title: HT29_treated_rep2 [HT29_P3]

city: Urbana

first: Paul

last: Hergenrother

state: IL

address: 600 S. Mathews

institute: University of Illinois

data_processing:
The libraries were quantitated by qPCR and sequenced on one lane for 151 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina), which trims off adaptors and removes sequences less than 35 nt
Each sample's fastq file was run through Trimmomatic 0.36 to first remove any remaining standard Illumina TruSeq SE v3 adapters, then trim bases from both ends with quality scores below 28, and finally to remove reads shorter than 30 bp (parameters ILLUMINACLIP:$EBROOTTRIMMOMATIC/adapters/TruSeq3-SE.fa:2:15:10 LEADING:28 TRAILING:28 MINLEN:30)
The spliced read aligner Salmon (v0.8.2) was used to align sequencing reads to NCBI’s GRCh38.p11 transcriptome. Counts were summarized to the gene level (Annotation release 108) using tximport (v 1.6.0) and the “lengthScaledTPM” method.
The counts were normalized using the TMM method from edgeR (v 3.20.5) and then transformed to log2 counts per million (logCPM) with prior.count = 3.
Genome_build: NCBI GRCh38.p11
Supplementary_files_format_and_content: Salmon's quant.sf output files are provided per sample and normalized logCPM values for genes that passed filtering thresholds are provided in the supplementary file "Llabani_etal2019_logCPM_values.xlsx"

growth_protocol: HT29 cells were grown in McCoy’s 5A media; A549 cells were grown in RPMI 1640 media. All media were supplemented with 10% FBS (Gemini), penicillin (50 IU/ml), streptomycin (50 μg/ml) and glutamine (2 mM) (Cellgro).

extract_protocol:
RNA was extracted with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. DNAse digestion was performed using the accompanying RNAse free DNAse set.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

treatment_protocol: HT29 cells were treated with DMSO or 10 µM ferroptocide for 6 hr; A549 cells were treated with DMSO or 2.5 µM ferroptocide for 6 hr

value: epithelial, colorectal adenocarcinoma cells

tag: treatment

value: 10 µM ferroptocide for 6 hr


title: HT29_treated_rep1 [HT29_P2]

status: Public on Apr 22 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: HT29_control_rep2 [HT29_D3]

value: DMSO for 6 hr


title: HT29_control_rep1 [HT29_D2]


title: A549_treated_rep2 [A549_P3]

value: lung epithelial carcinoma cells

value: 2.5 µM ferroptocide for 6 hr


title: A549_control_rep2 [A549_D3]


title: A549_control_rep1 [A549_D2]


title: BB19_embryo_1_131216_CGATGT

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

country: Israel

institute: Technion

data_processing:
Filter sequences with irrelevant barcodes
Split relevant sequences by barcode
Remove the linker from each sequence. Trim additional 3 bases.
Merge identical reads.
Sequences were aligned to gene transcripts using Bowtie, aloowing multiple alignments.
DEseq package in R (http://www.r-project.org) was used from the data obtained from bowtie to identify differentially expressed genes.
Genome_build: WS220/ce10

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: worms were grown at 20°C on enriched NGM with OP50 as food

extract_protocol:
Synchronized Embryos or L4 larval worms were washed several times to avoid contamination with bacteria, snap-freezed at liquid nitrogen, and grinded to powder in a liquid nitrogen -prechilled mortar and pestle. High-molecular weight and Low-molecular weight RNA fractions were isolated using miRVana miRNA isolation kit Applied Biosystems (Ambion).
libraries were prepared from the high molecular weight fraction by means of SMARTer® Stranded RNA-Seq Kit (Clontech Laboratories) after ribosomal depletion by Ribozero kit (Epicenter)

treatment_protocol: Embryos were isolated from gravid N2 adults by treatment with sodium hypochlorite solution. To obtain synchronized L4 worms, embryos were incubated in M9 media without food at 20 °C for 24h. Hutched synchronized L1 were grown until they reached L4 larval stage.

tag: strain

tag: Stage

value: Embryo

tag: bio replicate no


title: BB19_embryo_2_051216_TTAGGC


title: RNA-Seq PT PBS 4h

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: AD-HIES patients PBS 4h

data_processing:
Sequenced reads were aligned to the mm9 or hg19 genome assembly using Bowtie 0.12.9 and Tophat 2.1.1
Aligned reads are converted to bam format using samtools. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes.
Genome_build: mm9 or hg19

source_name: purified peripheral blood

growth_protocol: The USA 300 clinical isolate (FPR3757) of MRSA or the S. pyogenes NZ131 strain were used for all experiments. S. aureus bacteria were grown overnight at 37o C in a shaking incubator in tryptic soy broth, diluted 1:10, and mid-logarithmic growth phase bacteria were obtained after an additional 2 h of culture. S. pyogenes were grown in Todd Hewitt Broth under static conditions. Bacteria were pelleted and washed twice with PBS. Bacterial concentrations were estimated by measuring absorbance at 600 nm, and the absolute CFU was determined by plating dilutions on blood agar plates. For infection, mice were lightly anesthetized with ketamine/xylazine and received an intratracheal instillation of 50 l of S. aureus (2 x 107 CFU). For neutrophil depletion experiments, mice were injected i.p. with 1 mg 1A8 (anti-Ly6G) mAb or 2A3 isotype control mAb 2 days prior to MRSA infection. For blocking type I interferon responses, mice were injected with 1 mg MAR1-5A3 (anti-IFNAR1) or MOPC-21 isotype control mAbs on each of 2 days prior to infection. All depletion antibodies and isotype controls were from BioXCell.  S. aureus were quantified after infection by homogenizing one lung lobe in 1 ml PBS, followed by plating serial dilutions on blood agar plates. Mouse splenic CD4+ T cells were purified with a Stem Cell Technologies negative selection CD4+ T cell isolation kit and co-cultured with bone marrow-derived dendritic cells (cultured with GM-CSF for 7 days) at 1:1 ratio with or without Staphylococcal entertoxin B (SEB, 0.05 μg/ml, List Biological Laboratories, >95% pure, 14 EU/mg) and in the presence of either IL-21R-Fc blocking agent or control Fc (20 μg/ml) for 24 h; RNA was then isolated.  For intracellular staining of IL-21, human CD4+ T cells were purified from peripheral blood (Dynabeads Untouched negative selection CD4+ T cell kit, Invitrogen) and co-cultured at a 5:1 ratio with monocyte-derived DCs that had been cultured for 6 days in GM-CSF (800 U/ml) plus IL-4 (400 U/ml). At 72 h, cultures were treated with Golgi Plug for 4 h and stained for detection of intracellular IL-21 (clone 3A3-N2.1) by flow cytometry.

extract_protocol:
KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems, Wilmington, MA), and each library was indexed using barcoded primers (BIOO Scientific, Austin, TX). Barcoded PCR products were purified on 2% E-Gel, 250-400 bp fragments were purified, quantified on Qbit (Invitrogen), mixed, and sequenced on HiSeq2000 or HiSeq2500 platform.
PCR products were barcoded (indexed) and sequenced on HiSeq2000 or HiSeq2500 platform.

treatment_protocol: WT mice were treated intratracheally with 2 x 107 heat-killed S. aureus (HKSA, InVivoGen). Lung cells were isolated after one day by digestion with collagenase (1 mg/ml) and DNaseI (1 mg/ml) and were enriched first on a 44%/67% Percoll gradient. Neutrophils were then purified (80-90%) with a mouse neutrophil isolation kit (Miltenyi Biotec) and were used directly in either MRSA killing assays or were in vitro stimulated with IL-21 and then RNA isolated for RT-PCR analysis.

tag: tissue

value: purified peripheral blood

value: neutrophils

tag: disease state

value: AD-HIES patients

value: PBS 4h


title: SBR1

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

description:
SBR1
PolyA RNA
Cells were encapsulated and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 2(?).
processed data file: genes.tsv

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

organism: Mus musculus

source_name: Small Intestine

extract_protocol: 10x Genomics Chromium single cell preparation.

tag: strain/background

value: Distal small intestine (ileum)

tag: age

value: 8-12 weeks

value: Small bowel resection


title: SBR2

description:
SBR2
PolyA RNA
Cells were encapsulated and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 2(?).
processed data file: genes.tsv


title: RNA-Seq PT IFNb 4h

description: AD-HIES patients IFNb 4h

value: IFNb 4h


title: RNA-Seq ND IL21+IFNb 4h

description: normal donor IL21+IFNb 4h

value: Normal Donors

value: IL21+IFNb 4h


title: RNA-Seq ND IFNb 4h

description: normal donor IFNb 4h


title: BB19_L4_220816_GCCAAT


title: Sham2

description:
Sham2
PolyA RNA
Cells were encapsulated and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 2(?).
processed data file: genes.tsv

value: Sham surgery


title: RNA-Seq PT IL21+IFNb 4h

description: AD-HIES patients IL21+IFNb 4h


title: ILCP.WT.2

first: Margaret

middle: C

last: Cam

data_processing:
Basecalling by RTA 1.18.66.3, Illumina instrument run time analysis software, Demultiplexing Bcl2fastq 2.17, Barcode demultiplexed allowing 1 mismatch
The raw RNA-Seq fastq reads were aligned to mouse genome (mm10) using STAR (STAR_2.5.2b) on 2-pass mode with mouse gencode (release M12) gtf
Genome_build: mm10
Supplementary_files_format_and_content: Genes were quantified using RSEM-1.2.23 and further analyzed for gene expression changes using limma-voom with quantile normalization and batch correction using ComBat. The gene and sample-specific normalization factors were then used to correct counts to generate bigwig files used for further visualization.

source_name: ILCP

growth_protocol: samples were isolated by cell sorting from bone marrow single cell suspensions

extract_protocol:
RNA was extracted using RNeasy plus micro kit (Qiagen)
mRNA sequencing libraries were prepared using the SMARTer Ultra Low Input RNA Kit v3 (Clontech) and Nextera XT DNA library preparation kit (Illumina)

tag: strain background

tag: genotype/variation

value: bone marrow

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1+ IL-7Ra+

tag: batch


title: Sham3

description:
Sham3
PolyA RNA
Cells were encapsulated and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 2(?).
processed data file: genes.tsv


title: RNA-Seq ND IL21 4h -2

description: normal donor IL21 4h

value: IL21 4h


title: Sham1

description:
Sham1
PolyA RNA
Cells were encapsulated and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 2(?).
processed data file: genes.tsv


title: G007-LK.GDC-0973.3

city: Oslo

first: Martin

middle: Frank

last: Strand

address: Prinsensgate 7

country: Norway

institute: Høyskolen Kristiania

description:
HCT-15-combination-treatment-Counts.txt
DESeq2-normalized-counts.txt
G007MEKi-DMSO.txt
G007MEKi-G007.txt
G007MEKi-MEKi.txt

data_processing:
Reads were aligned using STAr aligner 2.5.0 and counts generated using cufflinks 2.2.1 .
DEG's and normalized counts were generated using the DESeq2 package in R
Genome_build: Homo sapiens (UCSC hg19)
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample, normalized counts, and Differentially expressed gene (DEG's)
Supplementary_files_format_and_content: HCT-15-combination-treatment-Counts.txt: gene counts
Supplementary_files_format_and_content: DESeq2-normalized-counts.txt: normalized gene counts
Supplementary_files_format_and_content: G007-DMSO.txt: DEG's from DESeq2
Supplementary_files_format_and_content: MEKi-DMSO.txt: DEG's from DESeq2
Supplementary_files_format_and_content: G007MEKi-DMSO.txt: DEG's from DESeq2
Supplementary_files_format_and_content: G007MEKi-G007.txt: DEG's from DESeq2
Supplementary_files_format_and_content: G007MEKi-MEKi.txt: DEG's from DESeq2
Supplementary_files_format_and_content: MEKi-G007.txt: DEG's from DESeq2

source_name: Colorectal adenocarcinoma

extract_protocol:
Total RNA was isolated using GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma Aldrich), followed by DNaseI (Sigma Aldrich) treatment for 15 min, according to the manufacturer’s instructions.
The libraries were subsequently sequenced on the HiSeq2500 (Illumina Inc.) at the Genomics Core Facility Oslo (Oslo University Hospital, Norway).

treatment_protocol: Sequencing libraries were generated from three biological replicates of cultured HCT-15 cells treated with DMSO (0.02%), G007-LK (1µM), GDC-0973 (1µM) or G007-LK and GDC-0973 for 24 hours using the Illumina TruSeq stranded mRNA kit (Illumina Inc.).

value: G007-LK and GDC-0975


title: A549_treated_rep1 [A549_P2]

value: lung epithelial carcinoma cells

value: 2.5 µM ferroptocide for 6 hr


title: RNA-Seq ND PBS 4h

description: normal donor PBS 4h

value: purified peripheral blood


title: c-EILP.WT.2

value: Tcf7GFP Zbtb16GFP

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1- Zbtb16high Flt3low


title: c-EILP.WT.3


title: cNK_CD8_rep1

city: Hefei

first: Xiaolei

last: Hao

state: Anhui

address: huangshan Road 443

country: China

institute: Institute of Immunology, USTC

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using hisat2 v2.1.0 with parameters --threads 28 --dta -t
Read counts were computed using Rsubread using default settings
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: cNK cells

extract_protocol:
NK cells were sorted by use of BD Aria II sorter and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: splenocytes

tag: genotype


title: cNK_CD8_rep3


title: G007-LK.GDC-0973.2

value: G007-LK and GDC-0974


title: cNK_CD8_rep2


title: cNK_B6_rep3

value: wild type


title: c-EILP.WT.1


title: CX-1 cells expressing RAB3C

type: RNA

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Gene expression data from CX-1 cells expressing RAB3C

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: DSMZ

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with blasticidin for two weeks.  Stably transduced cells were use for this experiment.

value: CX-1 cells

tag: expression


title: CX-1 cells expressing vector control

description: Gene expression data from CX-1 cells expressing control vector

value: vector


title: G007-LK.GDC-0973.1

value: G007-LK and GDC-0973


title: ILCP.WT.1


title: s-EILP.WT.2

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1- Zbtb16low Flt3high


title: cNK_B6_rep2


title: GDC-0973.3

description:
HCT-15-combination-treatment-Counts.txt
DESeq2-normalized-counts.txt
MEKi-DMSO.txt
G007MEKi-MEKi.txt
MEKi-G007.txt


title: s-EILP.WT.1


title: LrNK_CD8KO_rep2

source_name: LrNK cells

value: Liver Lymphocytes


title: LrNK_CD8KO_rep3


title: cNK_B6_rep1


title: LrNK_B6_rep4


title: GDC-0973.2


title: LrNK_CD8KO_rep1


title: R1-9 ES Cell #2

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

description: R1-9 ES Cell #2

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 2 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: R1-9 ES Cell

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: R1-9 ES cells were grown (~6 million cells) T75 flask, spent ES-medium was discarded, washed with PBS. 5.0 mL of TRIzol reagent (Invitrogen) was added, lysate was transferred to 15 mL tube, and stored at    80 0C. 1.0 mL aliquots were taken in 1.5 mL micro centrifuge tubes, 200 uL fresh chloroform was added to each tube, mixed gently and incubated for 2-3 min at 25 0C, and suspension centrifuged at 13000 rpm (table top centrifuge) for 10 min at 4 0C. Supernatant (upper aqueous layer) (about 500 uL) was transferred to a fresh tube. RNA was precipitated from the supernatant by mixing with equal volume of fresh isopropanol, and incubation for 5-10 min at 25 0C. Suspension centrifuged at 13000 rpm (table top centrifuge) for 15 min at 4 0C, supernatant was discarded, pellet washed with 70% alcohol, centrifuged at 13000 rpm for 5 min at 4 0C. Supernatant discarded and RNA pellet air-dried for 5 min, RNA redissolved in 50-100 uL DEPC-treated water

treatment_protocol: R1-9 mES cells were initially cultured on Mitomycin C inactivated mouse primary embryonic fibroblast cell layer, with DMEM-medium supplemented with Leukemia Inhibitory Factor (LIF) and 15% FBS, 1.0mM MEM non-essential amino acids, 100mM pyruvic acid, penicillin (50U/mL)-streptomycin (50   g/mL) and 55    M    -mercaptoethanol. The culture medium was changed every day. The cells were passaged when the colonies reached 60-70% confluence. About 40 million cells were grown on gelatin coated tissue culture plates (3 passages) to remove embryonic fibroblast feeders. Total RNA was extracted from the R1-9 mES cells using TRIzol (Invitrogen, USA) according to the manufacturer's protocol. Quality of the extracted RNA integrity was assessed by agarose gel electrophoresis.

value: Embryonic stem cell, R1-9 ES Cell

tag: gender

value: male

tag: development stage

value: embryo

tag: individual identifier

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: Universale Mouse Reference, 129ES Cell


title: R1-9 ES Cell #1

description: R1-9 ES Cell #1

tag: cell type


title: EILP.WT.3

value: bone marrow

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-


title: LrNK_B6_rep3

tag: strain


title: GDC-0973.1

tag: treatment


title: LrNK_B6_rep2


title: EILP.WT.2


title: G007-LK.3

description:
HCT-15-combination-treatment-Counts.txt
DESeq2-normalized-counts.txt
G007-DMSO.txt
G007MEKi-G007.txt
MEKi-G007.txt


title: G007-LK.2


title: EILP.WT.1


title: LrNK_B6_rep1


title: EILP.KO.2


title: CF_Ppos_8

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

description:
cystic fibrosis patient, Pseudomonas positive
SAMPLE CF17

data_processing:
Data were analyzed in excel using Ct values for each sample,  normalized to global means, and fold changes were calculated using the 2-ΔΔCT method
Data normalization: miRNA Ct values normalized to global mean ΔCt = (Ct_miRNA − Ct_global mean)
For fold change calculations, ΔΔCt based fold-change values were obtained using an average of control sample Ct values (2^-ΔΔCt, where -ΔΔCt = -[ΔCtsample -ΔCtavgcontrol])). A fold change of 40 was considered as cutoff.
The file Non-normalized_data.txt  contains raw Ct values. The file normalized_data.txt includes data  normalized to the global mean. Fold changes are calculated with the livak method (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])

label: SYBR Green

source_name: exhaled breath condensate

label_protocol: Small RNAs were retro-transcribed from 200 ng of total RNA using the miScript II RT kit (Qiagen). The expression of 1066 human miRNAs was assayed with the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z).

extract_protocol: MicroRNAs were purified from 0.5 mL of EBC with the Plasma/Serum RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada).

treatment_protocol: Exhaled breath condensates (EBC) were obtained from control patients (no Cystic Fibrosis, CF), patients with CF an Pseudomonas infection (Pseudomonas positive), and patients with CF without Pseudomonas infection (Pseudomonas negative). Total RNA was purified from EBCs and the expression of 1066 human miRNAs was detected with a PCR array.

value: exhaled breath condensate

tag: cf diagnosis

value: yes

tag: pseudomonas infection


title: CF_Ppos_9

description:
cystic fibrosis patient, Pseudomonas positive
SAMPLE CF18

tag: tissue


title: G007-LK.1


title: CF_Ppos_10

description:
cystic fibrosis patient, Pseudomonas positive
SAMPLE CF19


title: EILP.KO.1


title: CF_Pneg_9

description:
cystic fibrosis patient, Pseudomonas negative
SAMPLE CF16

value: no


title: RNA-Seq PT IL21 4h

description: AD-HIES patients IL21 4h

value: purified peripheral blood

value: neutrophils

tag: disease state

value: AD-HIES patients

value: IL21 4h


title: GSF-896-Adr-1-RIP-24June_S14_R1_001

description:
FLAG antibody (Sigma-Aldrich) was used for the RIP-seq on strain BB21 adr-1 (tm668) I; adr-2 (ok735) III- negative control after RIP-seq
Supp_Table5.xlsx

tag: Stage

value: Young Adult

tag: bio replicate no


title: DMSO.3

description:
HCT-15-combination-treatment-Counts.txt
DESeq2-normalized-counts.txt
G007-DMSO.txt
MEKi-DMSO.txt
G007MEKi-DMSO.txt

value: DMSO


title: CF_Ppos_7

description:
cystic fibrosis patient, Pseudomonas positive
SAMPLE CF15


title: DMSO.2


title: ALP.WT.3

source_name: ALP

tag: strain background

tag: genotype/variation

value: Lin- Kit+ 2B4+ a4b7- Flt3high IL-7Ra+


title: ALP.WT.2

tag: sorting profile

tag: batch


title: DMSO.1


title: GSF-896-Adr1-RIP-30Mar_S11_R1_001


title: GFP_low_2w4w_Sample3

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw RNA-seq reads were mapped against the human genome (hg19) and rRNA sequences using ContextMap (version 2.7.9).
Number of read fragments per gene (Ensembl version 75) were determined from the mapped RNA-seq reads using featureCounts (version 1.4.6-p3).
Genome_build: hg19
Supplementary_files_format_and_content: Counts in tab delimited text file generated using featureCounts (version 1.4.6-p3) against Ensembl v75 annotation.  Tab delimited text file include gene level FPKM values for each sample against Ensembl v75 annotation.

molecule: polyA RNA

source_name: Brain

growth_protocol: GBM 3D organoids were prepared as described (Hubert et al., 2016). Briefly, 1,000 dissociated GBM cells were embedded in a Matrigel (BD Biosciences) droplet of 20 µl, and cultivated for 4 days in neural stem cell media (Neurocult NS-A proliferation media (human), in 6 cm dishes. Cultures were then transferred for further growth onto an orbital shaker inside a tissue incubator.

extract_protocol:
GBM cells that were grown as 3D organoids were gently triturated with Pasteur pipettes of decreasing tip diameter. Cells were pelleted and resuspended in FACS buffer, and debris was removed by pelleting cells at 155 g for 6 min through a phase of 2% BSA in Hibernate-E LF. Cells were resuspended in FACS buffer and passed through a 70 µm mesh filter. DAPI (Invitrogen) was added to cell suspensions at a concentration of 5 µg/ml to stain dead cells. Cell suspensions were analyzed by flow cytometry (BD LSRII) or sorted by FACS (BD FACSAria IIu), and data was evaluated with FACSDiva and FlowJo software.
RNA from FACS sorted GBM cells (GFP-high and -low) was isolated with RNeasy (QIAGEN), and cDNA libraries for Illumina next-generation sequencing were either prepared with NEBNext Ultra Directional RNA Library Prep Kit (NEB E7420) for 2wk2wk samples, or with NuGEN Ovation amplification followed by NEBNext Ultra DNA Library Prep Kit (NEB 7370) for 2wk4wk samples. Sequencing was performed on Illumina HiSeq2500 devices in rapid run mode with paired 50 bp reads.

treatment_protocol: For Dox-on pulsing, doxycycline was added to the culture media for a final concentration of 1 µg/ml.

value: Brain

value: GBM cells in 3D organoid culture

tag: cell state

value: proliferative


title: GSF-896-Adr-1-Input-24June_S5_R1_001

description:
FLAG antibody (Sigma-Aldrich) was used for the RIP-seq on strain BB21 adr-1 (tm668) I; adr-2 (ok735) III- negative control total input
Supp_Table5.xlsx


title: GSF-896-76-RIP-30Mar_S10_R1_001

description:
FLAG antibody (Sigma-Aldrich) was used for the RIP-seq on strain HH76 adr-1(tm668) I blmEx1[3XFLAG-adr-1 genomic, rab3::gfp::unc-54] - after RIP-seq
Supp_Table5.xlsx


title: CF_Pneg_8

description:
cystic fibrosis patient, Pseudomonas negative
SAMPLE CF12


title: ALP.WT.1


title: CF_Ppos_4

description:
cystic fibrosis patient, Pseudomonas positive
SAMPLE CF11


title: GFP_low_2w2w_Sample3


title: CF_Pneg_7

description:
cystic fibrosis patient, Pseudomonas negative
SAMPLE CF10


title: HL1_ATACseq

city: Houston

first: Ashish

last: Kapoor

state: TX

address: 1825 Pressler St. Rm SRB 530C

institute: University of Texas Health Science Center at Houston

library_source: genomic

data_processing:
To process the ATAC-seq data, the adapter sequences (CTGTCTCTTATACACATCT)  were trimmed from the raw reads using cutadapt (ver. 1.12) with parameters “-q 3,3 -m 35”.
The trimmed reads were mapped to hg19 for AC16 and mm9 for HL1 with Bowtie2 (version 2.2.3), with the options “-X 2000 --dovetail --no-mixed --no-discordant –t”
Duplicated reads were removed using samtools (ver. 1.3.1) with the “rmdup” command, and only properly paired and mapped reads with MAPQ score>30 were retained
All reads mapping to the + strand were offset by +5bp and all reads mapping to the - strand were offset by -4bp, to account for the 9bp duplication of the target site by Tn5 transposase
Peaks and read density signals were calculated using MACS2 (ver. 2.1.0.20150731) with the parameters “–nomodel –shift -50 –extsize 100 --keep-dup all"
Genome_build: GRCh37, GRCm38, hg19, mm9
Supplementary_files_format_and_content: Tab-delimited text files for gene expression; narrowPeak and bigWig for ATAC-seq

molecule: genomic DNA

growth_protocol: HL1 cells were grown as described in Claycomb et al (Proc Natl Acad Sci U S A. 1998;95(6):2979-2984). AC16 cells were grown as described in Davidson et al. (J Mol Cell Cardiol. 2005;39(1):133-147).

extract_protocol:
Total RNA was isolated from HL1 and AC16 cells using RNeasy Mini kit (Qiagen) following the manufacturer’s instructions that included the on-column DNase treatment using the RNase-Free DNase set (Qiagen).  RNA quality was assessed using the Bioanalyzer RNA kit (Agilent Technologies) prior to sequencing library preparation. Nuclei were isolated from HL1 and AC16 cells following the lysis protocol by Buenrostro et al. (Nat Methods. 2013;10(12):1213-1218).
Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina) was used to generate indexed sequencing libraries following the manufacturer’s protocols.  A sample from each library was used to assess library fragment size distribution by electrophoresis, using BioAnalyzer High Sensitivity DNA Assay (Agilent Technologies), and to assess library concentration by qPCR, using the KAPA library quantification kit (KAPA Biosystems).  Equimolar amounts of libraries were pooled and sequenced on an Illumina HiSeq 2500 instrument using standard protocols for paired end 100bp reads with a desired sequencing depth of ~75 million paired end reads per library.  RNA-seq for both cell lines were performed in technical duplicates. ATAC-seq was performed on fresh unfixed HL1 and AC16 cells (~50,000 cells each) following the published protocol (Buenrostro et al. Nat Methods. 2013;10(12):1213-1218).  A sample from each indexed library was used to assess library fragment size distribution by 2% agarose TAE gel electrophoresis and to assess library concentration by qPCR using the KAPA library quantification kit (KAPA Biosystems).  Equimolar amounts of libraries were pooled and sequenced on an Illumina HiSeq 2500 instrument using standard protocols for paired end 50bp sequencing with a desired sequencing depth of ~150 million paired end reads per library.

tag: cell line


title: HL1_RNAseq_rep2

data_processing:
For the RNA-seq data, kallisto (ver. 0.43.1) was used to estimate abundance of mRNA transcripts for each of the replicates
GENCODE human transcript sequences (release 25 mapped to GRCh37) and mouse transcript sequences (release 12 mapped to GRCm38) were used as a reference for quantification
Transcripts per million (TPM) values were estimated by Kallisto directly from the raw reads with the default settings
Gene level TPMs were obtained by aggregating isoform level expression
Genome_build: GRCh37, GRCm38, hg19, mm9
Supplementary_files_format_and_content: Tab-delimited text files for gene expression; narrowPeak and bigWig for ATAC-seq


title: GFP_low_2w4w_Sample2


title: HL1_RNAseq_rep1


title: GSF-896-76-RIP-24June_S13_R1_001


title: GSF-896-76-Input-30Mar_S1_R1_001

description:
FLAG antibody (Sigma-Aldrich) was used for the RIP-seq on strain HH76 adr-1(tm668) I blmEx1[3XFLAG-adr-1 genomic, rab3::gfp::unc-54] - total input
Supp_Table5.xlsx


title: GSF-896-76-Input-24June_S4_R1_001


title: CF_Ppos_6

description:
cystic fibrosis patient, Pseudomonas positive
SAMPLE CF14


title: CF_Pneg_6

description:
cystic fibrosis patient, Pseudomonas negative
SAMPLE CF09


title: CF_Ppos_3

description:
cystic fibrosis patient, Pseudomonas positive
SAMPLE CF08


title: GFP_low_2w2w_Sample2


title: RNA-Seq ND HKSA 24h

description: normal donor HKSA 24h

value: Normal Donors

value: HKSA 24h


title: GFP_low_2w4w_Sample1


title: CF_Ppos_5

description:
cystic fibrosis patient, Pseudomonas positive
SAMPLE CF13


title: RNA-Seq ND IL21+HKSA 24h

description: normal donor IL21+HKSA 24h

value: IL21+HKSA 24h


title: GSF-896-134-RIP-30Mar_S12_R1_001

description:
FLAG antibody (Sigma-Aldrich) was used for the RIP-seq on strain HH134 adr-1(tm668);adr-2(ok735) I blmEx1[3XFLAG-adr-1 genomic, rab3::gfp::unc-54] - after RIP-seq
Supp_Table5.xlsx


title: GSF-896-134-RIP-24June_S15_R1_001


title: CF_Pneg_5

description:
cystic fibrosis patient, Pseudomonas negative
SAMPLE CF06


title: GSF-896-134-Input-30Mar_S3_R1_001

description:
FLAG antibody (Sigma-Aldrich) was used for the RIP-seq on strain HH134 adr-1(tm668);adr-2(ok735) I blmEx1[3XFLAG-adr-1 genomic, rab3::gfp::unc-54] - total input
Supp_Table5.xlsx


title: GFP_high_2w4w_Sample3

value: quiescent


title: CF_Ppos_2

description:
cystic fibrosis patient, Pseudomonas positive
SAMPLE CF07

value: exhaled breath condensate


title: RNA-Seq ND IL21 24h

description: normal donor IL21 24h


title: RNA-Seq ND Control 24h

description: normal donor Control 24h

value: Control 24h


title: GFP_high_2w2w_Sample3


title: CF_Pneg_4

description:
cystic fibrosis patient, Pseudomonas negative
SAMPLE CF05

value: yes

value: no


title: RNA-Seq ND IL21+HKSA 4h

description: normal donor IL21+HKSA 4h

value: purified peripheral blood

value: neutrophils

value: IL21+HKSA 4h


title: GSF-896-134-Input-24June_S6_R1_001

value: Young Adult


title: GSF-896-Adr-1-Input-30Mar_S2_R1_001


title: GFP_high_2w4w_Sample2


title: CF_Pneg_3

description:
cystic fibrosis patient, Pseudomonas negative
SAMPLE CF04


title: RNA-Seq ND HKSA 4h

description: normal donor HKSA 4h

value: HKSA 4h


title: CF_Ppos_1

description:
cystic fibrosis patient, Pseudomonas positive
SAMPLE CF03


title: GFP_high_2w2w_Sample2


title: RNA-Seq IL21R-Fc

description: Wild-type IL21R-Fc

source_name: total lung tissue

value: total lung tissue


title: RNA-Seq ND IL21 4h

description: normal donor IL21 4h

value: IL21 4h


title: GFP_low_2w2w_Sample1

value: Brain

value: GBM cells in 3D organoid culture


title: GFP_high_2w4w_Sample1


title: CF_Pneg_2

description:
cystic fibrosis patient, Pseudomonas negative
SAMPLE CF02


title: RNA-Seq Il21rKO MRSA 24h

description: Il21rKO MRSA 24h

value: Il21r knock-out

value: Il21rKO MRSA 24h


title: RNA-Seq Control-Fc

description: Wild-type Control-Fc

value: Control Fc

value: Control-Fc


title: ILCpro_WT.sc

data_processing:
Basecalling by RTA 1.12.4.2, Illumina instrument run time analysis software, Demultiplexing Bcl2fastq 2.17, Barcode demultiplexed allowing 1 mismatch
The raw RNA-Seq reads were aligned to mouse genome (mm10) using STAR (STAR_2.5.1b)
10x genomics data analysis was performed with the Cellranger v2.0.1 software using the default parameters. Cells with extremely low number of UMI counts were filtered out.
Genome_build: mm10

extract_protocol: 10x Genomics Single Cell Chromium v2 mRNA libraries were made and sequenced on the NextSeq with v2 chemistry

value: bone marrow

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+


title: GFP_high_2w2w_Sample1

value: quiescent


title: RNA-Seq ND Control 4h

description: normal donor Control 4h

value: Normal Donors

value: Control 4h


title: AC16_ATACseq


title: control_noCF_10

description:
control patient no CF
SAMPLE C10

value: exhaled breath condensate

value: no


title: CF_Pneg_1

description:
cystic fibrosis patient, Pseudomonas negative
SAMPLE CF01

value: yes


title: RNA-Seq Il21rKO MRSA 4h

description: Il21rKO MRSA 4h

value: neutrophils

value: Il21rKO MRSA 4h


title: AC16_RNAseq_rep2


title: ALP.sc

value: Lin- Kit+ 2B4+ a4b7- Flt3high IL-7Ra+


title: control_noCF_8

description:
control patient no CF
SAMPLE C08


title: RNA-Seq WT MRSA 24h

description: Wild-type MRSA 24h

value: total lung tissue

value: Wild-type

value: MRSA 24h


title: AC16_RNAseq_rep1


title: RNA-Seq WT MRSA 4h

description: Wild-type MRSA 4h

value: MRSA 4h


title: control_noCF_7

description:
control patient no CF
SAMPLE C07


title: WT Replicate 2

city: Wuhan

first: Jie

last: Gao

state: Hubei

address: No.1, Shizishan Street

institute: Huazhong Agricultural University

data_processing:
NGS QC Toolkit v2.3.3 used for clean reads with default settings
Clean reads were mapped to TAIR10.36 with HISAT2. The BnMAGL8.1 CDS sequence was added into the reference genome as "gene112".
featureCounts used to measure the gene expression levels ("featureCounts" "-M" "-T" "4" "-t" "CDS" "-g" "gene_id" "-a" "TAIR10.36.gtf" "-o" "mul.TAIR10.36.txt" "W2_.sort.bam" "W3_.sort.bam" "W4_.sort.bam" "O1_.sort.bam" "O2_.sort.bam" "O3_.sort.bam" )
DESeq2 used to discover differentially expressed genes. P value < 0.01 was used as a threshold.
Supplementary_files_format_and_content: excel file containg reads count for each sample

organism: Arabidopsis thaliana

source_name: flower buds in stage 6-9

growth_protocol: Plants were grown in a green house (8 h dark and 16 h light, 23 °C)

extract_protocol:
Total RNA was extracted from young flower buds (stage 6-9) with Tiangen RNA-pure extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background ecotype

value: Col

value: flower buds

tag: anther development stage

tag: genotype

value: WT


title: control_noCF_6

description:
control patient no CF
SAMPLE C06


title: WT Replicate 3


title: RNA-Seq WT IL21 24h

description: Wild-type IL21 24h

tag: cell type


title: WT Replicate 1


title: control_noCF_5

description:
control patient no CF
SAMPLE C05


title: control_noCF_4

description:
control patient no CF
SAMPLE C04


title: RNA-Seq WT PBS 24h

description: Wild-type PBS 24h

tag: treatment

value: PBS 24h


title: BnA9::BnMAGL8.1 Replicate 3


title: RNA-Seq Il21rKO MRSA 0h

description: Il21rKO MRSA 0h

value: Il21r knock-out

value: Il21rKO MRSA 0h


title: ILCpro_KO.sc

value: bone marrow

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+


title: BnA9::BnMAGL8.1 Replicate 2


title: RNA-Seq WT IL21 7h

description: Wild-type IL21 7h

value: IL21 7h


title: RNA-Seq WT PBS 7h

description: Wild-type PBS 7h

value: PBS 7h


title: control_noCF_3

description:
control patient no CF
SAMPLE C03

value: exhaled breath condensate

tag: cf diagnosis

value: no


title: control_noCF_2

description:
control patient no CF
SAMPLE C02

tag: pseudomonas infection


title: RNA-Seq WT MRSA 0h

description: Wild-type MRSA 0h

tag: tissue

value: neutrophils

value: MRSA 0h


title: KBM7.DpnI.Dam_LMNB1.clone_5.5.G1_S.64.library_KIN2094_34

status: Public on Apr 21 2019

city: Utrecht

first: Koos

last: Rooijers

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Combined DamID and transcriptomic measurement of 48 single cells

data_processing:
Demultiplexing of raw data (previously demultiplexed on Illumina index) was done using on the barcodes. DamID reads contain in read1, from 5’ to 3’: a 3nt UMI, a 6nt or 8nt barcode, followed by gDNA for the remainder of the read. Transcriptomic measurements contain in read1, from 5’ to 3’: a 6nt UMI, an 8nt barcode, followed by unalignable sequence, usually polyT. Read2 of the transcriptomic measurements contains mRNA sequence. For demultiplexing of the single-cell samples from the libraries, refer to “sample_barcodes.tsv” files with tables of barcode sequences for each sample.
gDNA obtained from DamID reads (in read1) were prepended with dinucleotide ‘GA’ (the 5’ half of the DpnI recognition motif), or ‘AG’ (the 5’ half of the AluI recognotion motif), and were aligned using bowtie2 (v2.3.2), using parameters ‘--seed 42 --very-sensitive -N 1’. Only unique alignments with mapping quality (BAM MAPQ) >= 10 were kept. DamID were further processed and only reads aligning to ‘GATC’ sequences were kept. mRNA reads from transcriptome measurements (in read2) were aligned using tophat2 (v2.1.1) using parameters ‘--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200’ to a transcriptome (options ‘--GTF’ and ‘--transcriptome-index’) obtained from GENCODE (v26) supplemented with ERCC mRNA spike-in sequences.
For DamID data, at most one read per sample, per GATC, per strand was taken. For transcriptomic measurements, reads and unique UMIs were counted per gene (according to the “intersection-strict” algorithm of `htseq-count` [http://htseq.readthedocs.io/en/master/count.html]). For each gene, the number of unique observed UMIs was trimmed by starting at the UMI with highest read count and setting UMIs with Hamming distance of 1 to zero, and iteratively filtering all UMI sequences (in case of equal read counts for a UMI, ties were broking by lexicographic sorting of the UMIs). The number of observed distinct UMIs after trimming was taken as the transcript count for that gene.
Genome_build: Data was aligned to hg19 (GRCh37), including mitochondrial genome, sex chromosomes and unassembled contigs. Transcriptome measurements were aligned to a transcriptome obtained from GENCODE (v26) [https://www.gencodegenes.org/releases/grch37_mapped_releases.html] supplemented with ERCC mRNA spike-in sequences [https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095047.txt]
Supplementary_files_format_and_content: Processed data files ‘genomic_counts.tsv.gz’ contain, for each single-cell sample, the (UMI-unique) counts per 100-kb bin for each chromosome (the first three columns in the file indicate chromosome, start and end positions).   Processed data files ‘transcriptomic_counts.tsv.gz’ contain, for each single-cell sample, the (UMI-unique) counts per ENSEMBL gene ID.  Processed data files ‘genomic_signal.in_silico_population.rpkm.wig.gz’ contain an in silico population profile of all samples passing our cutoffs, with values expressed as reads per kilobase per million reads/UMIs (RPKM), in WIG format. These files are useful for visual inspection of the genomic profiles, e.g. via the UCSC genome browser.

molecule: other

source_name: KBM7 cell line

growth_protocol: Haploid KBM7 cells were cultured in suspension in IMDM (Gibco) supplemented with 10% Fetal Bovine Serum (FBS; Sigma) and 1% Pen/Strep (Gibco). The same Shield1-inducible Dam-LMNB1 and Dam stable clonal KBM7 cell lines were used as in [Kind, J. et al. Genome-wide maps of nuclear lamina interactions in single human cells. Cell 163, 134-147, (2015)]. Cells were split every 3 days.

extract_protocol:
4 μL mineral oil was dispensed manually into each well of a 384-well plate using a multichannel pipet. 100 nL of unique CEL-Seq primer was dispensed per well using the mosquito HTS robot (TTP Labtech). The NanodropII robot (BioNex) was used for all subsequent dispensing steps at 12 p.s.i. pressure. After sorting, 100 nL lysis mix was added (0.8 U RNase inhibitor (Clontech, 2313A), 0.07 % Igepal, 1 mM dNTPs, 1:500,000 ERCC RNA spike-in mix (Ambion, 4456740)). Each single cell was lysed at 65 °C for 5 minutes and 150 nL reverse transcription mix was added (1x First Strand Buffer (Invitrogen, 18064-014), 10 mM DTT (Invitrogen, 18064-014), 2 U RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen, 10777019), 10 U SuperscriptII (Invitrogen, 18064014)) and the plate was incubated at 42 °C for 1 hour, 4 °C for 5 minutes and 70 °C for 10 minutes. Next, 1.92 μL of second strand synthesis mix was added (1x second strand buffer (Invitrogen, 10812014), 192 μM dNTPs, 0.006 U E. coli DNA ligase (Invitrogen, 18052019), 0.013 U RNAseH (Invitrogen, 18021071)) and the plate was incubated at 16 °C for 2 hours. 500 nL of protease mix was added (1x NEB CutSmart buffer, 1.21 mg/mL ProteinaseK (Roche, 000000003115836001)) and the plate was incubated at 50 °C for 10 hours and 80 °C for 20 minutes. Next, 230 nL DpnI mix was added (1x NEB CutSmart buffer, 0.2 U NEB DpnI) and the plate was incubated at 37 °C for 4 hours and 80 °C for 20 minutes. Finally, 50 nL of DamID2 adapters were dispensed (final concentrations varied between 32 and 128 nM), together with 450 nL of ligation mix (1x T4 Ligase buffer (Roche, 10799009001), 0.14 U T4 Ligase (Roche, 10799009001)) and the plate was incubated at 16 °C for 12 hours and 65 °C for 10 minutes. Contents of all wells with different primers and adapters was pooled and incubated with 0.8 volume magnetic beads (CleanNA, CPCR-0050) diluted 1:4 or 1:8 with bead binding buffer (20% PEG8000, 2.5M NaCl) for 10 minutes, washed twice with 80% ethanol and resuspended in 7 μL nuclease-free water before in vitro transcription at 37 °C for 14 hours using the MEGAScript T7 kit (Invitrogen, AM1334). Library preparation was done as described in the CEL-Seq protocol with minor adjustments[Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 17, 77, (2016).]. Amplified RNA (aRNA) was cleaned and size-selected by incubating with 0.8 volume magnetic beads (CleanNA) for 10 min, washed twice with 80% ethanol and resuspended in 22 μL nuclease-free water, and fragmented at 94 °C for 2 minutes in 0.2 volume fragmentation buffer (200 mM Tris-acetate pH 8.1, 500 mM KOAc, 150 mM MgOAc). Fragmentation was stopped by addition of 0.1 volume fragmentation STOP buffer (0.5 M EDTA pH8) and quenched on ice. Fragmented aRNA was incubated with 0.8 volume magnetic beads (CleanNA) for 10 minutes, washed twice with 80% ethanol and resuspended in 12 μL nuclease-free water.
Library preparation was done as previously described[Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 17, 77, (2016).] using 5 μL of aRNA and PCR cycles varied between 8 and 10. Libraries were run on the Illumina NextSeq platform with high output 75 bp paired-end sequencing.

treatment_protocol: Expression of Dam-LMNB1 and Dam constructs was induced in the KBM7 cells with 0.5 nM Shield1 (Glixx laboratories, 02939) 15 hours prior to harvesting. KBM7 cells were harvested in PBS (in-house production), stained with 0.5 μg/mL DAPI (Sigma) for live/dead selection. Single cells were sorted based on small forward and side-scatter values (30% of total population).

value: DpnI

tag: damid adapter concentration in nanomolar

tag: dam-fusion


title: KBM7.DpnI.Dam_LMNB1.clone_5.5.G1_S.64.library_KIN2094_36


title: KBM7.DpnI.Dam_LMNB1.clone_5.5.G1_S.64.library_KIN2094_35


title: KBM7.DpnI.Dam_only.clone_5.8.G1_S.32.library_KIN1660_5

value: Dam


title: KBM7.DpnI.Dam_only.clone_5.8.G1_S.64.library_KIN1660_6


title: KBM7.DpnI.Dam_LMNB1.clone_14.G1_S.64.library_KIN2094_31


title: KBM7.DpnI.Dam_LMNB1.clone_14.G1_S.64.library_KIN2094_30


title: KBM7.AluI.wt.wt.G1_S.128.library_KIN1687_14

description: gDNA digested with AluI restriction enzyme of 24 single cells

value: AluI


title: KBM7.DpnI.Dam_LMNB1.clone_14.G1_S.64.library_KIN2094_33


title: mESC.DpnI.Dam_Ring1B.clone_18.Unsorted.differentiation_day3.32.library_KIN3147_6

description: Combined DamID and transcriptomic measurement of 92 single cells (sequenced in across two runs)

data_processing:
Demultiplexing of raw data (previously demultiplexed on Illumina index) was done using on the barcodes. DamID reads contain in read1, from 5’ to 3’: a 3nt UMI, a 6nt or 8nt barcode, followed by gDNA for the remainder of the read. Transcriptomic measurements contain in read1, from 5’ to 3’: a 6nt UMI, an 8nt barcode, followed by unalignable sequence, usually polyT. Read2 of the transcriptomic measurements contains mRNA sequence. For demultiplexing of the single-cell samples from the libraries, refer to “sample_barcodes.tsv” files with tables of barcode sequences for each sample.
gDNA obtained from DamID reads (in read1) were prepended with dinucleotide ‘GA’ (the 5’ half of the DpnI recognition motif), or ‘AG’ (the 5’ half of the AluI recognotion motif), and were aligned using bowtie2 (v2.3.2), using parameters ‘--seed 42 --very-sensitive -N 1’. Only unique alignments with mapping quality (BAM MAPQ) >= 10 were kept. DamID were further processed and only reads aligning to ‘GATC’ sequences were kept. mRNA reads from transcriptome measurements (in read2) were aligned using tophat2 (v2.1.1) using parameters ‘--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200’ to a transcriptome (options ‘--GTF’ and ‘--transcriptome-index’) obtained from GENCODE (v26) supplemented with ERCC mRNA spike-in sequences.
For DamID data, at most one UMI-unique read (or two in the case of genotype-ambiguous alignment) per sample, per GATC, per strand was taken. For transcriptomic measurements, reads and unique UMIs were counted per gene (according to the “intersection-strict” algorithm of `htseq-count` [http://htseq.readthedocs.io/en/master/count.html]). For each gene, the number of unique observed UMIs was trimmed by starting at the UMI with highest read count and setting UMIs with Hamming distance of 1 to zero, and iteratively filtering all UMI sequences (in case of equal read counts for a UMI, ties were broking by lexicographic sorting of the UMIs). The number of observed distinct UMIs after trimming was taken as the transcript count for that gene.
Genome_build: Data was aligned to a reference made by imputing 129S1/SvImJ SNPs (obtained from the Sanger mouse genome project [ftp://ftp-mouse.sanger.ac.uk/current_snps/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz]) onto mm10, as well as a reference made by imputing CAST_EiJ SNPs (obtained from the Sanger mouse genome project [ftp://ftp-mouse.sanger.ac.uk/current_snps/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz]) onto mm10. References for alignment included mitochondrial genome, sex chromosomes and unassembled contigs. Transcriptome measurements were aligned using transcript annotations obtained from ENSEMBL (release 89) [ftp://ftp.ensembl.org/pub/release-89/gtf/mus_musculus/Mus_musculus.GRCm38.89.gtf.gz] supplemented with ERCC mRNA spike-in sequences [https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095047.txt]. Reads were assigned to a genotype based on which reference yielded a better alignment. The best alignment for a read was chosen using the smallest edit distance (‘NM’ tag in the BAM file) and the largest alignment score (‘AS’ tag in the BAM file). Reads with equally good alignments on the two references were considered “ambiguous”.
Supplementary_files_format_and_content: Processed data files ‘genomic_counts.tsv.gz’ contain, for each single-cell sample, the (UMI-unique) counts per 100-kb bin for each chromosome (the first three columns in the file indicate chromosome, start and end positions).  Processed data files ‘transcriptomic_counts.tsv.gz’ contain, for each single-cell sample, the (UMI-unique) counts per ENSEMBL gene ID.  'genomic_counts’ and ‘transcriptomic_counts’ are given for each parental allele separately in ‘unique_*’ files, and counts where the genotype of origin could not be resolved are given in ‘ambiguous_*’ files.  Processed data files ‘genomic_signal.in_silico_population.rpkm.wig.gz’ contain an in silico population profile of all samples passing our cutoffs (summed across alleles and counts with ambiguous genotype), with values expressed as reads per kilobase per million reads/UMIs (RPKM), in WIG format. These files are useful for visual inspection of the genomic profiles, e.g. via the UCSC genome browser.

source_name: mESC cell line, clone 18

growth_protocol: F1 hybrid 129/Sv:CAST/EiJ mouse embryonic stem cells (mESCs)[Peric-Hupkes, D. et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Molecular cell 38, 603-613, (2010)] were cultured on irradiated primary mouse embryonic fibroblasts (MEFs), in ES cell culture media; G-MEM (Gibco) supplemented with 10% FBS (Sigma), 1% Pen/Strep (Gibco), 1x GlutaMAX (Gibco), 1x non-essential amino acids (Gibco), 1x sodium pyruvate (Gibco), 0.1 mM β-mercaptoethanol (Sigma) and 103 U/mL ESGROmLIF (EMD Millipore, ESG1107). Cells were split every 3 days. Expression of constructs was suppressed by addition of 1 mM indole-3-acetic acid (IAA; Sigma, I5148). 2i F1 hybrid 129/Sv:Cast/EiJ mESCs were cultured for 2 weeks on primary MEFs in 2i ES cell culture media; 48% DMEM/F12 (Gibco) and 48% Neurobasal (Gibco), supplemented with 1x N2 (Gibco), 1x B27 supplement (Gibco), 1x non-essential amino acids (Gibco), 1% Pen/Strep (Gibco), 0.1 mM β-mercaptoethanol (Sigma), 0.5% BSA (Sigma), 1 μM PD0325901 (Axon Medchem, 1408), 3 μM CHIR99021 (Axon Medchem, 1386) and 103 U/mL ESGROmLIF (EMD Milipore). Cells were split every 3 days. Expression of constructs was suppressed by addition of 1mM IAA (Sigma). The stable mESC clones were differentiated by culturing them on gelatin-coated 6 well plates after MEF depletion, in monolayer differentiation media; IMDM (Gibco) supplemented with 15% FBS (Sigma), 1% Pen/Strep (Gibco), 1x GlutaMAX (Gibco), 1x non-essential amino acids (Gibco), 50 μg/mL ascorbic acid (Sigma, A4544) and 37.8 μL/L monothioglycerol (Sigma, M1753). Expression of constructs was suppressed by addition of 1 mM IAA (Sigma). After MEF depletion, one confluent 6 well of mESCs was split 1:15 on 6 gelatin-coated wells of a 6-well plate in differentiation media for 3 days. The medium was changed every other day.

extract_protocol:
F1 mESCs expressing Dam-LMNB1, Dam or Dam-RING1B were collected in plain or 2i ES cell culture media and stained with 30 μg/mL Hoechst 34580 (Sigma, 63493) for 45 minutes at 37 °C. mESC singlets were sorted based on forward and side-scatter properties, and in mid-S phase of the cell cycle based on DNA content histogram. Differentiated F1 mESCs expressing Dam-RING1B were collected in differentiation media and stained with 30 μg/mL Hoechst 34580 for 45 minutes at 37 °C. The same cells were stained with 1 μg/mL propidium iodide (Sigma) for live/dead selection. Differentiated mESCs singlets were sorted based on forward and side-scatter properties, and in G1, S and G2/M phase of the cell cycle based on DNA content histogram. One cell was sorted per well of 384-well plates (Biorad, HSP3801) using the BD FACSJazz cell sorter. Wells contained 4 μL mineral oil (Sigma) and 100 nL of 15 ng/μL unique CELseq primer. 4 μL mineral oil was dispensed manually into each well of a 384-well plate using a multichannel pipet. 100 nL of unique CEL-Seq primer was dispensed per well using the mosquito HTS robot (TTP Labtech). The NanodropII robot (BioNex) was used for all subsequent dispensing steps at 12 p.s.i. pressure. After sorting, 100 nL lysis mix was added (0.8 U RNase inhibitor (Clontech, 2313A), 0.07 % Igepal, 1 mM dNTPs, 1:500,000 ERCC RNA spike-in mix (Ambion, 4456740)). Each single cell was lysed at 65 °C for 5 minutes and 150 nL reverse transcription mix was added (1x First Strand Buffer (Invitrogen, 18064-014), 10 mM DTT (Invitrogen, 18064-014), 2 U RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen, 10777019), 10 U SuperscriptII (Invitrogen, 18064014)) and the plate was incubated at 42 °C for 1 hour, 4 °C for 5 minutes and 70 °C for 10 minutes. Next, 1.92 μL of second strand synthesis mix was added (1x second strand buffer (Invitrogen, 10812014), 192 μM dNTPs, 0.006 U E. coli DNA ligase (Invitrogen, 18052019), 0.013 U RNAseH (Invitrogen, 18021071)) and the plate was incubated at 16 °C for 2 hours. 500 nL of protease mix was added (1x NEB CutSmart buffer, 1.21 mg/mL ProteinaseK (Roche, 000000003115836001)) and the plate was incubated at 50 °C for 10 hours and 80 °C for 20 minutes. Next, 230 nL DpnI mix was added (1x NEB CutSmart buffer, 0.2 U NEB DpnI) and the plate was incubated at 37 °C for 4 hours and 80 °C for 20 minutes. Finally, 50 nL of DamID2 adapters were dispensed (final concentrations varied between 32 and 128 nM), together with 450 nL of ligation mix (1x T4 Ligase buffer (Roche, 10799009001), 0.14 U T4 Ligase (Roche, 10799009001)) and the plate was incubated at 16 °C for 12 hours and 65 °C for 10 minutes. Contents of all wells with different primers and adapters was pooled and incubated with 0.8 volume magnetic beads (CleanNA, CPCR-0050) diluted 1:4 or 1:8 with bead binding buffer (20% PEG8000, 2.5M NaCl) for 10 minutes, washed twice with 80% ethanol and resuspended in 7 μL nuclease-free water before in vitro transcription at 37 °C for 14 hours using the MEGAScript T7 kit (Invitrogen, AM1334). Library preparation was done as described in the CEL-Seq protocol with minor adjustments[Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 17, 77, (2016).]. Amplified RNA (aRNA) was cleaned and size-selected by incubating with 0.8 volume magnetic beads (CleanNA) for 10 min, washed twice with 80% ethanol and resuspended in 22 μL nuclease-free water, and fragmented at 94 °C for 2 minutes in 0.2 volume fragmentation buffer (200 mM Tris-acetate pH 8.1, 500 mM KOAc, 150 mM MgOAc). Fragmentation was stopped by addition of 0.1 volume fragmentation STOP buffer (0.5 M EDTA pH8) and quenched on ice. Fragmented aRNA was incubated with 0.8 volume magnetic beads (CleanNA) for 10 minutes, washed twice with 80% ethanol and resuspended in 12 μL nuclease-free water.
Library preparation was done as previously described[Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 17, 77, (2016).] using 5 μL of aRNA and PCR cycles varied between 8 and 10. Libraries were run on the Illumina NextSeq platform with high output 75 bp paired-end sequencing.

treatment_protocol: Expression of Dam-LMNB1 or Dam constructs was induced in the F1 mESCs by IAA washout with PBS (in-house production) 12 hours prior to harvesting.

tag: restriction enzyme


title: KBM7.DpnI.Dam_LMNB1.clone_14.G1_S.128.library_KIN1660_8


title: KBM7.DpnI.Dam_LMNB1.clone_14.G1_S.64.library_KIN1660_7


title: mESC.DpnI.Dam_Ring1B.clone_18.Unsorted.serum.32.library_KIN2966_31


title: mESC.DpnI.Dam_Ring1B.clone_18.Unsorted.differentiation_day3.32.library_KIN3147_11

description: Combined DamID and transcriptomic measurement of 92 single cells


title: mESC.DpnI.Dam_only.clone_C8.Unsorted.differentiation_day3.32.library_KIN2965_9

source_name: mESC cell line, clone C8


title: control_noCF_9

description:
control patient no CF
SAMPLE C09


title: BnA9::BnMAGL8.1 Replicate 1

value: Col


title: control_noCF_1

description:
control patient no CF
SAMPLE C01


title: mESC.DpnI.Dam_only.clone_C8.midS.2i.64.library_KIN2199_20


title: mESC.DpnI.Dam_only.clone_C8.midS.serum.64.library_KIN2199_15


title: mESC.DpnI.Dam_only.clone_C8.midS.serum.64.library_KIN1687_12


title: mESC.DpnI.Dam_LmnB1.clone_E6.G2_M.serum.64.library_KIN2440_33

source_name: mESC cell line, clone E6


title: mESC.DpnI.Dam_only.clone_C8.midS.2i.64.library_KIN1687_11


title: mESC.DpnI.Dam_LmnB1.clone_B2.G2_M.serum.64.library_KIN2440_37

source_name: mESC cell line, clone B2


title: mESC.DpnI.Dam_LmnB1.clone_B2.G2_M.serum.64.library_KIN2440_36


title: mESC.DpnI.Dam_LmnB1.clone_B2.midS.serum.64.library_KIN1687_10


title: mESC.DpnI.Dam_LmnB1.clone_E6.G2_M.serum.64.library_KIN2440_31


title: mESC.DpnI.Dam_LmnB1.clone_E6.G2_M.serum.64.library_KIN2440_30


title: mESC.AluI.Dam_only.clone_C8.G2_M.serum.64.library_KIN2199_13

description: Combined AluI readout and transcriptomic measurement of 48 single cells


title: mESC.DpnI.Dam_LmnB1.clone_B2.G2_M.serum.64.library_KIN2440_35


title: mESC.AluI.Dam_only.clone_C8.G2_M.serum.64.library_KIN2199_14


title: Patient11-first

city: Cincinnati

first: Xiaoting

last: Zhu

state: OH

address: 3333 burnet avenue,MLC7024

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequence reads were aligned to the reference genome GRCh37 by using standard Illumina sequence analysis pipeline. The aligned reads were quantified and converted to relative gene expression level represented by FPKM (fragments per kilobase million).
The differential expression was analyzed by comparing the second sample to first using the DESeq2 Bioconductor package. Significant differentially expressed genes (DEGs) were identified based on false discovery rate (FDR) adjusted p-values < 0.1.
Ingenuity® Pathway Analysis (IPA, Qiagen, Redwood City, CA) was used to produce comprehensive analysis of the DEGs in the context of biological processes and pathways.
Genome_build: GRCh37
Supplementary_files_format_and_content: "SecondSample_vs_FirstSample.all.gene.result.xls" gives  gene expression in FPKM and differential gene expression.

source_name: peripheral blood

extract_protocol:
Total RNA was extracted using PAXgene Blood RNA Kit (Qiagen, Hilden, Germany), including DNase I treatment according to the manufacturer’s instructions. The eluted RNA was again treated with DNase I and cleaned using the RNA Clean & Concentrator kit (Zymo, Irvine, CA) to remove trace amounts of genomic DNA. The RNA quality was measured by using Bioanalyzer RNA 6000 Nano Kit (Agilent, Santa Clara, CA). Globin-Zero Gold kit (Illumina, San Diego, CA) was used to enrich non-globin coding and non-coding RNAs from blood-derived total RNA. To ensure high reproducibility of the process, the automated SMARTer Apollo system (Takara, Mountain View, CA) was used to deplete globin and rRNA from 1 µg total RNA.
The NEBNext Ultra Directional RNA Library Prep kit (New England BioLabs, Ipswich, MA)  was used for library preparation.

treatment_protocol: The first peripheral blood sample was obtained from each patient within 24 hours of ICH symptom onset or last known normal. For the current study, a second peripheral blood sample was collected from each patient 72 hours (+/- 6 hours) following the first. At the time of each blood draw, 2.5 milliliters of blood was collected in PAXgene® (Preanalytix, Hombrechtikon, Switzerland) blood RNA tubes. Consistent with the manufacturer’s instructions, the tubes were gently inverted eight to ten times, stored at room temperature for two hours, and then frozen. The samples were stored at -80 C until the time of RNA extraction.

value: blood

tag: disease

value: Intracerebral hemorrhage


title: Patient11-second


title: Patient10-first


title: Patient9-second


title: Patient9-first


title: Patient8-first


title: Patient8-second


title: Patient7-second


title: Patient7-first


title: Patient6-second


title: Patient10-second


title: Patient5-second


title: Medic_shoot_nonmyco_pot8

city: Prague 2

first: Jan

last: Konečný

address: Albertov 6

department: Experimental Plant Biology

country: Czech Republic

institute: Faculty of Science, Charles University

description: 35 dpp; 12/2014-02/2015; harvested 11-12 a.m.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized using GeneChip® Hybridization, Wash, and Stain Kit according to manufacturers instruction.

scan_protocol: GeneChips were scanned using the Genechip scanner 7G 3000.

data_processing: The data were normalized with the RMA algorithm, than the trimmed mean was scaled to 1000. The data processing was performed by Genevestigator curators (Nebion, Zurich, Switzerland).

organism: Medicago truncatula

source_name: whole shoots

label_protocol: Biotinylated cRNA were prepared according to the GeneChip® 3â€™ IVT Express Kit Labeling Assay from 100 ng of total RNA, Array Format 49 (standard).

growth_protocol: Plant were grown in 2.5L pots filled with a substrate mix consisting of autoclaved clay granules (zeolite) 1-2.5mm, autoclaved sand, and gamma irradiated local soil mixed in a ratio of 9:9:2 (v:v:v) under glasshouse conditions (25/15°C day/night, 14h photoperiod, minimum of 150 mikromol photons m-2 s-1), and inoculated either with a mycorrhizal (pot-produced with leek as a host plant) inoculum of Rhizophagus irregularis SYM5 (90 ml per pot) or mock inoculum produced under the same conditions as the mycorrhizal inoculum. All plants were additionally inoculated with a suspension of Sinorhizobium meliloti strain 10 isolated from the field soil used to prepare the planting mixture (10 billion cells per pot). The plants were grown for a total of five week, from the 3th week onwards each pot received 65 mL Long-Ashton nutrient solution with reduced (20%) of the P concentration (i.e., 0.26 mM P) weekly. Root colonization by the mycorrhizal fungus reached 44% of the root length colonized in the mycorrhizal treatment, whereas no colonization was detected in the mock-inoculated plants. This was further confirmed by qPCR with Rhizophagus-specific TaqMan probe on cDNA obtained from the RNA extracts.

extract_protocol: Homogenized powder (3 g) + 80°C mixture of phenol (4 mL) & extraction buffer (4 mL; 1.95 g of 100mM Tris, 0.0424 g of 100mM LiCl, 0.372 g of 10mM EDTA and 1 g of 1% SDS per 100 mL of DEPC-treated water (0.1% DEPC), adjusted to pH = 6). Mixed, heated. + chlorophorm (4 mL), mixed and centrifuged; supernatant taken, mixed with additional chlorophorm (4 mL; repeated 3 times). Supernatant (2 mL) + 8M LiCl (0.68 mL) on ice overnight. Pellet resuspended in 75% EtOH (0.5 mL), centrifuged; pellet diluted in RNase-free H2O (250 uL) + 96% EtOH (500 uL) + 3M NaAcetate (25 uL) and on ice for 1 hour. Centrifuged and pellet diluted in RNase-free H2O (100 uL).

treatment_protocol: Both variants were treated with rhizobial solution, half of pots (myco) treated with cutted roots of leek (Allium porum) infected with Rhizophagus irregularis, the other half of pots with cutted roots of non-infected leek. Upon harvest, the shoots and roots were cleaned of soil in ice-cold water and flash-frozen in liquid nitrogen. Samples were homogenized in liquid nitrogen with a mortar and pestle.

tag: symbiosis

value: rhizobial (strain 10)


title: Medic_shoot_myco_pot4

value: rhizobial (strain 10) and mycorrhizal (R. i. SYM5)


title: Patient5-first


title: Medic_root_myco_pot6

source_name: whole roots


title: Patient4-second


title: AMC_07

city: Davis

first: Keith

last: Dunaway

state: CA

address: 3318 Tupper Hall

department: MMI

institute: UC Davis

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring protocol

data_processing: Data pre-processing utilized nSolver Analysis Software 3.0 and involved background subtraction of the mean + 2 standard deviations from negative controls as well as normalization to the geometric mean of the top 100 genes with the highest expression

organism: Rattus norvegicus

source_name: hypothalamus

label_protocol: Nanostring protocol

extract_protocol: miRNeasy kit (Qiagen)

value: augmented maternal care

tag: Sex

value: Male

tag: age


title: Control_01

value: Control


title: Control_04


title: Control_05


title: Control_02


title: Control_03


title: Medic_shoot_nonmyco_pot7


title: Medic_shoot_nonmyco_pot9


title: Patient3-second


title: Patient6-first


title: Medic_root_myco_pot4


title: Medic_root_nonmyco_pot8


title: Patient3-first


title: AMC_05


title: Medic_shoot_myco_pot6


title: AMC_06


title: Patient4-first


title: Medic_shoot_myco_pot5


title: AMC_04


title: Medic_root_nonmyco_pot9


title: Medic_root_myco_pot5


title: Patient2-second


title: Patient2-first


title: Medic_root_nonmyco_pot7


title: AMC_03


title: AMC_01


title: Patient1-second


title: AMC_02


title: Patient1-first


title: Mof_CreER_WT_rMof_D-3_4OHT_Input

status: Public on Apr 20 2019

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

data_processing:
Basecalls performed using Bcl2fastq
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3);
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script

source_name: Brown preadipocyte cell

growth_protocol: Primary brown preadipocytes were isolated from interscapular BAT of newborn Mof(flox/flox);CreER mice) and immortalized with SV40T-expressing retroviruses generated from the pBabeneo-large T plasmid

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15-18 cycles and library fragments of 200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For culture, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 1~2 days before ChIP-seq.

value: BAT isolated brown preadipocytes

tag: stage of adipogenesis

value: preadipocytes

tag: chip antibody


title: Mof_CreER_Vec_D-3_Mock_H4K16ac

value: anti-H4K16ac (Millipore, 07-329)


title: Mof_CreER_Vec_D-3_4OHT_H4K16ac


title: Mof_CreER_Vec_D-3_4OHT_MLL4


title: Mof_CreER_K274R_rMof_D-3_4OHT_Input


title: Mof_CreER_WT_rMof_D-3_4OHT_H4K16ac


title: Mof_CreER_Vec_D-3_4OHT_Input


title: Mof_CreER_Vec_D-3_Mock_MLL4


title: Mof_CreER_WT_rMof_D-3_4OHT_MLL4


title: MC3T3-E1-undifferentiated-1

city: Birmingham

first: Qiling

last: He

state: AL

address: 1825 University Blvd, Shelby Building

department: Microbiology

institute: University of Alabama at Birmingham

description: MC3T3-E1 pre-osteoblast cell line ( ATCC, CRL-2593)

hyb_protocol: 3.0 µg of RNA at 100ng/µL was used to hybridize ssDNA. Standard Affymetrix protocols were followed for hyb, wash, and stain

scan_protocol: Standard Affmetrix protocol for scanning was performed by using the Affymetrix 3000 7G scanner with autoloader. The acquisition and initial quantification of array images were performed by running Affymetrix GeneChip® Command Console® Software (AGCC)

data_processing:
Data analysis was performed using Agilent's GeneSpring GX software with the selection of the Affymetrix Exon Expression. After the normalization using RMA-16 method, data were filtered on expression (20.0 - 100.0)th Percentile and were processed to unpaired T Test. P-value was computed by selection of Asymptotic and corrected by Benjamini-Hochberg method. 2874 genes was selected by corrected p-value cut-off 0.05 and Fold change cut-off 1.5 to form the matrix table.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

label: Biotin

source_name: calvaria

label_protocol: Biotin

growth_protocol: MC3T3-E1 were maintained in α-MEM without ascorbic acid (Invitrogen, A10490-01) supplemented with 10% MSC-qualified FBS (Invitrogen,12763025), media were changed every 3 to 4 days.

extract_protocol: Total cellular RNA of the MC3T3-E1 and Osteoblasts differentiated from MC3T3-E1 was isolated using Trizol (invitrogen, 15596026 ) according to the manufacturer’s instructions. Integrity and concentration of RNA was evaluated using an Agilent 2100 Bioanalyzer in combination with the Nano Eukaryotic RNA chip. All RNA samples had an average RNA Integrity Number (RIN) of 9.9.

treatment_protocol: Osteoblasts was induced from confluent MC3T3-E1 for 14 days in DMEM with 10% FBS, 1mM sodium pyruvate, 0.1 μM dexamethasone, 0.2 mM L-Ascorbic acid-2 phosphate, 10mM β-glycerophosphate. Media were changed every 3 to 4 days.

value: new born

tag: strain

tag: cell line


title: MC3T3-E1-14 days of osteoblast differentiated-3

description: Osteoblasts differentiated from MC3T3-E1 pre-osteoblast cell line ( ATCC, CRL-2593)

value: osteoblast induction


title: MC3T3-E1-undifferentiated-3


title: MC3T3-E1-14 days of osteoblast differentiated-1


title: MC3T3-E1-14 days of osteoblast differentiated-2


title: MC3T3-E1-undifferentiated-2


title: sox13_dna: human plasmid DNA sequencing human UTR backgrounds

city: Seattle

first: Georg

last: Seelig

state: WA

address: 3946 W Stevens Way NE

department: Electrical Engineering

institute: University of Washington

data_processing:
DNA and RNA sequences distinguished using internal sequence tags
Sequences sorted based on human-derived background sequence tags
DNA and full length (long isoform) RNA used to build sequence map
RNA mapped back to the full-length sequences and the isoform and site of polyadenylation recorded
RNA short and long isoform ratios calculated for each unique library sequence
Genome_build: Reporter UTR background sequence designs based on Human build 37 GRCh37
Supplementary_files_format_and_content: CSV files contain reporter 3'UTR sequences and isoform calculations. Numpy matrix files contain polyadenylation site positions.

source_name: plasmid alternative polyadenylation reporter

growth_protocol: HEK293T cells were cultured on ECM-coated plates in Dubelco's DMEM media supplemented with FBS (5%), penicillin (.05%), and streptomycin (.05%)

extract_protocol:
RNA was extracted from transiently transfected cells 36-48 hours later using the Qiagen Rneasy kits. The purified RNA was then polyA purified using the NEB PolyA Spin kit (magnetic-bead-based protocol).
Library specific priming sites were used to append Illumina adapter sequences and to amplify the library. Amplification was conducted in a light-cycler and samples removed early to minimize PCR bias.

treatment_protocol: Plated cells were seeded on ECM-coated plates and grown to ~90% confluency for 24-36 hours. Plasmid DNA was complexed with Lipofectamine 3000 reagent and transiently transfected.

tag: passages

tag: molecule

value: reporter DNA


title: snhg6_dna: human plasmid DNA sequencing human UTR backgrounds

tag: cell type


title: hspe1_dna: human plasmid DNA sequencing human UTR backgrounds


title: Mof_CreER_Vec_D-3_Mock_Input


title: Mof_CreER_K274R_rMof_D-3_4OHT_H4K16ac


title: Mof_CreER_K274R_rMof_D-3_4OHT_MLL4


title: tomm5_dna: human_tomm5 plasmid DNA sequencing


title: whammp2_dna: human plasmid DNA sequencing human UTR backgrounds


title: aars_dna: human plasmid DNA sequencing human UTR backgrounds


title: atr_dna: human plasmid DNA sequencing human UTR backgrounds


title: Ramos_48hrs_human HDL(40nM)_2

city: Chicago

first: Colby

middle: Shad

last: Thaxton

address: 303 E Chicago, Tarry 16-703

department: Urology

institute: Northwestern University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized to quantiles using Illumina software.

source_name: Ramos cells

label_protocol: Cy3 cRNA were prepared using the Ambion Message Amp kit for Illumina Arrays

extract_protocol: RNA was extracted using Qiagen's Rneasy Mini RNA isolation kit.

treatment_protocol: Ramos cells were treated with HDL NPs, human HDL or PBS (NT) for 48 hours prior to RNA isolation and processing.

tag: cell line type

value: Burkitt's lymphoma

tag: passage number

tag: treatment

value: human HDL (40nM)


title: Ramos_48hrs_human HDL(40nM)_1


title: Ramos_48hrs_NT_3

value: PBS


title: Ramos_48hrs_HDL-NP(40nM)_3

value: HDL NP (40nM)


title: Ramos_48hrs_human HDL(40nM)_3


title: Tonsil_3_3_14_11

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_G

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: Normal tonsil

label_protocol: 300 ng of total RNA was reverse-transcribed, amplified, and biotin-labeled using an Illumina TotalPrep RNA Amplification kit (Ambion).

extract_protocol: Total RNA was extracted using the RNAqueous kit (Ambion, Austin, TX).

treatment_protocol: Cell suspensions were quickly thawed, washed and pelleted from cryopreservation solution, and magnetically depleted of cells expressing CD19 and/or CD20. Total RNA was extracted, the RNA integrity number (RIN) was determined on an Agilent Bioanalyzer, and samples with an RIN >= 7 proceeded to labeling and hybridization.

tag: tissue

value: normal tonsil

tag: cell fraction

value: non-B cells


title: T133

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_C


title: Tonsil_5_3_17_11

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_J


title: Ramos_48hrs_HDL-NP(40nM)_1


title: Kidney_7M_Cre(+)_2

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description: Gene expression data of PRCC-TFE3 expressing kidney

hyb_protocol: Each sample was hybridized to Affymetrix mouse Gene ST 2.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.  Wash and stain were performed on Affymetrix Fluidics Station 450

scan_protocol: Each chip was scanned on Affymetrix GeneChip scanner 3000 with AutoLoader.  Data were collected using Affymetrix AGCC software.

data_processing: Partek Genomics Suite 6.6 was used for RMA-based data normalization and the subsequent data analysis, including PCA and ANOVA

source_name: kidney from 7 month old PRCC-TFE3;KSP-Cre+ mouse

label_protocol: RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >7).  100 ng of RNA was reverse transcribed, amplified and sense strand cDNA was fragmented and labeled using Affymetrix’s GeneChip WT Plus Reagent Kit  following manufacturer’s suggested protocol.

growth_protocol: Mice were housed in Frederick National Laboratory for Cancer Research animal facilities

extract_protocol: Total RNA was isolated from flash frozen mouse kidneys using TRIzol reagent.

treatment_protocol: Mice were euthanized by CO2 asphyxiation for analyses according to the NCI-Frederick Animal Care and Use Committee guidelines.

value: kidney

value: 7 months-old

tag: genotype

value: PRCC-TFE3;KSP-Cre+ mouse


title: Kidney_7M_Cre(+)_3


title: Tonsil_7_6_8_10

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_L


title: Kidney_7M_Cre(-)_1

description: Gene expression data of control kidney

source_name: kidney from 7 month old PRCC-TFE3;KSP-Cre- mouse

value: PRCC-TFE3;KSP-Cre- mouse


title: Kidney_7M_Cre(-)_2

description: Gene expression data of control kidney


title: Kidney_4M_Cre(+)_4

source_name: kidney from 4 month old PRCC-TFE3;KSP-Cre+ mouse

value: 4 months-old


title: Ramos_48hrs_HDL-NP(40nM)_2


title: Kidney_7M_Cre(+)_4


title: Kidney_4M_Cre(+)_3


title: Tonsil_1_4_4

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_F


title: Tonsil_4_3_17_11

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_I


title: T135

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_D


title: Kidney_7M_Cre(-)_3

description: Gene expression data of control kidney


title: Tonsil_5_6_8_10

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_K


title: Kidney_7M_Cre(+)_1


title: Tonsil_3_3_28

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_H


title: T136

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_E


title: T127

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_A


title: Ramos_48hrs_NT_2


title: Ramos_48hrs_NT_1


title: T132

description:
Normal tonsil. Sample titles indicate uniqueness only.
6116709003_B


title: post-engraftment colon 2

city: St Louis

first: Samantha

last: Morris

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

description:
post2
polyA RNA
Nuclei were encapsulated and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v3 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 3.0.2 using a custom pre-mRNA mm10 reference package
processed data file: post.genes.tsv

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 or hg19 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: colon

extract_protocol: 10x Genomics Chromium single cell preparation.

value: large intestine

value: 7 weeks


title: post-engraftment colon 1

description:
post1
polyA RNA
Nuclei were encapsulated and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v3 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 3.0.2 using a custom pre-mRNA mm10 reference package.
processed data file: post.genes.tsv


title: FSP1 fibroblasts [3052_1_FSP]

city: Nashville

first: Sarika

last: Saraswati

state: TN

address: 1161 21st Avenue South, MCN C2217

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

data_processing:
Purified RNA was sent to Vanderbilt sequencing core (VANTAGE), paired end sequencing was performed at 75X depth.
Raw data (FASTQ files) were uploaded to CLC Genomic Workbench 8 (Qiagen) and data quality assessment performed.
Sequences were aligned to the Grmc38 platform of the Mus musculus genome using Tuxedo Suite, followed by normalization (RPKM).
Data were annotated using Ensemble Release 83 and quantified at the gene level using CuffDiff.
Genome_build: Grmc38 platform of the Mus musculus genome
Supplementary_files_format_and_content: Excel

source_name: FSP1 fibroblasts

extract_protocol:
Cells were isoated with Liberase TH enzyme digestion and sorted by FACS
VANTAGE at Vanderbilt performed mRNA enrichment and cDNA library preparation utilizing the Illumina Tru-seq stranded mRNA sample prep kit. Sequencing was performed at Single Read 50 HT bp on the Illumina HiSeq 2500. QC reports for sequencing quality and per sample yield was provided. The file deliverable is a demultiplexed FASTQ containing the PF reads.

treatment_protocol: cells were isolated 10 day following injury and sorted by GFP expression; RNA was isolated

tag: strain background

tag: genotype/variation

value: FSP1-GFP transgenic mice

value: 12 week old mice

value: injured heart after myocardial infarction


title: Uninjured fibroblasts [3052_6_uninjured]

source_name: Uninjured fibroblasts

treatment_protocol: cells were isolated and plated for 4 hours before collecting RNA

value: WT mice

value: uninjured heart


title: aSMA fibroblasts [3052_5_SMA-GFP]

source_name: aSMA fibroblasts

value: aSMA-GFP transgenic mice


title: Kidney_4M_Cre(+)_1


title: T144

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_J


title: Kidney_4M_Cre(-)_3

description: Gene expression data of control kidney

source_name: kidney from 4 month old PRCC-TFE3;KSP-Cre- mouse


title: T145

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_K


title: T121

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_E


title: post-engraftment colon 3

description:
post3
polyA RNA
Nuclei were encapsulated and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v3 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 3.0.2 using a custom pre-mRNA mm10 reference package
processed data file: post.genes.tsv


title: MEF AS D6 Rep B

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

data_processing:
BCL files were converted to FASTQ using bcl2fastq v2.19
Sequences were aligned to Mus musculus 10 (mm10) genome using Spliced Transcripts Alignment to a Reference (STAR), available through the SureCell RNA Single Cell App v1.1.0 in Illumina Basespace.
Droplets containing only single were selected using double knee plot in BaseSpace
Genome_build: mm10
Supplementary_files_format_and_content: .csv files containing UMI counts per genes (columns) for single cell (row).
Supplementary_files_format_and_content: The file 'IrrMEFs_CellID.csv' contains barcode information ("CellID") and sample information ("Sample", "Treatment", and "Timepoint") for each irradiated mouse embryonic fibroblast. These cells were removed before performing downstream Monocle analysis.

source_name: Mouse Embryonic Fibroblasts

growth_protocol:
MEF or mESCs were cultured in ESC Media (knockout DMEM, 15% FBS, L-glutamine, Pen/Strep, NEAA, 2-mercaptoethanol, and leuemia inhibitory factor) with or without small molecules (Ascorbic acid, SGC0946, CHIR-99021, and PD-032501).
Postnatal brain cells were cultured in neural basal medium supplmented with B27 (wo/ Vit A), Pen/Strep, L-glutamine, NEAA, 20ng/mL EGF, and 20ng/mL FGF2.  Postnatal brain cells repogramming was done in ESC media with small molecules.

extract_protocol:
Cells were resuspended into single cell suspension and encapsulated into droplets containing library components via Bio-Rad ddSeq Single-Cell Isolator.
Library were prepared using Illumina Bio-Rad SureCell WTA 3' Library Kit according to manufacturer's instruction.
Single-Cell RNA Sequencing

treatment_protocol: Reprogramming cultures were plated on irradiated MEFs and treated with 2ug/mL doxycycline, 50ug/mL ascorbic acid, and 5uM of SGC09456 on Day 0. CHIR-99021 and PD-0325901 (2i) was added 12 hours later. Media containing chemicals and doxycycline was replaced on day 2 and day 4 of reprogramming.

tag: timepoint

value: Day 6

value: AS

value: Embryonic


title: MEF AS D6 Rep A

tag: age


title: MEF AS D4 Rep B

value: Day 4


title: Kidney_4M_Cre(-)_4

description: Gene expression data of control kidney

value: kidney


title: MEF AS D4 Rep A


title: T146

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_L

value: normal tonsil

value: non-B cells


title: MEF S2 D6 Rep B


title: T137

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_G


title: T134

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_F


title: Kidney_4M_Cre(-)_1

description: Gene expression data of control kidney

value: PRCC-TFE3;KSP-Cre- mouse


title: T3_5_14_10

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_C


title: Kidney_4M_Cre(+)_2

description: Gene expression data of PRCC-TFE3 expressing kidney

value: 4 months-old

value: PRCC-TFE3;KSP-Cre+ mouse


title: T141

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_H


title: T1_3_28

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_A


title: MEF S2 D6 Rep A


title: Kidney_4M_Cre(-)_2

description: Gene expression data of control kidney


title: T117

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_D


title: T143

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_I


title: 1112851_B

source_name: B-cell fraction of follicular lymphoma

treatment_protocol: Cell suspensions were quickly thawed, washed and pelleted from cryopreservation solution, and magnetically sorted by negative selection into nominal B (CD3-depleted) and non-B (NB; CD19- and CD20-depleted) fractions. The desired enrichment of the respective fractions was determined by flow cytometry for CD19+ and/or CD20+ cells in the B fraction, and CD3+ cells in the NB fraction, as well as by depletion of CD20+ B cells from the NB fraction. Total RNA was extracted from fractions, and then the RNA integrity number (RIN) was determined on an Agilent Bioanalyzer. Only those samples with an RIN >= 6.6 proceeded to labeling and hybridization.

tag: patient id

tag: tissue source

value: untreated follicular lymphoma

value: B cells


title: 1112851_non-B

source_name: non-B-cell fraction of follicular lymphoma


title: T2_3_28

description:
Normal tonsil. Sample titles indicate uniqueness only.
6071820046_B


title: MEF S2 D4 Rep A


title: 1112935_non-B


title: MEF A2 D6 Rep B


title: MEF A2 D6 Rep A


title: MEF A2 D4 Rep B


title: MEF A2 D4 Rep A


title: MEF S2 D4 Rep B


title: MEF FBS D12 Rep B

value: Day 12


title: 1112995_B


title: MEF FBS D9 Rep A

value: Day 9


title: MEF FBS D9 Rep B


title: MEF FBS D6 Rep B


title: MEF FBS D6 Rep A


title: 1112995_non-B


title: 1112935_B


title: 1157284_B


title: MEF FBS D12 Rep A


title: 1113069_B


title: MEF FBS D3 Rep A

value: Day 3


title: MEF FBS D3 Rep B


title: 1113069_non-B


title: ESCs A2S Rep A

source_name: V6.5 Mouse Embryonic Stem Cells

value: Day 2


title: 1112904_non-B


title: 1113058_non-B


title: 1113058_B


title: 1112997_B


title: ESCs Rep B


title: 1112958_B


title: ESCs Rep A


title: 1112997_non-B


title: ESCs A2S Rep B


title: 1112957_B


title: 1112908_B


title: 1112904_B


title: 1157284_non-B


title: 1112908_non-B


title: 1112958_non-B


title: MEF Rep A


title: MEF A2S D6 Rep B


title: MEF A2S D4 Rep B


title: MEF A2S D6 Rep A


title: MEF A2S D4 Rep A


title: MEF Rep B


title: 1113048_B


title: 1113048_non-B


title: MEF A2S D2 Rep B


title: NH025_W1118 01

city: Edmonton

first: Kirst

last: King-Jones

state: Alberta

address: 116th Street and 85th Avenue

department: Biological Sciences

country: Canada

institute: University of Alberta

data_processing:
 Sequencing data was analysed using Arraystar 4.0 (DNAstar), MS Access and DAVID GO Tools.
Supplementary_files_format_and_content: FPKM

organism: Drosophila melanogaster

source_name: Ring glands

growth_protocol: Animals were raised on a standard media. Newly molted third instar larvae were staged and ring glands were manually dissected 40 hours after molting

extract_protocol:
50 ring glands were manually dissected in 1x PBS and stored in trizol. Samples were flash-frozen in liquid nitrogen and stored at -800C until needed. RNA samples were extracted using Qiagen Rneasy kit
Library was prepared using Ovation Drosophila RNA-Seq system

tag: sample age

value: 40hr after L2/L3 molting

tag: sample size

value: 50 ring glands/sample


title: NH026_W1118 02


title: NH024_IRP1B 3R3Q 02


title: 1113080_non-B


title: NH023_IRP1B 3R3Q 01


title: NH022_IRP1B C447S 02


title: NH021_IRP1B C447S 01


title: 1113080_B


title: 1112975_B


title: 1112991_B


title: 1112991_non-B


title: 1112914_B


title: 1112914_non-B


title: NH020_IRP1B WT 02


title: 1112957_non-B


title: NH019_IRP1B WT 01


title: 1113055_non-B


title: 1112975_non-B


title: 1113055_B


title: 1113078_B


title: NH018_IRP1A 3R3Q 02


title: NH017_IRP1A 3R3Q 01


title: NH016_IRP1A C450S 02


title: NH015_IRP1A C450S 01


title: NH014_IRP1A WT 02


title: NH013_IRP1A WT 01


title: 1112989_non-B


title: 1112989_B


title: 1113003_B


title: 1113047_non-B


title: s8_Vecadpos_GFPpos

city: Monterotondo

first: Christophe

last: Lancrin

state: RM

address: Via Ramarini 32

department: EMBL Rome

country: Italy

institute: EMBL

data_processing:
Quality check with Fastqc
Adaptor clipping with FASTX-clipper version 1.0.1
Synchronisation of clipped files with FASTQ-paired-end-joiner version 2.0.0
Splitting with FASTQ-paired-end-splitter version 1.0.0
Mapping with RNA star
Genome_build: mm10
Supplementary_files_format_and_content: Htseq-count text file with raw count numbers for each sample

growth_protocol: Not applicable. The cells were not grown.

extract_protocol:
Cells from miR144/451+/GFP E11.5 YS were FACS sorted into tube strips with lysis buffer containing 0.2% Triton X-100, oligo-dT Primer and dNTP mix and after snap frozen on dry-ice. RT & template-switching, PCR preamplification (14 cycles of amplification) were performed as described in the Smart-seq2 protocol (Picelli S et al, 2014, PMID: 24385147 )
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Not applicable. The cells were not treated.

value: Endothelial-Erythroid

tag: number of cells

tag: strain


title: s7_Vecadpos_GFPpos

tag: cell type


title: 1113047_B


title: 1113061_non-B


title: s6_Vecadneg_GFPpos

value: Erythroid


title: s5_Vecadneg_GFPpos


title: s3_Vecadpos_GFPneg

value: Endothelial


title: 1113061_B


title: s2_Vecadpos_GFPneg


title: 1112989_B_2


title: 1112924_B


title: s4_Vecadneg_GFPpos


title: s1_Vecadpos_GFPneg


title: tomm5_rna: human_tomm5 RNA sequencing

tag: passages

tag: molecule

value: reporter RNA


title: alien1_rna: fully_randomized_1_alien1 RNA sequencing


title: apa_six_rna: human_six RNA sequencing


title: alien2_rna: fully_randomized_2_alien2 RNA sequencing


title: alien2_dna: fully_randomized_2_alien2 plasmid DNA sequencing

value: reporter DNA


title: 1113056_B


title: alien1_dna: fully_randomized_1_alien1 plasmid DNA sequencing


title: 1113056_non-B

value: non-B cells


title: 1113054_B


title: 1113054_non-B


title: 1113065_B


title: 1112989_non-B_2


title: 1171965_non-B


title: DLD cells 4h DMSO

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

country: United Kingdom

institute: University of Oxford

description: Biological replicate 1 of 1.

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and stored in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenPIX 4200A (Molecular Devices) instrument.

data_processing:
1. TIF-files of scanned arrays were analyzed using the GenePix Pro 7 (Molecular Devices) software.
2. Ratios of  Cy3/Atto635 fluorescence signals were calculated for individual spots based on mean fluorescence signal (background fluorescence substraction).
3. Cy3 532/Atto635 ratios were normalized to Cy3 532/Atto635 values of tRNA standards (e.g. median Cy3 532/Atto635 ratios of the four tRNA standards E. coli tRNALys2, yeast tRNAAla5, E. coli tRNATyr2, Yeast tRNAPhe3) for individual blocks.
4. Normalized Cy3 532/Atto635 ratios for individual blocks were averaged, representing final Cy3 532/Atto635 ratios.

source_name: cultivated cells

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (4 pmol each; E. coli tRNALys2, E. coli tRNATyr2, yeast tRNAAla5, yeast tRNAPhe3) were added to 2 µg extracted total RNA prior to deacetylation.
2. For  abundance arrays total RNA was deacylated for 45 min at 37°C with 100 mM Tris-HCl (pH 9); For tRNA charging arrays total RNA  was oxidized with periodate and thereafter treated for 45 min at 37°C with 100 mM Tris-HCl (pH 9) for tRNA deacetylation; tRNA standards were added prior the deacylation step.
3. Cy3 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 16h at 16°C in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol:
Cells were cultivated at 37°C and 5% CO2 supplemented with 10% FCS (PAN Biotech) and 2 mM L-glutamine (Gibco) until 70 to 80% confluency.
Cell were grown independently for each biological experiment and checked frequently for mycoplasma contamination.

extract_protocol: Total RNA for total tRNA arrays was extracted using TriReagent (Sigma-Aldrich) and for arrays to determine the charged fraction with acidic phenol (pH 4.5) according to manufacturer's protocol

treatment_protocol: Cells were treated with 4-hydroxytamoxifen to activate c-myc.

tag: cell line

value: DLD-1 (ATCC CCL-221)

tag: treatment

value: charging 4h DMSO

tag: patient identifier

value: untreated


title: DLD cells 4h pol3 inhibition

description: Biological replicate 1 of 1.

value: charging 4h pol3 inhibition


title: DLD cells 0h pol3 inhibition

description: Biological replicate 1 of 1.

value: charging 0h pol3 inhibition


title: 1113065_non-B

value: untreated follicular lymphoma

tag: cell fraction


title: DLD cells 0h DMSO

description: Biological replicate 1 of 1.

value: charging 0h DMSO


title: Time 24 Repeat 2

city: Frederick

first: Barry

middle: Richard

last: O'Keefe

state: Maryland

address: Bldg. 562, Rm. 201, NCI at Frederick

department: Center for Cancer Research

institute: National Cancer Institute

description: bPGN treated

scan_protocol: NanoString Technology

data_processing:
Platform used was: nCounter® PanCancer Pathways Panel, CAT# XT-CSO-PATH1-12, nSOLVER, Advanced Analysis. Data were normalized to Time 0 for each repeat.
RCC files include Raw number of mRNA molecules per 100 ng of total RNA

source_name: HCT-116 human cell line

growth_protocol: RPMI 10%FBS

extract_protocol: miRVANA Paris RNA extraction

treatment_protocol: small molecule treatment. 50 nM bPGN

tag: time


title: 1112922_non-B

city: Houston


title: Time 1 Repeat 2

description: bPGN treated


title: 1112922_B

value: B cells


title: 1113050_non-B


title: 1155434_B


title: DLD cells charging 4h pol3 inhibition

description: Biological replicate 1 of 1.


title: 1155434_non-B


title: 1113050_B


title: 1171965_B