title: BJ9446,BJ9447,BJ9448, Mouse sperm, scHi-C


title: BJ9452,BJ9453,BJ9454, Mouse sperm, scHi-C

status: Public on Mar 08 2025

type: SRA

city: Beijing

first: Heming

last: Xu

address: Yiheyuan Road

country: China

institute: Peking University

library_source: genomic

data_processing:
Hi-C reads of mouse (sperm, mESC) and human (sperm) single-cell samples were mapped to GRCm38 and GRCh38 reference genome separately using BWA-mem29. Contacts were extract with “hickit” package (https://github.com/lh3/hickit, version r291). Contact ends with more than 10 other contact ends within 1 Kb were regard as promiscuous and removed with custom scripts. Contacts with less than 5 other contacts in their 10Mb L0.5 neighborhood were regard as isolated contacts and also removed.
For all cell types, samples with more than 30,000 remaining contacts were kept for downstream analysis. For diploid samples like mESCs, haplotype of contacts was phased according to SNP sites and imputed. For each sample, each chromosome is treated as a polymer chain, each chromosome is evenly divided into 20kb sections, each section is treated as a particle of the polymer chain, and contacts of the sample were used as restraints to search for the optimal x, y, z spatial coordinates of particles by the Force-Directed Graph (FDG) algorithm implemented by “hickit”. 5 models with different random initiate seeds were generated simultaneously and 3 of these models with lowest mean mutual root mean square deviation (RMSD) were selected candidates. The mean mutual RMSD of these 3 models is defined as RMSD of the sample. Samples with RMSD larger than 2 were excluded from structure-based analysis. For samples passed quality control, we randomly picked 1 model from 3 candidates to represent their 3D genome structures.
Assembly: GRCh38, GRCm38
Supplementary files format and content: 3dg file: each line sequentially listing the chromosome name, start position, x, y, and z coordinates, delimited by tab characters
Supplementary files format and content: pairs file: A tab-separated file recording contacts that conforms to 4DN Consortium standards

molecule: genomic DNA

organism: Mus musculus

source_name: Sperm cells

extract_protocol:
All animal experimental procedures were carried out following the Institutional Animal Care and Use Committee (IACUC) guidelines of Peking University. 10–12-week-old C57BL/6J male mice were purchased from Peking University Laboratory Animal Centre.
The single-cell preamplification product was diluted with water to 5 ng/uL. 2 μL of each diluted sample was transposed by the addition of 3 μL Transposition Mixture (1 μL 5 X TTBL, 0.25 μL TTE Mix V50 (Vazyme TD501), 1.75 μL water) and incubated at 55 °C for 10 min. Transposition was stopped by adding 1.25 μL 0.2% SDS and then the plate was incubated at room temperature for 10 min. Then, 2 μL 5 μM i5 unique dual (UD) index and 2 μL 5 μM i7 unique dual (UD) index were added in each well. Next, the sperm Hi-C library was amplified for 10 cycles of PCR with 9.75 uL KAPA PCR mix (Roche, KK2102) (4 uL 5× KAPA HiFi GC Buffer, 0.6 uL dNTP Mix (10 mM each), 4 uL KAPA HiFi DNA Polymerase (1 U/uL) and 4.75 uL water). The barcoded single-cell libraries were then pooled and purified with 0.6× and 0.15× VAHTS DNA Clean Beads (Vazyme, N411-02). The final libraries were sequenced with paired-end 150bp reads on a NovaSeq X plus (Illumina) platform according to the manufacturer’s instructions.

tag: cell type

value: Sperm cells


title: BJ9443,BJ9444,BJ9445, Mouse sperm, scHi-C


title: HS793,HS794,HS795, Human sperm, scHi-C

organism: Homo sapiens


title: BJ9440,BJ9441,BJ9442, Mouse sperm, scHi-C


title: HS784,HS785,HS786, Human sperm, scHi-C


title: HS790,HS791,HS792, Human sperm, scHi-C


title: BJ9437,BJ9438,BJ9439, Mouse sperm, scHi-C


title: HS781,HS782,HS783, Human sperm, scHi-C


title: HS787,HS788,HS789, Human sperm, scHi-C


title: BJ9434,BJ9435,BJ9436, Mouse sperm, scHi-C


title: BJ9431,BJ9432,BJ9433, Mouse sperm, scHi-C


title: HS778,HS779,HS780, Human sperm, scHi-C


title: HS775,HS776,HS777, Human sperm, scHi-C


title: BJ9428,BJ9429,BJ9430, Mouse sperm, scHi-C


title: HS772,HS773,HS774, Human sperm, scHi-C


title: BJ9425,BJ9426,BJ9427, Mouse sperm, scHi-C


title: HS769,HS770,HS771, Human sperm, scHi-C


title: BJ9422,BJ9423,BJ9424, Mouse sperm, scHi-C


title: HS766,HS767,HS768, Human sperm, scHi-C


title: BJ9419,BJ9420,BJ9421, Mouse sperm, scHi-C


title: HS763,HS764,HS765, Human sperm, scHi-C


title: BJ9416,BJ9417,BJ9418, Mouse sperm, scHi-C


title: HS760,HS761,HS762, Human sperm, scHi-C


title: BJ9413,BJ9414,BJ9415, Mouse sperm, scHi-C


title: HS757,HS758,HS759, Human sperm, scHi-C


title: BJ9407,BJ9408,BJ9409, Mouse sperm, scHi-C


title: HS751,HS752,HS753, Human sperm, scHi-C


title: BJ9404,BJ9405,BJ9406, Mouse sperm, scHi-C


title: BJ9401,BJ9402,BJ9403, Mouse sperm, scHi-C


title: BJ9395,BJ9396,BJ9397, Mouse sperm, scHi-C


title: BJ9392,BJ9393,BJ9394, Mouse sperm, scHi-C


title: BJ9389,BJ9390,BJ9391, Mouse sperm, scHi-C


title: HS736,HS737,HS738, Human sperm, scHi-C


title: HS739,HS740,HS741, Human sperm, scHi-C


title: HS742,HS743,HS744, Human sperm, scHi-C


title: BJ9398,BJ9399,BJ9400, Mouse sperm, scHi-C


title: BJ9383,BJ9384,BJ9385, Mouse sperm, scHi-C


title: HS748,HS749,HS750, Human sperm, scHi-C


title: HS745,HS746,HS747, Human sperm, scHi-C


title: BJ9380,BJ9381,BJ9382, Mouse sperm, scHi-C


title: BJ9386,BJ9387,BJ9388, Mouse sperm, scHi-C


title: HS727,HS728,HS729, Human sperm, scHi-C


title: HS730,HS731,HS732, Human sperm, scHi-C


title: BJ9377,BJ9378,BJ9379, Mouse sperm, scHi-C


title: HS733,HS734,HS735, Human sperm, scHi-C


title: BJ9410,BJ9411,BJ9412, Mouse sperm, scHi-C


title: BJ9374,BJ9375,BJ9376, Mouse sperm, scHi-C


title: HS754,HS755,HS756, Human sperm, scHi-C


title: HS718,HS719,HS720, Human sperm, scHi-C


title: BJ9371,BJ9372,BJ9373, Mouse sperm, scHi-C


title: BJ9368,BJ9369,BJ9370, Mouse sperm, scHi-C


title: HS715,HS716,HS717, Human sperm, scHi-C


title: BJ9365,BJ9366,BJ9367, Mouse sperm, scHi-C


title: HS712,HS713,HS714, Human sperm, scHi-C


title: HS709,HS710,HS711, Human sperm, scHi-C


title: BJ9362,BJ9363,BJ9364, Mouse sperm, scHi-C


title: HS706,HS707,HS708, Human sperm, scHi-C


title: BJ9359,BJ9360,BJ9361, Mouse sperm, scHi-C


title: BJ9356,BJ9357,BJ9358, Mouse sperm, scHi-C


title: BJ9350,BJ9351,BJ9352, Mouse sperm, scHi-C


title: HS724,HS725,HS726, Human sperm, scHi-C


title: HS703,HS704,HS705, Human sperm, scHi-C


title: HS700,HS701,HS702, Human sperm, scHi-C


title: BJ9353,BJ9354,BJ9355, Mouse sperm, scHi-C


title: HS691,HS692,HS693, Human sperm, scHi-C


title: BJ9347,BJ9348,BJ9349, Mouse sperm, scHi-C


title: HS697,HS698,HS699, Human sperm, scHi-C


title: BJ9344,BJ9345,BJ9346, Mouse sperm, scHi-C


title: HS694,HS695,HS696, Human sperm, scHi-C


title: HS685,HS686,HS687, Human sperm, scHi-C


title: HS688,HS689,HS690, Human sperm, scHi-C


title: BJ9338,BJ9339,BJ9340, Mouse sperm, scHi-C


title: HS682,HS683,HS684, Human sperm, scHi-C


title: BJ9341,BJ9342,BJ9343, Mouse sperm, scHi-C


title: BJ9335,BJ9336,BJ9337, Mouse sperm, scHi-C


title: HS679,HS680,HS681, Human sperm, scHi-C


title: BJ9332,BJ9333,BJ9334, Mouse sperm, scHi-C


title: HS676,HS677,HS678, Human sperm, scHi-C


title: BJ9326,BJ9327,BJ9328, Mouse sperm, scHi-C


title: HS721,HS722,HS723, Human sperm, scHi-C


title: HS670,HS671,HS672, Human sperm, scHi-C


title: BJ9323,BJ9324,BJ9325, Mouse sperm, scHi-C


title: BJ9320,BJ9321,BJ9322, Mouse sperm, scHi-C


title: HS667,HS668,HS669, Human sperm, scHi-C


title: HS664,HS665,HS666, Human sperm, scHi-C


title: HS661,HS662,HS663, Human sperm, scHi-C


title: HS658,HS659,HS660, Human sperm, scHi-C


title: BJ9311,BJ9312,BJ9313, Mouse sperm, scHi-C


title: HS655,HS656,HS657, Human sperm, scHi-C


title: HS649,HS650,HS651, Human sperm, scHi-C


title: BJ9305,BJ9306,BJ9307, Mouse sperm, scHi-C


title: BJ9308,BJ9309,BJ9310, Mouse sperm, scHi-C


title: BJ9302,BJ9303,BJ9304, Mouse sperm, scHi-C


title: HS652,HS653,HS654, Human sperm, scHi-C


title: BJ9299,BJ9300,BJ9301, Mouse sperm, scHi-C


title: HS673,HS674,HS675, Human sperm, scHi-C


title: HS640,HS641,HS642, Human sperm, scHi-C


title: HS637,HS638,HS639, Human sperm, scHi-C


title: HS646,HS647,HS648, Human sperm, scHi-C


title: BJ9290,BJ9291,BJ9292, Mouse sperm, scHi-C


title: BJ9296,BJ9297,BJ9298, Mouse sperm, scHi-C


title: BJ9329,BJ9330,BJ9331, Mouse sperm, scHi-C


title: HS634,HS635,HS636, Human sperm, scHi-C


title: HS643,HS644,HS645, Human sperm, scHi-C


title: BJ9293,BJ9294,BJ9295, Mouse sperm, scHi-C


title: BJ9287,BJ9288,BJ9289, Mouse sperm, scHi-C


title: BJ9317,BJ9318,BJ9319, Mouse sperm, scHi-C


title: BJ9284,BJ9285,BJ9286, Mouse sperm, scHi-C


title: HS628,HS629,HS630, Human sperm, scHi-C


title: HS631,HS632,HS633, Human sperm, scHi-C


title: HS625,HS626,HS627, Human sperm, scHi-C


title: BJ9278,BJ9279,BJ9280, Mouse sperm, scHi-C


title: BJ9275,BJ9276,BJ9277, Mouse sperm, scHi-C


title: BJ9314,BJ9315,BJ9316, Mouse sperm, scHi-C


title: BJ9272,BJ9273,BJ9274, Mouse sperm, scHi-C


title: HS619,HS620,HS621, Human sperm, scHi-C


title: BJ9269,BJ9270,BJ9271, Mouse sperm, scHi-C


title: HS622,HS623,HS624, Human sperm, scHi-C


title: HS613,HS614,HS615, Human sperm, scHi-C


title: HS616,HS617,HS618, Human sperm, scHi-C


title: HS610,HS611,HS612, Human sperm, scHi-C


title: BJ9266,BJ9267,BJ9268, Mouse sperm, scHi-C


title: BJ9263,BJ9264,BJ9265, Mouse sperm, scHi-C


title: HS604,HS605,HS606, Human sperm, scHi-C


title: BJ9260,BJ9261,BJ9262, Mouse sperm, scHi-C


title: BJ9257,BJ9258,BJ9259, Mouse sperm, scHi-C


title: HS601,HS602,HS603, Human sperm, scHi-C


title: BJ9254,BJ9255,BJ9256, Mouse sperm, scHi-C


title: BJ9251,BJ9252,BJ9253, Mouse sperm, scHi-C


title: BJ9248,BJ9249,BJ9250, Mouse sperm, scHi-C


title: HS592,HS593,HS594, Human sperm, scHi-C


title: HS595,HS596,HS597, Human sperm, scHi-C


title: BJ9281,BJ9282,BJ9283, Mouse sperm, scHi-C


title: HS589,HS590,HS591, Human sperm, scHi-C


title: BJ9245,BJ9246,BJ9247, Mouse sperm, scHi-C


title: BJ9242,BJ9243,BJ9244, Mouse sperm, scHi-C


title: BJ9239,BJ9240,BJ9241, Mouse sperm, scHi-C


title: HS583,HS584,HS585, Human sperm, scHi-C


title: BJ9236,BJ9237,BJ9238, Mouse sperm, scHi-C


title: HS580,HS581,HS582, Human sperm, scHi-C


title: BJ9233,BJ9234,BJ9235, Mouse sperm, scHi-C


title: BJ9230,BJ9231,BJ9232, Mouse sperm, scHi-C


title: HS571,HS572,HS573, Human sperm, scHi-C


title: HS607,HS608,HS609, Human sperm, scHi-C


title: BJ9224,BJ9225,BJ9226, Mouse sperm, scHi-C


title: HS598,HS599,HS600, Human sperm, scHi-C


title: HS574,HS575,HS576, Human sperm, scHi-C


title: HS565,HS566,HS567, Human sperm, scHi-C


title: BJ9221,BJ9222,BJ9223, Mouse sperm, scHi-C


title: HS562,HS563,HS564, Human sperm, scHi-C


title: BJ9215,BJ9216,BJ9217, Mouse sperm, scHi-C


title: BJ9218,BJ9219,BJ9220, Mouse sperm, scHi-C


title: BJ9206,BJ9207,BJ9208, Mouse sperm, scHi-C


title: BJ9212,BJ9213,BJ9214, Mouse sperm, scHi-C


title: HS553,HS554,HS555, Human sperm, scHi-C


title: HS556,HS557,HS558, Human sperm, scHi-C


title: HS550,HS551,HS552, Human sperm, scHi-C


title: HS559,HS560,HS561, Human sperm, scHi-C


title: HS586,HS587,HS588, Human sperm, scHi-C


title: HS547,HS548,HS549, Human sperm, scHi-C


title: HS544,HS545,HS546, Human sperm, scHi-C


title: BJ9200,BJ9201,BJ9202, Mouse sperm, scHi-C


title: BJ9203,BJ9204,BJ9205, Mouse sperm, scHi-C


title: BJ9194,BJ9195,BJ9196, Mouse sperm, scHi-C


title: BJ9227,BJ9228,BJ9229, Mouse sperm, scHi-C


title: HS538,HS539,HS540, Human sperm, scHi-C


title: HS577,HS578,HS579, Human sperm, scHi-C


title: BJ9191,BJ9192,BJ9193, Mouse sperm, scHi-C


title: HS568,HS569,HS570, Human sperm, scHi-C


title: BJ9188,BJ9189,BJ9190, Mouse sperm, scHi-C


title: BJ9185,BJ9186,BJ9187, Mouse sperm, scHi-C


title: BJ9182,BJ9183,BJ9184, Mouse sperm, scHi-C


title: HS532,HS533,HS534, Human sperm, scHi-C


title: HS526,HS527,HS528, Human sperm, scHi-C


title: HS529,HS530,HS531, Human sperm, scHi-C


title: BJ9209,BJ9210,BJ9211, Mouse sperm, scHi-C


title: BJ9179,BJ9180,BJ9181, Mouse sperm, scHi-C


title: HS523,HS524,HS525, Human sperm, scHi-C


title: HS517,HS518,HS519, Human sperm, scHi-C


title: BJ9176,BJ9177,BJ9178, Mouse sperm, scHi-C


title: HS520,HS521,HS522, Human sperm, scHi-C


title: HS514,HS515,HS516, Human sperm, scHi-C


title: BJ9170,BJ9171,BJ9172, Mouse sperm, scHi-C


title: BJ9167,BJ9168,BJ9169, Mouse sperm, scHi-C


title: BJ9197,BJ9198,BJ9199, Mouse sperm, scHi-C


title: HS541,HS542,HS543, Human sperm, scHi-C


title: BJ9161,BJ9162,BJ9163, Mouse sperm, scHi-C


title: BJ9164,BJ9165,BJ9166, Mouse sperm, scHi-C


title: HS502,HS503,HS504, Human sperm, scHi-C


title: HS508,HS509,HS510, Human sperm, scHi-C


title: HS535,HS536,HS537, Human sperm, scHi-C


title: BJ9158,BJ9159,BJ9160, Mouse sperm, scHi-C


title: HS499,HS500,HS501, Human sperm, scHi-C


title: HS511,HS512,HS513, Human sperm, scHi-C


title: BJ9155,BJ9156,BJ9157, Mouse sperm, scHi-C


title: HS505,HS506,HS507, Human sperm, scHi-C


title: HS496,HS497,HS498, Human sperm, scHi-C


title: BJ9152,BJ9153,BJ9154, Mouse sperm, scHi-C


title: BJ9149,BJ9150,BJ9151, Mouse sperm, scHi-C


title: BJ9173,BJ9174,BJ9175, Mouse sperm, scHi-C


title: HS493,HS494,HS495, Human sperm, scHi-C


title: HS490,HS491,HS492, Human sperm, scHi-C


title: BJ9143,BJ9144,BJ9145, Mouse sperm, scHi-C


title: BJ9140,BJ9141,BJ9142, Mouse sperm, scHi-C


title: HS487,HS488,HS489, Human sperm, scHi-C


title: HS484,HS485,HS486, Human sperm, scHi-C


title: HS478,HS479,HS480, Human sperm, scHi-C


title: BJ9137,BJ9138,BJ9139, Mouse sperm, scHi-C


title: BJ9131,BJ9132,BJ9133, Mouse sperm, scHi-C


title: BJ9128,BJ9129,BJ9130, Mouse sperm, scHi-C


title: HS475,HS476,HS477, Human sperm, scHi-C


title: HS472,HS473,HS474, Human sperm, scHi-C


title: BJ9125,BJ9126,BJ9127, Mouse sperm, scHi-C


title: HS469,HS470,HS471, Human sperm, scHi-C


title: HS466,HS467,HS468, Human sperm, scHi-C


title: BJ9119,BJ9120,BJ9121, Mouse sperm, scHi-C


title: HS460,HS461,HS462, Human sperm, scHi-C


title: BJ9113,BJ9114,BJ9115, Mouse sperm, scHi-C


title: HS463,HS464,HS465, Human sperm, scHi-C


title: BJ9146,BJ9147,BJ9148, Mouse sperm, scHi-C


title: BJ9110,BJ9111,BJ9112, Mouse sperm, scHi-C


title: HS451,HS452,HS453, Human sperm, scHi-C


title: BJ9116,BJ9117,BJ9118, Mouse sperm, scHi-C


title: BJ9104,BJ9105,BJ9106, Mouse sperm, scHi-C


title: HS454,HS455,HS456, Human sperm, scHi-C


title: HS457,HS458,HS459, Human sperm, scHi-C


title: HS448,HS449,HS450, Human sperm, scHi-C


title: BJ9107,BJ9108,BJ9109, Mouse sperm, scHi-C


title: BJ9101,BJ9102,BJ9103, Mouse sperm, scHi-C


title: HS481,HS482,HS483, Human sperm, scHi-C


title: HS439,HS440,HS441, Human sperm, scHi-C


title: BJ9134,BJ9135,BJ9136, Mouse sperm, scHi-C


title: BJ9098,BJ9099,BJ9100, Mouse sperm, scHi-C


title: BJ9122,BJ9123,BJ9124, Mouse sperm, scHi-C


title: HS442,HS443,HS444, Human sperm, scHi-C


title: BJ9095,BJ9096,BJ9097, Mouse sperm, scHi-C


title: BJ9092,BJ9093,BJ9094, Mouse sperm, scHi-C


title: HS436,HS437,HS438, Human sperm, scHi-C


title: BJ9089,BJ9090,BJ9091, Mouse sperm, scHi-C


title: HS427,HS428,HS429, Human sperm, scHi-C


title: HS433,HS434,HS435, Human sperm, scHi-C


title: BJ9074,BJ9075,BJ9076, Mouse sperm, scHi-C


title: BJ9086,BJ9087,BJ9088, Mouse sperm, scHi-C


title: HS424,HS425,HS426, Human sperm, scHi-C


title: BJ9077,BJ9078,BJ9079, Mouse sperm, scHi-C


title: BJ9071,BJ9072,BJ9073, Mouse sperm, scHi-C


title: HS418,HS419,HS420, Human sperm, scHi-C


title: BJ9083,BJ9084,BJ9085, Mouse sperm, scHi-C


title: BJ9068,BJ9069,BJ9070, Mouse sperm, scHi-C


title: BJ9080,BJ9081,BJ9082, Mouse sperm, scHi-C


title: HS430,HS431,HS432, Human sperm, scHi-C


title: HS421,HS422,HS423, Human sperm, scHi-C


title: HS445,HS446,HS447, Human sperm, scHi-C


title: BJ9065,BJ9066,BJ9067, Mouse sperm, scHi-C


title: BJ9062,BJ9063,BJ9064, Mouse sperm, scHi-C


title: HS412,HS413,HS414, Human sperm, scHi-C


title: HS403,HS404,HS405, Human sperm, scHi-C


title: BJ9053,BJ9054,BJ9055, Mouse sperm, scHi-C


title: HS400,HS401,HS402, Human sperm, scHi-C


title: BJ9050,BJ9051,BJ9052, Mouse sperm, scHi-C


title: HS409,HS410,HS411, Human sperm, scHi-C


title: BJ9056,BJ9057,BJ9058, Mouse sperm, scHi-C


title: BJ9059,BJ9060,BJ9061, Mouse sperm, scHi-C


title: HS397,HS398,HS399, Human sperm, scHi-C


title: HS385,HS386,HS387, Human sperm, scHi-C


title: HS394,HS395,HS396, Human sperm, scHi-C


title: BJ9038,BJ9039,BJ9040, Mouse sperm, scHi-C


title: BJ9035,BJ9036,BJ9037, Mouse sperm, scHi-C


title: HS388,HS389,HS390, Human sperm, scHi-C


title: HS391,HS392,HS393, Human sperm, scHi-C


title: HS415,HS416,HS417, Human sperm, scHi-C


title: BJ9047,BJ9048,BJ9049, Mouse sperm, scHi-C


title: BJ9044,BJ9045,BJ9046, Mouse sperm, scHi-C


title: HS376,HS377,HS378, Human sperm, scHi-C


title: HS373,HS374,HS375, Human sperm, scHi-C


title: HS406,HS407,HS408, Human sperm, scHi-C


title: BJ9041,BJ9042,BJ9043, Mouse sperm, scHi-C


title: HS382,HS383,HS384, Human sperm, scHi-C


title: HS367,HS368,HS369, Human sperm, scHi-C


title: BJ9020,BJ9021,BJ9022, Mouse sperm, scHi-C


title: HS379,HS380,HS381, Human sperm, scHi-C


title: BJ9026,BJ9027,BJ9028, Mouse sperm, scHi-C


title: BJ9032,BJ9033,BJ9034, Mouse sperm, scHi-C


title: HS358,HS359,HS360, Human sperm, scHi-C


title: BJ9005,BJ9006,BJ9007, Mouse sperm, scHi-C


title: HS352,HS353,HS354, Human sperm, scHi-C


title: HS349,HS350,HS351, Human sperm, scHi-C


title: HS340,HS341,HS342, Human sperm, scHi-C


title: BJ9002,BJ9003,BJ9004, Mouse sperm, scHi-C


title: BJ8492,BJ8493,BJ8494, Mouse sperm, scHi-C


title: BJ9029,BJ9030,BJ9031, Mouse sperm, scHi-C


title: BJ9023,BJ9024,BJ9025, Mouse sperm, scHi-C


title: BJ8483,BJ8484,BJ8485, Mouse sperm, scHi-C


title: BJ9008,BJ9009,BJ9010, Mouse sperm, scHi-C


title: HS361,HS362,HS363, Human sperm, scHi-C


title: BJ8486,BJ8487,BJ8488, Mouse sperm, scHi-C


title: HS370,HS371,HS372, Human sperm, scHi-C


title: HS343,HS344,HS345, Human sperm, scHi-C


title: BJ8489,BJ8490,BJ8491, Mouse sperm, scHi-C


title: HS334,HS335,HS336, Human sperm, scHi-C


title: HS364,HS365,HS366, Human sperm, scHi-C


title: BJ9014,BJ9015,BJ9016, Mouse sperm, scHi-C


title: HS337,HS338,HS339, Human sperm, scHi-C


title: BJ9017,BJ9018,BJ9019, Mouse sperm, scHi-C


title: HS355,HS356,HS357, Human sperm, scHi-C


title: BJ9011,BJ9012,BJ9013, Mouse sperm, scHi-C


title: HS346,HS347,HS348, Human sperm, scHi-C


title: HS331,HS332,HS333, Human sperm, scHi-C


title: BJ8480,BJ8481,BJ8482, Mouse sperm, scHi-C


title: HS325,HS326,HS327, Human sperm, scHi-C


title: BJ8477,BJ8478,BJ8479, Mouse sperm, scHi-C


title: BJ8495,BJ8496,BJ9001, Mouse sperm, scHi-C


title: BJ8474,BJ8475,BJ8476, Mouse sperm, scHi-C


title: HS328,HS329,HS330, Human sperm, scHi-C


title: BJ8471,BJ8472,BJ8473, Mouse sperm, scHi-C


title: HS322,HS323,HS324, Human sperm, scHi-C


title: HS316,HS317,HS318, Human sperm, scHi-C


title: BJ8468,BJ8469,BJ8470, Mouse sperm, scHi-C


title: HS319,HS320,HS321, Human sperm, scHi-C


title: HS313,HS314,HS315, Human sperm, scHi-C


title: BJ8465,BJ8466,BJ8467, Mouse sperm, scHi-C


title: BJ8462,BJ8463,BJ8464, Mouse sperm, scHi-C


title: BJ8453,BJ8454,BJ8455, Mouse sperm, scHi-C


title: HS307,HS308,HS309, Human sperm, scHi-C


title: HS310,HS311,HS312, Human sperm, scHi-C


title: BJ8456,BJ8457,BJ8458, Mouse sperm, scHi-C


title: BJ8459,BJ8460,BJ8461, Mouse sperm, scHi-C


title: BJ8444,BJ8445,BJ8446, Mouse sperm, scHi-C


title: HS295,HS296,HS297, Human sperm, scHi-C


title: HS301,HS302,HS303, Human sperm, scHi-C


title: HS292,HS293,HS294, Human sperm, scHi-C


title: HS304,HS305,HS306, Human sperm, scHi-C


title: BJ8438,BJ8439,BJ8440, Mouse sperm, scHi-C


title: HS286,HS287,HS288, Human sperm, scHi-C


title: BJ8450,BJ8451,BJ8452, Mouse sperm, scHi-C


title: HS280,HS281,HS282, Human sperm, scHi-C


title: BJ8447,BJ8448,BJ8449, Mouse sperm, scHi-C


title: HS298,HS299,HS300, Human sperm, scHi-C


title: BJ8441,BJ8442,BJ8443, Mouse sperm, scHi-C


title: HS283,HS284,HS285, Human sperm, scHi-C


title: BJ8432,BJ8433,BJ8434, Mouse sperm, scHi-C


title: HS289,HS290,HS291, Human sperm, scHi-C


title: BJ8435,BJ8436,BJ8437, Mouse sperm, scHi-C


title: BJ8429,BJ8430,BJ8431, Mouse sperm, scHi-C


title: BJ8420,BJ8421,BJ8422, Mouse sperm, scHi-C


title: HS274,HS275,HS276, Human sperm, scHi-C


title: HS268,HS269,HS270, Human sperm, scHi-C


title: HS277,HS278,HS279, Human sperm, scHi-C


title: HS271,HS272,HS273, Human sperm, scHi-C


title: BJ8423,BJ8424,BJ8425, Mouse sperm, scHi-C


title: BJ8417,BJ8418,BJ8419, Mouse sperm, scHi-C


title: HS265,HS266,HS267, Human sperm, scHi-C


title: BJ8426,BJ8427,BJ8428, Mouse sperm, scHi-C


title: BJ8414,BJ8415,BJ8416, Mouse sperm, scHi-C


title: BJ8411,BJ8412,BJ8413, Mouse sperm, scHi-C


title: HS259,HS260,HS261, Human sperm, scHi-C


title: BJ8408,BJ8409,BJ8410, Mouse sperm, scHi-C


title: BJ8405,BJ8406,BJ8407, Mouse sperm, scHi-C


title: HS262,HS263,HS264, Human sperm, scHi-C


title: HS253,HS254,HS255, Human sperm, scHi-C


title: BJ8399,BJ8400,BJ8401, Mouse sperm, scHi-C


title: HS256,HS257,HS258, Human sperm, scHi-C


title: HS247,HS248,HS249, Human sperm, scHi-C


title: BJ8402,BJ8403,BJ8404, Mouse sperm, scHi-C


title: HS241,HS242,HS243, Human sperm, scHi-C


title: HS244,HS245,HS246, Human sperm, scHi-C


title: BJ8386,BJ8387,BJ8388, Mouse sperm, scHi-C


title: HS232,HS233,HS234, Human sperm, scHi-C


title: HS238,HS239,HS240, Human sperm, scHi-C


title: BJ8379,BJ8380,BJ8381, Mouse sperm, scHi-C


title: BJ8395,BJ8397,BJ8398, Mouse sperm, scHi-C


title: BJ8382,BJ8383,BJ8385, Mouse sperm, scHi-C


title: HS235,HS236,HS237, Human sperm, scHi-C


title: BJ8376,BJ8377,BJ8378, Mouse sperm, scHi-C


title: BJ8389,BJ8390,BJ8391, Mouse sperm, scHi-C


title: HS229,HS230,HS231, Human sperm, scHi-C


title: HS220,HS221,HS222, Human sperm, scHi-C


title: BJ8369,BJ8370,BJ8371, Mouse sperm, scHi-C


title: BJ8373,BJ8374,BJ8375, Mouse sperm, scHi-C


title: HS214,HS215,HS216, Human sperm, scHi-C


title: HS226,HS227,HS228, Human sperm, scHi-C


title: HS250,HS251,HS252, Human sperm, scHi-C


title: BJ8366,BJ8367,BJ8368, Mouse sperm, scHi-C


title: HS223,HS224,HS225, Human sperm, scHi-C


title: HS208,HS209,HS210, Human sperm, scHi-C


title: BJ8359,BJ8361,BJ8362, Mouse sperm, scHi-C


title: HS217,HS218,HS219, Human sperm, scHi-C


title: BJ8356,BJ8357,BJ8358, Mouse sperm, scHi-C


title: BJ8363,BJ8364,BJ8365, Mouse sperm, scHi-C


title: BJ8353,BJ8354,BJ8355, Mouse sperm, scHi-C


title: BJ8346,BJ8347,BJ8349, Mouse sperm, scHi-C


title: BJ8392,BJ8393,BJ8394, Mouse sperm, scHi-C


title: HS211,HS212,HS213, Human sperm, scHi-C


title: HS205,HS206,HS207, Human sperm, scHi-C


title: BJ8350,BJ8351,BJ8352, Mouse sperm, scHi-C


title: HS202,HS203,HS204, Human sperm, scHi-C


title: HS199,HS200,HS201, Human sperm, scHi-C


title: HS196,HS197,HS198, Human sperm, scHi-C


title: BJ8340,BJ8341,BJ8342, Mouse sperm, scHi-C


title: BJ8343,BJ8344,BJ8345, Mouse sperm, scHi-C


title: BJ8337,BJ8338,BJ8339, Mouse sperm, scHi-C


title: HS193,HS194,HS195, Human sperm, scHi-C


title: BJ8333,BJ8334,BJ8335, Mouse sperm, scHi-C


title: HS187,HS188,HS189, Human sperm, scHi-C


title: HS181,HS182,HS183, Human sperm, scHi-C


title: BJ8323,BJ8325,BJ8326, Mouse sperm, scHi-C


title: BJ8320,BJ8321,BJ8322, Mouse sperm, scHi-C


title: BJ8317,BJ8318,BJ8319, Mouse sperm, scHi-C


title: BJ8327,BJ8328,BJ8329, Mouse sperm, scHi-C


title: BJ8330,BJ8331,BJ8332, Mouse sperm, scHi-C


title: BJ8314,BJ8315,BJ8316, Mouse sperm, scHi-C


title: HS166,HS167,HS168, Human sperm, scHi-C


title: HS184,HS185,HS186, Human sperm, scHi-C


title: HS178,HS179,HS180, Human sperm, scHi-C


title: BJ8304,BJ8305,BJ8306, Mouse sperm, scHi-C


title: HS169,HS170,HS171, Human sperm, scHi-C


title: HS172,HS173,HS174, Human sperm, scHi-C


title: BJ8301,BJ8302,BJ8303, Mouse sperm, scHi-C


title: HS190,HS191,HS192, Human sperm, scHi-C


title: HS175,HS176,HS177, Human sperm, scHi-C


title: BJ8310,BJ8311,BJ8313, Mouse sperm, scHi-C


title: HS154,HS155,HS156, Human sperm, scHi-C


title: HS157,HS158,HS159, Human sperm, scHi-C


title: HS163,HS164,HS165, Human sperm, scHi-C


title: BJ8307,BJ8308,BJ8309, Mouse sperm, scHi-C


title: HS160,HS161,HS162, Human sperm, scHi-C


title: BJ8292,BJ8293,BJ8294, Mouse sperm, scHi-C


title: BJ8295,BJ8296,BJ8297, Mouse sperm, scHi-C


title: BJ8286,BJ8287,BJ8288, Mouse sperm, scHi-C


title: BJ8289,BJ8290,BJ8291, Mouse sperm, scHi-C


title: BJ8298,BJ8299,BJ8300, Mouse sperm, scHi-C


title: HS145,HS146,HS147, Human sperm, scHi-C


title: HS151,HS152,HS153, Human sperm, scHi-C


title: HS148,HS149,HS150, Human sperm, scHi-C


title: HS139,HS140,HS141, Human sperm, scHi-C


title: HS142,HS143,HS144, Human sperm, scHi-C


title: BJ8283,BJ8284,BJ8285, Mouse sperm, scHi-C


title: HS133,HS134,HS135, Human sperm, scHi-C


title: HS136,HS137,HS138, Human sperm, scHi-C


title: HS130,HS131,HS132, Human sperm, scHi-C


title: BJ8271,BJ8272,BJ8273, Mouse sperm, scHi-C


title: BJ8274,BJ8275,BJ8276, Mouse sperm, scHi-C


title: BJ8268,BJ8269,BJ8270, Mouse sperm, scHi-C


title: BJ8265,BJ8266,BJ8267, Mouse sperm, scHi-C


title: HS127,HS128,HS129, Human sperm, scHi-C


title: HS124,HS125,HS126, Human sperm, scHi-C


title: BJ8256,BJ8257,BJ8258, Mouse sperm, scHi-C


title: HS118,HS119,HS120, Human sperm, scHi-C


title: HS121,HS122,HS123, Human sperm, scHi-C


title: HS115,HS116,HS117, Human sperm, scHi-C


title: BJ8253,BJ8254,BJ8255, Mouse sperm, scHi-C


title: BJ8262,BJ8263,BJ8264, Mouse sperm, scHi-C


title: HS112,HS113,HS114, Human sperm, scHi-C


title: BJ8259,BJ8260,BJ8261, Mouse sperm, scHi-C


title: BJ8250,BJ8251,BJ8252, Mouse sperm, scHi-C


title: HS109,HS110,HS111, Human sperm, scHi-C


title: HS106,HS107,HS108, Human sperm, scHi-C


title: BJ8280,BJ8281,BJ8282, Mouse sperm, scHi-C


title: BJ8277,BJ8278,BJ8279, Mouse sperm, scHi-C


title: HS103,HS104,HS105, Human sperm, scHi-C


title: BJ8244,BJ8245,BJ8246, Mouse sperm, scHi-C


title: HS100,HS101,HS102, Human sperm, scHi-C


title: BJ8241,BJ8242,BJ8243, Mouse sperm, scHi-C


title: BJ8247,BJ8248,BJ8249, Mouse sperm, scHi-C


title: HS97,HS98,HS99, Human sperm, scHi-C


title: BJ8235,BJ8236,BJ8237, Mouse sperm, scHi-C


title: HS94,HS95,HS96, Human sperm, scHi-C


title: BJ8232,BJ8233,BJ8234, Mouse sperm, scHi-C


title: BJ8229,BJ8230,BJ8231, Mouse sperm, scHi-C


title: Stiff

city: Palo Alto

first: Sangkyun

last: Cho

state: California

address: 240 Pasteur Dr, Room 3200, Biomedical Innovations Building

country: USA

institute: Stanford University

description:
Library name: SC3
10X Genomics scRNA-seq platform

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were performed using the standard CellRanger pipeline.
Assembly: hg38 (human) and mm10 (mouse)
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

source_name: iPSC

extract_protocol:
In vitro samples (scRNA-seq): cultured cells were dissociated using accutase for 3 min (STEMCELL Technologies), washed with 1X DPBS (Gibco), strainer-filtered (40 and 70 µm Flowmi) to remove debris, and re-suspended in 0.04% BSA. In vivo samples (snRNA-seq): snap-frozen apical tissue slices were cut into smaller pieces (< 1 mm^3) on a pre-cooled surface on ice using a clean cold razor, and gently homogenized over two rounds using a Dounce homogenizer. The isolated nuclei were then strainer-filtered (40 and 70 µm Flowmi) to remove debris and re-suspended in Diluted Nuclei Buffer (10X Genomics).
After single-cell/nucleus isolation, libraries were constructed following exactly the instructions in the User Guides provided by the manufacturer: 10X Chromium Single Cell 3' v3.1 protocol for the in vitro samples, and 10X Chromium Single Cell Multiome ATAC + GEX (the snRNA-seq GEX portion only) for the in vivo samples.

tag: cell line

value: iPSC

value: iPSC-cardiac fibroblasts

tag: treatment

value: Pre-stimulation with TGF-beta


title: HS88,HS89,HS90, Human sperm, scHi-C


title: BJ8226,BJ8227,BJ8228, Mouse sperm, scHi-C


title: BJ8238,BJ8239,BJ8240, Mouse sperm, scHi-C


title: BJ8217,BJ8218,BJ8219, Mouse sperm, scHi-C


title: HS85,HS86,HS87, Human sperm, scHi-C


title: BJ8220,BJ8221,BJ8222, Mouse sperm, scHi-C


title: Soft_TGFbi

description:
Library name: SC2
10X Genomics scRNA-seq platform


title: BJ8211,BJ8212,BJ8213, Mouse sperm, scHi-C


title: Stiff_TGFbi

description:
Library name: SC4
10X Genomics scRNA-seq platform


title: HS82,HS83,HS84, Human sperm, scHi-C


title: BJ8214,BJ8215,BJ8216, Mouse sperm, scHi-C


title: HS79,HS80,HS81, Human sperm, scHi-C


title: BJ8205,BJ8206,BJ8207, Mouse sperm, scHi-C


title: BJ8208,BJ8209,BJ8210, Mouse sperm, scHi-C


title: right atrial appendage, post-operative AF, patient nr. 1409

city: Chicago

first: Igor

last: Efimov

state: Illinois

address: 303 E Superior St

institute: Northwestern University

library_source: transcriptomic

data_processing:
Sequence reads underwent trimming with Trimmomatic v0.36 to eliminate potential adapter sequences and low-quality nucleotides.
The trimmed reads were then aligned to the Homo sapiens GRCh38 reference genome from ENSEMBL using the STAR aligner v2.5.2b.
Unique gene hit counts were determined using featureCounts from the Subread package v1.5.2, and the results were summarized and reported based on the gene_id feature in the annotation file.
Only unique reads that mapped within exon regions were included in the counts.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: comma-separated text file includes raw counts for each Sample
Supplementary files format and content: comma-separated text file include TPM values for each Sample

molecule: total RNA

source_name: human patient right atrial appendage biopsy

extract_protocol:
Right atrial appendages were obtained from patients undergoing cardiac surgery. Tissues were immediately flash frozen in liquid nitrogennd and stored at -80 °C. Total mRNA was extracted from 40 mg of tissue with RNeasy Fibrous Tissue Mini Kit (Qiagen). RNA purity and yield were quality checked with Agilent Bioanalyzer to satisfy RIN >7 and total RNA amount 3-5 μg.
TruSeq RNA Library Prep Kit (Illumina)

tag: tissue

tag: Sex

value: female

tag: age

tag: diagnosis group

value: post-operative AF


title: BJ8202,BJ8203,BJ8204, Mouse sperm, scHi-C


title: right atrial appendage, post-operative AF, patient nr. 1394

value: human patient right atrial appendage biopsy

value: male


title: right atrial appendage, post-operative AF, patient nr. 1377


title: HS73,HS74,HS75, Human sperm, scHi-C


title: BJ8196,BJ8197,BJ8198, Mouse sperm, scHi-C


title: HS91,HS92,HS93, Human sperm, scHi-C


title: right atrial appendage, post-operative AF, patient nr. 1346


title: BJ8190,BJ8191,BJ8192, Mouse sperm, scHi-C


title: BJ8223,BJ8224,BJ8225, Mouse sperm, scHi-C


title: Soft

description:
Library name: SC1
10X Genomics scRNA-seq platform


title: BJ8199,BJ8200,BJ8201, Mouse sperm, scHi-C


title: BJ8187,BJ8188,BJ8189, Mouse sperm, scHi-C


title: right atrial appendage, post-operative AF, patient nr. 1280


title: HS70,HS71,HS72, Human sperm, scHi-C


title: BJ8181,BJ8182,BJ8183, Mouse sperm, scHi-C


title: BJ8184,BJ8185,BJ8186, Mouse sperm, scHi-C


title: BJ8178,BJ8179,BJ8180, Mouse sperm, scHi-C


title: BJ8193,BJ8194,BJ8195, Mouse sperm, scHi-C


title: HS64,HS65,HS66, Human sperm, scHi-C


title: HS67,HS68,HS69, Human sperm, scHi-C


title: right atrial appendage, post-operative AF, patient nr. 1267


title: right atrial appendage, post-operative AF, patient nr. 1258


title: HS76,HS77,HS78, Human sperm, scHi-C


title: right atrial appendage, post-operative AF, patient nr. 1246


title: right atrial appendage, sinus rhythm, patient nr. 1430

value: sinus rhythm


title: BJ8166,BJ8167,BJ8168, Mouse sperm, scHi-C


title: BJ8175,BJ8176,BJ8177, Mouse sperm, scHi-C


title: HS58,HS59,HS60, Human sperm, scHi-C


title: BJ8172,BJ8173,BJ8174, Mouse sperm, scHi-C


title: BJ8163,BJ8164,BJ8165, Mouse sperm, scHi-C


title: HS61,HS62,HS63, Human sperm, scHi-C


title: BJ8169,BJ8170,BJ8171, Mouse sperm, scHi-C


title: HS55,HS56,HS57, Human sperm, scHi-C


title: BJ8157,BJ8158,BJ8159, Mouse sperm, scHi-C


title: BJ8160,BJ8161,BJ8162, Mouse sperm, scHi-C


title: BJ8151,BJ8152,BJ8153, Mouse sperm, scHi-C


title: right atrial appendage, sinus rhythm, patient nr. 1426


title: HS49,HS50,HS51, Human sperm, scHi-C


title: BJ8145,BJ8146,BJ8147, Mouse sperm, scHi-C


title: right atrial appendage, sinus rhythm, patient nr. 1391


title: right atrial appendage, sinus rhythm, patient nr. 1398


title: BJ8154,BJ8155,BJ8156, Mouse sperm, scHi-C


title: HS52,HS53,HS54, Human sperm, scHi-C


title: BJ8142,BJ8143,BJ8144, Mouse sperm, scHi-C


title: BJ8139,BJ8140,BJ8141, Mouse sperm, scHi-C


title: right atrial appendage, sinus rhythm, patient nr. 1380


title: BJ8148,BJ8149,BJ8150, Mouse sperm, scHi-C


title: right atrial appendage, sinus rhythm, patient nr. 1322


title: HS43,HS44,HS45, Human sperm, scHi-C


title: BJ8130,BJ8131,BJ8132, Mouse sperm, scHi-C


title: HS40,HS41,HS42, Human sperm, scHi-C


title: BJ8136,BJ8137,BJ8138, Mouse sperm, scHi-C


title: BJ8127,BJ8128,BJ8129, Mouse sperm, scHi-C


title: BJ8133,BJ8134,BJ8135, Mouse sperm, scHi-C


title: BJ8124,BJ8125,BJ8126, Mouse sperm, scHi-C


title: HS37,HS38,HS39, Human sperm, scHi-C


title: right atrial appendage, sinus rhythm, patient nr. 1291


title: HS46,HS47,HS48, Human sperm, scHi-C


title: BJ8121,BJ8122,BJ8123, Mouse sperm, scHi-C


title: BJ8118,BJ8119,BJ8120, Mouse sperm, scHi-C


title: HS34,HS35,HS36, Human sperm, scHi-C


title: right atrial appendage, sinus rhythm, patient nr. 1309


title: BJ8109,BJ8110,BJ8111, Mouse sperm, scHi-C


title: right atrial appendage, sinus rhythm, patient nr. 1191


title: HS31,HS32,HS33, Human sperm, scHi-C


title: BJ8112,BJ8113,BJ8114, Mouse sperm, scHi-C


title: BJ8115,BJ8116,BJ8117, Mouse sperm, scHi-C


title: right atrial appendage, paroxysmal AF, patient nr. 1535

value: paroxysmal AF


title: BJ8100,BJ8101,BJ8102, Mouse sperm, scHi-C


title: BJ8103,BJ8104,BJ8105, Mouse sperm, scHi-C


title: BJ8106,BJ8107,BJ8108, Mouse sperm, scHi-C


title: HS25,HS26,HS27, Human sperm, scHi-C


title: HS28,HS29,HS30, Human sperm, scHi-C


title: HS22,HS23,HS24, Human sperm, scHi-C


title: right atrial appendage, paroxysmal AF, patient nr. 1381


title: right atrial appendage, paroxysmal AF, patient nr. 1230


title: right atrial appendage, paroxysmal AF, patient nr. 1067


title: BJ8085,BJ8086,BJ8087, Mouse sperm, scHi-C


title: BJ8091,BJ8092,BJ8093, Mouse sperm, scHi-C


title: BJ8094,BJ8095,BJ8096, Mouse sperm, scHi-C


title: BJ8088,BJ8089,BJ8090, Mouse sperm, scHi-C


title: HS16,HS17,HS18, Human sperm, scHi-C


title: HS19,HS20,HS21, Human sperm, scHi-C


title: BJ8082,BJ8083,BJ8084, Mouse sperm, scHi-C


title: right atrial appendage, persistent AF, patient nr. 2205

value: persistent AF


title: HS13,HS14,HS15, Human sperm, scHi-C


title: right atrial appendage, persistent AF, patient nr. 2202


title: BJ8076,BJ8077,BJ8078, Mouse sperm, scHi-C


title: GFP_ctrl_2

city: Munich

first: Ali

last: Rezaei

address: Feodor-Lynen-Strasse 17

country: Germany

institute: LMU

description: Library name: GFP-ctrl-2

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format. Software Information: SOAPnuke (Version v1.5.2); Parameters -l 15 -q 0.2 -n 0.05.
Assembly: GRCh38.p14
Supplementary files format and content: Count table as CSV file; rows are gene names while each column corresponds to a unique sample in the study.

source_name: smNPC

growth_protocol: Human neurons were generated by doxycycline-mediated induction of NGN2 expression in small neural precursor cells (smNPC). The smNPCs are maintained in expansion medium containing N2B27 medium supplemented with CHIR (3 uM), PMA (0.5 uM) and ascorbic acid (64 mg/L). For treatment, smNPCs are differentiated into iNeurons through NGN2 expression induced by doxycycline (2.5 ug/mL). After induction, smNPCs differentiate into iNeurons within 5 days.

extract_protocol:
On day 19, RNA was isolated using Qiagen RNeasy Micro Kit according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using BGI in house mRNA-Seq Library Prep Kit following manufacturer's protocols (sample QC, mRNA Isolation, mRNA Fragmentation, cDNA Synthesis, End Repair, Add A and Adaptor Ligation, PCR, Library QC, Circularization). Libraries were paired-end sequenced with a read length of 100 bp and an average depth of 20 million reads.

treatment_protocol: iNeurons are transduced with GA149x-GFP and GFP lentiviral constructs on day 7, media change to remove excess virus on day 8, and CD (2.5 mg/mL) treatments were initiated at day 10. CD was added to the media at the same concentration every other day.

value: smNPC

value: neuron

tag: genotype

value: GFP transduction

value: Vehicle


title: HS10,HS11,HS12, Human sperm, scHi-C


title: BJ8073,BJ8074,BJ8075, Mouse sperm, scHi-C


title: GFP_ctrl_3

description: Library name: GFP-ctrl-3


title: right atrial appendage, persistent AF, patient nr. 2097


title: BJ8097,BJ8098,BJ8099, Mouse sperm, scHi-C


title: right atrial appendage, paroxysmal AF, patient nr. 1529


title: GFP_ctrl_1

description: Library name: GFP-ctrl-1


title: T61342_TG

description: Library name: T61342

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor (adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered ""Clean Reads"" are saved in FASTQ format.  Software Information: SOAPnuke (Version v1.5.2); Parameters -l 15 -q 0.2 -n 0.05
Software of HISAT use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these alignment positions to align the remaining sequences of each read to extend the alignment area. Software Information: HISAT2 (Version: v2.0.4); Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8
Expression quantification: We used Bowtie2[1] to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM[2] to calculate the gene expression level of each sample. Software Information: Bowtie2 (version: v2.2.5); Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200; Official Website: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml RSEM: (version: v1.2.8); Parameters：-p 8 --forward-prob 0.5 --paired-end; Official Website: http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html References: [1] Langmead, B. et al. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012); [2] Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).
Assembly: mm10
Supplementary files format and content: count table as CSV file; rows are gene names while each column corresponds to a unique sample in the study

source_name: neocortex

growth_protocol: two weeks after ASO injection, TDP-43ΔNLS transgene expression was induced by switching mice to chow without doxycycline

extract_protocol:
30 mg/sample was used with the RNEasy Plus Mini Kit from Qiagen
RNA libraries for RNA-seq were prepared using BGI in house mRNA-Seq Library Prep Kit following manufacturer's protocols (sample QC, mRNA Isolation, mRNA Fragmentation, cDNA Synthesis, End Repair, Add A and Adaptor Ligation, PCR, Library QC, Circularization). Libraries were paired-end sequenced with a read length of 100 bp and an average depth of 20 million reads.

treatment_protocol: single intracereboventricular ASO injection as described in the experimental design section

value: neocortex

value: TG

value: non-targeting ASO

tag: batch

value: A


title: BJ8070,BJ8071,BJ8072, Mouse sperm, scHi-C

value: Sperm cells


title: HS1,HS2,HS3, Human sperm, scHi-C


title: GFP_CD_4

description: Library name: GFP-CD-4

value: CD


title: B3

city: XuZhou

first: xinxing

last: huang

state: JiangSu

address: 209 Tongshan Road

institute: university

description: Library name: NC-3

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: mmu10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: BV2 cells were cultured for 24 h after passage

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: Incubate for 24 h after adding LPS to the medium

value: dopamine cells

tag: stimulation

value: LPS stimulates for 24 h

value: treated with extracellular vesicles from control microglia


title: right atrial appendage, persistent AF, patient nr. 2060

value: human patient right atrial appendage biopsy

value: female


title: BJ8067,BJ8068,BJ8069, Mouse sperm, scHi-C


title: BJ8061,BJ8062,BJ8063, Mouse sperm, scHi-C


title: BJ8079,BJ8080,BJ8081, Mouse sperm, scHi-C


title: HS7,HS8,HS9, Human sperm, scHi-C


title: GFP_CD_2

description: Library name: GFP-CD-2


title: GFP_CD_3

description: Library name: GFP-CD-3


title: BJ8064,BJ8065,BJ8066, Mouse sperm, scHi-C


title: HS4,HS5,HS6, Human sperm, scHi-C


title: T61340_TG

description: Library name: T61340


title: right atrial appendage, persistent AF, patient nr. 1747

value: male


title: GFP_CD_1

description: Library name: GFP-CD-1


title: B2

description: Library name: NC-2


title: B1

description: Library name: NC-1


title: T61331_WT

description: Library name: T61331

value: WT


title: BJ8058,BJ8059,BJ8060, Mouse sperm, scHi-C


title: BJ8055,BJ8056,BJ8057, Mouse sperm, scHi-C


title: GA_ctrl_3

description: Library name: GA-ctrl-3

value: smNPC

value: poly(GA) transduction


title: A3

description: Library name: SIX2-3

value: treated with extracellular vesicles from SIX2 overexpressing microglia


title: A2

description: Library name: SIX2-2


title: BJ8052,BJ8053,BJ8054, Mouse sperm, scHi-C


title: T61345_WT

description: Library name: T61345


title: BJ8049,BJ8050,BJ8051, Mouse sperm, scHi-C


title: T60303_TG

description: Library name: T60303


title: GA_ctrl_2

description: Library name: GA-ctrl-2

value: neuron

value: Vehicle


title: T61334_WT

description: Library name: T61334

value: neocortex


title: A1

description: Library name: SIX2-1


title: GA_ctrl_1

description: Library name: GA-ctrl-1


title: T61333_WT

description: Library name: T61333

value: non-targeting ASO


title: T_69524_TG

description: Library name: T_69524

value: TG

value: B


title: BJ8043,BJ8044,BJ8045, Mouse sperm, scHi-C

value: Sperm cells


title: GA_CD_3

description: Library name: GA-CD-3

value: CD


title: T_69523_WT

description: Library name: T_69523


title: BJ8046,BJ8047,BJ8048, Mouse sperm, scHi-C


title: Melanoma tumor cells, donor 3, rep 2

city: La Jolla

first: Maayan

last: Baron

state: CA

address: 9500 Gilman Dr.

institute: University of California San Diego

description: Library name: BS03229A

data_processing:
Quality control was also performed as described previously (Baron et al 2016). The raw matrix count was first transformed to UMIs (Unique Molecular Identifiers) to correct for library preparation duplications. Cells with >750 distinct UMIs, mitochondrial transcripts <20% and ribosomal transcripts <30% were selected for analysis. UMI counts for the selected cells were normalized by the total number of transcripts per cell, and a scale factor equivalent to the median number of transcripts across all cells was applied (transcripts per median, TPM).
Assembly: hg19
Supplementary files format and content: mtx files and tab files for gene names

source_name: skin

extract_protocol:
Melanoma tumors were collected post-operatively from two patients who consented and signed IRB. To obtain single-cell suspensions, samples were washed in PBS and cut into small pieces (4-5 mm3) followed by dissociation using the Miltenyi human tumor dissociation kit according to manufacturer instructions. Red blood cells were depleted using ACK lysis buffer for 3 minutes. Dead cells were removed, if needed, using the Milyenty dead cell separator.
Single cell encapsulation and library preparation were performed using the inDrop platform followed by sequencing on an Illumina NextSeq. Sequencing reads were de-multiplexed, aligned and counted using a custom pipeline as described previously (Baron et al 2020) to produce a raw count matrix for each tumor.

value: skin


title: Melanoma tumor cells, donor 3, rep 1

description: Library name: BS03155A


title: GA_ctrl_4

description: Library name: GA-ctrl-4


title: BJ8040,BJ8041,BJ8042, Mouse sperm, scHi-C


title: T_70261_TG

description: Library name: T_70261


title: Melanoma tumor cells, donor 2

description: Library name: BS02594A


title: BJ8037,BJ8038,BJ8039, Mouse sperm, scHi-C


title: GA_CD_4

description: Library name: GA-CD-4


title: T_69531_TG

description: Library name: T_69531


title: RNA-seq of Synovium in patients with rheumatoid arthritis-GCK3

city: Shanghai

first: Li

last: Cheng

state: Shanghai

address: 500 Quxi Road, Shanghai 200011

department: Department of Rehabilitation Medicine

institute: The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
The raw paired-end fastq reads underwent filtering by TrimGalore to eliminate adapters and low-quality bases, which was accomplished through the utilization of the Cutadapt tool.
The resulting clean reads were then aligned to the genome using HISAT2, followed by reference-guided transcriptome assembly and gene expression quantification utilizing StringTie.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene_count values, gene_tpm value for each Sample

source_name: synovium

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424)
High-quality RNA samples were used to construct a sequencing library.

value: synovium

tag: subject status

value: patient with rheumatoid arthritis

value: not determined

value: ginsenoside CK treatment.


title: GA_CD_2

description: Library name: GA-CD-2


title: HDR_100 mGy_2

city: Seoul

first: Yeonghoon

last: Son

address: 75, Nowon-ro

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences (KIRAMS)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Human coronary artery endothelial cells

growth_protocol: HCAEC cells were maintained in EGM-2 MV Microvascular Endothelial Cell Growth Medium-2 BulletKit with antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: Human coronary artery endothelial cells were exposed to 100 mGy ionizing radiation at 6 mGy/h (low-dose-rate) or 288 mGy/h (high-dose-rate). After 72 h, total RNA was extracted from sham or irradiated cells for Quant-Seq 3'mRNA-Seq, and bioinformatic analyses were performed using Metascape. Gene profiling was validated using qPCR.

value: Human coronary artery endothelial cells

value: Primary cell

value: WT

value: High-dose-rate irradiation 100 mGy (288 mGy/h)


title: RNA-seq of Synovium in patients with rheumatoid arthritis-GCK2


title: HDR_100 mGy_1


title: BJ8031,BJ8032,BJ8033, Mouse sperm, scHi-C


title: Melanoma tumor cells, donor 1

description: Library name: BS01487A


title: GA_CD_1

description: Library name: GA-CD-1

value: smNPC

value: neuron

value: poly(GA) transduction


title: BJ8034,BJ8035,BJ8036, Mouse sperm, scHi-C


title: T_69526_TG

description: Library name: T_69526

value: neocortex

value: non-targeting ASO


title: BJ8025,BJ8026,BJ8027, Mouse sperm, scHi-C


title: T_70260_WT

description: Library name: T_70260

value: B


title: HDR_0 mGy_1

value: Non treatment


title: T_70256_WT

description: Library name: T_70256


title: HDR_0 mGy_2


title: T_69527_WT

description: Library name: T_69527


title: BJ8028,BJ8029,BJ8030, Mouse sperm, scHi-C

value: Sperm cells


title: RNA-seq of Synovium in patients with rheumatoid arthritis-GCK1


title: RNA-seq of Synovium in patients with rheumatoid arthritis-dex2

value: dexamethasone treatment.


title: RNA-seq of Synovium in patients with rheumatoid arthritis-dex3

value: synovium


title: BJ8022,BJ8023,BJ8024, Mouse sperm, scHi-C


title: BJ8019,BJ8020,BJ8021, Mouse sperm, scHi-C


title: LDR_100 mGy_2

value: Low-dose-rate irradiation 100 mGy (6 mGy/h)


title: T_70263_TG

description: Library name: T_70263

value: TG


title: RNA-seq of Synovium in patients with rheumatoid arthritis-dex1

value: patient with rheumatoid arthritis

value: not determined


title: LDR_100 mGy_1

value: Human coronary artery endothelial cells

value: Primary cell


title: T_70262_WT

description: Library name: T_70262

value: WT


title: BJ8016,BJ8017,BJ8018, Mouse sperm, scHi-C


title: RNA-seq of Synovium in patients with rheumatoid arthritis-control3

value: no treatment


title: LDR_0 mGy_2


title: T_69532_WT

description: Library name: T_69532


title: T_70264_WT

description: Library name: T_70264


title: RNA-seq of Synovium in patients with rheumatoid arthritis-control2


title: RNA-seq of Synovium in patients with rheumatoid arthritis-control1


title: T_70267_TG

description: Library name: T_70267


title: si_1

city: London

first: Prabhakar

last: Rajan

address: Charterhouse Sq

department: BCI

country: United Kingdom

institute: QMUL

data_processing:
Reads were aligned to the genome using STAR v2.7.3a in dual pass mode
Transcripts were assembled and quantified in TPM using Stringtie v2.1.1
Read normalisation was performed using DESeq2 v1.34.0
Assembly: hg38
Supplementary files format and content: Matrix tables with raw and normalized gene counts for every gene and every sample

growth_protocol: PC3M cells were obtained from ATCC and their identities were confirmed by Short Tandem Repeat (STR) profiling (DDC Medical). Cells were incubated at 37oC, 5% CO2 in a humidified incubator. Cells were maintained at sub-confluency in RPMI-1640 medium (21875-034, Gibco) containing 2 mM L-glutamine, supplemented with 10% foetal calf serum (FCS) (Gibco), 100 units/ml penicillin and 100 µg/ml streptomycin (15140-122, Gibco) and regularly tested for the presence of mycoplasma.

extract_protocol:
After 72 hours siRNA treatment cells were washed 3x in PBS and then RNA was extracted from cells using Qiagen Rneasy mini kit (QIAgen 74004). To exclude genomic contamination, total RNA was treated with DNAse I (AMPD1, Sigma).
True-seq Illumina
RNA-Seq, 75bp (30M reads plexed) Nextseq 500

treatment_protocol: PC3M cells were transfected with 25nM non-silencing (NSI) or HNRNPA2B1 targeting siRNA with RNAiMax (13778-075, Thermo Fisher Scientific) according to the manufacturers’ instructions

value: Prostate Cancer Cell Line


title: si_3


title: BeWo cell, forsklin to to induce differentiation of BeWo to sycytiotrophoblast (STB)

type: RNA

city: Hradec Kralove

first: Mohammed

last: Ali

address: Čechova 722/2, 50002 Hradec Králové 2

department: pharmacology and Toxicology

country: Czech Republic

institute: Charles university

description: Cells

data_processing:
The data were analyzed using R statistical software and functions integrated with tidyverse package. The graphs were created using the packages ggplot2, ggbeeswarm, ggpubr, ggprism, ggrepel, and ggtext. The statistical evaluation was performed by R stat functions or the rstatix package. The gene expression data were processed on the principle of delta-delta Ct method. The interplate calibrator reaction was analyzed in each run in triplicates and the mean value was subtracted from Ct values in all analyses and the dCt values were generated. For the normalization mean of the dCt values of reference gene expression of B2M, GAPDH, and YWHAZ was used. The normalized dCtNORM values were acquired by subtraction of dCt value of the target gene from the dCt value of the reference gene. These values were re-scaled to the median of the reference group and presented as log2 of expression corresponding to a difference between dCtNORM of the sample and the median of dCtNORM values of the reference group.
Processed data: The values in the matrix table represent log₂-transformed normalized gene expression values, calculated using the ΔΔCt (delta-delta Ct) method. Ct values were adjusted by subtracting the mean Ct of an interplate calibrator reaction, ensuring consistency across runs. Gene expression was normalized using the mean ΔCt of reference genes (B2M, GAPDH, and YWHAZ), generating ΔCtNORM values. These values were then re-scaled to the median of the reference group and presented as log₂ expression values, corresponding to the difference between the ΔCtNORM of the sample and the median ΔCtNORM of the reference group.

label: FAM

source_name: BeWo cells, choriocarcinoma cell line isolated form human placetna

label_protocol: cDNA was prepared using the iScript Advanced cDNA Synthesis Kit (Bio-Rad). The reaction mixture was prepared by adding 4 µL of 5× iScript Advanced Reaction Mix, 1 µL of iScript Advanced Reverse Transcriptase, 10 µL of RNA (500 ng per 1 µL), and 5 µL of nuclease-free water, making a total reaction volume of 20 µL. cDNA synthesis was performed using a T100 Thermal Cycler, with the following conditions: 20 minutes at 46°C for reverse transcription, followed by 1 minute at 95°C to inactivate reverse transcriptase

growth_protocol: Human placental samples from first-trimester, term, and preterm births were obtained directly from patients and subsequently isolated for analysis. Rat placentas were collected at gestation days 12, 15, and 20, followed by isolation for further processing. Primary trophoblast cells were isolated from term placentas and cultured under standard cell culture conditions. BeWo cells were maintained under normal culture conditions and harvested for RNA extraction.

extract_protocol: RNA was extracted using TRI Reagent. For tissue samples, 1 mL of TRI Reagent per 100 mg of tissue was used, while for cell culture samples, 1 mL of TRI Reagent per 25 cm² flask was used. Samples were homogenized, and chloroform (200 µL per 1 mL of TRI Reagent used) was added to the homogenized sample, followed by vigorous shaking for 15 seconds. The sample was then centrifuged at 12,000 g for 15 minutes at 4°C, resulting in the formation of three phases: an aqueous phase containing RNA, an interphase containing proteins, and an organic phase containing lipids and DNA. The aqueous phase was carefully collected, ensuring no contamination from the interphase. 2-Propanol (500 µL per 1 mL of TRI Reagent used) was added to the collected aqueous phase, mixed, and left to stand at room temperature for 10 minutes. The sample was then centrifuged at 12,000 g for 10 minutes at 4°C, forming an RNA pellet. The supernatant was removed, and the pellet was washed with 75% ethanol (1 mL per 1 mL of TRI Reagent used), followed by centrifugation at 12,000 g for 5 minutes at 4°C. This ethanol wash was repeated twice to ensure purity. The remaining ethanol was carefully removed with a pipette and allowed to evaporate without drying the pellet completely. The RNA pellet was then dissolved in 20 µL of API (Aqua pro injectione). 1.5 µL of the isolated RNA was transferred to a separate vial for purity assessment. 1 µL of RNA was loaded onto a Nanodrop spectrophotometer, and absorbance was measured to determine RNA purity. The optimal 260/280 ratio was 1.8 – 2.2, indicating high RNA purity, while an optimal 260/230 ratio was >1.7. Lower 260/280 ratios indicated protein or DNA contamination, whereas lower 260/230 ratios suggested organic solvent contamination

treatment_protocol: For primary trophoblast cells, cells were initially seeded for 8 hours to allow attachment as cytotrophoblasts (CTB). They then underwent spontaneous differentiation into syncytiotrophoblasts (STB) over 72 hours in culture, with daily medium changes. For BeWo cells, they remained as cytotrophoblasts upon seeding. Differentiation into syncytiotrophoblasts was induced by forskolin (50 µM) treatment. Since forskolin was dissolved in DMSO, a 0.05% DMSO control was included for BeWo cytotrophoblast cells to account for any solvent effects.

value: Cells


title: BJ8010,BJ8011,BJ8012, Mouse sperm, scHi-C


title: CTCT-AID_ZNF143KO

first: Mo

last: Zhang

address: 800 Dongchuan Road

institute: Shanghai Jiaotong University

data_processing:
The HiC-Pro (v3.0.0) was used for Hi-C pre-process that includes reads alignment to GRCh37/hg19, building contact maps, and ICE normalization on contact maps. 10Kb, 25Kb, 100Kb, 200Kb, 500Kb, 1Mb ICE normalized interaction matrix was generated.
The juicer2juicebox script from HiC-Pro suite was used to transform .validPairs file generated from HiC-Pro to .hic file that can be used by Juicer tools. Hic2cool (v0.8.3) was used to convert .hic file to .cool file.
The loops were searched from 4kb to 2Mb distance to diagonal using Chromosight (v1.6.3) detect function with the the parameter --min-dist 40,000 –max-dis 2,000,000.
Aggregate peak analysis (APA) for loops was using coolpup.py (v1.0.0)  with default parameter, and the matrix is visualized by plotpup.py from coolpup.py.
TAD domains were called using Juicer tools Arrowhead function at 10kb resolution. Aggregate domain analysis (ADA) for TAD was calculated by a custom python script.
The directionality score was calculated by Fan-C (v0.9.10) directionality function with the widow-size as 4,000,000.
Hi-C eigenvector and Pearson value were computed using Juicer tool eigenvector and pearsons function with 100Kb resolution.
Assembly: hg19
Supplementary files format and content: hic, bedpe

growth_protocol: Human HEC-1-B cells and derived cell lines were cultured in MEM, 200mM L-Glutamine, Earle’s Balanced Salts (Hyclone) supplemented with 1mM sodium pyruvate (Sigma), 1% penicillin-streptomycin (Gibco) and 10% fetal bovine serum (Gibco). Human HCT-116 RAD21-AID-mClover cells (Natsume et al., 2016) were cultured in RPMI Medium 1640 L-Glutamine (Gibco), 1% penicillin-streptomycin (Gibco 15140122) and 10% fetal bovine serum (Gibco). The cells were cultured at 37°C in the incubator supplied with 5% (v/v) of CO2.

extract_protocol:
About 5 million cross-linked cells were lysed with lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% NP-40) to obtain nuclei. Nuclei were incubated with SDS and quenched by adding Triton X-100. Samples DNA was digested with MboI (NEB R0147M) for overnight at 37℃. After heat inactivation at 62℃, restriction fragment overhangs were filled and marked with biotin-14-dATP (Thermo 19524016), dCTP, dTTP, dGTP, and DNA Polymerase I, Large (Klenow) Fragment (NEB M0210L). After Proximity ligation using T4 DNA ligase (NEB M0202S), samples were reverse cross-links at 68℃ for overnight. DNA samples were precipitated with ethanol and then sonicated to fragmentize DNA. DNA fragment size selection was performed by using AMPure XP Beads (Beckman A63881), and 300-500 bp DNA fragments were used for the next step. M-280 Streptavidin beads (Thermo 11206D) were used to select DNA fragments marked with biotin.
Library construction steps were performed while DNA samples were still bound to the bead interval with strict washing. NEB end-repair module (NEB E6050S) was used to blunt DNA end and dA-Tailing DNA reaction performed with Klenow exo- (NEB M0212S). Illumina U-type adaptors were adopted to add adaptor for DNA, and USER enzyme (NEB M5505S) was used for adaptor cleavage. After 10-12 of cycles PCR amplification, DNA samples were purified with AMPure XP Beads (Beckman A63881).
In situ Hi-C

treatment_protocol: In order to degrade protein labeled with AID in TiR1 expression cells, IAA was added to final concentration of 500 μM for 6-24 hours.

value: IAA, 0h

value: Human Uterine Adenocarcinoma Cells

value: CTCF-AID, ZNF143KO


title: LDR_0 mGy_1

value: Non treatment


title: BJ8013,BJ8014,BJ8015, Mouse sperm, scHi-C

value: Sperm cells


title: 1391_TG

description: Library name: 1391

source_name: thoracic spinal cord

extract_protocol:
30 mg/sample was used with the RNEasy Plus Mini Kit from Qiagen
RNA libraries for RNA-seq were prepared using BGI in house mRNA-Seq Library Prep Kit following manufacturer's protocols (sample QC, mRNA Isolation, mRNA Fragmentation, cDNA Synthesis, End Repair, Add A and Adaptor Ligation, PCR, Library QC, Circularization). Libraries were paired-end sequenced with a read length of 100 bp and an average depth of 20 million reads .

value: thoracic spinal cord


title: si_2


title: BJ8007,BJ8008,BJ8009, Mouse sperm, scHi-C


title: BJ8001,BJ8002,BJ8003, Mouse sperm, scHi-C


title: BJ8004,BJ8005,BJ8006, Mouse sperm, scHi-C


title: CTCF-AID_ZNF143KO_CTCF-Degron

value: IAA, 24h


title: 1394_WT

description: Library name: 1394


title: T_70252_TG

description: Library name: T_70252

value: neocortex

value: non-targeting ASO

value: B


title: BeWo cell, DMSO-treated (CTB) used to compare to FSK-treated cells (model of STB)

description: Cells


title: CTCT-AID_WT

value: CTCF-AID


title: NSI_3


title: CTCT-AID_CTCF-Degron


title: NSI_2


title: 1352_WT

description: Library name: 1352


title: ZNF143KO_


title: NSI_1


title: Primary cell, syncytiotrophoblast (STB)

description: Cells

source_name: Primary cells, spontaneously differentiated trophoblast cells isolated from human term placenta


title: 1339_TG

description: Library name: 1339

value: TG


title: Primary cell, cytotrophoblast (CTB) used to compare to syncytiotrophoblast (STB)

description: Cells

source_name: Primary cells, trophoblast cells isolated from human term placenta


title: WT

value: wild type


title: 1316_WT

description: Library name: 1316

value: WT


title: metastatic > 5 metastases 4

city: Adelaide

first: Stefano

last: Mangiola

state: SA

address: North Terrace

department: SAiGENCI

country: Australia

institute: University of Adelaide

description: Library name: BCB-0106

data_processing:
Quality control and filtering were performed for each sample independently. The empty droplets were identified using barcodeRanks below the inflection point. The mitochondrial gene names were downloaded using AnnotationDbi (mapIds) and EnsDb.Hsapiens.v86. Scuttle was used for calculating cell quality metrics (perCellQCMetrics) with default parameters. The function isOutlier was used with default parameters to label outlier cells based on the fraction of mitochondrial transcription and ribosomal genes.
DoubletFinder (v3) was used with default parameters to identify and filter out doublets.
We identified variable genes using Seurat. We estimated the cell cycle phase using CellCycleScoring. Using principal component analysis (PCA) and UMAP dimensionality reduction, we checked that the cell cycle was not a major confounder for cell distribution and grouping. We scaled counts cell-wise and removed the residual mitochondrial and ribosomal content unwanted variation using SI-GA-E5 as the reference sample (as it was of good quality according to previous analyses and sequencing output), using SCT transform
We separated the macro clusters lymphoid, myeloid, and b-cells for independent integration, clustering, and marker gene selection. For each macro cluster, the unwanted sample-wise technical variation was removed using an anchor strategy implemented in Seurat
The curated cell annotation was based on a consensus between the identified markers and the label transfer described above (using pbmc_multimodal as reference). The classification of the gamma delta population was refined using an ad hoc signature.
Assembly: GRCh38-3.0.0
Supplementary files format and content: SingleCellExperiment with metadata

source_name: blood

extract_protocol: Single Cell V3 Protocol

value: blood

value: PBMC

tag: age primary_tumour_diagnosis

tag: race

value: Caucasian

tag: cells

value: Female

tag: alive or_dead

value: A

tag: sample id_2


title: Guard Cell, ABA 60 minutes, Replicate 3

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

data_processing:
Alignment using TopHat2 to the Darmor genome
Assembly: B. napus Darmor line
Supplementary files format and content: Read count matrix

organism: Brassica napus

source_name: Leaf

extract_protocol:
RNA was extracted using the RNeasy Plant Mini Kit (Qiagen).
Standard single-stranded Illumina protocols.

value: Leaf

value: Guard Cell

value: ABA 60 minutes


title: Rat placenta gestation day 20, female fetus

description: Rat placenta

organism: Rattus norvegicus

source_name: Rat placentas, gestation day 20

value: placenta


title: Rat placenta gestation day 20, male fetus

description: Rat placenta


title: 1300_WT

description: Library name: 1300

value: thoracic spinal cord


title: Guard Cell, ABA 60 minutes, Replicate 2


title: Rat placenta gestation day 20 used to compare GD12 GD15

description: Rat placenta


title: 1254_WT

description: Library name: 1254


title: Rat placenta gestation day 15

description: Rat placenta

source_name: Rat placentas, gestation day 15


title: metastatic > 5 metastases 3

description: Library name: BCB-0108

value: D


title: Guard Cell, ABA 15 minutes, Replicate 3

value: ABA 15 minutes


title: 1270_TG

description: Library name: 1270


title: Rat placenta gestation day 12

description: Rat placenta

source_name: Rat placentas, gestation day 12


title: Guard Cell, ABA 60 minutes, Replicate 1


title: Guard Cell, ABA 15 minutes, Replicate 2


title: metastatic > 5 metastases 2

description: Library name: BCB-0160


title: 1252_WT

description: Library name: 1252


title: Guard Cell, ABA 15 minutes, Replicate 1


title: oligometastatic < 5 metastases 5

description: Library name: BCB-0105


title: oligometastatic < 5 metastases 4

description: Library name: BCB-0104


title: Guard Cell, Control Replicate 3

value: Control


title: metastatic > 5 metastases 1

description: Library name: BCB-0137

value: Asian


title: 1239_TG

description: Library name: 1239

value: TG


title: Term used to comapre to PTB

description: Human placenta

source_name: Term, late gestation


title: oligometastatic < 5 metastases 3

description: Library name: BCB-0109


title: Preterm birth (PTB)

description: Human placenta

source_name: Preterm birth, pathological


title: 1244_TG

description: Library name: 1244


title: Guard Cell, Control Replicate 2


title: 1238_WT

description: Library name: 1238


title: Term used to comapre to FT

description: Human placenta


title: oligometastatic < 5 metastases 2

description: Library name: BCB-0099


title: 1227_TG

description: Library name: 1227


title: Guard Cell, Control Replicate 1


title: oligometastatic < 5 metastases 1

description: Library name: BCB-0097


title: First-trimester (FT)

description: Human placenta

source_name: First-trimester, early gestation


title: Mettl14 knockout, replicate2, scRNAseq

status: Public on Mar 07 2025

city: Philadelphia

first: Yachen

last: Shen

address: 3400 Civic Center Blvd, Philadelphia, PA 19104

institute: University of Pennsylvania

description:
Library name: Sampel6
Drop-seq

data_processing:
Single cell raw sequencing data was demultiplexed with bcl2fastq2 (Illumina) with adaptor trimming turned off. Additional processing was performed using drop-seq tools v.2.5.1 (Saunders et al., 2018) with GRCm39 as the reference genome, and GENCODE vM.25 GTF as the annotation file.
Assembly: mm10
Supplementary files format and content: raw counts, each file is a raw counts table for cells obtained from one Drop-seq run (single-cell).

source_name: arcuate nucleus of hypothalamus

extract_protocol:
For micro-dissected hypothalamic arcuate-median eminence complex (ARC–ME) samples, 4 pairs of postnatal day 0 CTRL and NKO mice were dissected, then brains were rapidly extracted and cooled in ice-cold Hibernate-A medium. To obtain coronal sections containing the ARC–ME region, each brain was immersed in melted 3% low melting point agarose dissolved in DMEM kept at 37°C in a custom cryo mold. The agarose mold was placed on ice for 5-10 mins to solidify. Slicing was performed using a Leica VT 1200S vibratome in ice-cold DMEM:F12 medium at 0.1 mm/s speed and 1 mm vibration amplitude. The 250 μm-thick brain slices were separated from the agarose by gentle pipetting and the continuous six slices from around Bregma -0.96 to – 2.80 mm were collected. The ARC–ME was micro-dissected by knife cuts at its visually approximated dorsolateral borders and pooled by each mouse. Pooled ARC–ME samples were digested by papain solution for 30 min at 37 °C with gentle agitation. After washing with 5 ml Hibernate A medium, the tissues were triturated with fire-polished glass Pasteur pipettes into a single-cell suspension within Hibernate A medium. To remove debris, the single-cell suspension was loaded on a 2-layer gradient and centrifuged at 100 g for 6 min at 4C, and cells were filtered through a 70-μm cell strainer in (Hughes et al., 2020)DPBS with 0.01% BSA (w/v). A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted using an automated cell counter (Invitrogen) and manual.
Single-cell libraries were constructed as per the Dropseq protocol (Macosko et al., 2015) with minor modifications. Briefly, each sample was loaded onto 2-3 droplet generation runs, and cell suspensions and droplets were kept on ice prior to droplet encapsulation and droplet breakage. After exonuclease I treatment, samples were performed with second strand synthesis as previously described(Hughes et al., 2020). In the cDNA PCR amplification stage, around 4,000 beads were combined in a single PCR tube reaction and purified individually using 0.6x AMPure XP beads. cDNA across multiple runs of the same sample were pooled together and used as input for tagmentation, where the tagment reaction time was increased to 6 min. Final samples were purified twice with 0.6x AMPure XP beads. Sequencing library fragment sizes were quantified by bioanalyzer, and concentrations were quantified by qPCR (KAPA). Samples were pooled, loaded at 2.0-2.2 pM, and sequenced on a Next-Seq 550 (Illumina) with a 20 bp Read 1 and 64 bp Read 2. The custom Read 1 primer was spiked into the usual Illumina sequencing primer well at the manufacturer’s recommended concentration.

treatment_protocol: tissue obtained from control and Nkx2.1-CreTg/+::Mettl14f/f

value: arcuate nucleus of hypothalamus

value: Mettl14 Knockout


title: Control, replicate4, scRNAseq

description:
Library name: Sampel4
Drop-seq


title: Mettl14 knockout, replicate4, scRNAseq

description:
Library name: Sampel8
Drop-seq


title: Mettl14 knockout, replicate1, scRNAseq

description:
Library name: Sampel5
Drop-seq


title: Mettl14 knockout, replicate3, scRNAseq

description:
Library name: Sampel7
Drop-seq


title: Control, replicate3, scRNAseq

description:
Library name: Sampel3
Drop-seq


title: Control, replicate2, scRNAseq

description:
Library name: Sampel2
Drop-seq


title: E8 NES nanobody R1

city: Exeter

first: Akshay

last: Bhinge

address: Stocker Road

department: CBS

institute: Living Systems Institute, University of Exeter

description:
Library name: E8_nes_R1
polyA purified total RNA

data_processing:
Raw reads were processed using minimap2.
Gene counts were generated using Flair.
Assembly: hg19
Supplementary files format and content: tab-separated gene counts

source_name: iPSC-derived

growth_protocol: Healthy iPSCs were grown on matrigel in StemFlex and dissociated into small colonies with 0.1 mM EDTA when 70% confluent. Cells were plated as colonies in a 1:6 split.

extract_protocol:
Total RNA was harvested using Qiazol
Libraries were constructed using the ONT ligation sequencing kit according to the manufacturer's protocol.
RNA-seq ONT long-read

treatment_protocol: iPSCs were plated as colonies onto Matrigel and treated with neuronal differentiation media (DMEM/F12:Neurobasal in a 1:1 ratio, HEPES 10mM, N2 supplement 1%, B27 supplement 1%, L-glutamine 1%, ascorbic acid 5uM) supplemented with SB431542 (40uM), CHIR9921 (3uM) and LDN8312 (0.2uM) from day 0 till day 4. Cells were caudalized by treatment with 0.1uM retinoic acid starting at day 2 and ventralized with 1uM purmorphamine starting at day 4 and continued till day 8. On day 8, motor neuron progenitors (MNPs) were re-plated onto poly-D-lysine/laminin coated wells. Differentiation was induced by treating the cells with N2B27 media supplemented with retinoic acid, purmorphamine and DAPT 10uM. DAPT treatment was stopped at day 13 and media was changed to N2B27 supplemented with BDNF 10ng/ml, GDNF 10ng/ml. Doxycycline 1ug/ml was added to the media at day 20 to induce control nanobody expression. Samples were collected at day 40.

value: iPSC-derived

value: motor neurons

value: NES

value: differentiation into motor neurons


title: Control, replicate1, scRNAseq

description:
Library name: Sampel1
Drop-seq


title: E8 NES nanobody R2

description:
Library name: E8_nes_R2
polyA purified total RNA

treatment_protocol: iPSCs were plated as colonies onto Matrigel and treated with neuronal differentiation media (DMEM/F12:Neurobasal in a 1:1 ratio, HEPES 10mM, N2 supplement 1%, B27 supplement 1%, L-glutamine 1%, ascorbic acid 5uM) supplemented with SB431542 (40uM), CHIR9921 (3uM) and LDN8312 (0.2uM) from day 0 till day 4. Cells were caudalized by treatment with 0.1uM retinoic acid starting at day 2 and ventralized with 1uM purmorphamine starting at day 4 and continued till day 8. On day 8, motor neuron progenitors (MNPs) were re-plated onto poly-D-lysine/laminin coated wells. Differentiation was induced by treating the cells with N2B27 media supplemented with retinoic acid, purmorphamine and DAPT 10uM. DAPT treatment was stopped at day 13 and media was changed to N2B27 supplemented with BDNF 10ng/ml, GDNF 10ng/ml. Doxycycline 1ug/ml was added to the media at day 20 to induce NES nanobody expression. Samples were collected at day 40.


title: E8 Control nanobody R2

description:
Library name: E8_ctrl_R2
polyA purified total RNA

treatment_protocol: iPSCs were plated as colonies onto Matrigel and treated with neuronal differentiation media (DMEM/F12:Neurobasal in a 1:1 ratio, HEPES 10mM, N2 supplement 1%, B27 supplement 1%, L-glutamine 1%, ascorbic acid 5uM) supplemented with SB431542 (40uM), CHIR9921 (3uM) and LDN8312 (0.2uM) from day 0 till day 4. Cells were caudalized by treatment with 0.1uM retinoic acid starting at day 2 and ventralized with 1uM purmorphamine starting at day 4 and continued till day 8. On day 8, motor neuron progenitors (MNPs) were re-plated onto poly-D-lysine/laminin coated wells. Differentiation was induced by treating the cells with N2B27 media supplemented with retinoic acid, purmorphamine and DAPT 10uM. DAPT treatment was stopped at day 13 and media was changed to N2B27 supplemented with BDNF 10ng/ml, GDNF 10ng/ml. MNs were transduced with AAV expressing the NES nanobody at day 20. Samples were collected at day 40.


title: E5 Control nanobody R1

description:
Library name: E5_ctrl_R1
polyA purified total RNA

treatment_protocol: iPSCs were plated as colonies onto Matrigel and treated with neuronal differentiation media (DMEM/F12:Neurobasal in a 1:1 ratio, HEPES 10mM, N2 supplement 1%, B27 supplement 1%, L-glutamine 1%, ascorbic acid 5uM) supplemented with SB431542 (40uM), CHIR9921 (3uM) and LDN8312 (0.2uM) from day 0 till day 4. Cells were caudalized by treatment with 0.1uM retinoic acid starting at day 2 and ventralized with 1uM purmorphamine starting at day 4 and continued till day 8. On day 8, motor neuron progenitors (MNPs) were re-plated onto poly-D-lysine/laminin coated wells. Differentiation was induced by treating the cells with N2B27 media supplemented with retinoic acid, purmorphamine and DAPT 10uM. DAPT treatment was stopped at day 13 and media was changed to N2B27 supplemented with BDNF 10ng/ml, GDNF 10ng/ml. MNs were transduced with AAV expressing the control nanobody at day 20. Samples were collected at day 40.


title: E8 Control nanobody R1

description:
Library name: E8_ctrl_R1
polyA purified total RNA


title: E5 Control nanobody R2

description:
Library name: E5_ctrl_R2
polyA purified total RNA


title: E5 NES nanobody R1

description:
Library name: E5_nes_R1
polyA purified total RNA


title: metastatic > 5 metastases 5

description: Library name: BCB-0102

value: blood

value: PBMC

value: Caucasian

value: Female


title: Fetal brain

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

institute: University of Missouri

data_processing:
The Cell Ranger pipeline (v. 3.0.1) was used to process the data including genrating the read count data. R pacakge Seurat was used analyze cell clusters.
Assembly: Sscrofa11.1
Supplementary files format and content: gzipped text files for barcodes, features and read counts.

molecule: nuclear RNA

organism: Sus scrofa

source_name: Fetal brain

extract_protocol:
Single nuclei were isolated from the samples using Pure Prep Nuclei Isolation kit (Product No. NUC-201, Sigma, St. Louis, MO, USA) as per manufacturer’s instructions.
The nuclei were used to prepare sequencing libraries using 10X Genomics Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 at the University of Missouri Genomics Technology Core according to manufacturer’s specifications.
10X Genomics Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1. Each library was sequenced to a depth of 20,000 paired-end (single-indexing) reads per nucleus.

value: Fetal brain

tag: developmental stage

value: Gestation day 45

tag: breed

value: Landrace x Large White


title: E5 NES nanobody R2

description:
Library name: E5_nes_R2
polyA purified total RNA

tag: cell line

tag: cell type


title: Placenta

source_name: Placenta

tag: tissue

value: Placenta


title: 4165_WC_5

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

data_processing:
Raw sequencing reads were aligned to the hg19 genome reference using our in-house pipeline (https://github.com/ndu-UCSD/LJI_RNA_SEQ_PIPELINE_V2). Briefly, FASTQ files were merged and filtered using fastp (v0.20.1), reads were aligned using STAR (v2.7.3a) and further processed using SAMtools (v0.1.19–44428cd), bamCoverage (v3.3.1), and Qualimap (v.2.2.2-dev). From this pipeline, raw counts and transcripts per million (TPM) reads were provided as output. Lowly expressed genes were removed for subsequent analysis (<=10 raw read counts). Differential expression was assessed using the DESeq2 Bioconductor package (v1.36.0)(56) in an R v4.2.1 environment with gene expression called differential with an FDR<0.05. Before fold change calculations, the 5% TPM quantile was calculated per gene and batch year (2021 and 2022) to prevent inflated fold change estimates caused by measurements close to zero. For genes of which the 5% quantile was equal to zero, TPM+0.1 was applied before fold change calculations. Spearman correlation analysis was performed using the correlation package (v0.8.4)(57). Pathway enrichment analysis was performed using Metascape and the Gene Ontology (GO) gene sets(58). Motif enrichment analysis was performed using HOMER findMotifs.pl (v4.11.1) with all genes with at least 10 raw counts as background(59).
Assembly: hg38
Supplementary files format and content: "2021 2022 PBMC gene expression raw_count.csv" contains raw count values per sample and gene
Supplementary files format and content: "2021 2022 PBMC gene expression tpm.csv" contains TPM values per sample and gene

source_name: Blood

extract_protocol:
2 million PBMC were lysed using QIAzol Lysis Reagent (Qiagen). Samples were stored at -80C until RNA extraction. RNA was extracted using the miRNeasy Mini Kit (Qiagen) including DNase treatment according to the manufacturer's instructions. The Smart-seq2 protocol was used to perform full-length bulkRNAseq. Briefly, RNA was captured using oligo-poly(dT)-30 primers and reverse transcription was performed using 50-template switching oligos (LNA technologies, Exicon). cDNA was pre-amplified using PCR and purified twice by magnetic beads (volume ratio 0.6x and 0.8x Ampure-XP magnetic beads, Beckman Coulter). cDNA was measured using capillary electrophoresis (Fragment analyzer, Advance analytical).
0.5 ng of cDNA was used to generate indexed Illumina libraries (Nextera XT library preparation kit, Illumina). Each library's fragment size was measured by capillary electrophoresis (Fragment analyzer, Advance analytical) and was quantified (Picogreen, Thermofisher). Libraries were pooled at equal molar concentration and sequenced paired-end to a minimum depth of 15 million reads with each a length of 100 base pairs.

value: Blood

tag: infancy vaccine

value: aP

tag: donor

tag: days post_booster


title: 4164_WC_3


title: 4166_WC_5


title: 4164_WC_1


title: 4166_WC_3


title: 4166_WC_2


title: 4165_WC_2


title: 4164_WC_5


title: 4166_WC_1


title: 4165_WC_4


title: 4166_WC_4


title: 4165_WC_3


title: 4164_WC_4


title: NeMECiS_plasmid_library

first: Jake

last: Cornwall-Scoones

address: 1 Midland Rd

institute: The Francis Crick Institute

description: Library name: NeMECiS_plasmid_library

library_source: other

data_processing:
A white-list of all 15,625 possible barcode concatemers was generated using a custom script. These were appended with left and right adaptor sequences to establish amplicons.fa, containing sequences each of length 163bp, labelled with the corresponding composition and ordering of CRE fragments. These have a generic form:    [TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG][AGCA][NNNNNNNN][GATT][NNNNNNNN][AGCA][NNNNNNNN][GATT][GATTAATAAAGGAAATTTATTTCATTGCAATAGTGTGTTGGAATTTGTGTCTCTCA][CTGTCTCTTATACACATCTCCGAGCCCACGAGAC]  [Nextera Rd1][Golden Gate overhang][8bp-BC sequence][Golden Gate overhang][8bp-BC sequence] [Golden Gate overhang][8bp-BC sequence][Golden Gate overhang][polyA terminator sequence ][Nextera Rd2]  Bowtie 2 was used for barcode calling. Index files were generated using the command: bowtie2-build amplicons.fa Global alignment of barcode concatemers for each fastq file from the NextSeq 500 demultiplexed output was achieved by running the following command, trimming alignment to exclude Nextera adaptors:  bowtie2 --threads 32 --trim-to 3:96 -x amplicons -1 fastq_file_read1.fastq -2 fastq_file_read2.fastq From the alignments recorded in the .sam file output, a custom python script was used to generate a count-matrix for each barcode in each sample. Here, reads by barcode were counted that had a perfect match (CIGAR output of 96M), and successfully aligned to a member of the white-list.
A Bayesian inference framework was used to calculate the (distribution) of (log) ZsGreen fluorescence for each synCRE by condition and replicate. In brief this performs the following steps: - Assume each synCRE produces a log fluorescence profile that is normally distributed - Pool of synCREs are parameterised by their relative densities in the pool, and the mean and variance of their log ZsGreen levels. - Sort bins are calibrated using measured flow distributions of sorted pools. - Finite number effects are simulated through sequential binomial sampling: (1) finite number of sorted cells; (2) finite number of reads. - Posterior probability distribution of each synCRE’s mean, variance and density given observed read-counts in each of the sorted bins and the unsorted population is inferred using the NUTS sampler (STAN)
https://github.com/jakesorel/NeMECiS
The GEO submission relates to folders "inference<https://github.com/jakesorel/NeMECiS/tree/main/inference>" and "alignment<https://github.com/jakesorel/NeMECiS/tree/main/alignment>"
Assembly: FASTA file is on series record.
Supplementary files format and content: Processed data csv file for plasmid library has the following structure. Rows are unique synCREs.  'Pos1', 'Pos2', 'Pos3' = fragment identities in positions 1,2,3 (from furthest to nearest the promoter) “Counts” = number of reads aligned by synCRE 'fragment_combination' = Combination of fragments in the synCRE (5’-3’) 'barcode_combination’= Combination of barcodes in the synCRE (5’-3’) BC_concatemer_seq' = Barcode concatemer aligned sequence 'BC1_seq' = Breakdown thereof for barcode 1 'synCRE_seq' = Full 608bp synCRE sequence 'Frag1_seq’ = Breakdown thereof for Fragment 1
Supplementary files format and content: Processed data csv files for neural progenitors has the following structure. Rows are unique synCREs.  'Pos1', 'Pos2', 'Pos3' = fragment identities in positions 1,2,3 (from furthest to nearest the promoter)  'estimated_mean_log_ZsGreen' = Bayesian inference of max-likelihood mean logZsGreen 'estimated_mean_log_ZsGreen_se' = Bayesian inference of standard error thereof 'passes_QC' = Passes quality control in this sample  'passes_QC_all_samples' = Passes quality control across all samples 'estimated_proportion_of_pool' = Bayesian estimate of max-likelihood relative density of this synCRE in the unsorted pool 'estimated_proportion_of_pool_se' = Standard error thereof 'estimated_std_log_ZsGreen' = Bayesian estimate of max-likelihood log ZsGreen standard deviation 'estimated_std_log_ZsGreen_se' = Standard error thereof  'Bin1_Counts_L001' = Read counts in Bin 1 and NextSeq sequencing lane L001 'Bin1_Counts' = Read counts in Bin 1, aggregated over sequencing lanes 'fragment_combination' = Combination of fragments in the synCRE (5’-3’) 'barcode_combination’= Combination of barcodes in the synCRE (5’-3’) BC_concatemer_seq' = Barcode concatemer aligned sequence 'BC1_seq' = Breakdown thereof for barcode 1 'synCRE_seq' = Full 608bp synCRE sequence 'Frag1_seq’ = Breakdown thereof for Fragment 1

molecule: other

organism: synthetic construct

growth_protocol: Plasmid library: Cloning product was transformed using 25uL Endura Electrocompetent Cells (60242-1) and grown at 28ºC (170rpm) in 1L L-Broth supplemented with Carbenicillin.  Neural progenitors: All experiments were carried out using the HM1 mouse embryonic stem cell (mESC) line, maintained at 37°C with 5% CO2. mESCs were maintained in ESGRO Complete PLUS Clonal Grade Medium (Merck Millipore, Cat No. SF001-500P) supplemented with 1% Penicillin/Streptomycin (Gibco, Cat No. 15140122) on CellBIND tissue-culture plates (Corning, Cat No. 3335) coated with 0.15% gelatin (Gibco, Cat no. G1393-100ML). Infected, selected cells (see below) were expanded for one passage in ESGRO and Puromycin Dihydrochloride. 200mm tissue culture plates were coated with 1:100 Vitronectin diluted in DMEM-F12 (-/-) (Gibco, Cat No. 21331-020) for 1 hour. Per replicate, a total of  6x10^7 cells cells were plated in N2B27 supplemented with bFGF as above. After 48 hours, media was changed into N2B27 supplemented with bFGF and CHIR99021 as above. After a further 20 hours, cells were dissociated with StemPro Accutase (Gibco, Cat No. A1110501), centrifuged, and re-plated at a 1:1 ratio in N2B27 supplemented with 100 nM RA (Sigma, Cat. No. R2625, additionally supplementing the media for half of the cells with 500 nM SAG (Merck, Cat. No. 566660-5mg), onto plates coated with 1:100 GelTrex diluted in DMEM-F12 (-/-) (Gibco, Cat No. 21331-020). Media was changed daily. After 72 hours, cells were dissociated with StemPro Accutase, centrifuged and resuspended in 0.5% BSA (Sigma-Aldrich, Cat No. A7979-50ML) in PBS (Gibco, Cat. No. 14190-094). 30% of each sample was immediately pelletted and frozen, and the remaining cells were flow sorted, as described below.  24 hours before flow sorting, 10mL polypropylene tubes were incubated with 100% Fetal Bovine Serum. Prior to sorting, samples were supplemented with 10 ng/ml DAPI (Invitrogen, Cat No. D1306). Samples were run on MoFlo XDP and BD InFlux. Sorted events were gated on live singlets (FSC-A vs SSC-A; SSC-A vs SSC-H; FSC-A vs DAPI). Four bins of ZsGreen intensity were established for each sample (two replicates, each for 0 nM and 500 nM SAG), demarcating the following percentile bins, following an optimal binning strategy (de Boer et al., 2020). FBS in polypropylene tubes was decanted and samples were sort according to the above gating strategy. To assess sort quality and calibrate downstream analysis, 10 L of each sorted sample, as well as the unsorted pool, were extracted and run on the BD LSRFortessa Cell Analyzer.

extract_protocol:
Plasmid library: 200mL of the OD600=1.0 bacterial culture was extracted using the Qiagen Plasmid Plus Maxi Kit (12963), according to manufacturer’s instructions. Neural progenitors: To extract genomic DNA, sorted cells for the NeMECiS screen were pelleted in 1.5mL DNA LoBind microfuge tubes (Eppendorf, Cat No. Z666548) by centrifugation for 10 minutes at 500g. Genomic DNA was extracted for sorted and unsorted pellets using a Quick-DNA Miniprep Plus Kit according to the manufacturer’s instructions (Zymo Research, Cat No. D4069), dividing each sorted sample into six columns each. Each column was eluted in 75 L of the supplied elution buffer (10 mM Tris-HCl, pH 8.5, 0.1 mM EDTA) pre-warmed to 60ºC, into 1.5mL DNA LoBind microfuge tubes, pooling the samples of the same origin to bring the total eluted gDNA to 450uL.
Barcode concatemers were amplified by PCR using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, Cat. No M0541L) by combining on ice: 450 L gDNA, 500 L 2X master mix, 5 L each of 100 M Nextera-adaptor primers (indexing each sample, see below), and 40 L nuclease-free water. Amplification was carried out under the following program: 5 minutes at 72°C, 30 seconds at 98°C, followed by 17 cycles of 30 seconds at 98°C, 30 seconds at 63 °C and 60 seconds at 72°C, and subsequently 5 minutes at 72°C. At this step, all PCR products were pooled. The pooled amplicon DNA was then cleaned up using 1.8x v/v of AMPureXP beads (Beckman Coulter, Cat. No. A63882) and eluted in 50 L EB buffer (10 mM Tris-Cl, pH 8.5). Library concentration was determined using the KAPA Library Quanitification Complete Kit Universal (Roche, Cat No. 07960140001) according to manufacturer’s instructions, using the QuantStudio 12K Flex Real-Time PCR System for qPCR (Applied Biosystems, Cat No. 4471087). 50% of the amplified sequence was further amplified using NEBNext High-Fidelity 2X PCR Master Mix and P5 (AATGATACGGCGACCACCGA) and P7 primers (CAAGCAGAAGACGGCATACGAGAT) using the same programme as above, then re-quantified as above to establish a concentration in excess of 1nM. Size spectra were examined with a Bioanalyzer using the DNA High Sensitivity DNA Kit (Agilent, Part No. 5067-4626) to confirm library quality. The plasmid library was sequenced using the Illumina MiniSeq Sequencer on a ‘High Output’ run using the MiniSeq High Output Reagent Kit (300-cycles) (Illumina, Cat No. FC-420-1003) according to the manufacturer’s instructions. The neural progenitor library was sequenced using the Illumina NextSeq 500 Sequencer on a ‘High Output’ run using the NextSeq 500/550 High Output Kit v2.5 (300 Cycles) (Illumina, Cat No. 20024908) according to the manufacturer’s instructions.  Sequence demultiplexing was performed with the built-in software by supplying the corresponding indexing sequences for each sample.

treatment_protocol: In duplicate, 10^7 mESCs were infected with the NeMECiS lentivirus library in ESGRO at MOI<1, maintained in CellBIND T175 flasks (Corning, CatNo. 3292). After 48 hours, media was changed into ESGRO supplemented with 1ug/mL Puromycin Dihydrochloride (Gibco, Cat No. 12122530).


title: 4163_WC_4


title: 4163_WC_5


title: 4165_WC_1


title: 4163_WC_2


title: 4163_WC_1


title: 4162_WC_5


title: 4162_WC_1


title: 4164_WC_2


title: 4162_WC_2


title: 4162_WC_4


title: 4140_WC_5


title: 4140_WC_4


title: 4139_WC_5


title: 4140_WC_2


title: 4139_WC_4


title: 4138_WC_3


title: 4092_WC_5


title: 4140_WC_3


title: 4139_WC_3


title: 4092_WC_3


title: 4162_WC_3


title: 4090_WC_5


title: 4092_WC_2


title: 4139_WC_1


title: 4163_WC_3


title: 4138_WC_1


title: 4138_WC_4


title: 4139_WC_2


title: 4091_WC_4


title: 4138_WC_2


title: 4091_WC_1


title: 4092_WC_1


title: 4090_WC_4


title: 4091_WC_5


title: 4090_WC_2


title: 4090_WC_3


title: 4138_WC_5


title: 4091_WC_2


title: 4140_WC_1


title: 4091_WC_3


title: 4089_WC_5


title: 4089_WC_3


title: 4089_WC_4


title: 4089_WC_2


title: 4089_WC_1


title: 4054_WC_4


title: 4055_WC_5


title: 4055_WC_3


title: 4054_WC_5


title: 4054_WC_3


title: 4054_WC_2


title: 4054_WC_1


title: 4090_WC_1


title: 4021_WC_2


title: 4092_WC_4


title: 4021_WC_5


title: 4021_WC_3


title: 4020_WC_4

value: wP


title: 4055_WC_2


title: 4020_WC_3


title: 4019_WC_4


title: 4020_WC_1


title: 4020_WC_2


title: 4019_WC_5


title: 4019_WC_3


title: 4055_WC_4


title: 4021_WC_4


title: 4021_WC_1


title: 4020_WC_5


title: 4019_WC_2


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