title: R318: Bone Marrow CD34+ cells - mast cell leukemia - rep3

description: Total Momonuclear Cells were isolated from a bone marrow aspirate at the time of diagnosis using Ficoll. CD34+ cells were further purified by Fluorescence-activated cell sorting.

value: mast cell leukemia


title: R321: Bone Marrow CD34+ cells - healthy - rep3

status: Public on Apr 14 2020

type: RNA

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: Cells were purchased from Lonza (Basel, Switzerland), cat # LON2M-101B

hyb_protocol: Affymetrix GeneChip®Human Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip WT Pico Reagent Kit User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: CD34+ cells isolated from healthy human bone marrow

label_protocol: 500pg of total RNA were amplified and labeled using the GeneChip WT Pico Reagent Kit (Catalog Number 902622,Affymetrix, Santa Clara, CA)

growth_protocol: mononuclear cells were isolated from bone marrow aspirates using Ficoll and frozen in FCS + 10% DMSO until sorting

extract_protocol: RNA was isolated using the Rneasy micro elute kit (Quiagen) according to the manufacturer's protocol

treatment_protocol: cells were incubated with fluorecence-labeled antibodies against CD45 and CD34 and sorted on a BD FACSAria I

tag: gender

value: male

tag: immune phenotype

tag: diagnosis

value: Healthy

tag: tissue

value: Bone Marrow


title: 200597: Healthy individual, with Globin-Block 19

type: SRA

city: Kiel

first: Florian

last: Uellendahl-Werth

address: Rosalind-Franklin-Straße 12

department: Institute of Clinical Molecular Biology (IKMB)

country: Germany

institute: Christian-Albrechts Universität zu Kiel

library_source: transcriptomic

data_processing:
Bases were called and samples demultiplexed with an Illumina 1.8+ pipeline.
Reads were aligned with STAR (2.5.2b-2) on usegalaxy.eu
Alignments were sumarized on transcript level by htseq-count (0.9.1) yielding raw counts and with StringTie (1.3.4d) yielding TPM. TPM values were not computed from the raw counts. The intention was to check if the findings hold irrespective of the read summarizer.
The summarized read tables were merged into one file using R and the data.table package.
Genome_build: GRCh38.87
Supplementary_files_format_and_content: Tab separated values (tsv) with EnsemblID transcripts, sample name (name of the raw data), if the sample was treated with Globin-Block (condition), and the ensembl gene ID and the gene name.

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
PAXgene Blood RNA Kit; Pellets from PAXgene Blood RNA Tubes are washed, resuspended, and incubated in optimized buffers together with proteinase K to digest proteins. Lysates are applied to a PAXgene 96 Filter Plate and centrifuged to remove residual cell debris. Ethanol is added to the flow-through to adjust binding conditions, and the lysates are applied to a PAXgene 96 RNA Plate. RNA is selectively bound to the PAXgene 96 RNA membrane as contaminants pass through. Residual DNA is removed through a DNase I digestion on the PAXgene 96 membrane. Remaining contaminants are removed in three efficient wash steps and RNA is eluted in Buffer BR5. (from manufacturer’s guide)
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit with 50 ng RNA input. Optional “Globin Block Module” used in samples with “yes” in the column “Globin Block applied”. Poly(A) RNA is reverse transcribed with poly(T)-Primers. RNA is digested and the second strand is synthesized by random priming. cDNA is purified. Illumina adapters are added. The PCR was run with 15 cycles.

tag: globin-block applied

value: yes

tag: identifier

value: Whole Blood


title: R319: Bone Marrow CD34+ cells - healthy - rep1


title: 200594: Healthy individual, with Globin-Block 16


title: 200595: Healthy individual, with Globin-Block 17


title: 200596: Healthy individual, with Globin-Block 18


title: 200593: Healthy individual, with Globin-Block 15


title: 200591: Healthy individual, with Globin-Block 13


title: 200592: Healthy individual, with Globin-Block 14


title: IL-33KO male lung ILC2s_naive_biological rep 1 (Fig5)

city: San Francisco

first: Catherine

middle: Anne

last: Steer

state: California

address: 3333 California Street, Suite 385, Box 1348

department: Laboratory Medicine

country: USA

institute: University of California San Francisco

hyb_protocol: cDNA was prepared from total RNA using Nugen Pico WTA kit according to the manufacturer's protocol. Fragmented cDNA was labeled and hybridized to Affymetrix GeneChip Mouse Gene 2.0ST Array. Washing and staining were performed by Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were analyzed by Expression Console software by Affymetrix. Normalization was performed using RMA algorithm (by FlexArray 1.6.3).

label: biotin

organism: Mus musculus

source_name: IL-33KO male lung ILC2s_naive

label_protocol: Labeling was performed using Nugen Encore biotin kit according to the manufacturer's instructions.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: Sex

value: Male

value: lung

tag: cell type

value: innate lymphoid cells (ILC2s)

tag: genotype

value: Knockout


title: Male lung ILC2s_naïve_biological rep 2 (Fig5)

source_name: Male lung ILC2s_naïve

value: Wildtype


title: Male lung ILC2s_naïve_biological rep 3 (Fig5)


title: IL-33KO male lung ILC2s_naive_biological rep 2 (Fig5)


title: 200598: Healthy individual, with Globin-Block 20


title: R131: Bone Marrow CD34+ cells - mast cell leukemia - rep2

source_name: CD34+ cells isloated from the bone marrow of a patient with mast cell leukemia

value: female

value: mast cell leukemia with associated acute myeloid Leukemia


title: R1213: Bone Marrow CD34+ cells - mast cell leukemia - rep1


title: 200599: Healthy individual, with Globin-Block 21


title: 200590: Healthy individual, with Globin-Block 12


title: 200587: Healthy individual, with Globin-Block 10


title: 200589: Healthy individual, with Globin-Block 11


title: Male lung ILC2s_naïve_biological rep 1 (Fig5)


title: 200586: Healthy individual, with Globin-Block 9


title: 200584: Healthy individual, with Globin-Block 7


title: 200585: Healthy individual, with Globin-Block 8


title: D10 neonatal lung ILC2s_naive_biological rep 3 (Fig1)

source_name: D10 neonatal lung ILC2s_naive

treatment_protocol: For effector adults, mice were injected intranasally with IL-33 for three consecutive days and then ILC2s were isolated one day after the last treatment.

tag: developmental stage

value: Neonate (10 days)


title: D10 neonatal lung ILC2s_naive_biological rep 1 (Fig1)


title: Male lung ILC2s_effector_biological rep 3 (Fig1)

source_name: Male lung ILC2s_effector

tag: treatment

value: Effector


title: Male lung ILC2s_effector_biological rep 2 (Fig1)


title: Female lung ILC2s_effector_biological rep 2 (Fig1)

source_name: Female lung ILC2s_effector

value: Female


title: Male lung ILC2s_effector_biological rep 1 (Fig1)


title: 200583: Healthy individual, with Globin-Block 6


title: 200582: Healthy individual, with Globin-Block 5


title: D10 neonatal lung ILC2s_naive_biological rep 2 (Fig1)


title: 200581: Healthy individual, with Globin-Block 4


title: Female lung ILC2s_effector_biological rep 3 (Fig1)


title: 200580: Healthy individual, with Globin-Block 3


title: 100673: Healthy individual, no Globin-Block 91

value: no


title: 200578: Healthy individual, with Globin-Block 1


title: 100672: Healthy individual, no Globin-Block 90


title: 200579: Healthy individual, with Globin-Block 2


title: 100671: Healthy individual, no Globin-Block 89


title: Male lung ILC2s_naïve_biological rep 3 (Fig1)

value: Naïve


title: Female lung ILC2s_effector_biological rep 1 (Fig1)


title: Female lung ILC2s_naïve_biological rep 3 (Fig1)

source_name: Female lung ILC2s_naïve


title: Male lung ILC2s_naïve_biological rep 2 (Fig1)


title: 100667: Healthy individual, no Globin-Block 85


title: 100668: Healthy individual, no Globin-Block 86


title: 100669: Healthy individual, no Globin-Block 87


title: 100664: Healthy individual, no Globin-Block 83


title: 100666: Healthy individual, no Globin-Block 84


title: Female lung ILC2s_naïve_biological rep 1 (Fig1)


title: Male lung ILC2s_naïve_biological rep 1 (Fig1)


title: BP394_KO

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix GeneChip® scanner

data_processing: GeneChip™ Mouse Gene 2.0 ST Array, Affymetrix console, RMA normalization

source_name: Pancreatic Cancer, Bap1 KO

label_protocol: Biotin

growth_protocol: F12/DMEM supplemented with EGF

extract_protocol: RNeasy Mini Kit (Qiagen)

value: F

tag: cell line

value: pancreatic cancer cell line

value: Bap1 KO; KrasG12D


title: Female lung ILC2s_naïve_biological rep 2 (Fig1)


title: 100663: Healthy individual, no Globin-Block 82


title: BP650_KO

value: M


title: BP466_KO


title: 100670: Healthy individual, no Globin-Block 88

value: Whole Blood


title: PA3636_WT

source_name: Pancreatic Cancer, Bap1 WT

value: Bap1 WT; KrasG12D


title: 100662: Healthy individual, no Globin-Block 81


title: PA3635_WT


title: Atp7b -/- liver 3mth rep 3

city: Houston

first: Clavia

middle: Ruth

last: Wooton-Kee

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Gene expression from Atp7b -/-  liver

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Data was processed in R using the affy-package.

source_name: liver of 3 month old Atp7b-/- C57Bl/6

label_protocol: Microarray processing using a GeneChip Mouse 430 2.0 (Affymetrix) was performed in the Genomic and RNA Profiling Core at Baylor College of Medicine

extract_protocol: 100 mg liver samples were extracted and placed in Trizol followed by RNA isolation using an Rneasy kit.

treatment_protocol: Supplemental ZN was given to 4 mutant mice.

value: liver

tag: strain

tag: age

value: 3 month

tag: agent


title: PA3632_WT


title: Atp7b -/- liver 3mth rep 4 with ZN

description: Gene expression from Atp7b -/-  liver + ZN

value: Zn treated


title: Atp7b -/- liver 3mth rep 4

description: Gene expression from Atp7b -/-  liver


title: 100660: Healthy individual, no Globin-Block 80


title: 100659: Healthy individual, no Globin-Block 79


title: Seedlings, Wildtype Col-0 Rep 3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
Gene expression data from 17 day old wild type seedlings grown
WT3_CTRL_3

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Aragene-1_0-type from Affymetrix. A Custom CDF Version 16 with TAIR-ID based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

organism: Arabidopsis thaliana

source_name: WT seedling grown on MS medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: RNA was extracted from 17-day-old wild-type and naa20-1 seedlings grown on 1xMS medium under short day conditions (100 µE, 8.5h light,).

extract_protocol: RNA was extracted with the peqGOLD Total RNA Kit (Peqlab, Germany) according to the manufacturers protocol.

treatment_protocol: not applicable

value: WT

value: seedlings


title: Seedlings, Wildtype Col-0 Rep 1

description:
Gene expression data from 17 day old wild type seedlings grown
WT1_CTRL_1


title: Seedlings, Wildtype Col-0 Rep 2

description:
Gene expression data from 17 day old wild type seedlings grown
WT2_CTRL_2


title: Atp7b -/- liver 3mth rep 3 with ZN


title: Atp7b -/- liver 3mth rep 1

description: Gene expression from Atp7b -/-  liver


title: Atp7b -/- liver 3mth rep 2

description: Gene expression from Atp7b -/-  liver


title: Seedlings, Mutant naa20-1 Rep 3

description:
Gene expression data from 17 day old naa20-1 mutant seedlings grown
naa20_CTRL_4

source_name: naa20-1 mutant seedling grown on MS medium


title: thoracic aortic aneurysm plasma sample 7

city: Vilnius

first: Raimundas

last: Ražanskas

address: Sauletėkio al. 7

department: Institute of Biotechnology, Life Sciences Center

country: Lithuania

institute: Vilnius University

description:
Pl-TAA 7
Plasma_miRNA_RC_DeseqRC.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
Raw FASTQ files were processed with custom R scripts. Briefly, identical sequences were counted and collapsed, adapter sequences were trimmed and reads shorter than 16 nt and longer than 28 nt were removed. Remaining reads were aligned to human miRNA hairpin sequences from miRBase v22 using Bowtie v1.1.2 with parameters -a -v 0. Additional alignment cycles with modified parameter --3 X were performed to include miRNA sequences with 1, 2 or 3 non-template 3’-terminal nucleotides. Any aligned sequence was accepted as mature miRNA if its 5’-terminal mapped to hairpin no further than 1 nt in either direction from the 5’ start position of corresponding mature miRNA (according to mirBase v22).
Data normalization and differential miRNA expression analyses were performed with R package DeSeq2.
Genome_build: hs_ref_GRCh38.p7
Supplementary_files_format_and_content: tab-delimited text file includes raw counts and DeSeq2 normalized values of mature miRNAs in each sample.
Supplementary_files_format_and_content: tab-delimited text, aorta tissue miRNA raw and DeSeq2 normalized counts
Supplementary_files_format_and_content: tab-delimited text, blood plasma miRNA raw and DeSeq2 normalized counts

source_name: plasma

extract_protocol:
RNA from tissues and plasma were extracted using Mirvana Ambion and Mirvana Paris kit, respectively.
cDNA libraries for sequencing were prepared using NEXTflex Small RNA-Seq v3 kit. Ligation reactions of 3′ and 5′ adapters were performed using 1,6 µg of total RNA or 10,5 µL of each RNA samples isolated from aortic tissues or blood plasma, respectively. 18 or 23 PCR cycles of amplification were performed to generate cDNA from tissue or plasma mRNAs, respectively.

tag: condition of thoracic aorta

value: thoracic aorta aneurysm

value: female


title: 100656: Healthy individual, no Globin-Block 77


title: thoracic aortic aneurysm plasma sample 8

description:
Pl-TAA 8
Plasma_miRNA_RC_DeseqRC.txt.gz

value: male


title: 100658: Healthy individual, no Globin-Block 78


title: thoracic aortic aneurysm plasma sample 6

description:
Pl-TAA 6
Plasma_miRNA_RC_DeseqRC.txt.gz


title: Seedlings, Mutant naa20-1 Rep 2

description:
Gene expression data from 17 day old naa20-1 mutant seedlings grown
naa20_CTRL_3


title: plasma sample from independent group of healthy patients 7

description:
Pl-Ctrl 7
Plasma_miRNA_RC_DeseqRC.txt.gz

value: healthy thoracic aorta


title: plasma sample from independent group of healthy patients 6

description:
Pl-Ctrl 6
Plasma_miRNA_RC_DeseqRC.txt.gz


title: 100655: Healthy individual, no Globin-Block 76

value: no


title: Atp7b -/- liver 3mth rep 1 with ZN


title: 100654: Healthy individual, no Globin-Block 75


title: thoracic aortic aneurysm tissue 7

description:
TAA 7
Aorta_miRNA_RC_DeseqRC.txt.gz

source_name: thoracic aorta tissue


title: plasma sample from independent group of healthy patients 5

description:
Pl-Ctrl 5
Plasma_miRNA_RC_DeseqRC.txt.gz


title: thoracic aortic aneurysm tissue 6

description:
TAA 6
Aorta_miRNA_RC_DeseqRC.txt.gz


title: thoracic aortic aneurysm tissue 8

description:
TAA 8
Aorta_miRNA_RC_DeseqRC.txt.gz


title: Seedlings, Mutant naa20-1 Rep 1

description:
Gene expression data from 17 day old naa20-1 mutant seedlings grown
naa20_CTRL_1


title: 100653: Healthy individual, no Globin-Block 74


title: thoracic aortic aneurysm tissue 5

description:
TAA 5
Aorta_miRNA_RC_DeseqRC.txt.gz


title: 100652: Healthy individual, no Globin-Block 73


title: heart transplat donor aorta tissue 4

description:
Ctrl 6
Aorta_miRNA_RC_DeseqRC.txt.gz


title: MRC-5_siPeriostin

city: Saga

first: Tomohito

last: Yoshihara

state: Saga

country: Japan

institute: Saga Univercity

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MRC-5, periostin siRNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using theRNAiso plus kit (Takara Bio) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: MRC-5 cell


title: Atp7b -/- liver 3mth rep 2 with ZN

description: Gene expression from Atp7b -/-  liver +ZN


title: heart transplat donor aorta tissue 3

description:
Ctrl 5
Aorta_miRNA_RC_DeseqRC.txt.gz


title: wildtype liver 3mth rep 3

description: Gene expression from liver

source_name: liver of 3 month old C57Bl/6

value: wildtype


title: MRC-5_siControl

source_name: MRC-5, control siRNA


title: wildtype liver 3mth rep 4

description: Gene expression from liver


title: wildtype liver 3mth rep 2

description: Gene expression from liver


title: wildtype liver 3mth rep 1

description: Gene expression from liver


title: non-aneurysmal sample collected 3 months after the surgery 3

description:
Pl-Op 3
Plasma_miRNA_RC_DeseqRC.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
Raw FASTQ files were processed with custom R scripts. Briefly, identical sequences were counted and collapsed, adapter sequences were trimmed and reads shorter than 16 nt and longer than 28 nt were removed. Remaining reads were aligned to human miRNA hairpin sequences from miRBase v22 using Bowtie v1.1.2 with parameters -a -v 0. Additional alignment cycles with modified parameter --3 X were performed to include miRNA sequences with 1, 2 or 3 non-template 3’-terminal nucleotides. Any aligned sequence was accepted as mature miRNA if its 5’-terminal mapped to hairpin no further than 1 nt in either direction from the 5’ start position of corresponding mature miRNA (according to mirBase v22).
Data normalization and differential miRNA expression analyses were performed with R package DeSeq2.
Genome_build: hs_ref_GRCh38.p7
Supplementary_files_format_and_content: tab-delimited text file includes raw counts and DeSeq2 normalized values of mature miRNAs in each sample.

value: thoracic aorta aneurysm after surgery

value: plasma


title: 100651: Healthy individual, no Globin-Block 72

source_name: Whole Blood


title: 100650: Healthy individual, no Globin-Block 71


title: non-aneurysmal sample collected 3 months after the surgery 2

description:
Pl-Op 2
Plasma_miRNA_RC_DeseqRC.txt.gz


title: non-aneurysmal sample collected 3 months after the surgery 1

description:
Pl-Op 1
Plasma_miRNA_RC_DeseqRC.txt.gz


title: 100649: Healthy individual, no Globin-Block 70


title: thoracic aortic aneurysm plasma sample 5

description:
Pl-TAA 5
Plasma_miRNA_RC_DeseqRC.txt.gz

source_name: thoracic aortic aneurysm plasma sample


title: thoracic aortic aneurysm plasma sample 4

description:
Pl-TAA 4
Plasma_miRNA_RC_DeseqRC.txt.gz


title: thoracic aortic aneurysm plasma sample 3

description:
Pl-TAA 3
Plasma_miRNA_RC_DeseqRC.txt.gz


title: plasma sample from independent group of healthy patients 4

description:
Pl-Ctrl 4
Plasma_miRNA_RC_DeseqRC.txt.gz


title: plasma sample from independent group of healthy patients 2

description:
Pl-Ctrl 2
Plasma_miRNA_RC_DeseqRC.txt.gz


title: non-aneurysmal sample collected 3 months after the surgery 4

description:
Pl-Op 4
Plasma_miRNA_RC_DeseqRC.txt.gz


title: plasma sample from independent group of healthy patients 1

description:
Pl-Ctrl 1
Plasma_miRNA_RC_DeseqRC.txt.gz


title: 100647: Healthy individual, no Globin-Block 68


title: DC3_Replicate2

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description: Illumina Human HT-12 BeadArray

hyb_protocol: Standard Illumina hybridization protocol for cRNA target (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

source_name: Peripheral Blood

label_protocol: Ambion TotalPrep cRNA target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from PBMC and isolated cell samples in parallel, using Qiagen Rneasy reagents on a QIACube instrument.

value: Peripheral Blood


title: 100648: Healthy individual, no Globin-Block 69

value: Whole Blood


title: PBMC_Replicate2

description: Illumina Human HT-12 BeadArray

value: PBMC


title: DC2_Replicate2

description: Illumina Human HT-12 BeadArray


title: plasma sample from independent group of healthy patients 3

description:
Pl-Ctrl 3
Plasma_miRNA_RC_DeseqRC.txt.gz


title: 100645: Healthy individual, no Globin-Block 66


title: MonocyteTotal_Replicate2

description: Illumina Human HT-12 BeadArray

value: Monocyte


title: DC1_Replicate2

description: Illumina Human HT-12 BeadArray


title: 100644: Healthy individual, no Globin-Block 65


title: thoracic aortic aneurysm tissue 4

description:
TAA 4
Aorta_miRNA_RC_DeseqRC.txt.gz

source_name: thoracic aortic aneurysm tissue

value: thoracic aorta tissue


title: MonocyteCD16+_Replicate2

description: Illumina Human HT-12 BeadArray

value: MonocyteNonclassical


title: thoracic aortic aneurysm tissue 1

description:
TAA 1
Aorta_miRNA_RC_DeseqRC.txt.gz


title: MonocyteCD16-_Replicate2

description: Illumina Human HT-12 BeadArray

value: MonocyteClassical


title: Neutrophil_Replicate2

description: Illumina Human HT-12 BeadArray

value: Neutrophil


title: thoracic aortic aneurysm tissue 3

description:
TAA 3
Aorta_miRNA_RC_DeseqRC.txt.gz

value: thoracic aorta aneurysm


title: thoracic aortic aneurysm plasma sample 1

description:
Pl-TAA 1
Plasma_miRNA_RC_DeseqRC.txt.gz


title: thoracic aortic aneurysm tissue 2

description:
TAA 2
Aorta_miRNA_RC_DeseqRC.txt.gz


title: B_Replicate2

description: Illumina Human HT-12 BeadArray

value: B


title: 100646: Healthy individual, no Globin-Block 67


title: healthy aortic tissue collected in coronary artery bypass procedure 1

description:
Ctrl 3
Aorta_miRNA_RC_DeseqRC.txt.gz

value: male


title: NK_Replicate2

description: Illumina Human HT-12 BeadArray

value: NK


title: 100642: Healthy individual, no Globin-Block 63

value: no


title: heart transplant donor aorta tissue 2

description:
Ctrl 2
Aorta_miRNA_RC_DeseqRC.txt.gz

source_name: heart transplant donor aorta tissue

value: healthy thoracic aorta

value: female


title: CD8+T_Replicate2

description: Illumina Human HT-12 BeadArray


title: 100641: Healthy individual, no Globin-Block 62


title: 100639: Healthy individual, no Globin-Block 60


title: CD4+T_Replicate2

description: Illumina Human HT-12 BeadArray


title: heart transplant donor aorta tissue 1

description:
Ctrl 1
Aorta_miRNA_RC_DeseqRC.txt.gz


title: 100640: Healthy individual, no Globin-Block 61


title: 100636: Healthy individual, no Globin-Block 58


title: healthy aortic tissue collected in coronary artery bypass procedure 2

description:
Ctrl 4
Aorta_miRNA_RC_DeseqRC.txt.gz


title: 100643: Healthy individual, no Globin-Block 64


title: 100634: Healthy individual, no Globin-Block 56


title: 100635: Healthy individual, no Globin-Block 57


title: 100638: Healthy individual, no Globin-Block 59


title: 100633: Healthy individual, no Globin-Block 55


title: PBMC_Replicate1

description: Illumina Human HT-12 BeadArray


title: Rptor WT_4

city: BALTIMORE

first: KAUSHAL

middle: VIJAY

last: ASRANI

state: MD

address: 1550 ORLEANS

institute: JOHNS HOPKINS MEDICINE

description: RAPTOR WT#4

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Biotin labeling was performed using the GeneChip WT Pico Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform, with junction probes, annotated as JUC~  in the meta-probeset file, excluded. Affymetrix's na35 probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
probe group file: MTA-1_0.r3.pgf
meta-probeset file: MTA-1_0.na35.mm10.probeset.csv

source_name: wild-type epidermis

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: Mouse epidermal tissue dissected from E18.5 mouse embryos

extract_protocol: E18.5 embryonic littermates were manually classified as wild-type or Rptor cKO and were additionally validated by genotyping. Mouse epidermis was separated from the dermis following incubation of E18.5 embryonic skin with 3.8% Ammonium thiocynate for 10 minutes at room temperature. The epidermal sheet was homogenized in TRIzol and total RNA prepared using the TRIzol RNA extraction and RNeasy purification protocol.

tag: genotype/variation

value: wild-type

value: epidermis


title: 100632: Healthy individual, no Globin-Block 54

description:
globinblock_rawcounts.csv
Outlier


title: DC1_Replicate1

description: Illumina Human HT-12 BeadArray

value: Peripheral Blood


title: blastocyst (natural cycle)

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

institute: Max Planck Institute Muenster

description:
equivalent of 20 embryos (after in vivo fertilization and in vitro culture in KSOM(aa))
embryos were lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water; volume equivalent to 20 embryos was used for labeling and hybridization

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit was used, for 16 h (+/- 1h) at 45°C with 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The robust multiarray averaging method was applied for background correction, normalization, and probe summarization using the Affymetrix Expression Console.

source_name: preimplantation embryo

label_protocol: Biotinylated cDNA was prepared using GeneChip WT Pico kit, reverse-transcribing 20 micrograms cRNA and, of these, subjecting 5.5 micrograms to labeling.

growth_protocol: Metaphase II oocytes from B6C3F1 females or zygotes from B6C3F1 x CD1 mating were collected from the oviducts; oocytes were lysed immediately for gene expression analysis; pronuclear-stage oocytes were cultured in pools in KSOM(aa) medium using a 4-well plate under 5% CO2 in air at 37 degrees C. Embryos were collected for lysis at the desired stage.

extract_protocol: Oocytes or embryos with zona pellucida were lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water according to the manufacturer's instructions. The volume equivalent to 20 oocytes or embryos was processed further.

treatment_protocol: The donors of the oocytes or embryos were subjected to 1) ovarian stimulation a.k.a. superovulation (PMSG 10 IU, hCG 10 IU, 48 hours apart); or 2) no ovarian stimulation.

tag: ovarian stimulation

tag: genetic background

value: B6C3F1 x CD1

value: Theiler stage 5; 4 days post fertilization

tag: cell numberd

value: equivalent of 20 embryos with approx.32 cells each


title: DC3_Replicate1

description: Illumina Human HT-12 BeadArray

tag: tissue


title: MonocyteTotal_Replicate1

description: Illumina Human HT-12 BeadArray

value: Monocyte


title: Rptor WT_6

description: RAPTOR WT#6


title: NK_Replicate1

description: Illumina Human HT-12 BeadArray


title: 100631: Healthy individual, no Globin-Block 53

tag: globin-block applied

value: Whole Blood


title: Rptor cKO_2

description: RAPTOR NULL#2

source_name: Rptor cKO epidermis

value: Rptor cKO


title: DC2_Replicate1

description: Illumina Human HT-12 BeadArray


title: 4-cell (natural cycle)

value: Theiler stage 3; 2 days post fertilization

value: equivalent of 20 embryos with 4 cells each


title: 8-cell (natural cycle)

value: Theiler stage 3; 3 days post fertilization

value: equivalent of 20 embryos with 8 cells each


title: MonocyteCD16+_Replicate1

description: Illumina Human HT-12 BeadArray

value: MonocyteNonclassical


title: Rptor cKO_3

description: RAPTOR NULL#3


title: 1-cell (natural cycle)

value: Theiler stage 1; 0 days post fertilization

value: equivalent of 20 embryos with 1 cell each


title: 2-cell late (natural cycle)

value: Theiler stage 2; 1 days post fertilization

value: equivalent of 20 embryos with 2 cells each


title: blastocyst (PMSG+48h+hCG)


title: morula (PMSG+48h+hCG)

value: Theiler stage 3-4; 3 days post fertilization

value: equivalent of 20 embryos with approx. 16 cells each


title: 100630: Healthy individual, no Globin-Block 52

value: no

tag: identifier


title: morula (natural cycle)

value: B6C3F1 x CD1


title: 2-cell early (natural cycle)


title: MonocyteCD16-_Replicate1

description: Illumina Human HT-12 BeadArray

value: Peripheral Blood

value: MonocyteClassical


title: Rptor WT_5

description: RAPTOR WT#5

value: wild-type

value: epidermis


title: Rptor cKO_1

description: RAPTOR NULL#1

value: Rptor cKO


title: 8-cell (PMSG+48h+hCG)


title: B_Replicate1

description: Illumina Human HT-12 BeadArray

value: B


title: oocyte MII (natural cycle)

description:
equivalent of 20 oocytes (after natural mating with vasectomized males)
oocytes were lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water; volume equivalent to 20 oocytes was used for labeling and hybridization

source_name: unfertilized oocyte

value: metaphase II, unfertilized

value: equivalent of 20 oocytes


title: 100628: Healthy individual, no Globin-Block 50

value: Whole Blood


title: 100629: Healthy individual, no Globin-Block 51


title: 100627: Healthy individual, no Globin-Block 49


title: HepG2_Fr-4_Seq

city: Wako

first: Itoshi

last: Nikaido

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

library_source: genomic

data_processing:
(Fr-1 ~ Fr-5, and RNA) Sequenced reads were trimmed with retaining last 50 bps using fastx_trimmer (-l 50).
(Fr-1 ~ Fr-5) Sequenced reads were mapped to hg38 whole genome using hisat2 v2.0.4 (samtools 0.1.19)  with parameters -p 24, then sorted and converted to bed.
(Fr-1 ~ Fr-5) Sequence reads were scaled to their read counts using wiggletools "scale".
(Fr-1 ~ Fr-5) Bam data were converted to wig (bam2wig.py -t 8500000000 -u -s hg38.chrom.sizes) and evaluate Fr-5/Fr-1 ratio using wiggletools "ratio" and "log 2"
(RNA-seq) TPM of each gene was evaluated using sailfish (SailfishBeta-0.10.0_CentOS5) quant -p 20 -l SR, and -i "hg38 gene of ensembl76"
Genome_build: hg38
Supplementary_files_format_and_content: wig format data and tab-delimited text files include TPM of each gene

molecule: genomic DNA

source_name: HepG2 cells

growth_protocol: HepG2 cells were cultured in a minimum essential medium with alpha-modification supplemented with 10% fetal bovine serum.

extract_protocol:
Cell extracts for the chromatin fractionation were prepared as follows: treatment with formaldehyde, solubilization, and fragmentation by sonication. Total RNA was prepared using an RNeasy MinElute Cleanup Kit (#74204, Qiagen).
The DNA in the fractions was sheared with an LE220 Focused-ultrasonicator (Covaris), and converted to a sequence library using a KAPA Hyper Library Preparation Kit (KAPA Biosystems). Total RNA from HepG2 cells was converted to a sequence library using a KAPA Stranded mRNA-seq Kit (KAPA Biosystems).

value: hepatocyte carcinoma

tag: fractional distribution

value: the 4th upper  fraction


title: HepG2_Fr-3_Seq

tag: cell type

value: the 3rd upper  fraction


title: HepG2_Fr-2_Seq

value: the 2nd upper  fraction


title: 100626: Healthy individual, no Globin-Block 48


title: 4-cell (PMSG+48h+hCG)

value: Theiler stage 3; 2 days post fertilization

value: equivalent of 20 embryos with 4 cells each


title: E14_KO

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

department: Research center

country: China

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Neural progenitor cells

growth_protocol: Neural progenitors were isolated from WT and STAT3 conditional KO (Nes-cre driven) brains at embryonic day 11 and 14. Cells were cultured in suspension for 3 days before total RNA isolation.

extract_protocol:
Suspension cultured neural progenitors were collected by centrifugation at 400g for 5 min. RNA was harvested using Trizol reagent. cDNA was obtained using the M-MLV Reverse Transcriptase kit from Promega according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: embryonic stage

tag: genotype

value: Stat3 cKO


title: WGABS_10pg_old_2

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to mouse genome mm9 by bismark.
Only uniquely mapped reads were kept for down-stream analyses.
Calling of mC was performed by scripts in bismark.
Genome_build: mm9
Supplementary_files_format_and_content: bismark output cov files

source_name: human brain gDNA

extract_protocol:
DNA was purified using Qiagen's Puregene kit and sonicated to about 200 bp.
Methylated adapters were added with the NEBNext DNA library prep kit. Libraries were bisulfite converted with the Zymo EZ DNA Methylation Lightning kit.

tag: technology

value: WGA-BS

tag: dna amount

value: 10 pg


title: 2-cell late (PMSG+48h+hCG)

value: B6C3F1 x CD1

value: Theiler stage 2; 1 days post fertilization

value: equivalent of 20 embryos with 2 cells each


title: E11_WT

tag: strain

value: WT


title: Pico_4ng

source_name: mouse ESCs

value: BS-Seq

value: 4 ng


title: E14_WT


title: 2-cell early (PMSG+48h+hCG)

tag: age


title: CD4+T_Replicate1

description: Illumina Human HT-12 BeadArray

value: Peripheral Blood


title: WGABS_10pg_old_1


title: CD8+T_Replicate1

description: Illumina Human HT-12 BeadArray


title: 1-cell (PMSG+48h+hCG)

value: Theiler stage 1; 0 days post fertilization

value: equivalent of 20 embryos with 1 cell each


title: Monocyte derived macrophages, CF_rep6

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
Reads quality was evaluated using FastQC (version 0.11.2, Babraham Institute Cambridge, UK) tool.
After adapter trimming reads were mapped to the human Ensembl GRCh38 build reference genome using bowtie version 1.1.2. Then the coordinates are compared to miRBase annotation version 21 (Griffiths‐Jones et al, 2004).
This pipeline was performed using sRNAbench command line tool with “genome mapping mode” from sRNAtoolbox suite of software (Rueda et al., 2015).
Subsequently, the differential expressed microRNAs analysis was performed with the sRNAbenchDE pipeline from sRNAtoolbox suite. The module generates an expression matrix with and uses the R/Bioconductor package edgeR (Robinson et al., 2010) to infer differential expression.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: miRNA_abundances.txt (Tab-delimited text file includes sample abundance measurements output of the microRNA-level created with sRNAbenchDE tool)

source_name: monocyte derived macrophages

extract_protocol:
Total RNA was extracted using QIAGEN miRNeasy kit and treated with RNAse free DNAse set (QIAGEN)
Libraries were prepared for sequencing according to Illumina TruSeq Small RNA Library Preparation Kit.

tag: individual

value: cystic fibrosis (CF)

value: blood

value: monocyte derived macrophages


title: Rheb cKO_6

scan_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

source_name: Rheb cKO_epidermis

growth_protocol: Mouse epidermal tissue dissected frm E18.5 mouse embryos

extract_protocol: E18.5 embryonic littermates were manually classified as wild-type or Rheb cKO and were additionally validated by genotyping. Mouse epidermis was separated from the dermis following incubation of E18.5 embryonic skin with 3.8% Ammonium thiocynate for 10 minutes at room temperature. The epidermal sheet was homogenized in TRIzol and total RNA prepared using the TRIzol RNA extraction protocol.

tag: strain background

value: Rheb cKO

tag: developmental stage

value: epidermis


title: Rheb WT_3

source_name: Rheb WT_epidermis

treatment_protocol: Mouse epidermis was separated from the dermis following incubation of E18.5 embryonic skin with 3.8% Ammonium thiocynate for 10 minutes at room temperature.

tag: genotype/variation


title: Rheb cKO_5


title: Rheb WT_2

value: wild-type


title: oxBS_100ng_3

value: oxBS-Seq


title: Rheb cKO_4


title: Rheb WT_1


title: 100625: Healthy individual, no Globin-Block 47

value: no

value: Whole Blood


title: oocyte MII (PMSG+48h+hCG)

description:
equivalent of 20 oocytes (after superovulation, no mating)
oocytes were lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water; volume equivalent to 20 oocytes was used for labeling and hybridization

tag: ovarian stimulation

tag: genetic background

value: metaphase II, unfertilized

value: equivalent of 20 oocytes


title: oxBS_100ng_2


title: Monocyte derived macrophages, CF_rep5

tag: tissue


title: E11_KO

value: Stat3 cKO


title: Monocyte derived macrophages, CF_rep3


title: 100621: Healthy individual, no Globin-Block 43

tag: globin-block applied


title: 100622: Healthy individual, no Globin-Block 44

tag: identifier


title: 100623: Healthy individual, no Globin-Block 45


title: Control_gDNA_100ng

value: BS-Seq


title: WGABS_5cell

value: WGA-BS


title: 100624: Healthy individual, no Globin-Block 46


title: oxBS_100ng_1


title: 100619: Healthy individual, no Globin-Block 41


title: Monocyte derived macrophages, CF_rep4


title: oxBS_100ng_ctrl


title: Control_gDNA_10pg

value: 10 pg


title: 100620: Healthy individual, no Globin-Block 42


title: Monocyte derived macrophages, CF_rep2


title: WGABS_10pg_3


title: Control_gDNA_10pg_negative


title: Monocyte derived macrophages, CF_rep1


title: Monocyte derived macrophages, CTRL_rep6

value: control


title: 100618: Healthy individual, no Globin-Block 40


title: WGABS_10pg_2


title: 100617: Healthy individual, no Globin-Block 39


title: AAV-p-MAEGI

city: West Haven

first: Ryan

middle: D

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

description: 10x single cell RNA-seq (3' polyA capture), CD45+ cells isolated by FACS from E0771 tumors in C57BL/6J mice, treated by AAV-p-MAEGI

data_processing:
Raw sequencing output was  preprocessed by Cell Ranger 1.3 (10x Genomics) (Zheng et al., 2017b) using cellranger mkfastq, count, and aggr (no normalization mode). *I1*.fastq.gz = sample index, *R1*fastq.gz = cell barcode + UMI, *R2*.fastq.gz = transcript
Genome_build: mm10
Supplementary_files_format_and_content: tsne-loadings.MAEGI.txt: t-SNE embedding on cells with at least 2000 UMIs, after ALRA imputation. aggregated.counts.csv: aggregated raw count matrix from Cell Ranger

source_name: CD45+ cells within E0771 tumors

extract_protocol:
10x Genomics Chromium Single-cell 3' RNA-seq  (v2)
10x Genomics Chromium Single-cell 3' RNA-seq  (v2)

value: CD45+ cells within E0771 tumors

tag: treatment

value: AAV-p-MAEGI


title: Control_5cell_negative


title: 100616: Healthy individual, no Globin-Block 38

source_name: Whole Blood


title: AAV-Vector

description: 10x single cell RNA-seq (3' polyA capture), CD45+ cells isolated by FACS from E0771 tumors in C57BL/6J mice, treated by AAV-Vector

value: AAV-Vector


title: NMDA polyribosomes 3a

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description:
processed data header: 2905_NMDA
Synapt_Genes_proteinCoding_DE.tsv

data_processing:
Basecalls performed using CASAVA v1.8.2
Aligment STAR v 2.5.2b
The quality control, read processing and filtering, visualization of the results, and counting of reads for the Genecode vM6 basic annotation was performed using custom scripts utilizing elements of the HTseq, RSeQC, BEDtools and SAMtools packages.
Differential expression analyses between the NMDA-R stimulated (NMDA) polysome RNA and unstimulated Total RNA samples was performed using the DESeq2 Bioconductor R package.
Genome_build: mm10 (GRCm38)

source_name: synaptoneurosomes

extract_protocol:
polisomal fractions were separated on sucrose density gradient; ribo-depleted total RNA and polysome RNA were extracted using phenol/chloroform
RNA libraries were prepared according to TruSeq RNA Library Prep kit v2 protocol (Illumina, RS-122-2001, instruction number 15026495 Rev. D)

treatment_protocol: NMDA-R receptors on synaptoneurosomes were stimulated at 37°C using NMDA(50 µM)/glutamate(10 µM) mix for 30 sec, followed by addition of APV (120 µM) and incubation for 20 min

value: FVB

value: hippocampus& adjacent part of cortex

value: 6-8 weeks

tag: molecule

value: polyribosome


title: Monocyte derived macrophages, CTRL_rep4

value: blood

tag: cell type

value: monocyte derived macrophages


title: 100615: Healthy individual, no Globin-Block 37

description:
globinblock_rawcounts.csv
Outlier

data_processing:
Bases were called and samples demultiplexed with an Illumina 1.8+ pipeline.
Reads were aligned with STAR (2.5.2b-2) on usegalaxy.eu
Alignments were sumarized on transcript level by htseq-count (0.9.1) yielding raw counts and with StringTie (1.3.4d) yielding TPM. TPM values were not computed from the raw counts. The intention was to check if the findings hold irrespective of the read summarizer.
The summarized read tables were merged into one file using R and the data.table package.
Genome_build: GRCh38.87
Supplementary_files_format_and_content: Tab separated values (tsv) with EnsemblID transcripts, sample name (name of the raw data), if the sample was treated with Globin-Block (condition), and the ensembl gene ID and the gene name.

extract_protocol:
PAXgene Blood RNA Kit; Pellets from PAXgene Blood RNA Tubes are washed, resuspended, and incubated in optimized buffers together with proteinase K to digest proteins. Lysates are applied to a PAXgene 96 Filter Plate and centrifuged to remove residual cell debris. Ethanol is added to the flow-through to adjust binding conditions, and the lysates are applied to a PAXgene 96 RNA Plate. RNA is selectively bound to the PAXgene 96 RNA membrane as contaminants pass through. Residual DNA is removed through a DNase I digestion on the PAXgene 96 membrane. Remaining contaminants are removed in three efficient wash steps and RNA is eluted in Buffer BR5. (from manufacturer’s guide)
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit with 50 ng RNA input. Optional “Globin Block Module” used in samples with “yes” in the column “Globin Block applied”. Poly(A) RNA is reverse transcribed with poly(T)-Primers. RNA is digested and the second strand is synthesized by random priming. cDNA is purified. Illumina adapters are added. The PCR was run with 15 cycles.

value: no

value: Whole Blood


title: Monocyte derived macrophages, CTRL_rep5


title: NMDA polyribosomes 2a

description:
processed data header: 1609_NMDA
Synapt_Genes_proteinCoding_DE.tsv


title: unstim. Total 2b

description:
processed data header: 1609_Total
Synapt_Genes_proteinCoding_DE.tsv

value: total RNA


title: Monocyte derived macrophages, CTRL_rep3


title: NMDA polyribosomes 1a

description:
processed data header: 0310_NMDA
Synapt_Genes_proteinCoding_DE.tsv


title: Monocyte derived macrophages, CTRL_rep2


title: unstim. Total 1b

description:
processed data header: 0310_Total
Synapt_Genes_proteinCoding_DE.tsv


title: 8W_MI_Sham_s_rep2 [miRNA-seq]

city: Gwangju

first: Do Han

last: Kim

address: 123, Cheomdangwagi-ro, Buk-gu

country: South Korea

institute: Gwangju Institute of Science and Technology

description:
MI_Sham_8w-3_RPM
processed data file: miR_FC_P-val_RPM.txt

data_processing:
The reads from the sequencer were processed and aligned to Mus musculus (mm10) using Tophat v2.0.13 which incorporates the Bowtie v2.2.3 algorithm. After aligning the reads to the genome, Cufflinks v2.2.1 was used to assemble aligned reads into transcripts and to estimate their abundance. In case of other parameters for Tophat and Cufflinks, default options were used.
The preprocessed and clustered reads were aligned to Mus musculus matured and precursor miRNAs obtained from miRBase v21.
The relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) from Cufflinks. The reads for each miRNA were normalized by the total reads of each individual sample as the standardized to RPM (reads per million)
Genes with zeroed FPKM and RPM values in all samples were excluded. To facilitate log2 transformation, 1 was added to each FPKM and RPM value of filtered genes. Filtered data were log2-transformed and subjected to quantile normalization
Statistical significance of the differential expression data was determined using independent t-tests and fold changes in which the null hypothesis was that no difference exists among groups.
Genome_build: The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from the UCSC table browser. Mus musculus matured and precursor miRNAs obtained from miRBase v21.
Supplementary_files_format_and_content: tab-delimited text files include FPKM, RPM values for each Sample

source_name: 8W_MI_Sham_s_heart left ventricles

extract_protocol:
For RNA-sequencing, 1 μg of total RNA extracted from pooled mouse LV of MI or sham animals was used to construct cDNA libraries using the TruSeq RNA library kit (Illumina). For small RNA-sequencing, 1 μg of total RNA from the pooled LV of MI and sham was isolated using a miRNeasy Mini kit (Qiagen) and libraries were prepared using a TruSeq RNA library preparation kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: 8 Week Sham for MI

value: Heart left ventricles


title: 100614: Healthy individual, no Globin-Block 36

city: Kiel

first: Florian

last: Uellendahl-Werth

institute: Christian-Albrechts Universität zu Kiel

description:
globinblock_rawcounts.csv
Outlier


title: 8W_MI_Sham_s_rep3 [miRNA-seq]

description:
MI_Sham_8w-5_RPM
processed data file: miR_FC_P-val_RPM.txt


title: 100613: Healthy individual, no Globin-Block 35


title: 8W_MI_Sham_s_rep1 [miRNA-seq]

description:
MI_Sham_8w-1_RPM
processed data file: miR_FC_P-val_RPM.txt


title: 100612: Healthy individual, no Globin-Block 34


title: Monocyte derived macrophages, CTRL_rep1


title: WGABS_10pg_1

tag: technology

value: WGA-BS


title: 1W_MI_Sham_s_rep3 [miRNA-seq]

description:
MI_Sham_1w-5_RPM
processed data file: miR_FC_P-val_RPM.txt

source_name: 1W_MI_Sham_s_heart left ventricles

value: 1 Week Sham for MI


title: 1W_MI_Sham_s_rep2 [miRNA-seq]

description:
MI_Sham_1w-3_RPM
processed data file: miR_FC_P-val_RPM.txt


title: 1W_MI_Sham_s_rep1 [miRNA-seq]

description:
MI_Sham_1w-1_RPM
processed data file: miR_FC_P-val_RPM.txt


title: Normal 4

city: Miami

first: Maria

middle: E

last: Figueroa

state: FL

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

description:
59180_myCpG
Bisulfite sequencing (ERRBS)

data_processing:
Reads were created by CASAVA 1.8.2 from the HiSeq2000, and these are all reads which pass filter.
Reads were filtered from the adapter sequences using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website (2011) (https://github.com/seqan/flexbar).
Reads were aligned to whole genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained.
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X and at most 500X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis. *myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_myCpG.txt: Tab-delimited text files with the following column headers: chrBase chr base strand coverage freqC freqT.

source_name: Peripheral blood (PB) cells

extract_protocol:
Genomic DNA were isolated using the AllPrep DNA/RNA kit from Qiagen (Valencia, CA) according to manufacturer’s instructions.
ERRBS libraries were constructed as described in Akalin A et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet. 2012;8(6):e1002781.

value: Peripheral blood (PB) cells

tag: status of low-risk mds

value: Normal

tag: time point

tag: gender

value: not applicable

tag: wbc

tag: hgb

tag: plt

tag: bone marrow blast count

tag: mutation


title: Normal 3

description:
59178_myCpG
Bisulfite sequencing (ERRBS)

tag: age


title: unstim. Total 3b

description:
processed data header: 2905_Total
Synapt_Genes_proteinCoding_DE.tsv

tag: strain

tag: tissue


title: 1D_MI_Sham_s_rep3 [miRNA-seq]

description:
MI_Sham_1d-5_RPM
processed data file: miR_FC_P-val_RPM.txt

source_name: 1D_MI_Sham_s_heart left ventricles

value: 1 Day Sham for MI


title: 1D_MI_Sham_s_rep1 [miRNA-seq]

description:
MI_Sham_1d-1_RPM
processed data file: miR_FC_P-val_RPM.txt


title: 100610: Healthy individual, no Globin-Block 32

address: Rosalind-Franklin-Straße 12

tag: globin-block applied

tag: identifier


title: 1D_MI_Sham_s_rep2 [miRNA-seq]

description:
MI_Sham_1d-3_RPM
processed data file: miR_FC_P-val_RPM.txt


title: 100609: Healthy individual, no Globin-Block 31


title: Normal 2

description:
59176_myCpG
Bisulfite sequencing (ERRBS)


title: 8W_MI_s_rep3 [miRNA-seq]

description:
MI_8w-7_RPM
processed data file: miR_FC_P-val_RPM.txt

source_name: 8W_MI_s_heart left ventricles

value: 8 Week MI


title: Normal 1

description:
59174_myCpG
Bisulfite sequencing (ERRBS)


title: 8W_MI_s_rep2 [miRNA-seq]

description:
MI_8w-4_RPM
processed data file: miR_FC_P-val_RPM.txt


title: MSK058_Progressive_BL

description:
13205_myCpG
Bisulfite sequencing (ERRBS)

value: Progressive

value: baseline

value: male

value: No mutation

tag: patient id


title: 8W_MI_s_rep1 [miRNA-seq]

description:
MI_8w-2_RPM
processed data file: miR_FC_P-val_RPM.txt


title: 1W_MI_s_rep3 [miRNA-seq]

description:
MI_1w-6_RPM
processed data file: miR_FC_P-val_RPM.txt

source_name: 1W_MI_s_heart left ventricles

value: 1 Week MI


title: 1W_MI_s_rep2 [miRNA-seq]

description:
MI_1w-2_RPM
processed data file: miR_FC_P-val_RPM.txt


title: MSK045_Progressive_FU

description:
13199_myCpG
Bisulfite sequencing (ERRBS)

tag: cell type

value: follow-up


title: 1W_MI_s_rep1 [miRNA-seq]

description:
MI_1w-10_RPM
processed data file: miR_FC_P-val_RPM.txt

tag: Stage


title: 100607: Healthy individual, no Globin-Block 29

value: no

value: Whole Blood


title: 1D_MI_s_rep3 [miRNA-seq]

description:
MI_1d-9_RPM
processed data file: miR_FC_P-val_RPM.txt

source_name: 1D_MI_s_heart left ventricles

value: 1 Day MI


title: 100606: Healthy individual, no Globin-Block 28


title: 1D_MI_s_rep2 [miRNA-seq]

description:
MI_1d-4_RPM
processed data file: miR_FC_P-val_RPM.txt

value: Heart left ventricles


title: 100611: Healthy individual, no Globin-Block 33


title: 8W_MI_Sham_rep3

description:
MI_Sham_8w-5_FPKM
processed data file: Gene_FC_P-val_FPKM.txt

source_name: 8W_MI_Sham_heart left ventricles

value: 8 Week Sham for MI


title: 1D_MI_s_rep1 [miRNA-seq]

description:
MI_1d-2_RPM
processed data file: miR_FC_P-val_RPM.txt


title: MSK049_Progressive_FU

description:
13182_myCpG
Bisulfite sequencing (ERRBS)

value: female


title: 100604: Healthy individual, no Globin-Block 26


title: 8W_MI_Sham_rep2

description:
MI_Sham_8w-3_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: MSK043_Progressive_BL

description:
13178_myCpG
Bisulfite sequencing (ERRBS)

value: Peripheral blood (PB) cells


title: 8W_MI_Sham_rep1

description:
MI_Sham_8w-1_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: 100603: Healthy individual, no Globin-Block 25


title: 1W_MI_Sham_rep2

description:
MI_Sham_1w-3_FPKM
processed data file: Gene_FC_P-val_FPKM.txt

source_name: 1W_MI_Sham_heart left ventricles

value: 1 Week Sham for MI


title: MSK034_Stable_BL

description:
13174_myCpG
Bisulfite sequencing (ERRBS)

value: Stable

value: DNMT3A, TET1


title: 100602: Healthy individual, no Globin-Block 24


title: 1W_MI_Sham_rep3

description:
MI_Sham_1w-5_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: 100608: Healthy individual, no Globin-Block 30


title: 1D_MI_Sham_rep3

description:
MI_Sham_1d-5_FPKM
processed data file: Gene_FC_P-val_FPKM.txt

source_name: 1D_MI_Sham_heart left ventricles

value: 1 Day Sham for MI


title: MSK028_Stable_FU

description:
13172_myCpG
Bisulfite sequencing (ERRBS)


title: MSK061_Progressive_FU

description:
12907_myCpG
Bisulfite sequencing (ERRBS)

value: Progressive


title: 100601: Healthy individual, no Globin-Block 23


title: MSK035_Stable_FU

description:
13195_myCpG
Bisulfite sequencing (ERRBS)

value: Same


title: 100600: Healthy individual, no Globin-Block 22


title: 100605: Healthy individual, no Globin-Block 27


title: MSK041_Stable_FU

description:
12901_myCpG
Bisulfite sequencing (ERRBS)

value: male


title: 1D_MI_Sham_rep2

description:
MI_Sham_1d-3_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: 8W_MI_rep2

description:
MI_8w-4_FPKM
processed data file: Gene_FC_P-val_FPKM.txt

source_name: 8W_MI_heart left ventricles

value: 8 Week MI


title: 8W_MI_rep3

description:
MI_8w-7_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: 8W_MI_rep1

description:
MI_8w-2_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: 1D_MI_Sham_rep1

description:
MI_Sham_1d-1_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: MSK040_Stable_BL

description:
12899_myCpG
Bisulfite sequencing (ERRBS)

value: baseline

value: No mutation


title: 1W_MI_rep3

description:
MI_1w-6_FPKM
processed data file: Gene_FC_P-val_FPKM.txt

source_name: 1W_MI_heart left ventricles

value: 1 Week MI


title: 1W_MI_rep2

description:
MI_1w-2_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: MSK032_Stable_BL

description:
12897_myCpG
Bisulfite sequencing (ERRBS)

value: UNK

value: CBL


title: 100597: Healthy individual, no Globin-Block 19

value: no

value: Whole Blood


title: 100598: Healthy individual, no Globin-Block 20


title: 100599: Healthy individual, no Globin-Block 21


title: 1D_MI_rep3

description:
MI_1d-9_FPKM
processed data file: Gene_FC_P-val_FPKM.txt

source_name: 1D_MI_heart left ventricles

value: 1 Day MI

value: Heart left ventricles


title: MSK027_Stable_BL

description:
12895_myCpG
Bisulfite sequencing (ERRBS)

value: Peripheral blood (PB) cells

value: female


title: 1W_MI_Sham_rep1

description:
MI_Sham_1w-1_FPKM
processed data file: Gene_FC_P-val_FPKM.txt

value: 1 Week Sham for MI


title: 1D_MI_rep2

description:
MI_1d-4_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: 100596: Healthy individual, no Globin-Block 18


title: 1D_MI_rep1

description:
MI_1d-2_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: MSK048_Progressive_BL

description:
12500_myCpG
Bisulfite sequencing (ERRBS)


title: 100595: Healthy individual, no Globin-Block 17


title: 100594: Healthy individual, no Globin-Block 16


title: MSK039_Stable_FU

description:
12498_myCpG
Bisulfite sequencing (ERRBS)

value: Stable

value: follow-up


title: 1W_MI_rep1

description:
MI_1w-10_FPKM
processed data file: Gene_FC_P-val_FPKM.txt


title: MSK033_Stable_FU

description:
12496_myCpG
Bisulfite sequencing (ERRBS)

value: Same

value: NRAS


title: MSK024_Stable_BL

description:
12494_myCpG
Bisulfite sequencing (ERRBS)


title: MSK023_Stable_FU

description:
12492_myCpG
Bisulfite sequencing (ERRBS)

value: male


title: 100590: Healthy individual, no Globin-Block 12


title: MSK031_Stable_FU

description:
11260_myCpG
Bisulfite sequencing (ERRBS)

value: TET1, TET2


title: 100591: Healthy individual, no Globin-Block 13


title: MSK054_Progressive_BL

description:
11268_myCpG
Bisulfite sequencing (ERRBS)

value: Progressive

value: baseline

value: No mutation


title: MSK022_Stable_BL

description:
11256_myCpG
Bisulfite sequencing (ERRBS)


title: R3_T20

city: Kent

first: Manabu

last: Kurokawa

state: OH

address: 222 Cunningham Hall

institute: Kent State

hyb_protocol: Followed manufacturer's protocol (11322355 Rev. A)

data_processing: Illumina Genome Studio was used to generate normalized intensity ratios. Raw expression data was background corrected using detection p-values, quantile normalized, and log-transformed. Genes with no detected spots across all samples as determined by presence/absence calling were removed. Illumina IDs that mapped to the same gene symbol were collapsed by selecting the probe with the highest standard deviation across all samples.

growth_protocol: Cells grown in RPMI + 10% FBS

extract_protocol: Ambion RNAqueous

treatment_protocol: Cells treated with 1 uM lapatinibi for 0, 10, 20 hrs

tag: group

value: Drug Resistant

value: 20 Hr

tag: agent

value: lapatinib

tag: cell line


title: R4_T20

scan_protocol: Followed manufacturer's protocol (11322355 Rev. A)

tag: time point


title: S2_T20

label_protocol: Followed manufacturer's protocol (11322355 Rev. A)

value: Drug Naiive


title: S4_T20


title: 100589: Healthy individual, no Globin-Block 11

value: no

value: Whole Blood


title: S3_T20


title: R1_T20


title: R2_T20


title: R3_T10

value: 10 Hr


title: R4_T10


title: 100593: Healthy individual, no Globin-Block 15


title: R2_T10


title: S1_T20


title: 100592: Healthy individual, no Globin-Block 14


title: 100586: Healthy individual, no Globin-Block 9


title: S3_T10


title: S4_T10


title: S2_T10


title: R1_T10


title: 100587: Healthy individual, no Globin-Block 10


title: R3_T0

value: 0 hr


title: MSK056_Progressive_FU

description:
11226_myCpG
Bisulfite sequencing (ERRBS)

value: Peripheral blood (PB) cells

tag: status of low-risk mds

tag: gender

tag: wbc


title: 100585: Healthy individual, no Globin-Block 8


title: 100584: Healthy individual, no Globin-Block 7


title: MSK030_Stable_BL

description:
11220_myCpG
Bisulfite sequencing (ERRBS)

value: Stable

value: female

tag: hgb

tag: plt

tag: bone marrow blast count


title: MSK025_Stable_FU

description:
11216_myCpG
Bisulfite sequencing (ERRBS)

value: follow-up

tag: age

tag: mutation


title: R1_T0


title: MSK019_Progressive_FU

description:
11080_myCpG
Bisulfite sequencing (ERRBS)

value: KRAS, IDH2


title: 100583: Healthy individual, no Globin-Block 6

tag: globin-block applied

tag: tissue


title: R4_T0


title: 100581: Healthy individual, no Globin-Block 4

tag: identifier


title: R2_T0


title: S1_T10


title: S4_T0


title: MSK010_Stable_FU

description:
11078_myCpG
Bisulfite sequencing (ERRBS)

tag: cell type

tag: patient id


title: MSK008_Stable_FU

description:
11074_myCpG
Bisulfite sequencing (ERRBS)

value: male

value: Same


title: 100580: Healthy individual, no Globin-Block 3


title: MSK037_Stable_BL

description:
11222_myCpG
Bisulfite sequencing (ERRBS)

value: baseline


title: 100579: Healthy individual, no Globin-Block 2


title: MSK006_Stable_FU

description:
11072_myCpG
Bisulfite sequencing (ERRBS)


title: 100578: Healthy individual, no Globin-Block 1


title: 100582: Healthy individual, no Globin-Block 5


title: MSK017_Progressive_FU

description:
10925_myCpG
Bisulfite sequencing (ERRBS)

value: Progressive


title: S2_T0

tag: group


title: MSK009_Stable_BL

description:
11076_myCpG
Bisulfite sequencing (ERRBS)

value: No mutation


title: siMASTL_48h_rep4.

city: Turku

first: Elisa

last: Närvä

address: Tykistökatu 6

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

description: Replicate 4

hyb_protocol: Each cRNA (750 ng) was hybridized on HumanHT-12 v4 Expression Bead Chip microarray (Illumina Sentrix) at 58°C for 19 hours accordingly to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide protocol (part # 11322355, rev. A).

scan_protocol: Arrays were scanned with Illumina Bead Array Reader (Factor=1.0, PMT=520, Filter = 100 %) and results were processed with GenomeStudio v.2011.1; Gene Expression Module v.1.9.0.

data_processing: The data were preprocessed using the Bioconductor lumi package (Du et al 2008). Gene expression intensities were transformed using the variance stabilizing transformation (VST) and normalized using the quantile normalization method.

source_name: cell

label_protocol: RNA (500 ng) was amplified using Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) continued by in vitro transcription reaction and biotionylation. The quality of the cRNA was validated with electrophoresis (Agilent Bioanalyzer).

growth_protocol: human MDA-MB-231 (human triple-negative adenocarcinoma, ATCC) were cultured on Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich) supplemented with 10 % fetal bovine serum (FBS, Sigma), 2 mM l-glutamine (Sigma-Aldrich) and 1 % MEM non-essential amino acid solution (Sigma-Aldrich), in + 37°C, 5 % CO2.

extract_protocol: mRNA was extracted using Rneasy Mini Kit (Qiagen) including DNase digestion in column.

treatment_protocol: Transfections of siRNAs were performed by using Lipofectamine® RNAiMAX transfection reagent (Invitrogen) according to manufacturer’s protocol. The used siRNAs were AllStars Neg. Control siRNA (1027281, Qiagen), Hs_MASTL_6 FlexiTube siRNA (SI02653014, sequence ACGCCTTATTCTAGCAAATTA, Qiagen)

value: epithelial cell

tag: disease

value: breast adenocarcinoma

tag: timepoint

tag: sirna

value: MASTL


title: S3_T0

value: Drug Naiive

tag: time point

tag: agent

value: lapatinib

tag: cell line


title: S1_T0


title: siMASTL_24h_rep3.

description: Replicate 3


title: siControl_24h_rep2.

description: Replicate 2

value: control


title: siControl_48h_rep3.

description: Replicate 3


title: siMASTL_48h_rep1.

description: Replicate 1


title: siMASTL_48h_rep3.

description: Replicate 3


title: siControl_48h_rep4.

description: Replicate 4


title: MSK004_Stable_FU

description:
10918_myCpG
Bisulfite sequencing (ERRBS)

tag: status of low-risk mds

tag: gender

tag: wbc

tag: hgb


title: Co6

middle: Eugenia

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

institute: University of Miiami

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Adapter sequences were filtered out using the cutadapt software (Marcel Martin (2011)) (http://journal.embnet.org/index.php/embnetjournal/article/view/200)
Reads were aligned to the hg19 genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool.
Genome_build: hg19
Supplementary_files_format_and_content: The myCpG.txt is a tab-delimited text file that contains the location of the CpG, total read coverage on the C base, percentage of bisulfite-converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The column headers are: chrBase, chr, base, strand, coverage, freqC, freqT.

source_name: control_CD34+ fraction of Bone marrow

growth_protocol: We used a two-dimensional “monolayer” system to differentiate human pluripotent stem cells (iPS) into “primitive” hematopoietic progenitor cells (hHPCs) as described (Mills et al. 2014). On day minus 1, iPS clones  were cultured in 100 x 20 mm petri dishes in the presence of 0.5 mM EDTA to reach a 5-10% confluency. On day 0, StemMACS iPS-Brew XF medium was replaced by complete hematopoietic differentiation medium supplemented with 5 ng/ml BMP4 (Peprotech), 50 ng/ml VEGF165 (Peprotech) and 1 μM GSK-3β inhibitor (CHIR99021, Sigma Aldrich). On day 2, this medium was replaced by hematopoietic differentiation medium serum free medium mixed 1:1 with complete StemPro34 medium and supplemented with 1% nonessential amino acids, 1mM L-glutamine, 0.5mg/ml Penicillin-Streptomycin, 0.1mM β-Mercaptoethanol, 1% Insulin-Transferrin-Selenium (ThermoFisher Scientific), 10% bovine serum albumin (BSA, Hyclone, ThermoFisher Scientific) fraction V, and 50 μg/ml ascorbic acid (Sigma Aldrich). This medium was further supplemented with 5ng/ml BMP4, 50ng/ml VEGF165 and 20ng/ml of bFGF. This medium was replaced on day 4 by hematopoietic differentiation medium supplemented with 50ng/ml VEGF165 and 5ng/ml bFGF, on day 6 by hematopoietic differentiation medium supplemented with 50ng/ml VEGF165, 50ng/ml bFGF, 50ng/ml SCF, and 5ng/ml Flt3LG, and on day 8 by hematopoietic differentiation medium supplemented with 50 ng/ml VEGF165, 50ng/ml bFGF, 50ng/ml SCF, 5ng/ml Flt3LG, 10ng/ml Interleukin-6 (IL-6, Peprotech) and 50ng/ml thrombopoietin (TPO, kindly provided by Kirin, Japon). hHPCs sorted at day 10-16 (depending on cell expension) were suspended in serum-free medium supplemented with 50ng/ml SCF, 5ng/ml FLT3LG, 10ng/ml IL-3, 10ng/ml IL-6, 50ng/ml TPO, 1U/ml EPO, 10ng/ml GM-CSF, 10ng/ml G-CSF and 10ng/ml M-CSF (all from Peprotech) for 10 days, with this medium being renewed every 2 days.

extract_protocol:
Twenty-five ng of high-molecular weight genomic DNA of CD34+ from control or patient A iPS clones were used to perform the ERRBS assay as described (Park et al. 2014) and sequenced on a HiSeq 3000 Illumina sequencer
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012).

value: Healthy Control

value: bone marrow

value: CD34+C43+ iPSCs


title: siControl_48h_rep1.

description: Replicate 1


title: Co5


title: HPD1

first: Juan

last: Domínguez-Bendala

address: 1450 NW 10th Ave Miami

department: Department of Surgery

institute: Diabetes Research Institute, University of Miami, Miller School of Medicine

description: Cell specific Barcodes

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger v3.0.2 -mkfastq command
Subsequent UMI and cell barcode de-convolution along with mapping to respective genome was performed using 10X Genomics’ cellranger v3.0.2 software package to generate the final digital gene expression matrices
10X Output files were then converted into Seurat objects using Seurat v3.0.0, cells were thresholded, genes normalized and scaled.
Normalized data was used for principal component analysis and t-stochastic neighbour embedding analysis
Normalized data was integrated into a human pancreas single-cell transcriptome, and further comparitive analysis performed.
The barcode/UMI information is being captured in R1, while transcript/biological info is being captured in R2; UMI: 10bp + Barcode:16bp
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are tsv and mtx gene expression matrix files which are inputs for Seurat v3.0.0 for analysis
Supplementary_files_format_and_content: Supplementary files contain Cellranger output files, which have been renamed to ensure clarity. Change file names (of filtered information) to 'matrix.mtx.gz', 'barcodes.tsv.gz' and 'features.tsv.gz' after seperating files into donor specific folders. This is necessary, to allow Seurat to read these files. Seruat cannot read files named in their current form. Detailed information is available here: https://github.com/JDBLab/Pancreas_ductal_scRNAseq
Supplementary_files_format_and_content: alk3n3_gene_expression_matrix.csv: a gene expression count matrix of all the 3 samples compiled into one file.

source_name: Human Exocrine Pancreas

growth_protocol: Cells cultured overnight

extract_protocol:
Single live cells were extracted from cryopreservation buffer using a dead-cell removal kit (Miltenyi, USA)
Single cell RNA libraries were generated using the Chromium Single Cell 3’ kit (10X Genomics, CA, USA).
10x Genomics microfuidics mediated single cell RNA-seq

value: ALK3+ Cells

tag: number of cells

value: Exocrine Pancreas


title: siControl_24h_rep3.

description: Replicate 3


title: HPD2

description: Cell specific Barcodes


title: Post-THC-S2

city: New Haven

first: Ke

last: Xu

description:
SA1218-85_HHT
Single-cell RNAseq
processed data file: barcodes.tsv
processed data file: genes.tsv

data_processing:
The Cell Ranger Single-Cell Software Suite (versions 2.0.0 and 2.1.0 for the discovery and validation patients respectively) were used to perform sample demultiplexing, barcode processing and single-cell gene counting.
Only genes with at least one UMI count detected in at least one cell were retained for analysis; single cells were excluded when >10% of reads mapped to mitochondrial RNA t; cells with fewer than 370 expressed genes or greater than 100,000 reads were also discarded.
Data normalization was performed using a standard protocol in Seurate.
Batch effects were then removed using an empirical Bayesian framework (ComBat function in R package sva).
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes.tsv, Barcodes.tsv, and Matrix.mtx for each sample

source_name: PBMC

extract_protocol:
PBMCs from THC- (N=2) and THC+ samples (N=2) from fresh whole blood were isolated at the same time using a standard protocol. The cells were washed twice with phosphate-buffered saline containing 0.04% bovine serum albumin, and the final cell concentration was adjusted to 1000 cells/mL for library preparation. 5000 cells/sample were prepared for single cell capture.
We used the 10X Genomics Chromium Single Cell 3' v2.0 platform to prepare individually barcoded single-cell RNA-Seq libraries following the manufacturer’s protocol. Library size was confirmed with Agilent Bioanalyzer High Sensitivity DNA assay (PN:5067-4626), Invitrogen dsDNA HS qubit assay to evaluate dsDNA quantity (PN:Q32854), and KAPA qPCR analysis (KAPA Biosystems LIB Quant Kit, Illumina/LC480, PN:KK4854) to evaluate quantity of sequencable transcripts.

treatment_protocol: Subjects received 0.03 mg/kg of THC, the principal active ingredient of cannabis.

value: PBMC

tag: race

value: Caucasian

tag: age

tag: treatment

value: THC

tag: subject id


title: Pre-THC-S2

description:
SA1218-60_HHT
Single-cell RNAseq
processed data file: barcodes.tsv
processed data file: genes.tsv

tag: cell type

value: male


title: Co3

tag: tissue


title: siControl_24h_rep1.

description: Replicate 1

tag: disease


title: siMASTL_24h_rep1.

description: Replicate 1

tag: timepoint


title: Co1


title: MSK002_Stable_FU

description:
10915_myCpG
Bisulfite sequencing (ERRBS)

value: Peripheral blood (PB) cells

value: Stable

value: follow-up

value: female

tag: plt

tag: bone marrow blast count

tag: mutation

tag: patient id


title: MSK001_Stable_BL

description:
10914_myCpG
Bisulfite sequencing (ERRBS)

tag: status of low-risk mds

tag: time point

value: baseline

value: No mutation


title: MSK007_Stable_BL

description:
10821_myCpG
Bisulfite sequencing (ERRBS)

tag: gender

tag: wbc


title: K562-IR w/ imatinib, replicate 2

city: İzmir

first: Seda

last: Baykal Köse

address: İnciraltı

department: Medical Biology and Genetics

country: Turkey

institute: Dokuz Eylul University

description:
K562-IR, K562-derived drug resistant sub-clone, has been obtained in our laboratory via clonal selection under pressure of increasing doses of imatinib.
9389333061_H

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was exported from Illumina GenomeStudio as background corrected, and then preprocessed by Bioconductor lumi package (version 2.12.0). It was VST transformed and quantile normalized.

source_name: Imatinib resistant K562 cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol:
complete RPMI 1640
All the cells were cultured in the RPMI 1640 medium with %10 FBS and %1 penicilin/streptomycin (complete medium).

extract_protocol: Cells were collected in triplicate and embedded directly in RNAlater solution (Invitrogen, Ambion, #AM7021). RNA extractions were done by AROS Applied Biotechnology (Denmark) before the analysis.

treatment_protocol:
supplemented with 10µM imatinib continuously
imatinib dissolved in water was added in every new passage to be 10µM at final concentration into the resistant cell line culture flasks (except K562-IR w/o imatinib samples)

value: chronic myeloid leukemia cell

tag: cell line


title: MSK018_Progressive_BL

description:
10823_myCpG
Bisulfite sequencing (ERRBS)

value: Progressive

tag: hgb

value: NRAS


title: MSK015_Progressive_FU

description:
10923_myCpG
Bisulfite sequencing (ERRBS)

tag: age

value: SF3B1, EZH2, ASXL1, CBL


title: K562-IR w/ imatinib, replicate 3

description:
K562-IR, K562-derived drug resistant sub-clone, has been obtained in our laboratory via clonal selection under pressure of increasing doses of imatinib.
9389333061_L

value: bone marrow


title: K562-IR w/o imatinib, replicate 3

description:
K562-IR, K562-derived drug resistant sub-clone, has been obtained in our laboratory via clonal selection under pressure of increasing doses of imatinib.
9389333061_K

treatment_protocol: imatinib dissolved in water was added in every new passage to be 10µM at final concentration into the resistant cell line culture flasks (except K562-IR w/o imatinib samples)


title: Pre-THC-S1

description:
sa1184_HHT
Single-cell RNAseq
processed data file: barcodes.tsv
processed data file: genes.tsv

tag: race

tag: treatment


title: K562-IR w/ imatinib, replicate 1

description:
K562-IR, K562-derived drug resistant sub-clone, has been obtained in our laboratory via clonal selection under pressure of increasing doses of imatinib.
9389333061_D

tag: cell type


title: Post-THC-S1

description:
sa1184_65_HHT
Single-cell RNAseq
processed data file: barcodes.tsv
processed data file: genes.tsv

tag: subject id


title: MSK005_Stable_BL

description:
10819_myCpG
Bisulfite sequencing (ERRBS)


title: MSK003_Stable_BL

description:
10817_myCpG
Bisulfite sequencing (ERRBS)


title: A5

source_name: CMML_CD34+ fraction of Bone marrow

tag: disease

value: chronic myelomonocytic leukemia (CMML)

tag: tissue

value: CD34+C43+ iPSCs


title: A4


title: A3


title: MSK014_Progressive_BL

description:
9821_myCpG
Bisulfite sequencing (ERRBS)

source_name: Peripheral blood (PB) cells

tag: plt

value: SF3B1, EZH2, ASXL1


title: MSK016_Progressive_BL

description:
9823_myCpG
Bisulfite sequencing (ERRBS)

tag: bone marrow blast count


title: HiC CLL ID R2

city: New York

first: Nishana

last: Mayilaadumveettil

state: New York

address: 31st Street & East River DR, Receiving Department BLDG Smilow Floor 03, RM 307 (Jane Skok Laboratory)

department: Pathology

institute: NYU Langone health

description: HiC in cells treated with IAA and Dox for 4 days. Replicate 2 of 2

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the GRCm38/mm10 assembly of mouse genome using bowtie2
Reads with quality < 30 and duplicates were removed using Samtools/1.3 for ChIP-seq
Peaks were called using Macs/1.4
rwas counts were obtained using Htseq in genes for RNAseq or peaks for ChIP-seq
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization.

source_name: CLL ID

growth_protocol: Mouse embryonic stem cells E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and all clones derived from these were cultured under feeder-free conditions in 0.1% gelatin (Sigma ES-006-B) coated dishes (Falcon, 353003) at 37°C and 5% CO2 in a humidified incubator. The cells were grown in DMEM (Thermo Fisher, 11965-118) supplemented with 15% fetal bovine serum (Thermo Fisher, SH30071.03), 100 U/ml penicillin - 100 μg/ml streptomycin (Sigma, P4458), 1 X GlutaMax supplement (Thermo Fisher, 35050-061), 1 mM sodium pyruvate (Thermo Fisher, 11360-070), 1 X MEM non-essential amino-acids (Thermo Fisher, 11140-50), 50 μM b-mercaptoethanol (Sigma, 38171), 104 U/ml leukemia inhibitory factor (Millipore, ESG1107), 3 μM CHIR99021 (Sigma, SML1046) and 1 μM MEK inhibitor PD0325901 (Sigma, PZ0162). The cells were passaged every alternate day by dissociation with TrypLE (Thermo Fisher, 12563011).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen 74104) as per the manufacturer's protocol.
ChIP-seq libraries were constructed using the Illumina Nextera DNA Sample prep kit. RNA seq libraries were prepared using standard Illumina protocols. Hi-C libraries were prepared as per the Arima kit guidelines.

treatment_protocol: For degradation of endogenous CTCF, 500 μM indole-3-acetic acid/IAA (Sigma, I5148) was added to the media. Expression of transgenes were achieved by the addition of doxycycline (Dox, 1 μg/ml) (Sigma, D9891) to the media. The cells were treated with IAA and/or Dox for 2 days for RNA seq and ChIP seq and 4 days for HiC.

value: Mouse embryonic stem cells

tag: parental cell line

tag: strain

value: 129/Ola, XY

tag: genotype/variation

value: CTCF-AID, Tir1, Flag-CLL-mRuby 2 transgene at Tigre

tag: kit

value: Arima


title: Spindle-shaped K562-IR cells, replicate 3

description:
K562-IR, K562-derived drug resistant sub-clone, has been obtained in our laboratory via clonal selection under pressure of increasing doses of imatinib.
9389333061_J

source_name: Spindle-shaped imatinib resistant K562 cell line


title: BisSeq_MLV_virions_rep2

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description:
bisulfite-treated RNA from MLV virions
BisSeq_pNCA_proviral.txt
viral_m5C_position_fraction.txt
virion RNA

data_processing:
Adapter sequences and reads less than 30 bases were removed using the program FastX clipper.
Reads were mapped to a bisulfite-converted version of the pNCA proviral sequence (i.e., all cytosines were changed to thymines) using Bowtie 1, allowing for up to three mismatches. To more easily visualize on the IGV browser, a randomly selected subset of 10 million clipped reads was aligned to the MLV sequence.Candidate m5C sites were identified using the bam-readcount tool and visually inspected on the IGV browser.
Supplementary_files_format_and_content: tab-delimited text file showing the m5C fraction of candidate m5C sites on the MLV genome; text file of bisulfite-converted MLV proviral sequence used for alignment

organism: Murine leukemia virus

source_name: murine leukemia virus

growth_protocol: Mouse embryonic fibroblasts (NIH3T3 cells; ATCC) were cultured in DMEM containing 100 U/mL penicillin-streptomycin, 10% fetal bovine serum, and 2 mM L-glutamine.

extract_protocol:
To prepare virus for bisulfite sequencing, viral particles were first concentrated by sedimenting filtered media from infected cells through 2-mL cushions of 20% sucrose and viral RNAs isolated using Trizol (Invitrogen. For infected cellular samples, total RNA was extracted in Trizol.
Cellular and viral RNAs were DNase treated. Additionally, cellular samples were subjected to RiboMinus (Thermo) treatment to deplete ribosomal RNAs. The Zymogen EZ RNA Methylation kit protocol was followed to convert unmethylated cytosines to uracil. Recovered RNA was used to generate sequencing libraries with the TruSeq Stranded mRNA kit (Illumina). cDNA libraries were amplified by 12 cycles of PCR, loaded onto a HiSeq 2000 Illumina sequencer, and sequenced for 100 bases at The University of Chicago Genomics Facility.
RNA bisulfite sequencing

treatment_protocol: NIH3T3 cells were infected (20:1 multiplicity of infection) with murine leukemia virus (MLV) particles produced from HEK293T cells in media containing 8 μg/mL hexadimethrine bromide (Polybrene; American Bioanalytical).

tag: passages


title: K562-IR w/o imatinib, replicate 1

description:
K562-IR, K562-derived drug resistant sub-clone, has been obtained in our laboratory via clonal selection under pressure of increasing doses of imatinib.
9389333061_C


title: Spindle-shaped K562-IR cells, replicate 2

description:
K562-IR, K562-derived drug resistant sub-clone, has been obtained in our laboratory via clonal selection under pressure of increasing doses of imatinib.
9389333061_F


title: Dog 3: Canine primary sublingual epithelial cells, 20 µg/ml D. farinae extract + 0.1 µM calcitriol (D3C4)

city: Merelbeke

first: Michael

last: Pelst

address: Salisburylaan 133

country: Belgium

institute: Ghent University

data_processing:
Sequencing read quantity and quality was checked using FastQC (v0.11.8). Contamination was determined using FastQ Screen (v0.14.0). Adapter trimming and removal of reads having a quality score lower than 20 or containing any ambiguities, was done using cutadapt (v2.5). The remaining high-quality reads were mapped on the CanFam3.1 reference dog genome using STAR (v2.7.2) and features were count at the gene level using RSEM (v1.3.1).
Differential expression analyses of the RNA-sequencing data were done in R using the edgeR (v3.26.8) package. For each analysis, feature counts were normalized using edgeR’s standard normalization method.
To remove uninformative low-count features, those having less than 1 cpm (counts per million) in the number of samples equivalent to the size of the smallest group were discarded.
Statistical testing was done by fitting a general linear model, followed by a quasi-likelihood F-test.
Differentially expressed features were considered statistically significant when having a fold-change of at least 2 (doubling or halving between the compared groups) and a false discovery rate (FDR or adjusted p-value according to Benjamini-Hochberg) smaller than or equal to 0.05.
Genome_build: CanFam3.1 reference dog genome
Supplementary_files_format_and_content: xlsx

organism: Canis lupus familiaris

source_name: Epithelial cells isolated from the sublingual mucosa

growth_protocol: Sublingual biopsies of approximately 0.5x0.5 cm were sampled within 3 hours after euthanasia from 6 privately-owned dogs that were euthanized for medical reasons unrelated to the study (Supplementary Table A). Oral consent to use the corpse for scientific purposes was given by all dog owners. Of one dog, one half of the sublingual biopsy was processed for immunohistochemistry. This sample was submerged in Methocel® MC (Merck), snap-frozen in liquid nitrogen and stored at -80°C. To isolate sublingual cells, biopsies were briefly submerged in 70% ethanol, washed 3 times with Ca2+- and Mg2+-free Dulbecco’s PBS (DPBS, Thermofisher Scientific, Waltham, MA, USA) and incubated in 4 mg/ml Dispase II (Thermofisher Scientific) in DPBS on ice. After 16-24h incubation, the epithelial layer was carefully separated from the underlying subepithelial tissue, followed by incubation of the epithelial and subepithelial tissue in DPBS with 0.25% trypsin (Thermofisher Scientific) and 2.65 mM EDTA for 20 min at room temperature (RT; 18-22°C). Subsequently, cell suspensions were resuspended, trypsin was neutralized with an equal volume of 5% fetal calf serum (FCS) (Merck, Burlington, MA, USA) in DPBS and the cells were filtered over a 70 µm cell strainer (Merck). After centrifugation (400g, 10 min, 18°C), cells were counted and 2.5x105 cells/cm2 were seeded in a culture flask in sublingual epithelial cell culture medium (SECCM; ¾ DMEM, ¼ nutrient mixture F12-Ham (Thermofisher Scientific), 5% FCS, 2 nM 3,3’,5-triiodo-L-thyronine sodium salt, 5 µg/ml recombinant human insulin, 10 ng/ml recombinant human epidermal growth factor, 0.4 µg/ml hydrocortisone, 100 nM L-isoproterenol hydrochloride (Merck), 100 U/ml penicillin, 100 µg/ml streptomycin and 100 µg/ml gentamicin (Thermofisher Scientific)) (27,28). During the first 7 days of culture, the SECCM was supplemented with 2.5 µg/ml amphotericin B (Thermofisher Scientific) and medium was changed daily. Thereafter, medium was replaced every 2-3 days. Cells were expanded, split (0.25% trypsin, 1 mM EDTA in DPBS) at 70-90% confluency and used at passage 2-7 for the experiments. The sublingual epithelial cells were shown to be free of Mycoplasma infection during routine testing using the LookOut® Mycoplasma PCR Detection Kit (Merck) according to the manufacturer’s instructions.

extract_protocol:
RNA extraction and DNase treatment of the samples was performed using the RNeasy mini kit (Qiagen) and RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions. Extracted RNA was stored at -80°C.
Total RNA concentration was measured using the Quant-iT RiboGreen RNA Assay Kit (Thermofisher Scientific). RNA quality was inspected using an RNA 6000 Nano chip on a BioAnalyser (Agilent Technologies, Santa Clara, CA, USA). For each sample, a sequencing library was constructed using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) starting from 500 ng total RNA and amplified by 14 PCR cycles. Quality and size distribution of the libraries were checked on a BioAnalyser (Agilent Technologies) using the high sensitivity Quant-iT dsDNA Assay Kit (Thermofisher Scientific) and a High Sensitivity DNA chip. Library concentration was determined according to Illumina’s Sequencing Library qPCR Quantification Guide on a LightCycler 480 (Roche Life Science, Penzberg, Germany).

treatment_protocol: Canine primary sublingual epithelial cells were seeded in SECCM in a 24-well plate at 30,000 cells/well and incubated overnight at 37°C and 5% CO2. Thereafter, Dermatophagoides farinae extract, TLR ligands, calcitriol or control medium was added for 24h to the cultured cells, the supernatant was collected and stored at -20°C. The products, listed in Table 1, were added in a volume of 400 µl sublingual epithelial cell stimulation medium (SECSM) (¾ DMEM, ¼ Ham’s F-12, 100 U/ml penicillin, 100 µg/ml streptomycin and 100 µg/ml gentamicin). Since calcitriol was dissolved in ethanol, the control wells for calcitriol contained an equal volume of this solvent. To analyze the effect of D. farinae extract in combination with calcitriol, cells were incubated without stimulus, with 20 µg/ml D. farinae extract or with both D. farinae extract and 0.1 µM in SECSM. Additionally, after 6h incubation with 0.1 µM calcitriol and 20 µg/ml D. farinae extract, sublingual epithelial cells were lysed in RLT buffer (RNeasy mini kit, Qiagen, Hilden, Germany) and stored at -80°C.

tag: sample id

value: Dog 3

value: 20 ug/ml D. farinae extract + 0.1 uM calcitriol


title: A1


title: K562, replicate 3

description:
Standard K562 cell line incubated in complete media
9389333061_I

source_name: K562, a BCR-ABL-positive human CML cell line (ATCC)

tag: cell line


title: K562-IR w/o imatinib, replicate 2

description:
K562-IR, K562-derived drug resistant sub-clone, has been obtained in our laboratory via clonal selection under pressure of increasing doses of imatinib.
9389333061_G


title: Dog 5: Canine primary sublingual epithelial cells, 20 µg/ml D. farinae extract + 0.1 µM calcitriol (D5C4)

value: Dog 5

value: Epithelial cells isolated from the sublingual mucosa


title: Spindle-shaped K562-IR cells, replicate 1

description:
K562-IR, K562-derived drug resistant sub-clone, has been obtained in our laboratory via clonal selection under pressure of increasing doses of imatinib.
9389333061_B


title: Dog 4: Canine primary sublingual epithelial cells, 20 µg/ml D. farinae extract + 0.1 µM calcitriol (D4C4)

value: Dog 4


title: HiC CLL ID R1

description: HiC in cells treated with IAA and Dox for 4 days. Replicate 1 of 2


title: Normal Control Donor Serum Sample 22

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters, PMT of 600, and a pixel size of 5um.

data_processing:
The GPR files were imported into Invitrogen's Prospector v5.2.3 microarray analysis software.  Individual results were characterized into disease and control groups and then linearly normalized for group-to-group analysis of differential expression.  Further significance analysis was performed using Random Forest (RF).
[Matrix files]  Normalized fluorescence intensities are presented in Relative Fluorescent Units (RFUs).

label: Alexa Fluor 647

molecule: other

source_name: Normal Control Donor Serum Sample 22

label_protocol: Probing and analysis of microarrays was performed with strict adherence to suggested manufacturer protocols.  (See Invitrogen and Molecular Devices online.)

extract_protocol: All STRIDE hip fracture repair plasma samples were provided by Johns Hopkins University, and all control serum samples were purchased from BioServe, a commercial biofluid repositiory. All samples were drawn and stored under proper conditions, and collected and used with IRB approval.

tag: individual

value: control

tag: gender

value: FEMALE

tag: sample type

value: serum


title: K562, replicate 2

description:
Standard K562 cell line incubated in complete media
9389333061_E

value: chronic myeloid leukemia cell


title: BisSeq_MLV_virions_rep1


title: ChIP CTCF ID M2

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 48 h. Mock treated with DMSO befpre ChIP.  Replicate 2 of 2

source_name: CTCF ID + Mock treatment

value: CTCF-AID, Tir1, Flag-CTCF-mRuby 2 transgene at Tigre

value: Nextera

tag: chip antibody

value: Anti-Flag M2 Magnetic Beads; Sigma (M8823)


title: K562, replicate 1

description:
Standard K562 cell line incubated in complete media
9389333061_A

tag: cell type

value: bone marrow


title: Dog 4: Canine primary sublingual epithelial cells, 0.1 µM calcitriol (D4C3)

tag: treatment

value: 0.1 uM calcitriol


title: Normal Control Donor Serum Sample 23

source_name: Normal Control Donor Serum Sample 23

tag: age


title: Normal Control Donor Serum Sample 20

source_name: Normal Control Donor Serum Sample 20

value: MALE


title: ChIP CTCFL ID M2

source_name: CTCFL ID + Mock treatment

tag: tissue

value: Mouse embryonic stem cells

value: 129/Ola, XY

value: CTCF-AID, Tir1, Flag-CTCFL-mRuby 2 transgene at Tigre


title: ChIP CTCF ID R2

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 48 h. Chromatin was treated with Rnase befpre ChIP.  Replicate 2 of 2

source_name: CTCF ID + Rnase treatment


title: Dog 5: Canine primary sublingual epithelial cells, 0.1 µM calcitriol (D5C3)


title: ChIP CTCF ID R1

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 48 h. Chromatin was treated with Rnase befpre ChIP.  Replicate 1 of 2


title: A2

tag: disease

value: chronic myelomonocytic leukemia (CMML)

value: CD34+C43+ iPSCs


title: ChIP CTCFL ID M1

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 48 h. Mock treated with DMSO befpre ChIP.  Replicate 1 of 2


title: Normal Control Donor Serum Sample 25

source_name: Normal Control Donor Serum Sample 25


title: Normal Control Donor Serum Sample 24

source_name: Normal Control Donor Serum Sample 24


title: Dog 1: Canine primary sublingual epithelial cells, 20 µg/ml D. farinae extract + 0.1 µM calcitriol (D1C4)

value: Dog 1

value: Epithelial cells isolated from the sublingual mucosa

value: 20 ug/ml D. farinae extract + 0.1 uM calcitriol


title: Dog 2: Canine primary sublingual epithelial cells, 20 µg/ml D. farinae extract + 0.1 µM calcitriol (D2C4)

value: Dog 2


title: Dog 3: Canine primary sublingual epithelial cells, 0.1 µM calcitriol (D3C3)

value: Dog 3


title: ChIP CTCF ID M1


title: JSC15-3 shALDH1A3 #3

city: Tokyo

first: Ryuhei

last: Kawakami

address: 3-8-31, Ariake,Koto-ku

institute: JFCR

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

source_name: Human Patient-derived Gastric Cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: Patient-derived gastric cancer cells were cultured in vitro in dishes and then total RNA was isolated.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: 5-FU: 3 mM, 7-day treatment (JSC15-3), 3 mM, 6-day treatment (JSC17-2) and 1 mM, 6-day treatment (JSC17-7) | SN38: 30 nM,  7-day treatment (JSC15-3) | shRNAs: introduced by using lentivirus and selected by 1 mg/mL puromycin for 8 days (JSC15-3)

value: Patient-derived Gastric Cancer

value: shALDH1A3 #3


title: HiC LCL ID R2

description: HiC in cells treated with IAA and Dox for 24 h. Replicate 2 of 2

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the GRCm38/mm10 assembly of mouse genome using bowtie2
Reads with quality < 30 and duplicates were removed using Samtools/1.3 for ChIP-seq
Peaks were called using Macs/1.4
raw counts were obtained using Htseq in genes for RNAseq or peaks for ChIP-seq
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization.

source_name: LCL ID

value: mouse ES cells E14Tg2a

value: CTCF-AID, Tir1, Flag-LCL-mRuby 2 transgene at Tigre

value: Arima

tag: agent

value: IAA and Dox

tag: time point


title: Normal Control Donor Serum Sample 21

source_name: Normal Control Donor Serum Sample 21

value: control

value: MALE

value: serum


title: ChIP CTCFL ID R2

source_name: CTCFL ID + Rnase treatment

value: Mouse embryonic stem cells

tag: parental cell line

tag: strain

value: 129/Ola, XY

value: CTCF-AID, Tir1, Flag-CTCFL-mRuby 2 transgene at Tigre

value: Nextera

value: Anti-Flag M2 Magnetic Beads; Sigma (M8823)


title: Dog 2: Canine primary sublingual epithelial cells, 0.1 µM calcitriol (D2C3)

value: Epithelial cells isolated from the sublingual mucosa

value: 0.1 uM calcitriol


title: Dog 4: Canine primary sublingual epithelial cells, 20 µg/ml D. farinae extract (D4C2)

value: Dog 4

value: 20 ug/ml D. farinae extract


title: Dog 1: Canine primary sublingual epithelial cells, 0.1 µM calcitriol (D1C3)

value: Dog 1