title: KYSE180_BRD4

value: BRD4 (Diagenode, C15410337)


title: Lg63_P2

status: Public on Mar 05 2021

type: SRA

city: Shenzhen

first: Yizhe

last: Tang

state: Guangdong Province

address: 3002 Sun Gang West Road, Futian District

country: China

institute: Shenzhen Second People's Hospital Department of Geriatrics

description:
LP
gene_count.txt
gene_fpkm.txt

library_source: transcriptomic

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: gene_fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: gene_count.txt: Tab-delimited text file includes raw gene counts for every gene and every sample.

molecule: total RNA

organism: Mus musculus

source_name: hypothalamus

growth_protocol: Five-week-old ICR female mice were fed on a control low fat diet (LFD, 10% kcal fat) or high-fat high-sucrose (HFHS, 45% kcal fat with sucrose) diet for five weeks before mating. The dams were keeping with the same diets of the pregestational one during the gestation and lactation. Ten pups per litter were adapted on the day of production.

extract_protocol:
Mice hypothalamus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent with 3 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

treatment_protocol: During the postnatal (P) 4 to 16, pups from dams feeding with LFD or HFHS were peripherally injected with PBS (vehicle) or 4-PBA daily. Thus there were offspring from LFD fed dams receiving vehicle (referred to as LP) or from HFHS fed dams receiving vehicle (referred to as HP) or 4-PBA (referred to as HA).

tag: strain

value: ICR

tag: genotype

value: wild type

tag: tissue

value: hypothalamus

tag: age

value: postnatal day 21

tag: Sex

value: male

tag: treatment

value: LFD lactation+neonatal PBS


title: Oral Cancer, Buccal Mucosa [RCC_OC_18]

type: RNA

city: Thiruvananthapuram

first: S

last: Kannan

state: Kerala

address: Medical College Campus

department: Cancer Research

country: India

institute: Regional Cancer Centre

description: miRNA Expression

hyb_protocol: The dried Cy3 labelled sample was re-suspended in nuclease-free water, denatured and mixed with the hybridizing buffer. Incubated the mixture at 100°C for 5 minutes and immediately snap cooled in ice. The hybridizing mixture was then pipetted onto the microarray slide installed in the hybridization cassette. Then the cassette was kept for hybridization in the rotary oven at 55°C for 20 hours. After the hybridization, slides were washed sequentially with pre-warmed gene expression washing buffers 1 &2.

scan_protocol: Hybridized microarrays were scanned with a DNA microarray scanner (Agilent G2565BA) and features were extracted using the Agilent Feature Extraction (AFE) image analysis tool (version A.9.5.3) with default protocols and settings.

data_processing: Data pre-processing and differential expression analysis of the microRNA and gene expression data were done in R using available Bioconductor AgiMicroRna package.The Total Gene Signal provided by the Agilent Feature Extraction image analysis software was used for data analysis. Data were normalized between arrays using the quantile method.The image analysis software attached a flag to each feature that identifies different quantification errors of the signal and which was used to filter out microRNAs data that do not reach a minimum quality.

organism: Homo sapiens

source_name: Tissue-Cancer-Buccal

label_protocol: The miRNA Complete Labeling Kit of Agilent was used to generates fluorescently-labeled miRNA with a sample input of 100 ng of total RNA. This method involved the ligation of one Cyanine 3-pCp molecule to the 3' end of a RNA molecule with greater than 90% efficiency.

extract_protocol: Total RNA was prepared from tissue samples using miRVana miRNA isolation kit as per manufacturer’s protocol. The quality and quantity of the isolated RNA was checked using UV-Vis Spectrophotometer.

treatment_protocol: After obtaining the signed informed consent from the eligible patients, incision biopsy of tumor was taken from each patient either during the investigative biopsy procedure or surgical excision of the lesion. Normal mucosa was also collected from patients undergoing oral and maxillofacial surgery for reasons other than cancer.

value: Buccal Mucosa

tag: gender

value: Female


title: Normal, Buccal Mucosa [RCC_OC_17]

description: miRNA Expression

source_name: Tissue-Normal-Buccal


title: Oral Cancer, Buccal Mucosa [RCC_OC_16]

description: miRNA Expression


title: Normal, Tongue Mucosa [RCC_OC_22]

description: miRNA Expression

source_name: Tissue-Normal-Tongue

value: Tongue Mucosa

value: Male


title: Hg43_A1

description:
HA
gene_count.txt
gene_fpkm.txt

value: HFHS lactation+neonatal 4-PBA


title: Colon_tissue_MDF-SD39C08

city: New York

first: Simone

last: Dallari

state: NY

address: 550 1st Ave

country: USA

institute: New York University Grossman School of Medicine

data_processing:
Reads were mapped by Bowtie (v2.3.1) to the mm10 reference genome
Normalized count tables were generated in R (v3.5.1) using DESeq2 (v1.18.1)
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample, obtained from DESeq2

source_name: Colon

growth_protocol: Piece of colonic (colon mid-section) and small intestinal (duodenum, jejunum, and ileum mid-section combined) were collected, snap frozen, and conserved at -80 until extraction

extract_protocol:
RNA for each sample was then isolated with the RNeasy Plus Mini Kit (Qiagen) following the protocol with on column DNAse Digestion (Qiagen).
RNA libraries were prepared using standard CelSeq2 protocols.

treatment_protocol: Germ free mice were left uninfected or mono infected with several enteric viruses. Tissues were collected 28 days post infection

value: Colon

tag: infection

value: MDF


title: Lg42_P1

description:
LP
gene_count.txt
gene_fpkm.txt


title: Hg13_P3

description:
HP
gene_count.txt
gene_fpkm.txt

value: HFHS lactation+neonatal PBS


title: KYSE180_BRDT

first: Xin

last: Wang

state: Guangdong

address: 1068, Xueyuan Road

department: Institute of Synthetic Biology

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

library_source: genomic

data_processing:
Alignment was done using Bowtie (1.0.0) with parameters: --chunkmbs 200 -a -m 1 --best --strata.
Sam/bam files were processed using samtools (1.9). Bigwig files were generated using bamCoverage from Deeptools (3.3.2).
Peaks were called using MACS2 (2.1.1). Broad peak calling mode was used for BRDT, BRD4 and histone modifications while narrow peak calling mode was used for p63.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing signal strength (normalized to RPKM) across genome.

molecule: genomic DNA

source_name: Esophageal squamous cell carcinoma

growth_protocol: KYSE180 cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% Penicillin and Streptomycin.

extract_protocol:
Cells were crosslinked using 1% formaldehyde for 20 minutes. Subsequently, fixed cells were lysed, sheared and subjected to immunoprecipitation with respective antibodies. The immunocomplexes were captured and the DNA extraction was done using phenol/chloroform/isoamyl.
ChIP-seq libraries were constructed using the KAPA HyperPrep kit according to the manufacturer’s manual.

tag: cell line

value: ESCC cell line KYSE180

tag: chip antibody

value: BRDT (Cell Signaling, #65133)


title: Colon_tissue_MuAstV-SD31C09

value: MuAstV


title: Normal, Buccal Mucosa [RCC_OC_15]

description: miRNA Expression


title: Colon_tissue_MAdV2-SD39C05


title: RMC099-Rnf219_sh50_2

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

description: processed data file: ES_Rnf219.sh50.xlsx

data_processing:
We first evaluated each RNA-seq data quality using FastQC (version 0.11.8) and confirmed that all datasets are qualified for following analysis. The RNA-seq reads were aligned to mouse reference genome (mm10/GRCm38) using HISAT2 (version 2.1.0). The mouse reference genome sequence was downloaded from ENSEMBL (Mus Musculus GRCm38/mm10). Then we used featureCounts (version 2.0.0) to count reads or read pairs for each protein-coding gene annotated in GENCODE (vM23)34.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: *.bw: bigWig files
Supplementary_files_format_and_content: ES_Rnf219.sh50.xlsx: Excel file

source_name: murine embryonic stem cells

extract_protocol:
ES cells (V6.5) were infected with lentivirus carrying either Non-targeting shRNA or Cnot10 shRNA in the presence of 8 ug/ml of polybrene. 24 hours later, ES cells were selected with 2 ug/ml of puromycin for additional 48 hours and then were grown one passage off feeders for 30 min before harvesting. Total RNA was isolated with the RNeasy (74106 Qiagen) kit, treated with DNase I (M0303L NEB), and re-purified with RNeasy. For total RNA-seq analyses, 2.5 µg of total RNA was depleted of ribosomal RNA with the Ribo-Zero kit from Epicentre (#RZH1046). Ribosomal RNA-depleted samples were used for library preparation with the TruSeq RNA Sample Prep Kit (FC-122-1001 Illumina) for next-generation sequencing.
TruSeq RNA Sample Prep Kit (FC-122-1001 Illumina).

value: C57BL/6 (female) x 129/S (male)

tag: cell type

value: mES

tag: shRNA

value: Rnf219 shRNA


title: Normal, Buccal Mucosa [RCC_OC_19]

description: miRNA Expression


title: METTL3-KD Input

city: Beijing

first: wei

last: wang

address: 17 Nanli, Panjiayuan, Chaoyang District

department: Thoracic Surgery

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

description:
Input
processed data file: Methylated_RNA_sites.mRNA.xlsx

data_processing:
Library strategy: MeRIP-seq
Basecalls performed using CASAVA version 1.8.
Reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19.
RNAs were detected and annotated with CIRI software.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Methylated_RNA_sites.mRNA.xlsx: Excel format; Number of raw junction read.

source_name: K180 Cell

growth_protocol: Cells are cultured in 1640 medium.

extract_protocol: RNA extraction protocol.

treatment_protocol: With or without METTL3 shRNA.

value: Esophageal squamous cell carcinoma cells

tag: antibody


title: Oral Cancer, Buccal Mucosa [RCC_OC_14]

description: miRNA Expression


title: shControl Input

value: shControl


title: Lg63_P3

description:
LP
gene_count.txt
gene_fpkm.txt

value: ICR

value: wild type

value: hypothalamus

value: postnatal day 21

value: male

value: LFD lactation+neonatal PBS


title: RMC097-SHC_2

value: Non-targeting


title: RMC098-Rnf219_sh50_1


title: Normal, Buccal Mucosa [RCC_OC_12]

description: miRNA Expression

value: Buccal Mucosa

value: Male


title: METTL3-KD IP

description:
IP
processed data file: Methylated_RNA_sites.mRNA.xlsx


title: RMC096-SHC-1


title: shControl IP


title: RNA-seq of mES total RNA after Cnot10 shRNA replicate 2

description: processed data file: ES_Cnot10.xlsx

data_processing:
We first evaluated each RNA-seq data quality using FastQC (version 0.11.8) and confirmed that all datasets are qualified for following analysis. The RNA-seq reads were aligned to mouse reference genome (mm10/GRCm38) using HISAT2 (version 2.1.0). The mouse reference genome sequence was downloaded from ENSEMBL (Mus Musculus GRCm38/mm10). Then we used featureCounts (version 2.0.0) to count reads or read pairs for each protein-coding gene annotated in GENCODE (vM23)34.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: *.bw: bigWig files
Supplementary_files_format_and_content: ES_Cnot10.xlsx: Excel file


title: Colon_tissue_MAdV2-SD26C06

value: Colon


title: RNA-seq of mES total RNA after Cnot10 shRNA replicate 1

description: processed data file: ES_Cnot10.xlsx


title: Colon_tissue_MAdV2-SD26C05


title: Normal, Buccal Mucosa [RCC_OC_10]

description: miRNA Expression

value: Female


title: Colon_tissue_MAdV1-SD42C09


title: Oral Cancer, Buccal Mucosa [RCC_OC_9]

description: miRNA Expression


title: Colon_tissue_MAdV2-SD39C04


title: Colon_tissue_MAdV2-SD26C07


title: Colon_tissue_MAdV2-SD39C03


title: RNA-seq of mES total RNA after non-targeting shRNA replicate 1

description: processed data file: ES_Cnot10.xlsx


title: Oral Cancer, Buccal Mucosa [RCC_OC_13]

description: miRNA Expression


title: Oral Cancer, Tongue Mucosa [RCC_OC_11]

description: miRNA Expression

source_name: Tissue-Cancer-Tongue

value: Tongue Mucosa


title: Oral Cancer, Buccal Mucosa [RCC_OC_8]

description: miRNA Expression


title: RNA-seq of mES total RNA after non-targeting shRNA replicate 2

description: processed data file: ES_Cnot10.xlsx

value: C57BL/6 (female) x 129/S (male)


title: Colon_tissue_MAdV1-SD42C07


title: Colon_tissue_MAdV1-SD42C08


title: Oral Cancer, Buccal Mucosa [RCC_OC_7]

description: miRNA Expression


title: H3K27me3_4hpi_Rep3

city: Chicago

first: Mary

last: Hummel

state: IL

address: 303 E. Chicago Ave

institute: Northwestern University

description: ChIPseq

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using HOMER
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: bigWig files

organism: Human betaherpesvirus 5

growth_protocol: Kasumi-3 were grown in RPMI-1640 medium (ATCC 30-2001) supplemented with 20% fetal bovine serum (Corning) and 1,000 Units/ml Penicillin-Streptomycin (Gibco)

extract_protocol:
After fixation, cells were lysed and sonication with Covaris Focused-ultrasonicator at 10% Duty Cycle, 140 peak, 200 cycles per burst, 360 seconds. ChIP was performed by incubating the sonicated sample with either Rpb1 NTD (D8L4Y) Rabbit mAb #14958, Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173, or Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 (Cell Signaling Technologies) and the protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit.
Libraries were prepared with the KAPA HTP Library Preparation Kit multiplexed with NEXTflex DNA Barcodes (Bio Scientific) and size selected with AMPure XB beads (Beckman Coulter) to have fragments 250-450 bp in length. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequencing was performed with Illumina NextSeq technology (50bp single- end reads).

treatment_protocol: Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1. Extracellular virus was inactivated at 4 hours post infection. Cells were either collected and fixed  immediately (4hpi) or left in culture for additional 24 hours.

value: HCMV infected, 4 hr


title: Colon_tissue_MAdV1-SD26C04


title: Oral Cancer, Buccal Mucosa [RCC_OC_6]

description: miRNA Expression


title: H3K27me3_4hpi_Rep2

description: ChIPseq

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 (Cell Signaling Technologies)


title: MQ24_10_r2

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: Gene expression after 24 hours of exposure to 10 µg/ml of rCNT

hyb_protocol: Labeled cRNA samples were hybridised onto the Agilent 2-colour 8x60k arrays according to the manufacturer's recommendations and hybridized for 17 hours at 65°C. After hybridization, slides were washed following the manufacturer's recommendations (Agilent).

scan_protocol: Slides were scanned with Agilent microarray scanner G2505C and data were extracted using the Agilent Feature Extraction software (V12.02.2)

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and data were normalized with quantile normalization. This experiment was performed as a two-colour experiment, but data were analyzed as single-channel arrays. Raw data files are available as a tar archive on the series record.

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/ml, 24 hours, replicate 2

label_protocol: Samples were amplified using the T7 RNA polymerase method. cRNAs were labelled with Cy3 or Cy5 following the manufacturer's protocol (Agilent).

growth_protocol: THP-1 cells (DSMZ ACC 16) were grown in culture flasks in  RPMI media ( supplemented with 10% FBS, 2 mM ultraglutamine and 1% penicillin-streptomycin, Gibco). Cells were PMA differentiated (50 nM) for 48 hours on six-well plates (1.0x10^6 cells/well). Media was replaced at 24 hours for fresh, complete RPMI including PMA. After 48h PMA was removed by fresh media without PMA.

extract_protocol: Cells were harvested and lysed with lysing buffer (Qiagen). Total RNA was extracted and purified with the Rneasy Mini Kit by Qiagen following the kits' instructions.

treatment_protocol: Stock solution (1mg of rCNT /ml of RPMI) was vortexed and sonicated in a bath sonicator at RT for 3 x 15 min and diluted to final concentrations of 5, 10 and 20 µg/mL with complete RPMI. Dilutions were further vortexed and sonicated for 15 minutes prior to exposure. Cells were exposed to rCNT for 24, 48 or 72 hours. Untreated controls had the same treatment without the rCNTs. Exposures were performed as triplicates.

value: THP-1 monocytes

tag: differentiation

value: PMA differentiated macrophage

tag: dose

value: 10 µg/ml

tag: exposure time

value: 24 hours

value: rCNT


title: MQ48_20_r3

description: Gene expression after 48 hours of exposure to 20 µg/ml of rCNT

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/ml, 48 hours, replicate 3

value: 20 µg/ml

value: 48 hours


title: MQ24_20_r1

description: Gene expression after 24 hours of exposure to 20 µg/ml of rCNT

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/ml, 24 hours, replicate 1


title: Colon_tissue_MAdV1-SD26C03


title: MQ24_ctrl_r1

description: Gene expression after 24 hours without rCNT treatment

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/ml, 24 hours, replicate 1

value: 0 µg/ml

value: untreated


title: H3K27Ac_4hpi_Rep3

description: ChIPseq

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies)


title: H3K27me3_4hpi_Rep1

description: ChIPseq


title: Colon_tissue_CW3-SD36C07


title: Normal, Buccal Mucosa [RCC_OC_3]

description: miRNA Expression

value: Buccal Mucosa

value: Male


title: Colon_tissue_CW3-SD36C06

value: Colon


title: H3K27Ac_4hpi_Rep1

description: ChIPseq


title: H3K27Ac_4hpi_Rep2

description: ChIPseq


title: MQ24_5_r1

description: Gene expression after 24 hours of exposure to 5 µg/ml of rCNT

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/ml, 24 hours, replicate 1

value: 5 µg/ml


title: Colon_tissue_CW3-SD31C06


title: Normal, Buccal Mucosa [RCC_OC_4]

description: miRNA Expression


title: Pol2_4hpi_Rep3

description: ChIPseq

value: HCMV infected, 24 hr

value: Rpb1 NTD (D8L4Y) Rabbit mAb #14958 (Cell Signaling Technologies)


title: Normal, Buccal Mucosa [RCC_OC_1]

description: miRNA Expression


title: Oral Cancer, Buccal Mucosa [RCC_OC_2]

description: miRNA Expression


title: SNJM10

city: new york

first: Mamta

last: Giri

state: new york

address: 1470 madison ave

department: Institute of Personalized medicine

institute: Mount Sinai hospital

data_processing:
FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish
Cell barcodes and unique molecular identifiers (UMIs) were extracted and “Raw” UMI matrix generated for each sample
extracted cell-barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger
Genome_build: danRer11

organism: Danio rerio

source_name: Intestinal dissection

growth_protocol: zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed

extract_protocol:
After 24 hours of DSS/BZA treatment, zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly, cells were dissociated and digested using standard collagenase and DNAse protocols, and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads
Library construction was performed as per 10X Genomics v2 and v3 chemistry kits (see descriptors for applications).

treatment_protocol: 6dpf zebrafish larvae were single- treated with 0.075% Dextran Sodium Sulphate (DSS) or co-treated with DSS+ 10uM Bazedoxifene (BZA) in egg water for 24 hours, in a 37C incubator

value: Intestine

value: 2X DSS+BZA

tag: genotype/variation

tag: 10x chemistry


title: Oral Cancer, Tongue Mucosa [RCC_OC_5]

description: miRNA Expression

value: Tongue Mucosa


title: Colon_tissue_CW3-SD26C09


title: Pol2_4hpi_Rep2

description: ChIPseq


title: SNJM09

value: 2X DSS


title: MQ72_ctrl_r3

description: Gene expression after 72 hours without rCNT treatment

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/ml, 72 hours, replicate 3

value: THP-1 monocytes

value: PMA differentiated macrophage

value: 72 hours


title: MQ48_10_r2

description: Gene expression after 48 hours of exposure to 10 µg/ml of rCNT

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/ml, 48 hours, replicate 2

value: 10 µg/ml

value: 48 hours

value: rCNT


title: MQ24_10_r3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/ml, 24 hours, replicate 3

value: 24 hours


title: SNJM08

value: untreated


title: MQ48_5_r2

description: Gene expression after 48 hours of exposure to 5 µg/ml of rCNT

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/ml, 48 hours, replicate 2


title: Colon_tissue_CR6-SD39C07


title: MQ48_ctrl_r2

description: Gene expression after 48 hours without rCNT treatment

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/ml, 48 hours, replicate 2

value: 0 µg/ml


title: MQ72_5_r3

description: Gene expression after 72 hours of exposure to 5 µg/ml of rCNT

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/ml, 72 hours, replicate 3


title: Pol2_4hpi_Rep1

description: ChIPseq


title: SNJM07

value: wildtype


title: input_4hpi_Rep3

description: ChIPseq

value: HCMV infected, 4 hr


title: Colon_tissue_CR6-SD39C06

source_name: Colon

value: Colon


title: Colon_tissue_CW3-SD26C08


title: SNJM06


title: input_4hpi_Rep2

description: ChIPseq


title: SNJM05

value: wildtype 2X


title: Colon_tissue_CR6-SD33C10


title: MQ24_5_r2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/ml, 24 hours, replicate 2

value: 5 µg/ml


title: MQ24_ctrl_r3

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/ml, 24 hours, replicate 3


title: Colon_tissue_CR6-SD33C09


title: 4hr_K3_Unsorted_Rep3

description: RNA-seq

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: tab-delimited file with read counts per gene
Supplementary_files_format_and_content: bigWig files

source_name: Total RNA_infected K3 cells_4hpi

extract_protocol:
Infected Kasumi-3 cells were collected and lysed in Trizol. Total RNA was prepared using the Direct-zol RNA miniprep kit (Zymo Research) with an on-column DNase digestion step according to the manufacturer’s instructions.
RNA was rRNA depleted with Ribo-zero (Illumina) and RNA-seq libraries were prepared with TrueSeq Stranded mRNA (Illumina). RNA-seq libraries were sequenced on the Illumina NextSeq 500 Sequencing System (50 bp single-end reads, 50 million reads/sample)

treatment_protocol: Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1. Extracellular virus was inactivated at 4 hours post infection. At 4 hr post-infection, virus was inactivated and cells were either collected immediately (4hpi) or left in culture for additional 24 hours.

tag: rna type

value: total RNA


title: Colon_tissue_CR6-SD30C10

tag: tissue


title: 4hr_K3_Unsorted_Rep2

description: RNA-seq


title: Colon_tissue_CR6-SD30C09


title: SNJM04

value: Intestine

value: 1X DSS


title: Colon_tissue_CW3-SD31C07


title: SNJM02


title: 4hr_K3_Unsorted_Rep1

description: RNA-seq


title: SNJM01


title: GFPP3R3

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
The CpG_Me pipeline (https://github.com/ben-laufer/CpG_Me) was used to perform all data processing steps.
Trim Galore was used to trim adapters and methylation bias.
FastQ Screen was used to screen for sample contamination.
Bismark was used align to the reference genome, remove PCR duplicates, calculate coverage, extract CpG methylation, and generate genome-wide cytosine reports (CpG count matrices).
Picard Tools was used to calculate insert size metrics.
MultiQC was used for quality control.
Genome_build: hg38
Supplementary_files_format_and_content: Bismark genome-wide cytosine reports (CpG count matrices)

source_name: SH-SY5Y cells

growth_protocol: Cells were grown and differentiated according the protocol from Shipley et al. (PMID: 26967710)

extract_protocol:
DNA was isolated from flash frozen cell pellets using the QIAamp DNA Micro kit (Qiagen)
Accel-NGS Methyl-Seq DNA Library Kit

treatment_protocol: Cells were transfected with piggyBac plasmids via Lipofectamine 3000

tag: genotype

value: GFP

tag: differentiation phase

value: Phase 3

tag: cell line replicate


title: GFPP3R2


title: input_4hpi_Rep1

description: ChIPseq

tag: treatment


title: SNJC03

data_processing:
FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish
Cell barcodes and unique molecular identifiers (UMIs) were extracted and “Raw” UMI matrix generated for each sample
extracted cell-barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger
Genome_build: danRer11

extract_protocol:
After 24 hours of DSS treatment, zebrafish larval intestines were dissected from untreated and DSS-treated fish. Single cell suspensions were generated as described in Methods. Briefly, cells were dissociated and digested using standard collagenase and DNAse protocols, and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads
Library construction was performed as per 10X Genomics v2 chemistry kit.
10X chromium

treatment_protocol: 6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours, in a 37C incubator

tag: status

value: DSS treated


title: Chat positive sample 2

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: Sorted ILC2s

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

tag: chat sorting gate

value: positive


title: MQ48_20_r1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/ml, 48 hours, replicate 1

tag: cell line

value: THP-1 monocytes

value: PMA differentiated macrophage

value: 20 µg/ml

value: 48 hours


title: MQ48_5_r1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/ml, 48 hours, replicate 1

value: rCNT


title: MQ72_5_r1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/ml, 72 hours, replicate 1

value: 72 hours


title: MQ72_ctrl_r2

description: Gene expression after 72 hours of without rCNT treatment

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/ml, 72 hours, replicate 2

value: 0 µg/ml

value: untreated


title: Chat positive sample 1


title: Chat positive sample 3


title: SNJM03

source_name: Intestinal dissection

value: wildtype


title: GFPP3R1

tag: cell type


title: MQ24_20_r2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/ml, 24 hours, replicate 2

value: 24 hours


title: Chat negative sample 3

value: negative


title: SNZF2

value: Intestine


title: GFPP1R3

value: Phase 1


title: SNJC02

value: untreated ctrl


title: Chat negative sample 2


title: Chat negative sample 1


title: SNJCZ2


title: MQ24_10_r1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/ml, 24 hours, replicate 1

value: 10 µg/ml


title: GFPP1R2

value: GFP


title: SNZF1


title: MQ72_10_r1

description: Gene expression after 72 hours of exposure to 10 µg/ml of rCNT

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/ml, 72 hours, replicate 1


title: GFPP1R1


title: MQ72_ctrl_r1

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/ml, 72 hours, replicate 1


title: MQ48_5_r3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/ml, 48 hours, replicate 3

value: 5 µg/ml


title: MQ48_10_r3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/ml, 48 hours, replicate 3

value: THP-1 monocytes


title: Mammary epithelium cKO4

city: beijing

first: chunlei

last: shao

address: yuanmingyuan west road

institute: china agricultural university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts.
Reads mapping to the reference genome
Novel transcripts prediction. The mapped reads of each sample were assembled by StringTie (v1.3.3b)  (Mihaela Pertea.et al. 2015) in a reference-based approach.
Quantification of gene expression level. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene.
Differential expression analysis
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: mammary gland

extract_protocol:
RNA was harvested using Trizol reagent from mammary epithelium. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mammary gland

tag: age

value: pregnancy day 14.5


title: SNJCZ1


title: GFPGR3

value: Growth


title: GFPGR2


title: Pol2_24hpi_Rep2

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using HOMER
Genome_build: hg19
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: bigWig files

organism:
Homo sapiens
Human betaherpesvirus 5

source_name: Pol2_24hpi GFP+

extract_protocol:
After fixation, cells were lysed and sonication with Covaris Focused-ultrasonicator at 10% Duty Cycle, 140 peak, 200 cycles per burst, 360 seconds. ChIP was performed by incubating the sonicated sample with Rpb1 NTD (D8L4Y) Rabbit mAb #14958 (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies) and the protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit.
Libraries were prepared with the KAPA HTP Library Preparation Kit multiplexed with NEXTflex DNA Barcodes (Bio Scientific) and size selected with AMPure XB beads (Beckman Coulter) to have fragments 250-450 bp in length. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequencing was performed with Illumina NextSeq technology (50bp single- end reads).

treatment_protocol: Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1 or mock-infected. Extracellular virus was inactivated at 24 hours post infection. HCMV-infected cells were sorted for GFP expression and live cells. Mock-infected cells were sorted for live cells. Cells were then fixed with 1% of Formaldehyde in PBS fand quenched with 0.125 M glycine.

value: live GFP+ infected, 24hpi

tag: chip antibody

value: Rpb1 NTD (D8L4Y) Rabbit mAb #14958 (Cell Signaling Technologies)


title: Pol2_24hpi_Rep1


title: MQ72_5_r2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/ml, 72 hours, replicate 2

tag: differentiation

value: PMA differentiated macrophage

tag: dose

value: 72 hours

value: rCNT


title: GFPGR1


title: Mammary epithelium cKO2


title: 3LP3R3

value: Phase 3


title: Total_RNA_Infected_K3_Rep2

description: RNA-seq

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: tab-delimited file with read counts per gene
Supplementary_files_format_and_content: bigWig files

source_name: Total RNA Infected K3

extract_protocol:
The cDNA was quantitated by qubit and processed into NGS libraries using the Swift BioSciences ACCEL-NGS® 1S PLUS DNA LIBRARY KIT in combination with the Swift BioSciences 1S Unique Dual Indexing Kit. Library QC (quality and quantity) was done by Bio-analyzer and the pool of libraries was sequenced on the Illumina NextSeq using Illumina reagents and protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 24 hr post-infection, HCMV infected cells were sorted for GFP expression and live cells while mock-infected cells were sorted for live cells. Newly synthesized RNA was labeled for 4 hr with 5-ethynyl uridine.   A portion of the RNA was saved for analysis of steady state RNA, and the nascent RNA was purified by biotinylation of EU-labeled RNA and selection on Streptavidin beads.  cDNA was prepared from each of the four RNA populations and the cDNA was purified with a Qiagen minElute PCR purification kit.

value: HCMV infected, 24 hr, EU-labeled total RNA

value: steady state RNA


title: Mammary epithelium WT4


title: Total_RNA_Infected_K3_Rep3

description: RNA-seq


title: 3LP3R2

source_name: SH-SY5Y cells


title: Total_RNA_Infected_K3_Rep1

description: RNA-seq


title: Mammary epithelium WT2


title: Mammary epithelium WT3


title: MQ72_20_r2

description: Gene expression after 72 hours of exposure to 20 µg/ml of rCNT

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/ml, 72 hours, replicate 2

value: 20 µg/ml

tag: exposure time


title: Nascent_RNA_Infected_K3_Rep3

description: RNA-seq

source_name: Nascent RNA Infected K3

value: HCMV infected, 24 hr, EU-labeled, biotinylated RNA purified

value: nascent RNA


title: Mammary epithelium cKO3


title: Mammary epithelium WT1


title: Nascent_RNA_Infected_K3_Rep2

description: RNA-seq


title: MQ24_ctrl_r2

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/ml, 24 hours, replicate 2

value: 0 µg/ml

value: 24 hours

value: untreated


title: 3LP1R3

value: Phase 1


title: MQ72_20_r3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/ml, 72 hours, replicate 3

value: THP-1 monocytes


title: Mammary epithelium cKO1

value: mammary gland

value: pregnancy day 14.5


title: 3LP1R2


title: Nascent_RNA_Infected_K3_Rep1

description: RNA-seq


title: MQ72_10_r2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/ml, 72 hours, replicate 2

value: 10 µg/ml


title: 3LP1R1


title: RNA-unstim-mixed-R1.bam

city: Los Angeles

first: Quen

last: Cheng

state: CA

address: 611 Charles E Young Dr E

institute: UCLA

description: MixedLigands-RNAseq-counts.txt

data_processing:
Samples were sequenced and base calls performed on Illumina NovaSeq 6000 (samples 50-60) and Illumina HiSeq 2500 (remaining samples)
Reads were trimmed of adapter sequences and low-quality reads (q<30), then mapped to mm10 genome with bowtie2 (ChIP) or STAR (RNA)
Aligned reads were filtered based on mapping score (MAPQ ≥ 30) by Samtools. For ChIP-seq, duplicated reads were removed using Picard MarkDuplicates.
For ChIP-seq, MACS2 version 2.1.0 was used to identify peaks for each sample using pooled input samples as control, FDR < 0.01, and extension size of average fragment length. These peaks were merged to generate a single reference peak file, and the number of reads that fell into each peak was counted using deeptools multiBigwigSummary with extension size of average fragment length
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq raw count tables are provided (unnormalized), generated by the featureCounts function in the Subread package.
Supplementary_files_format_and_content: ChIP-seq count tables are provided, normalized to sequencing depth by the multiBigWigSummary command from the deepTools package.

molecule: polyA RNA

source_name: MLE12 cell line

growth_protocol: MLE-12 cells obtained from ATCC (Manassas, VA) were cultured in DMEM (Corning Inc., Corning, NY) supplemented with 10% FBS, 100 IU/ml penicillin, 100 𝜇g/ml streptomycin, 2 mM L-glutamine at 370C at 5% CO2.

extract_protocol:
STAT1 ChIP was performed on lysed and sonicated chromatin using rabbit anti-STAT1 (Cell Signaling Technologies, Danvers, MA; CST-9172). Total RNA was extracted by Trizol according to manufacturer's instructions.
Libraries were prepared according to manufacturer's instructions: ChIP-seq with NEBNext Ultra II DNA Library Prep Kit (New England Biolabs E7645), RNA-seq samples 50-60 with Illumina TruSeq mRNA kit (Illumina), and for remaining RNA-seq samples KAPA Stranded mRNA-seq Library Preparation kit (KAPA Biosystems)

treatment_protocol: Recombinant murine IFN-b (PBL Assay Science, Piscataway, NJ) and IFN-γ (BD Biosciences, San Jose, CA) were used for stimulation.

tag: replicate

tag: assay

value: mRNA-seq

tag: stimulus

tag: timepoint

tag: column header


title: RNA-unstim-mixed-R2.bam

description: MixedLigands-RNAseq-counts.txt


title: MQ48_ctrl_r1

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/ml, 48 hours, replicate 1

value: PMA differentiated macrophage

value: 48 hours


title: MQ24_5_r3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/ml, 24 hours, replicate 3

value: 5 µg/ml

value: rCNT


title: 3LP3R1

tag: genotype

tag: differentiation phase

value: Phase 3

tag: cell line replicate


title: 3LGR3

value: Growth


title: MQ48_20_r2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/ml, 48 hours, replicate 2

value: 20 µg/ml

tag: treatment


title: MQ72_20_r1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/ml, 72 hours, replicate 1

tag: cell line

value: 72 hours


title: 24hr_K3_Infected_Rep3

description: ATACseq

source_name: HCMV infected_24 hpi

extract_protocol:
Cells were collected and resuspended in 50 μl of a transposase mix that included 25 μl of 2x Nextera Tagment DNA buffer (Illumina), 2.5 μl Nextera Tn5 transposase (Illumina), 0.5 μl digitonin 5% (Invitrogen), and 22μl of H2O. The reaction was carried at 37°C for 30 min. DNA was purified with Qiagen MinElute PCR purification kit and eluted in 10μl of buffer EB.
DNA libraries were amplified by using NEBNext High-Fidelity (New England Biolabs) and barcoded primers. The number of amplification cycles were calculated by qPCR and kept under 11 to prevent saturation. Libraries were purified with Qiagen MinElute PCR purification kit and sized selected with AMPure XB beads (Beckman Coulter) . Library quality control was assessed by Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and the libraries were sequenced with Illumina NextSeq technology (75bp single-end reads, 100 million reads/sample).

treatment_protocol: Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1 or mock-infected. Extracellular virus was inactivated at 24 hours post infection. HCMV-infected cells were sorted for GFP expression and live cells. Mock-infected cells were sorted for live cells.

value: HCMV infected, 24 hr

tag: barcode


title: 24hr_K3_Infected_Rep2

description: ATACseq


title: RNA-mix-4h-R2.bam

description: MixedLigands-RNAseq-counts.txt

value: IFN-Beta (1 U/ml) + IFN-gamma (1 ng/ml)


title: 3LGR2

tag: cell type


title: RNA-mix-4h-R1.bam

description: MixedLigands-RNAseq-counts.txt


title: 3LGR1


title: RNA-mix-2h-R1.bam

description: MixedLigands-RNAseq-counts.txt


title: MHC I high patient SCLC_9

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Raw sequencing data were aligned to hg19 version of human genome and mm10 version of mouse genome with Star aligner (v. 2.6.1).
Viper RNA-seq processing pipeline (Cornwell et al., 2018; PMID: 29649993) was used to generate normalized expression values.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: FFPE

extract_protocol:
Up to 10 consecutive FFPE 5µM sections were macrodissected or whole slide scraped and pooled into a single tube for downstream DNA and RNA isolation. DNA and RNA were co-extracted using the Qiagen AllPrep kit (Qiagen Cat No./ID: 80204). DNA and RNA were qualified and quantified using Nanodrop and Qbit to determine concentration and Agilent Bioanalyzer to determine quality. DNA and RNA samples with less than 100ng were excluded from downstream analysis.
RNA sequencing libraries were prepared using the TruSeq Illumina Stranded Total Gold with RiboZero using 100 ng of total RNA. Libraries were sequenced on the Novaseq.

tag: mhc class i status

value: high

tag: sorted population

tag: source

value: FFPE


title: 24hr_K3_Infected_Sorted_Rep2

description: RNA-seq

source_name: Total RNA_HCMV infected K3 cells_24hpi

extract_protocol:
Infected Kasumi-3 cells were collected and lysed in Trizol. Total RNA was prepared using the Direct-zol RNA miniprep kit (Zymo Research) with an on-column DNase digestion step according to the manufacturer’s instructions.
RNA was rRNA depleted with Ribo-zero (Illumina) and RNA-seq libraries were prepared with TrueSeq Stranded mRNA (Illumina). RNA-seq libraries were sequenced on the Illumina NextSeq 500 Sequencing System (50 bp single-end reads)

tag: rna type

value: total RNA


title: 24hr_K3_Infected_Rep1

description: ATACseq


title: RNA-gamma1-4h-R2.bam

description: MixedLigands-RNAseq-counts.txt

value: IFN-gamma (1 ng/ml)


title: 24hr_K3_Infected_Sorted_Rep1

description: RNA-seq


title: MQ48_10_r1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/ml, 48 hours, replicate 1

value: THP-1 monocytes

tag: differentiation

tag: dose

tag: exposure time


title: MHC I high patient SCLC_8


title: MQ24_20_r3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/ml, 24 hours, replicate 3

value: 24 hours


title: MQ48_ctrl_r3

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/ml, 48 hours, replicate 3

value: 0 µg/ml

value: untreated


title: Ad-shRNA Cklf1 rep3

city: Nanchang

first: Yanyu

last: Dean

address: Lushanzhong888, Changbei district

institute: Jiangxi Agricultural University

data_processing:
Trimmed, clean reads were mapped to the rat reference genome (Rnor_6.0) using the SOAP2 software and allowing five mismatches(Li et al., 2009).
Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
A FDR of no more than 0.05 (FDR ≤ 0.05) and a difference ratio of the FPKM between controls and CKLF1 samples of no less than 1 (|log2 ratio| ≥ 1) were adopted as the significance thresholds to identify DEGs.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: txt files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: Rat vascular smooth muscle cells

growth_protocol: Vascular smooth muscle cells with passage number four were transfected with overexpression of CKLF1 adenovirus particles overnight and then cultivated in the complete media. Until the confluence reached 75%, the cells in each well was starved with the media supplemented with 0.2% FCS for next 24 - 32 h. An adenovirus carrying green fluorescence protein was used as the negative control. For cells carrying with shRNA Cklf1 or shRNA Scramble, an additional treatment with 25 μg/L TNFɑ for 24 h were performed.Total RNA were extracted and generated by deep sequencing, in triplicate, on an Illumina X Ten platform.

extract_protocol:
Total RNA of 12 samples were isolated from adenovirus treated primary vascular smooth cells using Trizol reagent (Invitrogen) according to the manufacturer's instruction.
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primed reverse transcription. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation is then performed. After the previous step, adaptors are ligated to the end of these fragments. Next, ligation products were selected by size and purified on TAE-agarose gel. Finally, the fragments are enriched by PCR amplification, then purified by magnetic beads and dissolved in the appropriate amount of Epstein-Barr solution. During the QC step, Agilent 2100 Bioanaylzer are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina X Ten platform.

tag: Sex

value: male

tag: genotype/variation

value: knockdown of Cklf1

tag: strain

value: Sprague-Dailey


title: Ad-shRNA Cklf1 rep1


title: RNA-gamma1-4h-R1.bam

description: MixedLigands-RNAseq-counts.txt

tag: replicate

tag: assay

value: mRNA-seq

tag: stimulus

tag: timepoint

tag: column header


title: TTYH2-ECS-NM-Barcode1+2

city: Stanford

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description:
TTYH2-ECS-NM_S11
processed data file:
TTHY2-ECS-ShapeMapper2.txt.gz

data_processing:
Paired-end reads were first filtered by AfterQC and then mapped and demultiplexed by cutadapt 1.17 to read and trim the barcodes
The multiplexed reads were processed by ShapeMapper to detect DMS reactivity
Genome_build: synthetic constructs
Supplementary_files_format_and_content: txt file's content includes mutation counts, reactivity, profile, and log; pdf file's content is graph of reactivity, mutation rate, and histogram of analysis statistics; shape file list reactivity; map file is reactivty with standard error mapped with seqeuence

source_name: In vitro transcribed RNA

growth_protocol: In vitro experiments, no growth protocol involved.

extract_protocol:
RNA were in vitro transcribed using T7 RNA polymerase and DNA templates, and purified by AMpure RNA beads
RNA libraries were prepared for sequencing using methods described in bioRxiv 840884; doi: https://doi.org/10.1101/840884

treatment_protocol: RNA were treated by Dimethyl sulfide (DMS) as described in bioRxiv 840884; doi: https://doi.org/10.1101/840884

tag: treatment

value: Untreated


title: Ad-shRNA scramble rep3

value: control sample


title: NEIL1-NM2

description:
Neil1-L1-NM-2_S3
processed data file:
NEIL1-ShapeMapper2.txt.gz


title: RNA-beta1-4h-R2.bam

description: MixedLigands-RNAseq-counts.txt

tag: cell line

value: IFN-Beta (1 U/ml)


title: TTYH2-ECS-DMS-Barcode1+2

description:
TTYH2-ECS-DMS_S9
processed data file:
TTHY2-ECS-ShapeMapper2.txt.gz

value: Dimethyl sulfide (DMS) treatment


title: MHC I high patient SCLC_7

tag: mhc class i status


title: RNA-gamma1-2h-R1.bam

description: MixedLigands-RNAseq-counts.txt


title: MHC I high patient SCLC_5

tag: sorted population


title: MHC I high patient SCLC_6

tag: source


title: RNA-beta1-4h-R1.bam

description: MixedLigands-RNAseq-counts.txt


title: NEIL1-DMS2

description:
Neil1-L1-DMS-2_S1
processed data file:
NEIL1-ShapeMapper2.txt.gz


title: NEIL1-NM1

description:
Neil1-L1-NM-1_S4
processed data file:
NEIL1-ShapeMapper2.txt.gz


title: Ad-shRNA Cklf1 rep2


title: Ad-Cklf1 rep2

value: overexpression of Cklf1


title: MHC I high patient SCLC_4

value: high


title: MHC I high patient SCLC_3

value: FFPE


title: Ad-shRNA scramble rep1


title: RNA-beta1-2h-R1.bam

description: MixedLigands-RNAseq-counts.txt


title: Ad-Cklf1 rep3


title: CoTECH_agg_NIH3T3_exp2_RNA

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.

source_name: cultured NIH3T3

growth_protocol: NIH3T3 was cultured at 37 °C with 5% CO2 and was maintained in high glucose DMEM

extract_protocol:
following CoTECH protocol
After PCR enrichment using Q5 polymerase, the 300-1,000 bp fragments were isolated using the 1.5% (w/v) agarose gel and purified once with 0.8 x AMpure XP beads

treatment_protocol: The NIH3T3 was dissociated by 0.1% Trypsin digestion, and aliquot of cell numbers were directly used for CoTECH

tag: background strain

tag: chip antibody

tag: protocol

value: CoTECH


title: NEIL1-DMS1

description:
Neil1-L1-DMS-1_S2
processed data file:
NEIL1-ShapeMapper2.txt.gz


title: Ad-Cklf1 rep1


title: CoTECH_agg_NIH3T3_exp1_RNA


title: MHC I high patient SCLC_1


title: Ad-GFP rep3


title: MHC I lo/neg patient SCLC_3

value: low/neg


title: NIH3T3_insitu

value: low-input ChIP-seq method (PMID:31471188)


title: HT29ERβ H3K27AC ChIP-Seq rep 2

city: Stockholm

first: Rajitha

last: Indukuri

state: Sweden

address: Tomtebodavägen 23a, Solna

country: Sweden

institute: Scilifelab

data_processing:
ChIP-Seq reads were mapped to the human reference genome assembly hg38 (GRCh38) using STAR with the alignIntronMax flag set to 1. H3K27AC binding sites were identified by HOMER applying a false discovery rate (FDR) less than 0.001 and four-fold enrichment over control (Input) cut-off. Only peaks that were present in at least 2 out of 3 replicates were considered for downstream analysis. HOMER was used to perform de novo motif analysis of NFR centered peaks. Differential binding was performed by EdgeR between mock and ERβ, normalized using TMM normalization.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph

source_name: colon

growth_protocol: Cells were cultured in Dulbecco's modified Eagle’s medium (Sigma-Aldrich) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (P/S) and 1% blasticidine (Sigma Aldrich)

extract_protocol:
Cells were crosslinked with formaldehyde and nuclear chormatin fractions were separted and immunoprecipitated with H3K27AC anitboides. Magnetic beads were used to pull down the immunoprecipitated DNA and separted by column preparation.
The libraries of ChIP DNA were prepared by using the kit NEB Next Ultra II DNA Library Prep Kit for Illumina following user instrcutions

treatment_protocol: All Cells were treated with 10 nM 17β-estradiol (E2, Sigma-Aldrich) dissolved in DMSO for 2h before ChIP experiment.

value: H3K27AC antibody, Abcam, cat no:Ab4729, lot no:GR321937-1, rabbit polyclonal,

tag: transfection

value: stably transfected with ERβ


title: HT29ERβ H3K27AC ChIP-Seq rep 3


title: Ad-GFP rep2

tag: Sex


title: MHC I lo/neg patient SCLC_2


title: CoTECH_agg_NIH3T3_exp2_DNA


title: CoTECH_agg_NIH3T3_exp1_DNA


title: HT29ERβ H3K27AC ChIP-Seq rep 1


title: Ad-GFP rep1

tag: genotype/variation


title: MHC I low/neg patient SCLC_1


title: HT29M H3K27AC ChIP-Seq rep 3

value: stably transfected with empty vector


title: BAF155/170 deletion_rep2

city: Singapore

first: Manvendra

middle: K.

last: Singh

address: 8 College Road

department: Programme in Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS MEDICAL SCHOOL

data_processing:
Fastqc v0.11.7 was used to check the quality of the bases in the reads
cutadapt v1.18 was used to remove the base pairs if the adapter contamination is >= 10%
Paired end fastq sequence reads from each sample were aligned to mouse reference genome (GRCm38) using ultrafast RNA-seq aligner STAR
Mapped sequencing reads were quantified and assigned to genomic features via feature count option in R package Rsubread
Differential expression of genes identified between control and KO samples using LIMMA R package
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited file with featurecounts values for all samples

source_name: Neural Crest cells

extract_protocol:
Neural crest cells isolation using fluorescence-activated cell sorting (FACS)
RNA from collected neural crest cells was extracted using FavorPrep™ RNA isolation kit (Catalog no. FATRK001). Subsequently, strand-specific poly(A) RNAseq libraries were generated using NEBNext. Ultra™ II Directional RNA Library Prep Kit with sample purification beads from Illumina (NEB, Catalog no. E7795S).

tag: cell type

value: Neural Crest cells

tag: genotype

value: BAF155/170 deletion


title: BAF155/170 deletion_rep3


title: HT29M H3K27AC ChIP-Seq rep 2


title: MHC I high patient SCLC_2


title: SW480ERβ H3K27AC ChIP-Seq rep 2


title: Parkin-mutation carrier midbrain

city: Berlin

first: Malte

last: Spielmann

address: Ihnestraße 63

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
RNA, nuclear
Parkin-mutation carrier midbrain

data_processing:
Cell Ranger v3 mkfastq
Cell Ranger v3 count
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI count matrix

source_name: Parkin midbrain

extract_protocol:
The left hemi-midbrain was removed. This midbrain block was then snap-frozen at -120°C and cryosectioned at ~15 μm thickness in the transverse plane. The resulting sections were stored at -80°C. Addapted 10x Genomics protocol for nuclei isolation was used to extract the nuclei. Sorted nuclei were processed using the Chromium Next GEM Single Cell 3’ Kit v3.1 to generate the cDNA libraries
The sample was prepared for sequencing using standard Illumina protocol and sequenced on Illumina NovaSeq 6000-S2

tag: tissue

value: Midbrain

tag: disease state

value: Parkinson's disease

tag: age at death

value: M


title: DS1-PRJ-HCMV-22

first: David

last: Strugatsky

address: 615 CHARLES E YOUNG DR S

department: MIMG

description: snoRNA

data_processing:
Sequencing quality was examined by FastQC
The raw sequences were trimmed off 5’, 3’-adaptor bases using cutadapt.
The trimmed sequences were aligned to the manually curated reference of SnoRNAs in Ensemble by Novoalign at maximum mismatch <= 2.
SnoRNAs were measured as raw counts and normalized as tag counts per million of total aligned SnoRNA reads (TPM/CPM).
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: snoRNA raw counts in Excel format.

source_name: total RNA isolated from human cytomegalovirus virions

growth_protocol: Human fibroblast MRC-5 cells were seeded on 18x175 cm2 flasks in Eagle’s Minimum Essential Medium supplemented with 10% fetal bovine serum and 100U/ml of Penicillin-Streptomycin and cultured until they reached ~80-90% confluency, about a week. The cells were then infected with HCMV (AD169 strain). The growth media were replaced with fresh ones 4 days after infection. The media containing secreted HCMV virions were collected at 8 days post infection.

extract_protocol:
The growth media from infected MRC-5 cells were spun on SW28 rotor (Beckman) at 80,000 x g for 1 hour at 4°C. The supernatant was discarded and the pellet in each tube was resuspended in 50 µl of cold phosphate buffered saline (PBS). About 0.7 ml of combined pellet suspension from all ultracentrifuge tubes was loaded on 15%-50% linear gradient of sucrose made in PBS and spun in SW41 (Beckman) rotor at 80,000 x g for 1 hour at 4°C. About 1 ml of visible virus-containing band was collected into a new tube and mixed with 10 ml of sterile PBS solution in order to dilute sucrose. The virions were concentrated at 80,000 x g for 1 hour at 4°C and resuspended in 0.1 ml of PBS and used for total RNA isolation. 3 µg of total RNA isolated from RNase pre-treated virions was used for snoRNA library preparation.
Total RNA of each sample was used to prepare the SnoRNA-sequencing library in the following steps: 1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~170-370bp PCR amplified fragments (corresponding to ~50-250 nt small RNAs). The libraries are qualified and quantified using Agilent BioAnalyzer2100.

tag: sample type

value: human cytomegalovirus virions


title: Control_rep3

value: control


title: SW480ERβ H3K27AC ChIP-Seq rep 1


title: CoTECH_preAmplification_RNA

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.

source_name: cell line

growth_protocol: K562 was cultured at 37 °C with 5% CO2 and was maintained in high glucose DMEM

extract_protocol:
folloing CoTECH protocol
After PCR enrichment using Q5 polymerase, the 300-1,000 bp fragments were isolated using the 1.5% (w/v) agarose gel and purified once with 0.8 x AMpure XP beads
ChIP-seq and RNA-seq

treatment_protocol: The K562 was dissociated by 0.1% Trypsin digestion, and aliquot of cell numbers were directly used for CoTECH


title: Control_rep2


title: CoTECH_nopreAmplification_RNA


title: SW480M H3K27AC ChIP-Seq rep 2


title: CoTECH_preAmplification_DNA


title: Control_rep1


title: HT29M H3K27AC ChIP-Seq rep 1


title: BAF155/170 deletion_rep1


title: SW480M H3K27AC ChIP-Seq rep 1


title: Unstimulated osteoblast 12 day, rep2

city: Adelaide

first: Vasilios

last: Panagopoulos

state: SA

address: North Terrace,

department: Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using iscan control software

data_processing: The data were normalized using Illumina GenomeStudio software (Version 1.9.0)

label: biotin

source_name: unstimulated osteoblast cells

label_protocol: Biotinylated cRNA were prepared using standard kit for Illumina arrays

extract_protocol: RNA was extracted with Rneasy minikit in accordance with the prescribed protocol provided with the kit. RNA yield and purity were quantified by Nanodrop spectrophotometric measurement.

treatment_protocol: Osteoblasts from one donor were treated with or without 5µg/ml SBP for 12 days in osteogenic DMEM mineralization medium.

value: bone (iliac crrest)

value: osteoblast

tag: treatment

value: unstimulated


title: Unstimulated osteoblast 12 day, rep1


title: RNA_TX1072_XXdXic_d4_r2

status: Public on Mar 04 2021

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

data_processing:
An “N-Masked” genome of the mouse reference genome mm10 was generated using SNPsplit (0.3.2). For this, all the polymorphic sites of the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 were masked by ambiguity nucleobase ‘N’ as described previously (Pacini et al. 2020, Barros de Andrade E Sousa et al. 2019).
The reads were aligned using STAR (2.7.5a) with options [–outSAMattributes NH HI NM MD] to the N-masked mm10 genome (Dobin et al. 2013).
SAM files were translated into BAM files, filtered for properly paired reads and sorted using samtools (1.10) with options [view -b -h -f 3 -q 7] and [sort] (Li et al. 2009)
Blacklisted regions for mm10 (ENCODE Project Consortium 2012) were removed using bedtools (2.29.2) with options [intersect -v] (Quinlan and Hall 2010).
Duplicates were marked and removed using Picard (2.18.25) with options [MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE] (http://broadinstitute.github.io/picard)
BAM files were split according to the strand of the reads using a custom shell script
BigWig tracks were created using deepTools (2.0) with options [bamCoverage -e -bs 10 --normalizeUsing CPM -ignore chrX chrY] for TT-seq and [bamCoverage -bs 10 --normalizeUsing CPM -ignore chrX chrY] for RNA-seq (Ramírez et al. 2016). They were then visualized using the UCSC Genome Browser (Kent et al. 2002).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig: Coverage tracks

source_name: Mouse embryonic stem cells

growth_protocol: TX1072 XXΔXic and TX1072 XO Cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901, Axon).

extract_protocol:
The lysates were pre-cleared by centrifugation and per 10.000.000 cells supplemented with 2.4ng equimolar mix of in vitro transcribed S4U-labelled and unlabeled ERCC spike-ins, as described by Schwalb et al., 2016. Total RNA was extracted from Trizol with chloroform. In short, 200ul chloroform was mixed per ml lysate and phase separated by centrifugation in phase-lock tubes. RNA was precipitated from the aqueous phase with Isopropanol supplemented with 0.1 mM DTT and centrifugation for 10 minutes at 16.000x g and 4°C. The RNA pellet was washed once with 75% Ethanol and resuspended in Nuclease free water. Residual genomic DNA was removed in solution with DNaseI (Qiagen) following the manufacturer’s guidelines. The total RNA was purified for a second round with the Direct-zol RNA Miniprep Plus kit (Zymo Research) by following the manufacturer’s guidelines but in addition including 100 mM DTT in all wash buffers to prevent oxidation of S4U-labeled RNA. For each TT-seq reaction 300ug of purified RNA was divided over 2 Covaris MicroTubes and fragmented on the Covaris S2 platform for 10 s, 1% duty cycle, intensity 2, 1 cycle, 200 cycles/burst. Each corresponding sample was pooled and 3ug taken aside for quality control (BioAnalzyer fragment size check and spike-in qRT-PCR) and for NGS as input total RNA.  The remaining S4U-treated RNA (~260ul) was biotinylated by adding to 400 ul Biotin-HPDP (0.5ug/ul in DMSO)  100 ul 10x Biotinylation buffer and incubated for 1.5 hours on a thermoblock at 37°C with 750 rpm agitation. To clean up any unreacted Biotin-HPDP, the biotinylated RNA was extracted with phenol:chloroform (PCI) 5:1, pH 4.5) (Ambion). For this an equal volume of PCI was mixed with the biotinylated RNA and phase separated by centrifuging in phase-lock tubes at 12,000x g for 5 min. The aqueous phase was collected, mixed with an equal volume of Isoproponol and 1:10 volume of 5 M NaCl, and centrifuged at 16,000x g for 15 min 4°C to precipitate the biotinylated RNA. The RNA pellet was washed twice with 500ul 75% ethanol and dissolved in 50ul RNase-free water. Nascent biotinylated RNAs were enriched with MACS streptavidin μBeads.
Nascent RNA samples were subjected to strand-specific RNA-seq library preparation with the KAPA RNA HyperPrep kit with RiboErase (Illumina, #KR1351), which included 1st and 2nd strand synthesis and ribosomal RNA depletion, by following the manufacturers guidelines. The libraries were subjected to Illumina NGS PE75 (for TX1072 XXΔXic) on the HiSeq 4000 platform or PE100 (for TX1072 XO) on the NovaSeq 500 platform with approximately 100 million fragments per sample.

treatment_protocol: Differentiation was induced for 0, 2 or 4 days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol in fibronectin-coated (10 μg/ml) tissue culture plates. Cells were metabolically labeled with culture medium containing 750 μM 4-Thiouridine (S4U) (Sigma Aldrich) for 5 minutes at 37 °C and 5% CO2.

tag: cell line

value: TX1072 XXdXic

tag: condition

value: Day 4

tag: replicate

tag: strain background

value: CAST / C57BL/6

tag: assay

value: RNA-seq

value: Mouse embryonic stem cells


title: RNA_TX1072_XXdXic_d0_r2

value: Day 0


title: RNA_TX1072_XXdXic_d0_r1


title: TT_TX1072_XXdXic_d4_r2

data_processing:
Library strategy: TT-seq
An “N-Masked” genome of the mouse reference genome mm10 was generated using SNPsplit (0.3.2). For this, all the polymorphic sites of the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 were masked by ambiguity nucleobase ‘N’ as described previously (Pacini et al. 2020, Barros de Andrade E Sousa et al. 2019).
The reads were aligned using STAR (2.7.5a) with options [–outSAMattributes NH HI NM MD] to the N-masked mm10 genome (Dobin et al. 2013).
SAM files were translated into BAM files, filtered for properly paired reads and sorted using samtools (1.10) with options [view -b -h -f 3 -q 7] and [sort] (Li et al. 2009)
Blacklisted regions for mm10 (ENCODE Project Consortium 2012) were removed using bedtools (2.29.2) with options [intersect -v] (Quinlan and Hall 2010).
Duplicates were marked and removed using Picard (2.18.25) with options [MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE] (http://broadinstitute.github.io/picard)
BAM files were split according to the strand of the reads using a custom shell script
BigWig tracks were created using deepTools (2.0) with options [bamCoverage -e -bs 10 --normalizeUsing CPM -ignore chrX chrY] for TT-seq and [bamCoverage -bs 10 --normalizeUsing CPM -ignore chrX chrY] for RNA-seq (Ramírez et al. 2016). They were then visualized using the UCSC Genome Browser (Kent et al. 2002).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig: Coverage tracks

value: TT-seq


title: Unstimulated osteoblast 12 day, rep3


title: RNA_TX1072_XXdXic_d4_r1


title: TT_TX1072_XXdXic_d4_r1


title: TT_TX1072_XXdXic_d2_r2

value: Day 2


title: MQ72_10_r3

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and data were normalized with quantile normalization. This experiment was performed as a two-colour experiment, but data were analyzed as single-channel arrays. Raw data files are available as a tar archive on the series record.

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/ml, 72 hours, replicate 3

extract_protocol: Cells were harvested and lysed with lysing buffer (Qiagen). Total RNA was extracted and purified with the Rneasy Mini Kit by Qiagen following the kits' instructions.

value: THP-1 monocytes

tag: differentiation

value: PMA differentiated macrophage

tag: dose

value: 10 µg/ml

tag: exposure time

value: 72 hours

value: rCNT


title: SBP stimulated osteopblast 12 day, rep2

source_name: SBP stimulated osteoblast cells

value: bone (iliac crest)

value: SBP


title: TT_TX1072_XXdXic_d0_r2


title: SBP stimulated osteopblast 12 day, rep1

value: osteoblast


title: TT_TX1072_XXdXic_d2_r1


title: SBP stimulated osteopblast 12 day, rep3


title: ATAC_TX1072_XO_d4_r2

data_processing:
Read sequences were trimmed using Trim Galore (0.6.4) with options [--paired --nextera] (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
An “N-Masked” genome of the mouse reference genome mm10 was generated using SNPsplit (0.3.2). For this, all the polymorphic sites of the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 were masked by ambiguity nucleobase ‘N’ as described previously (Pacini et al. 2020, Barros de Andrade E Sousa et al. 2019).
The trimmed FASTQ files were aligned to the masked mm10 genome using bowtie2 (2.3.5) with the options [--local --very-sensitive-local -X 2000] (Langmead and Salzberg 2012)
SAM files were translated into BAM files, filtered for paired and mapped reads and sorted using samtools (1.10) with options [view -b -h -f 2 -q 20] and [sort] (Li et al., 2009).
Mitochondrial reads were removed using a custom Python script.
Blacklisted regions for mm10 (ENCODE Project Consortium 2012) were removed using bedtools (2.29.2) with options [intersect -v] (Quinlan and Hall 2010).
Duplicates were marked and removed using Picard (2.18.25) with options [MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE] (http://broadinstitute.github.io/picard)
BigWig tracks were created using deepTools2 (3.4.1) with options [bamCoverage -e -bs 10 --normalizeUsing CPM -ignore chrX chrY] (Ramírez et al. 2016) and visualized using the UCSC Genome Browser (Kent et al. 2002).
Peaks were called using MACS2 (2.1.2) with options [callpeak -f BAMPE -g mm -q 0.05] (Zhang et al. 2008).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig: Coverage tracks
Supplementary_files_format_and_content: narrowPeak: Peak files

growth_protocol: TX1072 XXΔXic and TX1072 XO Cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901, Axon) at a density of 1.56*10^4 cells/cm2 (Day 0) or 2.4*10^4 cells/cm2 (Day 2 and 4).

extract_protocol:
Per reaction, 60.000 cells were collected and lysed in 50 μl cold RSB plus buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1 % Igepal CA-630, 0.01% Digitonin). The lysis was washed out using 1 ml of cold RSB buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). Nuclei were then pelleted via centrifugation (500 x g, 10 min, 4 °C) and the supernatant aspirated. Subsequently, they were resuspended in 50 μl Transposase Mix (1x TD buffer (Illumina), 100 nM Nextera Tn5 Transposase (Illumina), 33% PBS, 0.01% Digitonin, 0.1% H2O) and incubated at 37 °C  for 30 minutes at 1000 rpm. The reaction was stopped by adding 2.5 μl 10% SDS and purified using the DNA Clean & Concentrator Kit (Zymo).
20 ul of the transposed DNA was amplified using the NEBNext High-Fidelity 2x PCR Master mix with i5 and i7 Nextera barcoded primers for 12 cycles. The PCR product was size-selected using NGS Clean beads (CleanNA), by adding them at first at a 70%-ratio and transferring the supernatant. Afterwards, the beads were added once more at a 180%-ratio and the PCR product was eluted from the beads in 20 μl H2O. The success of the transposition was verified with the BioAnalyzer High Sensitivity DNA system (Agilent Technologies). Sequencing libraries were pooled in equimolar ratios and sequenced paired-end 75 bp on the HiSeq 4000 platform yielding approximately 25.000.000 fragments per sample.

treatment_protocol: Differentiation was induced for 0, 2 or 4 days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol in fibronectin-coated (10 μg/ml) tissue culture plates.

value: TX1072 XO

value: ATAC-seq


title: ATAC_TX1072_XO_d2_r2


title: RNA_TX1072_XXdXic_d2_r1

value: TX1072 XXdXic


title: ATAC_TX1072_XO_d0_r2

value: CAST / C57BL/6


title: ATAC_TX1072_XO_d2_r1


title: pA_RNA_TX1072_XX_d2

data_processing:
An “N-Masked” genome of the mouse reference genome mm10 was generated using SNPsplit (0.3.2). For this, all the polymorphic sites of the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 were masked by ambiguity nucleobase ‘N’ as described previously (Pacini et al. 2020, Barros de Andrade E Sousa et al. 2019).
The reads were aligned using STAR (2.7.5a) with options [–outSAMattributes NH HI NM MD] to the N-masked mm10 genome (Dobin et al. 2013).
SAM files were translated into BAM files, filtered for properly paired reads and sorted using samtools (1.10) with options [view -b -h -f 3 -q 7] and [sort] (Li et al. 2009)
Blacklisted regions for mm10 (ENCODE Project Consortium 2012) were removed using bedtools (2.29.2) with options [intersect -v] (Quinlan and Hall 2010).
Duplicates were marked and removed using Picard (2.18.25) with options [MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE] (http://broadinstitute.github.io/picard)
BAM files were split according to the strand of the reads using a custom shell script
BigWig tracks were created using deepTools2 (3.4.1) ( with options [bamCoverage -bs 10 --normalizeUsing CPM -ignore chrX chrY] for RNA-seq (Ramírez et al. 2016).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig: Coverage tracks

growth_protocol: TX1072 XX Cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901, Axon).

extract_protocol:
Cells were lysed directly in the plate by adding up to 1 ml of Trizol (Invitrogen). RNA was isolated using the Direct-Zol RNA Miniprep Kit (Zymo Research) following the manufacturer’s instructions with on-column DNAse digestion.
Total RNA was subjected to strand-specific RNA-seq library preparation with the TruSeq® RNA Sample Preparation Kit v2 (Illumina), which included polyadenylated RNA enrichment using oligo-dT magnetic beads, by following the manufacturers guidelines.

treatment_protocol: Differentiation was induced for 2 days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol in fibronectin-coated (10 μg/ml) tissue culture plates.

value: TX1072 XX

value: RNA-seq


title: ATAC_TX1072_XO_d0_r1

value: Day 0

value: Mouse embryonic stem cells


title: ATAC_TX1072_XXdXic_d4_r2

value: Day 4


title: CoTECH_nopreAmplification_DNA

tag: chip antibody


title: ATAC_TX1072_XXdXic_d2_r1

value: Day 2


title: ATAC_TX1072_XXdXic_d2_r2


title: ATAC_TX1072_XXdXic_d4_r1


title: ATAC_TX1072_XO_d4_r1


title: RNA_TX1072_XXdXic_d2_r2


title: IDH_mut [RNA-Seq]

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University of Freiburg Medical Center

description: Bulk RNA library from GL261 cells

data_processing:
Instrument Model: Illumina HighSeq4000
Pipeline version: bcl2fastq 2.20.0.422
Sequencing kit: HiSeq 3000/4000 SE
Sequencing software: HCS HD 3.4.0.38
Basecall softwares: RTA 2.7.7
BaseQual encoding Phred+33
Read alignment and transcript quantification were conducted using usegalaxy.eu with RNA-STAR v2.7.5b and featureCounts v1.6.4+galaxy2
Genome_build: mm10
Supplementary_files_format_and_content: filtered and unfiltered counts files and metadata

source_name: GL261 episomally overexpressing R132H IDH1

growth_protocol: Cells were grown in DMEM medium substituted with 10% Fetal bovine serum, 100 U/ml Penicilin and Streptomycin.

extract_protocol:
RNA was extracted using PicoPure™ RNA-Isolation kit, Thermo Fisher Scientific
Libraries were prepared from cell lysates.
Illumina TruSeq Stranded RNA

treatment_protocol: GL261 glioma cell lines were episomally expressing wildtype or R132H-mutated Isocitrate Dehydrogenase 1.

value: GL261 cell line


title: ATAC_TX1072_XXdXic_d0_r2


title: IDH_wt [RNA-Seq]

description: Bulk RNA library from GL261 cells

source_name: GL261 episomally overexpressing wildtype IDH1

value: wildtype


title: RH4_4

description:
10x Genomics Library prepared with the 10x Single Cell 3' v2 Kit
Mm_CD45_IDH_SMAR_6mice_filtered_feature_bc_matrix.h5

data_processing:
Instrument Models: Illumina HighSeq4000 and NOVASEQ6000
Pipeline version: bcl2fastq 2.20.0.422
Sequencing kits: HiSeq 3000/4000 PE and S2
Sequencing software: HCS HD 3.4.0.38 and HCS 1.6.0
Basecall softwares: RTA 2.7.7 and RTA v3.4.4
BaseQual encoding Phred+33
Read alignment and transcript quantification were conducted using cellRanger v3.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: filtered and unfiltered counts files and metadata
Supplementary_files_format_and_content: cell metadata table
Supplementary_files_format_and_content: Seurat object

source_name: brain tumor xenograft

growth_protocol: C57BL/6J wild-type (wt) mice were purchased from Charles River. Mice were bred according to local regulatory authorities (breeding approval reference Z124I02). All mice were 7-10 weeks of age at use. Mice were kept under specific pathogen-free conditions at the animal facility of the DKFZ Heidelberg.

extract_protocol:
Tumors were dissociated after d7 (early) and d28 (late) and FACS purified based on CD45-expression using anti-CD45.2 (clone 30-F11, BioLegend, San Diego, USA)
10x libraries were prepared from FACS-purified CD45+ cells in a single run.
10x Single Cell 3' v2 Kit

treatment_protocol: 1 x 10E4 GL261 tumor cells were diluted in 2 µl sterile PBS (Sigma-Aldrich) and stereotactically implanted into the right hemisphere of 7-10 weeks old female C57BL/6J mice (coordinates: 2 mm right lateral of the bregma and 1 mm anterior to the coronal suture with an injection depth of 3mm below the dural surface) using a 10µl Hamilton micro-syringe driven by a fine step stereotactic device (Stoelting).

tag: time point

value: late timepoint

value: GL261 episomally overexpressing R132H-mutated IDH1 xenograft

value: FACS-sorted CD45+ cells


title: TT_TX1072_XXdXic_d0_r1

value: TT-seq

tag: cell type


title: ATAC_TX1072_XXdXic_d0_r1


title: RH4_2

tag: genotype


title: RH4_1


title: RH4_3


title: RH3_1


title: RH3_4


title: RH2_2


title: RH2_4


title: RH1_4


title: RH2_3


title: RH1_3


title: RH2_1


title: RH1_2


title: WT4_3

value: GL261 episomally overexpressing wildtype IDH1 xenograft


title: WT4_4


title: WT3_2


title: WT3_4


title: WT3_3


title: WT4_1


title: WT4_2


title: WT3_1


title: WT2_3


title: WT2_4


title: WT1_4


title: WT2_2


title: WT1_3


title: WT1_2


title: RH1_1


title: RH3_3


title: coculture.shEphB6.31.3

city: Padova

first: Marco

last: Montagner

state: PD

address: viale G. Colombo, 3

country: Italy

institute: University of Padua

description:
shEphB6 sequence: CCGGCGAGAGGTTGACCCTACATATCTCGAGATATGTAGGGTCAACCTCTCGTTTTT
HOO649A24

data_processing:
Biological replicate libraries were prepared using the polyA KAPA mRNA HyperPrep Kit and sequenced on Illumina HiSeq 4000 platform, generating ~24 million 100bp single-end reads per sample. Read quality trimming and adaptor removal was carried out using Trimmomatic (version 0.36).
The RSEM package (version 1.3.30)  in conjunction with the STAR alignment algorithm (version 2.5.2a)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl human GRCh38.89 version transcriptome. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.18.1)
Genome_build: Ensembl mouse GRCm38.89
Supplementary_files_format_and_content: Tab delimited text files containing normalised data. Rows represent Ensembl mouse genes and columns represent individual samples.

source_name: Culture on plastic

growth_protocol: MLNL medium (low-glucose DMEM/1% FCS)

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen) following manifacturer's protocol
RNA samples were assessed for quantity and integrity using the NanoDrop 8000 spectrophotometer v.2.0 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyser (Agilent Technologies), respectively. Biological replicate libraries were prepared using the polyA KAPA mRNA HyperPrep Kit and sequenced on Illumina HiSeq 4000 platform, generating ~24 million 100bp single-end reads per sample.

treatment_protocol: D2.0R-EGFP-shControl or D2.0R-EGFP-shEphB6 (1,8x105 cells/well) were plated on top of AT1-like cells (1,36x106 cells/sample) in MLNL medium (in 60 mm dish) for three days before separation by Fluorescence-Activated Cell Sorter (FACS) based on EGFP signal. EGFP-+cells (D2.0R cells) were subjected to analysis.

value: D2.0R-EGFP-shEphB6 cells cocultured with AT1-like cells


title: coculture.shEphB6.31.1

description:
shEphB6 sequence: CCGGCGAGAGGTTGACCCTACATATCTCGAGATATGTAGGGTCAACCTCTCGTTTTT
HOO649A22


title: WT1_1


title: coculture.shCtrl.3

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
HOO649A18

value: D2.0R-EGFP-shControl cells cocultured with AT1-like cells


title: coculture.shEphB6.35.2

description:
shEphB6 sequence: CCGGCCACAGCCTGAGCAAACAAATCTCGAGATTTGTTTGCTCAGGCTGTGGTTTTTG
HOO649A29


title: coculture.shCtrl.1

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
HOO649A16


title: monoculture.shCtrl.1

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
HOO649A4

value: D2.0R-EGFP-shControl cells cultivated on plastic


title: monoculture.shCtrl.2

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
HOO649A5


title: RH3_2


title: WT2_1


title: shEPHB6_3

description:
shEphB6 sequences: CCGGCGAGAGGTTGACCCTACATATCTCGAGATATGTAGGGTCAACCTCTCGTTTTT, CCGGCCCTGGACTACATCTACTGATCTCGAGATCAGTAGATGTAGTCCAGGGTTTTT, CCGGCCACAGCCTGAGCAAACAAATCTCGAGATTTGTTTGCTCAGGCTGTGGTTTTTG
SAH606A9

source_name: Breast cancer cells isolated from mouse lungs

extract_protocol:
Lungs and primary tumors were harvested from mice, immersed in PBS, and promptly chopped with scissors to small fragments. Minced lungs were then added to digestion solution (PBS buffer with 75mg/ml TM Liberase, Roche 05401151001, 75mg/ml TH Liberase, Roche 05401127001, 12.5mg/ml DNAse, Sigma-Aldrich DN25) for 1hr at 37°C, rocking. Digested lung pieces were spun down for 5’ at 1300rpm, re-suspended in calcium- and magnesium-free PBS plus 1mM EDTA by vigorous pipetting until the solution was homogeneous and eventually filtered through a 70mm cell strainer to remove undigested fibrous tissue. In the case of stiffer tissues, such as primary tumors, tissue fragments were also mechanically disrupted by passing them through needles of decreasing thickness. Cells were then pelleted and red blood cells lysed with Red Blood Cells Lysis Solution (Miltenyi Biotec, 130-094-183) following manufacturer protocol. After washing, cells were re-suspended in FACS buffer (PBS, 2mM EDTA, 3%BSA) and labelled with CD45-APC antibody for 30min (eBiosciences, 30-F11, 1:400) to avoid contamination from leukocytes during sorting. Samples were then washed repeatedly, filtered through a 70mm cell strainer and kept on ice during fluorescence-activated cell sorting.  Total RNA was extracted with RNeasy Plus Micro kit (Qiagen) following manufacturer protocol. RNA samples were assessed for quantity and integrity using the NanoDrop 8000 spectrophotometer V2.0 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyser (Agilent Technologies), respectively.
RNA samples were assessed for quantity and integrity using the NanoDrop 8000 spectrophotometer v.2.0 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyser (Agilent Technologies), respectively. Biological replicate libraries were prepared using the polyA KAPA mRNA HyperPrep Kit and sequenced on Illumina HiSeq 4000 platform, generating ~24 million 100bp single-end reads per sample.

treatment_protocol: D2.0R-EGFP-shControl (1x106 cells/mouse) or a mix of D2.0R-EGFP-shEphB6 cells (three population, each with a different shRNA sequwence) were injected in the tail vein of nude athymic BALB/c mice. After two weeks, lungs were harvested and digested into a single-cell suspension as described above. CD45-/EGFP+ cells were sorted directly into lysis buffer and total RNA was extracted with RNeasy Plus Micro Kit (Qiagen) following the manufacturer’s instructions.

value: Isolated from lungs


title: shEPHB6_1

description:
shEphB6 sequences: CCGGCGAGAGGTTGACCCTACATATCTCGAGATATGTAGGGTCAACCTCTCGTTTTT, CCGGCCCTGGACTACATCTACTGATCTCGAGATCAGTAGATGTAGTCCAGGGTTTTT, CCGGCCACAGCCTGAGCAAACAAATCTCGAGATTTGTTTGCTCAGGCTGTGGTTTTTG
SAH606A7


title: Ad-shRNA scramble rep2

data_processing:
Trimmed, clean reads were mapped to the rat reference genome (Rnor_6.0) using the SOAP2 software and allowing five mismatches(Li et al., 2009).
Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
A FDR of no more than 0.05 (FDR ≤ 0.05) and a difference ratio of the FPKM between controls and CKLF1 samples of no less than 1 (|log2 ratio| ≥ 1) were adopted as the significance thresholds to identify DEGs.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: txt files include FPKM values for each Sample.

source_name: Rat vascular smooth muscle cells

extract_protocol:
Total RNA of 12 samples were isolated from adenovirus treated primary vascular smooth cells using Trizol reagent (Invitrogen) according to the manufacturer's instruction.
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primed reverse transcription. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation is then performed. After the previous step, adaptors are ligated to the end of these fragments. Next, ligation products were selected by size and purified on TAE-agarose gel. Finally, the fragments are enriched by PCR amplification, then purified by magnetic beads and dissolved in the appropriate amount of Epstein-Barr solution. During the QC step, Agilent 2100 Bioanaylzer are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina X Ten platform.

tag: Sex

value: male

tag: genotype/variation

value: control sample

tag: strain

value: Sprague-Dailey


title: shCtrl_2

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
SAH606A2


title: coculture.shEphB6.35.3

description:
shEphB6 sequence: CCGGCCACAGCCTGAGCAAACAAATCTCGAGATTTGTTTGCTCAGGCTGTGGTTTTTG
HOO649A30


title: coculture.shCtrl.2

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
HOO649A17


title: SNI10

city: Chapel Hill

first: Jesse

last: Niehaus

state: NC

address: 116 Manning Drive, 7008B Mary Ellen Jones Building

department: Neuroscience Center

institute: University of North Carolina at Chapel Hill

data_processing:
Cells and UMIs demultiplexed, quality filtered, and poly-A trimmed using FASTQ files were converted to BAM format, tagged with cell and molecular barcodes, quality-filtered, trimmed, polyA-trimmed, and converted back to FASTQ as previously described (Macosko et al., 2015; Shekhar et al., 2016). Reads were aligned to a mouse-human hybrid genome (mm10-hg19) using STAR (Dobin et al., 2013), then sorted, merged, and exon-tagged as described (Macosko et al., 2015; Shekhar et al., 2016). Bead synthesis errors were corrected as described (Shekhar et al., 2016), and BAM files were separated into those containing mouse or human reads. UMIs were determined to be species-specific if >90% of the transcripts came from that species or considered a doublet if neither species achieved 90% specificity. UMIs were not considered if the transcript count sum (mouse+human) was less than 500. Gene expression matrices were then created using only the mouse-specific UMIs, as described (Macosko et al., 2015; Shekhar et al., 2016). Gene expression matrices were combined from multiple biological replicates; data values for one or more replicates that did not detect a given gene were assigned to zero. Processing steps utilized the Drop-seq Toolkit v1.12 where possible. Drop-seq_tools-2.3
Cells expressing fewer than 400 unique genes or whose mitochondrial transcripts exceeded 10% of total transcripts were removed. Genes were removed if they were not represented in at least 30 cells with at least 3 transcripts. We then performed two rounds of batch correction (by animal cohort and Drop-seq day) using ComBat (Johnson et al., 2007). The resulting gene expression matrix was median centered and log-transformed to generate our finalized dataset.
Clusters were established and optimized using “significant” principal components (PCs) as described previously (Loo et al., 2019; Shekhar et al., 2016). Briefly, eigenvalues were calculated from randomly permutating out dataset (n=1000). PCs with eigenvalues greater than those generated from random permutations were used for clustering (n = 60). Louvain-Jaccard clustering was performed with a silhouette score-optimized (Pearson correlation distance) nearest neighbor parameter as described previously (Loo et al., 2019; Shekhar et al., 2016). This resulted in 20 cell clusters.
To resolve cell types with more specificity, the above pipeline was performed a second time on each of the initial 20 clusters. The second clustering iteration was identical to the first with two key cluster refinement exceptions. First, a set of oligodendrocyte-related genes were removed for the second round of clustering (with the exception of the two initial clusters that were classified as oligodendrocytes) in order to remove unwanted signal caused by myelin debris. Second, clusters lacking at least one marker gene (enriched by > 1.0 log10 fold-change compared to other clusters) were merged with the next most similar cluster (Pearson correlation). This resulted in 69 clusters transcriptionally distinct clusters. After annotating each of the 69 clusters, three low-quality clusters were removed based on signs of doublets (expressing genes from two cell types), resulting in 66 final clusters.
Genome_build: mm10hg19 hybrid
Supplementary_files_format_and_content: tab-delineated .txt; gene expression matrix

source_name: L1-6 mouse spinal cord

extract_protocol:
Animals were perfused with aCSF supplemented with ion channel inhibitors. Lumbar spinal cord segments were dissected and dissociated in aCSF supplemented with 2mg/mL Collagenase + 2mg/mL Protease from streptomyces griseus. A percoll gradient was used to isolate cells from debris. Cells were then methanol fixed and stored in -80 before being rehydrated for Drop-seq.
Drop-seq was carried out as described (Loo et al 2019). RNAs were captured with Chemgenes oligodT barcoded beads (Macosko2015). Reverse transcription was performed using Maxima H Minus Reverse Transcriptase (ThermoFisher; EP0751). Libraries were amplified with KAPA Hi-Fi master mix and tagged using a Nextera XT DNA sample preparation kit (N701-N707, N711, N712, N714-N726)
Single-cell RNA seq (Drop-seq); Pooled libraries

tag: spike-ins

value: Human embryonic kidney cell

tag: dropseq day

tag: cohort


title: coculture.shEphB6.31.2

description:
shEphB6 sequence: CCGGCGAGAGGTTGACCCTACATATCTCGAGATATGTAGGGTCAACCTCTCGTTTTT
HOO649A23

tag: cell line

tag: treatment


title: SNI07


title: SNI09


title: SNI05


title: SNI02


title: SI10


title: SNI03


title: SI06


title: SI08


title: SNI01


title: SI09


title: monoculture.shCtrl.3

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
HOO649A6


title: shEPHB6_2

description:
shEphB6 sequences: CCGGCGAGAGGTTGACCCTACATATCTCGAGATATGTAGGGTCAACCTCTCGTTTTT, CCGGCCCTGGACTACATCTACTGATCTCGAGATCAGTAGATGTAGTCCAGGGTTTTT, CCGGCCACAGCCTGAGCAAACAAATCTCGAGATTTGTTTGCTCAGGCTGTGGTTTTTG
SAH606A8


title: shCtrl_3

description:
shControl sequence: CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTT
SAH606A3


title: SI04


title: SNI08


title: SI02


title: SI03


title: SI01


title: SNI06


title: SI05


title: shEPHB6_4

description:
shEphB6 sequences: CCGGCGAGAGGTTGACCCTACATATCTCGAGATATGTAGGGTCAACCTCTCGTTTTT, CCGGCCCTGGACTACATCTACTGATCTCGAGATCAGTAGATGTAGTCCAGGGTTTTT, CCGGCCACAGCCTGAGCAAACAAATCTCGAGATTTGTTTGCTCAGGCTGTGGTTTTTG
SAH606A10