title: 1_18

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_18


title: 1_17

status: Public on Feb 28 2022

type: protein

city: Philadelphia

first: Scott

last: Canna

address: The Children’s Hospital of Philadelphia Department of Pediatrics Philadelphia

country: USA

institute: Children's Hospital of Philadelphia

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_17

hyb_protocol: Somalogic standard protocol

scan_protocol: Somalogic standard protocol

data_processing: Post-normalization, all samples met predefined acceptance criteria and were included in the analysis. A complete description of the normalization and calibration procedures is available at: www.somalogic.com/wp-content/uploads/2017/03/SSM-071-Rev-0-Technical-Note-SOMAscan-Data-Standardization.pdf.

molecule: protein

organism: Homo sapiens

source_name: sJIA/MAS/ILD

label_protocol: Somalogic standard protocol

extract_protocol: not provided

tag: tissue

value: serum

tag: disease

value: sJIA-LD

tag: Sex

value: M

tag: age(year)

tag: hospital

value: NIH

tag: sample quality hemolysis score


title: 1_16

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_16

source_name: sJIA/ILD


title: 4_17

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
4_17

value: Active sJIA, no MAS

value: F

value: Stanford


title: 1_15

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_15


title: 1_13

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_13

source_name: sJIA/severe ILD


title: 1_11

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_11


title: 1_12

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_12


title: 1_14

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_14


title: SCC_NodalMet [D678]

type: SRA

city: Omaha

first: Marissa

last: Lobl

state: NE

address: 4014 Leavenworth St.

institute: UNMC

description:
D678
tumor DNA
Instrument model: Sentosa SQ301

library_source: genomic

data_processing:
Library strategy: DNA-Seq
Base-calling and signal processing were done using the Sentosa SQ Suite software
Alignment was done according to manufacturer instructions using the Sentosa instrument to a minimum quality control level of 85%
Filtering was done to 0.05 variant allele frequency and above
Genome_build: hg19
Supplementary_files_format_and_content: *.copy.xlsx: Excel files with sample id and mutation details.

molecule: genomic DNA

source_name: Human SCC cells

extract_protocol:
Macro-dissections were made on unstained tissue sections and genomic DNA was isolated using the Maxwell FFPE DNA isolation KIT (Promega Corp)
Libraries were prepared using the automated setting on the Sentosa SX101 instrument

tag: cell type

value: Human SCC

value: Cutaneous squamous cell carcinoma

tag: tumor location

value: nodal metastasis


title: SCC_NodalMet [D757]

description:
D757
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_NodalMet [D714]

description:
D714
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_NodalMet [D672]

description:
D672
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_NodalMet [D676]

description:
D676
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_NodalMet [D680]

description:
D680
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_NodalMet [D674]

description:
D674
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_NodalMet [D719_50]

description:
D719_50
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_NodalMet [D682]

description:
D682
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_NodalMet [D684]

description:
D684
tumor DNA
Instrument model: Sentosa SQ301


title: DMD-CO_day56_3 [GC115822]

city: Leuven

first: Yoke Chin

last: Chai

state: Leuven

address: Herestraat 49, ON5

department: Development & Regeneration

country: Belgium

institute: KU Leuven

library_source: transcriptomic

data_processing:
The raw sequence files generated (.fastq files) underwent quality control analysis using FastQC v0.11.7 (Andrews, 2010). Adapters were filtered with ea-utils fastq-mcf v1.05 (Aronesty, 2011)). Splice-aware alignment was performed with HiSat2 against the human reference genome hg38 using the default parameters. Reads mapping to multiple loci in the reference genome were discarded. Resulting BAM alignment files were handled with Samtools v1.5. (Li et al., 2009). Quantification of reads per gene was performed with HT-seq Count v2.7.14.
Genome_build: hg38
Supplementary_files_format_and_content: HT-seq Count

molecule: total RNA

source_name: DMD patient derived hiPSC

growth_protocol: hiPSC colonies were cultured in E8flex medium till confluent. The cells were then seeded into microwells to promote embryoid bodies (EBs) formation. The EBs  were then differentiated into cardiac organoids and maintained up to 93 days. At day 56, the DMD-CO and DMD-Iso-CO were harvested form RNA sequencing analysis.

extract_protocol:
The organoids were harvested in lysis buffer and the total RNA was extracted for sequencing analysis at the GenomicsCore of KU Leuven using single-read sequencing technique on the HiSeq4000 platform (Illumina Inc.).
RNA (>10 μg) extracted from DMD-CO and DMD-Iso-CO on day 56 were verified and processed by the Genomics Core (KU Leuven – UZ Leuven). As quality control, the RNA concentration was measured with Nanodrop and quality was checked with Bioanalyzer. The Lexogen QuantSeq 3' mRNA-Seq library prep kit was used according the manufacturer's protocol with 500 ng input. After the prep the libraries were measured with Qubit and put on the Fragment analyzer so the libraries can be pooled equimolar to 2 nM. The pool was then quantified with qPCR and a final pool (2 nM) was made for single-read sequencing on the HiSeq4000 (Illumina Inc). The settings were 51-8-8.

tag: genotype/variation

value: Contains specific DMD point mutation

value: DMD patient derived hiPSC


title: DMD-Iso-CO_day56_1 [GC115823]

value: DMD point mutation was corrected via CRISPR/Cas technology


title: DMD-Iso-CO_day56_3 [GC115825]


title: DMD-Iso-CO_day56_2 [GC115824]


title: 1_10

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_10


title: DMD-CO_day56_2 [GC115821]


title: 1_09

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_09


title: 1_08

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_08


title: 1_06

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_06


title: 1_07

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_07

source_name: Still's/lung nodules


title: DMD-CO_day56_1 [GC115820]


title: 1_04

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_04


title: 1_05

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_05


title: NHEK_C10orf99_rep3

city: Singapore

first: Vipin

last: Narang

address: 8A Biomedical Grove

country: Singapore

institute: Singapore Immunology Network

data_processing:
The 2 × 151 bp paired-end reads from Illumina sequencing were quality checked using fastqc (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) and after quality checks mapped to the GRCh38 human genome assembly using the STAR alignment tool (Dobin et al., 2013). Reads mapped to genes were counted in each sample using featureCounts (Liao et al., 2014), where the reference gene annotations were obtained from GENCODE v26 (Harrow et al., 2012).
Genome_build: GRCh38
Supplementary_files_format_and_content: geneCounts.txt

molecule: polyA RNA

source_name: Normal Human Epidermal Keratinocytes (NHEK)

growth_protocol: NHEKs (Kurabo, Osaka, Japan) were inoculated at a concentration of 2,500 cells/cm2 in culture medium, HuMedia-KG2 (Kurabo) supplemented with insulin (10 μg/mL), human epidermal growth factor (0.1 ng/mL), hydrocortisone (0.5 μg/mL), bovine pituitary extract (0.4% v/v), gentamicin (50 μg/mL), and amphotericin B (50 ng/mL). The culture was maintained at 37°C in a humidified chamber containing 5% CO2.

extract_protocol:
Total RNA was extracted from primary cultured normal human epidermal keratinocytes (NHEK) following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) followed by a Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany).
RNA was analyzed on Agilent Bioanalyser for quality assessment with RNA Integrity Number (RIN) range from 9.6 to 9.8 and median of RIN 9.8. cDNA libraries were prepared using 2 ng of total RNA using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1. Addition of 20 µM TSO; 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (Illumina) (31 samples/lane).

treatment_protocol: The human C10orf99 expression vector was generated by inserting a C10orf99 open reading frame (NM_207373) into the multiple cloning sites of pIRES-EGFP (Clontech Laboratories, Mountain View, CA, USA). According to the manufacturer's instructions, the human C10orf99 expression vector (or the mock vector) was transfected using Lipofectamine 3000 (Thermo Fisher Scientific, Waltham, MA). The cells were harvested before and after 2-day culture.

tag: transfection


title: NHEK_C10orf99_rep2


title: NHEK_C10orf99_rep1


title: NHEK_empty_vector_rep3

value: Empty vector-transfected


title: 1_02

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_02

source_name: sJIA/Lung disease

value: CCHMC/Grom


title: 1_03

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_03


title: 1_01

description:
We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.
1_01


title: NHEK_empty_vector_rep1


title: NHEK_empty_vector_rep2


title: siRNA_TUB_rep1b_VL9_S5_L001_R1_001.fastq.gz

city: Buffalo

first: Vincent

middle: J.

last: Lynch

state: NY

address: 551 Cooke Hall

department: Department of Biological Sciences

institute: University at Buffalo, SUNY

description: Sample "_TUB_rep1b_VL9_" not used in final analysis

data_processing:
All sequencing data were uploaded and analyzed on the Galaxy platform (https://usegalaxy.org/; Version 20.01). Individual reads for particular samples ("_rep1a" and "_rep1b") were concatenated using the “Concatenate datasets” tool (version 1.0.0). We used HISAT2 (version 2.1.0+galaxy5) (Kim, Langmead and Salzberg, 2015) to align reads to the Human hg38 reference genome using “Single-end” option, and reporting alignments tailored for transcript assemblers including StringTie. Transcripts were assembled and quantified using StringTie (v1.3.6) (Pertea et al., 2015, 2016), with reference file to guide assembly and the “reference transcripts only” option, and output count files for differential expression with DESeq2/edgeR/limma-voom. Differentially expressed genes were identified using DESeq2 (version 2.11.40.6+galaxy1) (Anders and Huber, 2010; Love, Huber and Anders, 2014). The reference file for StringTie guided assembly was wgEncodeGencodeBasicV33.
Genome_build: hg38
Supplementary_files_format_and_content: Unmodified DESeq2 output

source_name: Endometrial Stromal Fibroblasts

growth_protocol: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (CS-FBS; 12676029, Thermo Fisher Scientific), 1% L-glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1x insulin-transferrin-selenium (ITS; 41400045, Thermo Fisher Scientific)

extract_protocol:
48 hours post treatment cells were washed with PBS, trypsinized (0.05% Trypsin-EDTA; 15400-054, Thermo Fisher Scientific) and total RNA was extracted using RNeasy Plus Mini Kit (74134, QIAGEN) following the manufacturer’s protocol. RNA from knockdown and control samples were DNase treated with TURBO DNA-free Kit (AM1907, Thermo Fisher Scientific).
RNA-Seq libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human (RS-122-2201, Illumina Inc.) following manufacturer’s protocol. Library quality and quantity were checked on 2100 Bioanalyzer and the pool of libraries was sequenced on Illumina HiSEQ4000 (single-end 50bp) using manufacturer’s reagents and protocols. Quality control, Ribo-Zero library preparation and Illumina sequencing were performed at the Genomics Facility at The University of Chicago.

treatment_protocol: 2x105 cells were plated per well of a 6-well plate and 18 hours later cells in 1750μl of Opti-MEM (31985070, Thermo Fisher Scientific) were transfected with 50nM of siRNA targeting a specific transcription factor (Silencer Select Pre-Designed siRNAs, Thermo Fisher Scientific; see list below for cat. numbers) and 9μl of Lipofectamine RNAiMAX (133778-150, Invitrogen) in 250μl Opti-MEM. BlockIT Fluorescent Oligo (44-2926, Thermo Fisher Scientific) was used as a scrambled non-targeting RNA control. Cells were incubated in the transfection mixture for 6 hours. Then, cells were washed with PBS and incubated in the maintenance medium overnight. Cells in the control wells were checked under the microscope for fluorescence the next day. 48 hours post treatment cells were washed with PBS, trypsinized (0.05% Trypsin-EDTA; 15400-054, Thermo Fisher Scientific) and total RNA was extracted using RNeasy Plus Mini Kit (74134, QIAGEN) following the manufacturer’s protocol. The knockdown experiment was done in 3 biological replicates. To test for the efficiency of the knockdown, cDNA was synthesized from 100-200ng RNA using Maxima H Minus First Strand cDNA Synthesis Kit (K1652, Thermo Fisher Scientific) following the manufacturer’s protocol. qRT-PCR was performed using QuantiTect SYBR Green PCR (204143, QIAGEN). GAPDH housekeeping gene was used for normalization. See list of used primers below. Samples that showed >70% KD efficiency were used for RNA-Seq.

tag: catalog#

value: T HESCs (ATCC CRL-4003)

tag: cell line

value: T-HESC

tag: tag

value: TUB


title: NHEK_untreated_rep3

value: Untreated


title: siRNA_TUB_rep2a_VL17_S19_L001_R1_001.fastq.gz


title: NHEK_untreated_rep1


title: NHEK_untreated_rep2


title: siRNA_TUB_rep3b_VL25_S21_L001_R1_001.fastq.gz


title: siRNA_TUB_rep3a_VL25_S27_L001_R1_001.fastq.gz


title: siRNA_TUB_rep1a_VL9_S11_L001_R1_001.fastq.gz

description: Sample "_TUB_rep1a_VL9_" not used in final analysis


title: siRNA_Ctrl11_rep3b_VL26_S28_L001_R1_001.fastq.gz


title: siRNA_Ctrl11_rep3a_VL26_S22_L001_R1_001.fastq.gz


title: siRNA_Ctrl11_rep1b_VL10_S6_L001_R1_001.fastq.gz


title: siRNA_Ctrl11_rep2b_VL18_S14_L001_R1_001.fastq.gz


title: siRNA_Ctrl11_rep2a_VL18_S20_L001_R1_001.fastq.gz


title: siRNA_MLLT11_rep3b_VL-160_S45_L006_R1_001.fastq.gz

treatment_protocol: 2x105 cells were plated per well of a 6-well plate and 18 hours later cells in 1750μl of Opti-MEM (31985070, Thermo Fisher Scientific) were transfected with 50nM of siRNA targeting a specific transcription factor (see list below) and 9μl of Lipofectamine RNAiMAX (133778-150, Invitrogen) in 250μl Opti-MEM. BlockIT Fluorescent Oligo (44-2926, Thermo Fisher Scientific) was used as a scrambled non-targeting RNA control. Cells were incubated in the transfection mixture for 6 hours. Then, cells were washed with PBS and incubated in the maintenance medium overnight. Cells in the control wells were checked under the microscope for fluorescence the next day. 48 hours post treatment cells were washed with PBS, trypsinized (0.05% Trypsin-EDTA; 15400-054, Thermo Fisher Scientific) and total RNA was extracted using RNeasy Plus Mini Kit (74134, QIAGEN) following the manufacturer’s protocol. The knockdown experiment was done in 3 biological replicates. To test for the efficiency of the knockdown, cDNA was synthesized from 100-200ng RNA using Maxima H Minus First Strand cDNA Synthesis Kit (K1652, Thermo Fisher Scientific) following the manufacturer’s protocol. qRT-PCR was performed using QuantiTect SYBR Green PCR (204143, QIAGEN). GAPDH housekeeping gene was used for normalization. See list of used primers below. Samples that showed >70% KD efficiency were used for RNA-Seq.

tag: sirna


title: siRNA_MLLT11_rep3a_VL-160_S45_L006_R1_001.fastq.gz


title: siRNA_MLLT11_rep2a_VL-155_S40_L006_R1_001.fastq.gz


title: siRNA_MLLT11_rep2b_VL-155_S40_L006_R1_001.fastq.gz


title: siRNA_MLLT11_rep1a_VL-151_S36_L006_R1_001.fastq.gz


title: siRNA_MLLT11_rep1b_VL-151_S36_L006_R1_001.fastq.gz


title: siRNA_PHB_rep3b_VL-159_S44_L006_R1_001.fastq.gz

value: PHB


title: siRNA_PHB_rep3a_VL-159_S44_L006_R1_001.fastq.gz


title: siRNA_PHB_rep2a_VL-154_S39_L006_R1_001.fastq.gz


title: siRNA_TUB_rep2b_VL17_S13_L001_R1_001.fastq.gz


title: siRNA_PHB_rep2b_VL-154_S39_L006_R1_001.fastq.gz


title: siRNA_HOXA4_rep3a_VL-164_S49_L006_R1_001.fastq.gz


title: siRNA_PHB_rep1a_VL-150_S35_L006_R1_001.fastq.gz


title: siRNA_HOXA4_rep3b_VL-164_S49_L006_R1_001.fastq.gz


title: siRNA_PHB_rep1b_VL-150_S35_L006_R1_001.fastq.gz


title: siRNA_HOXA4_rep1a_VL-149_S34_L006_R1_001.fastq.gz


title: siRNA_HOXA4_rep2b_VL-153_S38_L006_R1_001.fastq.gz


title: siRNA_HOXA4_rep1b_VL-149_S34_L006_R1_001.fastq.gz


title: siRNA_RORB_rep3a_VL-163_S48_L006_R1_001.fastq.gz

value: RORB


title: siRNA_RORB_rep3b_VL-163_S48_L006_R1_001.fastq.gz


title: siRNA_Ctrl11_rep1a_VL10_S12_L001_R1_001.fastq.gz


title: siRNA_RORB_rep2b_VL-158_S43_L006_R1_001.fastq.gz


title: siRNA_HOXA4_rep2a_VL-153_S38_L006_R1_001.fastq.gz


title: siRNA_RORB_rep1b_VL-148_S33_L006_R1_001.fastq.gz


title: siRNA_RORB_rep1a_VL-148_S33_L006_R1_001.fastq.gz


title: siRNA_RXRA_rep3a_VL-162_S47_L006_R1_001.fastq.gz

value: RXRA


title: siRNA_RXRA_rep3b_VL-162_S47_L006_R1_001.fastq.gz


title: siRNA_RXRA_rep2b_VL-157_S42_L006_R1_001.fastq.gz


title: siRNA_RXRA_rep2a_VL-157_S42_L006_R1_001.fastq.gz


title: siRNA_RXRA_rep1a_VL-147_S32_L006_R1_001.fastq.gz


title: siRNA_RXRA_rep1b_VL-147_S32_L006_R1_001.fastq.gz


title: siRNA_Ctrl10_rep4b_VL-165_S50_L006_R1_001.fastq.gz

description: Ctrl10_rep4a/b is for RXRA, RORB, HOXA4 replicates 3a/b


title: siRNA_RORB_rep2a_VL-158_S43_L006_R1_001.fastq.gz


title: siRNA_Ctrl10_rep3b_VL-161_S46_L006_R1_001.fastq.gz

description: Ctrl10_rep2a/b is for HOXA4, PHB, MLLT11 replicates 2a/b


title: siRNA_Ctrl10_rep3a_VL-161_S46_L006_R1_001.fastq.gz

description: Ctrl10_rep3a/b is for RXRA, RORB replicates 2a/b and PHB, MLLT11 replicates 3a/b


title: siRNA_Ctrl10_rep2a_VL-156_S41_L006_R1_001.fastq.gz


title: siRNA_Ctrl10_rep2b_VL-156_S41_L006_R1_001.fastq.gz


title: siRNA_Ctrl10_rep1b_VL-152_S37_L006_R1_001.fastq.gz

description: Ctrl10_rep1a/b is for RXRA, RORB, HOXA4, PHB, MLLT11 replicates 1a/b


title: siRNA_Ctrl10_rep1a_VL-152_S37_L006_R1_001.fastq.gz


title: siRNA_Ctrl10_rep4a_VL-165_S50_L006_R1_001.fastq.gz


title: siRNA_FLI1_rep2b_VL-140_S25

treatment_protocol: 2x105 cells were plated per well of a 6-well plate and 18 hours later cells in 1750μl of Opti-MEM (31985070, Thermo Fisher Scientific) were transfected with 50nM of siRNA targeting a specific transcription factor (Silencer Select Pre-Designed siRNAs, Thermo Fisher Scientific; see list below for cat. numbers) and 9μl of Lipofectamine RNAiMAX (133778-150, Invitrogen) in 250μl Opti-MEM. BlockIT Fluorescent Oligo (44-2926, Thermo Fisher Scientific) was used as a scrambled non-targeting RNA control. Cells were incubated in the transfection mixture for 6 hours. Then, cells were washed with PBS and incubated in the maintenance medium overnight. Cells in the control wells were checked under the microscope for fluorescence the next day. 48 hours post treatment cells were washed with PBS, trypsinized (0.05% Trypsin-EDTA; 15400-054, Thermo Fisher Scientific) and total RNA was extracted using RNeasy Plus Mini Kit (74134, QIAGEN) following the manufacturer’s protocol. The knockdown experiment was done in 3 biological replicates. To test for the efficiency of the knockdown, cDNA was synthesized from 100-200ng RNA using Maxima H Minus First Strand cDNA Synthesis Kit (K1652, Thermo Fisher Scientific) following the manufacturer’s protocol. qRT-PCR was performed using TaqMan Fast Universal PCR Master Mix 2X (4352042, Thermo Fisher Scientific), with primers for a specific transcription factor and Malat as a control housekeeping gene. See list of used primers below. Samples that showed >70% KD efficiency were used for RNA-Seq.

value: T HESC


title: siRNA_FLI1_rep3a_VL-145_S30


title: siRNA_FLI1_rep3b_VL-145_S30


title: DorsalSkin_ASAL_Lice_Tank2_Fish2

type: RNA

city: St. John's

first: Albert

last: Caballero Solares

state: NL

address: 0 Marine Lab Road

department: Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: For each array, an equal quantity (825 ng) of an individual fish Cy5-labeled and reference Cy3-labeled aRNA were fragmented and co-hybridized to a 44K microarray [consortium for Genomic Research on All Salmonids Project (cGRASP)-designed Agilent 44K salmonid oligonucleotide microarray (GEOaccession #GPL11299)] at 65 °C for 17 h with rotation (10 rpm) using an Agilent hybridization oven. The array slides were washed immediately after hybridization as per the manufacturer’s instructions, and dried by centrifuging at 200 × g for 5 min at room temperature.

scan_protocol: Microarray slides were immediately scanned at 5-μm resolution using a SureScan Microarray Scanner System (Agilent) and Microarray Scan Control Software v.9.1 following the built-in Agilent HD 2-color gene expression microarray scan protocol.

data_processing: The signal intensity data were extracted and subjected to linear and LOESS normalization using Agilent Feature Extraction Software v12.0 (Agilent). Probes of low quality (e.g., signal not above background) or with absent values in more than 25% of all 24 arrays were removed from the dataset, and the missing values were imputed using GeneSpring Software v14.9 (Agilent).

organism: Salmo salar

source_name: Dorsal skin tissue, ASAL-injected, Lice-infected,  tank number,  individual fish

label_protocol: One microgram of DNaseI-treated and column-purified RNA from each individual fish and the common reference pool was in vitro-transcribed into aRNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, ThermoFisher Scientific, Waltham, MA, USA), following the manufacturer’s instructions. The resulting aRNAs were quality-checked and quantified using agarose gel electrophoresis and ND-1000 UV spectrophotometry (NanoDrop). Twenty micrograms of each aRNA sample were precipitated overnight using a standard ethanol precipitation method and re-suspended in coupling buffer (Ambion). Common reference and individual fish aRNAs were labeled with Cy3 and Cy5, respectively, following the manufacturer’s instructions. The labeled aRNA concentration and labeling efficiency were measured using the microarray feature in the ND-1000 UV spectrophotometer.

growth_protocol:
Atlantic salmon smolts were transported from a local salmon farm to the Dr. Joe Brown Aquatic Research Building [JBARB, Ocean Sciences Centre (OSC), Memorial University, NL, Canada]. Smolts were held in 3,800-L fiberglass tanks until transferred to the 620-L tanks used in the trials. While in the 3,800-L tanks, the salmon were PIT (passive integrated transponder; Easy AV, Avid Identification Systems, Norco, CA, USA)-tagged for growth monitoring and identification during experimentation. When they reached the desired initial weight [238.9 ± 45.2 g, mean weight ± standard deviation (SD)], salmon were randomly distributed into 2 and 4 tanks at JBARB and the Cold-Ocean Deep-Sea Research Facility (CDRF, OSC), respectively. All tanks were connected to the same flow-through seawater system (12 L/min), and monitored daily for water quality. The seawater was pumped from Logy Bay (NL) and subjected to filtration, temperature adjustment, and UV treatment before reaching header tanks inside JBARB; then, it was distributed to the JBARB tanks and the CDRF. Water from JBARB is UV-treated and oxygenated again inside CDRF, before reaching the CDRF's tanks. CDRF has an Aquatic Containment Level 3-certified (Canadian Food Inspection Agency) biocontainment facility equipped with the same 620-L fiberglass tanks used at JBARB. The photoperiod was 24-h light in both buildings. Fish were fed with EWOS Dynamic S feed (5 mm; 27% fat, 46% protein) using automatic feeders (AVF6 Vibratory Feeder; Pentair Aquatic Eco-Systems, Inc., Nanaimo, BC, Canada) at a daily ration of 1% body weight. Water temperature and dissolved oxygen levels were relatively constant (~10-11 ºC and ≥ 10 mg/L) throughout the acclimation and trial periods. Thirty-five salmon were allocated in each of the tanks at CDRF and 15 in each of the tanks at JBARB. CDRF's fish were destined for the Lepeophtheirus salmonis challenge trial, and those at JBARB to serve as no-lice infection controls.
immune challenges: The salmon at CDRF were challenged with Lepeophtheirus salmonis copepodids (at a 50 lice/fish ratio) after an acclimation period of 79 days. Four weeks after sea lice exposure, when lice were at the pre-adult stage, lice-infected salmon (CDRF) and non-infected salmon (JBARB) were fasted for 24 h and then subjected to an intraperitoneal (IP) injection of either phosphate-buffered saline (PBS; Gibco/ThermoFisher Scientific, Mississauga, ON, Canada), a solution of polyriboinosinic polyribocytidylic acid (pIC; 2 μg/μL; Sigma-Aldrich, Oakville, ON, Canada), or a suspension of formalin-killed Aeromonas salmonicida [ASAL; PBS-washed and pelleted commercial vaccine (Furogen dip, Novartis Canada, Charlottetown, PE, Canada), resuspended in PBS at an optical density of 1.0 at 600 nm wavelength]. For each tank at CDRF, 6 fish were injected with PBS, 6 with pIC, and 6 with ASAL at a dose of 1 μL/g of fish (wet mass). For each tank at JBARB, 4 fish were injected with PBS, 4-5 fish with pIC, and 4-5 fish with ASAL.
sample collection: At 24 h post-injection, all injected salmon were euthanized by immersion in a seawater bath with 400 mg/L MS-222 (Syndel Laboratories, Vancouver, BC, Canada) and dissected for tissue sample collection. Two 1-cm2 dorsal skin samples were taken from every lice-infected salmon (CDRF): one sample around a louse attachment site and another sample from an adjacent intact skin area (i.e., no lice attached or damaged). Dorsal skin samples (also 1 cm2) from non-infected salmon (JBARB) were taken from the area directly posterior to the dorsal fin and dorsal to the lateral line. Skin samples were immediately flash-frozen with liquid nitrogen and stored at -80 ºC until processed for RNA extraction.

extract_protocol:
Dorsal skin samples were homogenized in TRIzol reagent (Invitrogen/Life Technologies, Burlington, ON, Canada) with stainless steel beads (5 mm; QIAGEN, Mississauga, ON, Canada) using a TissueLyser II (QIAGEN), and subjected to RNA extraction following manufacturers’ instructions. Thirty micrograms of each total RNA sample were treated with 6.8 Kunitz units of DNaseI (RNase-Free DNase Set, QIAGEN) and then column-purified by using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions. The total RNA concentration and purity were assessed by ND-1000 UV spectrophotometry (NanoDrop, Wilmington, DE, USA), and the RNA integrity was examined by 1% agarose gel electrophoresis. RNA samples with tight 18S and 28S ribosomal RNA bands and high A260/280 and A260/230 ratios (> 1.8) were used in transcriptional analyses.
The common reference was prepared using pools of equal quantities of RNA from the 24 selected salmon for the present study (i.e., 6 PBS/no lice, 6 PBS/lice, 6 ASAL/no lice, and 6 ASAL/lice salmon), plus 6 pIC/no lice and 6 pIC/lice salmon. It should be noted that the present microarray study did not analyze the dorsal skin transcriptome response to pIC. The microarray data from each of the 12 pIC-injected salmon included in the RNA pool (i.e., channel 2) has contributed to another study and will be part of a separate GEO submission.

value: Dorsal skin

tag: life stage

value: Juvenile

source_name: Dorsal skin RNA pool, all biological replicates of all injection (PBS, ASAL, pIC)/infection (no lice, lice) groups, 6 biological replicates per group (36 biological replicates in total)


title: DorsalSkin_ASAL_NoLice_Tank33_Fish5

source_name: Dorsal skin tissue, ASAL-injected, Not lice-infected,  tank number,  individual fish


title: DorsalSkin_ASAL_Lice_Tank12_Fish1


title: DorsalSkin_PBS_Lice_Tank5_Fish4

source_name: Dorsal skin tissue, PBS-injected, Lice-infected,  tank number,  individual fish


title: DorsalSkin_PBS_Lice_Tank2_Fish5


title: DorsalSkin_PBS_Lice_Tank12_Fish6


title: siRNA_FLI1_rep2a_VL-140_S25


title: DorsalSkin_ASAL_Lice_Tank5_Fish4


title: DorsalSkin_ASAL_NoLice_Tank30_Fish4


title: DorsalSkin_ASAL_Lice_Tank8_Fish5


title: DorsalSkin_PBS_Lice_Tank2_Fish2


title: DorsalSkin_PBS_Lice_Tank8_Fish4


title: Input

city: xi'an

first: xin

last: wang

address: yanta west road 76

country: China

institute: xi'an jiaotong university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36)
ChIP-seq reads were aligned to the mm10 genome assembly using STAR(Version 2.5.3.a) with default parameters
The MACS2 software(version 2.1.1) was used for peak calling.
The homer was used for motifs analysis
Genome_build: mm10
Supplementary_files_format_and_content: peak

organism: Mus musculus

source_name: Treg cells from the lymph nodes of WT mice

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The library products corresponding to 100-300 bps were enriched, quantified and finally sequenced on PE150 model.

treatment_protocol: CD4+CD25+ Treg cells were sorted from the lymph nodes of wild-type mice

tag: strain

value: lymph nodes

value: Treg cells


title: DorsalSkin_ASAL_NoLice_Tank33_Fish2


title: DorsalSkin_ASAL_NoLice_Tank33_Fish3


title: DorsalSkin_ASAL_Lice_Tank8_Fish7


title: DorsalSkin_PBS_NoLice_Tank33_Fish2

source_name: Dorsal skin tissue, PBS-injected, Not lice-infected,  tank number,  individual fish


title: DorsalSkin_ASAL_NoLice_Tank30_Fish2


title: DorsalSkin_ASAL_NoLice_Tank30_Fish3


title: DorsalSkin_ASAL_Lice_Tank12_Fish4


title: DorsalSkin_PBS_NoLice_Tank33_Fish3


title: DorsalSkin_PBS_Lice_Tank5_Fish3


title: DorsalSkin_PBS_NoLice_Tank30_Fish3


title: siRNA_FLI1_rep1b_VL-135_S20


title: DorsalSkin_PBS_NoLice_Tank30_Fish4


title: DorsalSkin_PBS_NoLice_Tank30_Fish1


title: Ip


title: Rep2_PDL1_Low

city: shanghai

first: Baiwen

last: Chen

address: south  chongqing road

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Library strategy: CRISPR screen
The raw reads were trimmed with fastx_trimmer in FASTX-Toolkit and sgRNA sequences were counted by MAGeCK.
Enriched genes were retrieved with MAGeCK test subcommand.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files including count summary

source_name: Raw 264.7 cells

extract_protocol:
Genomic DNA were isolated from PD-L1-low, PD-L1-High and pre-sort cell populations,sgDNA sequences were PCR- amplified and subjected to Illumina sequencing.
Libraries were prepared for sequencing using standard Illumina protocols

tag: pd-l1 expression status

value: Low


title: siRNA_FLI1_rep1a_VL-135_S20


title: siRNA_ETV6_rep3b_VL-144_S29


title: Rep2_Pre_sort

value: pre-sort


title: Rep1_PDL1_Low


title: DorsalSkin_PBS_NoLice_Tank33_Fish4

tag: tissue


title: KO3_Adipo

city: ChengDu,SiChuan

first: Caojie

last: Liu

address: No.14,3Rd Section Of Ren Min Nan Rd.

institute: West China Hospital of Stomatology, Sichuan University

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

source_name: bone marrow mesenchymal stem cells

extract_protocol:
Primary MSCs were isolated by flushing the bone marrow of femurs, tibiae and humeri. The bone marrow suspension was cultured in 21cm2 petri dish in alpha minimum Eagle’s medium (α-MEM, HyClone) with 10% fetal bovine serum (FBS, Gibco), 100 units/mL penicillin and 100 μg/mL streptomycin. Incubated at 37°C with 5% CO2, the culture medium was changed every 48 hours. MSCs at passage 3 were applied for the subsequent research.  For the osteogenic induction, MSCs were cultured with osteogenic medium supplemented with 50μM ascorbic acid (Sigma), 10nM dexamethasone (Sigma), and 10mM β-glycerophosphate (Sigma). For adipogenic induction, MSCs were treated with adipogenic medium containing 10μg/ml insulin (Sigma), and 1μM dexamethasone (Sigma), 0.5μM isobutylmethylxanthin (Sigma).
RNA libiaries were prepared for sequencing using standard Illumina protocols.

value: bone marrow

value: bone marrow mesenchymal stem cells

tag: age

value: 4 weeks old

tag: treatment

value: Adipo induction

tag: genotype

value: Chd7 KO


title: siRNA_ETV6_rep3a_VL-144_S29

value: T HESCs (ATCC CRL-4003)


title: Rep1_PDL1_High

value: High


title: siRNA_ETV6_rep2b_VL-139_S24


title: WT3_Adipo

value: WT


title: KO1_Adipo


title: WT1_Adipo


title: Rep1_Pre_sort


title: siRNA_ETV6_rep1b_VL-134_S19


title: Rep2_PDL1_High


title: KO3_Osteo

value: Osteo induction


title: WT3_Osteo


title: siRNA_C11orf9_rep3b_VL-143_S28


title: siRNA_ETV6_rep1a_VL-134_S19


title: KO1_Osteo


title: WT2_Osteo


title: siRNA_C11orf9_rep2b_VL-138_S23


title: KO2_Adipo


title: WT control, 113

city: Irapuato

first: Alfredo

last: Herrera Estrella

state: Guanajuato

address: Libr. Norte carr. León, Km 9.6

department: LANGEBIO

country: Mexico

institute: CINVESTAV

description: Processed data file column-name: 113

data_processing:
Preprocessing with Reaper (Kraken)
Alingment to T. atroviride genome with Bowtie
Normalization
Differential expresion analysis with EdgeR and Limma packages
Genome_build: Trichoderma atroviride v2.0 (https://mycocosm.jgi.doe.gov/Triat2/Triat2.home.html)
Supplementary_files_format_and_content: smallRNA_processed_data.xlsx

organism: Trichoderma atroviride

source_name: Mycelium

growth_protocol: PDA medium in Petri dishes, complete darkness at 27°C

extract_protocol:
TRIzol RNA extraction
Illumina TruSeq small RNA sample prep V2
small RNA-Seq

treatment_protocol: Mycelium frozen in liquid nitrogen

value: Wild type

tag: protocol

value: growing alone

tag: time

value: Control

tag: replicate

value: Mycelium


title: dcr2 vs A. alternata (C), 111

description: Processed data file column-name: 111

value: mutant strain

value: co-cultured with Alternaria alternata

value: Contact


title: dcr2 control, 114

description: Processed data file column-name: 114


title: WT2_Adipo

tag: cell type


title: dcr2 vs A. alternata (BC), 110

description: Processed data file column-name: 110

value: Before contact


title: dcr2 vs A. alternata (AC), 112

description: Processed data file column-name: 112

value: After contact


title: WT vs A. alternata (AC), 109

description: Processed data file column-name: 109


title: siRNA_C11orf9_rep1b_VL-133_S18

value: T HESC


title: WT vs A. alternata (BC), 107

description: Processed data file column-name: 107


title: siRNA_C11orf9_rep1a_VL-133_S18


title: dcr2 control, 106

description: Processed data file column-name: 106


title: WT control, 105

description: Processed data file column-name: 105


title: siRNA_BRCA_rep3b_VL-142_S27

value: BRCA


title: dcr2 vs A. alternata (AC), 104

description: Processed data file column-name: 104


title: KO2_Osteo

value: bone marrow

value: bone marrow mesenchymal stem cells

value: 4 weeks old


title: siRNA_BRCA_rep3a_VL-142_S27

value: T HESCs (ATCC CRL-4003)


title: WT1_Osteo

value: WT


title: dcr2 vs A. alternata (BC), 102

description: Processed data file column-name: 102


title: siRNA_C11orf9_rep3a_VL-143_S28


title: siRNA_BRCA_rep2b_VL-137_S22


title: WT vs A. alternata (C), 100

description: Processed data file column-name: 100


title: WT vs A. alternata (BC), 99

description: Processed data file column-name: 99


title: WT vs A. alternata (AC), 101

description: Processed data file column-name: 101


title: siRNA_C11orf9_rep2a_VL-138_S23


title: WT control, 97

description: Processed data file column-name: 97


title: siRNA_BRCA_rep1b_VL-132_S17


title: dcr2 vs A. alternata (AC), 96

description: Processed data file column-name: 96


title: WT vs A. alternata (C), 108

description: Processed data file column-name: 108


title: siRNA_BRCA_rep1a_VL-132_S17


title: WT vs A. alternata (C), 92

description: Processed data file column-name: 92


title: WT vs A. alternata (BC), 91

description: Processed data file column-name: 91


title: dcr2 vs A. alternata (C), 103

description: Processed data file column-name: 103


title: siRNA_Ctrl9_rep2b_VL-141_S26


title: siRNA_Ctrl9_rep2a_VL-141_S26


title: siRNA_Ctrl9_rep1b_VL-136_S21


title: siRNA_Ctrl9_rep1a_VL-136_S21


title: siRNA_BRCA_rep2a_VL-137_S22


title: dcr2 control, 98

description: Processed data file column-name: 98


title: dcr2 vs A. alternata (C), 95

description: Processed data file column-name: 95


title: siRNA_PRRX2_rep3a_VL-130_S17_L004_R1_001.fastq.gz


title: dcr2 vs A. alternata (BC), 94

description: Processed data file column-name: 94


title: siRNA_PRRX2_rep3b_VL-130_S17_L001_R1_001.fastq.gz


title: siRNA_PRRX2_rep2b_VL-126_S13_L001_R1_001.fastq.gz


title: siRNA_PRRX2_rep2a_VL-126_S13_L004_R1_001.fastq.gz


title: WT vs A. alternata (AC), 93

description: Processed data file column-name: 93


title: siRNA_Ctrl9_rep3b_VL-146_S31


title: siRNA_Ctrl9_rep3a_VL-146_S31


title: miRNA46

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

data_processing:
Basecalling was performed using the default Illumina software
trimming was performed using the trim_galore software v0.6.6 and the parameters -length 16
mapping was performed using the miRDeep2 mapper.pl script (last update 21/04/2016). A bowtie index for hg38 was used.
known and novel miRNAs were quantified using the miRDeep2.pl script v2.0.1.3. Mature and hairpin human miRNA sequences were downloaded from miRBase. MiRNAs annotated for all primate species were used as reference for the discovery step.
Genome_build: hg38
Supplementary_files_format_and_content: the csv file is the direct output from the miRDeep script
Supplementary_files_format_and_content: Raw counts and normalized counts

source_name: serum sample

extract_protocol:
Venous blood samples were extracted, centrifugued and serum was homogeneized with TRIzol (Thermo Fisher). miRNA was extracted using the miRNeasy kit (Quiagen).
Library construction and sequencing was externalized to BGI Genomics (Beijin, China)
Standard BGI protocol for miRNA sequencing was applied

value: blood

tag: disease


title: miRNA44


title: miRNA43


title: miRNA45


title: miRNA42


title: siRNA_PRRX2_rep1a_VL-122_S9_L004_R1_001.fastq.gz


title: miRNA41


title: siRNA_PRRX2_rep1b_VL-122_S9_L001_R1_001.fastq.gz


title: control 3T3-L1  -rep2

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

hyb_protocol: Each Cyanine-3-labeled RNA samples were hybridized onto microarray for 20h at 55°C in hybridization rotating oven (Agilent Technologies).

scan_protocol: Acquisition and analysis of hybridization intensities were performed using Agilent DNA Microarray Scanner G2505C. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: The scanned images were analyzed with Feature Extraction Software (version 10.10.1.1) using default parameters (protocol miRNA_1010_Sep10 and Grid: 046066_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: murine 3T3-L1 adipocytes

label_protocol: 100 ng of total RNA with miRNA Spike-In (microRNA Spike-In Kit, Agilent Technologies) added were taken for labeling reaction. miRNA was labeled with Cyanine 3-pCp using the Complete Labeling and Hyb Kit (Agilent Technologies) according to the manufacturer’s procedure. The labeled RNA samples were purified on Micro Bio-Spin 6 columns to remove DMSO and unbound Cyanine 3-pCp.

growth_protocol: Adipogenic differentiation in 3T3-L1 cells was carried out free of contamination, using young stock. Cells were seeded and grown until appr. 100% confluence and for further 48 hours, in DMEM with high glucose, supplemented with 10% NBCS (New-Born Calf serum, Invitrogen) and an antibiotic-antimycotic mixture (Life Technologies), in controlled humidified air with 5% CO2, at 37oC. After this time, a differentiating medium was applied, which consisted of DMEM enriched with 10% fetal bovine serum (FBS, Fetal Bovine serum, Invitrogen) and supplemented with prodifferentiative agents (0.5 mmol/l isobutyl-methylxanthine, 1 µmol/l dexamethasone, 2 µmol/l insulin and 2 µmol/l rosiglitazone). After 3 days, this medium was replaced with DMEM supplemented with 10% FBS and insulin (in the concentration indicated above) and the cells were maintained in this medium for further 3 days. The last 2 days of incubation was performed in 10%FBS/DMEM.

extract_protocol: Total RNA, which also included miRNA, was isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s procedure. RNA quality was determined using Agilent 2100 Bioanalyzer (USA) and RNA 6000 Nano Kit (Agilent, Germany). All RNA samples taken for microarray analysis were of high quality (RIN was  between 9.5 and 10.0).

treatment_protocol: The cells were exposed to IL-6 at concentrations 1 ng/ ml. This concentration reflects post-exercise systemic cytokine levels and  increases insulin-stimulated glucose transport in mouse myotubes in vitro. IL-6 was added to the medium at the time of differentiation induction, and after that the medium was changed every 24 h, to support a fresh bolus of the experimental factor. IL-6 (recombinant, expressed in E.coli and suitable for cell culture) were purchased from Sigma-Aldrich (St. Louis, MO, USA).

value: 3T3-L1 Mouse Embryonic Fibroblasts

tag: stage of differentiation

value: on 8th day of adipogenic differentiation


title: siRNA_HRK1_rep3b_VL-129_S16_L001_R1_001.fastq.gz

tag: catalog#


title: siRNA_HRK1_rep3a_VL-129_S16_L004_R1_001.fastq.gz

tag: cell line


title: treated IL-6 3T3-L1 -rep2


title: control 3T3-L1  -rep4


title: control 3T3-L1  -rep1


title: miRNA40


title: treated IL-6 3T3-L1 -rep1


title: control 3T3-L1  -rep3


title: miRNA39


title: siRNA_HRK1_rep2b_VL-125_S12_L001_R1_001.fastq.gz


title: siRNA_HRK1_rep2a_VL-125_S12_L004_R1_001.fastq.gz


title: miRNA38


title: miRNA37


title: siRNA_HRK1_rep1a_VL-121_S8_L004_R1_001.fastq.gz


title: siRNA_HRK1_rep1b_VL-121_S8_L001_R1_001.fastq.gz


title: miRNA36


title: siRNA_GLI1_rep3b_VL-128_S15_L001_R1_001.fastq.gz


title: miRNA35


title: siRNA_GLI1_rep3a_VL-128_S15_L004_R1_001.fastq.gz


title: miRNA34


title: miRNA33


title: siRNA_GLI1_rep2b_VL-124_S11_L001_R1_001.fastq.gz


title: siRNA_GLI1_rep2a_VL-124_S11_L004_R1_001.fastq.gz


title: siRNA_GLI1_rep1b_VL-120_S7_L001_R1_001.fastq.gz


title: miRNA32


title: siRNA_GLI1_rep1a_VL-120_S7_L004_R1_001.fastq.gz


title: miRNA31


title: miRNA30


title: siRNA_Ctrl8_rep3b_VL-131_S18_L001_R1_001.fastq.gz


title: miRNA29


title: siRNA_Ctrl8_rep3a_VL-131_S18_L004_R1_001.fastq.gz


title: miRNA28


title: siRNA_Ctrl8_rep2a_VL-127_S14_L004_R1_001.fastq.gz


title: siRNA_Ctrl8_rep1b_VL-123_S10_L001_R1_001.fastq.gz


title: miRNA27


title: siRNA_Ctrl8_rep2b_VL-127_S14_L001_R1_001.fastq.gz


title: miRNA26


title: miRNA24


title: siRNA_Ctrl8_rep1a_VL-123_S10_L004_R1_001.fastq.gz


title: miRNA25


title: miRNA23


title: siRNA_THAP5_rep3a_VL-82_S34


title: siRNA_THAP5_rep3b_VL-82_S34


title: miRNA21


title: siRNA_THAP5_rep2b_VL-73_S25


title: siRNA_THAP5_rep2a_VL-73_S25


title: miRNA20


title: miRNA22


title: miRNA19


title: siRNA_THAP5_rep1b_VL-66_S18


title: siRNA_THAP5_rep1a_VL-66_S18


title: miRNA17


title: siRNA_TGIF2_rep3b_VL-81_S33


title: siRNA_TGIF2_rep3a_VL-81_S33


title: miRNA15


title: siRNA_TGIF2_rep2a_VL-72_S24


title: siRNA_TGIF2_rep2b_VL-72_S24


title: miRNA18


title: miRNA14


title: miRNA13


title: miRNA11


title: siRNA_TGIF2_rep1b_VL-65_S17


title: siRNA_TERF1_rep3b_VL-80_S32


title: siRNA_TERF1_rep3a_VL-80_S32


title: siRNA_TGIF2_rep1a_VL-65_S17


title: miRNA12


title: siRNA_TERF1_rep2b_VL-71_S23


title: miRNA9


title: miRNA10


title: miRNA8


title: siRNA_TERF1_rep2a_VL-71_S23


title: miRNA7


title: siRNA_TERF1_rep1a_VL-64_S16


title: miRNA6


title: siRNA_TERF1_rep1b_VL-64_S16


title: siRNA_TCFL5_rep3b_VL-85_S37


title: miRNA16


title: miRNA4


title: siRNA_TCFL5_rep3a_VL-85_S37


title: miRNA3


title: siRNA_TCFL5_rep2b_VL-79_S31


title: siRNA_TCFL5_rep1b_VL-63_S15


title: miRNA2


title: miRNA1


title: siRNA_POU6F1_rep3b_VL-84_S36


title: siRNA_TCFL5_rep1a_VL-63_S15


title: siRNA_POU6F1_rep3a_VL-84_S36


title: siRNA_POU6F1_rep1b_VL-61_S13


title: siRNA_POU6F1_rep2a_VL-77_S29


title: siRNA_POU6F1_rep1a_VL-61_S13


title: siRNA_POU6F1_rep2b_VL-77_S29


title: siRNA_ELK4_rep3a_VL-76_S28


title: siRNA_ELK4_rep3b_VL-76_S28


title: siRNA_ETV6_rep2a_VL-139_S24


title: COPD rep4

city: Beijing

first: Chunxiao

last: Li

address: Huayuan road

institute: Peking University

data_processing:
The sequencing data were filtered with SOAPnuke (v1.5.2) (Li et al., 2008)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) was more than 20%; (3) Removing reads whose unknown base ('N' base) ratio was more than 5%, and afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)(Kim et al., 2015). Bowtie2 (v2.2.5)(Langmead and Salzberg, 2012) was applied to align the clean reads to the reference coding gene set，and then expression level of gene was calculated by RSEM (v1.2.12)(Li and Dewey, 2011).
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Genome_build: mm9
Supplementary_files_format_and_content: gene_counts_matrix.txt
Supplementary_files_format_and_content: gene_expression_TPM.txt

source_name: gastrocnemius

extract_protocol:
Total RNA was extracted from the muscle tissues using Trizol (Invitrogen, Carlsbad, California, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, and then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, and then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from the previous step were amplified by PCR, and products were purified by Ampure XP Beads, and then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from the previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: gastrocnemius

value: 8 weeks-old

value: wild type

tag: disease state

value: COPD


title: COPD rep5


title: siRNA_ELK4_rep2b_VL-69_S21

tag: sirna


title: miRNA5


title: COPD rep3


title: siRNA_ELK4_rep2a_VL-69_S21


title: siRNA_ELK4_rep1a_VL-60_S12


title: COPD rep1


title: COPD rep2


title: siRNA_ELK4_rep1b_VL-60_S12


title: Ctrl rep5

value: control


title: siRNA_TCFL5_rep2a_VL-79_S31


title: siRNA_E2F3_rep3b_VL-75_S27


title: siRNA_E2F3_rep3a_VL-75_S27


title: Ctrl rep3


title: Ctrl rep2


title: siRNA_E2F3_rep2b_VL-68_S20


title: Ctrl rep4


title: siRNA_E2F3_rep2a_VL-68_S20


title: Ctrl rep1


title: siRNA_E2F3_rep1b_VL-59_S11


title: siRNA_E2F3_rep1a_VL-59_S11


title: siRNA_Ctrl7_rep1a_VL-86_S38

description: Ctrl7_rep1a/b is for POU6F1, TCFL5 replicates 3a/b


title: Notreated1

city: Shen Zhen

first: Shaohua

last: Ma

state: Guangdong Sheng

address: nanshan street

institute: Tsinghua University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) .
Bowtie2 (v2.2.5)  was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: xlsx file include raw counts, TPM, and FPKM values for each sample

source_name: gluteus maximus tissue

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular

value: Defect only

value: balb/c

value: gluteus maximus


title: Normal3

value: Untreated


title: Notreated3


title: Normal2


title: Lowbeads2

value: Treated with Matrigel LDB-MSCs for one month


title: siRNA_Ctrl6_rep3b_VL-83_S35

description: Ctrl6_rep3a/b is for TCFL5 replicates 2a/b and TERF1, TGIF2, THAP5 replicates 3a/b

value: T HESC


title: siRNA_Ctrl6_rep3a_VL-83_S35


title: siRNA_Ctrl7_rep1b_VL-86_S38


title: siRNA_Ctrl6_rep2a_VL-74_S26

description: Ctrl6_rep2a/b is for TERF1, TGIF2, THAP5 replicates 2a/b


title: Bulkgel2

value: Treated with Matrigel HDG-MSCs for one month


title: Highbeads3

value: Treated with Matrigel HDB-MSCs for one month


title: Highbeads1


title: Lowbeads1


title: Bulkgel1


title: siRNA_Ctrl5_rep3b_VL-78_S30

description: Ctrl5_rep3a/b is for E2F3, ELK4 replicates 3a/b and POU6F1 replicates 2a/b

value: T HESCs (ATCC CRL-4003)


title: siRNA_Ctrl6_rep1a_VL-67_S19

description: Ctrl6_rep1a/b is for TCFL5, TERF1, TGIF2, THAP5 replicates 1a/b


title: siRNA_Ctrl6_rep1b_VL-67_S19


title: siRNA_Ctrl6_rep2b_VL-74_S26


title: siRNA_Ctrl5_rep3a_VL-78_S30


title: Patient 55 [UCI95]

data_processing:
Basecalling was performed using the default Ion Torrent software
trimming was performed using the fastp software v0.20.1 and the parameters -f 3, -r, -M 15
Counts were calculated using the pseudoalignment tool salmon v1.4.0 with the default parameters for mapping-based quantification and the hg38 salmon partial index
Reads were loaded in R using the tximport library
Genome_build: hg38
Supplementary_files_format_and_content: the csv file was generated based on the txi matrix imported in R.
Supplementary_files_format_and_content: Raw counts

source_name: blood sample

extract_protocol:
Venous blood samples were extracted in TEMPUS tubes (Thermo Fisher). After centrifugation, pellets were homogeneized in Trizol and total RNA was extracted by isopropanol precipitation.
Libraries were prepared using the Ion Ampliseq Trascriptome Human Gene Expression Kit (Ion Torrent)
Amplification of known human transcripts

value: blood


title: Patient 54 [UCI90]


title: Patient 56 [UCI96]


title: siRNA_Ctrl5_rep2b_VL-70_S22

description: Ctrl5_rep2a/b is for E2F3, ELK4 replicates 2a/b


title: Patient 53 [UCI80]


title: siRNA_Ctrl5_rep2a_VL-70_S22


title: siRNA_Ctrl5_rep1b_VL-62_S14

description: Ctrl5_rep1a/b is for E2F3, ELK4, POU6F1 replicates 1a/b


title: siRNA_Ctrl5_rep1a_VL-62_S14


title: Patient 52 [UCI73]


title: siRNA_STAT5B_rep3b_VL-57_S30

description: Sample "_STAT5B_rep3b_VL57_" not used in final analysis

tag: tag


title: Patient 50 [UCI41]


title: Patient 49 [UCI37]


title: Patient 51 [UCI52]


title: siRNA_STAT5B_rep3a_VL-57_S30

description: Sample "_STAT5B_rep3a_VL57_" not used in final analysis


title: Patient 48 [UCI36]


title: siRNA_STAT5B_rep2b_VL-47_S20


title: siRNA_STAT5B_rep2a_VL-47_S20


title: Patient 47 [UCI33]


title: Patient 46 [UCI25]


title: siRNA_STAT5B_rep1a_VL-37_S9


title: siRNA_STAT5B_rep1b_VL-37_S9


title: 3h2_50

city: Changsha

first: Kaixuan

state: Hunan

address: 87 Xiangya Road, Kaifu District

institute: Xiangya Hospital Central South University

data_processing:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq®RNA Sample Preparation Kit (Illumina, USA)  following TruSeq®RNA Sample Preparation Guide.
Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, USA). The library construction and sequencing was performed at Shanghai Biotechnology Corporation.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: bladder tissue

extract_protocol:
The rats were anesthetized with intraperitoneal injection of 2% pentobarbital sodium (0.2ml/100g) and then killed by visceral blood collection. An abdominal incision was made to expose the urinary bladder with stereoscope. The obtained bladder tissues were washed with pre-cooled isotonic normal saline and then cut into pieces. Washed away the visible clots, and removed the connective tissue, fat and pollutants. Removed the components likely to interfere the required targets. Centrifugated at 4℃, 1000 rpm for 2min, and removed the supernatant. Separated the tissue, one was for RNA extraction according to the specification of the RNA extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Sprague-Dawley rats

value: 25mg/kg/day ketamine hydrochloride injection


title: 2L4_50


title: siRNA_RUNX1T1_rep3a_VL-56_S29


title: siRNA_RUNX1T1_rep3b_VL-56_S29


title: Patient 45 [UCI17]


title: Patient 44 [CV215]


title: Patient 43 [CV213]


title: 2h_50


title: O3-1_50

value: normal saline


title: o1_50


title: Patient 41 [CoV045]


title: Patient 42 [CoV048]


title: siRNA_RUNX1T1_rep1b_VL-36_S8


title: siRNA_RUNX1T1_rep2a_VL-46_S18


title: o2_50


title: siRNA_RUNX1T1_rep2b_VL-46_S18


title: siRNA_RUNX1T1_rep1a_VL-36_S8


title: Patient 39 [CoV042]


title: TM15_liver [F_plus]

city: Grugliasco

first: Dominga

last: Soglia

state: Torino

address: largo Braccini 2

department: Veterinary science

country: Italy

institute: Università degli Studi di Torino

data_processing:
Libraries were then processed with Illumina cBot for cluster generation on the flowcell, following the manufacturer’s instructions and sequenced on paired-end mode
The CASAVA 1.8.2 version of the Illumina pipeline was used to processed raw data for both format conversion and de-multiplexing.
Trimming (removing lower quality bases and adapters) using ERNE1 and Cutadapt2 softwares.
Alignments with TopHat2. Reads alignment on reference genome/transcriptome (with default parameters).
Execute transcripts count with provided annotation file (.GFF/.GTF) (Cufflinks3). Quality control by using RSeqQC4 package:
Genome_build: Gallus gallus reference genome (v.4.0) database
Supplementary_files_format_and_content: comparisons of genes/transcripts expression between CT and TM groups in each tissue (Cuffdiff file)

organism: Gallus gallus

source_name: liver parenchyma (L; central right lobe)

growth_protocol: 80 one-day-old male broiler chicks (Ross 708) were raised in 10 pens (8 birds/pen)

extract_protocol:
The total RNA of each homogenized sample was extracted using the TRIzol® method (Invitrogen, Carlsbad, CA, USA).
The TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA) was used for library preparation following the manufacturer’s instructions, starting with 1µg of RNA

treatment_protocol: fed with two diets (5 pens/diet): a control diet (CT) and an isonitrogenous and isoenergetic TM diet, obtained by partially replacing soybean meal, corn gluten meal, and soybean oil with 15% levels of full-fat TM larva meal

value: liver

tag: diet

value: Tenebrio molitor dietary inclusion (15%)


title: CT_breast [M_minus]

source_name: breast (B; central Pectoralis major)

tag: tissue

value: breast

value: standard


title: Patient 38 [CoV040]


title: TM15_breast [M_plus]


title: siRNA_NR1H3_rep2a_VL-55_S28

source_name: Endometrial Stromal Fibroblasts


title: Patient 37 [CoV039]


title: siRNA_NR1H3_rep1b_VL-35_S7


title: Patient 36 [CoV037]


title: TM15_jejunum  [D_plus]

source_name: approximately 5 cm length of the jejunum proximal tract adjacent to the Meckel’s diverticulum

value: jejunum


title: siRNA_KDM5B_rep3b_VL-54_S27


title: CT_jejunum  [D_minus]


title: Patient 35 [CoV036]


title: CT_liver [F_minus]


title: Patient 34 [CoV035]


title: siRNA_NR1H3_rep1a_VL-35_S7


title: CT_caecum [C_minus]

source_name: the apex of the caecum

value: caecum


title: TM15_caecum [C_plus]


title: Patient 33 [CoV034]


title: Patient 40 [CoV043]


title: siRNA_KDM5B_rep2b_VL-44_S17


title: Patient 32 [CoV33]


title: siRNA_KDM5B_rep2a_VL-44_S17


title: siRNA_KDM5B_rep1b_VL-34_S6


title: siRNA_NR1H3_rep2b_VL-55_S28


title: Liver wildtype rep4

city: Dallas

first: Lara

last: Bideyan

state: TX

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

data_processing:
For RNA-Seq, aata quality analysis was performed via FastQC
The reads were aligned to the mm10 genome using STAR (version 2.6.0c).
Differential expression analysis was performed with DESeq2 and genes were classified as significantly regulated if adjusted P value < 0.05.
Genes were annotated using biomaRt package in R (https://www.R-project.org/).
Genome_build: mm10
Supplementary_files_format_and_content: excel file showing the RNA-Seq results from DESeq2
Supplementary_files_format_and_content: csv file showing the normalized counts from RNA-Seq for each gene for each sample obtained from DESeq2

source_name: Left lobe of liver

extract_protocol:
Total RNA from frozen tissue was extracted through TRIzol (Invitrogen) and Qiagen RNeasy Mini Kit.
Total RNA libraries were made with Universal Plus mRNA-Seq Library Preparation Kit (NuGEN).

treatment_protocol: Mice were fasted 6 hours before sacrifice.

tag: age

value: 18 weeks old

value: wild type


title: Liver wildtype rep3


title: Patient 30 [CoV31]


title: siRNA_KDM5B_rep1a_VL-34_S6


title: siRNA_Ctrl4_rep2b_VL-48_S21

description: Ctrl4 is for KDM5B, NR1H3, RUNX1T1, STAT5B


title: Liver wildtype rep2


title: Liver wildtype rep1


title: Patient 29 [CoV30]


title: Patient 28 [CoV29]


title: Liver Brap knockout rep4

value: Brap liver knockout


title: siRNA_KDM5B_rep3a_VL-54_S27

value: T HESC


title: siRNA_Ctrl4_rep2a_VL-48_S21


title: siRNA_Ctrl4_rep1b_VL-38_S10


title: Patient 27 [CoV28]


title: siRNA_Ctrl4_rep1a_VL-38_S10


title: Liver Brap knockout rep3


title: Liver Brap knockout rep2


title: Liver Brap knockout rep1


title: Patient 31 [CoV32]


title: siRNA_HOXA7_rep3b_VL-52_S25


title: siRNA_HOXA7_rep3a_VL-52_S25


title: siRNA_HOXA7_rep2b_VL-42_S15

description: Sample "_HOXA7_rep2b_VL42_" not used in final analysis


title: Patient 23 [CoV24]


title: siRNA_HOXA7_rep2a_VL-42_S15

description: Sample "_HOXA7_rep2a_VL42_" not used in final analysis


title: P_OE

city: changzhou

first: runzi

last: sun

state: Jiangsu

address: 185 juqian street

institute: soochow university

description: bulk RNAseq of AIM2 over expressing HCC cell line

data_processing:
raw data were processed by standard bulk RNAseq pipeline
alignment, convert, and count reads.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: in vitro cell line

growth_protocol: HCC cells are growth in DMEM with 10% FBS and 1% PS

extract_protocol:
standard total RNA-seq
illumina RNAseq library protocol

treatment_protocol: lentivirus is transduced following the protocol

value: hepatocellular carcinoma cell line

tag: treatment

value: AIM2 over-expressing


title: Patient 22 [CoV23]


title: siRNA_HOXA7_rep1b_VL-32_S4

value: T HESCs (ATCC CRL-4003)


title: Patient 21 [CoV22]

value: blood


title: siRNA_HOXA7_rep1a_VL-32_S4


title: Patient 19 [CoV20]


title: siRNA_FOXF1_rep3b_VL-51_S24

description: Sample "_FOXF1_rep3b_VL51_" not used in final analysis


title: Patient 18 [CoV19]


title: Patient 17 [CoV18]


title: siRNA_FOXF1_rep2b_VL-41_S14


title: siRNA_FOXF1_rep3a_VL-51_S24

description: Sample "_FOXF1_rep3a_VL51_" not used in final analysis


title: Patient 26 [CoV27]


title: Patient 16 [CoV17]


title: Patient 25 [CoV26]


title: siRNA_FOXF1_rep2a_VL-41_S14


title: P_NC_OE

description: bulk RNAseq of control vector transduced HCC cell line

value: control vector transduced


title: Patient 24 [CoV25]


title: Patient 15 [CoV16]


title: siRNA_FOXF1_rep1a_VL-31_S3


title: Patient 13 [CoV14]


title: Patient 20 [CoV21]


title: siRNA_ERF_rep3b_VL-50_S23

value: ERF


title: ATAC-seq AML_BCORWT_R2

city: Boston

first: Eva

middle: Johanna

last: Schaefer

state: MASSACHUSETTS

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Raw RNA-seq reads were mapped to the GRCh38 build of the human genome by STAR (Dobin et al., 2013). Gene counts were obtained using featureCounts (Liao et al., 2014). Normalization and differential gene expression analysis was performed using the R package DESeq2 (Love et al., 2014). Genome build: Hg38.
ChIP-seq and ATAC-seq alignments and peak calling were performed using the ChiLin pipeline (Qin et al., 2016). Reads were mapped to the hg19 human reference genome with BWA (Li and Durbin, 2009). Mapped reads were indexed and sorted using samtools (Li et al., 2009). Peaks were called with MACS2 (Version 2.1.1, https://github.com/macs3-project/MACS; (Zhang et al., 2008)) at -q 0.01. The --SPMR option was used to generate bedgraph and bigwig files normalized to 1 million reads. Genome build: Hg19.
mERRBS FASTQ files were generated by using the Illumina pipeline. Adapter sequences were filtered out using the FAR software (Dodt, M, Ahmed R, Dieterich C. FAR -- flexible adapter remover. FAR project website (2011)) (http://sourceforge.net/projects/theflexibleadap/). Reads were aligned to the hg19 genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool. Genome build: Hg19.
Supplementary_files_format_and_content: matrix of raw RNA-seq counts; gene counts were obtained using featureCounts (Liao et al., 2014). Genome build: Hg38.
Supplementary_files_format_and_content: ChIP-seq and ATAC-seq bw files normalized to 1 million reads; bw files  were generated using the MACS2 --SPMR option  (Version 2.1.1, https://github.com/macs3-project/MACS; (Zhang et al., 2008)). Genome build: Hg19.
Supplementary_files_format_and_content: methylation call file (myCpG.txt); tab-delimited text file that contains the location of the CpG, total read coverage on the C base, percentage of bisulfite-converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The column headers are: chrBase, chr, base, strand, coverage, freqC, freqT. Genome build: Hg19.

source_name: primary AML cells

growth_protocol: K562 , KG1, MV4-11, and OCI-AML3 cells were cultured in RPMI-1640 medium (Gibco™) with 10% fetal bovine serum (FBS, Sigma-Aldrich) and 1% penicillin-streptomycin-glutamine (PSG, Gibco™) at 37°C and 5% CO2. Primary AML samples were obtained with informed consent from patients with newly diagnosed or relapsed acute myeloid leukemia. Leukemic blasts were isolated from whole blood using CD3 depletion and ficoll density gradient separation. Cell viability and sample purity was determined by trypan blue staining and FACS analyses.

extract_protocol:
ATAC-seq experiments were performed using an adjusted version of the Omni-ATAC protocol (Corces et al., 2017). 100,000 cells were resuspended in 50 ul cold ATAC-resuspension buffer (RSB, 10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2 in water) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and incubated on ice for 3 minutes. After lysis, 1 ml ATAC-RSB containing 0.1% Tween-20 was added to the mixture and centrifuged for 10 minutes at 1,500 RCF in a pre-chilled (4 °C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 ul transposition mix (2.5 ul transposase Tn5 (100 nM final), 25 ul 2x TD buffer, 16.5 ul 1x PBS, 0.5 ul 1% Digitonin, 0.5 ul 10% Tween-20 in water) (Corces et al., 2017). Transposition reactions were incubated at 37 °C for 30 minutes in a thermomixer.
Libraries were made according to protocol described by Buenrostro et al. (Buenrostro et al., 2015).  35-bp paired-end reads were sequenced on an Illumina NextSeq 500 system.

tag: genotype

value: BCORWT


title: CD90neg3

city: Melbourne

first: Jacky

middle: Yisheng

state: Victoria

address: 50 Flemington Rd

department: Cellular Biology

country: Australia

institute: MCRI

description: cd90AllCounts.txt [RNA260719-5]

data_processing:
For bulk sequencing data sequenced reads were mapped to GrCh38 whole human genome with the Spliced Transcript Alignment to a Reference (STAR) software using default parameters. Nonuniquely mapping reads and read pairs with unpaired alignments were excluded.
For single cell data, sequenced reads were mapped to the GrCh38 whole human genome with cell ranger software using the default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: count matrix for bulk sequencing data, features and barcodes and count matrix for single cell data

source_name: Human embryonic stem cell derived CD104+ EPCAM+ FOXN1+ cells

growth_protocol: Neonatal human thymic stromal cells were grown on Geltrex-coated cell cutlure plate and cultured with a chemically defined serum- and ablbumin-free medium.

extract_protocol:
RNA was isolated using the ISOLATEII RNA micro-Kit (Bioline, BIO-52075) as described by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 5 ng/ml KGF

value: Embryonic stem cell

tag: isolated population

value: CD104+ GFP+ EPCAM+ CD90-

tag: itgb4 antibody

value: Conjugated monoclonal mouse anti-human antibodies:CD104-APC (1:50, clone 422325, Invitrogen)

tag: epcam antibody

value: Conjugated monoclonal mouse anti-human antibodies:EPCAM-PeCy7 (1:200, clone 12c2, BioLegend), EPCAM-BV421(1:50, clone 9C4, BioLegend)

tag: cd90 antibody

value: Conjugated monoclonal mouse anti-human antibodies:CD90-PE (1:100, clone 5e10, Biolegend), CD90-BV421 (1:50, clone 5e10, Biolegend)


title: ATAC-seq AML_BCORWT_R1


title: CD90neg2

description: cd90AllCounts.txt [RNA301019-4]


title: CD90pos3

description: cd90AllCounts.txt [RNA260719-4]

value: CD104+ GFP+ EPCAM+ CD90+


title: CD90neg1

description: cd90AllCounts.txt [RNA301019-2]


title: CD90pos2

description: cd90AllCounts.txt [RNA301019-3]


title: CD90pos1

description: cd90AllCounts.txt [RNA301019-1]


title: siRNA_ERF_rep2b_VL-40_S13

data_processing:
All sequencing data were uploaded and analyzed on the Galaxy platform (https://usegalaxy.org/; Version 20.01). Individual reads for particular samples ("_rep1a" and "_rep1b") were concatenated using the “Concatenate datasets” tool (version 1.0.0). We used HISAT2 (version 2.1.0+galaxy5) (Kim, Langmead and Salzberg, 2015) to align reads to the Human hg38 reference genome using “Single-end” option, and reporting alignments tailored for transcript assemblers including StringTie. Transcripts were assembled and quantified using StringTie (v1.3.6) (Pertea et al., 2015, 2016), with reference file to guide assembly and the “reference transcripts only” option, and output count files for differential expression with DESeq2/edgeR/limma-voom. Differentially expressed genes were identified using DESeq2 (version 2.11.40.6+galaxy1) (Anders and Huber, 2010; Love, Huber and Anders, 2014). The reference file for StringTie guided assembly was wgEncodeGencodeBasicV33.
Genome_build: hg38
Supplementary_files_format_and_content: Unmodified DESeq2 output

extract_protocol:
48 hours post treatment cells were washed with PBS, trypsinized (0.05% Trypsin-EDTA; 15400-054, Thermo Fisher Scientific) and total RNA was extracted using RNeasy Plus Mini Kit (74134, QIAGEN) following the manufacturer’s protocol. RNA from knockdown and control samples were DNase treated with TURBO DNA-free Kit (AM1907, Thermo Fisher Scientific).
RNA-Seq libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human (RS-122-2201, Illumina Inc.) following manufacturer’s protocol. Library quality and quantity were checked on 2100 Bioanalyzer and the pool of libraries was sequenced on Illumina HiSEQ4000 (single-end 50bp) using manufacturer’s reagents and protocols. Quality control, Ribo-Zero library preparation and Illumina sequencing were performed at the Genomics Facility at The University of Chicago.


title: Patient 10 [CoV11]

tag: disease


title: Patient 11 [CoV12]


title: siRNA_ERF_rep2a_VL-40_S13


title: siRNA_ERF_rep3a_VL-50_S23


title: ATAC-seq K562_BCORKO_BCORL1KO_R3

source_name: K562 cell line


title: HTS-15 KGF CD104+EPCAM-

description: htsAllCounts.txt [RNA03032021-24]

source_name: Cultured human thymic stromal cells

value: thymus

value: Single positive CD104+EPCAM-


title: siRNA_FOXF1_rep1b_VL-31_S3


title: ATAC-seq K562_BCORKO_BCORL1KO_R2


title: Patient 14 [CoV15]


title: siRNA_ERF_rep1b_VL-30_S2


title: ATAC-seq K562_BCORKO_BCORL1KO_R1


title: Patient 8 [CoV9]


title: Patient 12 [CoV13]


title: HTS-15 KGF CD104-EPCAM-

description: htsAllCounts.txt [RNA03032021-27]

value: Double negative CD104-EPCAM-


title: Patient 7 [CoV8]


title: siRNA_ERF_rep1a_VL-30_S2

value: T HESC


title: HTS-15 KGF CD104+EPCAM+

description: htsAllCounts.txt [RNA03032021-23]

value: Double positive CD104+ EPCAM+


title: HTS-15 KGF (3) unsort

description: htsAllCounts.txt [RNA03032021-20]

value: Unsorted


title: ATAC-seq MV411_parental_R2

source_name: MV411 cell line

value: WT


title: Patient 6 [CoV7]

value: blood


title: ATAC-seq MV411_parental_R1


title: siRNA_CENPT_rep2b_VL-39_S12

description: Sample "_CENPT_rep2a_VL39_" not used in final analysis

value: T HESCs (ATCC CRL-4003)

value: CENPT


title: siRNA_CENPT_rep3a_VL-49_S22

description: Sample "_CENPT_rep2b_VL39_" not used in final analysis


title: HTS-7 KGF CD104-EPCAM-

description: htsAllCounts.txt [RNA03032021-7]


title: Patient 9 [CoV10]


title: Patient 5 [CoV6]


title: HTS-7 KGF CD104+EPCAM-

description: htsAllCounts.txt [RNA03032021-6]


title: Patient 3 [CoV3]


title: HTS-7 KGF CD104+EPCAM+

description: htsAllCounts.txt [RNA03032021-5]


title: ATAC-seq KG1_parental_R1

source_name: KG1 cell line


title: siRNA_CENPT_rep1b_VL-29_S1


title: Patient 2 [CoV2]


title: siRNA_CENPT_rep1a_VL-29_S1


title: ATAC-seq K562_KDM2BKO_R2


title: HTS-10 KGF unsort

description: htsAllCounts.txt [RNA03032021-4]


title: siRNA_CENPT_rep3b_VL-49_S22


title: siRNA_Ctrl3_rep3b_VL-53_S26

description: Ctrl3 is for CENPT, ERF, FOXF1, HOXA7


title: HTS-10 KGF CD104+EPCAM-

description: htsAllCounts.txt [RNA03032021-2]


title: ATAC-seq K562_KDM2BKO_R1


title: siRNA_Ctrl3_rep3a_VL-53_S26

description: Ctrl3 is for CENPT, ERF, FOXF1, HOXA7


title: ATAC-seq OCIAML3_parental_R2

source_name: OCIAML3 cell line


title: HTS-7 KGF unsort

description: htsAllCounts.txt [RNA03032021-8]


title: Patient 4 [CoV4]


title: HTS-10 KGF CD104+EPCAM+

description: htsAllCounts.txt [RNA03032021-1]


title: D6_NegCtrl [D6_N3_S28_L002]

city: South San Francisco

first: Jacob

middle: Cameron

last: Kimmel

state: CA

address: 1170 Veterans Blvd

department: Computing

institute: Calico Life Sciences, LLC

data_processing:
base calling: bcl2fastq
alignment: kallisto quant
differential expression: sleuth
normalization: kallisto quant
Genome_build: mm10
Supplementary_files_format_and_content: h5ad [Samples, Genes] matrix of TPM values.

growth_protocol: Cells grown in 6-well plates in DMEM supplemented with 10%FBS and 1% Pen/Strep.

extract_protocol:
RNAlater, TRIzol, Zymo DirectZol columns
NEB Ultra II Directional RNA Library Prep Kit

treatment_protocol: Doxcycline at 0 or 4 ug/mL in media

tag: cell line background

tag: day

tag: reprogramming treatment

value: NegCtrl


title: D6_NegCtrl [D6_N3_S28_L001]


title: ATAC-seq OCIAML3_parental_R1


title: ATAC-seq K562_PCGF1KO_R1


title: D6_NegCtrl [D6_N2_S27_L002]


title: siRNA_CENPT_rep2a_VL-39_S12

city: Buffalo

first: Vincent

address: 551 Cooke Hall

institute: University at Buffalo, SUNY

tag: catalog#

tag: cell line


title: siRNA_Ctrl3_rep2a_VL-43_S16

description: Ctrl3 is for CENPT, ERF, FOXF1, HOXA7

tag: tag


title: ATAC-seq KG1_parental_R2


title: ATAC-seq K562_BCORKO_R2

value: BCORKO


title: siRNA_Ctrl3_rep1b_VL-33_S5

description: Ctrl3 is for CENPT, ERF, FOXF1, HOXA7


title: HTS-10 KGF CD104-EPCAM-

description: htsAllCounts.txt [RNA03032021-3]


title: ATAC-seq K562_BCORKO_R1


title: Patient 1 [CoV1]


title: D6_NegCtrl [D6_N1_S26_L002]


title: D6_NegCtrl [D6_N1_S26_L001]


title: siRNA_Ctrl3_rep1a_VL-33_S5

description: Ctrl3 is for CENPT, ERF, FOXF1, HOXA7


title: ATAC-seq K562_WT_R2


title: siRNA_YY1_rep3b_VL-106_S55

growth_protocol: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (CS-FBS; 12676029, Thermo Fisher Scientific), 1% L-glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1x insulin-transferrin selenium (ITS; 41400045, Thermo Fisher Scientific)

value: T-HESC

tag: sirna


title: ATAC-seq K562_WT_R1


title: ATAC-seq K562_PCGF1KO_R2


title: siRNA_Ctrl3_rep2b_VL-43_S16

description: Ctrl3 is for CENPT, ERF, FOXF1, HOXA7


title: D6_Pulse [D6_Dx3_S25_L002]

value: Pulse


title: D8-3

city: Chicago

first: Jennillee

last: Wallace

state: IL

address: 1735 W Harrison St

institute: Rush University Medical Center

data_processing:
Raw reads were trimmed to remove Truseq adapters and bases from the 3’ end with quality scores less than 20 using cutadapt (Martin, 2011); trimmed reads shorter than 40bp were be discarded. Trimmed reads were  aligned to the reference genome in a splice-aware manner using the STAR aligner (Dobin et al., 2013). ENSEMBL gene expression were quantified  FeatureCounts (Liao et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text of gene expression: unnormalized counts

source_name: M-MDMs

growth_protocol: monocytes were differentiated into monocyte derived macrophages with M-CSF only (M-MDMs) or further skewed with addition of IL-4 (M2a-MDMs), then treated with cART (Drug A or T) or 7 days

extract_protocol:
RNA was extracted using Qiagen miRNAeasy kit following the manufacturer's instructions.
Universal Plus mRNA-Seq Library Preparation Kit with NuQuant (Tecan 0520-A01)

tag: individual (donor name)

tag: cell type

value: macrophages (MDMs)

tag: treatment (proteins)

value: 1 (M-CSF only)

tag: treatment (cart drug)

value: T (Triumeq)


title: D8-4

value: 2 (M-CSF and addition of IL-4 to skew to M2a-MDMs)

value: Control


title: siRNA_YY1_rep3a_VL-106_S55


title: D8-6


title: siRNA_YY1_rep2b_VL-100_S49


title: D7-6


title: D8-2

value: A (Atripla)


title: D6_Pulse [D6_Dx2_S24_L002]


title: ChIP-seq MV411_parental_H3K27me3

extract_protocol:
For histone ChIP-seq analysis, cells were cross-linked for 10 min with 1% formaldehyde at room temperature on a shaker at 850rpm. Crosslinked nuclei were quenched with 0.125 M glycine for 5 minutes at room temperature and washed with PBS (containing protease inhibitor and HDAC inhibitor Sodium Butyrate (NaBut)). For ChIP-seq analysis of BCOR, BCORL1, RNF2, KDM2B, and SUZ12, cells were first fixed with 2 mM DSG for 45 min at RT, followed by formaldehyde cross-linking as described above. After fixation, pellets were resuspended in 500 ul of 1% SDS (50 mM Tris-HCl pH 8, 10 mM EDTA) and sonicated in 1 ml AFA fiber millitubes for 25 minutes using a Covaris E220 instrument (setting: 75 peak incident power, 5% duty factor and 200 cycles per burst). Chromatin was immunoprecipitated using primary antibody and Dynabeads® Protein A/G.
ChIP-seq libraries were made using the ThruPLEX DNA-seq 48D Rubicon kit and purified. 75-bp single-end reads were sequenced on an Illumina NextSeq instrument.

tag: genotype

value: parental

tag: chip antibody


title: D6_NegCtrl [D6_N2_S27_L001]


title: D8-5


title: siRNA_YY1_rep2a_VL-100_S49


title: D8-1


title: D6_Pulse [D6_Dx2_S24_L001]


title: siRNA_YY1_rep1b_VL-94_S43


title: ChIP-seq K562_KDM2BKO_H2AK119ub


title: D6_Pulse [D6_Dx1_S23_L002]


title: ChIP-seq K562_KDM2BKO_H3K27me3


title: siRNA_YY1_rep1a_VL-94_S43


title: D7-4


title: ChIP-seq K562_KDM2BKO_H3K27ac


title: D7-5


title: D6_Pulse [D6_Dx1_S23_L001]


title: D6_Pulse [D6_Dx3_S25_L001]


title: ChIP-seq K562_WT_KDM2B


title: D5_Pulse [D5_Dx3_S22_L002]


title: D5_Pulse [D5_Dx3_S22_L001]


title: siRNA_PPARD_rep3b_VL-105_S54

value: PPARD


title: D7-2


title: siRNA_PPARD_rep3a_VL-105_S54


title: D7-3


title: D5_Pulse [D5_Dx2_S21_L002]


title: D6-5


title: D5_Pulse [D5_Dx2_S21_L001]


title: siRNA_PPARD_rep2b_VL-99_S48


title: D6-6


title: ChIP-seq OCIAML3_parental_H3K27me3


title: ChIP-seq MV411_parental_H3K27ac


title: ChIP-seq K562_KDM2BKO_R1_BCOR

value: BCOR


title: D7-1


title: ChIP-seq KG1_parental_H3K27me3

value: WT


title: siRNA_PPARD_rep1b_VL-93_S42


title: siRNA_PPARD_rep2a_VL-99_S48


title: D5_Pulse [D5_Dx1_S20_L002]


title: D6-4


title: D4_Pulse [D4_Dx3_S19_L001]


title: D4_Pulse [D4_Dx3_S19_L002]


title: ChIP-seq KG1_parental_H3K27ac


title: siRNA_PPARD_rep1a_VL-93_S42


title: siRNA_Ctrl2_rep3b_VL-107_S56

description: Ctrl2 is for PPARD and YY1


title: D4_Pulse [D4_Dx2_S18_L002]


title: siRNA_Ctrl2_rep3a_VL-107_S56

description: Ctrl2 is for PPARD and YY1


title: D5_Pulse [D5_Dx1_S20_L001]


title: D6-1


title: ChIP-seq MV411_parental_BCOR


title: ChIP-seq KG1_parental_BCOR


title: ChIP-seq OCIAML3_parental_H3K27ac


title: D4_Pulse [D4_Dx2_S18_L001]


title: D6-3


title: D4_Pulse [D4_Dx1_S17_L001]


title: ChIP-seq AML_BCORWT_input

value: BCORWT


title: D5-3


title: D5-5


title: siRNA_Ctrl2_rep1b_VL-95_S44

description: Ctrl2 is for PPARD and YY1

value: T HESCs (ATCC CRL-4003)


title: D6-2


title: ChIP-seq OCIAML3_parental_BCOR


title: ChIP-seq AML_BCORWT_H3K27me3


title: siRNA_Ctrl2_rep1a_VL-95_S44

description: Ctrl2 is for PPARD and YY1


title: D4_Pulse [D4_Dx1_S17_L002]


title: D5-6


title: siRNA_Ctrl2_rep2a_VL-101_S50

description: Ctrl2 is for PPARD and YY1


title: ChIP-seq AML_BCORWT_H3K27ac


title: D5-4


title: siRNA_Ctrl2_rep2b_VL-101_S50

description: Ctrl2 is for PPARD and YY1


title: siRNA_ESRRA_rep3b_VL-103_S52

value: ESRRA


title: D3_NegCtrl [D3_ND3_S16_L002]

value: NegCtrl


title: ChIP-seq K562_BCORL1KO_BCORL1


title: ChIP-seq AML_BCORWT_BCOR


title: siRNA_ESRRA_rep3a_VL-103_S52


title: D3_NegCtrl [D3_ND3_S16_L001]


title: D5-1


title: siRNA_ESRRA_rep2b_VL-97_S46


title: D3_NegCtrl [D3_ND1_S14_L002]


title: ChIP-seq K562_BCORKO_R2_BCORL1

value: BCORKO


title: siRNA_ESRRA_rep2a_VL-97_S46

value: T-HESC


title: D5-2


title: D3_NegCtrl [D3_ND2_S15_L001]


title: siRNA_ESRRA_rep1b_VL-91_S40


title: ChIP-seq K562_WT_BCORL1


title: D3_NegCtrl [D3_ND2_S15_L002]


title: siRNA_ESRRA_rep1a_VL-91_S40


title: ChIP-seq K562_BCORKO_R1_BCORL1


title: D4-3


title: siRNA_DRAP1_rep3b_VL-102_S51


title: D4-2


title: ChIP-seq K562_BCORKO_BCORL1KO_SUZ12


title: D4-5


title: D4-6


title: D4-4


title: D3_Pulse [D3_DxPos_S7_L002]

value: Pulse


title: siRNA_DRAP1_rep3a_VL-102_S51


title: D3_Pulse [D3_DxPos_S7_L001]


title: D3_NegCtrl [D3_ND1_S14_L001]


title: D4-1

value: macrophages (MDMs)


title: ChIP-seq K562_BCORPUFDTr_BCOR

value: BCORPUFDTr


title: ChIP-seq K562_KDM2BKO_R2_BCOR


title: D3_Pulse [D3_DxPos3_S13_L002]


title: D3-6

value: T (Triumeq)


title: siRNA_DRAP1_rep2b_VL-96_S45


title: D3-5

value: 2 (M-CSF and addition of IL-4 to skew to M2a-MDMs)


title: ChIP-seq AML_BCORPUFDTr_H3K27me3


title: siRNA_DRAP1_rep1b_VL-90_S39


title: D3_Pulse [D3_DxPos3_S13_L001]


title: ChIP-seq AML_BCORPUFDTr_H3K27ac


title: ChIP-seq K562_WT_SUZ12


title: ChIP-seq AML_BCORPUFDTr_BCOR


title: D3-4

value: Control


title: D3-3

value: 1 (M-CSF only)


title: D3-2

value: A (Atripla)


title: ChIP-seq K562_BCORKO_BCORL1KO_H2AK119ub


title: siRNA_Ctrl1_rep3b_VL-104_S53

description: Ctrl1 is for DRAP1 and ESRRA


title: D3_Pulse [D3_DxPos2_S8_L001]


title: siRNA_DRAP1_rep1a_VL-90_S39


title: D3_Pulse [D3_DxPos2_S8_L002]


title: D1_NegCtrl [D1_ND3_S6_L002]


title: siRNA_Ctrl1_rep3a_VL-104_S53

description: Ctrl1 is for DRAP1 and ESRRA


title: D3-1


title: D1_NegCtrl [D1_ND3_S6_L001]


title: ChIP-seq K562_BCORKO_BCORL1KO_H3K27me3


title: D1_NegCtrl [D1_ND2_S5_L002]


title: siRNA_Ctrl1_rep2b_VL-98_S47

description: Ctrl1 is for DRAP1 and ESRRA


title: ChIP-seq K562_BCORKO_BCORL1KO_H3K27ac


title: siRNA_DRAP1_rep2a_VL-96_S45


title: D2-6


title: siRNA_Ctrl1_rep2a_VL-98_S47

description: Ctrl1 is for DRAP1 and ESRRA


title: D1_NegCtrl [D1_ND2_S5_L001]


title: ChIP-seq K562_PCGF1KO_input


title: D2-5


title: siRNA_Ctrl1_rep1b_VL-92_S41

description: Ctrl1 is for DRAP1 and ESRRA


title: D2-4


title: D1_NegCtrl [D1_ND1_S4_L002]


title: ChIP-seq K562_BCORKO_input


title: ChIP-seq K562_WT_input


title: siRNA_Ctrl1_rep1a_VL-92_S41

description: Ctrl1 is for DRAP1 and ESRRA


title: D1_NegCtrl [D1_ND1_S4_L001]


title: D2-3


title: D1_Pulse [D1_Dx3_S3_L001]


title: MKC8866_24h_R3

city: Galway

first: Afshin

last: Samali

address: Newcastle Road, Biosciences Research Building

department: Apoptosis Research Centre

country: Ireland

institute: NUIG Galway

description: IRE1 inhibition

data_processing:
Sequenced reads were assessed in a quality control step with FastQC, MultiQC. Followed by adapter sequences trimming with TrimGalore.
Reads were aligned with reference genome using STAR. > 80% of uniquely mapped reads for each library.
Reads/counts per gene were summarized with FeatureCounts.
Genome_build: GRCh38 (Ensembl 99)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: breast cancer cell line

growth_protocol: MDA-MB-231 cells were seeded at density 2 × 104 cells per mm2 24 hours before treatment. Cultured in DMEM high glucose (Sigma-Aldrich, D6429) supplemented with 10% FBS and 2 mM L-glutamine at 37 °C, 5% CO2 in a humidified incubator.

extract_protocol:
RNA was isolated using Rneasy columns (Qiagen, 74104) according to the manufacturer’s protocol. RNA integrity was checked using the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols at EMBL Genomics Core facility in Heidelberg

treatment_protocol: Cells were treated with DMSO (control) or MKC8866 (IRE1 inhibitor) for the indicated time.

tag: treatment

tag: treatment duration

value: 24 hours


title: D2-2


title: MKC8866_24h_R2

description: IRE1 inhibition


title: D1_Pulse [D1_Dx3_S3_L002]


title: D1_Pulse [D1_Dx2_S2_L002]


title: MKC8866_24h_R1

description: IRE1 inhibition


title: ChIP-seq K562_PCGF1KO_H2AK119ub


title: D2-1


title: ChIP-seq K562_WT_H2AK119ub


title: ChIP-seq K562_BCORKO_H2AK119ub


title: DMSO_24h_R2

description: control

value: DMSO 20 μM


title: D1_Pulse [D1_Dx1_S1_L002]


title: D1_Pulse [D1_Dx2_S2_L001]


title: DMSO_24h_R3

description: control


title: ChIP-seq K562_BCORKO_BCOR

value: BCOR


title: ChIP-seq K562_WT_BCOR

value: WT


title: D1_Pulse [D1_Dx1_S1_L001]


title: DMSO_24h_R1

description: control


title: ChIP-seq K562_PCGF1KO_BCOR


title: MKC8866_8h_R3

description: IRE1 inhibition

value: 8 hours


title: D8_PosCtrl [220113_PosCtrl3_S31_L002]

value: PosCtrl


title: ChIP-seq K562_WT_RING1B


title: D8_PosCtrl [220113_PosCtrl3_S31_L001]


title: ChIP-seq K562_BCORKO_H3K27me3


title: D8_PosCtrl [220113_PosCtrl2_S30_L002]


title: DMSO_8h_R3

description: control


title: MKC8866_8h_R2

description: IRE1 inhibition


title: ChIP-seq K562_WT_H3K27me3


title: ChIP-seq K562_PCGF1KO_H3K27me3


title: D8_PosCtrl [220113_PosCtrl1_S29_L002]


title: MKC8866_8h_R1

description: IRE1 inhibition


title: ChIP-seq K562_PCGF1KO_H3K27ac


title: D8_PosCtrl [220113_PosCtrl1_S29_L001]


title: ChIP-seq K562_WT_H3K27ac


title: D8_NegCtrl [220113_NegCtrl3_S34_L002]

value: NegCtrl


title: 48h_1299_5_Scr_1uM_PTC

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

data_processing:
[trimming and alignment]  Quality control was performed with FastQC and adapter sequences were removed using Trimgalore v0.6.5. Reads were then aligned to the Ensembl  GRCh38 human reference genome using STAR v2.6.1 with gene count quantification mode, retaining only uniquely mapped reads.
[post-processing and filtering]  Lowly expressed genes (CPM < 1) were filtered out via a custom-made script in R and further biotype filtering was performed in R with the Bioconductor packages NOISeq and biomaRt, removing residual highly expressed mitochondrial and ribosomal RNA. Trimmed mean of M-values (TMM) normalization was applied to the dataset prior to differential expression (DE) analysis, performed using the Bioconductor package edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: raw, unfiltered gene counts

source_name: Medulloblastoma

growth_protocol: ICb1299 were cultured in DMEM (high glucose, GlutaMAX™, ThermoFisher) supplemented with 10% foetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (Gibco). CHLA-01-Med MB cells were grown in DMEM-F12 (Gibco) supplemented with B27 (Gibco), 20 ng/mL human epidermal growth factor (EGF, Peprotech) and 10 ng/mL human basic fibroblast growth factor (FGF, Peprotech)

extract_protocol:
Total RNA was extracted with RNA/DNA/Protein Purification Plus kit (Norgen), polyA mRNA was selected and library prepared using the NEBNext Ultra II Directional RNA Library Prep kit.
Libraries were size selected, multiplexed and 75bp paired-end sequences were obtained with HiSeq4000 (Illumina)

treatment_protocol: Cells were treated with 1uM PTC-209 (PTC, Tocris), 100nM PD325901 (PD, Tocris) or DMSO for the reported time.

tag: knockdown

value: Scramble

value: 48h of PTC-209 1uM treatment


title: D8_PosCtrl [220113_PosCtrl2_S30_L001]


title: D8_NegCtrl [220113_NegCtrl3_S34_L001]


title: 48h_1299_5_shC_1uM_PTC


title: 48h_1299_5_Scr_DMSO

value: 48h of DMSO treatment


title: D8_NegCtrl [220113_NegCtrl2_S33_L002]


title: RNA-seq K562_PCGF1KO_R1

extract_protocol:
Total RNA was extracted according to the manufacturer’s recommendations using RNeasy Plus Mini Kit (Qiagen, Cat#74134) or High Pure RNA Isolation Kit (Roche, Cat#11828665001).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely dual indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 550 with single-end 75bp reads or a NovaSeq 6000 with 50bp read pairs.


title: RNA-seq K562_PCGF1KO_R2


title: ChIP-seq K562_BCORKO_H3K27ac

value: BCORKO


title: RNA-seq K562_BCORKO_R2


title: D8_NegCtrl [220113_NegCtrl2_S33_L001]


title: 28h_1299_5_shC_100nM_PD

value: 28h of PD325901 100nM treatment


title: RNA-seq K562_BCORKO_R1


title: D8_NegCtrl [220113_NegCtrl1_S32_L001]


title: 28h_1299_5_shC_1uM_PTC

value: 28h of PTC-209 1uM treatment


title: DMSO_8h_R2

description: control


title: DMSO_8h_R1

description: control


title: D8_Pulse [220113_3d_pulse_6_S12_L002]

value: Pulse


title: RNA-seq K562_WT_R2


title: 28h_1299_5_shC_DMSO

value: 28h of DMSO treatment


title: RNA-seq K562_WT_R1


title: 28h_1299_5_Scr_100nM_PD


title: D8_Pulse [220113_3d_pulse_6_S12_L001]


title: 28h_1299_5_Scr_1uM_PTC


title: D8_Pulse [220113_3d_pulse_5_S11_L002]


title: 48h_1299_5_shC_DMSO


title: Tulipa gesneriana 'Red Power' stage 4 rep1

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for base calling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two stages was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate .  Genes with |fold change| >2 and P-value<0.05 were assigned as differentially expressed.

organism: Tulipa gesneriana

source_name: bulb

extract_protocol:
The bulbs of Tulipa gesneriana at different stages were collected for RAN isolation using plant RNA purification kit (Tiangen, Beijing, China). RNA purity and integrity were assessed using the NanoPhotometer® Spectrophotometer (IMPLEN, CA, USA) and the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: bulb

tag: treatment time

value: 'Red Power' bulb development stage 4

value: Red Power


title: 48h_1299_4_Scr_DMSO


title: 28h_1299_5_Scr_DMSO


title: D8_Pulse [220113_3d_pulse_4_S10_L002]

tag: cell line background

tag: day


title: D8_Pulse [220113_3d_pulse_5_S11_L001]

tag: reprogramming treatment


title: Tulipa gesneriana 'Red Power' stage 2 rep2

value: 'Red Power' bulb development stage 2


title: Tulipa gesneriana 'Red Power' stage 3rep1

value: 'Red Power' bulb development stage 3


title: D8_Pulse [220113_3d_pulse_4_S10_L001]


title: D8_NegCtrl [220113_NegCtrl1_S32_L002]


title: Tulipa gesneriana 'Red Power' stage 3 rep2


title: Tulipa gesneriana 'Red Power' stage 4 rep2


title: 48h_1299_4_shC_1uM_PTC

tag: cell line


title: 48h_1299_4_Scr_1uM_PTC


title: Tulipa gesneriana 'Red Power' stage 2 rep1


title: 48h_1299_4_shC_DMSO


title: Tulipa gesneriana 'Red Power' stage 1 rep2

value: 'Red Power' bulb development stage 1


title: D8_Pulse [220113_3d_pulse_2_S36_L002]


title: D8_Pulse [220113_3d_pulse_2_S36_L001]


title: 28h_1299_4_shC_1uM_PTC


title: Tulipa gesneriana 'Red Power' stage 1 rep1


title: Tulipa gesneriana 'Ad Rem' bulb stage 5 rep2

value: 'Ad Rem' bulb development stage 4

value: Ad Rem


title: 28h_1299_4_shC_DMSO