title: B_S1_L002

city: Palo Alto

first: Nidhi

last: Bhutani

state: California

address: 240 Pasteur Drive

department: Orthopaedic Surgery

institute: Stanford

description: Parse Biosciences

data_processing:
Sequencing files were processed using the Parse Biosciences Pipeline (v1.0.3) and aligned to the human GRCh38 genome to obtain count matrices.
The count matrix was loaded into R (v4.3.0) using the Seurat package (v4.3.0.1) to cluster, visualize and analyze the dataset.
Assembly: hg38
Supplementary files format and content: CSV files containing count matrices, annotation barcodes, cell metadata and gene IDs/names

source_name: Blood (PBMC)

extract_protocol:
PBMC samples from OA patients and healthy donors (n = 2 per group) were enriched for B-cells using the magnetic-activated cell sorting (MACS) bead isolation kit from (Human Pan B cell isolation kit 130-101-638, Miltenyi Biotec) according to manufacturer’s instructions
Cells were fixed and cDNA libraries were generated using the Evercode WT Mini v1 kit (Parse Biosciences, Seattle) according to manufacturer’s instructions

value: Blood (PBMC)

value: B cells

tag: disease state

value: Healthy + Osteoarthitis


title: Bovine,RNA-seq,8cell,siDuxA control,rep1

status: Public on May 01 2025

type: SRA

city: Yangling

first: zhang

last: yong

state: Shanxi

address: No.3 Taicheng Road

country: China

institute: Northwest A&F University

library_source: transcriptomic

data_processing:
We aligned all RNA-seq datasets to distinct genomes (bovine, bosTau9) utilizing Hisat2 v2.1.1. The quantification of gene expression was subsequently performed using StringTie 2.2.1.
Assembly: bosTau9
Supplementary files format and content: BigWig files of each stage

molecule: total RNA

organism: Bos grunniens x Bos taurus

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 96 hpi (16-cell), 132 hpi (morula). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
For the generation of Smart-seq2 libraries, zona pellucida-free oocytes or embryos lysis in a 708 buffer containing RNase inhibitor, following the Smart-seq2 protocol as described (Picelli,2013). After completion of purification and fragmentation, the library was quantificatied and sequenced.

tag: cell type

tag: treatment

value: control 8-cell embryo


title: Bovine,RNA-seq,D7_ICM,rep2

source_name: Inner cell mass

value: Inner cell mass


title: Slide4_B

city: University of Oxford

first: Agne

last: Antanaviciute

address: MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Raw sequence data were processed using 10X genomics Space Ranger pipeline
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz - list of spatial barcodes
Supplementary files format and content: features.tsv.gx - list of gene names
Supplementary files format and content: matrix.mtx.gx - gene expression count data in Matrix Market Exchange format
Supplementary files format and content: scale_factors_json.json - scale factors for image to spot coordinates in json format
Supplementary files format and content: tissue_hires_image.jpeg - tissue H&E image
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

organism: Homo sapiens

source_name: duodenum endoscopic biopsy

growth_protocol: Ex vivo (human tissue samples)

extract_protocol:
Endoscopic biopsies of duodenal mucosa - fresh frozen in OCT - 10μm sections cut on cryostat
10x visium spatial transcriptomics following manufacturer protocol

treatment_protocol: Active and treated celiac disease vs controls

tag: tissue

value: duodenum endoscopic biopsy

tag: study subject_id

value: Active celiac disease


title: Slide4_A


title: Bovine,RNA-seq,8cell,siKLF17,rep2

value: siKLF17 8-cell embryo


title: A549,HSV-1,ChIP-2

city: hangzhou

first: Hongyu

last: Lin

address: Zijingang Campus of Zhejiang University, 866 Yuhangtang Road, Xihu District

institute: Zhejiang University School of Medicine

library_source: genomic

data_processing:
The clean reads were aligned to human genome (GRCh38.p14) using BWA mem (v 0.7.12), and the IP enriched peaks were then analyzed by MACS2 (version 2.1.0).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

growth_protocol: DMEM/F-12, supplemented with 10% (v/v) FBS. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Infected A549 cells were collected, fixed and undergone chromatin cross-linking according to the manufacturer’s instructions using the SimpleChIP® Enzymatic Chromatin IP Kit
The purified DNA was then used to construct a ChIP-seq library by Novogene (Beijing, China)

treatment_protocol: A549 cells were infected with HSV-1 for 8 hours

tag: cell line

tag: antibody


title: Bovine,RNA-seq,8cell,siKLF17 control,rep2


title: Bovine,RNA-seq,8cell,rep2


title: A549,HSV-1,ChIP-1


title: Slide3_A


title: Bovine,RNA-seq,8cell,siDuxA,rep1

value: siDUXA 8-cell embryo


title: Slide3_B


title: Slide2_D

value: Treated celiac disease


title: Slide2_C

value: Control


title: Bovine,RNA-seq,6-8cell,rep1

source_name: 6-cell to 8-cell

value: 6-cell to 8-cell


title: Slide4_C


title: Bovine,RNA-seq,8cell,rep4


title: Bovine,RNA-seq,8cell,rep3


title: Slide3_D


title: Slide2_A


title: Bovine,RNA-seq,8cell,siDuxA control,rep2


title: Bovine,RNA-seq,4cell,rep1


title: Bovine,RNA-seq,4cell,rep4


title: Slide3_C


title: Slide1_B


title: Bovine,RNA-seq,6-8cell,rep2


title: Bovine,RNA-seq,4cell,rep3


title: Bovine,RNA-seq,4cell,rep2


title: Bovine,RNA-seq,16cell,rep2


title: Bovine,RNA-seq,2cell,rep1


title: Slide1_D


title: Slide4_D


title: UPN9_BM_baseline_TCR

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: National Institutes of Health

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the cellranger analysis pipeline.
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
T cell receptor and B cell receptor VDJ analysis: Cellranger
VDJ of T cells and B cells were infered with cellranger vdj pipeline to get TCR and BCR contig annotations.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human bone marrow

extract_protocol: Libraries of gene expression (BMMNCs and Lineage-CD34+HSPCs) and TCR/BCR sequencing for patients and healthy donors were generated using Genomics Chromium Single Cell 5' Solution Kit from 10XGenomics v1 and v1.1.

treatment_protocol:
Patients were treated with horse ATG, cyclosprorine, and eltrombopag (starting from day 1) for 6 months.
Primary end point is 6 month after IST treatment, and response to treatment is evaluated.

value: Human bone marrow

value: BMMNCs

tag: Sex

value: Male

tag: age

tag: response at_primary_end_point

value: Responder

tag: library type

value: VDJ (TCR)


title: UPN9_BM_6M_TCR

description: 10x Genomics


title: Slide1_A


title: Slide1_C


title: Bovine,RNA-seq,2cell,rep4


title: Bovine,RNA-seq,2cell,rep3


title: Bovine,RNA-seq,8cell,rep1


title: UPN7_BM_6M_TCR

description: 10x Genomics


title: UPN8_BM_baseline_TCR

description: 10x Genomics


title: UPN7_BM_baseline_TCR

description: 10x Genomics


title: Bovine,RNA-seq,2cell,rep2


title: Slide2_B


title: UPN6_BM_baseline_TCR

description: 10x Genomics

value: Female

value: Off study


title: bovine,H3K4me3,D7_TE,rep2

data_processing:
Initially, all reads underwent processing through TrimGalore (v.0.6.4) to eliminate reads with a minimum mapping quality of 20 and remove adapters. Subsequently, Bowtie2 (v2.3.4) (Langmead,2013)  was employed to map the filtered reads onto the genome (bovine, bosTau9). Removal of multiple mapped reads and duplicates was accomplished using MarkDuplicates.jar. The downstream calculation of Reads Per Kilobase Per Million of sequenced reads (RPKM) was performed exclusively on uniquely mapped reads. To mitigate batch and cell type variations in comparisons, RPKM values of CUT&RUN data underwent further normalization via z-score transformation.
Assembly: bosTau9
Supplementary files format and content: BigWig files of each stage

source_name: Trophectoderm

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.   Approximately 0.8 ×107 bovine sperm were purified employing a Puresperm 40/80 gradient column (Nidacon).  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 132 hpi (morula). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
CUT&RUN experiments were conducted following the established protocols with specific adaptations in cell permeabilization, DNA purification, and library construction steps, as previously described (Hainer, S. J., 2019;Patty, B. J. & Hainer, 2021).  In the ULI-NChIP-seq method, each reaction utilized 0.8 × 107 sperms. All collected cells underwent a thorough washing process with DPBS-0.001% BSA. The ULI-NChIP procedure followed the established protocol (Lismer,2021).For sequencing, the sequence libraries were constructed using the KAPA Hyper Prep Kit for the Illumina platform (Roche, KK8504) following the provided guidelines.

value: Trophectoderm


title: UPN9_BM_3M_TCR

description: 10x Genomics


title: Bovine,RNA-seq,16cell,rep1


title: UPN8_BM_6M_TCR

description: 10x Genomics


title: bovine,H3K4me3,Zygote,rep2


title: bovine,H3K4me3,Morula,rep1

source_name: Morula

value: Morula


title: bovine,H3K4me3,Morula,rep2


title: bovine,H3K4me3,Zygote,rep1


title: bovine,H3K4me3,D7_TE,rep1


title: bovine,H3K4me3,D7_ICM,rep2

value: Inner cell mass


title: UPN5_BM_baseline_TCR

description: 10x Genomics


title: UPN4_BM_baseline_repeat_TCR

description: 10x Genomics


title: UPN4_BM_baseline_TCR

description: 10x Genomics


title: bovine,H3K4me3,D7_ICM,rep1


title: UPN6_BM_3M_TCR

description: 10x Genomics


title: UPN3_BM_6M_TCR

description: 10x Genomics

value: Nonresponder


title: bovine,H3K4me3,8cell,rep1


title: bovine,H3K4me3,4cell,rep2


title: UPN3_BM_baseline_TCR

description: 10x Genomics


title: UPN2_BM_6M_TCR

description: 10x Genomics


title: UPN2_BM_baseline_TCR

description: 10x Genomics


title: bovine,H3K4me3,16cell,rep2


title: bovine,H3K4me3,16cell,rep1


title: UPN20_BM_baseline_TCR

description: 10x Genomics


title: bovine,H3K4me3,4cell,rep1


title: UPN1_BM_6M_TCR

description: 10x Genomics


title: bovine,H3K27me3,Zygote,rep2

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.   Approximately 0.8 ×106 bovine sperm were purified employing a Puresperm 40/80 gradient18 column (Nidacon). The sperm then underwent two washes with 2 ml of HEPES-TALP and subsequent lysis using GA buffer (TIANamp Genomic DNA Kit, DP304-03, up to 200 μL), supplemented with 20 μL of Proteinase K (20 mg/mL) and 20 μL of DTT (1M). The sperm genome was released at 56°C for 9-10 hours with shaking and following the extraction protocol of the TIANamp Genomic DNA Kit (Catalog No. DP304-03). The bovine sperm WGBS library was generated as described15. Briefly, purified DNA and unmethylated lambda DNA control were mixed and fragmented to 350 bp. End-repair, dA- tailing, and ligation were carried out using the NEBNext End Repair Module, dA-Tailing Module, and NEB T4 ligase. The adaptor-ligated DNA within the size range of 300-600 bp was selected through magnetic bead separation. Bisulfite conversion was then performed using the EZ DNA methylation-Gold Kit (Zymo Research, D5005), following the manufacturer’s instructions.  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 132 hpi (morula). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
CUT&RUN experiments were conducted following the established protocols with specific adaptations in cell permeabilization, DNA purification, and library construction steps, as previously described (Hainer, S. J., 2019;Patty, B. J. & Hainer, 2021).  In the ULI-NChIP-seq method, each reaction utilized 0.8 × 107 sperms. All collected cells underwent a thorough washing process with DPBS-0.001% BSA. The ULI-NChIP procedure followed the established protocol (Lismer,2021).For sequencing, the sequence libraries were constructed using the KAPA Hyper Prep Kit for the Illumina platform (Roche, KK8504) following the provided guidelines.


title: UPN20_BM_6M_TCR

description: 10x Genomics


title: bovine,H3K27me3,Zygote,rep1


title: UPN1_BM_baseline_TCR

description: 10x Genomics


title: bovine,H3K27me3,Morula,rep2


title: bovine,H3K27me3,Morula,rep1


title: UPN19_BM_baseline_TCR

description: 10x Genomics


title: bovine,H3K27me3,D7_TE,rep2


title: UPN18_BM_6M_TCR

description: 10x Genomics


title: UPN19_BM_6M_TCR

description: 10x Genomics


title: bovine,H3K27me3,D7_TE,rep1


title: UPN18_BM_baseline_TCR

description: 10x Genomics


title: bovine,H3K4me3,8cell,rep2


title: bovine,H3K27me3,D7_ICM,rep1


title: UPN17_BM_baseline_TCR

description: 10x Genomics


title: bovine,H3K27me3,8cell,rep2


title: UPN16_BM_6M_TCR

description: 10x Genomics


title: UPN17_BM_6M_TCR

description: 10x Genomics


title: bovine,H3K27me3,8cell,rep1


title: bovine,H3K27me3,D7_ICM,rep2


title: bovine,H3K27me3,4cell,rep1


title: bovine,H3K27me3,4cell,rep2


title: bovine,H3K27me3,2cell,rep2


title: bovine,DNAme,D7_TE,rep2

data_processing:
Initial treatment of all PBAT and WGBS datasets involved the use of cutadapt v1.11, whereby low- quality reads and adapters were removed prior to mapping. Bismark (v0.24.1; bowtie2 2.3.5.1) was then employed to align the filtered reads to genomes (bovine, bosTau9). Removal of multi-mapped reads and PCR duplicates was achieved using Bismark. CpG methylation calling was executed with bismark methylation extractor.
Assembly: bosTau9
Supplementary files format and content: bigwig files of each stage

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.  Approximately 0.8 ×106 bovine sperm were purified employing a Puresperm 40/80 gradient18 column (Nidacon). The sperm then underwent two washes with 2 ml of HEPES-TALP and subsequent lysis using GA buffer (TIANamp Genomic DNA Kit, DP304-03, up to 200 μL), supplemented with 20 μL of Proteinase K (20 mg/mL) and 20 μL of DTT (1M). The sperm genome was released at 56°C for 9-10 hours with shaking and following the extraction protocol of the TIANamp Genomic DNA Kit (Catalog No. DP304-03). The bovine sperm WGBS library was generated as described15. Briefly, purified DNA and unmethylated lambda DNA control were mixed and fragmented to 350 bp. End-repair, dA- tailing, and ligation were carried out using the NEBNext End Repair Module, dA-Tailing Module, and NEB T4 ligase. The adaptor-ligated DNA within the size range of 300-600 bp was selected through magnetic bead separation. Bisulfite conversion was then performed using the EZ DNA methylation-Gold Kit (Zymo Research, D5005), following the manufacturer’s instructions.  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 96 hpi (16-cell), 132 hpi (morula), and 168-180 hpi (blastocyst). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
Approximately 0.8 ×106 bovine sperm were purified employing a Puresperm 40/80 gradient18 column (Nidacon). The sperm then underwent two washes with 2 ml of HEPES-TALP and subsequent lysis using GA buffer (TIANamp Genomic DNA Kit, DP304-03, up to 200 μL), supplemented with 20 μL of Proteinase K (20 mg/mL) and 20 μL of DTT (1M). The sperm genome was released at 56°C for 9-10 hours with shaking and following the extraction protocol of the TIANamp Genomic DNA Kit (Catalog No. DP304-03). The bovine sperm WGBS library was generated as described15. Briefly, purified DNA and unmethylated lambda DNA control were mixed and fragmented to 350 bp. End-repair, dA- tailing, and ligation were carried out using the NEBNext End Repair Module, dA-Tailing Module, and NEB T4 ligase. The adaptor-ligated DNA within the size range of 300-600 bp was selected through magnetic bead separation. Bisulfite conversion was then performed using the EZ DNA methylation-Gold Kit (Zymo Research, D5005), following the manufacturer’s instructions.  To produce the PBAT library, zona pellucida-free oocytes and embryos underwent rigorous washing in DPBS-0.001% BSA. Subsequently, lysis in a buffer with 20 mg/mL proteinase K (QIAGEN, 19131) at 37°C for 1 hour. The mixture was then combined with spike-in λ-DNA (Promega, D150A) at a mass ratio of 1:200 and subjected to the EpiTect Fast Bisulfite Conversion Kit (Zymo Research, D5006), following the manufacturer’s protocol.


title: bovine,DNAme,D7_TE,rep1


title: UPN14_BM_3M_TCR

description: 10x Genomics


title: UPN14_BM_GEM_baseline_TCR

description: 10x Genomics


title: UPN14_BM_6M_TCR

description: 10x Genomics


title: UPN15_BM_3M_TCR

description: 10x Genomics


title: UPN13_BM_6M_TCR

description: 10x Genomics


title: bovine,DNAme,D7_ICM,rep1


title: UPN15_BM_baseline_TCR

description: 10x Genomics


title: bovine,DNAme,Morula,rep2


title: UPN12_BM_GEM_baseline_TCR

description: 10x Genomics


title: bovine,DNAme,Morula,rep1


title: UPN11_BM_baseline_TCR

description: 10x Genomics


title: bovine,DNAme,Ama_TBE_8cell,rep2

value: α-amanitin treated 8-cell embryo


title: bovine,DNAme,Ama_TBE_8cell,rep1


title: UPN114_BM_HD4_TCR

description: 10x Genomics


title: UPN113_BM_HD3_TCR

description: 10x Genomics


title: bovine,DNAme,8cell,rep2


title: UPN16_BM_baseline_TCR

description: 10x Genomics


title: bovine,DNAme,8cell,rep1


title: UPN112_BM_HD2_TCR

description: 10x Genomics


title: UPN11_BM_6M_TCR

description: 10x Genomics


title: bovine,DNAme,4cell,rep2


title: UPN111_BM_HD1_TCR

description: 10x Genomics


title: bovine,DNAme,4cell,rep1


title: bovine,H3K27me3,2cell,rep1


title: UPN10_BM_6M_TCR

description: 10x Genomics


title: UPN10_BM_baseline_TCR

description: 10x Genomics


title: bovine,DNAme,2cell,rep2


title: UPN13_BM_GEM_baseline_TCR

description: 10x Genomics


title: bovine,DNAme,2cell,rep1


title: UPN9_BM_3M_BCR

description: 10x Genomics

value: VDJ (BCR)


title: UPN12_BM_6M_TCR

description: 10x Genomics


title: bovine,DNAme,Zygote,rep1

source_name: Zygote

value: Zygote


title: bovine,ATAC-seq,Zygote,rep2

data_processing:
Initially, all reads underwent processing through TrimGalore (v.0.6.4) to eliminate reads with a minimum mapping quality of 20 and remove adapters. Subsequently, Bowtie2 (v2.3.4) (Langmead,2013)  was employed to map the filtered reads onto the genome (bovine, bosTau9). Removal of multiple mapped reads and duplicates was accomplished using MarkDuplicates.jar. The downstream calculation of Reads Per Kilobase Per Million of sequenced reads (RPKM) was performed exclusively on uniquely mapped reads. To mitigate batch and cell type variations in comparisons, RPKM values underwent further normalization via z-score transformation.
Assembly: bosTau9
Supplementary files format and content: BigWig files of each stage

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.   Approximately 0.8 ×106 bovine sperm were purified employing a Puresperm 40/80 gradient18 column (Nidacon).  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 132 hpi (morula). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of zygotes and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant.  The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
We prepared libraries of oocytes and early embryos utilizing the TruePrep DNA Library Prep Kit V2 from Illumina (Vazyme Biotech, TD502), with slight modifications (Wu, J. et al. ,2018). Briefly, oocytes or embryos without zona pellucida were transferred into a 0.2-mL conventional, low-binding tube (Axygen, PCR-02D-L-C) with a small volume of DPBS-0.001% BSA. After incubation with 6 μL lysis buffer (10 mM Tris-HCl pH = 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.5% IGEPAL CA-630) on ice for 10-30 min, 4 μL ddH2O, 4 μL 5 × TTBL, and 5 μL TTE mix V5 were added to the sample. The mixture was incubated at 37°C for 30 min, followed by mixing with 5 μL of 5 × TS stop buffer and further incubation at room temperature for 5 min. The sample was then mixed with 103 μL nuclease-free water and 2 μL of 20 ng/μL carrier RNA (Qiagen, 1068337) and transferred to a phase-lock tube (Qiagen,129056), containing 130 μL of phenol: chloroform: isoamyl alcohol (25:24:1). After centrifugation, the supernatant was transferred to a new low-binding 1.5-mL tube containing 1 μL glycogen, 13 μL of 3 M sodium acetate, and 130 μL isopropanol for DNA precipitation at -20°C overnight. Following centrifugation, the precipitated DNA was washed twice with 500 μL ice-cold 80% ethanol and dissolved in 20 μL of nuclease-free H2O. PCR was performed to amplify the libraries, which were then purified with 1.3 × AMPure beads (Beckman, A63882). Subsequently, all miniATAC-seq libraries were sequenced using Illumina Novaseq-6000 with paired-ended 150-bp reads.


title: UPN9_BM_baseline_BCR

description: 10x Genomics


title: bovine,ATAC-seq,Zygote,rep1


title: UPN8_BM_6M_BCR

description: 10x Genomics


title: bovine,ATAC-seq,Morula,rep2


title: bovine,DNAme,D7_ICM,rep2


title: UPN7_BM_6M_BCR

description: 10x Genomics


title: UPN9_BM_6M_BCR

description: 10x Genomics


title: bovine,DNAme,Zygote,rep2


title: bovine,ATAC-seq,Morula,rep1


title: UPN7_BM_baseline_BCR

description: 10x Genomics


title: UPN6_BM_3M_BCR

description: 10x Genomics


title: bovine,ATAC-seq,D7_TE,rep1


title: bovine,ATAC-seq,D7_TE,rep2


title: bovine,ATAC-seq,D7_ICM,rep1


title: UPN4_BM_baseline_BCR

description: 10x Genomics


title: UPN5_BM_baseline_BCR

description: 10x Genomics


title: bovine,ATAC-seq,D7_ICM,rep2


title: UPN6_BM_baseline_BCR

description: 10x Genomics


title: bovine,ATAC-seq,8cell,rep2


title: bovine,ATAC-seq,8cell,rep1


title: UPN3_BM_6M_BCR

description: 10x Genomics


title: UPN3_BM_baseline_BCR

description: 10x Genomics


title: UPN2_BM_6M_BCR

description: 10x Genomics


title: bovine,ATAC-seq,4cell,rep2


title: bovine,ATAC-seq,4cell,rep1


title: UPN2_BM_baseline_BCR

description: 10x Genomics


title: bovine,ATAC-seq,2cell,rep2


title: UPN8_BM_baseline_BCR

description: 10x Genomics


title: UPN20_BM_baseline_BCR

description: 10x Genomics


title: VSMC, Pulmonary, scCLEAN, Patient 4

city: New Orleans

first: Amitabh

middle: C

last: Pandey

state: LA

address: 1430 Tulane Ave

department: Medicine, Section of Cardiology

institute: Tulane University School of Medicine

description:
Library name: VSMC_pulmonary_P4_scCLEAN_S32_L004_R1_001
10xv3 + MAS-Seq + scCLEAN

data_processing:
The demultiplexing, UMI counting, and aggregations were performed with CellRanger v6.0.0 for Illumina sequenced data and pigeon v1.3.0 was used for PacBio sequenced data.
Assembly: GRCh38; GENCODE v32
Supplementary files format and content: tarball for each dataset; h5 files for Illumina processed samples and tab separated and matrix files for PacBio processed samples

source_name: Coronary and pulmonary arteries

extract_protocol:
single cell supsension was achieved and these cells were then ready for the library construct. Cell viablity was assessed using Countess system.
Chromium Next GEM Single Cell 3ʹ Kit v3.1

value: Coronary and pulmonary arteries

value: vascular smooth muscle cells

value: polyA RNA


title: bovine,ATAC-seq,2cell,rep1


title: UPN20_BM_6M_BCR

description: 10x Genomics

value: Human bone marrow


title: UPN1_BM_6M_BCR

description: 10x Genomics

value: BMMNCs


title: UPN1_BM_baseline_BCR

description: 10x Genomics

value: Male


title: VSMC, Pulmonary, scCLEAN, Patient 3

description:
Library name: VSMC_pulmonary_P3_scCLEAN_S30_L004_R1_001
10xv3 + MAS-Seq + scCLEAN


title: UPN19_BM_6M_BCR

description: 10x Genomics

value: Responder


title: VSMC, Pulmonary, 10xv3, Patient 3

description:
Library name: VSMC_pulmonary_P3_10xv3_control_S14_L002_R1_001
10xv3 + MAS-Seq


title: VSMC, Pulmonary, 10xv3, Patient 4

description:
Library name: VSMC_pulmonary_P4_10xv3_control_S16_L002_R1_001
10xv3 + MAS-Seq


title: UPN19_BM_baseline_BCR

description: 10x Genomics


title: UPN18_BM_6M_BCR

description: 10x Genomics


title: VSMC, Pulmonary, 10xv3, Patient 2

description:
Library name: VSMC_pulmonary_P2_10xv3_control_S12_L002_R1_001
10xv3 + MAS-Seq


title: UPN18_BM_baseline_BCR

description: 10x Genomics


title: UPN17_BM_6M_BCR

description: 10x Genomics


title: VSMC, Pulmonary, 10xv3, Patient 1

description:
Library name: VSMC_pulmonary_P1_10xv3_control_S10_L002_R1_001
10xv3 + MAS-Seq


title: UPN16_BM_6M_BCR

description: 10x Genomics


title: UPN17_BM_baseline_BCR

description: 10x Genomics


title: VSMC, Coronary, scCLEAN, Patient 4

description:
Library name: VSMC_coronary_P4_scCLEAN_S31_L004_R1_001
10xv3 + MAS-Seq + scCLEAN


title: VSMC, Coronary, 10xv3, Pateint 4

description:
Library name: VSMC_coronary_P4_10xv3_control_S15_L002_R1_001
10xv3 + MAS-Seq


title: UPN16_BM_baseline_BCR

description: 10x Genomics


title: VSMC, Coronary, 10xv3, Patient 3

description:
Library name: VSMC_coronary_P3_10xv3_control_S13_L002_R1_001
10xv3 + MAS-Seq


title: UPN15_BM_baseline_BCR

description: 10x Genomics


title: UPN15_BM_3M_BCR

description: 10x Genomics


title: UPN14_BM_6M_BCR

description: 10x Genomics


title: UPN13_BM_6M_BCR

description: 10x Genomics


title: UPN14_BM_3M_BCR

description: 10x Genomics


title: VSMC, Coronary, scCLEAN,  Patient 1

description:
Library name: VSMC_coronary_P1_scCLEAN_S25_L004_R1_001
10xv3 + MAS-Seq + scCLEAN


title: VSMC, Coronary, 10xv3, Patient 1

description:
Library name: VSMC_coronary_P1_10xv3_control_S9_L002_R1_001
10xv3 + MAS-Seq


title: UPN14_BM_GEM_baseline_BCR

description: 10x Genomics


title: PBMC, scCLEAN, sample 4

description:
Library name: pbmc_10xv3_scCLEAN_rep3_full_S4_L001_R1_001
10xv3 + MAS-Seq + scCLEAN

source_name: PBMC

value: PBMC

value: immune


title: VSMC, Coronary 10xv3, Patient 2

description:
Library name: VSMC_coronary_P2_10xv3_control_S11_L002_R1_001
10xv3 + MAS-Seq


title: VSMC, Pulmonary, scCLEAN, Patient 1

description:
Library name: VSMC_pulmonary_P1_scCLEAN_S26_L004_R1_001
10xv3 + MAS-Seq + scCLEAN


title: VSMC, Pulmonary, scCLEAN, Patient 2

description:
Library name: VSMC_pulmonary_P2_scCLEAN_S28_L004_R1_001
10xv3 + MAS-Seq + scCLEAN


title: PBMC, scCLEAN, sample 2

description:
Library name: pbmc_10xv3_scCLEAN_rep1_full_S2_L001_R1_001
10xv3 + MAS-Seq + scCLEAN


title: UPN12_BM_GEM_baseline_BCR

description: 10x Genomics

value: Female


title: PBMC, 10xv3, control, sample 1

description:
Library name: pbmc_10xv3_Control_full_S1_L001_R1_001
10xv3 + MAS-Seq


title: UPN13_BM_GEM_baseline_BCR

description: 10x Genomics


title: UPN12_BM_6M_BCR

description: 10x Genomics


title: PBMC, scCLEAN, sample 3

description:
Library name: pbmc_10xv3_scCLEAN_rep2_full_S3_L001_R1_001
10xv3 + MAS-Seq + scCLEAN


title: RNA_langerhans_cells_naive_rep4

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

data_processing:
File were demultiplexed with bcl2fastq and mapped with STAR to mouse genome mm10.
Homer was used to create tag directories and do follow up analysis with analyzeRepeats and getDiffExpression.
Assembly: mm10
Supplementary files format and content: RNAseq_DC_KC_LC_genes_tpm.txt: tab delimited text
Supplementary files format and content: DEG_RNAseq_DC_KC_LC_genes.txt: tab delimited text

organism: Mus musculus

source_name: ear skin

extract_protocol:
Langerhans Cells (DAPI- lineage(NK1.1, TCRb, gdTCR)- Ly6G- CD11c+ CD64- CD11b+ CD24+), dendritic cells (DC1: DAPI- lineage(NK1.1, TCRb, gdTCR)- Ly6G- CD11c+ CD64- CD11b- CD24; DC2: DAPI- lineage(NK1.1, TCRb, gdTCR)- Ly6G- CD11c+ CD64- CD11b+ CD24-) and keratinocytes (DAPI- lineage(NK1.1, TCRb, gdTCR)- Ly6G- CD45- CD34- CD49f+ Sca-1+) from the mouse ear of unassociated mice and mice treated with BHI-tween were sorted with a Sony MA900 sorter.
RNA was extracted using the Qiagen miRNeasy kit, and sequencing library was prepared using Tecan SoLo total RNA kit for mouse.
Libraries were sequenced as 2 x 150bp reads on a Illumina NextSeq 2000 using the P3 200 cycle kit

value: ear skin

value: Langerhans cells

tag: strain

value: naive


title: VSMC, Coronary, scCLEAN, Patient 3

description:
Library name: VSMC_coronary_P3_scCLEAN_S29_L004_R1_001
10xv3 + MAS-Seq + scCLEAN


title: VSMC, Coronary, scCLEAN, Patient 2

description:
Library name: VSMC_coronary_P2_scCLEAN_S27_L004_R1_001
10xv3 + MAS-Seq + scCLEAN


title: RNA_DC1_DC2_naive_rep2


title: RNA_langerhans_cells_naive_rep5


title: UPN114_BM_HD4_BCR

description: 10x Genomics


title: UPN11_BM_baseline_BCR

description: 10x Genomics


title: UPN11_BM_6M_BCR

description: 10x Genomics


title: UPN112_BM_HD2_BCR

description: 10x Genomics


title: RNA_langerhans_cells_naive_rep3


title: UPN113_BM_HD3_BCR

description: 10x Genomics


title: UPN111_BM_HD1_BCR

description: 10x Genomics


title: RNA_langerhans_cells_naive_rep2


title: RNA_langerhans_cells_naive_rep1


title: UPN10_BM_6M_BCR

description: 10x Genomics


title: mESC siStag3_Rep 3

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

institute: University College London

data_processing:
Reads were quality controlled using FASTQC software
Transcript level count data (transcript length adjusted) was quantified using salmon (Patro et al., 2017) then imported and summarised in R at the gene-level into R using tximport (Soneson et al., 2015).
Differential expression analysis performed using DESeq2 (Love et al., 2014).
Assembly: GRCm39
Supplementary files format and content: raw counts - gene level

source_name: embryo

growth_protocol: mESCs were grown on plates coated with Fibronectin in 'ES 2i media' (DMEM:F12/Neurobasal 1:1, 1X KnockOut Serum Replacement, 1X N2 supplement, 1X B27 supplement, 2mM Glutamax, 1X Pen-Strep, 10mM HEPES, 1µM PD0325901, 3µM CHIR99021, 0.1 mM BMe) and freshly added mouse recombinant LIF (1000U/ml).

extract_protocol:
Total RNA was isolated using NEB Monarch RNA prep kit (New England BioLabs). The RNA concentration and RIN (RNA integrity number) was assessed with a combination of NanoDrop 1000 (Thermo Scientific) and Agilent RNA 6000 Nano Bioanalyzer chip assay (Agilent).
Libraries were prepared from 200ng total RNA using a KAPA mRNA HyperPrep kit (KK8580) and Roche SeqCap Adapter kit (KR1317) according to the manufacturer’s instructions. The libraries were quantified using an Agilent DNA High Sensitivity Bioanalyzer chip assay and pooled together at equimolar concentrations. The final pooled library was quantified using a KAPA qPCR Library Quantification assay (07960140001).

treatment_protocol: siRNA knockdowns (KDs) were performed for 48hr in 6-well plates where 200,000 cells were seeded and 50pmol siRNA was transfected using 7.5µl RNAiMax Lipofectamine in 300µl Optimem at the time of seeding. The next day, media was changed, and the cells were transfected a second time with an additional 50pmol siRNA.

value: embryo

value: E14 mESCs

value: embryonic stem cells

tag: genotype

value: Stag3 knockdown

value: siRNA to Stag3


title: UPN10_BM_baseline_BCR

description: 10x Genomics

value: VDJ (BCR)


title: mESC siStag3_Rep 1


title: UPN9_CD34_6M

description: 10x Genomics

value: FACS sorted Linjeage-CD34+ bone marrow


title: UPN9_CD34_baseline

description: 10x Genomics

value: Human bone marrow


title: mESC siLuc_Rep 2

value: siLuc control

value: siRNA control (luciferase)


title: UPN9_CD34_baseline_repeat

description: 10x Genomics

value: Male

value: Responder


title: UPN8_CD34_6M

description: 10x Genomics


title: mESC untreated_Rep2

value: wildtype


title: UPN9_CD34_3M

description: 10x Genomics


title: RNAseq_CD8_CCR6_pos_BHI_tween_rep5_R1

data_processing:
File were demultiplexed with bcl2fastq and mapped with STAR to mouse genome mm10.
Homer was used to create tag directories and do follow up analysis with analyzeRepeats and getDiffExpression.
Assembly: mm10
Supplementary files format and content: rnaseq_CCR6neg_HSV_vs_CCR6pos_BHI_tpm.txt: tab delimited text
Supplementary files format and content: DEG_rnaseq_CCR6neg_HSV_vs_CCR6pos_BHI.txt: tab delimited text

extract_protocol:
CD8+ T cells (CD45+CD90.2+TCRb+CD8+CD4-) from the mouse ear skin of mice treated with BHI-tween were sorted with a Sony MA900 sorter.
RNA was extracted using the Qiagen miRNeasy kit, and sequencing library was prepared using Tecan SoLo total RNA kit for mouse.
Libraries were sequenced as 1 x 150bp reads on a Illumina NextSeq 2000 using the P3 200 cycle kit

value: CD8+ T cells (CCR6+)


title: mESC untreated_Rep1


title: RNAseq_CD8_CCR6_pos_BHI_tween_rep3_R1

value: ear skin


title: UPN7_CD34_6M

description: 10x Genomics


title: UPN7_CD34_baseline

description: 10x Genomics


title: UPN6_CD34_baseline

description: 10x Genomics

value: Female

value: Off study


title: UPN6_CD34_3M_repeat

description: 10x Genomics


title: RNAseq_CD8_CCR6_pos_BHI_tween_rep2_R1


title: UPN4_CD34_baseline

description: 10x Genomics


title: UPN3_CD34_baseline

description: 10x Genomics

value: Nonresponder


title: RNAseq_CD8_CCR6_neg_HSV1_rep5_R1

value: CD8+ T cells (CCR6-)


title: UPN3_CD34_6M

description: 10x Genomics


title: mESC siLuc_Rep 3

value: embryo

value: E14 mESCs

value: embryonic stem cells


title: mESC siStag3_Rep 2

value: Stag3 knockdown

value: siRNA to Stag3


title: RNAseq_CD8_CCR6_neg_HSV1_rep4_R1


title: mESC siLuc_Rep 1


title: UPN2_CD34_baseline

description: 10x Genomics

value: Human bone marrow

value: FACS sorted Linjeage-CD34+ bone marrow


title: UPN8_CD34_baseline

description: 10x Genomics


title: UPN6_CD34_3M

description: 10x Genomics


title: mESC untreated_Rep3


title: RNAseq_CD8_CCR6_neg_HSV1_rep3_R1


title: RNAseq_CD8_CCR6_pos_BHI_tween_rep4_R1


title: RNAseq_CD8_CCR6_neg_HSV1_rep2_R1


title: UPN2_CD34_6M

description: 10x Genomics


title: UPN1_CD34_baseline

description: 10x Genomics


title: RNAseq_CD8_CCR6_neg_HSV1_rep1_R1


title: UPN20_CD34_baseline

description: 10x Genomics


title: RNA_langerhans_cells_BHI_tween_rep4

data_processing:
File were demultiplexed with bcl2fastq and mapped with STAR to mouse genome mm10.
Homer was used to create tag directories and do follow up analysis with analyzeRepeats and getDiffExpression.
Assembly: mm10
Supplementary files format and content: RNAseq_DC_KC_LC_genes_tpm.txt: tab delimited text
Supplementary files format and content: DEG_RNAseq_DC_KC_LC_genes.txt: tab delimited text
Supplementary files format and content: RNAseq_DC_KC_LC_ERV_families.txt: tab delimited text
Supplementary files format and content: RNAseq_DC_KC_LC_repeats.txt: tab delimited text

value: Langerhans cells


title: RNA_langerhans_cells_BHI_tween_rep3


title: UPN1_CD34_6M

description: 10x Genomics

value: Male


title: UPN19_CD34_6M

description: 10x Genomics

value: Responder


title: RNA_langerhans_cells_BHI_tween_rep2


title: RNA_langerhans_cells_BHI_tween_rep5


title: UPN19_CD34_baseline

description: 10x Genomics


title: RNA_keratinocytes_naive_rep5

value: keratinocytes

value: naive


title: RNA_langerhans_cells_BHI_tween_rep1

value: ear skin


title: RNAseq_CD8_CCR6_pos_BHI_tween_rep1_R1

value: CD8+ T cells (CCR6+)


title: UPN17_CD34_baseline

description: 10x Genomics

value: Female


title: RNA_keratinocytes_naive_rep3


title: UPN18_CD34_6M

description: 10x Genomics


title: UPN17_CD34_6M

description: 10x Genomics


title: UPN18_CD34_baselin

description: 10x Genomics


title: RNA_keratinocytes_naive_rep4


title: RNA_keratinocytes_naive_rep2


title: UPN20_CD34_6M

description: 10x Genomics


title: UPN16_CD34_GEM_baseline

description: 10x Genomics


title: RNA_keratinocytes_naive_rep1


title: UPN15_CD34_baseline

description: 10x Genomics

value: Off study


title: RNA_keratinocytes_BHI_tween_rep5


title: RNA_keratinocytes_BHI_tween_rep4


title: RNA_keratinocytes_BHI_tween_rep2


title: UPN14_CD34_baseline

description: 10x Genomics


title: UPN14_CD34_6M

description: 10x Genomics


title: UPN15_CD34_3M

description: 10x Genomics


title: UPN13_CD34_baselin

description: 10x Genomics


title: RNA_DC1_DC2_naive_rep5


title: UPN13_CD34_baseline_repeat

description: 10x Genomics


title: UPN14_CD34_3M

description: 10x Genomics


title: RNA_keratinocytes_BHI_tween_rep1


title: UPN13_CD34_6M

description: 10x Genomics


title: UPN12_CD34_baseline

description: 10x Genomics


title: RNA_DC1_DC2_naive_rep4


title: RNA_DC1_DC2_naive_rep1


title: UPN12_CD34_baseline_repeat

description: 10x Genomics


title: RNA_DC1_DC2_BHI_tween_rep5


title: UPN12_CD34_6M

description: 10x Genomics


title: RNA_DC1_DC2_BHI_tween_rep4


title: UPN11_CD34_baselin

description: 10x Genomics


title: RNA_DC1_DC2_BHI_tween_rep3


title: UPN11_CD34_baseline_repeat

description: 10x Genomics


title: RNA_DC1_DC2_BHI_tween_rep2


title: RNA_keratinocytes_BHI_tween_rep3


title: UPN11_CD34_6M

description: 10x Genomics


title: RNA_DC1_DC2_BHI_tween_rep1


title: UPN114_CD34_GEM_HD4

description: 10x Genomics


title: CD8 T cells, scRNA_VDJ_lane4

description:
HTO_details_README.txt
filtered_contig_annotations.csv

data_processing:
Illumina files were converted to FASTQ files using bcl-output command and data were filtered and mapped to mm10 reference genome by using cellranger 7.0.0 (10X Genomics).
Data were normalized in Seurat (v. 5.0.2). Cells with 200 – 4000 RNAs, less than 5% of mitochondrial RNA and less than 20,000 RNA reads were kept for further analysis. Hashtag libraries were demultiplexed using Seurat’s HTODemux and negative and doublet cells were filtered out.
Assembly: mm10
Supplementary files format and content: HTO_details_README.txt: File with HTO hash tag key
Supplementary files format and content: scRNA_seq_cellranger_aggr_processed.tar.gz: tar folder with cellranger aggr output including matrix.mtx, barcodes.csv and features.csv
Supplementary files format and content: filtered_contig_annotations.csv: filtered contigs from VDJ analysis (output from cellranger vdj)
Supplementary files format and content: scRNAseq_final_filtered.rds: final Seurat object with VDJ data

extract_protocol:
To sort CD8+ T cells, single cell suspensions from ear pinnae skin of WT mice exposed to BHI-tween 14 days prior, or infected with HSV-1 7 days prior were stained with antibodies against CD45, lineage (CD11b, NK1.1, gdTCR), CD90.2, TCRb, CD4, CD8b, and DAPI for 30 minutes at 4°C. CD8+ T cells were sorted as DAPI- lineage- CD45+ CD90.2+ TCRb+ CD4- CD8b on a FACSAria. Each sample was additionally stained with an unique TotalSeq C hash tag antibdoy from Biolegend prior to sorting.
Libraries were prepared using a Chromium Single Cell 5’ Reagent kits following manufacturer’s instructions including HTO and VDJ libraries.
Libraries were then sequenced on an Illumina NextSeq 2000 (NextSeq 2000 P3 Reagents (200 Cycles), Illumina).

value: CD8 T cells

value: mixed sample (BHI-tween and HSV-1 treated)

value: VDJ


title: CD8 T cells, scRNA_VDJ_lane3


title: UPN113_CD34_GEM_HD3

description: 10x Genomics


title: CD8 T cells, scRNA_VDJ_lane2

description:
scRNA_seq_cellranger_aggr_processed.tar.gz
scRNAseq_final_filtered.rds
HTO_details_README.txt


title: UPN111_CD34_GEM_HD1

description: 10x Genomics


title: RNA_DC1_DC2_naive_rep3


title: UPN10_CD34_GEM_baseline

description: 10x Genomics


title: UPN10_CD34_GEM_baseline_repeat

description: 10x Genomics


title: CD8 T cells, scRNA_HTO_lane3

library_source: other

molecule: protein

value: HTO


title: CD8 T cells, scRNA_VDJ_lane1


title: CD8 T cells, scRNA_HTO_lane2


title: CD8 T cells, scRNA_HTO_lane4


title: UPN9_BM_6M

description: 10x Genomics

value: BMMNCs


title: UPN10_CD34_GEM_6M

description: 10x Genomics


title: CD8 T cells, scRNA_HTO_lane1


title: UPN9_BM_3M

description: 10x Genomics


title: CD8 T cells, scRNA_GEX_lane4

value: GEX


title: UPN8_BM_6M

description: 10x Genomics

value: Human bone marrow


title: UPN9_BM_GEM_baseline

description: 10x Genomics


title: CD8 T cells, scRNA_GEX_lane3


title: CD8 T cells, scRNA_GEX_lane2


title: UPN8_BM_GEM_baseline

description: 10x Genomics


title: CD8 T cells, scRNA_GEX_lane1


title: RNAseq_whole_tissue_ear_Sepi_rep4

data_processing:
File were demultiplexed with bcl2fastq and mapped with STAR to mouse genome mm10.
Homer was used to create tag directories and do follow up analysis with analyzeRepeats and getDiffExpression.
Assembly: mm10
Supplementary files format and content: RNAseq_whole_tissue_genes_tpm.txt: tab delimited text
Supplementary files format and content: DEG_whole_tissue_genes.txt: tab delimited text
Supplementary files format and content: RNAseq_whole_tissue_ERV_families.txt: tab delimited text

extract_protocol:
Punch biopsy from whole ear tissue of untreated mice or mice treated with either BHI-tween or S.epi were collected and digested.
RNA was extracted using the Qiagen miRNeasy kit, and sequencing library was prepared using Tecan SoLo total RNA kit for mouse.
Libraries were sequenced as 2 x 150bp reads on a Illumina NextSeq 2000 using the P3 200 cycle kit

value: S. epi


title: UPN7_BM_6M

description: 10x Genomics


title: UPN7_BM_GEM_baseline

description: 10x Genomics


title: UPN112_CD34_GEM_HD2

description: 10x Genomics

value: FACS sorted Linjeage-CD34+ bone marrow


title: RNAseq_whole_tissue_ear_Sepi_rep2


title: UPN6_BM_GEM_baseline

description: 10x Genomics


title: UPN6_BM_3M

description: 10x Genomics


title: RNAseq_whole_tissue_ear_Sepi_rep1


title: UPN5_BM_GEM_baseline

description: 10x Genomics

value: Male


title: RNAseq_whole_tissue_ear_Ctrl_rep5


title: UPN4_BM_GEM_baseline

description: 10x Genomics


title: RNAseq_whole_tissue_ear_Ctrl_rep4


title: RNAseq_whole_tissue_ear_Ctrl_rep3


title: RNAseq_whole_tissue_ear_BHI_rep5


title: UPN4_BM_GEM_baseline_repeat

description: 10x Genomics


title: RNAseq_whole_tissue_ear_Ctrl_rep2


title: UPN3_BM_GEM_baseline

description: 10x Genomics

value: Nonresponder


title: UPN3_BM_6M

description: 10x Genomics


title: UPN2_BM_GEM_baseline

description: 10x Genomics

value: Responder


title: UPN1_BM_6M

description: 10x Genomics


title: RNAseq_whole_tissue_ear_BHI_rep2


title: RNAseq_whole_tissue_ear_BHI_rep3


title: UPN19_BM_GEM_baseline

description: 10x Genomics


title: tkmh12

type: genomic

city: New Delhi

first: Tapan

last: Mondal

state: DELHI

address: LBS Centre, Pusa

country: India

institute: ICAR-National Institute for Plant Biotechnology

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner

data_processing:
Axiom_OsSNPnks.20140127.annot.db
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: biotin

organism: Oryza sativa

source_name: deepwater rice

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted usimg CTAB method and quality and quantity were assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: phenotype

value: Elongation ability


title: RNAseq_whole_tissue_ear_Ctrl_rep1

value: ear skin

value: naive


title: tkmh11


title: RNAseq_whole_tissue_ear_Sepi_rep3


title: UPN20_BM_6M

description: 10x Genomics


title: UPN18_BM_GEM_baseline

description: 10x Genomics


title: RNAseq_whole_tissue_ear_BHI_rep4


title: UPN1_BM_GEM_baseline

description: 10x Genomics


title: UPN20_BM_GEM_baseline

description: 10x Genomics


title: tkmh10


title: bovine,DNAme,Sperm,rep1

organism: Bos grunniens

source_name: Sperm

value: Sperm


title: bovine,DNAme,Sperm,rep2


title: UPN2_BM_6M

description: 10x Genomics

value: Female


title: RNAseq_whole_tissue_ear_BHI_rep1


title: UPN19_BM_6M

description: 10x Genomics


title: UPN17_BM_6M

description: 10x Genomics


title: tkmh9


title: UPN18_BM_6M

description: 10x Genomics


title: UPN17_BM_GEM_baseline

description: 10x Genomics


title: tkmh8


title: UPN16_BM_GEM_baseline

description: 10x Genomics


title: UPN16_BM_6M

description: 10x Genomics


title: tkmh7


title: tkmh6


title: tkmh5


title: UPN15_BM_3M

description: 10x Genomics

value: Off study


title: tkmh4


title: UPN15_BM_GEM_baseline

description: 10x Genomics


title: UPN14_BM_6M

description: 10x Genomics


title: tkmh1


title: tkmh3


title: UPN14_BM_3M

description: 10x Genomics


title: tkmg11


title: UPN13_BM_6M

description: 10x Genomics


title: UPN12_BM_6M

description: 10x Genomics


title: tkmg12


title: UPN14_BM_GEM_baseline

description: 10x Genomics


title: UPN12_BM_GEM_baseline

description: 10x Genomics


title: tkmg10


title: tkmg9


title: tkmg8


title: UPN11_BM_6M

description: 10x Genomics


title: UPN11_BM_GEM_baseline

description: 10x Genomics


title: UPN114_BM_GEM_HD4

description: 10x Genomics


title: tkmg6


title: UPN113_BM_GEM_HD3

description: 10x Genomics


title: tkmg5


title: tkmh2


title: tkmg4


title: UPN111_BM_GEM_HD1

description: 10x Genomics


title: UPN112_BM_GEM_HD2

description: 10x Genomics


title: tkmg3


title: UPN13_BM_GEM_baseline

description: 10x Genomics


title: tkmg1


title: UPN10_BM_GEM_6M

description: 10x Genomics


title: UPN10_BM_GEM_baseline

description: 10x Genomics


title: Fetal Thymocytes 2

first: Abdulvasey

last: Mohammed

state: CA

address: 240 Pasteur Dr

department: Pediatrics

data_processing:
Sequencing data were trimmed using Trim Galore v 0.6.6 with a Quality Phred score cutoff of 20.
Expression levels of transcripts were quantified using selective alignment in Salmon v1.8.0, with human genome GRCh38.p14 used to construct the reference transcriptome.
Transcript counts were summed for gene count quantification.
Assembly: GRCh38.p14
Supplementary files format and content: Count matrix of number of reads mapping to genes across all samples.

source_name: Thymocytes

extract_protocol:
Human fetal thymus and lung samples (pcw 16 -18) were mechanically dissected into <2 mm^3 pieces using surgical scissors. Human fetal bronchus samples (pcw 16 -18) were opened longitudinally and mechanically scraped with scalpel to harvest the inner epithelial layer of bronchus and esophagus, respectively. All tissue samples were enzymatically digested with DNAse (10 mg/ml) and Liberase (2.5 mg/ml, Sigma Aldrich) per 10 g tissue using a tissue dissociator (gentleMACS, C tube, program m_spleen_02 (Miltenyi), 1-3 runs depending on tissue). For fetal thymic tissue (16-18 pcw) only, thymocytes were isolated from cell suspension using Human CD45 MicroBeads (Miltenyi) while other immune cells were depleted using LD depletion columns (Miltenyi),108 cells/column, according to the manufacturer’s instructions. Single cell suspensions of all tissues, (CD45-depleted thymus, bronchus and lung) were enriched for epithelial cells using Human CD326 (EPCAM) Microbeads and LS positive selection columns (Miltenyi) according to the manufacturer’s instructions. Quality control for thymocyte depletion and epithelial cell enrichment for thymic single cell suspensions was performed by flow cytomery on Beckman FACSAria II with CD45-APC, CD3-FITC, CD205-PE, EPCAM-APC, and Live Dead-Near InfraRed-APC-Cy7 prior to MACS purification. Due to epitope blockage from magnetic bead antibodies, additional markers, i.e. CD7-AF647 (thymocytes) and CD105-PerCP/Cy5.5 (thymic mesenchymal cells) were used to assess post enrichment purity. Total RNA was extracted from thymocytes and EPCAM positive selected epithelial cells using the Qiagen RNeasy kit.
Takara SMART-Seq v4 Ultra low Input RNA kit
500pg-5ng of total RNA input were used followed by pooling of 2-12 samples into Hiseq4000 and NovaSeq6000 lanes at a 2 x 100 bp read length.

value: Thymocytes


title: tkmf11


title: tkmf12


title: tkmf9


title: Fetal Thymocytes 1


title: tkmg7


title: OXC9-04-12

city: Oxford

first: Jakub

last: Scaber

state: Oxfordshire

address: West Wing, John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

data_processing:
fastq quality control was performed using fastqc and fastq-screen
Mapping against Ensembl genome version 101 was performed with STAR using the 2-pass method using a standard hg38 genome, with the following options on first pass: “--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNoverReadLmax 0.04 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9”. Mapping statistics were generated using the Picard toolkit.
Assembly: hg38
Supplementary files format and content: tab-delimited counts file

source_name: induced pluripotent stem cell derived neurons

extract_protocol:
iPSC-MNs for RNA sequencing were harvested on day in vitro 39. RNA extraction was performed using the QIAGEN RNeasy Micro kit. RNA abundance and quality were assessed using nanodrop and the Bioanalyzer Nano RNA kit.
Library preparation was done using Illumina Truseq and paired-end sequencing with a read length of 150bp was performed on the Illumina NovaSeq 6000.

tag: collection day

value: male

value: C9orf72 expansion


title: OXC9-02-03

value: induced pluripotent stem cell derived neurons

value: female


title: OXC9-02-02


title: tkmg2


title: tkmf8


title: tkmf6


title: Control_840

value: Healthy Control


title: Control_OX3-6


title: OXC9-01-07


title: tkmf5


title: tkmf10


title: Control_841


title: tkmf7


title: tkmf4


title: tkmf3


title: HiChIP_H3K27ac_SKMEL-1128 rep 1

city: New York

first: Elissa

middle: WP

last: Wong

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

data_processing:
HiChIP reads were aligned to the hg19 genome using Juicer pipeline (v1.7.6) with default settings. MAPQ30 threshold .hic files were used for the subsequent analyses.
HiC-DC+ was run on both pooled and individual replicates of HiChIP data to find significant interactions at 25 kb resolutions.
Assembly: hg19
Supplementary files format and content: bedpe
Library strategy: HiChIP

source_name: skin

growth_protocol: All cells lines were cultured in media supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. All cells were cultured at 37 ºC in 5% CO2.

extract_protocol:
15 x 106 cells were cross-linked with 1% formaldehyde for 10 min. Fixation was quenched with 125 mM glycine. Cells were washed once with PBS and lysed for 30 min using in situ Hi-C lysis buffer [10mM Tris-HCl (pH 7.5), 10mM NaCl, 0.2% NP-40 and 1x complete EDTA-free protease inhibitors (Roche)]. Nuclei were treated with 0.5% SDS followed by 1.25% Triton X-100 before digesting with 400 U MboI (NEB) for 4 hr. Restriction enzyme digested overhangs were filled in with biotin-dATP (Thermo fisher scientific) and ligated at 16 °C overnight. Nuclei were sonicated in nuclear lysis buffer [50mM Tris-HCl (pH 7.5), 10mM EDTA, 0.5% SDS and 1x EDTA-free protease inhibitor (Roche)] using Covaris E220 with the following parameter: peak power = 140 W, duty factor = 5%, cycle per burst = 200 and time = 4 min. Pull-down with anti-H3K27ac antibody (Abcam, ab4729) was performed by diluting sheared chromatin to 0.16% SDS in buffer with Pierce ChIP-grade magnetic beads. ChIP reaction was washed 3x LiCl buffer [250mM LiCl, 10mM Tris-HCl (pH 8.0), 1% sodium deoxycholate, 1% NP-40 and 1mM EDTA], 1x RIPA wash buffer [500mM LiCl, 50mM HEPES-KOH (pH 7.6), 0.7% sodium deoxycholate, 1% NP-40 and 1mM EDTA] and 1x TE [10mM Tris-HCl (pH 8.0) and 1mM EDTA] + 50 mM NaCl. Chromatin was eluted in 50 mM sodium bicarbonate (pH 8.0) with 1% SDS and reverse cross-linked with proteinase K at 65’C overnight. Streptavidin C1 beads (Thermo fisher scientific) were used to capture biotinylated DNA. Beads were washed twice with tween wash buffer [5 mM Tris-HCl (pH 7.5), 0.5mM EDTA. 1M NaCl and 0.05% Tween 20].
To build library for Illumina NovaSeq 6000 sequencing, Tn5 (Illumina) was used for tagmentation and amplified with Nextera Ad1_noMX and Ad2.X primers using 2x Phusion high-fidelity PCR mix (NEB). AMPure beads (Beckman coulter) were used for double-sided size selection (0.5x and 1x of the PCR volume) and purification of library DNA
sequenced with PE75 500M reads.

treatment_protocol: no treatment was performed

value: skin

value: melanoma

value: no treatment

value: H3K27ac antibody


title: tkmf2


title: tkmf1


title: HiChIP_H3K27ac_SKMEL-23 rep 2


title: HiChIP_H3K27ac_SKMEL-23 rep 1


title: tkme12


title: HiC_501mel shNIPBL_#2 6D rep 2

data_processing:
HiChIP reads were aligned to the hg19 genome using Juicer pipeline (v1.7.6) with default settings. MAPQ30 threshold .hic files were used for the subsequent analyses.
HiC-DC+ was run on both pooled and individual replicates of Hi-C data to find significant interactions at 10 kb resolutions.
HiC-DC+ normalized scores (observed over expected counts) was used to show Hi-C interactions in plots.
Assembly: hg19
Supplementary files format and content: .hic files

extract_protocol:
Arima Hi-C kit (Arima genomics) was used for all Hi-C experiments. Standard input protocol was followed with 3 x 106 cells for each condition. Proximally ligated DNA was fragmented to around 400bp by Covaris E220 focused ultrasonicator (peak power = 140 W, duty factor = 10%, cycle per burst = 200) for 70 sec. Fragmented DNA was sized selected to have a distribution between ~200-600bp using AMPure XP beads (Beckman Coulter).
~ 2µg of size-selected DNA was used for library preparation using KAPA hyper prep kit (KAPA biosystems) and TruSeq DNA unique dual indexes (Illumina). The number of PCR cycle used for library amplification was determined by KAPA library quantification kit for Illumina platform (KAPA biosystems).
Each Hi-C library was sequenced to obtain 500M reads PE100 with biological duplicates to achieve a total of 1 B reads for each condition.

treatment_protocol: Cells that were transduced with lentivirus carrying puromycin-resistant shRNA plasmids were treated with 2 µg/ml puromycin.

value: shNIPBL_#2, 6D


title: tkme10

value: Elongation ability


title: tkme11


title: tkme9


title: tkme8


title: tkme6


title: HiC_501mel shLuc 6D rep 1

value: shLuc, 6D


title: tkme7


title: CUTNRUN_501mel_pLKO_NIPBL_#2_6D_H3K36me3

data_processing:
CUTNRUN-seq reads were aligned to hg19 using BWA (v0.7.17-r1188). Unmapped and low MAPQ reads (< 30) were filtered out using SAMtools (v1.9) and PCR duplicates were removed using Picard tools (v2.18.16). Depth normalized bigWig tracks were generated using deepTools (v3.1.1) bamCoverage with `bamCoverage -b ${input_bam} -o ${output_bigwig} --normalizeUsing RPGC --ignoreForNormalization chrX chrM -bl hg19-blacklist.v2.bed`.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: Cut&Run

extract_protocol:
CUT&RUN was performed using CUT&RUN assay kit (Cell signaling technology). Briefly, 0.25 x 106 live cells were immobilized on activated Concanavalin A beads and permeabilized with digitonin. Cell:bead suspension was washed with 1x wash buffer supplemented with spermidine and protease inhibitor cocktail and incubated with 1 µg of antibody at 4 °C overnight. The following antibodies were used: anti-H3K4me1 (Thermo fisher scientific/Invitrogen, 710795), anti-H3K4me3 (Thermo fisher scientific/Invitrogen, PA5-27029), anti-H3K27ac (Abcam, ab4729), anti-H3K27me3 (Cell signaling technology, 9733BF), anti-H3K9me3 (Abcam, ab176916), anti-H3K36me3 (Active motif, 61021) and anti-CTCF (Cell signaling technology, 3418F) antibodies. Antibody-targeted digestion of chromatin was performed by incubation of pAG-MNase at 4 °C for 1 hr and activation by calcium chloride at 4 °C for 30 min. MNase cleavage was stopped by addition of 1x stop buffer. Digested chromatin was allowed to diffuse out of cells at 37 °C for 20 min and DNA was purified by Nucleospin gel and PCR clean-up spin column (Takara bio).
Sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (KAPA Biosystems).
Barcoded libraries were run on NovaSeq 6000 in a PE100 run. An average of 25 M reads were generated per sample.

value: H3K36me3 antibody


title: HiC_501mel shLuc 6D rep 2


title: CUTNRUN_501mel_pLKO_NIPBL_#2_6D_H3K27ac


title: tkme4


title: CUTNRUN_501mel_pLKO_NIPBL_#2_6D_H3K4me3

value: H3K4me3 antibody


title: tkme5


title: CUTNRUN_501mel_pLKO_NIPBL_#1_6D_H3K27ac

value: shNIPBL_#1, 6D


title: tkme3


title: CUTNRUN_501mel_pLKO_NIPBL_#2_6D_H3K4me1

value: H3K4me1 antibody


title: tkme2


title: tkme1


title: HiChIP_H3K27ac_SKMEL-1128 rep 2


title: CUTNRUN_501mel_pLKO_NIPBL_#1_6D_H3K4me1


title: CUTNRUN_501mel_pLKO_Luc_6D_CTCF

value: CTCF antibody


title: tkmd11


title: tkmd10


title: CUTNRUN_501mel_pLKO_Luc_6D_H3K27me3

value: H3K27me3 antibody


title: CUTNRUN_501mel_pLKO_Luc_6D_H3K36me3


title: tkmd9


title: tkmd8


title: HiC_501mel shNIPBL_#2 6D rep 1


title: CUTNRUN_501mel_pLKO_Luc_6D_H3K9me3

value: H3K9me3 antibody


title: CUTNRUN_501mel_pLKO_Luc_6D_H3K27ac


title: tkmd5


title: CUTNRUN_501mel_pLKO_Luc_6D_H3K4me3


title: tkmd6


title: 4Cseq_501mel shNIPBL_#2 6D ULK4_int31 rep2

data_processing:
R1 was used for analysis. From the single-end reads, non-reading primers at the 3’ end were trimmed using Cutadapt (v3.7). A maximum error-rate of 0.15 was allowed and trimmed reads shorter than 40 bp were discarded. 5’ end of the trimmed reads was further trimmed until primary restriction enzyme site (RE1; EcoRI or NlaIII) using R.
Only reads containing RE1 next to the viewpoint were considered for downstream analysis. Bowtie2 (v2.4.5) was used for aligning the trimmed reads to the human genome (hg19) while SAMtools (v1.14) (parameter: -q 1 -bSu) was used to filter for high-quality uniquely mapped reads.
Fragment maps of the hg19 genome were generated for each restriction enzyme pair. Blind fragments (which have RE1 on both ends) were excluded from the analysis. Aligned reads were assigned to overlapping fragment ends. Fragment read counts were depth normalized to have 1 M reads on the cis chromosome where the viewpoint is located. The top 3 fragments with the highest read counts corresponding to the undigested and self-ligated fragments (usually the ones closest to the viewpoint) were excluded when calculating depth normalization.
For smoothening, running mean across the fragment read counts were calculated using sliding window sized 21 (averaging 10 fragments left and right to the fragment of interest).
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: 4C-seq

extract_protocol:
In brief, 10 x 106 cells were fixed with 1% formaldehyde for 10 min. Cross-linking was quenched with 200 mM glycine and cells were lysed with NP-40 lysis buffer [10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2% NP-40 and 1x complete EDTA-free protease inhibitors (Roche)] for 20 min on ice. Nuclei were incubated with 0.5 % SDS at 65 °C for 10 min followed by 1.25 % Triton X-100 at 37 °C for 15 min. Nuclei were digested with 500 U EcoRI (ALKATI viewpoint) or NlaIII (ULK4 intron 31 viewpoint) overnight. qPCR was performed using primers that span restriction enzyme cut site at the bait versus uncut control region to confirm the efficiency of restriction enzyme digestion to over 90%. Digested chromatin was ligated at 16 °C overnight, reverse cross-linked and purified. For efficient PCR amplification and next generation sequencing, a second round of restriction enzyme digestion was performed using 10 µg 3C product and 100 U DpnII (for both ALKATI and ULK4 intron 31 viewpoints) at 37 °C for 5 hr. Sample was ligated overnight at 16 °C, ethanol precipitated at -80 °C and purified with QIAquick PCR purification column.
Inverse PCR was performed using 4C_ALKATI_EcoRI or 4C_ULK4int31_NlaIII (reading) and 4C_ALKATI_DpnII or 4C_ULK4int31_DpnII (non-reading) primers with 2x Phusion high-fidelity PCR mix (NEB). Each 4C sample was amplified in 4 PCR reactions, each containing 200 ng of 4C DNA template for 18 cycles. A second round of PCR was performed to add P5 and P7 adapters as well as index sequences for multiplex sequencing. Double-sided size selection was performed using AMPure XP beads (Beckman coulter) with 0.5x and 1x of the PCR volume.
Sequencing was performed on Illumina NovaSeq 6000 sequencer PE75. Each sample was sequenced to generate 10 M reads.


title: CUTNRUN_501mel_pLKO_Luc_6D_H3K4me1


title: tkmd4


title: 4Cseq_501mel shNIPBL_#2 6D ULK4_int31 rep1


title: CUTNRUN_501mel_pLKO_NIPBL_#1_6D_H3K4me3


title: CUTNRUN_501mel_pLKO_NIPBL_#2_6D_H3K27me3


title: tkmd7


title: tkmd2


title: tkmd1


title: tkmc12


title: 4Cseq_501mel shNIPBL_#2 6D ALKATI rep2


title: 4Cseq_501mel shNIPBL_#2 6D ALKATI rep1


title: tkmd3


title: 4Cseq_501mel shLuc 6D ULK4_int31 rep2

value: shLuc


title: 4Cseq_501mel shLuc 6D ULK4_int31 rep1


title: tkmd12


title: tkmc11


title: 4Cseq_501mel shLuc 6D ALKATI rep2


title: tkmc10


title: tkmc8


title: tkmc7


title: 4Cseq_501mel shLuc 6D ALKATI rep1


title: Huh-7 cells, siRNA-3

city: Shanghai

first: Jiawen

last: Jiang

address: 130 Dongan Road, Xuhui District

institute: Fudan University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2
The mapped reads of each sample were assembled by StringTie
To identify DEGs between two different samples, the expression level of each transcript was calculated according to the TPM method. RSEM was used to quantify gene abundances.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
TRIzol reagent (Solarbio) was used to extract their RNAs.1 ug of RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeqTM RNA sample preparation Kit of Illumina following manufacturer's protocols.

value: Hepatocellular carcinoma cells

value: WT

value: siRNA

tag: time

value: 48 hours


title: Huh-7 cells, siRNA-1


title: Huh-7 cells, si-NC

value: si-NC


title: tkmc6


title: tkmc5


title: tkmc2


title: mitochondrial RNA of Hep-3B, 12 hours

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
Gene annotated in GENCODE were quantified using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Mitochondria Isolation Kit for Cultured Cells (Thermo Fisher) and TRIzol reagent (Solarbio) was used to isolate the mitochondria and their RNAs.1 ug of mitochondrial RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeqTM RNA sample preparation Kit of Illumina following manufacturer's protocols.

value: hepatocellular carcinoma cells

value: hypoxia cell model

value: 12 hours


title: mitochondrial RNA of Huh-7, 12 hours


title: mitochondrial RNA of Huh-7, 6 hours

value: 6 hours


title: tkmc3

value: Elongation ability


title: tkmb10


title: tkmc4


title: mitochondrial RNA of Huh-7, 0 hour

value: 0 hour


title: mitochondrial RNA of Hep-3B, 0 hour


title: mitochondrial RNA of PHH, 6 hours

source_name: PHH

value: PHH

value: primary human hepatocytes


title: tkmb12


title: tkmb11


title: tkmc9


title: tkmc1


title: mitochondrial RNA of Hep-3B, 6 hours


title: Obese, well controlled, replicate 4

city: Baltimore

first: Rulin

last: Wang

state: Maryland

address: 1650 Orleans Street

institute: Johns Hopkins University

description: 10x Genomics

data_processing:
Cell Ranger v6.0.0 was used to demultiplex the FASTQ reads and align them to the Human gemone.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD4+ T cell

extract_protocol:
We isolated PBMCs using the Ficoll-Paque centrifugation method (Amersham) from normal weight and obese children with asthma. Cells were stained with a UV excitable LIVE/DEAD (Invitrogen) discriminator and then treated with human IgG (Rockland) to block Fc receptors. Cells then underwent surface staining (Table E1) to isolate CD4+ cells. Single cells were identified followed by live-dead discrimination. Live cells were excluded for CD14+ populations, CD19+ populations and inclusion of CD3+ populations to remove monocytes, B-lymphocytes and identify T-lymphocytes, respectively. From the CD3+ population, CD8+ populations were removed and CD4+ population sorted and isolated into Dulbecco’s phosphate buffered saline with 0.1% bovine serum albumin.
Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1

value: asthma

tag: condition

value: obese

tag: clinical phenotype

value: well controlled

value: CD4+ T cell

value: 8-17 years old


title: mitochondrial RNA of PHH, 12 hours

tag: cell type

value: WT


title: mitochondrial RNA of PHH, 0 hour

tag: treatment


title: tkmb9


title: tkmb8


title: tkmb6


title: Obese, well controlled, replicate 3

description: 10x Genomics

tag: disease state


title: tkmb4


title: Obese, poorly controlled, replicate 4

description: 10x Genomics

value: poorly controlled


title: tkmb2


title: tkmb1


title: Obese, poorly controlled, replicate 2

description: 10x Genomics


title: Obese, poorly controlled, replicate 3

description: 10x Genomics


title: Normal weight, well controlled, replicate 4

description: 10x Genomics

value: normal


title: tkma10


title: tkma8


title: Obese, well controlled, replicate 1

description: 10x Genomics


title: Obese, poorly controlled, replicate 1

description: 10x Genomics


title: tkma12


title: tkma9


title: tkma7


title: Normal weight, well controlled, replicate 1

description: 10x Genomics


title: Normal weight, well controlled, replicate 2

description: 10x Genomics


title: Normal weight, poorly controlled, replicate 4

description: 10x Genomics


title: tkma11


title: Normal weight, poorly controlled, replicate 2

description: 10x Genomics


title: tkma6


title: Normal weight, well controlled, replicate 3

description: 10x Genomics


title: tkma5


title: Normal weight, poorly controlled, replicate 3

description: 10x Genomics


title: Normal weight, poorly controlled, replicate 1

description: 10x Genomics


title: tkmb7


title: Obese, well controlled, replicate 2

description: 10x Genomics


title: tkmb5


title: tkma4


title: tkmb3


title: NCCLu-475

city: Goyang-si

first: namhee

last: yu

state: Gyeonggi-do

address: 323, Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National cancer center

data_processing:
Quality filtering and adapter trimming: FASTQC and Trimmomatic(Version 0.39) (standard parameters)
Mapping with STAR(version 2.7.0a)
Quantification with RSEM (v1.2.31 )
Assembly: GRCh37/hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

source_name: Lung cancer patient derived cells

growth_protocol: Pleural effusions, pericardium effusions, ascites and tissues were obtained by lung cancer patients at National Cancer Center. All experiments utilizing human material were approved by NCC IRB. For liquid samples, effusions were transferred to conical tube and centrifuged at 120 x g for 10 min. The cell pellet was resuspended in RPMI and carefully layered onto LSM (Lymphocyte Separation Medium, #091692249 MP Biomedicals, France). After centrifugation at 400 x g for 30 min at room temperature, interphase layer between RPMI and LSM including tumor cells was harvested and washed with RPMI. For tissue sample, tumor tissues were minced finely and washed with RPMI. After washing, cells from effusion or tissue were cultured in AR-5 medium (5% FBS, 1 X GlutaMAX (Thermo Fisher Scientific), 1 X ITS (Insulin-Transferrin-Selenium, Thermo Fisher Scientific), 1% Penicillin/streptomycin, 50 nM hydrocortisone, 1 mM Sodium Pyruvate and 1 ng/ml EGF in RPMI) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was purified from cultured cell using RNeasy® mini kit, and AllPrep DNA/RNA Mini kit (Qiagen, German) and handled by QIAcube automatic instrument (Qiagen, German).
For RNA-seq analysis, we prepared mRNA sequencing libraries as paired-end reads with a length of 100 bases using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to the manufacturers’ protocols. Briefly, mRNA molecules were purified and fragmented from 2 μg of total RNA. The libraries were sequenced as paired-end reads (2 × 150 bp) using the NovaSeq 6000 (Illumina).

treatment_protocol: non-treatment

tag: tissue

value: lung cancer derived cells

tag: disease

value: Lung cancer


title: tkma3


title: tkma2


title: NCCLu-465


title: NCCLu-468


title: NCCLu-464


title: NCCLu-462


title: hongyang

city: Zhengzhou

first: Miaomiao

address: Hanghai east road

institute: Zhengzhou Fruit Research Institute, CAAS

description: Actinidia chinensis cv. hongyang

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: hongyang V3 genome
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Actinidia chinensis

source_name: leaf

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

value: leaf

tag: cultivar

value: hongyang

value: wildtype


title: NCCLu-452


title: NCCLu-453


title: HCT116, 8 Hours DMSO, CTRL, Rep3

city: Evanston

first: vadim

last: backman

state: IL

address: 2170 Campus Drive, Silverman Hall 3627

department: Bioengineering

institute: Northwestern University

data_processing:
RNA-seq reads were preprocessed with FastQC v.0.12.0 and aligned with STAR v.2.6.0using the --quantMode TranscriptomeSAM parameter to human reference genome GRCh38 (Ensembl). Aligned samples were converted to binary alignment map (BAM) files, sorted, and indexed using SAMtools v.1.6. Coverage files were generated as BigWigs for the postive and negative strand using DeepTools v.3.1.1 BamCoverage utility and normalized by either CPM or RPGC. Coverage files were later merged for ease of analysis. Alignment statistics were generated using SAMtools Flagstat utility. Aligned and processed BAMs were then quantified to generate a counts table using the rsem-calculate-expression command from RSEM v.1.3.3 or the htseq-count command from HTSeq v.2.0.2 and the Homo_sapiens.GRCh38.111.gtf (Ensembl) genome annotation. Differential gene expression analysis was performed using DESeq2 v.1.44.0 in R. Intron-centric differential expression analysis was performed using the Intron Differences To Exon or INDEX package (https://github.com/Shians/index) and Superintronic package (https://github.com/sa-lee/superintronic) in R.
Analysis was performed following the recommendations of35 (Zheng Y et al (2020). Protocol.io) with some modifications. Reads were trimmed with Trim Galore v.0.6.10 and either mapped to the human reference genome GRCh38 (Ensembl) or to a custom hg38 reference that includes a 45 KB rDNA repeat for mapping to ribosomal DNA using Bowtie2 v.2.5.4 with the following parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Duplicate reads were marked and removed using Picard v.2.21.4. To account for variation in sequencing depth, once duplicates were removed, replicates were downsampled to the lowest common read depth for a given antibody, either 1 million reads, 2 million reads, or 10 million reads. Aligned and dedupped samples were converted to binary alignment map (BAM) files, sorted, and indexed using SAMtools v.1.624. BAM files were converted using Samtools and BED files were converted using Bedtools v.2.30.0. BigWig coverage was generated using Deeptools v.3.1.1 bamCoverage and either CPM or RPGC normalization. BAMs from downsampled replicates were merged for final consensus peak calling. Peaks were called on BAMs with MACS2 v. 2.2.9.1 using the -q 0.1 --keep-dup all parameters.
Assembly: hg38
Supplementary files format and content: tab delimited file containing peak calls from MACS2
Supplementary files format and content: merged BigWig files containing  CPM normalized coverage for each sample

growth_protocol: HCT116-POLR2A-AID2, HCT116-POLR1A-AID, and HCT116 cells were grown in McCoy’s 5A Modified Medium  supplemented with 10% FBS and penicillin-streptomycin (100 μg/ml) All cells were cultured under recommended conditions at 37°C and 5% CO2. Lines in this study were maintained between passage 5 and 20. Cells were allowed at least 48 hours to re-adhere and recover from trypsin-induced detachment prior to experiments. All experiments  were performed at a confluence between 40–70%.

extract_protocol:
Three technical replicates (treated in separate dishes on the same day) were harvested for each condition. At 6 hours, cells were harvested at ~10 x 106 cells per sample and transferred to 1.7 mL Eppendorf tubes. Samples were centrifuged and media was aspirated, followed by snap freezing in N2. Later, total RNA was extracted with an miRNeasy kit.
The Illumina Stranded Total RNA Library Preparation Kit was used to prepare sequencing libraries. The kit procedure was performed without modifications. This procedure includes rRNA depletion, remaining RNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation.

treatment_protocol: To induce expression of OsTIR1 in HCT116-POLR1A-AID, 1 μg/ml of doxycycline was added to cells 24 hours prior to auxin treatment. HCT116-POLR1A-AID cells were treated with 500 μM Indole-3-acetic acid sodium salt  to degrade endogenous POLR1A. HCT116-POLR2A-AID2 cells were treated with 1 µM  5-phenyl-indole-3-acetic acid to degrade endogenous POLR2A. HCT116 “WT” cells were treated with either 5 µg/mL Actinomycin D or % v/v DMSO equal to the highest DMSO concentration in each experiment. Treatment times varied between 1 hour and 8 hours.

tag: cell line

value: human collecteral

value: DMSO


title: HCT116, 8 Hours DMSO, CTRL, Rep2


title: NCCLu-445


title: Pol2, 8 hours Aux, Rep3

value: 1 µM 5-PH-IAA


title: Pol2, 8 hours Aux, Rep2


title: NCCLu-441


title: NCCLu-438


title: Pol2, 8 hours Aux, Rep1


title: NCCLu-436


title: Pol1, 8 hours Aux, Rep3

value: 500 µM IAA


title: NCCLu-434


title: NCCLu-433


title: Pol1, 8 hours Aux, Rep2


title: NCCLu-470


title: NCCLu-432


title: tkma1

value: Elongation ability


title: ActD, 6 hours ActD, Rep3

value: 5 µg/mL Actinomycin D


title: ActD, 6 hours ActD, Rep2


title: NCCLu-451


title: NCCLu-417


title: transgenic line of AaBAM3.1

description: transgenic line of AaBAM3.1

value: transgenic line of AaBAM3.1


title: HCT116, 8 Hours DMSO, CTRL, Rep1


title: NCCLu-413


title: P9 Tracheal, current-smoker

first: Ahmed

last: Alhendi

address: 5 University St

institute: UCL

description: 10x Genomics

data_processing:
The 10x raw data were processed using Cellranger v7.1.0
Assembly: human genome ex-GRCh38-2020-A
Supplementary files format and content: Tab-separated files and matrix files

source_name: Tracheal

extract_protocol:
Single cell suspensions were obtained from the tracheal brushes as per previously described protocols (dx.doi.org/10.17504/protocols.io.qubdwsn)
Single cell RNA libraries were prepared using 10x Chromium 5' V2 Gene Expression kit. The single cell suspension was loaded with the master mix, partitioning oil and gel beads into the chip to generate GEMs (gel bead-in emulsion), containing 10x barcoded cDNA from poly-A RNA. The pooled cDNA was then cleaned up using Silane Dynabeads, amplified by PCR and separated by size for 5' gene expression library construction.

value: Tracheal

value: Airway epithelial cells

tag: age

value: Current smoker


title: NCCLu-412


title: P6 Tracheal, never-smoker

description: 10x Genomics

value: Never smoker


title: P4 Tracheal, current-smoker

description: 10x Genomics


title: A431 cells,RBM3_3

city: luzhou

first: yi

last: peng

address: xianglinlu

institute: 西南医科大学

description:
A431_RBM3_3
AR4

data_processing:
Raw sequencing data was processed through the following steps to obtain high-quality clean data:  Removal of adapter sequences and reads without inserts Trimming of low-quality bases (quality score < 20) at the 3' end, and removal of entire reads if any remaining base has a quality score < 10 Removal of reads with N ratio > 10% Removal of reads shorter than 20 bp Quality control was performed using fastp software (https://github.com/OpenGene/fastp)
Clean data was aligned to the reference genome to obtain mapped data for downstream analyses. Alignment was done using HiSat2 software (http://ccb.jhu.edu/software/hisat2/index.shtml), and quality assessment of the alignment results was conducted (sequencing saturation, gene coverage, read distribution, etc.).
RSEM software (http://deweylab.github.io/RSEM/) was used to quantify gene and transcript expression levels, generating Read Counts data.
For samples with biological replicates, differential expression analysis was performed using DESeq2 software (http://bioconductor.org/packages/stats/bioc/DESeq2/). For samples without replicates, DEGseq software (https://www.rdocumentation.org/packages/DEGseq/versions/1.26.0) was used. Differentially expressed genes were filtered using the criteria of FDR < 0.05 and |log2FC| ≥ 1.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: A431 cells were maintained in  DMEM medium supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from C918 cells using the QIAzol Lysis Reagent. 1.5 μg of total RNA was used for subsequent library construction.
Libraries were constructed using the Illumina® Stranded mRNA Prep Ligation Kit according to the manufacturer's instructions.

value: human cell line (epidermoid carcinoma)

value: rbm3 overexpression


title: NCCLu-407

value: lung cancer derived cells

value: Lung cancer


title: NCCLu-410


title: NCCLu-411


title: P8 Tracheal, current-smoker

description: 10x Genomics


title: NCCLu-406


title: A431 cells,RBM3_1

description:
A431_RBM3_1
AR2


title: A431 cells,RBM3_2

description:
A431_RBM3_2
AR3


title: NCCLu-408


title: A431 cells,Egfp_3

description:
A431_EGFP_3
AG3

value: egfp


title: NCCLu-403


title: A431 cells,Egfp_2

description:
A431_EGFP_2
AG2


title: Pol1, 8 hours Aux, Rep1


title: NCCLu-398


title: C918 cells, TTC_3

growth_protocol: C918 cells were maintained in  RPMI 1640 medium supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: For the treatment group, a 100 mM stock solution of TTC was prepared in PBS, and then diluted in the culture medium to a final concentration of 400 μM. For the control group, an equivalent volume of PBS was added to the culture medium. Cells were treated for 24 hours.

value: Human Uveal menolama cells

value: WT


title: A431 cells,Egfp_1

description:
A431_EGFP_1
AG1


title: NCCLu-397


title: ActD, 6 hours ActD, Rep1

value: human collecteral


title: NCCLu-420


title: NCCLu-405


title: NCCLu-393


title: C918 cells, TTC_2


title: C918 cells, TTC_1


title: NCCLu-389


title: NCCLu-388


title: NCCLu-384


title: NCCLu-383


title: C918 cells, con_2

value: pbs


title: C918 cells, con_1


title: NCCLu-376


title: NCCLu-379


title: NCCLu-375


title: Pv1

city: Lisbon

first: Henrique

last: Silveira

address: Rua da Junqueira, 100

department: Global Health and Tropical Medicine

country: Portugal

institute: Instituto de Higiene e Medicina Tropical, IHMT, UNL

data_processing:
Illumina reads were checked for quality control using FastQC v0.11.5 and trimmed for low-quality reads with Trimmomatic v.0.36.
High quality paired-end reads were assembled against the AdarC3 assembly genome using HISAT2 v2.1.0.
Transcript quantification was performed with featureCounts v1.5.3.
Genome_build: Anopheles-darlingi-Coari_AdarC3
Supplementary_files_format_and_content: tab-delimited matrix file include raw counts for each Sample

organism: Anopheles darlingi

source_name: midguts

extract_protocol:
Mosquito midguts were collected from mosquitoes submerged in ice-cold PBS and transferred to RNAlater (Ambion). RNA was harvested using Trizol reagent and treated with RNase-Free DNase I (Qiagen). RNA integrity was confirmed using 2100 Bioanalyzer (Agilent) and total RNA was used for library preparation and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A. darlingi mosquitoes  were: i) membrane-fed on P. vivax infected blood, ii) membrane-fed on blood with inactivated gametocytes or iii) fed on 10 % sugar solution.

value: 3-5 days old adult females

value: P. vivax-blood fed mosquitoes

tag: time-point

value: 18-24h after meal


title: Bl3

value: Non-infected blood-fed mosquitoes


title: NCCLu-371


title: NCCLu-370


title: Bl2


title: Pv2


title: NCCLu-365


title: NCCLu-368


title: Unf3

value: Sugar-fed mosquitoes


title: Bl1


title: NCCLu-363


title: Unf2


title: Unf1


title: NCCLu-360


title: C918 cells, con_3


title: NCCLu-359


title: NCP-W601-RUNX2-Round4-Rep2

city: Boston

first: Luca

last: Mariani

state: ma

address: 77 Avenue Pasteur

department: Medicine

institute: Harvard Medical School

description:
Library name: NCP-W601-RUNX2-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of RUNX2 for 4 rounds, Biological replicate 2

data_processing:
The forward (labeled ‘R1’) and reverse complement (labeled ‘R2’) 150-bp paired-end sequencing fastq reads were merged with PEAR in default setting (PMID: 24142950).
PCR duplicates were removed and the reads were trimmed at the 3’ end to remove the 6-bp UMIs. Since PIONEAR-seq libraries by design are 147-bp long, trimmed reads with different lengths were removed.
To extract the DNA sequence and the location of the tiles, the reads were aligned to the associated template  by the  R function pairwiseAlignment (default setting except: type='overlap’,  gapOpening=1000, gapExtension=0). This function furnishes an alignment score and the position of the base mismatches for each read. Given the template is 147-bp long and the random tile is 20-bp long, reads with an alignment score smaller than 127 were considered non-aligned and removed.
The position of the first and last mismatch were compared to assign the random tile position of each read
For each library, the read count of tiles at different position varies. To give the same weight to each tile position, the median read count of the library was used to resample the tiles at each psoition (Isotiling). To calculate motif enrichment the internal 16-bp of all the isotiles of the library were merged and compared to the associated input library by using the SELEX R package.
Assembly: Synthetic DNA
Supplementary files format and content: XXX_kmer_enrichment_table.txt' file is in txt format and contains a table showing:
Supplementary files format and content: the enrichment rank (Column 1: ID), the sequence of the enriched k-mer (column 2: Kmer), the k-mer count observed in the assessed library (column 3: ObservedCount), the expected k-mer count inferred from the associated input library used as background set (Column 4: ExpectedCount), their relative k-mer count increase, which is a measure of k-mer enrichment and is defined as the ration between the expected and observed counts (Column 5: Increase).
Library strategy: SELEX

molecule: other

organism: synthetic construct

source_name: synthetic DNA

extract_protocol:
Amplicon DNA
Sequencing libraries were prepared by adding to the selected libraries (1) 5' end Unique Molecular Identifies (UMIs), (2) llumina adaptors (IAs), (2) TRUseq dual barcodes (BCs) and (2) Illumina sequencing promoters P5 and P7 (P5/P7) by PCR amplification with custom primers.  10 ng of DNA was used as starting material samples. Libraries were with KAPA HiFi HotStart ReadyMix PCR Kit amplified by using 2 consecutive 6-cycle PCR runs (first cycle for UMIs and IAs, second cycle for BCs and P5/P7)  on the thermocycler. Post amplification libraries were size selected at ~3000bp in length by Azenta using AMPure XP beads. Libraries were validated by using both the Tapestation D1000 and  Qubit.

treatment_protocol: DNA Libraries were PCR amplified, assembled on in vitro reconstituted histone octamers to form nucleosome and incubated with GST-tagged transcription factors. TF-bound elements were selected by glutathione beads followed by PCR amplification. The treatment was repetead for 4 rounds.

value: synthetic DNA

value: DNA assembled onto nucleosomes


title: NCP-W601-RUNX2-Round4-Rep1

description:
Library name: NCP-W601-RUNX2-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of RUNX2 for 4 rounds, Biological replicate 1


title: NCP-W601-PU1-Round4-Rep1

description:
Library name: NCP-W601-PU1-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of PU1 for 4 rounds, Biological replicate 1


title: NCP-W601-ZNF143-Round4-Rep1

description:
Library name: NCP-W601-ZNF143-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of ZNF143 for 4 rounds, Biological replicate 1


title: Pv3


title: NCP-W601-PAX7-Round4-Rep1

description:
Library name: NCP-W601-PAX7-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of PAX7 for 4 rounds, Biological replicate 1


title: NCP-W601-PAX7-Round4-Rep2

description:
Library name: NCP-W601-PAX7-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of PAX7 for 4 rounds, Biological replicate 2


title: NCCLu-356


title: NCP-W601-OCT4-Round4-Rep2

description:
Library name: NCP-W601-OCT4-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of OCT4 for 4 rounds, Biological replicate 2


title: NCCLu-357


title: Syngeneic Placenta Erythroid Cells E19.5 3

type: RNA

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

hyb_protocol: 200ng of total RNA was hybridized with NanoString Mouse Immunology V1 panel according to the manufacturer's protocols.

scan_protocol: Automated scanning was performed on the NanoString Sprint system

data_processing: We performed QC on the raw data, normalized gene expression using 15 housekeeping genes, performed background thresholding (removed the genes with less expressiom that the mean of POS_D controls in all samples).

source_name: Placenta

growth_protocol: We collected mouse semi-allogeneic and syngeneic placentas at E12.5 at E19.5

extract_protocol: We extracted  Ter-119 Erythroid cells from murine placenta via Ter-119 magnetic separation

tag: day of development

tag: pregnancy type

value: Syngeneic


title: Syngeneic Placenta Erythroid Cells E19.5 1


title: Semi-allogeneic Placenta Erythroid Cells E19.5 3

value: Semi-allogeneic


title: Syngeneic Placenta Erythroid Cells E19.5 2


title: NCP-W601-GST-Round4-Rep2

description:
Library name: NCP-W601-GST-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of GST for 4 rounds, Biological replicate 2


title: Semi-allogeneic Placenta Erythroid Cells E19.5 2


title: NCP-W601-OCT4-Round4-Rep1

description:
Library name: NCP-W601-OCT4-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of OCT4 for 4 rounds, Biological replicate 1


title: NCP-W601-KLF4-Round4-Rep1

description:
Library name: NCP-W601-KLF4-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of KLF4 for 4 rounds, Biological replicate 1


title: NCCLu-353


title: NCP-W601-GST-Round4-Rep1

description:
Library name: NCP-W601-GST-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of GST for 4 rounds, Biological replicate 1


title: NCP-W601-GATA4-Round4-Rep1

description:
Library name: NCP-W601-GATA4-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of GATA4 for 4 rounds, Biological replicate 1


title: NCCLu-352


title: Semi-allogeneic Placenta Erythroid Cells E19.5 1