title: 6[4]10_WT_HTT-634.486_HIP_female_rep1

description: Library name: zQ175.231.K1033


title: 6[4]10_zQ175_NTC_HIP_male_rep1

status: Public on May 05 2026

type: SRA

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

description: Library name: zQ175.230.90

library_source: transcriptomic

data_processing:
Libraries for RNA-seq were sequenced using an Illumina NovaSeq X Plus and Illumina NovaSeq 6000
Custom genome and gene annotation were created to include transgenic sequences for EGFP, WPRE, nZFP   viral components as well as Htt1a transcript. GRCm38 genome fasta and GRCm38 version 76 gtf were used as a base for the custom genome and annotation.
Pre-alignment QC metrics such as read coverage, percent of un-mapped reads and GC contents were computed in Omicsoft
Omicsoft aligner was used to map the reads to the custom genome and RSEM software from Omicsoft was used to quantify gene and transcript expression
Adapter and quality trimming were performed in Omicsoft using the following settings: Trimming , Mode=TrimByQuality, ReadTrimQuality=2; AverageQualityCutoff=10, EnablePolyRateCutoff=True, PolyRateCutoff=80. FilterSource IlluminaAdapters,Human.rRNA,Human.tRNA,Ercc
Assembly: GRCm38HD.EGFP_WPRE_ZFPs_tdTomatoStiff custom genome assembly and GRCm38.76.Htt1a_EGFP_WPRE_ZFPs_tdTomatoStiff custom gene annotation
Supplementary files format and content: Tab-delimited file containing counts for genes

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Hippocampal brain tissues were dissected from all mice at 6 or 10 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using Illumina RNA preparation with polyA selection

treatment_protocol: The study involved four groups of mice: untreated mice, mice treated with non-targeting siRNA (NTC), mice administrated with HTT-10150 siRNA, and mice treated with both HTT-634 and HTT-486. Three distinct treatment strategies were employed: 2[4]6 - treatment at 2 months, sacrifice at 6 months; 6[4]10 -  treatment at 6 months, sacrifice at 10 months; 2+6[8]10 - treatment at 2 and 6 months, sacrifice at 10 months.

tag: tissue

value: Hippocampus

tag: genotype

tag: treatment

value: NTC

tag: Sex

value: male

tag: age

value: 10 months

tag: age at_treatment

value: 6 months

tag: sample group


title: 6[4]10_WT_HTT-10150_HIP_female_rep1

description: Library name: zQ175.231.K1043

value: Wild Type

value: female


title: 6[4]10_zQ175_HTT-634.486_HIP_male_rep1

description: Library name: zQ175.230.38


title: 6[4]10_WT_Untreated_HIP_female_rep1

description: Library name: zQ175.228.K1068

value: Untreated


title: 2[4]6_zQ175_Untreated_HIP_female_rep4

description: Library name: zQ175.170.K1030

value: 2 months


title: 2[4]6_zQ175_Untreated_HIP_male_rep3

description: Library name: zQ175.172.K1039


title: 2[4]6_zQ175_NTC_HIP_female_rep4

description: Library name: zQ175.170.K1028


title: 2[4]6_zQ175_HTT-634.486_HIP_female_rep4

description: Library name: zQ175.170.K1015


title: 2[4]6_zQ175_Untreated_HIP_male_rep4

description: Library name: zQ175.172.K1041


title: 2[4]6_zQ175_HTT-10150_HIP_female_rep4

description: Library name: zQ175.170.K1012


title: scRNA-seq of HPV-OPSCC; NCI_6

city: Bethesda

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

description: Library name: NCI_6

library_source: transcriptomic single cell

data_processing:
The resulting fastq files were processed using cellranger multi (-f 10,000; version 7.1.0) with a custom reference combining human reference genome GRCh38 and Ensembl annotation (version 98) with HPV types 6, 11, 16, 18, 33, 35 and 56 genome sequences and annotations obtained from PaVe53 and default parameters otherwise.
Assembly: human reference genome GRCh38 and Ensembl annotation (version 98) with HPV types 6, 11, 16, 18, 33, 35 and 56 genome sequences and annotations obtained from PaVe53 and default parameters otherwise.
Supplementary files format and content: Cellranger output files:  sample_id_filtered_feature_bc_matrix.h5

molecule: polyA RNA

organism: Homo sapiens

source_name: orophyngeal carcinoma

extract_protocol:
Fresh carcinoma sample were digested using the Human Tumor Dissociation Kit and the gentleMACS Dissociator (Miltenyi Biotec) per manufacturer recommendations. Cells were washed in 1× PBS, filtered (70 μm) and quantified using acridine orange + propidium iodide (AO/PI) staining on a Cellometer Auto 2000 (Nexcelom). Cells were concentrated to 1000 cells/μL and loaded onto the Chromium Controller (10X Genomics) with a target of 6,000 cells per sample.
Cells were mixed with barcoded gelbeads and 5′ GEM Kit v2 reagents (10X Genomics), and single-cell capture was performed. Following reverse transcription, cDNA was amplified, and gene expression libraries were constructed according to the manufacturer’s recommendations. Each fragmented DNA library was loaded into a sequencing lane on a NovaSeq or NextSeq system (Illumina) and was sequenced with pair-end reads of 75 bp.

value: orophyngeal carcinoma

tag: cell type

value: whole-tissue digest

value: mixed

value: treatment-naïve


title: scRNA-seq of HPV-OPSCC; NCI_12

description: Library name: NCI_12


title: scRNA-seq of HPV-OPSCC; NCI_11

description: Library name: NCI_11


title: scRNA-seq of HPV-OPSCC; NCI_22

description: Library name: NCI_22


title: scRNA-seq of HPV-OPSCC; NCI_15

description: Library name: NCI_15


title: scRNA-seq of HPV-OPSCC; NCI_10

description: Library name: NCI_10


title: scRNA-seq of HPV-OPSCC; NCI_21

description: Library name: NCI_21


title: scRNA-seq of HPV-OPSCC; NCI_9

description: Library name: NCI_9


title: scRNA-seq of HPV-OPSCC; NCI_5

description: Library name: NCI_5


title: scRNA-seq of HPV-OPSCC; NCI_4

description: Library name: NCI_4


title: scRNA-seq of HPV-OPSCC; NCI_8

description: Library name: NCI_8


title: scRNA-seq of HPV-OPSCC; NCI_13

description: Library name: NCI_13


title: 2[4]6_WT_HTT-634.486_HIP_female_rep4

description: Library name: zQ175.169.K1017


title: scRNA-seq of HPV-OPSCC; NCI_7

description: Library name: NCI_7


title: scRNA-seq of HPV-OPSCC; NCI_14

description: Library name: NCI_14


title: scRNA-seq of HPV-OPSCC; NCI_3

description: Library name: NCI_3


title: 2[4]6_WT_Untreated_HIP_female_rep4

description: Library name: zQ175.169.K1029


title: 2[4]6_WT_Untreated_HIP_female_rep3

description: Library name: zQ175.168.K1027


title: 2[4]6_WT_HTT-10150_HIP_female_rep4

description: Library name: zQ175.168.K1025


title: 2[4]6_WT_NTC_HIP_male_rep4

description: Library name: zQ175.166.K1144


title: 2[4]6_WT_HTT-634.486_HIP_male_rep4

description: Library name: zQ175.166.K1128


title: 2[4]6_WT_NTC_HIP_female_rep4

description: Library name: zQ175.168.K1011


title: 2[4]6_WT_HTT-10150_HIP_male_rep4

description: Library name: zQ175.166.K1122


title: 2[4]6_zQ175_NTC_HIP_male_rep4

description: Library name: zQ175.164.K1206


title: 2[4]6_zQ175_HTT-10150_HIP_male_rep4

description: Library name: zQ175.164.K1199


title: 2[4]6_zQ175_HTT-634.486_HIP_male_rep4

description: Library name: zQ175.164.K1201


title: 2[4]6_WT_Untreated_HIP_male_rep4

description: Library name: zQ175.166.K1159


title: RZ734_Pool_1

city: Darlinghurst

first: Peter

middle: C

last: Allen

state: New South Wales

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: Library name: RZ734_Pool_1

data_processing:
Sequence reads were aligned using 10x Genomics’s CellRanger software
CellBender was used to adjust for ambient RNA
RZ7## Samples were demultiplexed using a combination of Demuxalot and Vireo  Doublet detection was performed using a combination of Demuxalot, Vireo, scDblFinder, scds, and Solo
Integration was performed using scVI correcting for batch effects (10x Chemistry & poolID)  For quality control and downstream analyses, both scanpy (.h5ad) and seurat (.rds) were used.
Assembly: GRCh38, Gencode release 44, Ensemble 110
Supplementary files format and content: BAL_FINAL.rds: Seurat Object with the entire dataset
Supplementary files format and content: BAL_FINAL.h5ad: Scanpy Object with the entire dataset
Supplementary files format and content: BAL_FINAL_metadata.txt: Metadata for each cell barcode
Supplementary files format and content: mlm_umap_embeddings.csv: UMAP embeddings for the monocyte-derived clusters
Supplementary files format and content: ipf_allen2022.full_score.gz: scDRS results for each cell using the Richard Allen et al. 2022 IPF GWAS summary statistics

source_name: Lung

extract_protocol:
Bronchoalveolar lavage (BAL) samples were collected at ILD diagnosis from either the right middle lobe or lingula according to American Thoracic Society guidelines and fresh-frozen for downstream analysis.
Libraries pertaining to the BAL_scRNA samples were processed using the 10x Genomics Chromium Single Cell 3’ Library (v2, PN-120233; 10X Genomics) and sequenced on an Illumina NextSeq 500 using a 150-cycle NextSeq 500/550 High Output Reagent Kit v2 (FC-404-2002; Illumina).  Libraries pertaining to RZ7## samples were processed using the 10x Genomics Chromium Single Cell 3’ Library (v3, 10X-1000078; 10x Genomics) and sequenced on an Illumina NovaSeq 6000 using a 200-cycle S4 Reagent Kit.

value: Lung

value: Bronchoalveolar lavage


title: RZ734_Pool_2

description: Library name: RZ734_Pool_2


title: RZ725_Pool4

description: Library name: RZ725_Pool4


title: BAL_scRNA_Sample15

description: Library name: BAL_scRNA_Sample15


title: BAL_scRNA_Sample10

description: Library name: BAL_scRNA_Sample10


title: RZ734_Pool_3

description: Library name: RZ734_Pool_3


title: BAL_scRNA_Sample3

description: Library name: BAL_scRNA_Sample3


title: 2[4]6_WT_HTT-10150_HIP_male_rep3

description: Library name: zQ175.163.M2005


title: RZ725_Pool5

description: Library name: RZ725_Pool5


title: BAL_scRNA_Sample18

description: Library name: BAL_scRNA_Sample18


title: 2[4]6_WT_NTC_HIP_male_rep3

description: Library name: zQ175.163.M2020


title: 2[4]6_WT_Untreated_HIP_male_rep3

description: Library name: zQ175.163.M2023


title: 2[4]6_WT_HTT-634.486_HIP_male_rep2

description: Library name: zQ175.162.M2011


title: 2[4]6_WT_HTT-634.486_HIP_male_rep3

description: Library name: zQ175.163.M2010


title: 2[4]6_WT_Untreated_HIP_male_rep2

description: Library name: zQ175.162.M2034


title: 2[4]6_WT_HTT-10150_HIP_male_rep2

description: Library name: zQ175.162.M2004


title: 2[4]6_zQ175_HTT-634.486_HIP_male_rep3

description: Library name: zQ175.161.M2062


title: 2[4]6_WT_NTC_HIP_male_rep2

description: Library name: zQ175.162.M2022


title: 2[4]6_zQ175_HTT-10150_HIP_male_rep3

description: Library name: zQ175.161.M2050


title: 2[4]6_zQ175_NTC_HIP_male_rep3

description: Library name: zQ175.161.M2071


title: 2[4]6_zQ175_Untreated_HIP_male_rep2

description: Library name: zQ175.161.M2073


title: H3K9bhb-shBDH1-IP-2

city: Wuhan

first: Jin

last: Xu

address: 115 East Lake Road, Wuhan, Hubei, 430071, P. R. China

country: China

institute: Wuhan university

library_source: genomic

data_processing:
Raw sequencing files were filtered using Fastp, and then aligned against the human reference genome (GRCh38/hg38) using STAR(version 2.7.6a).
MACS2 identified the H3K9bhb and H3K9ac-enriched regions in each immunoprecipitation sample with the corresponding input library as control.
Tracks of signal were computed using MACS2 bdgcmp module with parameter ‘-m FE’, and then visualized using the Integrative Genomics Viewer (IGV) visualization tool.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

source_name: Jurkat

extract_protocol:
DNA was purified using the phenol-chloroform extraction and ethanol precipitation.
Library preparation was done using the VAHTS Universal DNA Library Prep Kit for Illumina V4 (Vazyme).

tag: cell line

value: Jurkat

value: T-ALL cell lines

tag: chip antibody


title: H3K9bhb-shBDH1-input-1


title: H3K9bhb-shcontrol-input-2


title: H3K9ac-shBDH1-IP


title: H3K9bhb-shBDH1-input-2


title: H3K9bhb-shcontrol-IP-2


title: H3K9ac-shBDH1-input


title: H3K9bhb-shcontrol-IP-1


title: H3K9bhb-shBDH1-IP-1


title: H3K9bhb-shcontrol-input-1


title: H3K9ac-shcontrol-input


title: 2[4]6_zQ175_NTC_HIP_male_rep2

description: Library name: zQ175.160.T3264

value: Hippocampus


title: H3K9ac-shcontrol-IP


title: 2[4]6_zQ175_HTT-634.486_HIP_male_rep2

description: Library name: zQ175.160.M2056


title: DSP-1001660008760-D-A06.dcc Patient 1 Macrophages Invasive front

city: Bordeaux

first: Hamid-Reza

last: Rezvani

address: 2 Rue Dr Hoffmann Martinot

country: France

institute: Bordeaux Institute of Oncology (BRIC)

description: Library name: DSP-1001660008760-D-A06.dcc

data_processing:
Following a pooling purification, the final library was sequenced on a Novaseq6000 (Illumina) using a dual-index workflow.
The quality control (QC) of NGS data was assessed prior analysis to ensure the data robustness and to eliminate problematic AOIs. Different parameters were analyzed and notably the raw read threshold, alignment, and sequencing saturation. Segments with less than 1000 reads, less than 80% of raw reads, and or less than 50% of sequencing saturation were eliminated. Moreover, segments with exceptionally low signal (< 1% of panel genes detected above the limit of quantification, based on negative control probes) were excluded.
Assembly: hg38
Supplementary files format and content: File name is "21019220628_rawdata.csv". File contains the count matrix.
Supplementary files format and content: File name is "21019220628_metadata.csv". File contains the sample metadata.
Library strategy: Spatial Transcriptomics

source_name: Macrophages

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) skin specimens were obtained from a cohort of three patients with cutaneous squamous cell carcinoma (cSCC). For each patient, tissue blocks contained histologically distinct regions corresponding to (i) healthy skin, (ii) peritumoral skin, (iii) actinic keratosis (AK) and/or in situ cSCC, (iv) advanced tumor core, (v) advanced invasive cSCC. Hematoxylin and eosin–stained sections were reviewed by a board-certified dermatopathologist to confirm diagnoses and to guide region selection.
Spatial transcriptomics was carried out through the Nanostring Technologies GeoMx Digital Spatial Profiling (GeoMx DSP). The protocol has five steps: standard FFPE tissue preparation; tissue incubation with a mixture of visualization markers (VMs) and DSP probes; imaging and region of interest (ROI) selection; ultraviolet (UV) exposure; and oligo collection step. This is then quantified using the Nanostring nCounter® system. Briefly, tissue sections were stained with a CD68/PanCK/Vimentin/Sytox panel to visualize tissue architecture and guide the selection of regions of interest (ROIs) for analysis. For each slide, ROIs were drawn in order to analyze the expression of the WTA gene panel in the healthy regions, AK/cSCC in situ, advanced cSCC, and invasive front. Each ROI was further segmented in 3 to 5 AOIs (area of illumination) based on the PanCK, CD68, and Vimentin staining. AOIs enriched for PanCK marked epithelial/tumor regions; CD68-enriched AOIs captured macrophage-rich regions; and PanCK⁺/Vimentin⁺ AOIs were used as an operational proxy for the invasive front, consistent with the local histopathology. The gene expression of each AOI was analyzed on the GeoMX DSP (NanoString®) using the Whole Transcriptome Atlas (WTA) panel. This panel covers the expression of 18695 protein-coding genes. Slides were incubated overnight with in situ hybridization (ISH) probes conjugated to unique DNA indexing-oligonucleotides via a UV-photocleavable linker. Each AOI was then illuminated with a UV laser to precisely release and collect the DNA barcode in a 96-well plate. GeoMx DSP aspirates in the plate contain photocleaved DNA oligos comprised of an analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. A PCR was performed on these aspirates to add Illumina adapter sequences and unique dual sample indices.

tag: group

value: Invasive front

value: Macrophages


title: A498 shRNF26_3

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

growth_protocol: A498 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: kidney

value: A498 cells

value: renal clear cell carcinoma cells

value: the treat group of knockdown of RNF26 by shRNA

value: transfection infection


title: 2[4]6_zQ175_HTT-10150_HIP_male_rep2

description: Library name: zQ175.160.M2052

value: male

value: 6 months

value: 2 months


title: T47D cells, plus hox plus estradiol, rep1

city: Charlestown

first: Dennis

last: Sgroi

state: MA

department: Pathology

institute: MGH

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality using FastQC
Trimmed reads were mapped with STAR and aligned to GRCh37/hg19 assembly
Duplicate reads were marked using Picard MarkDuplicates
Read count extraction was done using HTSeq
Assembly: hg19
Supplementary files format and content: tab delimited text file containing raw counts for each sample

growth_protocol: T47D and T47D-HOXB13 cells were plated in phenol-free DMEM supplemented with 10%FBS and antibiotics for 24 hrs.

extract_protocol:
RNA was harvested using Rneasy mini plus kit.
RNA sent to Novogene Inc for RNA library prep and RNA sequencing.

treatment_protocol: Media was then changed to phenol-free DMEM supplemented with 10% charcoal-stripped FBS and antibiotics for 72 hrs and then pulsed with 2nM estradiol or vehicle (ethanol) for 24 hrs.

value: Epithelial cells

value: ectopic HOXB13 expression

value: estradiol


title: T47D cells, plus hox plus estradiol, rep3


title: 2[4]6_WT_NTC_HIP_female_rep3

description: Library name: zQ175.159.M2036

value: Wild Type

value: NTC

value: female


title: T47D cells, plus hox, rep1

value: vehicle (ethanol)


title: T47D cells, normal, rep3

value: WT


title: T47D cells, plus estradiol, rep2


title: T47D cells, plus hox plus estradiol, rep2


title: T47D cells, plus hox, rep3


title: 2[4]6_WT_HTT-10150_HIP_female_rep2

description: Library name: zQ175.158.M2008

value: Hippocampus


title: T47D cells, plus estradiol, rep1


title: A498 shcontrol_1

value: kidney

value: the control group of knockdown of RNF26 by shRNA


title: 2[4]6_WT_Untreated_HIP_female_rep2

description: Library name: zQ175.158.M2024

value: Untreated


title: A498 shcontrol_3

value: A498 cells

value: renal clear cell carcinoma cells


title: A498 shRNF26_2

value: the treat group of knockdown of RNF26 by shRNA

value: transfection infection


title: T47D cells, normal, rep2


title: T47D cells, normal, rep1


title: T47D cells, plus estradiol, rep3


title: 2[4]6_WT_HTT-10150_HIP_female_rep3

description: Library name: zQ175.159.M2025

value: 6 months

value: 2 months


title: T47D cells, plus hox, rep2

value: Epithelial cells

value: ectopic HOXB13 expression


title: 2[4]6_WT_HTT-634.486_HIP_female_rep3

description: Library name: zQ175.159.M2012

value: Wild Type


title: 2[4]6_WT_HTT-634.486_HIP_female_rep2

description: Library name: zQ175.158.M2003


title: A498 shcontrol_2


title: A498 shRNF26_1


title: 2[4]6_zQ175_NTC_HIP_male_rep1

description: Library name: zQ175.156.T3267

value: NTC

value: male


title: ATAC_wt_rep1

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

description: Library name: ATAC_wt_rep1

data_processing:
For ATAC-seq data, reads were aligned to the human genome (UCSC hg19) using bowtie2 (version 2.5.4). SAM files were then converted into BAM files and indexed. Peaks were finally called with macs2 (version 2.2.9.1) with BAM files as input. The heatmap matrix was generated using computeMatrix (version 3.5.4) and illustrated with plotHeatmap software.
Assembly: NCBI hg19
Supplementary files format and content: gzipped wig file suitable for uploading to UCSC

growth_protocol: Human A375 cell were cultured in DMEM medium (Hyclone), supplemented with 10 % (v/v) FBS (VivaCell) and 10 U/ml (1×) Penicillin-Streptomycin (Gibco). Cells were cultured at 37 °C in a 5 % CO2 humidified incubator, and were passaged every three days.

extract_protocol:
~2 × 107 of cells were collected, cross-linked with 2% formaldehyde, quenched by adding excess pre-chilled glycine and finally cleaned with PBS.
ATAC-seq experiments were performed as previously described. Briefly, 10^6 cells were used for one experiment. Cells were washed twice with 1 ml of cold PBS and spined down at low rotations. The cell pellets were resuspended and incubated in cold lysis buffer to release nuclei, followed by centrifugation to discard supernatant. The nuclei were then fragmented and tagged with transposase. After transposition, DNA products were purified and libraries were constructed using the Hyperactive ATAC-seq library prep kit for illumina (Vazyme, TD711). The ATAC-seq libraries were sequenced using an Illumina Novaseq X plus platform at 2 × 150 bp mode.

treatment_protocol: No special treatment was performed to cultured cells.

value: Malignant Melanoma

value: wildtype


title: ATAC_wt_rep2

description: Library name: ATAC_wt_rep2


title: ATAC_del3_rep2

description: Library name: ATAC_del3_rep2

value: RFX5 del -/-


title: 2[4]6_WT_NTC_HIP_female_rep2

description: Library name: zQ175.158.M2009

value: Hippocampus

value: female


title: 2[4]6_zQ175_HTT-634.486_HIP_male_rep1

description: Library name: zQ175.156.M2080


title: ATAC_del1_rep2

description: Library name: ATAC_del1_rep2


title: ATAC_del2_rep2

description: Library name: ATAC_del2_rep2


title: ATAC_del3_rep1

description: Library name: ATAC_del3_rep1


title: 2[4]6_zQ175_Untreated_HIP_male_rep1

description: Library name: zQ175.153.M2030

value: Untreated


title: ATAC_del2_rep1

description: Library name: ATAC_del2_rep1


title: 2[4]6_zQ175_HTT-10150_HIP_male_rep1

description: Library name: zQ175.153.M2027


title: 2[4]6_WT_HTT-634.486_HIP_male_rep1

description: Library name: zQ175.146.M2047


title: 2[4]6_WT_NTC_HIP_female_rep1

description: Library name: zQ175.145.T3263


title: 4C_VEGFA_del3_rep2

description: Library name: 4C_VEGFA_del3_rep2

data_processing:
For QHR-4C data, Viewpoint primer sequence were first removed and duplicated paired-end reads caused by PCR were then removed by FastUniq (version 1.1). Only the unique reads were used to align to the human genomes using the Bowtie2 software. SAM files were then converted into BAM files and the reads per million (RPM) value was calculated using the r3Cseq program (version 3.20) in the R package (4.3.3).
Assembly: NCBI hg19
Supplementary files format and content: gzipped bedgraph files can be uploaded to UCSC
Library strategy: 4C-Seq

extract_protocol:
For one experiment, a 10 cm dish of cells at ~80 % confluency was collected, cross-linked with 2% formaldehyde and quenched by adding excess pre-chilled glycine. The cells were then collected with centrifuge and permeabilized with 4C permeabilization buffer supplemented with 1 × proteinase inhibitor.
The cells were digested with DpnII for a total of 16 h followed by in-nuclei ligation for 20 h. The ligated samples were then reverse cross-linked and purified, finally eluted into distilled water. The purified ligation products were then fragmented to ~200-1,000 bp using the SCIENTZ Sonication system (10 % energy, with working time 10 s and resting time of 50 s, 2 cycles). Fragmented products were then linear-amplified to formulate target sequences in single strand that are tagged with 5’ biotin primers. Target sequences were captured with Streptavidin Magnetic Beads (ThermoFisher, 65001) according to the manufacturer’s instructions. Adaptor was then ligated to the 3’ end of the tagged DNA. Finally, the QHR-4C libraries were generated by PCR amplification on beads with a pair of PCR primers that suits the Illumina sequencing criteria. Samples of same viewpoint with different barcode or index were purified in one column. The PCR products were purified with PCR purification kit (Qiagen).


title: 4C_VEGFA_del3_rep1

description: Library name: 4C_VEGFA_del3_rep1


title: 2[4]6_WT_HTT-10150_HIP_male_rep1

description: Library name: zQ175.146.M2041


title: 2[4]6_WT_HTT-634.486_HIP_female_rep1

description: Library name: zQ175.145.M2051


title: 4C_VEGFA_del2_rep2

description: Library name: 4C_VEGFA_del2_rep2


title: 2[4]6_WT_NTC_HIP_male_rep1

description: Library name: zQ175.146.M2077


title: 4C_VEGFA_del2_rep1

description: Library name: 4C_VEGFA_del2_rep1


title: 4C_PCDHb5_del3_rep1

description: Library name: 4C_PCDHb5_del3_rep1


title: 2.6[8]10_zQ175_HTT-10150_HIP_male_rep2

description: Library name: zQ175.78.32

value: 10 months

value: 2+6 months


title: 4C_PCDHb5_del2_rep2

description: Library name: 4C_PCDHb5_del2_rep2


title: 4C_PCDHb5_WT_rep1

description: Library name: 4C_PCDHb5_WT_rep1

value: widltype


title: 2.6[8]10_WT_NTC_HIP_male_rep2

description: Library name: zQ175.75.3


title: 2[4]6_zQ175_HTT-634.486_HIP_female_rep3

description: Library name: zQ175.151.M2074


title: ATAC_del1_rep1

description: Library name: ATAC_del1_rep1


title: 4C_PCDHb14_WT_rep2

description: Library name: 4C_PCDHb14_WT_rep2


title: 4C_VEGFA_del1_rep2

description: Library name: 4C_VEGFA_del1_rep2


title: 2.6[8]10_zQ175_HTT-634.486_HIP_male_rep2

description: Library name: zQ175.78.29


title: 4C_VEGFA_del1_rep1

description: Library name: 4C_VEGFA_del1_rep1


title: 2.6[8]10_WT_HTT-634.486_HIP_male_rep2

description: Library name: zQ175.75.9


title: 2.6[8]10_zQ175_Untreated_HIP_male_rep2

description: Library name: zQ175.78.34


title: 4C_PCDHb5_WT_rep2

description: Library name: 4C_PCDHb5_WT_rep2


title: 2[4]6_WT_HTT-10150_HIP_female_rep1

description: Library name: zQ175.145.T3260


title: 4C_PCDHb5_del1_rep1

description: Library name: 4C_PCDHb5_del1_rep1


title: 4C_PCDHb14_del3_rep2

description: Library name: 4C_PCDHb14_del3_rep2


title: 2.6[8]10_WT_HTT-10150_HIP_female_rep1

description: Library name: zQ175.66.10


title: 4C_PCDHb14_del1_rep2

description: Library name: 4C_PCDHb14_del1_rep2


title: 4C_PCDHb5_del3_rep2

description: Library name: 4C_PCDHb5_del3_rep2


title: 2[4]6_WT_Untreated_HIP_female_rep1

description: Library name: zQ175.145.M2224


title: 4C_PCDHb14_del1_rep1

description: Library name: 4C_PCDHb14_del1_rep1


title: 2.6[8]10_WT_HTT-10150_HIP_male_rep2

description: Library name: zQ175.75.2


title: 4C_PCDHb5_del2_rep1

description: Library name: 4C_PCDHb5_del2_rep1


title: 4C_PCDHb12_del3_rep1

description: Library name: 4C_PCDHb12_del3_rep1


title: 6[4]10_WT_HTT-10150_STR_female_rep4

description: Library name: zQ175.250.D24922

data_processing:
Libraries for RNA-seq were sequenced using an Illumina NovaSeq 2 x 150 bp
Custom genome and gene annotation were created to include transgenic sequences for EGFP, WPRE, nZFP   viral components as well as Htt1a transcript. GRCm38 genome fasta and GRCm38 version 76 gtf were used as a base for the custom genome and annotation.
Pre-alignment QC metrics such as read coverage, percent of un-mapped reads and GC contents were computed in Omicsoft
Omicsoft aligner was used to map the reads to the custom genome and RSEM software from Omicsoft was used to quantify gene and transcript expression
Adapter and quality trimming were performed in Omicsoft using the following settings: Trimming , Mode=TrimByQuality, ReadTrimQuality=2; AverageQualityCutoff=10, EnablePolyRateCutoff=True, PolyRateCutoff=80. FilterSource IlluminaAdapters,Human.rRNA,Human.tRNA,Ercc
Assembly: GRCm38HD.EGFP_WPRE_ZFPs_tdTomatoStiff custom genome assembly and GRCm38.76.Htt1a_EGFP_WPRE_ZFPs_tdTomatoStiff custom gene annotation
Supplementary files format and content: Tab-delimited files containing counts and FPKM values for genes

source_name: Corpus Striatum

extract_protocol:
Brain striatal tissues were dissected from all mice at 6 or 10 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using Illumina RNA preparation with polyA selection

treatment_protocol: There were three treatment groups in this study: untreated mice, mice treated with non-targeting siRNA (NTC), and mice treated with siRNAs targeting HTT-10150. Three distinct treatment strategies were employed: 2[4]6 - treatment at 2 months, sacrifice at 6 months; 6[4]10 -  treatment at 6 months, sacrifice at 10 months; 2+6[8]10 - treatment at 2 and 6 months, sacrifice at 10 months.

value: Corpus Striatum


title: 6[4]10_WT_NTC_STR_female_rep4

description: Library name: zQ175.249.59

value: 6 months


title: 6[4]10_zQ175_NTC_STR_female_rep4

description: Library name: zQ175-254-167


title: 4C_PCDHb5_del1_rep2

description: Library name: 4C_PCDHb5_del1_rep2


title: 4C_PCDHb12_WT_rep2

description: Library name: 4C_PCDHb12_WT_rep2


title: 2.6[8]10_zQ175_HTT-634.486_HIP_female_rep2

description: Library name: zQ175.74.33


title: 6[4]10_WT_HTT-10150_STR_female_rep3

description: Library name: zQ175.249.57


title: 4C_PCDHb14_del2_rep2

description: Library name: 4C_PCDHb14_del2_rep2


title: 6[4]10_zQ175_HTT-10150_STR_male_rep4

description: Library name: zQ175.251.189


title: 6[4]10_WT_NTC_STR_male_rep4

description: Library name: zQ175.245.144


title: 4C_PCDHb14_WT_rep1

description: Library name: 4C_PCDHb14_WT_rep1


title: 6[4]10_zQ175_HTT-10150_STR_female_rep4

description: Library name: zQ175.247.181


title: 6[4]10_zQ175_Untreated_STR_male_rep4

description: Library name: zQ175.253.115


title: 6[4]10_zQ175_NTC_STR_male_rep4

description: Library name: zQ175.251.168


title: 4C_PCDHb12_del3_rep2

description: Library name: 4C_PCDHb12_del3_rep2


title: 4C_PCDHb14_del2_rep1

description: Library name: 4C_PCDHb14_del2_rep1


title: 4C_PCDHb12_del1_rep2

description: Library name: 4C_PCDHb12_del1_rep2


title: 6[4]10_WT_HTT-10150_STR_male_rep3

description: Library name: zQ175.245.143


title: 4C_PCDHb14_del3_rep1

description: Library name: 4C_PCDHb14_del3_rep1


title: 6[4]10_zQ175_Untreated_STR_female_rep4

description: Library name: zQ175.247.174


title: 6[4]10_WT_NTC_STR_female_rep3

description: Library name: zQ175.244.2166


title: 4C_PCDHb12_del2_rep2

description: Library name: 4C_PCDHb12_del2_rep2


title: 6[4]10_WT_Untreated_STR_male_rep4

description: Library name: zQ175.245.162


title: 4C_PCDHb12_del2_rep1

description: Library name: 4C_PCDHb12_del2_rep1


title: 6[4]10_WT_HTT-10150_STR_female_rep2

description: Library name: zQ175.244.2163


title: 4C_KLF9_WT_rep1

description: Library name: 4C_KLF9_WT_rep1


title: 4C_PCDHb12_del1_rep1

description: Library name: 4C_PCDHb12_del1_rep1


title: 4C_KLF9_WT_rep2

description: Library name: 4C_KLF9_WT_rep2


title: 6[4]10_WT_HTT-10150_STR_male_rep4

description: Library name: zQ175.246.169


title: 6[4]10_WT_NTC_STR_female_rep2

description: Library name: zQ175.243.2152


title: 4C_KLF9_del3_rep2

description: Library name: 4C_KLF9_del3_rep2


title: 4C_KLF9_del3_rep1

description: Library name: 4C_KLF9_del3_rep1


title: 4C_KLF9_del2_rep1

description: Library name: 4C_KLF9_del2_rep1


title: 4C_KLF9_del1_rep1

description: Library name: 4C_KLF9_del1_rep1


title: 4C_HES1_WT_rep2

description: Library name: 4C_HES1_WT_rep2


title: 4C_HES1_del3_rep1

description: Library name: 4C_HES1_del3_rep1


title: 4C_KLF9_del1_rep2

description: Library name: 4C_KLF9_del1_rep2


title: 4C_KLF9_del2_rep2

description: Library name: 4C_KLF9_del2_rep2


title: 4C_HES1_WT_rep1

description: Library name: 4C_HES1_WT_rep1


title: 4C_HES1_del1_rep2

description: Library name: 4C_HES1_del1_rep2


title: 4C_HES1_del3_rep2

description: Library name: 4C_HES1_del3_rep2


title: 4C_HES1_del2_rep1

description: Library name: 4C_HES1_del2_rep1


title: 4C_HES1_del2_rep2

description: Library name: 4C_HES1_del2_rep2


title: 6[4]10_WT_Untreated_STR_female_rep3

description: Library name: zQ175.243.2142


title: 6[4]10_zQ175_NTC_STR_female_rep3

description: Library name: zQ175.2237.178


title: 6[4]10_WT_Untreated_STR_male_rep1

description: Library name: zQ175.240.88


title: 4C_HES1_del1_rep1

description: Library name: 4C_HES1_del1_rep1


title: 6[4]10_WT_HTT-10150_STR_male_rep1

description: Library name: zQ175.241.28


title: 6[4]10_WT_Untreated_STR_male_rep3

description: Library name: zQ175.242.17


title: 4C_CADM1_WT_rep2

description: Library name: 4C_CADM1_WT_rep2


title: 6[4]10_WT_Untreated_STR_female_rep2

description: Library name: zQ175.243.1474


title: 6[4]10_WT_HTT-10150_STR_male_rep2

description: Library name: zQ175.242.16


title: 6[4]10_WT_NTC_STR_male_rep3

description: Library name: zQ175.242.22


title: 6[4]10_WT_NTC_STR_male_rep2

description: Library name: zQ175.241.15


title: 4C_CADM1_WT_rep1

description: Library name: 4C_CADM1_WT_rep1


title: 6[4]10_zQ175_HTT-10150_STR_female_rep2

description: Library name: zQ175.237.124


title: 6[4]10_zQ175_NTC_STR_female_rep2

description: Library name: zQ175.237.84


title: 4C_CADM1_del3_rep1

description: Library name: 4C_CADM1_del3_rep1


title: 6[4]10_zQ175_Untreated_STR_female_rep1

description: Library name: zQ175.236.142


title: 4C_CADM1_del2_rep2

description: Library name: 4C_CADM1_del2_rep2


title: 4C_CADM1_del1_rep2

description: Library name: 4C_CADM1_del1_rep2


title: 4C_CADM1_del1_rep1

description: Library name: 4C_CADM1_del1_rep1


title: 6[4]10_WT_Untreated_STR_male_rep2

description: Library name: zQ175.241.39


title: 6[4]10_zQ175_NTC_STR_male_rep3

description: Library name: zQ175.234.2140


title: 6[4]10_zQ175_NTC_STR_female_rep1

description: Library name: zQ175.236.96


title: 6[4]10_zQ175_HTT-10150_STR_male_rep3

description: Library name: zQ175.234.2132


title: 6[4]10_zQ175_HTT-10150_STR_female_rep1

description: Library name: zQ175.236.99


title: 6[4]10_zQ175_Untreated_STR_female_rep3

description: Library name: zQ175.238.113


title: 6[4]10_zQ175_NTC_STR_male_rep2

description: Library name: zQ175.233.184


title: 6[4]10_zQ175_Untreated_STR_male_rep3

description: Library name: zQ175.234.2108


title: 6[4]10_WT_NTC_STR_male_rep1

description: Library name: zQ175.240.107


title: 6[4]10_zQ175_NTC_STR_male_rep1

description: Library name: zQ175.230.90


title: 6[4]10_zQ175_Untreated_STR_male_rep2

description: Library name: zQ175.233.121


title: 6[4]10_WT_HTT-10150_STR_female_rep1

description: Library name: zQ175.231.K1043


title: 6[4]10_zQ175_HTT-10150_STR_male_rep2

description: Library name: zQ175.233.154


title: 6[4]10_zQ175_Untreated_STR_male_rep1

description: Library name: zQ175.230.102


title: 6[4]10_zQ175_HTT-10150_STR_male_rep1

description: Library name: zQ175.230.74


title: 6[4]10_WT_NTC_STR_female_rep1

description: Library name: zQ175.232.K1063


title: 2[4]6_zQ175_HTT-10150_STR_female_rep4

description: Library name: zQ175.170.K1012

value: 2 months


title: 2[4]6_zQ175_Untreated_STR_female_rep4

description: Library name: zQ175.170.K1030


title: 2[4]6_zQ175_NTC_STR_female_rep4

description: Library name: zQ175.170.K1028


title: T-cells from rheumatoid arthritis patients

city: Yerevan

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Yerevan

address: Khorenatsi 1

department: Research and Development

country: Armenia

institute: PerikLab

description: Library name: S15177Nr3

data_processing:
Barcode processing, gene UMI counting and aggregation were made using the BD Rhapsody pipeline v2.2 (https://bd-rhapsody-bioinfo-docs.genomics.bd.com/release_notes.html).
Assembly: BD Rhapsody's RhapRef_Human_WTA_2025-03
Supplementary files format and content: Sample-demultiplexed (via SampleTag HTOs) 10X-like feature, barcode and matrix files containing RNA and ADT data.
Library strategy: CITE-seq

source_name: female (n =4)

extract_protocol:
Human mononuclear cells were isolated by Ficoll density gradient centrifugation. T cells were isolated from the mononuclear cells using CD3 magnetic sorting.
Library was performed according to the manufacter’s instructions (BD Rhapsody™ System mRNA Whole Transcriptome Analysis (WTA), AbSeq, and Sample Tag Library Preparation Protocol).

treatment_protocol: T-cells were incubated with TNF-a at the concentration of 20 ng/µl for 20h.

value: T-cells

value: Blood

tag: instrument

value: BD Rhapsody


title: 2[4]6_zQ175_Untreated_STR_male_rep3

description: Library name: zQ175.172.K1039


title: 2[4]6_WT_Untreated_STR_female_rep4

description: Library name: zQ175.169.K1029

value: Wild Type


title: 2.6[8]10_zQ175_NTC_HIP_female_rep2

description: Library name: zQ175.74.35

value: NTC


title: 2[4]6_WT_Untreated_STR_female_rep3

description: Library name: zQ175.168.K1027


title: 2[4]6_WT_HTT-10150_STR_female_rep4

description: Library name: zQ175.168.K1025


title: 2[4]6_WT_NTC_STR_female_rep4

description: Library name: zQ175.168.K1011


title: 2[4]6_WT_Untreated_STR_male_rep4

description: Library name: zQ175.166.K1159

value: male


title: HiC_del3_rep2

description: Library name: HiC_del3_rep2

data_processing:
For Hi-C data, the HiC-Pro toolkit was utilized to map raw FASTQ reads to the human reference genome assembly (GRCh37/hg19). Following alignment, the allValidPairs files were converted to hic format files with the hicpro2juicebox script from the HiC-Pro package, allowing subsequent analysis with Juicer tools. These hic files were further transformed to the cooler format via hic2cool (v0.8.3), and the contact matrix was normalized to a contact depth of 100 million based on cis-interactions using the Knight-Ruiz (KR) normalization method. Hi-C contact maps for specific genomic regions were generated using the fancplot module from the FAN-C toolkits, while differential contact heatmaps were constructed using Seaborn, a Python library. At a resolution of 100-Kb, the cis-Eigenvector 1 values and Pearson’s correlation matrix were computed using the Juicer software. The cis-Eigenvector 1 values were subsequently converted into the bedGraph format for visualization in the UCSC genome browser. Scatterplots with heat density representations were created using the R package ggpointdensity (v0.1.0). Topologically associating domains (TADs) were identified using the Hidden Markov Models (HMM) algorithm, as previously described. The dense contact matrix was processed using the DI_from_matrix script to calculate the Directionality Index (DI) score. This DI score was then used to predict the hidden states of genomic bins via HMM models. Adjacent bins with the same state were merged into regions. Regions containing fewer than 3 bins or with a median posterior bin probability lower than 0.99 were filtered out using a Perl script. TADs were ultimately defined as regions extending from an upstream boundary to a downstream boundary. The DI score was also converted to the bedGraph format for visualization in the UCSC genome browser. Chromatin loops were identified in the contact matrix using Chromosight (v1.6.3), with a minimum genomic distance threshold of 4 Kb for loop detection. Specific loops were further analyzed using the Aggregate Peak Analysis (APA) with cooltools (v0.6.1) (Open2C) and coolpup.py (v1.1.0).
Assembly: NCBI hg38
Supplementary files format and content: gzipped fpkm_tracking files containing FPKM values for each gene

extract_protocol:
~2 × 107 of cells were collected, cross-linked with 2% formaldehyde, quenched by adding excess pre-chilled glycine and finally cleaned with PBS.
The cross-linked samples were then suspended and lysed in lysis buffer followed by sufficient digestion with MboI. Digested products were then heat de-activated, end repaired and tagged with biotin-14-dATP (Thermofisher, 19524016). Fragments ligation was then performed followed with reverse cross-link and purification of DNA. Ligation products were then sonicated using the SCIENTZ Sonication system (10 % energy, with working time 10 s and resting time of 50 s, 2 cycles) and size selection was performed to generate fragments with size ~300-500 bp. Afterwards, Sonicated products tagged with biotin were pulled down with Streptavidin Magnetic Beads (ThermoFisher, 65001) according to the manufacturer’s instructions. The captured products were then end repaired ,3’ d(A) tailed on beads followed with adaptor ligation. The Hi-C library was finally constructed by PCR amplification.

value: Malignant Melanoma


title: HiC_del3_rep1

description: Library name: HiC_del3_rep1

value: RFX5 del -/-


title: HiC_WT_rep2

description: Library name: HiC_WT_rep2

value: wildtype


title: HiC_del1_rep1

description: Library name: HiC_del1_rep1


title: HiC_del2_rep1

description: Library name: HiC_del2_rep1


title: HiC_del1_rep2

description: Library name: HiC_del1_rep2


title: 2[4]6_WT_NTC_STR_male_rep4

description: Library name: zQ175.166.K1144


title: HiC_del2_rep2

description: Library name: HiC_del2_rep2


title: 2[4]6_zQ175_NTC_STR_male_rep4

description: Library name: zQ175.164.K1206


title: 2[4]6_zQ175_HTT-10150_STR_male_rep4

description: Library name: zQ175.164.K1199


title: 2[4]6_WT_Untreated_STR_male_rep3

description: Library name: zQ175.163.M2023


title: 2[4]6_WT_HTT-10150_STR_male_rep4

description: Library name: zQ175.164.K1122


title: 2[4]6_WT_NTC_STR_male_rep3

description: Library name: zQ175.163.M2020T3304


title: 2[4]6_WT_HTT-10150_STR_male_rep3

description: Library name: zQ175.163.M2005


title: 2[4]6_WT_Untreated_STR_male_rep2

description: Library name: zQ175.162.M2034


title: 6[4]10_WT_Untreated_STR_female_rep4

description: Library name: zQ175.249.76

value: female


title: 2[4]6_WT_NTC_STR_male_rep2

description: Library name: zQ175.162.M2022


title: 2[4]6_WT_HTT-10150_STR_male_rep2

description: Library name: zQ175.162.M2004


title: 2[4]6_zQ175_Untreated_STR_male_rep2

description: Library name: zQ175.161.M2073

value: Untreated


title: ChIP_RFX5_del3_rep2

description: Library name: ChIP_RFX5_del3_rep2

library_source: other

data_processing:
For ChIP-seq data, reads were aligned to the human genome (UCSC hg19) using bowtie2 (version 2.5.4). SAM files were then converted into BAM files and indexed. Peaks were finally called with macs2 (version 2.2.9.1) with BAM files as input. Heatmap matrix was generated using computeMatrix (version 3.5.4) and illustrated with plotHeatmap software.
Assembly: NCBI hg19
Supplementary files format and content: gzipped wig files can be uploaded to UCSC

molecule: protein

extract_protocol:
For one experiment, a 10 cm dish of cells at ~80 % confluency was collected and cross-linked with 1 % formaldehyde in 10% FBS/PBS followed by wash with PBS supplemented with 1 × proteinase inhibitor.
Cells were then resuspended in lysis buffer and sonicated to ~100-10000 bp using the SCIENTZ Sonication system (10 % energy, with working time 10 s and resting time of 50 s, 10 cycles). The sonicated samples were then centrifuged to remove insoluble debris and precleaned with protein-A agarose beads (Millipore, 16-157) for 1 h with slow rotation to remove non-specificity binding. Samples were then incubated with 2 μg of antibodies against CTCF (CST, 3418S), RAD21 (Abcam, Ab992), RFX5 (Rockland, 200401194) and H3K27ac (CST, 8173S) overnight on a rotator at 4 °C to form antibody-protein-DNA complex. The complex was formulated with protein A-agarose beads and cleaned with low salt buffer, high salt buffer, no salt buffer, LiCl buffer and TE buffer in turn, and finally eluted into elution buffer (1 % SDS, 0.1 M NaHCO3). Reverse cross-link and DNA purification were then performed and the samples were prepared into libraries using the VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme, ND610) following the manufacturer’s instruction.


title: ChIP_CTCF_del2_rep4

description: Library name: ChIP_CTCF_del2_rep4

value: CST 3418S


title: ChIP_CTCF_del2_rep2

description: Library name: ChIP_CTCF_del2_rep2


title: ChIP_CTCF_del3_rep2

description: Library name: ChIP_CTCF_del3_rep2


title: ChIP_CTCF_del3_rep3

description: Library name: ChIP_CTCF_del3_rep3


title: ChIP_CTCF_WT_rep6

description: Library name: ChIP_CTCF_WT_rep6


title: ChIP_CTCF_WT_rep5

description: Library name: ChIP_CTCF_WT_rep5


title: ChIP_CTCF_WT_rep2

description: Library name: ChIP_CTCF_WT_rep2


title: ChIP_RFX5_WT_reo1

description: Library name: ChIP_RFX5_WT_reo1


title: ChIP_CTCF_WT_rep3

description: Library name: ChIP_CTCF_WT_rep3


title: ChIP_RFX5_del1_rep2

description: Library name: ChIP_RFX5_del1_rep2


title: ChIP_CTCF_del2_rep3

description: Library name: ChIP_CTCF_del2_rep3


title: ChIP_RFX5_del2_rep2

description: Library name: ChIP_RFX5_del2_rep2


title: ChIP_CTCF_WT_rep4

description: Library name: ChIP_CTCF_WT_rep4


title: ChIP_CTCF_del3_rep4

description: Library name: ChIP_CTCF_del3_rep4


title: ChIP_RFX5_del3_rep1

description: Library name: ChIP_RFX5_del3_rep1


title: ChIP_RFX5_del2_rep1

description: Library name: ChIP_RFX5_del2_rep1


title: ChIP_CTCF_WT_rep1

description: Library name: ChIP_CTCF_WT_rep1


title: ChIP_RFX5_del1_rep1

description: Library name: ChIP_RFX5_del1_rep1


title: ChIP_CTCF_del3_rep1

description: Library name: ChIP_CTCF_del3_rep1


title: ChIP_CTCF_del2_rep1

description: Library name: ChIP_CTCF_del2_rep1


title: 6[4]10_zQ175_Untreated_STR_female_rep2

description: Library name: zQ175.2237.133

value: 10 months


title: 4C_CADM1_del3_rep2

description: Library name: 4C_CADM1_del3_rep2


title: 4C_PCDHb12_WT_rep1

description: Library name: 4C_PCDHb12_WT_rep1

value: widltype


title: 2[4]6_zQ175_HTT-10150_STR_male_rep2

description: Library name: zQ175.160.M2052

value: Corpus Striatum


title: 2[4]6_zQ175_NTC_STR_male_rep3

description: Library name: zQ175.161.M2071

value: 6 months


title: ChIP_CTCF_del1_rep4

description: Library name: ChIP_CTCF_del1_rep4


title: ChIP_CTCF_del1_rep2

description: Library name: ChIP_CTCF_del1_rep2


title: 2[4]6_WT_NTC_STR_female_rep2

description: Library name: zQ175.158.M2009

value: 2 months


title: ChIP_H3K27ac_del1_rep2

description: Library name: ChIP_H3K27ac_del1_rep2

value: CST 8173S


title: 2[4]6_zQ175_Untreated_STR_male_rep1

description: Library name: zQ175.153.M2030


title: ChIP_H3K27ac_del3_rep2

description: Library name: ChIP_H3K27ac_del3_rep2


title: ChIP_H3K27ac_del2_rep2

description: Library name: ChIP_H3K27ac_del2_rep2


title: ChIP_CTCF_del1_rep3

description: Library name: ChIP_CTCF_del1_rep3


title: 2[4]6_zQ175_HTT-10150_STR_male_rep3

description: Library name: zQ175.161.M2050


title: 2[4]6_WT_NTC_STR_female_rep3

description: Library name: zQ175.159.M2036


title: ChIP_CTCF_del1_rep1

description: Library name: ChIP_CTCF_del1_rep1


title: 2[4]6_WT_HTT-10150_STR_female_rep2

description: Library name: zQ175.158.M2008


title: 2[4]6_zQ175_NTC_STR_male_rep2

description: Library name: zQ175.160.T3264


title: 2[4]6_WT_HTT-10150_STR_female_rep3

description: Library name: zQ175.159.M2025


title: ChIP_H3K27ac_del2_rep1

description: Library name: ChIP_H3K27ac_del2_rep1


title: ChIP_H3K27ac_WT_rep2

description: Library name: ChIP_H3K27ac_WT_rep2


title: ChIP_H3K27ac_WT_rep1

description: Library name: ChIP_H3K27ac_WT_rep1


title: 2[4]6_zQ175_NTC_STR_male_rep1

description: Library name: zQ175.156.T3267


title: ChIP_H3K27ac_del3_rep1

description: Library name: ChIP_H3K27ac_del3_rep1


title: 2[4]6_WT_Untreated_STR_female_rep2

description: Library name: zQ175.158.M2024


title: ChIP_H3K27ac_del1_rep1

description: Library name: ChIP_H3K27ac_del1_rep1


title: 2[4]6_zQ175_HTT-10150_STR_male_rep1

description: Library name: zQ175.153.M2027


title: 4C_CADM1_del2_rep1

description: Library name: 4C_CADM1_del2_rep1


title: ChIP_RAD21_WT_rep2

description: Library name: ChIP_RAD21_WT_rep2

value: Abcam ab992


title: HiC_WT_rep1

description: Library name: HiC_WT_rep1


title: 2[4]6_zQ175_HTT-10150_STR_female_rep3

description: Library name: zQ175.151.M2028


title: 2[4]6_zQ175_Untreated_STR_female_rep1

description: Library name: zQ175.148.M2054


title: ChIP_RAD21_WT_rep1

description: Library name: ChIP_RAD21_WT_rep1


title: 2[4]6_zQ175_Untreated_STR_male_rep4

description: Library name: zQ175.170.K1041


title: 2[4]6_zQ175_NTC_STR_female_rep2

description: Library name: zQ175.149.M2065


title: ChIP_RAD21_de2_rep2

description: Library name: ChIP_RAD21_de2_rep2


title: ChIP_RAD21_del3_rep1

description: Library name: ChIP_RAD21_del3_rep1


title: ChIP_RAD21_del2_rep1

description: Library name: ChIP_RAD21_del2_rep1


title: 2[4]6_zQ175_Untreated_STR_female_rep2

description: Library name: zQ175.148.M2059


title: RNA_WT_rep1

description: Library name: RNA_WT_rep1

data_processing:
For RNA-seq data, reads were aligned to human genome (hg38_tran) using Hisat2 (version 2.2.1) to generate SAM files and converted into BAM files using samtools (version 1.2.1). the FPKM value was calculated using BAM file as input with the Cufflinks software (version 2.2.1). Gene count matrix was generated using featureCounts (version 2.0.3). DEG was calculated with DESeq2 and clustered with clusterProfiler (version 4.14.6).
Assembly: NCBI hg38
Supplementary files format and content: gzipped fpkm_tracking files containing FPKM values for each gene

extract_protocol:
Cells at ~80 % confluency were collected into Trizol reagents (ThermoFisher) for RNA-seq experiments. Total RNA was isolated and precipitated with trichloromethane and isopropyl alcohol, followed by wash with 70 % ethanol. For each RNA-seq experiment, 1 μg of total RNA was used to generate mRNA using mRNA capture bead kit (Vazyme, N403) following the manufacturer’s instructions.
The extracted mRNA was then washed and heat fragmented to an average size of ~150-250 bp using the RNA-seq library Prep kit (Vazyme, NR606). Fragmented RNA was then reverse-transcribed followed with synthesis of second strand cDNA. Afterwards, the cDNA was purified with Ampure XP Beads (Beckman). The purified cDNA was then end-repaired and phosphorylated at the 5’ end. Adaptor was then added to both ends of cDNA and redundant adaptor were removed using Ampure XP Beads (Beckman). The processed cDNA was finally amplified by PCR to generate sequencing libraries. All RNA-seq experiments were performed with at least 2 biological replicates. deletion and their wildtype control cells were experimented in the same round.


title: 2[4]6_zQ175_HTT-10150_STR_female_rep1

description: Library name: zQ175.148.M2038


title: RNA_WT_rep2

description: Library name: RNA_WT_rep2


title: ChIP_RAD21_del1_rep1

description: Library name: ChIP_RAD21_del1_rep1


title: ChIP_RAD21_del1_rep2

description: Library name: ChIP_RAD21_del1_rep2


title: 2[4]6_zQ175_NTC_STR_female_rep1

description: Library name: zQ175.148.M2045


title: 2[4]6_WT_NTC_STR_male_rep1

description: Library name: zQ175.146.M2077


title: 2[4]6_zQ175_HTT-10150_STR_female_rep2

description: Library name: zQ175.149.M2037


title: RNA_del3_rep2

description: Library name: RNA_del3_rep2


title: 2[4]6_WT_Untreated_STR_male_rep1

description: Library name: zQ175.146.M2079


title: 2[4]6_zQ175_NTC_STR_female_rep3

description: Library name: zQ175.151.M2032


title: 2[4]6_WT_HTT-10150_STR_male_rep1

description: Library name: zQ175.146.M2041


title: T-cells from healty donors

description: Library name: S15177Nr2

value: T-cells

value: Blood

value: BD Rhapsody


title: 2[4]6_WT_NTC_STR_female_rep1

description: Library name: zQ175.145.T3263

value: Wild Type

value: NTC


title: RNA_del3_rep1

description: Library name: RNA_del3_rep1

value: Malignant Melanoma

value: RFX5 del -/-


title: 2[4]6_zQ175_Untreated_STR_female_rep3

description: Library name: zQ175.149.M2057

value: female


title: ChIP_RAD21_del3_rep2

description: Library name: ChIP_RAD21_del3_rep2


title: 6[4]10_WT_Untreated_STR_female_rep1

description: Library name: zQ175.228.K1068

value: Untreated


title: 2[4]6_WT_Untreated_STR_female_rep1

description: Library name: zQ175.145.M2224


title: RNA_del2_rep3

description: Library name: RNA_del2_rep3


title: RNA_del2_rep2

description: Library name: RNA_del2_rep2


title: 2+6[8]10_zQ175_Untreated_STR_female_rep4

description: Library name: zQ175.91.215

value: 2+6 months


title: RNA_del1_rep2

description: Library name: RNA_del1_rep2


title: RNA_del2_rep1

description: Library name: RNA_del2_rep1


title: RNA_del1_rep3

description: Library name: RNA_del1_rep3


title: 2+6[8]10_WT_NTC_STR_male_rep4

description: Library name: zQ175.89.27

value: male

value: 10 months


title: 2+6[8]10_WT_HTT-10150_STR_male_rep5

description: Library name: zQ175.89.26

value: Corpus Striatum


title: 2+6[8]10_zQ175_NTC_STR_female_rep4

description: Library name: zQ175.88.151


title: 2+6[8]10_WT_Untreated_STR_male_rep4

description: Library name: zQ175.89.8


title: 2+6[8]10_zQ175_HTT-10150_STR_female_rep4

description: Library name: zQ175.88.135


title: 2+6[8]10_zQ175_NTC_STR_female_rep3

description: Library name: zQ175.87.159


title: 2+6[8]10_zQ175_HTT-10150_STR_female_rep3

description: Library name: zQ175.87.156


title: 2+6[8]10_zQ175_Untreated_STR_female_rep3

description: Library name: zQ175.87.145


title: 6[4]10_zQ175_HTT-10150_STR_female_rep3

description: Library name: zQ175.238.94

value: 6 months


title: RNA_del1_rep1

description: Library name: RNA_del1_rep1


title: RNA_del3_rep3

description: Library name: RNA_del3_rep3


title: 2+6[8]10_WT_HTT-10150_STR_male_rep4

description: Library name: zQ175.86.226


title: 4C_RUNX1_del3_rep2

description: Library name: 4C_RUNX1_del3_rep2


title: 4C_VEGFA_WT_rep2

description: Library name: 4C_VEGFA_WT_rep2

value: widltype


title: 4C_VEGFA_WT_rep1

description: Library name: 4C_VEGFA_WT_rep1


title: 4C_RUNX1_WT_rep1

description: Library name: 4C_RUNX1_WT_rep1


title: 4C_RUNX1_del3_rep1

description: Library name: 4C_RUNX1_del3_rep1


title: hESC Perturb jan_7_GEX_G4_sg_B9

city: Cambridge

first: Reuben

last: Saunders

address: 455 Main St

institute: Whitehead Institute

description: Library name: jan_7_GEX_G4_sg_B9

data_processing:
Cell Ranger
Assembly: GRCh38
Supplementary files format and content: 10x H5AD

source_name: H1 hESC

extract_protocol: 10x 5' scRNA-seq

value: H1 hESC

value: hESC

value: CRISPRi


title: hESC Perturb jan_6_GEX_E3_sg_D10

description: Library name: jan_6_GEX_E3_sg_D10


title: hESC Perturb jan_6_GEX_F3_sg_C10

description: Library name: jan_6_GEX_F3_sg_C10


title: hESC Perturb jan_7_GEX_B4_sg_G9

description: Library name: jan_7_GEX_B4_sg_G9


title: hESC Perturb jan_7_GEX_C4_sg_F9

description: Library name: jan_7_GEX_C4_sg_F9


title: hESC Perturb jan_6_GEX_D3_sg_E10

description: Library name: jan_6_GEX_D3_sg_E10


title: hESC Perturb jan_6_GEX_B3_sg_G10

description: Library name: jan_6_GEX_B3_sg_G10


title: hESC Perturb jan_7_GEX_E4_sg_D9

description: Library name: jan_7_GEX_E4_sg_D9


title: hESC Perturb jan_7_GEX_A4_sg_H9

description: Library name: jan_7_GEX_A4_sg_H9


title: hESC Perturb jan_6_GEX_A3_sg_H10

description: Library name: jan_6_GEX_A3_sg_H10


title: hESC Perturb jan_6_GEX_H3_sg_A10

description: Library name: jan_6_GEX_H3_sg_A10


title: hESC Perturb jan_8_GEX_F5_sg_C8

description: Library name: jan_8_GEX_F5_sg_C8


title: hESC Perturb jan_6_GEX_G3_sg_B10

description: Library name: jan_6_GEX_G3_sg_B10


title: hESC Perturb jan_8_GEX_B5_sg_G8

description: Library name: jan_8_GEX_B5_sg_G8


title: hESC Perturb jan_8_GEX_C5_sg_F8

description: Library name: jan_8_GEX_C5_sg_F8


title: hESC Perturb jan_7_GEX_F4_sg_C9

description: Library name: jan_7_GEX_F4_sg_C9


title: hESC Perturb jan_7_GEX_D4_sg_E9

description: Library name: jan_7_GEX_D4_sg_E9


title: hESC Perturb jan_7_GEX_H4_sg_A9

description: Library name: jan_7_GEX_H4_sg_A9


title: 2+6[8]10_WT_NTC_STR_male_rep3

description: Library name: zQ175.85.254


title: hESC Perturb jan_8_GEX_A5_sg_H8

description: Library name: jan_8_GEX_A5_sg_H8


title: 4C_RUNX1_del2_rep2

description: Library name: 4C_RUNX1_del2_rep2


title: 4C_RUNX1_WT_rep2

description: Library name: 4C_RUNX1_WT_rep2


title: hESC Perturb jan_8_GEX_D5_sg_E8

description: Library name: jan_8_GEX_D5_sg_E8


title: hESC Perturb jan_6_GEX_C3_sg_F10

description: Library name: jan_6_GEX_C3_sg_F10


title: hESC Perturb jan_8_GEX_E5_sg_D8

description: Library name: jan_8_GEX_E5_sg_D8


title: hESC Perturb jan_4_GEX_E2_sg_D11

description: Library name: jan_4_GEX_E2_sg_D11


title: hESC Perturb jan_4_GEX_F2_sg_C11

description: Library name: jan_4_GEX_F2_sg_C11


title: hESC Perturb jan_4_GEX_G2_sg_B11

description: Library name: jan_4_GEX_G2_sg_B11


title: 2+6[8]10_WT_HTT-10150_STR_male_rep3

description: Library name: zQ175.85.242


title: hESC Perturb jan_4_GEX_B2_sg_G11

description: Library name: jan_4_GEX_B2_sg_G11


title: 4C_RUNX1_del2_rep1

description: Library name: 4C_RUNX1_del2_rep1


title: hESC Perturb jan_3_GEX_H1_sg_A12

description: Library name: jan_3_GEX_H1_sg_A12


title: 2+6[8]10_WT_Untreated_STR_female_rep4

description: Library name: zQ175.84.45


title: hESC Perturb jan_3_GEX_E1_sg_D12

description: Library name: jan_3_GEX_E1_sg_D12


title: 2+6[8]10_WT_Untreated_STR_male_rep3

description: Library name: zQ175.85.241


title: hESC Perturb jan_4_GEX_A2_sg_H11

description: Library name: jan_4_GEX_A2_sg_H11


title: hESC Perturb jan_3_GEX_C1_sg_F12

description: Library name: jan_3_GEX_C1_sg_F12


title: 2+6[8]10_WT_NTC_STR_female_rep4

description: Library name: zQ175.83.34


title: 4C_RUNX1_del1_rep2

description: Library name: 4C_RUNX1_del1_rep2


title: 4C_IL6_WT_rep1

description: Library name: 4C_IL6_WT_rep1


title: hESC Perturb jan_4_GEX_C2_sg_F11

description: Library name: jan_4_GEX_C2_sg_F11


title: hESC Perturb jan_4_GEX_D2_sg_E11

description: Library name: jan_4_GEX_D2_sg_E11


title: hESC Perturb jan_3_GEX_F1_sg_C12

description: Library name: jan_3_GEX_F1_sg_C12


title: 4C_RUNX1_del1_rep1

description: Library name: 4C_RUNX1_del1_rep1


title: hESC Perturb jan_17_GEX_H12_sg_A1

description: Library name: jan_17_GEX_H12_sg_A1


title: hESC Perturb jan_3_GEX_B1_sg_G12

description: Library name: jan_3_GEX_B1_sg_G12


title: hESC Perturb jan_3_GEX_A1_sg_H12

description: Library name: jan_3_GEX_A1_sg_H12


title: 4C_IL6_del3_rep2

description: Library name: 4C_IL6_del3_rep2


title: hESC Perturb jan_17_GEX_G12_sg_B1

description: Library name: jan_17_GEX_G12_sg_B1


title: 4C_IL6_del3_rep1

description: Library name: 4C_IL6_del3_rep1


title: 2+6[8]10_zQ175_NTC_STR_male_rep4

description: Library name: zQ175.82.48


title: hESC Perturb jan_17_GEX_C12_sg_F1

description: Library name: jan_17_GEX_C12_sg_F1


title: hESC Perturb jan_17_GEX_F12_sg_C1

description: Library name: jan_17_GEX_F12_sg_C1


title: 4C_IL6_del2_rep1

description: Library name: 4C_IL6_del2_rep1


title: 2+6[8]10_WT_Untreated_STR_female_rep3

description: Library name: zQ175.83.41


title: hESC Perturb jan_3_GEX_D1_sg_E12

description: Library name: jan_3_GEX_D1_sg_E12


title: 2+6[8]10_zQ175_NTC_STR_male_rep3

description: Library name: zQ175.81.55


title: hESC Perturb jan_3_GEX_G1_sg_B12

description: Library name: jan_3_GEX_G1_sg_B12


title: 4C_IL6_del2_rep2

description: Library name: 4C_IL6_del2_rep2


title: 4C_IL6_WT_rep2

description: Library name: 4C_IL6_WT_rep2


title: 2+6[8]10_zQ175_HTT-10150_STR_male_rep4

description: Library name: zQ175.82.32


title: hESC Perturb jan_17_GEX_D12_sg_E1

description: Library name: jan_17_GEX_D12_sg_E1


title: hESC Perturb jan_17_GEX_A12_sg_H1

description: Library name: jan_17_GEX_A12_sg_H1


title: hESC Perturb jan_17_GEX_B12_sg_G1

description: Library name: jan_17_GEX_B12_sg_G1


title: 2+6[8]10_zQ175_Untreated_STR_male_rep3

description: Library name: zQ175.81.64


title: 2+6[8]10_zQ175_Untreated_STR_male_rep4

description: Library name: zQ175.82.63


title: hESC Perturb jan_16_GEX_F11_sg_C2

description: Library name: jan_16_GEX_F11_sg_C2


title: 4C_IL6_del1_rep2

description: Library name: 4C_IL6_del1_rep2


title: 2+6[8]10_zQ175_HTT-10150_STR_male_rep3

description: Library name: zQ175.81.40


title: 2+6[8]10_WT_NTC_STR_female_rep3

description: Library name: zQ175.80.51


title: hESC Perturb jan_16_GEX_G11_sg_B2

description: Library name: jan_16_GEX_G11_sg_B2


title: 2[4]6_WT_HTT-10150_STR_female_rep1

description: Library name: zQ175.145.T3260

value: 2 months


title: hESC Perturb jan_17_GEX_E12_sg_D1

description: Library name: jan_17_GEX_E12_sg_D1


title: hESC Perturb jan_16_GEX_E11_sg_D2

description: Library name: jan_16_GEX_E11_sg_D2


title: hESC Perturb jan_16_GEX_D11_sg_E2

description: Library name: jan_16_GEX_D11_sg_E2


title: 2+6[8]10_WT_Untreated_STR_female_rep2

description: Library name: zQ175.80.46


title: 4C_HLADPA1_WT_rep1

description: Library name: 4C_HLADPA1_WT_rep1


title: hESC Perturb jan_16_GEX_B11_sg_G2

description: Library name: jan_16_GEX_B11_sg_G2


title: hESC Perturb jan_16_GEX_C11_sg_F2

description: Library name: jan_16_GEX_C11_sg_F2


title: 2+6[8]10_WT_HTT-10150_STR_female_rep2

description: Library name: zQ175.83.10


title: hESC Perturb jan_16_GEX_H11_sg_A2

description: Library name: jan_16_GEX_H11_sg_A2


title: hESC Perturb jan_16_GEX_A11_sg_H2

description: Library name: jan_16_GEX_A11_sg_H2


title: 2+6[8]10_zQ175_NTC_STR_male_rep2

description: Library name: zQ175.78.36


title: 4C_IL6_del1_rep1

description: Library name: 4C_IL6_del1_rep1


title: hESC Perturb jan_14_GEX_H10_sg_A3

description: Library name: jan_14_GEX_H10_sg_A3


title: 4C_HLADPA1_WT_rep2

description: Library name: 4C_HLADPA1_WT_rep2


title: 2+6[8]10_WT_NTC_STR_male_rep2

description: Library name: zQ175.75.3


title: 2+6[8]10_zQ175_Untreated_STR_male_rep2

description: Library name: zQ175.78.34


title: 2+6[8]10_zQ175_HTT-10150_STR_male_rep2

description: Library name: zQ175.78.32


title: 2+6[8]10_WT_HTT-10150_STR_male_rep2

description: Library name: zQ175.75.2


title: hESC Perturb jan_14_GEX_F10_sg_C3

description: Library name: jan_14_GEX_F10_sg_C3


title: hESC Perturb jan_14_GEX_G10_sg_B3

description: Library name: jan_14_GEX_G10_sg_B3


title: hESC Perturb jan_14_GEX_E10_sg_D3

description: Library name: jan_14_GEX_E10_sg_D3


title: 2+6[8]10_zQ175_NTC_STR_female_rep2

description: Library name: zQ175.74.35


title: 2+6[8]10_zQ175_Untreated_STR_female_rep2

description: Library name: zQ175.74.30


title: hESC Perturb jan_14_GEX_C10_sg_F3

description: Library name: jan_14_GEX_C10_sg_F3


title: hESC Perturb jan_14_GEX_D10_sg_E3

description: Library name: jan_14_GEX_D10_sg_E3


title: hESC Perturb jan_14_GEX_B10_sg_G3

description: Library name: jan_14_GEX_B10_sg_G3


title: 2+6[8]10_WT_HTT-10150_STR_female_rep1

description: Library name: zQ175.73.16


title: hESC Perturb jan_14_GEX_A10_sg_H3

description: Library name: jan_14_GEX_A10_sg_H3


title: 2+6[8]10_WT_NTC_STR_female_rep2

description: Library name: zQ175.73.17


title: 2+6[8]10_WT_Untreated_STR_female_rep1

description: Library name: zQ175.73.12


title: hESC Perturb jan_13_GEX_H9_sg_A4

description: Library name: jan_13_GEX_H9_sg_A4


title: hESC Perturb jan_13_GEX_G9_sg_B4

description: Library name: jan_13_GEX_G9_sg_B4


title: 2+6[8]10_zQ175_Untreated_STR_male_rep1

description: Library name: zQ175.72.28


title: 2+6[8]10_zQ175_HTT-10150_STR_male_rep1

description: Library name: zQ175.71.27


title: hESC Perturb jan_13_GEX_F9_sg_C4

description: Library name: jan_13_GEX_F9_sg_C4


title: 2+6[8]10_zQ175_NTC_STR_male_rep1

description: Library name: zQ175.71.21


title: hESC Perturb jan_13_GEX_E9_sg_D4

description: Library name: jan_13_GEX_E9_sg_D4


title: 4C_HLADPA1_del2_rep1

description: Library name: 4C_HLADPA1_del2_rep1


title: 4C_ETS1_del3_rep2

description: Library name: 4C_ETS1_del3_rep2


title: 4C_ETS1_del1_rep1

description: Library name: 4C_ETS1_del1_rep1


title: 4C_ETS1_WT_rep2

description: Library name: 4C_ETS1_WT_rep2


title: 4C_HLADPA1_del3_rep1

description: Library name: 4C_HLADPA1_del3_rep1


title: 4C_ETS1_del2_rep2

description: Library name: 4C_ETS1_del2_rep2


title: 4C_HLADPA1_del1_rep1

description: Library name: 4C_HLADPA1_del1_rep1


title: 4C_ETS1_del2_rep1

description: Library name: 4C_ETS1_del2_rep1


title: 4C_ETS1_del1_rep2

description: Library name: 4C_ETS1_del1_rep2


title: 4C_ETS1_del3_rep1

description: Library name: 4C_ETS1_del3_rep1


title: 4C_ETS1_WT_rep1

description: Library name: 4C_ETS1_WT_rep1


title: 4C_HLADPA1_del2_rep2

description: Library name: 4C_HLADPA1_del2_rep2


title: 4C_HLADPA1_del3_rep2

description: Library name: 4C_HLADPA1_del3_rep2


title: fetal_adrenal_6wpf

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description: Library name: fetal_adrenal_6wpf

data_processing:
Sequence data was demultiplexed and fastqs produced using Cell Ranger (v.7.1.0)
UMI counts were read into R (v.4.4.1) and secondary analysis was performed using Seurat (v.5.1.0)1. UMI count tables were first loaded into R by using the Read10x function, and Seurat objects were built from each sample, one per alignment.
For mixed samples: The sum of UMI counts for each alignment was totaled for each cell for both human and mouse counts. The total UMIs for human alignment were then compared with the mouse alignment. Any cell with greater than twofold assignment of UMIs to human than mouse was designated as a human cell. Similarly, any cell with twofold higher mouse counts than human would be designated mouse.
For each sample a minimum number of genes = 2,000 and maximum genes = 10,000 were set as well as a maximum mitochondrial content of 25% and cells outside those bounds were excluded. A minimum UMI was set on a per-sample basis to exclude low-quality cells by assigning a minimum cutoff based on an inspection of a ranked plot of UMI per sample. Minimum UMI cutoffs were as follows: MT21_DZLCplusCap, MT18_APLCplusCap – 103.5; A78_L, HS108 – 103.6; HS97, T24_d45 – 103.7;  HS26H, HS46, HS12H – 103.9; A176_CD10_d7_RSPO3_ACTH, A176_CD10_d14_Base_ACTH, MT3_3m_APplusCap – 104.  For all other samples a minimum of 103.8 UMI/cell was set.
Cell cycle state was assigned using Seurat’s CellCycleScoring function. Samples were scaled using SCTransform 2, regressing “S.Score” and “G2M.Score”. Layers were integrated using Harmony method 3 within Seurat’s IntegrateLayers function. The first 30 dimensions were used for FindNeighbors, FindClusters and RunUMAP to generate an integrated object containing all cells.
Assembly: GRCh38, (additionally for samples containing mouse cells, also against GRCm38)
Supplementary files format and content: Processed files are seurat object for each sample individually prior to integration

source_name: adrenal

growth_protocol: APLCs were induced using established methods. DZLCs were induced from APLCs using RSPO3 + SB-431542.

extract_protocol:
Cells were encapsulated using 10X's chromium system using manufacturer's protocol
Libraries were created using 10X's 3.1 NextGEM kits following manufacturer's protocols.

value: adrenal

value: fetal


title: fetal_adrenal_5wpf

description: Library name: fetal_adrenal_5wpf


title: adult_adrenal_17yo_rep_1

description: Library name: adult_adrenal_17yo_rep_1

value: adult


title: adult_adrenal_38yo

description: Library name: adult_adrenal_38yo


title: 2+6[8]10_WT_HTT-10150_STR_male_rep1

description: Library name: zQ175.70.19

value: Wild Type


title: fetal_adrenal_19wpf

description: Library name: fetal_adrenal_19wpf


title: adult_adrenal_17yo_rep_2

description: Library name: adult_adrenal_17yo_rep_2


title: fetal_adrenal_8wpf_2

description: Library name: fetal_adrenal_8wpf_2


title: adult_adrenal_50yo

description: Library name: adult_adrenal_50yo


title: DZLC_d21

description: Library name: DZLC_d21

source_name: iPSC-derived

value: iPSC-derived

value: DZLC


title: fetal_adrenal_8wpf_1

description: Library name: fetal_adrenal_8wpf_1


title: TZLC

description: Library name: TZLC

value: TZLC


title: DZLC_d45

description: Library name: DZLC_d45


title: fetal_adrenal_17wpf

description: Library name: fetal_adrenal_17wpf


title: 2+6[8]10_WT_Untreated_STR_male_rep1

description: Library name: zQ175.69.13

value: Untreated

value: 2+6 months


title: 4C_EGFR_del3_rep2

description: Library name: 4C_EGFR_del3_rep2

value: Malignant Melanoma

value: RFX5 del -/-


title: hESC Perturb jan_13_GEX_D9_sg_E4

description: Library name: jan_13_GEX_D9_sg_E4


title: hESC Perturb jan_4_GEX_H2_sg_A11

description: Library name: jan_4_GEX_H2_sg_A11


title: 4C_EGFR_WT_rep2

description: Library name: 4C_EGFR_WT_rep2


title: 2+6[8]10_WT_NTC_STR_male_rep1

description: Library name: zQ175.70.15

value: Corpus Striatum

value: NTC

value: male

value: 10 months


title: 4C_EGFR_WT_rep1

description: Library name: 4C_EGFR_WT_rep1

value: widltype


title: hESC Perturb jan_13_GEX_C9_sg_F4

description: Library name: jan_13_GEX_C9_sg_F4

value: H1 hESC

value: hESC

value: CRISPRi


title: hESC Perturb jan_13_GEX_B9_sg_G4

description: Library name: jan_13_GEX_B9_sg_G4


title: hESC Perturb jan_13_GEX_A9_sg_H4

description: Library name: jan_13_GEX_A9_sg_H4


title: DZLC_CapLC_tx_d87

description: Library name: DZLC_CapLC_tx_d87


title: 2+6[8]10_WT_Untreated_STR_male_rep2

description: Library name: zQ175.69.14


title: APLC_CapLC_tx_d55

description: Library name: APLC_CapLC_tx_d55

value: APLC


title: 2+6[8]10_zQ175_Untreated_STR_female_rep1

description: Library name: zQ175.68.27

value: female


title: hESC Perturb jan_12_GEX_H8_sg_A5

description: Library name: jan_12_GEX_H8_sg_A5


title: 4C_EGFR_del3_rep1

description: Library name: 4C_EGFR_del3_rep1


title: hESC Perturb jan_12_GEX_F8_sg_C5

description: Library name: jan_12_GEX_F8_sg_C5


title: hESC Perturb jan_12_GEX_G8_sg_B5

description: Library name: jan_12_GEX_G8_sg_B5


title: 4C_EGFR_del2_rep2

description: Library name: 4C_EGFR_del2_rep2


title: 4C_EGFR_del2_rep1

description: Library name: 4C_EGFR_del2_rep1


title: 4C_EGFR_del1_rep2

description: Library name: 4C_EGFR_del1_rep2


title: 2+6[8]10_zQ175_HTT-10150_STR_female_rep1

description: Library name: zQ175.68.20


title: 2+6[8]10_zQ175_NTC_STR_female_rep1

description: Library name: zQ175.68.19


title: 2+6[8]10_WT_NTC_STR_female_rep1

description: Library name: zQ175.66.3

value: Wild Type


title: 2+6[8]10_zQ175_HTT-10150_STR_female_rep2

description: Library name: zQ175.68.26


title: 4C_AXL_WT_rep2

description: Library name: 4C_AXL_WT_rep2


title: 4C_EGFR_del1_rep1

description: Library name: 4C_EGFR_del1_rep1


title: hESC Perturb jan_12_GEX_E8_sg_D5

description: Library name: jan_12_GEX_E8_sg_D5


title: hESC Perturb jan_12_GEX_D8_sg_E5

description: Library name: jan_12_GEX_D8_sg_E5


title: hESC Perturb jan_12_GEX_C8_sg_F5

description: Library name: jan_12_GEX_C8_sg_F5


title: 4C_AXL_WT_rep1

description: Library name: 4C_AXL_WT_rep1


title: hESC Perturb jan_12_GEX_B8_sg_G5

description: Library name: jan_12_GEX_B8_sg_G5


title: 4C_AXL_del3_rep1

description: Library name: 4C_AXL_del3_rep1


title: hESC Perturb jan_12_GEX_A8_sg_H5

description: Library name: jan_12_GEX_A8_sg_H5


title: hESC Perturb jan_10_GEX_H7_sg_A6

description: Library name: jan_10_GEX_H7_sg_A6


title: 4C_AXL_del3_rep2

description: Library name: 4C_AXL_del3_rep2


title: hESC Perturb jan_10_GEX_G7_sg_B6

description: Library name: jan_10_GEX_G7_sg_B6


title: 4C_AXL_del2_rep1

description: Library name: 4C_AXL_del2_rep1


title: 4C_AXL_del2_rep2

description: Library name: 4C_AXL_del2_rep2


title: 4C_AXL_del1_rep2

description: Library name: 4C_AXL_del1_rep2


title: hESC Perturb jan_10_GEX_E7_sg_D6

description: Library name: jan_10_GEX_E7_sg_D6


title: 4C_AXL_del1_rep1

description: Library name: 4C_AXL_del1_rep1


title: hESC Perturb jan_10_GEX_D7_sg_E6

description: Library name: jan_10_GEX_D7_sg_E6


title: hESC Perturb jan_10_GEX_C7_sg_F6

description: Library name: jan_10_GEX_C7_sg_F6


title: 4C_ANKRD1_WT_rep2

description: Library name: 4C_ANKRD1_WT_rep2


title: 4C_ANKRD1_WT_rep1

description: Library name: 4C_ANKRD1_WT_rep1


title: hESC Perturb jan_10_GEX_B7_sg_G6

description: Library name: jan_10_GEX_B7_sg_G6


title: 4C_HLADPA1_del1_rep2

description: Library name: 4C_HLADPA1_del1_rep2


title: APLC_CapLC_tx_d90

description: Library name: APLC_CapLC_tx_d90

value: iPSC-derived


title: FZLC

description: Library name: FZLC

value: FZLC


title: hESC Perturb jan_10_GEX_A7_sg_H6

description: Library name: jan_10_GEX_A7_sg_H6


title: 4C_ANKRD1_del3_rep2

description: Library name: 4C_ANKRD1_del3_rep2


title: 4C_ANKRD1_del3_rep1

description: Library name: 4C_ANKRD1_del3_rep1


title: Anca9_XETG00088__0029041__Region_8__20240719__095642

type: RNA

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: The Xenium samples underwent 15 rounds of   fluorescent probe hybridization, imaging, and probe removal. The Xenium   Analyzer captured a Z-stack of images every cycle and in every channel,   which needed to be processed and stitched to build a spatial map of the   transcripts across the tissue section. Decoding of transcripts was   performed using a Xenium codebook (a collection of codewords that were   assigned to genes in the gene panel). In order to assign mRNAs to cells,   the spatial boundaries of cells were defined by nuclear expansion   (Default segmentation). Xenium was run on a commercial instrument.

scan_protocol: Xenium In Situ Analyzer

data_processing:
Baysor (v0.6.2) was used to re-segment cells with prior being default segmentations (cell_boundaries.parquet). Scanpy (v1.10.1) workflows were used for normalization to the median the downstream analysis.  The processed anndata object (processed_data.h5ad) contains cells after re-segmentation and integration. .X contains log-normalized counts.
Gene expression

label: Xenium Human Custom Probe Set

source_name: 5 µm kidney section

label_protocol: Xenium Human Probe Set

extract_protocol: 5 μm sections from FFPE were taken each for Xenium.

value: kidney

tag: subject group

value: ANCA

tag: number of samples in the slide


title: Anca8_XETG00088__0029041__Region_7__20240719__095642


title: 4C_ANKRD1_del2_rep2

description: Library name: 4C_ANKRD1_del2_rep2

value: Malignant Melanoma


title: GDM3

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

description: Library name: Sample 8

data_processing:
Raw reads were aligned to the human genome (GRCh38) using Bowtie2. Gene-level counts were generated with HTSeq, and differential expression analysis was performed using DESeq2 via the SARTools pipeline.
Assembly: GRCh38
Supplementary files format and content: .txt files containing normalised counts

source_name: Gingival Crevicular Fluid

extract_protocol:
RNA was extracted from pooled GCF paper strips using TRIzol LS Reagent, followed by quantification with Qubit and quality assessment with Fragment Analyzer.
Libraries were prepared using the Collibri Stranded RNA Library Prep Kit (Thermo Fisher, A39003024) following the manufacturer's protocol. Library quality was assessed using a Fragment Analyzer.

value: Gingival Crevicular Fluid

tag: trimester

value: first

tag: gdm status_at_end_of_pregnancy

value: gestational diabetes mellitus (GDM)


title: GDM4

description: Library name: Sample 9


title: GDM2

description: Library name: Sample 7


title: GDM5

description: Library name: Sample 10


title: Anca7_XETG00088__0029041__Region_6__20240719__095642


title: 4C_ANKRD1_del2_rep1

description: Library name: 4C_ANKRD1_del2_rep1

value: RFX5 del -/-


title: GDM1

description: Library name: Sample 6


title: Anca6_XETG00088__0029041__Region_5__20240719__095642


title: 4C_ANKRD1_del1_rep2

description: Library name: 4C_ANKRD1_del1_rep2


title: CTL5

description: Library name: Sample 5

value: healthy


title: Control 2

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: DZNE Göttingen

description: Library name: Sample 2

data_processing:
sequencing reads were mapped with bowtie2 to GrCM38/mm10 genome
Peaks were called using  MACS2.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes differentially expressed peaks

source_name: primary hippocampal neurons

growth_protocol: primary hippocampal neurons were maintained in Neurobasal medium supplemented with 1% B27 and antibiotics in a humidified chamber at 37°C

extract_protocol:
RNA was isolated using the Zymo RNA clean & Concentrator-5 Kit.
ChIP-seq libraries were prepared using  NEBNext Ultra II DANN Library Prep Kit for Illumina.

treatment_protocol: Cells with fixed with 5% PFA for 10 minutes. After quenching and cell lysis, chromatin was sonicated for 30 cycles.

value: primary hippocampal neurons

value: WT

value: Anti-h3k27me3 (07-449, Millipore)


title: NeuID knockdown 1

description: Library name: Sample 7

value: NeuID knockdown


title: NeuID knockdown 4

description: Library name: Sample 10


title: Control 5

description: Library name: Sample 5


title: Control 6

description: Library name: Sample 6


title: NeuID knockdown 6

description: Library name: Sample 12


title: NeuID knockdown 5

description: Library name: Sample 11


title: Control 3

description: Library name: Sample 3


title: knoockdown input

description: Library name: Sample 14


title: Control 1

description: Library name: Sample 1


title: NeuID knockdown 2

description: Library name: Sample 8


title: Control 4

description: Library name: Sample 4


title: NeuID knockdown 3

description: Library name: Sample 9


title: Control input

description: Library name: Sample 13


title: Anca5_XETG00088__0029041__Region_4__20240719__095642


title: Anca2_XETG00088__0029040__Region_6__20240719__095642


title: Anca3_XETG00088__0029040__Region_7__20240719__095642


title: CTL2

description: Library name: Sample 2


title: CTL3

description: Library name: Sample 3


title: 4C_ANKRD1_del1_rep1

description: Library name: 4C_ANKRD1_del1_rep1


title: CTL4

description: Library name: Sample 4


title: Anca4_XETG00088__0029041__Region_3__20240719__095642


title: CTL1

description: Library name: Sample 1


title: Anca1_XETG00088__0029040__Region_5__20240719__095642


title: Patient 8 AK/In situ

description: Library name: 10-S2210320-PRE

data_processing:
The resulting FASTQ files were processed towards a gene expression count matrix using the HTG EdgeSeq Reveal Software. The quality control (QC) of NGS data was assessed prior analysis to ensure the data robustness.
Assembly: hg38
Supplementary files format and content: File name is "21019221207_HTGseq_rawdata.xlsx". File contains the count matrix. Sample names allow the reconstruction of metadata regarding specimen origin (SAIN = heatlhy skin, PRE = Actinic keratosis/In situ cSCC, TUM = tumor).

source_name: Actinic keratosis/In situ cSCC

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) skin specimens were obtained from a cohort of eight patients with cutaneous squamous cell carcinoma (cSCC). For each patient, tissue blocks contained histologically distinct regions corresponding to (i) healthy skin, (ii) actinic keratosis (AK) and/or in situ cSCC, and (iii) advanced invasive cSCC. Hematoxylin and eosin–stained sections were reviewed by a board-certified dermatopathologist to confirm diagnoses and to guide region selection. The three regions of interest (healthy, AK/in situ cSCC, and advanced cSCC) were macro-dissected separately from 5-µm FFPE unstained sections using annotated reference slides. Care was taken to minimize cross-contamination between regions. Sections were then subjected to lysis and Proteinase K treatment for 20min at 56°C. After protein inactivation, DNase digestion was performed at 37°C for 30 min and the quantitative nuclease protection assay was run using the HTG EdgeSeq Processors. Adapters and sample tags were finally added in a PCR amplification.
The resulting libraries were sequenced using on an Illumina NextSeq 2000 (Flow cell P2 - 100 cycles).

value: Actinic keratosis/In situ cSCC


title: Anca0_XETG00088__0029040__Region_4__20240719__095642


title: Patient 8 Tumoral

description: Library name: 10-S2210320-TUM

source_name: cSCC tumor

value: cSCC tumor


title: control2_XETG00088__0029041__Region_1__20240719__095642

value: Control


title: Patient 8 Healthy

description: Library name: 10-S2210320-SAIN

source_name: Healthy skin

value: Healthy skin


title: control1_XETG00088__0029040__Region_3__20240719__095641


title: Patient 7 AK/In situ

description: Library name: 10-S2210959-PRE


title: Marc-145 cells exposured with DON rep4

city: Jinzhong

first: Ruiyan

last: Niu

address: Shanxi Agricultural University, Taigu District, Jinzhong City, Shanxi Province

institute: Shanxi Agricultural University

description: Library name: D4

data_processing:
RNA-seq
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Macaca mulatta

source_name: Kidney

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Kidney

value: Epithelial-like


title: Marc-145 cells exposured with DON rep5

description: Library name: D5


title: Marc-145 cells co-exposured to DON and PRRSV rep2

description: Library name: VD2


title: Marc-145 cells co-exposured to DON and PRRSV rep4

description: Library name: VD4


title: Marc-145 cells co-exposured to DON and PRRSV rep5

description: Library name: VD5


title: Marc-145 cells co-exposured to DON and PRRSV rep1

description: Library name: VD1


title: Marc-145 cells co-exposured to DON and PRRSV rep3

description: Library name: VD3


title: Marc-145 cells exposured with DON rep3

description: Library name: D3


title: Patient 7 Tumoral

description: Library name: 10-S2210959-TUM


title: Marc-145 cells exposured with DON rep2

description: Library name: D2


title: Patient 7 Healthy

description: Library name: 10-S2210959-SAIN


title: spatial gene expression profiling of HPV-OPSCC; NCI_22

description: This data was generated using the 10x Genomics Xenium platform

hyb_protocol: The tissue sections were first deparaffinized and de-crosslinked according to the 10x Genomics Demonstrated Protocol CG000580. Subsequently, probe hybridization, ligation, amplification and subsequent steps were performed as outlined in the 10X user guide (CG000582). The custom probe set was then used in the hybridization step.

scan_protocol: A Xenium run was set-up as per Xenium Analyzer user guide (CG000584) running instrument software v1.6.1.0 and onboard analysis software v1.6.0.8 (10x Genomics). Digital images were acquired of the hematoxylin and eosin-stained tissue section used for spatial transcriptomic analysis and annotation of tumor parenchyma and stroma (malignant samples) or non-malignant epithelium and stroma (non-malignant samples) was performed by an anatomic pathologist. Xenium data was processed using the Space Range software (10x Genomics)

data_processing:
Sample_ID_seurat_xenium.rds is an R data file containing a seurat object containing the spatial gene expression information and can be read using the R readRDS function.
Sample_ID_transcripts.csv.gz is a space ranger output file that contains information about all transcripts assiged to individual cells. For instance, it specifies if a transcript overlaps with the nucleus of a given cell.

source_name: orophyngeal carcinoma

treatment_protocol: Xenium In Situ Technology from 10X Genomics was used to spatially detect gene expression using a custom probe set that included HPV16 genes. Tissue sections of 5 μm thickness from FFPE blocks were placed on Xenium slides.

value: orophyngeal carcinoma

value: whole-tissue sections from FFPE blocks

value: mixed

value: treatment-naïve


title: control0_XETG00088__0029040__Region_2__20240719__095641

value: kidney


title: Patient 6 AK/In situ

description: Library name: 10-S2202680-PRE


title: Marc-145 cells exposured with DON rep1

description: Library name: D1


title: spatial gene expression profiling of HPV-OPSCC; NCI_21

extract_protocol: The tissue sections were first deparaffinized and de-crosslinked according to the 10x Genomics Demonstrated Protocol CG000580. Subsequently, probe hybridization, ligation, amplification and subsequent steps were performed as outlined in the 10X user guide (CG000582). The custom probe set was then used in the hybridization step.


title: spatial gene expression profiling of HPV-OPSCC; NCI_15


title: Patient 6 Tumoral

description: Library name: 10-S2202680-TUM


title: Marc-145 cells infected with PRRSV rep5

description: Library name: V5


title: spatial gene expression profiling of HPV-OPSCC; NCI_14


title: TIM3+ CX3CR1+ cells, WT 849

city: Saint Louis

first: Sunnie

last: Hsiung

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 4.0.3-8 software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: spleen

growth_protocol: Tcf7-cKO mice on a B6 background were infected with LCMV clone 13. Splenocytes were harvested on day 35 post-infection and purified using FACS.

extract_protocol:
Cells were lysed in Trizol and RNA was extracted using Direct-zol RNA miniprep kit (Zymo Research).
Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol.

value: spleen


title: TIM3+ CX3CR1– cells, WT 849


title: TIM3+ CX3CR1– cells, KO 940


title: TIM3+ CX3CR1+ cells, KO 945


title: TIM3+ CX3CR1+ cells, KO 874


title: TIM3+ CX3CR1– cells, KO 945


title: TIM3+ CX3CR1– cells, KO 876


title: TIM3+ CX3CR1– cells, KO 874


title: TIM3+ CX3CR1– cells, WT 850


title: TIM3+ CX3CR1+ cells, WT 853


title: TIM3+ CX3CR1+ cells, KO 940


title: TIM3+ CX3CR1+ cells, KO 876


title: TIM3+ CX3CR1– cells, WT 856


title: TIM3+ CX3CR1+ cells, WT 850


title: TIM3+ CX3CR1– cells, WT 853


title: Marc-145 cells infected with PRRSV rep4

description: Library name: V4


title: Patient 6 Healthy

description: Library name: 10-S2202680-SAIN


title: TIM3+ CX3CR1+ cells, WT 856


title: Patient 5 Tumoral

description: Library name: 10-S2228101-TUM


title: Marc-145 cells infected with PRRSV rep2

description: Library name: V2


title: spatial gene expression profiling of HPV-OPSCC; NCI_10


title: spatial gene expression profiling of HPV-OPSCC; NCI_12


title: Patient 4 AK/In situ

description: Library name: 10-S2216712-PRE


title: Marc-145 cells infected with PRRSV rep3

description: Library name: V3


title: Marc-145 cells infected with PRRSV rep1

description: Library name: V1


title: spatial gene expression profiling of HPV-OPSCC; NCI_8


title: Patient 5 AK/In situ

description: Library name: 10-S2228101-PRE


title: spatial gene expression profiling of HPV-OPSCC; NCI_9


title: Patient 5 Healthy

description: Library name: 10-S2228101-SAIN


title: Marc-145 cells control group rep5

description: Library name: C5


title: spatial gene expression profiling of HPV-OPSCC; NCI_6


title: Marc-145 cells control group rep4

description: Library name: C4


title: Marc-145 cells control group rep3

description: Library name: C3


title: Patient 4 Tumoral

description: Library name: 10-S2216712-TUM


title: Patient 4 Healthy

description: Library name: 10-S2216712-SAIN


title: Patient 3 AK/In situ

description: Library name: 10-S2202105-PRE


title: spatial gene expression profiling of HPV-OPSCC; NCI_4


title: spatial gene expression profiling of HPV-OPSCC; NCI_3


title: Marc-145 cells control group rep1

description: Library name: C1


title: Marc-145 cells control group rep2

description: Library name: C2


title: Patient 3 Tumoral

description: Library name: 10-S2202105-TUM


title: Patient 3 Healthy

description: Library name: 10-S2202105-SAIN


title: Patient 2 AK/In situ

description: Library name: 10-S2203938-PRE


title: Patient 2 Tumoral

description: Library name: 10-S2203938-TUM


title: CMP11_CNS_WT_4

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: Library name: 677T_D4

data_processing:
The sequences in raw FASTQ files were aligned to the EMSEMBL GRCm38.p6 mouse reference transcriptome105 and quantified using Kallisto (v0.46.1).
Assembly: GRCm38
Supplementary files format and content: Gzipped kallisto output

source_name: CNS

growth_protocol: Adult mice were used on a C57Bl/6J background (The Jackson Laboratory, #000664). B6(Cg)-Zbtb46tm2Mnz/J (The Jackson Laboratory, #026850) were bred to AHR-Flox mice to generate Zbtb46CreAHRfl (AHRZBTB) and KLF4-Flox mice to generate Zbtb46CreKLF4fl (KLF4ZBTB). Ahrtm3.1Bra/J (AHR-Flox) mice were purchase from Jackson laboratory (The Jackson Laboratory, #006203)96. KLF4-Flox and FADS3KO mice were kingly donated by Dr. Florent Ginhoux and Dr. J. Thomas Brenna, respectively. C57BL/6-Tg (Tcra2D2, Tcrb2D2)1Kuch/J (The Jackson Laboratory, #006912) were used for co-coculture with BMDCs. B6.D2N-Ahrd/J (The Jackson Laboratory, #002921) were used for in vitro experiments38,39. B6(cg)-Zbtb46tm1(BBEGF)Mnz/J (The Jackson Laboratory, #019506) were used for generate FADS3 chimeras. Tg(CAG-Kaede)15Kgwa mice on a C57Bl/6J background were obtained from RIKEN BRC, Japan. All mice were housed in a conventional, pathogen-free facility at the Brigham and Women’s Hospital (BWH) – Harvard Medical School (HMS) in sterile autoclaved cages with irradiated food and acidified, autoclaved water. Mouse handling and weekly cage changes were performed by investigators or mouse husbandry staff wearing sterile gowns, masks and gloves in a sterile biosafety hood. All experiments were reviewed and approved by Institutional Animal Care and Use Committee (IACUC) at Brigham and Women’s Hospital – Harvard Medical School.

extract_protocol:
Sorted cells were lysed on extraction buffer and RNA was isolated using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific, #KIT0204).
RNA was suspended in 10 µL of nuclease free water at a concentration of 0.5-1 ng/µL and sequenced using or SMARTSeq2104 at the Broad Institute.

value: CNS

value: Dendritic Cells


title: CMP9_CNS_CTRL_4

description: Library name: 677T_B12


title: CMP11_CNS_AHR_4

description: Library name: 677T_D8

value: FADS3 Knockout


title: CMP11_CNS_WT_2

description: Library name: 677T_D2

value: WT


title: CMP9_CNS_IAA_3

description: Library name: 677T_C3

value: IAA


title: CMP11_Spleen_AHR_4

description: Library name: 677T_C12

source_name: Spleen

value: Spleen


title: CMP11_Spleen_WT_4

description: Library name: 677T_C8


title: CMP11_CNS_AHR_3

description: Library name: 677T_D7


title: CMP9_CNS_CTRL_2

description: Library name: 677T_B10


title: CMP11_CNS_AHR_2

description: Library name: 677T_D6


title: CMP11_Spleen_WT_3

description: Library name: 677T_C7


title: CMP11_Spleen_AHR_2

description: Library name: 677T_C10


title: CMP11_Spleen_AHR_1

description: Library name: 677T_C9


title: CMP11_Spleen_WT_1

description: Library name: 677T_C5


title: CMP11_Spleen_WT_2

description: Library name: 677T_C6


title: CMP9_CNS_IAA_4

description: Library name: 677T_C4


title: CMP11_Spleen_AHR_3

description: Library name: 677T_C11


title: CMP11_CNS_WT_1

description: Library name: 677T_D1


title: CMP11_CNS_AHR_1

description: Library name: 677T_D5


title: CMP9_CNS_CTRL_3

description: Library name: 677T_B11


title: CMP9_CNS_IAA_2

description: Library name: 677T_C2


title: CMP9_CNS_IAA_1

description: Library name: 677T_C1


title: CMP11_CNS_WT_3

description: Library name: 677T_D3


title: Patient 1 Healthy

description: Library name: 10-S2210388-SAIN


title: Patient 1 Tumoral

description: Library name: 10-S2210388-TUM

value: cSCC tumor


title: Patient 1 AK/In situ

description: Library name: 10-S2210388-PRE

value: Actinic keratosis/In situ cSCC


title: CMP9_CNS_CTRL_1

description: Library name: 677T_B9

value: Control


title: QAG370-QAG372-QAG373, scRNAseq

city: Madrid

first: Jose Luis

last: Ruiz-Sepulveda

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Translational Research

country: Spain

institute: CNIO

description: 10x Genomics; CMO-OLIGOS for each of mouse QAG370:1-2-3-4, QAG372:5-6-7-8, QAG373:9-10-11-12

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina RTA software  (RTA v2). Conversion of BCL files to FASTQ format was performed with "cellranger mkfastq" (10xGenomics), a wrapper for "bcl2fastq" (Illumina).
The bollito pipeline (García-Jimeno et al., 2022) was used to perform the initial steps of the single-cell analysis, checking cell-level quality control by removing outlier cells based on read counts, number of expressed genes and the percentage of mitochondrial counts distributions. All of its parameters were set as default (random seed:4848, minimum number of genes detected per cell: 500, maximum number of genes detected per cell: 100000, minimum percentage of reads mapping to mitochondrial gene: 8, minimum percentage of reads mapping to the ribosomal genome: 40).
The samples were merged into a single object.
Seurat v4.3.0 was employed to exclude cells with low quality (those with fewer than 2,500 UMIs) or cells identified as potential multiplets (those with more than 27500 UMIs). Only cells expressing a minimum of 50 house-keeping genes from a curated list specific to quality control (Tirosh et al., 2016) were retained for analysis.
The expression levels were normalized to log transcripts per 10,000 cells (TP10K).
Variable genes were identified with FindVariableFeatures, selecting 2,500 genes using the ‘vst’ method. The data was then  scaled with ScaleData, followed by a PCA conducted with RunPCA. We utilized RunUMAP for the UMAP embedding, opting for 16 dimensions based on an elbow plot, while keeping the remaining parameters at their default settings.
Cell annotation was conducted using SingleR v2.0.0. using as the ImmGen mouse reference dataset obtained from the previously mentioned package with its ImmGenData() function. Cells labels were kept to its general names (i.e., 'T cell (T.4FP3+25+)' to just 'T cell' )
Assembly: mm10
Supplementary files format and content: Samples' cell barcodes, genes/features and  metadata (supplementary) as tab-separated values files
Supplementary files format and content: Samples' expression values as matrix files

source_name: Breast cancer

growth_protocol: All animal experiments were performed in the CNIO (Spanish National Cancer Research Centre) in accordance with protocols approved by the Research Ethics and Animal Welfare Committee on Animal Experimentation of the Instituto de Salud Carlos III (PROEX 387/15 and PROEX 206.7/21). Experiments were performed in accordance with the guidelines stated in the International Guiding Principles for Biomedical Research Involving Animals developed by the Council for International Organizations of Medical Sciences. MMTV-PyMT mice (FVB/N-Tg (MMTV-PyVT)634Mul/J) and BALB/c were bred at the CNIO Animal Facility. Mouse strains were maintained under specific pathogen-free conditions at the CNIO Animal Facility. Animals were kept in a climate-controlled environment (22±2ºC) with cycles of 12h light/dark and with ad libitum access to food and water.

extract_protocol:
Tumors were extracted from mice and dissagregated using Tumor Dissociation Kit, mouse (Miltenyi, #130-096-730). Single cell tumor cell suspension were stained with DAPI and DAPI- cells were sorted in BD-FACS-ARIA into PBS. After that, three different tumors were multiplexed using oligo labeling was by 3’CellPlex Kit Set A (10xGenomics, cat no. 1000261). Next, a secondary sort of DAPI- cells was executed with the BD FACS ARIA to further enrich for viable cells. Multiplexed-single-cell suspensions sourced from three distinct tumors were processed together into one sample, which was drop encapsulated with Chromium device (10xGenomics). Finally, it was sequenced in Illumina Nextseq 550 (with v2.5 reagent kit)
Cell multiplexed samples were processed with the "Chromium Next GEM Single Cell 3' Kit v3.1" (10xGenomics  PN-1000268). Generation of gel beads in emulsion (GEMs), barcoding, post GEM-RT clean-up, cDNA amplification and both 3’ Gene Expression and Cell Multiplexing library construction were all performed as recommended by the manufacturer.

treatment_protocol: Treatments with the different drugs were started at 7th weeks of age of MMTV-PyMT mouse models. Anti-VEGFA clone B20-4.1.1 or Isotype mouse IgG2a clone C1.18.4 were prepared in 1x PBS and administered at 5 mg/kg intraperitoneally twice per week during 6 weeks

value: Breast cancer