title: C128_A3_L1_38wUW_RepM


title: C128_A7_L1_38wUW_RepM

status: Public on Feb 02 2023

type: SRA

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

library_source: transcriptomic

data_processing:
Following quality controls , reads were mapped to the Mus musculus transcriptome (ENSEMBL version 101) using Salmon v 0.13.1 and RNA-seq data were analysed using Seurat packages (v 4.0.1) on R (v 4.0.3).
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of gene expression read counts matrix per gene/cell.

molecule: total RNA

organism: Mus musculus

source_name: Murine Epidermal cells

extract_protocol:
Flow citometry was used to sort tomato positive epidermal cells
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).

treatment_protocol: Lrig1-EGFP-ires-CreERT2 Rosa26-fl/STOP/fl-tdTomato mice received a single topical application of hydroxytamoxifen on tail skin prior to wounding.

tag: strain

value: CBA C57BL/6 mixed

tag: cell type

value: Keratinocytes

tag: plate

tag: population

tag: time

tag: replicate

value: RepM

tag: batch


title: C119_H8_L1_38w_RepL

value: RepL


title: C128_A10_L1_38wUW_RepM


title: C119_H9_L1_38w_RepL


title: C128_A11_L1_38wUW_RepM


title: C128_C1_L1_38wUW_RepM


title: C119_H6_L1_38w_RepL


title: C119_H12_L1_38w_RepL_MBULK


title: C119_H7_L1_38w_RepL


title: C119_H2_L1_38w_RepL


title: C128_B5_L1_38wUW_RepM


title: C119_H11_L1_38w_RepL


title: C119_H10_L1_38w_RepL


title: C119_H1_L1_38w_RepL


title: C119_G9_L1_38w_RepL


title: C119_G8_L1_38w_RepL


title: C128_A9_L1_38wUW_RepM


title: C119_G4_L1_38w_RepL


title: C119_G7_L1_38w_RepL


title: C119_G6_L1_38w_RepL


title: C119_G3_L1_38w_RepL


title: C119_G2_L1_38w_RepL


title: C119_G11_L1_38w_RepL


title: C119_G10_L1_38w_RepL


title: C119_G12_L1_38w_RepL


title: C129_B5_L1_38wUW_RepN

value: RepN


title: C129_C2_L1_38wUW_RepN


title: C119_G1_L1_38w_RepL


title: C119_F8_L1_38w_RepL


title: C119_F11_L1_38w_RepL


title: C119_F12_L1_38w_RepL


title: C119_F4_L1_38w_RepL


title: C119_F3_L1_38w_RepL


title: C119_F10_L1_38w_RepL


title: C119_F2_L1_38w_RepL


title: C119_F1_L1_38w_RepL


title: C119_E9_L1_38w_RepL


title: C129_B6_L1_38wUW_RepN


title: C119_E3_L1_38w_RepL


title: C119_E7_L1_38w_RepL


title: C119_E4_L1_38w_RepL


title: C119_E11_L1_38w_RepL


title: C119_E1_L1_38w_RepL


title: C119_E2_L1_38w_RepL


title: C119_E12_L1_38w_RepL


title: C119_D9_L1_38w_RepL


title: C119_F9_L1_38w_RepL


title: C119_D8_L1_38w_RepL


title: C119_D7_L1_38w_RepL


title: C119_D2_L1_38w_RepL


title: C119_D12_L1_38w_RepL


title: C119_D3_L1_38w_RepL


title: C119_D4_L1_38w_RepL


title: C119_D11_L1_38w_RepL


title: C119_D10_L1_38w_RepL


title: C119_C6_L1_38w_RepL


title: C119_C7_L1_38w_RepL


title: C119_C3_L1_38w_RepL


title: C119_C10_L1_38w_RepL


title: C119_C11_L1_38w_RepL


title: C119_C1_L1_38w_RepL


title: C119_C12_L1_38w_RepL


title: C119_B7_L1_38w_RepL


title: C119_B8_L1_38w_RepL


title: C119_B9_L1_38w_RepL


title: C119_B6_L1_38w_RepL


title: C119_B10_L1_38w_RepL


title: C119_B12_L1_38w_RepL


title: C119_B4_L1_38w_RepL


title: C119_B11_L1_38w_RepL


title: C119_D1_L1_38w_RepL


title: C119_A6_L1_38w_RepL


title: C119_A8_L1_38w_RepL


title: C119_A11_L1_38w_RepL


title: C119_A4_L1_38w_RepL


title: C119_A3_L1_38w_RepL


title: C119_A10_L1_38w_RepL


title: C118_B9_L1_38w_RepI

value: RepI


title: C119_A2_L1_38w_RepL


title: C118_B7_L1_38w_RepI


title: C118_B4_L1_38w_RepI


title: C118_B11_L1_38w_RepI


title: C118_B10_L1_38w_RepI


title: C119_A9_L1_38w_RepL


title: C118_A8_L1_38w_RepI


title: C118_B3_L1_38w_RepI


title: C118_A7_L1_38w_RepI


title: C118_A9_L1_38w_RepI


title: C118_A6_L1_38w_RepI


title: C118_A4_L1_38w_RepI


title: C118_A3_L1_38w_RepI


title: C118_A5_L1_38w_RepI


title: C119_A12_L1_38w_RepL


title: C114_H3_L1_38w_RepI_IDTILL


title: C118_A12_L1_38w_RepI


title: C114_H1_L1_38w_RepI


title: C119_B3_L1_38w_RepL


title: C114_G6_L1_38w_RepI__IDTILL


title: C114_G5_L1_38w_RepI__IDTILL


title: C119_B2_L1_38w_RepL


title: C114_G5_L1_38w_RepI


title: C118_B12_L1_38w_RepI


title: C114_G2_L1_38w_RepI


title: C114_G2_L1_38w_RepI_IDTILL


title: C114_G1_L1_38w_RepI


title: C114_F6_L1_38w_RepI


title: C114_F5_L1_38w_RepI


title: C114_F2_L1_38w_RepI_IDTILL


title: C114_F4_L1_38w_RepI


title: C114_F3_L1_38w_RepI


title: C114_F4_L1_38w_RepI_IDTILL


title: C114_F1_L1_38w_RepI_IDTILL


title: C118_A11_L1_38w_RepI


title: C114_F3_L1_38w_RepI_IDTILL


title: C114_F2_L1_38w_RepI


title: C114_E6_L1_38w_RepI


title: C114_E5_L1_38w_RepI


title: C114_F1_L1_38w_RepI


title: C114_E4_L1_38w_RepI__IDTILL


title: C114_E4_L1_38w_RepI


title: C114_E3_L1_38w_RepI__IDTILL


title: C114_G3_L1_38w_RepI__IDTILL


title: C114_E3_L1_38w_RepI


title: C114_G4_L1_38w_RepI


title: C114_E2_L1_38w_RepI


title: C114_E1_L1_38w_RepI_IDTILL


title: C114_G3_L1_38w_RepI


title: C114_E1_L1_38w_RepI


title: C114_D9_L1_38w_RepI


title: C114_D8_L1_38w_RepI


title: C114_D7_L1_38w_RepI


title: C114_D3_L1_38w_RepI


title: C114_D10_L1_38w_RepI


title: C114_D11_L1_38w_RepI


title: C114_C9_L1_38w_RepI


title: C114_C7_L1_38w_RepI


title: C114_C12_L1_38w_RepI


title: C114_C3_L1_38w_RepI


title: C114_C10_L1_38w_RepI


title: C114_B9_L1_38w_RepI


title: C114_E2_L1_38w_RepI_IDTILL


title: C114_B8_L1_38w_RepI


title: C114_B7_L1_38w_RepI


title: C114_A8_L1_38w_RepI


title: C114_A9_L1_38w_RepI


title: C114_B12_L1_38w_RepI


title: C114_A7_L1_38w_RepI


title: C114_A10_L1_38w_RepI


title: C114_A2_L1_38w_RepI


title: C328_H7_PR12_PRT_t0_S181

treatment_protocol: Lrig1-EGFP-ires-CreERT2 Rosa26-fl/STOP/fl-tdTomato mice received a single topical application of hydroxytamoxifen on tail skin prior to PRT4165 or veichle treatment.

tag: treatment

tag: timetreatment


title: C328_H3_PR12_PRT_t0_S149


title: C328_H4_PR12_PRT_t0_S157


title: C328_H6_PR12_PRT_t0_S173


title: C328_H5_PR12_PRT_t0_S165


title: C114_C8_L1_38w_RepI


title: C328_G8_PR12_PRT_t0_S188


title: C328_G5_PR12_PRT_t0_S164


title: C328_G7_PR12_PRT_t0_S180


title: C328_G6_PR12_PRT_t0_S172


title: C114_B10_L1_38w_RepI


title: C328_G4_PR12_PRT_t0_S156


title: C328_G3_PR12_PRT_t0_S148


title: C328_G11_PR12_PRT_t0_S212


title: C328_G1_PR12_PRT_t0_S132


title: C328_F8_PR12_PRT_t0_S187


title: C328_G10_PR12_PRT_t0_S204


title: C328_F9_PR12_PRT_t0_S195


title: C328_F6_PR12_PRT_t0_S171


title: C328_F5_PR12_PRT_t0_S163


title: C328_F7_PR12_PRT_t0_S179


title: C328_H2_PR12_PRT_t0_S141


title: C328_F3_PR12_PRT_t0_S147


title: C328_F11_PR12_PRT_t0_S211


title: C328_F10_PR12_PRT_t0_S203


title: C328_F1_PR12_PRT_t0_S131


title: C328_F4_PR12_PRT_t0_S155


title: C328_E8_PR12_PRT_t0_S186


title: C328_E7_PR12_PRT_t0_S178


title: C328_G9_PR12_PRT_t0_S196


title: C328_G2_PR12_PRT_t0_S140


title: C328_E9_PR12_PRT_t0_S194


title: C328_E6_PR12_PRT_t0_S170


title: C328_E3_PR12_PRT_t0_S146


title: C328_E5_PR12_PRT_t0_S162


title: C328_E11_PR12_PRT_t0_S210


title: C328_E2_PR12_PRT_t0_S138


title: C328_E12_PR12_PRT_t0_S218


title: C328_E10_PR12_PRT_t0_S202


title: C119_A7_L1_38w_RepL


title: C328_E1_PR12_PRT_t0_S130


title: C328_F2_PR12_PRT_t0_S139


title: C328_D5_PR12_PRT_t0_S161


title: C328_D6_PR12_PRT_t0_S169


title: C328_D2_PR12_PRT_t0_S137


title: C328_D12_PR12_PRT_t0_S217


title: C328_D4_PR12_PRT_t0_S153


title: C328_D3_PR12_PRT_t0_S145


title: C328_D7_PR12_PRT_t0_S177


title: C328_D11_PR12_PRT_t0_S209


title: C328_D10_PR12_PRT_t0_S201


title: C328_C9_PR12_PRT_t0_S192


title: C328_C8_PR12_PRT_t0_S184


title: C328_D1_PR12_PRT_t0_S129


title: C328_C7_PR12_PRT_t0_S176


title: C328_C6_PR12_PRT_t0_S168


title: C328_E4_PR12_PRT_t0_S154


title: C328_C4_PR12_PRT_t0_S152


title: C328_C3_PR12_PRT_t0_S144


title: C328_C2_PR12_PRT_t0_S136


title: C328_C11_PR12_PRT_t0_S208


title: C328_D9_PR12_PRT_t0_S193


title: C328_C1_PR12_PRT_t0_S128


title: C328_C10_PR12_PRT_t0_S200


title: C328_B9_PR12_PRT_t0_S191


title: C328_D8_PR12_PRT_t0_S185


title: C328_B8_PR12_PRT_t0_S183


title: C328_B7_PR12_PRT_t0_S175


title: C328_B6_PR12_PRT_t0_S167


title: C328_B2_PR12_PRT_t0_S135


title: C328_B4_PR12_PRT_t0_S151


title: C328_B3_PR12_PRT_t0_S143


title: C328_B1_PR12_PRT_t0_S127


title: C328_B11_PR12_PRT_t0_S207


title: C328_C5_PR12_PRT_t0_S160


title: C328_B10_PR12_PRT_t0_S199


title: C328_A4_PR12_PRT_t0_S150


title: C328_A6_PR12_PRT_t0_S166


title: C328_A5_PR12_PRT_t0_S158


title: C328_A3_PR12_PRT_t0_S142


title: C320_G4_PR9_AC_t0_S60


title: C119_C9_L1_38w_RepL


title: C320_G5_PR9_AC_t0_S68


title: C320_G10_PR9_AC_t0_S108


title: C328_A2_PR12_PRT_t0_S134


title: C320_G1_PR9_AC_t0_S36


title: C328_B5_PR12_PRT_t0_S159


title: C320_F6_PR9_AC_t0_S75


title: C320_F9_PR9_AC_t0_S99


title: C320_G2_PR9_AC_t0_S44


title: C320_F7_PR9_AC_t0_S83


title: C320_F4_PR9_AC_t0_S59


title: C320_F3_PR9_AC_t0_S51


title: C320_F2_PR9_AC_t0_S43


title: C320_F10_PR9_AC_t0_S107


title: C320_F5_PR9_AC_t0_S67


title: C320_F1_PR9_AC_t0_S35


title: C328_A7_PR12_PRT_t0_S174


title: C320_E9_PR9_AC_t0_S98


title: C320_E7_PR9_AC_t0_S82


title: C320_E5_PR9_AC_t0_S66


title: C320_E6_PR9_AC_t0_S74


title: C320_E4_PR9_AC_t0_S58


title: C320_E2_PR9_AC_t0_S42


title: C320_E3_PR9_AC_t0_S50


title: C320_G3_PR9_AC_t0_S52


title: C320_E12_PR9_AC_t0_S122


title: C320_E11_PR9_AC_t0_S114


title: C320_E1_PR9_AC_t0_S34


title: C320_D9_PR9_AC_t0_S97


title: C320_D8_PR9_AC_t0_S89


title: C320_D6_PR9_AC_t0_S73


title: C118_A10_L1_38w_RepI


title: C320_D7_PR9_AC_t0_S81


title: C320_D5_PR9_AC_t0_S65


title: C320_D4_PR9_AC_t0_S57


title: C320_C8_PR9_AC_t0_S88


title: C320_D3_PR9_AC_t0_S49


title: C320_D1_PR9_AC_t0_S33


title: C320_C7_PR9_AC_t0_S80


title: C320_D2_PR9_AC_t0_S41


title: C320_C5_PR9_AC_t0_S64


title: C320_D12_PR9_AC_t0_S121


title: C320_C6_PR9_AC_t0_S72


title: C320_C12_PR9_AC_t0_S120


title: C320_C2_PR9_AC_t0_S40


title: C320_C3_PR9_AC_t0_S48


title: C320_C11_PR9_AC_t0_S112


title: C320_C1_PR9_AC_t0_S32


title: C320_B9_PR9_AC_t0_S95


title: C320_B6_PR9_AC_t0_S71


title: C320_B5_PR9_AC_t0_S63


title: C320_B4_PR9_AC_t0_S55


title: C320_B3_PR9_AC_t0_S47


title: C320_B2_PR9_AC_t0_S39


title: C320_B11_PR9_AC_t0_S111


title: C320_B1_PR9_AC_t0_S31


title: C320_A6_PR9_AC_t0_S70


title: C320_A4_PR9_AC_t0_S54


title: C320_C9_PR9_AC_t0_S96


title: C320_A2_PR9_AC_t0_S38


title: C329_H2_PR12_PRT_t0


title: C329_H3_PR12_PRT_t0


title: C320_C4_PR9_AC_t0_S56


title: C329_G9_PR12_PRT_t0


title: C329_G2_PR12_PRT_t0


title: C329_G3_PR12_PRT_t0


title: C329_G6_PR12_PRT_t0


title: C329_G8_PR12_PRT_t0


title: C329_G5_PR12_PRT_t0


title: C329_F8_PR12_PRT_t0


title: C329_G4_PR12_PRT_t0


title: C329_G10_PR12_PRT_t0


title: C329_G11_PR12_PRT_t0


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title: C329_E1_PR12_PRT_t0


title: C329_D9_PR12_PRT_t0


title: C329_D7_PR12_PRT_t0


title: C329_D6_PR12_PRT_t0


title: C329_D5_PR12_PRT_t0


title: C329_D3_PR12_PRT_t0


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title: C329_D4_PR12_PRT_t0


title: C329_D2_PR12_PRT_t0


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title: C329_A4_PR12_PRT_t0


title: C329_A7_PR12_PRT_t0


title: C329_A5_PR12_PRT_t0


title: C329_A3_PR12_PRT_t0


title: C329_A2_PR12_PRT_t0


title: C319_G9_PR9_AC_t0


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title: C319_G2_PR9_AC_t0


title: C319_G6_PR9_AC_t0


title: C319_G3_PR9_AC_t0


title: C319_G4_PR9_AC_t0


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title: C319_F1_PR9_AC_t0


title: C319_E9_PR9_AC_t0


title: C319_E7_PR9_AC_t0


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title: C319_E3_PR9_AC_t0


title: C319_E2_PR9_AC_t0


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title: C319_E11_PR9_AC_t0


title: C319_E12_PR9_AC_t0


title: C319_D8_PR9_AC_t0


title: C319_D9_PR9_AC_t0


title: C319_D6_PR9_AC_t0


title: C319_D3_PR9_AC_t0


title: C319_D4_PR9_AC_t0


title: C319_F10_PR9_AC_t0


title: C319_D5_PR9_AC_t0


title: C319_D12_PR9_AC_t0


title: C319_D1_PR9_AC_t0


title: C319_C7_PR9_AC_t0


title: C319_C9_PR9_AC_t0


title: C319_D11_PR9_AC_t0


title: C319_D10_PR9_AC_t0


title: C319_C8_PR9_AC_t0


title: C319_C6_PR9_AC_t0


title: C319_E5_PR9_AC_t0


title: C319_C4_PR9_AC_t0


title: C319_C3_PR9_AC_t0


title: C319_C5_PR9_AC_t0


title: C319_C12_PR9_AC_t0


title: C319_C11_PR9_AC_t0


title: C319_D7_PR9_AC_t0


title: C319_C2_PR9_AC_t0


title: C319_C1_PR9_AC_t0


title: C319_C10_PR9_AC_t0


title: C319_B4_PR9_AC_t0


title: C319_B5_PR9_AC_t0


title: C319_B3_PR9_AC_t0


title: C319_D2_PR9_AC_t0


title: C319_B7_PR9_AC_t0


title: C319_B11_PR9_AC_t0


title: C319_B2_PR9_AC_t0


title: C319_A7_PR9_AC_t0


title: C319_B1_PR9_AC_t0


title: C319_B10_PR9_AC_t0


title: C319_A4_PR9_AC_t0


title: C319_A3_PR9_AC_t0


title: C319_A11_PR9_AC_t0


title: C319_A5_PR9_AC_t0


title: C319_B9_PR9_AC_t0


title: C82_H7_L1_1w_RepG_Replicate2

extract_protocol:
Flow citometry was used to sort tomato positive epidermal cells.
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).

treatment_protocol: Lrig1-EGFP-ires-CreERT2 Rosa26-fl/STOP/fl-tdTomato mice received a single topical application of hydroxytamoxifen on tail skin prior wounding.


title: C319_A2_PR9_AC_t0


title: C82_H6_L1_1w_RepG_Replicate2


title: C82_H9_L1_1w_RepG_Replicate2


title: C82_H8_L1_1w_RepG_Replicate2


title: C319_B8_PR9_AC_t0


title: C319_B6_PR9_AC_t0


title: C82_H11_L1_1w_RepG_Replicate2


title: C82_H5_L1_1w_RepG_Replicate2


title: C82_H10_L1_1w_RepG_Replicate2


title: C82_H1_L1_1w_RepG_Replicate2


title: C82_G9_L1_1w_RepG_Replicate2


title: C82_H2_L1_1w_RepG_Replicate2


title: C82_G4_L1_1w_RepG_Replicate2


title: C82_G5_L1_1w_RepG_Replicate2


title: C82_G7_L1_1w_RepG_Replicate2


title: C82_G8_L1_1w_RepG_Replicate2


title: C82_G3_L1_1w_RepG_Replicate2


title: C82_G6_L1_1w_RepG_Replicate2


title: C82_G10_L1_1w_RepG_Replicate2


title: C82_F9_L1_1w_RepG_Replicate2


title: C82_G2_L1_1w_RepG_Replicate2


title: C82_H4_L1_1w_RepG_Replicate2


title: C82_G1_L1_1w_RepG_Replicate2


title: C82_H3_L1_1w_RepG_Replicate2


title: C82_G11_L1_1w_RepG_Replicate2


title: C82_F7_L1_1w_RepG_Replicate2


title: C82_F8_L1_1w_RepG_Replicate2


title: C82_F3_L1_1w_RepG_Replicate2


title: C82_F1_L1_1w_RepG_Replicate2


title: C82_F11_L1_1w_RepG_Replicate2


title: C82_F10_L1_1w_RepG_Replicate2


title: C82_E6_L1_1w_RepG_Replicate2


title: C82_F4_L1_1w_RepG_Replicate2


title: C82_F5_L1_1w_RepG_Replicate2


title: C82_E9_L1_1w_RepG_Replicate2


title: C82_E8_L1_1w_RepG_Replicate2


title: C82_E4_L1_1w_RepG_Replicate2


title: C82_E5_L1_1w_RepG_Replicate2


title: C82_E7_L1_1w_RepG_Replicate2


title: C82_D7_L1_1w_RepG_Replicate2


title: C82_E10_L1_1w_RepG_Replicate2


title: C82_D5_L1_1w_RepG_Replicate2


title: C82_E2_L1_1w_RepG_Replicate2


title: C82_E11_L1_1w_RepG_Replicate2


title: C82_D4_L1_1w_RepG_Replicate2


title: C82_E1_L1_1w_RepG_Replicate2


title: C82_D3_L1_1w_RepG_Replicate2


title: C82_F6_L1_1w_RepG_Replicate2


title: C82_D2_L1_1w_RepG_Replicate2


title: C82_F2_L1_1w_RepG_Replicate2


title: C82_D11_L1_1w_RepG_Replicate2


title: C82_D10_L1_1w_RepG_Replicate2


title: C82_C5_L1_1w_RepG_Replicate2


title: C82_C8_L1_1w_RepG_Replicate2


title: C82_E3_L1_1w_RepG_Replicate2


title: C82_C9_L1_1w_RepG_Replicate2


title: C82_C7_L1_1w_RepG_Replicate2


title: C82_C3_L1_1w_RepG_Replicate2


title: C82_C4_L1_1w_RepG_Replicate2


title: C82_C6_L1_1w_RepG_Replicate2


title: C82_C1_L1_1w_RepG_Replicate2


title: C82_C10_L1_1w_RepG_Replicate2


title: C82_C11_L1_1w_RepG_Replicate2


title: C82_C2_L1_1w_RepG_Replicate2


title: C82_B9_L1_1w_RepG_Replicate2


title: C82_D9_L1_1w_RepG_Replicate2


title: C82_D6_L1_1w_RepG_Replicate2


title: C82_B7_L1_1w_RepG_Replicate2


title: C82_B6_L1_1w_RepG_Replicate2


title: C82_B3_L1_1w_RepG_Replicate2


title: C82_B2_L1_1w_RepG_Replicate2


title: C82_B8_L1_1w_RepG_Replicate2


title: C82_D1_L1_1w_RepG_Replicate2


title: C82_B11_L1_1w_RepG_Replicate2


title: C82_B1_L1_1w_RepG_Replicate2


title: C82_B10_L1_1w_RepG_Replicate2


title: C81_H9_L1_1w_RepG_Replicate1


title: C81_H7_L1_1w_RepG_Replicate1


title: C82_A5_L1_1w_RepG_Replicate2


title: C81_H3_L1_1w_RepG_Replicate1


title: C82_A4_L1_1w_RepG_Replicate2


title: C82_A3_L1_1w_RepG_Replicate2


title: C81_H4_L1_1w_RepG_Replicate1


title: C81_H6_L1_1w_RepG_Replicate1


title: C81_H5_L1_1w_RepG_Replicate1


title: C81_H12_L1_1w_RepG_Replicate1


title: C81_H10_L1_1w_RepG_Replicate1


title: C81_G9_L1_1w_RepG_Replicate1


title: C81_H11_L1_1w_RepG_Replicate1


title: C81_G5_L1_1w_RepG_Replicate1


title: C81_G6_L1_1w_RepG_Replicate1


title: C82_B4_L1_1w_RepG_Replicate2


title: C82_B5_L1_1w_RepG_Replicate2


title: C81_G8_L1_1w_RepG_Replicate1


title: C81_G7_L1_1w_RepG_Replicate1


title: C81_G4_L1_1w_RepG_Replicate1


title: C81_G3_L1_1w_RepG_Replicate1


title: C81_G2_L1_1w_RepG_Replicate1


title: C81_G1_L1_1w_RepG_Replicate1


title: C81_G12_L1_1w_RepG_Replicate1


title: C81_F8_L1_1w_RepG_Replicate1


title: C81_F7_L1_1w_RepG_Replicate1


title: C81_F2_L1_1w_RepG_Replicate1


title: C81_F3_L1_1w_RepG_Replicate1


title: C81_H1_L1_1w_RepG_Replicate1


title: C81_F10_L1_1w_RepG_Replicate1


title: C81_F11_L1_1w_RepG_Replicate1


title: C81_F5_L1_1w_RepG_Replicate1


title: C81_F4_L1_1w_RepG_Replicate1


title: C81_F6_L1_1w_RepG_Replicate1


title: C81_E6_L1_1w_RepG_Replicate1


title: C81_F1_L1_1w_RepG_Replicate1


title: C81_E9_L1_1w_RepG_Replicate1


title: C81_E8_L1_1w_RepG_Replicate1


title: C81_E4_L1_1w_RepG_Replicate1


title: C81_E3_L1_1w_RepG_Replicate1


title: C81_G11_L1_1w_RepG_Replicate1


title: C81_G10_L1_1w_RepG_Replicate1


title: C81_E2_L1_1w_RepG_Replicate1


title: C81_E12_L1_1w_RepG_Replicate1


title: C81_E1_L1_1w_RepG_Replicate1


title: C81_E11_L1_1w_RepG_Replicate1


title: C81_E10_L1_1w_RepG_Replicate1


title: C81_D9_L1_1w_RepG_Replicate1


title: C81_D6_L1_1w_RepG_Replicate1


title: C81_D7_L1_1w_RepG_Replicate1


title: C81_F9_L1_1w_RepG_Replicate1


title: C81_D5_L1_1w_RepG_Replicate1


title: C81_D4_L1_1w_RepG_Replicate1


title: C81_E7_L1_1w_RepG_Replicate1


title: C81_D12_L1_1w_RepG_Replicate1


title: C81_D3_L1_1w_RepG_Replicate1


title: C81_E5_L1_1w_RepG_Replicate1


title: C81_D2_L1_1w_RepG_Replicate1


title: C81_D11_L1_1w_RepG_Replicate1


title: C81_C7_L1_1w_RepG_Replicate1


title: C81_C9_L1_1w_RepG_Replicate1


title: C81_D1_L1_1w_RepG_Replicate1


title: C81_C5_L1_1w_RepG_Replicate1


title: C81_D10_L1_1w_RepG_Replicate1


title: C81_C8_L1_1w_RepG_Replicate1


title: C81_C3_L1_1w_RepG_Replicate1


title: C81_C4_L1_1w_RepG_Replicate1


title: C81_C2_L1_1w_RepG_Replicate1


title: C81_C11_L1_1w_RepG_Replicate1


title: C81_C10_L1_1w_RepG_Replicate1


title: C81_B7_L1_1w_RepG_Replicate1


title: C81_B9_L1_1w_RepG_Replicate1


title: C81_D8_L1_1w_RepG_Replicate1


title: C81_B8_L1_1w_RepG_Replicate1


title: C81_C1_L1_1w_RepG_Replicate1


title: C81_B3_L1_1w_RepG_Replicate1


title: C81_B4_L1_1w_RepG_Replicate1


title: C81_B2_L1_1w_RepG_Replicate1


title: C81_B1_L1_1w_RepG_Replicate1


title: C81_A9_L1_1w_RepG_Replicate1


title: C81_B11_L1_1w_RepG_Replicate1


title: C81_A6_L1_1w_RepG_Replicate1


title: C81_A5_L1_1w_RepG_Replicate1


title: C81_A7_L1_1w_RepG_Replicate1


title: C81_A8_L1_1w_RepG_Replicate1


title: C81_A10_L1_1w_RepG_Replicate1


title: C77_H8_L1_9w_RepF_Replicate2


title: C81_A4_L1_1w_RepG_Replicate1


title: C81_A2_L1_1w_RepG_Replicate1


title: C81_B5_L1_1w_RepG_Replicate1


title: C81_A12_L1_1w_RepG_Replicate1


title: C77_H9_L1_9w_RepF_Replicate2


title: C77_H6_L1_9w_RepF_Replicate2


title: C81_C12_L1_1w_RepG_Replicate1


title: C77_H12_L1_9w_RepF_Replicate2


title: C77_H7_L1_9w_RepF_Replicate2


title: C77_H3_L1_9w_RepF_Replicate2


title: C77_H11_L1_9w_RepF_Replicate2


title: C81_A3_L1_1w_RepG_Replicate1


title: C77_H10_L1_9w_RepF_Replicate2


title: C77_H2_L1_9w_RepF_Replicate2


title: C77_H4_L1_9w_RepF_Replicate2


title: C77_G9_L1_9w_RepF_Replicate2


title: C77_H1_L1_9w_RepF_Replicate2


title: AMuV2

city: Shenyang

first: Xiaoxue

last: Wang

state: Liaoning

address: 120 Dongling Road, Shenhe District

department: Rice Research Institute

country: China

institute: Shenyang Agricultural University

description: fpkm, readcount

data_processing:
The clustering of the index-coded samples is performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations are sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads are generated.
Raw data (raw reads) of fastq format are firstly processed through in-house perl scripts.
Index of the reference genome is built using Bowtie v2.2.3 and paired-end clean reads are aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 is used to count the reads numbers mapped to each gene.
Genome_build: Genome_build: TAIR 10
Supplementary_files_format_and_content: fpkm, read counts

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Seedlings of wild type (Col-0) and skip-1 mutant were grown under 16 hour light/ 8 hour dark photocyles (LD) with cool white fluorescent light (70 Âµmol m-2 s-1) at 22oC for the day and 18oC for the night.

extract_protocol:
Total RNA is extracted with Takara RNAiso Plus (Takara, Cat# 9108)
Sequencing libraries are generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes are added to attribute sequences to each sample. The library quality is assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: 13-day-old seedlings were treated with 0 or 100 uM ABA for 3 hours.

tag: material

value: mutant (Mu or skip-1)

tag: aba concentration

value: 100 uM ABA

tag: replication

value: rep 2

tag: ecotype


title: AMuV1

description: fpkm, readcount

value: rep 1


title: 0MuV2

description: fpkm, readcount

value: 0 uM ABA


title: C77_G8_L1_9w_RepF_Replicate2


title: 0MuV1

description: fpkm, readcount


title: C81_A11_L1_1w_RepG_Replicate1


title: C77_G5_L1_9w_RepF_Replicate2


title: AWTV2

description: fpkm, readcount

value: wild type (WT)


title: C77_G7_L1_9w_RepF_Replicate2


title: AWTV1

description: fpkm, readcount


title: C77_G3_L1_9w_RepF_Replicate2


title: C77_G4_L1_9w_RepF_Replicate2


title: 0WTV2

description: fpkm, readcount


title: C77_G2_L1_9w_RepF_Replicate2


title: 0WTV1

description: fpkm, readcount


title: C77_G10_L1_9w_RepF_Replicate2


title: C77_F9_L1_9w_RepF_Replicate2


title: C77_F8_L1_9w_RepF_Replicate2


title: C77_G1_L1_9w_RepF_Replicate2


title: C77_F7_L1_9w_RepF_Replicate2


title: C77_F6_L1_9w_RepF_Replicate2


title: C77_F5_L1_9w_RepF_Replicate2


title: C77_F3_L1_9w_RepF_Replicate2


title: C77_F2_L1_9w_RepF_Replicate2


title: C77_G12_L1_9w_RepF_Replicate2


title: C77_F11_L1_9w_RepF_Replicate2


title: C77_F12_L1_9w_RepF_Replicate2


title: C77_F4_L1_9w_RepF_Replicate2


title: C81_B6_L1_1w_RepG_Replicate1


title: C77_F10_L1_9w_RepF_Replicate2


title: XKYC9.1d_KC_27wk

city: Boston

first: Elliot

last: Akama-Garren

state: MA

address: 200 Longwood Ave

country: USA

institute: Harvard Medical School

data_processing:
FASTQ files were aligned using BWA-mem to the GRCm38.ERCC genome
Counts were generated using featureCounts
Assembly: mm10
Supplementary files format and content: comma seperated value file contains raw counts for each Sample

molecule: polyA RNA

source_name: Pancreas

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using QuantSeq 3’ mRNA-seq Library Kit (Lexogen) following manufacturer's protocols.

tag: tissue

value: Pancreas

tag: genotype

value: KC


title: XKYC9.1a_KC_27wk


title: C77_G11_L1_9w_RepF_Replicate2


title: XKPC19.2b_KC_30wk_tumor


title: C77_F1_L1_9w_RepF_Replicate2


title: XKYC6.3d_KC_25wk


title: Normoxia_CD11bhiDCs, biological rep3

type: RNA

city: Ann Arbor

first: Antonia

middle: P.

last: Popova

state: Michigan

address: 1150 W. Medical Center Dr., Room 3570, MSRBII, Box 5688

department: Pediatrics

institute: University of Michigan Medical School

description: Gene expression data from CD11bhi DCs flow sorted from neonatal mouse lungs after normoxia

hyb_protocol: Hybridization of the samples to Affymetrix GeneChip arrays was performed by the University of Michigan Sequencing core according to the Affymetrix manual instructions.

scan_protocol: Scanning of Affymetrix GeneChip arrays was performed by the University of Michigan Sequencing core according to the Affmetrix manual instructions.

data_processing: The expression values for each gene were calculated using a robust multi-array average (RMA). Weighted linear models were fitted to the data and computed the contrasts of interest. Probesets with variance less than 0.04 were filtered out. Probesets with a fold change of 1.5 or greater and an adjusted p-value of 0.05 or less were selected. P-values were adjusted for multiple comparisons using false discovery rate Benjamini and Hochberg. The oligo and limma packages of Bioconductor were impremented in the R statistical environment.

label: biotin

source_name: Normoxia-exposed neonatal lung CD11bhi DCs

label_protocol: Labelling was performed by the University of Michigan Sequencing core using the Affymetrix WT Pico Reagent Kit

growth_protocol: Two-day old wild type C57BL/6J mice were exposed to air or 75% oxygen for 14 days using a polypropylene chamber coupled to an oxygen controller and sensor. Dams were exchanged between air and hyperoxia daily. Lungs were analyzed immediately hyperoxia.

extract_protocol: Total RNA was extracted from flow sorted neonatal lung CD103+ DC and CD11bhi DCs using the RNeasy Plus Micro Kit (Qiagen).

treatment_protocol: Lungs were perfused with PBS containing EDTA (0.5 mM) to remove circulating cells in the vasculature, then minced and digested with Liberase TM (100 µg/mL; Roche, Indianapolis, IN), collagenase XI (250 µg/mL), hyaluronidase 1a (1 mg/mL), and DNase I (200 µg/mL; Sigma, St. Louis, MO) for 1 hour at 37oC. Cells were filtered and treated with RBC lysis buffer (BD Biosciences, Franklin Lakes NJ) and kept on ice in media containing 10% serum. Dead cells were stained with DAPI. Lung cells were then stained with fluorescent-labeled antibodies against various leukocyte surface markers (CD45, F4/80, CD11c, CD103, and CD11b). Appropriate isotype-matched controls and Fluorescence Minus One (FMO) controls were used in all experiments. Antibodies were purchased from Biolegend (San Diego, CA). Cells were flow sorted by FACSAria II (BD Biosciences) flow cytometer. Flow sorting purity was >95%. Flow sorted CD103+DCs and CD11b+DCs were used for a gene array (Affymetrix Gene Chip (Affymetrix, CA)) by University of Michigan Sequence Core.

value: lung

tag: condition

value: Normoxia

value: CD11bhi DCs

tag: age

value: 16 day old


title: Normoxia_CD103+DCs, biological rep1

description: Gene expression data from CD103+ DCs flow sorted from neonatal mouse lungs after normoxia

source_name: Normoxia-exposed neonatal lung CD103+ DCs

value: CD103+ DCs

tag: strain


title: Normoxia_CD11bhiDCs, biological rep2

tag: cell type


title: Hyperoxia_CD103+DCs, biological rep3

description: Gene expression data from CD103+ DCs flow sorted from neonatal mouse lungs after hyperoxia

source_name: Hyperoxia-exposed neonatal lung CD103+ DCs

value: Hyperoxia


title: Hyperoxia_CD103+DCs, biological rep2


title: Normoxia_CD103+DCs, biological rep2


title: Hyperoxia_CD103+DCs, biological rep1


title: Hyperoxia_CD11bhiDCs, biological rep1

description: Gene expression data from CD11bhi DCs flow sorted from neonatal mouse lungs after hyperoxia

source_name: Hyperoxia-exposed neonatal lung CD11bhi DCs


title: Hyperoxia_CD11bhiDCs, biological rep2


title: Normoxia_CD103+DCs, biological rep3


title: Hyperoxia_CD11bhiDCs, biological rep3


title: Normoxia_CD11bhiDCs, biological rep1


title: C77_E9_L1_9w_RepF_Replicate2

value: CBA C57BL/6 mixed

value: Keratinocytes

tag: plate


title: XKYC6.2b_WT_47wk

value: WT


title: C77_E8_L1_9w_RepF_Replicate2

tag: population


title: XKYC12.1d_WT_28wk


title: XKYC5.2a_XKC_30wk

value: XKC


title: C77_E7_L1_9w_RepF_Replicate2

tag: time


title: C77_E6_L1_9w_RepF_Replicate2

tag: replicate


title: C77_E5_L1_9w_RepF_Replicate2


title: XKPC24.1e_XKPC_24wk

value: XKPC


title: XKYC4.3f_XKC_67wk_non.tumor


title: C77_E4_L1_9w_RepF_Replicate2


title: XKYC4.3f_XKC_67wk_tumor


title: C77_E3_L1_9w_RepF_Replicate2


title: C77_E2_L1_9w_RepF_Replicate2


title: XKPC33.1I_WT_28wk


title: XKPC32.1a_WT_26wk


title: XKPC21.2b_KPC_18wk_tumor

value: KPC


title: C77_E12_L1_9w_RepF_Replicate2


title: XKPC21.2b_KPC_18wk_non.tumor


title: C77_E11_L1_9w_RepF_Replicate2


title: XKPC21.2a_KPC_13wk_tumor


title: XKPC24.2f_XKPC_34wk


title: C77_D9_L1_9w_RepF_Replicate2


title: XKPC21.2a_KPC_13wk_non.tumor


title: C77_E10_L1_9w_RepF_Replicate2


title: XKPC24.2d_XKPC_18wk_non.tumor


title: C77_D6_L1_9w_RepF_Replicate2


title: C77_D8_L1_9w_RepF_Replicate2


title: C77_E1_L1_9w_RepF_Replicate2


title: XKPC19.2I_KC_24wk


title: C77_D5_L1_9w_RepF_Replicate2


title: XKPC17.4d_KC_38wk_tumor


title: XKPC19.2b_KC_30wk_non.tumor


title: XKPC17.4a_KPC_29wk


title: C77_D3_L1_9w_RepF_Replicate2


title: C77_D12_L1_9w_RepF_Replicate2


title: XKPC16.2a_XKPC_18wk


title: C77_D10_L1_9w_RepF_Replicate2


title: XKPC18.2f_KC_27wk


title: C77_D11_L1_9w_RepF_Replicate2


title: C77_D4_L1_9w_RepF_Replicate2


title: XKPC18.1a_KC_47wk


title: XKPC17.4h_KPC_17wk


title: XIAK9.1a_KiC_24wk

value: KiC


title: XKPC14.6e_XKC_23wk


title: XKPC17.4d_KC_38wk_non.tumor


title: C77_C8_L1_9w_RepF_Replicate2


title: C77_C9_L1_9w_RepF_Replicate2


title: XKPC11.1e_XKC_28wk


title: XIAK8.2d_WT_AP_10wk

value: Caerulein


title: C77_C7_L1_9w_RepF_Replicate2


title: C77_C3_L1_9w_RepF_Replicate2


title: XIAK8.2c_iC_AP_10wk

value: iC


title: XIAK8.2b_WT_AP_10wk

value: Pancreas


title: C77_C2_L1_9w_RepF_Replicate2


title: C77_C5_L1_9w_RepF_Replicate2


title: C77_C4_L1_9w_RepF_Replicate2


title: XIAK6.2a_KiC_45wk_tumor


title: XKPC14.7e_XKC_29wk


title: C77_C6_L1_9w_RepF_Replicate2


title: XIAK6.2e_KiC_25wk_tumor


title: XIAK4.1f_iC_35wk


title: C77_C10_L1_9w_RepF_Replicate2


title: C77_C12_L1_9w_RepF_Replicate2


title: C77_C1_L1_9w_RepF_Replicate2


title: C77_B9_L1_9w_RepF_Replicate2


title: XIAK6.2e_KiC_25wk_non.tumor


title: C77_D1_L1_9w_RepF_Replicate2


title: C77_B8_L1_9w_RepF_Replicate2


title: XIAK26.1c_iC_26wk


title: XIAK6.2a_KiC_45wk_non.tumor


title: C77_B7_L1_9w_RepF_Replicate2


title: XIAK26.1a_iC_26wk


title: C77_B6_L1_9w_RepF_Replicate2


title: XIAK20.1e_KiC_23wk


title: XIAK8.2a_iC_AP_10wk


title: C77_B5_L1_9w_RepF_Replicate2


title: C77_B4_L1_9w_RepF_Replicate2


title: C77_B3_L1_9w_RepF_Replicate2


title: XIAK16.2h_KiC_22wk


title: C77_B2_L1_9w_RepF_Replicate2


title: C77_C11_L1_9w_RepF_Replicate2


title: XIAK16.4d_KiC_34wk


title: C77_B12_L1_9w_RepF_Replicate2


title: C77_B11_L1_9w_RepF_Replicate2


title: C77_B10_L1_9w_RepF_Replicate2


title: C77_B1_L1_9w_RepF_Replicate2


title: C77_A8_L1_9w_RepF_Replicate2


title: C77_A9_L1_9w_RepF_Replicate2


title: C77_A7_L1_9w_RepF_Replicate2


title: XIAK16.6a_KiC_36wk


title: OptoTranscriptomics_Control_45min_Rep_3

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

data_processing:
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Assembly: GRCm38
Supplementary files format and content: .tar.gz zipped directories with kallisto output (pseudoaligned read counts and tpm measures of trancripts) containing .h5 and .tsv files

source_name: brain

extract_protocol:
Trizol
illumina TrueSeq

value: brain

tag: brain region

value: hippocampus

tag: sub region

value: vHC

tag: animalid

tag: group

value: OptoTranscriptomics

tag: virus

value: Control

value: Stimulation

tag: timepoint

tag: stimulation frequency

tag: Sex

value: Male


title: OptoTranscriptomics_Control_1h30min_Rep_4

tag: tissue

tag: genotype

tag: treatment


title: C77_A6_L1_9w_RepF_Replicate2

tag: strain

value: CBA C57BL/6 mixed


title: OptoTranscriptomics_Control_1h30min_Rep_5


title: OptoTranscriptomics_ChR2_1h30min_Rep_4


title: OptoTranscriptomics_Control_45min_Rep_5


title: OptoTranscriptomics_Control_45min_Rep_4


title: OptoTranscriptomics_ChR2_45min_Rep_3


title: OptoTranscriptomics_ChR2_1h30min_Rep_3


title: OptoTranscriptomics_Control_1h30min_Rep_3


title: C77_A3_L1_9w_RepF_Replicate2

tag: cell type

value: Keratinocytes


title: C77_A4_L1_9w_RepF_Replicate2

tag: plate


title: C77_A2_L1_9w_RepF_Replicate2

tag: population


title: OptoTranscriptomics_Control_45min_Rep_2


title: C77_A12_L1_9w_RepF_Replicate2

tag: time


title: OptoTranscriptomics_ChR2_45min_Rep_2

tag: replicate


title: OptoTranscriptomics_ChR2_45min_Rep_4

tag: brain region


title: OptoTranscriptomics_ChR2_1h30min_Rep_2

tag: sub region


title: C77_A11_L1_9w_RepF_Replicate2


title: OptoTranscriptomics_Control_1h30min_Rep_2

tag: animalid


title: OptoTranscriptomics_ChR2_1h30min_Rep_1

tag: group


title: C76_H9_L1_9w_RepF_Replicate1


title: OptoTranscriptomics_Control_45min_Rep_1

tag: virus


title: OptoTranscriptomics_ChR2_45min_Rep_1

tag: timepoint


title: C76_H8_L1_9w_RepF_Replicate1


title: C76_H7_L1_9w_RepF_Replicate1


title: C77_A5_L1_9w_RepF_Replicate2


title: C76_H4_L1_9w_RepF_Replicate1


title: C76_H5_L1_9w_RepF_Replicate1


title: OptoTranscriptomics_Control_1h30min_Rep_1

tag: stimulation frequency


title: C76_H11_L1_9w_RepF_Replicate1


title: C76_H12_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 57]

city: Beijing

first: qian

middle: qian

last: zhang

address: Datun road, chaoyang district

department: State Key Laboratory of Brain and Cognitive Science

institute: Institute of Biophysics

description: FPKM.csv

data_processing:
STAR (STAR 2.5.3a) was used to align the paired-end reads to the reference genome GRCm38 primary assembly with default settings. Reads were counted using featureCounts (featureCounts 1.5.3).
The R package, scater (Single-cell analysis toolkit for gene expression data in R, version 1.6.3), was employed for quality control, normalization and data visualization.
Gene expression was normalized to the number of fragments per kilobase million (FPKM value) using Scater package.
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM.csv: Comma-separated text file includes FPKM values.

source_name: chemical induced neurons

extract_protocol:
We collected the single-cell RNA from the in vivo patch-clamped neurons. To obtain transcriptome data from single neurons, the patch pipette solution was modified as follows (in mM): 123 K-gluconate, 12 KCl, 10 HEPES, 0.2 EGTA, 4 MgATP, 0.3 NaGTP, 10 sodium phosphocreatine, 20 μg/mL glycogen, and 1 U/μL recombinant RNase inhibitor (Cadwell et al., 2017). Approximately 0.1% Texas Red as a tip indicator and 6 μM calcium indicator dye Oregon Green BAPTA-1 (OGB-1) was added for membrane rupture and inner extraction. All neuron-related reagents were RNase-free. The electrode resistance ranged from 2 to 4 MΩ. The cell membrane was ruptured via negative pressure with a calcium influx indicated by OGB-1. The extracted soma of the neuron was confirmed as the electrode was pulled out of the tissue and then transferred to ice-cold lysis buffer immediately after breaking the tip within the tube. The sample was stored at -80 ºC for at most one week before the next step of processing.
Illumina HiSeq4000

value: Chemical-induced neurons

tag: age

value: 12 weeks


title: CiNs_BW12_RNA-seq [cell 58]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 60]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 61]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 62]

description: FPKM.csv


title: C76_G9_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 56]

description: FPKM.csv


title: C77_A10_L1_9w_RepF_Replicate2


title: C76_H10_L1_9w_RepF_Replicate1


title: C76_H1_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 54]

description: FPKM.csv


title: C76_G8_L1_9w_RepF_Replicate1


title: C76_G6_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 52]

description: FPKM.csv


title: C76_G4_L1_9w_RepF_Replicate1


title: C76_G3_L1_9w_RepF_Replicate1


title: C76_H6_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 59]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 50]

description: FPKM.csv


title: C76_G2_L1_9w_RepF_Replicate1


title: C76_G11_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 48]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 47]

description: FPKM.csv


title: C76_G10_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 49]

description: FPKM.csv


title: C76_F9_L1_9w_RepF_Replicate1


title: C76_F7_L1_9w_RepF_Replicate1


title: C76_F8_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 55]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 44]

description: FPKM.csv


title: C76_F5_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 53]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 45]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 43]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 41]

description: FPKM.csv


title: C76_F4_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 46]

description: FPKM.csv


title: C76_F6_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 51]

description: FPKM.csv


title: C76_G5_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 40]

description: FPKM.csv


title: C76_F2_L1_9w_RepF_Replicate1


title: C76_F3_L1_9w_RepF_Replicate1


title: C76_F12_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 39]

description: FPKM.csv


title: C76_F11_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 38]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 37]

description: FPKM.csv


title: C76_F10_L1_9w_RepF_Replicate1


title: C76_F1_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 36]

description: FPKM.csv


title: C76_E9_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 35]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 42]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 32]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 33]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 27]

description: FPKM.csv


title: C76_E7_L1_9w_RepF_Replicate1


title: C76_E6_L1_9w_RepF_Replicate1


title: C76_E8_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 28]

description: FPKM.csv


title: C76_E4_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 25]

description: FPKM.csv


title: C76_E3_L1_9w_RepF_Replicate1


title: C76_E2_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 24]

description: FPKM.csv


title: C76_E12_L1_9w_RepF_Replicate1


title: C76_E11_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 22]

description: FPKM.csv


title: C76_E10_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 21]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 20]

description: FPKM.csv


title: C76_E1_L1_9w_RepF_Replicate1


title: C76_D9_L1_9w_RepF_Replicate1


title: C76_D8_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 34]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 19]

description: FPKM.csv


title: C76_E5_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 26]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 16]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 14]

description: FPKM.csv


title: C76_D4_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 23]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 17]

description: FPKM.csv


title: C76_D6_L1_9w_RepF_Replicate1


title: C76_D5_L1_9w_RepF_Replicate1


title: C76_D7_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 13]

description: FPKM.csv


title: C76_D3_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 15]

description: FPKM.csv


title: C76_D12_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 10]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 11]

description: FPKM.csv


title: C76_D10_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 9]

description: FPKM.csv


title: C76_D1_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 8]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 18]

description: FPKM.csv


title: C76_C9_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 7]

description: FPKM.csv


title: C76_C7_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 6]

description: FPKM.csv


title: C76_C6_L1_9w_RepF_Replicate1


title: C76_C5_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 5]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 12]

description: FPKM.csv


title: C76_D2_L1_9w_RepF_Replicate1


title: C76_D11_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 4]

description: FPKM.csv


title: CiNs_BW12_RNA-seq [cell 3]

description: FPKM.csv


title: C76_C3_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 2]

description: FPKM.csv


title: C76_C12_L1_9w_RepF_Replicate1


title: C76_C11_L1_9w_RepF_Replicate1


title: CiNs_BW12_RNA-seq [cell 1]

description: FPKM.csv


title: C76_C2_L1_9w_RepF_Replicate1


title: PDGFRA_R1

city: Vancouver

first: Ryan

last: Flannigan

state: BC

address: 2660 Oak St, Vancouver, BC V6H 3Z6

country: Canada

institute: University of British Columbia

data_processing:
RNA reads mapped to reference genome with STAR aligner (v2.7.1.a)
Gene counts were quantified with STAR aligners, `--quant Mode`
rawcounts.tsv were generated by joining of each samples count table with R's merge.data.frame function.
Assembly: GRCH38-84
Supplementary files format and content: Tab Separated File. Each Row represent a gene and each colum represent a sample in our dataset

organism: Homo sapiens

source_name: Testis

extract_protocol:
TrypLE Express Enzymatic dissociation
MGI RNA Directional Library Prep

tag: cell line

value: primary peritubular myoid cells PDGFRA

value: myoid

tag: derivation

value: primary isolated


title: C76_B9_L1_9w_RepF_Replicate1


title: DL01-HPSC_R3

source_name: Human induced pluripotent stem cell line

value: hiPSC line DL01

value: hiPSC

value: undifferentiated


title: PDGFRA_R2


title: 11-10-myoid_R1

value: hiPSC line 11-10

value: hiPSC-derived


title: C76_B8_L1_9w_RepF_Replicate1


title: C76_C1_L1_9w_RepF_Replicate1


title: 11-10-HPSC_R3


title: C76_B7_L1_9w_RepF_Replicate1


title: C76_B6_L1_9w_RepF_Replicate1


title: DL01-HPSC_R2


title: DL01-HPSC_R1


title: C76_C4_L1_9w_RepF_Replicate1


title: 11-10-myoid_R2


title: C76_B4_L1_9w_RepF_Replicate1


title: 11-10-myoid_R3


title: C76_B12_L1_9w_RepF_Replicate1


title: C76_B11_L1_9w_RepF_Replicate1


title: DL01-myoid_R3


title: C76_B2_L1_9w_RepF_Replicate1


title: C76_B10_L1_9w_RepF_Replicate1


title: DL01-myoid_R2


title: C76_B1_L1_9w_RepF_Replicate1


title: 11-10-HPSC_R1


title: DL01-myoid_R1


title: PDGFRA_R3


title: C76_A8_L1_9w_RepF_Replicate1


title: C76_A9_L1_9w_RepF_Replicate1


title: C76_A6_L1_9w_RepF_Replicate1


title: C76_A7_L1_9w_RepF_Replicate1


title: C76_A5_L1_9w_RepF_Replicate1


title: C76_A4_L1_9w_RepF_Replicate1


title: C76_A3_L1_9w_RepF_Replicate1


title: mNETseq, A549, PolII

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Adapters were trimmed with Cutadapt v1.9.1
Mapping to the hg19 genome was performed with Tophat2 v2.1.0
Extraction of properly paired and properly mapped reads was done with SAMtools v1.3.1
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
Bigwig files were generated with Bedtools version 2.23 genomecov and the UCSC bedGraphToBigWig tool.
Assembly: hg19
Supplementary files format and content: Bigwig: genome-coverage files for all samples
Library strategy: mNET-Seq

molecule: genomic DNA

growth_protocol: A549 cells (ATCC) were cultured in DMEM (Corning) supplemented with L-glutamine (2 mM), penicillin (100 U/mL), streptomyocin (100 μg/mL) and 10% fetal calf serum (FCS; Gibco) at 37 °C in a 5% CO2 humidified atmosphere

extract_protocol:
Nascent RNAs for mNET-seq were purified from Pol II IP products of solublilized chromatin.
Libraries were prepared using Illumina's TruSeq Small RNA Library Preparation Kit.

treatment_protocol: PPP1R13L knockdown was achieved by inserting with CRISPR/Cas9 an indel mutation

tag: chip antibody

value: Anti RNA polymerase II antibody, MABI0601, MBL International

tag: genotype

value: Wild-type

tag: treatment


title: mNETseq, KO, PolII

value: PPP1R13L knockdown


title: KO, p53-CS, R2

library_source: genomic

data_processing:
Adapters were trimmed with Cutadapt v1.9.1
Mapping to the hg19 genome was performed with Bowtie2 v2.3.4
Extraction of properly paired and properly mapped reads was done with SAMtools v1.3.1
PCR deduplication was performed with Picard MarkDuplicates tool
Peak calling was performed with MACS2 version 2.1.1.20160309
Bigwig files were generated with Bedtools version 2.23 genomecov and the UCSC bedGraphToBigWig tool.
Assembly: hg19
Supplementary files format and content: Bigwig: genome-coverage files for all samples

extract_protocol:
DNA were purified from chromatin IP products.
Libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit.

value: Anti-p53 antibody, 9282S, Cell Signaling


title: KO, PolII, R2

value: Anti RNA polymerase II antibody, NBP2-32080, Novus Biologicals


title: KO, DMSO, p53, 8h


title: C76_A2_L1_9w_RepF_Replicate1

tag: strain

value: CBA C57BL/6 mixed

tag: cell type

tag: plate


title: C76_A12_L1_9w_RepF_Replicate1

value: Keratinocytes

tag: time

tag: population

tag: replicate


title: C76_B3_L1_9w_RepF_Replicate1


title: KO, DMSO, p53-SC

value: Anti-p53 antibody, sc-126, Santa Cruz


title: KO, DMSO, p53, 6h


title: C76_A11_L1_9w_RepF_Replicate1


title: KO, DMSO, p53-CS, R2


title: C61_H8_L1_0w_RepC_Replicate2


title: C61_H9_L1_0w_RepC_Replicate2


title: KO, DMSO, PolII, R2


title: KO, DMSO, PolII, 8h


title: KO, p53-SC


title: KO, DMSO, PolII, 6h


title: 11-10-HPSC_R2


title: C61_H6_L1_0w_RepC_Replicate2


title: C61_H5_L1_0w_RepC_Replicate2


title: C61_H4_L1_0w_RepC_Replicate2


title: Input, KO, R2


title: Input, KO, DMSO, p53-SC


title: C61_H3_L1_0w_RepC_Replicate2


title: Input, KO, DMSO, R2


title: Input, KO, DMSO, 8h


title: C61_H12_L1_0w_RepC_Replicate2


title: C61_H11_L1_0w_RepC_Replicate2


title: Input, KO, DMSO, 6h


title: Input, A549, p53-SC


title: C61_H10_L1_0w_RepC_Replicate2


title: Input, A549, R2


title: Input, A549, DMSO, p53-SC


title: C61_H1_L1_0w_RepC_Replicate2


title: C61_G9_L1_0w_RepC_Replicate2


title: C61_H7_L1_0w_RepC_Replicate2


title: Input, A549, DMSO, R2


title: Input, A549, DMSO, 8h


title: Input, KO, p53-SC


title: C61_G6_L1_0w_RepC_Replicate2


title: A549, p53-SC


title: C61_G8_L1_0w_RepC_Replicate2


title: A549, p53-CS, R2


title: C61_G2_L1_0w_RepC_Replicate2


title: C61_G3_L1_0w_RepC_Replicate2


title: A549, DMSO, p53, 8h


title: C61_G11_L1_0w_RepC_Replicate2


title: C61_G4_L1_0w_RepC_Replicate2


title: C61_G12_L1_0w_RepC_Replicate2


title: A549, PolII, R2


title: A549, DMSO, p53, 6h


title: C61_H2_L1_0w_RepC_Replicate2


title: C61_G10_L1_0w_RepC_Replicate2


title: Input, A549, DMSO, 6h


title: A549, DMSO, p53-SC


title: C61_F9_L1_0w_RepC_Replicate2


title: C61_F8_L1_0w_RepC_Replicate2


title: A549, DMSO, p53-CS, R2


title: A549, DMSO, PolII, R2


title: C61_F7_L1_0w_RepC_Replicate2


title: C61_F6_L1_0w_RepC_Replicate2


title: A549, DMSO, PolII, 8h


title: A549, DMSO, PolII, 6h


title: C61_F5_L1_0w_RepC_Replicate2


title: C61_F4_L1_0w_RepC_Replicate2


title: C61_F3_L1_0w_RepC_Replicate2


title: C61_F11_L1_0w_RepC_Replicate2


title: C61_F2_L1_0w_RepC_Replicate2


title: C61_F10_L1_0w_RepC_Replicate2


title: C61_F1_L1_0w_RepC_Replicate2


title: C61_E9_L1_0w_RepC_Replicate2


title: embryos, control (biol rep 2)

city: Chongqing

first: Guoliang

last: Chen

state: Chongqing

address: No. 174, Shazheng Street

department: Bioengineering College

institute: Chongqing University

data_processing:
Following sequencing, data was trimmed for both adaptor and quality using a combination of ea-utils and Btrim.
Sequencing reads were then aligned to the genome (Ensembl Danio_rerio.GRCz11.92 with and without unplaced contigs) using Tophat2/HiSat2 and counted via HTSeq.
Gene counts were determined using featureCounts v1.6.2 and differential expression analysis was performed using DESeq2 v1.14.1, using a adjusted p-value cut off of <0.05.
Assembly: Ensembl Danio_rerio.GRCz11.92
Supplementary files format and content: All_gene_counts.csv
Supplementary files format and content: counts; CK1(control (biol rep 1)), CK2(control (biol rep 2)),  SYP1(SYP-3343 (biol rep 1)), SYP2 (SYP-3343 (biol rep 2))

organism: Danio rerio

source_name: whole embryos

extract_protocol:
The samples were homogenized completely, then the total RNA was extracted using the TRIzol® reagent (Invitrogen, USA) according to the manufacturer’s protocol.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

tag: developmental stage

value: embryos

tag: tissue

value: whole embryos

value: WT

value: untreated


title: C61_F12_L1_0w_RepC_Replicate2


title: embryos, SYP-3343 (biol rep 2)

value: SYP-3343 exposure


title: embryos, control (biol rep 1)


title: embryos, SYP-3343 (biol rep 1)


title: C61_E8_L1_0w_RepC_Replicate2


title: BMSC-shRac1+OGD Sample E1

city: wenzhou

first: huang

middle: dong

last: dong

address: juyi street 105

institute: wenzhou medical university

description:
BMSC-shRac1+OGD
With shRac1 lentivirus infection and OGD treatment
Sample E1

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling
We used the StringTie software (v1.2.3) to estimate the abundance of the gene level and transcript level, referring to the official database information, then to calculate FPKM the gene or transcript level separately and to find the difference using Ballgown software.
Sequenced reads was filtered through Solexa CHASTITY, and to match to the corresponding reference genome Rnor6, by Hisat2 software（v2.0.4）
Genome_build: Rnor6
Supplementary_files_format_and_content: Xlsx include FPKM values for all samples

organism: Rattus norvegicus

source_name: Bone marrow mesenchymal stem cells

growth_protocol: BMSC cells without OGD were maintained in high glucose DMEM supplemented with 10% fetal bovine serum in a normal incubator with 5% CO2 at 37 ℃ and BMSC cells with OGD were maintained in sugar-free DMEM in a humidiﬁed atmosphere with 5% CO2, 1% O2, at 37 ℃.

extract_protocol:
The whole RNA of BMSC cell lines was harvested using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel electrophoresis, then quantified and examined by  Agilent 2100 Bioanalyzer.1-2 ug of total RNA was selected for each sample for sequencing library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: group BMSC: normal BMSC without treatment; group BMSC-shLuci: BMSC received shLuci lentivirus only; group BMSC-shRac1: BMSC received shRac1 lentivirus only; group BMSC-shLuci+OGD: BMSC received shLuci lentivirus and OGD 12 h/R 24 h treatment; group BMSC-shRac1: BMSC received shRac1 lentivirus and OGD 12 h/R 24 h treatment;

value: Sprague dawley rat

value: Femoral bone marrow

tag: passages


title: BMSC-shRac1+OGD Sample E2

description:
BMSC-shRac1+OGD
With shRac1 lentivirus infection and OGD treatment
Sample E2


title: BMSC-shRac1+OGD Sample E3

description:
BMSC-shRac1+OGD
With shRac1 lentivirus infection and OGD treatment
Sample E3


title: C61_E7_L1_0w_RepC_Replicate2


title: BMSC-shLuci+OGD Sample D2

description:
BMSC-shLuci+OGD
With shLuci lentivirus infection and OGD treatment
Sample D2


title: BMSC-shLuci+OGD Sample D1

description:
BMSC-shLuci+OGD
With shLuci lentivirus infection and OGD treatment
Sample D1


title: BMSC-shLuci+OGD Sample D3

description:
BMSC-shLuci+OGD
With shLuci lentivirus infection and OGD treatment
Sample D3


title: BMSC-shRac1 Sample C2

description:
BMSC-shRac1
With shRac1 lentivirus infection and without OGD treatment
Sample C2


title: BMSC-shRac1 Sample C3

description:
BMSC-shRac1
With shRac1 lentivirus infection and without OGD treatment
Sample C3


title: C61_E5_L1_0w_RepC_Replicate2


title: BMSC-shRac1 Sample C1

description:
BMSC-shRac1
With shRac1 lentivirus infection and without OGD treatment
Sample C1


title: C61_E4_L1_0w_RepC_Replicate2


title: C61_E3_L1_0w_RepC_Replicate2


title: BMSC-shLuci Sample B3

description:
BMSC-shLuci
With shLuci lentivirus infection and without OGD treatment
Sample B3


title: BMSC-shLuci Sample B2

description:
BMSC-shLuci
With shLuci lentivirus infection and without OGD treatment
Sample B2


title: BMSC-shLuci Sample B1

description:
BMSC-shLuci
With shLuci lentivirus infection and without OGD treatment
Sample B1


title: C61_E2_L1_0w_RepC_Replicate2


title: BMSC Sample A3

description:
BMSC
Without lentivirus infection and OGD treatment
Sample A3


title: C61_E12_L1_0w_RepC_Replicate2


title: BMSC Sample A2

description:
BMSC
Without lentivirus infection and OGD treatment
Sample A2


title: C61_E10_L1_0w_RepC_Replicate2


title: C61_E1_L1_0w_RepC_Replicate2


title: scRNAseq EOMs DMD 12months

city: CRETEIL

first: Valentina

last: TAGLIETTI

address: RUE GENERAL SERRAIL

country: France

institute: INSERM

description: scRNAseq

data_processing:
Sequence analysis with Cell Ranger Single Cell Software Suite 3.0.2 by 10X Genomics
Raw base call files were demultiplexed with the cellranger mkfastq pipeline into library specific FASTQ files
The FASTQ files for each library were then processed independently with the cellranger count pipeline.
Assembly: rn6
Supplementary files format and content: For each sample, set of 3 files in format 10X (list of cell barcodes, list of genes and expression matrix (raw counts))

source_name: Extraocular, muscle

extract_protocol:
muscle enzymatic digestion - 10x Genomics Chromium Next GEM Single Cell 3' V3.1
Chromium Next GEM Single Cell 3' Library kit v3.1

tag: disease state

value: wild-type

value: 12 months

value: Total cells from extraocular muscles


title: scRNAseq EOMs WT 12months

description: scRNAseq

value: DMD


title: scRNAseq TA DMD 12months

description: scRNAseq

source_name: Tibialis anterior, muscle

value: Total cells from tibialis anterior


title: C61_D7_L1_0w_RepC_Replicate2


title: C61_D6_L1_0w_RepC_Replicate2


title: hEB_D16_TCBPA2

city: 北京市

first: Renjun

last: Yang

state: 北京

address: 双清路18号林业大学北门

institute: RCEES

data_processing:
Remove the reads containing the connector
Remove reads with unknown base N content greater than 5%
Remove low-quality reads (we define reads with a mass value of less than 15 Accounting for more than 20% of the total base number of the reads as low-quality reads).The filtered "clean reads" is saved in fastq format
Software information: soapnuke， version： v1.5.2
Genome_build: GCF_000001405.39_GRCh38.p13
Supplementary_files_format_and_content: txt, gene expression level

source_name: Human embryonic stem cells

growth_protocol: Embryoid bodies were cultured on ultra-low adsorption plate, and the medium was E6. The differentiation process lasted 16 days.

extract_protocol:
RNA was extracted with RNA extraction kit
Total RNA was processed by mRNA enrichment method. MRNA enrichment: the mRNA with Polya tail was enriched by magnetic beads with oligodt. The obtained RNA was fragmented with the interrupt buffer, and the random N6 primers were reverse transcribed, and then the cDNA ⼆ strand was synthesized to form double stranded DNA. The ends of the synthesized double stranded DNA were flattened and phosphorylated at the 5 'end, the 3' end formed a protruding "a" sticky end, and then connected to a bubbly joint with protruding "t" at the 3 'end. The ligation products were amplified by PCR with specific primers. The PCR product was thermally denatured into a single strand, and then the single strand DNA was cyclized with ⼀ segment bridge primers to obtain a single strand circular DNA library. The constructed library was qualified for quality inspection and sequenced.

treatment_protocol: Two replicates were exposed to HFRS for 16 days

value: ES-derived embryoid body cells

value: treated with TCBPA for 16 days


title: C61_D8_L1_0w_RepC_Replicate2

value: CBA C57BL/6 mixed


title: hEB_D16_TCBPA1

address: 双清路18号林业大学北门


title: AGH149_9

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: MD

address: 6 Center Drive, 6/230

institute: NIH, NICHD

description:
H3 ChIP-seq (+SM) Repl. 3
Biological replicate 3

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Occupancies profiles of Histone H3, Rpb3, Rpb1, Gcn4, TBP and myc-tagged Spt7, Srb6 and Eaf1 were created using custom R programs.
The processed data were converted to the bigwig files supplied here: different DNA length exclusion limits were used in the processing (listed with Processed Data Files)
Assembly: SacCer3

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM). For anchor away strains, cells were treated with rapamycin for 90 min before adding SM or no SM.

extract_protocol:
Sonicated chromatin extracts were immunoprecipitated with anti-histone H3, anti-Gcn4 (home-made), anti-TBP (from Joseph Reese's lab), anti-myc (Sigma, Cat# 11667203001), anti-Rpb1 (Biolegend, Cat#664906) and anti-Rpb3 (NeoClone, Cat# W0012). Immunoprecipitated chromatin were treated with proteinase K and DNA were extracted with chloroform and precipitated with iso-propanol.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.

treatment_protocol: Cells were fixed with formaldhyde and sonicated with bioruptor. The detail was described previously in Qiu et al., Genome Research 26:211-225 (2006) and Rawal et al., Genes and Development 32:695-710 (2018)

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5-delta::hphMX4 EAF1-FRB::natMX4

value: Formaldehyde-fixed and sonicated


title: scRNAseq TA WT 12months

description: scRNAseq


title: C61_D5_L1_0w_RepC_Replicate2

source_name: Murine Epidermal cells

value: Keratinocytes


title: hEB_D16_TBBPS2

address: 双清路18号林业大学北门

value: treated with TBBPS for 16 days


title: AGH149_8

description:
H3 ChIP-seq (+SM) Repl. 2
Biological replicate 2


title: C61_D4_L1_0w_RepC_Replicate2


title: hEB_D16_TBBPA2

address: 双清路18号林业大学北门

value: treated with TBBPA for 16 days


title: AGH149_7

description:
H3 ChIP-seq (+SM) Repl. 1
Biological replicate 1


title: hEB_D16_DMSO2

address: 双清路18号林业大学北门

value: treated with DMSO for 16 days


title: C61_D3_L1_0w_RepC_Replicate2


title: C61_E11_L1_0w_RepC_Replicate2


title: hEB_D16_TBBPS1

address: 双清路18号林业大学北门


title: BMSC Sample A1

description:
BMSC
Without lentivirus infection and OGD treatment
Sample A1


title: C61_D9_L1_0w_RepC_Replicate2


title: hEB_D16_DMSO1

address: 双清路18号林业大学北门


title: AGH149_3

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5-delta::hphMX4


title: C61_D2_L1_0w_RepC_Replicate2


title: hEB_D16_BHEE1

address: 双清路18号林业大学北门

value: treated with TBBPA-BHEE for 16 days


title: C61_D12_L1_0w_RepC_Replicate2


title: AGH149_2


title: hEB_D16_BDBPE1

address: 双清路18号林业大学北门

value: treated with TBBPA-BDBPE for 16 days


title: hEB_D16_BAE1

address: 双清路18号林业大学北门

value: treated with TBBPA-BAE for 16 days


title: hEB_D16_TBBPA1

address: 双清路18号林业大学北门


title: hEB_D16_BDBPE2

address: 双清路18号林业大学北门


title: C61_E6_L1_0w_RepC_Replicate2


title: AGH149_6

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 eaf1-delta::hphMX4


title: hEB_D8_TCBPA2

address: 双清路18号林业大学北门

value: treated with TCBPA for 8 days


title: AGH149_1


title: C61_D10_L1_0w_RepC_Replicate2


title: C61_D1_L1_0w_RepC_Replicate2


title: hEB_D8_TBBPS2

address: 双清路18号林业大学北门

value: treated with TBBPS for 8 days


title: hEB_D8_TCBPA1

address: 双清路18号林业大学北门


title: AGH149_5


title: hEB_D8_TBBPA2

address: 双清路18号林业大学北门

value: treated with TBBPA for 8 days


title: hEB_D8_TBBPA1

address: 双清路18号林业大学北门

value: ES-derived embryoid body cells


title: C61_C9_L1_0w_RepC_Replicate2


title: C61_C8_L1_0w_RepC_Replicate2


title: hEB_D8_TBBPS1

address: 双清路18号林业大学北门


title: AGH149_4


title: AGH149_15

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: E. coli BL21 whole genome, control

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description:
Ecoli_ctrl
modP1_difference.RDS, modP2_difference.RDS, modQ_difference.RDS

data_processing:
For plasmid libraries, reads were base called in super-accuracy mode (dna_r9.4.1_450bps_sup_prom) with demultiplexing, using Guppy 6.0.7 and default parameters.
Read depth was downsampled to 400x per plasmid with ont_fast5_api v4.0.1 (https://github.com/nanoporetech/ont_fast5_api), first filtering for read quality with Filtong v0.2.1 (https://github.com/rrwick/Filtlong).
DNA modification motif discovery and classification was performed with Nanodisco v1.0.3, down-sampling read depth to 400x per plasmid, aligning reads to the pET15b vector containing the relevant mod insert.
For genomic DNA libraries of E. coli and A. pleuropneumoniae, reads were basecalled in high-accuracy mode (dna_r9.4.1_450bps_hac_prom) with demultiplexing, using Guppy 6.1.5 and default parameters, and downsampled to a read depth of 400x per sample.
DNA modification motif discovery and classification was performed with Nanodisco v1.0.3, aligning reads to the E. coli and A. pleuropneumoniae complete genomes.
Assembly: pET15b plasmid (EMD Millipore, catalog number: 69661),  E. Coli genome (ASM584v2),  A. pleuropneumoniae genome (57675_E01)
Supplementary files format and content: RDS objects containing methylation current difference values computed by Nanodisco
Library strategy: Transposase (DNA sequencing)

organism: Escherichia coli

source_name: bacterial culture

growth_protocol: A. pleuropneumoniae isolates were grown on BBL™ blood agar base supplemented with thiamine HCl (0.0005%), NADH (0.0025%), oleic acid bovine albumin complex (5%) consisting of 4.75% bovine serum albumin (Fraction V) in normal saline (with the saline containing 5% NaOH and 0.06% oleic acid) and heat inactivated horse serum (1%) (termed BA/SN) or brain heart infusion (BHI, Oxoid) agar containing β-nicotinamide adenine dinucleotide, NAD (0.01%) at 37°C for 24 h. Escherichia coli strains (DH5α and BL21) were grown overnight in lysogeny broth (LB) supplemented with ampicillin at 100 µg/ml or chloramphenicol at 20 µg/ml as required at 37 °C in a shaker at 200 rpm. For mutant selection, A. pleuropneumoniae strains were grown overnight on BHI-NAD plates with 1 µg/ml of chloramphenicol. The Type III methyltransferase genes were cloned into the pET15b vector (Novagen).

extract_protocol:
Genomic DNA was isolated using the Sigma GenElute kit, or plasmid DNA isolated with the Qiagen miniprep kit.
Nanopore sequencing libraries were prepared from 400 ng of DNA per sample with the Rapid DNA Barcoding kit (RBK004) according to manufacturer’s instructions. A 500 ng pool of 6 indexed plasmid libraries was sequenced on 1 PromethION R9.4.1 flow cells (FLO-PRO002) on a PromethION 24 instrument running MinKNOW 22.03.4. For genomic DNA libraries of E. coli and A. pleuropneumoniae, a 500 ng pool of 10 indexed samples was sequenced on 1 PromethION R9.4.1 flow cells (FLO-PRO002) on a PromethION 24 instrument running MinKNOW 22.08.6.

value: bacterial culture

value: control


title: AGH149_14

value: Formaldehyde-fixed and sonicated


title: C61_C7_L1_0w_RepC_Replicate2

value: CBA C57BL/6 mixed

value: Keratinocytes


title: E. coli BL21 whole genome, modQ overexpression

description:
Ecoli_modQ
modQ_difference.RDS

value: modQ overexpression


title: hEB_D8_DMSO2

address: 双清路18号林业大学北门

value: treated with DMSO for 8 days


title: hEB_D8_DMSO1

address: 双清路18号林业大学北门


title: E. coli BL21 whole genome, modP2 overexpression

description:
Ecoli_modP2
modP2_difference.RDS

value: modP2 overexpression


title: C61_D11_L1_0w_RepC_Replicate2


title: hEB_D16_BAE2

address: 双清路18号林业大学北门


title: hEB_D8_BHEE2

address: 双清路18号林业大学北门

value: treated with TBBPA-BHEE for 8 days


title: AGH149_12

description:
H3 ChIP-seq (no SM) Repl. 3
Biological replicate 3


title: C61_C6_L1_0w_RepC_Replicate2


title: C61_C5_L1_0w_RepC_Replicate2


title: E. coli BL21 whole genome, modP1 overexpression

description:
Ecoli_modP1
modP1_difference.RDS

value: modP1 overexpression


title: AGH149_11

description:
H3 ChIP-seq (no SM) Repl. 2
Biological replicate 2


title: pET15b_modQ plasmid, from E. coli DH5a strain, no modQ induction control

description:
pET15b_modQ_DH5a
pET15b_modQ_difference.RDS


title: C61_C4_L1_0w_RepC_Replicate2


title: hEB_D8_BHEE1

address: 双清路18号林业大学北门


title: AGH149_10

description:
H3 ChIP-seq (no SM) Repl. 1
Biological replicate 1


title: pET15b_modQ plasmid, from E. coli BL21 strain, modQ overexpression

description:
pET15b_modQ_BL21
pET15b_modQ_difference.RDS


title: C61_C3_L1_0w_RepC_Replicate2


title: hEB_D8_BDBPE1

address: 双清路18号林业大学北门

value: treated with TBBPA-BDBPE for 8 days


title: AGH149_16

description:
H4-ac ChIP-seq (+SM) Repl. 3
Biological replicate 3

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5-delta::hphMX4 EAF1-FRB::natMX4


title: C61_C2_L1_0w_RepC_Replicate2


title: hEB_D8_BAE2

address: 双清路18号林业大学北门

value: treated with TBBPA-BAE for 8 days


title: AGH149_13


title: AGH148_23

description:
H4-ac ChIP-seq (+SM) Repl. 2
Biological replicate 2


title: C61_C12_L1_0w_RepC_Replicate2


title: pET15b_modP1 plasmid, from E. coli DH5a strain, no modP1 induction (control)

description:
pET15b_modP1_DH5a
pET15b_modP1_difference.RDS


title: pET15b_modP1 plasmid, from E. coli BL21 strain, modP1 overexpression

description:
pET15b_modP1_BL21
pET15b_modP1_difference.RDS


title: AGH148_22

description:
H4-ac ChIP-seq (+SM) Repl. 1
Biological replicate 1


title: C61_C10_L1_0w_RepC_Replicate2


title: hEB_D2_TBBPS2

address: 双清路18号林业大学北门

value: treated with TBBPS for 2 days


title: hEB_D2_TCBPA2

address: 双清路18号林业大学北门

value: treated with TCBPA for 2 days


title: AGH148_18

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5-delta::hphMX4


title: hEB_D2_TCBPA1

address: 双清路18号林业大学北门

value: ES-derived embryoid body cells


title: hEB_D8_BDBPE2

address: 双清路18号林业大学北门


title: hEB_D8_BAE1

address: 双清路18号林业大学北门


title: C61_B9_L1_0w_RepC_Replicate2


title: pET15b_modP2 plasmid, from E. coli DH5a strain, no modP2 induction control

description:
pET15b_modP2_DH5a
pET15b_modP2_difference.RDS

value: bacterial culture


title: hEB_D2_TBBPS1

address: 双清路18号林业大学北门


title: C61_B8_L1_0w_RepC_Replicate2


title: AGH148_21

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 eaf1-delta::hphMX4


title: AGH148_20

value: Formaldehyde-fixed and sonicated


title: hEB_D2_TBBPA2

address: 双清路18号林业大学北门

value: treated with TBBPA for 2 days


title: pET15b_modP2 plasmid, from E. coli BL21 strain, modP2 overexpression

description:
pET15b_modP2_BL21
pET15b_modP2_difference.RDS


title: C61_C11_L1_0w_RepC_Replicate2

value: CBA C57BL/6 mixed

value: Keratinocytes


title: Co3_Control, replicate_3

city: Shanghai

first: Ping

last: Zheng

state: Shanghai

address: 490 South Chuanhuan Road

department: Neurosurgery

institute: Shanghai Pudong New area People's Hospital

description: Gene expression in healthy control human blood

hyb_protocol: Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

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

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.Genespring (version 14.8,Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “Detected” were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs. Finally, Hierarchical Clustering was performed to display the distinguishable genes' expression pattern among samples.

source_name: whole blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the Blood RNA Purification kit (Qiagen, USA) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-ND-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from 12 TBI and 4 healthy volunteers was collected, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: whole blood

tag: gender

value: F

tag: condition

value: healthy control


title: C61_B7_L1_0w_RepC_Replicate2


title: C61_C1_L1_0w_RepC_Replicate2


title: AGH148_17


title: C61_B6_L1_0w_RepC_Replicate2


title: AGH148_19


title: C61_B5_L1_0w_RepC_Replicate2


title: hEB_D2_DMSO2

address: 双清路18号林业大学北门

tag: cell line

value: treated with DMSO for 2 days


title: Co1_Control, replicate_1

value: M

tag: age


title: AGH149_21

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: hEB_D2_DMSO1

address: 双清路18号林业大学北门


title: hEB_D2_BHEE2

address: 双清路18号林业大学北门

value: treated with TBBPA-BHEE for 2 days


title: C61_B4_L1_0w_RepC_Replicate2


title: Co2_Control, replicate_2


title: hEB_D2_TBBPA1

address: 双清路18号林业大学北门


title: hEB_D2_BHEE1

address: 双清路18号林业大学北门


title: AGH149_19

description:
H4-ac ChIP-seq (no SM) Repl. 3
Biological replicate 3


title: C61_B2_L1_0w_RepC_Replicate2


title: C61_B12_L1_0w_RepC_Replicate2


title: Se4_Severe TBI, replicate_4

description: Gene expression within 24hr in TBI human blood

value: traumatic brain injury


title: AGH149_18

description:
H4-ac ChIP-seq (no SM) Repl. 2
Biological replicate 2


title: AGH149_22


title: Se2_Severe TBI, replicate_2


title: Se3_Severe TBI, replicate_3


title: hEB_D2_BDBPE2

address: 双清路18号林业大学北门

value: treated with TBBPA-BDBPE for 2 days


title: hEB_D2_BDBPE1

address: 双清路18号林业大学北门


title: hEB_D2_BAE2

address: 双清路18号林业大学北门

value: treated with TBBPA-BAE for 2 days


title: AGH148_9

description:
H3-ac ChIP-seq (+SM) Repl. 3
Biological replicate 3

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5-delta::hphMX4 EAF1-FRB::natMX4


title: hEB_D2_BAE1

address: 双清路18号林业大学北门

value: ES-derived embryoid body cells


title: Mo4_Moderate TBI, replicate_4


title: C61_B10_L1_0w_RepC_Replicate2


title: C61_B11_L1_0w_RepC_Replicate2


title: AGH149_20


title: AGH149_17

description:
H4-ac ChIP-seq (no SM) Repl. 1
Biological replicate 1


title: C61_B3_L1_0w_RepC_Replicate2


title: Se1_Severe TBI, replicate_1


title: C61_B1_L1_0w_RepC_Replicate2


title: AGH148_8

description:
H3-ac ChIP-seq (+SM) Repl. 2
Biological replicate 2


title: Mo2_Moderate TBI, replicate_2


title: Mo1_Moderate TBI, replicate_1


title: AGH148_3

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5-delta::hphMX4


title: C61_A8_L1_0w_RepC_Replicate2


title: C61_A7_L1_0w_RepC_Replicate2


title: AGH148_6

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 eaf1-delta::hphMX4

value: Formaldehyde-fixed and sonicated


title: C61_A6_L1_0w_RepC_Replicate2

value: CBA C57BL/6 mixed


title: AGH148_1

description:
H3-ac ChIP-seq (+SM) Repl. 1
Biological replicate 1


title: Mi4_Mild TBI, replicate_4


title: C61_A5_L1_0w_RepC_Replicate2

value: Keratinocytes


title: AGH148_5


title: AGH148_7


title: Mi2_Mild TBI, replicate_2

value: whole blood


title: C61_A9_L1_0w_RepC_Replicate2


title: Mo3_Moderate TBI, replicate_3


title: Severe patient 6

city: Boadilla del Monte

first: CARMELA

last: PABLO-TORRES JIMÉNEZ

state: Urbanización Montepríncipe

address: Urbanización Montepríncipe

country: Spain

institute: SAN PABLO CEU UNIVERSITY

description: Gene expression data from CD3+ cells

hyb_protocol: The fragmented and labeled cDNA of all the samples was hybridized (4 samples for each strip) for 20 hours at 48ºC

scan_protocol: Gene chips were stained and imaged using GeneAtlas System

data_processing: CEL raw files were normalized and transformed into expression measures using Expression Console Software (Affymetrix). The Robust Multi‐array Average (RMA) algorithm was used for background correction, normalization, and summarization of the probe‐set level expression of the samples.

source_name: CD3+ cells from a severe allergic subject

label_protocol: Single-stranded cDNA was fragmented by UDG and APE1 and labeled by TdT using DNA labeling reagent that was covalently linked to biotin

extract_protocol: RNA was extracted from Ficoll®‐isolated CD3+ using RNeasy® Mini Kit (Qiagen, Hilden, Germany) with DNase treatment following manufacturer procedure. RNA concentration was determined using a NanoDrop™ 2000/2000c Spectrophotometer

value: CD3+ cells

value: Severe

value: Older than 18


title: hEB_D16_BHEE2

address: 双清路18号林业大学北门

value: treated with TBBPA-BHEE for 16 days


title: Severe patient 7

description: Gene expression data from CD3+ cells


title: Mi1_Mild TBI, replicate 1

value: F


title: ced-3(n1286) embryos biol rep 3

first: Alla

last: Grishok

address: 72 E Concord

institute: Boston University

data_processing:
Trimmed reads containing adapter, poly-N or with low quality from raw data with Novogene perl scripts.
Index of the reference genome was built using Hisat2 v2.0.5
(Stringtie- 1.3.3b) was used to count the read numbers mapped to each gene
Assembly: WBcel235 (NCBI, GCF_000002985.6_WBcel235_genomic.fa)
Supplementary files format and content: genes.readcount.txt is a 7 x 46660 matrix of read counts for all samples

organism: Caenorhabditis elegans

source_name: ced-3(n1286) mutant embryos

growth_protocol: Starved L1 worms grown in solid NGM with E. coli OP50 food at 20 °C were chunked, grown to egg-laying adults, alkaline hypochlorite solution applied to synchronize L1 progeny, which were allowed to grow to egg-laying adults. Alkaline hypochlorite solution was used to extract specifically eggs from the synchronized population of egg-laying adults.

extract_protocol:
miRNeasy kit (Qiagen) following standard procedures for total RNA extraction, including the optional wash with RWT buffer
Strand-specific libraries were generated using NEBNextUltra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Ribosomal RNA was depleted. In order to select cDNA fragments of preferentially 250-300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then USER Enzyme (NEB, USA) was used to digest the second strand with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.

value: embryos


title: Wild-type L3 worms biol replicate 1

description: Wild-type L3 worms

data_processing:
FASTQ files were preprocessed by Novogene as follows: (1) Get rid of reads of which more than 50% bases has a base quality score no more than 5; (2) Get rid of reads containing N > 10%;  (3) Get rid of reads with 5' primer contaminants; (4) Get rid of reads without 3' primer and reads without the insert tag; (5) Trim 3' primer sequence; (6) Get rid of reads with polyA/T/G/C. Small RNA adapter sequences: RNA 5’ Adapter (RA5), part: 5'-GTTCAGAGTTCTACAGTCCGACGATC-3' RNA 3' Adapter (RA3), part: 5'-AGATCGGAAGAGCACACGTCT-3'
Analysis was done using QuasR version 1.34, including qAlign(maxHits = 50)
and including QuasR function qExportWig(strand="+") for sense and qExportWig(strand="-") for antisense reads
Assembly: WBcel235/ce11 (UCSC, ce11.fa)
Supplementary files format and content: WT1Plus.wig.gz and WT2Plus.wig.gz are the output of qExportWig from QuasR and correspond to a WIG file viewable in a genome browser showing reads on the + sense strand
Supplementary files format and content: WT1Minus.wig.gz and WT2Minus.wig.gz are the output of qExportWig(strand="-") and correspond to a WIG file viewable in a genome browser showing reads on the - antisense strand

source_name: whole worm

growth_protocol: Starved L1 worms grown in solid NGM with E. coli OP50 food at 20 °C were chunked, grown to egg-laying adults, alkaline hypochlorite solution applied to synchronize L1 progeny, which were allowed to grow to the L3 stage

extract_protocol:
miRNeasy kit following standard procedures for total RNA extraction
Libraries with insertions between 18 - 40 bp were size selected. Illumina sequencing was performed with SE50

treatment_protocol: Alkaline hypochlorite solution was used to synchronize worm populations

value: whole worm


title: AGH148_4


title: C61_A4_L1_0w_RepC_Replicate2

first: Andrea

last: Lauria

institute: University of Turin

data_processing:
Following quality controls , reads were mapped to the Mus musculus transcriptome (ENSEMBL version 101) using Salmon v 0.13.1 and RNA-seq data were analysed using Seurat packages (v 4.0.1) on R (v 4.0.3).
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of gene expression read counts matrix per gene/cell.

extract_protocol:
Flow citometry was used to sort tomato positive epidermal cells.
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).


title: ced-3(n1286) embryos biol rep 2

treatment_protocol: Alkaline hypochlorite solution was used to extract specifically eggs from the synchronized population of egg-laying adults.


title: Wild-type L3 worms biol replicate 2

description: Wild-type L3 worms


title: Mi3_Mild TBI, replicate_3

value: M

value: traumatic brain injury


title: Severe patient 1

description: Gene expression data from CD3+ cells


title: C61_A3_L1_0w_RepC_Replicate2


title: Severe patient 2

description: Gene expression data from CD3+ cells


title: AGH148_2


title: ced-3(n1286) embryos biol rep 1


title: C61_A2_L1_0w_RepC_Replicate2


title: Severe patient 3

description: Gene expression data from CD3+ cells


title: Severe patient 5

description: Gene expression data from CD3+ cells


title: AGH148_15

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: dot-1.1(knu339); ced-3(n1286) embryos biol rep 3

source_name: dot-1.1(knu339); ced-3(n1286) mutant embryos


title: AGH148_12

description:
H3-ac ChIP-seq (no SM) Repl. 3
Biological replicate 3


title: AGH148_13


title: Mild patient 9

description: Gene expression data from CD3+ cells

source_name: CD3+ cells from a mild allergic subject

value: Mild


title: C61_A11_L1_0w_RepC_Replicate2


title: AGH148_14


title: C61_A10_L1_0w_RepC_Replicate2


title: C60_H9_L1_0w_RepC_Replicate1


title: dot-1.1(knu339); ced-3(n1286) embryos biol rep 1


title: ced-3(n1286) embryos biol rep 3 [ced5]

data_processing:
FASTQ files were trimmed and preprocessed using FASTP (with parameter --length_required 7)
Remaining analysis used QuasR version 1.34, including qAlign(maxHits = 50)
including QuasR function qCount(orientation = "same") for sense and qCount(orientation = "opposite") for antisense reads
Assembly: WBcel235 (NCBI, GCF_000002985.6_WBcel235_genomic.fa)
Supplementary files format and content: rawReadsNCBIced3VSdot1ced3.csv is a 8 x 32239 matrix of counts outputted by qCount(orientation="same"). It is the read counts for sense reads.
Supplementary files format and content: rawReadsNCBIced3vsdot1ced3antisense.csv is a 8 x 32239 matrix of counts outputted by qCount(orientation="opposite"). It is the read counts for antisense reads.

extract_protocol:
miRNeasy kit following standard procedures for total RNA extraction, including the optional wash with RWT buffer
Libraries with insertions between 18 - 40 bp were size selected. Illumina sequencing was performed with SE50


title: AGH148_11

description:
H3-ac ChIP-seq (no SM) Repl. 2
Biological replicate 2


title: C60_H8_L1_0w_RepC_Replicate1


title: AGH148_10

description:
H3-ac ChIP-seq (no SM) Repl. 1
Biological replicate 1


title: Mild patient 8

description: Gene expression data from CD3+ cells


title: Mild patient 5

description: Gene expression data from CD3+ cells


title: ced-3(n1286) embryos biol rep 2 [ced4]


title: C60_H7_L1_0w_RepC_Replicate1


title: Mild patient 7

description: Gene expression data from CD3+ cells


title: Mild patient 6

description: Gene expression data from CD3+ cells


title: dot-1.1(knu339); ced-3(n1286) embryos biol rep 2


title: C60_H6_L1_0w_RepC_Replicate1


title: ced-3(n1286) embryos biol rep 1 [ced1]


title: Co4_Control, replicate_4

value: healthy control


title: dot-1.1(knu339); ced-3(n1286) embryos biol rep 3 [dot5]


title: Mild patient 4

description: Gene expression data from CD3+ cells


title: C60_H3_L1_0w_RepC_Replicate1


title: dot-1.1(knu339); ced-3(n1286) embryos biol rep 2 [dot4]


title: Mild patient 3

description: Gene expression data from CD3+ cells


title: C60_H2_L1_0w_RepC_Replicate1


title: Arabidopsis_cauline - SS1 antibody m6A-IP-seq

city: Seattle

first: Andrew

middle: Ben

last: Stergachis

state: WA

address: 1959 NE Pacific St

department: Medical Genetics

institute: University of Washington

description: m6A-IP seq

data_processing:
Reads were aligned to their corresponding genome using bwa (0.7.12).
Peaks were called using MACS2 (q-value 0.01) with either input and/or IgG IP-seq control as background
Genome_build: dm6 for S2-DSRC and Drosophila embryo samples; TAR19 for Arabidopsis samples; Creinhardtii_281_v5_0_nonnuclear for C.reinhardtii
Supplementary_files_format_and_content: narrowPeak files, called peaks of signal enrichment

source_name: A. thaliana cauline leaves

extract_protocol: Cauline leaves were collected from three separate flowering col-0 Arabidopsis thaliana plants and combined together. Two biological replicates were obtained from plants grown 3 months apart from each other. Approximately 1 g of Cauline leaves was combined with 1.2 mL of Buffer A supplemented with 1% sodium dodecyl sulfate (Sigma L3771), 0.5% polyvinylpyrrolidone (Sigma PVP40) and fresh 1% 2-Mercaptoethanol (Sigma M3148) in a Dounce homogenizer. Tissue was ground using a “B” pestle until homogenous. The lysate was transferred in 200 μl aliquots to 1.5 mL microfuge tubes and all samples were mixed with 3 μl Proteinase K and incubated for 1 hour at 50°C. The DNA was purified by adding 200 μl (1:1) of phenol:chloroform:isoamyl alcohol 25:24:1 (saturated with 10mM Tris, pH 8.0, 1mM EDTA) then mixed by vigorous tube inversions and incubated for 10 min at RT.

tag: m6a-mtase treatment

value: Untreated

tag: anti-dna-m6a antibody

value: SS1 - Synaptic System Ab. 202 003


title: Mild patient 2

description: Gene expression data from CD3+ cells

tag: genotype


title: dot-1.1(knu339); ced-3(n1286) embryos biol rep 1 [dot1]


title: Arabidopsis_cauline - MP1 antibody m6A-IP-seq

description: m6A-IP seq

value: MP1 - Millipore Sigma ABE572


title: C60_H10_L1_0w_RepC_Replicate1

city: Turin

address: Via Accademia Albertina, 13

tag: strain

value: CBA C57BL/6 mixed

value: Keratinocytes


title: Mild patient 1

description: Gene expression data from CD3+ cells

value: CD3+ cells


title: dEmbryo_45min - Input Control

description: IP-seq

organism: Drosophila melanogaster

source_name: Drosophila 45 minute embryos

growth_protocol: Baker's yeast paste 3 days prior to collection, with daily exchange of fresh 100 mm molasses agar plates.

extract_protocol: Timed egg lays were used to stage embryos by adding a fresh molasses agar plate with yeast paste to the collection cage for 30 minutes; this was then replaced with a fresh plate for the next collection cycle. The plate was submerged in 1X PBS and the eggs were dislodged with a paint brush then inverted over a funnel into an egg basket and rinsed with additional PBS. The egg basket was then inverted over a 50 mL conical tube and the eggs were collected with PBS and pelleted for 3 min at 300 x g. The PBS was removed and the eggs were transferred with a wide bore pipette tip in approximately 1 mL of PBS to a 1.5 mL microfuge tube and pelleted for 2 min at 500 x g. The PBS was removed and the egg pellet was flash frozen in liquid nitrogen and stored at -80°C. On average, the embryo pellets were frozen 15 minutes after removal of the agar plate from the collection cage yielding embryos between 15 and 45 minutes of development (referred hereafter as 45min embryos). The pellets were transferred to 1.2 mL of Buffer A supplemented with 1% sodium dodecyl sulfate, 0.5% polyvinylpyrrolidone and fresh 1% 2-Mercaptoethanol, and DNA was extracted as described for cauline leaves.

value: Input Control


title: Control patient 8

description: Gene expression data from CD3+ cells

source_name: CD3+ cells from a non allergic subject

value: Control

value: Older than 18


title: C60_H1_L1_0w_RepC_Replicate1

tag: cell type


title: Arabidopsis_cauline - Input Control

description: IP-seq


title: Arabidopsis_cauline - IgG antibody IP-seq

description: IP-seq

value: IgG - Cell Signaling Technology 7076


title: C60_G9_L1_0w_RepC_Replicate1

tag: plate


title: dEmbryo_45min - SS1 antibody m6A-IP-seq

description: m6A-IP seq


title: C60_G8_L1_0w_RepC_Replicate1

tag: time


title: AGH146_18

description: Biological replicate 3

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Occupancies profiles of Histone H3, Rpb3, Rpb1, Gcn4, TBP and myc-tagged Spt7, Srb6 and Eaf1 were created using custom R programs.
The processed data were converted to the bigwig files supplied here. Bigwig files for each sample have a  DNA length exclusion limit is: 50 - 300 bp.
Bigwig files for the merged replicates of the H3 ChIP samples were made with DNA length exclusion of 50-200 bp. These files were used for the IGV view figure in our manuscript. These merged files are available on the series record.
Assembly: SacCer3
Supplementary files format and content: bigWig

source_name: myc ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta

tag: chip antibody

value: myc

tag: treatment

value: Formaldehyde-fixed and sonicated


title: Control patient 7

description: Gene expression data from CD3+ cells


title: AGH146_20

description: Biological replicate 2

source_name: myc ChIP-seq (+SM) Repl. 2

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4


title: AGH146_19

description: Biological replicate 1

source_name: myc ChIP-seq (+SM) Repl. 1


title: S2-DRSC (0.075U Hia5) - IgG antibody IP-seq

description: IP-seq

source_name: S2-DRSC cells

growth_protocol: 1X Schneider’s Drosophila Medium (Gibco 21720-024) supplemented with 10% HI FBS (Gibco 16140-063) and 1% Pen Strep (Gibco 15140-122) at room temperature in 75 cm2 flasks to approximately 90% confluency and >95% viability.

extract_protocol: Three million S2 cells were pelleted at 250 x g   for 5 minutes then resuspended in 60 μl of Buffer A (15 mM Tris, pH 8.0; 15 mM   NaCl; 60 mM KCl; 1mM EDTA, pH 8.0; 0.5 mM EGTA, pH 8.0; 0.5 mM Spermidine). 60  μl of cold 2X Lysis buffer (0.1 % IGEPAL CA-630 in Buffer A) was added to each   sample and mixed by gentle flicking then kept on ice for 10 minutes. Samples were   pelleted at 4°C for 5 min at 350 x g and the supernatant was removed.

value: 0.075 Units for 10 minutes

tag: replicate


title: C60_G7_L1_0w_RepC_Replicate1

tag: population


title: dEmbryo_45min - MP1 antibody m6A-IP-seq

description: m6A-IP seq


title: C60_G6_L1_0w_RepC_Replicate1


title: S2-DRSC (0.075U Hia5) - MP1 antibody m6A-IP-seq

description: m6A-IP seq


title: AGH148_16

value: MATa his3-delta1 leu2-delta met15-delta ura3-delta fpr1-delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5-delta::hphMX4


title: AGH146_21

description: Biological replicate 3


title: Control patient 6

description: Gene expression data from CD3+ cells

tag: tissue


title: AGH146_16

description: Biological replicate 1


title: Control patient 5

description: Gene expression data from CD3+ cells


title: S2-DRSC (Untreated) - SS2 antibody m6A-IP-seq

description: m6A-IP seq

value: SS2 - Synaptic System Ab. 202 111


title: C60_G5_L1_0w_RepC_Replicate1


title: Control patient 3

description: Gene expression data from CD3+ cells


title: Control patient 4

description: Gene expression data from CD3+ cells


title: C60_G4_L1_0w_RepC_Replicate1


title: S2-DRSC (Untreated) - SS1 antibody m6A-IP-seq

description: m6A-IP seq

value: Untreated


title: Control patient 2

description: Gene expression data from CD3+ cells


title: AGH146_15

description: Biological replicate 3

source_name: myc ChIP-seq (no SM) Repl. 3


title: S2-DRSC (Untreated) - AB1 antibody m6A-IP-seq

description: m6A-IP seq

value: AB1 - Abcam ab151230


title: S2-DRSC (Untreated) - AM1 antibody m6A-IP-seq

description: m6A-IP seq

value: AM1 - Active Motif 61756


title: C60_G2_L1_0w_RepC_Replicate1

value: CBA C57BL/6 mixed


title: AGH146_14

description: Biological replicate 2

source_name: myc ChIP-seq (no SM) Repl. 2


title: C60_G3_L1_0w_RepC_Replicate1

source_name: Murine Epidermal cells

value: Keratinocytes


title: AGH146_13

description: Biological replicate 1

source_name: myc ChIP-seq (no SM) Repl. 1


title: AGH146_12

description: Biological replicate 3

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 EAF1-myc13::HIS3MX6


title: AGH146_17

description: Biological replicate 2


title: human pericyte cells, MTG, scr_2

city: Auckland

first: Maize

last: Cao

address: 3A Symonds Street

country: New Zealand

institute: University of Auckland

data_processing:
Raw data quality control was applied using FastQC software and then trimmed with Trimmomatic.
Reads were aligned to the GRCh38 reference genome with HISAT2 and quantified with StringTie.
Count data was imported into the R software environment  with the tximport package to perform differential expression analysis using DESeq2 and differential exon usage analysis using DEXSeq.
Assembly: GRCh38
Supplementary files format and content: comma-separated values files include DEG analysis results and DEU analysis results

source_name: brain

extract_protocol:
RNA was isolated and purified using the RNAqueous®-Micro Total RNA Isolation Kit following manufacturer's recommendations
0.5-1μg RNA per sample was used as input material. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations
150 bp paired-end reads

value: brain

tag: brain region

value: middle temporal gyrus

value: brain pericytes

value: scr


title: human pericyte cells, MTG, siTDP_2

value: siTDP


title: human pericyte cells, MTG, scr_3


title: S2-DRSC (Untreated) - MP1 antibody m6A-IP-seq

description: m6A-IP seq

value: MP1 - Millipore Sigma ABE572


title: human pericyte cells, MTG, siTDP_3


title: C60_G12_L1_0w_RepC_Replicate1


title: S2-DRSC (0.6U Hia5) - SS2 antibody m6A-IP-seq

description: m6A-IP seq

value: 0.6 Units for 10 minutes


title: AGH146_11

description: Biological replicate 2

value: myc

value: Formaldehyde-fixed and sonicated


title: human pericyte cells, MTG, scr_1


title: S2-DRSC (0.6U Hia5) - SS1 antibody m6A-IP-seq

description: m6A-IP seq

value: SS1 - Synaptic System Ab. 202 003


title: C60_G11_L1_0w_RepC_Replicate1


title: AGH146_10

description: Biological replicate 1


title: C60_G10_L1_0w_RepC_Replicate1


title: human pericyte cells, MTG, siTDP_1


title: AGH146_9

description: Biological replicate 3


title: human pericyte cells, MC, siTDP_6

value: motor cortex


title: S2-DRSC (0.6U Hia5) - AB1 antibody m6A-IP-seq

description: m6A-IP seq


title: human pericyte cells, MC, scr_6


title: C60_G1_L1_0w_RepC_Replicate1


title: S2-DRSC (0.6U Hia5) - AM1 antibody m6A-IP-seq

description: m6A-IP seq


title: C60_F8_L1_0w_RepC_Replicate1


title: C60_F9_L1_0w_RepC_Replicate1


title: AGH146_7

description: Biological replicate 1


title: AGH146_8

description: Biological replicate 2


title: S2-DRSC (0.6U Hia5) - MP1 antibody m6A-IP-seq

description: m6A-IP seq


title: AGH146_6

description: Biological replicate 3

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 EAF1-myc13::HIS3MX6 gcn5delta::kanMX4


title: human pericyte cells, MC, scr_5