title: 10x lib 70, donor N282, cytopenia

description:
Library name: 10x_lib_70_donor_N282_blood_sample_175
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 69, donor N280, MDS

status: Public on Jan 06 2025

type: SRA

city: Rehovot

first: Liran

last: Shlush

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description:
Library name: 10x_lib_69_donor_N280_blood_sample_173
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model

library_source: transcriptomic single cell

data_processing:
Count matrices were generated using 10x Genomics' Cell Ranger v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
As each 10x scRNA library contained pooled cells of multiple individuals, both Vireo (https://github.com/single-cell-genetics/vireo) and Souporcell (https://github.com/wheaton5/souporcell) were used (on each 10x library separately) to cluster cells based on SNPs found in the sequenced RNA. Cells that were identified as doublets by Vireo or Souporcell were discarded. Resulting clusters were matched to targeted genotype data obtained for each donor.
Cells with high mitochondrial content (>20%), platelet signature (PPBP > 0.2%), neutrophil signature (LCN2, CAMP, LTF), erythrocyte signature (HBB, HBA1, HBA2), or with low signature of nuclear RNAs were excluded. As part of additional doublet detection, cells were excluded if their UMI count was higher than 2.5-fold of their cluster median computed (thereby compensating for variable cell sizes across types), as well as if they exhibited high expression of both monocyte and MEBEMP gene programs.
Assembly: GRCh38-3.0.0
Supplementary files format and content: h5ad file (https://anndata.readthedocs.io/en/stable/) containing count matrix and cell metadata.

molecule: polyA RNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Peripheral blood was drawn into lithium-heparin tubes. PBMCs were isolated via Ficoll, using Lymphoprep filled Sepmate tubes (StemCell technologies), followed by CD34 magnetic bead-based enrichment using the EasySep human CD34 positive selection kit II (StemCell technologies). 3-6 individual samples were pooled on each experiment day such that CD34-enrichment was performed on the entire pool of PBMCs produced. Few samples were not pooled due to logistical issues of timing blood donations, as sampling was restricted to fresh blood.
Single cell RNA libraries were generated using the 10x Genomics scRNA-seq platform (Chromium Next Gem single cell 3’ reagent kit V3.1) according to the manufacturer's instructions, except that we "super-loaded" each chromium chip lane, loading cells at a significantly higher concentration than recommended, with an expected yield of ~20-25k single cells.

tag: tissue

value: peripheral blood

tag: Sex

value: female

tag: cell type

value: PBMC

tag: age

tag: disease state

value: MDS

tag: batch


title: 10x lib 65, donor N272, normal

description:
Library name: 10x_lib_65_donor_N272_blood_sample_168
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model

value: normal


title: 10x lib 60, donor N260, normal

description:
Library name: 10x_lib_60_donor_N260_blood_sample_161
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model

value: male


title: 10x lib 77, donor N319, normal

description:
Library name: 10x_lib_77_donor_N319_blood_sample_200
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 65, donor N79, normal

description:
Library name: 10x_lib_65_donor_N79_blood_sample_167
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 77, donor N318, normal

description:
Library name: 10x_lib_77_donor_N318_blood_sample_199
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 74, donor N308, normal

description:
Library name: 10x_lib_74_donor_N308_blood_sample_196
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 74, donor N307, normal

description:
Library name: 10x_lib_74_donor_N307_blood_sample_195
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 58, donor N251, MDS/MPN

description:
Library name: 10x_lib_58_donor_N251_blood_sample_159
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model

value: MDS/MPN


title: 10x lib 55, donor N257, MDS

description:
Library name: 10x_lib_55_donor_N257_blood_sample_157
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 76, donor N322, normal

description:
Library name: 10x_lib_76_donor_N322_blood_sample_203
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 55, donor N249, MDS

description:
Library name: 10x_lib_55_donor_N249_blood_sample_155
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 74, donor N306, normal

description:
Library name: 10x_lib_74_donor_N306_blood_sample_194
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 75, donor N251, MDS/MPN

description:
Library name: 10x_lib_75_donor_N251_blood_sample_193
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 73, donor N298, cytopenia

description:
Library name: 10x_lib_73_donor_N298_blood_sample_189
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model

value: cytopenia


title: 10x lib 48, donor N243, MDS/MPN

description:
Library name: 10x_lib_48_donor_N243_blood_sample_152
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 72, donor N55, normal

description:
Library name: 10x_lib_72_donor_N55_blood_sample_187
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 72, donor N292, normal

description:
Library name: 10x_lib_72_donor_N292_blood_sample_184
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 71, donor N290, normal

description:
Library name: 10x_lib_71_donor_N290_blood_sample_182
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 73, donor N296, cytopenia

description:
Library name: 10x_lib_73_donor_N296_blood_sample_188
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 71, donor N288, normal

description:
Library name: 10x_lib_71_donor_N288_blood_sample_180
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 71, donor N289, cytopenia

description:
Library name: 10x_lib_71_donor_N289_blood_sample_181
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 46, donor N239, cytopenia

description:
Library name: 10x_lib_46_donor_N239_blood_sample_148
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 46, donor N109, normal

description:
Library name: 10x_lib_46_donor_N109_blood_sample_147
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 77, donor N320, normal

description:
Library name: 10x_lib_77_donor_N320_blood_sample_201
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 45, donor N235, MDS/MPN

description:
Library name: 10x_lib_45_donor_N235_blood_sample_145
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 71, donor N287, cytopenia

description:
Library name: 10x_lib_71_donor_N287_blood_sample_179
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 70, donor N284, cytopenia

description:
Library name: 10x_lib_70_donor_N284_blood_sample_177
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 60, donor N259, normal

description:
Library name: 10x_lib_60_donor_N259_blood_sample_160
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 58, donor N250, MDS

description:
Library name: 10x_lib_58_donor_N250_blood_sample_158
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 53, donor N257, MDS

description:
Library name: 10x_lib_53_donor_N257_blood_sample_157
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 43, donor N175, normal

description:
Library name: 10x_lib_43_donor_N175_blood_sample_141
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 41, donor N228, cytopenia

description:
Library name: 10x_lib_41_donor_N228_blood_sample_140
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 44, donor N235, MDS/MPN

description:
Library name: 10x_lib_44_donor_N235_blood_sample_145
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 55, donor N122, normal

description:
Library name: 10x_lib_55_donor_N122_blood_sample_156
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 53, donor N249, MDS

description:
Library name: 10x_lib_53_donor_N249_blood_sample_155
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 40, donor N164, normal

description:
Library name: 10x_lib_40_donor_N164_blood_sample_138
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 53, donor N122, normal

description:
Library name: 10x_lib_53_donor_N122_blood_sample_156
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 51, donor N248, MDS

description:
Library name: 10x_lib_51_donor_N248_blood_sample_154
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 48, donor N179, normal

description:
Library name: 10x_lib_48_donor_N179_blood_sample_153
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 47, donor N179, normal

description:
Library name: 10x_lib_47_donor_N179_blood_sample_153
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 47, donor N243, MDS/MPN

description:
Library name: 10x_lib_47_donor_N243_blood_sample_152
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 48, donor N242, MDS

description:
Library name: 10x_lib_48_donor_N242_blood_sample_151
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 47, donor N242, MDS

description:
Library name: 10x_lib_47_donor_N242_blood_sample_151
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 46, donor N116, MDS

description:
Library name: 10x_lib_46_donor_N116_blood_sample_146
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 38, donor N211, MDS

description:
Library name: 10x_lib_38_donor_N211_blood_sample_132
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 42, donor N99, normal

description:
Library name: 10x_lib_42_donor_N99_blood_sample_144
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 46, donor N240, MDS/MPN

description:
Library name: 10x_lib_46_donor_N240_blood_sample_149
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 48, donor N241, MDS

description:
Library name: 10x_lib_48_donor_N241_blood_sample_150
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 36, donor N205, MDS

description:
Library name: 10x_lib_36_donor_N205_blood_sample_126
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 36, donor N204, MDS

description:
Library name: 10x_lib_36_donor_N204_blood_sample_125
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 43, donor N159, normal

description:
Library name: 10x_lib_43_donor_N159_blood_sample_143
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 47, donor N241, MDS

description:
Library name: 10x_lib_47_donor_N241_blood_sample_150
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 43, donor N91, cytopenia

description:
Library name: 10x_lib_43_donor_N91_blood_sample_142
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 42, donor N159, normal

description:
Library name: 10x_lib_42_donor_N159_blood_sample_143
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 42, donor N91, cytopenia

description:
Library name: 10x_lib_42_donor_N91_blood_sample_142
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 42, donor N175, normal

description:
Library name: 10x_lib_42_donor_N175_blood_sample_141
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 43, donor N99, normal

description:
Library name: 10x_lib_43_donor_N99_blood_sample_144
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 40, donor N165, cytopenia

description:
Library name: 10x_lib_40_donor_N165_blood_sample_139
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 40, donor N78, normal

description:
Library name: 10x_lib_40_donor_N78_blood_sample_137
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 33, donor N193, cytopenia

description:
Library name: 10x_lib_33_donor_N193_blood_sample_118
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 34, donor N189, cytopenia

description:
Library name: 10x_lib_34_donor_N189_blood_sample_119
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 39, donor N157, normal

description:
Library name: 10x_lib_39_donor_N157_blood_sample_135
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 40, donor N131, normal

description:
Library name: 10x_lib_40_donor_N131_blood_sample_136
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 38, donor N88, normal

description:
Library name: 10x_lib_38_donor_N88_blood_sample_134
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 38, donor N212, MDS

description:
Library name: 10x_lib_38_donor_N212_blood_sample_133
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 37, donor N181, MDS/MPN

description:
Library name: 10x_lib_37_donor_N181_blood_sample_131
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 32, donor N187, MDS

description:
Library name: 10x_lib_32_donor_N187_blood_sample_113
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 36, donor N206, cytopenia

description:
Library name: 10x_lib_36_donor_N206_blood_sample_127
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 37, donor N180, MDS

description:
Library name: 10x_lib_37_donor_N180_blood_sample_128
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 32, donor N186, MDS

description:
Library name: 10x_lib_32_donor_N186_blood_sample_112
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 35, donor N201, MDS

description:
Library name: 10x_lib_35_donor_N201_blood_sample_123
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 34, donor N194, MDS

description:
Library name: 10x_lib_34_donor_N194_blood_sample_120
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 34, donor N197, cytopenia

description:
Library name: 10x_lib_34_donor_N197_blood_sample_122
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 36, donor N203, MDS

description:
Library name: 10x_lib_36_donor_N203_blood_sample_124
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 34, donor N196, cytopenia

description:
Library name: 10x_lib_34_donor_N196_blood_sample_121
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 30, donor N181, MDS/MPN

description:
Library name: 10x_lib_30_donor_N181_blood_sample_105
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 30, donor N180, cytopenia

description:
Library name: 10x_lib_30_donor_N180_blood_sample_104
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 37, donor N207, cytopenia

description:
Library name: 10x_lib_37_donor_N207_blood_sample_129
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 37, donor N208, cytopenia

description:
Library name: 10x_lib_37_donor_N208_blood_sample_130
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 26, donor N171, normal

description:
Library name: 10x_lib_26_donor_N171_blood_sample_94
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 33, donor N192, MDS/MPN

description:
Library name: 10x_lib_33_donor_N192_blood_sample_117
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 33, donor N191, MDS

description:
Library name: 10x_lib_33_donor_N191_blood_sample_116
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 26, donor N168, normal

description:
Library name: 10x_lib_26_donor_N168_blood_sample_91
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 17, donor N91, cytopenia

description:
Library name: 10x_lib_17_donor_N91_blood_sample_64
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 22, donor N153, normal

description:
Library name: 10x_lib_22_donor_N153_blood_sample_75
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 32, donor N188, MDS

description:
Library name: 10x_lib_32_donor_N188_blood_sample_114
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 33, donor N190, cytopenia

description:
Library name: 10x_lib_33_donor_N190_blood_sample_115
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 31, donor N60, MDS/MPN

description:
Library name: 10x_lib_31_donor_N60_blood_sample_110
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 32, donor N185, MDS

description:
Library name: 10x_lib_32_donor_N185_blood_sample_111
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 31, donor N48, MDS/MPN

description:
Library name: 10x_lib_31_donor_N48_blood_sample_109
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 31, donor N209, MDS

description:
Library name: 10x_lib_31_donor_N209_blood_sample_108
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 31, donor N12, MDS

description:
Library name: 10x_lib_31_donor_N12_blood_sample_107
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 3, donor N81, cytopenia

description:
Library name: 10x_lib_3_donor_N81_blood_sample_9
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 2, donor N74, normal

description:
Library name: 10x_lib_2_donor_N74_blood_sample_4
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 2, donor N76, normal

description:
Library name: 10x_lib_2_donor_N76_blood_sample_5
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: monogyne, SB/SB, spring-reared gyne, ovary, BHM-9-2, biol rep 4

city: Griffin

first: Brendan

last: Hunt

state: GA

address: 1109 Experiment St

department: Entomology

country: USA

institute: University of Georgia

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (v0.6.5)
Trimmed sequence reads were aligned to SNVBB1 using STAR (v2.7.3a) via the 2-pass alignment procedure
Read count normalization was performed via CPM using edgeR
Assembly: GCA_009650705.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes CPM values for all samples in each tissue

organism: Solenopsis invicta

source_name: ovary

extract_protocol:
RNA was harvested using Rneasy micro kit (brains) and Rneasy minit kit (ovaries) with Dnase treatment. 1.6 ng and 8.0 ng of total RNA was used to make each brain and ovary library respectively.
Organs from a single gyne from each colony were used to prepare libraries following the Smart-seq2 protocol developed for low input RNA sequencing applications

value: ovary

tag: genotype

value: SB/SB

tag: treatment

value: Spring-reared


title: monogyne, SB/SB, spring-reared gyne, ovary, BHM-5-1, biol rep 5


title: 10x lib 3, donor N80, normal

description:
Library name: 10x_lib_3_donor_N80_blood_sample_7
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: monogyne, SB/SB, spring-reared gyne, ovary, BHM-10-1, biol rep 1


title: monogyne, SB/SB, spring-reared gyne, ovary, BHM-6-1, biol rep 8


title: monogyne, SB/SB, spring-reared gyne, ovary, BHM-7-1, biol rep 3


title: monogyne, SB/SB, spring-reared gyne, ovary, BHM-8-1, biol rep 7


title: monogyne, SB/SB, spring-reared gyne, brain, BHM-6-1, biol rep 8

source_name: brain

value: brain


title: monogyne, SB/SB, spring-reared gyne, brain, BHM-5-1, biol rep 5


title: 10x lib 3, donor N82, cytopenia

description:
Library name: 10x_lib_3_donor_N82_blood_sample_10
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: monogyne, SB/SB, spring-reared gyne, ovary, BHM-3-2, biol rep 6


title: 10x lib 17, donor N130, MDS

description:
Library name: 10x_lib_17_donor_N130_blood_sample_60
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: monogyne, SB/SB, spring-reared gyne, ovary, BHM-4-1, biol rep 2


title: monogyne, SB/SB, spring-reared gyne, brain, BHM-9-2, biol rep 4


title: monogyne, SB/SB, spring-reared gyne, brain, BHM-4-1, biol rep 2


title: monogyne, SB/SB, spring-reared gyne, brain, BHM-10-1, biol rep 1


title: monogyne, SB/SB, overwintered gyne, ovary, M18-7-3, biol rep 8

value: Overwintered


title: monogyne, SB/SB, overwintered gyne, ovary, M18-4-2, biol rep 6


title: monogyne, SB/SB, overwintered gyne, ovary, M18-2-3, biol rep 7


title: monogyne, SB/SB, overwintered gyne, ovary, M18-6-2, biol rep 5


title: monogyne, SB/SB, overwintered gyne, ovary, M18-1-2, biol rep 4


title: 10x lib 3, donor N78, normal

description:
Library name: 10x_lib_3_donor_N78_blood_sample_8
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 2, donor N77, normal

description:
Library name: 10x_lib_2_donor_N77_blood_sample_6
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: monogyne, SB/SB, overwintered gyne, ovary, M18-9-2, biol rep 3


title: monogyne, SB/SB, overwintered gyne, brain, M18-7-3, biol rep 8


title: monogyne, SB/SB, spring-reared gyne, brain, BHM-8-1, biol rep 7


title: monogyne, SB/SB, overwintered gyne, ovary, M18-3-2, biol rep 1


title: monogyne, SB/SB, overwintered gyne, brain, M18-2-3, biol rep 7


title: monogyne, SB/SB, overwintered gyne, brain, M18-4-2, biol rep 6


title: monogyne, SB/SB, spring-reared gyne, brain, BHM-3-2, biol rep 6


title: monogyne, SB/SB, spring-reared gyne, brain, BHM-7-1, biol rep 3


title: seedling, cry1_Blue_2

city: Shanghai

first: Yuhan

last: Hao

address: #300 Fenglin Road

country: China

institute: CAS Center for Excellence in Molecular Plant Science

data_processing:
Illumina software used for basecalling.
Sequenced reads were processed using Trimmomatic(Version0.36), The reads containing poly-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2(Version2.2.1.0).
Then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks TopHat（version:2.2.1）
FPKM and read counts valueof each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(Version1.18.0)(2012) functions estimateSizeFactors and nbinomTest.
Assembly: TAIR10.1_NCBI
Supplementary files format and content: Excel files include FPKM values for each Sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
total RNA was isolated using RNAiso Plus kit (Takara Bio, Shiga, Japan)
The RNA library generation process followed the manufacturer’s protocol for the Illumina TruseqTM RNA sample prep Kit

value: seedling

value: 10 DAY OLD

value: blue light


title: monogyne, SB/SB, overwintered gyne, brain, M18-9-2, biol rep 3


title: seedling, cry1_Dark_3

value: dark


title: seedling, cry1_Dark_2


title: seedling, cry1_Blue_1


title: monogyne, SB/SB, overwintered gyne, brain, M18-1-2, biol rep 4


title: monogyne, SB/SB, overwintered gyne, brain, M18-3-2, biol rep 1


title: seedling, WT_Blue_3

value: Wild-type


title: seedling, cry1_Blue_3


title: monogyne, SB/SB, overwintered gyne, ovary, M18-5-2, biol rep 2


title: monogyne, SB/SB, overwintered gyne, brain, M18-5-2, biol rep 2


title: seedling, WT_Blue_1


title: seedling, WT_Dark_3


title: seedling, WT_Blue_2


title: seedling, WT_Dark_2


title: seedling, WT_Dark_1


title: seedling, cry1_Dark_1


title: JC_2_99 (21PG55-3)

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

description: Gpig.scRNAseq.counts.all.tsv.gz

data_processing:
For the guinea pig single-cell RNA-Seq data, adapters and low-quality reads were removed using Trimgalore with default parameters. Subsequently, high-quality reads were aligned to the guinea pig Ensembl reference genome (v.Cavpor.3.0.105, Cavia porcellus, obtained from the Ensembl website)using the HISAT2 aligner (v 2.2.0) with default settings. Only uniquely mapped reads were retained for gene expression quantification. Raw read counts were tentatively quantified using featureCounts (v1.6.3) based on Ensembl reference annotation.
Considering the incomplete guinea pig reference annotation, we decided to update the guinea pig gene annotation using the following steps: 1. Ensembl transcripts belonging to “lincRNA”, “processed_pseudogene”, “protein_coding”, and “pseudogenes” were selected as the guided annotation. The mapping bam files were used as input for Stringtie (v1.3.3b) for each individual sample. After the initial assembly, the transcripts were merged using 'stringtie --merge' and compared with the guided annotation using 'gffcompare -r'. Transcripts that overlapped with multiple reference genes were excluded, as well as transcripts with a length less than 200 bp and 'class codes' identified by gffcompare equal to ‘e’, ‘s’, ‘x’ were removed in downstream analysis. Transcripts with class codes 'j', 'k', '=', 'm', 'n', 'o', 'p', 'y' were assigned to corresponding reference genes. Novel transcripts with no clear reference annotation were blasted against human and mouse transcripts of protein coding and lncRNA with parameters '-max_target_seqs 1 -outfmt 6 -num_threads 25 -evalue 1e-20 -strand plus -max_hsps 1' to find the most similar human or mouse reference genes. If there were no orthologous genes of matched reference genes in the guinea pig Ensembl annotation, they were added. Other novel transcripts with known orthologous genes in the guinea pig Ensembl annotation were reassigned to known annotated genes based on whether the novel transcripts fell within the nearby loci (± 3 kb) of the current annotation.
Assembly: Cavpor.3.0.105
Supplementary files format and content: tab-delimited text file include raw count for each Sample

organism: Cavia porcellus

source_name: embryo

growth_protocol: Hartley guinea pigs (Charles River Labs, Laval, Québec) were housed in the Animal Care Facility at the CRCHUM, maintained at 21 °C with 30-70 % humidity under a 12 h light cycle, and fed with Teklad Global Guinea Pig Diet 2040 pellets, water, and hay ad libitum.

extract_protocol:
Briefly, embryos were flushed from the oviduct (E3.5) or uterine horns (E4-E5.75) using 5-10 ml of warm M2 medium (MR-015-D, Sigma Aldrich) supplemented with 1 % Penicillin-Streptomycin (15130122, Life Technologies), washed and briefly kept in M2 drops covered with Ovoil TM (10029, Vitrolife) at the incubator at 5 % O2 5 % CO2 at 37.5 °C prior to being fixed in PFA 4 % for 15 min or single cell picking. E6 embryos were collected at E5.75 and incubated in similar conditions for 6 h to reach the desirable embryonic day, as implantation occurs around E6, and obtaining embryos by flushing the uterus was challenging.
Embryos collected from E3-E5.75 were obtained through the flushing female guinea pigs and placed in M2 drops under mineral oil until further processing. Zona pellucida was removed using tyrodes, and subsequent single-cell dissociation was achieved through enzymatic digestion with TrypLE Express (12604-013, Gibco, Life Technologies) followed by isolation using fine glass capillaries. Libraries were prepared using the Smartseq2 protocol, following established procedures 14–16. The quantity and quality of the cDNA libraries were assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies). Approximately 1 ng of cDNA per cell was transformed into a single-cell library using the Nextera XT DNA Library prep kit (Illumina FC-131-1096) and following the manual instructions with slight modifications. In brief, 1 ng of cDNA (in a maximum of 5 µl of sample volume) underwent tagmentation with 2 µl of TD and 1 µl of ATM at 55 °C for 5 min. Upon completion of the program, the reaction was promptly halted by adding 1 µl of 2 % SDS and incubating for 5 min at RT. Amplification was carried out using 3 µl of NMP per sample and adding 1 µl of each dual-indexed (i7 and i5; Illumina) primer. Individual Nextera XT libraries were pooled and then purified using magnetic beads. Indexed sequence libraries were combined for multiplexing (384 samples per lane). The sequencing was performed using the NovoSeq6000 paired-end.

treatment_protocol: Embryos at each stage were retrieved from at least 3 separate Hartley guinea pig females (~500 grams, 2-3 months of age) between days 3.5 and 5.75 after natural mating.

value: embryo

tag: developmental stage

value: Late blastocyst

tag: time

value: embryo in vitro day E5.75


title: JC_2_98 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_97 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_96 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst


title: monogyne, SB/SB, overwintered gyne, brain, M18-6-2, biol rep 5


title: JC_2_95 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_91 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_92 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_93 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_9 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 16 cell

value: embryo in vitro day E4


title: JC_2_90 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_89 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_87 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_81 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_8 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_88 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_78 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Early blastocyst

value: embryo in vitro day E5


title: JC_2_85 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_82 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_79 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_86 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_83 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_84 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_77 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_80 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: qs864, positive, wt433

city: Waterville

first: Suegene

last: Noh

state: ME

address: 5717 Mayflower Hill

department: Biology

institute: Colby College

data_processing:
Quality control of sequencing reads was performed using fastp v.0.23.1 (Chen et al. 2018). Reference data were obtained from DictyBase (Chisholm et al. 2006; Fey et al. 2009) on January 16, 2023, and included a reference genome (FASTA), a gene annotation file (GTF), and a Gene Ontology (GO) annotation file. The reference genome was indexed and reads were aligned to the indexed reference using STAR v.2.7.5c (Dobin et al. 2013). To process the alignments and check the quality, only reads mapped in proper pairs were included and sorted by read query using SAMtools v.1.3.1 (Danecek et al. 2021). Read groups were added using SAMtools and subsequently counted using htseq-count v.0.11.2 (Anders et al. 2015). The count table was generated with the -s reverse flag and reads were required to have a minimum alignment quality score of 20.
Assembly: DictyBase (downloaded January 16, 2023)
Supplementary files format and content: Tab-delimited file of raw counts per gene for each sample

organism: Dictyostelium discoideum

source_name: whole organism

extract_protocol:
All cells were collected into RNAlater (Qiagen). Subsequent total RNA extractions from each sample were performed with RNeasy plus Mini kits (Qiagen).
Illumina stranded mRNA-seq libraries were prepared and sequenced as 151 bp paired-end reads at University of Minnesota Genome Center (UMGC).
Libraries were barcoded, pooled, and sequenced across three lanes to minimize lane (batch) effects.

value: whole organism

tag: cell line

tag: infection

value: infected

value: pos


title: JC_2_75 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: qs864, 360mpi, wt433


title: JC_2_74 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: qs864, negative, wt433

value: uninfected

value: neg


title: JC_2_76 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_94 (21PG55-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: qs864, negative, delta433


title: qs864, 360mpi, delta433


title: JC_2_73 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: qs864, 090mpi, wt433


title: qs864, 090mpi, delta433


title: JC_2_72 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: qs4, positive, wt433


title: qs864, positive, delta433


title: JC_2_70 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_71 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: qs4, 360mpi, wt433


title: JC_2_7 (21PG50-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 8 cell

value: embryo in vitro day E3.5


title: qs4, positive, delta433


title: qs4, 360mpi, delta433


title: JC_2_69 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: qs4, 090mpi, wt433


title: qs4, negative, delta433


title: JC_2_67 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: primary astrocytes, 3222401L13Rik KD 6

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Data was analysed using in-house built pipeline
Raw reads were processed and demultiplexed using bcl2fastq (v2.20.2).
Quality control of raw sequencing data was done using FastQC (v0.11.5).
Reads were aligned to the mouse (mm10) genome with the STAR aligner (v2.5.2b)
feature Counts (v1.5.1) was used to generate read counts
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: Primary mouse astrocytes

growth_protocol: Primary mouse astrocytes were isolated from p1 mice and cultured in Neurobasal+ medium containing B27+ supplement and antibiotics in humified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was isolated using Tri reagent (Sigma), followed by purification with the RNA Clean & Concentrator-5 kit (Zymo)
Libraries were generated from 300 ng RNA with the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara)

treatment_protocol: Cells were treated on DIV12 with 50 nM control or 3222401L13Rik KD Gapmers using Lipofectamine RNAiMAX in medium without antibiotics for 48 hours.

value: Primary mouse astrocytes

tag: strain

value: 3222401L13Rik KD Gapmers


title: JC_2_68 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: JC_2_65 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_63 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_64 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: qs4, 090mpi, delta433


title: JC_2_66 (21PG42-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: primary astrocytes, 3222401L13Rik KD 5


title: JC_2_61 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: primary astrocytes, 3222401L13Rik KD 4


title: JC_2_60 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: primary astrocytes, 3222401L13Rik KD 2


title: primary astrocytes, 3222401L13Rik KD 1


title: JC_2_59 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_6 (21PG50-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: qs4, negative, wt433


title: JC_2_58 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: primary astrocytes, control 4

value: Control Gapmers


title: JC_2_57 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: primary astrocytes, control 5


title: JC_2_62 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_55 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_56 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: primary astrocytes, control 3


title: WT-tobra3

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

data_processing:
Removed adaptor with cutadapt and kept only 10-40-mers
Mapped the reads on the organism's transcriptome - Bowtie (parameters: -v 2 -y -a -m 1 --best --strata -p 18)
Kept only the mapped reads - samtools (parameters: -F 4 -f 0,16 -h)
Assembly: N16961
Supplementary files format and content: txt files with the count of reads detected for each CDS

organism: Vibrio cholerae

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen).  RNA depleted for rRNA was used for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA preparation kits

value: bacteria

value: WT

value: Tobramycin


title: primary astrocytes, control 2


title: JC_2_54 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: WT-tobra2


title: JC_2_53 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: WT-tobra1


title: primary astrocytes, 3222401L13Rik KD 3


title: JC_2_51 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_5 (21PG50-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_52 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: WT2


title: JC_2_50 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: WT3


title: JC_2_49 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: WT1


title: JC_2_46 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_47 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: tgt3

value: delta-tgt


title: tgt-tobra2


title: tgt-tobra1


title: tgt2


title: tgt-tobra3


title: JC_2_48 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Early blastocyst


title: JC_2_44 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E5


title: JC_2_45 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: primary astrocytes, control 1


title: tgt1


title: JC_2_43 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_41 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: DNMT3A_overexpresion_1_RRBS

city: Shenzhen

first: Aixia

last: Zhai

state: Guangdong

address: 92 Fuhua Road, Futian District

department: The Eighth Affiliated Hospital

institute: Sun Yat-sen University

description: Library name: DNMT3A_overexpresion_1_RRBS

library_source: genomic

data_processing:
The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

molecule: genomic DNA

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Genomic DNA degradation and contamination was validated by agarose gels. DNA purity was checked using NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).
A total amount of 1.5 μg genomic DNA spiked with moderate lambda DNA were handled by MspI, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to DNA as per manufacturer’s instructions. Then these DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research)

treatment_protocol: HepG2 cell line overexpressing DNMT3A was constructed by lentivirus

value: Human hepatocellular carcinoma cells

value: DNMT3A overexpression


title: DNMT3A_overexpresion_2_RRBS

description: Library name: DNMT3A_overexpresion_2_RRBS


title: JC_2_4 (21PG50-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_372 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_39 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: control_3_RRBS

description: Library name: control_3_RRBS


title: control_2_RRBS

description: Library name: control_2_RRBS


title: control_1_RRBS

description: Library name: control_1_RRBS


title: JC_2_38 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Small_Intestine I3C

type: RNA

city: Columbia

first: Prakash

last: Nagarkatti

state: South Carolina

address: 6439 Garners Ferry Road, Basic Science Bldg 1, Rm C-26

department: Department of Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine Columbia

description: Gene expression data from IECs from BALB/cJmice  treated with I3C alone

hyb_protocol: The GeneChip™ Hybridization, Wash, and Stain kit was used with the Affymetrix® Hybridization Oven and Affymetrix® Fluidics Station on the 450 protocol to prepare Affymetrix® GeneChip® arrays

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Microarray intensity was quantified, and differential expression was analyzed using Applied Biosystems Transcription Analysis Console (TAC) 4.0 software. The heat maps were generated using TAC 4.0 software

source_name: Small_Intestine I3C

label_protocol: cDNA fragments were labeled using the Affymetrix® genechip WT terminal labeling kit.

growth_protocol: BALB/cJ (8-10 weeks) were purchased from the Jackson Laboratory, and housed in specific pathogen-free conditions, under 12-hour light/12-hour dark cycles in an Association for Assessment and Accreditation of Laboratory Animal Care–accredited (AAALAC-accredited) animal facility at the University of South Carolina School of Medicine. Mice were provided with unlimited access to water and fed a regular chow diet.

extract_protocol: IECs were isolated from control and experimental animals. A total RNA was purified from ileal epithelial cells of control and experimental mice using the Qiagen RNA easy kit. After removal of DNA upon recombinant DNAse I treatment, Polyadenylated controls were prepared, and 1 mg of RNA was converted to complementary DNA (cDNA). These cDNA were purified, quantified and subsequently fragmented into 40-70 base pairs (bp).

treatment_protocol: Colitis in susceptible BALB/cJ mice was induced by intrarectal injections of TNBS (50 μL of 1 mg TNBS in 50% ethanol) under light isoflurane anesthesia. Mice in treatment groups received 100 μL i.p. injections of I3C (40 mg/kg in 0.05% DMSO/corn oil) 24 hours before TNBS injection and continued every day until completion of the experiment

value: Intestinal epitheial cells


title: JC_2_370 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Small_Intestine TNBS+I3C

description: Gene expression data from IECs from TNBS-induced colitis mice ((BALB/cJ)) treated with I3C

source_name: Small_Intestine TNBS+I3C


title: JC_2_37 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_368 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_369 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: DNMT3A_overexpresion_3_RRBS

description: Library name: DNMT3A_overexpresion_3_RRBS


title: JC_2_366 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Small_Intestine Vehicle

description: Gene expression data from IECs from vehicle group ((BALB/cJ))

source_name: Small_Intestine Vehicle


title: Small_Intestine TNBS

description: Gene expression data from IECs from TNBS-induced colitis mice (BALB/cJ)

source_name: Small_Intestine TNBS


title: JC_2_367 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_42 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_40 (21PG33-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_362 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 95, donor N413, MDS/MPN

description: Library name: 10x_lib_95_donor_N413_blood_sample_240

value: peripheral blood

value: male

value: PBMC

value: MDS/MPN


title: JC_2_360 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_364 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_363 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_361 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_359 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 94, donor N204, MDS

description: Library name: 10x_lib_94_donor_N204_blood_sample_239

value: female

value: MDS


title: JC_2_36 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: MDAMB231_DMSO_R2

type: genomic

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

description: DMSO Treated Replicate 2

hyb_protocol: hybing was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

scan_protocol: scanning was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

data_processing: The raw intensity data extracted from the CEL files were normalized with cyclic loess normalization and log transformed.

label: biotin

source_name: Breast

label_protocol: labeling was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

growth_protocol: Cells were collected as describled in the manuscript Gahramanov et al.

extract_protocol: genomic DNA was extracted as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

treatment_protocol: cell were treated as described in the manuscript Gahramanov et al.

value: MDA MB 231

value: DMSO Treated


title: MDAMB231_PG_Drug_R1

description: PG drug treaterd Replicate 1

value: Pioglitazone Drug Treated


title: BT20_T72_untreated

description: 72h after Untreated

value: Untreated


title: JC_2_357 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst

value: embryo in vitro day E5.5


title: 10x lib 93, donor N259, normal

description: Library name: 10x_lib_93_donor_N259_blood_sample_238

value: normal


title: MDAMB231_PG_Drug_R2

description: PG drug Treated Replicate 2


title: BT20_T0

description: T0 Timepoint for BT20


title: JC_2_371 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Early blastocyst

value: embryo in vitro day E5


title: BT20_T48_treated

description: 48h after Treated

value: HDAC Drug Treated


title: BT20_T72_treated

description: 72h after Treated


title: JC_2_356 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: MDAMB231_DMSO_R1

description: DMSO Treated Replicate 1


title: BT20_T48_untreated

description: 48h after Untreated


title: MDAMB231_T0

description: T0 Timepoint for MDAMB231


title: JC_2_365 (21PG33-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 91, donor N367, MDS/MPN

description: Library name: 10x_lib_91_donor_N367_blood_sample_235

value: peripheral blood


title: 10x lib 90, donor N367, MDS/MPN

description: Library name: 10x_lib_90_donor_N367_blood_sample_235

value: male


title: JC_2_355 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_354 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_358 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 89, donor N405, MDS

description: Library name: 10x_lib_89_donor_N405_blood_sample_233

value: PBMC


title: 10x lib 92, donor N382, MDS

description: Library name: 10x_lib_92_donor_N382_blood_sample_237


title: JC_2_353 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_352 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 89, donor N281, MDS/MPN

description: Library name: 10x_lib_89_donor_N281_blood_sample_232

value: MDS/MPN


title: 10x lib 94, donor N413, MDS/MPN

description: Library name: 10x_lib_94_donor_N413_blood_sample_240


title: 10x lib 92, donor N192, MDS/MPN

description: Library name: 10x_lib_92_donor_N192_blood_sample_236

value: female


title: 10x lib 89, donor N279, MDS

description: Library name: 10x_lib_89_donor_N279_blood_sample_231

value: MDS


title: JC_2_351 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: JC_2_35 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: JC_2_350 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_349 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 87, donor G12, MDS/MPN

description: Library name: 10x_lib_87_donor_G12_blood_sample_229


title: 10x lib 90, donor N191, MDS

description: Library name: 10x_lib_90_donor_N191_blood_sample_234


title: 10x lib 86, donor N280, MDS

description: Library name: 10x_lib_86_donor_N280_blood_sample_228


title: JC_2_348 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 86, donor N264, normal

description: Library name: 10x_lib_86_donor_N264_blood_sample_227


title: JC_2_347 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_346 (20PG4-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 86, donor N1, normal

description: Library name: 10x_lib_86_donor_N1_blood_sample_226


title: JC_2_345 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_344 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: ANTH_K562_HiC_dauno_rep4

city: Chapel Hill

first: Marielle

last: Bond

state: NC

address: 116 Manning Dr

department: Genetics

institute: UNC Chapel Hill

data_processing:
Hi-C maps for each sample were generated using the Juicer pipeline as initially described in Rao et al. 2014 (version 1.5.6).
Merged Hi-C maps for each treatment  were generated using Juicer (version 1.5.6).
Loops were called from individual maps at 5kb resolution using SIP (-res 5000 -factor 1 -fdr 0.05 -t 2000 -g 1, version 1.6.1)
Loops were called from merged maps at 5kb resolution using SIP (-res 5000 -factor 1 -fdr 0.05 -t 2000 -g 1, version 1.6.1)
Counts for merged loops were extracted from Hi-C files of each sample using hictoolsr (no normalization, 10kb resolution)
Raw counts were used as input for differential analysis with DESeq2 (LRT, design =~ rep + treat). Significant results were determined based on an absolute LFC greater than 2 and an adjusted p-value below 0.05.
Assembly: hg38
Supplementary files format and content: hic files

growth_protocol: K562 cells were cultured in RPMI 1640 + L-Glutamine (Gibco), 10% fetal bovine serum (Biowest), and 1% Penicillin-Streptomycin (Gibco). Cell density and culture conditions were maintained according to the ENCODE Cell Culture Guidelines

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min, quenched with 2.0M glycine for 5 min, washed in PBS, and split into 3x106 cell pellet aliquots
in situ Hi-C

treatment_protocol: K562 cells were treated for 2 hours with aclarubicin (sc-200160), daunorubicin (Sanofi-Aventis), or amrubicin (sc-207289). All of these drugs were dissolved according to the manufacturer's formulation.

value: Human leukemia

value: WT

value: daunorubicin


title: ANTH_K562_HiC_dauno_rep3


title: JC_2_343 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst


title: JC_2_342 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E5.5


title: ANTH_K562_HiC_dauno_rep1


title: JC_2_34 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_341 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: ANTH_K562_HiC_control_rep3


title: ANTH_K562_HiC_control_rep4


title: JC_2_340 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 88, donor N403, MDS/MPN

description: Library name: 10x_lib_88_donor_N403_blood_sample_230


title: ANTH_K562_HiC_control_rep2


title: JC_2_339 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: ANTH_K562_HiC_control_rep1


title: ANTH_K562_HiC_acla_rep4

value: aclarubicin


title: ANTH_K562_HiC_acla_rep3


title: JC_2_337 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_336 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: ANTH_K562_HiC_acla_rep2


title: JC_2_335 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 98, donor N422, MDS/MPN

description: Library name: 10x_lib_98_donor_N422_blood_sample_245


title: JC_2_334 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: ANTH_K562_HiC_acla_rep1


title: 10x lib 97, donor N421, MDS

description: Library name: 10x_lib_97_donor_N421_blood_sample_244


title: JC_2_333 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_332 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 97, donor N339, MDS

description: Library name: 10x_lib_97_donor_N339_blood_sample_242


title: JC_2_331 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: ANTH_K562_HiC_dauno_rep2


title: JC_2_330 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 97, donor N418, cytopenia

description: Library name: 10x_lib_97_donor_N418_blood_sample_243

value: cytopenia


title: 10x lib 96, donor N417, cytopenia

description: Library name: 10x_lib_96_donor_N417_blood_sample_241


title: 10x lib 84, donor N376, MDS

description: Library name: 10x_lib_84_donor_N376_blood_sample_224


title: JC_2_338 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_33 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 84, donor N365, cytopenia

description: Library name: 10x_lib_84_donor_N365_blood_sample_223


title: 10x lib 66, donor N31, normal

description: Library name: 10x_lib_66_donor_N31_blood_sample_171

value: normal


title: 10x lib 68, donor N279, MDS

description: Library name: 10x_lib_68_donor_N279_blood_sample_172


title: JC_2_328 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 67, donor N31, normal

description: Library name: 10x_lib_67_donor_N31_blood_sample_171


title: 10x lib 66, donor N274, MDS

description: Library name: 10x_lib_66_donor_N274_blood_sample_170


title: 10x lib 67, donor N274, MDS

description: Library name: 10x_lib_67_donor_N274_blood_sample_170


title: JC_2_325 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_327 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_326 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_324 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_323 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 67, donor N147, normal

description: Library name: 10x_lib_67_donor_N147_blood_sample_169


title: JC_2_322 (21PG65-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Late blastocyst

value: embryo in vitro day E6


title: 10x lib 64, donor N272, normal

description: Library name: 10x_lib_64_donor_N272_blood_sample_168

value: peripheral blood


title: JC_2_321 (21PG65-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 64, donor N79, normal

description: Library name: 10x_lib_64_donor_N79_blood_sample_167

value: PBMC


title: JC_2_32 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_319 (21PG65-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 63, donor N267, normal

description: Library name: 10x_lib_63_donor_N267_blood_sample_165

value: male


title: 10x lib 62, donor N97, normal

description: Library name: 10x_lib_62_donor_N97_blood_sample_166


title: JC_2_318 (21PG65-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_329 (20PG3-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 62, donor N267, normal

description: Library name: 10x_lib_62_donor_N267_blood_sample_165


title: 10x lib 63, donor N266, normal

description: Library name: 10x_lib_63_donor_N266_blood_sample_164


title: JC_2_317 (21PG65-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_316 (21PG65-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_315 (21PG65-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 63, donor N265, MDS

description: Library name: 10x_lib_63_donor_N265_blood_sample_163


title: 10x lib 62, donor N266, normal

description: Library name: 10x_lib_62_donor_N266_blood_sample_164


title: JC_2_314 (21PG65-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 61, donor N261, normal

description: Library name: 10x_lib_61_donor_N261_blood_sample_162


title: JC_2_311 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_312 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_313 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 59, donor N260, normal

description: Library name: 10x_lib_59_donor_N260_blood_sample_161


title: 10x lib 59, donor N259, normal

description: Library name: 10x_lib_59_donor_N259_blood_sample_160


title: JC_2_310 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 57, donor N251, MDS/MPN

description: Library name: 10x_lib_57_donor_N251_blood_sample_159

value: MDS/MPN


title: JC_2_31 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_320 (21PG65-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 66, donor N147, normal

description: Library name: 10x_lib_66_donor_N147_blood_sample_169


title: 10x lib 62, donor N265, MDS

description: Library name: 10x_lib_62_donor_N265_blood_sample_163

value: MDS


title: 10x lib 63, donor N97, normal

description: Library name: 10x_lib_63_donor_N97_blood_sample_166


title: 10x lib 56, donor N251, MDS/MPN

description: Library name: 10x_lib_56_donor_N251_blood_sample_159


title: JC_2_308 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: JC_2_309 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 54, donor N257, MDS

description: Library name: 10x_lib_54_donor_N257_blood_sample_157

value: female


title: 10x lib 57, donor N250, MDS

description: Library name: 10x_lib_57_donor_N250_blood_sample_158


title: 10x lib 56, donor N250, MDS

description: Library name: 10x_lib_56_donor_N250_blood_sample_158


title: JC_2_307 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_305 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 54, donor N122, normal

description: Library name: 10x_lib_54_donor_N122_blood_sample_156


title: JC_2_306 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 52, donor N122, normal

description: Library name: 10x_lib_52_donor_N122_blood_sample_156


title: JC_2_304 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 54, donor N249, MDS

description: Library name: 10x_lib_54_donor_N249_blood_sample_155


title: 10x lib 52, donor N249, MDS

description: Library name: 10x_lib_52_donor_N249_blood_sample_155


title: JC_2_303 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 50, donor N248, MDS

description: Library name: 10x_lib_50_donor_N248_blood_sample_154


title: JC_2_300 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 49, donor N248, MDS

description: Library name: 10x_lib_49_donor_N248_blood_sample_154


title: JC_2_3 (21PG50-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 8 cell

value: embryo in vitro day E3.5


title: JC_2_30 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: 10x lib 29, donor N179, normal

description: Library name: 10x_lib_29_donor_N179_blood_sample_106


title: 10x lib 28, donor N181, MDS/MPN

description: Library name: 10x_lib_28_donor_N181_blood_sample_105


title: JC_2_299 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 28, donor N180, cytopenia

description: Library name: 10x_lib_28_donor_N180_blood_sample_104


title: JC_2_297 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 28, donor N184, normal

description: Library name: 10x_lib_28_donor_N184_blood_sample_103


title: JC_2_298 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 29, donor N183, normal

description: Library name: 10x_lib_29_donor_N183_blood_sample_102


title: 10x lib 28, donor N178, normal

description: Library name: 10x_lib_28_donor_N178_blood_sample_100


title: JC_2_296 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 29, donor N182, normal

description: Library name: 10x_lib_29_donor_N182_blood_sample_101


title: 10x lib 52, donor N257, MDS

description: Library name: 10x_lib_52_donor_N257_blood_sample_157


title: 10x lib 27, donor N175, normal

description: Library name: 10x_lib_27_donor_N175_blood_sample_99


title: JC_2_294 (21PG35-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst

value: embryo in vitro day E5.25


title: JC_2_302 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_293 (21PG35-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_291 (21PG35-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 25, donor N176, normal

description: Library name: 10x_lib_25_donor_N176_blood_sample_98


title: JC_2_301 (21PG65-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 27, donor N174, normal

description: Library name: 10x_lib_27_donor_N174_blood_sample_97


title: JC_2_290 (21PG35-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 27, donor N173, normal

description: Library name: 10x_lib_27_donor_N173_blood_sample_96


title: JC_2_292 (21PG35-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 27, donor N172, normal

description: Library name: 10x_lib_27_donor_N172_blood_sample_95


title: JC_2_29 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 25, donor N169, normal

description: Library name: 10x_lib_25_donor_N169_blood_sample_92


title: JC_2_288 (21PG45-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E5.5


title: JC_2_289 (21PG35-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 25, donor N167, normal

description: Library name: 10x_lib_25_donor_N167_blood_sample_90


title: JC_2_287 (21PG45-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 24, donor N165, cytopenia

description: Library name: 10x_lib_24_donor_N165_blood_sample_88

value: cytopenia


title: 10x lib 25, donor N166, normal

description: Library name: 10x_lib_25_donor_N166_blood_sample_89

value: normal


title: 10x lib 24, donor N164, normal

description: Library name: 10x_lib_24_donor_N164_blood_sample_87


title: JC_2_286 (21PG45-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_284 (21PG45-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_295 (21PG35-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 24, donor N162, normal

description: Library name: 10x_lib_24_donor_N162_blood_sample_85


title: JC_2_281 (21PG45-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 24, donor N161, normal

description: Library name: 10x_lib_24_donor_N161_blood_sample_84


title: 10x lib 23, donor N48, MDS

description: Library name: 10x_lib_23_donor_N48_blood_sample_83


title: JC_2_282 (21PG45-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_280 (21PG45-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 21, donor N159, normal

description: Library name: 10x_lib_21_donor_N159_blood_sample_82


title: 10x lib 23, donor N157, normal

description: Library name: 10x_lib_23_donor_N157_blood_sample_81


title: JC_2_28 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_278 (21PG45-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_279 (21PG45-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 23, donor N160, normal

description: Library name: 10x_lib_23_donor_N160_blood_sample_80


title: 10x lib 27, donor N170, normal

description: Library name: 10x_lib_27_donor_N170_blood_sample_93


title: JC_2_277 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Late blastocyst

value: embryo in vitro day E5.75


title: JC_2_276 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 21, donor N156, normal

description: Library name: 10x_lib_21_donor_N156_blood_sample_78

value: peripheral blood


title: JC_2_275 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 23, donor N154, normal

description: Library name: 10x_lib_23_donor_N154_blood_sample_76

value: PBMC


title: JC_2_274 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 21, donor N155, normal

description: Library name: 10x_lib_21_donor_N155_blood_sample_77


title: JC_2_285 (21PG45-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 19, donor N147, normal

description: Library name: 10x_lib_19_donor_N147_blood_sample_73

value: male


title: JC_2_273 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 19, donor N150, normal

description: Library name: 10x_lib_19_donor_N150_blood_sample_72


title: JC_2_272 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 21, donor N152, normal

description: Library name: 10x_lib_21_donor_N152_blood_sample_74


title: JC_2_271 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 24, donor N163, normal

description: Library name: 10x_lib_24_donor_N163_blood_sample_86


title: 10x lib 20, donor N151, MDS

description: Library name: 10x_lib_20_donor_N151_blood_sample_71


title: JC_2_283 (21PG45-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 20, donor N148, normal

description: Library name: 10x_lib_20_donor_N148_blood_sample_69


title: JC_2_269 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_270 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 23, donor N158, normal

description: Library name: 10x_lib_23_donor_N158_blood_sample_79


title: 10x lib 19, donor N146, normal

description: Library name: 10x_lib_19_donor_N146_blood_sample_68


title: 10x lib 19, donor N145, normal

description: Library name: 10x_lib_19_donor_N145_blood_sample_67


title: 10x lib 20, donor N144, normal

description: Library name: 10x_lib_20_donor_N144_blood_sample_66


title: JC_2_266 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_267 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_26 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 19, donor N143, normal

description: Library name: 10x_lib_19_donor_N143_blood_sample_65


title: 10x lib 20, donor N149, cytopenia

description: Library name: 10x_lib_20_donor_N149_blood_sample_70


title: JC_2_268 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_25 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 18, donor N91, cytopenia

description: Library name: 10x_lib_18_donor_N91_blood_sample_64


title: JC_2_23 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 16 cell

value: embryo in vitro day E4


title: JC_2_24 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: 10x lib 16, donor N134, normal

description: Library name: 10x_lib_16_donor_N134_blood_sample_62

value: female


title: 10x lib 18, donor N133, normal

description: Library name: 10x_lib_18_donor_N133_blood_sample_61


title: 10x lib 15, donor N17, normal

description: Library name: 10x_lib_15_donor_N17_blood_sample_58


title: JC_2_227 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 18, donor N130, MDS

description: Library name: 10x_lib_18_donor_N130_blood_sample_60

value: MDS


title: 10x lib 16, donor N113, normal

description: Library name: 10x_lib_16_donor_N113_blood_sample_59


title: JC_2_228 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_226 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_27 (21PG40-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_225 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 15, donor N16, normal

description: Library name: 10x_lib_15_donor_N16_blood_sample_57


title: 10x lib 14, donor N129, normal

description: Library name: 10x_lib_14_donor_N129_blood_sample_56


title: 10x lib 14, donor N128, normal

description: Library name: 10x_lib_14_donor_N128_blood_sample_55


title: JC_2_224 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_222 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 15, donor N127, normal

description: Library name: 10x_lib_15_donor_N127_blood_sample_54


title: JC_2_221 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_223 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 15, donor N126, normal

description: Library name: 10x_lib_15_donor_N126_blood_sample_53


title: 10x lib 14, donor N125, normal

description: Library name: 10x_lib_14_donor_N125_blood_sample_52


title: JC_2_220 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 14, donor N124, normal

description: Library name: 10x_lib_14_donor_N124_blood_sample_51


title: JC_2_22 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 13, donor N122, normal

description: Library name: 10x_lib_13_donor_N122_blood_sample_50


title: 10x lib 16, donor N131, normal

description: Library name: 10x_lib_16_donor_N131_blood_sample_63


title: 10x lib 12, donor N18, normal

description: Library name: 10x_lib_12_donor_N18_blood_sample_49


title: JC_2_218 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_219 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 13, donor N123, normal

description: Library name: 10x_lib_13_donor_N123_blood_sample_48


title: JC_2_215 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_217 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 12, donor N121, normal

description: Library name: 10x_lib_12_donor_N121_blood_sample_47


title: 10x lib 13, donor N120, normal

description: Library name: 10x_lib_13_donor_N120_blood_sample_46


title: JC_2_213 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_214 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 13, donor N118, normal

description: Library name: 10x_lib_13_donor_N118_blood_sample_44


title: 10x lib 12, donor N119, normal

description: Library name: 10x_lib_12_donor_N119_blood_sample_45


title: JC_2_212 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 10, donor N109, normal

description: Library name: 10x_lib_10_donor_N109_blood_sample_42


title: JC_2_211 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 12, donor N117, normal

description: Library name: 10x_lib_12_donor_N117_blood_sample_43


title: JC_2_210 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_21 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 11, donor N116, MDS

description: Library name: 10x_lib_11_donor_N116_blood_sample_41


title: JC_2_209 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 10, donor N115, normal

description: Library name: 10x_lib_10_donor_N115_blood_sample_40


title: JC_2_208 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_207 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 10, donor N112, normal

description: Library name: 10x_lib_10_donor_N112_blood_sample_38


title: 10x lib 11, donor N111, normal

description: Library name: 10x_lib_11_donor_N111_blood_sample_37


title: 10x lib 11, donor N110, normal

description: Library name: 10x_lib_11_donor_N110_blood_sample_36


title: JC_2_205 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_216 (21PG75-4)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 11, donor N108, normal

description: Library name: 10x_lib_11_donor_N108_blood_sample_35


title: 10x lib 10, donor N107, cytopenia

description: Library name: 10x_lib_10_donor_N107_blood_sample_34


title: JC_2_203 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 9, donor N106, normal

description: Library name: 10x_lib_9_donor_N106_blood_sample_32


title: JC_2_201 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 8, donor N99, normal

description: Library name: 10x_lib_8_donor_N99_blood_sample_33


title: 10x lib 9, donor N105, normal

description: Library name: 10x_lib_9_donor_N105_blood_sample_31


title: 10x lib 9, donor N104, normal

description: Library name: 10x_lib_9_donor_N104_blood_sample_30


title: JC_2_199 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 8, donor N100, normal

description: Library name: 10x_lib_8_donor_N100_blood_sample_26


title: 10x lib 6, donor N95, normal

description: Library name: 10x_lib_6_donor_N95_blood_sample_25


title: JC_2_20 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 9, donor N101, normal

description: Library name: 10x_lib_9_donor_N101_blood_sample_27


title: 10x lib 10, donor N114, normal

description: Library name: 10x_lib_10_donor_N114_blood_sample_39


title: JC_2_204 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 8, donor N103, normal

description: Library name: 10x_lib_8_donor_N103_blood_sample_29


title: JC_2_198 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 7, donor N94, normal

description: Library name: 10x_lib_7_donor_N94_blood_sample_24


title: JC_2_202 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_206 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_197 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_195 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_200 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_194 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_2 (21PG50-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 8 cell

value: embryo in vitro day E3.5


title: 10x lib 7, donor N93, normal

description: Library name: 10x_lib_7_donor_N93_blood_sample_23


title: 10x lib 7, donor N92, normal

description: Library name: 10x_lib_7_donor_N92_blood_sample_22


title: JC_2_196 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst


title: 10x lib 7, donor N90, normal

description: Library name: 10x_lib_7_donor_N90_blood_sample_21


title: 10x lib 8, donor N102, normal

description: Library name: 10x_lib_8_donor_N102_blood_sample_28


title: JC_2_192 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Early blastocyst

value: embryo in vitro day E5.25


title: 10x lib 7, donor N97, normal

description: Library name: 10x_lib_7_donor_N97_blood_sample_20


title: JC_2_180 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: 10x lib 6, donor N98, normal

description: Library name: 10x_lib_6_donor_N98_blood_sample_19

value: normal


title: 10x lib 4, donor N87, cytopenia

description: Library name: 10x_lib_4_donor_N87_blood_sample_17

value: cytopenia


title: JC_2_18 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 5, donor N86, cytopenia

description: Library name: 10x_lib_5_donor_N86_blood_sample_16


title: JC_2_178 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_179 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 4, donor N85, cytopenia

description: Library name: 10x_lib_4_donor_N85_blood_sample_15


title: JC_2_177 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 6, donor N92, normal

description: Library name: 10x_lib_6_donor_N92_blood_sample_22


title: JC_2_175 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 4, donor N59, cytopenia

description: Library name: 10x_lib_4_donor_N59_blood_sample_13


title: JC_2_19 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_174 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 1, donor N37, normal

description: Library name: 10x_lib_1_donor_N37_blood_sample_3


title: JC_2_171 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 1, donor N35, normal

description: Library name: 10x_lib_1_donor_N35_blood_sample_2


title: JC_2_173 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 5, donor N79, normal

description: Library name: 10x_lib_5_donor_N79_blood_sample_12


title: JC_2_191 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 5, donor N89, normal

description: Library name: 10x_lib_5_donor_N89_blood_sample_18


title: JC_2_17 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_169 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 1, donor N235, MDS/MPN

description: Library name: 10x_lib_1_donor_N235_blood_sample_1

value: MDS/MPN


title: GSC 83 cells, ALKBH5-KO, polysome

city: Xiamen

first: Tianzhi

last: Huang

address: No. 4221, Xiang'an South Road, Xiang'an District

department: State Key Laboratory of Cellular Stress Biology

institute: Xiamen University

description:
Library name: Sample 4
Column name in Polysome_count.FPKM_all_samples.csv: KO_A5_1_ZX_poly_Count, KO_A5_1_ZX_poly_FPKM

data_processing:
All samples were sequenced by Illumina NovaSeq 6000. Raw data quality control was generated using FastQC Reports (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Mapping and FPKM of sequencing data were performed with HISAT2 and stringtie against the new version of the human genome GRCh38. Mapping was done with default parameters. For comparisons of gene expression within and between samples, FPKM values were determined. we mainly used the Poly-seq and RNA-seq data to calculate TEs of mRNAs using the formula FPKMpoly/FPKMtotal. To improve the accuracy of the analyses, genes with an FPKM>1 were retained for further analysis.
FC was used as the threshold for translation efficiency variance analysis. We consider a gene to have a difference in translation efficiency when it met |log2(FC)| > 0.5.
Assembly: Human GRCh38
Supplementary files format and content: Matrix table with raw gene counts and FPKM value for every gene and every sample
Library strategy: Polysome-seq

source_name: GSC 83

growth_protocol: Patient-derived glioma stem-like cells (GSCs), which were previously characterized, were cultured as non-adherent spheroids in DMEM/F12 medium (Thermo Fisher Scientific), supplemented with B27 (2%, Thermo Fisher Scientific), penicillin and streptomycin (1%, Thermo Fisher Scientific), Heparin (5 μg/ml, Sigma-Aldrich), EGF (20 ng/ml, Peprotech), and bFGF (20 ng/ml, Peprotech).

extract_protocol:
Subsequently, the cells layered onto a sucrose gradient tube ranging from 10% to 45%, then centrifuged at 36,000 rpm using a Beckman SW-41Ti rotor for 3 hours at 4°C. Peak fractions were isolated based on A260 optical density using a gradient fractionation station. mRNAs associated with ribosomes were extracted as polysome fractions and purified using TRIzol Reagent. Poly-A selected mRNAs were subsequently isolated and utilized for library preparation.
RNA libraries were prepared by LC-Bio Technology CO., Ltd(hangzhou, China).

treatment_protocol: ALKBH5 KO or control GSC 83 cells were subjected to cycloheximide (CHX) treatment at a concentration of 100 μg/ml for 15 minutes at 37°C. Following treatment, cells were collected and resuspended in pre-cooled PBS (0.01 M) supplemented with 100 μg/mL CHX. The cells underwent three washing cycles and were centrifuged to eliminate the supernatant and lysed in lysis buffer.

value: GSC 83

value: glioblastoma stem cell

value: ALKBH5 knockout


title: GSC 83 cells, ALKBH5-KO, input

description:
Library name: Sample 3
Column name in Polysome_count.FPKM_all_samples.csv: KO_A5_1_ZX_input_Count, KO_A5_1_ZX_input_FPKM


title: JC_2_168 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 16 cell


title: 10x lib 5, donor N84, normal

description: Library name: 10x_lib_5_donor_N84_blood_sample_14

value: peripheral blood

value: PBMC


title: GSC 83 cells, Control, polysome

description:
Library name: Sample 2
Column name in Polysome_count.FPKM_all_samples.csv: Control_ZX_poly_Count, Control_ZX_poly_FPKM

value: WT


title: JC_2_170 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: JC_2_176 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_166 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: GSC 83 cells, Control, input

description:
Library name: Sample 1
Column name in Polysome_count.FPKM_all_samples.csv: Control_ZX_input_Count, Control_ZX_input_FPKM


title: JC_2_165 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_167 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 4, donor N88, normal

description: Library name: 10x_lib_4_donor_N88_blood_sample_11

value: male


title: JC_2_172 (21PG32-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RA-FLS 3

city: Wenzhou

first: Wu

last: Gan

address: Chashan Street, Ouhai District

institute: Wenzhou Medical University

description: Library name: RA3

data_processing:
The library preparations were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150 bp paired-end reads were generated.
All peak calling was performed with MACS2 (version 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
Peaks were adjusted to the same size (500 bp) centered peak summits and motif discoveries of these loci sequences were performed using findMotifsGenome.pl program in HOMER v4.11 software with ‘-len 8,10,12,14 -gc -size given -homer2 -dumpFasta’.
The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene. ChIPseeker (Yu et al., 2015) was used to retrieve the nearest genes around the peak and annotate genomic region of the peak. Peak-related genes can be confirmed by ChIPseeker, and then Gene Ontology (GO) enrichment analysis was performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by peak-related genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of peak related genes in KEGG pathways.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: fibroblast-like synoviocytes

extract_protocol:
CUT&Tag assay was conducted using Hieff NGS G-Type In-Situ DNA Binding Profiling Library Prep Kit for Illumina (12598, Yeasen, China), following the manufacturer’s instruction (three independent samples of each group). Briefly, cells were harvested and bound to concanavalin A-coated magnetic beads, reacted with primary antibody against H3K9la, secondary antibody of anti-rabbit IgG, and pA/G-Transposome Mix to activate transposase. FLSs were lysed by proteinase K and DNA was extracted, amplified and purified for library construction using Hieff NGS Tagment Index Kit (12416, Yeasen, China)
The library construction using Hieff NGS Tagment Index Kit (12416, Yeasen, China),

tag: subject status

value: RA patient

value: fibroblast-like synoviocytes

tag: cut&tag antibody

value: H3K9la, (PTMbio, #PTM-1419RM )


title: JC_2_162 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RA-FLS 1

description: Library name: RA1


title: HC-FLS 3

description: Library name: HC3

value: healthy controls


title: JC_2_163 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: HC-FLS 2

description: Library name: HC2


title: JC_2_161 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: HC-FLS 1

description: Library name: HC1


city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: PM_CLW_RMC_Tissue_Input_for_H3K4me1.WI_22461

data_processing:
Data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore
ChIP-Seq reads were mapped to the humangenome build UCSC hg38 using bowtie2 and duplicate reads were removed
Peaks were called using MACS2
tdf files were generated using BEDTools
Assembly: hg38
Supplementary files format and content: tag density files (tdf)

source_name: kidney

extract_protocol:
Frozen tissue kept on dry ice was placed in tissue pulverizer in liquid nitrogen, then crushed. 200 mg of the powdered tissue were added into the 5 mL PBS solution containing 10% of protease & phosphatase inhibitors (Sigma #P8340, Sigma #P5726, & Sigma #P0044). Crosslinking was performed using 37% Formaldehyde with a final concentration 1.5% (Fisher Scientific #CAS 7732-18-5) for 20 minutes at room temperature. Reaction was stopped using 0.5 mL 10X Glycine for 5 minutes at room temperature. After a 5-minutes centrifugation at 1,500 rpm, pellet was washed with PBS and resuspended in a PBS solution containing 10% of protease & phosphatase inhibitors. Tissue lysate was obtained using Qiagen tissue homogenizer 25 Hz for 20 seconds. Then, after a 5-minutes centrifugation at 1,500 rpm, pellet was resuspended into a buffer containing 5mM PIPES pH 8, 85mM KCl, and 0.5% NP40. Cell lysate was obtained after incubation for 15 minutes on ice. After a 5-minutes centrifugation at 4,500 rpm, pellet was resuspended into a buffer containing 50mM Tris-HCl pH8, 10mM EDTA, and 1% SDS. Nuclear lysate was obtained after incubation for 10 minutes on ice. Sonication was performed using Bioruptor® Plus for 30 to 40 cycles of 30 seconds on and 30 seconds off. Quality of sonication was checked using a solution of 5M NaCl and RNase A (Novagen #70856) for 30 minutes at 37°C. Then, Proteinase K (Novagen #71049) helped remove any protein overnight at 65°C. DNA was purified using QIAquick PCR purification kit. Quantification of DNA was performed using Nanodrop®. DNA shearing was controlled by electrophoresis: samples were considered if the majority of DNA belonged to 100 and 400 bp.
Rubicon ThruPLEX Plasma-Seq library preparation system (p/n R400492)

value: kidney

tag: tumor type

tag: patient id

tag: chip antibody

value: input


title: JC_2_160 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

tag: tissue


description: Library name: PM_CLW_RMC_Tissue_Input_for_H3K27me3.WI_22460


title: JC_2_16 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4


title: JC_2_159 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RA-FLS 2

description: Library name: RA2

tag: cell type


title: JC_2_157 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC_Tissue_Input_for_H3K27ac_4me3.WI_22459


description: Library name: PM_CLW_RMC36T_Tissue_SNF5_Deficient_H3K4me1.WI_22458

value: RMC tumor


description: Library name: PM_CLW_RMC36N_Tissue_SNF5_Proficient_H3K4me1.WI_22457

value: Adjacent normal


title: JC_2_156 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_155 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC30T_Tissue_SNF5_Deficient_H3K4me1.WI_22454


description: Library name: PM_CLW_RMC31T_Tissue_SNF5_Deficient_H3K4me1.WI_22456


title: JC_2_153 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC30N_Tissue_SNF5_Proficient_H3K4me1.WI_22453


title: JC_2_154 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC31N_Tissue_SNF5_Proficient_H3K4me1.WI_22455


title: JC_2_152 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC4T_Tissue_SNF5_Deficient_H3K4me1.WI_22452


title: JC_2_151 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_150 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC2T_Tissue_SNF5_Deficient_H3K4me1.WI_22450


title: JC_2_164 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC4N_Tissue_SNF5_Proficient_H3K4me1.WI_22451


title: JC_2_15 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC2N_Tissue_SNF5_Proficient_H3K4me1.WI_22449


description: Library name: PM_CLW_RMC36T_Tissue_SNF5_Deficient_H3K27me3.WI_22448


title: JC_2_149 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_148 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_158 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_147 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz