice, rep3

city: Hangzhou

first: yihang

last: Pan

state: Zhejiang

address: erkang road

institute: Zhejiang University

description: Library name: WT_H2O_3

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:hisat2-2.2.1) 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.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) 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: Ensembl_v101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: hepatic Kupffer cells

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTM Reverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM 6000 at the (LC Sceiences, USA) following the vendor's recommended protocol.

value: hepatic Kupffer cells


title: Kupffer cells, wild type mice, rep2

description: Library name: WT_H2O_2


title: Kupffer cells, wild type mice, rep1

description: Library name: WT_H2O_1


title: maize crown root, inoculum WEL_N_W, Drought, plantID_602

description:
Library name: plantID_602
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

source_name: crown root


title: HK2-TEAD1-rep2_S24

description: Library name: HK2-TEAD1-rep2_S24


title: Kupffer cells, hepcidin-1 knockout mice, rep3

description: Library name: KO_H2O_3


title: su005 Post Tumor 1

value: su005 Post Tumor 1


title: UOK121-H3K27ac-rep2_S28

description: Library name: UOK121-H3K27ac-rep2_S28


title: maize crown root, inoculum SVR_N_W, Drought, plantID_613

description:
Library name: plantID_613
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: SVR


title: su001 Post Tumor 5  rep 2

value: su001 Post Tumor 5  rep 2


title: Kupffer cells, hepcidin-1 knockout mice, rep2

description: Library name: KO_H2O_2


title: maize crown root, inoculum TRI_G_D, Drought, plantID_601

description:
Library name: plantID_601
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: su001 Post Tumor 4  rep 2

value: su001 Post Tumor 4  rep 2


title: HK2-TEAD1-rep1_S8

description: Library name: HK2-TEAD1-rep1_S8


title: HK2-H3K9me3-rep2_S33

description: Library name: HK2-H3K9me3-rep2_S33


title: maize crown root, inoculum WEL_G_W, Drought, plantID_600

description:
Library name: plantID_600
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live


title: su001 Post Tumor 3  rep 2

value: su001 Post Tumor 3  rep 2


title: su001 Post Tumor 6  rep 2

value: su001 Post Tumor 6  rep 2


title: HK2-H3K27ac-rep1_S4

description: Library name: HK2-H3K27ac-rep1_S4


title: maize crown root, inoculum CWR_G_W, Drought, plantID_595

description:
Library name: plantID_595
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: CWR

value: gamagrass


title: maize crown root, inoculum SVR_G_W, Drought, plantID_596

description:
Library name: plantID_596
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: TRPM2 Mg KO+Bilirubin 2

city: Hefei

first: Shuaijie

last: Sun

address: The First Affiliated Hospital of USTC

institute: Department of Anesthesiology,First Affiliated Hospital of USTC

description:
Library name: Sample6
10x Genomics

data_processing:
For scRNA-seq data processing, raw reads were aligned to mouse reference genome GRCm39 using the Cell Ranger software (v8.0.0) to generate cell × gene matrices. The FASTQ files were processed using the standard workflow of cellranger to generate gene expression count matrices for each sample. The raw count matrices from all samples were merged using Scanpy (V1.9.6), followed by quality control.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain cells

extract_protocol:
Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion).
ScRNA-seq libraries were subsequently prepared following the manufacturer’s protocol of Chromium Next GEM Single Cell 3’ Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode.

value: brain cells


title: su001 Post Tumor 1 rep 2

description:
Xenium Transcript Counts
FFPE-derived human patient tissue specimens analyzed using 10x Xenium in situ

value: su001 Post Tumor 1 rep 2


title: TRPM2 Mg KO+Bilirubin 1

description:
Library name: Sample5
10x Genomics


title: HK2-1perinput-rep1_S34

description: Library name: HK2-1perinput-rep1_S34

value: input


title: maize crown root, inoculum CWR_N_W, Drought, plantID_606

description:
Library name: plantID_606
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root


title: maize crown root, inoculum SVR_G_W, Drought, plantID_593

description:
Library name: plantID_593
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: Drought


title: su001 Pre Tumor 2  rep 1

value: su001 Pre Tumor 2  rep 1


title: maize crown root, inoculum TRI_N_D, Drought, plantID_592

description:
Library name: plantID_592
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: TRI


title: su001 Pre Tumor 1  rep 1

value: su001 Pre Tumor 1  rep 1


title: WT+Bilirubin 2

description:
Library name: Sample4
10x Genomics


title: WT+Bilirubin 1

description:
Library name: Sample3
10x Genomics


title: maize crown root, inoculum TRI_G_D, Drought, plantID_591

description:
Library name: plantID_591
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: su001 Post Tumor 6  rep 1

value: su001 Post Tumor 6  rep 1


title: WT+Vehicle 2

description:
Library name: Sample2
10x Genomics


title: maize crown root, inoculum CWR_N_D, Drought, plantID_587

description:
Library name: plantID_587
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: WT+Vehicle 1

description:
Library name: Sample1
10x Genomics


title: su001 Post Tumor 5  rep 1

value: su001 Post Tumor 5  rep 1


title: Kupffer cells, hepcidin-1 knockout mice, rep1

description: Library name: KO_H2O_1

value: hepatic Kupffer cells


title: HK2-H3K9me3-rep1_S14

description: Library name: HK2-H3K9me3-rep1_S14

value: kidney; Cortex; Proximal tubule


title: su001 Post Tumor 2  rep 2

value: su001 Post Tumor 2  rep 2


title: maize crown root, inoculum SVR_G_D, Drought, plantID_586

description:
Library name: plantID_586
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live

value: SVR


title: su001 Post Peri 1  rep 1

description:
Xenium Transcript Counts
transcripts file and parquet file available on GSMnnn
FFPE-derived human patient tissue specimens analyzed using 10x Xenium in situ

value: su001 Post Peri 1  rep 1


title: su001 Post Node 1  rep 1

value: su001 Post Node 1  rep 1


title: maize crown root, inoculum Mock, Drought, plantID_583

description:
Library name: plantID_583
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: mock


title: maize crown root, inoculum SVR_N_D, Drought, plantID_581

description:
Library name: plantID_581
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: su001 Post Tumor 3  rep 1

value: su001 Post Tumor 3  rep 1


title: Curio Spatial transcriptomics of left nodose ganglion tile 2

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description: Library name: LNG1-3_A0045_002_F2R2

data_processing:
Fastq data was aligned to GRCm38 mm10 ensembl 100
Assembly: GRCm38
Supplementary files format and content: For snRNAseq the gene expression data matrix is stored in standard HDF5 format. For spatial transcriptomics the gene expression data is stored in seurat RDS files
Supplementary files format and content: For spatial datasets we provide the bead barcode information for each tile as .txt files
Library strategy: Spatial Transcriptomics

source_name: Left Nodose Ganglion

extract_protocol:
For snRNAseq: Mice were euthanized and the nodose ganglia were immediately extracted and snap frozen on dry ice pooling overnight-fasted left, overnight-fasted right, ad libitum fed left, and ad libitum fed right nodose ganglia into four separate tubes. Each sample was separately homogenized in 500µL homogenization buffer in a dounce homogenizer on ice. Samples were centrifuged at 900 r.c.f at 4°C for 10 minutes. The supernatant was removed and pellets were resuspended in a 1:1 mixture of homogenization buffer and 50% Optiprep diluted in iodixanol dilution media. These suspensions were then layered on top of 450µL 29% Optiprep diluted in iodixanol dilution medium and were centrifuged at 13,500 r.c.f, at 4°C for 20 minutes. The supernatant was removed, and pellets were resuspended in 1mL PBS containing 0.04% BSA. Resuspended samples were centrifuged at 900 r.c.f for 10 minutes at 4°C and supernatant was removed. Samples were resuspended in 100µL of different cell multiplexing oligo (CMO; from the 10X Genomics 3’ CellPlex kit) and incubated for 5 minutes at room temperature. After incubation, 1.9mL resuspension buffer (PBS with 1% BSA and 0.4U/µL RNasin) was added to each sample, and the mixture centrifuged at 900 r.c.f for 10 minutes, and then the supernatant was removed. Another 1mL resuspension buffer was added, the mixture centrifuged at 900 r.c.f for 4 minutes and then the supernatant removed. Nuclei pellets were resuspended in 100µL resuspension buffer each and then combined. The pooled sample was centrifuged at 900 r.c.f for 10 minutes, the top 50µL of supernatant removed, and the pellet resuspended in the rest of the supernatant. For spatial transcriptomics: The left and right nodose ganglia from six mice were dissected and snap frozen on dry ice. Three nodose ganglia in the same orientation were placed on a single disposable base mould and embedded by adding chilled bubble free optimal cutting temperature compound. The samples, comprising 6 left nodose ganglia and 3 right nodose ganglia in total, were stored at -80°C until sectioned on a cryostat at -20°C into 10µm sections. The 10µm section was mounted to a pre chilled 3mm by 3mm Curio Seeker tile slide for high-resolution spatial transcriptomics.
For snRNAseq: libraries were generated by following the Chromium Next GEM Single Cell 3’ v3.1 Dual Index protocols, with feature barcode technology for cell multiplexing. For spatial transcriptomics libraries were generated according to the Curio Seeker Spatial Mapping Kit (3x3) user guides.

value: Left Nodose Ganglion

value: Ad libitum fed


title: maize crown root, inoculum CWR_G_D, Drought, plantID_575

description:
Library name: plantID_575
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

data_processing:
UMIs were removed from all sequences and added to the read headers using UMI-tools. Next, cutadapt version 4.2 was used to remove the first four bases of each read, remove poly-A tails (if present), remove spurious poly-G runs using the --nextseq-trim=10 parameter, and remove adapter sequences. Reads that were <10 bp long or that aligned to maize rRNA gene sequences were removed; the remaining reads were aligned to the maize reference genome B73 RefGen_v550 using HISAT2 version 2.2.1. Aligned reads were converted to BAM format, sorted, and indexed using samtools version 1.9. We then used UMI-tools to de-duplicate reads that both shared a UMI and had identical mapping coordinates. Finally, we used the FeatureCounts function of the subread package version 2.0.5 with the maize genome annotation version Zm00001eb.1 and parameters -O --fraction -M --primary -g ID -t gene to generate a table of gene expression estimates.
Assembly: maize reference genome B73 RefGen_v5
Supplementary files format and content: tab-delimited FeatureCounts output (transcript counts per sample/library)

extract_protocol:
Macherey-Nagel NucleoSpin RNA Plant kit + Invitrogen DNA-Free kit
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root

value: CWR

value: gamagrass

value: Drought


title: Curio Spatial transcriptomics of right nodose ganglion tile 1

description: Library name: RNG4-6_A0051_045_F3R3

source_name: Right Nodose Ganglion

value: Right Nodose Ganglion


title: su001 Post Tumor 4  rep 1

value: su001 Post Tumor 4  rep 1


title: su001 Post Tumor 2  rep 1

value: su001 Post Tumor 2  rep 1


title: single nucleus RNA sequencing of mouse nodose ganglia gene expression library

description:
Library name: nodose_ganglion_pooled_gex
Library consists of 4 samples

data_processing:
Fastq data was aligned to GRCm38 mm10 ensembl 100
Assembly: GRCm38
Supplementary files format and content: For snRNAseq the gene expression data matrix is stored in standard HDF5 format. For spatial transcriptomics the gene expression data is stored in seurat RDS files
Supplementary files format and content: For spatial datasets we provide the bead barcode information for each tile as .txt files

source_name: Nodose Ganglion (left and right)

value: Nodose Ganglion (left and right)

value: ad libitum fed and overnight fast


title: maize crown root, inoculum SVR_N_W, Drought, plantID_578

description:
Library name: plantID_578
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live


title: AtcS_Mutant_Day4_rep5

city: Richmond

first: Daniel

last: Miller

state: Virginia

address: 1101 E Marshall Street

department: Microbiology and Immunology

institute: Virginia Commonwealth University

data_processing:
Quality control, trimming, and merging of paired sequence reads using FastQC, cutadapt , and FLASH. Gene assignment was performed using Bowtie 2.
Assembly: Genome assembly ASM818v1
Supplementary files format and content: reads_table.csv (show reads without normalization)

organism: Treponema denticola

source_name: Bacterial cells

growth_protocol: Treponema denticola ATCC 35405 and atcS mutant used in this study were grown in new oral spirochete (NOS) media under anerobic conditions (5% H2, 5% CO2, 90% N2) at 37C.

extract_protocol:
RNA extraction via TRIzol method. Total RNA quantity and integrity were determined using an Agilent Bioanalyzer RNA Pico assay. All samples passed quality control assessment with RNA Integrity Numbers (RIN) above 9. Ribosomal reduction was then performed on all samples using Illumina’s Ribo-Zero rRNA Removal Kit. The resulting depleted RNA was assessed using an Agilent Bioanalyzer RNA Pico assay to confirm efficient rRNA removal.
Kit to sequencing libraries - Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
For Sequencing - NextSeq 1000/2000 P1 Reagents (300 Cycles. Read length is 150bp x 150bp for sequencing, Paired End.

treatment_protocol: T. denticola 35405 and atcS mutant were grown for 4 days in NOS under anerobic conditions at 37C.

value: Bacterial cells

value: atcS gene deletion


title: maize crown root, inoculum TRI_G_W, Drought, plantID_572

first: Maggie

last: Wagner

address: 1200 Sunnyside Avenue

institute: University of Kansas

description:
Library name: plantID_572
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: TRI


title: su001 Post Tumor 1 rep 1

value: su001 Post Tumor 1 rep 1


title: K4

city: hangzhou

first: zhiqi

last: xie

address: huzhou street 51

institute: Hangzhou city university

description: Library name: Sample 6

data_processing:
The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina). The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4). The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization. Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and count values for each samples

source_name: bone marrow

extract_protocol:
Total RNA was extracted using Trizol 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.
library preparation according to Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® ). Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina novaseq6000.

value: bone marrow

value: bone marrow cells

value: 34.7 mM KCl


title: AtcS_Mutant_Day4_rep4


title: maize crown root, inoculum WEL_N_D, Drought, plantID_571

city: Lawrence

description:
Library name: plantID_571
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root

value: WEL


title: K2

description: Library name: Sample 5


title: Bl6/NZB Lactation day 21 replicate 3

city: New York

first: Edmund

middle: C

last: Jenkins

state: NY

address: 1468 Madison Avenue

department: Heme/Onc

institute: Icahn School of Medicine at Mt. Sinai

description: 10x Genomics Chromium

data_processing:
fastq files were analyzed using the Cellranger count pipeline. Cell pupulations were identifies using the Loupe Browser
Assembly: GRCm38/mm10

molecule: nuclear RNA

source_name: Mammary Gland

growth_protocol: Samples are from freshly isolated snap frozen tissue

extract_protocol:
Freshly isolated snap frozen Inguinal mammary glands were submitted to GENEWIZ, LLC, NJ, USA for nuclei isolation and GEM (Gel Bead-based Emulsion) single cell RNA seq analysis on the 10x Genomics platform. Analysis was performed using the Cellranger (10xGenomics) count pipeline.
10X Genomics Chromium automated single cell gene expression by chromium connect

value: Mammary Gland

value: Lactation D21


title: maize crown root, inoculum TRI_G_W, Drought, plantID_568

description:
Library name: plantID_568
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: gamagrass

value: Drought


title: AtcS_Mutant_Day4_rep3


title: K1

description: Library name: Sample 4


title: Bl6/NZB Lactation day 21 replicate 2

description: 10x Genomics Chromium


title: AtcS_Mutant_Day4_rep2


title: C4

description: Library name: Sample 3

value: untreated


title: Bl6/NZB Lactation day 21 replicate 1

description: 10x Genomics Chromium


title: AtcS_Mutant_Day4_rep1


title: maize crown root, inoculum WEL_G_W, Drought, plantID_555

description:
Library name: plantID_555
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: single nucleus RNA sequencing of mouse nodose ganglia CMO library

city: Cambridge

description:
Library name: nodose_ganglion_pooled_CMO
CMO barcodes to demultiplex the snRNAseq library

value: Nodose Ganglion (left and right)


title: Curio Spatial transcriptomics of left nodose ganglion tile 1

description: Library name: LNG4-6_A0045_018_F1R1

value: Left Nodose Ganglion

value: Ad libitum fed


title: Wild_type_Day4_rep5

value: Bacterial cells

value: Wild type


title: Bl6/NZB Vigin replicate 3

description: 10x Genomics Chromium

value: Virgin


title: Con1

description: Library name: Sample 1


title: Bl6/NZB Vigin replicate 2

description: 10x Genomics Chromium


title: maize crown root, inoculum SVR_G_D, Drought, plantID_544

description:
Library name: plantID_544
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live

value: SVR


title: Wild_type_Day4_rep4


title: maize crown root, inoculum WEL_G_D, Drought, plantID_542

description:
Library name: plantID_542
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: CITE_NRAS_aPD1

city: Leuven

first: Jean-Christophe

last: Marine

address: Herestraat

country: Belgium

institute: VIB-KULeuven

description: Library name: NRO010

data_processing:
The raw sequencing reads were processed by CellRanger (v. 7.2.0, 10x Genomics)
Assembly: mm10
Supplementary files format and content: h5 for RNA expression, csv for protein expression
Library strategy: CITE-seq

source_name: melanoma

extract_protocol:
10X Genomics
The scRNA-Seq libraries were prepared using the GemCode Single Cell 5’ Gel Bead and Library kit, version Next GEM 2 according to the manufacturer’s instructions (10x Genomics, CG000331)

value: melanoma


title: maize crown root, inoculum TRI_G_D, Drought, plantID_541

description:
Library name: plantID_541
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: TRI


title: Wild_type_Day4_rep3


title: Bl6/NZB Vigin replicate 1

description: 10x Genomics Chromium


title: CITE_NRAS_control

description: Library name: NRO009


title: Bl6/c57 Lactation day 21 replicate 3

description: 10x Genomics Chromium


title: Wild_type_Day4_rep2


title: maize crown root, inoculum CWR_N_D, Drought, plantID_540

description:
Library name: plantID_540
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root

value: CWR


title: sc_NRAS_aPD1_aNK_1_1

description: Library name: NRO008

data_processing:
The raw sequencing reads were processed by CellRanger (v. 7.2.0, 10x Genomics)
Assembly: mm10
Supplementary files format and content: h5 for RNA expression, csv for protein expression

value: TME


title: Wild_type_Day4_rep1


title: maize crown root, inoculum CWR_G_W, Drought, plantID_538

description:
Library name: plantID_538
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: Caenorhabditis_elegans_embryo_kuls54_H3K9me3_ChIP_seq_R2

city: Guangzhou

first: shiyu

last: cai

address: No. 135 Xingang Xi Road, Haizhu District

institute: Sun Yat-sen University

description: Library name: kuls54_H3K9me3_ChIP_R2

data_processing:
The sequencing reads were processed using Trim Galore (v0.6.10 ) to remove adapters and filter out low-quality sequences.
Alignment was performed against the Caenorhabditis elegans reference genome (WS292 ) using Bowtie2.
Duplicate reads were removed using sambamba (v1.0.0 ). BAM files from replicates were merged with samtools (v1.19.2 ), and read counts were normalized using the RPKM (Reads Per Kilobase per Million mapped reads) method.the ChIP/input ratio was calculated using bamcompare.
Peak calling was performed with MACS2 (v3.0.1,--broad-cutoff 0.1)
Assembly: WBcel235 (WS292)
Supplementary files format and content: bigwig
Supplementary files format and content: broadPeak

organism: Caenorhabditis elegans

source_name: embryo

extract_protocol:
worm embryos were crosslinked in 2% formaldehyde for 30 min. Crosslinking was quenched with 125 mM glycine for 5 min at room temperature and washed three times with M9 (3g/L KH2PO4, 6g/L Na2HPO4, 5g/L NaCl, 1 mM MgSO4). Crosslinked samples were suspended by FA buffer (50 mM Tris/HCl pH 7.5, 1 mM EDTA, 1 % Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl) with 1X complete protease inhibitor (Roche, 4693132001) and sonicated for three 8-min cycles (30 s on and 30 s off per cycle) with Diagenode Bioruptor on high amplitude. Lysates were precleared with protein A/G (Santa Cruz, SC-2003). 5% samples were saved for input. The rest of the lysate was immunoprecipitated with 2 μl of rabbit anti-H3K9me3 antibody (Millipore, 07-523) overnight at 4 °C. The next day, the samples were incubated with 20 μL protein A/G beads for 2h at 4 °C. Beads were extensively washed by FA  buffer two times, FA-500 buffer (50 mM Tris/HCl pH 7.5, 1 mM EDTA, 1 % Triton X-100, 0.1% sodium deoxycholate, 500 mM NaCl) two times, LiCl buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris/HCl pH 8.0) one time and TE buffe (10 mM Tris/HCl pH 8.0, 1 mM EDTA) 2 times. Washed samples were eluted with elution buffer (1% SDS, 100 mM NaHCO3) for 30 min at room temperature. The samples were de-crosslinked with 200 mM NaCl at 65 °C for 4 h. For input DNA, input samples were treated with RNase A (Thermofisher, EN0531) at 65 °C for 30 min. All DNA samples were purified by E.Z.N.A. Gel Extraction Kit (Omega, D2500).
ChIP-seq libraries were made using IVAHTS Universal DNA Library Prep Kit for lllumina V3 (Vazyme, ND607) according to the manufacturer’s instructions.

value: embryo


title: maize crown root, inoculum CWR_N_W, Drought, plantID_549

description:
Library name: plantID_549
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: Con2

description: Library name: Sample 2

value: bone marrow

value: bone marrow cells


title: Bl6/c57 Lactation day 21 replicate 2

description: 10x Genomics Chromium

value: Mammary Gland

value: Lactation D21


title: maize crown root, inoculum CWR_G_D, Drought, plantID_536

description:
Library name: plantID_536
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: gamagrass

value: Drought


title: Bl6/c57 Lactation day 21 replicate 1

description: 10x Genomics Chromium


title: Caenorhabditis_elegans_embryo_gwls4_H3K9me3_ChIP_seq_R2

description: Library name: gwls4_H3K9me3_ChIP_R2


title: Bl6/c57 Vigin replicate 3

description: 10x Genomics Chromium


title: maize crown root, inoculum SVR_G_W, Drought, plantID_529

description:
Library name: plantID_529
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: sc_NRAS_control

description: Library name: NRO005


title: Caenorhabditis_elegans_embryo_N2(for_transgenes)_H3K9me3_ChIP_seq_R2

description: Library name: N2(for_transgenes)_H3K9me3_ChIP_R2

value: WT


title: sc_NRAS_aPD1

description: Library name: NRO006


title: sc_YUMM_5_2_aPD1_aNK_1_1

description: Library name: NRO004

value: YUMM 5.2


title: maize crown root, inoculum TRI_N_W, Drought, plantID_521

description:
Library name: plantID_521
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: Bl6/c57 Vigin replicate 2

description: 10x Genomics Chromium

value: Virgin


title: Caenorhabditis_elegans_embryo_kuls54_H3K9me3_ChIP_seq_R1

description: Library name: kuls54_H3K9me3_ChIP_R1


title: Bl6/c57 Vigin replicate 1

description: 10x Genomics Chromium


title: Caenorhabditis_elegans_embryo_gwls4_H3K9me3_ChIP_seq_R1

description: Library name: gwls4_H3K9me3_ChIP_R1


title: sc_YUMM_5_2_aNK1_1

description: Library name: NRO002


title: Caenorhabditis_elegans_embryo_N2(for_transgenes)_H3K9me3_ChIP_seq_R1

description: Library name: N2(for_transgenes)_H3K9me3_ChIP_R1


title: maize crown root, inoculum CWR_N_W, Drought, plantID_518

description:
Library name: plantID_518
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live


title: sc_NRAS_aNK_1_1

description: Library name: NRO007


title: sc_YUMM_5_2_aPD1

description: Library name: NRO001


title: Caenorhabditis_elegans_embryo_kuls54_H3K9me3_Input_seq

description: Library name: kuls54_H3K9me3_Input


title: maize crown root, inoculum Mock, Drought, plantID_512

description:
Library name: plantID_512
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: mock


title: Caenorhabditis_elegans_embryo_gwls4_H3K9me3_Input_seq

description: Library name: gwls4_H3K9me3_Input


title: Mousec_v

city: SHANGHAI

first: Fudi

last: Wang

state: SHANGHAI

address: 320, YUEYANG ROAD

description: Library name: Mousec_v

data_processing:
Quality control of the sequencing data was performed using FastQC (v0.11.8).
TrimGalore (v0.6.10) was employed for the trimming of sequence reads.
The RNA-seq reads were aligned to mm10 reference genome using the STAR software (v2.7.11b).
Raw read counts were subjected to variance stabilizing transformation (VST) using the DESeq2 (v1.44).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Bone marrow

growth_protocol: BMDMs were prepared from three mice. At day4 of differentiation, 7x105 macrophages were seeded into 6-well plates.

extract_protocol:
Total RNA was extracted according to the protocol from manufacturer and qualified on a NanoDrop™ OneC Microvolume UV-Vis Spectrophotometer (Thermo Scientific™ 840274200).
Three biological replicates per treatment group with a total of 200 ng RNA per sample were sent to Novogene Co. (Sacramento, CA, USA) for sample quality control, library preparation, and sequencing.
Complementary DNA library construction and sequencing were performed for each sample on an Illumina Novaseq 6000 platform with paired-end 150-bp reads.

treatment_protocol: Cells were treated with 2µM thiothixene or DMSO for 24 hours at day 6. Drug-treated macrophages were washed with PBS once and cells were lysed with 0.5 ml TRIzol™ Reagent (ThermoFisher 15596026).

value: Bone marrow

value: BMDM

value: Macrophage

value: DMSO


title: maize crown root, inoculum SVR_N_D, Drought, plantID_527

description:
Library name: plantID_527
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: crown root

value: SVR


title: Colon Cancer_578

city: Palma

first: Ramon

middle: Maria

last: Rodriguez

state: Balearic Islands

address: Edificio S, Hospital Universitario Son Espases, Carretera de Valldemossa, 79

department: Oncology and hematology

country: Spain

institute: Institut d'Investigació Sanitària Illes Balears

description: Gene expression data from patiets with colon cancer

hyb_protocol: Samples were hybridized with GeneChip Human Clariom S Pico Arrays (Affymetrix, Thermo Fisher Scientific) and scanned at the Genomic Core Facility of the The Health Research Institute of the Balearic Islands (IdISBa)

scan_protocol: Array scanning was performed by using the GeneChip Scanner 3000 7G according to the manufacturer's instruction (Affymetrix, Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software using default analysis settings.

source_name: Human colon cancer

label_protocol: Double-stranded cDNA was generated from the amplified cRNA with the GeneChip Pico Reagent Kit (Affymetrix, Thermo Fisher Scientific) and then fragmented and biotin-labeled.

extract_protocol: RNeasy Plus Kit was used for extraction of total RNA according to the manufacturer's instructions.

tag: disease state

value: Human colon cancer

value: Colon

tag: age

value: Male

tag: histological features diagnostic

tag: bmi

tag: ethnicity

value: White/Mediterranean


title: maize crown root, inoculum WEL_N_W, Drought, plantID_509

description:
Library name: plantID_509
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: tissue

value: WEL


title: Mouseb_v

description: Library name: Mouseb_v

tag: cell line

tag: cell type


title: Caenorhabditis_elegans_embryo_N2(for_transgenes)_H3K9me3_Input_seq

description: Library name: N2(for_transgenes)_H3K9me3_Input

value: embryo


title: Colon Cancer_577

tag: Sex


title: Mousea_v

description: Library name: Mousea_v


title: maize crown root, inoculum WEL_G_W, Drought, plantID_500

description:
Library name: plantID_500
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

tag: plant id

tag: inoculum type

tag: inoculum origin

value: gamagrass

value: Drought


title: Caenorhabditis_elegans_embryo_secp-2(ths431)_H3K9me3_ChIP_seq-R2

description: Library name: secp-2(ths431)_H3K9me3_ChIP_R2

tag: genotype


title: Colon Cancer_575

tag: unsaturated/saturated fa ratio


title: sc_YUMM_5_2_control

description: Library name: NRO003

value: melanoma

value: YUMM 5.2

value: TME


title: maize crown root, inoculum SVR_N_D, Drought, plantID_520

description:
Library name: plantID_520
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: live

tag: inoculum conditioning_host

tag: inoculum conditioning_water

tag: testphase water_treatment


title: Caenorhabditis_elegans_embryo_secp-2(ths431)_H3K9me3_ChIP_seq-R1

description: Library name: secp-2(ths431)_H3K9me3_ChIP_R1


title: Mousec_4

description: Library name: Mousec_4

value: Bone marrow

value: BMDM

tag: treatment

value: Thiothixene 2 µM