title: HCT116 cells, shMIB1, replicate2

city: Seoul

first: Junyoung

last: Park

address: 84, Heukseok-ro

department: Department of Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Low-quality reads were filtered based on the following criteria: reads containing more than 10% of skipped bases (marked as ‘N’s), reads containing more than 40% of bases with quality scores of less than 20, and reads with average quality scores for each read of less than 20.
The filtering process was performed using in-house scripts. Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.4.0b.
Gene expression levels were measured using Cufflinks v2.1.1 and the gene annotation database of the species. For differentially expressed gene (DEG) analysis, gene-level count data were generated using HTSeq-count v0.6.1p1. Based on the calculated read count data, DEGs were identified using the R package ‘TCC’.
The normalization factors were calculated using the iterative DEGES/edgeR method. The Q-value was calculated based on the P-value using the p.adjust function of the R package, with default parameter settings. The DEGs were identified based on a Q-value threshold of less than 0.05 for correcting errors caused by multiple testing.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each sample
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: Colon

extract_protocol:
RNA was extracted using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
mRNA molecules were purified and fragmented from 0.1-1 ug of total RNA using oligo (dT) magnetic beads. Fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. Double-stranded cDNA was prepared by using this cDNA as a template for second strand synthesis. After a sequential process of end repair, A-tailing, and adpter ligation, cDNA libraries were amplifed using PCR.

value: Colon

tag: cell line

value: Adenocarcinoma

value: MIB1 knockdown


title: MEF+shTip60#3_day7_rep1

status: Public on Nov 22 2022

type: SRA

city: Stanford

first: Justyna

middle: A.

last: Janas

state: CA

address: 265 Campus Drive

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Raw reads were trimmed for base call quality (PHRED score ≥ 21) using skewer 0.2.2 (Jiang et al., 2014).
Transcript quantification was performed using mm10 reference transcriptome and salmon 1.4.0 (Patro et al., 2017).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tsv files containig TPM values

molecule: total RNA

organism: Mus musculus

source_name: MEF+shTip60#2 day7

growth_protocol: Homozygous TauEGFP knock-in mice (Tucker et al., 2001) were bred with C57B/6 mice (Jackson Laboratory). Mouse embryonic fibroblasts (MEFs) were isolated from embryonic day (E)13.5 heterozygous embryos and maintained in DMEM (Invitrogen) supplemented with 10% cosmic calf serum.

extract_protocol:
RNA was harvested using Trizol.
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit or TruSeq mRNA Library Prep Kit, following standard protocols.

treatment_protocol: MEFs were transduced with indicated lentiviruses. rtTA and Ascl1+rtTA transduced MEFs were treated with doxycycline (dox) two days post-infection to induce transgene expression. The cells were transferred into N3 medium (DMEM/F12, N2 supplement, insulin) containing dox the following day. The medium was refreshed every 3 days.

tag: genotype

tag: cell type

value: E13.5 fibroblast

tag: time post-infection

value: 7 days

tag: time post-dox


title: Ascl1_H2AZ_tauPos_day5_rep3

library_source: genomic

data_processing:
Library strategy: Cut&Tag
Reads were trimmed using cutadapt and aligned with Bowtie2 (v 2.3.5.1) to mm10 reference genome.
Peaks were called using MACS2. Reproducible peaks for each condition were identified using IDR (idr≤0.1) or by overlap thresholding (for histone Cut&Tag). Reproducible peaks were aggregated, read counts for each region were obtained using featureCounts package followed by normalization and differential accessibility analysis using DESeq2.
Bigwig files were produced with deepTools (Ramirez et al., 2014).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file containing normalized read counts as determined for the aggregated peak set; tar containing normalized average signal files

molecule: genomic DNA

source_name: Ascl1_H2AZ_tauPos day5

growth_protocol: Mouse embryonic fibroblasts (MEFs) were isolated from embryonic day (E)13.5 heterozygous TauEGFP embryos, or E13.5 homozygous Tip60/Kat5 conditional KO (cKO) embryos, and maintained in DMEM (Invitrogen) supplemented with 10% cosmic calf serum.

extract_protocol: Cells at different times of neuronal induction were subjected to Cut&Tag following the previously described protocol (Kaya-Okur et al., 2019). Where indicated, day5 TauEGFP cells were sorted using BD FACS-Aria II sorter.

treatment_protocol: MEFs were transduced with indicated lentiviruses. shRNA-infected populations were selected for 2 days in 2 mg/ml puromycin. The cells were treated with doxycycline (dox) two days post-infection to induce transgene expression, and transferred into N3 medium (DMEM/F12, N2 supplement, insulin) containing dox the following day. The medium was refreshed every 3 days.

tag: time post-induction

tag: antibody

value: H2A.Z (Active Motif, 39113)


title: MEF+shTip60#2_day7_rep2


title: DN_nr_d0_3

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

country: Germany

institute: Technical University of Munich

description:
L31_S3
counts_expression_matrix_batchA.tsv

data_processing:
Demultiplexing: Reads were demultipled with the bcl2fastq software (v2.20.0.422).
Pipeline: Reads were processed using snakemake pipelines as indicated under (https://gitlab.lrz.de/ImmunoPhysio/bulkSeqPipe). Parameters are provided in the configuration (see "config.yaml").
Filtering: Reads were filtered using Trimmomatic v0.36.
Mapping: STAR v2.5.3a was used for mapping to annotation release #91 and genome build #38 from Mus musculus (Ensembl). Multimapped reads were discarded.
Differential expression: DESeq2 v1.24.0 was used for differential expression analysis. Differences for genes with a Basemean > 50, an absolute log2 fold change >1, an adjusted p-value <0.05 and more than 10 counts in at least 2 samples were considered significant.
Assembly: GRCm38 (release 91)
Supplementary files format and content: The .tsv files contain the read counts for each gene (rows) in each sample (columns).

source_name: small intestine lamina propria

extract_protocol:
Small intestines were removed, digested using 240 mg/ml Liberase TL and 150 μg/mL DNase I, DPs and DNs were sorted with an Aria Fusion and RNA was harvested using Agencourt RNAdvance Cell v.2 kit.
TotalRNA was isolated using the RNAdvance Cell v2 kit (Beckmann-Coulter). cDNA synthesis was performed with the SMART-Seq v4 Ultra Low Input RNA kit (takara) following the manufacturers protocol with 14 cycles of PCR amplification. Input amount were 9.5µl of each RNA sample. cDNA was measured with Bioanalyzer DNA HS Chip (Agilent) and 300pg of amplified cDNA were used for library preparation with the Nextera XP DNA library Preparation Kit (Illumina). Libraries were analyzed with a Bioanalyzer DNA HS Chip (Agilent) and quantified by qPCR following guidelines from Illumina and using Kapa SYBR mastermix (Kapa Biosystems). After the normalization of all libraries to 2nM, 14 samples each were pooled and sequenced on three single-end runs (1x100bp, dual-index) on a HiSeq2500 (Illumina) using HiSeq Rapid v2 chemistry (Illumina).

treatment_protocol: C57BL/6 mice received 5x103 CD45.1 congenic INTEGRA OT-1 T-cells (day -1), an Lm-Ova infection (1000 cfu i.v., day 0), and tamoxifen (100 mg/kg in corn oil i.p.) on days 24 and 25. Mice were re-challenged with VSV-Ova (2x106 pfu i.v.) on day 32 and samples were collected after 2 and 8 days and for mice without re-infection.

tag: tissue

value: small intestine lamina propria

value: CD8+ T cell

value: CD103-ERT2-Cre-zsGreen (INTEGRA)

tag: group

value: no-reinfection

tag: subpopulation

value: DN

tag: time

tag: batch

value: A

tag: mouse

tag: replicate

tag: zsgreen

value: Neg

tag: lane

tag: ID


title: DN_nr_d0_1

description:
L29_S1
counts_expression_matrix_batchA.tsv

tag: cell line


title: rtTA_H2AZ_day2_rep2

source_name: rtTA_H2AZ day2

tag: genotype


title: MEF+Ascl1+shNTC_day2_b2_rep2

source_name: MEF+Ascl1+shNTC day2

tag: cell type

value: 4 days

value: 2 days


title: DN_wt_d2_2

description:
L35_S7
counts_expression_matrix_batchA.tsv

value: VSV-wt


title: DN_nr_d0_2

description:
L30_S2
counts_expression_matrix_batchA.tsv


title: DP_ova_d2_4

description:
L14_S14
counts_expression_matrix_batchA.tsv

value: VSV-OVA

value: DP

value: Pos


title: HCT116 cells, shNC, replicate1

organism: Homo sapiens

value: Colon

value: Adenocarcinoma

value: Control

tag: treatment

value: shNC


title: MEF+shNTC_day7_rep2

source_name: MEF+shNTC day7

value: E13.5 fibroblast

tag: time post-infection

value: 7 days

tag: time post-dox


title: rtTA_H2AZ_day2_rep1

tag: time post-induction

tag: antibody

value: H2A.Z (Active Motif, 39113)


title: HCT116 cells, shNC, replicate2

tag: tissue


title: DP_ova_d2_2

description:
L12_S12
counts_expression_matrix_batchA.tsv

value: small intestine lamina propria

value: CD8+ T cell

value: CD103-ERT2-Cre-zsGreen (INTEGRA)

tag: group

tag: subpopulation


title: Ascl1_Tip60_tauPos_day5_rep2

source_name: Ascl1_Tip60_tauPos day5


title: Ascl1_Tip60_day2_rep2

source_name: Ascl1_Tip60 day2


title: MEF+shTip60#3_day4_rep2

source_name: MEF+shTip60#2 day4


title: DP_ova_d2_1

description:
L11_S11
counts_expression_matrix_batchA.tsv

tag: time

tag: batch

value: A


title: MEF+shNTC_day7_rep1


title: DP_ova_d2_3

description:
L13_S13
counts_expression_matrix_batchA.tsv

tag: mouse

tag: replicate


title: 6-2PA1_NP_n2

city: Suwon

first: Su Bin

last: Lim

state: Gyeonggi-do

address: Worldcup-Ro 164, Yeongtong-Gu

institute: Ajou University School of Medicine

description: PANC1, deltaNP63, n=2

data_processing:
Altanalyze 2.1.4.4
Assembly: human genome in Ensembl (version EnsMart72)
Supplementary files format and content: tab-delimited text files include transcript-level expression values (TPMs) for mRNAs for all samples

extract_protocol:
Total RNA from cancer cells was extracted using RNeasy plus mini kit (Qiagen)
RNA libraries were prepared using Illumina TruSeq Stranded mRNA Sample Prep Kit

value: biol rep 2

value: Pancreatic cancer cell line

value: deltaNp63 O/E


title: MEF+shTip60#3_day4_rep1

value: 4 days


title: HCT116 cells, shMIB1, replicate1

value: MIB1 knockdown


title: 5PA1_TAP_n1

description: PANC1, TAp63, n=1

value: biol rep 1

value: TAp63 O/E


title: rtTA_Tip60_day2_rep2

source_name: rtTA_Tip60 day2


title: MEF+shTip60#2_day4_rep2


title: 4-2PA1_Mock_n2

description: PANC1, Mock, n=2

value: Mock


title: DP_wt_d2_4

description:
L9_S9
counts_expression_matrix_batchA.tsv

value: VSV-wt

value: DP

tag: zsgreen

value: Pos

tag: lane


title: 4PA1_Mock_n1

description: PANC1, Mock, n=1

tag: cell line


title: DP_wt_d2_3

description:
L8_S8
counts_expression_matrix_batchA.tsv

tag: genotype

tag: ID


title: MEF+shNTC_day4_rep2

source_name: MEF+shNTC day4

tag: cell type

value: E13.5 fibroblast


title: MEF+Ascl1+shTip60#3_day2_b1_rep2

source_name: MEF+Ascl1+shTip60#3 day2

tag: time post-infection

value: 2 days


title: 6PA1_NP_n1

description: PANC1, deltaNP63, n=1


title: DP_wt_d2_2

description:
L7_S7
counts_expression_matrix_batchA.tsv

value: small intestine lamina propria


title: MEF+shTip60#2_day4_rep1

tag: time post-dox


title: MEF+shNTC_day4_rep1


title: MEF+Ascl1+shTip60#3_day2_b1_rep1


title: 3AS1_NP_n1

description: ASPC1, deltaNP63, n=1


title: MEF+Ascl1+shTip60#2_day2_b1_rep2

source_name: MEF+Ascl1+shTip60#2 day2


title: 5-2PA1_TAP_n2

description: PANC1, TAp63, n=2


title: Ascl1_Tip60_day2_rep1

tag: time post-induction


title: 3-2AS1_NP_n2

description: ASPC1, deltaNP63, n=2


title: 2-2AS1_TAP_n2

description: ASPC1, TAp63, n=2


title: DP_wt_d2_5

description:
L10_S10
counts_expression_matrix_batchA.tsv

value: CD8+ T cell


title: DP_nr_d0_3

description:
L3_S3
counts_expression_matrix_batchA.tsv

value: CD103-ERT2-Cre-zsGreen (INTEGRA)

value: no-reinfection


title: MEF+Ascl1+shTip60#2_day2_b1_rep1


title: DP_nr_d0_2

description:
L2_S2
counts_expression_matrix_batchA.tsv

value: A


title: WT_Spleen_Tconv

city: Suita

first: Mara

middle: Anais

last: Llamas-Covarrubias

state: Osaka

address: 3-1 Yamadaoka

department: Department of Genome Informatics

country: Japan

institute: Osaka University

data_processing:
FASTQ files were aligned to the mouse reference genome, filtered and counted for barcode and unique molecular identifiers (UMIs) by the 10x Genomics software Cell Ranger v.5.0
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Spleens were obtained and after tissue disruption, Tconv cells were sorted as CD3+, GFP- Tcells
libraries were produced according to 10x Genomics single cell VDJ and Gene expresion protocol

value: Spleen

tag: mouse model

value: WT

value: Tconv


title: 2AS1_TAP_n1

description: ASPC1, TAp63, n=1

value: Pancreatic cancer cell line


title: MEF+Ascl1+shNTC_day2_b1_rep2

value: 4 days


title: rtTA_Tip60_day2_rep1

tag: antibody


title: ZAC_Spleen_Treg

data_processing:
FASTQ files were aligned to the mouse reference genome, filtered and counted for barcode and unique molecular identifiers (UMIs) by the 10x Genomics software Cell Ranger v.5.0
Hashtag demultiplexing was performed in ZAC samples by the method integrated in Seurat v4.0 R package
Batch correction and data integration was performed by the R package Canek
The identification of cell clusters based on gene expression data was performed in the integrated data set by Seurat v4.0
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

tag: tissue

value: ZAC

value: Treg


title: DP_nr_d0_1

description:
L1_S1
counts_expression_matrix_batchA.tsv

tag: group

tag: subpopulation


title: 1-2AS1_Mock_n2

description: ASPC1, Mock, n=2

value: biol rep 2

value: Mock


title: MEF+Ascl1+shNTC_day2_b1_rep1


title: ZAC_Spleen_Tconv


title: DP_wt_d2_1

description:
L6_S6
counts_expression_matrix_batchA.tsv

value: VSV-wt

value: DP

tag: time

tag: batch

value: Pos


title: WT_Spleen_Treg


title: Cornea with culture and FFPE 2

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.73
Reads were mapped to the human reference genome (Gencode, GRCh38.p13, all regions, release 39) with RNA STAR (Galaxy Version 2.7.8a) using the corresponding Gencode main annotation file.
Reads mapped to the reference genome were counted with featureCounts (Galaxy Version 2.0.1) using the aforementioned annotation files.
The outputs of featureCounts were imported to RStudio (Version 2022.02.0+443). Gene symbols were determined based on the ENSEMBL database (release 105, download on 01/19/2022).
Assembly: hg38

source_name: cornea

extract_protocol:
RNA extraction from corneal samples was performed by a commercial provider (GenXPro) as previously described. Briefly, total RNA was isolated using the Quick-RNA FFPE Kit (Zymo Research). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer).
MACE RNA-Seq

value: Cornea with culture and FFPE

value: cornea


title: MEF+rtTA+shNTC_day2_b1_rep2

source_name: MEF+rtTA+shNTC day2

value: E13.5 fibroblast

value: 2 days


title: MEF+rtTA+shNTC_day2_b1_rep1


title: Acup2

city: Beijing

first: Xiaodong

last: Liu

address: 11 E 3rd N ring RD

country: China

institute: Beijing University of Chinese Medicine

description: Acupuncture 24 hour after bupivacaine injection

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene,
Genome_build: mm10
Supplementary_files_format_and_content: excel files include gene counts and FPKM values for each Sample

source_name: Gastrocnemius muslce

extract_protocol:
Muslce tissues were removed and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Gastrocnemius muslce

tag: age

value: 6-7 months

value: wild type


title: Acup3


title: Cornea with culture and FFPE 3


title: Acup1


title: Cornea without culture with FFPE 3

value: Cornea without culture and with FFPE


title: Cornea with culture and FFPE 1


title: Pkd1_clone_21_Cre

first: Roman

last: Pichler

address: Hugstetter Str. 55

department: Nephrology

institute: University clinic Freiburg

description: Cre transduction

data_processing:
Raw sequence analysis on the Galaxy platform and usegalaxy.eu server
Reads were trimmed with Trim Galore! version 0.4.3.0 and quality was analyzed with FastQC version 0.67
Reads were aligned to the genome build mm10+GRCm38.89 using RNA STAR version 2.5.2b-2
Gene counts were calculated with featureCounts version 1.6.0.3
Differentially expressed genes (DEG) between Cre and Flp conditions were determined using DESeq2 version 2.11.40.1
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Gene raw counts calculated with featureCounts version 1.6.0.3, DESeq2 analysis, tab-delimited files

source_name: Cell culture

growth_protocol: Pkd1 iREC clones were cultured in MEF medium containing DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 10% (v/v) FBS (fetal bovine serum), penicillin/streptomycin and glutamine, and were maintained in a humidified atmosphere of 5% CO2

extract_protocol:
Total RNA was extracted with QIAzol Lysis Reagent (Qiagen) and isolated using the RNeasy Plus Universal Mini Kit
Library construction by Eurofinsgenomics

treatment_protocol: Cells were seeded in MEFM and grown until confluency

value: iRECs

value: Pkd1 knockout (Pkd1 -/-)


title: Pkd1_clone_21_Flp

description: Flp transduction

value: Pkd1 wild type (Pkd1 fl/fl)


title: Inju3

description: Bupivacaine injecion injuduced muscular injury


title: Pkd1_clone_7_Flp

description: Flp transduction


title: Cornea without culture with FFPE 2


title: iPSC-CM, R14del_rep2

city: Barcelona

first: Malgorzata

middle: Ewa

last: Rogaska

address: C/ del Dr. Aiguader, 88

country: Spain

institute: CRG

data_processing:
RNA-seq reads were processed for alternative splicing and expression analysis using vast-tools, version 2.2.2 , available on github (https://github.com/vastgroup/vast-tools)
Alternative splicing analysis: From the primary vast-tools output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW for cassette exon [CE], microexon [MIC] and alternative 5'/3'-ss events or coverage less than 15 reads for intron retention [IR] events; score 4 other than OK/B1 for CE and MIC events or less than 0.05 for IR events). Significantly differential AS was assessed using a 2-tailed unpaired Wilcoxon–Mann–Whitney test. The FDR was estimated using the Benjamini–Hochberg method. A p-value < 0.05 fdr<0.12 and PSI difference >5 was considered significant
Assembly: hg38
Supplementary files format and content: All files are in tab-delimited format. File Splicing_R14del.tab contains filtered PSI values and results of differential AS analysis with dPSI per event and associated p-value and FDR.

source_name: iPSC-CM

extract_protocol:
RNA mini kit (Qiagen)
Sequencing libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina

treatment_protocol: CM differentiation (Wnt activation/inhibition using small molecules)

value: iPSC-CM

value: Day 45 post differentiation

value: MUT


title: iPSC-CM, R14del_rep1


title: iPSC-CM, Parental_rep3

value: WT


title: iPSC-CM, R14del_rep3


title: Inju2


title: Pkd1_clone_7_Cre

description: Cre transduction


title: Cornea without culture with FFPE 1


title: iPSC-CM, Parental_rep2


title: 1AS1_Mock_n1

description: ASPC1, Mock, n=1

tag: replicate

value: biol rep 1

value: Pancreatic cancer cell line

value: Mock


title: Inju1


title: iPSC-CM, Parental_rep1

tag: cell line


title: Pkd1_clone_4_Flp

description: Flp transduction

tag: genotype


title: Cornea with culture 8

value: Cornea with culture

value: cornea


title: CCD18Co siLTBP2 rep3 [AG_12_S12]

city: Berlin

first: Ambre

middle: Manon

last: Giguelay

state: Berlin

address: Hannoversche Str. 28

department: Cell Biology/Single Cells

institute: Berlin Institute for Health

data_processing:
Basecalling and demultiplexing were performed with Illumina software Dragen 3.8.4 (default parameters of bcl2fastq command)
Alignment with STAR 2.7.1a (2 passes)
Read count extraction with HTSeq-count 0.11.2
Genome_build: Ensembl Homo_sapiens.GRCh38.104
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: CCD18Co cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% Penicilline/streptomycine (Gibco, Invitrogen, Life Technologies) at 37°C in 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using Monarch Total RNA Miniprep Kit (New England Biolabs #T2010S)
RNA libraries were prepared for sequencing using standard Illumina protocols (RNA Stranded Total RNA prep Ligation with Ribo-Zero plus kit)

treatment_protocol: Cells were transfected during 6h with siRNA against LTBP2 (Dharmacon #L-011078-00-005) or non target sequence (Dharmacon #D-001810-10-05) using lipofectamine 2000 (Thermofisher #11668027). 48h hours after transfection,  cells were washed twice with PBS and frozen.

tag: treatment

value: siLTBP2 48h


title: Pkd1_clone_4_Cre

description: Cre transduction

tag: cell type


title: Sham3

description: Saline injection

value: Gastrocnemius muslce


title: Cornea with culture 7


title: Sham2

description: Saline injection

value: 6-7 months


title: CCD18Co siNT rep3 [AG_11_S11]

value: siNT 48h


title: CCD18Co siLTBP2 rep2 [AG_10_S10]


title: WT3

description: naïve control

value: wild type


title: CCl4_library1, scRNA-seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

library_source: transcriptomic single cell

data_processing:
Sequencing data filtered and gene expression matrix was obtained using DNBelab C Series scRNA analysis-software (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software).
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

source_name: colon

extract_protocol:
The colon tissues were enzymatically digested into single-cell suspensions using Multi Tissue Dissociation Kits (Miltenyi Biotec)
The single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured bead collection, reverse transcription, cDNA amplification, and purification.

value: colon

value: CCl4 for 6 weeks


title: CCD18Co siNT rep2 [AG_09_S9]


title: Cornea with culture 4


title: WT1

description: naïve control


title: CCD18Co siLTBP2 rep1 [AG_08_S8]


title: WT2

description: naïve control


title: control_library1, scRNA-seq

value: control


title: Sham1

description: Saline injection


title: Cornea with culture 3


title: Cornea with culture 2


title: Cornea with culture 9


title: CCD18Co siNT rep1 [AG_07_S7]


title: CCl4_library2, scRNA-seq


title: Cornea with culture 6


title: LN-tet-AR, doxycycline, ChIP-AR

status: Public on Nov 21 2022

city: Boston

first: Maryam

last: Labaf

state: MA

address: 100 William T Morrissey Blvd

department: Biology

institute: University of Massachusetts Boston

data_processing:
Raw reads were processed for quality control using fastqc (v.0.11.5)
Raw reads were aligned to human hg19 using BWA (v0.7.5a)
Peaks were called using MACS3 v3.0.0a6 with the significance cut-off q-value <=0.05
The bedGraph files from MACS were converted into bigwig files using UCSC tools (version 372)
Assembly: Human hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: LNCaP-tet-AR

growth_protocol: LN-tet-AR cells are cultured routinely in 10% tetracycline-free FBS containing RPMI1640 and passed every 5-6 days

extract_protocol:
Cells were crosslinked with formaldehyde and then sonicated. DNA were immunoprecipitated with AR antibody and protein A beads. After reverse crosslinking, DNA were purified with Qiagen PCR purification kit.
ChIP DNA Library were prepared with NEBNext ChIP-Seq Library Prep Reagent set for Illumina and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1)

treatment_protocol: LN-tet-AR cells were grown in 5%CSS and treated with 0.25 ug/ml doxycycline for 2 days and stimulated with 0.1 nM DHT for 4 hours.

value: LNCaP-tet-AR

value: Prostate Cancer Cell Line (generated from LNCaP)

value: 0.25 ug/ml doxycycline


title: LN-tet-AR, vehicle, ChIP-AR

value: vehicle


title: CRISPR screen Brunello Library Input

first: Sizun

last: Jiang

address: 3 Blackfan Circle

institute: BIDMC/Harvard

description: Brunello Library input plasmid

data_processing:
CRISPR: Adapters from sgRNA reads were trimmed with cutadapt
CRISPR: Trimmed sgRNA reads were counted based on the Brunello library, with MAGeCK.
CRISPR: Beta scores for each gene was computed after normalizing based on essentail genes with  MAGeCKFlute
CRISPR: Differential beta scores between CRISPR screen conditions were computed to identify relative selection of genes in EBV-positive and negative NPCs
HiChIP: HiChIP library reads were mapped onto hg19 using HiC-Pro
HiChIP: Significant loops were identified with mango and normalized for restriction enzyme fragment sizes wit hichipper
HiChIP: Identified loops were quality controlled by  1) Merging anchors within 2kb of each other, 2) Removing loops <5kb , 3) Removing loops with FDR > 0.01, 4) Removing loops with >4 PETs in one replicate but 0 in other, 5) Removing loops not annotated as enhancers (by H3K27ac ChIP seq peaks) or promoter/genebody.
HiChIP: Normalized loops were visualized on the WashU genome browser
Genome_build: hg19
Supplementary_files_format_and_content: CRISPR: count tables of each condition, as well as input library
Supplementary_files_format_and_content: HiChIP: Loops that can be visualized on the WashU genome browser

organism: synthetic construct

source_name: Brunello Library input

growth_protocol: All cells were grown in RPMI supplemented with 10% FBS, 1% PenStrep and 1% L-Glutamine.

extract_protocol:
CRISPR Screen: After 28 days, cells were harvested, and genomic DNA was extracted by using the Blood and Cell culture DNA Maxi Kit (QIAGEN) according to manufacturer’s instructions.    HiChIP: 15 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature, followed by adding 125mM glycine for 5 min to stop reaction. Cross-linked cells were then lysed with 500ul ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40, 1X Roche protease inhibitors) with rotation at 4° C for 30 min. Nuclei was extracted by spin down at 2500g for 5 min followed by another wash with Hi-C lysis buffer. 375U MboI enzyme was used to cleave cross-linked DNA with shaking at 800RPM,37 ˚C for 2 hr. Over hanged DNA ends were filled in with 37.5 μL of 0.4 mM biotin-dATP (Thermo Fisher 19524016), 4.5 μL of a dCTP, dGTP, and dTTP mix at 10 mM each, and 10 μL of 5 U/μL DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210) with shaking at 600RPM, 37° C for 1 hr. 10 μL of 400 U/μL T4 DNA Ligase was used for proximity DNA ligation at 4° C overnight. After ligation DNA was sonicated by using a Covaris M220 using the samples following parameters: Peak Power = 75, Duty Factor = 10 Cycles/Burst = 200, Time = 4 min, fragmented were then diluted 10 times with CHIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 7.5, 167 mM NaCl) samples were precleared with 60 μL Protein A Dynabeads at 4° C for 1hr and DNA- protein complexes were captured  with 8uL H3K27Ac antibody (Abcam ab4729) with rotation at 4° C overnight. The next day Chromatin Immunoprecipitation complexes were captured with 60 μL of Protein A beads with rotation at 4° C for 2hr. Beads were then captured with magnet and washed sequentially with Low Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 7.5, 150 mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 7.5, 500 mM NaCl), and LiCl Wash Buffer (10 mM Tris-HCl pH 7.5, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, make fresh) each wash was done at room temperature with 3 times by adding 500 μL of a wash buffer. DNA were then eluted twice each with 150μL of fresh prepared DNA Elution Buffer (50 mM sodium bicarbonate pH 8.0, 1% SDS). Eluted DNA were combined. Samples were reverse cross-linked by incubation at 55° C for 45 min followed by 67° C for 1.5 hr with shaking at 800RPM. DNA were then purified with PCR purification Kit (Qiagen).
CRISPR Screen: Extracted DNA was then used as PCR template for sgRNA amplification. Multiple PCR covering all the genomic DNA was performed according to protocols from Broad Institute. For each PCR mix contains 10g genomic DNA, 1.5ul Ex Taq Polymerase, 10ul 10x reaction buffer,8ul dNTP, 0.5ul P5 Primer Mix (100uM), 10ul P7 primer (5uM), water was then added to top up reaction system to 100ul. Thermal cycler condition was set at: an initial 95˚C 1 min followed by  95˚C 30s, 53˚C 30s, 72˚C 30s for total of 28 cycles and a final extension at 72˚C 10 min. Amplified sgRNAs were purified with AMPure XP-beads (Beckman Coulter) according to manufacturer’s instructions.    HiChIP: 50ng post-CHIP DNA was used for downstream library prep. Biotin dATP labeled DNA was captured with 5μL Streptavidin C-1 beads (Thermo Fisher) and DNA was then transposed with 2.5 μL of Tn5 at 55° C with interval shaking for 10 min. Beads were then washed with 500 μL 50 mM EDTA and incubated at 50° C for 30 minutes shaking at 300rpm followed by wash two times each in 500 μL 50 mM EDTA then Tween Wash Buffer at 55° C for 2 min. Beads were lastly washed in 500ul 10 mM Tris. DNA was further amplified with PCR reaction. After wash beads were re-suspended with 23 μL ddH2O, 25 μL 2X Phusion HF (New England Biosciences), 1 μL of each Nextera Ad1_noMX and Nextera Ad2.X at 12.5 μM. PCR was running on thermal cycler at condition: an initial 72° C for 5 min, 98° C for 1 min followed by  98° C for 15 s, 63° C for 30 s for 8 cycles, and final extension at 72° C for 1 min. After PCR amplification Two-sided size selection with Ampure XP beads were performed for DNA size selection and purification, purified DNA was quantified

treatment_protocol: CRISPR Screen was performed as described below: 130 million Cas9 expressing C666 and NP69 cells were infected with CRISPR sgRNA Brunello library lentivirus at a multiplicity of infection (MOI) of 0.3.  Infection was performed in 12 well plates with spin infection at 300g for 2 hr at 30℃ in the presence of 4ug/ml polybrene. After infection plates were then returned to incubator for another 6 hr and cells were re-seeded into a large flash at a confluence of 10%. 48 hr later cells were selected with puromycin at 3ug/ml. Cell culture media was changed every 3 days and cells passaged until a confluency of 80%. At least 40 million cells were passaged out each time to maintain adequate sgRNA library complexity.

value: Brunello Library input


title: H3K27ac-Siah2 cells

city: Houston

first: Laure

last: Maneix

state: TX

address: One Baylor Plaza, MS230, Alkek building, Room N830

department: Huffington Center on Aging

institute: Baylor College of Medicine

description: CT 10364

data_processing:
Sequence reads were obtained from the Illumina Genome Analyzer Pipeline using Basespace (Next Seq 500) or the Baylor College of Medicine Genomic and RNA Profiling Core server (HiSeq 2500).
Sequences were aligned to the human reference genome hg19 with bowtie using default parameters.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm (http://liulab.dfci.harvard.edu/MACS/), version 2.
Genome_build: hg19
Supplementary_files_format_and_content: The SAM file with the alignments was converted to BAM format and then sorted using samtools. Sorted alignments were converted to WIG format using a perl script.

source_name: MM.1S cells (ATCC #CRL-2974)

growth_protocol: MM.1S cells were obtained from ATCC (#CRL-2974) and cultured in RPMI 1640 medium at 37°C in a humidified atmosphere containing 5% CO2 following vendor's recommendations.

extract_protocol:
ChIP assays were carried out according to an optimized version of the protocol provided with the iDeal ChIP-seq Kit for Transcription Factors (Diagenode). Following proteasome inhibition for 3 h with 25 µM Lactacystin, 60 nM Bortezomib, 60 nM Carfilzomib or 0.1% v/v DMSO control, MM.1S, MM.1S-Siah2, MM.1S-shHDAC3, and control cells were collected in 50 mL conical tubes, counted, and assessed for cell viability. For each immunoprecipitation, 25 million cells were harvested, washed once in sterile 1X PBS (Phosphate-Buffered Saline), resuspended in 1% formaldehyde in PBS solution, and fixed for 10 min. at room temperature with gentle end-over-end rotation on a Hula mixer (10 rpm).
Cross-linking reaction was quenched by adding glycine at a final concentration of 125 mM to the fixation solution for additional mixing (5 min, 10 rpm). After incubation, fixed samples were washed once in sterile 1X ice-cold PBS and stored on ice until further processing. Cell lysis was carried out with ice-cold lysis buffers iL1b and iL2, according to vendor’s protocol for suspension cells. After centrifugation, nuclear pellets were resuspended in SDS-containing shearing buffer iS1b supplemented with protease inhibitor cocktail at a concentration of 1.5 million cells per 100 µl buffer iS1b. Nuclear cell suspension was split into 250 µl aliquots and chromatin was sheared using a Bioruptor Pico water bath sonicator (Diagenode). To ensure generation of 150-300 bp DNA fragments suitable for next generation sequencing, the Bioruptor Pico sonicator was set at 10 cycles, each cycle 30 s “ON” and 30 s “OFF”, and kept at 4°C. After sonication, samples were centrifuged (10 min, 16,000 g, 4°C) to remove nuclear membrane debris and insoluble fraction. Supernatant (sonicated chromatin) was stored at -80°C into “Input” aliquots or used immediately in immunoprecipitation (IP) reactions, which were carried out with 2 µg of antibodies/IP and DiaMag Protein A-coated magnetic beads (30 µl/IP) under constant rotation on a Hula mixer (10 rpm). The ChIP-grade primary antibodies used in this study were the following: anti-H3K4me1 antibody (Abcam, ab8895), anti-H3K4me3 antibody (Abcam, ab8580), anti-H3K27ac antibody (Diagenode, C15410196), and anti-HDAC3 antibody (Millipore Sigma, 17-10238).
After immunoprecipitation overnight at 4°C, the immunoprecipitated complexed were captured with a magnetic rack, washed, and eluted according to Diagenode’s protocol. ChIP and “Input” samples were then de-crosslinked overnight at 65°C in a temperature-controlled water bath. The next day, ChIP and “Input” DNA was recovered and purified using iPure beads provided in the manufacturer’s kit. Finally, a 55%-25% DNA fragment double size selection was performed using Agencourt AMPure XP beads (Beckman Coulter) and final amounts of size-selected DNA were measured on a Qubit fluorometer (Thermo Fisher Scientific). The purified and size-selected DNA was then included in library preparation for next generation sequencing.
Single-indexed DNA libraries were constructed with the Ultra Next DNA library prep kit I and II (New England Biolabs (NEB), E7370S and E7645S) and prepared for multiplex sequencing using NEBNext Multiplex oligos (E7335S and E7500S) following manufacturer’s instructions. Library quality control, including assessment of fragment size distribution and quantification by qPCR, and library sequencing was conducted by the Baylor College of Medicine Genomic and RNA Profiling Core. The size distribution of the final libraries were confirmed by electrophoretic analysis on an Agilent Bioanalyzer 2100 prior to sequencing. Briefly, 1.8 pM of equimolarly pooled libraries with 1% PhiX control spike-in were loaded onto a NextSeq 500 high output v2.5 flow cell (Illumina, 20024906) and analyzed on a Illumina NextSeq 500 sequencing system. The flow cell was sequenced in a 75 bp single-end run, enabling the generation of a minimum of 25 million reads per sample. DNA libraries prepared for sequencing on a Illumina HiSeq 2500 were processed identically for quality control. After equimolar pooling of the individual samples, a 10 pM library with 5% PhiX control spike-in was sequenced on a Illumina HiSeq 2500 instrument as a 1 x 50 bp single-end sequencing run (25 million reads per sample) in rapid run mode (v.2). Clustering and sequencing performance were controlled as previously described (Sweeney M.A. et al., Sci. Rep, 2020, PMID 32811853). Libraries were sequenced on the Genome Analyzer following Illumina's protocols for ChIP-seq with HiSeq 2500 or NextSeq 500.

treatment_protocol: Treatment was performed with the proteasome inhibitors lactacystin (6µM; Cayman Chemical, # 70980), bortezomib (60 nM; Selleckchem, # PS-341), carfilzomib (60 nM; Selleckchem, # PR-171), or 0.1% (v/v) DMSO (mock) for three hours. For each treatment, cells were incubated in 75cm2 flasks with an average of 50 million cells per flask.

value: Siah2 overexpressing cells

value: B lymphoblast

tag: disease

value: IgA lambda myeloma

tag: gender

value: Female

tag: molecule subtype

value: ChIP DNA


title: H3K4me3-Lactacystin

description: CT 2571

value: Lactacystin (25 µM)

value: Parental cells


title: H3K27ac-Control cells

description: CT 10363

value: Control cells for Siah2 overexpression


title: BIV infection Replicate 2_dye_swap

type: RNA

city: Pulawy

first: Magdalena

last: Materniak-Kornas

address: Partyzantow 57

department: Biochemistry

country: Poland

institute: National Veterinary Research Institute

description: Biological replicate 2_dye_swap/ Technical replicate 1

hyb_protocol: The dye assigned to the control and treated samples was reversed for the other four arrays (dye swap). After labeling and volume reduction the sample from uninfected BoMac cell was combined with sample from BoMac/BIV cell and diluted in 120µl of SlideHyb glass array Hybridization buffer 1 (Ambion) and incubated at 70oC from 5 min. Following this step hybridization was carried out using HybArray12 (Perkin Elmer) under following steps: O-ring conditioning at 75oC for 2 min; probe introduction at 75oC, step down hybridization of 42oC for 6h, 35oC for 6h, 30oC for 6h, followed by washing steps ( 5X w 2XSSC/0.1%SDS, 37oC, 5X 0.2XSSC/0.1%SDS, 25oC, 5X 0.2XSSC, 25oC) at 37oC, 25oC and 25oC, respectively

scan_protocol: ScannerModel: ProScanArray Serial No.: 61456 Images were quantified using ScanArray Express,

data_processing: ScanArray Express was used for background subtraction and LOWESS normalization.

label: Alexa 647

organism: Bos taurus

source_name: BoMac

label_protocol: Superscript Indirect cDNA Labeling System, Invitrogen_  Alexa 555 and Alexa 647 dye

growth_protocol: The BoMac cells were maintained in RPMI1640 medium supplemented with 7 % FCS and 1x antibiotic antimycotic solution (Sigma).

extract_protocol: total RNA extraction using RNeasy MiniKit (Qiagen)

treatment_protocol: 24 hours before infection the cells were seeded into P6 plate at 1.5 x 10^6 cells/well and infected next day, by incubating cells with the BIV containing supernatant at MOI 10 for 18 hours at 370C with 5% CO2. Simultaneously uninfected BoMac cultures were incubated in virus-free media in similar manner (uninfected control)

value: bovine macrophages cell line

tag: infection stage

value: uninfected control

label: Alexa 555

source_name: BoMac/BIV FL112

value: BIV infected


title: RNA-seq_Lactacystin #1

data_processing:
Sequence reads were obtained from the Illumina Genome Analyzer Pipeline using the Baylor College of Medicine Genomic and RNA Profiling Core server.
RNA-seq fastq files were processed with Cutadapt ver.1.12 in order to trim for adaptor sequences then sequence reads were mapped to the human reference genome hg19 using TopHat2/Bowtie2 ver.2.1.0 with default parameters.
Gene expression changes were quantified with Cufflinks and Cuffdiff ver.2.1.1.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample and log2 (fold change Treated vs Control) values.

extract_protocol:
Total RNAs were extracted with Qiagen RNeasy Mini kit (Cat. #74106) following vendor's protocol. An additional step of on column DNase I digestion was performed during RNA extraction in order to eliminate potential traces of genomic DNA (RNase-Free DNase Set, Qiagen, Cat. #79254).
Kapa Biosystems Stranded RNA-seq Kit with RiboErase (HMR) (Cat. # KK8483) was used with 1 ug of total RNA for the construction of sequencing libraries according to recommended protocol. ERCC RNA Spike-In control Mix 1 (Life Technologies, Cat. #4456740) has been included during library prep to assess platform dynamic range and lower limit of detection. Desired library insert size was 200 bp. The size distribution of the final libraries were confirmed by electrophoretic analysis on an Agilent Bioanalyzer 2100 prior to sequencing. Libraries were sequenced on the Illumina Genome Analyzer following the manufacturer's protocols for RNA-seq with HiSeq2500 in Rapid Run Mode using the HiSeq Rapid SBS v2 flow cell.

treatment_protocol: Treatment was performed with 6 µM of the proteasome inhibitor lactacystin (Cayman Chemical, # 70980) or 0.1% (v/v) DMSO (mock) for six hours. For each condition, cells were treated in 25cm2 flasks with an average of 3-4 million cells per flask.

value: Lactacystin (6 uM)


title: H3K4me1-DMSO

description: CT 2565


title: H3K4me1-Lactacystin

description: CT 2570


title: H3K4me3-DMSO

description: CT 2566


title: H3K27ac-DMSO (Control for Lactacystin)

description: CT 2734


title: RNA-seq_Lactacystin #2


title: BIV infection Replicate 1_dye_swap (technical repeat)

description: Biological replicate 1_dye_swap/ Technical replicate 2


title: RNA-seq_Control for Lactacystin #2


title: BIV infection Replicate 1

description: Biological replicate 1/ Technical replicate1


title: BIV infection Replicate 1_dye_swap

description: Biological replicate 1_dye_swap/ Technical replicate1


title: RNA-seq_Control for Lactacystin #1


title: BIV infection Replicate 2 (technical repeat)

description: Biological replicate 2 /Technical replicte 2


title: H3K27ac-Lactacystin

description: CT 2739


title: Sample 24 Liver FFPE biopsy

city: Copenhagen

first: Kasper

middle: Thystrup

last: Karstensen

address: A. C. Meyers Vænge 15

country: Denmark

institute: Aalborg University

data_processing:
STAR aligner (v. 2.5.0a) was used for raw read mapping and gene quantification, using the Ensembl release 92 of Homo sapiens as reference genome and for gene modelling.
To account for fragment amplification during library preparation mean gene count values were assessed across each disease group. Genes with a minimum mean count of 5 in 70% of the samples in one or more disease groups, were included for further analysis.
The DESeq2 package (v. 1.24.0) was used for count normalization and differential expression analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw gene count matrix

source_name: Liver FFPE biopsy

extract_protocol:
Total RNA from liver biopsies was purified using RNeasy FFPE Kit (Qiagen) according to the manufacturer’s instructions, and RNA quality was assessed using the Experion automated electrophoresis system (BioRad).
Total RNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (Illumina). The input for each sample was 100ng total RNA, except for sample 22 and 23 where 50ng were used. RNAseq was performed on …Ω using a HiSeq SBS Kit v4 250 cycle (2x125 bp paired end sequencing), providing un-stranded paired-end raw reads in FASTQ format.

tag: diagnosis

value: Normal

value: Liver


title: BIV infection Replicate 2

description: Biological replicate 2/ Technical replicate 1


title: Sample 23 Liver FFPE biopsy

tag: tissue


title: Sample 22 Liver FFPE biopsy


title: Sample 20 Liver FFPE biopsy


title: Sample 21 Liver FFPE biopsy


title: BIV infection Replicate 1 (technical repeat)

description: Biological replicate 1/ Technical replicate 2


title: LN-tet-AR, doxycycline, DHT0.1nM, ChIP-AR

value: LNCaP-tet-AR

value: Prostate Cancer Cell Line (generated from LNCaP)

value: 0.25 ug/ml doxycycline 0.1 nM DHT


title: control_library2, scRNA-seq

value: colon

value: control


title: Sample 18 Liver FFPE biopsy


title: Sample 16 Liver FFPE biopsy


title: Sample 15 Liver FFPE biopsy


title: Sample 12 Liver FFPE biopsy


title: Sample 11 Liver FFPE biopsy


title: Sample 9 Liver FFPE biopsy


title: Sample 10 Liver FFPE biopsy


title: Sample 3 Liver FFPE biopsy


title: Sample 2 Liver FFPE biopsy


title: Sample 5 Liver FFPE biopsy


title: Sample 14 Liver FFPE biopsy


title: Ascl1_Tip60_tauPos_day5_rep1

data_processing:
Library strategy: Cut&Tag
Reads were trimmed using cutadapt and aligned with Bowtie2 (v 2.3.5.1) to mm10 reference genome.
Peaks were called using MACS2. Reproducible peaks for each condition were identified using IDR (idr≤0.1) or by overlap thresholding (for histone Cut&Tag). Reproducible peaks were aggregated, read counts for each region were obtained using featureCounts package followed by normalization and differential accessibility analysis using DESeq2.
Bigwig files were produced with deepTools (Ramirez et al., 2014).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file containing normalized read counts as determined for the aggregated peak set; tar containing normalized average signal files

source_name: Ascl1_Tip60_tauPos day5

value: E13.5 fibroblast

tag: time post-induction

tag: antibody


title: Sample 8 Liver FFPE biopsy


title: Sample 13 Liver FFPE biopsy


title: Sample 4 Liver FFPE biopsy


title: Sample 6 Liver FFPE biopsy


title: MEF+shTip60#2_day7_rep1

data_processing:
Raw reads were trimmed for base call quality (PHRED score ≥ 21) using skewer 0.2.2 (Jiang et al., 2014).
Transcript quantification was performed using mm10 reference transcriptome and salmon 1.4.0 (Patro et al., 2017).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tsv files containig TPM values

source_name: MEF+shTip60#2 day7

extract_protocol:
RNA was harvested using Trizol.
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit or TruSeq mRNA Library Prep Kit, following standard protocols.

tag: time post-infection

value: 7 days

tag: time post-dox


title: Sample 19 Liver FFPE biopsy


title: ANFX8549

city: Ljubljana

first: Ales

last: Maver

address: Slajmerjeva 3

country: Slovenia

institute: Clinical institute of medical genetics Ljubljana Slovenia

data_processing:
Demultiplexing and adaptor trimming was performed using the Illumina BCL2Fastq software
Alignments to the human reference genome (hg19) were performed  using bowtie and tophat algorithms
Transcript abundances were then estimated using read counts function in Subread package for R, followed by intersample normalization by variance modelling at the observational level (voom) approach implemented in limma Bioconductor package.
Differences in gene expression were estimated using linear modelling and significance estimation procedures in limma.
Assembly: hg19, mm10

source_name: Peripheral blood

extract_protocol:
Whole blood samples were collected into Tempus™ Blood RNA tubes (Thermo Fisher Scientific, Waltham, MA, USA) or PAXgene blood tubes (Qiagen, Hilden, Germany) containing RNA stabilizing reagent. Total RNA was isolated using QuickGene blood cell kit (RB-S) and Fujifilm QuickGene-810 automated system (Fujifilm Life Sciences, Tokyo, Japan) or PAXgene Blood miRNA Kit and fully automated QIAcube system (Qiagen), according to manufacturer’s isolation protocol. The purity of isolated RNA was assessed using the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific) and integrity was determined on Agilent 2100 Bioan+alyzer using RNA 6000 Nano LabChip kit (Agilent Technologies, Santa Clara, CA, USA). All samples used for library preparation had RNA integrity values greater than 7.0. Extracted RNA samples were stored at -80ºC before further processing.
We performed library preparation using the TrueSeq stranded total RNA sample preparation kit (Illumina, San Diego, CA, USA), according to the manufacturer’s protocol. After Ribo-Zero rRNA depletion, the remaining RNA was purified, fragmented, and primed for first strand cDNA synthesis with reverse transcriptase (SuperScript II) and random primers, followed by second strand cDNA synthesis performed in the presence of dUTP. Blunt ended double strand DNA was 3’ adenylated and multiple indexing adapters (T-tailed) were ligated to the ends of the ds cDNA. Fragments with adapter molecules on both ends were selectively enriched with 15 cycles of PCR reaction. 44 libraries were normalized to the final concentration of 10 nM and then pooled in equimolar concentrations. Sequencing was performed on the Illumina Hiseq 2000 sequencing system in 2×100 sequencing cycles using pair-end sequencing mode.

value: Peripheral blood

tag: anaphylaxis stage/severity

value: allergic/no anaphylaxis

tag: individual


title: Hi-C in E13.5 XY supporting cells rep1

first: Irene

last: Mota-Gomez

address: Hannoversche strasse 28

institute: Max Delbruck Center

data_processing:
Base calling with standard Illumina Software.
Paired-end reads from all Hi-C experiments were aligned to mm10 genome, processed and filtered using Juicer (Durand et al. 2016) using standard parameters in order to construct Knight-Ruiz (KR) normalized Hi-C matrices.
For each pair of fastq files, juicer was run individually and then merged with the mega.sh function in order to generate one replicate.
Assembly: mm10 assembly
Supplementary files format and content: Multiresolution hic files.

source_name: E13.5 XY supporting cells

growth_protocol: Gonads were dissected from E10.5 or E13.5 embryos in 1XPBS, and the mesonephros was removed using syringe tips.

extract_protocol:
Fixed nuclei were extracted adding ice-cold custom-made lysis buffer containing the following components: 50mM Tris HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1.15% Triton X-100, 25X Protease Inhibitor in MilliQ water. Extracted nuclei were then collected, snap frozen and stored at -80 °C or further processed with the following steps: digestion with Mbo I RE, re-ligation of the digested fragments, de-crosslinking and DNA purification.
The Hi-C library was sheared using Covaris sonicator and the following parameters: 2 cycles, each 50’’, 10% duty, 4 intensity, 200 cycles/burst, temperature: 4°C. Sheared sample was then treated following the NEBNext Ultra DNA Library Prep kit for Illumina guidelines (end repair, dA-tailing, adaptor ligation, PCR enrichment of Adaptor ligated DNA, DNA purification).

treatment_protocol: Embryonic tissue was resuspended in Trypsin, dissociated to make a single-cell-suspension using a cell-strainer and finally pelleted. Tissue pellet was then fixed in a 2% PFA/FCS/PBS solution by incubation at room temperature for 10 minutes while tumbling. To stop the fixation process, the sample was quenched on ice and 1.425M Glycine was added.

tag: developmental stage

value: Gonad


title: Hi-C in E13.5 XY supporting cells rep2


title: Hi-C in E10.5 XY supporting cells rep1

source_name: E10.5 XY supporting cells

value: Sf1-eGFP (Nr5a1-eGFP)


title: ANFX8602

value: severe anaphylaxis


title: Sample 17 Liver FFPE biopsy


title: ANFX8616


title: ANFX8839


title: Sample 7 Liver FFPE biopsy


title: ANFX8617


title: ANFX8615

value: mild to moderate anaphylaxis


title: Sample 1 Liver FFPE biopsy


title: ANFX8548


title: ANFX8255


title: ANFX8298


title: ANFX8254


title: ANFX8597


title: ANFX8297


title: ANFX8835


title: ANFX8380


title: ANFX8370


title: ANFX8375


title: Hi-C in E10.5 XX supporting cells rep1

source_name: E10.5 XX supporting cells


title: ANFX8373


title: ANFX8300


title: ANFX8251


title: ANFX7623


title: BIV infection Replicate 2_dye_swap (technical repeat)

description: Biological replicate 2_dye_swap /Technical replicte 2

value: bovine macrophages cell line

value: uninfected control

value: BIV infected


title: ANFX7583


title: i729_i518

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: Mouse hypothalamus Rxfp4-EYFP, sample 381

data_processing:
Sequenced reads were trimmed for adapter sequence using cutadapt, mapped to the primary mouse genome (GRCm38) using STAR, and raw counts generated with featureCounts.
Gene expression modelling and normalised counts per million were generated using Seurat (v4.0.2).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes raw count values for all samples.

source_name: Hypothalamus

extract_protocol:
Cells were sorted directly into individual wells of 96-well plates containing lysis buffer using an Influx Cell Sorter, sorting for EYFP-positive and DraQ5-negative. 384 YFP-positive cells were isolated and processed using a Smart-Seq2 protocol.
The library was constructed using the Nextera XT DNA preparation kit and Nextera XT 96-Index kit.

treatment_protocol: Mice were sacrificed by cervical dislocation and the hypothalamus dissected into Hibernate-A medium supplemented with 0.25% GlutaMAX and 2% B27. Tissue digested in Hibernate-A medium without calcium containing 20 U/mL Papain and 1% GlutaMAX for 30 min at 37oC under agitation (Thermomixer, 500 rpm). After digestion, tissue was triturated in Hibernate-A medium with 3.5 U/mL DNase I. The trituration supernatant was loaded on a BSA gradient prepared in Hibernate-A medium, spun for 5 min at 300 rcf, and the pellet resuspended in Hibernate-A medium + 1% BSA. The cell suspension was filtered through a 70 µm cell strainer into a fresh tube.

value: Hypothalamus

tag: expression


title: i729_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 384


title: i729_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 383


title: i729_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 379


title: i729_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 382


title: ANFX8550


title: ANFX8614


title: i729_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 376


title: i729_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 377


title: i729_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 375


title: i729_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 374


title: i729_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 373


title: i729_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 372


title: i729_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 371


title: i728_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 368


title: i729_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 369


title: i729_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 370


title: i728_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 367


title: i728_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 363


title: i728_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 365


title: i728_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 359


title: i728_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 362


title: i728_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 361


title: i728_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 357


title: i728_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 360


title: i728_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 364


title: i728_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 358


title: i729_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 380


title: i729_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 378


title: i728_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 353


title: i728_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 355


title: i728_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 356


title: i727_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 350


title: i728_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 354


title: i727_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 351


title: i727_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 352


title: i728_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 366


title: i727_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 349


title: i727_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 348


title: i727_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 345


title: i727_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 347


title: i727_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 344


title: i727_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 346


title: i727_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 342


title: i727_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 339


title: i727_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 340


title: i727_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 338


title: i727_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 343


title: i726_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 336


title: i727_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 341


title: i727_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 337


title: i726_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 333


title: i726_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 330


title: i726_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 332


title: i726_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 331


title: i726_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 334


title: i726_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 335


title: i726_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 329


title: i726_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 328


title: i726_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 327


title: i726_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 326


title: vtc4∆ 3

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

source_name: cultures

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

tag: lab strain number

tag: genotype/variation

value: h- vtc4[delta]::kanMX

value: vegetative growth


title: WT 3

value: h-


title: vtc4∆ 1


title: vtc4∆ 2


title: i726_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 325


title: i726_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 323


title: WT 2


title: i726_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 324


title: i726_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 322


title: Lung, Delta_Post-vac, rep6

city: Silver Spring

first: Hang

last: Xie

state: Maryland

address: 10993 New Hampshire Ave WO 52/72 Rm 1324

institute: US Food and Drug Administration, Center for Biologics Evaluation and Research

description:
Test group 6
SAMPLE 39

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://dataanalysis.qiagen.com/pcr/arrayanalysis.php?wuid=b4d56157-c14b-4fd9-a99c-8ddecd502e64&logindata=&customerdata=&customeremail=&platform=catalogArray&format=X
Normalization was performed using GUSB as the internal housekeeping gene.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping gene).
Fold Change worksheet reports test/control (i.e., NY/Naive) ratios.

label: SYBR Green

source_name: Lung

label_protocol: Reverse transcription was performed using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific). Quantitative real-time PCR were performed in Stratagene MX3000p using RT² Profiler™ PCR Array Mouse Hypoxia Signaling Pathway kit (QIAgen) following the Manufacturer’s instructions. The cycling conditions are: hold for 10 min at 95°C, followed by 40 cycles of 15 s at 95°C and 60 s at 60°C.

extract_protocol: Total RNA was extracted using QIAgen RNeasy Plus Mini Kit

value: Whole lung homogenate

tag: genotype

value: K18-hACE2 transgenic

tag: infection

tag: activation agent

value: Post-vac sera transfer with Delta challenge

tag: time

value: dpi 5 after Delta challenge

tag: group

value: Test group 6


title: i726_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 321


title: Lung, Delta_Post-vac, rep5

description:
Test group 6
SAMPLE 38


title: i724_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 319


title: Lung, Delta_Post-vac, rep4

description:
Test group 6
SAMPLE 37


title: i724_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 318


title: Lung, Delta_Post-vac, rep3

description:
Test group 6
SAMPLE 36


title: Lung, Delta_Post-vac, rep2

description:
Test group 6
SAMPLE 35


title: i724_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 317


title: Lung, Delta_Post-vac, rep1

description:
Test group 6
SAMPLE 34


title: i724_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 315


title: i724_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 314


title: Lung, Kappa_Post-vac, rep6

description:
Test group 5
SAMPLE 33

value: Post-vac sera transfer with Kappa challenge

value: dpi 5 after Kappa challenge

value: Test group 5


title: Lung, Kappa_Post-vac, rep4

description:
Test group 5
SAMPLE 31


title: Lung, Kappa_Post-vac, rep5

description:
Test group 5
SAMPLE 32


title: i724_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 316


title: i724_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 313


title: i724_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 312


title: Lung, Kappa_Post-vac, rep1

description:
Test group 5
SAMPLE 28


title: Lung, NY_Post-vac, rep6

description:
Test group 4
SAMPLE 27

value: Post-vac sera transfer with NY challenge

value: dpi 5 after NY challenge

value: Test group 4


title: Lung, Kappa_Post-vac, rep3

description:
Test group 5
SAMPLE 30


title: i724_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 311


title: i724_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 310


title: Lung, Kappa_Post-vac, rep2

description:
Test group 5
SAMPLE 29


title: WT 1


title: i724_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 309


title: i724_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 308


title: i724_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 320


title: Lung, NY_Post-vac, rep5

description:
Test group 4
SAMPLE 26


title: Lung, NY_Post-vac, rep4

description:
Test group 4
SAMPLE 25


title: Lung, NY_Post-vac, rep3

description:
Test group 4
SAMPLE 24


title: i724_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 307


title: i724_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 306


title: Lung, NY_Post-vac, rep1

description:
Test group 4
SAMPLE 22


title: Lung, Delta_Mock, rep6

description:
Test group 3
SAMPLE 21

value: Mock transfer with Delta challenge

value: Test group 3


title: i723_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 304

value: Hypothalamus


title: i724_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 305


title: Lung, Delta_Mock, rep4

description:
Test group 3
SAMPLE 19


title: Lung, NY_Post-vac, rep2

description:
Test group 4
SAMPLE 23


title: Lung, Delta_Mock, rep5

description:
Test group 3
SAMPLE 20


title: i723_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 303


title: i723_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 301


title: i723_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 300


title: Lung, Delta_Mock, rep3

description:
Test group 3
SAMPLE 18


title: Lung, Kappa_Mock, rep6

description:
Test group 2
SAMPLE 15

value: Mock transfer with Kappa challenge

value: Test group 2


title: Lung, Delta_Mock, rep1

description:
Test group 3
SAMPLE 16


title: i723_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 299


title: i723_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 298


title: i723_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 297


title: Lung, Delta_Mock, rep2

description:
Test group 3
SAMPLE 17


title: i723_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 295


title: Lung, Kappa_Mock, rep5

description:
Test group 2
SAMPLE 14


title: i723_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 292


title: i723_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 296


title: Lung, Kappa_Mock, rep3

description:
Test group 2
SAMPLE 12


title: i723_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 294


title: Lung, Kappa_Mock, rep2

description:
Test group 2
SAMPLE 11


title: Lung, Kappa_Mock, rep1

description:
Test group 2
SAMPLE 10


title: i723_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 293


title: i723_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 302


title: i723_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 291


title: i723_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 290


title: Lung, NY_Mock, rep4

description:
Test group 1
SAMPLE 7

value: Mock transfer with NY challenge

value: Test group 1


title: Lung, NY_Mock, rep3

description:
Test group 1
SAMPLE 6

value: Whole lung homogenate

value: K18-hACE2 transgenic


title: i722_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 288


title: Lung, NY_Mock, rep2

description:
Test group 1
SAMPLE 5


title: Lung, NY_Mock, rep1

description:
Test group 1
SAMPLE 4


title: Lung, Kappa_Mock, rep4

description:
Test group 2
SAMPLE 13


title: Lung, Naive, rep2

description:
Control
SAMPLE 2

value: control

value: naïve

value: no infection

value: Control


title: i722_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 286


title: i722_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 284


title: Lung, Naive, rep3

description:
Control
SAMPLE 3


title: Lung, Naive, rep1

description:
Control
SAMPLE 1


title: i722_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 285


title: i722_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 282


title: i722_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 283


title: Lung, NY_Mock, rep6

description:
Test group 1
SAMPLE 9


title: i722_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 281


title: D-18-m-Endo-1

city: Hamburg

first: Tianran

last: Zhang

address: Falkenried 94

institute: University Medical Center Hamburg-Eppendorf

data_processing:
The quality of the bulk RNA-seq reads was assessed using FastQC (v0.11.5).
The reads were aligned to the mouse reference genome (mm10) with Bowtie2 (v2.3.3.1) using RSEM (v1.3.0) with the default parameters.  The function rsem-calculate-expression was used to align the reads and quantify the gene and isoform abundance.
Assembly: mm10
Supplementary files format and content: plain file including read count and transcripts per million (TPM) value

source_name: Glomerular endothelial cells

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 148ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.

tag: cell type

value: Glomerular endothelial cells

value: BTBR ob/ob

tag: treatment

value: BTBR ob/ob (DN)

value: 18 weeks

tag: Sex

value: male


title: i722_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 280

tag: tissue


title: D-18-m-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 151ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: Lung, NY_Mock, rep5

description:
Test group 1
SAMPLE 8

value: dpi 5 after NY challenge


title: D-18-m-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 149ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-18-f-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 147ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.

value: female


title: i722_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 279

value: Hypothalamus


title: D-18-f-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 145ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-18-f-Endo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 144ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i722_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 276


title: i722_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 287


title: i723_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 289


title: i722_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 275


title: C-18-m-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 143ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.

value: BTBR +/+

value: BTBR WT (control)


title: i722_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 274


title: C-18-m-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 141ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-18-m-Endo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 142ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i722_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 273


title: C-18-m-Endo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 140ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-18-f-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 139ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i721_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 272


title: C-18-f-Endo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 138ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i721_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 269


title: C-18-f-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 137ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i721_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 270


title: i722_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 278


title: D-18-m-Podo-2

source_name: Podocytes

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 133ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.

value: Podocytes


title: i722_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 277

extract_protocol:
Cells were sorted directly into individual wells of 96-well plates containing lysis buffer using an Influx Cell Sorter, sorting for EYFP-positive and DraQ5-negative. 384 YFP-positive cells were isolated and processed using a Smart-Seq2 protocol.
The library was constructed using the Nextera XT DNA preparation kit and Nextera XT 96-Index kit.


title: i721_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 266


title: i721_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 267


title: i721_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 265


title: D-18-m-Podo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 132ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-18-f-Endo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 146ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i721_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 268


title: D-18-f-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 130ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i721_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 263


title: i721_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 264


title: D-18-m-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 135ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-18-f-Podo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 128ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i721_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 262


title: C-18-m-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 127ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-18-m-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 126ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i721_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 260


title: D-18-f-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 131ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-18-m-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 125ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i721_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 271


title: i721_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 259


title: C-18-m-Podo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 124ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i721_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 258


title: i720_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 256


title: i721_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 257


title: C-18-f-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 123ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-18-f-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 122ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-18-f-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 121ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 255


title: D-18-m-Mesa-4

source_name: Mesangail cells

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 119ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.

value: Mesangail cells


title: D-18-f-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 129ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-18-m-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 116ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 253

extract_protocol:
Cells were sorted directly into individual wells of 96-well plates containing lysis buffer using an Influx Cell Sorter, sorting for EYFP-positive and DraQ5-negative. 384 YFP-positive cells were isolated and processed using a Smart-Seq2 protocol.
The library was constructed using the Nextera XT DNA preparation kit and Nextera XT 96-Index kit.


title: i720_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 252


title: D-18-m-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 117ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-18-f-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 115ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 254


title: i720_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 251


title: i721_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 261


title: D-18-f-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 113ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 250


title: D-18-f-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 112ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 249


title: D-18-f-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 114ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 247


title: C-18-m-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 110ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-18-m-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 111ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 246


title: C-18-m-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 109ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 244


title: i720_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 245


title: C-18-m-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 108ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 243


title: C-18-f-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 107ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-18-f-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 106ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-18-f-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 105ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 241


title: D-12-m-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 103ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.

value: 12 weeks


title: D-12-m-Endo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 102ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i719_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 239


title: i719_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 240


title: D-12-m-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 101ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i720_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 248


title: D-12-f-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 99ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-12-m-Endo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i719_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 238

extract_protocol:
Cells were sorted directly into individual wells of 96-well plates containing lysis buffer using an Influx Cell Sorter, sorting for EYFP-positive and DraQ5-negative. 384 YFP-positive cells were isolated and processed using a Smart-Seq2 protocol.
The library was constructed using the Nextera XT DNA preparation kit and Nextera XT 96-Index kit.


title: D-12-f-Endo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 98ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-12-f-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 97ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-12-f-Endo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 96ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i719_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 236


title: i719_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 235


title: C-12-m-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 95ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i719_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 232


title: i719_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 234


title: i719_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 231


title: i720_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 242


title: C-12-m-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 93ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-12-m-Endo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 94ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i719_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 230


title: C-12-m-Endo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 92ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i719_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 229


title: i719_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 228


title: C-12-f-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 91ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-12-f-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 89ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i719_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 237


title: C-12-f-Endo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 90ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-12-f-Endo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 88ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i719_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 226


title: i719_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 227


title: i719_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 225


title: D-12-m-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 86ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-12-m-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 85ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i719_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 233


title: D-12-m-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 87ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i718_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 224


title: D-12-m-Podo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 84ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i718_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 221


title: D-12-f-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 83ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i718_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 222

extract_protocol:
Cells were sorted directly into individual wells of 96-well plates containing lysis buffer using an Influx Cell Sorter, sorting for EYFP-positive and DraQ5-negative. 384 YFP-positive cells were isolated and processed using a Smart-Seq2 protocol.
The library was constructed using the Nextera XT DNA preparation kit and Nextera XT 96-Index kit.


title: D-12-f-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 82ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i718_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 219


title: D-12-f-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 81ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i718_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 220


title: i718_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 218


title: i718_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 217


title: D-12-f-Podo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 80ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-12-m-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 78ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-12-m-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 79ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i718_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 215


title: i718_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 214


title: C-12-m-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 77ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: C-12-m-Podo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 76ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i718_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 213


title: C-12-f-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 75ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i718_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 223


title: C-12-f-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 74ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i718_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 212


title: i718_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 210


title: C-12-f-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 73ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i716_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 208


title: i718_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 209


title: i716_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 207


title: D-12-m-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 68ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-12-m-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 67ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i718_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 216


title: D-12-f-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 65ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: D-12-m-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 70ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i716_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 205


title: D-12-f-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 63ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacturer's protocols.


title: i716_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 203


title: i716_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 202