title: E6_6_3 (smallseq)


title: E6_5_13 (smallseq)

status: Public on Sep 06 2024

type: SRA

city: Stockholm

first: Cheng

last: Zhao

address: Solnavägen 1, 171 77 Solna

department: Department of Clinical Science

country: Sweden

institute: Karolinska institute

library_source: transcriptomic

data_processing:
SncRNA reads were processed using a modified version of the Small-Seq pipeline. First, the UMIs (8bp associated with the unique molecular identifiers) were removed from sequence reads and appended to the reads' name using umi_tools (v0.4.4). Then, cutadapt (v1.17) was used to remove adapter and polyA sequences (parameters: -e 0.1 -o 3 -m 18 -M 81 -u 2). The setting of "-M 81" was chosen because our small RNA sequencing had a maximum read length of 101 base pairs. Additionally, at least 10-base pair trimming of adapter or polyA sequences was performed to ensure that the reads originated from short transcripts.  The resulting clean reads were aligned to GRCh38-3.0.0  using bowtie (v1.0.0) with the following parameters: "-a --best --strata -v 2 -m 50 -S -q -p 2".  To avoid false positive mapping, reads with a length less than 20 base pairs and with one or more mismatches were excluded and reads with lengths between 20 and 40 base pairs and two mismatches were also filtered out. Mismatches located at the last base pair of reads were disregarded, considering the "CCA" addition in tRNA maturation and miRNA modification dynamics. In addition, unmapped reads underwent recursive soft clipping by 1 nucleotide from the 3' end and were then mapped to the reference genome using Bowtie with parameters ”-a --best --strata -v 1 -m 50 “ until the soft-clipped read length reached 3 nucleotides, the same procedure for 5’ end of reads was subsequently performed.  Any reads with a  mapping length of less than 17 base pairs were discarded. PCR amplicons were collapsed, and RNA molecules were counted using UMI-tools with the "dedup --method directional" option. Deduplicated soft-clipped reads were remapped onto the genome using the same procedure as above to recover multiple mapping information dampened by the "dedup" process. Annotation coordinates on the genome were then extracted from Mirbase V22 (miRNA), Gencode V39 (snoRNA, snRNA, rRNA, and others),  GtRNAdb V19 (tRNA), piBase V3.0 to assign the reads to their corresponding categories. The reads were assigned to each category in a hierarchical manner based on their overlap with the above annotations. If a read was mapped to more than one category, we assigned it to only one category based on the following order of priority: miRNA, rRNA, snoRNA, snRNA, tRNA, piRNA, and other types of transcripts. Subsequently, cell quality filtering was implemented based on three criteria: First, each cell required a minimum of 0.5 million sequenced reads. Second, the proportion of mitochondrial associated UMIs was required to be less than 25%. Third, the number of expressed miRNA molecules per cell was required to be more than 100. Data generated using Co-seq were only used for data integration and were excluded from downstream analysis to minimise introduction of batch differences from library preparation and as such introduce technical errors.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: embryo

extract_protocol:
Supernumerary human embryos donated to research by patients attending CReATe Fertility Centre, with study approval by Veritas IRB (protocol number 16580) and regional ethics board (2018/691-31 and 20.126) were utilised. Embryos were thawed using the Vit Kit-Thaw (FujiFilm). A total of 87 embryos were cultured from embryonic days 3-7 in a SAGE 1-step medium. Embryos were then dissociated into single cells as previously described using TrypLE enzyme solution and micromanipulation with glass capillaries. Cells were manually collected into individual 8-strip PCR tubes containing 2 uL of lysis buffer (0.13% Triton X-100, 1.33 U/ul Recombinant RNase inhibitor, 2.0 uM 5.8S rRNA-masking oligonucleotide) and stored at -80°C until further processing. To identify embryonic lineages based on transcriptomic signatures, single-cell mRNA-sncRNA Co-seq was performed as previously described and validated on mouse embryos. Briefly, individual cells were collected into 4uL of lysis buffer. After cell lysis at 72°C for 20 minutes, lysates were split into two equal 2 µL halves, with one half allocated to sncRNA sequencing and the other to SmartSeq. Each half was prepared following the original Small-seq and SmartSeq2 protocols, using 22 amplification cycles during the first PCR of SmartSeq2. This approach enabled the association of mRNA markers of cell lineage with corresponding sncRNA profiles.
Small-seq Library Preparation and Sequencing:The remaining, non-Coseq sncRNA libraries were generated using the Small-seq protocol as previously described. Briefly, cells were thawed and incubated at 72°C for 20 minutes followed by 3’ adapter ligation at 30°C for 6h followed by 4°C for 10h. Free adapters were then removed by 5’ deadenylation followed by digestion of RT primer-3’ adapter duplexes by lambda exonuclease. The 5’ adapter was ligated at 37°C for 1h, followed by reverse transcription with Superscript II (ThermoFisher Scientific) at 42°C for 1h. Two PCRs were performed, first to amplify the cDNA products (12 cycles) and second to barcode the libraries for multiplexing (12 cycles). The resulting pooled libraries (~150 nt) were processed with the DNA Clean & Concentrator (Zymo) at a 7x buffer:DNA ratio, eluted in 50 uL, analysed by 2100 Bioanalyzer (Agilent) and quantified by Qubit DNA High Sensitivity (ThermoFisher Scientific). Libraries were sequenced on either NovaSeq or NextSeq 550 100 bp SE or PE for a sequencing depth of 2 million reads per cell. During the following analysis, only the forward read was used from PE data. Co-seq to capture sncRNA and mRNA from a single-cell: Briefly, individual cells were collected into 4uL of lysis buffer. After cell lysis at 72°C for 20 minutes, lysates were split into two equal 2 µL halves, with one half allocated to sncRNA sequencing and the other to SmartSeq. Each half was prepared following the original Small-seq and SmartSeq2 protocols, using 22 amplification cycles during the first PCR of SmartSeq2. This approach enabled the association of mRNA markers of cell lineage with corresponding sncRNA profiles.

tag: tissue

value: embryo

tag: developmental stage

value: embryo in vitro day E6


title: E6_5_19 (smallseq)


title: E6_6_28 (smallseq)


title: E6_5_12 (smallseq)


title: E6_5_11 (smallseq)


title: E6_5_10 (smallseq)


title: E6_4_9 (smallseq)


title: E6_4_6 (smallseq)


title: E6_4_4 (smallseq)


title: E6_6_12 (smallseq)


title: E6_4_3 (smallseq)


title: E6_4_5 (smallseq)


title: E6_4_12 (smallseq)


title: E6_4_10 (smallseq)


title: E6_4_11 (smallseq)


title: E6_5_21 (smallseq)


title: E6_5_20 (smallseq)


title: E6_6_50 (smallseq)


title: E6_4_1 (smallseq)


title: E6_3_7 (smallseq)


title: E6_3_8 (smallseq)


title: E6_3_6 (smallseq)


title: E6_3_5 (smallseq)


title: E6_3_29 (smallseq)


title: E6_3_28 (smallseq)


title: E6_3_4 (smallseq)


title: E6_3_26 (smallseq)


title: E6_3_24 (smallseq)


title: E6_3_25 (smallseq)


title: E6_3_21 (smallseq)


title: E6_3_20 (smallseq)


title: E6_3_22 (smallseq)


title: E6_4_2 (smallseq)


title: E6_3_19 (smallseq)


title: E6_3_1 (smallseq)


title: E6_30_9 (smallseq)


title: E6_30_8 (smallseq)


title: E7_12_14 (smallseq)

value: embryo in vitro day E7


title: E7_12_17 (smallseq)


title: E6_3_17 (smallseq)


title: E6_30_20 (smallseq)


title: E6_3_18 (smallseq)


title: E6_30_3 (smallseq)


title: E6_30_10 (smallseq)


title: E6_3_27 (smallseq)


title: E6_3_30 (smallseq)


title: E6_30_12 (smallseq)


title: E6_30_1 (smallseq)


title: E6_29_7 (smallseq)


title: E6_29_9 (smallseq)


title: E6_3_23 (smallseq)


title: E6_29_55 (smallseq)


title: E6_29_54 (smallseq)


title: E6_29_56 (smallseq)


title: E6_29_52 (smallseq)


title: E6_29_51 (smallseq)


title: E6_29_50 (smallseq)


title: E6_3_2 (smallseq)


title: E6_29_5 (smallseq)


title: E6_29_48 (smallseq)


title: E6_29_47 (smallseq)


title: E6_29_46 (smallseq)


title: E6_29_42 (smallseq)


title: E6_29_41 (smallseq)


title: E6_29_6 (smallseq)


title: E6_29_4 (smallseq)


title: E6_29_43 (smallseq)


title: E6_29_40 (smallseq)


title: E6_29_39 (smallseq)


title: E6_29_38 (smallseq)


title: E6_29_35 (smallseq)


title: E6_29_36 (smallseq)


title: E6_29_33 (smallseq)


title: E6_29_37 (smallseq)


title: E6_29_34 (smallseq)


title: E6_29_53 (smallseq)


title: E6_29_32 (smallseq)


title: E6_29_27 (smallseq)


title: E6_29_31 (smallseq)


title: E6_29_29 (smallseq)


title: E6_29_30 (smallseq)


title: E6_29_26 (smallseq)


title: E6_29_3 (smallseq)


title: E6_29_28 (smallseq)


title: E6_29_24 (smallseq)


title: E6_29_49 (smallseq)


title: E6_29_21 (smallseq)


title: E6_29_45 (smallseq)


title: E6_29_25 (smallseq)


title: E6_29_20 (smallseq)


title: E6_29_2 (smallseq)


title: E6_29_44 (smallseq)


title: E6_29_18 (smallseq)


title: E6_29_15 (smallseq)


title: E6_29_17 (smallseq)


title: E6_29_13 (smallseq)


title: E6_29_10 (smallseq)


title: E6_29_12 (smallseq)


title: E6_29_14 (smallseq)


title: E6_29_11 (smallseq)


title: E6_29_1 (smallseq)


title: E6_28_11 (smallseq)


title: E6_2_9 (smallseq)


title: E6_27_9 (smallseq)


title: E6_28_10 (smallseq)


title: E6_27_6 (smallseq)


title: E6_27_7 (smallseq)


title: E6_28_17 (smallseq)


title: E6_27_3 (smallseq)


title: E6_27_14 (smallseq)


title: E6_27_4 (smallseq)


title: E6_27_10 (smallseq)


title: E6_27_2 (smallseq)


title: E6_26_13 (smallseq)


title: E6_27_5 (smallseq)


title: E6_29_19 (smallseq)


title: E6_26_4 (smallseq)


title: E6_25_9 (smallseq)


title: E6_2_6 (smallseq)


title: E6_26_9 (smallseq)


title: E6_25_10 (smallseq)


title: E6_2_5 (smallseq)


title: E6_24_9 (smallseq)


title: E6_24_6 (smallseq)


title: E6_25_3 (smallseq)


title: E6_24_12 (smallseq)


title: E6_24_5 (smallseq)


title: E6_24_18 (smallseq)


title: E6_24_17 (smallseq)


title: E6_27_12 (smallseq)


title: E6_24_20 (smallseq)


title: E6_24_15 (smallseq)


title: E6_24_11 (smallseq)


title: E6_23_9 (smallseq)


title: E6_24_10 (smallseq)


title: E6_23_7 (smallseq)


title: E6_23_6 (smallseq)


title: E6_23_8 (smallseq)


title: E6_2_4 (smallseq)


title: E6_23_39 (smallseq)


title: E6_25_13 (smallseq)


title: E6_23_45 (smallseq)


title: E6_23_21 (smallseq)


title: E6_24_19 (smallseq)


title: E6_23_19 (smallseq)


title: E6_23_30 (smallseq)


title: E6_23_13 (smallseq)


title: E6_2_3 (smallseq)


title: E6_22_7 (smallseq)


title: E6_22_8 (smallseq)


title: E6_22_23 (smallseq)


title: E6_22_4 (smallseq)


title: E6_22_6 (smallseq)


title: E6_22_20 (smallseq)


title: E6_22_2 (smallseq)


title: E6_22_14 (smallseq)


title: E6_22_15 (smallseq)


title: E6_22_17 (smallseq)


title: E6_22_11 (smallseq)


title: E6_22_13 (smallseq)


title: E6_22_21 (smallseq)


title: E6_21_2 (smallseq)


title: E6_23_23 (smallseq)


title: E6_23_14 (smallseq)


title: E6_21_16 (smallseq)


title: E6_21_5 (smallseq)


title: E6_21_4 (smallseq)


title: E6_22_12 (smallseq)


title: E6_2_2 (smallseq)


title: E6_21_15 (smallseq)


title: E6_21_1 (smallseq)


title: E6_2_10 (smallseq)


title: E6_21_6 (smallseq)


title: E6_2_1 (smallseq)


title: E6_1_9 (smallseq)


title: E6_1_8 (smallseq)


title: E6_22_18 (smallseq)


title: E6_17_8 (smallseq)


title: E6_17_3 (smallseq)


title: E6_17_6 (smallseq)


title: E6_17_2 (smallseq)


title: E6_17_1 (smallseq)


title: E6_22_10 (smallseq)


title: E6_16_9 (smallseq)


title: E6_16_6 (smallseq)


title: E6_16_5 (smallseq)


title: E6_1_7 (smallseq)


title: E6_16_4 (smallseq)


title: E6_16_38 (smallseq)


title: E6_16_28 (smallseq)


title: E6_16_27 (smallseq)


title: E6_16_31 (smallseq)


title: E6_16_32 (smallseq)


title: E6_16_26 (smallseq)


title: E6_16_33 (smallseq)


title: E6_16_25 (smallseq)


title: E6_16_29 (smallseq)


title: E6_16_24 (smallseq)


title: E6_16_22 (smallseq)


title: E6_16_20 (smallseq)


title: E6_16_2 (smallseq)


title: E6_16_23 (smallseq)


title: E6_16_19 (smallseq)


title: E6_16_17 (smallseq)


title: E6_16_18 (smallseq)


title: E6_16_14 (smallseq)


title: E6_16_15 (smallseq)


title: E6_16_12 (smallseq)


title: E6_16_7 (smallseq)


title: E6_16_13 (smallseq)


title: E6_16_11 (smallseq)


title: E6_16_37 (smallseq)


title: E6_16_10 (smallseq)


title: E6_1_3 (smallseq)


title: E6_1_5 (smallseq)


title: E6_12_9 (smallseq)


title: E6_12_7 (smallseq)


title: E6_12_8 (smallseq)


title: E6_12_6 (smallseq)


title: E6_12_4 (smallseq)


title: E6_12_2 (smallseq)


title: E6_12_3 (smallseq)


title: E6_12_22 (smallseq)


title: E6_16_21 (smallseq)


title: E6_12_19 (smallseq)


title: E6_12_23 (smallseq)


title: E6_12_18 (smallseq)


title: E6_12_21 (smallseq)


title: E6_12_14 (smallseq)


title: E6_12_15 (smallseq)


title: E6_12_12 (smallseq)


title: E6_12_13 (smallseq)


title: E6_12_11 (smallseq)


title: E6_12_1 (smallseq)


title: E6_11_9 (smallseq)


title: E6_11_7 (smallseq)


title: E6_11_4 (smallseq)


title: E6_11_6 (smallseq)


title: E6_11_3 (smallseq)


title: E6_11_21 (smallseq)


title: E6_11_5 (smallseq)


title: E6_11_2 (smallseq)


title: E6_11_20 (smallseq)


title: E6_12_5 (smallseq)


title: E6_11_17 (smallseq)


title: E6_11_18 (smallseq)


title: E6_11_22 (smallseq)


title: E6_11_15 (smallseq)


title: E6_11_16 (smallseq)


title: E6_11_19 (smallseq)


title: E6_11_12 (smallseq)


title: E6_10_23 (smallseq)


title: E6_1_11 (smallseq)


title: E6_11_14 (smallseq)


title: E6_11_11 (smallseq)


title: E6_11_10 (smallseq)


title: E6_10_22 (smallseq)


title: E6_10_19 (smallseq)


title: E6_11_1 (smallseq)


title: E6_11_13 (smallseq)


title: E6_10_18 (smallseq)


title: E6_10_16 (smallseq)


title: E6_10_20 (smallseq)


title: E6_10_17 (smallseq)


title: E6_10_14 (smallseq)


title: E6_10_13 (smallseq)


title: E6_10_11 (smallseq)


title: E5_8_9 (smallseq)

value: embryo in vitro day E5


title: E5_8_7 (smallseq)


title: E5_8_8 (smallseq)


title: E5_8_6 (smallseq)


title: E5_8_21 (smallseq)


title: E5_8_4 (smallseq)


title: E5_8_3 (smallseq)


title: E5_8_2 (smallseq)


title: E5_8_5 (smallseq)


title: E5_8_19 (smallseq)


title: E5_8_20 (smallseq)


title: E5_8_18 (smallseq)


title: E5_8_15 (smallseq)


title: E5_8_14 (smallseq)


title: E5_8_16 (smallseq)


title: E5_8_13 (smallseq)


title: E5_8_12 (smallseq)


title: E6_10_15 (smallseq)


title: E5_8_1 (smallseq)


title: E5_7_8 (smallseq)


title: E5_7_9 (smallseq)


title: E5_7_7 (smallseq)


title: E5_8_10 (smallseq)


title: E5_7_6 (smallseq)


title: E5_7_31 (smallseq)


title: E5_7_4 (smallseq)


title: E5_7_5 (smallseq)


title: E5_7_30 (smallseq)


title: E5_7_3 (smallseq)


title: E5_7_28 (smallseq)


title: E5_7_25 (smallseq)


title: E5_7_29 (smallseq)


title: E5_7_24 (smallseq)


title: E5_7_23 (smallseq)


title: E5_7_21 (smallseq)


title: E5_7_20 (smallseq)


title: E5_7_19 (smallseq)


title: E5_7_2 (smallseq)


title: E5_7_17 (smallseq)


title: E5_7_22 (smallseq)


title: E5_7_16 (smallseq)


title: E5_7_14 (smallseq)


title: E5_7_13 (smallseq)


title: E5_7_12 (smallseq)


title: E5_7_11 (smallseq)


title: E5_7_10 (smallseq)


title: E5_6_6 (smallseq)


title: E5_6_4 (smallseq)


title: E5_6_5 (smallseq)


title: E5_6_12 (smallseq)


title: E5_6_2 (smallseq)


title: E5_6_3 (smallseq)


title: E5_6_11 (smallseq)


title: E5_6_10 (smallseq)


title: E5_5_5 (smallseq)


title: E5_6_1 (smallseq)


title: E5_5_3 (smallseq)


title: E5_7_18 (smallseq)


title: E5_5_2 (smallseq)


title: E5_5_18 (smallseq)


title: E5_5_6 (smallseq)


title: E5_5_16 (smallseq)


title: E5_5_15 (smallseq)


title: E5_5_19 (smallseq)


title: E5_5_17 (smallseq)


title: E5_7_15 (smallseq)


title: E5_6_9 (smallseq)


title: E5_5_1 (smallseq)


title: E5_5_10 (smallseq)


title: E5_4_8 (smallseq)


title: E5_5_11 (smallseq)


title: E5_4_7 (smallseq)


title: E5_4_9 (smallseq)


title: E5_4_4 (smallseq)


title: E5_4_6 (smallseq)


title: E5_5_9 (smallseq)


title: E5_4_3 (smallseq)


title: E5_4_20 (smallseq)


title: E5_5_4 (smallseq)


title: E5_5_22 (smallseq)


title: E5_4_18 (smallseq)


title: E5_4_2 (smallseq)


title: E5_4_14 (smallseq)


title: E5_4_15 (smallseq)


title: E5_4_12 (smallseq)


title: E5_5_12 (smallseq)


title: E5_4_10 (smallseq)


title: E5_4_11 (smallseq)


title: E5_3_9 (smallseq)


title: E5_4_1 (smallseq)


title: E5_3_7 (smallseq)


title: E5_3_4 (smallseq)


title: E5_3_5 (smallseq)


title: E5_3_2 (smallseq)


title: E5_3_3 (smallseq)


title: E5_3_13 (smallseq)


title: E5_3_12 (smallseq)


title: E5_4_5 (smallseq)


title: E5_3_1 (smallseq)


title: E5_3_11 (smallseq)


title: E5_27_8 (smallseq)


title: E5_27_9 (smallseq)


title: E5_4_13 (smallseq)


title: E5_27_3 (smallseq)


title: E5_27_19 (smallseq)


title: E5_27_11 (smallseq)


title: E5_27_2 (smallseq)


title: E5_27_1 (smallseq)


title: E5_26_8 (smallseq)


title: E5_26_4 (smallseq)


title: E5_26_35 (smallseq)


title: E5_26_33 (smallseq)


title: E5_3_6 (smallseq)


title: E5_26_31 (smallseq)


title: E5_26_9 (smallseq)


title: E5_26_25 (smallseq)


title: E5_26_26 (smallseq)


title: E5_26_29 (smallseq)


title: E5_3_10 (smallseq)


title: E5_26_32 (smallseq)


title: E5_26_23 (smallseq)


title: E5_26_22 (smallseq)


title: E5_26_21 (smallseq)


title: E5_2_9 (smallseq)


title: E5_26_19 (smallseq)


title: E5_26_2 (smallseq)


title: E5_26_16 (smallseq)


title: E5_26_10 (smallseq)


title: E5_26_13 (smallseq)


title: E5_2_7 (smallseq)


title: E5_26_1 (smallseq)


title: E5_25_27 (smallseq)


title: E5_25_30 (smallseq)


title: E5_25_26 (smallseq)


title: E5_25_25 (smallseq)


title: E5_25_21 (smallseq)


title: E5_26_28 (smallseq)


title: E5_25_2 (smallseq)


title: E5_25_15 (smallseq)


title: E5_25_11 (smallseq)


title: E5_25_10 (smallseq)


title: E5_25_18 (smallseq)


title: E5_26_24 (smallseq)


title: E5_24_6 (smallseq)


title: E5_24_44 (smallseq)


title: E5_24_41 (smallseq)


title: E5_24_4 (smallseq)


title: E5_26_17 (smallseq)


title: E5_24_46 (smallseq)


title: E5_24_34 (smallseq)


title: E5_24_40 (smallseq)


title: E5_24_38 (smallseq)


title: E5_24_33 (smallseq)


title: E5_24_3 (smallseq)


title: E5_24_36 (smallseq)


title: E5_24_30 (smallseq)


title: E5_24_10 (smallseq)


title: E5_24_1 (smallseq)


title: E5_24_12 (smallseq)


title: E5_23_3 (smallseq)


title: E5_23_4 (smallseq)


title: E5_24_7 (smallseq)


title: E5_23_22 (smallseq)


title: E5_24_18 (smallseq)


title: E5_22_9 (smallseq)


title: E5_23_1 (smallseq)


title: E5_23_25 (smallseq)


title: E5_22_5 (smallseq)


title: E5_22_4 (smallseq)


title: E5_2_24 (smallseq)


title: E5_22_38 (smallseq)


title: E5_22_35 (smallseq)


title: E5_22_36 (smallseq)


title: E5_22_34 (smallseq)


title: E5_22_32 (smallseq)


title: E5_22_33 (smallseq)


title: E5_22_3 (smallseq)


title: E5_22_31 (smallseq)


title: E5_22_30 (smallseq)


title: E5_22_28 (smallseq)


title: E5_22_26 (smallseq)


title: E5_22_20 (smallseq)


title: E5_22_23 (smallseq)


title: E5_22_7 (smallseq)


title: E5_22_18 (smallseq)


title: E5_22_17 (smallseq)


title: E5_2_22 (smallseq)


title: E5_23_26 (smallseq)


title: E5_22_15 (smallseq)


title: E5_22_1 (smallseq)


title: E5_22_11 (smallseq)


title: E5_22_12 (smallseq)


title: E5_22_16 (smallseq)


title: E5_22_13 (smallseq)


title: E5_2_21 (smallseq)


title: E5_22_27 (smallseq)


title: E5_22_25 (smallseq)


title: E5_2_20 (smallseq)


title: E5_22_29 (smallseq)


title: E5_22_14 (smallseq)


title: E5_2_17 (smallseq)


title: E5_2_15 (smallseq)


title: E5_2_14 (smallseq)


title: E5_2_16 (smallseq)


title: E5_2_13 (smallseq)


title: E5_2_11 (smallseq)


title: E5_2_12 (smallseq)


title: E5_22_21 (smallseq)


title: E5_2_10 (smallseq)


title: E5_20_9 (smallseq)


title: E5_20_8 (smallseq)


title: E5_20_7 (smallseq)


title: E5_20_5 (smallseq)


title: E5_20_6 (smallseq)


title: E5_20_4 (smallseq)


title: E5_20_3 (smallseq)


title: E5_20_21 (smallseq)


title: E5_20_19 (smallseq)


title: E5_20_2 (smallseq)


title: E5_20_22 (smallseq)


title: E5_20_16 (smallseq)


title: E5_20_17 (smallseq)


title: E5_20_18 (smallseq)


title: E5_2_18 (smallseq)


title: E5_20_14 (smallseq)


title: E5_20_15 (smallseq)


title: E5_19_47 (smallseq)


title: E5_20_11 (smallseq)


title: E5_19_41 (smallseq)


title: E5_20_10 (smallseq)


title: E5_20_1 (smallseq)


title: E5_20_13 (smallseq)


title: E5_19_40 (smallseq)


title: E5_19_4 (smallseq)


title: E5_19_37 (smallseq)


title: E5_19_33 (smallseq)


title: E5_19_3 (smallseq)


title: E5_2_1 (smallseq)


title: E5_19_23 (smallseq)


title: E5_19_25 (smallseq)


title: E5_19_21 (smallseq)


title: E5_19_18 (smallseq)


title: E5_19_15 (smallseq)


title: E5_20_20 (smallseq)


title: E5_19_10 (smallseq)


title: E5_18_21 (smallseq)


title: E5_18_16 (smallseq)


title: E5_16_9 (smallseq)


title: E5_16_5 (smallseq)


title: E5_16_7 (smallseq)


title: E5_16_6 (smallseq)


title: E5_16_11 (smallseq)


title: E5_1_6 (smallseq)


title: E5_1_5 (smallseq)


title: E5_14_9 (smallseq)


title: E5_14_3 (smallseq)


title: E5_14_6 (smallseq)


title: E5_14_15 (smallseq)


title: E5_14_2 (smallseq)


title: E5_14_13 (smallseq)


title: E5_14_4 (smallseq)


title: E5_14_1 (smallseq)


title: E5_14_14 (smallseq)


title: E5_13_5 (smallseq)


title: E5_13_4 (smallseq)


title: E5_1_8 (smallseq)


title: E5_13_3 (smallseq)


title: E5_14_12 (smallseq)


title: E5_14_11 (smallseq)


title: E5_13_11 (smallseq)


title: E5_13_1 (smallseq)


title: E5_1_7 (smallseq)


title: E5_13_14 (smallseq)


title: E5_1_3 (smallseq)


title: E5_1_4 (smallseq)


title: E5_12_7 (smallseq)


title: E5_12_6 (smallseq)


title: E5_12_5 (smallseq)


title: E5_12_9 (smallseq)


title: E5_14_16 (smallseq)


title: E5_12_20 (smallseq)


title: E5_12_21 (smallseq)


title: E5_12_4 (smallseq)


title: E5_12_3 (smallseq)


title: E5_12_18 (smallseq)


title: E5_12_17 (smallseq)


title: E5_12_19 (smallseq)


title: E5_12_13 (smallseq)


title: E5_12_14 (smallseq)


title: E5_12_12 (smallseq)


title: E5_12_15 (smallseq)


title: E5_12_11 (smallseq)


title: E5_12_1 (smallseq)


title: E5_11_2 (smallseq)


title: E5_12_10 (smallseq)


title: E5_1_12 (smallseq)


title: E5_11_11 (smallseq)


title: E5_1_1 (smallseq)


title: E5_10_6 (smallseq)


title: E5_1_17 (smallseq)


title: E5_10_3 (smallseq)


title: E5_1_10 (smallseq)


title: E4_9_9 (smallseq)

value: embryo in vitro day E4


title: E4_9_6 (smallseq)


title: E5_1_2 (smallseq)


title: E4_9_5 (smallseq)


title: E5_12_2 (smallseq)


title: E4_9_4 (smallseq)


title: E4_9_3 (smallseq)


title: E4_9_13 (smallseq)


title: E4_9_14 (smallseq)


title: E4_9_2 (smallseq)


title: E4_9_12 (smallseq)


title: E4_9_1 (smallseq)


title: E4_9_10 (smallseq)


title: E4_9_11 (smallseq)


title: E4_8_8 (smallseq)


title: E4_8_9 (smallseq)


title: E4_8_7 (smallseq)


title: E4_8_5 (smallseq)


title: E4_8_3 (smallseq)


title: E4_8_4 (smallseq)


title: HEK293, Prm1 negative, Replicate 3, Hi-C

city: Haifa

first: Noam

last: Kaplan

address: Efron 1

country: Israel

institute: Technion - Israel Institute of Technology

library_source: genomic

data_processing:
readpair fastq files were processed using distiller-nf v0.34 to create interaction maps in mcool format.
Assembly: hg38
Supplementary files format and content: mcool, separately pooled for all Prm1 positive and all Prm1 negative samples

molecule: genomic DNA

growth_protocol: HEK293 cells were cultured under standard conditions. Cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cultures were kept at 37°C in a humidified atmosphere containing 5% CO2. Cells were passaged every 2-3 days to maintain exponential growth. Cell density was monitored to ensure optimal confluency of 70-80% before transfection experiments.

extract_protocol:
Hi-C libraries were prepared using FLIE Hi-C protocol. Cells were crosslinked with 2% formaldehyde. The cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630) to permeabilize the nuclei. The nuclei were digested with DpnII restriction enzyme, following by end-filling with biotin-14-dATP, dCTP, dGTP, and dTTP with Klenow. Blunt ends were ligated with T4 DNA ligase, and the formaldehyde crosslinking was reversed by proteinase K (10 mg/ml). DNA was purified using phenol-chloroform and ethanol precipitation, sonicated to an average size of 200 bp, and biotin was removed from non-ligated DNA ends with T4 polymerase. Biotinylated chimeric DNA strands were pulled down using streptavidin beads (Dynabeads C1).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: HEK293 cells were plated 24 hours before transfection in 10 mm plates. They were then transfected with Prm1-mCherry plasmid and incubated for 72 hours before proceeding with the Hi-C sample preparation.

tag: cell line


title: E4_8_2 (smallseq)


title: E4_8_15 (smallseq)


title: HEK293, Prm1 negative, Replicate 1, Hi-C


title: HEK293, Prm1 positive, Replicate 3, Hi-C


title: E4_8_13 (smallseq)


title: HEK293, Prm1 positive, Replicate 1, Hi-C


title: HEK293, Prm1 positive, Replicate 2, Hi-C


title: HEK293, Prm1 negative, Replicate 2, Hi-C


title: E4_8_12 (smallseq)


title: E4_8_16 (smallseq)


title: Late RA-gastruloid, replicate 2

city: Seattle

first: Riddhiman

last: Garge

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings
Fastqc was performed to estimate the quality of the reads. Adapter trimming and filtering for low quality reads was performed using Trimmomatic v0.39 either in paired-end or single end mode trimming low-quality reads (<2) at the ends and applying a 4 base sliding window across reads retaining reads with average quality above 15
Depending on the species, trimmed reads were then aligned using STAR to either the human GRCh38 or mouse GRCm39 reference assemblies. Count matrix was generated with FeatureCounts using default settings
Assembly: hg38 for Human, mm39 for Mouse
Supplementary files format and content: Processed files include a count matrix processed from FeatureCounts for both human and mouse datasets

molecule: polyA RNA

extract_protocol:
Total RNA from each sample were isolated using the Qiagen AllPrep DNA/RNA kit (Qiagen #80204). Approximately, 500ng of total RNA was used as input for library preparation
mRNAs were constructed using the NEBNext UltraII RNA Library Prep Kit for Illumina (NEB #E7770).


title: Late RA-gastruloid, replicate 1


title: E4_8_11 (smallseq)


title: E4_8_10 (smallseq)


title: E4_8_14 (smallseq)


title: Early RA-gastruloid, replicate 2


title: E4_8_1 (smallseq)


title: E4_7_9 (smallseq)


title: Primed RUES2_GLR ESCs, replicate 2


title: Early RA-gastruloid, replicate 1


title: E4_7_6 (smallseq)


title: E4_7_7 (smallseq)


title: Primed RUES2_GLR ESCs, replicate 1


title: Primed H9 ESCs, replicate 2


title: E4_8_6 (smallseq)


title: E4_7_5 (smallseq)


title: Primed H9 ESCs, replicate 1


title: Naive H9 ESCs, replicate 2


title: E4_7_3 (smallseq)


title: E4_7_4 (smallseq)


title: E4_7_15 (smallseq)


title: Naive H9 ESCs, replicate 1


title: E4_7_2 (smallseq)


title: scRNA-seq_day90-CerebralOrganoid_HC-2

city: Utrecht

first: Ronald Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Only reads containing a barcode and UMI were considered. The barcodes gave a number of unique molecular identifiers (UMIs) per cell, which constitutes the read count per cell. The counts contain both spliced, mRNA molecules with a poly-A tail, as well as unspliced, pre-RNA molecules with a poly-A stretch in their introns, RNA reads. The reads were aligned to the human genome (Ensemble GRCh38-2020-A) using the cellranger (v6.1.1) pipeline. The count files were used as input for the Scanpy (v1.8.1) pipeline (Virshup et al., 2021, 2023; Wolf et al., 2018)
Assembly: Ensemble GRCh38-2020-A
Supplementary files format and content: tab separated files with barcodes, features, and matrix of cells with exonic and intronic reads.

source_name: day 90 iPSC-derived cerebral organoid cell

growth_protocol: iPSC derive cerebral organoids were generated as reported previously (Lancaster & Knoblich, 2014; Ormel et al., 2018).

extract_protocol:
After washing with PBS, eight organoids were cut in small pieces. Then, papain and DNAse I (Worthington) were mixed in DMEM/F-12, added to the organoids and then this mix was put on an orbital shaker at 50 rpm to incubate for 25 minutes in total at 37⁰C. Every 10 minutes, the cell suspension was vigorously pipetted up and down. Afterwards, the reaction was quenched with DMEM/F-12 supplemented with 2% FBS. Doublets and clumps were removed with cell strainers: first with those containing 100 µm pores and then 70 µm pores. Finally, the cell suspension was centrifuged for 5 minutes at 300 rcf and resuspended in 250 microlitre mix of DMEM/F-12 with 40% FBS, counted and checked for cell viability, and then frozen in DMEM/F-12 with 40% FBS and 15% DMSO.
Cells were sequenced by Single Cell Discoveries (Utrecht, The Netherlands) according the 10X Genomics single cell 3' gel bead kit version 3 (Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3). In short, cell suspensions were thawed, the cells were washed and filtered one more time to ensure single cells. Cells were put on a Chromium single cell 3’ chip, where single cells were linked to a Single cell 3’ v3 gel bead and were separated from other cells by oil. Then, beads were dissolved, primers were released and the cell was lysed. The beads were coated with strands containing an Illumina TruSeq read 1, a 16 nucleotide (nt) 10X barcode, a 12 nt unique molecular identifier (UMI) and a 30 nt poly(dT)VN tail. The poly-A tails of the mRNA molecules aligned with the poly-T tails. The barcode diversity was 3.5 million. There was a different barcode per cell and a different UMI per mRNA molecule. The DNA primer was elongated to match the mRNA molecule by reverse transcription followed by template switch oligo priming and mRNA transcript extension. Then, single cell partitions were pooled again. Silane magnetic beads were used to extract the first-strand cDNA and the barcoded cDNA was amplified by PCR to complete the library preparation. P5, P7, a sample index, and TruSeq Read 2 (read 2 primer sequence) were added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The 16 bp 10x Barcode and 12 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sequencing was performed on Illumina Nextseq 2000. Sequencing depth was set at 50,000 reads per cell for 5,000 cells per sample.

tag: cell type

tag: genotype

value: age-matched healthy control


title: E4_7_14 (smallseq)


title: E4_7_13 (smallseq)


title: scRNA-seq_day90-CerebralOrganoid_C9-patient-4

description: 10X Genomics

value: day 90 iPSC-derived cerebral organoid cell

value: ALS/FTD patient carrying the C9ORF72 hexanucleotide repeat expansion on one allele


title: E4_7_11 (smallseq)


title: Multiplexed sample

city: Mexico City

first: Marti

last: Wilson-Verdugo

state: Mexico City

address: Ciudad Universitaria

country: Mexico

institute: Instituto de Fisiologia Celular

data_processing:
FASTQ files were processed with the BD Rhapsody Targeted Gene Expression Analysis Pipeline within the Seven Bridges Genomics cloud server
Assembly: GRCh38
Supplementary files format and content: Comma-delimited table containing DBEC normalized gene molecules per cell
Supplementary files format and content: Comma-delimited table containing the BD Rhapsody Pipeline sample tag assigned to each sample for demultiplexing

source_name: Peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from EDTA-anticoagulated peripheral blood by density gradient centrifugation using lymphoprep (Axis-Shield, OSLO, Norway) according to manufacturer’s instructions. Vials with 25 million PBMCs were cryopreserved until used. For scRNA-seq library preparation, samples were thawed and incubated overnight at 37ºC with RPMI with 10% of Bovine serum. The next day, the samples were labeled with molecular markers using Sample Tag (1-7) BD Human Single Cell Multiplexing Kit (Cat, 633781, San Jose, California) following manufacturer’s instructions. Then, the samples were sorted to purify live/CD45(+)/CD15(-) cells. These cells pull together to ensure at least 5,700 cells from each sample with a total of 40,000 cells. To capture mRNA, we used the BD Rhapsody Express Single Cell Analysis System, following manufacturer’s instructions for the BD Rhapsody Express Targeted library workflow. Briefly, the sorted cells were loaded on the cartridge with the Cell Capture Beads provided by the kit; then, the cells were lysed to capture all messenger RNA.
cDNA synthesis and the library preparation were performed following manufacturer’s instructions from the BD Rhapsody Immune Response Targeted Panel (Human) kit, (Cat, 633750, San Jose, California), which contains 399 genes for profiling human immune cells: naïve and memory CD4+, CD8+, Monocytes, Dendritic Cells, gamma-delta T, mast cells, B cells, NK and NKT cells.
Targeted scRNA-seq

value: Peripheral blood

value: Peripheral blood mononuclear cells

tag: treatment

value: Multiplexed:Control (baseline), Control (t = 6 months), Zinc (baseline), Zinc (t = 6 months), Selenium (baseline), Selenium (t = 6 months), Zinc + selenium (t = 6 months)


title: scRNA-seq_day90-CerebralOrganoid_C9-patient-1

description: 10X Genomics


title: scRNA-seq_day90-CerebralOrganoid_HC-3

description: 10X Genomics


title: E4_7_10 (smallseq)


title: scRNA-seq_day90-CerebralOrganoid_HC-1

description: 10X Genomics


title: E4_7_12 (smallseq)


title: E5_2_2 (smallseq)


title: scRNA-seq_day90-CerebralOrganoid_C9-patient-2

description: 10X Genomics


title: Late gastruloid, replicate 1

organism: Mus musculus


title: E4_7_1 (smallseq)


title: Early gastruloid, replicate 2


title: Primed EpiLCs, replicate 1


title: E4_6_3 (smallseq)


title: Early gastruloid, replicate 1


title: E4_6_5 (smallseq)


title: Naive mESCs, replicate 2


title: Naive mESCs, replicate 1


title: E4_6_13 (smallseq)


title: E4_6_14 (smallseq)


title: E4_6_4 (smallseq)


title: E4_6_9 (smallseq)


title: E4_6_12 (smallseq)


title: Late gastruloid, replicate 2


title: E4_6_1 (smallseq)


title: E4_6_10 (smallseq)


title: E4_6_7 (smallseq)


title: U251_model_GK_M2

city: Jiangsu province

first: Wei

last: Xiao

address: N0.58 Kangyuan Road, Jiangning Industrial town, Economic and development zone, Lianyun District

country: China

institute: State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process

data_processing:
Demultiplexing and basecalling performed using CASAVA version 1.8.2
QC was performed on the FASTQ files using FastQC(v0.11.5) software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens(hg19) whole genome using HISAT2(v2.1.0).
Sequence reads aligned to the human genome were imported into HTseq(v0.11.3) for sequence read counting.
Sequence reads mapped to different isoforms of individual genes were pooled together, and then were input into the DESeq(v1.36.0) differential expression analysis program to normalize and determine expression levels and differentially expressed genes.
Genome_build: Homo sapiens
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each gene per sample

source_name: cell line: Human astroglioma cell line U251

growth_protocol: The human macrophage cell line THP-1 was maintained in RPMI 1640 medium (HyClone, USA), while the human umbilical vein endothelial cell line HUVEC-T1 and the human astroglioma cell line U251 were cultured in Modified Eagle’s medium (MEM) (HyClone, USA), both media supplemented with 10% fetal bovine serum (FBS, ExCell Bio, China). The human megakaryoblastic cell line MEG-01 was cultured in RPMI 1640 medium supplemented with 20% FBS. The human neuroblastoma cell line SH-SY5Y was cultured in (EMEM) (HyClone, USA) supplemented with 15% FBS. The human microglialcell line HMC3 was cultured in special culture medium (Procell, China). All media were supplemented with 1% penicillin, and 1% streptomycin (HyClone, UT, USA)1% penicillin, and 1% streptomycin (HyClone, UT, USA). All cell lines were authenticated and tested negative for mycoplasma contamination.

extract_protocol:
The cell lysates were directly reverse transcribed and amplified into double stranded cDNAs, which were subsequently added adaptors by Tn5 transposase. The purified and fragmented products were used for library construction and sequencing.
RNA libraries were prepared for sequencing using Illumina protocols

treatment_protocol: After seeding cells into the 96well plates following growth protocol. MEG-01 was cultured in medium containing 100 ng/mL PMA (Sigma-Aldrich, Germany) for 3 days. HUVECs-T1 and HMC3 inflammatory model were built by stimulating cells with 5 ng/mL IL-1β (GenScript, China) for 24 h. U251 was induced fibrosis related reactions with 10 ng/ml TGF-β (GenScript, China) for 24h. SH-SY5Y cell was cultured in medium containing 10 µM RA (Sigma-Aldrich, Germany) for 10 days. After 10 days, SH-SY5Y cell culture medium was replaced with sugar free medium and treated with hypoxia for 4 hours, then replaced medium and incubated for 24 hours with 5% CO2 at 37°C to build SH-SY5Y OGD model. THP-1 cell was differentiated into resting (M0) macrophages by 24 h incubation with 100 ng/ml PMA (Sigma-Aldrich, Germany) followed by treating with 1 µg/mL LPS (Sigma-Aldrich) for 24 h to polarize into M1 macrophages. Meanwhile, THP-1 cell was incubated in medium with 80 μg/mL oxLDL for 24 h to form foam cells. All cells harvested at the indicated time point.


title: U251_model_GK_H2


title: U251_model_GK_L2


title: E4_5_8 (smallseq)


title: U251_model_GK_H1


title: U251_model_GB_M2


title: E4_5_5 (smallseq)


title: Primed EpiLCs, replicate 2


title: U251_model_GK_L1


title: E4_5_4 (smallseq)


title: E4_6_6 (smallseq)


title: U251_model_GB_M1


title: E4_6_2 (smallseq)


title: U251_model_GB_L2


title: U251_model_GB_L1


title: E4_5_2 (smallseq)


title: U251_model_GK_M1


title: E4_5_10 (smallseq)


title: U251_model_GB_H2


title: U251_model_GB_H1


title: U251_model_GA_M,2


title: E4_5_1 (smallseq)


title: E4_5_7 (smallseq)


title: U251_model_GA_M


title: E4_4_6 (smallseq)


title: E4_4_9 (smallseq)


title: E4_4_5 (smallseq)


title: E4_4_4 (smallseq)


title: U251_model_GA_L1


title: U251_model_GA_L2


title: U251_model_GA_H2


title: E4_4_20 (smallseq)


title: E4_4_21 (smallseq)


title: U251_model_EGB761_M1


title: U251_model_GA_H1


title: U251_model_EGB761_M2


title: E4_4_19 (smallseq)


title: E4_5_3 (smallseq)


title: E4_4_18 (smallseq)


title: U251_model_EGB761_H2


title: E4_4_17 (smallseq)


title: E4_4_16 (smallseq)


title: U251_model_EGB761_H1


title: U251_model_DMSO_M1


title: E4_4_14 (smallseq)


title: E4_4_15 (smallseq)


title: E4_4_22 (smallseq)


title: E4_4_13 (smallseq)


title: E4_4_12 (smallseq)


title: E4_4_2 (smallseq)


title: U251_model_DMSO_H2


title: U251_model_EGB761_L2


title: U251_model_DMSO_L1


title: U251_model_DGMIsolvent_M2


title: U251_model_EGB761_L1


title: E4_2_9 (smallseq)


title: E4_4_1 (smallseq)


title: U251_model_DMSO_H1


title: E4_4_10 (smallseq)


title: U251_model_DGMIsolvent_L1


title: U251_model_DGMIsolvent_L2


title: E4_2_7 (smallseq)


title: E4_2_6 (smallseq)


title: U251_model_DGMIsolvent_H2


title: E4_2_5 (smallseq)


title: U251_model_DMSO_M2


title: U251_model_DMSO_L2


title: U251_model_DGMI_M2


title: E4_2_4 (smallseq)


title: E4_2_3 (smallseq)


title: U251_model_DGMI_M1


title: E4_2_2 (smallseq)


title: E4_2_11 (smallseq)


title: U251_model_DGMI_L2


title: E4_4_11 (smallseq)


title: U251_model_DGMIsolvent_M1


title: U251_model_DGMI_L1


title: E4_2_10 (smallseq)


title: E4_1_6 (smallseq)


title: U251_model2

value: TGFb


title: E4_1_4 (smallseq)


title: E4_1_3 (smallseq)


title: E4_1_7 (smallseq)


title: U251_model_DGMI_H2


title: U251_model4


title: E4_12_8 (smallseq)


title: E4_12_9 (smallseq)


title: U251_model3


title: E4_2_1 (smallseq)


title: E4_1_5 (smallseq)


title: U251_model_DGMI_H1


title: U251_model1


title: U251_ctrl3

value: untreated


title: E4_1_2 (smallseq)


title: U251_ctrl2


title: U251_ctrl1


title: U251_ctrl4


title: U251_model_DGMIsolvent_H1


title: THP1_LPSmodel7

source_name: cell line: Human macrophage cell line THP-1


title: E4_12_5 (smallseq)


title: THP1_LPSmodel8


title: E4_1_13 (smallseq)


title: THP1_LPSmodel5


title: E4_1_16 (smallseq)


title: E4_1_15 (smallseq)


title: E4_1_14 (smallseq)


title: THP1_LPSmodel6


title: THP1_LPSmodel4


title: E4_1_11 (smallseq)


title: E3_6_6 (smallseq)

value: embryo in vitro day E3


title: THP1_LPSmodel2


title: E3_5_5 (smallseq)


title: E3_5_4 (smallseq)


title: E4_1_10 (smallseq)


title: THP1_LPSmodel_GK_M2


title: THP1_LPSmodel1


title: E3_5_3 (smallseq)


title: THP1_LPSmodel_GK_M1


title: E3_5_1 (smallseq)


title: E3_3_3 (smallseq)


title: THP1_LPSmodel_GB_M2


title: THP1_LPSmodel_GK_L2


title: E3_3_5 (smallseq)


title: THP1_LPSmodel_GB_L2


title: E3_5_2 (smallseq)


title: E3_3_2 (smallseq)


title: E3_3_1 (smallseq)


title: E3_2_7 (smallseq)


title: THP1_LPSmodel_GK_H1


title: E3_2_6 (smallseq)


title: THP1_LPSmodel_GB_H2


title: THP1_LPSmodel_GB_M1


title: THP1_LPSmodel3


title: THP1_LPSmodel_GB_H1


title: E3_2_5 (smallseq)


title: THP1_LPSmodel_GA_M2


title: THP1_LPSmodel_GK_L1


title: E3_2_4 (smallseq)


title: E3_2_2 (smallseq)


title: THP1_LPSmodel_GA_L2


title: E3_1_5 (smallseq)


title: THP1_LPSmodel_GA_M1


title: E3_3_4 (smallseq)


title: THP1_LPSmodel_GK_H2


title: E3_1_4 (smallseq)


title: THP1_LPSmodel_GA_L1


title: E3_1_2 (smallseq)


title: THP1_LPSmodel_GB_L1


title: E3_1_1 (smallseq)


title: E7_44_9 (coseq-smallseq)


title: THP1_LPSmodel_GA_H2


title: THP1_LPSmodel_EGB761_M2


title: THP1_LPSmodel_EGB761_M1


title: THP1_LPSmodel_EGB761_L2


title: E7_44_8 (coseq-smallseq)


title: E7_44_7 (coseq-smallseq)


title: THP1_LPSmodel_EGB761_H2


title: THP1_LPSmodel_EGB761_L1


title: E7_44_6 (coseq-smallseq)


title: E7_44_5 (coseq-smallseq)


title: THP1_LPSmodel_EGB761_H1


title: E7_44_48 (coseq-smallseq)


title: THP1_LPSmodel_DMSO_M2


title: E7_44_45 (coseq-smallseq)


title: E7_44_44 (coseq-smallseq)


title: E7_44_47 (coseq-smallseq)


title: THP1_LPSmodel_GA_H1


title: E7_44_43 (coseq-smallseq)


title: THP1_LPSmodel_DMSO_H2


title: THP1_LPSmodel_DMSO_L1


title: THP1_LPSmodel_DMSO_L2


title: THP1_LPSmodel_DGMIsolvent_M2


title: E7_44_42 (coseq-smallseq)


title: E7_44_41 (coseq-smallseq)


title: THP1_LPSmodel_DMSO_H1


title: E7_44_40 (coseq-smallseq)


title: THP1_LPSmodel_DGMIsolvent_M1


title: THP1_LPSmodel_DGMIsolvent_L2


title: E7_44_36 (coseq-smallseq)


title: E7_44_35 (coseq-smallseq)


title: THP1_LPSmodel_DGMIsolvent_L1


title: E7_44_38 (coseq-smallseq)


title: E7_44_37 (coseq-smallseq)


title: THP1_LPSmodel_DGMIsolvent_H1


title: THP1_LPSmodel_DGMI_M2


title: THP1_LPSmodel_DGMIsolvent_H2


title: E7_44_32 (coseq-smallseq)


title: E7_44_31 (coseq-smallseq)


title: THP1_LPSmodel_DMSO_M1


title: THP1_LPSmodel_DGMI_L2


title: THP1_LPSmodel_DGMI_M1


title: E7_44_30 (coseq-smallseq)


title: THP1_LPSmodel_DGMI_L1


title: THP1_LPSmodel_DGMI_H2


title: E7_44_29 (coseq-smallseq)


title: E7_44_3 (coseq-smallseq)


title: E7_44_27 (coseq-smallseq)


title: THP1_LPSmodel_DGMI_H1


title: E7_44_26 (coseq-smallseq)


title: E7_44_34 (coseq-smallseq)


title: E7_44_25 (coseq-smallseq)


title: THP1_LDLmodel7


title: E7_44_23 (coseq-smallseq)


title: E7_44_22 (coseq-smallseq)


title: THP1_LDLmodel4


title: THP1_LDLmodel6


title: THP1_LDLmodel3


title: THP1_LDLmodel5


title: E7_44_19 (coseq-smallseq)


title: THP1_LDLmodel1


title: E7_44_15 (coseq-smallseq)


title: THP1_LDLmodel8


title: THP1_LDLmodel_GK_M1


title: E7_44_14 (coseq-smallseq)


title: THP1_LDLmodel2


title: E7_44_18 (coseq-smallseq)


title: THP1_LDLmodel_GK_L2


title: E7_44_28 (coseq-smallseq)


title: THP1_LDLmodel_GK_M2


title: THP1_LDLmodel_GK_L1


title: E7_44_12 (coseq-smallseq)


title: E7_44_13 (coseq-smallseq)


title: E7_44_11 (coseq-smallseq)


title: THP1_LDLmodel_GK_H2


title: THP1_LDLmodel_GK_H1


title: E7_44_10 (coseq-smallseq)


title: THP1_LDLmodel_GB_M2


title: E7_44_1 (coseq-smallseq)


title: THP1_LDLmodel_GB_M1


title: E6_43_6 (coseq-smallseq)


title: E7_44_21 (coseq-smallseq)


title: THP1_LDLmodel_GB_L2


title: E6_43_7 (coseq-smallseq)


title: E6_43_5 (coseq-smallseq)


title: THP1_LDLmodel_GB_L1


title: THP1_LDLmodel_GB_H2


title: E6_43_4 (coseq-smallseq)


title: E6_43_31 (coseq-smallseq)


title: E6_43_29 (coseq-smallseq)


title: THP1_LDLmodel_GA_M1


title: THP1_LDLmodel_GB_H1


title: THP1_LDLmodel_GA_L2


title: THP1_LDLmodel_GA_M2


title: THP1_LDLmodel_GA_L1


title: E6_43_27 (coseq-smallseq)


title: E6_43_24 (coseq-smallseq)


title: THP1_LDLmodel_GA_H2


title: THP1_LDLmodel_GA_H1


title: E6_43_26 (coseq-smallseq)


title: E6_43_23 (coseq-smallseq)


title: E6_43_20 (coseq-smallseq)


title: E6_43_22 (coseq-smallseq)


title: THP1_LDLmodel_EGB761_M1


title: THP1_LDLmodel_EGB761_M2


title: E6_43_19 (coseq-smallseq)


title: E6_43_36 (coseq-smallseq)


title: THP1_LDLmodel_EGB761_L2


title: E6_43_2 (coseq-smallseq)


title: THP1_LDLmodel_EGB761_L1


title: THP1_LDLmodel_DMSO_M1


title: E6_43_13 (coseq-smallseq)


title: E6_43_18 (coseq-smallseq)


title: THP1_LDLmodel_DMSO_L2


title: E6_43_16 (coseq-smallseq)


title: THP1_LDLmodel_DMSO_M2


title: E6_43_12 (coseq-smallseq)


title: E6_43_14 (coseq-smallseq)


title: THP1_LDLmodel_EGB761_H2


title: THP1_LDLmodel_DMSO_L1


title: E6_42_9 (coseq-smallseq)


title: E6_43_11 (coseq-smallseq)


title: THP1_LDLmodel_DMSO_H3


title: THP1_LDLmodel_EGB761_H1


title: THP1_LDLmodel_DMSO_H2


title: E6_42_7 (coseq-smallseq)


title: THP1_LDLmodel_DGMIsolvent_M2


title: E6_42_4 (coseq-smallseq)


title: THP1_LDLmodel_DGMIsolvent_M1


title: E6_42_32 (coseq-smallseq)


title: E6_42_30 (coseq-smallseq)


title: E6_42_29 (coseq-smallseq)


title: E6_42_3 (coseq-smallseq)


title: THP1_LDLmodel_DGMIsolvent_H2


title: E6_42_26 (coseq-smallseq)


title: THP1_LDLmodel_DGMIsolvent_L1


title: E6_42_24 (coseq-smallseq)


title: THP1_LDLmodel_DGMIsolvent_H1


title: THP1_LDLmodel_DGMIsolvent_L2


title: THP1_LDLmodel_DGMI_M2


title: E6_42_28 (coseq-smallseq)


title: E6_42_23 (coseq-smallseq)


title: THP1_LDLmodel_DGMI_M1


title: E6_42_22 (coseq-smallseq)


title: THP1_LDLmodel_DGMI_L1


title: E6_42_21 (coseq-smallseq)


title: THP1_LDLmodel_DGMI_L2


title: E6_42_20 (coseq-smallseq)


title: THP1_LDLmodel_DGMI_H2


title: THP1_LDLmodel_DMSO_H1


title: E6_42_19 (coseq-smallseq)


title: THP1_LDLmodel_DGMI_H1


title: E6_42_18 (coseq-smallseq)


title: THP1_ctrl14


title: THP1_ctrl13


title: E6_42_17 (coseq-smallseq)


title: E6_42_16 (coseq-smallseq)


title: E6_42_15 (coseq-smallseq)


title: E6_42_14 (coseq-smallseq)


title: THP1_ctrl11


title: E6_42_12 (coseq-smallseq)


title: E6_42_13 (coseq-smallseq)


title: THP1_ctrl9


title: THP1_ctrl8


title: THP1_ctrl6


title: THP1_ctrl7


title: THP1_ctrl4


title: THP1_ctrl3


title: E6_41_47 (coseq-smallseq)


title: THP1_ctrl2


title: E6_41_44 (coseq-smallseq)


title: THP1_ctrl1


title: E6_41_43 (coseq-smallseq)


title: THP1_ctrl12


title: SY5Y_model_GK_M2

source_name: cell line: Human neuroblastoma cell line SH-SY5Y


title: E6_41_42 (coseq-smallseq)


title: THP1_ctrl10


title: SY5Y_model_GK_L2


title: E6_41_41 (coseq-smallseq)


title: SY5Y_model_GK_M1


title: SY5Y_model_GK_L1


title: E6_42_10 (coseq-smallseq)


title: SY5Y_model_GK_H2


title: E6_41_40 (coseq-smallseq)


title: E6_41_5 (coseq-smallseq)


title: THP1_ctrl5


title: E6_41_4 (coseq-smallseq)


title: E6_41_6 (coseq-smallseq)


title: E6_41_39 (coseq-smallseq)


title: E6_41_37 (coseq-smallseq)


title: E6_41_46 (coseq-smallseq)


title: E6_41_38 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_B6D2F1_Testis_H3K4me3_Millipore_04_745

city: BeiJing

first: Yuqing

last: Guo

state: BeiJing

address: Peking University, No.5 Yiheyuan Road, Haidian District, Beijing, China

department: Biomedical Pioneering Innovation Center

institute: Peking University

description: scNanoSeq-CUT&Tag of B6D2F1_Testis (H3K4me3)

data_processing:
Base calling was performed to convert the electrical signals into raw fastq files using Guppy (v6.5.7). The raw fastq data were demultiplexed into single cell files according to the single-cell barcodes sequence using nanoplexer (v0.1). Two successive demultiplexing processes were performed on the outer barcodes and inner barcodes.Reads with low quality (q<7) and short length (<100 bp) were filtered using NanoFilt (v2.8.0). Adaptors were trimmed using cutadapt (v3.5). The clean reads were next mapped to reference genome of human (hg38) and mouse (mm10) using minimap2 (v2.26-r1175). Reads with low mapping quality (mapQ<30) and not primary alignment were filtered using samtools (v1.3). Then the aligned reads were sorted by coordinate and PCR duplicates were removed using samtools. To obtain chromatin modification signals, the aligned bam files were converted to bed format using the 'bamtobed' command of bedtools (v2.30.0). Then, we extracted the two ends of the long reads, centring on each end and extending 50bp on both sides respectively. The produced bed files recorded the chromatin modification signals for each single cell. The fragments file was read into ArchR (v1.0.1) for analysis. Peak calling was performed using SEACR (v1.3).
Assembly: hg38 for human; mm10 for mouse
Supplementary files format and content: Bigwig files recorded scNanoSeq-CUT&Tag signal strength tracks. Bed files recorded coordinates of scNanoSeq-CUT&Tag peaks. bedgraph.gz files recorded scNanoSeq-CUT&Tag signal strength tracks preduced in this expreiment.
Library strategy: scNanoSeq-CUT&Tag

source_name: Testis

growth_protocol: The human chronic myelogenous leukemia (CML) cell line K562 was grown in RPMI1640 medium (Gibco; 11875093) supplemented with 15% fetal bovine serum (FBS), 1% penicillin-streptomycin (Gibco, 15140122) and 2mM GlutaMAX (Gibco, 35050061). The human embryonic kidney cell line HEK293T and the mouse embryonic fibroblast cell line 3T3 were both grown in DMEM medium (Gibco, 11995040) supplemented with 10% FBS and 1% penicillin-streptomycin. The two human B-lymphocyte cell lines GM12878 and HG002 (NA24385) were both grown in RPMI1640 medium supplemented with 15% FBS and 1% penicillin-streptomycin. The human T-lymphocyte cell line H9 was grown in RPMI1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin. The human foreskin fibroblast cell line HFF1 was grown in DMEM medium supplemented with 15% FBS and 1% penicillin-streptomycin. All cell lines were validated to be free of mycoplasma contamination (Yeasen, 40612ES25).

extract_protocol:
Firstly, the scCUT&Tag was performed as pervious described with some modifications. Approximately 50,000 to 300,000 cells were collected, washed and incubated with specific antibodies against chromatin modifications or transcription factors. After tagmentation by pG-Tn5, single cells were sorted into 96-well plate containing cell lysis buffer with 24bp cell barcodes in each well and processed to preamplification to obtain long-read amplicons. And then the PCR product of 48 cells with different cell barcodes was pooled, purified and processed to further PCR amplification with sample barcodes introduced during amplification. Finally, the purified DNA with different barcodes can be pooled together for library construction.
Approximately 1ug of purified DNA was diluted to a volume of 48 μl for library construction by using SQK-LSK110 Ligation Sequencing kit according to the manufacturer's protocol.

value: Testis

value: testis

tag: chip antibody

value: H3K4me3 (Millipore,#04-745)


title: SY5Y_model_GK_H1


title: scNanoSeq-CUT&Tag_B6D2F1_blood_H3K4me3_Millipore_04_745

source_name: Blood

value: Blood

value: blood


title: E6_41_45 (coseq-smallseq)

value: embryo

value: embryo in vitro day E6


title: SY5Y_model_GB_M2


title: SY5Y_model_GB_M1


title: E6_41_35 (coseq-smallseq)


title: E6_41_36 (coseq-smallseq)


title: E6_41_29 (coseq-smallseq)


title: E6_41_24 (coseq-smallseq)


title: SY5Y_model_GB_L1


title: E6_41_30 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_HFF1_RAD21_GeneTex_GTX106012

description: scNanoSeq-CUT&Tag of HFF1 (RAD21)

value: Human embryonic fibroblast

value: RAD21 (GeneTex,#GTX106012)


title: E6_41_23 (coseq-smallseq)


title: SY5Y_model_GB_H2


title: E6_41_20 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_HFF1_CTCF_Millipore_07_729

description: scNanoSeq-CUT&Tag of HFF1 (CTCF)

value: CTCF (Millipore,#07-729)


title: scNanoSeq-CUT&Tag_K562_drug_treatment_DMSO_H3K27ac_Abcam_ab4729

description: scNanoSeq-CUT&Tag of K562_drug_treatment_DMSO (H3K27ac)

treatment_protocol: The K562 cells were treated with 5 μM 5-azacytidine (5-AZA, Sigma, cat. no. A2385) for 5 days and the medium was exchanged every 2 days. For the control group, DMSO with the same volume of 5-azacytidine was added to the medium. The collected cells were washed and the clean cells were for  scNanoSeq-CUT&Tag experiment.  As for isolation of mouse blood cells, the 3 ml of whole blood from 8-week-old male B6D2F1 was firstly mixed with 30 ml of 1x red blood cell lysis buffer, incubated at room temperature for 15 min, and centrifuged at 400 x g for 20 min to remove red blood cells. And then the cell pellets were washed twice with 10ml of PBS and were stained with the following antibodies: APC-Cy7 anti-mouse CD45 (Biolegend, 103115), PE anti-mouse CD3 (Biolegend, 100205), CD19 (Biolegend, 115537), FITC anti-mouse CD4 (Biolegend, 100405), APC anti-mouse CD8a (Biolegend, 100711). After that the free antibodies were washed away, the cells were filtered with a 40 μm filter and resuspended with 500 ul of PBS buffer containing 0.5% BSA for subsequent cell sorting. Finally, CD45+ immune cells, CD45+CD3+CD19-CD4+ T cells, CD45+CD3+CD19-CD8+ T cells, CD45+CD3-CD19+ B cells, CD45+CD3-CD19- monocytes were collected for subsequent scNanoSeq-CUT&Tag experiment. As for isolation for testicular cells, the testes from 8-week-old male B6D2F1 mouse were collected and dissociated into single cell suspension with 0.5mg/ml of collagenase type I, 0.25% of trypsin and 5mg/ml of DNase I. After that the digestion was stopped by adding 0.5 ml of FBS, the cells were filtered through a 70 μm filter and were washed twice with PBS. Finally, the clean testicular cells were used for scNanoSeq-CUT&Tag experiment.

value: Lymphoblast

value: H3K27ac (Abcam,#ab4729)

value: DMSO


title: E6_41_19 (coseq-smallseq)


title: SY5Y_model_GB_H1


title: E6_41_28 (coseq-smallseq)


title: E6_41_16 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_K562_drug_treatment_5AZA_H3K27ac_Abcam_ab4729

description: scNanoSeq-CUT&Tag of K562_drug_treatment_5AZA (H3K27ac)


title: SY5Y_model_GA_M2


title: scNanoSeq-CUT&Tag_HFF1_H3K9me3_Abcam_ab8898

description: scNanoSeq-CUT&Tag of HFF1 (H3K9me3)

value: H3K9me3 (Abcam,#ab8898)


title: E6_41_13 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_HFF1_H3K27me3_CST_9733T

description: scNanoSeq-CUT&Tag of HFF1 (H3K27me3)


title: E6_41_11 (coseq-smallseq)


title: SY5Y_model_GA_M1


title: SY5Y_model_GB_L2


title: SY5Y_model_GA_L2


title: E6_41_27 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_HFF1_H3K27ac_Abcam_ab4729

description: scNanoSeq-CUT&Tag of HFF1 (H3K27ac)


title: E6_41_1 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_HFF1_H3K36me3_Abcam_ab9050

description: scNanoSeq-CUT&Tag of HFF1 (H3K36me3)


title: SY5Y_model_GA_L1


title: scNanoSeq-CUT&Tag_HFF1_H3K4me3_Millipore_04_745

description: scNanoSeq-CUT&Tag of HFF1 (H3K4me3)


title: E6_40_6 (coseq-smallseq)


title: E6_40_7 (coseq-smallseq)


title: SY5Y_model_GA_H2


title: scNanoSeq-CUT&Tag_H9_RAD21_GeneTex_GTX106012

description: scNanoSeq-CUT&Tag of H9 (RAD21)


title: E6_40_5 (coseq-smallseq)


title: E6_41_14 (coseq-smallseq)


title: E6_40_23 (coseq-smallseq)


title: E6_40_24 (coseq-smallseq)


title: SY5Y_model_GA_H1


title: scNanoSeq-CUT&Tag_H9_CTCF_Millipore_07_729

description: scNanoSeq-CUT&Tag of H9 (CTCF)


title: E6_41_12 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_H9_H3K9me3_Abcam_ab8898

description: scNanoSeq-CUT&Tag of H9 (H3K9me3)


title: E6_40_21 (coseq-smallseq)


title: E6_40_20 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_H9_H3K27me3_CST_9733T

description: scNanoSeq-CUT&Tag of H9 (H3K27me3)


title: E6_40_9 (coseq-smallseq)


title: SY5Y_model_EGB761_M1


title: E6_40_2 (coseq-smallseq)


title: E6_40_19 (coseq-smallseq)


title: SY5Y_model_EGB761_L2


title: E6_40_17 (coseq-smallseq)


title: E6_40_8 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_H9_H3K36me3_Abcam_ab9050

description: scNanoSeq-CUT&Tag of H9 (H3K36me3)


title: E6_40_18 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_H9_H3K27ac_Abcam_ab4729

description: scNanoSeq-CUT&Tag of H9 (H3K27ac)


title: SY5Y_model_DMSO_M2


title: SY5Y_model_EGB761_M2


title: E6_40_11 (coseq-smallseq)


title: E6_40_15 (coseq-smallseq)


title: E6_40_14 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_H9_H3K4me3_Millipore_04_745

description: scNanoSeq-CUT&Tag of H9 (H3K4me3)


title: E5_32_9 (coseq-smallseq)

value: embryo in vitro day E5


title: scNanoSeq-CUT&Tag_HG002_CTCF_Millipore_07_729

description: scNanoSeq-CUT&Tag of HG002 (CTCF)


title: E6_40_4 (coseq-smallseq)


title: SY5Y_model_DMSO_L1


title: SY5Y_model_EGB761_L1


title: E6_40_13 (coseq-smallseq)


title: SY5Y_model_DMSO_H2


title: E5_32_4 (coseq-smallseq)


title: SY5Y_model_DMSO_H1


title: SY5Y_model_DMSO_M1


title: E6_40_12 (coseq-smallseq)


title: SY5Y_model_DMSO_L2


title: scNanoSeq-CUT&Tag_HG002_RAD21_GeneTex_GTX106012

description: scNanoSeq-CUT&Tag of HG002 (RAD21)


title: E5_32_5 (coseq-smallseq)


title: E5_32_7 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_HG002_H3K9me3_Abcam_ab8898

description: scNanoSeq-CUT&Tag of HG002 (H3K9me3)


title: E6_40_16 (coseq-smallseq)


title: E6_40_1 (coseq-smallseq)


title: E5_32_3 (coseq-smallseq)


title: E5_32_28 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_HG002_H3K27me3_CST_9733T

description: scNanoSeq-CUT&Tag of HG002 (H3K27me3)


title: scNanoSeq-CUT&Tag_HG002_H3K36me3_Abcam_ab9050

description: scNanoSeq-CUT&Tag of HG002 (H3K36me3)


title: E5_32_31 (coseq-smallseq)


title: SY5Y_model_DGMIsolvent_M1


title: E5_32_29 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_HG002_H3K27ac_Abcam_ab4729

description: scNanoSeq-CUT&Tag of HG002 (H3K27ac)


title: SY5Y_model_DGMIsolvent_L2


title: SY5Y_model_DGMIsolvent_M2


title: SY5Y_model_DGMIsolvent_L1


title: E5_32_20 (coseq-smallseq)


title: E5_32_27 (coseq-smallseq)


title: E5_32_24 (coseq-smallseq)


title: E5_32_2 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_GM12878_RAD21_GeneTex_GTX106012

description: scNanoSeq-CUT&Tag of GM12878 (RAD21)


title: E5_32_19 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_HG002_H3K4me3_Millipore_04_745

description: scNanoSeq-CUT&Tag of HG002 (H3K4me3)


title: E5_32_18 (coseq-smallseq)


title: SY5Y_model_DGMIsolvent_H1


title: scNanoSeq-CUT&Tag_GM12878_H3K9me3_Abcam_ab8898

description: scNanoSeq-CUT&Tag of GM12878 (H3K9me3)


title: SY5Y_model_DGMI_M2


title: E5_32_17 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_GM12878_H3K27me3_CST_9733T

description: scNanoSeq-CUT&Tag of GM12878 (H3K27me3)


title: SY5Y_model_DGMIsolvent_H2


title: E5_32_15 (coseq-smallseq)


title: E5_32_22 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_GM12878_CTCF_Millipore_07_729

description: scNanoSeq-CUT&Tag of GM12878 (CTCF)


title: E5_32_16 (coseq-smallseq)


title: E5_31_5 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_GM12878_H3K27ac_Abcam_ab4729

description: scNanoSeq-CUT&Tag of GM12878 (H3K27ac)


title: E5_32_23 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_GM12878_H3K36me3_Abcam_ab9050

description: scNanoSeq-CUT&Tag of GM12878 (H3K36me3)


title: SY5Y_model_DGMI_M1


title: E5_32_21 (coseq-smallseq)


title: E5_31_19 (coseq-smallseq)


title: E5_31_24 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_293T_RAD21_GeneTex_GTX106012

description: scNanoSeq-CUT&Tag of 293T (RAD21)

value: Human embryonic kidney


title: SY5Y_model_DGMI_L2


title: E5_31_22 (coseq-smallseq)


title: SY5Y_model_DGMI_L1


title: scNanoSeq-CUT&Tag_293T_CTCF_Millipore_07_729

description: scNanoSeq-CUT&Tag of 293T (CTCF)


title: E5_30_6 (coseq-smallseq)


title: E5_31_14 (coseq-smallseq)


title: E5_30_2 (coseq-smallseq)


title: E5_32_13 (coseq-smallseq)


title: SY5Y_model6

value: OGD


title: SY5Y_model_DGMI_H1


title: E5_30_7 (coseq-smallseq)


title: SY5Y_model_DGMI_H2


title: scNanoSeq-CUT&Tag_GM12878_H3K4me3_Millipore_04_745

description: scNanoSeq-CUT&Tag of GM12878 (H3K4me3)


title: scNanoSeq-CUT&Tag_293T_H3K9me3_Abcam_ab8898

description: scNanoSeq-CUT&Tag of 293T (H3K9me3)


title: SY5Y_model5


title: E5_30_11 (coseq-smallseq)


title: E5_30_14 (coseq-smallseq)


title: E5_30_15 (coseq-smallseq)


title: E5_31_23 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_293T_H3K27me3_CST_9733T

description: scNanoSeq-CUT&Tag of 293T (H3K27me3)


title: SY5Y_model4


title: E4_30_9 (coseq-smallseq)

value: embryo in vitro day E4


title: scNanoSeq-CUT&Tag_293T_H3K36me3_Abcam_ab9050

description: scNanoSeq-CUT&Tag of 293T (H3K36me3)


title: SY5Y_model3


title: E4_30_6 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_293T_H3K4me3_Millipore_04_745

description: scNanoSeq-CUT&Tag of 293T (H3K4me3)


title: E4_30_5 (coseq-smallseq)


title: E4_30_7 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_293T_H3K27ac_Abcam_ab4729

description: scNanoSeq-CUT&Tag of 293T (H3K27ac)


title: E5_30_3 (coseq-smallseq)


title: E4_30_4 (coseq-smallseq)


title: E4_30_3 (coseq-smallseq)


title: E4_30_2 (coseq-smallseq)


title: E4_30_10 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_K562_RAD21_GeneTex_GTX106012

description: scNanoSeq-CUT&Tag of K562 (RAD21)


title: SY5Y_model1


title: SY5Y_ctrl2

value: untreated


title: E5_30_12 (coseq-smallseq)


title: scNanoSeq-CUT&Tag_K562_H3K9me3_Abcam_ab8898

description: scNanoSeq-CUT&Tag of K562 (H3K9me3)


title: E4_30_1 (coseq-smallseq)


title: E7_44_8 (coseq-mRNA)

data_processing:
Read quality was firstly checked by FastQC. Subsequently, we aligned high-quality reads to the human GRCh38 reference genome (v.3.0.0, GRCh38, obtained from the 10X Genomics website) using the STAR aligner (v2.5.1b) with default settings. Raw read counts were quantified using the rsem-calculate-expression from RSEM (v1.3.0) with the option of " --single-cell-prior". To filter low quality cells, a cut-off based on the number of expressed genes (nGene) of 750 and percentage of mitochondrial genes (percent.mito) of 0.3 was used, leaving 103 cells post-filtering. Gene expression was normalised based on the library size excluding mitochondrial ncRNAs.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
single-cell mRNA-sncRNA Co-seq was performed as previously described and validated on mouse embryos. Briefly, individual cells were collected into 4uL of lysis buffer. After cell lysis at 72°C for 20 minutes, lysates were split into two equal 2 µL halves, with one half allocated to sncRNA sequencing and the other to SmartSeq. Each half was prepared following the original Small-seq and SmartSeq2 protocols, using 22 amplification cycles during the first PCR of SmartSeq2. This approach enabled the association of mRNA markers of cell lineage with corresponding sncRNA profiles.
Co-seq to capture sncRNA and mRNA from a single-cell.

value: embryo in vitro day E7


title: scNanoSeq-CUT&Tag_K562_CTCF_Millipore_07_729

description: scNanoSeq-CUT&Tag of K562 (CTCF)


title: E7_44_6 (coseq-mRNA)


title: scNanoSeq-CUT&Tag_K562_H3K36me3_Abcam_ab9050

description: scNanoSeq-CUT&Tag of K562 (H3K36me3)


title: E7_44_7 (coseq-mRNA)


title: SY5Y_ctrl1


title: MEG01_model_GK_M2

source_name: cell line: Human megakaryoblastic cell line MEG-01


title: scNanoSeq-CUT&Tag_K562_H3K27me3_CST_9733T

description: scNanoSeq-CUT&Tag of K562 (H3K27me3)


title: scNanoSeq-CUT&Tag_K562_H3K27ac_Abcam_ab4729

description: scNanoSeq-CUT&Tag of K562 (H3K27ac)


title: E7_44_45 (coseq-mRNA)


title: MEG01_model_GK_L2


title: mouse neuron nuclei, 50000 cells, Replicate 4, Hi-C

data_processing:
readpair fastq files were processed using distiller-nf v0.34 to create interaction maps in mcool format.
Assembly: hg38, mm10
Supplementary files format and content: mcool for 5k hap1, 10k hap1, 4x50k mouse neurons (pooled), 1x50 mouse neurons (WT4/Rep1)

source_name: forebrain

treatment_protocol: Mouse forebrain was dissected and minced using homogenizer in 5 ml homogenization buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, 1mM DTT, 0.15mM spermine, 0.5mM spermidine), 7 µl RNase Inhibitor (Promega N2611) and 300 µl 5% IGEPAL. The sample was filtered through a 40 µm strainer, mixed with 5 ml of 50% iodixanol (Sigma D1556), underlaid with a gradient of 30% and 40% iodixanol, and centrifuged at 4,600g for 1 hour in a swinging bucket centrifuge at 4°C. Nuclei were collected at the 30%-40% interface. The nuclei were transferred to a 2 ml tube and centrifuged 10 min at 1,000g and 4°C. Nuclei were then FACS-sorted into 4 tubes of 50,000 nuclei each. Finally, nuclei were transferred to freezing buffer (0.32M sucrose, 5mM CaCl2, 0.1mM EDTA, 10mM tris HCl, 3mM Mg(Ac)2) and frozen in -80°C.  5,000 and 10,000 Hap1 human haploid cells (Horizon Discovery) were FACS-sorted to ensure accurate cell counts following formaldehyde crosslinking and quenching as described in the FLIE Hi-C protocol.

value: forebrain

value: neurons

value: frozen nuclei


title: E7_44_41 (coseq-mRNA)

value: embryo


title: MEG01_model_GK_M1


title: E7_44_32 (coseq-mRNA)


title: E7_44_38 (coseq-mRNA)


title: E7_44_40 (coseq-mRNA)


title: MEG01_model_GK_L1


title: E7_44_26 (coseq-mRNA)


title: mouse neuron nuclei, 50000 cells, Replicate 3, Hi-C


title: E7_44_25 (coseq-mRNA)


title: scNanoSeq-CUT&Tag_K562_H3K4me3_Millipore_04_745

description: scNanoSeq-CUT&Tag of K562 (H3K4me3)

value: H3K4me3 (Millipore,#04-745)


title: E7_44_48 (coseq-mRNA)


title: E7_44_22 (coseq-mRNA)


title: mouse neuron nuclei, 50000 cells, Replicate 2, Hi-C


title: MEG01_model_GK_H2


title: mouse neuron nuclei, 50000 cells, Replicate 1, Hi-C


title: MEG01_model_GK_H1


title: E7_44_21 (coseq-mRNA)


title: E6_43_7 (coseq-mRNA)

value: embryo in vitro day E6


title: MEG01_model_GB_M2


title: E7_44_15 (coseq-mRNA)


title: MEG01_model_GB_M1


title: mouse_mirmOTSTEO_sample_9_a (control)

data_processing:
Read quality was firstly checked by FastQC. Subsequently, we aligned high-quality reads to the mouse mm10 reference genome (mm10-2020-A, obtained from the 10X Genomics website) using the STAR aligner (v2.5.1b) with default settings. Raw read counts were quantified using the rsem-calculate-expression from RSEM (v1.3.0) with the option of " --single-cell-prior". Low-quality cells were filtered out by discarding those with fewer than 3000 expressed genes or with a percentage of mitochondrial genes higher than 0.1.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: All mouse experiments were approved by the Centre de Recherche du Centre Hospitalier de l’Universite de Montreal (CRCHUM) Comite Institutionnel de Protection des Animaux du CHUM (CIPA) under the protocol number IP21005SPs. To induce ovulation, C57BL/6 x DBA F1 females were injected with 5 IU of pregnant mare’s serum gonadotropin (PMSG), followed by 5 IU of human chorionic gonadotropin (hCG) 48 hours later. Super-ovulated females were placed with C57BL/6 x DBA F1 male mice for mating immediately following the hCG injection and sacrificed using isoflurane anaesthetic and cervical dislocation 45 to 48 hours later.

extract_protocol:
Upon reaching the desired developmental stage (8 cell (E2.5) or 32 cell (E3.5)), several control and mimic-treated mouse embryos (3-5 embryos/group/timepoint) were collected for single cell dissociation and isolation. Embryos were briefly transferred into Tyrodes solution (Millipore, ref # MR-004-D) to digest the zona pellucida, then were dissociated through trituration in TrypLE (Life Technologies, ref # 12604-013) and picked with fine glass capillaries. Individual cells were dispensed in 4.1 uL Smart-Seq2 lysis buffer and stored at -80°C until library preparation.
Following removal from -80°C storage and thawing, cell lysis (thermocycler, 72°C for 3 minutes) and reverse transcription were performed. This was followed by two polymerase chain reactions (PCRs), the first to amplify the cDNA product (20 cycles) and second with indexes to barcode the libraries for multiplexing (11 cycles). Sample purification, downstream library preparation, sequencing with a NextSeq550 and data analysis using in-house pipelines were all performed as described in Petropoulos et al., 2016

treatment_protocol: At E1.5, uteri were dissected and flushed with 37°C EmbryoMax M2 medium (Sigma-Aldrich, cat # MR-015-D) to collect 2 cell embryos. These embryos were placed in pre-equilibrated EmbryoMax KSOM Media (Sigma-Aldrich, cat # MR-121-D) droplets covered with EmbryoMax Filtered Light Mineral Oil (Sigma-Aldrich, cat # ES-005-C). At this point, mirVana™ custom miRNA mimics (Invitrogen™ (ThermoFisher Scientific)) designed to replicate the actions of miR-381-3p were added directly to media droplets containing 2 cell embryos at a final concentration of either 5 µM or 10 µM. In parallel, a scrambled negative control mimic (Invitrogen™ (ThermoFisher Scientific), cat # 4464058) at the same concentration was used. Embryos were cultured with their respective treatments to later stages of preimplantation development in a normoxic incubator at 37°C (5% CO2, 20% O2).

value: 8 cell

value: control


title: SY5Y_model2


title: E6_43_8 (coseq-mRNA)


title: E6_43_5 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_8_a (control)


title: E6_43_4 (coseq-mRNA)


title: E6_43_36 (coseq-mRNA)


title: E6_43_25 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_88_a (control)


title: E6_43_41 (coseq-mRNA)


title: MEG01_model_GB_L2


title: E7_44_20 (coseq-mRNA)


title: E6_43_34 (coseq-mRNA)


title: E6_43_22 (coseq-mRNA)


title: MEG01_model_GB_L1


title: mouse_mirmOTSTEO_sample_86_b (control)

value: 32 cell


title: MEG01_model_GB_H2


title: MEG01_model_GB_H1


title: mouse_mirmOTSTEO_sample_87_a (control)


title: E6_43_18 (coseq-mRNA)


title: E6_43_24 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_86_a (miR381mimic_treated)


title: E6_43_2 (coseq-mRNA)


title: E6_43_15 (coseq-mRNA)


title: E6_42_7 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_85_b (control)


title: MEG01_model_GA_M1


title: E6_43_13 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_85_a (miR381mimic_treated)


title: E6_42_32 (coseq-mRNA)


title: E6_42_31 (coseq-mRNA)


title: MEG01_model_GA_L2


title: E6_42_29 (coseq-mRNA)


title: MEG01_model_GA_L1


title: E6_42_24 (coseq-mRNA)


title: MEG01_model_GA_H2


title: E6_42_23 (coseq-mRNA)


title: E6_42_22 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_84_a (miR381mimic_treated)


title: mouse_mirmOTSTEO_sample_83_b (control)


title: E6_42_21 (coseq-mRNA)


title: E6_42_20 (coseq-mRNA)


title: MEG01_model_GA_H1


title: E6_42_19 (coseq-mRNA)


title: MEG01_model_GA_M2


title: MEG01_model_EGB761_M2


title: E6_42_17 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_83_a (miR381mimic_treated)


title: E6_42_16 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_82_a (miR381mimic_treated)


title: MEG01_model_EGB761_M1


title: mouse_mirmOTSTEO_sample_82_b (control)


title: E6_42_13 (coseq-mRNA)


title: MEG01_model_EGB761_L2


title: E6_42_15 (coseq-mRNA)


title: E6_42_12 (coseq-mRNA)


title: E6_42_11 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_81_b (control)


title: mouse_mirmOTSTEO_sample_84_b (control)


title: E6_41_8 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_81_a (miR381mimic_treated)


title: E6_41_5 (coseq-mRNA)


title: E6_41_7 (coseq-mRNA)


title: MEG01_model_EGB761_L1


title: E6_41_47 (coseq-mRNA)


title: MEG01_model_EGB761_H2


title: mouse_mirmOTSTEO_sample_80_a (miR381mimic_treated)


title: E6_41_44 (coseq-mRNA)


title: E6_41_45 (coseq-mRNA)


title: E6_41_46 (coseq-mRNA)


title: MEG01_model_EGB761_H1


title: MEG01_model_DMSO_M2


title: E6_41_41 (coseq-mRNA)


title: E6_41_42 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_7_a (control)


title: mouse_mirmOTSTEO_sample_79_a (miR381mimic_treated)


title: MEG01_model_DMSO_M1


title: MEG01_model_DMSO_L2


title: mouse_mirmOTSTEO_sample_79_b (control)


title: E6_41_40 (coseq-mRNA)


title: E6_41_4 (coseq-mRNA)


title: MEG01_model_DMSO_L1


title: MEG01_model_DMSO_H2


title: E6_41_39 (coseq-mRNA)


title: E6_41_37 (coseq-mRNA)


title: E6_41_34 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_77_b (control)


title: E6_41_33 (coseq-mRNA)


title: E6_41_32 (coseq-mRNA)


title: MEG01_model_DGMIsolvent_M1,2


title: E6_41_35 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_80_b (control)


title: E6_41_36 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_78_a (miR381mimic_treated)


title: E6_41_31 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_78_b (control)


title: E6_41_27 (coseq-mRNA)


title: MEG01_model_DGMIsolvent_M1


title: mouse_mirmOTSTEO_sample_76_b (control)


title: MEG01_model_DMSO_H1


title: E6_41_23 (coseq-mRNA)


title: E6_41_29 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_76_a (miR381mimic_treated)


title: MEG01_model_DGMIsolvent_L1,2


title: mouse_mirmOTSTEO_sample_75_b (control)


title: Pooled cells with thymus specific, islet specific, and HEL specific T cells_replicate 1

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

description: 10x genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using cell ranger software v7.0.1
Assembly: mm10
Supplementary files format and content: tab separated value and matrix files

source_name: Secondary lymphoid tissues

extract_protocol:
Tissues were mechanically meshed through 70um strainer to generate single cells suspensions
Libraries for single-cell gene expression and sequencing were prepared at the McDonnell Genome Institute (MGI) at Washington University using the 3v3.1 methods. Specifically, cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.

value: Secondary lymphoid tissues

value: Immune cells

value: WT NOD, NOD.HEL TCRtg


title: MEG01_model_DGMIsolvent_H1,2


title: KidneyPT Iron Overload 4

city: New York

first: Katherine

last: Xu

state: NY

address: 1150 St. Nicholas Ave., Room 408A/B

department: Medicine

institute: Columbia University Medical Center

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
A pseudoalignment was performed to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Differentially expressed genes were tested between Spns-KO versus Control samples, and Iron Overload versus Control samples, using DESeq2 (R package, version 1.36.0) from RNA-seq counts data.
Assembly: Mouse: GRCm38
Supplementary files format and content: Tab-delimited text file includes estimated counts of each transcript for each Sample

source_name: kidney

extract_protocol:
Total RNA was extracted by Trizol and in vitro biotinylation of RNA was prepared by using EZ-link Biotin HPDP (Pierce Biotechnology, #21341), and subsequently purified using µMACS Streptavidin Kit (Miltenyi Biotec, Cat#: 130-074-101). RNA concentration and integrity for each sample were assessed on RNA 6000 Pico Chips using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Poly-A pull-down was used to enrich mRNAs)
Libraries were prepared using paired-end 100bp reads for each sample with Illumina TruSeq® RNA prep kits (Illumina, San Diego, CA).
Thio-uracil labeled RNA-seq. Libraries were sequenced using Illumina NovaSeq6000 at the Columbia Genome Center.

treatment_protocol: Genetic Iron Overload Model: Spns1 fl/fl mice were bred with Megalin-CreERT to create Megalin-CreERT;Spns1 f/f deleting Spns1 in proximal tubules. Uprtf/+ mice were bred into this construct to result in Uprt-induced biotinlyation of nasent RNA. Dietary Iron Overload Model: mice containing one allele of Uprt (for biotinylation of nascent RNA) were injected with 12mg of iron sucrose daily for 3 days and euthanized 1 week later.

value: kidney

tag: Sex

value: female

value: proximal tubule

value: Spns1 WT

value: Iron Overload


title: mouse_mirmOTSTEO_sample_74_b (control)


title: mouse_mirmOTSTEO_sample_77_a (miR381mimic_treated)


title: MEG01_model_DGMIsolvent_H1


title: E6_41_30 (coseq-mRNA)


title: KidneyPT Iron Overload 3


title: E6_40_7 (coseq-mRNA)


title: MEG01_model_DGMI_M2


title: E6_40_6 (coseq-mRNA)


title: KidneyPT Iron Overload 2


title: Pooled cells with thymus specific, islet specific, and HEL specific T cells_replicate 2

description: 10x genomics


title: mouse_mirmOTSTEO_sample_74_a (miR381mimic_treated)


title: MEG01_model_DGMI_M1


title: mouse_mirmOTSTEO_sample_73_b (control)


title: KidneyPT Iron Overload 1


title: MEG01_model_DGMI_L2


title: MEG01_model_DGMIsolvent_L1


title: KidneyPT Spns1-WT Control 5

value: Control


title: E6_41_22 (coseq-mRNA)


title: E6_40_22 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_73_a (miR381mimic_treated)


title: E6_40_3 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_75_a (miR381mimic_treated)


title: KidneyPT Spns1-WT Control 4


title: E6_40_9 (coseq-mRNA)


title: MEG01_model_DGMI_H2


title: E6_40_21 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_72_b (control)


title: MEG01_model_DGMI_H1


title: E6_40_19 (coseq-mRNA)


title: KidneyPT Spns1-WT Control 3


title: mouse_mirmOTSTEO_sample_71_b (control)


title: E6_40_16 (coseq-mRNA)


title: KidneyPT Spns1-WT Control 1


title: mouse_mirmOTSTEO_sample_71_a (miR381mimic_treated)


title: KidneyPT Spns1-KO 4

value: Spns1 KO


title: E6_40_14 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_72_a (miR381mimic_treated)


title: E6_40_13 (coseq-mRNA)


title: MEG01_model_DGMI_L1


title: mouse_mirmOTSTEO_sample_70_a (miR381mimic_treated)


title: MEG01_model1

value: PMA


title: MEG01_model3


title: E6_40_11 (coseq-mRNA)

value: embryo


title: mouse_mirmOTSTEO_sample_70_b (control)


title: KidneyPT Spns1-KO 2


title: MEG01_model2


title: mouse_mirmOTSTEO_sample_6_a (control)


title: E6_40_10 (coseq-mRNA)


title: MEG01_ctrl4

value: untreated


title: KidneyPT Spns1-KO 1


title: mouse_mirmOTSTEO_sample_69_b (control)


title: KidneyPT Spns1-WT Control 2


title: mouse_mirmOTSTEO_sample_69_a (miR381mimic_treated)


title: MEG01_model4


title: Intestinal lamina propria cells from lactating mice

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

data_processing:
10x Genomics Chromium Flex scRNA-seq processed using cellranger multi v7.2.0, Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv and refdata-gex-mm10-2020-A
Assembly: mm10
Supplementary files format and content: Cell Ranger Feature Barcode Matrices H5 format

source_name: intestine

extract_protocol:
Using FACSAria III Cell Sorter (BD), CD45-positive and EPCAM-negative cells (Immune cells) and  CD45-negative and EPCAM-negative cells (Mesenchymal cells) were enriched by cell sorting from nulliparous and lactating mice. For each sample, one million cells were fixed for 22 hours at 4°C, quenched and stored at -80°C according to 10X genomic Fixation of Cells & Nuclei for Chromium Fixed RNA profiling (CG000478, 10X Genomics, Pleasanton, CA) using the Chromium Next GEM Single Cell Fixed RNA Sample preparation kit (PN-1000414, 10X Genomics).
250,000 cells per sample were used for probe hybridization using the Chromium Fixed RNA Kit, Mouse WTA probes (PN-1000496, 10X Genomics), pooled at equal numbers and washed following the Pooled Wash Workflow following the Chromium Fixed RNA Profiling Reagent kit protocol (CG000527, 10X Genomics). GEMs were generated using Next GEM ChipQ (PN-1000422, 10X Genomics) on Chromium X (10X Genomics) with a target of 10,000 cells recovered
Libraries prepared according to the manufacturer instructions (CG000527, 10X Genomics). Sequencing was performed using NovaSeq S4 lane PE150 (Illumina) with a target of 15,000 reads per cell. Alignment of the samples was performed with the 10x Genomics Cell Ranger 7.1.0 multi pipeline.

value: intestine

value: immune cells and mesenchymal cells

tag: strain


title: MEG01_ctrl3


title: E5_32_5 (coseq-mRNA)

value: embryo in vitro day E5


title: MEG01_ctrl2


title: Intestinal lamina propria cells from nulliparous mice


title: KidneyPT Spns1-KO 3


title: mouse_mirmOTSTEO_sample_68_b (control)

value: 32 cell

value: control


title: mouse_mirmOTSTEO_sample_68_a (miR381mimic_treated)

value: 8 cell


title: MEG01_ctrl1


title: MI_7D

city: Guangzhou

first: fu

last: Ai

state: Guangdong

address: Jingxijiedao

institute: Southern Medical University

data_processing:
Reads containing barcodes were de-multiplexed to generate single cell profiles by custom scripts. Trimmed paired-end reads were mapped to a mouse mm10 genome reference genome with bowtie2. Duplicate reads were removed using picard. Only uniquely reads>1000 cells will be remained. Peaks were called uing macs2 2.2.7.1 with nolambda、nomedel and broad parameters. Bigwig files were generated using the Deeptools BamCoverage，reads were normalized to 1000000.
Assembly: mm10
Supplementary files format and content: The processed files were bigwig files and bed files.

source_name: tissue

growth_protocol: Both the MI surgery mice and Sham surgery mice heart were divided into infarct zone.For each sample, the same zone from 1 mice samples were pooled together.The heart tissue were minced into 1-3 mm pieces on ice with sterilized scissors in 2mL tubes containing 1mL 5%FBS (with 10mM sodium butyrate) and  washed twice with 1mL cold HBSS (with 10mM sodium butyrate) to remove excessive blood. Next, tissues were individually digested with 1mL 0.075% Collagenase Ⅱ（Sigma-Aldrich，#C6885)  at 37°C for 8-15min in the rotate wheel with 40rpm/min and cells were collected by centrifugation at 500g for 5min at 4°C. This step was repeated for 3-4 times until tissue was fully digested.To get rid of blood cells, cells were suspended with 1mL  RBC (erythrocyte lysis buffer, 155mM NH4Cl, 10mM KHCO3and 0.01mM EDTA in sterilized ddH2O) and incubated on ice for 3min. RBC buffer was removed by centrifugation at 500g for 5min at 4°C and the cells were then resuspended with 1mL 5%FBS (10mM sodium butyrate).Cell suspensions were stained in 5%FBS (10mM sodium butyrate) with fluorochrome-labeled antibodies anti-F4/80-APC (Biolegend ,123116 , 1:100), anti-CD45-PE-cy7 (Biolegend ,103114, 1:400), 7-AAD （invitrogen,00699350,1:100）.Cells sorted on a FACSAriaIII.FSC-W vs FSC-A was used excluded doublets and dead cells removed by 7-AAD. Macrophages were identifified as CD45+ F4/80+ cells. Gating strategy for those markers was set based on background auto-fluorescence measured in unstained controls.The dissociated cells were binding with Concanavalin A coated magnetic beads (Con-A beads)  for 15 min at RT.As for the Con-A beads,they were washed with 1 mL Binding Buffer (400 μl 1 M HEPES pH 7.9, 200 μl 1 M KCl, 20 μl 1 M CaCl2, 20 μl 1 M MnCl2, and the final volume to 20 ml with ddH2O) 1-2 times, and were then resuspended with adequate Binding Buffer and applied to the cell mixture.Then the cells were cross-linked with 0.25% formaldehyde at 4℃ for 5 min and quenched by addition of 35 mM Glycine at 4℃ for 5 min followed by methyl alcohol fixation. Samples were stored at  80 ℃ for later use.

extract_protocol:
Adequate cells were took out from -80℃ and washed thrice with 0.1% BSA/PBS(10mM sodium butyrate) 5 min each time.Cells were resuspended with 80 µl Antibody Buffer (mix 4 µL 0.5 M EDTA with 1 mL 0.01% Digitonin-Wash Buffer (Dig-Wash Buffer) supplemented with cocktail, 10 mM sodium butyrate and 0.05% Triton X-100) and added primary antibody.The mixture incubated at 4℃ for 4 h in a rotate wheel with 30 rpm/min . Then cells were washed twice with 180 µL Dig-Wash Buffer .The secondary antibody were incubate in the same buffer and condition except the duration for 10 min.Cells were split into 96-well plates with 1,000-2,000 cells per tube in 80 µl Dig-Wash Buffer (with 0.05% Triton-X, cocktail, and 10 mM sodium butyrate) containing 0.83 µM PAT-T5 and 0.83 µM PAT-T7, and incubated at 4°C for 1 h. Free PAT was then dislodged with 180 µL Dig-Wash Buffer containing 0.05% Triton X-100 three times at 5 min per time. The reaction was activated by suspending cells with 10 µL cold Reaction Buffer (10 mM TAPS-NaOH pH 8.3, 5 mM MgCl2, 10% DMF, 0.05% Triton-X, 0.01% Digtonin and supplemented with cocktail, 10 mM sodium butyrate) in each tube. The reaction was gently mixed once after 30 min incubation and stopped by adding 8 µl 50 mM EDTA followed by further incubation at 4°C for 10 min after mixing well. Cells were combined and washed with 0.1% BSA/PBS three times, then passed through a 40 µm cell strainer to remove cell clumps. 20-25 cells were sorted into each well of a new 96-well plate which contains 3µL Lysis Buffer (0.1 mg/ml Proteinase K,10 mM Tris-HCl pH 8.5 and 0.05% SDS) and incubated at 55°C for 3 h in a PCR cycler.
Library enrichment was performed using two steps of PCR amplification as previously described(60). Briefly, the first step was performed by the addition of 0.5 μL 50 μM Truseq connector primer mix (Connector primer F:5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCTTCGTCGGCAGCGTCTCCACGC-3′, Connector primer R:5′-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTCTCGTGGGCTCGGCTGTCCCTGT-3′), 10 µL 5 × Q5 reaction buffer, 10 µL 5 × Q5 high GC enhancer, 1 µL 10 mM dNTP, 23.5 µL 1 mM MgCl2, 0.3 µL Q5 polymerase (NEB M0491S) to the 3 μL CoBATCH cell lysis in each tube and the reaction was set up . Then 0.5 μL 20 U/µl ExoI (NEB M0293S) was added and the reaction was incubated at 37°C for 30 min, and 72°C for 20 min. The second PCR enrichment was performed by the addition of 1 µl 10 mM Truseq index P5, 1 µl Truseq index P7, 2 µl 5 × Q5 reaction buffer, 2 µl 5 × Q5 high GC enhancer, 0.5 µl 10 mM dNTP, 3.5 µl 1 mM MgCl2, 0.1 µl Q5 polymerase (NEB M0491S) to the mixture, and the reaction was set up by incubation at 95°C for 5 min, 5-7 cycles of amplification (95°C for 30 s, 63°C for 30 s, 72°C for 1 min), and final 72°C extension for 5 min. Finally, the PCR products were purified and selected by SPRI beads for 200-1000 bp.

value: tissue

value: macrophage/monocyte

value: myocardial infarction


title: MI_3D


title: HUVECT1_model_GK_M1

source_name: cell line: Human umbilical vein endothelial cell line HUVECT1


title: mouse_mirmOTSTEO_sample_67_b (control)


title: Sham_7D


title: mouse_mirmOTSTEO_sample_67_a (miR381mimic_treated)


title: E5_32_31 (coseq-mRNA)


title: Sham_3D


title: E5_32_16 (coseq-mRNA)


title: E5_32_23 (coseq-mRNA)


title: E5_32_6 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_66_b (control)


title: HUVECT1_model_GK_L2


title: E5_32_15 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_66_a (miR381mimic_treated)


title: mouse_mirmOTSTEO_sample_65_b (control)


title: HUVECT1_model_GK_H2


title: CD45+ of partial tumor volume 16/2 Gy RT (PI16/2), 16GY part , mice 2

city: Fontenay-Aux-Roses

first: Fabien

last: Milliat

address: 31 avenue de la division Leclerc

country: France

institute: IRSN

description: 10X Genomics

data_processing:
The demultiplexing, bar coded processing, gene counting and agregation were made using the Cell Ranger Software (Pipeline Version cellranger-6.0.2 10X gennomics) with the Chemistry Single Cell 3' v3 and the tracriptome version mm10-2020-A
Assembly: mm10-2020-A
Supplementary files format and content: table-separated values and matrix files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: tumor

extract_protocol:
2 days after RT, mice were euthanized, and tumor tissues collected. Single-cell suspensions were prepared and CD45+ cells were positively selected using CD45 MicroBeads and viability (at least 85% of cell viability and >90% of CD45+ cell) was checked before encapsulation.
Cells were encapsulated using the 10x Chromium Controller system and a Chromium Next GEM Single Cell 3ʹ Dual Index Kit v3.1. Reverse transcription and libraries were prepared according to the manufacturer's instruction.

treatment_protocol: MC38 cells were subcutaneously injected into the right hind flank of C57BL/6 Female mice aged 8 weeks. After 11 days, the mice were divided into different groups: control tumors (Ctrl), total tumor irrdiated at 2 Gy RT (TI2) or 16 Gy RT (TI16), partial tumor volume 16/0 Gy RT (PI16/0), and partial tumor volume 16/2 Gy RT (PI16/2). Portions irradiated at 16 Gy and 0 Gy (unirradiated) from PI16/0 tumors are respectively called PI16/0 16Gy and PI16/0 0Gy. Portions irradiated at 16 Gy and 2 Gy from PI16/2 tumors are respectively called PI16/2 16Gy and PI16/2 2Gy.

value: tumor

value: Murine MC-38 Colon Carcinoma Epithelial Cell line from C57BL6


title: CD45+ of partial tumor volume 16/2 Gy RT (PI16/2), 16GY part , mice 1

description: 10X Genomics


title: E5_32_32 (coseq-mRNA)


title: HUVECT1_model_GK_M2


title: E5_32_4 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_65_a (miR381mimic_treated)


title: E5_31_3 (coseq-mRNA)


title: CD45+ of partial tumor volume 16/2 Gy RT (PI16/2), 2GY part , mice 2

description: 10X Genomics


title: HUVECT1_model_GB_M1


title: HUVECT1_model_GB_M2


title: mouse_mirmOTSTEO_sample_64_b (control)


title: CD45+ of partial tumor volume 16/2 Gy RT (PI16/2), 2GY part , mice 1

description: 10X Genomics


title: mouse_mirmOTSTEO_sample_64_a (miR381mimic_treated)


title: HUVECT1_model_GB_L2


title: HUVECT1_model_GK_L1


title: mouse_mirmOTSTEO_sample_63_b (control)


title: E5_31_1 (coseq-mRNA)


title: CD45+ of partial tumor volume 16/0 Gy RT (PI16/0), 16GY part , mice 2

description: 10X Genomics


title: mouse_mirmOTSTEO_sample_5_a (control)


title: mouse_mirmOTSTEO_sample_63_a (miR381mimic_treated)


title: E5_31_24 (coseq-mRNA)


title: E5_32_14 (coseq-mRNA)


title: HUVECT1_model_GB_H2


title: CD45+ of partial tumor volume 16/0 Gy RT (PI16/0), 16GY part , mice 1

description: 10X Genomics


title: HUVECT1_model_GB_L1


title: E5_30_9 (coseq-mRNA)


title: CD45+ of partial tumor volume 16/0 Gy RT (PI16/0), 0GY part , mice 2

description: 10X Genomics


title: mouse_mirmOTSTEO_sample_4_a (control)


title: E5_30_7 (coseq-mRNA)


title: E5_30_8 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_3_a (control)


title: CD45+ of partial tumor volume 16/0 Gy RT (PI16/0), 0GY part , mice 1

description: 10X Genomics


title: HUVECT1_model_GK_H1


title: HUVECT1_model_GB_H1


title: CD45+ of total tumor volume at 16Gy, mice 2

description: 10X Genomics

value: total tumor volume at 16Gy


title: HUVECT1_model_GA_M2


title: E5_30_3 (coseq-mRNA)


title: E5_31_20 (coseq-mRNA)


title: HUVECT1_model_GA_M1


title: E5_30_15 (coseq-mRNA)


title: mouse_mirmOTSTEO_sample_2_a (control)


title: HUVECT1_model_GA_L2


title: mouse_mirmOTSTEO_sample_30_a (control)


title: CD45+ of total tumor volume at 2Gy, mice 2

description: 10X Genomics

value: total tumor volume at 2Gy


title: mouse_mirmOTSTEO_sample_29_a (control)


title: HUVECT1_model_GA_L1


title: CD45+ of total tumor volume at 2Gy, mice 1

description: 10X Genomics


title: E5_30_10 (coseq-mRNA)


title: CD45+ of Control tumor mice 4

description: 10X Genomics

value: Control


title: E4_30_7 (coseq-mRNA)

value: embryo in vitro day E4


title: HUVECT1_model_EGB761_M2


title: E4_30_9 (coseq-mRNA)

value: embryo


title: CD45+ of Control tumor mice 3

description: 10X Genomics


title: E4_30_1 (coseq-mRNA)


title: HUVECT1_model_GA_H1


title: HUVECT1_model_GA_H2


title: CD45+ of total tumor volume at 16Gy, mice 1

description: 10X Genomics


title: mouse_mirmOTSTEO_sample_27_a (control)


title: Hashtag labeling Heart

city: Aachen

first: Tore

last: Bleckwehl

address: Pauwelsstrasse 30

department: Klinik fuer Nieren- und Hochdruckkrankheiten, rheumatologische und immunologische Erkrankungen (Medizinische Klinik II)

country: Germany

institute: RWTH Uniklinik

library_source: other

data_processing:
For the demultiplexing of CellPlex and Hashtag based sample labeling, sequencing reads were mapped to the reference genome GRCh38-2020-A applying the the cellranger multi pipeline (version 7.1.0) with default setting and the used sample barcodes for the corresponding tagging method
Assembly: GRCh38-2020-A
Supplementary files format and content: raw_feature_bc_matrix, multiplexing_assignment_tables

molecule: other

source_name: Heart

extract_protocol:
For PBMC isolation blood was collected from patients into EDTA-tubes and mixed 1:1 with PBS. EDTA-blood was then carefully layered on to Ficoll-Paque Plus (1:1,5) and centrifuged (400 G, 40 min, RT). After centrifugation the PBMC-Layer was aspirated, resuspended in FACS-Buffer (PBS, 2% FCS, 2mM EDTA) and centrifuged (300 G, 10 min, RT). The supernatant was discarded and cells were resuspended in 300 µl FACS Buffer. At this step, PBMC were counted and ~0.5x106 cells were taken for each Bulk-RNA sequencing and WES. The remaining cells were stained with CD14-PE, CD16-APC, CD4-FITC, CD8-PE Cy7 and CD19-BB700 (30 min, 4°C, protected from light). Afterwards, cells were washed once with FACS Buffer (400 g, 5 min, 4°C) before staining PBMC with a unique CellPlex-Oligo (100 µl, 5 min, RT) for each patient. Subsequently cells were washed twice, before sorting a unique PBMC population for each patient (CD14 Monocytes, CD16 Monocytes, CD4 T-Cells, CD8 T-Cells, CD19 B-Cells) using a BD FACSMelody Cell Sorter. For lymphocytes Dapi, CD16 and CD14 positive cells were excluded to avoid dead cell and monocyte contamination. For monocytes Dapi, CD4 and CD8 positive cells were excluded to avoid dead cell and lymphocyte contamination. After sorting, PBMC were pooled and immediately loaded onto a Chromium Next GEM Chip G for snRNA-seq (10x, 3’ v3.1). For heart samples, Snap frozen tissue was crushed using a mortar and pestle, resuspended in 500 µl nuclei lysis Buffer (NLB, EZ lysis Buffer NUC101, Sigma-Aldrich with 1 Tab/10 ml  of Complete Protease Inhibitor, Roche and 10 µl/ml Recombinant RNase Inhibitor 2313A, Takara Bio and 10µl/ml Superase In RNase Inhibitor, Thermofisher) and homogenized with dounce tissue grinder pestles. The homogenized solution was spun down, supernatant discarded and the pellet resuspended in 4 ml nuclei resuspension buffer (NRB, PBS, 1% BSA, 10 µl/ml Protector RNase Inhibitor, Rochel). The suspension was then filtered via a 40 µm cell strain and centrifuged (500 G, 4°C, 5 min). Supernatant was discarded, and cells resuspended in 200 µl Nuclei resuspension Buffer (NRB, PBS, 1% BSA, 10 µl/ml Protector RNase Inhibitor, Rochel) with 3 µl of a unique TotalSeq anti-Nuclear Pore Complex Antibody Hashtag-Antibody for each sample (4°C, 20 min). Subsequently samples were washed with 1 ml NRB, centrifuged (500 G, 4°C, 5 min) and resuspended in 100 µl of a unique CellPlex Oligo for each sample (RT, 5 min). Cells were washed once more with NRB (500 G, 4°C, 5 min) before proceeding to Fluorescent-activated Nuclei-sorting of DAPI positive nuclei with a Sony SH800S. 5 minutes prior to sorting nuclei were stained with DAPI (Sigma-Aldrich). After sorting, nuclei were pooled and immediately loaded onto a Chromium Next GEM Chip G for snRNA-seq (10x, 3’ v3.1).
Single cell RNA (3’ v3.1, Dual Index) and 3’ CellPlex library preparation was performed according to the manufacturer's instructions. Hashtag-Libraries were prepared as described by Stoeckius et al.

value: Heart


title: CD45+ of Control tumor mice 1

description: 10X Genomics


title: HUVECT1_model_EGB761_M1


title: HUVECT1_model_EGB761_L2


title: mouse_mirmOTSTEO_sample_25_a (control)

source_name: embryo


title: CellPlex labeling Heart


title: Mga_KO_IFN-g_2

city: Houston

first: Chang

last: Yang

state: Texas

address: 6565 MD Anderson BLVD

department: Experimental Radiation Oncology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
The raw reads were first processed using AfterQC (Version 0.9.7, https://github.com/OpenGene/AfterQC) for data filtering, trimming, error removing and quality control.
Genome mapping was carried out using HISAT2 software (v2.1.0) with the mouse reference genome (UCSC GRCm38/mm10).
Reads in features were counted using htseq-count (v0.6.1p1) as a part of HTSeq (https://htseq.readthedocs.io/en/latest/).
Expression of the transcripts or genes was normalized as FPKM (fragments per kilobase of transcript per million mapped reads) for quantification.
Assembly: UCSC GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

growth_protocol: 4T1 WT and Mga KO cells were cultured in DMEM medium with 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, 74104)  according to the manufacturer’s instructions.
The libraries were prepared with NEBNext Ploy(A) mRNA Magnetic Isolation Module (E7490L, New England Biolabs), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L, New England Biolabs) and NEBNext Multiplex Oligos for illumina (E6609S, New England Biolabs)

treatment_protocol: With or without IFN-g stimulation (100ng/ml) for 24 hours

value: epithetial cell

value: Mga KO

value: IFN-g


title: Mga_KO_IFN-g_3


title: mouse_mirmOTSTEO_sample_28_a (control)


title: mouse_mirmOTSTEO_sample_23_a (control)


title: HUVECT1_model_EGB761_L1