title: D-12-f-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 64ng 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_i513

status: Public on Nov 21 2022

type: SRA

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 201

library_source: transcriptomic

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.

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: Hypothalamus

tag: expression


title: i718_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 211


title: i716_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 199


title: C-12-m-Mesa-2

city: Hamburg

first: Tianran

last: Zhang

address: Falkenried 94

country: Germany

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: Mesangail cells

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 59ng 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: Mesangail cells

tag: genotype

value: BTBR +/+

tag: treatment

value: BTBR WT (control)

tag: time

value: 12 weeks

tag: Sex

value: male


title: i716_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 198


title: C-12-m-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 60ng 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-Podo-1

source_name: Podocytes

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 72ng 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

value: female


title: i716_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 197


title: D-12-m-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 69ng 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 ob/ob

value: BTBR ob/ob (DN)


title: i716_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 206


title: C-12-m-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 58ng 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-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 57ng 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-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 56ng 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_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 196


title: C-12-f-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 55ng 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_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 195


title: i716_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 204


title: i716_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 193


title: D-12-f-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 62ng 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-06-m-Endo-3

source_name: Glomerular endothelial cells

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 52ng 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: Glomerular endothelial cells

value: 6 weeks


title: i715_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 191


title: C-12-f-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 54ng 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-06-m-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 53ng 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_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 194


title: D-06-m-Endo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 50ng 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: i715_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 192


title: i716_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 200


title: i715_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 189


title: D-06-f-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 49ng 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-06-m-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 51ng 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: i715_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 190


title: D-06-f-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 47ng 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-06-f-Endo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 46ng 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-06-f-Endo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 48ng 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: i715_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 186

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: i715_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 188


title: i715_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 187


title: i715_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 184


title: C-06-m-Endo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 44ng 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-06-m-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 45ng 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-06-m-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 43ng 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: i715_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 182


title: i715_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 179


title: C-06-f-Endo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 41ng 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: i715_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 178


title: i715_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 180


title: C-06-m-Endo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 42ng 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: i715_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 181


title: i715_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 185


title: C-06-f-Endo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 38ng 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: i715_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 177


title: C-06-f-Endo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 40ng 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-06-m-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 37ng 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-06-m-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 36ng 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: i714_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 176


title: i714_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 175


title: D-06-m-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 35ng 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: i714_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 174


title: i714_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 173


title: D-06-f-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 32ng 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-06-f-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 33ng 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-06-f-Endo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 39ng 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-06-m-Podo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 34ng 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: i714_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 172


title: i714_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 171


title: D-06-f-Podo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 30ng 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-06-f-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 31ng 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-06-m-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 28ng 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: i714_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 168

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: i714_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 170


title: C-06-m-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 29ng 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: i714_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 166


title: i714_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 164


title: C-06-m-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 27ng 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: i714_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 165


title: i714_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 169


title: C-06-f-Podo-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 24ng 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: i714_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 163


title: C-06-f-Podo-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 25ng 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-06-m-Podo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 26ng 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-06-f-Podo-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 22ng 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-06-f-Podo-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 23ng 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: LN-tet-AR cells,doxycyline, DHT 10nM, repeat 3

city: Boston

first: Maryam

last: Labaf

state: MA

address: 100 William T Morrissey Blvd

department: Biology

country: USA

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 Ensembl, GRCh37 using STAR (v2.5.3a)
Gene level read counts was produced by featureCounts from Subread (v1.6.2) package
Assembly: Ensembl GRCH37
Supplementary files format and content: tab-deliminated text files include raw gene counts

organism: Homo sapiens

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:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
TruSeq® Strnd Total RNA LT (Illumina) was used for RNA-Seq library construction.

treatment_protocol: LN-tet-AR cells were grown in 5% CSS and treated with or without 0.25 ug/ml doxycycline for 2 days and stimulated with or without 0.1 nM DHT or 10 nM DHT for 24 hours before collection.

tag: cell line

value: LNCaP-tet-AR

value: prostate cancer cell line (generated from LNCaP)

value: 0.25 ug/ml doxycycline 10 nM DHT


title: D-06-m-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 20ng 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: i714_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 162


title: D-06-m-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 19ng 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: i712_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 160


title: LN-tet-AR cells,doxycyline, DHT 10nM, repeat 2


title: LN-tet-AR cells,doxycyline, DHT 10nM, repeat 1


title: i712_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 159


title: D-06-m-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 17ng 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-06-f-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 15ng 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-06-m-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 18ng 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: i712_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 158


title: LN-tet-AR cells,doxycyline, DHT 0.1nM, repeat 3

value: 0.25 ug/ml doxycycline 0.1 nM DHT


title: LN-tet-AR cells,doxycyline, DHT 0.1nM, repeat 2


title: D-06-f-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 13ng 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: i712_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 157


title: LN-tet-AR cells,doxycyline, DHT 0.1nM, repeat 1


title: D-06-f-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 14ng 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-06-m-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 10ng 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-06-f-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 12ng 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-06-m-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 8ng 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-06-m-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 9ng 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: i712_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 156

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: C-06-m-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 7ng 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: LN-tet-AR cells,doxycyline, repeat 3

value: 0.25 ug/ml doxycycline


title: i714_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 161

value: Hypothalamus


title: C-06-f-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 5ng 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: i712_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 155


title: C-06-f-Mesa-3

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 4ng 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 +/+


title: LN-tet-AR cells,doxycyline, repeat 2


title: i712_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 154


title: C-06-f-Mesa-1

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 2ng 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 WT (control)


title: C-06-f-Mesa-2

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 3ng 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: LN-tet-AR cells,doxycyline, repeat 1

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
TruSeq® Strnd Total RNA LT (Illumina) was used for RNA-Seq library construction.


title: i712_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 153


title: LN-tet-AR cells, DHT 10nM, repeat 3

value: 10 nM DHT


title: FUS-ERG Ba/F3 AzaR3-1

city: Otsu

first: Ai

last: Asai

state: Shiga

address: setatsukinowacho

department: hematology

country: Japan

institute: Shiga university of medical science JAPAN

description:
Expression_Profile.mm10.gene.txt
Novel_splicing_variant_list.txt

data_processing:
Analyze the quality control of the sequenced raw reads. Overall readsꆯ quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.Transcript is assembled by StringTie with aligned reads. This process provides information of known transcripts, novel transcripts, and alternative splicing transcripts.
Expression profiles are represented as read count and normalization values which are calculated based on transcript length and depth of coverage. Normalization values are provided as FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) / RPKM (Reads Per Kilobase of transcript per Million mapped reads) and TPM(Transcripts Per Kilobase Million).
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
Assembly: mm10
Supplementary files format and content: Text files include FPKM and TPM values for each Sample

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, Hilden, Germany).14-23 ug of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA) was used to prepare libraries.

value: pro B cells

value: FUS-ERG

value: After 3rd  Azacitidine


title: FUS-ERG Ba/F3 AzaR3-2


title: i712_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 152


title: empty Ba/F3 AzaR3-1

value: empty

value: After 3rd Azacitidine


title: empty Ba/F3 AzaR3-2


title: LN-tet-AR cells, DHT 10nM, repeat 1


title: i712_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 150


title: i712_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 149


title: LN-tet-AR cells, DHT 0.1nM, repeat 3

value: 0.1 nM DHT


title: Non-infarcted regions of the left ventricle from mice with experimental MI treated with liraglutide, biol rep 2

city: Toronto

first: Chi Kin

last: Wong

address: 600 University Avenue

country: Canada

institute: LTRI

data_processing:
Sequence alignment was performed in STAR-2.7.9a with default parameters
A count table was compiled and subject to differential analysis in DESeq2
Assembly: mm10
Supplementary files format and content: A count table stored in count_table.csv

molecule: polyA RNA

source_name: Left ventricle

extract_protocol:
RNA was prepared by homogenizing tissues in TRIzol followed by standard ethanol precipitation.
Sequencing libraries were constructed using TruSeq stranded mRNA library preparation kit per manufacturer's instructions.

treatment_protocol: Male C57BL/6J mice were subjected to ligation of the left anterior descending (LAD) coronary artery to induce myocardial infarction. Sham-operated mice underwent the same procedure by moving the suture underneath the LAD coronary artery but without tying off the vessel. The atria, infarcted left ventricle, and non infarcted left ventricle were isolated 3 days post-MI for RNA extraction.

value: Left ventricle

value: male

value: Liraglutide


title: Non-infarcted regions of the left ventricle from mice with experimental MI treated with liraglutide, biol rep 3


title: Non-infarcted regions of the left ventricle from mice with experimental MI treated with liraglutide, biol rep 1


title: Non-infarcted regions of the left ventricle from mice with experimental MI treated with PBS, biol rep 1

value: PBS


title: Non-infarcted regions of the left ventricle from mice with experimental MI treated with PBS, biol rep 2


title: Non-infarcted regions of the left ventricle from mice with experimental MI treated with PBS, biol rep 3


title: i712_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 148


title: Infarcted regions of the left ventricle from mice with experimental MI treated with liraglutide, biol rep 3


title: Infarcted regions of the left ventricle from mice with experimental MI treated with PBS, biol rep 3


title: Infarcted regions of the left ventricle from mice with experimental MI treated with PBS, biol rep 2


title: i712_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 147


title: LN-tet-AR cells, DHT 0.1nM, repeat 1

value: LNCaP-tet-AR

value: prostate cancer cell line (generated from LNCaP)


title: Infarcted regions of the left ventricle from mice with experimental MI treated with liraglutide, biol rep 2


title: LN-tet-AR cells, DHT 10nM, repeat 2


title: Infarcted regions of the left ventricle from mice with experimental MI treated with PBS, biol rep 1


title: LN-tet-AR cells, vehicle, repeat 3

value: vehicle


title: i712_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 151

value: Hypothalamus


title: LN-tet-AR cells, vehicle, repeat 2


title: i712_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 146


title: Atria from mice with experimental MI treated with PBS, biol rep 3

source_name: Heart atria

value: Heart atria


title: Atria from mice with experimental MI treated with liraglutide, biol rep 3


title: LN-tet-AR cells, vehicle, repeat 1


title: Atria from mice with experimental MI treated with PBS, biol rep 2


title: LN-tet-AR cells, DHT 0.1nM, repeat 2


title: C-12-m-Mesa-4

extract_protocol:
RNA was harvested using RNeasy Micro Kit(Qiagen). 61ng 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

value: BTBR +/+

value: BTBR WT (control)

value: 12 weeks


title: i711_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 144


title: Atria from mice with experimental MI treated with liraglutide, biol rep 2


title: Ubiquitin-Lactacystin

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: CUT & RUN DNA

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Sequence reads were obtained from the Illumina Genome Analyzer Pipeline using Basespace.
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.

molecule: genomic DNA

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:
CUT and RUN was performed with a CUT&RUN assay kit according to the vendor's specifications (Cell Signaling Technology, 86652). Following proteasome inhibition for 3 h with 25 µM Lactacystin or 0.1% v/v DMSO control, cells were collected in conical tubes, counted, and assessed for cell viability. 250,000 MM.1S cells were used per condition and lysed in 4% digitonin. Capturing of DNA/protein complexes was performed with the following antibodies: 2 µl of anti-MYC antibody (Cell Signaling Technology, 13987) per condition, 2 µl of anti-FLAG antibody (Sigma-Aldrich, Clone M2, F1804) per condition for MM.1S cells stably transduced with 3xFLAG-ubiquitin, and as a negative control 5 µl of rabbit IgG isotype control (Cell Signaling Technology, 66362) per condition.
Single-indexed DNA libraries were prepared with the Ultra Next DNA library prep kit II (NEB, E7645S) and multiplexed for sequencing using NEBNext Multiplex oligos (E7500S). The protocol for DNA library preparation was adapted from previous publications and specifically optimized for CUT and RUN samples (Skene P.J. & Henikoff S., eLife, 2016, PMID 28079019; Liu N. et al., Cell, 2018, PMID 29606353). 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 was confirmed by electrophoretic analysis on an Agilent Bioanalyzer 2100 prior to sequencing. Pooled libraries 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 paired-end run, enabling the generation of a minimum of 19 million reads per sample. Clustering and sequencing performance were controlled as previously described (Sweeney M.A. et al., Sci. Rep, 2020, PMID 32811853).

treatment_protocol: Treatment was performed with the proteasome inhibitor lactacystin (6µM; Cayman Chemical, # 70980) or 0.1% (v/v) DMSO (mock) for three hours.

value: Lactacystin (25 uM)

value: 3XFlag-ubiquitin cells

value: B lymphoblast

tag: disease

value: IgA lambda myeloma

tag: gender

value: Female


title: Ubiquitin-DMSO

description: CUT & RUN DNA


title: i711_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 143


title: Atria from mice with experimental MI treated with liraglutide, biol rep 1

value: male


title: H3K27ac-Lactacystin-shHDAC3 cells

description: CT 14120

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.

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: Lactacystin (25 µM)

value: sh HDAC3 cells

tag: molecule subtype

value: ChIP DNA


title: Infarcted regions of the left ventricle from mice with experimental MI treated with liraglutide, biol rep 1

value: Left ventricle

value: Liraglutide


title: i712_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 145

value: Hypothalamus


title: i711_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 140


title: RNA-seq in XY E13.5 WT gonads rep1

city: Berlin

first: Irene

last: Mota-Gomez

address: Hannoversche strasse 28

institute: Max Delbruck Center

data_processing:
Base calling with standard Illumina Software.
Fastq files were mapped to mm10 genome using STAR version 2.7.10a with parameters (-- outFilterMultimapNmax 1).
Gene expression was quantified using featureCounts from subREAD package with default parameters.
Sample scaling and differential gene expression analysis were performed using the R package DESeq2.
Assembly: mm10
Supplementary files format and content: Counts.csv = Merged matrix containing counts from all samples in the different columns.
Supplementary files format and content: DEseq2.csv = Differential gene expression analysis, direct output from DESeq2.

source_name: E13.5 XY Gonads

growth_protocol: E13.5 gonads were microdissected in 1XPBS and separated from mesonephros using syringes and snapped frozen in liquid N.

extract_protocol:
RNA was extracted using RNase Micro kit (Qiagen).
RNA-seq libraries were performed using the NEBNext Ultra II Directional RNA library prep kit for Illumina including the Poly(A) magnetic isolation module.

value: WT

tag: developmental stage

value: gonads


title: RNA-seq in XY E13.5 Fgf9 Δ306 gonads rep2

value: Fgf9 <delta>306


title: RNA-seq in XY E13.5 Fgf9 Δ306 gonads rep3


title: H3K27ac-DMSO-shHDAC3 cells

description: CT 14117

value: shHDAC3 cells


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

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 XX 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.

value: Gonad


title: RNA-seq in XY E13.5 WT gonads rep3


title: RNA-seq in XY E13.5 WT gonads rep2


title: RNA-seq in XY E13.5 Fgf9 Δ306 gonads rep1


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


title: Hi-C in E10.5 XY supporting cells rep2

source_name: E10.5 XY supporting cells

value: Sf1-eGFP (Nr5a1-eGFP)


title: i711_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 138


title: Hi-C in E10.5 XX supporting cells rep2

source_name: E10.5 XX supporting cells


title: MYC-DMSO

description: CUT & RUN DNA

value: Parental cells


title: H3K27ac-DMSO-Non Silencing cells

description: CT 14111

value: Non Silencing cells

value: B lymphoblast


title: i711_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 137


title: i711_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 141


title: cumulus cells, Sphk1/2 knockout 3, 2h

city: New York city

first: Feifei

last: Yuan

state: NY

institute: Columbia University

description: Sample 12

data_processing:
Quality Control: Raw Data are processed with Perl scripts to ensure the quality of data used in following analysis. The adopted filter criteria are: 1) Filter out adaptor-polluted reads. (Reads contains more than 5 adapter-polluted bases are regarded as adaptor-polluted reads and are filtered out. As for paired-end sequencing data, reads from two ends are filtered out if any read of the paired-end reads are adaptor-polluted); 2) Filter out low-quality reads. (Reads with the number of bases whose phred Quality value was no more than 19 accounting for more than 15% are regarded as low-quality reads and are filtered out.) 3) Filter out reads with the number of N basesaccounting for more than 5 %. As for paired-end sequencing data, reads from two ends are filtered out if any read of the paired-end reads should be filtered out according to the abovecriteria. The Clean Data is abotained after filtering, and statistics analyses are performed on its quantity and quality, including Q30 statistics, data quantity statistics, base content statistics, etc.
Mapping the Sequencing Reads to Reference Genomes: The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). And Clean Data were mapped to the reference genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml). HISAT2 is a specialized software for transcriptome sequencing reads mapping, can identify exon-exon junctions by splitting the mapped reads and mapping them to the reference genome again. Moreover, HiSAT2 is more accurater and faster.
Assembly: GRCm38.90
Supplementary files format and content: tab-delimited text files include FPKM values for each sampe.

source_name: cumulus cells

growth_protocol: Mural granulosa cells and cumulus cells were collected form WT (control) and Sphk1/2 knockout mice at 2 h post-hCG.

extract_protocol:
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.RNA degradation and contamination was detected by 1% agarose gels; RNA purity was checked using the Qubit® 3.0 Flurometer（Life Technologies,   CA, USA）; RNA integrity and concentration was assessed using the RNA Nano 6000 Assay   Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: cumulus cells

value: Sphk1/2 knockout

value: 2 h post-hCG


title: i711_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 139


title: cumulus cells, Sphk1/2 knockout 2, 2h

description: Sample 11


title: i711_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 142


title: i711_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 136


title: HDAC3-Bortezomib

description: CT 14730

value: Bortezomib (60 nM)

value: IgA lambda myeloma

value: Female


title: mural granulosa cells, Sphk1/2 knockout 3, 2h

description: Sample 6

source_name: mural granulosa cells

value: mural granulosa cells


title: cumulus cells, Control 1, 2h

description: Sample 7


title: cumulus cells, Control 3, 2h

description: Sample 9


title: mural granulosa cells, Sphk1/2 knockout 2, 2h

description: Sample 5


title: cumulus cells, Sphk1/2 knockout 1, 2h

description: Sample 10


title: i711_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 135

value: Hypothalamus


title: HDAC3-DMSO (Control for Carfilzomib)

description: CT 15558

value: ChIP DNA


title: cumulus cells, Control 2, 2h

description: Sample 8

value: WT


title: HDAC3-DMSO (Control for Bortezomib)

description: CT 14727


title: i711_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 133


title: i711_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 134


title: HDAC3-Lactacystin

description: CT 13305

value: Lactacystin (25 µM)


title: H3K27ac-Lactacystin-Non Silencing cells

description: CT 14114


title: mural granulosa cells, Sphk1/2 knockout 1, 2h

description: Sample 4


title: mural granulosa cells, Control 3, 2h

description: Sample 3


title: mural granulosa cells, Control 2, 2h

description: Sample 2


title: i711_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 132


title: i715_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 183


title: HDAC3-DMSO (Control for Lactacystin)

description: CT 13303


title: Atria from mice with experimental MI treated with PBS, biol rep 1

value: Heart atria

value: male

value: PBS


title: H3K27ac-Carfilzomib

description: CT 15559

value: Carfilzomib (60 nM)

value: Parental cells


title: i711_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 130


title: i711_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 129


title: fPTS3_1, small-sample ATAC-seq, female

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 94). Transcript per million (TPM) and expected counts were generated by RSEM. All samples are of high percentage of uniquely mapped reads (> 80%) and are included for downstream analysis. Unless otherwise specified, the computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform
ATAC-seq data was processed using the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). In brief, The illumina adapters (-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT) were removed using cutadapt. Trimmed pair-ended reads were mapped mm10 (iGenomes) using BOWTIE2. Duplicated reads were marked by Picard and removed by Samtools (-F1804, -q 30). Peak calling was performed using MACS2 after the reads were shifted. Peaks falling into the blacklist regions were removed based on mm10-blacklist
Assembly: Ensemble release 94 and mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Kidney

growth_protocol: All animal work was conducted in accordance with NIH animal protocol (H-0047R4). 6- to 8-week-old male and female C57BL/6 mice from Taconic were used throughout the study.

extract_protocol:
2-5 tubules were collected for either RNA extraction (Direct-zol RNA MicroPrep kit, Zymo Research) or ATAC-seq.
Trizol-extracted RNA was eluted in 10 µl water and immediately proceeded to cDNA generation using the SMARTer V4 Ultra Low RNA Kit (Takara Bio). cDNA was generated with 10-12 PCR cycles. 1 ng of the resulting cDNA was “tagmented” and barcoded by using the Nextera XT DNA Sample Preparation Kit (Illumina) to generate sequencing libraries for high throughput sequencing. Libraries were purified by AmPure XP magnetic beads (Beckman Coulter), and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). An equal amount of index libraries were pooled and sequenced (paired-end 50 bp) on an Illumina platform.

value: female

value: Kidney

value: Proximal tubule cells


title: fPTS3_4, small-sample ATAC-seq, female


title: fPTS2_4, small-sample ATAC-seq, female


title: fPTS2_2, small-sample ATAC-seq, female


title: fPTS3_2, small-sample ATAC-seq, female


title: fPTS2_3, small-sample ATAC-seq, female


title: fPTS3_3, small-sample ATAC-seq, female


title: i710_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 128


title: fPTS2_1, small-sample ATAC-seq, female


title: fPTS1_3, small-sample ATAC-seq, female


title: H3K27ac-DMSO (Control for Bortezomib)

description: CT 14726

value: B lymphoblast


title: fPTS1_2, small-sample ATAC-seq, female


title: i710_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 127


title: fPTS1_4, small-sample ATAC-seq, female


title: H3K27ac-Bortezomib

description: CT 14729

value: Bortezomib (60 nM)


title: AD2(+)_single_cell_RNAseq

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

data_processing:
Raw data were processed with the Cell Ranger pipeline (v.6.0.1).
Sequencing reads were aligned using STAR aligner and UMIs were counted for each gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output

source_name: Enriched CD3+, CD14+/CD16+, and CD19+ cells from a 34-year-old with celiac disease and atopic dermatitis being treated with Dupilumab (a 600 mg loading dose 30 days after vaccination and were then maintained at 300 mg q.2 weeks till the analysis)

extract_protocol:
Single cells were captured into Gel Bead-in-EMulsions using a 10x chromium controller.
Single-cell 5’ biased transcriptome libraries were prepared using a 5’ Library & Gel Bead Kit (PN-1000014) according to the 10x Genomics manual

tag: subject status

value: Europe Am

value: Male

value: heparinized blood

value: PBMC cells


title: i710_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 126

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.

value: Hypothalamus


title: i711_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 131


title: mural granulosa cells, Control 1, 2h

description: Sample 1

value: mural granulosa cells

value: WT

value: 2 h post-hCG


title: i710_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 125


title: mPTS3_4, small-sample ATAC-seq, male

value: male


title: AD1(-)_single_cell_RNAseq

source_name: Enriched CD3+, CD14+/CD16+, and CD19+ cells from a 57-year-old with atopic dermatitis controlled by intermittent topical treatment with 0.05% Fluocinonide

value: Asian Am

value: Female


title: mPTS3_3, small-sample ATAC-seq, male


title: H3K27ac-DMSO (Control for Carfilzomib)

description: CT 15557

value: Parental cells

value: IgA lambda myeloma

value: ChIP DNA


title: Con#4_single_cell_RNAseq

source_name: Enriched CD3+, CD14+/CD16+, and CD19+ cells from a 53-year-old asymptomatic COVID-19 convalescent individual 131 days post positive test

value: Eurpian Am


title: mPTS3_2, small-sample ATAC-seq, male

value: Kidney

value: Proximal tubule cells


title: i714_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 167

source_name: Hypothalamus


title: Con#3_single_cell_RNAseq

source_name: Enriched CD3+, CD14+/CD16+, and CD19+ cells from a 57-year-old asymptomatic COVID-19 convalescent individual 94 days post positive test


title: i710_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 124


title: mPTS1_4, small-sample ATAC-seq, male


title: mPTS3_1, small-sample ATAC-seq, male


title: Si-Rap1B5

city: Milwaukee

first: Magdalena

last: Chrzanowska

state: WI

address: 8733 W. Watertown Plank Road

department: Blood Research Institute

institute: Versiti

data_processing:
Samples were demulitplexed using Illumina BaseSpace
Expression was quantified using Salmon v1.3.0
Expression was summarized to the gene level using tximport v1.18
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: CSV file of non-normalized read counts per gene

source_name: HUVEC

growth_protocol: siRap1B- or siControl-transfected HUVECs, cultured in growth media (EGM-2, Lonza) were treated with TNF-α for 12 hours.

extract_protocol:
For each biological replicate RNA was extracted from 300,000 cells grown in parallel dishes using TRIzol™ reagent.
Libraries were prepared using SMART-Seq2

tag: transfection

value: 12 hour TNF-alpha


title: mPTS1_3, small-sample ATAC-seq, male


title: i710_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 122


title: mPTS2_3, small-sample ATAC-seq, male


title: mPTS2_4, small-sample ATAC-seq, male


title: fPTS1_1, small-sample ATAC-seq, female

value: female


title: i710_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 120


title: mPTS2_2, small-sample ATAC-seq, male


title: mPTS1_1, small-sample ATAC-seq, male


title: mPTS1_2, small-sample ATAC-seq, male


title: Si-Rap1B4


title: Si-Rap1B3


title: mPTS2_1, small-sample ATAC-seq, male


title: Si-Rap1B2


title: Si-Rap1B1


title: i710_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 123


title: i710_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 121


title: scRNAseq_Zfp281KO_1

first: Sofia

last: Hu

email: sofiahu@mit.edu, xsu@cpdr.org

address: 500 Main Street

institute: MIT

description: scRNAseq for Zfp281KO cells (replicate 1)

library_source: transcriptomic single cell

data_processing:
scRNAseq: Cellranger (v.3.1.0) mkfastq and count pipelines were used for: demultiplexing, converting to fastq format, combining sequencing results, alignment to GRCm38 (mm10) genome assembly and gene annotation, barcode processing, and UMI counting.
ChIPseq: Reads were aligned to the mm10 reference genome using BWA-MEM (v.0.7.16a) with default parameters. Reads per genomic content (RPGC)-normalized bigWig files were generated for each IP using the bamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads --extendReads 150. Background signal was subtracted from each sample ChIP using the bigwigCompare function with the parameter –operation subtract (ex. Klf4 ChIP signal in Klf4-/- cells was subtracted from Klf4 ChIP signal in WT cells and from Klf4 ChIP signal in Zfp281-/- cells).
V6.5 mouse embryonic stem cells (mESC) were cultured on tissue culture-treated 10cm plates pre-coated with 0.2% gelatin in phosphate-buffered saline (PBS+B39). ESC were cultured in Dulbecco’s Modified Eagle Medium (Fisher), plus 10% fetal bovine serum, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x β-mercaptoethanol, and 1000 U ml-1 leukemia inhibitor factor. All cells were grown at 37C and 5% CO2 and passaged every two days to maintain 10-70% confluency.
Assembly: mm10
Supplementary files format and content: scRNAseq: filtered feature-barcode matrix in MEX format
Supplementary files format and content: ChIPseq: bigWig format

source_name: mouse embryonic stem cell

growth_protocol: V6.5 mouse embryonic stem cells (mESC) were cultured on tissue culture-treated 10cm plates pre-coated with 0.2% gelatin in phosphate-buffered saline (PBS). ESC were cultured in Dulbecco’s Modified Eagle Medium (Fisher), plus 10% fetal bovine serum, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x β-mercaptoethanol, and 1000 U ml-1 leukemia inhibitor factor. All cells were grown at 37C and 5% CO2 and passaged every two days to maintain 10-70% confluency.

extract_protocol:
scRNAseq: Single-cell suspension of V6.5 mESC was made by treatment with 0.25% trypsin followed by inactivation in complete medium. Single-cell isolation and library preparation was done using a 10x Genomics Chromium machine in 3’ RNA digital gene expression mode.
ChIP-seq: Cells were crosslinked in 1% formaldehyde on a rocker at room temperature for 10 minutes. Crosslinking was quenched with 250 mM glycine on a rocker at room temperature for 5 minutes. After cell lysis, chromatin was Maase-treated and sonicated using a Covaris220 evolution solicitor. ChIPseq libraries were prepared using NEB UltraII kit from 6-10 ng of DNA. Libraries were prepared by the MIT BioMicro Center.

value: mouse embryonic stem cell

value: embryonic stem cell line

tag: chip antibody


title: Si-C5

value: Si-Control


title: scRNAseq_Klf4KO_1

description: scRNAseq for Klf4KO cells (replicate 1)


title: scRNAseq_WT_2

description: scRNAseq for WT cells (replicate 2)


title: scRNAseq_Klf4KO_2

description: scRNAseq for Klf4KO cells (replicate 2)


title: i710_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 117

value: Hypothalamus


title: scRNAseq_WT_1

description: scRNAseq for WT cells (replicate 1)

value: WT


title: Si-C4


title: i710_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 116


title: Si-C3


title: i710_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 115


title: DTA_WT1

city: Shanghai

first: Junjie

address: 600 Yishan Road

country: China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
After sequencing, generated reads were filtered and mapped to the reference genome using HISAT2 (v2.0.4)and assembled using StringTie (v1.3.4d) with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (v0.9.8) and the expression levels of all transcripts were calculated by Stringtie and ballgown.
Differential gene analysis was performed by DESeq2 software and then subjected to enrichment analysis of GO functions.
Assembly: Mus_musclus.GRCm38 V99
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cortical bone tissue

extract_protocol:
Total cortical bone RNA from 4 weeks WT and DTAhet mice was extracted using Trizol reagent (Thermofisher), quantified and purified using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent).
Following purification, mRNA library was constructed, fragmented, amplified and loaded into the nanoarray and sequencing was performed on Illumina Novaseq™ 6000 platform following the vendor’s recommender protocol.

value: cortical bone tissue

value: Wild-type

tag: age

value: 4 weeks old


title: Si-C2


title: scRNAseq_Zfp281KO_2

description: scRNAseq for Zfp281KO cells (replicate 2)


title: KO_Bm_4w,scRNAseq

first: Peng

last: Ding

address: No.600, Yishan Road

department: Orthopaedics

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

description: 10x Genomics

data_processing:
The final library pool was sequenced on the Illumina NovaSeq 6000 platform and the sequencing data were processed using the Cell Ranger software (10X Genomics).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Bone marrow

extract_protocol:
Bone marrow cells from WT and DTAhet mice were isolated by flushing the bone marrow cavities of mice femurs and tibias wit PBS.
Single-cell RNA sequencing (scRNA-seq) was performed using 10X Genomics Chromium platform. Related operations including Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT cleanup, complementary DNA amplification and library construction were all carried out following the manufacturer’s protocol. Clustering analysis, proportion analysis, RNA velocity, myeloid trajectory analysis lymphoid trajectory analysis was performed.150-base-pair paired-end reads was applied.

value: Bone marrow

value: Bone marrow cells

value: Dmp1cre DTAfl/+


title: DTA_WT3


title: i710_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 114


title: Si-C1


title: ICI_nov21

city: Los Angeles

first: Melissa

middle: G

last: Lechner

state: CA

address: 10833 Le Conte Ave, CHS 57-154

department: Div of Endocrinology, Diabetes, and Metabolism

institute: UCLA Geffen School of Medicine

description: scRNAseq, intrathyroidal immune cells from immune checkpoint inhibitor treated NOD strain mice

data_processing:
The reads are first mapped to mm10 (mouse) reference using cellranger software from 10x Genomics
Filtered output matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used for downstream analysis with Seurat
Cells with a mitochondiral gene percentage greater than or equal to 30 were removed
The raw counts and metadata from the Seurat object after IntegrateData and ScaleData step across samples are provided as processed data file
Subsequent clustering are descibed in the full manuscript
Genome_build: mm10
Supplementary_files_format_and_content: mouse_irae_iso_integrated_counts.csv

source_name: NOD mice

extract_protocol: Chromium Single Cell GEM, Library & Gel Bead Kit

treatment_protocol: 4-6 week old male and female NOD.WT mice were treated twice weekly with anti-PD-1 (clone RPM1-14) and anti-CTLA-4 (clone 9D9) antibodies or isotype control antibodies by intraperitoneal injection for four weeks. Mice were euthanized, perfused with PBS, and then fresh thyroid tissue collected. Thyroid tissue was dissociated into a single cell suspension by collagenase digestion followed by passage through a 40um filter. CD45+ live single cells were isolated by FACS and used for single cell sequencing.

value: CD45+ mouse primary immune cells isolated from thyroid tissue

value: anti-PD-1 + anti-CTLA-4 antibody

value: 5' sequencing

tag: cell number


title: DTA_KO2

tag: tissue


title: ISO

description: scRNAseq, intrathyroidal immune cells from NOD strain mice treated with isotype control antibodies (clones 2A3, MPC11)

value: Isotype control antibody treatment  (clones 2A3, MPC11)


title: OTX2_2

city: Tel Aviv

first: Mai

last: Eshel

address: Klatzkin 35

department: Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

data_processing:
Sequenced reads were aligned to the human genome (hg19) using Bowtie2
OTX2 peaks were detected using MACS2; 6461 peaks detected
Genome_build: hg19
Supplementary_files_format_and_content: processed file contains the genomic coordinates of the 6461 peaks (bed format)

source_name: hES-RPE

growth_protocol: For RPE differentiation, hESCs colonies (Hes1 hES) were picked up using collagenase IV (1 mg/ml; 200 U/mg, Gibco-BRL, Gaithersburg, MD), and cultured using differentiation protocol including treatment with nicotinamide and activinA. After 6-10 weeks in suspension, pigmented clusters were triturated, plated on gelatin (Sigma) coated plates (Corning Incorporated, Corning, NY), and cultured in Knock out medium with 10mM nicotinamide for 3-5 weeks. The RPE cell lines were further propagated using TrypLE Select (Gibco-BRL). The cells were passaged every 2 weeks.

extract_protocol:
Sonicated chromatin from hES-RPE cells was immunoprecipitated with rabbit anti-Otx2 (Abcam, ab21990).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit.

value: ES-derived RPE cells

value: rabbit anti-Otx2 (Abcam, ab21990)


title: i707_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 112

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.

tag: expression


title: OTX2_1

tag: cell type


title: L1HFA060360: MLN cells co-cultured with anti-CD3, anti-CD28 antibodies rep2

city: Wuxi

first: Sai

middle: sai

last: Feng

state: State/Province

address: Lihu Avenue No1800

department: School of Food Science and Technology

institute: Jiangnan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm39 whole genome using hisat2
Transcripts Per Kilobase of exon model per Million mapped reads (TPM) were calculated using a protocol from Liao et al., Bioinformatics, 2014.
Expression matrix was calculated using a script in trinity from Grabherr et al., Nature Biotechnology, 2019.
Genome_build: Build by hisat2-build
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts, FPKM and TPM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Gene expression file including TMM values (based on TPM) for every gene and every sample

source_name: mesenteric lymph node cells

growth_protocol: MLN cells were cultured in RPIM1640 supplemented with 5% FBS, 3 mmol/l L-glutamine, 10 mmol/L Hepes, 0.05 mmol/L β-Mercaptoethanol, 0.1% (v/v) penicillin/streptomycin (Sigma-Aldrich) with or without stimulus (1 mmol/L anti-CD3 and anti-CD28 antibodies)

extract_protocol: RNA was extracted using Trizol reagent.

tag: strain

value: mesenteric lymph node cells

value: coculture with anti-CD3, anti-CD28 antibodies for 3 days

tag: genotype

value: wild type


title: WT_Bm_4w,scRNAseq

description: 10x Genomics


title: L1HFA060361: MLN cells co-cultured with anti-CD3, anti-CD28 antibodies rep3

tag: treatment


title: L1HFA060359: MLN cells co-cultured with anti-CD3, anti-CD28 antibodies rep1


title: i710_i508

first: Fiona

institute: University of Cambridge

description: Mouse hypothalamus Rxfp4-EYFP, sample 118

value: Hypothalamus


title: i707_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 111


title: L1HFA060358: MLN cells co-cultured with Bifidobacterium bifidum and anti-CD3, anti-CD28 antibodies rep3

value: coculture with Bifidobacterium bifidum and anti-CD3, anti-CD28 antibodies for 3 days


title: OTX2_input1


title: OTX2_input2


title: L1HFA060356: MLN cells co-cultured with Bifidobacterium bifidum and anti-CD3, anti-CD28 antibodies rep1


title: L1HFA060357: MLN cells co-cultured with Bifidobacterium bifidum and anti-CD3, anti-CD28 antibodies rep2


title: i707_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 110


title: LHX2_input_2_A

data_processing:
Sequenced reads were aligned to the human genome (hg19) using Bowtie2
LHX2 peaks were detected using MACS2; 1278 peaks detected
Genome_build: hg19
Supplementary_files_format_and_content: processed file contains the genomic coordinates of the 1278 peaks (bed format)

extract_protocol:
Sonicated chromatin from hES-RPE cells was immunoprecipitated with rabbit anti-Lhx2 (Millipore, ABE1402) or gout anti-Lhx2 (Santa Cruz,  sc-19344)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit.


title: L1HFA060351: MLN cells co-cultured with Clostridium butyricum rep3

value: coculture with Clostridium butyricum for 3 days


title: DTA_KO3

value: cortical bone tissue


title: L1HFA060350: MLN cells co-cultured with Clostridium butyricum rep2


title: i707_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 109


title: i710_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 113


title: L1HFA060349: MLN cells co-cultured with Clostridium butyricum rep1


title: L1HEK190244: MLN cells co-cultured with Akkermansia muciniphila AH39 rep1

value: coculture with Akkermansia muciniphila AH39 for 3 days


title: LHX2_input_1_A


title: i707_i516

description: Mouse hypothalamus Rxfp4-EYFP, sample 107


title: input_LHX2_M


title: i707_i515

description: Mouse hypothalamus Rxfp4-EYFP, sample 106


title: DN-Wnt1

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Demultiplexing with cellranger v3.1.0 mkfastq, bcl2fastq v2.20.0.422
Barcode and UMI deconvolution, mapping with cellranger v3.1.0 count
Genome_build: mm10
Supplementary_files_format_and_content: .h5 files (HDF5) for cellranger of deconvoluted gene expression matrix

source_name: Mouse mammary tumor

growth_protocol: mammary tumors were harvested and used for dissociation when they reached 1.5 cm2

extract_protocol: 10X 3' Gene Expression

treatment_protocol: MMTV-Wnt1 and K8iKOR-Wnt1 tumors were from animals injected with tamoxifen (2 mg for 3 consecutive days) at 8 weeks of age. Tumors were harvested when they reaced 1.5 cm2 (ranging from 3-12 months of age)

tag: strain background

value: FVB

tag: cell types

value: whole tumor - epithelia, stroma


title: ICI_CD45pos_m1b

extract_protocol:
Chromium Single Cell GEM, Library & Gel Bead Kit
10x Genomics single cell RNA-Seq


title: ip_Lhx2_2_A

value: gout anti-Lhx2 (Santa Cruz, sc-19344)


title: MMTV-Wnt1

value: tamoxifen injected at 8 wks


title: ICI_CD45pos_m1a

value: CD45+ mouse primary immune cells isolated from thyroid tissue

value: anti-PD-1 + anti-CTLA-4 antibody


title: ICI_CD45pos_m1

value: 5' sequencing


title: i707_i517

last: Gribble

address: Box 289 Addenbrooke's Hospital, Hills Road

description: Mouse hypothalamus Rxfp4-EYFP, sample 108


title: i707_i511

description: Mouse hypothalamus Rxfp4-EYFP, sample 104


title: L1HEK190246: MLN cells co-cultured with Akkermansia muciniphila AH39 rep2


title: i707_i510

description: Mouse hypothalamus Rxfp4-EYFP, sample 103


title: mPROseq_WT_ESC_c1_BR1

description:
mPROseq
nascent RNA

data_processing:
Library strategy: PRO-Seq
scRNAseq: Cellranger (v.3.1.0) mkfastq and count pipelines were used for: demultiplexing, converting to fastq format, combining sequencing results, alignment to GRCm38 (mm10) genome assembly and gene annotation, barcode processing, and UMI counting.
scATACseq: Cellranger ATAC (v.1.1.0) mkfastq and count pipelines were used for demultiplexing sequencing results and converting to fastq format, as well as alignment to GENCODE vM17 basic genome annotation, barcode processing, and UMI counting.
mPROseq: Raw reads were processed using fastxtoolkit (v.0.0.13). Fastq files were converted to fasta format using the fastq_to_fasta command with parameter -n. Adapter sequence was removed using fastx_clipper with parameters -n -a ATCTCGTATGCCGTCTTCTGCTTG -l 14. PCR duplicates were removed using fastx_collapser with default parameters. The 6bp unique molecular identifier (UMI) was removed using fastx_trimmer (-f 7). Then, libraries were demultiplexed using fastx_barcode_splitter with parameters --mismatches 2 --partial 1. Library barcodes were trimmed using fastx_trimmer (-f 10). The reverse complement of trimmed sequences were obtained using fastx_reverse_complement and aligned to the mm10 reference genome using Bowtie2 (v.2.3.5.1) with parameter --sensitive-local -f. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads -e 150.
ATACseq: Reads were trimmed for adapter sequences using TrimGalore (v.0.6.5) (--paired --nextera). Paired-end reads were aligned to the mm10 reference genome using Bowtie2 (v.2.3.5.1) (--very-sensitive -k 10) and filtered for autosomal, properly-paired, mapped read pairs with mapping quality >= 30 using samtools (v.1.10) view (-b -h -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30). Peak calling was performed separately for each sample using Genrich (-a 10 -j -r -e chrM,chrY), excluding ENCODE blacklisted regions (ENCFF547MET.bed, downloaded from https://www.encodeproject.org/files/ENCFF547MET/). Peaks called in each sample were collated, and overlapping peaks were merged to generate a consensus list of peaks using bedtools merge. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads.
RNAseq: Reads were trimmed for adapter sequences using TrimGalore (--paired --illumina --length 20). Sequences were trimmed for read quality using fastq_quality_filter in fastxtoolkit (-Q33 -q 30 -p 90). Paired-end reads were aligned to the mm10 reference genome using hisat2 (v.2.2.0) (--rna-strandness FR). Aligned reads were counted to GENCODE vM15 genomic transcripts using featureCounts in the subread package (v.1.6.2) using default parameters. Reads per genomic content (RPGC)-normalized bigWig files were generated from bam files using the BamCoverage function in the deeptools package (v.3.0.1) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --centerReads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .tar archives include barcodes.tsv, features.tsv, and matrix.mtx files.
Supplementary_files_format_and_content: bigWig coverage files

source_name: mouse embryonic stem cell V6.5

growth_protocol: V6.5 mouse embryonic stem cells (ESC) were cultured on tissue culture-treated 10cm plates pre-coated with 0.2% gelatin in phosphate-buffered saline (PBS). ESC were cultured in Dulbecco’s Modified Eagle Medium (Fisher), plus 10% fetal bovine serum, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x β-mercaptoethanol, and 1000 U ml-1 leukemia inhibitor factor. All cells were grown at 37C and 5% CO2 and passaged every two days to maintain 10-70% confluency.

extract_protocol: scRNAseq: Single-cell suspension of V6.5 mESC was made by treatment with 0.25% trypsin followed by inactivation in complete medium. Single-cell isolation and library preparation was done using a 10x Genomics Chromium machine in 3’ RNA digital gene expression mode. scATACseq: Single-nuclei suspension of V6.5 mESC was isolated following the 10x Genomics nuclei isolation protocol (CG000169 Rev D). mPROseq: The PROseq protocol established in Mahat et al. 2016 was modified to enable small cell input and performed. ATACseq: Library preparation was performed according to protocol established in Buenrostro et al. 2013 (PMID 24097267), Buenrostro et al. 2015 (PMID 25559105). RNAseq: RNA was extracted by standard Trizol protocol. rRNA-depleted RNA sequencing libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche 08098140702) to manufacturer’s instructions.

tag: cell line

value: embryonic stem cell line

tag: subpopulation

value: unsorted

value: WT

tag: biological replicate


title: mPROseq_WT_ESC_c1_BR4

description:
mPROseq
nascent RNA


title: mPROseq_WT_ESC_c1_BR3

description:
mPROseq
nascent RNA


title: i707_i508

description: Mouse hypothalamus Rxfp4-EYFP, sample 102


title: LHX2_KD_2

data_processing:
Sequenced reads were mapped to the homo sepians genome (hg19), using TopHat v2.0.10
Genes were identified using a .gtf obtained from Ensembl release 82. Per gene reads were counted using HTSeq.
Normalization and detection of differentially expressed genes were done using DEseq2
Genome_build: hg19
Supplementary_files_format_and_content: Excel table with gene count

extract_protocol:
RNA was extracted using the QIAshredder and the RNeasy kits (QIAGEN)
Sequencing libraries were prepared using the INCPM mRNA protocol

treatment_protocol: The downregulation of Lhx2 was constructed using pGIPZ vectors (Thermo Fisher Scientific). Four different pGIPZ vectors containing four different shRNA sequences targeting Lhx2 mRNA (NM_004789) were examined for their downregulation efficiency using qRT-PCR. Two of the four vectors which showed the strongest effect were then used. A sh-non-silencing pGIPZ vector (RHS4531) was used as a negative control. To produce the infectious viruses, the 293T packaging cell line was co-transfected using jetPEI (Polyplus) with the lentiviral backbone plasmids shLhx2-pGIPZ or the sh-non-silencing-pGIPZ, packaging plasmid pCMVΔR8.2 and envelope plasmid pVSV-G. After 72hr, the virus particles in the medium were collected and filtrated through a 0.45 μm pore size filter. 2.5x10^5 hRPE-ES cells were seeded in 24 well plate and were grown for 14d to achieve full differentiation. For the infection, cells were incubated with virus-containing medium in the presence of 100 μg/ml polybrene (hexadimethrine bromide; Sigma) for 30min in 37°C followed by centrifugation (30min, 37°C, 1100xg). Medium was afterwards replaced with fresh growth medium. After 24hr 10 μg/ml puromycin (Sigma) was added for additional 5 days followed by harvesting for RNA isolation.

value: ES-derived RPE cells

value: 14d in differentiation conditions


title: mPROseq_Zfp281KO_ESC_c1_BR4

description:
mPROseq
nascent RNA

value: Zfp281 KO


title: K8iKOR-Wnt1


title: i707_i507

description: Mouse hypothalamus Rxfp4-EYFP, sample 101

value: Hypothalamus


title: mPROseq_WT_ESC_c1_BR2

description:
mPROseq
nascent RNA


title: mPROseq_Zfp281KO_ESC_c1_BR3

description:
mPROseq
nascent RNA


title: LHX2_KD_1


title: mPROseq_Zfp281KO_ESC_c1_BR1

description:
mPROseq
nascent RNA


title: mPROseq_Zfp281KO_ESC_c1_BR2

description:
mPROseq
nascent RNA


title: i707_i513

description: Mouse hypothalamus Rxfp4-EYFP, sample 105


title: ip_LHX2_M

value: rabbit anti-Lhx2 (Millipore, ABE1402)


title: mPROseq_Klf4KO_ESC_c1_BR4

description:
mPROseq
nascent RNA

value: Klf4 KO


title: mPROseq_Klf4KO_ESC_c1_BR2

description:
mPROseq
nascent RNA


title: mPROseq_Klf4KO_ESC_c1_BR3

description:
mPROseq
nascent RNA


title: H3K27ac HiChIP C17 Replicate 2

first: Sizun

last: Jiang

address: 3 Blackfan Circle

institute: BIDMC/Harvard

description: HiChIP DNA

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

source_name: EBV-associated nasopharyngeal carcinoma cell line

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: EBV Positive NPC Cell Line

tag: hichip antibody

value: H3K27ac, Abcam ab4729


title: i707_i506

description: Mouse hypothalamus Rxfp4-EYFP, sample 100


title: i707_i503

description: Mouse hypothalamus Rxfp4-EYFP, sample 98


title: mPROseq_Klf4KO_ESC_c1_BR1

description:
mPROseq
nascent RNA


title: H3K27ac HiChIP C17 Replicate 1

description: HiChIP DNA


title: NS_sh_2

value: non specific sh-RNA


title: i706_i522

description: Mouse hypothalamus Rxfp4-EYFP, sample 96


title: i707_i502

description: Mouse hypothalamus Rxfp4-EYFP, sample 97


title: HDAC3-Carfilzomib

description: CT 15560

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)

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.

value: Carfilzomib (60 nM)

value: Parental cells

value: B lymphoblast

tag: disease

value: IgA lambda myeloma

tag: gender

value: Female

tag: molecule subtype

value: ChIP DNA


title: i707_i505

description: Mouse hypothalamus Rxfp4-EYFP, sample 99


title: CRISPR screen NP69 Replicate 1

description:
CRISPR sgRNA inserted DNA
NP69_counts.count.txt

source_name: SV40 immortalized nasopharyngeal epithelial cells

value: EBV Negative nasopharyngeal epithelial cells

tag: crispr library

value: Brunello


title: CRISPR screen NP69 Replicate 2


title: H3K27ac HiChIP C666-1 Replicate 1

description: HiChIP DNA


title: NS_sh_1

value: ES-derived RPE cells

tag: age


title: i706_i520

description: Mouse hypothalamus Rxfp4-EYFP, sample 94

tag: tissue


title: CRISPR screen C666-1 Replicate 2

description:
CRISPR sgRNA inserted DNA
C666_counts.count.txt


title: i706_i518

description: Mouse hypothalamus Rxfp4-EYFP, sample 93

tag: expression


title: H3K27ac HiChIP C666-1 Replicate 2

description: HiChIP DNA

tag: cell type


title: CRISPR screen C666-1 Replicate 1


title: i706_i517

description: Mouse hypothalamus Rxfp4-EYFP, sample 92


title: i706_i521

description: Mouse hypothalamus Rxfp4-EYFP, sample 95