title: Bmp4 embryonic KO plate 12

description:
4n_x7_p16
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Bmp4 embryonic KO plate 33

status: Public on May 21 2024

type: SRA

city: Rehovot

first: Markus

last: Mittnenzweig

state: Shfela

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description:
4n_x10_p13
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos

library_source: transcriptomic single cell

data_processing:
MARS-seq data was processed as detailed in the MARS-seq2.0 protocol (Keren-Shaul et al. 2019):
see https://github.com/tanaylab/MARS-SEQ for computational pipeline
1. bcl2fastq/2.15.0.4
2. Pool_barcode (4 bps) and well_barcode (7 bps) plus UMI barcode (8 bps) were removed from Read 1 and Read 2 (respectively)
3. Read 1 sequences were mapped to the mm10 genome using star aligner
4. Demultiplexing and construction of mRNA count matrix were based on 4bp plate barcode, 7bp well barcode and 8bp UMI barcode
read1 structure: 52bp mRNA, 4bp plate barcode was added to the fastq header
read2 structure: 7W.8R, i.e. first 7bp contain the cell barcode and next 8bp are UMI
Assembly: mm10
Supplementary files format and content: Tab-separated text file for each 384-well plate containing UMI counts per gene per single cell. Supplementary files contain metadata for each processed single cell
10x scRNA-seq data from ex utero embryos was processed using Cell Ranger v6.2.1
After initial demultiplexing, reads were aligned and counted using cellranger count with default settings
Supplementary files format and content: filtered feature barcode matrix in .mtx format (10x output of cellranger count pipeline)

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryo

growth_protocol: control and mutant mESCs were cultured on irradiated mouse embryonic fibroblasts (MEFs) with standard serum medium for 2-3 days and replaced with 2i+LIF medium containing an additional 1 mM PD0325901 and 3 mM CHIR99021 for another growth of 10-12 hours.

extract_protocol:
Genetically manipulated embryos were dissected in ice-cold 1×PBS, followed by imaging in a drop of DMEM medium supplemented with 10% foetal bovine serum (FBS) under a Nikon Eclipse Ti2 inverted microscope. Embryos were then rinsed in ice-cold 1×PBS, transferred into an Eppendorf tube containing 35 µl 0.25% Trypsin/0.02% EDTA Solution A, and incubated at 37 °C for 5 min with 2-3 times pipetting. Trypsinization was stopped by adding 10% FBS/DMEM medium. Cell suspensions were filtered through a 35 µm strainer before sorting.
Single-cell cDNA libraries were prepared using the MARS-Seq method as described (Keren-Shaul et al., 2019). Briefly, reverse transcription was performed in individual wells of the sorted 384-well plate to get complementary DNA (cDNA). Subsequently, all liquid from each 384-well plate was pooled and converted to double-stranded DNA, transcribed using T7 RNA polymerase, and fragmented. A unique plate adaptor was added to each library to be sequenced together, and RNA::ssDNA (plate adaptor) ligation was performed. The purified ligates were applied to a second RT step with a primer complementary to the ligated adaptor, and the library is completed by cDNA enrichment through PCR amplification. Library concentration and profile were evaluated before sequencing.
10x ex utero: Cultured embryos were prepared for sequencing at different developmental stages after two days in culture: late streak and early head fold, assessed by light microscopy. Six similar embryos were selected for each developmental stage, pooled and dissociated using Trypsin-EDTA solution A 0.25% (Biological Industries; 030501B) for 5 minutes at 37℃. Trypsin was neutralized with media including 10% FBS and cells were washed and re-suspended in 1x PBS (calcium and magnesium free) with 400 μg/ml BSA. Cell suspension was than filtered with a 100 μm cell strainer to avoid cell clumps. Single cell viability was determined by trypan blue staining, before being diluted to a final concentration of 1000 cells/μl. Single-cell RNA-seq libraries were generated for each pool of embryos separately using 10x Genomics Chromium v3 system (5000 cell target cell recovery) and sequenced on Illumina NovaSeq 6000 platform according to the manufacturer’s instructions.

treatment_protocol: (1) To obtain whole-embryo mutants, mESCs were injected into tetraploid B6D2F x B6D2F1 E3.5 blastocysts and surgically implanted into E2.5 postcoitum pseudo-pregnant Hsd:ICR (CD-1) females following standard procedures. Females were sacrificed at embryonic day 7.5-9.5 based on the design of the experiment. (2) For ex utero experiments - Pre-gastrulating embryos were dissected at E5.5, their Reichert's membrane removed and individually placed into separate wells of 8-well glass bottom/ibiTreat μ-plates (iBidi; 80827/80826) filled with 250 μl of EUCM (consisted of 25% DMEM (GIBCO 11880; includes 1mg/mL D-glucose and pyruvate, without phenol red and without L-glutamine) supplemented with 1x Glutamax (GIBCO, 35050061), 100 units/ml penicillin/100 μg/ml streptomycin (Biological industries; 030311B) and 11 mM HEPES (GIBCO, 15630056), plus 50% Rat Serum (RS) (Rat whole embryo culture serum, ENVIGO Bioproducts B-4520) and 25% Human Umbilical Cord Blood Serum (HCS) that is prepared in-house. Media was pre-heated for an hour in an incubator with 5% CO2 at 37 °C. Embryos were cultured statically with 5% CO2 at 37℃. Total volume of media was replaced every 24 hrs, and embryos were monitored by morphological assessment daily. (3) Elf5 ExE-KO mutants: Infection of nascent blastocysts were performed using B6D2F1 (C57BL/6xDBA) (Envigo)/Cas9-GFP embryos. In brief, 3-4-week old B6D2F1 females were hormone primed by an intraperitoneal (i.p.) injection of pregnant mare serum gonadotropin (PMSG, Vetmarket) followed 46 hr later by an injection of human chorionic gonadotropin (hCG, Sigma) and mating with homozygote Cas9-GFP males. Embryos were harvested at the zygote stage, and cultured in KSOM medium until the blastocyst stage. For efficient infection of the trophectoderm, zona pellucida was removed in acidic Tyrode’s solution (Sigma). Next, 15-20 embryos were incubated with lentiviruses, described above, in KSOM for 4-5 hrs. The transduced blastocysts were washed, and then transferred to each recipient female generated after mating with vasectomized CD1 males (Envigo); the day of injection was considered as 2.5dpc. Mice were handled in accordance with institutional guidelines and approved by the Institutional Animal Care and Use Committee (IACUC).

tag: tissue

value: Mouse embryo

tag: genotype

value: Host cells and injected mESC-derived Bmp4 KO cells

tag: developmental stage


title: Bmp4 embryonic KO plate 9

description:
4n_x7_p13
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Bmp4 embryonic KO plate 10

description:
4n_x7_p14
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Bmp4 embryonic KO plate 6

description:
4n_x7_p7
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Bmp4 embryonic KO plate 8

description:
4n_x7_p11
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Bmp4 embryonic KO plate 11

description:
4n_x7_p15
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Bmp4 embryonic KO plate 7

description:
4n_x7_p8
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Bmp4 embryonic KO plate 2

description:
4n_x7_p2
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Bmp4 embryonic KO plate 1

description:
4n_x7_p1
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Elf5 KO plate 43

description:
p5_elf5_sc_exp8_sg2_sg3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos

value: Extraembryonic-ectoderm-specific Elf5 KO embryos


title: Bmp4 embryonic KO plate 4

description:
4n_x7_p5
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Elf5 KO plate 42

description:
p4_elf5_sc_exp8_sg2_sg3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Bmp4 embryonic KO plate 23

description:
4n_x10_p2
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Bmp4 embryonic KO plate 26

description:
4n_x10_p5
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Elf5 KO plate 39

description:
p1_elf5_sc_exp8_sg2_sg3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Bmp4 embryonic KO plate 18

description:
4n_x8_p5
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Elf5 KO plate 36

description:
elf5_sg2_sg3_exp6_p4
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 33

description:
elf5_sg2_sg3_exp6_p1
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 32

description:
p3_elf5_exp5_sg2_sg3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 35

description:
elf5_sg2_sg3_exp6_p3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 38

description:
elf5_sg2_sg3_exp6_p6
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 34

description:
elf5_sg2_sg3_exp6_p2
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Bmp4 embryonic KO plate 5

description:
4n_x7_p6
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Elf5 KO plate 37

description:
elf5_sg2_sg3_exp6_p5
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 31

description:
p2_control_exp5_sg2_sg3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 30

description:
p11_DB4GC_e1b
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Bmp4 embryonic KO plate 3

description:
4n_x7_p3
MARS-seq of tetraploid complementary assay of embryonic Bmp4-KO embryos


title: Elf5 KO plate 23

description:
p7_DB4GC_control_e3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 27

description:
p1_elf5_exp4_sg2_3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 44

description:
p1_elf5_sc_exp7_sg2_sg3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 26

description:
p8_DB4GC_control_e3b
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 29

description:
p1_control_exp5_sg2_sg3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 28

description:
p2_elf5_exp4_sg2_3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 21

description:
p6_DB4GC_control_e2c
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 22

description:
p6_DB4GC_control_e4_exp6
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 41

description:
p3_elf5_sc_exp8_sg2_sg3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 18

description:
p4_DB4GC_e7_exp6
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 40

description:
p2_elf5_sc_exp8_sg2_sg3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 20

description:
p5_DB4GC_e7b_exp6
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 19

description:
p5_DB4GC_control_e2b
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 17

description:
p4_DB4GC_control_e2
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 25

description:
p7b_DB4GC_control_e4c_exp6
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 15

description:
p3_DB4GC_control_e1_b
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 14

description:
p2_DB4GC_e5b_exp6
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 16

description:
p3_DB4GC_e5c_exp6
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 13

description:
p2_DB4GC_control_e1_cont
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 11

description:
p1_DB4GC_e5_exp6
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 9

description:
elf5_sc_exp3_p9
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 12

description:
p10_DB4GC_e1
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 10

description:
p1_DB4GC_control_e1
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 24

description:
p7_DB4GC_control_e4b_exp6
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 8

description:
elf5_sc_exp3_p8
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 7

description:
elf5_sc_exp3_p7
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 6

description:
elf5_sc_exp3_p6
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 3

description:
elf5_sc_exp3_p3
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 4

description:
elf5_sc_exp3_p4
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 5

description:
elf5_sc_exp3_p5
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 2

description:
elf5_sc_exp3_p2
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Elf5 KO plate 1

description:
elf5_sc_exp3_p1
MARS-seq of extraembryonic-ectoderm-specific Elf5 KO embryos


title: Wildtype plate 151

description:
lin_trace_p7_exp1
MARS-seq of wildtype embryos

value: Wildtype embryo


title: Wildtype plate 152

description:
lin_trace_p9_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 150

description:
lin_trace_p6_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 145

description:
lin_trace_p15_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 144

description:
lin_trace_p13_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 146

description:
lin_trace_p2_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 143

description:
lin_trace_p12_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 147

description:
lin_trace_p3_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 149

description:
lin_trace_p5_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 142

description:
lin_trace_p11_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 140

description:
lin_trace_p1_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 138

description:
roni2e
MARS-seq of wildtype embryos


title: Wildtype plate 141

description:
lin_trace_p10_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 137

description:
roni2_p
MARS-seq of wildtype embryos


title: Wildtype plate 139

description:
EXE33_P1
MARS-seq of wildtype embryos


title: Wildtype plate 136

description:
roni2_e_002
MARS-seq of wildtype embryos


title: Wildtype plate 133

description:
EXE28_P8
MARS-seq of wildtype embryos


title: Wildtype plate 134

description:
EXE28_P9
MARS-seq of wildtype embryos


title: Wildtype plate 131

description:
EXE28_P6
MARS-seq of wildtype embryos


title: Wildtype plate 129

description:
EXE28_P4
MARS-seq of wildtype embryos


title: Wildtype plate 128

description:
EXE28_P3
MARS-seq of wildtype embryos


title: Wildtype plate 130

description:
EXE28_P5
MARS-seq of wildtype embryos


title: Wildtype plate 148

description:
lin_trace_p4_exp1
MARS-seq of wildtype embryos


title: Wildtype plate 125

description:
EXE28_P1
MARS-seq of wildtype embryos


title: Wildtype plate 127

description:
EXE28_P2
MARS-seq of wildtype embryos


title: Wildtype plate 126

description:
EXE28_P10
MARS-seq of wildtype embryos


title: Wildtype plate 124

description:
EXE27_P1
MARS-seq of wildtype embryos


title: Wildtype plate 121

description:
EXE25_P8
MARS-seq of wildtype embryos


title: Wildtype plate 122

description:
EXE25_P9
MARS-seq of wildtype embryos


title: Wildtype plate 123

description:
EXE26_P1
MARS-seq of wildtype embryos


title: Wildtype plate 120

description:
EXE25_P7
MARS-seq of wildtype embryos


title: Wildtype plate 117

description:
EXE25_P4
MARS-seq of wildtype embryos


title: Wildtype plate 115

description:
EXE25_P2
MARS-seq of wildtype embryos


title: Wildtype plate 113

description:
EXE25_P10
MARS-seq of wildtype embryos


title: Wildtype plate 116

description:
EXE25_P3
MARS-seq of wildtype embryos


title: Wildtype plate 114

description:
EXE25_P11
MARS-seq of wildtype embryos


title: Wildtype plate 119

description:
EXE25_P6
MARS-seq of wildtype embryos


title: Wildtype plate 118

description:
EXE25_P5
MARS-seq of wildtype embryos


title: Wildtype plate 112

description:
EXE25_P1
MARS-seq of wildtype embryos


title: Wildtype plate 109

description:
EXE24_P7
MARS-seq of wildtype embryos


title: Wildtype plate 110

description:
EXE24_P8
MARS-seq of wildtype embryos


title: Wildtype plate 107

description:
EXE24_P5
MARS-seq of wildtype embryos


title: Wildtype plate 108

description:
EXE24_P6
MARS-seq of wildtype embryos


title: Wildtype plate 111

description:
EXE24_P9
MARS-seq of wildtype embryos


title: Wildtype plate 135

description:
roni2_e_001
MARS-seq of wildtype embryos


title: Wildtype plate 132

description:
EXE28_P7
MARS-seq of wildtype embryos


title: Wildtype plate 106

description:
EXE24_P4
MARS-seq of wildtype embryos


title: Wildtype plate 105

description:
EXE24_P3
MARS-seq of wildtype embryos


title: Wildtype plate 103

description:
EXE24_P19
MARS-seq of wildtype embryos


title: Wildtype plate 104

description:
EXE24_P2
MARS-seq of wildtype embryos


title: Wildtype plate 100

description:
EXE24_P16
MARS-seq of wildtype embryos


title: Wildtype plate 102

description:
EXE24_P18
MARS-seq of wildtype embryos


title: Wildtype plate 99

description:
EXE24_P15
MARS-seq of wildtype embryos


title: Wildtype plate 97

description:
EXE24_P13
MARS-seq of wildtype embryos


title: Wildtype plate 98

description:
EXE24_P14
MARS-seq of wildtype embryos


title: Wildtype plate 96

description:
EXE24_P12
MARS-seq of wildtype embryos


title: Wildtype plate 95

description:
EXE24_P11
MARS-seq of wildtype embryos


title: Wildtype plate 94

description:
EXE24_P10
MARS-seq of wildtype embryos


title: Wildtype plate 92

description:
EXE23_P9
MARS-seq of wildtype embryos


title: Wildtype plate 93

description:
EXE24_P1
MARS-seq of wildtype embryos


title: PGC plate 13

description:
190401_P03
MARS-seq of FACS-sorted Oct4-positive cells

value: transgenic OCT4-EGFP reporter cells


title: Wildtype plate 91

description:
EXE23_P8
MARS-seq of wildtype embryos


title: PGC plate 10

description:
190814_P01
MARS-seq of FACS-sorted Oct4-positive cells


title: PGC plate 9

description:
190703_P02_OG2
MARS-seq of FACS-sorted Oct4-positive cells


title: PGC plate 7

description:
190625_P01_OG2
MARS-seq of FACS-sorted Oct4-positive cells


title: PGC plate 6

description:
190416_P03
MARS-seq of FACS-sorted Oct4-positive cells


title: PGC plate 8

description:
190703_P01_OG2
MARS-seq of FACS-sorted Oct4-positive cells


title: PGC plate 5

description:
190416_P02
MARS-seq of FACS-sorted Oct4-positive cells


title: Wildtype plate 86

description:
EXE23_P3
MARS-seq of wildtype embryos


title: Wildtype plate 87

description:
EXE23_P4
MARS-seq of wildtype embryos


title: Wildtype plate 101

description:
EXE24_P17
MARS-seq of wildtype embryos


title: Wildtype plate 88

description:
EXE23_P5
MARS-seq of wildtype embryos


title: Wildtype plate 84

description:
EXE23_P13
MARS-seq of wildtype embryos


title: PGC plate 2

description:
190108_P03
MARS-seq of FACS-sorted Oct4-positive cells


title: Wildtype plate 82

description:
EXE23_P11
MARS-seq of wildtype embryos


title: Wildtype plate 85

description:
EXE23_P2
MARS-seq of wildtype embryos


title: PGC plate 3

description:
190301_P04
MARS-seq of FACS-sorted Oct4-positive cells


title: Wildtype plate 81

description:
EXE23_P10
MARS-seq of wildtype embryos


title: Wildtype plate 80

description:
EXE23_P1
MARS-seq of wildtype embryos


title: Wildtype plate 251

description:
20191217_ICR_e7.5_p9
MARS-seq of wildtype embryos


title: PGC plate 11

description:
190814_P02
MARS-seq of FACS-sorted Oct4-positive cells


title: Wildtype plate 89

description:
EXE23_P6
MARS-seq of wildtype embryos


title: Wildtype plate 90

description:
EXE23_P7
MARS-seq of wildtype embryos


title: Wildtype plate 83

description:
EXE23_P12
MARS-seq of wildtype embryos


title: Wildtype plate 250

description:
20191217_ICR_e7.5_p8
MARS-seq of wildtype embryos


title: Wildtype plate 79

description:
EXE22_p9_e4
MARS-seq of wildtype embryos


title: Wildtype plate 78

description:
EXE22_p8_e3c
MARS-seq of wildtype embryos


title: Wildtype plate 249

description:
20191217_ICR_e7.5_p7
MARS-seq of wildtype embryos


title: PGC plate 4

description:
190416_P01
MARS-seq of FACS-sorted Oct4-positive cells


title: Wildtype plate 76

description:
EXE22_p6_e3
MARS-seq of wildtype embryos


title: Wildtype plate 248

description:
20191217_ICR_e7.5_p6
MARS-seq of wildtype embryos


title: Wildtype plate 77

description:
EXE22_p7_e3b
MARS-seq of wildtype embryos


title: Wildtype plate 247

description:
20191217_ICR_e7.5_p5
MARS-seq of wildtype embryos


title: Wildtype plate 74

description:
EXE22_p4_e2_placenta_e2
MARS-seq of wildtype embryos


title: Wildtype plate 245

description:
20191217_ICR_e7.5_p3
MARS-seq of wildtype embryos


title: PGC plate 1

description:
190108_P01
MARS-seq of FACS-sorted Oct4-positive cells


title: Wildtype plate 73

description:
EXE22_p2_e1
MARS-seq of wildtype embryos


title: Wildtype plate 75

description:
EXE22_p5_e2b_placenta_e3
MARS-seq of wildtype embryos


title: Wildtype plate 244

description:
20191217_ICR_e7.5_p2
MARS-seq of wildtype embryos


title: Wildtype plate 246

description:
20191217_ICR_e7.5_p4
MARS-seq of wildtype embryos


title: Wildtype plate 243

description:
20191217_ICR_e7.5_p16
MARS-seq of wildtype embryos


title: Wildtype plate 72

description:
EXE22_p10_e4b_placenta_e5
MARS-seq of wildtype embryos


title: Wildtype plate 40

description:
EXE29_P1
MARS-seq of wildtype embryos


title: Wildtype plate 47

description:
EXE18_P11_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 236

description:
20191217_ICR_e7.5_p1
MARS-seq of wildtype embryos


title: Wildtype plate 233

description:
190710_173
MARS-seq of wildtype embryos


title: Wildtype plate 240

description:
20191217_ICR_e7.5_p13
MARS-seq of wildtype embryos


title: Wildtype plate 238

description:
20191217_ICR_e7.5_p11
MARS-seq of wildtype embryos


title: Wildtype plate 22

description:
EXE_EXP8_E6.5_NOVA_701
MARS-seq of wildtype embryos


title: Wildtype plate 52

description:
EXE18_P5_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 41

description:
EXE29_P2
MARS-seq of wildtype embryos


title: Wildtype plate 234

description:
190710_175
MARS-seq of wildtype embryos


title: Wildtype plate 237

description:
20191217_ICR_e7.5_p10
MARS-seq of wildtype embryos


title: Wildtype plate 43

description:
EXE31_p1
MARS-seq of wildtype embryos


title: Wildtype plate 241

description:
20191217_ICR_e7.5_p14
MARS-seq of wildtype embryos


title: Wildtype plate 49

description:
EXE18_P2_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 239

description:
20191217_ICR_e7.5_p12
MARS-seq of wildtype embryos


title: Wildtype plate 21

description:
EXE_EXP8_E6.5_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 242

description:
20191217_ICR_e7.5_p15
MARS-seq of wildtype embryos


title: Wildtype plate 42

description:
EXE30_P1
MARS-seq of wildtype embryos


title: Wildtype plate 235

description:
190710_176
MARS-seq of wildtype embryos


title: Wildtype plate 232

description:
190710_172
MARS-seq of wildtype embryos


title: Wildtype plate 231

description:
190710_169
MARS-seq of wildtype embryos


title: Wildtype plate 19

description:
EXE_exp14_spatial_p2_E6.5_e5_e6_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 16

description:
EXE_EXP13_E7.5_P1_E4_e5
MARS-seq of wildtype embryos


title: Wildtype plate 18

description:
EXE_exp14_spatial_p1_E6.5_e1_e2_e3_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 228

description:
190710_166
MARS-seq of wildtype embryos


title: Wildtype plate 71

description:
EXE22_p1_placenta_e1
MARS-seq of wildtype embryos


title: Wildtype plate 229

description:
190710_167
MARS-seq of wildtype embryos


title: Wildtype plate 17

description:
EXE_EXP13_E7.5_P1_E6_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 38

description:
P3_EXE16_E6.5_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 15

description:
EXE_EXP13_E7.5_P1_E1_E2_E3_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 8

description:
EXE_EXP10_E7.0_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 230

description:
190710_168
MARS-seq of wildtype embryos


title: Wildtype plate 226

description:
190710_164
MARS-seq of wildtype embryos


title: Wildtype plate 227

description:
190710_165
MARS-seq of wildtype embryos


title: Wildtype plate 223

description:
190527_P156
MARS-seq of wildtype embryos


title: Wildtype plate 218

description:
190527_P150
MARS-seq of wildtype embryos


title: Wildtype plate 216

description:
190527_P146
MARS-seq of wildtype embryos


title: Wildtype plate 225

description:
190710_114
MARS-seq of wildtype embryos


title: Wildtype plate 215

description:
190527_P105
MARS-seq of wildtype embryos


title: Wildtype plate 224

description:
190710_112
MARS-seq of wildtype embryos


title: Wildtype plate 212

description:
190527_P102
MARS-seq of wildtype embryos


title: Wildtype plate 210

description:
190527_P100
MARS-seq of wildtype embryos


title: Wildtype plate 206

description:
190506_P126
MARS-seq of wildtype embryos


title: Wildtype plate 220

description:
190527_P152
MARS-seq of wildtype embryos


title: Wildtype plate 214

description:
190527_P104
MARS-seq of wildtype embryos


title: Wildtype plate 213

description:
190527_P103
MARS-seq of wildtype embryos


title: Wildtype plate 217

description:
190527_P148
MARS-seq of wildtype embryos


title: Wildtype plate 211

description:
190527_P101
MARS-seq of wildtype embryos


title: Wildtype plate 219

description:
190527_P151
MARS-seq of wildtype embryos


title: Wildtype plate 204

description:
190506_P124
MARS-seq of wildtype embryos


title: Wildtype plate 209

description:
190506_P129
MARS-seq of wildtype embryos


title: Wildtype plate 203

description:
190506_P120
MARS-seq of wildtype embryos


title: Wildtype plate 205

description:
190506_P125
MARS-seq of wildtype embryos


title: Wildtype plate 2

description:
190908_E8.5_roni_NOVA
MARS-seq of wildtype embryos


title: Wildtype plate 222

description:
190527_P155
MARS-seq of wildtype embryos


title: Wildtype plate 202

description:
190506_P119
MARS-seq of wildtype embryos


title: Wildtype plate 221

description:
190527_P153
MARS-seq of wildtype embryos


title: Wildtype plate 208

description:
190506_P128
MARS-seq of wildtype embryos


title: Wildtype plate 207

description:
190506_P127
MARS-seq of wildtype embryos


title: Wildtype plate 200

description:
190313_P16
MARS-seq of wildtype embryos


title: Wildtype plate 201

description:
190506_P118
MARS-seq of wildtype embryos


title: Wildtype plate 198

description:
190313_P14
MARS-seq of wildtype embryos


title: Wildtype plate 199

description:
190313_P15
MARS-seq of wildtype embryos


title: Wildtype plate 197

description:
190313_P13
MARS-seq of wildtype embryos


title: Wildtype plate 196

description:
190313_P12
MARS-seq of wildtype embryos


title: Wildtype plate 194

description:
190313_P10
MARS-seq of wildtype embryos


title: Wildtype plate 187

description:
190313_P03
MARS-seq of wildtype embryos


title: Wildtype plate 190

description:
190313_P06
MARS-seq of wildtype embryos


title: Wildtype plate 191

description:
190313_P07
MARS-seq of wildtype embryos


title: Wildtype plate 195

description:
190313_P11
MARS-seq of wildtype embryos


title: Wildtype plate 192

description:
190313_P08
MARS-seq of wildtype embryos


title: Wildtype plate 193

description:
190313_P09
MARS-seq of wildtype embryos


title: Wildtype plate 189

description:
190313_P05
MARS-seq of wildtype embryos


title: Wildtype plate 188

description:
190313_P04
MARS-seq of wildtype embryos


title: Wildtype plate 184

description:
190311_P03
MARS-seq of wildtype embryos


title: Wildtype plate 185

description:
190313_P01
MARS-seq of wildtype embryos


title: Wildtype plate 180

description:
190307_P15
MARS-seq of wildtype embryos


title: Wildtype plate 183

description:
190311_P02
MARS-seq of wildtype embryos


title: Wildtype plate 178

description:
190307_P13
MARS-seq of wildtype embryos


title: Wildtype plate 179

description:
190307_P14
MARS-seq of wildtype embryos


title: Wildtype plate 182

description:
190311_P01
MARS-seq of wildtype embryos


title: Wildtype plate 181

description:
190307_P16
MARS-seq of wildtype embryos


title: Wildtype plate 177

description:
190307_P12
MARS-seq of wildtype embryos


title: Wildtype plate 175

description:
190307_P10
MARS-seq of wildtype embryos


title: Wildtype plate 176

description:
190307_P11
MARS-seq of wildtype embryos


title: Wildtype plate 186

description:
190313_P02
MARS-seq of wildtype embryos


title: Wildtype plate 174

description:
190307_P09
MARS-seq of wildtype embryos


title: Wildtype plate 172

description:
190304_P02
MARS-seq of wildtype embryos


title: Wildtype plate 173

description:
190304_P03
MARS-seq of wildtype embryos


title: Wildtype plate 170

description:
190223_P10
MARS-seq of wildtype embryos


title: Wildtype plate 167

description:
190223_P07
MARS-seq of wildtype embryos


title: Wildtype plate 168

description:
190223_P08
MARS-seq of wildtype embryos


title: Wildtype plate 169

description:
190223_P09
MARS-seq of wildtype embryos


title: Wildtype plate 171

description:
190304_P01
MARS-seq of wildtype embryos


title: Wildtype plate 164

description:
190223_P04
MARS-seq of wildtype embryos


title: Wildtype plate 166

description:
190223_P06
MARS-seq of wildtype embryos


title: Wildtype plate 163

description:
190223_P03
MARS-seq of wildtype embryos


title: Wildtype plate 161

description:
190223_P01
MARS-seq of wildtype embryos


title: Wildtype plate 156

description:
190214_P01
MARS-seq of wildtype embryos


title: Wildtype plate 159

description:
190214_P04
MARS-seq of wildtype embryos


title: Wildtype plate 160

description:
190214_P05
MARS-seq of wildtype embryos


title: Wildtype plate 155

description:
181209_P04
MARS-seq of wildtype embryos


title: Wildtype plate 70

description:
exe21_p5
MARS-seq of wildtype embryos


title: Wildtype plate 162

description:
190223_P02
MARS-seq of wildtype embryos


title: Wildtype plate 69

description:
exe21_p4
MARS-seq of wildtype embryos


title: Wildtype plate 157

description:
190214_P02
MARS-seq of wildtype embryos


title: Wildtype plate 158

description:
190214_P03
MARS-seq of wildtype embryos


title: Wildtype plate 67

description:
exe21_p2
MARS-seq of wildtype embryos


title: Wildtype plate 154

description:
181209_P03
MARS-seq of wildtype embryos


title: Wildtype plate 153

description:
181209_P01
MARS-seq of wildtype embryos


title: Wildtype plate 66

description:
exe21_p1
MARS-seq of wildtype embryos


title: Wildtype plate 65

description:
exe19_p9
MARS-seq of wildtype embryos


title: Wildtype plate 68

description:
exe21_p3
MARS-seq of wildtype embryos


title: Wildtype plate 64

description:
exe19_p8
MARS-seq of wildtype embryos


title: Wildtype plate 62

description:
exe19_p5
MARS-seq of wildtype embryos


title: Wildtype plate 165

description:
190223_P05
MARS-seq of wildtype embryos


title: Wildtype plate 63

description:
exe19_p6
MARS-seq of wildtype embryos


title: Wildtype plate 61

description:
exe19_p4
MARS-seq of wildtype embryos


title: Wildtype plate 60

description:
exe19_p3
MARS-seq of wildtype embryos


title: Wildtype plate 58

description:
exe19_p11_NOVAseq
MARS-seq of wildtype embryos


title: Wildtype plate 59

description:
exe19_p2
MARS-seq of wildtype embryos


title: Wildtype plate 54

description:
EXE18_P8
MARS-seq of wildtype embryos


title: Wildtype plate 55

description:
EXE18_P9
MARS-seq of wildtype embryos


title: Wildtype plate 57

description:
exe19_p10
MARS-seq of wildtype embryos


title: Wildtype plate 56

description:
exe19_p1
MARS-seq of wildtype embryos


title: Wildtype plate 53

description:
EXE18_P6
MARS-seq of wildtype embryos


title: Wildtype plate 50

description:
EXE18_P3
MARS-seq of wildtype embryos


title: Wildtype plate 48

description:
EXE18_P12
MARS-seq of wildtype embryos


title: Wildtype plate 45

description:
EXE18_P1
MARS-seq of wildtype embryos


title: Wildtype plate 46

description:
EXE18_P10
MARS-seq of wildtype embryos


title: Wildtype plate 39

description:
P4_EXE16_E6.5
MARS-seq of wildtype embryos


title: Wildtype plate 44

description:
EXE17_E5.5_P1
MARS-seq of wildtype embryos


title: Wildtype plate 36

description:
P1_EXE16_E6.5
MARS-seq of wildtype embryos


title: Wildtype plate 34

description:
EXE5_E4cont-E6_E6.5_2
MARS-seq of wildtype embryos


title: Wildtype plate 35

description:
EXE5_E6cont-E7_E6.5_3
MARS-seq of wildtype embryos


title: Wildtype plate 33

description:
EXE5_E1-E4_E6.5_1
MARS-seq of wildtype embryos


title: Wildtype plate 32

description:
EXE4_M1E1-E4,M2E1-E2_E5.5_1
MARS-seq of wildtype embryos


title: Wildtype plate 30

description:
EXE3_m2e1-e3_E6.5_4
MARS-seq of wildtype embryos


title: Wildtype plate 29

description:
EXE3_e4-e5_E6.5_3
MARS-seq of wildtype embryos


title: Wildtype plate 31

description:
EXE3_m2e3cont-m3e1-e2_E6.5_5
MARS-seq of wildtype embryos


title: Wildtype plate 23

description:
EXE1_e1-3_E6.25_1
MARS-seq of wildtype embryos


title: Wildtype plate 27

description:
EXE3_e1_E6.5_1
MARS-seq of wildtype embryos


title: Wildtype plate 28

description:
EXE3_e2-3_E6.5_2
MARS-seq of wildtype embryos


title: Wildtype plate 25

description:
EXE2_e4_E7.5_3
MARS-seq of wildtype embryos


title: Wildtype plate 51

description:
EXE18_P4
MARS-seq of wildtype embryos


title: Wildtype plate 14

description:
EXE_EXP12_E7.5_4
MARS-seq of wildtype embryos


title: Wildtype plate 12

description:
EXE_EXP12_E7.5_2
MARS-seq of wildtype embryos


title: Wildtype plate 26

description:
EXE2_e5_E7.5_4
MARS-seq of wildtype embryos


title: Wildtype plate 9

description:
EXE_EXP11_E7.5_1
MARS-seq of wildtype embryos


title: Wildtype plate 24

description:
EXE2_e3_E7.5_2
MARS-seq of wildtype embryos


title: Wildtype plate 20

description:
EXE_exp15_spatial_p1_E6.5_e1_e2_e3_m1e2
MARS-seq of wildtype embryos


title: Wildtype plate 10

description:
EXE_EXP11_E7.5_2
MARS-seq of wildtype embryos


title: Wildtype plate 11

description:
EXE_EXP12_E7.5_1
MARS-seq of wildtype embryos


title: Wildtype plate 7

description:
EXE_EXP10_E7.0_2
MARS-seq of wildtype embryos


title: Wildtype plate 6

description:
EXE_EXP10_E7.0_1
MARS-seq of wildtype embryos


title: Wildtype plate 37

description:
P2_EXE16_E6.5
MARS-seq of wildtype embryos


title: Wildtype plate 5

description:
EXE_6_E7.5_P3_e5_e6_e7
MARS-seq of wildtype embryos


title: Wildtype plate 3

description:
EXE_6_E7.5_P1_e1_e2
MARS-seq of wildtype embryos


title: Wildtype plate 4

description:
EXE_6_E7.5_P2_e3_e4
MARS-seq of wildtype embryos


title: Wildtype plate 1

description:
190908_E8.5_roni_EE02
MARS-seq of wildtype embryos


title: Dermal CD45+ Lin- cells

status: Public on May 20 2024

city: Solna

first: Itziar

last: Martinez Gonzalez

address: Biomedicum C7, Solnavägen 9

country: Sweden

institute: Karolinska Institute

data_processing:
Post-processing and quality control were performed by Single Cell Discoveries. Reads were aligned to GRCh38 reference assembly using STARsolo
Assembly: GRCh38
Supplementary files format and content: Seurat object

organism: Homo sapiens

source_name: Skin

extract_protocol:
Healthy skin tissues were obtained as excess materials from plastic surgery of the breast or abdomen. Skin sheets were incubated overnight at 4 °C with 0.2% (weight/volume (wt/vol)) Dispase II (Roche) in PBS to enable the separation of dermis from epidermis. The dermis was cut into fine pieces and incubated in IMDM with 0.5% (wt/vol) collagenase D (Roche), 50 U ml−1 DNAse I (Sigma-Aldrich) and 0.5% (vol/vol) FCS for 2 h at 37 °C. Dermal cell suspensions were filtered through a 70-μm nylon mesh strainer. 1583 CD45+ Lin- cells were directly sorted in 384-well plates, frozen and sent to Single Cell Discoveries for further processing of their pipeline based on CEL-Seq2 (Muraro et al., 2016).
1583 cells were directly sorted in 384-well plates, frozen and sent to Single Cell Discoveries for further processing of their pipeline based on CEL-Seq2 (Muraro et al., 2016).

value: Skin

tag: cell type

value: Dermal CD45+ Lin- cells


title: PanIN1134

type: RNA

city: Baltimore

first: Luciane

middle: Tsukamoto

last: Kagohara

state: MD

address: 1650 Orleans St - Rm 485

department: Oncology

country: USA

institute: Johns Hopkins University

description: RNA in situ hybridization was performed at 10x Genomics facilities following manufacturer’s instructions. Sections were placed on the Xenium slides and deparaffinized and decrosslinked for optimal probe hybridization. The probes that hybridized to transcripts in the sample were ligated, amplified and conjugated to fluorescent probes in the Xenium Analyzer. The fluorescence captured by the device was preprocessed for visualization using the Xenium Explorer software. Finally, the sections were stained with hematoxylin and eosin and scanned

scan_protocol: Transcript detection and quantification was conducted using the Xenium Analyzer platform

data_processing:
Outputs from the Xenium Analyzer were analyzed in R using Seurat software. Expression values were normalized using SCTransform in Seurat. Clustering was conducted in Seurat using Louvain clustering.
Assembly: GRCh38
Supplementary files format and content: de_gene_groups.csv: differentially expressed genes from clustering result
Supplementary files format and content: analysis.h5: compressed clustering information
Supplementary files format and content: analysis.zarr.zip: compressed clustering information
Supplementary files format and content: cell_boundaries.csv.gz: compressed dimensions of cell boundaries
Supplementary files format and content: cell_boundaries.parquet: dimensions of cell boundaries
Supplementary files format and content: cell_feature_matrix.h5: compressed cell expression data
Supplementary files format and content: cell_feature_matrix.zarr.zip: compressed cell expression data
Supplementary files format and content: cells.csv.gz: compressed cell locations
Supplementary files format and content: cells.parquet: cell locations
Supplementary files format and content: cells.zarr.zip: compressed cell locations
Supplementary files format and content: experiment.xenium: executable file to open data in Xenium Explorer
Supplementary files format and content: gene_panel.json: gene panel list
Supplementary files format and content: metrics_summary.csv: summarized cell metrics
Supplementary files format and content: morphology.ome.tif: slide image
Supplementary files format and content: morphology_focus.ome.tif: slide image
Supplementary files format and content: morphology_mip.ome.tif: slide image
Supplementary files format and content: nucleus_boundaries.csv.gz: compressed dimensions of nuclear boundaries
Supplementary files format and content: nucleus_boundaries.parquet: dimensions of nuclear boundaries
Supplementary files format and content: transcripts.csv.gz: compressed transcript loactions
Supplementary files format and content: transcripts.parquet: transcript loactions
Supplementary files format and content: transcripts.zarr.zip: compressed transcript loactions
Supplementary files format and content: cell_feature_matrix/barcodes.tsv.gz: cell barcode names
Supplementary files format and content: cell_feature_matrix/features.tsv.gz: gene expression feature names
Supplementary files format and content: cell_feature_matrix/matrix.mtx.gz: gene expression matrix

source_name: Pancreatic Intraductal Neoplasm

extract_protocol:
There was no extraction protocol used.
The capture probe panel was comprised of the 10x Genomic 280 gene breast cancer panel with the addition of 100 additional custom probes.

tag: subject

tag: organism

value: human

value: pancreas


title: PanIN1132

hyb_protocol: RNA in situ hybridization was performed at 10x Genomics facilities following manufacturer’s instructions. Sections were placed on the Xenium slides and deparaffinized and decrosslinked for optimal probe hybridization. The probes that hybridized to transcripts in the sample were ligated, amplified and conjugated to fluorescent probes in the Xenium Analyzer. The fluorescence captured by the device was preprocessed for visualization using the Xenium Explorer software. Finally, the sections were stained with hematoxylin and eosin and scanned


title: Wildtype plate 13

description:
EXE_EXP12_E7.5_3
MARS-seq of wildtype embryos


title: Rloop_N_1

status: Public on May 01 2024

city: Riverside

first: feng

last: tang

state: CA

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

library_source: genomic

data_processing:
Trim Galore was used to remove low-qualified bases and adapter-containing reads from raw spKAS-seq data. Duplicated reads were removed using Picard MarkDuplicates.
Trimmed reads were aligned to the human hg19 reference genome using Bowtie2 with the default configuration
Definitions of R-loops by spKAS-seq were performed by following previously reported procedures (PMID: 36449625)
Assembly: hg19
Supplementary files format and content: bed files were genereated using bedtools by merging the peaks of two replicates
Supplementary files format and content: bw files were generated using deeptools
Library strategy: spKAS-seq

molecule: genomic DNA

source_name: HEK293T cells

growth_protocol: Cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Invitrogen) and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2. For genomic DNA extraction, the cells were harvested at 80% confluence. Cell lines used in this study were examined for a mycoplasma contamination test using e-Myco Mycoplasma PCR Detection Kit (Bulldog Bio. Inc.).

extract_protocol:
The purified genomic DNA was subsequently mixed with 5 μl of 20 mM dibenzocyclooctyne-PEG4-biotin conjugate (Sigma-Aldrich, 760749) and 10 μl of 10× phosphate-buffered saline (PBS), and the total volume was adjusted to 100 μl with 25 mM K3BO3. The resulting mixture was shaken gently at 37°C for 1.5 h, followed by addition of 5 μl of 10 mg/mL RNase A (Thermo Fisher Scientific, 12091039), and the mixture was shaken at 37°C for another 5 min. After the reaction, the DNA was isolated using the DNA Clean & Concentrator-5 kit (Zymo Research, D4013) and fragmented by sonication to 150 to 350 base pairs (bp). The sonicated DNA was employed for enrichment using 10 μl of Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific, 65001). The beads were washed with 1× binding and washing (B&W) buffer (5 mM tris-HCl, pH 7.4, 0.5 mM EDTA, 1 M NaCl, and 0.05% Tween 20), resuspended in 95 μl of 2× B&W buffer, and mixed with the sonicated DNA. The suspension was incubated at room temperature for 15 min. The beads were then washed once with 1× B&W buffer, twice with 100 mM NaOH solution to denature the dsDNA and remove the DNA strands that are not labeled by N3-kethoxal, and once again with 1× B&W buffer. The DNA was eluted from the beads by heating the beads in 10 μl H2O at 95°C for 10 min.
The ensuing enriched DNA and the corresponding input were employed for library construction using the Accel-NGS Methyl-Seq DNA Library Kit (Swift, 30024) following the manufacturer’s instructions. Subsequently, the purified DNA libraries were assessed using an Agilent 2100 Bioanalyzer and multiplexed for sequencing on a MGISEQ-2000 platform (BGI).
PROTOCOL: Strand-specific kethoxal-assisted single-stranded DNA (ssDNA) sequencing (spKAS-seq)

treatment_protocol: spKAS-seq was conduceted following previously published procedures with minor modifications (PMID: 36449625), where N2-heptynyl-dG was added to the culture medium until its final concentration reached 10 μM. After a 3-h incubation, the cells were treated with 5 mM N3-kethoxal dissolved in the culture medium for 10 min at 37°C, then harvested for genomic DNA isolation using the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific, K182002).

tag: cell line

value: HEK293T cells

value: Human embryonic kidney

value: WT

tag: treatment

value: N2-heptynyl-dG  treatment


title: PanIN1131_S1A


title: Rloop_1


title: E10.5 Chd4 WT-4 heart ATAC

status: Public on Apr 18 2024

city: Chapel Hill

first: Wei

last: Shi

state: NC

address: 221 Fordham Hall

department: Biology

institute: UNC-Chapel Hill

data_processing:
Libraries were run on a NovaSeq 6000 (Illumina) with 2×150 bp paired end reads.
Pooled libraries were then sequenced to a depth of 100 million reads per sample. Reads were aligned to the mm10 reference genomes using BWA-MEM and peaks were called using HOMERv4.10.3. Annotation and analysis were performed using ChIP-Seeker v1.20.0.
Assembly: mm10
Supplementary files format and content: Bed files of differential peaks
Supplementary files format and content: BedGraph files of differential peaks

source_name: Heart

extract_protocol:
Four hearts at E10.5 were pooled per genotype per replicate, and were then dissociated into single cells. 40,000 viable cells were taken for were lysed to isolate nuclei, which were treated with Tn5 transposase (Nextera DNA Sample Prep Kit, Illumina) to isolate DNA. Fragmented DNA was then amplified using bar-coded PCR primers and libraries were seuqenced.
Dissociated embryonic cardiac cells were lysed to isolate nuclei, which were treated with Tn5 transposase (Nextera DNA Sample Prep Kit, Illumina) to isolate DNA Fragmented DNA was then amplified using bar-coded PCR primers and libraries were pooled.

value: Heart


title: E10.5 Chd4 WT-1 heart ATAC


title: E10.5 Chd4 WT-3 heart ATAC


title: E10.5 Chd4 CMko-4 heart ATAC


title: E10.5 Chd4 CMko-2 heart ATAC


title: E10.5 Chd4 CMko-3 heart ATAC


title: Br8492

status: Public on Apr 27 2024

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

library_source: transcriptomic

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline with Aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv, barcode, feature, and matrix files for each donor.
Library strategy: Spatial Transcriptomics

source_name: brain (hippocampus)

extract_protocol:
Anterior hippocampus was dissected from fresh frozen postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. Tissue was permeabilized and cDNA was synthesized to incorporate positional barcode.
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions

value: brain (hippocampus)


title: PanIN1144


title: Br8667


title: E10.5 Chd4 CMko-1 heart ATAC


title: Br6423


title: PanIN1131_S1C


title: Br2720


title: Br8325


title: Br3942_VSPG


title: A498 Sunitinib-resistant replicate 2 [42veh2]

status: Public on Apr 17 2024

city: Rockville

first: Alexis

middle: L

last: Norris

address: 7500 Standish Place

institute: US FDA

data_processing:
Base calling with bcl2fastq2 version 2.19.0
Sequencing reads were trimmed using trimmomatic (version 0.36.6; parameters: SLIDINGWINDOW:4:20 MINLEN:50)
Trimmed reads were aligned to GRCh38/hg38 using HISAT2 (version 2.1.0; parameters: --n-ceil L,0.0,0.15 --mp 6,2 --no-softclip --np 1 --rdg 5,3 --rfg 5,3 --sp 2,1 --score-min L,0.0,-0.2 --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000).
Gene counts were estimated using featureCounts (version 1.6.3; parameters: -s 1 -t 'exon' -g 'gene_id' -J -Q 12 --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0) with GENCODE gene annotation (GENCODE version 33; Ensembl version 99).
Assembly: hg38
Supplementary files format and content: tab-delimited text file include gene counts for each Sample

molecule: polyA RNA

growth_protocol: Two human advanced renal cell carcinoma cell lines A498 and 786-O were purchased from ATCC. They were cultured in DMEM growth media containing 25mM glucose and glutamine supplemented with 10% heat-inactivated foetal bovine serum and 1% penicillin-streptomycin at 37⁰C in a humidified atmosphere of 5% CO2. Sunitinib (SU11248) malate was purchased from Selleckchem. For the development of sunitinib-resistant cells, parental cells were exposed to increasing concentrations of sunitinib. In brief, the RCC cell lines were treated with varying concentrations of sunitinib (0, 1, 2, 3, 4, 5, 7, 10, 20, and 50μM). With the passage of time of every four days, it has been observed that A498 cells showed stable growth and eventually became confluent at a concentration of 2µM, while 798-O cells showed stable growth to confluence at a concentration of 4µM. It can be assumed that cells that grew to confluence had developed stable sunitinib-resistance after a period of four months or >20 passages. The cells were constantly in sunitinib containing medium throughout the selection process.

extract_protocol:
Total RNA was isolated from cultured cells according to the QIAGEN RNeasy mini kit protocol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Sample prep kit.

value: advanced clear cell renal cell carcinoma (ccRCC)

tag: drug resistance

value: Sunitinib

tag: batch


title: A498 Sunitinib-resistant replicate 1 [42veh1]


title: 786-O parental replicate 3 [7_veh3]


title: Br6522


title: ATAC-seq in fish 30 hpf tail bud replicate 1

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

data_processing:
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024.
Raw ATAC-seq paired-end reads were processed with CutAdapt version 4.1 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15) to remove Nextera adapters and bad quality bases.
Filtered reads were mapped on mm39 for mouse samples and danRer11 where alternative contigs were removed for fish samples with bowtie2 version 2.4.5 with the following parameters: --very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000. Only pairs mapping concordantly outside of mitochondria were kept (Samtools v1.16.1)
PCR duplicates were removed by Picard version 3.0.0 (http://broadinstitute.github.io/picard/index.html). BAM files were converted to BED with bedtools version 2.30.0. Peaks were called and coverage was generated by MACS2 version 2.2.7.1 with --nomodel --keep-dup all --shift -100 --extsize 200 --call-summits -B. Coverages were normalized to million mapped reads.
Assembly: mm39
Assembly: danRer11
Supplementary files format and content: *narrowPeak.gz: peaks from MACS2
Supplementary files format and content: *bw: coverage from MACS2 normalized to million mapped reads

organism: Danio rerio

source_name: tail bud

extract_protocol:
Mouse and fish tissues were isolated and placed into 1x PBS containing 10% FCS on ice. Collagenase (Sigma-Aldrich C9697) was added to 50ug/ml and incubated at 37º for 20 minutes with shaking at 900rpm.
Cells were washed 3x in 1x PBS. The number of cells was counted and viability confirmed to be greater than 90%. An input of 50000 cells was then processed according to previous description.

value: tail bud

tag: Sex

tag: Stage

value: 30 hpf

value: wild type

tag: strain

value: AB, Tu, TL


title: ATAC-seq in fish 30 hpf trunk replicate 1

source_name: trunk

value: trunk


title: ATAC-seq in fish 30 hpf cloaca replicate 1

source_name: cloaca

value: cloaca


title: Br8325_VSPG


title: 786-O parental replicate 2 [7_veh2]


title: Br6471


title: E10.5 Chd4 WT-2 heart ATAC


title: 786-O parental replicate 1 [7_veh1]


title: 786-O Sunitinib-resistant replicate 2 [74veh2]


title: 786-O Sunitinib-resistant replicate 3 [74veh3]


title: Br3942


title: A498 Sunitinib-resistant replicate 3 [42veh3]


title: Br6432


title: A498 parental replicate 3 [4_veh3]


title: A498 parental replicate 1 [4_veh1]


title: 786-O Sunitinib-resistant replicate 1 [74veh1]


title: nonSMA39

status: Public on Apr 16 2024

city: Albuquerque

first: Douglas

middle: Jay

last: Perkins

state: NM

address: MSC10 5550, 1 University of New Mexico

department: Center for Global Health

institute: University of New Mexico

data_processing:
Raw data were quality-controlled and filtered using fastp
Sequences were aligned to the human reference genome (GRCh38.p13) using the STAR sofware version 2.5
HTSeq v0.6.1 was used to generate read counts mapped to each gene.
Differential expression analysis of the two clinical conditions (non-SMA vs SMA) was performed using EdgeR (3.16.5) package, utilizing a negative binomial (NB) based statistical model
Assembly: GRCh38.p13
Supplementary files format and content: excel files includes Mapped reads stats for each sample
Supplementary files format and content: excel  files includes raw read counts for each sample
Supplementary files format and content: excel  files includes Quality control summary for each sample

source_name: blood

extract_protocol:
Total RNA was batch-isolated using E.Z.N.A® Total RNA Kit (Omega Bio-Tek Inc.), treated with RNase-free DNase I (New England Biolabs Inc.), and further processed using RNA Clean & Concentrator (ZYMO Research Corp.).
Only samples with RNA integrity number (RIN) >8 were used for library preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: MALE

tag: genetic variants

value: HbAA

tag: time

value: Day 0

value: blood


title: nonSMA38


title: nonSMA40


title: nonSMA36

value: FEMALE


title: nonSMA41


title: nonSMA35


title: nonSMA37


title: nonSMA34


title: nonSMA33


title: nonSMA32


title: nonSMA31


title: nonSMA27

value: HbAS


title: nonSMA28


title: nonSMA29

value: HbSS


title: nonSMA26


title: nonSMA30


title: nonSMA25


title: nonSMA23


title: nonSMA22


title: nonSMA21


title: nonSMA20


title: A498 parental replicate 2 [4_veh2]


title: nonSMA15


title: nonSMA17


title: nonSMA18


title: nonSMA14


title: nonSMA16


title: nonSMA13


title: nonSMA12


title: nonSMA10


title: nonSMA11


title: nonSMA7


title: nonSMA9


title: nonSMA6


title: nonSMA4


title: nonSMA8


title: nonSMA2


title: nonSMA3


title: nonSMA5


title: nonSMA1


title: SMA25


title: SMA23


title: SMA22


title: SMA24


title: nonSMA19


title: SMA21


title: SMA20


title: SMA18


title: SMA17


title: SMA16


title: SMA15


title: SMA14


title: SMA10


title: SMA12


title: SMA13


title: SMA8


title: SMA9


title: SMA7


title: SMA6


title: SMA1


title: SMA2


title: SMA5


title: SMA3


title: Pancreas, KCIL17-Rafl/fl, replicate4

status: Public on Apr 15 2024

city: Houston

first: Lourdes

middle: Susana

last: Castro Pando

state: Texas

address: 7777 Greenbriar Drive, Apt 2050

institute: UT MD ANDERSON CANCER CTR.

description: 10X Genomics

data_processing:
The raw data was processed using cell ranger count (Cell Ranger v2.1.1; 10x Genomics) based on the mm10 mouse reference genome
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: pancreas

extract_protocol:
Single-cell suspensions were prepared by mincing murine pancreas followed by digestion with Collagenase P (4 mg/mL), Dispase (4mg/mL) and DNAse (0.5 mg/mL) and incubation for 5-10 minutes at 37°C in a shaker. Samples were then filtered through a 70-μm and 40-μm strainer and stained with L/D aqua (Thermo Fisher) at Room temperature for 10 minutes. Samples were resuspended in PBS with 0.004% bovine serum albumin and sorted for live cells using Aria II sorter. Cell viability was measured using Trypan Blue. Single-cell suspensions were loaded in a 10x Genomics (Pleasanton, CA) Chromium instrument to generate gel beads in emulsion.
The raw data was processed using cell ranger count (Cell Ranger v2.1.1; 10x Genomics) based on the mm10 mouse reference genome

value: pancreas

value: epithelial and immune cells


title: SMA4


title: Pancreas, KC, replicate3

description: 10X Genomics

value: KC


title: Pancreas, KC, replicate1

description: 10X Genomics


title: Pancreas, KC, replicate4

description: 10X Genomics


title: Pancreas, KCIL17-Rafl/fl, replicate3

description: 10X Genomics


title: Pancreas, KC, replicate2

description: 10X Genomics


title: Pancreas, KCIL17-Rafl/fl, replicate2

description: 10X Genomics


title: Progressing papilloma (early carcinoma) 8, scRNAseq

status: Public on Mar 22 2024

city: San Francisco

first: MARK

middle: ALAN

last: TAYLOR

department: Hellen Diller Family Comprehensive Cancer Center

institute: UCSF

description:
EK-3502-8h12-PAP-CA4
chemotherapy_additional_samples.RDS

data_processing:
Reads generated by 10x Genomics sequencing were demultiplexed using default settings by Cell Ranger’s mkfastq function (version 2.0, 10x Genomics). Demultiplexed reads were aligned and assigned to the mm10 (GRCm38) mouse reference provided by 10x Genomics and converted to sample-specific unique molecular identifier (UMI) count matrices using the count function with default settings. Count data for each sample were independently quality-controlled. Minimally, all cells were required to express at least 200 genes, with at least 20% of reads aligning, and retained genes were required to be detected in at least 3 cells. We filtered stressed or dying cells with more than 10-17% of UMIs generated from mitochondrial genes. We then analyzed sequencing curves of cells ordinated by UMI detection and gene number in order to detect lower elbows indicating low-complexity libraries (empty droplets) and upper elbows indicating an artifactually rapid increase in well-wise UMI detection (multiplets). We filtered cells falling below and above these thresholds, respectively. The lower threshold ranged between 250-750 and the upper between 2500-6000 .  We integrated and normalized count data using R/Seurat v.2.3. To normalize, we used the NormalizeData function to scale UMIs by dividing each cell by the total number of counts per cell, multiplying by a scaling factor of 10000, and converting to a log scale. We then passed these data to the R software package Monocle3. We then included all genes in dimensionality reduction with principal components, limiting the reduced hyperspace to 100 dimensions. Together, the first 3 PCs explained 34% of the data, so the data were subsequently projected onto a 3-D manifold using the uMAP method. However, upon inspection of sample arrangement in this space, we observed that FACS was strongly confounded by batch. In particular, unsorted cells were colinear with the first batch, and sorted cells with the second batch. To reduce this technical variability while preserving biological variability, we implemented a mutual nearest neighbor method to identify hyperdimensional batch-specific planes and resolve these planes into a single mutually uniform plane. We then used these batch-corrected data for all downstream analyses.
Assembly: mm10
Supplementary files format and content: .rds R objects containing cell dataset (CDS)-formatted data

source_name: papilloma

extract_protocol:
Single-cell suspensions of dorsal back skin were prepared by carefully removing subcutaneous fat and floating the intact tissue dermal side down in 0.25% Trypsin/EDTA (Invitrogen, 25200-056) solution with gentle rocking for 1 h at 37°C. Trypsin activity was neutralized with 10% chelexed FBS in Ca2+ free PBS (Hyclone, SH30028.02). The epithelial skin layer was then scraped into suspension and agitated to dissociate cells. To obtain single-cell suspensions of skin tumors, lesions were finely chopped into very small pieces with a sterile scalpel and then enzymatically digested in 0.25% Trypsin-EDTA with gentle agitation for 1 hour at 37°C. Individually, each disaggregated cell suspension sample was then passed through a sterile 40 µm filter, centrifuged at 300 g for 5 min to pellet cells, and resuspended in 10% chelexed FBS in Ca2+ free PBS prior to flow cytometry. Cell samples were collected and analyzed using a FACSAria III, and appropriate gating was used to exclude doublets. DAPI staining was used to assess cell viability, and only viable, DAPI-negative cells were selected for subsequent analysis. Within each sample type, three populations of viable cells were evaluated: unsorted global cell populations, Lgr6eGFP+ stem cells (gated on positive eGFP expression), and tdTomato+ Lgr6+ stem cell-derived progeny cells (gated on positive tdTomato expression). FACS sorted cells were collected in Ca2+ free, PBS-containing 1% chelexed Ca2+ free FBS, centrifuged at 300 g to pellet the cells before final resuspension in 35 µl 1% chelexed Ca2+ free PBS, and stored on ice prior to scRNA-sequencing library preparation which occurred within 2-3 h of sample collection.
scRNAseq libraries from samples were prepared using the 10x Genomics Chromium extraction and preparation protocol according to the manufacturer’s instructions and sequenced on a Novaseq S4 sequencer (Illumina).

value: papilloma

value: FVB


title: Progressing papilloma (early carcinoma) 7, scRNAseq

description:
EK-3502-7g12-PAP-CA3
chemotherapy_additional_samples.RDS


title: Progressing papilloma (early carcinoma) 6, scRNAseq

description:
EK-3502-6f12-PAP-CA2
chemotherapy_additional_samples.RDS


title: Progressing papilloma (early carcinoma) 5, scRNAseq

description:
EK-3502-5e12-PAP-CA1
chemotherapy_additional_samples.RDS


title: SMA19


title: Papilloma 2, scRNAseq

description:
EK-3502-2b12-PAP2
chemotherapy_additional_samples.RDS


title: SMA11


title: Papilloma 4, scRNAseq

description:
EK-3502-4d12-PAP4
chemotherapy_additional_samples.RDS


title: Papilloma 3, scRNAseq

description:
EK-3502-3c12-PAP3
chemotherapy_additional_samples.RDS


title: Squamous cell carcinoma 3 treated with control vehicle, scRNAseq

description:
EK-3796_01
chemotherapy_additional_samples.RDS

source_name: carcinoma

value: carcinoma


title: Papilloma 1, scRNAseq

description:
EK-3502-1a12-PAP1
chemotherapy_additional_samples.RDS


title: Squamous cell carcinoma 4 treated with control vehicle, scRNAseq

description:
EK-3796_02
chemotherapy_additional_samples.RDS


title: Squamous cell carcinoma 4 treated with cisplatin, scRNAseq

description:
EK-3796_04
chemotherapy_additional_samples.RDS


title: Squamous cell carcinoma 2 treated with cisplatin, scRNAseq

description:
EK-3205_04
chemotherapy_additional_samples.RDS


title: Squamous cell carcinoma 3 treated with cisplatin, scRNAseq

description:
EK-3796_03
chemotherapy_additional_samples.RDS


title: Squamous cell carcinoma 2 treated with control vehicle, scRNAseq

description:
EK-3205_02
chemotherapy_additional_samples.RDS


title: FACS sorted, global cell population from normal back skin (non-lineage traced), scRNAseq

description:
NO_TAM_BS
integrated_corrected_cds_v3.RDS

source_name: normal back skin

value: normal back skin

value: FVB Lgr6eGFPtdTomato


title: Squamous cell carcinoma 1 treated with control vehicle, scRNAseq

description:
EK-3205_01
chemotherapy_additional_samples.RDS


title: FACS sorted, Lgr6 derived progeny cells (tomato+) from lineage-traced normal back skin, scRNAseq

description:
PROGENY
integrated_corrected_cds_v3.RDS


title: FACS sorted, global cell population from lineage-traced normal back skin, scRNAseq

description:
TAM_BS
integrated_corrected_cds_v3.RDS

source_name: tumor-adjacent normal skin

value: tumor-adjacent normal skin


title: Pancreas, KCIL17-Rafl/fl, replicate1

description: 10X Genomics


title: FACS sorted, Lgr6+ cells (GFP+) cells from lineage-traced normal back skin, scRNAseq

description:
LGR6
integrated_corrected_cds_v3.RDS


title: FACS sorted, Lgr6 derived progeny cells (tomato+) cells from lineage-traced normal skin adjacent to tumor, scRNAseq

description:
Skin_Progeny
integrated_corrected_cds_v3.RDS


title: FACS sorted, Lgr6 derived progeny cells (tomato+) cells from lineage-traced papilloma, scRNAseq

description:
PAP_Progeny
integrated_corrected_cds_v3.RDS


title: FACS sorted, Lgr6+ cells (GFP+) cells from lineage-traced normal skin adjacent to tumor, scRNAseq

description:
Skin_Lgr6
integrated_corrected_cds_v3.RDS


title: FACS sorted, global cell population from lineage traced SCC, contains Lgr6GFP+ and Tomato+ progeny cells, scRNAseq

description:
CA_US
integrated_corrected_cds_v3.RDS


title: FACS sorted, Lgr6+ cells (GFP+) cells from lineage-traced squamous cell carcinoma, scRNAseq

description:
CA_Lgr6
integrated_corrected_cds_v3.RDS


title: FACS sorted, global cell population from lineage traced papillomas, contain Lgr6GFP+ and Tomato+ progeny cells, scRNAseq

description:
PAP_US
integrated_corrected_cds_v3.RDS


title: RNAseq_earlyBlast_Xist-KO_Female_rep10

status: Public on Mar 15 2024

city: Boston

first: Chunyao

last: Wei

state: MA

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
On the HiSeq 2500, HiSeq 4000 and NovaSeq platform, intensity extraction from images, base calling and quality score assignment during the sequencing was performed by software RTA and RTA2, respectively.
Raw data was first examined using Trim Galore (The Babraham Bioinformatics Group) to remove adapters from reads using the following parameters: (--stringency 8 --phred33 -e 0.2 --paired --length 43 --r1 44 --r2 44), followed by the PCR duplication removal and subsequent base trimming from the 5’end of reads (22nt from read1 and 5nt from read2). Pre-processed reads were aligned to two parental mouse genomes separately using STAR (v2.7.10a) in the 2-pass mode, with the allowance of 1 mismatch in every 20 bases and a maximum of 6 mismatches per read pair. Non-canonical introns were not considered. Reads with overlapping mates were only considered with at least 5 nucleotide overlap. All discordant read pairs where two mates were aligned to different chromosomes were discarded. The coordinates of rRNA genes in mm10 mouse genome were downloaded from RepeatMasker track (v4.0.7) in UCSC genome browser and all the reads mapping to these regions were masked and ignored in the final output files (including bam, bed and bw files).
To quantify overall expression of each given gene, all unique aligned read pairs overlapping with gene exons were counted using featureCounts (v1.5.0-p1).
For allelic gene analysis, each unique aligned read that covered strain specific SNPs or indels was analyzed and the alignment quality between two alleles was compared to determine its allelic origin. Each experiment yielded three tracks: cas, mus, and composite (neutral, cas and mus combined). For better visualization of gene expression between alleles, read mapping coordinates in different parental genomes were also converted to matched coordinates in mm10 mouse genome.  Similar to overall expression quantification, only the allelic read overlapping with gene exons were considered for allelic read counts of this gene. Allelic expression level of a given gene was thus calculated by splitting its overall expression in accordance with the allelic expression ratio, which was defined by the ratio of total allelic read count from one allele relative to that of the other allele.
assembly: mm10
processed data files format and content: alignment .bw files showing RNA coverage on + and - strand from M. castaneus (cas) reads, M. musculus (mus) reads and compsoite (comp) reads.
processed data files format and content: .txt files showing gene read counts from M. castaneus (cas) reads, M. musculus (mus) reads and compsoite (comp) reads.

organism:
Mus musculus
Mus musculus castaneus

source_name: Single preimplantation embryo

extract_protocol:
Single embryo was flushed out from the mouse oviduct, and immediately lysed in 1ul lysis solution containing 1% NP-40 and 4U RNase inhibitor
A combination of 1ul of 5x 1st strand buffer and 0.1 ul of RNA spike-in or water was added into the single embryo lysis, followed by the incubation at 82C for 12 minutes. After quick chill on ice, the RNAs were next end repaired by adding 1ul PNK solution (70mM tris-HCl pH7.6, 10mM MgCl2, 15mM DTT, 4 units/ul RNase Inhibitor) containing 2 units of T4 PNK and by incubating at 37C for 10 minutes. The RNA samples were further incubated at 37C for 5 minutes after the addition of 0.5ul mix containing 1 unit of PolyA polymerase and 3 picomole ATP. Before reverse transcription, 1ul of pre-RT mix (5uM R-dT Primer (TTTCCCTACACGACGCTCTTCCGATCTNNNNNNTTTTTTTTTTTTTTTVVN), 6.25mM dNTPs, 15mM EDTA) was added to samples, followed by the heat up at 72C for 2 minutes. After RNA denaturation, samples were immediately chilled on ice, followed by the addition of 5.5ul freshly made RT mix containing 1X 1st strand Buffer, 10mM DTT, 2U/ul RNase inhibitor, 2M Betaine, 1uM GGrG oligo (iCiGiCGGAGTTCAGACGTGTGCTCTTCCGATCTrGrG+G) and 20U/ul Superscript II reverse transcriptase II. Samples were then incubated with the following temperature setting: 40C for 5 mins, 42C for 30 mins, Two cycles of 50C for 2 mins followed by 42C for 2mins, and 15 mins at 70C. First strand cDNA libraries were next amplified by 15 cycles of first round PCR (F: GTGACTGGAGTTCAGACGTGTGCTCTTC; R: ACACTCTTTCCCTACACGACGCTCTTC) in a total volume of 30ul PCR reactions and purified with Ampure XP beads at 1:1 ratio. Purified cDNAs from the PCR (13.5ul) were mixed with 130ng of RNA probes in total 30ul of hybridization buffer (10mM Tris-HCl, pH8.0, 0.5M NaCl, 5mM EDTA and 0.2% SDS), and incubated at the following temperatures: 94C for 2 mins, followed by ramp down to 50C with 1C down per 50 seconds, and finally at 50C for 5 mins. Meanwhile, 100ul of streptavidin C1 beads were washed, pre-blocked and warmed to 50C. To delete ribosomal cDNAs, samples and beads were mixed at 50 C and incubated for another 5 mins at 50 C, and immediately put on a magnetic rack. Supernatant was collected and purified with Ampure XP beads. The purified cDNAs were further amplified by 9 cycles of PCR with Multiplex oligos (NEB). The final PCR product was purified and subject to sequencing.

value: Single preimplantation embryo

value: Paternal Xist-KO

value: Female

value: CAST/EiJ x 129S1/SvImJ (Xist-KO)

value: early blastocyst


title: RNAseq_earlyBlast_Xist-KO_Female_rep12


title: Squamous cell carcinoma 1 treated with cisplatin, scRNAseq

description:
EK-3205_03
chemotherapy_additional_samples.RDS


title: RNAseq_earlyBlast_Xist-KO_Female_rep9


title: RNAseq_4C_Xist-KO_Female_rep13


title: RNAseq_4C_Xist-KO_Female_rep11


title: RNAseq_4C_Xist-KO_Male_rep12

value: wild type (CM)

value: Male


title: RNAseq_late2C_Xist-KO_Male_rep21

value: late 2-cell


title: RNAseq_late2C_Xist-KO_Male_rep23


title: RNAseq_late2C_Xist-KO_Female_rep22


title: RNAseq_earlyBlast_Xist-KO_Female_rep11


title: RNAseq_late2C_Xist-KO_Male_rep20


title: RNAseq_earlyBlast_Xist-KO_Male_rep8


title: RNAseq_4C_Xist-KO_Male_rep10


title: RNAseq_late2C_Xist-KO_Female_rep19


title: FACS sorted, Lgr6+ cells (GFP+) cells from lineage-traced papilloma, scRNAseq

description:
PAP_Lgr6
integrated_corrected_cds_v3.RDS


title: RNAseq_earlyBlast_CM_Female_rep13

value: CAST/EiJ x C57BL/6J


title: FACS sorted, Lgr6 derived progeny cells (tomato+) cells from lineage-traced squamous cell carcinoma, scRNAseq

description:
CA_Progeny
integrated_corrected_cds_v3.RDS


title: RNAseq_late2C_Xist-KO_Female_rep18


title: RNAseq_earlyBlast_CM_Male_rep7


title: RNAseq_earlyBlast_CM_Female_rep9


title: RNAseq_earlyBlast_CM_Male_rep8


title: RNAseq_earlyBlast_CM_Male_rep5


title: RNAseq_earlyBlast_CM_Male_rep10


title: RNAseq_earlyBlast_CM_Male_rep12


title: RNAseq_earlyBlast_CM_Male_rep2


title: RNAseq_earlyBlast_CM_Female_rep3


title: RNAseq_16C_CM_Female_rep12


title: RNAseq_earlyBlast_CM_Male_rep4


title: RNAseq_16C_CM_Female_rep13


title: RNAseq_16C_CM_Female_rep14


title: RNAseq_earlyBlast_CM_Male_rep1


title: RNAseq_16C_CM_Male_rep8


title: RNAseq_16C_CM_Female_rep9


title: RNAseq_16C_CM_Male_rep4


title: RNAseq_16C_CM_Male_rep5


title: RNAseq_16C_CM_Female_rep1


title: RNAseq_16C_CM_Male_rep7


title: RNAseq_16C_CM_Male_rep3


title: RNAseq_8C_CM_Female_rep11


title: RNAseq_16C_CM_Male_rep11


title: RNAseq_16C_CM_Female_rep6


title: RNAseq_8C_CM_Female_rep9


title: RNAseq_earlyBlast_CM_Female_rep11


title: RNAseq_8C_CM_Female_rep10


title: RNAseq_8C_CM_Female_rep8


title: RNAseq_earlyBlast_CM_Female_rep6


title: RNAseq_8C_CM_Female_rep6


title: RNAseq_8C_CM_Female_rep7


title: RNAseq_8C_CM_Male_rep5


title: RNAseq_8C_CM_Male_rep4


title: RNAseq_8C_CM_Female_rep2


title: RNAseq_8C_CM_Male_rep3


title: RNAseq_16C_CM_Male_rep10


title: RNAseq_8C_CM_Female_rep1


title: RNAseq_4C_CM_Male_rep8


title: RNAseq_4C_CM_Female_rep5


title: RNAseq_4C_CM_Female_rep3


title: RNAseq_4C_CM_Male_rep7


title: RNAseq_4C_CM_Male_rep6


title: RNAseq_16C_CM_Female_rep2


title: RNAseq_4C_CM_Female_rep2


title: RNAseq_4C_CM_Female_rep1


title: RNAseq_late2C_CM_Male_rep9


title: RNAseq_late2C_CM_Male_rep7


title: RNAseq_late2C_CM_Male_rep10


title: RNAseq_late2C_CM_Male_rep4


title: RNAseq_late2C_CM_Female_rep3


title: RNAseq_late2C_CM_Male_rep6


title: RNAseq_late2C_CM_Female_rep5


title: RNAseq_late2C_CM_Female_rep1


title: RNAseq_earlyBlast_MC_Male_rep9

value: wild type (MC)

value: C57BL/6J x CAST/EiJ


title: RNAseq_earlyBlast_MC_Male_rep11


title: RNAseq_late2C_CM_Female_rep2


title: RNAseq_earlyBlast_MC_Female_rep8


title: RNAseq_earlyBlast_MC_Male_rep6


title: RNAseq_earlyBlast_MC_Male_rep7


title: RNAseq_4C_CM_Female_rep4


title: RNAseq_earlyBlast_Xist-KO_Female_rep3


title: RNAseq_8C_MC_Female_rep14


title: RNAseq_8C_MC_Male_rep12


title: RNAseq_earlyBlast_Xist-KO_Female_rep2


title: RNAseq_earlyBlast_MC_Female_rep5


title: RNAseq_8C_Xist-KO_Female_rep1


title: RNAseq_late2C_CM_Female_rep8


title: RNAseq_earlyBlast_MC_Male_rep3


title: RNAseq_earlyBlast_MC_Female_rep4


title: RNAseq_earlyBlast_MC_Male_rep2


title: RNAseq_earlyBlast_Xist-KO_Male_rep1


title: RNAseq_earlyBlast_MC_Female_rep10


title: RNAseq_earlyBlast_MC_Female_rep1


title: RNAseq_16C_MC_Male_rep8


title: RNAseq_16C_MC_Male_rep4


title: RNAseq_16C_MC_Female_rep7


title: RNAseq_16C_MC_Female_rep6


title: RNAseq_16C_MC_Male_rep1


title: RNAseq_8C_MC_Male_rep9


title: RNAseq_16C_MC_Female_rep5


title: RNAseq_8C_MC_Male_rep11


title: RNAseq_16C_MC_Female_rep3


title: RNAseq_8C_MC_Female_rep10


title: RNAseq_8C_MC_Female_rep15


title: RNAseq_16C_MC_Female_rep2


title: RNAseq_8C_MC_Male_rep8


title: RNAseq_8C_MC_Male_rep6


title: RNAseq_8C_MC_Female_rep5


title: RNAseq_8C_MC_Male_rep4


title: RNAseq_8C_MC_Male_rep3


title: RNAseq_8C_MC_Male_rep2


title: RNAseq_4C_MC_Male_rep17


title: RNAseq_4C_MC_Female_rep16


title: RNAseq_4C_MC_Female_rep15


title: RNAseq_4C_MC_Female_rep11


title: RNAseq_4C_MC_Male_rep12


title: RNAseq_8C_MC_Female_rep1


title: RNAseq_4C_MC_Male_rep13


title: RNAseq_4C_MC_Male_rep10


title: RNAseq_4C_MC_Female_rep4


title: RNAseq_4C_MC_Male_rep9


title: RNAseq_4C_MC_Female_rep14


title: RNAseq_4C_MC_Female_rep6


title: RNAseq_4C_MC_Male_rep7


title: RNAseq_4C_MC_Male_rep5


title: RNAseq_4C_MC_Male_rep1


title: RNAseq_4C_MC_Male_rep3


title: RNAseq_8C_MC_Female_rep7


title: RNAseq_4C_MC_Male_rep2


title: RNAseq_late2C_MC_Female_rep8


title: RNAseq_late2C_MC_Male_rep7


title: RNAseq_4C_MC_Male_rep8


title: RNAseq_late2C_MC_Male_rep5


title: RNAseq_late2C_MC_Male_rep10


title: RNAseq_late2C_MC_Female_rep6


title: RNAseq_late2C_MC_Male_rep4


title: RNAseq_late2C_MC_Male_rep2


title: RNAseq_late2C_MC_Male_rep1


title: RNAseq_early2C_MC_Male_rep6

value: early 2-cell


title: RNAseq_late2C_MC_Male_rep3


title: RNAseq_early2C_MC_Female_rep5


title: RNAseq_early2C_MC_Male_rep2


title: RNAseq_early2C_MC_Female_rep4


title: RNAseq_early2C_MC_Male_rep3


title: RNAseq_late2C_MC_Male_rep9


title: RNAseq_zygote_MC_ rep3

value: unknown


title: RNAseq_zygote_MC_ rep4


title: RNAseq_earlyBlast_Xist-KO_Male_rep5


title: RNAseq_early2C_MC_Female_rep1


title: RNAseq_8C_Xist-KO_Female_rep13


title: RNAseq_earlyBlast_Xist-KO_Male_rep7


title: RNAseq_earlyBlast_Xist-KO_Male_rep6


title: RNAseq_zygote_MC_ rep1


title: RNAseq_8C_Xist-KO_Male_rep12


title: RNAseq_zygote_MC_ rep2


title: RNAseq_8C_Xist-KO_Female_rep10


title: RNAseq_8C_Xist-KO_Female_rep7


title: RNAseq_8C_Xist-KO_Male_rep6


title: RNAseq_8C_Xist-KO_Male_rep9


title: RNAseq_8C_Xist-KO_Male_rep4


title: RNAseq_8C_Xist-KO_Female_rep11


title: RNAseq_8C_Xist-KO_Male_rep8


title: RNAseq_8C_Xist-KO_Male_rep3


title: RNAseq_4C_Xist-KO_Female_rep8


title: RNAseq_4C_Xist-KO_Female_rep9


title: RNAseq_8C_Xist-KO_Male_rep2


title: RNAseq_8C_Xist-KO_Female_rep5


title: RNAseq_4C_Xist-KO_Male_rep6


title: RNAseq_4C_Xist-KO_Female_rep4


title: RNAseq_4C_Xist-KO_Male_rep5


title: RNAseq_earlyBlast_Xist-KO_Female_rep4


title: RNAseq_4C_Xist-KO_Male_rep2


title: RNAseq_4C_Xist-KO_Male_rep3


title: RNAseq_4C_Xist-KO_Male_rep1


title: RNAseq_late2C_Xist-KO_Male_rep14


title: RNAseq_late2C_Xist-KO_Female_rep13


title: RNAseq_late2C_Xist-KO_Male_rep12


title: RNAseq_late2C_Xist-KO_Male_rep16


title: RNAseq_late2C_Xist-KO_Male_rep8


title: RNAseq_late2C_Xist-KO_Male_rep9


title: RNAseq_late2C_Xist-KO_Male_rep11


title: RNAseq_late2C_Xist-KO_Female_rep7


title: RNAseq_late2C_Xist-KO_Male_rep15


title: RNAseq_late2C_Xist-KO_Male_rep10


title: RNAseq_late2C_Xist-KO_Male_rep5


title: RNAseq_4C_Xist-KO_Female_rep7


title: RNAseq_late2C_Xist-KO_Male_rep2


title: RNAseq_late2C_Xist-KO_Male_rep1


title: RNAseq_diff_dTAG_24H_rep1

status: Public on Mar 08 2024

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description: rnaseq_RA_differentiation.gene_counts.txt

data_processing:
ChIP-seq: ZFP143 ChIP-seq reads were mapped to the mm10 mouse reference genome assembly using bwa mem. Calibrated CTCF ChIP-seq reads were mapped to the mm10 mouse and hg38 human reference genome assemblies using bwa mem. Uniquely mapped reads with MAPQ > 10 mapped in proper read pairs were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. Scaling factors for calibrated CTCF ChIP-seq normalisation were calculated as described previously (Greulich et al., 2021). The bigwig coverage tracks were generated using the “bamCoverage” and "bamCompare" functions from the deepTools. TT-seq: TT-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Uniquely mapped reads with MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. The reads were split by strand using SAMtools as described previously (Gregersen et al., 2020). Gene counts were obtained using the ”htseq-count” function from HTSeq. Bigwig coverage tracks were generated separately for forward and reverse strands using the "bamCoverage" function from deepTools. Hi-C: Hi-C reads were mapped to the mm10 mouse reference genome assembly using bwa mem with the Open2C distiller-nf pipeline. Mapped reads were parsed using pairtools with the “walks-policy” parameter set to “mask” and the “max_mismatch_bp” parameter set to 1. Read pairs were then binned into Hi-C contact matrices. Iterative correction of the matrices and removal of low coverage bins was performed using the "balance" function from cooler. 4C-seq: 4C-seq reads were processed as previously described (Haarhuis et al., 2017; van de Werken et al., 2012) using custom R scripts. The sequencing data were demultiplexed per viewpoint and mapped to the mm10 mouse reference genome assembly using the bwa aln and bwa samse. To generate the read counts per RE fragment, for each fragment we counted the number of mapped reads that have the same start or end coordinates as the fragment. To obtain 4C contact profiles, the counts were normalised to the total number of overlaps detected per million reads. ATAC-seq: ATAC-seq reads were mapped to the mm10 mouse reference genome assembly bwa mem. Uniquely mapped reads that were not mapped to mitochondrial DNA and had MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. RNA-seq: RNA-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Read counts per gene were obtained using the "quantMode" parameter in STAR.
Assembly: mm10
Supplementary files format and content: ChIP-seq: normalized signal tracks in bigWig format; peaks in BED format. TT-seq: normalized signal tracks in bigWig format; read counts per gene in TXT format. Hi-C: contact matrices in MCOOL and HIC formats. 4C-seq: viewpoint coordinates in TXT format; normalized coverage per fragment in TSV format. RNA-seq: read counts per gene in TXT format.

growth_protocol: Mouse Embryonic Stem Cells E14Tg2A (129/Ola) cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10 × 4 U of Leukaemia Inhibitory Factor (LIF) (Millipore), MEK inhibitor PD0325901 (1 μM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 μM, Cayman Chemical) and 1-Thioglycerol (1.5 × 10−4 M, Sigma-Aldrich). The cell lines were passaged every 2 days in daily culture.

extract_protocol:
ChIP-seq: Chromatin was cross-linked using 1% FA final concentration. Chromatin was sheared on a Bioruptor Plus sonication instrument and immunoprecipitated by different antibodies. DNA was purified using the MiniElute PCR purification kit from Qiagen. TT-seq: Libraries for TTchem-seq were prepared following a published protocol (Gregersen et al., 2020). Cells were labelled with 2 mM of the uridine analog 4-thiouridine (4sU) for 10 min. Total RNA was isolated and fragmented. The 4sU-biotin labelled RNA was enriched using µMacs Streptavidin Kit (Miltenyi). Hi-C: Hi-C data were generated using as a previous published protocol (Rao et al., 2014) with minor modifications (Haarhuis et al., 2017). Cells were harvested and crosslinked using 2% formaldehyde. Crosslinked DNA was digested in nucleus using MboI (NEB), and biotinylated nucleotides were incorporated at the restriction overhangs and joined by blunt-end ligation. The ligated DNA was enriched in a streptavidin pull-down 4C-seq: 4C-seq was performed as previously described (Geeven et al., 2018; van de Werken et al., 2012) using a two-step PCR method for indexing described first in (Haarhuis et al., 2017). MboI (NEB) was used as the first restriction enzyme and Csp6I (NEB) as the second restriction enzyme. ATAC-seq: Cells were washed in cold PBS and subjected to lysis using a 2x lysis buffer. Subsequently, the cells were centrifuged, and the resulting pellet was treated with 2xTD buffer and 2 uL of transposon mix. RNA-seq: RNA was first isolated using standard RNA isolation procedure from Qiagen RNeasy Mini Kit (Qiagen), including a DNaseI treatment.
ChIP-seq: Libraries were prepared following the KAPA HTP Library Preparation Kit (Roche). TT-seq: Libraries were prepared using KAPA RNA HyperPrep and KAPA Dual-Indexed Adapter kits (Roche) using dual indexing adapters. Hi-C: Hi-C libraries were prepared using a standard end-repair and A-tailing method. 4C-seq: 4C-seq libraries were prepared using a two-step PCR method for indexing described first in (Haarhuis et al., 2017). ATAC-seq: PCR amplification was conducted using KAPA HiFi HotStart ReadyMix (Roche). Fragments ranging from 200 to 700 bp were purified utilising AMPure XP beads (Beckman Coulter). RNA-seq: Libraries were prepared following the TruSeq Stranded mRNA kit (Illumina) with TruSeq RNA Single Indexes set A (Illumina).

treatment_protocol: For the knock-in of the FKBP sequence at the genes of interest, cells were transfected with the plasmids containing the gRNA sequence and the donor plasmid designed to include the FKBP-2xHA-P2A-GFP in between two homology arms for the gene of interest. To induce ZFP143 degradation, the cells were treated with 500 nM dTAG-V1 or DMSO as a control.

value: Embryonic Stem Cell


title: RNAseq_late2C_Xist-KO_Male_rep4


title: RNAseq_diff_dTAG_24H_rep2


title: RNAseq_diff_dTAG_24H_RA_24H_rep1


title: RNAseq_late2C_Xist-KO_Male_rep3


title: RNAseq_late2C_Xist-KO_Female_rep17


title: RNAseq_diff_DMSO_24H_rep1

value: DMSO


title: ATACseq_gastruloids_dTAG@72H_96H_rep1

description: ATAC-seq samples were shallowly sequenced to perform deconvolution, but not downstream analyses. Therefore, these samples do not have any processed data files.

source_name: Whole gastruloid

value: Whole gastruloid

tag: collection time


title: RNAseq_diff_DMSO_24H_RA_24H_rep1

value: DMSO+RA


title: ATACseq_gastruloids_dTAG@48H_96H_rep1


title: RNAseq_late2C_Xist-KO_Male_rep6

value: Single preimplantation embryo


title: ATACseq_gastruloids_dTAG@48H_72H_rep1


title: ATACseq_gastruloids_DMSO@72H_rep1


title: H3K27Ac_ChIP_3SL2h_Rep2

status: Public on Mar 04 2024

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description:
formaldehyde cross-linked
processed data file:
BMDM_ChIP_H3K27Ac_TFmerge.txt, BMDM_ChIP_H3K27Ac_AllMerged.txt

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
For p300, SREBP and LXR ChIP-seq experiments peaks were called with HOMER for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Only peaks with > 16 normalized tags (normalized to total tags of 1e7) were kept. Overlapping peak sets were determined using mergePeaks command. The pooled tag directory from two replicates was used for track visualization. To annotate p300 signal in ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 200 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential p300 signal > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For H3K27ac analysis: To annotate H3K27ac signal around ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 1000 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal or chromatin accessibility with > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For p65 and ATAC-Seq analysis of data from GSE79423 and GSE109965 respectively: Relevant raw FASTQ files were mapped to mm10 genome with Bowtie2 with default parameters (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010). For p65 peaks were called with HOMER findPeaks for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Peak files across various timepoints for vehicle and KLA treated timepoints were merged using HOMER mergePeaks. Merged peaks were annotated for H3K27ac and p300 signal as indicated. For ATAC-Seq, mm10 mapped, IDR defined peaks from GSE109965, for both vehicle and KLA treatment conditions, were used. Peaks were merged using HOMER mergePeaks, then merged peak file was used for further analysis as indicated in text.
To identify motifs enriched in peak regions over the background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. The background sequences were either from random genome sequences or from peaks from the comparing condition indicated in the main text and in the figure legends.
Genome_build: mm10
Supplementary files format and content: Processed files include peak text files (ChIP-Seq, ATAC, and H3K27Ac peak or region data, using default HOMER parameters). Peak or region files BMDM_ChIP_p300_AllTFmerged.txt and BMDM_ChIP_H3K27Ac_AllTFmerged.txt are summed transcription factor peak files annotated with normalized tag counts from either p300 or H3K27Ac ChIP-seq data as indicated. Peak files BMDM_ChIP_p300_ATACmerged.txt and BMDM_ChIP_H3K27Ac_ATACmerged.txt are summed ATAC-Seq peak files annotated with normalized tag counts from either p300 or H3K27Ac ChIP-seq data. Peak annotation, with p300 and H3K27Ac tag directories, was done using HOMER annotatePeaks command, with option -size 200 or -size 1000, respectively. All genomic coordinates are relative to mm10 mouse assembly.

source_name: H3K27Ac ChIP-seq 3'SL2h

growth_protocol: Bone marrow derived macrophages (BMDMs): Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

extract_protocol:
For H3K27ac ChIP-seq, culture media was removed and plates were washed once with PBS and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For p300, LXR and SREBP ChIP-seq, cells were crosslinked with 3mM DSG (ProteoChem) in PBS for 30 minutes at room temperature, and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then pelleted at 700 X G for 5 minutes at 4°C. Crosslinked cells were stored at –80°C until ready for ChIP-seq library preparation. Fixed cells were thawed on ice, resuspended in either ice-cold LB3 (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail, 1mM Na-Butyrate, for H3K27ac ChIP) or ice-cold RIPA-NR lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% Na-Deoxycholate, 0.1% SDS, 1% NP-40, 1x protease inhibitors, for p300, LXR, and SREBP ChIP). Frozen crosslinked nuclei were resuspended in wash buffer (10mM HEPES/KOH pH7.9, 85mM KCl, 1mM EDTA, 0.2% IGEPAL CA-630, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) for 5minutes on ice. Cells were spun down and then resuspended in RIPA-NR lysis buffer. Chromatin was sheared by sonication. Samples were sonicated in a 96 Place microTUBE Rack (Covaris cat#500282) using a Covaris E220 for 12 cycles (samples in LB3) or 18 cycles (samples in RIPA-NR buffer) with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. The LB3 lysate was diluted 1.1-fold with ice-cold 10% Triton X-100 after sonication. One percent of the lysate was kept as ChIP input. For each immunoprecipitation, aliquots of diluted lysate equivalent to 500,000 cells (for H3K27ac ChIP) or 1-2 million cells  (for p300, SREBP ChIP), 20 µl of Dynabeads Protein A (for rabbit polyclonal antibodies) or Dynabeads protein A/G (for p300, LXR, and SREBP ChIP) bound to specific antibodies for H3K27ac (2 μg, Active Motif, 39133), p300 (2 μg, Millipore, cat# 05-257,Diagenode, cat# C15200211), LXR (Santa Cruz Biotechnology: sc-1000X, sc- 133221X, sc-271064X) , and SREBP (2 μg, Santa Cruz Biotechnology: sc-8984X, Thermo Fisher Scientific: PA1-337, R&D Systems: AF7119) were combined and rotated overnight at 4°C. For H3K27ac ChIP, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA) and twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20). For p300, LXR and SREBP ChIP, beads were washed three times with RIPA-NR buffer (20 mM Tris-HCl/pH7.5, 150 mM NaCl, 0.1% SDS, 1% NP-40, 0.4 % Na-Deoxycholate, 1 mM EDTA, 0.5mM EGTA, 0.5mM DTT), six times with RIPA-LiCl buffer (10 mM Tris-HCl/pH 7.5, 250 mM LiCl, 1% NP-40, 0.7% Na-Deoxycholate, 1 mM EDTA), three times with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), and one time with IDTE (10mM Tris-HCl pH 8.0, 0.1mM EDTA). Bead complexes were resuspended in 25 μl TT (10 mM Tris/HCl pH 8.0, 0.05% Tween-20, 1x protease inhibitor cocktail) and sequencing libraries were prepared on-bead as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit with reaction volumes reduced by half, essentially as previously described (Heinz et al., 2018). Libraries were eluted and crosslinks reversed by adding to the 46.5 μl NEB reaction 20 μl water, 4 μl 10% SDS, 4.5 μl 5M NaCl, 3 μl 0.5 M EDTA, and 1 μl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 65C for 30 minutes to overnight in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries cleaned by adding 2 μl SpeedBeads 3 EDAC in 61 μl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 μl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 25 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 50 μl reaction volume using NEBNext Ultra II PCR master mix and 0.5 μM each Solexa 1GA and Solexa 1GB primers. Libraries were cleaned up with SpeedBeads as above using 36.5 μl 20% PEG 8000/1.5 M NaCl and 2 μl SpeedBeads. After ethanol washing and drying, PCR amplified libraries were eluted from the SpeedBeads using 20 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween- 20. Next, libraries were size selected 250-500 bp using gel extraction using 10% TBE acrylamide gels. Libraries were single-end sequenced using either a HiSeq 4000 or a NextSeq 500 to a depth of 10-20 million reads.

treatment_protocol: The following day after replating BMDMs, fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with or without 100 µg/ml 3'SL , with 10 ng/ml of LPS for 1 – 24 hours as indicated. For LXR and SREBP experiments cells were treated with 1uM GW3965.

value: bone marrow derived macrophages

value: 3'SL for 2 hours

tag: antibody

value: H3K27Ac (Vendor:Active Motif, cat# 39133)


title: H3K27Ac_ChIP_3SL6h_Rep2

source_name: H3K27Ac ChIP-seq 3'SL6h

value: 3'SL for 6 hours


title: ATACseq_gastruloids_DMSO@96H_rep1

tag: tissue


title: H3K27Ac_ChIP_PBS2_Rep2

source_name: H3K27Ac ChIP-seq PBS

value: vehicle PBS treatment


title: RNAseq_diff_dTAG_24H_RA_24H_rep2

tag: genotype


title: NB35-BM1

status: Public on Mar 03 2024

first: Shenglin

last: Mei

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 5.0.0). Human genome hg19 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts. Quality control metrics were used to select cells with total UMI more than 700.
Assembly: GRCh38/hg38
Supplementary files format and content: count matrix in csv

source_name: bone marrow

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Single cells from neuroblastoma bone metastatic and non-metastatic  samples subjected to RBC lysis were surface stained with anti-CD235-PE (Biolegend) for 30 min at 4°C. Cells were washed once with 2% FBS-PBS (v/v) followed by DAPI staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI-neg/CD235-neg) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument. All flow cytometry data were analyzed using FlowJo software (Treestar, San Carlos, CA).

value: neuroblastoma

tag: patient id

value: yes

tag: metastatic

value: metastatic


title: NB34_BM


title: NB37-BM5

value: non-metastatic


title: NB33-BM3


title: BM7


title: BM10

value: no


title: NB21-BM2R


title: NBBM6


title: BM6


title: RNAseq_diff_DMSO_24H_rep2

tag: cell type


title: NBBM5


title: RNAseq_diff_DMSO_24H_RA_24H_rep2


title: NBBM3


title: H3K27Ac_ChIP_3SL_LPS6h_Rep2

source_name: H3K27Ac ChIP-seq Input 3SL LPS

value: 3SL LPS treatment


title: H3K27Ac_ChIP_3SL_LPS2h_Rep2

source_name: H3K27Ac ChIP-seq Input 3SL


title: NBBM2


title: NBBM1


title: H3K27Ac_ChIP_LPS6h_Rep2

source_name: H3K27Ac ChIP-seq LPS6h

value: LPS for 6 hours


title: NBBM4