title: C57BL/6 mice with sham_4

city: Beijing

first: Guangda

last: Zheng

address: No. 5, North Line Pavilion, Xicheng District

institute: Guang anmen Hospital

description: small RNA

data_processing:
Undergoing fastp for the quality control, clean reads then were mapped to reference genome via STAR (for mRNA and lncRNA) and bowtie (for miRNA), followed by the quantification using Salmon tool.
We used mirtop for miRNA annotation.
For mRNA and lncRNA, desq2 tool was utilized in the analysis of differentially-expressed genes.
For miRNA, differentially-expressed analysis was processed by edgR and desq2.
The functional potential of differentially-expressed genes was predicted by Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: left spinal cord

extract_protocol:
Samples of spinal cord were homogenized in 1 mL TRIzol reagent (Invitrogen, USA) for 5 min at room temperature, followed by chloroform (Sigma-Aldric, USA) extraction for 2 min and isopropanol (Sigma-Aldric, USA) precipitation for 10 min. The purity of total RNA was determined using Aglient 2100 Bioanalyzer (Aglient, USA).
Total RNA was fragmented and reversely transcribed into cDNA using TIANSeq RNA Frag/cDNA Synthesis Module (TIANGEN, Beijing, China) after rRNA was removed by TIANSeq rRNA Depletion Kit (TIANGEN, Beijing, China). cDNA library construction was performed by TIANSeq Fast DNA Library (illumina) Kit (TIANGEN, Beijing, China) after the purification and enrichment of cDNA fragments using TIANSeq Size Selection DNA Beads (TIANGEN, Beijing, China). RNA-sequencing was processed using a high-throughput sequencing platform (illumine, USA) to obtain sequencing reads of each sample.

value: left spinal cord

value: injected with equivalent normal saline in  the intramedullary space of the left femur


title: 270

status: Public on Oct 11 2025

type: SRA

city: Chapel Hill

first: Shehzad

middle: Z.

last: Sheikh

address: 111 Mason Farm Road

department: Department of Medicine

country: USA

institute: University of North Carolina School of Medicine

description: Library name: 270

library_source: transcriptomic

data_processing:
Salmon was used to quantify transcript expression. Quality control metrics based on distributions of sequencing quality, sequencing error rate, and A/T/G/C base, and RNA integrity number (RIN), were used to exclude low-quality samples
Assembly: hg19
Supplementary files format and content: rownames contain the gene name. colnames conatin the sample names. Matrix values are the rounded transcript expression.

molecule: polyA RNA

organism: Homo sapiens

source_name: Colon

extract_protocol:
Total RNA was isolated from frozen tissue in Trizol and total RNA purification kit (Norgen Biotek).
PolyA enrichment, library preparation, and sequencing (150 bp paired end reads) on the NovaSeq sequencer was performed by Novogene (https://www.novogene.com).

tag: tissue

value: Colon

tag: Sex

value: Male

tag: disease

value: NIBD

tag: age

tag: sample year

tag: tin scores


title: 331

description: Library name: 331


title: Nonresponder 0M [0M_10]

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

country: Japan

institute: Tsukuba university

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 20.0.0; Qiagen, Redwood City, CA).
Assembly: hg19

molecule: total RNA

source_name: Whole blood cells

extract_protocol:
Silica-membrane-based RNA isolation and purification in a spin-column format were performed using the PAXgene Blood RNA kit (Qiagen). Extracted RNA was globin-cleared using the Ambion GLOBINclear kit (Thermo Fisher, Waltham, MA). Then, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) and converted to an Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Whole blood cells

tag: group

value: Nonresponder 0M


title: C57BL/6 mice with sham_3

country: China

description: small RNA

organism: Mus musculus

tag: strain

tag: treatment


title: 261

description: Library name: 261

value: Female


title: Region_4_left

type: RNA

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

description:
fresh frozen single-cell spatial transcriptomics
F_4 = Region_4_left

hyb_protocol: Probe hybridization was performed at 50°C overnight using the pre-designed, 247-probe Xenium Mouse Brain Gene Expression base panel (10X Genomics, Cat# 1000462) in tandem with a custom 50-probe add-on panel (10X Genomics, Cat# 1000464) against select L6b target genes. On the next day, slides underwent wash steps to remove any unhybridized probes, followed by a 2-h ligation step at 37°C to anneal probes to their specific mRNA target. Probes were then enzymatically amplified via rolling circle amplification PCR for 2-h at 37°C. After subsequent washing, quenching steps were performed to reduce background autofluorescence, followed by a DAPI nuclear stain. The slide cassettes were then loaded onto the Xenium Analyzer instrument for quantification.

scan_protocol: Instrument buffers and reagents were prepared as according to the Xenium Analyzer User Guide (10X Genomics). Following instrument initialization, slides and consumables were loaded onto the Xenium Analyzer, and regions of interest were selected after a preliminary sample scan. Once the Xenium Analyzer run began, slides underwent iterative rounds of image acquisition where probe-specific fluorescent oligos were added, hybridized to the amplified probe sequence, imaged and gently removed. mRNA-specific puncta were decoded into their corresponding gene IDs and assigned a quality score. Using the DAPI nuclear stain, cell boundaries were segmented and transcripts were spatially assigned to cells at a sub-50nm XY localization precision. After approximately 2 days of on-instrument imaging and analysis, Xenium data was collected for downstream analysis.

data_processing:
Xenium In Situ Analyzer performs automated onboard analysis which includes DAPI-based segmentation of nuclei via deep-learning, then expansion of the segmentation masks. A cell-by-gene matrix of segmented nuclei is generated for analysis. Xenium In Situ Analyzer output was re-segmented using Xenium Ranger (v3.1) to adjust nuclear expansion to 5 um. Post-processing in R with custom scripts and Seurat.
Processed data files:  xen_l6b_analysis.rds.gz, countsTableXenium.txt.gz, metaDataXenium.txt.gz

source_name: brain hemisection

extract_protocol: Brain hemispheres were then immediately embedded into OCT molds and snap frozen in methylbutane cooled by liquid nitrogen. Frozen tissue samples were processed according to recommendations in the Xenium In Situ for Fresh Frozen Tissues – Tissue Preparation Guide (10X Genomics). To summarize, six 10μm hemisections spanning the AP axis (bregma = -1.22mm, -2.18mm, -3.08mm, -3.64mm,) were collected from each animal. Tissue was sectioned using a cryostat and placed within the 12 × 24mm capture frame on a Xenium slide. Slides were subsequently stored at −80°C until use. Prepared slides were fixed and permeabilized as per the Xenium In Situ for Fresh Frozen Tissues – Fixation & Permeabilization protocol (10X Genomics).

tag: genotype

value: WT mouse

value: brain hemisection


title: Region_5_left

description:
fresh frozen single-cell spatial transcriptomics
F_5 = Region_5_left


title: C57BL/6 mice with sham_2

description: small RNA


title: Region_3_left

description:
fresh frozen single-cell spatial transcriptomics
F_3 = Region_3_left


title: Responder 0M [0M_6]

value: Responder 0M


title: C57BL/6 mice with sham_1

description: small RNA


title: 252

description: Library name: 252


title: 0M in AE case [0M_7]

value: 0M in AE case


title: 264

description: Library name: 264


title: Responder 0M [0M_5]


title: Region_2_left

description:
fresh frozen single-cell spatial transcriptomics
F_2 = Region_2_left


title: C57BL/6 mice with BCP_4

description: small RNA

value: treated with the transplant of mouse lung cancer cells (LL/2) in  the intramedullary space of the left femur


title: Responder 0M [0M_4]


title: 248

description: Library name: 248


title: Region_5_right

description:
fresh frozen single-cell spatial transcriptomics
M_5 = Region_5_right


title: Region_4_right

description:
fresh frozen single-cell spatial transcriptomics
M_4 = Region_4_right


title: 235

description: Library name: 235


title: Nonresponder 0M [0M_3]


title: C57BL/6 mice with BCP_2

description: small RNA


title: Nonresponder 0M [0M_2]


title: 205

description: Library name: 205


title: Region_3_right

description:
fresh frozen single-cell spatial transcriptomics
M_3 = Region_3_right


title: C57BL/6 mice with BCP_1

description: small RNA


title: Region_2_right

description:
fresh frozen single-cell spatial transcriptomics
M_2 = Region_2_right


title: Eggshell_Colour_Brown_rep141

status: Public on Oct 10 2025

type: genomic

first: Bingjie

last: Zhang

address: Beijing HaiDian District, Mingyuanxilu No.2

institute: China Agricultural University

description:
41716
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations.

data_processing:
Convert the chip CSV file containing genotype information into a PLINK-readable format using R. Then, use PLINK to filter the data based on genotype quality control criteria, including sample call rate, SNP call rate, minor allele frequency (MAF), and Hardy-Weinberg equilibrium (HWE). Perform quality control on the raw genotype data for all samples to generate a filtered PLINK file. Finally, use PLINK to convert this file into a VCF format for subsequent genome-wide association analysis.
primary data description: From the 600K Affymetrix panel, 571,185 high-quality and segregating SNPs were retained for 200 samples.

label: biotin

molecule: genomic DNA

organism: Gallus gallus

source_name: Chicken blood,Eggshell colour, brown

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: We conducted a cross between White Leghorn roosters (n=15) and recessive white hens (n=58) to generate the F1 generation. In the F1 generation, 24 male chickens and 82 female chickens were mated to produce the F2 generation, in which a segregation of eggshell color phenotypes was observed.

extract_protocol: DNA extraction using the phenol-chloroform method.

treatment_protocol: The absorbance values of the eggshell dissolution liquid were measured at 412 nm and 670 nm using a multifunctional microplate reader.

value: Blood

tag: eggshell colour

value: brown


title: Eggshell_Colour_Brown_rep140

description:
41741
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep139

description:
41635
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: 255

description: Library name: 255


title: Eggshell_Colour_White_rep18

description:
41831
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array

source_name: Chicken blood,Eggshell colour, white

value: white


title: Eggshell_Colour_Brown_rep138

description:
41545
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep137

description:
41731
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep136

description:
41777
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep135

description:
41578
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep133

description:
41520
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep17

description:
41586
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep130

description:
41782
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep132

description:
28817
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep134

description:
41856
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep131

description:
41658
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep129

description:
41598
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: C57BL/6 mice with BCP_3

description: small RNA


title: Eggshell_Colour_Brown_rep127

description:
41588
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep128

description:
41579
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep125

description:
41792
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep124

description:
28855
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep123

description:
41804
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep122

description:
28849
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Responder 0M [0M_1]


title: Eggshell_Colour_Brown_rep120

description:
41602
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep119

description:
41633
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep118

description:
41601
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: 200

description: Library name: 200


title: Eggshell_Colour_Brown_rep115

description:
41639
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep116

description:
41747
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep114

description:
41650
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep112

description:
41532
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep111

description:
41669
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep107

description:
41603
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep108

description:
41493
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep104

description:
41555
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep105

description:
41613
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep16

description:
28811
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep103

description:
41554
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep102

description:
41717
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep126

description:
41654
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep100

description:
41793
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep121

description:
41518
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep97

description:
41546
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep98

description:
41563
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep96

description:
41724
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep117

description:
41621
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep95

description:
41722
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep113

description:
41477
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep94

description:
41626
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep92

description:
41448
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep93

description:
41819
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep110

description:
41550
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep89

description:
41715
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep91

description:
41537
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep88

description:
41761
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep87

description:
41873
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep86

description:
41848
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep106

description:
41662
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep109

description:
41663
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep84

description:
41584
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep83

description:
41760
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep101

description:
41543
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep81

description:
28810
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep15

description:
41426
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep79

description:
41585
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep99

description:
41611
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep78

description:
41670
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep90

description:
41440
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep75

description:
41839
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep77

description:
41620
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep76

description:
41439
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep80

description:
41614
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep82

description:
41745
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep74

description:
41615
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep73

description:
28851
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep72

description:
28830
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep71

description:
41566
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep69

description:
28842
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep70

description:
41649
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep68

description:
41529
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep66

description:
41429
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep67

description:
28840
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep85

description:
41725
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep13

description:
41814
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep65

description:
41691
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep64

description:
41408
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep63

description:
41790
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep62

description:
41697
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep60

description:
28836
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep61

description:
41438
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep58

description:
41416
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep59

description:
41524
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep12

description:
41443
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep57

description:
41702
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep56

description:
41695
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep52

description:
41704
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep55

description:
41817
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep53

description:
41465
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep54

description:
41471
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep10

description:
41895
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep51

description:
41740
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep50

description:
41627
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep14

description:
41519
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep48

description:
41684
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep49

description:
41657
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep47

description:
41710
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep9

description:
41744
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep8

description:
41832
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep45

description:
41453
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep43

description:
41706
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep46

description:
28819
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep44

description:
41884
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep42

description:
41878
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep41

description:
41877
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep39

description:
41810
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep40

description:
41473
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep36

description:
41444
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep38

description:
41610
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep7

description:
41413
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep11

description:
41785
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep34

description:
41843
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep37

description:
41854
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep35

description:
41489
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep31

description:
28804
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep33

description:
41432
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep32

description:
41591
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep27

description:
41759
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep29

description:
41796
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep26

description:
41812
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep28

description:
41883
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep5

description:
41800
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep25

description:
41830
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep4

description:
41786
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep24

description:
41781
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep23

description:
41864
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep22

description:
41847
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep18

description:
41488
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep21

description:
41701
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep20

description:
41574
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep19

description:
41723
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep17

description:
41809
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep16

description:
41592
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep2

description:
41495
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep3

description:
41542
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep14

description:
28854
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep15

description:
41818
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep13

description:
41685
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep11

description:
28834
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep8

description:
41842
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep9

description:
28839
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep30

description:
41549
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep6

description:
41850
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep4

description:
41490
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep3

description:
41816
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep1

description:
41882
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep6

description:
28843
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep1

description:
41865
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep5

description:
41820
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Td9-A12,Cre

first: Luzi

last: Yang

address: 38 Xueyuan Road, Haidian District

institute: Peking University Health Science Ce

data_processing:
After sequencing, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads.
RNA-seq reads were aligned to GrCM38/mm10 added Cre with STAR 2.7.9a aligner.
Reads counts were calculated via FeatureCounts v2.0.1.
Assembly: GrCM38/mm10 added Cre
Supplementary files format and content: Td9_miR122_C.txt includes raw counts for each Sample.

source_name: Liver

extract_protocol:
RNA was harvested using TransZol Up Plus RNA Kit(TransGen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  mRNA-seq Library Prep Kit  following manufacture's protocols.

value: Liver


title: Td9-A10,Cre


title: Td9-A11,Cre


title: Td9-A4,Cre-miR122


title: Eggshell_Colour_Brown_rep166

description:
41530
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep35

description:
41479
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep34

description:
51408
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Td9-A1,Cre-miR122


title: Eggshell_Colour_White_rep33

description:
41622
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep10

description:
41643
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep165

description:
41696
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep31

description:
51659
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep30

description:
28803
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep29

description:
28833
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep28

description:
51461
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep27

description:
41769
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep164

description:
41891
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep7

description:
41460
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep26

description:
28835
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep162

description:
41735
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep2

description:
41496
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep25

description:
41497
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep161

description:
41636
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep160

description:
41690
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep159

description:
41605
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: 8MGBA S-SETMAR  control biol rep 2

city: Tours

first: Sylvaine

last: Renault

address: 10 bld Tonnelé

country: France

institute: INSERM U1253

data_processing:
performed on use.Galaxy.org
Sequence reads were trimmed with Trimmomatic (Galaxy Version 0.38.0)
Reads were mapped with HISAT2 (Galaxy Version 2.4.2+galaxy0).
Expression level of transcripts was quantified with htseq-count (Galaxy Version 0.9.1)
Differential expression was performed with DESEQ2(Galaxy Version (Galaxy Version 2.11.40.8)
Assembly: GRCH38.p11
Supplementary files format and content: table-delimited text file includes  raw counts for each file (Htcount_SETMAR)
Supplementary files format and content: table-delimited text file includes  DEGs with LogFC, pvalue, pvalue-adjusted issued from comparison of Htcount 8MBGA versus 8MGBA S-SETMAR (Deseq_SETMAR)

growth_protocol: 8MGBA (human GB, #ACC-432 DSMZ)  and 8MGBA S-SETMAR cells were cultured in Minimum Essential Medium (MEM, ThermoFisher) supplemented with 10% Fetal Bovine Serum (FBS, ThermoFisher) and maintained in 5% CO2at 37°C

extract_protocol:
RNA were extracted with Direct-Zol RNA miniprep kit (Zymo Research).
RNA-seq libraries were performed using TruSeq Stranded mRNA kit (Illumina). Indexed samples were sequenced on  Illumina HiSeq 1500 to obtain single end reads.

treatment_protocol: no treatment

tag: cell line

value: astrocytes


title: 8MGBA S-SETMAR  control biol rep 3


title: Td9-A2,Cre-miR122


title: Eggshell_Colour_Brown_rep158

description:
41589
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: 8MGBA S-SETMAR  control biol rep 1


title: Eggshell_Colour_Brown_rep156

description:
41494
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep24

description:
41461
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: 8MGBA control biol rep 2


title: 8MGBA control biol rep 1


title: 8MGBA control biol rep 3


title: Eggshell_Colour_White_rep32

description:
41726
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: SP04_480

city: Fuzhou

first: Nathaniel

last: Weygant

state: Fujian

address: Qiuyang street

department: Academy of Integrative Medicine

institute: FJTCM

description: Library name: Sample 8

data_processing:
Qubit2.0 Fluorometer was used for preliminary quantification, and the library was diluted to 1.5ng/SYMBOL for ul.
Agilent 2100 bioanalyzer was used to detect the insert size of the library.
After passing the library inspection, different libraries were pooled according to the effective concentration and the required amount of target data for off-machine processing, followed by Illumina sequencing, resulting in 150 bp paired-end reads.
The image data obtained from the high-throughput sequencing instrument for sequencing fragments were converted into sequence data through CASAVA base calling. HISAT2 v2.0.5 was used to construct an index for the reference genome, and paired-end clean reads were aligned to the reference genome using HISAT2 v2.0.5. featureCounts (1.5.0-p3) was used to calculate the reads mapped to each gene.
Assembly: Subsequently, the FPKM of each gene was calculated based on its length, and the reads mapped.
Supplementary files format and content: tab-delimited text files including raw counts data for each samples

source_name: colon

growth_protocol: SW480 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1× penicillin/streptomycin at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Cells were carefully washed with PBS, suspended in 1.5 ml of TRIzol reagent per 1×107 cells, and transfered to an RNase-free 15 ml centrifuge tube and snap frozen in liquid nitrogen.
The NEBNext® UltraTM RNA Library Prep Kit (Illumina) to establish the RNA libraries.

treatment_protocol: SW480 was digested with 0.2% trypsin-EDTA and then seeded in a 6 well plate and incubated at 37°C overnight. The next day, 1 x 107 TU of lentivirus was added when the cell confluence reached 50%. After infection, the medium was replaced and puromycin (MCE, HY-B1743; 4μg/ml) was added to each well. Puromycin selection was maintained until the Western blot confirmed stable overexpression of SPOCK1.

value: colon

value: human  CRC cell

value: epithelial cell

tag: batch


title: Eggshell_Colour_White_rep23

description:
41596
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: SP03_480

description: Library name: Sample 7


title: Eggshell_Colour_Brown_rep155

description:
41628
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: SP01_480

description: Library name: Sample 5


title: Eggshell_Colour_White_rep22

description:
41678
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep153

description:
28850
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Ct04_480

description: Library name: Sample 4


title: Eggshell_Colour_Brown_rep163

description:
41531
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Ct03_480

description: Library name: Sample 3


title: Eggshell_Colour_Brown_rep151

description:
41776
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep152

description:
41857
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Ct02_480

description: Library name: Sample 2


title: Eggshell_Colour_Brown_rep150

description:
41671
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep21

description:
41597
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep157

description:
41659
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep149

description:
41557
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Ct01_480

description: Library name: Sample 1


title: B3 MYT3MT

city: Nashville

first: guoqiang

last: Gu

state: Tennessee

address: 9415D Medical Research Building IV

department: Department of Cell and Developmental Biology

institute: Vanderbilt University Medical Center

description:
Library name: 8960-GG-3
indrop

library_source: transcriptomic single cell

data_processing:
DropEst was used to generate count matrices.
Cells with low unique mapping reads (<500), low proportion of expressed genes (<100), or high proportion of mitochondrial RNAs (>10%) will be excluded.
Reads were normalized using UMI-filtered counts.
Cell subpopulations were identified and visualized by UMAP using Seurat based on the first 30 principal components generated from the top 2000 highly variable genes.
Assembly: GRCh38
Supplementary files format and content: tab-separated values files and matrix files

source_name: pancreas islet

growth_protocol: Human donor islets were from IIDP or the Nationwide Children's Hospital, Columbus, OH. Islets were stained with dithizone to verify islet purity, stained with DAPI or Trypan blue to examine viability, and tested for glucose responsiveness. Only islets with >80% purity, >95% viability, and a stimulation index above 2.0 were used for studies.

extract_protocol:
Each shRNA was expressed in one lentiviral DNA construct under the control of a U6 promoter, which also expresses eGFP for monitoring transfection. Islets were dissociated into single cells, washed with standard CMRL islet media (CMRL1066 with 10% heat-inactivated FBS, 1X antibiotics, and 1X L-glutamine) and resuspended in VPM media (50% CMRL1066 + 50% Vasculife Basal Media, 10% heat-inactivated FBS, 1X antibiotics, 0.5X Glutamax, 2.5 mM HEPES, 0.5X sodium pyruvate plus rh VEGF LifeFactor, rh EGF LifeFactor, rh FGF basic LifeFactor, rh IGF-1 LifeFactor, Ascorbic Acid LifeFactor, Hydrocortisone Hemisuccinate LifeFactor, Heparin Sulfate LifeFactor, Gentamicin/Amphotericin, L-glutamine LifeFactor B, and iCell Endothelial Cells Medium Supplement). Cells (200,000 in 200 μL) were aliquoted into one prepared Aggrewells 96-well plate, mixed with 40-50 ng of lentivirus. The plate was centrifuged at 200g for 5 min and left undisturbed in a cell culture incubator for 5 days. The PSIs were then recovered for downstream studies. Wells preparation uses 100ul/well of anti-adhesive rinsing solution (96-well late, Nacali #4860-900SP).
dissociated PSIs with ~80-90% single cells and <5% dead cells were used for InDrop. The end library was sequenced with Novaseq 6000 (Illumina), targeting 120 million reads per sample.

treatment_protocol: Single cells were infected with lentivirus expressing control or targeting shRNA, made into pseudo-islets in 5days. Pseudo-islets were dissociated into single cells again for routine InDrop-based scRNA-seq.

value: pancreas islet

value: MYT3 mutated


title: Eggshell_Colour_Brown_rep147

description:
41833
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: B3 MYT1MT

description:
Library name: 8960-GG-2
indrop

value: MYT1 mutated


title: Eggshell_Colour_Brown_rep148

description:
41732
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep146

description:
41661
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep145

description:
41677
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: HD_74A_2 Lane 1

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description:
Library name: Sample 7
HD_74A_2_raw_peak_expression.h5
HD_74A_2_fragments.tsv.gz
HD_74A_2_fragments.tsv.gz.tbi

library_source: genomic single cell

data_processing:
The barcoded processing and gene counting were made using the Cell Ranger ATAC software v2.0.0 [Zheng2017]. Cells with less than3000 or greater than 40000 reads were excluded; cells with less than 3000 or greater than 3000 features were excluded; cells with a TSS enrichment score below 3 were excluded; cells with a percentage above 0.25% of fragments from the blacklist were excluded.
Post-alignment processing and visualisation was performed using Seurat v5.1 [Hao2023] and Signac v1.14.0 [Stuart2021] . Data was normalised using the term frequency inverse document frequency (TF-IDF) with a scale factor of 10000 [Cusanovich2015].
The clustering was performed using SLM [Waltman2013]; ClustAssess[Shahsavari2022] was used for identifying stable clusters; the identification of markers was performed per cluster vs its complement using the Wilcoxon rank sum test. The genes with average log-foldchange less than 0.5 and with and adjusted pvalue greater than 0.05 were discarded as markers.
The visualisation and community accessible overview were complied using ClustAssess.
Assembly: GRCh38 (Ensembl 93 from pre-built Cell Ranger reference 3.1.0)
Supplementary files format and content: count matrix containing raw peak by gene expression (hdf5)
Supplementary files format and content: tsv file containing the fragment information

source_name: HD

extract_protocol:
Cells were harvested using accutase, spun down, and resuspented in 2 mL of PBS for cell counting. Nuclei from 2 x106 cells were isolated following the manufacturer's instructions. The number of nuclei was then assessed by using Countess II.
Approximately 16,000 nuclei were incubated with the transposase enzyme, loaded into Chromium Next GEM Chip H Single Cell Kit (10x Genomics), and snATAC libraries were generated with Chromium Single Cell ATAC Reagent Kits User Guide v1.1 (10x Genomics) according to manufacturer’s instructions.

value: HD

value: induced neural stem cells

tag: sample group

value: healthy


title: B3 Control

description:
Library name: 8960-GG-1
indrop

value: wild type


title: SP02_480

description: Library name: Sample 6


title: HD_74A_1 Lane 2

description:
Library name: Sample 6
HD_74A_1_raw_peak_expression.h5
HD_74A_1_fragments.tsv.gz
HD_74A_1_fragments.tsv.gz.tbi


title: HD_74A_1 Lane 1

description:
Library name: Sample 5
HD_74A_1_raw_peak_expression.h5
HD_74A_1_fragments.tsv.gz
HD_74A_1_fragments.tsv.gz.tbi


title: Eggshell_Colour_Brown_rep144

description:
41590
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: HD_74A_2 Lane 2

description:
Library name: Sample 8
HD_74A_2_raw_peak_expression.h5
HD_74A_2_fragments.tsv.gz
HD_74A_2_fragments.tsv.gz.tbi


title: Eggshell_Colour_White_rep20

description:
41791
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_White_rep19

description:
28831
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: 105_2g_2 Lane 2

description:
Library name: Sample 4
105_2g_2_raw_peak_expression.h5
105_2g_2_fragments.tsv.gz
105_2g_2_fragments.tsv.gz.tbi

value: PMS


title: 105_2g_2 Lane 1

description:
Library name: Sample 3
105_2g_2_raw_peak_expression.h5
105_2g_2_fragments.tsv.gz
105_2g_2_fragments.tsv.gz.tbi


title: Eggshell_Colour_Brown_rep154

description:
41427
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: 105_2g_1 Lane 2

description:
Library name: Sample 2
105_2g_1_raw_peak_expression.h5
105_2g_1_fragments.tsv.gz
105_2g_1_fragments.tsv.gz.tbi


title: Eggshell_Colour_Brown_rep143

description:
28805
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: Eggshell_Colour_Brown_rep142

description:
41535
Hybrid offspring with bidirectional selection for white and brown egg shells.
600K Affymetrix Axiom Chicken Genotyping Array


title: HD_7HA_DMSO

description:
Library name: Sample 4
healthy control

data_processing:
The barcoded processing and gene counting were made using the Cell Ranger software v7.1.0 [Zheng2017]. Cells with less than 3000 or more than 60000 reads were excluded; cells with less than 1000 features were excluded; cells with less than 2% and more than 10% reads incident to mitochondrial genes were excluded; cells with less than 15% and more than 40% reads incident to ribosomal protein genes were excluded.
Post-alignment processing and visualisation was performed using Seurat v5.1 [Hao2023]. Data was normalised using log-normalisation with a scale factor of 10000 [Lun2016].
The clustering was performed using SLM [Waltman2013]; ClustAssess[Shahsavari2022] was used for identifying stable clusters; the identification of markers was performed per cluster vs its complement using the Wilcoxon rank sum test. The genes with average log-foldchange less than 0.5 and with and adjusted pvalue greater than 0.05 were discarded as markers.
The visualisation and community accessible overview were complied using ShinyCell [Ouyang2021] and ClustAssess.
Assembly: GRCh38 (Ensembl 93 from pre-built Cell Ranger reference 3.1.0)
Supplementary files format and content: count matrix containing raw gene expression (hdf5)

molecule: nuclear RNA

source_name: induced neural stem cells

growth_protocol: iNSCs are maintained in neural induction media consisting of DMEM/F12 and neural basal (1:1), supplemented with N2 (1X), B27 (1X), 1% glutamax, CHIR99021 (3 uM), SB-431542 (3 uM), and hLIF (5 uM). iNSCs are grown on growth factor reduced matrigel coated tissue culture plastic.

extract_protocol:
Cells were harvested using accutase, spun down, and resuspented in 2 mL of PBS for cell counting.
10,000 cells were loaded into Chromium Next GEM Chip G Single Cell Kit (10x Genomics), and scRNA libraries were generated with Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to manufacturer’s instructions.


title: 105_2g_1 Lane 1

description:
Library name: Sample 1
105_2g_1_raw_peak_expression.h5
105_2g_1_fragments.tsv.gz
105_2g_1_fragments.tsv.gz.tbi


title: P7hLPS14h heart6

city: changsha

first: yan

last: tan

address: 138 Tongzpo Road

institute: XiangYa School of Medicine

data_processing:
RNA sequencing was performed on a BGISEQ-500 platform (BGI, Guangdong, China).
After removing reads with low quality, the clean reads were aligned to a mouse genome (mm10) with HiSat2 software (version 2.0.4) and Bowtie2 (version 2.2.5) and sorted with RSEM (version 1.2.12).
The fragments per kilobase of exon model per million mapped fragments (FPKM) estimate for each detected gene was determined with StringTie (version 1.3.3.13) software. The count information acquired from the files created by StringTie was further taken as the input of DESeq2 (version 1.4.5) for differentially expressed gene (DEG) identification.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample；Matrix table with raw gene counts for every gene and every sample

source_name: heart tissue

growth_protocol: Male C57BL/6J mice were maintained on a 12-hour light-dark cycle in a pathogen-free facility at Central South University(Changsha,Hunan, China).

extract_protocol:
Heart tissues were dissected, harvested in TRIzol reagent, The RNA quality and quantity were tested with 1% agarose gels, a NanoDrop and an Agilent 2100 bioanalyzer (Thermo Fisher Scientific).
cDNA libraries were constructed using an MGIEasy RNA Library Prep Kit V3.0 (96 RXN) (MGI, 1000005272)

treatment_protocol: Six replicate of control heart group was PBS treated as control;Six replicate of P7h heart group was poly(I:C) priming for 7 hours;Six replicate of P7hLPS4h heart group was poly(I:C) priming for 7 hours and then LPS treated for 4 hours;Six replicate of P7hLPS14h heart group was poly(I:C) priming for 7 hours and then LPS treated for 14 hours.

value: heart tissue

value: Poly(I:C) 7h+LPS 14h

value: 8-10 weeks


title: HD_7HA_ABT_263

description:
Library name: Sample 3
healthy control

value: senolytic treatement


title: P7hLPS14h heart5


title: 105_2g_DMSO

description:
Library name: Sample 2
PMS


title: 105_2g_ABT_263

description:
Library name: Sample 1
PMS


title: P7hLPS14h heart4


title: C24

description: Library name: Sample 25

data_processing:
Quality checks were performed using FastQC (v0.12.1), summarised with MultiQC (v1.14). Reads were then subsampled. Alignment to the human reference genome (build GRCh38.p13) was performed using STAR (v2.7.10a) with default parameters. The counts of the aligned reads corresponding to exons were obtained using featureCounts program against the exon annotations obtained from the ensembl database (annotation file Homo_sapiens.GRCh38.101.gtf). MA plots, JSIs and PCA were performed as further quality checks.
The resulting expression values were normalised using quantile normalisation [Bolstad2003] and noise levels were assessed using noisyR count matrix approach [Moutsopoulos2021].
Differential expression analysis was performed using edgeR (v3.34.1) [Robinson2010] and DESeq2 1.32.0 [Love2014].
The visualisation, and community accessible overview were complied using bulkAnalyseR [Moutsopoulos2023].
Assembly: hg38 (GRCh38.p13)
Supplementary files format and content: csv count matrix containing raw gene expression
Supplementary files format and content: csv count matrix containing normalised and denoised gene expression

growth_protocol: iNSCs are maintained in neural induction media consisting of DMEM/F12 and neural basal (1:1), supplemented with N2 (1X), B27 (1X), 1% glutamax, CHIR99021 (3 µM), SB-431542 (3 µM), and hLIF (5 µM). iNSCs are grown on growth factor reduced matrigel coated tissue culture plastic.

extract_protocol:
Qiagen RNeasy Kit
standard Illumina protocol

tag: condition

value: individual control iNSC treated with CM from individual PMS treated with senolytic


title: P7hLPS14h heart3


title: C23

description: Library name: Sample 24


title: C22

description: Library name: Sample 23


title: P7hLPS14h heart1


title: P7hLPS4h heart6

value: Poly(I:C) 7h+LPS 4h


title: C21

description: Library name: Sample 22


title: P7hLPS4h heart5


title: C18_2

description: Library name: Sample 19


title: C20

description: Library name: Sample 21


title: C19

description: Library name: Sample 20


title: P7hLPS4h heart2


title: P7hLPS4h heart4


title: P7hLPS4h heart1


title: C16

description: Library name: Sample 16


title: P7h heart5

value: Poly(I:C) 7h


title: P7h heart6


title: P7h heart4


title: C18

description: Library name: Sample 18


title: C13

description: Library name: Sample 13

value: individual control iNSC treated with CM from individual PMS


title: P7h heart2


title: C15

description: Library name: Sample 15


title: C17

description: Library name: Sample 17


title: C12

description: Library name: Sample 12


title: P7hLPS14h heart2


title: C14

description: Library name: Sample 14


title: P7h heart3


title: C10

description: Library name: Sample 10


title: P7h heart1


title: control heart5

value: PBS


title: C9

description: Library name: Sample 9


title: C8

description: Library name: Sample 8


title: C11

description: Library name: Sample 11


title: control heart4


title: control heart3


title: P7hLPS4h heart3


title: C7

description: Library name: Sample 7


title: control heart2


title: C6

description: Library name: Sample 6

value: base iNSC


title: control heart1


title: C5

description: Library name: Sample 5


title: OE-NC9

city: Shanghai

first: Y

last: Su

address: No. 1200, Huatuo Road, Shanghai University of Traditional Chinese Medicine

description: Library name: Sample 20

data_processing:
Illumina NovaSeq 6000
Rawreads were obtained following mRNA-Seq sequencing.
The adapter sequences were removed using the Cutadapt program.
The data quantity of the clean data was quantified using the FastQC program, including the proportions of bases with quality scores of Q20 and Q30.
The clean data were aligned to the reference genome using the HISAT2 program.
Reads were assembled into transcripts and gene expression levels were analyzed using the StringTie program.
Expression analysis of differentially expressed genes was conducted using edgeR or DEGseq.
GO and KEGG pathway analyses of differentially expressed genes were performed using the clusterProfiler.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: liver

growth_protocol: constant humidity (60 ± 5%), temperature (24 ± 1°C), and a 12h light/dark cycle (6AM to 6PM light)

extract_protocol:
mRNA was extracted using the KAPA Stranded mRNA-Seq Kit.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: TDO knockdown and overexpression MHCC-97H, Huh7 cells and their empty control cells were subcutaneously injected into both armpits of nude mice.

value: liver

value: BALB/C

value: 4 weeks

value: male


title: OE-NC8

institute: Shanghai University of Traditional Chinese Medicine

description: Library name: Sample 19


title: C4

description: Library name: Sample 4

value: induced neural stem cells


title: OE-NC6

description: Library name: Sample 18


title: C3

description: Library name: Sample 3


title: C2

description: Library name: Sample 2


title: control heart6

value: wild type


title: C1

description: Library name: Sample 1


title: VCaP_11OHTE_Rep3

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

institute: Laval University

description: Library name: Sample 63

data_processing:
Raw sequencing data were trimmed using trimmomatic v0.39
Quality of trimmed reads was analyzed using FastQC (v0.12.1)
Qc results were merged using MultiQC (v1.23)
Assembly: Reads were pseudo-aligned to the human reference genome GRCh38 using Kallisto (v0.46.1).
Supplementary files format and content: Raw counts and normalized counts were generated using DESeq2 (v.1.42.1).

source_name: VCaP

growth_protocol: VCaP (CVCL_2235) were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, 1% L-glutamine, 1 mM sodium pyruvate;  LAPC4 (CVCL_4744) were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, 1% L-glutamine; DU145 (CVCL_0105) were maintained in EMEM supplemented as above and with 1% MEM Non-essential amino acid, 1 mM sodium pyruvate. All cells were maintained at 37°C with 5% CO₂ and cultured for a maximum of four months.

extract_protocol:
Total RNA was extracted with a RNEasy plus mini kit (Qiagen, Toronto, ON, Canada). RNA quantification and quality control were done with a NanoDrop spectrophotometer and Agilent 2100 BioAnalyzer , respectively. Samples had an RNA Integrity Number ≥ 9.5.
RNA sequencing libraries were prepared using NEBNext Ultra II Directional RNA library with NEBNext Poly(A) mRNA (New England Biolabs, Whitby, ON, Canada)

treatment_protocol: Cells were hormone-deprived for 72 hours in phenol-red free medium supplemented with 2% charcoal-stripped serum (CSS). Cells were then treated with 10 nM of an androgen or vehicle only (containing 0.05 % DMSO), with or without 10 µM enzalutamide

value: VCaP

value: Prostate cancer CRPC model

value: AR positive

value: 11OHT 10 nM + enzalutamide 10 uM)

tag: time


title: VCaP_11OHTE_Rep2

description: Library name: Sample 62


title: OE8

description: Library name: Sample 14

tag: tissue


title: OE9

description: Library name: Sample 15

tag: Sex


title: OE-NC1

description: Library name: Sample 16


title: VCaP_11OHT_Rep3

description: Library name: Sample 60

value: 11OHT 10 nM


title: OE2

description: Library name: Sample 12


title: OE-NC2

description: Library name: Sample 17


title: OE1

description: Library name: Sample 11


title: VCaP_11OHTE_Rep1

description: Library name: Sample 61


title: KD-NC10

description: Library name: Sample 10


title: OE6

description: Library name: Sample 13


title: VCaP_11OHT_Rep1

description: Library name: Sample 58


title: VCaP_11OHT_Rep2

description: Library name: Sample 59


title: VCaP_11KTE_Rep3

description: Library name: Sample 57

value: 11KT 10 nM + enzalutamide 10 uM)


title: VCaP_11KTE_Rep2

description: Library name: Sample 56


title: VCaP_11KTE_Rep1

description: Library name: Sample 55


title: KD-NC9

description: Library name: Sample 9


title: VCaP_11KT_Rep2

description: Library name: Sample 53

value: 11KT 10 nM


title: KD-NC5

description: Library name: Sample 7


title: VCaP_11KT_Rep1

description: Library name: Sample 52


title: KD-NC1

description: Library name: Sample 6


title: KD10

description: Library name: Sample 5


title: KD-NC6

description: Library name: Sample 8


title: KD9

description: Library name: Sample 4


title: VCaP_R1881E_Rep3

description: Library name: Sample 51

value: R1881 10 nM + enzalutamide 10 uM)


title: KD6

description: Library name: Sample 3


title: VCaP_R1881E_Rep2

description: Library name: Sample 50


title: KD5

description: Library name: Sample 2


title: VCaP_R1881E_Rep1

description: Library name: Sample 49


title: KD1

description: Library name: Sample 1


title: VCaP_R1881_Rep3

description: Library name: Sample 48


title: VCaP_R1881_Rep2

description: Library name: Sample 47


title: Stroma_IgG

city: St. Louis

first: Liang

last: Ma

state: MO

address: 660 S. Euclid Ave

department: Medicine, Obstetrics and Gynecology

institute: Washington University

description:
Library name: Stroma_IgG_GATAGCCAAT-ACCAACACAG
Stroma_IgG-LIB062172_22H52CLT4_S457_L004.RPKMnorm.bigwig

library_source: genomic

data_processing:
Reads were aligned to the mm10 mouse genome using the Bowtie2 read aligner.
Aligned reads were extracted and converted to a sorted bam file using SAMtools. Scaled BigWig files were generated using Deeptools.
Merged bam files for replicates of input, IgG, and Sall1 in luminal epithelia and stroma.
ChIP peaks were called using Macs2 using IgG samples as background control.
Assembly: mus musculus mm10
Supplementary files format and content: Merged BigWig files (RPKM normalized) for replicates of input, IgG and Sall1 in luminal epithalia and stroma.
Supplementary files format and content: Macs2 narrowPeak files for Sall1 binding in luminal epithelia and stroma, called using Sall1 replicates against IgG background binding.

source_name: uterine stroma

growth_protocol: Female mice were considered 0.5 days post-coitum (dpc) pregnant upon observation of vaginal plugs after mating. 3.5 dpc pregnancy timepoint was confirmed by presence of blastocysts upon PBS flush of uterine horns.

extract_protocol:
Uterine luminal epithelium was isolated by cutting horns into ~4mm segments, opening segments longitudinally to form sheets, shaking sheets in 1mL 1% w/v trypsin in calcium and magnesium free HBSS in 15mL conical tubes for 1.5hr at 4C on a shaking platform, followed by  30 min. shaking at room temperature. 4mL additional HBSS was added to each tube and tubes were shaken vigorously by hand to encourage LE sheets to detach. Contents of each tube was poured onto a 6cm dish. The large chunks were removed with tweezers and placed in new tube for subsequent stromal processing. HBSS was collected from the dish by pipetting and spun at 9,000xG for 5 minutes. Supernatant was removed and remaining pellet was considered isolated LE. To isolate uterine stroma, remaining uterine chunks were incubated in 1mL 0.25% trypsin with 1mg/mL collagenase in HBSS at 37C on a platform shaker at 200rpm for 30 minutes. 3mL additional HBSS was then added to each tube, and 5mL serological pipette was used to pipette up and down at least 25 times to release the stromal cells into solution. This was then again moved to a 6cm petri dish, and large chunks (serous and muscle layers) were removed with tweezers and discarded. Remaining solution was passed through a 100um nylon filter (cell strainer), strainer was rinsed with 1mL full serum hESC growth media, and solution was transferred to tubes and spun at 9,000xG for 5 minutes. Pellets were washed once with 500uL full serum hESC growth media to inhibit remaining trypsin, and solutions were spun again at 9,000xG for 5 minutes. Supernatant was removed and remaining pellet was considered isolated uterine stroma. Uterine luminal epithelia and stroma was washed with cold PBS (+Ca/Mg) and crosslinked for 30 minutes at room temperature with 2mM di(N succinimidyl) glutarate, followed by incubation with 1% formaldehyde for 10 minutes. Chromatin was extracted from isolated nuclei and sheared to 100-1000bp using a Covaris ME220. Primary antibody was incubated overnight for ChIP reactions. Crosslinks were reversed by adding NaCl and heating at 65 °C for 15 h, RNase A was added and incubated for 2 h at 37 °C, and Proteinase K added and incubated 2 h at 63 °C. DNA was isolated using the MinElute PCR Purification Kit (Qiagen 28004).
Libraries were made using NEBNext Ultra II Library Kit (E7645) and sequenced on an Illumina Nova Seq at a depth of 100 million paired end reads.

value: uterine stroma

tag: developmental stage

value: 3.5 dpc

tag: antibody

value: IgG (Cell Signaling 2729)


title: VCaP_R1881_Rep1

description: Library name: Sample 46


title: Stroma_Sall1_rep1

description:
Library name: Stroma_Sall1_rep1_TGGTGAAGAT-ACCTTACAGC
Stroma_Sall1_1_2_merged_RPKMnorm.bigwig
Stroma_Sall1_1_2_peaks_over_IgG_peaks.narrowPeak

value: Sall1 (Abcam 31526)


title: Stroma_Input_rep1

description:
Library name: Stroma_Input_rep1_GGAATGTCAT-ACAGGAACAC
Stroma_Input_1_2_merged_RPKMnorm.bigwig


title: LE_IgG_rep2

description:
Library name: LE_IgG_rep2_CGAGAGAAAT-ACGGAAGAGA
LE_IgG_1_2_merged_RPKMnorm.bigwig

source_name: uterine luminal epithelia

value: uterine luminal epithelia


title: VCaP_DMSO_Rep2

description: Library name: Sample 44

value: DMSO


title: LAPC4_11OHTE_Rep3

description: Library name: Sample 42


title: VCaP_DMSO_Rep3

description: Library name: Sample 45


title: VCaP_DMSO_Rep1

description: Library name: Sample 43


title: Stroma_Sall1_rep2

description:
Library name: Stroma_Sall1_rep2_GGTGTACAAT-ACAGACGCTA
Stroma_Sall1_1_2_merged_RPKMnorm.bigwig
Stroma_Sall1_1_2_peaks_over_IgG_peaks.narrowPeak


title: LE_IgG_rep1

description:
Library name: LE_IgG_rep1_TTCCAGGTAT-ACCAGTGCTT
LE_IgG_1_2_merged_RPKMnorm.bigwig


title: LE_Input_rep2

description:
Library name: LE_Input_rep2_TTACCGACAT-ACCGAATACG
LE_Input_1_2_merged_RPKMnorm.bigwig


title: VCaP_11KT_Rep3

description: Library name: Sample 54


title: LAPC4_11OHT_Rep3

description: Library name: Sample 39


title: LE_Sall1_rep2

description:
Library name: LE_Sall1_rep2_TCGTCTGAAT-ACGTCCTTGA
LE_Sall1_1_2_merged_RPKMnorm.bigwig
LE_Sall1_1_2_peaks_over_IgG.narrowPeak


title: LE_Sall1_rep1

description:
Library name: LE_Sall1_rep1_CACGCAATAT-ACCCTTCCAT
LE_Sall1_1_2_merged_RPKMnorm.bigwig
LE_Sall1_1_2_peaks_over_IgG.narrowPeak


title: LE_Input_rep1

description:
Library name: LE_Input_rep1_CGGCATTAAT-ACGTCAGTCA
LE_Input_1_2_merged_RPKMnorm.bigwig


title: LAPC4_11OHT_Rep2

description: Library name: Sample 38


title: LAPC4_11OHT_Rep1

description: Library name: Sample 37


title: 7824 stroma

description:
Library name: Sample 24
sample.7824_st

data_processing:
RNA-seq reads were aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were then imported into the R/Bioconductor package EdgeR1 and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma2. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights3.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions.
Assembly: Ensembl release 101 primary assembly
Supplementary files format and content: tab-delimited text files includes raw transcript counts for each sample

source_name: Uterine stroma

growth_protocol: Female mice were considered 0.5 days post-coitum (dpc) pregnant upon observation of vaginal plubs after mating. 3.5dpc pregnancy timepoint was confirmed by presence of blastocysts upon PBS flush of uterine horns. 4.5dpc pregnancy timepoint was confirmed by presence of implantation sites during Chicago blue tail vein injection procedure.

extract_protocol:
Uterine luminal epithelium was isolated by cutting horns into ~4mm segments, opening segments longitudinally to form sheets, shaking sheets in 1mL 1% w/v trypsin in calcium and magnesium free HBSS in 15mL conical tubes for 1.5hr at 4C o a shaking platform, followed by  30 min. shaking at room temperature. 4mL additional HBSS was added to each tube and tubes were shaken vigorously by hand to encourage LE sheets to detach. Contents of each tube was poured onto a 6cm dish. The large chunks were removed with tweezers and placed in new tube for subsequent stromal processing. HBSS was collected from the dish by pipetting and spun at 9,000xG for 5 minutes. Supernatant was removed and remaining pellet was considered isolated LE. To isolate uterine stroma, remaining uterine chunks were incubated in 1mL 0.25% trypsin with 1mg/mL collagenase in HBSS at 37C on a platform shaker at 200rpm for 30 minutes. 3mL additional HBSS was then added to eachy tube, and 5mL serological pipette was used to pipette up and down at least 25 times to release the stromal cells into solution. This was then again moved to a 6cm petri dish, and large chunks (serous and muscle layers) were removed with tweezers and discarded. Remaining solution was passed through a 100um nylon filter (cell strainer), strainer was rinsed with 1mL full serum hESC growth media, and solution was transferred to tubes and spun at 9,000xG for 5 minutes. Pellets were washed once with 500uL full serum hESC growth media to inhibit remaining trypsin, and solutions were spun again at 9,000xG for 5 minutes. Supernatant was removed and remaining pellet was considered isolated uterine stroma. Uterine luminal epithelia and stroma was washed with cold PBS and RNA was isolated using Qiagen RNeasy kit with Dnase treatment.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Uterine stroma

value: Sall1 fl/fl; Pgr-cre+

value: pregnancy 4.5dpc

value: seq request 8/31/22


title: 7824 LE

description:
Library name: Sample 23
sample.7824_le

source_name: Uterine luminal epithelium

value: Uterine luminal epithelium


title: LAPC4_11KTE_Rep2

description: Library name: Sample 35

value: Prostate cancer CRPC model

value: AR positive


title: 7351 stroma

description:
Library name: Sample 22
sample.7351_st


title: 7351 LE

description:
Library name: Sample 21
sample.7351_le


title: Stroma_Input_rep2

description:
Library name: Stroma_Input_rep2_GGACATCAAT-ACTACCTGCA
Stroma_Input_1_2_merged_RPKMnorm.bigwig

value: wild type


title: LAPC4_11KTE_Rep1

description: Library name: Sample 34

value: 11KT 10 nM + enzalutamide 10 uM)


title: 7349 stroma

description:
Library name: Sample 20
sample.7349_st


title: LAPC4_11OHTE_Rep2

description: Library name: Sample 41

value: 11OHT 10 nM + enzalutamide 10 uM)


title: LAPC4_11KT_Rep1

description: Library name: Sample 31

value: 11KT 10 nM


title: LAPC4_R1881E_Rep3

description: Library name: Sample 30

value: R1881 10 nM + enzalutamide 10 uM)


title: control 7.20.22 stroma

description:
Library name: Sample 18
sample.control_7.20.22_st

value: Sall1 fl/fl


title: LAPC4_R1881E_Rep2

description: Library name: Sample 29


title: LAPC4_R1881E_Rep1

description: Library name: Sample 28


title: control 4.4.22 LE

description:
Library name: Sample 15
sample.control_4.4.22_le


title: 7349 LE

description:
Library name: Sample 19
sample.7349_le


title: LAPC4_11OHTE_Rep1

description: Library name: Sample 40


title: control 3.22.22 LE

description:
Library name: Sample 13
sample.control_3.22.22_le


title: LAPC4_11KT_Rep2

description: Library name: Sample 32


title: 7210 stroma

description:
Library name: Sample 12
sample.7210.uterine.stroma

value: pregnancy 3.5dpc

value: seq request 4/27/22


title: control 3.22.22 stroma

description:
Library name: Sample 14
sample.control_3.22.22_st


title: control 4.4.22 stroma

description:
Library name: Sample 16
sample.control_4.4.22_st


title: 7210 LE

description:
Library name: Sample 11
sample.7210.uterine.le


title: LAPC4_DMSO_Rep3

description: Library name: Sample 24


title: LAPC4_11KT_Rep3

description: Library name: Sample 33


title: LAPC4_DMSO_Rep2

description: Library name: Sample 23


title: LAPC4_11KTE_Rep3

description: Library name: Sample 36


title: 7141 stroma

description:
Library name: Sample 10
sample.7141.uterine.stroma


title: PIC_CITE TCR Library 3

first: Jonathan

middle: Morris

last: Urbach

state: Massachusetts

address: 400 Technology Sq Rm 851

institute: Ragon Institute of MGH, MIT and Harvard

description:
Library name: VDJ_3
TCR

data_processing:
Demultiplexing using bcl2fastq version 2.19.1.403 and the sample sheet (SampleSheet_PIC_CITE_20250224.csv).
CellRanger (version 9.0.0) multianalysis specifying "Gene Expression", "Antibody Capture", and "VDJ-T" feature types with refdata-gex-GRCh38-2020-A as the genomic reference, refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0 as the VDJ reference, and file feature_reference.PIC_CITE_20250224.0.csv as the feature reference.
Seurat processing in R: counts from the "sample_filtered_feature_bc_matrix/matrix.mtx.gz" file generated by CellRanger were imported into R using the readMM() function from the Matrix package and used to construct a Seurat object for analysis. Demultiplexing of cells on the basis of hashtag oligos to assign cells to time points was performed using the HTODemux() function from Seurat. Matching of cells with tetramer barcodes was also performed using HTODemux() as well, and tetramer barcode/participant/response associations were mapped using the table in Participant_Response_Sample_metadata.tsv. TCR counts were imported from the "multi/vdj_t/all_contig_annotations.json" file using the jsonlite R package. For clustering, dimensionality reduction, differential expression, and other analysis, genes matching the following regular expression "^TR[ABDG][VJC]" were removed so that clustering would not be driven by clonotype-specific TCR gene expression. Only cells that were unambiguously assigned to a by HTO (HTO_classification.global == "Singlet") were included in the filtered data set.
Assembly: GRCh38-2020-A
Supplementary files format and content: tsv: tab separated values, tsv.gz: gzip-compressed tab-separated values, and json data format.
Library strategy: CITE-seq

source_name: PBMC

extract_protocol:
Epitope-specific CD8+ T cells were isolated by FACS.
10x Genomics Chromium GEM-X Single Cell 5' Reagent Kit v3 (Dual Index) library construction protocol with feature barcodes

treatment_protocol: Longitudinal samples from before and after administration of broadly neutralizing anti HIV1 antibodies (3BNC117 and/or 10-1074) in the context of analytical treatment interruption.

value: PBMC

value: CD8+ T cells

value: bNAb treatment & ATI


title: PIC_CITE TCR Library 2

description:
Library name: VDJ_2
TCR


title: 7141 LE

description:
Library name: Sample 9
sample.7141.uterine.le

value: Sall1 fl/fl; Pgr-cre+


title: PIC_CITE TCR Library 4

description:
Library name: VDJ_4
TCR


title: LAPC4_DMSO_Rep1

description: Library name: Sample 22

value: DMSO


title: DU145_11OHTE_Rep3

description: Library name: Sample 21

value: AR negative


title: 7211 stroma

description:
Library name: Sample 8
sample.7211.uterine.stroma

value: Uterine stroma


title: LAPC4_R1881_Rep3

description: Library name: Sample 27

value: Prostate cancer CRPC model


title: control 7.20.22 LE

description:
Library name: Sample 17
sample.control_7.20.22_le

value: Uterine luminal epithelium

value: pregnancy 4.5dpc

value: seq request 8/31/22


title: LAPC4_R1881_Rep1

description: Library name: Sample 25

value: AR positive


title: 7211 LE

description:
Library name: Sample 7
sample.7211.uterine.le


title: PIC_CITE Gene Expression Library 2

description:
Library name: GEX_2
RNA


title: LAPC4_R1881_Rep2

description: Library name: Sample 26


title: DU145_11OHTE_Rep1

description: Library name: Sample 19

value: 11OHT 10 nM + enzalutamide 10 uM)


title: 7209 stroma

description:
Library name: Sample 6
sample.7209.uterine.stroma


title: DU145_11OHT_Rep3

description: Library name: Sample 18

value: 11OHT 10 nM


title: PIC_CITE ADT Library 3

description:
Library name: ADT_3
ADT

library_source: other

molecule: protein


title: PIC_CITE Gene Expression Library 1

description:
Library name: GEX_1
RNA


title: PIC_CITE ADT Library 4

description:
Library name: ADT_4
ADT


title: PIC_CITE ADT Library 2

description:
Library name: ADT_2
ADT


title: PIC_CITE ADT Library 1

description:
Library name: ADT_1
ADT


title: DU145_11OHT_Rep2

description: Library name: Sample 17


title: CITE-seq TCR library 2

description:
Library name: TCR2
TCR
filtered_contig_annotations.csv

data_processing:
Demultiplexing using bcl2fastq version 2.19.1.403 and the provided sample sheet.
CellRanger multianalysis specifying "Gene Expression", "Antibody Capture", and "VDJ-T" feature types with refdata-gex-GRCh38-2020-A as the genomic reference and refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0 as the VDJ reference.
Seurat processing in R: counts from the "sample_filtered_feature_bc_matrix/matrix.mtx.gz" file generated by CellRanger were imported into R using the readMM() function from the Matrix package and used to construct a Seurat object for analysis. Demultiplexing of cells on the basis of hashtag oligos to assign cells to time points was performed using the HTODemux() function from Seurat. Samples corresponding to the top 5% of  counts for the A03_FLU_IK9 and A03_EBV_RK9 were removed from the data set because staining for those specificities was poor. TCR counts were imported from the "multi/vdj_t/filtered_contig_annotations.csv" file. For clustering, dimensionality reduction, differential expression, and other analysis, genes matching the following regular expression "^TR[ABDG][VJC]" were removed so that clustering would not be driven by clonotype-specific TCR gene expression. Only cells that were unambiguously assigned to a by HTO (HTO_classification.global == "Singlet") were included in the filtered data set.
Assembly: GRCh38-2020-A
Supplementary files format and content: tsv: tab separated values and tsv.gz: gzip-compressed tab-separated values.
Library strategy: CITE-seq

extract_protocol:
Epitope-specific CD8+ T cells were isolated by FACS.
10x Genomics Chromium Next GEM Single Cell 5' Reagent Kit v2 (Dual Index) library construction protocol with feature barcodes

treatment_protocol: Longitudinal samples from a participant undergoing analytical treatment interruption.

value: T cells

value: ATI


title: CITE-seq TCR library 3

description:
Library name: TCR3
TCR
filtered_contig_annotations.csv


title: 7214 stroma

description:
Library name: Sample 4
sample.7214.uterine.stroma

value: Sall1 fl/fl

value: pregnancy 3.5dpc

value: seq request 4/27/22


title: CITE-seq TCR library 1

description:
Library name: TCR1
TCR
filtered_contig_annotations.csv

value: PBMC


title: PIC_CITE TCR Library 1

description:
Library name: VDJ_1
TCR

value: CD8+ T cells

value: bNAb treatment & ATI


title: SA-WTSS2

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: single-stranded RNA, unphosphorylated CACUUUCACUUCUCCCUUUUAGUUUCC

data_processing:
Reads were first trimmed of adapters and low-complexity sequences with cutadapt 1.14 (-O 5 -f fastq --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT)
Trimmed reads were then sorted with fastq-tools (fastq-sort)
Trimmed reads were mapped against RepBase with STAR v2.4.0j to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 10 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Remaining reads were mapped to the appropriate genome build (hg19) using STAR aligner (--outFilterMultimapNmax 10 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
featureCounts was used to count reads according to gencode v19 annotations (-s 2 -M)
Assembly: hg19
Supplementary files format and content: bigwigs contain RPM-normalized read densities of uniquely-mapped reads
Supplementary files format and content: counts text files contain output from featureCounts

source_name: human embryonic kidney

growth_protocol: 1X Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37°C in a 5% CO2

extract_protocol:
poly(A) selection
Illumina stranded mRNA, part# 15031047 Revision E

treatment_protocol: 2.5 μL Lipofectamine 2000 and 125 μL Opti-MEM medium were combined with a mixture of 1 μg RNA (either ssRNA or 3p-RNA) and 125 μL Opti-MEM per well of a 6-well plate. After 5 min at room temperature, the solution was added drop-wise to cells grown to 70-90% confluence in 2 mL DMEM

value: human embryonic kidney

value: embryonic kidney

value: wildtype

value: transfection


title: DU145_11OHT_Rep1

description: Library name: Sample 16

value: Prostate cancer CRPC model

value: AR negative


title: DU145_11KTE_Rep3

description: Library name: Sample 15

value: 11KT 10 nM + enzalutamide 10 uM)


title: SA-WTSS1


title: PIC_CITE Gene Expression Library 3

description:
Library name: GEX_3
RNA


title: 7208 stroma

description:
Library name: Sample 2
sample.7208.uterine.stroma

value: Uterine stroma


title: CITE-seq Gene Expression library 3

description:
Library name: GEX3
RNA
HEAL_FILTERED_RNA_COUNTS.tsv.gz


title: DU145_11KTE_Rep2

description: Library name: Sample 14


title: 7208 LE

description:
Library name: Sample 1
sample.7208.uterine.le

value: Uterine luminal epithelium


title: DU145_11OHTE_Rep2

description: Library name: Sample 20

value: 11OHT 10 nM + enzalutamide 10 uM)


title: CITE-seq Gene Expression library 1

description:
Library name: GEX1
RNA
HEAL_FILTERED_RNA_COUNTS.tsv.gz

value: T cells

value: ATI


title: CITE-seq Gene Expression library 2

description:
Library name: GEX2
RNA
HEAL_FILTERED_RNA_COUNTS.tsv.gz


title: PIC_CITE Gene Expression Library 4

description:
Library name: GEX_4
RNA


title: SA-WT3P1

description: single-stranded RNA, tri-phopshorylated TAATACGACTCACTATAGGAAACTAAAAGGGAGAAGTGAAAGTG and CACTTTCACTTCTCCCTTTTAGTTTCCTATAGTGAGTCGTATTA


title: DU145_11KT_Rep3

description: Library name: Sample 12

value: 11KT 10 nM


title: 7214 LE

description:
Library name: Sample 3
sample.7214.uterine.le

value: Sall1 fl/fl

value: pregnancy 3.5dpc

value: seq request 4/27/22


title: DU145_11KTE_Rep1

description: Library name: Sample 13


title: SA-KOSS2

value: PARP13 knockout, homozygous


title: WT 3 + 4NQO

city: Tucson

first: Justin

last: Wilson

state: AZ

address: 1515 N Campbell Ave

department: Immunobiology

institute: The University of Arizona

description: Library name: WT002R2

data_processing:
Data was processed by Novogene
Assembly: Genome build/assembly prepared by Novogene
Supplementary files format and content: txt file contains FPKM values for each sample

source_name: tongue

extract_protocol:
Tongue tissue was homogenized using Qiagen RNAeasy Plus kits per manufacturer's instructions.
RNA libraries were constructed by Novogene for sequencing

treatment_protocol: Mice were treated with 100 μg/ml 4NQO for 20 weeks in drinking water ad libitum. Tongues were excised for RNA extraction.

value: tongue

value: WT


title: WT 2 + 4NQO

description: Library name: WT002L2


title: DU145_11KT_Rep2

description: Library name: Sample 11


title: CITE-seq ADT library 2

description:
Library name: ADT2
ADT
HEAL_FILTERED_ADT_COUNTS.tsv.gz
HEAL_FILTERED_HTO_COUNTS.tsv.gz
HEAL_FILTERED_TET_COUNTS.tsv.gz

value: PBMC


title: WT 1 + 4NQO

description: Library name: WT002L1


title: CITE-seq ADT library 1

description:
Library name: ADT1
ADT
HEAL_FILTERED_ADT_COUNTS.tsv.gz
HEAL_FILTERED_HTO_COUNTS.tsv.gz
HEAL_FILTERED_TET_COUNTS.tsv.gz


title: Aim2 KO 3 + 4NQO

description: Library name: KO630R1

value: AIM2 KO


title: DU145_R1881E_Rep3

description: Library name: Sample 9

value: Prostate cancer CRPC model

value: R1881 10 nM + enzalutamide 10 uM)


title: CITE-seq ADT library 3

description:
Library name: ADT3
ADT
HEAL_FILTERED_ADT_COUNTS.tsv.gz
HEAL_FILTERED_HTO_COUNTS.tsv.gz
HEAL_FILTERED_TET_COUNTS.tsv.gz


title: SA-KO3P2

value: human embryonic kidney

value: embryonic kidney

value: transfection


title: Aim2 KO 2 + 4NQO

description: Library name: KO630L1


title: BMDM, Alpk1-/-, ADP-Hep, replicate 3

first: Yuanhanyu

last: Luo

state: Beijing

address: No.7, Science Park Road, Zhongguancun Life Science Park, Beijing

institute: National Institute of Biological Sciences

description:
Library name: Sample12
Column name in BMDM_raw_count.csv: KO-A-12_R1_001

data_processing:
Raw reads were quality-checked using FastQC
Adapter trimming was done with Trim Galore using default parameters.
Clean reads were aligned to the mm10/hg38 genome using STAR
Read counts were generated using featureCounts package.TPM quantification was performed using RSEM.
Differential expression analysis was conducted using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Primary Mouse bone marrow derived macrophages(BMDMs)

extract_protocol:
RNA was extracted using the Vazyme RNA extraction kit (RC112-01) and protocols.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep, Ligation kit (20040534), following manufacturer's protocols.

treatment_protocol: Cells were treated with 100 μM ALPK1 agonist (ADP-Hep) or PBS for 4 h.

value: Macrophage

value: Alpk1 knockout

value: ADP-Hep

value: 4 h


title: DU145_R1881E_Rep2

description: Library name: Sample 8

value: AR negative


title: SA-KO3P1


title: BMDM, Alpk1-/-, ADP-Hep, replicate 2

description:
Library name: Sample11
Column name in BMDM_raw_count.csv: KO-A-11_R1_001

value: Primary Mouse bone marrow derived macrophages(BMDMs)


title: Aim2 KO 1 + 4NQO

description: Library name: KO63000