title: ∆rpoS, high osmolarity, 120min, rep D


title: ∆rpoS, high osmolarity, 90min, rep C

status: Public on Aug 23 2023

type: SRA

city: Claremont

first: Daniel

last: Stoebel

state: CA

address: 301 Platt Blvd

department: Biology

country: USA

institute: Harvey Mudd College

library_source: transcriptomic

data_processing:
Sequencing reads from each sample in a pool were demultiplexed based on their associated barcode sequence using custom scripts.  Up to 1 mismatch in the barcode was allowed provided it did not make assignment of the read to a different barcode possible. Barcode sequences were removed from the first read as were terminal G’s from the second read that may have been added by SMARTScribe during template switching.
Reads were aligned to the NCBI E. coli K-12 MG1655 genome (RefSeq assembly GCF_000005855.2) using BWA v0.7.17 (Li, 2013).
Reads were counted with htseq-count v2.0.1 (Anders et al., 2015).
Assembly: RefSeq assembly GCF_000005855.2
Supplementary files format and content: Processed data are the output of htseq-count

molecule: total RNA

organism: Escherichia coli

source_name: Strain K-12, substrain BW27786

extract_protocol:
200 μL of culture was pelleted and resuspended in 500 μL of Trizol heated to 65°C and then stored at -80°C until use. Samples were purified on a column using the Zymo Direct-Zol RNA Miniprep kit. They then went through two DNase I treatments using Turbo DNA-free (Invitrogen) for 30 minutes each at 37˚C to ensure that all DNA was degraded. The samples were further purified on a column using the Zymo RNA Clean and Concentrator Kit and again stored at -80˚C until they were ready to be sent to get sequenced.
Illumina cDNA libraries were generated using a modified version of the RNAtag-seq protocol (Shishkin et al., 2015). Briefly, 500 ng to 1 μg of total RNA was fragmented, depleted of genomic DNA, dephosphorylated, and ligated to DNA adapters carrying 5’-AN8-3’ barcodes of known sequence with a 5’ phosphate and a 3’ blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (Epicentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcoded adaptor with addition of an adapter to the 3’ end of the cDNA by template switching using SMARTScribe (Clontech) as described (Zhu et al., 2001); (ii) PCR amplification using primers whose 5’ ends target the constant regions of the 3’ or 5’ adaptors and whose 3’ ends contain the full Illumina P5 or P7 sequences. cDNA libraries were sequenced on the Illumina [NextSeq 500] platform to generate paired end reads.

treatment_protocol: For RNA isolation, strains were inoculated from -80°C frozen cultures and grown aerobically overnight in 5 mL of Luria-bertani (LB) broth (1% tryptone, 0.5% yeast extract, 1% NaCl) at 37˚C with shaking at 225 rpm. The next morning, 250μL of each culture was diluted in 25mL of LB and continued to grow at 37˚C with shaking at 225 rpm until the OD600 of the culture reached approximately  0.3. At this point, samples were taken for RNA and protein isolation and then the culture was exposed to the stressor of interest: for low temperature, they were moved to a 15°C shaking water bath; for high osmolarity, 3mL of 5M NaCl was added to the cultures; or they were left to continue growing to reach stationary phase.

tag: cell line

value: Strain K-12, substrain BW27786

tag: genotype

value: delta-rpoS

tag: treatment

value: low tempearture


title: ∆rpoS, high osmolarity, 30min, rep A


title: ∆rpoS, stationary phase, 120min, replicate LSP_E

value: wild-type


title: ∆rpoS, stationary phase, 180min, replicate LSP_E


title: ∆rpoS, high osmolarity, 0min, rep A


title: ∆rpoS, stationary phase, 240min, replicate LSP_E


title: ∆rpoS, stationary phase, 180min, replicate LSP_C


title: ∆rpoS, stationary phase, 120min, replicate LSP_C


title: ∆rpoS, stationary phase, 90min, replicate LSP_E


title: ∆rpoS, stationary phase, 0min, replicate LSP_E


title: ∆rpoS, stationary phase, 240min, replicate LSP_C


title: ∆rpoS, stationary phase, 300min, replicate LSP_C


title: ∆rpoS, stationary phase, 90min, replicate LSP_C


title: ∆rpoS, stationary phase, 300min, replicate LSP_A


title: ∆rpoS, stationary phase, 240min, replicate LSP_A


title: ∆rpoS, stationary phase, 120min, replicate LSP_A


title: ∆rpoS, stationary phase, 0min, replicate LSP_C


title: ∆rpoS, low temperature, 90 mins, rep short_B


title: ∆rpoS, low temperature, 120 mins, rep short_B


title: ∆rpoS, low temperature, 150 mins, rep short_B


title: ∆rpoS, stationary phase, 90min, replicate LSP_A


title: ∆rpoS, stationary phase, 0min, replicate LSP_A


title: ∆rpoS, stationary phase, 180min, replicate LSP_A


title: ∆rpoS, low temperature, 60 mins, rep short_B


title: ∆rpoS, low temperature, 150 mins, rep short_A


title: ∆rpoS, low temperature, 30 mins, rep short_B


title: ∆rpoS, stationary phase, 300min, replicate LSP_E


title: ∆rpoS, low temperature, 120 mins, rep short_A


title: ∆rpoS, low temperature, 90 mins, rep short_A


title: ∆rpoS, low temperature, 30 mins, rep short_A


title: ∆rpoS, low temperature, 60 mins, rep short_A


title: ∆rpoS, low temperature, 0 mins, rep short_A


title: ∆rpoS, low temperature, 150 mins, rep short_1


title: ∆rpoS, low temperature, 120 mins, rep short_1


title: ∆rpoS, low temperature, 90 mins, rep short_1


title: ∆rpoS, low temperature, 30 mins, rep short_1


title: ∆rpoS, stationary phase, 150min, replicate SP_C


title: UMCV38-T

city: Oklahoma City

first: Hiroshi

middle: Y

last: Yamada

state: Oklahoma

department: Medicine

institute: OUHSC

data_processing:
Samples were normalized and pooled onto a 150 paired end run on Illumina’s NextSeq 2000.
Illumina Seq paired fastq files were aligned in Strand NGS software version 2.1 (www.strand-ngs.com) using human assembly.
Reads were normalized using DESeq. The normalized read counts were log-transformed and base-lined to the data set, resulting in normalized signal values.
Differential gene expression of the normalized signal values between the control and experimental group was determined with a 2-fold cutoff using a moderated t test, p < 0.05.
Assembly: Strand NGS software version 2.1 (www.strand-ngs.com) using human assembly

organism: Homo sapiens

source_name: colon

extract_protocol:
Tissue RNA and DNA were extracted with Trizol (ThermoFischer/Invitrogen) and stored at -80oC until use.
Stranded RNA-seq libraries were constructed using NEBNext poly(A) mRNA isolation kit with the SWIFT RNA Library Kit and the established protocols.
The library construction was accomplished with 500 ng of RNA or 4 ng-200 ng of DNA. During library construction, each of the libraries was indexed in order to multiplex for sequencing.

tag: tissue

value: colon

tag: cell type

value: cancer

tag: race

value: white


title: ∆rpoS, stationary phase, 90min, replicate SP_C


title: UMCV36-T


title: UMCV30-T

value: Black


title: ∆rpoS, stationary phase, 60min, replicate SP_C


title: UMCV30-N

value: normal-looking mucosa


title: UMCV29-T


title: ∆rpoS, low temperature, 0 mins, rep short_B


title: UMCV27-T


title: ∆rpoS, stationary phase, 0min, replicate SP_C


title: ∆rpoS, stationary phase, 150min, replicate SP_B


title: ∆rpoS, stationary phase, 60min, replicate SP_B


title: ∆rpoS, stationary phase, 30min, replicate SP_C


title: ∆rpoS, stationary phase, 90min, replicate SP_B


title: UMCV27-N


title: KTM_081

value: white, non-hispanic


title: KTM_084


title: ∆rpoS, stationary phase, 30min, replicate SP_B


title: KTM_077


title: ∆rpoS, stationary phase, 0min, replicate SP_B


title: ∆rpoS, low temperature, 0 mins, rep short_1


title: KTM_076

value: American Indian


title: ∆rpoS, stationary phase, 120min, replicate SP_C


title: ∆rpoS, low temperature, 60 mins, rep short_1


title: ∆rpoS, stationary phase, 150min, replicate SP_A


title: ∆rpoS, stationary phase, 120min, replicate SP_A


title: ∆rpoS, stationary phase, 90min, replicate SP_A


title: KTM_075


title: ∆rpoS, stationary phase, 60min, replicate SP_A


title: ∆rpoS, stationary phase, 120min, replicate SP_B


title: KTM_050


title: KTM_037


title: KTM_025


title: UMCV26-N


title: wild-type, high osmolarity, 180min, rep D


title: ∆rpoS, stationary phase, 0min, replicate SP_A


title: ∆rpoS, stationary phase, 30min, replicate SP_A


title: wild-type, high osmolarity, 120min, rep D


title: wild-type, high osmolarity, 90min, rep D


title: UMCV25-N


title: UMCV24-T


title: UMCV24-N


title: wild-type, high osmolarity, 60min, rep D


title: wild-type, high osmolarity, 0min, rep D


title: wild-type, high osmolarity, 30min, rep D


title: wild-type, high osmolarity, 180min, rep C


title: UMCV23-T


title: KTM_072


title: UMCV22-N


title: wild-type, high osmolarity, 90min, rep C


title: UMCV23-N


title: UMCV22-T


title: wild-type, high osmolarity, 120min, rep C


title: KTM_069


title: wild-type, high osmolarity, 30min, rep C


title: wild-type, high osmolarity, 0min, rep C


title: wild-type, high osmolarity, 60min, rep C


title: UMCV25-T


title: UMCV21-N


title: UMCV20-T


title: UMCV21-T


title: wild-type, high osmolarity, 180min, rep A

value: high osmolarity


title: UMCV19-N


title: wild-type, high osmolarity, 60min, rep A


title: wild-type, high osmolarity, 120min, rep A


title: UMCV16-N


title: wild-type, high osmolarity, 0min, rep A


title: UMCV15-N


title: UMCV15-T


title: UMCV13-T


title: UMCV14-T


title: wild-type, stationary phase, 240min, replicate LSP_E


title: wild-type, stationary phase, 180min, replicate LSP_E


title: UMCV19-T


title: wild-type, stationary phase, 120min, replicate LSP_E


title: UMCV13-N


title: UMCV17-N


title: wild-type, high osmolarity, 90min, rep A


title: wild-type, high osmolarity, 30min, rep A


title: wild-type, stationary phase, 300min, replicate LSP_E


title: UMCV12-N


title: wild-type, stationary phase, 300min, replicate LSP_C


title: UMCV20-N


title: UMCV10-T


title: wild-type, stationary phase, 240min, replicate LSP_C


title: wild-type, stationary phase, 0min, replicate LSP_E


title: UMCV10-N


title: UMCV12-T


title: wild-type, stationary phase, 90min, replicate LSP_E


title: UMCV9-T


title: UMCV9-N


title: wild-type, stationary phase, 120min, replicate LSP_C


title: wild-type, stationary phase, 0min, replicate LSP_C


title: UMCV8-T


title: wild-type, stationary phase, 300min, replicate LSP_A


title: UMCV8-N


title: wild-type, stationary phase, 180min, replicate LSP_A


title: wild-type, stationary phase, 240min, replicate LSP_A


title: UMCV7-T


title: UMCV6-T


title: UMCV11-N


title: wild-type, stationary phase, 120min, replicate LSP_A


title: wild-type, stationary phase, 180min, replicate LSP_C


title: UMCV6-N


title: wild-type, stationary phase, 0min, replicate LSP_A


title: wild-type, stationary phase, 90min, replicate LSP_A


title: wild-type, low temperature, 60 mins, rep short_B


title: UMCV4-N


title: wild-type, low temperature, 90 mins, rep short_B


title: KTM_122


title: UMCV2-N


title: UMCV4-T


title: KTM_110


title: wild-type, low temperature, 120 mins, rep short_B


title: UMCV1-T


title: UMCV3-T


title: UMCV3-N


title: wild-type, low temperature, 150 mins, rep short_B


title: wild-type, low temperature, 30 mins, rep short_B


title: UMCV1-N


title: wild-type, stationary phase, 90min, replicate LSP_C


title: KM37


title: wild-type, low temperature, 120 mins, rep short_A


title: CWR22-Rv1 cells, siSETD7, repeat 2

city: Boston

first: Zifeng

last: Wang

state: Massachusetts

address: 100 Morrissey Blvd, ISC/4610

department: CPCT

institute: UMASS Boston

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (v2.0.1) from GRCh37 Ensembl reference.
Gene level read counts was produced by setting the parameter 'quantMode' as 'GeneCounts' in STAR
Assembly: GRCh37
Supplementary files format and content: tab-deliminated text files include raw gene counts

source_name: CWR22-Rv1 cells

growth_protocol: CWR22-Rv1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol
RNA libraries for RNA-seq were prepared using TruSeq Strnd Total,RNA LT (Illumina)  mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: transfected with 20nM siRNA of SETD7, MLL for 3 days

value: CWR22-Rv1 cells

value: Prostate cancer cell line

value: SETD7 knockdown


title: wild-type, low temperature, 90 mins, rep short_A


title: CWR22-Rv1 cells, siSETD7, repeat 3


title: wild-type, low temperature, 30 mins, rep short_A


title: CWR22-Rv1 cells, siSETD7, repeat 1


title: wild-type, low temperature, 0 mins, rep short_A


title: CWR22-Rv1 cells, siNTC, repeat 3

value: siNTC


title: wild-type, low temperature, 150 mins, rep short_1

value: stationary phase


title: wild-type, low temperature, 150 mins, rep short_A

value: Strain K-12, substrain BW27786


title: wild-type, low temperature, 0 mins, rep short_B


title: CWR22-Rv1 cells, siNTC, repeat 2


title: CWR22-Rv1_Veh_ChIP_SETD7

description: CWR22-Rv1, SETD7, CST

library_source: genomic

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.17-r1188) with aln and samse or sampe sub-commands.
Samtools (version 1.9) was used to convert sam files to bam format.
MACS2 (version 2.1.4) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 357).
Assembly: hg19
Supplementary files format and content: bigWig, bed

molecule: genomic DNA

growth_protocol: CWR22-Rv1,LNCaP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were crosslinked with 1% formaldehyde and then sonicated. DNA were immunoprecipitatted with antibody and protein A/G beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).

treatment_protocol: LNCaP cells were treated with vehicle and GSK2879552  together with or without PFI-2 for 4hrs

tag: chip antibody

value: vehicle


title: CWR22-Rv1 cells, siNTC, repeat 1


title: A2xCt2

city: LUND

middle: P

last: Brink

address: Naturvetarvagen 14

department: Applied Microbiology

country: Sweden

institute: Lund University

data_processing:
Base-calling: The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite.
Filtering: TrimGalore (v0.6.1) running cutadapt (v2.3)
Read alignment: Hisat2 (v2.2.1)
Mapping statistics: were assessed with RSeQC
Differential gene expression: DEseq2 (R-package)
Assembly: JAOEGQ000000000
Supplementary files format and content: tsv file with the results of the DEseq2 analysis for each of the genes predicted in the genome annotation. Includes raw counts and DEseq2-normalized counts from each of the 12 samples, and calculated differential expression data for four compared conditions (g2_vs_g1, x2_vs_x1, x1_vs_g1, x2_vs_g2)

organism: Rhodotorula toruloides

source_name: nitrogen-starvation (time point 2), xylose, biological replicate C

growth_protocol: YNB (without ammonium sulfate) supplemented with glucose and ammonium sulfate to a carbon-to-nitrogen (C/N) ratio of 80 g/g

extract_protocol:
RNeasy Mini Kit (Qiagen, Germany; Purification of Total RNA from Yeast protocol); Precellys evolution bead mill (Bertin Instruments, Montigny-le-Bretonneux, France) for 4 cycles à 45 s at 6000 rpm
Illumina TruSeq Stranded mRNA library kit with Poly-A selection

treatment_protocol: Quenching by liquid nitrogen

tag: strain

tag: growth condition

value: nitrogen-starvation

tag: sugar

value: xylose


title: CWR22-Rv1_shCTL_ChIP_FOXA1

description: CWR22-Rv1, FOXA1, ABCAM

value: shCTL


title: A2xBt2

source_name: nitrogen-starvation (time point 2), xylose, biological replicate B


title: A2xCt1

source_name: exponential growth (time point 1), xylose, biological replicate C

value: exponential growth


title: A2xAt2

source_name: nitrogen-starvation (time point 2), xylose, biological replicate A


title: wild-type, low temperature, 60 mins, rep short_A

value: wild-type


title: wild-type, low temperature, 120 mins, rep short_1

value: delta-rpoS


title: wild-type, stationary phase, 150min, replicate SP_C


title: wild-type, stationary phase, 120min, replicate SP_C


title: wild-type, low temperature, 30 mins, rep short_1


title: wild-type, stationary phase, 90min, replicate SP_C


title: wild-type, low temperature, 90 mins, rep short_1


title: A2xAt1

source_name: exponential growth (time point 1), xylose, biological replicate A


title: wild-type, stationary phase, 60min, replicate SP_C


title: wild-type, low temperature, 0 mins, rep short_1


title: wild-type, low temperature, 60 mins, rep short_1


title: A2gCt2

source_name: nitrogen-starvation (time point 2), glucose, biological replicate C

value: glucose


title: wild-type, stationary phase, 0min, replicate SP_C


title: CWR22-Rv1_shSETD7_ChIP_FOXA1

description: CWR22-Rv1, FOXA1, ABCAM


title: wild-type, stationary phase, 150min, replicate SP_B


title: A2gBt2

source_name: nitrogen-starvation (time point 2), glucose, biological replicate B


title: A2gAt2

source_name: nitrogen-starvation (time point 2), glucose, biological replicate A


title: wild-type, stationary phase, 120min, replicate SP_B


title: wild-type, stationary phase, 90min, replicate SP_B


title: A2gCt1

source_name: exponential growth (time point 1), glucose, biological replicate C


title: wild-type, stationary phase, 60min, replicate SP_B


title: A2xBt1

source_name: exponential growth (time point 1), xylose, biological replicate B


title: A2gAt1

source_name: exponential growth (time point 1), glucose, biological replicate A


title: wild-type, stationary phase, 30min, replicate SP_B


title: wild-type, stationary phase, 0min, replicate SP_B


title: wild-type, stationary phase, 150min, replicate SP_A


title: wild-type, stationary phase, 30min, replicate SP_C


title: wild-type, stationary phase, 90min, replicate SP_A


title: wild-type, stationary phase, 60min, replicate SP_A


title: wild-type, stationary phase, 120min, replicate SP_A


title: SW480 (negative control)

city: Bloomington

first: Ahmed

middle: H

last: Ghobashi

state: IN

institute: Indiana University

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.11.9)
Reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.4.2. The Bam file was generated and sorted using samtools (V 1.15.1)
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.01
Assembly: hg38
Supplementary files format and content: NarrowPeak(called peaks)(except for Input sample)
Library strategy: CUT&RUN

growth_protocol: SW480 cells were maintained in McCoy 5A media supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
CUT&RUN was performed  using a commercial kit's protocol (EpiCypher CUTANA pAG-MNase for ChIC/CUT&RUN, 15-1116)
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep kit for Illumina (NEB) as per the manufacturer's protocol

value: Primary colorectal cancer cells

tag: antibody

value: HA  (CUTANA)™


title: SW480 PTENKD (HA-EZH2 WT)


title: SW480 EV KD  (HA-EZH2 WT)


title: SW480  (negatoive control)

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.11.9)
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.4.2.The Bam file was generated and sorted using samtools (V 1.15.1)
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.01
Assembly: hg38
Supplementary files format and content: tab-delimited text (called peaks)(except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, the experiment were perforemd using Diagenode iDeal ChIP-seq Kit (C01010055, for transcription factors) as per the manufacturer's protocol..
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep kit for Illumina (NEB) as per the manufacturer's protocol

value: FLAG (sigma)


title: SW480 EV KD  (HA-EZH2 PN (S21A)


title: SW480 PTENKD_EZH2i _R1 (FLAG-β-catenin WT)


title: wild-type, low temperature, 90 mins, rep long_D


title: wild-type, stationary phase, 0min, replicate SP_A


title: SW480 PTENKD_EZH2i _R2 (FLAG-β-catenin WT)


title: SW480 PTENKD (HA-EZH2 PN (S21A)


title: wild-type, low temperature, 300 mins, rep long_D


title: SW480 EV KD_EZH2i_R2 (FLAG-β-catenin WT)


title: A2gBt1

source_name: exponential growth (time point 1), glucose, biological replicate B


title: wild-type, low temperature, 240 mins, rep long_D


title: SW480 EV KD_EZH2i_R1 (FLAG-β-catenin WT)


title: wild-type, low temperature, 180 mins, rep long_D


title: SW480 PTENKD _R2 (FLAG-β-catenin WT)


title: SW480 PTENKD _R1 (FLAG-β-catenin WT)


title: wild-type, low temperature, 120 mins, rep long_D


title: ∆rpoS, low temperature, 90 mins, rep long_D


title: SW480 EV KD_R2 (FLAG-β-catenin WT)


title: wild-type, low temperature, 0 mins, rep long_D


title: wild-type, stationary phase, 30min, replicate SP_A


title: SW480 PTENKD_EZH2i _R3

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.11.9)
An index of the hg38 genome was created, and reads were aligned with STAR (v2.7.10a) with the additional parameter --quantMode GeneCounts to generate count matrix
Deseq2 (v3.24.0) was used for differential expression analysis. Gene Set Enrichment Analysis using the Molecular Signatures Database collections and database were run with clusterProfiler (v1.38.3) and volcanoplot was visualized with EnhancedVolcano.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count values for each sample

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEB NextUltra DNA Library following the manufacturer's protocol.

treatment_protocol: Cells were treated with 2 μM EZH2 inhibitor (GSK503 (Sigma, SML2718) ) for 72 hours

value: PTEN knockdown

value: EZH2 inhibitor

tag: time

value: 72 hours


title: SW480 EV KD_R1 (FLAG-β-catenin WT)


title: SW480 PTENKD_EZH2i _R1


title: SW480 EV KD_EZH2i_R2

value: WT


title: SW480 EV KD_EZH2i_R3


title: SW480 PTENKD _R1

value: Untreated


title: SW480 PTENKD _R3


title: SW480 EV KD_EZH2i_R1


title: SW480 PTENKD_EZH2i _R2


title: HB13151 SYC233

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

description:
HB13151
5hmC_Seal

data_processing: The raw 5hmC-Seal data were summarized using the pipelines that we previously described. Briefly, raw sequencing reads were trimmed and filtered for low-quality bases using the FASTX Toolkit (v 0.0.14), followed by alignment to hg19 using Bowtie2 (v 2.2.6) with the end-to-end alignment mode [39]. Read pairs were concordantly aligned with fragment length ≤500 bp and with up to one ambiguous base and up to four mismatched bases per 100 bp. Aligned read pairs were then sorted, indexed and deduplicated using Picard (v 2.6.0). Alignments with mapping quality score ≥ 10 were counted for gene bodies, and histone modifications.

source_name: Tissue

extract_protocol:
Genomic DNA was isolated from tissues using the QIAamp DNA Mini Kit (Qiagen, Germany). DNA fragmentation was done by sonication, and quality and quantity examined with standard molecular biology protocols using Qubit (Thermo Fisher, USA).
Approximately 50 ng per sample was used to construct the 5hmC-Seal library as we previously described, followed by the NGS on the NextSeq 500 platform (PE39) at the University of Chicago Genomics Facility. On average 25 million read counts were obtained for each sample.

tag: tissue type

value: Normal

tag: population


title: NU01308 SYC322

description:
NU01308
5hmC_Seal

value: GBM

value: White


title: NU00681 SYC345

description:
NU00681
5hmC_Seal

value: More than one race


title: SW480 EV KD_R1


title: SW480 EV KD_R2


title: SW480 EV KD_R3


title: SW480 PTENKD _R2


title: ∆rpoS, low temperature, 120 mins, rep long_C

value: Strain K-12, substrain BW27786

value: stationary phase


title: ∆rpoS, low temperature, 180 mins, rep long_C

value: wild-type


title: wild-type, low temperature, 120 mins, rep long_C


title: ∆rpoS, low temperature, 300 mins, rep long_C


title: ∆rpoS, low temperature, 0 mins, rep long_D

value: delta-rpoS


title: ∆rpoS, low temperature, 240 mins, rep long_D


title: NU01249 SYC336

description:
NU01249
5hmC_Seal


title: wild-type, low temperature, 180 mins, rep long_C


title: ∆rpoS, low temperature, 180 mins, rep long_D


title: ∆rpoS, low temperature, 90 mins, rep long_C


title: wild-type, low temperature, 300 mins, rep long_C


title: ∆rpoS, low temperature, 240 mins, rep long_C


title: wild-type, low temperature, 0 mins, rep long_C


title: wild-type, low temperature, 90 mins, rep long_C


title: ∆rpoS, low temperature, 300 mins, rep long_D


title: wild-type, low temperature, 90 mins, rep long_B


title: wild-type, low temperature, 240 mins, rep long_C


title: ∆rpoS, low temperature, 120 mins, rep long_D


title: NU01139 SYC341

description:
NU01139
5hmC_Seal


title: wild-type, low temperature, 300 mins, rep long_B


title: NU01126 SYC335

description:
NU01126
5hmC_Seal


title: wild-type, low temperature, 240 mins, rep long_B


title: ∆rpoS, low temperature, 0 mins, rep long_C


title: NU00983 SYC239

description:
NU00983
5hmC_Seal


title: NU00951 SYC240

description:
NU00951
5hmC_Seal

value: Refused, not reported


title: NU00919 SYC241

description:
NU00919
5hmC_Seal


title: NU00915 SYC242

description:
NU00915
5hmC_Seal


title: NU00866 SYC283

description:
NU00866
5hmC_Seal

value: Unknown


title: ∆rpoS, low temperature, 90 mins, rep long_B


title: wild-type, low temperature, 120 mins, rep long_B


title: wild-type, low temperature, 0 mins, rep long_B


title: wild-type, low temperature, 90 mins, rep long_A


title: NU00859 SYC285

description:
NU00859
5hmC_Seal


title: NU00839 SYC288

description:
NU00839
5hmC_Seal


title: NU00843 SYC287

description:
NU00843
5hmC_Seal


title: NU00835 SYC289

description:
NU00835
5hmC_Seal


title: NU00860 SYC284

description:
NU00860
5hmC_Seal


title: NU00845 SYC286

description:
NU00845
5hmC_Seal


title: wild-type, low temperature, 180 mins, rep long_B


title: NU01004 SYC238

description:
NU01004
5hmC_Seal


title: ∆rpoS, low temperature, 0 mins, rep long_B


title: wild-type, low temperature, 180 mins, rep long_A


title: wild-type, low temperature, 240 mins, rep long_A


title: NU00793 SYC291

description:
NU00793
5hmC_Seal


title: ∆rpoS, low temperature, 240 mins, rep long_B


title: ∆rpoS, low temperature, 120 mins, rep long_B


title: wild-type, low temperature, 300 mins, rep long_A


title: ∆rpoS, low temperature, 180 mins, rep long_B


title: ∆rpoS, low temperature, 300 mins, rep long_B


title: NU00773 SYC292

description:
NU00773
5hmC_Seal


title: NU00764 SYC293

description:
NU00764
5hmC_Seal


title: wild-type, low temperature, 120 mins, rep long_A


title: wild-type, low temperature, 0 mins, rep long_A


title: ∆rpoS, low temperature, 90 mins, rep long_A


title: NU00715 SYC298

description:
NU00715
5hmC_Seal


title: NU00826 SYC290

description:
NU00826
5hmC_Seal

value: Black


title: NU00734 SYC296

description:
NU00734
5hmC_Seal


title: NU00696 SYC280

description:
NU00696
5hmC_Seal


title: ∆rpoS, low temperature, 120 mins, rep long_A


title: ∆rpoS, low temperature, 240 mins, rep long_A


title: ∆rpoS, low temperature, 180 mins, rep long_A


title: ∆rpoS, low temperature, 0 mins, rep long_A


title: NU00625 SYC282

description:
NU00625
5hmC_Seal


title: NU00434 SYC303

description:
NU00434
5hmC_Seal


title: NU00440 SYC278

description:
NU00440
5hmC_Seal


title: NU01251 SYC337

description:
NU01251
5hmC_Seal


title: NU00341 SYC310

description:
NU00341
5hmC_Seal


title: NU00408 SYC306

description:
NU00408
5hmC_Seal


title: NU00400 SYC307

description:
NU00400
5hmC_Seal


title: NU00483 SYC302

description:
NU00483
5hmC_Seal


title: NU00334 SYC311

description:
NU00334
5hmC_Seal


title: NU00382 SYC277

description:
NU00382
5hmC_Seal


title: NU00387 SYC308

description:
NU00387
5hmC_Seal


title: NU00423 SYC304

description:
NU00423
5hmC_Seal


title: ∆rpoS, low temperature, 300 mins, rep long_A


title: NU00620 SYC300

description:
NU00620
5hmC_Seal


title: NU00328 SYC312

description:
NU00328
5hmC_Seal


title: NU00413 SYC305

description:
NU00413
5hmC_Seal


title: NU00544 SYC301

description:
NU00544
5hmC_Seal


title: NU00323 SYC313

description:
NU00323
5hmC_Seal


title: NU00318 SYC314

description:
NU00318
5hmC_Seal


title: NU00313 SYC315

description:
NU00313
5hmC_Seal


title: NU00351 SYC309

description:
NU00351
5hmC_Seal


title: NU00348 SYC276

description:
NU00348
5hmC_Seal


title: NU00295 SYC316

description:
NU00295
5hmC_Seal


title: NU00266 SYC318

description:
NU00266
5hmC_Seal


title: NU00265 SYC274

description:
NU00265
5hmC_Seal


title: NU00273 SYC275

description:
NU00273
5hmC_Seal


title: NU00280 SYC317

description:
NU00280
5hmC_Seal


title: NU00210 SYC272

description:
NU00210
5hmC_Seal


title: NU00252 SYC273

description:
NU00252
5hmC_Seal


title: NU00160 SYC269

description:
NU00160
5hmC_Seal


title: NU00153 SYC268

description:
NU00153
5hmC_Seal


title: NU00184 SYC270

description:
NU00184
5hmC_Seal


title: NU00123 SYC257

description:
NU00123
5hmC_Seal


title: NU00140 SYC258

description:
NU00140
5hmC_Seal


title: NU00118 SYC254

description:
NU00118
5hmC_Seal


title: HU13062 SYC243

description:
HU13062
5hmC_Seal


title: 82370 SYC249

description:
82370
5hmC_Seal


title: HU13260 SYC234

description:
HU13260
5hmC_Seal


title: 5427 SYC250

description:
5427
5hmC_Seal


title: HU13144 SYC232

description:
HU13144
5hmC_Seal


title: NU00109 SYC251

description:
NU00109
5hmC_Seal


title: NU00121 SYC256

description:
NU00121
5hmC_Seal


title: NU00119 SYC255

description:
NU00119
5hmC_Seal


title: 5246 SYC244

description:
5246
5hmC_Seal


title: 5482 SYC245

description:
5482
5hmC_Seal


title: 5511 SYC248

description:
5511
5hmC_Seal


title: YOUNG3

city: mudanjiang

first: shanshan

last: hu

address: Mudanjiang City, Heilongjiang Province

country: China

institute: Hongqi Hospital Affiliated to Mudanjiang Medical College

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: anterior lens capsule

extract_protocol: RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: anterior lens capsule


title: YOUNG2


title: YOUNG1


title: EGCG3


title: EGCG2


title: EGCG1


title: AGED3


title: Scgb1a1+,CD24low single cell 286

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Genome_build: mm10
Supplementary_files_format_and_content: The detected number of RNA moelcules per well (i.e., single cell)  for each gene is listed.

source_name: Scgb1a1+,CD24low cell

extract_protocol:
RNAs from cell lysate in each well was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: Single cells were isolated in wells respectively

tag: age

value: 4 month


title: Scgb1a1+,CD24low single cell 285


title: AGED2


title: AGED1


title: Scgb1a1+,CD24low single cell 284


title: Scgb1a1+,CD24low single cell 281


title: Scgb1a1+,CD24low single cell 279


title: Scgb1a1+,CD24low single cell 280


title: Scgb1a1+,CD24low single cell 278


title: Scgb1a1+,CD24low single cell 275


title: Scgb1a1+,CD24low single cell 274


title: Scgb1a1+,CD24low single cell 277


title: Scgb1a1+,CD24low single cell 283


title: Scgb1a1+,CD24low single cell 270


title: Scgb1a1+,CD24low single cell 271


title: Scgb1a1+,CD24low single cell 269


title: Scgb1a1+,CD24low single cell 272


title: Scgb1a1+,CD24low single cell 264


title: Scgb1a1+,CD24low single cell 265


title: Scgb1a1+,CD24low single cell 263


title: Scgb1a1+,CD24low single cell 266


title: Scgb1a1+,CD24low single cell 282


title: Scgb1a1+,CD24low single cell 261


title: Scgb1a1+,CD24low single cell 273


title: Scgb1a1+,CD24low single cell 268


title: Scgb1a1+,CD24low single cell 259


title: Scgb1a1+,CD24low single cell 260


title: Scgb1a1+,CD24low single cell 276


title: Scgb1a1+,CD24low single cell 258


title: Scgb1a1+,CD24low single cell 257


title: Scgb1a1+,CD24low single cell 267


title: Scgb1a1+,CD24low single cell 256


title: Scgb1a1+,CD24low single cell 255


title: Scgb1a1+,CD24low single cell 262


title: Scgb1a1+,CD24low single cell 253


title: Scgb1a1+,CD24low single cell 252


title: Scgb1a1+,CD24low single cell 250


title: Scgb1a1+,CD24low single cell 249


title: Scgb1a1+,CD24low single cell 248


title: Scgb1a1+,CD24low single cell 247


title: Scgb1a1+,CD24low single cell 245


title: Scgb1a1+,CD24low single cell 254


title: Scgb1a1+,CD24low single cell 243


title: Scgb1a1+,CD24low single cell 240


title: Scgb1a1+,CD24low single cell 241


title: Scgb1a1+,CD24low single cell 242


title: Scgb1a1+,CD24low single cell 238


title: Scgb1a1+,CD24low single cell 237


title: Scgb1a1+,CD24low single cell 246


title: Scgb1a1+,CD24low single cell 239


title: Scgb1a1+,CD24low single cell 234


title: Scgb1a1+,CD24low single cell 236


title: Scgb1a1+,CD24low single cell 235


title: Scgb1a1+,CD24low single cell 231


title: Scgb1a1+,CD24low single cell 232


title: Scgb1a1+,CD24low single cell 233


title: Scgb1a1+,CD24low single cell 229


title: Scgb1a1+,CD24low single cell 230


title: Scgb1a1+,CD24low single cell 227


title: Scgb1a1+,CD24low single cell 228


title: Scgb1a1+,CD24low single cell 244


title: Scgb1a1+,CD24low single cell 251


title: Scgb1a1+,CD24low single cell 225


title: Scgb1a1+,CD24low single cell 224


title: Scgb1a1+,CD24low single cell 223


title: Scgb1a1+,CD24low single cell 226


title: Scgb1a1+,CD24low single cell 221


title: Scgb1a1+,CD24low single cell 220


title: Scgb1a1+,CD24low single cell 222


title: 24 [Young, WT]

city: Madison

first: Cynthia

middle: A

last: Kelm-Nelson

state: WI

address: 1300 University Avenue, 416 Medical Sciences Center

department: Surgery

institute: University of Wisconsin- Madiso

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, contamination and low-quality reads were removed. Goblin (alpha and beta) were removed. Reads were mapped to the annotated rat (Rattus Norvegicus) genome in Ensembl.
Technical quality was determined using several parameters. Briefly, trimming software skewer was used to preprocess raw fastq files. Combined cycle base quality, per cycle base frequencies and average base quality, relative 3-Kmer diversity, Phred quality distribution, mean quality distribution, average read length and read occurrence distribution were used as additional quality control measures on the read data. Additionally, the biological coefficient of variation was estimated to be approximately 0.12.
Gene analysis was performed with the glm using the EdgeR Bioconductor Package, v. 3.9. The p-value cutoff was set to 0.05 for significance. A Benjamini-Hochberg correction was applied to control the False Discovery Rate (FDR).
RSEM approach for normalizing RNA seq data was used
Supplementary files format and content: tab-delimited text files include raw values for each sample.

organism: Rattus norvegicus

source_name: whole blood

extract_protocol:
Whole blood was collected and stored in RNALater at -80. Whole Blood RNA was harvested using the Invitrogen RiboPure Blood Kit (Cat#AM1928). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole blood

tag: Sex

value: Male

value: Young


title: Scgb1a1+,CD24low single cell 219


title: 22 [Young, WT]

value: WT


title: 23 [Young, Pink1-/-]


title: Scgb1a1+,CD24low single cell 218


title: Scgb1a1+,CD24low single cell 215


title: 649B [Old, Pink1-/-]

value: Old


title: 13 [Young, WT]


title: Scgb1a1+,CD24low single cell 212


title: Scgb1a1+,CD24low single cell 214


title: Scgb1a1+,CD24low single cell 216


title: 4 [Young, Pink1-/-]


title: 14 [Young, Pink1-/-]


title: 15 [Young, WT]


title: Scgb1a1+,CD24low single cell 211


title: 10B [Young, Pink1-/-]


title: Scgb1a1+,CD24low single cell 217


title: 078B [Old, Pink1-/-]


title: Scgb1a1+,CD24low single cell 208


title: Scgb1a1+,CD24low single cell 213


title: RNA-3S-3, RNAseq

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

data_processing:
RNA analysis: Quality-filtered NGS reads were aligned to the genome using RSEM (version 1.2.28). The TPM values for annotated transcripts were estimated using the “rsem-calculate-expression” function of RSEM (version 1.2.28) with a strand-specific strategy.
Assembly: Mm10 (GRCm38) for the mouse reads mapping
Supplementary files format and content: The TPM value of each gene and each sample generaed by RSEM were included in the .txt file.

source_name: Sperm

extract_protocol:
12 male mice of C57BL/6J strain at 24-month-old were used to extract brains, hearts, livers, bone marrow, PBMCs and sperms. Red cells in bone marrow were removed by Red Blood Cell Lysis Buffer (Beyotime). PBMCs were isolated from blood using Ficoll-Paque PLUS (GE Healthcare). The motile spermatozoa were isolated from the mouse epididymal tail by collecting cells floating in the upper layer of RPMI 1640 (Thermo Fisher Scientific). The isolated tissues were immediately put into liquid nitrogen for quick freezing. The whole organs were cut into small pieces and ground into powder by tissue homogenizer in presence of liquid nitrogen to avoid heating. All ground tissue samples were stored at -80℃ prior to DNA isolation. Genomic DNA from the mouse brain, bone marrow, heart, liver and PBMCs was isolated using TIANamp Genomic DNA kit (Tiangen, DP304) with RNaseA treatment according to the manufacturer’s protocols. Genomic DNA from sperm cells was extracted using Sperm DNA Purification Kit (Simgen, 4202050) following the manufacturer’s instructions. All DNA samples were eluted in UltraPure™ DNase/RNase-Free Distilled Water (Invitrogen), measured the concentration using SMA6000 (Merinton) and stored at -20. Total RNA was isolated with TRNzol (TIANGEN, Beijing).
ncRNAseq:The RNA samples were used for RNA-seq library construction using rRNA depletion and a strand-specific strategy. The library construction and sequencing using the Illumina NovaSeq 6000 platform with the PE150 strategy on the 10-GB scale were outsourced to Novogene Corporation (Beijing).
SSiNGLe method; SSiNGLe-AP method; ncRNA-seq

value: Sperm

tag: development stage

value: 3 months


title: Scgb1a1+,CD24low single cell 210


title: 016A [Old, Pink1-/-]


title: Scgb1a1+,CD24low single cell 209


title: RNA-3S-2, RNAseq


title: 394 [Old, WT]


title: 211 [Old, WT]


title: RNA-3S-1, RNAseq


title: Scgb1a1+,CD24low single cell 207


title: 25 [Old, WT]


title: RNA-3P-2, RNAseq

source_name: PBMC

value: PBMC


title: RNA-3P-3, RNAseq


title: RNA-3P-1, RNAseq


title: Scgb1a1+,CD24low single cell 205


title: Scgb1a1+,CD24low single cell 206


title: RNA-3M-3, RNAseq

source_name: Bone marrow

value: Bone marrow


title: MHCC-97H cells, Treat, 16h, rep1

city: Nanning

first: Lichuan

last: Wu

state: China

address: N0. 100, Daxue East Road

department: School of Medicine

institute: Guangxi University

data_processing:
Remove Reads containing connectors
Remove low-quality Reads (including Reads with a removal ratio of N greater than 10%; remove Reads with a mass of value below 10 with an alkali base accounting for more than 50% of the entire Read)
Compare Clean Reads with reference genomes using HISAT2 software
Assemble the reads on using StringTie comparison, and reconstruct the Transcriptome for subsequent analysis
Assembly: Homo_sapiens.GRCh38_release95.genome.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: liver

growth_protocol: MHCC-97H cells were cultured in DMEM supplemented with 10% fetal  bovine serum (FBS) and 1% penicillin-streptomycin

extract_protocol:
Total RNA was harvested using Rneasy mini plus kit (Qiagen)
Enrichment of mRNA with Oligo (dT) Beads, Adding Fragmentation Buffer to Randomly Break mRNA, Using mRNA as a template, synthesize the first cDNA strand and second strand, and purify the cDNA, The purified double stranded cDNA is then subjected to end repair, A-tailed addition, and sequencing connectors are connected. Then, AMPure XP beads are used for fragment size selection, and finally, a cDNA library is obtained through PCR enrichment

treatment_protocol: MHCC-97H cells were treated with 6j (10 μM) or solvent control for 16 h

value: liver

tag: cell line

value: liver cancer cell

value: compound 6j


title: MHCC-97H cells, Treat, 16h, rep2


title: RNA-3M-1, RNAseq


title: RNA-3L-3, RNAseq

source_name: Liver

value: Liver


title: MHCC-97H cells, Control, 16h, rep3


title: Scgb1a1+,CD24low single cell 204

tag: genotype


title: Scgb1a1+,CD24low single cell 203


title: RNA-3H-3, RNAseq

source_name: Heart

value: Heart


title: RNA-3L-1, RNAseq


title: Scgb1a1+,CD24low single cell 202


title: MHCC-97H cells, Control, 16h, rep2

tag: treatment


title: RNA-3H-2, RNAseq

tag: tissue


title: RNA-3H-1, RNAseq


title: MHCC-97H cells, Control, 16h, rep1

tag: cell type


title: Scgb1a1+,CD24low single cell 201


title: RNA-3B-3, RNAseq

source_name: Brain

value: Brain


title: MHCC-97H cells, Treat, 16h, rep3


title: RNA-3B-2, RNAseq


title: CWR22-Rv1 cells, siMLL1, repeat 2

source_name: CWR22-Rv1 cells

value: CWR22-Rv1 cells

value: Prostate cancer cell line

value: MLL1 knockdown


title: Scgb1a1+,CD24low single cell 200

value: 4 month


title: RNA-3M-2, RNAseq


title: Medulloblastoma Sample HSJD_EPIC_390

type: genomic

city: Esplugues de Llobregat

first: Soledad

last: Gómez-González

state: Barcelona

address: Santa Rosa, 39-57, 4a planta

department: Oncology

country: Spain

institute: Hospital Sant Joan de Déu

hyb_protocol: 600ng of genomic DNA was bisulfite converted using EZ DNA Methylation Kit (Zymo) following manufacturer's protocol. 4uL of bisulfite-converted DNA were hybridized to Infinium HumanMethylationEPIC BeadChip following Illumina Infinium HD Methylation protocol

scan_protocol: Chip analysis was performed using Illumina iScan® System (SY-101-1001)  scanner and the intensities of the images were extracted using GenomeStudio (2011.1) Methylation module (v 1.8) software

data_processing:
Bioconductor (Version 3.15) package minifi (Version 1.42.0) using function 'preprocessIllumina'  Average beta
Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy5

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Genomic DNA was isolated using Gentra Pure gene Tissue kit for fresh-frozen samples and QIAamp DNA FFPE kit for FFPE samples (Qiagen Technologies).

tag: sample type

value: Medulloblastoma

tag: sample subtype

value: non-WNT/non-SHH

tag: material

value: Fresh-Frozen


title: Medulloblastoma Sample HSJD_EPIC_420

label: Cy5 and Cy6


title: RNA-3L-2, RNAseq

tag: strain


title: CWR22-Rv1 cells, siNTC, repeat 2 control for siMLL

value: siNTC


title: Scgb1a1+,CD24low single cell 197


title: Medulloblastoma Sample HSJD_EPIC_264

data_processing:
Bioconductor (Version 3.15) package minifi (Version 1.42.0) using function 'preprocessIllumina'  Average beta
matrix processed value definition: Average Beta

label: Cy5 and Cy3


title: RNA-3B-1, RNAseq

value: 3 months


title: Medulloblastoma Sample HSJD_EPIC_375

label: Cy5 and Cy4


title: CWR22-Rv1 cells, siMLL1, repeat 1


title: CWR22-Rv1 cells, siNTC, repeat 1 control for siMLL


title: Medulloblastoma Sample HSJD_EPIC_262

value: FFPE


title: Scgb1a1+,CD24low single cell 198


title: Scgb1a1+,CD24low single cell 196


title: LNCaP_GSK_PFI_ChIP_FOXA1

description: LNCaP, FOXA1, ABCAM

source_name: LNCaP

value: LNCaP

tag: chip antibody

value: GSK2879552  together with or without PFI-2


title: Ependymoma Sample HSJD_EPIC_252

value: Ependymoma

value: EP


title: RNA-22S-3, RNAseq

value: Sperm

value: 22 months


title: RNA-22S-1, RNAseq


title: Scgb1a1+,CD24low single cell 195


title: RNA-22P-3, RNAseq

value: PBMC


title: Medulloblastoma Sample HSJD_EPIC_244

value: WNT


title: Scgb1a1+,CD24low single cell 199


title: Scgb1a1+,CD24low single cell 194


title: Scgb1a1+,CD24low single cell 193


title: Medulloblastoma Sample HSJD_EPIC_238


title: RNA-22P-2, RNAseq


title: Scgb1a1+,CD24low single cell 192


title: RNA-22M-3, RNAseq

value: Bone marrow


title: RNA-22P-1, RNAseq


title: LNCaP_DMSO_ChIP_FOXA1

description: LNCaP, FOXA1, ABCAM

value: Prostate cancer cell line

value: DMSO


title: LNCaP_GSK_ChIP_FOXA1

description: LNCaP, FOXA1, ABCAM


title: RNA-22S-2, RNAseq


title: CWR22-Rv1_Veh_ChIP_FOXA1

description: CWR22-Rv1, FOXA1, ABCAM

value: Veh


title: Scgb1a1+,CD24low single cell 190

value: 4 month


title: Scgb1a1+,CD24low single cell 191


title: CEL211011EL_AML_4_GEX

city: Portland

first: Evan

middle: F.

last: Lind

state: OR

address: Mail Code L220, 3181 SW Sam Jackson Park Road

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

description:
10x Genomics 3' mRNA
CEL211011EL_AML_4_GEX

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0.
Assembly: mm10
Supplementary files format and content: cellranger derived feature, barcode, matrix files

source_name: spleen

extract_protocol:
Spleens from mice were collected from healthy WT or AML mice and processed for single cell suspensions. In brief, spleens were mechanicaly disrupted using frosted tip glass slides and filtered using 70 um mesh filters. Filtered suspensions were ACK treated to remove RBCs before incubation with ADTs according to manufacturer's instructions (BioLegend). After ADT surface stains cell suspensions were resuspended at 1,000 cells per µL with 1X PBS 0.04% BSA before transfer to OHSU MPSSR for sequencing.
scRNA-seq 3'GEX v3 (10x Genomics)
Library was performed according to the manufacter’s instructions (Single Cell 3'GEX v3 protocol, 10x Genomics).

tag: condition

value: AML

value: spleen

tag: model

value: GEMM


title: Medulloblastoma Sample HSJD_EPIC_226

value: Medulloblastoma

value: SHH

value: Fresh-Frozen


title: RNA-22M-1, RNAseq


title: Medulloblastoma Sample HSJD_EPIC_239

value: non-WNT/non-SHH


title: Scgb1a1+,CD24low single cell 189


title: CEL211011EL_AML_1_GEX

description:
10x Genomics 3' mRNA
CEL211011EL_AML_1_GEX


title: Medulloblastoma Sample HSJD_EPIC_220


title: CEL211011EL_AML_2_GEX

description:
10x Genomics 3' mRNA
CEL211011EL_AML_2_GEX


title: Medulloblastoma Sample HSJD_EPIC_212


title: RNA-22L-3, RNAseq

value: Liver


title: RNA-22L-1, RNAseq


title: RNA-22M-2, RNAseq


title: ATRT Sample HSJD_EPIC_163

value: ATRT

value: FFPE


title: ATRT Sample HSJD_EPIC_155


title: Medulloblastoma Sample HSJD_EPIC_159


title: Scgb1a1+,CD24low single cell 185


title: Scgb1a1+,CD24low single cell 188


title: CEL211011EL_WT_2_GEX

description:
10x Genomics 3' mRNA
CEL211011EL_WT_2_GEX

value: WT healthy


title: Scgb1a1+,CD24low single cell 186


title: RNA-22H-3, RNAseq

value: Heart

value: 22 months


title: Scgb1a1+,CD24low single cell 187


title: CEL211011EL_WT_1_GEX

description:
10x Genomics 3' mRNA
CEL211011EL_WT_1_GEX


title: RNA-22H-2, RNAseq


title: CEL211011EL_AML_3_GEX

description:
10x Genomics 3' mRNA
CEL211011EL_AML_3_GEX


title: Medulloblastoma Sample HSJD_EPIC_211


title: CEL211011EL_WT_4_GEX

description:
10x Genomics 3' mRNA
CEL211011EL_WT_4_GEX


title: ATRT Sample HSJD_EPIC_153


title: RNA-22H-1, RNAseq


title: Scgb1a1+,CD24low single cell 184


title: ATRT Sample HSJD_EPIC_145


title: CEL211011EL_AML_4_ADT

description:
protein ADT
10x Genomics ADT
CEL211011EL_AML_4_ADT

library_source: other

molecule: protein


title: CEL211011EL_WT_3_GEX

description:
10x Genomics 3' mRNA
CEL211011EL_WT_3_GEX


title: Medulloblastoma Sample HSJD_EPIC_128


title: Scgb1a1+,CD24low single cell 182


title: CEL211011EL_AML_3_ADT

description:
protein ADT
10x Genomics ADT
CEL211011EL_AML_3_ADT


title: Scgb1a1+,CD24low single cell 183


title: RNA-22B-2, RNAseq

value: Brain


title: CEL211011EL_AML_2_ADT

description:
protein ADT
10x Genomics ADT
CEL211011EL_AML_2_ADT


title: Medulloblastoma Sample HSJD_EPIC_119


title: CEL211011EL_WT_4_ADT

description:
protein ADT
10x Genomics ADT
CEL211011EL_WT_4_ADT


title: Scgb1a1+,CD24low single cell 181


title: RNA-19S-2, RNAseq

value: Sperm

value: 19 months


title: ATRT Sample HSJD_EPIC_115


title: CEL211011EL_AML_1_ADT

description:
protein ADT
10x Genomics ADT
CEL211011EL_AML_1_ADT


title: RNA-19S-3, RNAseq


title: Scgb1a1+,CD24low single cell 179

value: 4 month


title: RNA-19S-1, RNAseq


title: CEL211011EL_WT_3_ADT

description:
protein ADT
10x Genomics ADT
CEL211011EL_WT_3_ADT


title: ATRT Sample HSJD_EPIC_111


title: Scgb1a1+,CD24low single cell 178


title: RNA-22B-3, RNAseq


title: ATRT Sample HSJD_EPIC_109


title: RNA-19P-3, RNAseq

value: PBMC


title: CEL211011EL_WT_2_ADT

description:
protein ADT
10x Genomics ADT
CEL211011EL_WT_2_ADT

value: spleen


title: CEL211011EL_WT_1_ADT

description:
protein ADT
10x Genomics ADT
CEL211011EL_WT_1_ADT

value: GEMM


title: Scgb1a1+,CD24low single cell 177


title: Medulloblastoma Sample HSJD_EPIC_121

value: Medulloblastoma


title: ATRT Sample HSJD_EPIC_106

value: SHH


title: RNA-19P-2, RNAseq


title: Scgb1a1+,CD24low single cell 180


title: Scgb1a1+,CD24low single cell 176


title: RNA-19P-1, RNAseq


title: ATRT Sample HSJD_EPIC_086


title: Scgb1a1+,CD24low single cell 173


title: Scgb1a1+,CD24low single cell 174


title: Scgb1a1+,CD24low single cell 175


title: RNA-19M-3, RNAseq

value: Bone marrow


title: T_WT_3

city: San Francisco

first: Robert

last: Raffai

state: California

address: 4150 Clement St

institute: University of California San Francisco

data_processing:
Aligned with STAR v 2.7.5c
Assembly: GRCm38
Supplementary files format and content: gene by read counts table text file

source_name: Spleen

growth_protocol: CD4+ T cells were collected from spleens of age-matched male mice that are 6- to 12-week-old. Cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, 1% GlutaMAX, and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA were collected using the Qiagen RNeasy Mini Kit.
Universal Plus mRNA-Seq library preparation kit

treatment_protocol: Cells were stimulated with anti-CD3/anti-CD28 beads and 5 ng/mL of recombinant murine IL-2 while also treated with 2 x 10^9 particles/mL of EKO-BMDM-exo, or WT-BMDM-exo, or PBS for 18 hours.

value: Spleen

value: CD4+ T cells

value: WT

tag: treatment 1

value: Stimulated w/ anti-CD3/anti-CD28 beads and 5 ng/mL murine IL-2

tag: treatment 2

value: WT-BMDM-exo


title: T_PBS_3

value: PBS


title: RNA-19M-2, RNAseq


title: Medulloblastoma Sample HSJD_EPIC_081

value: non-WNT/non-SHH

value: Fresh-Frozen


title: Scgb1a1+,CD24low single cell 172

tag: age


title: RNA-19M-1, RNAseq


title: Ependymoma Sample HSJD_EPIC_100

value: Ependymoma

value: EP


title: T_PBS_2


title: RNA-19L-3, RNAseq

value: Liver

value: 19 months


title: ATRT Sample HSJD_EPIC_082

value: ATRT


title: Ependymoma Sample HSJD_EPIC_077


title: Medulloblastoma Sample HSJD_EPIC_075


title: T_WT_1


title: T_PBS_1


title: T_WT_2


title: Scgb1a1+,CD24low single cell 171

value: 4 month


title: Scgb1a1+,CD24low single cell 169


title: RNA-19L-2, RNAseq


title: T_EKO_2

value: EKO-BMDM-exo


title: Scgb1a1+,CD24low single cell 170


title: Medulloblastoma Sample HSJD_EPIC_058

value: Medulloblastoma


title: T_EKO_3


title: ETMR Sample HSJD_EPIC_069

value: ETMR


title: RNA-19L-1, RNAseq


title: RNA-19H-3, RNAseq

value: Heart


title: Scgb1a1+,CD24low single cell 168


title: RNA-19H-2, RNAseq


title: Ependymoma Sample HSJD_EPIC_052

value: FFPE


title: T_EKO_1

value: Spleen

value: CD4+ T cells

value: WT


title: RNA-19H-1, RNAseq


title: Scgb1a1+,CD24low single cell 166


title: Scgb1a1+,CD24low single cell 167


title: Medulloblastoma Sample HSJD_EPIC_051


title: RNA-19B-3, RNAseq

value: Brain


title: Scgb1a1+,CD24low single cell 165


title: WT_BMDM_2

data_processing:
Reads aligned following exceRpt smallRNA-seq pipeline v.4.6.3
Assembly: mm9
Supplementary files format and content: read counts per miRNA table

growth_protocol: Bone marrow cells were collected from age-matched male mice that are 6- to 12-week-old. Cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% GlutaMAX, and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA were collected using the Qiagen RNeasy Mini Kit.
NEB SmallRNA Library Prep for Illumina Sequencing

treatment_protocol: Cells were treated with 25 ng/mL recombinant murine M-CSF every two days for six days total.

value: Bone marrow

value: Bone marrow derived macrophages

value: Macrophage differentiation w/ M-CSF


title: WT_BMDM_1


title: RNA-19B-2, RNAseq


title: Scgb1a1+,CD24low single cell 164


title: RNA-19B-1, RNAseq


title: EKO_BMDM_3

value: ApoE-KO


title: Scgb1a1+,CD24low single cell 163


title: RNA-12S-3, RNAseq

value: Sperm

value: 12 months


title: EKO_BMDM_2


title: RNA-22L-2, RNAseq

value: Liver

value: 22 months


title: Scgb1a1+,CD24low single cell 162

value: 4 month


title: Ependymoma Sample HSJD_EPIC_053

value: Ependymoma

value: EP

value: Fresh-Frozen


title: Scgb1a1+,CD24low single cell 161


title: RNA-12S-2, RNAseq


title: WT_BMDM_3


title: RNA-12S-1, RNAseq


title: Medulloblastoma Sample HSJD_EPIC_049

value: Medulloblastoma

value: non-WNT/non-SHH


title: Medulloblastoma Sample HSJD_EPIC_048


title: Medulloblastoma Sample HSJD_EPIC_047


title: Medulloblastoma Sample HSJD_EPIC_046


title: Medulloblastoma Sample HSJD_EPIC_050


title: Scgb1a1+,CD24low single cell 160


title: mpk7_ko3 imbibed seeds rep2

city: Shenzhen

first: Xi

last: Chen

address: No.97in Buxin road, Dapeng district, Shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.20.0, -z 4 -q 20 -u 30 -n 10).
Clean reads were mapped to the Arabidopsis reference genome using the software Hisat2 (version 2.1.0).
Feature Counts (version 2.0.1) was used to count the reads using these common parameters (-p -t exon -g gene_id).
Raw counts were normalized with DEseq2 (version 1.34.0) to compare gene expression in different samples.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include count values for each Sample

organism: Arabidopsis thaliana

source_name: seed

growth_protocol: Arabidopsis seeds were sown in a soil mixture and grown in a growth chamber (Hipoint, FH-1300) under a 16-h-light/8-h-dark cycle (23°C/20°C) with 55-60% humidity. Freshly harvested seeds were immediately used for seed dormancy and germination assay or stored in a cabinet (Huayuxiandai, HYXD-180KWS) with constant conditions (dark, 50% humidity, 22°C) for after-ripening treatment.

extract_protocol:
RNA was extracted from dry and imbibed seeds using FastPure Plant Total RNA Isolation Kit (Polysaccharides and Polyphenolics-rich) (Vazyme Biotech, Nanjing, China) according to the manufacturer’s instructions. RNA-Seq library preparation and sequencing were performed at Novogene Biotech
Library preparation and sequencing were completed at Novogene Biotech (Beijing, China) using an Illumina NovaSeq 6000-PE150

treatment_protocol: Freshly harvested seeds were immediately sampled (dry seeds) or imbibed in saturated filter paper for 6 h prior to sample (imbibed seeds).

value: seed

tag: ecotype

value: MPK7 Knock out

value: seeds after imbibition for 6 hours


title: RNA-12P-3, RNAseq

value: PBMC

tag: development stage


title: mpk7_ko3 imbibed seeds rep3


title: Scgb1a1+,CD24low single cell 159


title: Medulloblastoma Sample HSJD_EPIC_044


title: mpk7_ko3 imbibed seeds rep1


title: RNA-12P-2, RNAseq


title: Scgb1a1+,CD24low single cell 158


title: mkk3-1 imbibed seeds rep3

value: MKK3 knock out


title: RNA-12P-1, RNAseq


title: Scgb1a1+,CD24low single cell 157


title: Medulloblastoma Sample HSJD_EPIC_043

value: WNT


title: RNA-12M-3, RNAseq

value: Bone marrow


title: EKO_BMDM_1

value: Bone marrow derived macrophages

value: ApoE-KO

value: Macrophage differentiation w/ M-CSF


title: Medulloblastoma Sample HSJD_EPIC_042


title: mkk3-1 imbibed seeds rep2


title: Scgb1a1+,CD24low single cell 156


title: Medulloblastoma Sample HSJD_EPIC_041


title: mkk3-1 imbibed seeds rep1


title: RNA-12M-2, RNAseq

value: 12 months


title: Scgb1a1+,CD24low single cell 155

value: 4 month


title: RNA-12M-1, RNAseq


title: Col imbibed seeds rep3

value: WT


title: Medulloblastoma Sample HSJD_EPIC_045


title: Medulloblastoma Sample HSJD_EPIC_040


title: Scgb1a1+,CD24low single cell 154


title: Col imbibed seeds rep2


title: RNA-12L-3, RNAseq

value: Liver


title: Medulloblastoma Sample HSJD_EPIC_039

value: SHH

value: Fresh-Frozen


title: Medulloblastoma Sample HSJD_EPIC_038

value: Medulloblastoma

value: non-WNT/non-SHH


title: Scgb1a1+,CD24low single cell 153


title: Col imbibed seeds rep1

value: seed


title: Scgb1a1+,CD24low single cell 152


title: RNA-12L-2, RNAseq


title: Scgb1a1+,CD24low single cell 151


title: RNA-12L-1, RNAseq


title: Cerebellum Sample HSJD_EPIC_037

value: Cerebellum


title: mpk7_ko3 dry seeds rep3

value: MPK7 Knock out

value: freshly harvested dry seeds


title: RNA-12H-3, RNAseq

value: Heart


title: Medulloblastoma Sample HSJD_EPIC_036


title: mpk7_ko3 dry seeds rep2


title: Scgb1a1+,CD24low single cell 150


title: RNA-12H-2, RNAseq


title: mpk7_ko3 dry seeds rep1


title: Medulloblastoma Sample HSJD_EPIC_035


title: Scgb1a1+,CD24low single cell 149


title: Medulloblastoma Sample HSJD_EPIC_034


title: Scgb1a1+,CD24low single cell 148


title: mkk3-1 dry seeds rep3

value: MKK3 knock out


title: Medulloblastoma Sample HSJD_EPIC_033


title: mkk3-1 dry seeds rep2


title: Scgb1a1+,CD24low single cell 147


title: RNA-12B-2, RNAseq

value: Brain


title: RNA-12H-1, RNAseq


title: Scgb1a1+,CD24low single cell 146


title: Medulloblastoma Sample HSJD_EPIC_031


title: Col dry seeds rep3


title: Scgb1a1+,CD24low single cell 145


title: RNA-12B-1, RNAseq


title: control3

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

molecule: polyA RNA

source_name: cerebral cortex (bulk lysate)

extract_protocol:
frozen tissue was homogenized in Trizol, then RNA was extracted with an Invitrogen PureLink RNA extraction kit.
oligo-dT

value: cerebral cortex (bulk lysate)


title: Col dry seeds rep2


title: Medulloblastoma Sample HSJD_EPIC_030


title: Col dry seeds rep1


title: Medulloblastoma Sample HSJD_EPIC_028

value: WNT


title: Neuronal Bmal1KO 3


title: SHL2-sh3_FRAS202423562-1r

city: hongkong

first: Yasi

last: PAN

address: Rm701, LiKS Med Sci Bldg, PWH, Shatin

country: Hong Kong

institute: the Chinese University of Hong Kong

data_processing:
Illumina HiSeq 4000
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each samples
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: HKCI2 cell line

extract_protocol:
RNA was extracted and treated with DNase I. After passing quality control, the libraries were generated and sequenced with the Illumina HiSeq 4000 (PE150) according to the protocol from the company (Epibiotek).
Illumina HiSeq 4000

tag: cell line

value: HKCI2 cell line

value: NAFLD-HCC


title: Scgb1a1+,CD24low single cell 142

value: 4 month

tag: genotype


title: RNA-12B-3, RNAseq

value: 12 months


title: Scgb1a1+,CD24low single cell 143


title: SHL2-sh2_FRAS202423561-1r


title: Medulloblastoma Sample HSJD_EPIC_027


title: Neuronal Bmal1KO 1


title: control2


title: mkk3-1 dry seeds rep1

tag: treatment


title: Medulloblastoma Sample HSJD_EPIC_032


title: Medulloblastoma Sample HSJD_EPIC_026

value: SHH


title: SHL2-nc-2_FRAS202423560-1r


title: control1

tag: tissue


title: SHL2-nc-1_FRAS202423559-1r

tag: cell type


title: Scgb1a1+,CD24low single cell 140


title: Medulloblastoma Sample HSJD_EPIC_029

tag: sample type

value: Fresh-Frozen


title: Medulloblastoma Sample HSJD_EPIC_025

value: Medulloblastoma

tag: sample subtype


title: Scgb1a1+,CD24low single cell 144


title: Scgb1a1+,CD24low single cell 139


title: Medulloblastoma Sample HSJD_EPIC_024

value: non-WNT/non-SHH

tag: material


title: Scgb1a1+,CD24low single cell 138

tag: strain


title: Medulloblastoma Sample HSJD_EPIC_023


title: GS.789

city: Rotterdam

first: Martine

last: Lamfers

state: Zuid Holland

address: Wytemaweg 80

department: Neurosurgery

country: Netherlands

institute: Erasmus MC

data_processing:
Optical duplicates and adaptors were removed with clumpify and fastx-toolkit, respectively
reads were mapped to the human reference genome GRCh38 with STAR2.6
gene-expression matrices were generated with HTSeq
Assembly: GRCh38
Supplementary files format and content: Text files including count data for each Sample

source_name: Brain tumor

growth_protocol: GBM cell cultures were maintained in Neuro Sphere(NS) medium (DMEM-F12, Pen/strep 1%, B27 2%, bFGF 20 ng/mL, EGF 20 ng/mL and Heparin 5ug/mL) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using Trizol (ThermoFisher Scientific). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA stranded mRNA library prep kit following manufacturer's protocols.

value: Brain tumor

value: Glioblastoma

value: GBM - IDH WT

value: STUPP


title: GS.785


title: Neuronal Bmal1KO 2


title: Lungs, UC_3

city: Palo Alto

first: Avnesh

last: Thakor

state: Default

address: 3155 Porter Drive

institute: Stanford University

data_processing:
Sequenced reads were trimmed for adaptor sequence,
Then mapped to mouse genome Mus Musculus using HISTAT
HTSeq was used to generate the raw read counts
DESeq2 was used for differential gene expression analysis
Assembly: (GRCm39/mm39)
Supplementary files format and content: tab-delimited text file include FPKM values for all samples
Supplementary files format and content: tab-delimited text file include raw counts for all samples

source_name: Lungs

extract_protocol:
total RNA was extracted from each replicate using the RNAeasy minikit (qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lungs

value: LPS with hUC-MSCs


title: Scgb1a1+,CD24low single cell 141

source_name: Scgb1a1+,CD24low cell


title: GS.359


title: Medulloblastoma Sample HSJD_EPIC_022


title: GS.295


title: Medulloblastoma Sample HSJD_EPIC_021


title: Lungs, UC_1


title: Lungs, BM_4

value: LPS with hBM-MSCs


title: Scgb1a1+,CD24low single cell 135


title: Scgb1a1+,CD24low single cell 136


title: Lungs, BM_3


title: GS.851


title: Medulloblastoma Sample HSJD_EPIC_020


title: Medulloblastoma Sample HSJD_EPIC_019


title: Lungs, UC_4


title: Medulloblastoma Sample HSJD_EPIC_012

value: FFPE


title: Lungs, BM_2


title: Scgb1a1+,CD24low single cell 134


title: Scgb1a1+,CD24low single cell 133


title: Lungs, UC_2


title: Scgb1a1+,CD24low single cell 132


title: GS.828


title: GS.824


title: Scgb1a1+,CD24low single cell 131


title: GS.820


title: Medulloblastoma Sample HSJD_EPIC_009


title: Lungs, BM_1


title: GS.832


title: Ependymoma Sample HSJD_EPIC_006

value: Ependymoma

value: EP


title: Medulloblastoma Sample HSJD_EPIC_007

value: WNT


title: Lungs, AD_4

value: LPS with hAD-MSCs


title: Scgb1a1+,CD24low single cell 129

value: 4 month


title: GS.741


title: Scgb1a1+,CD24low single cell 130


title: Lungs, AD_3


title: Scgb1a1+,CD24low single cell 128


title: Lungs, LPS_4

value: LPS


title: Lungs, AD_2


title: GS.802


title: GS.636


title: Hic_Nitrogen-deprivation_N2_replicat1

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

institute: Hainan normal university

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean Hi-C data were first processed using HiC-Pro with minimal CIS distance of 4000 bp. Contact maps were constructed with bin sizes of 5kb, 10 kb, 20 kb, 40kb and 100 kb and converted to hic files (https://doi.org/10.1016/j.cels.2016.07.002) using HiC-Pro’s built-in script. The chromosome-scale heat maps were plotted using HiCPlotter. Significant intra-chromosomal interactions were identified with the program HICUPPS (with parameter settings -m 1024 -r 5000,10000 -k VC_SQRT -f 0.001,0.001 -p 4,2 -i 7,5 -t 0.02,1.5,1.75,2 -d 20000,20000). Significant interactions were merged within replicates using custom scripts. Differential interactions were identified using edgeR (quasi-likelihood method with p value of 0.2). Obtained interactions combined with other genomic datasets were visualized using Sushi.
Assembly: Nannochloropsis oceanica IMET1

organism: Nannochloropsis oceanica strain IMET1

source_name: Cells

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into the modified f/2 liquid medium, which was prepared with 35 g L-1 sea salt (Realocean, USA), 1 g L-1 NaNO3, 67 mg L-1 NaH2PO4*H2O, 3.65 mg L-1 FeCl3*6H2O, 4.37 mg l-1 Na2EDTA*2H2O, trace metal mix (0.0196 mg L-1 CuSO4*5H2O, 0.0126 mg L-1 NaMoO4*2H2O, 0.044 mg L-1 ZnSO4*7H2O, 0.01mg L-1 CoCl2, and 0.36 mg L-1 MnCl2*4H2O), and vitamin mix (2.5 µg L-1 VB12, 2.5 µg L-1 biotin, and 0.5 µg L-1 thiamine HCl).The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm).

extract_protocol:
For Hi-C experiments in N. oceanica, about 2 g samples were ground to powder in liquid nitrogen for the Hi-C experiment. Chromatin extraction was performed as described previously method. The procedure for the Hi-C experiment, including chromatin digestion, labelling of DNA ends, DNA ligation, purification and fragmentation, was as described previously(cell for hi-c method). DNA libraries were constructed using an Illumina TruSeq DNA Sample Prep Kit and sequenced on an Illumina HiSeq 3000 system. Hi-C experiments and sequencing were performed with two biological replicates.  Hi-C read mapping and normalization.
Hic libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm). The seed cultures were bubbled with air-level CO2. At the logarithmic phase (OD750=2.5), cells were harvested by centrifugation, one was sampled for RNA extraction as control (C0) with three replicates and the other was washed with fresh medium (nitrogen-free) for three times before being used for the following experiments. Cell pellets were inoculated into Nitrogen-free (for sampling of mRNA-seq, ChIP-seq and HiC-seq) and Nitrogen-repletion f/2 medium (for physiological measurement). Cultures started with the same initial cell concentration of OD750 = 2.5 and were exposed to continuous illumination of 50±5 μmol m−2 s−1. Cell aliquots were collected  for sampling of mRNA-seq, ChIP-seq and HiC-seq after being transferred to the designated conditions for one and two days  as nitrogen-deprivation samples (N1 and N2) with three replicates

value: Nitrogen-deprivation for 2 days


title: Medulloblastoma Sample HSJD_EPIC_005

value: Medulloblastoma

value: Fresh-Frozen


title: Ependymomaendymoma Sample HSJD_EPIC_004


title: Scgb1a1+,CD24low single cell 127


title: Lungs, LPS_5


title: Hic_Nitrogen-deprivation_N2_replicat2


title: GS.507

value: Brain tumor


title: Lungs, LPS_2


title: Hic_Nitrogen-deprivation_N1_replicat2

value: Nitrogen-deprivation for 1 day


title: Scgb1a1+,CD24low single cell 124


title: GS.502

value: Glioblastoma

value: GBM - IDH WT


title: Scgb1a1+,CD24low single cell 125


title: Lungs, AD_1

value: Lungs


title: Hic_Nitrogen-deprivation_N1_replicat1


title: Scgb1a1+,CD24low single cell 126


title: GS.353

value: STUPP


title: GS.944


title: Lungs, C_3

value: No treatment


title: Lungs, LPS_3


title: Scgb1a1+,CD24low single cell 122


title: GS.799


title: Hic_Nitrogen-repletion_C0_replicat2

value: Nitrogen-repletion


title: Hic_Nitrogen-repletion_C0_replicat1


title: Lungs, LPS_1


title: Lungs, C_2


title: GS.786


title: Scgb1a1+,CD24low single cell 120


title: GS.365


title: Scgb1a1+,CD24low single cell 137


title: Lungs, C_1


title: Scgb1a1+,CD24low single cell 119


title: Scgb1a1+,CD24low single cell 121


title: seedlings, RNAPII_S5P_rep1

city: Regensburg

first: Simon

last: Obermeyer

address: Universitätsstraße 31

country: Germany

institute: University Regensburg

data_processing:
Reads were trimmed using Trimmomatic (v0.39)  followed by alignment to the TAIR10
genome (https://www.arabidopsis.org/) using Bowtie2  using the preset mode --local --
very-sensitive-local. Alignment files were converted to .bam files containing only alignments
with MAPQ score >10, sorted and indexed using the samtools suite (v1.16.1). Coverage
tracks were calculated using deepTools ‘bamCoverage’. Peaks were called using the MACS3 callpeak function with RNAPII-S2P and RNAPII-S5P as control, respectively, with the following arguments -g 119481543 -B -q 0.01 --nomodel.
Assembly: TAIR10
Supplementary files format and content: coverage tracks
Supplementary files format and content: peak files

source_name: seedlings

growth_protocol: Seeds of Arabidopsis thaliana Col-0 were sown on solid 0.5x MS medium and grown a plant incubator with long day settings with 16h light (110 μmol∙m-2·s-1) at 21°C and 8h darkness at 18°C.

extract_protocol:
Arabidopsis plants were crosslinked with formaldehyde and used for isolation of nuclei, before chromatin was sheared using a Bioruptor Pico device. Immunoprecipitation was carried out using magnetic Dynabeads Protein A. Elongation factor ChIPs were performed with previously described antibodies directed against purified, recombinant domains of elongation factors
Libraries were prepared using the NEBnext UltraII Library preparation kit with 6bp NEBNext Multiplex Oligonucleotides for Illumina according to the manufacturer

treatment_protocol: For heat stress treatment the plates were transferred to a water bath set to 44°C for 10 min and snap frozen in liquid nitrogen

value: seedlings

tag: chip antibody


title: seedlings, RNAPII_S5P_rep2


title: GS.772


title: GS.691


title: Scgb1a1+,CD24low single cell 123


title: seedlings, RNAPII_S2P_rep2


title: GS.627


title: seedlings, RNAPII_S2P_rep1


title: Myonuclei, Muscle Overload, snRNA-Seq, rep1

city: Cincinnati

first: Douglas

last: Millay

state: OH

address: 3333 Burnet Ave Cincinnati, OH 45229

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Cellranger/5.0.1
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Quality control, data normalization, gene expression visualization, integration, and dimensionality reduction was performed using Seurat/4.3.0 SCTransform workflow.
Assembly: mm10
Supplementary files format and content: RDS

molecule: nuclear RNA

source_name: Myonuclei, Muscle Overload

growth_protocol: HSArtTA; TREH2B-GFP mice were fed with Dox diet five days prior to synergist ablation, then isolated myonuclei one week after surgery.

extract_protocol: Chromium Next GEM Single Cell 3Ê¹ Kit v3.1

treatment_protocol: Muscles were obtained from mice and then minced, homogenized, and processed through a series of steps. The nuclei were sorted using a FACS cell sorter. Further details could be found in method session in this paper.

value: Skeletal muscle

tag: muscle type

value: Plantaris

value: Myonuclei

value: HSArtTA; TRE-H2B-GFP

value: Muscle Overload

tag: gender

value: Male


title: Myonuclei, Sham, snRNA-Seq, rep1

source_name: Myonuclei, Sham

value: Sham


title: Scgb1a1+,CD24low single cell 117

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Genome_build: mm10
Supplementary_files_format_and_content: The detected number of RNA moelcules per well (i.e., single cell)  for each gene is listed.

value: 4 month


title: seedlings, RNAPII_INPUT

description: input


title: Myonuclei, Sham, RNA-Seq, rep4

description:
all_transcript_counts.RDS
sample-metadata.csv

data_processing:
nf-core/rnaseq v3.11.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt/v3.4
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Ribosomal RNA sequences were subsequently removed from the aligned data using SortMeRNA v4.3.4
The resulting alignments were sorted and indexed using SAMtools v1.16.1
Transcript quantification was performed using Salmon/1.9.0.
Transcripts were annotated using a modified GTF file obtained from gencode (vM24) containing both intronic and exonic regions for genes.
Reads were imported into DESeq2 using the tximport command from the tximport package. All differential expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: RDS

growth_protocol: Pax7rtTA; TREH2B-GFP mice were fed with Dox diet twelve days without surgery performed.

extract_protocol:
mRNA isolation was performed using the Direct-zol RNA Microprep kit (Zymo research R2060).
RNA libraries were prepared using Nextera XT Sample preparation kit

value: Pax7rtTA; TRE-H2B-GFP


title: Myonuclei, Muscle Overload, snRNA-Seq, rep2


title: GS.607

value: Brain tumor


title: GS.598

value: Glioblastoma


title: seedlings, spt16_rep4

description:
spt16_coverage.bw
spt16_S2P_summits.bed
spt16_S5P_summits.bed


title: Myonuclei, Sham, RNA-Seq, rep3

data_processing:
nf-core/rnaseq v3.11.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt/v3.4
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR v/2.7.9a
Ribosomal RNA sequences were subsequently removed from the aligned data using SortMeRNA v4.3.4
The resulting alignments were sorted and indexed using SAMtools v1.16.1
Transcript quantification was performed using Salmon/1.9.0.
Transcripts were annotated using a modified GTF file obtained from gencode (vM24) containing both intronic and exonic regions for genes.
Reads were imported into DESeq2 using the tximport command from the tximport package. All differential expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: RDS


title: Scgb1a1+,CD24low single cell 116

extract_protocol:
RNAs from cell lysate in each well was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.


title: siRNA of INO80 #3

city: Tokyo

first: Imari

last: Mimura

address: 7-3-1 Hongo Bunkyo-ku

institute: The University of Tokyo

data_processing:
Remove low quality reads to make adaptor sequences
Mapping for Hisat2/v2.0.1
Gene expression counting (HT-seq/V 0.6.1)
Compare gene expression between groups(DEGSeq/V1.38.0)
Assembly: Human hg19
Supplementary files format and content: .gz file

source_name: Human Kidney-2

growth_protocol: DMEM/H12, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2.0 ug of total RNA was used for the construction of sequencing libraries.
Total RNA 500ng was used making poly-A selection.RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic isolation module following manufacturer's protocols. cDNA synthesis and libraries for NGS was performed using NEBNext Ultra II Directional RNA Library Prep Kit. NGS was illumina Hiseq 2×150bp. Pair-end sequencing ; 20,000,000reads for one sample.

treatment_protocol: transfection with RNAiMax for 48hours using siRNA of INO80.

value: Human Kidney-2

value: renal proximal tubular cell

value: knockdown

value: siRNA of INO80 knockdown


title: seedlings, spt16_rep3


title: siRNA of INO80 #2


title: Myonuclei, Sham, RNA-Seq, rep2


title: Scgb1a1+,CD24low single cell 114


title: seedlings, spt16_rep2


title: Myonuclei, Sham, RNA-Seq, rep1


title: siRNA of INO80 #1


title: Scgb1a1+,CD24low single cell 113


title: seedlings, spt16_rep1


title: Scgb1a1+,CD24low single cell 118


title: seedlings, spt16_INPUT

description: input


title: siRNA of control #3

value: WT

value: siRNA of control knockdown


title: Myonuclei, Muscle Overload, Mymk KO, RNA-Seq, rep3

source_name: Myonuclei, Muscle Overload, Mymk KO

growth_protocol: MyomakerloxP/loxP; Pax7CreER mice were treated with tamoxifen  five days prior to synergist ablation, then isolated myonuclei one week after surgery.

value: Skeletal muscle

value: MyomakerloxP/loxP; Pax7CreER

value: Muscle Overload, Mymk KO


title: Scgb1a1+,CD24low single cell 111


title: Scgb1a1+,CD24low single cell 115


title: Myonuclei, Muscle Overload, Mymk KO, RNA-Seq, rep2

value: Plantaris

value: Myonuclei


title: siRNA of control #2


title: siRNA of control #1


title: Scgb1a1+,CD24low single cell 110


title: Scgb1a1+,CD24low single cell 109


title: NU01308 SYC176

city: Chicago

first: Wei

last: Zhang

address: 680 N Lake Shore Drive, Suite 1400

institute: Northwestern University

description:
NU01308
Ribo-Zero Transcriptome

data_processing: Raw sequencing reads were trimmed and filtered for low-quality bases and reads (quality score  20 for a minimum of 90% bases) using the FASTX Toolkit (v 0.0.14), followed by alignment to the human genome reference (GRCh37/hg19 without chromosome X, Y and Mitochondria) using the spliced aligner Tophat (v 2.1.0) with the default paired-end mode. Read pairs were concordantly aligned with ≤ 2 mismatches. Aligned read pairs with mapping quality score ≥ 20 were counted for genomic features according to the start and end coordinates derived from the ENCODE-derived annotation files (hg19) using FeatureCounts from Subread (v 1.6.1) with strand information.

source_name: Tissue

extract_protocol:
Total RNA was isolated (~1 ug/sample ) , followed by treatment with the Ribo-Zero Gold rRNA Removal Kit (Illumina, Inc., USA) . The cDNA libraries were prepared using the TrueSeq Stranded Total RNA Library Prep Kit (Illumina, Inc., USA).
The next-generation sequencing (NGS) was performed on the Illumina HiSeq 4000 platform (PE50) at the University of Chicago Genomics Facility. Approximately 24 million read pairs were generated from each library.

tag: tissue type

value: GBM

tag: population

value: White


title: seedlings, ssrp1_rep2

description:
ssrp1_coverage.bw
ssrp1_S2P_summits.bed
ssrp1_S5P_summits.bed

value: seedlings


title: seedlings, ssrp1_rep4


title: Myonuclei, Muscle Overload, GFP-, RNA-Seq, rep3

source_name: Myonuclei, Muscle Overload, GFP-

growth_protocol: Pax7rtTA; TREH2B-GFP mice were fed with Dox diet five days prior to synergist ablation, then isolated myonuclei one week after surgery.

value: Pax7rtTA; TRE-H2B-GFP

value: Muscle Overload, GFP-

value: Male


title: Scgb1a1+,CD24low single cell 108

city: Suita

first: Katsuyuki

last: Shiroguchi

address: 6-2-3 Furuedai

institute: RIKEN

tag: age

value: 4 month


title: seedlings, ssrp1_rep1

tag: ecotype


title: NU00681 SYC143

description:
NU00681
Ribo-Zero Transcriptome

value: More than one race


title: Scgb1a1+,CD24low single cell 112


title: Scgb1a1+,CD24low single cell 107


title: HB13151 SYC82

description:
HB13151
Ribo-Zero Transcriptome

value: Normal


title: seedlings, ssrp1_INPUT

description: input


title: Scgb1a1+,CD24low single cell 106


title: Myonuclei, Muscle Overload, GFP+, RNA-Seq, rep3

source_name: Myonuclei, Muscle Overload, GFP+

value: Muscle Overload, GFP+


title: Scgb1a1+,CD24low single cell 105


title: NU01249 SYC173

description:
NU01249
Ribo-Zero Transcriptome


title: Myonuclei, Muscle Overload, Mymk KO, RNA-Seq, rep1


title: NU01251 SYC174

description:
NU01251
Ribo-Zero Transcriptome


title: seedlings, elf7_rep4

description:
elf7_coverage.bw
elf7_S2P_summits.bed
elf7_S5P_summits.bed


title: Myonuclei, Muscle Overload, GFP+, RNA-Seq, rep2


title: Scgb1a1+,CD24low single cell 104


title: seedlings, ssrp1_rep3


title: Myonuclei, Muscle Overload, GFP+, RNA-Seq, rep1

growth_protocol: Pax7rtTA; TREH2B-GFP mice were treated with Dox from P18 to P28

treatment_protocol: Muscles were obtained from mice and then minced, homogenized, and processed through a series of steps. The nuclei were then labeled with anti-PCM1 and further processed before finally using a FACS cell sorter to separate the PCM1-labeled myonuclei fractions. Further details could be found in method session in this paper.


title: Scgb1a1+,CD24low single cell 103


title: NU01139 SYC90

description:
NU01139
Ribo-Zero Transcriptome


title: seedlings, elf7_rep2


title: seedlings, elf7_rep1


title: Myonuclei, GFP-, RNA-Seq, rep2

source_name: Myonuclei, GFP-

value: TA + Gastroc

value: GFP-

value: pooled male and female


title: Myonuclei, Muscle Overload, GFP-, RNA-Seq, rep2

data_processing:
nf-core/rnaseq v3.11.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR v/2.7.9a
Ribosomal RNA sequences were subsequently removed from the aligned data using SortMeRNA v4.3.4
The resulting alignments were sorted and indexed using SAMtools v1.16.1
Transcript quantification was performed using Salmon/1.9.0.
Transcripts were annotated using a modified GTF file obtained from gencode (vM24) containing both intronic and exonic regions for genes.
Reads were imported into DESeq2 using the tximport command from the tximport package. All differential expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: RDS

value: Skeletal muscle


title: Scgb1a1+,CD24low single cell 102


title: NU01126 SYC172

description:
NU01126
Ribo-Zero Transcriptome


title: Myonuclei, GFP-, RNA-Seq, rep3


title: Myonuclei, Muscle Overload, GFP-, RNA-Seq, rep1


title: Scgb1a1+,CD24low single cell 101


title: NU01004 SYC167

description:
NU01004
Ribo-Zero Transcriptome


title: NU00983 SYC166

description:
NU00983
Ribo-Zero Transcriptome


title: seedlings, elf7_INPUT

description: input


title: Scgb1a1+,CD24low single cell 100


title: seedlings, spt5_rep4

description:
spt5_coverage.bw
spt5_S2P_summits.bed
spt5_S5P_summits.bed


title: NU00951 SYC163

description:
NU00951
Ribo-Zero Transcriptome

value: Refused, not reported


title: seedlings, spt5_rep3


title: Scgb1a1+,CD24low single cell 99


title: Myonuclei, GFP+, RNA-Seq, rep3

source_name: Myonuclei, GFP+

value: GFP+


title: seedlings, elf7_rep3


title: Myonuclei, GFP+, RNA-Seq, rep2

value: Myonuclei


title: seedlings, spt5_rep2


title: Myonuclei, GFP+, RNA-Seq, rep1


title: NU00919 SYC162

description:
NU00919
Ribo-Zero Transcriptome

value: GBM


title: Scgb1a1+,CD24low single cell 98


title: NU00915 SYC161

description:
NU00915
Ribo-Zero Transcriptome

value: White


title: seedlings, spt5_rep1

value: seedlings


title: Scgb1a1+,CD24low single cell 97


title: seedlings, spt5_INPUT

description: input


title: Scgb1a1+,CD24low single cell 95


title: Myonuclei, GFP-, RNA-Seq, rep1

value: Pax7rtTA; TRE-H2B-GFP


title: Scgb1a1+,CD24low single cell 96


title: NU00860 SYC159

description:
NU00860
Ribo-Zero Transcriptome

value: Unknown


title: genomic DNA from peripheral blood leukocytes_SRS2

city: Seongnam-si

first: Hwa Young

last: Kim

state: Gyeonggi-do

address: 82, Gumi-ro 173 Beon-gil

country: South Korea

institute: Seoul National University Bundang Hospital

description: peripheral blood leukocytes sample of genomic imprinting disorders (SRS, IC1 loss of methylation)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEpic Beadchip kits using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Ilumina iScan scanner

data_processing:
Illumina GenomeStudio v2011.1
Average Beta, Unmethylated and methylated signal intensities in supplementary file

source_name: peripheral blood leukocytes 19

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood samples using Qiagen DNeasy Kit according to standard instructions

value: Male

value: peripheral blood leukocytes

tag: disease state

value: SRS, IC1 loss of methylation


title: genomic DNA from peripheral blood leukocytes_SRS1

source_name: peripheral blood leukocytes 18

value: Female


title: NU00859 SYC158

description:
NU00859
Ribo-Zero Transcriptome


title: BMDM, MPLA, 4h, biol rep 2

city: Nashville

first: Margaret

middle: Ann

last: Mcbride

state: Tennessee

address: 1211 Medical Center Drive

department: Anesthesiology

institute: Vanderbilt University Medical Center

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. STAR-software was used to align reads to the reference genome. Expression levels were quantified using FPKM.
Reads that met the following citeria were removed. 1. reads containing adapters; 2., reads containing N > 10% (N represents base that could not be determined); 3. low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Assembly: mm10
Supplementary files format and content: excel file including raw counts for each sample
Supplementary files format and content: excel file including FPKM  for each sample

source_name: bone marrow-derived macrophage

growth_protocol: Murine bone marrow-servied macrophages were cultured from whole bone marrow and maintained in RPMI 1640 supplemented with 10% FBS, 1% antibiotic/anitbmycotic solution, and 10ug/mL murine macrophage colony stimulating factor

extract_protocol:
Total RNA was isolated under an RNase-free environment using the RNeasy Mini Kit (Qiagen, Hilden, Germany) which included a DNAse treatment step. Total RNA quality and concentration were verified with a Thermo Scientific NanoDrop 2000 spectrophotometer.
Sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s protocol.

treatment_protocol: BMDM were treated with β-glucan (5μg/mL), MPLA (1μg/mL), or lactated Ringers solution or DMSO (1uL/mL) in supplemnted RPMI for 4h, 24h, or 3 days (3dp) prior to RNA harvest. The 3dp groups were treated as specifiec for 24 hours, after which the BMDM were washed with PBS and the supplemented RPMI without the treatment was replaced.  The BMDM then rested for 3 additional days prior to RNA harvest.

value: bone marrow-derived macrophage

tag: Sex

value: WT

value: 4hrs post 1microg/mL MPLA


title: BMDM, MPLA, 24h, biol rep 2

tag: genotype

value: 24hrs post 1microg/mL MPLA


title: NU00845 SYC157

description:
NU00845
Ribo-Zero Transcriptome


title: genomic DNA from peripheral blood leukocytes_BWS13

description: peripheral blood leukocytes sample of genomic imprinting disorders (BWS, IC1 gain of methylation)

source_name: peripheral blood leukocytes 17

value: BWS, IC1 gain of methylation


title: Scgb1a1+,CD24low single cell 94

value: 4 month


title: BMDM, MPLA, 24h, biol rep 1

tag: treatment


title: BMDM, MPLA, 4h, biol rep 1


title: genomic DNA from peripheral blood leukocytes_BWS12

description: peripheral blood leukocytes sample of genomic imprinting disorders (BWS, IC2 loss of methylation)

source_name: peripheral blood leukocytes 16

tag: tissue

value: BWS, IC2 loss of methylation


title: Scgb1a1+,CD24low single cell 93

source_name: Scgb1a1+,CD24low cell


title: Scgb1a1+,CD24low single cell 92


title: NU00839 SYC155

description:
NU00839
Ribo-Zero Transcriptome


title: BMDM, DMSO control, 3dp, biol rep 1

tag: cell type

value: 3 days post 0.1% DMSO for 24 hrs


title: genomic DNA from peripheral blood leukocytes_BWS11

source_name: peripheral blood leukocytes 15


title: BMDM, MPLA then LPS, biol rep 3

value: 3 days post 1microg/mL MPLA for 24 hours, then restimulated 4 hours prior to harvest with 100ng/mL LPS


title: BMDM,DMSO control, 3dp, biol rep 2


title: Scgb1a1+,CD24low single cell 91


title: genomic DNA from peripheral blood leukocytes_BWS10

source_name: peripheral blood leukocytes 14


title: Scgb1a1+,CD24low single cell 90


title: BMDM, MPLA then LPS, biol rep 2


title: NU00866 SYC160

description:
NU00866
Ribo-Zero Transcriptome

value: GBM


title: NU00835 SYC154

description:
NU00835
Ribo-Zero Transcriptome

value: White


title: NU00826 SYC153

description:
NU00826
Ribo-Zero Transcriptome

value: Black


title: BMDM, MPLA then LPS, biol rep 1


title: genomic DNA from peripheral blood leukocytes_BWS8

source_name: peripheral blood leukocytes 12


title: Scgb1a1+,CD24low single cell 89


title: genomic DNA from peripheral blood leukocytes_BWS9

source_name: peripheral blood leukocytes 13


title: Scgb1a1+,CD24low single cell 88


title: NU00793 SYC152

description:
NU00793
Ribo-Zero Transcriptome


title: BMDM, LPS, 4hr, biol rep 6

value: 4hrs post 100ng/mL LPS


title: Scgb1a1+,CD24low single cell 87


title: NU00773 SYC150

description:
NU00773
Ribo-Zero Transcriptome

value: Refused, not reported


title: BMDM, LPS, 4hr, biol rep 5

value: Male


title: NU00764 SYC149

description:
NU00764
Ribo-Zero Transcriptome


title: Scgb1a1+,CD24low single cell 86


title: genomic DNA from peripheral blood leukocytes_BWS6

source_name: peripheral blood leukocytes 10

value: peripheral blood leukocytes


title: NU00843 SYC156

description:
NU00843
Ribo-Zero Transcriptome


title: NU00734 SYC146

description:
NU00734
Ribo-Zero Transcriptome


title: genomic DNA from peripheral blood leukocytes_BWS4

source_name: peripheral blood leukocytes 8

value: Female


title: NU00715 SYC145

description:
NU00715
Ribo-Zero Transcriptome

source_name: Tissue


title: BMDM, LPS, 4hr, biol rep 4

value: bone marrow-derived macrophage


title: Scgb1a1+,CD24low single cell 84


title: BMDM, MPLA, 3dp, biol rep 2

value: WT

value: 3 days post 1microg/mL MPLA for 24 hours


title: BMDM, MPLA, 3dp, biol rep 3


title: NU00696 SYC144

description:
NU00696
Ribo-Zero Transcriptome

value: More than one race


title: genomic DNA from peripheral blood leukocytes_BWS3

source_name: peripheral blood leukocytes 7


title: Scgb1a1+,CD24low single cell 83


title: BMDM, MPLA, 3dp, biol rep 1


title: NU00625 SYC142

description:
NU00625
Ribo-Zero Transcriptome

value: Unknown


title: genomic DNA from peripheral blood leukocytes_BWS2

source_name: peripheral blood leukocytes 6


title: genomic DNA from peripheral blood leukocytes_BWS7

source_name: peripheral blood leukocytes 11


title: BMDM, NS control, 3dp, biol rep 6

value: 3 days post 0.1% NS for 24 hrs


title: NU00620 SYC141

description:
NU00620
Ribo-Zero Transcriptome


title: genomic DNA from peripheral blood leukocytes_BWS1

source_name: peripheral blood leukocytes 5

value: BWS, IC2 loss of methylation


title: BMDM, NS control, 3dp, biol rep 5


title: Scgb1a1+,CD24low single cell 82

value: 4 month


title: NU00544 SYC139

description:
NU00544
Ribo-Zero Transcriptome


title: NU00483 SYC137

description:
NU00483
Ribo-Zero Transcriptome


title: Scgb1a1+,CD24low single cell 80


title: genomic DNA from peripheral blood leukocytes_BWS5

source_name: peripheral blood leukocytes 9


title: BMDM, NS control, 3dp, biol rep 4


title: Scgb1a1+,CD24low single cell 85


title: genomic DNA from peripheral blood leukocytes_control 3

description: normal peripheral blood leukocytes sample

source_name: peripheral blood leukocytes 3

value: normal


title: genomic DNA from peripheral blood leukocytes_control 2

source_name: peripheral blood leukocytes 2


title: NU00440 SYC134

description:
NU00440
Ribo-Zero Transcriptome

value: GBM


title: BMDM, β-glucan then LPS, biol rep 3

source_name: bone marrow-derived macrophage

value: 3 days post 5microg/mL Beta-Glucan for 24 hours, then restimulated 4 hours prior to harvest with 100ng/mL LPS


title: BMDM, β-glucan then LPS, biol rep 2


title: Scgb1a1+,CD24low single cell 78


title: NU00434 SYC133

description:
NU00434
Ribo-Zero Transcriptome


title: genomic DNA from peripheral blood leukocytes_control 1

source_name: peripheral blood leukocytes 1


title: BMDM, β-glucan then LPS, biol rep 1


title: Scgb1a1+,CD24low single cell 77

source_name: Scgb1a1+,CD24low cell


title: NU00423 SYC130

description:
NU00423
Ribo-Zero Transcriptome

value: White


title: NU00413 SYC129

description:
NU00413
Ribo-Zero Transcriptome


title: Scgb1a1+,CD24low single cell 76


title: Scgb1a1+,CD24low single cell 81


title: BMDM, LPS, 4hr, biol rep 3

value: 4hrs post 100ng/mL LPS


title: Scgb1a1+,CD24low single cell 75


title: BMDM, LPS, 4hr, biol rep 2