title: F508delCFBE41o, siLMTK2, TGFβ1 (Urban_3_4_S12)

city: Pittsburgh

first: Donald

middle: B.

last: DeFranco

state: PA

address: 7041 Biomedical Sciences Tower 3

department: Department of Pharmacology and Chemical Biology

institute: University of Pittsburgh

description: F508delCFBE41o- miRseq

data_processing:
RNA sequencing reads were imported into CLC Genomics Workbench 11 (Qiagen, Valencia, CA, USA) and an initial quality control report of each read was performed.
Adapter trimming from the sequence reads was performed using the following adapter sequences: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Trimmed sequence reads mapping was performed using human GRCh38/hg38 as a reference genome and using the sequence and annotation from ENSEMBL version 86. Expression values were scaled to TPM and only mapped reads were considered.
PCA plot was obtained and differential expression was performed using four different groups: (1) siCTRL-transfected cells with vehicle treatment, (2) siCTRL-transfected cells with TGF-β1 treatment, (3) siLMTK2-transfected cells with vehicle treatment, and (4) siLMTK2-transfected cells with TGF-β1 treatment.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx, differential gene expression

source_name: Parental CFBE41o- Cells

growth_protocol: Immortalized human bronchial epithelial cell models: parental CFBE41o- (with no CFTR transduction) were cultured in Minimum Essential Media (MEM) containing 10% Fetal bovine serum (FBS), 50µg/mL streptomycin, 50U/mL Penicillin, 2mM L-Glutamine). Cells were split at 90% confluency  were seeded (~1 million/well)  on 6-well culture plates (Corning) coated with 10% collagen (PureCol, Type I Bovine Collagen Solution, Advanced BioMatrix) in Opti-MEM (1X Opti-MEM Reduced Serum Medium, gibco, Life Technologies) and incubated with the optimized transfection mixture containing 50nM of siRNA (siLMTK2 or siCTRL), at 37ºC for 24 h. Next day, cells were trypsinized and transferred to Transwell filters (air-liquid interface) and cultured for 5 days.

extract_protocol:
Total RNA was isolated from cell lysate using the Quick-RNA Miniprep Kit (Zymo Research, R1054) according to the manufacturer’s instructions, with additional on-column DNase treatment with the RNase-free DNase Set (Zymo) to remove contaminating genomic DNA
1 μg of total RNA was used with the Illumina TruSeq Stranded Total RNA sample preparation kit (Illumina, San Diego, CA, USA), following manufacturer’s instruction.
3′ and 5’ adapters were ligated to total input RNA. Reverse transcription followed by polymerase chain reaction (PCR) was used to create cDNA constructs. This process selectively enriches those fragments that have adapter molecules on both ends. PCR was performed with primers that anneal to the ends of the adapters. cDNA libraries were then purified using QIAquick PCR purification kit (Qiagen). The cDNA libraries were validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorometer. Quality was examined using Agilent Bioanalyzer Tapestation 2200. The cDNA libraries were pooled at a final concentration of 1.8pM. Cluster generation and 75 bp paired-end read sequencing was performed on Illumina NextSeq 500’s (Illumina).

treatment_protocol: Human TGF-b1 (Sigma, St. Louis, MO) or vehicle control (4 mM HCl+1 mg/mL BSA) was used at concentration (15 ng/mL) for the treatment of cells on 24mm inserts (basolaterally) for 24 hour

value: Immortalized (CFBE41o-) Cells

tag: transfection


title: F508delCFBE41o, siCTRL, TGFβ1 (Urban_3_2_S10)

status: Public on Aug 11 2020

type: SRA

country: USA

description: F508delCFBE41o- miRseq

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: siCTRL

tag: treatment


title: F508delCFBE41o, siLMTK2, vehicle (Urban_3_3_S11)

description: F508delCFBE41o- miRseq

value: vehicle (HCL+BSA)


title: F508delCFBE41o, siLMTK2, TGFβ1 (Urban_2_4_S8)

description: F508delCFBE41o- miRseq


title: RNA-seq from untreated cells, rep 1

city: Berkeley

first: Timothy

middle: J

last: Eisen

state: CALIFORNIA

address: Stanley Hall

institute: UC Berkeley

data_processing:
Adapter trimming, cutadapt v1.18, cutadapt -j 10 -u 8 -m 10 -a TCGTATGCCGTCTTCTGCTTG
Alignment, STAR v2.7.1a, --alignIntronMax 1 --outSAMtype BAM SortedByCoordinate --genomeDir $star_index --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique --readFilesIn $directory/${filename}_trimmed_fastq.txt --outFileNamePrefix $directory/${filename}_ > $directory/${filename}_stdOut_logFile.txt
Indexing, samtools v1.9, samtools index
Counting reads, featureCounts, featureCounts -T 10 -s 1 -f -a $gtf_file -o $directory/${filename}_featureCounts.txt $directory/${filename}_Aligned.sortedByCoord.out.bam
Genome_build: SacCer3
Supplementary_files_format_and_content: Tab-delimited tables of reads per gene model

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast lysate from o/n culture

growth_protocol: Three individual yeast colonies were picked and grown o/n in liquid culture. Each colony culture was dilituded to mediawithand without  10uM radicicol and grown o/n. Cultures were further diluted to 0.001 OD600 in 100ml media and grown for 24 hours and collected for ribosome profiling or RNA-seq

extract_protocol:
Samples were rapidly collected using filtration and ground to a fine powder using a Freezer/Mill (SPEX SamplePrep) and stored at -80 °C.
To prepare RNA-seq libraries with fragment sizes that matched the ribosome profiling libraries, 25 µg of total RNA was poly(A)-selected, digested into 27–33 nt fragments, and used to prepare libraries in parallel with the ribosome-protected fragments. For ribosome profiling libraries, aliquots of lysate were digested with 1 U/μL RNase I (Ambion) for 30 min at room temperature and then run on a 10–50% sucrose gradient to purify monosomes (Subtelny et al., 2014). RNAs from both RNA-seq and ribosome profiling were then size-selected, ligated to adapters, reverse-transcribed, and amplified (Subtelny et al., 2014).

treatment_protocol: 10uM radicicol treatment o/n prior to further diliution to 0.001 OD600 and an additional o/n growth

value: untreated

tag: sequenced molecule

value: poly(A)-selected, fragmented RNA


title: F508delCFBE41o, siLMTK2, vehicle (Urban_2_3_S7)

description: F508delCFBE41o- miRseq


title: F508delCFBE41o, siCTRL, vehicle (Urban_3_1_S9)

description: F508delCFBE41o- miRseq


title: F508delCFBE41o, siCTRL, TGFβ1 (Urban_2_2_S6)

description: F508delCFBE41o- miRseq


title: RNA-seq from radicicol cells, rep 2

value: 10 µM radicicol pre-treatment


title: F508delCFBE41o, siLMTK2, vehicle (Urban_1_3_S3)

description: F508delCFBE41o- miRseq


title: F508delCFBE41o, siLMTK2, TGFβ1 (Urban_1_4_S4)

description: F508delCFBE41o- miRseq


title: F508delCFBE41o, siCTRL, vehicle (Urban_1_1_S1)

description: F508delCFBE41o- miRseq


title: F508delCFBE41o, siCTRL, TGFβ1 (Urban_1_2_S2)

description: F508delCFBE41o- miRseq


title: kidney vessels isolated at P10_early life MatSep, bio rep2

type: RNA

city: Lexinton

first: Analia

middle: S

last: Loria

state: KY

address: 900 S Limestone

department: Pharmacology

institute: U of Kentucky

description:
MS_P10_17
Kidney vessels isolated at P10 from littermate that had exposure to early life stress.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing:
Data were processed using RMA and medium normalization implemented in Partek Genomics suite software. Gene level expression were summarized from the corrected intensities without log2 transformation.
probe group file: RaGene-2_0-st-v1.pgf

label: biotin

organism: Rattus norvegicus

source_name: kidney vessels isolated at P10, early life MatSep

label_protocol: Purified RNA samples were quantified and labeled using WT-IVT whole transcriptome amplification procedure following Affymetrix rat array protocol.

growth_protocol: Kidney vessels were isolated after exposure to chronic behavioral stress at postnatal day 10 (P10) and at later in life after normal growth and development (postnatal day, P180).

extract_protocol: Kidney vessels were frozen in liquid nitrogen immediately after isolation, and stored at −80 C till RNA extraction. Cellular total RNA was prepared using Trizol reagents.

tag: tissue

value: renal vessels

tag: age

tag: Sex

value: male

value: maternal separation


title: HCEC miR-184 rep1

city: Wenzhou

first: Qiongjie

last: CAO

state: Zhejiang

address: 270 Xueyuan Road

country: China

institute: Wenzhou Medical University

description: Gene expression in HCECs 48 hours post transfection with miR-184

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k

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

source_name: human corneal epithelial cell, transfected with 50 nM microRNA-184, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent)

growth_protocol: The SV40-immortalized human corneal epithelial cells (HCECs) were kept in DMEM/F12 medium (Thermo Fisher Scientific) that was supplemented with 10% fetal bovine serum (Thermo Fisher Scientific), 10 ng/mL insulin (Sigma-Aldrich), and 10 ng/mL EGF (Sigma) in a humidiﬁed incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted by using the Trizol Reagent (Invitrogen) following the manufacturer's recommendations.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: HCECs were seeded onto 6-, 24-, or 96-well plates one day before the transfections were performed. Cells were transfected with either 50 nM miR-184 mimic for miR-184 overexpression, or a negative control (NC), using a transfection reagent (Lipofectamine RNAiMAX; Invitrogen).

tag: cell line


title: SCR-2_ATAC-seq

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

library_source: genomic

data_processing:
ATAC-Seq reads alignment using Bowtie v2.2.6
Sort/remove duplicates using Sambamba v0.6.5
Convert to bam using Samtools v1.2.0
Count feature coverage around features using Deeptools v2.0.0
Count feature coverages using Rsubread v1.26.1
Trim reads/ quality control using Trim Galore v0.4.2
RNA-Seq reads alignment using STAR v2.5.3a
Count feature coverage around transcriptomic features using fetureCounts v1.5.0
Count feature coverages using igvtools v2.3.91
Detect differential regions using DESeq2 v1.16.1
Genome_build: hg19/panTro4/gorGor3/rheMac3/mm9
Supplementary_files_format_and_content: TDF format, read coverage

molecule: genomic DNA

source_name: H7 hESC-CM, scramble

growth_protocol: Pluripotent cells were grown on Matrigel-coated plates (1:100 Matrigel in E8 medium) using chemically defined E8 medium. The medium was changed daily and cells were passaged every 3-4 days using EDTA or Accutase. Cardiomyocytes were maintained in RPMI + B27+ with media change every other day.

extract_protocol:
For RNA-seq, RNA was isolated using miRNeasy kit (Qiagen) following the manufacture’s protocol. For ATAC-seq, 100,000 cells were centrifuged 500 g for 5 min at room temperature. The cell pellet was resuspended in 50 ml lysis buffer (10 mM Tris–Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Igepal CA-630) and centrifuged immediately 500 g for 10 min at 4°C. The cell pellet was resuspended in 50 ml transposase mixture (25 ul 2×TD buffer, 22.5 μl dH2O, and 2.5 μl Illumina Tn5 transposase or with final concentration of 100 nM Atto-590-labeled in-house Tn5) and incubated at 37°C for 30 min. After transposition, the mixture was purified with the Qiagen Mini-purification kit and eluted in 10 ul Qiagen EB elution buffer. For transgenic BANCR embryos plasmid vector construction (pRP[Exp]-BetaMHC>hBANCR) and purification, pronuclear plasmid injection of FVB embryos, harvesting and genotyping of E16 embryos were performed by Cyagen Biosciences (Santa Clara, CA,USA). Total RNA was isolated from extracted embryo hearts that were plasmid positive (n=2) or negative (n=2).
Total RNA was submitted to a core facility (Stanford Functional Genomics) for library preparation and Illumina sequencing. For ATAC-seq, sequencing libraries were prepared following the original ATAC-seq protocol (Buenrostro, J. D. et al. Nat Methods 10, 1213-1218 (2013)). The HiChIP protocol was performed as previously described (Mumbach, M. R. et al. Nat Methods 13, 919-922 (2016)).

treatment_protocol: Cardiomyocytes were differentiated from human and NHP pluripotent cells. Briefly, differentiation medium consisted of RPMI-1640 media (11875-085, Life Technologies) supplemented with B27® minus insulin (A1895601, Life Technologies) (RPMI + B27-). To this medium, various small molecules were added over a week-long timetable as previously described. On the first day (D0) of differentiation, 6 µM CHIR 99021 (C-6556, LC Laboratories) was added. On D2, media was aspirated and replaced with RPMI + B27-. On D3, media was aspirated and replaced with 5 µM of IWR-1 (S7086, Selleck Chemicals) in RPMI + B27-. Media was replaced with RPMI + B27- on D5 and RPMI plus B27 supplemented with insulin (17504-044, Life Technologies) (RPMI + B27+) on D7.

value: H7 hESC-CM

tag: gender

value: female

tag: differentiation days


title: HCEC NC rep1

description: Gene expression in HCECs 48 hours post transfection with NC

source_name: human corneal epithelial cell, transfected with 50 nM NC, replicate 1

value: negative control


title: SCR-1_ATAC-seq


title: kidney vessels isolated at P10_early life MatSep, bio rep3

description:
MS_P10_22
Kidney vessels isolated at P10 from littermate that had exposure to early life stress.


title: BKD-1_ATAC-seq

source_name: H7 hESC-CM, BANCR knockdown


title: F508delCFBE41o, siCTRL, vehicle (Urban_2_1_S5)

description: F508delCFBE41o- miRseq


title: BOE-2_ATAC-seq

source_name: H7 hESC-CM, BANCR overexpression


title: kidney vessels isolated at P10_early life MatSep, bio rep4

description:
MS_P10_23
Kidney vessels isolated at P10 from littermate that had exposure to early life stress.


title: kidney vessels isolated at P10_early life MatSep, bio rep5

description:
MS_P10_24
Kidney vessels isolated at P10 from littermate that had exposure to early life stress.


title: kidney vessels isolated at P180_early life MatSep, bio rep2

description:
MS_6mo_5
Kidney vessels isolated at P180 from littermate that had exposure to early life stress.

source_name: kidney vessels isolated at P180, early life MatSep


title: kidney vessels isolated at P180_early life MatSep, bio rep3

description:
MS_6mo_6
Kidney vessels isolated at P180 from littermate that had exposure to early life stress.


title: kidney vessels isolated at P180_early life MatSep, bio rep4

description:
MS_6mo_10
Kidney vessels isolated at P180 from littermate that had exposure to early life stress.


title: BKD-3_RNA-seq

description: abundance data: BOE.SCR.BKD.read.counts.txt


title: BKD-1_RNA-seq


title: kidney vessels isolated at P180_early life MatSep, bio rep5

description:
MS_6mo_11
Kidney vessels isolated at P180 from littermate that had exposure to early life stress.


title: kidney vessels isolated at P10_no MatSep control, bio rep3

description:
C_P10_19
Kidney vessels isolated at P10 from littermate that was not exposed to early life stress.

source_name: kidney vessels isolated at P10, P10 age control

value: no maternal separation


title: kidney vessels isolated at P10_no MatSep control, bio rep4

description:
C_P10_20
Kidney vessels isolated at P10 from littermate that was not exposed to early life stress.


title: BKD-2_ATAC-seq


title: kidney vessels isolated at P10_early life MatSep, bio rep1

description:
MS_P10_16
Kidney vessels isolated at P10 from littermate that had exposure to early life stress.


title: kidney vessels isolated at P10_no MatSep control, bio rep2

description:
C_P10_15
Kidney vessels isolated at P10 from littermate that was not exposed to early life stress.


title: kidney vessels isolated at P180_early life MatSep, bio rep1

description:
MS_6mo_4
Kidney vessels isolated at P180 from littermate that had exposure to early life stress.


title: SCR-3_RNA-seq


title: kidney vessels isolated at P10_no MatSep control, bio rep1

description:
C_P10_14
Kidney vessels isolated at P10 from littermate that was not exposed to early life stress.


title: SCR-2_RNA-seq


title: BOE-1_ATAC-seq


title: kidney vessels isolated at P10_no MatSep control, bio rep5

description:
C_P10_21
Kidney vessels isolated at P10 from littermate that was not exposed to early life stress.


title: kidney vessels isolated at P180_no MatSep control, bio rep5

description:
C_6mo_9
Kidney vessels isolated at P180 from littermate that was not exposed to early life stress.

source_name: kidney vessels isolated at P180, 6 mo age control


title: SCR-1_RNA-seq


title: Sample_23: genomic DNA from neonatal sepsis NS_9

type: genomic

city: Paterna

first: María José

last: Garzón Garzón

address: Carrer del Catedràtic Agustín Escardino Benlloch, 9

country: Spain

institute: EpiDisease SL

description: plasma from neonates

hyb_protocol: The bisulphite treatment of DNA was followed by a whole genome amplification step, enzymatic endpoint fragmentation, precipitation and resuspension, and finally, the hybridization to Illumina Infinium Human Methylation850 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina HiScan SQ scanner

data_processing: House-made R scripts

label: biotin and DNP

source_name: Whole-blood sample 23

label_protocol: The nucleotides incorporated for the single base extension were labeled with biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP)

extract_protocol: Genomic DNA was isolated with All-In-One DNA/RNA Miniprep Kit (BS88203, Bio Basic Canda Inc, Canada, USA) following the manufacturer's instructions

value: Whole blood

tag: sample group

value: Nosocomial sepsis


title: Sample_22: genomic DNA from healthy control C_6

description: plasma from neonates

source_name: Whole-blood sample 22

value: Control


title: BOE-3_RNA-seq


title: Sample_21: genomic DNA from neonatal sepsis NS_8

description: plasma from neonates

source_name: Whole-blood sample 21


title: kidney vessels isolated at P180_no MatSep control, bio rep3

description:
C_6mo_3
Kidney vessels isolated at P180 from littermate that was not exposed to early life stress.


title: BOE-2_RNA-seq


title: kidney vessels isolated at P180_no MatSep control, bio rep2

description:
C_6mo_2
Kidney vessels isolated at P180 from littermate that was not exposed to early life stress.


title: kidney vessels isolated at P180_no MatSep control, bio rep1

description:
C_6mo_1
Kidney vessels isolated at P180 from littermate that was not exposed to early life stress.


title: kidney vessels isolated at P180_no MatSep control, bio rep4

description:
C_6mo_8
Kidney vessels isolated at P180 from littermate that was not exposed to early life stress.


title: BKD-2_RNA-seq


title: Sample_20: genomic DNA from neonatal sepsis NS_7

description: plasma from neonates

source_name: Whole-blood sample 20


title: Sample_19: genomic DNA from healthy control C_5

description: plasma from neonates

source_name: Whole-blood sample 19


title: BOE-1_RNA-seq


title: Sample_18: genomic DNA from neonatal sepsis VS_6

description: plasma from neonates

source_name: Whole-blood sample 18

value: Vertical sepsis


title: Human fetal stomatch Fetus-2

description: abundance data: fetal_tissues_read_counts.txt

source_name: Human fetal stomatch Fetus-2

value: fetal stomatch Fetus


title: Sample_17: genomic DNA from neonatal sepsis VS_5

description: plasma from neonates

source_name: Whole-blood sample 17


title: Sample_16: genomic DNA from neonatal sepsis NS_6

description: plasma from neonates

source_name: Whole-blood sample 16


title: Human fetal pancreas Fetus-2

source_name: Human fetal pancreas Fetus-2

value: fetal pancreas Fetus


title: Sample_15: genomic DNA from healthy control C_4

description: plasma from neonates

source_name: Whole-blood sample 15


title: Sample_14: genomic DNA from neonatal sepsis VS_4

description: plasma from neonates

source_name: Whole-blood sample 14


title: Human fetal liver Fetus-2

source_name: Human fetal liver Fetus-2

value: fetal liver Fetus


title: Human fetal left ventricle proximal Fetus-2

value: fetal left ventricle proximal Fetus


title: Sample_13: genomic DNA from neonatal sepsis NS_5

description: plasma from neonates

source_name: Whole-blood sample 13


title: Human fetal left ventricle distal Fetus-2

value: fetal left ventricle distal Fetus


title: Sample_12: genomic DNA from healthy control C_3

description: plasma from neonates

source_name: Whole-blood sample 12


title: Human fetal brain Fetus-2

source_name: Human fetal brain Fetus-2

value: fetal brain Fetus


title: Sample_11: genomic DNA from neonatal sepsis VNS_2

description: plasma from neonates

source_name: Whole-blood sample 11

value: Vertical+Nosocomial sepsis


title: Human fetal stomatch Fetus-1

source_name: Human fetal stomatch Fetus-1

value: male


title: Sample_9: genomic DNA from neonatal sepsis NS_4

description: plasma from neonates

source_name: Whole-blood sample 9


title: Sample_7: genomic DNA from healthy control C_2

description: plasma from neonates

source_name: Whole-blood sample 7


title: Sample_8: genomic DNA from neonatal sepsis NS_3

description: plasma from neonates

source_name: Whole-blood sample 8


title: Sample_6: genomic DNA from neonatal sepsis VS_2

description: plasma from neonates

source_name: Whole-blood sample 6


title: Human fetal pancreas Fetus-1

source_name: Human fetal pancreas Fetus-1


title: Human fetal left ventricle proximal Fetus-1


title: Human fetal left ventricle distal Fetus-1


title: Human fetal liver Fetus-1

source_name: Human fetal liver Fetus-1


title: Sample_5: genomic DNA from neonatal sepsis NS_2

description: plasma from neonates

source_name: Whole-blood sample 5


title: Human fetal kidney Fetus-1

source_name: Human fetal kidney Fetus-1

value: fetal kidney Fetus


title: Human fetal brain Fetus-1

source_name: Human fetal brain Fetus-1


title: Sample_3: genomic DNA from neonatal sepsis VNS_1

description: plasma from neonates

source_name: Whole-blood sample 3


title: Human fetal skeletal muscle Fetus-2

source_name: Human fetal skeletal muscle Fetus-2

value: fetal skeletal muscle Fetus


title: Sample_2: genomic DNA from neonatal sepsis VS_1

description: plasma from neonates

source_name: Whole-blood sample 2


title: Sample_4: genomic DNA from healthy control C_1

description: plasma from neonates

source_name: Whole-blood sample 4


title: Human iPSC Fetus-2

description: abundance data: primates.read.counts.txt

source_name: Human iPSC Fetus-2

value: iPSC Fetus

value: female


title: Human iPSC Fetus-1

source_name: Human iPSC Fetus-1


title: Sample_1: genomic DNA from neonatal sepsis NS_1

description: plasma from neonates

source_name: Whole-blood sample 1


title: Human fetal kidney Fetus-2

source_name: Human fetal kidney Fetus-2


title: OE2_1

city: St. Louis

first: Xuemin

last: Wang

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Illumina Casava 1.8 software used for basecalling.
Three types reads were filtered: reads with adapter; contain N (no exact base information) reads; low-quality reads.
Based on HISAT2 software.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Oryza sativa

source_name: OE, root

growth_protocol: Soil-grown,10-h lighting and 14-h dark at room temperature.

extract_protocol:
Total RNA was extracted using a Trizol reagent (TransGene Biotech, Beijing, China) following the manufacturer’s instruction, and DNA contaminated was removed using RNase-free DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Dongjin

value: root

value: seven-day-old

tag: genotype

value: dgk1 OE


title: OE2_3


title: OE2_2


title: Sample_10: genomic DNA from neonatal sepsis VS_3

description: plasma from neonates

source_name: Whole-blood sample 10

value: Whole blood

value: Vertical sepsis


title: Human fetal skeletal muscle Fetus-1

source_name: Human fetal skeletal muscle Fetus-1


title: dgk1_3

source_name: dgk, root

value: dgk1 KO


title: NZB ES cells

city: Freiburg

first: Manching

last: Ku

address: Mathildenstrasse 1

department: Hematology and Oncology

country: Germany

institute: Medical Center - University of Freiburg

data_processing:
Basecalling softwares version was HiSeq Control Software 2.2.38 and RTA 1.18.61
BCL files to fastq files conversion and demultiplexing were done using CASAVA v1.8.2
Reads are aligned to reference genome using STAR (v2.2.0c)
Gene expression was quantified using aligned reads to exons of RefSeq transcripts using HOMER
differential gene expression was determined with edgeR
Genome_build: mm9
Supplementary_files_format_and_content: B6_NOD_ES_RNASeq_ChIPSeq_Processed_File.xlsx

organism: Mus musculus

source_name: NZB ES cells

growth_protocol: Cells were isolated from mouse embryos

extract_protocol:
embryonic stem cells were isolated from embryos and analyzed using mRNA-Seq
Nucleospin RNA XS kit (Macherey-Nagel)
mRNA was selected by poly-dT magnetic beads, then RNA was fragmented and reverse-transcribed preserving strand information, and cDNA was end-repaired, adenylated, adapter-ligated and PCR amplified
RNA-Seq (RNA-Seq libraries were sequenced on Illumina HiSeq2500 at single-end 50-bp (base pair), resulting 25-30 million reads per library)

treatment_protocol: ES cells were grown in the presence of 2i

tag: strain

value: NZB

value: Embryonic stem cells


title: NOD5 ES cells

source_name: NOD ES cells

value: NOD


title: v6.5 ES cells

source_name: v6.5 ES cells


title: NOD1 ES cells


title: B6 ES cells

source_name: B6 ES cells


title: NOD_Blastocyst2

description: [[done]]

data_processing:
Basecalling softwares version was HiSeq Control Software 2.2.38 and RTA 1.18.61
BCL files to fastq files conversion and demultiplexing were done using CASAVA v1.8.2
Reads are aligned to reference genome using STAR (v2.2.0c)
Gene expression was quantified using aligned reads to exons of RefSeq transcripts using HOMER
differential gene expression was determined with edgeR
Genome_build: mm10
Supplementary_files_format_and_content: Excel file RPKM values for each Sample
Tab-delimited text file containing read counts used as input to differential gene expression

source_name: NOD blastocyst

growth_protocol: Cells were isolated from mouse blastocysts

extract_protocol:
mouse blastocyst was isolated from mouse and analyzed using Takara Clontech SMART-Seq low input RNA-Seq
whole blastocysts were used as input without isolating RNA
Clontech Takara Bio Smart-Seq V4 ultra-low input RNA-Seq library preparation kit was used to prepare RNA-Seq libraries
RNA-Seq (RNA-Seq libraries were sequenced on Illumina HiSeq2500 at single-end 50-bp (base pair), resulting 25-30 million reads per library)

treatment_protocol: no treatment

value: whole blastocyst


title: dgk1_2


title: NOD_Blastocyst1

description: [[done]]


title: dgk1_1


title: WT3

source_name: WT, root

value: wild-type


title: WT2


title: WT1


title: B6_Blastocyst

description: [[done]]

source_name: B6 blastocyst


title: NOD ES cells H3K4me3 ChIP

data_processing:
Basecalling softwares version was HiSeq Control Software 2.2.38 and RTA 1.18.61
BCL files to fastq files conversion and demultiplexing were done using CASAVA v1.8.2
Reads are aligned to reference genome using STAR (v2.2.0c)
Genome_build: mm9
Supplementary_files_format_and_content: Homer annotated peak file

source_name: NOD ES cells H3K4me3 ChIP

extract_protocol:
embryonic stem cells were isolated from embryos and analyzed using ChIP-Seq
ES cells were crosslinked with formaldehyde, then sonicate to fragment chromatin, and then subjected to antibody against perspective histone modification
ChIP DNA was end-repaired, then phosphorylated and an A was added. Illumina adapters were ligated and then PCR amplified to generate the sequencing library.
ChIP-Seq libraries were sequenced on Illumina HiSeq2500 at single-end 50-bp (base pair), resulting 25-30 million reads per library)

tag: mark

tag: chip antibody

value: anti-H3K4me3, Abcam ab8580, lot GR240214-2


title: SMA early symptomatic mouse brain, poly-RIBOseq, P5, rep 2

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

description:
ribosome profiling of polysomes from aSMA early symptomatic mouse brain at P5
SMN_SMA_rpf_table.txt

data_processing:
Library strategy: Ribo-seq
Raw reads were processed by removing 5’ adapters, discarding reads shorter than 20 nucleotides and trimming the first nucleotide (using Trimmomatic v0.36). Reads mapping on rRNAs and tRNAs (downloaded from the SILVA rRNA and the Genomic tRNA databases respectively) were removed. The remaining reads were aligned to the mouse transcriptome (Ensembl v81, corresponding to GENCODE mouse M6) with Bowtie2 (v2.2.6) employing the default settings. All reads aligning to the very same region were collapsed to avoid potential PCR duplicates, and only strand-specific reads were kept.  The number of ribosome protected fragments was determined with samtools idxstats.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text files including a brief annotation and transcript-specific counts of ribosome protected fragments

molecule: cytoplasmic RNA

source_name: SMA early symptomaticl mouse brain, ribosome profiling from polysomes, biological replicate 2

growth_protocol: The ‘Taiwanese’ mouse model of severe SMA was used in this study (Hsieh-Li et al., 2000; Riessland et al., 2010; Somers et al., 2015). All mice were on a congenic FVB background, with colonies at the University of Edinburgh established from breeding pairs purchased from Jackson Labs. ‘Taiwanese’ SMA mice (Smn-/-; SMN2tg/0) carry two copies of SMN2 on one allele and are on a null murine Smn background. Phenotypically normal heterozygous (Smn+/-;SMN2tg/0) littermates were used as controls. Litters were retrospectively genotyped using standard PCR protocols. All mice were housed within the animal care facilities in Edinburgh under standard SPF conditions. All animal procedures and breeding were performed in accordance with University of Edinburgh institutional guidelines and under appropriate project and personal licenses granted by the UK Home Office.

extract_protocol:
Cytoplasmic lysates were prepared pulverizing frozen mouse brains in a pestle and mortar cooled by liquid nitrogen and dissolving the powder in lysis buffer.   Active ribosome profiling: Lysates were clarified by two following centrifugations.    Ribosome profiling of polysomes: the lysates were loaded in a 15-50% linear sucrose gradient and polysomes separated by ultracentrifugation.   Ribosome profiling of SMN-primed ribosomes: after centrifugation to remove tissue debris, nuclei and mitochondria, the absorbance at 260 nm was measured. The concentration of NaCl was adjusted to 150 mM and endonuclease digestion was performed with RNAse I (5U/Unit of absorbance at 260nm in the lysate) at room temperature for 45 min. The reaction was stopped with SUPERase-In RNase inhibitor (Thermo Fisher Scientific). The digested lysates were centrifuged for 70 min at 100,000 rpm (TLA100.2 rotor, 4°C) and the ribosome pellet solubilized in 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 150 mM NaCl, 1% Triton X-100, 600 U/mL RiboLock RNase Inhibitor (Thermo Scientific), 0.2 mg/mL cycloheximide, Protease Inhibitor Cocktail. Ribosomes associated to SMN were obtained by immunoprecipitation using mouse anti-SMN antibody or anti-IgG as a control for unspecific binding. Briefly, the ribosome suspension was incubated with 2 μL of antibody for 1 h and 40 min in orbital rotation at 4°C. Then 100 μL of Dynabeads Protein G (Life technologies) were added and the sample was incubated for 1 hr at 4°C in orbital rotation. The supernatant was removed using a magnetic stand and the beads were washed 2 times for 5 min with washing buffer (10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 150 mM NaCl, 1% Triton X-100, 0.2 mg/mL cycloheximide, Protease Inhibitor Cocktail) before extraction of RNA with Trizol.
Ribosome profiling of polysomes: Polysomal fractions were pooled and digested with Rnase I for 2h at 4°C. Ribosome Protected Fragments (RPFs) were extracted with acid-phenol:chloroform:isoamylalcohol and isopropanol precipitation and size selected (25-35 nt) by UREA Page. RPFs were treated to remove 3’ phosphate, ligated to the 3’ adaptor and purified by UREA page. Ligated RPFs were retrotranscribed and the cDNA circularized. Libraries were finally amplified by PCR using Illumina PCR Primer Index. Libraries were sequenced on an Illumina HiSeq2500.   Active Ribosome Profiling: the RNA absorbance of the lysate (at 260 nm) was measured by Nanodrop ND-1000 UV-VIS Spectrophotometer and the lysate diluted to 1.7 a.u. A260/µL. RNase I digestion was performed for 45 mitues. The reaction was added directly to the RiboLace beads and the suspension incubated on a wheel for at least 1 hour in orbital rotation, 3 rpm at 4°C. After incubation, the tubes were kept on ice on a magnetic stand for 5 min to capture the beads–bounded-ribosomes. The supernatant was discarded (unbound fraction) and beads washed two times with 500 µL of a buffer. Ribosome Protected Fragments (RPFs) were extracted with acid-phenol:chloroform:isoamylalcohol and isopropanol precipitation and size selected (25-35 nt) by UREA Page. RPFs were treated to remove 3’ phosphate, ligated to the 3’ adaptor and purified by UREA page. Ligated RPFs were retrotranscribed and the cDNA circularized. Libraries were finally amplified by PCR using Illumina PCR Primer Index. Libraries were sequenced on an Illumina HiSeq2500.   Ribosome profiling of SMN-primed ribosomes: the ribosome protected fragments from both SMN and IgG immunoprecipitation were isolated and used for library preparation as described above. Libraries were sequenced on an Illumina HiSeq2500.

treatment_protocol: Neonatal mice were euthanized at P5 by overdose of anaesthetic, before decapitation to allow the brain to be removed. Following isolation, all tissues were immediately snap-frozen on dry ice and then transferred to -80 °C for storage.

value: Smn-/-; SMN2tg/0

tag: rna fraction

value: Poly-RIBOseq

tag: Stage

tag: replicate


title: B6 ES cells H3K4me3 ChIP

source_name: B6 ES cells H3K4me3 ChIP

tag: cell type


title: B6 ES cells H3K27ac ChIP

source_name: B6 ES cells H3K27ac ChIP

value: anti-H3K27Ac, Active Motif 39133, lot 31814008


title: SMA early symptomatic mouse brain, RiboLace RIBOseq, P5, rep 2

description:
active ribosome profiling with RiboLace from a SMA early symptomatic mouse brain at P5
SMN_SMA_rpf_table.txt

source_name: SMA early symptomatic mouse brain, active ribosome profiling with RiboLace, biological replicate 2

value: RiboLace-RIBOseq


title: SMA early symptomatic mouse brain, RiboLace RIBOseq, P5, rep 1

source_name: SMA early symptomatic mouse brain, active ribosome profiling with RiboLace, biological replicate 1


title: control mouse brain, IgG control ribosome profiling, P5, rep 1

description:
IgG control ribosome profiling from a control mouse brain at P5
SMN_SMA_rpf_table.txt

source_name: control mouse brain, IgG control ribosome profiling, biological replicate 1

value: Smn+/-; SMN2tg/0

value: IgG-RIBOseq


title: control mouse brain, SMN-specific ribosome profiling, P5, rep 2

description:
SMN-specific ribosome profiling from a control mouse brain at P5
SMN_SMA_rpf_table.txt

source_name: control mouse brain, SMN-specific ribosome profiling, biological replicate 2

value: SMN-RIBOseq


title: SMA early symptomatic mouse brain, poly-RIBOseq, P5, rep 1

description:
ribosome profiling of polysomes from a SMA early symptomatic mouse brain at P5
SMN_SMA_rpf_table.txt

source_name: SMA early symptomatic mouse brain, ribosome profiling from polysomes, biological replicate 1


title: control mouse brain, SMN-specific ribosome profiling, P5, rep 3

source_name: control mouse brain, SMN-specific ribosome profiling, biological replicate 3


title: control mouse brain, SMN-specific ribosome profiling, P5, rep 1

source_name: control mouse brain, SMN-specific ribosome profiling, biological replicate 1


title: WT Heart rep1

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

institute: CNIO

data_processing:
Sequenced on an Illumina HiSeq 2500 platform
For alignment and gene counting, we applied the Lexogen QuantSeq 2.2.3 pipeline provided by BlueBee, designed for use with the libraries described above
We decided to remove one of the WT heart replicates due to initial inferior RNA integrity and a failure to cluster with the rest of the WT heart samples. The differential expression analyses have been performed with DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Heart

extract_protocol:
Whole mount KO and WT embryos at E9.5 (21-23 pairs of somites) were placed in cold PBS. The whole heart along with surrounding SHF regions and a section of heart-proximal neural tube were dissected, snap-frozen and stored at -80 ºC. Per genotype and region, 3 replicates from 3 embryos each were extracted using TRI reagent (Sigma T9424) and homogenized with syringe and needle (25-30G)
Libraries were prepared using the QuantSeq 3’ mRNA-seq Library Prep Kit FWD (Lexogen)

value: Heart

value: WT


title: WT Neural Tube rep1

source_name: Neural Tube

value: Neural Tube


title: WT Neural Tube rep3


title: STAG2-KO Neural Tube rep3

value: STAG2 KO


title: STAG2-KO Neural Tube rep2


title: STAG2-KO Heart rep3


title: Rv1469KO_Rv1963c_D1_UT_U_3

city: Seattle

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

data_processing:
Raw FASTQ read data processing was carried out using a custom processing pipeline that harnesses the Bowtie 2 utilities, which is available at https://github.com/robertdouglasmorrison/DuffyNGS, and https://github.com/robertdouglasmorrison/DuffyTools, as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Genome_build: MT_H37Rv_V3
Supplementary_files_format_and_content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis

source_name: 7H9 broth culture

growth_protocol: Mycobacteria tuberculosis strains were grown on Middlebrook 7H9 medium (Difco) with 0.05% Tween 80 and ADC supplement.

extract_protocol:
RNA was isolated using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, frozen cell pellets Pellets were resuspended in Trizol, transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 sec in a FastPrep 120 homogenizer (Qbiogene) three times, with cooling on ice between steps. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a tube containing 300 mL chloroform and Heavy Phase Lock Gel (Eppendorf North America, Inc.), inverted for one minute, and centrifuged at max speed. The aqueous phase was then precipitated with 270 mL isopropanol and 270 mL high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was cleaned using an RNeasy kit following manufacturer’s recommendations (Qiagen). Messenger RNA was enriched using the RiboZero rRNA removal (bacteria) magnetic kit (Illumina Inc.) according to manufacturer's instructions.
Libraries were prepared for Illumina sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions and using the AMPure XP reagent (Agencourt Bioscience Corporation) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries associated with each replicate and multiplexing up to 48 libraries per sequencing run. The prepared libraries were quantified using the Kapa qPCR quantification kit, and were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit (Illumina Inc).

treatment_protocol: Bacteria were harvested at 1 day after being exposed to isoniazid (3.6μM) or no drug (as indicated in each sample title).

tag: treatment

value: untreated

tag: rv1963c induction state

value: Uninduced


title: Rv1469KO_Rv1963c_D1_UT_U_2


title: Rv1469KO_Rv1963c_D1_UT_I_2

value: Induced


title: Rv1469KO_Rv1963c_D1_UT_U_1


title: WT Heart rep2

tag: tissue

tag: age


title: STAG2-KO Neural Tube rep1


title: NOD ES cells H3K27ac ChIP

source_name: NOD ES cells H3K27ac ChIP

value: NOD

value: Embryonic stem cells


title: Rv1469KO_Rv1963c_D1_INH_U_3

value: isoniazid


title: Rv1469KO_Rv1963c_D1_UT_I_1


title: STAG2-KO Heart rep1


title: Rv1469KO_Rv1963c_D1_UT_I_3


title: Rv1469KO_Rv1963c_D1_INH_U_2


title: Rv1469KO_Rv1963c_D1_INH_U_1


title: WT Neural Tube rep2


title: Rv1469KO_Rv1963c_D1_INH_I_3


title: Brain Metastasis 2

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

data_processing:
RNA-seq pipeline description: Columbia Genome Center standard pipeline
Libraries were sequenced using Illumina HiSeq2500/4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat [1] (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation. We test for differentially expressed genes under various conditions using DESeq2. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2 normalized values for each sample

source_name: Brain Metastasis

extract_protocol:
RNA was prepared from snap-frozen tissues the using MagMAX-96 total RNA isolation kit and only RNA samples having between >200 ng and 1 ug and with an RNA integrity number (RIN) > 8 were used.
Libraries were prepared by the Columbia Genome Center. Poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). Libraries were prepared using TruSeq RNA library prep kit v2 or TruSeq Stranded mRNA library prep kit.

value: Mixed strain, predominantly C57BL/6

value: prostate

value: 7 months

value: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+

value: Intact, mouse with bone metastasis


title: Brain Metastasis 3

value: 9 months


title: Brain Metastasis 1


title: Normal Bone 3

data_processing:
RNA-seq pipeline description: Columbia Genome Center standard pipeline
Libraries were sequenced using Illumina HiSeq2500/4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation. We test for differentially expressed genes under various conditions using DESeq2. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2 normalized values for each sample

source_name: Bone

value: Bone

value: 5 months

value: Intact, un-induced mouse


title: Rv1469KO_Rv1963c_D1_INH_I_2


title: Normal Bone 2


title: CDC_Rv1963c_D1_UT_U_3


title: Rv1469KO_Rv1963c_D1_INH_I_1


title: CDC_Rv1963c_D1_UT_U_2


title: CDC_Rv1963c_D1_UT_U_1


title: Normal Bone 1

value: 10 months


title: CDC_Rv1963c_D1_UT_I_3


title: STAG2-KO Heart rep2

value: Heart

value: STAG2 KO


title: Normal Lung 3

source_name: Lung

value: Lung


title: CDC_Rv1963c_D1_UT_I_2

value: untreated

value: Induced


title: Normal Lung 2


title: CDC_Rv1963c_D1_UT_I_1


title: Lymph Node Metastasis 3

source_name: Lymph Node Metastasis

value: Lymph Node


title: Lymph Node Metastasis 2


title: CDC_Rv1963c_D1_INH_U_2

value: isoniazid

value: Uninduced


title: Lymph Node Metastasis 1

value: Mixed strain, predominantly C57BL/6


title: CDC_Rv1963c_D1_INH_U_3


title: CDC_Rv1963c_D1_INH_U_1


title: Lymph Node Metastasis 4

value: 8 months


title: CDC_Rv1963c_D1_INH_I_3


title: Bone Metastasis 9

source_name: Bone Metastasis

value: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+

value: Intact


title: CDC_Rv1963c_D1_INH_I_2


title: CDC_Rv1963c_D1_INH_I_1


title: Bone Metastasis 5

value: 9 months


title: Bone Metastasis 7


title: Bone Metastasis 6


title: Bone Metastasis 4


title: RIP IGF2BP1 AKD input rep1

city: Shanghai

first: Bi

last: Yan

address: Siping Road 1239

institute: Tongji university

description:
PolyA RNA
IGF2BP1 enrichment

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.7) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.4.2 ) with the default parameters.
The processed RNA-Seq reads were mapped to hg19 genome using STAR (v0.6.0). RefSeq genes were quantified to FPKM using Stringtie.
The processed RIP-Seq reads were mapped to hg19 genome using TopHat (v2.1.1) with default parameters.
FPKM for each sample and log2 fold change were calculated by using cuffdiff (v2.1.1).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *fpkm: Tab-delimited text files include FPKM values.

source_name: pluripotent stem cells

growth_protocol: For cell culture, hiF-T were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 2mM GlutaMAX (Millipore). Primed ESCs/iPSCs (pESCs/piPSCs) were cultured in hESM containing DMEM/F12 (Gibco) with 20% KnockOut SR (Gibco), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin(Millipore),8 ng/ml bFGF (Peprotech). Naïve ESCs/iPSCs (nESCs/niPSCs) were cultured in 5iLAF medium containing DMEM/F12: Neurobasal (1:1) (Gibco), 1% N2 supplement (Gibco), 2% B27 supplement (Gibco), 0.5% KnockOut SR (Gibco), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin(Millipore), 20ng/ml human LIF (Milipore), 8 ng/ml bFGF (Peprotech), 50 μg/ml BSA (Sigma) and the following cytokines and small molecules: PD0325901 (Selleck, 1 μM), SB590885 (Selleck, 0.5 μM), WH-4-023 (Selleck, 1 μM), Y-27632 (Selleck, 10 μM), and Activin A (Peprotech, 20 ng/ml) and passaged by Accutase (Sigma) every 4-5 days as previously reported. All hESCs were routinely cultured at 37 °C in 5% CO2, 5% O2.

extract_protocol:
For mRNA-seq, total RNAs were isolated from cells using TRizol (Invitrogen). To generate RNA sequencing libraries, KAPA Stranded mRNA-Seq Kit (KAPA) was used following the manufacturer’s instructions. For single cell RNAseq, cell clones were mechanically picked and washed with PBS supplemented with 0.5% BSA. Following the Covaris DNA shearing protocol for Smart-seq sequence library generation as previously described. Briefly, cells were lysed, RNAs with a polyadenylated tail were captured, reverse transcripted and preamplified.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: TJ-1# nESCs

tag: passages

tag: genotype/variation

value: ALPPL2 knockdown

tag: rip antibody


title: RIP IGF2BP1 AKD rep1

description:
PolyA RNA
IGF2BP1 enrichment


title: RIP IGF2BP1 AKD rep2

description:
PolyA RNA
IGF2BP1 enrichment


title: Normal Lung 1

value: Intact, un-induced mouse


title: Bone Metastasis 2


title: Bone Metastasis 3


title: Lung Metastasis 9

source_name: Lung Metastasis

value: lung

value: 5 months

value: Intact, mouse with bone metastasis


title: TJ-1# pESCs rep1

description: PolyA RNA

value: Embryo-derived pluripotent stem cells

value: Wild type


title: TJ-1# pESCs rep2

description: PolyA RNA


title: TJ-1# nESCs rep1

description: PolyA RNA


title: Lung Metastasis 7

value: Intact, mouse without bone metastasis


title: TJ-1# nESCs rep2

description: PolyA RNA


title: Lung Metastasis 8


title: Lung Metastasis 5


title: iCRISPR pESCs rep2

description: PolyA RNA


title: Lung Metastasis 4


title: iCRISPR pESCs rep1

description: PolyA RNA


title: Bone Metastasis 8


title: iCRISPR nESCs rep1

description: PolyA RNA


title: Lung Metastasis 3


title: RIP IGF2BP1 AKD input rep2

description:
PolyA RNA
IGF2BP1 enrichment


title: OCT4-ΔPE nESCs WT rep2

description:
PolyA RNA
OCT4-ΔPE TJ-1# nESCs

value: OCT4-<delta>PE TJ-1# nESCs


title: Lung Metastasis 2

value: 7 months


title: Lung Metastasis 1


title: OCT4-ΔPE nESCs WT rep1

description:
PolyA RNA
OCT4-ΔPE TJ-1# nESCs


title: OCT4-ΔPE nESCs AKD rep2

description:
PolyA RNA
OCT4-ΔPE TJ-1# nESCs


title: Primary Tumor 13

source_name: Prostate tumor, AP lobe

value: prostate

value: 10 months


title: Primary Tumor 12

value: Mixed strain, predominantly C57BL/6

value: 6 months


title: Bone Metastasis 1

value: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+

value: Intact


title: OCT4-ΔPE nESCs AKD rep1

description:
PolyA RNA
OCT4-ΔPE TJ-1# nESCs


title: Primary Tumor 11


title: RIP IGF2BP1 WT rep1

description:
PolyA RNA
IGF2BP1 enrichment

value: TJ-1# nESCs


title: Primary Tumor 9


title: Primary Tumor 10

value: 8 months


title: RIP IGF2BP1 WT input rep1

description:
PolyA RNA
IGF2BP1 enrichment


title: Lung Metastasis 6


title: iCRISPR nESCs rep2

description: PolyA RNA


title: nESCs IKO rep12

description:
PolyA RNA
scRNA-seq

value: IGF2BP1 Knockout


title: Primary Tumor 8

value: 9 months


title: Primary Tumor 7

source_name: Prostate tumor, DLP lobe


title: nESCs IKO rep10

description:
PolyA RNA
scRNA-seq


title: nESCs IKO rep11

description:
PolyA RNA
scRNA-seq


title: Primary Tumor 4


title: Primary Tumor 5


title: Primary Tumor 3


title: nESCs IKO rep9

description:
PolyA RNA
scRNA-seq


title: Primary Tumor 2


title: nESCs IKO rep7

description:
PolyA RNA
scRNA-seq


title: nESCs IKO rep6

description:
PolyA RNA
scRNA-seq


title: Primary Tumor 1


title: nESCs IKO rep5

description:
PolyA RNA
scRNA-seq


title: nESCs IKO rep3

description:
PolyA RNA
scRNA-seq


title: nESCs IKO rep4

description:
PolyA RNA
scRNA-seq


title: control replicate 4

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

data_processing:
Trimming was performed using BBDuk v36.92 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r forcetrimleft=11 useshortkmers=t mink=5 qtrim=t trimq=10 minlength=30).
Reads mapping to mouse rRNA transcripts (refseq) were removed using bwa v0.7.12 alignment and samtools v1.3.1.
Remaining reads were aligned to the mouse genome mm10 using TopHat v2.1.1 (parameter:--library-type fr-secondstrand), and reads in genes were counted with htseq-count v0.6.1 (parameter: -s yes) (reference data: illumina iGenomes, UCSC, mm10).
Genome_build: mm10
Supplementary_files_format_and_content: space-delimited text files with per gene read counts

source_name: splenic B220+ B cells

growth_protocol: For LPS-induced plasmablast differentiation assays splenic B220+ B cells were enriched using MACS technology (Miltenyi), according to the manufacturer’s instructions. Purified B cells were plated at a density of 150.000 cells/ml in IMDM medium (Life Technologies) supplemented with 10% fetal calf serum (Sigma), 50 µM 2-mercaptoethanol, 2 mM glutamine (Gibco), 100 U/ml penicillin (Sigma), 100 µg/ml streptomycin sulfate (Sigma).

extract_protocol:
After 4 days of LPS stimulation, the cells were FACS-sorted for CD22-CD138+ plasmablasts and RNA was harvested using Trizol reagent.
cDNA libraries for each of the samples were generated from 500 ng of total RNA using the QuantSeq 3′ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen) following the manufacturer’s instructions.

treatment_protocol: Splenic B220+ B cells isolated as described above were treated for 4 days with 25 µg/ml LPS (Sigma).

value: CD22-CD138+ sorted plasmablasts

value: 4 days LPS


title: control replicate 3


title: control replicate 2


title: nESCs IKO rep2

description:
PolyA RNA
scRNA-seq


title: nESCs IKO rep1

description:
PolyA RNA
scRNA-seq


title: Jagn1DB replicate 4

value: Jagn1fl/fl Mb1Cre+


title: Primary Tumor 6

value: Intact, mouse with bone metastasis


title: nESCs AKO rep9

description:
PolyA RNA
scRNA-seq

value: ALPPL2 Knockout


title: control replicate 1


title: Jagn1DB replicate 3


title: nESCs AKO rep8

description:
PolyA RNA
scRNA-seq


title: nESCs AKO rep7

description:
PolyA RNA
scRNA-seq


title: nESCs AKO rep6

description:
PolyA RNA
scRNA-seq


title: Jagn1DB replicate 1


title: nESCs IKO rep8

description:
PolyA RNA
scRNA-seq


title: Jagn1DB replicate 2


title: nESCs AKO rep3

description:
PolyA RNA
scRNA-seq


title: nESCs AKO rep5

description:
PolyA RNA
scRNA-seq


title: nESCs AKO rep1

description:
PolyA RNA
scRNA-seq


title: 293T WT rep2

description: PolyA RNA

source_name: human embryonic kidney cells

tag: cell line

value: Human embryonic kidney cells

value: Wild type


title: nESCs AKO rep2

description:
PolyA RNA
scRNA-seq


title: 293T AOE rep2

description: PolyA RNA

value: ALPPL2 overexpress


title: 293T AOE rep1

description: PolyA RNA


title: 293T WT rep1

description: PolyA RNA


title: nESCs AKO rep4

description:
PolyA RNA
scRNA-seq


title: hPSC_Lung organoid_SARS-CoV-2_imatinib_1 [LungOrganoid-10uM-Imatinib-1]

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel files storing RPKM per gene per sample

growth_protocol: Protocols for maintenance of hPSCs and generation of lung organoids were slightly modified from previous studies. The hESC line RUES2 was cultured on irradiated mouse embryonic fibroblasts (Global Stem, cat. no. GSC-6001G) at a density of 20,000- 25,000 cells/cm2 in a medium of DMEM/F12, 20% knockout serum replacement (Life Technologies), 0.1 mM β-mercaptoethanol (Sigma Aldrich) and 20 ng/ml bFGF (R&D Systems), and medium was changed daily. hESC cultures were maintained in an undifferentiated state at 37 °C in a 5% CO2/air environment until stem cells reached about 90% confluence.     hESC differentiation into endoderm was performed in serum-free differentiation (SFD) medium of DMEM/F12 (3:1) (Life Technologies) supplemented with N2 (Life Technologies), B27, 50 μg/ml ascorbic acid, 2 mM Glutamax, 0.4 μM monothioglycerol, 0.05% BSA at 37 °C in a 5% CO2/5% O2/95% N2 environment. hESCs were treated with Accutase and plated onto low attachment 6-well plates (Corning Incorporated, Tewksbury MA), resuspended in endoderm induction medium containing 10 μM Y-27632, 0.5 ng/ml human BMP4, 2.5 ng/ml human bFGF, 100 ng/ml human Activin A, for 72-76 hours dependent on the formation rates of endoderm cells. On day 3 or 3.5, the endoderm bodies were dissociated into single cells using 0.05% Trypsin/0.02% EDTA and plated onto fibronectin-coated, 24-well tissue culture plates (~100,000–150,000 cells/well). For induction of anterior foregut endoderm, the endoderm cells were cultured in SFD medium supplemented with 1.5 μM dorsomorphin dihydrochloride (R&D Systems) and 10 μM SB431542 (R&D Systems) for 36 hrs, and then switched to 36 hrs of 10 μM SB431542 and 1 μM IWP2 (R&D Systems) treatment. For induction of early stage lung progenitor cells (day 6–15), the resulting anterior foregut endoderm was treated with 3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human KGF, 10 ng/ml human BMP-4 and 50-60 nM all-trans retinoic acid (ATRA), in SFD medium for 8–10 d. The day 10–15 cultures were maintained in a 5% CO2/air environment. On days 15 and 16, the lung field progenitor cells were replated after one minute trypsinization onto fibronectin-coated plates, in the presence of SFD containing either a combination of five factors (3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human FGF7, 10 ng/ml human BMP4, and 50 nM ATRA). Day 16–25 cultures of late stage lung progenitor cells were maintained in SFD media containing 3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human KGF, in a 5% CO2/air environment. For differentiation of mature lung cells (day 25 to 55) in 3D culture, cultures were re-plated and embedded in 90% Matrigel after brief trypsinization in SFD media containing maturation components containing 3 μM CHIR99021, 10 ng/ml human FGF-10; 10 ng/ml human KGF, and DCI (50 nM Dexamethasone, 0.1 mM 8-bromo-cAMP (Sigma Aldrich ) and 0.1 mM IBMX (3,7-dihydro-1-methyl-3-(2-methylpropyl)-1H-purine-2,6-dione) (Sigma Aldrich).

extract_protocol:
At 24 hpi, hPSC-LOs were washed three times in PBS and lysed in TRIzol for RNA analysis.
Libraries were prepared using Illumina TruSeq stranded mRNA Sample Preparation kit.

treatment_protocol: hPSC-LOs were infected with SARS-CoV-2 at the indicated MOI and incubated for 24 hrs at 37°C. hPSC_LOs were treated with DMSO or 10 uM imatinib and infected with SARS-CoV-2 at indicated MOI.

tag: tissue/cell type

value: hPSC_Lung organoid


title: hPSC_Lung organoid_SARS-CoV-2_DMSO_2 [LungOrganoid-DMSO-2]


title: hPSC_Lung organoid_SARS-CoV-2_imatinib_3 [LungOrganoid-10uM-Imatinib-3]


title: hPSC_Lung organoid_SARS-CoV-2_DMSO_1 [LungOrganoid-DMSO-1]


title: hPSC_Lung organoid_SARS-CoV-2_DMSO_3 [LungOrganoid-DMSO-3]


title: Aspergillus niger wild type grown on D-glucose 2 hours, replicate 2 (re-analyzed)

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

hyb_protocol: Following fragmentation, 10 µg of cRNA was hybridized to Affymetrix A. niger Genome GeneChips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned.

data_processing: Microarray data was analyzed using the Bioconductor tool package version 2.8 (http://www.bioconductor.org/) together with house-made Perl (version .5.0) and Python (version 3.0) scripts. Probe intensities were normalized for background by the robust multi-array average (RMA) method using the R statistical language and environment. This method makes use of only perfect match (PM) probes. Normalization was processed by the quantiles algorithm. The median polish summary method was used to calculate the gene expression values.

organism: Aspergillus niger

source_name: A. niger wild type growing on D-glucose

label_protocol: Biotin-labeled antisense cRNA was produced from 2 µg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com)

growth_protocol: Aspergillus niger N402 was propagated and grown on complete medium (CM) or minimal medium (MM). Liquid cultures were grown in a rotary shaker at 250 rpm and 30C. Transfer experiment was performed by growing the strain for 16 h in 1 L Erlenmeyer flasks that contained 250 mL CM supplemented with 2% D-fructose as carbon source. The mycelium was harvested by filtration and washed with MM without a carbon source.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer.

treatment_protocol: One gram (wet weight) of the mycelium was transferred to 250 mL Erlenmeyer flasks containing 50 mL MM supplemented with 1% guar gum (Sigma-Aldrich) and incubated for 8 h, 24 h and 48 h.

tag: genotype

value: cspA1 (wild type)

value: mycelium

value: 2 hours

tag: substrate

value: 25 mM D-glucose


title: Aspergillus niger wild type grown on D-mannose 2 hours, replicate 1 (re-analyzed)

source_name: A. niger wild type growing on D-mannose

tag: strain

value: 25 mM D-mannose


title: Aspergillus niger wild type grown on D-glucose 2 hours, replicate 1 (re-analyzed)


title: Aspergillus niger wild type grown on D-mannose 2 hours, replicate 2 (re-analyzed)


title: Aspergillus niger wild type grown on guar-gum 2 hours, replicate 1 (re-analyzed)

source_name: A. niger wild type growing on guar-gum

value: 1% guar-gum


title: Aspergillus niger wild type grown on D-galactose 2 hours, replicate 1 (re-analyzed)

source_name: A. niger wild type growing on D-galactose

value: 25 mM D-galactose


title: Aspergillus niger wild type grown on D-galactose 2 hours, replicate 2 (re-analyzed)


title: Guar gum 24 hours biological rep1

description: Transcriptome of A. niger during guar gum degradation after 24 hour incubation

tag: process

value: guar gum degradation

tag: time

value: 24 hour


title: Guar gum 8 hours biological rep1

description: Transcriptome of A. niger during guar gum degradation after 8 hour incubation

value: 8 hour


title: Aspergillus niger wild type grown on mannan 2 hours, replicate 2 (re-analyzed)

source_name: A. niger wild type growing on mannan

value: 1% mannan


title: Aspergillus niger wild type grown on guar-gum 2 hours, replicate 2 (re-analyzed)


title: shRunx3-2_S14

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

description: 72 hr exposure

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include quantile normalized FPKM values for each Sample

source_name: Acute myeloid leukemia

growth_protocol: Cells were grown in Alpha MEM media with 20% FBS and 10 ng/mL GM-CSF

extract_protocol:
Total RNA was isolated from AML cells utilizing an RNA mini kit from Ambion. Isolated RNA was treated with DNAse 1 at 37°C for 20 minutes. The RNA was quantified and checked for purity and integrity prior to library construction.
RNA was prepared for sequencing utilizing a kit from Illumina

treatment_protocol: AML OCI-AML5 cells were treated with 1000 nM of OTX015 or 1000 nM of ARV-825 for 4 hours. OCI-AML5 cells were transduced with sh-NT or RUNX1 shRNA for 72 hours.

value: RUNX1 shRNA, 72 hrs exposure


title: Guar gum 48 hours biological rep2

description: Transcriptome of A. niger during guar gum degradation after 48 hour incubation

value: 48 hour


title: A549 12 hpi _rep2

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

description:
OAD13
A549-ATCC® CCL-185™

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38) using kallisto (0.44.0).
Genome_build: Human: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung epithelial cells

growth_protocol: Francisella tularensis spp. holarctica strain LVS (ATCC® 29684) were used for the infection. Bacterial cultures were grown at 37◦C to mid-log phase in TSBC (TSB Difco, supplemented with 0.1% cysteine, BD, France). The bacteria were washed with PBS and re-suspended in DMEM supplemented with 10% heat inactivated fetal bovine serum. A549 cells were seeded 20h prior to infection in six-well microtiter plates at a density of 10^6 cells per well

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and residual DNA was digested using RNase-free DNase (Qiagen).
Library construction using Illumina TruSeq chemistry

treatment_protocol: The cells were infected with the overnight LVS culture to at MOI of 20K, centrifuged at 600g for 5 minutes, and incubated at 37◦C for the indicated time. One-hour post infection the medium was replaced with DMED supplemented with 50ug/ml Gentamicin to kill extracellular bacteria. Thirty minutes later cells were washed three times with PBS and left with DMEM supplemented with 10% FBS

tag: agent

value: Francisella Tularensis

tag: time point

value: 12 hours


title: A549 6 hpi _rep2

description:
OAD12
A549-ATCC® CCL-185™

value: 6 hours


title: A549 24 hpi _rep2

description:
OAD14
A549-ATCC® CCL-185™

value: 24 hours


title: A549 3 hpi _rep2

description:
OAD11
A549-ATCC® CCL-185™

value: 3 hours


title: shRunx3-3_S15

description: 72 hr exposure


title: Guar gum 8 hours biological rep2

source_name: A. niger during guar gum degradation after 8 hour incubation

value: mycelium


title: Guar gum 48 hours biological rep1

source_name: A. niger during guar gum degradation after 48 hour incubation


title: shRunx3-1_S13

description: 72 hr exposure


title: hPSC_Lung organoid_SARS-CoV-2_imatinib_2 [LungOrganoid-10uM-Imatinib-2]

value: hPSC_Lung organoid


title: shNT-3_S12

description: 72 hr exposure

value: shNT, non-targeting shRNA, 72 hrs exposure


title: Aspergillus niger wild type grown on mannan 2 hours, replicate 1 (re-analyzed)

value: cspA1 (wild type)

value: 2 hours


title: A549 0.5hpi _rep2

description:
OAD09
A549-ATCC® CCL-185™

value: 0.5 hour


title: A549 1 hpi _rep2

description:
OAD10
A549-ATCC® CCL-185™

value: 1 hour


title: shNT-1_S10

description: 72 hr exposure


title: OCI-AML51uMOTX0152_S5

description: 4 hr treatment

value: OTX015 treated, 1000 nM, 4 hrs


title: A549 24 hpi _rep1

description:
OAD07
A549-ATCC® CCL-185™


title: OCI-AML51uMOTX0151_S4

description: 4 hr treatment


title: OCI-AML51uMARV2_S8

description: 4 hr treatment

value: ARV-825 treated, 1000 nM, 4 hrs


title: OCI-AML51uMARV1_S7

description: 4 hr treatment


title: OCI-AML5Control3_S3

description: 4 hr treatment

value: Control cells, no treatment


title: A549 mock _rep2

description:
OAD08
A549-ATCC® CCL-185™

value: uninfected


title: OCI-AML51uMOTX0153_S6

description: 4 hr treatment


title: A549 12 hpi _rep1

description:
OAD06
A549-ATCC® CCL-185™


title: A549 6 hpi _rep1

description:
OAD05
A549-ATCC® CCL-185™


title: LI_Day30C 3

city: Toronto

first: David

middle: G

last: Brooks

state: Ontario

address: 610 University Avenue

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
Base calling was performed using RTA 2.4.11
bcl2fastq2 2.19.1 was used to convert from bcl to fastq
reads were aligned to the GRCm38 genome using hisat2 2.1.0
samtools 1.3.1 was used to sort the alignment sam file from hisat2
genes counts were quantified using htseq-count 0.9.1
Genome_build: Genome_build: GRCm38 build 88
Supplementary_files_format_and_content: Tab delimited text file showing raw counts for each gene (by ensembl ID) for each sample

source_name: Large intestine

extract_protocol:
Small and large intestinal tissue was prepared by PBS washes, chopping, DTT digestion (IEL), collagenase/Dnase digestion (LPL). IEL and LPL were pooled, and then CD45+ live (PI-) cells were FACSsorted into RLT. RNA was isolated using a single cell RNA purification kit (Norgen Biotech Corp.) according to manufacturer’s instructions. SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) was used per manufacturer’s instructions for amplification of RNA and subsequent cDNA synthesis.
All samples proceeded through NexteraXT DNA Library Preparation (Illumina) using NexteraXT Index Kit V1 or V2 Set A (Illumina) following manufacturer’s instructions.

value: Large intestine

tag: cell type

value: CD45+ immune cells

value: 3 LCMV-Cl13 (chronic) infected


title: hPSC_Lung organoid_mock_2 [2B]

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: txt files storing raw read counts per gene per sample

source_name: hPSC_Lung organoid_mock

extract_protocol:
At 24 hpi, hPSC-LOs or hPSC-COs were washed three times in PBS and lysed in TRIzol for RNA analysis.
Libraries were prepared using Illumina TruSeq stranded mRNA Sample Preparation kit.

treatment_protocol: hPSC-LOs were infected with SARS-CoV-2 at the indicated MOI and incubated for 24 hrs at 37°C.

tag: treatment

value: Mock


title: hPSC_Lung organoid_SARS-CoV-2_1 [2D]

source_name: hPSC_Lung organoid_SARS-CoV-2


title: hPSC_Lung organoid_SARS-CoV-2_3 [2F]


title: OCI-AML51uMARV3_S9

description: 4 hr treatment


title: OCI-AML5Control2_S2

description: 4 hr treatment


title: LI_Day30A 1

value: LCMV-Armstrong (acute) infected


title: hPSC_Lung organoid_SARS-CoV-2_2 [2E]


title: A549 1 hpi _rep1

description:
OAD03
A549-ATCC® CCL-185™

value: Francisella Tularensis


title: A549 0.5hpi _rep1

description:
OAD02
A549-ATCC® CCL-185™


title: Guar gum 24 hours biological rep2

source_name: A. niger during guar gum degradation after 24 hour incubation

value: mycelium

value: guar gum degradation

value: 24 hour


title: A549 3 hpi _rep1

description:
OAD04
A549-ATCC® CCL-185™

value: 3 hours


title: OCI-AML5Control1_S1

description: 4 hr treatment


title: A549 mock _rep1

description:
OAD01
A549-ATCC® CCL-185™


title: Cut&Run Hhex control sample

city: Clayton

first: Sebastian

last: Scheer

address: 15 Innovation Walk

country: Australia

institute: Monash University

data_processing:
Library strategy: Cut&Run
Raw paired end fastq files were aligned to the UCSC mm10 genome with Bowtie2
Aligned bam files were then filtered to remove reads in black-listed regions
Bam files were filtered again to remove low quality reads
Macs2 was used to call peaks using both sample and input bam under default settings
Genome_build: UCSC mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: Enriched NK cells (STEMCELL negative NK cell enrichment kit) were cultured for 8 days in the presence of IL-15.

extract_protocol:
1 µg of anti-Hhex antibody (MAB83771, clone 2018B) was used to perform Cut&Run
MGITech MGIEasy DNA FS Library preparation kit V2 (according to the manufacturer's instructions: document revision A0)

treatment_protocol: 500,000 nuclei of each sample were isolated, taken up in Cut&Tag wash buffer, bound to ConA beads and Cut&Run was performed.

value: cultured NK cells

tag: ip antibody


title: Cut&Run Hhex IP sample

value: anti-Hhex antibody (MAB83771, clone 2018B)


title: hPSC_Lung organoid_mock_3 [2C]

value: hPSC_Lung organoid


title: shNT-2_S11

description: 72 hr exposure

value: shNT, non-targeting shRNA, 72 hrs exposure


title: LI_Day30C 2

tag: tissue


title: LI_Day30C 1


title: LI_Day30A 3


title: hPSC_Lung organoid_mock_1 [2A]


title: LI_Day30A 2


title: SI_Day30C 1

source_name: Small intestine

value: Small intestine


title: COVID_19 lung autopsy_3 [COVI19-Lung_64L-H3]

source_name: COVID_19 lung autopsy

tag: subject status

value: adult lung autopsy


title: Ovarian cancer, ADR-EF_batch2 (RNA-seq)

city: Pokfulam, Hong Kong

first: Alan

last: Wong

address: 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description:
OVCAR8-ADR treated with Erotinib and Fludarabine replicate 2.
OVCAR8-ADR-RNA-seq_rawcounts.csv

data_processing:
(Barcode NGS) fastq files preprocessed and analyzed using customized codes (https://github.com/AWHKU/CombiPIPE)
(RNA-seq) Trimmed pair-end adaptors by Trimmomatic 0.39
(RNA-seq) Aligned sequence reads by STAR aligner version 2.7
(RNA-seq) Extracted raw counts by Rsubread
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: excel files with NGS CPM barcode reads
csv files with RNA-seq raw counts

source_name: Ovarian cancer cells

growth_protocol: SK-N-MC-Cas9 cells were cultured in DMEM supplemented with 10% FBS and 1 X antibiotic-antimycotic (Life Technologies) at 37°C with 5% CO2. OVCAR8-ADR cells and OVCAR8-ADR-Cas9 cells were cultured in RPMI 1640 supplemented with 10% FBS and 1 X antibiotic-antimycotic at 37°C with 5% CO2.

extract_protocol:
For gRNA-library-transduced cell pool, genomic DNA was extracted from cells with DNeasy Blood and Tissue kit (Qiagen). For drug-treated OVCAR8-ADR cells, total RNAs were isolated by MiniBEST universal RNA extraction kit (Takara).
Barcode libraries from NGS and RNA libraries were prepared for sequencing using standard Illumina protocols.
Barcode NGS and RNA-seq

treatment_protocol: For the barcode libraries, SK-N-MC-Cas9 cells and OVCAR8-ADR-Cas9 cells were transduced by the lentiviruses with respective combinatorial gRNA libraries at a multiplicity of infection (MOI) of ~0.3-0.5. For the RNA-seq libraries, OVCAR8-ADR cells were treated with Azacitidine, Fludarabine, Erlotinib, Azacitidine+Fludarabine, Azacitidine+Erlotinib, Fludarabine+Erlotinib, and Azacitidine+Fludarabine+ Erlotinib.

value: Erlotinib(1.33 uM)+Fludarabine(0.3 uM)


title: SI_Day30A 3


title: COVID_19 lung autopsy_2 [COVI19-Lung_62L-H2]


title: Ovarian cancer, ADR-AF_batch2 (RNA-seq)

description:
OVCAR8-ADR treated with Azacitidine and Fludarabine replicate 2.
OVCAR8-ADR-RNA-seq_rawcounts.csv

value: Azacitidine(2.5 uM)+Fludarabine(0.3 uM)


title: LI_Day0 3

value: Large intestine

value: CD45+ immune cells

value: naïve


title: COVID_19 lung autopsy_1 [COVI19-Lung_59L-H1]


title: LI_Day0 2


title: YAK1 with Q578* variant replicate 4 [V4]

city: Minneapolis

first: Frank

middle: Wolfgang

last: Albert

state: MN

address: 6-160 Jackson Hall, 321 Church St SE

department: Department of Genetics, Cell Biology, & Development

institute: University of Minnesota

data_processing:
Using the trimmomatic software (Bolger et al., 2014), reads were trimmed of adapters and low quality bases and filtered to be at least 36 bp long.
Reads were then pseudo-aligned to the S. cerevisiae transcriptome (Ensembl build 93) and counted using kallisto (Bray et al., 2016).
We used RSeQC to calculate Transcript Integrity Numbers (TIN) which provided an estimation of alignment quality for each gene of each sample.
We excluded any gene with at least one read count of zero or at least one TIN of zero across the ten samples.
After filtering, 5,755 genes remained for analysis. Differential expression analysis was performed using the DESeq2 R package (Love et al., 2014), using the extraction batch information as covariate. DESeq2 provided, for each gene, the log2-fold change (YAK1Q578* vs. YAK1wt) and the p-value adjusted for multiple-testing using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995).
Genome_build: S. cerevisiae transcriptome (Ensembl build 93)
Supplementary_files_format_and_content: DE_RNAseq: Differential analysis result (YAK1_Q578* vs YAK1_wt) (same as in paper), tsv file
Supplementary_files_format_and_content: RNAseq_processed: 10 samples mRNA quantification (before batch correction), tsv file

source_name: Yeast S. cerevisiae BY4741 (Q578* in YAK1)

growth_protocol: We quantified RNA and protein from five biological replicates (different clones obtained after CRISPR-Swap) of YAK1_wt and YAK1_Q578*. For each of these 10 strains, fresh colonies were used to inoculate 5 ml of SC medium (completed with uracil, arginine, histidine, and leucine) and the culture was grown overnight at 30°C. The next day, 50 ml of SC media in an Erlenmeyer flask was inoculated with the overnight culture to an initial OD600 of 0.05 and were grown under shaking at 30°C. When the OD600 reached 0.35 – 0.45 (late log phase), four aliquots of 7 ml of the culture was transferred to a falcon tube, centrifuged, and washed with 1 ml of sterile PBS buffer at 30°C (Phosphate Buffered Saline, pH 7.5). The pellets were immediately frozen in liquid nitrogen. For each strain, one cell pellet was used for RNA sequencing.

extract_protocol:
RNA extraction was done in two batches that each contained equal numbers of clones from the two groups (first batch: clones 1 and 2 of BY YAK1_wt and clones 1 and 2 of BY YAK1_Q578*, second batch: clones 3, 4 and 5 of BY YAK1_wt and clones 3, 4 and 5 of BY YAK1_Q578*). We used ZR Fungal/Bacterial RNA mini-prep kit with DNase I digestion (Zymo Research R2014), following the kit manual. RNA was eluted in 50 µl of RNase/DNase free water, quantified, and checked for integrity on an Agilent 2200 TapeStation. All RNA Integrity Numbers were higher than 9.5 and all concentrations were above 120 ng/µl. The RNA samples were stored at -20°C until use.
Poly-A RNA selection was done using 550 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L), processing all samples in one batch. We prepared the library using NEB Ultra II Directional RNA library kit for Illumina (NEB E7760) used dual index primers (from NEBNext Multiplex Oligos for Illumina, NEB E7600S) for multiplexing, and amplified the library for ten cycles. The libraries were quantified using Qubit dsDNA HS Assay Kit (ThermoFisher Scientist Q32854) and pooled at equal mass for sequencing using 75-bp single-end reads on Illumina NextSeq 550 at UMGC.

tag: strain background

tag: yak1 variant

tag: batch


title: SI_Day30C 3

value: 3 LCMV-Cl13 (chronic) infected


title: LI_Day0 1


title: Ovarian cancer, ADR-AEF_batch1 (RNA-seq)

description:
OVCAR8-ADR treated with Azacitidine, Erotinib, and Fludarabine replicate 1.
OVCAR8-ADR-RNA-seq_rawcounts.csv

tag: cell line

value: Azacitidine(2.5 uM) + Erlotinib(1.33 uM) + Fludarabine (0.3 uM)


title: Ovarian cancer, ADR-EF_batch1 (RNA-seq)

description:
OVCAR8-ADR treated with Erotinib and Fludarabine replicate 1.
OVCAR8-ADR-RNA-seq_rawcounts.csv


title: SI_Day0 3


title: SI_Day0 2


title: SI_Day30C 2


title: Ovarian cancer, ADR-AEF_batch2 (RNA-seq)

description:
OVCAR8-ADR treated with Azacitidine, Erotinib, and Fludarabine replicate 2.
OVCAR8-ADR-RNA-seq_rawcounts.csv


title: YAK1 with Q578* variant replicate 2 [V2]


title: YAK1 with Q578* variant replicate 1 [V1]


title: YAK1 with Q578* variant replicate 3 [V3]


title: YAK1 from BY replicate 5 [B5]

source_name: Yeast S. cerevisiae BY4741 (WT)

value: Wild type


title: Healthy Lung autopsy [Healthy-lung]

description: Healthy-lung

source_name: Healthy Lung autopsy

value: healthy

tag: tissue/cell type


title: SI_Day30A 2

value: LCMV-Armstrong (acute) infected


title: YAK1 from BY replicate 3 [B3]


title: Murine embryo heart (littermate control)-2

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

description: abundance data: MBOE_read_counts.txt

data_processing:
ATAC-Seq reads alignment using Bowtie v2.2.6
Sort/remove duplicates using Sambamba v0.6.5
Convert to bam using Samtools v1.2.0
Count feature coverage around features using Deeptools v2.0.0
Count feature coverages using Rsubread v1.26.1
Trim reads/ quality control using Trim Galore v0.4.2
RNA-Seq reads alignment using STAR v2.5.3a
Count feature coverage around transcriptomic features using fetureCounts v1.5.0
Count feature coverages using igvtools v2.3.91
Detect differential regions using DESeq2 v1.16.1
Genome_build: hg19/panTro4/gorGor3/rheMac3/mm9
Supplementary_files_format_and_content: TDF format, read coverage

source_name: E16 FVB murine embryo heart littermate control-2

extract_protocol:
For RNA-seq, RNA was isolated using miRNeasy kit (Qiagen) following the manufacture’s protocol. For ATAC-seq, 100,000 cells were centrifuged 500 g for 5 min at room temperature. The cell pellet was resuspended in 50 ml lysis buffer (10 mM Tris–Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Igepal CA-630) and centrifuged immediately 500 g for 10 min at 4°C. The cell pellet was resuspended in 50 ml transposase mixture (25 ul 2×TD buffer, 22.5 μl dH2O, and 2.5 μl Illumina Tn5 transposase or with final concentration of 100 nM Atto-590-labeled in-house Tn5) and incubated at 37°C for 30 min. After transposition, the mixture was purified with the Qiagen Mini-purification kit and eluted in 10 ul Qiagen EB elution buffer. For transgenic BANCR embryos plasmid vector construction (pRP[Exp]-BetaMHC>hBANCR) and purification, pronuclear plasmid injection of FVB embryos, harvesting and genotyping of E16 embryos were performed by Cyagen Biosciences (Santa Clara, CA,USA). Total RNA was isolated from extracted embryo hearts that were plasmid positive (n=2) or negative (n=2).
Total RNA was submitted to a core facility (Stanford Functional Genomics) for library preparation and Illumina sequencing. For ATAC-seq, sequencing libraries were prepared following the original ATAC-seq protocol (Buenrostro, J. D. et al. Nat Methods 10, 1213-1218 (2013)). The HiChIP protocol was performed as previously described (Mumbach, M. R. et al. Nat Methods 13, 919-922 (2016)).

value: E16 FVB murine embryo heart

tag: gender

value: missing


title: Ovarian cancer, ADR-AE_batch2 (RNA-seq)

description:
OVCAR8-ADR treated with Azacitidine and Erlotinib replicate 2.
OVCAR8-ADR-RNA-seq_rawcounts.csv

value: Azacitidine(2.5 uM)+ Erlotinib(1.33 uM)


title: YAK1 from BY replicate 1 [B1]


title: SI_Day30A 1


title: YAK1 with Q578* variant replicate 5 [V5]


title: Ovarian cancer, ADR-AF_batch1 (RNA-seq)

description:
OVCAR8-ADR treated with Azacitidine and Fludarabine replicate 1.
OVCAR8-ADR-RNA-seq_rawcounts.csv


title: Murine embryo heart (littermate control)-1

description: abundance data: MBOE_read_counts.txt

source_name: E16 FVB murine embryo heart littermate control-1


title: Exon123 KO hESC-CM, HG12, RNA-seq

source_name: Exon123 KO hESC-CM

value: female

value: Exon123 KO hESC-CM

tag: genotype

value: Exon123 KO

tag: differentiation days


title: S24_LUHMES_diff_DopaNeuron_Methyl_mercury_3

city: Rockville

middle: Lee

last: Gerhold

state: MD

address: 9800 Medical Center Drive

department: Division of Preclinical Innovation

institute: NCATS/NIH

data_processing:
Fastq-gz files were delivered from the NHLBI sequencing core. All processing was performed at the NIH HPC resource. Paired end sequence reads files, three file pairs from three lanes per sample, were aligned to the Ensembl GRCh38 Human Genome sequence using STAR aligner.
Alignment BAM files for each biological sample were merged to a single BAM file for each biological sample.
Merged BAM files, one per sample, were analyzed by htseq-count script (HTSeq) to produce raw count files.
Individual count files for all samples were combined to produce the raw, unnormalized count matrix (See Raw Matrix File).
DESeq was used to normalize read counts to produce a normalized count matrix (see Normalized Matrix File).
Differential expression tests and further analysis are described in the associated publication.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw unnormalized matrix file. A tab delimited text file containing Ensembl Gene ids and Gene Symbols, one row per gene, 24 columns of data, one per sample. Values are un-normalized read counts per gene in each sample.
Supplementary_files_format_and_content: Normalized matrix file. A tab delimited text file containing Ensembl Gene ids and Gene Symbols, one row per gene, 24 columns of data, one per sample. Values are DESeq normalized read counts per gene in each sample.

source_name: dopa-neurons exposed to 0.5uM MHG

growth_protocol: LUHMES cells were grown in culture vessels coated with 50mg/ml each poly-L-ornithine and human fibronectin in Advanced DMEM/F12 medium containing 2 mM L-glutamine, 1X N2-supplement and 40 ng/ml bFGF. LUHMES differentiation was induced by 1mg/ml tetracycline and 1 mM cAMP contained in advanced DMEM/F12 medium with 2 mM L-glutamine, 1X N2-supplement, and 2ng/ml GDNF (Schildknecht et al. 2009).

extract_protocol:
Initial extraction and polyA enrichment were performed in the NCATS laboratories. Total RNA samples were prepared from cultured cells using Qiaquick kit (Qiagen, Germantown, MD) and selected for polyA+ transcripts using the Qiagen Oligotex midi kit. The resulting samples were then depleted of ribosomal sequences using two rounds of RiboZero Gold™, Illumina Inc. TruSeq Protocol by the NHLBI-NIH sequencing core (NHLBI-NIH DNA Sequencing and Genomics Core, Bethesda, MD, https://www.nhlbi.nih.gov/science/dna-sequencing-and-genomics-core).
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq)
RNA-Seq library production (TruSeq) for Hiseq 3000

treatment_protocol: For gene expression assays, 3 x 10e5 cells were cultured per well in 12 well plates with 2 mL medium to enable RNA extraction. Toxicant stock solutions in DMSO were diluted with culture medium to make 10X working solutions for each concentration and added to the cells at 10% of the volume in each well. Control cells were treated with 1% DMSO to match treatments. Cells were treated with DMSO or a toxicant for 6h prior to commencing RNASeq sample preparation.

value: Lund human mesencephalic (LUHMES) cell line

value: Dopaminergic Neurons Differentiated from LUHMES Cells

tag: compound treatment

tag: compound name

value: Methylmercury Chloride

tag: publication comp. abbr.

value: MHG

tag: toxicant dose

tag: teatment class

value: Toxicant

tag: cas#


title: Exon123 KO hESC-CM, HG11, RNA-seq

tag: cell type


title: Ovarian cancer, ADR-AE_batch1 (RNA-seq)

description:
OVCAR8-ADR treated with Azacitidine and Erlotinib replicate 1.
OVCAR8-ADR-RNA-seq_rawcounts.csv

tag: treatment


title: Exon123 KO hESC-CM, HG15, RNA-seq


title: Exon123 KO hESC-CM, HG16, RNA-seq


title: YAK1 from BY replicate 4 [B4]


title: SI_Day0 1

tag: strain

tag: tissue

value: Small intestine

value: CD45+ immune cells

value: naïve


title: MPNST_suz12_mut_Z3

city: Boston

first: Kenneth

middle: N

last: Ross

state: MA

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: MPNST tumors from zebrafish with wild type atrx in context of combined p53/nf1/suz12a/suz12b-deficiency

data_processing:
FastQC was used to evaluate read quality on raw RNA-Seq reads and trimmed reads.
Trimming of low quality reads and clipping of sequencing adapters was done using the program Trimmomatic version 0.36 and all reads shorter than 36bp after trimming were dropped (Trimmomatic was run with settings of ILLUMINACLIP:adapters/TruSeq3-PE-2.fa: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 AVGQUAL:10).
Reads were aligned to the zebrafish (Danio rerio) reference genome with TopHat version 2.1.0 using UCSC danRer10 and settings of -x 1 -g 1 -r 44 --mate-std-dev 223 (with values for the flags -r and --mate-std-dev coming from the mean fragment size).
Bam sorting and indexing was done with SamTools and duplicate reads were removed using Picard-tools (http://picard.sourceforge.net).
Aligned reads processed to Fragments Per Kilobase of exon per Million fragments mapped (FPKM) using cufflinks version 2.2.1 (http://cufflinks.cbcb.umd.edu/index.html) with the -G flag to use the danRer10 reference annotation to estimate isoform expression and not assemble novel transcripts and the flags --max-bundle-frags 4000000 -N --compatible-hits-norm.
Gene level counts were obtained with htseq-count version 0.9.1.
Differential gene expression was evaluated with the R Bioconductor package DESeq2 and normalized expression values for individual samples were obtained from DESeq2 using the variance stabilizing transform on the raw counts. The variance stabilizing transformed data were used for GSEA.
Genome_build: GRCz10
Supplementary_files_format_and_content: genes.fpkm_tracking files are tab delimited text files output by cufflinks in a generic FPKM tracking format with estimated gene-level expression values in the form of FPKM values and raw_count.txt files are tab delimited text files output by htseq-count with gene level counts

organism: Danio rerio

source_name: Zebrafish malignant peripheral nerve sheath tumors (MPNSTs)

growth_protocol: Zebrafish were raised and maintained according to standard procedures. They were derived from the p53/nf1-deficient background (Shin et al., Disease Models & Mechanisms, 2012). All zebrafish studies and maintenance were done in accord with Dana-Farber Cancer Institute IACUC-approved protocol (#02-107).

extract_protocol:
RNA was isolated from one half of p53/nf1/atrx-deficient MPNSTs and p53/nf1-deficient control MPNSTs using the AllPrep DNA/RNA Mini Kit from Qiagen (Hilden, Germany) and the other half was set asside for analysis by histopathology.
Library preparation, quality control, and next-generation sequencing were conducted by the Molecular Biology Core Facility of the Dana-Farber Cancer Institute following standard protocols.

treatment_protocol: The zebrafish atrx mutant lines were generated by the CRISPR-Cas9 genome editing system using the previous described protocol (Hwang et al., Nature Biotechnology, 2013). The plasmid constructs pDR274 (#42250) and pMLM3613 (#42251) were purchased from Addgene. Oligonucleotides 5’-TAG GTC CTG AGT TCC GTA ACA A-3’ and 5’-AAA CTT GTT ACG GAA CTC AGG A-3’ were annealed and cloned into the pDR274 vector to generate single guide RNAs (gRNAs) targeting atrx exon 4. Each embryo was injected with 1 nl of solution containing 25 ng/μl gRNA and 600 ng/μl Cas9 mRNA at the 1 cell stage. Mosaic F0 fish with germline mutation were identified, and stable mutant lines were established by outcrossing.

tag: atrx

value: wt


title: MPNST_suz12_mut_Z5


title: Exon4 KO hESC-CM, HG4, RNA-seq

source_name: Exon4 KO hESC-CM

growth_protocol: Pluripotent cells were grown on Matrigel-coated plates (1:100 Matrigel in E8 medium) using chemically defined E8 medium. The medium was changed daily and cells were passaged every 3-4 days using EDTA or Accutase. Cardiomyocytes were maintained in RPMI + B27+ with media change every other day.

value: Exon4 KO hESC-CM

value: Exon4 KO


title: Murine embryo heart (BANCR pos)-1

description: abundance data: MBOE_read_counts.txt

source_name: E16 FVB murine embryo heart with BANCR plasmid expression-1

value: E16 FVB murine embryo heart


title: MPNST_suz12_mut_Z2


title: S23_LUHMES_diff_DopaNeuron_Methyl_mercury_2


title: Exon4 KO hESC-CM, HG6, RNA-seq


title: S22_LUHMES_diff_DopaNeuron_Methyl_mercury_1


title: infected colon organoid in vitro

description: live single cell

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) plus virus sequence and to extract gene expression UMI counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: huES derived colon organoid

growth_protocol: The colon progenitor organoids were collected from the initial 2D cultures and embedded in a 100% Matrigel dome in a 24-well plate. Differentiation to mature colonic cell types was achieved by culturing these colon progenitor organoids in differentiation medium containing 600 nM LDN193189 (Axon), 3 μM CHIR99021 and 100 ng/ml hEGF in Advance DMEM F12 medium supplemented with 1X B27 supplement, 1X GlutaMax, 10 mM HEPES and 1X Pen-Strep. The differentiation medium were refreshed every 3 days for at least 40 days to achieve full colonic differentiation. The colon organoids were passaged and expanded every 10 – 14 days at 1:6 density. To passage the organoids, the Matrigel domes containing the organoids were scrapped off the plate and resuspended in cold splitting media (Advance DMEM F12 medium supplemented with 1X GlutaMax, 10 mM HEPES and 1X Pen-Strep). The organoids were mechanically dislodged from the Matrigel dome and fragmented by pipetting in cold splitting media. The old Matrigel and splitting media were removed after spinning down cells and the organoids were resuspended in 100% Matrigel. 50 µL Matrigel containing fragmentized colon organoids were plated in one well of a pre-warmed 24-well plate.

extract_protocol:
hPSC-COs were harvested by cell scraper, mixed with 20 µl Matrigel (Corning) and transplanted under the kidney capsule of 7-9 weeks old male NSG mice. At two weeks post-transplantation, SARS-Cov-2 pseudo-entry virus was inoculated locally at 1x10e3 FFU.
Library was constructed according to the user manual of Chromium Single Cell 3’ Library & Gel Bead Kit v2

treatment_protocol: To assay pseudotyped virus infection on colon organoids, COs were seeded in 24 well plates. Pseudotyped virus was added at MOI=0.01 plus polybrene at a final concentration of 8 μg/mL, and the plate centrifuged for 1 hr at 1200g.  At 3 hpi, the infection medium was replaced with fresh medium.

value: hPSC-COs

tag: infection

value: SARS-CoV-2 pseudo-entry virus


title: S18_LUHMES_diff_DopaNeuron_Rotenone_3

source_name: dopa-neurons exposed to 1uM ROT

tag: cell line

value: Rotenone

value: ROT


title: H7 hESC-CM, HG2, RNA-seq

source_name: H7 hESC-CM

value: female

value: hESC-CM

value: control


title: YAK1 from BY replicate 2 [B2]

tag: strain background

tag: yak1 variant

value: Wild type

tag: batch


title: nESCs WT rep13

description:
PolyA RNA
scRNA-seq

source_name: pluripotent stem cells

value: TJ-1# nESCs

tag: passages

tag: genotype/variation


title: Murine embryo heart (BANCR pos)-2

description: abundance data: MBOE_read_counts.txt

source_name: E16 FVB murine embryo heart with BANCR plasmid expression-2

tag: gender

value: missing


title: MPNST_suz12_mut_Z1


title: H7 hESC-CM, HG1, RNA-seq

tag: genotype

tag: differentiation days


title: S20_LUHMES_diff_DopaNeuron_6-HD_2

source_name: dopa-neurons exposed to 1uM 6HD

value: Lund human mesencephalic (LUHMES) cell line

value: Dopaminergic Neurons Differentiated from LUHMES Cells

tag: compound treatment

tag: compound name

tag: publication comp. abbr.

tag: toxicant dose

tag: teatment class

value: Toxicant


title: colon organoid in vitro

description: live single cell

tag: tissue