title: NIH3T3-Con-Rep_3

first: Savas

last: Tay

address: 5640 South Ellis Avenue, Chicago, IL 60637

department: PME

institute: University of Chicago

data_processing:
Basecalls performed using CASAVA
Sequenced reads were trimmed for adaptor sequence and aligned using STAR aligner with default settings
Transcript abundance was calculated using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts object with counts and annotations

source_name: RelA-/- Rela-DsRed 3T3s

growth_protocol: Cells were cultured in growth media and passaged at confluency for no more than 20 passages before use in a T25

extract_protocol:
Cells were detached with TrypLE, placed in 0.1% Triton-X 100 to lyse, and extraction-free RT and 10 cycles of pre-amplification performed using Superscript ii and KAPA HiFi respectively
cDNA libraries were prepared for sequencing using standard Illumina protocols from NexteraXT kit

treatment_protocol: Cells were loaded into custom microfluidic devices, stimulated with the indicated cytokine for two hours

tag: cell type

value: NIH3T3 immortalized MEFs

value: RelA-/- Rela-DsRed 3T3s

value: media


title: h10B_P

status: Public on Jan 01 2024

type: SRA

city: West Hollywood

first: Simon

last: Knott

state: California

address: 8687 Melrose Ave

department: BFG

country: USA

institute: Cedars Sinai

library_source: transcriptomic single cell

data_processing:
All immune cells following the single cell pipeline outlined in Methods
All non-immune cells following the single cell pipeline outlined in Methods
All TCR data
Assembly: hg38
Supplementary files format and content: H5AD file containing celltype, subtype, patient, batch, pCR and other metadata columns for each immune cell
Supplementary files format and content: H5AD file containing celltype, subtype, patient, batch, pCR and other metadata columns for each non-immune cell
Supplementary files format and content: CSV file containing TCR data

molecule: polyA RNA

organism: Homo sapiens

source_name: Breast

extract_protocol:
Human TNBC core needle biopsies were dissociated using the Miltenyi BiotecHuman Tumor Dissociation Kit, then CD45-positive cells were enriched using the Miltenyi Biotec anti-human CD45 microbeads and CD45-negative cells were obtained from the non-enriched portion
Single-cell gene expression and paired TCR (CD45-positive only) librarieswere prepared according to the 10X Genomics Single Cell 5’ v1 protocol.

tag: tissue

value: Breast

tag: age

value: adult

tag: Sex

value: female

tag: treatment

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


title: colonTreg_2-4_GvHD_Tcra_R1

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

description:
re-isolated
mTRA_Tx198-1-297-C-rp_A.RunAB.clonotypes.TRA.txt

library_source: transcriptomic

data_processing:
base calling: Base-calling and demultiplexing based on Illumina barcodes was carried out using the bcl2fastq Conversion Software (v1.8.4) provided by Illumina (Illumina INc., San Diego, California, USA).
paired-end read alignment: UMI-barcoded and paired TCR-sequencing reads were joined using PEAR (v0.9.11).
UMI-based generation of MIGs: Demultiplexing on the basis of UMI-barcodes and adaptor trimming was done using MIGEC (v1.2.9) resulting in consensus sequences of molecular identifier groups (MIGs).
MIG mapping: MIGs were mapped using MIXCR (v3.0.13).
Assembly: RepSeq.IO library v1.6
Supplementary files format and content: Mapping output of MIXCR
Library strategy: TCR-seq

molecule: total RNA

organism: Mus musculus

source_name: CD4+CD25+ regulatory T cells

growth_protocol: Splenocytes were stained with anti-CD25-PE and anti-PE UltraPure MicroBeads and enriched for CD25+ cells by MACS® (Miltenyi Biotec). The CD25+ fraction was further stained for CD8, CD4 and CD62L and Treg were sorted on a FACSAria IIuTM or a FACSAriaTM Fusion (BD Biosciences) as CD4+CD25highCD62L+ cells; purity of sorted cells was >98%. Polyclonal in vitro expansion of Treg was performed as recently described {Riegel, 2020 #61}. In brief, sorted Treg were cultured in DMEM (high glucose, Gibco/Invitrogen) with 10% FCS, 2mM L-glutamine, 10mM HEPES, 1% NEAA (PAN Biotech), 50U/ml penicillin, 50µg/ml streptomycin and 5x10-5 M 2-mercaptoethanol  (Gibco/Invitrogen) (cDMEM) in 96-U-well plates (1x104/well) and stimulated with CD3/CD28-beads (Treg-Expansion Kit, Miltenyi Biotec, 4 beads/cell) and rhIL-2 (2000 U/ml; Proleukin®, Chiron). Cultures received 100 µl/well fresh medium on d4, were restimulated on d7 with 1 bead/cell after transfer into 24-well-plates (1x106 cells/ml/well), fed and split on d10 as needed and harvested on d12. For allospecific in vitro expansion sorted Treg were seeded at 5x104/well in cDMEM together with 2,5x104/well (d0) or 1x104/well (restimulation on d7) anti-CD11c MicroBead-enriched (Miltenyi Biotec) and irradiated (30 Gy) CD11c+ DC  from BALB/c mice. Cells received fresh medium on d4 and d10 and were harvested on d12.

extract_protocol:
Total cellular RNA was isolated from Treg (freshly isolated, in vitro expanded, or re-isolated after BMT) using the RNeasy Mini Kit or the RNeasy Micro Kit (Qiagen). Following the manufacturer’s recommendations, samples originating from 500 to 500k cells were processed with the Micro Kit whereas the Mini Kit was applied to all samples exceeding 500k cells. RNA concentration and quality were simultaneously assessed using RNA Screentape Analysis or High Sensitivity RNA Screentape Analysis (Agilent), depending on the expected yield.
Total cellular RNA was obtained as described in section “RNA-seq library preparation”. TCR repertoire sequencing libraries for Illumina sequencing were prepared on the basis of {Mamedov, 2013 #7} and the protocol was adapted, as follows. For the generation of 5’RACE-ready cDNA total RNA ranging from 10 - 200 ng (low input) or 200 - 1000 ng (high input) in a total of 10 µl RNAse-free water was combined with 1 µL of 12 µM or 25 µM 5’-CDS Primer A in a total volume of 11 µL, respectively. Reactions were incubated at 72°C for 3 min followed by 42°C for 2 min for poly-dT primer annealing. Next, 1 µL of 10 µM (low input) or 50 µM (high input) TCR_UMI_Smarter template-switching oligo (TSO) was added at room temperature. RT Buffer Mix (5x First-Strand-Buffer Mix, 20mM dNTP, 100 mM DTT) was freshly prepared on ice before it was supplemented with RNaseOUT™ Recombinant Ribonuclease Inhibitor (40 U/µL) (Thermo Fisher Scientific) and SMARTScribe Reverse Transcriptase (100 U/µL) (Takara) at room temperature. A volume of 8 µL of the resulting reverse transcription master mix was added to each reaction. After homogenization, the 20 µL reactions were incubated at 42°C for 90 min followed by 70°C for 10 min and put on hold at 10°C in a hot-lid thermal cycler. Following reverse transcription, excess TSO was digested using Uracil-DNA Glycosylase (UDG) (New England Biolabs) by adding 4 µL of UDG master mix adjusted for TSO input amount and successive incubation at 37°C for 60 min. The master mix for PCR1 was prepared on ice using the Advantage 2 PCR Kit (Takara) along with primers specific for the constant regions of the Trac and Trbc loci as well as a universal forward primer specific for a binding sequence introduced via the TSO. 24 µL of RACE-ready cDNA were combined with 26 µL of PCR1 master mix and subjected to a two-step PCR program (95°C, 1min; 95°C, 30 s & 68°C, 70 s (x times); 68°C, 7 min; 8°C, hold). Depending on the RNA input amount, PCR cycle numbers ranged from 16 to 28. The 50 µL PCR product was purified with 27.5 µL of AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions. After elution in 23.5 µL of Monarch® DNA Elution Buffer (New England Biolabs), reactions were split into 10 µL technical replicates for successive extension PCR (PCR2). PCR2 master mix was assembled using the Advantage 2 PCR Kit (Takara) and gene-specific nested primers (Trac, Trbc loci) introducing Illumina Nextera XT i5 indices (S501, S502, S503, S508, S517, S520, S507), distinguishing Tcra from Tcrb libraries within each reaction. After addition of 36 µl PCR2 master mix, 4 µL of Nextera XT Index Kit v2 (Illumina) adapters were used for indexing libraries individually. Libraries were amplified using the same program as in PCR1 with 18 PCR cycles. Library purification was carried out using  AMPure XP beads (Beckman Coulter) at a volume ratio of 0.8 according to the manufacturer’s instructions. After final elution in 17 µL of Monarch® DNA Elution Buffer (New England Biolabs), concentration was measured with the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific) and fragment size profile was assessed using the High Sensitivity D1000 or D5000 ScreenTape Assay (Agilent). Libraries were stored at -20°C until sequencing (paired-end 300bp) on the Illumina MiSeq system. Oligonucleotide sequences are summarized in Supplemental Table 3, Libraries are summarized in Supplemental Tables 4-7.
poly-dT-primed, gene-specifically enriched TRA/TRB library preparation

treatment_protocol: Single cell suspensions from BM (femora and tibiae of both hind legs) and spleen were prepared. T cells were depleted from BM (T cell depleted bone marrow; TCDBM) by using anti-CD90.2 MicroBeads with the MidiMACS® system (Miltenyi Biotec). CD4+CD25- conventional T cells (Tconv) were isolated from splenocytes by depletion of CD25+ cells using anti-CD25-PE (all antibodies used in this study are listed in Supplemental Table 2)  and anti-PE UltraPure MicroBeads (Miltenyi Biotec), followed by enrichment of CD4+ cells from the CD25- fraction through labeling with anti-CD4 MicroBeads (Miltenyi Biotec) using the MidiMACS® system. For short-term (d7) FACS and RNA-seq experiments BALB/c recipients were lethally irradiated (8 Gy) on the day of BMT and transplanted i.v. with 2.5 x106 TCDBM cells and 1x106 Tconv from B6-CD45.1 mice with or without in vitro expanded allo or polyTreg from Foxp3gfp mice at a 1:1 ratio. Recipients of the ‘no GvHD’ group received TCDBM and Treg only. In long-term survival experiments lethally irradiated BALB/c recipients were transplanted with 2.5 x106 TCDBM on d0 and 0.25 x106 Tconv were administered on d2 for GvHD induction. Mice of the GvHD prophylaxis groups (allo or poly) received additional 0.25x106 in vitro expanded Treg from B6 WT mice on d0. Recipients were monitored daily, body weight and GvHD symptoms assessed twice weekly by non-blinded investigators applying a standardized scoring system (Cooke et al., 1996). Single cell suspensions from BM, spleen and mesenteric lymph nodes were prepared. Erythrocytes were lysed in splenic and BM cell suspensions. For leukocyte isolation from the liver, the organ was flushed with PBS through the portal vein and the gallbladder was removed before it was excised, transferred to a petri dish and dissected into small pieces using a scalpel. Fragments were suspended in RPMI (Lonza/Biozym)/5% FCS, strained and washed in RPMI w/o FCS before Percoll centrifugation (40%/80%; 800 x g/20 min/20°C, w/o break). Leukocytes were resuspended in RPMI/5% FCS, erythrocytes were lysed, cells were washed in RPMI/10% FCS and kept on ice until further use. For intestinal leukocyte isolation, large intestine was excised, cut into 0.5 cm pieces, incubated twice for 20 min at 37 °C in HBSS/5mM EDTA/1mM DTT (Sigma-Aldrich) followed by vigorous shaking to isolate intraepithelial leukocytes (IEL). For lamina propria leukocytes (LPL), the fragments were transferred to HBSS without phenol red containing calcium and magnesium with 5% FCS together with enzymes of the Lamina propria dissociation kit (Miltenyi Biotec) and incubated for 30 min at 37°C. The fragments were further mechanically dissociated using the GentleMACS system (protocol: m_intestine_01; Miltenyi Biotec), strained, washed and pooled together with IEL before Percoll (Sigma-Aldrich)  centrifugation (30%; 512 xg/15 min/20°C). For baseline (no BMT) colon Treg sorts IEL were not included (no Tregs in untreated animals) and colonic LPL were further enriched using anti-CD45 MicroBeads (Miltenyi Biotec) and the AutoMACS® system (Miltenyi Biotec). Splenocytes were enriched for CD25+ cells by MACS® using anti-CD25-PE and anti-PE UltraPure MicroBeads before sorting. Cells were further stained for CD8, CD4 and CD62L (also CD45 for colon-derived cells) and Treg were sorted on a FACSAriaTM IIu or a FACSAriaTM Fusion (Becton Dickinson). From spleen and liver, CD62L+ and CD62L– subpopulations were isolated, from colon, only CD62L–- cells were obtained (sorting strategy is shown in detail in Supplemental Fig.2a). For re-isolation of donor Treg on day 7 after transplantation, single cell suspensions from spleen, liver and colon were prepared as described, stained for H-2Kb, CD45.1, CD45.2, TCRβ and CD4 and sorted on a FACSAria IIuTM or a FACSAriaTM Fusion (for detailed sorting strategy see Supplemental Fig.2b). Staining was performed in PBS/2%FCS with anti-CD16/CD32 antibodies to block FcR-binding and DAPI (Sigma-Aldrich) or Fixable Viability Dye (Thermo Fisher) to exclude dead cells. Detailed information on all antibodies used in this study is listed in Supplemental Table 2. For staining of intracellular markers, the Foxp3/Transcription Factor Staining Buffer Set® (eBioscience) was used.  Multicolour FACS staining for surface markers was performed using Brilliant Stain Buffer (BD Biosciences) where applicable. Data was acquired on a FACSymphony® A5 SORP (Becton Dickinson) and analyzed using FlowJo® software (v10.7.1 or v10.8.0; Treestar Inc). For clustering and embedding of multiparameter flow cytometry data (as presented in Supplemental Fig.2a) FlowJo® plugins DownSample_v3.3 and UMAP_v3.1 were used. The UMAP plot in Supplemental Fig. 2a was created on the basis of 27 samples from spleen, liver and colon (all n=3) from 3 experimental groups: alloTreg prophylaxis, polyTreg prophylaxis and GvHD control and 3 independent experiments, with every sample representing a cell pool of 2-3 mice. Cells were stained for CD45.1, CD45.2, H-2kb, TER119, TCRβ, CD8α, CD4, CD19, Nkp46, CD11b, Ly6C, Gr-1 and CD25. Dead cells were excluded with DAPI. Samples were gated on live single CD45.1+TER119- and CD45.2+TER119- cells, downsampled to 15.000 cells each and assembled into one file.

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: poly

tag: model

value: GvHD

value: colon

tag: treg donor

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: alpha

tag: techn. replicate


title: 5-FU+FMT-3

city: Hangzhou

first: lu

last: huan

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University medical center

data_processing:
Illumina Casava1.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore-0.6.5, then mapped to mm10 whole genome using hisat2-2.2.1 with default parameters
sam files were transformed to bam files and filtered with samtools to get unique properly paired reads.
featureCounts v2.0.1 were used to get raw gene counts.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene

source_name: long-term hematopoietic stem cells

extract_protocol:
Total RNA was isolated with Trizol
First-strand cDNA synthesis  and cDNA libraries were constructed using the NEBNext Ultra TM  II RNA Library Prep  Kit  (New  England  Biolabs).
cDNA  quality  was  determined  on  Agilent  2100  BioAnalyzer  (Agilent  Technologies),  and  then  sequenced  on  NovaSeq  6000  device  (Illumina) to obtain pair-end 150 bp reads.

treatment_protocol: Mice were pre-conditioned with 5-FU (250 mg/kg body weight), and FMT (5 mg/kg body weight) was intravenously administered after  1, 4 and 7 days. Mice were sacrifised at day 8 and LT-HSCs were sorted as Lin-Sca1+c-Kit+CD150+C48-.

tag: cell type

value: long-term hematopoietic stem cells

tag: genotype

value: C57BL/6 WT

value: 5-FU pre-conditioned, followed by FMT treatment


title: ITGB1AKQ_C

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Sequenced reads were mapped to UCSC mm10 whole genome using STAR v2.7.4a with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.38.4
Assembly: UCSC mm10
Supplementary files format and content: rawcounts.txt = tab-delimited text files include rawcount values for each Sample

source_name: Embryonic endothelial cells eEnd2

growth_protocol: Transfected mouse embryonic endothelial eEnd2 cells were cultured in DMEM supplemented with 10% fetal calf serum and 2% antibiotics in humidified atmospher with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted by using the RNA and protein extraction kit (Macherey-Nagel) according to the manufacturer instruction.
Illumina Ribo-Zero plus

treatment_protocol: No treatment

tag: transfection

tag: cell line

value: Embryonic endothelial cells eEnd2


title: h09C_P

tag: tissue

tag: age

tag: Sex

tag: treatment

value: Pembrolizumab + Radiation


title: colonTreg_3-3_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-348-C-ra_A.RunAB.clonotypes.TRA.txt

tag: strain

tag: sampleID

tag: mouse (pool/culture no.)

value: allo


title: NIH3T3-Con-Rep_2

city: Chicago

state: IL

value: NIH3T3 immortalized MEFs

value: RelA-/- Rela-DsRed 3T3s

value: media


title: h09B_TCR

value: Breast

value: adult

value: female

tag: disease state


title: NIH3T3-Con-Rep_1


title: h09B_P

value: Pembrolizumab

value: Triple-receptor negative breast cancer


title: NIH3T3-PAM-Rep_3

value: 0.2 ng/mL PAM


title: 5-FU+FMT-2


title: h09A_TCR

value: Baseline


title: NIH3T3-PAM-Rep_2


title: 5-FU+Saline-1

value: 5-FU pre-conditioned, followed by PBS treatment


title: colonTreg_3-2_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-346-C-ra_ABC.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: type

tag: model

value: GvHD

value: colon

tag: treg donor

tag: recipient

value: alpha


title: NIH3T3-PAM-Rep_1


title: h07C_TCR

value: Pembrolizumab + Radiation


title: Control-2

value: long-term hematopoietic stem cells

value: C57BL/6 WT

value: Untreated


title: colonTreg_2-3_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-296-C-ra_AB.RunAB.clonotypes.TRA.txt

value: allo

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

tag: techn. replicate


title: 5-FU+Saline-3

tag: cell type

tag: genotype


title: colonTreg_2-2_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-294-C-ra_AB.RunAB.clonotypes.TRA.txt

tag: tissue


title: h09A_P

value: Breast

tag: age

tag: Sex


title: 5-FU+FMT-1

tag: treatment

value: 5-FU pre-conditioned, followed by FMT treatment


title: colonTreg_2-1_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-293-C-ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

tag: sampleID


title: NIH3T3-LPS-Rep_3

value: NIH3T3 immortalized MEFs

value: RelA-/- Rela-DsRed 3T3s

value: 100 ng/mL LPS


title: Control-1


title: NIH3T3-LPS-Rep_2


title: Female F2  (MaleDose2 x FemaleDose2) sample C

city: Montpellier

first: Brigitte

last: Boizet Bonhoure

address: 141 rue de la Cardonille

department: Human Genetic Institute

country: France

institute: CNRS UMR9002

description: 100 nt

data_processing:
Libraries were sequenced on a Novaseq 6000 (Illumina, San Diego, CA, USA) on one lane of a S4 flow cell in paired end 2*100nt mode according to the manufacturer’s instructions
For sequencing quality control, image analyses and base calling were performed using the NovaSeq Control Software and Real-Time Analysis component
Demultiplexing and trimming were performed using the Illumina's conversion software (bcl2fastq 2.20)
The raw data quality was assessed using FastQC (version 1.19) from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer). FastqScreen (version 0.15) was used to estimate the potential level of contamination
Assembly: For sequences alignment, the splice junction mapper, TopHat 2.1.1 and Bowtie 2.4.5 were used to align the RNA-Seq reads to the Mus musculus genome (NCBI mm39)
Supplementary files format and content: Samtools (v1.13) was used to sort the alignment files. Then, genes were counted with Featurecounts 2.0.3
Supplementary files format and content: Differentially expressed genes were identified using the Bioconductor, package DESeq2 1.32.0 ; Data were normalized using the DESeq2 normalization method

source_name: Ovary

extract_protocol:
RNA was extracted and purified using the TRIZOL technique (Invitrogen). RNA purity was confirmed by the A260/A280 and A260/A230 ratios of >1.8 and >2.0, respectively. RNA integrity of each sample was measured using an Agilent 2100 BioAnalyzer
RNA libraries were constructed using the Stranded mRNA Prep Ligation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

treatment_protocol: Two mixtures (doses 1, D1 and dose 2, D2) containing environmentally relevant doses of IBU/2hIBU + DCF + EE2 were added or not (control; C) to the drinking water of pregnant mice and their progeny from 8.5 days post-coitum (dpc) until animal sacrifice (8 week-old for females and 10 week-old for males)

value: Ovary


title: colonTreg_3-1_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-341-C-ra_A.RunAB.clonotypes.TRA.txt

tag: mouse (pool/culture no.)


title: 5-FU+Saline-2


title: h07C_P

value: adult

value: female

tag: disease state

value: Triple-receptor negative breast cancer


title: Female F2  (MaleDose2 x FemaleDose2) sample B

description: 100 nt


title: NIH3T3-IL-1-Rep_3

value: 0.2 ng/mL IL-1b


title: NIH3T3-LPS-Rep_1


title: NIH3T3-IL-1-Rep_2


title: h07B_P

value: Pembrolizumab


title: spleenTreg_7-5_noGvHD_Tcra_R1

description:
re-isolated
mTRA_248_Tx198-12-4214_S_rp_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: type

value: poly

tag: model

value: BMT control

value: spleen

value: alpha


title: spleenTreg_7-6_noGvHD_Tcra_R1

description:
re-isolated
mTRA_251_Tx198-12-4216_S_rp_A.RunAB.clonotypes.TRA.txt

tag: treg donor

tag: recipient


title: h07B_TCR


title: Control-3

value: long-term hematopoietic stem cells

value: C57BL/6 WT

value: Untreated


title: NIH3T3-IL-1-Rep_1

value: NIH3T3 immortalized MEFs


title: Female F2  (MaleDose2 x FemaleDose2) sample A

description: 100 nt


title: h06C_TCR

value: Breast

value: Pembrolizumab + Radiation


title: h07A_TCR

value: Baseline


title: spleenTreg_6-6_noGvHD_Tcra_R1

description:
re-isolated
mTRA_234_Tx198-10-4196_S_rp_A.RunAB.clonotypes.TRA.txt

tag: pcr1 cy. no.

tag: pcr2 cy. no.


title: h07A_P

value: adult


title: spleenTreg_7-4_noGvHD_Tcra_R1

description:
re-isolated
mTRA_254_Tx198-12-4205_S_rp_A.RunAB.clonotypes.TRA.txt

tag: chain

tag: techn. replicate


title: Female F2  (MaleDose2 x FemaleCTL) sample C

description: 100 nt

value: Ovary


title: spleenTreg_6-4_noGvHD_Tcra_R1

description:
re-isolated
mTRA_228_Tx198-10-4192_S_rp_AB.RunAB.clonotypes.TRA.txt


title: UD human keratinocytes, IgG for CUT&RUN

city: Evanston

first: Xiaomin

last: Bao

address: 633 Clark Street

department: Molecular Biosciences

institute: Northwestern University

library_source: genomic

data_processing:
For RNA-seq, adaptor trimming and quality control was performed using Trim Galore and FastQC, respectively. Alignment was performed using STAR and transcript quantification was performed using Salmon. Differential expression analysis was performed using DESeq2.
ChIP-seq adaptor trimming and quality control was performed using Trim Galore and FastQC, respectively. Alignment was performed using BWA-MEM. Bigwig files were generated using BEDTools and normalized based on counts per million reads. Differential analysis was performed using EdgeR via Diffbind.
Assembly: hg38
Supplementary files format and content: Processed RNA-seq data is presented as the DESeq2 output information, featuring the normalized counts for each gene.
Supplementary files format and content: Processed ChIP-seq data is presented as a bigWig file and/or MACS2 broadPeak file.

molecule: genomic DNA

source_name: Foreskin

growth_protocol: Keratinocytes were cultured from a mixture of multiple unidentified donors using a 1:1 mixture of Keratinocyte-SFM and 50% Medium 154. To induce differentiation, keratinocytes were seeded at 100% confluency and treated with 1.2 mM CaCl2 over 4 days.

extract_protocol:
RNA was extracted using Quick-RNA MiniPrep (Zymo Research) with DNase I treatment following the manufacturer protocol.
NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit were used to prepare RNA-seq libraries. NEBNext Ultra II DNA Library Prep Kit was used to prepare ChIP-seq and CUT&RUN libraries.

treatment_protocol: For the shRNA-mediated knockdown, shRNA lentivirus was added to the keratinocytes in addition to polybrene (20 ug/mL) and centrifuged at 1,250 rpm for 1 hour at 32oC. The keratinocytes were then selected with puromycin (2 ug/mL) for 48 hours.

value: Foreskin

tag: cell type

value: primary human neonatal keratinocytes

tag: genotype

value: UD control

value: Rabbit IgG (EpiCypher, 13-0042k)


title: h06C_P

tag: tissue

tag: age

value: female

value: Triple-receptor negative breast cancer


title: Female F2  (MaleDose2 x FemaleCTL) sample B

description: 100 nt

tag: treatment


title: Female F2  (MaleDose2 x FemaleCTL) sample A

description: 100 nt


title: UD human keratinocytes, PBRM1 sh3 for BRD7 CUT&RUN

value: UD PBRM1 knockdown

value: BRD7 (Bethyl, A700-221T)


title: spleenTreg_7-3_noGvHD_Tcra_R1

description:
re-isolated
mTRA_242_Tx198-12-4209_S_ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 Foxp3GFP+

value: allo

value: BMT control

value: spleen

value: alpha


title: spleenTreg_7-2_noGvHD_Tcra_R1

description:
re-isolated
mTRA_239_Tx198-12-4208_S_ra_A.RunAB.clonotypes.TRA.txt

tag: sampleID


title: h06B_P

value: Breast

tag: Sex

value: Pembrolizumab


title: h06B_TCR

value: adult

tag: disease state


title: Female F2  (MaleDose1 x FemaleCTL) sample C

description: 100 nt

value: Ovary


title: UD human keratinocytes, PBRM1 sh1 for BRD7 CUT&RUN

value: Foreskin


title: spleenTreg_6-5_noGvHD_Tcra_R1

description:
re-isolated
mTRA_231_Tx198-10-4193_S_rp_A.RunAB.clonotypes.TRA.txt

tag: mouse (pool/culture no.)

tag: type

value: poly


title: UD human keratinocytes, Control shB for BRD7 CUT&RUN (GFP)

value: primary human neonatal keratinocytes

value: UD control


title: h06A_TCR

value: female

value: Baseline


title: Female F2  (MaleDose1 x FemaleCTL) sample B

description: 100 nt


title: spleenTreg_7-1_noGvHD_Tcra_R1

description:
re-isolated
mTRA_245_Tx198-12-400_S_ra_A.RunAB.clonotypes.TRA.txt

tag: model

tag: treg donor


title: h06A_P

value: Triple-receptor negative breast cancer


title: Homozygous Untreated Replicate 1

city: New York

first: Sergei

last: Koralov

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU School of Medicine

data_processing:
Samples were sequenced using an sp100 Illumina Novaseq 6000 flow cell.
Reads were cleaned, trimmed, and then aligned using the STAR program.
featureCounts was used to generate count data for mapped reads.
Assembly: mm10
Supplementary files format and content: tab-delimited csv file

source_name: Bone Marrow

growth_protocol: At 8 weeks bone marrow was collected from mice and cultured for ~ 24 hours in alpha-MEM media. Following, non-adherent bone marrow progenitor cells were collected for RNA extraction.

extract_protocol:
Qiagen RNeasy Plus Micro Kit
RNA libraries were prepared using the Cloentech Low Input PolyA protocol

treatment_protocol: Mice received either no treatment or SCFA treatment in drinking water until about 8 weeks of age.

value: Bone Marrow

tag: cell line

value: Progenitors

value: R26STAT3Cstopfl/fl CD4Cre

value: Untreated


title: Female F2  (MaleCTL x FemaleDose2) sample C

description: 100 nt


title: Female F2  (MaleCTL x FemaleDose2) sample B

description: 100 nt


title: spleenTreg_6-2_noGvHD_Tcra_R1

description:
re-isolated
mTRA_222_Tx198-10-4183_S_ra_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

value: allo

value: BMT control

value: spleen

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.


title: UD human keratinocytes, PBRM1 sh2 for BRD7 CUT&RUN

tag: cell type

value: UD PBRM1 knockdown

value: BRD7 (Bethyl, A700-221T)


title: UD human keratinocytes, Control shA for BRD7 CUT&RUN (non-targeting)

value: Foreskin

tag: genotype


title: h05C_P

tag: tissue

value: Breast

value: adult

value: Pembrolizumab + Radiation


title: h05C_TCR

tag: age

value: female


title: spleenTreg_6-1_noGvHD_Tcra_R1

description:
re-isolated
mTRA_219_Tx198-10-4181_S_ra_A.RunAB.clonotypes.TRA.txt

tag: chain

value: alpha

tag: techn. replicate


title: DF human keratinocytes, PIAS1 shA

value: primary human neonatal keratinocytes

value: DF PIAS1 knockdown

tag: treatment


title: liverTreg_7-6_noGvHD_Tcra_R1

description:
re-isolated
mTRA_252_Tx198-12-4216_L_rp_AB.RunAB.clonotypes.TRA.txt

tag: strain

tag: sampleID

value: poly

value: liver


title: liverTreg_7-5_noGvHD_Tcra_R1

description:
re-isolated
mTRA_249_Tx198-12-4214_L_rp_AB.RunAB.clonotypes.TRA.txt

tag: mouse (pool/culture no.)


title: h05B_TCR

tag: Sex

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


title: DF human keratinocytes, Control shB for PIAS1 KD (GFP)

value: DF control


title: liverTreg_7-4_noGvHD_Tcra_R1

description:
re-isolated
mTRA_255_Tx198-12-4205_L_rp_AB.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: type

tag: model

value: BMT control

tag: treg donor


title: h05B_P


title: DF human keratinocytes, Control shA for PIAS1 KD (non-targeting)


title: Female F2  (MaleCTL x FemaleDose1) sample B

description: 100 nt

value: Ovary


title: Female F2  (MaleCTL x FemaleDose1) sample A

description: 100 nt


title: liverTreg_6-5_noGvHD_Tcra_R1

description:
re-isolated
mTRA_232_Tx198-10-4193_L_rp_AB.RunAB.clonotypes.TRA.txt

tag: recipient

tag: pcr1 cy. no.


title: h05A_TCR

value: Baseline


title: DF human keratinocytes, PIAS1 shB

value: Foreskin

tag: cell type


title: h04C_TCR

value: Breast


title: CA95_3_DHT

city: Rochester

first: Liewei

last: Wang

state: MN

address: 200 2st Str SW

department: Neurology

institute: Mayo Clinic

description:
CA95_3
AR_PGxeQTL_rawcount.txt

data_processing:
Raw RNA sequencing reads were aligned to the human genome GRCh37 (hg19) using STAR[24], and gene counts were performed using HTSEQ
Assembly: GRCh37
Supplementary files format and content: tab deliminated text file of gene counts per sample

source_name: Blood

growth_protocol: LCLs were cultured in RPMI 1640 supplemented with 15% FBS and 1% penicillin/streptomycin, under 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted with the RNeasy RNA extraction kit per manufacturer's instruction (Qiagen). RNA integrity was examined by Agilent Bioanalyzer
polyA enrichment; RNA-seq libraries were prepared with the TruSeq2 RNA Library Prep Kit v2 (Illumina).

treatment_protocol: Prior to DHT/Enz treatment, all cells were grown in 5% charcoal-stripped media for 24 h, then either DHT in Ethanol (final concentration 10nM) or Enz in DMSO (final concentration 100nM), combination of both drugs, or pure vehicle of 0.1%DMSO/0.1%Ethanol was added to the culture and incubated for 8 hours before harvesting by centrifugation and snap frozen in trizol lysis buffer.

value: Blood

tag: cell line

value: B lymphoblastoid cell line

value: DHT


title: liverTreg_6-6_noGvHD_Tcra_R1

description:
re-isolated
mTRA_235_Tx198-10-4196_L_rp_AB.RunAB.clonotypes.TRA.txt

tag: tissue

tag: pcr2 cy. no.

value: alpha


title: liverTreg_6-4_noGvHD_Tcra_R1

description:
re-isolated
mTRA_229_Tx198-10-4192_L_rp_AB.RunAB.clonotypes.TRA.txt

tag: chain


title: Female F2  (MaleDose1 x FemaleCTL) sample A

description: 100 nt


title: Female F2  (MaleCTL x FemaleCTL) sample C

description: 100 nt


title: Female F2  (MaleCTL x FemaleDose2) sample A

description: 100 nt


title: liverTreg_7-3_noGvHD_Tcra_R1

description:
re-isolated
mTRA_243_Tx198-12-4209_L_ra_AB.RunAB.clonotypes.TRA.txt

value: allo

tag: techn. replicate


title: CA95_2_Enz

description:
CA95_2
AR_PGxeQTL_rawcount.txt

tag: treatment

value: Enz


title: h05A_P

tag: age

value: adult

value: female


title: h04C_P

value: Pembrolizumab + Radiation


title: Female F2  (MaleCTL x FemaleCTL) sample A

description: 100 nt


title: AML, Sample 1

city: Philadelphia

first: Peter

last: Kurre

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

data_processing:
Cell Ranger 7.0.1. was used to map the sequencing data. Cell Ranger consists of a set of analysis pipelines developed by 10x Genomics to process the single-cell RNA-sequencing output. The raw sequencing data (FASTQ files) was mapped to the mouse reference genome 2020-A (GRCm38, GENCODE vM23/Ensembl 98), provided by 10x Genomics, using the cellranger count pipeline. For the downstream analysis, the filtered count matrices were used.
Preprocessing:  The data from all samples were loaded in R (version 4.2.2) and processed using the Seurat package (version 4.3.0 – Hao et al. Cell 2021). Cells with low UMI counts were filtered out. The filtering thresholds were determined independently for each library to exclude outliers (A1: 1800 UMIs/cell; A2: 3000 UMIs/cell; A3: 1800 UMIs/cell; B1: 2000 UMIs/cell; B3: 2000 UMIs/cell). Cells with more than 10% mitochondrial genes were also removed. Cells from library B2 were excluded due to the low quality of the library.  The dataset was normalized for sequencing depth per cell and log-transformed using a scaling factor of 10,000. Principal component analysis (PCA) was performed on the 2,000 most variable features. The first 29 PCs were used to generate the UMAP. Cell cycle was scored using the CellCycleScoring function of Seurat. Inspection of the UMAP revealed differential distribution assigned to cell cycle. Cell cycle effects were then regressed out using the vars.to.regress parameter in Seurat’s ScaleData function. After regression, principal component analysis (PCA) was performed again on the 2,000 most variable features, and the first 27 PCs were used for dimensionality reduction and clustering. Batch effects between libraries were removed using the Harmony package (version 0.1.1).
Pseudobulk analysis: Differentially expressed genes between conditions (AML vs PBS) were calculated using the Wilcoxon rank sum test as implemented in the FindAllMarkers function in Seurat with parameters logfc.threshold = 0.1, return.thresh = 0.01 and min.pct = 0.1. We then performed an over-representation analysis of the significantly differentially expressed genes using the enricher function in the clusterProfiler package (version 4.6.2) with the collections “MH: hallmark gene sets”, “M2: curated gene sets”, “M5: ontology gene sets” and “M8: cell type signature gene sets” from the Mouse Molecular Signatures Database.
Cell type annotation and differential expression analysis:  We annotated cells using gene signatures for HSPCs identified in Pietras et al, 2015. The gene signature for each population was defined by the top 100 genes ranked by the Significance Analysis of Microarrays (SAM) scores. We calculated a module score for each cell based on the average expression levels of every gene signature, subtracted by the aggregated expression of randomly selected control genes using Seurat’s AddModuleScore function. Each cell was assigned to the population with the highest positive score. Cells with only negative scores were annotated as “Unclassified”. Differentially expressed genes between conditions (AML vs PBS) per cell type were calculated using the Wilcoxon rank sum test as implemented in the FindAllMarkers function in Seurat with parameters logfc.threshold = 0.25, return.thresh = 0.01 and min.pct = 0.1. Over-representation analysis of the resulting gene lists was performed using the collections “MH: hallmark gene sets”, “M2: curated gene sets” and “M5: ontology gene sets”.
Assembly: mm10-2020-A
Supplementary files format and content: tab separated values and matrix files

source_name: Bone marrow

growth_protocol: C1498 cells were cultured in vitro using DMEM media supplemented with 10% FBS and 1% P/S.

extract_protocol:
At sacrifice, hind legs were dissected and bone marrow (BM) cells were harvested by flushing both femur and tibia. Whole BM cells were subjected to RBC lysis and were lineage-depleted using a magnetic-activated cell sorting (MACS)-based method with EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (StemCell Technologies). Lineage-depleted BM cells were stained and HSPCs were fluorescence-activated cell sorting (FACS)-sorted using the FACSAria Fusion sorter (BD). RNA were extracted from HSPCs using RNeasy Micro Plus Kit (Qiagen) according to manufactuer's protocol.
Library were constructed using Chromium GEM V3 chemistry (10X Genomics) according to manufacturer's protocol

value: Bone marrow

value: N/A - in vivo

value: HSPC (Lin- cKit+ Sca1+)

tag: genotype

value: C1498 AML


title: CA95_4_EnzDHT

description:
CA95_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: h04B_TCR

value: Pembrolizumab

value: Triple-receptor negative breast cancer


title: Female F2  (MaleCTL x FemaleDose1) sample C

description: 100 nt

value: Ovary


title: liverTreg_6-3_noGvHD_Tcra_R1

description:
re-isolated
mTRA_226_Tx198-10-4190_L_ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

value: BMT control

value: liver


title: h04B_P

value: Breast

tag: Sex

tag: disease state


title: h04A_TCR

value: Baseline


title: CA93_3_DHT

description:
CA93_3
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line

value: DHT


title: Female F1  Dose 2 sample B

description: 100 nt

value: Dose 2


title: Female F1  Dose 2 sample A

description: 100 nt


title: Female F1  Dose 2 sample C

description: 100 nt


title: liverTreg_7-2_noGvHD_Tcra_R1

description:
re-isolated
mTRA_240_Tx198-12-4208_L_ra_AB.RunAB.clonotypes.TRA.txt

tag: type

value: allo

tag: model

tag: treg donor

value: alpha


title: CA93_4_EnzDHT

description:
CA93_4
AR_PGxeQTL_rawcount.txt

tag: cell type


title: liverTreg_7-1_noGvHD_Tcra_R1

description:
re-isolated
mTRA_246_Tx198-12-400_L_ra_AB.RunAB.clonotypes.TRA.txt

tag: recipient

tag: pcr1 cy. no.


title: CA93_2_Enz

description:
CA93_2
AR_PGxeQTL_rawcount.txt

tag: tissue

tag: cell line

value: Enz


title: CA95_1_Veh

description:
CA95_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: CA90_4_EnzDHT

description:
CA90_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: h04A_P

value: adult

value: female


title: h03C2_P

value: Pembrolizumab + Radiation

value: Triple-receptor negative breast cancer


title: CA90_3_DHT

description:
CA90_3
AR_PGxeQTL_rawcount.txt


title: Female F1  Dose 1 sample A

description: 100 nt

value: Ovary

value: Dose 1


title: CA93_1_Veh

description:
CA93_1
AR_PGxeQTL_rawcount.txt


title: liverTreg_6-2_noGvHD_Tcra_R1

description:
re-isolated
mTRA_223_Tx198-10-4183_L_ra_AB.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

value: BMT control

value: liver

tag: pcr2 cy. no.

tag: chain

tag: techn. replicate


title: h03C2_TCR

value: Breast

tag: age

tag: treatment


title: Female F2  (MaleCTL x FemaleCTL) sample B

description: 100 nt


title: Female F1  Dose 1 sample C

description: 100 nt


title: liverTreg_6-1_noGvHD_Tcra_R1

description:
re-isolated
mTRA_220_Tx198-10-4181_L_ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

tag: sampleID


title: colonTreg_7-5_noGvHD_Tcra_R1

description:
re-isolated
mTRA_250_Tx198-12-4214_C_rp_A.RunAB.clonotypes.TRA.txt

tag: mouse (pool/culture no.)

value: poly

value: colon


title: Female F1  Dose 1 sample B

description: 100 nt


title: colonTreg_7-6_noGvHD_Tcra_R1

description:
re-isolated
mTRA_253_Tx198-12-4216_C_rp_A.RunAB.clonotypes.TRA.txt


title: CA90_2_Enz

description:
CA90_2
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line


title: h03B2_TCR

tag: Sex

value: Pembrolizumab

tag: disease state


title: h03B2_P


title: CA90_1_Veh

description:
CA90_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: h03B1_TCR


title: CA87_4_EnzDHT

description:
CA87_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: Female F1  Control sample B

description: 100 nt


title: colonTreg_6-6_noGvHD_Tcra_R1

description:
re-isolated
mTRA_236_Tx198-10-4196_C_rp_A.RunAB.clonotypes.TRA.txt

tag: type

tag: model

value: alpha


title: colonTreg_7-4_noGvHD_Tcra_R1

description:
re-isolated
mTRA_256_Tx198-12-4205_C_rp_A.RunAB.clonotypes.TRA.txt

tag: treg donor


title: Female F1  Control sample C

description: 100 nt


title: colonTreg_6-5_noGvHD_Tcra_R1

description:
re-isolated
mTRA_233_Tx198-10-4193_C_rp_A.RunAB.clonotypes.TRA.txt

tag: recipient


title: colonTreg_6-4_noGvHD_Tcra_R1

description:
re-isolated
mTRA_230_Tx198-10-4192_C_rp_A.RunAB.clonotypes.TRA.txt

tag: pcr1 cy. no.


title: CA87_3_DHT

description:
CA87_3
AR_PGxeQTL_rawcount.txt

tag: tissue

tag: cell type

value: DHT


title: h03B1_P

value: adult

value: female


title: h03A2_TCR

value: Baseline

value: Triple-receptor negative breast cancer


title: CA87_2_Enz

description:
CA87_2
AR_PGxeQTL_rawcount.txt

tag: cell line

value: Enz


title: colonTreg_7-3_noGvHD_Tcra_R1

description:
re-isolated
mTRA_244_Tx198-12-4209_C_ra_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

value: allo

value: BMT control

tag: pcr2 cy. no.

tag: chain


title: CA87_1_Veh

description:
CA87_1
AR_PGxeQTL_rawcount.txt


title: Male F2  (MaleDose2 x FemaleDose2) sample A

description: 100 nt

source_name: Testis

value: Testis


title: h03A2_P

value: Breast

tag: age


title: Male F2  (MaleDose2 x FemaleDose2) sample B

description: 100 nt

tag: treatment


title: h03A1_TCR


title: Male F2  (MaleDose2 x FemaleCTL) sample C

description: 100 nt


title: h03A1_P


title: colonTreg_7-2_noGvHD_Tcra_R1

description:
re-isolated
mTRA_241_Tx198-12-4208_C_ra_A.RunAB.clonotypes.TRA.txt

tag: strain

value: colon

tag: techn. replicate


title: colonTreg_7-1_noGvHD_Tcra_R1

description:
re-isolated
mTRA_247_Tx198-12-400_C_ra_A.RunAB.clonotypes.TRA.txt

tag: sampleID

tag: mouse (pool/culture no.)


title: Female F1  Control sample A

description: 100 nt

value: Ovary


title: colonTreg_6-3_noGvHD_Tcra_R1

description:
re-isolated
mTRA_227_Tx198-10-4190_C_ra_AB.RunAB.clonotypes.TRA.txt


title: Male F2  (MaleDose2 x FemaleCTL) sample B

description: 100 nt


title: h02C_TCR

tag: Sex

value: Pembrolizumab + Radiation

tag: disease state


title: CA86_2_Enz

description:
CA86_2
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line


title: Male F2  (MaleDose2 x FemaleCTL) sample A

description: 100 nt


title: CA86_4_EnzDHT

description:
CA86_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: h02C_P


title: colonTreg_6-2_noGvHD_Tcra_R1

description:
re-isolated
mTRA_224_Tx198-10-4183_C_ra_AB.RunAB.clonotypes.TRA.txt

tag: type

tag: model

value: alpha


title: Male F2  (MaleDose2 x FemaleDose2) sample C

description: 100 nt


title: colonTreg_6-1_noGvHD_Tcra_R1

description:
re-isolated
mTRA_221_Tx198-10-4181_C_ra_A.RunAB.clonotypes.TRA.txt

tag: treg donor

tag: recipient


title: Male F2  (MaleDose1 x FemaleCTL) sample C

description: 100 nt

tag: tissue


title: Male F2  (MaleDose1 x FemaleCTL) sample B

description: 100 nt


title: CA84_4_EnzDHT

description:
CA84_4
AR_PGxeQTL_rawcount.txt

tag: cell type


title: h02B_TCR

value: adult

value: Pembrolizumab


title: h02B_P

value: female


title: polyTreg_7_donor_Tcra_R1

description:
expanded
mTRA_238_Tx198-12-245_d12_rp_A.RunAB.clonotypes.TRA.txt

value: poly

value: in vitro

value: donor

tag: pcr1 cy. no.


title: CA84_3_DHT

description:
CA84_3
AR_PGxeQTL_rawcount.txt

tag: cell line

value: DHT


title: h02A_TCR

value: Baseline

value: Triple-receptor negative breast cancer


title: Male F2  (MaleDose1 x FemaleCTL) sample A

description: 100 nt

value: Testis


title: Male F2  (MaleCTL x FemaleDose2) sample C

description: 100 nt


title: CA86_3_DHT

description:
CA86_3
AR_PGxeQTL_rawcount.txt


title: CA84_2_Enz

description:
CA84_2
AR_PGxeQTL_rawcount.txt

value: Enz


title: polyTreg_4_donor_Tcra_R1

description:
expanded
mTRA_103_Tx198-4-208_d11_rp_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: pcr2 cy. no.

tag: chain


title: CA84_1_Veh

description:
CA84_1
AR_PGxeQTL_rawcount.txt

tag: treatment

value: Veh


title: Male F2  (MaleCTL x FemaleDose2) sample B

description: 100 nt


title: h01C_TCR

value: Breast

tag: age

value: Pembrolizumab + Radiation


title: polyTreg_3_donor_Tcra_R1

description:
expanded
mTRA_Tx198-2-d12-rp_AB.RunAB.clonotypes.TRA.txt

tag: strain

tag: techn. replicate


title: Male F2  (MaleCTL x FemaleDose2) sample A

description: 100 nt


title: CA86_1_Veh

description:
CA86_1
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line


title: polyTreg_2_donor_Tcra_R1

description:
expanded
mTRA_Tx198-1-d13-rp_AB.RunAB.clonotypes.TRA.txt

tag: sampleID

tag: mouse (pool/culture no.)

value: alpha


title: h01C_P

value: adult

tag: Sex

tag: disease state


title: h02A_P

value: female


title: CA79_4_EnzDHT

description:
CA79_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: Male F2  (MaleCTL x FemaleDose1) sample C

description: 100 nt


title: CA79_3_DHT

description:
CA79_3
AR_PGxeQTL_rawcount.txt


title: polyTreg_1_donor_Tcra_R1

description:
expanded
mTRA_176_Treg_d14_poly_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 WT

tag: type

value: poly

tag: model

value: in vitro


title: CA79_2_Enz

description:
CA79_2
AR_PGxeQTL_rawcount.txt


title: alloTreg_7_donor_Tcra_R1

description:
expanded
mTRA_237_Tx198-12-245_d12_ra_A.RunAB.clonotypes.TRA.txt

value: allo

value: donor

tag: treg donor

tag: recipient


title: polyTreg_6_donor_Tcra_R1

description:
expanded
mTRA_218_Tx198-10-241_d12_rp_A.RunAB.clonotypes.TRA.txt

tag: tissue


title: h01A_TCR

value: Baseline

value: Triple-receptor negative breast cancer


title: h01A_P


title: alloTreg_6_donor_Tcra_R1

description:
expanded
mTRA_217_Tx198-10-241_d12_ra_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: pcr1 cy. no.


title: Male F2  (MaleCTL x FemaleCTL) sample C

description: 100 nt

value: Testis


title: CA79_1_Veh

description:
CA79_1
AR_PGxeQTL_rawcount.txt

tag: cell line

tag: cell type

value: Veh


title: CA77_4_EnzDHT

description:
CA77_4
AR_PGxeQTL_rawcount.txt


title: ES2 cells, ASO-IT1-3

city: Beijing

first: Pengfei

last: Zhao

address: No.17, Panjiayuan Nanli, South Huawei Road

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
We conducted quality control on the raw data from high-throughput sequencing platforms using FastQC (v0.11.9) (Andrews, 2010).
Subsequently, we employed fastp (v0.22.0) (Chen Shifu et al., 2018) to trim and remove potential sequencing adapters from the raw sequencing data (raw reads).
This process also involved eliminating reads with low-quality bases and those with a high ratio of ambiguous bases in the original sequences. After quality control, reads with a minimum length of 75 base pairs were retained as clean reads for subsequent bioinformatics analysis pipelines.
Assembly: GRCh38

growth_protocol: ES2 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA purification, reverse transcription, library construction and sequencing were performed in Sequanta Technologies Co., Ltd at Shanghai according to the manufacturer's instructions.
The mRNA-focused sequencing libraries from 1µg total RNA were prepared using Illumina VAHTS® Universal V6 RNA-seq Library Prep Kit (Vazyme).

value: epithelial ovarian cancer cells

tag: genotype

value: RUNX1-IT1 knockdown


title: CA77_3_DHT

description:
CA77_3
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line

tag: treatment

value: DHT


title: alloTreg_4_donor_Tcra_R1

description:
expanded
mTRA_102_Tx198-4-208_d11_ra_A.RunAB.clonotypes.TRA.txt

tag: pcr2 cy. no.

tag: chain

value: alpha


title: alloTreg_3_donor_Tcra_R1

description:
expanded
mTRA_Tx198-2-d12-ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

tag: techn. replicate


title: ES2 cells, ASO-IT1-2


title: Male F2  (MaleCTL x FemaleCTL) sample A

description: 100 nt


title: Male F2  (MaleCTL x FemaleCTL) sample B

description: 100 nt


title: Male F2  (MaleCTL x FemaleDose1) sample A

description: 100 nt


title: CA77_1_Veh

description:
CA77_1
AR_PGxeQTL_rawcount.txt


title: alloTreg_2_donor_Tcra_R1

description:
expanded
mTRA_Tx198-1-d13-ra_AB.RunAB.clonotypes.TRA.txt

tag: sampleID

tag: mouse (pool/culture no.)


title: Male F2  (MaleCTL x FemaleDose1) sample B

description: 100 nt


title: CA71_4_EnzDHT

description:
CA71_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: ES2 cells, ASO-IT1-1


title: Lung, AT2 origin, Pten H1047R, chromatin, rep 2

city: NEW YORK

first: Ashley

middle: M

last: Laughney

state: New York

address: 413 East 69th Street

department: Physiology, Biophysics, and Systems Biology

institute: Weill Cornell Medicine

data_processing:
Bulk ATAC-seq raw reads were processed using the standard nf-core ATAC-seq pipeline. Library quality was assessed using the nf-core quality-control report unique mapped reads, GC-content, and peak annotation. Loess normalization was used for differential accessibility testing to minimize technical batch effects.
Assembly: mm10
Supplementary files format and content: .txt: comma separated text file. This contains the consensus peak annotations for  ATAC chromatin peaks across all replicates.

source_name: Lung

extract_protocol:
Established Omni-ATAC extraction protocol
Established Omni-ATAC library construction protocol

value: Lung


title: alloTreg_1_donor_Tcra_R1

description:
expanded
mTRA_196_Treg_d14_allo_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 WT


title: ES2 cells, ASO-C-3

value: Control


title: CA71_3_DHT

description:
CA71_3
AR_PGxeQTL_rawcount.txt


title: Male F1  Dose 2 sample A

description: 100 nt

value: Dose 2


title: Lung, AT2 origin, Pten H1047R, chromatin, rep 1


title: Male F1  Dose 1 sample C

description: 100 nt

value: Dose 1


title: Lung, AT2 origin, Pten E545K, chromatin, rep 2


title: CA77_2_Enz

description:
CA77_2
AR_PGxeQTL_rawcount.txt

value: Enz


title: 19994X64 infiltrative BCC

city: Salt Lake City

first: Doug

last: Grossman

state: Utah

address: Huntsman Cancer Institute, 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 106 and a reference database was created using STAR version 2.7.9a
A custom Perl script (smallRNA_pe_umi_extractor.pl) from https://github.com/HuntsmanCancerInstitute/UMIScripts was used to trim adapters and extract the Unique Molecular Index (UMI)
The trimmed reads were aligned to the reference database using STAR options optimized for shorter miRNA reads
A second Perl script (bam_umi_dedup.pl) removed PCR duplicates from the aligned BAM file
Mapped reads were assigned to miRNAs in miRbase release 22.1 using featureCounts version 1.6.3
Differentially expressed miRNA in miRbase were identified using a 5% false discovery rate with DESeq2 version 1.36.0
Assembly: GRCm39
Supplementary files format and content: FeatureCount ouput files combined into a single tab-delimited count matrix

source_name: skin

extract_protocol:
Whole RNA was isolated using a RecoverAll kit (Thermo Fisher Scientific, AM1975), quantitated by ScreenTape Assay (Agilent), converted to cDNA  for sequencing.
Small RNA sequencing libraries were prepared from 10-100 ng of total RNA using the Qiagen QIAseq miRNA Library Kit

value: infiltrative BCC


title: Lung, AT2 origin, Pten E545K, chromatin, rep 1


title: Male F1  Dose 1 sample B

description: 100 nt


title: CA71_2_Enz

description:
CA71_2
AR_PGxeQTL_rawcount.txt


title: CA70_4_EnzDHT

description:
CA70_4
AR_PGxeQTL_rawcount.txt


title: 19994X63 infiltrative BCC


title: 19994X62 infiltrative BCC


title: Male F1  Dose 2 sample C

description: 100 nt


title: Male F1  Dose 1 sample A

description: 100 nt


title: ES2 cells, ASO-C-2


title: Male F1  Control sample C

description: 100 nt


title: Lung, AT2 origin, Pten loss, chromatin, rep 2


title: Male F1  Dose 2 sample B

description: 100 nt


title: 19994X61 infiltrative BCC


title: Lung, AT2 origin, Pten loss, chromatin, rep 1


title: CA70_2_Enz

description:
CA70_2
AR_PGxeQTL_rawcount.txt


title: 19994X60 infiltrative BCC


title: Male F1  Control sample B

description: 100 nt


title: Lung, AT2 origin, WT, chromatin, rep 2


title: Male F1  Control sample A

description: 100 nt


title: 19994X59 infiltrative BCC


title: ES2 cells, ASO-C-1


title: Lung, AT2 origin, WT, chromatin, rep 1


title: CA70_1_Veh

description:
CA70_1
AR_PGxeQTL_rawcount.txt


title: 19994X58 infiltrative BCC


title: CA67_4_EnzDHT

description:
CA67_4
AR_PGxeQTL_rawcount.txt


title: CA71_1_Veh

description:
CA71_1
AR_PGxeQTL_rawcount.txt


title: CA67_3_DHT

description:
CA67_3
AR_PGxeQTL_rawcount.txt


title: Lung, de novo LUAD, chromatin, rep 3


title: 18913X3, MC38 Tumor-infiltrating CD45+ cells, B. uniformis gavage, female

first: W. Zac

last: Stephens

state: UT

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

institute: University of Utah

description: 10X Genomics

data_processing:
Reads were first demultiplexed then count matrices created with with 10X Genomics Cell Ranger pipeline
Assembly: mm10
Supplementary files format and content: 3 files are provided for each sample, in one archive. The cell barcodes, the gene identifiers and the matrix of counts.

source_name: tumor

extract_protocol:
MC38 tumors stained with CD45-PE and MACS sorted for CD45+ cells, then RNA was extracted according to the 10x Genomics 5' Expression library kit.
Libraries were prepared according to the 10x Genomics 5' Expression kit.

value: tumor

value: B. uniformis gavage


title: 18913X4, MC38 Tumor-infiltrating CD45+ cells, B. uniformis gavage, male

description: 10X Genomics


title: 19994X57 infiltrative BCC


title: 19994X56 infiltrative BCC


title: CA67_2_Enz

description:
CA67_2
AR_PGxeQTL_rawcount.txt


title: Lung, de novo LUAD, chromatin, rep 2


title: 18913X1, MC38 Tumor-infiltrating CD45+ cells, PBS gavage, female

description: 10X Genomics

value: PBS gavage


title: 19994X55 infiltrative BCC


title: Lung, AT2 origin, SCLC genotype, chromatin, pooled


title: 19994X54 infiltrative BCC


title: Lung, de novo LUAD, chromatin, rep 1


title: CA66_3_DHT

description:
CA66_3
AR_PGxeQTL_rawcount.txt


title: CA67_1_Veh

description:
CA67_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: 19994X53 infiltrative BCC


title: CA66_2_Enz

description:
CA66_2
AR_PGxeQTL_rawcount.txt


title: CA70_3_DHT

description:
CA70_3
AR_PGxeQTL_rawcount.txt


title: 19994X52 infiltrative BCC


title: Lung, de novo SCLC, chromatin, rep 1

value: PNEC-RPMT


title: Dbp mouse submandibular gland replicate 1 Cut-taq

city: shenzhen

first: yang

last: kaibin

address: No.1066 Xueyuan Road, Nanshan District

institute: shenzhen university

description:
Dbp rep1
The submandibular gland of  control mice

data_processing:
bowtie2
hisat2
samtools
cufflinks
bowtie2
Assembly: mm10
Supplementary files format and content: text files include FPKM values for each sample
Supplementary files format and content: bigWig files were generated from bed files using bamCoerage tool
Supplementary files format and content: BED (Browser Extensible Data)
Library strategy: CUT&tag

source_name: submandibular gland

extract_protocol:
For RNA-seq, we euthanized mice aged 6-8 weeks using the neck dislocation method, cut the skin along the neck to expose the submandibular gland, and then remove the gland tissue. Total RNAs were extracted using the Trizol method. Library construction and sequencing were performed on the DNBSEQ-T7 platform at the Geneplus Co, Shenzhen, China. Final data were presented as FPKM value for each gene. Tissue samples were collected at ZT3, ZT9 and ZT15 (10:00 am, 4:00 pm, and 10:00 pm).
For Cut-taq, the mouse submandibular gland was minced and digested with Worthington Collagenase I at 0.2% concentration for 25-30 minutes at 37°C. The sample was filtered through a Falcon 40um filter, and the remaining tissue was incubated with 1x Gibco Trypsin/EDTA at 37°C for 20 minutes. After filtration, the sample was resuspended in PBS and centrifuged at 500 g for 5 minutes to obtain the supernatant. Standard operations were performed according to the instructions ofTD901-TD902 from Hyperactive In-Situ Chip Library Prep Kit for IIIumina. The 150 bp paired-end DNA sequencing was performed on the Illumina NovaSeq 6000 system (Haplox Genomics Center, Jiangxi, China).
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kitfor Illumina following manufacturer's protocols.
The 150 bp paired-end DNA sequencing was performed on the Illumina NovaSeq 6000 system (HaploX Genomics Center, Jiangxi, China) according to the manufacturer's instructions.
Library was performed according to the manufacter’s instructions (Single Cell RNA Library Kit Cell/Tissue for Matrix V2 protocol GEXSCOPE). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: submandibular gland

value: Dbp mouse


title: 19994X51 infiltrative BCC


title: Nr1d1 mouse submandibular gland replicate 2 Cut-taq

description:
Nr1d1 rep2
The submandibular gland of  control mice

value: Nr1d1 mouse


title: CA66_1_Veh

description:
CA66_1
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line


title: Lung, PNEC origin, LUAD genotype, chromatin, pooled

value: Lung

value: PNEC-ERPMT


title: 18913X2, MC38 Tumor-infiltrating CD45+ cells, PBS gavage, male

description: 10X Genomics


title: Nr1d1 mouse submandibular gland replicate 1 Cut-taq

description:
Nr1d1 rep1
The submandibular gland of  control mice


title: CA63_4_EnzDHT

description:
CA63_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: 19994X50 infiltrative BCC


title: 19994X49 infiltrative BCC


title: Bmal1 mouse submandibular gland replicate 2 Cut-taq

description:
Bmal1 rep2
The submandibular gland of  control mice

value: Bmal1 mouse


title: Bmal1 mouse submandibular gland replicate 1 Cut-taq

description:
Bmal1 rep1
The submandibular gland of  control mice


title: mutant 3, E10.5, FNP/MxP

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

data_processing:
Following sequencing, reads were demultiplexed, and FASTQ files processed using two distinct bioinformatic pipelines. Two pipelines were used to help reduce false positives. In the first approach, FASTQ files were mapped to the mm10 genome using STAR Aligner (Dobin et al., 2013) with default settings. Gene expression was then quantified using StringTie (Pertea et al., 2016; Pertea et al., 2015), with the following settings: -e (expression estimation mode), -G (mm10 reference annotation file), -A (gene abundances). Following quantification, count matrices were produced using the prepDE.py script, available from StringTie, and used as input for DESeq2 (Love et al., 2014). Differential gene expression analysis was conducted in DESeq2 using the DESeqDataSetFromMatrix function. For the second approach, FASTQ files were pseudo-aligned to the mm10 genome using the kallisto (Bray et al., 2016) quant function with the following settings: -b 50, --single, -l 100, -s 20. After alignment, differential gene expression analysis was conducted using sleuth (Pimentel et al., 2017), along with the sleuth_prep function and the following settings: full_model = genotype, gene_model = TRUE, read_bootstrap_tpm = TRUE, extra_bootstrap_summary = TRUE, transformation_function = function(x) log2(x + 0.05)). The resulting ‘sleuth object’ was then subjected to the sleuth_fit function, followed by the sleuth_wt function to calculate differentially expressed genes between genotypes. The kallisto-sleuth pipeline output was used, along with ggplot2 (Wickham, 2016) and ggrepel, to generate and visualize differentially expressed genes by volcano plot. Genes that both had, 1) a fold-change greater or less than +1.25 or -1.25, respectively, and an adjusted p-value less than 0.05 (pipeline 1), and 2) a q-value less than 0.1 (pipeline 2) (Table S1), were used for ontology, enrichment, and pathway analysis using the Enrichr platform (Chen et al., 2013; Kuleshov et al., 2016; Xie et al., 2021).
Assembly: mm10

source_name: Microdissected frontonasal and maxillary prominence

extract_protocol: Tissue preparation, cDNA library generation, and sequencing: E10.5 bulk frontonasal and maxillary prominence tissue from three control and three Tfap2Δ/NCKO littermates were processed for RNA-seq as previously described (Van Otterloo et al., 2016). After PCR-genotyping, samples stored in RNAlater (ThermoFisher) were processed for RNA (Norgen Biotek) and further purified with the RNAeasy kit (Qiagen). mRNA quality was determined with DNA Analysis ScreenTape (Agilent Technologies), and cDNA libraries were generated using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina). Samples were sequenced on the Illumina HiSeq2500 platform as 150-bp single-end reads. Library construction and sequencing was carried out by the Genomics and Microarray Core on the University of Colorado Anschutz Medical Campus.

value: Tfap2a;Tfap2b;Wnt1CRE mutant


title: E11.5 FNP/MxP/MdP sonicated chromatin, Input

data_processing:
Following sequencing and demultiplexing, FASTQ files were mapped to the mm10 genome using BWA (Li and Durbin, 2009), followed by sam to bam file conversion using Samtools (Li et al., 2009). To identify ‘enriched’ regions (i.e., regions with significantly more reads in the TFAP2 IP versus input), MACS2 (Zhang et al., 2008) was utilized with the following settings: -f BAM, -g mm, --keep-dup 2 (Table S2, Tab 3). Motif and peak annotation were completed using the findMotifsGenome.pl and the annotatePeaks.pl functions in HOMER (Heinz et al., 2010). Heatmap visualization of enriched regions was completed using the bamCoverage, computeMatrix and plotHeatmap function in deepTools (Ramirez et al., 2016), with the following settings: -of ‘bigwig’, --ignoreDuplicates, -bs 25, --normalizeUsing RPKM (for bamCoverage); reference-point, -b 3000, -a 3000 –referencePoint center (for computeMatrix); --whatToShow ‘heatmap and colorbar’, --missingDataColor 1, --kmeans 7, --refPointLabel “peak” (for plotHeatmap). For computeMatrix (Fig. 5E) the following scaled bigwig datasets were downloaded from GEO (Barrett et al., 2013) and used (along with the MACS2 generated ‘TFAP2-bound’ bed file): GSM2371708, E10.5 frontonasal prominence H3K4me2; GSM2371717, E10.5 frontonasal prominence H3K27ac; GSM2371732, E10.5 frontonasal prominence ATAC-seq; GSM2371713, E10.5 frontonasal prominence H3K27me3 (peak-cluster annotations in Table S2, Tab 3) (Minoux et al., 2017). Additional datasets used for analysis included: GSM2371710, E10.5 mandibular prominence H3K4me2; GSM2371719, E10.5 mandibular prominence H3K27ac; GSM2371734, E10.5 mandibular prominence ATAC-seq; GSM2371715, E10.5 mandibular prominence H3K27me3. The Integrative Genomics Viewer (Robinson et al., 2011) was used for gene level visualization of these datasets at Alx1/3/4 loci. Pathway analysis was conducted using GREAT (McLean et al., 2010) with the following setting: ‘Basal plus extension’, ‘Proximal 5 kb upstream, 1 kb downstream, plus Distal: up to 100 kb’.
Assembly: mm10

source_name: Microdissected frontonasal, maxillary, and mandibular prominences

extract_protocol: Chromatin immunoprecipitation (ChIP) was conducted, essentially as previously described (Van Otterloo et al., 2022), with the exception that full facial prominences were used, rather than just isolated ectoderm. Further modifications included the use of an anti-TFAP2A antibody (5 µg of sc-184, Santa Cruz Biotechnology) and Dynabeads (ThermoFisher Scientific). Following precipitation and subsequent quality control analysis (ScreenTape analysis, Agilent), samples (i.e., sc-184 IP and input DNA) were sequenced on the Illumina HiSeq 2500 platform as 150-bp single-end reads. Library construction and sequencing was carried out by the Genomics and Microarray Core at the University of Colorado Anschutz Medical Campus.

tag: age

value: wild-type

tag: antibody

value: none (input)


title: E11.5 FNP/MxP/MdP sonicated and SC184 immunoprecipated chromatin

value: Microdissected frontonasal, maxillary, and mandibular prominences


title: mutant 2, E10.5, FNP/MxP

value: Microdissected frontonasal and maxillary prominence


title: CA63_2_Enz

description:
CA63_2
AR_PGxeQTL_rawcount.txt

value: Enz


title: 3T3_met50

city: Guangzhou

first: Yicong

last: Xu

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

description: The 50% methanol-fixed cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

data_processing:
The adapter sequences and low-quality reads were removed using fastp.
The processed reads were aligned to the genome using STAR.
The duplicate reads with identical sequences were removed using Picard.
The transcripts were assembled and quantified using HTSeq.
Assembly: hg38;mm10
Supplementary files format and content: Tab-separated matrix files of counts for bulk samples
Supplementary files format and content: HDF5 matrix files of counts for the single-cell samples

source_name: Cell line

growth_protocol: The cells were cultured in RPMI 1640 medium or DMEM supplemented with 10% fatal bovine serum and 1% penicillin–streptomycin. Adherent cells were detached by 0.25% Trypsin-EDTA at 37℃ for 3min and quenched with growth medium. All the cells were maintained in 37℃ with 5% CO2.

extract_protocol:
The methanol fixed cells were kept in -20℃ for 30min and pelleted at 500×g for 5min at 4℃. After two further washes with 1ml of ice-cold wash-resuspension buffer I, permeabilized cells were resuspended in 20ul of ice-cold wash-resuspension buffer II.
The cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

treatment_protocol: The cultured cells were washed twice with 1ml of ice-cold PBS and resuspended in 200ul of ice-cold PBS, 800ul of methanol were added dropwise and gently mixed.

value: Cell line

value: Embryonic fibroblast cells

value: WT

value: Fixed by 50% methanol


title: CA66_4_EnzDHT

description:
CA66_4
AR_PGxeQTL_rawcount.txt


title: Dbp mouse submandibular gland replicate 2 Cut-taq

description:
Dbp rep2
The submandibular gland of  control mice

value: submandibular gland

value: Dbp mouse


title: CA63_3_DHT

description:
CA63_3
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line

value: DHT


title: 19994X48 infiltrative BCC

value: infiltrative BCC


title: 19994X47 infiltrative BCC


title: CA63_1_Veh

description:
CA63_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: 3T3_met40

description: The 40% methanol-fixed cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

value: Fixed by 40% methanol


title: 3T3_met30

description: The 30% methanol-fixed cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

value: Fixed by 30% methanol


title: control 2, E10.5, FNP/MxP

value: control


title: control 1, E10.5, FNP/MxP


title: CA62_2_Enz

description:
CA62_2
AR_PGxeQTL_rawcount.txt


title: Ovary BCAS2 cKO, rep3

first: xiaohong

last: Yao

address: No. 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

description:
cKO3
The function of granulosa cells.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Mus musculus GRCm39
Supplementary files format and content: fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: ovary

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
The library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer.

value: ovary

value: BCAS2 cKO


title: 19994X44 infiltrative BCC


title: Ovary BCAS2 cKO, rep2

description:
cKO2
The function of granulosa cells.


title: mutant 1, E10.5, FNP/MxP

value: Microdissected frontonasal and maxillary prominence

value: Tfap2a;Tfap2b;Wnt1CRE mutant


title: control 3, E10.5, FNP/MxP


title: 19994X43 infiltrative BCC


title: CA62_3_DHT

description:
CA62_3
AR_PGxeQTL_rawcount.txt


title: Lung, de novo SCLC, chromatin, rep 2

value: Lung

value: PNEC-RPMT


title: CA62_1_Veh

description:
CA62_1
AR_PGxeQTL_rawcount.txt


title: 19994X42 micronodular BCC

value: micronodular BCC


title: 19994X45 infiltrative BCC


title: C2C12 cells si-USF2 rep2

city: Shenzhen Shi

first: zishuai

last: wang

state: Guangdong Sheng

address: Peng Fei Lu

institute: caas

data_processing:
FastQC: For assessing the quality of raw sequencing data
Trimmomatic: To remove adapter sequences and low-quality bases.
HISAT2:For mapping reads to a reference genome.
featureCounts:To count the number of reads that align to each gene.
DESeq2: A R package for detecting differentially expressed genes.
Assembly: mm10
Supplementary files format and content: tab-delimated file including raw-reads count for each sample
Supplementary files format and content: tab-delimated file including TPM for each sample

growth_protocol: C2C12 myoblasts were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco, USA) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin (PS, Thermo Scientific, USA) at 37 °C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, Shanghai, China).
HiScript III 1st Strand cDNA Synthesis kit (+gDNA wiper) (R312-01, Vazyme, Nanjing, China) was used to generate cDNA following the manufacturer’s instructions

treatment_protocol: siRNA-NC and siRNA-USF2 mimics were transfected into C2C12 myoblast cells following lipofectamine 3000 protocol

value: mouse myoblast cell

value: WT

tag: sirna


title: C2C12 cells si-USF2 rep1


title: Ovary WT, rep3

description:
ctl3
The function of granulosa cells.


title: C2C12 cells si-USF2 rep3


title: CA59_4_EnzDHT

description:
CA59_4
AR_PGxeQTL_rawcount.txt

value: Blood

value: EnzDHT


title: 19994X40 micronodular BCC


title: Ovary WT, rep1

description:
ctl1
The function of granulosa cells.


title: CA59_3_DHT

description:
CA59_3
AR_PGxeQTL_rawcount.txt

value: B lymphoblastoid cell line

value: DHT


title: Ovary WT, rep2

description:
ctl2
The function of granulosa cells.


title: CA59_2_Enz

description:
CA59_2
AR_PGxeQTL_rawcount.txt

value: Enz


title: 19994X41 micronodular BCC


title: C2C12 cells siRNAcontrol 3

value: siRNA-NC


title: 19994X46 infiltrative BCC

value: infiltrative BCC


title: CA62_4_EnzDHT

description:
CA62_4
AR_PGxeQTL_rawcount.txt


title: CA59_1_Veh

description:
CA59_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: 19994X39 micronodular BCC


title: Ovary BCAS2 cKO, rep1

description:
cKO1
The function of granulosa cells.

value: ovary


title: C2C12 cells siRNAcontrol 2


title: Ovary, SRSF1 cKO, rep3

description:
cKO3
The function of granulosa cells.

value: SRSF1 cKO


title: 19994X38 micronodular BCC


title: CA58_3_DHT

description:
CA58_3
AR_PGxeQTL_rawcount.txt


title: CA58_4_EnzDHT

description:
CA58_4
AR_PGxeQTL_rawcount.txt


title: C2C12 cells siRNAcontrol 1


title: N_14_G-R-_replicate_3

city: New Haven

first: Shangqin

last: Guo

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

data_processing:
After quality control, the clean reads were mapped to mouse genome (mm10) using Cufflinks.
Genes expression level were quantitated with HTSeq.
Differentially expressed genes (DEGs) were identified with DESeq2. An absolute log2 fold change >1 and the adjusted p-value (FDR) significance score <0.05 were used as thresholds to identify DEGs.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: MEF

growth_protocol: We performed bulk RNA-seq of control (EV), Actin overexpressed (Actin)  and NLS-actin OE (NLA-Actin) in mouse MEF and day 4 reporgramming cells. We also performed bulk RNA-seq of green positive or red positive reporogramming cells with or witiour NLS-actin under day 10 and day 14.

extract_protocol:
Total RNA with polyA+ selection was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), from three replicates of each group.
RNA-seq was performed at Illumina Hiseq 2500 platform that included quality control, library preparation, fragmentation and PCR enrichment of target RNA according to standardized procedures.
150 bp paired-end raw reads were initially processed to obtain clean reads by removing adaptor sequences, low quality sequences, empty reads.

treatment_protocol: Total RNA was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), from two or three replicates of each group.

tag: time

value: 14 days

value: MEF

value: reprogramming

value: NLS-Actin OE

tag: group

value: G-R-


title: 19994X36 micronodular BCC

tag: tissue

value: micronodular BCC


title: Ovary, WT, rep3

description:
ctl3
The function of granulosa cells.

value: WT


title: Ovary, SRSF1 cKO, rep1

description:
cKO1
The function of granulosa cells.


title: CA58_2_Enz

description:
CA58_2
AR_PGxeQTL_rawcount.txt

value: Blood


title: CA58_1_Veh

description:
CA58_1
AR_PGxeQTL_rawcount.txt


title: 19994X35 micronodular BCC


title: N_14_G+R-_replicate_3

value: G+R-


title: CA57_4_EnzDHT

description:
CA57_4
AR_PGxeQTL_rawcount.txt

value: B lymphoblastoid cell line

value: EnzDHT


title: Ovary, WT, rep1

description:
ctl1
The function of granulosa cells.


title: N_14_G-R-_replicate_1


title: N_14_G-R-_replicate_2


title: Ovary, WT, rep2

description:
ctl2
The function of granulosa cells.


title: CA57_3_DHT

description:
CA57_3
AR_PGxeQTL_rawcount.txt

value: DHT


title: 19994X33 micronodular BCC


title: N_14_G+R-_replicate_2


title: 19994X32 nodular BCC

value: nodular BCC


title: CA57_2_Enz

description:
CA57_2
AR_PGxeQTL_rawcount.txt

value: Enz


title: DMP1-Cre Mfn2 mice

city: hangzhou

first: Zhaoming

last: Ye

address: 88 jiefang road

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

description: 10x Genomics

data_processing:
Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) was used to process the raw data and generate the UMI matrix.
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

growth_protocol: A total of 1× 10^6 LLC cells were resuspended in 10μL PBS and injected into the bone marrow cavity of the right tibia of DMP1-Cre Mfn2-/- mice, DMP1-Cre Rhot1-/- mice, and wild-type mice. After two weeks, the tumors were dissected.

extract_protocol:
Tumor tissues were dissected from DMP1-Cre Mfn2-/- mice, DMP1-Cre Rhot1-/- mice, or wild-type mice and washed with ice-cold PBS. Tumors were enzymatically dissociated in DMEM medium supplemented with collagenase type IV (2 mg/ml, Sigma), DNase (0.1 mg/ml, Sigma), hyaluronidase (0.1 mg/ml, Sigma), and BSA (1 mg/ml, Sigma) at 37 °C for 1h and then filtrated through 70 μm filters (Falcon) to obtain single cells suspensions. Cells were washed in PBS and incubated with Zombie Aqua™ Fixable Viability Kit (Biolegend, Cat# 423107) for dead cell exclusion using Beckman MoFlo Astrios EQs and Summit v6.3.1 software (3 tumors from 3 mice mixed 1:1:1 for each group).
Barcoded scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Reagent Kit. The cells were loaded on a 10 X Chromium Controller (10X Genomics) to generate nanoliter-scale gel beads-in-emulsions (GEMs). Then, the GEMs were used to generate barcoded, full-length cDNA through reverse transcription reactions. Next, the barcoded, full-length cDNA was used for library construction via fragmentation, end repair, A-tailing, ligation to an index adaptor, and amplification by PCR. The final libraries were sequenced on a HiSeq X Ten platform (Illumina), and 150 bp paired-end reads were generated.

value: tumor cells and infiltrating cells

value: DMP1-Cre Mfn2

value: 8 weeks old


title: DMP1-Cre Rhot1 mice

description: 10x Genomics

value: DMP1-Cre Rhot1


title: Ovary, SRSF1 cKO, rep2

description:
cKO2
The function of granulosa cells.

value: ovary

value: SRSF1 cKO


title: 19994X37 micronodular BCC


title: CA57_1_Veh

description:
CA57_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: 19994X34 micronodular BCC


title: 19994X30 nodular BCC


title: N_14_G+R-_replicate_1

value: 14 days

value: MEF

value: reprogramming

value: NLS-Actin OE


title: CA56_4_EnzDHT

description:
CA56_4
AR_PGxeQTL_rawcount.txt

value: Blood


title: 19994X31 nodular BCC


title: mitochondria-recipient cells in intratibial LLC model

description: 10x Genomics

data_processing:
Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) was used to process the raw data and generate the UMI matrix.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

growth_protocol: A total of 1× 106 LLC cells were resuspended in 10μL PBS and injected into the bone marrow cavity of the right tibia of DMP1-Cre PhAM mice. After two weeks, the tumors were dissected.

extract_protocol:
Tumor tissues were dissected from DMP1-Cre PhAM mice and washed with ice-cold PBS. Tumors were enzymatically dissociated in DMEM medium supplemented with collagenase type IV (2 mg/ml, Sigma), DNase (0.1 mg/ml, Sigma), hyaluronidase (0.1 mg/ml, Sigma), and BSA (1 mg/ml, Sigma) at 37 °C for 1h and then filtrated through 70 μm filters (Falcon) to obtain single cells suspensions. Cells were washed in PBS and incubated with Zombie Aqua™ Fixable Viability Kit (Biolegend, Cat# 423107) for dead cell exclusion. Alive osteocyte-derived mitochondria recipient cells were sorted using Beckman MoFlo Astrios EQs and Summit v6.3.1 software according to the presence of Dendra2 signal and the absence of BV521.
Barcoded scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Reagent Kit. The cells were loaded on a 10 X Chromium Controller (10X Genomics) to generate nanoliter-scale gel beads-in-emulsions (GEMs). Then, the GEMs were used to generate barcoded, full-length cDNA through reverse transcription reactions. Next, the barcoded, full-length cDNA was used for library construction via fragmentation, end repair, A-tailing, ligation to an index adaptor, and amplification by PCR. The final libraries were sequenced on a HiSeq X Ten platform (Illumina), and 150 bp paired-end reads were generated.

value: mitochondria-recipient cells

value: DMP1-Cre PhAM


title: CA56_3_DHT

description:
CA56_3
AR_PGxeQTL_rawcount.txt

value: B lymphoblastoid cell line

value: DHT


title: N_14_G-R+_replicate_2

value: G-R+


title: tumor-infiltrating cell in intratibial LLC model

description: 10x Genomics

data_processing:
Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) was used to process the raw data and generate the UMI matrix.
Supplementary files format and content: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

growth_protocol: A total of 1× 106 LLC cells were resuspended in 10μL PBS and injected into the bone marrow cavity of the right tibia of CAG-ZsGreen mice. After two weeks, the tumors were dissected.

extract_protocol:
Tumor tissues were dissected from CAG-ZsGreen mice and washed with ice-cold PBS. Tumors were enzymatically dissociated in DMEM medium supplemented with collagenase type IV (2 mg/ml, Sigma), DNase (0.1 mg/ml, Sigma), hyaluronidase (0.1 mg/ml, Sigma), and BSA (1 mg/ml, Sigma) at 37 °C for 1h and then filtrated through 70 μm filters (Falcon) to obtain single cells suspensions. Cells were washed in PBS and incubated with Zombie Aqua™ Fixable Viability Kit (Biolegend, Cat# 423107) for dead cell exclusion. Alive tumor-infiltrating cells were sorted using Beckman MoFlo Astrios EQs and Summit v6.3.1 software according to the presence of ZsGreen signal and the absence of BV521.
Barcoded scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Reagent Kit. The cells were loaded on a 10 X Chromium Controller (10X Genomics) to generate nanoliter-scale gel beads-in-emulsions (GEMs). Then, the GEMs were used to generate barcoded, full-length cDNA through reverse transcription reactions. Next, the barcoded, full-length cDNA was used for library construction via fragmentation, end repair, A-tailing, ligation to an index adaptor, and amplification by PCR. The final libraries were sequenced on a HiSeq X Ten platform (Illumina), and 150 bp paired-end reads were generated.

value: tumor-infiltrating cells


title: 19994X29 nodular BCC

value: nodular BCC


title: 19994X28 nodular BCC


title: Early2c_MT2Mm_ko rep3

city: Shanghai

first: Wenju

last: Liu

address: 1239  siping road

institute: University of Tongji

data_processing:
Illumina NovaSeq 6000 System was used for basecalling and 150 bp paired-end reads were generated.
Sequenced reads were trimed for adaptor and low-quality sequence using cutadapt v1.18 and then mapped to GRCm38 whole genome using HISAT2 v2.1.0 with parameters "--rna-strandness RF --dta-cufflinks --no-discordant"
gene expression levels were quantified as FPKM by stringtie V1.3.4d with parameters “-e --rf”. Genes with FPKM <0.1 in all samples were filtered, and FPKM values of replicates were averaged.
Differences in expression were determined using Cuffdiff V2.2.1.
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files include FPKM values for each Sample

source_name: embryo

extract_protocol:
Total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions.
TruSeq Stranded Total RNA kit(illumine) was used to construct library of early embryonic development stage following the manufacturer’s instructions, each sample need approximately 150-200 embryos. In briefly, Ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with beads, and cleaved RNA fragments were copied into cDNA using reverse transcriptase and random primers. cDNA subjected to 12–15 cycles of PCR amplification. For small amount total RNA-Seq, we used a SMARTer Stranded Total RNA-Seq Kit version 2(Takara) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina NovaSeq 6000 platform with paired ends and 150-bp read lengths at Berry Genomics.

tag: developmental stage

value: embryo

value: MT2Mm KO


title: E_10_G-R-_replicate_3

value: 10 days

tag: cell line

value: WT

value: G-R-


title: Early2c_MT2Mm_ko rep2


title: N_14_G-R+_replicate_1

value: 14 days

tag: cell type


title: CA56_1_Veh

description:
CA56_1
AR_PGxeQTL_rawcount.txt

data_processing:
Raw RNA sequencing reads were aligned to the human genome GRCh37 (hg19) using STAR[24], and gene counts were performed using HTSEQ
Assembly: GRCh37
Supplementary files format and content: tab deliminated text file of gene counts per sample

extract_protocol:
Total RNA was extracted with the RNeasy RNA extraction kit per manufacturer's instruction (Qiagen). RNA integrity was examined by Agilent Bioanalyzer
polyA enrichment; RNA-seq libraries were prepared with the TruSeq2 RNA Library Prep Kit v2 (Illumina).

value: Veh


title: CA56_2_Enz

description:
CA56_2
AR_PGxeQTL_rawcount.txt

value: Enz


title: 19994X26 nodular BCC


title: Early2c_MT2Mm_ko rep1

tag: genotype


title: E_10_G-R-_replicate_1

value: MEF

value: reprogramming


title: WT mice

description: 10x Genomics

value: tumor cells and infiltrating cells

value: 8 weeks old


title: 19994X25 nodular BCC


title: N_14_G-R+_replicate_3

value: NLS-Actin OE


title: E_10_G-R-_replicate_2


title: CA52_3_DHT

description:
CA52_3
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line

tag: treatment

value: DHT


title: Early2c_MT2Mm_ctrl rep3

value: wild type


title: CA52_4_EnzDHT

description:
CA52_4
AR_PGxeQTL_rawcount.txt

value: EnzDHT


title: 19994X24 nodular BCC

value: nodular BCC


title: E_10_G-R+_replicate_3

value: 10 days

value: G-R+


title: CA52_2_Enz

description:
CA52_2
AR_PGxeQTL_rawcount.txt


title: CA52_1_Veh

description:
CA52_1
AR_PGxeQTL_rawcount.txt


title: 19994X23 nodular BCC


title: 19994X27 nodular BCC


title: Early2c_MT2Mm_ctrl rep1

value: embryo


title: Early2c_MT2Mm_ctrl rep2


title: E_10_G-R+_replicate_1

value: WT


title: 19994X21 superficial BCC

value: superficial BCC


title: E_10_G-R+_replicate_2


title: CA50_3_DHT

description:
CA50_3
AR_PGxeQTL_rawcount.txt


title: CA50_4_EnzDHT

description:
CA50_4
AR_PGxeQTL_rawcount.txt


title: E_14_G+R+_replicate_3

value: 14 days

value: G+R+


title: E_14_G+R+_replicate_2

value: MEF

value: reprogramming


title: Late1c_MT2Mm_ko rep3

value: MT2Mm KO


title: 19994X20 superficial BCC


title: Late1c_MT2Mm_ko rep2


title: Late1c_MT2Mm_ctrl rep3


title: E_14_G+R+_replicate_1


title: CA50_1_Veh

description:
CA50_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: E_14_G-R-_replicate_3

value: G-R-


title: CA40_4_EnzDHT

description:
CA40_4
AR_PGxeQTL_rawcount.txt

value: Blood

value: B lymphoblastoid cell line


title: 19994X18 superficial BCC


title: CA50_2_Enz

description:
CA50_2
AR_PGxeQTL_rawcount.txt

value: Enz


title: Late1c_MT2Mm_ctrl rep2

value: wild type


title: E_14_G-R-_replicate_2


title: CA40_3_DHT

description:
CA40_3
AR_PGxeQTL_rawcount.txt

value: DHT


title: 19994X22 superficial BCC


title: Late1c_MT2Mm_ctrl rep1


title: 19994X16 superficial BCC


title: E_14_G-R-_replicate_1


title: CA40_2_Enz

description:
CA40_2
AR_PGxeQTL_rawcount.txt


title: CA40_1_Veh

description:
CA40_1
AR_PGxeQTL_rawcount.txt


title: E_14_G+R-_replicate_2

value: G+R-


title: E_14_G+R-_replicate_3


title: VTIR2

city: Chongqing

first: Li

last: Guoxing

state: Chongqing

address: Street of shiyou Road, Yuzhong District, Chongqing, China

institute: Chongqing Medical University

description: VB12 treated I/R model, heart, I/R, B12 treatment

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 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software. The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml? t=example) in a reference-based approach[2].
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length).

value: heart

value: I/R, B12 treatment


title: Late1c_MT2Mm_ko rep1

value: embryo


title: 19994X14 superficial BCC

value: superficial BCC


title: E_14_G+R-_replicate_1

value: 14 days

value: WT


title: VTIR1


title: 19994X13 superficial BCC


title: 19994X12 superficial BCC


title: E_14_G-R+_replicate_3

value: MEF

value: G-R+


title: IR3

description: heart, I/R, normal water intake

value: I/R, normal water intake


title: E_14_G-R+_replicate_2

value: reprogramming


title: 19994X11 superficial BCC


title: CA29_3_DHT

description:
CA29_3
AR_PGxeQTL_rawcount.txt


title: CA29_2_Enz

description:
CA29_2
AR_PGxeQTL_rawcount.txt


title: CA29_1_Veh

description:
CA29_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: IR2

description: heart, I/R, normal water intake


title: VTIR3


title: IR1

description: heart, I/R, normal water intake


title: CA28_4_EnzDHT

description:
CA28_4
AR_PGxeQTL_rawcount.txt

value: Blood

value: EnzDHT


title: 19994X10 superficial BCC


title: E_14_G-R+_replicate_1


title: 19994X15 superficial BCC


title: VC3

description: heart, Sham operation, B12 treatment

value: Sham operation, B12 treatment


title: CA29_4_EnzDHT

description:
CA29_4
AR_PGxeQTL_rawcount.txt

value: B lymphoblastoid cell line


title: N_10_G-R-_replicate_3

value: 10 days

value: NLS-Actin OE

value: G-R-


title: 19994X17 superficial BCC


title: N_10_G-R-_replicate_2


title: 19994X8 control skin

value: control skin


title: CA28_3_DHT

description:
CA28_3
AR_PGxeQTL_rawcount.txt

value: DHT


title: VC2

description: heart, Sham operation, B12 treatment

value: heart


title: VC1

description: heart, Sham operation, B12 treatment


title: N_10_G-R-_replicate_1


title: 19994X7 control skin


title: 19994X9 control skin


title: N_10_G-R+_replicate_3


title: C2

description: heart, Sham operation, normal water intake

value: Sham operation ,normal water intake


title: N_10_G-R+_replicate_2


title: C1

value: WT


title: 19994X5 control skin


title: C3


title: CA24_3_DHT

description:
CA24_3
AR_PGxeQTL_rawcount.txt


title: 19994X3 control skin


title: N_14_G+R+_replicate_3

value: 14 days

value: MEF

value: G+R+


title: N_14_G+R+_replicate_2

value: reprogramming


title: CA24_1_Veh

description:
CA24_1
AR_PGxeQTL_rawcount.txt

value: Veh


title: CA24_2_Enz

description:
CA24_2
AR_PGxeQTL_rawcount.txt

value: Blood

value: Enz


title: Purkinje cells, nm3888-/-, rep3

city: La Jolla

first: Susan

last: Ackerman

state: CA

address: 9500 Gilman Drive

department: CMM

institute: UCSD

data_processing:
Fastp was used to trim adapter off of sequences
Bowtie2 was used to align files to the mm10 genome
Samtools FeatureCounts was used to count number of reads mapped at the gene level
DESeq2 was used for differential expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: cerebellum

extract_protocol:
Each cerebellum was homogenized using a dounce homogenizer in 1.5mL lysis buffer (1% NP-40, 100mM KCl, 50mM Tris pH 7.4, 12mM MgCl2, 0.1mg/mL cycloheximide, protease inhibitor cocktail (Sigma, 11836170001), 1mg/mL heparin, 5µL/mL RNAseOUT (ThermoFisher 10777019)). Ribosomes were then isolated as previously described (Sanz 2009) Briefly, lysates containing tagged ribosomes were incubated for 4 hours at 4˚C with 5µg rat anti-HA antibody (Roche, 11867423001) after which 400µL protein G-coupled dynabeads (Thermo Scientific, 10004D) were added to the lysate and incubated at 4˚C overnight. The following day ribosome-bound beads were washed three times with high salt buffer (0.3M KCl, 1% NP-40, 50mM Tris pH 7.4, 12mM MgCl2, 0.1mg/mL cycloheximide, 0.5mM DTT), and mRNA was isolated using buffer RLT and spin columns (Qiagen RNEasy Mini Kit). RNA was eluted in 30µL H2O
Libraries were constructed using the Kapa Stranded mRNA-Seq Kit (#KR0960) in accordance with manufacteur’s instructions.

value: cerebellum

value: Purkinje cells

value: 3 weeks

tag: Sex

value: Male

tag: antibody for_ip


title: Purkinje cells, nm3888-/-, rep4


title: 19994X2 control skin


title: CA19_4_EnzDHT

description:
CA19_4
AR_PGxeQTL_rawcount.txt

value: B lymphoblastoid cell line

value: EnzDHT


title: CA28_1_Veh

description:
CA28_1
AR_PGxeQTL_rawcount.txt


title: Purkinje cells, wild type, rep3

value: Wild type

value: Female


title: N_14_G+R+_replicate_1

value: NLS-Actin OE


title: 19994X1 control skin

value: control skin


title: 19994X6 control skin


title: HEK293T_input

city: Shanghai City

first: Peisong

last: Zhai

address: Zhizaoju Rd. No.639

institute: Shanghai Jiao Tong universisy medical school affiliated Shanghai ninth people's hospital

data_processing:
The quality control for sequencing data used Trimmomatic, blastn and NT databases. Bowtie2 was used to align the reads to the human genome. Strand cross-correlation (SCC) was used to assess the ChIRP pull-down quality. MACS2 was used to call the peaks.
Gene symbols and other information were annotated onto the peaks by chipseeker (v1.12.1). MEME-ChIP was used to analyse motifs in the peaks, and Tomtom was used to compare the motifs and to annotate them.
Manorm (v 1.18.0) was used to analyse differences in peak reads between groups (p value<0.01 and log2(M value)>1).
Statistical significance was analysed by the R package DiffBind
Assembly: mm10
Supplementary files format and content: Excel spreadsheet with peak name -log10(pvalue), peak location, length, fold enrichment -log10(qvalue), ect..
Library strategy: ChIRP-seq

growth_protocol: CAL27 and HEK-293T cells were cultured in high-glucose Dulbecco’s modified Eagle’s medium containing 10% foetal bovine serum and treated with 300μg/mL cetuximab in a humidified 37°C incubator with a 5% CO2 atmosphere.

extract_protocol:
ChIRP was carried out based on a standard ChIP assay using a SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling Technology, USA). Briefly, cells were first transfected with biotinylated miRNA (RiboBio, China). Within 24 h, cells were prepared by crosslinking with formaldehyde. Chromatin was segmented using micrococcal nuclease, and cell lysis was carried out via sonication to break the nuclear membrane. Total DNA template (20 µL) was collected after centrifugation and sample dilution. The remaining segmented chromatin was then incubated with streptavidin magnetic beads (Merck, Germany) overnight at 4°C. The samples were collected with a magnetic stand and washed several times before elution. The eluted samples were reverse crosslinked and subjected to DNA purification. Finally, each sample DNA was eluted in a total volume of 30 µL twice and stored with templates at -20°C before sequencing.
A total of 20 ng of DNA templates was used to build libraries for ChIRP-seq.

treatment_protocol: CAL27 and HEK293T cells were treated with 300μg/mL cetuximab. Cells were transfected with biotin labelled miR-451a probes before ChIRP according to the manufacturer's instruction.

value: Tongue carconoma cells

tag: chirp probe


title: 4FH_D4_NLS-Actin_replicate_2

value: MEF