title: Sample 1128 Normal_3_5_8_3


title: Sample 1125 Normal_3_5_7_6

status: Public on Jul 09 2023

type: SRA

city: Guangzhou

first: Xinyan

last: Yang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Developmental Biology

country: China

institute: Southern Medical University

library_source: genomic

data_processing:
library strategy: single-cell chromatin overall omic-scale landscape sequencing (scCOOL-seq)
Illumina CASAVA version 1.8 were used to the basecalling.
For RNA part, we used specific cell barcode (8 bp) in read 2 to separate single cell R2 reads and used read ID to extract the corresponding R1 reads. Template switch oligo (TSO) sequence, low quality bases and ployA tails were then removed. The clean R1 reads were mapped to human reference genome hg38 (downloaded from UCSC genome browser) with Hisat2 (v2.1.0) in single-end module with default settings. HTSeq package (v0.6.1) was used to count uniquely mapped reads and cell-specific barcodes were used to group the uniquely mapped reads. Finally, distinct UMIs for each gene were counted as the transcript copy number and normalized to TPM value. Gene expression level was shown as log2 (TPM/10+1).
For DNA part, we used Trim_galore (v 0.3.3) and Cutadapt (v 1.2.1) to remove adaptor sequence, low quality bases and 6 bp random primers in raw data. The clean reads were mapped to human reference genome hg38 using Bismark (v0.7.6) in paired-end and non_directional module. Due to a large number of chimeric reads generated during post-bisulfite adaptor tagging (PBAT) library construction, the unmapped read 1 and read 2 were realigned in single-end and non_directional module separately to rescue more reads. SAMtools (v0.1.18) was used to remove duplicate reads, only uniquely mapped reads were used for downstream analysis. Cytosines in WCG (W = A/T) context were used to reflect DNA methylation level, while those in GCH (H = A/C/T) context were used to reflect chromatin accessibility.
Assembly: hg38
Supplementary files format and content: text file
Supplementary files format and content: WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

molecule: genomic DNA

organism: Homo sapiens

source_name: testis

extract_protocol:
Here we performed single-cell multi-omics libraries referring to the methods of STRT-seq and scCOOL-seq. A mouth pipette was used to randomly pick human testicular cells and transferred into the 2.5 μl cell lysis buffer containing 4 U RNase inhibitor (Takara, Cat. 2313B), 0.25% IGEPAL CA-630 (Sigma, Cat. I3021), and in vitro methylation mix (1× GC reaction buffer, 160 μM S-adenosylmethionine and 2 U M.CviPI (NEB, Cat. M0227L). After gently vortexed for about 15 seconds, the lysate was incubated at 37°C for 20 mins and then at 65°C for 25 mins. To isolate DNA and RNA of the single cells, a 3 μl nuclear separation mixture containing 0.2 µl of Dynabeads Myone Carboxylic Acid (Invitrogen, Cat. 65011), 0.2% Tween-20 (Sigma, Cat. P1379), 1% Triton X-100 (Sigma, Cat. T8787), 4 U RNase inhibitor, 50 mM DTT and 2 µl of 5× Superscript II first-strand buffer (Invitrogen, Cat. 18064071), was added to above 2.5 μl cell lysis. The tube was placed on the magnet after mixing by vortexing and brief centrifugation. The nuclei (DNA) wrapped with magnetic beads and the cytoplasm in the supernatant were separated for subsequent use.
For RNA part, the preparation of single cell RNA-seq library was performed using the STRT-seq. Briefly, the above separated supernatant was transferred into the 4.5 μl reverse transcription (RT) mix containing 100 U SuperScript II reverse transcriptase (Invitrogen, Cat. 18064071), 4 U RNase inhibitor, 1 mM dNTPs (Takara, Cat. 4019), 60 mM MgCl2, 3 µM 8-bp barcode primer and 10 µM TSO primer, followed by incubation at 25°C for 5 min, 42°C for 60 min, 50°C for 30 min and 70°C for 10 min. The cDNA amplification and purification by 0.8× AMPure XP beads (Beckman, Cat. A63882) was then performed. Biotin PCR was further carried out and enriched. Finally, the single cell RNA-seq library was prepared according to the KAPA Hyper Prep Kits with PCR Library Amplication/Illumina series (KAPA, KK8054). The libraries were checked and sequenced with 150 bp pair-end reads on Illumina Hiseq 4000 (Novogene). For DNA part, the magnetic beads containing cell nuclei (DNA) were treated with 5 µl of protein lysis buffer consist of 2.5 µl M-digestion buffer (Zymo Research, Cat. D5044) and 0.5 µl of protease K (NEB, Cat. P8107S). The single cell DNA libraries were then constructed according to scCOOL-seq protocol with minor modifications. In brief, the bisulfite conversion was conducted by EZ-96 DNA Methylation-Direct MagPrep kit (Zymo Research, Cat. D5044). Four rounds of amplification were performed with Klenow exo- (ENzymics, Cat. NG202) and scBS-seq-P5-N6-oligo1 (CTACACGACGCTCTTCCGATCTNNNNNN). After purified by 0.8× AMPure XP beads, the products were used to synthesize the second strand using scBS-seq-P7-N6-oligo2 (AGACGTGTGCTCTTCCGATCTNNNNN). Finally, 16 cycles of PCR program were performed to complete the DNA library construction incorporated universal primers and index primers (New England Biolabs), followed by purification twice with 0.8× AMPure XP beads. The DNA libraries were pooled together and sequenced with 150 bp pair-end reads on Illumina Hiseq 4000 (Novogene).

tag: tissue

value: testis

tag: Sex

value: male

tag: condition

value: Normal


title: Sample 1129 Normal_3_5_8_4


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title: EPIC_MUT_AG221_7d_oxBS_Rep3

type: genomic

city: Huddinge

first: Anna

last: Palau

address: Hälsovägen 9

country: Sweden

institute: Karolinska Institutet

description: Sample 29

hyb_protocol: DNA methylation analysis was performed using Illumina’s Infinium MethylationEPIC assay (EPIC) according to the manufacturer’s protocol.

data_processing:
Data analysis was conducted using the ChAMP algorithm
Normalized Beta Value using BMIQ method

label: Cy5 and Cy3

growth_protocol: TF-1 IDH2WT/IDH2R140Q cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS), 1% GlutaMAX, 2 ng/mL human GM-CSF recombinant protein and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: Genomic DNA was extracted from TF-1 cell line and was subjected to bisulfite(BS)-treatment and oxidative BS (oxBS)-treatment using the EZ-96 DNA Methylation Kit (Zymo Research)

treatment_protocol: Where indicated, the TF-1 IDH2 mutant cells were treated with 5 µM AG-221 (MedChemExpress) without GM-CSF in the medium for 4 and 7 days using DMSO as vehicle.

tag: type of bisulfite conversion

value: oxBS

tag: cell line

value: TF-1 IDH2R140Q

tag: treatment

tag: time

value: 7 days


title: EPIC_MUT_DMSO_7d_oxBS_Rep3

description: Sample 32

scan_protocol: DNA methylation analysis was performed using Illumina’s Infinium MethylationEPIC assay (EPIC) according to the manufacturer’s protocol.

value: DMSO


title: Sample 849 Normal_2_3_4_5


title: EPIC_MUT_AG221_7d_oxBS_Rep2

description: Sample 28


title: Sample 848 Normal_2_3_4_4


title: EPIC_MUT_DMSO_7d_BS_Rep3

description: Sample 26

value: BS


title: EPIC_MUT_AG221_7d_oxBS_Rep1

description: Sample 27


title: Sample 846 Normal_2_3_4_2


title: Sample 858 Normal_2_3_6_2


title: EPIC_MUT_DMSO_7d_BS_Rep1

description: Sample 24


title: EPIC_MUT_AG221_7d_BS_Rep3

description: Sample 23


title: Sample 844 Normal_2_3_3_8


title: EPIC_MUT_DMSO_7d_BS_Rep2

description: Sample 25


title: Sample 845 Normal_2_3_4_1


title: Sample 843 Normal_2_3_3_7


title: EPIC_MUT_DMSO_7d_oxBS_Rep2

description: Sample 31


title: Sample 842 Normal_2_3_3_6


title: Sample 840 Normal_2_3_3_4


title: EPIC_MUT_AG221_7d_BS_Rep1

description: Sample 21


title: EPIC_MUT_DMSO_4d_oxBS_Rep1

description: Sample 19

value: 4 days


title: EPIC_MUT_AG221_4d_oxBS_Rep2

description: Sample 18


title: EPIC_MUT_DMSO_4d_oxBS_Rep2

description: Sample 20


title: Sample 841 Normal_2_3_3_5


title: Sample 839 Normal_2_3_3_3


title: EPIC_MUT_AG221_4d_oxBS_Rep1

description: Sample 17


title: Sample 847 Normal_2_3_4_3


title: EPIC_MUT_DMSO_7d_oxBS_Rep1

description: Sample 30


title: Sample 837 Normal_2_3_2_8


title: Sample 838 Normal_2_3_3_2


title: Sample 835 Normal_2_3_2_6


title: EPIC_MUT_DMSO_4d_BS_Rep2

description: Sample 15


title: EPIC_MUT_AG221_4d_BS_Rep3

description: Sample 13


title: Sample 834 Normal_2_3_2_5


title: EPIC_MUT_DMSO_4d_BS_Rep1

description: Sample 14


title: EPIC_MUT_DMSO_4d_BS_Rep3

description: Sample 16


title: EPIC_MUT_AG221_4d_BS_Rep2

description: Sample 12


title: Sample 836 Normal_2_3_2_7


title: Sample 833 Normal_2_3_2_4


title: EPIC_MUT_AG221_7d_BS_Rep2

description: Sample 22


title: EPIC_WT_oxBS_Rep1

description: Sample 9

value: TF-1 IDH2WT


title: EPIC_WT_oxBS_Rep2

description: Sample 10


title: EPIC_MUT_AG221_4d_BS_Rep1

description: Sample 11


title: Sample 830 Normal_2_3_2_1


title: Sample 832 Normal_2_3_2_3


title: Sample 829 Normal_2_3_12_8


title: EPIC_WT_BS_Rep3

description: Sample 8


title: Sample 828 Normal_2_3_12_7


title: Sample 827 Normal_2_3_12_6


title: EPIC_WT_BS_Rep1

description: Sample 6


title: EPIC_WT_BS_Rep2

description: Sample 7


title: EPIC_MUT_oxBS_Rep2

description: Sample 5


title: Sample 826 Normal_2_3_12_5


title: EPIC_MUT_oxBS_Rep1

description: Sample 4


title: EPIC_MUT_BS_Rep3

description: Sample 3


title: Sample 824 Normal_2_3_12_3


title: Sample 825 Normal_2_3_12_4


title: EPIC_MUT_BS_Rep2

description: Sample 2


title: EPIC_MUT_BS_Rep1

description: Sample 1


title: Sample 831 Normal_2_3_2_2


title: Sample 823 Normal_2_3_12_2


title: D4-ST3

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

library_source: transcriptomic

data_processing:
Low-quality reads were removed by fastp with default parameters
Remaining clean reads were align to the Human genome 38 (hg38) by Hisat2 with default parameters
Raw gene counts were generated by featurecount and then normalized by DEseq2
Assembly: hg38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

molecule: total RNA

source_name: TSC-ST

extract_protocol:
Total RNA  was extracted using TRIzol Reagent (15596018, Invitrogen) according to the instruction.
mRNA was purified with Oligo(dT)-attached magnetic beads, followed by fragmentation.The first strand and second cDNA were generated by random hexamer-primed reverse transcription. The cDNA was amplified by PCR and purified by Ampure XP Beads. The quality control of the products was verified by Agilent Technologies 2100 bioanalyzer.

value: TSC-ST

tag: cell type

value: Syncytiotrophoblast

tag: genotype

value: WT

value: TSC differentiation


title: Sample 818 Normal_2_3_11_2


title: D4-EVT4

source_name: TSC-EVT

value: TSC-EVT

value: Extravillous Trophoblasts


title: Sample 820 Normal_2_3_11_5


title: Sample 821 Normal_2_3_11_6


title: Sample 819 Normal_2_3_11_3


title: Sample 822 Normal_2_3_12_1


title: D4-EVT3


title: Sample 817 Normal_2_3_11_1


title: D4-EVT2


title: Sample 815 Normal_2_3_10_6


title: D4-A11-S4

source_name: TSCADM KO-ST

value: TSCADM KO-ST


title: Sample 814 Normal_2_3_10_5

value: testis


title: D4-A11-S2


title: D4-EVT1


title: Sample 812 Normal_2_3_10_3

value: male


title: D4-A11-S1


title: Sample 811 Normal_2_3_10_2

value: Normal


title: D4-A11-E4

source_name: TSCADM KO-EVT

value: TSCADM KO-EVT


title: D4-ST1


title: Sample 810 Normal_2_3_10_1


title: D4-A11-E3


title: D4-ST2


title: Sample 809 Normal_2_2_9_5


title: Sample 808 Normal_2_2_9_3


title: Sample 807 Normal_2_2_8_8


title: Sample 806 Normal_2_2_8_7


title: D2-ST4


title: D4-A11-E1


title: D2-ST3


title: Sample 805 Normal_2_2_8_4


title: Sample 804 Normal_2_2_8_2


title: D4-A11-E2


title: D4-A11-S3


title: D2-EVT4


title: D2-ST2


title: D2-ST1


title: Sample 803 Normal_2_2_8_1


title: Sample 802 Normal_2_2_7_8


title: Sample 813 Normal_2_3_10_4


title: D2-EVT3


title: Sample 800 Normal_2_2_7_4


title: D2-EVT1


title: Sample 798 Normal_2_2_7_2


title: D2-A11-S3


title: D2-A11-S4


title: Sample 799 Normal_2_2_7_3


title: Sample 797 Normal_2_2_6_8


title: D2-A11-S2


title: Sample 796 Normal_2_2_6_7


title: D2-A11-S1


title: Sample 794 Normal_2_2_5_8


title: D2-A11-E4


title: Sample 793 Normal_2_2_5_7


title: Sample 795 Normal_2_2_6_5


title: D2-A11-E3


title: Sample 791 Normal_2_2_5_4


title: Sample 792 Normal_2_2_5_6


title: D2-A11-E1


title: D2-A11-E2


title: Sample 801 Normal_2_2_7_6


title: Sample 816 Normal_2_3_10_7


title: D0-TSC3

source_name: TSC

value: TSC

value: Trophoblast Stem Cell

value: TSC culture


title: D0-TSC4


title: Sample 790 Normal_2_2_5_3


title: D2-EVT2


title: Sample 787 Normal_2_2_4_8


title: D0-TSC2


title: P2C2_pMXs_PU1_MSCV_Runx1_1%_input_rep1

city: Pasadena

first: Boyoung

last: Shin

state: CA

address: 1200 E. California Blvd

country: USA

institute: California Institute of Technology

data_processing:
Fastq files were aligned to the mouse reference genome GRCm38/mm10 using Bowtie2 (v3.5.1)
Mitochondrial reads using Samtools (v.1.9)
Reproducible peak calling was performed using a HOMER (v.4.11.1) adaptation of the Irreproducibility Discovery Rate (IDR) tool according to ENCODE guideline
Assembly: GRCm38/mm10
Supplementary files format and content: peak file (txt) for C&R and ChIP-seq

organism: Mus musculus

growth_protocol:
For pro-T cells obtained from OP9-Dll1 culture, Multipotent bone marrow progenitor cells were cultured with OP9-Dll1 cells in  OP9 medium (20% FBS, 2mM glutamine, 100 IU/ml penicillin, 100 mg/ml streptomycin, and 50 µM β-ME in α-MEM).   Cells were supplemented with  IL-7, Flt3-ligand  (10 ng/ml each) under 37 °C, 7% CO2 environment.
For Scid.adhd.2c2 (P2C2) cells, cells were maintained  in  P2C2 medium(10%  FBS, 2 mM glutamine, 100 IU/mL penicillin, 100 ug/mL streptomycin, 0.1 mM sodium pyruvate, non-essential amino acids, and 50 uM b-mercaptoethanol in RPMI1640) under 37 °C, 5% CO2 environment.

extract_protocol:
DNA was isolated using phenol-chloroform-isoamyl alcohol after CUT&RUN.  Zymo ChIP DNA Clean & Concentrator was used to clean eluted DNA after ChIP.
Sequencing libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit
CUT&RUN and ChIP-seq

treatment_protocol: For delivering retroviral vectors, bone-marrow progenitor cells were co-cultured with OP9-Dll1 for 2 days, then viral supernatant were supplemented with 8 ug/ml polybrene and centrifuged for 2 hours at 500g at 32'C

value: DN3-like Scid.adhd.2c2 (P2C2) cells

value: DN3-like cell line

value: pMXs-PU.1l-NGFR vector and MSCV_Runx1-HA_mCherry vectors were introduced for 2 days


title: Sample 785 Normal_2_2_4_5


title: D0-A11-4

source_name: TSCADM KO

value: TSCADM KO


title: Sample 786 Normal_2_2_4_6


title: D0-TSC1


title: Sample 789 Normal_2_2_5_2


title: Sample 788 Normal_2_2_5_1


title: TAU_microglia_rep3

city: Nagoya

first: Akira

last: Sobue

address: Furo-cho Chikusa-ku

country: Japan

institute: Nagoya university

data_processing:
The reference genome assemblies and gene annotations, the mouse genome version UCSC mm10  were retrieved from iGenomes
The Illumina adapter sequences, as well as low quality bases (quality score < 20), were trimmed from 3’-ends of the sequencing reads with the Trim Galore v0.5.0
The reads were qualified with FastQC v0.11.8 before and after trimming.
The processed reads were mapped on the reference genome assembly with HISAT2 v2.1.0
Mapping reads prepared with the stranded kit was processed by employing strand specificity information. The alignments on rDNA regions were removed with BEDTools v2.25.0. From mapping data, expressions of the individual annotated genes were quantified with StringTie v1.3.5
Assembly: mm10
Supplementary files format and content: MS Excel file including CPM values of the individual genes for each sample and the results of the differential expression analysis

source_name: isolated microglia

extract_protocol:
For the RNA-seq of the mouse samples, total RNA was extracted from MACS-isolated microglia of each models using an RNeasy Micro Kit (Qiagen, Hilden, Germany). The RNAs were sampled from cerebral cortices of 8-month-old AppNL-G-F/NL-G-F and 7-month-old rTg4510 mice and lumbar spinal cords of 5-month-old SODG93A mice together with the corresponding wild-type or non-Tg control mice, respectively.
Libraries were prepared by using TruSeq mRNA or TruSeq Stranded mRNA (Illumina, San Diego, CA, USA), and, from these libraries, 151-nt paired-end reads were sequenced on the HiSeq X Ten with the HiSeq X Reagent Kits (Illumina)

value: isolated microglia

value: rTg4512 (Tau)


title: P2C2_pMXs_Control_MSCV_Runx1_1%_input_rep1

value: pMXs-empty-control-NGFR vector and MSCV_Runx1-HA_mCherry vectors were introduced for 2 days


title: TTA_microglia_rep1

value: Ctrl (CamKII-tta)


title: TTA_microglia_rep3


title: TAU_microglia_rep2

value: rTg4511 (Tau)


title: Cervical cells [CC19]

city: tartu

first: Maire

last: Peters

department: Dept. of Obstetrics and gynecology

country: Estonia

institute: University of Tartu

data_processing:
The raw sequencing data were analysed with the nf-core pipeline version 3.5
Reads were aligned to the GRCh37 human genome with the STAR aligner (v2.7.10a)
read quantification was performed using RSEM (v1.3.3).
Assembly: GRCh37 human genome
Supplementary files format and content: "rsem.merged.gene_counts.tsv" This file contains the raw read count matrix. This file is tab separated file.
Supplementary files format and content: "rsem.merged.gene_tpm.tsv": This file contains the Transcript per million count matrix. This file is tab separated file.

molecule: polyA RNA

source_name: Cervical cells

extract_protocol:
Cervical cells’ RNA was isolated by RNeasy Micro kit (Qiagen) according to the manufacturer’s protocol
TruSeq Stranded mRNA Library Prep kit (Illumina)

tag: source

value: Cervical cells

tag: gender

value: Female

tag: age

tag: menstrual cycle_dating


title: Sample 781 Normal_2_2_3_6

value: testis

value: male


title: Sample 783 Normal_2_2_4_2

value: Normal


title: PBAT.P20-cKO.Rep1b

description: PBAT

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
We used Trim_galore (v 0.3.3) and Cutadapt (v 1.2.1) to remove adaptor sequence, low quality bases and 6 bp random primers in raw data. The clean reads were mapped to human reference genome hg38 or mouse reference genome mm10 using Bismark (v0.7.6) in paired-end and non_directional module. Due to a large number of chimeric reads generated during post-bisulfite adaptor tagging (PBAT) library construction, the unmapped read 1 and read 2 were realigned in single-end and non_directional module separately to rescue more reads. SAMtools (v0.1.18) was used to remove duplicate reads, only uniquely mapped reads were used for downstream analysis. Cytosines in WCG (W = A/T) context were used to reflect DNA methylation level.
Assembly: hg38 and mm10
Supplementary files format and content: The columns in CpG files represent "chr" "start" "end" "methylated rate".

extract_protocol:
HEK293T cells were first treated with 10 μM Decitabine dissolved in dimethylsulfoxide (DMSO) or DMSO (control) for 12 h, and then transfected with the expression vector containing hPRDM9b cDNA with a C-terminal FLAG tag. About 48 h after transfection, the cells were collected for PBAT and CUT&Tag assay, respectively.
PBAT library preparation. Briefly, 5 ng genomic DNA together with 60 pg unmethylated lambda DNA (ThermoFisher) were subjected to bisulfite conversion followed by column-based purification using the EZ DNA methylation–direct kit (Zymo Research, D5021). Next, the random priming, library amplification and sequencing were consistent with the method used in the preparation of single-cell DNA library.

value: Uhrf1 cKO


title: D0-A11-3

value: Trophoblast Stem Cell


title: P2C2_pMXs_PU1_MSCV_Runx1_aHA_ChIP_rep1

description: Rabbit anti-HA (sc-805 x)


title: Sample 780 Normal_2_2_3_5


title: D0-A11-2

value: TSC culture


title: Deci-hPRDM9.rep2

data_processing:
*library strategy: CUT&Tag
In brief, the adaptor sequences were trimmed using bbduk (v 38.18) and low-quality reads were removed by trimmomatic (v 0.39), with the length cut-off 35 bp. The clean reads were aligned to hg38 genome using bowtie2 (v 2.3.5.1) with the options (--very-sensitive --end-to-end). Then, the low-quality mapping reads were removed using SAMtools with the option (-q 35). The duplicated sequences were removed using Picard (v 2.23.0) and biological repeats were merged.
Bigwig files were generated using genomeCoverageBed from BEDTools (v 2.29.2) (scale factor = 60 million / <each sample’s total unique reads>) and bedGraphToBigWig (v 2.8). The enrichment of CUT&Tag data in different regions was calculated by the computeMatrix and plotProfile of deepTools (v 3.5.1).
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
NovoNGS ® CUT&Tag 2.0 High-Sensitivity Kit (Novoprotein, N259-YH01) was used to capture hPRDM9 binding sites according to the manufacturer’s instructions. In brief, 1× 10^5 HEK293T cells that ectopically expressed hPRMD9 were prepared and immobilized on conA beads. The beads were first incubated with a Flag primary antibody (Sigma, F1804), and followed by the incubation with a secondary antibody mouse anti-IgG (Abcam, ab6708). Then the beads were washed and incubated with pA-Tn5. Tn5 was activated by addition of Mg2+ and incubated at 37° C for 1 h. Reactions were stopped by the addition of 0.5M EDTA (10 µL), 10% SDS (3 µL) and 20 mg/mL Proteinase K (2.5 µL).
DNA was then extracted using phenolchloroform and used for CUT&Tag library construction. The library was quantified by Equalbit dsDNA HS Assay Kit (Vazyme, EQ111-01) using Qubit™ 4 Fluorometer (Invitrogen, Q33226). Sequencing was performed on NovaSeq platform at Novogene using paired-end 150-bp strategy.

value: Decitabine


title: PBAT.P20-cKO.Rep1c

description: PBAT


title: D0-A11-1


title: Sample 784 Normal_2_2_4_3


title: P2C2_pMXs_Control_MSCV_Runx1_aHA_ChIP_rep1

description: Rabbit anti-HA (sc-805 x)

value: DN3-like Scid.adhd.2c2 (P2C2) cells

value: DN3-like cell line


title: Deci-hPRDM9.rep3


title: Sample 779 Normal_2_2_3_3


title: Deci-hPRDM9.rep1


title: Sample 782 Normal_2_2_4_1


title: TAU_microglia_rep1

value: rTg4510 (Tau)


title: PBAT.P20-CTL.Rep2b

description: PBAT

value: Wild type


title: Sample 778 Normal_2_2_3_1


title: Cervical cells [CC16]


title: TTA_microglia_rep2

value: isolated microglia


title: PBAT.P20-cKO.Rep1a

description: PBAT


title: Cervical cells [CC17]


title: Cervical cells [CC15]

value: Proliferative


title: DMSO-hPRDM9.rep3

value: DMSO


title: Sample 777 Normal_2_2_2_8


title: PBAT.P20-CTL.Rep2a

description: PBAT


title: Cervical cells [CC14]


title: Cervical cells [CC18]


title: PBAT.P20-CTL.Rep1b

description: PBAT


title: DMSO-hPRDM9.rep1


title: Sample 775 Normal_2_2_2_5


title: DMSO-hPRDM9.rep2


title: Cervical cells [CC13]


title: Deci-DNA-6

description: PBAT


title: Cervical cells [CC12]


title: Sample 776 Normal_2_2_2_7


title: Sample 774 Normal_2_2_2_2


title: Sample 773 Normal_2_2_12_7


title: Deci-DNA-4

description: PBAT


title: Female Control E11.5, scRNA-seq

city: Berlin

first: Irene

last: Mota-Gomez

address: Hannoversche strasse 28

country: Germany

institute: Max Delbruck Center

description:
FemaleCtrl11.5_1
cells (rownames) ending in "_4" in the processed files
singlecell_counts_integrated.txt.gz
singlecell_metadata_integrated.txt

library_source: transcriptomic single cell

data_processing:
alignment using cellranger 6.1.1
counts matrices samples with two technical replicates were merged using Seurat
Filtering of low quality cells, blood cells and doublets
Integration of objects, further clean up of the data
Donstream DEG analysis using MAST
Assembly: mm10_v3.0.0 from 10X genomics
Supplementary files format and content: singlecell_counts_integrated.txt.gz
Supplementary files format and content: singlecell_metadata_integrated.txt

source_name: gonad and mesonephros

extract_protocol:
Three to four pairs of gonads per genotype, sex and stage were pooled and individual cell suspensions were performed using 0.05% Trypsin-EDTA  for 7 minutes at 37°C. Trypsin digestion was stopped by adding 5% BSAand solution was passed through a 40 µm Flowmi cell strainer . Finally, cells were collected by centrifugation (300g for 5 min at 4 °C) and the pellet was resuspended in PBS for cell counting and viability check and then fixed with Methanol (98%).
After rehydration of the cells, about 10,000 cells were loaded on a 10X Chromium controller and sc-RNA libraries were prepared using the Chromium Next Gem Single Cell 3’ Reagent Kit v3.1
scRNA-seq 3' 10X genomics platform

value: gonad and mesonephros

tag: strain

value: C57BL/6 x 129S4/SvJae


title: Deci-DNA-5

description: PBAT


title: Male Mutant E11.5, scRNA-seq

description:
MaleMut11.5_1
cells (rownames) ending in "_2" in the processed files
singlecell_counts_integrated.txt.gz
singlecell_metadata_integrated.txt


title: Cervical cells [CC10]

value: Cervical cells

value: Female

value: early-secretory


title: Sample 772 Normal_2_2_12_6

value: testis

value: male

value: Normal


title: Cervical cells [CC11]


title: Male Mutant E11.75 scRNA-seq

description:
MaleMut11.75
cells (rownames) ending in "_3" in the processed files
singlecell_counts_integrated.txt.gz
singlecell_metadata_integrated.txt


title: Sample 771 Normal_2_2_12_4


title: Male Control E11.5, scRNA-seq

description:
MaleCtrl11.5
cells (rownames) ending in "_1" in the processed files
singlecell_counts_integrated.txt.gz
singlecell_metadata_integrated.txt


title: Cervical cells [CC8]

value: late-secretory


title: DMSO-DNA-2

description: PBAT


title: Foxl2 UTR mutant,E11.5 gonad, replicate 3, RNA-seq

description:
Foxl2-gonad_rep3_11.5
COUNTS_Foxl2_MC_11.5.txt

data_processing:
The bulk RNA-seq reads were mapped to the mm10 mouse genome and counted with the align and featureCounts function from the R subread package
Only genes with 1 or more cpm (counts per million) in at least two of the samples were considered to be expressed and were used for further analysis.
Analysis of the differential gene expression was performed using EdgeR
Assembly: mm10
Supplementary files format and content: All the processed data files contain the RAW counts for each of the samples (indicated in the corresponding column names) and for each gene (GeneID or mgi_symbol columns), further analysis with EdgeR will normalize the data and generate the differential expression analysis found in extended data tables of the manuscript.

source_name: gonad tissue

extract_protocol:
For RNA-seq, total RNA was isolated from gonad-mesonephos complexes at E11.5 and from isolated gonads at E12.5 using the RNeasy Micro Kit
Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and  the Truseq stranded mRNA Library prep

value: gonad tissue

value: mutant, XY


title: Sample 770 Normal_2_2_12_3


title: PBAT.P20-CTL.Rep1a

description: PBAT


title: DMSO-DNA-1

description: PBAT


title: Cervical cells [CC7]


title: Foxl2 UTR mutant,E11.5 gonad, replicate 2, RNA-seq

description:
Foxl2-gonad_rep2_11.5
COUNTS_Foxl2_MC_11.5.txt


title: Sample 768 Normal_2_2_12_1


title: Sample 769 Normal_2_2_12_2


title: Foxl2 UTR mutant,E11.5 eye, replicate 3, RNA-seq

description:
Foxl2-eye_rep3_11.5
COUNTS_Foxl2_MC_11.5.txt

source_name: eye tissue

value: eye tissue


title: Cervical cells [CC4]

value: mid-secretory


title: Sample 767 Normal_2_2_11_7


title: Cervical cells [CC6]


title: BT67_H4K5ac_Input_3

city: Calgary

first: Ravinder

last: Bahia

state: Alberta

address: 3330 Hospital drive NW

department: Cell Biology and Anatomy

country: Canada

institute: University of Calgary

data_processing:
Base calls were performed using bcl2fastq for novaseq output
ChIP-seq reads were first trimmed for adapter sequences and low quality score bases using Trimmomatic
The resulting reads were mapped to the human reference genome (hg38) using BWA-MEM in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were marked using Picard tools (https://broadinstitute.github.io/picard/)
Peaks were called using MACS2 software suite. A “reference peak set” was obtained by merging ChIP-seq peaks from each samples using bed tools merge with parameters: -sorted -d -125. Peaks were associated with the nearest TSS of genes (+/- 20kb) using the annotate Peaks command from HOMER software suite (https://bedtools.readthedocs.io/).
peak enrichments were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM)
Assembly: hg38

growth_protocol: BT67 cells were cultured in stem cell enriched media supplemented with EGF (20ng/ml), bFGF (20ng/ml) and heparin sulfate (2µg/ml) in humidified atmosphere with 5% CO2 at 37C and were used within 10 passages after being thawed.

extract_protocol:
The crosslinked cells were lysed in hypotonic cell lysis buffer and nuclei were pelleted and lysed using 10% SDS (0.3% final concentration) and sonicated to achieve the chromatin size between 200-1000bp.
ChIP-seq libraries were prepared using NEB II ultra, w/o shearing kit.

treatment_protocol: For H3K27ac ChIP-seq, the BT67 romidepsin and DMSO treated cells anf for H4K5ac ChIP-seq the BT67 HDAC2 KO and AAVS1 control cells were crosslinked with 1% formaldehyde (F) for 10 minutes. For HDAC1/2 and SMAD3 ChIP-seq, the dual crosslinked (DCL) (crosslinking with 1% formaldehyde for 10 minutes followed by DSP (dithiobis(succinimidyl propionate)) crosslinking) BT 67 cells were used.

value: Brain tumour stem cell

tag: chip antibodies


title: Foxl2 UTR mutant,E11.5 gonad, replicate 1, RNA-seq

description:
Foxl2-gonad_rep1_11.5
COUNTS_Foxl2_MC_11.5.txt


title: BT67_H4K5ac_Input_2


title: Cervical cells [CC5]


title: Sample 764 Normal_2_2_11_4


title: Cervical cells [CC1]


title: BT67_H4K5ac_AAVS1_1

value: H4K5ac (abcam, cat#51997)


title: BT67_H4K5ac_Input_1


title: Foxl2 UTR mutant,E11.5 eye, replicate 2, RNA-seq

description:
Foxl2-eye_rep2_11.5
COUNTS_Foxl2_MC_11.5.txt


title: Sample 763 Normal_2_2_11_2


title: BT67_H4K5ac_HDAC2KO_3


title: DMSO-DNA-3

description: PBAT


title: Sample 766 Normal_2_2_11_6


title: Cervical cells [CC9]


title: BT67_H4K5ac_AAVS1_3


title: Cut&Run_H3K4me1_R1

city: Irvine

first: Paula Duyen

last: Pham

address: 4410 Natural Sciences

institute: UC Irvine

data_processing:
Paired-end fragments were trimmed using trimmomatic. Paired-end reads were aligned using Bowtie2 with options: --local --very-sensitive --dovetail --phred33 -I 10 -X 700. The fragments were filtered for a MAPQ score of 30 prior to calling peaks.
processed data files format and content: bigwig file
Library strategy: CUT&RUN

growth_protocol: cXEN cells were cultured in Advanced RPMI (Thermo Fisher,12633012) supplemented with 15% FBS (R&D Systems, S10250H), 2 mM Glutamax (Thermo Fisher, 35050061), 100 U/mL Pen/Strep (Thermo Fisher, 15140122), 0.1 mM 2(β)-ME (Sigma, M-3148).

extract_protocol: 500,000 cells was used for CUT&RUN following the standard protocol (Skene, P., 2017)

value: cXEN

value: Extraembryonic endoderm stem cells

tag: antibody

value: anti-H3K4me1 (ab8895, Abcam)


title: BT67_H4K5ac_HDAC2KO_1


title: Cut&Run_H3K27ac_R2

value: anti-H3K27ac (MABE647, EMD Millipore Sigma)


title: tdLN_BF10

city: Taipei

first: JuPei

last: Chen

address: No. 155, Sec. 2, Linong St. Beitou Dist.

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
All data processing steps are using QIAseq TCR Panel Immune Repertoire RNA Library Kit (version 2.01).
Trim reads: First trim from the reads the constant regions generated by the enrichment protocol, and move the UMI sequence to the read indentifier line.
Down-sample reads: Randomly discard the reads until the remaining reads contain about 8 reads per UMI.
Build consensus reas: Error corrected consensus reads are generated by grouping multiple reads that putatively came from the same input simple molecule, based on three factors: (1) the UMI tag sequence; (2) the endogenous sequence near the random fragmentation and UMI ligation site; and (3) the full read sequence.
Merge overlapping R1 and R2 reads: R1 being entirely VDJ sequence, and R2 being V-only.
Split reads by genes (TRAC, TRBC, TRDC, TRGC).
Align the reads to the V-region models and trim overhang regions.
Run IMSEQ to generate clonotype calls and quantities. (parameters: -ev 0.15 -ma -sfb)
Compute diversity metrics. (Total clonotype count, Clonotypes within the top 50% of UMIs, Shannon-Wiener diversity index, Inverse Simpson diversity index)
Assembly: mm10
Supplementary files format and content: QIAseqRNA-immune-repertoire-TCR.clonotypes file in .txt format for three sample groups.

source_name: Lymph node

growth_protocol: Primary CD8 T cells were isolated by MACS CD8 T cell microbeads from tumor, spleen, and LN.

extract_protocol:
Trizol protocol for tissue RNA extraction. Extracted RNA were quantificated by using Qubit fluorometer with Qubit RNA BR Assay Kit
Libraries were prepared using QIAseq Immune Repertoire RNA Library Kit (GeneGlobe configuration no.  IMMM-001Z-12) following the directions of the manufacturer.
QIASeqTargeted enrichment & sequencing

treatment_protocol: Tumor-bearing mice were treated the equivalent dose (30 mg/kg) of all components with 3 days interval for total 3 doses, followed by CD8 T cell isolation for TCR sequencing.

value: Lymph node

value: CD8 T cells

value: WT

value: BF10 fusion protein


title: Cut&Run_H3K4me3_R2

value: anti-H3K4me3 (39159, Active Motif)


title: Foxl2 UTR mutant,E11.5 eye, replicate 1, RNA-seq

description:
Foxl2-eye_rep1_11.5
COUNTS_Foxl2_MC_11.5.txt


title: tdLN_Ctl-IgG

value: Control IgG


title: Sample 759 Normal_2_2_1_5

value: testis

value: male

value: Normal


title: Cut&Run_FoxA2_R2

value: anti-FoxA2 (07-633, EMD Millipore Sigma)


title: Sample 765 Normal_2_2_11_5


title: Cervical cells [CC3]

value: Cervical cells

value: Female

value: mid-secretory


title: Cut&Run_FoxA2_R1

value: cXEN


title: Cervical cells [CC2]


title: Cut&Run_H3K4me3_R1

value: Extraembryonic endoderm stem cells


title: Cut&Run_H3K4me1_R2

value: anti-H3K4me1 (ab8895, Abcam)


title: BT67_H4K5ac_AAVS1_2

value: Brain tumour stem cell

value: H4K5ac (abcam, cat#51997)


title: Cut&Run_Sox17_R2

value: anti-Sox17 (AF1924, R&D Systems)


title: Sample 762 Normal_2_2_10_5


title: Sample 756 Normal_2_1_9_6


title: tdLN_CSF1R

value: Lymph node

value: CD8 T cells

value: WT

value: anti-CSF1R antibody


title: CD8_Spleen_BF10

source_name: Spleen

value: Spleen

value: BF10 fusion protein


title: Sample 761 Normal_2_2_1_7

value: testis

value: male

value: Normal


title: Cut&Run_H3K27ac_R1

value: anti-H3K27ac (MABE647, EMD Millipore Sigma)


title: Sample 758 Normal_2_2_1_4


title: Sample 760 Normal_2_2_1_6


title: tdLN_IL10


title: BT67_Input_3


title: Sample 754 Normal_2_1_7_1


title: CD8_TIL_CSF1R

source_name: Tumor

value: Tumor


title: BT67_H4K5ac_HDAC2KO_2


title: BT67_Input_2


title: Sample 753 Normal_2_1_6_6


title: BT67_HDAC2_3

value: HDAC2 (abcam, cat#ab12169)


title: CD8_Spleen_CSF1R


title: BT67_SMAD3_3

value: SMAD3 (abcam, cat#ab40854)


title: CD8_Spleen_IL10


title: Sample 757 Normal_2_1_9_7


title: CD8_TIL_IL10


title: BT67_SMAD3_2


title: Sample 751 Normal_2_1_6_3


title: BT67_HDAC2_1


title: Cut&Run_Sox17_R1

value: cXEN

value: Extraembryonic endoderm stem cells


title: Sample 755 Normal_2_1_9_5


title: Cut&Run_Gata6_R2

value: anti-Gata6 (5851S, Cell Signaling Technology)


title: CD8_TIL_BF10


title: Sample 68 NOA1_1_4_6

value: nonobstructive azoospermia (NOA)


title: Cut&Run_Gata6_R1


title: RNA_Sox17FKBP_FoxA2Mut_48h_R1

data_processing:
Samples are mapped to reference genome mm10 by Hisat2 using the following option: --no-mixed, --no-discordant, and others as default.  The bam file was processed to generate the raw count file by HTSeq using the following option: -a 10, --order=pos, -m intersection-strict, --stranded=reverse, --type=exon, --nonunique=none, --secondary-alignments=ignore, --supplementary-alignments=ignore.
processed data files format and content: tab-delimited text files include count values for each sample generated by htseq

extract_protocol: RNA was harvested using trizol. 1 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: cXEN cells were used as a model system to examine transcription factor functions in extraembryonic endoderm lineage differentiation. Acute degradation for the cXEN cells with Gata6 or Sox17 FKBPv degron tag was induced by treating the cells with 500 nM dTAGV1 (Tocris). dTAGV1 was kept in culture until harvest during the time course with times indicated in hours representing the amount of time dTAGV1 was in culture. For BMP4 treatment, cXEN cells were adapted to the N2B27 media with 1% FBS for 24h on 0.1% gelatin. The media was then changed to N2B27 without serum supplemented with 25 ng/ml BMP4 (R&D Systems, 314-BP-010/CF) and cultured for Day 1 (24h) and/or Day 3 (72h).


title: 22rv ko ip1

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by HISAT2 with uniquely mapped reads retained for the following analyses.
Normalization were performed by Deeptools.
Differential expression analysis was performed by DESeq2.
Peak calling was performed with exomePeak.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig normalized signal

source_name: prostate cancer cells

extract_protocol:
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.

tag: technology

value: FTO KO


title: BT67_SMAD3_1

value: Brain tumour stem cell


title: BT67_HDAC2_2


title: ATAC_XEN_R2

data_processing:
Paired-end fragments were trimmed using trimmomatic. Paired-end reads were aligned using Bowtie2 with options: --local --very-sensitive --dovetail --phred33 -I 10 -X 700. The fragments were filtered for a MAPQ score of 30 prior to calling peaks.
processed data files format and content: bigwig file

extract_protocol: 50,000 cells was used for ATAC following the Active Motif ATAC-seq Kit (53150)

tag: tissue


title: BT67_HDAC1_1

value: HDAC1 (abcam, cat# ab7028


title: ATAC_XEN_R1

extract_protocol: 50,000 cells was used for ATAC following manufacturer's instructions for the Active Motif ATAC-seq Kit (53150)


title: Sample 752 Normal_2_1_6_4

extract_protocol:
Here we performed single-cell multi-omics libraries referring to the methods of STRT-seq and scCOOL-seq. A mouth pipette was used to randomly pick human testicular cells and transferred into the 2.5 μl cell lysis buffer containing 4 U RNase inhibitor (Takara, Cat. 2313B), 0.25% IGEPAL CA-630 (Sigma, Cat. I3021), and in vitro methylation mix (1× GC reaction buffer, 160 μM S-adenosylmethionine and 2 U M.CviPI (NEB, Cat. M0227L). After gently vortexed for about 15 seconds, the lysate was incubated at 37°C for 20 mins and then at 65°C for 25 mins. To isolate DNA and RNA of the single cells, a 3 μl nuclear separation mixture containing 0.2 µl of Dynabeads Myone Carboxylic Acid (Invitrogen, Cat. 65011), 0.2% Tween-20 (Sigma, Cat. P1379), 1% Triton X-100 (Sigma, Cat. T8787), 4 U RNase inhibitor, 50 mM DTT and 2 µl of 5× Superscript II first-strand buffer (Invitrogen, Cat. 18064071), was added to above 2.5 μl cell lysis. The tube was placed on the magnet after mixing by vortexing and brief centrifugation. The nuclei (DNA) wrapped with magnetic beads and the cytoplasm in the supernatant were separated for subsequent use.
For RNA part, the preparation of single cell RNA-seq library was performed using the STRT-seq. Briefly, the above separated supernatant was transferred into the 4.5 μl reverse transcription (RT) mix containing 100 U SuperScript II reverse transcriptase (Invitrogen, Cat. 18064071), 4 U RNase inhibitor, 1 mM dNTPs (Takara, Cat. 4019), 60 mM MgCl2, 3 µM 8-bp barcode primer and 10 µM TSO primer, followed by incubation at 25°C for 5 min, 42°C for 60 min, 50°C for 30 min and 70°C for 10 min. The cDNA amplification and purification by 0.8× AMPure XP beads (Beckman, Cat. A63882) was then performed. Biotin PCR was further carried out and enriched. Finally, the single cell RNA-seq library was prepared according to the KAPA Hyper Prep Kits with PCR Library Amplication/Illumina series (KAPA, KK8054). The libraries were checked and sequenced with 150 bp pair-end reads on Illumina Hiseq 4000 (Novogene). For DNA part, the magnetic beads containing cell nuclei (DNA) were treated with 5 µl of protein lysis buffer consist of 2.5 µl M-digestion buffer (Zymo Research, Cat. D5044) and 0.5 µl of protease K (NEB, Cat. P8107S). The single cell DNA libraries were then constructed according to scCOOL-seq protocol with minor modifications. In brief, the bisulfite conversion was conducted by EZ-96 DNA Methylation-Direct MagPrep kit (Zymo Research, Cat. D5044). Four rounds of amplification were performed with Klenow exo- (ENzymics, Cat. NG202) and scBS-seq-P5-N6-oligo1 (CTACACGACGCTCTTCCGATCTNNNNNN). After purified by 0.8× AMPure XP beads, the products were used to synthesize the second strand using scBS-seq-P7-N6-oligo2 (AGACGTGTGCTCTTCCGATCTNNNNN). Finally, 16 cycles of PCR program were performed to complete the DNA library construction incorporated universal primers and index primers (New England Biolabs), followed by purification twice with 0.8× AMPure XP beads. The DNA libraries were pooled together and sequenced with 150 bp pair-end reads on Illumina Hiseq 4000 (Novogene).

tag: Sex


title: CD8_TIL_Ctl-IgG

value: CD8 T cells

value: WT

value: Control IgG


title: BT67_HDAC1_3


title: 22rv ko ip2


title: BT67_Input_1


title: RNA_Sox17FKBP_FoxA2Mut_48h_R2


title: CD8_Spleen_Ctl-IgG

value: Spleen


title: RNA_Sox17FKBP_FoxA2Mut_0h_R1

value: DMSO


title: Sample 67 NOA1_1_3_8

value: testis

value: male

tag: condition


title: 22rv wt ip2


title: RNA_Sox17FKBP_FoxA2Mut_0h_R2


title: Sample 66 NOA1_1_3_6


title: Sample 64 NOA1_1_3_3


title: RNA_Gata6FKBP_FoxA2Mut_48h_R1


title: 22rv wt input2

value: RNA-Seq


title: 22rv wt ip1


title: Sample 65 NOA1_1_3_4


title: BT67_HDAC1_2


title: RNA_Gata6FKBP_FoxA2Mut_48h_R2


title: 22rv ko input1


title: Sample 63 NOA1_1_3_2


title: RNA_Gata6FKBP_FoxA2Mut_0h_R1


title: RNA_Gata6FKBP_FoxA2Mut_0h_R2


title: RNA_N2B27_XEN_R2_plus_72h_BMP4

value: N2B27+25ng/mL BMP4


title: HPMEC, poly(I:C)+, NMN 0 mM (ctrl), rep 3

city: Tokyo

first: Anton

last: Kratz

address: Saisei Ikedayama Bldg. 5-10-25 Higashi Gotanda Shinagawa

institute: The Systems Biology Institute

data_processing:
The data integrity of the raw sequences were checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed with Trimmomatic 0.38 (http://www.usadellab.org/cms/?page=trimmomatic) to drop the reads with length shorter than 36bp. The trimmed reads were mapped against the reference genome GRCh38 using HISAT2 version 2.1.0 (https://ccb.jhu.edu/software/hisat2/index.shtml) and Bowtie2 2.3.4.1 aligner. The abundance of gene/transcript was calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for each sample.
After the read mapping, Stringtie was used for transcript assembly. Expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million). Annotation: NCBI_109.20200522
Assembly: GRCh38
Supplementary files format and content: Expression_Profile.GRCh38.gene.xlsx: For each gene, lists identifiers, raw counts, tags-per-million (TPM) and Fragment per Kilobase of transcript per Million mapped reads (FPKM)
Supplementary files format and content: Expression_Profile.GRCh38.transcript.xlsx: For each gene, lists identifiers, raw counts, tags-per-million (TPM) and Fragment per Kilobase of transcript per Million mapped reads (FPKM)

source_name: lung

growth_protocol: Human Pulmonary Microvascular Endothelial Cells (HPMEC) and Human Coronary Artery Endothelial Cells (HCAEC) were obtained from ScienCell Research Laboratories and maintained in Endothelial Cell Medium (ScienCell Research Laboratories) in a humidified atmosphere at 37°C with 5% CO2. The culture dishes and plates were pre-coated with fibronectin at a concentration of 2 μg/cm2. After the frozen vial was thawed in a 37° water bath, the entire amount was seeded in one 100 mm dish, followed by changing medium every 2-3 days and the cells were cultured until sufficient cell numbers were obtained. Cells were detached with 0.05% Trypsin EDTA, subcultured, and expanded culture was performed while subculturing was continued until the number of cells required for the test was obtained. Both cell lines were passaged twice after thawing and cells were spread onto 12-well tissue culture-treated plates and cultured for 2 days.

extract_protocol:
Total RNA was prepared with RNeasy Plus Mini Kit (QIAGEN) and subjected to reverse transcription with SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific) to obtain cDNA.
Library construction for whole transcriptome sequencing was performed using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA) according to the manufacturer's protocols

treatment_protocol: Cells were treated with or without 25 µg/ml poly(I:C) in a CO2 incubator for 6 hours and further cultured in fresh media containing 0, 0.1 (low), 1.0 (medium), 10.0 (high) mM NMN for 48 hours. In the group with poly I:C induction, the supernatant of the 6-well plate seeded with each cell was removed and replaced with poly I:C containing medium. On the other hand, in the group without Poly I:C induction, Poly I:C was replaced with a medium containing water for injection. After induction with poly I:C in a CO2 incubator for 6 hours, the supernatant was removed and the medium was replaced with a fresh media containing 0, 0.1 (low), 1.0 (medium), 10.0 (high) mM NMN and the cells were further cultured for 48 hours in a CO2 incubator.

value: lung

value: HPMEC

value: endothelial cells


title: HPMEC, poly(I:C)+, NMN 10 mM, rep 3


title: HPMEC, poly(I:C)+, NMN 0 mM (ctrl), rep 2


title: Sample 62 NOA1_1_3_1

data_processing:
library strategy: single-cell chromatin overall omic-scale landscape sequencing (scCOOL-seq)
Illumina CASAVA version 1.8 were used to the basecalling.
For RNA part, we used specific cell barcode (8 bp) in read 2 to separate single cell R2 reads and used read ID to extract the corresponding R1 reads. Template switch oligo (TSO) sequence, low quality bases and ployA tails were then removed. The clean R1 reads were mapped to human reference genome hg38 (downloaded from UCSC genome browser) with Hisat2 (v2.1.0) in single-end module with default settings. HTSeq package (v0.6.1) was used to count uniquely mapped reads and cell-specific barcodes were used to group the uniquely mapped reads. Finally, distinct UMIs for each gene were counted as the transcript copy number and normalized to TPM value. Gene expression level was shown as log2 (TPM/10+1).
For DNA part, we used Trim_galore (v 0.3.3) and Cutadapt (v 1.2.1) to remove adaptor sequence, low quality bases and 6 bp random primers in raw data. The clean reads were mapped to human reference genome hg38 using Bismark (v0.7.6) in paired-end and non_directional module. Due to a large number of chimeric reads generated during post-bisulfite adaptor tagging (PBAT) library construction, the unmapped read 1 and read 2 were realigned in single-end and non_directional module separately to rescue more reads. SAMtools (v0.1.18) was used to remove duplicate reads, only uniquely mapped reads were used for downstream analysis. Cytosines in WCG (W = A/T) context were used to reflect DNA methylation level, while those in GCH (H = A/C/T) context were used to reflect chromatin accessibility.
Assembly: hg38
Supplementary files format and content: text file
Supplementary files format and content: WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

source_name: testis


title: HPMEC, poly(I:C)+, NMN 10 mM, rep 1


title: 22rv ko input2


title: TTseq_TotalRNA_TF1_IDH2R140Q_7days_DMSO_Rep2

description: Total RNA

data_processing:
Paired-end 75-bp reads were first mapped to a single copy of the rDNA locus to remove rRNA-related sequences. Reads that did not map to the rDNA were then aligned to the GRCh38 genome assembly (Human Genome Reference Consortium) using STAR 2.6.0c (Dobin 2013) with the following specifications: outFilterMismatchNoverLmax 0.05, outFilterMultimapScoreRange 0, and alignIntronMax 500,000. Bam files were filtered with SAMtools (Li 2009) to remove alignments with MAPQ smaller than 7 (-q 7), and only proper pairs (-f99, -f147, -f83, -f163) were selected. Fragment counts for different features were calculated with HTSeq (Anders 2015). Further data processing was carried out using the R/Bioconductor environment.    Annotation of eRNAs: Annotation of enhancer RNAs (eRNAs), was done as described (Lidschreiber, 2021) with few modifications. In brief, genome-wide coverage was calculated from all TT-seq fragment midpoints in consecutive 200 bp bins throughout the genome. A two-state hidden Markov model with a Poisson-Log-Normal emission distribution was learned in order to segment the genome into ‘transcribed’ and ‘untranscribed’ states. Resulting transcribed units (TUs) were further filtered using a minimal expression threshold that was defined based on overlap with genes annotated in GENCODE (v21). The threshold was optimized using the Jaccard index criterion and resulted in ~26,000 TUs. TUs that overlapped at least 25% of an annotated protein-coding gene and overlapped with an annotated exon of the corresponding gene were classified as mRNAs. Remaining TUs were annotated as non-coding (nc)RNAs and further classified according to their genomic location relative to protein-coding genes: upstream antisense RNA (uaRNA), convergent RNA (conRNA), antisense RNA (asRNA), and intergenic RNA. ncRNAs located on the opposite strand of an mRNA were classified as asRNA if the TSS was located > 1 kbp downstream of the sense TSS, as uaRNA if the TSS was located < 1 kbp upstream of the sense TSS, and as conRNA if the TSS was located < 1 kbp downstream of the sense TSS. All remaining ncRNAs were classified as intergenic. We further classified intergenic and asRNAs as eRNAs, if their TSS ± 500 bp overlapped with an enhancer state annotated by GenoSTAN (Zacher 2017). In addition, we restricted our set of intergenic eRNAs to only those originating from regions with TT-seq detected transcription on both strands. The described approach was used to annotate eRNAs in TF-1 IDH2R140Q and TF-1 IDH2WT cells and annotations were subsequently merged to obtain a combined set of 4998 putative eRNAs (annotation_merged_eRNAs.gtf) used for all further analyses.
Assembly: Hg38
Supplementary files format and content: tab-delimited text files containing raw read counts (HTSeq) for protein-coding genes (RefSeq release 109.20190607), lncRNAs (RefSeq release 109.20190607) and eRNAs (annotation_merged_eRNAs.gtf).

source_name: TF-1 IDH2R140Q

extract_protocol:
Total RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was extracted according to Gressel at al., protocols.io, 2019.
Sequencing libraries were prepared with the Ovation Universal RNA-Seq System (NuGEN) following the manufacturer's’ instructions

treatment_protocol: Cells were labeled with 500 µM 4-thiouridine (4sU) (Sigma-Aldrich) for 15 min at 37 °C under 5% CO2. Cells were harvested using TRIzol (Life Technologies).Where indicated, the TF-1 IDH2 mutant cells were treated with 5 µM AG-221 (MedChemExpress) without GM-CSF in the medium for 4 and 7 days using DMSO as vehicle.

value: TF-1 IDH2R140Q

value: acute myeloid leukemia

value: 15 min 4sU

tag: method

value: RNA-seq

value: 7 days


title: HPMEC, poly(I:C)+, NMN 1 mM, rep 3

tag: cell line


title: TTseq_TotalRNA_TF1_IDH2R140Q_7days_DMSO_Rep1

description: Total RNA

tag: treatment


title: Sample 60 NOA1_1_2_7

value: nonobstructive azoospermia (NOA)


title: HPMEC, poly(I:C)+, NMN 10 mM, rep 2


title: RNA_N2B27_XEN_R1_plus_24h_BMP4

value: cXEN

value: Extraembryonic endoderm stem cells

tag: time


title: RNA_N2B27_XEN_R2_plus_24h_BMP4

tag: cell type


title: Sample 57 NOA1_1_2_4


title: RNA_N2B27_XEN_R1_plus_72h_BMP4

tag: genotype


title: Sample 59 NOA1_1_2_6


title: HPMEC, poly(I:C)+, NMN 0.1 mM, rep 3


title: HPMEC, poly(I:C)+, NMN 0 mM (ctrl), rep 1


title: Sample 56 NOA1_1_2_2


title: HPMEC, poly(I:C)+, NMN 1 mM, rep 2


title: HPMEC, poly(I:C)+, NMN 1 mM, rep 1


title: Sample 61 NOA1_1_2_8


title: 22rv wt input1

value: WT


title: HPMEC, poly(I:C)+, NMN 0.1 mM, rep 2


title: Sample 58 NOA1_1_2_5


title: RNA_N2B27_XEN_R1_0h_minusBMP4


title: TTseq_TotalRNA_TF1_IDH2R140Q_4days_AG221_Rep2

description: Total RNA

value: 4 days


title: TTseq_TotalRNA_TF1_IDH2R140Q_7days_AG221_Rep1

description: Total RNA


title: Sample 55 NOA1_1_2_1

value: testis


title: TTseq_TotalRNA_TF1_IDH2R140Q_4days_DMSO_Rep2

description: Total RNA

value: DMSO


title: HPMEC, poly(I:C)+, NMN 0.1 mM, rep 1


title: Sample 54 NOA1_1_12_8

value: male


title: RNA_XEN_R2


title: HPMEC, Poly(I:C)-, NMN 0 mM (ctrl), rep 3


title: TTseq_TotalRNA_TF1_IDH2R140Q_4days_AG221_Rep1

description: Total RNA


title: Sample 53 NOA1_1_12_7


title: TTseq_TotalRNA_TF1_IDH2R140Q_7days_AG221_Rep2

description: Total RNA


title: RNA_XEN_R1


title: RNA_Sox17FKBP_96h_R1


title: TTseq_TotalRNA_TF1_IDH2R140Q_4days_DMSO_Rep1

description: Total RNA


title: TTseq_LabeledRNA_TF1_IDH2R140Q_4days_DMSO_Rep2

description: 4sU-labeled RNA

value: TT-seq


title: HPMEC, Poly(I:C)-, NMN 0 mM (ctrl), rep 2

value: lung


title: HPMEC, Poly(I:C)-, NMN 10 mM, rep 3

value: HPMEC


title: LabeledRNA_TF1_IDH2R140Q_4days_DMSO_Rep1

description: 4sU-labeled RNA


title: HPMEC, Poly(I:C)-, NMN 10 mM, rep 2

value: endothelial cells


title: RNA_Sox17FKBP_96h_R2


title: HPMEC, Poly(I:C)-, NMN 0 mM (ctrl), rep 1


title: TTseq_LabeledRNA_TF1_IDH2R140Q_7days_DMSO_Rep1

description: 4sU-labeled RNA

value: TF-1 IDH2R140Q


title: Sample 52 NOA1_1_12_6


title: Sample 49 NOA1_1_12_3


title: RNA_Sox17FKBP_48h_R2


title: LabeledRNA_TF1_IDH2R140Q_7days_AG221_Rep2

description: 4sU-labeled RNA

value: acute myeloid leukemia


title: Sample 48 NOA1_1_12_2


title: RNA_N2B27_XEN_R2_0h_minusBMP4


title: RNA_Sox17FKBP_72h_R2


title: HPMEC, Poly(I:C)-, NMN 1 mM, rep 3


title: TTseq_LabeledRNA_TF1_IDH2R140Q_7days_DMSO_Rep2

description: 4sU-labeled RNA

value: 15 min 4sU


title: Sample 50 NOA1_1_12_4


title: LabeledRNA_TF1_IDH2R140Q_4days_AG221_Rep2

description: 4sU-labeled RNA


title: Sample 51 NOA1_1_12_5


title: RNA_Sox17FKBP_72h_R1


title: HPMEC, Poly(I:C)-, NMN 10 mM, rep 1


title: RNA_Sox17FKBP_24h_R1


title: Sample 45 NOA1_1_11_4


title: LabeledRNA_TF1_IDH2R140Q_4days_AG221_Rep1

description: 4sU-labeled RNA


title: TotalRNA_TF1_IDH2WT_Rep2

description: Total RNA

source_name: TF-1 IDH2WT

value: TF-1 IDH2WT

value: RNA-seq


title: Sample 44 NOA1_1_11_2

value: nonobstructive azoospermia (NOA)


title: Sample 43 NOA1_1_11_1


title: TotalRNA_TF1_IDH2WT_Rep1

description: Total RNA


title: HPMEC, Poly(I:C)-, NMN 0.1 mM, rep 1


title: RNA_Sox17FKBP_48h_R1

value: cXEN


title: LabeledRNA_TF1_IDH2R140Q_7days_AG221_Rep1

description: 4sU-labeled RNA

value: 7 days


title: TotalRNA_TF1_IDH2R140Q_Rep2

description: Total RNA


title: Sample 47 NOA1_1_12_1


title: HCAEC, poly(I:C)+, NMN 0 mM (ctrl), rep 3

source_name: coronary artery

value: coronary artery

value: HCAEC


title: TotalRNA_TF1_IDH2R140Q_Rep1

description: Total RNA


title: RNA_Sox17FKBP_0h_R1

value: Extraembryonic endoderm stem cells


title: HPMEC, Poly(I:C)-, NMN 1 mM, rep 1


title: Sample 41 NOA1_1_10_7

value: testis


title: LabeledRNA_TF1_IDH2WT_Rep2

description: 4sU-labeled RNA


title: Sample 40 NOA1_1_10_3

value: male


title: HPMEC, Poly(I:C)-, NMN 1 mM, rep 2


title: Sample 46 NOA1_1_11_5


title: RNA_Sox17FKBP_24h_R2


title: Sample 39 NOA1_1_10_1


title: RNA_Sox17FKBP_6h_R2


title: HPMEC, Poly(I:C)-, NMN 0.1 mM, rep 2


title: RNA_Sox17FKBP_6h_R1


title: HCAEC, poly(I:C)+, NMN 10 mM, rep 3


title: RNA_Gata6FKBP_72h_R2


title: Sample 38 NOA1_1_1_8


title: RNA_Sox17FKBP_0h_R2

value: DMSO


title: LabeledRNA_TF1_IDH2R140Q_Rep1

description: 4sU-labeled RNA

value: TT-seq


title: HCAEC, poly(I:C)+, NMN 10 mM, rep 2


title: Sample 42 NOA1_1_10_8


title: RNA_Gata6FKBP_72h_R1


title: Sample 36 NOA1_1_1_6


title: RNA_Gata6FKBP_96h_R2


title: HCAEC, poly(I:C)+, NMN 10 mM, rep 1


title: HPMEC, Poly(I:C)-, NMN 0.1 mM, rep 3

value: lung

value: HPMEC


title: LabeledRNA_TF1_IDH2WT_Rep1

description: 4sU-labeled RNA


title: HCAEC, poly(I:C)+, NMN 0 mM (ctrl), rep 2

value: endothelial cells


title: HCAEC, poly(I:C)+, NMN 1 mM, rep 3


title: Sample 37 NOA1_1_1_7


title: RNA_Gata6FKBP_96h_R1


title: LabeledRNA_TF1_IDH2R140Q_Rep2

description: 4sU-labeled RNA

value: TF-1 IDH2R140Q

value: acute myeloid leukemia


title: HCAEC, poly(I:C)+, NMN 0 mM (ctrl), rep 1


title: RNA_Gata6FKBP_48h_R2


title: HCAEC, poly(I:C)+, NMN 1 mM, rep 2


title: Runx1OE_ATAC_rep2

description:
ATAC-seq
Runx1OE_ATAC_genrich_narrowPeak.txt

data_processing:
Fastq files were aligned to the mouse reference genome GRCm38/mm10 using Bowtie2 (v3.5.1).
Mitochondrial reads using Samtools (v.1.9) or Picard (v.3.0.0).
Reproducible peak calling was performed using a HOMER (v.4.11.1) adaptation of the Irreproducibility Discovery Rate (IDR) tool according to ENCODE guideline.
Supplementary files format and content: GRCm38/mm10
Supplementary files format and content: Peak file (txt) for C&R,  ChIP-seq, and ATAC-seq

source_name: bone-marrow

growth_protocol: For pro-T cells obtained from OP9-Dll1 culture, Multipotent bone marrow progenitor cells were cultured with OP9-Dll1 cells in  OP9 medium (20% FBS, 2mM glutamine, 100 IU/ml penicillin, 100 mg/ml streptomycin, and 50 µM β-ME in α-MEM).   Cells were supplemented with  IL-7, Flt3-ligand  (10 ng/ml each) under 37 °C, 7% CO2 environment.

extract_protocol:
For delivering retroviral vectors, bone-marrow progenitor cells were co-cultured with OP9-Dll1 for 2 days, then viral supernatant were supplemented with 8 ug/ml polybrene and centrifuged for 2 hours at 500g at 32'C
DNA was isolated using phenol-chloroform-isoamyl alcohol after CUT&RUN.  Zymo ChIP DNA Clean & Concentrator was used to clean eluted DNA after ChIP and transposition (for ATAC).
Sequencing libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit for C&R and ChIP-seq. ATAC-seq library was generated by following previously published protocols (Buenrostro et al., 2015  PMID: 25559105).

treatment_protocol: For Scid.adhd.2c2 (P2C2) cells, cells were maintained  in  P2C2 medium(10%  FBS, 2 mM glutamine, 100 IU/mL penicillin, 100 ug/mL streptomycin, 0.1 mM sodium pyruvate, non-essential amino acids, and 50 uM b-mercaptoethanol in RPMI1640) under 37 °C, 5% CO2 environment.

value: bone-marrow

value: BM progenitor-derived T  progenitor cells (DNs) in Phase1 (cKit high)

value: Bcl2 transgenic

value: Cultured on OP9-Dll1 with IL-7 and Flt3l for total 4 days, MSCV_Runx1_NGFR and Banshee_shRandom_mCherr vectors ere introduced  from day3 to day4 (for 2 days)


title: EV_Control_ATAC_rep2

description:
ATAC-seq
EV_Control_ATAC_genrich_narrowPeak.txt

value: Cultured on OP9-Dll1 with IL-7 and Flt3l for total 4 days, MSCV_EV_NGFR and Banshee_shRandom_mCherr vectors ere introduced  from day3 to day4 (for 2 days)


title: Runx1OE_ATAC_rep1


title: Sample 35 NOA1_1_1_5

value: nonobstructive azoospermia (NOA)


title: EV_Control_ATAC_rep1


title: Sample 34 NOA1_1_1_2


title: RNA_Gata6FKBP_24h_R1

value: cXEN


title: RNA_Gata6FKBP_24h_R2

value: Extraembryonic endoderm stem cells


title: Sample 33 NOA1_1_1_1

value: testis


title: HCAEC, poly(I:C)+, NMN 1 mM, rep 1

value: coronary artery

value: HCAEC


title: HCAEC, poly(I:C)+, NMN 0.1 mM, rep 3


title: P2C2_pMXs_PU1_MSCV_Runx1_1%_input_rep3

source_name: DN3-like Scid.adhd.2c2 (P2C2) cells

value: DN3-like Scid.adhd.2c2 (P2C2) cells

value: DN3-like cell line

value: pMXs-PU.1l-NGFR vector and MSCV_Runx1-HA_mCherry vectors were introduced for 2 days


title: Sample 32 RNA_Normal_4_7

description:
exp.log2TPM.Normal.tsv.gz
Info.Normal.tsv.gz

data_processing:
library strategy: Single-cell tagged reverse transcription sequencing (STRT-seq)
Illumina CASAVA version 1.8 were used to the basecalling.
For RNA part, we used specific cell barcode (8 bp) in read 2 to separate single cell R2 reads and used read ID to extract the corresponding R1 reads. Template switch oligo (TSO) sequence, low quality bases and ployA tails were then removed. The clean R1 reads were mapped to human reference genome hg38 (downloaded from UCSC genome browser) with Hisat2 (v2.1.0) in single-end module with default settings. HTSeq package (v0.6.1) was used to count uniquely mapped reads and cell-specific barcodes were used to group the uniquely mapped reads. Finally, distinct UMIs for each gene were counted as the transcript copy number and normalized to TPM value. Gene expression level was shown as log2 (TPM/10+1).
For DNA part, we used Trim_galore (v 0.3.3) and Cutadapt (v 1.2.1) to remove adaptor sequence, low quality bases and 6 bp random primers in raw data. The clean reads were mapped to human reference genome hg38 using Bismark (v0.7.6) in paired-end and non_directional module. Due to a large number of chimeric reads generated during post-bisulfite adaptor tagging (PBAT) library construction, the unmapped read 1 and read 2 were realigned in single-end and non_directional module separately to rescue more reads. SAMtools (v0.1.18) was used to remove duplicate reads, only uniquely mapped reads were used for downstream analysis. Cytosines in WCG (W = A/T) context were used to reflect DNA methylation level, while those in GCH (H = A/C/T) context were used to reflect chromatin accessibility.
Assembly: hg38
Supplementary files format and content: text file
Supplementary files format and content: WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

value: male

value: Normal


title: HCAEC, poly(I:C)+, NMN 0.1 mM, rep 2

value: endothelial cells


title: P2C2_pMXs_Control_MSCV_Runx1_1%_input_rep3

value: pMXs-empty-control-NGFR vector and MSCV_Runx1-HA_mCherry vectors were introduced for 2 days


title: RNA_Gata6FKBP_48h_R1


title: Sample 31 RNA_Normal_4_6


title: RNA_Gata6FKBP_6h_R1


title: RNA_Gata6FKBP_6h_R2


title: HCAEC, poly(I:C)+, NMN 0.1 mM, rep 1


title: HCAEC, Poly(I:C)-, NMN 0 mM (ctrl), rep 3


title: P2C2_pMXs_PU1_MSCV_Runx1_aHA_ChIP_rep3

description:
Rabbit anti-HA (Stem cell technologies 3724S)
P2C2_pMXs_PU1_MSCV_Runx1OE_aHA_ChIP_IDR_rep1_rep3.txt


title: RNA_Gata6FKBP_0h_R2

value: DMSO


title: OP9_DN1_aIgG_CnR_rep4

description: guinea pig anti-IgG antibody (Antibodies-Online, ABIN101961)

data_processing:
Fastq files were aligned to the mouse reference genome GRCm38/mm10 using Bowtie2 (v3.5.1).
Mitochondrial reads using Samtools (v.1.9) or Picard (v.3.0.0).
Reproducible peak calling was performed using a HOMER (v.4.11.1) adaptation of the Irreproducibility Discovery Rate (IDR) tool according to ENCODE guideline.
Supplementary files format and content: GRCm38/mm10
Supplementary files format and content: Peak file (txt) for C&R,  ChIP-seq, and ATAC-seq
Library strategy: CUT&RUN

value: bone-marrow

value: BM progenitor-derived T  progenitor cells (cKit high CD25- DN1)

value: wild-type

value: Cultured on OP9-Dll1 with IL-7 and Flt3l for 5 days


title: P2C2_pMXs_Control_MSCV_Runx1_aHA_ChIP_rep3

description:
Rabbit anti-HA (Stem cell technologies 3724S)
P2C2_pMXs_Control_MSCV_Runx1OE_aHA_ChIP_IDR_rep1_rep3.txt


title: RNA_Gata6FKBP_0h_R1

value: cXEN


title: HCAEC, Poly(I:C)-, NMN 0 mM (ctrl), rep 2


title: Q1-2mix_IL10

data_processing:
For BulkRNA sequencing, libraries were sequenced on Illumina NovaSeq6000, with 150bp from read 1 & read 2,and at a depth of 50-72 million reads per sample.
Reads were cleaned and quality checked using Fastp v0.20.1
High-quality reads were then imported into STAR v2.7.5a for alignment into BAM files.
BAM files were imported into the RSEM v1.3.3 for expected counts, FPKM and TPM estimation.
Expected counts table was imported into the DESeq2 v1.30.0 for DEG analysis.
Genome_build: The mouse genome mm10 (GRCm38.101)
Supplementary_files_format_and_content: DESeq2 normalized abundance measurements in .csv file.

source_name: Orthotopic oral tumor tissue

growth_protocol: 5*106 of MTC-Q1 cancer cells were orthotopic injection in C57BL/6 mice.

extract_protocol:
Trizol protocol for tissue RNA extraction. Extracted RNA were quantificated by using Qubit fluorometer with Quant-iT RNA BR assay kit.
Libraries were prepared using QIAseq FastSelect RNA Removal Kit_Human Cyto & Mito rRNA + Illumina TruSeq Stranded mRNA Sample Prep Kit + limited cycles of PCR by KAPA HiFi Polymerase following the directions of the manufacturer. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The treatment of IL10/CSF1R fusion protein (twice per week) for totoal 6 doses when tumor size reach 100 mm3. Tumor tissues isolated (~100 mm3) isolated and total RNA were extracted by Trizol, followed by cDNA were sequenced by  Illumina NovaSeq6000.

value: recombinant IL10-Fc protein

value: Orthotopic oral tumor tissue

value: oral cancer


title: OP9_DN1_aIgG_CnR_rep3


title: Sample 28 RNA_Normal_4_3

value: testis


title: Sample 25 RNA_Normal_3_8


title: Sample 26 RNA_Normal_4_1


title: OP9_DN1_aRunx1_CnR_rep3

description:
Rabbit anti-Runx3 (provided from Dr. Levanon and Dr. Groner, Levanon et al., 2014)
DN1_Runx1_CnR_IDR_peaks_score10.txt


title: Sample 27 RNA_Normal_4_2


title: HCAEC, Poly(I:C)-, NMN 0 mM (ctrl), rep 1

value: coronary artery

value: HCAEC


title: HCAEC, Poly(I:C)-, NMN 10 mM, rep 3


title: HCAEC, Poly(I:C)-, NMN 10 mM, rep 2


title: Q1-2mix_BF10

value: IL10/CSF1R (BF10) fusion protein


title: HCAEC, Poly(I:C)-, NMN 10 mM, rep 1


title: Q1-2mix_Ctrl

value: Control isotype (IgG1-Fc)


title: OP9_DN1_aRunx1_CnR_rep2


title: Sample 24 RNA_Normal_3_7

value: male

value: Normal


title: IL10_CD45+

data_processing:
For Single-cell RNA sequencing, libraries were sequenced on Illumina NovaSeq 6000, with 150 bases from read 1 and read 2, and at a depth of 554-721 million reads per sample.
The data was processed with the Cell Ranger pipeline (version 5.0.1, 10X Genomics) and mapped to the mm10 (GENCODE vM23/Ensembl 98) genome assembly.
Genome_build: The mouse genome mm10 (GENCODE vM23/Ensembl 98)
Supplementary_files_format_and_content: Tab-delimited text files containing genes by barcode counts matrices, barcode file and gene list per sample and aggregated all sample using cellranger-aggr function.

growth_protocol: 5*10^6 of MTC-Q1 cancer cells were orthotopic injection in C57BL/6 mice.

extract_protocol:
Tumor tissues were dissociated by tumor dissociation kit (MACS) and remove dead cells by dead cell removal kit (MACS). CD45+ immune cell isolation were isolated by CD45+ microbeads.The single-cell suspension from tumor with the viability over 80% was loaded onto the 10 × Genomics Next GEM Chip G for target capture of ~10,000 cells/chip.
Libraries were prepared using a Chromium Next GEM Single Cell 3' Reagent Kit (v3.1 kit) following the directions of the manufacturer. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The treatment of IL10/CSF1R fusion protein (twice per week) for totoal 6 doses when tumor size reach 100 mm3

value: Oral tumor tissue

value: CD45+ cells


title: Sample 30 RNA_Normal_4_5


title: OP9_DN1_aRunx1_CnR_rep1

value: bone-marrow


title: Sample 23 RNA_Normal_3_6


title: Sample 29 RNA_Normal_4_4


title: Ctrl_CD45+


title: Phase1 pro-T cells, HTO-derived exp2

description: Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

data_processing:
Single-cell RNA-seq data were processed using 10X Cellranger 3.0.0 software. Standard cellranger-mm10-3.0.0 reference annotations were loaded to the pipeline for read mapping and gene quantification.
For hashtag data, Read 1 includes cell barcode and UMI; read 2 includes HTO (cell hashing) sequences. Valid cell barcodes identified in CellRanger pipeline from cDNA library data were used as cell IDs, and the HTO sequences were mapped to a 15 bases reference HTO list from in house hashtag_tool v1, count was quantified by UMI.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab separated txt and tsv table files and matrix files

extract_protocol:
single cell droplet RNA-seq library preparation was performed with 10x Chromium v3
Multiple samples were stained for surface markers and barcoded cell hashing antibodies separately.

value: BM progenitor-derived T  progenitor cells (DNs) in Phase1 (cKit high)

value: Bcl2 transgenic

value: Cultured on OP9-Dll1 with IL-7 and Flt3l for total 4-8 days. MSCV vector or E42 gRNA expressing vectors were delivered on day 2.


title: HCAEC, Poly(I:C)-, NMN 1 mM, rep 3

value: endothelial cells


title: Phase1 pro-T cells, mRNA-derived cDNA exp2

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CSF1R_CD45+

value: CSF1R antibody


title: HCAEC, Poly(I:C)-, NMN 1 mM, rep 2


title: P2C2_pMXs_PU1_MSCV_Runx1_1%_input_rep2

data_processing:
Fastq files were aligned to the mouse reference genome GRCm38/mm10 using Bowtie2 (v3.5.1)
Mitochondrial reads using Samtools (v.1.9)
Reproducible peak calling was performed using a HOMER (v.4.11.1) adaptation of the Irreproducibility Discovery Rate (IDR) tool according to ENCODE guideline
Assembly: GRCm38/mm10
Supplementary files format and content: peak file (txt) for C&R and ChIP-seq

extract_protocol:
DNA was isolated using phenol-chloroform-isoamyl alcohol after CUT&RUN.  Zymo ChIP DNA Clean & Concentrator was used to clean eluted DNA after ChIP.
Sequencing libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit
CUT&RUN and ChIP-seq

value: DN3-like Scid.adhd.2c2 (P2C2) cells

value: DN3-like cell line

value: pMXs-PU.1l-NGFR vector and MSCV_Runx1-HA_mCherry vectors were introduced for 2 days


title: HCAEC, Poly(I:C)-, NMN 1 mM, rep 1

value: coronary artery


title: Q1-2mix_CSF1R

value: Orthotopic oral tumor tissue

value: oral cancer


title: Sample 21 RNA_Normal_3_4

value: testis


title: P2C2_pMXs_Control_MSCV_Runx1_1%_input_rep2

value: pMXs-empty-control-NGFR vector and MSCV_Runx1-HA_mCherry vectors were introduced for 2 days


title: HCAEC, Poly(I:C)-, NMN 0.1 mM, rep 3

value: HCAEC


title: Sample 19 RNA_Normal_3_2

value: male

value: Normal


title: HCAEC, Poly(I:C)-, NMN 0.1 mM, rep 1


title: HCAEC, Poly(I:C)-, NMN 0.1 mM, rep 2


title: Sample 18 RNA_Normal_3_1


title: P2C2_pMXs_PU1_MSCV_Runx1_aHA_ChIP_rep2

description: Mouse anti-HA (sc-7392 x)


title: P2C2_pMXs_Control_MSCV_Runx1_aHA_ChIP_rep2

description: Mouse anti-HA (sc-7392 x)


title: Sample 22 RNA_Normal_3_5


title: AAV-GFAP-Gq-DREADD_106

city: Indianapolis

first: Stephanie

last: Philtjens

state: Indiana

address: 320 W. 15th Street, NB Bldg Rm 103

institute: Indiana University School of Medicine

description: single cell RNA sequencing

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v.3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v.3.0.2)
single-cell 3' gene counting, Cell Ranger Single Cell Software Suite (v.3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v.3.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package

source_name: Hippocampus and Cortex

extract_protocol:
8-week old C57BL/6J male mice were injected the AAV-GFAP-hM3D(Gq)-mCherry virus in the hippocampus and cortex using a stereotaxic instrument. They were given either CNO or Saccharin for 8 weeks in their drinking water. Upon tissue collection, the mice were euthanized and perfused using ice-cold PBS. The hippocampal and cortical tissue containing the virus was dissected, minced with a razor blade and incubated for 30 min in ice-cold Accutase at 4 degrees C. The dissociated tissue was centrifuged at 300g for 10 min at 4°C. The pellet was resuspended in ice-cold Hanks’ Balanced Salt solution (Life Technologies, Cat. No. 14025-092) and triturated with a 15 mL serological pipette. This step was repeated until the entire tissue was dissociated. Next, the sample was filtered first through a 70 μm cell strainer, followed by a 40 μm cell strainer. The cells were centrifuged at 300g for 5 min at 4°C. Myelin removal was performed following the Miltenyi’s Myelin Depletion Protocol. In short, the pellet obtained during cell isolation was resuspended in magnetic-activated cell sorting (MACS) buffer (0.5% BSA in PBS, Thermofisher, Cat. No. AM2618), myelin removal beads (Miltenyi Biotec, Cat. No. 130-096-733) were added, and the solution was incubated for 15 min at 4°C. The cells were centrifuged at 300g for 10 min at 4°C, the pellet was resuspended in MACS buffer and the solution was passed through LS columns (Miltenyi Biotec, Cat. No. 130-042-401). The cells were centrifuged at 300g for 15 min at 4°C, the pellet was resuspended in MACS buffer, centrifuged again at 300g for 15 min at 4°C and resuspended in PBS containing 0.01% BSA. The obtained single cells were subjected to droplet-based single cell RNA sequencing. The 10x Genomics ChromiumTM Single Cell 3’ Library & Gel Bead Kit v2 was used per manufacturer’s instructions. The libraries were sequenced on an Illumina NovaSeq 6000 SP.
10x Genomics ChromiumTM Single Cell 3’ Library & Gel Bead Kit v2  protocol

treatment_protocol: Mouse samples 104 and 105 were given CNO in their drinking water for 8 weeks, while sampples 106 and 107 were given saccharin in their drinking water

value: brain

tag: group

value: Saccharin

value: Gq-DREADD


title: AAV-GFAP-Gq-DREADD_105

description: single cell RNA sequencing

value: CNO


title: OP9_Phase1_Runx1OE_aIgG_CnR_rep2

value: bone-marrow

value: BM progenitor-derived T  progenitor cells (DNs) in Phase1 (cKit high)

value: Bcl2 transgenic

value: Cultured on OP9-Dll1 with IL-7 and Flt3l for total 4 days, MSCV_Runx1_control_mCherry vector was introduced  from day3 to day4 (for 2 days)


title: BT67_H3K27ac_romi_Input_3

data_processing:
Base calls were performed using bcl2fastq for novaseq output
ChIP-seq reads were first trimmed for adapter sequences and low quality score bases using Trimmomatic
The resulting reads were mapped to the human reference genome (hg38) using BWA-MEM in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were marked using Picard tools (https://broadinstitute.github.io/picard/)
Peaks were called using MACS2 software suite. A “reference peak set” was obtained by merging ChIP-seq peaks from each samples using bed tools merge with parameters: -sorted -d -125. Peaks were associated with the nearest TSS of genes (+/- 20kb) using the annotate Peaks command from HOMER software suite (https://bedtools.readthedocs.io/).
peak enrichments were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM)
Assembly: hg19

treatment_protocol: For H3K27ac ChIP-seq, the BT67 romidepsin and DMSO treated cells were crosslinked with 1% formaldehyde (F) for 10 minutes. For HDAC2 and SMAD3 ChIP-seq, the dual crosslinked (DCL) (crosslinking with 1% formaldehyde for 10 minutes followed by DSP (dithiobis(succinimidyl propionate)) crosslinking) BT 67 cells were used.

value: Brain tumour stem cell

value: romidepsin

value: 72 hours


title: OP9_Phase1_Runx1OE_aIgG_CnR_rep3


title: BT67_H3K27ac_romi_Input_1


title: OP9_Phase1_Runx1OE_aIgG_CnR_rep1

value: Cultured on OP9-Dll1 with IL-7 and Flt3l for total 4 days, MSCV_Runx1_mCherry vector was introduced  from day3 to day4 (for 2 days)


title: AAV-GFAP-Gq-DREADD_104

description: single cell RNA sequencing


title: Sample 15 RNA_Normal_2_2

value: testis


title: BT67_H3K27ac_romi_Input_2


title: Sample 16 RNA_Normal_2_3


title: BT67_H3K27ac_DMSO_Input_3

value: DMSO


title: BF10_CD45+

value: IL10/CSF1R fusion protein

value: Oral tumor tissue

value: CD45+ cells


title: Sample 20 RNA_Normal_3_3

value: male

value: Normal


title: G93A_B6_5M_C_rep3

data_processing:
The reference genome assemblies and gene annotations, the mouse genome version UCSC mm10  were retrieved from iGenomes
The Illumina adapter sequences, as well as low quality bases (quality score < 20), were trimmed from 3’-ends of the sequencing reads with the Trim Galore v0.5.0
The reads were qualified with FastQC v0.11.8 before and after trimming.
The processed reads were mapped on the reference genome assembly with HISAT2 v2.1.0
Mapping reads prepared with the stranded kit was processed by employing strand specificity information. The alignments on rDNA regions were removed with BEDTools v2.25.0. From mapping data, expressions of the individual annotated genes were quantified with StringTie v1.3.5
Assembly: mm10
Supplementary files format and content: MS Excel file including CPM values of the individual genes for each sample and the results of the differential expression analysis

source_name: isolated microglia

extract_protocol:
For the RNA-seq of the mouse samples, total RNA was extracted from MACS-isolated microglia of each models using an RNeasy Micro Kit (Qiagen, Hilden, Germany). The RNAs were sampled from cerebral cortices of 8-month-old AppNL-G-F/NL-G-F and 7-month-old rTg4510 mice and lumbar spinal cords of 5-month-old SODG93A mice together with the corresponding wild-type or non-Tg control mice, respectively.
Libraries were prepared by using TruSeq mRNA or TruSeq Stranded mRNA (Illumina, San Diego, CA, USA), and, from these libraries, 151-nt paired-end reads were sequenced on the HiSeq X Ten with the HiSeq X Reagent Kits (Illumina)

value: isolated microglia


title: AAV-GFAP-Gq-DREADD_107

description: single cell RNA sequencing

value: brain

value: Saccharin

value: Gq-DREADD


title: OP9_Phase1_Control_aIgG_CnR_rep1

value: bone-marrow

value: BM progenitor-derived T  progenitor cells (DNs) in Phase1 (cKit high)

value: Bcl2 transgenic

value: Cultured on OP9-Dll1 with IL-7 and Flt3l for total 4 days, MSCV_empty_control_mCherry vector was introduced  from day3 to day4 (for 2 days)


title: Sample 14 RNA_Normal_2_1


title: OP9_Phase1_Control_aIgG_CnR_rep2


title: WT_B6_5M_C_rep4

value: WT


title: G93A_B6_5M_C_rep2


title: Sample 13 RNA_Normal_1_7.2_5


title: BT67_H3K27ac_romi_3

extract_protocol:
The crosslinked cells were lysed in hypotonic cell lysis buffer and nuclei were pelleted and lysed using 10% SDS (0.3% final concentration) and sonicated to achieve the chromatin size between 200-1000bp.
ChIP-seq libraries were prepared using NEB II ultra, w/o shearing kit.

value: Brain tumour stem cell

value: romidepsin

value: 72 hours

value: H3K27ac (abcam, cat#ab177178)


title: BT67_H3K27ac_DMSO_Input_2

value: DMSO


title: OP9_Phase1_Runx1OE_aRunx1_CnR_rep2

description: Rabbit anti-Runx1 (ab23980)

value: Cultured on OP9-Dll1 with IL-7 and Flt3l for total 4 days, MSCV_Runx1_mCherry vector was introduced  from day3 to day4 (for 2 days)


title: G93A_B6_5M_C_rep4


title: BT67_H3K27ac_DMSO_Input_1


title: Sample 17 RNA_Normal_2_4

value: testis

value: male


title: Sample 12 RNA_Normal_1_6

value: Normal


title: OP9_Phase1_Runx1OE_aRunx1_CnR_rep3

description: Rabbit anti-Runx1 (ab23980)


title: Sample 11 RNA_Normal_1_5


title: WT_B6_5M_C_rep2

value: isolated microglia


title: OP9_Phase1_Runx1OE_aRunx1_CnR_rep1

description: Rabbit anti-Runx1 (ab23980)


title: Sample 9 RNA_Normal_1_3


title: BT67_H3K27ac_romi_1


title: OP9_Phase1_Control_aRunx1_CnR_rep2

description: Rabbit anti-Runx1 (ab23980)


title: WT_B6_5M_C_rep1


title: Sample 10 RNA_Normal_1_4


title: Sample 8 RNA_Normal_1_2


title: APP_B6_8M_C_rep4

value: App


title: G93A_B6_5M_C_rep1


title: BT67_H3K27ac_DMSO_3


title: OP9_Phase1_Control_aRunx1_CnR_rep1

description: Rabbit anti-Runx1 (ab23980)


title: BT67_H3K27ac_DMSO_2


title: APP_B6_8M_C_rep3


title: WT_B6_5M_C_rep3


title: Sample 7 RNA_Normal_1_1


title: BT67_H3K27ac_romi_2


title: BT67_H3K27ac_DMSO_1


title: Sample 5 RNA_NOA2_2

description:
exp.log2TPM.NOA2.tsv.gz
Info.NOA2.tsv.gz

value: nonobstructive azoospermia (NOA)


title: Thy_DN3_aHEB_CnR_rep1

description: Rabbit anti-HEB (Proteintech 14419-1-AP)

source_name: thymus

value: thymus

value: Thymic T progenitor cells after T-lineage commitment (cKit-CD44- CD25+ DN3)

value: wild-type


title: BT67_DMSO_3

data_processing:
Base calls were performed using bcl2fastq for novaseq output
NCBI RefSeq mRNA transcripts were quantified using kallisto 0.42.4 with a mean insert size of 180 and a std dev of 20
Supplementary files format and content: counts

extract_protocol:
Total RNA was extracted using the RNeasy Kit (Qiagen, cat# 74104) and quantified using Nanodrop.
RNA libraries were prepared using NEB ultra II directional mRNA library kit following manufacturer's protocols.

treatment_protocol: The BTSC line, BT67, was treated with 50picomolar dose of romidepsin and vehicle control for 72 hours and pellets were collected from three biological replicates


title: BT67_romidepsin_3


title: Thy_DN3_aIgG_CnR_rep3


title: WT_B6_8M_C_rep4


title: Sample 6 RNA_NOA2_3


title: BT67_romidepsin_2


title: Sample 3 RNA_NOA1_3

description:
exp.log2TPM.NOA1.tsv.gz
Info.NOA1.tsv.gz


title: Sample 4 RNA_NOA2_1


title: WT_B6_8M_C_rep3


title: OP9_DN1_aIgG_CnR_rep2

value: bone-marrow

value: BM progenitor-derived T  progenitor cells (cKit high CD25- DN1)

value: Cultured on OP9-Dll1 with IL-7 and Flt3l for 5 days


title: BT67_DMSO_2

value: Brain tumour stem cell


title: Sample 1 RNA_NOA1_1


title: WT_B6_8M_C_rep2

value: WT


title: BT67_romidepsin_1

value: romidepsin

value: 72 hours


title: OP9_DN1_aIgG_CnR_rep1


title: OP9_DN1_aRunx3_CnR_rep1

description: Rabbit anti-Runx3 (provided from Dr. Levanon and Dr. Groner, Levanon et al., 2014)


title: BT67_DMSO_1

value: DMSO


title: WT_B6_8M_C_rep1


title: OP9_DN1_aRunx3_CnR_rep2


title: Thy_DN3_aE2A_CnR_rep1

description: Rabbit anti-E2A (ab228699)


title: APP_B6_8M_C_rep2


title: APP_B6_8M_C_rep1


title: Lung squamous cell carcinoma from Patient 4

status: Public on Jul 08 2023

type: RNA

city: Botucatu

first: Natália

last: Bertoni

state: São Paulo

address: Av. Prof. Mário Rubens Guimarães Montenegro

department: Surgery and Orthopedics

country: Brazil

institute: São Paulo State University (UNESP)

hyb_protocol: Following labeling, the biotin-labeled sample were hybridized for 16 hr at 48ºC on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix GeneChips Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software.

label: biotin

source_name: Pool Tumor

label_protocol: Biotinylated cRNA were preprared according to the standard Affymetrix protocol from 130 ng total RNA (FlashTag™ Biotin HRS RNA Labeling Kit - Thermo Fisher Scientific, Walthmam, MA, USA).

extract_protocol: RNA from solid, fresh frozen tumor and normal tissues were isolated using the TRIzol® Reagent protocol (invitrogen/Thermo Fisher Scientific) followed by purification in the RNeasy® Mini Ki (Qiagen). RNA extraction from plasma was performed using the miRNeasy® Serum/Plasma Kit (Qiagen). All steps were performed as recommended by the manufacturers.

treatment_protocol: Surgically resected tumor and normal tissues were subject to histological frozen section analysis to ensure at least 90% presence of tumor or normal cells before RNA extraction. Peripheral blood was collected in BD Vacutainer® EDTA tube (Becton Dickinson, NJ, USA) and plasma samples were obtained before RNA extraction.

value: lung squamous cell carcinoma

tag: gender

value: Male

tag: smoking

value: Yes (50 packs/year)

tag: tumor grade

value: Moderately differentiated (50%) and Poorly differentiated (50%)

tag: tumor size

tag: nodal status

tag: distant metastasis

value: X

tag: Stage

value: IIIA


title: Lung squamous cell carcinoma from Patient 7

tag: tissue

value: Female

tag: age

value: Yes (2 straw cigarretes/day/60 years)

value: Moderately differentiated (100%)


title: Lung squamous cell carcinoma from Patient 6

value: Yes (3 straw cigarretes/day/50 years)

value: IIB


title: Sample 2 RNA_NOA1_2

value: testis

tag: Sex

value: male

tag: condition

value: nonobstructive azoospermia (NOA)


title: Plasma from Patient 4

source_name: Pool Plasma

value: plasma


title: Plasma from Patient 5

value: Yes (64 packs/year)

value: Poorly differentiated (85%) and Moderately differentiated (15%)

value: IB


title: Lung squamous cell carcinoma from Patient 2

value: lung squamous cell carcinoma

value: No.

value: IIA


title: Plasma from Patient 1

value: Male

value: Yes (15 straw cigarretes/day/58 years)

value: Moderately differentiated (70%) with Well differentiatd areas (30%)

value: X


title: Plasma from Patient 7

value: Female

value: Yes (2 straw cigarretes/day/60 years)

value: Moderately differentiated (100%)


title: Histologically normal lung Patient 3

source_name: Pool Normal

value: histologically normal lung

value: Former smoker (100 packs/year until 2016)


title: Plasma from Patient 6

value: Yes (3 straw cigarretes/day/50 years)

value: IIB


title: Histologically normal lung Patient 4

value: Yes (50 packs/year)

value: Moderately differentiated (50%) and Poorly differentiated (50%)

value: IIIA


title: Histologically normal lung Patient 6


title: Histologically normal lung Patient 1

value: IB


title: Histologically normal lung Patient 5

value: Yes (64 packs/year)

value: Poorly differentiated (85%) and Moderately differentiated (15%)


title: Plasma from Patient 8

value: plasma

value: Male

value: Former smoker (45 packs/year until 2008)

value: Well differentiated (100%)


title: Histologically normal lung Patient 2

value: Female

value: No.

value: X

value: IIA