title: RAW264.7 cells, Kdm7a gRNA (KO), M1 macrophage stimulated with LPS and interferon-γ for 48 hours., rep-2

description: Library name: Sample14

value: Kdm7a KO_M1

value: M1 macropage stimulation


title: SEP3tet_mock_rep1_R1

status: Public on Mar 03 2026

type: SRA

city: Berlin

first: Kerstin

last: Kaufmann

address: Philippstr. 11-13 (House 22)

department: Plant Cell and Molecular Biology

country: Germany

institute: Humboldt-Universitaet zu Berlin

library_source: genomic

data_processing:
Read were timmed with Trimmomatic v0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
Trimmed reads were mapped to the Arabidopsis genome using bowtie2 v2.2.5 with default parameters
Peak calling was done using MACS2 (version 2.2.7.1) comparing IP vs mock with defaults parameters except: -g 101274395
Wiggle tracks were generated by DeepTools with the command “bamCoverage” with parameters -bs 10 --skipNonCoveredRegions
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for mock samples)

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plants were growing at 22°C under the long-day condition (daily cycles of 16 hours with light and 8 hours in dark).

extract_protocol:
~1g inflorescence were collected as starting material. Then, tissue fixation and nuclei isolation were done according to the published protocol (Kaufmann, K., Muiño, J.M., Østerås, M., Farinelli, L., Krajewski, P., and Angenent, G.C. (2010a). Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat. Protoc. 5: 457–472.). Native SEP3 antibody and Dynabeads protein A (Thermo Fisher) were used for immunoprecipitation.
ChIP-seq library preparation was done with the ThruPlex DNA-Seq kit following the kit manual.

tag: tissue

value: inflorescence

tag: cell type

value: floral cells

tag: genotype

tag: chip antibody

value: pre-immune


title: DHODH_NT_2_1

city: Houston

first: Arun

last: Sreekumar

state: Texas

address: One Baylor Plaza

department: Molecular and Cell Biology

country: USA

institute: Baylor College of Medicine

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
Fastq files were run through fastqc for primary qc
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt (parameter- Default settings)
Trimmed sequence reads were mapped to GRCh38 using HISAT2
Read count extraction and normalization were performed using Feature Counts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Feature counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: 2B-MDA-PCa was cultured in BRFF-HPC1 media (AthenaES, Baltimore, MD) with 20% FBS (FBS, Hyclone Labs, Thermo Scientific, Rockford, IL) and 0.1% penicillin-streptomycin (Hyclone Labs, Thermo Scientific, Rockford, IL). MDA-PCa-2a cells were cultured in plates or flasks pre-coated with a fibronectin solution (AthenaES, Baltimore, MD).

extract_protocol:
RNA extraction was performed using the Aurum™ Total RNA Mini Kit (Bio-Rad).
Libraries were prepared using ABclonal mRNA-seq Library Prep Kit for Illumina (poly-A selection). RNA integrity and quantification was confirmed on the AATI Fragment Analyzer and quantitative PCR. Quality assessment and sequencing were performed by Novogene Corporation, Sacramento. Sequencing was performed using Illumina NovaSeq X Plus (PE150).

tag: cell line


title: SEP3wt_mock_rep1_R1


title: DHODH_NT_1_1

description: Library name: Sample 1


title: DHODH_KD1_2_1

description: Library name: Sample 5


title: DY 24hr LPS rep 3

city: St. Louis

first: Sharon

middle: Celeste

last: Morley

state: MO

address: 625 S Euclid

department: Pediatrics

institute: Washington University in St. Louis

description:
sample.dy3_24hr
group_dy_24hr-group_wt_24hr_Differential_Expression.tsv
group_dy_24hr-group_wt_24hr.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv

data_processing:
Basecalls and demultiplexing- bcl2fastq software and a custom python demultiplexing program
aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Gene counts derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated
Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05
For each contrast extracted with Limma, global perturbations in known KEGG pathways were detected using the R/Bioconductor package GAGE8 to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term
Assembly: Ensembl release 76 primary assembly
Supplementary files format and content: tsv files for KEGG signaling and metabolism pathway analysis statistics
Supplementary files format and content: tsv files of differentially expressed genes

organism: Mus musculus

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow was subjected to RBC lysis (BD pharmlyse) and incubated in complete DMEM (Gibco DMEM, 10% FBS, 1% pen/strep, 1% HEPES, 1% GlutaMAX) with 10% L929 conditioned medium for 6 days. Media was replenished every 2-4 days.

extract_protocol: RNA was extracted from BMDMs using the RNeasy Plus Mini Kit (Qiagen #74134) according to manufacturer instructions.

treatment_protocol: Treated samples were subjected to 100 ng/mL LPS for the indicated amount of time

value: Bone marrow-derived macrophages

tag: treatment

value: 24hr LPS


title: DY 24hr LPS rep 2

description:
sample.dy2_24hr
group_dy_24hr-group_wt_24hr_Differential_Expression.tsv
group_dy_24hr-group_wt_24hr.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv


title: RAW264.7 cells, Kdm7a gRNA (KO), M0 macrophages treated without stimulation for 48 hours, rep-2

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description: Library name: Sample11

data_processing:
The fastq data was processed by Trim_galore, Star mapping, and Rsem.
Assembly: mm10
Supplementary files format and content: Raw count all sample.txt containts all raw count data from 18 samples.

growth_protocol: RAW264.7 cells were cultured in Dulbecco-modified eagle’s medium (DMEM) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), and penicillin/streptomycin (P/S).

extract_protocol:
Total RNA was extracetd using Rneasy Mini kit folloing manufacturer's instructions.
poly(A) RNA was isolated and library was prepared using NEBNext Ultra II RNA Library Prep Kit for Ilumina following manufacturer's instructions.

treatment_protocol: RAW264.7 cells were polarized by expose to 2 ng/ml mouse IFN-γ and 0.1 µg/ml LPS (M1) or 20 ng/ml IL-4, IL-10, and IL-13 (from mouse) and 2 ng/ml human TGF-β1 (M2) during 48 hours.

value: Kdm7a KO_M0

value: Kdm7a Knockout

value: non-treatment


title: GW4064-3

city: Shanghai

first: Senlin

last: Zhao

address: 270 Dong An Road

department: Colorectal Surgery

country: China

institute: Cancer Hospital, Fudan University

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: GW4064 treatment group

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

value: subcutaneous xenograft

value: CRC cells

value: WT


title: BGLT3 sh2, Day14

city: Beijing

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

data_processing:
(Sample 51-54) All reads were aligned to reference Homo sapiens genome (Ensembl GRCh38.92) using tophat2, and uniquely mapped reads were retained for calculating gene counts by HTseq.
Differential gene expression analyses was conducted using DESeq2 with the P-value < 0.05 and |rlogFC| (sh1 versus Ctrl and sh2 versus Ctrl) > 0.3.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HSPC

growth_protocol: (Sample 51-54) For Poly(A)+ shRNA-seq on day 8 and day 14 of erythroid differentiation: CD34+ cells cultured in IMDM medium supplemented with 20% BIT,5ng/ml IL-3, 100 ng/ml SCF ,10^-6 M Hydrocortisone and 3 U/ml human EPO for 8 days. From days 8 through 14, SCF and EPO were included in the culture medium, and only EPO was included during days 14 to 18.

extract_protocol:
The harvested viral particles were added into the day 4 CD34+ plus with 8 µg/ml polybrene for 12 hours. Then the cells were replaced with fresh complete medium and subjected to the following experiments.
The cells were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: HSPC


title: SEP3tet_rep2__R1

description:
X57
SEP3tet_peaks.narrowPeak


title: RAW264.7 cells, Kdm7a gRNA (KO), M1 macrophage stimulated with LPS and interferon-γ for 48 hours., rep-3

description: Library name: Sample15


title: BGLT3 sh1, Day14


title: DY unstim rep 3

description:
sample.dy3
group_dy-group_wt_Differential_Expression.tsv
group_dy-group_wt.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv


title: DY 24hr LPS rep 1

description:
sample.dy1_24hr
group_dy_24hr-group_wt_24hr_Differential_Expression.tsv
group_dy_24hr-group_wt_24hr.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv


title: CON1

source_name: Control group

value: CON


title: RAW264.7 cells, Kdm7a gRNA (KO), M1 macrophage stimulated with LPS and interferon-γ for 48 hours., rep-1

description: Library name: Sample13


title: SEP3wt_rep1_R1

description:
X33
SEP3wt_peaks.narrowPeak


title: RAW264.7 cells, Kdm7a gRNA (KO), M0 macrophages treated without stimulation for 48 hours, rep-3

description: Library name: Sample12


title: RAW264.7 cells, control gRNA, M2 macrophage stimulated with Il-4, 10, 13 and Tgf-β1 for 48 hours., rep-3

description: Library name: Sample9

value: M2 macrophage stimulation


title: KSHV(+) iSLK.219 Cells; 72 Hours, sieIF5B, Replicate 3

city: Miami

first: Yuande

last: Tan

address: 1120 NW 14th Street

department: UNM Comprehensive Cancer Center

institute: Miami University

description:
Library name: S24
X024.RNAseq_S24

data_processing:
performed nextflow core/rnaseq with GRCh38 reference to output multiqc and counts of reads across all fastq samples.
used DESeq2 to normalized count data.
performed PCA analysis of samples using VSD data.
performed DESeq2 to differential analysis.
Assembly: GRCh38
Supplementary files format and content: tsv files including gene counts, transcript counts for each sample
Supplementary files format and content: tsv files including gene, transcript tpm for eacj sample

source_name: Renal Cell Carcinoma

growth_protocol: iSLKs were cultured DMEM supplemented with 10% FBS,  and 1% Pen-Step with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from cells using RLT buffer (RNeasy Kit Qiagen)
Library prep using Illumina TruSeq total stranded RNA with RiboZero Gold rRNA depletion. This approach will prepare libraries containing all RNA greater than ~200 bp regardless of polyA status.

treatment_protocol: Selection in iSLK.KSHV219 cells was conducted by culturing cells in the presence of 10mg/mL of puromycin 50 mg/mL of G418 and 50 mg/mL of Hygromycin B .

value: Renal Cell Carcinoma

value: KSHV (+) iSLK.242

value: Human Endothelial

value: eIF5B silenced


title: SEP3tet_rep1_R1

description:
X34
SEP3tet_peaks.narrowPeak

value: inflorescence

value: floral cells


title: DY unstim rep 1

description:
sample.dy1
group_dy-group_wt_Differential_Expression.tsv
group_dy-group_wt.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv

value: Bone marrow-derived macrophages


title: KSHV(+) iSLK.219 Cells; 72 Hours, sieIF5B, Replicate 1

description:
Library name: S22
X022.RNAseq_S22

value: KSHV (+) iSLK.240


title: KSHV(+) iSLK.219 Cells; 72 Hours, sieIF5B, Replicate 2

description:
Library name: S23
X023.RNAseq_S23

value: KSHV (+) iSLK.241


title: DY unstim rep 2

description:
sample.dy2
group_dy-group_wt_Differential_Expression.tsv
group_dy-group_wt.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv


title: WT 24hr LPS rep 3

description:
sample.wt3_24hr
group_dy_24hr-group_wt_24hr_Differential_Expression.tsv
group_dy_24hr-group_wt_24hr.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv

value: 24hr LPS


title: BXD-1425 ependymoma cell line 5-Azacytidine 2

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

data_processing:
Sequencing and base calling: RNA-seq libraries were sequenced on an Illumina HiSeq 2500 equipment (Illumina, San Diego, CA, USA) with base calling by CASAVA software (version 1.8.2, Illumina, San Diego, CA, USA).
Read alignment: Raw data were processed by TrimGalore package (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to trim the adapters, in following the RNA-seq library reads processed by FastQC tool (Andrews, 2010) and MultiQC (Ewels et al., 2016) and performed analysis of detection of differential expression in BXD-1425 cell line using processed reads aligned with the reference genome (Genome Reference Consortium Human GRCh38) through STAR package (Dobin and Gingeras, 2015).
Gene specific read counts: Gene specific read counts were determined with to FastQC tool (Andrews, 2010) and MultiQC (Ewels et al., 2016).
Assembly: Reads are in .fastq format and contain the raw base calls from sequencing.
Supplementary files format and content: Gene counts normalized are in .txt format and contain the number of counts normalized abundance measurements using DeSeq2 for every gene and every sample.

growth_protocol: BXD-1425 cell line was maintained in DMEM highGlucose medium (Gibco™, Thermo Fisher®, Carlsbad, CA, USA), supplemented with 5% FBS, 100U/ml penicillin, 100 μg/ml streptomycin and kept in a humid atmosphere containing 5% CO2 at 37ºC.

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA/Protein Mini kit (QIAGEN, Hilden, Germany) and RNA integrity was evaluated by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA), following manufacturer’s. specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: ependymoma

tag: time


title: RAW264.7 cells, control gRNA, M1 macrophage stimulated with LPS and interferon-γ for 48 hours., rep-3

description: Library name: Sample6

value: M1 macropage stimulation


title: RAW264.7 cells, Kdm7a gRNA (KO), M0 macrophages treated without stimulation for 48 hours, rep-1

description: Library name: Sample10

value: Kdm7a KO_M0

value: Kdm7a Knockout

value: non-treatment


title: BGLT3 sh2, Day8

value: HSPC


title: BGLT3 sh1, Day8


title: BXD-1425 ependymoma cell line 5-Azacytidine 3


title: RAW264.7 cells, control gRNA, M2 macrophage stimulated with Il-4, 10, 13 and Tgf-β1 for 48 hours., rep-1

description: Library name: Sample7

value: WT

value: M2 macrophage stimulation


title: RAW264.7 cells, control gRNA, M2 macrophage stimulated with Il-4, 10, 13 and Tgf-β1 for 48 hours., rep-2

description: Library name: Sample8


title: RAW264.7 cells, control gRNA, M1 macrophage stimulated with LPS and interferon-γ for 48 hours., rep-2

description: Library name: Sample5


title: RAW264.7 cells, control gRNA, M1 macrophage stimulated with LPS and interferon-γ for 48 hours., rep-1

description: Library name: Sample4


title: WT 24hr LPS rep 2

description:
sample.wt2_24hr
group_dy_24hr-group_wt_24hr_Differential_Expression.tsv
group_dy_24hr-group_wt_24hr.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv


title: KSHV(+) iSLK.219 Cells; 72 Hours, siControl, Replicate 2

description:
Library name: S20
X020.RNAseq_S20

value: Renal Cell Carcinoma

value: KSHV (+) iSLK.238

value: siControl


title: BXD-1425 ependymoma cell line 5-Azacytidine 1


title: WT unstim rep 3

description:
sample.wt3
group_dy-group_wt_Differential_Expression.tsv
group_dy-group_wt.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv


title: KSHV(+) iSLK.219 Cells; 72 Hours, siControl, Replicate 1

description:
Library name: S19
X019.RNAseq_S19

value: KSHV (+) iSLK.237

value: Human Endothelial


title: BXD-1425 ependymoma cell line Control 3

value: Medium


title: H9-TSC

city: Taipa, Macau

first: Siyi

last: FU

state: Taipa, Macau

address: Room 2003,  N22 Building

department: FHS

country: Macau

institute: University of Macau

data_processing:
Bulk RNA sequenced reads were trimmed for short or low-quality sequence, then mapped to hg38 whole genome using hisat2 with defalut parameters
Supplementary files format and content: hg38
Supplementary files format and content: excel files include FPKM counts for each sample of  RNA-seq

extract_protocol:
Bulk mRNA was extracted using RNeasy mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hES-derived trophoblast stem cells

tag: growth

value: BAP-TSC differentiation

value: Day 15


title: KSHV(+) iSLK.219 Cells; 72 Hours, siControl, Replicate 3

description:
Library name: S21
X021.RNAseq_S21

value: KSHV (+) iSLK.239


title: WT unstim rep 1

description:
sample.wt1
group_dy-group_wt_Differential_Expression.tsv
group_dy-group_wt.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv

value: Bone marrow-derived macrophages


title: WT 24hr LPS rep 1

description:
sample.wt1_24hr
group_dy_24hr-group_wt_24hr_Differential_Expression.tsv
group_dy_24hr-group_wt_24hr.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv

value: 24hr LPS


title: BXD-1425 ependymoma cell line Control 2

value: ependymoma


title: KSHV(+) iSLK.219 Cells; 48 Hours, sieIF5B, Replicate 3

description:
Library name: S18
X018.RNAseq_S18

value: KSHV (+) iSLK.236

value: eIF5B silenced


title: ENVY-TSC

source_name: ENVY

value: ENVY

value: WT


title: RAW264.7 cells, control gRNA, M0 macrophages treated without stimulation for 48 hours, rep-3

description: Library name: Sample3

value: non-treatment


title: BXD-1425 ependymoma cell line Control 1


title: H9-BAP3D

value: hES-derived trophoblast cells

value: BAP differentiation

value: Day 3


title: KSHV(+) iSLK.219 Cells; 48 Hours, siControl, Replicate 1

description:
Library name: S13
X013.RNAseq_S13

value: Renal Cell Carcinoma

value: KSHV (+) iSLK.231

value: Human Endothelial

value: siControl


title: RNA-Seq for EMF-treated hSCs - Rep2

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description: Library name: hSCs5

data_processing:
For quality control ofsequencing, two rounds of reading generated optimal metrics, with >85% of readspassing the filtering and 93% of reads with Q score>30; technical error rate was 0.32%.
Read pre-processing was performed with FastP (v.0.21) in default setting. The filteredreads were aligned on the reference human transcriptome annotations from Gencode v48(Build GRCh38) to be converted into quantifications of different transcripts present in thesamples.
The alignment was performed with Salmon tool (v.1.4) with default settings andwith seqBias and gcBias options to correct for hexamer priming and GC biases,respectively. A mean alignment rate of 95% was observed.
Assembly: hg38
Supplementary files format and content: Table of DESeq2 normalized counts

source_name: hSCs

extract_protocol:
Total RNA was extracted from SCs cultures by TriFast Il (Euroclone, Pero, Italy),according to the manufacturer’s protocol, then quantified with Nano-Drop2000 (ThermoFisher Scientific, Monza, Italy).
Each sample of 500 ng total RNA was processed to obtain a libraryof indexed fragments using an Illumina Stranded mRNA kit (San Diego, CA, USA).Equimolar quantities of indexed libraries for each sample were loaded for sequencing ontwo flow cells Illumina MidOutput 150 cycles and sequenced using IlluminaNextSeq550dx (RUO mode).

treatment_protocol: Cells were exposed to 50 Hz 0.1 T EMF (at room temperature) for 10-min treatment perday for 5 consecutive days (every 24 h, at the same daytime) mimicking the chronicexposure

value: hSCs

value: EMF


title: KSHV(+) iSLK.219 Cells; 48 Hours, sieIF5B, Replicate 2

description:
Library name: S17
X017.RNAseq_S17

value: KSHV (+) iSLK.235


title: KSHV(+) iSLK.219 Cells; 48 Hours, sieIF5B, Replicate 1

description:
Library name: S16
X016.RNAseq_S16

value: KSHV (+) iSLK.234


title: RAW264.7 cells, control gRNA, M0 macrophages treated without stimulation for 48 hours, rep-2

description: Library name: Sample2


title: KSHV(+) iSLK.219 Cells; 48 Hours, siControl, Replicate 3

description:
Library name: S15
X015.RNAseq_S15

value: KSHV (+) iSLK.233


title: KO3

city: Seoul

first: June

last: Yang

address: 145, Anam-ro, Seongbuk-gu, Seoul, Republic of Korea

department: Biotechnology

country: South Korea

institute: Korea University

data_processing:
Raw reads were preprocessed to remove low quality and adapter sequence before analysis.
Processed reads were aligned to the Mus musculus (mm10) using HISAT v2.1.0.
Transcript assembly of known transcripts was processed by String Tie v1.3.4d.
Expression abundance of transcript and gene were calculated as read count or FPKM value per sample.
Genes with one more than zeroed read count values in the samples were excluded.
Filtered data were log2-transformed and subjected to RLE Normalization.
Statistical significance of the differential expression data was determined using DESeq2 nbinomWaldTest.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: data2.xlsx: Excel spreadsheet format includes Gene ID, NCBI mRNA accession ID, Gene symbol, FPKM, TPM, Fold change, p-value and Read count.

source_name: BMDM

extract_protocol:
Total RNA was isolated from WT and MafB-deficient BMDMs using Qiazol reagent according to the manufacturer's instructions.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T‐attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582). Indexed libraries were then submitted to an Illumina NovaSeq (Illumina, Inc., San Diego, CA, USA), and the paired-end (2×100 bp) sequencing was performed by the Macrogen Incorporated.

treatment_protocol: Stimulated for 24 h with rmIL-4 (R&D systems).

value: Bone marrow-derived macrophages

tag: genotype/variation

value: MafB-deficient

value: IL-4 for 24h


title: KO2


title: RNA-Seq for EMF-treated hSCs - Rep3

description: Library name: hSCs6


title: RAW264.7 cells, control gRNA, M0 macrophages treated without stimulation for 48 hours, rep-1

description: Library name: Sample1

value: WT


title: ENVY-BAP3D

value: ENVY


title: KSHV(+) iSLK.219 Cells; 24 Hours, sieIF5B, Replicate 3

description:
Library name: S12
X012.RNAseq_S12

value: KSHV (+) iSLK.230

value: eIF5B silenced


title: RNA-Seq for EMF-treated hSCs - Rep1

description: Library name: hSCs4


title: ossh1_3, on the day of flowering, RNAseq

first: He

last: wei

state: Beijing

address: China agriculture university

institute: China agriculture university

description: WT vs ossh1

data_processing:
used HISAT2 (Kim et al. 2015) to align the clean reads to the reference genome
used RSEM (v1.3.1) (Li and Dewey 2011) software for gene expression quantification
the DEGs (fold change ≥ 1.2, FDR < 0.00001) were identified with DESeq2
Assembly: Os-Nipponbare-Reference-IRGSP-1.0, MSU7
Supplementary files format and content: tab-delimited text file inculdes read counts for each sample

organism: Oryza sativa

source_name: abscission zone

growth_protocol: All plants were grown in field conditions in Beijing or Sanya, Hainan province, China

extract_protocol:
Total RNA was extracted from various tissues of different plants as described in the text using TRIzol reagent (Thermo Fisher Scientific) and purified using the RNeasy Mini Kit (Qiagen)
Total RNA was isolated with three biological replicates each containing five plants
averagely generating about 6.69G Gb bases per sample
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep kit following manufacture's protcols

treatment_protocol: The treatment conditions for mutants and wild-type are the same

value: abscission zone

value: mutant


title: RNA-Seq for control hSCs - Rep2

description: Library name: hSCs2

value: Control


title: KSHV(+) iSLK.219 Cells; 24 Hours, sieIF5B, Replicate 2

description:
Library name: S11
X011.RNAseq_S11

value: Renal Cell Carcinoma

value: KSHV (+) iSLK.229

value: Human Endothelial


title: KSHV(+) iSLK.219 Cells; 48 Hours, siControl, Replicate 2

description:
Library name: S14
X014.RNAseq_S14

value: KSHV (+) iSLK.232

value: siControl


title: KO1


title: KSHV(+) iSLK.219 Cells; 24 Hours, sieIF5B, Replicate 1

description:
Library name: S10
X010.RNAseq_S10

value: KSHV (+) iSLK.228


title: WT2


title: RNA-Seq for control hSCs - Rep1

description: Library name: hSCs1

value: hSCs


title: ossh1_2, on the day of flowering, RNAseq

description: WT vs ossh1


title: ossh1_1, on the day of flowering, RNAseq

description: WT vs ossh1


title: WT_3, on the day of flowering, RNAseq

description: WT vs ossh1

value: wild type


title: WT1

value: Bone marrow-derived macrophages


title: KSHV(+) iSLK.219 Cells; 24 Hours, siControl, Replicate 2

description:
Library name: S8
X008.RNAseq_S8

value: KSHV (+) iSLK.226


title: Rabbit ear skin, normal skin, rep3

city: Wuhan

first: Zhuo-ran

state: Hubei

address: No. 1037 Luoyu Road, Hongshan District

department: Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering

institute: Huazhong University of Science and Technology (HUST)

description:
Library name: SAMPLES9
FPKM_anno.xls: NS3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platformand 150 bppaired-endreadswere generated.
Raw reads of fastq format were firstly processed using fastp (v 0.20.1) and the low quality reads were removed to obtain the cleanreads.The cleanreads were mapped to the reference genome using HISAT2 (v 2.1.0). FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count (v 0.11.2).
PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 (v 1.22.2). Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expressiongene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar.
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Oryctolagus cuniculus

source_name: Rabbit ear skin

growth_protocol: Rabbits were housed in an open animal laboratory with 2 rabbits in each cage. Except for the fasting treatment before the experiment, all animals were unrestricted in water and food intake. All animals underwent an adaptation period of at least 1 week prior to the experiment.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed usingtheAgilent2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Firstly, 0.5 mL of 50% oleic acid solution was applied to the 2 × 2 cm area at the opening of the ear tube in the rabbit ear, once a day for 14 days.  Starting from the 10th day, 100 μL C. acnes bacterial suspension (1 × 108 CFU/mL) was injected subcutaneously into the ear area coated with oleic acid, once every other day until the end of modeling.  If the stratum corneum exhibited thickening and abscesses were observed on the rabbit ear surface within 2 days following the cessation of the modeling process, the procedure is deemed successful. Subsequently, MNs was applied to the acne area on the 2nd day, once daily for a total of 5 times.  Finally, all rabbits were euthanized on the 7th day.

value: Rabbit ear skin


title: TAC_LA_4

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description:
Library name: TAC4
2 weeks post procedure

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Left atrium

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit
For each sample, isolated RNA was amplified and sequencing libraries were prepared using the Trio Low Input RNA Kit (Nugen)

treatment_protocol: Constriction of the transverse thoracic aorta or sham surgery was performed on 2-months-old wildtype mice.

value: Left atrium

value: Wild type

value: TAC procedure


title: WT3

value: WT

value: IL-4 for 24h


title: KSHV(+) iSLK.219 Cells; 24 Hours, siControl, Replicate 1

description:
Library name: S7
X007.RNAseq_S7

value: KSHV (+) iSLK.225


title: KSHV(+) iSLK.219 Cells; 24 Hours, siControl, Replicate 3

description:
Library name: S9
X009.RNAseq_S9

value: Renal Cell Carcinoma

value: KSHV (+) iSLK.227


title: oscct_3, on the day of flowering, RNAseq

description: CK vs oscct

value: abscission zone

value: oscct

value: mutant


title: TAC_LA_3

description:
Library name: TAC3
2 weeks post procedure


title: Rabbit ear skin, normal skin, rep1

description:
Library name: SAMPLES7
FPKM_anno.xls: NS1


title: KSHV(+) iSLK.219 Cells; 0 Hours, sieIF5B, Replicate 3

description:
Library name: S6
X006.RNAseq_S6

value: KSHV (+) iSLK.224

value: Human Endothelial

value: eIF5B silenced


title: WT_1, on the day of flowering, RNAseq

description: WT vs ossh1

value: wild type


title: Sham_LA_5

description:
Library name: Sham5
2 weeks post procedure

value: Sham procdure


title: TAC_LA_2

description:
Library name: TAC2
2 weeks post procedure


title: KSHV(+) iSLK.219 Cells; 0 Hours, sieIF5B, Replicate 2

description:
Library name: S5
X005.RNAseq_S5

value: KSHV (+) iSLK.223


title: Acne tissue from rabbit ears, treated with microneedles, rep3

description:
Library name: SAMPLES6
FPKM_anno.xls: H-P3

value: Rabbit ear skin


title: oscct_2, on the day of flowering, RNAseq

description: CK vs oscct


title: TAC_LA_1

description:
Library name: TAC1
2 weeks post procedure

value: Left atrium

value: Wild type


title: oscct_1, on the day of flowering, RNAseq

description: CK vs oscct


title: Acne tissue from rabbit ears, treated with microneedles, rep1

description:
Library name: SAMPLES4
FPKM_anno.xls: H-P1


title: KSHV(+) iSLK.219 Cells; 0 Hours, sieIF5B, Replicate 1

description:
Library name: S4
X004.RNAseq_S4

value: KSHV (+) iSLK.222


title: Acne tissue from rabbit ears, treated with microneedles, rep2

description:
Library name: SAMPLES5
FPKM_anno.xls: H-P2


title: Sham_LA_4

description:
Library name: Sham4
2 weeks post procedure


title: KSHV(+) iSLK.219 Cells; 0 Hours, siControl, Replicate 3

description:
Library name: S3
X003.RNAseq_S3

value: KSHV (+) iSLK.221

value: WT

value: siControl


title: Rabbit ear skin, normal skin, rep2

description:
Library name: SAMPLES8
FPKM_anno.xls: NS2


title: WT unstim rep 2

description:
sample.wt2
group_dy-group_wt_Differential_Expression.tsv
group_dy-group_wt.KEGG_Signaling_and_Metabolism_singleDirection_results.tsv

value: Bone marrow-derived macrophages


title: CK3, on the day of flowering, RNAseq

description: CK vs oscct

value: abscission zone

value: CK


title: KSHV(+) iSLK.219 Cells; 0 Hours, siControl, Replicate 2

description:
Library name: S2
X002.RNAseq_S2

value: Renal Cell Carcinoma

value: KSHV (+) iSLK.220


title: Acne tissue from rabbit ears, untreated, rep3

description:
Library name: SAMPLES3
FPKM_anno.xls: con3


title: CK2, on the day of flowering, RNAseq

description: CK vs oscct


title: KSHV(+) iSLK.219 Cells; 0 Hours, siControl, Replicate 1

description:
Library name: S1
X001.RNAseq_S1

value: KSHV (+) iSLK.219

value: Human Endothelial


title: CK1, on the day of flowering, RNAseq

description: CK vs oscct

value: wild type


title: Sham_LA_2

description:
Library name: Sham2
2 weeks post procedure

value: Sham procdure


title: PTX – 35 days post ptx IP P#2

status: Public on Mar 02 2026

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

description: Library name: PTX_35d_Paw_2

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq Fastq reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using htseq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Assembly: UCSC mouse genome build mm9
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Paw

extract_protocol:
Tissue samples were hind paw punch biopsies, L3-L5 DRG and lumbar area of spinal cord
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 3000 platform.

treatment_protocol: PTX (2mg/kg) was injected intraperitoneally twice, one day apart.

tag: strain

value: Paw

tag: Sex

value: Male

tag: age

value: 8-12 weeks


title: PTX – 35 days post ptx IP P#3

description: Library name: PTX_35d_Paw_3


title: PTX – 35 days post ptx IP D#3

description: Library name: PTX_35d_DRG_3

source_name: DRG

value: DRG


title: Sham_LA_3

description:
Library name: Sham3
2 weeks post procedure

value: Left atrium

value: Wild type


title: Sham_LA_1

description:
Library name: Sham1
2 weeks post procedure


title: PTX – 35 days post ptx IP S#3

description: Library name: PTX_35d_SC_3

source_name: Spine

value: Spine


title: Acne tissue from rabbit ears, untreated, rep2

description:
Library name: SAMPLES2
FPKM_anno.xls: con2

value: Rabbit ear skin


title: PTX – 22 days post ptx IP S#1

description: Library name: PTX_22d_SC_1


title: PTX – 35 days post ptx IP D#2

description: Library name: PTX_35d_DRG_2


title: PTX – 35 days post ptx IP S#2

description: Library name: PTX_35d_SC_2


title: PTX – 1 day post ptx IP S#1

description: Library name: PTX_1d_SC_1


title: PTX – 35 days post ptx IP S#1

description: Library name: PTX_35d_SC_1


title: PTX – 1 day post ptx IP S#3

description: Library name: PTX_1d_SC_3


title: TAC_LA_5

description:
Library name: TAC5
2 weeks post procedure

value: TAC procedure


title: PTX 1 day ipsi #3

description: Library name: PTX_1d_3

source_name: Spinal cord

value: Spinal cord


title: PTX – 22 days post ptx IP S#2

description: Library name: PTX_22d_SC_2


title: PTX – 35 days post ptx IP D#1

description: Library name: PTX_35d_DRG_1


title: PTX 1 day ipsi #2

description: Library name: PTX_1d_2


title: PTX 1 day control #3

description: Library name: PTX_1d_control_3


title: PTX 1 day control #2

description: Library name: PTX_1d_control_2


title: PTX 1 day ipsi #1

description: Library name: PTX_1d_1


title: PTX – 35 days post ptx IP P#1

description: Library name: PTX_35d_Paw_1


title: Acne tissue from rabbit ears, untreated, rep1

description:
Library name: SAMPLES1
FPKM_anno.xls: con1


title: PTX 7 days control #3

description: Library name: PTX_7d_control_3


title: PTX – 22 days post ptx IP S#3

description: Library name: PTX_22d_SC_3


title: PTX 7 days control #2

description: Library name: PTX_7d_control_2


title: PTX – 1 day post ptx IP S#2

description: Library name: PTX_1d_SC_2


title: PTX 7 days control #1

description: Library name: PTX_7d_control_1


title: PTX 22 days post-ptx P#3

description: Library name: PTX22_paw_3


title: PTX 7 days ipsi #2

description: Library name: PTX_7d_2


title: WT_2, on the day of flowering, RNAseq

description: WT vs ossh1

value: abscission zone

value: WT


title: PTX 1 day control #1

description: Library name: PTX_1d_control_1


title: PTX 7 days ipsi #3

description: Library name: PTX_7d_3


title: PTX 22 days post-ptx P#1

description: Library name: PTX22_paw_1


title: PTX 22 days post-ptx D#2

description: Library name: PTX22_DRG_2


title: PTX 22 days post-ptx D#3

description: Library name: PTX22_DRG_3


title: PTX 7 days post-ptx P#2

description: Library name: PTX7_paw_2


title: PTX 22 days post-ptx D#1

description: Library name: PTX22_DRG_1


title: PTX 7 days post-ptx P#3

description: Library name: PTX7_paw_3


title: PTX CONTROL 2 days post-ptx D#3

description: Library name: Cont2_DRG_3


title: PTX CONTROL 2 days post-ptx P#1

description: Library name: Cont2_paw_1


title: PTX 7 days post-ptx D#1

description: Library name: PTX7_DRG_1


title: PTX 2 days post-ptx P#1

description: Library name: PTX2_paw_1


title: PTX 22 days post-ptx P#2

description: Library name: PTX22_paw_2


title: PTX 2 days post-ptx P#3

description: Library name: PTX2_paw_3


title: PTX CONTROL 2 days post-ptx P#3

description: Library name: Cont2_paw_3


title: PTX CONTROL 2 days post-ptx P#2

description: Library name: Cont2_paw_2


title: PTX 7 days post-ptx P#1

description: Library name: PTX7_paw_1


title: PTX CONTROL 2 days post-ptx D#1

description: Library name: Cont2_DRG_1


title: PTX 7 days post-ptx D#3

description: Library name: PTX7_DRG_3


title: PTX 2 days post-ptx P#2

description: Library name: PTX2_paw_2


title: km3

description: Library name: km3

source_name: paw

extract_protocol:
Tissue samples were hind paw punch biopsies.
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 3000 platform.

value: paw

value: male

value: 8-16 weeks

value: vehicle


title: PTX CONTROL 2 days post-ptx D#2

description: Library name: Cont2_DRG_2


title: k-PTX4

description: Library name: k_PTX4

value: PTX-short


title: k-PTX3

description: Library name: k_PTX3


title: k-PTX1

description: Library name: k_PTX1


title: PTX 2 days post-ptx D#3

description: Library name: PTX2_DRG_3


title: kf4

description: Library name: kf4

value: female


title: kf3

description: Library name: kf3


title: PTX 2 days post-ptx D#2

description: Library name: PTX2_DRG_2

value: Male


title: kf2

description: Library name: kf2


title: PTX 7 days post-ptx D#2

description: Library name: PTX7_DRG_2

value: 8-12 weeks


title: PTX 7 days ipsi #1

description: Library name: PTX_7d_1


title: PTX 2 days post-ptx D#1

description: Library name: PTX2_DRG_1

value: DRG


title: CPM4

description: Library name: CPM4

value: Col+/TdT

value: PTX


title: km2

description: Library name: km2


title: k-PTX2

description: Library name: k_PTX2


title: kf1

description: Library name: kf1


title: CVM4

description: Library name: CVM4

value: Vehicle


title: CPM3

description: Library name: CPM3


title: CVM3

description: Library name: CVM3


title: Saline 6weeks

type: RNA

city: Kobe

first: Masafumi

last: Tsurutani

state: Hyogo

address: 2-2-3 Minatojima minami, Chuo-ku

department: Center for Biosystems Dynamics Research (BDR)

institute: RIKEN

description: Sections near the PVH in the hypothalamus of 4 control mice aged 6 weeks.

hyb_protocol: Xenium analysis was performed using the Prime 5K Mouse Pan Tissue, add-on custom panel and Pathways Assay Kit (cat#1000672) according to the Xenium protocol (CG000580 and CG000760).

scan_protocol: Imaging processing, decoding, quality score generation, and DAPI-based cell segmentation was automatically performed by Xenium Analyzer system according to the Xenium protocol (CG000584).

data_processing: Xenium Onboard Analysis: 3.0.0.15. R using Seurat v5.1.0 pakeges.

label: Xenium probe set

source_name: Hypothalamus of brain

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Brains from Saline and VPA-treated OT-Cre mice were processed as follows. Mice were anesthetized with an overdose of isoflurane and perfused transcardially with PBS, followed by 4% paraformaldehyde (PFA) in PBS. Brains were post-fixed in 4% PFA at 4 °C overnight and then sequentially dehydrated in PBS, 70% ethanol, 80% ethanol, 90% ethanol, and 100% ethanol before dissecting the hypothalamic region containing the PVH. Tissues were subsequently infiltrated with paraffin and embedded. Before sectioning, paraffin blocks were rehydrated according to the Xenium protocol (CG000578) and sectioned at 5 μm. A subset of sections was stained with DAPI to identify the PVH, and adjacent sections were mounted onto Xenium slides.

treatment_protocol: To generate a VPA-treated group of mice, pregnant females received a single intraperitoneal injection of sodium valproate (Sigma, #P4543) at 500 mg/kg on gestational day (GD) 12.5. Gestational timing was determined by the presence of a vaginal plug, which was designated as GD 0.5. For the saline-treated control group, pregnant females were injected with 10 mL/kg sterile saline at the same gestational stage.

value: Hypothalamus of brain

tag: tissue preservation method

value: FFPE

tag: Stage

value: healthy conrol


title: CVM2

description: Library name: CVM2


title: VPA 6weeks

description: Sections near the PVH in the hypothalamus of 3 VPA-treated mice aged 6 weeks.

value: VPA-treated


title: CVM1

description: Library name: CVM1


title: GFP-HA-KERP2, Input sample, Trial 3

city: Tokyo

first: Ruofan

last: Peng

state: Tokyo

address: 7-3-1 Hongo, Bunkyo-ku

department: International Health

institute: University of Tokyo

description:
Library name: Sample 6
GFP-HA-KERP2, Input sample, Trial 3

data_processing:
Raw sequencing reads were evaluated for quality using FastQC (v0.12.1), followed by adapter and low-quality base trimming with Trim Galore (v0.6.10). Clean reads were aligned to the Entamoeba histolytica reference genome (DDBJ accession numbers AP023109–AP023147) using Bowtie2 (v2.5.2) with the --very-sensitive -X 2000 setting. The resulting SAM files were converted to BAM format, sorted, and indexed using SAMtools (v1.18). PCR duplicates were marked and removed using Picard MarkDuplicates (v3.1.1). Enriched regions (peaks) were identified using MACS2 (v2.2.7.1) with --broad and --nomodel --extsize 200 parameters. Input DNA samples were used as background controls, and peaks with q-value < 0.05 were retained.
Assembly: DNA Data Bank of Japan (DDBJ) under AP023109-AP023147
Supplementary files format and content: CSV (peaks) formats

organism: Entamoeba histolytica

growth_protocol: Trophozoites were maintained axenically in Diamond’s BI-S-33 medium at 35.5°C

extract_protocol:
Samples were prepared as described in the description
ChIP and input DNA were subjected to end-repair and A-tailing using a commercial End Repair & A-tailing kit in a total volume of 30 µL. The reaction was performed in a thermal cycler with the following program: 20 °C for 30 minutes, 65 °C for 30 minutes, and held at 4 °C. Adaptors and ligation buffer were prepared and kept on ice during the incubation. For adaptor ligation, 30 µL of the end-repaired product was mixed with 5 µL of adaptor solution (or 2 µL for ChIP and 1 µL for input samples), 15 µL of ligation buffer, and 5 µL of DNA ligase in a total volume of 55 µL. The ligation reaction was incubated at 20 °C for 20 minutes. NEXTflex DNA barcoded adaptors were used for multiplexing. ollowing ligation, 44 µL of SPRIselect beads was added for size selection and cleanup. The sample was incubated at room temperature for 15 minutes, then placed on a magnetic stand for 2 minutes. Supernatant was discarded, and beads were washed twice with 150 µL of 80% ethanol. After removing residual ethanol and drying for 2 minutes, DNA was eluted in 10 µL of 10 mM Tris-HCl (pH 8.0), incubated for 2 minutes, and transferred to a new tube. Library amplification was carried out using the KAPA Library Amplification Kit in a 24 µL reaction volume containing 10 µL of purified library, 2.5 µL KAPA Library Amplification Primer Mix, and 11.5 µL of KAPA HiFi HotStart Ready Mix.

treatment_protocol: Transfect with pEhEx-GFP-HA-KERP2

value: Trophozoites

value: pEhEx-GFP-HA-KERP2 transfected


title: km1

description: Library name: km1

value: paw

value: male


title: CVF4

description: Library name: CVF4

value: 8-16 weeks


title: GFP-HA-KERP2, ChIP sample, Trial 3

description:
Library name: Sample 5
GFP-HA-KERP2, ChIP sample, Trial 3


title: CVF2

description: Library name: CVF2


title: GFP-HA-KERP2, Input sample, Trial 1

description:
Library name: Sample 2
GFP-HA-KERP2, Input sample, Trial 1


title: 45PM4

description: Library name: 45PM4


title: CVF3

description: Library name: CVF3


title: GFP-HA-KERP2, ChIP sample, Trial 1

description:
Library name: Sample 1
GFP-HA-KERP2, ChIP sample, Trial 1


title: GFP-HA-KERP2, ChIP sample, Trial 2

description:
Library name: Sample 3
GFP-HA-KERP2, ChIP sample, Trial 2


title: CVF1

description: Library name: CVF1


title: GFP-HA-KERP2, Input sample, Trial 2

description:
Library name: Sample 4
GFP-HA-KERP2, Input sample, Trial 2


title: Entamoeba hisolytica, psAP-mock, Trial 3

description:
Library name: Sample 6
psAP-mock_3

data_processing:
FastQC (ver0.11.8) was used to check the quality of all reads, and Trim Galore (ver0.6.4) was used to remove low‒quality reads. Filtering was done with default parameter values.
Each read obtained after filtering was mapped to the reference genome AmoebaDB‒EhistolyticaHM1IMSS‒Genome using STAR (ver2.7.4a). Mapping reads was done using the default parameter values.
FeatureCount (ver1.6.4) was used to calculate the number of counts for each gene defined by the gene ID.
Assembly: AmoebaDB‒EhistolyticaHM1IMSS release‒54
Supplementary files format and content: CSV (gene counts) formats
Supplementary files format and content: Gene_name, Read_count, p-value, q-value, Foldchange

extract_protocol:
Total RNA from E. histolytica trophozoites was extracted using the TRIzol reagent (Invitrogen) following the manufacturer’s protocol.
Library construction was processed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions.

treatment_protocol: Transfect with small interfering RNAs with the psAP-2-Gunma plasmid

value: psAP-mock


title: CPM1

description: Library name: CPM1


title: CPM2

description: Library name: CPM2


title: Entamoeba hisolytica, psAP-mock, Trial 2

description:
Library name: Sample 5
psAP-mock_2


title: Entamoeba hisolytica, psAP-mock, Trial 1

description:
Library name: Sample 4
psAP-mock_1


title: 45PM2

description: Library name: 45PM2


title: 45PM1

description: Library name: 45PM1


title: 45VM4

description: Library name: 45VM4


title: VPA 5weeks

description: Sections near the PVH in the hypothalamus of 2 VPA-treated mice aged 5 weeks.


title: Entamoeba hisolytica, KERP2-knockdown, Trial 3

description:
Library name: Sample 3
psAP-K2gs_3


title: 45VM3

description: Library name: 45VM3


title: Entamoeba hisolytica, KERP2-knockdown, Trial 2

description:
Library name: Sample 2
psAP-K2gs_2


title: 45VM1

description: Library name: 45VM1


title: 45PM3

description: Library name: 45PM3


title: Entamoeba hisolytica, KERP2-knockdown, Trial 1

description:
Library name: Sample 1
psAP-K2gs_1


title: 45VM2

description: Library name: 45VM2


title: 45VF4

description: Library name: 45VF4

value: female


title: F3516: gckp_rep3

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: gckp_rep3
Column name in salmon_gene_counts_raw.csv: gckp_rep3

data_processing:
Quality control was performed via FastQC (v0.11.8)
Trim Galore! (version 0.6.5) was used to trim the adapter sequences with a quality threshold of 20. The mouse genome reference was GRCm38.p6, and GENCODE release M25 was used as the transcriptome reference. The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts were obtained via Salmon (v1.2.1) for all the libraries. All the samples passed the quality control requirements, with > 90% of the reads uniquely mapped (>20 M uniquely mapped reads for each library) via the STAR aligner.
Differential expression analysis was performed via gene level read counts and the DESeq2 (v1.28.1) R package. Genes with fewer than 5 reads across all samples were filtered as inactive genes. A gene was considered differentially expressed if the adjusted p value was less than 0.05 and if the absolute log2-fold change was greater than 1.
Assembly: GRCm38.p6
Supplementary files format and content: CSV file including raw counts for all samples

organism: Mus

source_name: pancreas

growth_protocol: The cells were routinely cultured under standard 5% CO2, 37C conditions.The cell culture medium consisted of Dulbecco's modified Eagle medium (DMEM)+ GlutaMAX (#10566016; Gibco) supplemented with 10% FBS (#10082147; Gibco), NEAA (#11140050; Gibco) and 1% PenStrep (#1500--063; Gibco).

extract_protocol:
RNA extraction made with the Maxwell® 16 LEV simple RNA Purification Kit (Promega, AS1280) and the Maxwell® 16 instrument (AS2000).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: no treatment

value: pancreas

value: pancreatic cancer cell line

value: no treatment

tag: batch


title: A2569: gckp_rep4

description:
Library name: gckp_rep4
Column name in salmon_gene_counts_raw.csv: gckp_rep4


title: 45VF2

description: Library name: 45VF2


title: F3382: gckp_rep2

description:
Library name: gckp_rep2
Column name in salmon_gene_counts_raw.csv: gckp_rep2


title: F2464: gckp_rep1

description:
Library name: gckp_rep1
Column name in salmon_gene_counts_raw.csv: gckp_rep1


title: 45VF1

description: Library name: 45VF1


title: 45VF3

description: Library name: 45VF3


title: F3469: ckp_rep4

description:
Library name: ckp_rep4
Column name in salmon_gene_counts_raw.csv: ckp_rep4


title: F3207: ckp_rep3

description:
Library name: ckp_rep3
Column name in salmon_gene_counts_raw.csv: ckp_rep3


title: F4407: ckp_rep5

description:
Library name: ckp_rep5
Column name in salmon_gene_counts_raw.csv: ckp_rep5


title: PTX “short” 16d post-PTX IP female Paw #3

description: Library name: PTX_sh_F_Paw_16d_3

extract_protocol:
Tissue samples were hind paw punch biopsies and L3-L5 DRG
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 3000 platform.

treatment_protocol: PTX (3mg/kg) was injected intraperitoneally twice, one day apart

value: Paw

value: Female

value: 8-12 weeks

value: PTX (2x3mg/kg)


title: PTX “short” 16d post-PTX IP female Paw #2

description: Library name: PTX_sh_F_Paw_16d_2


title: F3056: ckp_rep2

description:
Library name: ckp_rep2
Column name in salmon_gene_counts_raw.csv: ckp_rep2


title: PTX “short” 26d post-PTX IP female Paw #3

description: Library name: PTX_sh_F_Paw_26d_3


title: F2987: ckp_rep1

description:
Library name: ckp_rep1
Column name in salmon_gene_counts_raw.csv: ckp_rep1


title: PTX “short” 26d post-PTX IP female Paw #1

description: Library name: PTX_sh_F_Paw_26d_1


title: A2929: cckp_rep4

description:
Library name: cckp_rep4
Column name in salmon_gene_counts_raw.csv: cckp_rep4


title: A2770: cckp_rep3

description:
Library name: cckp_rep3
Column name in salmon_gene_counts_raw.csv: cckp_rep3


title: PTX “short” 16d post-PTX IP female Paw #1

description: Library name: PTX_sh_F_Paw_16d_1


title: PTX “short” 6d post-PTX IP female Paw #3

description: Library name: PTX_sh_F_Paw_6d_3


title: A2712: cckp_rep1

description:
Library name: cckp_rep1
Column name in salmon_gene_counts_raw.csv: cckp_rep1


title: PTX “short” 6d post-PTX IP female Paw #1

description: Library name: PTX_sh_F_Paw_6d_1


title: PTX “short” 6d post-PTX IP female Paw #2

description: Library name: PTX_sh_F_Paw_6d_2


title: PTX “short” 26d post-PTX IP female Paw #2

description: Library name: PTX_sh_F_Paw_26d_2


title: A2716: cckp_rep2

description:
Library name: cckp_rep2
Column name in salmon_gene_counts_raw.csv: cckp_rep2


title: ex4velt_1

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

description: Library name: ex4velt_1

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Subsequent data analysis and visualization was performed using the R bioconductor package ballgown (https://www.bioconductor.org/packages/release/bioc/html/ballgown.html)
Assembly: Tair 10
Supplementary files format and content: tab-delimited text files including log2 quantile normalized FPKM values for each sample

source_name: Rosette leaves

growth_protocol: We used three natural Arabidopsis thaliana accessions from southern Spain, Bon, Moj and Vel; and the Col-0 reference. We conducted common garden experiments at El Castillejo Botanical Garden (36.46ºN, 5.30ºW, 326 m; El Bosque, Cádiz province). For each accession, we sowed 20 replicates with 250 seeds each in plastic pots (12×12×12 cm3) with drainage holes and filled with peat-reduced, high-quality substrate (Blumenerde, Gramoflor Ibérica SLU, Moixent, ES). We collected samples in vegetative, inductive (i.e. when shoot meristems become committed to flowering) and reproductive stages (bolting/flowering). In each sampling, we collected samples in the morning (between 10:00 and 10:30) and in the afternoon (between 15:30 and 16:00), we collected three replicates per accession pooling five plants to reduce bias . We kept the aerial part of rosettes for RNA extractions, discarding roots in all samples, and stalks for samples in the reproductive stage.  We used foil envelopes to store samples in liquid nitrogen using a cryogenic carrying flask (KGW-Isotherm, Karlsruhe, DE). Samples were later stored at -80ºC in a freezer in the laboratory until RNA extraction.

extract_protocol:
RNA was extracted using the  ISOLATE II RNA Plant Kit (Meridian Bioscience Inc., Cincinnati, OH, US).
The TruSeq RNA Sample Prep Kit v.2 (Illumina, San Diego, CA, US) was used for library preparation following the manufacturer's recommendations

value: Rosette leaves

tag: ecotype

value: vel

value: evening

tag: extraction


title: ex4velt_2

description: Library name: ex4velt_2

tag: tissue


title: ex4velt_3

description: Library name: ex4velt_3


title: PTX “short” 6d post-PTX IP female DRG #1

description: Library name: PTX_sh_F_D_6d_1

value: DRG


title: ex4velm_3

description: Library name: ex4velm_3

value: morning


title: PTX “short” 6d post-PTX IP female DRG #3

description: Library name: PTX_sh_F_D_6d_3


title: PTX “short” 6d post-PTX IP female DRG #2

description: Library name: PTX_sh_F_D_6d_2


title: PTX “short” 2d post-PTX IP female Paw #2

description: Library name: PTX_sh_F_Paw_2d_2


title: ex4velm_1

description: Library name: ex4velm_1


title: ex4velm_2

description: Library name: ex4velm_2


title: PTX “short” 2d post-PTX IP female Paw #3

description: Library name: PTX_sh_F_Paw_2d_3


title: PTX “short” 2d post-PTX IP female  DRG #1

description: Library name: PTX_sh_F_D_2d_1


title: PTX “short” 2d post-PTX IP female Paw #1

description: Library name: PTX_sh_F_Paw_2d_1


title: ex4col0t_2

description: Library name: ex4col0t_2


title: PTX “short” 2d post-PTX IP female  DRG #3

description: Library name: PTX_sh_F_D_2d_3


title: PTX “short” – LC IP 15 days post-PTX male Paw #2

description: Library name: PTX_Sh_Paw_15d_M2

value: Male

value: PTX-short


title: ex4col0t_1

description: Library name: ex4col0t_1


title: ex4col0m_3

description: Library name: ex4col0m_3


title: PTX “short” – LC IP 15 days post-PTX male Paw #3

description: Library name: PTX_Sh_Paw_15d_M3


title: ex4col0m_2

description: Library name: ex4col0m_2


title: PTX “short” 2d post-PTX IP female DRG #2

description: Library name: PTX_sh_F_D_2d_2


title: ex3velm_2

description: Library name: ex3velm_2


title: ex3velt_1

description: Library name: ex3velt_1


title: PTX “short” – LC IP 15 days post-PTX male Paw #1

description: Library name: PTX_Sh_Paw_15d_M1


title: PTX “short” – LC IP 6 days post-PTX male DRG #2

description: Library name: PTX_Sh_DRG_6d_M2


title: PTX “short” – LC IP 6 days post-PTX male Paw #3

description: Library name: PTX_Sh_Paw_6d_M3


title: ex3velt_2

description: Library name: ex3velt_2


title: ex4col0m_1

description: Library name: ex4col0m_1


title: PTX “short” – LC IP 6 days post-PTX male Paw #1

description: Library name: PTX_Sh_Paw_6d_M1


title: PTX “short” – LC IP 6 days post-PTX male Paw #2

description: Library name: PTX_Sh_Paw_6d_M2


title: ex3mojm_2

description: Library name: ex3mojm_2

value: moj


title: PTX “short” – LC IP 2 days post-PTX male Paw #3

description: Library name: PTX_Sh_Paw_2d_M3


title: PTX “short” – LC IP 6 days post-PTX male DRG #1

description: Library name: PTX_Sh_DRG_6d_M1


title: ex3velm_1

description: Library name: ex3velm_1


title: ex3mojt_3

description: Library name: ex3mojt_3


title: PTX “short” – LC IP 6 days post-PTX male DRG #3

description: Library name: PTX_Sh_DRG_6d_M3


title: PTX “short” – LC IP 2 days post-PTX male DRG #2

description: Library name: PTX_Sh_DRG_2d_M2


title: PTX “short” – LC IP 2 days post-PTX male DRG #1

description: Library name: PTX_Sh_DRG_2d_M1


title: ex3velt_3

description: Library name: ex3velt_3


title: ex3mojt_2

description: Library name: ex3mojt_2


title: ex3mojt_1

description: Library name: ex3mojt_1


title: ex3col0t_3

description: Library name: ex3col0t_3


title: PTX “short” – LC IP 2 days post-PTX male Paw #1

description: Library name: PTX_Sh_Paw_2d_M1


title: PTX “short” – LC IP 2 days post-PTX male DRG #3

description: Library name: PTX_Sh_DRG_2d_M3


title: ex3mojm_1

description: Library name: ex3mojm_1


title: WT control female Paw #3

description: Library name: WT_C_Paw_F3

value: Vehicle


title: PTX “short” – LC IP 2 days post-PTX male Paw #2

description: Library name: PTX_Sh_Paw_2d_M2


title: ex3col0t_2

description: Library name: ex3col0t_2


title: ex3col0t_1

description: Library name: ex3col0t_1


title: WT control female Paw #1

description: Library name: WT_C_Paw_F1


title: WT control female DRG #2

description: Library name: WT_C_DRG_F2


title: ex3col0m_3

description: Library name: ex3col0m_3


title: 10/2/20 – Nav1.8/LTbR CKO-rep3

description: Library name: CKO_3

extract_protocol:
Tissue samples were L3-L5 DRG
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 3000 platform.

treatment_protocol: PTX (6mg/kg) was injected intraperitoneally three times, two days apart.

value: male

value: 8-16 weeks

value: Water


title: ex3bont_2

description: Library name: ex3bont_2

value: bon


title: WT control female DRG #1

description: Library name: WT_C_DRG_F1


title: ex3col0m_1

description: Library name: ex3col0m_1


title: ex3bont_1

description: Library name: ex3bont_1


title: ex3col0m_2

description: Library name: ex3col0m_2


title: ex3bonm_1

description: Library name: ex3bonm_1


title: ex3bonm_2

description: Library name: ex3bonm_2


title: ex3mojm_3

description: Library name: ex3mojm_3


title: ex3bont_3

description: Library name: ex3bont_3


title: WT control female Paw #2

description: Library name: WT_C_Paw_F2

value: Paw


title: 10/1/20 – Nav1.8/LTbR CKO-rep2

description: Library name: CKO_2


title: ex3bonm_3

description: Library name: ex3bonm_3


title: ex2velt_3

description: Library name: ex2velt_3


title: 10/2/20 – LTbR-fl/fl-rep4

description: Library name: LTbR_4


title: 10/2/20 – LTbR-fl/fl-rep3

description: Library name: LTbR_3


title: ex2velt_1

description: Library name: ex2velt_1


title: 10/1/20 – LTbR-fl/fl-rep1

description: Library name: LTbR_1


title: 10/1/20 – LTbR-fl/fl-rep2

description: Library name: LTbR_2


title: 10/1/20 – Nav1.8/LTbR CKO-rep1

description: Library name: CKO_1


title: ex2velt_2

description: Library name: ex2velt_2


title: 9/25/20 – PTX Nav1.8/LTbR CKO-rep4

description: Library name: PTX_CKO_4

value: PTX


title: ex2velm_2

description: Library name: ex2velm_2


title: 9/25/20 – PTX LTbR-fl/fl-rep4

description: Library name: PTX_LTbR_4


title: ex2velm_3

description: Library name: ex2velm_3


title: WT control female DRG #3

description: Library name: WT_C_DRG_F3

value: Female

value: 8-12 weeks


title: 9/25/20 – PTX LTbR-fl/fl-rep3

description: Library name: PTX_LTbR_3


title: ex2mojm_3

description: Library name: ex2mojm_3

value: Rosette leaves


title: ex2velm_1

description: Library name: ex2velm_1

value: vel


title: ex2col0t_3

description: Library name: ex2col0t_3

value: evening


title: 9/24/20 – PTX Nav1.8/LTbR CKO-rep2

description: Library name: PTX_CKO_2

value: DRG


title: ex2mojt_2

description: Library name: ex2mojt_2


title: ex2mojt_3

description: Library name: ex2mojt_3


title: 9/24/20 – PTX LTbR-fl/fl-rep2

description: Library name: PTX_LTbR_2


title: 9/24/20 – PTX Nav1.8/LTbR CKO-rep1

description: Library name: PTX_CKO_1


title: 9/25/20 – PTX Nav1.8/LTbR CKO-rep3

description: Library name: PTX_CKO_3


title: PTX + LTbR antagonist (paw and spine – 1d and 4d during PTX) 6d post-PTX #2 Paw

description: Library name: PTX_LTBR_6d_Paw_2

treatment_protocol: PTX (2mg/kg) was injected intraperitoneally twice, one day apart. LTβR antagonist (15μg each) and IgG (10μg each) were injected simultaneously into hind paw (intraplantar (i.pl.)) and spinal cord (intrathecal (i.t.)).


title: ex2mojm_2

description: Library name: ex2mojm_2

value: morning


title: ex2col0t_2

description: Library name: ex2col0t_2


title: 9/24/20 – PTX LTbR-fl/fl-rep1

description: Library name: PTX_LTbR_1


title: ex2mojm_1

description: Library name: ex2mojm_1


title: PTX + LTbR antagonist (paw and spine – 1d and 4d during PTX) 6d post-PTX #1 Paw

description: Library name: PTX_LTBR_6d_Paw_1

value: Male


title: 10/2/20 – Nav1.8/LTbR CKO-rep4

description: Library name: CKO_4


title: ex2col0t_1

description: Library name: ex2col0t_1


title: ex2mojt_1

description: Library name: ex2mojt_1


title: ex2col0m_3

description: Library name: ex2col0m_3


title: ex2col0m_2

description: Library name: ex2col0m_2


title: PTX + LTbR antagonist (paw and spine – 1d and 4d during PTX) 6d post-PTX #2 Spine

description: Library name: PTX_LTBR_6d_SC_2

value: Spine


title: PTX + LTbR antagonist (paw and spine – 1d and 4d during PTX) 6d post-PTX #3 Spine

description: Library name: PTX_LTBR_6d_SC_3


title: PTX + LTbR antagonist (paw and spine – 1d and 4d during PTX) 6d post-PTX #3 Paw

description: Library name: PTX_LTBR_6d_Paw_3


title: ex2col0m_1

description: Library name: ex2col0m_1


title: ex2bont_3

description: Library name: ex2bont_3


title: PTX + LTbR antagonist (paw and spine – 1d and 4d during PTX) 6d post-PTX #1 Spine

description: Library name: PTX_LTBR_6d_SC_1


title: ex2bont_2

description: Library name: ex2bont_2


title: ex2bont_1

description: Library name: ex2bont_1


title: PTX + LTbR antagonist (paw and spine – 1d and 4d during PTX) 6d post-PTX #1 DRG

description: Library name: PTX_LTBR_6d_DRG_1


title: PTX + LTbR antagonist (paw and spine – 1d and 4d during PTX) 6d post-PTX #2 DRG

description: Library name: PTX_LTBR_6d_DRG_2


title: ex1velt_1

description: Library name: ex1velt_1


title: LTβR agonist 1 day #1

description: Library name: LTBetaR_1d_1

extract_protocol:
Tissue samples were hind paw punch biopsies, L3-L5 DRG and lumbar portion of spinal cord.
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 3000 platform.

treatment_protocol: LTβR agonistic antibody (10μg each) and IgG (10μg each) were injected into hind paw (intraplantar (i.pl.)).

value: Spinal cord


title: LTβR agonist 6 days (2x-1d,3d) #3

description: Library name: LTBetaR_6d_3


title: ex2bonm_3

description: Library name: ex2bonm_3


title: ex2bonm_1

description: Library name: ex2bonm_1


title: PTX + LTbR antagonist (paw and spine – 1d and 4d during PTX) 6d post-PTX #3 DRG

description: Library name: PTX_LTBR_6d_DRG_3


title: LTβR agonist 6 days (2x-1d,3d) #1

description: Library name: LTBetaR_6d_1


title: ex1velm_3

description: Library name: ex1velm_3


title: LTβR agonist 1 day #3

description: Library name: LTBetaR_1d_3


title: LTbR agonist P (2x – 1d, 3d; 6 days post first paw injection) #3

description: Library name: Paw_LTb_6d_3


title: ex1velt_3

description: Library name: ex1velt_3


title: LTβR agonist 1 day #2

description: Library name: LTBetaR_1d_2


title: LTbR agonist D (2x – 1d, 3d; 6 days post first paw injection) #3

description: Library name: DRG_LTb_6d_3


title: ex1velm_1

description: Library name: ex1velm_1


title: LTbR agonist P (2x – 1d, 3d; 6 days post first paw injection) #1

description: Library name: Paw_LTb_6d_1


title: ex1velt_2

description: Library name: ex1velt_2


title: LTβR agonist 6 days (2x-1d,3d) #2

description: Library name: LTBetaR_6d_2


title: ex1mojt_2

description: Library name: ex1mojt_2

value: moj


title: ex1velm_2

description: Library name: ex1velm_2


title: LTbR agonist D (2x – 1d, 3d; 6 days post first paw injection) #2

description: Library name: DRG_LTb_6d_2


title: ex2bonm_2

description: Library name: ex2bonm_2


title: ex1mojt_1

description: Library name: ex1mojt_1


title: ex1mojm_3

description: Library name: ex1mojm_3


title: LTbR agonist D (2x – 1d, 3d; 6 days post first paw injection) #1

description: Library name: DRG_LTb_6d_1


title: LTbR agonist P (2x – 1d, 3d; 6 days post first paw injection) #2

description: Library name: Paw_LTb_6d_2


title: LTbR agonist P (24 hrs. post paw injection) #3

description: Library name: Paw_LTb_24h_3


title: LTbR agonist P (24 hrs. post paw injection) #2

description: Library name: Paw_LTb_24h_2


title: ex1mojm_1

description: Library name: ex1mojm_1


title: ex1col0t_1

description: Library name: ex1col0t_1


title: ex1col0t_3

description: Library name: ex1col0t_3


title: LTbR agonist P (24 hrs. post paw injection) #1

description: Library name: Paw_LTb_24h_1


title: ex1mojm_2

description: Library name: ex1mojm_2


title: ex1col0m_2

description: Library name: ex1col0m_2


title: LTbR agonist D (24 hrs. post paw injection) #3

description: Library name: DRG_LTb_24h_3


title: LTbR agonist D (24 hrs. post paw injection) #2

description: Library name: DRG_LTb_24h_2


title: LTbR agonist D (24 hrs. post paw injection) #1

description: Library name: DRG_LTb_24h_1


title: ex1bont_3

description: Library name: ex1bont_3


title: ex1bont_2

description: Library name: ex1bont_2


title: ex1col0m_3

description: Library name: ex1col0m_3


title: ex1bonm_3

description: Library name: ex1bonm_3


title: LTbR control agonist D (24 hrs. post paw injection) #1

description: Library name: DRG_LTb_cont_1


title: ex1bont_1

description: Library name: ex1bont_1


title: LTbR control agonist P (24 hrs. post paw injection) #1

description: Library name: Paw_LTb_cont_1


title: LTbR control agonist D (24 hrs. post paw injection) #3

description: Library name: DRG_LTb_cont_3


title: ex1col0m_1

description: Library name: ex1col0m_1


title: p16high (Tom+) hepatocytes from CCl4 treated mice

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

description:
Library name: Hep_CCL4_Posi
10x Genomics Flex

data_processing:
The demultiplexing, barcoded processing, and gene counting were performed by conducting CellRanger software v7.2.0.
Assembly: Mouse mm10
Supplementary files format and content: TSV files for barcodes, features, and count matrix

source_name: Liver

extract_protocol:
To prepare hepatocyte suspensions of CCl4-treated male p16-Tom mice, PBS was perfused followed by liver excision and chopping into 5 mm2 pieces. The tissue fragments were fixed in Fix & Perm Buffer (10X Genomics) containing 4% formaldehyde (Polysciences) at 4°C with moderate agitation for 16–20 hours. Fixation was stopped by adding 1.25 M glycine, and the fragments were washed with tissue resuspension buffer (0.496X PBS (Nacalai Tesque), 50 mM Tris-HCl pH 8.0, 0.02% (w/v) BSA (Sigma), and RNase inhibitors (TOYOBO). The tissues were dissociated into single cells using a gentleMACS Dissociator (Miltenyi) with 0.2 mg/mL of Liberase TL and TH (Roche). Dissociated cells were washed with tissue resuspension buffer, filtered through a 70 μm cell strainer, and stained with MitoBrilliant 646 (Tocris Bioscience, 1:5000 dilution) at 37°C for 30 minutes. Following staining, the cells were washed, and filtered, and nuclei were stained with 2 μg/mL of Hoechst dye (Dojindo). The cell suspension was analyzed using BD FACSAria III flow cytometer (BD Biosciences), and Hoechst+ /MitoBrilliant 646+ /Tom+ or Tom- hepatocytes were collected in Protein LoBind Tubes (Eppendorf).
Library preparation for single-cell transcriptomes of isolated hepatocytes was performed using the Chromium Fixed RNA Kit (10X Genomics, Mouse Transcriptome) following the manufacturer’s protocol. Three pairs of customized tdTomato probes were added to the probe set for quantifying tdTomato expression. Probe sequences: tdTomato-1 TACAGGAACAGGTGGTGGCGGCCCT, TTTACGGATGTCAACGTCACAC, tdTomato-2 AACACAGTGCACACCACGCCACGTT, GCCTGACAACGGGCCACAACTCCTC, tdTomato-3 AGGACGTCCCGCGCAGAATCCAGGT, GGCAACACAGGCGAGCAGCCAAGGA.

value: Liver

tag: cell type

value: p16high (Tom+) hepatocytes


title: LTbR control agonist P (24 hrs. post paw injection) #3

description: Library name: Paw_LTb_cont_3


title: ex1bonm_2

description: Library name: ex1bonm_2


title: Joma_n2 transfected with siRNA LKB1

city: La Tronche

first: Chantal

last: Thibert

address: Site Santé - Allée des Alpes

country: France

institute: Institute for Advanced Biosciences

description:
Library name: Joma_n2_siL
The processed data file contains values of FPKM, raw read count (read_count) and normalized read count (norm_read_count)  for each samples

data_processing:
The raw data were filtered, low-quality sequence data removed, and quality controlled with SOAPnuke v2.3. The clean data were saved in FASTQ format for subsequent bioinformatics analysis.
Genome and gene alignments. The clean reads were aligned to the reference genome sequence Mus musculus (version: GCF_000001635.27_GRCm39) using HISAT2 software (v2.0.4). The software Bowtie2 v2.2.5 was used to align the clean reads to the reference gene sequence (transcriptome).
Gene Expression Quantification. RSEM v1.2.8 was used to calculate the gene expression levels in each sample. Fragments per kilobase of exon model per million mapped fragments (FPKM) values were used to estimate the level of gene expression. The genes with a mean FPKM > 0.5 were considered expressed in the group.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: csv  files include RNA expression values of FPKM, raw read count (read_count) and normalized read count (norm_read_count) for each samples
Supplementary files format and content: csv  files include gene expression values of FPKM, raw read count (read_count) and normalized read count (norm_read_count) for each samples

source_name: JoMa 1.3

growth_protocol: A 1:1 mixture of Dulbecco’s Modified Eagle’s Medium (DMEM; 4,500 mg/L glucose, L-glutamine, sodium pyruvate) and Ham’s F-12 was used as the basal medium. The medium was supplemented with 1% N2 supplement (Invitrogen), 2% B27 supplement (Invitrogen), 10 ng/mL epidermal growth factor (EGF; from?), 1 ng/mL fibroblast growth factor (from?), 1% penicillin–streptomycin (Invitrogen), and 10% chick embryo extract.

extract_protocol:
Total RNA was extracted using TRIzol™ (Invitrogen™), and reverse-transcribed with the iScript™ Reverse Transcription Supermix (Bio-Rad). Quantitative polymerase chain reaction (qPCR) was performed using SsoAdvanced Universal SYBR Green Supermix (Bio-Rad) and CFX CONNECT (Bio-Rad).
RNA-Seq libraries were constructed with Optimal Dual-mode mRNA Library Prep Kit from Beijing Genomics Institute (BGI). A sequence read length of 150 bp was obtained by sequencing on the DNBSEQ T7 platform using the pair-end method (30M clean reads per library).

treatment_protocol: Lkb1 knockdown was performed using siRNAs from Dharmacon (ON-TARGETplus Mouse Stk11 SMART Pool and ON-TARGETplus Non-targeting Pool as control). siRNAs were transfected using jetPRIME (Ozyme) or RNAiMax lipofectamine (Invitrogen) with 60 nM siRNA final. For progenitor cells, experiments were performed 72 hours after transfection.

value: JoMa 1.3

value: Neural crest stem cells

tag: genotype

value: Lkb1 KD

value: siRNA LKB1


title: p16low (Tom-) hepatocytes from CCl4 treated mice

description:
Library name: Hep_CCL4_Nega
10x Genomics Flex

value: p16low (Tom-) hepatocytes


title: ex1bonm_1

description: Library name: ex1bonm_1

value: bon


title: snRNA-seq, arcopallium

city: San Francisco

first: Michael

last: Brainard

state: CA

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

description: Library name: ARCO

data_processing:
FASTQ files were aligned to the Bengalese finch reference genome (lonStrDom2, GCF_005870125.1) using cellranger v7.1.0. Included also in the alignment index were gene models with extended 3' UTRs as described in Colquitt et al., eLife, 2023. Ambient RNA was removed using cellbender v0.3.2 with a false positive rate of 0.01. Using Seurat v5.2.1, nuclei were removed that had greater than 2% mitochondrial reads, greater than 20,000 UMIs, and less than 1000 UMIs. Doublets were removed using two methods. First, nuclei were demultiplexed by their genotype using souporcell v1.0, which assigns each nucleus to an individual bird and estimates whether a nucleus is a doublet or singlet. Second, we performed doublet detection using DoubletFinder v2.0.4. Nuclei were retained if they were called a singlet in both approaches. Gene expression was then normalized using SCTransform, transformed via principal components analysis, then reduced using uniform manifold approximate projection (UMAP) and the first 30 PCs. Clustering was performed iteratively on progressively smaller subgroups to identify subclusters. First, clustering was performed on the entire dataset using Louvain clustering with multilevel refinement and a resolution of 0.2 using the Seurat function FindClusters. At this level, major cell classes were identified based on marker gene expression (e.g. glutamatergic and GABAergic neurons, astrocytes, oligodendrocytes, etc.). Glutamatergic neurons were subsetted and reprocessed via SCTransform, PCA, UMAP, and clustering to identify clusters belonging to regional domains, nidopallium and arcopallium. Glutamatergic neurons in each region were then similarly reprocessed to identify region-specific subclusters. GABAergic neurons were not subdivided by region but were similarly subsetted and reprocessed as the glutamatergic neurons.
Assembly: lonStrDom2, GCF_005870125.1
Supplementary files format and content: Cellranger output files: filtered_feature_bc_matrix.h5

organism: Lonchura striata

source_name: arcopallium

extract_protocol:
Adult (>120 days post hatch) male Bengalese finches were euthanized via isoflurane overdose then decapitated. The brain was dissected out into ice-cold ACSF (152 mM choline chloride, 2.5 mM KCl, 1.1 mM NaH2PO4, 25 mM NaCO3, 35 mM glucose, 10 mM HEPES, 3 mM MgSO4*7H2O, and 0.5 mM CaCl2*2H2O) bubbled with carbogen. The brain was then sectioned in ice-cold carbogenated ACSF either coronally or sagittally using a Leica VT1000 vibratome at 300 um. Areas of interest were microdissected out, placed in cryovials, frozen in liquid nitrogen, then transferred to -80C for long-term storage.  500 uL ice-cold lysis buffer (10 mM Trizma pH 7.4 (Sigma, T2194), 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40) was added to each cryovial, and the tissue was transferred to 2 mL glass dounces (Kimble). Samples were dounced 15 times using a loose pestle then 15 times using a tight pestle. 900 uL sucrose cushion buffer (Sigma, NUC201-1KT) was added to each sample and was slowly mixed by pipetting 20 times. 500 uL sucrose cushion buffer was added to a new 2 mL tube, then the 1400 uL of tissue/lysis/sucrose bufffer was carefully layered on top. Samples were centrifuged for 45 minutes at 13,000xg at 4C. All but 100 uL supernatant was discarded, 300 uL nuclei suspension buffer (1x PBS, 1% UltraPure BSA (ThermoFisher, AM2616), and 0.5% RNase inhibitor (Clontech, 2313A)) was added, then the pellet was gently resuspended by pipetting. Samples were centrifuged for 5 minutes at 550xg at 4C. All but 70 uL of supernatant was discarded, the pellet was resuspended, and the sample was passed through a 40 um FlowMi filter (Bel-Air). Nuclei were counted on a C-Chip and standardized to 400-700 nuclei / uL.
Nuclei were added to target recovery 10,000 nuclei onto a Next GEM Chip G microfluidics chip as part of the Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics). Following multiplexing, libraries were sequenced on two lanes of an Illumina NovaSeq S4 200 flow cell (101 cycles R1, 12 cycles I1, 24 cycles I2, 101 cycles R2) at the UCSF Center for Advanced Technology.

value: arcopallium

value: male

value: >120 days post hatch


title: LTbR control agonist P (24 hrs. post paw injection) #2

description: Library name: Paw_LTb_cont_2

value: Paw

value: 8-12 weeks


title: Joma_n2 transfected with siRNA control

description:
Library name: Joma_n2_siC
The processed data file contains values of FPKM, raw read count (read_count) and normalized read count (norm_read_count)  for each samples

value: WT

value: siRNA control


title: Joma_n1 transfected with siRNA control

description:
Library name: Joma_n1_siC
The processed data file contains values of FPKM, raw read count (read_count) and normalized read count (norm_read_count)  for each samples


title: snRNA-seq, Rostral nidopallium

description: Library name: NR

source_name: rostral nidopallium

value: rostral nidopallium


title: Joma_n1 transfected with siRNA LKB1

description:
Library name: Joma_n1_siL
The processed data file contains values of FPKM, raw read count (read_count) and normalized read count (norm_read_count)  for each samples


title: snRNA-seq, Caudal nidopallium

description: Library name: NC

source_name: caudal nidopallium

value: caudal nidopallium


title: snRNA-seq, HVC

description: Library name: HVC

source_name: HVC

value: HVC


title: snRNA-seq, RA

description: Library name: RA

source_name: robust nucleus of the arcopallium

value: robust nucleus of the arcopallium


title: LTbR control agonist D (24 hrs. post paw injection) #2

description: Library name: DRG_LTb_cont_2

value: DRG

value: Male


title: homo rep 4

city: nanjing

first: wang

last: ziyang

address: 12 Xuefu Road, Pukou District

institute: nanjing university

description:
Library name: sample8
DP_homo_4

data_processing:
Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300-400bp use magnetic beads followed by PCR amplified for 10-15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform (PE150) using NovaSeq Reagent Kit. OR the sequencing library was performed on DNBSEQ platform (PE150) using DNBSEQ Reagent Kit (FCL PE150) version 3.0.
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 or DEGseq. DEGs with |log2FC|≥1 and FDR < 0.05(DESeq2) or FDR < 0.001 (DEGseq) were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value < 0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and Python scipy software, respectively.
All the alternative splice events that occurred in our sample were identified by using recently releases program rMATS. Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention events.
Assembly: GRCm39
Supplementary files format and content: TPM values for each sample

source_name: basilar membrane

extract_protocol:
Total RNA from P6 cochlear basilar membrane was extracted using RNAiso Plus (Takara Bio) according the manufacturer’s instructions.
Library construction was performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions. The RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1 μg of total RNA.

value: basilar membrane

value: Dnajc17 cKO


title: snRNA-seq, LMAN

description: Library name: LMAN

source_name: lateral magnocellular nucleus of the anterior nidopallium


title: Multiome, Bengalese finch RA, GEX, biol rep 2

description: Library name: ra_rna_run3

data_processing:
FASTQ files were aligned to the Bengalese finch reference genome (lonStrDom2, GCF_005870125.1) using cellranger-arc v2.0.2. Included also in the alignment index were gene models with extended 3' UTRs as described in Colquitt et al., eLife, 2023. Ambient RNA was removed using cellbender v0.3.2 with a false positive rate of 0.05. Using Seurat v5.2.1, nuclei were retained that satisfied the following conditions: 1000 < number of GEX UMIs < 25,000, 1000 < number of ATAC fragments < 30,000, nucleosome signal < 2, and TSS enrichment >1.  Doublets were removed using two methods. First, nuclei were demultiplexed by their genotype using souporcell v1.0, which assigns each nucleus to an individual bird and estimates whether a nucleus is a doublet or singlet. Second, we performed doublet detection using DoubletFinder v2.0.4. Nuclei were retained if they were called a singlet in both approaches. Cluster labels were assigned using Seurat label transfer and labels from the snRNA-seq dataset.
Assembly: lonStrDom2, GCF_005870125.1
Supplementary files format and content: Cellranger-arc output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz

extract_protocol:
For snRNA/ATAC-seq samples, three to four adult (>120 dph) male Bengalese finches were anesthetized with isoflurane, transcardially perfused with ice-cold carbogenated ACSF, then decapitated. Brains were dissected out into ice-cold carbogenated ACSF then coronally sectioned using a Leica VT1000 vibratome at 300 um. Areas of interest were microdissected out, placed in cryovials, frozen in liquid nitrogen, then transferred to -80C for long-term storage. Nuclei were isolated using a modified version of the Optiprep method. Several stable buffers were prepared before nuclei isolation and stored a 4C: 1.079x Homogenization Buffer Stable Solution ("HBS", 260 mM sucrose, 30 mM KCl, 10 mM MgCl2, 20 mM Tricine-KOH pH 7.8), Diluent Buffer (150 mM KCl, 30 mM MgCl2, 120 mM Tricine-KOH pH 7.8), 50% iodixanol solution (diluted from 60% Optiprep Density Gradient Medium, Sigma, D1556, using Diluent Buffer), and 5X ATAC-RSB (50 mM Tris-HCl pH 7.5, 50 mM NaCl, 15 mM MgCl2). On the day of nuclei isolation, the following buffers were prepared: 1x Homogenization Buffer Unstable Solution ("HBU", HBS to 1x, 1 mM DTT, 0.5 mM spermidine, 0.15 mM spermine, 0.3\% NP-40, 1 U/uL Protector RNase Inhibitor (Sigma 3335402001), 1x Complete Protease Inhibitor (prepared from a 25x solution consisting of one tablet (Sigma, 11697498001) dissolved in 2 mL nuclease-free water)), 30% Iodixanol Solution and 40% Iodixanol Solution (both diluted from 50% iodixonal solution using 1x Homogenization Buffer Unstable Solution), and ATAC-RSB-Tween (1x ATAC-RSB, 0.1\% Tween-20, 1% BSA, and 1 U/uL Protector RNase Inhibitor). Samples from different birds were pooled and 1 mL 1x HBU was added. Samples were incubated on ice for 5 minutes, then transferred to a 2 mL glass dounce (Kimble). Samples were homogenized with 15 strokes of the loose pestle, then 15 strokes of the tight pestle. Samples were transferred to 2 mL tubes then centrifuged for 5 minutes at 350xg at 4C using a swing-out rotor. All but 200 uL of supernatant was removed, the total volume was brought up to 400 uL using 1x HBU, then the pellet was gently resuspended by pipetting. 400 uL 50% iodixanol solution was added and mixed well by pipetting. 600 uL 30% iodixanol solution was layered underneath the 25% iodixonal/tissue layer, followed by 600 uL 40% iodixanol solution underneath the 30% layer. In a pre-chilled swing-out rotor, samples were centrifuged for 20 minutes at 10,000xg at 4C with the brake off. Starting at the top of the solution, enough solution was aspirated off to leave ~200-300 uL above the interface between the 30% and 40% iodixanol layers, which contains nuclei. 200 uL of the nuclei band was aspirated and transferred to a clean 1.5 mL tube containing 1 mL of ATAC-RSB-Tween. Nuclei were centrifuged for 10 minutes at 500xg at 4C using a swing-out rotor. The entire supernatant was carefully removed, followed by addition of 12 uL Nuclei Resuspension Buffer (10X Genomics) and gentle resuspension by pipetting.
Nuclei were counted and their concentrations were adjusted to 800-12,000 nuclei/uL. The nuclei were then loaded onto a Next GEM Chip J (10X Genomics) at numbers targeting 2,500 to 10,000 recovered nuclei. Sequencing libraries for each region were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The libraries were then pooled, and sequenced on an Illlumina NovaSeq S4 200 flow cell at the UCSF CAT.

tag: library type

value: mRNA


title: homo rep 1

description:
Library name: sample5
DP_homo_1


title: homo rep 2

description:
Library name: sample6
DP_homo_2


title: Multiome, Bengalese finch RA, ATAC, biol rep 2

description: Library name: ra_atac_run3

library_source: genomic single cell

value: ATAC


title: Multiome, Bengalese finch Arco, GEX, biol rep 2

description: Library name: arco_rna_run3

value: arcopallium


title: homo rep 3

description:
Library name: sample7
DP_homo_3


title: Multiome, Bengalese finch Arco, ATAC, biol rep 1

description: Library name: arco_atac_run2


title: hete rep 3

description:
Library name: sample3
DP_hete_3


title: Multiome, Bengalese finch Arco, GEX, biol rep 1

description: Library name: arco_rna_run2


title: hete rep 4

description:
Library name: sample4
DP_hete_4


title: Multiome, Bengalese finch RA, GEX, biol rep 1

description: Library name: ra_rna_run2


title: Multiome, Bengalese finch Arco, ATAC, biol rep 2

description: Library name: arco_atac_run3


title: hete rep 2

description:
Library name: sample2
DP_hete_2


title: Multiome, Bengalese finch RA, ATAC, biol rep 1

description: Library name: ra_atac_run2


title: hete rep 1

description:
Library name: sample1
DP_hete_1


title: Multiome, Bengalese finch NC, ATAC, biol rep 2

description: Library name: nc_atac_run2


title: Multiome, Bengalese finch NC, GEX, biol rep 2

description: Library name: nc_rna_run2