title: GBM8_batch_3223

data_processing:
Paired-end reads from mouse model were mapped to the UCSC mm10 mouse transcriptome using Bowtie. Expression values were calculated by RSEM in paired-end mode using parameters, from which TPM values for each gene were extracted. Reads from 10x were aligned using CellRanger
We examined as quality control the number of genes detected in each cell. We observed a bimodal distribution and conservatively excluded sequenced cells with fewer than 3,000 detected genes.
For the remaining cells, we calculated Eavg(i) = log2(mean(TPMi,1...n)+1) for each gene, and excluded genes with Eavg < 4
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Comma-separated value containing TPM values (transcript-per-million reads).


title: 000789FFD3_IL

status: Public on Apr 23 2021

type: SRA

city: La Jolla

first: Daniel

last: Munro

state: CA

address: 9500 Gilman Drive

department: Psychiatry

country: USA

institute: UC San Diego

library_source: transcriptomic

data_processing:
Reads were first trimmed for adapter and poor-quality base calls using cutadapt
Reads were then aligned to the Ensembl Rat Transcriptome using RSEM
Upper quantile adjusted was applied to estimated gene read counts using DESeq2
Samples were filtered based on low reads counts, mismatched genotypes, and expression PCA outliers
Genes were eliminated if less than 25% of libraries had more than one read or if the total number of reads among all libraries for the gene was less than 100
Read counts were log base 2 transformed after the addition of 1 to each read count (to avoid taking the log of zero)
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Tab-separated table with row names (Ensembl gene IDs) and column names (sample IDs) containing log2(read count + 1) values

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Brain region: Infralimbic cortex

growth_protocol: All rats were group housed under standard laboratory conditions.

extract_protocol:
1) Brain region dissection: Brains were taken out of a minus 80 degree freezer and cryosectioned into 60um sections, which were mounted onto RNase-free glass slides. Slides were stored in minus 80 degree until dissection. During dissection, slides were placed on a minus 20 degree cold plate. One drop (approximately 50 ul) of RNAlater was placed on the brain region of interest. Each brain region then was dissected out under a dissecting video camera by using a pair of fine tipped forceps with the assistance of an 18 gauge needle with a bent tip. Bilateral tissue of the same brain region from each rat was immediately transferred into 350 ul Buffer RLT (containing beta-mercaptoethanol) and placed on dry ice. Tissue was stored in minus 80 degree before RNA extraction. 2) RNA extraction: Tissue was thawed on ice and homogenized by using a clean stainless steel bead using Qiagen TissueLyser (40Hz, 3 min). AllPrep DNA/RNA mini kit (Qiagen) was used to extract RNA. Samples were processed by using the QIAcube robot following standard protocols. The optional DNase digestion step was included for RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: All rats were naïve to behavioral or pharmacology treatment.

tag: population

value: Heterogeneous Stock

tag: Sex

value: M

tag: rat batch

tag: brain region

value: Infralimbic cortex


title: 000789FFAC_IL


title: hiPSCs_D20X_HP_repB

city: Leuven

first: Marino

last: Caruso

address: Herestraat 49

department: Oncology

country: Belgium

institute: KULeuven

description: High-polysome (HP) RNA extract

data_processing:
Library strategy: polysome profiling
 Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument.
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
sequence read were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads will be mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts will be calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fall within exon regions will be counted.
Supplementary_files_format_and_content: Table of gene hit counts for each replicate

molecule: total RNA

organism: Homo sapiens

source_name: HC3X hiPSCs-derived Hepatocyte-like cells

growth_protocol: HC3X iPSCs were cultured on hESCs qualified-Matrigel coated vessels in mTESR PLUS medium supplemented with 1% penicillin-streptomycin. Cells were passaged every 5-6 days by accutase detachment and plated at a 1/10 dilution. Cells were replated in medium supplemented with 10uM ROCK inhibitor (Y27632) for the first 24h.

extract_protocol:
ReliaPrep RNA extraction (Promega Z6010)
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol:
STD and HC3X in vitro hepatogenic differentiation
TotRNA: Cell lysis
High-Polysome (HP) RNA: Cell lysis, sucrose density fractionation, selection of high-polysome containing fractions

tag: cell type

value: HC3X hiPSCs

tag: treatment

value: D20 HC3X hepatogenic differentiation

tag: replicate

value: B


title: GBM8_batch_3222

city: Rehovot

first: Rony

last: Chanoch

state: Israel

address: Weizmann Institute of Science, 234 Herzl Street

country: Israel

institute: Weizmann Instititue

organism: Mus musculus

source_name: Glioblastoma single cell

extract_protocol:
For mice samples, collected brains were mechanically and enzymatically dissociated using a papain-based brain tumor dissociation kit (Miltenyi Biotec) supplemented with 0.1% typeI collagenase (Thermo Fisher Scientific) / PBS. The dissociated cells were first stained with calcein Blue AM (Thermo Fisher Scientific) and Zombie NIR (BioLegend) for 25 min at 4 ℃, and with anti-mouse CD16/32 (BD Biosciences) for 5min. After washing cells with ice-cold 1% BSA / PBS, the cells were then stained with a combination of following antibodies; PerCP anti-mouse CD45 (clone 30-F11, BD Biosciences), phycoerythrin (PE) anti-mPdgfra (clone APA5, BioLegend), Allophycocyanin (APC) anti-mPodoplanin (clone 8.1.1, BioLegend), and APC anti-CD11b (clone M1/70, BioLegend), for 30 min at 4 ℃. Sorting was performed with Becton Dickinson Influx cytometer (Becton Dickinson). Side scatter (SSC) width versus forward scatter (FSC) area, and Trigger Pulse Width versus FSC criteria were used to discriminate doublets and gate only singleton cells. Viable single cells were identified as calcein blue AM positive and Zombine NIR negative. We sorted viable CD45 negative/ GFP positive or CD45 positive/ CD11b positive single-cells into 96-well plates containing 5uL of TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen immediately after sorting and stored at -80 ℃ prior to whole transcriptome amplification, library preparation and sequencing.
Libraries from isolated single cells from mouse model were generated based on the Smart-seq2 protocol (Picelli 2014) with the following modifications. RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter) before oligo-dT primed reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 768 cells with unique barcodes were combined and sequenced with paired-end, 38-base reads, using a NextSeq 500 sequencer (Illumina). Comma-seperated file containing TPM values (transcript-per-million reads) for 6608 genes across 679 cells. For the cell lines, scRNA-seq libraries were generated using the 10X Genomics Chromium Single Cell 3’ Kit v2 and the 10x Chromium Controller (10x Genomics) according to the 10X Single Cell 3’ v2 protocol. The cell lines were processed as a pool that consisted of 6 total cell lines, 4 of which were used in this study (MGG23, MGG75, MGH143, MGG18). Two of the used cell lines, MGG23 and MGH143 were profiled again in a different pool. Briefly, we generated a single cell suspension of the pool in 0.04% PBS-BSA (95% viability) and loaded approximately 10,500 single cells to the Chromium Controller with a targeted recovery of 6,000 cells. Single cells, reagents and single gel beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized droplets and subjected to reverse transcription. Droplets were broken and the barcoded cDNAs were purified with DynaBeads and amplified by 12 cycles of PCR (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, 72°C for 1 min] x 12; 72°C for 1 min). The amplified cDNA was fragmented, end-repaired, ligated with index adaptors, and size-selected with clean-ups between each step using the SPRIselect Reagent Kit (Beckman Coulter). Quality control of the resulting barcoded libraries was performed with the Agilent TapeStation and by PCR with primers specific to the P5 and P7 sequence (NEBNext Library Quant Kit for Illumina, New England Biolabs).
single cell RNA-seq

tag: strain


title: THP-1-veh-5

city: Cambridge

first: Eric

middle: Scott

last: Lightcap

state: MA

address: 40 Landsdowne Street

institute: Takeda Pharmaceuticals

data_processing:
Raw fastq files were processed using the RNA-seq pipeline within Array Studio. Briefly, reads with bad qualities, or from IlluminaAdapters, Ercc, rRNA and tRNA were first filtered from raw data, the cleaned reads were then aligned to the genome through OmicSoft Aligner (OSA). The reads mapped to the exonic region were counted for each gene and then normalized into FPKM for the downstream analysis.
Genome_build: mouse NCBI genome build 38 and human NCBI genome build 37
Supplementary_files_format_and_content: The reads count and FPKM value of each gene in each sample are uploaded as the processed data files

source_name: cell line

growth_protocol: Cell lines THP-1, CT26, MC-38, B16F10, A20 were generated by re-plating at various densities from 80,000 to 200,000 cells per well in 12-well plates, in matched media supplemented with 10%FBS and/or 0.05mM β-Mercaptoethanol for 24 hour before treated with compounds. Cell lines HCT116, Colo205, MDA-MB-231 were generated by re-plating at 200,000 cells per well in 24-well plates, in matched media supplemented with 10%FBS for 24 hour before treated with compounds.

extract_protocol:
Cell pellets were collected after centrifuge, flash frozen on dry ice, and total RNA was extracted using RNeasy Mini Kit (Qiagen, 74104). Illumina TruSeq RNA Library Prep Kit (Cat#RS-122-2001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNAseq libraries were prepared for sequencing using standard Illumina protocols. Briefly, first polyA containing mRNA molecules were purified using oligo-dT attached magnetic beads from total RNA and then fragmented. The fragmented mRNA were reverse transcribed into first strand cDNA with reverse transcriptase and random primers. Then the RNA template were removed and replaced by synthesis of the second strand cDNA. Then the end of the cDNA fragments were repaired into blunt ends and adenylated at 3’ ends. Then the indexing adapters were ligated to the ends of cDNA fragments, and the DNA fragments with adapters on both ends were enriched and amplified by PCR. After clean-up, the PCR products go through quality control and quantitation to get the final library. Sequencing were run on Novaseq S4 platform: PE150.

treatment_protocol: THP-1, CT26, MC-38, B16F10, and A20 were seeded as triplets and treated with 1uM TAK-981 for 16 hours. HCT116, Colo205, and MDA-MB-231 were seeded as triplets and treated with 1uM TAK-981 or 1 uM ML-792 for 16 hours.

tag: cell line

value: DMSO

tag: dosage

tag: timepoint


title: hiPSCs_D20X_TotRNA_repB

description: Total cytoplasmic RNA extract

data_processing:
 Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument.
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
sequence read were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads will be mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts will be calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fall within exon regions will be counted.
Supplementary_files_format_and_content: Table of gene hit counts for each replicate


title: GBM8_batch_3221


title: GBM8_batch_3226


title: hiPSCs_D20X_HP_repA

description: High-polysome (HP) RNA extract

value: A


title: 000789FF94_IL


title: 000789FF7D_IL


title: THP-1-veh-4


title: HCT116-veh-2


title: 00078A2667_Acbc

description: Removed: genotype mismatch

source_name: Brain region: Nucleus accumbens core

value: Nucleus accumbens core


title: 00077EA7E6_IL


title: hiPSCs_D20X_TotRNA_repC

description: Total cytoplasmic RNA extract

value: C


title: hiPSCs_D20_TotRNA_repC

description: Total cytoplasmic RNA extract

value: D20 STD hepatogenic differentiation


title: GBM8_batch_3217


title: 00077E8336_IL


title: 000789FFF0_IL


title: GBM8_batch_3215


title: 00078A2496_Acbc

value: F


title: GBM8_batch_3219


title: hiPSCs_D20_HP_repA

description: High-polysome (HP) RNA extract


title: 00077E76C6_IL

description: Removed: expression outlier


title: 00078A2463_Acbc


title: 00077E76FE_IL


title: GBM8_batch_3220


title: hiPSCs_D20_TotRNA_repA

description: Total cytoplasmic RNA extract


title: 00078A2315_Acbc


title: 00077E67B5_IL


title: GBM8_batch_3213


title: GBM8_batch_3212


title: hiPSCs_D20_HP_repC

description: High-polysome (HP) RNA extract


title: hiPSCs_D12X_TotRNA_repC

description: Total cytoplasmic RNA extract

value: D12 HC3X hepatogenic differentiation


title: GBM8_batch_3218


title: 00078A2595_Acbc


title: 00078A261F_Acbc


title: GBM8_batch_3216


title: 00078A1F34_Acbc


title: GBM8_batch_3210


title: GBM8_batch_3214


title: 00078A1A2B_Acbc


title: hiPSCs_D20X_TotRNA_repA

description: Total cytoplasmic RNA extract


title: 00078A1A16_Acbc


title: hiPSCs_D12X_HP_repC

description: High-polysome (HP) RNA extract


title: hiPSCs_D20_HP_repB

description: High-polysome (HP) RNA extract


title: 00078A22EB_Acbc


title: GBM8_batch_3211


title: hiPSCs_D20_TotRNA_repB

description: Total cytoplasmic RNA extract


title: 00078A22DF_Acbc


title: 00078A19B7_Acbc


title: hiPSCs_D12X_HP_repB

description: High-polysome (HP) RNA extract


title: GBM8_batch_3204


title: hiPSCs_D12X_TotRNA_repB

description: Total cytoplasmic RNA extract


title: GBM8_batch_3209


title: 00078A1B05_Acbc

description: Removed: expression outlier


title: GBM8_batch_3208


title: hiPSCs_D12X_TotRNA_repA

description: Total cytoplasmic RNA extract


title: hiPSCs_D12X_HP_repA

description: High-polysome (HP) RNA extract


title: GBM8_batch_3207


title: hiPSCs_D12_HP_repB

description: High-polysome (HP) RNA extract

value: D12 STD hepatogenic differentiation


title: GBM8_batch_3199


title: 00078A1942_Acbc


title: 00078A193E_Acbc


title: hiPSCs_D12_HP_repC

description: High-polysome (HP) RNA extract


title: GBM8_batch_3198


title: 00078A19C0_Acbc


title: hiPSCs_D12_TotRNA_repC

description: Total cytoplasmic RNA extract


title: GBM8_batch_3206


title: 00078A18F7_Acbc


title: GBM8_batch_3205


title: hiPSCs_D12_TotRNA_repB

description: Total cytoplasmic RNA extract


title: GBM8_batch_3203


title: 00078A19B5_Acbc


title: GBM8_batch_3194


title: 00078A19A7_Acbc


title: GBM8_batch_3193


title: hiPSCs_D12_HP_repA

description: High-polysome (HP) RNA extract


title: A549 cells, LCMV infected at an MOI of 0.01, biological replicate 2

city: Wuhan

first: Qingxing

last: Wang

state: Wuchang

address: NO 44 in xiaohongshan Central District, Wuhan, China

country: China

institute: Wuhan institude of virology, CAS

data_processing:
The sequencing quality were assessed with FastQC (v0.11.8) and then low quality data were filtered using SOAPnuke (v1.3.0).
The clean reads were then aligned to the reference genome using STAR(v2.7.0d) with default parameters.
The processed reads from each sample were aligned using STAR against the reference genome.
The gene expression analyses were performed with Htseq (v0.11.2).
DESeq2 (v 1.26.0) was used to analyze the differentially expressed genes (DEGs) between samples. Q value was used to conduct significance analysis. Parameters for classifying significantly DEGs are 2-fold differences in the transcript abundance and q < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: human lung cell line

extract_protocol:
A549 cells were infected with LCMV at an MOI of 0.01 or mock-treated. At 36 hours post infection, cells were collected and total RNA was extracted with Trizol (Tiangen, Beijing) and RNA level was assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and NanoPhotometer spectrophotometer (Implen). Triplicate samples of all assays were used to construct independent libraries, followed by sequencing and analysis. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing. NEB Next Poly (A) mRNA Magnetic Isolation Module kit was used to enrich the poly (A) tailed mRNA.
The mRNA was fragmented into ~200 base pair pieces. The first-strand cDNA was synthesized from the mRNA fragments using reverse transcriptase and random hexamer primers, and then the second-strand cDNA was synthesized using DNA polymerase I and RNaseH. The end of the cDNA fragment was subjected to an end repair process that included the addition of a single ‘‘A’’ base, followed by ligation of the adapters. Products were purified and enriched by polymerase chain reaction (PCR) to amplify the library DNA. The final libraries were quantified using Qubit 2.0 Fluorometer (Invitrogen) and an Agilent 2100 Bioanalyzer. After quantitative reverse transcription-PCR validation, libraries were subjected to paired-end sequencing with pair end 150-base pair reading length on an Illumina Novaseq 6000 (Illumina).

value: epithelial

tag: agent

value: LCMV


title: GBM8_batch_3202


title: 00078A1979_Acbc


title: 00078A18A7_Acbc

description: Removed: genotype mismatch


title: A549 cells, LCMV infected at an MOI of 0.01, biological replicate 1


title: hiPSCs_D12_TotRNA_repA

description: Total cytoplasmic RNA extract


title: GBM8_batch_3201


title: 00078A1875_Acbc


title: GBM8_batch_3200


title: hiPSCs_D0_HP_repC

description: High-polysome (HP) RNA extract

source_name: HC3X hiPSCs non differentiated

value: CTRL non treated


title: A549 cells, mock infected, biological replicate 2

value: mock


title: 00078A194B_Acbc

value: Heterogeneous Stock

value: M


title: hiPSCs_D0_TotRNA_repC

description: Total cytoplasmic RNA extract

value: HC3X hiPSCs


title: 00078A1863_Acbc

description: Removed: expression outlier


title: hiPSCs_D0_HP_repB

description: High-polysome (HP) RNA extract


title: 00078A1937_Acbc


title: hiPSCs_D0_TotRNA_repB

description: Total cytoplasmic RNA extract


title: GBM8_batch_3197


title: hiPSCs_D0_HP_repA

description: High-polysome (HP) RNA extract


title: GBM8_batch_3196


title: 00078A192C_Acbc


title: 00078A1837_Acbc


title: 00078A181B_Acbc


title: 00078A1816_Acbc


title: 00078A1905_Acbc


title: hiPSCs_D0_TotRNA_repA

description: Total cytoplasmic RNA extract


title: GBM8_batch_3195


title: A549 cells, LCMV infected at an MOI of 0.01, biological replicate 3


title: GBM11_batch_390


title: 00078A18CF_Acbc


title: 00078A189F_Acbc


title: A549 cells, mock infected, biological replicate 3


title: GBM11_batch_396


title: GBM11_batch_395


title: 00078A179C_Acbc


title: GBM11_batch_391


title: Subject RC01, household contact control

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
FastQC was used for checking raw read QC.
Adapter clipping was performed using Cutadapt (v2.4) with default settings.
RNA-Seq reads’ alignment was performed using HISAT2 (v2.1.0) on GRCh38 reference genome analysis set.
The gene read quantification was performed using HTSeq-count (v0.9.1) with setting “–stranded reverse”. The gene annotation used for quantification was Ensembl version 94.
Genome_build: GRCh38, Ensembl gene annotation 94
Supplementary_files_format_and_content: CSV format, gene raw read and CPM counts

source_name: whole blood

extract_protocol:
Whole blood was collected in PAXgene tubes and frozen. RNA was extracted automatically using a QIAcube with the PAXgene Blood miRNA Kit. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) including poly(A) enrichment. Additionally, globin reduction was performed using GLOBINclear kit (Cat#AM1980). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA cDNA was synthesized. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. Libraries were sequenced on the Illumina NovaSeq6000 System with a 150bp paired-end protocol.

tag: tissue

value: whole blood

tag: subject

tag: disease state

value: household contact control

tag: time point

value: HHC

tag: ridley-jopling classification


title: Subject RC23, household contact control


title: Subject RC12, household contact control


title: Subject RC18, household contact control


title: Subject RC08, household contact control


title: 00078A186C_Acbc

tag: population


title: GBM11_batch_394


title: 00078A1731_Acbc

tag: Sex


title: 00078A1732_Acbc

tag: rat batch


title: GBM11_batch_384


title: GBM11_batch_385


title: GBM11_batch_388


title: GBM11_batch_386


title: Subject RC16, household contact control


title: GBM11_batch_387


title: A549 cells, mock infected, biological replicate 1


title: GBM11_batch_393


title: 00078A1772_Acbc

tag: brain region


title: Subject RC07, household contact control


title: 00078A1707_Acbc


title: 00078A16DF_Acbc


title: GBM11_batch_392


title: Subject RC13, household contact control


title: GBM11_batch_39


title: GBM11_batch_381


title: Subject RC11, household contact control


title: 00078A1807_Acbc


title: GBM11_batch_389


title: 00078A17F7_Acbc


title: Subject RC03, household contact control


title: 00078A17A7_Acbc


title: Subject RC33, household contact control


title: Subject RC30, household contact control


title: GBM11_batch_382


title: Subject RC36, household contact control


title: GBM11_batch_383


title: Subject RC21, household contact control


title: Subject RC35, household contact control


title: Subject RC25, household contact control


title: 00078A0A43_Acbc

description: Removed: expression outlier


title: GBM11_batch_380


title: 00078A0AEA_Acbc


title: GBM11_batch_38


title: Subject RC34, household contact control


title: GBM11_batch_379


title: GBM11_batch_375


title: 00078A02DF_Acbc


title: Subject RC37, household contact control


title: GBM11_batch_374


title: Subject RC26, household contact control


title: GBM11_batch_378


title: 00078A096C_Acbc


title: 00078A087B_Acbc


title: GBM11_batch_377


title: Subject RC04, household contact control


title: 00078A16D3_Acbc


title: GBM11_batch_376


title: Subject RC24, household contact control


title: 00078A09B1_Acbc


title: 00078A07A2_Acbc

description: Removed: low read count


title: Subject RC40, household contact control


title: Subject RC10, household contact control


title: Subject RC39, household contact control


title: 00078A022D_Acbc


title: Subject RC31, household contact control


title: 00078A0255_Acbc


title: 00078A0246_Acbc


title: 00078A02CB_Acbc


title: GBM11_batch_373


title: 00078A0224_Acbc

description: Removed: genotype mismatch


title: GBM11_batch_372


title: GBM11_batch_37


title: 00078A021A_Acbc


title: GBM11_batch_370


title: Subject RL16, leprosy progressor second timepoint

value: leprosy progressor

value: Second

value: BT


title: Subject RL01, leprosy progressor second timepoint

value: PN


title: Subject RL33, leprosy progressor second timepoint


title: 00078A0215_Acbc

value: Nucleus accumbens core


title: GBM11_batch_369


title: GBM11_batch_371


title: 00078A01FE_Acbc

value: F


title: Subject RL08, leprosy progressor second timepoint


title: Subject RL34, leprosy progressor second timepoint


title: GBM11_batch_367


title: 00078A01D8_Acbc


title: Subject RL21, leprosy progressor second timepoint


title: 00078A01DB_Acbc


title: Subject RL35, leprosy progressor second timepoint


title: Subject RL11, leprosy progressor second timepoint


title: Subject RL07, leprosy progressor second timepoint


title: 00078A01C0_Acbc


title: 00078A01A6_Acbc


title: Subject RC28, household contact control


title: 00078A0139_Acbc


title: 00078A0189_Acbc


title: Subject RC15, household contact control


title: GBM11_batch_361


title: GBM11_batch_363


title: 00078A0138_Acbc


title: GBM11_batch_366


title: GBM11_batch_360


title: Subject RC09, household contact control


title: Subject RC20, household contact control


title: 00078A0127_Acbc


title: Subject RC17, household contact control


title: GBM11_batch_359


title: 00078A00BF_Acbc


title: GBM11_batch_357


title: 00078A00AC_Acbc

description: Removed: expression outlier


title: 00078A0244_Acbc


title: Subject RC19, household contact control


title: GBM11_batch_362


title: 00078A0166_Acbc


title: Subject RC14, household contact control


title: 00078A0085_Acbc


title: Subject RC22, household contact control


title: GBM11_batch_356


title: GBM11_batch_36


title: GBM11_batch_355


title: GBM11_batch_354


title: Subject RC27, household contact control


title: 00078A0058_Acbc


title: GBM11_batch_353


title: Subject RC29, household contact control


title: 00078A0041_Acbc


title: Subject RC32, household contact control


title: GBM11_batch_358


title: GBM11_batch_368


title: 00078A002C_Acbc

description: Removed: low read count


title: GBM11_batch_352


title: GBM11_batch_351


title: 000789FFF9_Acbc


title: Subject RC06, household contact control


title: 000789FFF0_Acbc


title: Subject RC05, household contact control


title: 000789FF94_Acbc


title: Subject RL16, leprosy progressor first timepoint

value: First


title: Subject RL01, leprosy progressor first timepoint


title: Subject RC02, household contact control


title: GBM11_batch_350


title: 000789FF6E_Acbc


title: 000789FFD3_Acbc


title: Subject RC38, household contact control


title: Subject RL07, leprosy progressor first timepoint


title: 000789FFAC_Acbc


title: GBM11_batch_344


title: GBM11_batch_349


title: GBM11_batch_347


title: 00077EA7E6_Acbc


title: 00077E8336_Acbc


title: GBM11_batch_345


title: Subject RL21, leprosy progressor first timepoint


title: GBM11_batch_343


title: Subject RL11, leprosy progressor first timepoint


title: 000789FFF8_Acbc

description: Removed: too many zero counts


title: 00077E76C6_Acbc

description: Removed: expression outlier


title: GBM11_batch_342


title: GBM11_batch_35


title: Subject RL33, leprosy progressor first timepoint


title: 000789FF7D_Acbc


title: GBM11_batch_346


title: 00077E67B5_Acbc


title: GBM11_batch_348


title: Subject RL35, leprosy progressor first timepoint


title: Subject RL37, leprosy progressor second timepoint


title: Moss animal whole animal(s) (Sample1845)

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (3D-DNA, Juicer)
Centromere position identification (repeat sequence mapping or structural analysis, 3D-DNA/JBAT)
Aggregate chromosome analysis (3D-DNA)
Variant calling (DRAGEN pipeline)
Chromosome-length variant phasing (3D-DNA)
Genome_build: In addition to those generate as part of the study, the following existing genome builds were used: GRCg6a (domestic chicken); Xla.v91 (African clawed frog); AaegL5.0 (Yellow fever mosquito), CpipJ3 (Southern domestic mosquito); Release_6_plus_ISO1_MT (fruit fly, with chromosome arms merged for ACA analysis resulting in Release_6_plus_ISO1_MT_merged); WBcel235 (C. elegans); sacCer3 (baker's yeast); arahy.Tifrunner.gnm2.J5K5 (ground nut); 161010_Chinese_Spring_v1.0_pseudomolecules (bread wheat).
Supplementary_files_format_and_content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary_files_format_and_content: hic: contact maps generated by aligning Hi-C data to corresponding chromosome-length reference sequences. In addition to standard contact maps generated for all genomic positions across chromosomes the uploaded files include ACA (aggregate chromosome analysis) maps and phasing contact maps representing interactions between positions on the genome that contain heterogyzous SNPs. For more details see Hoencamp et al., Supplement.
Supplementary_files_format_and_content: wig: tracks showing the alignment frequency of Hi-C reads from read pairs that contain centromere repeat-specifc sequences.
Supplementary_files_format_and_content: bedpe: Files describing the tentative position of centromeres in chromosome-length genome assemblies, identified either by mapping repeat sequences associated with the centromere or via analysis of the contact map for evidence of centromere-to-telomere folding axis. For details see Hoencamp et al., Supplement.
Supplementary_files_format_and_content: vcf.gz: Variants (specifically SNPs) identivied by the DRAGEN variant calling pipeline from aligning Hi-C data to chromosome-length references generated via Hi-C-guided assembly and phased using the 3D-DNA Hi-C-guided phasing module.

molecule: genomic DNA

organism: Cristatella mucedo

source_name: 30 whole animals

extract_protocol:
Extraction protocol is described as part of the library construction protocol.
The Hi-C libraries were prepared following the in situ Hi-C strategy (Rao, Huntley et al., 2014). Briefly, cells or tissue were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. Afterward DNA was handled according to standard Illumina library construction protocol. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on various Illumina instruments following the manufacturer's protocols. Fpr the tammar wallaby, a short insert-size PCR-free DNA-Seq library was prepared following the ClaSeek protocol.

value: 30 whole animals


title: GBM11_batch_341


title: Subject RL34, leprosy progressor first timepoint


title: Subject RL08, leprosy progressor first timepoint


title: GBM11_batch_340


title: GBM11_batch_34


title: Bread wheat leaves (Sample4080, Sample4081)

description: Sample4080, Sample4081

organism: Triticum aestivum

source_name: leaves (genotype: Julius)

value: leaves


title: GBM11_batch_339


title: GBM11_batch_338


title: Subject RL23, leprosy progressor second timepoint


title: Subject RL25, leprosy progressor second timepoint


title: GBM11_batch_336


title: Subject RL30, leprosy progressor second timepoint


title: Subject RL31, leprosy progressor second timepoint


title: GBM11_batch_337


title: Subject RL10, leprosy progressor second timepoint


title: Subject RL25, leprosy progressor first timepoint


title: GBM11_batch_335


title: GBM11_batch_334


title: Subject RL23, leprosy progressor first timepoint


title: GBM11_batch_333


title: GBM11_batch_332


title: Subject RL30, leprosy progressor first timepoint


title: Subject RL31, leprosy progressor first timepoint


title: Subject RL10, leprosy progressor first timepoint


title: GBM11_batch_329


title: GBM11_batch_330


title: Subject RL40, leprosy progressor second timepoint


title: Subject RL38, leprosy progressor second timepoint


title: Subject RL39, leprosy progressor second timepoint


title: GBM11_batch_328


title: GBM11_batch_33


title: GBM11_batch_326


title: GBM11_batch_325


title: GBM11_batch_327


title: Subject RL36, leprosy progressor second timepoint


title: Subject RL32, leprosy progressor second timepoint


title: GBM11_batch_324


title: Subject RL29, leprosy progressor second timepoint


title: Subject RL26, leprosy progressor second timepoint


title: Subject RL28, leprosy progressor second timepoint


title: GBM11_batch_331


title: GBM11_batch_320


title: Subject RL37, leprosy progressor first timepoint


title: Subject RL22, leprosy progressor second timepoint


title: Subject RL27, leprosy progressor second timepoint


title: GBM11_batch_32


title: GBM11_batch_321


title: Subject RL24, leprosy progressor second timepoint


title: Subject RL20, leprosy progressor second timepoint


title: GBM11_batch_322


title: Subject RL19, leprosy progressor second timepoint


title: GBM11_batch_319


title: Subject RL18, leprosy progressor second timepoint


title: GBM11_batch_317


title: GBM11_batch_323


title: Subject RL15, leprosy progressor second timepoint


title: Subject RL17, leprosy progressor second timepoint

value: TT


title: GBM11_batch_316


title: GBM11_batch_315


title: GBM11_batch_365


title: GBM11_batch_364


title: Subject RL14, leprosy progressor second timepoint

value: I


title: Subject RL13, leprosy progressor second timepoint


title: GBM11_batch_314


title: GBM11_batch_313


title: GBM11_batch_312


title: Subject RL12, leprosy progressor second timepoint


title: Subject RL09, leprosy progressor second timepoint


title: GBM11_batch_311


title: GBM11_batch_310


title: Subject RL06, leprosy progressor second timepoint


title: GBM11_batch_31


title: Subject RL05, leprosy progressor second timepoint


title: Subject RL04, leprosy progressor second timepoint


title: GBM11_batch_318


title: Subject RL03, leprosy progressor second timepoint


title: Single CD44+ CD51-TNCs (A-H) and Single CD44- CD51-TNCs (I-P) PB2

city: Utrecht

first: Judith

middle: Anne

last: Vivié

state: Utrecht

address: Uppsalalaan 8

department: Single Cell Sequencing Facility

institute: Hubrecht Institute

data_processing:
Paired end reads obtained by CEL-seq2 were aligned to the transcriptome using bwa mem (version 0.7.15) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode and UMI information: the first 6 bases correspond the Unique Molecular Identifier (UMI), the next 8 basepairs to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: mm10
Supplementary_files_format_and_content: *.TranscriptCounts.tsv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number of the experiment, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: Bone marrow

extract_protocol:
Cells were sorted into mineral oil (Sigma Aldrich) and cells were lysed at 65 ℃ for 5 minutes
mRNA was processed using the previously described SORTseq method. Resulting DNA libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing

treatment_protocol: Bone marrow were enzymatically dissociated using collagenase IV (2mg/mL) and dispase (1mg/mL) and single cells were sorted into mineral oil.


title: Single CD44- CD51-TNCs (1) PB-B1


title: Subject RL02, leprosy progressor second timepoint


title: Single CD44+ CD51-TNCs (1) PB-A1


title: Subject RL12, leprosy progressor first timepoint


title: Subject RL28, leprosy progressor first timepoint


title: MGG23_TF_siTEAD4_OSM3

source_name: MGG23 bulk RNA


title: Subject RL24, leprosy progressor first timepoint


title: MGG23_TF_siTEAD4_OSM1


title: Subject RL20, leprosy progressor first timepoint


title: MGG23_TF_siTEAD4_BSA3


title: Subject RL15, leprosy progressor first timepoint


title: MGG23_TF_siTEAD4_BSA2


title: Subject RL18, leprosy progressor first timepoint


title: MGG23_TF_siTEAD4_BSA1


title: MGG23_TF_siTEAD2_OSM3


title: Subject RL19, leprosy progressor first timepoint


title: Subject RL17, leprosy progressor first timepoint


title: MGG23_TF_siTEAD2_OSM1


title: Single CD44+ CD51-TNCs (A-H) and Single CD44- CD51-TNCs (I-P) PB1


title: Subject RL40, leprosy progressor first timepoint


title: MGG23_TF_siTEAD2_BSA2


title: Subject RL22, leprosy progressor first timepoint


title: Subject RL13, leprosy progressor first timepoint


title: Subject RL27, leprosy progressor first timepoint


title: MGG23_TF_siTEAD2_BSA3


title: MGG23_TF_siTEAD4_OSM2


title: MGG23_TF_siTEAD2_BSA1


title: Subject RL26, leprosy progressor first timepoint


title: MGG23_TF_siTAZ_OSM2


title: MGG23_TF_siTAZ_OSM3


title: MGG23_TF_siTAZ_OSM1


title: MGG23_TF_siTEAD2_OSM2


title: MGG23_TF_siTAZ_BSA3


title: MGG23_TF_siTAZ_BSA2


title: MGG23_TF_siTAZ_BSA1


title: Subject RL02, leprosy progressor first timepoint


title: Subject RL39, leprosy progressor first timepoint


title: Subject RL32, leprosy progressor first timepoint


title: Subject RL09, leprosy progressor first timepoint


title: Subject RL04, leprosy progressor first timepoint


title: MGG23_TF_siSTAT3_OSM2


title: MGG23_TF_siSTAT3_OSM1


title: Subject RL06, leprosy progressor first timepoint


title: MGG23_TF_siSTAT3_OSM3


title: Subject RL36, leprosy progressor first timepoint


title: Subject RL29, leprosy progressor first timepoint


title: MGG23_TF_siSTAT3_BSA1


title: MGG23_TF_siRELA_OSM3


title: MGG23_TF_siSTAT3_BSA2


title: Subject RL03, leprosy progressor first timepoint


title: Subject RL38, leprosy progressor first timepoint


title: Sea squirt tissue (Sample2441)

organism: Ciona intestinalis

source_name: tissue

value: tissue


title: MGG23_TF_siRELA_OSM2


title: MGG23_TF_siSTAT3_BSA3


title: Sea squirt tissue (Sample2441, Sample2444)

description: Sample2441, Sample2444


title: MGG23_TF_siRELA_BSA3


title: Arctic lamprey muscle (Sample3820)

organism: Lethenteron camtschaticum

source_name: muscle

value: muscle


title: MGG23_TF_siRELA_OSM1


title: Red-bellied piranha muscle (Sample2033)

organism: Pygocentrus nattereri


title: Acropora millepora stony coral branch fragments (Sample1884, Sample1992)

description: Sample1884, Sample1992

organism: Acropora millepora

source_name: branch

value: branch


title: MGG23_TF_siRELA_BSA1


title: MGG23_TF_siRELA_BSA2


title: Peanut leaves (Sample2455)

organism: Arachis hypogaea

source_name: leaves (genotype: Tiftrunner)


title: MGG23_TF_siJUN_OSM3


title: MGG23_TF_siJUN_OSM2


title: MGG23_TF_siJUN_OSM1


title: MGG23_TF_siJUN_BSA3


title: MGG23_TF_siJUN_BSA2


title: MGG23_TF_siFOS_OSM3


title: MGG23_TF_siJUN_BSA1


title: Trained, intact, head kidney, fish 5

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays.

scan_protocol: Arrays were scanned with Agilent microarray scanner.

data_processing: Global normalization was performed by equalizing the mean intensities of all microarrays. The individual values for each feature were divided to the mean value of all samples and expression ratios (ER) were calculated. Log2-ER were normalized with the locally weighted non-linear regression (Lowess).

organism: Salmo salar

source_name: Head kidney

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was fed with commercial feed.

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen).

value: Head kidney

tag: training

value: Trained

tag: challenge

value: intact


title: Trained, intact, head kidney, fish 3


title: Trained, intact, head kidney, fish 6


title: MGG23_TF_siFOS_OSM2


title: Control, intact, head kidney, fish 6

value: Control


title: Control, intact, head kidney, fish 5


title: MGG23_TF_siFOS_BSA2


title: MGG23_TF_siFOS_BSA3


title: MGG23_TF_siFOS_OSM1


title: Trained, intact, head kidney, fish 1


title: Control, intact, head kidney, fish 4


title: Control, intact, head kidney, fish 1


title: Control, intact, head kidney, fish 2


title: MGG23_TF_siCTR_OSM3


title: Control, intact, head kidney, fish 3


title: MGG23_TF_siFOS_BSA1


title: Trained, P salmonis challenged, head kidney, fish 6

value: Piscirickettsia salmonis


title: MGG23_TF_siCTR_BSA3


title: Trained, intact, head kidney, fish 4


title: Trained, intact, head kidney, fish 2


title: Trained, P salmonis challenged, head kidney, fish 2


title: Trained, P salmonis challenged, head kidney, fish 4


title: Trained, P salmonis challenged, head kidney, fish 5


title: Subject RL05, leprosy progressor first timepoint

value: whole blood

value: leprosy progressor

value: BT


title: Trained, P salmonis challenged, head kidney, fish 3


title: MGG23_TF_siCEBPb_OSM3


title: MGG23_TF_siCEBPb_OSM1


title: Trained, P salmonis challenged, head kidney, fish 1


title: MGG23_TF_siCEBPb_OSM2


title: MGG23_TF_siCTR_OSM2


title: Control, P salmonis challenged, head kidney, fish 5


title: MGG23_TF_siCTR_OSM1


title: Control, P salmonis challenged, head kidney, fish 6


title: Control, P salmonis challenged, head kidney, fish 4


title: MGG23_TF_siCEBPb_BSA2


title: Control, P salmonis challenged, head kidney, fish 3


title: MGG23_MGG75_OSM

source_name: MGG23, MGG75 cell-line


title: MGG23_TF_siCEBPb_BSA1


title: Control, P salmonis challenged, head kidney, fish 2


title: Tardigrade whole animal(s) (Sample3840)

organism: Hypsibius dujardini

source_name: whole animals

value: whole animals


title: MGG75

source_name: MGG75 GBM cell-line


title: MGH143

source_name: MGH143 GBM cell-line


title: MGG23_TF_siCTR_BSA2


title: MGG23

source_name: MGG23 GBM cell-line


title: MGG18

source_name: MGG18 GBM cell-line


title: MGG23_TF_siCTR_BSA1


title: Control, P salmonis challenged, head kidney, fish 1


title: MGG23_TF_siCEBPb_BSA3


title: S018

city: Montpellier

first: Jacques

last: Colinge

address: 208, avenue des Apothicaires

country: France

institute: Inserm

description:
S018
ncounts.txt

data_processing:
Adaptor trimming using trimmomatic
reads alignment with STAR (default parameters and 2 passes)
reads counts with HTSeq 0-7-2
reads count normalization using edgeR
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized reads count per sample

source_name: PCNSL

extract_protocol:
RNA was extracted using RNeasy Blood and Tissue Kit (Qiagen) and quantified by spectrophotometry using the Nanodrop 2000 (ThermoFisher Scientific) and 2100 Bioanalyzer (Agilent). Quality was checked by Fragment analyzer (RIN > 7). 400 ng was used for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions. DNA library were prepared with the TruSeq Stranded mRNA Sample Preparation Kit.

value: brain

tag: type

value: tumor


title: S020

description:
S020
ncounts.txt


title: S022

description:
S022
ncounts.txt


title: S005

description:
S005
ncounts.txt


title: S011

description:
S011
ncounts.txt


title: S003

description:
S003
ncounts.txt


title: S015

description:
S015
ncounts.txt


title: S009

description:
S009
ncounts.txt


title: 32

description:
P342_032
ncounts.txt


title: S007

description:
S007
ncounts.txt


title: 31

description:
P342_031
ncounts.txt


title: 22

description:
P342_022
ncounts.txt


title: 25

description:
P342_025
ncounts.txt


title: 12

description:
P342_012
ncounts.txt


title: 11

description:
P342_011
ncounts.txt


title: C57BL/6_Spleen_TAK-981-001-J_7.5 mg/kg_8hr_repl.3

data_processing:
Raw fastq files were processed using the RNA-seq pipeline within Array Studio. Briefly, reads with bad qualities, or from IlluminaAdapters, Ercc, rRNA and tRNA were first filtered from raw data, the cleaned reads were then aligned to the genome through OmicSoft Aligner (OSA). The reads mapped to the exonic region were counted for each gene and then normalized into FPKM for the downstream analysis.
Genome_build: mouse NCBI genome build 38
Supplementary_files_format_and_content: The reads count and FPKM value of each gene in each sample are uploaded as the processed data files

source_name: Spleen

growth_protocol: Mouse B16-F10 melanoma cells were grown in DMEM medium containing 10% FBS. Mouse A20 B-lymphoma cells were grown in RPMI-1640 medium containing 10%FBS and 0.05 mM 2-mercaptoethanol. When preparation of tumor cell inoculation, the cells were harvested and washed in DMEM or RPMI medium. Then 0.1 million of B16-F10 cells in 0.1ml DMEM medium or 1 million of A20 cells in 0.1 ml RPMI medium were inoculated subcutaneously into C57BL/6 or BALB/c mice in flank respectively.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When tumor volumes were around 500 mm^3, C57BL/6 bearing B16-F10 tumors and BALB/c mice bearing A20 tumors were given one dose of TAK-981 at 2.5 mg/kg, 5 mg/kg, 7.5 mg/kg, or 15 mg/kg intravenously, each dose level had 4-hour and 8-hour time points, and each time point had three mice per group. By 4 hours and 8 hours post TAK-981 treatment, samples of whole of blood, tumor, and spleen were harvested for further analysis.

tag: strain

tag: treatment

value: 7.5 mg/kg


title: 15

description:
P342_015
ncounts.txt


title: C57BL/6_Spleen_TAK-981-001-J_7.5 mg/kg_4hr_repl.3

tag: dosage


title: 3

description:
P342_003
ncounts.txt


title: 13

description:
P342_013
ncounts.txt


title: A20_TAK-981

data_processing:
Raw fastq files were first mapped to the genome through Cell Ranger  ( version 2.1.1), and the QC filtered quantified mtx files were then processed using Seurat (v2) for the downstream cell clustering, maker gene identification, and gene expression analysis using the default parameters.
Genome_build: mouse NCBI genome build 38
Supplementary_files_format_and_content: The reads count of each gene in each sample is uploaded into mtx format

source_name: Subcutaneous tumor

growth_protocol: A20 cells were grown in RPMI 1640 media supplemented with 10% fetal bovine serum.  Balb/c mice were inouclated with 1x10^6 cells per mouse in the subcutaneous space along the left flank.  Tumor growth was monitored using verneir calipers.  Treatment begain when volumes reach approximately 300mm^3.

extract_protocol:
Single cell RNA libraries were generated from A20 tumors derived from tumor-bearing Balb/c mice 8 h after treatment with vehicle or 7.5 mg/kg TAK-981 using the Chromium Single Cell 5’ kit (10X Genomics) following Dead Cell Removal (Miltenyi). Cells were loaded onto the Chromium Controller (10 X Genomics) to target capture of ~3,000 GEMs (Gel Bead-in Emulsions) per sample for downstream analysis, following the manufacturer’s specifications.
The sequencing libraries were evaluated for quality on the Agilent TapeStation (Agilent Technologies), and quantified by using Qubit 2.0 Fluorometer (Invitrogen) and pooled libraries were quantified using qPCR (Applied Biosystems) prior to loading onto an Illumina (Illumina) sequencing platform.

treatment_protocol: Mice received IV injections of either 20% HPbCD (hydroxy- beta- cyclodextrin) as a vehicle control or TAK-981 at 7.5mg/kg.  8 hours following administration of either vehicle or TAK-981 tumors were excised by blunt dissection and dispersed into single-cells by mechanical separation through a 70uM filter.

value: Balb/c


title: C57BL/6_Spleen_TAK-981-001-J_7.5 mg/kg_8hr_repl.1


title: A20_Veh

value: 20% HPbCD


title: S010

description:
S010
ncounts.txt


title: C57BL/6_Spleen_TAK-981-001-J_7.5 mg/kg_4hr_repl.1


title: C57BL/6_Spleen_TAK-981-001-J_7.5 mg/kg_8hr_repl.2


title: C57BL/6_Spleen_TAK-981-001-J_15.0 mg/kg_8hr_repl.3


title: C57BL/6_Spleen_TAK-981-001-J_15.0 mg/kg_8hr_repl.2


title: C57BL/6_Spleen_TAK-981-001-J_7.5 mg/kg_4hr_repl.2


title: C57BL/6_Spleen_20% HPbCD_._8hr_repl.3

description: C57BL/6_Spleen_20% HPbCD_._8hr


title: C57BL/6_Spleen_TAK-981-001-J_15.0 mg/kg_8hr_repl.1


title: C57BL/6_Spleen_20% HPbCD_._4hr_repl.2

description: C57BL/6_Spleen_20% HPbCD_._4hr


title: C57BL/6_Spleen_TAK-981-001-J_15.0 mg/kg_4hr_repl.3


title: C57BL/6_Spleen_20% HPbCD_._8hr_repl.2

description: C57BL/6_Spleen_20% HPbCD_._8hr


title: C57BL/6_Spleen_TAK-981-001-J_15.0 mg/kg_4hr_repl.2


title: C57BL/6_Spleen_TAK-981-001-J_15.0 mg/kg_4hr_repl.1


title: C57BL/6_Spleen_20% HPbCD_._4hr_repl.3

description: C57BL/6_Spleen_20% HPbCD_._4hr


title: C57BL/6_Spleen_20% HPbCD_._8hr_repl.1

description: C57BL/6_Spleen_20% HPbCD_._8hr


title: C57BL/6_Spleen_20% HPbCD_._4hr_repl.1

description: C57BL/6_Spleen_20% HPbCD_._4hr


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_7.5 mg/kg_8hr_repl.3


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_7.5 mg/kg_8hr_repl.2


title: Yellow fever mosquito whole animal(s) (SAMN08028734)

organism: Aedes aegypti

source_name: whole pupae

value: whole pupae


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_7.5 mg/kg_8hr_repl.1


title: 10

description:
P342_010
ncounts.txt


title: Baker's yeast cells (Sample4076)

organism: Saccharomyces cerevisiae

source_name: cells

value: cells


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_7.5 mg/kg_4hr_repl.1


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_7.5 mg/kg_4hr_repl.3


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_5.0 mg/kg_4hr_repl.3

value: 5.0 mg/kg


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_7.5 mg/kg_4hr_repl.2


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_5.0 mg/kg_8hr_repl.3


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_5.0 mg/kg_4hr_repl.2


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_5.0 mg/kg_8hr_repl.2


title: RNA-seq-SAEC_Ruxolitinib_rep2

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples

source_name: small airway epithelial cells (SAEC)

growth_protocol: Human small airway epithelial cells (SAEC) obtained from Lifeline Technology (FC-0016) were expanded using the complete BronchiaLifeTM media kit (Lifeline Technology, LL-0023). All culture wares were pre-coated in 30 mg/ml of Fibronectin (ThermoFisher Scientific, 33016015) for at least 1h at room temperature.

extract_protocol:
Total RNA was isolated from the cytokine-stimulated cells using PureLink™ RNA Mini Kit (Invitrogen) and libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301).
Libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: Cytokines (10 ng/ml; Human IFNb, 300-02BC; Human IFNg, 300-02; Human IL6, 200-06; Human IL7, 200-07; Human Growth hormone, 100-40, Peprotech; Human IFNa2b, 78077.1, Stem Cell Technologies; Human IFNl3, 5259-IL-025, R&D systems) were treated in respective culture media and the cells were incubated for 12hr in 5% CO2 atmosphere at 37°C. Jak inhibitors, 10 mM of either Baricitinib (HY-15315A, MedChemExpress) or Ruxolitinib (HY-50856A, MedChemExpress), were added to BronchiLiafeTM media with or without IFNb and incubated for 12hrs.

tag: cell type

value: small airway epithelial cells (SAEC)

value: Ruxolitinib


title: RNA-seq-SAEC_Ruxolitinib_rep3


title: RNA-seq-SAEC_Ruxolitinib_rep1


title: RNA-seq-SAEC_IL7_rep2


title: RNA-seq-SAEC_IL7_rep1


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_5.0 mg/kg_4hr_repl.1


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_2.5 mg/kg_8hr_repl.3

value: 2.5 mg/kg


title: RNA-seq-SAEC_IL6_rep2


title: RNA-seq-SAEC_IL6_rep3


title: RNA-seq-SAEC_IL6_rep1


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_2.5 mg/kg_8hr_repl.2


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_2.5 mg/kg_8hr_repl.1


title: Yellow fever mosquito whole animal(s) (SAMN08028733, SAMN08028734, SAMN08028735)


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_2.5 mg/kg_4hr_repl.3


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_2.5 mg/kg_4hr_repl.2


title: RNA-seq-SAEC_IFNl3_rep2


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_2.5 mg/kg_4hr_repl.1


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_5.0 mg/kg_8hr_repl.1


title: RNA-seq-SAEC_IL7_rep3


title: RNA-seq-SAEC_IFNl3_rep1


title: RNA-seq-SAEC_IFNg_rep3

value: IFNg


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_15.0 mg/kg_8hr_repl.2


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_15.0 mg/kg_8hr_repl.3


title: RNA-seq-SAEC_IFNg_rep2


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_15.0 mg/kg_4hr_repl.3


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_15.0 mg/kg_8hr_repl.1


title: RNA-seq-SAEC_IFNb_Ruxolitinib_rep3


title: RNA-seq-SAEC_IFNg_rep1


title: RNA-seq-SAEC_IFNb_Ruxolitinib_rep2


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_15.0 mg/kg_4hr_repl.2


title: C57BL/6_Tumor(B16F10)_TAK-981-001-J_15.0 mg/kg_4hr_repl.1


title: C57BL/6_Tumor(B16F10)_20% HPbCD_._8hr_repl.2

description: C57BL/6_Tumor(B16F10)_20% HPbCD_._8hr


title: RNA-seq-SAEC_IFNl3_rep3


title: RNA-seq-SAEC_IFNb_rep2

value: IFNb


title: C57BL/6_Tumor(B16F10)_20% HPbCD_._8hr_repl.1

description: C57BL/6_Tumor(B16F10)_20% HPbCD_._8hr


title: C57BL/6_Tumor(B16F10)_20% HPbCD_._4hr_repl.3

description: C57BL/6_Tumor(B16F10)_20% HPbCD_._4hr


title: C57BL/6_Tumor(B16F10)_20% HPbCD_._4hr_repl.2

description: C57BL/6_Tumor(B16F10)_20% HPbCD_._4hr


title: C57BL/6_Tumor(B16F10)_20% HPbCD_._4hr_repl.1

description: C57BL/6_Tumor(B16F10)_20% HPbCD_._4hr


title: RNA-seq-SAEC_IFNb_rep1


title: C57BL/6_Blood_TAK-981-001-J_7.5 mg/kg_8hr_repl.3

source_name: Blood


title: RNA-seq-SAEC_IFNb_Baricitinib_rep2


title: RNA-seq-SAEC_IFNb_Baricitinib_rep1


title: C57BL/6_Blood_TAK-981-001-J_7.5 mg/kg_8hr_repl.2


title: RNA-seq-SAEC_IFNa_rep2

value: IFNa


title: C57BL/6_Blood_TAK-981-001-J_7.5 mg/kg_8hr_repl.1


title: C57BL/6_Tumor(B16F10)_20% HPbCD_._8hr_repl.3

description: C57BL/6_Tumor(B16F10)_20% HPbCD_._8hr


title: RNA-seq-SAEC_IFNb_Ruxolitinib_rep1


title: C57BL/6_Blood_TAK-981-001-J_7.5 mg/kg_4hr_repl.3


title: RNA-seq-SAEC_IFNb_Baricitinib_rep3


title: RNA-seq-SAEC_IFNa_rep3


title: C57BL/6_Blood_TAK-981-001-J_5.0 mg/kg_8hr_repl.2


title: RNA-seq-SAEC_Control_rep4

value: Control


title: RNA-seq-SAEC_GH_rep3

value: Growth hormone


title: C57BL/6_Blood_TAK-981-001-J_7.5 mg/kg_4hr_repl.1


title: RNA-seq-SAEC_GH_rep2


title: RNA-seq-SAEC_Control_rep3


title: C57BL/6_Blood_TAK-981-001-J_5.0 mg/kg_8hr_repl.3


title: C57BL/6_Blood_TAK-981-001-J_5.0 mg/kg_8hr_repl.1


title: RNA-seq-SAEC_IFNb_rep3


title: RNA-seq-SAEC_IFNa_rep1


title: C57BL/6_Blood_TAK-981-001-J_7.5 mg/kg_4hr_repl.2


title: RNA-seq-SAEC_Control_rep1


title: C57BL/6_Blood_TAK-981-001-J_5.0 mg/kg_4hr_repl.2


title: RNA-seq-SAEC_Baricitinib_rep3

value: Baricitinib


title: RNA-seq-SAEC_Baricitinib_rep1


title: RNA-seq-SAEC_Baricitinib_rep2


title: C57BL/6_Blood_TAK-981-001-J_2.5 mg/kg_8hr_repl.3


title: C57BL/6_Blood_TAK-981-001-J_2.5 mg/kg_8hr_repl.2


title: RNA-seq-SAEC_GH_rep1


title: ChIP-seq-SAEC_IFNb_Ruxolitinib_H3K27ac

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Quality filtering and alignment of the raw reads was done using Trimmomatic27 (version 0.36) and Bowtie28 (version 1.2.2) and Samtools29 (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome hg19. Homer30 (version 4.8.2) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer31 (version 2.5.3) was used for visualization.  (Langmead et al., Nature methods, 2012)  with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools (Broad Institute. Picard, http://broadinstitute.github.io/picard/.) to remove duplicates. Homer software (Heinz et al., Mol. Cell, 2010) was applied  for the generation of bedGraph files.
Genome_build: hg19

extract_protocol:
Chromatin was fixed with formaldehyde (1% final concentration) for 15 min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: H3K27ac (Abcam, ab4729), RNA polymerase II (Abcam, ab5408), H3K4me1 (Active Motif, 39297) and H3K4me3 (Millipore, 07-473). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 3000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard Illumina protocols.


title: C57BL/6_Blood_TAK-981-001-J_2.5 mg/kg_8hr_repl.1


title: ChIP-seq-SAEC_IFNb_Ruxolitinib_PolII


title: C57BL/6_Blood_TAK-981-001-J_2.5 mg/kg_4hr_repl.3


title: ChIP-seq-SAEC_IFN-b_PolII_rep2

value: IFN-b


title: C57BL/6_Blood_TAK-981-001-J_2.5 mg/kg_4hr_repl.2


title: RNA-seq-SAEC_Control_rep2


title: C57BL/6_Blood_TAK-981-001-J_2.5 mg/kg_4hr_repl.1


title: ChIP-seq-SAEC_IFN-b_PolII_rep1


title: C57BL/6_Blood_TAK-981-001-J_15.0 mg/kg_8hr_repl.3


title: C57BL/6_Blood_TAK-981-001-J_15.0 mg/kg_8hr_repl.2


title: C57BL/6_Blood_TAK-981-001-J_15.0 mg/kg_4hr_repl.2


title: C57BL/6_Blood_TAK-981-001-J_15.0 mg/kg_8hr_repl.1


title: ChIP-seq-SAEC_Control_PolII_rep2


title: ChIP-seq-SAEC_IFN-b_H3K27ac_rep2


title: C57BL/6_Blood_TAK-981-001-J_5.0 mg/kg_4hr_repl.3


title: C57BL/6_Blood_TAK-981-001-J_15.0 mg/kg_4hr_repl.3


title: ChIP-seq-SAEC_IFN-b_H3K4me1_rep1


title: ChIP-seq-SAEC_IFN-b_H3K4me3_rep1


title: C57BL/6_Blood_TAK-981-001-J_5.0 mg/kg_4hr_repl.1


title: C57BL/6_Blood_TAK-981-001-J_15.0 mg/kg_4hr_repl.1


title: ChIP-seq-SAEC_Control_PolII_rep1


title: ChIP-seq-SAEC_Control_H3K27ac_rep2


title: ChIP-seq-SAEC_Control_H3K27ac_rep1


title: C57BL/6_Blood_20% HPbCD_._8hr_repl.3

description: C57BL/6_Blood_20% HPbCD_._8hr


title: C57BL/6_Blood_20% HPbCD_._8hr_repl.2

description: C57BL/6_Blood_20% HPbCD_._8hr


title: ChIP-seq-SAEC_Control_H3K4me3_rep1


title: ChIP-seq-SAEC_Control_H3K4me3_rep2


title: C57BL/6_Blood_20% HPbCD_._8hr_repl.1

description: C57BL/6_Blood_20% HPbCD_._8hr


title: ChIP-seq-SAEC_Control_H3K4me1_rep2


title: ChIP-seq-SAEC_Control_H3K4me1_rep1


title: C57BL/6_Blood_20% HPbCD_._4hr_repl.2

description: C57BL/6_Blood_20% HPbCD_._4hr


title: ChIP-seq-SAEC_IFN-b_H3K27ac_rep1


title: C57BL/6_Blood_20% HPbCD_._4hr_repl.1

description: C57BL/6_Blood_20% HPbCD_._4hr


title: human brain vascular pericyte cell line (HBVP)

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

data_processing:
The sequence reads were aligned to the human genome (GRCh38) using Tophat2 software (version 2.1.1).  The gene counts were summarized using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with counts values for each sample

source_name: Brain

extract_protocol:
RNA was extracted from sub-confluent 10-cm plates using RNeasy mini kit (Qiagen, Cat No. 74104). RNA quality (RNA integrity number, RIN) and quantity was measured in a Bioanalyzer 2100 (Agilent) using the Agilent RNA 6000 Nano Kit (part number 5067-1511).
The sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S, New England Biolabs), with 200 ng of total RNA as input.

value: Brain

tag: age

value: adult


title: Balb/c_Spleen_TAK-981-001-J_7.5 mg/kg_8hr_repl.3

value: Balb/c

value: 7.5 mg/kg


title: human brain cell line 940

description: human brain cell line 940

tag: tissue


title: Balb/c_Spleen_TAK-981-001-J_7.5 mg/kg_8hr_repl.2


title: Balb/c_Spleen_TAK-981-001-J_7.5 mg/kg_8hr_repl.1


title: human brain cell line 622

description: human brain cell line 622


title: Balb/c_Spleen_TAK-981-001-J_7.5 mg/kg_4hr_repl.3


title: human brain cell line 787

description: human brain cell line 787


title: human brain cell line 618

description: human brain cell line 618


title: Balb/c_Spleen_TAK-981-001-J_7.5 mg/kg_4hr_repl.1


title: Balb/c_Spleen_TAK-981-001-J_7.5 mg/kg_4hr_repl.2


title: human brain cell line 619

description: human brain cell line 619


title: Balb/c_Spleen_TAK-981-001-J_15.0 mg/kg_8hr_repl.3


title: Balb/c_Spleen_TAK-981-001-J_15.0 mg/kg_8hr_repl.2


title: C57BL/6_Blood_20% HPbCD_._4hr_repl.3

description: C57BL/6_Blood_20% HPbCD_._4hr

value: 20% HPbCD


title: human brain cell line 556

description: human brain cell line 556


title: human brain cell line 496

description: human brain cell line 496


title: Balb/c_Spleen_TAK-981-001-J_15.0 mg/kg_8hr_repl.1


title: Balb/c_Spleen_TAK-981-001-J_15.0 mg/kg_4hr_repl.3


title: human brain cell line 489

description: human brain cell line 489


title: Balb/c_Spleen_TAK-981-001-J_15.0 mg/kg_4hr_repl.1


title: human brain cell line 350

description: human brain cell line 350


title: Balb/c_Spleen_TAK-981-001-J_15.0 mg/kg_4hr_repl.2


title: Balb/c_Spleen_20% HPbCD_._8hr_repl.3

description: Balb/c_Spleen_20% HPbCD_._8hr


title: human brain cell line 333

description: human brain cell line 333


title: human brain cell line 347

description: human brain cell line 347


title: human brain cell line 810

description: human brain cell line 810


title: human brain cell line 281

description: human brain cell line 281


title: Balb/c_Spleen_20% HPbCD_._8hr_repl.2

description: Balb/c_Spleen_20% HPbCD_._8hr


title: Balb/c_Spleen_20% HPbCD_._8hr_repl.1

description: Balb/c_Spleen_20% HPbCD_._8hr


title: human brain cell line 238

description: human brain cell line 238


title: Balb/c_Spleen_20% HPbCD_._4hr_repl.3

description: Balb/c_Spleen_20% HPbCD_._4hr


title: human brain cell line 234

description: human brain cell line 234


title: human brain cell line 273

description: human brain cell line 273


title: Balb/c_Spleen_20% HPbCD_._4hr_repl.2

description: Balb/c_Spleen_20% HPbCD_._4hr


title: Balb/c_Spleen_20% HPbCD_._4hr_repl.1

description: Balb/c_Spleen_20% HPbCD_._4hr


title: human brain cell line 339

description: human brain cell line 339


title: Balb/c_Tumor(A20)_TAK-981-001-J_7.5 mg/kg_8hr_repl.2


title: Input Decitabine

city: Los Angeles

first: Jiong

last: Li

state: CA - California

department: School of Dentistry

institute: UCLA

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.2.0.
The unique mapped reads was used for peak calling by MACS2 with default setting
Supplementary_files_format_and_content: wig file

source_name: Bladder cancer cells

growth_protocol: 10% FBS in DMEM

extract_protocol:
10–50 mg of genomic DNA for each sample was sonicated and used for the ligation of barcoded Illumina adapters. A total of 5 mg adaptor ligated DNA was used for immunoprecipitation by 5-Methylcytosine (5-mC) Rabbit mAb (Cell Signaling 28692S).
Sequencing libraries were generated using a DNA SMART ChIP-Seq Kit (Clonetech 634865) and pooling immunoprecipitated DNA from 3 independent samples.

treatment_protocol: 5637 cells were treated with 100nM DEC or with DEC and cisplatin combined daily for 72 hours

tag: cell line

value: 5637 cells

tag: chip antibody

tag: agent

value: Decitabine


title: Input Decitabine and Cisplatin

value: Decitabine and Cisplatin


title: Decitabine and Cisplatin

value: 5-Methylcytosine (5-mC) Rabbit mAb (Cell Signaling 28692S)


title: Mock

value: Mock


title: M. viscosa challenged, vaccinated, spleen, fish 20

value: Spleen

value: Vaccine

value: Moritella viscosa


title: M. viscosa challenged, vaccinated, spleen, fish 22


title: M. viscosa challenged, vaccinated, spleen, fish 18


title: Balb/c_Blood_TAK-981-001-J_7.5 mg/kg_8hr_repl.3

tag: time point


title: Input Mock


title: Balb/c_Blood_TAK-981-001-J_7.5 mg/kg_8hr_repl.2


title: Balb/c_Blood_TAK-981-001-J_7.5 mg/kg_8hr_repl.1


title: A20-TAK-3

source_name: cell line

value: 1 uM

tag: timepoint


title: A20-TAK-2


title: Balb/c_Tumor(A20)_TAK-981-001-J_7.5 mg/kg_4hr_repl.3


title: Balb/c_Tumor(A20)_TAK-981-001-J_7.5 mg/kg_4hr_repl.2


title: Balb/c_Tumor(A20)_TAK-981-001-J_7.5 mg/kg_8hr_repl.3


title: Decitabine


title: M. viscosa challenged, saline, spleen, fish 13

value: Saline


title: M. viscosa challenged, vaccinated, skin, fish 22

source_name: Skin

value: Skin


title: M. viscosa challenged, vaccinated, spleen, fish 14


title: M. viscosa challenged, saline, spleen, fish 24


title: M. viscosa challenged, saline, spleen, fish 14


title: M. viscosa challenged, saline, spleen, fish 4


title: M. viscosa challenged, vaccinated, skin, fish 20


title: Balb/c_Blood_TAK-981-001-J_7.5 mg/kg_4hr_repl.3


title: M. viscosa challenged, vaccinated, skin, fish 18


title: Balb/c_Tumor(A20)_TAK-981-001-J_7.5 mg/kg_4hr_repl.1


title: Balb/c_Blood_TAK-981-001-J_7.5 mg/kg_4hr_repl.2


title: B16F10-TAK-3


title: A20-TAK-1


title: A20-veh-6

value: DMSO


title: Balb/c_Blood_TAK-981-001-J_7.5 mg/kg_4hr_repl.1


title: A20-veh-5


title: Balb/c_Tumor(A20)_TAK-981-001-J_7.5 mg/kg_8hr_repl.1


title: Balb/c_Tumor(A20)_TAK-981-001-J_5.0 mg/kg_8hr_repl.3

value: 5.0 mg/kg


title: B16F10-TAK-2


title: Balb/c_Tumor(A20)_TAK-981-001-J_5.0 mg/kg_8hr_repl.2


title: B16F10-TAK-1


title: M. viscosa challenged, saline, skin, fish 24


title: M. viscosa challenged, saline, skin, fish 13


title: M. viscosa challenged, saline, skin, fish 4


title: M. viscosa challenged, vaccinated, head kidney, fish 22

source_name: Head kidney

value: Head kidney


title: M. viscosa challenged, vaccinated, head kidney, fish 20


title: B16F10-veh-5


title: Balb/c_Blood_TAK-981-001-J_5.0 mg/kg_8hr_repl.2

value: Balb/c


title: Balb/c_Tumor(A20)_TAK-981-001-J_5.0 mg/kg_8hr_repl.1


title: M. viscosa challenged, saline, skin, fish 14


title: B16F10-veh-6


title: MC38-TAK-3


title: B16F10-veh-4


title: MC38-TAK-2


title: MC38-TAK-1


title: M. viscosa challenged, vaccinated, head kidney, fish 18


title: Balb/c_Blood_TAK-981-001-J_5.0 mg/kg_8hr_repl.1


title: Balb/c_Tumor(A20)_TAK-981-001-J_5.0 mg/kg_4hr_repl.2


title: Balb/c_Tumor(A20)_TAK-981-001-J_5.0 mg/kg_4hr_repl.3


title: M. viscosa challenged, vaccinated, head kidney, fish 14


title: M. viscosa challenged, saline, head kidney, fish 13


title: M. viscosa challenged, saline, head kidney, fish 14


title: M. viscosa challenged, saline, head kidney, fish 24


title: Balb/c_Blood_TAK-981-001-J_5.0 mg/kg_8hr_repl.3


title: M. viscosa challenged, saline, head kidney, fish 4


title: Balb/c_Blood_TAK-981-001-J_5.0 mg/kg_4hr_repl.3


title: MC38-veh-5


title: SAV challenged, vaccinated, spleen, fish 1

value: Salmon alphavirus


title: Balb/c_Blood_TAK-981-001-J_5.0 mg/kg_4hr_repl.2


title: MC38-veh-4


title: SAV challenged, vaccinated, spleen, fish 12


title: Balb/c_Blood_TAK-981-001-J_5.0 mg/kg_4hr_repl.1


title: Balb/c_Tumor(A20)_TAK-981-001-J_2.5 mg/kg_8hr_repl.3

value: 2.5 mg/kg


title: CT26-TAK-3


title: CT26-TAK-2


title: Balb/c_Tumor(A20)_TAK-981-001-J_5.0 mg/kg_4hr_repl.1


title: SAV challenged, vaccinated, spleen, fish 11


title: CT26-veh-6


title: Balb/c_Tumor(A20)_TAK-981-001-J_2.5 mg/kg_8hr_repl.2


title: CT26-TAK-1


title: Balb/c_Blood_TAK-981-001-J_2.5 mg/kg_8hr_repl.3


title: SAV challenged, saline, spleen, fish 14


title: SAV challenged, saline, spleen, fish 11


title: CT26-veh-5


title: M. viscosa challenged, vaccinated, skin, fish 14


title: SAV challenged, vaccinated, spleen, fish 10


title: SAV challenged, saline, spleen, fish 15


title: CT26-veh-4


title: Balb/c_Blood_TAK-981-001-J_2.5 mg/kg_8hr_repl.2


title: MC38-veh-6


title: Balb/c_Tumor(A20)_TAK-981-001-J_2.5 mg/kg_8hr_repl.1


title: Balb/c_Tumor(A20)_TAK-981-001-J_2.5 mg/kg_4hr_repl.2


title: Balb/c_Blood_TAK-981-001-J_2.5 mg/kg_8hr_repl.1


title: Neuro-2a soma 3

city: Haifa

first: Martin

last: Mikl

address: Abba Khoushy 199

department: Department of Human Biology

institute: University of Haifa

data_processing:
Library strategy: Amplicon sequencing
bcl2fastq v2.20
fastq files (read 2) were mapped to the synthetic library variants (library sequences contained in processed data file) using custom-made python scripts
UMIs per library variant were determined from read 1 using custom-made python scripts and reported in the processed data file
Genome_build: no mapping against a genome (synthetic library)
Supplementary_files_format_and_content: One csv file containing the sequences of the synthetic library and counts for each library variant in all 12 samples

source_name: Neuro-2a cell line

extract_protocol:
Soma and neurite fractions were collected and RNA isolated using the Zymo Direct-ZOL RNA Miniprep kit followed by cDNA synthesis using Invitrogen SuperScriptIV, both according to the manufacturer's protocol.
A first PCR reaction was performed (using Kapa Hifi Ready mix) to specifically amplify reporter cDNA (15=20 cycles). In a second PCR step, Illumina adapters were added (12 cycles).

tag: compartment

value: soma

tag: biological replicate


title: SAV challenged, saline, spleen, fish 1


title: SAV challenged, vaccinated, head kidney, fish 10


title: Neuro-2a soma 2


title: Balb/c_Blood_TAK-981-001-J_2.5 mg/kg_4hr_repl.3


title: Neuro-2a neurite 2

value: neurite


title: Neuro-2a neurite 1


title: Balb/c_Blood_TAK-981-001-J_2.5 mg/kg_4hr_repl.2


title: SAV challenged, saline, head kidney, fish 14


title: Balb/c_Blood_TAK-981-001-J_2.5 mg/kg_4hr_repl.1


title: SAV challenged, vaccinated, head kidney, fish 12


title: Neuro-2a soma 1


title: CAD neurite 2

source_name: CAD cell line

value: CAD


title: CAD neurite 3


title: SAV challenged, saline, head kidney, fish 15


title: SAV challenged, vaccinated, head kidney, fish 13


title: SAV challenged, saline, head kidney, fish 11


title: Balb/c_Tumor(A20)_TAK-981-001-J_15.0 mg/kg_8hr_repl.3


title: Balb/c_Tumor(A20)_TAK-981-001-J_2.5 mg/kg_4hr_repl.3


title: CAD neurite 1


title: SAV challenged, vaccinated, head kidney, fish 11


title: Balb/c_Tumor(A20)_TAK-981-001-J_15.0 mg/kg_8hr_repl.2


title: SAV challenged, saline, head kidney, fish 10


title: Before challenge, vaccinated, spleen, fish 4

value: Before challenge


title: Balb/c_Tumor(A20)_TAK-981-001-J_15.0 mg/kg_8hr_repl.1


title: Balb/c_Tumor(A20)_TAK-981-001-J_2.5 mg/kg_4hr_repl.1


title: CAD soma 3


title: Balb/c_Blood_TAK-981-001-J_15.0 mg/kg_8hr_repl.3


title: CAD soma 1


title: Balb/c_Blood_TAK-981-001-J_15.0 mg/kg_8hr_repl.2


title: Before challenge, vaccinated, spleen, fish 2


title: Balb/c_Blood_TAK-981-001-J_15.0 mg/kg_8hr_repl.1


title: Neuro-2a neurite 3


title: Balb/c_Tumor(A20)_TAK-981-001-J_15.0 mg/kg_4hr_repl.3


title: CD34pos_N1AcSpd_2 [RNA-seq]

city: Cologne

first: Franziska

last: Metge

address: Joseph-Stelzmann-Str 9b

department: Bioinformatics Corefacility

country: Germany

institute: Max Planck Institute for Biology of Ageing

description:
processed data file:
rnaSeq_counts.tsv
differential_translation.CD34neg_N1AcSpd.vs.CD34pos_N1AcSpd.results.tsv
differential_translation.CD34pos.vs.CD34pos_N1AcSpd.results.tsv

data_processing:
adapters were trimmed using flexbar version 3.0.3 (-as TGGAATTCTCGGGTGCCAAGG  -at 0.2  -q TAIL -qt 25 -u 5 )
RNA-seq:
trimmed reads were are mapped to the genome using STAR version 2.7.3a
transcript abundance was estimated using featureCounts version v2.0.0
Ribo-Seq:
Trimmed reads aligning to t-rna and r-rna were removed using bowtie version 1.2.3 (bowtie -v2 small_rna –un cleaned.fastq > /dev/null)
remaining reads were are mapped to the genome using STAR version 2.7.3a
Ribo-Seq data was analyzed using R-packages riboWaltz (1.1.0)
differential translation was calculated using R-package Riborex (2.4.0)
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: counts, differential_translation results

growth_protocol: 3D-3C organoid cultures were cultured for 2 weeks and sorted to obtain alpha6+CD34- and alpha6+CD34+ cells

extract_protocol:
RNA-seq: Sorted cells were frozen in liquid nitrogen and lyszed in 300µl lysis buffer (10mM NaCl, 10mM MgCl2, 10mM Tris-HCl pH7.5, 1% triton X-100, 1% sodium deoxycholate, 1mM DTT, 0.1mg/ml cycloheximide). 1µg of total RNA was extracted using the Direct-zol RNA Microprep Kit (Zymo Research) according to manufacturer's instruction.
RNA-seq: Libraries were prepared using the NEBNext® UltraTM RNA Library Preparation Kit for Illumina (NEB) including hybridization-based ribo depletion according to manufacturer’s instructions. Library validation and quantification were performed using TapeStation analysis (Agilent). Equimolar amounts of the library were pooled. The pool was quantified using the KAPA Library Quantification Kit (Peqlab) and the ABI Prism® 7900HT Sequence Detection System (Applied Biosystems) and sequenced on an Illumina NovaSeq6000 sequencer.
Ribo-Seq: Sorted cells were frozen in liquid nitrogen and lyszed in 300µl lysis buffer (10mM NaCl, 10mM MgCl2, 10mM Tris-HCl pH7.5, 1% triton X-100, 1% sodium deoxycholate, 1mM DTT, 0.1mg/ml cycloheximide). For the isolation of ribosome-protected fragments, the samples were incubated with RNase I and S7. Ribosomal proteins were digested by proteinase K for 1h at 65°C. RNA fragments were purified by acid-phenol:chloroform extraction and precipitated by the addition of cold ethanol.
Ribo-Seq: The fragmented RNA pellets were resuspended in nuclease free water and treated with T4 Polynucleotide kinase (NEB) for 90 min at 37°C. Size selection of the fragmented RNA was performed using PAGE. Gel slices in the range of 24 36 nt were excised using X Tracta Tips (Biozym). After purification, RNA fragments were resuspended in nuclease free water. Sequencing libraries were prepared using the Small RNA Seq Library Prep Kit (Lexogen) according to manufacturer’s instructions. Amplification was done using 16 PCR cycles. The pool of all libraries was size-selected using the BluePippin device (SAGE-Science) with a 3% DF Marker Q3 Kit (SAGE-Science). The range of 135 180 bp was selected. The pool was quantified using the KAPA Library Quantification Kit (Peqlab) and the ABI Prism® 7900HT Sequence Detection System (Applied Biosystems) and sequenced on an Illumina NovaSeq6000 sequencer.

treatment_protocol: w/ or w/o 72h N1-acetylspermidine

tag: mouse id

value: HFSC organoid culture

tag: cell subtype

value: N1-acetylspermidine for 72h


title: Before challenge, saline, spleen, fish 4

value: Spleen

tag: challenge


title: Balb/c_Tumor(A20)_TAK-981-001-J_15.0 mg/kg_4hr_repl.2


title: CD34neg_N1AcSpd_2 [RNA-seq]

description:
processed data file:
rnaSeq_counts.tsv
differential_translation.CD34neg_N1AcSpd.vs.CD34pos_N1AcSpd.results.tsv
differential_translation.CD34neg.vs.CD34neg_N1AcSpd.results.tsv


title: Before challenge, saline, spleen, fish 3


title: Balb/c_Tumor(A20)_TAK-981-001-J_15.0 mg/kg_4hr_repl.1


title: Before challenge, vaccinated, spleen, fish 1

value: Vaccine


title: CD34pos_2 [RNA-seq]

description:
processed data file:
rnaSeq_counts.tsv
differential_translation.CD34neg.vs.CD34pos.results.tsv
differential_translation.CD34pos.vs.CD34pos_N1AcSpd.results.tsv


title: Before challenge, saline, spleen, fish 2


title: Balb/c_Blood_TAK-981-001-J_15.0 mg/kg_4hr_repl.2


title: Balb/c_Blood_TAK-981-001-J_15.0 mg/kg_4hr_repl.3


title: Before challenge, vaccinated, spleen, fish 3


title: Before challenge, saline, spleen, fish 1


title: Balb/c_Blood_TAK-981-001-J_15.0 mg/kg_4hr_repl.1


title: CD34neg_2 [RNA-seq]

description:
processed data file:
rnaSeq_counts.tsv
differential_translation.CD34neg.vs.CD34pos.results.tsv
differential_translation.CD34neg.vs.CD34neg_N1AcSpd.results.tsv


title: CD34pos_1 [RNA-seq]


title: Before challenge, vaccinated, skin, fish 4


title: CD34pos_N1AcSpd_1 [RNA-seq]


title: Balb/c_Tumor(A20)_20% HPbCD_._8hr_repl.3

description: Balb/c_Tumor(A20)_20% HPbCD_._8hr

value: 20% HPbCD


title: CD34neg_1 [RNA-seq]


title: Before challenge, vaccinated, skin, fish 1


title: CAD soma 2


title: CD34neg_N1AcSpd_1 [RNA-seq]


title: Before challenge, vaccinated, skin, fish 3


title: CD34pos_N1AcSpd_2 [Ribo-seq]

description:
processed data file:
riboSeq_counts.tsv
differential_translation.CD34neg_N1AcSpd.vs.CD34pos_N1AcSpd.results.tsv
differential_translation.CD34pos.vs.CD34pos_N1AcSpd.results.tsv


title: CD34pos_2 [Ribo-seq]

description:
processed data file:
riboSeq_counts.tsv
differential_translation.CD34neg.vs.CD34pos.results.tsv
differential_translation.CD34pos.vs.CD34pos_N1AcSpd.results.tsv


title: Balb/c_Blood_20% HPbCD_._8hr_repl.3

description: Balb/c_Blood_20% HPbCD_._8hr


title: Before challenge, vaccinated, skin, fish 2


title: Balb/c_Tumor(A20)_20% HPbCD_._8hr_repl.2

description: Balb/c_Tumor(A20)_20% HPbCD_._8hr


title: Balb/c_Tumor(A20)_20% HPbCD_._8hr_repl.1

description: Balb/c_Tumor(A20)_20% HPbCD_._8hr


title: CD34neg_2 [Ribo-seq]

description:
processed data file:
riboSeq_counts.tsv
differential_translation.CD34neg.vs.CD34pos.results.tsv
differential_translation.CD34neg.vs.CD34neg_N1AcSpd.results.tsv


title: Before challenge, saline, skin, fish 2

value: Saline


title: CD34neg_N1AcSpd_2 [Ribo-seq]

description:
processed data file:
riboSeq_counts.tsv
differential_translation.CD34neg_N1AcSpd.vs.CD34pos_N1AcSpd.results.tsv
differential_translation.CD34neg.vs.CD34neg_N1AcSpd.results.tsv


title: CD34pos_N1AcSpd_1 [Ribo-seq]


title: Before challenge, saline, skin, fish 3

value: Skin


title: Before challenge, saline, skin, fish 4


title: CD34pos_1 [Ribo-seq]


title: A20-veh-4

value: DMSO


title: Balb/c_Tumor(A20)_20% HPbCD_._4hr_repl.2

description: Balb/c_Tumor(A20)_20% HPbCD_._4hr


title: Index7OtC3513+cells-mice

city: Lubbock

first: Beverly

middle: S

last: Chilton

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

description:
rRNA depleted
Index7_Otc3513

data_processing:
Paired-end 106 nucleotide reads were subjected to species-specific mapping against the mouse (mm10) and human (hg38) reference genomes
sequencing depth was a minimum of 40 million reads
Comparison of expression (fpkm_tracking) and differential expression analysis was conducted withcufflinks.cuffdiff (2.2.1).
Exon quantification was performed to show the relative expression of all known HLTF/Hltf exons in control tumr and control microenvironment (mouse)
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: tab-delimited text files for RPKM vlaues for human and mouse for each sample

organism:
Homo sapiens
Mus musculus

source_name: primary CDX tumor

extract_protocol:
primary CDX tumor x 3 biological replicates for test and control mice = 6 total samples were flashfrozen and sent to Otogenetics for RNAseq
Random-primed cDNA (rRNA depleted) using standard Illumina Protocols

value: human tumor and mouse microenvironment cells

tag: host mouse background strain

tag: human cell line

value: HCT116 cells HLTF+/+

tag: mouse genotype

value: test Hltf -/- mouse


title: Index5OtC3511+cells-mice

description:
rRNA depleted
Index5_OtC3511


title: Balb/c_Blood_20% HPbCD_._8hr_repl.2

description: Balb/c_Blood_20% HPbCD_._8hr

tag: strain

value: Balb/c

tag: treatment

tag: dosage


title: Acvr2aPRcre_4

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

data_processing:
Sequenced reads in FASTQ files were mapped to mm10 whole genome using HISAT2 (Galaxy tool version 2.1.0). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.2).  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: mouse uterine tissues

growth_protocol: For fertility analyses, 6-week-old female mice were mated to WT males of proven fertility for 6 months and the total number of pups was quantified. Smad1flox/flox and Smad5flox/flox mice were previously generated and described. To generate Smad1/5 cKO females, female mice carrying homozygous Smad1flox/flox; Smad5flox/flox alleles were crossed to males carrying the double Smad1flox/flox; Smad5flox/flox alleles and the progesterone receptor-cre (PRcre/+). A similar breeding scheme was used to generate Acvr2aflox/flox-PRcre/+ and Acvr2bflox/flox-PRcre/+ mice using Acvr2aflox/flox and Acvr2bflox/flox mice that were generated in collaboration with Dr. Se-Jin Lee. The mice were maintained on a hybrid C57BL/6J and 129S5/SvEvBrd genetic background. Animal handling and experimental studies were performed following the NIH Guide for the Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committee of Baylor College of Medicine.

extract_protocol:
Uterine tissues were collected from control, Smad1/5 cKO, and Acvr2a cKO mice at 3.5dpc of pseudopregnancy and immediately snap frozen on dry ice or fixed in formalin. Mice were determined to be 3.5dpc pseudopregnant according to the levels of serum progesterone. RNA was extracted from the tissues, processed in Trizol and isolated with the Direct-zol RNA extraction kit (Zymo).
Quality control of the samples was determined by assessing the RNA Integrity Number (RIN) and then used for library preparation and sequencing. Sequencing (>20M reads per sample) was performed by Novogene Corporation (Santa Cruz, CA), on the Illumina Platform (PE150).

tag: tissue

value: uterine

tag: genotype/variation


title: Before challenge, vaccinated, head kidney, fish 1

value: Head kidney


title: Balb/c_Blood_20% HPbCD_._8hr_repl.1

description: Balb/c_Blood_20% HPbCD_._8hr


title: Before challenge, saline, head kidney, fish 4


title: Balb/c_Tumor(A20)_20% HPbCD_._4hr_repl.3

description: Balb/c_Tumor(A20)_20% HPbCD_._4hr


title: Index14OtC3222+cells+mice

description:
rRNA depleted
Index14_OtC3222

value: control Hltf +/+ mouse


title: Before challenge, vaccinated, head kidney, fish 4


title: CD34neg_N1AcSpd_1 [Ribo-seq]

tag: cell type


title: Before challenge, saline, skin, fish 1


title: CD34neg_1 [Ribo-seq]


title: Before challenge, vaccinated, head kidney, fish 3


title: Before challenge, vaccinated, head kidney, fish 2


title: Balb/c_Blood_20% HPbCD_._4hr_repl.3

description: Balb/c_Blood_20% HPbCD_._4hr


title: Index15OtC3223+cells+mice

description:
rRNA depleted
Index15_OtC3223


title: Before challenge, saline, head kidney, fish 1


title: Before challenge, saline, head kidney, fish 3


title: RPF replicate 3

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

description: ribosome-protected mRNA fragments

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10
Genome read mapping using bowtie (1.2.2), parameters: -l 16 -n 1 -e 50 -m 1—strata—best y
Read counting using bedtools, version 2.17.0, parameter: -s
Genome_build: U00096.3, NCBI
Supplementary_files_format_and_content: Unique read counts per gene and million mapped reads RPM

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: Cells were cultured in LB medium and collected at OD600 of 0.5.

extract_protocol:
Cells were freeze-ruptured (Retch Mill) and 100 A260 units of ribosome-bound mRNA complex was digested with micrococal nuclease (10 units/µl, Fermentas) for 10 min, RT in 10 mM Tris pH 9.2 containing 50 mM NH4Cl, 10 mM MgCl2, 0.2% triton X-100 and 20 mM CaCl2 to obtain monosomes.
RNA-size selection and generation of the cDNA libraries was performed as described (Ingolia et al, 2009; doi: 10.1126/science.1168978). Frgments with a size of 20-35-nt RNA were size selected on a denaturing 15% polyacrylamide gel.

tag: passenge


title: Acvr2aPRcre_2


title: Acvr2aPRcre_1


title: AF357425_Low_RIP_Seq

description: RNA from Fibrillarin pulldown

data_processing:
Raw FASTQ files of long RNAseq samples and RIPseq samples was processed using the LUMC BioWDL RNAseq pipeline version 1.1.0 (https://github.com/biowdl/RNA-seq/tree/v1.1.0), which comprises FASTQ preprocessing, alignment and read quantification.
Cutadapt (version 2.4) was used for adapters clipping.
Reads were further aligned to the mouse reference genome GRCm38 using the STAR aligner (version 2.6.0c)
Gene raw read quantification was performed using htseq-count (v0.9.1) with the Ensembl mouse gene annotation version 96.
StringTie (v1.3.4) was used to calculate transcripts per million (TPM) of all genes with default settings.
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV, raw read count generated by Htseq-count

source_name: Ear

growth_protocol: Fibroblasts were isolated from ear-clippings of C57BL/6 mice. Cells were expanded using culture media (DMEM with 10% heat-inactivated fetal calf serum and 1% PenStrep).

extract_protocol:
After transfection, RNA from whole cell lysates (Long RNA seq) or from fibrillarin pulldown (RIP-seq), was isolated by standard TRIzol-chloroform extraction. Ribosomal RNA depletion was performed on RIP-seq samples prior to sequencing.
Long RNA library (H/M/R) and RIP RNA library (B08)
DNBseq Eukaryotic Long RNA and Eukaryotic Transcriptome resequencing

treatment_protocol: Cells were cultured for 48 hours with KN93 to synchronize the cell cycle and subsequently transfected with gapmers against AF357425 or a scrambled control for 24 hours

value: Primary ear fibroblasts

tag: rip antibody

value: Fibrillarin Antibody Abcam, Cat. Nr. ab5821

value: AF357425 inhibition


title: Balb/c_Blood_20% HPbCD_._4hr_repl.1

description: Balb/c_Blood_20% HPbCD_._4hr

tag: time point


title: AF357425_Low_Long_RNA_Seq

description: Total RNA


title: Before challenge, saline, head kidney, fish 2

value: Before challenge


title: Smad1/5 Prcre_4

value: Smad1/5 Prcre


title: Balb/c_Blood_20% HPbCD_._4hr_repl.2

description: Balb/c_Blood_20% HPbCD_._4hr


title: AF357425_High_RIP_Seq

description: RNA from Fibrillarin pulldown

value: AF357425 overexpression


title: MET-3

city: Beijing

first: Ping

address: Yong An Road No.95

institute: Beijing Friendship Hospital

hyb_protocol: standard Affymentrix protocol

scan_protocol: standard Affymentrix protocol

data_processing:
Affymetrix® Expression Console™ software (v.1.0)
Partek Genomics Suite 6.6
RMA normalization
Histogram analysis and PCA analysis
Differentially Expressed Genes Between Groups
raw CEL data for each gene and each sample

label: biotin

source_name: Hepatic progenitor cells

label_protocol: standard Affymentrix protocol

growth_protocol: Hepatic progenitor cells were cultured in 10%FBS DMEM/F12 with 1ng/ml EGF and 0.5ng/ml SCF.

extract_protocol:
Total RNA was isolated by TRIzol Reagent and RNA Neasy Mini Kit.
Target prepared by GeneChip WT PLUS Reagent kit.

treatment_protocol: Hepatic progenitor cells were treated with 1ng/ml TGF-b1 in 10%FBS DMEM/F12 for 16 days to induce epithelial-mesenchymal transition.  The 16-day TGF-b1-treated cells were cultured in 10%FBS DMEM/F12 with 1ng/ml EGF and 0.5ng/ml SCF for 7 days to induce mesenchymal-epithelial transition.

value: In vitro cultured hepatic progenitor cells

value: SD Rat


title: RPF replicate 2

description: ribosome-protected mRNA fragments


title: Sea gooseberry tissue (Sample1830)

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (3D-DNA, Juicer)
Centromere position identification (repeat sequence mapping or structural analysis, 3D-DNA/JBAT)
Aggregate chromosome analysis (3D-DNA)
Variant calling (DRAGEN pipeline)
Chromosome-length variant phasing (3D-DNA)
Genome_build: In addition to those generate as part of the study, the following existing genome builds were used: GRCg6a (domestic chicken); Xla.v91 (African clawed frog); AaegL5.0 (Yellow fever mosquito), CpipJ3 (Southern domestic mosquito); Release_6_plus_ISO1_MT (fruit fly, with chromosome arms merged for ACA analysis resulting in Release_6_plus_ISO1_MT_merged); WBcel235 (C. elegans); sacCer3 (baker's yeast); arahy.Tifrunner.gnm2.J5K5 (ground nut); 161010_Chinese_Spring_v1.0_pseudomolecules (bread wheat).
Supplementary_files_format_and_content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary_files_format_and_content: hic: contact maps generated by aligning Hi-C data to corresponding chromosome-length reference sequences. In addition to standard contact maps generated for all genomic positions across chromosomes the uploaded files include ACA (aggregate chromosome analysis) maps and phasing contact maps representing interactions between positions on the genome that contain heterogyzous SNPs. For more details see Hoencamp et al., Supplement.
Supplementary_files_format_and_content: wig: tracks showing the alignment frequency of Hi-C reads from read pairs that contain centromere repeat-specifc sequences.
Supplementary_files_format_and_content: bedpe: Files describing the tentative position of centromeres in chromosome-length genome assemblies, identified either by mapping repeat sequences associated with the centromere or via analysis of the contact map for evidence of centromere-to-telomere folding axis. For details see Hoencamp et al., Supplement.
Supplementary_files_format_and_content: vcf.gz: Variants (specifically SNPs) identivied by the DRAGEN variant calling pipeline from aligning Hi-C data to chromosome-length references generated via Hi-C-guided assembly and phased using the 3D-DNA Hi-C-guided phasing module.

organism: Pleurobrachia bachei

source_name: tissue

extract_protocol:
Extraction protocol is described as part of the library construction protocol.
The Hi-C libraries were prepared following the in situ Hi-C strategy (Rao, Huntley et al., 2014). Briefly, cells or tissue were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. Afterward DNA was handled according to standard Illumina library construction protocol. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on various Illumina instruments following the manufacturer's protocols. Fpr the tammar wallaby, a short insert-size PCR-free DNA-Seq library was prepared following the ClaSeek protocol.

value: tissue


title: Smad1/5 Prcre_3


title: Smad1/5 Prcre_2


title: Smad1/5 Prcre_1


title: FL12: Rat liver - fibrosis

city: 成都

first: 熊

last: 肖

address: 四川省成都市文江区万春镇

institute: 成都中医药大学附属第五人民医院

data_processing:
Using next-generation sequencing technology to perform RNA-seq analysis on an Illumina genome analyzer IIx.
The original reads containing more than 2-N bases were first discarded. Short reads of less than 16nt, the adapters and low-quality bases in the original sequencing reads were removed by the FASTX-Toolkit (Version 0.0.13).
Clean Reads was compared with the GRCH38 genome using TopHat2 allowing 4 mismatches.
Unique locational reads were used for gene reads count and FPKM (number of locational fragments per million segments per 1000 base transcript)
Genome_build: GRch38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Rattus norvegicus

source_name: Rat liver

extract_protocol:
TRIzol (Invitrogen, Carlsbad, California, USA) was used to extracted total RNA from rat liver tissues, and purified by the manufacturer's instructions.
Utilize NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, Ma, USA) to quantify total RNA and according Agilent 2100 system and RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA) to determine RNA integrity. To achieve accurate lncRNA analysis, the Ribosomal RNA was removed using the Thermo Fisher Scientific Central Ribonucleic Acid Removal Kit. Using next-generation sequencing technology to perform RNA-seq analysis on an Illumina genome analyzer IIx.

value: liver

tag: disease state

value: fibrosis


title: FF Control_3

value: Control


title: FL5: Rat liver - fibrosis

address: 四川省成都市文江区万春镇

institute: 成都中医药大学附属第五人民医院


title: RPF replicate 1

description: ribosome-protected mRNA fragments


title: MET-2


title: FF Control_2


title: AF357425_High_Long_RNA_Seq

description: Total RNA


title: FF Control_1


title: Brownbanded bamboo shark blood (Sample1575)

organism: Chiloscyllium punctatum

source_name: blood

value: blood


title: OVC EMT-3

value: 1ng/ml TGF-beta1


title: Burmese python blood (Sample0838)

organism: Python bivittatus


title: CL6: Rat liver - normal

address: 四川省成都市文江区万春镇

institute: 成都中医药大学附属第五人民医院

value: normal


title: OVC EMT-1


title: CONT-2


title: Gfap sgPlxnb1 3

status: Public on Apr 22 2021

city: Boston

first: Michael

last: Wheeler

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
The reads are aligned to GrCM38 mouse genome using STAR (2.7.3)
The aligned reads were quantified using RSEM (v1.3)
Genome_build: GrCM38
Supplementary_files_format_and_content: Tab delimited gene expression table

organism: Mus musculus

source_name: Flow cytometry sorted astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were created according to the manufacturer's protocol for the NEB kit (#E6420)

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: WT C57Bl/6

tag: Sex

value: Female


title: FL2: Rat liver - fibrosis

address: 四川省成都市文江区万春镇

institute: 成都中医药大学附属第五人民医院


title: Itgam sgSema4d 2


title: CL7: Rat liver - normal

address: 四川省成都市文江区万春镇

institute: 成都中医药大学附属第五人民医院


title: Gfap sgPlxnb1 1


title: Gfap sgPlxnb2 2


title: Gfap sgPlxnb2 1


title: Chinese muntjac blood (Sample1296)

organism: Muntiacus reevesi