title: C9-4_Ab_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

status: Public on May 23 2023

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N 5th St

institute: TGen

description:
C7_NonStimulated_FTD27_1_V7_Sattler_IPSC_microglia_S40
genecounts_Stim_Master.csv

data_processing:
base calling was performed using Illumina' bcl2fastq software
adapter trimming was performed using cutadapt to remove the first 3 bases from end of R2, as specifed by Takara Bio
reads were aligned to the human genome using STAR v.2.7.10a with default options
alignment (BAM) fies from STAR were converted into gene counts tables using featureCounts v. 1.6.4 with default options
Assembly: GRCh38
Supplementary files format and content: raw gene counts tables from featureCounts

source_name: cell line

growth_protocol:
IPSCs were differentiated into microglia following an established protocol (McQuade et al., 2018). Briefly, iPSCs were maintained in mTeSR Plus Kit (Stemcell Technologies # 05825) in 10cm dishes. At DIV -1 of HPCs differentiation, five to seven day old iPSCs cultures were then used to generate cluster of differentiating 43 positive (CD43+) hematopoietic progenitor cells (HPCs) following a 12 day commercially available kit (STEMdiff Hematopoietic Kit; Stemcell Technologies # 05310). IPSCs were cleaned and 1/3 dish was gently dissociated with dispase (Stemcell Technologies # 07923) for 12-15 minutes at 37°C. IPSCs were then collected and spun down at 500rpm for 1-2 minutes and resuspended in 2mL of mTeSR Plus media with 20 µM ROCK inhibitor Y-27632 (Stemcell Technologies # 72304). Matrigel, hESC-Qualified Matrix (Corning # 354277) coated six well plates were used to start the HPC differentiation. Using a 5mL serological pipette, one drop or two drops of iPSCs were seeded per well into matrigel. Then, next day, on DIV 0 of HPCs differentiation, wells with 80 small colonies per well were selected to start HPCs differentiation. IPSCs were fed following the manufacturer’s instructions. On DIV 12 of HPCs differentiation, only the non-adherent HPCs were transferred to a new six well plate to start microglia differentiation (DIV 12/0).
Matrigel, GFR (growth factor reduced) Membrane Matrix (Corning # 356231) coated six well plates were prepared to start microglia differentiation (DIV12/0). HPCs were differentiated into microglia for 28 days using serum free media conditions. HPCs in suspension were collected and spun down at 300 xG for 6 minutes and resuspended into microglia basal media (MBM, 2mL/well) containing: DMEM/F12 no phenol (Gibco # 11-039-021), 2% Insulin Transferin Selenite (Gibco # 41400045), 2% B27 (Gibco # 17504-044), 0.5% N2 (Gibco # 17502-048), 1% Glutamax (Gibco # 35050-061), 1% NEAA (Gibco # 11140-050), 1% Pen/Strep (Gibco # 15140-122), 400μM 1-Thioglycerol (Sigma # M1753), 5μg/mL human insulin (Sigma # I2643) and supplemented with 3 growth factors (GFs): 100ng/mL human recombinant interleukin-34 (IL-34; Peprotech # 200-34), 25ng/mL macrophage colony-stimulating factor (M-CSF; Gibco # PHC9501) and 50ng/mL transforming growth factor β1 (TGFβ1; Miltenyi Biotec # 130-108-969) (MBM + 3GFs); cytokines and growth factors known to be essential for the development of microglia (Butovsky et al., 2014, Greter et al., 2012, Wang et al., 2012, Abud et al., 2017, Pandya et al., 2017, Abutbul et al., 2012, Chen et al., 2002, Elmore et al., 2014). Microglia differentiation starts (DIV 12/0) once the HPCs are transferred and plated at a density of 200 000 cells per well of a six well. Cells will predominantly grow in suspension. On DIV 2, 4, 6, 8 and 10 of microglia differentiation, 1mL of MBM + 3GFs media was added to each well. On DIV 12, a partial media change was done. IPSC-MGs from one six well plate were spun down at 300 xG for 6 minutes and resuspended into MBM + 3 GFs and split back into the same six well plate. On DIV 14, 16, 18, 20, 22, 24, 1mL media was added per well. On DIV 25, MBM + 3GFs was changed to maturation media composed of MBM supplemented with the 5 growth factors (MBM +5 GFs): 100ng/mL IL34, 25ng/mL M-CSF and 50ng/ml TGFβ1, 100ng/mL cluster of differentiation 200 (CD200; Novoprotein # C31150UG) and100ng/mL fracktaline chemokine C-X3-C motif ligand 1 (CX3CL1; Peprotech # 300-31) (MBM + 5 GFs). The presence of CD200 and CX3CL1 in the culture media, both glial and neuronal molecules are critical for microglia maturation and maintenance of an in vivo-like microglia resting state phenotype in an in vitro setting (Barclay et al., 2002, Kim et al., 2011, Kierdorf and Prinz, 2013) (Figure 1A). At DIV 28, IPSC-MG reached maturation. 1mL of MBM + 5GFs media was added to the cultures every other day. Mature cells were used for experimentation within 10 days (DIV 28-DIV38).
For cortical neuron differentiation, 70% confluent iPS cells maintained in mTeSR Plus media on 10 cm dishes were used for embryoid bodies (EBs) formation. The cells were cultured in low attachment six well plates (Greiner bio-one # 657970) using WiCell Medium containing: DMEM/F12 (Gibco #11330057), 25% knock out serum replacement (Gibco # 10828-028), 1.3% L-glutamine (Gibco # 35050-061), 1.3% NEAA (Gibco # 11140-050), 0.1mM 2-Mercaptoethanol (Sigma# M3148) and placed on a shaker in the incubator for 8 days to allow EBs formation. EBs were then resuspended in Forebrain Neural Induction Media (FB-NIM) containing: DMEM/F12, 1% N2 supplement (Gibco # 17502-048), 1% NEAA, 2ug/mL heparin (Sigma # H3149), 10 μg/mL bFGF (Stemcell Technologies # 78003) and plated on to T25 flasks coated with basement membrane matrigel (Corning # 356234) to allow formation of neuronal rosettes. Neuronal rosettes were maintained in FB-NIM for the next 10 days and then, collected and maintained in suspension on a shaker with half FB-NIM media changes every other day to allow for neurosphere growth. Neurospheres were maintained for 20 days in FB-NIM and then resuspended using forebrain neuronal differentiation media (FB-DM) containing:  Neurobasal Medium (Corning # 21103-049), 2% B27 (Gibco # 17504-044), 10 ug/mL BDNF (Stem cell technologies # 78005), 10 ug/mL GDNF (Stem cell technologies # 78058), 1μg/mL laminin (Life technologies # 23017-015), 3.3 μg/mL cAMP (Stem cell technologies # 73884), 3.52 μg/mL Ascorbic acid (Stem cell technologies # 72132 ), 0.5mM L-glutamine and 1% NEAA and then plated on to T25 flasks. iPSC cortical neurons were harvested on DIV 65-72 for RNA sequencing analysis.

extract_protocol:
RNA was isolated with RNeasy Mini Kit (QIAGEN-74104) following the manufacturer’s instructions. RNA samples were measured for quantity with Quant-iT Ribogreen RNA Assay (Thermo Fisher, Cat. No. R11490) and quality with Agilent High Sensitivity RNA ScreenTape and buffer (Agilent, Cat. No. 5067-5579 & 5067-5580).
For each RNA sample, an indexed, Illumina-compatible, double-stranded cDNA whole transcriptome library was synthesized from 1 μg of total whole transcriptome library was synthesized from 1 μg of total Prep Kit – HI Mammalian (Takara Bio, Cat. No. 634876) and SMARTer RNA Unique Dual Index Kit (Takara Bio, Cat. No. 634418). Library preparation included ribosomal RNA depletion, RNA fragmentation (94◦ C for 3 min), cDNA synthesis, and a 12-cycle unique dual indexing enrichment PCR.

treatment_protocol: On DIV 28-30 iPSC-MG from 4 C9orf72 ALS/FTD patient lines and 5 control lines were plated on to 4 chambers glass slides as described above. For LPS stimulation - One hour after plating, iPSC-MGs were treated for 6 h with LPS (100ng/mL). All iPSC-MG were then collected and sent for RNA sequencing analysis. For Aβ (1-40) stimulation - iPSC-MGs were treated for 2 h with vehicle (DMSO) or 1µM Aβ (1-40) TAMRA (human Aβ, AnaSpec # AS-60488; (Paolicelli et al., 2017)) prepared in microglia basal media with growth factors. All iPSC-MGs were collected at 2 hours and sent for RNA sequencing analysis.

value: cell line

tag: cell line

value: iPSC

value: iPSC- microglia

value: vehicle treatment, 2h


title: C9-7_Ab_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

type: SRA

country: USA

description:
C9_NonStimulated_092_5_V9_Sattler_IPSC_microglia_S42
genecounts_Stim_Master.csv

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: C9-4_Ab, iPSC-MG, C9orf72, day 28-30/40-42

description:
C8_AB_1to40_stimulated_FTD27_1_V8_Sattler_IPSC_microglia_S41
genecounts_Stim_Master.csv

value: 1uM Ab (1-40) TAMRA treatment, 2 h


title: C9-7_Ab, iPSC-MG, C9orf72, day 28-30/40-42

description:
C10_AB_1to40_stimulated_092_5_V10_Sattler_IPSC_microglia_S43
genecounts_Stim_Master.csv


title: BCM-2277_107010

status: Public on Jul 18 2023

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

library_source: transcriptomic single cell

data_processing:
Basecalling: BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14)
QC: Fastq files containing the read were analyzed with FastQC v.0.11.8 to identify any quality concerns with the raw data.
Alignment: Fastq files were aligned independently to the merged human/mouse hg19mm10 genome provided by 10X using CellRanger v6 "count" algorithm with the expected number of cells set to 5000.
Mouse Cell Removal: An in-house R script and the 10X-generated GEM file were used to identify and remove all mouse and multiplet cell barcodes from each PDX sample by using the CellRanger script "subset_bam".  The remaining reads were converted back to fastq files using the CellRanger script "bamtofastq".  These new filtered fastq files were then re-aligned independently to the GRCh38 human genome using the CellRanger "count" algorithm, however, this time the Force Cells option was set to the exact number of remaining human cells for each sample.
Dead Cell Removal: An in-house R script using the Seurat v4 R package was used to identify and remove barcodes associated with dead or poor quality cells.  The 10X "subset_bam" and "bamtofastq" scripte were once again used to filter the bam files for each sample to generate fastq files containing only the reads from good quality human cells.
Alignment: Each sample was re-aligned to the human GRCh38 genome provided by 10X using the CellRanger "count" algorithm with the Force Cells option set to the exact number of good quality cells identified in the previous step.
Assembly: GRCh38
Supplementary files format and content: The process data files include the 10X formatted features.tsv.gz, barcodes.tsv.gz, and matrix.mtx.gz files that can be imported directly into R using the Seurat package.

source_name: Basal-like triple-negative breast cancer patient-derived xenograft

growth_protocol: PDX tumors were grown orthotopically in NSG mice for 8 weeks.

extract_protocol: 10x Genomics Chromium kit

treatment_protocol:
Carboplatin Resistant:  Mice with PDXs were grown and treated three times spaced out every 4 days with 40mg/kg of carboplatin. Once the tumors regrew they were passaged to new recipient mice and then treated with another set of carboplatin. This proceeded until the tumors no longer responded to carboplatin; at this point they were termed carboplatin-resistant.
Tamoxifen Resistant: Mice harboring PDX tumors were given tamoxifen citrate chow. These PDXs were passaged under tamoxifen citrate selection until no difference in growth rate between treated and untreated tumors was observed. These models were then termed "tamoxifen resistant."
Tamoxifen citrate: Chow was replaced with Tamoxifen citrate chow from Envigo (600mg/kg) for 2 weeks prior to tumor excision.
Estradiol Withdrawal (EWD): Ovariectomy was performed and no exogenous estrogen pellet was provided.
Estrogen pellet:Two milligram slow-release estrogen pellets were implanted subcutaneously as an exogenous source of estrogen.
Ovariectomy (OVX): Both ovaries were surgically removed from mice to withdraw the primary source of estrogen.

tag: biomaterial provider

value: Baylor College of Medicine

value: PDX

value: Untreated

value: PDX mammary tumor


title: C9-3_Ab_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
A4_NonStimulated_FTD16_15_C9_v5_Sattler_IPSC_microglia_S24
genecounts_Stim_Master.csv


title: C9-3_Ab, iPSC-MG, C9orf72, day 28-30/40-42

description:
A5_AB_1to40_stimulated_FTD16_15_C9_v6_Sattler_IPSC_microglia_S25
genecounts_Stim_Master.csv


title: BCM-7821-107713


title: Control-7_Ab, iPSC-MG, control, day 28-30/40-42

description:
C6_AB_1to40_stimulated_Healthy_Control_V6_Sattler_IPSC_microglia_S39
genecounts_Stim_Master.csv

value: Control


title: Control-7_Ab_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
C5_NonStimulated_Healthy_Control_V5_Sattler_IPSC_microglia_S38
genecounts_Stim_Master.csv


title: BCM-15057-107684

source_name: ER+ breast cancer patient-derived xenograft

value: Estrogen pellet


title: Control-6_Ab, iPSC-MG, control, day 28-30/40-42

description:
AB_1to40_stimulated_JH082_Control_v2_Sattler_IPSC_microglia_S10
genecounts_Stim_Master.csv


title: Control-5_Ab, iPSC-MG, control, day 28-30/40-42

description:
C4_AB_1to40_stimulated_CS14_V4_Sattler_IPSC_microglia_S37
genecounts_Stim_Master.csv


title: Control-5_Ab_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
C3_NonStimulated_CS14_V3_Sattler_IPSC_microglia_S36
genecounts_Stim_Master.csv


title: Control-2_Ab, iPSC-MG, control, day 28-30/40-42

description:
AB_1to40_stimulated_CS03_Control_v4_Sattler_IPSC_microglia_S5
genecounts_Stim_Master.csv


title: Control-2_Ab_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
NonStimulated_CS03_Control_v3_Sattler_IPSC_microglia_S4
genecounts_Stim_Master.csv


title: Control-1_Ab, iPSC-MG, control, day 28-30/40-42

description:
C2_AB_1to40_stimulated_CS83_V2_Sattler_IPSC_microglia_S35
genecounts_Stim_Master.csv


title: BCM-7482_107157


title: C9-7_LPS, iPSC-MG, C9orf72, day 28-30/40-42

description:
B8_LPS_stimulated_092_5_V8_Sattler_IPSC_microglia_S33
genecounts_Stim_Master.csv

value: 100ng/mL LPS treatment, 6 h


title: Control-1_Ab_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
C1_NonStimulated_CS83_V1_Sattler_IPSC_microglia_S34
genecounts_Stim_Master.csv


title: C9-7_LPS_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
B7_NonStimulated_092_5_V7_Sattler_IPSC_microglia_S32
genecounts_Stim_Master.csv

value: vehicle treatment, 6h


title: C9-4_LPS, iPSC-MG, C9orf72, day 28-30/40-42

description:
B6_LPS_stimulated_FTD27_1_V6_Sattler_IPSC_microglia_S31
genecounts_Stim_Master.csv


title: C9-3_LPS, iPSC-MG, C9orf72, day 28-30/40-42

description:
A2_LPS_stimulated_FTD16_15_C9_v14_Sattler_IPSC_microglia_S22
genecounts_Stim_Master.csv


title: C9-1_LPS, iPSC-MG, C9orf72, day 28-30/40-42

description:
LPS_stimulated_CSOBUU_C9_v11_Sattler_IPSC_microglia_S12
genecounts_Stim_Master.csv


title: Control-5_LPS, iPSC-MG, control, day 28-30/40-42

description:
B4_LPS_stimulated_CS14_V4_Sattler_IPSC_microglia_S29
genecounts_Stim_Master.csv


title: C9-1_LPS_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
NonStimulated_CSOBUU_C9_v10_Sattler_IPSC_microglia_S11
genecounts_Stim_Master.csv


title: Control-5_LPS_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
B3_NonStimulated_CS14_V3_Sattler_IPSC_microglia_S28
genecounts_Stim_Master.csv


title: Control-7_LPS, iPSC-MG, control, day 28-30/40-42

description:
B2_LPS_stimulated_Healthy_Control_V2_Sattler_IPSC_microglia_S27
genecounts_Stim_Master.csv


title: C9-1_Ab_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
NonStimulated_CSOBUU_C9_v7_Sattler_IPSC_microglia_S14
genecounts_Stim_Master.csv


title: Control-7_LPS_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
B1_NonStimulated_Healthy_Control_V1_Sattler_IPSC_microglia_S26
genecounts_Stim_Master.csv


title: C9-3_LPS_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
A1_NonStimulated_FTD16_15_C9_v13_Sattler_IPSC_microglia_S21
genecounts_Stim_Master.csv


title: Control-6_LPS, iPSC-MG, control, day 28-30/40-42

description:
LPS_stimulated_JH082_Control_v5_Sattler_IPSC_microglia_S7
genecounts_Stim_Master.csv


title: Control-2_LPS, iPSC-MG, control, day 28-30/40-42

description:
LPS_stimulated_CS03_Control_v2_Sattler_IPSC_microglia_S2
genecounts_Stim_Master.csv


title: Control-1_LPS, iPSC-MG, control, day 28-30/40-42

description:
LPS_stimulated_CS83_CONTROL_v8_Sattler_IPSC_microglia_S14
genecounts_Stim_Master.csv


title: Control-6_Ab_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
NonStimulated_JH082_Control_v1_Sattler_IPSC_microglia_S9
genecounts_Stim_Master.csv


title: Control-6_LPS_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
NonStimulated_JH082_Control_v4_Sattler_IPSC_microglia_S6
genecounts_Stim_Master.csv


title: Cortical-12, iPSC cortical neurons, day 65-72

description:
CS83_p33_20_CNs_S34
genecounts_Master.csv

value: iPSC-cortical neurons

value: no treatment, only differentiated cells


title: Control-2_LPS_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
NonStimulated_CS03_Control_v1_Sattler_IPSC_microglia_S1
genecounts_Stim_Master.csv


title: Cortical-10_2, iPSC cortical neurons, day 65-72

description:
CS1HKR_p24_18_CNs_S17
genecounts_Master.csv


title: Cortical-11, iPSC cortical neurons, day 65-72

description:
CS0YJY_p23_19_CNs_S26
genecounts_Master.csv

value: Sporadic ALS


title: C9-1_Ab, iPSC-MG, C9orf72, day 28-30/40-42

description:
AB_1to40_stimulated_CSOBUU_C9_v8_Sattler_IPSC_microglia_S15
genecounts_Stim_Master.csv


title: Cortical-8, iPSC cortical neurons, day 65-72

description:
092_5_p25_15_CNs_S22
genecounts_Master.csv


title: Cortical-9, iPSC cortical neurons, day 65-72

description:
Progranulin_16_CNs_S29
genecounts_Master.csv

value: Mutant Progranulin


title: C9-4_LPS_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
B5_NonStimulated_FTD27_1_V5_Sattler_IPSC_microglia_S30
genecounts_Stim_Master.csv

value: cell line


title: Cortical-6, iPSC cortical neurons, day 65-72

description:
FTD_26pt5_p39_13_CNs_S23
genecounts_Master.csv

value: iPSC


title: Cortical-5_3, iPSC cortical neurons, day 65-72

description:
FTD_27_1_p35_10_CNs_2_S4
genecounts_Master.csv


title: Cortical-4_2, iPSC cortical neurons, day 65-72

description:
034_p29_9_CNs_S18
genecounts_Master.csv


title: Cortical-4_1, iPSC cortical neurons, day 65-72

description:
034_p21_8_CNs_S16
genecounts_Master.csv


title: Cortical-5_1, iPSC cortical neurons, day 65-72

description:
FTD_27pt1_p33_11_CNs_S27
genecounts_Master.csv


title: Cortical-3_1, iPSC cortical neurons, day 65-72

description:
JH082_p19_7_CNs_S32
genecounts_Master.csv


title: Cortical-7, iPSC cortical neurons, day 65-72

description:
078_p30_14_CNs_S21
genecounts_Master.csv


title: Cortical-2_3, iPSC cortical neurons, day 65-72

description:
CS03_p26_3_CNs_S24
genecounts_Master.csv


title: C9-7, iPSC-MG, C9orf72, day 28/40

description:
092_5_p24_2_Microglia_S14
genecounts_Master.csv

value: iPSC- microglia


title: C9-6, iPSC-MG, C9orf72, day 28/40

description:
CS1HKR_p25_20_Microglia_S10
genecounts_Master.csv


title: Cortical-2_2, iPSC cortical neurons, day 65-72

description:
CS03_p21_d68_5_CNs_S19
genecounts_Master.csv


title: Cortical-2_1, iPSC cortical neurons, day 65-72

description:
CS03_p21_4_CNs_S20
genecounts_Master.csv


title: Cortical-1_2, iPSC cortical neurons, day 65-72

description:
CS25_p31_2_CNs_S28
genecounts_Master.csv


title: Cortical-3_2, iPSC cortical neurons, day 65-72

description:
JH082_p30_6_CNs_S25
genecounts_Master.csv


title: Cortical-10_1, iPSC cortical neurons, day 65-72

description:
CS1HKR_p23_17_CNs_S33
genecounts_Master.csv


title: C9-2, iPSC-MG, C9orf72, day 28/40

description:
CS5_MNZ_p24_24_Microglia_S8
genecounts_Master.csv


title: C9-1, iPSC-MG, C9orf72, day 28/40

description:
CSO_BUU_p25_25_Microglia_S12
genecounts_Master.csv


title: C9-3, iPSC-MG, C9orf72, day 28/40

description:
FTD_16_15_p20_26_Microglia_S13
genecounts_Master.csv


title: Control-6, iPSC-MG, control, day 28/40

description:
JH082_p28_1_Microglia_S11
genecounts_Master.csv


title: C9-5, iPSC-MG, C9orf72, day 28/40

description:
FTD_26pt5_p40_7_Microglia_S6
genecounts_Master.csv


title: Cortical-1_1, iPSC cortical neurons, day 65-72

description:
CS25_p24_1_CNs_S30
genecounts_Master.csv


title: Control-2_2, iPSC-MG, control, day 28/40

description:
CS03_p23_5_Microglia_S9
genecounts_Master.csv


title: Control-2_1, iPSC-MG, control, day 28/40

description:
CS03_p23_21_Microglia_S3
genecounts_Master.csv


title: IA414

status: Public on May 09 2023

city: Chicago

first: Issam

middle: A

last: Awad

state: IL

address: 5841 S Maryland Avenue MC 3026, J 341 MC 3026, J 341

department: Neurological Surgery

institute: University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.11.7
Adapter trimming: cutadapt 1.14
Alignment: sRNAbench version 10/14
Differentially expressed miRNA analysis: DESeq2 with R version 3.4
Assembly: miRBase 22 mature microRNAs
Supplementary files format and content: tab-delimited text file include matrix with reads  mapped to mature miRNA from sense strand summarized by sRNAbench.

source_name: blood plasma

extract_protocol:
RNAs was extracted using an RNA isolation kit (miRNeasy Serum/Plasma Kit (Qiagen, Venlo, Netherlands).
RNA libraries were prepared for sequencing using commercially available Illumina small RNA-Seq kits (San Diego, California, USA),

value: blood plasma

tag: disease state

value: Healthy

tag: molecule subtype

value: small RNA


title: IA413


title: IA397


title: IA214


title: IA215


title: IA412

value: Cerebral cavernous malformation


title: IA411


title: IA396


title: Cortical-5_2, iPSC cortical neurons, day 65-72

description:
FTD_27pt1_p36_12_CNs_S31
genecounts_Master.csv


title: C9-4, iPSC-MG, C9orf72, day 28/40

description:
FTD_27pt1_p33_8_Microglia_S2
genecounts_Master.csv


title: IA299


title: IA390


title: IA209


title: IA210


title: IA391


title: IA301


title: IA208


title: IA410


title: IA395


title: Control-5, iPSC-MG, control, day 28/40

description:
CS14_p23_6_Microglia_S1
genecounts_Master.csv


title: Control-1, iPSC-MG, control, day 28/40

description:
CS83_p34_22_Microglia_S5
genecounts_Master.csv


title: IA302


title: IA322


title: KJ261


title: IA393


title: IA285


title: Control-1_LPS_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
NonStimulated_CS83_CONTROL_v7_Sattler_IPSC_microglia_S13
genecounts_Stim_Master.csv


title: IA279


title: IA213


title: IA394


title: IA212


title: IA211


title: IA-351_S25

data_processing:
Raw sequencing QC assessement: FastQC v0.11.7
Adapter trimming: cutadapt 1.14
Alignment: sRNAbench version 10/14
Differentially expressed miRNA analysis: DESeq2 with R version 3.4
Assembly: miRBase 22 mature microRNAs
Supplementary files format and content: tab-delimited text files include reads mapped to mature miRNA from sense strand summarized by sRNAbench for each Sample.

organism: Mus musculus

tag: strain background


title: IA-350_S24


title: IA-353_S26

value: WT


title: IA-343_S13


title: IA-346_S21


title: IA-342_S31


title: IA300


title: IA-340_S30


title: IA-341_S12


title: IA-338_S29


title: IA-339_S11


title: IA-336_S28


title: IA-335_S9


title: IA298


title: IA-332_S26


title: IA-333_S8


title: IA-334_S27


title: IA-337_S10


title: IA-331_S7


title: IA-330_S25


title: IA-328_S6


title: IA-327_S5


title: IA-325_S24


title: IA306


title: IA-348_S22


title: IA-324_S23


title: IA-314_S4


title: IA-349_S23


title: IA-313_S22


title: IA-311_S21


title: IA-312_S3


title: IA-309_S20


title: IA-308_S1


title: IA-271_S5


title: IA-273_S7


title: IA-270_S4


title: IA-275_S9


title: IA-272_S6


title: IA-268_S2


title: IA-267_S1


title: IA-269_S3


title: VASA_all_hypocotyl, rep2, snRNAseq

status: Public on Apr 04 2023

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

country: Germany

institute: Heidelberg University

description:
VASA-seq
VASAseq-barcodes.tsv
VASAseq-features.tsv

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the  STAR v2.7.8a with “--soloFeatures GeneFull --alignIntronMax 10000 --alignMatesGapMax 10000” options for Libraries DSNucseq2, UHE-DS, and using Cell Ranger software v6.0.1 with “--include-introns” option and “--alignIntronMax 10000 --alignMatesGapMax 10000” alignment option for Libraries WT and d14.
Transgene sequence (H4-GFP, H2B-RFP) were added to the genome for Libraries DSNucseq2 and UHE-DS. ERCC 92 RNA Spike-In information were added to the genome for Libraries UHE-DS (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip). Nuclear arabidopsis genome were used in Libraries WT and d14.
Cell barcodes for 10x Chromium were obtained from (3M-february-2018.txt.gz, https://github.com/10XGenomics/cellranger/tree/master/lib/python/cellranger/barcodes). Well barcodes for VASA-seq were obtained from Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/; Accession ID: GSE112438, celseq2_bc.csv.gz)
Assembly: tair10 / araport11 annotation
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Seurat object RDS file

organism: Arabidopsis thaliana

source_name: hypocotyl

growth_protocol: Arabidopsis were grown on 0.8% w/v agar in 1/2 Murashige and Skoog (MS) medium supplemented with 1% w/v sucrose. Seedlings were grown in short-day conditions (SD; 10 h light and 14 h darkness) for at 21-22 degrees for 4 weeks (Library: DSNucseq2, UHE-DS) or 19 days (Library: WT, d14).

extract_protocol:
Hypocotyls were dissected from Arabidopsis and collected on petri dishes kept on ice. 2ml of 1x nuclei isolation buffer (CelLytic ™ PN Isolation/Extraction Kit, Sigma #CELLYTPN1) supplemented with 20 µl RiboLock RNase inhibitor 40 U/µL (ThermoFisher #EO0381) and Hoechst 33342 at 10 µg/ml final concentration were prepared and minimum amount of buffer was applied to the hypocotyls to submerge the collected hypocotyls. Hypocotyls were chopped using razor blades (Wilkinson Sword) for several minutes (up to 5 min.) and transferred on a gentle shaker in at 4 degrees for 15 min. Samples were then filtered through a 50 µm filter (CellTrics, Sysmex #04-004-2327) and passed to a low protein binding tube (Eppendorf #0030108132). Nuclei were further purified in FANS with 405-nm laser, and collectively sorted into a tube for 10x Genomics application.  Single nuclei were sorted into the single well of 384-well plates for VASA-seq application with GFP and RFP signal information, where ERCC spike-in controls and well-specific barcodes are included in each well. O21-24, P21-24 wells (barcodes: "AGTTGGAC", "AGTGCAGA", "CTCTGTCT", "CTCTGCTA", "TAGTTGCG", "AGGCTAAC") were kept blank for quality control.
10x Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). FANS collected nuclei were applied without dilution, resulted in about 6,000 nuclei application. For VASA-seq, plates were processed according to the published VASA-plate protocol (doi: 10.1038/s41587-022-01361-8).

value: hypocotyl

value: nucleus


title: VASA_all_hypocotyl, rep3, snRNAseq


title: VASA_all_hypocotyl, rep1, snRNAseq


title: IA-274_S8


title: VASA_cambium, rep2, snRNAseq

value: cambium enriched nucleus


title: VASA_cambium, rep1, snRNAseq


title: VASA_cambium, rep3, snRNAseq


title: d14, snRNAseq

description:
10x Genomics
WTd14-10x-barcodes.tsv
WTd14-10x-features.tsv


title: 10x_all_hypocotyl, snRNAseq

description:
10x Genomics
10x-all_hypocotyl_barcodes.tsv
10x-all_hypocotyl_features.tsv


title: craniofacial tissues - H3K4me3_rep2

status: Public on Mar 15 2023

city: Berkeley

first: Laura

middle: E

last: Cook

state: California

address: 1 Cyclotron Road

department: Biosciences

institute: Lawrence Berkeley National Laboratory

library_source: genomic

data_processing:
CASAVA (v1.8.2) for base calling and preliminary quality analysis
Raw data were processed by adapter trimming and low quality read removal using  Cutadapt v1.9.1  to generate clean data for subsequent analysis. This process includes removing adapter sequences, 5' or 3' end of bases of quality (QPhred) scores below 20, reads where 'N' is above 10\% and reads that are less than 75 bp long after trimming.
Sequencing reads were aligned to the fat-tailed dunnart genome with Bowtie2 v.2.3.5.1 (parameters: -q -X 2000 --very-sensitive).
Aligned reads were filtered to remove low-quality and unpaired reads using Samtools v.1.9 (parameters: -q 30 -f 2) and multiple-mapping reads by the MarkDuplicates tool from picard v.2.23.1.
Enriched regions were called on the aligned reads using MACS2 v.2.1.1 (parameter: -f BAMPE, -g 2740338543) using total DNA input as control and retaining all statistically significant enrichment regions (FDR-corrected P < 0.01).
Genome_build: smiCra1
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: peak files

molecule: genomic DNA

organism: Sminthopsis crassicaudata

source_name: craniofacial tissues

extract_protocol:
Chromatin immunoprecipitation was performed using the MAGnify Chromatin Immunoprecipitation System (Thermo Fisher, 492024) according to manufacturer's instructions. Briefly, frozen dunnart tissue samples were diced quickly with two razor blades in cold dPBS (Gibco) followed by crosslinking in 1\% formaldehyde solution (Sigma) for 10 minutes. I then added 0.125 M glycine and incubated for 5 minutes at room temperature to neutralize the formaldehyde. Chromatin was fragmented to 300bp average size by sonication on a Covaris S2 using the following parameters: duty cycle = 5%, intensity = 2, cycles per burst = 200, cycle time = 60 seconds, cycles = 10, temperature = 4°C, power mode = frequency sweeping, degassing mode = continuous. In each ChIP experiment, I used sheared chromatin from each replicate for immunoprecipitation with antibodies against H3K4me3 (abcam ab8580) and H3K27ac (abcam ab4729). An input control was included for each replicate. DNA was purified according to kit instructions using a DynaMag PCR Magnet (Thermo Fisher).
Illumina sequencing libraries were prepared from ChIP-enriched DNA by GENEWIZ (Suzhou, China). Libraries were constructed following the manufacturer’s protocol (NEBNext UltraTMII DNA Library Prep Kit for Illumina). For each sample, a minimum of 10 ng of ChIP product was used and libraries were multiplexed and sequenced on an Illumina HiSeq instrument according to manufacturers instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150 paired-end configuration.

tag: developmental stage

value: day of birth (<24 hours old)

value: craniofacial tissues from 27 heads

tag: antibody


title: craniofacial tissues - input_rep2

value: input


title: WT, snRNAseq


title: craniofacial tissues - H3K27ac_rep2


title: craniofacial tissues - H3K27ac_rep1

value: craniofacial tissues from 26 heads


title: craniofacial tissues - H3K4me3_rep1


title: IA-310_S2


title: craniofacial tissues - input_rep1


title: IA-307_S19


title: mnp-20-0765

status: Public on Jan 30 2023

type: genomic

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: CNS tumor tissue

label_protocol: Illumina

extract_protocol: DNA from FFPE tissue was extracted using a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: "material"

value: FFPE tissue

tag: "tumor type"

value: Ependymoma, WHO grade II

tag: "patient age (years)"

tag: "patient gender"

value: male

tag: "tumor location"

value: spinal cord


title: mnp-20-1303

value: female


title: mnp-20-1132

value: Myxopapillary ependymoma (MPE)


title: mnp-20-0711


title: si-circGLIS3 transfected fibroblasts, 2

status: Public on Feb 06 2023

type: RNA

city: Stockholm

first: Yongjian

last: Chen

address: Solnavägen 1

country: Sweden

institute: Karolinska Institutet

description:
Fibroblasts transfected with si-circGLIS3
processed.txt

hyb_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

data_processing:
Expression data were analyzed by using Transcriptome Analysis Console 4.0. The follwoing criteria were used for data analysis:  Array Type: Clariom_S_Human  Analysis Type: Expression (Gene)  Analysis Version: version 2  Summarization Method: Gene Level - SST-RMA  Pos vs Neg AUC Threshold: 0,7  Genome Version: hg38 (Homo sapiens)  Annotation: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv  Condition (Comparison): circRNA kd; ctr
Expression Analysis Settings:  • Gene-Level Fold Change < -2 or > 2  • Gene-Level P-Value < 0,05  • Anova Method: ebayes  • A Probeset (Gene/Exon) is considered expressed if ≥ 50% samples have DABG values below DABG Threshold.  • DABG < 0,05

label: biotin

label_protocol: One hundred fifty nanograms of total RNA was used to prepare cDNA following the GeneChip WT PLUS Reagent Kit labeling protocol

growth_protocol: Human dermal fibroblasts (hDFs) isolated from plastic surgery skin were cultured in DMEM medium (Gibco™) supplemented with 10% fetal bovine serum (FBS, Gibco™) and 1% penicillin/streptomycin (Gibco™) at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from the cells using TRIzol reagent (ThermoFisher Scientific).

treatment_protocol: Third passage hDFs were seeded in 24-well plates. At 60-70% confluence, cells were transfected with siRNA control, si-circGLIS3, p-Ctrl, p-circGLIS3 or p-circGLIS3_RNA using Lipofectamine 3000 (ThermoFisher Scientific). After 24 hours, cells were harvested for RNA extraction.

value: Skin

value: Fibroblasts

value: si-circGLIS3 knockdown


title: mnp-20-1290


title: mnp-20-0057


title: mnp-20-0839

value: cerebellum, fourth ventricle, pons


title: mnp-20-1206

value: cerebellum


title: MM1S_C24_rep2

status: Public on Jan 25 2023

city: Nanjing

first: jun

last: wang

state: Jiangsu

address: No. 163 Xianlin Avenue, Qixia District

department: IMB

country: China

institute: Nanjing University

data_processing:
Fastq files were aligned to the hg19 human genome using STAR v2.4.2 with parameters: --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM. Transcript abundance was estimated with salmon v0.1.19 to quantify the transcriptome defined by Gencode v22. Gene level counts were summed across isoforms and genes with low counts (maximum expression < 10) were filtered for the downstream analyses. Raw read counts were used for differential gene expression analysis by DESeq2 v1.38.2 where size normalization factor was estimated based on median-of-ratios.
Assembly: hg19
Supplementary files format and content: tab delimited matrix of gene level count estimates

source_name: MM1.S cells

growth_protocol: MM1.S cells were grown in the RPMI1640 base medium plus 10% FBS and 1% antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit. 1 ug of total RNA for the construction of the pooled sequencing libraries.
NEBNext Ultra II RNA library Prep kit (NEB, #E7770) was used.

treatment_protocol: MM1.S cells were treated with DMSO, 0.5 µM of C24, MS177N1, MS177 for 24h and collected for RNAseq.

value: MM1.S cells treated with 0.5 uM of C24 for 24h


title: mnp-20-0754


title: si-circGLIS3 transfected fibroblasts, 1

scan_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

source_name: Fibroblasts transfected with si-circGLIS3


title: MM1S_C24_rep1


title: mnp-20-0119


title: MM1S_MS177_rep2

value: MM1.S cells treated with 0.5 uM of MS177 for 24h


title: MM1S_DMSO_rep2

value: MM1.S cells treated with DMSO for 24h


title: MM1S_DMSO_rep1


title: MM1S_MS177_rep1


title: MM1S_MS177N1_rep1

value: MM1.S cells treated with 0.5 uM of MS177N1 for 24h


title: MM1S_C24_H3K27me3

data_processing:
Fastq files were mapped to the reference genome (hg19) using bowtie2.3.5.
The non-primary alignment, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively
Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Deeptools (v3.3.0) was used to generate bigwig files, heatmaps and averaged plotting of CUT&RUN signals.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

growth_protocol: MM1.S cells were grown in RPMI1640 plus 10% FBS and 1% antibiotics.

extract_protocol:
DNA purification was carried out with the PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup Kit, #T1030).
Libraries were prepared by NEBNext Ultra II kit (NEB, #E7645L)

treatment_protocol: Fresh 0.5 million  cells was collected, washed and bound to ConA beads. Cell:bead sample was incubated with indicating antibodies over night and then washed, treated with pAG-Mnase followed by adding 2mM CaCl2 to activate pAG-Mnase. Solubilized chromatin was then released using the CUT&RUN stop buffer.

tag: chip antibody

value: Rabbit anti-H3k27me3 (CST 9733)

tag: treatment condition


title: MM1S_MS177_EZH2

tag: cell line

value: Rabbit anti-EZH2 (CST 5246)


title: MM1S_DMSO_H3K27me3


title: MM1S_MS177_H3K27me3


title: si-ctrl transfected fibroblasts, 3

description:
Fibroblasts transfected with siRNA control
processed.txt

tag: tissue

tag: cell type

value: Control


title: si-ctrl transfected fibroblasts, 2

source_name: Fibroblasts transfected with siRNA control

tag: genotype


title: MM1S_DMSO_EZH2


title: si-ctrl transfected fibroblasts, 1


title: MM1S_MS177N1_rep2

tag: treatment


title: MM1S_H3K27me3

value: NO


title: si-circGLIS3 transfected fibroblasts, 3


title: MM1S_EZH2


title: input_endometrium,middle secretory phase of control,rep3

status: Public on Oct 16 2022

city: Lanzhou

first: Wenxin

last: Gao

state: 甘肃

address: East west road no. 1

institute: Lanzhou university

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer and wer e quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software(v1.9.3).
clean reads of input libraries were aligned to reference genome (UCSC hg19) by STAR software
clean reads of all libraries were aligned to the reference genome using Hisat2 software
Methylated sites on RNAs which called peaks were id entified by MACS software
Differentially methylated sites were identified using diffReps
Assembly: HG19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: middle secretory phase endometrium

extract_protocol:
RNA was isolated from endometrial tissue of control group and RIF group by TRIzol Reagent
GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) was used to construct RNA libraries for IP and input samples by following the manufacturer’s instructions.

value: middle secretory phase endometrium

tag: diagnosis

value: control

value: none (input)


title: input_endometrium,middle secretory phase of control,rep1


title: E14.5 Brain KO repl2

status: Public on Dec 20 2022

city: Montpellier

first: Pierre-François

last: Roux

address: 208 rue des Apothicaires

country: France

institute: Inserm

description:
KO-607
RNA-seq paired

data_processing:
Quality of raw data has been evaluated with FastQC.
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on reference genome using standard options.
Quantification of gene and isoform abundances has been done with rsem 1.2.28.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files including expecting counts, TPM and FPKM.

source_name: Brain

extract_protocol:
Mouse embryo brains were dissected, flash frozen in liquid nitrogen, and RNA was extracted using Trizol reagent.
Libraries were prepared from the extracted RNA using the KAPA Stranded mRNA-Seq Kit.

tag: genotype/variation

value: E4f1 KO

value: Brain


title: input_endometrium,middle secretory phase of RIF,rep2

value: RIF


title: E14.5 Brain WT repl1

description:
WT-601
RNA-seq paired

value: WT


title: E14.5 Brain WT repl3

description:
WT-164
RNA-seq paired


title: E14.5 Brain KO repl1

description:
KO-605
RNA-seq paired


title: endometrium,middle secretory phase of control,rep3

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer and wer e quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software(v1.9.3).
clean reads of input libraries were aligned to reference genome (UCSC hg19) by STAR software
clean reads of all libraries were aligned to the reference genome using Hisat2 software
Methylated sites on RNAs which called peaks were id entified by MACS software
Differentially methylated sites were identified using diffReps
Assembly: HG19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Library strategy: MeRIP-seq


title: input_endometrium,middle secretory phase of control,rep2


title: endometrium,middle secretory phase of control,rep2


title: endometrium,middle secretory phase of control,rep1


title: input_endometrium,middle secretory phase of RIF,rep3


title: endometrium,middle secretory phase of RIF,rep2


title: endometrium,middle secretory phase of RIF,rep3


title: input_endometrium,middle secretory phase of RIF,rep1


title: MM1S_C24_EZH2


title: T265 MEKi 24hr RNA rep2

status: Public on Sep 20 2022

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

data_processing:
Illumina RTA (1.18.64) software was used for basecalling.
Bcl2fastq (v2.17) software was used for demultiplexing.
Trimmomatic (0.36) was used to trim the reads for adaptors.
STAR (2.6.1) was used for alignment.
RSEM (1.2.31) or PartekFlow was used for transcriptomic quantification.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited files include raw counts for each sample.

molecule: polyA RNA

source_name: T265 cells

growth_protocol: Human MPNST cell lines, T265 and ST88-14, were maintained in DMEM10 (DMEM supplemented with 10% FBS, 100 U/mL penicillin, 100 ug/mL streptomycin, and L-Glutamine). MPNST cell line PT2002 was cultured in RPMI10 (RPMI supplemented with 10% FBS, 100 U/mL penicillin, 100 ug/mL streptomycin, and L-Glutamine). Open reading frame (ORF) of human SUZ12 (NM_015355, GenScript, Piscataway, NJ) was cloned into the pLVX-TetOne-Puro vector (Takara Bio) using In-Fusion HD (Takara Bio). MPNST cell lines were infected with lentiviral particles generated using either pLVX-TetOne-Puro-SUZ12 or empty vector (pLVX-TetOne-Puro-EV), followed by puromycin selection (T265-SUZ12: 1 ug/mL, ST88-14-SUZ12: 5 ug/mL, and PT2002-SUZ12: 1 ug/mL). Dox-inducible Cas9-expressing MPNST cells were transduced with the lentivirus of gRNAs that target the exon of human FOXC1 genes and selected with puromycin (Invitrogen).

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To restore a functional PRC2 in human MPNST cells that are deficient of SUZ12, cell lines transduced with Dox-inducible ORF of human SUZ12 were treated with Dox (0.5 ug/mL) for 5 consecutive days and Dox was replenished every other day. To knockout FOXC1 in T265 cells, Dox-inducible Cas9-expressing T265 cells that were transduced with gRNAs targeting the exon of FOXC1 were treated with Dox (0.5 ug/mL) for 7 days. Dox was replenished every other day. Small molecule inhibitor of MEK, trametinib (100 nM), was used to treat T265 cells for 8 or 24 hours.

value: MPNST

tag: transduced with

value: treated with trametinib for 24 hours


title: T265 MEKi 24hr RNA rep3


title: T265 MEKi 24hr RNA rep1


title: T265 DMSO 24hr RNA rep2

value: DMSO


title: T265 MEKi 8hr RNA rep3

value: treated with trametinib for 8 hours


title: T265 DMSO 24hr RNA rep1


title: E14.5 Brain KO repl3

description:
KO-242
RNA-seq paired

tag: developmental stage


title: T265 MEKi 8hr RNA rep2


title: T265 DMSO 8hr RNA rep3


title: T265 DMSO 8hr RNA rep2


title: endometrium,middle secretory phase of RIF,rep1

tag: antibody


title: E14.5 Brain WT repl2

description:
WT-608
RNA-seq paired


title: T265 DMSO 8hr RNA rep1


title: T265 DMSO 24hr RNA rep3


title: T265-Cas9 FOXC1 plus Dox RNA rep1

value: gRNAs targeting the exon of FOXC1

value: treated with Dox for 7 days


title: T265-Cas9 FOXC1 no Dox RNA rep1

value: untreated


title: PT2002-SUZ12 plus Dox RNA rep1

source_name: PT2002 cells

value: transduced with Dox-inducible SUZ12-ORF

value: treated with Dox for 5 days


title: PT2002-SUZ12 plus Dox RNA rep2


title: T265-Cas9 FOXC1 plus Dox RNA rep2


title: T265-Cas9 FOXC1 no Dox RNA rep2


title: ST88-14-SUZ12 plus Dox RNA rep1

source_name: ST88-14 cells


title: T265-SUZ12 plus Dox RNA rep2


title: PT2002-SUZ12 no Dox RNA rep1


title: PT2002-SUZ12 no Dox RNA rep2


title: ST88-14-SUZ12 no Dox RNA rep1


title: T265-SUZ12 no Dox RNA rep1


title: PT2002-SUZ12 plus Dox FOXC1

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome using bwa and then use the MACS2 for peak calling
Assembly: hg19
Supplementary files format and content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.
Supplementary files format and content: peak text files

growth_protocol: Human MPNST cell lines, T265 and ST88-14, were maintained in DMEM10 (DMEM supplemented with 10% FBS, 100 U/mL penicillin, 100 ug/mL streptomycin, and L-Glutamine). MPNST cell line PT2002 was cultured in RPMI10 (RPMI supplemented with 10% FBS, 100 U/mL penicillin, 100 ug/mL streptomycin, and L-Glutamine). Open reading frame (ORF) of human SUZ12 (NM_015355, GenScript, Piscataway, NJ) was cloned into the pLVX-TetOne-Puro vector (Takara Bio) using In-Fusion HD (Takara Bio). MPNST cell lines were infected with lentiviral particles generated using either pLVX-TetOne-Puro-SUZ12 or empty vector (pLVX-TetOne-Puro-EV), followed by puromycin selection (T265-SUZ12: 1 ug/mL, ST88-14-SUZ12: 5 ug/mL, and PT2002-SUZ12: 1 ug/mL).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody following the Active Motif's instructions of the ChIP-IT High Sensitivity Kit.
Libraries were prepared according to Illumina's TruSeq ChIP Sample Preparation Guide.

treatment_protocol: To restore a functional PRC2 in human MPNST cells that are deficient of SUZ12, cell lines transduced with Dox-inducible ORF of human SUZ12 were treated with Dox (0.5 ug/mL) for 5 consecutive days and Dox was replenished every other day.

tag: growth protocol

value: FOXC1 (Invitrogen PA1-807)


title: T265-SUZ12 plus Dox FOXC1 rep2


title: T265-SUZ12 no Dox RNA rep2


title: PT2002-SUZ12 no Dox FOXC1


title: ST88-14-SUZ12 no Dox FOXC1


title: T265 MEKi 8hr RNA rep1


title: ST88-14-SUZ12 plus Dox FOXC1


title: T265-SUZ12 no Dox FOXC1 rep2


title: Met2_Resection_lane4

data_processing:
The 10X scRNA-Seq libraries from human samples were aligned to the hg19 human genome using the Cell Ranger pipeline (version 3.0.2) with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5 for each sample from Cell Ranger output

extract_protocol:
Human tumors were collected from the operation room and placed in DMEM. Tissue was cut into 1 mm3 pieces and placed into dissociation medium in 50 mL tubes containing 20 mL DMEM, 10 mg Collagenase type I, and 50 mg Dispase II and DNaseI and processed on a GentleMACS dissociator followed by incubation at 37°C incubator for 45 min., with 170 rpm shaking. The dissociation process was stopped by adding 10mL DMEM containing 10% FBS. Samples were centrifuged at 300 x g for 5 minutes at 4°C. Supernatants were removed and cell pellets were re-suspended into DMEM. Suspensions were filtered with 40 µm cell strainers and centrifuged at 300 x g for 5 minutes at 4°C. Pellets were resuspended into 100 ul of 1X PBS/0.1% BSA. PI positive viable cells were counted to determine the cell concentration for droplet based single-cell RNA sequencing (scRNA-seq).
Library synthesis was performed according to manufacturer’s instructions to generate barcoded cDNA libraries for scRNA-seq. Ten thousand viable cells per lane from each sample were loaded using the 10X Chromium platform version 3 chemistries (3’) (10X Genomics).

tag: tumor type

tag: tumor stage

value: metastasis

tag: surgery type

value: resection

tag: gender

value: male


title: Met2_Resection_lane3


title: Met2_Resection_lane2


title: Met2_Resection_lane1


title: Met1_Resection_lane7

value: female


title: Met1_Resection_lane6


title: T265-SUZ12 plus Dox RNA rep1


title: ST88-14-SUZ12 plus Dox RNA rep2


title: Met1_Resection_lane3


title: Met1_Resection_lane5


title: Met1_Resection_lane1


title: Met1_Resection_lane4


title: Primary_Resection_lane2

value: primary


title: Primary_Resection_lane3


title: Primary_Resection_lane4


title: Primary_Resection_lane1


title: Met1_Resection_lane2


title: ST88-14-SUZ12 no Dox RNA rep2


title: Primary_Biopsy_lane2

value: biopsy


title: PT2002-SUZ12 plus Dox H3K4me3

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome using bwa and then use the MACS2 for peak calling
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.
Supplementary_files_format_and_content: peak text files

tag: chip antibody

value: H3K4me3 (Cell Signaling 9751S)


title: Primary_Biopsy_lane1

value: MPNST


title: PT2002-SUZ12 no Dox H3K4me3


title: PT2002-SUZ12 plus Dox H3K27ac

value: H3K27ac (Abcam ab4729)


title: PT2002-SUZ12 plus Dox H3K27me3

value: H3K27me3 (Millipore 07-449)


title: PT2002-SUZ12 no Dox H3K27ac


title: PT2002-SUZ12 plus Dox input


title: ST88-14-SUZ12 plus Dox H3K4me3


title: PT2002-SUZ12 no Dox input


title: ST88-14-SUZ12 no Dox H3K4me3


title: ST88-14-SUZ12 no Dox H3K27ac


title: ST88-14-SUZ12 plus Dox H3K27ac


title: ST88-14-SUZ12 plus Dox H3K27me3


title: ST88-14-SUZ12 no Dox H3K27me3


title: ST88-14-SUZ12 plus Dox input


title: ST88-14-SUZ12 no Dox input


title: T265 input

value: not transduced


title: T265 FOXC1


title: T265-SUZ12 no Dox H3K4me3


title: T265-SUZ12 no Dox FOXC1 rep1


title: T265-SUZ12 plus Dox FOXC1 rep1


title: T265-SUZ12 no Dox H3K27ac


title: T265-SUZ12 plus Dox H3K4me3


title: T265-SUZ12 plus Dox H3K27ac


title: T265-SUZ12 plus Dox H3K27me3


title: T265-SUZ12 no Dox H3K27me3


title: T265 siC H3K27ac

data_processing:
Basecalls performed using CASAVA version 1.4
CUT&RUN reads were aligned to the hg19 and S. cerevisiae yeast genome using bwa and then use the MACS2 for peak calling
Assembly: hg19 and S. cerevisiae yeast
Supplementary files format and content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.
Supplementary files format and content: peak text files
Library strategy: CUT&RUN

growth_protocol: Human MPNST cell line T265 was maintained in DMEM10 (DMEM supplemented with 10% FBS, 100 U/mL penicillin, 100 ug/mL streptomycin, and L-Glutamine).

extract_protocol:
Cells were fixed with 0.1% formaldehyde for 2 min at room temperature and protein-DNA complexes were enriched with antibody following the Cell Signaling Techmology's instructions of the CUT&RUN assay Kit.
Libraries were prepared according to Cell Signaling Technology's SimpleChIP ChIP-seq DNA library Prep Kit for Illumina Guide.

treatment_protocol: To knock down the target protein, siRNA targeting FOXC1 was used with RNAiMAX in a reverse transfection experiment.

value: malignant peripheral nerve sheath tumors (MPNST)

value: transfected with control siRNA

value: H3K27ac (Active Motif, 39133)

value: siControl


title: PT2002-SUZ12 no Dox H3K27me3

value: transduced with Dox-inducible SUZ12-ORF

value: untreated


title: T265-SUZ12 no Dox input


title: T265 siF H3K27ac

value: transfected with siRNA that targets human FOXC1


title: PT2002-SUZ12 plus Dox ATAC rep1

data_processing:
Basecalls performed using CASAVA version 1.4
Data was analyzed by Encode ATAC-seq pipeline
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.

extract_protocol:
Chromatin extraction and ATAC-seq was performed as previously described by William J Greenleaf and Howard Y Chang's group (Nature Methods. 960 | VOL.14 NO.10 | OCTOBER 2017, PMID 28846090).
Libraries were prepared according to the protocol from William J Greenleaf and Howard Y Chang's group using Illumina's Nextera DNA library prep kit.

value: treated with Dox for 5 days


title: T265 siC input


title: T265 siF input


title: PT2002-SUZ12 plus Dox ATAC rep2


title: PT2002-SUZ12 no Dox ATAC rep2


title: PT2002-SUZ12 no Dox ATAC rep1


title: ST88-14-SUZ12 plus Dox ATAC rep1


title: ST88-14-SUZ12 no Dox ATAC rep1


title: T265-SUZ12 plus Dox ATAC rep2


title: ST88-14-SUZ12 plus Dox ATAC rep2


title: ST88-14-SUZ12 no Dox ATAC rep2


title: T265-SUZ12 plus Dox ATAC rep1


title: hu14.18-IL2, scRNAseq

status: Public on Sep 01 2022

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: h5 files and matrix files

source_name: CD45+ cells

extract_protocol:
Neuroblastoma tumors were freshly processed into single cell suspensions and enriched via CD45 magnetic bead positive selection (Stem Cell Technologies). The viability of samples was confirmed to be >80% prior to further processing. Three individual mouse samples per treatment group were pooled.
About 10,000 cells from each treatment group were loaded with the goal of capturing 6,000 cells using the 10X Genomics 3’ v3.1 chemistry. We followed the manufacturer’s instructions for library generation. The cDNA libraries were sequenced on the NextSeq2000 with a target depth of approximately 50,000 reads per cell.

value: CD45+ cells

tag: strain

value: A/J

tag: age

value: 4-6 weeks old

value: NXS-2 cells orthotopically injected hu14.18-IL2


title: hu14.18-IL15, scRNAseq

description: 10x Genomics

value: female

value: NXS-2 cells orthotopically injected hu14.18-IL15


title: T265-SUZ12 no Dox ATAC rep2

tag: cell line

value: MPNST


title: T265-SUZ12 plus Dox input

tag: cell type


title: T265-SUZ12 no Dox ATAC rep1


title: 22RV1_HA_EZH2_TAD_WT

status: Public on Aug 29 2022

source_name: 22Rv1 cells

growth_protocol: 22Rv1 cells, either the parental cells or those with the stably expressed HA-tagged EZH2 (carrying WT TAD domain or the TAD-transactivation-dead mutant (FA), were grown in the RPMI1640 base medium plus 10% FBS and 1% antibiotics. For EZH2 and H3K27me3 CUT&RUN, IgG was used as negative control; and for anti-HA CUT&RUN, 22Rv1 cells with empty vector (EV) were used as negative control. For compound treatment, cells were treated for 24 hours with either DMSO (control) or 2.5 µM of MS177.

treatment_protocol: 1 million of cells was collected, washed and bound to ConA beads. Cell:bead sample was incubated with the indicated antibodies overnight and then washed and treated with pAG-MNase, followed by adding 2mM CaCl2 to activate pAG-MNase. Solubilized chromatin was then released using the CUT&RUN stop buffer.

value: 22Rv1 cells

tag: antibody used

value: Rabbit anti-HA (CST 3724)

tag: treatment condition

value: stably expressed HA-tagged EZH2 (carrying WT TAD domain)


title: 22RV1_HA_EZH2_TAD_mutant(FA)

value: stably expressed HA-tagged EZH2 (carrying the TAD-transactivation-dead mutant (FA))


title: 22RV1_MS177_EZH2

value: Rabbit anti-EZH2 (CST 5246)

value: 2.5 µM of MS177 treatment for 24h


title: 22RV1_DMSO_H3K27me3

value: Rabbit anti-H3k27me3 (CST 9733)

value: DMS0 treatment for 24h


title: 22RV1_DMSO_AR

value: Rabbit anti-AR (santa cruz sc-816)


title: 22RV1_HA_negative control

value: stably expressed EV (control)


title: 22RV1_EZH2_rep2


title: 22RV1_DMSO_EZH2


title: 22RV1_H3K27me3_ab1

tag: treatment

value: CST


title: 22RV1_MS177N1_rep1

data_processing:
Fastq files were aligned to the GRCh38 human genome (GRCh38.d1.vd1.fa) using STAR v2.4.2 with parameters: --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM. Transcript abundance was estimated with salmon v0.1.19 to quantify the transcriptome defined by Gencode v22. Gene level counts were summed across isoforms and genes with low counts (maximum expression < 10) were filtered for the downstream analyses. Raw read counts were used for differential gene expression analysis by DESeq2 v1.38.2 where size normalization factor was estimated based on median-of-ratios.
Assembly: hg19
Supplementary files format and content: tab delimited matrix of gene level count estimates

growth_protocol: 22Rv1 cells were grown in the RPMI1640 base medium plus 10% FBS and 1% antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit. 1 ug of total RNA for the construction of the pooled sequencing libraries.
NEBNext Ultra II RNA library Prep kit (NEB, #E7770) was used

treatment_protocol: 22Rv1 cells were first cultured under the ligand-starved conditions for three days by using the Phenol red free RPMI-1640 base medium supplemented with the charcoal-stripped serum, followed by treatment with either vehicle (DMSO), 10 nM of dihydrotestosterone (DHT), or 10 nM of DHT together with compounds, which were either DMSO or 2.5 µM of MS177 (EZH2-targeting degrader), C24 (the EZH2 catalytic inhibitor) or MS177N1 (the inactive non-PROTAC analog of MS177).

value: 2.5 µM of MS177N1 treatment for 24h


title: 22RV1_MS177_rep1


title: 22RV1_C24_rep2

value: 2.5 µMof C24 treatment for 24h


title: 22RV1_DMSO_rep1

value: DMSO treatment for 24h


title: 22RV1_shEZH2_rep2

value: EZH2 knock-down


title: 22RV1_DMSO_rep2


title: 22RV1_shEZH2_rep1


title: hu14.18-IL21, scRNAseq

description: 10x Genomics

value: CD45+ cells

value: A/J

value: 4-6 weeks old

value: female

value: NXS-2 cells orthotopically injected hu14.18-IL21


title: 22RV1_MS177_AR

value: 22Rv1 cells


title: 22RV1_MS177_H3K27me3


title: Control, scRNAseq

description: 10x Genomics

value: NXS-2 cells orthotopically injected Vehicle


title: 22RV1_shEV_rep1

value: control


title: 231_sg14_S11_R1/2

status: Public on Aug 02 2022

data_processing:
Library strategy: CUT&RUN
Raw sequencing reads were first trimmed by Trim Galore to remove low-quality and adaptor bases, and were mapped to hg19 human genome using bowtie2.3.5
The non-primary alignment, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard “MarkDuplicates” function (ver2.20.4), and bedtools (v2.28.0), respectively
Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g hs/mm --keep-dup 1). Distribution of peaks was calculated by “annotatePeak” function of HOMER
Deeptools (v3.3.0) was used to make bigwig files, heatmaps, and averaged plotting of CUT&RUN signals. Genomic binding profiles were generated using the deepTools “bamCompare” functions
Profiles of CUT&RUN read densities were displayed in the Integrative Genomics Viewer
Genome_build: hg19

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 and 293T were cultured in DMEM medium supplemented with 10% fetal bovine serum plus 1% penicillin–streptomycin

extract_protocol: Libraries were prepared by NEBNext Ultra II kit (NEB, #E7645L)

value: H3P16-OH_Rabbit1,rabbit anti H3P16-OH antibody was generated by Abclonal Company

value: MDA-MB-231 cells

value: Treated with inducible sgRNA EglN2-14


title: 231_sg13_S10_R1/2

value: Treated with inducible sgRNA EglN2-13


title: 231_Ctrl_S9_R1/2

value: Treated with inducible sgRNA control


title: 22RV1_H3K27me3_ab2

value: Rabbit anti-H3k27me3 (Millipore 07-449)

value: MP


title: 22RV1_MS177N1_rep2

value: 2.5 µm of MS177N1 treatment for 24h


title: 231_hypoxia_KDM5A-1_S9

value: rabbit anti-KDM5A  (abcam, ab70892)

value: Treated with hypoxia


title: 231_hypoxia_EglN2-1_S7

value: Rabbit anti-EglN2 (Abcam, ab113077)


title: 231_hypoxia_H3K4ME3-2_S12

value: rabitt anti H3K4me3 (EpiCypher, 15-1016)


title: 22RV1_C24_rep1

value: 2.5 µM of C24 treatment for 24h


title: 231_hypoxia_EglN2-2_S8


title: 231_hypoxia_H3K4ME3-1_S11


title: 22RV1_MS177_rep2

value: 2.5 µM of MS177 treatment for 24h


title: 231_Hypoxia_H3K4me3_S5


title: 293_sg13_OH_S2

source_name: 293T cells

value: H3P16-OH_Rabbit2,rabbit anti H3P16-OH antibody was generated by Abclonal Company

value: 293T cells

value: Treated with sgRNA EglN2-13


title: 231_hypoxia_sg13_OH_S8

value: Treated with sgRNA EglN2-13+hypoxia


title: 231_ctrl_H3K4me3_S4 (2)

value: MDA-MB-231 cells


title: 22RV1_shEV_rep2

value: 22Rv1 cells

value: control


title: 231_hypoxia_Ctrl_OH_S7

value: Treated with sgRNA control+hypoxia


title: 231_sg14_OH_S6

value: Treated with sgRNA EglN2-14


title: 231_Ctrl_OH_S4

value: Treated with sgRNA control


title: 231_sg13_OH_S5


title: 293T_EglN2si2_3_S9

data_processing:
The fastq files were aligned to the GRCh38 human genome (GRCh38.d1.vd1.fa) using STAR v2.4.2 with the following parameters: --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM. Transcript abundance for each sample was estimated with salmon v0.1.19  to quantify the transcriptome defined by Gencode v22. Gene level counts were summed across isoforms and genes with low counts (maximum expression < 10) were filtered for the downstream analyses
Genome_build: hg19

value: Treated with siRNA EglN2-2


title: 231_hypoxia_KDM5A-2_S10

value: rabbit anti-KDM5A  (abcam, ab70892)


title: 293T_EglN2si2_1_S7


title: 293T_EglN2si1_2_S5

value: Treated with siRNA EglN2-1


title: 293_ctrl_3_S3

value: Treated with siRNA control


title: 293T_EglN2si2_2_S8


title: 293T_EglN2si1_3_S6


title: 293T_EglN2si1_1_S4


title: 293_ctrl_2_S2


title: 293T_KDM5Ash2_3_S18

value: Treated with shRNA KDM5A-2


title: 293T_KDM5Ash2_2_S17


title: 293T_KDM5Ash2_1_S16


title: 293T_KDM5Ash1_3_S15

value: Treated with shRNA KDM5A-1


title: 293_ctrl_1_S1


title: 293T_KDM5Ash1_2_S14


title: 293T_KDM5Ash1_1_S13


title: 293T_scr_3_S12

value: Treated with shRNA control


title: 293T_scr_2_S11


title: 293_sg14_OH_S3

value: H3P16-OH_Rabbit2,rabbit anti H3P16-OH antibody was generated by Abclonal Company


title: 293T_scr_1_S10


title: 293_ctrl_OH_S1

value: 293T cells


title: 231_EglN2si2_2_S8


title: 231_EglN2si2_3_S9


title: 231_EglN2si2_1_S7


title: 231_EglN2si1_2_S5


title: 231_EglN2si1_3_S6


title: 231_ctrl_2_S2


title: 231_EglN2si1_1_S4


title: 231_ctrl_3_S3


title: 231_KDM5Ash2_3_S18


title: 231_KDM5Ash2_2_S17


title: 231_KDM5Ash2_1_S16


title: 231_KDM5Ash1_2_S14


title: 231_KDM5Ash1_3_S15


title: 231_scr_3_S12


title: 231_KDM5Ash1_1_S13


title: 231_scr_2_S11


title: 231_scr_1_S10


title: 293T_siEglN2_1_KDM5A_S7


title: 293T_siEglN2_4_KDM5A_S8

value: Treated with siRNA EglN2-4


title: 293T_siEglN2_1_H3K4ME3_S5

value: rabitt anti H3K4me3 (EpiCypher, 15-1016)


title: 231_siEglN2_2_KDM5A_S7

value: MDA-MB-231 cells


title: 231_EglN2si1_KDM5A_S8


title: 231_siEglN2_3_H3K4ME4_S1

value: Treated with siRNAEglN2-3


title: 231_ctrl_KDM5A_S7


title: 231_siEglN2_1_H3K4ME3_S2


title: 231_Ctrl_H3K4ME3_S4


title: 231_siEglN2_2_H3K4ME3_S3


title: 231_ctrl_1_S1


title: 293_h3k4me3_CUT-RUN_S1


title: 293_H3K4ME3-R1/2


title: 293_KDM5A-1-2_CUT-RUN_S8


title: 293_lgG_CUT-RUN_S7

value: rabitt anti IgG (CST, 2729S)


title: 293_KDM5A-1-1_CUT-RUN_S7


title: 293T_EgLN2_2_S2

value: Rabbit anti-EglN2 (Abcam, ab113077)


title: 293_3_CUT-RUN_S9

value: H3P16-OH_Rabbit1,rabbit anti H3P16-OH antibody was generated by Abclonal Company


title: 293T_EgLN2_1_S1


title: 293_H3OH-R1/2


title: 293T_Ctrl_KDM5A_S6


title: 231_IgG_S2


title: 293T_siEglN2_4_H3K4ME3_S6


title: 231_H3K4ME3_1_S3


title: 231_KDM5A-1-2_CUT-RUN_S8


title: 231_KDM5A-1-1_CUT-RUN_S7


title: 293T_Ctrl_H3K4ME3_S3


title: 231_lgG_CUT-RUN_S1


title: 231_EGLN2-2_CUT-RUN_S6


title: 293_lgG_S1


title: 231_1-01_CUT-RUN_S4


title: 231_EGLN2-1_CUT-RUN_S5


title: 231_0-96_CUT-RUN_S3


title: 231_0-49_CUT-RUN_S2


title: Genomic DNA from myxopapillary ependymoma 116

status: Public on Apr 25 2022

city: Hamburg

first: Michael

last: Bockmayr

address: Martinistr. 52

department: Pediatric Hematology and Oncology

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing: Statistical analysis was performed using the minfi package version 1.30.0 with the statistical programming language R version 3.6.0

label: Cy5 and Cy3

source_name: myxopapillary ependymoma 116

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

tag: Sex

value: female

tag: mpe subtype

value: B

tag: material

value: FFPE

tag: pfs [years]

tag: pfs status

value: NED

tag: localization

value: lumbar

tag: histology

value: myxoid


title: Genomic DNA from myxopapillary ependymoma 118

source_name: myxopapillary ependymoma 118

value: male

value: thoracolumbar

value: tanycytic


title: Genomic DNA from myxopapillary ependymoma 115

source_name: myxopapillary ependymoma 115

tag: resection

value: GTR


title: Genomic DNA from myxopapillary ependymoma 114

source_name: myxopapillary ependymoma 114

value: A

value: papillary


title: Genomic DNA from myxopapillary ependymoma 109

source_name: myxopapillary ependymoma 109

value: lumbosacral


title: Genomic DNA from myxopapillary ependymoma 110

source_name: myxopapillary ependymoma 110


title: Genomic DNA from myxopapillary ependymoma 67

source_name: myxopapillary ependymoma 67


title: Genomic DNA from myxopapillary ependymoma 66

source_name: myxopapillary ependymoma 66

value: thoracic

value: STR


title: Genomic DNA from myxopapillary ependymoma 108

source_name: myxopapillary ependymoma 108


title: Genomic DNA from myxopapillary ependymoma 113

source_name: myxopapillary ependymoma 113


title: Genomic DNA from myxopapillary ependymoma 51

source_name: myxopapillary ependymoma 51

value: relapsed

value: sacral


title: Genomic DNA from myxopapillary ependymoma 83

source_name: myxopapillary ependymoma 83

value: female


title: Genomic DNA from myxopapillary ependymoma 112

source_name: myxopapillary ependymoma 112


title: 15291X50

status: Public on Apr 04 2022

city: Salt Lake City

first: Sujee

last: Jeyapalina

state: Utah

address: 500 Foothill Dr

institute: Department of Veteran Affairs

data_processing:
STAR 2.6.1b
featureCounts 1.6.3 Ensemble v94
sva 3.40.0
DESeq2 1.32.0
Genome_build: GRCh38.94
Supplementary_files_format_and_content: Count matrix

source_name: Whole-Blood

extract_protocol:
Whole-blood collected in PAXgene blood RNA tubes.
Total RNA underwent ribosomal depletion and library prep using Illumina TruSeq Stranded RNA Kit with Rob-Zero Gold.

tag: patient

tag: time point

tag: rin


title: 15291X48


title: Genomic DNA from myxopapillary ependymoma 64

source_name: myxopapillary ependymoma 64

tag: age


title: 15291X47


title: 231_h3k4me3_CUT-RUN_S1

source_name: MDA-MB-231 cells

value: rabitt anti H3K4me3 (EpiCypher, 15-1016)

tag: cell line

value: MDA-MB-231 cells


title: 15291X49


title: 15291X44


title: 15291X43


title: 15291X46


title: 15291X42


title: 15291X41


title: 15291X45


title: 15291X40


title: 15291X39


title: 15291X35


title: 15291X37


title: 15291X34


title: 15291X36


title: 15291X33


title: 15291X38


title: Genomic DNA from myxopapillary ependymoma 65

source_name: myxopapillary ependymoma 65

value: B

value: FFPE


title: 15291X32


title: 15291X30


title: Genomic DNA from myxopapillary ependymoma 23

source_name: myxopapillary ependymoma 23

value: NED


title: 15291X31


title: 15291X27


title: 15291X28


title: 15291X26


title: 15291X23


title: 15291X24


title: 15291X21


title: 15291X25


title: 15291X20


title: 15291X22


title: 15291X19


title: 15291X18


title: 15291X16


title: 15291X12


title: 15291X13


title: 15291X15


title: 15291X14


title: 15291X11


title: 15291X9


title: 15291X8


title: 15291X4


title: 15291X10


title: 15291X29


title: 15291X7


title: 15291X3


title: 15291X6


title: 15291X2


title: 15291X5


title: 15291X1


title: 14526X45


title: 14526X44


title: 14526X46


title: 15291X17


title: 14526X43


title: 14526X41


title: 14526X42


title: 14526X39


title: 14526X37


title: 14526X40


title: 14526X36


title: 14526X35


title: 14526X33


title: 14526X34


title: 14526X31


title: 14526X32


title: 14526X29


title: 14526X27


title: 14526X26


title: 14526X25


title: 14526X30


title: 14526X23


title: 14526X24


title: 14526X47


title: 14526X20


title: 14526X22


title: 14526X21


title: 14526X16


title: 14526X17


title: 14526X15


title: 14526X13


title: 14526X19


title: 14526X38


title: 14526X14


title: 14526X11


title: 14526X12


title: 14526X10


title: 14526X28


title: 14526X6


title: 14526X8


title: 14526X9


title: 14526X5


title: 14526X1


title: 14526X3


title: 14526X4


title: 14526X2


title: Skin_biopsy_Control/Pyoderma_case3

status: Public on Mar 23 2022

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler

scan_protocol: Cartridges were run on a Nanostring Sprint machine

data_processing:
Data were analyzed with nSolver software version 4.0
raw counts for our analysis

label: fluorescent probe

organism: Canis lupus familiaris

source_name: archival skin biopsy

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol

extract_protocol: RNA was isolated from 30 micron curls from archival skin biopsies using Qiagen FFPE RNEasy kit with Deparaffinization solution per the manufacturer's instructions.

tag: disease status

value: Control/Pyoderma


title: 14526X18


title: 14526X7


title: liver biopsy [Liv277]

status: Public on Jan 09 2022

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: liver biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol:
All human liver biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

value: N

value: Y

tag: steatohepatitis (y, n, na)

tag: fibrosis (y, n, na)


title: liver biopsy [Liv276]


title: liver biopsy [Liv246]


title: liver biopsy [Liv293]


title: liver biopsy [Liv262]


title: liver biopsy [Liv240]


title: liver biopsy [Liv247]


title: liver biopsy [Liv239]


title: liver biopsy [Liv257]


title: liver biopsy [Liv258]


title: liver biopsy [Liv279]


title: liver biopsy [Liv248]


title: liver biopsy [Liv243]


title: liver biopsy [Liv245]


title: liver biopsy [Liv268]


title: liver biopsy [Liv292]


title: liver biopsy [Liv280]


title: liver biopsy [Liv301]


title: liver biopsy [Liv304]


title: liver biopsy [Liv242]


title: liver biopsy [Liv334]


title: liver biopsy [Liv286]


title: liver biopsy [Liv331]


title: liver biopsy [Liv326]


title: liver biopsy [Liv321]


title: liver biopsy [Liv241]


title: liver biopsy [Liv275]


title: liver biopsy [Liv250]


title: liver biopsy [Liv303]


title: liver biopsy [Liv259]


title: liver biopsy [Liv269]


title: liver biopsy [Liv244]


title: liver biopsy [Liv322]


title: liver biopsy [Liv314]


title: liver biopsy [Liv306]


title: liver biopsy [Liv316]


title: liver biopsy [Liv310]


title: liver biopsy [Liv337]


title: liver biopsy [Liv237]


title: liver biopsy [Liv272]


title: liver biopsy [Liv329]


title: liver biopsy [Liv336]


title: liver biopsy [Liv320]


title: liver biopsy [Liv309]


title: liver biopsy [Liv311]


title: liver biopsy [Liv255]


title: liver biopsy [Liv265]


title: liver biopsy [Liv324]


title: liver biopsy [Liv252]


title: liver biopsy [Liv295]


title: liver biopsy [Liv315]


title: liver biopsy [Liv332]


title: liver biopsy [Liv273]


title: liver biopsy [Liv261]


title: liver biopsy [Liv285]


title: liver biopsy [Liv333]


title: liver biopsy [Liv299]


title: liver biopsy [Liv271]


title: liver biopsy [Liv302]


title: liver biopsy [Liv327]


title: liver biopsy [Liv278]


title: liver biopsy [Liv312]


title: liver biopsy [Liv266]


title: liver biopsy [Liv284]


title: liver biopsy [Liv256]


title: liver biopsy [Liv283]


title: liver biopsy [Liv297]


title: liver biopsy [Liv281]


title: liver biopsy [Liv290]


title: liver biopsy [Liv282]


title: liver biopsy [Liv298]


title: liver biopsy [Liv264]


title: liver biopsy [Liv328]


title: liver biopsy [Liv319]


title: liver biopsy [Liv318]


title: liver biopsy [Liv308]


title: liver biopsy [Liv307]


title: liver biopsy [Liv317]


title: liver biopsy [Liv335]


title: liver biopsy [Liv238]


title: liver biopsy [Liv289]


title: liver biopsy [Liv254]


title: liver biopsy [Liv296]


title: liver biopsy [Liv260]


title: liver biopsy [Liv251]


title: liver biopsy [Liv274]


title: liver biopsy [Liv294]


title: liver biopsy [Liv267]


title: liver biopsy [Liv253]


title: liver biopsy [Liv263]


title: liver biopsy [Liv325]


title: liver biopsy [Liv287]


title: liver biopsy [Liv249]


title: liver biopsy [Liv288]


title: liver biopsy [Liv330]


title: liver biopsy [liver193]


title: liver biopsy [liver29]


title: liver biopsy [liver194]


title: liver biopsy [liver235]


title: liver biopsy [liver51]


title: liver biopsy [Liv300]


title: liver biopsy [liver230]


title: liver biopsy [liver34]


title: liver biopsy [liver40]


title: liver biopsy [liver12]


title: liver biopsy [liver36]


title: liver biopsy [liver213]


title: liver biopsy [Liv270]


title: liver biopsy [liver4]


title: liver biopsy [liver107]


title: liver biopsy [liver43]


title: liver biopsy [liver148]


title: liver biopsy [liver190]


title: liver biopsy [Liv313]


title: liver biopsy [liver221]


title: liver biopsy [liver191]


title: liver biopsy [liver127]


title: liver biopsy [liver72]


title: liver biopsy [liver115]


title: liver biopsy [liver69]


title: liver biopsy [liver31]


title: liver biopsy [liver217]


title: liver biopsy [liver73]


title: liver biopsy [liver114]


title: liver biopsy [liver13]


title: liver biopsy [liver134]


title: liver biopsy [liver123]


title: liver biopsy [liver183]


title: liver biopsy [liver1]


title: liver biopsy [liver225]


title: liver biopsy [liver196]


title: liver biopsy [liver26]


title: liver biopsy [liver108]


title: liver biopsy [liver133]


title: liver biopsy [liver199]


title: liver biopsy [liver129]


title: liver biopsy [liver75]


title: liver biopsy [liver54]


title: liver biopsy [liver215]


title: liver biopsy [liver111]


title: liver biopsy [liver192]


title: liver biopsy [liver233]


title: liver biopsy [liver2]


title: liver biopsy [liver96]


title: liver biopsy [liver41]


title: liver biopsy [liver228]


title: liver biopsy [liver119]


title: liver biopsy [liver10]


title: liver biopsy [liver20]


title: liver biopsy [liver33]


title: liver biopsy [liver207]


title: liver biopsy [liver198]


title: liver biopsy [liver216]


title: liver biopsy [liver53]


title: liver biopsy [liver80]


title: liver biopsy [liver56]


title: liver biopsy [liver49]


title: liver biopsy [liver59]


title: liver biopsy [liver155]


title: liver biopsy [liver11]


title: liver biopsy [liver95]


title: liver biopsy [liver68]


title: liver biopsy [liver231]


title: liver biopsy [liver65]


title: liver biopsy [liver105]


title: liver biopsy [liver159]


title: liver biopsy [liver25]


title: liver biopsy [liver210]


title: liver biopsy [liver77]


title: liver biopsy [liver124]


title: liver biopsy [liver88]


title: liver biopsy [liver142]


title: liver biopsy [liver165]


title: liver biopsy [liver141]


title: liver biopsy [liver171]


title: liver biopsy [liver203]


title: liver biopsy [liver35]


title: liver biopsy [liver46]


title: liver biopsy [liver102]


title: liver biopsy [liver202]


title: liver biopsy [liver126]


title: liver biopsy [Liv323]


title: liver biopsy [liver19]


title: liver biopsy [liver8]


title: liver biopsy [liver167]


title: liver biopsy [liver120]


title: liver biopsy [liver44]


title: liver biopsy [liver82]


title: liver biopsy [liver137]


title: liver biopsy [liver42]


title: liver biopsy [liver223]


title: liver biopsy [liver76]


title: liver biopsy [liver112]


title: liver biopsy [liver85]


title: liver biopsy [liver186]


title: liver biopsy [liver153]


title: liver biopsy [liver100]


title: liver biopsy [liver93]


title: liver biopsy [liver94]


title: liver biopsy [liver122]


title: liver biopsy [liver97]


title: liver biopsy [liver32]


title: liver biopsy [liver170]


title: liver biopsy [liver143]


title: liver biopsy [liver23]


title: liver biopsy [liver89]


title: liver biopsy [liver157]


title: liver biopsy [liver116]


title: liver biopsy [liver168]


title: liver biopsy [liver179]


title: liver biopsy [liver173]


title: liver biopsy [liver222]


title: liver biopsy [liver5]


title: liver biopsy [liver219]


title: liver biopsy [liver92]


title: liver biopsy [liver15]


title: liver biopsy [liver214]


title: liver biopsy [liver226]


title: liver biopsy [liver184]


title: liver biopsy [liver90]


title: liver biopsy [liver201]


title: liver biopsy [liver84]


title: liver biopsy [liver70]


title: liver biopsy [liver151]


title: liver biopsy [liver218]


title: liver biopsy [liver37]


title: liver biopsy [liver27]


title: liver biopsy [liver164]


title: liver biopsy [liver57]


title: liver biopsy [liver160]


title: liver biopsy [liver38]


title: liver biopsy [liver130]


title: liver biopsy [liver30]


title: liver biopsy [liver128]


title: liver biopsy [liver220]


title: liver biopsy [liver189]


title: liver biopsy [liver132]


title: liver biopsy [liver195]


title: liver biopsy [liver154]


title: liver biopsy [liver64]


title: liver biopsy [liver86]


title: liver biopsy [liver211]


title: liver biopsy [liver39]


title: liver biopsy [Liv291]


title: liver biopsy [liver52]


title: liver biopsy [liver212]


title: liver biopsy [liver99]


title: liver biopsy [liver66]


title: liver biopsy [liver125]


title: liver biopsy [liver81]


title: liver biopsy [liver55]


title: liver biopsy [liver104]


title: liver biopsy [liver74]


title: liver biopsy [liver229]


title: liver biopsy [liver208]


title: liver biopsy [liver91]


title: liver biopsy [liver78]


title: liver biopsy [liver172]


title: liver biopsy [liver188]


title: liver biopsy [liver22]


title: liver biopsy [liver206]


title: liver biopsy [liver103]


title: liver biopsy [liver178]


title: liver biopsy [liver234]


title: liver biopsy [liver135]


title: liver biopsy [liver146]


title: liver biopsy [liver58]


title: liver biopsy [liver209]


title: liver biopsy [liver24]


title: liver biopsy [Liv305]


title: liver biopsy [liver79]


title: liver biopsy [liver174]


title: liver biopsy [liver232]


title: liver biopsy [liver28]


title: liver biopsy [liver156]


title: liver biopsy [liver182]


title: liver biopsy [liver110]


title: liver biopsy [liver197]


title: liver biopsy [liver60]


title: liver biopsy [liver224]


title: liver biopsy [liver113]


title: liver biopsy [liver62]


title: liver biopsy [liver71]


title: liver biopsy [liver144]


title: liver biopsy [liver17]


title: liver biopsy [liver200]


title: liver biopsy [liver16]


title: liver biopsy [liver7]


title: liver biopsy [liver205]


title: liver biopsy [liver175]


title: liver biopsy [liver14]


title: liver biopsy [liver180]


title: liver biopsy [liver6]


title: liver biopsy [liver9]


title: liver biopsy [liver152]


title: liver biopsy [liver63]


title: liver biopsy [liver162]


title: liver biopsy [liver176]


title: liver biopsy [liver158]


title: liver biopsy [liver45]


title: EOL1_MS177_replicate_1

status: Public on Dec 29 2021

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed. Raw read counts were used for differential gene expression analysis by DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates

source_name: EOL1  cells

growth_protocol: EOL1, MV4;11, MOLM13 and MM1S cells were grown in RPMI1640 plus 10% FBS and 1% antibiotics.

treatment_protocol: For compound treatment studies, EOL1 cells were treated with either DMSO, 0.5 µM of C24 or 0.5 µM of MS177 for 16h experiments and collected; MV4;11, MOLM13 and MM1S cells were treated with either DMSO o 2.5 µM of C24, MS177N1 or MS177 for 24h and collected.

tag: agent


title: EOL1_MS177_replicate_2


title: liver biopsy [liver109]


title: liver biopsy [liver48]


title: liver biopsy [liver147]


title: liver biopsy [liver131]


title: liver biopsy [liver117]


title: liver biopsy [liver61]


title: liver biopsy [liver150]


title: liver biopsy [liver98]


title: liver biopsy [liver177]


title: liver biopsy [liver138]


title: liver biopsy [liver185]


title: liver biopsy [liver87]


title: EOL1_C24_replicate_2


title: liver biopsy [liver187]


title: liver biopsy [liver149]


title: liver biopsy [liver18]


title: liver biopsy [liver166]


title: liver biopsy [liver101]


title: liver biopsy [liver204]


title: liver biopsy [liver3]


title: liver biopsy [liver145]


title: liver biopsy [liver21]


title: liver biopsy [liver106]


title: EOL1_C24_replicate_1


title: liver biopsy [liver227]


title: liver biopsy [liver121]


title: EOL1_DMSO_replicate_2

value: DMSO


title: liver biopsy [liver181]


title: MV4-11_DMSO_EZH2_ChIP_with_spikein

data_processing:
All reads were mapped to both drosophila dm3 and human hg19 reference genomes using the STAR aligner. All mismatches are extended and low quality sequences are trimmed at this step. Non-primary alignment and PCR duplicates were then removed by samtools. Scaling factors are calculated and normalization is done by the bamCompare function of deeptools  with bin size 10 and read length 250.
Alignment files in the bam format were transformed into read coverage files (bigwig format) using DeepTools. Scaling factors are calculated, and normalization is done by the bamCompare function of deeptools with bin size 10 and read length 250.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: MV4;11 cells

growth_protocol: EOL1 and MV4;11 cells were grown in RPMI1640 plus 10% FBS and 1% antibiotics. For treatment, EOL1 cells were treated with either DMSO, 0.5 µM of C24 or 0.5 µM of MS177 for 16h experiments and collected; MV4;11 cells were treated with either DMSO or 2.5 µM of MS177 for 24h and collected.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies against EZH2 (CST 5246) or H3K27me3 (CST 9733) together with H2Av (Active motif 39715; for Drosophila spike-in chromatin)
Libraries were prepared by NEBNext Ultra II kit (NEB, #E7645L)

treatment_protocol: For ChIP-seq experiments, cells were grown in regular medium and collected, followed by cell fixation with 1% of formaldehyde, sonication, antibody enrichment, ChIP DNA recovery, library generation and parallel sequencing.

tag: antibody

value: Rabbit anti-EZH2 (CST 5246), Rabbit anti-H2Av (Active motif 39715)


title: MV4-11_DMSO_H3K27me3_ChIP_with_spikein

value: Rabbit anti-H3k27me3 (CST 9733), Rabbit anti-H2Av (Active motif 39715)


title: MV4-11_DMSO_input_for_H3K27me3

value: n/a (input)


title: MV4-11_MS177_H3K27me3_ChIP_with_spikein


title: EOL1_MS177_H3K27me3_ChIP_with_spikein

source_name: EOL1 cells


title: EOL1_DMSO_input_for_EZH2


title: MV4-11_DMSO_input_for_EZH2


title: MV4-11_MS177_EZH2_ChIP_with_spikein


title: EOL1_C24_H3K27me3_ChIP_with_spikein


title: EOL1_DMSO_replicate_1


title: EOL-1_sgEZH2_1

description: 1 ug/ml doxcycline treatment for 4 days

growth_protocol: EOL-1 and MV4;11 cells were grown in RPMI1640 plus 10% FBS and 1% antibiotics.

treatment_protocol: treat doxcycline (1µg/ml) for 4 days

tag: treatment


title: EOL-1_sgEZH2_2

description: 1 ug/ml doxcycline treatment for 4 days


title: EOL1_DMSO_input_for_H3K27me3


title: EOL1_C24_EZH2_ChIP_with_spikein


title: EOL1_MS177_EZH2_ChIP_with_spikein


title: MV4-11_sgcMyc_1_2

description: 1 ug/ml doxcycline treatment for 4 days


title: EOL1_DMSO_H3K27me3_ChIP_with_spikein

value: Rabbit anti-H3k27me3 (CST 9733) and Rabbit anti-H2Av (Active motif 39715)


title: EOL-1_sgEV_1

description: 1 ug/ml doxcycline treatment for 4 days

value: sgEV


title: MV4-11_sgcMyc_5_2

description: 1 ug/ml doxcycline treatment for 4 days


title: EOL-1_sgEV_2

description: 1 ug/ml doxcycline treatment for 4 days


title: MV4-11_EV_2

description: 1 ug/ml doxcycline treatment for 4 days

value: EV


title: MV4-11_sgcMyc_5_1

description: 1 ug/ml doxcycline treatment for 4 days


title: MV4-11_sgcMyc_1_1

description: 1 ug/ml doxcycline treatment for 4 days


title: MV4-11_shEZH2_1

description: 1 ug/ml doxcycline treatment for 4 days


title: MV4-11_sgEV_2

description: 1 ug/ml doxcycline treatment for 4 days


title: PDX_H3K27ac

data_processing:
Library strategy: CUT&RUN
Fastq files were mapped to the reference genome (hg19) using bowtie2.3.5.
The non-primary alignment, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively
Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Deeptools (v3.3.0) was used to generate bigwig files, heatmaps and averaged plotting of CUT&RUN signals.
Genome_build: hg19

source_name: PDX #68555 cells

growth_protocol: EOL-1 and MV4;11 cells were grown in RPMI1640 plus 10% FBS and 1% antibiotics. PDX #68555 cells  was freshly thawed from liquid nitrogen.

treatment_protocol: Fresh 1 million  cells was collected, washed and bound to ConA beads. Cell:bead sample was incubated with indicating antibodies over night and then washed, treated with pAG-Mnase followed by adding 2mM CaCl2 to activate pAG-Mnase. Solubilized chromatin was then released using the CUT&RUN stop buffer.

tag: antibody used

value: Rabbit anti-H3K27ac (abcam ab4729)


title: MV4_cMyc_ab2

value: Rabiit anti-cMyc (abcam ab32072)


title: PDX_H3K27me3

value: Rabbit anti-H3k27me3 (CST 9733)


title: EOL-1_cMyc_ab2

source_name: EOL-1 cells


title: MV4-11_sgEV_1

description: 1 ug/ml doxcycline treatment for 4 days


title: MV4-11_shEZH2_2

description: 1 ug/ml doxcycline treatment for 4 days


title: MOLM13_DMSO_replicate_2

source_name: MOLM13 cells


title: MOLM13_DMSO_replicate_1


title: MV411_MS177_replicate_1


title: MV4-11_EV_1

description: 1 ug/ml doxcycline treatment for 4 days


title: EOL1_DMSO_EZH2_ChIP_with_spikein


title: PDX_EZH2

value: Rabbit anti-EZH2 (CST 5246)


title: PDX_cMyc

value: Rabbit anti-cMyc (CST 3873)


title: EOL-1_HA_EZH2

value: Rabbit anti-HA (CST 3724)


title: EOL-1_cMyc_ab1


title: MV411_C24_replicate_1


title: MOLM13_C24_replicate_2


title: MOLM13_MS177_replicate_1


title: MOLM13_MS177N1_replicate_1


title: MV4_HA_EZH2


title: MV411_MS177_replicate_2


title: MV411_DMSO_replicate_2


title: MOLM13_MS177N1_replicate_2


title: MV4_cMyc_ab1


title: MV411_MS177N1_replicate_2


title: MOLM13_MS177_replicate_2


title: MV411_C24_replicate_2


title: MV411_MS177N1_replicate_1


title: N67

status: Public on Dec 25 2021

city: Beijing

first: Fengjie

last: Liu

address: No.8 Xishiku Street, Xi Cheng District

department: Dermatology and Venereology

institute: Peking University First Hospital

data_processing:
MF skin-biopsy sequencing data produced by Illumina HiSeq 4000 and cell line sequencing data produced by BGISEQ-500 called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
After filtering raw reads via SOAPnuke,clean reads were mapped to the human hg38 reference genome via HISAT.
For sequence data of skin-biopsy samples, gene expression levels were calculated by summarizing the transcript levels belonging to the same gene estimated by Kallisto,which was quantified by TPM（transcripts per million）.
For sequence data of cell lines,clean reads were aligned to the reference gene sequence using Bowtie2 and gene expression levels were calculated by RSEM,which was normalized as FPKM（fragments per kilobase million）.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM/FPKM values for 49 MF skin-biopsy samples and 14 CTCL cell-line samples

source_name: lymphocytes

growth_protocol: HH  and Myla cells were cultured in RPMI 1640 medium with 10% fetal bovine serum , containing 100 U/mL penicillin and 0.1 mg/mL streptomycin

extract_protocol:
200ng total RNA samples were extracted from lesional skin biopsies obtained from 49 patients with MF (26 LCT, 23 NLCT) using Trizol reagent; from control HH cells and PEG10-silienced HH cells , control Myla cells and  PEG10-overexpressed Myla cells  using EZNA total RNA kit II (Omega Bio-tek) ,respectively.
RNA libraries were prepared for sequencing using standard Illumina and BGISEQ protocols

treatment_protocol: HH cells  were subjected with lentivirus-mediated transfection of vectors expressing PEG10-shRNA(shPEG10-1 and shPEG10-2)  or scrambled shRNA(sh0), and then cultured  to produce stable PEG10 knockdown cell line.  Myla cells  were subjected with lentivirus-mediated transfection of empty vetors and PEG10 expression vectors ( RF1b, RF1b/2, RF1b/2+CNF) , and then cultured  to produce stable PEG10 overexpression cell line.

tag: tumor

value: MF

tag: tissue

value: skin

tag: dissease state

value: NLCT

tag: Sex

value: M

tag: onset age (yr)

tag: duration of disease (yr)

tag: tnmb staging (t)

tag: tnmb staging (n)

tag: tnmb staging (m)

tag: tnmb staging (b)

tag: tnmb  stage

value: IIB

tag: pfs time (mo)

tag: progression

tag: os time(mo)

tag: survival


title: MOLM13_C24_replicate_1

tag: agent


title: N458

value: F


title: MV411_DMSO_replicate_1

value: DMSO


title: N407


title: N69


title: liver biopsy [liver139]

value: Y

tag: steatohepatitis (y, n, na)

value: N

tag: fibrosis (y, n, na)


title: N58

tag: tumor

tag: tissue


title: N531

tag: dissease state

tag: Sex

value: IIIA


title: N559

tag: onset age (yr)

tag: duration of disease (yr)


title: N470

tag: tnmb staging (t)

tag: tnmb staging (n)


title: N266

tag: tnmb staging (m)

tag: tnmb staging (b)


title: N526

tag: tnmb  stage

tag: pfs time (mo)


title: N168

tag: progression

tag: os time(mo)


title: N178

tag: survival


title: N103


title: N30

value: IIIB


title: N325


title: N235


title: N104


title: N251


title: N141


title: N139


title: N295


title: L520_2

value: LCT

tag: lct

value: IVB


title: L446


title: L520


title: L5


title: L431


title: N28


title: L355


title: L381


title: L492


title: L457


title: N292


title: L42


title: L487


title: L40


title: L284


title: L314


title: L321


title: L262


title: L268


title: L260


title: L236


title: L529


title: L176


title: L107


title: L149


title: L112


title: lPEG10_OE1

source_name: CTCL cell line(Myla)

value: stage IIA


title: lPEG10_OE2


title: sPEG10_OE2


title: vec_3


title: vec_2


title: shPEG10_3

source_name: CTCL cell line (HH)

value: peripheral blood

value: stage IVB


title: vec_1


title: shPEG10_2


title: sh0_3


title: shPEG10_1


title: L318


title: sh0_2


title: sh0_1


title: L25