title: Patient 1 month after treatment with guideline based therapy_100

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

institute: Tsukuba university

description: Library name: 100_1

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 20.0.0; Qiagen, Redwood City, CA).
Assembly: hg19
Supplementary files format and content: excel files include expression values of total counts, RPKM, TPM, and CPM for each sample

source_name: Whole blood cells

extract_protocol:
Silica-membrane-based RNA isolation and purification in a spin-column format were performed using the PAXgene Blood RNA kit (Qiagen). Extracted RNA was globin-cleared using the Ambion GLOBINclear kit (Thermo Fisher, Waltham, MA). Then, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) and converted to an Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). CD19, CD56, CD123, and CD235a antibodies was used to obtain remaining eosinophils. Total RNA from eosinophils was extracted using TRIzol™ Reagent (Invitrogen). Then, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) and converted to an Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole blood cells


title: chicken hindlimb ID3, 7days11hours, 04

status: Public on Dec 08 2025

type: SRA

city: Yokohama

first: Satomi

last: Ono

state: Kanagawa

address: B-17, 4259, Nagatsuta-cho, Midori-ku

country: Japan

institute: Institute of Science Tokyo

library_source: transcriptomic

data_processing:
Read 1 reads were processed with fastp (version 0.21.0) using the following parameters: --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31.
The trimmed reads were then mapped to the chicken reference sequences of GCF_000002315.6_rna.fna, using BWA mem (version 0.7.17-r1188)  with the default parameters.
The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0).
Assembly: GCF_000002315.6_rna.fna
Supplementary files format and content: CSV

molecule: total RNA

organism: Gallus gallus

source_name: Interdigital region 3 of chicken hindlimb

extract_protocol:
RNA was extracted using TRIzol-LS Reagent (Molecular Research Center) in combination with an AcroPrep Advance 96-well Long Tip Filter Plate for Nucleic Acid Binding (Pall) as previously described (Ujibe, K., Nishimura, K., Kashima, M., and Hirata, H. (2021). Direct-TRI: High-throughput RNA-extracting Method for all Stages of Zebrafish Development. Bio-protocol 11(17): e4136. DOI: 10.21769/BioProtoc.4136.). 180 ng of total RNA were used for the construction of libraries.
RNA-Seq library preparation were conducted according to the Lasy-Seq ver. 1.1 protocol.

treatment_protocol: Chicken embryos from HH30 to HH31 incubated for 7 days +4 hours, +6 hours, +8 hours, and +11 hours (each 6 samples) were dissected and immersed in RNAlater (Sigma-Aldrich), then interdigital region 3 (ID3) were dissected.

tag: tissue

tag: treatment

value: Incubation for 7days and 11hours


title: ChIP-Seq_mES_MED4_CTDP1-12h_rep2

city: Beijing

first: Dexun

last: Ji

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

country: China

institute: Peking University

description: Library name: Sample 16

library_source: genomic

data_processing:
ChIP-seq reads with spike-in were trimmed by Cutadapt (v3.4) and aligned to the mm10 and hg19 genomes using Bowtie2 (v2.3.5.1) in end-to-end mode. Downstream analyses utilized uniquely mapped reads.
RNA-seq reads were trimmed by Cutadapt (v3.4) and aligned to the mm10-dm6 merged genome by STAR (v2.7.10a). Downstream analyses included gene counting by featureCounts (v2.0.1) with spike-in normalization.
Assembly: mm10, hg19, dm6
Supplementary files format and content: Processed bigWig files for each sample in ChIP-seq
Supplementary files format and content: spike-in normalized counts for each sample in RNA-seq

molecule: genomic DNA

organism: Mus musculus

source_name: cell culture

growth_protocol: The cell were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma, D5796) with 15 % fetal bovine serum (FBS) (GeminiBio, 900-108), also supplemented with 1 mM L-glutamine (Gibco, 25030081), 1× nucleosides (Millipore, ES-008-D), 1× nonessential amino acids (Gibco, 11140050), 1× penicillin/ streptomycin (Gibco, 15140122), 1 mM Sodium Pyruvate (Gibco, 11360070), 0.1 mM β-mercaptoethanol (Sigma, M3148), 3 μM CHIR99021 (Selleck, S1036) and 1 μM PD0325901 (Selleck, S1263), 1000 U/ml mouse leukemia inhibiting factor (mLIF) (Milipore, ESG1107). All the cells were cultured in 0.2 % gelatin-coated plates at 37°C and 5% CO2 under humid environment.

extract_protocol: ChIP–seq and RNA-seq were performed as previously described (PMID: 40038320) with two biological replicates per sample.

treatment_protocol: For RPB1 degradation, cells were treated with 2 μg/mL Dox for 13 hours, followed by 1 μM dTAG-13 for the final indicated minutes. For CTDP1-mCherry expression, cells were treated with 2 μg/mL Dox for 12 hours.

value: cell culture

tag: cell line

value: mESC

tag: cell type

value: Teton-WT CTDP1-mCherry


title: ChIP-Seq_mES_MED4_CTDP1-12h_rep1

description: Library name: Sample 15


title: Old, d7, rep6, collagenase-treated hematoma, HTO

city: Berlin

first: Anne

last: Noom

address: Augustenburger Pl. 1

country: Germany

institute: Charité - Universitätsmedizin

description:
Library name: Od7_6c_CSP
10x Genomics
Od7_6c_output_filtered.h5

library_source: other

data_processing:
Sequencing data were processed using the CellRanger pipeline (v7.1.0)
Assembly: mm10
Supplementary files format and content: CellRanger output files: output_filtered_cellblender_0_01.h5

molecule: protein

source_name: Femur

extract_protocol:
The bone marrow was flushed from murine femora using a syringe with PBS containing 2% FCS and passed through a 70um cell strainer. Red blood cells were lysed using ACK lysis buffer for 1 min at RT, followed by washing with PBS + 2% FCS. Cortical bone fragments were subjected to digestion buffer (HBSS with 2 mg/mL collagenase IV and 1 mg/mL DNase II) at 37C for 30 min with gentle shaking. Following digestion, cells were passed through a 70um strainer, washed and resuspended in PBS + 0.04% BSA. Viable single cells were counted using trypan blue and used for downstream single-cell libraries.
Single-cell suspensions from bone marrow and cortical bone were processed using 10x Genomics Chromium Single Cell 3' v3 chemistry (10x Genomics) according to the manufacturer's protocol. Cells were first labeled with TotalSeq-B hashtag oligonucleotide (HTO) antibodies (BioLegend) for multiplexing. After washing to remove unbound antibodies, labeled cells were loaded into the Chromium Controller for droplet encapsulation. Libraries for both gene expression (GEX) and HTO were generated from the same Gel Bead-in Emulsion (GEM) reaction. Following reverse transcription, GEMs were broken and cDNA was purified. Separate amplification and indexing steps were performed for GEX and HTO libraries, which were then pooled and sequenced according to the 10x Genomics recommendations.

value: Femur

tag: Sex

value: Female

tag: age

tag: injured?

value: Yes

tag: library type

value: HTO

tag: hto

value: TotalSeq-B0301 anti-mouse Hashtag 1 (BM), TotalSeq-B0303 anti-mouse Hashtag 3 (CB), TotalSeq-B0304 anti-mouse Hashtag 4 (H)


title: chicken hindlimb ID3, 7days11hours, 03

value: Interdigital region 3 of chicken hindlimb


title: Patient before treatment with guideline based therapy_100

description: Library name: 100_0

organism: Homo sapiens


title: A01

city: Santa Cruz

first: Vikas

last: Peddu

email: vpeddu@ucsc.edu, dkim142@ucsc.edu

state: CA

address: 1156 High Street

department: Biomolecular engineering

country: USA

institute: University of California Santa Cruz

data_processing:
We assembled a transcriptome of ~5.5 million transcripts, annotated with the corresponding ENSEMBL transcript IDs, UCSC genome browser repeat instance names, and novel gene IDs from IsoQuant. Transcript counts were aggregated to the gene level for GENCODE genes, and to the repeat ‘family’ level for repeat elements as previously described
Assembly: HG38
Supplementary files format and content: Counts matrix

molecule: polyA RNA

source_name: Plasma

extract_protocol:
Norgen Biotek Plasma/Serum Circulating and Exosomal RNA purification slurry format kit(20)
Illumina libraries were prepared using full-length cDNA generated from the isolated plasma RNA of healthy, Barrett’s esophagus, and esophageal cancer samples using the SMART-Seq HT kit from Takara Bio USA. Final libraries were prepared with the Nextera XT Prep Kit from Illumina and sequenced on an Illumina Novaseq using a 2x151 sequencing chemistry.

value: Plasma

value: cell-free RNA

tag: genotype

value: adenocarcinoma


title: Patient 1 month after treatment with guideline based therapy_99

description: Library name: 99_1


title: ChIP-Seq_mES_MED1_deadCTDP1-12h_rep2

description: Library name: Sample 14

value: Teton-MT CTDP1-mCherry


title: Old, d7, rep6, GEX

description:
Library name: Od7_6_GEX
10x Genomics
6Od7_output_filtered.h5

library_source: transcriptomic single cell

value: mRNA


title: chicken hindlimb ID3, 7days11hours, 01


title: Old, d7, rep6, HTO

description:
Library name: Od7_6_CSP
10x Genomics
6Od7_output_filtered.h5


title: chicken hindlimb ID3, 7days11hours, 02


title: Patient before treatment with guideline based therapy_99

description: Library name: 99_0


title: ChIP-Seq_mES_MED1_deadCTDP1-12h_rep1

description: Library name: Sample 13


title: Old, d7, rep5, collagenase-treated hematoma, GEX

description:
Library name: Od7_5c_GEX
10x Genomics
Od7_5c_output_filtered.h5


title: ChIP-Seq_mES_MED1_CTDP1-12h_rep2

description: Library name: Sample 12


title: ChIP-Seq_mES_MED1_CTDP1-12h_rep1

description: Library name: Sample 11


title: chicken hindlimb ID3, 7days08hours, 06

value: Incubation for 7days and 8hours


title: Patient 1 month after treatment with guideline based therapy_98

description: Library name: 98_1

value: Whole blood cells


title: Patient before treatment with guideline based therapy_98

description: Library name: 98_0


title: Old, d7, rep5, collagenase-treated hematoma, HTO

description:
Library name: Od7_5c_CSP
10x Genomics
Od7_5c_output_filtered.h5


title: ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-60min_rep2

description: Library name: Sample 10

value: RPB1-GFP, Teton-MT CTDP1-dTAG-mCherry


title: chicken hindlimb ID3, 7days08hours, 04


title: Old, d7, rep4, collagenase-treated hematoma, GEX

description:
Library name: Od7_4c_GEX
10x Genomics
Od7_4c_output_filtered.h5


title: chicken hindlimb ID3, 7days08hours, 05


title: ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-40min_rep2

description: Library name: Sample 8

value: cell culture


title: Old, d7, rep4, collagenase-treated hematoma, HTO

description:
Library name: Od7_4c_CSP
10x Genomics
Od7_4c_output_filtered.h5


title: Old, d7, rep7, HTO

description:
Library name: Od7_7_CSP
10x Genomics
7Od7_output_filtered.h5


title: Patient before treatment with guideline based therapy_97

description: Library name: 97_0


title: Patient 1 month after treatment with guideline based therapy_96

description: Library name: 96_1


title: chicken hindlimb ID3, 7days08hours, 03


title: chicken hindlimb ID3, 7days08hours, 02


title: Old, d7, rep4, GEX

description:
Library name: Od7_4_GEX
10x Genomics
4Od7_output_filtered.h5


title: ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-40min_rep1

description: Library name: Sample 7

value: mESC


title: Old, d7, rep4, HTO

description:
Library name: Od7_4_CSP
10x Genomics
4Od7_output_filtered.h5


title: Patient before treatment with guideline based therapy_96

description: Library name: 96_0


title: chicken hindlimb ID3, 7days08hours, 01


title: Old, d7, rep3, GEX

description:
Library name: Od7_3_GEX
10x Genomics
3Od7_output_filtered.h5


title: Old, d7, rep3, HTO

description:
Library name: Od7_3_CSP
10x Genomics
3Od7_output_filtered.h5


title: Patient before treatment with guideline based therapy_95

description: Library name: 95_0


title: Old, d7, rep2, GEX

description:
Library name: Od7_2_GEX
10x Genomics
2Od7_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_97

description: Library name: 97_1


title: ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-0min_rep2

description: Library name: Sample 4


title: chicken hindlimb ID3, 7days06hours, 05

value: Incubation for 7days and 6hours


title: Patient 1 month after treatment with guideline based therapy_94

description: Library name: 94_1


title: ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-60min_rep1

description: Library name: Sample 9


title: ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-20min_rep1

description: Library name: Sample 5


title: chicken hindlimb ID3, 7days06hours, 04


title: chicken hindlimb ID3, 7days06hours, 03


title: ChIP-Seq_mES_RPB1NTD_CTDP1-13h_dTAG-0min_rep2

description: Library name: Sample 2


title: Old, d3, rep7, collagenase-treated hematoma, GEX

description:
Library name: Od3_7c_GEX
10x Genomics
Od3_7c_output_filtered.h5

value: Femur


title: chicken hindlimb ID3, 7days06hours, 02


title: Patient 1 month after treatment with guideline based therapy_93

description: Library name: 93_1


title: Patient before treatment with guideline based therapy_94

description: Library name: 94_0


title: ChIP-Seq_mES_RPB1NTD_CTDP1-13h_dTAG-0min_rep1

description: Library name: Sample 1


title: Patient 1 month after treatment with guideline based therapy_95

description: Library name: 95_1


title: chicken hindlimb ID3, 7days06hours, 06


title: Old, d7, rep2, HTO

description:
Library name: Od7_2_CSP
10x Genomics
2Od7_output_filtered.h5

value: Female


title: Old, d3, rep7, GEX

description:
Library name: Od3_7_GEX
10x Genomics
7Od3_output_filtered.h5

value: Yes


title: Patient 1 month after treatment with guideline based therapy_92

description: Library name: 92_1


title: chicken hindlimb ID3, 7days04hours, 06

value: Incubation for 7days and 4hours


title: WT-28-2

first: Mengfei

last: Song

address: 北京市海淀区颐和园路5号

institute: Peking university

description:
Library name: WT-28-2
WT-28-2

data_processing:
After removing reads with adapter sequences and low quality by fastp, the high-quality reads were mapped to the TAIR10 genome assembly of Arabidopsis thaliana using HISAT2 (version 2.1.0) with parameters “--dta --min-intronlen 50 --max-intronlen 6000”. Only unique mapping and MAPQ score > 20 reads were kept using SAMtools version 1.6 for subsequent analysis.
Assembly: TAIR10
Supplementary files format and content: text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: total seedlings

extract_protocol:
Total RNA from 9-d-old WT and mutant seedlings were isolated using RNeasy Plant Mini Kits (Sigma). Three biological replicates for each sample were subjected to RNA-seq.
Poly (A) RNA from 1 μg total RNA was used to generate the cDNA library according to the TruSeq RNA Sample Prep Kit protocol. The library was then sequenced using a HiSeq Xten system (Illumina).

value: total seedlings

tag: developmental stage

value: 9-day-old seedlings grown under continuous white light at 28 tm

value: WT


title: ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-20min_rep2

description: Library name: Sample 6


title: WT-28-3

address: 北京市海淀区颐和园路5号

description:
Library name: WT-28-3
WT-28-3


title: chicken hindlimb ID3, 7days06hours, 01

value: Interdigital region 3 of chicken hindlimb


title: Old, d3, rep7, HTO

description:
Library name: Od3_7_CSP
10x Genomics
7Od3_output_filtered.h5

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1 (BM), TotalSeq-B0303 anti-mouse Hashtag 3 (CB), TotalSeq-B0304 anti-mouse Hashtag 4 (H)


title: ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-0min_rep1

description: Library name: Sample 3


title: Patient 1 month after treatment with guideline based therapy_91

description: Library name: 91_1


title: WT-28-1

address: 北京市海淀区颐和园路5号

description:
Library name: WT-28-1
WT-28-1


title: Old, d3, rep6, collagenase-treated hematoma, GEX

description:
Library name: Od3_6c_GEX
10x Genomics
Od3_6c_output_filtered.h5

value: mRNA


title: chicken hindlimb ID3, 7days04hours, 05


title: Old, d3, rep6, collagenase-treated hematoma, HTO

description:
Library name: Od3_6c_CSP
10x Genomics
Od3_6c_output_filtered.h5


title: pklpif4-28-3

address: 北京市海淀区颐和园路5号

description:
Library name: pklpif4-28-3
pklpif4-28-3


title: chicken hindlimb ID3, 7days04hours, 04


title: Patient before treatment with guideline based therapy_93

description: Library name: 93_0


title: Patient before treatment with guideline based therapy_91

description: Library name: 91_0


title: pklpif4-28-2

address: 北京市海淀区颐和园路5号

description:
Library name: pklpif4-28-2
pklpif4-28-2


title: chicken hindlimb ID3, 7days04hours, 03


title: Old, d3, rep6, GEX

description:
Library name: Od3_6_GEX
10x Genomics
6Od3_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_90

description: Library name: 90_1


title: chicken hindlimb ID3, 7days04hours, 02


title: Old, d3, rep7, collagenase-treated hematoma, HTO

description:
Library name: Od3_7c_CSP
10x Genomics
Od3_7c_output_filtered.h5


title: pklpif4-28-1

address: 北京市海淀区颐和园路5号

description:
Library name: pklpif4-28-1
pklpif4-28-1


title: Old, d3, rep6, HTO

description:
Library name: Od3_6_CSP
10x Genomics
6Od3_output_filtered.h5


title: Patient before treatment with guideline based therapy_90

description: Library name: 90_0


title: chicken hindlimb ID3, 7days04hours, 01


title: Old, d3, rep5, collagenase-treated hematoma, GEX

description:
Library name: Od3_5c_GEX
10x Genomics
Od3_5c_output_filtered.h5


title: pkl-28-3

address: 北京市海淀区颐和园路5号

description:
Library name: pkl-28-3
pkl-28-3


title: Patient 1 month after treatment with guideline based therapy_89

description: Library name: 89_1


title: chicken hindlimb ID3, noggin, 12h_06

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer’s protocol. 180 ng of total RNA were used for the construction of  libraries.
RNA-Seq library preparation were conducted according to the Lasy-Seq ver. 1.1 protocol.

treatment_protocol: Noggin beads were implanted in the left/right ID3 and PBS beads in the right/left ID3 (6 samples) at HH30.  After 12 hours of incubation, embryos were immersed in RNAlater (Sigma-Aldrich), then interdigital region 3 (ID3) were dissected.

value: Noggin soaked bead implantation


title: Old, d3, rep5, collagenase-treated hematoma, HTO

description:
Library name: Od3_5c_CSP
10x Genomics
Od3_5c_output_filtered.h5


title: Patient before treatment with guideline based therapy_92

description: Library name: 92_0

value: Whole blood cells


title: chicken hindlimb ID3, pbs, 12h_06

value: PBS soaked bead implantation


title: Patient before treatment with guideline based therapy_89

description: Library name: 89_0


title: pkl-28-1

address: 北京市海淀区颐和园路5号

description:
Library name: pkl-28-1
pkl-28-1


title: Patient 1 month after treatment with guideline based therapy_88

description: Library name: 88_1


title: pif4-28-2

address: 北京市海淀区颐和园路5号

description:
Library name: pif4-28-2
pif4-28-2


title: Old, d3, rep5, HTO

description:
Library name: Od3_5_CSP
10x Genomics
5Od3_output_filtered.h5


title: Patient before treatment with guideline based therapy_88

description: Library name: 88_0


title: chicken hindlimb ID3, noggin, 12h_05


title: Old, d3, rep5, GEX

description:
Library name: Od3_5_GEX
10x Genomics
5Od3_output_filtered.h5


title: Old, d3, rep4, collagenase-treated hematoma, GEX

description:
Library name: Od3_4c_GEX
10x Genomics
Od3_4c_output_filtered.h5


title: chicken hindlimb ID3, pbs, 12h_04


title: pif4-28-1

address: 北京市海淀区颐和园路5号

description:
Library name: pif4-28-1
pif4-28-1


title: Old, d3, rep4, collagenase-treated hematoma, HTO

description:
Library name: Od3_4c_CSP
10x Genomics
Od3_4c_output_filtered.h5


title: cR_WT-3

address: 北京市海淀区颐和园路5号

description:
Library name: cR_WT-3
cR_WT-3

value: 9-day-old seedlings grown under continuous red light


title: Patient 1 month after treatment with guideline based therapy_87

description: Library name: 87_1


title: Patient 1 month after treatment with guideline based therapy_86

description: Library name: 86_1


title: Old, d3, rep3, GEX

description:
Library name: Od3_3_GEX
10x Genomics
3Od3_output_filtered.h5


title: Patient before treatment with guideline based therapy_87

description: Library name: 87_0


title: cR_WT-2

address: 北京市海淀区颐和园路5号

description:
Library name: cR_WT-2
cR_WT-2


title: pkl-28-2

address: 北京市海淀区颐和园路5号

description:
Library name: pkl-28-2
pkl-28-2


title: Patient before treatment with guideline based therapy_86

description: Library name: 86_0


title: chicken hindlimb ID3, pbs, 12h_05


title: chicken hindlimb ID3, pbs, 12h_03


title: Old, d3, rep2, GEX

description:
Library name: Od3_2_GEX
10x Genomics
2Od3_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_85

description: Library name: 85_1


title: Old, d3, rep3, HTO

description:
Library name: Od3_3_CSP
10x Genomics
3Od3_output_filtered.h5


title: chicken hindlimb ID3, pbs, 12h_02


title: cR_pklpif4-3

address: 北京市海淀区颐和园路5号

description:
Library name: cR_pklpif4-3
cR_pklpif4-3


title: cR_WT-1

address: 北京市海淀区颐和园路5号

description:
Library name: cR_WT-1
cR_WT-1


title: pif4-28-3

address: 北京市海淀区颐和园路5号

description:
Library name: pif4-28-3
pif4-28-3


title: Old, d3, rep2, HTO

description:
Library name: Od3_2_CSP
10x Genomics
2Od3_output_filtered.h5


title: chicken hindlimb ID3, noggin, 12h_02


title: Old, d0, rep7, GEX

description:
Library name: Od0_7_GEX
10x Genomics
7Od0_output_filtered.h5


title: chicken hindlimb ID3, noggin, 12h_04


title: chicken hindlimb ID3, pbs, 12h_01


title: Patient 1 month after treatment with guideline based therapy_84

description: Library name: 84_1


title: Patient before treatment with guideline based therapy_85

description: Library name: 85_0


title: cR_pklpif4-1

address: 北京市海淀区颐和园路5号

description:
Library name: cR_pklpif4-1
cR_pklpif4-1


title: Old, d0, rep7, HTO

description:
Library name: Od0_7_CSP
10x Genomics
7Od0_output_filtered.h5


title: Patient before treatment with guideline based therapy_84

description: Library name: 84_0


title: chicken hindlimb ID3, noggin, 12h_01


title: cR_pkl-3

address: 北京市海淀区颐和园路5号

description:
Library name: cR_pkl-3
cR_pkl-3


title: Old, d0, rep6, GEX

description:
Library name: Od0_6_GEX
10x Genomics
6Od0_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_83

description: Library name: 83_1


title: chicken hindlimb ID3, noggin, 12h_03


title: Patient before treatment with guideline based therapy_83

description: Library name: 83_0


title: cR_pkl-2

address: 北京市海淀区颐和园路5号

description:
Library name: cR_pkl-2
cR_pkl-2


title: Old, d0, rep6, HTO

description:
Library name: Od0_6_CSP
10x Genomics
6Od0_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_82

description: Library name: 82_1


title: Old, d0, rep5, HTO

description:
Library name: Od0_5_CSP
10x Genomics
5Od0_output_filtered.h5


title: Old, d0, rep5, GEX

description:
Library name: Od0_5_GEX
10x Genomics
5Od0_output_filtered.h5


title: cR_pkl-1

address: 北京市海淀区颐和园路5号

description:
Library name: cR_pkl-1
cR_pkl-1


title: cR_pklpif4-2

address: 北京市海淀区颐和园路5号

description:
Library name: cR_pklpif4-2
cR_pklpif4-2


title: cR_pif4-2

address: 北京市海淀区颐和园路5号

description:
Library name: cR_pif4-2
cR_pif4-2


title: Old, d0, rep4, GEX

description:
Library name: Od0_4_GEX
10x Genomics
4Od0_output_filtered.h5


title: Patient before treatment with guideline based therapy_81

description: Library name: 81_0


title: cR_pif4-1

address: 北京市海淀区颐和园路5号

description:
Library name: cR_pif4-1
cR_pif4-1


title: Old, d0, rep4, HTO

description:
Library name: Od0_4_CSP
10x Genomics
4Od0_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_81

description: Library name: 81_1


title: T1Cje_placenta_trisomic_Dam16_embryo9

type: RNA

city: Bethesda

first: Laura

middle: L

last: Baxter

state: MD

address: 35A Convent Drive

department: NHGRI

institute: NIH

description: Gene expression data from mouse E18.5 placenta

hyb_protocol: Arrays were washed and stained using the GeneTitan Hybridization, Wash, and Stain kit with streptavidin-phycoerythrin protocol according to the manufacturer's instructions.           Arrays were scanned using the GeneTitan automated microarray system.

data_processing: Microarray data were analyzed using Transcriptome Analysis Console (TAC) software (version 4.0.0) (Thermo Fisher Scientific) using RMA normalization

label: biotin

source_name: Mouse E18.5 placenta

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate using Mouse Clariom S HT arrays (Cat. No. 902970, Thermo Fisher Scientific) and the GeneTitan automated microarray system.

growth_protocol: Mouse placentas were collected at E18.5 (late gestation), snap frozen, and stored at -80°C until RNA extraction.

extract_protocol: RNA was processed and hybridized on Mouse Clariom S HT 96-array plates (902970; ThermoFisher Scientific) using GeneChip WT Plus Reagent Kits following the manufacturer’s protocol (902281; ThermoFisher Scientific).

value: TS

tag: model


title: Patient 1 month after treatment with guideline based therapy_80

description: Library name: 80_1


title: T1Cje_placenta_euploid_Dam16_embryo8

scan_protocol: Arrays were scanned using the GeneTitan automated microarray system.

value: EUP


title: ChIPseq_Input_pkl_rep3

address: 北京市海淀区颐和园路5号

data_processing:
Illumina bcl-convert v3.7.5 software used for basecalling.
After removing reads with adapter sequences and low quality by fastp, the high-quality reads were mapped to the TAIR10 genome assembly of Arabidopsis thaliana using HISAT2 (version 2.1.0) with parameters “--dta --min-intronlen 50 --max-intronlen 6000”. Only unique mapping and MAPQ score > 20 reads were kept using SAMtools version 1.6 for subsequent analysis.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
After removing reads with adapter sequences and low quality by fastp, the high-quality reads were mapped to the TAIR10 genome assembly of Arabidopsis thaliana using bowtie2 (version 2.3.3) with default parameters.
Peak calling was performed using MACS2 (version 2.2.5) with the following parameters: --keep-dup 1 --gsize 1.2e8 --qvalue 0.05.
The alignments were converted to bigWig files using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 5 --normalizeUsing CPM”.
Supplementary files format and content: Bigwig files were generated using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 5 --normalizeUsing CPM”.
Supplementary files format and content: peak text files
Supplementary files format and content: Hi-C matrices in .hic format produced by juicer software

extract_protocol:
Total RNA from 9-d-old WT and mutant seedlings grown in continuous white light were isolated using RNeasy Plant Mini Kits (Sigma). Three biological replicates for each sample were subjected to RNA-seq.
Poly (A) RNA from 1 μg total RNA was used to generate the cDNA library according to the TruSeq RNA Sample Prep Kit protocol. The library was then sequenced using a HiSeq Xten system (Illumina).

value: 9-day-old seedlings grown under continuous white light

tag: chip antibody

value: IgG (PP64, Millipore)

value: pkl mutant


title: ChIPseq_Input_pkl_rep2

address: 北京市海淀区颐和园路5号


title: T1Cje_placenta_trisomic_Dam16_embryo4

value: Female


title: Old, d0, rep2, GEX

description:
Library name: Od0_2_GEX
10x Genomics
2Od0_output_filtered.h5

value: Femur

value: Yes


title: T1Cje_placenta_euploid_Dam16_embryo7

value: Male


title: Patient before treatment with guideline based therapy_80

description: Library name: 80_0


title: ChIPseq_Input_pkl_rep1

address: 北京市海淀区颐和园路5号

value: total seedlings


title: cR_pif4-3

address: 北京市海淀区颐和园路5号

description:
Library name: cR_pif4-3
cR_pif4-3


title: Patient 1 month after treatment with guideline based therapy_79

description: Library name: 79_1


title: Patient before treatment with guideline based therapy_82

description: Library name: 82_0


title: Old, d0, rep1, HTO

description:
Library name: Od0_1_CSP
10x Genomics
1Od0_output_filtered.h5

value: HTO


title: Patient before treatment with guideline based therapy_79

description: Library name: 79_0


title: T1Cje_placenta_euploid_Dam16_embryo1


title: Old, d0, rep1, GEX

description:
Library name: Od0_1_GEX
10x Genomics
1Od0_output_filtered.h5


title: ChIPseq_Input_WT_rep2

address: 北京市海淀区颐和园路5号

value: Col-0 ecotype


title: Young, d7, rep1, GEX

description:
Library name: Yd7_f1_GEX
10x Genomics
1Yd7_output_filtered.h5

value: mRNA


title: Patient 1 month after treatment with guideline based therapy_78

description: Library name: 78_1


title: ChIPseq_Input_WT_rep1

address: 北京市海淀区颐和园路5号


title: Old, d0, rep2, HTO

description:
Library name: Od0_2_CSP
10x Genomics
2Od0_output_filtered.h5

value: TotalSeq-B0301 anti-mouse Hashtag 1 (BM), TotalSeq-B0303 anti-mouse Hashtag 3 (CB), TotalSeq-B0304 anti-mouse Hashtag 4 (H)


title: Young, d7, rep1, HTO

description:
Library name: Yd7_f1_CSP
10x Genomics
1Yd7_output_filtered.h5


title: Young, d7, rep2, contralateral, GEX

description:
Library name: Yd7_c2_GEX
10x Genomics
Yd7_2_cl_output_filtered.h5

value: No


title: ChIPseq_H3K4me3_pkl_rep3

address: 北京市海淀区颐和园路5号

value: anti-H3K4me3 endogenous antibody


title: T1Cje_placenta_trisomic_Dam16_embryo2


title: T1Cje_placenta_trisomic_Dam16_embryo3


title: Patient before treatment with guideline based therapy_78

description: Library name: 78_0

value: Whole blood cells


title: Patient 1 month after treatment with guideline based therapy_77

description: Library name: 77_1


title: T1Cje_placenta_trisomic_Dam15_embryo6

value: TS


title: Patient before treatment with guideline based therapy_77

description: Library name: 77_0


title: ChIPseq_Input_WT_rep3

address: 北京市海淀区颐和园路5号


title: ChIPseq_H3K4me3_pkl_rep1

address: 北京市海淀区颐和园路5号


title: Young, d7, rep1, contralateral, GEX

description:
Library name: Yd7_c1_GEX
10x Genomics
Yd7_1_cl_output_filtered.h5


title: T1Cje_placenta_trisomic_Dam15_embryo5


title: T1Cje_placenta_euploid_Dam15_embryo4

value: EUP


title: T1Cje_placenta_trisomic_Dam15_embryo3


title: Young, d7, rep2, contralateral, HTO

description:
Library name: Yd7_c2_CSP
10x Genomics
Yd7_2_cl_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_76

description: Library name: 76_1


title: ChIPseq_H3K4me3_WT_rep3

address: 北京市海淀区颐和园路5号

value: 9-day-old seedlings grown under continuous white light


title: Young, d7, rep1, contralateral, HTO

description:
Library name: Yd7_c1_CSP
10x Genomics
Yd7_1_cl_output_filtered.h5


title: T1Cje_placenta_trisomic_Dam15_embryo1


title: ChIPseq_H3K4me3_WT_rep2

address: 北京市海淀区颐和园路5号


title: T1Cje_placenta_trisomic_Dam15-2_embryo7


title: Young, d7, rep7, GEX

description:
Library name: Yd7_7_GEX
10x Genomics
7Yd7_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_75

description: Library name: 75_1


title: Patient before treatment with guideline based therapy_75

description: Library name: 75_0


title: Young, d7, rep7, HTO

description:
Library name: Yd7_7_CSP
10x Genomics
7Yd7_output_filtered.h5


title: T1Cje_placenta_trisomic_Dam15-2_embryo6


title: Young, d7, rep6, GEX

description:
Library name: Yd7_6_GEX
10x Genomics
6Yd7_output_filtered.h5


title: ChIPseq_H3K4me3_pkl_rep2

address: 北京市海淀区颐和园路5号


title: ChIPseq_H3K4me2_pkl_rep3

address: 北京市海淀区颐和园路5号

value: anti-H3K4me2 endogenous antibody


title: Patient 1 month after treatment with guideline based therapy_74

description: Library name: 74_1


title: T1Cje_placenta_euploid_Dam15_embryo2


title: T1Cje_placenta_euploid_Dam15-2_embryo5


title: Patient before treatment with guideline based therapy_74

description: Library name: 74_0


title: Young, d7, rep6, HTO

description:
Library name: Yd7_6_CSP
10x Genomics
6Yd7_output_filtered.h5


title: Young, d7, rep5, GEX

description:
Library name: Yd7_5_GEX
10x Genomics
5Yd7_output_filtered.h5


title: ChIPseq_H3K4me2_pkl_rep1

address: 北京市海淀区颐和园路5号

value: pkl mutant


title: Patient 1 month after treatment with guideline based therapy_73

description: Library name: 73_1


title: ChIPseq_H3K4me2_WT_rep3

address: 北京市海淀区颐和园路5号


title: T1Cje_placenta_trisomic_Dam15-2_embryo4

value: Female


title: T1Cje_placenta_euploid_Dam15-2_embryo3


title: Patient before treatment with guideline based therapy_76

description: Library name: 76_0


title: Young, d7, rep5, HTO

description:
Library name: Yd7_5_CSP
10x Genomics
5Yd7_output_filtered.h5

value: Femur


title: Patient before treatment with guideline based therapy_73

description: Library name: 73_0


title: T1Cje_placenta_trisomic_Dam11_embryo4

description: Gene expression data from mouse E18.5 placenta


title: T1Cje_placenta_euploid_Dam11_embryo3


title: ChIPseq_H3K4me2_WT_rep2

address: 北京市海淀区颐和园路5号


title: ChIPseq_H3K4me3_WT_rep1

address: 北京市海淀区颐和园路5号


title: T1Cje_placenta_euploid_Dam11_embryo2


title: Young, d7, rep4, GEX

description:
Library name: Yd7_4_GEX
10x Genomics
4Yd7_output_filtered.h5

value: Yes


title: Patient 1 month after treatment with guideline based therapy_72

description: Library name: 72_1


title: Young, d7, rep4, HTO

description:
Library name: Yd7_4_CSP
10x Genomics
4Yd7_output_filtered.h5


title: Patient before treatment with guideline based therapy_72

description: Library name: 72_0


title: ChIPseq_H3K4me2_WT_rep1

address: 北京市海淀区颐和园路5号


title: ChIPseq_H3K4me2_pkl_rep2

address: 北京市海淀区颐和园路5号


title: ChIPseq_H3K4me1_pkl_rep3

address: 北京市海淀区颐和园路5号

value: anti-H3K4me1 endogenous antibody


title: Patient 1 month after treatment with guideline based therapy_71

description: Library name: 71_1


title: T1Cje_placenta_trisomic_Dam11_embryo1

value: Male


title: ChIPseq_H3K4me1_pkl_rep2

address: 北京市海淀区颐和园路5号

value: total seedlings


title: Young, d3, rep2, HTO

description:
Library name: Yd3_f2_CSP
10x Genomics
2Yd3_output_filtered.h5

value: HTO


title: Patient before treatment with guideline based therapy_71

description: Library name: 71_0


title: ChIPseq_H3K4me1_pkl_rep1

address: 北京市海淀区颐和园路5号


title: T1Cje_placenta_euploid_Dam11-2_embryo5


title: T1Cje_placenta_trisomic_Dam11-2_embryo7


title: ChIPseq_H3K4me1_WT_rep3

address: 北京市海淀区颐和园路5号

value: Col-0 ecotype


title: Young, d3, rep1, HTO

description:
Library name: Yd3_f1_CSP
10x Genomics
1Yd3_output_filtered.h5

value: TotalSeq-B0301 anti-mouse Hashtag 1 (BM), TotalSeq-B0303 anti-mouse Hashtag 3 (CB), TotalSeq-B0304 anti-mouse Hashtag 4 (H)


title: Patient 1 month after treatment with guideline based therapy_70

description: Library name: 70_1


title: Young, d3, rep1, GEX

description:
Library name: Yd3_f1_GEX
10x Genomics
1Yd3_output_filtered.h5

value: mRNA


title: Patient before treatment with guideline based therapy_70

description: Library name: 70_0


title: ChIPseq_H3K4me1_WT_rep2

address: 北京市海淀区颐和园路5号


title: T1Cje_placenta_euploid_Dam11-2_embryo4


title: Young, d3, rep2, contralateral, GEX

description:
Library name: Yd3_c2_GEX
10x Genomics
Yd3_2_cl_output_filtered.h5

value: No


title: ChIPseq_H3K4me1_WT_rep1

address: 北京市海淀区颐和园路5号


title: Young, d3, rep2, GEX

description:
Library name: Yd3_f2_GEX
10x Genomics
2Yd3_output_filtered.h5


title: T1Cje_placenta_trisomic_Dam11-2_embryo2


title: T1Cje_placenta_trisomic_Dam11-2_embryo1


title: Patient before treatment with guideline based therapy_69

description: Library name: 69_0

value: Whole blood cells


title: T1Cje_placenta_trisomic_Dam10_embryo9

value: TS


title: ChIPseq_Input_hy5_rep3

address: 北京市海淀区颐和园路5号

value: IgG (PP64, Millipore)

value: hy5 mutant


title: Young, d3, rep1, contralateral, GEX

description:
Library name: Yd3_c1_GEX
10x Genomics
Yd3_1_cl_output_filtered.h5


title: Young, d3, rep2, contralateral, HTO

description:
Library name: Yd3_c2_CSP
10x Genomics
Yd3_2_cl_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_68

description: Library name: 68_1


title: Patient before treatment with guideline based therapy_68

description: Library name: 68_0


title: ChIPseq_Input_hy5_rep1

address: 北京市海淀区颐和园路5号

value: 9-day-old seedlings grown under continuous white light


title: Patient 1 month after treatment with guideline based therapy_67

description: Library name: 67_1


title: T1Cje_placenta_trisomic_Dam10_embryo8


title: ChIPseq_Input_hy5_rep2

address: 北京市海淀区颐和园路5号


title: Patient before treatment with guideline based therapy_67

description: Library name: 67_0


title: Young, d3, rep7, HTO

description:
Library name: Yd3_7_CSP
10x Genomics
7Yd3_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_69

description: Library name: 69_1


title: ChIPseq_PKL_hy5_rep2

address: 北京市海淀区颐和园路5号

value: anti-PKL endogenous antibody


title: T1Cje_placenta_trisomic_Dam10_embryo7


title: Young, d3, rep7, contralateral, GEX

description:
Library name: Yd3_7_Cl_GEX
10x Genomics
Yd3_7_cl_output_filtered.h5

value: Female


title: Young, d3, rep7, GEX

description:
Library name: Yd3_7_GEX
10x Genomics
7Yd3_output_filtered.h5

value: Femur


title: ChIPseq_PKL_hy5_rep3

address: 北京市海淀区颐和园路5号


title: Patient 1 month after treatment with guideline based therapy_66

description: Library name: 66_1


title: ChIPseq_PKL_hy5_rep1

address: 北京市海淀区颐和园路5号


title: T1Cje_placenta_euploid_Dam10_embryo4

value: EUP


title: T1Cje_placenta_trisomic_Dam10_embryo6


title: Patient before treatment with guideline based therapy_66

description: Library name: 66_0


title: Young, d3, rep7, contralateral, HTO

description:
Library name: Yd3_7_Cl_CSP
10x Genomics
Yd3_7_cl_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_65

description: Library name: 65_1


title: T1Cje_placenta_euploid_Dam9_embryo10


title: ChIPseq_Input_pifQ_rep3

address: 北京市海淀区颐和园路5号

value: pifQ mutant


title: Young, d3, rep1, contralateral, HTO

description:
Library name: Yd3_c1_CSP
10x Genomics
Yd3_1_cl_output_filtered.h5


title: T1Cje_placenta_euploid_Dam10_embryo2

value: Male


title: ChIPseq_Input_pifQ_rep2

address: 北京市海淀区颐和园路5号

value: total seedlings


title: Young, d3, rep5, HTO

description:
Library name: Yd3_5_CSP
10x Genomics
5Yd3_output_filtered.h5

value: Yes

value: HTO


title: T1Cje_placenta_euploid_Dam9_embryo8


title: Patient before treatment with guideline based therapy_65

description: Library name: 65_0


title: T1Cje_placenta_trisomic_Dam9_embryo7


title: Young, d0, rep5, GEX

description:
Library name: Yd0_5_GEX
10x Genomics
5Yd0_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_64

description: Library name: 64_1


title: ChIPseq_Input_pifQ_rep1

address: 北京市海淀区颐和园路5号


title: ChIPseq_PKL_pifQ_rep3

address: 北京市海淀区颐和园路5号


title: Young, d0, rep5, HTO

description:
Library name: Yd0_5_CSP
10x Genomics
5Yd0_output_filtered.h5

value: TotalSeq-B0301 anti-mouse Hashtag 1 (BM), TotalSeq-B0303 anti-mouse Hashtag 3 (CB), TotalSeq-B0304 anti-mouse Hashtag 4 (H)


title: Patient before treatment with guideline based therapy_64

description: Library name: 64_0


title: Patient 1 month after treatment with guideline based therapy_63

description: Library name: 63_1


title: ChIPseq_PKL_pifQ_rep2

address: 北京市海淀区颐和园路5号


title: Young, d3, rep5, GEX

description:
Library name: Yd3_5_GEX
10x Genomics
5Yd3_output_filtered.h5

value: mRNA


title: Young, d0, rep4, GEX

description:
Library name: Yd0_4_GEX_rep_2
10x Genomics
4Yd0_output_filtered.h5


title: Young, d0, rep2, contralateral, GEX

description:
Library name: Yd0_4_GEX
10x Genomics
4Yd0_output_filtered.h5

value: No


title: ChIPseq_PKL_pifQ_rep1

address: 北京市海淀区颐和园路5号


title: T1Cje_placenta_trisomic_Dam9_embryo5

description: Gene expression data from mouse E18.5 placenta


title: ChIPseq_Input_jaw-5D_rep3

address: 北京市海淀区颐和园路5号

value: jaw-5D mutant


title: Patient before treatment with guideline based therapy_63

description: Library name: 63_0

value: Whole blood cells


title: T1Cje_placenta_trisomic_Dam9_embryo2

value: TS


title: Young, d0, rep4, HTO

description:
Library name: Yd0_4_CSP_rep_2
10x Genomics
Yd0_2_cl_output_filtered.h5


title: Young, d0, rep2, contralateral, HTO

description:
Library name: Yd0_4_CSP
10x Genomics
Yd0_2_cl_output_filtered.h5


title: ChIPseq_Input_jaw-5D_rep2

address: 北京市海淀区颐和园路5号

value: IgG (PP64, Millipore)


title: T1Cje_placenta_euploid_Dam9_embryo3


title: Patient 1 month after treatment with guideline based therapy_62

description: Library name: 62_1


title: Patient before treatment with guideline based therapy_62

description: Library name: 62_0


title: Young, d0, rep3, GEX

description:
Library name: Yd0_3_GEX_rep_2
10x Genomics
3Yd0_output_filtered.h5


title: ChIPseq_Input_jaw-5D_rep1

address: 北京市海淀区颐和园路5号

value: 9-day-old seedlings grown under continuous white light


title: T1Cje_placenta_trisomic_Dam9_embryo1


title: Patient 1 month after treatment with guideline based therapy_61

description: Library name: 61_1


title: Ts66Yah_placenta_trisomic_Dam19_embryo6


title: ChIPseq_PKL_jaw-5D_rep3

address: 北京市海淀区颐和园路5号

value: anti-PKL endogenous antibody


title: T1Cje_placenta_euploid_Dam9_embryo6

value: Female


title: Ts66Yah_placenta_trisomic_Dam19_embryo7


title: Patient before treatment with guideline based therapy_61

description: Library name: 61_0


title: Ts66Yah_placenta_trisomic_Dam19_embryo5


title: ChIPseq_PKL_jaw-5D_rep2

address: 北京市海淀区颐和园路5号


title: Patient 1 month after treatment with guideline based therapy_60

description: Library name: 60_1


title: ChIPseq_PKL_jaw-5D_rep1

address: 北京市海淀区颐和园路5号


title: Ts66Yah_placenta_euploid_Dam19_embryo3


title: Patient before treatment with guideline based therapy_60

description: Library name: 60_0


title: Young, d0, rep1, contralateral, GEX

description:
Library name: Yd0_2_GEX
10x Genomics
2Yd0_output_filtered.h5

value: Femur


title: Patient 1 month after treatment with guideline based therapy_59

description: Library name: 59_1


title: Young, d0, rep2, HTO

description:
Library name: Yd0_3_CSP
10x Genomics
Yd0_1_cl_output_filtered.h5


title: ChIPseq_PKL_WT_rep2

address: 北京市海淀区颐和园路5号

value: Col-0 ecotype


title: ChIPseq_PKL_WT_rep3

address: 北京市海淀区颐和园路5号


title: Patient before treatment with guideline based therapy_59

description: Library name: 59_0


title: Young, d0, rep1, contralateral, HTO

description:
Library name: Yd0_2_CSP
10x Genomics
2Yd0_output_filtered.h5


title: Ts66Yah_placenta_euploid_Dam18_embryo10

value: EUP


title: Young, d0, rep1, GEX

description:
Library name: Yd0_1_GEX
10x Genomics
1Yd0_output_filtered.h5


title: Patient 1 month after treatment with guideline based therapy_58

description: Library name: 58_1


title: Young, d0, rep2, GEX

description:
Library name: Yd0_3_GEX
10x Genomics
3Yd0_output_filtered.h5


title: Ts66Yah_placenta_euploid_Dam18_embryo9


title: ChIPseq_PKL_WT_rep1

address: 北京市海淀区颐和园路5号


title: Ts66Yah_placenta_trisomic_Dam18_embryo6


title: Patient before treatment with guideline based therapy_58

description: Library name: 58_0


title: Ts66Yah_placenta_euploid_Dam18_embryo5


title: Ts66Yah_placenta_euploid_Dam19_embryo1

value: Male


title: Patient 1 month after treatment with guideline based therapy_57

description: Library name: 57_1


title: HiC_hy5_rep1

address: 北京市海淀区颐和园路5号

value: total seedlings


title: sc_day2

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

description: Library name: Sample4

data_processing:
The scRNA-seq raw data were processed using CellRanger software (v 7.1.0) from the 10× Genomics website. Sequencing reads from each sample were aligned to the GRCm38 reference genome using the cellranger count module to perform sequence alignment, quality filtering, barcode and UMI counting, and generating of filtered feature-barcode matrices.
Assembly: GRCm38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: mouse primary embryonic stem cells

extract_protocol:
EBs collected at four time points (days 2, 8, 12, and 16) were dissociated into single-cell suspensions. Following centrifugation at 450 × g for 3 min, cells were washed once with No LIF medium and resuspended in DMEM containing 10% v/v FBS. The suspensions were filtered twice with a 70-μm strainer. Cell number and viability were assessed using the Countess Ⅱ Automated Cell Counter. The resulting single-cell suspensions were subjected to single-cell RNA sequencing using the 10× Genomics platform
Library was constructed under manufacture's instruction (Chromium Single Cell 3’ Library & Single Cell 3ʹ v3 Gel Beads)

value: mouse primary embryonic stem cells

value: ES derived cells

value: Dlx2 overexpression

value: dox induction


title: Young, d0, rep3, HTO

description:
Library name: Yd0_3_CSP_rep_2
10x Genomics
Yd0_1_cl_output_filtered.h5

value: Yes

value: mRNA


title: HiC_hy5_rep2

address: 北京市海淀区颐和园路5号


title: HiC_pifQ_rep2

address: 北京市海淀区颐和园路5号


title: Ts66Yah_placenta_euploid_Dam15_embryo7


title: sc_day8

description: Library name: Sample3


title: Patient before treatment with guideline based therapy_57

description: Library name: 57_0

value: Whole blood cells


title: HiC_pifQ_rep1

address: 北京市海淀区颐和园路5号


title: HiC_jaw-5D_rep2

address: 北京市海淀区颐和园路5号


title: Patient 1 month after treatment with guideline based therapy_56

description: Library name: 56_1


title: sc_day12

description: Library name: Sample2


title: sc_day16

description: Library name: Sample1


title: Ts66Yah_placenta_trisomic_Dam18_embryo3

value: TS


title: Patient before treatment with guideline based therapy_56

description: Library name: 56_0


title: Young, d0, rep1, HTO

description:
Library name: Yd0_1_CSP
10x Genomics
1Yd0_output_filtered.h5

value: HTO

value: TotalSeq-B0301 anti-mouse Hashtag 1 (BM), TotalSeq-B0303 anti-mouse Hashtag 3 (CB), TotalSeq-B0304 anti-mouse Hashtag 4 (H)


title: HiC_jaw-5D_rep1

address: 北京市海淀区颐和园路5号

value: 9-day-old seedlings grown under continuous white light


title: HiC_pkl_rep2

address: 北京市海淀区颐和园路5号

value: pkl mutant


title: Patient 1 month after treatment with guideline based therapy_55

description: Library name: 55_1


title: Ts66Yah_placenta_trisomic_Dam15_embryo5

value: Female


title: HiC_pkl_rep1

address: 北京市海淀区颐和园路5号


title: Ts66Yah_placenta_euploid_Dam15_embryo2


title: HiC_WT_rep2

address: 北京市海淀区颐和园路5号

value: Col-0 ecotype


title: GFP+dox_rep2

description: Library name: Sample16

data_processing:
Quanlity filtering using fastp v 0.20.0) with default parameters.
Trimmed data were mapped against the mouse genome (Mus musculus, GRCm38) using HISAT2 v 2.1.0
Differentially expressed genes (DEGs) analysis was performed using the DESeq2 1.18.1 package in R3.4.3, DEGs were called by FDR < 0.05 and fold change > 2.
Assembly: CRCm38.91
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Msx1-tdTomato mESCs

growth_protocol: Msx1-tdTomato mESCs were maintained in DMEM supplemented with 15% FBS, 1%NEAA, 1% GlutaMAX, 1% Pen-Strep, 0.1mM 2-Mercaptoethanol, and 1000U/ml LIF.

extract_protocol:
Total RNAs were extracted from cells using the TRI Reagent (Sigma-Aldrich), 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Stable inducible mESCs were induced to form embyoid bodies (EBs) using the hanging drop method, with or without 1μg/ml Doxycycline (Dox, TAKARA) treatment.

value: Msx1-tdTomato mESCs

value: mESCs derived EB cells

value: Inducible GFP overexpression

value: EB formation with Dox induction


title: Ts66Yah_placenta_euploid_Dam15_embryo3

value: EUP

value: Male


title: Patient 1 month after treatment with guideline based therapy_54

description: Library name: 54_1


title: Ts66Yah_placenta_euploid_Dam15_embryo1


title: GFP+dox_rep1

description: Library name: Sample15


title: Patient before treatment with guideline based therapy_54

description: Library name: 54_0


title: Ts66Yah_placenta_trisomic_Dam15_embryo6


title: Ts66Yah_placenta_euploid_Dam13_embryo8


title: RNA-seq_pkl_rep3

address: 北京市海淀区颐和园路5号

value: total seedlings


title: Dlx2-dox_rep2

description: Library name: Sample14

value: Inducible Dlx2 overexpression

value: EB formation without Dox induction


title: Patient 1 month after treatment with guideline based therapy_53

description: Library name: 53_1

value: Whole blood cells


title: Ts66Yah_placenta_euploid_Dam13_embryo3


title: Patient before treatment with guideline based therapy_53

description: Library name: 53_0


title: GFP-dox_rep2

description: Library name: Sample18


title: Dlx2+dox_rep2

description: Library name: Sample12


title: GFP-dox_rep1

description: Library name: Sample17


title: Patient 1 month after treatment with guideline based therapy_52

description: Library name: 52_1


title: Patient before treatment with guideline based therapy_55

description: Library name: 55_0


title: RNA-seq_pkl_rep1

address: 北京市海淀区颐和园路5号


title: Dlx2+dox_rep1

description: Library name: Sample11


title: Ts66Yah_placenta_euploid_Dam12_embryo8


title: Ts66Yah_placenta_trisomic_Dam12_embryo6

value: TS


title: HiC_WT_rep1

address: 北京市海淀区颐和园路5号


title: Ts66Yah_placenta_euploid_Dam12_embryo2


title: ES_rep2

description: Library name: Sample10

value: mESCs

value: WT

value: untreated


title: E6_7d_Dox_Washout 2

city: Solna

first: Jasper

last: Panten

address: Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

description: Library name: E6_7d_Dox_Washout

data_processing:
Library strategy: EM-Seq
Processing of DNA methylation was performed using the methylseq nextflow pipeline with the --emseq option (v2.3.0, NextFlow v22.10.6). Reads were trimmed using TrimGalore! (v0.6.7) and aligned to the same N-masked genome (GRCm38) using bismarck (v0.24.0), and used SNP_split (v0.5.0) to assign mapped reads to parental genomes, similar to the RNA-Seq data. We finally used bismark_methylation_extractor from the bismarck software to generate base-level methylation counts for both haplotypes.
Assembly: GRCm38
Supplementary files format and content: Bismarck coverage file

organism: Mus

growth_protocol: NPCs were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in NPC media (N2B27 media supplemented with with FGF2 (10 ng/mL) and EGF (10 ng/mL, both Peprotech)).

extract_protocol:
Genomic DNA (gDNA) from >1M NPC was extracted using column-based DNeasy Blood & Tissue Kit (Qiagen).
DNA integrity was tested on a 0.8% agarose gel and 200 ng of high-quality gDNA was used to prepare libraries according to the NEBNext® Enzymatic Methyl-seq Kit following the section for large insert libraries with minor modifications. A total of 55-100 ng of DNA was used per library, including a spike-in of pUC and Lambda DNA as a control for methylation efficiency. Samples were fragmented using the Covaris S2 System to achieve an average fragment size of 350-400 bp and barcoded using 5 PCR cycles for 100 ng input and 6 PCR cycles for 55 ng input.

treatment_protocol: Xist expression in TX1072 was induced by addition of doxycycline (1 µg/mL) to the NPC media. Culture media supplemented with doxycycline was renewed every 24h. For doxycycline wash-out, doxycycline-containing media was removed, and cells were refreshed with doxycycline-free culture media.

tag: strain

value: C57BL6/J x CAST/EiJ

value: neural progenitor cell

value: Xptet / R26rtTA

value: Dox (7d) - washout

tag: enrichment

value: Untargeted


title: E6_21d_Dox_Washout 2

description: Library name: E6_21d_Dox_Washout

value: Dox (21d) - washout


title: Patient before treatment with guideline based therapy_52

description: Library name: 52_0


title: Patient before treatment with guideline based therapy_51

description: Library name: 51_0


title: ES_rep1

description: Library name: Sample9

value: Msx1-tdTomato mESCs


title: Dlx2-dox_rep1

description: Library name: Sample13

value: mESCs derived EB cells


title: E6_21d_Dox 2

description: Library name: E6_21d_Dox

value: Dox (21d)


title: Ts66Yah_placenta_euploid_Dam11_embryo3

value: EUP

value: Male


title: Ts66Yah_placenta_trisomic_Dam11_embryo4

value: Female


title: D16_Msx1+_rep2

description: Library name: Sample8

value: Inducible Dlx2 overexpression

value: EB formation with Dox induction and FACS


title: Patient 1 month after treatment with guideline based therapy_50

description: Library name: 50_1

value: Whole blood cells


title: Patient before treatment with guideline based therapy_50

description: Library name: 50_0


title: D16_Msx1+_rep1

description: Library name: Sample7


title: E6_7d_Dox 2

description: Library name: E6_7d_Dox

value: Dox (7d)


title: Ts65Dn_placenta_euploid_Dam137_embryo8


title: E6_No_Dox 2

description: Library name: E6_No_Dox

value: Control


title: Patient 1 month after treatment with guideline based therapy_49

description: Library name: 49_1


title: Ts65Dn_placenta_euploid_Dam137_embryo6


title: D16_Msx1-_rep1

description: Library name: Sample5


title: Ts65Dn_placenta_trisomic_Dam137_embryo5

value: TS


title: Patient 1 month after treatment with guideline based therapy_51

description: Library name: 51_1


title: RNA-seq_pkl_rep2

address: 北京市海淀区颐和园路5号

value: total seedlings

value: 9-day-old seedlings grown under continuous white light

value: pkl mutant


title: Patient before treatment with guideline based therapy_49

description: Library name: 49_0


title: embryo52

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1H5

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz) were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType EndToEnd. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1). The embryo RNA-Sequencing data was pre-processed as described above (Allele-specific preprocessing of RNA-Sequencing data), using the SNPs between C57BL/6J and JF1 mice (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz). To confirm the annotated genotypes of the embryos, the rtTA transgene was included in the reference genome, and any embryo with >150 mapped transgene reads was considered rtTA-positive. For developmental staging, principal component analysis (prcomp, stats v4.2.0) was performed on total read counts after size-factor normalization (estimateSizeFactors, DESeq2, v1.36.0) and subsetting on highly variable genes (getTopHVGs, scran, v1.24.1). The first principal component separated embryo stages as determined by morphological staging and was used as a developmental pseudotime.
Assembly: GRCm39
Supplementary files format and content: delimited text files

source_name: whole embryo

extract_protocol:
Single embryos were picked and washed three times with transfer buffer (1X- PBS, 0.4% BSA) and transferred into 0.2 ml PCR tubes containing 2μl of lysis buffer (0.7% Triton X-100, 2U/μl RNasin (Promega), 1μl of oligo-dT30VN primer (10 μM 5'-aagcagtggttatcaacgcagagtact30vn-3') and 1 μl of 10 mM dNTP mix (Thermo Fisher).
Illumina libraries were prepared by using a modified smart-seq2 protocol [Picelli 2014] using SuperScript IV RT and tagmentation procedure as previously described [Henning 2018]. The RT reaction mix was as follows: 2 μl SSRT IV 5x buffer; 0.5 μl 100 mM DTT; 2 μl 5 M betaine; 0.1 μl 1 M MgCl2; 0.25 μl 40 U/μl RNAse inhibitor; 0.25 μl SSRT IV; 0.1 μl 100 uM TSO, 1.15 μl RNase-free H2O. RT thermal conditions: 52 °C 15 min, 80 °C 10 min. cDNA was generated using 16 PCR cycles. The cDNA cleanup (0.6x SPRI ratio) was carried out omitting the ethanol wash steps and the elution volume was 13 μl of H2O. For tagmentation, the sample input was normalized to 0.2 ng/μl. Obtained libraries that passed the QC step were pooled in equimolar amounts.
Libraries were sequenced at 50 bp paired-end on NextSeq 2000 platform.

treatment_protocol: Embryos were derived from natural mating between C57BL/6 TX males Xptet/Y; R26rtTA/WT (whole embryo RNA-seq) or Xptet/Y; R26rtTA/rtTA  with wild type JF1 females. Embryos were harvested at E2.5 and E3.5 and cultured in vitro in the presence of Doxycycline for 24 hours.

value: JF1 x C57BL6/J (Xptet/Y; R26rtTA/WT)

value: whole embryo

value: embryonic cells

value: Xptet

value: 24h doxycycline

tag: batch

tag: embryo stage


title: Ts65Dn_placenta_trisomic_Dam137_embryo4


title: D8_Msx1+_rep2

description: Library name: Sample4

value: Msx1-tdTomato mESCs

value: mESCs derived EB cells


title: Patient 1 month after treatment with guideline based therapy_48

description: Library name: 48_1


title: Ts65Dn_placenta_euploid_Dam137_embryo3

value: EUP

value: Male


title: embryo51

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1G7

tag: tissue

value: Xptet / R26rtTA


title: Patient before treatment with guideline based therapy_48

description: Library name: 48_0

value: Whole blood cells


title: D8_Msx1+_rep1

description: Library name: Sample3

value: Inducible Dlx2 overexpression

tag: treatment

value: EB formation with Dox induction and FACS


title: Ts65Dn_placenta_trisomic_Dam137_embryo1

value: TS


title: D8_Msx1-_rep2

description: Library name: Sample2

tag: cell line


title: embryo50

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1G5

tag: cell type


title: embryo49

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1F7


title: D8_Msx1-_rep1

description: Library name: Sample1


title: D16_Msx1-_rep2

description: Library name: Sample6


title: embryo48

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1F5


title: embryo53

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1H6


title: Ts65Dn_placenta_euploid_Dam125_embryo8

description: Gene expression data from mouse E18.5 placenta

tag: Sex


title: Patient before treatment with guideline based therapy_47

description: Library name: 47_0


title: CutTagDlx2+dox_rep1

description: Library name: Sample16

data_processing:
CUT&Tag reads were trimmed using cutadapt 4.4
Paired-end reads were aligned to the mm10 reference genome using Bowtie2 (v 2.3.5.1)
Peak calling was executed using SEACR 1.3
All statistically significantly enriched regions, referred to as peaks, identified in CUT&Tag data were annotated to genes using the R package ChIPseeker. Enriched motifs were calculated using Homer suite
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Single-cell suspensions were incubated with ConA magnetic beags (Bangs Labratories), followed by antibodies incubation. After tagmentation by pA-Tn5 transposon, the DNA was extracted by phenol-chloroform-isoamyl alcohol (ThermoFisher).
CUT&Tag libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme).

value: Inducible GFP overexpression

value: EB formation with Dox induction


title: Patient 1 month after treatment with guideline based therapy_46

description: Library name: 46_1


title: Ts65Dn_placenta_trisomic_Dam125_embryo5

value: Female


title: embryo47

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1E6

value: JF1 x C57BL6/J (Xptet/Y; R26rtTA/WT)


title: Patient before treatment with guideline based therapy_46

description: Library name: 46_0


title: CutTagDlx2+dox_rep2

description: Library name: Sample15


title: embryo46

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1E5

value: whole embryo


title: CutTagDlx2-dox_rep1

description: Library name: Sample14

value: EB formation without Dox induction


title: Ts65Dn_placenta_euploid_Dam125_embryo4


title: Patient 1 month after treatment with guideline based therapy_45

description: Library name: 45_1


title: Patient before treatment with guideline based therapy_45

description: Library name: 45_0


title: embryo45

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1D6

value: embryonic cells


title: Ts65Dn_placenta_euploid_Dam125_embryo1


title: CutTagDlx2-dox_rep2

description: Library name: Sample13


title: Patient 1 month after treatment with guideline based therapy_47

description: Library name: 47_1


title: Patient 1 month after treatment with guideline based therapy_44

description: Library name: 44_1


title: embryo43

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1B6

value: 24h doxycycline


title: Ts65Dn_placenta_trisomic_Dam113_embryo7


title: CutTag-IgG_rep1

description: Library name: Sample12

value: Msx1-tdTomato mESCs


title: CutTag-IgG_rep2

description: Library name: Sample11

value: mESCs derived EB cells


title: embryo42

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1A6


title: Ts65Dn_placenta_trisomic_Dam113_embryo5


title: Ts65Dn_placenta_euploid_Dam113_embryo4

value: EUP


title: H3K9me3_rep1

description: Library name: Sample10


title: TxrttaTigre_1.14 Dox (24h)

description: Library name: 1.14_plus

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz) were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). For the E6, CL30/CL30.7 and CL31/CL31.16, the mm10 genome was used  (GRCm38). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1).
Allele-specific expression per gene was calculated from genotype-assigned read counts. First, lowly expressed genes with an average allelic read count < 10 were excluded (summing both haplotypes). Escape of an X-linked gene was generally quantified as the fraction of read counts on the inactivated X against the total read count across both active and inactive X (Xi / (Xi + Xa), allelic ratio, also known as d-score).
Assembly: GRCm38
Supplementary files format and content: delimited text file

growth_protocol: ESCs were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in 2i-containing ESC media (DMEM, 15% FBS, 0.1 mM β-mercaptoethanol, 1,000 U/mL−1 leukaemia inhibitory factor (LIF), CHIR99021 (3 µM), and PD0325901 (1 µM)).

extract_protocol:
RNA was extracted from > 1M NPCs using the RNeasy kit and on-column DNAse digestion (Qiagen). RNA integrity was measured using the Bioanalyzer Nano Kit.
Only high-quality RNA was used for subsequent library preparation using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L, New England Biolabs (NEB), Ipswich, MA, USA) implemented on the liquid handling robot Beckman i7. Obtained libraries that passed the QC step were pooled in equimolar amounts; and the pools were loaded on the Illumina sequencer NextSeq 500 or NextSeq 2000 and sequenced bi-directionally, generating ~500 million paired-end reads, each 75 bases long.

treatment_protocol: Xist expression in TX1072 was induced by addition of doxycycline (1 µg/mL) to the media.

value: C57BL6/J x CAST/EiJ

value: ES cells

value: Dox (24h)


title: Patient before treatment with guideline based therapy_44

description: Library name: 44_0

value: Whole blood cells


title: Patient before treatment with guideline based therapy_43

description: Library name: 43_0


title: Ts65Dn_placenta_trisomic_Dam113_embryo1

value: Male


title: H3K27ac_rep1

description: Library name: Sample8

value: Inducible Dlx2 overexpression


title: Ts65Dn_placenta_euploid_Dam113_embryo2


title: TxrttaTigre_1.14 Control

description: Library name: 1.14_minus

value: Xptet / R26rtTA

value: Control


title: Patient 1 month after treatment with guideline based therapy_42

description: Library name: 42_1


title: embryo44

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1D5


title: H3K27ac_rep2

description: Library name: Sample7

value: EB formation with Dox induction


title: ExE_Dox_6

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1H2

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz) were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType EndToEnd. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1). The RNA-Sequencing data was pre-processed as described above (Allele-specific preprocessing of RNA-Sequencing data), using the SNPs between C57BL/6 and JF1 mice (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz). To confirm the annotated genotypes of the embryos, the rtTA transgene was included in the reference genome, and any embryo with >150 mapped transgene reads was considered rtTA-positive.
Assembly: GRCm39
Supplementary files format and content: delimited text files

source_name: Extra-embryonic tissue

extract_protocol:
Extra-embryonic tissues were dissected in PBS and collected in 150µl of 1x RNA Protection Reagent (NEB #T2011-1), snap-frozen and stored at -70C. RNA extraction was performed using the Monarch Total RNA Miniprep Kit (T2010S, NEB) following the protocol for mammalian whole blood RNA extraction with a few modifications. RNA was eluted in 30µl of water.
Illumina libraries were prepared by using a modified smart-seq2 protocol [Picelli 2014] using SuperScript IV RT and tagmentation procedure as previously described [Henning 2018]. The RT reaction mix was as follows: 2 μl SSRT IV 5x buffer; 0.5 μl 100 mM DTT; 2 μl 5 M betaine; 0.1 μl 1 M MgCl2; 0.25 μl 40 U/μl RNAse inhibitor; 0.25 μl SSRT IV; 0.1 μl 100 uM TSO, 1.15 μl RNase-free H2O. RT thermal conditions: 52 °C 15 min, 80 °C 10 min. cDNA was generated using 16 PCR cycles. The cDNA cleanup (0.6x SPRI ratio) was carried out omitting the ethanol wash steps and the elution volume was 13 μl of H2O. For tagmentation, the sample input was normalized to 0.2 ng/μl. Obtained libraries that passed the QC step were pooled in equimolar amounts.
Libraries were sequenced at 50 bp paired-end on NextSeq 2000 platform.

treatment_protocol: C57BL/6 TX males Xptet/Y; R26rtTA/WT or Xptet/Y; R26rtTA/rtTA were mated with wild type JF1 females. Xist was induced by adding doxycycline (1g/L of Dox and 100g/L of sucrose) to the drinking water of pregnant females 3.5 days post-coitum. The water bottles were changed every 48h and protected from light. Non-induced embryos were obtained from pregnant females provided with water containing only sucrose. After 5-days of Dox treatment (E8.5 post-coitum), embryos were dissected from the uteri of the pregnant females.

value: JF1 x C57BL6/J (Xptet/Y; R26rtTA/R26rtTA)

value: Extra-embryonic tissue

value: extra-embryonic cells

value: 5-days Doxycycline


title: Patient before treatment with guideline based therapy_42

description: Library name: 42_0


title: H3K27ac_rep3

description: Library name: Sample6


title: ExE_Dox_NoRtta_2

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1H1

value: JF1 x C57BL6/J (Xptet/Y; R26rtTA/WT)

value: Xptet


title: Patient 1 month after treatment with guideline based therapy_43

description: Library name: 43_1


title: Patient 1 month after treatment with guideline based therapy_41

description: Library name: 41_1


title: Ts65Dn_placenta_trisomic_Dam42_embryo6

value: TS

value: Female


title: ExE_Dox_5

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1G2


title: LAP2_rep1

description: Library name: Sample5

value: Msx1-tdTomato mESCs

value: mESCs derived EB cells


title: ExE_Dox_4

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1G1


title: Patient before treatment with guideline based therapy_41

description: Library name: 41_0


title: Ts65Dn_placenta_trisomic_Dam42_embryo5


title: Ts65Dn_placenta_euploid_Dam113_embryo3

value: EUP


title: Ts65Dn_placenta_trisomic_Dam42_embryo4


title: Ts65Dn_placenta_euploid_Dam42_embryo2


title: H3K9me3_rep2

description: Library name: Sample9


title: Patient 1 month after treatment with guideline based therapy_40

description: Library name: 40_1

value: Whole blood cells


title: LAP2_rep2

description: Library name: Sample4


title: Patient before treatment with guideline based therapy_40

description: Library name: 40_0


title: IgG_rep1

description: Library name: Sample3


title: IgG_rep2

description: Library name: Sample2


title: Patient 1 month after treatment with guideline based therapy_39

description: Library name: 39_1


title: Ts65Dn_placenta_euploid_Dam42_embryo3

value: Male


title: ExE_NoDox_8

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1E2

value: No treatment


title: ExE_NoDox_9

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1F2

value: Xptet / R26rtTA


title: Ts65Dn_placenta_trisomic_Dam18_embryo7


title: Ts65Dn_placenta_trisomic_Dam18_embryo6


title: IgG_rep3

description: Library name: Sample1

value: Inducible Dlx2 overexpression


title: Ts65Dn_placenta_trisomic_Dam42_embryo1


title: Patient 1 month after treatment with guideline based therapy_38

description: Library name: 38_1


title: Rep 2: RT Day 3, FTY720 Day 3, RT+FTY720 Day 3 CITE-seq VDJ

city: Portland

first: Wesley

last: Rosales

state: OR

address: 4805 NE Glisan St

institute: Earle A. Chiles Research Institute

description: Library name: 4_RT-D3_FTY720-D3_RTFTY720-D3_V

data_processing:
BCL output files were deultiplexed into fastq files via Illumina Bcl2Fastqv2.20
Cellranger v8.0.1 multi command was used to process fastqs into count matrices
Cellranger v8.0.1 vdj command was used to process fastqs into filtered contig files
Assembly: mm39
Supplementary files format and content: Cellranger multi on each library: barcodes.tsv.gz, features.tsv.gz, matrix.tsv.gz. Post cellranger internal filtering. In combination these produce gene count matrix and HTO information for downstream analyses
Supplementary files format and content: Cellranger vdj on each library: filtered_contig_annotations.csv. Contains post-filtered TCR contig information for TCR analysis.
Library strategy: CITE-seq

source_name: Tumor

growth_protocol: The MC38 murine colorectal cancer cell line was cultured in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin solution, 1% L-glutamine 200 mmol/L, 1% sodium pyruvate, 1% HEPES, and 1% MEM nonessential amino acids at 37°C with 5% CO2.

extract_protocol:
Tumors were manually dissociated using surgical scissors and the contents were transferred into Miltenyi Biotec gentleMACS C tubes containing enzyme digestion mixture, consisting of with 250 U/ml collagenase IV, 30 U/ml DNase I, 5 mM CaCl2, 5% heat-inactivated FBS, and HBSS. Dissociated tumors in collagenase cocktail were shaken at 37°C for 30 minutes. Samples were washed with RPMI containing 10% FBS and 2 mM EDTA. Digested contents were filtered through 70 µm cell strainers and washed in RPMI containing 10% FBS and 2 mM EDTA. Samples were enriched magnetically using CD4/CD8 TIL MicroBeads. Samples were then stained with viability dye, CD90.2-Alexa Fluor 700, and Totalseq hashtag antibodies. Kaede green or red live CD90.2+ cells were sorted using a Symphony S6 cell sorter with a 100µM nozzle.
Library construction was performed using the 10X Genomics Chromium GEM-X Single Cell 5' Reagent v3 with Feature Barcode technology for Cell Surface Protein protocol (CG000734).

treatment_protocol: Mice were randomized to treatment groups on day 7. On day 14, tumor bearing mice were photoconverted by exposing the TdLN to a 405 nm LED light source using a collimator for 5 min. Tumor from these mice were immediately treated with CT-guided radiation using the Small Animal Radiation Research Platform (SARRP). The SARRP delivered a single dose of 12 Gy to an isocenter within the tumor using a 10 mm x 10 mm collimator at beam angles designed to minimize dose delivery to normal tissues. FTY720 (10µg) was injected intraperitoneally into umor bearing mice on day 15.

value: Tumor

value: CD90+ T-cells

value: Kaedehet

value: RT Day 3, FTY720 Day 3, RT+FTY720 Day 3


title: ExE_Dox_3

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1E1

value: JF1 x C57BL6/J (Xptet/Y; R26rtTA/R26rtTA)

value: Extra-embryonic tissue

value: extra-embryonic cells

value: 5-days Doxycycline


title: Patient before treatment with guideline based therapy_38

description: Library name: 38_0

extract_protocol:
Silica-membrane-based RNA isolation and purification in a spin-column format were performed using the PAXgene Blood RNA kit (Qiagen). Extracted RNA was globin-cleared using the Ambion GLOBINclear kit (Thermo Fisher, Waltham, MA). Then, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) and converted to an Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). CD19, CD56, CD123, and CD235a antibodies was used to obtain remaining eosinophils. Total RNA from eosinophils was extracted using TRIzol™ Reagent (Invitrogen). Then, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) and converted to an Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ExE_NoDox_7

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1D2


title: Rep 2: RT Day 3, FTY720 Day 3, RT+FTY720 Day 3 CITE-seq HTO

description: Library name: 4_RT-D3_FTY720-D3_RTFTY720-D3_H

value: TotalSeq™-C0301 (RT D3 Red), TotalSeq™-C0302 (RT D3 Green), TotalSeq™-C0303 (FTY720 D3 Red), TotalSeq™-C0304 (FTY720 D3 Green), TotalSeq™-C0305 (RT+FTY720 Red), TotalSeq™-C0306 (RT+FTY720 Green)


title: ExE_Dox_2

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1D1


title: Rep 2: RT Day 3, FTY720 Day 3, RT+FTY720 Day 3 CITE-seq GEX

description: Library name: 4_RT-D3_FTY720-D3_RTFTY720-D3_M


title: Ts65Dn_placenta_trisomic_Dam18_embryo5

description: Gene expression data from mouse E18.5 placenta

value: TS


title: Patient 1 month after treatment with guideline based therapy_37

description: Library name: 37_1


title: ExE_Dox_NoRtta_1

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1F1

value: JF1 x C57BL6/J (Xptet/Y; R26rtTA/WT)

value: Xptet


title: Ts65Dn_placenta_euploid_Dam18_embryo4

value: EUP


title: Ts65Dn_placenta_euploid_Dam18_embryo3

value: Female


title: ExE_NoDox_5

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1C1

value: No treatment


title: ExE_NoDox_6

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1C2

value: Xptet / R26rtTA


title: Rep 2: NT Day 1, RT Day 1, NT Day 3 CITE-seq VDJ

description: Library name: 3_NT-D1_RT-D1_NT-D3_V

value: NT Day 1, RT Day 1, NT Day 3


title: Patient before treatment with guideline based therapy_39

description: Library name: 39_0

value: Whole blood cells


title: Patient 1 month after treatment with guideline based therapy_36

description: Library name: 36_1


title: Ts65Dn_placenta_trisomic_Dam18_embryo2


title: Ts65Dn_placenta_euploid_Dam125_embryo7

value: Male


title: Rep 2: NT Day 1, RT Day 1, NT Day 3 CITE-seq GEX

description: Library name: 3_NT-D1_RT-D1_NT-D3_M

value: Tumor

value: CD90+ T-cells

value: Kaedehet


title: ExE_NoDox_4

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1B2

value: JF1 x C57BL6/J (Xptet/Y; R26rtTA/R26rtTA)

value: Extra-embryonic tissue


title: Ts65Dn_placenta_euploid_Dam18_embryo1


title: ExE_NoDox_3

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1B1

value: extra-embryonic cells


title: Patient before treatment with guideline based therapy_36

description: Library name: 36_0


title: Patient 1 month after treatment with guideline based therapy_35

description: Library name: 35_1


title: ExE_Dox_1

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1A3

value: 5-days Doxycycline


title: Ts65Dn_placenta_trisomic_Dam11_embryo8

value: TS


title: Rep 1: RT Day 3, FTY720 Day 3, RT+FTY720 Day 3 CITE-seq VDJ

description: Library name: 2_RT-D3_FTY720-D3_RTFTY720-D3_V

value: RT Day 3, FTY720 Day 3, RT+FTY720 Day 3


title: Patient before treatment with guideline based therapy_35

description: Library name: 35_0


title: Patient 1 month after treatment with guideline based therapy_34

description: Library name: 34_1


title: Rep 1: RT Day 3, FTY720 Day 3, RT+FTY720 Day 3 CITE-seq GEX

description: Library name: 2_RT-D3_FTY720-D3_RTFTY720-D3_M


title: Ts65Dn_placenta_trisomic_Dam11_embryo7


title: Rep 1: NT Day 1, RT Day 1, NT Day 3 CITE-seq VDJ

description: Library name: 1_NT-D1_RT-D1_NT-D3_V


title: Rep 2: NT Day 1, RT Day 1, NT Day 3 CITE-seq HTO

description: Library name: 3_NT-D1_RT-D1_NT-D3_H

value: TotalSeq™-C0301 (NT D1 Red), TotalSeq™-C0302 (NT D1 Green), TotalSeq™-C0303 (RT D1 Red), TotalSeq™-C0304 (RT D1 Green), TotalSeq™-C0305 (NT D3 Red), TotalSeq™-C0306 (NT D3 Green)


title: Patient before treatment with guideline based therapy_37

description: Library name: 37_0


title: Ts65Dn_placenta_euploid_Dam11_embryo5

value: EUP


title: Patient before treatment with guideline based therapy_34

description: Library name: 34_0


title: ExE_NoDox_1

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1A1


title: Ts65Dn_placenta_trisomic_Dam11_embryo6


title: Rep 1: NT Day 1, RT Day 1, NT Day 3 CITE-seq HTO

description: Library name: 1_NT-D1_RT-D1_NT-D3_H


title: Ts65Dn_placenta_euploid_Dam11_embryo4

value: Female


title: Rep 1: NT Day 1, RT Day 1, NT Day 3 CITE-seq GEX

description: Library name: 1_NT-D1_RT-D1_NT-D3_M


title: Patient 1 month after treatment with guideline based therapy_33

description: Library name: 33_1


title: E6 NoDox H3K27me3 (rep2)

description: Library name: E6NoDoxr3_H3K27me3

data_processing:
Paired-end reads were mapped with Bowtie2 (v2.3.4.1) using an N-masked genome reference (--very-sensitive -X 1000 --no-mixed --no-discordant). Low-quality and mitochondrial reads were filtered using Samtools (v1.9). Genotype assignment was performed with SNPsplit (v0.3.4), followed by duplicate removal with Picard Tools (v2.20.8). Three BAM files were generated: C57BL/6, CASTEiJ, and total reads (allelic and unassigned). BigWig files were generated from each BAM file using bamCoverage with scale factors calculated based on 10 kb binned coverage data using edgeR.
Assembly: Mouse mm10
Supplementary files format and content: BigWig files containing scale factor-normalized coverage tracks for genome browser visualization.
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed based on the protocol described in Skene and Henikoff, 2017. Mnase-digested DNA fragments were purified via ethanol precipitation and size selection using Ampure XP beads.
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Kit.

treatment_protocol: Xist expression in NPCs was induced by addition of doxycycline (1 µg/mL) to the NPC media. Culture media supplemented with doxycycline was renewed every 24h. For doxycycline wash-out, doxycycline-containing media was removed, and cells were refreshed with doxycycline-free culture media.

value: C57BL6/J x CAST/EiJ

value: neural progenitor cell

value: Control

tag: antibody


title: Patient before treatment with guideline based therapy_33

description: Library name: 33_0

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 20.0.0; Qiagen, Redwood City, CA).
Assembly: hg19
Supplementary files format and content: excel files include expression values of total counts, RPKM, TPM, and CPM for each sample

value: Whole blood cells


title: E6 NoDox H3K27me3 (rep1)

description: Library name: E6NoDoxr2_H3K27me3

value: Xptet / R26rtTA


title: Rep 1: RT Day 3, FTY720 Day 3, RT+FTY720 Day 3 CITE-seq HTO

description: Library name: 2_RT-D3_FTY720-D3_RTFTY720-D3_H

value: Tumor

value: TotalSeq™-C0301 (RT D3 Red), TotalSeq™-C0302 (RT D3 Green), TotalSeq™-C0303 (FTY720 D3 Red), TotalSeq™-C0304 (FTY720 D3 Green), TotalSeq™-C0305 (RT+FTY720 Red), TotalSeq™-C0306 (RT+FTY720 Green)


title: Ts65Dn_placenta_trisomic_Dam11_embryo3


title: ExE_NoDox_2

description: Library name: AACMHH2HV_4585_EMBRYOS_24s001670-1-1_loda_lane1A2

value: No treatment


title: Mouse KPC tumor, intratumoral VIVIT, rep3

city: Stanford

first: Chuner

last: Guo

address: 257 Campus Dr

department: Surgery

institute: Stanford University

description:
Library name: vivit3
instrument model: Singular G4

data_processing:
Cell Ranger (v9.0.0) was used to perform alignment, barcode processing, demultiplexing, and single cell 3' gene counting.
Assembly: mm10
Supplementary files format and content: Cell Ranger output feature barcode matrices (HDF5 format), fragment files (tsv.gz), and the corresponding fragment file tabix indices (tsv.gz.tbi).

source_name: pancreas

extract_protocol:
Tissues were minced and digested using a 1:1 ratio of Collagenase Type IV (Cat#17104019; Thermo Fisher) and Collagenase Type II (Cat#17101015; Thermo Fisher) at a concentration of 1500 U/mL in DMEM (Cat#10569010; Thermo Fisher) for 90 minutes at 37°C. Tissue pieces were agitated at 150 rpm during enzymatic digestion using an orbital shaker. Collagenase activity was stopped using DMEM with FBS, and digested tissue was strained through 100 μm (Cat#4620E99; Corning) and 40 μm cell strainers (Cat#4620F05; Corning). Cells were centrifuged at 1500 rpm / 524 rcf for 5 minutes at 4°C resulting in a single-cell suspension. Samples were resuspended with 0.04% UltraPure BSA (Cat# AM2618; Thermo Fisher).
scRNA-seq libraries were made following the 10x Genomics Single Cell 3' Reagent Kits User Guide (v3 Chemistry) for control1 and vivit1. The remaining 4 libraries were made following the 10x Genomics GEM-X Universal 3' Gene Expression v4 4-plex Reagent Kits User Guide.

value: pancreas


title: Patient before treatment with guideline based therapy_32

description: Library name: 32_0


title: E6 7dDox H3K27me3 (rep2)

description: Library name: E67dDoxr3_H3K27me3

value: Dox (7d)


title: Dp16_placenta_euploid_Dam81_embryo10

value: Male


title: E6 7dDox H3K27me3 (rep1)

description: Library name: E67dDoxr2_H3K27me3


title: Dp16_placenta_euploid_Dam81_embryo9


title: E6 7dD7dWO H3K27me3 (rep2)

description: Library name: E67dD7dWOr3_H3K27me3

value: Dox (7d) - washout (7d)


title: Patient 1 month after treatment with guideline based therapy_31

description: Library name: 31_1


title: Dp16_placenta_euploid_Dam81_embryo7


title: E6 7dD7dWO H3K27me3 (rep1)

description: Library name: E67dD7dWOr2_H3K27me3


title: Mouse KPC tumor, intratumoral VIVIT, rep1

description:
Library name: vivit1
instrument model: Singular G4


title: Mouse KPC tumor, intratumoral saline control, rep3

description:
Library name: control3
instrument model: Singular G4


title: Mouse KPC tumor, intratumoral saline control, rep2

description:
Library name: control2
instrument model: Singular G4


title: E6 21dDox H3K27me3 (rep2)

description: Library name: E621dDoxr3_H3K27me3

value: Dox (21d)


title: Patient 1 month after treatment with guideline based therapy_30

description: Library name: 30_1


title: Patient before treatment with guideline based therapy_31

description: Library name: 31_0


title: Mouse KPC tumor, intratomural saline control, rep1

description:
Library name: control1
instrument model: Singular G4


title: Dp16_placenta_euploid_Dam81_embryo6

description: Gene expression data from mouse E18.5 placenta


title: Patient before treatment with guideline based therapy_30

description: Library name: 30_0


title: E6 21dD7dWO H3K27me3 (rep2)

description: Library name: E621dD7dWOr3_H3K27me3

value: Dox (21d) - washout (7d)


title: Dp16_placenta_trisomic_Dam81_embryo2

value: TS


title: Mouse KPC tumor, intratumoral AF12198 + IL12 (GEX)

description: Library name: combo_GEX

data_processing:
Cell Ranger ARC (v2.0.0) was used to perform alignment, barcode processing, peak calling, and counting of both ATAC and GEX molecules.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (gzipped format)

extract_protocol:
Single nuclei were extracted as previously described (Foster DS, Griffin M, Januszyk M, Delitto D, Norton JA, Longaker MT. Optimized Nuclei Isolation from Fresh and Frozen Solid Tumor Specimens for Multiome Sequencing. J Vis Exp. 2023. doi: 10.3791/65831. PMID: 37902368).
Libraries were made following the 10x Genomoics Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide.


title: Mouse KPC tumor, intratumoral AF12198 + IL12 (ATAC)

description: Library name: combo_ATAC

library_source: genomic single cell


title: Mouse KPC tumor, intratumoral VIVIT, rep2

description:
Library name: vivit2
instrument model: Singular G4


title: Patient 1 month after treatment with guideline based therapy_32

description: Library name: 32_1


title: Dp16_placenta_trisomic_Dam81_embryo11


title: Patient 1 month after treatment with guideline based therapy_29

description: Library name: 29_1


title: E6 21dDox H3K27me3 (rep1)

description: Library name: E621dDoxr2_H3K27me3


title: Dp16_placenta_euploid_Dam81_embryo5

value: EUP


title: Mouse KPC tumor, intratumoral IL12 (ATAC)

description: Library name: IL12_ATAC


title: Patient before treatment with guideline based therapy_29

description: Library name: 29_0


title: Patient 1 month after treatment with guideline based therapy_28

description: Library name: 28_1


title: E6 NoDox H2AK119ubi (rep2)

description: Library name: E6NoDoxr3_H2AK119ubi


title: Patient before treatment with guideline based therapy_28

description: Library name: 28_0


title: E6 NoDox H2AK119ubi (rep1)

description: Library name: E6NoDoxr2_H2AK119ubi


title: Patient 1 month after treatment with guideline based therapy_27

description: Library name: 27_1


title: Dp16_placenta_euploid_Dam81_embryo1


title: Dp16_placenta_euploid_Dam63_embryo4


title: Mouse KPC tumor, intratumoral AF12198, multiome (ATAC)

description: Library name: AF12198_ATAC


title: E6 7dDox H2AK119ubi (rep2)

description: Library name: E67dDoxr3_H2AK119ubi


title: E6 7dDox H2AK119ubi (rep1)

description: Library name: E67dDoxr2_H2AK119ubi


title: Mouse KPC tumor, intratumoral IL12 (GEX)

description: Library name: IL12_GEX


title: Dp16_placenta_trisomic_Dam57_embryo5


title: Mouse KPC tumor, intratumoral AF12198, multiome (GEX)

description: Library name: AF12198_GEX


title: Patient before treatment with guideline based therapy_27

description: Library name: 27_0


title: Mouse KPC tumor, intratumoral saline control, multiome (ATAC)

description: Library name: control_ATAC


title: E6 7dD7dWO H2AK119ubi (rep2)

description: Library name: E67dD7dWOr3_H2AK119ubi


title: Dp16_placenta_euploid_Dam57_embryo6


title: Patient 1 month after treatment with guideline based therapy_26

description: Library name: 26_1


title: Dp16_placenta_euploid_Dam57_embryo4


title: Mouse KPC tumor, intratumoral saline control, multiome (GEX)

description: Library name: control_GEX


title: E6 7dD7dWO H2AK119ubi (rep1)

description: Library name: E67dD7dWOr2_H2AK119ubi


title: Dp16_placenta_trisomic_Dam57_embryo3

value: Female


title: E6 21dDox H2AK119ubi (rep2)

description: Library name: E621dDoxr3_H2AK119ubi

value: C57BL6/J x CAST/EiJ


title: Patient before treatment with guideline based therapy_26

description: Library name: 26_0


title: Dp16_placenta_trisomic_Dam63_embryo3


title: Patient 1 month after treatment with guideline based therapy_25

description: Library name: 25_1


title: Dp16_placenta_trisomic_Dam57_embryo1


title: Dp16_placenta_euploid_Dam57_embryo2


title: E6 21dD7dWO H2AK119ubi (rep2)

description: Library name: E621dD7dWOr3_H2AK119ubi

value: neural progenitor cell


title: Mouse KPC tumor, control

description: Library name: tumor

data_processing:
Cell Ranger (v6.0.0)  was used to perform alignment, barcode processing, and single cell 3' gene counting.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (gzipped format)

extract_protocol:
Tissues were minced and digested using a 1:1 ratio of Collagenase Type IV (Cat#17104019; Thermo Fisher) and Collagenase Type II (Cat#17101015; Thermo Fisher) at a concentration of 1500 U/mL in DMEM (Cat#10569010; Thermo Fisher) for 90 minutes at 37°C. Tissue pieces were agitated at 150 rpm during enzymatic digestion using an orbital shaker. Collagenase activity was stopped using DMEM with FBS, and digested tissue was strained through 100 μm (Cat#4620E99; Corning) and 40 μm cell strainers (Cat#4620F05; Corning). Cells were centrifuged at 1500 rpm / 524 rcf for 5 minutes at 4°C resulting in a single-cell suspension. Samples were resuspended with 0.04% UltraPure BSA (Cat# AM2618; Thermo Fisher).
scRNA-seq libraries were made following the 10x Genomoics Single Cell 3' Reagents Kits User Guide (v3 Chemistry).


title: E6 21dDox H2AK119ubi (rep1)

description: Library name: E621dDoxr2_H2AK119ubi


title: Patient 1 month after treatment with guideline based therapy_24

description: Library name: 24_1


title: Mouse pancreas, suture ligated to induce pancreatitis

description: Library name: pancreatitis


title: Dp16_placenta_euploid_Dam47_embryo10


title: Mouse pancreas, normal

description: Library name: normal


title: E6 21dD7dWO H2AK119ubi (rep1)

description: Library name: E621dD7dWOr2_H2AK119ubi


title: E6 21dD7dWO H3K27me3 (rep1)

description: Library name: E621dD7dWOr2_H3K27me3


title: Patient before treatment with guideline based therapy_24

description: Library name: 24_0


title: Dp16_placenta_trisomic_Dam47_embryo9


title: Dp16_placenta_trisomic_Dam47_embryo8


title: MU636M - Replicate 3_sRNA

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

description: Library name: MU636M_C_sRNA

data_processing:
Raw paired-end (PE)  and single-end reads from M. lusitanicus RNA-seq datasets were quality-checked using FastQC v0.11.9
Adapters were removed with Trim Galore! V.0.4.3.1
Reads with a Phred quality score (q) ≤32 and/or a total length < 20 nt were removed from the analysis
Assembly: Mucor lusitanicus (CBS 277.49) v2 (https://mycocosm.jgi.doe.gov/pages/search-for-genes.jsf?organism=Mucci2)
Supplementary files format and content: Spreadsheet including counts, log2FC, differential expression statistics and functional annotation for every gene

organism: Mucor lusitanicus

source_name: Spores&Macrophages

growth_protocol: MU636 and MU412 spores were co-incubated with J774A.1 murine macrophages at an MOI of 1.5:1 for 1 hour at 37 °C.

extract_protocol:
Total RNA was extracted using the mirVana kit (AM1561) and treated with DNase (Sigma, On-Column DNaseI treatment set)
NEBNext® Ultra™ Directional RNA Library Prep Kit

value: Spores

tag: co-culture

value: J774A.1 murine macrophages

value: Wild-type strain


title: B16F10 shRNA OSGEP#2 replicat3

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

description: Library name: N3-O2

data_processing:
Raw reads were demultiplexed and adapter-trimmed using Illumina bcl2fastq conversion software v2.20. They were processed within our custom nextflow RNAseq pipeline inspired from nf-core/rnaseq. We used TrimGalore to trimm a single base at 5' and 3' ends of each read and to perform a quality based trimming after removing poly-G tails. Then, we did the STAR alignment and Salmon quantification
Assembly: Genome Reference reference genome fa and the annotations from Ensembl release genes
Supplementary files format and content: Raw counts from Salmon

source_name: Cell

growth_protocol: B16F10 were cultured in a humidified incubator at 37°C with 5% CO2, grown in Dulbecco’s modified Eagle’s medium (DMEM, LONZA) supplemented with 1% glutamine and 1% penicillin-streptomycin and 10% FBS (GIBCO)

extract_protocol:
Cells were washed three times with cold PBS and lysed in RIP buffer (150 mmol/L KCl, 25 mmol/L Tris pH 7.4, 5 mmol/L EDTA,0.5 mmol/L DTT, 0.5%NP40) supplemented with protease inhibitor for 30min at 4°C. Lysates were cleared by centrifugation at 10.000G for 15min at 4°C. 1mg of lysate were mixed with anti-FLAG anti-A/G protein conjugated magnetic beads (MedeChemExpress, #HY-K0207, #HY-K0202 respectively) according manufacturer’s instruction. Binding reaction was incubated on rotation overnight at 4°C. Beads were washed 4 times with RIP buffer and elution was completed with buffer elution A (0.15M glycine, pH3). After 10min, neutralization buffer (1M TrisHCl pH8.0) was added and followed by incubation with 10mg/mL of proteinase K (FischerScientific, #10103533) at 55°C for 1h. The RNA bound to FLAG-RIG was extracted using TRIzol protocol (Invitrogen)
Library preparation was performed using 10 ng of total RNA following the Illumina Stranded Total RNA Ligation with Ribo-Zero Plus protocol  (Illumina). The final library profiles were assessed using the QIAxcel Advanced System (Qiagen), and concentrations were measured by qPCR using the SYBR Fast KAPA Kit.Indexed Libraries were pooled in equimolar ratios, and the pooled library was sequenced on the NovaSeq 6000 platform using an S2 flow cell with paired-end 150 bp reads, with 50 Mi fragments sequenced per sample.

value: Cell

value: melanoma

value: KD OSGEP


title: Patient 1 month after treatment with guideline based therapy_23

description: Library name: 23_1

value: Whole blood cells


title: MU636M - Replicate 2_sRNA

description: Library name: MU636M_B_sRNA


title: B16F10 shRNA OSGEP#1 replicat3

description: Library name: N3-O1


title: Dp16_placenta_euploid_Dam47_embryo7

data_processing: Microarray data were analyzed using Transcriptome Analysis Console (TAC) software (version 4.0.0) (Thermo Fisher Scientific) using RMA normalization

extract_protocol: RNA was processed and hybridized on Mouse Clariom S HT 96-array plates (902970; ThermoFisher Scientific) using GeneChip WT Plus Reagent Kits following the manufacturer’s protocol (902281; ThermoFisher Scientific).


title: Patient before treatment with guideline based therapy_23

description: Library name: 23_0


title: MU636M - Replicate 1_sRNA

description: Library name: MU636M_A_sRNA


title: Mouse KPC tumor, treated with AF12198

description: Library name: tumor_AF12198

value: pancreas


title: Patient before treatment with guideline based therapy_25

description: Library name: 25_0


title: B16F10 shRNA Ctrl replicat3

description: Library name: N3-CTRL

value: WT


title: Patient before treatment with guideline based therapy_22

description: Library name: 22_0


title: B16F10 shRNA OSGEP#2 replicat2

description: Library name: N2-O2


title: MU636C - Replicate 3_sRNA

description: Library name: MU636C_C_sRNA

source_name: Spores


title: MU636C - Replicate 2_sRNA

description: Library name: MU636C_B_sRNA


title: Patient 1 month after treatment with guideline based therapy_21

description: Library name: 21_1


title: Dp16_placenta_trisomic_Dam47_embryo5

value: Male


title: Dp16_placenta_trisomic_Dam47_embryo4


title: MU636C - Replicate 1_sRNA

description: Library name: MU636C_A_sRNA


title: Patient before treatment with guideline based therapy_21

description: Library name: 21_0


title: B16F10 shRNA Ctrl replicat2

description: Library name: N2-CTRL


title: Dp16_placenta_euploid_Dam47_embryo1


title: MU412M - Replicate 3_sRNA

description: Library name: MU412M_C_sRNA

value: Mutant strain (r3b2delta)


title: Patient 1 month after treatment with guideline based therapy_20

description: Library name: 20_1


title: MU412M - Replicate 2_sRNA

description: Library name: MU412M_B_sRNA


title: B16F10 shRNA OSGEP#1 replicat1

description: Library name: N1-O1


title: Patient before treatment with guideline based therapy_20

description: Library name: 20_0


title: Patient 1 month after treatment with guideline based therapy_22

description: Library name: 22_1


title: Dp16_placenta_trisomic_Dam34_embryo5


title: MU412M - Replicate 1_sRNA

description: Library name: MU412M_A_sRNA