title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-5UP)

value: Male

value: Duplication

value: Description:very nice biopsy, variation in fiber size and several hypercontracted or centrally nucleated fibers. We also found focal fatty replacement and many areas of attempted regeneration, characteristic of an early stage dystrophy


title: SW-69 (297A-A2NW)

status: Public on Jan 14 2018

type: RNA

city: Chicago

first: Steven

middle: R

last: White

state: IL

address: 5841 S. Maryland Ave

department: Medicine

country: USA

institute: University of Chicago

description:
Mechanical injury: Mechanical injury (MI) was produced by rake tines which were 0.3 mm in diameter and spaced 0.4 mm apart). Cells then were washed in culture medium to remove debris and incubated for 8 or 24 hr in standard medium. Control cells without MI were collected at the same time intervals.  Cyclic stretch (CS) injury was performed using FX-4000T Flexcell Tension Plus system 18% elongation, at 0.5 Hz continuously for either 8 or 24 hr. Control cells were incubated on BioFlex plates for the same time intervals but not subjected to CS. For dual injury, cells were seeded (1 x 106 cells/well) onto collagen-IV coated flexible bottom BioFlex plates. When confluent, plates were washed with culture medium and mechanical rake injury done as in preceding experiments prior to mount plates into the Flexcell system and exposed to CS of the desired magnitude and durations.
Cell culture: Primary human airway epithelial cells (AEC) in submersion and differentiated airway epithelial cells (dAEC) in air liquid interface culture system were grown and maintained as described (White SR et al., Am J Physiol Lung Cell Mol Physiol 2008;295(6):L1018-1027; 2009;297(1):L164-173; 2010; 299(5): L681â€“L693).
Cell ID: Cell ID refers to a number assigned based on the collection from a donor human lung. Cells with the same ID number came from the same lung at the same time.
Culture condition: Condition refers to submersion or air liquid interface as described in cell culture references. All cells in ALI were grown in this for 3 weeks. All cells in submersion were grown to > 95% confluence.
Mechanical injury: Mechanical injury (MI) was produced by rake tines which were 0.3 mm in diameter and spaced 0.4 mm apart). Cells then were washed in culture medium to remove debris and incubated for 8 or 24 hr in standard medium. Control cells without MI were collected at the same time intervals.  Cyclic stretch (CS) injury was performed using FX-4000T Flexcell Tension Plus system 18% elongation, at 0.5 Hz continuously for either 8 or 24 hr. Control cells were incubated on BioFlex plates for the same time intervals but not subjected to CS. For dual injury, cells were seeded (1 x 106 cells/well) onto collagen-IV coated flexible bottom BioFlex plates. When confluent, plates were washed with culture medium and mechanical rake injury done as in preceding experiments prior to mount plates into the Flexcell system and exposed to CS of the desired magnitude and durations.
Cell culture: Primary human airway epithelial cells (AEC) in submersion and differentiated airway epithelial cells (dAEC) in air liquid interface culture system were grown and maintained as described (White SR et al., Am J Physiol Lung Cell Mol Physiol 2008;295(6):L1018-1027; 2009;297(1):L164-173; 2010; 299(5): L681â€“L693).
Cell ID: Cell ID refers to a number assigned based on the collection from a donor human lung. Cells with the same ID number came from the same lung at the same time.
Culture condition: Condition refers to submersion or air liquid interface as described in cell culture references. All cells in ALI were grown in this for 3 weeks. All cells in submersion were grown to > 95% confluence.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GenomeStudio software licensed by Illumina Inc.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human asthmatic airway epithelial cell

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: human asthmatic airway epithelial cell

tag: cell id

tag: culture condition

value: air-liquid interface culture

tag: injury duration hr

tag: mechanical injury

value: Sham


title: Asynchronous remodeling in DMD (MIDO-DYS_Pos-6UP)

city: DC

first: mamta

last: giri

state: Washington. DC

address: 111 Michigan Ave

department: Center for Genetic Medicine

institute: CNMC

hyb_protocol: hybridized to Affymetrix microarrays,

scan_protocol: Standard Affymetrix protocol

data_processing: Expression console, Partek Genomics Suite, HCE 3.0

label: Biotin

source_name: vastus lateralis

label_protocol: Ten micrograms of total RNA was then reverse-transcribed into double stranded cDNA using a T7-oligo-dT primer, and cRNA was produced using two biotinylated nucleotide precursors. A 4-fold amplification of starting material (total RNA) to biotinylated cRNA was set as the minimum threshold for continuing with microarray hybridizations

extract_protocol:
Biopsies were taken generally at the time of diagnosis and were typically from the vastus lateralis
RNA was isolated using standard Trizol reagent and methods, and quality of RNA was assessed by gel electrophoresis and/or Agilent Bioanalyzer

tag: age

value: vastus lateralis

tag: pathology

value: severe

tag: Sex

value: F

tag: mutation

value: 2 found

tag: pathology note

value: nice biopsy, considerable fatty replacement, remaining fascicles show a DYSTROPHIC picture.


title: SW-71 (468A-A2NW)


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-7UP)

value: Description:nice biopsy, small rounded fibers with frequent central nuclei, increased endomysial fibrosis, several areas of focal inflammation, necrotic cells, degeneration, early stage dystrophy


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-17UP)

value: Description:nice biopsy, severe dystrophy, endomysial fibrosis, degen/regen, fiber size variation.


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-6UP)

value: moderate

value: Description:very nice biopsy, fiber size variation, hypercontracted fibers, cells with central nuclei, small areas of active regen and necrosis, ealry stage dystrophy


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-3UP)

value: Description:Very nice biopsy, fiber size variation, several necrotic fibers and large areas of grouped regeneration, numerous central nuclei, one large area of all rounded fibers, mid stage dystrophy


title: Asynchronous remodeling in DMD (MIDO-DYS_Neg-5UP)

value: mild

value: Mutaion found by exome seq

value: Nice biopsy, although artifactual space between fibers. Mild dystrophy/myopathy. Mild fiber size variation, few central nuclei.


title: Asynchronous remodeling in DMD (MIDO-DYS_Pos-2UP)

value: mod

value: M

value: 1 found

value: nice biopsy, dysferlin-like with inflammation (both vascular, endomysial, and necrotic fibers). many fibers with infiltrating cells; great for a pathology study of inflammatory cells types.


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-4UP)

value: vastus lateralis

value: Male

value: nice biopsy, severe dystropy, fiber size variation, necrotic fibers, regeneration


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-16UP)

value: severe

value: Description:nice biopsy, severe dystrophy, fiber size variation, necrosis, fibrosis


title: SW-66 (483A-S2NW)

value: human asthmatic airway epithelial cell

value: submersion

value: Sham


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-15UP)

value: moderate

value: Duplication

value: nice biopsy, fiber size variation, endomysial fibrosis. looks relatively mild for DMD with larger fibers with less endomysial fibrosis than typical


title: SW-65 (468A-S2NW)


title: SW-64 (312A-S2NW)


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-13UP)

value: Description:good condition. It showed fiber size variation, many hypercontracted fibers, cells with central nuclei, numerous areas of active regeneration and several necrotic fibers, mid stage dystrophy


title: SW-67 (267A-A2NW)

value: air-liquid interface culture


title: SW-72 (483A-A2NW)


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-10UP)

value: Description:nice biopsy, severe mid/end stage dystrophy, very extensive fibrosis (endomysial, perimysial). A strange large fibrotic blood vessel with a second fibrotic blood vessel inside of it? Fiber size variation, rounded fibers, failed regeneration


title: SW-63 (297A-S2NW)


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-11UP)

value: Description:nice biopsy, young child with DYSTROPHIC process, central nuclei, fiber size variation


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-12UP)

value: Exon 3-6 deletion

value: nice biopsy, dystrophic, fiber size variation, degen/regen, focal fatty infiltration and fibrosis, many fascicles with little or no endomysial fibrosis


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-1UP)

value: vastus lateralis

value: nice biopsy, DMD like, degen/regen, endomysial fibrosis


title: Asynchronous remodeling in DMD (MIDO-CTRL_Pos-5UP)

description: Normal


title: SW-74 (268A-S8NW)


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-9UP)

value: Male

value: Description:nice biopsy, mid stage severe dystrophy, fiber size variation, endomysial fibrosis, fiber size variation, failed regeneration


title: Asynchronous remodeling in DMD (MIDO-CTRL_Pos-3UP)

description: Normal


title: SW-62 (268A-S2NW)


title: SW-60 (483A-A0NW)


title: Asynchronous remodeling in DMD (MIDO-CTRL_Pos-2UP)

description: Normal


title: Asynchronous remodeling in DMD (MIDO-CTRL_Pos-6UP)

description: Normal


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-8UP)

value: M

value: Deletion Exons 13-41

value: Good (#2 Description:Myopathic, 2nd:nice biopsy, fiber size variation, variable fibrosis, minor fatty replacement, numerous central nuclei, areas of degen/regen


title: SW-61 (267A-S2NW)

value: human asthmatic airway epithelial cell

value: submersion

value: Sham


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-6UP)

value: mild

value: Deletion Exons 45-53

value: nice biopsy, variable endomysial fibrosis, many hypercontracted fibers, central nuclei, early stage DYSTROPHIC


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-1UP)

value: Deletion Exons 48-49

value: nice biopsy; very mild dystrophy; some fiber size variation; few focal areas have increased fibrosis


title: SW-58 (312A-A0NW)

value: air-liquid interface culture


title: Asynchronous remodeling in DMD (MIDO-CTRL_Pos-4UP)

description: Normal


title: SW-57 (297A-A0NW)


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-3UP)

value: Deletion Exons 45-47

value: excellent condition. It showed fiber size variation, mild fibrosis, numerous central nuclei, 1-2 hypercontracted fibers, and a few small areas of regeneration. This pathology is characteristic of an early stage dystrophy


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-15UP)

value: vastus lateralis

value: Duplication Exons 51-55

value: nice biopsy, mild dystrophy with many central nuclei. Not much endomysial fibrosis, but more extensive perimysial fibrosis/fatty replacement. No overt degeneration.


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-14UP)

value: severe

value: M

value: Deletion Exons 61-79

value: Biopsy not great, freeze artefact, mid stage DUchenne?


title: SW-59 (468A-A0NW)

value: human asthmatic airway epithelial cell


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-10UP)

value: Deletion Exons 45-48

value: nice biopsy, relatively static mild myopathy, some fiber size variation


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-11UP)

value: moderate

value: Deletion Exons 5-9

value: Very little muscle in biopsy, few focal regions of poorly preserved, atrophic fibers


title: SW-55 (267A-A0NW)

value: Sham


title: SW-56 (268A-A0NW)

value: air-liquid interface culture


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-12UP)

value: Deletion Exon 49

value: biopsy OK, varying fiber orientation, considerable endomysial fat, central nuclei, isolated areas of degen/regen


title: SW-54 (483A-S0NW)

value: submersion


title: SW-51 (297A-S0NW)


title: SW-49 (267A-S0NW)


title: SW-48 (483A-A24W)

value: MI


title: SW-53 (468A-S0NW)


title: SW-45 (297A-A24W)


title: SW-46 (312A-A24W)


title: SW-44 (268A-A24W)


title: SW-43 (267A-A24W)


title: SW-50 (268A-S0NW)


title: SW-52 (312A-S0NW)


title: Asynchronous remodeling in DMD (MIDO-DMD_Pos-14UP)

value: vastus lateralis

value: Male

value: nice biopsy, although some freeze artefact. early stage DMD with focal grouped necrosis, some fiber size variation but little fibrosis, young child


title: SW-47 (468A-A24W)


title: SW-41 (468A-S24W)


title: SW-42 (483A-S24W)


title: SW-36 (483A-A8W)


title: SW-33 (297A-A8W)


title: SW-37 (267A-S24W)


title: SW-39 (297A-S24W)


title: SW-38 (268A-S24W)


title: SW-34 (312A-A8W)


title: SW-32 (268A-A8W)


title: SW-29 (468A-S8W)


title: SW-28 (312A-S8W)


title: SW-31 (267A-A8W)


title: SW-35 (468A-A8W)


title: SW-27 (297A-S8W)


title: SW-24 (483A-A2W)


title: SW-26 (268A-S8W)


title: SW-22 (312A-A2W)


title: SW-30 (483A-S8W)


title: SW-23 (468A-A2W)


title: SW-25 (267A-S8W)


title: SW-21 (297A-A2W)


title: Asynchronous remodeling in DMD (MIDO-CTRL_Pos-1UP)

description: Normal


title: SW-17 (468A-S2W)


title: SW-15 (297A-S2W)


title: SW-16 (312A-S2W)


title: SW-20 (268A-A2W)


title: SW-11 (468A-A0W)


title: SW-10 (312A-A0W)


title: SW-19 (267A-A2W)


title: SW-14 (268A-S2W)


title: SW-06 (483A-S0W)


title: SW-08 (268A-A0W)


title: SW-09 (297A-A0W)


title: SW-12 (483A-A0W)


title: Clostridium difficile - anaerobic - Replicate 3

city: Silver Spring

first: Paul

last: Carlson

state: MD

address: 10903 New Hampshire Ave

department: DBPAP

institute: Food and Drug Administration

hyb_protocol: Agilent manufacturer protocols were followed using supplied reagents

data_processing: data were median normalized and log transformed

organism: Clostridioides difficile 630

source_name: Clostridium difficile in vitro culture

extract_protocol: RNA eas extracted using hot phenol extraction methodology.  RNA was treated with Dnase prior to use.

tag: strain

value: Clostridium difficile in vitro culture


title: Clostridium difficile - 2% oxygen - Replicate 2

scan_protocol: Agilent manufacturer protocols were followed using supplied reagents


title: Clostridium difficile - 2% oxygen - Replicate 1

label_protocol: Agilent manufacturer protocols were followed using supplied reagents


title: SW-07 (267A-A0W)


title: Clostridium difficile - 2% oxygen - Replicate 3


title: SW-18 (483A-S2W)


title: SW-02 (268A-S0W)


title: Clostridium difficile - anaerobic - Replicate 1


title: SW-04 (312A-S0W)


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-4UP)

value: M

value: Deletion Exons 45-47

value: Nice biopsy. Large fiber size variation. Splitting and central nuclei.Lobulated fibers.Increase in both endo and perymisial connective. Some adipose infiltraction. End stage dystrophy.


title: Tgd.Sp#3_RNA-seq

status: Public on Jan 13 2018

type: SRA

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Total Splenic gdT cells

library_source: transcriptomic

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.3
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM12)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

organism: Mus musculus

source_name: Spleen

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

value: 6 weeks old

tag: sorting markers

value: Spleen

tag: cell type

value: gd T cells


title: Clostridium difficile - anaerobic - Replicate 2


title: SW-05 (468A-S0W)

value: human asthmatic airway epithelial cell


title: Treg.4.FP3+.Nrplo.Co#1_RNA-seq

description: Colonic FoxP3+ Nrplo Tregs

source_name: Colon

value: Colon

value: ab T cells


title: SW-03 (297A-S0W)


title: Treg.4.25hi.Sp#1_RNA-seq

description: Splenic CD25+ Tregs


title: SW-01 (267A-S0W)


title: Tgd.Sp#4_RNA-seq

description: Total Splenic gdT cells


title: Tgd.g2+d17.LN#1_RNA-seq

description: Vg2+ CD27neg.LN

source_name: Lymph Node

value: Lymph Node


title: Tgd.g2+d17.LN#2_RNA-seq

description: Vg2+ CD27neg.LN


title: Tgd.g2+d1.LN#2_RNA-seq

description: Vg2+ CD27+.LN


title: Tgd.g2+d17.24a+.Th#2_RNA-seq

description: Vg2+ Scart2+ immature thymocytes

source_name: Thymus

value: Thymus


title: Tgd.g2+d1.24a+.Th#1_RNA-seq

description: Vg2+ Scart2-  immature thymocytes


title: Tgd.g2+d1.LN#1_RNA-seq

description: Vg2+ CD27+.LN


title: Tgd.g1.1+d1.24a+.Th#2_RNA-seq

description: Vg1.1+  Scart2-  immature thymocytes


title: Tgd.g1.1+d1.24a+.Th#1_RNA-seq

description: Vg1.1+  Scart2-  immature thymocytes


title: Tgd.g1.1+d1.LN#1_RNA-seq

description: Vg1.1+ CD27+.LN


title: Treg.4.FP3+.Nrplo.Co#2_RNA-seq

description: Colonic FoxP3+ Nrplo Tregs


title: Treg.4.25hi.Sp#2_RNA-seq

description: Splenic CD25+ Tregs


title: Asynchronous remodeling in DMD (MIDO-BMD_Pos-7UP)

value: mild

value: nice biopsy, variable endomysial fibrosis, many hypercontracted fibers, central nuclei, early stage DYSTROPHIC


title: T8.Tem.LCMV.d180.Sp#2_RNA-seq

description: Splenic CD8+ Effector Memory, LCMV d180

value: 32 weeks old


title: Tgd.g2+d1.24a+.Th#2_RNA-seq

description: Vg2+ Scart2-  immature thymocytes


title: T8.TN.P14.Sp#1_RNA-seq

description: Splenic Triple Negative CD8+ P14 T cells


title: Tgd.g1.1+d1.LN#2_RNA-seq

description: Vg1.1+ CD27+.LN


title: T8.Tcm.LCMV.d180.Sp#2_RNA-seq

description: Splenic CD8+ Central Memory, LCMV d180


title: T8.TN.P14.Sp#2_RNA-seq


title: T8.Tcm.LCMV.d180.Sp#1_RNA-seq

description: Splenic CD8+ Central Memory, LCMV d180


title: T8.MP.LCMV.d7.Sp#2_RNA-seq

description: Splenic CD8+ Memory Precursor, LCMV d7

value: 7 weeks old


title: T8.IEL.LCMV.d7.Gut#2_RNA-seq

description: Gut IEL CD8+ , LCMV d7

source_name: Gut

value: Gut


title: T.DN4.Th#2_RNA-seq

description: Thymic preT DN4


title: T.ISP.Th#2_RNA-seq

description: Intermediate Single-Positive Thymocytes


title: T8.IEL.LCMV.d7.Gut#1_RNA-seq

description: Gut IEL CD8+ , LCMV d7


title: T.DP.Th#2_RNA-seq

description: Double Positive Thymocytes


title: T.8.Th#2_RNA-seq

description: CD8+ Thymocytes


title: SW-40 (312A-S24W)

value: submersion

value: MI


title: T8.MP.LCMV.d7.Sp#1_RNA-seq

description: Splenic CD8+ Memory Precursor, LCMV d7


title: T.ISP.Th#1_RNA-seq

description: Intermediate Single-Positive Thymocytes


title: T.DP.Th#1_RNA-seq

description: Double Positive Thymocytes


title: T.8.Th#1_RNA-seq

description: CD8+ Thymocytes


title: T.DN4.Th#1_RNA-seq

description: Thymic preT DN4


title: 3355-Tumor

city: Taipei

first: Jer-Wei

last: Chang

address: 5F-13, No.27, Sec.2, Fuxing S. Rd.,

country: Taiwan

institute: Mao Ying Genetech Inc.

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

data_processing:
RMA expression values derived from Expression Console software.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: breast cancer tissue

label_protocol: Affymetrix standard protocol.

growth_protocol: Not applicable.

extract_protocol: Total RNA was prepared from tumors and normal breast tissues by using TRIzol reagent.

treatment_protocol: Not applicable.

value: female

value: 46 yr

tag: patient disease state

value: breast cancer

tag: cancer stage

value: IIB

value: breast cancer tissue

tag: patient identifier


title: T.4.Th#2_RNA-seq

description: CD4+ Thymocytes

value: 6 weeks old


title: T.4.Sp.aCD3+CD40.18hr#2_RNA-seq

description: Splenic Activated CD4+ Tcells, aCD3+CD40 18 hr

value: Spleen


title: T.4.Sp.aCD3+CD40.18hr#1_RNA-seq

value: ab T cells


title: T.4.Th#1_RNA-seq

description: CD4+ Thymocytes


title: T.4.Nve.Sp#2_RNA-seq

description: Splenic Na<ef>ve CD4+ T cells


title: 3355-Normal

source_name: breast tumor adjacent normal tissue

value: breast tumor adjacent normal tissue


title: T.4.Nve.Fem.Sp#2_RNA-seq

description: Female Splenic Na<ef>ve CD4+ T cells


title: 3297-Tumor

value: 56 yr

value: IIIA


title: 3297-Normal


title: proB.FrBC.BM#1_RNA-seq

description: Bone Marrow Fr. BC (Pro-B)

source_name: Bone Marrow

value: Bone Marrow

value: B cells


title: STHSC.150-.BM#2_RNA-seq

value: Stem Cells


title: 3232-Normal

value: 47 yr

value: I


title: 3197-Tumor

value: 34 yr

value: IIA


title: 3232-Tumor

value: female


title: 3156-Tumor

value: 35 yr

value: breast cancer


title: proB.FrBC.BM#2_RNA-seq

description: Bone Marrow Fr. BC (Pro-B)


title: 3159-Normal

value: 55 yr


title: proB.CLP.BM#1_RNA-seq

description: Bone Marrow Common Lymphoid Progenitor

value: 6 weeks old


title: 2985-Normal

value: 46 yr


title: preT.DN3.Th#2_RNA-seq

description: Thymic preT DN3

value: Thymus

value: ab T cells


title: STHSC.150-.BM#1_RNA-seq


title: T.4.Nve.Fem.Sp#1_RNA-seq

description: Female Splenic Na<ef>ve CD4+ T cells

value: Spleen


title: 2972-Tumor

value: breast cancer tissue


title: 2943-Tumor


title: 3156-Normal

value: IIB

value: breast tumor adjacent normal tissue


title: 3197-Normal


title: T.4.Nve.Sp#1_RNA-seq

description: Splenic Na<ef>ve CD4+ T cells


title: 2943-Normal


title: 2985-Tumor


title: preT.DN2a.Th#2_RNA-seq

description: Thymic preT DN2a


title: proB.CLP.BM#2_RNA-seq

description: Bone Marrow Common Lymphoid Progenitor

value: Bone Marrow

value: B cells


title: preT.DN1.Th#1_RNA-seq

description: Thymic preT DN1


title: preT.DN1.Th#2_RNA-seq

description: Thymic preT DN1


title: 2972-Normal

value: I


title: proB.FrA.BM#2_RNA-seq

description: Bone Marrow Fr. A (Pre-Pro-B)


title: NKT.Sp.LPS.3hr#2_RNA-seq

description: Splenic Natural Killer T cells, LPS 3hr

value: 8 weeks old


title: proB.FrA.BM#1_RNA-seq

description: Bone Marrow Fr. A (Pre-Pro-B)


title: NKT.Sp.LPS.3hr#1_RNA-seq

description: Splenic Natural Killer T cells, LPS 3hr


title: 2910-Normal

value: 36 yr

value: IIA


title: preT.DN3.Th#1_RNA-seq

description: Thymic preT DN3


title: preT.DN2b.Th#2_RNA-seq

description: Thymic preT DN2b


title: 2910-Tumor

value: female


title: NKT.Sp.LPS.3d#2_RNA-seq

description: Splenic Natural Killer T cells, LPS  3d


title: 2780-Normal

value: 56 yr

value: breast cancer


title: 2780-Tumor


title: preT.DN2b.Th#1_RNA-seq

description: Thymic preT DN2b

value: 6 weeks old


title: NKT.Sp.LPS.18hr#1_RNA-seq

description: Splenic Natural Killer T cells, LPS 18hr


title: SW-13 (267A-S2W)

value: human asthmatic airway epithelial cell

value: submersion

value: MI


title: NKT.Sp.LPS.18hr#2_RNA-seq

value: Spleen

value: ab T cells


title: NKT.Sp#3_RNA-seq

description: Splenic Natural Killer T cells


title: NK.27+11b+.Sp#2_RNA-seq

description: Splenic CD27+ CD11b+ Natural Killer

value: Innate Lymphocytes


title: NK.27+11b-.Sp#2_RNA-seq

description: Splenic CD27+ CD11b- Natural Killer


title: 2397-Tumor

value: 44 yr

value: breast cancer tissue


title: 2917-Tumor

value: 47 yr

value: IIIA


title: 2917-Normal

value: breast tumor adjacent normal tissue


title: 2706-Normal

value: 55 yr


title: NK.27+11b+.BM#1_RNA-seq

description: Bone Marrow CD27+ CD11b+ Natural Killer

value: Bone Marrow


title: 2454-Tumor

value: female

value: 33 yr

value: IIA


title: 2451-Tumor

value: 56 yr

value: breast cancer

value: IIB


title: NK.27+11b+.BM#2_RNA-seq

description: Bone Marrow CD27+ CD11b+ Natural Killer

value: 6 weeks old


title: NK.27+11b-.BM#2_RNA-seq

description: Bone Marrow CD27+ CD11b- Natural Killer


title: 2706-Tumor


title: NK.27+11b-.BM#1_RNA-seq

description: Bone Marrow CD27+ CD11b- Natural Killer


title: NK.27-11b+.Sp#2_RNA-seq

description: Splenic CD27- CD11b+ Natural Killer

value: Spleen


title: 2365-Tumor

value: 54 yr


title: NK.27+11b-.Sp#1_RNA-seq

description: Splenic CD27+ CD11b- Natural Killer

value: Innate Lymphocytes


title: 3159-Tumor


title: 2451-Normal


title: 2397-Normal

value: 44 yr


title: NK.27-11b+.BM#2_RNA-seq

description: Bone Marrow CD27- CD11b+ Natural Killer


title: NK.27-11b+.BM#1_RNA-seq

description: Bone Marrow CD27- CD11b+ Natural Killer


title: 2297-Normal


title: MMP4.135+.BM#2_RNA-seq

value: Stem Cells


title: 2454-Normal


title: 2280-Normal

value: I


title: 2297-Tumor

value: IIIA

value: breast cancer tissue


title: 2280-Tumor


title: 2190-Tumor


title: MMP4.135+.BM#1_RNA-seq


title: 2353-Normal

value: breast tumor adjacent normal tissue


title: MMP3.48+.BM#1_RNA-seq

value: Bone Marrow


title: 2353-Tumor

value: female


title: MMP2.150+48+.BM#1_RNA-seq


title: 2181-Normal

value: 53 yr


title: 2181-Tumor


title: MF.PC#3_RNA-seq

description: Peritoneal Macrophages

source_name: Peritoneal Cavity

value: Peritoneal Cavity

value: Macrophages


title: MMP3.48+.BM#2_RNA-seq


title: 2190-Normal

value: breast cancer


title: 2146-Tumor

value: IIA


title: MF.Fem.PC#2_RNA-seq

description: Female Peritoneal Macrophages

value: 6 weeks old


title: 2146-Normal


title: 2365-Normal


title: 2110-Tumor

value: 43 yr

value: IIIC


title: 2110-Normal


title: MF.pIC.Alv.Lu#2_RNA-seq

description: Alveolar Macrophages, Poly IC

source_name: Lung

value: CD45+ CD11c+ SiglecF+

value: Lung


title: MF.Alv.Lu#2_RNA-seq

description: Alveolar Macrophages


title: MF.Fem.PC#1_RNA-seq

description: Female Peritoneal Macrophages


title: LTHSC.34+.BM#2_RNA-seq

value: Stem Cells


title: LTHSC.34+.BM#1_RNA-seq


title: low glucose replicate 3

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. The bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data
Reads were trimmed for quality using a minimum phred value of 20 and minimum length of 20 using Fastx-Trimmer
Reads were mapped with STAR (Dobin et al, 2013) to the human genome downloaded from Ensembl (GRCh37).
FeatureCounts (Liao et al, 2014) was used to count reads mapped to gene bodies on the correct strand with a minimum mapping quality of 10 using Ensembl genome annotation (Homo_sapiens.GRCh37.75.gtf).
Genome_build: GRCh37
Supplementary_files_format_and_content: Expression count matrix

source_name: low glucose, HepG2

growth_protocol: HepG2 cells from ATCC at passage 9 were maintained in Dulbecco’s modified Eagle’s medium (DMEM) basal glucose (Gibco, Carlsbad, USA) supplemented with 10% fetal bovine serum (GE Healthcare, Chicago, USA) and penicillin and streptomycin (Gibco) (100 UI and 100 g/mL, respectively).

extract_protocol:
Cells were disrupted with TRIzol (Qiagen, Hilde, Germany). RNA was isolated from TRIzol homogenates using the Direct-zol Kit (Zymo Research, Irvine, USA). RNA was quantified on Qubit (Thermo Fisher, Waltham, USA) and its quality was evaluated on the MultiNA bioanalyzer (Shimadzu, Kyoto, Japan).
NEBNext® Poly(A) mRNA Magnetic Isolation Module was used to enrich mRNA from 1 μg of total RNA. We used the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (San Diego, USA) to generate barcoded libraries. Libraries were quantified on the MultiNA bioanalyzer (Shimadzu) and pooled to equimolar ratios for sequencing.

treatment_protocol: The cells were cultivated for 48 h in normoglycemic (LG) or hyperglycemic (HG) medium, containing D-glucose (Sigma, St. Louis, USA) up to a final concentration of 20 mM. Cells under LG and HG conditions were then treated with 1.0 mM VPA (Sigma) for another 12 h and compared with the respective untreated controls.

tag: cell line

value: HepG2 cells

tag: medium

value: Glucose 5.5 mM

tag: treatment

value: control


title: low glucose replicate 1


title: low glucose VPA replicate 2

source_name: low glucose VPA, HepG2

value: VPA 1 mM


title: MF.Alv.Lu#1_RNA-seq

description: Alveolar Macrophages

tag: tissue


title: MF.PC#4_RNA-seq

description: Peritoneal Macrophages


title: low glucose replicate 2


title: low glucose VPA replicate 3


title: low glucose VPA replicate 1


title: high glucose VPA replicate 3

source_name: high glucose VPA, HepG2

value: Glucose 20 mM


title: 2102-Normal

value: female

value: 46 yr

value: IIIA

value: breast tumor adjacent normal tissue


title: high glucose VPA replicate 2


title: LEC.SLN#3_RNA-seq

description: Subcutaneous Lymph Node Lymphatic Endothelial Cell

source_name: Subcutaneous Lymph Node

value: CD45- CD31+ PDPN+

value: Subcutaneous Lymph Node

value: Stromal Cells


title: 2102-Tumor

value: breast cancer

value: breast cancer tissue


title: high glucose VPA replicate 1


title: ILC3.NKp46+.SI#2_RNA-seq

description: Lamina Propria NKp46+ ILC3

source_name: Lamina Propia

value: 6 weeks old

value: CD45lo  CD3-CD19- NK1.1- Thy1+ NKp46+ CCR6-

value: Lamina Propia

value: Innate Lymphocytes


title: LEC.SLN#2_RNA-seq


title: high glucose replicate 2

source_name: high glucose, HepG2

value: HepG2 cells


title: high glucose replicate 3

value: control


title: MC.heparinase.PC#3_RNA-seq

value: Peritoneal Cavity

value: Mast Cells


title: ILC3.NKp46-CCR6-.SI#2_RNA-seq

description: Lamina Propria DN ILC3

value: CD45lo CD3-CD19- NK1.1- Thy1+ NKp46- CCR6-


title: LTHSC.34-.BM#1_RNA-seq

value: Bone Marrow

value: Stem Cells


title: high glucose replicate 1

value: Glucose 20 mM


title: ILC3.CCR6+.SI#2_RNA-seq

description: Lamina Propria CCR6+ ILC3

value: CD45lo  CD3-CD19- NK1.1- Thy1+ NKp46- CCR6+


title: LTHSC.34-.BM#2_RNA-seq


title: ILC2.SI#2_RNA-seq

description: ST2+ ILC2 siLP

source_name: Small Intestine

value: Small Intestine


title: ILC3.NKp46+.SI#1_RNA-seq

description: Lamina Propria NKp46+ ILC3


title: IAP.SLN#2_RNA-seq

description: Subcutaneous Lymph Node IAP

value: CD45- CD31- PDPN- ITGA7+

value: Subcutaneous Lymph Node

value: Stromal Cells


title: mycellial culture, on Alkyl Esther medium (AE) without glycerol , 7 days incubation at room temperature (RT) in the dark

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

country: Germany

institute: Technische Universität München

data_processing:
RNA-seq reads were mapped on the reference genome using tophat2 (v2.0.8).
The interval for allowed intron lengths were set to min 20 nt and max 1 kb (Kim, 2013, Trapnell et al., 2009).
Cufflinks was used  to determine the abundance of transcripts in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) and calculated differentially expressed genes using cuffdiff (Trapnell et al., ,2012, Trapnell et al., 2010).
The gene models were included as raw junctions. Genes with a minimum of fourfold increase or decrease in expression (|log2 of the FPKM values +1| ≥ 2) between the two experimental conditions were considered as regulated.
Genome_build: Ramularia collo-cygni Urug2: http://www.ebi.ac.uk/ena/data/view/FJUY01000001-FJUY01000078
Supplementary_files_format_and_content: tab-delimited text file holding FPKM values for each sample

organism: Ramularia collo-cygni

source_name: mycellial culture

growth_protocol: The isolates were grown on 6 different conditions : “control” which is the same as used for the genome sequencing, i.e growing on AE medium for 7 days; “old”, growing the isolates on AE for 14 days instead of 7 days.; “PH5”, growing it on AE buffered with HCl until pH = 5, for 7 days; “PH9”, growing it on AE buffered with NaOH until pH = 9, for 7 days; “NoG”, growing it on AE without glycerol, for 7 days; “BSagar”, growing it on Barley Straw Agar medium (BSagar) (40g of grounded barley straw, 20 g of agar for 1000 mL of final volume), for 7 days.

extract_protocol:
Total RNA was extracted from R. collo-cygni mycelium from the 6 different conditions using TRIzol reagent (Invitrogen, Karlsruhe, Germany). RNA integrity was confirmed using a 2100 Bioanalyzer RNA Nanochip with the RNA 6000 Nano Kit (5067-1511) following the manufacturer’s protocol (Agilent, Santa Clara, CA, USA).
The RNA-seq library preparation was performed using the TruSeq Stranded mRNA Library Prep Kit (RS-122- 2101) (Illumina San Diego, California 92122 U.S.A.) following the manufacturer’s protocol.
The prepared library (Insert size: about 180 bp) was subjected to high-throughput sequencing using the Illumina HiSeq2500 using 1 lane and multiplexed paired-end read (read 1: 101 cycles, index read: 7 cycles, read 2: 101 cycles). The sequencing was performed using the TruSeq Rapid PE Cluster Kit (PE-402-4001) and the TruSeq Rapid SBS Kits - HS (200 cycles) (FC-402-4001) (Illumina San Diego, California 92122 U.S.A.).

tag: genotype

value: wild type

tag: dpi

tag: culture condition


title: mycellial culture, on BSAgar, 7 days incubation at RT in the dark


title: mycellial culture, on AE, 14 days incubation at RT in the dark


title: IAP.SLN#1_RNA-seq

description: Subcutaneous Lymph Node IAP

tag: age

value: 6 weeks old


title: mycellial culture, on AE, 7 days incubation at RT in the dark


title: mycellial culture, on AE pH 5, 7 days incubation at RT in the dark


title: mycellial culture, on AE pH 9, 7 days incubation at RT in the dark


title: ILC3.CCR6+.SI#1_RNA-seq

description: Lamina Propria CCR6+ ILC3

value: Lamina Propia


title: X2T2_DNA_29_30_1

type: mixed

city: Nahant

first: Jennifer

last: Bowen

state: Massachusetts

address: 430 Nahant Rd.

department: Marine and Environmental Sciences

institute: Northeastern University

description:
X2T2DNA30
environmental DNA extracted from marsh sediments

hyb_protocol: Samples were hybridized to duplicate arrays by overnight incubation at 64°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4300) Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing:
Quality control was employed to remove noise by eliminating features in which the Cy3 signal was not at least twice the value of the control probes.
Cy3/Cy5 fluorescence intensities were standardized to the highest Cy3/Cy5 fluorescence across the each probe set (normalized fluorescence ratio; FRN) The 4 probesets are as follows: NosZ, WNosZ, NorB, AOAamoA

molecule: other

organism: synthetic construct

source_name: Universal Internal Standard + 70-mer

label_protocol: Hybridization targets were prepared by digesting environmental DNA  with a four cutter restriction enzyme. The digested environmental DNA was labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (1000 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: DNA was extracted from sediment samples using a MoBio PowerSoil RNA Isolation Kit (MoBio, Carlsbad, CA, USA) with a DNA Isolation Accessory Kit according to manufacturer’s instructions

tag: sample type

value: universal standard 20mer DNA oligo + 70mer oligo

molecule: genomic DNA

organism: sediment metagenome

source_name: marsh sediments

value: sediment samples

tag: geographical location

value: Great Sippewissett Marsh

tag: location (n)

tag: location (w)


title: X2T2_DNA_29_30_2


title: ILC2.ST2-.SI#2_RNA-seq

description: ST2- ILC2 siLP

tag: strain

tag: sorting markers

value: Innate Lymphocytes


title: GN.Thio.PC#1_RNA-seq

description: Thio-induced Peritoneal Neutrophil

value: CD11b+ Ly6G+

value: Peritoneal Cavity

tag: cell type

value: Granulocytes


title: GN.BM#2_RNA-seq

description: Bone Marrow Neutrophil

value: Bone Marrow


title: GN.Sp#4_RNA-seq

description: Splenic Neutrophil

source_name: Spleen

value: Spleen


title: GN.Thio.PC#2_RNA-seq

description: Thio-induced Peritoneal Neutrophil


title: ILC2.ST2-.SI#1_RNA-seq

description: ST2- ILC2 siLP


title: X2S1_DNA_29_30_1

description:
X2S1DNA30
environmental DNA extracted from marsh sediments


title: X2T2_DNA_0_1_2

description:
X2T2DNA1
environmental DNA extracted from marsh sediments


title: FRC.CD140a+.Madcam-.CD35-.SLN#1_RNA-seq

description: Subcutaneous Lymph Node Fibroblastic Reticular Cell

value: CD45- CD31- CD35- MadCAM- PDPN+ CD140+


title: X2S1_DNA_29_30_2


title: X2S1_DNA_0_1_2

description:
X2S1DNA1
environmental DNA extracted from marsh sediments


title: X2S2_DNA_29_30_2

description:
X2S2DNA30
environmental DNA extracted from marsh sediments


title: FRC.CD140a+.Madcam-.CD35-.SLN#3_RNA-seq


title: X2T2_DNA_0_1_1


title: GN.BM#1_RNA-seq

description: Bone Marrow Neutrophil


title: X2S2_DNA_0_1_2

description:
X2S2DNA1
environmental DNA extracted from marsh sediments


title: X2S2_DNA_0_1_1


title: ILC2.SI#1_RNA-seq

description: ST2+ ILC2 siLP

value: Small Intestine


title: X1T2_DNA_29_30_2

description:
X1T2DNA30
environmental DNA extracted from marsh sediments


title: FRC.CD140a+.Madcam-.CD35-.SLN#2_RNA-seq


title: X1T2_DNA_29_30_1


title: NK.27+11b+.Sp#1_RNA-seq

description: Splenic CD27+ CD11b+ Natural Killer


title: Ep.MECHi.Th#1_RNA-seq

description: Thymic Medullary Epithelial cells, MHCIIhi

source_name: Thymus

value: Thymus


title: DC.pDC.Sp#2_RNA-seq

description: Splenic Plasmacytoid

source_name: Splenic

value: CD45lo CD11b+

value: Splenic

value: Dendritic cells


title: X2S1_DNA_0_1_1


title: DC.pDC.Sp#1_RNA-seq

description: Splenic Plasmacytoid

value: 6 weeks old


title: DC.8+.Sp#2_RNA-seq

description: Spleenic CD8+

value: CD45+ MHCII+ CD11c+ CD8+ CD4-


title: X2S2_DNA_29_30_1

value: universal standard 20mer DNA oligo + 70mer oligo


title: DC.8+.Sp#3_RNA-seq

description: Spleenic CD8+


title: GN.Sp#3_RNA-seq

description: Splenic Neutrophil


title: Ep.MECHi.Th#2_RNA-seq

value: Stromal Cells


title: DC.4+.Sp#1_RNA-seq

description: Splenic CD4+

value: CD45+ MHCII+ CD11c+ CD8- CD4+


title: X1T1_DNA_0_1_2

description:
X1T1DNA1
environmental DNA extracted from marsh sediments

value: sediment samples

value: Great Sippewissett Marsh


title: X1T1_DNA_29_30_2

description:
X1T1DNA30
environmental DNA extracted from marsh sediments


title: X1S2_DNA_29_30_2

description:
X1S2DNA30
environmental DNA extracted from marsh sediments


title: X1T2_DNA_0_1_1

description:
X1T2DNA1
environmental DNA extracted from marsh sediments


title: DC.8+.Sp#1_RNA-seq

description: Spleenic CD8+


title: X1S2_DNA_29_30_1


title: +/- RA time-course, RA series, day 8

city: Münster

first: Boris

last: Greber

address: Von-Esmarch-Str. 54

institute: Max Planck Institute for Molecular Biomedicine

description: SAMPLE 24

hyb_protocol: 18 hours according to manufacturer's instructions (Illumina)

scan_protocol: Default settings on a HiScan SQ (Illumina)

data_processing: Cubic spline normalization with background subtration in GenomeStudio (Illumina)

source_name: HuES6 cells subjected to atrial cardiac differentiation protocol - RA-treated - day 8

label_protocol: Illumina TotalPrep RNA Amplification Kit (Thermo); 14h of in-vitro transcription

growth_protocol: Undifferentiated hESCs (HuES6 background) were grown to full confluency in chemically defined FTDA medium (PMID 22860038). Differentiation was initiated after replating cells at 500,000 cells per well in Matrigel-coated 24-well plates.

extract_protocol: Machery Nagel NucleoSpin RNA isolation kits with on-column DNA-digestion.

treatment_protocol: The baseline directed cardiac differentiation conditions were as described (Zhang et al., 2015, PMID 25639979 - monolayer format). In the +/- DOX (= +/- ISL1) time series, a subset of samples received 0.2 µg/ml doxycycline on days 3 and 4, to mimic endogenous ISL1 expression during this time frame. In the +/- RA time series, a subset of samples received 0.5 µg/ml retinoic acid on days 3 and 4 of differentiation, to induce an atrial cardiomyocyte phenotype, in contrast to the default protocol that mostly yields ventricular-like cells. The purpose of these comparisons was to assess to which extent RA-untreated ISL1 knockout cells mimic the atrial phenotype induced by RA in wild-type hES cells.

value: differentiated cell line

tag: time-point

value: day 8


title: X1T2_DNA_0_1_2


title: +/- RA time-course, RA series, day 4

description: SAMPLE 21

source_name: HuES6 cells subjected to atrial cardiac differentiation protocol - RA-treated - day 4

value: day 4


title: +/- RA time-course, day 3

description: SAMPLE 16

source_name: HuES6 cells subjected to cardiac differentiation protocol - day 3

value: day 3


title: X1T1_DNA_29_30_1


title: +/- RA time-course, RA series, day 5

description: SAMPLE 22

source_name: HuES6 cells subjected to atrial cardiac differentiation protocol - RA-treated - day 5

value: day 5


title: +/- RA time-course, no-RA series, day 4

description: SAMPLE 17

source_name: HuES6 cells subjected to default cardiac differentiation protocol - day 4


title: +/- RA time-course, no-RA series, day 8

description: SAMPLE 20

source_name: HuES6 cells subjected to default cardiac differentiation protocol - day 8


title: BEC.SLN#2_RNA-seq

description: Subcutaneous Lymph Node Blood Endothelial Cell

value: CD45- CD31+ PDPN- PNAd+

value: Subcutaneous Lymph Node


title: +/- RA time-course, RA series, day 6

description: SAMPLE 23

source_name: HuES6 cells subjected to atrial cardiac differentiation protocol - RA-treated - day 6

value: day 6


title: +/- RA time-course, no-RA series, day 5

description: SAMPLE 18

source_name: HuES6 cells subjected to default cardiac differentiation protocol - day 5


title: +/- DOX time-course, DOX series, day 8

description: SAMPLE 12

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - ISL1-induced - day 8


title: DC.4+.Sp#3_RNA-seq

description: Splenic CD4+

value: Splenic


title: DC.4+.Sp#2_RNA-seq

description: Splenic CD4+

value: Dendritic cells


title: X1S2_DNA_0_1_1

description:
X1S2DNA1
environmental DNA extracted from marsh sediments


title: +/- DOX time-course, no-DOX series, day 8

description: SAMPLE 11

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - non-ISL1-induced - day 8


title: +/- DOX time-course, DOX series, day 6

description: SAMPLE 10

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - ISL1-induced - day 6


title: +/- RA time-course, day 2

description: SAMPLE 15

source_name: HuES6 cells subjected to cardiac differentiation protocol - day 2

value: day 2


title: +/- RA time-course, no-RA series, day 6

description: SAMPLE 19

source_name: HuES6 cells subjected to default cardiac differentiation protocol - day 6


title: +/- DOX time-course, DOX series, day 5

description: SAMPLE 8

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - ISL1-induced - day 5


title: +/- DOX time-course, no-DOX series, day 5

description: SAMPLE 7

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - non-ISL1-induced - day 5


title: X1T1_DNA_0_1_1

source_name: Universal Internal Standard + 70-mer

source_name: marsh sediments


title: +/- RA time-course, day 1

description: SAMPLE 14

source_name: HuES6 cells subjected to cardiac differentiation protocol - day 1

value: day 1


title: B1b.PC#1_RNA-seq

description: Peritoneal B1b

source_name: Peritoneal Cavity

value: 6 weeks old

value: Peritoneal Cavity

value: B cells


title: X1S1_DNA_29_30_2

description:
X1S1DNA30
environmental DNA extracted from marsh sediments

value: universal standard 20mer DNA oligo + 70mer oligo

value: sediment samples


title: B.T3.Sp#2_RNA-seq

description: Splenic T3

source_name: Spleen

value: Spleen


title: +/- DOX time-course, no-DOX series, day 6

description: SAMPLE 9

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - non-ISL1-induced - day 6

value: differentiated cell line


title: X1S2_DNA_0_1_2

value: Great Sippewissett Marsh


title: B.T2.Sp#2_RNA-seq

description: Spleinc  T2


title: E1786-APP-E4-HFD-F

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

data_processing:
The libraries were sequenced on Illumina HiSeq2000 at the Functional Genomics Core, UPenn, Philadelphia
All sequencing datasets, FASTQ files in this study have been processed using Subread-featureCounts-limma/voom pipeline
differential expression analyzed by edgeR (v3.14.0) package
Co-expression networks were created with a raw count exclusion so that genes below 5 reads per million mapped were removed to eliminate noise. Samples were separated by sex and clustered by gene expression profile to identify the outliers
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include reads values for each sample and a file with the differentially expressed genes.

source_name: Cortex from brain

growth_protocol: APP/PS1ΔE9 mice were bred to targeted replacement APOE3 +/+ and APOE4 +/+ mice to generate APP/PS1ΔE9/APOE3 +/+ and APP/PS1ΔE9/APOE4 +/+ (referred to as APP/E3 and APP/E4, respectively). Males and females were randomly assigned to Normal diet (ND, Prolab Isopro RMH 3000, Lab Diet) or HFD (D12079B RD Western Diet, Research Diets) at a mean age of 3.5 months and fed for a 3 month period.

extract_protocol:
Mice were anesthetized with Avertin (250 mg/kg of body weight, i.p.) and perfused transcardially with cold 0.1 M PBS, pH 7.4. The left hemisphere was fixed in 4% paraformaldehyde for histology and the cortex was dissected from the other and snap frozen on dry ice for RNA and protein isolation.
RNA was isolated from the frontal cortex and purified using RNeasy mini kit (Qiagen). RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies) and samples with RIN > 8 were used for library construction. Sequencing libraries were generated using mRNA Library Prep Reagent Set (Illumina).

treatment_protocol: HFD supplemented 40% calories from fat; 16.8% from protein and 42.6% from carbohydrates. Fat was provided as anhydrous milk fat and corn oil. The mice had free access to water and food. After 3 months of feeding, behavior was assessed at mean age of 14.7 months.

value: brain

tag: brain region

value: frontal cortex

tag: diet

value: HFD

tag: gender

value: F


title: +/- DOX time-course, day 2

description: SAMPLE 3

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - day 2


title: +/- DOX time-course, no-DOX series, day 4

description: SAMPLE 5

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - non-ISL1-induced - day 4

value: day 4


title: E1758-APP-E4-ND

value: ND

value: M


title: +/- DOX time-course, day 1

description: SAMPLE 2

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - day 1


title: E1784-APP-E4-HFD-F


title: B.T1.Sp#2_RNA-seq

description: Splenic T1


title: E1783-APP-E4-HFD-F


title: B.T2.Sp#1_RNA-seq

description: Spleinc  T2


title: E1756-APP-E4-ND-F


title: E1750-APP-E4-HFD


title: BEC.SLN#3_RNA-seq

source_name: Subcutaneous Lymph Node

value: CD45- CD31+ PDPN- PNAd+

value: Subcutaneous Lymph Node

value: Stromal Cells


title: BEC.SLN#1_RNA-seq

value: 6 weeks old


title: C2T2_DNA_29_30_2

description:
C2T2DNA30
environmental DNA extracted from marsh sediments


title: C2T2_DNA_0_1_2

description:
C2T2DNA1
environmental DNA extracted from marsh sediments


title: +/- DOX time-course, DOX series, day 4

description: SAMPLE 6

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - ISL1-induced - day 4


title: E1746-APP-E4-ND


title: B1b.PC#2_RNA-seq

description: Peritoneal B1b

value: Peritoneal Cavity

value: B cells


title: X1S1_DNA_0_1_1

description:
X1S1DNA1
environmental DNA extracted from marsh sediments

value: universal standard 20mer DNA oligo + 70mer oligo

value: sediment samples


title: X1S1_DNA_29_30_1


title: E1701-APP-E4-HFD-M


title: E1694-APP-E4-ND-F


title: +/- DOX time-course, day 3

description: SAMPLE 4

source_name: HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene subjected to cardiac differentiation protocol - day 3

value: differentiated cell line

value: day 3


title: +/- RA time-course, day 0

description: SAMPLE 13

source_name: Undifferentiated wild-type HuES6 cells

value: undifferentiated cell line (HuES6)

value: day 0


title: F1382-APP-E3-HFD-M

value: brain

value: frontal cortex

value: HFD


title: B.PB.Sp#2_RNA-seq

description: Splenic  Plasmablasts

value: sorted on GFPlo CD138+ MHCIIhi (dump:NK1.1- TCRb- Gr1- CD11b-)

value: Spleen


title: E1676-APP-E4-HFD-M

value: M


title: E1757-APP-E4-ND

value: ND


title: B.PB.Sp#1_RNA-seq

description: Splenic  Plasmablasts


title: X1S1_DNA_0_1_2

value: Great Sippewissett Marsh


title: E1674-APP-E4-HFD


title: E1760-APP-E4-ND-M


title: E1673-APP-E4-ND-F

value: F


title: B.Sp#4_RNA-seq

description: Splenic  B cells

value: 6 weeks old


title: E1691-APP-E4-HFD-M


title: C2T2_DNA_29_30_1


title: C2T1_DNA_0_1_1

description:
C2T1DNA1
environmental DNA extracted from marsh sediments


title: E1749-APP-E4-ND-F


title: E1648-APP-E4-ND-F


title: +/- DOX time-course, day 0

description: SAMPLE 1

source_name: Undifferentiated HuES6 cells with endogenous ISL1 knockout and inducible ISL1 rescue transgene


title: B.mem.Sp#1_RNA-seq

description: Splenic Memory

value: B cells


title: C2S3_DNA_29_30_2

description:
C2S3DNA30
environmental DNA extracted from marsh sediments

value: universal standard 20mer DNA oligo + 70mer oligo


title: E1612-APP-E4-ND


title: C2T2_DNA_0_1_1

value: sediment samples


title: E1678-APP-E4-ND-M


title: D2047-APP-E3-ND


title: B.GC.CC.Sp#1_RNA-seq

description: Splenic Germinal Center Centrocytes

value: CD19+B220+IgD-Fas+CD38-CXCR4lo CD86hi


title: C2T1_DNA_29_30_1

description:
C2T1DNA30
environmental DNA extracted from marsh sediments


title: D1914-APP-E3-HFD-F


title: E1741-APP-E4-ND-F


title: C2S3_DNA_0_1_1

description:
C2S3DNA1
environmental DNA extracted from marsh sediments


title: B.GC.CC.Sp#2_RNA-seq

description: Splenic Germinal Center Centrocytes


title: C2S1_DNA_29_30_2

description:
C2S1DNA30
environmental DNA extracted from marsh sediments


title: D1910-APP-E3-HFD


title: E1593-APP-E4-ND-F


title: C2S1_DNA_29_30_1


title: B.PC.Sp#2_RNA-seq

description: Splenic Plasma cells

source_name: Splenic

value: sorted on GFPhi CD138+ MHCIIlo (dump:NK1.1- TCRb- Gr1- CD11b-)

value: Splenic


title: D1909-APP-E3-ND-M


title: D1904-APP-E3-ND-F


title: B.GC.CB.Sp#1_RNA-seq

description: Splenic  Germinal Center Centroblasts

value: CD19+B220+IgD-Fas+CD38-CXCR4hi CD86lo


title: E1618-APP-E4-HFD-F

value: brain


title: C2S1_DNA_0_1_1

description:
C2S1DNA1
environmental DNA extracted from marsh sediments


title: C2T1_DNA_0_1_2


title: B.FrE.BM#2_RNA-seq

description: Bone Marrow Fr. E (newly formed B)

source_name: Bone Marrow

value: Bone Marrow


title: D1879-APP-E3-ND-F

value: frontal cortex


title: B.PC.BM#1_RNA-seq

description: Bone Marrow Plasma cells


title: C2S1_DNA_0_1_2

source_name: Universal Internal Standard + 70-mer


title: C2S3_DNA_29_30_1

source_name: marsh sediments


title: C2T1_DNA_29_30_2


title: C1T2_DNA_29_30_1

description:
C1T2DNA30
environmental DNA extracted from marsh sediments


title: D1920-APP-E3-ND


title: E1667-APP-E4-HFD-F

value: HFD


title: B.MZ.Sp#2_RNA-seq

description: Splenic Marginal Zone

value: Spleen


title: E1672-APP-E4-HFD-F


title: D1912-APP-E3-ND

value: M


title: B.MZ.Sp#1_RNA-seq

description: Splenic Marginal Zone


title: E1669-APP-E4-HFD-F


title: D1863-APP-E3-HFD-F


title: B.GC.CC.Sp#3_RNA-seq

description: Splenic Germinal Center Centrocytes


title: B.Fo.Sp#1_RNA-seq

description: Splenic Follicular


title: D1906-APP-E3-HFD


title: B.GC.CB.Sp#2_RNA-seq

description: Splenic  Germinal Center Centroblasts


title: D1842-APP-E3-HFD-F


title: B.Fo.Sp#3_RNA-seq

description: Splenic Follicular


title: D1841-APP-E3-HFD-F


title: C1T1_DNA_29_30_2

description:
C1T1DNA30
environmental DNA extracted from marsh sediments


title: D1903-APP-E3-ND-F

value: ND


title: D1864-APP-E3-HFD-F


title: B.FrE.BM#1_RNA-seq

description: Bone Marrow Fr. E (newly formed B)


title: C1T1_DNA_0_1_2

description:
C1T1DNA1
environmental DNA extracted from marsh sediments

value: Great Sippewissett Marsh


title: D1791-APP-E3-HFD


title: C1T1_DNA_29_30_1


title: D1901-APP-E3-ND-F

value: F


title: D1789-APP-E3-HFD


title: C1T2_DNA_29_30_2


title: D1889-APP-E3-HFD-F


title: D1861-APP-E3-ND-F


title: C2S3_DNA_0_1_2


title: B.Fo.Sp#2_RNA-seq

description: Splenic Follicular

value: 6 weeks old


title: D1776-APP-E3-ND


title: B.Fo.Sp#4_RNA-seq

description: Splenic Follicular

value: B cells


title: D1862-APP-E3-HFD-F


title: HS1

city: Yangzhou

first: Yifan

last: Liu

address: No.58 Cangjie road

country: China

institute: Institute of Poultry Science, Chinese Academy of Agricultural Science

data_processing:
The raw sequencing data firstly went through a data clean process to remove low quality adaptors, having quality values less than 20, 5’ and 3’ primer contaminants, N adaptors, polyA adaptors, sequences without insert tags and adaptors shorter than 17 nt.
The sequences matching Gallus gallus miRBase were considered known miRNAs, and the expression of all miRNAs was assayed.
Genome_build: gg4.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample ...

organism: Gallus gallus

source_name: chicken testis

extract_protocol:
Total RNA was extracted from each testis sample using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina®, following manufacturer’s recommendations.

tag: breed

value: Beijing-you

tag: sperm motility

value: high

value: chicken testis


title: C1T2_DNA_0_1_1

description:
C1T2DNA1
environmental DNA extracted from marsh sediments

value: universal standard 20mer DNA oligo + 70mer oligo

value: sediment samples


title: C1S2_DNA_29_30_2

description:
C1S2DNA30
environmental DNA extracted from marsh sediments


title: B.GC.CB.Sp#3_RNA-seq

description: Splenic  Germinal Center Centroblasts

value: CD19+B220+IgD-Fas+CD38-CXCR4hi CD86lo

tag: tissue


title: D1865-APP-E3-ND-M

value: brain

tag: genotype


title: C1T2_DNA_0_1_2


title: D1847-APP-E3-ND-F


title: LS1

value: low


title: D1840-APP-E3-HFD-F

value: frontal cortex


title: C1S2_DNA_0_1_1

description:
C1S2DNA1
environmental DNA extracted from marsh sediments


title: B.Fem.Sp#1_RNA-seq

description: Female Splenic  B cells


title: LS2


title: D1785-APP-E3-ND-F


title: C1S1_DNA_29_30_1

description:
C1S1DNA30
environmental DNA extracted from marsh sediments


title: D1792-APP-E3-HFD-M

value: HFD


title: C1S2_DNA_29_30_1


title: C1S2_DNA_0_1_2


title: Day 4 Prdm1 null_2

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

country: United Kingdom

institute: Oxford University

description: Day 4 MEC Prdm1 null TAM replicate 2

data_processing: Background subtraction followed by Rank invariant normalization using Gene Expression Module V1.9.0 of Illumina GenomeStudio

source_name: mammary epithelial cultures

label_protocol: Total RNA was labeled according to the standard Illumina protocol

growth_protocol: Mammary epithelial cultures

extract_protocol: RNA was extracted using QIAGEN Rneasy mini kit with on-column DNase I treatment in accordance with the prescribed protocol provided with the kit.

treatment_protocol: 4OH Tamoxifen (TAM) on D0 of culture


title: X2T1_DNA_29_30_2

description:
X2T1DNA30
environmental DNA extracted from marsh sediments


title: Day 3 Wild type_3

description: Day 3 MEC Wild type TAM replicate 3

value: Wild type


title: Day 4 Wild type_3

description: Day 4 MEC Wild type TAM replicate 3


title: Day 4 Prdm1 null_1

description: Day 4 MEC Prdm1 null TAM replicate 1


title: Day 3 Wild type_1

description: Day 3 MEC Wild type TAM replicate 1


title: KEA100_CD44ΔBTcl1tg_n3

city: Salzburg

first: Julia

middle: Christine

last: Gutjahr

address: Müllner Hauptstraße 48

department: Department of Internal Medicine III, Paracelsus Medical University

country: Austria

institute: SCRI-LIMCR

description: Genexpression data from isolated CD5+/CD19+ cells from spleen of CD44ΔB Tcl1 tg mouse

hyb_protocol: 3,8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom S mouse arrays for 16 h at 45 ° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

scan_protocol: signals were measured with an Affymetrix GeneChip Scanner 3000 7G, controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software.

label_protocol: of total RNA was used to generate double-stranded cDNA. 15 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin. (Affymetrix GeneChip WT PLUS Reagent Kit User Manual)

growth_protocol: Tcl1 tg mice and CD44ΔB tcl1 tg mice were sacrificed at end stage of disease.

extract_protocol: Total RNA was extracted with RNeasy Mini Extraction Kit (Qiagen) including Dnase digestion

treatment_protocol: CD5+/CD19+ cells were freshly isolated from spleen of Tcl1 tg and CD44ΔB Tcl1 tg mice.

tag: genotype/variation

value: CD44deltaB Tcl1 tg

value: CD5+/CD19+ cells

tag: age in days


title: X2T1_DNA_29_30_1

tag: sample type

value: Great Sippewissett Marsh


title: HS2


title: C1T1_DNA_0_1_1

tag: geographical location


title: KEA101_CD44wtTcl1tg_n3

description: Genexpression data from isolated CD5+/CD19+ cells from spleen of Tcl1 tg mouse

value: Tcl1 tg


title: KEA106_CD44wtTcl1tg_n4

source_name: isolated CD5+/CD19+ cells from spleen of Tcl1 tg mouse


title: Day 4 Prdm1 null_3

description: Day 4 MEC Prdm1 null TAM replicate 3


title: Day 3 Prdm1 null_2

description: Day 3 MEC Prdm1 null TAM replicate 2


title: Day 4 Wild type_1

description: Day 4 MEC Wild type TAM replicate 1


title: X2T1_DNA_0_1_2

description:
X2T1DNA1
environmental DNA extracted from marsh sediments

tag: location (n)


title: C1S1_DNA_0_1_2

description:
C1S1DNA1
environmental DNA extracted from marsh sediments

tag: location (w)


title: KEA103_CD44ΔBTcl1tg_n4

source_name: isolated CD5+/CD19+ cells from spleen of CD44ΔB Tcl1 tg mouse

tag: strain


title: Day 3 Prdm1 null_3

description: Day 3 MEC Prdm1 null TAM replicate 3


title: Day 3 Prdm1 null_1

description: Day 3 MEC Prdm1 null TAM replicate 1


title: KEA67_CD44ΔBTcl1tg_n1


title: C1S1_DNA_29_30_2


title: Wbec-CD-Au4-miRNA4

city: Columbia

first: William

middle: James

last: Becker

state: South Carolina

address: 6439 Garners Ferry Rd.

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

description: miRNA gene expression data in mouse CD4+ T cells.

hyb_protocol: Prelabeled spike control oligonucleotides were spiked in to the controls used for labeling and hybridization, as well as for data normalization purposes. The hybridization mixture contained premixed hybridization controls (bioB, bioC, bioD, and cre). Each labeled sample was hybridized to the array at 48 °C and 60 rpm for 16 h, then washed, and stained with fluorescent-conjugated streptavidin on a Fluidics Station.

scan_protocol: The stained chip was washed and scanned on GeneArray 2500 Scanner.

data_processing: Affymetrix Power Tools (APT) was used to generate Robust MultiArray Average (RMA) values as well as detection above background (DABG) p-values.

source_name: Mouse CD4+ cells draining from syngeneic graft 10 days post-transplant

label_protocol: Total RNA containing small RNA were labeled with biotin using FlashTag Biotin HSR RNA labeling kit.

extract_protocol: Qiagen miRNeasy Mini Kit.

treatment_protocol: Cells were labeled with PE labeled anti-mouse CD4 (clone GK1.5) for magnetic bead isolation of CD4+ cells.

tag: strain/background

value: female

value: purified CD4+ T cells

tag: group

value: syngeneic graft


title: Wbec-CD-Al4-miRNA4

source_name: Mouse CD4+ cells draining from allograft 10 days post-transplant

tag: cell type

value: allogenic graft


title: C1S1_DNA_0_1_1


title: Wbec-CD-N4-miRNA4

source_name: Mouse CD4+ cells isolated from naïve lymph nodes

value: naive


title: KEA71_CD44ΔBTcl1tg_n2


title: Day 3 Wild type_2

description: Day 3 MEC Wild type TAM replicate 2


title: Day 4 Wild type_2

description: Day 4 MEC Wild type TAM replicate 2


title: KEA138_CD44wtTcl1tg_n2


title: X2T1_DNA_0_1_1

value: universal standard 20mer DNA oligo + 70mer oligo


title: RNAseq_mouseComboTest_MEPMPLW515L_RuxJQ1_rep1

status: Public on Jan 12 2018

city: Manhattan

first: Ross

last: Levine

state: NY

address: RRL

institute: MSKCC

description: Table_RNAseq_MEP_MPLW515L_mouse_VehRuxJQ1combo_rawcounts.txt

data_processing:
STAR 2.4.2a was used to align the RNA-seq samples to the reference genome (mm10) and to count the number of reads mapping to each gene in the Ensembl GRCm38.80 gene model.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text of read count for each transcript and condition

source_name: MEP MPLW515L MPN

growth_protocol: MEPs were sorted from healthy (MigR1) or MPLW515L-diseased mice.

extract_protocol:
Total RNA was purified with RNeasy Mini kit (Qiagen).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

tag: treatment


title: RNAseq_mouseMEP_JAK2V617F_AIV6_CrePos_rep2

description: Table_RNAseq_mouseMEP_JAK2V617F_CrePos_CreNeg.txt

source_name: MEP


title: RNAseq_mouseMEP_JAK2V617F_AJB2_CrePos_rep3


title: RNAseq_mouseComboTest_MEPMPLW515L_RuxJQ1_rep2


title: RNAseq_mouseComboTest_MEPMPLW515L_JQ1_rep2


title: RNAseq_mouseMEP_JAK2V617F_AIV2_CrePos_rep1


title: RNAseq_mouseMEP_JAK2V617F_AJB3_CreNeg_rep3


title: RNAseq_mouseComboTest_MEPMPLW515L_JQ1_rep1


title: RNAseq_mouseComboTest_MEPMPLW515L_Vehicle_rep3

value: Vehicle


title: RNAseq_mouseMEP_JAK2V617F_AIV1_CreNeg_rep1


title: RNAseq_mouseComboTest_MEPMPLW515L_Rux_rep2

value: Ruxolitinib


title: E14.5 knockout ovary, biological rep-3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression data from E14.5 mouse ovary that lacks Coup-tfII

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Expression Console Software (AGCC; Version 1.2) using the MAS5 algorithm to generate .CHP files.

source_name: E14.5 ovary without Coup-tfII

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours.

extract_protocol: RNA extraction was performed using PicoPure RNA Isolation kit (Life technologies, USA)

treatment_protocol: Dams carrying embryos were injected tamoxifen at the dose of 2 mg/10 g body weight once daily at E11.5 and E12.5. Ovaries from embryos were collected at E14.5 and 16.5 and snap-frozen.

value: C57BL/6, Swiss Webster, and B6129SF1/J mixed

value: Coup-tfII knockout

value: ovary

tag: embryonic day


title: E16.5 control ovary, biological rep-2

description: Gene expression data from E16.5 mouse ovary

source_name: E16.5 ovary with Coup-tfII

value: control


title: KEA50_CD44wtTcl1tg_n1


title: E16.5 control ovary, biological rep-1


title: E16.5 knockout ovary, biological rep-1

description: Gene expression data from E16.5 mouse ovary that lacks Coup-tfII

source_name: E16.5 ovary without Coup-tfII


title: E14.5 knockout ovary, biological rep-1


title: E14.5 control ovary, biological rep-2

description: Gene expression data from E14.5 mouse ovary

source_name: E14.5 ovary with Coup-tfII


title: E14.5 control ovary, biological rep-1


title: RNAseq_mouseMEP_JAK2V617F_AIV7_CreNeg_rep2


title: E16.5 control ovary, biological rep-4


title: E14.5 control ovary, biological rep-3


title: E14.5 knockout ovary, biological rep-2


title: E16.5 knockout ovary, biological rep-4


title: E16.5 control ovary, biological rep-3


title: E16.5 knockout ovary, biological rep-2


title: E16.5 knockout ovary, biological rep-3


title: RNAseq_mouse_BMT637MigR1IMEP

description: Table_RNAseq_mouse_BMT637MPLvsMIGR1_6samples_rawcounts.txt

source_name: MEP control MIGR1


title: RNAseq_mouseComboTest_MEPMPLW515L_Vehicle_rep1


title: RNAseq_mouse_BMT637MigR1IIIMEP


title: RNAseq_mouseComboTest_MEPMPLW515L_Rux_rep1


title: RNAseq_mouseComboTest_MEPMPLW515L_Vehicle_rep2


title: RNAseq_mouse_BMT637MPLIIMEP


title: RNAseq_mouse_BMT637MPLIMEP


title: RNAseq_mouse_BMT637MigR1IIMEP


title: TS23

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
Bcl converion and demultiplexing using CASAVA 1.8.2. Adapter masked fastq files were generated.
Quality filter by FASTX Toolkit 0.0.13 (fastq_quality_filter: -Q33 -q 20 -p 80 was used as a parameter, fastq_quality_trimmer: -Q33 -t 20 -l 10 was used as a parameter). Fastq files were generated.
Read alignment using Tophat 2.0.9 using mm10 reference genome. BAM files were generated.
FPKM calculation using Cufflinks 2.2.1. Plain text (can be read by excel) files were generated. Both Tophat and Cufflinks used UCSC mm10 gtf file as guided annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: xls files for FPKM values for each sample

source_name: IAV LM AM

growth_protocol: The double transgenic GM-CSF (DTGM) mice were bred on the wild-type C57BL/6J background. Littermate control (LM) mice were defined as being single transgenic littermates of DTGM mice that were only positive for the SCGB1A1-rTA and thereby did not have the CMV-GM-CSF gene.  All mice were maintained on an ad libitum feeding.

extract_protocol:
Single cell suspensions were obtained from bronchoalveolar lavage (BAL) fluid on day 8 post-infection. Single cell suspensions from lung digests were placed at 4C and then surface stained in Hank's Buffered Saline Solution with 3% fetal bovine serum with fluorochrome-conjugated monoclonal antibodies and then stained with a fixable viability dye. For fluorescence-activated cell sorting BAL cells were recovered and placed at 4C and then surface stained in Hank's Buffered Saline Solution (HBSS) with 3% FBS with fluorochrome-conjugated monoclonal antibodies and 7-aminoactinomycin D (7-AAD) was used to assess viability just prior to acquisition. Alveolar macrophages (AM) were defined as 7-AAD-neg, CD45-pos, CD11c-pos, SiglecF-pos, CD11b-neg, whereas exudative macrophages (EM) were defined as  7-AAD-neg, CD45-pos, SiglecF-neg, CD11b-pos.  All flow cytometric data were collected using an LSR II (Becton Dickinson, BD) instrument, and all FACS-sorting was performed using a FACSAria (BD) High Speed cell sorter. Cells were sorted directly into RNA-Bee to isolate RNA for further RNA-sequencing (RNA-seq).   RNA was phase separated using chloroform and the aqueous phase containing RNA was removed following centrifugation and precipitated overnight at -20C using ice cold isopropanol. RNA was washed with 75% ethanol then solubilized in RNase-free water. Optical density values of extracted RNA were measured using NanoDrop (Thermo Fisher Scientific) to confirm an A260:A280 ratio above 1.9. RNA integrity number (RIN) was measured using BioAnalyzer (Agilent) RNA 6000 Pico Kit to confirm RIN above 7. The cDNA libraries were prepared using the SMARTer® Ultra® Low Input RNA Kit for Sequencing - v3 (Clontech) followed by Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
The cDNA libraries were prepared using the NEXTflex™ Rapid RNA Sequencing Kit and NEXTflex™ RNA-Seq Barcodes – 24 Kit (BioO Scientific) as per the manufacturer’s instructions. The final product was assessed for its size distribution using Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). Six libraries were pooled per HiSeq lane, followed by on-board cluster generation on a Rapid Run single-end flow cell and subsequent 50 cycles sequencing (v3 sequencing kit) according to the manufacturer's instructions (HiSeq 2500, Illumina).

treatment_protocol: Young adult (8-12 week old) mice were infected intranasally with influenza A virus (A/PR8/8/34) on Day 0. DTGM mice and LM controls were exposed to 1 mg/mL doxycycline in drinking water starting at day 3 post-infection, and doxycycline-containing drinking water was replenished every 2–3 days. Both male and female mice were used for all experiments; all mice were sex- and age-matched to control mice

value: littermate control

value: airway alveolar macrophage

tag: infection

value: influenza A virus-infected (A/puerto rico/8/34)

tag: Sex

value: M

tag: age

value: 8-12 weeks-old


title: TS35

value: F


title: TS34

source_name: IAV LM EM

value: airway exudative macrophage


title: TS26


title: TS27


title: TS31

source_name: IAV DTGM AM

value: double transgenic GM-CSF (DTGM)


title: TS33


title: TS32

source_name: IAV DTGM EM


title: TS38


title: TS29


title: TS36


title: TS24


title: TS25


title: TS30


title: TS28


title: TS37


title: RNAseq_mouse_BMT637MPLIIIMEP


title: TS15


title: TS21


title: TS17


title: TS16


title: TS18


title: TS22


title: TS14


title: TS11


title: TS13


title: TS12


title: JS170744

city: West Haven

first: Matthew

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

description:
Negative control TimeLapse experiment with neither chemical treatment nor s4U treatment. For the processed data files, reads of combined replicates (JS170744 and JS170745) filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)
MEF1707-MM.0.min.bedGraph
MEF1707-MM.0.pos.bedGraph
MEF1707-MM.1.min.bedGraph
MEF1707-MM.1.pos.bedGraph
MEF1707-MM.2.min.bedGraph
MEF1707-MM.2.pos.bedGraph
MEF1707-MM.3.min.bedGraph
MEF1707-MM.3.pos.bedGraph
MEF1707-MM.4.min.bedGraph
MEF1707-MM.4.pos.bedGraph
MEF1707-MM.5.min.bedGraph
MEF1707-MM.5.pos.bedGraph

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the GRCm38 or GRCh38 genome (MEF or K562, respectively) using STAR aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCm38
Genome_build: GRCh38

source_name: immortalized MEFs

growth_protocol: MEF cells were grown in DMEM containing 1% penicillin/streptomycin, 10% FBS, at 37°C. K562 cells were grown in RPMI containing 1% penicillin/streptomycin, 10% FBS, at 37°C.

extract_protocol:
MEF RNA was harvested with Trizol reagent, followed by chloroform extraction and ethanol precipitation. K562 RNA was harvested with a modified RNeasy protocol as described in the methods section. Chemically treated RNAs were treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in the methods section. MTS-enriched RNAs for transient transcriptome studies were prepared using a modified protocol from Duffy et al. Mol Cell (2015), as described in the methods section.
Libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian (Takara Bio USA, cat. 635005).

treatment_protocol: s4U plus and minus MEF cells had their media replaced with growth media supplemented with 1 mM s4U or left unsupplemented, respectively. HS and NHS cells were incubated during this 1h feed at 42°C and 37°C, respectively. For transcriptome-wide studies, s4U plus and minus K562 cells had their growth media supplemented with 100 µM s4U for 4h or left unsupplemented, respectively.  For transient transcriptome studies, s4U plus and minus K562 cells had their growth media supplemented with 1 mM s4U for 5min or left unsupplemented, respectively.

value: F1:129S1/CastEiJ x 129S1

tag: heat shock

value: No

tag: s4u feed

tag: chemical treatment


title: JS170743

description: Heat shock MEF negative control TimeLapse experiment with neither s4U treatment nor chemical treatment.

value: Yes


title: JS170745


title: RNAseq_humanSET2_RuxJQ1_rep2

description: Table_RNAseq_SET2cellline_human_VehRuxJQ1combo_rawcounts.txt

source_name: SET-2 cell line

tag: genotype


title: RNAseq_humanSET2_JQ1_rep3


title: RNAseq_humanSET2_Rux_rep1


title: JS170733

description:
MEF TimeLapse experiment. For the processed data files, reads of combined replicates (JS170732 and JS170733) filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)
MEF1707-PP.0.min.bedGraph
MEF1707-PP.0.pos.bedGraph
MEF1707-PP.1.min.bedGraph
MEF1707-PP.1.pos.bedGraph
MEF1707-PP.2.min.bedGraph
MEF1707-PP.2.pos.bedGraph
MEF1707-PP.3.min.bedGraph
MEF1707-PP.3.pos.bedGraph
MEF1707-PP.4.min.bedGraph
MEF1707-PP.4.pos.bedGraph
MEF1707-PP.5.min.bedGraph
MEF1707-PP.5.pos.bedGraph


title: RNAseq_humanSET2_RuxJQ1_rep3


title: RNAseq_humanSET2_RuxJQ1_rep1


title: JS170737

description:
Negative control TimeLapse experiment with chemical treatment but no s4U treatment. For the processed data files, reads of combined replicates (JS170736 and JS170737) filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)
MEF1707-MP.0.min.bedGraph
MEF1707-MP.0.pos.bedGraph
MEF1707-MP.1.min.bedGraph
MEF1707-MP.1.pos.bedGraph
MEF1707-MP.2.min.bedGraph
MEF1707-MP.2.pos.bedGraph
MEF1707-MP.3.min.bedGraph
MEF1707-MP.3.pos.bedGraph
MEF1707-MP.4.min.bedGraph
MEF1707-MP.4.pos.bedGraph
MEF1707-MP.5.min.bedGraph
MEF1707-MP.5.pos.bedGraph


title: JS170736


title: JS170734

description: Heat shock MEF negative control TimeLapse experiment with chemical treatment but no s4U treatment.


title: JS170730

description:
Heat shocked MEF TimeLapse experiment. For the processed data files, reads of combined replicates (JS170730 and JS170731) were filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)
HS_MEF_1707.0.min.bedGraph
HS_MEF_1707.0.pos.bedGraph
HS_MEF_1707.1.min.bedGraph
HS_MEF_1707.1.pos.bedGraph
HS_MEF_1707.2.min.bedGraph
HS_MEF_1707.2.pos.bedGraph
HS_MEF_1707.3.min.bedGraph
HS_MEF_1707.3.pos.bedGraph
HS_MEF_1707.4.min.bedGraph
HS_MEF_1707.4.pos.bedGraph
HS_MEF_1707.5.min.bedGraph
HS_MEF_1707.5.pos.bedGraph


title: JS170731


title: JS170738

description: Heat shock MEF negative control TimeLapse experiment with s4U treatment but no chemical treatment.


title: RNAseq_humanSET2_DMSO_rep2

value: Vehicle


title: JS170739


title: JS170742


title: RNAseq_humanSET2_DMSO_rep3


title: BS019 CO_neural progenitors

city: New York City

first: Sylvie

last: Janssens

address: 1452 Madison Avenue

department: Department for Developmental and Regenerative Biology

institute: Mount Sinai School of Medicine

description:
RRBS
bisulfite converted DNA

library_source: genomic

data_processing:
Raw sequencing reads were trimmed by 10 bp at each end and aligned to the human genome build hg19/GRCh37 using BSMAP (Xi and Li, 2009).
Methylation levels at CpGs were determined with the mCall package from MOABS (Sun et al., 2014). Only CpGs covered by 5 or more reads were used for analysis.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bed files containing chromosomal positions and methylation scores of CpGs

source_name: CO_neural progenitors

growth_protocol: organoids were grown for 16 weeks, dissociated and grown as two-dimensional culture for 1 week

extract_protocol:
DNA was extracted with phenol-chloroform and subsequent NaCl/ethanol precipitation. 200 ng of genomic DNA were fragmented with a Covaris S2 for 6 min using the following program: duty cycle 5%; intensity 5; cycle per burst 200. The sheared DNA was purified with the DNA Clean & Concentrator kit from Zymo Research according to the manufacturer’s recommendations. Bisulfite conversion of DNA was then conducted with the EZ DNA Methylation-Gold kit (Zymo Research) following the manufacturer's protocol and eluted in 15 µl low TE buffer.
WGBS libraries were generated using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences) following the manufacturer’s protocol. RRBS library construction was performed as described before by Boyle et al., 2012

treatment_protocol: ZIKV 1MOI, 72h

tag: tissue

value: cerebral organoid derived neural progenitors

tag: parental cell type

value: H9 derived - WiCell (WAO9)

tag: treatment & infection status

value: ZIKVpos


title: RNAseq_humanSET2_DMSO_rep1


title: JS170741

description:
Negative control TimeLapse experiment with no chemical treatment but with s4U treatment. For the processed data files, reads of combined replicates (JS170740 and JS170741) filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)
MEF1707-PM.0.min.bedGraph
MEF1707-PM.0.pos.bedGraph
MEF1707-PM.1.min.bedGraph
MEF1707-PM.1.pos.bedGraph
MEF1707-PM.2.min.bedGraph
MEF1707-PM.2.pos.bedGraph
MEF1707-PM.3.min.bedGraph
MEF1707-PM.3.pos.bedGraph
MEF1707-PM.4.min.bedGraph
MEF1707-PM.4.pos.bedGraph
MEF1707-PM.5.min.bedGraph
MEF1707-PM.5.pos.bedGraph


title: BS018 CO_neural progenitors

description:
RRBS
bisulfite converted DNA

value: MOCK


title: RNAseq_humanSET2_JQ1_rep1


title: BS017 CO_neurons

description:
RRBS
bisulfite converted DNA

value: cerebral organoid derived neurons

value: ZIKVneg


title: BS020 CO_neural progenitors

description:
RRBS
bisulfite converted DNA


title: JS170740


title: RNAseq_humanSET2_Rux_rep3

value: Ruxolitinib


title: RNAseq_humanSET2_JQ1_rep2


title: BS015 CO_neurons

description:
RRBS
bisulfite converted DNA


title: BS016 CO_neurons

description:
RRBS
bisulfite converted DNA


title: BS014 CO_astrocytes

description:
RRBS
bisulfite converted DNA

value: cerebral organoid derived astrocytes


title: BS013 CO_astrocytes

description:
RRBS
bisulfite converted DNA


title: BS010 CDI_neurons

description:
RRBS
bisulfite converted DNA

value: iPSC derived neurons

value: CDI - Caucasian ethnicity


title: BS008 GIBCO_neural progenitors

description:
RRBS
bisulfite converted DNA

source_name: GIBCO_neural progenitors

value: hESC derived neural progenitors

value: GIBCO - H9


title: BS007 GIBCO_neural progenitors

description:
RRBS
bisulfite converted DNA


title: JS170704

description: Negative control expeimernt for K562 TimeLapse-seq with neither s4U treatment nor chemical treatment.

source_name: immortalized K562s


title: BS006 CDI_neurons

description:
RRBS
bisulfite converted DNA


title: JS170714

description:
Reads of combined replicates (JS170713 and JS170714) filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)
K562_4h_TL.0.min.bedGraph
K562_4h_TL.0.pos.bedGraph
K562_4h_TL.1.min.bedGraph
K562_4h_TL.1.pos.bedGraph
K562_4h_TL.2.min.bedGraph
K562_4h_TL.2.pos.bedGraph
K562_4h_TL.3.min.bedGraph
K562_4h_TL.3.pos.bedGraph
K562_4h_TL.4.min.bedGraph
K562_4h_TL.4.pos.bedGraph
K562_4h_TL.5.min.bedGraph
K562_4h_TL.5.pos.bedGraph


title: BS004 CDI_astrocytes

description:
RRBS
bisulfite converted DNA

value: iPSC derived astrocytes


title: JS170716

description: Negative control expeimernt for K562 TimeLapse-seq with  s4U treatment but no chemical treatment.


title: JS170703


title: JS170715


title: humanZFY-full.unbound

city: Palo Alto

first: Zheng

last: Zuo

state: CA

address: Stanford

department: Genetics

institute: Stanford university

data_processing:
Library strategy: Spec-seq
Binding site extraction: For each sequencing read, the binding site is embedded in the middle with prefixed flanking sequences. So I used unix command "sed -n 's/^.*TCAC.\(.................\)AGAT.*/\1/p' ZFY.bound.raw" to extract the binding site content.
Variant reads counting and sorting: For each randomized binding site, its number in Bound and Unbound portions were counted separately. The Bound/Unbound ratio was supposedly porportional to its relative binding affinity, and the negative logarithm of this ratio indicates the relative binding energy in kT unit.
Energy logo visualization: Based on the binding energy for particular reference and all its single variants, an energy logo can be generated to indicate the specificity of particular protein-DNA interactions.
Energy matrix regression: http://stormo.wustl.edu/cgi-bin/gsahota/sampling.pl
Energy logo visualization: http://stormo.wustl.edu/EnergyModel
Supplementary_files_format_and_content: All processed data were saved in excel files, including the sequence, bound reads, unbound reads, Bound/Unbound ratio, relative binding energy for each variant.

source_name: humanZFY-full

extract_protocol:
After EMSA, DNA fragments were cut and extracted by gel extraction buffer at 50C for 30mins.
For each portion of DNA fragment, PE1-Genetics and indexed PE2 PCR primers were used to PCR amplify extracted DNA by at least 8 cycles (95C 15s, 52C 15s, 72C 30s)
For each particular sample, there are two raw data files, i.e., bound reads and unbound reads with different Illumina Index. The processed data file was based on analysis of Bound and Unbound data together.

treatment_protocol: All EMSA reactions were done in 12% Tris-glycine gel, 200V, 30mins

tag: experimental condition

value: In vitro protein-DNA binding reactions

tag: dna library composition

tag: recombinant protein

value: human ZFY DNA binding domain


title: BS005 CDI_neurons

description:
RRBS
bisulfite converted DNA


title: humanZFY-full.bound


title: BS003 CDI_astrocytes

description:
RRBS
bisulfite converted DNA


title: BS012 CO_astrocytes

description:
RRBS
bisulfite converted DNA


title: JS170713

value: No

value: Yes


title: JS170701

description: Negative control expeimernt for K562 TimeLapse-seq without s4U treatment.


title: humanZFY(F9-F13).unbound

value: human ZFY DNA binding domain (F9-F13)


title: humanZFY(F11-F13).bound

value: human ZFY DNA binding domain (F11-F13)


title: humanZFY(F9-F13).bound


title: BS002 MOCK

description:
WGBS
bisulfite converted DNA

source_name: Whole organoids

value: whole organoid

value: H9 derived - WiCell (WAO9)


title: BS001 ZIKV

description:
WGBS
bisulfite converted DNA

value: ZIKV


title: humanZFY(F11-F13).unbound


title: JS170702


title: BS011 GIBCO_neural progenitors

description:
RRBS
bisulfite converted DNA

value: ZIKVneg


title: Control rep2

city: Antwerp

last: Krivoshiev

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

data_processing:
Reads were mapped to the human reference genome (UCSC hg19) and only reads that were uniquely mapped and mapped concordantly in pairs were retained.
Alignment, mapping, and annotation steps were performed with CLC Genomics Workbench (CLC Bio, DEN) using default parameters.
Samples were normalised by quantile normalisation.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited txt with Expression values|Normalized expression values|Transcripts annotated|Detected transcripts|Exon length|Unique gene reads|Total gene reads|Unique exon reads|Total exon reads|Ratio of unique to total (exon reads)|Unique exon-exon reads|Total exon-exon reads|Unique intron reads|Total intron reads |Ratio of intron to total gene reads|Exons|RPKM|Chromosome|Chromosome region start|Chromosome region end

source_name: Human Hepatocellular Carcinoma Cell Line (HepG2)

growth_protocol: The human hepatocellular carcinoma cell line, HepG2 (ATCC HB-8065), was maintained as a monolayer in T-25 Nunc culture flasks in Minimum Essential Medium supplemented with Earle's salts (Gibco, USA), 1 mM sodium pyruvate, 4 mM l-glutamine, 1% non-essential amino acids, 50 IU/ml penicillin, 50 mg/ml streptomycin, and 10% heat-inactivated foetal bovine serum (FBS). Cells were cultured in a 37 °C incubator under 5% CO2, and once reaching 70–80% confluency, were passaged using 0.25% trypsin/ethylenediaminetetraacetic acid (EDTA), without reaching a maximum of 25 passages.

extract_protocol:
The combined TRIzol (Invitrogen, USA) and RNeasy (Qiagen, GER) approach was adopted for RNA isolation as it yields high RNA quality required for RNA-seq. This involved extracting RNA from cells with TRIzol as per manufacturer's instructions through to phase separation, at which point the RNA in the aqueous phase was treated as lysate and then subjected to RNA clean up using the RNeasy kit according to manufacturer's instructions. RNA was stored at − 80 °C prior to library preparation.
Sequencing libraries were prepared using the TruSeq® Stranded mRNA Sample Preparation kit (Illumina, USA) following the manufacturer's protocol.
Prepared libraries were 2 × 50 bp paired-end sequenced using the Illumina HiSeq® 1500 platform (Illumina, USA).

treatment_protocol: 3 × 105 HepG2 cells were seeded per well in 6-well plates and allowed to culture for 72 h for acclimatisation after detachment/reattachment. The number of seeding cells was optimised to allow for the necessary amount of RNA to be extracted after treatments while cells were at 70–80% confluency by the end of treatments to prevent over-confluency. 2.5 μM and 125 μM TBOEP in 0.1% DMSO were used for exposures to low and high concentrations respectively (concentrations at which there was an absence of cytotoxicity). Final DMSO concentrations in treatments did not exceed 0.1%, equivalent or even lower than the final concentrations used in other MOA transcriptomic studies of other chemicals in HepG2 cells. Control treatments included cells treated with 0.1% DMSO only. Cells were exposed for 72 h before RNA isolation. Treatments were conducted as triplicates, involving separate seeding of cells (thus forming three separate cell populations), separate treatment of each cell population with compound solutions made up independently between replicates, and separate RNA isolations and sequencing reactions for each population of cells.

value: DMSO

tag: concentration

value: 0.1 percent

tag: passages

tag: cell line


title: TBOEP 125uM rep3

tag: treatment

value: TBOEP


title: TBOEP 2.5uM rep1


title: Control rep1


title: TBOEP 125uM rep1


title: TBOEP 125uM rep2


title: Control rep3


title: TBOEP 2.5uM rep2


title: day 7 wound macrophage- biological replicate- 7

city: Columbus

first: Sashwati

last: Roy

state: OH

department: Surgery

institute: Ohio State University

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes  •Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing:
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: day 7 wound macrophages

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Pico Amplification Kit, Module 2 (Affymetrix)

extract_protocol: Extraction of total RNA was performed using miRVana isolation kit according to the manufacturer's instructions.

tag: cell type

value: macrophage

tag: stress

value: wounding

tag: time

value: day 7


title: day 7 wound macrophage- biological replicate- 5


title: day 3 wound macrophage- biological replicate- 1

source_name: day 3 wound macrophages

value: day 3


title: WT_Morphine_4

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: Sample 12

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequencing reads obtained from Periaqueductal gray region brain cells were mapped to mm10 using TopHat2v2.1.0. Counts of reads mapping to genes were obtained using HTSeq-count against Ensembl v75 annotation. Differential expression was done using the voom-limma R package at FDR cutoff of 0.05 (5% False Discovery Rate) and a log fold change cutoff of < -0.05 or > 0.05 was applied.
Genome_build: mm10
Supplementary_files_format_and_content: Counts in tab delimited text files generated using HTSeq-count against Ensembl v75 annotation

molecule: polyA RNA

source_name: Brain cells

growth_protocol: Four biological replicates per group were used for the RNA-Seq studies. PAG punches from two animals were pooled per biological replicate (four 14-gauge punches per sample).

extract_protocol:
Total RNA was isolated with TRIzol and the integrity was confirmed with an Agilent 2100 Bioanalyzer (53).
mRNA-Seq libraries were prepared using a TruSeq RNA sample preparation kit v2 (Illumina).

value: brain

tag: brain region

value: Periaqueductal gray region

tag: Sex

value: Male

value: wildtype

value: morphine


title: KO_Morphine_2

description: Sample 14

value: RGSz1 KO


title: KO_Morphine_1

description: Sample 13


title: day 7 wound macrophage- biological replicate- 6


title: day 3 wound macrophage- biological replicate- 4


title: TBOEP 2.5uM rep3


title: KO_Morphine_4

description: Sample 16


title: BS009 CDI_astrocytes

description:
RRBS
bisulfite converted DNA

value: iPSC derived astrocytes

value: CDI - Caucasian ethnicity


title: day 7 wound macrophage- biological replicate- 8


title: BM from non-tumor bearing NOD-SCID mice with fibroblasts

city: Saint Louis

first: Sreeraj

last: Pillai

state: MO

address: 660 S Euclid Avenue, CB 8109

institute: Washington University School of Medicine

description: BM collected tinia and femur

hyb_protocol: Hybridization was done following NuGEN’s recommendations using Affymetrix fluidic stations and Affymetrix hybridization, wash and stain kit.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Affymetrix CEL files were imported into Partek Genomics Suite v6.5 and processed using the RMA algorithm without probe filtering.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Control, bone marrow

label_protocol: lablelling was done using NuGEN Encore Biotin module.

extract_protocol: BM from the four long bones of each animal was pooled and cells were pelleted down from the entire volume of BM collected which was used for RNA extraction.  Total RNA was isolated from BM samples using Trizol reagent (Invitrogen) according to manufacturer’s protocol.  The extracted RNA was quantified and qualitatively assessed using an Agilent Bioanalyzer and RNA NanoChip assay. cDNA synthesis and amplification was performed using the Ovation Pico SL kit from NuGEN.

tag: phenotype

value: Non-tumor bearing

value: Bone marrow


title: Splenic metastatic tumor WHIM17B29

description: Tumor tissue

source_name: PDX, spleenic metastatic tumor

value: Tumor bearing

value: Tumor


title: Primary xenograft tumor WHIM17B29

description: Tumor tissue

source_name: PDX, primary breast tumor


title: KO_Morphine_3

description: Sample 15

tag: genotype


title: BM from PDX mice WHIM17C1182

description: BM collected tinia and femur

source_name: Tumor bearing PDX, bone marrow

tag: tissue


title: BM from non tumor bearing NOD-SCID mice

description: BM collected tinia and femur


title: BM from PDX mice WHIM17C1180

description: BM collected tinia and femur


title: WT_Morphine_3

description: Sample 11


title: BM from PDX mice WHIM17B29

description: BM collected tinia and femur


title: KO_Naive_3

description: Sample 7

value: naïve


title: BM from PDX mice WHIM17B1188

description: BM collected tinia and femur


title: day 3 wound macrophage- biological replicate- 3

value: macrophage


title: WT_Morphine_1

description: Sample 9


title: KO_Naive_4

description: Sample 8


title: WT_Morphine_2

description: Sample 10


title: WT_Naive_4

description: Sample 4


title: KO_Naive_1

description: Sample 5


title: BM from PDX mice WHIM17B1141

description: BM collected tinia and femur


title: WT_Naive_1

description: Sample 1


title: WT_Naive_2

description: Sample 2


title: WT_Naive_3

description: Sample 3


title: BM from WHIM17B1139

description: BM collected tinia and femur


title: BM from PDX mice WHIM17A1384

description: BM collected tinia and femur


title: KO_Naive_2

description: Sample 6


title: RNAseq_humanSET2_Rux_rep2

value: Ruxolitinib


title: WT_MK_24hr_1

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description:
251486836642
WT BMDCs were Mock treated and harvested at 24 hours. Replicate number 1

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: BMDCs were prepared from WT or Il-1r-/- mice. Cells from both genotypes were infected with WNV (MOI 2.5). Total RNA was harvested at 24 and 48 hours post-treatment from these and time-matched mock control cells from the appropriate genotype. Relative gene expression levels were determined by Agilent Whole-Genome mouse microarray (4x44K chip)

extract_protocol: Total RNA was extracted from BMDCs using 350 ml/sample buffer RLT in 350 ml of RNA extraction buffer (RLT, Qiagen), and total RNA was extracted using an RNeasy kit (Qiagen).

treatment_protocol: WT or IL-1R KO BMDCs were either mock-treated or pre-treated with 100 ng IL-1b for 24 hours. Cells were then either mock-infected or infected with WNV at an MOI of 2.5.

tag: genotype/variation

value: WT

value: bone marrow-derived dendritic cells (BMDCs)

value: Mock

tag: timepoint

tag: replicate