title: HCT116-Control rep 2

tag: cell type

value: Colon

tag: disease state

value: colorectal carcinoma

tag: p53 genotype

value: wildtype

value: no treatment


title: ANTHER-WTLD16:00_rep1

status: Public on Mar 30 2021

type: SRA

city: Shanghai

first: Jingbin

last: Li

address: 800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

description: ANTHER_All counts.txt

library_source: transcriptomic

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to rice  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: Tigr7
Supplementary_files_format_and_content: TXT file contain counts for each sample

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: Stage 12 anther

growth_protocol: Oryza sativa L. ssp. japonica 9522 curtiva was grown in paddy fields of Shanghai (China) from June–August).

extract_protocol:
Total RNA, excluding miRNAs, was extracted using TRIzol (Life Technologies) for RNA sequencing according to the manufacturer’s protocol. C
DNA libraries were prepared with the FastQuant RT Kit with DNase (Tiangen), according to manufacturer’s instructions.

treatment_protocol: By the middle of August (initiation of reproductive development), the daylength is ~14.5 h (LD photoperiod). Rice plots (WT and csa) were divided into two groups, and SD photoperiod (12 h light) was simulated by covering plants in one group with lightproof plastic film from 18:00 to 6:00 of next day.

tag: genotype

value: WT

tag: tissue

value: Anther

tag: development stage

value: Stage 12

tag: treatment

value: long day photoperiod

tag: collection time


title: HCT116-Control rep 1

city: Rochester

first: Julia

last: Freewoman

state: NY

address: 1 Lomb Memorial Dr

department: Thomas H. Gosnell School of Life Sciences

country: USA

institute: Rochester Institute of Technology

data_processing:
University of Rochester Genomics Research Center (URGRC) sequenced the samples and the resulting raw reads were cleaned using Trimmomatic-0.32 with a cutoff 25 bp for the read size
The filtered fastq were further cleaned by FASTX-toolkit (version 0.0.13) with a quality score cutoff of 28. Then, cutadapt (version 1.10) was used to filter out all reads greater than 50bp.
Reads in the FASTQ files were aligned to the human genome assembly hg19 using TopHat (version 2.1.1) with the default setting.
The resulting BAM files were sorted by SAM-tools (version 1.3.1) for visualization in the UCSC Genome Browser.
Following the Cufflinks (version 2.2.1) pipleline for version 2.0 and greater CuffDiff2 was used for differential expression analysis.
For DESeq2 (version 2_1.24.0, ref. 33), read counts for each gene were calculated using htseq-count (version 0.10.0, ref. 32) using the bam files produced by TopHat and sorted by Samtools (version 1.9) by position. Following the tutorial of the Bioconductor package DESeq2 was used for differential expression analysis.
Genome_build: HG19
Supplementary_files_format_and_content: matrix_deseq2.txt.   Matrix of the normalized count values from DESeq2 from the counts command with the first column as the name of gene and following columns the normalized count values for each replicate
Supplementary_files_format_and_content: matrix_cuffdiff2.txt.   Matrix of the FPKM values from CuffDiff2 from the repFpkmMatrix call along with the featureNames with the first column as the name of gene and following columns the normalized count values for each replicate.

organism: Homo sapiens

source_name: Colon Cancer Cells

growth_protocol: HCT116 p53 cells were grown in recommended McCoy’s 5a modified media with 10% FBS and 1X antibiotic mix. Cells were grown in the media at 37º C with 5% CO2 in a 35 mm plates until 70-80% confluence

extract_protocol:
RNA was extracted following the instruction of the QUIAGEN RNeasy Mini Kit and the QIAshredder (QIAGEN) was used during the RNeasy Kit’s lyse and homogenization stage. The RNA concentration was determined using NanoDrop (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 6, 12 or 24 hours prior to RNA extraction, the media was changed and 2 ml of fresh media, along with fluorouracil (5-FU) (with final concentration of 375 µM) or 2uL dimethyl sulphoxide (DMSO) were added to the cells. The DMSO-treated samples were used as controls because DMSO is the solvent of 5-FU. Non-treatment controls were also set up. For each treatment and each time point, two biological replicates were performed.

tag: cell line

tag: time


title: ANTHER-csaLD16:00_rep2

description: ANTHER_All counts.txt

value: csa


title: PT45_Ep_1

city: New York

first: Sagar

last: Chhangawala

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

data_processing:
fastq files were aligned using STAR (v2.5.0b, default parameters)
Read counting was performed using htseq-count (v0.9.1, parameters: --stranded=no -t exon)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file that contains gene IDs and read counts for each sample

molecule: polyA RNA

source_name: PDAC EpCAM+ primary tumor

extract_protocol:
DNA and RNA were extracted from same samples of each of the EpCAM+ and EpCAM- subpopulations using Qiagen All-prep DNA/RNA micro kit (Qiagen Cat # 80284) following manufacturer’s standard guidelines.
Library was constructed using QuantSeq FWD HT Kit (015.384) based on manufacturer's protocol
Quant-seq

tag: tumor differentiation

value: moderately diff

tag: margin status

value: Positive

tag: tumor stage

value: T3 N1

tag: adjuvant therapy

value: Yes

tag: radiotherapy

value: No

tag: recurrence status


title: CTL_11

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

data_processing:
STAR 2.7.3a aligner
Ensembl Transcripts release 100 annotations
Genome_build: hg38
Supplementary_files_format_and_content: Matrix with raw gene counts before normalization

source_name: Human control tissue

extract_protocol:
RNAs were isolated using the Qiagen RNeasy Mini Kit per manufacturer’s instructions.
the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® was used and mRNA enriched using oligo(dT) beads.
Constructed cDNA libraries that pass a library quality control test (consists of Qubit, LabChip fragment analysis, and qPCR steps) are sequenced on an Illumina NovaSeq 6000 PE150 platform.

tag: Sex

value: Female

value: CTL

tag: tumor

value: PA

tag: age


title: ANTHER-csaSD04:00_rep2

description: ANTHER_All counts.txt

value: short day photoperiod


title: PA_27

source_name: Human tumor tissue


title: ANTHER-csaSD04:00_rep1

description: ANTHER_All counts.txt


title: PolII_HAP1_UV_4h_R2

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Library strategy: mNET-seq
Adapters were trimmed with Cutadapt v1.13
Mapping to the hg38 genome was performed with STAR v2.6.1d.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1
Mapped reads were de-duplicated with Picard (ChIRP-seq)
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
Bigwig files were generated with the Deeptools2 v2.5.0.1 bamCoverage tool
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

growth_protocol: HAP1 cells were maintained in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10% fetal bovine serum and 100 μg/ml of penicillin and streptomycin.

extract_protocol:
DNA for ChIRP-seq were purified from chromatin IP products. Nascent RNAs for mNET-seq were purified from Pol II IP products of solublilized chromatin.
For ChIRP-seq, libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions. For mNET-seq, libraries were prepared according to the protocols of NEBNext small RNA library preparation kit (NEB)

treatment_protocol: Cells were irradiated with UV light (254 nm, 40 J/m2) with Stratalinker (Fischer Bioblock Scientific)

tag: antibody

value: MABIO601:Anti-RNA Polymerase II CTD mAb. MBL International Corporation

value: Wild-type


title: PT42_Ep_1

value: Free

value: T3 N0


title: PT42_Eff_1

source_name: PDAC EpCAM- primary tumor


title: PolII_HAP1_UV_2h_R2

tag: genotype


title: PolII_HAP1_UV_1h_R2


title: ANTHER-csaSD16:00_rep2

description: ANTHER_All counts.txt

tag: tissue

value: Anther


title: PA_25

value: Male


title: PA_26


title: PT41_Eff_1


title: PolII_HAP1_UV_1h_R1


title: ANTHER-csaSD16:00_rep1

description: ANTHER_All counts.txt

tag: development stage

value: Stage 12


title: PA_28


title: PT4_Ep_1

value: moderately to poorly diff


title: PT43_Ep_1

value: moderately diff


title: PolII_HAP1_UV_0h_R2


title: PA_23


title: ANTHER-WTSD04:00_rep2

description: ANTHER_All counts.txt

value: WT

tag: treatment


title: PolII_HAP1_UV_0h_R1


title: PT43_Eff_1

value: T3 N1


title: PT4_Eff_1

value: Positive

value: Yes


title: PA_22

value: Female


title: PT39_Ep_1

value: No


title: ANTHER-WTSD04:00_rep1

description: ANTHER_All counts.txt

tag: collection time


title: ANTHER-WTSD16:00_rep1

description: ANTHER_All counts.txt


title: ANTHER-WTSD16:00_rep2

description: ANTHER_All counts.txt


title: PA_21

value: PA


title: PolII_7SK-KO_UV_4h_R2

tag: cell line

value: 7SK KO


title: PA_20


title: PolII_7SK-KO_UV_2h_R2

value: MABIO601:Anti-RNA Polymerase II CTD mAb. MBL International Corporation


title: PA_19


title: PolII_7SK-KO_UV_1h_R2


title: PT39_Eff_1


title: LEAF-csaLD04:00_rep1

description: LEAF_All counts.txt

source_name: Rice flag leaf at Stage 12 of anther development

value: csa

value: Flag leaf

value: long day photoperiod


title: PT41_Ep_1


title: PT37_Ep_1

value: Free


title: PolII_7SK-KO_UV_1h_R1


title: PT37_Eff_1


title: PA_18

value: Male


title: LEAF-csaLD00:00_rep1

description: LEAF_All counts.txt

value: Stage 12


title: PA_16


title: PT35_Ep_1

value: T2 N1


title: PolII_7SK-KO_UV_0h_R2


title: PT36_Ep_1

value: moderately diff


title: PolII_7SK-KO_UV_0h_R1


title: PT35_Eff_1


title: CTL_10


title: LEAF-csaLD20:00_rep2

description: LEAF_All counts.txt


title: IP_HAP1_UV-_R2

library_source: genomic

data_processing:
Library strategy: ChIRP-seq
Adapters were trimmed with Cutadapt v1.13
Mapping to the hg38 genome was performed with STAR v2.6.1d.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1
Mapped reads were de-duplicated with Picard (ChIRP-seq)
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
Bigwig files were generated with the Deeptools2 v2.5.0.1 bamCoverage tool
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

molecule: genomic DNA

value: Biotinylated oligonucleotides against 7SK snRNA

value: Wild-type


title: CTL_9


title: IP_HAP1_UV+_R2


title: LEAF-csaLD04:00_rep2

description: LEAF_All counts.txt


title: LEAF-csaLD20:00_rep1

description: LEAF_All counts.txt


title: LEAF-csaLD16:00_rep2

description: LEAF_All counts.txt


title: PT34_Eff_1

value: moderately to poorly diff

value: Positive

value: T3 N1


title: IP_HAP1_UV-_R1


title: IP_HAP1_UV+_R1


title: PT33_Ep_1

value: Yes

value: No


title: PA_17

value: PA


title: LEAF-csaLD12:00_rep2

description: LEAF_All counts.txt


title: PA_15

value: Female


title: PA_24


title: PA_14


title: CTL_8


title: LEAF-csaLD00:00_rep2

description: LEAF_All counts.txt

value: csa


title: IP_7SK-KO_UV+_R2

value: 7SK KO


title: PT33_Eff_1


title: LEAF-csaLD12:00_rep1

description: LEAF_All counts.txt

value: Flag leaf

value: long day photoperiod


title: IP_7SK-KO_UV-_R2


title: LEAF-csaLD16:00_rep1

description: LEAF_All counts.txt


title: LEAF-csaLD08:00_rep2

description: LEAF_All counts.txt


title: IP_7SK-KO_UV+_R1


title: PA_13

value: Male

value: Glioblastoma


title: PT34_Ep_1


title: PA_12


title: PT32_Ep_1


title: PT32_Eff_1


title: PA_11


title: IP_7SK-KO_UV-_R1


title: PT31_Ep_1


title: LEAF-WTLD04:00_rep2

description: LEAF_All counts.txt

value: WT

value: Stage 12


title: Input_HAP1_R2


title: LEAF-csaLD08:00_rep1

description: LEAF_All counts.txt


title: PT26_Ep_1

value: poorly diff

value: Free


title: PA_9


title: PA_10


title: LEAF-WTLD04:00_rep1

description: LEAF_All counts.txt


title: Input_HAP1_R1

value: Wild-type


title: Input_7SK-KO_R2


title: LEAF-WTLD00:00_rep2

description: LEAF_All counts.txt


title: PT26_Eff_1


title: LEAF-WTLD00:00_rep1

description: LEAF_All counts.txt


title: Input_7SK-KO_R1


title: PA_7


title: PA_8


title: PT25_Ep_1

value: moderately diff

value: Positive


title: LEAF-WTLD20:00_rep2

description: LEAF_All counts.txt


title: PA_6

value: Yes


title: JMJ28np5-OE_rep2

city: Taipei

first: Fu-Yu

last: Hung

address: Institute of Plant Biology, National Taiwan University

country: Taiwan

institute: NTU, IPB

data_processing:
The raw sequence data were processed and map the reads to the Arabidopsis genome (TAIR10)  by CLC genome work banch
To determine the correlation between biological repeats, Pearson correlation was computed using CLC software on normalized signal intensity. The DEGs were caculated by CLC.
The DEGs were caculated by CLC genome work banch.
Genome_build: TAIR 10
Supplementary_files_format_and_content: excel files

organism: Arabidopsis thaliana

source_name: 14 days old plants

growth_protocol: The Arabidopsis seedlings were grown under Long-day conditions at 22°C and harvested after 14 days.

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

tag: eco-type

value: seedlings

value: 14 days old


title: PT25_Eff_1

tag: tumor differentiation

value: T3 N1

value: No


title: JMJ28np5-OE_rep1


title: PT24_Ep_1

tag: margin status


title: PA_5

value: PA


title: jmj28_rep2


title: PA_4

value: Female


title: PT24_Eff_1

tag: tumor stage


title: PT31_Eff_1

tag: adjuvant therapy


title: LEAF-WTLD16:00_rep1

description: LEAF_All counts.txt

value: Flag leaf

value: long day photoperiod


title: PA_3


title: jmj28_rep1


title: PA_2

value: Male


title: WT_rep1

value: WT


title: PT23_Ep_1

tag: radiotherapy


title: PT21_Ep_1

value: T3 N0

tag: recurrence status


title: WT_rep2


title: JMJ28pro::JMJ28:3xFLAG_input

data_processing:
The raw sequence data were processed using the Illumina sequence data analysis pipeline GAPipeline 1.3.2. Bowtie2 was then employed to map the reads to the Arabidopsis genome (TAIR10).
To determine the correlation between biological repeats, Pearson correlation was computed using R statistical software on normalized signal intensity for ChIP binding peaks. The alignments were first converted to Wiggle (WIG) files using MACS2. The data were then imported into the Integrated Genome Viewer (IGV) for visualization. The program ChIPseeker2 was used to identify ChIP-enriched domains (peaks).
Genome_build: TAIR 10
Supplementary_files_format_and_content: Bed files

growth_protocol: The transgenic Arabidopsis seedlings were grown under Long-day conditions at 22°C and harvested after 14 days.

extract_protocol:
2 ng of DNA was pooled to ensure that there are enough starting DNA for library construction. Two biological replicates were prepared and sequenced for each ChIP-seq experiment. The ChIP DNA was first tested by qRT-PCR and then used to prepare ChIP-seq libraries.
End repair, adaptor ligation, and amplification were carried out using the Nebnext DNA Sample Prep kit according to the manufacturer's protocol.

value: seedling


title: PT21_Eff_1

value: poorly diff


title: LEAF-WTLD08:00_rep2

description: LEAF_All counts.txt

value: Stage 12


title: LEAF-WTLD12:00_rep2

description: LEAF_All counts.txt


title: JMJ28pro::JMJ28:3xFLAG_2


title: PT20_Ep_1

value: moderately to poorly diff

value: Free


title: LEAF-WTLD08:00_rep1

description: LEAF_All counts.txt


title: JMJ28pro::JMJ28:3xFLAG_1


title: PT20_Eff_1

value: Yes


title: LEAF-WTLD20:00_rep1

description: LEAF_All counts.txt


title: LEAF-csaSD04:00_rep2

description: LEAF_All counts.txt

value: csa

value: short day photoperiod


title: 143B-EC-8042-rep3

city: Oviedo

first: Rene

last: Rodríguez

state: Asturias

address: Av. Roma s/n

department: Sarcomas and Experimental Therapeutics

country: Spain

institute: Health Research Institute of Asturias (ISPA)

data_processing:
Pseudo-aligment and quantification were made with Salmon algorithm v1.2.1
Correlation analysis, principal component study and differential expression analysis were performed with DESeq2 package v1.24.0. Differential gene expression analyses were done using the parametric Wald test, with Benjamini-Hochberg adjustment (padj). Genes with padj <0.01 and a log2 fold change of ±1 were considered significantly expressed genes (DEGs).
fgsea package v1.10.1 was used for gene set enrichment of KEGG pathways and GO terms (Cellular Component - Biological Processes - Molecular Function)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files that include TPM values and raw counts per transcript

source_name: osteosarcoma cell line

growth_protocol: Cells cultured in DMEM 4.5g/l glucose + 10% FBS + 1X glutamax + 1X penicilyn/streptomicyn

extract_protocol:
Total RNA was extracted using the EURx Universal RNA Purification Kit (Ref: E3598)
NEBNext® Ultra Directional RNA protocol was used to prepare libraries for Illumina Novaseq 6000 paired-end 150bp sequencing

treatment_protocol: 24 hours treatment with either DMSO (control), 25 nM mithramycin, 25 mM Mithramycin A loaded in polymeric nanoparticles, 100 nM EC8042 or 300 nM EC8042

tag: cell type

value: tumor cell line


title: 143B-EC-8042-rep1


title: LEAF-WTLD12:00_rep1

description: LEAF_All counts.txt


title: LEAF-csaSD00:00_rep2

description: LEAF_All counts.txt


title: LEAF-WTLD16:00_rep2

description: LEAF_All counts.txt


title: LEAF-csaSD04:00_rep1

description: LEAF_All counts.txt


title: PT18_Ep_1

value: Positive

value: No


title: PT18_Eff_1


title: 143B-control-rep2

value: vehicle (DMSO)


title: PT23_Eff_1

value: T3 N1


title: LEAF-csaSD00:00_rep1

description: LEAF_All counts.txt

value: Flag leaf


title: 143B-control-rep3


title: PT17_Ep_1


title: PA_1

tag: Sex

value: Male

tag: tumor

value: PA


title: 143B-control-rep1


title: PT17_Eff_1


title: LEAF-csaSD20:00_rep2

description: LEAF_All counts.txt


title: T-5H-FC-EC-8042-rep3

source_name: myxoid liposarcoma model

value: mesenchymal stem cell-derived tumor model


title: 143B-EC-8042-rep2


title: PT16_Ep_1


title: PT16_Eff_1


title: LEAF-csaSD20:00_rep1

description: LEAF_All counts.txt


title: T-5H-FC-EC-8042-rep1


title: LEAF-csaSD16:00_rep2

description: LEAF_All counts.txt


title: PT14_Eff_1


title: LEAF-csaSD12:00_rep1

description: LEAF_All counts.txt


title: PT14_Ep_1


title: T-5H-FC-EC-8042-rep2


title: PT13_Ep_1


title: T-5H-FC-NP_MTA-rep2

value: 25 mM Mithramycin A loaded in polymeric nanoparticles


title: LEAF-csaSD12:00_rep2

description: LEAF_All counts.txt


title: T-5H-FC-free_MTA-rep3

value: 25 mM Mithramycin A


title: T-5H-FC-NP_MTA-rep3


title: PT13_Eff_1

value: poorly diff


title: PT12_Ep_1

value: moderately to poorly diff


title: T-5H-FC-free_MTA-rep2


title: LEAF-csaSD08:00_rep2

description: LEAF_All counts.txt

value: Stage 12


title: LEAF-WTSD04:00_rep2

description: LEAF_All counts.txt

value: WT


title: T-5H-FC-free_MTA-rep1


title: LEAF-csaSD08:00_rep1

description: LEAF_All counts.txt

value: csa


title: LEAF-WTSD04:00_rep1

description: LEAF_All counts.txt

value: short day photoperiod


title: PT10_Ep_1

value: Free

value: T3 N0

value: Yes


title: T-5H-FC-control-rep2

value: vehicle (DMSO)


title: LEAF-WTSD00:00_rep2

description: LEAF_All counts.txt


title: T-5H-FC-control-rep3


title: PT10_Eff_1

value: No


title: LEAF-WTSD00:00_rep1

description: LEAF_All counts.txt

value: Flag leaf


title: LEAF-WTSD20:00_rep1

description: LEAF_All counts.txt


title: LEAF-WTSD20:00_rep2

description: LEAF_All counts.txt


title: T-5H-FC-control-rep1


title: IMR-32 Oct-1Z_rep3

city: Moscow

first: Tatiana

last: Portseva

address: Vavilova street 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

data_processing:
Sequencing on the Illumina NovaSeq6000 SP on one side, reading length 100 bp.
After control Illumina NovaSek (101 cycle with end of fragments) using NovaSeq SP reagents. FASTQ files were obtained using bcl2fastq v2.20 Conversion Software (Illumina).
Recording format quality data strings - Phred 33.
Data were generated by deep sequencing, in triplicate, using Illumina NovaSeq. Mapping reads to the human genome (hg38) using hisat program.  The htseq-count utility calculated the number of reads that were mapped to known genes (ncbi - entrezID). The obtained values (cpm - countpermillion) for each gene for each library were combined into one matrix for further analysis.
Filtration, normalization by the method (TMM), variance estimation and evaluation of differentially expressed genes were performed in the edgeR module. Genes in which cpm did not exceed 1 in any three libraries were considered low-expressing. After filtering the low-expressing genes, 15,108 entries remained. RNA-Seq data confirmed that approximately 8% of the transcripts showed differential expression between the WT and Oct-1 overexpressed differentiating neuroblastoma cells, with FDR<0.01 (p-value adjusted for multiple testing).
Genome_build: hg38
Supplementary_files_format_and_content: bcl2fastq v2.20 Conversion Software

source_name: neuroblastoma cell line IMR32

growth_protocol: IMR32 cells growth in the MEM medium, 10% FCS, 5% CO2

extract_protocol:
differentiation in vitro with 2.5 mkM BrdU in the MEM medium, 10 % FCS during b16 days
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IMR32 total RNA was harvested using Trizol reagent.

value: neuroblastoma cell line IMR32 differentiating in vitro during 16 days

value: pLenti 5 - Oct-1Z stably overexpressed

value: treated with 2.5 mkM BrdU for 16-days


title: IMR-32 Oct-1Z_rep2


title: IMR-32 WT_rep3

value: wild type


title: LEAF-WTSD08:00_rep2

description: LEAF_All counts.txt


title: LEAF-WTSD12:00_rep2

description: LEAF_All counts.txt


title: LEAF-WTSD08:00_rep1

description: LEAF_All counts.txt


title: YN146 Doublet Control

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

description:
rawCounts.csv
normalizedCounts.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCh38
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
normalizedCounts.csv: remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+0.25) CPM

source_name: PBMC

growth_protocol: in vivo

extract_protocol:
RNA was extracted from flow-sorted classical monocyte (CD14++CD16-) singlet and doublets using the Qiagen RNeasy Mini kit in combination with the Qiagen QIAshredder kit per the manufacturer’s protocol. RNA quality was assessed using a Fragment Analyzer (Advanced Analytical Technologies, Inc., Ankeny, IA) and 3ng of RNA was used for RNA-Seq.
cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, Japan). DNA libraries were generated using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA).
Libraries were pooled at 2nM and sequenced using a paired end, 50. cycle, rapid run design on an Illumina HiSeq 2500

tag: condition

value: Control

value: monocyte doublet

tag: donor


title: PT12_Eff_1

value: moderately to poorly diff

value: T3 N1


title: Human CD4+ T cells_ki0100022_CMV-_batch4_VDJ

city: Atlanta

first: Haydn

last: Kissick

address: 1462 Clifton Rd.

institute: Emory University

description:
TCR VDJ
processed.vdj.csv
processed.meta.data.matrix.csv

data_processing:
Cell Ranger cellranger mkfastq command was used for basecalling to generate Fastq files.
Cell Ranger cellranger count command was used for alignment, filtering, barcode counting, UMI counting.
Cell Ranger cellranger vdj command was used to generate VDJ sequences and annotations.
Normalized counts were obtained via Seurat.
Genome_build: GRCH38
Supplementary_files_format_and_content: csv files containing:
1.processed.ADT.matrix.csv:  antibody-derived tags expression matrix (normalized counts) of equally sampled CD4+ T cells from 4 pairs of age and sex matched CMV+ and CMV- healthy subjects.
2.processed.gene.matrix.csv:  gene expression matrix (normalized counts) of equally sampled CD4+ T cells from 4 pairs of age and sex matched CMV+ and CMV- healthy subjects.
3.processed.meta.data.matrix.csv:  metadata of the ADT and gene expression matrix.
4.processed.vdj.csv:  a spreadsheet containing VDJ sequencing data (V gene, J gene, CDR3 sequence, clonotype ID) of CD4+ T cells from 4 pairs of age and sex matched CMV+ and CMV- healthy subjects.

source_name: Human CD4+ T cells

extract_protocol:
Peripheral blood samples were drawn. PBMC were isolated from whole blood by means of density gradient centrifugation. CD4+ T cells were extracted using MACS negative CD4+ T cell isolation kit.
Gene expression libraries and feature barcoding libraries were prepared using Chromium Single Cell 3′ V3 Reagent Kits with Cell Surface Protein Feature Barcoding Technology for Cell Surface Protein (10X Genomics). VDJ libraries were prepared using Chromium Single Cell V(D)J V1 Reagent Kits (10X Genomics). The sequencing of gene expression libraries was conducted as a custom configuration (26x8x91bp) on the Illumina HiSeq3000 with a depth of 50,000 reads per targeted cell. The sequencing of VDJ libraries was conducted as PE150 on the Illumina HiSeq3000 with a depth of 5,000 reads per targeted cell. The sequencing of 10X feature barcode libraries was conducted as a custom configuration (26x8x25bp) on the Illumina HiSeq3000 with a depth of 5,000 reads per targeted cell. Junk cells with low read depth were removed and the remaining libraries were sequenced to a depth of 60M to 190M reads per sample in total.

tag: feature barcode

value: Biolegend TotalSeq™-C:CD57, CD27, CD28, CD244, CD45RO, PD-1, CD45RA, CCR7, CD39, CD25

tag: batch

value: batch 4

tag: sample id

tag: cmv serology status

value: CMV-

value: CD4+ T cells


title: T-5H-FC-NP_MTA-rep1

tag: cell line

value: mesenchymal stem cell-derived tumor model

tag: treatment

value: 25 mM Mithramycin A loaded in polymeric nanoparticles


title: Human CD4+ T cells_ki0100022_CMV-_batch4_gene

description:
total RNA
processed.gene.matrix.csv
processed.meta.data.matrix.csv


title: YN146 Singlet Control

description:
rawCounts.csv
normalizedCounts.csv

value: monocyte singlet


title: Human CD4+ T cells_ki0100022_CMV-_batch4_ADT

description:
ADT (antibody-derived tags)
processed.ADT.matrix.csv
processed.meta.data.matrix.csv

molecule: other


title: VP618 Doublet Psoriasis

description:
rawCounts.csv
normalizedCounts.csv

value: Psoriasis


title: IMR-32 WT_rep2

tag: genotype


title: LEAF-WTSD12:00_rep1

description: LEAF_All counts.txt

value: WT

tag: tissue

value: Flag leaf

tag: development stage

value: Stage 12

value: short day photoperiod

tag: collection time


title: LEAF-WTSD16:00_rep2

description: LEAF_All counts.txt


title: LEAF-WTSD16:00_rep1

description: LEAF_All counts.txt


title: VP618 Singlet Psoriasis

description:
rawCounts.csv
normalizedCounts.csv


title: IMR-32 WT_rep1

value: neuroblastoma cell line IMR32 differentiating in vitro during 16 days

value: wild type

value: treated with 2.5 mkM BrdU for 16-days


title: RP076 Doublet Psoriasis

description:
rawCounts.csv
normalizedCounts.csv

value: monocyte doublet


title: Human CD4+ T cells_ki0100020_CMV+_batch4_gene

value: CMV+


title: Human CD4+ T cells_ki0100110_CMV-_batch3_VDJ

value: Biolegend TotalSeq™-C:CD57, CD27, CD28, CD244, CD45RO, PD-1, CD45RA, CCR7, CD39, CD25

value: batch 3


title: Patient 73

type: RNA

city: Beijing

first: Chuzhong

address: 119 South Fourth Ring West Road, Fengtai

institute: Beijing Neurosurgical Institute

description: Gene expression of tissue

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Non-Functioning Pituitary Adenoma  (NFPA) tissue

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: According to the manufacturer's protocol, total RNA was extracted and purified using the phenol-free mirVana™ miRNA isolation kit (Cat#AM1561, Ambion, Austin, Texas, USA).

treatment_protocol: All tissue samples were immediately snap-frozen in liquid nitrogen and stored at −80°C.

tag: tissue type

value: tumor tissue

tag: gender

value: male

tag: invasiveness

value: Yes


title: Human CD4+ T cells_ki0100020_CMV+_batch4_ADT

value: batch 4

tag: cell type

value: CD4+ T cells


title: LN097 Singlet Control

description:
rawCounts.csv
normalizedCounts.csv

value: Control

value: monocyte singlet


title: Human CD4+ T cells_ki0100110_CMV-_batch3_ADT

value: CMV-


title: LN097 Doublet Control

description:
rawCounts.csv
normalizedCounts.csv


title: HP025 Doublet Psoriasis

description:
rawCounts.csv
normalizedCounts.csv

value: Psoriasis


title: Human CD4+ T cells_ki0100110_CMV-_batch3_gene


title: Human CD4+ T cells_ki0100111_CMV+_batch3_VDJ


title: Human CD4+ T cells_ki0100111_CMV+_batch3_ADT


title: Human CD4+ T cells_ki0100020_CMV+_batch4_VDJ


title: HN647 Doublet Control

description:
rawCounts.csv
normalizedCounts.csv


title: RP076 Singlet Psoriasis

description:
rawCounts.csv
normalizedCounts.csv


title: Human CD4+ T cells_ki0100111_CMV+_batch3_gene


title: Patient 72

description: Gene expression of tissue

value: female


title: Human CD4+ T cells_ki0100015_CMV-_batch2_VDJ

value: batch 2


title: HN647 Singlet Control

description:
rawCounts.csv
normalizedCounts.csv


title: Patient 66

description: Gene expression of tissue


title: Patient 70

description: Gene expression of tissue


title: GN305 Singlet Control

description:
rawCounts.csv
normalizedCounts.csv


title: Human CD4+ T cells_ki0100015_CMV-_batch2_ADT


title: Human CD4+ T cells_ki0100015_CMV-_batch2_gene


title: Patient 71

description: Gene expression of tissue


title: Patient 65

description: Gene expression of tissue


title: Patient 68

description: Gene expression of tissue


title: Patient 62

description: Gene expression of tissue


title: GN305 Doublet Control

description:
rawCounts.csv
normalizedCounts.csv


title: Patient 63

description: Gene expression of tissue


title: Patient 64

description: Gene expression of tissue


title: IMR-32 Oct-1Z_rep1

value: neuroblastoma cell line IMR32 differentiating in vitro during 16 days

value: pLenti 5 - Oct-1Z stably overexpressed


title: Patient 61

description: Gene expression of tissue


title: Patient 67

description: Gene expression of tissue


title: HP025 Singlet Psoriasis

description:
rawCounts.csv
normalizedCounts.csv


title: EN446 Doublet Control

description:
rawCounts.csv
normalizedCounts.csv

value: monocyte doublet


title: EN446 Singlet Control

description:
rawCounts.csv
normalizedCounts.csv


title: Human CD4+ T cells_ki0100021_CMV+_batch2_VDJ

value: CMV+


title: Patient 59

description: Gene expression of tissue


title: DN550 Doublet Control

description:
rawCounts.csv
normalizedCounts.csv


title: Human CD4+ T cells_ki0100021_CMV+_batch2_gene

value: Biolegend TotalSeq™-C:CD57, CD27, CD28, CD244, CD45RO, PD-1, CD45RA, CCR7, CD39, CD25


title: DN550 Singlet Control

description:
rawCounts.csv
normalizedCounts.csv


title: Patient 57

description: Gene expression of tissue


title: CN628 Doublet Control

description:
rawCounts.csv
normalizedCounts.csv


title: Human CD4+ T cells_ki0100022_CMV-_batch1_gene

value: batch 1


title: CN628 Singlet Control

description:
rawCounts.csv
normalizedCounts.csv


title: Human CD4+ T cells_ki0100022_CMV-_batch1_VDJ


title: Human CD4+ T cells_ki0100022_CMV-_batch1_ADT


title: BP508 Doublet Psoriasis

description:
rawCounts.csv
normalizedCounts.csv


title: Human CD4+ T cells_ki0100020_CMV+_batch1_VDJ


title: Human CD4+ T cells_ki0100020_CMV+_batch1_ADT


title: BP508 Singlet Psoriasis

description:
rawCounts.csv
normalizedCounts.csv


title: BN450 Doublet Control

description:
rawCounts.csv
normalizedCounts.csv


title: Patient 60

description: Gene expression of tissue

value: tumor tissue


title: BN450 Singlet Control

description:
rawCounts.csv
normalizedCounts.csv


title: Human CD4+ T cells_ki0100021_CMV+_batch2_ADT


title: Patient 56

description: Gene expression of tissue

value: male


title: PMH1065_rCSF

city: Durham

first: John

middle: R.

last: Perfect

state: North Carolina

address: 303 Research Drive, Rm.337

department: Division of Infectious Diseases

institute: Duke University School of Medicine

data_processing:
The quality filtering and adaptor trimming were performed using Cutadapt (v 1.12).
Paired-read alignment for RNA-seq data was carried out against the gene set for C. neoformans var. grubii H99 (CNA3) excluding non-coding RNAs and mitochondria genes, using STAR (v 2.5.3a).
The expected count, TPM, and FPKM for each gene were estimated with RSEM (v1.2.31).
Genome_build: CNA3 (GCA_000149245.3)
Supplementary_files_format_and_content: Tab-delimited text files include length, Effective length, Expected count, TPM, and FPKM For each gene.

organism: Cryptococcus neoformans

source_name: yeast cell

growth_protocol: (1) aCSF: yeast cells incubated in aCSF at 37oC for 24 hours. Cells were harvested by centrifugation at 3000 RPM and stored at -800C. (2) rCSF: yeast cells were inoculated intracisternally into 2-3 kg New Zealand White rabbits receiving daily cortisone acetate. Each yeast strain was inoculated into three separate rabbits. Rabbit CSF was withdrawn (1-2ml) after 24 and 96 hours in the rabbit subarachnoid space.  rCSF containing the same strain were pooled, centrifuged to pellet the cells and the cell pellets were stored at -800C. (3) YPD / CAP:  yeast cells were grown for 24 hours in yeast peptone dextrose broth (YPD) or capsule-inducing media (CAP), centrifuged to collect the cell pellet, and store at -800C. (4) Human CSF (hCSF): yeasts per ml of CSF (1-5mls) was directly withdrawn under a lumbar puncture as standard of care, centrifuged to pellet and stored at -80C until RNA isolation was performed.

extract_protocol:
These lyophilized samples were treated with Trizol and total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions.
Library preparation was prepared by shearing the RNA and adapted for Illumina sequencing using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, CA) for YPD and CAP conditions or the Tag-Seq Protocol (Shishkin et al Nat Methods 2015) for the in vivo CSF and aCSF samples.

tag: isolate

tag: strain

value: VNI

value: Rabbit CSF

tag: day

tag: repeat


title: PMH1063_rCSF

value: VNBII

tag: condition


title: Patient 55

description: Gene expression of tissue

value: Yes


title: Human CD4+ T cells_ki0100020_CMV+_batch1_gene

tag: feature barcode

tag: batch

tag: sample id

value: CD4+ T cells


title: PMH1051_rCSF


title: PMH1040_rCSF


title: Patient 53

description: Gene expression of tissue


title: Patient 54

description: Gene expression of tissue


title: Patient 51

description: Gene expression of tissue


title: PMH1033_rCSF


title: Patient 49

description: Gene expression of tissue


title: Patient 58

description: Gene expression of tissue


title: Patient 50

description: Gene expression of tissue


title: Patient 52

description: Gene expression of tissue


title: PMH1063_rCSF_D4


title: Patient 48

description: Gene expression of tissue


title: PMH1033_rCSF_D4


title: Patient 47

description: Gene expression of tissue


title: NRH5045_rCSF

value: VNBI


title: PBS_3_PBS_Day 6

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profiling after 6 days PBS

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: Mock

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from harvested lungs using Trizol/phenol chloroform extraction followed by precipitation.  RNA quality assessed using Agilent Bioanalyzer.

treatment_protocol: Mice were vaccinated with either NAV-PBS or NAV-DPBS and exposed to either PBS or H1N1 influena virus.   At 3 or 6 days post-viral infection lung tissue was harvested and RNA isolated for microarray analysis.

value: Lung

tag: vaccine

value: PBS

tag: infection

tag: time

value: post-viral infection day 6


title: PBS_4_PBS_Day 6

tag: tissue


title: NRH5030_rCSF


title: Patient 45

description: Gene expression of tissue

value: female


title: PBS_2RP_Day_3

description: Gene expression profiling after 3 days influenza infection

source_name: PBS Day 3

value: virus strain H1N1

value: post-viral infection day 3


title: Patient 44

description: Gene expression of tissue


title: NRH5030_rCSF_D4


title: PBS_2_PBS_Day 6


title: Patient 46

description: Gene expression of tissue


title: Patient 43

description: Gene expression of tissue


title: PBS_NP_Day_6

description: Gene expression profiling after 6 days influenza infection

source_name: PBS Day 6


title: PBS_DP_Day_6


title: Patient 42

description: Gene expression of tissue


title: Patient 39

description: Gene expression of tissue

value: No


title: PBS_1_PBS_Day 6


title: NRH5027_rCSF_D4


title: NAV_PBS_NP_Day_6_replicate

source_name: NAV PBS Day 6

value: NAV-PBS


title: NAV_DPBS_LP_Day_6

source_name: NAV DPBS Day 6

value: NAV-DPBS


title: Patient 38

description: Gene expression of tissue

value: tumor tissue


title: Patient 40

description: Gene expression of tissue


title: NAV_PBS_DP_Day_3

source_name: NAV PBS Day 3


title: NRH5010_rCSF


title: NRH5010_rCSF_D4


title: H99_rCSF_b2


title: Patient 69

description: Gene expression of tissue


title: NRH5027_rCSF


title: NAV_PBS_DP_Day_6


title: H99_rCSF_b2_D4


title: Patient 41

description: Gene expression of tissue


title: PMH1065_aCSF_r2

value: Artificial CSF


title: PMH1065_aCSF

value: VNI


title: PMH1063_aCSF_r3


title: NAV_PBS_LP_Day_3


title: Patient 37

description: Gene expression of tissue

value: male


title: Patient 36

description: Gene expression of tissue


title: Patient 35

description: Gene expression of tissue


title: Patient 34

description: Gene expression of tissue


title: NAV_DPBS_NP_Day_6


title: NAV_PBS_LP_Day_6


title: Patient 33

description: Gene expression of tissue


title: NAV_DPBS_LP_Day_3

source_name: NAV DPBS Day 3


title: Patient 32

description: Gene expression of tissue


title: PMH1063_aCSF

value: VNBII


title: PBS_LP_Day_3


title: NAV_DPBS_DP_Day_3


title: Patient 29

description: Gene expression of tissue


title: NAV_PBS_2RP_Day_6


title: Patient 28

description: Gene expression of tissue

value: Yes


title: PMH1051_aCSF_r2


title: PMH1051_aCSF


title: PMH1063_aCSF_r2


title: LEAF-csaSD16:00_rep1

description: LEAF_All counts.txt

tag: genotype

value: csa

value: Flag leaf

tag: development stage

value: Stage 12

tag: treatment

value: short day photoperiod

tag: collection time


title: Patient 30

description: Gene expression of tissue

tag: tissue type

tag: gender

tag: invasiveness


title: NAV_DPBS_RP_Day_3

value: Lung


title: PBS_LP_Day_6

value: PBS

value: post-viral infection day 6


title: PMH1040_aCSF

tag: isolate

tag: strain

tag: day


title: Patient 25

description: Gene expression of tissue


title: NAV_PBS_NP_Day_3

value: virus strain H1N1

value: post-viral infection day 3


title: Patient 27

description: Gene expression of tissue

value: female


title: PMH1033_aCSF_r2

tag: condition

tag: repeat


title: PMH1033_aCSF


title: PMH1040_aCSF_r2


title: NAV_DPBS_DP_Day_6

value: NAV-DPBS


title: NRH5045_aCSF_r2

value: VNBI


title: NRH5030_aCSF_r2

value: Artificial CSF


title: NRH5045_aCSF


title: Patient 31

description: Gene expression of tissue

value: tumor tissue


title: NAV_PBS_2RP_Day_6_replicate

value: NAV-PBS


title: NRH5030_aCSF


title: PBS_DP_Day_3


title: Patient 21

description: Gene expression of tissue


title: PBS_RP_Day_3


title: NAV_DPBS_2RP_Day_6


title: NAV_DPBS_NP_Day_3


title: PBS_RP _Day_6


title: Patient 24

description: Gene expression of tissue

value: male

value: No


title: PBS_NP_Day_3


title: NRH5027_aCSF_r2


title: Patient 19

description: Gene expression of tissue


title: NAV_DPBS_2RP_Day_3


title: NRH5027_aCSF


title: Patient 20

description: Gene expression of tissue


title: NRH5010_aCSF_r2

value: VNI


title: NAV_PBS_NP_Day_6


title: H99_aCSF


title: Patient 18

description: Gene expression of tissue

value: Yes


title: Patient 17

description: Gene expression of tissue


title: H99_aCSF_r2


title: Patient 14

description: Gene expression of tissue


title: NRH5010_aCSF


title: Patient 16

description: Gene expression of tissue


title: NAV_DPBS_RP_Day_6


title: PBS_2RP_Day_6


title: NAV_PBS_RP_Day_3


title: Prim5_Nuc_CAGE

city: Birmingham

first: Sanjana

last: Pillay

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

data_processing:
Library strategy: LQ-CAGE sequencing
The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis.
CAGEr starts from mapped reads and does quality filtering, normalization, removal of the additional 5’ end G nucleotide (added during the CAGE protocol) and the frequency of the usage of start sites (Haberle et al., 2015).
Genome_build: Zv9
Supplementary_files_format_and_content: CTSS files in bedGraph format

organism: Danio rerio

source_name: 24hpf stage embryo

growth_protocol: Wild-type male and female zebrafish (AB-strain) were set up in breeding tanks overnight and the eggs were collected the next day as soon as (~10 min) they were laid (important to get synchronised embryos). About 100-500 (depending upon the stage) embryos were collected for each developmental stage (64 cell, 256 cell, 1000 cell, shield, 24hpf, 50hpf). The embryos were treated with Pronase (protease from Streptomyces griseus, Sigma-Aldrich) to remove the chorion, 1mL of Pronase working solution (1mg/mL) was added to 2-3 ml of fish water containing embryos.

extract_protocol:
RNA was extracted using the Rneasy mini kit
The conventional method used for 5’-cap analysis, also called cap trapping method (Carninci et al., 1996), targets all capped mRNAs by chemical modification of the 5’ end (cap) followed by its biotinylation and then a pulldown using streptavidin-coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ-CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.

treatment_protocol: Dechorionated embryos were then washed twice with 1 X PBS (Phosphate buffer solution, ThermoFisher). RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally, collected and labelled as the nuclear fraction.

value: zebrafish embryos

tag: Stage

tag: fraction

value: Nuclear

tag: molecule type

value: capped RNAs


title: Patient 15

description: Gene expression of tissue


title: Patient 22

description: Gene expression of tissue


title: Prim5_Cyt_CAGE

value: Cytosolic


title: Shield_Cyt_CAGE

source_name: Shield stage embryo

value: Shield


title: NAV_PBS_2RP_Day_3

value: Lung

tag: vaccine

tag: infection

value: virus strain H1N1

tag: time


title: Shield_Nuc_CAGE

tag: tissue


title: NAV_PBS_RP_Day_6

value: post-viral infection day 6


title: Patient 26

description: Gene expression of tissue

value: female


title: Negative control+Bleomycin 2

city: Wuhan

first: Li-Mei

last: Liang

state: Hubei

address: 1277 JieFang Avenue

department: Department of Respiratory and Critical Care Medicine, Union Hospital

institute: Huazhong University of Science and Technology

data_processing:
The genome of human genome version of hg38 was used as reference. The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3).The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters.
The processed reads from each sample were aligned using HISAT2 against the reference genome. The gene expression analyses were performed with StringTie (v1.3.3b). DESeq(v1.28.0) was used to analyze the DEGs between samples
Then a p-value was obtained, which was corrected by FDR method. And Corrected P-value (q-value) was calculated by correcting using BH method. p-value or q-value were used to conduct significance analysis. Parameters for classifying significantly DEGs are ≥2-fold differences (|log2FC|≥1, FC: the fold change of expressions) in the transcript abundance and p ≤ 0.05.
The annotation of the DEGs were perfomed based on the information obtained from the database of ENSEMBL, NCBI, Uniprot, GO, and KEGG.
Genome_build: Homo_sapiens.GRCh38.dna.toplevel.REF.fa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Matrix table with raw gene counts for every gene and every sample.

source_name: Mesothelial cells

growth_protocol: The human PMC line Met-5A was obtained from the American Type  Culture Collection (ATCC, Manassas, VA, USA). PMCs were cultured in RPMI 1640  medium (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS).Culture media contained 100 U/ml penicillin and 100  μg/ml streptomycin and maintained at 37 °C in a humidified atmosphere containing 5% CO2.  The cells were sub-cultured at 1:3 ratios, and culture medium was changed every 2 days.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The samples were assessed  with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After transfection with SRSF6 siRNAs or negative control siRNAs, Met-5A were incubated with bleomycin (0.2 µg/ml) for 24 h.

value: mesothelium

tag: cell type

value: epithelial virus transformed

tag: transfection

value: negative control siRNA for 48 h

tag: treatment

tag: cell line


title: SRSF6 KD+Bleomycin 2

value: SRSF6 siRNA for 48 h

value: incubated with bleomycin (0.2 µg/ml) for 24 h


title: Patient 13

description: Gene expression of tissue

tag: tissue type

value: tumor tissue

tag: gender

value: male

tag: invasiveness


title: Negative control+Bleomycin 1


title: Patient 10

description: Gene expression of tissue

value: No


title: Dome_Cyt_CAGE

source_name: Dome stage embryo

value: zebrafish embryos

value: Dome


title: Patient 12

description: Gene expression of tissue

value: Yes


title: Dome_Nuc_CAGE

value: Nuclear

value: capped RNAs


title: 1000Cell_Cyt_CAGE

source_name: 1000Cell stage embryo

value: Cytosolic


title: Pooled_5geno_6tp_3rep_3000-5000nt_fract

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

description:
Pooled sample of total RNA extracted from barley infected first leaves (PO:0007094) of five barley genotypes [CI 16151 (Mla6, Rar3, Bln1); m18982 (mla6, Rar3, Bln1); m11526 (Mla6, rar3, Bln1); m19089 (Mla6, Rar3, bln1); m19028 (mla6, Rar3, bln1)] across 6 timepoints (0, 16, 20, 24, 32, 48 HAI) following infection with powdery mildew fungus (Blumeria graminis f. sp. hordei; isolate 5874).  Sample was SAGE-ELF size selected to generate 3000-5000 nt fragments for library preperation.
Hordeum vulgare L. (Barley) + Blumeria graminis f. sp. hordei (Bgh)

data_processing:
Library strategy: Iso-Seq
Conversion of BAX to BAM: BAX files obtained from SMRT sequencing were converted to BAM files using SMRT Linkv6.0.0.47841 and default arguments.
Conversion of Subreads to CCS: Subreads were converted into circular consensus sequences by SMRT Linkv6.0.0.47841 using ccs utility.
Polishing CCS to generate transcripts: CCS were first categorized into complete and incomplete sequences. The complete full length sequences were polished and converted into full length sequences by SMRT Linkv6.0.0.47841.
Error correcting transcripts: Short reads were aligned to the full length sequences and indels were corrected using HECIL, LorDEC, HALC, COLORMAP.
Genome_build: Barley (Mascher 2017) and Blumeria (Ensembl Fungi Assembly EF 1, INSDC Assembly GCA_000151065.1) (Spanu 2010).
Supplementary_files_format_and_content: Full length transcriptome in fasta format.

organism:
Hordeum vulgare
Blumeria hordei

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: CI 16151 and its derived mutant barley lines were maintained via single seed descent. Genotypes were grown in separate trays (19.5 x 27.5-cm) in a climate-controlled greenhouse using a split plot design. Each tray consisted of six rows of 16 seedlings, with rows randomly assigned to one of six harvest timepoints (0, 16, 20, 24, 32, and 48 HAI).

extract_protocol:
Total RNA was isolated from 0.5 g of each pool using a hot (60˚C) phenol / guanidine thiocyanate method (Caldo et al., 2004).
The pooled sample (90 experimental units) was SAGE-ELF size selected to generate 6 PacBio cDNA Iso‐Seq Library Preparations [fragment sizes: 1) non-fractionated 2) 1000-1500 nt 3) 1500-2000 nt 4) 2000-3000 nt 5) 3000-5000 nt 6) > 5000 nt].  The non-fractionated as well as the three smallest fragment libraries were each loaded onto 3 SMRT cells, and the two largest fragment libraries were each loaded onto 2 SMRT cells for a total of 16 SMRT cells.

treatment_protocol: Seven days after sowing, seedling trays were inoculated at 16:00 with a high density of Bgh isolate 5874 (AVRa1, AVRa6, vira8, AVRa12, vira13, AVRLa) and positioned randomly in a controlled growth chamber (18°C, 8 h darkness, 16 h light). Rows of seedlings were harvested at the assigned time points, pooled, and immediately placed into liquid nitrogen. The entire procedure was replicated three times in successive weeks resulting in 90 experimental units (5 genotypes x 6 timepoints x 3 replications).

tag: fragment size

value: leaf

tag: plant genotype

value: mixed sample:CI 16151 (Mla6, Rar3, Bln1); m18982 (mla6, Rar3, Bln1); m11526 (Mla6, rar3, Bln1); m19089 (Mla6, Rar3, bln1); m19028 (mla6, Rar3, bln1) (non-demultiplexed)

tag: fungal isolate

value: Bgh isolate 5874

tag: timepoint

value: mixed sample:0, 16, 20, 24, 32, 48 HAI (non-demultiplexed)

tag: replication

value: 3 replicates per genotype / timepoint combination


title: Patient 11

description: Gene expression of tissue

value: female


title: Pooled_5geno_6tp_3rep_greater5000nt_fract

description:
Pooled sample of total RNA extracted from barley infected first leaves (PO:0007094) of five barley genotypes [CI 16151 (Mla6, Rar3, Bln1); m18982 (mla6, Rar3, Bln1); m11526 (Mla6, rar3, Bln1); m19089 (Mla6, Rar3, bln1); m19028 (mla6, Rar3, bln1)] across 6 timepoints (0, 16, 20, 24, 32, 48 HAI) following infection with powdery mildew fungus (Blumeria graminis f. sp. hordei; isolate 5874).  Sample was SAGE-ELF size selected to generate > 5000 nt fragments for library preperation.
Hordeum vulgare L. (Barley) + Blumeria graminis f. sp. hordei (Bgh)


title: 256Cell_Cyt_CAGE

source_name: 256Cell stage embryo

tag: Stage

tag: fraction

tag: molecule type


title: Pooled_5geno_6tp_3rep_2000-3000nt_fract

description:
Pooled sample of total RNA extracted from barley infected first leaves (PO:0007094) of five barley genotypes [CI 16151 (Mla6, Rar3, Bln1); m18982 (mla6, Rar3, Bln1); m11526 (Mla6, rar3, Bln1); m19089 (Mla6, Rar3, bln1); m19028 (mla6, Rar3, bln1)] across 6 timepoints (0, 16, 20, 24, 32, 48 HAI) following infection with powdery mildew fungus (Blumeria graminis f. sp. hordei; isolate 5874).  Sample was SAGE-ELF size selected to generate 2000-3000 nt fragments for library preperation.
Hordeum vulgare L. (Barley) + Blumeria graminis f. sp. hordei (Bgh)


title: Pooled_5geno_6tp_3rep_1500-2000nt_fract

description:
Pooled sample of total RNA extracted from barley infected first leaves (PO:0007094) of five barley genotypes [CI 16151 (Mla6, Rar3, Bln1); m18982 (mla6, Rar3, Bln1); m11526 (Mla6, rar3, Bln1); m19089 (Mla6, Rar3, bln1); m19028 (mla6, Rar3, bln1)] across 6 timepoints (0, 16, 20, 24, 32, 48 HAI) following infection with powdery mildew fungus (Blumeria graminis f. sp. hordei; isolate 5874).  Sample was SAGE-ELF size selected to generate 1500-2000 nt fragments for library preperation.
Hordeum vulgare L. (Barley) + Blumeria graminis f. sp. hordei (Bgh)


title: Pooled_5geno_6tp_3rep_1000-1500nt_fract

description:
Pooled sample of total RNA extracted from barley infected first leaves (PO:0007094) of five barley genotypes [CI 16151 (Mla6, Rar3, Bln1); m18982 (mla6, Rar3, Bln1); m11526 (Mla6, rar3, Bln1); m19089 (Mla6, Rar3, bln1); m19028 (mla6, Rar3, bln1)] across 6 timepoints (0, 16, 20, 24, 32, 48 HAI) following infection with powdery mildew fungus (Blumeria graminis f. sp. hordei; isolate 5874).  Sample was SAGE-ELF size selected to generate 1000-1500 nt fragments for library preperation.
Hordeum vulgare L. (Barley) + Blumeria graminis f. sp. hordei (Bgh)


title: 1000Cell_Nuc_CAGE


title: 256Cell_Nuc_CAGE


title: 64Cell_Cyt_CAGE

source_name: 64Cell stage embryo


title: Pooled_5geno_6tp_3rep_non_fract

description:
Pooled sample of total RNA extracted from barley infected first leaves (PO:0007094) of five barley genotypes [CI 16151 (Mla6, Rar3, Bln1); m18982 (mla6, Rar3, Bln1); m11526 (Mla6, rar3, Bln1); m19089 (Mla6, Rar3, bln1); m19028 (mla6, Rar3, bln1)] across 6 timepoints (0, 16, 20, 24, 32, 48 HAI) following infection with powdery mildew fungus (Blumeria graminis f. sp. hordei; isolate 5874).  Sample was not size fractionated prior to library preparation.
Hordeum vulgare L. (Barley) + Blumeria graminis f. sp. hordei (Bgh)

value: non-fractionated


title: SET1_yck2_R3

status: Public on Mar 29 2021

city: Seoul

first: Yong-Sun

last: Bahn

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

data_processing:
The sequenced reads were trimmed to remove the adaptor sequence and masked for low-complexity or low-quality sequence by using Cutadapt v2.4 with Python 3.5.2 with adapter sequence i7: TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGC and i5: GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTA
The reads were aligned to the genome sequence of Candida albicans SC5314 (from Stanford University) strain retrieved from the Stanford University (http://www-sequence.stanford.edu/group/candida/) using Hisat2 v2.1.0 with the Hisat, and Bowtie2 algorithm
Hisat2 was performed with “-p 30” and “--dta -1” option and other parameters set as default. Aligned reads were converted and sorted using Samtools v0.1.19 with “-Sb -@ 8” for converting, and “-@ 20 –m 2000000000” option for sorting and other parameters set as default
Transcript assembly and abundance estimation were performed by Stringtie v1.3.6 by using “-p 12” option, and also “-B” option to run the Ballgown
Assembled transcripts were merged to single GTF file, and the relative transcript abundances were displayed via FPKM (Fragments Per Kilobase of exon per Million fragments mapped)
The read count matrix was generated by python script ‘prepDE.py’ and analyzed by DESeq2. Differential expression analysis was performed using DESeq2 v1.24.0 with default sets with the Ballgown
Genome_build: Candida albicans SC5314 (from Stanford University)
Supplementary_files_format_and_content: Excel file includes FPKM value for each Sample.

organism: Candida albicans SC5314

source_name: SC5314_total RNA

growth_protocol: Candida albicans WT and yck2Δ mutant strains were inoculated into 50 ml of YPD medium liquid medium and cultured overnight at 30°C in a shaking incubator. Cells were sub-innoculated in fresh YPD medium until OD600 indicated 0.6.

extract_protocol:
Incubated cells were spun down, frozen in liquid nitrogen and lyophilized overnight. Total RNA was isolated by trizol extraction method using Easy-blue (iNtRON). The prepared total RNAs were purified with RNeasy Mini Kit (QIAGEN). The concentration was measured by Quant-IT RiboGreen (Invitrogen).
The quality of the RNA was verified by the TapeStation RNA screentape (Agilent) and the RNA Integrity Number (RIN) greater than 7.0 was used to construct the cDNA library (TruSeq mRNA Sample Prep kit, Illumina).

treatment_protocol: YPD basal condition

tag: medium

value: YPD medium

tag: background strain

tag: genotype


title: 64Cell_Nuc_CAGE

tag: tissue


title: SRSF6 KD+Bleomycin 1

value: mesothelium

tag: cell type

value: epithelial virus transformed

tag: transfection

value: SRSF6 siRNA for 48 h

tag: treatment

value: incubated with bleomycin (0.2 µg/ml) for 24 h


title: Patient 9

description: Gene expression of tissue

source_name: Non-Functioning Pituitary Adenoma  (NFPA) tissue

tag: tissue type

value: tumor tissue

tag: gender

value: male

value: No


title: Patient 4

description: Gene expression of tissue

tag: invasiveness


title: Patient 6

description: Gene expression of tissue


title: SET1_WT_R3

value: wildtype


title: SET1_WT_R2


title: Patient 8

description: Gene expression of tissue


title: SET1_yck2_R1


title: Patient 3

description: Gene expression of tissue


title: SET1_yck2_R2


title: Patient 2

description: Gene expression of tissue


title: Patient 1

description: Gene expression of tissue


title: Patient 5

description: Gene expression of tissue


title: SET1_WT_R1


title: Human, treatment-naive rectal cancer, TM214

first: Julio

last: Garcia-Aguilar

department: Colorectal Surgery

institute: Memorial Sloan Kettering Cancer Center

description: gene expression from pre-treatment rectal adenocarcinoma

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetrix

data_processing: Data were profiled by Affymetrix U133 Plus 2.0 Array platform (Affymetrix, Santa Clara, CA). A background correction using robust multi-array average (RMA) method was performed on the microarray data followed by quantile normalization. Only perfectly matched probes were taken into account and expression measure was calculated using median polish algorithm.

label: biotin

source_name: Rectal cancer patients accrued through clinical trial number NCT00335885

label_protocol: standard Affymetrix protocol

growth_protocol: Not applicable

extract_protocol: Pre-treatment biopsies of patients were obtained. All the specimens were stored as formalin-fixed-paraffin-embedded (FFPE) blocks and ten slides of 10-micron thickness were cut per block. A pathologist reviewed the hematoxylin and eosin (H&E) slides of all the sections to confirm the boundaries of the malignant epithelia. The tumor enriched areas were macro-dissected from unstained slides guided by the H&E slides. DNA & RNA were extracted from FFPE sections using AllPrep DNA/RNA FFPE kit (Qiagen Inc., Valencia, CA). Total RNA was amplified to generate cDNA libraries using the Ovation FFPE WTA System (NuGEN Technologies, San Carlos, CA).

treatment_protocol: Not applicable

tag: kras_mutant or wild_type

value: KRAS-mutant


title: Human, treatment-naive rectal cancer, TM222

source_name: Rectal cancer patients accrued through clinical trial number NCT00335890


title: Human, treatment-naive rectal cancer, TM210

source_name: Rectal cancer patients accrued through clinical trial number NCT00335883

value: KRAS-wild-type


title: Human, treatment-naive rectal cancer, TM224

source_name: Rectal cancer patients accrued through clinical trial number NCT00335892


title: Patient 7

last: Li

description: Gene expression of tissue


title: Human, treatment-naive rectal cancer, TM201

source_name: Rectal cancer patients accrued through clinical trial number NCT00335876


title: Human, treatment-naive rectal cancer, TM223

source_name: Rectal cancer patients accrued through clinical trial number NCT00335891


title: Human, treatment-naive rectal cancer, TM198

source_name: Rectal cancer patients accrued through clinical trial number NCT00335874


title: Human, treatment-naive rectal cancer, TM200

source_name: Rectal cancer patients accrued through clinical trial number NCT00335875


title: Human, treatment-naive rectal cancer, TM219

source_name: Rectal cancer patients accrued through clinical trial number NCT00335888


title: Human, treatment-naive rectal cancer, TM218

source_name: Rectal cancer patients accrued through clinical trial number NCT00335887


title: Human, treatment-naive rectal cancer, TM208

source_name: Rectal cancer patients accrued through clinical trial number NCT00335881


title: Human, treatment-naive rectal cancer, TM202

source_name: Rectal cancer patients accrued through clinical trial number NCT00335877


title: Human, treatment-naive rectal cancer, TM211

source_name: Rectal cancer patients accrued through clinical trial number NCT00335884


title: Human, treatment-naive rectal cancer, TM216

source_name: Rectal cancer patients accrued through clinical trial number NCT00335886


title: Human, treatment-naive rectal cancer, TM205

source_name: Rectal cancer patients accrued through clinical trial number NCT00335878


title: Human, treatment-naive rectal cancer, TM197

source_name: Rectal cancer patients accrued through clinical trial number NCT00335873


title: Human, treatment-naive rectal cancer, TM187

source_name: Rectal cancer patients accrued through clinical trial number NCT00335868


title: Human, treatment-naive rectal cancer, TM220

source_name: Rectal cancer patients accrued through clinical trial number NCT00335889


title: Human, treatment-naive rectal cancer, TM209

source_name: Rectal cancer patients accrued through clinical trial number NCT00335882


title: Human, treatment-naive rectal cancer, TM196

source_name: Rectal cancer patients accrued through clinical trial number NCT00335872


title: Human, treatment-naive rectal cancer, TM184

source_name: Rectal cancer patients accrued through clinical trial number NCT00335866


title: Human, treatment-naive rectal cancer, TM206

source_name: Rectal cancer patients accrued through clinical trial number NCT00335879


title: Human, treatment-naive rectal cancer, TM190

source_name: Rectal cancer patients accrued through clinical trial number NCT00335870


title: Human, treatment-naive rectal cancer, TM194

source_name: Rectal cancer patients accrued through clinical trial number NCT00335871


title: Patient 23

description: Gene expression of tissue

source_name: Non-Functioning Pituitary Adenoma  (NFPA) tissue


title: Human, treatment-naive rectal cancer, TM188

source_name: Rectal cancer patients accrued through clinical trial number NCT00335869


title: Human, treatment-naive rectal cancer, TM185

source_name: Rectal cancer patients accrued through clinical trial number NCT00335867


title: Human, treatment-naive rectal cancer, TM183

source_name: Rectal cancer patients accrued through clinical trial number NCT00335865


title: Human, treatment-naive rectal cancer, TM207

source_name: Rectal cancer patients accrued through clinical trial number NCT00335880


title: Human, treatment-naive rectal cancer, TM179

source_name: Rectal cancer patients accrued through clinical trial number NCT00335862


title: Human, treatment-naive rectal cancer, TM178

source_name: Rectal cancer patients accrued through clinical trial number NCT00335861


title: Human, treatment-naive rectal cancer, TM182

source_name: Rectal cancer patients accrued through clinical trial number NCT00335864


title: Human, treatment-naive rectal cancer, TM174

source_name: Rectal cancer patients accrued through clinical trial number NCT00335859


title: Human, treatment-naive rectal cancer, TM171

source_name: Rectal cancer patients accrued through clinical trial number NCT00335856


title: Human, treatment-naive rectal cancer, TM169

source_name: Rectal cancer patients accrued through clinical trial number NCT00335855


title: Human, treatment-naive rectal cancer, TM173

source_name: Rectal cancer patients accrued through clinical trial number NCT00335858


title: Human, treatment-naive rectal cancer, TM180

source_name: Rectal cancer patients accrued through clinical trial number NCT00335863


title: Human, treatment-naive rectal cancer, TM175

source_name: Rectal cancer patients accrued through clinical trial number NCT00335860


title: Human, treatment-naive rectal cancer, TM166

source_name: Rectal cancer patients accrued through clinical trial number NCT00335854


title: Human, treatment-naive rectal cancer, TM172

source_name: Rectal cancer patients accrued through clinical trial number NCT00335857


title: Human, treatment-naive rectal cancer, TM165

source_name: Rectal cancer patients accrued through clinical trial number NCT00335853


title: Human, treatment-naive rectal cancer, TM142

source_name: Rectal cancer patients accrued through clinical trial number NCT00335842


title: Human, treatment-naive rectal cancer, TM152

source_name: Rectal cancer patients accrued through clinical trial number NCT00335847


title: Human, treatment-naive rectal cancer, TM140

source_name: Rectal cancer patients accrued through clinical trial number NCT00335840


title: Human, treatment-naive rectal cancer, TM147

source_name: Rectal cancer patients accrued through clinical trial number NCT00335845


title: Human, treatment-naive rectal cancer, TM148

source_name: Rectal cancer patients accrued through clinical trial number NCT00335846


title: Human, treatment-naive rectal cancer, TM158

source_name: Rectal cancer patients accrued through clinical trial number NCT00335848


title: Human, treatment-naive rectal cancer, TM164

source_name: Rectal cancer patients accrued through clinical trial number NCT00335852


title: Human, treatment-naive rectal cancer, TM159

source_name: Rectal cancer patients accrued through clinical trial number NCT00335849


title: Human, treatment-naive rectal cancer, TM143

source_name: Rectal cancer patients accrued through clinical trial number NCT00335843


title: Human, treatment-naive rectal cancer, TM146

source_name: Rectal cancer patients accrued through clinical trial number NCT00335844


title: Human, treatment-naive rectal cancer, TM141

source_name: Rectal cancer patients accrued through clinical trial number NCT00335841


title: Human, treatment-naive rectal cancer, TM135

source_name: Rectal cancer patients accrued through clinical trial number NCT00335837


title: Human, treatment-naive rectal cancer, TM136

source_name: Rectal cancer patients accrued through clinical trial number NCT00335838


title: Human, treatment-naive rectal cancer, TM137

source_name: Rectal cancer patients accrued through clinical trial number NCT00335839


title: Human, treatment-naive rectal cancer, TM163

source_name: Rectal cancer patients accrued through clinical trial number NCT00335851


title: Human, treatment-naive rectal cancer, TM134

source_name: Rectal cancer patients accrued through clinical trial number NCT00335836


title: Human, treatment-naive rectal cancer, TM126

source_name: Rectal cancer patients accrued through clinical trial number NCT00335835


title: Human, treatment-naive rectal cancer, TM119

source_name: Rectal cancer patients accrued through clinical trial number NCT00335831


title: Human, treatment-naive rectal cancer, TM125

source_name: Rectal cancer patients accrued through clinical trial number NCT00335834


title: Human, treatment-naive rectal cancer, TM120

source_name: Rectal cancer patients accrued through clinical trial number NCT00335832


title: Human, treatment-naive rectal cancer, TM114

source_name: Rectal cancer patients accrued through clinical trial number NCT00335829


title: Human, treatment-naive rectal cancer, TM116

source_name: Rectal cancer patients accrued through clinical trial number NCT00335830


title: Human, treatment-naive rectal cancer, TM106

source_name: Rectal cancer patients accrued through clinical trial number NCT00335824


title: Human, treatment-naive rectal cancer, TM160

source_name: Rectal cancer patients accrued through clinical trial number NCT00335850


title: Human, treatment-naive rectal cancer, TM112

source_name: Rectal cancer patients accrued through clinical trial number NCT00335828


title: Human, treatment-naive rectal cancer, TM107

source_name: Rectal cancer patients accrued through clinical trial number NCT00335825


title: N4 rep1

city: shenyang

first: lv

last: chengzhou

state: liaoing

address: nanjingbeijie 155

department: thyroid surgery

institute: the first hospital of china medical university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low  quality bases which will affect the following assembly and analysis. Thus, to get high quality  clean reads, reads were further filtered by fastp  (version 0.18.0)
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome  RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean  reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the  reference genome using HISAT2.2.4 with “-rna-strandness RF” and other parameters set as  a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a  reference-based approach. For each transcription region, a FPKM (fragment per kilobase of  transcript per million mapped reads) value was calculated to quantify its expression  abundance and variations, using StringTie software.
Genome_build: GRCh38.release 94
Supplementary_files_format_and_content: all.genes.expression; circRNAs detailed sequence list

source_name: adjacent normal tissue

extract_protocol:
Thyroid cancer and adjacent normal tissue were collected, physiological saline cleaning, liquid nitrogen quick freezing, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: Papillary Thyroid cancer

value: Normal tissue adjacent to tumor

tag: tumor stage

value: T2N1aM0, I

tag: Sex

tag: age


title: N2 rep1

value: T3bN1aM0, I


title: N3 rep1


title: N1 rep1

value: T4aN1bM0, I

value: female


title: Human, treatment-naive rectal cancer, TM092

source_name: Rectal cancer patients accrued through clinical trial number NCT00335819


title: Human, treatment-naive rectal cancer, TM096

source_name: Rectal cancer patients accrued through clinical trial number NCT00335820


title: T4 rep1

source_name: Thyroid cancer

value: Tumor tissue


title: Human, treatment-naive rectal cancer, TM103

source_name: Rectal cancer patients accrued through clinical trial number NCT00335822


title: Human, treatment-naive rectal cancer, TM110

source_name: Rectal cancer patients accrued through clinical trial number NCT00335826


title: Human, treatment-naive rectal cancer, TM101

source_name: Rectal cancer patients accrued through clinical trial number NCT00335821


title: Human, treatment-naive rectal cancer, TM088

source_name: Rectal cancer patients accrued through clinical trial number NCT00335817


title: Human, treatment-naive rectal cancer, TM111

source_name: Rectal cancer patients accrued through clinical trial number NCT00335827


title: Human, treatment-naive rectal cancer, TM091

source_name: Rectal cancer patients accrued through clinical trial number NCT00335818


title: Human, treatment-naive rectal cancer, TM104

source_name: Rectal cancer patients accrued through clinical trial number NCT00335823


title: T3 rep1


title: T2 rep1


title: TF ChIP-seq from transverse colon (ENCLB821IFF)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR449SEF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR449SEF
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB821IFF
fragmentation methods: none
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens female adult (51 years) transverse colon tissue

tag: antibody

value: CTCF

value: transverse colon

value: tissue

tag: description

value: EnTEX:Colon - Transverse

tag: biosample encode accession

tag: dev stage

value: adult

value: 51 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS555CAN at ENCODE; https://www.encodeproject.org/ENCBS555CAN/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: TF ChIP-seq from transverse colon (ENCLB277MTN)

description:
https://www.encodeproject.org/experiments/ENCSR449SEF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR449SEF
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB277MTN
fragmentation methods: none
size range: 200-600


title: Control ChIP-seq from breast epithelium (ENCLB413DYE)

description:
https://www.encodeproject.org/experiments/ENCSR776ZDB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR776ZDB
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB413DYE
size range: 200-600

source_name: Homo sapiens male adult (54 years) breast epithelium tissue

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue

value: male

value: 54 year

value: ENCBS353DWM at ENCODE; https://www.encodeproject.org/ENCBS353DWM/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: CD44 WT Hs578T rep 3

city: Minneapolis

first: Sarah

last: Munro

state: MN

address: 117 Pleasant Street SE

institute: University of Minnesota

description:
Hs578T_CD44positive_3
Hs578T_CD44positive_9
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt

data_processing:
Fastq files were mapped to the hg38 human reference genome using HiSat2 (v. 2.1.0).
Counts were estimated using the Subread featureCounts (v1.6.2) tool using the gencode.v28.GRCh38.annotation.gtf annotation.
Count data were filtered to only keep genes that were less than 300 nt in length and had a cpm (counts per million) value greater than 1 cpm in at least 2 sample replicates across all experimental conditions.
Genome_build: GRCh38
Supplementary_files_format_and_content: CD44_KO_subread.txt: Tab-delimited text file includes abundance measurements.

growth_protocol: Hs578T and MDA-MB-231 cells were grown per ATCC recommendations in Dulbecco's Modified Eagle's Medium, 10% fetal bovine serum, and 1% Pen/Strep.

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen #74104) and 2000ng RNA was submitted per sample. Twelve dual-indexed Illumina TruSeq stranded mRNA libraries were pooled for sequencing on 1 lane of a HiSeq 2500 using v4 chemistry to generate 2x50 bp paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CD44 was deleted from the Hs578T and MDA-MB-231 cells using CRISPR/Cas9 -based techniques and sorted to generate populations of CD44 knockout cells. Knockout was confirmed by flow cytometry and Western blot.

tag: cell line

tag: cell type

value: Breast cancer cell line

tag: cd44 status

value: wild-type


title: CD44 WT MDA-MB-231 rep 2

description:
231_CD44positive_2
231_CD44positive_3
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt


title: Control ChIP-seq from lower leg skin (ENCLB074GHC)

description:
https://www.encodeproject.org/experiments/ENCSR010HMS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR010HMS
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2019-02-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB074GHC
size range: 200-600

source_name: Homo sapiens male adult (37 years) lower leg skin tissue

value: lower leg skin

value: EnTEX:Skin - Sun Exposed (Lower leg)

value: 37 year

value: ENCBS851XJZ at ENCODE; https://www.encodeproject.org/ENCBS851XJZ/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Control ChIP-seq from lower leg skin (ENCLB572CEK)

description:
https://www.encodeproject.org/experiments/ENCSR010HMS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR010HMS
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2019-02-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB572CEK
size range: 200-600

value: tissue

value: adult

value: Bradley Bernstein, Broad


title: Control ChIP-seq from breast epithelium (ENCLB284LHQ)

description:
https://www.encodeproject.org/experiments/ENCSR776ZDB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR776ZDB
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB284LHQ
size range: 200-600

source_name: Homo sapiens male adult (54 years) breast epithelium tissue originated from breast epithelium

value: EnTEX:Breast Epithelium - Mammary Tissue

value: Kristin Ardlie

value: ENCBS548VTE at ENCODE; https://www.encodeproject.org/ENCBS548VTE/


title: CD44 KO MDA-MB-231 rep 2

description:
231_CD44negative_2
231_CD44negative_4
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt

value: knockout


title: CD44 WT Hs578T rep 2

description:
Hs578T_CD44positive_2
Hs578T_CD44positive_5
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt


title: ImmatureB_KO_4

city: Montreal

first: Anastasia

last: Nijnik

state: Quebec

address: Rm 368 - 3649 Promenade Sir William Osler

department: Physiology

country: Canada

institute: McGill University

data_processing:
The high quality of sequence reads was confirmed using FastQC tool.
low-quality bases were trimmed from read extremities using Trimmomatic v.0.33.
Trimmed reads were then mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.9 in conjunction with Bowtie 1.0.0 algorithms.
Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters.
We retained genes that had an expression level of minimum 5 counts per million reads (CPM) in at least 3 of the samples, and performed quantile normalization with the preprocessCore package to remove batch effects. TMM normalization and differential gene expression analyses were conducted using the edgeR Bioconductor package (R version 3.4.2).
Pairwise comparisons were performed between samples across different mouse genotypes and genes with changes in expression ≥ |1.5| folds and Benjamini-Hochberg adjusted p values ≤ 0.01 were considered significant.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with CPM values after quantile normalization
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene in each sample as generated by featureCounts (gene annotation: UCSC mm9)

source_name: Immature B cells

growth_protocol: The mice were maintained under specific pathogen-free conditions. Test and control groups were bred as littermates and co-housed together.

extract_protocol:
Bone marrow was flushed in PBS supplemented with 0.1% BSA and 2mM EDTA, filtered through 40μm cell-strainers, and subjected to red blood cell lysis in ACK buffer (0.15M NH4Cl, 10mM KHCO3, 0.1mM EDTA). The samples were stained with: biotin-conjugated antibodies against lineage markers [anti-CD3ε (145-2C11, BioLegend), anti-CD11b (M1/70, BioLegend), anti-CD11c (N418, BioLegend), anti-Ly-6G/Ly-6C (Gr-1) (RB6-8C5, BioLegend), anti-NK-1.1 (PK136, BioLegend), and anti-TER-119 (TER-119, BioLegend)], followed by APC-eFluor 780-conjugated Streptavidin (eBioscience), Alexa Fluor 488-conjugated anti-IgD (11-26c.2a, BioLegend), APC-conjugated anti-CD43 (S7, BD Biosciences), PE-conjugated anti-IgM (II/41, eBioscience), PE-Cy7-conjugated anti-CD19 (6D5, BioLegend), and PerCP-Cy5.5-conjugated anti-CD45R/B220 (RA3-6B2, BioLegend) antibodies. DAPI was added immediately before sorting for dead cell exclusion. Cell sorting was performed on FACSAria and analyzed with FACS Diva software (BD Biosciences). The cells were sorted using FACS into pre-B and immature B cells, gating on B220+CD3-CD11b-NK1.1-CD11c-TER119-Gr1-, and IgM-IgD-CD19+CD43- for pre-B cells, and CD19+IgM+IgD- for immature B cells.
RNA was isolated from the FACS-sorted cells using the MagMAX total RNA kit (Ambion, Life Technologies), and quality assessed using Bioanalyzer RNA Pico chips (Agilent). rRNA depletion and library preparation were performed using the SMARTer Stranded RNA-Seq kit (Takara Clontech). The libraries were sequenced on an Illumina HiSeq 4000 sequencer in paired-end 50bp configuration. Cells from multiple mice were pooled to achieve yields of >1.7ng of RNA per sample, and 3-4 independent samples were analyzed per genotype for each cell-type.

tag: strain

tag: gender

value: m

tag: tissue

value: Bone marrow

value: Immature B cells (Bone marrow cells sorted by gates B220+CD3-CD11b-NK1.1-CD11c-TER119-Gr1-CD19+IgM+IgD-)

tag: genotype

value: Bap1 fl/fl mb1-Cre


title: Control ChIP-seq from K562 (ENCLB017CIY)

description:
https://www.encodeproject.org/experiments/ENCSR418YQO/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-E2F4 tagged K562 cell line.
experiment encode accession: ENCSR418YQO
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB017CIY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens K562 cell line stably expressing C-terminal eGFP-tagged E2F4

tag: line

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to E2F4

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Kevin White, UChicago

value: Kevin White

tag: passage number

value: ENCBS107UAM at ENCODE; https://www.encodeproject.org/ENCBS107UAM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: CD44 WT MDA-MB-231 rep 3

description:
231_CD44positive_3
231_CD44positive_7
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt

value: Breast cancer cell line

value: wild-type


title: CD44 WT Hs578T rep 1

description:
Hs578T_CD44positive_1
Hs578T_CD44positive_1
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt


title: CD44 KO Hs578T rep 2

description:
Hs578T_CD44negative_2
Hs578T_CD44negative_2
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt


title: T1 rep1

tag: subject status

value: Papillary Thyroid cancer

tag: tissue type

value: Tumor tissue

tag: tumor stage

value: T4aN1bM0, I

tag: Sex

tag: age


title: CD44 KO MDA-MB-231 rep 3

description:
231_CD44negative_3
231_CD44negative_8
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt

value: knockout


title: Control ChIP-seq from skin epidermis (ENCLB260CDB)

description:
https://www.encodeproject.org/experiments/ENCSR436NLU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq of keratinocyte basal cell carcinoma female adult (66 years). Note that tissue excised from donor is cancerous.
experiment encode accession: ENCSR436NLU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-09-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB260CDB
size range: 200-600

source_name: Homo sapiens female adult (66 years) skin epidermis tissue with basal cell carcinoma

value: skin epidermis

value: tissue

tag: description

value: BCC tumor tissue collected during keratinocyte carcinoma removal surgery under supervision of Maryam Asgari.

tag: biosample encode accession

value: keratinocyte carcinoma surgical removal

tag: dev stage

value: adult

value: 66 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Maryam M. Asgari, MD, MPH

value: ENCBS649ZPH at ENCODE; https://www.encodeproject.org/ENCBS649ZPH/

value: Derived from ENCODE donor ENCDO017WNO; https://www.encodeproject.org/ENCDO017WNO/


title: PreB_KO_4

source_name: Pre B cells

tag: strain

value: m

value: Bone marrow

tag: cell type

value: Pre B cells (Bone marrow cells sorted by gates B220+CD3-CD11b-NK1.1-CD11c-TER119-Gr1-IgM-IgD-CD19+CD43-)

value: Bap1 fl/fl mb1-Cre


title: TF ChIP-seq from MM.1S (ENCLB386APH)

description:
https://www.encodeproject.org/experiments/ENCSR703KWN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR703KWN
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR264HOB
encode release date: 2017-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB386APH
fragmentation methods: sonication (generic)
size range: 300-600
nucleic acid starting quantity: 13
nucleic acid starting quantity units: ng

source_name: Homo sapiens MM.1S immortalized cell line

tag: antibody

value: cell line

value: The parent cell line, MM.1, was established from peripheral blood of a multiple myeloma patient who had become resistant to steroid-based therapy. this line is sensitive to dexamethasone

value: female

value: 42 year

value: immunoglobulin A lambda myeloma

tag: link

value: ENCBS981ZAE at ENCODE; https://www.encodeproject.org/ENCBS981ZAE/

value: Derived from ENCODE donor ENCDO697GBW; https://www.encodeproject.org/ENCDO697GBW/

value: ENCODE dbxrefs Cellosaurus CVCL_8792; http://web.expasy.org/cellosaurus/CVCL_8792


title: PreB_KO_3

tag: gender

tag: tissue

tag: genotype


title: CD44 KO Hs578T rep 1

description:
Hs578T_CD44negative_1
Hs578T_CD44negative_10
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt

tag: cell line

value: Breast cancer cell line

tag: cd44 status

value: knockout


title: CD44 WT MDA-MB-231 rep 1

description:
231_CD44positive_1
231_CD44positive_11
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt

value: wild-type


title: TF ChIP-seq from MM.1S (ENCLB473LOX)

description:
https://www.encodeproject.org/experiments/ENCSR703KWN/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR703KWN
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR264HOB
encode release date: 2017-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB473LOX
fragmentation methods: sonication (generic)
size range: 300-600
nucleic acid starting quantity: 4
nucleic acid starting quantity units: ng

tag: line

value: adult

tag: health state

value: Bradley Bernstein, Broad


title: CD44 KO Hs578T rep 3

description:
Hs578T_CD44negative_3
Hs578T_CD44negative_6
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt


title: PreB_KO_2

tag: age

value: f


title: ImmatureB_KO_3

value: m

value: Bone marrow

value: Immature B cells (Bone marrow cells sorted by gates B220+CD3-CD11b-NK1.1-CD11c-TER119-Gr1-CD19+IgM+IgD-)


title: PreB_KO_1

value: Pre B cells (Bone marrow cells sorted by gates B220+CD3-CD11b-NK1.1-CD11c-TER119-Gr1-IgM-IgD-CD19+CD43-)

value: Bap1 fl/fl mb1-Cre


title: PreB_HET_4

value: Bap1 fl/+ mb1-Cre


title: PreB_HET_3


title: ImmatureB_WT_2

value: 9w 4d

value: Bap1 fl/+


title: PreB_WT_2


title: PreB_WT_3


title: Input_BaF3_BAP1_FLAGx3

data_processing:
Reads quality filtered according to the Illumina pipeline
Experimental and input control sequence reads were mapped to the mouse mm9 reference genome assembly with Bowtie 1.0.0 using the following settings: --best mm9.
Chromatin binding sites of BAP1 were identified using peak detection algorithm MACS (version 1.4.2, default parameters), with comparisons for read enrichment against control input DNA from the same cells.
The resulting binding sites were filtered to remove regions with < 5 fold enrichment compared to the input DNA and < 5 normalized tag counts within 200bp to the peak summit.
Genome_build: mm9

source_name: Ba/F3 cell line stably expressing triple-FLAG-tagged murine BAP1

growth_protocol: Murine B cell lineage precursor cell line Ba/F3 was maintained at 0.5-2 x10^6 cells/mL in RPMI-1640 (Wisent) with 10% Fetal Calf Serum (FCS, Wisent), 2mM L-Glutamine, 100μg/mL streptomycin, 100U/mL penicillin (Wisent), and 5% WEHI conditioned media as the source of IL-3. Ba/F3 cell lines stably expressing triple-FLAG-tagged murine BAP1 and CRISPR-Cas9 targeted Bap1 knockout cell lines were maintained under 2μg/mL puromycin selection (Wisent).

extract_protocol:
Cells were crosslinked for 10 min at room temperature with 1% formaldehyde added in culture medium. Crosslink was stopped with ice-cold PBS containing 0.125M glycine for 5min. Nuclei were prepared by sequential incubation on ice for 5min in buffer A [10mM Tris-HCl (pH 8), 10mM EDTA, 0.25% Triton X-100], and for 30min in buffer B [10mM Tris-HCl (pH 8), 1mM EDTA, 200mM NaCl] (all buffers include proteases inhibitors). Nuclei were resuspended in sonication buffer [10mM Tris-HCl (pH 8), 1mM EDTA, 0.5% SDS, 0.5% Triton X-100, 0.05% NaDOC, 140mM NaCl] and sonicated with a Branson Digital Sonifier (Branson Ultrasonics) to an average size of 250bp (12 cycles of 30 seconds  at 80%, with 30 seconds rest in cooled circulating water). Sonicated chromatin from the equivalent of 5x10^6 cells per ChIP was incubated overnight on a rotating platform at 4°C with 40μL of Dynabeads Protein G (Invitrogen, Life Technologies) conjugated with antibodies: anti-BAP1 (Cell Signaling Technology, D1W9B, 52.8 μg), anti-FLAG M2 (Sigma, F1804, 5 μg) or anti-H2AK119Ub (Cell Signaling Technology, D27C4, 5 μg). Immune complexes with anti-BAP1 and anti-H2AK119Ub antibodies were washed sequentially for 2min at room temperature with 1ml of the following buffers: Wash 1 [0.5% NP-40, 150mM KCl, 1mM EDTA, 10mM Tris-HCl pH8]; Wash 2 [0.5% Triton, 0.1% NaDOC, 100mM NaCl, 10mM Tris-HCl pH8]; Wash 3A [0.5% Triton, 0.1% NaDOC, 400mM NaCl, 10mM Tris-HCl pH8]; Wash 3B [0.5% Triton, 0.1% NaDOC, 500mM NaCl, 10mM Tris-HCl pH8]; and Wash 4 [0.5% NaDOC, 0.5% NP-40, 250mM LiCl, 1mM EDTA, 10mM Tris-HCl pH8]. Immune complexes with anti-FLAG antibody was washed sequentially for 2min at room temperature with 1ml of the following buffers: Wash B [1% Triton X-100, 0.1% SDS, 150mM NaCl, 2mM EDTA, 20mM Tris-HCl pH 8]; Wash C [1% Triton X-100, 0.1% SDS, 500mM NaCl, 2mM EDTA, 20mM Tris-HCl pH 8]; Wash D [1% NP-40, 250mM LiCl, 1mM EDTA, 10mM Tris-HCl pH 8]; and TEN buffer [50mM NaCl, 10mM Tris-HCl pH 8, 1mM EDTA]. After de-crosslinking by overnight incubation at 65°C, the ChIP and Input DNA was purified with Qiaquick PCR Cleanup kit following manufacturer’s instructions (Qiagen).
ChIP-seq libraries were prepared using the Illumina TruSeq kit and sequenced on an Illumina HiSeq 4000 sequencer in paired-end 50bp configuration, with input DNA from the same cells sequenced as negative control.

treatment_protocol: For CRISPR-Cas9 edited samples: Plasmid pSpCas9(BB)-2A-GFP (PX458) was obtained from Addgene (#48138). gRNAs targeting Bap1 were designed using the Zhang lab software (http://crispr.mit.edu): gRNA_Bap1_Exon4_ Chr14:32,066,155: gcaaatggatcgaagagcgc and gRNA_Bap1_Exon5_Chr14:32,066,654: ggcgtgagtggcacaagagt. The gRNAs were ligated into the BbsI (NEB) digested PX458 plasmid, and the resulting plasmids were transformed into DH5α competent cells, purified using PureLink HiPure Plasmid Filter Midiprep Kit (Invitrogen), and verified by Sanger sequencing. To introduce the constructed plasmid into Ba/F3 cells, nucleofection was performed using Amaxa Cell Line Nucleofector Kit V (Lonza) according to the manufacturer’s protocols.  Single GFP+ cells were sorted 48 hours after the nucleofection and then expanded over two weeks to generate single cell clones. The loss of BAP1 protein expression in the cell line clones was validated via Western blotting, with the following antibodies: anti-BAP1 (D7W7O, Cell Signaling Technology), anti-β-Actin (D6A8, Cell Signaling Technology), HRP-conjugated anti-mouse-Ig (eB144, Rockland), and HRP-conjugated anti-rabbit-Ig (eB182, Rockland).

tag: chip antibody


title: CD44 KO MDA-MB-231 rep 1

description:
231_CD44negative_1
231_CD44negative_12
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt


title: ImmatureB_KO_2


title: Anti_H2AK119ub_BaF3_BAP1KO4

source_name: Ba/F3 cell line with CRISPR-Cas9 targeted Bap1 knockout

value: anti-H2AK119Ub (Cell Signaling Technology, D27C4)


title: ImmatureB_KO_1


title: ImmatureB_WT_4


title: Input_BaF3_BAP1KO3


title: Anti_BAP1_BaF3_WT

source_name: WT Ba/F3 cell line

value: anti-BAP1 (Cell Signaling Technology, D1W9B)


title: ImmatureB_HET_4