title: BJ_cell_001_HiC


title: GM12878_cell_222_RNA

status: Public on Jan 15 2024

type: SRA

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description: Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice

library_source: transcriptomic single cell

data_processing:
RNA reads were mapped to hg38 transcriptome reference using hisat2.
Hi-C reads were processed and analysed using Dip-C and hickit package.
Files with .e.allValidPairs.gz and .e.hic suffixes were generated using the human genome assembly corrected for Philadelphia chromosome (ehap.hg38.genome.fa.gz).
We pooled Hi-C samples for each cell line.
We generated three replicate structures (_1.3dg.gz, _2.3dg.gz and _3.3dg.gz) per cell reconstructed with different random seeds (1-3).
Assembly: hg38
Supplementary files format and content: .hic
Supplementary files format and content: .3dg
Supplementary files format and content: .allValidPairs

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Viable cells were picked into a single tube containing 7 μL soft cell lysis buffer (25 mM Tris pH8.3, 30 mM NaCl, 0.45% IGEPAL-CA630, 1 U/μL SUPERaseIn) supplemented with 0.25 μL magnetic beads, then incubate on ice for 30 min, after incubation, vortex for 1 min. Centrifuge at 500 x g for 5 min at 4°C, then take 5 μL supernatant to a new tube. The supernatant was proceeded to Smart-seq2 reverse transcription and amplification5. Nuclei was proceeded to chromosome conformation capture.
simultaneous 3D genome and gene expression by LiMCA
Smart-seq2 for LiMCA RNA library; Dip-C protocol for LiMCA Hi-C library

tag: tissue

value: blood

tag: cell line

value: Lymphoblastoid

tag: cell type

tag: genotype

value: WT


title: p119-bc_003_rna

description:
mOSN
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz

library_source: transcriptomic

data_processing:
RNA reads were mapped to mm10 transcriptome reference using hisat2.
Gene expression were quantified using RSEM.
Hi-C reads were processed and analysed using Dip-C and hickit package.
We generated three replicate structures (_1.3dg.gz, _2.3dg.gz and _3.3dg.gz) per cell reconstructed with different random seeds (1-3).
We pooled Hi-C samples for each group.
Assembly: mm10
Supplementary files format and content: .hic
Supplementary files format and content: .3dg
Supplementary files format and content: .allValidPairs.txt.gz

organism: Mus musculus

source_name: mouse olfactory epithelium

extract_protocol:
The main olfactory epithelium was dissected and minced to small pieces, then was dissociated into single cell suspension with the Papain Dissociation System (Worthington Biochemical, Cat. #LK003150) at 37°C for 15 min, during incubation, titration every 5 min with wide-bore pipette tip according to previously described2. Then filtered with 30 μm strainer (MACS), then wash twice with ice-cold 1 x PBS.
simultaneous 3D genome and gene expression by LiMCA
Smart-seq2 for LiMCA RNA library; Dip-C protocol for LiMCA Hi-C library

value: mouse olfactory epithelium

tag: age

value: postnatal day 119

tag: strain

value: bc

tag: treatment


title: p119-bc_004_rna

description:
progenitor-2
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: BJ_cell_008_HiC

library_source: genomic

molecule: genomic DNA

source_name: foreskin

value: foreskin

value: human fibroblast cell line

value: BJ


title: GM12878_cell_220_RNA


title: p119-bc_002_rna

description:
iOSN
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: GM12878_cell_219_RNA


title: GM12878_cell_221_RNA


title: GM12878_cell_218_RNA


title: p119-bc_005_rna


title: GM12878_cell_217_RNA


title: GM12878_cell_216_RNA


title: p111-bc_007_rna

value: postnatal day 111


title: GM12878_cell_214_RNA


title: p111-bc_006_rna

description:
progenitor-1
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: p111-bc_005_rna


title: GM12878_cell_213_RNA


title: p111-bc_003_rna


title: GM12878_cell_212_RNA


title: p111-bc_002_rna


title: GM12878_cell_211_RNA


title: p111-bc_001_rna


title: GM12878_cell_210_RNA


title: p070-bdf1_015_rna

value: postnatal day 70


title: GM12878_cell_209_RNA


title: p119-bc_001_rna


title: p070-bdf1_014_rna


title: GM12878_cell_208_RNA


title: p070-bdf1_013_rna


title: p070-bdf1_012_rna


title: GM12878_cell_215_RNA


title: p111-bc_004_rna


title: p070-bdf1_011_rna


title: p070-bdf1_010_rna


title: p070-bdf1_008_rna


title: p070-bdf1_009_rna


title: GM12878_cell_202_RNA


title: GM12878_cell_206_RNA


title: GM12878_cell_205_RNA


title: GM12878_cell_203_RNA


title: GM12878_cell_207_RNA


title: p070-bdf1_006_rna


title: GM12878_cell_200_RNA


title: GM12878_cell_199_RNA


title: p070-bdf1_007_rna


title: p070-bdf1_004_rna


title: p070-bdf1_005_rna


title: p070-bdf1_003_rna


title: GM12878_cell_198_RNA


title: p070-bdf1_002_rna


title: GM12878_cell_197_RNA


title: p070-bdf1_001_rna


title: GM12878_cell_196_RNA


title: p060-bdf1_051_rna

value: postnatal day 60


title: GM12878_cell_195_RNA


title: GM12878_cell_194_RNA


title: p060-bdf1_050_rna


title: GM12878_cell_193_RNA


title: GM12878_cell_204_RNA


title: GM12878_cell_192_RNA


title: p060-bdf1_048_rna


title: p060-bdf1_049_rna


title: p060-bdf1_047_rna


title: GM12878_cell_191_RNA


title: GM12878_cell_190_RNA


title: p060-bdf1_046_rna


title: GM12878_cell_188_RNA


title: p060-bdf1_045_rna


title: GM12878_cell_187_RNA


title: p060-bdf1_042_rna


title: p060-bdf1_043_rna


title: GM12878_cell_201_RNA


title: p060-bdf1_041_rna


title: GM12878_cell_189_RNA


title: GM12878_cell_185_RNA


title: GM12878_cell_183_RNA


title: GM12878_cell_184_RNA


title: p060-bdf1_039_rna


title: GM12878_cell_182_RNA


title: p060-bdf1_044_rna


title: p060-bdf1_038_rna


title: p060-bdf1_037_rna


title: GM12878_cell_180_RNA


title: p060-bdf1_036_rna


title: GM12878_cell_179_RNA


title: GM12878_cell_178_RNA


title: p060-bdf1_035_rna


title: p060-bdf1_034_rna


title: p060-bdf1_032_rna


title: GM12878_cell_177_RNA


title: GM12878_cell_176_RNA


title: p060-bdf1_033_rna


title: GM12878_cell_186_RNA


title: p060-bdf1_031_rna


title: GM12878_cell_174_RNA


title: p060-bdf1_030_rna


title: p060-bdf1_029_rna


title: p060-bdf1_040_rna


title: GM12878_cell_173_RNA


title: p060-bdf1_028_rna


title: GM12878_cell_172_RNA


title: GM12878_cell_171_RNA


title: p060-bdf1_027_rna


title: GM12878_cell_181_RNA


title: GM12878_cell_170_RNA


title: p060-bdf1_026_rna


title: p060-bdf1_025_rna


title: GM12878_cell_168_RNA


title: GM12878_cell_167_RNA


title: p060-bdf1_024_rna


title: GM12878_cell_169_RNA


title: p060-bdf1_023_rna


title: p060-bdf1_022_rna


title: GM12878_cell_165_RNA


title: GM12878_cell_175_RNA


title: p060-bdf1_021_rna


title: GM12878_cell_164_RNA


title: GM12878_cell_162_RNA


title: p060-bdf1_020_rna


title: p060-bdf1_019_rna


title: GM12878_cell_161_RNA


title: p060-bdf1_018_rna


title: GM12878_cell_163_RNA


title: p060-bdf1_017_rna


title: GM12878_cell_159_RNA


title: GM12878_cell_158_RNA


title: p060-bdf1_014_rna


title: p060-bdf1_016_rna


title: p060-bdf1_015_rna


title: GM12878_cell_157_RNA


title: p060-bdf1_012_rna


title: GM12878_cell_156_RNA


title: p060-bdf1_011_rna


title: p060-bdf1_013_rna


title: GM12878_cell_154_RNA


title: GM12878_cell_155_RNA


title: p060-bdf1_010_rna


title: p060-bdf1_008_rna


title: p060-bdf1_007_rna


title: GM12878_cell_151_RNA


title: GM12878_cell_150_RNA


title: p060-bdf1_006_rna


title: GM12878_cell_160_RNA


title: GM12878_cell_149_RNA


title: p060-bdf1_005_rna


title: GM12878_cell_166_RNA


title: GM12878_cell_148_RNA


title: p060-bdf1_004_rna


title: p060-bdf1_003_rna


title: GM12878_cell_146_RNA


title: GM12878_cell_147_RNA


title: p060-bdf1_002_rna


title: p060-bdf1_001_rna


title: GM12878_cell_145_RNA


title: p028-bdf1_070_rna

value: postnatal day 28


title: GM12878_cell_143_RNA


title: GM12878_cell_144_RNA


title: GM12878_cell_152_RNA


title: p028-bdf1_069_rna


title: GM12878_cell_153_RNA


title: p060-bdf1_009_rna


title: GM12878_cell_142_RNA


title: p028-bdf1_068_rna


title: GM12878_cell_141_RNA


title: p028-bdf1_066_rna


title: p028-bdf1_067_rna


title: GM12878_cell_139_RNA


title: p028-bdf1_065_rna


title: GM12878_cell_135_RNA


title: p028-bdf1_063_rna


title: GM12878_cell_138_RNA


title: p028-bdf1_062_rna


title: GM12878_cell_136_RNA


title: p028-bdf1_061_rna


title: p028-bdf1_064_rna


title: GM12878_cell_137_RNA


title: p028-bdf1_060_rna


title: GM12878_cell_133_RNA


title: p028-bdf1_057_rna


title: GM12878_cell_131_RNA


title: GM12878_cell_132_RNA


title: p028-bdf1_058_rna


title: p028-bdf1_059_rna


title: GM12878_cell_129_RNA


title: GM12878_cell_140_RNA


title: GM12878_cell_130_RNA


title: p028-bdf1_055_rna


title: p028-bdf1_056_rna


title: p028-bdf1_053_rna


title: GM12878_cell_127_RNA


title: p028-bdf1_054_rna


title: GM12878_cell_128_RNA


title: p028-bdf1_052_rna


title: GM12878_cell_125_RNA


title: GM12878_cell_134_RNA


title: p028-bdf1_051_rna


title: GM12878_cell_124_RNA


title: GM12878_cell_123_RNA


title: p028-bdf1_050_rna


title: p028-bdf1_047_rna


title: GM12878_cell_121_RNA


title: GM12878_cell_122_RNA


title: p028-bdf1_049_rna


title: GM12878_cell_118_RNA


title: p028-bdf1_045_rna


title: p028-bdf1_043_rna


title: p028-bdf1_046_rna


title: GM12878_cell_119_RNA


title: GM12878_cell_116_RNA


title: GM12878_cell_126_RNA


title: p028-bdf1_044_rna


title: GM12878_cell_117_RNA


title: p028-bdf1_048_rna


title: p028-bdf1_042_rna


title: GM12878_cell_115_RNA


title: p028-bdf1_041_rna


title: p028-bdf1_039_rna


title: p028-bdf1_038_rna


title: GM12878_cell_113_RNA


title: p028-bdf1_040_rna


title: GM12878_cell_111_RNA


title: GM12878_cell_112_RNA


title: GM12878_cell_120_RNA


title: p028-bdf1_037_rna


title: p028-bdf1_036_rna


title: p028-bdf1_035_rna


title: GM12878_cell_109_RNA


title: GM12878_cell_110_RNA


title: GM12878_cell_108_RNA


title: GM12878_cell_107_RNA


title: GM12878_cell_104_RNA


title: p028-bdf1_031_rna


title: GM12878_cell_103_RNA


title: p028-bdf1_030_rna


title: p028-bdf1_029_rna


title: GM12878_cell_105_RNA


title: GM12878_cell_102_RNA


title: p028-bdf1_028_rna


title: GM12878_cell_101_RNA


title: GM12878_cell_114_RNA


title: p028-bdf1_027_rna


title: GM12878_cell_100_RNA


title: p028-bdf1_026_rna


title: GM12878_cell_099_RNA


title: p028-bdf1_025_rna


title: GM12878_cell_098_RNA


title: GM12878_cell_097_RNA


title: p028-bdf1_024_rna


title: p028-bdf1_034_rna


title: p028-bdf1_023_rna


title: p028-bdf1_022_rna


title: GM12878_cell_106_RNA


title: p028-bdf1_032_rna


title: p028-bdf1_020_rna


title: p028-bdf1_021_rna


title: GM12878_cell_096_RNA


title: GM12878_cell_095_RNA


title: GM12878_cell_094_RNA


title: p028-bdf1_033_rna


title: GM12878_cell_092_RNA


title: p028-bdf1_017_rna


title: GM12878_cell_091_RNA


title: GM12878_cell_090_RNA


title: p028-bdf1_018_rna


title: GM12878_cell_093_RNA


title: GM12878_cell_088_RNA


title: p028-bdf1_014_rna


title: p028-bdf1_016_rna


title: p028-bdf1_015_rna


title: p028-bdf1_013_rna


title: GM12878_cell_086_RNA


title: p028-bdf1_012_rna


title: p028-bdf1_011_rna


title: p028-bdf1_009_rna


title: GM12878_cell_083_RNA


title: p028-bdf1_010_rna


title: p028-bdf1_008_rna


title: p028-bdf1_019_rna


title: GM12878_cell_081_RNA


title: GM12878_cell_082_RNA


title: GM12878_cell_080_RNA


title: p028-bdf1_006_rna


title: p028-bdf1_007_rna


title: GM12878_cell_087_RNA


title: GM12878_cell_078_RNA


title: p028-bdf1_005_rna


title: GM12878_cell_089_RNA


title: GM12878_cell_084_RNA


title: p028-bdf1_004_rna


title: GM12878_cell_076_RNA


title: GM12878_cell_077_RNA


title: GM12878_cell_085_RNA


title: GM12878_cell_075_RNA


title: p028-bdf1_002_rna


title: In vitro spheroids from primary hepatocytes from donor mice replicate 2b

city: Solna

first: Nuria

last: Vilarnau

state: Outside AUS/NZ

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

data_processing:
Libraries were sequenced in Hiseq3000 single read 50bp
The raw flowcell were then demultiplexed, and every Fastq file were first trimmed to eliminate bad quality reads and aligned using tophat2 to Mouse genome
The resulting BAM files were indexed, sorted, and all duplicated reads removed with Umitools dedup and Samtools.
The counts were then calculated using featurecounts
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts for each sample
Supplementary files format and content: tab-delimited text file include TPM values for all samples

molecule: total RNA

source_name: In vitro spheroids

extract_protocol:
Total RNA isolated with Rneasy kit from QIAGEN
Samples were prepared with Smartseq3 tehnologies according to manufacturer's instructions
Bulk RNAseq

value: In vitro spheroids

value: Primary murine hepatocytes from albino C57BL/6N mice

value: Hepatocyte

value: WT Albino


title: GM12878_cell_074_RNA

value: blood


title: GM12878_cell_072_RNA

value: Lymphoblastoid


title: GM12878_cell_073_RNA

value: WT


title: GM12878_cell_079_RNA


title: In vitro spheroids from primary hepatocytes from donor mice replicate 2c


title: In vitro spheroids from primary hepatocytes from donor mice replicate 2a


title: p028-bdf1_001_rna

value: mouse olfactory epithelium


title: GM12878_cell_071_RNA


title: p028-bdf1_003_rna


title: In vitro spheroids from primary hepatocytes from donor mice replicate 1c


title: GM12878_cell_069_RNA


title: GM12878_cell_068_RNA


title: GM12878_cell_070_RNA


title: p014-bdf1_054_rna

value: postnatal day 14


title: GM12878_cell_067_RNA


title: In vitro spheroids from primary hepatocytes from donor mice replicate 1b


title: p014-bdf1_055_rna


title: GM12878_cell_066_RNA


title: In vitro spheroids from primary hepatocytes from donor mice replicate 1a


title: GM12878_cell_065_RNA


title: p014-bdf1_053_rna


title: p014-bdf1_052_rna


title: Endogenous liver from donor mice replicate 3c

source_name: Endogenous liver

value: Endogenous liver

value: Liver tissue


title: GM12878_cell_064_RNA


title: GM12878_cell_063_RNA


title: GM12878_cell_062_RNA


title: Endogenous liver from donor mice replicate 3b


title: GM12878_cell_060_RNA


title: GM12878_cell_061_RNA


title: p014-bdf1_050_rna


title: p014-bdf1_051_rna


title: GM12878_cell_059_RNA


title: GM12878_cell_058_RNA


title: Endogenous liver from donor mice replicate 2c


title: Endogenous liver from donor mice replicate 2b


title: p014-bdf1_048_rna


title: GM12878_cell_057_RNA


title: GM12878_cell_056_RNA


title: Endogenous liver from donor mice replicate 2a


title: GM12878_cell_055_RNA


title: GM12878_cell_054_RNA


title: p014-bdf1_047_rna


title: GM12878_cell_052_RNA


title: Endogenous liver from donor mice replicate 1c


title: GM12878_cell_053_RNA


title: GM12878_cell_051_RNA


title: p014-bdf1_046_rna


title: Endogenous liver from donor mice replicate 3a


title: p014-bdf1_045_rna

description:
unknown
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: Endogenous liver from donor mice replicate 1b


title: GM12878_cell_048_RNA


title: GM12878_cell_046_RNA


title: Iris tissue without explants for control replicate 3c

description:
Iris_3c
Iris is not included in matrix pm_matrix_corrected_average_over1.txt because iris samples are deemed as not relevant once the correction for contaminating iris tissue in the explants is removed via deconvolution, as explained in the study.

source_name: Iris

value: Iris


title: Endogenous liver from donor mice replicate 1a


title: GM12878_cell_047_RNA


title: p014-bdf1_044_rna


title: GM12878_cell_049_RNA


title: p014-bdf1_049_rna


title: GM12878_cell_045_RNA


title: GM12878_cell_044_RNA


title: p014-bdf1_042_rna


title: Iris tissue without explants for control replicate 3b

description:
Iris_3b
Iris is not included in matrix pm_matrix_corrected_average_over1.txt because iris samples are deemed as not relevant once the correction for contaminating iris tissue in the explants is removed via deconvolution, as explained in the study.


title: p014-bdf1_043_rna


title: GM12878_cell_043_RNA


title: Iris tissue without explants for control replicate 3a

description:
Iris_3a
Iris is not included in matrix pm_matrix_corrected_average_over1.txt because iris samples are deemed as not relevant once the correction for contaminating iris tissue in the explants is removed via deconvolution, as explained in the study.


title: GM12878_cell_042_RNA


title: p014-bdf1_041_rna


title: GM12878_cell_041_RNA


title: p014-bdf1_040_rna


title: GM12878_cell_040_RNA


title: Iris tissue without explants for control replicate 2c

description:
Iris_2c
Iris is not included in matrix pm_matrix_corrected_average_over1.txt because iris samples are deemed as not relevant once the correction for contaminating iris tissue in the explants is removed via deconvolution, as explained in the study.


title: GM12878_cell_038_RNA


title: GM12878_cell_039_RNA


title: GM12878_cell_037_RNA


title: p014-bdf1_039_rna


title: GM12878_cell_050_RNA


title: Iris tissue without explants for control replicate 2a

description:
Iris_2a
Iris is not included in matrix pm_matrix_corrected_average_over1.txt because iris samples are deemed as not relevant once the correction for contaminating iris tissue in the explants is removed via deconvolution, as explained in the study.


title: GM12878_cell_035_RNA


title: GM12878_cell_036_RNA


title: GM12878_cell_033_RNA


title: GM12878_cell_031_RNA


title: Iris tissue without explants for control replicate 1c

description:
Iris_1c
Iris is not included in matrix pm_matrix_corrected_average_over1.txt because iris samples are deemed as not relevant once the correction for contaminating iris tissue in the explants is removed via deconvolution, as explained in the study.


title: Iris tissue without explants for control replicate 1b

description:
Iris_1b
Iris is not included in matrix pm_matrix_corrected_average_over1.txt because iris samples are deemed as not relevant once the correction for contaminating iris tissue in the explants is removed via deconvolution, as explained in the study.


title: p014-bdf1_037_rna


title: p014-bdf1_036_rna


title: Iris tissue without explants for control replicate 1a

description:
Iris_1a
Iris is not included in matrix pm_matrix_corrected_average_over1.txt because iris samples are deemed as not relevant once the correction for contaminating iris tissue in the explants is removed via deconvolution, as explained in the study.


title: GM12878_cell_030_RNA


title: Isolated primary hepatocytes from donor mouse livers replicate 3c

source_name: Liver

value: Liver


title: GM12878_cell_029_RNA


title: GM12878_cell_028_RNA


title: GM12878_cell_027_RNA


title: p014-bdf1_035_rna


title: p014-bdf1_034_rna


title: GM12878_cell_025_RNA


title: p014-bdf1_033_rna


title: Iris tissue without explants for control replicate 2b

description:
Iris_2b
Iris is not included in matrix pm_matrix_corrected_average_over1.txt because iris samples are deemed as not relevant once the correction for contaminating iris tissue in the explants is removed via deconvolution, as explained in the study.


title: GM12878_cell_024_RNA


title: GM12878_cell_026_RNA


title: Isolated primary hepatocytes from donor mouse livers replicate 3a


title: Isolated primary hepatocytes from donor mouse livers replicate 3b


title: p014-bdf1_032_rna


title: Isolated primary hepatocytes from donor mouse livers replicate 2c


title: GM12878_cell_023_RNA


title: p014-bdf1_038_rna


title: GM12878_cell_022_RNA


title: GM12878_cell_034_RNA


title: GM12878_cell_018_RNA


title: p014-bdf1_031_rna


title: Isolated primary hepatocytes from donor mouse livers replicate 2b


title: p014-bdf1_030_rna


title: Isolated primary hepatocytes from donor mouse livers replicate 2a


title: GM12878_cell_016_RNA


title: GM12878_cell_019_RNA


title: GM12878_cell_017_RNA


title: GM12878_cell_015_RNA


title: p014-bdf1_027_rna


title: GM12878_cell_013_RNA


title: GM12878_cell_014_RNA


title: Isolated primary hepatocytes from donor mouse livers replicate 1a


title: Isolated primary hepatocytes from donor mouse livers replicate 1b


title: GM12878_cell_012_RNA


title: GM12878_cell_011_RNA


title: GM12878_cell_020_RNA


title: p014-bdf1_025_rna


title: GM12878_cell_007_RNA


title: GM12878_cell_008_RNA


title: p014-bdf1_024_rna


title: p014-bdf1_026_rna


title: GM12878_cell_010_RNA


title: GM12878_cell_009_RNA


title: Explants at 2 months post-transplant replicate 6b

value: Explants (spheroids engrafted in ACE of recipient mice)


title: p014-bdf1_029_rna


title: Isolated primary hepatocytes from donor mouse livers replicate 1c


title: GM12878_cell_006_RNA


title: Explants at 2 months post-transplant replicate 6c

source_name: Explants (spheroids engrafted in ACE of recipient mice


title: Explants at 2 months post-transplant replicate 6a


title: p014-bdf1_028_rna


title: p014-bdf1_023_rna


title: p014-bdf1_022_rna


title: GM12878_cell_005_RNA


title: GM12878_cell_003_RNA


title: GM12878_cell_004_RNA


title: GM12878_cell_021_RNA


title: GM12878_cell_001_RNA


title: Explants at 2 months post-transplant replicate 5c


title: p014-bdf1_021_rna


title: eHAP_cell_042_RNA

source_name: eHAP

value: eHAP


title: Explants at 2 months post-transplant replicate 5b


title: GM12878_cell_002_RNA


title: p014-bdf1_020_rna


title: eHAP_cell_041_RNA


title: Explants at 2 months post-transplant replicate 5a


title: eHAP_cell_040_RNA


title: p014-bdf1_019_rna


title: Explants at 2 months post-transplant replicate 4c


title: Explants at 2 months post-transplant replicate 4b


title: eHAP_cell_038_RNA


title: p014-bdf1_018_rna


title: eHAP_cell_036_RNA


title: Explants at 2 months post-transplant replicate 4a


title: p014-bdf1_017_rna


title: Explants at 2 months post-transplant replicate 2c


title: eHAP_cell_034_RNA


title: eHAP_cell_033_RNA


title: eHAP_cell_032_RNA


title: eHAP_cell_035_RNA


title: p014-bdf1_016_rna


title: eHAP_cell_028_RNA


title: p014-bdf1_015_rna


title: eHAP_cell_030_RNA


title: eHAP_cell_029_RNA


title: p014-bdf1_014_rna


title: eHAP_cell_027_RNA


title: eHAP_cell_031_RNA


title: Explants at 2 months post-transplant replicate 1c


title: eHAP_cell_039_RNA


title: p014-bdf1_013_rna


title: eHAP_cell_026_RNA


title: eHAP_cell_025_RNA


title: p014-bdf1_012_rna


title: eHAP_cell_023_RNA


title: eHAP_cell_024_RNA


title: eHAP_cell_037_RNA


title: eHAP_cell_022_RNA


title: Explants at 2 months post-transplant replicate 2b


title: p014-bdf1_010_rna


title: IgG-CUT&Tag of DEK-KO E14TG2a cells repeat 2

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

institute: central south university

data_processing:
For CUT&Tag analysis, the CUT&Tag Fastq read files were aligned to the mm10 reference genome using Bowtie2, utilizing the default parameters. To identify Dek-wt peaks, biological replicates were merged, and peak calling was carried out using MACS2 (version 2.2.6) with specific settings (--keep-dup all -g mm -P-value ≤ 1e–5) against the IgG data. The generation of CUT&Tag bedgraph files involved the subtraction of IgG signals from the experimental group signals using Deeptools' bamCompare, with the inclusion of --skipNAs and --scaleFactorsMethod readCount options. The CUT&Tag bedgraph files were then subjected to normalization by calculating the reads per million (RPM), and the resulting bigwig files were generated using bedGraphToBigWig.
bigWig files were generated using bamCoverage.
Assembly: mm10
Supplementary files format and content: bigWig files

growth_protocol: Mouse E14TG2a ESCs (a kind gift from M. Zhang’s laboratory, Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China) were cultured on gelatin-coated dishes in DMEM (High Glucose, with Sodium Pyruvate, with L-Alanyl-L-Glutamine) (Vivacell) supplemented with 15% fetal bovine serum (Vistech), 1× non-essential amino acids (Gibco), 100 μM β-mercaptoethanol (Sigma), and 1000 U/mL of leukemia inhibitory factor (LIF) (Millipore). The cells were incubated at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
The CUT&Tag was performed following the protocol provided by the Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit (Yeasen). A total of 50,000 cells were harvested and subjected to two rounds of washing using washing buffer (composed of 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1× Protease inhibitor cocktail). Subsequently, the cells were incubated with activated Concanavalin A coated magnetic beads. To this, 0.5 μg of primary antibody was added and allowed to incubate on a rotating platform at 4 °C for a duration of 16 hours. Following this, 0.5 μL of secondary antibody was introduced and incubated for an additional hour. After a thorough washing step, the cells were treated with pA/G-Tn5 transposase at 37°C for 1 hour. Subsequently, DNA extraction was carried out by DNA selection beads
To amplify libraries, 16 μL CUT&Tag DNA was mixed with 1 μL of a uniquely barcoded i5, 1 μL a uniquely barcoded i7 primer, using a different barcode for each sample, 7 μL ddH2O, and 25 μL 2× Ultima Amplification Mix, and run the following cycling conditions with lid heat on: 72 °C for 3 min; 95 °C for 30 s; 12 cycles of 95 °C for 10 s, 55 °C for 30 s and 72 °C for 30 s; final extension at 72 °C for 5 min and hold at 4 °C. Post-PCR clean-up was performed by adding 1.2× volume of DNA selection beads (60 μL), and libraries were incubated with beads for 5 min at RT, washed twice gently in 80% ethanol, and eluted in 20 μL EB buffer.

value: mouse embryonic stem cell

value: Dek-WT

value: IgG CUT&Tag antibody


title: IgG-CUT&Tag of DEK-KO E14TG2a cells repeat 1


title: eHAP_cell_021_RNA


title: eHAP_cell_019_RNA


title: p014-bdf1_009_rna


title: p014-bdf1_011_rna


title: H3K27me3-CUT&Tag of DEK-KO E14TG2a cells repeat 2

value: H3K27me3 CUT&Tag antibody


title: eHAP_cell_017_RNA


title: Explants at 2 months post-transplant replicate 1a

value: Primary murine hepatocytes from albino C57BL/6N mice

value: Hepatocyte


title: eHAP_cell_016_RNA


title: Explants at 2 months post-transplant replicate 2a

value: WT Albino


title: eHAP_cell_020_RNA


title: Explants at 2 months post-transplant replicate 1b


title: eHAP_cell_015_RNA


title: H3K27me3-CUT&Tag of DEK-KO E14TG2a cells repeat 1


title: eHAP_cell_013_RNA


title: p014-bdf1_008_rna


title: p014-bdf1_006_rna


title: p014-bdf1_007_rna


title: eHAP_cell_012_RNA


title: H3K27ac-CUT&Tag of DEK-KO E14TG2a cells repeat 2

value: H3K27ac CUT&Tag antibody


title: H3K27ac-CUT&Tag of DEK-KO E14TG2a cells repeat 1


title: eHAP_cell_011_RNA

value: WT


title: p014-bdf1_005_rna

value: mouse olfactory epithelium


title: eHAP_cell_010_RNA


title: H3K9me3-CUT&Tag of DEK-KO E14TG2a cells repeat 2

value: H3K9me3 CUT&Tag antibody


title: eHAP_cell_009_RNA


title: eHAP_cell_018_RNA


title: eHAP_cell_008_RNA


title: eHAP_cell_007_RNA


title: H3K9me3-CUT&Tag of DEK-KO E14TG2a cells repeat 1


title: p014-bdf1_003_rna

value: postnatal day 14


title: eHAP_cell_006_RNA


title: H3K9ac-CUT&Tag of DEK-KO E14TG2a cells repeat 2

value: H3K9ac CUT&Tag antibody


title: eHAP_cell_014_RNA


title: p014-bdf1_002_rna


title: eHAP_cell_005_RNA


title: eHAP_cell_004_RNA


title: H3K9ac-CUT&Tag of DEK-KO E14TG2a cells repeat 1


title: eHAP_cell_003_RNA


title: p014-bdf1_001_rna


title: DEK-CUT&Tag of DEK-KO E14TG2a cells repeat 2

value: DEK CUT&Tag antibody


title: p014-bc_043_rna

value: bc


title: K562_cell_063_RNA

source_name: bone marrow

value: bone marrow


title: DEK-CUT&Tag of DEK-KO E14TG2a cells repeat 1


title: eHAP_cell_002_RNA

value: eHAP


title: p014-bc_042_rna


title: K562_cell_062_RNA


title: K562_cell_060_RNA


title: IgG-CUT&Tag of Parental E14TG2a cells repeat 2

value: mouse embryonic stem cell


title: p014-bc_041_rna


title: K562_cell_061_RNA


title: p014-bdf1_004_rna


title: K562_cell_059_RNA


title: IgG-CUT&Tag of Parental E14TG2a cells repeat 1

value: Dek-WT


title: p014-bc_040_rna


title: K562_cell_057_RNA


title: K562_cell_058_RNA


title: p014-bc_039_rna


title: H3K27me3-CUT&Tag of Parental E14TG2a cells repeat 2


title: K562_cell_056_RNA


title: K562_cell_055_RNA


title: p014-bc_038_rna


title: K562_cell_053_RNA


title: eHAP_cell_001_RNA


title: H3K27ac-CUT&Tag of Parental E14TG2a cells repeat 2


title: K562_cell_054_RNA


title: H3K27me3-CUT&Tag of Parental E14TG2a cells repeat 1


title: p014-bc_037_rna


title: K562_cell_051_RNA


title: K562_cell_050_RNA


title: H3K9me3-CUT&Tag of Parental E14TG2a cells repeat 2


title: K562_cell_048_RNA


title: p014-bc_036_rna


title: H3K27ac-CUT&Tag of Parental E14TG2a cells repeat 1


title: p014-bc_035_rna


title: K562_cell_047_RNA


title: K562_cell_046_RNA


title: H3K9ac-CUT&Tag of Parental E14TG2a cells repeat 2


title: p014-bc_034_rna


title: K562_cell_045_RNA


title: K562_cell_044_RNA


title: p014-bc_033_rna


title: K562_cell_043_RNA


title: H3K9ac-CUT&Tag of Parental E14TG2a cells repeat 1


title: K562_cell_052_RNA


title: K562_cell_042_RNA


title: p014-bc_032_rna


title: K562_cell_041_RNA


title: p014-bc_031_rna


title: K562_cell_040_RNA


title: DEK-CUT&Tag of Parental E14TG2a cells repeat 1


title: K562_cell_039_RNA


title: K562_cell_038_RNA


title: K562_cell_037_RNA


title: DEK-CUT&Tag of Parental E14TG2a cells repeat 2


title: p014-bc_030_rna


title: K562_cell_049_RNA


title: H3K9me3-CUT&Tag of Parental E14TG2a cells repeat 1


title: p014-bc_028_rna


title: p014-bc_029_rna


title: K562_cell_034_RNA


title: K562_cell_032_RNA


title: K562_cell_033_RNA


title: K562_cell_031_RNA


title: p014-bc_027_rna


title: K562_cell_030_RNA


title: K562_cell_029_RNA


title: p014-bc_026_rna


title: K562_cell_027_RNA


title: K562_cell_028_RNA


title: K562_cell_036_RNA


title: p014-bc_024_rna


title: p014-bc_023_rna


title: K562_cell_022_RNA


title: K562_cell_024_RNA


title: K562_cell_021_RNA


title: K562_cell_025_RNA


title: K562_cell_020_RNA


title: K562_cell_019_RNA


title: K562_cell_018_RNA


title: K562_cell_026_RNA


title: p014-bc_021_rna


title: p014-bc_025_rna


title: K562_cell_017_RNA


title: p014-bc_020_rna


title: K562_cell_023_RNA


title: K562_cell_016_RNA


title: p014-bc_022_rna


title: p014-bc_019_rna


title: K562_cell_014_RNA


title: K562_cell_013_RNA


title: K562_cell_012_RNA


title: p014-bc_018_rna


title: K562_cell_035_RNA


title: K562_cell_011_RNA


title: A. selago x A millepora offspring s2xm1

city: Austin

first: Christopher

last: Peterson

state: TX

address: 2415 Speedway #C0930

department: Integrative Biology

country: USA

institute: University of Texas

data_processing:
WGBS reads trimmed with Trim Galore 0.6.7
Trimmed adult WGBS reads aligned to Amil v2.1 with Bismark v 0.24.2 with with mapping parameters -N 1 --score_min L,0,-0.8
md-RAD reads trimmed and aligned with Bowtie2 v. 2.5.0
Adult WGBS and md-RAD alignments variant called with ANGSD 0.940
Fixed SNP differences between adults were determine from variant calls, then used to create N-masked reference genomes for each pair of parents, with SNPsplit’s genome preparation script
Offspring WGBS files aligned to parent-specific masked genomes, using Bismark v 0.24.2.
Offspring alignments separated by parental alleles using SNPsplit v 0.6
Methylation calls extracted from adult WGBS alignments and offspring allele-specific alignments using Bismark’s methylation extraction script.
Assembly: Acroproa millepora, v2.1
Supplementary files format and content: Gzipped tab separated coverage file, created by Bismark’s methylation extraction script; Columns are: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Supplementary files format and content: Offspring have separate coverage files for each allele-specific alignment

organism: Acropora selago x Acropora millepora

source_name: Larval Pool

growth_protocol: Specimens of A. millepora and A. selago were collected and placed into raceways 7 days before spawning. Sperm and egg were collected from each colony on the night of spawning and separated to be fertilized in controlled crosses. Larvae were kept at 27 °C for 5 days until larval development completed. After development, we fixed larvae from each successful cross in 100% Ethanol and stored at -80 °C.

extract_protocol:
DNA was extracted from adult corals and from individual and pooled larvae (approximately 10 larvae per pool).  Samples were lysed through bead beating and 2-hour incubation with CTAB buffer at 65 °C. Subsequently, an organic DNA extraction is performed using phenol:chloroform:isoamyl alcohol (25:24:1). DNA was then cleaned using the Zymo Clean & Concentrate kit.
Whole genome bisulfite (WGBS) preparation was only completed on adult coral samples and pooled larvae using the Zymo-Seq WGBS Library Kit.

value: Larval Pool

tag: protocol

value: whole genome bisulfite-seq

value: Offspring


title: K562_cell_010_RNA


title: p014-bc_017_rna


title: p014-bc_016_rna


title: K562_cell_015_RNA


title: K562_cell_009_RNA


title: A. selago x A millepora offspring s1xm2


title: K562_cell_008_RNA


title: K562_cell_007_RNA


title: A. selago x A millepora offspring s1xm1


title: p014-bc_014_rna


title: K562_cell_005_RNA


title: K562_cell_006_RNA


title: p014-bc_015_rna


title: A. millepora offspring m2xm1

organism: Acropora millepora


title: K562_cell_004_RNA


title: p014-bc_013_rna


title: p014-bc_012_rna


title: A. millepora offspring m1xm2


title: K562_cell_003_RNA


title: A. selago x A millepora offspring s2xm2


title: BJ_cell_063_RNA

value: foreskin

value: human fibroblast cell line

value: BJ


title: K562_cell_002_RNA

value: WT


title: md-RAD_A. millepora adult 1

description:
lane1-A3-C_S3_L001_1.trim_bismark_bt2_pe.deduplicated.bismark.cov.gz
Both whole genome bisulfite-seq and md-RAD data were in the generation of the processed data files.

data_processing:
WGBS reads trimmed with Trim Galore 0.6.7
Trimmed adult WGBS reads aligned to Amil v2.1 with Bismark v 0.24.2 with with mapping parameters -N 1 --score_min L,0,-0.8
md-RAD reads trimmed and aligned with Bowtie2 v. 2.5.0
Adult WGBS and md-RAD alignments variant called with ANGSD 0.940
Fixed SNP differences between adults were determine from variant calls, then used to create N-masked reference genomes for each pair of parents, with SNPsplit’s genome preparation script
Offspring WGBS files aligned to parent-specific masked genomes, using Bismark v 0.24.2.
Offspring alignments separated by parental alleles using SNPsplit v 0.6
Methylation calls extracted from adult WGBS alignments and offspring allele-specific alignments using Bismark’s methylation extraction script.
Assembly: Acroproa millepora, v2.1
Supplementary files format and content: Gzipped tab separated coverage file, created by Bismark’s methylation extraction script; Columns are: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Supplementary files format and content: Offspring have separate coverage files for each allele-specific alignment
Library strategy: md-RAD

source_name: Coral Fragment

value: Coral Fragment

value: md-RAD

value: Parent


title: BJ_cell_059_RNA


title: p014-bc_009_rna

value: mouse olfactory epithelium

value: postnatal day 14


title: BJ_cell_058_RNA


title: p014-bc_011_rna

value: bc


title: K562_cell_001_RNA

value: bone marrow


title: BJ_cell_062_RNA


title: md-RAD_A. millepora adult 2

description:
lane1-A4-D_S4_L001_1.trim_bismark_bt2_pe.deduplicated.bismark.cov.gz
Both whole genome bisulfite-seq and md-RAD data were in the generation of the processed data files.


title: A. millepora adult 1


title: hb52_KCl_3

type: RNA

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description: Gene expression after 1 d KCl treatment

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings treated with KCl

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Maxwell RSC RNA kit (Promega) following the manufacturer's recommendations.

treatment_protocol: 5 day-old Arabidopsis Col-0 wild-type and hb52-KO grown in N-free MS (Murashige and Skoog) liquid medium with 10 mM ammonium were treated with 10 mM KNO3 or 10 mM KCl (control) for 1 day.

value: Whole seedlings

value: 10 mM KCl


title: BJ_cell_061_RNA

description: Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice


title: WT_KNO3_1

description: Gene expression after 1 d KNO3 treatment

source_name: Arabidopsis seedlings treated with KNO3

value: Col-0 wild-type

value: 10 mM KNO3


title: p014-bc_010_rna

description:
mOSN
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: hb52_KCl_1

description: Gene expression after 1 d KCl treatment


title: WT_KCl_3

description: Gene expression after 1 d KCl treatment


title: WT_KNO3_3


title: hb52_KNO3_1


title: hb52_KNO3_2


title: p014-bc_007_rna

description:
iOSN
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: BJ_cell_060_RNA


title: A. millepora adult 2

value: whole genome bisulfite-seq


title: WT_KCl_1

description: Gene expression after 1 d KCl treatment


title: WT_KCl_2

description: Gene expression after 1 d KCl treatment


title: BJ_cell_057_RNA


title: BJ_cell_054_RNA


title: BJ_cell_053_RNA


title: p014-bc_008_rna


title: BJ_cell_052_RNA


title: BJ_cell_056_RNA


title: Drosophila_whole body, wild-type strain w1118, 10 day-old_male

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

description: CH ATAC-seq

library_source: genomic single cell

data_processing:
For each sequenced CHATAC-seq library, we obtained two FASTQ files, one of which contained combinatorial index for HY(768 indices) and Tn5 (384 indices) in specific base positions. We filtered reads with more than one mismatch in each index and trimmed adaptor sequences using trimmomatic(version 0.3.8). After that, reads from Drosophila  were aligned to D.melanogaster dm6 genome(UCSC) using BWA (version 0.7.15).  Taking the 9-bp duplication caused by Tn5 transposase into account, we shifted aligned reads + 4bp and -5bp for each positive and negative strand using alignmentSieve(deeptools 3.5.1).Then we used snaptools(version 1.4.8) to keep nonduplicate fragments with high mapping quality (MAPQ > 30) and proper length(<1000 bp) and extracted fragment files from the snap files. Subsequent analysis was performed by ArchR (version 1.0.2). We created arrow files from fragment files by ‘createArrowFiles function’ and constructed customized genome using ‘createGenomeAnnotation’ and ‘createGeneAnnotation function’.
Assembly: D.melanogaster dm6 genome(UCSC)
Supplementary files format and content: BED files recording coordinates of fragments captured by scATAC-seq

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
Samples were  subjected to manual pulverization via grinded in liquid nitrogen. The pulverized tissues were aliquoted into  1.5 ml lysis buffer  [10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sangon Biotech), 0.1% IGEPAL-CA630 (Sigma Aldrich) and 0.01% Digitonin (Thermo Scientific) in water], and followed by incubation for 3 minutes on ice for nuclei extraction.
Library preparations were performed with the CH ATAC-seq protocol

treatment_protocol: Hypothermal shocked

value: whole body

value: wild-type

value: 10 days

tag: Sex

value: male


title: Drosophila_whole body, wild-type strain w1118, 10 day-old_female

description: CH ATAC-seq

value: Female


title: BJ_cell_055_RNA

value: foreskin

value: human fibroblast cell line

value: BJ

value: WT


title: hb52_KCl_2

description: Gene expression after 1 d KCl treatment


title: HMCB cells, siAHCYL1, biol rep 3

city: Chicago

first: Jing

last: Chen

state: IL

address: 900 E 57th St

institute: University of Chicago

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the human GRCh38 using the STAR aligner. The aligned reads were then assigned to genes using RSEM.
The aligned reads were then assigned to genes using RSEM
Assembly: GRCh38
Supplementary files format and content: table delimited text file containing the expression of genes

source_name: HMCB

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purificationThe library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: HMCB

value: melanoma cell line

value: Nras Q61K

value: AHCYL1 siRNA


title: HMCB cells, siAHCYL1, biol rep 2


title: BJ_cell_051_RNA


title: p014-bc_006_rna

value: mouse olfactory epithelium

value: postnatal day 14

value: bc


title: p014-bc_004_rna


title: p014-bc_005_rna


title: BJ_cell_049_RNA


title: BJ_cell_050_RNA


title: p014-bc_003_rna


title: WT_KNO3_2

value: Whole seedlings

value: Col-0 wild-type

value: 10 mM KNO3


title: BJ_cell_047_RNA


title: BJ_cell_046_RNA


title: HMCB cells, siNC, biol rep 3

value: siNC


title: HMCB cells, siAHCYL1, biol rep 1


title: BJ_cell_045_RNA


title: hb52_KNO3_3


title: BJ_cell_048_RNA


title: BJ_cell_044_RNA


title: HMCB cells, siNC, biol rep 1


title: p014-bc_001_rna


title: BJ_cell_043_RNA


title: BJ_cell_042_RNA


title: BJ_cell_041_RNA


title: HMCB cells, siNC, biol rep 2


title: p007-bdf1_081_rna

description:
progenitor-2
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz

value: postnatal day 7


title: BJ_cell_039_RNA


title: BJ_cell_040_RNA


title: p007-bdf1_079_rna


title: Parasympathetic neurons from S2 FD iPSCs, day 30, biol rep 3

city: Athens GA

first: Nadja

last: Zeltner

state: GA

address: 325 Riverbend road

institute: University of Georgia

data_processing:
Analyses were done on the Galaxy platform (www.usegalaxy.org)
Low quality bases were trimmed using Trimmomatic (version 0.38)
Reads were mapped to the human genome using HISAT2 (version 2.2.1)
Reads per gene were counted using HTSeq (version 0.9.1). Minimum alignment quality value of 10
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts per gene

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and purified following the manufacturer's protocol
Library was prepared using the kit NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) following the standard protocol

value: iPSC

value: FD

tag: time point

value: day 30


title: p007-bdf1_080_rna


title: BJ_cell_038_RNA

value: foreskin

value: human fibroblast cell line

value: BJ


title: Parasympathetic neurons from S2 FD iPSCs, day 30, biol rep 2


title: BJ_cell_036_RNA

value: WT


title: BJ_cell_035_RNA


title: Parasympathetic neurons from S2 FD iPSCs, day 30, biol rep 1


title: BJ_cell_034_RNA


title: p007-bdf1_078_rna


title: BJ_cell_033_RNA


title: BJ_cell_031_RNA


title: p007-bdf1_077_rna


title: Parasympathetic neurons from H9 hPSCs, day 30, biol rep 2

value: hPSC


title: BJ_cell_032_RNA


title: Parasympathetic neurons from H9 hPSCs, day 30, biol rep 3


title: p007-bdf1_076_rna


title: p014-bc_002_rna


title: BJ_cell_030_RNA


title: Parasympathetic neurons from H9 hPSCs, day 30, biol rep 1


title: BJ_cell_028_RNA


title: BJ_cell_027_RNA


title: BJ_cell_026_RNA


title: BJ_cell_029_RNA


title: p007-bdf1_075_rna


title: p007-bdf1_072_rna

description:
progenitor-1
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: Schwann cell progenitors from H9 hPSCs, day 16, biol rep 1

value: day 16


title: BJ_cell_037_RNA


title: p007-bdf1_073_rna

value: mouse olfactory epithelium


title: p007-bdf1_074_rna


title: Schwann cell progenitors from H9 hPSCs, day 16, biol rep 3


title: BJ_cell_025_RNA


title: WPM_48

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

data_processing:
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Sequences were trimmed for adaptor seuqences and masked for low-complexity and low-quality
150 nt paired-end reads were assembled into transcript isoforms and mapped to the pig genome (version GRCm38) using Kallisto v0.43 (Bray et al., 2016)
Genome_build: Sus scrofa genome (version 10)
Supplementary_files_format_and_content: xls format,  transcripts per million (TPM) values for each sample, one column per sample
rodriguez_wean22amy48_counts.xlsx

organism: Sus scrofa

source_name: Amygdala

extract_protocol:
RNA was extracted from all samples using standards protocols. TRIzol reagent (Life Technologies, Grand Island, New York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina Inc, San Diego, CA, USA). Read 1 aligns to the antisense strand and read 2 aligns to the sense strand. The libraries were sequenced on a NovaSeq 6000. Pair-ended reads of length 150bp were sequenced. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

tag: feeding

value: Weaned

value: P

value: Male

value: 22 day old

value: Amygdala


title: BJ_cell_023_RNA


title: Schwann cell progenitors from H9 hPSCs, day 16, biol rep 2


title: Sympathetic precursors from H9 hPSCs, day 14, biol rep 3

value: day 14


title: BJ_cell_021_RNA


title: BJ_cell_020_RNA


title: BJ_cell_019_RNA


title: p007-bdf1_070_rna

value: postnatal day 7


title: Sympathetic precursors from H9 hPSCs, day 14, biol rep 1


title: WPM_47


title: WPM_46


title: BJ_cell_018_RNA


title: p007-bdf1_069_rna


title: WPM_45


title: p007-bdf1_068_rna


title: Neural crest cells from H9 hPSCs, day 10, biol rep 2

value: day 10


title: BJ_cell_024_RNA


title: BJ_cell_022_RNA


title: BJ_cell_017_RNA


title: p007-bdf1_066_rna


title: BJ_cell_016_RNA


title: Neural crest cells from H9 hPSCs, day 10, biol rep 1


title: p007-bdf1_071_rna


title: p007-bdf1_064_rna


title: WPM_43


title: BJ_cell_014_RNA


title: BJ_cell_013_RNA


title: p007-bdf1_063_rna


title: WPF_40

value: Female


title: WPF_38


title: BJ_cell_010_RNA


title: WPM_44


title: Neural crest cells from H9 hPSCs, day 10, biol rep 3


title: p007-bdf1_062_rna


title: BJ_cell_008_RNA


title: BJ_cell_015_RNA


title: WCM_35

value: C


title: BJ_cell_011_RNA

value: foreskin


title: p007-bdf1_067_rna


title: p007-bdf1_065_rna


title: BJ_cell_007_RNA

value: human fibroblast cell line


title: p007-bdf1_060_rna


title: WPF_39


title: BJ_cell_009_RNA

value: BJ


title: WPF_42


title: p007-bdf1_059_rna

value: WT


title: WPF_37


title: WCM_36


title: p007-bdf1_058_rna


title: p007-bdf1_057_rna


title: WPF_41


title: BJ_cell_006_RNA


title: WCM_33


title: BJ_cell_012_RNA


title: p007-bdf1_061_rna


title: BJ_cell_005_RNA


title: p007-bdf1_055_rna


title: p007-bdf1_056_rna


title: BJ_cell_004_RNA


title: WCM_32


title: WCM_34


title: p007-bdf1_054_rna


title: WCF_30


title: BJ_cell_003_RNA


title: BJ_cell_002_RNA


title: WCF_29


title: p007-bdf1_052_rna


title: WCM_31


title: p007-bdf1_053_rna


title: p007-bdf1_051_rna


title: WCF_28


title: p007-bdf1_050_rna


title: BJ_cell_001_RNA


title: WCF_27


title: p007-bdf1_047_rna


title: Sympathetic precursors from H9 hPSCs, day 14, biol rep 2

value: hPSC


title: WCF_25


title: p007-bdf1_049_rna


title: A549_PAX5-flag input_rep_1

city: Tianjin

first: Yan

middle: Xue

last: miao

state: Tianjin

address: 22 Qixiangtai Road,Heping District,Tianjin,China

department: Department of Immunologyc

institute: Tianjin Medical University

description: A549_PAX5 flag_input_rep_1

data_processing:
Basecalls performed using CASAVA version 1.4
Data were filtered using Trimmomatic
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2-2.3.5
peaks were called using MACS2
Genome_build: hg38
Supplementary_files_format_and_content: bw files were generated using deepTools>-bamCoverage

source_name: A549 cell line expressing PAX5-flag

growth_protocol: A549 cell line expressing PAX5-flag vector and cultured in 1640 medium containg 10%FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and PAX5-flag-DNA complexes were isolated with flag antibody.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: human lung cancer cell line

tag: chip antibody


title: p007-bdf1_048_rna

source_name: mouse olfactory epithelium

value: mouse olfactory epithelium


title: A549_PAX5-flag ChIP-seq_rep_1

description: A549_PAX5 flag_IP_rep_1

value: Anti-Flag® M2 Affinity Gel (A2220, sigma)


title: WCF_26

value: Weaned


title: NPM_24

value: Nursed

value: P

value: Male


title: A549_PAX5-flag input_rep_2

description: A549_PAX5 flag_input_rep_2


title: p007-bdf1_046_rna


title: NPM_23

value: 22 day old

value: Amygdala


title: p007-bdf1_045_rna

value: postnatal day 7


title: p007-bdf1_044_rna


title: NPM_22


title: A549_PAX5-flag ChIP-seq_rep_2

description: A549_PAX5 flag_IP_rep_2


title: p007-bdf1_043_rna


title: NPM_21


title: NPM_20


title: NPM_19


title: p007-bdf1_042_rna


title: p007-bdf1_041_rna


title: NPF_18

value: Female


title: p007-bdf1_039_rna


title: p007-bdf1_040_rna


title: NPF_16


title: NPF_17


title: Naïve, hub, expt 2

city: Cambridge

first: Colin

middle: YC

last: Lee

address: Wellcome Genome Campus, Hinxton

country: United Kingdom

institute: Molecular Immunity Unit

description: BCR sequencing

data_processing:
MiSeq libraries were prepared using Illumina protocols and sequenced using 300 bp paired-ended MiSeq (Illumina). Raw MiSeq reads were filtered for base quality (median Phred score > 32) using QUASR (http://sourceforge.net/projects/quasr/). MiSeq forward and reverse reads were merged together if they contained identical overlapping regions of >50 bp, or otherwise discarded. Universal barcoded regions were identified in reads and orientated to read from V-primer to constant region primer. The barcoded region within each primer was identified and checked for conserved bases (i.e., the T’s in NNNNTNNNNTNNNNT). Primers and constant regions were trimmed from each sequence, and sequences were retained only if there was >80% sequence certainty between all sequences obtained with the same barcode, otherwise discarded. The constant region allele with highest sequence similarity was identified by 10-mer matching to the reference constant region genes from the IMGT database, and sequences were trimmed to give only the region of the sequence corresponding to the variable (V–D–J) regions. Isotype usage information for each IgH was retained throughout the analysis hereafter. Sequences without complete reading frames and non-immunoglobulin sequences were removed and only reads with significant similarity to reference IgHV and J genes from the IMGT database were retained using BLAST. IGHV and IGHJ genes and mutational status were determined for each BCR using IMGT/V-QUEST. All scripts to perform the BCR-seq processing can be found at https://github.com/clatworthylab/bulkBCRseq.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Fasta file containing reconstructed BCR sequences
Library strategy: BCR-seq (bulk)

source_name: Rostral-rhinal hub

extract_protocol:
RNA were extracted from the tissues using RNA pure link mini kit (Thermo Fisher) as per the manufacturer’s instructions.
Reverse transcription (RT) was performed in two steps: first, 1 μl barcoded reverse primer mix (10 μM per each primer), 1 μl dNTP (10 mM) and 14 μl RNA template (up to 500 ng) were mixed and heated to 65 °C for 5 min followed by an immediate transfer to ice for at least 1 min. Second, mixture 2 including 4 μl 5× First-Strand Buffer, 1 μl DTT (0.1 M), 1 μl RNaseOUT (Thermo Scientific) and 1 μl SuperScriptIII (Life Technologies) was added and incubated at 50 °C for 60 min followed by 15 min inactivation at 70 °C. cDNA was cleaned up with Agencourt AMPure XP beads and PCR amplified with V-gene multiplex primer mix (10 μM each forward primer) and 3′ universal reverse primer (10 μM) using KAPA protocol (KAPA Biosystems) and the thermal cycling conditions: 1 cycle (95 °C for 5 min); 5 cycles (98 °C for 5 s, 72 °C for 2 min); 5 cycles (98 °C for 5 s, 65 °C for 10 s, 72 °C for 2 min); 30 cycles (98 °C for 20 s, 60 °C for 1 min, 72 °C for 2 min) and 1 step (72 °C for 7 min). Primers are listed in Supplementary Table 1 of Fitzpatrick et al 2020 PMID: 33149302 (doi.org/10.1038/s41586-020-2886-4).

treatment_protocol: Where indicated, VSV infected mice were treated with anti-LFA1/VLA-4 or isotype control antibodies beginning at d6 post-infection.

value: Rostral-rhinal hub

tag: time

value: naïve (day 0)


title: 21dpi VSV, hub, expt 2, isotype

description: BCR sequencing

value: day 21

value: Isotype control antibody


title: Week 3 VSV, spleen, rep 2

description: BCR sequencing

source_name: Spleen

value: Spleen


title: NPF_14


title: Week 3 VSV, spleen, rep 5

description: BCR sequencing


title: 21dpi VSV, hub, expt 2, anti-LFA1-VLA4

description: BCR sequencing


title: p007-bdf1_037_rna

value: WT


title: Week 3 VSV, spleen, rep 1

description: BCR sequencing


title: 6dpi VSV, hub, expt 2

description: BCR sequencing

value: day 6


title: Week 3 VSV, spleen, rep 3

description: BCR sequencing


title: Week 3 VSV, sinus, rep 5

description: BCR sequencing

source_name: Dural venous sinus

value: Dural venous sinus


title: NPF_15


title: Week 3 VSV, sinus, rep 4

description: BCR sequencing


title: Mia PaCa-2 cells stably expressing a siRNA targeting cytidine deaminase (CDA), clone 3

city: Toulouse

first: Pierre

last: Cordelier

address: 2, avenue Hubert Curien

country: France

institute: Cancer Research Center of Toulouse

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.
Assembly: GRCh38/hg38
Supplementary files format and content: Text file with raw counts

source_name: Pancreas tumor

growth_protocol: cancer cells were obtained from the ATCC and cultured in Dulbecco Modified Eagle Medium (DMEM) 4.5 g/L glucose containing 10% Fetal Bovine Serum (FBS), 100 IU/mL penicillin, 100 µg/mL streptomycin and 250 ng/mL fungizone (AB) and 100 µg/mL normocin (Invivogen) to avoid mycoplasma  contamination. Cells were incubated at 37°C with 5% CO2

extract_protocol:
Total RNA was extracted with RNeasy kit (Qiagen) according to the manufacturer’s instructions; quality and quantity were measured on a Nanodrop system (ThermoFisher Scientific)
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

value: Pancreas tumor

value: Mia PaCa-2

value: cancer cells


title: Week 3 VSV, spleen, rep 4

description: BCR sequencing


title: NCM_13

value: Nursed

value: C


title: p007-bdf1_036_rna

value: mouse olfactory epithelium


title: p007-bdf1_035_rna


title: Mia PaCa-2 cells stably expressing a siRNA targeting cytidine deaminase (CDA), clone 1


title: Mia PaCa-2 cells stably expressing a control siRNA, clone 3


title: Mia PaCa-2 cells stably expressing a siRNA targeting cytidine deaminase (CDA), clone 2


title: Week 3 VSV, sinus, rep 3

description: BCR sequencing


title: p007-bdf1_034_rna


title: NCM_12

value: Male

value: 22 day old

value: Amygdala


title: NCM_11


title: Week 3 VSV, sinus, rep 2

description: BCR sequencing


title: Mia PaCa-2 cells stably expressing a control siRNA, clone 2


title: p007-bdf1_038_rna

value: postnatal day 7


title: p007-bdf1_033_rna


title: NCM_10


title: Mia PaCa-2 cells stably expressing a control siRNA, clone 1


title: Week 3 VSV, hub, rep 4

description: BCR sequencing

value: Rostral-rhinal hub


title: Week 3 VSV, hub, rep 5

description: BCR sequencing

value: day 21


title: p007-bdf1_031_rna


title: NCM_08


title: p007-bdf1_030_rna


title: NCF_07

value: Female


title: Week 3 VSV, hub, rep 3

description: BCR sequencing


title: Week 3 VSV, hub, rep 2

description: BCR sequencing


title: p007-bdf1_029_rna


title: NCF_06


title: Islet_67 (SAMN12496804), HTO

city: Farmington

first: Eishani

middle: Kumar

last: Sokolowski

state: CT

address: 263 Farmington Avenue

institute: University of Connecticut Health Center

description: 10x Genomics

data_processing:
Illumina base call files for all libraries were converted to FASTQ using Illumina’s bcl2fastq.
The FASTQ files were then associated with the gene expression libraries, aligned to the GRCh38.93 reference genome and merged, including all transcribed unitary pseudogenes, using the 10x Genomics Cell Ranger’s count pipeline.
FASTQ files representing the HTO libraries were then processed into hashtag-count matrices using CITE-seq-Count.
Sample identities were determined using demuxlet, and demultiplexed based on enrichment of HTO using Seurat.
Assembly: hg38
Supplementary files format and content: Tab-delimited values and matrix files.
Supplementary files format and content: Text file (Barcodes_Treatment.txt) associating barcodes with treatment conditions in each sample.

source_name: Pancreatic Islets

growth_protocol: Fresh human cadaveric pancreatic islets were procured from Prodo Labs or the Integrated Islet Distribution Program (IIDP). Upon arrival, cells were transferred into PIM(S) media (Prodo Labs) supplemented with PIM(ABS) (Prodo Labs) and PIM(G) (Prodo Labs) and incubated in a T-150 non-tissue culture treated flask (VWR) for recovery at 37°C and 5% CO2 overnight.

extract_protocol:
Islets were treated with Accutase for 8-10 min at 37°C to generate a single cell suspension. Cells were then washed and suspended in Staining buffer (PBA, 2%BSA, 0.01%TweenS).
Islets were incubated with Fc Blocking reagent (FcX, BioLegend) 10 minutes at 4 ̊C, before adding 0.5ug of a unique Cell Hashing antibody (TotalseqTM-A0251 to A0257 anti-human hashtag antibody, Biolegend) for 20 minutes at 4 ̊C, and then washed 2 times with Staining buffer, and once with PBS+0.04%BSA. Cell viability was assessed on a Countess II automated cell counter (ThermoFisher), and up to 30,000 cells (~5,000 cells from each hash-tagged (HTO) sample) were loaded onto one lane of a 10X Chromium Controller. One single cell suspension was loaded twice i.e. across 2 lanes on the 10x chip, and 2 gene expression and 2 HTO libraries were generated in total, which were processed into a single set of gene expression and HTO outputs. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform V3 chemistry and according to the manufacturer’s protocol (#GC000103).

treatment_protocol: The media was changed to CMRL (10% FBS, 1% Glutamax) supplemented with either 0.025%v DMSO, 250nM thapsigargin or 25 U/mL of IL1β + 1000 U/mL of IFNγ (R&D Systems) for 24-hr incubation at 37°C and 5% CO2.

value: Pancreatic Islets

tag: unos id

tag: library type

value: Hashtag (multiplexed)


title: Islet_116 (SAMN16114998) & Islet_117 (SAMN16122047), HTO

description: 10x Genomics


title: Islet_168 (SAMN29494287), HTO

description: 10x Genomics


title: p007-bdf1_028_rna

value: WT


title: NCF_05


title: Islet_162 (SAMN25980818), HTO

description: 10x Genomics


title: p007-bdf1_027_rna


title: Week 3 VSV, hub, rep 1

description: BCR sequencing


title: Week 3 VSV, cLN, rep 5

description: BCR sequencing

source_name: Cervical lymph node

value: Cervical lymph node


title: Week 3 VSV, cLN, rep 4

description: BCR sequencing


title: Week 3 VSV, sinus, rep 1

description: BCR sequencing

value: Dural venous sinus


title: p007-bdf1_026_rna


title: NCF_03


title: Islet_116 (SAMN16114998) & Islet_117 (SAMN16122047), GEX

description: 10x Genomics

value: Gene Expression (multiplexed)


title: p007-bdf1_032_rna


title: NCM_09


title: Islet_67 (SAMN12496804), GEX

description: 10x Genomics


title: p007-bdf1_025_rna


title: Islet_168 (SAMN29494287), GEX

description: 10x Genomics


title: Week 3 VSV, cLN, rep 3

description: BCR sequencing


title: NCF_01


title: Week 3 VSV, cLN, rep 1

description: BCR sequencing


title: Week 3 VSV, cLN, rep 2

description: BCR sequencing


title: mg_invivo_ascl1_oe

city: Seattle

first: Amy

middle: Moreda

last: Tresenrider

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: single Cell RNA sequencing library prepared from whole cells using a 10x 3' v3.1 Dual Index Gene Expression kit.

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
See SAMPLES
Assembly: GRCm38
Supplementary files format and content: Count Matrix (RDS file), Cell Metadata (comma separated values- .csv), Gene Metadata (comma separated values- .csv), Monocle3 cds object (RDS file), Count matrix from 10x (.mtx),

source_name: FACs sorted Muller glia from dissected retina

growth_protocol: The Muller glia were cultured as in Todd et al. Sci Adv. (2022)

extract_protocol:
Retinas were harvested and those cells expressing GFP were collected by FACs 21 days after NMDA administration.
Sorted cells were subjected to the standard 10x workflow for Single Cell 3' v3.1 Dual Index Gene Expression kit.

treatment_protocol: To induce Ascl1 in MG in vivo, tamoxifen was given intraperitoneally at 1.5mg per 100μl for four consecutive days. Intravitreal injections were performed on isoflurane anesthetized mice using a 32-gauge Hamilton syringe. All intravitreal injections were done at 2μl, and contained either NMDA (Sigma, #M3262-100MG) or TSA (Tocris #1406/1). NMDA injections were done in 1μl volume at a concentration of 100mM. TSA injections were given in 1μl volume at a concentration of 1μg/μl.

value: Glast-CreER:LNL-tTA;TetO-mAscl1-ires-GFP from mixed backgrounds of C57BL/6 and B6SJF1


title: Islet_150 (SAMN21845647), GEX

description: 10x Genomics


title: p007-bdf1_024_rna


title: p007-bdf1_021_rna


title: Week 3 VSV, skull BM, rep 4

description: BCR sequencing

source_name: Skull bone marrow

value: Skull bone marrow


title: Islet_162 (SAMN25980818), GEX

description: 10x Genomics


title: Islet_148, SAMN20926064, 24 Hr Cytokines

data_processing:
The paired-end (2x150 bp) RNA-seq FASTQ files for each islet were aligned against the human genome (GRCh38/hg38) using STAR.
Raw counts were generated using QoRTs.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file (ERS_RNA-seq_Raw_Count_Matrix.txt) that includes the raw count matrix for all the 24 Hr DMSO and 24 Hr Thapsigargin treated samples.
Supplementary files format and content: Tab-delimited text file (CYT_RNA-seq_Raw_Count_Matrix.txt) that includes the raw count matrix for all the 24 Hr Untreated and 24 Hr Cytokines treated samples.

extract_protocol:
Total RNA was extracted and purified from 2,000–3,000 IEQs using TRIzol (Life Technologies). ERCC Mix 1 or Mix 2 spike-ins were then randomly added to each sample (Thermo Fisher, catalog #4456740).
Human islet RNA-seq libraries were prepared from total RNA using the stranded TruSeq kit (Illumina).

value: 24 Hr Cytokines


title: Islet_150 (SAMN21845647), HTO

description: 10x Genomics


title: mg_timecourse_ascl1_oe

description: single nucleus RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Brotman Baty sci-RNA-seq demultiplexing and processing pipelines (https://github.com/bbi-lab/bbi-dmux; https://github.com/bbi-lab/bbi-sci). The hashes were incorporated into the output and further analysis was performed using Monocle3
See SAMPLES
Assembly: GRCm38
Supplementary files format and content: Count Matrix (RDS file), Cell Metadata (comma separated values- .csv), Gene Metadata (comma separated values- .csv), Monocle3 cds object (RDS file), Count matrix from 10x (.mtx),

source_name: Muller glia from dissected retina

extract_protocol:
In a 24-well plate, the cells were  rinsed with 200ul HBSS, followed by a 1 minute room-temperature incubation with 200ul of Accutase. Accutase was removed, and the cells were incubated at 37°C for 5 minutes. Cells were then resuspended in 200 uL of 1% tet-FBS-reduced growth medium with a wide-bore P200 pipette tip to isolate single cells.
The library was prepared by the original sci-RNA-seq2 protocol  (Cao et al., 2017) in combination with hashing as presented by sci-Plex (Srivatsan et al., 2019). Nuclei were fixed in the presence of a barcoded polyA DNA oligo. A reverse transcription reaction with barcoded RT primers captured 3'-polyAdenylated transcripts and the barcoded oligo. Using FACs, nuclei were sorted into wells of 96-well plates where second strand synthesis was followed by tagmentation of dsDNA. PCR was performed with barcoded primers and the library was size-selected. The unique combination of barcodes in the RT and PCR steps enable the reconstruction of individual cells in silico.

treatment_protocol: Retinal cells were dissociated,  cultured until confluent (~7 days), and then frozen. Cells were thawed and cultured for 1-7 days before being induced to express Ascl1 through 2 ug/mL of doxycycline for 1-5 days before being harvested.

value: Muller glia from dissected retina

value: rtTa:tetO-Ascl1-ires-GFP (a gift from M. Nakafuku, U. Cincinnati)


title: NCF_04

value: Nursed

value: C

value: 22 day old


title: NCF_02

value: Amygdala


title: p007-bdf1_023_rna

data_processing:
RNA reads were mapped to mm10 transcriptome reference using hisat2.
Gene expression were quantified using RSEM.
Hi-C reads were processed and analysed using Dip-C and hickit package.
We generated three replicate structures (_1.3dg.gz, _2.3dg.gz and _3.3dg.gz) per cell reconstructed with different random seeds (1-3).
We pooled Hi-C samples for each group.
Assembly: mm10
Supplementary files format and content: .hic
Supplementary files format and content: .3dg
Supplementary files format and content: .allValidPairs.txt.gz

value: mouse olfactory epithelium

value: postnatal day 7


title: Week 3 VSV, skull BM, rep 5

description: BCR sequencing

value: day 21


title: p007-bdf1_022_rna


title: mg_pulse_ascl1_oe

extract_protocol:
In a 48-well plate, the cells were  rinsed with 200ul HBSS and then 200ul of Accutase. Accutase was removed, and the cells were incubated at 37°C for 5 minutes. Cells were then resuspended in 200 uL of 1% tet-FBS-reduced growth medium with a wide-bore P200 pipette tip to isolate single cells.
The library was prepared by the original sci-RNA-seq2 protocol  (Cao et al., 2017) in combination with hashing as presented by sci-Plex (Srivatsan et al., 2019). Nuclei were fixed in the presence of a barcoded polyA DNA oligo. A reverse transcription reaction with barcoded RT primers captured 3'-polyAdenylated transcripts and the barcoded oligo. Using FACs, nuclei were sorted into wells of 96-well plates where second strand synthesis was followed by tagmentation of dsDNA. PCR was performed with barcoded primers and the library was size-selected. The unique combination of barcodes in the RT and PCR steps enable the reconstruction of individual cells in silico.

treatment_protocol: Retinal cells were dissociated,  cultured until confluent (~7 days), and then frozen. Cells were thawed and cultured for 1-2 days before being induced to express Ascl1 through 2 ug/mL of doxycycline for 1-5 days. Cells were harvested 5 days from the start of Ascl1 expression.


title: Week 3 VSV, skull BM, rep 3

description: BCR sequencing


title: Islet_149, SAMN21399152, 24 Hr Cytokines

value: Pancreatic Islets


title: p007-bdf1_017_rna

extract_protocol:
The main olfactory epithelium was dissected and minced to small pieces, then was dissociated into single cell suspension with the Papain Dissociation System (Worthington Biochemical, Cat. #LK003150) at 37°C for 15 min, during incubation, titration every 5 min with wide-bore pipette tip according to previously described2. Then filtered with 30 μm strainer (MACS), then wash twice with ice-cold 1 x PBS.
simultaneous 3D genome and gene expression by LiMCA
Smart-seq2 for LiMCA RNA library; Dip-C protocol for LiMCA Hi-C library

value: WT


title: Week 3 VSV, skull base, rep 5

description: BCR sequencing

source_name: Skull base

value: Skull base


title: p007-bdf1_020_rna


title: mg_screen_ascl1_oe

treatment_protocol: Retinal cells were dissociated,  cultured until confluent (~7 days), and then frozen. Cells were thawed and cultured for 1-2 days before being induced to express Ascl1 through 2 ug/mL of doxycycline for 1-5 days. At the same time, cells were also exposed to one of 92 different compounds from the Tocriscreen Stem Cell Library at a dose of 0.1 uM, 1 uM, or 10 uM. Cells were harvested 5 days from the start of Ascl1 expression + drug treatment.


title: Islet_147, SAMN20923891, 24 Hr Cytokines


title: p007-bdf1_019_rna


title: Islet_103, SAMN14331402, 24 Hr Cytokines


title: Week 3 VSV, skull BM, rep 2

description: BCR sequencing


title: Islet_146, SAMN20821183, 24 Hr Cytokines


title: p007-bdf1_015_rna


title: Islet_99, SAMN14206475, 24 Hr Cytokines


title: Week 3 VSV, skull BM, rep 1

description: BCR sequencing


title: p007-bdf1_018_rna


title: Week 3 VSV, skull base, rep 2

description: BCR sequencing


title: p007-bdf1_016_rna


title: Week 3 VSV, skull base, rep 4

description: BCR sequencing


title: Week 3 VSV, skull base, rep 1

description: BCR sequencing


title: E95_Brd4_cKO2 (HiSeq4000)

city: San Francisco

first: Angelo

last: Pelonero

state: CA

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

description: Single cell transcriptomes from cardiogenic region from E9.5 Brd4 flox homozygous; Mef2c-AHF-Cre heterozygous mouse embryo

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite (3.0.2) from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v3 according to specifications in the tutorials (https://satijalab.org/seurat/pbmc3k_tutorial.html)
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene-cellbarcode expression matrix in csv format

source_name: Embryonic mouse heart at E9.5

growth_protocol: Timed matings were set up between male mice that were compound heterozygous for the Brd4 floxed allele and Mef2c-AHF-cre allele and Brd4 floxed homozygous female mice. Morning of plug detection was considered E0.5 and embryos were harvested at embryonic day (E)9.5

extract_protocol:
35ul of single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN- 1000121) and Chromium i7 Multiplex Kit (PN-120262).

treatment_protocol: Embryos were dissected in PBS and 1% FBS on ice. Cardiogenic tissue regions were microdissected and dissociated in 200ul TryplE for 5 minutes at 37C followed by brief trituration and incubation for an additional 5 minutes. TryplE was quenched with 600ul PBS/1% FBS and centrifuged at 150 rcf for 3 minutes and resuspended in 35ul of PBS/1% FBS

value: Embryonic mouse heart at E9.5

value: Brd4 flox/flox; Mef2c-AHF-cre

tag: specific heart region

value: Cardiogenic region

tag: additional cell lineages present in dataset

value: Non-cardiac mesoderm, ectoderm and endoderm


title: Islet_100, SAMN14217400, 24 Hr Cytokines

value: 24 Hr Cytokines


title: Week 1 VSV, spleen, rep 5

description: BCR sequencing

tag: tissue

value: Spleen

value: day 7


title: p007-bdf1_012_rna


title: Week 3 VSV, skull base, rep 3

description: BCR sequencing

tag: cell line


title: E95_Brd4_flox2 (HiSeq4000)

description: Single cell transcriptomes from cardiogenic region from E9.5 Brd4 flox homozygous mouse embryo

value: Brd4 flox/flox


title: Islet_97, SAMN14121359, 24 Hr Cytokines

tag: cell type


title: p007-bdf1_014_rna

tag: genotype


title: Islet_144, SAMN20523746, 24 Hr Cytokines


title: Week 1 VSV, spleen, rep 4

description: BCR sequencing


title: Islet_96, SAMN14120450, 24 Hr Cytokines


title: p007-bdf1_013_rna

tag: age


title: E95_Brd4_cKO1 (HiSeq4000)

tag: strain


title: p007-bdf1_011_rna

tag: treatment


title: Islet_93, SAMN13938639, 24 Hr Cytokines


title: Islet_94, SAMN13972304, 24 Hr Cytokines


title: p007-bdf1_010_rna


title: E95_Brd4_flox1 (HiSeq4000)


title: Islet_95, SAMN14085642, 24 Hr Cytokines


title: Islet_92, SAMN13926317, 24 Hr Cytokines


title: p007-bdf1_008_rna


title: co-SHI-B3 (ATAC-seq)

city: shanghai

first: deng

middle: li

last: Hong

address: 280 chongqing south road

institute: shanghai jiao tong univerisity

data_processing:
All reads were aligned to the mm 10 genomes Burrows-Wheeler Aligner mem after adapter sequences were trimmed by Trim_Galore. Low-quality reads were filtered. PCR duplicates and reads mapped to the mitochondrial or chrY were removed.
Peak calling was performed using MACS2 with options -f BAM, -g mm, --nomodel, --shift -100 and –extsize 200. The samples were normalised using bamCoverage function from deepTools to visualise the signal in IGV.
The read count matrix was generated using deepTools with 10 kb bins applied to the genome. Log (FPKM+1) was used for analysing the overall similarity/dissimilarity among samples.
A principal component analysis was conducted using Diffbind with all samples across the haematopoietic development.
The motifs were determined in each differential peak using HOMER and top-ranked significant motifs were selected in each differential peak
Genome_build: mm10
Supplementary_files_format_and_content: Peak calling was performed using MACS2, The motifs were determined in each differential peak using HOMER

source_name: HSPC

extract_protocol:
HSPCs were lysed in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 10 min and spun at 4 °C for nuclear preparations. The supernatant was discarded. Nuclei were then incubated with Tn5 transposome and tagmentation buffer at 37 °C for 30 min (Vazyme Biotech)
The tagmentation products were purified and amplified by polymerase chain reaction (PCR). Amplification was achieved with 10 cycles by using the following conditions: 72 °C for 5 min; 98 °C for 30 s; thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; and 72 °C for 5 min. Libraries were purified with a PCR purification kit (Qiagen) and fragments were enriched with 0.5× and 1.0× VAHTS DNA Clean Beads (Vazyme Biotech) after the amplification.

treatment_protocol: E12.5 FL-HSPCs were cultured with E16.5 hepatocytes-conditioned media (co-SHI) or basic media (SHI) , after 2 hours, the HSPCs were collected for ATAC seq.

tag: developmental stage

value: LSK


title: Islet_86, SAMN13515839, 24 Hr Cytokines


title: Week 1 VSV, spleen, rep 1

description: BCR sequencing


title: Week 1 VSV, spleen, rep 3

description: BCR sequencing


title: Week 1 VSV, spleen, rep 2

description: BCR sequencing


title: co-SHI-B2 (ATAC-seq)


title: p007-bdf1_007_rna


title: co-SHI-B1 (ATAC-seq)


title: Week 1 VSV, sinus, rep 5

description: BCR sequencing

value: Dural venous sinus


title: Islet_82, SAMN13186657, 24 Hr Cytokines


title: Week 1 VSV, sinus, rep 4

description: BCR sequencing


title: MRC5_CSC_R1

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

institute: Inserm 1052

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. After fragmentation 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K v2  Microarrays (Agilent-026655) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried briefly in acetonitrile.

scan_protocol: Whole Human Genome Microarrays 4x44K v2 (Agilent Technologies)  were scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).Fluorescent signals were extracted and normalized with the Feature Extraction software version 10.5.1.1 (Agilent Technologies),

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MRC5 fibroblast treated with CSC during 6 days

label_protocol: cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's recommandations, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MRC5 normal human fibroblasts (ATCC) were cultured in Dulbecco′s modified Eagle′s medium (DMEM, Life Technologies) with GlutaMax and supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin/streptomycin (ThermoFisher Scientific). Cells were maintained at 37°C under a 5% CO2 atmosphere. All experiments were carried out on cells at early passages (between 22 and 28).

extract_protocol: Total RNA was extracted from MRC5 cells using NucleoSpin® RNA (Macherey Nalgen) following the manufacturer's recommendations

treatment_protocol: MRC5 cells were cultured with DMSO or Cigaret Smoke Condensate (CSC) at 40µg/ml during 6 days

value: Normal human fibroblast cells


title: MRC5_CTRL_R3

source_name: MRC5 fibroblast treated with DMSO


title: p007-bdf1_006_rna

city: Beijing

first: Xiaoliang

last: Xie

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

value: mouse olfactory epithelium


title: Islet_81, SAMN13134368, 24 Hr Cytokines


title: p007-bdf1_005_rna

value: postnatal day 7


title: p007-bdf1_009_rna


title: Week 1 VSV, sinus, rep 2

description: BCR sequencing


title: Week 1 VSV, sinus, rep 3

description: BCR sequencing


title: SHI-C1 (ATAC-seq)


title: p007-bdf1_003_rna


title: Week 1 VSV, sinus, rep 1

description: BCR sequencing


title: Islet_75, SAMN12833535, 24 Hr Cytokines


title: 8w BM3 (ATAC-seq)


title: MRC5_CTRL_R1


title: Islet_149, SAMN21399152, 24 Hr Untreated

value: 24 Hr Untreated


title: 8w BM2 (ATAC-seq)

value: 8 week


title: p007-bdf1_002_rna

value: WT


title: Islet_148, SAMN20926064, 24 Hr Untreated

value: Pancreatic Islets


title: MRC5_CSC_R2


title: SHI-C3 (ATAC-seq)


title: MRC5_CTRL_R2


title: Islet_147, SAMN20923891, 24 Hr Untreated


title: MRC5_CSC_R3


title: Week 1 VSV, hub, rep 4

description: BCR sequencing

value: Rostral-rhinal hub


title: p007-bdf1_001_rna


title: Week 1 VSV, hub, rep 5

description: BCR sequencing


title: Week 1 VSV, hub, rep 1

description: BCR sequencing


title: 8w BM1 (ATAC-seq)


title: p007-bc_020_rna

value: bc


title: SHI-C2 (ATAC-seq)


title: 6w BM3 (ATAC-seq)

value: 6 week


title: Islet_146, SAMN20821183, 24 Hr Untreated


title: Islet_78, SAMN12924398, 24 Hr Cytokines


title: Week 1 VSV, cLN, rep 5

description: BCR sequencing

value: Cervical lymph node


title: p007-bc_019_rna


title: p007-bdf1_004_rna


title: Islet_144, SAMN20523746, 24 Hr Untreated


title: 6w BM2 (ATAC-seq)


title: Week 1 VSV, cLN, rep 4

description: BCR sequencing


title: p007-bc_018_rna


title: 6w BM1 (ATAC-seq)


title: Islet_103, SAMN14331402, 24 Hr Untreated


title: Week 1 VSV, cLN, rep 3

description: BCR sequencing


title: Week 1 VSV, cLN, rep 2

description: BCR sequencing


title: 4w BM2 (ATAC-seq)

value: 4 week


title: p007-bc_016_rna


title: 4w BM3 (ATAC-seq)


title: p007-bc_017_rna


title: Islet_100, SAMN14217400, 24 Hr Untreated


title: Islet_99, SAMN14206475, 24 Hr Untreated


title: 4w BM1 (ATAC-seq)


title: Islet_97, SAMN14121359, 24 Hr Untreated


title: Islet_96, SAMN14120450, 24 Hr Untreated


title: p007-bc_014_rna


title: p007-bc_015_rna


title: p007-bc_013_rna


title: Week 1 VSV, skull BM, rep 5

description: BCR sequencing

value: Skull bone marrow


title: 3w BM1 (ATAC-seq)

value: 3 week


title: Week 1 VSV, cLN, rep 1

description: BCR sequencing

value: day 7


title: Week 1 VSV, skull BM, rep 4

description: BCR sequencing


title: 3w BM2 (ATAC-seq)

value: LSK


title: Islet_95, SAMN14085642, 24 Hr Untreated


title: 1w BM3 (ATAC-seq)

value: 1 week


title: Week 1 VSV, skull BM, rep 3

description: BCR sequencing


title: p007-bc_012_rna


title: Islet_94, SAMN13972304, 24 Hr Untreated


title: Week 1 VSV, skull BM, rep 2

description: BCR sequencing


title: p007-bc_011_rna


title: p007-bc_010_rna


title: 1w BM2 (ATAC-seq)


title: p007-bc_009_rna


title: 1w BM1 (ATAC-seq)


title: Week 1 VSV, skull base, rep 3

description: BCR sequencing

value: Skull base


title: Islet_92, SAMN13926317, 24 Hr Untreated


title: Week 1 VSV, skull BM, rep 1

description: BCR sequencing


title: Week 1 VSV, skull base, rep 5

description: BCR sequencing


title: p007-bc_008_rna

value: mouse olfactory epithelium


title: Week 1 VSV, skull base, rep 2

description: BCR sequencing


title: p007-bc_007_rna

value: postnatal day 7


title: Islet_86, SAMN13515839, 24 Hr Untreated

value: 24 Hr Untreated


title: Perinatal BM1 (ATAC-seq)

value: Perinatal


title: Islet_81, SAMN13134368, 24 Hr Untreated


title: p007-bc_006_rna

value: WT


title: Perinatal BM2 (ATAC-seq)


title: Islet_82, SAMN13186657, 24 Hr Untreated

value: Pancreatic Islets


title: p007-bc_005_rna


title: E16.5 FL3 (ATAC-seq)


title: Islet_78, SAMN12924398, 24 Hr Untreated


title: Naïve, spleen, rep 5

description: BCR sequencing

value: Spleen

value: naïve (day 0)


title: Islet_75, SAMN12833535, 24 Hr Untreated


title: Islet_93, SAMN13938639, 24 Hr Untreated


title: Islet_149, SAMN21399152, 24 Hr Thapsigargin

value: 24 Hr Thapsigargin


title: E16.5 FL1 (ATAC-seq)


title: p007-bc_004_rna

value: bc


title: E16.5 FL2 (ATAC-seq)


title: Week 1 VSV, skull base, rep 1

description: BCR sequencing


title: Naïve, spleen, rep 2

description: BCR sequencing


title: p007-bc_003_rna


title: Islet_147, SAMN20923891, 24 Hr Thapsigargin


title: p007-bc_002_rna


title: Naïve, spleen, rep 1

description: BCR sequencing


title: p007-bc_001_rna


title: Islet_148, SAMN20926064, 24 Hr Thapsigargin


title: p003-bdf1_041_rna

value: postnatal day 3


title: E12.5 FL1 (ATAC-seq)


title: Naïve, spleen, rep 4

description: BCR sequencing


title: E12.5 PL3 (ATAC-seq)


title: Naïve, sinus, rep 5

description: BCR sequencing

value: Dural venous sinus


title: Islet_144, SAMN20523746, 24 Hr Thapsigargin


title: Islet_146, SAMN20821183, 24 Hr Thapsigargin


title: Perinatal BM3 (ATAC-seq)


title: Naïve, sinus, rep 4

description: BCR sequencing


title: E12.5 PL2 (ATAC-seq)


title: Islet_86, SAMN13515839, 24 Hr Thapsigargin


title: Naïve, sinus, rep 3

description: BCR sequencing


title: p003-bdf1_039_rna


title: Naïve, spleen, rep 3

description: BCR sequencing


title: E12.5 PL1 (ATAC-seq)


title: Islet_82, SAMN13186657, 24 Hr Thapsigargin


title: p003-bdf1_038_rna


title: E12.5 FL3 (ATAC-seq)


title: E12.5 FL2 (ATAC-seq)


title: Islet_81, SAMN13134368, 24 Hr Thapsigargin


title: Naïve, sinus, rep 1

description: BCR sequencing


title: Islet_78, SAMN12924398, 24 Hr Thapsigargin


title: p003-bdf1_037_rna


title: 8w BM3 (RNA-seq)

data_processing:
Trim Galore was used to deal with raw data with the parameters “--quality 20 --fastqc --length 20 --stringency 1”
The clean reads were then aligned to the reference genome of mouse (GRCm38) using STAR v2.7 in the 1-pass mode with the parameters “–outSAMtype BAM SortedByCoordinate.
The aligned reads were assigned to genes using GENCODE annotations and htseq-count version 0.6.1p1 with the parameters “-m union -s no”.
Counts were normalised to FPKM and Log (FPKM+1)
Genome_build: mouse (GRCm38)
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

extract_protocol:
Total RNA was isolated from highly purified HSPCs using Tri Pure Isolation Reagent (Roche), as recommended by the manufacturer
The high-quality samples were selected for library construction using the Illumia Truseq RNA Pre kit.

value: 8 week

value: HSPC


title: p003-bdf1_040_rna


title: 8w BM2 (RNA-seq)


title: p003-bdf1_036_rna


title: 8w BM1 (RNA-seq)


title: p003-bdf1_035_rna


title: p003-bdf1_034_rna


title: 6w BM3 (RNA-seq)

value: 6 week


title: Naïve, hub, rep 5

description: BCR sequencing

value: Rostral-rhinal hub


title: Islet_75, SAMN12833535, 24 Hr Thapsigargin


title: p003-bdf1_033_rna


title: Naïve, hub, rep 3

description: BCR sequencing


title: Naïve, hub, rep 4

description: BCR sequencing


title: 6w BM2 (RNA-seq)


title: 6w BM1 (RNA-seq)


title: Islet_149, SAMN21399152, 24 Hr DMSO

value: 24 Hr DMSO


title: 4w BM3 (RNA-seq)

value: 4 week


title: Naïve, hub, rep 1

description: BCR sequencing


title: p003-bdf1_032_rna

value: mouse olfactory epithelium


title: Naïve, sinus, rep 2

description: BCR sequencing


title: Naïve, hub, rep 2

description: BCR sequencing


title: Islet_146, SAMN20821183, 24 Hr DMSO


title: Islet_147, SAMN20923891, 24 Hr DMSO


title: p003-bdf1_031_rna


title: Naïve, cLN, rep 5

description: BCR sequencing

value: Cervical lymph node


title: Naïve, cLN, rep 4

description: BCR sequencing


title: 4w BM2 (RNA-seq)


title: p003-bdf1_030_rna


title: 4w BM1 (RNA-seq)


title: Islet_86, SAMN13515839, 24 Hr DMSO


title: Naïve, cLN, rep 3

description: BCR sequencing


title: Islet_148, SAMN20926064, 24 Hr DMSO


title: Naïve, cLN, rep 2

description: BCR sequencing


title: 3w BM2 (RNA-seq)

value: 3 week


title: 3w BM3 (RNA-seq)


title: p003-bdf1_028_rna

value: WT


title: Islet_82, SAMN13186657, 24 Hr DMSO

value: Pancreatic Islets


title: Naïve, cLN, rep 1

description: BCR sequencing


title: 3w BM1 (RNA-seq)


title: Islet_81, SAMN13134368, 24 Hr DMSO


title: p003-bdf1_026_rna


title: 1w BM3 (RNA-seq)

value: 1 week


title: Islet_75, SAMN12833535, 24 Hr DMSO


title: p003-bdf1_025_rna


title: 1w BM2 (RNA-seq)


title: Islet_78, SAMN12924398, 24 Hr DMSO


title: Naïve, skull BM, rep 4

description: BCR sequencing

value: Skull bone marrow

value: naïve (day 0)


title: Naïve, skull BM, rep 3

description: BCR sequencing


title: Islet_99, SAMN14206475, 24 Hr Cytokines

data_processing:
The paired-end (2x150 bp) ATAC-seq FASTQ files for each islet were trimmed using Trimmomatic.
Alignment was performed against the human genome (GRCh38/hg38) using BWA-MEM.
Duplicate reads were removed and the remaining reads were shifted by 9bp to account for the binding site of Tn5.
Technical replicates were merged using SAMtools.
Peaks were called using MACS2.
Separate consensus peaksets for ER stress (ERS) and pro-inflammatory cytokine (CYT) samples were generated by considering peaks that were present in at least 2 samples, and those peaks that mapped to ENCODE Exclusion List regions were excluded using DiffBind.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file (ERS_ATAC-seq_Consensus_Peakset_Raw_Counts.txt) that includes the raw counts for the consensus peakset generated using all the 24 Hr DMSO and 24 Hr Thapsigargin treated samples.
Supplementary files format and content: Tab-delimited text file (CYT_ATAC-seq_Consensus_Peakset_Raw_Counts.txt) that includes the raw counts for the consensus peakset generated using all the 24 Hr Untreated and 24 Hr Cytokines treated samples.

extract_protocol:
50 islet equivalents (50,000 cells) per sample were transposed in triplicate using 2.5 μL Transposase (Illumina). Sample purification was then performed using the Qiagen Minelute kit.
Human islet ATAC-seq libraries were prepared following the Active motif ATAC prep kit (Active motif catalog# 53150).

value: 24 Hr Cytokines


title: Islet_144, SAMN20523746, 24 Hr DMSO


title: p003-bdf1_024_rna

value: postnatal day 3


title: 1w BM1 (RNA-seq)


title: Naïve, skull BM, rep 2

description: BCR sequencing


title: Islet_153, SAMN22818629, 24 Hr Cytokines


title: Perinatal BM3 (RNA-seq)

value: Perinatal


title: p003-bdf1_023_rna


title: p003-bdf1_029_rna


title: p003-bdf1_022_rna


title: Islet_152, SAMN22021186, 24 Hr Cytokines


title: Naïve, skull BM, rep 1

description: BCR sequencing


title: p003-bdf1_027_rna


title: Naïve, skull BM, rep 5

description: BCR sequencing


title: p003-bdf1_021_rna


title: Islet_125, SAMN17035384, 24 Hr Cytokines


title: Perinatal BM1 (RNA-seq)


title: Naïve, skull base, rep 5

description: BCR sequencing

value: Skull base


title: Islet_151, SAMN21855451, 24 Hr Cytokines


title: Naïve, skull base, rep 4

description: BCR sequencing


title: p003-bdf1_020_rna


title: Islet_106, SAMN15314807, 24 Hr Cytokines


title: E16.5 FL3 (RNA-seq)

value: HSPC


title: Naïve, skull base, rep 3

description: BCR sequencing


title: Islet_99, SAMN14206475, 24 Hr Untreated

value: 24 Hr Untreated


title: p003-bdf1_019_rna


title: p003-bdf1_018_rna


title: Naïve, skull base, rep 2

description: BCR sequencing


title: E16.5 FL1 (RNA-seq)


title: Islet_153, SAMN22818629, 24 Hr Untreated


title: Naïve, skull base, rep 1

description: BCR sequencing


title: Islet_152, SAMN22021186, 24 Hr Untreated


title: p003-bdf1_017_rna


title: E12.5 FL3 (RNA-seq)


title: Perinatal BM2 (RNA-seq)


title: E12.5 FL2 (RNA-seq)


title: p003-bdf1_016_rna


title: Islet_151, SAMN21855451, 24 Hr Untreated


title: E12.5 FL1 (RNA-seq)


title: FaDu-2

city: Shanghai

first: Lixiao

address: No.85 Wujin road, Hongkou district, Shnaghai,200080, China

department: Otorhinolaryngology head and neck surgery

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: FaDu cell line

extract_protocol:
Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hypopharyngeal tumor cell

value: FaDu

tag: shRNA


title: shNSUN2-3


title: Islet_125, SAMN17035384, 24 Hr Untreated


title: p003-bdf1_015_rna


title: shNSUN2-2


title: FaDu-3


title: E12.5 PL3 (RNA-seq)


title: Islet_151, SAMN21855451, 24 Hr Thapsigargin

value: 24 Hr Thapsigargin


title: E12.5 PL2 (RNA-seq)


title: p003-bdf1_012_rna

value: mouse olfactory epithelium


title: p003-bdf1_013_rna


title: E16.5 FL2 (RNA-seq)


title: p003-bdf1_014_rna


title: p003-bdf1_011_rna


title: E12.5 PL1 (RNA-seq)


title: shNSUN2-1


title: Islet_148, SAMN20926064, 24 Hr Thapsigargin