title: Day 85 OPC

first: Xitiz

last: Chamling

state: MD

address: 400 N. Broadway

institute: Johns Hopkins University School of Medicine

description: single cell from 10X

data_processing:
Cell Ranger 2.1.0 pipeline was used to generate count matrices according to manufacturer recommendations
processed reads were aligned to GRCh38 using the STAR RNA aligner
exons were tagged using the Homo_sapiens.GRCh38.88.gtf annotations file
Genome_build: hg19
Supplementary_files_format_and_content: 10x filtered feature-barcode matrix where rows and columns are barcodes and genes. Created by running cellranger mat2csv on filtered_gene_bc_matrices_h5.h5

source_name: stem cell derived PDGFRα+ cells

growth_protocol: hOPCs differentiattion from hES and hIPSCs was initiated using a dual SMAD inhibition and addition of 100 nM all-trans RA. From day 8 to day 12, differentiating cells were maintained in neural induction media supplemented with RA (100nM) and SAG (1 mM). At day 12, adherent cells were lifted and cultured in low-attachment plates to favor sphere aggregation. At day 30, spheres were plated into poly-L-ornithine/laminin-coated dishes in a media supplemented with, B27 (Thermo Fisher, 12587010), N2 supplement (Thermo Fisher, 17502048), PDGF-AA, neurotrophin-3, HGF, and T3. Once a significant number of tdTomato+ OPCs were visible around day 65-70, a PDGF media without mitogens (PDGF-AA, HGF, NT-3) was used to drive oligodendrocyte maturation.

extract_protocol:
Differentiating hOPC cultures were were dissociated into single cell suspension by incubating in accutase for ~45 minutes. The single cell suspension was then passed through a ~70 uM cell strainer. To purify PDGFRα expressing cells, the dissociated cells were resuspended in MACS buffer and CD90.2 (THY1.2) or O4 microbeads and incubated at room temperature for 15 minutes for cell binding. Please note that the hES cells used here are knock-in reporter cell lines where the PDGFRα drives the expression of tdTomato and CD90.2, allowing hES-derived OPCs to be purified using CD90.2 microbeads. After incubation with the beads, cells are generally run through the MS column twice without additional supplementation of MicroBeads to increase the purity and achieve ~90% tdTomato+ cells. The purified PDGFRα-tdTomato+ cells are then used to single cell capture by 10X.
10x Genomics Single Cell 3' v2 according to Manufacturers Recommendation

value: hES-derived OPCs

tag: age

value: day 85


title: KRAB_rep1_HbF_high

status: Public on Dec 22 2020

type: SRA

city: Boston

last: Liu

state: MA

address: 300 Longwood Avenue

department: Hematology/Oncology

country: USA

institute: Boston Children's Hospital

description:
KRAB_deconvolved_scores.bedgraph
KRAB_neglog10_pvals.bedgraph
KRAB_raw_scores.bed

library_source: genomic

data_processing:
Library strategy: CRISPR Screen
DESeq2 was then used to compare the sgRNA counts between sorted and unsorted samples
sgRNA counts were used as input into CRISPR-SURF Count with the following parameters: -nuclease cas9, -pert indel (for Cas9 samples) or -pert crispri (for dCas9 samples). With the resulting output, CRISPR-SURF Deconvolution was applied with the following parameters: -pert cas9, -sim_n 1000, and the perturbation range parameter -range 7 (for Cas9) or -range 20 (for dCas9). The CRISPR-SURF deconvolution analysis provides p-values and statistical power for the CRISPR dense perturbation data.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph contains the raw score, deconvoluted score, or p value of each sgRNA

molecule: genomic DNA

organism: Homo sapiens

source_name: HUDEP-2 cells

extract_protocol:
genomic DNA was extracted using the Qiagen Blood and Tissue kit. sgRNA integrant PCR to amplify spacer sequences was performed with Herculase II reaction buffer (1X), forward and reverse primers (0.5 μM each), dimethyl sulfoxide (DMSO) (8%), deoxynucleotide triphosphates (dNTPs) (0.25 μM each), Herculase II Fusion DNA Polymerase (0.5 reactions) using the following cycling conditions: 95°C for 2 min; 20 cycles of 95°C for 15 s, 60°C for 20 s, 72°C for 30 s; 72°C for 5 min. Multiple reactions of no more than 200 ng each were used to amplify from 6.6 ug gDNA (~1x106 cell genomes) per pool. Samples were subjected to additional rounds of PCR to add sequencing adaptors and indices before Illumina sequencing.
sgRNA integrant PCR to amplify spacer sequences was performed with Herculase II reaction buffer (1X), forward and reverse primers (0.5 μM each), dimethyl sulfoxide (DMSO) (8%), deoxynucleotide triphosphates (dNTPs) (0.25 μM each), Herculase II Fusion DNA Polymerase (0.5 reactions) using the following cycling conditions: 95°C for 2 min; 20 cycles of 95°C for 15 s, 60°C for 20 s, 72°C for 30 s; 72°C for 5 min. Multiple reactions of no more than 200 ng each were used to amplify from 6.6 ug gDNA (~1x106 cell genomes) per pool. Samples were subjected to additional rounds of PCR to add sequencing adaptors and indices before Illumina sequencing.

treatment_protocol: HUDEP-2 cells were transduced with lentivirus encoding various Cas9 or dCas9 variants to produce stably expressing cells. The cells were then transduced with the sgRNA lentivirus library and selected with 1 μg/ml puromycin. Cells were transduced at MOI of 0.3. Cell numbers were maintained throughout the experiment with at least 1000 cells per spacer sequence. After sgRNA transduction, cells were cultured in EDM2 medium for 12 days.

tag: cell line

tag: tissue

value: Erythroid

tag: crispr

tag: hbf-sorted population

value: high

tag: differentiation stage

value: Day 12


title: RMS_breast tumor_140 [VMT267]

city: Lyon

first: Virginie

last: MARCEL

address: 28 rue Laennec

country: France

institute: Cancer Research Center of Lyon

library_source: transcriptomic

data_processing:
library strategy: RiboMethSeq
Adatper sequences were removed with Trimmomatic v0.36. Reads shorter than 17 nucleotides were discarded.
Reads were aligned to the human rRNA sequence with Bowtie 2.
5' end reads were counted at each rRNA nucleotide position
Genome_build: NR_046235
Supplementary_files_format_and_content: Raw counts of 5' end reads on each position of the rRNA subunits

molecule: total RNA

source_name: RMS_breast tumor

extract_protocol:
RNAeasy kit (Qiagen)
Total RNA was first subjected to partial alkaline hydrolysis to generate RNA fragments ranging from 50 to 100 bp. Libraries were then prepared using NEBNext Multiplex Small RNA Library Prep Set

value: primary breast tumour

tag: subtype

value: ER+ HER2-

tag: p53 status

value: WT

tag: Stage

value: Stage 3

tag: molecule subtype

value: ribosomal RNA


title: 6498 nodules soybean 21 Days 2

type: RNA

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

description: nodules soybean 21 dpi infected by a B. japonicum blr1880 mutant

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2–2.5 µg of labeled cDNA from culture-grown bacteria, and 6 -7.5 µg of total bacteroid cDNA were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich, St. Louis, USA) in addition to the described composition. Hybridization was done overnight at 48°C. The amount of bacteroid cDNA was estimated from the proportion of bacterial:plant RNA in nodules (Bioanalyzer, Agilent technologies, Palo Alto CA).

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed using the mas5 algorithm described in the Affymetrix statistical algorithms description document (http://www.affymetrix.com). Normalized signal values from the arrays were then analyzed using Genespring GX 7.3 (Agilent Technologies,CA, USA). For culture-grown bacteria or bacteroids, only those genes which are “present” (i.e., expressed, based on the detection P-value ≤ 0.06) in 80% of all replicates were further considered. For experiments comparing different conditions amongst culture-grown bacteria or bacteroids, each chip was normalized to the median. Values below 0.01 were set to 0.01. For statistical comparisons, the student t-test with a P-value threshold of 0.01 was applied. Genes were considered as differentially expressed if the fold change (FC) was higher than 2, when comparing different conditions amongst culture-grown bacteria or symbiotic bacteria.

label: biotin

organism: Bradyrhizobium japonicum

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix).  The double amounts of labeling reagent and terminal deoxynucleotide transferase was used for fragmented cDNA from bacteroids. The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: Cells were grown to mid-exponential phase (OD600 of 0.4-0.5) and stationary phase (OD600 of 2) in VMM minimal medium. For harvesting, cultures were rapidly transferred to cold tubes containing one tenth of the culture volume of “stop solution” (10% Tris-HCl-buffered phenol [pH 8] in ethanol), centrifuged for 5 min (10,800 × g; 4°C), the supernatant was decanted, and cells were frozen in liquid nitrogen and stored at −80°C. Nodules from 5 soybean plants were collected for each GeneChip hybridization experiment. Nodules were harvested 21 post inoculation (dpi) and immediately frozen in liquid nitrogen.

extract_protocol: Total RNA was isolated using the hot phenol extraction procedure described previously (Babst et al. 1996). For RNA isolation from symbiotically grown bacteria, approximately 10 frozen nodules were placed in a 2-ml Eppendorf tube, disrupted and homogenized using a TissueLyzer (Qiagen, Valencia, CA) (3 times for 50 sec; 30 Hertz) with a tungsten carbide bead (3 mm; Qiagen) (Pessi et al. MPMI, 2007). RNA integrity was checked by agarose gel electrophoresis. Precipitated RNA (100 µg) was treated with 20 units of RQ1 DNase I (Promega, Madison, USA) for 30 min at 37°C in a reaction volume of 200 µl. SUPERase•InTM (100 units; Ambion,Huntingdon, UK) was included in the reaction to inhibit potential RNase activity. RNA samples were cleaned up with RNeasy spin columns (Qiagen). cDNA was synthesized. according to the Affymetrix antisense genome array protocol for E. coli (http://www.affymetrix.com). For reverse transcription, MMLV reverse transcriptase RNase H minus (Promega, Madison, USA) was used in the supplied reaction buffer. The resulting cDNA was spectrophotometrically quantified and fragmented according to the Affymetrix manual except that the time for fragmentation by DNase I was shortened to 3 min. For control, 200 ng of DNase I-treated cDNA were separated on a 4-to–20% acrylamide gradient gel and stained with SYBR green II (Molecular Probes, Inc., Eugene, OR, USA). Ideally, the fragmented cDNA migrated in a range that corresponded to 50–200 bp of the 50-bp ladder (Fermentas International Inc., Burlington, Canada). RNA was isolated from the roots of soybean plants as described above, and cDNA was fragmented and labeled according to the protocol for free-living bacteria.

tag: strain

tag: genotype/variation

value: blr1880 mutant

tag: growth condition

value: nodules

tag: medium

value: soybean

tag: time

value: 21 Days


title: Ng-2

city: Changsha

first: Lvyun

last: Zhu

state: Hunan

address: 109 Deya Road, Kaifu District

department: College of Liberal Arts and Sciences

country: China

institute: National University of Defense Technology

description: Mock buffer, normal gravity, replicate 2

data_processing:
Sequence quality was examined using the FastQC software.
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to the reference genome using Hisat2 software (v2.0.4).
The transcript abundances for each sample were estimated with StringTie (v1.2.3), and the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0).
The differentially expressed genes and transcripts were filtered using R package Ballgown.
The novel genes and transcripts were predicted from assembled results by comparing them to the reference annotation using StringTie and Ballgown.
Genome_build: Danio rerio (assembly GRCz10)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: embryos

extract_protocol:
After 12 hours post fertilization (hpf), total RNA from each sample was extracted using TRIzol reagent and quantified by a NanoDrop ND-1000 instrument and agarose gel electrophoresis.
1–2 μg total RNA was used to prepare the sequencing library in the following steps: 1) Total RNA is enriched by oligo(dT) magnetic beads (rRNA removed); 2) RNA-seq library is prepared using a KAPA Stranded RNA-Seq Library Prep Kit, which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific.

treatment_protocol: One-cell stage embryos were microinjected with 2 nL (1 mg/μL) poly I:C or microinjection buffer (0.5% phenol red, 240 mM KCl, and 40 mM HEPES at pH 7.4) control using a microinjector (ASI MPPI-3) and then subjected immediately to the simulated microgravity conditions generated by RCCS or the normal gravity conditions in cell culture dish.

value: Wild-type AB

tag: gravity conditoin

value: Normal gravity

tag: stimulation

value: Mock buffer


title: HUVEC DMSO + IL-6 2

city: Albany

first: Alejandro

middle: Pablo

last: Adam

state: NY

address: 43 New Scotland Ave

department: Molecular and Cellular Physiology

institute: Albany Medical College

description: Non-ribosomal RNA

data_processing:
Trimming with trim galore v0.4.4
Alignment with salmon v 0.8.2
Import into R with tximport
Fold-change analysis with DESeq2
Annotation with biomart and EnsDb.Hsapiens.v86
Genome_build: Genome Reference Consortium Human Build 38
Supplementary_files_format_and_content: csv file with counts per million reads mapped (CPM)

source_name: HUVEC

growth_protocol: Grown at confluency in EGM-2 media

extract_protocol:
Trizol
GENEWIZ Riibo--Zero workflow

treatment_protocol: Post-confluent (48h) monolayers

tag: cell type

value: HUVEC

tag: treatment


title: RMS_breast tumor_139 [VMT266]

tag: tissue

value: TNBC


title: Cas9_rep_3_HbF_high

description:
Cas9_deconvolved_scores.bedgraph
Cas9_neglog10_pvals.bedgraph
Cas9_raw_scores.bed

tag: cell line

value: Erythroid

tag: crispr


title: HUVEC DMSO + IL-6 1

description: Non-ribosomal RNA


title: Ng-1

description: Mock buffer, normal gravity, replicate 1


title: RMS_breast tumor_138 [VMT265]


title: HUVEC DMSO 3

description: Non-ribosomal RNA

value: DMSO


title: Cas9_rep_2_presort

tag: hbf-sorted population

value: presort

tag: differentiation stage

value: Day 12


title: HUVEC DMSO + IL-6 3

description: Non-ribosomal RNA


title: RMS_breast tumor_137 [VMT264]

value: primary breast tumour

tag: subtype

tag: p53 status


title: HUVEC DMSO 2

description: Non-ribosomal RNA


title: M1KO_844

city: Baltimore

first: Guang

middle: William

last: Wong

address: 855 N Wolfe Street

department: School of Medicine

institute: The Johns Hopkins University

data_processing:
Illumina CASAVA performed base-calling of Illumina NovaSeq 6000 150bp paired-end data producing FASTQ files.
Data were filtered to remove reads containing adaptors, with N>10% of bases, or error rates > 0.02%.
STAR v2.5 performed mapping to mm10 with mismatch=2 and the MMP option.
HTSeq v0.6.1, with -m union setting, quantified the reads to FPKM
DESeq2 v2_1.6.3 performed diffferential analysis using the negative binomial distribution, where FDR adjustment was by the Benjamini and Hochberg algorithm.
Genome_build: NCBI mm10
Supplementary_files_format_and_content: Processed data supplementary file, Wong_FPKM_Values.zip, is a zipped .txt file of the FPKM values used in the DESeq2 differential analysis.  A sample's FPKM column name corresponds to its title with "_fpkm" (e.g. M1WT_769_fpkm)

organism: Mus musculus

source_name: Kidney

extract_protocol:
Whole kidneys from the anatomical left were immediately excised from euthanized WT and CTRP1-deficient mice and flash frozen in liquid nitrogen. Total RNA was isolated using Trizol reagent (Thermo Fisher Scientific, Carlsbad, CA.)  per the manufacturer's protocol. RNA samples were subjected to DNASE I (New England Biolabs, Ipswwich, MA.) digestion to remove genomic DNA contamination using the manufacturer's protocol. A 3M (pH 5.2) sodium actetate (Quality Biological, Gaithersburg, MD.) precipation was performed after DNASE I digestion to purify RNA samples.  In brief, sodium acetate was added at 1/10 the volume of the sample followed by the addition of 2.5 volumes of ice cold 100% ethanol and mixed throroughly. The samples were incubated at -80 ° C overnight. The samples were centrifuged at 12,000 x g for 20 minutes at 4° C and the supernantant was decanted. The RNA pellets were washed twice using 1ml of ice cold 75% ethanol and centrifuged at 12,000 x g at 4° C. A quick spin was performed to removed any traces of residual ethanol in the pellet using a very fine pipette tip. The pellets were air dryed and reconsitituted in sterile filtered molecular biology grade water (Quality Biological, Gaithersburg, MD). The RNA quality number (RQN) of total RNA was determined for each sample before RNA-seq analysis was performed by Novogene.
Quality-controlled total RNA was purified to mRNA with poly-T magnetic beads, fragmented, and then reverse transcribed into cDNA.  Fragments of 150~200bp were selected and the library PCR amplified.

treatment_protocol: The Ctrp1 KO (-/-) mouse strain used for this research project (B6;129S5-C1qtnf1tm1Lex/Mmucd, identification number 032164-UCD) was obtained from the Mutant Mouse Regional Resource Center (MMRRC), an NCRR-NIH funded strain repository, and was donated to the MMRRC by Genentech, Inc. The Ctrp1 gene is located on mouse chromosome 11 and comprises 4 exons. The largest exon, exon 4 (which codes for 61% of the full-length protein), was targeted by homologous recombination. A total of 679 bp, spanning the coding region of exon 4 and a portion (162 bp) of the 3’UTR, was deleted. Heterozygous mice were recovered from cryo-preserved embryos. Since the ES cells were derived from the 129S5/Sv mouse strain, we backcrossed Ctrp1 KO mice to the C57BL/6J genetic background for >6 generations. All Ctrp1-KO (-/-) and WT (+/+) littermate controls used in this study were generated by intercrossing Ctrp1 heterozygous (+/-) mice. Male and female Ctrp1 KO mice and WT littermate controls were housed in polycarbonate cages on a 12-h light-dark photocycle with ad libitum access to water and food.

value: kidney

tag: age

value: 49 weeks

tag: genotype


title: Cas9_rep_2_HbF_high

value: high


title: RMS_breast tumor_135 [VMT262]

value: ER+ HER2-

value: WT

tag: Stage

value: Stage 3

tag: molecule subtype

value: ribosomal RNA


title: Cas9_rep_1_presort


title: HUVEC DMSO 1

description: Non-ribosomal RNA


title: RMS_breast tumor_134 [VMT261]

value: Stage 2


title: MITF-X6-rep4

city: reykjavik

first: Ramile

last: Dilshat

address: Sturlugata 8

department: Biochemistry and Molecular biology

country: Iceland

institute: University of Iceland

data_processing:
RNA-seq reads were aligned using Kallisto with --bootstrap 100
Differential expressed genes were called using Sleuth
Genome_build: GRCh38
Supplementary_files_format_and_content: count file generated from Kallisto

molecule: polyA RNA

source_name: SkMel28_MITF knock out - Cas-gRNA-X6

extract_protocol:
RNA was extracted using TRIZOL reagent and treated with DNase I.
mRNA was isolated using NEBNext Poly(A) mRNA isolation module (E7490, NEB) with using approximately 1µg total RNA. Then, RNA-Sequencing library was generated using NEBNext Ultra Directional RNA library Kit (E7420S, NEB) with isolated mRNA as input.

value: skin melanoma cell line

value: MITF knock out - Cas-gRNA-X6


title: Cas9_rep_1_HbF_high


title: M1KO_770

tag: strain


title: MITF-X6-rep3


title: RMS_breast tumor_136 [VMT263]


title: M1KO_754


title: MITF-X6-rep2


title: M1WT_842

value: wild type


title: RMS_breast tumor_132 [VMT259]

value: MT


title: RMS_breast tumor_133 [VMT260]


title: MITF-X6-rep1


title: M1WT_821


title: RMS_breast tumor_131 [VMT258]

value: TNBC


title: M1WT_799


title: M1WT_769


title: RMS_breast tumor_130 [VMT257]


title: EV-SKmel28-rep4


title: EV-SKmel28-rep3


title: M1KO_823


title: RMS_breast tumor_129 [VMT256]


title: EV-SKmel28-rep2


title: RMS_breast tumor_128 [VMT255]


title: Treatment_2_rep_C_day_2

city: Peoria

first: Christopher

last: Dunlap

state: IL

address: 1815 N. University st

department: Crop Bioprotection Research Unit

institute: USDA-ARS

data_processing:
Raw sequencing reads were checked for adapters and quality trimmed to Q30 using Genomics Workbench (version 10.0.1) (Qiagen, Inc, Germantown, MD, USA). The reads were mapped to the B. bassiana strain D1-5 reference genome (GenBank accession no. ANFO01000000) using the 85% length alignment and 85% similarity.  Expression values were normalized using RPKM and a separate General Linear Model with a negative binomial distribution under Genomics Workbench. Statistical comparisons of differential gene expression between treatments were conducted pairwise with Wald tests and Bonferroni corrected P-values determined under Genomics Workbench. Differentially expressed genes with False discovery rate (FDR) adjusted p-value (< 0.005) and log2(fold change, FC) > 2 or < -2 were used for the final data set.
Supplementary_files_format_and_content: rpkm values

organism: Beauveria bassiana

source_name: Strain GHA ARSEF 201

growth_protocol: Three independent biological samples (i.e., whole culture in shake flasks) were collected for each fermentation time (i.e., days 1, 2, and 3) were collected (1 mL), centrifuged at 16,000g for 5 minutes to pellet the cells, the supernatant decanted and the pellet flash-frozen in liquid nitrogen. The pellet was homogenized with a mortar and pestle under liquid nitrogen. Total RNA was extracted with a Qiagen RNAeasy Kit (Germantown, MD, USA). RNA quality was confirmed using an Agilent 2200 tapestation. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA), and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA integrity number (RIN) was considered acceptable if greater than 6. The library preparation and sequencing were performed by Brigham Young University DNA sequencing center. The mRNA was selected with an oligo poly dT selection, and the library was prepared with an Illumina TruSeq RNA library kit. The final library was sequenced with an Illumina HiSeq 2500 with 50 cycle single read sequencing V4.

extract_protocol:
qiagen
cDNA

value: Strain GHA ARSEF 201

value: 20% glucose

tag: time

value: day 2


title: RMS_breast tumor_127 [VMT254]

value: primary breast tumour


title: Flag empty vector overexpression

city: Bei jing

first: zhimin

last: jiang

address: No.2 Yuanmingyuan West Road, Haidian District, Beijing

department: college of Veterinary medicine

institute: China agriculture university

description: The cells were transfected with FLAG-tagged RIG-I or IFI16 constructs and infected with PR8 (MOI = 2) for 12 hr, the FLAG empty vector as the negative control.

data_processing:
The callpeak file is generated by MACS version 2.1.1.20160309 to analyse the maximum duplicate fragments and Redundant rate .
Genome_build: PR8/H1N1 genome
Supplementary_files_format_and_content: callpeak

source_name: RIG-I knockout 293T cells

extract_protocol:
1 mL Tri-reagent (Sigma) was added to each sample, and RNA was harvested according to the manufacturer’s instructions. RNA was eluted from beads and examined by  RNA-seq
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: HEK293T cells were transfected with FLAG-tagged RIG-I or IFI16 constructs and infected with PR8 (MOI = 2) for 12 hr. Cells were disrupted in IP lysis buffer(25U RNasin) and lysates were then incubated with 30 mL/sample anti-FLAG agarose bead overnight with rotation at 4 C. Beads were collected by centrifugation, washed ten times with NT2 buffer.resuspended in 250 mL of DNase digestion buffer (40 mM Tris  [pH 8.0], 10 mM MgSO4, 1 mM CaCl2), and treated with 25U RNasin (Promega) and 2U DNase I (NEB) at 37 C for 20 min. Beads were then washed and resuspended in 100 mL NT2 buffer and treated with 4 units proteinase K at 55 C for 30 min. ( as described in the Thapa et al., 2016, Cell Host & Microbe 20, 674–681).

tag: iav strain

value: Viral RNA


title: Treatment_2_rep_C_day_1

value: day 1


title: RMS_breast tumor_126 [VMT252]


title: Treatment_2_rep_A_day_3

value: day 3


title: Treatment_2_rep_B_day_1


title: RMS_breast tumor_125 [VMT251]

value: ER+ HER2-


title: Treatment_2_rep_B_day_2


title: Treatment_2_rep_A_day_2


title: RMS_breast tumor_122 [VMT248]

value: WT


title: RMS_breast tumor_123 [VMT249]


title: RMS_breast tumor_124 [VMT250]

value: Stage 3


title: CD14+_monocytes_*03:01/*13:01_28

city: Solna

first: Leonid

last: Padyukov

address: Visionsgatan 18

department: Division of Rheumatology, Department of Medicine

country: Sweden

institute: Karolinska Institutet

data_processing:
Raw read quality was evaluated using FastQC. Pre-filtering on quality of reads using cutadapt (version 1.9.1) was applied (-q 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 40).
Filtered reads were aligned to the hg38 assembly, containing the MHC reference haplotype PGF (GENCODE release 28 (GRCh38.p12)), using STAR in two-pass mode (version 2.5.4b) with default settings. STAR was also used to obtain the gene counts.
Counts of genes in the MHC region (chr6: 28,500,000-33,500,000) were replaced with counts obtained from AltHapAlignR. In short, unmapped reads and reads mapped to the MHC region (using MHC reference haplotype PGF) were extracted and realigned to all available MHC reference haplotypes (APD, COX, DBB, MANN, MCF, QBL, SSTO) independently using STAR in two-pass mode.
Raw expression counts obtained from STAR (non-MHC genes) and AltHapAlignR (MHC genes) were adjusted for library size using the R package DESeq2 (version 1.26.0). Pre-filtering of low count genes was performed to keep only genes that had at least 50 counts in total over all samples. The counts were regularized-logarithm transformed for principal component analysis (PCA). For each specific cell subset, RIN score was highly correlated with principal component 1 and used as covariate as binary category (< 7 and > 7) in the analyses. The default DESeq2 options were used, including log fold change shrinkage using apeglm and independent hypothesis weighting.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix tables per cell type with normalized gene counts for every gene and every sample

extract_protocol:
Buffy coats were processed by density gradient centrifugation using Ficoll (GE Healthcare Bio-Sciences AB, Uppsala, Sweden) and PBMCs were subsequently recovered. CD4+, CD8+, and CD14+ cells were isolated from the PBMCs via positive selection using CD4, CD8 or CD14 Microbeads (Miltenyi Biotec Norden AB, Lund, Sweden) on the autoMACS Pro Separator (Miltenyi Biotec Norden AB). Total RNA was extracted with the RNeasy Mini kit (Qiagen AB, Sollentuna, Sweden) according to manufacturer’s instructions.
The RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq stranded total RNA sample preparation kit with ribosomal depletion using RiboZero (2 x 125 bp) and sequenced on an Illumina HiSeq 2500 sequencer (SNP&SEQ Technology Platform, Uppsala, Sweden).

value: Blood

tag: Sex

value: F

tag: hla-drb1 alleles


title: CD14+_monocytes_*03:01/*15:01_31

tag: cell type


title: CD14+_monocytes_*03:01/*15:01_30

tag: tissue


title: Treatment_2_rep_A_day_1

tag: treatment


title: CD14+_monocytes_*01:01/*04:01_32


title: RMS_breast tumor_121 [VMT247]

value: ribosomal RNA


title: RMS_breast tumor_120 [VMT246]


title: Treatment_2_rep_C_day_3


title: CD14+_monocytes_*03:01/*15:01_17


title: CD14+_monocytes_*04:01/*14:01_24


title: Treatment_1_rep_C_day_3

value: 10% glucose


title: CD14+_monocytes_*01:01/*04:01_27


title: CD14+_monocytes_*01:01/*04:01_15


title: Treatment_2_rep_B_day_3


title: Treatment_1_rep_C_day_2


title: RMS_breast tumor_119 [VMT245]


title: Treatment_1_rep_C_day_1


title: Treatment_1_rep_B_day_3


title: RMS_breast tumor_117 [VMT243]


title: CD14+_monocytes_*04:01/*07:01_9


title: Treatment_1_rep_B_day_2


title: CD14+_monocytes_*03:01/*04:01_10


title: CD8+_Tcells_*01:01/*04:01_32


title: RMS_breast tumor_118 [VMT244]


title: RMS_breast tumor_115 [VMT240]


title: Treatment_1_rep_B_day_1


title: CD8+_Tcells_*03:01/*15:01_31


title: CD8+_Tcells_*03:01/*15:01_30


title: RMS_breast tumor_112 [VMT236]


title: Treatment_1_rep_A_day_2


title: Treatment_1_rep_A_day_3


title: RMS_breast tumor_116 [VMT241]


title: CD8+_Tcells_*03:01/*13:01_28


title: RMS_breast tumor_113 [VMT238]

value: LumiNAl


title: RMS_breast tumor_111 [VMT235]

value: MT


title: Treatment_1_rep_A_day_1


title: CD8+_Tcells_*03:01/*04:01_26


title: CD8+_Tcells_*01:01/*04:01_27


title: RMS_breast tumor_109 [VMT233]

value: Stage 1


title: RMS_breast tumor_110 [VMT234]

value: TNBC


title: CD8+_Tcells_*04:01/*09:01_25


title: CD8+_Tcells_*04:01/*04:04_22


title: CD8+_Tcells_*03:01/*13:01_23


title: RMS_breast tumor_107 [VMT231]


title: CD8+_Tcells_*04:08/*07:01_29


title: control serum,biological replicate 4

city: Kalyani

first: Bishnupriya

last: Chhatriya

state: West Bengal

address: PO NSS

country: India

institute: National Institute of Biomedical Genomics

description: miRNa expression data from healthy individual.

hyb_protocol: Biotinylated RNA were hybridized on Affymetrix GeneChip® miRNA 4.0 Arrays at 48 °C and 60 rpm for 16 h . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: Data were processed using R bioconductor Packages.

label: Biotin

source_name: Serum

label_protocol: RNA were biotinylated using the FlashTag Biotin HSR RNA Labelling kit (Affymetrix) according to manufacturer’s instructions.

extract_protocol: miRNA was isolated using miRNeasy kit from QIAGEN with glycogen method.

value: 50 years

tag: gender

value: Male

tag: disease

value: healthy


title: RMS_breast tumor_106 [VMT230]

value: primary breast tumour

value: Stage 2


title: RMS_breast tumor_105 [VMT229]


title: CD8+_Tcells_*03:01/*13:01_20


title: RMS_breast tumor_108 [VMT232]


title: patient serum,biological replicate 4

description: miRNA expression data from chronic pancreatitis patient.

value: 53 years

value: chronic pancreatitis


title: RMS_breast tumor_104 [VMT228]

value: WT


title: CD8+_Tcells_*03:01/*04:01_16


title: CD8+_Tcells_*03:01/*13:01_18


title: patient serum,biological replicate 2

value: 49 years


title: patient serum,biological replicate 3

value: 52 years


title: control serum,biological replicate 2

value: 40 years


title: control serum,biological replicate 3

value: 56 years


title: S2R+ M3(2.5%FEx) #2

city: Bloomington

first: Andrew

last: Zelhof

state: IN

address: 1001 East Third St

institute: Indiana University

description:
geneCounts.tsv
fex2_2

data_processing:
Demultiplexing of the reads was performed with bcl2fastq version 2.20.0 pipeline
Adapters and low quality bases were trimmed using Trimmomatic (version 0.36) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17
Reads were mapped to the Drosophila melanogaster dmel_r6.30 using Hisat2 (version 2.1.0)
Mapped reads were counted using Samtools (version version 1.9 ) and featureCounts (version 1.6.4)
R (version 3.6.0) and DESeq2 (version 1.24.0) were used to perform differential expresison analysis.
Genome_build: Drosophila melanogaster dmel_r6.30
Supplementary_files_format_and_content: tab-delimited text file of raw count values for each Sample ...

organism: Drosophila melanogaster

growth_protocol: S2R+ cells were cultured in the respective media and subcultured when they have reached cell density of no more than 8 million cells/mL back to a seeding density of 2 million cells/mL.

extract_protocol:
50 million cells were collected from a 10mL culture (5 million cells/mL), in triplicates. The cells were pelleted and total RNA was extracted using Trizol according to manufacturer's protocol. Total RNA were subsequently cleaned using Qiagen RNAeasy kit according to manufacturer's protocol.
First, the integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were processed using the following steps. From each sample, 1ug of total RNA was used for library preparation following the Illumina TruSeq Stranded mRNA library preparation kit protocol. The cleaned adapter ligated libraries were pooled and loaded on the NextSeq 500 with a 75 cycle sequencing module to generate paired-end reads.

tag: developmental stage

value: embryonic

value: Oregon-R

value: cultured in M3 + 2.5% Fex


title: CD8+_Tcells_*04:01/*14:01_12

value: Blood

value: F


title: S2R+ M3(2.5%FEx) #3

description:
geneCounts.tsv
fex2_3


title: CD8+_Tcells_*01:01/*04:01_15


title: EV-SKmel28-rep1

tag: cell line

value: skin melanoma cell line


title: CD8+_Tcells_*04:01/*07:01_7


title: S2R+ M3(2.5%FEx) #1

description:
geneCounts.tsv
fex2_1


title: S2R+ M3(10%FEx) #3

description:
geneCounts.tsv
fex10_3

value: cultured in M3 + 10% Fex


title: RMS_breast tumor_100 [VMT224]

tag: subtype

tag: p53 status

value: Stage 3

value: ribosomal RNA


title: RMS_breast tumor_102 [VMT226]

value: primary breast tumour

value: TNBC


title: S2R+ M3(10%FEx) #1

description:
geneCounts.tsv
fex10_1


title: CD8+_Tcells_*04:01/*13:03_8

tag: age


title: RMS_breast tumor_103 [VMT227]

tag: Stage


title: RMS_breast tumor_99 [VMT223]

value: LumiNAl

tag: molecule subtype


title: RMS_breast tumor_98 [VMT222]

value: MT


title: CD8+_Tcells_*03:01/*15:01_4


title: RMS_breast tumor_97 [VMT221]


title: S2R+ M3(10%FEx) #2

description:
geneCounts.tsv
fex10_2

tag: strain


title: S2R+ (M3BPYE10% FCS) #3

description:
geneCounts.tsv
S2R_3

value: cultured in M3 + BPYE + 10% FCS


title: control serum,biological replicate 1

value: Male

value: healthy


title: CD8+_Tcells_*03:01/*15:01_3


title: S2R+ (M3BPYE10% FCS) #2

description:
geneCounts.tsv
S2R_2


title: RMS_breast tumor_101 [VMT225]

value: WT


title: RMS_breast tumor_95 [VMT219]

value: Stage 2


title: CD8+_Tcells_*03:01/*04:01_1


title: S2R+ (M3BPYE10% FCS) #1

description:
geneCounts.tsv
S2R_1

value: embryonic

value: Oregon-R


title: CD8+_Tcells_*01:01/*04:01_5

value: Blood


title: CD4+_Tcells_*01:01/*04:01_32

value: F


title: RMS_breast tumor_94 [VMT218]


title: CD4+_Tcells_*03:01/*15:01_30


title: RMS_breast tumor_93 [VMT217]


title: CD4+_Tcells_*04:08/*07:01_29


title: RMS_breast tumor_92 [VMT216]


title: SMARCA4KO_SMARCA2dtag_3h_dTAG47_A

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Pro-Seq-single-rep-raw-counts-genebody-SMARCA4KO-SMARCA2-dtag.txt

data_processing:
Library strategy: PRO-seq
Read trimming was performed using Skewer (Jiang et al., 2014) for ATAC-seq and ChIP-seq data, Trimmomatic (Bolger et al., 2014) for RNA-seq data or cutadapt for Pro-seq data (Martin, 2011).
ATACseq and ChIP-seq: Read mapping was performed to GRCh38/hg38 using Bowtie2 (Langmead and Salzberg, 2012) and the “-very sensitive” parameter. Only unique reads with a mapping quality > 30 and alignment to the nuclear genome were included in the downstream analyses.
ATAC-seq: Peak calling was performed using MACS2 (Zhang et al., 2008) with the “-nomodel” and “extsize 147” parameters. Peaks overlapping blacklisted features defined in the ENCODE project (Hoffman et al., 2013) were discarded from the analyses.
Pro-seq: Raw reads (FASTQ) were trimmed using cutadapt v1.9.1 -a "TGGAATTCTCGGGTGCCAAGG" --minimum-length=10; trimmed reads were converted to reverse complements using fastx_reverse_complement v0.0.14; Read mapping was performed to a concatenated hg38_dm6_rDNA-U13369 genome using bowtie2 (Langmead and Salzberg, 2012) and filtered by a MAPQ value of 20; number of reads aligning to dm6 were counted with "samtools view | awk '$3 ~ /dm6_/ {++dm6_count}'" and normalization factor alpha=1e6/dm6_count (see PMID: 25437568); only 3' base (Pol II active center) was retained in BED files with "bedtools v2.26.0 bamtobed | awk '($6 == "+") {print $1,$3-1,$3,$4,$5,$6}; ($6 == "-") {print $1,$2,$2+1,$4,$5,$6}'"
RNA-seq: Read mapping was performed using STAR (Dobin et al.,2013) and the Ensembl transcript annotation from version e100 April2020 as reference transcriptome.
Genome_build: hg38
Supplementary_files_format_and_content: txt, raw read counts per region per sample
csv, raw read counts per region per sample
tsv, raw read counts per gene per sample

growth_protocol: HAP1 wildtype (Horizon Discovery C631) and knock-out cells were grown in Iscove's Modified Dulbecco's Medium (IMDM, Thermo Fisher Scientific, 21980-032 or Sigma I3390) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific 10500064) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122) at 37 °C and 5% CO2.

extract_protocol:
ATAC-seq was performed according to Buenrostro et al. with small adaptations (Buenrostro et al., 2015). In brief, 50,000 cells (1:2 drosophila S2 cells : HAP1 cells) were resuspended in 25 µl transposase reaction mix (0.02% digitonin (Promega G9441), 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer. On-plate ATAC-seq was performed as described for ATAC-seq, but without Drosophila spike-ins and performing transposase reaction on the plate. ChIP-seq and RNA-seq was performed as described in Schick et al., 2019. Pro-seq was performed as described in Jaeger et al., 2020.
ATAC-seq: 1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880). The libraries were checked on a Bioanalyzer instrument using High Sensitivity DNA Chips (Agilent), quantified using Qubit dsDNA HS Assay kit (Thermo Fisher Scientific, Q32854) and pooled. Libraries were sequenced using the Illumina HiSeq3000/4000 platform with the 75 bp paired-end configuration.   ChIP-seq: NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs E7645) was used for the library preparation as described by manufacturer protocol. The quality control of the ChIP samples was confirmed prior to sequencing on Bioanalyzer (Agilent Cat no. 5067-4626). Samples were sequenced on a HiSeq 3000/4000 platform using 50 bp single read configuration.  RNA-seq: RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts. Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-base-pair, single-end mode.  PRO-seq: Finally, RNA was reverse transcribed using RP1 primer with Superscript III and cDNA subjected to a 4x-dilution series test PCR to determine the optimal PCR cycle number for final sequencing library amplification. Full scale amplification with RPI-x indexing primers was then performed in 2x 50 µl reactions per sample for a total of 11-19 cycles. DNA was ethanol precipitated and subjected to 2x 1.1:1 AMPure XP bead left-side size selection according to manufacturer instructions. DNA concentration was determined using the Qubit dsDNA Hs kit and library size distribution was measured with Bioanalyzer. Libraries were pooled to equal molar ratios and sequenced on a HiSeq 3000/4000 system in 50SR mode, yielding ~60 mio reads per sample.

treatment_protocol: Cells were either treated with DMSO, 300 nM dTAG47, 1 µM BRM014, 3 µM ACBI1 or 3 µM cis-ACBI1 for the indicated time.

tag: genotype

value: SMARCA4 KO

tag: dtag

value: SMARCA2 dTAG

value: 3h dTAG47


title: RMS_breast tumor_90 [VMT214]

value: ribosomal RNA


title: RMS_breast tumor_91 [VMT215]

value: primary breast tumour

value: Stage 1


title: SMARCA4KO_SMARCA2dtag_3h_DMSO_B

value: DMSO


title: SMARCA4KO_SMARCA2dtag_3h_DMSO_A


title: CD4+_Tcells_*03:01/*13:01_28

tag: Sex


title: WT_SMARCA4dTAG_3h_dTAG47_A

description: Pro-Seq-single-rep-raw-counts-WT-SMARCA4-dtag-dtag-timecourse.txt, Pro-Seq-single-rep-raw-counts-genebody-WT-SMARCA4-dtag.txt

value: wild-type

value: SMARCA4 dTAG


title: WT_SMARCA4dTAG_3h_dTAG47_B


title: RMS_breast tumor_114 [VMT239]

value: TNBC

value: Stage 3


title: CD4+_Tcells_*04:01/*09:01_25

tag: hla-drb1 alleles


title: CD4+_Tcells_*03:01/*13:01_21

tag: cell type


title: WT_SMARCA4dTAG_3h_DMSO_A


title: CD4+_Tcells_*01:01/*04:01_27

tag: tissue


title: SMARCA4KO_SMARCA2dtag_3h_dTAG47_B

tag: treatment


title: WT_SMARCA4dTAG_3h_DMSO_B


title: RMS_breast tumor_89 [VMT213]

value: WT


title: RMS_breast tumor_86 [VMT210]

value: LumiNAl


title: CD4+_Tcells_*03:01/*15:01_31


title: patient serum,biological replicate 1

value: 55 years

tag: gender

value: Male

value: chronic pancreatitis


title: WT_DMSO_1h_B

description: Pro-Seq-single-rep-raw-counts-BRM014-timecourse.txt, Pro-Seq-single-rep-raw-counts-genebody-BRM014.txt


title: WT_DMSO_1h_A


title: RMS_breast tumor_96 [VMT220]

value: Stage 2


title: CD4+_Tcells_*03:01/*04:01_19

value: Blood

value: F


title: RMS_breast tumor_85 [VMT209]

value: MT


title: RMS_breast tumor_84 [VMT208]

value: ribosomal RNA


title: RMS_breast tumor_83 [VMT207]

value: primary breast tumour


title: CD4+_Tcells_*03:01/*15:01_17


title: RMS_breast tumor_87 [VMT211]


title: WT_BRM014_1h_B

value: 1h BRM014


title: WT_BRM014_30min_B

value: 30min BRM014


title: RMS_breast tumor_88 [VMT212]

value: Stage 1


title: CD4+_Tcells_*03:01/*04:01_16


title: CD4+_Tcells_*03:01/*13:01_23


title: CD4+_Tcells_*03:01/*13:01_20


title: RMS_breast tumor_80 [VMT204]


title: RMS_breast tumor_82 [VMT206]


title: RMS_breast tumor_81 [VMT205]


title: RNA_ref_ctrl_1 [VMT193]

value: pool of different origins


title: WT_BRM014_10min_B

value: wild-type

value: 10min BRM014


title: HAP1_SMARCC2_KO_DMSO_2_S67585

data_processing:
Read trimming was performed using Skewer (Jiang et al., 2014) for ATAC-seq and ChIP-seq data, Trimmomatic (Bolger et al., 2014) for RNA-seq data or cutadapt for Pro-seq data (Martin, 2011).
ATACseq and ChIP-seq: Read mapping was performed to GRCh38/hg38 using Bowtie2 (Langmead and Salzberg, 2012) and the “-very sensitive” parameter. Only unique reads with a mapping quality > 30 and alignment to the nuclear genome were included in the downstream analyses.
ATAC-seq: Peak calling was performed using MACS2 (Zhang et al., 2008) with the “-nomodel” and “extsize 147” parameters. Peaks overlapping blacklisted features defined in the ENCODE project (Hoffman et al., 2013) were discarded from the analyses.
Pro-seq: Raw reads (FASTQ) were trimmed using cutadapt v1.9.1 -a "TGGAATTCTCGGGTGCCAAGG" --minimum-length=10; trimmed reads were converted to reverse complements using fastx_reverse_complement v0.0.14; Read mapping was performed to a concatenated hg38_dm6_rDNA-U13369 genome using bowtie2 (Langmead and Salzberg, 2012) and filtered by a MAPQ value of 20; number of reads aligning to dm6 were counted with "samtools view | awk '$3 ~ /dm6_/ {++dm6_count}'" and normalization factor alpha=1e6/dm6_count (see PMID: 25437568); only 3' base (Pol II active center) was retained in BED files with "bedtools v2.26.0 bamtobed | awk '($6 == "+") {print $1,$3-1,$3,$4,$5,$6}; ($6 == "-") {print $1,$2,$2+1,$4,$5,$6}'"
RNA-seq: Read mapping was performed using STAR (Dobin et al.,2013) and the Ensembl transcript annotation from version e100 April2020 as reference transcriptome.
Genome_build: hg38
Supplementary_files_format_and_content: txt, raw read counts per region per sample
csv, raw read counts per region per sample
tsv, raw read counts per gene per sample

value: SMARCC2 KO

value: DMSO


title: CD4+_Tcells_*03:01/*15:01_14


title: CD4+_Tcells_*03:01/*13:01_13


title: HAP1_SMARCC1_KO_DMSO_2_S67584

value: SMARCC1 KO


title: WT_BRM014_10min_A


title: CD4+_Tcells_*04:01/*14:01_12


title: WT_BRM014_1h_A


title: RMS_breast tumor_79 [VMT186]

value: Stage 3


title: CD4+_Tcells_*03:01/*15:01_11


title: WT_BRM014_30min_A


title: HAP1_ARID2_KO_DMSO_2_S67583

description: rnaseq_deseq_ARID2KO_clone_counts_raw.tsv

value: ARID2 KO


title: CD4+_Tcells_*03:01/*13:01_18


title: RMS_breast tumor_78 [VMT185]

value: TNBC


title: CD4+_Tcells_*01:01/*04:01_15

value: Blood


title: V32

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to rn5 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted from uterine samples using a Qiagen RNeasy Lipid kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BPA administered by oral gavage from gestation day (GD) 6 through the start of labor and then by oral gavage to pups from postnatal day (PND) 1 (day of birth = PND 0) until experiment termination at PND365 was examined in Sprague-Dawley rats from the NCTR breeding colony (Sprague-Dawley/CD23/NctrBR). BPA doses were 2.5, 25, 250, 2,500, and 25,000 μg/kg body weight (bw)/day. A vehicle (0.3% carboxymethylcellulose (CMC)) control group and two doses (0.05 and 0.5 μg/kg bw/day) of the orally active estrogen ethinyl estradiol (EE2) were also included. n=4 per group

value: Sprague-Dawley

value: uterus


title: V31


title: CD4+_Tcells_*04:01/*07:01_9

value: F


title: RMS_breast tumor_77 [VMT184]

value: primary breast tumour

value: LumiNAl

value: WT

value: Stage 2

value: ribosomal RNA


title: HAP1_WT_SMARCA4_F1_dTAG_47_6h_2_S67626

value: wild-type

value: SMARCA4 dTAG

value: 6h dTAG47


title: CD4+_Tcells_*03:01/*04:01_10


title: HAP1_WT_SMARCA4_F1_dTAG_47_3h_2_S67625

value: 3h dTAG47


title: V30


title: CD4+_Tcells_*04:01/*13:03_8


title: V29


title: V27


title: HAP1_WT_SMARCA4_F1_dTAG_47_2h_2_S67631

value: 2h dTAG47


title: CD4+_Tcells_*03:01/*13:01_6


title: RMS_breast tumor_75 [VMT181]

value: MT

value: Stage 3


title: CD4+_Tcells_*04:01/*07:01_7


title: CD4+_Tcells_*01:01/*04:01_5


title: HAP1_WT_DMSO_2_S67618

value: DMSO


title: RMS_breast tumor_73 [VMT178]


title: HAP1_SMARCA4_KO_DMSO_2_S67619

description: rnaseq_deseq_BRG_clone_counts_raw.tsv,rnaseq_deseq_WT_clone_counts_raw.tsv

value: SMARCA4 KO


title: V26

value: Sprague-Dawley


title: HAP1_SMARCA2_KO_DMSO_2_S67620

value: SMARCA2 KO


title: RMS_breast tumor_71 [VMT175]


title: V25

value: uterus


title: RMS_breast tumor_76 [VMT183]

value: primary breast tumour


title: RNA_ref_ctrl_2 [VMT194_ctrl]

value: pool of different origins


title: PBMCs_*01:01/*04:01_32

source_name: PBMCs

value: Blood

value: PBMCs

value: F


title: RMS_breast tumor_70 [VMT174]

value: WT

value: ribosomal RNA


title: HAP1_WT_SMARCA4_F1_dTAG_47_24h_2_S67627

value: wild-type

value: SMARCA4 dTAG

value: 24h dTAG47


title: V28


title: V24

source_name: BPA 250


title: HAP1_CC1_CC2_F1_dTAG_47_72h_2_S67629

value: SMARCC1 KO

value: SMARCC2 dTAG

value: 72h dTAG47


title: RMS_breast tumor_69 [VMT173]

value: MT

value: Stage 3


title: PBMCs_*03:01/*15:01_30


title: PBMCs_*03:01/*15:01_31


title: V23

value: Sprague-Dawley


title: HAP1_CC1_CC2_F1_dTAG_47_3h_2_S67634

value: 3h dTAG47


title: V22

value: uterus


title: HAP1_CC1_CC2_F1_dTAG_47_2h_2_S67633

value: 2h dTAG47


title: PBMCs_*04:08/*07:01_29

value: Blood


title: RMS_breast tumor_72 [VMT176]

value: primary breast tumour


title: V21


title: RMS_breast tumor_67 [VMT171]

value: TNBC

value: Stage 2


title: RMS_breast tumor_68 [VMT172]

value: WT

value: ribosomal RNA


title: HAP1_CC1_CC2_F1_dTAG_47_24h_2_S67628


title: RMS_breast tumor_66 [VMT170]

value: LumiNAl


title: PBMCs_*03:01/*13:01_28

value: PBMCs

value: F


title: V20

source_name: BPA 25


title: PBMCs_*01:01/*04:01_27


title: HAP1_CC1_CC2_F1_DMSO_2_S67630

value: SMARCC1 KO

value: SMARCC2 dTAG

value: DMSO


title: V19


title: HAP1_CC1_CC2_F1_dTAG_47_6h_2_S67635

value: 6h dTAG47


title: PBMCs_*03:01/*04:01_26


title: RMS_breast tumor_64 [VMT168]

value: Stage 3


title: V18

value: Sprague-Dawley


title: PBMCs_*04:01/*09:01_25


title: V17

value: uterus


title: HAP1_BRG_BRM_C8_dTAG_47_6h_2_S67623

value: SMARCA4 KO

value: SMARCA2 dTAG


title: PBMCs_*04:01/*14:01_24

value: Blood


title: HAP1_BRG_BRM_C8_dTAG_47_3h_2_S67624

value: 3h dTAG47


title: PBMCs_*03:01/*13:01_23


title: HAP1_BRG_BRM_C8_dTAG_47_2h_2_S67617

value: 2h dTAG47


title: V16

source_name: BPA 2.5


title: RMS_breast tumor_74 [VMT179]

value: primary breast tumour

value: WT

value: Stage 2


title: V14


title: RMS_breast tumor_62 [VMT166]

value: LumiNAl

value: ribosomal RNA


title: RMS_breast tumor_61 [VMT165]

value: MT


title: PBMCs_*04:01/*04:04_22

value: PBMCs

value: F


title: RMS_breast tumor_59 [VMT163]


title: RMS_breast tumor_65 [VMT169]


title: V15


title: PBMCs_*03:01/*13:01_20


title: PBMCs_*03:01/*13:01_21


title: V13


title: RMS_breast tumor_60 [VMT164]

value: TNBC


title: HAP1_BRG_BRM_C8_DMSO_2_S67632

value: DMSO


title: HAP1_WT_SMARCA4_F1_dTAG_47_72h_2_S67654

value: wild-type

value: SMARCA4 dTAG

value: 72h dTAG47


title: HAP1_BRG_BRM_C8_dTAG_47_24h_2_S67622

value: SMARCA4 KO

value: SMARCA2 dTAG

value: 24h dTAG47


title: CD4+_Tcells_*03:01/*04:01_1

value: Blood


title: RMS_breast tumor_58 [VMT162]

value: primary breast tumour

value: Stage 3


title: RMS_breast tumor_57 [VMT161]

value: WT

value: Stage 2


title: RMS_breast tumor_63 [VMT167]

value: ribosomal RNA


title: V11

value: Sprague-Dawley

value: uterus


title: HAP1_BRG_BRM_C8_dTAG_47_72h_2_S67621


title: HAP1_WT_SMARCA4_F1_DMSO_2_S67650


title: V12


title: PBMCs_*03:01/*04:01_19

value: PBMCs

value: F


title: HAP1_WT_DMSO_1_S67639

value: DMSO


title: PBMCs_*03:01/*13:01_18


title: V9


title: HAP1_SMARCC2_KO_DMSO_1_S67648

value: SMARCC2 KO


title: PBMCs_*03:01/*15:01_17


title: V10


title: RMS_breast tumor_54 [VMT158]

value: LumiNAl


title: RMS_breast tumor_55 [VMT159]


title: PBMCs_*03:01/*04:01_16


title: HAP1_SMARCA4_KO_DMSO_1_S67644


title: V8


title: V7


title: HAP1_SMARCC1_KO_DMSO_1_S67643

value: SMARCC1 KO


title: PBMCs_*03:01/*15:01_14


title: PBMCs_*01:01/*04:01_15


title: V6


title: PBMCs_*04:01/*14:01_12


title: HAP1_SMARCA2_KO_DMSO_1_S67645

value: SMARCA2 KO


title: HAP1_BRG_BRM_C8_dTAG_47_72h_1_S67636

value: SMARCA4 KO

value: SMARCA2 dTAG

value: 72h dTAG47


title: V5


title: PBMCs_*03:01/*15:01_11

value: Blood


title: RMS_breast tumor_51 [VMT155]

value: primary breast tumour

value: TNBC

value: MT

value: Stage 3


title: RMS_breast tumor_56 [VMT160]

value: ribosomal RNA


title: RMS_breast tumor_50 [VMT154]

value: WT

value: Stage 2


title: PBMCs_*03:01/*04:01_10

value: PBMCs

value: F


title: V4

source_name: control

value: Sprague-Dawley

value: uterus


title: HAP1_BRG_BRM_C8_dTAG_47_3h_1_S67641

value: 3h dTAG47


title: HAP1_BRG_BRM_C8_dTAG_47_6h_1_S67640

value: 6h dTAG47


title: V3


title: RMS_breast tumor_53 [VMT157]


title: PBMCs_*04:01/*07:01_9


title: V2


title: RMS_breast tumor_48 [VMT151]


title: RMS_breast tumor_47 [VMT150]

value: LumiNAl


title: PBMCs_*04:01/*07:01_7


title: HAP1_BRG_BRM_C8_dTAG_47_24h_1_S67637

value: SMARCA4 KO

value: SMARCA2 dTAG

value: 24h dTAG47


title: HAP1_BRG_BRM_C8_dTAG_47_2h_1_S67638

value: 2h dTAG47


title: V1


title: RMS_breast tumor_52 [VMT156]

value: primary breast tumour


title: HAP1_ARID2_KO_DMSO_1_S67642

value: ARID2 KO

value: DMSO


title: PBMCs_*03:01/*13:01_6

value: Blood


title: T198

city: Shanghai

first: rui

last: Dong

address: 399 Wan Yuan Road

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

description: one sample from homo pleuropulmonary blastoma tissue

data_processing:
Using Cell ranger software (10X Genomics, version 2.1.1), the data of raw basecall files were split, counted, combined mathematically, and reanalyzed. Cells with less than 10% UMI in whole genes were filtered out.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for gene and every cell

source_name: human  pleuropulmonary blastoma tissue

extract_protocol:
Tumor smple was fragmented and digested with collagenase IV (Gibco) and DNase I (Sigma). Cell fragments and red blood cells in the single cell suspension were removed with Human lymphocyte separation fluid (CL5020; Cedarlane).  And single cells were suspended in PBS containing 1% BSA. Cells were loaded on a Chromium Controller instrument.
RNA libraries were prepared for sequencing with standard Illumina NovaSeq 6000

value: 46 months

value: female

tag: disease state

value: Type III PPB

value: tumor


title: HAP1_A2_A4_F5_dTAG_47_72h_2_S67646

value: SMARCA4 dTAG

value: 72h dTAG47


title: RMS_breast tumor_45 [VMT148]

value: WT

value: Stage 1

value: ribosomal RNA


title: WT_2_3

description: novaseq05_7_190723_A00394_0298_BHH5CLDSXX.s_3_358_258.001

value: skin melanoma cell line

value: MITF-FLAG-overexpression


title: PBMCs_*01:01/*04:01_5

value: PBMCs

value: F


title: RMS_breast tumor_46 [VMT149]

value: primary breast tumour

value: TNBC

value: MT

value: Stage 3


title: PBMCs_*03:01/*15:01_3

value: Blood


title: RMS_breast tumor_44 [VMT146]


title: WT_2_2

description: novaseq05_7_190723_A00394_0298_BHH5CLDSXX.s_3_350_250.001


title: PBMCs_*03:01/*04:01_2


title: RMS_breast tumor_43 [VMT145]

value: LumiNAl


title: HAP1_A2_A4_F5_dTAG_47_6h_2_S67653

value: ARID2 KO

value: 6h dTAG47


title: PBMCs_*03:01/*04:01_1


title: HAP1_A2_A4_F5_dTAG_47_3h_2_S67652

value: SMARCA4 dTAG

value: 3h dTAG47


title: HAP1_A2_A4_F5_dTAG_47_2h_2_S67651

value: 2h dTAG47


title: WT_2_1

description: novaseq05_7_190723_A00394_0298_BHH5CLDSXX.s_2_342_242.001


title: RMS_breast tumor_42 [VMT144]

value: WT


title: RMS_breast tumor_41 [VMT143]

value: Stage 2

value: ribosomal RNA


title: HAP1_A2_A4_F5_DMSO_2_S67649

value: DMSO


title: EV_1_2

description: novaseq05_7_190723_A00394_0298_BHH5CLDSXX.s_4_389_289.001

value: skin melanoma cell line

value: empty-vector-FLAG-overexpression


title: EV_1_1

description: novaseq05_7_190723_A00394_0298_BHH5CLDSXX.s_4_381_281.001


title: HAP1_A2_A4_F5_dTAG_47_24h_2_S67647

value: 24h dTAG47


title: DM8_S25 Interstitium

city: Indianapolis

first: Michael

middle: T

last: Eadon

address: 950 W Walnut St

data_processing:
For Illumina Sequencing data, FastQC for sequencing quality check
Adapter sequences were removed with cutadapt (1.14+)
Reads were aligned to the human referece genome Hg38 using STAR with parameters ajusted to short reads and Integrative Genomics Viewer (IGV) alignment.
Expression counts determined by edgeR / rbamtools
The remaining processing and normalization steps described on the paper were not performed on the provided processed data
Genome_build: Hg38
Supplementary_files_format_and_content: csv

extract_protocol:
Kidney tissue was obtained from a clinical biopsy, placed in Michels solution and frozen on OCT within 24 h. 20 um of cross-sectional biopsy tissue was cut on a cryotome and placed in Arcturus Picopure extraction buffer. RNA was extracted according to protocol.
Nephrectomies were obtained and frozen on OCT within 24 h. 20 um of cross-sectional biopsy tissue was cut on a cryotome and placed in Arcturus Picopure extraction buffer. RNA was extracted according to protocol.
SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input
RNA seq, 10 millions input reads per sample

value: Kidney

tag: disease

value: Diabetic Nephropathy

tag: tissue source

value: Biopsy

tag: segment

value: DM8_S25 Interstitium

tag: storage

value: OCT at -80C

value: Male


title: RMS_breast tumor_49 [VMT152]

value: primary breast tumour

tag: subtype

value: TNBC

tag: p53 status

value: MT

value: Stage 3


title: EV_1_3

description: novaseq05_7_190723_A00394_0298_BHH5CLDSXX.s_2_334_234.001

tag: cell line


title: RMS_breast tumor_40 [VMT142]

value: WT

tag: Stage

tag: molecule subtype


title: DM3_S20 Interstitium

value: DM3_S20 Interstitium


title: RMS_breast tumor_38 [VMT140]

value: LumiNAl

value: Stage 2

value: ribosomal RNA


title: DM4_S21 Interstitium

value: DM4_S21 Interstitium


title: HAP1_WT_SMARCA4_F1_dTAG_47_6h_1_S67610

tag: genotype

value: wild-type

tag: dtag

value: SMARCA4 dTAG

value: 6h dTAG47


title: RMS_breast tumor_39 [VMT141]


title: siMITF_2

description: novaseq09_191030_A00841_0045_AHTYHNDSXX.s_3_356_256.001

value: skin melanoma cell line

value: siMITF


title: DM2_S19 Interstitium

value: Kidney

value: Diabetic Nephropathy

value: Biopsy

value: DM2_S19 Interstitium

value: OCT at -80C


title: siMITF_3

description: novaseq09_191030_A00841_0045_AHTYHNDSXX.s_1_301_201.001


title: HAP1_WT_SMARCA4_F1_dTAG_47_3h_1_S67609

value: 3h dTAG47


title: RMS_breast tumor_37 [VMT139]

value: primary breast tumour

value: WT

value: Stage 3


title: DM1_S18 Interstitium

value: DM1_S18 Interstitium

value: Male


title: RMS_breast tumor_36 [VMT138]

value: LumiNAl

value: MT

value: ribosomal RNA


title: 18-0010 Interstitium

value: Reference

value: Nephrectomy

value: 18-0010 Interstitium


title: HAP1_WT_SMARCA4_F1_dTAG_47_2h_1_S67612

value: wild-type

value: SMARCA4 dTAG

value: 2h dTAG47


title: HAP1_WT_SMARCA4_F1_dTAG_47_24h_1_S67607

value: 24h dTAG47


title: siMITF_1

description: novaseq09_191030_A00841_0045_AHTYHNDSXX.s_1_316_216.001

value: skin melanoma cell line

value: siMITF


title: RMS_breast tumor_35 [VMT137]

value: primary breast tumour


title: DM5_S22 Interstitium

value: Kidney

value: Diabetic Nephropathy

value: Biopsy

value: DM5_S22 Interstitium

value: OCT at -80C


title: siCTRL_2

description: novaseq09_191030_A00841_0045_AHTYHNDSXX.s_3_348_248.001

value: siCTRL


title: HAP1_WT_SMARCA4_F1_DMSO_1_S67605

value: DMSO


title: RMS_breast tumor_34 [VMT136]

value: LumiNAl

value: WT

value: Stage 2

value: ribosomal RNA


title: HAP1_WT_SMARCA4_F1_dTAG_47_72h_1_S67608

value: wild-type

value: SMARCA4 dTAG

value: 72h dTAG47


title: 18-0010 CD

value: Reference

value: Nephrectomy

value: Male


title: siCTRL_1

description: novaseq09_191030_A00841_0045_AHTYHNDSXX.s_1_308_208.001

value: skin melanoma cell line


title: 18-0010 DCT

value: Kidney


title: RMS_breast tumor_33 [VMT135]

value: primary breast tumour

value: MT

value: Stage 3


title: HAP1_CC1_CC2_F1_dTAG_47_72h_1_S67614

value: SMARCC1 KO

value: SMARCC2 dTAG


title: HAP1_CC1_CC2_F1_dTAG_47_3h_1_S67615

value: 3h dTAG47


title: RMS_breast tumor_32 [VMT133]

value: WT


title: RMS_breast tumor_31 [VMT132]

value: LumiNAl


title: HAP1_CC1_CC2_F1_dTAG_47_6h_1_S67616

value: 6h dTAG47


title: 18-0010 Proximal Tubule

value: 18-0010 Proximal Tubule

value: OCT at -80C


title: 18-0010 Glom


title: ATAC-seq in LNCaP

first: Fei

last: Li

address: 320 Yue-Yang Road Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

data_processing:
The approach used or ATAC-seq data processing was quite similar to that used for ChIP-seq data processing. However, the peak calling step differed due to the lack of input control files. In brief, after raw reads were trimmed with TrimGalore-0.5.0, Bowtie2 was used for mapping the reads to the hg19 genome.
SAMtools was further utilized for bam file sorting and indexing. The bamCoverage function in deepTools was used to generate .bw files with counts per million (CPM) normalization
R package Diffbind was used to identify overlapped peaks between AR ChIP-seq-generated peaks in LNCaP cells and ATAC-seq-generated peaks in all four cell lines, respectively. Then, both-open peaks were defined by overlapping the above generated peaks in all four cell lines. To further identify specific prostate-open peaks, we employed the intersect function in bedtools to exclude peaks that emerged in any of the three lung cell lines in LNCaP cells.
Genome_build: hg19
Supplementary_files_format_and_content: narrowpeak files were generated from MACS2 and bw files were generated from DeepTools

source_name: Human prostate cancer cell line

extract_protocol:
To reduce the amount of contaminating mitochondrial DNA, we performed a previously reported optimized ATAC-seq protocol. In brief, 50,000 cells were collected and washed once with PBS. Cells were then lysed in 50 μL of ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% NP-40; 0.1% Tween 20; and 0.01% digitonin) for 3 minutes on ice. Immediately after lysis, nuclei were washed with 1 mL of wash buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.1% Tween 20) and then centrifuged at 500g for 10 minutes at 4°C.
To prepare sequencing libraries, a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) was utilized for the following steps.

value: LNCaP


title: ATAC-seq in H1437

source_name: Human lung cancer cell line


title: ATAC-seq in A549


title: ATAC-seq in H2126


title: siCTRL_3

description: novaseq09_191030_A00841_0045_AHTYHNDSXX.s_4_388_288.001

value: siCTRL


title: 18-0010 Bulk

value: Reference

value: Nephrectomy


title: Input_mix for AR_ChIP-seq

data_processing:
Raw fastq files were first trimmed to remove adaptors using TrimGalore-0.5.0 with the following parameter settings: -q 25 --phred33 --length 35 -e 0.1 --stringency 4. Trimmed fastq files were then mapped to hg19 genome utilizing Bowtie241. Sambamba_v0.6.6 was conducted to remove duplicates. For IGV visualization, deepTools was then performed using function bamCoverage to generate normalized CPM .bw files. For peak calling, MACS2 was utilized with -q 0.05 parameter setting. DeepTools was further applied for heatmap visualization with the function of computeMatrix and plotHeatmap.
Genome_build: hg19
Supplementary_files_format_and_content: narrowpeak files were generated from MACS2 and bigwig files were generated from DeepTools

source_name: Human cell mix (A549, H1437, H2126 and LNCaP)

extract_protocol:
ChIP-seq was performed as previously described. In brief, 10 million cells were fixed with 1% formaldehyde at room temperature for 10 minutes with rotation. Then, 125 mM glycine was added to quench the formaldehyde at room temperature for 5 minutes. Cells were washed with cold PBS. The supernatants were then removed, and 880 μL of ice-cold cell lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, 1× proteinase inhibitor) was added and incubated at 4°C for 30 minutes with rotation. An 880 μL cell lysate was transferred into a Covaris milliTUBE 1 mL AFA Fiber vial and sheared in a Covaris S220 ultrasonicator (fill level: 10, duty cycle: 5, PIP: 140, cycles/BURST: 200, time: 4 minutes). Clarified samples were collected by centrifugation at 16,100 rcf for 15 minutes at 4°C. After preclearing using 20 µL of protein G beads (Invitrogen, 10003D), 3 µL of anti-AR antibody was added (Abcam, ab108341) for immunoprecipitation overnight. To bind the anti-AR antibody, 60 μL of protein G beads was added and incubated with rotation for two hours at 4°C. The beads were washed twice each with Low Salt Wash Buffer, High Salt Wash Buffer and LiCl Wash Buffer and resuspended in 100 μL of freshly prepared DNA Elution Buffer (50 mM NaHCO3 and 1% SDS). The ChIP sample beads were placed on a magnet, and the supernatant was collected into a new tube. The above elution step was repeated with another 100 μL volume of elution buffer. The samples were then digested with 10 μL of Proteinase K (Invitrogen, 25530049) with incubation at 67°C for 4 hours. DNA was purified with DNA Clean & ConcentratorTM-5 (Zymo Research, D4004).
One nanogram of eluted DNA was used as input for library construction with a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503). Libraries were sequenced with the Illumina NovaSeq sequencing system (PE 2×150 bp reads) at Berry Genomics.

tag: antibody


title: HAP1_CC1_CC2_F1_dTAG_47_2h_1_S67598

value: 2h dTAG47


title: HAP1_CC1_CC2_F1_dTAG_47_24h_1_S67613

value: 24h dTAG47


title: RMS_breast tumor_29 [VMT129]

data_processing:
library strategy: RiboMethSeq
Adatper sequences were removed with Trimmomatic v0.36. Reads shorter than 17 nucleotides were discarded.
Reads were aligned to the human rRNA sequence with Bowtie 2.
5' end reads were counted at each rRNA nucleotide position
Genome_build: NR_046235
Supplementary_files_format_and_content: Raw counts of 5' end reads on each position of the rRNA subunits

source_name: RMS_breast tumor

extract_protocol:
RNAeasy kit (Qiagen)
Total RNA was first subjected to partial alkaline hydrolysis to generate RNA fragments ranging from 50 to 100 bp. Libraries were then prepared using NEBNext Multiplex Small RNA Library Prep Set

value: primary breast tumour

value: TNBC

value: ribosomal RNA


title: RMS_breast tumor_30 [VMT130]

value: Stage 3


title: 18-0009 Interstitium

value: Kidney

value: 18-0009 Interstitium

value: Male


title: RMS_breast tumor_28 [VMT128]

value: WT


title: HAP1_CC1_CC2_F1_DMSO_1_S67611

value: SMARCC1 KO

value: SMARCC2 dTAG

value: DMSO


title: AR_ChIP-seq in LNCaP

value: LNCaP

value: anti-AR antibody (Abcam, ab108341)


title: HAP1_BRG_BRM_C8_DMSO_1_S67599

value: SMARCA4 KO

value: SMARCA2 dTAG


title: 18-0009 CD

value: Reference

value: Nephrectomy

value: OCT at -80C


title: RMS_breast tumor_27 [VMT127]

value: primary breast tumour

value: Stage 2


title: HAP1_A2_A4_F5_dTAG_47_72h_1_S67602

value: ARID2 KO

value: SMARCA4 dTAG

value: 72h dTAG47


title: 18-0009 DCT

value: Kidney

value: Male


title: 18-0010 TAL


title: AR_ChIP-seq in H1437


title: RMS_breast tumor_26 [VMT126]

value: TNBC

value: MT

value: Stage 3

value: ribosomal RNA


title: AR_ChIP-seq in H2126

value: anti-AR antibody (Abcam, ab108341)


title: 18-0009 TAL


title: RMS_breast tumor_25 [VMT124]

value: WT


title: AR_ChIP-seq in A549


title: HAP1_A2_A4_F5_dTAG_47_6h_1_S67604

value: 6h dTAG47


title: 18-0009 Proximal Tubule

value: Reference

value: 18-0009 Proximal Tubule


title: HAP1_A2_A4_F5_dTAG_47_3h_1_S67603

value: 3h dTAG47


title: 18-0009 Glom

value: Nephrectomy

value: OCT at -80C


title: ELLi_RNAseq_rep2

city: San Diego

first: George

last: Sen

state: CA

address: 9500 Gilman Drive

institute: UCSD

data_processing:
NOVASEQ pair-end reads were trimmed and filtered using Partek Flow. High quality reads were aligned using TopHat v2.1.0 for alignment into BAM files.
BAM files were imported into the RNA-seq pipeline of Partek Genomic Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 85 2019-05-02). Exclusions include a mininum reads of 10 in one out of 4 samples. RPKM values were log2-transformed with an offset value of 0.000001.
Genome_build: hg19
Supplementary_files_format_and_content: log2 RPKM

source_name: Human epidermal keratinocyte

growth_protocol: Primary keratinocytes were grown on culture dishes in keratinocyte EPILIFE medium (Life technologies).

extract_protocol:
RNA was isolated using GeneJET RNA purification kit (Thermo Scientific).
RNA-seq libraries were prepared with NEBNext Ultra II RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: ELL siRNA knockdown and continued culturing in growth medium for four days

tag: cell type

value: keratinocyte

value: transfected with ELL siRNA

tag: timepoints

value: 4 days


title: RMS_breast tumor_24 [VMT122]

first: Virginie

last: MARCEL

address: 28 rue Laennec

tag: tissue

value: primary breast tumour


title: RMS_breast tumor_23 [VMT120]


title: ELLi_RNAseq_rep1

tag: treatment


title: HAP1_A2_A4_F5_dTAG_47_24h_1_S67601

value: ARID2 KO

value: SMARCA4 dTAG

value: 24h dTAG47


title: 18-0008 Interstitium

value: Kidney

value: 18-0008 Interstitium

tag: gender

value: Female


title: 18-0009 Bulk

tag: disease

value: Male


title: CTLi_RNAseq_rep2

treatment_protocol: CTL siRNA knockdown and continued culturing in growth medium for four days

value: transfected with control siRNA


title: HAP1_A2_A4_F5_DMSO_1_S67600

value: DMSO


title: RMS_breast tumor_22 [VMT119]

value: Stage 3

value: ribosomal RNA


title: CTLi_RNAseq_rep1


title: 18-0008 CD

value: Reference

tag: tissue source

value: Nephrectomy


title: WT_DMSO_input

value: wild-type

tag: bait


title: RMS_breast tumor_21 [VMT118]

value: WT


title: WT_DMSO_H3K27ac


title: RMS_breast tumor_20 [VMT117]


title: NFYA_CUTRUN_CD34_KO32_rep2

city: Boston

last: Liu

address: 300 Longwood Avenue

institute: Boston Children's Hospital

data_processing:
Library strategy: CUT&RUN
Data was processed with CUT&RUNTools, which incorporates the following softwares
Reads were trimmed with trimmomatic 0.36 to remove low quality reads and adapter sequences. (ILLUMINACLIP:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25)
Bowtie2 (v2.2.9) was used to align reads to reference genome
Aligned reads were marked for duplicates with Picard 2.8.0 MarkDuplicates function.
Samtools 1.3.1 was used to remove duplicate reads, sort and index alignment files. DNA fragments larger than 120 bp were removed
MACS2 v2.1 was used to call peaks based on alignment file
bigwig was generated using bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file is a binary format of Wig file, value represents pile-up signal of mapped reads

source_name: CD34+ HSPC derived erythroid precursors

extract_protocol:
Briefly, 1 million cells were collected and frozen in 10% DMSO in FBS, as necessary. Frozen cells were thawed, pelleted, and washed once with PBS, and  processed according to the following steps: 1) addition of 0.5 mL of NE buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1% Triton X-100, 20% Glycerol and 1x protease inhibitor cocktails from Sigma) for nuclei isolation. Nuclei were pelleted at 600 x g for 3 min, resuspended with 0.4 mL of NE buffer. 2) 25 uL BioMagPlus Concanavalin A beads slurry was washed twice and resuspended in 200uL Binding Buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2), and   Binding Buffer is added to the nuclei suspension. The mixture was thoroughly mixed on a rocker for 10 min to allow binding to nuclei to the beads. 3) The nuclei were pelleted with a magnet stand and blocked with Wash Buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.1% BSA and 1x protease inhibitor cocktails from Sigma) supplemented with 2 mM EDTA. After washing once with Wash Buffer, nuclei were resuspended in 200 uL Wash buffer containing 2 ug of antibody, and incubated overnight to allow antibody binding. 4) The next day, wash the nuclei twice on a magnet stand with wash buffer and incubate with 1:1000 pA-MN in 200 uL Wash Buffer. After 1 hr, wash twice to remove unbound pA-MN. 5) Resuspend the nuclei in 150 uL Wash Buffer, chill on a 0°C metal block that sits in water-ice mixture. Add 3 uL 100 mM CaCl2 to activate pA-MN, and incubate at 0°C for 60 min. 6) The reaction was stopped by adding 150 uL 2XSTOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 mg/mL RNase A and 40 mg/mL glycogen). The protein-DNA complex was released by centrifugation and then digested by proteinase K at 50°C overnight. DNA was extracted by ethanol precipitation, followed by Qubit fluorometer and bioanalyzer quality control.
Library preparation of CUT&RUN was performed using NEB Ultra II library preparation kit with important modifications. Briefly, less than 30 ng DNA is used as input. End prep was performed at 20°C for 30 min and then 50°C for 60min (instead of 65°C for 30 min in the manual). The reduced temperature prevents melting of short DNA fragments. 5 pmol adaptor was added and ligated to end prep products at 20°C for 15 min. USER enzyme was then used to cleave the uracil in the loop. 1.7x volume of AMPure beads were used to purify the ligation product. The use of 1.7x beads is essential for recovery of short fragments. To amplify the library, the ligation product was mixed with 2x Ultra II Q5 mix, universal primer and index primers. PCR was carried out as follows: 98°C 30 s, 12 cycles of 98°C 10s and 65°C 10s, and final extension 65°C 5 min. The PCR product was subjected twice to double size selection  with 0.8x and then 1.2x AMPure beads. The purified library was quantified with Qubit and Tapestation. Libraries were pooled at similar molar amount and sequenced using Nextseq500 platform. Paired-end sequencing, read length 42 bp x 2, 6 bp index was performed. For detailed protocol please see: dx.doi.org/10.17504/protocols.io.wvgfe3w

value: CD34+ HSPC derived erythroid precursors (Primary cells, adult)

value: BCL11A KO

value: NFYA


title: RMS_breast tumor_19 [VMT116]

city: Lyon

institute: Cancer Research Center of Lyon

value: primary breast tumour

value: TNBC


title: WT_SMARCA4dTAG_DMSO_H3K27ac_72

value: SMARCA4 dTAG


title: HAP1_A2_A4_F5_dTAG_47_2h_1_S67606

value: ARID2 KO

value: 2h dTAG47


title: 18-0008 TAL

source_name: Kidney

value: Kidney

tag: segment

tag: storage

value: OCT at -80C

value: Female


title: NFYA_CUTRUN_CD34_KO72_rep2


title: 18-0008 Proximal Tubule

value: 18-0008 Proximal Tubule


title: RMS_breast tumor_18 [VMT112]

tag: subtype

tag: p53 status

value: Stage 3

value: ribosomal RNA


title: WT_SMARCA4dTAG_DMSO_IgG

value: DMSO

value: IgG


title: RMS_breast tumor_17 [VMT111]

value: WT

tag: Stage


title: NFYA_CUTRUN_CD34_aavs72_rep2

value: CD34+ HSPC derived erythroid precursors (Primary cells, adult)

value: AAVS1 KO


title: 18-0008 Glom

value: Reference

value: Nephrectomy


title: TBP_CUTRUN_CD34_KO32_rep2

value: BCL11A KO

value: TBP


title: RMS_breast tumor_16 [VMT110]

value: primary breast tumour

value: LumiNAl

tag: molecule subtype


title: 18-0008 Bulk

value: Kidney


title: 18-0007 Interstitium

value: 18-0007 Interstitium

value: OCT at -80C


title: WT_SMARCA4dTAG_DMSO_ARID1A

tag: genotype

value: wild-type

value: SMARCA4 dTAG


title: RMS_breast tumor_15 [VMT109]

value: MT

value: Stage 3

value: ribosomal RNA


title: WT_SMARCA4dTAG_DMSO_BRD4

tag: dtag

value: DMSO


title: TBP_CUTRUN_CD34_KO72_rep2

value: CD34+ HSPC derived erythroid precursors (Primary cells, adult)

tag: antibody


title: 18-0008 DCT

value: Female


title: WT_SMARCA4dTAG_dTAG47_72h_H3K27ac

value: 72h dTAG47


title: WT_SMARCA4dTAG_dTAG47_72h_IgG

value: IgG


title: RMS_breast tumor_14 [VMT108]

value: WT


title: RMS_breast tumor_13 [VMT107]

value: Stage 2


title: TBP_CUTRUN_CD34_AAVS32_rep2

tag: cell type

value: AAVS1 KO

value: TBP


title: 18-0007 CD

value: Kidney

value: Reference

value: Nephrectomy


title: TBP_CUTRUN_CD34_AAVS72_rep2


title: 18-0007 DCT

value: OCT at -80C


title: NFYA_CUTRUN_CD34_AAVS32_rep2

value: NFYA


title: WT_SMARCA4dTAG_dTAG47_72h_BRD4

value: wild-type

value: SMARCA4 dTAG


title: 18-0007 TAL


title: RMS_breast tumor_11 [VMT105]

value: primary breast tumour

value: Stage 3

value: ribosomal RNA


title: MDA_567: siTFEB_2

city: Saint John

first: Thomas

last: Pulinilkunnil

state: New Brunswick

address: 100 Tucker park road

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

data_processing:
Paired-end reads were pseudoaligned to the Homo sapiens GRCh38 transcriptome and quantified using kallisto
Transcripts were summarized to gene-level counts with the R package tximport and testing for differential gene expression was completed with DESeq2. Testing for differential expression was conducted only on genes with an average estimated count of greater than 0.3.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include summarized gene-level abundance values (TPM) for each sample as determined by tximport

source_name: Breast Cancer Cells

growth_protocol: MDA-MB-231 cells were grown in DMEM High Glucose + 9% FBS prior to treatment

extract_protocol:
RNA was extracted using the Qiagen RNeasy mini kit according to the manufacturer’s instructions
Libraries were constructed using NEBNext DNA Library Prep Master Mix Set for Illumina accroding to manufacturers instructions

treatment_protocol: Cells were transfected for 48 hours with 10 nM of either control siRNA or two separate siRNA's targeting TFEB using 2µL Lipofectamine RNAiMAX per plate and diluted in Opti-MEM

tag: cell line

tag: sirna


title: 18-0007 Proximal Tubule

tag: tissue

value: 18-0007 Proximal Tubule

value: Female


title: WT_SMARCA4dTAG_dTAG47_72h_ARID1A

tag: treatment

value: 72h dTAG47


title: RMS_breast tumor_12 [VMT106]

value: WT


title: MDA_566: siTFEB_2


title: 18-0007 Glom

tag: disease

tag: gender


title: MDA_565: siTFEB_1


title: WT_SMARCA4dTAG_DMSO_H3K27ac

value: DMSO

tag: bait


title: WT_SMARCA4dTAG_72h_dTAG_input


title: RMS_breast tumor_9 [VMT103]


title: MDA_564: siTFEB_1


title: RMS_breast tumor_8 [VMT102]

value: LumiNAl

value: Stage 2


title: WT_SMARCA4dTAG_72h_dTAG_H3K27ac


title: RMS_breast tumor_7 [VMT101]

value: Stage 1


title: 18-0006 Interstitium

value: Kidney

value: Reference

tag: tissue source

tag: segment

value: Interstitium


title: 18-0006 CD

value: Nephrectomy

value: Collecting Duct

tag: storage

value: OCT at -80C


title: WT_SMARCA4dTAG_6h_dTAG_input

value: wild-type

value: SMARCA4 dTAG

value: 6h dTAG47


title: 18-0006 TAL

value: Thin Ascending Limb


title: WT_SMARCA4dTAG_6h_dTAG_H3K27ac


title: MDA_568: siTFEB_2


title: WT_SMARCA4dTAG_DMSO_input


title: RMS_breast tumor_5 [JJD41_B2325]

value: primary breast tumour

tag: subtype

value: TNBC

tag: p53 status

value: MT

value: Stage 3

value: ribosomal RNA


title: RMS_breast tumor_4 [JJD39_B2323]

value: LumiNAl

value: WT

tag: Stage

tag: molecule subtype


title: 18-0006 Proximal Tubule

value: Kidney

value: Proximal Tubule

value: Female


title: WT_SMARCA4dTAG_3h_dTAG_input

tag: genotype

tag: dtag

value: 3h dTAG47


title: RMS_breast tumor_10 [VMT104]


title: 18-0006 Glom

value: Reference

value: Nephrectomy

value: Glomerulus


title: MDA_561: siCTRL

value: siCTRL


title: MDA_559: siCTRL


title: WT_SMARCA4dTAG_3h_dTAG_H3K27ac

value: wild-type

value: SMARCA4 dTAG


title: 18-0007 Bulk

value: OCT at -80C


title: 18-0006 Bulk

value: Bulk


title: WT_SMARCA4dTAG_24h_dTAG_input

value: 24h dTAG47


title: RMS_breast tumor_2 [JJD36_B2320]

value: primary breast tumour

value: TNBC

value: MT

value: Stage 3


title: 18-0004 Interstitium

value: Kidney

value: 18-0004 Interstitium

value: Male


title: WT_SMARCA4dTAG_24h_dTAG_H3K27ac


title: MDA_563: siTFEB_1


title: MDA_562: siCTRL


title: RMS_breast tumor_6 [VMT100]

value: LumiNAl

value: Stage 2

value: ribosomal RNA


title: RMS_breast tumor_1 [JJD35_B2319]

value: WT


title: HeLa-iCas9 cells, day 12 of iCas9 induction, repeat2

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

description:
nosgRNA_HeLa_D12_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

data_processing:
library strategy: tRNA-seq
Read were trimmed using homerTool
Alignment was done to the genome and mature tRNA using Bowtie2 (Langmead and Salzberg, 2012) with parameters --very-sensitive-local. Read aligned with equal alignment score to the genome and mature tRNA were annotated as mature tRNA. Reads aligned to multiple tRNA genes were randomly assigned when mapping to identical anticodon, and discarded from the analysis if aligned to different anticodon.
Read count was done using BedTools-coverage count (Quinlan and Hall, 2010).
Variant calling for detection of mutation and indels was done using samtools (Li et al., 2009) command “mpileup” with the parameters: “-A -q1 -d100000”.
Genome_build: hg19
Supplementary_files_format_and_content: read counts of mature tRNA and reads with Indel mutation in the vicinity (5 nt up and downstream) of the sgRNA targeting site, and the maximal read coverage in that location

source_name: HeLa iCas9 - no sgRNA

growth_protocol: HeLa- iCas9 with single sgRNAs  cells (targeteing 4 different human tRNA families) were grown in DMEM + NEAA (Life Technologies; 10938-025) - Dulbecco’s Modified Eagle medium with 4.5mg/ml D-Glucose and Non-Essential amino acids. Supplemented with 10% FBS, 1% penicillin/ streptomycin (P/S), 1% L-Glutamine and 1% Sodium Pyruvate.   The medium was supplemented with 200µg/ml Hygromycin (for iCas9 selection, Thermo Fisher; 10687010), 2µg/ml Puromycin (for sgRNA selection, Sigma-Aldrich; 58-58-2) and 1µg/ml Doxycycline (for iCas9 induction, Sigma-Aldrich; 10592-13-9). Upon iCas9 induction, each cell population was samples every 4 days, and fresh medium containing all  antibiotics was replaced every two days for 12 days.

extract_protocol:
RNA was extracted using TRI-reagent (Sigma-Aldirch), according to standard protocol.
tRNA sequencing protocol was adapted from Zheng et al., 2015 (Zheng et al., 2015) with minor modification. Small RNA was isolated using SPRI-beads (Agencourt AMPure XP, Beckman Coulter), using dual side size-selection protocol. First RNA and beads were mixed at 1:1.8 ratio, collection the supernatant. The small RNA was isolated by mixing the clear supernatant with bead at 1:0.8 ratio, with addition of X1.34 isopropanol. Small RNA was treated for modification removal using AlkB wt, and D135S, a kind gift from Prof. Tao Pan. Reverse transcription was done using TGIRT™-III Enzyme, with the indicated primers. 3’ adaptor was ligated to the cDNA using T4 ligase (NEB). The cDNA was purified using Dynabeads myOne SILANE (life Technologies) after each step.  The library was amplified using NEBNext PCR mix and cleaned using SPRI-beads. Samples were pooled and sequenced using NextSeq illumina. primers: Reverse-transcription DNA:5’-CACGACGCTCTTCCGATCTT  -3’,  Reverse-transcription RNA:5’-rArGrArUrCrGrGrArArGrArGrCrGrUrCrGrUrG-3’,  3’ adaptor:5’-  CGTCATAGATCGGAAGAGCACA-3’.

treatment_protocol: Cells were centrifuged for 3 minutes at 2000rpm. The medium was removed and cell pellet was freezed at -80°C until RNA extraction.

value: HeLa

tag: crispr construct

value: iCas9- nosgRNA

tag: icas9 induction time

value: Day 12

tag: repeat

value: repeat 2

value: tRNA


title: 18-0004 DCT

tag: tissue

value: Reference

value: Nephrectomy

value: OCT at -80C


title: SMARCC1KO_SMARCC2dTAG_DMSO_H3K27ac

value: SMARCC1 KO

value: SMARCC2 dTAG

tag: treatment

value: DMSO


title: HeLa-iCas9 cells, day 12 of iCas9 induction, repeat1

description:
nosgRNA_HeLa_D12_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

tag: cell line

value: repeat 1


title: HeLa-iCas9 cells, day 8 of iCas9 induction, repeat2

description:
nosgRNA_HeLa_D8_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: Day 8


title: SMARCC1KO_SMARCC2dTAG_DMSO_IgG

value: IgG


title: 18-0004 CD

value: Kidney

tag: disease

tag: gender

value: Male


title: MDA_560: siCTRL

tag: sirna

value: siCTRL


title: miRNA-seq_liver_STZ_12w_3

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

country: Japan

institute: Chuo University

description:
non coding small RNA seq
liver_STZ_12w_3
DIAR STZ 12w liver

data_processing:
Processed by CAP-MIRSeq. See setup files, run_info.txt, sample_info.txt, tool_info.txt
Genome_build: mm10
Supplementary_files_format_and_content: generated Excel file

source_name: liver

extract_protocol:
Total RNA was extracted by RNeasy mini kit (Qiagen).
1) Filter Small RNA: Separate RNA segment of different size by PAGE gel,select 18-30nt stripe and recycle. 2) Adaptor  ligation: Prepare connection system, blend and centrifuge, connect warmly for a period of time. 3) RT-PCR: Prepare  reverse transcription system, connect warmly for a period on PCR on PCR instrument, then PCR amplification. 4) Purify  PCR products: Recover the Purified PCR construct by PAGE gel, dissolve the recylced products in EB solution. Finally,  label to finish the library construction. 5) Library quality testing: Use Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-  TimePCR System to test quality and production of the prepared library.

treatment_protocol: Excision of liver tissue, and exosome rich fraction extracted by Exoquick (System Biosciences).

tag: disease state

value: hepatocellular carcinoma

value: liver

tag: time

value: 12 weeks


title: HeLa-iCas9 cells, day 8 of iCas9 induction, repeat1

description:
nosgRNA_HeLa_D8_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: HeLa

value: iCas9- nosgRNA


title: RMS_breast tumor_3 [JJD37_B2321]

value: primary breast tumour

tag: subtype

value: TNBC

value: MT

value: Stage 3

value: ribosomal RNA


title: miRNA-seq_liver_STZ_12w_2

description:
non coding small RNA seq
liver_STZ_12w_2
DIAR STZ 12w liver


title: SMARCC1KO_SMARCC2dTAG_DMSO_BRD4

value: SMARCC1 KO

value: SMARCC2 dTAG

value: DMSO

tag: bait


title: HeLa-iCas9 cells, day 4 of iCas9 induction, repeat2

description:
nosgRNA_HeLa_D4_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: Day 4

value: repeat 2

value: tRNA


title: SMARCC1KO_SMARCC2dTAG_DMSO_ARID1A


title: miRNA-seq_liver_STZ_10w_3

description:
non coding small RNA seq
liver_STZ_10w_3
DIAR STZ 10w liver

value: 10 weeks


title: 18-0004 Glom

value: Kidney

value: Reference

tag: tissue source

value: Nephrectomy

tag: segment

tag: storage

value: OCT at -80C

value: Male


title: HeLa-iCas9 cells, day 4 of iCas9 induction, repeat1

description:
nosgRNA_HeLa_D4_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: HeLa

value: iCas9- nosgRNA

value: repeat 1

tag: molecule subtype


title: HeLa-iCas9 cells, before iCas9 induction, repeat2

description:
nosgRNA_HeLa_D0_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

tag: crispr construct

value: Day 0


title: miRNA-seq_liver_STZ_10w_2

description:
non coding small RNA seq
liver_STZ_10w_2
DIAR STZ 10w liver

value: hepatocellular carcinoma

value: liver


title: 18-0004 Bulk


title: SMARCC1KO_SMARCC2dTAG_dTAG47_72h_IgG

tag: genotype

value: SMARCC1 KO

tag: dtag

value: SMARCC2 dTAG

value: 72h dTAG47

value: IgG


title: HeLa-iCas9 cells, before iCas9 induction, repeat1

description:
nosgRNA_HeLa_D0_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

tag: icas9 induction time

tag: repeat

value: tRNA


title: miRNA-seq_liver_STZ_10w_1

description:
non coding small RNA seq
liver_STZ_10w_1
DIAR STZ 10w liver

tag: tissue

value: 10 weeks


title: miRNA-seq_liver_STZ_6w_3

description:
non coding small RNA seq
liver_STZ_6w_3
DIAR STZ 6w liver

value: 6 weeks


title: SMARCC1KO_SMARCC2dTAG_dTAG47_72h_BRD4

tag: treatment


title: 18-0003v2 Interstitium

value: Kidney

tag: disease

value: Reference

value: 18-0003v2 Interstitium

tag: gender

value: Female


title: SMARCC1KO_SMARCC2dTAG_dTAG47_72h_ARID1A


title: 18-0003v2 CD

value: Nephrectomy

value: OCT at -80C


title: miRNA-seq_liver_STZ_12w_1

description:
non coding small RNA seq
liver_STZ_12w_1
DIAR STZ 12w liver

tag: disease state

value: 12 weeks


title: 18-0004 TAL

value: Male


title: 18-0003v2 DCT


title: 18-0004 Proximal Tubule

value: 18-0004 Proximal Tubule


title: miRNA-seq_liver_STZ_6w_1

description:
non coding small RNA seq
liver_STZ_6w_1
DIAR STZ 6w liver

value: hepatocellular carcinoma

value: liver

tag: time


title: HeLa-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat2

description:
SerCGAsgRNA_HeLa_D8_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

source_name: HeLa iCas9 - SerCGA sgRNA

tag: cell line

value: HeLa

value: iCas9- SerCGAsgRNA

value: Day 8

value: repeat 2


title: miRNA-seq_liver_CTR_12w_3

description:
non coding small RNA seq
liver_CTR_12w_3
DIAR control 12w liver

value: normal control


title: SMARCA4KO_SMARCA2dTAG_DMSO_H3K27ac

value: SMARCA4 KO

value: SMARCA2 dTAG

value: DMSO

tag: bait


title: HeLa-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat1

description:
SerCGAsgRNA_HeLa_D8_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: repeat 1

value: tRNA


title: 18-0003v2 Proximal Tubule

value: Kidney

value: Reference

tag: tissue source

value: Nephrectomy

value: 18-0003v2 Proximal Tubule

value: Female


title: SMARCC1KO_SMARCC2dTAG_dTAG47_72h_H3K27ac

value: SMARCC1 KO

value: SMARCC2 dTAG

value: 72h dTAG47


title: SMARCA4KO_SMARCA2dTAG_DMSO_input


title: 18-0003v2 TAL

tag: segment

value: OCT at -80C


title: SMARCA4KO_SMARCA2dTAG_DMSO_H3K27ac_72


title: miRNA-seq_liver_CTR_12w_2

description:
non coding small RNA seq
liver_CTR_12w_2
DIAR control 12w liver

value: liver

value: 12 weeks


title: 18-0003v2 Glom

tag: storage


title: HeLa-iCas9-SerCGA sgRNA cells, day 12 of iCas9 induction, repeat2

description:
SerCGAsgRNA_HeLa_D12_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: HeLa

value: iCas9- SerCGAsgRNA

value: Day 12

value: repeat 2

tag: molecule subtype


title: SMARCA4KO_SMARCA2dTAG_DMSO_IgG

value: SMARCA4 KO

value: SMARCA2 dTAG

value: DMSO

value: IgG


title: HeLa-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat1

description:
SerCGAsgRNA_HeLa_D4_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

tag: crispr construct

value: Day 4

value: repeat 1

value: tRNA


title: SMARCA4KO_SMARCA2dTAG_DMSO_BRD4

tag: genotype


title: 18-0003v2 Bulk

value: Kidney

value: Reference

value: Nephrectomy

value: Female


title: HeLa-iCas9-SerCGA sgRNA cells, before iCas9 induction, repeat2

description:
SerCGAsgRNA_HeLa_D0_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: Day 0


title: 17-0002 Interstitium

value: Interstitium

value: OCT at -80C


title: miRNA-seq_liver_CTR_10w_3

description:
non coding small RNA seq
liver_CTR_10w_3
DIAR control 10w liver

value: normal control

value: liver

value: 10 weeks


title: miRNA-seq_liver_STZ_6w_2

description:
non coding small RNA seq
liver_STZ_6w_2
DIAR STZ 6w liver

value: hepatocellular carcinoma

value: 6 weeks


title: miRNA-seq_liver_CTR_10w_2

description:
non coding small RNA seq
liver_CTR_10w_2
DIAR control 10w liver


title: miRNA-seq_liver_CTR_12w_1

description:
non coding small RNA seq
liver_CTR_12w_1
DIAR control 12w liver

value: 12 weeks


title: 17-0002 CD

value: Collecting Duct


title: HeLa-iCas9-SerCGA sgRNA cells, day 12 of iCas9 induction, repeat1

description:
SerCGAsgRNA_HeLa_D12_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: HeLa

value: iCas9- SerCGAsgRNA

value: Day 12


title: HeLa-iCas9-SerCGA sgRNA cells, before iCas9 induction, repeat1

description:
SerCGAsgRNA_HeLa_D0_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: repeat 1

value: tRNA


title: 17-0002 TAL

value: Kidney

value: Reference

value: Nephrectomy

value: Thin Ascending Limb


title: HeLa-iCas9-ProCGG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ProCGGsgRNA_HeLa_D12_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

source_name: HeLa iCas9 - ProCGG sgRNA

value: iCas9- ProCGGsgRNA

value: repeat 2


title: miRNA-seq_liver_CTR_10w_1

description:
non coding small RNA seq
liver_CTR_10w_1
DIAR control 10w liver

value: normal control

value: liver


title: miRNA-seq_liver_CTR_6w_3

description:
non coding small RNA seq
liver_CTR_6w_3
DIAR control 6w liver


title: HeLa-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat2

description:
SerCGAsgRNA_HeLa_D4_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: Day 4


title: 17-0002 Proximal Tubule

value: Proximal Tubule

value: OCT at -80C

value: Female


title: miRNA-seq_liver_CTR_6w_2

description:
non coding small RNA seq
liver_CTR_6w_2
DIAR control 6w liver

value: 6 weeks


title: SMARCA4KO_SMARCA2dTAG_72h_dTAG_H3K27ac

value: SMARCA4 KO

tag: dtag

value: SMARCA2 dTAG

value: 72h dTAG47


title: 17-0002 Glom

value: Glomerulus


title: HeLa-iCas9-ProCGG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ProCGGsgRNA_HeLa_D8_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: HeLa

tag: icas9 induction time

value: Day 8

value: tRNA


title: HeLa-iCas9-ProCGG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ProCGGsgRNA_HeLa_D12_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: Day 12

tag: repeat

value: repeat 1


title: SMARCA4KO_SMARCA2dTAG_6h_dTAG_H3K27ac

value: 6h dTAG47


title: SMARCA4KO_SMARCA2dTAG_6h_dTAG_input


title: 17-0002 Bulk

tag: tissue

value: Kidney

value: Reference

value: Nephrectomy

value: Bulk


title: SMARCA4KO_SMARCA2dTAG_DMSO_ARID1A

tag: treatment

value: DMSO


title: HeLa-iCas9-ProCGG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ProCGGsgRNA_HeLa_D4_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: iCas9- ProCGGsgRNA

value: Day 4

value: repeat 2


title: HeLa-iCas9-ProCGG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ProCGGsgRNA_HeLa_D8_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv


title: 17-0001 Interstitium

tag: disease

value: Interstitium

value: OCT at -80C

value: Female


title: SMARCA4KO_SMARCA2dTAG_dTAG47_72h_IgG

value: SMARCA4 KO

value: SMARCA2 dTAG

value: 72h dTAG47

value: IgG


title: HeLa-iCas9-ProCGG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ProCGGsgRNA_HeLa_D4_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: HeLa

value: repeat 1

value: tRNA


title: SMARCA4KO_SMARCA2dTAG_72h_dTAG_input


title: miRNA-seq_blood_STZ_12w_1

description:
non coding small RNA seq
blood_STZ_12w_1
DIAR STZ 12w serum

source_name: exosome

value: hepatocellular carcinoma

value: serum exosome

value: 12 weeks


title: miRNA-seq_blood_STZ_12w_2

description:
non coding small RNA seq
blood_STZ_12w_2
DIAR STZ 12w serum


title: SMARCA4KO_SMARCA2dTAG_dTAG47_72h_BRD4


title: HeLa-iCas9-ProCGG sgRNA cells, before iCas9 induction, repeat2

description:
ProCGGsgRNA_HeLa_D0_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: Day 0


title: miRNA-seq_blood_STZ_12w_3

description:
non coding small RNA seq
blood_STZ_12w_3
DIAR STZ 12w serum


title: HeLa-iCas9-ProCGG sgRNA cells, before iCas9 induction, repeat1

description:
ProCGGsgRNA_HeLa_D0_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: iCas9- ProCGGsgRNA


title: 17-0001 TAL

value: Kidney

value: Reference

value: Nephrectomy

value: Thin Ascending Limb

tag: gender


title: miRNA-seq_blood_STZ_10w_3

description:
non coding small RNA seq
blood_STZ_10w_3
DIAR STZ 10w serum

tag: disease state

value: 10 weeks


title: 17-0001 Proximal Tubule

value: Proximal Tubule

value: OCT at -80C

value: Female


title: HeLa-iCas9-LeuTAG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_HeLa_D12_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

source_name: HeLa iCas9 - LeuTAG sgRNA

value: iCas9- LeuTAGsgRNA

value: Day 12

value: repeat 2


title: SMARCA4KO_SMARCA2dTAG_dTAG47_72h_ARID1A

value: SMARCA4 KO

value: SMARCA2 dTAG

value: 72h dTAG47


title: SMARCA4KO_SMARCA2dTAG_3h_dTAG_input

value: 3h dTAG47


title: miRNA-seq_blood_STZ_10w_2

description:
non coding small RNA seq
blood_STZ_10w_2
DIAR STZ 10w serum

value: hepatocellular carcinoma

value: serum exosome

tag: time


title: 17-0001 Glom

value: Kidney

value: Glomerulus


title: miRNA-seq_liver_CTR_6w_1

description:
non coding small RNA seq
liver_CTR_6w_1
DIAR control 6w liver

value: normal control

value: liver

value: 6 weeks