title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 04h - rep3

description:
A549_OE_FOXO3.rnaseq.dex.04h.rep3
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 01h - rep1

status: Public on Feb 22 2021

type: SRA

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

country: USA

institute: Duke University

description:
A549_OE_FOXO3.rnaseq.dex.01h.rep1
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

library_source: transcriptomic

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned against the latest mouse reference genome (GRCh38) using the aligner STAR v2.4.1a following the proposed 2-pass strategy, removing alignments containing non-canonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical)
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Differential expression analysis was performed using DESeq2 (v1.22.0) running on R (v3.5.1). Briefly, raw counts were imported and filtered to remove genes with low or no expression, that is, keeping genes having two or more counts per million (CPMs) in two or more samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited files with TPM gene counts

molecule: total RNA

organism: Homo sapiens

source_name: Modified A549_FOXO3 Overexpressed and treated with DEX for 01h

extract_protocol:
Harvested plates at timepoints (0,0.5, 1, 2 3, 4, 5, 6, 7, 8, 10, 12) by removing media, washing with 3 mL PBS twice, and lysing with RLT+ beta-mercaptoethanol
Cleaned total RNA with Qiagen RNA midiprep kits, and used Illumina mRNA prep kits

treatment_protocol:
Seeded out 10 M seed stock of A549 cells. Changed media after 48 hours. Performed a 1:10 split into 10 plates after 72 hours. Performed a6:12 split into 12 plates 72 hours later. Performed a final 12:48 split into 12 plates and into 12 6-well plates
Treated with 3 uL of 100 uM Dexamethasone dissolved in Ethanol for 12 hours. After 12 hours, removed the media containing dexamethasone and replaced with media that did not contain dex

tag: cell line background

tag: tissue/cell type

value: adenocarcinomic human alveolar basal epithelial

tag: genotype/variation

value: FOXO3 Overexpressed

tag: treatment

value: dexamethasone (DEX)

tag: time point


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 01h - rep2

description:
A549_OE_FOXO3.rnaseq.dex.01h.rep2
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: MR diet 6h 4242_MR_6

city: Baton Rouge

first: Thomas

middle: W

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

institute: Pennington Biomedical Research Center

description:
MR diet 6h
4242_MR_6

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, 3.5.2(2018-12-2), Rstudio V1.2.1511 and biomaRt V2.38.0
DESeq2  V1.22.2 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: mouse- GRCm38.84
Supplementary_files_format_and_content: tab-delimited text containing raw counts and DESeq2 normalized counts

organism: Mus musculus

source_name: liver

growth_protocol: Mice were obtained from JAX at 7 weeks of age, adapted to a reverse light cycle and put on Control diet at 8 weeks of age. Food was removed during lights on and restored at lights off. On the day of the experiment, mice were fed Control or MR diet for either 3 or 6 hours. There were 8 mice in each group.  Animals were sacrificed  using CO2 inhalation and decapitation.

extract_protocol:
Flash frozen liver was dissected and a small piece was placed in Trizol. After homogenization, BCP was added, samples were vortexed vigorously, and then spun. The aqueous phase was combined with an equal volume of ethanol and the sample was processed through a Qiagen RNeasy column according to the manufacturer's instructions. mRNA was stored at -80°C and samples were diluted to 100ng/µl for RNAseq.
Lexogen Quant-Seq
indexed and pooled samples, 50bp forward read

treatment_protocol: The diets used consisted of standard diet containing elemental amino acids with a methionine concentration of either 0.86% methionine (control) or 0.17% methionine (MR; Dyets).

tag: gender

value: Male

tag: strain

tag: age

value: 2 months


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 00h - rep3

description:
A549_OE_FOXO3.rnaseq.dex.00h.rep3
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOXO3 Overexpressed and treated with DEX for 00h


title: sc3

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: DZNE Göttingen

description: synaptic RNAs, total and small

data_processing:
Illumina’s bcl2fastq (v2.20.2) was used for adapter trimming and converting the base calls
Trimming of 3’ adapters for smallRNASeq data was done using cutadapt (v1.11.0)
totalRNASeq reads were aligned using the STAR aligner (v2.5.2b)
smallRNASeq reads were aligned using the mapper.pl script from mirdeep2 (v2.0.1.2) which uses bowtie (v1.1.2)
TotalRNASeq read counts were generated using featureCounts (v1.5.1)
smallRNA read counts were generated with the quantifier.pl script from mirdeep2 (v2.0.1.2)
All read counts were normalized according to library size to transcript per million (TPM)
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing raw and normalized read counts

source_name: Hippocampus primary culture from E17 mouse

growth_protocol: cells were seeded on PDMS (coated with 0.5mg/ml PDL in borate buffer) and cultured in Neurobasal Plus with GlutaMax, Penicilin/Strep and B27 Plus supplement

extract_protocol:
Synaptosome RNA was extracted via Trizol, synaptic RNA from microfluidic chambers was isolated with the GenElute™ Single Cell RNA Purification Kit after cutting the synaptic compartment out of the chamber
Synaptosome small RNA libraries were done via NEBNext Small RNA Library Prep Kit, synaptosome toal RNA libraries via Illumina Truseq total RNA kit. Microfluidic total RNA libraries were prepared with Takara´s SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian, microfluidic chamber small RNA with Takara´s  SMARTer smRNA-Seq Kit for Illumina

treatment_protocol: as indicated, samples were treated with 50mM of KCl for 2h

value: DIV14 from E17

tag: stimulation


title: 2

description: synaptic RNAs, total and small


title: MR diet 6h 4239_MR_6

description:
MR diet 6h
4239_MR_6


title: Control diet 6h 4241_con_6

description:
Control diet 6h
4241_con_6


title: Control diet 6h 4238_con_6

description:
Control diet 6h
4238_con_6


title: Control diet 6h 4234_con_6

description:
Control diet 6h
4234_con_6


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 00h - rep2

description:
A549_OE_FOXO3.rnaseq.dex.00h.rep2
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Control diet 3h 4233_con_3

description:
Control diet 3h
4233_con_3


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 12h - rep3

description:
A549_OE_FOXO1.rnaseq.dex.12h.rep3
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOXO1 Overexpressed and treated with DEX for 12h

value: FOXO1 Overexpressed


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 12h - rep1

description:
A549_OE_FOXO3.rnaseq.dex.12h.rep1
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOXO3 Overexpressed and treated with DEX for 12h


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 00h - rep1

description:
A549_OE_FOXO3.rnaseq.dex.00h.rep1
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Control diet 6h 4231_con_6

description:
Control diet 6h
4231_con_6


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 12h - rep2

description:
A549_OE_FOXO1.rnaseq.dex.12h.rep2
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: MR diet 6h 4229_MR_6

description:
MR diet 6h
4229_MR_6


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 12h - rep1

description:
A549_OE_FOXO1.rnaseq.dex.12h.rep1
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 08h - rep3

description:
A549_OE_FOXO1.rnaseq.dex.08h.rep3
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOXO1 Overexpressed and treated with DEX for 08h


title: MR diet 6h 4228_MR_6

description:
MR diet 6h
4228_MR_6


title: Modified A549 cells with FOXO3 Overexpressed and treated with DEX for 01h - rep3

description:
A549_OE_FOXO3.rnaseq.dex.01h.rep3
processed data file: A549_OE_FOXO3.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: MR diet 3h 4223_MR_3

description:
MR diet 3h
4223_MR_3


title: Control diet 6h 4222_con_6

description:
Control diet 6h
4222_con_6


title: Control diet 3h 4220_con_3

description:
Control diet 3h
4220_con_3


title: Control diet 6h 4221_con_6

description:
Control diet 6h
4221_con_6


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 04h - rep3

description:
A549_OE_FOXO1.rnaseq.dex.04h.rep3
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOXO1 Overexpressed and treated with DEX for 04h


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 08h - rep2

description:
A549_OE_FOXO1.rnaseq.dex.08h.rep2
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: MR diet 6h 4219_MR_6

description:
MR diet 6h
4219_MR_6


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 08h - rep1

description:
A549_OE_FOXO1.rnaseq.dex.08h.rep1
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 04h - rep2

description:
A549_OE_FOXO1.rnaseq.dex.04h.rep2
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 01h - rep1

description:
A549_OE_FOXO1.rnaseq.dex.01h.rep1
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOXO1 Overexpressed and treated with DEX for 01h


title: MR diet 3h 4216_MR_3

description:
MR diet 3h
4216_MR_3


title: Control diet 3h 4218_con_3

description:
Control diet 3h
4218_con_3


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 00h - rep3

description:
A549_OE_FOXO1.rnaseq.dex.00h.rep3
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOXO1 Overexpressed and treated with DEX for 00h


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 00h - rep2

description:
A549_OE_FOXO1.rnaseq.dex.00h.rep2
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: MR diet 6h 4214_MR_6

description:
MR diet 6h
4214_MR_6


title: Control diet 3h 4215_con_3

description:
Control diet 3h
4215_con_3


title: MR diet 3h 4209_MR_3

description:
MR diet 3h
4209_MR_3


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 01h - rep2

description:
A549_OE_FOXO1.rnaseq.dex.01h.rep2
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Control diet 3h 4217_con_3

description:
Control diet 3h
4217_con_3


title: MR diet 3h 4210_MR_3

description:
MR diet 3h
4210_MR_3


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 12h - rep3

description:
A549_OE_FOSL2.rnaseq.dex.12h.rep3
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOSL2 Overexpressed and treated with DEX for 12h

value: FOSL2 Overexpressed


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 00h - rep1

description:
A549_OE_FOXO1.rnaseq.dex.00h.rep1
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: MR diet 3h 4208_MR_3

description:
MR diet 3h
4208_MR_3


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 12h - rep2

description:
A549_OE_FOSL2.rnaseq.dex.12h.rep2
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Control diet 3h 4205_con_3

description:
Control diet 3h
4205_con_3


title: MR diet 3h 4204_MR_3

description:
MR diet 3h
4204_MR_3


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 08h - rep3

description:
A549_OE_FOSL2.rnaseq.dex.08h.rep3
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOSL2 Overexpressed and treated with DEX for 08h


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 04h - rep3

description:
A549_OE_FOSL2.rnaseq.dex.04h.rep3
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOSL2 Overexpressed and treated with DEX for 04h


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 08h - rep1

description:
A549_OE_FOSL2.rnaseq.dex.08h.rep1
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 04h - rep1

description:
A549_OE_FOXO1.rnaseq.dex.04h.rep1
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 08h - rep2

description:
A549_OE_FOSL2.rnaseq.dex.08h.rep2
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOXO1 Overexpressed and treated with DEX for 01h - rep3

description:
A549_OE_FOXO1.rnaseq.dex.01h.rep3
processed data file: A549_OE_FOXO1.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_shSELP2_S62_L004

city: Tel Aviv

first: Ronit

last: Satchi-Fainaro

address: Klatzkin 35

department: physiology and pharmacology

country: Israel

institute: Tel Aviv University

description:
CD11b positive cells, glioblastoma cells and T cells from P-Selectin knockdown  GL261 tumors
Exp2_shSELP2
P-Selectin shRNA  GL261 tumors
second_data_set_counts_table.csv

data_processing:
Gene counts were obtained by aligning reads to the mm10 genome using CellRanger software (v1.3 10× Genomics). To remove doublets and poor-quality cells, we removed cells that contained more than 10% mitochondrially derived transcripts, or where less than 500 genes were detected. Among the retained cells, we considered only genes that are present in >30 cells and have >60 transcripts summed across all the selected cells, yielding 5,457 cells and 9,505 genes.
Genome_build: mm10
Supplementary_files_format_and_content: Transcript count for each library was normalized to the median of the transcript counts across all cells. For PCA and clustering, we used a log-transformed expression matrix. The top 12 and 8 PCs were included for subsequent tSNE analysis, determined by a drop in the proportion of variance explained by subsequent PCs. We confirmed that the resulting analyses were not particularly sensitive to this choice.
Supplementary_files_format_and_content: Column names starting with "NC" belongs to sample number 1 (negative control) and column names starting with "shSELP" blong to sample number 2 (shSELP treated)

source_name: P-selectin shRNA GL261 glioblastoma tumors

extract_protocol:
For samples Exp1, only CD11b postive cells were isolated on day 21 post tumor inoculation using magnetic beads cell separation. For Exp2, CD11b postive cells and the remaining CD45 positive cells were isolated on day 16 post tumor inoculation using magnetic beads cell separation. CD11b positive, CD45 positive and cancer cells were mixed in equal amounts. Cells were isolated from negative control or P-Selectin knockdown GL261 glioblastoma tumors and were encapsulated into droplets.
Libraries were prepared using Chromium Single Cell 3′ Reagent Kits v2 according to manufacturer’s protocol (10× Genomics). The generated single cell RNA-seq libraries were sequenced using a 75 cycle Nextseq 500 high output V2 kit.
single cell RNA-seq

tag: tissue

value: Glioblastoma Tumor

tag: genotype

value: P-Selectin knockdown


title: Exp2_shSELP2_S62_L003


title: Exp2_shSELP2_S62_L002


title: Exp2_shSELP2_S62_L001


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 04h - rep1

description:
A549_OE_FOSL2.rnaseq.dex.04h.rep1
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 04h - rep2

description:
A549_OE_FOSL2.rnaseq.dex.04h.rep2
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_shSELP2_S6_L003


title: Exp2_shSELP2_S6_L001


title: Exp2_shSELP2_S6_L002


title: Exp2_shSELP2_S6_L004


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 01h - rep2

description:
A549_OE_FOSL2.rnaseq.dex.01h.rep2
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOSL2 Overexpressed and treated with DEX for 01h


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 01h - rep3

description:
A549_OE_FOSL2.rnaseq.dex.01h.rep3
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_shSELP1_S52_L003

description:
CD11b positive cells, glioblastoma cells and T cells from P-Selectin knockdown  GL261 tumors
Exp2_shSELP1
P-Selectin shRNA  GL261 tumors
second_data_set_counts_table.csv


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 00h - rep3

description:
A549_OE_FOSL2.rnaseq.dex.00h.rep3
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_FOSL2 Overexpressed and treated with DEX for 00h


title: Exp2_shSELP1_S52_L004


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 00h - rep1

description:
A549_OE_FOSL2.rnaseq.dex.00h.rep1
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 12h - rep1

description:
A549_OE_FOSL2.rnaseq.dex.12h.rep1
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_shSELP1_S5_L004


title: Exp2_shSELP1_S5_L003


title: Exp2_shSELP1_S5_L002


title: A549 cells treated with DEX for 08h - rep2

description:
A549_OE_ctrl.rnaseq.dex.08h.rep2
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 cells treated with DEX for 08h

value: GFP only


title: A549 cells treated with DEX for 08h - rep3

description:
A549_OE_ctrl.rnaseq.dex.08h.rep3
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 01h - rep1

description:
A549_OE_FOSL2.rnaseq.dex.01h.rep1
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_NC2_S42_L004

description:
CD11b positive cells, glioblastoma cells and T cells from negative control  GL261 tumors
Exp2_NC2
Negative control shRNA GL261 tumors
second_data_set_counts_table.csv

source_name: Negative control shRNA GL261 glioblastoma tumors

value: Negative control


title: Exp2_NC2_S42_L003


title: A549 cells treated with DEX for 04h - rep3

description:
A549_OE_ctrl.rnaseq.dex.04h.rep3
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 cells treated with DEX for 04h


title: A549 cells treated with DEX for 04h - rep2

description:
A549_OE_ctrl.rnaseq.dex.04h.rep2
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with FOSL2 Overexpressed and treated with DEX for 00h - rep2

description:
A549_OE_FOSL2.rnaseq.dex.00h.rep2
processed data file: A549_OE_FOSL2.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_NC2_S42_L002


title: Exp2_NC2_S42_L001


title: A549 cells treated with DEX for 01h - rep3

description:
A549_OE_ctrl.rnaseq.dex.01h.rep3
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 cells treated with DEX for 01h


title: Exp2_shSELP1_S52_L001


title: Exp2_NC2_S4_L003


title: Exp2_NC2_S4_L002


title: Exp2_shSELP1_S52_L002


title: Exp2_NC2_S4_L004


title: A549 cells treated with DEX for 01h - rep2

description:
A549_OE_ctrl.rnaseq.dex.01h.rep2
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 00h - rep1

description:
A549_OE_ctrl.rnaseq.dex.00h.rep1
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 cells treated with DEX for 00h


title: A549 cells treated with DEX for 12h - rep2

description:
A549_OE_ctrl.rnaseq.dex.12h.rep2
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: A549 cells treated with DEX for 12h


title: A549 cells treated with DEX for 12h - rep3

description:
A549_OE_ctrl.rnaseq.dex.12h.rep3
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_NC1_S32_L004

description:
CD11b positive cells, glioblastoma cells and T cells from negative control  GL261 tumors
Exp2_NC1
Negative control shRNA GL261 tumors
second_data_set_counts_table.csv


title: A549 cells treated with DEX for 12h - rep1

description:
A549_OE_ctrl.rnaseq.dex.12h.rep1
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_NC1_S32_L003


title: Exp2_shSELP1_S5_L001

description:
CD11b positive cells, glioblastoma cells and T cells from P-Selectin knockdown  GL261 tumors
Exp2_shSELP1
P-Selectin shRNA  GL261 tumors
second_data_set_counts_table.csv


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 12h - rep2

description:
A549_OE_CEBPD.rnaseq.dex.12h.rep2
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_CEBPD Overexpressed and treated with DEX for 12h

value: CEBPD Overexpressed


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 12h - rep1

description:
A549_OE_CEBPD.rnaseq.dex.12h.rep1
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: A549 cells treated with DEX for 08h - rep1

description:
A549_OE_ctrl.rnaseq.dex.08h.rep1
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_NC1_S32_L002


title: Exp2_NC1_S32_L001


title: A549 cells treated with DEX for 04h - rep1

description:
A549_OE_ctrl.rnaseq.dex.04h.rep1
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 08h - rep3

description:
A549_OE_CEBPD.rnaseq.dex.08h.rep3
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_CEBPD Overexpressed and treated with DEX for 08h


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 08h - rep2

description:
A549_OE_CEBPD.rnaseq.dex.08h.rep2
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 12h - rep3

description:
A549_OE_CEBPD.rnaseq.dex.12h.rep3
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_NC1_S3_L003


title: Exp2_NC2_S4_L001

description:
CD11b positive cells, glioblastoma cells and T cells from negative control  GL261 tumors
Exp2_NC2
Negative control shRNA GL261 tumors
second_data_set_counts_table.csv


title: Exp2_NC1_S3_L002


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 08h - rep1

description:
A549_OE_CEBPD.rnaseq.dex.08h.rep1
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_NC1_S3_L004


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 04h - rep2

description:
A549_OE_CEBPD.rnaseq.dex.04h.rep2
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_CEBPD Overexpressed and treated with DEX for 04h


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 04h - rep1

description:
A549_OE_CEBPD.rnaseq.dex.04h.rep1
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp2_NC1_S3_L001


title: Exp1_shSELP2_S3_L004

description:
CD11b positive cells from negative control GL261 tumors
Exp1_shSELP 2
P-Selectin shRNA  GL261 tumors
first_data_set_counts_table.csv


title: Exp1_shSELP2_S3_L002


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 01h - rep1

description:
A549_OE_CEBPD.rnaseq.dex.01h.rep1
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_CEBPD Overexpressed and treated with DEX for 01h


title: Exp1_shSELP2_S3_L001


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 01h - rep2

description:
A549_OE_CEBPD.rnaseq.dex.01h.rep2
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp1_shSELP2_S3_L003


title: Exp1_shSELP2_S2_L004


title: Exp1_shSELP2_S2_L003


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 00h - rep2

description:
A549_OE_CEBPD.rnaseq.dex.00h.rep2
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_CEBPD Overexpressed and treated with DEX for 00h


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 00h - rep3

description:
A549_OE_CEBPD.rnaseq.dex.00h.rep3
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 00h - rep1

description:
A549_OE_CEBPD.rnaseq.dex.00h.rep1
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp1_shSELP2_S2_L002


title: Exp1_shSELP2_S2_L001

description:
CD11b positive cells from P-Selectin knockdown GL261 tumors
Exp1_shSELP 2
P-Selectin shRNA  GL261 tumors
first_data_set_counts_table.csv


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 12h - rep3

description:
A549_OE_CEBPB.rnaseq.dex.12h.rep3
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_CEBPB Overexpressed and treated with DEX for 12h

value: CEBPB Overexpressed


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 12h - rep2

description:
A549_OE_CEBPB.rnaseq.dex.12h.rep2
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp1_NC1_S7_L004

description:
CD11b positive cells from negative control GL261 tumors
Exp1_NC8
Negative control shRNA GL261 tumors
first_data_set_counts_table.csv


title: Exp1_NC1_S7_L003

description:
CD11b positive cells from negative control GL261 tumors
Exp1_NC1
Negative control shRNA GL261 tumors
first_data_set_counts_table.csv


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 04h - rep3

description:
A549_OE_CEBPD.rnaseq.dex.04h.rep3
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 12h - rep1

description:
A549_OE_CEBPB.rnaseq.dex.12h.rep1
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with CEBPD Overexpressed and treated with DEX for 01h - rep3

description:
A549_OE_CEBPD.rnaseq.dex.01h.rep3
processed data file: A549_OE_CEBPD.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 08h - rep3

description:
A549_OE_CEBPB.rnaseq.dex.08h.rep3
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_CEBPB Overexpressed and treated with DEX for 08h


title: Exp1_NC1_S3_L004


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 08h - rep2

description:
A549_OE_CEBPB.rnaseq.dex.08h.rep2
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp1_NC1_S3_L002


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 04h - rep3

description:
A549_OE_CEBPB.rnaseq.dex.04h.rep3
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_CEBPB Overexpressed and treated with DEX for 04h


title: Exp1_NC1_S3_L001


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 04h - rep2

description:
A549_OE_CEBPB.rnaseq.dex.04h.rep2
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp1_NC1_S3_L003


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 04h - rep1

description:
A549_OE_CEBPB.rnaseq.dex.04h.rep1
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: Exp1_NC1_S7_L001


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 01h - rep3

description:
A549_OE_CEBPB.rnaseq.dex.01h.rep3
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_CEBPB Overexpressed and treated with DEX for 01h


title: L42034: Setdb1fl/fl

city: Dresden

first: Sebastian

last: Zeissig

state: Saxony

address: Fetscherstraße 105

department: Center for Regenerative Therapies (CRTD)

institute: TU Dresden

data_processing:
bcl2fastq2 2.19.1 for demultiplexing
Alignment of the reads to the mouse reference (mm10) was done with GSNAP (v2018-07-04) and the use of standard parameters. Ensembl gene annotation version 92 was used to detect splice sites.
The uniquely aligned reads were counted with featureCounts (v1.6.3) and the same Ensembl annotation.
Genome_build: mm10
Supplementary_files_format_and_content: bfx1355.counts.mm10.e92.xlsx is a tab separated table from the featureCounts output. Each row corresponds to a gene and each column is a sample. The remaining columns are gene information from Ensembl, such as ID, start and end coordinates, length and strand information.

source_name: intestinal epithelial crypt cells

extract_protocol:
Crypts from the distal third of mouse small intestines were isolated by scraping off villi and incubating in 2mM EDTA in PBS for 30 minutes at 4°C. Isolated crypts were resuspended in RTL Buffer (supplemented with b-mercaptoethanol, Qiagen). Total RNA was isolated using RNeasy Mini Kit (Qiagen).
mRNA was isolated from 500 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation custom adaptors were used (Adaptor-Oligo 1: 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 1:0.9. Dual indexing was done during the following PCR enrichment (12 cycles, 65°C) using custom amplification primers carrying the same sequence for i7 and i5 index (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (1:0.9), libraries were quantified using the Fragment Analyzer (Agilent).

treatment_protocol: Mice received intraperitoneal injections of 1mg tamoxifen in sunflower oil for 2 consecutive days.

value: 8 weeks

value: 2x1mg tamoxifen in sunflower oil

tag: timepoint

value: day 2

tag: cell type

value: intestinal epithelial crypt cells


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 01h - rep1

description:
A549_OE_CEBPB.rnaseq.dex.01h.rep1
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

value: adenocarcinomic human alveolar basal epithelial


title: L42032: Villin-CreERT2 Setdb1fl/fl

value: Villin-CreERT2 Setdb1fl/fl


title: L42031: Setdb1fl/fl


title: L42033: Setdb1fl/fl


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 01h - rep2

description:
A549_OE_CEBPB.rnaseq.dex.01h.rep2
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

value: dexamethasone (DEX)


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 00h - rep3

description:
A549_OE_CEBPB.rnaseq.dex.00h.rep3
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

source_name: Modified A549_CEBPB Overexpressed and treated with DEX for 00h


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 00h - rep2

description:
A549_OE_CEBPB.rnaseq.dex.00h.rep2
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: L42030: Villin-CreERT2 Setdb1fl/fl


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 00h - rep1

description:
A549_OE_CEBPB.rnaseq.dex.00h.rep1
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: L42028: Setdb1fl/fl


title: L42029: Villin-CreERT2 Setdb1fl/fl


title: Exp1_NC1_S7_L002


title: L42027: Villin-CreERT2 Setdb1fl/fl


title: Modified A549 cells with CEBPB Overexpressed and treated with DEX for 08h - rep1

description:
A549_OE_CEBPB.rnaseq.dex.08h.rep1
processed data file: A549_OE_CEBPB.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt


title: L42026: Villin-CreERT2 Setdb1fl/fl


title: TC32-shSA1 rep3

city: Indianapolis

first: Xiongbin

last: Lu

state: Indiana

address: 980 W. Walnut Street, R3-C218D	MMGE

institute: Indiana University School of Medicine

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 4000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to Gencode 25 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: GENCODE 25 GRCh38
Supplementary_files_format_and_content: Raw counts

source_name: Ewing sarcoma cell line

extract_protocol:
Total mRNA was isolated using Direct-zol RNA extraction kit (Zymo Research) and 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Both SA2-intact TC71 and SA2-mutated TC32 Ewing sarcoma cells were treated with or without doxycycline-induced SA1 knockdown for 72 h

tag: sa2 mutation

value: Mutated

tag: shRNA

value: SA1 shRNA


title: L42025: Setdb1fl/fl


title: TC32-shSA1 rep2


title: TC32-shSA1 rep1


title: TC32-shNT rep2

value: Control shRNA


title: TC71-shSA1 rep3

value: Wild type


title: TC71-shSA1 rep2


title: D3a-FO-rep1

city: Cambridge

first: Vinay

middle: S

last: Mahajan

state: MA

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

data_processing:
bcl2fastq
rsem
Genome_build: mm10
Supplementary_files_format_and_content: gene level expression estimates were generated using RSEM-1.2.29

source_name: Follicular B (B2) cells

growth_protocol: Cells were FACS sorted into RLT + 1% BME

extract_protocol:
Qiagen RNeasy Micro Plus kit
Kapa RNA HyperPrep with RiboErase

value: CD19-Cre+/- Dnmt3a-fl/fl

value: 4 weeks


title: WT-B1a-rep2

source_name: Peritoneal B1 B cells

value: Wild-type


title: D3a-FO-rep2


title: WT-FO-rep2


title: WT-B1a-rep1


title: A549 cells treated with DEX for 00h - rep3

description:
A549_OE_ctrl.rnaseq.dex.00h.rep3
processed data file: A549_OE_ctrl.rnaseq.dex.featurecounts.genes.TPM.selected_samples.surrogate_variables_reduced.corrected_ln.protein_coding.txt

value: GFP only


title: TC71-shSA1 rep1


title: TC71-shNT rep3


title: D3a-B1a-rep1


title: TC71-shNT rep1


title: TC71-shNT rep2


title: D3a-B1a-rep2


title: WT_B1a_H3K27Ac S51

description:
WT_B1a_H3K27Ac
WT_B1a_H3K27Ac

library_source: genomic

data_processing:
bcl2fastq
Bowtie2 v2.2.5
macs2
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs

molecule: genomic DNA

source_name: B1 cells

extract_protocol:
n/a
CUT&RUN (PMID: 29651053)
CUT&RUN (Nature Protocols 2018. 13 (5): 1006–19)

tag: antibody


title: WT_B1a_H3K27Ac S50

description:
WT_B1a_H3K27Ac
WT_B1a_H3K27Ac


title: WT_B1a_H3K27Ac S49

description:
WT_B1a_H3K27Ac
WT_B1a_H3K27Ac


title: TC32-shNT rep3


title: WT-FO-rep1


title: TC32-shNT rep1


title: WT_proB2_H3K27Ac S71

description:
WT_proB2_H3K27Ac
WT_proB2_H3K27Ac

source_name: proB2 cells


title: WT_proB2_H3K27Ac S72

description:
WT_proB2_H3K27Ac
WT_proB2_H3K27Ac


title: WT_proB2_H3K27Ac S70

description:
WT_proB2_H3K27Ac
WT_proB2_H3K27Ac


title: WT_proB2_H3K27Ac S69

description:
WT_proB2_H3K27Ac
WT_proB2_H3K27Ac


title: WT_proB2_H3K4me3 S68

description:
WT_proB2_H3K4me3
WT_proB2_H3K4me3


title: WT_proB2_H3K4me3 S67

description:
WT_proB2_H3K4me3
WT_proB2_H3K4me3


title: Input of Arabidopsis thaliana Dex:NTT_GFP rep2

city: Orsay

first: Maria Victoria

last: Gomez-Roldan

address: bat 630

country: France

institute: CNRS

data_processing:
Preprocessing of sequenced reads for quality was performed using FASTQC
ChipSeq were aligned onto TAIR10 genome with bwa-mem software
only reads with mapQ > 30 and uniquely mapped were kept using Samtools
reads identified as PCR duplicates were discarded using Picard Toolkit
The MACS2 (version 2.1.2) software was used to identify significantly enriched regions (q-value <10e-10)
Genome_build: TAIR10 (release 43 from Ensembl database)
Supplementary_files_format_and_content: peaks calling results file are in BED (6 col) format file

organism: Arabidopsis thaliana

source_name: seven-days old seedlings

growth_protocol: Arabidopsis (Arabidopsis thaliana) genotypes (accession Columbia-0, Col-0) were grown under a 16-h-light/8-h-dark condition at 22°C in a growth room. For seed germination, sterilized seeds were incubated at 4°C for 2 days and sown on Murashige and Skoog (MS) medium plates containing 1% sucrose and 0.8% agar.

extract_protocol:
Chromatin was sonicated to an average length of 300 bp and immunoprecipitated (overnight at 4 °C) with an anti-GFP antibody (Clontech 632592). The chromatin was then reverse-crosslinked (RNase and proteinase K digestion) and DNA was extracted with phenol-chloroform.
Precipitated DNA (10ng of IP or input DNA) was used for ChIP-seq library construction using a NEBNext® Ultra DNA Library Prep Kit for Illumina®. Single-end sequencing of IP and input samples were performed using GAIIx Illumina® (read length of 50 bp)

treatment_protocol: ChIP assays were performed as described by Jégu et al. (2017). Briefly, seven-days old seedlings of Dex:TT1-GFP and Dex:NTT-GFP lines were transferred to MS liquid medium supplied with 1µM Dex. After 8 h treatment, seedlings were crosslinked with 1% formaldehyde and the reaction was stopped with glycine (2mM)

tag: build

tag: chip antobody


title: WT_proB2_H3K4me3 S66

description:
WT_proB2_H3K4me3
WT_proB2_H3K4me3


title: WT_B1a_H3K27Ac S52

description:
WT_B1a_H3K27Ac
WT_B1a_H3K27Ac


title: ChipSeq of Arabidopsis thaliana Dex:NTT_GFP rep2

description: NTT (TF) peak calling on TAIR10 genome

value: anti-GFP antibody (Clontech 632592)


title: Input of Arabidopsis thaliana Dex:NTT_GFP rep1


title: ChipSeq of Arabidopsis thaliana Dex:NTT_GFP rep1

description: NTT (TF) peak calling on TAIR10 genome


title: WT_B2_H3K27Ac S45

description:
WT_B2_H3K27Ac
WT_B2_H3K27Ac

source_name: B2 cells


title: WT_proB2_H3K4me3 S65

description:
WT_proB2_H3K4me3
WT_proB2_H3K4me3


title: WT_proB2_H3K4me1 S64

description:
WT_proB2_H3K4me1
WT_proB2_H3K4me1


title: WT_B2_H3K27Ac S44

description:
WT_B2_H3K27Ac
WT_B2_H3K27Ac


title: WT_B2_H3K27Ac S43

description:
WT_B2_H3K27Ac
WT_B2_H3K27Ac


title: Input of Arabidopsis thaliana Dex:TT1_GFP


title: ChipSeq of Arabidopsis thaliana Dex:TT1_GFP

description: TT1 (TF) peak calling on TAIR10 genome


title: WUS-GR+CMV + DEX 2 RNA-seq

city: Hefei

first: Zhong

last: Zhao

state: Anhui

address: Huangshan Road 443

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 cDNA using BWA with parameters -e 60 -i 15 -q 10 -t 4
Reads Per Kilobase of transcript per Megabase of library size (RPKM) were calculated.
Genome_build: TAIR10
Supplementary_files_format_and_content: spreadsheet include numbers of mapped reads,RPKM values for each Sample as well as log2 RPKM ratios, p-values and FDR for multipairwise comparisons

source_name: 5-week adult plant

growth_protocol: Seeds pretreated for 2 days at 4°C were grown in soil in the greenhouse for another 4-weeks  (22°C, 16 h light /8 h dark photoperiod).

extract_protocol:
Plant tissues were flash frozen in liquid nitrogen, and Total RNA from apices were isolated using the mirVana™ miRNA Isolation Kit (lifetechnology). 10 μg of totalRNA were subject to DNase I treatment and mRNA was purified by Dynabeads® mRNA DIRECT™ Purification Kit(lifetechnology).
Strand-specific RNA-seq libraries were prepared using the NEB Next Ultra RNA Library Prep Kit for Illumina following the manufacturer’s instructions and were sequenced on the Illumina Hi-Seq2500 platform to obtain 2×100-bp paired end reads.

treatment_protocol: For virus infections, leaves of 3-week-old PUBI10:Mcherry-GR-Linker-WUS plants were mechanically dusted with carborundum and inoculated with CMV RNA (100 ng/μl).Systemically infected apexes from plants were harvested 8 days after infection. The shoot apices were collected and removing older flowers. The shoot apexes with or without CMV infection were treated with CHX (10 μM) alone or CHX+ DEX (15μM) for 2 hours, and then total RNA were isolated from the shoot apexes.

tag: developmental stage

value: 5-week adult plant

value: shoot apexes


title: WT_B2_H3K4me3 S42

description:
WT_B2_H3K4me3
WT_B2_H3K4me3


title: WUS-GR+CMV + DEX 1 RNA-seq


title: WUS-GR+CMV + CHX 2 RNA-seq


title: WT_B2_H3K4me3 S40

description:
WT_B2_H3K4me3
WT_B2_H3K4me3


title: WUS-GR+CMV + CHX 1 RNA-seq


title: WT_proB2_H3K4me1 S63

description:
WT_proB2_H3K4me1
WT_proB2_H3K4me1


title: FP-RMS Rh30 cells grow as xenografts_1

type: RNA

first: Corinne

middle: Mary

last: Linardic

state: NC

address: Box 102382, DUMC

department: Pediatrics

institute: DUKE UNIVERSITY

hyb_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip HG-U133_Plus_2 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: The CEL files of all samples were normalized by RMA Robust Multi-Array algorithm.

label: biotin

source_name: FP-RMS Rh30 cells grow as xenografts

growth_protocol: FP-RMS Rh30 cells grow as adherent. For sphere, Rh30 cells were cultured in Neurobasal media supplemented with 1X B27, 80 ng/ml bFGF, 40 ng/ml EGF, and 50µg/ml insulin. For xenograft, Rh30 cells grown as adherent cultures or as spheres were resuspended in Matrigel (BD Biosciences), implanted subcutaneously into the flanks of immunodeficient SCID/beige mice

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions. The RNA were analyzed with Agilent 2100 Bioanalyzer G2939A

tag: cell line

value: PAX3-FOXO1 fusion protein positive

tag: growth method

value: xenograft


title: WUS-GR-MOCK + DEX2 RNA-seq


title: WT_B2_H3K4me1 S39

description:
WT_B2_H3K4me1
WT_B2_H3K4me1


title: WUS-GR-MOCK + DEX1 RNA-seq


title: WUS-GR-MOCK + CHX 2 RNA-seq


title: FP-RMS Rh30 cells grow as spheres_1

source_name: FP-RMS Rh30 cells grow as spheres

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip HG-U133_Plus_2 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

value: spheres


title: WT_B2_H3K4me1 S38

description:
WT_B2_H3K4me1
WT_B2_H3K4me1


title: FP-RMS Rh30 cells grow as adherent_3

source_name: FP-RMS Rh30 cells grow as adherent

value: adherent


title: FP-RMS Rh30 cells grow as spheres_3


title: FP-RMS Rh30 cells grow as xenografts_3


title: WUS-GR-MOCK + CHX 1 RNA-seq


title: D3a_B2_H3K27Ac S36

description:
D3a_B2_H3K27Ac
D3a_B2_H3K27Ac


title: D3a_B2_H3K27Ac S35

description:
D3a_B2_H3K27Ac
D3a_B2_H3K27Ac


title: FP-RMS Rh30 cells grow as spheres_2


title: FP-RMS Rh30 cells grow as adherent_2


title: FP-RMS Rh30 cells grow as adherent_1


title: FP-RMS Rh30 cells grow as xenografts_2


title: HEK293T-DRIP-Restriction_enzymes_S96

city: Wuhan

first: Kaiwei

last: Liang

state: Hubei

address: # 185 Dong Hu Road

institute: Wuhan University

description: DRIP-seq with S9.6 in HEK293T cells with restriction enzymes digestion

data_processing:
Library strategy: DRIP-seq
DRIP-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the first 50 nucleotides. The resulting reads were normalized with total reads aligned for visualization.
Genome_build: hg38
Genome_build: Escherichia coli K-12 substr. MG1655
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

growth_protocol: HEK293T cells were obtained from ATCC and maintained in Dulbecco’s modified Eagle’s media (DMEM; Life Technologies) supplemented with 10% fetal bovine serum (FBS; LONSERA) and 1X penicillin-streptomycin (Life Technologies) at 5% CO2 in 37 °C. The wild-type Pol II and slow Pol II (R749H) mutant HEK293T cell lines were established with pOG44 (Invitrogen) and pCDNA5-Pol-II plasmids. The stable cell lines were cultured in DMEM supplemented with 10% FBS.

extract_protocol: For DRIP-seq library preparation, the RNA molecules were digested with NEB RNase A for 1 hour at 37 °C and the DNA molecules were recovered with ethanol precipitation. The libraries were prepared with the NEBNext Ultra DNA library prep kit for Illumina, followed by LabChip analysis and next-generation sequencing.

treatment_protocol: After induction with 2.0 μg/mL doxycycline for 16 hours, WT and slow Pol II cells were treated with 2.5 μg/mL α-amanitin (Santa Cruz) for 42 hours to degrade the endogenous Pol II

value: Derived from embryonic kidney

tag: tag

value: WT

tag: library strategy

value: DRIP-seq

tag: digestion

value: Restriction enzymes


title: WT_B2_H3K4me3 S41

description:
WT_B2_H3K4me3
WT_B2_H3K4me3

tag: strain


title: HEK293T-DRIP-Restriction_enzymes_InPUT

description: InPUT for HEK293T DNA with restriction enzymes digestion


title: D3a_B2_H3K27Ac S34

description:
D3a_B2_H3K27Ac
D3a_B2_H3K27Ac


title: WT_B2_H3K4me1 S37

description:
WT_B2_H3K4me1
WT_B2_H3K4me1


title: D3a_B2_H3K4me3 S33

description:
D3a_B2_H3K4me3
D3a_B2_H3K4me3


title: HEK293T-DRIP-Fragmentase_InPUT

description: InPUT for HEK293T DNA with dsDNA fragmentase digestion

value: dsDNA fragmentase


title: HEK293T-DRIP-Fragmentase_S96

description: DRIP-seq with S9.6 in HEK293T cells with dsDNA fragmentase digestion


title: D3a_B2_H3K4me3 S32

description:
D3a_B2_H3K4me3
D3a_B2_H3K4me3


title: D3a_B2_H3K4me3 S31

description:
D3a_B2_H3K4me3
D3a_B2_H3K4me3


title: HEK293T-Slow-POL2-DOX-a-Amanitin (CUT&Tag)

description: R-Loop CUT&Tag analysis with 2HBD and Anti-HisTag in slow Pol II cells after DOX and alpha-amanitin treatment

data_processing:
Library strategy: CUT&Tag
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches. The aligned reads were normalized to total reads aligned (reads per million, r.p.m.). The track files were made with the bamCoverage command from deeptools 3.3.0. For spike-in normalization, the reads were also aligned to the E.coil genome by Bowtie2 with the options (--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred 33 -I 10 -X 700). The Rnase A treated group was normalized to its non-treated counterpart by scale factors.
Genome_build: hg38
Genome_build: Escherichia coli K-12 substr. MG1655
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

extract_protocol: The CUT&Tag tagmentation products were purified with 1X Sera-Mag carboxylate-modified magnetic beads (Sigma-Aldrich, GE24152105050350), and were eluted in 10 μL 0.1% Tween-20. The eluent was mixed with 10 U Bst 2.0 WarmStart DNA polymerase (NEB, M0538) in 1X Q5 polymerase reaction buffer, and was incubated at 65 °C for 30 minutes to complete the strand displacement reaction. The reaction was then stopped by incubation at 80 °C for 20 minutes. To perform the library preparation, the mixture was mixed with a universal i5 primer and a uniquely barcoded i7 primer, and was amplified with Q5 high-fidelity master mix (NEB, M0492). The libraries were size-selected with 0.56-0.85´ Sera-Mag carboxylate-modified magnetic beads, and were subjected to LabChip DNA analysis and Illumina sequencing. The  RNA was purified with the Sera-Mag carboxylate-modified magnetic beads and was subjected to strand-specific RNA-seq library preparation. Libraries were made with the NEBNext ultra RNA library prep kit for Illumina and subjected to next-generation sequencing.

value: Slow Pol II (R749H)

value: Anti-HisTag

value: CUT&Tag


title: D3a_B2_H3K4me1 S30

description:
D3a_B2_H3K4me1
D3a_B2_H3K4me1

value: CD19-Cre+/- Dnmt3a-fl/fl


title: D3a_B2_H3K4me1 S29

description:
D3a_B2_H3K4me1
D3a_B2_H3K4me1


title: HEK293T-WT-POL2-DOX-a-Amanitin (CUT&Tag)

description: R-Loop CUT&Tag analysis with 2HBD and Anti-HisTag in WT Pol II cells after DOX and alpha-amanitin treatment


title: HEK293T-Rloop-S96-HISTAG-RNaseH (CUT&Tag)

description: R-Loop CUT&Tag analysis with the S9.6 antibody and RNase H

value: Rnase H


title: HEK293T-DRIPc-Fragmentation-2HBD

description: DRIPc-seq with 2HBD in HEK293T cells with dsDNA fragmentase digestion

data_processing:
Library strategy: DRIPc-seq
DRIPc-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the first 50 nucleotides. The resulting reads were normalized with total reads aligned for visualization. The heatmap were generated with the indicated regions with the computeMatrix and plotHeatmap commands from deeptools 3.3.0. The read numbers at indicated regions were counted by the multicov command from bedtools v2.25.0 or HTseq-count.
Genome_build: hg38
Genome_build: Escherichia coli K-12 substr. MG1655
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

extract_protocol:
RNA was extacted by Trizol
For DRIPc-seq library preparation, the DNA molecules were digested with NEB DNase I for 1 hour at 37 °C and the RNA molecules were recovered with ethanol precipitation. The libraries were prepared with the NEBNext ultra directional RNA library prep kit and subjected to LabChip analysis and next-generation sequencing.

value: DRIPc-seq


title: WT_proB2_H3K4me1 S62

description:
WT_proB2_H3K4me1
WT_proB2_H3K4me1

value: Wild-type


title: HEK293T-Rloop-S96-HISTAG-NoRNaseH (CUT&Tag)

description: R-Loop CUT&Tag analysis with the S9.6 antibody


title: HEK293T-Rloop-2XHBD-HISTAG-RNaseH (CUT&Tag)

description: R-Loop CUT&Tag analysis with 2HBD, Anti-GST and RNase H


title: D3a_B2_H3K4me1 S28

description:
D3a_B2_H3K4me1
D3a_B2_H3K4me1


title: D3a_B1_H3K27Ac S27

description:
D3a_B1_H3K27Ac
D3a_B1_H3K27Ac


title: HEK293T-Rloop-2XHBD-HISTAG-NoRNaseH (CUT&Tag)

description: R-Loop CUT&Tag analysis with 2HBD and Anti-HisTag


title: D3a_B1_H3K27Ac S25

description:
D3a_B1_H3K27Ac
D3a_B1_H3K27Ac


title: D3a_B1_H3K4me3 S24

description:
D3a_B1_H3K4me3
D3a_B1_H3K4me3


title: D3a_B1_H3K4me3 S22

description:
D3a_B1_H3K4me3
D3a_B1_H3K4me3


title: HEK293T-H3K27ac (ChIP-seq)

description: ChIP-seq with H3K27ac antibody in HEK293T cells

data_processing:
ChIP-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the first 50 nucleotides. The resulting reads were normalized with total reads aligned for visualization. The heatmaps were generated with the indicated regions with the computeMatrix and plotHeatmap commands from deeptools 3.3.0
Genome_build: hg38
Genome_build: Escherichia coli K-12 substr. MG1655
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

extract_protocol: For ChIP-seq library preparation, the DNA was amplified with the NEBNext Ultra DNA library prep kit for Illumina, followed by LabChip analysis and next-generation sequencing.

value: ChIP-seq


title: D3a_B1_H3K27Ac S26

description:
D3a_B1_H3K27Ac
D3a_B1_H3K27Ac


title: D3a_B1_H3K4me3 S23

description:
D3a_B1_H3K4me3
D3a_B1_H3K4me3


title: D3a_B1_H3K4me1 S21

description:
D3a_B1_H3K4me1
D3a_B1_H3K4me1


title: HEK293T-DRIPc-Fragmentation-S96

description: DRIPc-seq with S9.6 in HEK293T cells with dsDNA fragmentase digestion


title: D3a_B1_H3K4me1 S20

description:
D3a_B1_H3K4me1
D3a_B1_H3K4me1


title: R-Loop-CUT-Tag-HEK293T-2HBD-Anti-HisTag-Rep2

data_processing:
Library strategy: CUT&Tag
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches. The aligned reads were normalized to total reads aligned (reads per million, r.p.m.). The track files were made with the bamCoverage command from deeptools 3.3.0. For spike-in normalization, the reads were also aligned to the E.coil genome by Bowtie2 with the options (--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred 33 -I 10 -X 700). The Rnase A treated group was normalized to its non-treated counterpart by scale factors.
TT-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the 50 bp read. The resulting reads were normalized to total reads aligned (reads per million, r.p.m) for each strand with deeptools 3.3.0
PRO-seq reads were mapped to the human genome (UCSC hg38) using Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches (35). Aligned reads were then converted to strand-specific bigwig files with the bamCoverage command from deeptools 3.3.0. PRO-seq genome browser track examples show coverage of the entire length of the read for visualization. The read counts at indicated regions were calculated by bedtools multicov (version 2.25.0). The heatmap were generated with the indicated regions with ngs.plot or the computeMatrix command from deeptools 3.3.0.
DRIPc-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the first 50 nucleotides. The resulting reads were normalized with total reads aligned for visualization. The heatmap were generated with the indicated regions with the computeMatrix and plotHeatmap commands from deeptools 3.3.0. The read numbers at indicated regions were counted by the multicov command from bedtools v2.25.0 or HTseq-count.
Chromatin-associated RNA reads were aligned to the human genome (UCSC hg18) using Bowtie 1.1.2. For track files, reads were normalized by r.p.m). Reads at all of the protein-coding genes were counted by HTseq-count with the union model.
Genome_build: hg38
Genome_build: Escherichia coli K-12 substr. MG1655
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

growth_protocol: HEK293T cells were obtained from ATCC and maintained in Dulbecco’s modified Eagle’s media (DMEM; Life Technologies) supplemented with 10% fetal bovine serum (FBS; LONSERA) and 1X penicillin-streptomycin (Life Technologies) at 5% CO2 in 37 °C.

extract_protocol:
Total RNA was extracted using Trizol.
The CUT&Tag tagmentation products were purified with 1X Sera-Mag carboxylate-modified magnetic beads (Sigma-Aldrich, GE24152105050350), and were eluted in 10 μL 0.1% Tween-20. The eluent was mixed with 10 U Bst 2.0 WarmStart DNA polymerase (NEB, M0538) in 1X Q5 polymerase reaction buffer, and was incubated at 65 °C for 30 minutes to complete the strand displacement reaction. The reaction was then stopped by incubation at 80 °C for 20 minutes. To perform the library preparation, the mixture was mixed with a universal i5 primer and a uniquely barcoded i7 primer, and was amplified with Q5 high-fidelity master mix (NEB, M0492). The libraries were size-selected with 0.56-0.85´ Sera-Mag carboxylate-modified magnetic beads, and were subjected to LabChip DNA analysis and Illumina sequencing. The  RNA was purified with the Sera-Mag carboxylate-modified magnetic beads and was subjected to strand-specific RNA-seq library preparation. Libraries were made with the NEBNext ultra RNA library prep kit for Illumina and subjected to next-generation sequencing.

treatment_protocol: 4SU labeling was performed for TT-seq

tag: cell line origin


title: R-Loop-CUT-Tag-HEK293T-2HBD-Anti-GST-RNaseA-Rep2

description: R-Loop CUT&Tag analysis with 2HBD, Anti-GST and RNase A

value: Anti-GST


title: R-Loop-CUT-Tag-HEK293T-2HBD-Anti-HisTag-RNaseA-Rep2


title: R-Loop-CUT-Tag-HEK293T-2HBD-Anti-GST-Rep2

description: R-Loop CUT&Tag analysis with 2HBD and Anti-GST


title: R-Loop-CUT-Tag-HEK293T-S96-Rep2


title: WT_proB2_H3K4me1 S61

description:
WT_proB2_H3K4me1
WT_proB2_H3K4me1


title: WT_B1_H3K4me3 S18

description:
WT_B1_H3K4me3
WT_B1_H3K4me3


title: WT_B1_H3K4me3 S16

description:
WT_B1_H3K4me3
WT_B1_H3K4me3


title: HEK293T-R-Loop-S96-BUFFER5-Tagmentation

description: R-Loop CUT&Tag analysis with S9.6 antibody and tagmentation buffer 5


title: HEK293T-R-Loop-S96-BUFFER6-Tagmentation

description: R-Loop CUT&Tag analysis with S9.6 antibody and tagmentation buffer 6


title: WT_B1_H3K4me3 S17

description:
WT_B1_H3K4me3
WT_B1_H3K4me3


title: WT_B1_H3K4me3 S15

description:
WT_B1_H3K4me3
WT_B1_H3K4me3


title: R-Loop-CUT-Tag-HEK293T-S96-RNaseA-Rep2

description: R-Loop CUT&Tag analysis with the S9.6 antibody and RNase A


title: WT_B1_H3K4me3 S14

description:
WT_B1_H3K4me3
WT_B1_H3K4me3


title: HEK293T-R-Loop-S96-BUFFER4-Tagmentation

description: R-Loop CUT&Tag analysis with S9.6 antibody and tagmentation buffer 4


title: HEK293T-R-Loop-S96-BUFFER2-Tagmentation

description: R-Loop CUT&Tag analysis with S9.6 antibody and tagmentation buffer 2


title: HEK293T-R-Loop-S96-BUFFER8-Tagmentation

description: R-Loop CUT&Tag analysis with S9.6 antibody and tagmentation buffer 8


title: WT_B1_H3K4me3 S13

description:
WT_B1_H3K4me3
WT_B1_H3K4me3


title: WT_B1_H3K4me1 S12

description:
WT_B1_H3K4me1
WT_B1_H3K4me1


title: HEK293T-R-Loop-S96-BUFFER1-Tagmentation

description: R-Loop CUT&Tag analysis with S9.6 antibody and tagmentation buffer 1


title: R-Loop-CUT-Tag-HEK293T-S96-RNaseA


title: WT_B1_H3K4me1 S11

description:
WT_B1_H3K4me1
WT_B1_H3K4me1


title: WT_B1_H3K4me1 S10

description:
WT_B1_H3K4me1
WT_B1_H3K4me1


title: D3a_B1_H3K4me1 S19

description:
D3a_B1_H3K4me1
D3a_B1_H3K4me1


title: R-Loop-CUT-Tag-HEK293T-S96


title: HEK293T-R-Loop-S96-BUFFER3-Tagmentation

description: R-Loop CUT&Tag analysis with S9.6 antibody and tagmentation buffer 3


title: DEK_cKO_H3K4me3

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

data_processing:
library strategy: CUT&Tag, similar to ChIP-Seq
Illumina Casava1.7 software used for basecalling.
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 with -×2000
Reads that aligned to the mitochondrial genome were filtered and PCR duplicates were removed with picard MarkDuplicates.
The bam file generated by the unique mapped reads as an input file, using MACS2 software for callpeak with cutoff qvalue < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files

source_name: cKO-Bone marrow-LSK cells

growth_protocol: We used  Dekfl/fl (floxp) and Dekfl/fl,Tie2-Cre (cKO) mice at 12 weeks of age (homeostatic condition).

extract_protocol:
Cells were harvested and washed twice in 1 mL wash buffer (20 mM HEPES PH 7.5, 150 mM Nacl, 0.5 mM Spermidine, 1x PIC (Bimake)), and then resuspended in 300 μL wash buffer. Concanavalin A coated beads were activated by washing twice in binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM MnCl2, 1 mM CaCl2). 10 μL activated beads were then added to the cell suspension. After 30 min’s incubation at room temperature, the supernatant was removed and the beads were resuspended in 50 μL antibody buffer (20 mM HEPES pH 7.5,150 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 2 mM EDTA, 0.1% BSA, 1x PIC). Then 0.5 μL antibody (H3K27ac, H3K9ac, H3K4me3, or DEK) was added and incubated for 2 hours at room temperature. After the supernatant was gently removed on DynaMag (Thermo), the beads were resuspended in 100 μL Dig wash buffer (20 mM HEPES pH 7.5,150 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 1x PIC) containing 1 μL Guinea Pig anti-Rabbit IgG antibody. After incubation for 1 hr at room temperature, the beads were then washed three times in 800 μL Dig wash buffer, followed by resuspended in 100 μL Dig 300 wash buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.0125% Digitonin, 1x PIC). Then 0.04 μM pA-Tn5 adapter complex (Vazyme S603) was added and incubated for 1 h at room temperature. Beas were washed three times in 800 μL Dig 300 wash buffer and resuspended in 300 μL tagmentation buffer (20 mM HEPES pH 7.5, 300 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 10 mM MgCl2, 1x PIC) and incubated for 1 hr at 37°C. And then 10 µL of 0.5 M EDTA, 3 µL of 10% SDS and 1 µL of 20 mg/mL Proteinase K were added and incubated at 55°C for 1 hr to stop tagmentation.The DNA was extracted by PCI and amplified with i5 and i7 primers (Vazyme, TD202) by 16-18 cycles’ PCR.
DNA libraries were prepared for sequencing using standard Illumina protocols. The amplified products were purified by Ampure XP beads to remove >1 kb fragment and to enrich the 200-1000 bp fragments for high-throughput sequencing.

treatment_protocol: About 50,000 LSK cells or 20,000 HSC were isolated by FACS

tag: age

value: 3 months

value: Dekfl/fl,Tie2-Cre (cKO)

value: cKO-Bone marrow-LSK cells

tag: experiment type

value: H3K4me3 CUT&Tag


title: Dek_cKO_H3K9ac

source_name: cKO-Bone marrow-HSC

tag: genotype

value: cKO-Bone marrow-HSC

value: H3K9ac CUT&Tag


title: WT_proB1_H3K27Ac S9

description:
WT_proB1_H3K27Ac
WT_proB1_H3K27Ac

source_name: proB1 cells


title: HEK293T-R-Loop-S96-BUFFER7-Tagmentation

description: R-Loop CUT&Tag analysis with S9.6 antibody and tagmentation buffer 7

value: Derived from embryonic kidney

value: WT


title: Dek_fl_H3K9ac

source_name: fl-Bone marrow-HSC

value: Dekfl/fl  (fl)

tag: cell type

value: fl-Bone marrow-HSC


title: R-Loop-CUT-Tag-HEK293T-2HBD-noABS-RNaseA

description: R-Loop CUT&Tag analysis with 2HBD and RNase A

value: no


title: DEK_fl_H3K4me3

source_name: fl-Bone marrow-LSK cells

value: fl-Bone marrow-LSK cells


title: WT_proB1_H3K27Ac S8

description:
WT_proB1_H3K27Ac
WT_proB1_H3K27Ac


title: R-Loop-CUT-Tag-HEK293T-2HBD-noABS

description: R-Loop CUT&Tag analysis with 2HBD


title: Dek_cKO_H3K27ac

value: H3K27ac CUT&Tag


title: WT_proB1_H3K27Ac S7

description:
WT_proB1_H3K27Ac
WT_proB1_H3K27Ac


title: DEK2

value: DEK CUT&Tag


title: R-Loop-CUT-Tag-HEK293T-2HBD-Anti-HisTag-RNaseA

value: Anti-HisTag


title: Dek_fl_H3K27ac


title: DEK3


title: WT_proB1_H3K4me3 S6

description:
WT_proB1_H3K4me3
WT_proB1_H3K4me3

value: Wild-type


title: R-Loop-CUT-Tag-HEK293T-2HBD-Anti-GST-RNaseA

value: Anti-GST


title: WT_proB1_H3K4me3 S4

description:
WT_proB1_H3K4me3
WT_proB1_H3K4me3


title: Dek_cKO2 [ATAC-seq]

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 with -×2000
Reads that aligned to the mitochondrial genome were filtered and PCR duplicates were removed with picard MarkDuplicates.
The bam file generated by the unique mapped reads as an input file, using MACS2 software for callpeak with cutoff qvalue < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files

extract_protocol:
About 20,000 HSC (Lin-Sca-1+c-Kit+CD48-CD150+) in bone marrow were isolated by FACS and resuspended in 35 mL lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and incubated on ice for 10 min with 3 times vortex.
DNA libraries were prepared for sequencing using standard Illumina protocols. DNA fragmentation was conducted by adding 10 mL 5×TTBL, 5 mL×TTE Mix and shaking at 37℃ for 30 min. Fragmented DNA was purified using 1.8×AMPure beads, barcoded with dual indexes and PCR amplified.Size selection and purification of DNA fragments were done using AMPure beads. Size distribution and molarity of these sequencing library were determined by Agilent 2100 bioanalyzer and Qubit (Thermo Fisher Scientific). Sequencing was performed using Hiseq-PE150 (Illumina) by Novogene.

treatment_protocol: We used  Dekfl/fl (floxp) and Dekfl/fl,Tie2-Cre (cKO) mice at 12 weeks of age (homeostatic condition).

value: 3 months

value: Bone marrow-Hematopoietic stem cells (HSC)


title: Dek_cKO1  [ATAC-seq]

value: Dekfl/fl,Tie2-Cre (cKO)


title: R-Loop-CUT-Tag-HEK293T-2HBD-Anti-HisTag


title: Dek_cKO3 [ATAC-seq]


title: Dek_fl3 [ATAC-seq]


title: R-Loop-CUT-Tag-HEK293T-2HBD-Anti-GST


title: Dek_fl2 [ATAC-seq]


title: Dek_fl1 [ATAC-seq]


title: WT_proB1_H3K4me1 S3

description:
WT_proB1_H3K4me1
WT_proB1_H3K4me1


title: WT_proB1_H3K4me1 S2

description:
WT_proB1_H3K4me1
WT_proB1_H3K4me1


title: HEK293T-2HBD-DRIPc-seq

description: DRIPc-seq with GST-His6-2XHBD in HEK293T cells

data_processing:
Library strategy: DRIPc-seq
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches. The aligned reads were normalized to total reads aligned (reads per million, r.p.m.). The track files were made with the bamCoverage command from deeptools 3.3.0. For spike-in normalization, the reads were also aligned to the E.coil genome by Bowtie2 with the options (--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred 33 -I 10 -X 700). The Rnase A treated group was normalized to its non-treated counterpart by scale factors.
TT-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the 50 bp read. The resulting reads were normalized to total reads aligned (reads per million, r.p.m) for each strand with deeptools 3.3.0
PRO-seq reads were mapped to the human genome (UCSC hg38) using Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches (35). Aligned reads were then converted to strand-specific bigwig files with the bamCoverage command from deeptools 3.3.0. PRO-seq genome browser track examples show coverage of the entire length of the read for visualization. The read counts at indicated regions were calculated by bedtools multicov (version 2.25.0). The heatmap were generated with the indicated regions with ngs.plot or the computeMatrix command from deeptools 3.3.0.
DRIPc-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the first 50 nucleotides. The resulting reads were normalized with total reads aligned for visualization. The heatmap were generated with the indicated regions with the computeMatrix and plotHeatmap commands from deeptools 3.3.0. The read numbers at indicated regions were counted by the multicov command from bedtools v2.25.0 or HTseq-count.
Chromatin-associated RNA reads were aligned to the human genome (UCSC hg18) using Bowtie 1.1.2. For track files, reads were normalized by r.p.m). Reads at all of the protein-coding genes were counted by HTseq-count with the union model.
Genome_build: hg38
Genome_build: Escherichia coli K-12 substr. MG1655
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples


title: Dek_cKO2 [RNA-seq]

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: polyA RNA

extract_protocol:
About 800 HSC (Lin-Sca-1+c-Kit+CD48-CD150+) were isolated by FACS and the mRNA library constructed using Smart-Seq V4 Ultra Low Input RNA Kit for sequencing (Takara) according to the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue source

value: Bone marrow

value: Hematopoietic stem cells (HSC)

tag: cell states

value: Quiescent

tag: intervention

value: Dek-knockout


title: IgG_CUT_Tag_HEK293T

description: CUT&Tag analysis with rabbit IgG

value: Derived from embryonic kidney

value: WT

tag: antibody

value: IgG


title: Dek_cKO1  [RNA-seq]


title: WT_proB1_H3K4me1 S1

description:
WT_proB1_H3K4me1
WT_proB1_H3K4me1


title: Dek_fl3 [RNA-seq]

value: Control


title: Dek_fl4 [RNA-seq]


title: DEK1

value: Dekfl/fl  (fl)

value: fl-Bone marrow-HSC


title: HEK293T_chromatin_RNA_rep2

description: Chromatin-associated RNA-seq with HEK293T

data_processing:
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches. The aligned reads were normalized to total reads aligned (reads per million, r.p.m.). The track files were made with the bamCoverage command from deeptools 3.3.0. For spike-in normalization, the reads were also aligned to the E.coil genome by Bowtie2 with the options (--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred 33 -I 10 -X 700). The Rnase A treated group was normalized to its non-treated counterpart by scale factors.
TT-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the 50 bp read. The resulting reads were normalized to total reads aligned (reads per million, r.p.m) for each strand with deeptools 3.3.0
PRO-seq reads were mapped to the human genome (UCSC hg38) using Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches (35). Aligned reads were then converted to strand-specific bigwig files with the bamCoverage command from deeptools 3.3.0. PRO-seq genome browser track examples show coverage of the entire length of the read for visualization. The read counts at indicated regions were calculated by bedtools multicov (version 2.25.0). The heatmap were generated with the indicated regions with ngs.plot or the computeMatrix command from deeptools 3.3.0.
DRIPc-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the first 50 nucleotides. The resulting reads were normalized with total reads aligned for visualization. The heatmap were generated with the indicated regions with the computeMatrix and plotHeatmap commands from deeptools 3.3.0. The read numbers at indicated regions were counted by the multicov command from bedtools v2.25.0 or HTseq-count.
Chromatin-associated RNA reads were aligned to the human genome (UCSC hg18) using Bowtie 1.1.2. For track files, reads were normalized by r.p.m). Reads at all of the protein-coding genes were counted by HTseq-count with the union model.
Genome_build: hg38
Genome_build: Escherichia coli K-12 substr. MG1655
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples


title: Dek_fl2 [RNA-seq]


title: WT_B2 TAB-Seq

description: TABSEQ

data_processing:
bcl2fastq
cutadapt
bismark
methpipe
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs with estimated CpG modification levels

growth_protocol: Cells were FACS sorted and frozen in DNA/RNA shield prior to DNA extraction

extract_protocol:
Qiagen minElute DNA purification kit
WGBS libraries were prepared using the Pico Methyl-Seq™ Library Prep Kit (Zymo Research). For TAB-Seq, 5hmC's in genomic DNA were protected using the Wisegene (catalog #K001) kit and the DNA was subsequently processed using the Pico Methyl-Seq™ Library Prep Kit (Zymo Research) following manufacturer's instructions.
WGBS or TABSEQ

tag: cells


title: Dek_fl1 [RNA-seq]


title: WT_proB1_H3K4me3 S5

description:
WT_proB1_H3K4me3
WT_proB1_H3K4me3


title: MKRN3_2

city: Shanghai

first: Menghuan

last: Zhang

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp software.
The sequencing reads was aligned to mus musculus genomic reference (GRCm38) using HISAT2.
Read counts were summarized at the gene level in each sample with HTSeq.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: GT1-7 cells

growth_protocol: GT1-7 cells were cultured in DMEM/F12 (1:1) supplemented with 10% fetal bovine serum (FBS), 50units/ml penicillin and 50μg/ml streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were tranfected with empty vectors or MKRN3 expressing vectors using lipo2000. Six hours after transfection, Medium was change to complete medium and continue to culture for 48 hours before harvast for RNA-seq.

tag: stain

tag: tissue

value: Hypothalamic neuronal cell line

value: MKRN3 overexpressed GT1-7


title: MKRN3_3


title: HEK293T_chromatin_RNA_rep1

tag: cell line


title: MKRN3_1


title: HEK293T-TTseq-rep2

description: TT-seq with HEK293T cells

data_processing:
Library strategy: TT-seq
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches. The aligned reads were normalized to total reads aligned (reads per million, r.p.m.). The track files were made with the bamCoverage command from deeptools 3.3.0. For spike-in normalization, the reads were also aligned to the E.coil genome by Bowtie2 with the options (--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred 33 -I 10 -X 700). The Rnase A treated group was normalized to its non-treated counterpart by scale factors.
TT-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the 50 bp read. The resulting reads were normalized to total reads aligned (reads per million, r.p.m) for each strand with deeptools 3.3.0
PRO-seq reads were mapped to the human genome (UCSC hg38) using Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches (35). Aligned reads were then converted to strand-specific bigwig files with the bamCoverage command from deeptools 3.3.0. PRO-seq genome browser track examples show coverage of the entire length of the read for visualization. The read counts at indicated regions were calculated by bedtools multicov (version 2.25.0). The heatmap were generated with the indicated regions with ngs.plot or the computeMatrix command from deeptools 3.3.0.
DRIPc-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the first 50 nucleotides. The resulting reads were normalized with total reads aligned for visualization. The heatmap were generated with the indicated regions with the computeMatrix and plotHeatmap commands from deeptools 3.3.0. The read numbers at indicated regions were counted by the multicov command from bedtools v2.25.0 or HTseq-count.
Chromatin-associated RNA reads were aligned to the human genome (UCSC hg18) using Bowtie 1.1.2. For track files, reads were normalized by r.p.m). Reads at all of the protein-coding genes were counted by HTseq-count with the union model.
Genome_build: hg38
Genome_build: Escherichia coli K-12 substr. MG1655
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples


title: HEK293T-TTseq-rep1

description: TT-seq with HEK293T cells


title: Dek_cKO3 [RNA-seq]


title: WT_proB1

description: WGBS

value: Wild-type


title: control_1

value: wild-type


title: WT_proB2

description: WGBS


title: HEK293T-Proseq-rep2

description: PRO-seq with HEK293T cells

data_processing:
Library strategy: Pro-seq
CUT&Tag reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches. The aligned reads were normalized to total reads aligned (reads per million, r.p.m.). The track files were made with the bamCoverage command from deeptools 3.3.0. For spike-in normalization, the reads were also aligned to the E.coil genome by Bowtie2 with the options (--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred 33 -I 10 -X 700). The Rnase A treated group was normalized to its non-treated counterpart by scale factors.
TT-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the 50 bp read. The resulting reads were normalized to total reads aligned (reads per million, r.p.m) for each strand with deeptools 3.3.0
PRO-seq reads were mapped to the human genome (UCSC hg38) using Bowtie version 1.1.2, allowing only uniquely mapping reads with up to three mismatches (35). Aligned reads were then converted to strand-specific bigwig files with the bamCoverage command from deeptools 3.3.0. PRO-seq genome browser track examples show coverage of the entire length of the read for visualization. The read counts at indicated regions were calculated by bedtools multicov (version 2.25.0). The heatmap were generated with the indicated regions with ngs.plot or the computeMatrix command from deeptools 3.3.0.
DRIPc-seq reads were aligned to the human genome (UCSC hg38) with Bowtie 1.1.2, allowing only uniquely mapping reads with up to three mismatches within the first 50 nucleotides. The resulting reads were normalized with total reads aligned for visualization. The heatmap were generated with the indicated regions with the computeMatrix and plotHeatmap commands from deeptools 3.3.0. The read numbers at indicated regions were counted by the multicov command from bedtools v2.25.0 or HTseq-count.
Chromatin-associated RNA reads were aligned to the human genome (UCSC hg18) using Bowtie 1.1.2. For track files, reads were normalized by r.p.m). Reads at all of the protein-coding genes were counted by HTseq-count with the union model.
Genome_build: hg38
Genome_build: Escherichia coli K-12 substr. MG1655
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples


title: control_2


title: control_3


title: 1-b

description: synaptic RNAs, total and small

data_processing:
Illumina’s bcl2fastq (v2.20.2) was used for adapter trimming and converting the base calls
Trimming of 3’ adapters for smallRNASeq data was done using cutadapt (v1.11.0)
totalRNASeq reads were aligned using the STAR aligner (v2.5.2b)
smallRNASeq reads were aligned using the mapper.pl script from mirdeep2 (v2.0.1.2) which uses bowtie (v1.1.2)
TotalRNASeq read counts were generated using featureCounts (v1.5.1)
smallRNA read counts were generated with the quantifier.pl script from mirdeep2 (v2.0.1.2)
All read counts were normalized according to library size to transcript per million (TPM)
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing raw and normalized read counts

source_name: Hippocampus primary culture from E17 mouse

extract_protocol:
Synaptosome RNA was extracted via Trizol, synaptic RNA from microfluidic chambers was isolated with the GenElute™ Single Cell RNA Purification Kit after cutting the synaptic compartment out of the chamber
Synaptosome small RNA libraries were done via NEBNext Small RNA Library Prep Kit, synaptosome toal RNA libraries via Illumina Truseq total RNA kit. Microfluidic total RNA libraries were prepared with Takara´s SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian, microfluidic chamber small RNA with Takara´s  SMARTer smRNA-Seq Kit for Illumina

value: DIV14 from E17

tag: stimulation


title: 11-b

description: synaptic RNAs, total and small


title: 42

description: synaptic RNAs, total and small


title: HEK293T-Proseq-rep1

description: PRO-seq with HEK293T cells


title: D3a_B2

description: WGBS

value: CD19-Cre+/- Dnmt3a-fl/fl


title: 4

description: synaptic RNAs, total and small


title: WT_B2

description: WGBS


title: 7

description: synaptic RNAs, total and small


title: Syn14young3cntr

description: synaptic RNAs, total and small

source_name: Hippocampus, tissue from adult mice brain

value: 3 month


title: 5

description: synaptic RNAs, total and small


title: D3a_B1

description: WGBS


title: HiPSC [methyl-seq]

city: Seoul

first: Kinarm

last: Ko

address: 120, Neungdong-ro, Gwangjin-gu

country: South Korea

institute: Konkuk University

data_processing:
bismark_v0.16.3
bowtie2-2.1.0
samtools-1.3
Genome_build: hg19

source_name: Induced pluripotent stem cells

growth_protocol: Pluripotent stem cells were cultured on matrigel coated plated using mTeSR

extract_protocol:
DNA extraction was performed using standard protocols
SureSelectXT   Methyl-Seq Target   Enrichment System for   Illumina Multiplexed   Sequencing
Agilent SureSelect XT Methyl-Seq

value: Human induced pluripotent stem cells


title: Syn2young1cntr

description: synaptic RNAs, total and small


title: WT_B1 TAB-Seq

description: TABSEQ

source_name: B1 cells


title: WT_B1

description: WGBS


title: Syn8young2cntr

description: synaptic RNAs, total and small


title: PgHiPSC [methyl-seq]

value: Parthenogenetic induced pluripotent stem cells


title: WtFib [methyl-seq]

source_name: Fibroblasts

value: Skin Fibroblast


title: Syn14y3cntr

description: synaptic RNAs, total and small


title: Stom3.S.Pylorus.24hr.neg

city: Utrecht

first: Joep

last: de Ligt

address: Universiteitsweg 100

department: Genetics

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Illumina software used for basecalling.
Sequenced reads mappend and analysed as specified here;https://github.com/UMCUGenetics/RNASeq/releases/tag/2.1.0
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file with metadata
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Stomach

growth_protocol: Organoids from human the small intestine, colon, liver ducts, pancreas and stomach were grown is expansion medium as described in earlier publications (23, 48–50). Small intestine, colon, liver and pancreas organoids were grown in Matrigel (BD

extract_protocol:
Total RNA was extracted using the RNAeasy mini kit (Qiagen) according to manufecter's protocol including DNAse treatment.
Library preparation was started with 500ng of Total RNA using the Truseq Stranded Total RNA kit with Ribo-Zero Human/Mouse/Rat set A and B by Illumina (Cat. RS-122-2201 and RS-122-2202
Libraries were equimolar pooled to 2 nM. And sequenced on the Illumina Nextseq, 1x75bp high output, and 1.0-1.4 pM of library pools was loaded.

treatment_protocol: On day 3 post splitting xpansion medium was replaced by Wnt inhibitory medium, lacking Wnt and/or R-spondin (see Table 7) and addition of DKK1 (200 ng/μl - Peprotech) and IWP2 (3 μM - Tocris).

tag: line

value: Pylorus

value: Stomach

tag: timepoint (hr)

tag: wnt yes or no

value: no


title: Stom2.S.Corpus.24hr.neg

value: Corpus


title: PgFib [methyl-seq]

value: Parthenogenetic fibroblast


title: Syn2y1cntr

description: synaptic RNAs, total and small

tag: strain


title: Stom1.S.Cardia.24hr.neg

value: Cardia


title: Syn8y2cntr

description: synaptic RNAs, total and small

tag: age


title: Stom3.S.Pylorus.6hr.neg


title: AgHiPSC [methyl-seq]

value: Androgenetic induced pluripotent stem cells


title: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description: Torrin replicate 3

data_processing:
Raw fastq files were aligned to Ensembl reference zv11 using STAR
Aligned reads were cleaned using samtools
Normalized read counts were obtained using HTSeq and edgeR
Genome_build: Danio Rerio Ensembl zv11
Supplementary_files_format_and_content: Counts per million normalized reads are available as a tab-delimited file (Normalized_expression.txt), and include YapS87A and WT samples from GSE71681

organism: Danio rerio

source_name: 36hpf zebrafish eyes

extract_protocol:
Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol.
polyA RNA; RNA libraries were prepared using standard Illumina protocols.
Illumina HiSeq 2000; 50bp Single-end reads

tag: treatment

value: Torrin

value: eyes


title: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1

description: Torrin replicate 1


title: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2

description: Torrin replicate 2


title: Stom2.S.Corpus.6hr.neg


title: HiPSC

data_processing:
Illumina Casava1.8.2 software used for basecalling
Check the rRNA ratio using Fastq screen v0.11.1
Using bowtie to align RNA-seq data to reference genome(human hg19) and get histogram for insert size
Using Tophat v2.0.13 to mapping the read to reference(hg19) and generate bam files
Fragments Per Kilobase of transcript per Million(FPKM) was calculated from mapped reads using cufflinks v2.2.0.
Genome_build: hg19
Supplementary_files_format_and_content: "expression.csv.gz" contains FPKM values for genes

growth_protocol: Human induced pluripotent stem cells were cultured on matrigel coated plated using mTeSR.

extract_protocol:
RNA extraction was performed using QIAGEN standard protocols. Illumina TruSeq Stranded mRNA Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3

description:
Matched control samples are WT samples from GSE71681
Wnt2b replicate 3

tag: genotype

value: Wnt2ba overexpression


title: AgFib [methyl-seq]

tag: cell type

value: Androgenetic fibroblast


title: Stom1.S.Cardia.6hr.neg


title: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1

description: DMSO Control replicate 1

value: DMSO control


title: WtFib


title: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2

description:
Matched control samples are WT samples from GSE71681
Wnt2b replicate 2


title: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1

description:
Matched control samples are WT samples from GSE71681
Wnt2b replicate 1


title: PgHiPSC


title: YapS87A, replicate2

description:
from GSE71681
YapS87A replicate 2

value: YapS87A overexpression


title: Stom3.S.Pylorus.0hr.pos

value: yes


title: Stom2.S.Corpus.0hr.pos


title: YapS87A, replicate1

description:
from GSE71681
YapS87A replicate 1


title: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3

description:
from GSE71681
Control_3

value: Gal4 Control for Wnt2b and YapS87A


title: SI3.W.76.6hr.neg

source_name: Intestine

value: Intestine


title: Stom1.S.Cardia.0hr.pos


title: G82D18B

city: Cincinnati

first: Biplab

last: Dasgupta

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: run1768_lane2_indexD705-D507=G82D18B-human_align

data_processing:
Post Binary Alignment/Map (BAM) aligned files of RNASeq data were analyzed using Avadis® NGS software, Version 1.3.0. Reads were filtered to remove 1) duplicate reads, 2) non-primary-matched reads and 3) reads with alignment scores <95. Quantification was performed on the filtered reads against the RefSeq annotation.
Data normalization was performed with DESeq. The sequencing depth is estimated by the read count of the gene with the median read count ratio across all genes. The method is based on the negative binomial distribution, which allows for less restrictive variance parameter assumptions than does the Poisson distribution. The false discovery rate (FDR) was calculated according to the Benjamini and Hochberg algorithm.  1.5 FC with an FDR of 0.05 was used as selection criteria
Supplementary_files_format_and_content: Tab-delimited text files include DESeq normalized values for each sample.

source_name: Brain Tumor

extract_protocol:
Rneasy Mini Kit from Qiagen
RNA-Seq as per Illumina protocol

value: Brain Tumor

value: acquired resistant cells

tag: time point

value: day 18


title: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1

description:
from GSE71681
Control_1


title: SI3.W.76.24hr.neg

value: no


title: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1

description: NICD replicate 1

value: NICD overexpression


title: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2

description: DMSO Control replicate 2


title: G82D18A

description: run1768_lane2_indexD704-D508=G82D18A-human_align


title: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3

description: DMSO Control replicate 3


title: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6

description: NICD Control replicate 6

value: NICD Control


title: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 1

description: NICD Control replicate 1


title: G68D18B

description: run1768_lane2_indexD706-D505=G68D18B-human_align


title: SI3.W.76.0hr.pos


title: G82D1A

description: run1773_lane92_indexD707-D504=G82D1A-human_align

value: parental

value: day 1


title: YapS87A, replicate3

description:
from GSE71681
YapS87A replicate 3


title: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 5

description: NICD Control replicate 5


title: Pan3.W.N15.24hr.neg

source_name: Pancreas

value: Pancreas


title: PgFib

value: Parthenogenetic fibroblast


title: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2

description:
from GSE71681
Control_2

value: eyes


title: Pan3.W.N15.6hr.neg


title: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2

description: NICD replicate 2


title: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 3

description: Rab11a DN replicate 3

value: Rab11aDN overexpression


title: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 1

description: Rab11a DN Control replicate 1

value: Rab11aDN Control