title: st9_sox3_we_rep2

city: Irvine

first: Ken

last: Cho

address: University of California, Irvine

institute: University of California, Irvine

data_processing:
The multiplexed libraries were sequenced on the Novaseq 6000.   The version of Novaseq control software was NVCS ver 1.7.0 with real time analysis software, RTA 3.4.4.
For ChIP-seq, reads were aligned to Xenopus tropicalis v10.0 genome (Xenbase) using Bowtie2 v2.4.4. For RNA-seq, reads were aligned to Xenopus tropicalis v10.0 genome (Xenbase) using STAR v2.7.3a
For ChIP-seq, PCR duplicates were removed from aligned bam files using Samtools v1.10. For RNA-seq, RSEM v1.3.3 was used to calculate raw counts and expression values in transcripts per million (TPM)
For non-histone ChIP-seq, peaks were called using Macs2 v2.7.1 followed by IDR analysis using idr v2.0.4.2 in anaconda v4.11.0. For histone ChIP-seq, peaks were called using Macs2 v2.7.1 followed by reproduciable peak analysis using overlap method in Bedtools v2.29.2. For RNA-seq, differential expression analysis was performed using edgeR v3.36.0 in R v4.1.2
For ChIP-seq, bigwig files were generated from PCR deduplicated bam using Deeptools v3.5.0
Assembly: Xenopus tropicalis v10.0 (Xenbase)
Supplementary files format and content: For ChIP-seq, IDR peak bed files were included. For RNA-seq, raw count files were included

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Xenopus tropicalis embryos were obtained by in vitro fertilization according to Ogino et al. (2006) and staged according to Nieuwkoop and Faber (1994). All embryos were cultured in 1/9X Marc’s modified Ringers (MMR) at 25C.

extract_protocol:
For embryo dissection, animal caps or vegetal mass explants were dissected from late blastula embryos in 1X MMR, TSA treatment to embryos were maintained during dissection
For ChIP-seq, NEBNext Ultra II DNA library prep (E7645S) protocol was followed. For RNA-seq, NEBNext Ultra II RNA library prep (E7770S) protocol was followed.

treatment_protocol: For a-Amanitin injection, 1-cell staged embryos were injected at 6pg/embryo. For TSA/ VPA treatment, 4-cell staged embryos were immersed in 100nM TSA/ 10 mM VPA in 1/9 MMR or equavalent volume of DMSO/ H2O

value: whole embryo

value: Sox3 (Zhang et al., Development, 2003)

tag: genotype

value: wildtype

value: untreated


title: st10.5_vg_vpa_rna_rep2

status: Public on Mar 27 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

source_name: vegetal mass cells

tag: tissue

value: vegetal mass cells

tag: treatment

value: VPA (10mM)


title: Pt1Dx_FAM98C.G228S_XVseq

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

description: XV-seq

data_processing:
For demultiplexing, we used cellranger-7.0.0 mkfastq or bcl2fastq v2.20.0.422, with identical results.
For alignment of scRNA-seq data and to generate gene expression matrices, we used cellranger-7.0.0 count.
For the analysis of XV-seq data, we used IronThrone-GoT.
Assembly: hg38
Supplementary files format and content: counts.tsv: tab-separated transcript counts per cell
Supplementary files format and content: norm.tsv: tab-separated normalized transcript counts per cell
Supplementary files format and content: metadata.tsv: tab-separated metadata per cell
Supplementary files format and content: FilteredCells.txt: tab-separated number of UMIs with wildtype or mutant genotyping calls per cell
Library strategy: XV-seq

molecule: polyA RNA

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
mRNA was extracted and hybridized to polyT oligos on 10x Genomics or Seq-Well beads.
10x Genomics 3' v3 or v3.1, or Seq-Well S3 library construction methods were used to construct single-cell RNA-sequencing libraries. From the full-length cDNA, XV-seq was used to enrich and sequence mutation sites of interest (similar to Genotyping of Transcriptomes, GoT).

value: Bone marrow

tag: Sex

value: Male

tag: age

tag: disease state

value: Diagnosis

tag: bone marrow_involvement

value: Yes


title: Th0_rep3

city: Barcelona

first: Pere

last: Santamaria

address: C/Rosselló 149-153

country: Spain

institute: IDIBAPS

description:
Non activated, Th0 (CD4+/CD44-/CXCR5-/PD-1-) cells from KLH-immunized mice
TFH_Th0_Raw_counts.xlsx

data_processing:
Contaminant rRNA filtering with Bowtie2 (2.2.5)
Mouse samples: Alignment with STAR 2.5.3a to the GENCODE  release 16 of the Mus musculus genome (mm10 assembly)
Human samples: Alignment with STAR 2.5.3a to the GENCODE  release 29 of the Homo sapiens genome (hg38 assembly)
Raw count of reads per gene was obtained with Partek “Quantify to annotation model (Partek E/M)” tool
Counts were normalized by CPM
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheets (xlsx) containing raw counts

organism: Mus musculus

source_name: Th0 (non activated) T cells

extract_protocol:
RNA purification using Rneasy Mini kit (QIAGEN)
TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer's protocol (Illumina, San Diego, CA)

treatment_protocol: Samples are obtained from mice that have been immunized with KLH.

tag: strain

value: NOD

tag: cell type

value: T cell

value: KLH immunization


title: A33728 cells grown for 8h at 30ºC rep 1 [d139014.D_8h]

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Reads were aligned to a S. cerevisiae transcriptome with STAR version 2.5.3a and gene expression was quantified with RSEM version 1.3.0. Transcript per million (TPM) values were offset by +1 and transformed to log 2 space.
Assembly: SacCer3 plus spike-ins with an ensembl annotation
Supplementary files format and content: allegra_l2tpm.txt.gz is a tab-delimited text file of log2 tpm data

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: 8 hours growth at 30ºC in YEPD

extract_protocol:
RNeasy kit (Qiagen)
Illumina Truseq followed by Roche KAPA

value: yeast

tag: strain source

value: Fink Lab

tag: strain genotype

value: MATa/alpha, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+

tag: temperature


title: st10.5_vg_vpa_rna_rep1


title: st10.5_vg_h2o_rna_rep2


title: A2587 cells grown for 8h at 30ºC rep 2 [d139013.H_8h_2]

value: Nasmyth Lab


title: Pt5Dx_BioRep3_scRNAseq

description:
10x Genomics 3' v3.1
Pt5Dx_counts.tsv
Pt5Dx_norm.tsv
Pt5Dx_metadata.tsv

library_source: transcriptomic single cell

data_processing:
For demultiplexing, we used cellranger-7.0.0 mkfastq or bcl2fastq v2.20.0.422, with identical results.
For alignment of scRNA-seq data and to generate gene expression matrices, we used cellranger-7.0.0 count.
For the analysis of XV-seq data, we used IronThrone-GoT.
Assembly: hg38
Supplementary files format and content: counts.tsv: tab-separated transcript counts per cell
Supplementary files format and content: norm.tsv: tab-separated normalized transcript counts per cell
Supplementary files format and content: metadata.tsv: tab-separated metadata per cell
Supplementary files format and content: FilteredCells.txt: tab-separated number of UMIs with wildtype or mutant genotyping calls per cell

value: No


title: Th0_rep2


title: st10.5_vg_h2o_rna_rep1


title: Th0_rep1


title: A2587 cells grown for 8h at 30ºC rep 1 [d139012.H_8h]


title: Pt5Dx_BioRep1_scRNAseq


title: st10.5_ac_vpa_rna_rep2

source_name: animal cap cells

value: animal cap cells


title: A33728 cells grown for 6h at 30ºC rep 2 [d139011.D_6h_2]

growth_protocol: 6 hours growth at 30ºC in YEPD


title: st10.5_ac_vpa_rna_rep1

value: wildtype


title: A2587 cells grown for 10h at 30ºC rep 2 [d139017.H_10h_2]

growth_protocol: 10 hours growth at 30ºC in YEPD


title: Pt1Rem_BioRep3_scRNAseq

description:
10x Genomics 3' v3.1
Pt1Rem_counts.tsv
Pt1Rem_norm.tsv
Pt1Rem_metadata.tsv

value: Remission


title: Pt1Dx_TET2.Q960_XVseq

description: XV-seq


title: Tet_Basal_rep1

description:
Unstimulated Tetramer+ CD4+ T cells from pMHCII-NP-treated NOD mice
Tet_TF_Basal_Stim_Raw_counts.xlsx

source_name: Unstimulated Tetramer+ CD4+ T cells

treatment_protocol: Samples are obtained from mice that have received intravenously 10 doses of pMHCII-NPs.  Stimulated cells have been cultured with aCD3/CD28 beads previous to RNA extraction.

value: pMHCII-NPs


title: A33728 cells grown for 6h at 30ºC rep 1 [d139010.D_6h]


title: st10.5_ac_h2o_rna_rep2

value: untreated


title: Pt1Rem_BioRep2_scRNAseq

value: Bone marrow


title: TFH_rep1

description:
T follicular helper (CD4+/CXCR5+/PD-1+) cells from KLH-immunized mice
TFH_Th0_Raw_counts.xlsx

source_name: T follicular helper cells


title: A2587 cells grown for 6h at 30ºC rep 2 [d139009.H_6h_2]


title: st10.5_ac_h2o_rna_rep1


title: Pt1Rem_BioRep1_scRNAseq

value: Male


title: A33728 cells grown for 8h at 30ºC rep 2 [d139015.D_8h_2]


title: Pt1Dx_ASXL1.L697fs_XVseq

description: XV-seq

value: Diagnosis


title: Tet_rep3_B6

description:
Tetramer+ CD4+ T cells from pMHCII-NP-treated B6 mice
B6_Tet+_Tet-_Raw_counts.xlsx

source_name: Tetramer+ CD4+ T cells

treatment_protocol: Samples are obtained from mice that have received intravenously 10 doses of pMHCII-NPs.


title: A33728 cells grown for 4h at 30ºC rep 2 [d139007.D_4h_2]

growth_protocol: 4 hours growth at 30ºC in YEPD


title: Pt1Dx_BioRep3_scRNAseq

description:
10x Genomics 3' v3.1
Pt1Dx_counts.tsv
Pt1Dx_norm.tsv
Pt1Dx_metadata.tsv

value: Yes


title: Tet_rep2_B6


title: Pt1Dx_BioRep2_scRNAseq


title: st10.5_hdac1_DMSO_we

library_source: genomic

molecule: genomic DNA

value: whole embryo

tag: antibody

value: HDAC1 (Cell Signaling, 34589S)

value: DMSO solvent control


title: Tet_rep1_B6

value: T cell


title: A2587 cells grown for 6h at 30ºC rep 1 [d139008.H_6h]

value: yeast


title: st10.5_hdac1_TSA_we

value: TSA (100nM)


title: st9_hdac1_TSA_we


title: A33728 cells grown for 4h at 30ºC rep 1 [d139006.D_4h]

value: Fink Lab

value: MATa/alpha, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+


title: A2587 cells grown for 4h at 30ºC rep 1 [d139005.H_4h]

value: Nasmyth Lab


title: Tconv_rep2_B6

description:
Conventional Tet- CD4+ T cells from pMHCII-NP-treated B6 mice
B6_Tet+_Tet-_Raw_counts.xlsx

source_name: Conventional T cells


title: Pt16Dx_BioRep2_scRNAseq

description:
10x Genomics 3' v3.1
Pt16Dx_counts.tsv
Pt16Dx_norm.tsv
Pt16Dx_metadata.tsv


title: TFH_rep2

value: NOD

value: KLH immunization


title: A33728 cells grown for 2h at 30ºC rep 2 [d139004.D_2h_2]

growth_protocol: 2 hours growth at 30ºC in YEPD


title: A33728 cells grown for 2h at 30ºC rep 1 [d139003.D_2h]


title: Pt16Dx_BioRep1_scRNAseq


title: Tconv_rep1_B6

value: pMHCII-NPs


title: st10.5_hdac2_we

value: HDAC2 (Cell Signaling, 57156S)

value: wildtype

value: untreated


title: st9_hdac2_we


title: Tet_rep4

description:
Tetramer+ CD4+ T cells from pMHCII-NP-treated NOD mice
NOD_Tet+_Tet-_Raw_counts.xlsx


title: Tet_rep3


title: Pt15Dx_BioRep6_scRNAseq

description:
10x Genomics 3' v3.1
Pt15Dx_counts.tsv
Pt15Dx_norm.tsv
Pt15Dx_metadata.tsv

value: Bone marrow

value: Male

value: Diagnosis


title: A2587 cells grown for 2h at 30ºC rep 1 [d139001.H_2h]


title: A2587 cells grown for 2h at 30ºC rep 2 [d139002.H_2h_2]


title: Pt14Dx_BioRep3_scRNAseq

description:
10x Genomics 3' v3.1
Pt14Dx_counts.tsv
Pt14Dx_norm.tsv
Pt14Dx_metadata.tsv

value: Yes


title: A2589 cells treated with alpha factor for 9h at 30ºC [d113036.af.p.9]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with 5 μg/mL for 9 hours and refreshed with 2 μg/mL every 2 hours

value: MATa, bar1::HisG, leu2-3, ura3, trp1-1, his3, ade2, can1-100, GAL, psi+,


title: Pt15Dx_BioRep5_scRNAseq


title: Tet_rep2

value: T cell


title: Tconv_rep3_B6


title: Tet_rep1


title: st9_hdac1_DMSO_we

value: whole embryo

value: HDAC1 (Cell Signaling, 34589S)

value: DMSO solvent control


title: Pt14Dx_BioRep2_scRNAseq


title: Pt16Dx_BioRep3_scRNAseq


title: A2589 cells treated with alpha factor for 8h at 30ºC [d113035.af.p.8]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with 5 μg/mL for 8 hours and refreshed with 2 μg/mL every 2 hours

value: yeast


title: Tconv_rep4

description:
Conventional Tet- CD4+ T cells from pMHCII-NP-treated NOD mice
NOD_Tet+_Tet-_Raw_counts.xlsx


title: TFH_rep3


title: st10.5_vg_dmso_rna_rep1

treatment_protocol: For a-Amanitin injection, 1-cell staged embryos were injected at 6pg/embryo. For TSA treatment, 4-cell staged embryos were immersed in 100nM TSA in 1/9 MMR or equavalent volume of DMSO

tag: chip antibody


title: st10.5_ac_tsa_rna_rep2

value: TSA (100nM)


title: Pt14Dx_BioRep1_scRNAseq


title: Tconv_rep3

value: NOD


title: A2589 cells treated with alpha factor for 6h at 30ºC [d113034.af.p.6]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with 5 μg/mL for 6 hours and refreshed with 2 μg/mL every 2 hours

value: Nasmyth Lab


title: Pt15Dx_BioRep7_scRNAseq


title: st10.5_ac_tsa_rna_rep1


title: Pt12Rel_BioRep2_scRNAseq

description:
10x Genomics 3' v3.1
Pt12Rel_counts.tsv
Pt12Rel_norm.tsv
Pt12Rel_metadata.tsv

value: Relapse


title: st10.5_vg_tsa_rna_rep2


title: A2589 cells treated with alpha factor for 2h at 30ºC [d113032.af.p.2]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with 5 μg/mL for 2 hours


title: st10.5_vg_tsa_rna_rep1


title: st10.5_vg_dmso_rna_rep2


title: Pt12Rel_BioRep1_scRNAseq


title: st10.5_ac_dmso_rna_rep2


title: A2589 cells treated with alpha factor for 0h at 30ºC [d113031.af.p.0]

growth_protocol: Log-phase culture grown at 30ºC in YEPD


title: Pt12Dx_BioRep2_scRNAseq

description:
10x Genomics 3' v3.1
Pt12Dx_counts.tsv
Pt12Dx_norm.tsv
Pt12Dx_metadata.tsv

value: No


title: A2589 cells treated with DMSO for 9h at 30ºC [d113030.af.m.9]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with equivalent volume (as alpha factor) of DMSO for 9 hours


title: Pt12Dx_BioRep1_scRNAseq


title: st10.5_panh3kac_vg_tsa_rep2

value: wildtype

value: panH3Kac (Active Motif, 39139)


title: NPCs p53 -/- alone repeat 3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Raw reads were aligned using TopHat v.2.0.11 and assigned to genomic features using HTSeq v.0.6.1.
Genome_build: Mus musculus mm9
Supplementary_files_format_and_content: tab delimited file containing unfiltered raw counts from HTSeq

source_name: Neural progenitor cells

growth_protocol: NPCs were isolated from the SVZ of P9–P12 mouse brains and routinely grown DMEM/F12supplemented with 0.25% FBS, N2, 20 ng/ml EGF, 10 ng/ml bFGF and 35 μg/ml bovine pituitary extract.

extract_protocol:
RNA was isolated using RNeasy mini kit
Libraries were prepared using the Truseq mRNA stranded kit

treatment_protocol: NPCs were plated either alone or onto endothelial monolayers for 48h before collection

tag: culture conditions

value: laminin coated plates for 48h


title: A2589 cells treated with DMSO for 8h at 30ºC [d113029.af.m.8]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with equivalent volume (as alpha factor) of DMSO for 8 hours


title: st10.5_panh3kac_vg_tsa_rep1


title: NPCs p53+/+ co-culture repeat 3

value: co-culture for 48h

value: wild type


title: A2589 cells treated with DMSO for 6h at 30ºC [d113028.af.m.6]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with equivalent volume (as alpha factor) of DMSO for 6 hours


title: A2589 cells treated with alpha factor for 4h at 30ºC [d113033.af.p.4]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with 5 μg/mL for 4 hours and refreshed with 2 μg/mL every 2 hours


title: st10.5_panh3kac_vg_dmso_rep2


title: NPCs p53+/+ alone repeat 3


title: Pt10Rel_BioRep1_scRNAseq

description:
10x Genomics 3' v3
Pt10Rel_counts.tsv
Pt10Rel_norm.tsv
Pt10Rel_metadata.tsv

value: Bone marrow

value: Male

value: Yes


title: A2589 cells treated with DMSO for 4h at 30ºC [d113027.af.m.4]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with equivalent volume (as alpha factor) of DMSO for 4 hours

value: MATa, bar1::HisG, leu2-3, ura3, trp1-1, his3, ade2, can1-100, GAL, psi+,


title: Tconv_rep2

value: T cell

value: pMHCII-NPs


title: st10.5_ac_dmso_rna_rep1

growth_protocol: Xenopus tropicalis embryos were obtained by in vitro fertilization according to Ogino et al. (2006) and staged according to Nieuwkoop and Faber (1994). All embryos were cultured in 1/9X Marc’s modified Ringers (MMR) at 25C.

value: DMSO solvent control


title: st10.5_panh3kac_vg_dmso_rep1

description: st105_panh3kac_vg_dmso_overlap2reps_peaks.narrowPeak


title: Pt10Dx_BioRep4_scRNAseq

description:
10x Genomics 3' v3
Pt10Dx_counts.tsv
Pt10Dx_norm.tsv
Pt10Dx_metadata.tsv

value: Diagnosis


title: A2589 cells treated with DMSO for 2h at 30ºC [d113026.af.m.2]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with equivalent volume (as alpha factor) of DMSO for 2 hours

value: yeast


title: NPCs p53 -/- co-culture repeat 2


title: Pt10Dx_BioRep3_scRNAseq


title: Tconv_rep1

value: NOD


title: st10.5_panh3kac_ac_tsa_rep2

value: TSA (100nM)


title: NPCs p53 -/- alone repeat 2


title: NPCs p53 -/- co-culture repeat 3


title: st10.5_panh3kac_ac_tsa_rep1


title: Pt10Dx_BioRep2_scRNAseq

value: No


title: A2589 cells treated with DMSO for 0h at 30ºC [d113025.af.m.0]

value: Nasmyth Lab


title: NPCs p53+/+ co-culture repeat 2


title: NPCs p53+/+ alone repeat 2


title: st10.5_panh3kac_ac_dmso_rep2

value: wildtype

value: panH3Kac (Active Motif, 39139)


title: A2596 cells grown for 8h at 37ºC [d8503.65.15.2.8h]

growth_protocol: Growth at 37ºC for 8 hours in YEPD

value: MATa, cdc15-2, leu2-3, ura3, trp1-1, omns, ade1


title: Pt10Dx_BioRep1_scRNAseq


title: st10.5_panh3kac_ac_dmso_rep1

description: st105_panh3kac_ac_dmso_overlap2reps_peaks.narrowPeak


title: Pt10Rel_BioRep2_scRNAseq

value: Relapse


title: A2596 cells grown for 6h at 37ºC [d8502.65.15.2.6h]

growth_protocol: Growth at 37ºC for 6 hours in YEPD


title: NPCs p53 -/- co-culture repeat 1

value: co-culture for 48h


title: st10.5_panh3kac_we_rep2

source_name: whole embryos

value: untreated


title: NPCs p53 -/- alone repeat 1

value: laminin coated plates for 48h


title: A2596 cells grown for 4h at 37ºC [d8501.65.15.2.4h]

growth_protocol: Growth at 37ºC for 4 hours in YEPD


title: BM5_BioRep3_scRNAseq

description:
10x Genomics 3' v3.1
BM_counts.tsv
BM_norm.tsv
BM_metadata.tsv

value: Bone marrow

value: Male

value: HealthyDonor


title: NPCs p53+/+ co-culture repeat 1

value: wild type


title: BM4_BioRep3_scRNAseq


title: A2596 cells grown for 2h at 37ºC [d8500.65.15.2.2h]

growth_protocol: Growth at 37ºC for 2 hours in YEPD


title: st9_h3k18ac_we_rep1

value: H3K18ac(Cell Signaling, 13998)


title: st10.5_panh3kac_we_rep1

description: st105_panh3kac_we_overlap2reps_peaks.narrowPeak


title: NPCs p53+/+ alone repeat 1


title: BM4_BioRep2_scRNAseq


title: BM4_BioRep1_scRNAseq


title: st9_sox3_we_rep1

description: st9_sox3_we_idr_0.05_filtered_peaks.narrowPeak

value: Sox3 (Zhang et al., Development, 2003)


title: A2587 cells grown for 9h at 37ºC [d8499.65.WT.9h]

growth_protocol: Growth at 37ºC for 9 hours in YEPD, kept between OD600 = 0.2 and OD600 = 0.8

value: yeast


title: A2596 cells grown for 9h at 37ºC [d8504.65.15.2.9h]

growth_protocol: Growth at 37ºC for 9 hours in YEPD


title: A2587 cells grown for 8h at 37ºC [d8498.65.WT.8h]

growth_protocol: Growth at 37ºC for 8 hours in YEPD, kept between OD600 = 0.2 and OD600 = 0.8


title: st10.5_hdac1_we_rep2

value: HDAC1 (Cell Signaling, 34589S)


title: PC9 cells, Nil Unsorted biol rep 3

city: Durham

first: Christian

last: Cerda-Smith

state: NC

address: 450 Research Drive, LSRC C134, PO Box 3813, Duke University

department: Pharmacology and Cancer Biology

institute: Duke University

description:
Nil_unsorted_3
Nil-High_vs_Nil-Low_beta.gene_summary.txt
E3-Ligase_sgRNA_Library_forMAGeCKcount.csv
Nil-High_vs_Nil-Low.countsummary.txt
Nil-High_vs_Nil-Low.count_normalized.txt

data_processing:
Demultiplexed fastq.gz files were concatenated across lanes for each sample.
Raw sequencing reads were then aligned against a database of sgRNA sequences (containing the sgRNA name, trimmed sgRNA sequence, and target gene name) and a normalized counts table was generated utilizing the MAGeCK (v0.5.9.2) count sub-command with default settings.
Gene level enrichment or depletion was then evaluated across samples using the MAGeCK (v0.5.9.2) MLE sub-command with the normalized counts table as input, default settings.
Assembly: hg38
Supplementary files format and content: Concatenated across sequencing flowcell lanes (L001, L002, L003, L004) for each Sample.fastq.gz
Supplementary files format and content: tab-delimited text files include normalized sgRNA counts for each Sample, summary of counts data for each sample, or beta scores for gene-level enrichment or depletion comparison between samples. Comma-separated values file contains library of trimmed sgRNA sequences for raw read alignment.

source_name: Lung

growth_protocol: PC9 cells were maintained in RPMI 1640 (Life Technologies) supplemented with 10% FBS, 10 mM Hepes, 1 mM sodium pyruvate, and 0.2% glucose. Cells were grown at 37 °C in 5% CO2.

extract_protocol:
gDNA was recovered from fixed cells utilizing Arcturus PicoPure DNA Extraction Kit, according to manufacturer instructions.
DNA-seq (sgRNA) libraries were PCR-amplified from gDNA using NEBNext Ultra II Q5 Master Mix (New England BioLabs) according to manufacturer instructions, using the following primers: FWD 5′- AATGATACGGCGACCACCGAGATCTACACAATTTCTTGGGTAGTTTGCAGTT, Rev 5′- CAAGCAGAAGACGGCATACGAGAT(6 bp index sequence)GACTCGGTGCCACTTTTTCAA. Amplified libraries were purified using SPRIselect beads (Beckman Coulter) using right-sided selection of 0.75x then to 1.2x the original volume. Each sample was quantified using the Quant-iT dsDNA Broad Range Assay Kit (Thermo). Samples were pooled and sequenced on a NextSeq 500 (Illumina) with 20bp single-end sequencing using the following custom read and index primers: Custom Read 5′- GATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCG, Custom Index 5′- GCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTC.
DNA-seq

treatment_protocol: PC9 cells with stable expression of Cas9 were transduced at a low multiplicity of infection ~0.3 at greater than 3,000x coverage with a custom lentiviral sgRNA library targeting 593 known or predicted human E3 ligases (5 sgRNAs per gene, 2,965 total) and non-targeting controls (50 total). 24 hours following transduction, media was replaced with fresh media containing 2 ug/mL puromycin and cells selected for 48 hours. Cells were passaged and maintained above 3,000x coverage for 7 days post-transduction to allow for stable integration and Cas9-directed knockout of target genes. Cells were then split into triplicate conditions (7.5x106 cells per replicate) and treated with 5 µM Nilotinib immediately prior to incubation in 1% O2 for 24 hours. After hypoxic incubation, cells were fixed and permeabilized using the eBioscience Foxp3 Transcription Factor Staining Buffer Set (Thermo) according to manufacturer recommendations, with minor modifications. Fixed and permeabilized cells were incubated overnight at 4 °C, rotating with a PE-conjugated HIF-1α antibody (Biolegend) at 5 µL per 1,000,000 cells. For each replicate, stained cells were then sorted by Fluorescence Activated Cell Sorting (FACS), collecting the top and bottom 10% of HIF-1a expressing cells on the basis of PE signal; cell were collected in FBS-coated tubes, maintaining approximately 300x coverage per high and low population. An ungated control sample was also collected for each replicate.

value: Lung

tag: cell line

value: PC9 cells

value: Lung cancer cells

tag: transgene

value: Nilotinib, hypoxia

tag: facs-sorted cells

value: Unsorted


title: BM3_BioRep1_scRNAseq

description:
10x Genomics 3' v3
BM_counts.tsv
BM_norm.tsv
BM_metadata.tsv

tag: tissue


title: PC9 cells, Nil Unsorted biol rep 2

description:
Nil_unsorted_2
Nil-High_vs_Nil-Low_beta.gene_summary.txt
E3-Ligase_sgRNA_Library_forMAGeCKcount.csv
Nil-High_vs_Nil-Low.countsummary.txt
Nil-High_vs_Nil-Low.count_normalized.txt

tag: treatment


title: st10.5_hdac1_we_rep1

description: final.st105_hdac1_we_IDR0.05_in_merged_peaks.narrowPeak

value: wildtype


title: BM3_BioRep2_scRNAseq

tag: Sex


title: PC9 cells, Nil Unsorted  biol rep 1

description:
Nil_unsorted_1
Nil-High_vs_Nil-Low_beta.gene_summary.txt
E3-Ligase_sgRNA_Library_forMAGeCKcount.csv
Nil-High_vs_Nil-Low.countsummary.txt
Nil-High_vs_Nil-Low.count_normalized.txt


title: A2587 cells grown for 6h at 37ºC [d8497.65.WT.6h]

growth_protocol: Growth at 37ºC for 6 hours in YEPD, kept between OD600 = 0.2 and OD600 = 0.8

value: Nasmyth Lab


title: A2587 cells grown for 4h at 37ºC [d8496.65.WT.4h]

growth_protocol: Growth at 37ºC for 4 hours in YEPD, kept between OD600 = 0.2 and OD600 = 0.8


title: st9_hdac1_we_amanitin_rep2

value: a-Amanitin injected (6pg/embryo)


title: BM2_BioRep3_scRNAseq

value: Female

tag: age


title: BM5_BioRep1_scRNAseq

value: Bone marrow

tag: disease state


title: A2587 cells grown for 2h at 37ºC [d8495.65.WT.2h]

growth_protocol: Growth at 37ºC for 2 hours in YEPD, kept between OD600 = 0.2 and OD600 = 0.8


title: BM2_BioRep2_scRNAseq

tag: bone marrow_involvement


title: st9_hdac1_we_amanitin_rep1

tag: strain


title: A937 cells grown for 9h at 37ºC [d8494.64.20.1.9h]

tag: cell type

value: MATalpha, cdc20-1, ura3, trp1, leu2,  his3 , ade2, can1


title: st9_hdac1_we_ut_rep2

value: untreated


title: PC9 cells, Nil low biol rep 2

description:
Nil_Low_2
Nil-High_vs_Nil-Low_beta.gene_summary.txt
E3-Ligase_sgRNA_Library_forMAGeCKcount.csv
Nil-High_vs_Nil-Low.countsummary.txt
Nil-High_vs_Nil-Low.count_normalized.txt

value: Low


title: PC9 cells, Nil low  biol rep 1

description:
Nil_Low_1
Nil-High_vs_Nil-Low_beta.gene_summary.txt
E3-Ligase_sgRNA_Library_forMAGeCKcount.csv
Nil-High_vs_Nil-Low.countsummary.txt
Nil-High_vs_Nil-Low.count_normalized.txt


title: st9_hdac1_we_ut_rep1


title: BM1_BioRep3_scRNAseq

value: Male

value: HealthyDonor


title: PC9 cells, Nil High biol rep 3

description:
Nil_High_3
Nil-High_vs_Nil-Low_beta.gene_summary.txt
E3-Ligase_sgRNA_Library_forMAGeCKcount.csv
Nil-High_vs_Nil-Low.countsummary.txt
Nil-High_vs_Nil-Low.count_normalized.txt

value: High


title: A937 cells grown for 6h at 37ºC [d8492.64.20.1.6h]

value: yeast

tag: strain source


title: PC9 cells, Nil low biol rep 3

description:
Nil_Low_3
Nil-High_vs_Nil-Low_beta.gene_summary.txt
E3-Ligase_sgRNA_Library_forMAGeCKcount.csv
Nil-High_vs_Nil-Low.countsummary.txt
Nil-High_vs_Nil-Low.count_normalized.txt

value: Lung


title: st9_hdac1_we_rep2

value: HDAC1 (Cell Signaling, 34589S)


title: PC9 cells, Nil High biol rep 2

description:
Nil_High_2
Nil-High_vs_Nil-Low_beta.gene_summary.txt
E3-Ligase_sgRNA_Library_forMAGeCKcount.csv
Nil-High_vs_Nil-Low.countsummary.txt
Nil-High_vs_Nil-Low.count_normalized.txt

value: PC9 cells

value: Lung cancer cells


title: A937 cells grown for 4h at 37ºC [d8491.64.20.1.4h]

tag: strain genotype


title: st9_hdac1_we_rep1

description: final.st9_hdac1_we_IDR0.05_in_merged_peaks.narrowPeak


title: BM1_BioRep2_scRNAseq


title: A937 cells grown for 8h at 37ºC [d8493.64.20.1.8h]

tag: temperature


title: A937 cells grown for 2h at 37ºC [d8490.64.20.1.2h]


title: st8_hdac1_we_rep2


title: A2587 cells grown for 9h at 37ºC [d8489.64.WT.9h]


title: st8_hdac1_we_rep1

description: final.st8_hdac1_we_IDR0.05_in_merged_peaks.narrowPeak


title: PC9 cells, Nil High biol rep 1

description:
Nil_High_1
Nil-High_vs_Nil-Low_beta.gene_summary.txt
E3-Ligase_sgRNA_Library_forMAGeCKcount.csv
Nil-High_vs_Nil-Low.countsummary.txt
Nil-High_vs_Nil-Low.count_normalized.txt

value: Nilotinib, hypoxia


title: 1,25(OH)2D3,3

city: Iwaki

first: Yoshiaki

last: Kanemoto

state: Fukushima

address: kaminodai 57, jyobankamiyunagaya-town

country: Japan

institute: Jyoban Hospital

data_processing:
FPKM values were calculated from mapped reads by normalizing to total counts and transcript. Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
The list of differentially expressed genes detected by DESeq2 (basemean > 5 and fold-change < 0.25, or basemean > 5 and fold-change > 4) were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: GRCh38.p13.chromosomes
Supplementary files format and content: Reads on annotated genes were counted using featureCounts (version 1.6.1).

growth_protocol: HCT116 parent and VDRKO cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Add 1ml of TRIZOL per well and extract total RNA according to the manufacturer's instruction.
RNA libraries for RNA-seq were prepared using SMARTer stranded RNA-Seq kit v2(Clontech) according to the manufacturer's instruction.

treatment_protocol: Treatment of 1,25(OH)2D3 and/or antagonist post confluent cells on 6-well platefor 8hrs.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH30).

tag: genotype

value: WT


title: BM2_BioRep1_scRNAseq


title: A2587 cells grown for 6h at 37ºC [d8488.64.WT.6h]

value: Nasmyth Lab


title: 1,25(OH)2D3,1

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH28).


title: BM1_BioRep1_scRNAseq

value: Bone marrow


title: 1,25(OH)2D3,2

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH29).


title: A2587 cells grown for 4h at 37ºC [d8487.64.WT.4h]


title: Vehicle,3

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH27).

value: Vehicle


title: Vehicle,2

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH26).


title: A39000 cells grown for 9h at 37ºC rep 3 [d169054.cdc28-13 t:9]

value: Amon Lab


title: Vehicle,1

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH25).


title: stress sample 4

type: RNA

city: Bristol

first: Valentina

last: Mosienko

address: University Walk

institute: University of Bristol

description: total RNA enriched in small RNA

hyb_protocol: Hybridization was performed automatically for 16 hours at 42 °C followed by automatic biochip washing and signal measurement. The signal enhancement process was combined with streptavidin-phycoerythrin detection of biotin to maximize signal sensitivity.

scan_protocol: Array images were analysed using the Geniom Wizard software (Febit Biomed Gmbh). For each array, the median signal intensity was extracted from the raw data file such that for each miRNA seven intensity values have been calculated corresponding to each replicate copy of miRNA-Base on the array.

data_processing:
After background correction, median values were calculated from the seven replicate intensity values of each miRNA. Microarray data were analysed using R’s LIMMA package.
The order of the data in the raw data file is the same order in the sample data table.

label: biotin

source_name: stressed, amygdalae

label_protocol: Samples were labelled with biotin using microfluidic-based enzymatic on-chip labelling of miRNAs

extract_protocol: Total RNA enriched in small RNA was extracted using mirVANA kit (Applied Biosystems). RNA quantity and quality (A260/280 > 1.80) were measured using NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies)

treatment_protocol: Immediately after a 6-hour immobilisation stress, wild-type control and stressed mice were anaesthetized, intraperitoneally using sodium pentobarbital, and transcardially perfused with ice-cold phosphate buffered saline (PBS). Amygdalae were isolated using a dissecting microscope in ice-cold ACSF (Glucose 25 mM, NaCl 115 mM, NaH2PO4·H2O 1.2 mM, KCl 3.3 mM, CaCl2 2 mM, MgSO4 1 mM, NaHCO3 25.5 mM, pH 7.4) and stored in RNAlater (Qiagen) at -20 °C until further processing.

tag: gender

value: male

value: 12 weeks

tag: brain are

value: amygdala

tag: experimental condition

value: stressed


title: Patient_G

city: Leuven

first: Jan

last: Remsik

address: Campus Gasthuisberg, Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB

data_processing:
Raw FASTQ files for each patient were preprocessed using the SEQC pipeline using hg38 human genome and the default SEQC parameters for 10X Genomics to obtain the molecule count matrix. The SEQC pipeline aligns the reads to the genome, corrects barcode and unique molecular identifier (UMI) errors, resolves multi-mapping reads, and generates a molecule count matrix. SEQC also performs a number of filtering steps: (1) Identification of true cells from cumulative distribution of molecule counts per barcode, (2) removal of apoptotic cells identified at cells with >20% of molecules derived from the mitochondria, and (3) removal of low-complexity cells identified as cells where the detected molecules are aligned to a small subset of genes.
Cell doublets are a characteristic error source in droplet-based single-cell sequencing data where two cells are randomly co-encapsulated with the same barcode. To remove likely doublet cells we have employed unsupervised machine learning classifier DoubletDetection. T Each patient was processed separately.
Filtered count matrices for each patient were median size normalized. To avoid numerical issues counts were multiplied by 10,000 and log transformed with pseudo count of 1 with Scanpy.
Assembly: hg38
Supplementary files format and content: h5ad file of filtered and corrected data, used for downstream analyses in Remsik et al., 2022

source_name: CSF cell fraction isolated from a cancer patient without leptomeningeal metastasis

extract_protocol: CSF, collected from consented patients, was processed to isolate the sample into cell-free CSF and the cellular contents of the CSF:  The whole CSF sample was centrifuged at 600 x g for 5 minutes without brake at 4 ºC to pellet the cells, and the supernatant was saved as cell-free CSF. The pellet was resuspended, washed with PBS supplemented with 0.4% BSA twice and processed immediatelly. The cells were manually counted with a hematocytometer. scRNA-Seq was performed with 10X genomics system using Chromium Single Cell 3’ Library and Gel Bead Kit V2 (catalog no. 120234). Briefly, viability of cells was evaluated (viability 70-80%), aiming for targeting recovery of ~5,000 cells with 3.9% multiplet rate. In cases, where cell count was too low to target 5,000 cells, maximum volume (34 µl) was loaded in the microfluidic droplet generation device. After reverse transcription reaction emulsions were broken, barcoded cDNA was purified with DynaBeads, followed by 12-cycles of PCR amplification. The resulting amplified barcoded-cDNA library was fragmented to ~400-600 bp, ligated to sequencing adapter and PCR-amplified to obtain sufficient amount of material for next-generation sequencing. The final libraries were sequenced on an Illumina NovaSeq 6000 system (Read 1 – 28 cycles, Index Read – 8 cycles, and Read 2 – 96 cycles).

tag: metastatic site

value: leptomeninges/CSF


title: Patient_H


title: Patient_I


title: Patient_F


title: A2587 cells grown for 2h at 37ºC [d8486.64.WT.2h]

value: yeast


title: stress sample 1

description: total RNA enriched in small RNA


title: VDRKO, antagonist,3

description: V.KO.VDnega.AHposi_V.KO.VDnega.AHposi.3.

tag: cell line

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH23).

value: VDRKO

value: antagonist


title: Patient_J


title: A39000 cells grown for 9h at 37ºC rep 2 [d169053.cdc28-13 t:9]


title: stress sample 3

description: total RNA enriched in small RNA


title: Monocytes 24h, HTO-derived cDNA

city: Paris

first: Javiera

last: Villar

address: 25 rue d'Ulm

country: France

institute: Institut Curie

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where HTO sequences were concatenated and treated as Custom library with default settings (v3.1) and aligning to the hg38 genome.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: blood

extract_protocol:
Peripheral Blood Mononuclear Cells (PBMC) were prepared by centrifugation on a Ficoll gradient (Lymphoprep, StemCell). Blood CD14+ monocytes were isolated from healthy donors’ PBMC by positive selection using magnetic beads (Miltenyi).
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics).

tag: tissue

value: blood

value: CD14+ monocytes

value: M-CSF + IL4 + TNFa

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD298 + Anti Beta2M :DonorA--/TotalSeq-A0251 ; DonorB--/TotalSeq-A0252


title: Monocytes 48h, HTO-derived cDNA

tag: treatment


title: Monocytes 48h, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: stress sample 2

description: total RNA enriched in small RNA

tag: age


title: A2587 cells grown for 9h at 37ºC rep 2 [d169050.WT t:9]

value: Nasmyth Lab


title: control sample 3

description: total RNA enriched in small RNA

source_name: stress-naïve, amygdalae

value: control


title: Monocytes 24h, mRNA-derived cDNA


title: A2587 cells grown for 9h at 37ºC rep 3 [d169051.WT t:9]


title: VDRKO, 1,25(OH)2D3,3

description: V.KO.VDposi.AHnega_V.KO.VDposi.AHnega.3.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH22).


title: VDRKO, 1,25(OH)2D3+antagonist,3

description: V.KO.VDposi.AHposi_V.KO.VDposi.AHposi.3.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH24).


title: A39000 cells grown for 9h at 37ºC rep 1 [d169052.cdc28-13 t:9]

value: Amon Lab


title: control sample 4

description: total RNA enriched in small RNA

value: male

value: 12 weeks

value: amygdala


title: VDRKO, Vehicle,3

description: V.KO.VDnega.AHnega_V.KO.VDnega.AHnega.3.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH21).

value: Vehicle


title: A2587 cells grown for 9h at 37ºC rep 1 [d169049.WT t:9]

value: yeast


title: Monocytes 9h, mRNA-derived cDNA

value: blood


title: Monocytes 9h, HTO-derived cDNA

value: CD14+ monocytes


title: control sample 2

description: total RNA enriched in small RNA


title: control sample 1

description: total RNA enriched in small RNA


title: parent, 1,25(OH)2D3+antagonist,3

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH20).

value: WT


title: A39000 cells grown for 8h at 37ºC rep 3 [d169048.cdc28-13 t:8]


title: A39000 cells grown for 8h at 37ºC rep 2 [d169047.cdc28-13 t:8]


title: pst1_64_PD

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing: Reporter Code Count (RCC) and Reporter Library Files (RLF) generated by the nCounter SPRINT Profiler were imported into NanoString nSolver 4.0 Advanced Analysis software, version 2.0.134. The manufacturer’s recommended default parameters were used for imaging, quality control flagging, binding density, positive control linearity, and positive control limit of detection. Each sample in the intraoperative and postmortem cohorts was first normalized to the geometric mean determined by the six External RNA Controls Consortium (ERCC) synthetic RNA Spike-In Controls designated as positive controls (PosA to PosF), with default flagging of normalization factors (<0.3 and >3). These ERCC RNA Spike-In Controls were used both within each experiment and across all the nCounter experiments to create a standard baseline measurement of RNA samples across various samples and batches. We then applied normalization using the geometric mean of custom housekeeping genes, with default flagging of normalization factors (<0.1 and >10). Thirteen stably expressed housekeeping genes were selected for the intraoperative samples: CCDC127; UBE2D2; ASB7; LARS; MTO1; CSNK2A2; TADA2B; SUPT7L; CNOT10; AARS; FAM104A; CYC1; and RPL13. The geometric mean of the two most stable housekeeping genes, CYC1 and UBE2D2 were selected for normalization in the postmortem cohort. Normalized gene expression datasets were assessed using fold changes, p values, and enriched pathways.

source_name: prefrontal cortex

label_protocol: Because of the challenge of intraoperative tissue, comparisons between intraoperative and postmortem cohorts, and small samples, we chose the NanoString nCounter Human Neuropathology Panels. Gene expression profiles of intraoperative tissue collected during DBS-implantation surgery and postmortem frontal tissue were generated using identical NanoString nCounter Human Neuropathology Panels (NanoString Technologies, Inc., Seattle, WA). Human tissue samples were submitted to the Iowa NeuroBank Core in the Iowa Neuroscience Institute. Total RNA (100 ng per sample) was extracted using the RNeasy Plus Mini Kit (Qiagen, Germantown, MD) following the manufacturer’s protocol. The quality and concentration of RNA samples were quantified using NanoDrop (Thermo Scientific, Waltham, MA), Fragment Analyzer (Agilent, Clara, CA), and Bioanalyzer (Agilent) systems in the Iowa Neuroscience Institute and in the Iowa Institute of Human Genetics, Genomics Division. Samples with a Bioanalyzer RNA integrity number (an index of RNA quality control) of >3 were analyzed with the NanoString nCounter Human Neuropathology Panel and Custom CodeSet (C8574, C9676) assays, designed in consultation with the NanoString bioinformatics team. All intraoperative mRNA assays were performed on the NanoString nCounter SPRINT Profiler for image acquisition and data processing, without amplification or generation of cDNA (Geiss et al 2008). Due to instrumentation updates, the postmortem assays were performed using the NanoString nCounter MAX system, according to the manufacturer’s instructions. Gene expression profiles for a total of 780 genes were screened using target-specific biotinylated probes and barcoded reporter probes in the NanoString nCounter neurodegenerative cartridge.

extract_protocol: Intraoperative tissue was collected during previously scheduled DBS implantation surgery. All PD patients were off dopaminergic medication for the surgery. Since DBS electrode insertion requires a cortical incision, no additional cortical tissue was disrupted for the patients in this study. A standard coronal burr hole placement for usual clinical DBS trajectory and targeting was utilized. These were ~14-mm diameter holes, typically located over the middle frontal gyrus or rarely located over the lateral aspect of the superior frontal gyrus (i.e., Brodmann areas 8, 9/46). After dural opening, a corticotomy at the DBS insertion point was made bilaterally under direct vision to avoid visible blood vessels. Through this opening, ~2-mm cupped biopsy forceps (~the same diameter as a DBS insertion cannula) were used to grasp a small biopsy (~5 mg) from directly beneath the pial surface (Figure 1). The collected tissue was immediately passed off the sterile field and frozen in the operating room using dry ice. Samples were collected separately from the left and right hemispheres and pooled together for RNA extraction and downstream analysis. Due to the brevity of tissue collection, no meaningful additional time was added to the surgery. One to three 2-mm diameter stainless steel DBS implantation cannulas were then passed through the same cortical opening, and surgery commenced in the usual manner. No immediate or delayed complications from the tissue collection procedure were observed.  To compare gene expression profiles from our intraoperative tissue specimens with prior data, we collected postmortem samples from the superior/middle frontal gyrus (BA 8, 9/46), the same frontal region targeted in DBS patients. All postmortem frontal cortex tissue was obtained from the Iowa NeuroBank Core (https://medicine.uiowa.edu/inbc/), with informed consent forms signed by the next of kin as required by state law. The postmortem cases were PD patients or neurotypical control patients available for study without PD or ET.

value: prefrontal cortex

tag: cohort

value: postmortem

tag: diagnosis

value: PD

tag: age (yr)

tag: Sex

value: M


title: parent, 1,25(OH)2D3,3

tag: cell type

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH18).


title: parent, antagonist,3

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH19).

value: antagonist


title: A39000 cells grown for 8h at 37ºC rep 1 [d169046.cdc28-13 t:8]

tag: strain

tag: strain source

value: Amon Lab

tag: strain genotype

tag: temperature


title: Monocytes 3h, mRNA-derived cDNA

value: M-CSF + IL4 + TNFa

value: mRNA


title: pst1_61_Control

value: Control


title: A2587 cells grown for 8h at 37ºC rep 3 [d169045.WT t:8]

value: Nasmyth Lab


title: parent, Vehicle,3

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH17).

tag: genotype

value: Vehicle


title: pst1_47_PD


title: pst1_46_Control


title: A2587 cells grown for 8h at 37ºC rep 2 [d169044.WT t:8]

value: yeast


title: VDRKO, antagonist,2

description: V.KO.VDnega.AHposi_V.KO.VDnega.AHposi.2.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH15).

value: VDRKO


title: A2587 cells grown for 8h at 37ºC rep 1 [d169043.WT t:8]


title: pst1_48_PD

value: prefrontal cortex


title: xenograft SK-N-SH CD44neg rep1 Input, ChIP-seq

first: Agathe

last: Peltier

address: 26 rue d'Ulm

department: Centre de recherche

data_processing:
Alignment with Bowtie2 v2.1.0, default options
Quality filtering: Q > 20; duplicates kept
Peak calling with HMCan v1.40
Renormalization of wig profiles among all H3K27ac samples with an in-house R script
Assembly: hg19
Supplementary files format and content: bigWig files correspond to renormalized signal; score in .bed files correspond to the likelihood of a region to be enriched in H3K27ac or to be a binding site of a TF

source_name: Neuroblastoma

growth_protocol: Neuroblastoma cell lines were cultured  in RPMI (for PDX63) or DMEM ( for other cell lines) with 10% FCS (Eurobio) and 100 μg/ml penicillin/streptomycin.

extract_protocol:
Chromatin preparation and ChIP were performed with Ideal ChIP-seq kit for histones according to the supplier's protocol (Diagenode )
lllumina sequencing libraries were prepared from ChIP and input DNAs using the TruSeq ChIP library preparation kit according to the manufacturer’s protocol. Briefly, DNA were subjected to consecutive steps of end-repair, dA-tailing and ligation to TruSeq indexed

value: Neuroblastoma

value: SK-N-SH

value: Xenograft of cell line


title: xenograft SK-N-SH CD44neg rep2 Input, ChIP-seq


title: xenograft SK-N-SH CD44neg rep2 H3K27ac, ChIP-seq

value: ab4729 (rabbit polyclonal, Abcam)


title: pst1_45_Control

value: postmortem

value: M


title: xenograft SK-N-SH CD44neg rep1 H3K27ac, ChIP-seq


title: VDRKO, 1,25(OH)2D3,2

description: V.KO.VDposi.AHnega_V.KO.VDposi.AHnega.2.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH14).


title: pst1_44_PD

value: PD


title: Monocytes 3h, HTO-derived cDNA

value: blood

value: CD14+ monocytes

value: M-CSF + IL4 + TNFa

value: HTO

value: Anti CD298 + Anti Beta2M :DonorA--/TotalSeq-A0251 ; DonorB--/TotalSeq-A0252


title: xenograft SK-N-SH CD44pos rep2 Input, ChIP-seq


title: A39000 cells grown for 6h at 37ºC rep 1 [d169042.cdc28-13 t:6]

value: yeast

value: Amon Lab


title: A2587 cells grown for 6h at 37ºC rep 3 [d169041.WT t:6]

value: Nasmyth Lab


title: VDRKO, Vehicle,2

description: V.KO.VDnega.AHnega_V.KO.VDnega.AHnega.2.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH13).

value: VDRKO

value: Vehicle


title: pst1_42_Control

value: prefrontal cortex

value: Control


title: parent, 1,25(OH)2D3+antagonist,2

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH12).

value: WT


title: pst1_40_PD

value: postmortem

value: M


title: A2587 cells grown for 6h at 37ºC rep 2 [d169040.WT t:6]


title: xenograft SK-N-SH CD44pos rep1 Input, ChIP-seq

value: Neuroblastoma

value: SK-N-SH

value: Xenograft of cell line


title: pst1_39_PD

value: PD


title: VDRKO, 1,25(OH)2D3+antagonist,2

description: V.KO.VDposi.AHposi_V.KO.VDposi.AHposi.2.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH16).


title: parent, 1,25(OH)2D3,2

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH10).


title: xenograft SK-N-SH CD44pos rep1 H3K27ac, ChIP-seq

value: ab4729 (rabbit polyclonal, Abcam)


title: pst1_38_Control


title: xenograft SH-SY5Y rep2 Input, ChIP-seq


title: A2587 cells grown for 4h at 37ºC rep 3 [d169037.WT t:4]

value: yeast

value: Nasmyth Lab


title: parent, Vehicle,2

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH9).


title: A2587 cells grown for 4h at 37ºC rep 2 [d169036.WT t:4]


title: VDRKO, 1,25(OH)2D3+antagonist,1

description: V.KO.VDposi.AHposi_V.KO.VDposi.AHposi.1.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH8).

value: VDRKO


title: pst1_37_Control

value: prefrontal cortex

value: Control


title: xenograft SH-SY5Y rep1 Input, ChIP-seq


title: xenograft SK-N-SH CD44pos rep2 H3K27ac, ChIP-seq


title: int2_23_PD


title: int2_22_PD


title: A2587 cells grown for 4h at 37ºC rep 1 [d169035.WT t:4]


title: A39000 cells grown for 2h at 37ºC rep 3 [d169034.cdc28-13 t:2]

value: Amon Lab


title: int2_21_PD


title: parent, antagonist,2

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH11).

value: WT

value: antagonist


title: xenograft SH-SY5Y rep1 H3K27ac, ChIP-seq

value: Neuroblastoma


title: A2587 cells grown for 6h at 37ºC rep 1 [d169039.WT t:6]


title: VDRKO, Vehicle,1

description: V.KO.VDnega.AHnega_V.KO.VDnega.AHnega.1.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH5).

value: Vehicle


title: SK-N-SHm CD44neg Input, ChIP-seq

value: SK-N-SH

value: Cell line


title: A39000 cells grown for 2h at 37ºC rep 2 [d169033.cdc28-13 t:2]


title: int2_20_PD

value: PD

value: M


title: parent, 1,25(OH)2D3+antagonist,1

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH4).


title: SK-N-SHm CD44neg H3K27ac, ChIP-seq

value: ab4729 (rabbit polyclonal, Abcam)


title: A39000 cells grown for 4h at 37ºC rep 1 [d169038.cdc28-13 t:4]

value: yeast


title: SK-N-SHm CD44pos Input, ChIP-seq


title: xenograft SH-SY5Y rep2 H3K27ac, ChIP-seq

value: Xenograft of cell line


title: A2587 cells grown for 2h at 37ºC rep 3 [d169031.WT t:2]

value: Nasmyth Lab


title: int2_19_PD

value: prefrontal cortex


title: parent, antagonist,1

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH3).


title: VDRKO, antagonist,1

description: V.KO.VDnega.AHposi_V.KO.VDnega.AHposi.1.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH7).

value: VDRKO


title: SK-N-SHm CD44pos H3K27ac, ChIP-seq


title: SK-N-SH CD44neg Input, ChIP-seq


title: int2_17_ET

value: ET


title: VDRKO, 1,25(OH)2D3,1

description: V.KO.VDposi.AHnega_V.KO.VDposi.AHnega.1.

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH6).


title: A2587 cells grown for 2h at 37ºC rep 1 [d169029.WT t:2]


title: A2587 cells grown for 2h at 37ºC rep 2 [d169030.WT t:2]


title: SK-N-SH CD44neg H3K27ac, ChIP-seq

value: Neuroblastoma


title: parent, Vehicle,1

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH1).

value: WT

value: Vehicle


title: int2_15_ET

value: F


title: int2_12_PD

value: PD

value: M


title: Pt9Dx_TET2.Q1547_XVseq

description: XV-seq

source_name: Bone marrow

value: Bone marrow

value: Male

tag: disease state

value: Diagnosis

tag: bone marrow_involvement

value: No


title: parent, 1,25(OH)2D3,1

tag: cell line

value: Human cell line derived from colon cancer. Loss of the DNA mismatch repair gene (hMLH2).


title: Pt9Dx_TET2.E1437fs_XVseq

description: XV-seq

tag: tissue


title: int2_11_ET

value: prefrontal cortex


title: A39000 cells grown for 2h at 37ºC rep 1 [d169032.cdc28-13 t:2]

value: yeast

value: Amon Lab


title: SK-N-SH CD44pos Input, ChIP-seq

value: SK-N-SH

value: Cell line


title: HT29_METTL14 rep03

city: Shanghai

first: Yichao

last: Hou

address: 639 Zhi Zao Ju Road

country: China

institute: Shanghai Jiao Tong University

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 11.5 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: HT29 human colon cancer cells, METTL14, replicate 3

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

growth_protocol: HT29 human colon cancer cells were maintained in McCoy’s 5A supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: Total RNA was isolated from the HT29 human colon cancer cells by TRIzol reagent (Ambion) according to the manufacturer’s instructions. Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: stably infected with control transfectants or stable METTL14 overexpression

value: p53 mutant

value: HT29 colorectal cancer cell

value: stably infected with lentivirus carrying METTL14 overexpression (METTL14)


title: int1_18_PD


title: HT29_METTL14 rep02

source_name: HT29 human colon cancer cells, METTL14, replicate 2


title: int1_16_PD


title: HT29_METTL14 rep01

source_name: HT29 human colon cancer cells, METTL14, replicate 1


title: Pt9Dx_CUX1.L911fs_XVseq

description: XV-seq


title: SK-N-SH CD44pos H3K27ac, ChIP-seq

value: Neuroblastoma

value: ab4729 (rabbit polyclonal, Abcam)


title: P87

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

description: Single Cell 5' PE

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (refdata-cellranger-GRCh38-3.0.0) and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Assembly: refdata-cellranger-GRCh38-3.0.0
Supplementary files format and content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: skin

extract_protocol:
A 6mm punch biopsy was taken and processed immediately. The sample was cut into small pieces and digested in the C Tube (Miltenyi Biotec, Bergisch Gladbach, Germany) using the enzyme mix as provided by the Whole Skin Dissociation Kit for human (Miltenyi Biotec) in a total volume of 0,5ml RPMI medium with enzymatic supplements as described in the manufacturer's instructions. The sample was then incubated for a total of one hour in a water bath at 37°C. The sample was then further dissociated using the gentleMACS Dissociator (Miltenyi Biotec) running the program h_skin_01. After termination of the program steps 10-14 were conducted as detailed in the manufacturer's instructions. Finally, the cell pellet was resuspended in PBS with 0,08% BSA reaching a total volume of not more than 100µl. A cell aliquot was stained with trypan blue and cell numbers and percentages of dead cells were assessed by manual counting. Samples with not more than 30% dead cells were then subjected to scRNA-seq processing.
Single cell suspensions from skin isolates were processed for scRNA-seq using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit v1.1 (10X Genomics, Pleasanton, CA), according to the manufacturer’s suggestions.

value: skin

tag: condition 1

value: Covid-19 rash

tag: condition 2

value: psoriasis

value: ustekinumab


title: RNAseq in sgRUVBL1#2

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description: PE150 by NovaSeq6000

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling (for samples split between flowcells and later merged per run)
ChIP-seq reads were aligned to the GRCh38 genome assembly using BWA with the following configurations…
Aligned reads were then sorted by samtools (version 1.10) and duplicated reads were tagged and removed by Picard MarkDuplicates tool (version 2.21.1)
peaks were called using MACS2 (version 2.1.1) and --SPMR option was used to generate normalized pileup files for downstream analysis.
RNA-seq reads aligned to the GRCh38 genome assembly using STAR_2.6.0a, Aligned reads was normalized by edgeR bioconductor package and outputed as rpkm.txt file
Genome_build: Genome Reference Consortium GRCh38
Supplementary_files_format_and_content: bigwig file were generating using MACS2 and bdgToBW, scores represent pileup signals
Supplementary_files_format_and_content: raw count table in txt format of every sample in RNAseq project

source_name: A673 cells

growth_protocol: Cas9-expressing A673 cells transduced with sgCtrl or sgRUVBL1 and seleted in 1 ug/ml puromycine for 4 days.

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN) for RNAseq.
Eukaryotic mRNA directional library prep were used for RNAseq.

treatment_protocol: sgCtrl and sgRUVBL1 were cloned into ipUSEPR vector and transduced via lentiviral infection.

value: Ewing sarcoma

tag: sequencing type

value: RNA-seq

tag: transduction


title: Pt9Dx_BioRep2_scRNAseq

description:
Seq-Well S^3
Pt9Dx_counts.tsv
Pt9Dx_norm.tsv
Pt9Dx_metadata.tsv

value: Bone marrow

value: Male

tag: age

value: Diagnosis

value: No


title: HT29_vector rep3

source_name: HT29 human colon cancer cells, vector, replicate 3

tag: treatment

value: stably infected with lentivirus carrying control transfectants (vector)


title: HT29_vector rep2

source_name: HT29 human colon cancer cells, vector, replicate 2


title: RNAseq in sgRUVBL1#1

description: PE150 by NovaSeq6000


title: RNAseq in sgCtrl#2

description: PE150 by NovaSeq6000

value: sgCtrl


title: Pt9Dx_BioRep1_scRNAseq

tag: Sex


title: int1_13_ET

value: prefrontal cortex

tag: cohort

tag: diagnosis

value: ET

tag: age (yr)

value: F


title: METTL14_02

hyb_protocol: Configure the hybridization reaction solution according to the manufacturer’s instruction. Run on the PCR machine at 99°C for 5 minutes and 48°C for 5 minutes. Add hybridization solution to the chip and hybridize at 48°C and 60rpm for 16 hours.

scan_protocol: Washing the hybridization chip and scanned with GeneChip® Scanner 3000, Affymetrix, P/N 00-00212.

data_processing: Standardize data using RMA algorithm (R package).

source_name: HCT116 human colon cancer cells, stably expressing METTL14

label_protocol: 4µl 5X FlashTag Biotin HSR Ligation Mix and 2µl T4 DNA Ligase were added to the mixture in order. Then Run on the PCR machine at 25℃ for 30min. The reaction was terminated by 2.5µl HSR Stop Solution.

growth_protocol: Cells were cultured in the recommended medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. Then 1ug total RNA was treated with Poly(A) Polymerase Tailing Kit.

treatment_protocol: Cells were stably infected with lentivirus carrying control vector (Lv-vector) or METTL14  (Lv-METTL14).

value: HCT116 human colon cancer cell line

value: stably expressing METTL14


title: RNAseq in sgCtrl#1

description: PE150 by NovaSeq6000

tag: cell type


title: int1_8_PD

value: PD

value: M


title: int1_7_ET


title: MYC ChIPseq in sgRUVBL1#2

description: PE150 by NovaSeq6000


title: BM6_BioRep1_scRNAseq

description:
Seq-Well S^3
BM_counts.tsv
BM_norm.tsv
BM_metadata.tsv

value: HealthyDonor


title: METTL14_01


title: int1_6_PD


title: MYC ChIPseq in sgRUVBL1#1

description: PE150 by NovaSeq6000


title: METTL14_03


title: int1_5_ET


title: int1_4_PD


title: vector_02

source_name: HCT116 human colon cancer cells, stably expressing control vector

value: stably expressing control vector


title: MYC ChIPseq in sgCtrl#1

description: PE150 by NovaSeq6000

value: Ewing sarcoma


title: MYC ChIPseq in sgCtrl#2

description: PE150 by NovaSeq6000


title: HT29_vector rep1

source_name: HT29 human colon cancer cells, vector, replicate 1

value: p53 mutant

value: HT29 colorectal cancer cell


title: int1_3_ET


title: int1_2_PD


title: vector_01


title: Input for MYC ChIPseq

description: PE150 by NovaSeq6000


title: Unstimulated vs IL-4 stimulated cells from donor #3

city: Tampere

first: Ilkka

last: Junttila

state: Tampere

address: Arvo Ylpön katu 34

department: Institute of Medical and Life Science

country: Finland

institute: University of Tampere

description: Biological replicate 3 of 3. Flipped labeling.

hyb_protocol: Standard Agilent protocol

scan_protocol: Agilent Technologies Scanner G2505C - 5 microns per pixel

data_processing: Agilent Feature extraction version GE2_105_Dec08

source_name: neutrophils isolated from blood

label_protocol: Nugen Ovation V2, Nugen FL-Ovation cDNA Fluorescent Module

growth_protocol: Freshly isolated human neutrophils

extract_protocol: Qiagen RNAeasy (#74104) kit protocol

treatment_protocol: unstimulated or stimulated with 1ng/ml IL-4

tag: donor number

value: Donor 3

tag: stimulation type

tag: stimulation

value: Unstimulated


title: int1_9_ET


title: IL-4 stimulated cells vs Unstimulated from donor #3

description: Biological replicate 3 of 3.


title: int1_1_ET


title: vector_03

tag: genotype


title: Unstimulated vs IL-4 stimulated cells from donor #1

description: Biological replicate 1 of 3. Flipped labeling.

value: Donor 1


title: IL-4 stimulated cells vs Unstimulated from donor #2

description: Biological replicate 2 of 3.

value: Donor 2


title: Unstimulated vs IL-4 stimulated cells from donor #2

description: Biological replicate 2 of 3. Flipped labeling.


title: sgDGAT1a 3 bulk RNAseq

status: Public on Mar 26 2023

city: New York

first: Dianne

last: Lumaquin

state: NY

address: 417 E 68th ST

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequencing reads underwent quality control with FASTQC 0.11.9, trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11.
Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters.
Normalized counts derived from DESeq2 processing.
Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell-type specific marker genes as done previously using FindAllMarkers.
Assembly: GRCz11

organism: Danio rerio

source_name: Skin

extract_protocol:
Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter.
Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing (Takara) according to manufacturer's instructions.

value: Skin

value: melanoma

value: DGAT1a knockout


title: IL-4 stimulated cells vs Unstimulated from donor #1

description: Biological replicate 1 of 3.


title: sgDGAT1a 2 bulk RNAseq


title: sgDGAT1a 1 bulk RNAseq


title: sgNT 3 bulk RNAseq

value: WT


title: sgNT 2 bulk RNAseq


title: sgNT 1 bulk RNAseq


title: TEAZ scRNAseq

data_processing:
Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell-type specific marker genes as done previously using FindAllMarkers.
Counts matrix derived from Seurat
Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell-type specific marker genes as done previously using FindAllMarkers.
Assembly: GRCz11

extract_protocol:
Zebrafish tumors were dissected and dissociated for encapsulation
Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation, droplet-based scRNA-seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G (10x Genomics) into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles, i5 10 cycles, i7 10 cycles, Read2 90 cycles. Sequencing depth was approximately 51,000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.


title: D32_P1

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

data_processing:
The reads from fastq files were mapped to the human genome (Ensembl version 90) and quantified using Cell Ranger 3.1.0 (10x Genomics).
Cell Ranger was run with the expect number of cells parameter (expect-cells) set to 8,000.
Cell Ranger output matrices (i.e. genes.tsv and barcodes.tsv) were then input into R, the samples from the same batch were merged and genes with zero counts in all cells were discarded.
Genome_build: Human genome (Ensembl version 90). We provided to Cell Ranger a custom-built reference transcriptome generated by filtering the Ensembl transcriptome for the gene biotypes: protein coding, lincRNA and antisense.
Supplementary_files_format_and_content: Cell Ranger output matrices

source_name: Differentiated Human Embryonic Stem Cells (ESC)

growth_protocol: hES cell–derived photoreceptor progenitors differentiated from H1 ES cells on coated laminin (LN523 and LN521) on Costar 6 or 24 well plates.

extract_protocol:
Adherent cells were trypsinized using TrypLE for 8 minutes at 37oC. Generation and Barcoding of Gel Bead-In-Emulsions (GEMS) were performed according to standard 10X Genomics Reagent kit Protocol (Chromium Single Cell 3' Reagent kits).
RNA libraries were prepared for sequencing using standard 10X Genomics Protocol (Chromium Single Cell 3' Reagent kits)
D2 and D9 for H1 cells were processed in one batch; D22 and D32 H1 cells were processed in one batch; H9D9, H9D32, HS980D9 and HS980D32 were processed in one batch

value: H1 ES-derived photoreceptor progenitors

tag: passages

tag: type of laminin coating

value: Laminin 523 + Laminin 521

tag: time (rna was extracted from wells at day)

value: Day 32

tag: cell line


title: D22_P2

value: Day 22


title: D32_P2


title: F6_HFD_8w_liver

city: Beijing

first: Li

last: Wang

address: No.1 Tiantan Xili

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters GeneSpring GX to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: liver_miR-185-inh treated ApoE KO mice fed a high-fat diet after 8 w

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the NucleoSpin® RNA clean-up kit（MACHEREY-NAGEL,Germany）following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Livers were harvested and stored at -80 °C from ApoE KO mice, fed a high-fat diet, which were treated by ctrl-inh or miR-185-inh after 8 w.

value: ApoE KO

value: male

value: 8 weeks

tag: tissue

value: liver


title: F1_HFD_8w_liver


title: D22_P1


title: E11_HFD_8w_liver

source_name: liver_ctrl-inh treated ApoE KO mice fed a high-fat diet after 8 w

value: ctrl-inh


title: F12_HFD_8w_liver


title: F8_HFD_8w_liver


title: E3_HFD_8w_liver


title: F3_HFD_8w_liver


title: F10_HFD_8w_liver


title: Adult-DRG

city: Nantong

first: Sheng

last: Yi

state: Jiangsu, China

address: 19 Qixiu Road

institute: Nantong University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

organism: Rattus norvegicus

source_name: dorsal root ganglion

growth_protocol: Primary culture of SCs was maintained in DMEM containing 10% fetal bovine serum (complete medium) at 37°C under humidified 5% CO2.

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

tag: strain

value: Sprague Dawley

value: not determined

value: postnatal 8 weeks

tag: tissue/cell type

value: dorsal root ganglion


title: F7_HFD_8w_liver

tag: age

tag: treatment


title: E8_HFD_8w_liver

tag: Sex


title: F9_HFD_8w_liver


title: E4_HFD_8w_liver


title: E12_HFD_8w_liver


title: E9_HFD_8w_liver


title: P1-DRG

value: postnatal day 1


title: Adult-SN

source_name: sciatic nerve

value: sciatic nerve


title: E1_HFD_8w_liver


title: L523-D30_C2D3R2_L002

description: Sample 26

data_processing:
All reads were assessed for quality and (when necessary) adaptors were removed using Cutadapt.
RNA-Seq reads were aligned to hg38 (Ensembl Gene annotation build 79) using STAR 2.5.2b
Reads were quantified using featureCount v1.5.1
Genome_build: hg38 (Ensembl Gene annotation build 79)
Supplementary_files_format_and_content: tab-delimited text files include sample information, counts, and TPM values for each sample.

extract_protocol:
RNA extraction using Qiashredder (Qiagen; 79656) and RNeasy mini kit (Qiagen; 74106)
Libraries were constructed with TruSeq stranded total RNA library Prep Kit (Illumina).
Samples were multiplexed with 10 samples per lane and sequenced in Illumina HiSeq 3000 RNA sequencing platform (150bp pair-end reads)

value: ES-derived photoreceptor progenitors

value: Laminin 523 + Laminin 323


title: D9_P2_H1

value: H1 ES-derived photoreceptor progenitors

value: Day 9


title: L523-D30_C2D3R1_L001

description: Sample 25

value: Day 32


title: L523-D20_C2D2R3_L003

description: Sample 24

value: Day 22


title: D9_P1_H1

value: Laminin 523 + Laminin 521


title: D2_P2_H1

source_name: Undifferentiated Human Embryonic Stem Cells (ESC)

value: H1 undifferentiated ESC

value: Day 2


title: L523-D20_C2D2R2_L002

description: Sample 23


title: P1-SN


title: L523-D0_C2D1R3_L003

description: Sample 21


title: L523-D20_C2D2R1_L001

description: Sample 22


title: L523-D30_C2D3R3_L003

description: Sample 27


title: E2_HFD_8w_liver

value: ApoE KO

value: male

value: 8 weeks

value: liver


title: L523-D0_C2D1R2_L002

description: Sample 20


title: L523-D0_C2D1R1_L001

description: Sample 19


title: L521-D30_C1D3R3_L003

description: Sample 18

value: Laminin 521 + Laminin 323


title: L521-D30_C1D3R2_L002

description: Sample 17


title: liver, without treatment, rep3

city: Wuhan

first: Huanzhang

last: Niu

address: Jiefang Avenue 1277#

institute: Wuhan Union Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCH38/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Assembly: tab-delimited text file includes RPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: condition

value: Budd-Chiari syndrome

value: without treatment


title: L521-D20_C1D2R3_L003

description: Sample 15


title: liver, without treatment, rep4


title: liver, endovascular treatment, rep4

value: endovascular treatment


title: liver, endovascular treatment, rep2


title: liver, endovascular treatment, rep1


title: D2_P1_H1


title: L521-D20_C1D2R2_L002

description: Sample 14

value: ES-derived photoreceptor progenitors


title: NB4-IgG

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.1)
Peaks were identified using MACS2 (v2.0.10)
Assembly: hg38
Supplementary files format and content: peak text files
Library strategy: CUT-TAG

extract_protocol: HyperactiveUniversalCUT&TagAssayKitfor Illumina (Vazyme #TD903)

tag: chip antibody

value: IgG

tag: treat

value: untreated


title: NB4-LDB1


title: B6

city: Izumo

first: Ryosuke

last: Tanino

address: 89-1 Enya

department: Department of Internal Medicine

institute: Shimane University

description: Murine lungs were harvested from 6 mice of B6 after bronchoalveolar lavage fluid and exsanguinated under anesthesia. Total RNA was extracted from each lung and mixed for 6-biological-replicate.

hyb_protocol: Labelled aminoallyl-RNA pools were mixed with hybridization buffer, and hybridized for 16 h. Hybridization was followed by the instruction (Toray Industries, Inc.).

scan_protocol: 3D-Gene Scanner (Toray Industries Inc.) was used for mesuring intensity of Cy5 or Cy3. Images were quantified using 3D-Gene Extraction software (Toray Industries Inc.).

data_processing: Detected signals for each gene were normalized by global normalization method (Cy3/Cy5 ratio median=1).

source_name: Murine lung

label_protocol: Mixed total RNA was labeled with Cy5 or Cy3 by using Amino Allyl MessageAmp II aRNA Amplification Kit (Thermo Fisher Scientific).

extract_protocol: Lung sample (25 mg per mouse) were homogenized using TissuLyser II (Thermo Fisher Scientific). Total RNA was extracted using miRNeasy Mini Kit (Qiagen) following the instruction. Each total RNA (10 μg per mouse) from six mice was mixed up for the labeling.

value: C57BL/6JJcl (Clea Japan, Inc., Tokyo, Japan)

tag: room condition

value: Conventional conditions with food and water ad libitum.

value: Male


title: liver, without treatment, rep1


title: ME

description: Murine lungs were harvested from 6 mice of ME after bronchoalveolar lavage fluid and exsanguinated under anesthesia. Total RNA was extracted from each lung and mixed for 6-biological-replicate.

value: Mayumi-Emphysema mouse


title: liver, endovascular treatment, rep3


title: L521-D0_C1D1R3_L003

description: Sample 12

tag: cell type

value: H1 undifferentiated ESC


title: L521-D0_C1D1R2_L002

description: Sample 11

value: Day 2


title: L521-D0_C1D1R1_L001

description: Sample 10


title: poePro_wholefish_lineB_n5_rep3

city: Auburn University

first: Xu

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

data_processing:
The quality of raw reads were controlled using  FastQC.
Sequencing adapter sequences and low-quality bases were trimmed using Trimmomatic v0.36.
High-quality reads were mapped to the reference P. prolifica genome assembly by Tophat-2.1.1.
The raw RNA-seq counts for each gene were determined using BEDtools
Assembly: P. prolifica genome assembly (GenBank assembly accession JAPDDK000000000)
Supplementary files format and content: Gzipped, tab-delimiited text file inlcuding raw gene counts for every gene in all samples

organism: Poeciliopsis prolifica

source_name: juvenile wholefish

extract_protocol:
Total RNA samples were extracted from the whole body of juvenile P. prolifica (n = 3 for line A and n = 3 for line B) using the RNeasy Mini Plus kit (Qiagen, Redwood City, CA, USA).
For juvenile fish wholebody samples, standard double-strand RNA-seq libraries were constructed using the Illumina TruSeq RNA Library Prep Kit (Illumina, San Diego, CA, USA) and the NEXTFLEX Rapid RNA-Seq Kit for Illumina Sequencing (PerkinElmer, Hopkinton, MA, USA). To obtain information on the direction of transcription, single-strand RNA-seq libraries were prepared using the NEXTFLEX Rapid Directional RNA-Seq Kit (PerkinElmer, Hopkinton, MA, USA) and TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA, USA) following the manufacturer’s protocols.  libraries were sequenced in a 2×100 bp Paired-End (PE) setting on an Illumina HiSeq2000 machine. To characterize expression genes in the embryonic stages, total RNA samples were also extracted from early embryos at developmental stage 45 of P. prolifica line A and line B, and mRNA-seq libraries were prepared using the TruSeq RNA Library Prep kit v2 (Illumina, San Diego, CA, USA). After size check on an Agilent TapeStation 4200 using the High-Sensitive D1000 Screen Tape (Agilent Technologies, Santa Clara, CA, USA), the libraries were sequenced using a 2×125 bp PE format on an Illumina HiSeq2500 Sequencer .

value: line B

tag: cultured time

value: uncultured


title: L323-D30_C3D3R3_L003

description: Sample 9

value: Laminin 323

value: Day 32


title: L521-D30_C1D3R1_L001

description: Sample 16

value: Laminin 521 + Laminin 323


title: poePro_wholefish_lineB_n5_rep1


title: poePro_wholefish_lineB_n1_2


title: poePro_wholefish_lineB_n1_1


title: L323-D30_C3D3R2_L002

description: Sample 8


title: poePro_wholefish_lineA_n6_rep3

value: line A


title: HS980D32

value: HS980 ES-derived photoreceptor progenitors

value: Laminin 523 + Laminin 521


title: poePro_wholefish_lineA_n6_rep4


title: L323-D20_C3D2R3_L003

description: Sample 6

value: ES-derived photoreceptor progenitors

value: Day 22


title: liver, without treatment, rep2

value: liver

value: Budd-Chiari syndrome

value: without treatment


title: L323-D20_C3D2R2_L002

description: Sample 5


title: H9D32

value: H9 ES-derived photoreceptor progenitors


title: H9D9

value: Day 9


title: L521-D20_C1D2R1_L001

description: Sample 13


title: poePro_wholefish_lineB_n5_rep4

value: untreated


title: poePro_wholefish_lineA_n6_rep2


title: poePro_s40_placenta_lineB_n11

source_name: placenta


title: L323-D0_C3D1R3_L003

description: Sample 3

value: H1 undifferentiated ESC

value: Day 2


title: L323-D20_C3D2R1_L001

description: Sample 4


title: poePro_wholefish_lineA_n6_rep1

value: uncultured


title: poePro_s40_embryo_lineB_n11

source_name: embryo

value: line B


title: poePro_s40_placenta_lineA_n7


title: poePro_wholefish_lineA_n3_2


title: poePro_wholefish_lineB_n5_rep2


title: poePro_wholefish_lineA_n3_1


title: poePro_s40_embryo_lineA_n7


title: L323-D0_C3D1R1_L001

description: Sample 1

value: Laminin 323


title: L323-D30_C3D3R1_L001

description: Sample 7

value: Day 32


title: HS980D9


title: Human lung mast cells (donor 4)

status: Public on Mar 25 2023

city: Solna

first: Elin

last: Rönnberg Höckerlind

address: NKs Bioclinicum J7:30, Visionsgatan 4

department: Medicine (Solna)

country: Sweden

institute: Karolinska Institutet

description:
SmartSeq2
Plate 404

data_processing: Reads were aligned to the reference genome GRCh38 (primary assembly) using star/2.5.3a with default settings. Counts per gene  were calculated for each transcript using featureCounts from subread/1.5.2 using parameters -t exon -g gene_id

source_name: Lung

extract_protocol:
Single-cell suspensions were obtained by digesting the tissue as previously described (Ravindran et al. Front Immunol 2022). Briefly, human lung tissue was cut into small pieces and enzymatically digested for 45 min with DNase I and collagenase. Thereafter, the tissue was mechanically disrupted by shearing with a syringe, debris was removed by 30% Percoll centrifugation and red blood cells lysed with an ACK buffer. Thereaftar the mast cells were FACS sorted.
SmartSeq2
Sorted cells were processed using the Smart-seq2 protocolwith minor changes (Picelli et al., 2013).

value: Lung

value: mast cells

value: female


title: Human lung mast cells (donor 3)

description:
SmartSeq2
Plate 401


title: Human lung mast cells (donor 2)

description:
SmartSeq2
Plate 272


title: Human lung mast cells (donor 1)

description:
SmartSeq2
Plate 049-3

value: male


title: RNA-Seq of Adult Oenocyte_fruTrip-rep2

city: New Orleans

first: Jie

last: Sun

state: Louisiana

address: 1700 Tulane Ave

department: School of Medicine, Department of Biochemistry

institute: Tulane University

description:
fru_Trip-rep2
Using BDSC#31593 knock down Fru in oenocytes

data_processing:
QC: fastp 0.22.0
Align ot dme 6: bowtie2
Counts: RSEM 1.2.31
DEGs :edger 3.36.0; P ≤ 0.001 and a log2 fold change: 2
Assembly: dme6

organism: Drosophila melanogaster

source_name: Oenocyte

growth_protocol: 25 °C, 60% relative humidity, and 12-h light/dark cycle until eclosion, and then incubated at 29°C for 7 days

extract_protocol:
Zymo RNA  preparation kit.
NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina were used for library preparation.

value: Oenocyte

tag: genotype

value: prom-E800-Gal4,Fru-RNAi (BDSC#31593)


title: RNA-Seq of Adult Oenocyte_Ctrl-rep1

description:
Ctrl-rep1
the control of oenocyte

value: 25 °C, 60% relative humidity, and 12-h light/dark cycle until eclosion, and then incubated at 29°C for 7 days


title: RNA-Seq of Adult Oenocyte_fru330035-rep2

description:
fru_330035-rep2
Using VDRC330035 knock down Fru in oenocytes

value: prom-E800-Gal4,Fru-RNAi (VDRC330035)


title: RNA-Seq of Adult Oenocyte_fruTrip-rep1

description:
fru_Trip-rep1
Using BDSC#31593 knock down Fru in oenocytes


title: RNA-Seq of Adult Oenocyte_Ctrl-rep2

description:
Ctrl-rep2
the control of oenocyte


title: RNA-Seq of Adult Oenocyte_fru105005-rep1

description:
fru_105005-rep1
Using VDRC105005 knock down Fru in oenocytes

value: prom-E800-Gal4,Fru-RNAi (VDRC105005)


title: RNA-Seq of Adult Oenocyte_fruBOE-rep2

description:
fruB_OE-rep2
overexpression Fru in the oenocytes


title: RNA-Seq of Adult Oenocyte_fruBOE-rep1

description:
fruB_OE-rep1
overexpression Fru in the oenocytes


title: RNA-Seq of Adult Oenocyte_fru330035-rep1

description:
fru_330035-rep1
Using VDRC330035 knock down Fru in oenocytes


title: RNA-Seq of Adult Oenocyte_fru105005-rep2

description:
fru_105005-rep2
Using VDRC105005 knock down Fru in oenocytes


title: L323-D0_C3D1R2_L002

description: Sample 2

tag: passages


title: KOPTK1_I-BET151_treatment_72h_RNA-seq

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

data_processing:
The sequence reads were aligned to the reference human genome  hg19 (GRCh37-lite; http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/README.GRCh37-lite) using BWA-0.5.7 aln.
RNA-seq pair-end reads were aligned to an extended reference transcriptome that consists of the reference genome and annotated exon–exon junctions using BWA-0.5.7 aln. To generate the custom reference transcriptome (built from NCBI GRCh37-lite reference and Ensembl v75 annotations) and ‘reposition’ reads that spanned exon-exon junctions we used JAGuaR v 2.0.3.
For RPKM normalization, we used the total number of reads aligned into coding exons normalized by total exon length
Assembly: hg19a
Supplementary files format and content: RPKM_and_read_counts.xlsx

growth_protocol: KOPTK1 cell line were grown in RPMI 1640 media supplemented with 10% FBS, penicillin/streptomycin solution, and 2mM L-glutamine.

extract_protocol:
RNA was isolated from live cells with TRIzol reagent followed by purification over PureLink RNA mini kit columns (Invitrogen).
RNA-seq was performed using a poly A library construction protocol with strand specific cDNA synthesis and 8 cycles of PCR. Purification of polyA+ mRNA and mRNA(-) was done by Flow-through total RNA using MultiMACS 96 Separation Unit. For library Construction, 96-well Plate-based Strand-specific cDNA Synthesis using Maxima H Minus Strand Specific 96-well was used for Illumina MiSeq Sequencing.

treatment_protocol: KOPTK1 cells were seeded at 100,000 per well in 6 well-plate. DMSO (Sigma, D2650-100ML) and I-BET151 (Selleckchem, S2780) were dosed by direct addition to the culture media at 0.1%. I-BET151 was used at a final concentration of 0.5µM and cells were treated for 72 hours.

value: T-ALL cell

tag: time

value: 72 hours of treatment

value: Peripheral Blood

tag: disease state

value: T-cell Lymphoblastic Leukemia


title: KOPTK1_I-BET151_control_DMSO_72h_RNA-seq

tag: cell line

value: control


title: MDAMB231_m6A-seq_shNS_IP_rep2

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
Library strategy: m6A-seq
Raw reads from m6A-seq were also quality controlled by utilizing FastQC and mapped to the human transcriptome built with gene annotations (gencode v33) by use of STAR with parameters --outFilterMismatchNoverReadLmax 0.04 and --outFilterMultimapNmax 20.
The mapped reads were then passed to exomePeak (version 2.16) with default parameters to identify the potential m6A peaks.
The identified m6A peaks with fold enrichment ≥ 1 and FDR ≤ 0.05 were recognized as significant m6A methylated regions.
Genome_build: hg38
Supplementary_files_format_and_content: results from exomePeak

growth_protocol: MDA-MB-231 cells were grown to 80-90% confluence and total RNA was purified by Trizol (Qiagen) using manufacturers protocols.

extract_protocol:
Trizol (Qiagen) was used to isolate total RNA followed by PolyA RNA purification using PolyATtract® mRNA Isolation Systems kit (Promega) from MDA-MB-231 cells. The RNA was fragmented by incubating mRNA at a concentration of 1ug/ul with 10mM ZnCl2 in 10mM Tris-HCl pH 7.0 at 94C for 4 minutes. 10ug of fragmented RNA was then immunoprecipitated using 5ug anti-m6A antibody (Synaptics Systems). The immunoprecipitated RNA was purified by the RNeasy MinElute Cleanup Kit (Qiagen).
Agilent Bioanalyzer 2100 was used to determine the size and quality of both IP and input samples prior to RNA library construction using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) (KR0960m Kapa Biosystems) and sequenced on an Illumina Hiseq2500.


title: KOPTK1_I-BET151_treatment_72h_input

data_processing:
The sequence reads were aligned to the reference human genome  hg19 (GRCh37-lite; http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/README.GRCh37-lite) using BWA-0.5.7 aln.
In all the downstream analyses duplicate reads are removed and mapQ >= 5 is used
FindER.1.0.0b is used with IP-signal data and DNA input control data to call the peaks at FDR <=0.01 with minimum peak size 300bp and maximumpeaks within gap between peaks is 100bp are merged together.
Assembly: hg19 (GRCh37-lite) http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/README.GRCh37-lite
Supplementary files format and content: bigwig files were generated using UCSC utilities.

extract_protocol:
ChIP-seq libraries were constructed using Native ChIP-seq protocol with a validated anti-H3K27ac antibody (ab4729).
A customized version of paired-end sample Prep Kit from Illumina V.1.1 was used for sample preparation. Libraries were indexed, pooled and sequenced using paired-end 75nt sequencing chemistry on an Illumina HiSeq 2500 platform following the manufacturer’s protocols (Illumina, Hayward, CA).

tag: anatomic site

value: Pleural Effusion


title: KOPTK1_I-BET151_control_DMSO_72h_input


title: KOPTK1_I-BET151_treatment_72h_H3K27ac

value: anti-H3K27ac antibody (ab4729)


title: MDAMB231_m6A-seq_shNS_IP_rep1


title: MDAMB231_m6A-seq_shNS_input_rep1

value: input


title: MDAMB231_m6A-seq_shNS_input_rep2


title: KOPTK1_I-BET151_control_DMSO_72h_H3K27ac


title: MDAMB231_RIP-seq_YTHDC1_IP_rep2

description: RIP-seq

data_processing:
The human genome indexes were built with gene annotations (gencode v33) and the human GRCh38 reference genome sequences by using STAR (version 2.7.2b) and RSEM (version 1.2.31) software.
Then raw reads from RNA-seq were quality controlled through FastQC (version 0.11.5, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and mapped to the reference genome with built index by use of STAR.
After alignments, RSEM was used to estimate the read counts of transcripts. To identify YTHDC1 targeted transcripts, we kept the transcripts with read counts ≥ 5 in at least 50% samples and then perform batch effect correction by utilizing RUVSeq R package.
We then calculated the dispersion and fold change of transcripts of YTHDC1 IP versus input in MDA-MB-231 cells by use of DESeq2 with shrinkage estimators.
The transcripts with adjusted p-value ≤ 0.1 and fold change ≥ 2 were recognized as YTHDC1 bound targets.
Genome_build: hg38
Supplementary_files_format_and_content: results from DESeq2

growth_protocol: MDA-MB-231  cells were transduced with 3x flag-YTHDC1 by lentiviral transduction using an MOI of 4. 24 hours later, 2ug/ml puromycin was added and the cells were selected for 4 days before RNA immunoprecipitation.

extract_protocol:
Cells were washed with cold PBS and UV-crosslinked 3× at 120,000 μJ/cm2 using a 254nm lamp. Nuclear isolation buffer (320mM sucrose 10mM Tris-HCl pH 7.5, 5mM MgCl2, 1% Triton X-100 vol/vol) was added onto the dish and the cells were detached with a cell scraper. The cells were incubated on ice for 20 minutes on ice followed by pelleting of nuclei by centrifugation at 1500 × g for 15 minutes at 4°C. The pellet was resuspended in RIP buffer (150mM NaCl, 25mM Tris-HCl pH 7.4, 5mM EDTA, 0.5mM DTT, and 0.5% Tergitol NP40) containing HaltTM Protease (Thermo Fisher Scientific) and RiboLock (Thermo Fisher Scientific) RNase inhibitors and sonicated using a Qsonica Q800R3 sonicator to isolate nuclear contents. The lysate was centrifuged at 15,000 × g for 10 minutes at 4°C and the supernatant was pre-cleared by incubation with protein A/G beads for 1 hour at 4°C. The amount of protein in each sample was quantified using the Bio-Rad Protein Assay Kit (Bio-Rad). For each immunoprecipitation reaction, 5 μg of anti-flag antibody (F3165, Sigma-Aldrich) or normal mouse IgG (12-371, Millipore) was conjugated to 50 μl Protein A/G magnetic beads (Thermo Fisher Scientific) for 4 hours at 4°C. The beads were washed twice with RIP buffer and incubated with supernatant containing 500 μg protein from nuclear lysate overnight at 4°C. Meanwhile, supernatant containing 50 μg of protein (10% input) was saved for each RNA or protein input sample. The next day, the immunoprecipitation reactions were washed 3x with RIP buffer and resuspended in 100 μl PBS. For isolation of immunoprecipitated protein, 20 μl of beads were transferred to another 1.5 ml tube and 6.7 μl of 4x Laemli buffer was added and the sample was incubated at 95°C for 5 minutes. The remaining beads were then treated with DNase 1 (Thermo Fisher Scientific) followed by Proteinase K (Thermo Fisher Scientific) to remove unwanted DNA and uncrosslinked protein. The tube was then placed on a magnetic stand and the supernatant containing the immunoprecipitated protein fraction was transferred to a new tube and frozen at -80°C. Trizol was added to the remaining 80 μl of beads and RNA was isolated.
Samples were rRNA depleted followed by library construction using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) (KR0960m Kapa Biosystems) with 10 cycles of PCR amplification and sequenced on an Illumina Hiseq2500.


title: MDAMB231_RIP-seq_YTHDC1_IP_rep1

description: RIP-seq


title: MDAMB231_RIP-seq_YTHDC1_input_rep2

description: RIP-seq


title: MDAMB231_RIP-seq_YTHDC1_input_rep1

description: RIP-seq