title: CSC24h [dw_rna_seq_12]

city: Cape Town

first: Danicke

last: Willemse

state: Western Cape

address: Main Rd, Observatory, Cape Town, 7925

country: South Africa

institute: University of Cape Town

description:
dw_rna_seq_12
Diff_expression_24h_all_comparisons.csv

data_processing:
Sequencing reads were subjected to secondary data analysis using the Partek Flow (Partek Inc.) pipeline. In short, reads were filtered based on quality of Phred 30 with minimum read lengths of 25 nucleotides and aligned to the Mtb CDC1551 reference genome sequence (European Nucleotide Archive ASM858v1) using the RNA-seq aligner STAR v2.5.3a. Post-alignment quality assessment, transcript abundance estimation according to ASM858v1 transcriptome annotation by expectation-maximization algorithm, and sample read count normalization using TPM (Transcripts Per Kilobase Million) was done.
Read counts data (not normalized) were uploaded into the iDEP91 online RNA-seq analysis software(50) (Ge et al., 2018). The minimal counts per million (CPM) were kept at default of 0.5 in at least one library. Counts data were transformed for clustering and principal component analysis using EdgeR: log2(CPM+c) and pseudocount (c) of 4. Gene ID’s were not converted to Ensembl. Where multiple transcripts were present, full stops were replaced with underscores in the read counts files to enable recognition of the transcripts as distinct. Missing values imputation was done using the gene median. Principle component analysis was done. Differential Expressed genes were identified using the DESeq2 option on the iDEP91 software, with a FDR of 0.1 and minimum fold change of 2.0. Exposure to CSC was considered the main factor, reference DMSO used when comparing CSC versus DMSO and batch effect considered.
Supplementary_files_format_and_content: Partek Flow analysis results attached

organism: Mycobacterium tuberculosis

source_name: Culture

growth_protocol: Starter cultures were cultured in 7H9 OADC for 6 days, sub-cultured to OD 0.05 and allowed to grow for 4 days. Bacteria were collected, washed twice in 7H9 dextrose to remove catalase, re-suspended in 7H9 dextrose and sonicated to break up clumps. After filtering through a 0.2 micron cell strainer (Falcon) to remove clumps, the cultures were diluted to an OD of 0.2.

extract_protocol:
Cultures (30 ml), were collected, resuspended in 1 ml RNAProBlue solution, transferred to a 2 ml tube containing 0.2 mm matrix B beads (MP Biomedicals) and frozen at -80 °C. After defrosting, bacteria were lysed by bead beating at 3 800 rpm for 3 cycles of 30 s each using a BioSpec Mini-Beadbeater-24 and cellular debris removed by centrifugation at 15 000´g for 15 minutes. Chloroform (300 μl) was added and the reaction vortexed for 10 seconds (s). The Nucleospin RNA kit (Machery-Nagel) kit was used for RNA extraction according to manufacturer’s instructions.the RNA was also treated with Turbo DNase from the TURBO DNA-free Kit (Ambion) kit according to manufacturer’s instructions. Following inactivation of the DNase using inactivation reagent (Ambion), the RNA Clean & Concentrator Kit (Zymo) was used to get rid of the DNase buffer and RNA was eluted in RNase-free water.
The Zymo-Seq RiboFree Total RNA Library Kit was used for library preparation according to the manufacturer’s instructions. RNA (500 ng) was used and ribosomal depletion done for 30 minutes, followed by 14 cycles of PCR.
RNA-seq was done using the Illumina NextSeq 500 V2.5 kit according to the manufacturer’s instructions on the NextSeq 500 machine by the UTHSCSA Genome Sequencing Facility.

treatment_protocol: Cultures were split into 30 ml cultures and exposed to 50  μg/ml CSC or DMSO only (unexposed) for 3 and 24 hours

tag: bacterial strain

value: CSC 50 microg/ml

tag: time of treatment

tag: replicate experiment


title: CSC24h [dw_rna_seq_8]

status: Public on Apr 15 2021

type: SRA

department: Medicine

description:
dw_rna_seq_8
Left out of final analysis because of poor grouping in PCA

library_source: transcriptomic

molecule: total RNA

tag: treatment


title: A02_Brain_APP+-_Arg1fl+_LysMCreTg+_rep2

type: RNA

city: Lexington

first: Chao

last: Ma

state: KY

address: Sanders-Brown Bldg. R430, 800 S. Limestone St.

department: Department of Neuroscience

country: USA

institute: University of Kentucky

hyb_protocol: Panel codeset probes were hybridized with 100 ng of total RNA per sample according to manufacturer’s protocol.

scan_protocol: Hybridized RNA samples were loaded, scanned, and counted by the nCounter® SPRINT Profiler, Moffitt Cancer Center, Tampa, FL, US) according to the manufacturer’s protocol.

data_processing: The NanoString nCounter data analysis was performed using the nSolver™ Analysis Software (v4.0, NanoString Technologies, Inc.) according to the user manuals (MAN-C0019-08, MAN-10030-03). The nSolver was used for analyzing the mouse neuropathology panel by loading with an RLF file (NS_Mm_NeuroPath_v1.0). We performed the basic features of the nSolver analysis to generate the heat maps of differentially expressed gene transcripts (DEGs) with agglomerative clustering based on the normalized data. We also used it to export all normalized data. We also performed the advanced nSolver analysis based on the downloaded and installed online R package (nCounter_Advanced_Analysis_2.0.134) and a modified probe annotation file based on the original one provided by NanoString (NS_Mm_NeuroPath_v1.0_ProbeAnnotations). All RNA samples passed system QC parameters on imaging (fields of view > 75), binding density (0.1-2.25), and positive control linearity (R2 > 0.95). All RNA data passed the positive control limit of detection QC (0.5fM > 2*standard deviations above the arithmetic mean of the negative controls). The following basic threshold criteria were applied. A threshold count value of 10 was calculated as the gene transcript expression background (arithmetic mean of negative controls + 2*standard deviation). An observation frequency of 0.5 was applied for the background, indicating gene transcripts with counts lower than 10 were omitted if it happened to more than 50% of the samples. Therefore, 648 genes were above the background, and 122 genes were removed for falling below the background too frequently. A total of 6 house-keeping genes (Aars, Ccdc127, Cnot10, Csnk2a2, Lars, Mto1) were selected for data normalization by the geNorm algorithm. The p-values were adjusted for multiple testing by the false discovery rate (FDR) method of Benjamini and Hochberg correction. The matrix remodeling pathway was dropped from pathway scoring analysis due to less than five detected gene transcripts. In gene set analysis, a directed global significance score at ±1.3 was set as the cut-off value to reflect the top changed pathways further.

label: Nanostring

organism: Mus musculus

source_name: Brain Posterior Cortex

label_protocol: All RNA samples were loaded and labeled with gene transcript specific probes built in the nCounter® mouse neuropathology panel (v1.0, XT-CSO-MNROP1-12, 12 Reactions, NanoString Technologies, Inc.), then analyzed by the nCounter® Analysis System (nCounter® SPRINT Profiler, Moffitt Cancer Center, Tampa, FL, US) according to the manufacturer’s procedures for hybridization, detection, and scanning.

growth_protocol: The Cre-recombinase mice (B6.129P2-Lyz2tm1(cre)/fo /J; LysMcre promoter, Stock No: 004781) and arginase 1 mice (C57BL/6-Arg1tm1Pmu /J (Arg1fl), Stock No: 008817) were purchased from the Jackson Laboratory. The APP Tg2576 mice (APP+/-), Arg1 floxed mice (Arg1fl/fl), and LysMcreTg/+ were bred according to the Institutional Animal Care and Use Committee (IACUC) approved protocols. Thus, four groups of mice were maintained (nTg/Arg1+/+/LysMcreTg/+, nTg/Arg1fl/+/LysMcreTg/+, APP+/-/Arg1+/+/LysMcreTg/+, and APP+/-/Arg1fl/+/LysMcreTg/+). All mice were subjected to behavioral tests at the age of 15 months, followed by euthanasia and perfusion at 16-month-old age.

extract_protocol: Total RNA of the posterior cortex was extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN, #80004) according to the manufacturer’s protocol.

tag: gender

value: Male


title: FFPE colorectal cancer sample, OHP-res 4

type: genomic

city: Rionero in Vulture

first: Valentina

last: Condelli

state: PZ

address: Via Padre Pio, 1

country: Italy

institute: IRCCS CROB

description:
OHP-res 4
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation 850 Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned using Illumina HiScanSQ system, using standard recommended Illumina scanner setting

data_processing: Illumina Infinium 850K Human Methylation data were processed by R/Bioconductor environment

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: FFPE colorectal cancer sample

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from formalin-fixed, paraffin-embedded (FFPE) CRC specimens using QIAamp DNA Mini kit according to standard instructions

tag: disease state

value: metastatic CRC

tag: subgroup

value: first-line primary-resistant mCRC


title: DMSO24h [dw_rna_seq_11]

description:
dw_rna_seq_11
Diff_expression_24h_all_comparisons.csv

value: DMSO


title: DMSO3h [dw_rna_seq_5]

description:
dw_rna_seq_5
Diff_expression_3h_all_comparisons.csv


title: CSC3h [dw_rna_seq_10]

description:
dw_rna_seq_10
Diff_expression_3h_all_comparisons.csv


title: MHC-17-20

city: 昆明市

first: shaoxing

last: Dai

state: 云南

address: No.1 boda road chenggong, Kunming 650500 Yunnan,China

country: China

institute: Kunming University of Science and Technology

description: Chimera embryo cell of Macaca fascicularis

data_processing:
fastp was used to cut adapters and quality control
human and monkey cells were identified by two ways using the clean data. One way is to compare the number of identical hits of sequencing reads from each cell by blastp with the random selected 10000 reads against the human and monkey genome (Ensembl Homo_sapiens.GRCh38 and Macaca_fascicularis_5.0), respectively. Another way is to compare the reads counts of sequencing reads mapped to tdTomato vector.
hisat2  was used to map sequencing reads to the human or monkey genome with the default parameters.
The program stringtie with default parameters was used to assembly alignments into potential transcripts
Quantify the gene expression as transcripts per million mapped reads (TPM) value by the program stringtie
Genome_build: Homo_sapiens.GRCh38 and Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text file include TPM matrix for all samples

organism: Macaca fascicularis

source_name: embryo cell

extract_protocol:
The single-cell was washed in 30µL micro-drop of PBS-BSA solution and individual cells were picked into 0.2mL PCR tubes by micropipette for modified Smart2-seq,all the cDNA were quantified on a 2100 Bioanalyzer (Agilent) and Qubit 3.0.
The scRNA-seq libraries were generated using the TruePrepTM DNA Library Prep Kit V2 for Illumina®(Vazyme) . Briefly, we use 5-50ng cDNA constructing the libraries according to the manufacturer’s instructions.  cDNA molecules were preamplified and pooled followed by library construction. All libraries were quantified on a 2100 Bioanalyzer (Agilent) and realtime quantitative PCR, and then subjected to 150 bp paired-end sequencing on an Illumina Xten platform (sequenced by Novogene and Annoroad).

tag: tissue

value: embryo

tag: development stage

tag: lineage

value: PE


title: DMSO3h [dw_rna_seq_9]

description:
dw_rna_seq_9
Diff_expression_3h_all_comparisons.csv


title: CSC3h [dw_rna_seq_6]

description:
dw_rna_seq_6
Diff_expression_3h_all_comparisons.csv


title: CSC3h [dw_rna_seq_2]

description:
dw_rna_seq_2
Diff_expression_3h_all_comparisons.csv


title: DMSO24h [dw_rna_seq_7]

description:
dw_rna_seq_7
Left out of final analysis because of poor grouping in PCA


title: CSC24h [dw_rna_seq_4]

description:
dw_rna_seq_4
Diff_expression_24h_all_comparisons.csv


title: MHC-17-22

value: EXMC


title: MHC-17-16


title: DMSO3h [dw_rna_seq_1]

description:
dw_rna_seq_1
Diff_expression_3h_all_comparisons.csv


title: MHC-17-17

value: EPI


title: DMSO24h [dw_rna_seq_3]

description:
dw_rna_seq_3
Diff_expression_24h_all_comparisons.csv


title: MHC-17-12


title: MHC-17-13


title: MHC-17-15


title: MHC-17-11


title: MHC-17-19


title: MHC-17-14


title: MHC-17-1


title: E9-C-7A

value: TE


title: MHC-17-18


title: E9-C-9A


title: E9-C-6A


title: E9-C-33A


title: E9-C-8A


title: E9-C-22A


title: FFPE colorectal cancer sample, OHP-sens 4

description:
OHP-sens 4
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt

value: drug-sensitive mCRC


title: MHC-17-10


title: E9-C-21A


title: E9-C-20A


title: E9-C-1A


title: E9-C-19A


title: E9-C-18A


title: E9-C-17A


title: E9-C-2A


title: E9-C-3A


title: E9-C-23A


title: E9-C-5A


title: E9-C-16A


title: Normal fibroblasts 3

city: Guangzhou

first: Chonghui

last: Hu

state: Guangdong

address: 106 Zhongshan Er Road

department: Department of General Surgery

institute: Guangdong Provincial People's Hospital

data_processing:
bowtie2 (https://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2, v2.2.9) and Tophat (http://ccb.jhu.edu/software/tophat/index.shtml, v2.1.0) were performed to map clean reads to the reference genome of known species
Find_cric (https://github.com/marvin-jens/find_circ，Based on python 2.7) and CIRCexplorer2 (https://circexplorer2.readthedocs.io/en/latest/, v2.3.2) were performed to screen circRNA based on the alignment results.
A self-made program was performed to calculate the expression of circRNA by normalized to TPM (Transcripts per million).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with annotation for every gene

source_name: paired non-cancerous tissues

extract_protocol:
Cancer-associated fibroblasts (CAFs) and Primary normal fibroblasts (NFs) were isolated from pancreatic ductal carcinoma and paired non-cancerous tissues. The Human Tumor Dissociation Kit (Miltenyi Biotec 130-095-929) was used for the generation of single cells from dissociated tissues. Fibroblast populations were isolated by differential velocity adherent technique.
After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer® (Implen, cat.N60, Munich, Germany), ribosomal RNA was removed from 1 μg total RNA using Ribo-off® rRNA Depletion Kit (Human/Mouse/Rat, Vazyme, cat.N406-01, Nanjing, China) and purified using VAHTS® RNA Clean Beads (Vazyme, cat. N412, Nanjing, China). VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, cat.NR604-02, Nanjing, China) was used for lncRNA library construction following the manufacturer's protocol. The enriched ncRNAs were segmented with FRAG/PRIME Buffer. The first cDNA strand was generated by reverse transcription starting from -3 ’ , and the second cDNA strand with U was synthesized using the first cDNA strand. Single- or dual-index adapters were ligated to the fragments with ligase, and size selection was performed with VAHTS® DNA Clean Beads (Vazyme, cat.N411, Nanjing, China). The ligated products were amplified with PCR by the following conditions: Incubated at 37 ° C for 10 minutes to remove the U containing antisense chain, initial denaturation at 98℃ for 10 sec; 12-14 cycles of denaturation at 98℃ for 10 sec, annealing at 60℃ for 30 sec, extension at 72℃ for 30 sec, and then final extension at 72 ℃ for 5 min. The average insert size for the final cDNA library was 290bp (±50 bp). At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (Illumina Corporation， San Diego，USA) following the vendor's recommended protocol by Guangzhou Huayin Health Medical Group CO.,Ltd. (Guangzhou, China).

tag: cell type

value: primary normal fibroblasts


title: Cancer-associated firboblasts 5

source_name: Pancreatic Ductal Adenocarcinoma

value: primary cancer-associated firboblasts


title: Normal fibroblasts 2


title: FFPE colorectal cancer sample, OHP-sens 2

description:
OHP-sens 2
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: Cancer-associated firboblasts 3


title: E9-C-15A


title: Cancer-associated firboblasts 4


title: Cancer-associated firboblasts 2


title: E9-C-13A


title: RNA-seq PSCR Rep1

city: Ciudad de México

first: Pedro

middle: Antonio

last: Avila

state: CDMX

address: Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV

data_processing:
Quality control of all raw data were analyzed in FastQC and filtered for quality in Trim Galore! considering a phred quality score threshold of 30. The reads were mapped to the reference genome (Homo sapiens hg19) with Bowtie2 with default parameters. The unmapped and duplicate reads were filtered with SAMtools, with the following parameters: Minimum MAPQ quality score (-q) 20. The peaks of H2A.Z and acH2A.Z with respect to ChIP-seq input were determined with MACS, with the following parameters: build model --nomodel, composite broad regions --broad, set extension size --extsize 270 for H2A.Z and 249 for acH2A.Z, and peak detection based on q-value=0.05.
To visualize the ChIP-seq signal, deepTools2, was used with the following parameters: --binSize 25, method to use for scaling the largest sample to the smallest was read counts and compare the two files with compute difference of number of reads (subtract input from H2A.Z and acH2A.Z). The generated bigwig files were viewed in the IGV genome browser
The quality control of the raw data was analyzed in FastQC and were filtered for quality in Trim Galore! considering a phred quality score threshold of 30. The reads were mapped to the reference genome (Homo sapiens hg19) using TopHat with default parameters. The assembly of the transcripts and the determination of the differential expression were carried out using the Cufflinks suite. In addition, genes that had FPKM of zero were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: peak text files, bigwigs. RNA-seq: tab-delimited text files include FPKM values for each sample, transcript_differential_expression_testing.txt

source_name: H2A.Z shRNA scramble

growth_protocol: The PDAC cell line PANC-1 (ATCC® CRL-1469TM) were purchased from the American Type Culture Collection (ATCC) and cultured according to their protocols. The PANC-1 cell line was grown in DMEM medium (ATCC® 30-2002TM) supplemented with 10% fetal bovine serum and were cultured in a humid atmosphere, with 5% CO2 at 37ºC. The absence of mycoplasma was confirmed by PCR.

extract_protocol:
Phenol-chloroform extraction was performed for ChIP-seq and total RNA from PZT-1 and PANC-1 scramble was extracted using the TRIZOL reagent
Libraries were prepared for sequencing using standard Illumina protocols by Novogene.

tag: genotype

value: shRNA scramble

tag: cell line

value: pancreatic cancer cell line PANC-1


title: E9-C-14A


title: FFPE colorectal cancer sample, OHP-sens 3

description:
OHP-sens 3
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: RNA-seq PSCR Rep2

description: transcript_differential_expression_testing.txt


title: FFPE colorectal cancer sample, OHP-res 1

description:
OHP-res 1
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt


title: RNA-seq PZT-1 Rep2

source_name: H2A.Z knock-down clone

value: knock-down clone


title: RNA-seq PZT-1 Rep1


title: Input ChIP-seq PANC-1 Rep2

library_source: genomic

source_name: pancreatic cancer cell line PANC-1

value: wild type

tag: chip antibody


title: Input ChIP-seq PANC-1 Rep1


title: E9-C-12A


title: E9-C-4A


title: E9-C-11A


title: acH2A.Z ChIP-seq PANC-1 Rep1

value: anti-acH2A.Z (Abcam ab232908)


title: acH2A.Z ChIP-seq PANC-1 Rep2


title: H2A.Z ChIP-seq PANC-1 Rep2

value: anti-H2A.Z (Cell Signaling # 2718)


title: E9-C-10A


title: Cancer-associated firboblasts 1


title: H2A.Z ChIP-seq PANC-1 Rep1


title: E17-C-5


title: E17-C-9


title: E17-C-8


title: E17-C-6


title: E17-C-3


title: PBMC_infected [B85D75-07]

city: Durham

first: Daniel

last: Saban

state: NC

address: 2351 Erwin Rd, Duke Eye Center

institute: Duke University

description: Single-cell RNA-seq

data_processing:
The raw sequencing data were processed using 10x Genomics Cell Ranger software (v3.1.0).
BCL files were demultiplexed to generate FASTQ files.
FASTQ files were aligned with STAR aligner to the human genome reference GRCh38 from Ensembl database.
Feature barcode processing and UMI counting were then performed according to the standard workflow.
Gene expression matrices were created.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx files

source_name: PBMC

extract_protocol:
Frozen human PBMCs were recovered to perform single-cell RNA-seq.
10x Genomics Single Cell 5’ v1 chemistry was used to generate Gel Bead-In Emulsions (GEM), and perform post GEM-RT cleanup, cDNA amplification, as well as library construction.

treatment_protocol: PBMCs were collected from peripheral whole blood. PBMCs were cryopreserved.

tag: library index

value: PBMC

value: infected

tag: Sex

value: Female


title: E17-C-4

value: embryo


title: PBMC_hospitalized [EB057C-00]

description: Single-cell RNA-seq

value: hospitalized

value: Male


title: PBMC_infected [BAAF62-00]

description: Single-cell RNA-seq


title: PBMC_infected [BAAF62-14]

description: Single-cell RNA-seq


title: PBMC_hospitalized [936128-00]

description: Single-cell RNA-seq


title: PBMC_infected [82CCF5-14]

description: Single-cell RNA-seq


title: PBMC_exposed [80A16A-14]

description: Single-cell RNA-seq

value: exposed


title: PBMC_infected [B85D75-00]

description: Single-cell RNA-seq


title: PBMC_infected [BAAF62-07]

description: Single-cell RNA-seq


title: PBMC_infected [82CCF5-07]

description: Single-cell RNA-seq


title: PBMC_exposed [80A16A-00]

description: Single-cell RNA-seq


title: PBMC_exposed [7768E4-28]

description: Single-cell RNA-seq


title: E17-C-21

value: TE


title: E17-C-2


title: PBMC_healthy [77DA77-00]

description: Single-cell RNA-seq

value: healthy


title: PBMC_exposed [7768E4-14]

description: Single-cell RNA-seq


title: E17-C-20

value: EXMC


title: Normal fibroblasts 1

value: primary normal fibroblasts


title: PBMC_healthy [94D44E-00]

description: Single-cell RNA-seq


title: PBMC_infected [82CCF5-00]

description: Single-cell RNA-seq


title: PBMC_infected [7085CA-14]

description: Single-cell RNA-seq


title: FFPE colorectal cancer sample, OHP-sens 1

description:
OHP-sens 1
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt

value: metastatic CRC

value: drug-sensitive mCRC


title: PBMC_infected [7085CA-07]

description: Single-cell RNA-seq


title: PBMC_infected [7085CA-00]

description: Single-cell RNA-seq


title: E17-C-19


title: E17-C-17


title: PBMC_exposed [61BBAD-07]

description: Single-cell RNA-seq


title: E17-C-16


title: PBMC_exposed [61BBAD-14]

description: Single-cell RNA-seq


title: PBMC_healthy [655A91-00]

description: Single-cell RNA-seq


title: E17-C-15


title: PBMC_hospitalized [45FBA5-00]

description: Single-cell RNA-seq


title: PBMC_infected [450905-14]

description: Single-cell RNA-seq


title: PBMC_hospitalized [460F8D-00]

description: Single-cell RNA-seq


title: E17-C-12


title: PBMC_infected [450905-00]

description: Single-cell RNA-seq


title: PBMC_infected [40067F-14]

description: Single-cell RNA-seq


title: PBMC_exposed [7768E4-02]

description: Single-cell RNA-seq


title: PBMC_infected [40067F-07]

description: Single-cell RNA-seq


title: PBMC_infected [40067F-00]

description: Single-cell RNA-seq


title: E17-C-11


title: PBMC_healthy [52BA23-00]

description: Single-cell RNA-seq


title: E17-C-10


title: PBMC_hospitalized [2DB5F9-00]

description: Single-cell RNA-seq


title: PBMC_infected [2AD75E-14]

description: Single-cell RNA-seq


title: PBMC_infected [2AD75E-07]

description: Single-cell RNA-seq


title: E15-C-9


title: PBMC_exposed [61BBAD-00]

description: Single-cell RNA-seq


title: PBMC_infected [450905-07]

description: Single-cell RNA-seq


title: E15-C-8


title: PBMC_healthy [22CBD6-00]

description: Single-cell RNA-seq


title: PBMC_infected [180E1A-14]

description: Single-cell RNA-seq


title: E15-C-83


title: E15-C-7


title: PBMC_infected [180E1A-07]

description: Single-cell RNA-seq


title: E15-C-75


title: E15-C-79


title: PBMC_infected [0BF51C-14]

description: Single-cell RNA-seq


title: PBMC_infected [0BF51C-00]

description: Single-cell RNA-seq


title: PBMC_infected [180E1A-00]

description: Single-cell RNA-seq


title: PBMC_infected [0B943B-14]

description: Single-cell RNA-seq


title: PBMC_infected [0BF51C-07]

description: Single-cell RNA-seq


title: PBMC_infected [0B943B-00]

description: Single-cell RNA-seq


title: PBMC_infected [0B943B-03]

description: Single-cell RNA-seq


title: MH-17-T-57

description: PSCs in the Chimera embryo of Macaca fascicularis

source_name: Pluripotent stem cells (PSCs)

value: PSCs

value: PE


title: E15-C-73


title: E15-C-72


title: MH-17-T-54


title: E15-C-70


title: MH-17-T-56

value: EPI


title: MH-17-T-52


title: E15-C-6


title: MH-17-T-49


title: MH-17-T-45


title: MH-17-T-53


title: FFPE colorectal cancer sample, OHP-res 2

description:
OHP-res 2
matrix_signal_Unmeth_Meth_DetPval_FOLFOX.txt

value: first-line primary-resistant mCRC


title: E9-TD-9B


title: E9-TD-7B


title: E9-TD-6B


title: E15-C-67


title: E15-C-62


title: E9-TD-5B


title: E15-C-5


title: E9-TD-4B


title: E9-TD-3B


title: E9-TD-2B


title: E9-TD-1B


title: E9-TD-18B


title: E9-TD-17B


title: E15-C-51


title: E15-C-59


title: E15-C-52


title: E15-C-50


title: E9-TD-14B


title: E9-TD-13B


title: E9-TD-12B


title: E9-TD-8B


title: E9-TD-11B


title: E9-TD-10B


title: E15-C-41


title: E15-C-4


title: E15-C-40


title: E9-MH-TD-23


title: E9-MH-TD-22


title: E9-MH-TD-21


title: E9-MH-TD-20


title: E17-TD-8B


title: E17-TD-5B


title: E15-C-39


title: E17-TD-9B


title: E17-TD-4B


title: E17-TD-40B


title: E9-TD-16B


title: E17-TD-3


title: E17-TD-3B


title: E17-TD-37B


title: E15-C-37


title: E15-C-35


title: E15-C-38


title: E17-TD-35B


title: E17-TD-34B


title: E17-TD-33B


title: E15-C-34


title: E17-TD-30B


title: E17-TD-31B


title: E17-TD-2B


title: E17-TD-29B


title: E15-C-3


title: E15-C-32


title: E17-TD-27B


title: E15-C-31


title: E17-TD-25B


title: E17-TD-22B


title: E17-TD-20B


title: E15-C-36


title: E15-C-2


title: E17-TD-1


title: E17-TD-1B


title: E15-C-29


title: E17-TD-19B


title: E15-C-33


title: E17-TD-16B


title: E15-C-28


title: E17-TD-14B


title: E17-TD-28B


title: E15-C-26


title: E17-TD-12B


title: E17-TD-10B


title: E15-TD-9


title: E15-C-30


title: E15-TD-97


title: E15-TD-95


title: E15-TD-96


title: E17-TD-21B


title: E15-TD-94


title: E15-C-27


title: E15-C-22


title: E15-C-24


title: E15-TD-90


title: E17-TD-17B


title: E15-TD-88


title: E15-TD-8


title: E15-TD-87


title: E15-TD-86


title: E15-TD-85


title: E15-TD-84


title: E15-TD-83


title: E15-C-18


title: E15-C-1


title: E15-C-23


title: E15-TD-82


title: E15-TD-92


title: E15-TD-80


title: E15-C-16


title: E15-C-17


title: E15-C-15


title: E15-TD-75


title: E15-TD-78


title: E15-TD-7


title: E15-TD-76


title: E15-C-14


title: E15-C-21


title: E15-TD-73


title: E15-TD-74


title: E15-TD-71


title: FOXA1 ChIP-seq in EPZ-6438 & P5091 Combo LNCaP cells_rep #2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: LNCaP cells treated with 1 uM EPZ-6438 and 3 uM P5091 for 7 days. Replicate #2

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Peak-calling by HOMER v4.2
Genome_build: hg19
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file

source_name: prostate tumor

growth_protocol: LNCaP cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin

extract_protocol: Chromatin in nuclear fraction were sheared to 200-500bp using an Covaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antibody. DNA was then reverse crosslinked from protein and purified.  ChIP-seq libraries were prepared from 3-5ng ChIPped DNA by using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Postamplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000.

treatment_protocol: For m880-m883, LNCaP cells were infected with shCtrl or shFOXA1 along with control, HA-FOXA1, or HA-K295A for 5 days. For m944-m951, LNCaP cells were treated with either DMSO, 1 uM EPZ-6438, 3 uM P5091, or in combination for 7 days.

value: LNCaP

value: 1 uM EPZ-6438 and 3 uM P5091

tag: antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog number

tag: antibodylot/batch number


title: E15-TD-72


title: E15-C-19

description: Chimera embryo cell of Macaca fascicularis

value: embryo


title: E15-C-12


title: E15-TD-6


title: FOXA1 ChIP-seq in EPZ-6438 treated LNCaP cells_rep #2

description: LNCaP cells treated with 1 uM EPZ-6438 for 7 days. Replicate #2

tag: treatment


title: E15-C-11


title: E15-TD-77


title: E15-TD-70


title: E15-TD-69


title: E15-C-10


title: E13-C-8


title: FOXA1 ChIP-seq in P5091 treated LNCaP cells_rep #2

description: LNCaP cells treated with 3 uM P5091 for 7 days. Replicate #2


title: E15-TD-66


title: FOXA1 ChIP-seq in EPZ-6438 & P5091 Combo LNCaP cells_rep #1

description: LNCaP cells treated with 1 uM EPZ-6438 and 3 uM P5091 for 7 days. Replicate #1


title: E15-TD-67


title: E13-C-9


title: FOXA1 ChIP-seq in DMSO treated LNCaP cells_ rep #2

description: LNCAP cells treated with DMO for 7 days. Replicate #2

value: DMO


title: FOXA1 ChIP-seq in P5091 treated LNCaP cells_rep #1

description: LNCaP cells treated with 3 uM P5091 for 7 days. Replicate #1


title: E15-TD-64


title: E15-C-13


title: FOXA1 ChIP-seq in DMSO treated LNCaP cells_rep #1

description: LNCAP cells treated with DMO for 7 days. Replicate #1


title: FOXA1 ChIP-seq in EPZ-6438 treated LNCaP cells_rep #1

description: LNCaP cells treated with 1 uM EPZ-6438 for 7 days. Replicate #1


title: E13-C-7


title: E13-C-6


title: E15-TD-65


title: E13-C-5


title: E15-TD-63


title: HA ChIP-seq in shFoxA1+K295A LNCaP cells

description: LNCaP cells with stable expression of both shFoxA1 and K295A

tag: shRNA

value: HA


title: E13-C-4


title: E15-TD-62


title: E17-C-1


title: E13-C-46


title: E15-TD-60


title: HA ChIP-seq in shFoxA1+WT LNCaP cells

description: LNCaP cells with stable expression of both shFoxA1 and WT FOXA1


title: E15-TD-5


title: HA ChIP-seq in pGIPZ LNCaP cells

description: LNCaP cells with stable expression of pGIPZ control

value: stable expression of pGIPZ control


title: HA ChIP-seq in shFoxA1 LNCaP cells

description: LNCaP cells with stable expression of shFoxA1

value: stable expression of shFoxA1


title: E15-TD-56


title: E13-C-42


title: E15-TD-59


title: sox10-BRAFV600E;p53-/-_rep_9

city: New York

first: Richard

middle: Mark

last: White

state: NY

address: 1275 York Avenue MB 424

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

description: Zebrafish_processed_counts_table.xlsx [S6_S5]

data_processing:
quality control with FASTQC (Babraham Bioinformatics)
trimming with TRIMMOMATIC
reads were aligned to GRCz10 (Ensembl version 81) using STAR with --quantMode GeneCounts
quality control via SeQC
Differential expression was calculated with DESeq2
Genome_build: GRCz10, Ensembl version 81
Supplementary_files_format_and_content: CSV file with raw counts from STAR

organism: Danio rerio

source_name: Zebrafish melanoma

growth_protocol: Zebrafish were raised to adulthood in standard 28.5C aquatics chambers and tumors harvested when large enough for RNA extraction

extract_protocol:
Entire tumor was processed using Trizol RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transgenic construct injection at 1-cell state

tag: line

value: Tu (p53/--) background

tag: plasmid


title: PBMC_infected [2AD75E-00]

description: Single-cell RNA-seq

value: PBMC

tag: disease state

value: infected

value: Male


title: PBMC_hospitalized [0993F8-00]

description: Single-cell RNA-seq

value: hospitalized


title: E15-TD-54

tag: tissue

value: PSCs

tag: development stage


title: E13-C-41

tag: lineage

value: TE


title: E13-C-40

value: EPI


title: sox10-BRAFV600E;p53-/-_rep_12

description: Zebrafish_processed_counts_table.xlsx [S9_S8]


title: E15-TD-4

description: PSCs in the Chimera embryo of Macaca fascicularis


title: sox10-BRAFV600E;p53-/-_rep_10

description: Zebrafish_processed_counts_table.xlsx [S7_S6]


title: sox10-BRAFV600E;p53-/-_rep_8

description: Zebrafish_processed_counts_table.xlsx [S5_S4]


title: E15-TD-3

value: EXMC


title: sox10-BRAFV600E;p53-/-_rep_7

description: Zebrafish_processed_counts_table.xlsx [S4_S3]


title: E13-C-39

description: Chimera embryo cell of Macaca fascicularis


title: E13-C-3


title: E13-C-45


title: E15-TD-2


title: sox10-BRAFV600E;p53-/-_rep_6

description: Zebrafish_processed_counts_table.xlsx [S2_S2]


title: sox10-BRAFV600E;p53-/-_rep_11

description: Zebrafish_processed_counts_table.xlsx [S8_S7]


title: E13-C-38


title: E15-TD-29


title: E13-C-44


title: sox10-BRAFV600E;p53-/-_rep_5

description: Zebrafish_processed_counts_table.xlsx [S15_S12]


title: E13-C-37


title: E15-TD-28


title: E13-C-43


title: sox10-BRAFV600E;p53-/-_rep_4

description: Zebrafish_processed_counts_table.xlsx [S14_S11]


title: E15-TD-51


title: E15-TD-26


title: sox10-BRAFV600E;p53-/-_rep_3

description: Zebrafish_processed_counts_table.xlsx [S12_S10]


title: E13-C-35


title: sox10-BRAFV600E;p53-/-_rep_2

description: Zebrafish_processed_counts_table.xlsx [S10_S9]


title: E13-C-34


title: sox10-BRAFV600E;p53-/-_rep_1

description: Zebrafish_processed_counts_table.xlsx [S1_S1]


title: mitf-BRAFV600E;p53-/-_rep_6

description: Zebrafish_processed_counts_table.xlsx [M9_S17]


title: E15-TD-24


title: E13-C-33


title: E13-C-32


title: E15-TD-23


title: mitf-BRAFV600E;p53-/-_rep_5

description: Zebrafish_processed_counts_table.xlsx [M6_S16]


title: mitf-BRAFV600E;p53-/-_rep_4

description: Zebrafish_processed_counts_table.xlsx [M5_S15]


title: E13-C-30


title: E13-C-31


title: mitf-BRAFV600E;p53-/-_rep_3

description: Zebrafish_processed_counts_table.xlsx [M2_S14]


title: E15-TD-20


title: E15-TD-1


title: E13-C-29


title: E13-C-2


title: E13-C-36


title: E15-TD-19


title: E13-C-28


title: E15-TD-18


title: BiPNT.D3.cKit+.rep2(RNA-seq)

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

description: mRNA

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the genome (mm10) with bowtie2.
ATAC-seq reads were aligned to the mouse mm10 genome using bowtie247 with the options ‘-p 20– very-sensitive–end-to-end–no-unal–no-mixed -X 2000’. The multimapped reads were kept for TE analysis, but only the best alignment is reported for those reads, if more than one equivalent best alignment was found, then one random alignment was reported. Whereas the reads mapping to mitochondrial DNA or unassigned sequences were discarded.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig, *.genes.results (counts, TPMs, FPKMs)

source_name: PNT reprogramming cells D3

growth_protocol: For reprogramming of EpiSCs into naïve state, EpiSCs were passaged with Accutase into singular cell and seeded at a density of 5,000 cells per well of 24-well plate coated with FBS in N2B27+XAV939+FA medium with the addition of 5 μM Y-27632. The medium was replaced with Stage 1 medium and changed daily for the first 3 days. The Stage 2 medium was refreshed daily for the last 5 days.

extract_protocol: DNA was isolated for ATAC-seq. RNA was isolated for RNA-seq.

tag: cell type

value: PNT reprogramming cells

tag: ckit

value: cKit+

tag: time point


title: E15-TD-25


title: E15-TD-21


title: E15-TD-17


title: E13-C-27


title: BiPNT.D3.cKit+.rep1(RNA-seq)

description: mRNA


title: E15-TD-22


title: E13-C-26


title: BiPNT.D3.cKit-.rep2(RNA-seq)

description: mRNA

value: cKit-


title: E15-TD-15


title: P14_#2_cochlea and DRG

city: Boston

first: Rosalind

last: Segal

state: MA

address: 450 Brookline Ave

institute: Harvard Medical School

data_processing:
The demultiplexing and barcode analysis was performed using InDrops pipeline (https://github.com/indrops/indrops), using Genome Reference Consortium Mouse Build 38 (GRCm38) to estimate the molecular count matrix for the measured cells.
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix in tsv

molecule: polyA RNA

source_name: cochlea and DRG

extract_protocol:
Indrop Single cell v3
2 cochlea out of the inner ear and 6 lumbar DRGs (3 from each side) and 2 SN (1 from each side) per mouse were dissected. The dissections were done in ice-cold Ca2+-free HBSS solution (20mM HEPES in Ca2+-free HBSS). For all dissociations, enzyme mix included collagenase IV, papain and DNase I (Worthington Papain dissociation system) in HBSS solution with Ca2+ (20mM HEPES in HBSS with Ca2+ (Life Technologies) with only P14 dissociation also included trypsin. Tissues were incubated with the enzyme mix at 37C for 10-40min depending on the animal stage and triturated in between. Equal volume of ovomucoid inhibitor in EBSS was then added to stop the reaction. The cells were washed with 2% BSA in HBSS solution by spinning at 300rpm for 5-7min, resuspended with 2% BSA in HBSS. The cells were spinned through a tube with cell-strainer cap (Catalog# 352235) and loaded to FACS instrument for sorting for GFP+ glia and Neurog1cre, tdTomato+ neurons. After FACS, the cells were pelleted and resuspended in Optiprep/BSA solution (20% optiprep, 2% BSA in HBSS). An equal percentage of high GFP and low GFP glia from cochlea were combined. For both DRG+SN and cochlea samples, 2.5-5% neurons from the sorting were added to the glial cells to spike the runs as negative control. Cell mixes were loaded at 80,000 cells/ml concentration to the inDrop chip.

value: cochlea and DRG

tag: age


title: BiPNT.D3.cKit-.rep1(RNA-seq)

description: mRNA


title: E13-C-25

value: embryo


title: E13-C-24


title: P14_#1_cochlea and DRG


title: BiPNT.D3.cKit+(ATAC-seq)


title: E13-C-23


title: E15-TD-13


title: E18_#2_cochlea and DRG


title: E18_#3_cochlea and DRG


title: E15-TD-14


title: E13-C-22


title: E15-TD-136


title: E18_#1_cochlea and DRG


title: E13-C-21


title: Liver_KPC_7

city: Baltimore

first: Won Jin

last: Ho

state: MD

address: 1650 Orleans St. CRB I Rm 488

department: Oncology

institute: Johns Hopkins University

data_processing:
Illumina reads were processed through Illumina's Real-Time Analysis generating base calls and corresponding base call quality scores
FASTQ files were generated with bcl2fastq2
Resulting data was aligned to reference mouse genome M21 using salmon software
Values were normalized as reads per million and the resulting count data was log2 transformed
Genome_build: M21 (GRCm38.p6)
Supplementary_files_format_and_content: rds object with gene counts for every gene and every sample; R script is used to load and annotate the files based on the txt annotation file

source_name: KPC liver

extract_protocol:
Cells were trypsinized off culture plates, washed in PBS x2; normal lungs and livers were dissociated enzymatically into single cell suspensions, washed in PBS x2; KPC-bearing lungs and livers were dissociated enzymatically into single cell suspensions and enriched for CD45- populations, washed in PBS x2
Total RNA was extracted using Quick-RNA microprep kit, with DNAse I treatment. NEBNext Ultra II Directional RNA library prep kit was used to generate libraries. PolyRNA is first selected using oligodT beads. After cDNA synthesis, adapters are ligated for PCR enrichment.

value: liver

tag: strain

value: Non-immune cells enriched from KPC-bearing livers


title: E15-TD-135


title: Liver_KPC_6


title: E14_#3_cochlea and DRG


title: E15-TD-134


title: Liver_KPC_5


title: E13-C-19


title: E14_#2_cochlea and DRG


title: E15-TD-133


title: E14_#1_cochlea and DRG


title: E13-C-18


title: Liver_KPC_4


title: E15-TD-131


title: E13-C-17


title: BiPNT.D3.cKit-(ATAC-seq)


title: Liver_KPC_3


title: E15-TD-12


title: Liver_KPC_2


title: Liver_KPC_1


title: E15-TD-129


title: E13-C-16


title: PBS4

city: Copenhagen N

first: Atul

last: Anand

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Department of Pathology

country: Denmark

institute: Rigshospitalet

data_processing:
The raw data were first demultiplexed using CASAVA thereby creating FASTQ files.
The FASTQ files were processed using BBDUK from the BBMAP tool package for trimming remnant adaptor sequences, removal of low quality bases and reads and kmer-filtering.
aligned against the murine transcriptome (Mus_musculus.GRCm38.87), and then to the murine genome (Mus_musculus.GRCm38) using TOPHAT2
Quantification was done using the HTseq-count python module embedded in the HTSeq tool package
The edgeR R-package was used for transformation of the raw counts into counts per million (cpm), filtration of very low expressed genes
Genome_build: Mus_musculus.GRCm38
Genome_build: transcriptional: Mus_musculus.GRCm38.87
Supplementary_files_format_and_content: the limma R-package was used for calculating the statistics for the differential expression analysis. KEGG pathway analysis was done using DAVID

source_name: Brain

extract_protocol:
RNA extraction was performed using a Trizol protocol
The sequence libraries were prepared using an Illumina Truseq Stranded mRNA sample preparation kit (Illumina).

treatment_protocol: intrathecal treatment with PBS or CPG

value: PBS


title: E13-C-20


title: PBS2


title: E15-TD-128


title: E13-C-14


title: CPG5

value: CPG


title: E15-TD-127


title: Lung_KPC_5

source_name: KPC lung

value: lung

value: Non-immune cells enriched from KPC-bearing lungs


title: Lung_KPC_4


title: CPG4


title: CPG2


title: E15-TD-126


title: E13-C-12


title: Lung_KPC_3


title: E15-TD-125


title: CPG1


title: E15-TD-16


title: Lung_KPC_2


title: E13-C-10


title: PBS1


title: E15-TD-124


title: E13-C-15


title: E13-C-11


title: Lung_KPC_1


title: E15-TD-123


title: E13-C-13


title: E15-TD-122


title: Liver_NL_5

source_name: Normal liver

value: Dissociated normal liver


title: Mouse-165

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Raw reads were demultiplexed and mapped by CellRanger (v3.0.2) with the GRCm38 reference genome (in the mm10-2.1.0 reference database provided with CellRanger). Unique-molecular identifier (UMI) counts and loaded into R. Genes that are expressed in less than 3 cells in both samples or cells that have less than 200 or more than 2500 genes expressed were removed from the analysis. Cells having more than 5 percents of UMIs from the mitochondrial genes were also removed.
UMI counts were converted into log2 counts-per-million-UMIs (log2 CPM) values with an a-priori count of 5. We then used the t-distributed stochastic neighbor embedding (tSNE) function provided in the tsne R-package for dimentional reduction on the log2CPM values.
Genome_build: mm10
Supplementary_files_format_and_content: zipped sparse matrix of UMI counts

source_name: Tumor

growth_protocol: Tumors were induced after topical application of 2ul of a 5mM 4-hydroxytamoxifen solution

extract_protocol:
Sorted leukocytes were re-suspended at a concentration of 1×10^3 cells/ul and then loaded onto to the 10X ChromiumTM Single Cell 3’ Chip to be encapsulated forming Gel Beads in Emulsion (GEM). Then PolyA barcoded cDNA was generated after incubation with GEM at 53ºC for 45 minutes using a Thermocycler.
Single cell RNA sequencing libraries were prepared according to 10X Genomics protocol and using the ChromiumTM Single Cell 3’ Library and Gel Bead Kit (v2)

treatment_protocol: Tumors were collected 48 days post tamoxifen application, enzymatically digested (collagenase IV) for 45 minutes at 37 degrees to obtain single cell suspensions and stained with fluorescent-conjugated antibodies and a dead cell marker. Live tumor-infiltrating leukcoytes were then purified by flow-cytometry.

value: Tumor

tag: celltype

value: Live CD45+ cells

tag: infection


title: E15-TD-120

value: PSCs


title: Liver_NL_4


title: E11-C-9

source_name: embryo cell

value: TE


title: Liver_NL_3


title: E11-C-9A

value: EPI


title: E15-TD-11


title: Mouse-136


title: scRNAseq_Islets_IL1B

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: Islets

extract_protocol:
10x Genomics
10x Genomics

treatment_protocol: Pancreatic islets were harvested from mice, exposed to cytokines ex vivo, dissociated, and loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles).

value: 6 hours IL-1B treatement

value: Pancreas


title: scRNAseq_Islets_IL1B_IFNg

value: 6 hours IL-1B and IFNg treatement


title: E11-C-8


title: Liver_NL_2


title: scRNAseq_Islets_IFNg

value: 6 hours IFNg treatement


title: E15-TD-117


title: E11-C-7A

value: embryo


title: Lung_NL_5

source_name: Normal lung

value: Dissociated normal lung


title: E15-TD-119


title: epididymal adipose tissue, WD5 rep3

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Reads quality control using fastQC and Fastq-scren,
Read mapping using STAR_2.4.0a versus mm10 following ENCODE RNA-seq options,
Features quantification using featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -C" options using Ensembl GRCm38.83 release.
Genome_build: mm10
Supplementary_files_format_and_content: NormalizedData.txt: normalized count table

source_name: Epididymal Adipose tissue

growth_protocol: 3-weeks-old male mice were divided into 2 groups. Males from the first group were kept on CD and the males of the other group were fed a WD for 3-4 months. This first generation of WD males was named WD1. At four months-old, 4 to 6 independent males of each group were then crossed with 7-weeks old C57BL/6J female mice (CD-fed) obtained from Charles River (Charles River Laboratories, France). The male progenies were kept and subjected to the same experimental procedure. At 3-weeks old, they were fed a HFD and at 4-5 months crossed with a CD-female. This second generation of males was called WD2. This experimental design was repeated 3 times to obtain the WD5 group

extract_protocol:
Epididymal white adipose tissues were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1000 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 5-months old mice

tag: genotype

value: wild type

tag: diet

value: WD

tag: generation number in hfd

value: Epididymal Adipose tissue


title: epididymal adipose tissue, WD5 rep1


title: Lung_NL_4

value: lung


title: Liver_NL_1

value: liver

value: Dissociated normal liver


title: E11-C-8A


title: epididymal adipose tissue, WD5 rep2


title: mitf-BRAFV600E;p53-/-_rep_2

description: Zebrafish_processed_counts_table.xlsx [M11_S19]

value: Tu (p53/--) background


title: epididymal adipose tissue, WD1 rep3


title: E11-C-7


title: mitf-BRAFV600E;p53-/-_rep_1

description: Zebrafish_processed_counts_table.xlsx [M1_S13]


title: epididymal adipose tissue, WD1 rep2


title: E15-TD-115

description: PSCs in the Chimera embryo of Macaca fascicularis

value: PSCs


title: E11-C-6

value: TE


title: E15-TD-118

value: EPI


title: E15-TD-116


title: Lung_NL_1


title: Lung_NL_3


title: E11-C-6A


title: Lung_NL_2


title: E11-C-5


title: E15-TD-114

value: EXMC


title: E11-C-5A

value: PE


title: epididymal adipose tissue, WD1 rep1


title: E11-C-4


title: 2D_KPC_7

source_name: 2D culture

value: In vitro culture of KPC cells

value: pancreatic cancer


title: E15-TD-113


title: 2D_KPC_8


title: epididymal adipose tissue, CD rep3

value: CD


title: epididymal adipose tissue, CD rep2


title: 2D_KPC_5


title: E15-TD-112


title: E15-TD-111


title: E11-C-4A

value: embryo


title: 2D_KPC_6


title: epididymal adipose tissue, CD rep1

value: 5-months old mice


title: E11-C-3A


title: 2D_KPC_3


title: E15-TD-110


title: E11-C-37A


title: E15-TD-10


title: 56pit

first: Sander

middle: M

last: Houten

address: 1425 Madison Avenue, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina HiSeq2500 for base caling
Read alignment. STAR (release 2.4.0 g1)
gene-level read quantification via featureCounts v1.4.4
Genome_build: mouse genome mm10 (GRCm38.75)
Supplementary_files_format_and_content: text file containing read count per gene

source_name: pituitary, wt

extract_protocol:
RNA was isolated using QIAzol lysis reagent followed by purification using the RNeasy kit (Qiagen)
mRNA-focused cDNA libraries were generated using Illumina reagents (polyA capture), and samples were run on an Illumina HiSeq 2500 sequencer to yield a total read depth of approximately 46 million 100 nucleotide single-end reads per sample

tag: Sex

value: male

value: 18 weeks

value: wt

value: chow

value: pituitary


title: E15-TD-109


title: 66pit

source_name: pituitary, KLF14 KO

value: 21 weeks

value: KLF14 KO


title: 66IFAT

source_name: inguinal white adipose tissue, KLF14 KO

value: inguinal white adipose tissue


title: E11-C-36A

value: TE


title: 2D_KPC_2


title: E15-TD-108

source_name: Pluripotent stem cells (PSCs)

value: PSCs

value: EPI


title: 56IFAT

source_name: inguinal white adipose tissue, wt


title: E15-TD-104


title: E11-C-3


title: 2D_KPC_1


title: E11-C-34A


title: E15-TD-103


title: E11-C-33A


title: 50IFAT

value: 19 weeks


title: E15-TD-102


title: 2D_KPC_4

value: In vitro culture of KPC cells


title: E11-C-32A


title: 49pit


title: Mouse embryonic retinal progenitor cells - E14.5 DHS4D-GFP+mCherry

city: Aurora

first: Michael Kaufman

middle: L

last: Kaufman

state: CO

address: Fitzsimons Building,13001 East 17th Place

department: Department of Biomedical Informatics

institute: CU Cancer Center

description: single cell RNA

data_processing:
Demultiplexing of raw base calls was conducted with Cell Ranger 2.2
GFP and mCherry sequences were added to the mouse reference genome to enable alignment and detection of reads from the DHS-4D GFP plasmid.
The cellranger mkfastq and cellranger counts tools were used for alignment to mm10, filtering, barcode counting, and UMI counting.
Processed data files resulted in barcodes.tsv, genes.tsv, and matrix.mtx.
Following removal of doublets, we captured 1,843 cells and read depth was estimated to be approximately 250K reads per cell.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv - cell ranger generated barcoded cell indexes
Supplementary_files_format_and_content: genes.tsv - cell ranger generated IDs of quantified genes
Supplementary_files_format_and_content: matrix.mtx - cell ranger generated matrix of count values

source_name: whole E14.5 retina

extract_protocol:
Embryonic mouse retinas were cultured up to 48hrs following electroporation and then dissociated using the Worthington Papain Dissociation System (Worthington Biochemical Corporation, Lakewood, New Jersey, USA). Tissue was placed into activated papain tubes, prepared via manufacturer specifications, and incubated on a nutator at 37°C. Dissociation status of tissue was checked every 10 minutes and the cells gently triturated using a 1mL pipette 2-3 times. Just prior to achieving a final single cell suspension, warmed DNase solution was added dropwise, gently inverted to mix, and then incubated for 5 more minutes on rotator at 37°C. Next, prewarmed ovomucoid solution was slowly added dropwise and again gently inverted to mix. Cells were spun down for 5 minutes at 300 g and the supernatant carefully aspirated. Cells were then resuspended and washed with 1% FBS + PBS (without calcium or magnesium). After washing, cells were spun 5 minutes at 300 g and resuspended with 1% FBS + PBS for fluorescently activated cell sorting. GFP+(±Cherry) and Cherry-only cells were separately collected from cell sorter into 10% FBS+PBS (without calcium or magnesium), counted on a hemocytometer, and resuspended in 10% FBS + PBS.
To generate sequencing library GFP+ (±Cherry) and Cherry-only cells were mixed at a 40/60 ratio. Single cell suspension was then submitted for droplet based barcoding on the 10X Chromium using the Chromium Single Cell 3' Reagent Kit V2 (10X Genomics, Pleasanton, California, USA).
2x151 scRNAseq

value: retinal progenitor cells


title: 49IFAT


title: E13-TD-8


title: E11-C-35A


title: E11-C-31A

value: EXMC


title: E11-C-30

value: embryo


title: E13-TD-9


title: 48IFAT


title: 48pit


title: 35pit


title: invivo_LNP_12h_Rep2

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

data_processing:
Raw reads were trimmed and filtered using fastp version version 0.20.0
Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
transcripts per milion (tpm) were identified using kallisto
Genome_build: Mus musculus Ensembl GRCm38.p5
Supplementary_files_format_and_content: Tab-separated (abundance)

source_name: primary hepatocytes

growth_protocol: for in vitro:DMEM grwoth medium supplemented with 10% FBS and 1% P/S; in vivo samples were isolated from C58BL/6J animals

extract_protocol:
in vitro: Detachment with TryplE, wash with PBS, lysis in RLT buffer and RNA isolation following RNAeasy protocol; in vivo: primary hepatocyte isolation
total RNA

treatment_protocol: in vitro: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000; in vivo: LNP- or AAV-mediated delivery

value: tail vein

value: ABEmax7.10, LNP, 12h

value: primary hepatocytes


title: invivo_LNP_12h_Rep1


title: 50pit

value: male


title: E11-C-30A


title: Cerebral Cortex Sevo3 rep3

city: Shanghai

first: Ming

last: Jiang

address: Dong'an Road 130

institute: Fudan University

data_processing:
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm10
Supplementary_files_format_and_content: TPM values for each sample.

source_name: Cerebral Cortex

extract_protocol:
Fetal cerebral cortex were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cerebral Cortex

value: embryonic day 14.5

tag: treatment

value: treated with 2.5% sevoflurane and 97.5% Oxygen for 6 hours


title: E13-TD-7

first: shaoxing

last: Dai

address: No.1 boda road chenggong, Kunming 650500 Yunnan,China

institute: Kunming University of Science and Technology

data_processing:
fastp was used to cut adapters and quality control
human and monkey cells were identified by two ways using the clean data. One way is to compare the number of identical hits of sequencing reads from each cell by blastp with the random selected 10000 reads against the human and monkey genome (Ensembl Homo_sapiens.GRCh38 and Macaca_fascicularis_5.0), respectively. Another way is to compare the reads counts of sequencing reads mapped to tdTomato vector.
hisat2  was used to map sequencing reads to the human or monkey genome with the default parameters.
The program stringtie with default parameters was used to assembly alignments into potential transcripts
Quantify the gene expression as transcripts per million mapped reads (TPM) value by the program stringtie
Genome_build: Homo_sapiens.GRCh38 and Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text file include TPM matrix for all samples

extract_protocol:
The single-cell was washed in 30µL micro-drop of PBS-BSA solution and individual cells were picked into 0.2mL PCR tubes by micropipette for modified Smart2-seq,all the cDNA were quantified on a 2100 Bioanalyzer (Agilent) and Qubit 3.0.
The scRNA-seq libraries were generated using the TruePrepTM DNA Library Prep Kit V2 for Illumina®(Vazyme) . Briefly, we use 5-50ng cDNA constructing the libraries according to the manufacturer’s instructions.  cDNA molecules were preamplified and pooled followed by library construction. All libraries were quantified on a 2100 Bioanalyzer (Agilent) and realtime quantitative PCR, and then subjected to 150 bp paired-end sequencing on an Illumina Xten platform (sequenced by Novogene and Annoroad).


title: E11-C-2


title: 34IFAT

value: 21 weeks

value: wt

value: chow


title: E13-TD-4

value: PSCs


title: Cerebral Cortex Ctr2 rep2

value: treated with 100% Oxygen for 6 hours


title: 35IFAT

value: KLF14 KO

value: inguinal white adipose tissue


title: E13-TD-6

value: EPI


title: Cerebral Cortex Sevo2 rep2


title: Cerebral Cortex Ctr1 rep1


title: E15-TD-100


title: invivo_LNP_12h_Rep3


title: E11-C-2A


title: E11-C-29

value: TE


title: E11-C-29A

value: embryo


title: Cerebral Cortex Ctr3 rep3


title: E11-C-27


title: E13-TD-31


title: E13-TD-3

value: EXMC


title: 32IFAT


title: 33pit

value: pituitary


title: E11-C-28


title: ChIP-seq for Otx2

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

data_processing:
Raw reads were mapped xenopus tropicalis (v9.1) genome using CSBB-v3.0 (https://github.com/praneet1988/Computational-Suite-For-Bioinformaticians-and-Biologists)
Mapped reads in Bam format were used to call peaks using MACS2.
Mapped reads in Bam format were used to bigwigs using deeptools
Genome_build: xenopus tropicalis v9.1
Supplementary_files_format_and_content: bigwigs and bed

organism: Xenopus tropicalis

source_name: early gastrula embryo (st 10.5)

extract_protocol:
Lysates were clarified from sonicated nuclei of 2000-3000 fixed embryos and protein-DNA complexes were isolated by antibody.
Libraries were prepared for the Illumina GAIIx according to the manufacturer's instructions.

value: Nigerian A

tag: chip antibody

value: Otx2 (Sudou et al., 2012)

value: early gastrula embryo

tag: Stage


title: E13-TD-30

city: 昆明市

tag: tissue


title: ChIP-seq for Lim1/Lhx1

value: Lim1-Lhx1 (Sudou et al., 2012)


title: E13-TD-33

tag: development stage


title: 33IFAT

value: male


title: ChIP-seq for p300

value: p300 (Santa Cruz sc-585)


title: E13-TD-32

tag: lineage


title: E11-C-28A


title: 32pit

value: 21 weeks


title: Cerebral Cortex Sevo1 rep1

value: Cerebral Cortex

value: embryonic day 14.5

value: treated with 2.5% sevoflurane and 97.5% Oxygen for 6 hours


title: ChIP-seq for TLE

value: TLE (Santa Cruz sc-13373)


title: E13-TD-5

value: PSCs


title: 34pit

value: wt

value: chow


title: E11-C-27A

value: embryo

value: EPI


title: E11-C-25

value: TE


title: Input control of ChIP-seq for Otx2 and Lim1/Lhx1

value: Nigerian A


title: E11-C-26


title: E13-TD-2


title: Input control of ChIP-seq for Gsc


title: whole lung - Ctrl

city: Los Angeles

first: Fremont

last: Gao

state: California

address: 2011 Zonal Ave, HMR 903

institute: USC

description: scRNA

data_processing:
The 10x Genomics’ Cell Ranger pipeline was used to demultiplex raw base call (BCL) files into FASTQ files, perform alignment, filtering, barcode counting, and UMI counting, combine and normalize counts from multiple samples, generate feature-barcode matrices, run the dimensionality reduction, clustering, and gene expression analysis.
Quality control was done additionally in Partek Flow to filter out cells with excess mitochondrial reads and possible doublets and remove batch effects.
Loupe Browser was used for data visualization and analysis including identification of differentially expressed genes and marker genes, cell type classification, cell reclustering, cell counting, gene expression comparative analysis between different cell clusters at both cell and population levels.
To construct single cell pseudotime trajectory and to identify genes that change as the cells undergo transition, Monocle 3 algorithm was applied to the cells from clusters 4 to 11.
Genome_build: mm10
Supplementary_files_format_and_content: Feature -barcode-matrix files (H5) were generated using 10x genomics cell ranger.

growth_protocol: Control (Gli1-cre) and mutant (Gli1-cre;Alk5-f/f;Tgfbr2-f/f) mouse were bred and maintained as regulated by IACUC.

extract_protocol:
Neonatal lungs at PN14 were dissected and dissociated into single cell suspension by cold active protease (CAP).
The single cell suspension prepared above was loaded onto a Chromium Single-Cell instrument (10x Genomics) to generate single-cell barcoded droplets (GEMs) as detailed in manufacture’s protocol. The resulting libraries were pooled and sequenced across two lanes on an Illumina HiSeq2500 instrument in High-output mode by Novogene. Reads were aligned and subsequent analyses performed using the Cell Ranger (Pipeline).

treatment_protocol: Tamoxifen (8mg/mL in peanut oil) was administered by oral gavage to neonates at postnatal day 2 (P2, 400 μg each pup) with a plastic feeding needle.

value: control


title: E13-TD-26


title: Input control of ChIP-seq for TLE and p300

value: early gastrula embryo


title: whole lung - Mut

description: scRNA


title: E11-C-26A


title: E13-TD-27


title: Input control of ChIP-seq for H3K4me1 and H3K27ac


title: 31pit

value: KLF14 KO

value: pituitary


title: E13-TD-28


title: E11-C-25A


title: 31IFAT

value: male

value: inguinal white adipose tissue


title: E11-C-24A


title: E11-C-23


title: Nfia_rep2_RNA-seq

city: Fukuoka

first: Jun

last: Takouda

address: 3-1-1, Maidashi

country: Japan

institute: Kyushu University

data_processing:
ChIP and RNA sequencing were performed with 50-bp single-end sequencing by an Illumina Hiseq 2500.
Obtained reads were processed with the FASTX tool kit to remove short (<30 bp) and low-quality (quality score < 20) reads, followed by trimming of the adaptor sequence.
For further processing of RNA-seq data, the sequence reads were aligned to mm10 using TopHat. Cuffdiff, a program in Cufflinks, was used for differential gene expression analysis.
For further processing of ChIP-seq data,the sequence reads were aligned to the mouse genome  mm10 using Bowtie (v1), by which all redundant reads were removed from further analysis. SAM files were converted to the BAM format using SAMtools. Peak calling was performed using MACS (v1.4) with default parameters and the IgG library as control.
Genome_build: mm10
Supplementary_files_format_and_content:
BigWig files representing alignment of each samples
TXT files representing FPKM values of each samples

source_name: Neural stem/precursor cells

growth_protocol: Telencephalons of E11.5 fetal mice were tritutated in Hank's balanced salt solution by mild pippetting. After centifugation, the cell pellet was resuspended in N2-supplemented Dulbecco's Modified Eagle Medium /F-12, containing 10 ng/mL basic fibroblast growth factor and plated on dishes precoated with poly-L-ornithine/fiblonectin.

extract_protocol:
For ChIP-seq, cells were fixed with 1% formaldehyde-containing medium and suspended in lysis buffer. The lysates were sonicated with a sonicator. After centrifugation, the supernatant was collected. Dynabeads M-280 sheep anti-mouse IgG (Thermo Fisher, Cat# DB11202), with magnetic property, were pre-incubated with 5 μg of anti-Flag antibody (Sigma-Aldrich, Cat# F3165) and then incubated with sonicated chromatin with rotation at 4℃ overnight. The immunoprecipitated samples were washed and then eluted in elution buffer at 65℃ overnight. Samples were treated with RNase A at 37℃ for 1 h, followed by proteinase K at 55℃ 2 h. DNA was purified according to conventional PCI method. For RNA-seq, total RNA was extracted using Sepasol®-RNA I Super G (nacalai tesque, Cat# 09379-55), and then mRNA was further isolataed with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Cat#E7490) according to their standard procedure.
For ChIP-seq, libraries were made according to instructions in the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Cat# E7645S). For RNA-seq, purified mRNAs were supplied for library construction using the NEBNext Ultra Directional RNA library Prep Kit for illumine (New England and Biolabs, Cat# E7420) according to manufacturer’s protocols.

tag: cell type

value: NS/PCs

tag: developmental stage

value: E11 NS/PCs primary culture

value: ICR

value: Nfia-transduced


title: ChIP-seq for H3K27ac

value: H3K27ac (Abcam ab4729)


title: E13-TD-25

value: PSCs


title: Nfia_rep3_RNA-seq


title: ChIP-seq for H3K4me1

value: H3K4me1 (Abcam ab8895)


title: E13-TD-23


title: control_rep3_ RNA-seq


title: Nfia_rep1_RNA-seq


title: ChIP-seq for Gsc

value: Gsc (Yasuoka et al., 2014)


title: control_rep2_ RNA-seq


title: E11-C-24

value: embryo


title: E13-TD-22

value: EPI


title: E11-C-23A

value: TE


title: E11-C-22


title: Np95fl/fl:Stra8-Cre rep2

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

institute: Yokohama City University

data_processing:
Illumina sequencing reads of WGBS samples were mapped onto the mouse mm10 genome using BMap.
Quantification of DNA methylation levels of individual CpG sites was performed using MPTC and MethExport.
Methylation levels of each genomic feature were quantified using SeqMonk version 44.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix for methylation levels (%) of all CpG sites having at least 10x coverages.

source_name: Male germ cells

growth_protocol: Male germ cells were isolated from 21-day-old Np95fl/fl and Np95fl/fl:Stra8-Cre mouse testes.

extract_protocol:
Genomic DNA was isolated from testicular germ cells of Np95fl/fl and Np95fl/fl:Stra8-Cre mice by using the QIAGEN Allprep DNA/RNA Mini Kit according to the supplier’s protocol.
Two ug of genomic DNA was utilized for bisulfite conversion using the EpiTect Bisulfite Kit (QIAGEN).
Bisulfite-seq (PBAT)

treatment_protocol: Materials dissected out were immersed in phosphate-buffered saline (PBS), and repeatedly passed through a 1ml syringe without a needle, to dissociate seminiferous tubules. Dissociated tubules were manually picked by tweezers, immersed in accutase solution (Innovative Cell Technologies), and sheared by scissors, to dissociate germ cells. Cell suspension was filtrated with a 95 um mesh to remove interstitial cells including Leydig cells, blood vessels, and lymphatic vessels.

value: Male germ cells


title: E13-TD-21


title: E13-TD-24


title: E11-C-22A

value: PE


title: IgG_ChIP

value: IgG


title: control_rep1_ RNA-seq

value: control


title: E13-TD-20


title: Np95fl/fl:Stra8-Cre rep1


title: Np95fl/fl rep2


title: E13-TD-1


title: Nfia_ChIP

value: Flag


title: E11-C-21


title: E13-TD-19

value: EXMC


title: Np95fl/fl rep1


title: E11-C-20


title: E11-C-21A


title: E13-TD-18


title: E11-C-20A


title: E13-TD-17


title: nup54MB_9B4_rnaseq

city: Cambridge

first: Marzia

last: Munafo

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: RNA-seq library (rRNA depletion)

data_processing:
RNAseq, PRO-seq  and CLIPseq analysis
For RNA-seq, PRO-seq and CLIP-seq raw fastq files generated by Illumina sequencing were analysed by a pipeline developed in-house. In short, the first 5 bases of each 50 bp read were removed using fastx trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). After removal of reads mapping to Drosophila rRNA using STAR, high-quality reads were aligned to the Drosophila melanogaster genome release 6 (dm6; downloaded from Flybase) (Hoskins et al., 2015) using STAR (Dobin et al., 2013). For transposon-wide analysis, genome multi-mapping reads were randomly assigned to one location using option '--outFilterMultimapNmax 1000 --outSAMmultNmax 1 --outMultimapperOrder Random' and non-mapping reads were removed. For genome-wide analyses, multi-mapping reads were removed to ensure unique locations of reads. Normalization was achieved by calculating rpm (reads per million) using the deepTools2 bamCoverage. Differential expression analysis was performed using DESeq2 (Love et al., 2014) and plotting was done in R using ggplot2. For genes carrying “nearby transposon insertions”, we considered only gene promoters within -10 kb to +15 kb of a TE insertion on the same genomic strand. Coordinates used for the piRNA clusters are chrX:21631891-22282863 (flam) and chrX:21520428-21556793 (20A).
Genome_build: dm6

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: flies and cells were grown at 25°C

extract_protocol:
ovaries or cells were homogenized in Trizol and RNA extracted using Rneasy mini kit (qiagen); rRNA was depleted using ribopools
NEBNext Ultra Directional RNAseq

treatment_protocol: OSCs were treated with indicated siRNA

value: Ovary

tag: genotype/variation


title: nup54MB_w1118_het_rnaseq

description: RNA-seq library (rRNA depletion)

value: nup54MB/w1118 heterozygotes


title: E13-TD-16


title: halo-nxf1_clip

description: CLIP-seq library

data_processing:
Library strategy: CLIP-seq
RNAseq, PRO-seq  and CLIPseq analysis
For RNA-seq, PRO-seq and CLIP-seq raw fastq files generated by Illumina sequencing were analysed by a pipeline developed in-house. In short, the first 5 bases of each 50 bp read were removed using fastx trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). After removal of reads mapping to Drosophila rRNA using STAR, high-quality reads were aligned to the Drosophila melanogaster genome release 6 (dm6; downloaded from Flybase) (Hoskins et al., 2015) using STAR (Dobin et al., 2013). For transposon-wide analysis, genome multi-mapping reads were randomly assigned to one location using option '--outFilterMultimapNmax 1000 --outSAMmultNmax 1 --outMultimapperOrder Random' and non-mapping reads were removed. For genome-wide analyses, multi-mapping reads were removed to ensure unique locations of reads. Normalization was achieved by calculating rpm (reads per million) using the deepTools2 bamCoverage. Differential expression analysis was performed using DESeq2 (Love et al., 2014) and plotting was done in R using ggplot2. For genes carrying “nearby transposon insertions”, we considered only gene promoters within -10 kb to +15 kb of a TE insertion on the same genomic strand. Coordinates used for the piRNA clusters are chrX:21631891-22282863 (flam) and chrX:21520428-21556793 (20A).
Genome_build: dm6

source_name: ovarian somatic cells (OSC)

growth_protocol: cells were grown at 25°C

extract_protocol:
SMARTER Stranded RNAseq
SMARTER Stranded RNAseq

treatment_protocol: OSCs weretransfected with indicated plasmids

tag: cell line

value: OSC

value: Ovarian somatic cells


title: w1118_rnaseq

description: RNA-seq library (rRNA depletion)


title: E13-TD-15


title: RNAseq_HEK293-GR_siNON_dex_rep4

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

country: Finland

institute: University of Eastern Finland

description:
RNA-seq from siNON and dexamethasone-treated cells.
RNAseq-DEseq2_HEK293-GR_siNON-vs-siBCOR_EtOH-vs-dex.txt

data_processing:
For ChIP-seq, The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artefacts, trimming reads, quality filtering and collapsing identical reads). Preprocessed reads were aligned against human genome hg19 with Bowtie software (version 0.12.9) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19. Peak calling was done in HOMER (version 4.10.3) using findPeaks command (with parameters: -F 3, -tagTreshold 20, -minDist 350) and appropriate input as a control. Two replicates were compared with each other using bedTools (intersectBed) and only those binding sites found in both replicates were considered representative and used for further analysis. Representative BCOR binding sites from vehicle and dexamethasone samples were merged and sites with two-fold difference in RPKM-normalized ChIP-seq signal between vehicle- or dexamethasone-treatments were defined vehicle-enriched (V-enriched), dexamethasone-enriched (D-enriched), and shared (difference less than two-fold between vehicle and dexamethasone samples).
For RNA-seq, the quality of raw reads was analyzed by FastQC and trimmomatic (LEADING:5, TRAILING:5, MINLEN:36) and HOMER (homerTools trim -3 AAAAAAAA -mis 1 -min 36) were used for preprocessing raw reads (removal of artefacts, trimming reads, removing poly-A). Remaining reads were mapped to reference human transcriptome and genome (hg19) using tophat2. Table of transcript-level counts from exon regions was generated using HOMER (analyzeRepeats.pl rna hg19 -noadj -count exons).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq files of V-enriched, D-enriched and shared BCOR chromatin binding sites are in bed format. A text file with table of transcript-level counts is provided for RNA-seq data.

growth_protocol:
ChIP-seq: HEK293-GR cells were grown in steroid-depleted medium (DMEM supplemented with 2.5% (v/v) charcoal-treated FBS) for 2 days.
RNA-seq: HEK293-GR cells were grown on 6-well plates (300 000 cells/well) in regular growth medium for 24h after which the medium was replaced with steroid-depleted medium (DMEM supplemented with 2.5% (v/v) charcoal-treated FBS).

extract_protocol:
ChIP-seq: Chromatin fragments were purified using MiniElute columns (Qiagen), ChIP-seq libraries were prepared using NEBNext kit (New England Biolabs) and sequenced with HiSeq2000 at EMBL GeneCore (Heidelberg, Germany).
RNA-seq: Total RNA was extracted from four biological replicates using TriPure isolation reagent (Roche) and treated with DNAse. RNA-seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic isolation module (New England Biolabs) and sequenced with Illumina HiSeq2000 at EMBL GeneCore (Heidelberg, Germany).

treatment_protocol:
ChIP-seq: Cells were treated with vehicle (ethanol, EtOH) or dex (100 nM) for 1 h before harvesting. Then cells were fixed with 1% (v/v) formaldehyde for 10 min at room temperature. Chromatin was fragmented to ∼200–400 bp using sonication (Bioruptor UCD-300, Diagenode). Anti-BCOR antibodies (Bethyl Laboratories, A301-673A) were coupled to protein-A- beads (Millipore), fragmented chromatin was incubated with antibody-coupled beads overnight, washed, eluted and de-crosslinked in the presence of proteinase K (Fermentas).
RNA-seq: Cells were transfected with 20 nM ON-TARGETplus SMARTpool siRNAs (Dharmacon) against BCOR (siBCOR; L-004584–01-0005) for 72 h using Lipofectamine RNAiMAX (Invitrogen) reagent and exposed to 100 nM dex or equal volume of vehicle (ethanol, EtOH) for 6 h before collecting. ON-TARGETplus Non-Targeting Pool (GE Dharmacon, Lafayette, LA) was used as the control siRNA (siNON).

tag: medium

value: steroid-depleted medium, 48h

value: dexamethasone, 100nM, 6h

tag: transfection

value: siNON, 20nM, 72h


title: nxf1-halo_clip

description: CLIP-seq library


title: E11-C-1A

source_name: embryo cell


title: E13-TD-14

value: PSCs


title: MUT DMSO2

city: Pittsburgh

first: Xiaoran

last: Zhang

state: PA

address: 16 Sheridan Court

institute: upmc

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: normalized counts

source_name: Astrocytes

growth_protocol: Immortalized Astrocytes expressing IDH1 R132H was grown in DMEM with 10% FBS with 1% Pen-Strep at 37C with 5% CO2.

extract_protocol: none provided by the submitter

treatment_protocol: Cells are treated with 1uM ATRA or equivalent volume of DMSO for 48 hrs.


title: MUT RA 1

value: Immortalized Astrocytes expressing IDH1 R132H


title: osc_proseq_siyb

description: PRO-seq library

data_processing:
Library strategy: PRO-seq
RNAseq, PRO-seq  and CLIPseq analysis
For RNA-seq, PRO-seq and CLIP-seq raw fastq files generated by Illumina sequencing were analysed by a pipeline developed in-house. In short, the first 5 bases of each 50 bp read were removed using fastx trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). After removal of reads mapping to Drosophila rRNA using STAR, high-quality reads were aligned to the Drosophila melanogaster genome release 6 (dm6; downloaded from Flybase) (Hoskins et al., 2015) using STAR (Dobin et al., 2013). For transposon-wide analysis, genome multi-mapping reads were randomly assigned to one location using option '--outFilterMultimapNmax 1000 --outSAMmultNmax 1 --outMultimapperOrder Random' and non-mapping reads were removed. For genome-wide analyses, multi-mapping reads were removed to ensure unique locations of reads. Normalization was achieved by calculating rpm (reads per million) using the deepTools2 bamCoverage. Differential expression analysis was performed using DESeq2 (Love et al., 2014) and plotting was done in R using ggplot2. For genes carrying “nearby transposon insertions”, we considered only gene promoters within -10 kb to +15 kb of a TE insertion on the same genomic strand. Coordinates used for the piRNA clusters are chrX:21631891-22282863 (flam) and chrX:21520428-21556793 (20A).
Genome_build: dm6

extract_protocol:
nucei were extracted according to Mahat et al. 2016
Mahat, D.B., et al. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols 11, 1455–1476.


title: E11-C-19A

value: embryo


title: E11-C-18

value: TE


title: E13-TD-12

value: EPI


title: E11-C-19


title: MUT RA 2


title: osc_proseq_sinup58

description: PRO-seq library


title: RNAseq_HEK293-GR_siNON_dex_rep3


title: RNAseq_HEK293-GR_siNON_dex_rep2


title: E13-TD-11


title: E11-C-18A


title: osc_proseq_sinup54

description: PRO-seq library


title: RNAseq_HEK293-GR_siNON_EtOH_rep4

description:
RNA-seq from siNON and vehicle-treated cells.
RNAseq-DEseq2_HEK293-GR_siNON-vs-siBCOR_EtOH-vs-dex.txt

value: ethanol 6h


title: osc_proseq_sigfp

description: PRO-seq library


title: E11-C-1

description: Chimera embryo cell of Macaca fascicularis


title: E11-C-17


title: E13-TD-10


title: osc_rnaseq_02_sizuc

description: RNA-seq library (rRNA depletion)


title: E13-TD-13


title: E11-C-17A


title: RNAseq_HEK293-GR_siNON_EtOH_rep3


title: E11-TD-9B


title: E11-TD-8B


title: osc_rnaseq_02_sinup93

description: RNA-seq library (rRNA depletion)


title: RNAseq_HEK293-GR_siNON_EtOH_rep2


title: E11-C-16


title: osc_rnaseq_02_sinup62

description: RNA-seq library (rRNA depletion)


title: RNAseq_HEK293-GR_siNON_dex_rep1


title: E11-TD-7B


title: RNAseq_HEK293-GR_siNON_EtOH_rep1


title: osc_rnaseq_02_sigfp

description: RNA-seq library (rRNA depletion)


title: E11-C-16A


title: E11-C-15A


title: E11-TD-6B


title: RNAseq_HEK293-GR_siBCOR_dex_rep2

description:
RNA-seq from siBCOR and dexamethasone-treated cells.
RNAseq-DEseq2_HEK293-GR_siNON-vs-siBCOR_EtOH-vs-dex.txt

value: siBCOR, 20nM, 72h


title: RNAseq_HEK293-GR_siBCOR_dex_rep3


title: E11-C-14


title: nup58-clip-comb

description:
Sample 15
CLIP-seq library

data_processing:
Library strategy: CLIP-seq
Small RNA-seq, RNAseq  and CLIPseq analyses.
Raw fastq files generated by Illumina sequencing were analysed by a pipeline developed in-house. In short, for RNA-seq and CLIP-seq the first 5 bases of each 50 bp read were removed using fastx trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). After removal of rRNA mapped reads, high-quality reads were aligned to the Drosophila melanogaster genome release 6 (dm6; downloaded from Flybase) using STAR (Dobin et al. 2013). For transposon-wide analysis, genome multi-mapping reads were randomly assigned to one location using option '--outFilterMultimapNmax 1000 --outMultimapperOrder Random' and non-mapping reads were removed. Alignment files were then converted back to fastq format with samtools (Li et al. 2009) and re-aligned to the transposon consensus sequences allowing multi-mappers that were assigned to a random position. Generated bam alignment files were indexed using samtools index. For genome-wide analyses, multi-mapping reads were removed to ensure unique locations of reads. Normalization was achieved by calculating rpm (reads per million) using the deepTools2 bamCoverage function with 10 bp bin sizes (Ramirez et al. 2016). Reads mapping to genes were counted with htseq (Anders et al. 2015) and transposon derived reads were calculated using a custom script. Differential expression analysis was performed using custom built R scripts. Coordinates used for the piRNA clusters are chrX:21631891-22282863 (flam) and chrX:21520428-21556793 (20A).
For small RNA-seq, adapters were clipped from raw fastq files with fastx_clipper (adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) keeping only reads with at least 23 bp length. Then the first and last 4 bases were trimmed using seqtk (https://github.com/lh3/seqtk). After removal of cloning markers and 2S rRNA mapped reads, alignment was performed as described above and normalised to miRNA reads in the control library (set to rpm). Only high-quality small RNA reads with a length between 23 and 29 bp were used for further analysis of piRNA profiles.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: strand-specific bigWig files

growth_protocol: Cells were grown at 25°C.

extract_protocol: SMARTER Stranded RNAseq.

treatment_protocol: OSCs were transfected with indicated plasmids.


title: E11-C-15


title: E11-TD-3B


title: RNAseq_HEK293-GR_siBCOR_dex_rep1


title: E11-TD-2


title: mock-clip-comb

description:
Sample 13
CLIP-seq library


title: E11-C-14A


title: RNAseq_HEK293-GR_siBCOR_EtOH_rep4

description:
RNA-seq from siBCOR and vehicle-treated cells.
RNAseq-DEseq2_HEK293-GR_siNON-vs-siBCOR_EtOH-vs-dex.txt


title: E11-C-12


title: E11-TD-1


title: E11-C-12A


title: flamBG-homo-rnaseq

description:
Sample 10
RNA-seq library (rRNA depletion)

data_processing:
Small RNA-seq, RNAseq  and CLIPseq analyses.
Raw fastq files generated by Illumina sequencing were analysed by a pipeline developed in-house. In short, for RNA-seq and CLIP-seq the first 5 bases of each 50 bp read were removed using fastx trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). After removal of rRNA mapped reads, high-quality reads were aligned to the Drosophila melanogaster genome release 6 (dm6; downloaded from Flybase) using STAR (Dobin et al. 2013). For transposon-wide analysis, genome multi-mapping reads were randomly assigned to one location using option '--outFilterMultimapNmax 1000 --outMultimapperOrder Random' and non-mapping reads were removed. Alignment files were then converted back to fastq format with samtools (Li et al. 2009) and re-aligned to the transposon consensus sequences allowing multi-mappers that were assigned to a random position. Generated bam alignment files were indexed using samtools index. For genome-wide analyses, multi-mapping reads were removed to ensure unique locations of reads. Normalization was achieved by calculating rpm (reads per million) using the deepTools2 bamCoverage function with 10 bp bin sizes (Ramirez et al. 2016). Reads mapping to genes were counted with htseq (Anders et al. 2015) and transposon derived reads were calculated using a custom script. Differential expression analysis was performed using custom built R scripts. Coordinates used for the piRNA clusters are chrX:21631891-22282863 (flam) and chrX:21520428-21556793 (20A).
For small RNA-seq, adapters were clipped from raw fastq files with fastx_clipper (adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) keeping only reads with at least 23 bp length. Then the first and last 4 bases were trimmed using seqtk (https://github.com/lh3/seqtk). After removal of cloning markers and 2S rRNA mapped reads, alignment was performed as described above and normalised to miRNA reads in the control library (set to rpm). Only high-quality small RNA reads with a length between 23 and 29 bp were used for further analysis of piRNA profiles.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: strand-specific bigWig files

growth_protocol: Flies and cells were grown at 25°C.

extract_protocol:
Ovaries or cells were homogenized in Trizol and RNA extracted using RNeasy mini kit (Qiagen); rRNA was depleted using ribopools.
NEBNext Ultra Directional RNAseq.

treatment_protocol: OSCs were treated with indicated siRNA.

value: flamBG02658 homozygotes


title: RNAseq_HEK293-GR_siBCOR_dex_rep4


title: RNAseq_HEK293-GR_siBCOR_EtOH_rep3


title: flam-transhet-rnaseq

description:
Sample 12
RNA-seq library (rRNA depletion)


title: flamBG-het-rnaseq

description:
Sample 9
RNA-seq library (rRNA depletion)

value: flamBG02658 heterozygotes


title: E11-TD-2B


title: flamKG-het-rnaseq

description:
Sample 11
RNA-seq library (rRNA depletion)

value: flamKG00476 heterozygotes


title: E11-C-11


title: E11-TD-14B


title: RNAseq_HEK293-GR_siBCOR_EtOH_rep2


title: E11-C-11A


title: nup54-clip-comb

description:
Sample 14
CLIP-seq library


title: RNAseq_HEK293-GR_siBCOR_EtOH_rep1


title: ChIPseq_HEK293-GR_BCOR_dex_rep2

description:
ChIP-seq of BCOR in dexamethasone-treated cells.
ChIPseq_HEK293-GR_BCOR_D-enriched.bed
ChIPseq_HEK293-GR_BCOR_shared.bed

value: dexamethasone, 100nM, 1h

tag: antibody

value: anti-BCOR (Bethyl Laboratories, A301-673A)


title: E11-C-10A


title: E11-TD-1B


title: osc-rnaseq-sinup54

description:
Sample 6
RNA-seq library (rRNA depletion)

value: OSC


title: osc-rnaseq-siyb

description:
Sample 8
RNA-seq library (rRNA depletion)

value: Ovarian somatic cells


title: E11-C-10


title: E11-TD-10B


title: E11-TD-12B


title: E11-MH-TD-18


title: N3

city: Beijing

first: Li

last: Liu

state: State...

address: #5 Dong Dan San Tiao

institute: Peking Union Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mesocricetus auratus

source_name: kidney

extract_protocol:
After 48 transfection, total RNAs from transfected BHK21 cells were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: age

value: one day

value: transfected with STYK1/NOK


title: ChIPseq_HEK293-GR_BCOR_dex_rep1

value: steroid-depleted medium, 48h


title: ChIPseq_HEK293-GR_BCOR_EtOH_rep2

description:
ChIP-seq of BCOR in vehicle-treated cells.
ChIPseq_HEK293-GR_BCOR_V-enriched.bed
ChIPseq_HEK293-GR_BCOR_shared.bed

value: ethanol 1h


title: E11-TD-11B

value: PSCs

value: EXMC


title: ChIPseq_HEK293-GR_BCOR_EtOH_rep1


title: osc-rnaseq-sigfp

description:
Sample 5
RNA-seq library (rRNA depletion)


title: E11-MH-TD-17

value: TE


title: S3

city: Davis

first: Alexander

middle: Star

last: Nord

state: CA

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

data_processing:
Library strategy: MPRA
PE reads were trimmed using Ngmerge (v0.2_dev) in adaptor removal mode.
Reads from were aligned to the human and mouse genomes (GRCh38, GRCm38) using bwa mem v0.7.17.
Aligned reads in SAM format were converted to BAM format, and duplicates were removed using Picard Tools MarkDuplicates, v2.23.3.
Reads per amplicon were counted using samtools view -F 0x0400 v1.10
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: CSV, read counts per MPRA amplicon

source_name: Mouse cortex

extract_protocol:
Bulk forebrains were dissected from postnatal day (P)7 mice injected with the viral library at P0. Dissection included whole forebrain, separated into left and right hemispheres, after removing surface tissue and skull. Hemispheres were stored in RNAlater Stabilization Solution (Thermo Fisher #AM7020) for downstream dual DNA and RNA collection. Hemispheres were then physically homogenized and processed using the AllPrep DNA/RNA Mini Kit (Qiagen #80204) to collect total RNA and genomic DNA from the same tissue. RNA was treated on-column with 1 µL RNase-Free DNase (Qiagen #79254). First strand cDNA was synthesized from purified total RNA using the SuperScript VILO cDNA Synthesis Kit (Invitrogen #11755050) with random primers.
We amplified the variable regions of the reporter library from cDNA and genomic (g)DNA using PCR with Phusion Hot Start II High Fidelity DNA polymerase (Invitrogen #F549S) using primers flanking the variable region within pscAAV-Hsp68-EGFP (forward primer, Amplicon PCR Primer F: GATCACTCTCGGCATGGAC; reverse primer, Amplicon PCR Primer R: GATGGCTGGCAACTAGAAGG). PCR consisted of 30 cycles (or 35, for technical replicate Sample 4-35) at 60 °C for annealing and 1 min for extension. PCRs were then loaded onto a 1.0% agarose gel, the ~1-1.1 kb fragment excised, and gel fragment purified using the Promega Gel & PCR Cleanup system (#A9282). Purified gel fragments were then re-purified using the Qiagen MinElute PCR Purification Kit (#28004) to remove residual chemical contamination, and concentration and quality assessed with Nanodrop and the Qubit dsDNA High Sensitivity assay kit (Thermo Fisher #Q33230). Purified amplicons were prepared for sequencing using the Nextera XT DNA Library Preparation Kit (Illumina #FC-131-1001) using 1 ng of purified amplicon library per sample. Quality and concentration of sequencing libraries was assessed using an Agilent BioAnalyzer instrument. Each library was quantified and pooled for sequencing on the Illumina HiSeq 4000 using a paired end 150-bp sequencing strategy. The miniMPRA was sequenced on a MiSeq instrument since lower coverage was required due to lower library complexity.

treatment_protocol: C57BL/6 mice from Jackson Laboratories were used for mouse experiments. All procedures were performed in accordance with the ARVO statement for the Use of Animals in Ophthalmic and Vision Research and were approved by the University of California Animal Care and Use Committee (AUP #R200-0913BC). Surgery was performed under anesthesia, and all efforts were made to minimize suffering. Neonatal mice (on a C57BL6/J background) were injected in the prefrontal cortex in 2 separate locations with 0.5 µL of virus. Only the left side of brain was injected. A beveled 34-gauge needle (Hamilton syringes) was used to push through the skull and to inject virus into the brain. Virus was delivered slowly by hand over the course of 1 min. Mice were anesthetized on ice for 3-4 min prior to injection, and after injection mice were heated on a warm pad before being returned to the cage.

tag: genetic material

value: Mouse cortex RNA

tag: vehicle

value: AAV library


title: N2


title: E11-TD-13B

state: 云南


title: P3

value: transfected with pCMV-Myc


title: MUT DMSO1

value: Immortalized Astrocytes expressing IDH1 R132H


title: S4


title: P2


title: osc-rnaseq-sinup58

description:
Sample 7
RNA-seq library (rRNA depletion)


title: N1


title: osc-srna-siyb

description:
Sample 4
small RNA-seq library (19-28nt)

extract_protocol:
Cells were homogenized in Trizol and RNA extracted using Phenol/Chloroform.
Adapted from: Jayaprakash, Anitha D. et al. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39.21 (2011): e141. PMC. Web. 22 Oct. 2018.


title: osc-srna-sinup58

description:
Sample 3
small RNA-seq library (19-28nt)


title: E11-MH-TD-16

description: PSCs in the Chimera embryo of Macaca fascicularis

value: EPI


title: S2


title: osc-srna-sinup54

description:
Sample 2
small RNA-seq library (19-28nt)


title: E11-MH-TD-15


title: S1


title: osc-srna-sigfp

description:
Sample 1
small RNA-seq library (19-28nt)


title: P1


title: CAI-4 CO2 3

status: Public on Apr 14 2021

city: Canterbury

first: Campbell

last: Gourlay

state: Kent

address: School of Biosciences, University of Kent

department: School of Biosciences

institute: University of Kent

data_processing:
Illumina NextSeq 500 Real-Time Analysis software v2.4.11 used for basecalling.
Low quality ends (Phred score < 20) and any adaptor sequences were trimmed using TrimGalore! v0.4.3. Reads which became shorter than 40bp after trimming were removed from further analysis.
Processed reads were aligned with the reference C. albicans genome SC5314 version A21-s02-m09-r10 using HISAT2 v2.1.0 with single-end reads and reverse strand settings.
Number of mapped reads which overlapped CDS features in the genome (using the C. albicans_SC5314_version_A21-s02-m09-r10_features.gtf annotation file from Candida Genome Database) were determined using htseq-count v0.9.1 with default settings.
Differential gene expression analysis between conditions (0.03% and 5% CO2) was performed using DESeq2 v1.18.1 with default settings.
Genome_build: C. albicans genome SC5314 version A21-s02-m09-r10
Supplementary_files_format_and_content: tab-delimited text files include CDS feature counts for each sample.
Supplementary_files_format_and_content: xslx file with mean normalised counts and differentially expressed genes across all samples.

organism: Candida albicans

source_name: C. albicans biofilm_5% CO2

growth_protocol: CAI-4 cells were seeded onto a silicone surface and grown as a biofilm for 48hr in either 0.03% or 5% CO2 at 37oC in RPMI-1640 media.

extract_protocol:
Biofilms were washed twice with ice-cold PBS, RNA was extracted using the E.Z.N.A Yeast RNA Kit (Omega Bio-Tek, R6870-01).
mRNA-Seq libraries were prepared from 500ng total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina).

tag: strain

tag: environment

tag: mode of growth

value: Biofilm on silicone surface at 37oC

tag: biofilm stage

value: Mature (48hr growth)


title: LA-NPC_NR23

city: Guangzhou

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

description: Gene expression data from LA-NPC with no-response to induction chemotherapy

hyb_protocol: Total RNA was hybridized to Affymetrix Human Transcriptome Arrays 2.0 GeneChips (Affymetrix, Santa Clara, CA, USA) using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: All arrays were scanned with Affymetrix GeneChip® Scanner 3000 (Affymetrix). Raw data was obtained using Command Console Software 4.0 (Affymetrix) with default settings.

data_processing: Raw data were normalized using Transcriptome Analysis Console (version 4.0.1). We used empirical Bayes statistics implemented in eBayes in the 'limma package' to determine significant differentially expressed probes between response and no-response groups. Due to RNA from FFPE samples are highly and randomly fragmented, we used Fisher's exact test to confirm whether a transcript is indeed significant differentially expressed. Differential expressed transcripts were characterized according to the criterion of empirical Fold change ≥ 1.5, empirical Bayes test P-value <0.05, and Fisher p-value <0·05.

label: biotin

source_name: LA-NPC_94-Stable Disease

label_protocol: Total RNA was amplified, fragmentated, labeled with Ovation FFPE WTA System (NuGEN, San Carlos, CA, USA) and Encore Biotin Module (NuGEN) according to the manufacturer’s instructions.

growth_protocol: Nasopharyngeal carcinoma biopsy samples obtained through nasopharyngoscope before treatment.

extract_protocol: Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Germany).

tag: tissue

value: Nasopharyngeal carcinoma

tag: response

value: stable disease


title: LA-NPC_NR24

source_name: LA-NPC_95-Stable Disease


title: CAI-4 CO2 1


title: LA-NPC_NR19

source_name: LA-NPC_90-Stable Disease


title: LA-NPC_NR22

source_name: LA-NPC_93-Stable Disease