title: BRCA_28-1 (TEQUILA-seq)


title: Hela cells,generation3

status: Public on Jun 06 2023

type: SRA

city: Guangzhou

first: Hong

last: Lu

address: No. 601, West Huangpu Avenue, Tianhe District, Guangzhou

country: China

institute: jinan university

description: total RNA of Hela

library_source: transcriptomic

data_processing:
Then reads were mapped to transcripts using the hyperaccurate mapping algorithm FANSe3 in the next-generation sequencing analysis platform “Chi Cloud” (http://www.chi-biotech.com).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  algorithm FANSe3 in the next-generation sequencing analysis platform “Chi Cloud” (http://www.chi-biotech.com).
Trimmed sequence reads were mapped to algorithm FANSe3 in the next-generation sequencing analysis platform “Chi Cloud” (http://www.chi-biotech.com).
Read count extraction and normalization were performed using  algorithm FANSe3 in the next-generation sequencing analysis platform “Chi Cloud” (http://www.chi-biotech.com).
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Hela

growth_protocol: These cells were cultured in DMEM medium with 10% FBS and 1% penicillin/streptomycin. All cell lines culture environment was 37 °C, 5% CO2.

extract_protocol:
RNA was harvested using TRIzol RNA extraction reagent (Ambion, Austin,TX). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
For mRNA-seq, our study used two methods to construct the sequencing library, including Oligo (dT) method and the rRNA depletion method.
For RNA-degraded samples treated with RNase A, the library construction method of  rRNA depletion method was used.

tag: cell line

value: Hela

tag: cell type

value: cervical cancer cells

tag: genotype

value: WT

tag: treatment

value: Normal subculture without special treatment


title: Hela cells,generation2

description: total RNA of Hela


title: BRCA_24-1 (TEQUILA-seq)

city: Philadelphia

first: Yi

last: Xing

state: PA

address: 9054 Colket Translational Research Bldg. 3501 Civic Center Blvd.

department: Executive Director, Department of Biomedical and Health Informatics

country: USA

institute: The Children’s Hospital of Philadelphia

description:
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BRCA_TEQUILA-seq_N2_R0_abundance.esp
BRCA_TEQUILA-seq_N2_R0_updated.gtf

data_processing:
Basecalling was performed in fast mode with Guppy (version 4.0.15) for all Nanopore sequencing data in this study (https://community.nanoporetech.com/downloads). Basecalling of direct RNA and cDNA libraries were done using config files rna_r9.4.1_70bps_fast.cfg and dna_r9.4.1_450bps_fast.cfg respectively.
Reads were then mapped to either the SIRVome or hg19 reference genome using minimap2 (v2.17) with parameters “-a -x splice -ub -k 14 -w 4 --secondary=no” and either SIRV transcript annotations or GENCODE v34 annotations (https://www.gencodegenes.org/human/release_34lift37.html).
Alignment files (SAM format) were next processed by ESPRESSO (https://github.com/Xinglab/espresso) using default settings and either SIRV transcript annotations or GENCODE v34 annotations. Reads that either map to the mitochondrial genome or contain large continuous insertions (≥20 nt) in the raw alignment were filtered out by ESPRESSO.
Assembly: hg19, SIRVome
Supplementary files format and content: .esp files are tab-delimited matrices generated by ESPRESSO that contain read count estimates for all identified isoforms (rows) across all samples (columns); .gtf files generated by ESPRESSO are in GTF format and provide genomic coordinates for all identified transcript isoforms and their corresponding exons
Paired-end Illumina sequencing data with 150-bp read length for SH-SY5Y cells were generated from libraries prepared following the TruSeq Stranded mRNA protocol (Illumina, Cat. #20020595)
Reads from the 3 samples were pooled and aligned to the GRCh37/hg19 reference genome using STAR on two-pass mode with default settings and transcript annotations from GENCODE v34.
Exon skipping events were detected and quantified from short-read alignment files using rMATS (v4.1.1) with default settings.
Assembly: hg19
Supplementary files format and content: SH-SY5Y_SE.MATS.JC.txt is a tab-delimited file that contains coordinates and junction read counts associated with all identified exon skipping events

molecule: polyA RNA

growth_protocol:
Cell line was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA 30-4500 K™). Cell lines were cultured according to ATCC recommendations and were authenticated by the supplier.
See above

extract_protocol:
Total RNA of breast cancer cell lines was extracted using TRIzol reagent (Invitrogen, #15596018).
A 200 ng aliquot of total RNA was used as templates for cDNA synthesis following the SMART-seq2 protocol. Nanopore 1D libraries were constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. Briefly, cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 min and 65°C for 20 min. The cDNA was then purified with 1× volume of AMPure XP beads and eluted in 60 μl of nuclease-free water. Adapter ligation was performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, libraries were purified using 0.45× volumes of AMPure XP beads and short fragment buffer.
See above
See above

tag: lineage

value: Human breast cancer HER2 enriched

tag: nanopore library type

value: TEQUILA-seq


title: D18-182151

city: Cambridge

first: Dunaduan

last: Ma

state: Ma

address: 77 Massachusetts Ave

department: Koch Institute

institute: MIT

data_processing:
Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, sample contamination estimation, intergenic reads percentile calculation, intronic reads percentile calculation, UTR reads percentile calculation, gene coding reads percentile calculation, and rRNA contamination estimation. Besides, sense to antisense reads ratio was calculated to indicate strand specificity. Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.11.1.0.12 basing on log2(fpkm+1) values of the expressed coding genes to observe sample relationship and to detect outliers.
RNA-Seq mapping: against GRCm38/mm10 reference for mouse sequences using STAR/2.5.3a
Gene expression was quantitated using RSEM v. 1.3.0
Gene set enrichment analyses was performed by GSEA 2-2.0.13 basing on normalized expression values
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt file. Each gene per row and each sample per column(raw counts from RSEM)

organism: Mus musculus

source_name: Non-tumoral thymus

extract_protocol: Total RNA was isolated from primary cells or tumors, using the RNeasy Plus Mini Kit (Qiagen) and sequenced on an Illumina HiSeq2000. At least 5000 cells were sorted  directly  in lysis buffer for specifc T cell progenitor populations in the thymus while at least 5 million cells have used for RNA isolation form thymic lymphomas. Unless otherwise indicated samples from tumors were isolated without sorting specific polulations.

tag: tissue

value: Normal Thymus_DP


title: BRCA_25-1 (TEQUILA-seq)


title: D18-182152

value: Normal Thymus_DN1


title: Hela cells,generation1

description: total RNA of Hela


title: BRCA_29-2 (TEQUILA-seq)


title: BRCA_24-2 (TEQUILA-seq)


title: BRCA_23-2 (TEQUILA-seq)


title: A549 cells,generation10

description: total RNA of A549

value: Lung cancer cells


title: BRCA_23-1 (TEQUILA-seq)


title: D18-182155


title: D18-182150

value: Normal Thymus_DN4


title: BRCA_22-2 (TEQUILA-seq)


title: BRCA_26-1 (TEQUILA-seq)


title: D18-182149

value: Normal Thymus_DN3


title: D18-182148


title: BRCA_22-1 (TEQUILA-seq)


title: A549 cells,generation8

description: total RNA of A549


title: BRCA_21-2 (TEQUILA-seq)


title: A549 cells,generation9

description: total RNA of A549


title: D18-182147


title: BRCA_21-1 (TEQUILA-seq)


title: A549 cells,generation7

description: total RNA of A549


title: BRCA_19-2 (TEQUILA-seq)


title: D18-182146


title: BRCA_19-1 (TEQUILA-seq)


title: BRCA_20-2 (TEQUILA-seq)


title: BRCA_18-2 (TEQUILA-seq)

value: Human breast cancer basal B


title: A549 cells,generation6

description: total RNA of A549


title: D18-182145


title: BRCA_20-1 (TEQUILA-seq)


title: BRCA_17-2 (TEQUILA-seq)


title: BRCA_18-1 (TEQUILA-seq)


title: A549 cells,generation5

description: total RNA of A549


title: D18-182144


title: A549 cells,generation11

description: total RNA of A549


title: BRCA_16-1 (TEQUILA-seq)


title: BRCA_16-2 (TEQUILA-seq)


title: A549 cells,generation4

description: total RNA of A549


title: D18-182143


title: BRCA_15-2 (TEQUILA-seq)


title: BRCA_17-1 (TEQUILA-seq)


title: A549 cells,generation3

description: total RNA of A549


title: BRCA_15-1 (TEQUILA-seq)


title: BRCA_14-2 (TEQUILA-seq)


title: D18-182142


title: A549 cells,generation2

description: total RNA of A549


title: D18-182141


title: BRCA_13-2 (TEQUILA-seq)


title: BRCA_13-1 (TEQUILA-seq)


title: HCCLM3 cells,generation8

description: total RNA of HCCLM3

value: hepatocellular cells


title: A549 cells,generation1

description: total RNA of A549


title: D18-182139


title: BRCA_12-2 (TEQUILA-seq)


title: BRCA_12-1 (TEQUILA-seq)


title: BRCA_10-1 (TEQUILA-seq)

value: Human breast cancer basal A


title: BRCA_11-2 (TEQUILA-seq)


title: BRCA_10-2 (TEQUILA-seq)


title: HCCLM3 cells,generation6

description: total RNA of HCCLM3


title: D18-182137

value: Normal Thymus_DN2


title: HCCLM3 cells,generation5

description: total RNA of HCCLM3


title: HCCLM3 cells,generation4

description: total RNA of HCCLM3


title: BRCA_8-2 (TEQUILA-seq)


title: BRCA_9-2 (TEQUILA-seq)


title: D18-182136


title: BRCA_8-1 (TEQUILA-seq)


title: BRCA_9-1 (TEQUILA-seq)


title: BRCA_14-1 (TEQUILA-seq)


title: D18-182140


title: D18-182135


title: BRCA_7-1 (TEQUILA-seq)


title: BRCA_11-1 (TEQUILA-seq)


title: D18-182133


title: BRCA_6-2 (TEQUILA-seq)


title: HCCLM3 cells,generation1

description: total RNA of HCCLM3


title: D18-182134


title: BRCA_6-1 (TEQUILA-seq)


title: HCCLM3 cells,generation7

description: total RNA of HCCLM3


title: BRCA_5-2 (TEQUILA-seq)


title: D18-182138


title: BRCA_7-2 (TEQUILA-seq)


title: BRCA_5-1 (TEQUILA-seq)


title: D18-182132


title: HCCLM3 cells,generation2

description: total RNA of HCCLM3


title: BRCA_4-2 (TEQUILA-seq)


title: D18-182131


title: D18-182130


title: HCCLM6 cells,generation6

description: total RNA of HCCLM6


title: BRCA_3-1 (TEQUILA-seq)


title: BRCA_2-2 (TEQUILA-seq)


title: BRCA_2-1 (TEQUILA-seq)


title: BRCA_1-2 (TEQUILA-seq)


title: D18-182129


title: HCCLM6 cells,generation5

description: total RNA of HCCLM6


title: D18-182128


title: HCCLM6 cells,generation4

description: total RNA of HCCLM6


title: HCCLM3 cells,generation3

description: total RNA of HCCLM3


title: SH-SY5Y-3 (TEQUILA-seq_48h)

description:
SIRV1,SIRV3,SIRV5,SIRV4003,SIRV6003,SIRV8003,SIRV10002,SIRV12003,ERCC-00130,ERCC-00004,ERCC-00136,ERCC-00108,ERCC-00116,ERCC-00092,ERCC-00095,ERCC-00131,ERCC-00062,ERCC-00019,ERCC-00144,ERCC-00170,ERCC-00154,ERCC-00085,ERCC-00028,ERCC-00033,ERCC-00134,ERCC-00147,ERCC-00097,ERCC-00156,ERCC-00123,ERCC-00017,ERCC-00083,ERCC-00096,ERCC-00171,ERCC-00009,ERCC-00042,ERCC-00060,ERCC-00035,ERCC-00025,ERCC-00051,ERCC-00053,ERCC-00148,ERCC-00126,ERCC-00034,ERCC-00150,ERCC-00067,ERCC-00031,ERCC-00109,ERCC-00073,ERCC-00158,ERCC-00104,ERCC-00142,ERCC-00138,ERCC-00117,ERCC-00075  ENSG00000021776,ENSG00000116752,ENSG00000029363,ENSG00000122870,ENSG00000137656,ENSG00000106245,ENSG00000149187,ENSG00000048740,ENSG00000159409,ENSG00000101489,ENSG00000161082,ENSG00000140488,ENSG00000104859,ENSG00000111605,ENSG00000149532,ENSG00000101811,ENSG00000177613,ENSG00000150316,ENSG00000163510,ENSG00000273559,ENSG00000066044,ENSG00000107105,ENSG00000196361,ENSG00000162374,ENSG00000104413,ENSG00000103067,ENSG00000182944,ENSG00000162613,ENSG00000107164,ENSG00000089280,ENSG00000132463,ENSG00000177733,ENSG00000135486,ENSG00000139675,ENSG00000122566,ENSG00000170144,ENSG00000197451,ENSG00000092199,ENSG00000179172,ENSG00000138668,ENSG00000152795,ENSG00000169813,ENSG00000169045,ENSG00000126945,ENSG00000096746,ENSG00000165119,ENSG00000104824,ENSG00000143889,ENSG00000099783,ENSG00000125944,ENSG00000153187,ENSG00000105323,ENSG00000214753,ENSG00000240682,ENSG00000121774,ENSG00000112232,ENSG00000131773,ENSG00000088247,ENSG00000175324,ENSG00000181817,ENSG00000204392,ENSG00000170860,ENSG00000130520,ENSG00000106355,ENSG00000164167,ENSG00000130332,ENSG00000128534,ENSG00000007392,ENSG00000146963,ENSG00000108848,ENSG00000162385,ENSG00000152601,ENSG00000139793,ENSG00000076770,ENSG00000183496,ENSG00000176624,ENSG00000181588,ENSG00000135097,ENSG00000153944,ENSG00000183011,ENSG00000204356,ENSG00000139910,ENSG00000104967,ENSG00000169564,ENSG00000197111,ENSG00000183570,ENSG00000090097,ENSG00000132424,ENSG00000165630,ENSG00000110107,ENSG00000117360,ENSG00000134748,ENSG00000134186,ENSG00000136875,ENSG00000196504,ENSG00000110844,ENSG00000112739,ENSG00000101161,ENSG00000174231,ENSG00000164985,ENSG00000011304,ENSG00000117569,ENSG00000119314,ENSG00000179950,ENSG00000112531,ENSG00000125970,ENSG00000184672,ENSG00000161847,ENSG00000162437,ENSG00000078328,ENSG00000100320,ENSG00000182872,ENSG00000244462,ENSG00000183808,ENSG00000239306,ENSG00000162775,ENSG00000259956,ENSG00000134453,ENSG00000119446,ENSG00000122965,ENSG00000203867,ENSG00000086589,ENSG00000100461,ENSG00000112183,ENSG00000119707,ENSG00000139746,ENSG00000091009,ENSG00000106344,ENSG00000102317,ENSG00000184863,ENSG00000188739,ENSG00000132819,ENSG00000131051,ENSG00000173933,ENSG00000089682,ENSG00000126254,ENSG00000184898,ENSG00000155636,ENSG00000163694,ENSG00000173914,ENSG00000003756,ENSG00000004534,ENSG00000076053,ENSG00000265241,ENSG00000153250,ENSG00000076067,ENSG00000144642,ENSG00000147274,ENSG00000134597,ENSG00000170748,ENSG00000157110,ENSG00000166831,ENSG00000185946,ENSG00000205937,ENSG00000175467,ENSG00000075856,ENSG00000126461,ENSG00000139218,ENSG00000156304,ENSG00000213079,ENSG00000168066,ENSG00000099995,ENSG00000104897,ENSG00000183431,ENSG00000115524,ENSG00000087365,ENSG00000189091,ENSG00000143368,ENSG00000116560,ENSG00000061936,ENSG00000164609,ENSG00000119953,ENSG00000122692,ENSG00000144028,ENSG00000161981,ENSG00000124380,ENSG00000184209,ENSG00000060688,ENSG00000168566,ENSG00000104852,ENSG00000077312,ENSG00000131876,ENSG00000125835,ENSG00000125870,ENSG00000124562,ENSG00000167088,ENSG00000125743,ENSG00000100028,ENSG00000182004,ENSG00000139343,ENSG00000143977,ENSG00000128739,ENSG00000153914,ENSG00000096063,ENSG00000135250,ENSG00000184343,ENSG00000133226,ENSG00000167978,ENSG00000139767,ENSG00000136450,ENSG00000188529,ENSG00000116754,ENSG00000154548,ENSG00000161547,ENSG00000112081,ENSG00000116350,ENSG00000100650,ENSG00000124193,ENSG00000115875,ENSG00000263465,ENSG00000111786,ENSG00000117614,ENSG00000116001,ENSG00000151923,ENSG00000164548,ENSG00000136527,ENSG00000160201,ENSG00000161265,ENSG00000063244,ENSG00000163714,ENSG00000152332
SH-SY5Y_hg19_N2_R0_abundance.esp
SH-SY5Y_hg19_N2_R0_updated.gtf
SH-SY5Y_SIRV_N2_R0_abundance.esp
SH-SY5Y_SIRV_N2_R0_updated.gtf

growth_protocol:
SH-SY5Y human neuroblastoma cells (ATCC, #CRL-2266) were cultured in DMEM/F-12 (Gibco, #11330032) supplemented with 10% fetal bovine serum (FBS, Corning, #45000-734) and 100 U/ml penicillin-streptomycin (Gibco, #15140122). SH-SY5Y cells were maintained at 37°C in a humidified chamber with 5% CO2. The SH-SY5Y cell line was authenticated by short tandem repeat analysis and verified to be mycoplasma-free.
See above

extract_protocol:
Total RNA of  SH-SY5Y cell line was extracted using TRIzol reagent (Invitrogen, #15596018).
A 200 ng aliquot of total RNA was used as templates for cDNA synthesis following the SMART-seq2 protocol. Nanopore 1D libraries were constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. Briefly, cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 min and 65°C for 20 min. The cDNA was then purified with 1× volume of AMPure XP beads and eluted in 60 μl of nuclease-free water. Adapter ligation was performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, libraries were purified using 0.45× volumes of AMPure XP beads and short fragment buffer.
See above
See above

value: human neuroblastoma


title: HCCLM6 cells,generation3

description: total RNA of HCCLM6


title: D18-182126


title: HCCLM6 cells,generation8

description: total RNA of HCCLM6


title: SH-SY5Y-1 (TEQUILA-seq_48h)


title: BRCA_4-1 (TEQUILA-seq)


title: D18-182125


title: HCCLM6 cells,generation7

description: total RNA of HCCLM6


title: SH-SY5Y-3 (TEQUILA-seq_4h)


title: SH-SY5Y-2 (TEQUILA-seq_8h)


title: SH-SY5Y-1 (TEQUILA-seq_8h)


title: SH-SY5Y-2 (TEQUILA-seq_48h)


title: SH-SY5Y-3 (TEQUILA-seq_8h)


title: BRCA_3-2 (TEQUILA-seq)


title: HCCLM6 cells,generation2

description: total RNA of HCCLM6


title: D18-182124


title: SH-SY5Y-2 (TEQUILA-seq_4h)


title: MHCC97H cells, generation9

description: total RNA of MHCC97H


title: BRCA_1-1 (TEQUILA-seq)


title: SH-SY5Y-3 (1D cDNA)

description:
SH-SY5Y_hg19_N2_R0_abundance.esp
SH-SY5Y_hg19_N2_R0_updated.gtf
SH-SY5Y_SIRV_N2_R0_abundance.esp
SH-SY5Y_SIRV_N2_R0_updated.gtf

value: 1D cDNA


title: D18-182123


title: SH-SY5Y-2 (1D cDNA)


title: MHCC97H cells, generation8

description: total RNA of MHCC97H


title: SH-SY5Y-1 (1D cDNA)


title: D18-182127


title: D18-182122


title: SH-SY5Y-3 (direct RNA)

extract_protocol:
Total RNA of  SH-SY5Y cell line was extracted using TRIzol reagent (Invitrogen, #15596018).
20 μg total RNA were subjected to poly(A)+ RNA selection using the Dynabeads mRNA DIRECT purification kit (Invitrogen, #61011) following the manufacturer’s instructions. Approximately 500 ng of the resulting poly(A)+ RNA, along with 5 ng of SIRVs, were pooled as input for direct RNA library generation. Libraries were made by following the standard SQK-RNA002 protocol with the optional reverse transcription step included.
See above
See above

value: direct RNA


title: SH-SY5Y-2 (direct RNA)


title: Brain-2 (TEQUILA-seq)

description:
ENSG00000173406,ENSG00000132535,ENSG00000176884,ENSG00000197386,ENSG00000157193,ENSG00000186868,ENSG00000179915,ENSG00000133961,ENSG00000078328,ENSG00000196876
Brain_hg19_N2_R0_abundance.esp
Brain_hg19_N2_R0_updated.gtf

source_name: Human brain total RNA sample

growth_protocol: See above

extract_protocol:
Total RNA isolated by a modified guanidinium thiocyanate method by the supplier (Clontech)
A 200 ng aliquot of total RNA was used as templates for cDNA synthesis following the SMART-seq2 protocol. Nanopore 1D libraries were constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. Briefly, cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 min and 65°C for 20 min. The cDNA was then purified with 1× volume of AMPure XP beads and eluted in 60 μl of nuclease-free water. Adapter ligation was performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, libraries were purified using 0.45× volumes of AMPure XP beads and short fragment buffer.
See above
See above

value: Human brain total RNA sample


title: MHCC97H cells, generation6

description: total RNA of MHCC97H

value: WT


title: MHCC97H cells, generation7

description: total RNA of MHCC97H

value: Normal subculture without special treatment


title: D18-182120


title: SH-SY5Y-1 (direct RNA)


title: D18-182118


title: MHCC97H cells, generation5

description: total RNA of MHCC97H


title: HCCLM6 cells,generation1

description: total RNA of HCCLM6


title: Brain-1 (TEQUILA-seq)


title: Brain-2 (xGenLockdown-seq)

value: xGenLockdown-seq


title: MHCC97H cells, generation4

description: total RNA of MHCC97H


title: D18-182119


title: Brain-3 (xGenLockdown-seq)


title: SH-SY5Y-1 (TEQUILA-seq_4h)

value: TEQUILA-seq


title: MHCC97H cells, generation3

description: total RNA of MHCC97H


title: Brain-3 (1D cDNA)

description:
Brain_hg19_N2_R0_abundance.esp
Brain_hg19_N2_R0_updated.gtf


title: D18-182121


title: D18-182117

value: Normal Thymus_DP


title: Brain-2 (1D cDNA)


title: Brain-1 (1D cDNA)


title: MHCC97H cells, generation2

description: total RNA of MHCC97H


title: D18-182116


title: MHCC97H cells, generation1

description: total RNA of MHCC97H


title: D18-182115


title: Brain-1 (xGenLockdown-seq)


title: Brain-3 (TEQUILA-seq)


title: D18-182114


title: WT, m6A IP, r1, m6A-RIP-seq

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

data_processing:
Raw reads were trimmed with Trimmomatic-0.39
Trimmed reads were aligned to mouse genome and transcriptome (mm10, version M19, 2018-08-30) using HISAT (version 2.1.0).
Reads on each GENCODE annotated gene were counted using HTSeq and then differentially expressed genes were called using DESeq2 package
m6A marked genes were identified as differentially up-regulated genes comparing m6A IP sample with the corresponding Input samples
Assembly: mm10
Supplementary files format and content: text files include read counts for each Sample

source_name: B16F10 tumors

growth_protocol: 3×105 B16F10 tumor cells in 100 μL DPBS were injected subcutaneously into the flank

extract_protocol:
Tumors were harvested and minced into small pieces. Tumor tissue was submerged in RPMI with 10 U/mL DNase I (Thermo Fisher Scientific, EN0521) and 1 mg/ml collagenase IV (Gibco, 17104019) and digested at 37 °C for 1 hour. The suspension was filtered through a 70-mm cell strainer. Red blood cells were lysed with ACK Lysing Buffer (Gibco, A1049201) and resuspended in FACS buffer (DPBS with 2% FBS). Tumor-infiltrating lymphocytes were enriched by CD4 (TIL) Microbeads (Miltenyi Biotec, 130-116-475).  Enriched lymphocytes were stained with DAPI, CD45, and CD4. Live CD45+CD4+GFP+ Treg cells were sorted at 4 °C into Trizol. RNAs were isolated by chloroform and precipitated by isopropanol following the manufacturer’s protocol. Unfragmented total RNAs were subjected to m6A-RIP using the EpiMark N6-Methyladenosin Enrichment Kit (NEB, E1610S) following the manual. Enriched RNAs were recovered by RNA Clean & Concentrator (Zymo, R1014).
RNA libraries were constructed with the SMARTer Stranded Total RNA-Seq Kit v2 (Takara, 634412).

value: B16F10 tumors

value: CD45+ CD4+Foxp3-GFP+ Treg cells

tag: rip antibody

value: m6A Rabbit mAb (Cell Signaling, 56593)


title: D18-182113

value: Normal Thymus_DN1


title: MB.G4.4, scRNAseq

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing and preprocessing of the scRNA data was conducted with CellRanger v3.0.2.
After converting the raw 10X data to fastq format with CellRanger's mkfastq, the data was aligned against the human reference transcriptome GRCh38 with the CellRanger count function using default values.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cerebellar tumour tissue

extract_protocol:
Fresh tumour tissue retrieved from G3/G4 MB patients was minced utilising scalpels. It underwent enzymatic dissociation for 20 minutes at 37°C using Accutase solution (Sigma Aldrich) in addition to mechanical dissociation. The resulting cell suspensions were rinsed with PBS, and red blood cell lysis was performed using ACK lysis buffer in line with the manufacturer’s guidelines (Thermo Fisher). Next, 7-Aminoactinomycin D (Sigma Aldrich) was used as viability dye, and the stained cells were sorted with a BD FACSAria Fusion flow cytometer (BD Biosciences). Eventually, the concentration of sorted single cells was measured using Trypan Blue stain (0.4%; Thermo Fisher Scientific).
Chromium technology (10x Genomics) was employed for single-cell capture, barcoding and cDNA amplification. We used the Library Bead Kit and i7 Multiplex Hit for library generation and performed quality controls with a Tapestation 2000 instrument (Agilent Technologies).

value: cerebellar tumour tissue

value: Medulloblastoma G4 tumour cells


title: MB.G4.2, scRNAseq

description: 10x Genomics

source_name: cerebellar tumour tissue and spinal metastasis


title: D18-182112


title: MB.G4.3, scRNAseq

description: 10x Genomics


title: KO-2-3

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
10X Genomics CellRanger v3.0.2
Seurat v4
Genome_build: GRCh38.p12, Gencode v28
Supplementary_files_format_and_content: raw counts matrix for filtered cells/nuclei in H5AD format

source_name: induced pluripotent stem cells, wild type WTC-11 line from Gladstone Institute

growth_protocol: Cerebral organoid protocol from Stemcell Technologies and Lancaster et al., 2013

extract_protocol:
nuclei extraction method following Habib et al., 2017 and Ayhan et al., 2021
Chromium Single Cell 3’ v3
10X Chromium single-nuclei

value: CRISPR gene edited, isogenic to the wild type samples


title: Lin-Sca-1hic-kit+, control 1, 5mc

city: Tianjin

first: hanxiao

last: Yin

address: Weijin road 94

institute: nankai university

description: WGBS-seq

library_source: genomic

data_processing:
Sequencing data quality control. (1) Removal of adapter sequences. (2) If the average mass value of the entire read base is less than 15, remove the entire read. (3) Cut off bases with a mass value of less than 5 from the beginning and end of the sequence. (4) Sequences shorter than 80bp in length after removing clean.
Methylation level calculation and evaluation of oxidation conversion efficiency
Assembly: GRCm39
Supplementary files format and content: KO_vs_WT_DMR_and_DhMR.xlsx (First sheet is Identification and statistics of differential hydroxymethylation sites (DhMC). Second sheet is Identification and statistics of differential methylation sites (DMC).)

molecule: genomic DNA

source_name: bone marrow

extract_protocol:
Using standard extraction methods to extract DNA from LSK cells
Take approximately 1ug of complete genomic DNA, add Control lambda DNA, and fragment the DNA to approximately 250bp using a Bioruptor Pico non-contact ultrasound interrupter. The fragmented DNA is passivated and phosphorylated by enzymes such as polymerase and kinase, leading to the addition of an A base at the 3 'end and the connection of a 5-methylcytosine modified connector sequence. The connecting product is obtained through the EZ DNA Method Gold of ZYMO Research ™  After the Kit undergoes sulfite transformation and DNA purification, it undergoes low cycle PCR amplification to complete library construction.
After the construction of the library is completed, preliminary quantification is carried out and the library is diluted to 1.5ng/ul. Subsequently, the insert size of the library is detected using Agilent 2100 bioanalyzer. After the insert size meets expectations, qRT-PCR accurately quantifies the effective concentration of the library (the effective concentration of the library is higher than 2nM) to ensure the quality of the library
After passing the library inspection, the different libraries were pooled according to the effective concentration and target offline data volume requirements, and then Illumina sequencing was performed. The basic principle of sequencing is sequencing by synthesis.

value: bone marrow

value: hematopoietic stem/progenitor cells (LSK)


title: D18-182111

value: Normal Thymus_DN4


title: Lin-Sca-1hic-kit+, HDAC6 knockout 2, 5hmc

description: oxWGBS-seq

value: HDAC6 KO


title: Lin-Sca-1hic-kit+, HDAC6 knockout 1, 5mc

description: WGBS-seq


title: MB.G4.1, scRNAseq

description: 10x Genomics


title: Lin-Sca-1hic-kit+, control 2, 5hmc

description: oxWGBS-seq


title: MB.G3.1, scRNAseq

description: 10x Genomics

source_name: spinal metastasis

value: spinal metastasis

value: Medulloblastoma G3 tumour cells


title: MB.G3.2, scRNAseq

description: 10x Genomics


title: NIH3T3_SMO_ETOH_3

city: San Francisco

first: Vikas

last: Daggubati

state: CA

department: Radiation Oncology

institute: University of California, San Francisco

data_processing:
100 base pair single-ended sequencing on Illumina HiSeq 4000, basecalling with
Quality control performed by FASTQC
Reads were trimmed using Trimmomatic, removing leading and trailing bases with quality scores below 28, as well as any base that did not have an average quality score of 28 within a sliding window of 4 bases. Any read shorter than 75 bases was removed
Reads were mapped to GRCm38 or GRCh38 (depending on human or mouse origin) using HISAT2 default paramters
Differential analysis was performed using DESeq2 with "apeglm" parameters with a FDR of 0.05
Assembly: GRCm38, GRCh38
Supplementary files format and content: csv or xlsx files containing fold-change for identified genes, p-values, and FDR values

extract_protocol:
Qiagen Rneasy Mini Extraction
Illumina TruSeq stranded mRNA kit

value: Fibroblast

value: ETOH


title: KO-2-1


title: NIH3T3_SMO_ETOH_2


title: KO-2-2


title: WT, m6A IP, r2, m6A-RIP-seq

value: WT


title: WT-3

value: wild type


title: D18-182109

value: Normal Thymus_DN2


title: D18-182110

value: Normal Thymus_DN3


title: WT-2


title: WT, Input, r1, m6A-RIP-seq

value: B16F10 tumors

value: CD45+ CD4+Foxp3-GFP+ Treg cells


title: WT, Input, r2, m6A-RIP-seq


title: WT-1


title: NIH3T3_SMO_ETOH_1


title: D18-182108

value: Normal Thymus_DN1


title: NIH3T3_SMO_7a27_3


title: NIH3T3_SMO_7a27_2


title: D18-182107

value: Normal Thymus_DP


title: D18-182106


title: NIH3T3_SMO_7a27_1


title: NIH3T3_WT_ETOH_5

value: wildtype


title: D18-182104


title: D18-182105


title: D18-182103


title: Glioma-005 in vitro cultured before transfer

city: La Jolla

first: Kathryn

last: Lande

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

data_processing:
RNA sequencing was performed using the Illumina HiSeq 2500 platform on 51-bp single-end libraries prepared using the IlluminaTruSeq RNA sample preparation kit.
Reads from bulk RNA-seq of 005 GSCs were aligned to the GRCm39/mm39 mouse genome using STAR.
Expression values were TMM-normalized using edgeR::calcNormFactors, followed by conversion to log counts per million with edgeR::cpm.
Assembly: mm10
Supplementary files format and content: FPKM values for sample

source_name: Glioma in vitro

extract_protocol:
Glioma-005 RNA was isolated using Trizol
RNA-Seq cDNA library preparation

tag: strain

value: Glioma in vitro


title: NIH3T3_WT_ETOH_4


title: D18-182101


title: D18-182102


title: NIH3T3_WT_7a27_3


title: Male, saline [M6.PFC.SAL]

city: Minneapolis

first: Shirelle

middle: Xinyue

last: Liu

state: Minnesota

address: 75 E River Rd

institute: University of Minnesota

data_processing:
Quality control on raw sequence data was performed with FastQC.
Mapping of reads was performed via Hisat2 (version 2.1.0) using the rat genome (rn6) as reference.
Differentially expressed genes (DEGs) were identified by gene-wise negative binomial generalized linear models using the EdgeR feature in CLC Genomics Workbench p-value (q-value) < 0.05.
Feature counts was used for gene quantification
Assembly: rn6

organism: Rattus norvegicus

source_name: dorsalmedial prefrontal cortex (dmPFC)

extract_protocol:
Samples within each condition for each sex were randomly pooled in groups of three prior to RNA preparation. RNA was extractd using RNeasy Mini Kit (Qiagen). Isolated RNA was further purified and concentrated using the MinElute Cleanup Kit (Qiagen).
RNA was quantified using the RiboGreen RNA Assay kit (Invitrogen) and assessed for quality using capillary electrophoresis (Agilent BioAnalyzer 2100; Agilent). Barcoded libraries were constructed for each sample using the TruSeq RNA v2 kit (Illumina). Libraries were size- (200 bp) selected and sequenced (50bp paired-end read, ~20 million reads/library) using Illumina HiSeq 2500.

treatment_protocol: Experimetntal group received daily subcutanuoue morphine injection (5.0 mg/kg, 10 days); control group received saline injection. dmPFC was extracted 24 hours after the final injection.

value: dorsalmedial prefrontal cortex (dmPFC)

tag: Sex

value: Male

value: Saline


title: NIH3T3_WT_7a27_2


title: NIH3T3_WT_ETOH_6


title: Male, saline [M5.PFC.SAL]


title: NIH3T3_WT_7a27_1


title: Male, saline [M4.PFC.SAL]


title: Male, morphine [M3.PFC.MOR]

value: Morphine


title: NIH3T3_SMO_KO_SAG_2

value: SAG


title: NIH3T3_SMO_KO_SAG_3

value: Fibroblast


title: UKK2_hiPSC_Chir_48hr_R1

type: RNA

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

institute: University of Cologne

hyb_protocol: The samples were purified using magnetic beads and fragmented. 12,5 μg of fragmented RNA samples were hybridized on Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA). The microarray hybridization step was performed in an Affymetrix GeneChip Hybridization Oven-645 for 16 h at 45 °C and 60 rpm. Washing and staining of the hybridized arrays was completed using the GeneChip HWS Kit (Affymetrix, High Wycombe, United Kingdom) and Affymetrix GeneChip Fluidics Station-450.

scan_protocol: Stained arrays were scanned with Affymetrix Gene-Chip Scanner-3000-7G and evaluated for quality control with Affymetrix GCOS software

data_processing: All analyses were conducted using the Transcriptome Analysis Console software, version 4.0.2.

label: biotin

source_name: IMR90 hiPSC cells

label_protocol: The samples were amplified and labelled with biotin using GeneChip 3′ IVT Express Kit per the manufacturer’s instructions (Affymetrix, High Wycombe, UK).

growth_protocol: Cells were differentiated in RPMI 1640 GlutaMAX™ medium (Thermo Fisher Scientific, Germany) plus B-27™ Supplement, minus insulin (Thermo Fisher Scientific, Germany) supplemented with 10 µM Wnt activator small molecule CHIR99021 (R&D Systems, Minneapolis, USA).

extract_protocol: The cells were homogenised with TRIzol lysis reagent (Thermo Fisher Scientific, Germany), and the total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.

treatment_protocol: Cells were incubated (5 % CO2, 37 °C) with the test compounds at different concentrations and a DMSO concentration of 0.1 % or 0.5 %.

tag: gender

value: female

tag: state

value: proliferating state

tag: agent

value: Chir

tag: time point


title: UKK2_hiPSC_Chir_48hr_R2


title: UKK2_hiPSC_Chir_1hr_R3


title: Male, morphine [M2.PFC.MOR]


title: UKK2_hiPSC_Chir_48hr_R3


title: UKK2_hiPSC_Chir_24hr_R3


title: NIH3T3_SMO_KO_IHH_2

value: IHH


title: UKK2_hiPSC_Chir_24hr_R1


title: NIH3T3_SMO_KO_IHH_3


title: NIH3T3_SMO_KO_IHH_1


title: Female, saline [F6.PFC.SAL]

value: Female


title: Female, saline [F5.PFC.SAL]


title: Male, morphine [M1.PFC.MOR]


title: UKK2_hiPSC_Chir_24hr_R2


title: NIH3T3_SMO_KO_DHH_2

value: DHH


title: NIH3T3_SMO_KO_DHH_3


title: Female, saline [F4.PFC.SAL]


title: NIH3T3_SMO_KO_SAG_1


title: NIH3T3_SMO_KO_DHH_1


title: UKK2_hiPSC_Chir_1hr_R1


title: Female, morphine [F2.PFC.MOR]


title: Female, morphine [F1.PFC.MOR]


title: UKK2_hiPSC_Untreated_NA_R3

value: pluripotent state

value: Untreated


title: UKK2_hiPSC_Chir_1hr_R2


title: 97H 4saizhe mRNA-seq

description: total RNA of MHCC97H

value: hepatocellular cells

value: WT

value: RNA libraries for RNA-seq were prepared by Sagene Co. Ltd.


title: NIH3T3_SMO_KO_SHH_1

value: SHH


title: NIH3T3_SMO_KO_SHH_2


title: UKK2_hiPSC_Untreated_NA_R2


title: UKK2_hiPSC_Thalidomide_Day14_R3

data_processing: All analyses were conducted using the statistical software R, version 4.2.2. Pre-processing of the data consists of the three steps background correction, normalization, and summarization, using the frozen robust multi-array average (fRMA) algorithm. This yields expression values for 54675 probe sets. The R-packages affy, frma and hgu133plus2frmavecs were used.

value: Thalidomide


title: 97H 9 saizhe mRNA-seq

description: total RNA of MHCC97H


title: UKK2_hiPSC_Thalidomide_Day14_R2


title: NIH3T3_SMO_KO_SHH_3


title: UKK2_hiPSC_Thalidomide_Day4_R3


title: UKK2_hiPSC_Untreated_NA_R1


title: UKK2_hiPSC_Thalidomide_Day4_R2


title: 97H 3saizhe mRNA-seq

description: total RNA of MHCC97H


title: UKK2_hiPSC_Thalidomide_Day14_R1


title: NIH3T3_SMO_KO_2425_3


title: 97H 1 saizhe mRNA-seq

description: total RNA of MHCC97H


title: NIH3T3_SMO_KO_2425_1


title: Female, morphine [F3.PFC.MOR]

value: dorsalmedial prefrontal cortex (dmPFC)


title: TCF7L2_Nalm6_Pred_24hr_Rep3

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing data was processed with the publicly available nf-core/cutandrun pipeline (version 2.0).
The following customized parameters were used: genome: hg19; normalisation_mode: Spikein; peakcaller: macs2; run_narrow_peak: true.
NarrowPeaks with a p-value threshold of 0.05 were used to construct reproducible and consensus peak sets.
Reproducible peaks were defined as genomic intervals present in all three replicates within each experimental condition.
Assembly: hg19
Supplementary files format and content: narrowPeak files for each experimental sample
Library strategy: Cut & Run

source_name: Nalm6 (ALL cell line)

growth_protocol: Nalm6 cells were maintained with RPMI-1640 with 10% charcoal-stripped FBS, 2mM Glutamine, and Pen/Strep

extract_protocol:
Briefly, Nalm6 cells were processed using the CUTANA ChIC/CUT&RUN Kit (Version 3, Cat# 14-1048) exactly according to manufacturer's instructions
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with prednisolone at a concentration of 5uM (Nalm6 cells) or vehicle control for 24 hours

value: ALL

tag: antibody

value: TCF7L2 Rabbit mAb (Cell Signaling #2569)

value: PRED (5uM, 24hrs)

tag: replicate


title: NIH3T3_SMO_KO_20S_3

value: Fibroblast


title: NIH3T3_SMO_KO_20S_2


title: NIH3T3_SMO_KO_2425_2


title: TCF7L2_Nalm6_Pred_24hr_Rep2


title: TCF7L2_Nalm6_Pred_24hr_Rep1


title: UKK2_hiPSC_VPA_Day14_R3

value: female

value: proliferating state

value: VPA


title: UKK2_hiPSC_Thalidomide_Day1_R3


title: UKK2_hiPSC_Thalidomide_Day1_R1


title: UKK2_hiPSC_Thalidomide_Day4_R1


title: NIH3T3_SMO_KO_7B27_3


title: UKK2_hiPSC_VPA_Day14_R2


title: NIH3T3_SMO_KO_20S_1


title: UKK2_hiPSC_Thalidomide_Day1_R2


title: NIH3T3_SMO_KO_7B27_2


title: TCF7L2_Nalm6_Ctrl_Rep1


title: NIH3T3_SMO_KO_7B27_1


title: NIH3T3_SMO_KO_BSA_3

value: BSA


title: Nalm6_Dex_Ctrl_Rep2

data_processing:
Reads were mapped to the human genome using bowtie2
Differential enrichment analysis was performed using DESeq2
Assembly: hg19
Supplementary files format and content: text file of raw counts for each replicate

growth_protocol: Nalm6 and TLE1 KO cells were maintained with RPMI-1640 with 10% charcoal-stripped FBS, 2mM Glutamine, and Pen/Strep

extract_protocol:
RNA was extracted from cell lines using the Rneasy Mini Kit (Cat #74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nalm6 cells were treated with prednisolone at a concentration of 5uM for 24 hours. TLE1 KO cells were treated with CHIR-99021 at a concentration of 0.5uM for 24 hours. CEM cells  were treated with a Wnt agonist CHIR-99021 (2uM) or Prednisolone (10µM) for 24 hours.

tag: treatement


title: UKK2_hiPSC_VPA_Day14_R1


title: NIH3T3_SMO_KO_BSA_2

tag: cell line


title: Nalm6_Dex_Ctrl_Rep1

tag: cell type


title: NIH3T3_SMO_KO_BSA_1

tag: genotype


title: Nalm6_Dex_Ctrl_Rep3


title: Nalm6_Pred_24hr_Rep3


title: TCF7L2_Nalm6_Ctrl_Rep2

tag: treatment


title: UKK2_hiPSC_VPA_Day4_R3


title: UKK2_hiPSC_VPA_Day4_R1


title: TCF7L2_Nalm6_Ctrl_Rep3


title: UKK2_hiPSC_VPA_Day4_R2


title: UKK2_hiPSC_VPA_Day1_R3


title: Nalm6_Pred_24hr_Rep2


title: UKK2_hiPSC_VPA_Day1_R1


title: RNA-seq of Plasmodium blood stages: MZ Rep3

city: San Antonio

first: Evelien

middle: M

last: Bunnik

address: 7703 Floyd Curl Dr.

department: Microbiology, Immunology, and Molecular Genetics

institute: University of Texas Health Science Center at San Antonio

description: MZ 3 Rep3

data_processing:
RNA-seq data was processed as paired-end. Following quality assessment of the reads using FastQC (v0.11.8) (reads with a quality score > 30 were retained), adaptor sequences were trimmed using Trim-galore (v0.5.0). RNA-seq data was mapped to the P. falciparum 3D7 genome v3.0, release 44 using hisat2 (v2.1.0) with a maximum intron length of 2,500 bp. Reads were filtered with SAMtools (v1.9) to remove sequences that aligned to the genome more than once (option -q 10) and duplicates were removed using markduplicates from Picard (v2.18.29-SNAPSHOT). Bigwig files were generated with using bamCoverage from the deeptools suite (v3.2.0) and normalized using the RPGC option.
Assembly: P. falciparum 3D7 genome v3.0, release 44
Supplementary files format and content: bigwig files

organism: Plasmodium falciparum

extract_protocol:
RNA was isolated from merozoites and schizonts stored in TRI reagent using Zymo’s Direct-zol RNA microprep kit according to manufacturer’s instructions with DNase treatment. As an extra safe-guard step, isolated RNA was treated with DNase I (Invitrogen #AM1906) using the manufacturer’s protocol for rigorous DNase treatment. RNA quality was determined by Bioanalyzer, and its concentration determined by Qubit.
RNA samples with an RNA integrity number > 7 were used for library preparation. High quality, strand-specific libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) according to manufacturer’s instructions with the following modifications. Adaptor-ligated DNA was enriched by PCR with i7 index primers and i5 universal primer (NEBNext multiplex oligos for Illumina index primers set 1 and 2, NEB #E7335 and #E7500) using KAPA HiFi hot start ready mix (Roche # 07958919001) with the following program: initial denaturation at 98°C for 45 sec.; 9 cycles of (98°C for 15 sec., 55°C for 30 sec., 62°C for 30 sec.); and final extension at 62°C for 5 min. Libraries were purified using 0.9 volumes sparQ beads (QuantaBio #95196-060) according to manufacturer’s instructions and sequenced with the Illumina NextSeq500 to generate 75 bp paired end reads.

tag: Stage

value: Merozoite

tag: isolation

value: Magentically isolated schizonts (40 hpi) were incubated with E64 for 8 hours and then merozoites were mechanically released by filteration. Isolated merozoites were stored in 1 ml TRI reagent.


title: NIH3T3_SMO_KO_ETOH_2

value: ETOH


title: NIH3T3_SMO_KO_ETOH_1


title: RNA-seq of Plasmodium blood stages: MZ Rep1

description: MZ 1 Rep1


title: NIH3T3_SMO_KO_ETOH_3


title: RNA-seq of Plasmodium blood stages: SZ Rep3

description: SZ 3 Rep3

value: Schizont (40 hpi)

value: Schizonts (40 hpi) were magnetically seperated from uninfected and ring infected erythrocytes, then released from erythrocytes by saponin treatment. Isolated schizonts were stored in 1 ml TRI reagent.


title: UKK2_hiPSC_VPA_Day1_R2


title: CEM_Pred_24hr_Rep3

source_name: CEM (ALL cell line)

value: PRED (10uM, 24hrs)


title: RNA-seq of Plasmodium blood stages: MZ Rep2

description: MZ 2 Rep2


title: RNA-seq of Plasmodium blood stages: SZ Rep2

description: SZ 2 Rep2


title: UKK2_hiPSC_Isotretinoin_Day14_R3

value: Isotretinoin


title: NIH3T3_SMO_KO_DMSO_2

value: DMSO


title: NIH3T3_SMO_KO_DMSO_3


title: NIH3T3_SMO_KO_DMSO_1


title: CEM_Pred_24hr_Rep1


title: CEM_CHIR_24hr_Rep3


title: CEM_CHIR_24hr_Rep2


title: NIH3T3_WT_SAG_2

value: wildtype

value: SAG


title: ChIP-seq of Plasmodium blood stages: R input

description: 3D7 input R

data_processing:
Paired-end data generated for histone PTM ChIP-seq was treated as single-end data so that all ChIP-seq data could be processed in the same way, and only read one was processed for analysis. Following quality assessment of the reads using FastQC (v0.11.8) (reads with a quality score ³ 30 were retained), adaptor sequences were trimmed using Trim-galore (v0.5.0). ChIP-seq data were mapped to the P. falciparum 3D7 genome v3.0, release 44 or the P. berghei ANKA genome v3.0, release 49 with Bowtie2 (v2.3.5). Reads were filtered with SAMtools (v1.9) to remove sequences that aligned to the genome more than once (option -q 10) and duplicates were removed using markduplicates from Picard (v2.18.29-SNAPSHOT). Using bamCompare from the deeptools suite (v3.2.0), log2(ChIP/input) bigwig files with reads extended to 150 bp were generated from bam files. Input and no antibody bigwig files were generated with bamCoverage from deeptools (v3.2.0).
Assembly: P. falciparum 3D7 genome v3.0, release 44 or P. berghei ANKA genome v3.0, release 49
Supplementary files format and content: bigwig files showing log2(ChIP/input), except for input and no antibody samples which not normalized

extract_protocol:
Parasites were crosslinked with 1% paraformaldehyde. Crosslinked parasites were washed with 1 ml cold PBS containing protease inhibitors (cOmplete protease inhibitor cocktail) then incubated on ice with 1 ml nuclear extraction buffer [f.c.: 10 mM HEPES, 10 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 1 mM DTT, 200 mM AEBSF, cOmplete protease inhibitor cocktail, Phos Stop phosphatase inhibitor in nuclease-free water]. After 35 min., NP-40/IGEPAL was added to a final concentration of 0.25% and the solution was homogenized by passing the mixture seven times through a 26 G needle. Extracted nuclei were pelleted by centrifugation at 2,100 × g for 20 min. at 4°C. Supernatant was removed and the pelleted nuclei were resuspended in 130 µl of cold shearing buffer [f.c.: 0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 7.5, cOmplete protease inhibitor cocktail, Phos Stop phosphatase inhibitor in nuclease-free water] and transferred to a microTUBE. Chromatin was fragmented with an M220 sonicator (Covaris) with the following settings: 5% duty cycle, 75 W peak incident power, 200 cycles per burst at 6°C for 300 sec. Fragmented chromatin was transferred to a pre-lubricated, low binding 1.5 ml tube. The microTUBE was washed with 70 µl of shearing buffer after which the solution was combined with the fragmented chromatin for a total volume of 200 µl. For each developmental stage (schizont, merozoite, ring, and hepatic merozoite) 30 µl of sheared chromatin was collected at this point for use as an input sample and stored at -70°C until decrosslinking. Chromatin was diluted 1:1 in ChIP dilution buffer [f.c.: 30 mM Tris-HCl pH 8.0, 3 mM EDTA, 0.1% SDS, 300 mM NaCl, Triton X-100, supplemented with cOmplete protease inhibitor cocktail and Phos Stop phosphatase inhibitor in nuclease-free water] then precleared by incubation with protein A agarose/salmon sperm DNA beads (50 µl beads per 1 ml sheared chromatin) for 1 hour at 4°C with agitation to reduce non-specific background. Following the incubation, the beads were pelleted by centrifugation at 100 × g for 1 min. at RT. The supernatant containing the chromatin was moved to a new low-binding tube and incubated overnight at 4°C with agitation with 2 µg of antibody against the histone PTM of interest. Protein A agarose/salmon sperm DNA beads (25 µl beads per 500 µl sonicated chromatin) were washed with 500 µl ChIP dilution buffer and blocked with 1 mg/ml BSA for 1 hour at 4°C with agitation to reduce non-specific binding. Agarose beads were washed 3 times with 500 µl ChIP dilution buffer, then added to the chromatin suspension and incubated for 1 hour at 4°C with agitation. Agarose beads were pelleted by centrifugation at 100 × g for 1 min. at RT, and the supernatant was discarded. Beads were washed twice at 4°C for 15 min. with agitation 1 ml high salt wash buffer [f.c.: 1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 nM NaCl in nuclease-free water], 1 ml low salt wash buffer [f.c.: 1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, in nuclease-free water], and 1 ml lithium chloride wash buffer [f.c.: 0.25 M LiCl, 1% NP-40/IGEPAL, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0 in nuclease-free water]. Beads were then washed twice for 15 min. with TE buffer [f.c.: 10 mM Tris-HCl pH 8.0, 1 mM EDTA in nuclease-free water] at RT with agitation. Chromatin bound to agarose beads was eluted by incubating with 125 µl elution buffer [f.c.: 1% SDS, 0.1 M NaHCO3 in nuclease-free water] for 15 min. at RT with agitation. The elution was repeated, and fractions combined for a total of 250 µl. Samples were reverse crosslinked by adding NaCl to a final concentration of 0.5 M and incubating overnight at 45°C. RNase A was then added to a final concentration of 0.6 μg/ml and incubated at 37°C for 30 min. Samples were then incubated with EDTA (f.c.: 1 mM), Tris-HCl pH 7.5 (f.c.:4 mM), and proteinase K (0.8 U) for 2 hours at 45°C. DNA was isolated using 2 volumes sparQ beads according to manufacturer’s instructions. ChIP DNA was stored at -20°C until library preparation. Input samples were incubated with 0.6 μg RNase A per µl for 30 min. at 37°C, then incubated with 0.8 U proteinase K overnight at 45°C. DNA was isolated using 2 volumes sparQ beads according to manufacturer’s instructions and stored at -20°C until library preparation.
Libraries from ChIP samples were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB #E6040) or the NEBNext Ultra II DNA library prep kit for Illumina (NEB #E7645) according to manufacturer’s instructions with the following modification. Libraries were amplified using i7 index primers and i5 universal primer (NEBNext multiplex oligos for Illumina index primers set 1 and 2, NEB #E7335 and #E7500) with KAPA HiFi hot start ready mix with the following program: initial denaturation at 98°C for 45 sec.; 15 cycles of (98°C for 15 sec., 55°C for 30 sec., 62°C for 30 sec.); and final extension at 62°C for 5 min. Libraries were purified using 0.9 volumes sparQ beads according to manufacturer’s instructions. Libraires were sequenced with the Illumina HiSeq 2500 or Illumina NextSeq500 to generate 50 bp single-end reads or 75 bp paired-end reads, respectively.

value: Ring (4hpi)

tag: chip antibody

value: Cultures were synchronized to the ring stage by two sorbitol treatments then cultured for 25 hours in the presence of heparin (20 U/ml) to prevent reinvasion of erythrocytes. Once the majority of parasites had developed to the late schizont stage (fully segmented schizonts as assessed by Giemsa stain), the culture was centrifuged at 250 × g for 5 min. at RT to pellet the erythrocytes. The supernatant containing heparin was removed, and the erythrocytes resuspended in complete culture medium (5% hematocrit). The culture was incubated under normal growth conditions (37°C in an atmosphere of 5% O2, 5% CO2, and 90% N2) for 4 hours to allow reinvasion. Following the reinvasion window, mature parasites were removed from the culture by treatment with 5% sorbitol. To ensure complete removal of mature parasites, remaining trophozoite- and schizont-infected erythrocytes were removed by magnetic separation using a MidiMACS separator. Isolated ring stage (4 hpi) parasites were released from erythrocytes by saponin treatment.


title: RNA-seq of Plasmodium blood stages: SZ Rep1

description: SZ 1 Rep1


title: UKK2_hiPSC_Isotretinoin_Day14_R1


title: NIH3T3_WT_SAG_3

value: Fibroblast


title: CEM_Pred_24hr_Rep2

value: ALL


title: ChIP-seq of Plasmodium blood stages: MZ H3K18me

description: 3D7 H3K18me MZ

value: Magentically isolated schizonts (40 hpi) were incubated with E64 for 8 hours and then merozoites were mechanically released by filteration.


title: CEM_CHIR_24hr_Rep1


title: UKK2_hiPSC_Isotretinoin_Day4_R1

value: female

value: proliferating state


title: UKK2_hiPSC_Isotretinoin_Day4_R2


title: ChIP-seq of Plasmodium blood stages: SZ H3K18me

description: 3D7 H3K18me SZ

value: Schizonts (40 hpi) were magnetically seperated from uninfected and ring infected erythrocytes, then released from erythrocytes by saponin treatment.


title: NIH3T3_WT_SAG_1


title: NIH3T3_WT_IHH_3

value: IHH


title: CEM_Ctrl_Rep3


title: UKK2_hiPSC_Isotretinoin_Day4_R3


title: CEM_Ctrl_Rep2


title: ChIP-seq of Plasmodium blood stages: R H3K4me

description: 3D7 H3K4me R


title: UKK2_hiPSC_Isotretinoin_Day1_R2


title: ChIP-seq of Plasmodium blood stages: R H3K4me2

description: 3D7 H3K4me2 R


title: CEM_Ctrl_Rep1


title: NIH3T3_WT_IHH_1


title: UKK2_hiPSC_Isotretinoin_Day1_R3


title: UKK2_hiPSC_Isotretinoin_Day1_R1


title: UKK2_hiPSC_Buspirone_Day14_R2

value: Buspirone


title: UKK2_hiPSC_Buspirone_Day14_R3


title: NIH3T3_WT_DHH_3

value: DHH


title: Nalm6_Dex_24hr_Rep3

value: DEX (100nM, 24hrs)


title: ChIP-seq of Plasmodium blood stages: R H3K4me3

description: 3D7 H3K4me3 R


title: Nalm6_Dex_24hr_Rep2


title: ChIP-seq of Plasmodium blood stages: R H3K9ac

description: 3D7 H3K9ac R


title: UKK2_hiPSC_Buspirone_Day14_R1


title: ChIP-seq of Plasmodium blood stages: R H3K27ac

description: 3D7 H3K27ac R


title: Nalm6_Dex_24hr_Rep1


title: Nalm6_Pred_24hr_Rep1

value: PRED (5uM, 24hrs)


title: NIH3T3_WT_DHH_1


title: NIH3T3_WT_IHH_2


title: NIH3T3_WT_SHH_2

value: SHH


title: TLE1_KO_Dex_24hr_Rep2

source_name: CRISPR/Cas9 edited Nalm6 (ALL cell line)


title: NIH3T3_WT_SHH_1


title: TLE1_KO_Dex_24hr_Rep3


title: UKK2_hiPSC_Buspirone_Day4_R2


title: TLE1_KO_Dex_24hr_Rep1


title: NES_Retnla_Tumor_3

source_name: brain

tag: tissue

value: brain

value: Neuroepithelial cells

value: Retnla overexpression

value: dox


title: NIH3T3_WT_2425_3

value: wildtype


title: NES_Retnla_Tumor_2


title: UKK2_hiPSC_Buspirone_Day4_R1


title: NES_Retnla_Tumor_1


title: UKK2_hiPSC_Buspirone_Day4_R3


title: NIH3T3_WT_2425_1

value: Fibroblast


title: NIH3T3_WT_2425_2


title: UKK2_hiPSC_Buspirone_Day1_R3


title: NIH3T3_WT_SHH_3


title: UKK2_hiPSC_Buspirone_Day1_R2


title: UKK2_hiPSC_Buspirone_Day1_R1


title: NES_Retnla_Control_3

value: water


title: NES_Retnla_Control_1


title: NIH3T3_WT_20S_1


title: NIH3T3_WT_20S_2


title: UKK2_hiPSC_Dmso_Day14_R2

value: Dmso


title: UKK2_hiPSC_Dmso_Day4_R3

value: female


title: UKK2_hiPSC_Dmso_Day14_R1

value: proliferating state


title: UKK2_hiPSC_Dmso_Day4_R1


title: UKK2_hiPSC_Dmso_Day4_R2


title: NIH3T3_WT_20S_3


title: NES_Hsd11b1_Tumor_2

value: Hsd11b1 overexpression


title: NIH3T3_WT_7B27_3


title: NES_Hsd11b1_Tumor_1


title: BCC_Tumor_8

source_name: Skin

value: Skin

value: mixture

value: tumor

value: malignant


title: NIH3T3_WT_BSA_2

value: BSA


title: NIH3T3_WT_BSA_3


title: BCC_Tumor_7


title: BCC_Tumor_6


title: NES_Hsd11b1_Tumor_3


title: BCC_Tumor_9


title: NIH3T3_WT_7B27_1


title: NIH3T3_WT_BSA_1


title: NIH3T3_WT_DHH_2

value: DHH


title: NIH3T3_WT_7B27_2


title: NIH3T3_WT_ETOH_3

value: ETOH


title: BCC_Tumor_5


title: NIH3T3_WT_ETOH_2


title: BCC_Tumor_4


title: UKK2_hiPSC_Dmso_Day14_R3


title: NIH3T3_WT_ETOH_1


title: BCC_Tumor_3


title: UKK2_hiPSC_Dmso_Day1_R2


title: UKK2_hiPSC_Control_Day4_R3

value: Control


title: UKK2_hiPSC_Dmso_Day1_R3


title: UKK2_hiPSC_Control_Day14_R2


title: BCC_Tumor_2


title: UKK2_hiPSC_Control_Day4_R2


title: NIH3T3_WT_DMSO_2

value: DMSO


title: NES_Retnla_Control_2

value: brain

value: Neuroepithelial cells

value: Retnla overexpression


title: BCC_Tumor_1


title: NIH3T3_WT_DMSO_1

value: Fibroblast

value: wildtype


title: UKK2_hiPSC_Control_Day14_R1

value: female


title: BCC_Normal_9

value: normal


title: UKK2_hiPSC_Dmso_Day1_R1

value: proliferating state

value: Dmso


title: UKK2_hiPSC_Control_Day14_R3


title: BCC_Normal_8

value: Skin

value: mixture


title: UKK2_hiPSC_Control_Day4_R1


title: SMK_WT_C_TM2_SCI_EAE-1

first: Han

last: Gao

state: Guangdong

address: 600 Tianhe RD

institute: The Third Affiliated Hospital of Sun Yat-sen University

description: Sample multiplexing tag

data_processing:
Sequencing reads filtering and alignment were conducted using the BD RhapsodyTM Single-Cell Analysis system.
Read pairs with low sequencing quality are removed according to read length, mean base quality score, and highest single nucleotide frequency (SNF). Then the remaining reads were aligned to the mm10 genome by calling STAR.
BD Biosciences developed UMI adjustment recursive substitution error correction (RSEC) algorithm to remove artifact molecules.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell
Supplementary files format and content: Metadata for every cell

source_name: spinal cord

extract_protocol:
Spinal cords were enzymatically dissociated into single-cell suspensions with a papain-based Neural Dissociation Kits (Miltenyi, #130-092-628). Myeloid cells were enriched by positive selection with CD11b Microbeads (Miltenyi, #130-049-601) after myelin removal using Myelin Removal Beads (Miltenyi, #130-096-433), according to manufacturer’s protocols. Different single-cell suspension samples were mixed together using BDTM Single-cell Multiplexing Kits (BD, #633793) for high sample throughput and batch effects elimination purposes.
Library preparations were performed using the BD RhapsodyTM system according to the manufacturer’s protocol.
Sequencing was conducted using Illumina Novaseq 6000 PE150

value: spinal cord

value: myeloid cells

value: SCI and EAE


title: NIH3T3_WT_DMSO_3


title: WTA_WT_C_TM2_SCI_EAE-1

description: Single-cell transcriptome part4


title: BCC_Normal_5


title: UKK2_hiPSC_Control_Day1_R2


title: BCC_Normal_4


title: S1-CD4cre

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: MRC - Laboratory of Molecular Biology

description: 10x Genomics

data_processing:
For each library the reads were aligned to the mouse transcriptome (GRCm38) and expression calculated using the 10X Cellranger (v6.0.1) wrapper for the STAR aligner (Spliced Transcripts Alignment to a Reference, Alexander Dobin)
They were then combined with Cellranger.
Assembly: GRCm38
Supplementary files format and content: Cloupe file

source_name: Lung

extract_protocol:
FACS purified cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) to obtain nuclei extract
10X Single cell library preparation was performed using the 10X Genomics technology platform. The 10X Genomics Chromium Single Cell 3’ v3 protocol was followed to obtain separate 3’ libraries for each sample for subsequent sequencing.

treatment_protocol: Mice were anesthetized by isoflurane inhalation followed by the intranasal injection of papain (7.5 mg, Sigma-Aldrich #76216) in 40 ml PBS on days 0 and 14. On day 19, lung lymphocytes were isolated by FACS.

value: naive CD4+CD44-CD62L+CD25- T cells and CD4+CD44+CD62L-ST2+ effector T cells

value: Lung

tag: strain

tag: age

value: 6-8 weeks old


title: UKK2_hiPSC_Control_Day1_R1

tag: gender

value: Control


title: BCC_Normal_3


title: UKK2_hiPSC_Control_Day1_R3

tag: state


title: NEB, 3' OH and blocked oligo mix

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
For LIDAR, LIDAR3 and NEB samples: Adapter trimming with TrimGalore v0.6.4: --length 5 --paired --retain_unpaired -r 20 -r 100. For NEB samples, additional trimming step with Cutadapt v 4.2: cutadapt -A GATCGTCGG --minimum-length 5 --paired-filter any
Samples with UMI (LIDAR, LIDAR-3): UMIs were extracted using umi_tools v1.1.2 with the regex ".*(?<umi_1>.{7})CG(?P<umi_2>.{2})AG(?P<umi_3>.{2})GGG" and remaining constant bases were trimmed with Cutadapt (cutadapt --minimum-length 5 -g CGAGGGG), then TSO dimers were removed with Cutadapt (cutadapt -e 3 -b CGTCAGATGTGTATAAGAGACAG --discard-trimmed)
Reads were mapped sequentially with STAR v2.7.10a to consensus rRNA repeats (BK000964.3), snoRNA from GENCODE vM27, snRNA from GENCODE vM27, piRNA from piRbase v3.0 using bowtie2 ver2.5.0, and tRNA from GtRNAdb and tRNAscan-SE as curated by Nedialkova et al. using GSNAP ver 2019-02-26 with SNP database provided, then to a custom GRCm39 genome with all of the sequences above masked and provided as extra scaffolds, using STAR (paired reads with inserts > 100nt) or bowtie2 (paired reads with inserts < 100nt and single reads)
Samples with UMI (LIDAR, LIDAR-3): bam files were deduplicated using umi_tools dedup with method --unique
Only reads with fragment length >=15 were retained for downstream analysis
Assembly: GRCm39
Supplementary files format and content: tab delimited files include raw counts corresponding to each gene (counts.genes.txt) or biotype, including reads mapped to non-annotation regions (counts.biotypes.txt)

organism: synthetic construct

source_name: synthetic oligos

extract_protocol:
For ESC and NPC, cell pellets were resuspended in 1ml of TriPure and RNA was extracted following standard protocol. DNA was digested with Turbo DNase-I at 37°C for 30min, RNA was re-purified using TriPure, and resuspend in 10mM Bis/Tris pH=6.7, 0.1mM EDTA. For mouse sperm, sperm were resuspended in 120 ul of water and 66 μl of Sperm_lysis_buffer were added [120mM Tris-HCl (pH=8), 6.4M Guanidine-HCl, 5% Tween-20, 5% Triton-X-100, 120mM EDTA]. Proteins were digested by adding 6.6 μl of 20 mg/ml proteinase K and 6.6 μl of 1M DTT, followed by incubation at 60°C for 15 min under 600 rpm constant shaking. Volume was adjusted with water to 400 μl and 400 μl of TriPure were added. RNA was extracted by adding 120 μl of BCP Phase Separation Reagent and precipitated with isopropanol. DNA was digested with Turbo DNase-I at 37°C for 30min, RNA was re-purified using TriPure, and resuspend in modBTE buffer (10mM Bis/Tris pH=6.7, 0.1mM EDTA). For enrichment of <200nt RNAs, the Zymo RNA Clean and Concentrator-5 kit was used, starting from 1ug of total RNA. For enrichment of <50nt RNAs, 18ug of total RNA were run on a denaturing 12% polyacrylamide-urea gel, and bands between 10nt and 50nt were excised. Gel pieces were shredded trough pierced 0.5ml tubes, and RNA was elute from the gel by overnight incubation in 400μl RNA elution buffer (10mM Bis/Tris pH=6.7, 300mM NaCl, 10mM EDTA) at 4°C with constant rotation. Eluate was filtered though 5μm PVDF spin filters, and RNA was precipitated by adding 1μl of Glycoblue, 40μl of 3M NaOAc pH=5.2, and 1.1ml of ice-cold 100% EtOH, followed by incubation at -80°C for 1h. RNA was pelleted at 20000g for 30min (4°C), washed once with 1ml of 70% EtOH, once with 1ml of 80% EtOH, air-dried for 5 min, and resuspended in modBTE buffer.
LIDAR and LIDAR-3 library preparation  The desired amount of total and fractionated RNAs was diluted to 1μl and mixed with 0.4μl of 10μM LIDAR_RT_primer (/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNND). To anneal the LIDAR_RT_primer to the template RNA, samples were heated to 65°C for 5 min, then temperature was lowered to 4°C (0.5°C/s). To initiate retrotranscription, 6.28μl of RT_mix [25mM Tris-HCl pH=8.3, 20mM NaCl, 2.5mM MgCl2, 8mM DTT, 5% PEG-8000, 0.5mM dNTPs, 1mM GTP, 0.5 U/μl Murine RNase inhibitor, and 2U/μl Maxima H-minus Reverse Transcriptase – concentrations refer to a final volume of 8 μl] were added and samples were incubated at 25°C for 10 min. To further promote cDNA synthesis and template switch, temperature was raised to 42°C, 0.32μl of 50μM LIDAR_TSO_mix (equimolar ratio of the following oligos: /5Biosg/CGTCAGATGTGTATAAGAGACAGtgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhtgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhmtgNNcgNNagNNrGrGrG) were added, and samples were incubated at 42°C for 80 min, followed by 10 cycles at 50°C for 2 min and 42°C for 2 min, then at 85°C for 5 min. To pre-amplify and add adapters to cDNA, 12μl of KAPA_mix [1X KAPA HiFi HotStart buffer Ready Mix, 0.5μM LIDAR_preamp_f (TCGTCGGCAGCGTCAGATGTGTATAAGAGAC*A*G), and 0.1μM LIDAR_preamp_r (GTCTCGTGGGCTCGGAGA) – concentrations refer to a final volume of 20 μl]  were added and samples were incubated with the following PCR cycling conditions: denaturation (95°C for 3 min), 18 cycles of amplification (98°C for 20s, 70°C for 30s, 72°C for 30s), final extension (72°C for 5 min). Quality of adapter-containing libraries was assessed by loading 5ul on a 2% agarose gel. To generate the final libraries, 2μl of pre-amplified were diluted to 37μl with 10mM Tris-HCl pH=8, 0.5μl of each 10μM custom Nextera indexing primers was added, followed by 12μl of Q5_mix [1X Q5 buffer, 0.5mM dNTPs, 0.02 U/µl Q5 High-Fidelity DNA Polymerase (Cat. No M0491, New England Biolabs) – concentrations refer to a final volume of 50 μl]. Samples were incubated with the following PCR cycling conditions: denaturation (98°C for 30 sec), 18 cycles of amplification (98°C for 10s, 65°C for 20s, 72°C for 20s), final extension (72°C for 2 min). Indexed libraries were purified using 2.3X SPRI beads and eluted in 50μl of TE buffer (10mM Tris-HCl pH=8, 1mM EDTA).  For LIDAR-3, the LIDAR-3_RT_oligo was generated by mixing equimolar amounts of LIDAR-3_RT_sense (/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNNN) and LIDAR-3_RT_antisense (CdUGdUCdUCdUdUAdUACACAdUCdUCCGAG/3ddC/), followed by heating at 95°C for 5 min, and a slow cool down to 25°C (0.1°C/s). To prepare LIDARsp libraries, 1μl of input RNA was first denatured at 70°C for 2 min, then temperature was lowered to 50°C and 0.4μl of 1μM LIDAR-3_RT_oligo were added. Samples were incubated at 50°C for further 2min, then temperature was lowered to 4°C (0.5°C/s). To initiate retrotranscription, 6.28μl of RT_mix were added and samples were incubated at 25°C for 10 min. To further promote cDNA synthesis and template switch, temperature was raised to 42°C, 0.32μl of 50μM LIDAR_TSO_mix were added, and samples were incubated at 50°C for 80 min, followed by 10 cycles at 55°C for 2 min and 50°C for 2 min, then at 85°C for 5 min. LIDAR-3_RT_antisense was digested by adding 1ul of USER II enzyme and incubating at 37°C for 30 min. USER II was heat inactivated by incubation at 65°C for 10 min. To pre-amplify and add adapters to cDNA, 12μl of KAPAsp_mix [1X KAPA HiFi HotStart buffer Ready Mix, 2μM LIDAR_preamp_f (TCGTCGGCAGCGTCAGATGTGTATAAGAGAC*A*G), and 0.5μM LIDAR_preamp_r (GTCTCGTGGGCTCGGAGA) – concentrations refer to a final volume of 20 μl] were added and samples were incubated with the following PCR cycling conditions: denaturation (95°C for 3 min), 6 cycles of 3-step amplification (98°C for 20s, 63°C for 30s, 72°C for 30s), 12 cycles of 2-step amplification (98°C for 20s, 72°C for 50s), final extension (72°C for 5 min). Quality of adapter-containing libraries was assessed by loading 5ul on a 2% agarose gel. To generate the final libraries, 2μl of pre-amplified were diluted to 37μl with 10mM Tris-HCl pH=8, 1μl of each 10μM custom Nextera indexing primers was added, followed by 12μl of Q5sp_mix [1X Q5 buffer, 0.5mM dNTPs, 0.02 U/µl Q5 High-Fidelity DNA Polymerase – concentrations refer to a final volume of 50 μl]. Samples were incubated with the following PCR cycling conditions: denaturation (98°C for 30 sec), 7 cycles of amplification (98°C for 10s, 65°C for 20s, 72°C for 20s), final extension (72°C for 5 min). Indexed libraries were purified using 2.4X SPRI beads and eluted in 50μl of TE buffer (10mM Tris-HCl pH=8, 1mM EDTA).   Small RNA-seq and mRNA-seq library preparation  Small RNA libraries were prepared using the NEBnext Small RNA Library Prep Set for Illumina (Cat. No E7330S, New England Biolabs), following the standard protocol with the following parameters: 1) 1:2 dilution of 3’SR Adaptor, SR RT Primer, and 5’SR Adaptor 2) 15 indexing PCR cycles 3) cleanup of final libraries with QIAgen MinElute PCR purification kit, followed by a second cleanup with 2X SPRI. Libraries were analyzed on a 6% non-denaturing polyacrylamide gel.  For mRNA-seq libraries, polyA RNA was enriched from 2 μg total RNA using Dynabeads Oligo(dT)25. Poly-A-enriched fraction was used for library construction using the NEBnext Ultra II Directional Library Prep Kit for Illumina (Cat. No. E7760L, New England Biolabs), following the standard protocol but using half the reaction volumes recommended. Libraries were analyzed on a 2% agarose gel.  Both small RNA-seq and mRNA-seq libraries were quantified using NEBNext Library Quant Kit for Illumina (Cat. No E7630L, New England Biolabs). Libraries were sequenced on an Illumina NextSeq500 instrument.

treatment_protocol: C57BL/6 mouse embryonic stem cells (ESC) were purchased from ATCC (SCRC-1002) and maintained onto 1% gelatin-coated dishes in DMEM knockout medium supplemented with 15% ES-grade Fetal Bovine Serum, 1% GlutaMAX, 1% Non-essential aminoacids, 0.5% Penicillin/Streptomycin solution, 110μM β-mercaptoethanol, 100 units/ml Leukemia Inhibitory Factor (LIF), 3μM GSK-3 Inhibitor XVI, 1 μM MEK1/2 Inhibitor III. Cells were passaged through trypsinization (0.05%) every 2–3 days. Prior to neuronal progenitor cells (NPC) differentiation, embryonic stem cells that were maintained in N2B27 serum-free medium consisting of 1:1 mix of Neurobasal medium and DMEM/F12, supplemented with 1X N2, 1X B27, 1% GlutaMAX, 1% Non-essential aminoacids, 0.5% Penicillin/Streptomycin, 55μM β-mercaptoethanol, 100 units/ml Leukemia Inhibitory Factor (LIF), 3μM GSK-3 Inhibitor XVI, 1 μM MEK1/2 Inhibitor III. For NPC differentiation differentiation, Epiblast-like cells (EpiLC) were induced from ESC in N2B27 serum-free medium (without 2i and LIF) supplemented with 40μg/ml of BSA, and 10ng/ml bFGF for 72h. EpiLC were treated with 500nM SAG in N2B27 serum-free medium (without 2i and LIF) for 48h to generate NPC.

value: synthetic oligos

tag: input amount_(ng)


title: BCC_Normal_2


title: UKK2_hiPSC_untreated_Day 0_R3

value: pluripotent state

tag: agent

value: untreated

tag: time point

value: Day 0


title: UKK2_hiPSC_untreated_Day 0_R1

value: female


title: LIDAR, 8N oligo mix


title: UKK2_hiPSC_untreated_Day 0_R2


title: Spinal Cord H5/H5 Sample 1

city: Bar Harbor

first: George

middle: C

last: Murray

state: ME

address: 600 Main St.

department: Research

institute: The Jackson Laboratory

data_processing:
nf-core RNASeq pipline v3.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Quality was assessed using FASTQC
Trimmed sequence reads were mapped to GRCm38/mm10 using Star
Read count extraction and normalization were performed using RSEM
Assembly: GRCm38 - mm10
Supplementary files format and content: tab-delimited text files include RSEM expected counts, TPM, and FPKM values for each Sample

extract_protocol:
Total RNA was isolated from tissue using the NucleoMag RNA Kit (Macherey-Nagel) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in MR1 buffer (Macherey-Nagel) using a gentleMACS dissociator (Miltenyi Biotec Inc). RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA ScreenTape Assay (Agilent Technologies).
Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.
Libraries were sequenced 150 bp paired-end on an Illumina NovaSeq 6000 using the S4 Reagent Kit v1.5.

tag: Sex

value: F

tag: age (wk)


title: LIDAR3, 3' OH and blocked oligo mix

tag: cell line


title: WTA_WT_C_TM2_SCI_EAE-2

description: Single-cell transcriptome part5

tag: cell type


title: Spinal Cord H5/H5 Sample 2

value: M

tag: genotype


title: Bulk RNA-Seq, Control, Cd49f+ 17GW fetal tissue _2

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

description:
40 million PE reads
fetal_tissue_feature_counts.txt

data_processing:
Fastq files were first trimmed using Trimmomatic and mapped using STAR aligner with the paired end option selected (hg38)
We used FeatureCounts to assemble transcripts and generate raw count matrices. Following generation of raw count data, we used DESeq2 to normalize matrices and to determine differential gene expression statistics.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw expression values for each sample.

source_name: purified human fetal cells

growth_protocol: Human cortical organoids: Following 3D formation, spheroids were treated daily in neural induction media (DMEM/F12, KSR, NEAA, Glutamax, Pen/Strep, Beta-mercaptoethanol) supplemented with Dorsomorphin (Sigma, Cat. 142  P5499-25MG, 5 μM) and SB-431542 (Selleck Chemicals, Cat. S1067, 10 μM) for 6 days.  Following this treatment, organoids were treated daily with neural media supplemented with EGF (R&D Systems, Cat. 236-EG-01M, 20 ng/mL) and FGF2 (R&D Systems, Cat. 233-FB-01M, 20 ng/mL) for 10 days, and every other day for days 16-24. At day 25, organoids were treated every other day with neural media supplemented with BDNF (PeproTech, Cat. 450-02- 1mg, 20 ng/mL) and NT-3 (R&D Systems, Cat. 267-N3-005/CF, 20 ng/mL) to promote differentiation of progenitors. From day 43 onwards, organoids were fed every 3 days with neural media only.

extract_protocol:
RNA was harvested using miRneasy kit (Qiagen).
RNA libraries for RNA-seq were prepared using the NEB Next Ultra II kit using poly-A selection following manufacturer's protocols.

treatment_protocol:
Additon of ligands TGFB2, NLGN1, TSLP, DKK1, and BMP4
Purified human fetal tissue: Purified cells were spun and plated on poly-D-lysine-coated plastic coverslips in a Neurobasal/DMEM-based serum-free medium. We replaced the media every other day for 12 days with or without ligand addition.

value: purified human fetal cells

value: immature astrocytes

tag: treatment


title: BCC_Normal_1

value: Skin

value: mixture

value: wildtype

value: normal


title: Spinal Cord DBA/1J Sample 3

value: spinal cord

value: DBA-WT


title: Bulk RNA-Seq, Control, Cd49f+ 17GW fetal tissue _1


title: BCC_Normal_6


title: S2-CD4creADNPflox

description: 10x Genomics

value: naive CD4+CD44-CD62L+CD25- T cells and CD4+CD44+CD62L-ST2+ effector T cells

value: Lung

value: 6-8 weeks old


title: Spinal Cord DBA/1J Sample 2


title: LIDAR, 3' OH and blocked oligo mix

value: synthetic oligos


title: Bulk RNA-Seq, Control, Cd49f+ 19GW fetal tissue _2

value: Control


title: NEB,  8N oligo mix


title: keratinocytes, MPXV clade I, no2

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

description:
TPM_for_GEO_upload_skin.txt
skin_Congo_2

data_processing:
Sequencing was performed on an Illumina NextSeq500 platform in a 76-base single-end mode.
Illumina RTA version 2.11.3 and  bcl2fastq version 2.17 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt v3.4. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.9a with the GENCODE (release 36, GRCh38.p13) gtf file.
The raw counts for protein-coding genes were calculated using htseq-count v0.13.5 with the GENCODE gtf file.Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: Normal Human Epidermal Keratinocytes

growth_protocol: Normal human epidermal keratinocytes   NHEK-Ad (Normal Human Epidermal Kerationocytoes-Adult, Cat# 00192627, Lonza) were cultured with KGM-Gold Keratinocyte Growth Medium BulletKit (Cat# 00192060, Lonza). NHEK-Ad were seeded on 24-well cell culture plates (2.0×104 cells/2 cm2) and cultured for 7 days.    Human iPS cell-derived colon organoids   The iPS cell line, 1383D6, was maintained on 0.5 μg/cm2 recombinant human laminin 511 E8 fragments (iMatrix-511, Cat# 892 012, Nippi) with StemFit AK02N medium (Cat# RCAK02N, Ajinomoto) containing 10 μM Y-27632 (Cat# 034-24024FUJIFILM Wako Pure Chemical). To passage the cells, iPS cell colonies were treated with TrypLE Select Enzyme (Cat# 12563029, Thermo Fisher Scientific) for 10 min at 37°C. After the centrifugation, the cells were seeded on Matrigel® Growth Factor Reduced Basement Membrane (Cat# 354230, Corning)-coated cell culture plates (2.0×105 cells/4 cm2) and cultured for 2 days. To perform definitive endoderm differentiation, human iPS cells were treated with 100 ng/mL Activin A (Cat# 338-AC-01M, R&D Systems) and 10 μM Y-27632 in RPMI1640 medium (Cat# R8758-500, Sigma-Aldrich) supplemented with 1×B-27 Supplement Minus Vitamin A (Cat# 12587001, Thermo Fisher Scientific), 1×GlutaMAX (Cat# 35050-079, Thermo Fisher Scientific), and 1×Penicillin-Streptomycin for 3 days. To perform hindgut differentiation, the cells were treated with 200 ng/uL FGF2 (Cat# 160-0010-3, Katayama Chemical Industries) in RPMI1640 medium supplemented with 1×B-27 Supplement Minus Vitamin A, 1×GlutaMAX, and 1×Penicillin-Streptomycin for 4 days. To generate colon organoids, the cells were dissociated and embedded in Matrigel Growth Factor Reduced Basement Membrane to generate organoids. To perform colonic differentiation, the cells were treated with 3 μM CHIR99021 (Cat# 034-23103, FUJIFILM Wako Pure Chemical), 0.5 μM A-83-01 (Cat# 035-24113, FUJIFILM Wako Pure Chemical), 50 ng/mL Noggin (Cat# 120-10C, PeproTech), 30 ng/uL Forskolin (Cat# 063-02193, FUJIFILM Wako Pure Chemical), and 50 ng/ml EGF (Cat# AF-100-15, PeproTech) in advanced DMEM/F12 supplemented with 1×N2 (Cat# 141-08941, FUJIFILM Wako Pure Chemical), 1×B-27 Supplement Minus Vitamin A, 1×GlutaMAX, 0.05% bovine serum albumin, and 1×penicillin-streptomycin for 13 days. To perform the infection experiments, the colon organoids were recovered from Matrigel, and the suspension of colon organoids (small free-floating clumps) was seeded onto Matrigel-coated 24-well cell culture plates (1.0×105 cells/2 cm2) and cultured for 3 days.

extract_protocol:
Total RNA was isolated from infected keratinocytes and colon organoids using ISOGENE (NIPPON GENE).
The library preparation was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Human iPS cell-derived colon organoids or keratinocytes were infected with MPXV (0.05 multiplicity of infection (MOI)) and cultured for 72 h. Three MPXV strains (clade I/Zr-599, clade IIa/Liberia, clade IIb/MPXV-2022) were used in this experiment.

value: Normal Human Epidermal Keratinocytes

value: keratinocytes

value: wild type

value: MPXV clade I infected

tag: time

value: 3 dpi


title: Spinal Cord H4/H4 Sample 4

value: M


title: keratinocytes, MPXV clade I, no3

description:
TPM_for_GEO_upload_skin.txt
skin_Congo_3


title: Spinal Cord DBA/1J Sample 1


title: ZO1_capillary_3

first: Raleigh

middle: Miller

last: Linville

state: MA

address: 43 Vassar St

institute: Massachusetts Institute of Technology

data_processing:
Reads were aligned to GRCh38.p13 using STAR v2.7.10b
Reads were assigned to genes using Subread v2.0.6 to generate raw counts
The median of ratios method was used to generate normalized counts using DESeq2 v1.30.1
Assembly: hg38
Supplementary files format and content: txt file of raw counts
Supplementary files format and content: txt file of normalized counts

source_name: iPSC-derived endothelial cell

extract_protocol:
differentiation protocols: iECs and iBMECs were differentiation from the WTC-ZO1 iPSC line (AICS-0023 cl.20) following previously published protocols (see PMID: 36333694).  Standard culture mediums were used for the duration of experiments.
lentivirus production: For each transcription factor, a Gateway-compatible pShuttle vector containing untagged an ORF and a stop codon were obtained and inserted into a doxycycline-inducible backbone pLIX401 (Addgene # 41393) following Genecopoeia protocols.  A third-generation lentivirus system was employed using plasmids pRSV-Rev (Addgene #12253), pMDLg/pRRE (Addgene #12251), and pMD2.G (Addgene #12259).  A Lenti-X™ qRT-PCR Titration Kit (Takara #631235) was used to calculate physical titer following manufacturer guidelines, with functional titer determined using a control virus expression EYFP.
transduction protocol (iEC only): ~3350 iECs were plated into each well of a 96-well plate and immediately exposed to lentivirus particles at an MOI of ~3-5 (based on functional titer estimated using pLIX401.EYFP virus. Transduction efficiency was improved by using 10 ug/mL polybrene for 1 hour at RT at 800g in a swinging bucket centrifuge (spinfection), control iECs were not transduced but still exposed to polybrene.
transduction protocol: After 1 hour spinfection, media was replenished and cells were cultured for 48 hours. Then transduced cells were selected (0.5 ug/mL puromycin) for 3 days. Then expression of transgene was induced (10 ug/mL doxycycline) for 3 days.
Monolayers on 96 well plates were washed with 1xPBS, treated with 0.25% trypsin-EDTA for 10 minutes, and then spun down in a V-bottom 96 well plate (x3) to thoroughly wash.
SMART-Seq mRNA LP kit (Takara Bio #634769) was used according to manufacturer protocols.

value: iPSC-derived endothelial cell

tag: transduction

value: capillary combination (LEF1, KLF2, TSC22D1, FOXP1)

value: puromycin selection and doxycycline exposure

tag: culture time_prior_to_lysis

value: 8 days


title: Spinal Cord H4/H4 Sample 3

tag: tissue

value: spinal cord


title: Bulk RNA-Seq, Control, Cd49f+ 19GW fetal tissue _1

value: purified human fetal cells

value: immature astrocytes


title: ZO1_venous_3

value: venous combination (PPARD, FLI1, TSHZ2)


title: keratinocytes, MPXV clade IIb, no3

description:
TPM_for_GEO_upload_skin.txt
skin_2022_3

value: MPXV clade IIb infected


title: ZO1_capillary_1


title: Spinal Cord H4/H4 Sample 2

value: F


title: ZO1_capillary_2


title: Spinal Cord H4/H4 Sample 1


title: Spinal Cord H5/H5 Sample 3


title: Bulk RNA-Seq, Control, Cd49f+ 20GW fetal tissue _2

value: Control


title: Bulk RNA-Seq, Control, Cd49f+ 20GW fetal tissue _1


title: ZO1_arterial_3

value: arterial combination (PRDM16, HEY1)


title: ZO1_venous_2


title: UKK2_hiPSC_Isotretinoin_Day14_R2

value: female

value: proliferating state

value: Isotretinoin


title: keratinocytes, MPXV clade IIb, no2

description:
TPM_for_GEO_upload_skin.txt
skin_2022_2

value: Normal Human Epidermal Keratinocytes

value: keratinocytes

value: wild type

value: 3 dpi


title: ZO1_venous_1

value: iPSC-derived endothelial cell

value: puromycin selection and doxycycline exposure


title: Bulk RNA-Seq, Ligand exposed, Cd49f+ 17GW fetal tissue _3

value: Ligand cocktail-exposed


title: Spinal Cord H3/H3 Sample 4

value: spinal cord

value: M


title: Bulk RNA-Seq, Control, Cd49f+ 19GW fetal tissue _3

value: purified human fetal cells

value: immature astrocytes


title: ZO1_arterial_2

value: 8 days


title: keratinocytes, MPXV clade IIb, no1

description:
TPM_for_GEO_upload_skin.txt
skin_2022_1

value: MPXV clade IIb infected


title: Bulk RNA-Seq, Ligand exposed, Cd49f+ 17GW fetal tissue _2


title: Bulk RNA-Seq, Ligand exposed, Cd49f+ 17GW fetal tissue _1


title: keratinocytes, MPXV clade IIa, no3

description:
TPM_for_GEO_upload_skin.txt
skin_west_Africa_3

value: MPXV clade IIa infected


title: Spinal Cord H3/H3 Sample 3

value: F


title: keratinocytes, MPXV clade I, no1

description:
TPM_for_GEO_upload_skin.txt
skin_Congo_1

value: MPXV clade I infected


title: Spinal Cord H3/H3 Sample 2


title: keratinocytes, MPXV clade IIa, no1

description:
TPM_for_GEO_upload_skin.txt
skin_west_Africa_1


title: ZO1_control_3

value: doxycycline exposure


title: Bulk RNA-Seq, Ligand exposed, Cd49f+ 19GW fetal tissue _2


title: Bulk RNA-Seq, Ligand exposed, Cd49f+ 19GW fetal tissue _3


title: ZO1_control_2


title: Spinal Cord H3/H3 Sample 1


title: ZO1_control_1


title: Spinal Cord H2/H2 Sample 4


title: keratinocytes, mock, no2

description:
TPM_for_GEO_upload_skin.txt
skin_mock_2

value: Normal Human Epidermal Keratinocytes

value: mock


title: keratinocytes, mock, no3

description:
TPM_for_GEO_upload_skin.txt
skin_mock_3

value: keratinocytes

value: wild type


title: Spinal Cord H2/H2 Sample 3


title: Spinal Cord H2/H2 Sample 2


title: keratinocytes, mock, no1

description:
TPM_for_GEO_upload_skin.txt
skin_mock_1

value: 3 dpi


title: Bulk RNA-Seq, Ligand exposed, Cd49f+ 19GW fetal tissue _1


title: iBMEC_4

source_name: iPSC-derived brain microvascular endothelial-like cells

value: 2 days


title: iBMEC_3

value: iPSC-derived brain microvascular endothelial-like cells


title: ZO1_arterial_1

value: iPSC-derived endothelial cell

value: arterial combination (PRDM16, HEY1)

value: puromycin selection and doxycycline exposure


title: Bulk RNA-Seq, Ligand exposed, Cd49f+ 20GW fetal tissue _3

value: purified human fetal cells

value: immature astrocytes

value: Ligand cocktail-exposed


title: iBMEC_2


title: keratinocytes, MPXV clade IIa, no2

description:
TPM_for_GEO_upload_skin.txt
skin_west_Africa_2

value: MPXV clade IIa infected


title: colon organoids, MPXV clade I, no3

description:
TPM_for_GEO_upload_colon.txt
colon_Congo_3

source_name: iPS cell-derived colon organoids

value: iPS cell-derived colon organoids

value: colon organoids


title: colon organoids, MPXV clade I, no2

description:
TPM_for_GEO_upload_colon.txt
colon_Congo_2

value: MPXV clade I infected


title: Spinal Cord H2/H2 Sample 1

value: spinal cord

value: F


title: Spinal Cord H1/H1 Sample 2


title: Spinal Cord H1/H1 Sample 3

value: M


title: Bulk RNA-Seq, Ligand exposed, Cd49f+ 20GW fetal tissue _1


title: Bulk RNA-Seq, 8858.3, Control, day 90-120_6

description:
40 million PE reads
8858-3_feature_counts.txt

source_name: organoid

value: organoid

value: Control


title: iBMEC_1

value: 2 days


title: Bulk RNA-Seq, Ligand exposed, Cd49f+ 20GW fetal tissue _2


title: colon organoids, MPXV clade IIb, no3

description:
TPM_for_GEO_upload_colon.txt
colon_2022_3

value: wild type

value: MPXV clade IIb infected

value: 3 dpi


title: Bulk RNA-Seq, 8858.3, Control, day 90-120_5


title: Spinal Cord H1/H1 Sample 1


title: Bulk RNA-Seq, 8858.3, Control, day 90-120_4


title: Bulk RNA-Seq, 8858.3, Control, day 90-120_3


title: colon organoids, MPXV clade IIb, no2

description:
TPM_for_GEO_upload_colon.txt
colon_2022_2


title: Spinal Cord C57BL/6J Sample 2


title: G7 - Donor 1 confluency passage 2

city: Maastricht

first: Vanessa

last: LaPointe

address: Universiteitssingel 40

country: Netherlands

institute: MERLN Institute

description: 10x genomics

data_processing:
The BCL files resulting from sequencing were transformed to FASTQ files with 10× Genomics Cell Ranger mkfastq following its mapping with Cell Ranger count. During sequencing, Read 1 was assigned 28 bp, and were used for identification of the Illumina library barcode, cell barcode and unique molecular identifier (UMI). R2 was used to map the human reference genome GRCh38. Filtering of empty barcodes was done in Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Corneal endothelium

growth_protocol: Human corneal endothelial cells were isolated and cultured as previously reported.5 Briefly, the stripped endothelium–Descemet’s layer was incubated with 2 mg/ml collagenase A (Roche) solution in human endothelial serum free media (SFM) (Thermo Fisher Scientific) for 2–5 h at 37°C followed by a 5 min incubation in TrypLE express (Thermo Fisher Scientific) to generate small clumps of corneal endothelial cells. Cells from each cornea were seeded equally across 2 wells of a 24-well plate coated with fibronectin collagen (FNC) coating mix (Athena Enzyme Systems) in M5 stabilization media (human endothelial SFM (Thermo Fisher Scientific) supplemented with 5% fetal bovine serum (FBS), 100 U/mL penicillin–streptomycin, and 0.25 μg/mL amphotericin B) supplemented with 10 μM Y-27632 (STEMCELL Technologies). Subsequently, corneal endothelial cells were cultured in M4 proliferation medium (1:1 Ham’s F12 (Thermo Fisher Scientific) and M199 (Thermo Fisher Scientific) supplemented with 5% FBS, 20 μg/mL ascorbic acid (Sigma), 1 × ITS (Thermo Fisher Scientific), 10 ng/mL human recombinant bFGF (Sigma), and 10 μM Y-27632 (STEMCELL Technologies)); media was refreshed every other day. Upon reaching 90% confluency, after approximately 8–10 days of culture, cells were cultured in M5 stabilization media for 7 days. After this, corneal endothelial cells were treated with TripLE express and passaged into wells pre-coated with FNC-coating mix at a seeding density of 10,500 cells/cm2 in M5 stabilization medium. All cell culture was performed in incubators with humidified atmosphere of 37°C and 5% CO2.

extract_protocol: scRNAseq of primary cultured CECs wasperformedat Single Cell Discoveries (Utrecht, the Netherlands)followingstandard 10× Genomics 3’V3.1chemistry protocol.Cells were rehydrated and loaded on the 10× Chromium controller as follows. Approximately 10,000 cells were loaded per each sample. Sequencing libraries were prepared following a standard 10× Genomics protocol and sequenced with an Illumina NovaSeq 6000 platform; read length: 150 bp, paired-end.

value: Corneal endothelium

value: primary corneal endothelial cells

value: Caucasian Male

value: primary culture


title: G8 - Donor 2 confluency passage 1

description: 10x genomics


title: Spinal Cord C57BL/6J Sample 3


title: G9 - Donor 2 confluency passage 2

description: 10x genomics


title: colon organoids, MPXV clade IIa, no3

description:
TPM_for_GEO_upload_colon.txt
colon_west_Africa_3

value: MPXV clade IIa infected


title: G6 - Donor 1 confluency passage 1

description: 10x genomics


title: Bulk RNA-Seq, 8858.3, Control, day 90-120_2


title: Bulk RNA-Seq, 8858.3, Control, day 90-120_1


title: G5 - Donor 1 confluency passage 0

description: 10x genomics


title: Spinal Cord C57BL/6J Sample 1


title: Cerebellum H5/H5 Sample 3

source_name: cerebellum

value: cerebellum


title: colon organoids, MPXV clade IIb, no1

description:
TPM_for_GEO_upload_colon.txt
colon_2022_1

value: iPS cell-derived colon organoids

value: colon organoids