title: healthy_monocytes_autologous_serum_IFNa2b_6hrs_A

treatment_protocol: incubated with 20% autologous serum alone or in the presence of 1000 U/ml of IFNα2b (Schering Plough, Kenilworth, NJ) in 6-well plates at a concentration of 106 monocytes per well in 3 ml of media. After incubation for six hours at 37 ⁰C, cells were harvested and RNA was extracted.

value: healthy

value: monocyte

tag: treatment

value: autologous serum + IFNa2b


title: lupus_monocytes_posForMixedLymphocyteReaction_6h_A SLE29

status: Public on Jun 03 2014

type: RNA

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

country: USA

institute: Baylor Research Institute

hyb_protocol: cRNA was fragmented and hybridized to the HG-U133A & HG-U133B Affymetrix GeneChip® arrays that contain 45,000 probe sets at 45 ⁰C for 16 hours

scan_protocol: GeneChip arrays were washed, stained, and scanned according to protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA)

data_processing: To analyze the data from monocytes from untreated and treated SLE patients, 5 samples in each data set were used for final analysis, and compared to 5 samples from healthy donors.  Data were normalized to this set of healthy controls.  For each set of experiments, unsupervised clustering of samples was performed using the list of genes present in at least one sample to rule out technical variability.  For supervised analysis, an Affymetrix flag call of ‘present’ in 3 out of 5 samples from each cohort was used to designate the filter for a reliable intensity measurement from each individual gene chip.  These two lists combined were used as a quality control measure for class comparison, which was performed using a non- parametric ranking statistical analysis test (Mann Whitney) as well as a 2-fold difference in the average normalized value of healthy to test set.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: RNA was labeled using the GeneChip® Two-Cycle Target Labeling kit (Affimetrix, Santa Clara, CA) following the manufacturer’s recommended procedures

extract_protocol: RNA was extracted using either the RNeasy® Mini Kit (Qiagen, Valencia, CA), if >5x105 were recovered, or PicoPureTM RNA Isolation Kit (Molecular Devices Corporation, Sunnyvale, CA) when <5x105 cells were recovered

treatment_protocol: CFSE labeled CD4 T cells (1x105) were incubated with or without monocytes (2x104) in 96-well plates in complete RPMI medium. Cells were harvested at 0hrs (control) or six hours. After 6 hours of culture, harvested cells were enriched by depleting T cells with CD3 Dynabeads® (Invitrogen, Carlsbad, CA), and RNA was extracted for use in microarray testing.

tag: disease state

value: systemic lupus erythematosus

tag: cell type

value: monocytes positive For Mixed Lymphocyte Reaction

tag: time

tag: subject


title: lupus_monocytes_negForMixedLymphocyteReaction_6h_A SLE20

value: monocytes negative For Mixed Lymphocyte Reaction


title: healthy_monocytes_autologous_serum_SLE160_A

treatment_protocol: Blood monocytes isolated from healthy volunteers were incubated in RPMI supplemented with L-glutamine, Gentamicin, and Penicillin in 6-well plates (1,000,000 cells/well, 3 ml of medium) with either 20% autologous serum or 20% SLE sera from active and untreated patients. Cells were harvested and RNA was extracted after 6 hours incubation. In some experiments, blood monocytes isolated from healthy volunteers were incubated in RPMI supplemented with L-glutamine, Gentamicin, and Penicillin in 24-well plates (500,000 cells/well/1 ml of medium) with either 20% autologous serum or 20% SLE sera from active and untreated lupus patients.

value: autologous serum


title: lupus_monocytes_posForMixedLymphocyteReaction_+CD4 T cells_A SLE79

value: +CD4 T cells


title: healthy_monocytes_SLE_serum_SLE143_A

value: SLE serum


title: healthy_monocytes_SLE_serum_SLE145_A


title: lupus_monocytes_posForMixedLymphocyteReaction_0h_A SLE79


title: healthy_monocytes_autologous_serum_6hrs_A


title: healthy_monocytes_autologous_serum_SLE145_A


title: lupus_monocytes_posForMixedLymphocyteReaction_+CD4 T cells_A SLE29


title: lupus_monocytes_negForMixedLymphocyteReaction_+CD4 T cells_A SLE20


title: healthy_monocytes_autologous_serum_SLE143_A


title: lupus_monocytes_posForMixedLymphocyteReaction_6h_A SLE185


title: lupus_monocytes_posForMixedLymphocyteReaction_+CD4 T cells_A SLE183


title: lupus_monocytes_posForMixedLymphocyteReaction_6h_A SLE183


title: healthy_monocytes_SLE_serum_SLE160_A


title: lupus_monocytes_posForMixedLymphocyteReaction_+CD4 T cells_A SLE185


title: lupus_monocytes_posForMixedLymphocyteReaction_0h_A SLE183


title: lupus_monocytes_negForMixedLymphocyteReaction_6h_A SLE177


title: lupus_monocytes_negForMixedLymphocyteReaction_+CD4 T cells_A SLE177


title: IL4 DC-ND324-HKSE-12h

status: Public on Oct 22 2014

hyb_protocol: 750 ng of amplified labeled RNA were hybridized overnight to Illumina HT12 V3 beadchips (Illumina, San Diego, CA).

scan_protocol: Following hybridization, each chip was washed, blocked, stained, and scanned on an Illumina BeadStation 500 following the manufacturer’s protocols.

data_processing:
Matrix normalized data was Global Average Normalized per Illumina GenomeStudio and all signal <10 has been set to 10.
The data was generated using in-house code that uses GenomeStudio's Global Avg. Normalization algorithm. It calculates the avg signal for each sample and the avg signal for the dataset. Then the signals are multiplied by the factor: (avg dataset signal/avg sample signal). The net result is that all sample average and the dataset average are equal.
Matrix non-normalized data is the raw data computed from the chip by GenomeStudio.

source_name: IL4 DC_HKSE_12h

label_protocol: 250 ng of RNA from all samples passing quality control were amplified and labeled using the Illumina TotalPrep-96 RNA amplification kit (Ambion, Austin, TX).

growth_protocol:
Monocyte-derived dendritic cell cultures: Monocytes were obtained from frozen fraction 5 from healthy donor apheresis. Cells were thawed for one minute in a 37°C water bath and resuspended in 1x phosphate buffered saline (PBS). Cells were spun at 350g for 7 minutes, washed with 1x PBS, counted, washed again, and resuspended in PBS / 2% Fetal Bovine Serum (FBS) / 1mM EDTA at 5x107 cells/mL. Monocytes were then enriched using the EasySep Human Monocyte Enrichment Without CD16 Depletion Kit (#19058, StemCell Technologies) according to the manufacturer’s protocol. Once enriched, cells were counted and resuspended in serum-free CellGenix DC medium (#2005, CellGenix, Germany) / 1% Penicillin/Streptomycin at 1x106 cells/mL. GM-CSF (Leukine®, Genzyme Corporation) was added for all DC subsets at 200 ng/mL. For IL-4 DC, recombinant IL-4 was added at 50 ng/mL and cells were fed a full dose of GM-CSF and IL-4 at day 2 and day 4 of a 6-day culture. For IFN-alpha DC, IFN-alpha was added at 500U/mL, and cells were fed a full dose of GM-CSF and IFN-alpha at day 1 of a 3-day culture. Cell suspensions were injected into 72mL sterile culture bags (#2PF-0072-AC, AFC, Gaithersburg, MD) with a 60mL syringe and bags were closed with injection ports. Feeding of the cells during the culture was done with a 1mL syringe through the injection ports. Cells were cultured in an incubator at 37°C, 5% CO2.
Influenza Virus propagation: Madin Darby Canine Kidney (MDCK) cells were grown to of 80% confluent in 75 cm flask. The cells were infected with A/Brisbane/59/2007 IVR 148 (H1N1) strain at a ratio of 1:100 for 1 hour. The cells were washed twice and incubated for 48 to 72 hours with media (1 X Opti-MEM). Supernatant was harvested post-infection. The virus titer from the supernatant was assessed by plague assay. Experiments were performed under BSL-3 laboratory conditions.
Salmonella enterica culture: Bacteria were thawed and plated on a nutrient agar (Difco) plate with a sterile 10uL inoculating loop, incubated overnight at 37°C and subsequently stored at 4°C. A single colony was picked up from the agar plate and inoculated in 6mL Difco nutrient broth (in 15mL Falcon tube), and cultured overnight at 37°C on a shaker. After overnight expansion, bacter were brought in log phase by culturing 500uL of bacterial preparation in 4.5mL fresh broth for 1.5 hour at 37°C on a shaker. Bacteria concentration was measured using a standard curve, bacteria were heat-killed for 30 minutes in 72°C water bath and stored at -80°C until use.

extract_protocol: Total RNA was isolated from cell lysates using the RNeasy Mini-Kit (#74104, Qiagen) according to the manufacturer's instructions. Following extraction, an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) was used to measure RNA Integrity Numbers (RIN) for each sample. All samples with RIN values greater than seven were retained for further processing. RNA concentration was measured using a Nanodrop 1000 (Nanodrop Technologies, Wilmington, DE).

treatment_protocol:
Monocyte-derived dendritic cell stimulation: At the end of cultures, cells were collected with a 60 mL syringe, washed in 1x PBS and resuspended in complete RPMI at 1x106 cells/mL. To increase throughput, stimulations were conducted in 96 1mL deep-well plates (Greiner Bio-One) in a total volume of 500uL (5x105 cells). All stimuli used are summarized in Table S1. At the end of the stimulation period, cells were spun at 350g for 7 minutes, washed with 1x PBS, spun again and lysed in 600uL (1x106 cells) or 350uL (5x105) of RLT buffer (#79216, Qiagen). Cell lysates were stored at -80°C until extraction.
Monocyte-derived dendritic cell stimulation with pathogens: IL-4 and IFN-alpha DC were stimulated in vitro for 1, 2, 6, 12 or 24h with either live influenza virus H1N1 Brisbane (Multiplicity of Infection 5:1), heat-killed Salmonella enterica (108 cfu/mL, ATCC# 14028) or heat-killed Staphylococcus aureus (108 cfu/mL, Invivogen, #cat tlr-hksa) at 37°C, 5% CO2. All pathogen stimulations were conducted in 96-deep well plates as described above. At the end of incubation time, cells were washed twice with PBS, lysed in the plate 350 uL RLT buffer (RNEasy Kit, Qiagen) and stored at -80°C.

tag: donor id

tag: tissue

value: whole blood

tag: cell population

value: IL4 DC

tag: culture condition

value: HKSE

tag: dosage

tag: time point


title: lupus_monocytes_negForMixedLymphocyteReaction_0h_A SLE20


title: lupus_monocytes_posForMixedLymphocyteReaction_0h_A SLE185


title: lupus_monocytes_negForMixedLymphocyteReaction_0h_A SLE177


title: lupus_monocytes_negForMixedLymphocyteReaction_0h_A SLE170


title: lupus_monocytes_negForMixedLymphocyteReaction_6h_A SLE170


title: lupus_monocytes_negForMixedLymphocyteReaction_+CD4 T cells_A SLE142


title: lupus_monocytes_negForMixedLymphocyteReaction_0h_A SLE142


title: monocyte-healthy-19_A

extract_protocol: mDCs and monocytes from healthy volunteers were sorted on a FACSAria® (BD Bioscience, Franklin Lakes, NJ) as Lineage- CD11c+HLA-DR+ and CD14+HLA-DR+ cells, respectively. RNA was extracted from isolated cells using either the RNeasy® Mini Kit (Qiagen, Valencia, CA), if >5x105 were recovered, or PicoPureTM RNA Isolation Kit (Molecular Devices Corporation, Sunnyvale, CA) when <5x105 cells were recovered

treatment_protocol: none, healthy monocytes.


title: monocyte-healthy-1_A


title: lupus_monocytes_negForMixedLymphocyteReaction_+CD4 T cells_A SLE170


title: monocyte-healthy-11_A


title: lupus_monocytes_negForMixedLymphocyteReaction_6h_A SLE142


title: healthy_monocytes_ND140+AS+IFNa2b_1Hr_A

treatment_protocol: incubated with 20% autologous serum alone or in the presence of 1000 U/ml of IFNα2b (Schering Plough, Kenilworth, NJ) in 6-well plates at a concentration of 106 monocytes per well in 3 ml of media. After incubation for one hour at 37 ⁰C, cells were harvested and RNA was extracted. Identical experiments were done after the following incubation time points: six hours, twenty four hours, two days, and three days.

value: autologous serum IFNa2b


title: mDC-healthy-19_A

value: mDC


title: healthy_monocytes_ND140+AS+IFNa2b_24Hrs_A


title: mDC-healthy-6_A


title: monocyte-healthy-5_A


title: healthy_monocytes_ND140+AS_3days_A


title: mDC-healthy-1_A


title: healthy_monocytes_ND140+AS_6Hrs_A


title: healthy_monocytes_ND140+AS+IFNa2b_2days_A


title: mDC-healthy-5_A


title: healthy_monocytes_ND140+AS_1Hr_A


title: healthy_monocytes_ND140+AS_24Hrs_A


title: healthy_monocytes_AS+IFNa2b_6Hrs_A


title: healthy_monocytes_AS+IFNa2b_3days_A


title: healthy_monocytes_ND140+AS+IFNa2b_6Hrs_A


title: healthy_monocytes_ND140+AS+IFNa2b_3days_A


title: healthy_monocytes_AS_3days_A


title: healthy_monocytes_AS+IFNa2b_24Hrs_A


title: monocyte-healthy-6_A


title: mDC-healthy-11_A


title: healthy_monocytes_AS+IFNa2b_2days_A


title: healthy_monocytes_AS_6Hrs_A


title: healthy_monocytes_ND140+AS_2days_A


title: healthy_monocytes_AS_24Hrs_A


title: healthy_monocytes_autologous_serum_6hrs_B


title: healthy_monocytes_autologous_serum_IFNa2b_6hrs_B


title: lupus_monocyte_145_A

source_name: lupus monocytes

treatment_protocol: Monocytes were isolated from PBMCs from healthy donors and SLE patients by positive selection using MACS columns (Miltenyi Biotech Inc., Auburn, CA)

value: pediatric systemic lupus erythematosus


title: healthy_monocytes_AS_2days_A


title: lupus_monocyte_143_A


title: healthy_monocytes_SLE_serum_SLE145_B


title: lupus_monocyte_ 137_A

value: SLE 137


title: lupus_monocyte_144_A


title: healthy_monocyte_152_A

source_name: healthy monocytes


title: healthy_monocyte_99_A


title: healthy_monocyte_58_A


title: healthy_monocytes_SLE_serum_SLE160_B


title: healthy_monocytes_SLE_serum_SLE143_B


title: healthy_monocytes_autologous_serum_SLE160_B


title: healthy_monocyte_154_A


title: healthy_monocytes_autologous_serum_SLE145_B


title: lupus_monocyte_ 41_A

value: SLE 41


title: healthy_monocyte_104_A

value: healthy


title: lupus_monocytes_posForMixedLymphocyteReaction_+CD4 T cells_B SLE79

value: monocytes posForMixedLymphocyteReaction


title: healthy_monocytes_AS+IFNa2b_1Hr_A

value: monocyte


title: healthy_monocytes_autologous_serum_SLE143_B


title: lupus_monocytes_posForMixedLymphocyteReaction_0h_B SLE79

value: systemic lupus erythematosus


title: healthy_monocytes_AS_1Hr_A


title: lupus_monocytes_posForMixedLymphocyteReaction_6h_B SLE29


title: lupus_monocytes_posForMixedLymphocyteReaction_+CD4 T cells_B SLE29


title: lupus_monocytes_negForMixedLymphocyteReaction_6h_B SLE20


title: lupus_monocytes_posForMixedLymphocyteReaction_+CD4 T cells_B SLE185


title: lupus_monocytes_negForMixedLymphocyteReaction_0h_B SLE20


title: lupus_monocytes_negForMixedLymphocyteReaction_+CD4 T cells_B SLE20


title: lupus_monocytes_negForMixedLymphocyteReaction_0h_B SLE170


title: lupus_monocytes_posForMixedLymphocyteReaction_0h_B SLE185


title: lupus_monocytes_negForMixedLymphocyteReaction_0h_B SLE177


title: lupus_monocytes_negForMixedLymphocyteReaction_+CD4 T cells_B SLE142


title: lupus_monocytes_negForMixedLymphocyteReaction_+CD4 T cells_B SLE177


title: lupus_monocytes_posForMixedLymphocyteReaction_6h_B SLE79


title: lupus_monocytes_posForMixedLymphocyteReaction_+CD4 T cells_B SLE183


title: lupus_monocytes_negForMixedLymphocyteReaction_6h_B SLE177


title: lupus_monocytes_negForMixedLymphocyteReaction_0h_B SLE142


title: lupus_monocytes_negForMixedLymphocyteReaction_+CD4 T cells_B SLE170


title: lupus_monocytes_negForMixedLymphocyteReaction_6h_B SLE142


title: lupus_monocytes_posForMixedLymphocyteReaction_6h_B SLE185


title: monocyte-healthy-19_B


title: monocyte-healthy-5_B


title: monocyte-healthy-11_B


title: monocyte-healthy-1_B


title: lupus_monocytes_negForMixedLymphocyteReaction_6h_B SLE170


title: monocyte-healthy-6_B


title: lupus_monocytes_posForMixedLymphocyteReaction_6h_B SLE183


title: mDC-healthy-11_B


title: mDC-healthy-5_B


title: mDC-healthy-1_B


title: mDC-healthy-19_B


title: mDC-healthy-6_B


title: healthy_monocytes_ND140+AS+IFNa2b_3days_B


title: healthy_monocytes_ND140+AS+IFNa2b_6Hrs_B


title: healthy_monocytes_ND140+AS+IFNa2b_1Hr_B


title: healthy_monocytes_ND140+AS_3days_B


title: healthy_monocytes_ND140+AS_2days_B


title: healthy_monocytes_AS+IFNa2b_3days_B


title: healthy_monocytes_ND140+AS_6Hrs_B


title: healthy_monocytes_ND140+AS+IFNa2b_24Hrs_B


title: healthy_monocytes_ND140+AS_1Hr_B


title: healthy_monocytes_ND140+AS_24Hrs_B


title: healthy_monocytes_AS+IFNa2b_1Hr_B


title: healthy_monocytes_AS+IFNa2b_24Hrs_B


title: healthy_monocytes_AS_3days_B


title: healthy_monocytes_AS+IFNa2b_2days_B


title: healthy_monocytes_AS+IFNa2b_6Hrs_B


title: healthy_monocytes_ND140+AS+IFNa2b_2days_B


title: healthy_monocytes_AS_2days_B


title: healthy_monocytes_AS_1Hr_B


title: healthy_monocytes_AS_24Hrs_B


title: healthy_monocytes_AS_6Hrs_B


title: lupus_monocyte_ 41_B


title: lupus_monocyte_143_B


title: lupus_monocyte_145_B


title: healthy_monocyte_99_B


title: healthy_monocyte_154_B


title: lupus_monocyte_144_B


title: healthy_monocyte_58_B


title: lupus_monocyte_ 137_B


title: healthy_monocyte_152_B


title: healthy_monocyte_104_B


title: NCH-VK-86D_LAIV_D30

status: Public on Mar 31 2014

description:
NCH-VK-86D
7509310056_G

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with BeadArray Reader 500X

data_processing: The data were normalised using average normalization with GenomeStudio Version 4

source_name: whole blood_LAIV_D30

label_protocol: Biotinylated cRNA were prepared with the IlluminaÂ® TotalPrep-96 RNA Amplification Kit

extract_protocol: RNA was extracted with MagMAX RNA Isolation Kit. Quality control was performed with Agilent Bioanalyser.

tag: vaccine

value: LAIV

tag: age (years)

tag: gender

value: M

tag: race

value: W


title: NCH-VK-86C_LAIV_D7

description:
NCH-VK-86C
7509301165_J

source_name: whole blood_LAIV_D7


title: NCH-VK-86B_LAIV_24h

description:
NCH-VK-86B
7509301136_F

source_name: whole blood_LAIV_24h


title: NCH-VK-86A_LAIV_D0

description:
NCH-VK-86A
7509310040_L

source_name: whole blood_LAIV_D0


title: NCH-VK-73A_TIV_D0

description:
7509310056_I
NCH-VK-73A

source_name: whole blood_TIV_D0

value: TIV

value: A/Indian


title: NCH-VK-57A_TIV_D0

description:
7509310056_E
NCH-VK-57A

value: whole blood

value: F


title: NCH-VK-73D_TIV_D30

description:
7509310055_H
NCH-VK-73D

source_name: whole blood_TIV_D30


title: NCH-VK-59A_TIV_D0

description:
7509310055_I
NCH-VK-59A


title: NCH-VK-79B_LAIV_24h

description:
7509310056_D
NCH-VK-79B


title: NCH-VK-77A_LAIV_D0

description:
7509310056_A
NCH-VK-77A

value: Bi


title: NCH-VK-59C_TIV_D7

description:
7509310055_L
NCH-VK-59C

source_name: whole blood_TIV_D7


title: NCH-VK-62C_LAIV_D7

description:
7509310056_F
NCH-VK-62C


title: NCH-VK-84D_LAIV_D30

description:
7509310056_J
NCH-VK-84D


title: NCH-VK-68B_LAIV_24h

description:
7509310056_H
NCH-VK-68B


title: NCH-VK-76C_TIV_D7

description:
7509310056_C
NCH-VK-76C


title: NCH-VK-71A_TIV_D0

description:
7509310055_J
NCH-VK-71A


title: NCH-VK-76A_TIV_D0

description:
7509310055_F
NCH-VK-76A


title: NCH-VK-67D_LAIV_D30

description:
7509310055_B
NCH-VK-67D


title: NCH-VK-74D_LAIV_D30

description:
7509310055_K
NCH-VK-74D


title: NCH-VK-72D_TIV_D30

description:
7509310056_B
NCH-VK-72D


title: NCH-VK-66D_TIV_D30

description:
7509310055_G
NCH-VK-66D


title: NCH-VK-85B_TIV_24h

description:
7509310055_C
NCH-VK-85B

source_name: whole blood_TIV_24h


title: NCH-VK-64A_LAIV_D0

description:
7509310043_K
NCH-VK-64A


title: NCH-VK-66B_TIV_24h

description:
7509310055_D
NCH-VK-66B


title: NCH-VK-63B_TIV_24h

description:
7509310055_E
NCH-VK-63B


title: NCH-VK-72B_TIV_24h

description:
7509310043_L
NCH-VK-72B


title: NCH-VK-54B_LAIV_24h

description:
7509310055_A
NCH-VK-54B


title: NCH-VK-65A_LAIV_D0

description:
7509310043_J
NCH-VK-65A


title: lupus_monocytes_posForMixedLymphocyteReaction_0h_B SLE183


title: NCH-VK-81D_LAIV_D30

description:
7509310043_F
NCH-VK-81D


title: NCH-VK-61D_LAIV_D30

description:
7509310043_H
NCH-VK-61D


title: NCH-VK-75A_LAIV_D0

description:
7509310043_E
NCH-VK-75A


title: NHC-VK-68A_LAIV_D0

description:
7509310043_G
NHC-VK-68A


title: NCH-VK-59B_TIV_24h

description:
7509310040_K
NCH-VK-59B


title: NCH-VK-57C_TIV_D7

description:
7509310043_I
NCH-VK-57C


title: NCH-VK-77C_LAIV_D7

description:
7509310043_B
NCH-VK-77C


title: NCH-VK-55C_TIV_D7

description:
7509310040_J
NCH-VK-55C


title: NCH-VK-50A_TIV_D0

description:
7509310043_D
NCH-VK-50A


title: NCH-VK-55B_TIV_24h

description:
7509310040_G
NCH-VK-55B


title: NCH-VK-85C_TIV_D7

description:
7509310040_F
NCH-VK-85C


title: NHC-VK-60C_TIV_D7

description:
7509310043_C
NHC-VK-60C


title: NCH-VK-67B_LAIV_24h

description:
7509310040_H
NCH-VK-67B


title: NCH-VK-56A_LAIV_D0

description:
7509310040_I
NCH-VK-56A


title: NCH-VK-64B_LAIV_24h

description:
7509310040_E
NCH-VK-64B


title: NCH-VK-82B_LAIV_24h

description:
7509310040_C
NCH-VK-82B

value: A/Chinese


title: NCH-VK-65C_LAIV_D7

description:
7509310043_A
NCH-VK-65C


title: NCH-VK-57B_TIV_24h

description:
7509310035_I
NCH-VK-57B


title: NHC-VK-60B_TIV_24h

description:
7509310040_D
NHC-VK-60B


title: NCH-VK-72A_TIV_D0

description:
7509310035_J
NCH-VK-72A


title: NHC-VK-60A_TIV_D0

description:
7509310035_F
NHC-VK-60A


title: NCH-VK-65B_LAIV_24h

description:
7509310040_B
NCH-VK-65B


title: NCH-VK-79C_LAIV_D7

description:
7509310035_K
NCH-VK-79C


title: NCH-VK-85A_TIV_D0

description:
7509310035_H
NCH-VK-85A


title: NCH-VK-80C_LAIV_D7

description:
7509310040_A
NCH-VK-80C


title: NCH-VK-84A_LAIV_D0

description:
7509310035_L
NCH-VK-84A


title: NCH-VK-56C_LAIV_D7

description:
7509310035_D
NCH-VK-56C


title: NCH-VK-78A_TIV_D0

description:
7509310035_G
NCH-VK-78A


title: NCH-VK-69A_TIV_D0

description:
7509310035_C
NCH-VK-69A


title: NCH-VK-68D_LAIV_D30

description:
7509310035_B
NCH-VK-68D


title: NCH-VK-80B_LAIV_24h

description:
7509310035_A
NCH-VK-80B


title: NCH-VK-74C_LAIV_D7

description:
7509310032_L
NCH-VK-74C


title: NCH-VK-51B_LAIV_24h

description:
7509310032_F
NCH-VK-51B


title: NCH-VK-57D_TIV_D30

description:
7509310032_J
NCH-VK-57D


title: NCH-VK-53C_TIV_D7

description:
7509310032_H
NCH-VK-53C


title: NCH-VK-85D_TIV_D30

description:
7509310032_I
NCH-VK-85D


title: NCH-VK-56D_LAIV_D30

description:
7509301165_K
NCH-VK-56D


title: NCH-VK-70C_TIV_D7

description:
7509310032_K
NCH-VK-70C


title: NCH-VK-51A_LAIV_D0

description:
7509310032_C
NCH-VK-51A


title: NCH-VK-53A_TIV_D0

description:
7509310032_D
NCH-VK-53A


title: NCH-VK-69C_TIV_D7

description:
7509310032_E
NCH-VK-69C


title: NCH-VK-61B_LAIV_24h

description:
7509310032_A
NCH-VK-61B


title: NCH-VK-78C_TIV_D7

description:
7509301165_G
NCH-VK-78C


title: NCH-VK-69D_TIV_D30

description:
7509301165_E
NCH-VK-69D


title: NCH-VK-52B_LAIV_24h

description:
7509301165_B
NCH-VK-52B


title: NCH-VK-78B_TIV_24h

description:
7509301165_L
NCH-VK-78B


title: NCH-VK-50B_TIV_24h

description:
7509301136_L
NCH-VK-50B


title: NCH-VK-76B_TIV_24h

description:
7509310032_B
NCH-VK-76B


title: NCH-VK-52C_LAIV_D7

description:
7509301165_I
NCH-VK-52C


title: NCH-VK-83A_LAIV_D0

description:
7509301165_H
NCH-VK-83A


title: NCH-VK-79A_LAIV_D0

description:
7509301165_F
NCH-VK-79A


title: NCH-VK-51D_LAIV_D30

description:
7509301165_D
NCH-VK-51D

value: N


title: NCH-VK-80D_LAIV_D30

description:
7509301165_A
NCH-VK-80D


title: NCH-VK-61C_LAIV_D7

description:
7509301136_K
NCH-VK-61C


title: NCH-VK-63C_TIV_D7

description:
7509301136_I
NCH-VK-63C


title: NCH-VK-84B_LAIV_24h

description:
7509301165_C
NCH-VK-84B


title: NCH-VK-78D_TIV_D30

description:
7509301136_H
NCH-VK-78D


title: NCH-VK-65D_LAIV_D30

description:
7509301136_J
NCH-VK-65D


title: NCH-VK-67C_LAIV_D7

description:
7509301136_G
NCH-VK-67C


title: NCH-VK-66C_TIV_D7

description:
7509301136_E
NCH-VK-66C


title: NCH-VK-52A_LAIV_D0

description:
7509301136_C
NCH-VK-52A


title: NCH-VK-50C_TIV_D7

description:
7509301136_B
NCH-VK-50C


title: NCH-VK-67A_LAIV_D0

description:
7509301128_G
NCH-VK-67A


title: NCH-VK-63A_TIV_D0

description:
7509301128_L
NCH-VK-63A


title: NCH-VK-55A_TIV_D0

description:
7509301128_E
NCH-VK-55A


title: NCH-VK-66A_TIV_D0

description:
7509301128_H
NCH-VK-66A


title: NCH-VK-82C_LAIV_D7

description:
7509301136_D
NCH-VK-82C


title: NCH-VK-63D_TIV_D30

description:
7509301084_L
NCH-VK-63D


title: NCH-VK-62B_LAIV_24h

description:
7509301128_J
NCH-VK-62B


title: NCH-VK-81B_LAIV_24h

description:
7509301128_C
NCH-VK-81B


title: NCH-VK-52D_LAIV_D30

description:
7509301128_K
NCH-VK-52D


title: NCH-VK-58C_TIV_D7

description:
7509301084_E
NCH-VK-58C


title: NCH-VK-56B_LAIV_24h

description:
7509301084_F
NCH-VK-56B


title: NCH-VK-53D_TIV_D30

description:
7509301084_K
NCH-VK-53D


title: NCH-VK-55D_TIV_D30

description:
7509301128_F
NCH-VK-55D


title: NCH-VK-76D_TIV_D30

description:
7509301084_I
NCH-VK-76D


title: NCH-VK-83D_LAIV_D30

description:
7509301128_D
NCH-VK-83D


title: NCH-VK-81A_LAIV_D0

description:
7509301128_I
NCH-VK-81A


title: NCH-VK-53B_TIV_24h

description:
7509301084_C
NCH-VK-53B


title: NCH-VK-71C_TIV_D7

description:
7509301084_A
NCH-VK-71C


title: NCH-VK-61A_LAIV_D0

description:
7509301084_D
NCH-VK-61A


title: NCH-VK-51C_LAIV_D7

description:
7509301128_B
NCH-VK-51C


title: NCH-VK-69B_TIV_24h

description:
7509301084_G
NCH-VK-69B


title: NCH-VK-73C_TIV_D7

description:
7509301136_A
NCH-VK-73C


title: NCH-VK-80A_LAIV_D0

description:
7509301084_H
NCH-VK-80A


title: NCH-VK-58B_TIV_24h

description:
7509301084_J
NCH-VK-58B


title: NCH-VK-62A_LAIV_D0

description:
7509301084_B
NCH-VK-62A


title: NCH-VK-74A_LAIV_D0

description:
7509301075_L
NCH-VK-74A


title: NCH-VK-77D_LAIV_D30

description:
7509301128_A
NCH-VK-77D


title: NCH-VK-83C_LAIV_D7

description:
7509301075_K
NCH-VK-83C


title: NCH-VK-59D_TIV_D30

description:
7509301075_J
NCH-VK-59D


title: NCH-VK-82D_LAIV_D30

description:
7509301075_F
NCH-VK-82D


title: NCH-VK-64C_LAIV_D7

description:
7509301075_C
NCH-VK-64C


title: NCH-VK-50D_TIV_D30

description:
7509301065_K
NCH-VK-50D


title: NCH-VK-84C_LAIV_D7

description:
7509301065_C
NCH-VK-84C


title: NCH-VK-72C_TIV_D7

description:
7509301075_B
NCH-VK-72C


title: NCH-VK-58D_TIV_D30

description:
7509301075_D
NCH-VK-58D


title: NCH-VK-58A_TIV_D0

description:
7509301065_F
NCH-VK-58A


title: NCH-VK-70D_TIV_D30

description:
7509301065_J
NCH-VK-70D


title: NCH-VK-54D_LAIV_D30

description:
7509301075_I
NCH-VK-54D


title: NCH-VK-68C_LAIV_D7

description:
7509301075_G
NCH-VK-68C


title: NCH-VK-75B_LAIV_24h

description:
7509301075_A
NCH-VK-75B


title: NCH-VK-81C_LAIV_D7

description:
7509301065_G
NCH-VK-81C


title: NCH-VK-79D_LAIV_D30

description:
7509301065_I
NCH-VK-79D


title: NCH-VK-73B_TIV_24h

description:
7509301065_B
NCH-VK-73B


title: NCH-VK-82A_LAIV_D0

description:
7509301065_E
NCH-VK-82A


title: NCH-VK-62D_LAIV_D30

description:
7509301075_E
NCH-VK-62D


title: NCH-VK-64D_LAIV_D30

description:
7509301075_H
NCH-VK-64D


title: Normal-N_LJ_5

status: Public on Nov 18 2013

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: Preprocessing was carried out using GCRMA (through gcrma package from R/Bioconductor). Since samples were processed using two different kits, Combat was used to eliminate the batch effect. However, the presence of genes with small variance precluded successful estimation of the parameters in the sophisticated model used by Combat in this dataset. To circumvent this issue, genes with SD<0.2 were eliminated prior to Combat adjustment of the batch effect.

source_name: human skin biopsy

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

tag: condition

value: Normal

tag: patient

value: Normal skin biopsy

tag: kit

value: Affy


title: NCH-VK-83B_LAIV_24h

description:
7509301065_H
NCH-VK-83B


title: Normal-N_LJ_9


title: Normal-N_LJ_4


title: NCH-VK-54C_LAIV_D7

description:
7509301065_L
NCH-VK-54C


title: Normal-N_LJ_8


title: Normal-N_LJ_10


title: Normal-N_LJ_7


title: Normal-N_LJ_6


title: NHC-VK-60D_TIV_D30

description:
7509301065_D
NHC-VK-60D


title: Normal-N_LJ_2


title: Normal-N_LJ_1


title: Normal-N_LJ_3


title: Columbus Acute RSV 25

status: Public on Nov 12 2013

description: NCH 645

data_processing: The data were normalised using average normalization with Genome Studio version 1.9.0.

source_name: Columbus Acute RSV

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit.

tag: age

value: male

tag: sample group

value: acute Respiratory Syncytial Virus lower respiratory tract infection (RSV LRTI)


title: Columbus Acute RSV 27

description: NCH 574


title: Columbus Acute RSV 22

description: NCH 637


title: Columbus Acute RSV 23

description: NCH 639

value: female


title: Columbus Acute RSV 28

description: NCH 568


title: Columbus Acute RSV 21

description: NCH 635


title: Columbus Acute RSV 19

description: NCH 629


title: Columbus Acute RSV 3

description: NCH 506


title: Columbus Acute RSV 8

description: NCH 518


title: Columbus Acute RSV 7

description: NCH 514


title: Columbus Acute RSV 4

description: NCH 508


title: Columbus Acute RSV 10

description: NCH 532


title: Columbus Acute RSV 20

description: NCH 632


title: Columbus Acute RSV 9

description: NCH 524


title: Columbus Acute RSV 6

description: NCH 513


title: Columbus Acute RSV 17

description: NCH 560


title: NCH-VK-74B_LAIV_24h

description:
7509310032_G
NCH-VK-74B


title: Columbus Acute RSV 24

description: NCH 640


title: Columbus Acute RSV 5

description: NCH 512


title: Columbus Acute RSV 13

description: NCH 552


title: Columbus Acute RSV 18

description: NCH 595


title: Columbus Acute RSV 16

description: NCH 559


title: Columbus Acute RSV 1

description: NCH 503


title: Columbus Acute RSV 2

description: NCH 505


title: Columbus Acute RSV 15

description: NCH 556


title: Columbus Acute RSV 11

description: NCH 537


title: Columbus Acute RSV 14

description: NCH 553


title: Columbus Acute RSV 12

description: NCH 544


title: Columbus Acute RSV 26

description: NCH 563


title: Columbus healthy control 8

description: NCH 702

source_name: Columbus healthy control

value: healthy matched control


title: Columbus healthy control 5

description: NCH 685


title: Columbus healthy control 7

description: NCH 701


title: Columbus healthy control 4

description: NCH 684


title: Columbus healthy control 6

description: NCH 700


title: Columbus healthy control 2

description: NCH 678


title: Columbus healthy control 3

description: NCH 683


title: Dalls RSV 1-2 months follow up 15

data_processing: The data were normalised using average normalization with Genome Studio

source_name: Dalls RSV 1-2 months follow up

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep-96 RNA Amplification Kit

extract_protocol: RNA was extracted with MagMAX™ RNA Isolation Kit. Quality control was performed with Agilent Bioanalyser.

tag: age (months)

value: 1-2 month after the acute hospitalization in children with RSV

value: Whole blood


title: Dalls RSV 1-2 months follow up 19


title: Dalls RSV 1-2 months follow up 12


title: Dalls RSV 1-2 months follow up 21


title: Dalls RSV 1-2 months follow up 8


title: Dalls RSV 1-2 months follow up 20


title: Dalls RSV 1-2 months follow up 16


title: Dalls RSV 1-2 months follow up 14


title: Dalls RSV 1-2 months follow up 13


title: Dalls RSV 1-2 months follow up 11


title: Dalls RSV 1-2 months follow up 17


title: Dalls RSV 1-2 months follow up 18


title: Dalls RSV 1-2 months follow up 4


title: Dalls RSV 1-2 months follow up 9


title: Dalls RSV 1-2 months follow up 1


title: Columbus healthy control 1

description: NCH 672


title: Dalls RSV 1-2 months follow up 3


title: Dallas Influenza A 16

source_name: Dallas Influenza A

tag: diagnosis

value: acute human Influenza A lower respiratory tract infection (LRTI)


title: Dalls RSV 1-2 months follow up 2


title: Dalls RSV 1-2 months follow up 10


title: Dallas Influenza A 15


title: Dalls RSV 1-2 months follow up 6


title: Dalls RSV 1-2 months follow up 7


title: Dallas Influenza A 12


title: Dallas Influenza A 14


title: Dallas Influenza A 9


title: Dallas Influenza A 10


title: Dallas Influenza A 13


title: Dallas Influenza A 8


title: Dallas Influenza A 11


title: Dallas Influenza A 2


title: Dallas Acute HRV 30

source_name: Dallas Acute HRV

value: acute human Rhinovirus lower respiratory tract infection (HRV LRTI)


title: Dallas Influenza A 5


title: Dallas Acute HRV 28


title: Dallas Acute HRV 23


title: Dallas Influenza A 7


title: Dalls RSV 1-2 months follow up 5


title: Dallas Influenza A 4


title: Dallas Acute HRV 17


title: Dallas Acute HRV 27


title: Dallas Influenza A 3


title: Dallas Acute HRV 25


title: Dallas Influenza A 6


title: Dallas Acute HRV 29


title: Dallas Acute HRV 21


title: Dallas Acute HRV 19


title: Dallas Acute HRV 20


title: Dallas Acute HRV 24


title: Dallas Influenza A 1


title: Dallas Acute HRV 22


title: Dallas Acute HRV 16


title: Dallas Acute HRV 11


title: Dallas Acute HRV 10


title: Dallas Acute HRV 14


title: Dallas Acute HRV 13


title: Dallas Acute HRV 12


title: Dallas Acute HRV 9


title: Dallas Acute HRV 26


title: Dallas Acute HRV 6


title: Dallas Acute HRV 15


title: Dallas Acute HRV 4


title: Dallas Acute HRV 3


title: Dallas Acute HRV 2


title: Finnish Acute RSV 12

source_name: Finnish Acute RSV

value: acute Respiratory Syncytial Virus  lower respiratory tract infection (RSV LRTI)


title: Finnish Acute RSV 15


title: Dallas Acute HRV 5


title: Dallas Acute HRV 7


title: Dallas Acute HRV 1


title: Finnish Acute RSV 13


title: Finnish Acute RSV 16


title: Finnish Acute RSV 5


title: Finnish Acute RSV 11


title: Dallas Acute HRV 18


title: Finnish Acute RSV 10


title: Finnish Acute RSV 9


title: Finnish Acute RSV 8


title: Finnish Acute RSV 6


title: Finnish Acute RSV 7


title: Dallas Acute HRV 8


title: Finnish Acute RSV 3


title: Finnish Acute RSV 4


title: Dallas  Acute RSV 89

source_name: Dallas  Acute RSV


title: Finnish Acute RSV 2


title: Dallas  Acute RSV 91


title: Dallas  Acute RSV 90


title: Dallas  Acute RSV 85


title: Dallas  Acute RSV 78


title: Dallas  Acute RSV 86


title: Dallas  Acute RSV 84


title: Dallas  Acute RSV 88


title: Dallas  Acute RSV 79


title: Finnish Acute RSV 14


title: Dallas  Acute RSV 77


title: Dallas  Acute RSV 74


title: Finnish Acute RSV 1


title: Dallas  Acute RSV 73


title: Dallas  Acute RSV 67


title: Dallas  Acute RSV 87


title: Dallas  Acute RSV 69


title: Dallas  Acute RSV 75


title: Dallas  Acute RSV 82


title: Dallas  Acute RSV 76


title: Dallas  Acute RSV 83


title: Dallas  Acute RSV 80


title: Dallas  Acute RSV 72


title: Dallas  Acute RSV 64


title: Dallas  Acute RSV 62


title: Dallas  Acute RSV 61


title: Dallas  Acute RSV 71


title: Dallas  Acute RSV 70


title: Dallas  Acute RSV 63


title: Dallas  Acute RSV 65


title: Dallas  Acute RSV 81


title: Dallas  Acute RSV 68


title: Dallas  Acute RSV 66


title: Dallas  Acute RSV 60


title: Dallas  Acute RSV 59


title: Dallas  Acute RSV 49


title: Dallas  Acute RSV 50


title: Dallas  Acute RSV 51


title: Dallas  Acute RSV 47


title: Dallas  Acute RSV 54


title: Dallas  Acute RSV 48


title: Dallas  Acute RSV 56


title: Dallas  Acute RSV 55


title: Dallas  Acute RSV 53


title: Dallas  Acute RSV 52


title: Dallas  Acute RSV 58


title: Dallas  Acute RSV 36


title: Dallas  Acute RSV 46


title: Dallas  Acute RSV 45


title: Dallas  Acute RSV 42


title: Dallas  Acute RSV 44


title: Dallas  Acute RSV 43


title: Dallas  Acute RSV 37


title: Dallas  Acute RSV 34


title: Dallas  Acute RSV 39


title: Dallas  Acute RSV 41


title: Dallas  Acute RSV 57


title: Dallas  Acute RSV 38


title: Dallas  Acute RSV 33


title: Dallas  Acute RSV 32


title: Dallas  Acute RSV 35


title: Dallas  Acute RSV 24


title: Dallas  Acute RSV 23


title: Dallas  Acute RSV 29


title: Dallas  Acute RSV 40


title: Dallas  Acute RSV 25


title: Dallas  Acute RSV 28


title: Dallas  Acute RSV 19


title: Dallas  Acute RSV 20


title: Dallas  Acute RSV 27


title: Dallas  Acute RSV 22


title: Dallas  Acute RSV 26


title: Dallas  Acute RSV 15


title: Dallas  Acute RSV 14


title: Dallas  Acute RSV 9


title: Dallas  Acute RSV 21


title: Dallas  Acute RSV 7


title: Dallas  Acute RSV 10


title: Dallas  Acute RSV 4


title: Dallas  Acute RSV 5


title: Dallas  Acute RSV 18


title: Dallas  Acute RSV 30


title: Dallas  Acute RSV 31


title: Dallas  Acute RSV 6


title: Dallas  Acute RSV 17


title: Dallas  Acute RSV 12


title: Dallas  Acute RSV 11


title: Dallas  Acute RSV 8


title: Dallas  Acute RSV 16


title: Dallas  Acute RSV 3


title: Dallas healthy control 24

source_name: Dallas healthy control


title: Dallas healthy control 25


title: Dallas  Acute RSV 2


title: Finnish healthy control 8

source_name: Finnish healthy control


title: Dallas healthy control 26


title: Dallas  Acute RSV 1


title: Dallas healthy control 23


title: Finnish healthy control 3


title: Finnish healthy control 6


title: Finnish healthy control 2


title: Dallas healthy control 17


title: Dallas healthy control 19


title: Dallas healthy control 20


title: Dallas healthy control 16


title: Dallas healthy control 22


title: Dallas healthy control 13


title: Dallas healthy control 14


title: Dallas healthy control 18


title: Dallas healthy control 15


title: Dallas healthy control 9


title: Dallas healthy control 21


title: Dallas healthy control 10


title: Dallas healthy control 12


title: Dallas healthy control 7


title: Dallas healthy control 5


title: Dallas healthy control 27


title: Dallas healthy control 8


title: Dallas healthy control 11


title: CLIP_nohippuristanol_rep2_SantaCruzAb

status: Public on Jul 15 2013

type: SRA

city: Riverside

first: Fedor

last: Karginov

state: California

address: 900 University Ave

department: MCSB

institute: UC Riverside

description: Ago2-crosslinked RNA

library_source: transcriptomic

data_processing:
Basecalling with Illumina RTA 1.9.35
Sequenced reads were trimmed of the fixed 3` adaptor and 5` adaptor sequences.  The 5` RNA adaptor contains a 4-nucleotide random region (a "counting" barcode) that serves to count distinct 5` ligation events in the library preparation.  The count of such unique barcodes associated with each unique CLIPped RNA fragment (the insert sequence without adaptors) was used as its readcount, instead of the total read multiplicity.  This avoids PCR amplification bias in the quantitation.  The insert sequences without adaptors were mapped to the hg19 human genome assembly using Bowtie version 0.12.8 iteratively with 0, 1, and 2 mismatches, retaining the mapped reads from each stage and passing the non-mappers to the next stage, only allowing unique mappers.  Reads that did not map to the genome were processed with Tophat to identify reads mapping to RefSeq RNA and lincRNA splice junctions.  Reads mapping to identical genomic positions were collapsed and summed.  Combined reads were annotated for RefSeq, lincRNA, microRNA and RepeatMasker categories.  To identify peaks, reads from all replicates for each condition were pooled and used as input to Findpeaks version 4.0.  Parameters were set to denote peaks separated by valleys of 50% height or less, and to trim the sides of peaks dropping below 10% of peak height.  To identify peaks from two conditions (eg., +/- arsenite) that correspond to the same Ago2 binding site, while allowing for some differences (shifting) in their end coordinates, peaks from the two conditions that overlapped more than 50% of their width were designated as the same peak/binding location, and the union of their coordinates was used as the genomic coordinates for this "peak pair" or "combined peak".  This included pseudo-pairs, with a peak present in one condition and completely absent in the other.  Annotations for peaks were obtained as above, and the coordinates of combined peaks were used to re-extract readcounts from individual replicates under the peak.  Readcounts for the corresponding mRNAs from RNA-seq replicates were appended to the dataset, and peaks were filtered for the presence of greater than 10 readcounts across all CLIP replicates in an experiment (treatment and control), as well as greater than 10 readcounts of the corresponding mRNA.  CLIP readcounts were then normalized to the miRNA fraction (separately for each replicate), and RNA-seq readcounts were normalized across replicates by applying DESeq-derived sizing factors. Normalized replicate counts were padded with a value of 0.25, and the CLIP signal for each peak was then divided by the corresponding mRNA abundance in the replicate.
hg19
tab-delimited text file with Ago2 CLIP peak genomic coordinates, annotation and normalized natural log abundance and logratio of change in treatment

source_name: 293S cells

growth_protocol: 293S cells were grown in DMEM + 10% FBS  + penicillin/streptomycin, in adherent monolayer, to ~70% confluency.

extract_protocol: CLIP-seq - Ago2 crosslinking-immunoprecipitation of RNA

treatment_protocol: Where indicated, treated with 1 μM hippuristanol for 30 minutes

tag: treatment

value: no treatment (control)

tag: cell line

tag: antibody

tag: antibody manufacturer

value: Santa Cruz


title: RNAseq_nohippuristanol_rep1

data_processing:
Basecalling with Illumina RTA 1.9.35
Reads were trimmed to nucleotides 9-36 and reverse-complemented to obtain sense strand sequences, and mapped to the hg19 human genome assembly using Bowtie version 0.12.8 iteratively with 0, 1, and 2 mismatches, retaining the mapped reads from each stage and passing the non-mappers to the next stage, only allowing unique mappers.  Reads that did not map to the genome were processed with Tophat to identify reads mapping to RefSeq RNA and lincRNA splice junctions.  Combined reads were annotated for RefSeq, lincRNA, microRNA and RepeatMasker categories, and analyzed by DESeq.
hg19
tab-delimited text file with Ago2 CLIP peak genomic coordinates, annotation and normalized natural log abundance and logratio of change in treatment

extract_protocol: Trizol and NSR method


title: RNAseq_hippuristanol_rep1

value: hippuristanol


title: RNAseq_hippuristanol_rep2


title: CLIP_nohippuristanol_rep2_SigmaAb

description: Ago2-crosslinked RNA

value: Sigma


title: CLIP_hippuristanol_rep2_SantaCruzAb

description: Ago2-crosslinked RNA


title: CLIP_hippuristanol_rep2_SigmaAb

description: Ago2-crosslinked RNA


title: CLIP_nohippuristanol_rep2_AbnovaAb

description: Ago2-crosslinked RNA

value: Abnova


title: Dallas healthy control 4

tag: tissue


title: CLIP_hippuristanol_rep1_SigmaAb

description: Ago2-crosslinked RNA


title: Dallas healthy control 3


title: CLIP_nohippuristanol_rep1_SigmaAb

description: Ago2-crosslinked RNA


title: Dallas healthy control 6


title: CLIP_hippuristanol_rep1_SantaCruzAb

description: Ago2-crosslinked RNA


title: CLIP_nohippuristanol_rep1_SantaCruzAb

description: Ago2-crosslinked RNA


title: Dallas healthy control 2


title: Dallas healthy control 1


title: CLIP_hippuristanol_rep1_AbnovaAb

description: Ago2-crosslinked RNA


title: RNAseq_emetine

treatment_protocol: Where indicated, treated with 20 μg/mL emetine for 60 minutes

value: emetine


title: CLIP_nohippuristanol_rep1_AbnovaAb

description: Ago2-crosslinked RNA


title: CLIP_emetine_SigmaAb

description: Ago2-crosslinked RNA

data_processing:
Basecalling with Illumina RTA 1.8.70.0
Sequenced reads were trimmed of the fixed 3` adaptor and 5` adaptor sequences.  The 5` RNA adaptor contains a 4-nucleotide random region (a "counting" barcode) that serves to count distinct 5` ligation events in the library preparation.  The count of such unique barcodes associated with each unique CLIPped RNA fragment (the insert sequence without adaptors) was used as its readcount, instead of the total read multiplicity.  This avoids PCR amplification bias in the quantitation.  The insert sequences without adaptors were mapped to the hg19 human genome assembly using Bowtie version 0.12.8 iteratively with 0, 1, and 2 mismatches, retaining the mapped reads from each stage and passing the non-mappers to the next stage, only allowing unique mappers.  Reads that did not map to the genome were processed with Tophat to identify reads mapping to RefSeq RNA and lincRNA splice junctions.  Reads mapping to identical genomic positions were collapsed and summed.  Combined reads were annotated for RefSeq, lincRNA, microRNA and RepeatMasker categories.  To identify peaks, reads from all replicates for each condition were pooled and used as input to Findpeaks version 4.0.  Parameters were set to denote peaks separated by valleys of 50% height or less, and to trim the sides of peaks dropping below 10% of peak height.  To identify peaks from two conditions (eg., +/- arsenite) that correspond to the same Ago2 binding site, while allowing for some differences (shifting) in their end coordinates, peaks from the two conditions that overlapped more than 50% of their width were designated as the same peak/binding location, and the union of their coordinates was used as the genomic coordinates for this "peak pair" or "combined peak".  This included pseudo-pairs, with a peak present in one condition and completely absent in the other.  Annotations for peaks were obtained as above, and the coordinates of combined peaks were used to re-extract readcounts from individual replicates under the peak.  Readcounts for the corresponding mRNAs from RNA-seq replicates were appended to the dataset, and peaks were filtered for the presence of greater than 10 readcounts across all CLIP replicates in an experiment (treatment and control), as well as greater than 10 readcounts of the corresponding mRNA.  CLIP readcounts were then normalized to the miRNA fraction (separately for each replicate), and RNA-seq readcounts were normalized across replicates by applying DESeq-derived sizing factors. Normalized replicate counts were padded with a value of 0.25, and the CLIP signal for each peak was then divided by the corresponding mRNA abundance in the replicate.
hg19
tab-delimited text file with Ago2 CLIP peak genomic coordinates, annotation and normalized natural log abundance and logratio of change in treatment


title: RNAseq_noemetine


title: CLIP_noemetine_SigmaAb

description: Ago2-crosslinked RNA


title: CLIP_emetine_AbnovaAb

description: Ago2-crosslinked RNA


title: CLIP_emetine_SantaCruzAb

description: Ago2-crosslinked RNA


title: CLIP_noemetine_AbnovaAb

description: Ago2-crosslinked RNA


title: CLIP_noemetine_SantaCruzAb

description: Ago2-crosslinked RNA


title: CLIP_LOband_noarsenite_rep2

description:
Ago2-crosslinked RNA
The "LO" band was excised during the CLIP procedure.  These datasets were used to quantify miRNA abundance in the samples.

data_processing:
Basecalling with Illumina RTA 1.8.70.0
Four biological replicate "LO" libraries for the –arsenite and +arsenite conditions were processed separately.  Reads were trimmed of 3` adaptor and 5` adaptor sequences, including the random barcodes (thus using the total read multiplicity as the readcount), and mapped to the hg19 human genome assembly using Bowtie iteratively with 0, 1, and 2 mismatches, retaining the mapped reads from each stage and passing the non-mappers to the next stage.  Multiple mappers were allowed for this analysis.  Reads mapping to identical genomic positions were collapsed and summed, and annotated with miRBase version 18 microRNA genomic positions.  Reads mapping to different genomic loci of the same annotated miRNA (eg, let-7a-1 and let-7a-2) were further collapsed and summed.  The resulting miRNA counts were filtered for more than 10 reads across all replicates/conditions, and analysed for differential expression using the DESeq R package.  To obtain the top 50 miRNA seed families, miRNA counts were collapsed and summed for each miRNA family that shares a common 7mer seed (nucleotides 2-8 of mature -3p or -5p miRNAs), and processed by DESeq to yield normalized mean counts across replicates/conditions.
hg19
tab-delimited text file with DeSeq-processed microRNA abundances +/- arsenite, associated fold changes and p-values

treatment_protocol: Where indicated, treated with 1 mM sodium arsenite for 30 minutes

tag: antibody catalog #


title: CLIP_LOband_noarsenite_rep3


title: CLIP_hippuristanol_rep2_AbnovaAb

description: Ago2-crosslinked RNA


title: CLIP_LOband_arsenite_rep3

value: arsenite


title: CLIP_LOband_noarsenite_rep4


title: CLIP_LOband_noarsenite_rep1


title: CLIP_LOband_arsenite_rep1


title: RNAseq_arsenite_rep4

data_processing:
Basecalling with Illumina RTA 1.8.70.0
Reads were trimmed to nucleotides 9-36 and reverse-complemented to obtain sense strand sequences, and mapped to the hg19 human genome assembly using Bowtie version 0.12.8 iteratively with 0, 1, and 2 mismatches, retaining the mapped reads from each stage and passing the non-mappers to the next stage, only allowing unique mappers.  Reads that did not map to the genome were processed with Tophat to identify reads mapping to RefSeq RNA and lincRNA splice junctions.  Combined reads were annotated for RefSeq, lincRNA, microRNA and RepeatMasker categories, and analyzed by DESeq.
hg19
tab-delimited text file with Ago2 CLIP peak genomic coordinates, annotation and normalized natural log abundance and logratio of change in treatment


title: RNAseq_noarsenite_rep4


title: CLIP_LOband_arsenite_rep2


title: RNAseq_arsenite_rep3


title: RNAseq_noarsenite_rep2


title: RNAseq_noarsenite_rep3


title: RNAseq_arsenite_rep1


title: RNAseq_arsenite_rep2


title: RNAseq_noarsenite_rep1


title: CLIP_arsenite_rep4

description: Ago2-crosslinked RNA


title: CLIP_noarsenite_rep4

description: Ago2-crosslinked RNA


title: Dallas  Acute RSV 13


title: CLIP_noarsenite_rep2

description: Ago2-crosslinked RNA


title: CLIP_noarsenite_rep3

description: Ago2-crosslinked RNA


title: CLIP_arsenite_rep3

description: Ago2-crosslinked RNA


title: RNAseq_Sucrose_Gradient_arsenite_fraction8

description: sucrose-gradient-fractionated total RNA

data_processing:
Basecalling with Illumina RTA 1.13.48
Reads were processed as for RNA-seq in subseries1-3, with an added initial mapping step to the ERCC spike-in sequences.  ERCC scaling factors were calculated by linear regression of length-corrected counts for each ERCC RNA between samples.  Non-ERCC reads were then mapped further as above.  Exonic read counts were collapsed by gene, filtered for genes with 10 or more counts across all fractions for each condition (+/- arsenite), normalized to ERCC scaling factors, and further normalized to a total abundance of 1 across all fractions within a condition.
hg19
tab-delimited text file containing, per gene, normalized abundances in sucrose gradient fractions +/- arsenite, and the center-of-mass (COM) and COM shift upon arsenite


title: CLIP_arsenite_rep2

description: Ago2-crosslinked RNA


title: CLIP_noarsenite_rep1

description: Ago2-crosslinked RNA


title: RNAseq_Sucrose_Gradient_arsenite_fraction7

description: sucrose-gradient-fractionated total RNA


title: CLIP_arsenite_rep1

description: Ago2-crosslinked RNA


title: RNAseq_Sucrose_Gradient_arsenite_fraction6

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_arsenite_fraction4

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_arsenite_fraction3

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_arsenite_fraction1

description: sucrose-gradient-fractionated total RNA


title: CLIP_LOband_arsenite_rep4


title: RNAseq_Sucrose_Gradient_arsenite_fraction2

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_arsenite_fraction5

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_noarsenite_fraction7

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_noarsenite_fraction6

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_noarsenite_fraction8

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_noarsenite_fraction4

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_noarsenite_fraction5

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_noarsenite_fraction1

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_noarsenite_fraction3

description: sucrose-gradient-fractionated total RNA


title: RNAseq_Sucrose_Gradient_noarsenite_fraction2

description: sucrose-gradient-fractionated total RNA


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_H3K4me3

status: Public on Sep 14 2012

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone

value: primary cell

value: CD14-positive monocyte

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me3

tag: antibody targetdescription

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

tag: antibody vendorname

value: 1)abcam; 2)Millipore

tag: antibody vendorid

tag: controlid

tag: replicate

tag: softwareversion

tag: cell sex

value: F

value: Millipore

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_H3K27me3

status: Public on Sep 13 2012

value: rabbit polyclonal. Antibody Target:H3K27me3

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

tag: antibody

tag: treatment


title: RNAseq_nohippuristanol_rep2

value: no treatment (control)

tag: cell line


title: MDA Sharp1, biological replicate C

status: Public on Jul 19 2012

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from Sharp1-overexpressing MDA-MB-231 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: human metastatic breast cell line MDA-MB-231 overexpressing Sharp1

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.

growth_protocol: MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.

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

treatment_protocol: Cells were cultivated under normal growing conditions

tag: genotype/variation

value: cells overexpressing Sharp1


title: Placenta_term_11

status: Public on Sep 01 2011

type: genomic

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Exported from BeadStudio software v3.2, converted to M values using the Bioconductor package lumi, colour-adjusted, background-corrected and ssn normalized

label: Cy5 and Cy3

source_name: Placenta at term

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue collected from elective abortions and normal pregnancies

tag: tissue

value: Placenta at term

tag: disease state

value: normal


title: Placenta_term_14


title: Placenta_term_13


title: MDA shHIF, biological replicate C

description: Gene expression data from  MDA-MB-231 cells depleted of HIF1a and HIF2a

source_name: human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against HIF1a and HIF2a

value: cells depleted of HIF1a and HIF2a


title: MDA shHIF, biological replicate D


title: MDA Sharp1, biological replicate D


title: MDA shHIF, biological replicate A


title: Placenta_2ndtri_6

source_name: Placenta at second trimester

extract_protocol: Tissue collected from elective abortions and normal pregnancies. Tissue samples were incubated at 50C overnight with shaking in DNA extraction buffer (100 mM NaCl, 10 mM Tris.HCl pH8, 25 mM EDTA, 0.5% (w/v) SDS), containing 200 ug/ml proteinase K. DNA was isolated by two rounds of phenol:chloroform extraction, followed by RNAse A treatment, precipitation in absolute ethanol containing 10% (v/v) sodium acetate (3M, pH 5.2), and resuspended in 100 ul nuclease-free water (Ambion, Austin, TX, USA) or using salting out method followed by purification with Qiagen blood and tissue kit (Qiagen, Mississauga, ON, USA). DNA was stored at -20C.

value: Placenta at second trimester


title: Placenta_2ndtri_8


title: Placenta_2ndtri_7


title: Placenta_term_12


title: MDA Sharp1, biological replicate A


title: MDA Sharp1, biological replicate B


title: Placenta_term_10


title: Placenta_2ndtri_10


title: Placenta_term_8


title: Placenta_term_6


title: Placenta_2ndtri_4


title: MDA shHIF, biological replicate B


title: Placenta_2ndtri_2


title: Placenta_2ndtri_5


title: Placenta_2ndtri_3


title: Placenta_term_5


title: Placenta_term_9


title: Placenta_2ndtri_1


title: Placenta_term_4


title: Placenta_term_3


title: Placenta_term_7


title: Placenta_1sttri_12

source_name: Placenta at first trimester

value: Placenta at first trimester


title: Placenta_1sttri_18


title: Placenta_1sttri_11


title: Placenta_1sttri_17


title: Placenta_1sttri_14


title: Placenta_1sttri_10


title: Placenta_term_2


title: Placenta_1sttri_8


title: Placenta_1sttri_16


title: Placenta_1sttri_5


title: Placenta_1sttri_7


title: Placenta_1sttri_1


title: Placenta_1sttri_13


title: Placenta_1sttri_9


title: donor 3 vs Donor 4 (NT)

status: Public on Jun 19 2011

city: MONTPELLIER

first: Paul

last: Chuchana

address: 80 avenue Augustin Fliche

country: France

institute: INSERM

description: Sample 3 NT

hyb_protocol: Prior to hybridization, excess oligonucleotide was removed from the arrays by shaking them twice1min in 0.2% SDS. Arrays were then washed 2 times in distilled water.  The two labelled aRNA were added to microarray hybridization buffer version 2 (GE Healthcare) in a final concentration of 50% formamide, denaturated at 95°C for 3 min and applied to the microarrays in individual chambers of an automated slide processor (GE Healthcare). Hybridization was carried out at 37°C for 12 h. Hybridized slides were washed at 37°C successively with 1X SSC, 0.2% SDS for 10 min, twice with 0.1X SSC, 0.2% SDS for 10 min, with 0.1X SSC for 1 min and with isopropanol before air drying.

scan_protocol: Microarrays were immediately scanned at 10 µm resolution in both Cy3 and Cy5 channels with GenePix 4200AL scanner (Molecular Devices) with a variable PMT voltage to obtain maximal signal intensities with <0.1% probe saturation. ArrayVision software was used for feature extraction. Spots with high local background or contamination fluorescence were flagged manually. A local background was calculated for each spot as the median values of the fluorescence intensities of 4 squares surrounding the spot. This background was subtracting from the foreground fluorescence intensity.

data_processing:
Identification of differentially regulated genes was carried out using the EV (Expression Variation) method [Chuchana P., Marchand D., Nugoli M., Rodriguez C., Molinari N. et al. (2007) An adaptation of the LMS method to determine expression variations in profiling data. Nucleic Acids Res 35:e71 doi:10.1093], on paired data, i.e. LPS stimulated macrophages versus unstimulated macrophages from the same donor. This method can be used to analyze the signal with regards to noise by normalizing and constructing confidence bands of gene expression, and by fitting cubic spline curves to the Box–Cox transformation. The confidence bands, fitted to the actual variance of the data, include the genes devoid of significant variation, and are used to calculate EV, based on the confidence bandwidth. Each outlier is positioned according to the dispersion space (DS) and provides a measure of gene EV associated with a p-value. This model allows us to stabilize variance.
For each spot S, its orthogonal projection to the median O was determined and the distance between O and U d(O,U) (intersection of the segments O,U and the curve of the DS) measured. For each spot located along the O, S line, the value d(O,U) represents the unit of expression. Expression variation Ev#(S) thus corresponds to the d(O,S)/d(O,U) ratio. |EV#(S)| 1/41 defines the baseline for genes presenting no EV. If the ration is lower than one, the spot do not present expression variation and the measurement in noted NR.
The processed data file is linked as supplementary file on the Series record.

source_name: FV-NT

label_protocol: For the preparation of the labelled Cy3- and Cy5- aRNA target, one microgram of total RNA samples were amplified and synthesised using Amino Allyl Message Amp II aRNA amplification kit (Ambion), according the manufacturer’s instructions.

extract_protocol: Total RNA was then extracted from the fresh pooled monolayer in duplicate experiments, which includes a DNAse step, using the RNeasy® mini kit (Qiagen) according to the manufacturer’s instructions. RNA quantity and purity was quantified using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies) and assayed for degradation using an Agilent bioanalyser (Agilent technologies, Santa Clara, USA) according to the manufacturer’s instructions.

treatment_protocol: All samples were processed together the same day. Briefly, the mononuclear cell fraction was obtained by gradient centrifugation over Ficoll (Histopaque 1077, Sigma-Aldrich Chimie, Lyon, France) and monocytes were purified by CD14+ magnetic cell sorting (Miltenyi Biotech) according to manufacturer’s instructions. Monocytes were then seeded in 24-well plates at 106 cells per well (4 wells per donor) in complete Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10 % heat-inactivated human type AB (Cambrex) serum, ultra-glutamine 2 mM, penicillin 200 U/ml and streptomycin 200 pg/ml. Cells were cultured for 5 days (with pre-warmed complete medium change at day 3) to allow differentiation into macrophages. At day 5, two wells per donor were stimulated with 100 ng/ml lipopolysaccharide (LPS, Escherichia coli, Sigma) whereas the two other wells were left as unstimulated controls (medium change only). After 48 hours, all wells were washed with pre-warmed phosphate-buffered saline (PBS).

tag: cell type

value: monocytes/macrophages

tag: donor

tag: agent

value: untreated

source_name: OK-NT


title: donor 3 vs Donor 4 (LPS)

description: Sample 4 LPS

source_name: FV-LPS

value: LPS

source_name: OK-LPS


title: donor 1 vs Donor 2 (LPS)

description: Sample 2 LPS

source_name: BB-LPS

source_name: DB-LPS


title: Placenta_1sttri_6


title: donor 1 vs Donor 2 (NT)

description: Sample 1 NT

source_name: BB-NT

source_name: DB-NT


title: donor 5 vs Donor 6 (NT)

description: Sample 5 NT

source_name: PH-NT

source_name: RGB-NT


title: Placenta_1sttri_3


title: DroshaflflES_Tam_rep2

status: Public on Jun 25 2010

description: 5`-phosphorylated poly(A) RNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Standard tissue culture practice

extract_protocol: Global 5`-phosphate-dependent RACE in WT, Ago2-KO and Drosha-excised mouse ES cells and human 293S cells

treatment_protocol: 100nM 4-OH-tamoxifen for 4-9 days for the Drosha experiment

tag: genotype

value: Drosha flox/flox; CreER

value: with tamoxifen

value: embryonic stem cells


title: Placenta_term_1


title: DroshaflflES_Tam_rep1

description: 5`-phosphorylated poly(A) RNA


title: Placenta_1sttri_15


title: donor 5 vs Donor 6 (LPS)

description: Sample 6 LPS

source_name: PH-LPS

source_name: RGB-LPS


title: DroshaflflES_NoTam_rep2

description: 5`-phosphorylated poly(A) RNA

value: no tamoxifen


title: Ago2ko_ES_rep10

description: 5`-phosphorylated poly(A) RNA


title: Ago2ko_ES_rep9

description: 5`-phosphorylated poly(A) RNA


title: DroshaflflES_NoTam_rep1

description: 5`-phosphorylated poly(A) RNA


title: Ago2ko_ES_rep7

description: 5`-phosphorylated poly(A) RNA


title: Ago2ko_ES_rep5

description: 5`-phosphorylated poly(A) RNA


title: Ago2ko_ES_rep4

description: 5`-phosphorylated poly(A) RNA


title: Ago2ko_ES_rep3

description: 5`-phosphorylated poly(A) RNA


title: WT_ES_rep6

description: 5`-phosphorylated poly(A) RNA

value: WT


title: Ago2ko_ES_rep1

description: 5`-phosphorylated poly(A) RNA


title: WT_ES_rep5

description: 5`-phosphorylated poly(A) RNA


title: Ago2ko_ES_rep2

description: 5`-phosphorylated poly(A) RNA


title: Placenta_1sttri_2


title: WT_ES_rep4

description: 5`-phosphorylated poly(A) RNA


title: WT_ES_rep2

description: 5`-phosphorylated poly(A) RNA


title: 293S_rep7

description: 5`-phosphorylated poly(A) RNA

source_name: 293S cell line


title: 293S_rep6

description: 5`-phosphorylated poly(A) RNA


title: 293S_rep4

description: 5`-phosphorylated poly(A) RNA


title: 293S_rep3

description: 5`-phosphorylated poly(A) RNA


title: 293S_rep5

description: 5`-phosphorylated poly(A) RNA


title: WT_ES_rep1

description: 5`-phosphorylated poly(A) RNA


title: 293S_rep2

description: 5`-phosphorylated poly(A) RNA


title: 293S_rep1

description: 5`-phosphorylated poly(A) RNA


title: Placenta_1sttri_4


title: Ago2ko_ES_rep8

description: 5`-phosphorylated poly(A) RNA


title: Ago2ko_ES_rep6

description: 5`-phosphorylated poly(A) RNA


title: WT_ES_rep3

description: 5`-phosphorylated poly(A) RNA


title: WholeCerebellum_1month_p53--_Ink4c--_rep4

status: Public on Jan 17 2009

description:
Barcode used in pool: 5MLH
Raw data file: CSHL_FC12772_5_Medullo_4.fastq

data_processing: The reads were deconvoluted by barcode, collapsed to unique sequences, aligned to the genome and annotated.  Read-counts for miRNA sequences were cubic-spline normalized then log-transformed.  The R-project software (http://www.R-project.org), including Bioconductor were used for data analysis.

source_name: cerebellum

growth_protocol: Standard mouse facility

extract_protocol: Total RNA extraction by Trizol

value: P53-/-, Ink4c (p18) -/-; Tissue:cerebellum; Age:1 month


title: MBcells_Ptc+-_Ink4c--_rep1

description:
Barcode used in pool: 5MLA
Raw data file: CSHL_FC12772_4_Medullo_3.fastq

source_name: Purified GNP-like medulloblastoma cells from cerebellum

value: Ptch1+/-, Ink4c (p18) -/-; Tissue:MB cells; Age:variable


title: WholeCerebellum_1month_Ptc+-_Ink4c--_rep2

description:
Barcode used in pool: 5MLJ
Raw data file: CSHL_FC12772_5_Medullo_4.fastq

tag: Ptch1+/-, Ink4c (p18) -/-, age 1 month

value: Ptch1+/-, Ink4c (p18) -/-; Tissue:cerebellum; Age:1 month


title: MBcells_P53--_Ink4c--_rep1

description:
Barcode used in pool: 5MLD
Raw data file: CSHL_FC12772_4_Medullo_3.fastq

value: P53-/-, Ink4c (p18) -/-; Tissue:MB cells; Age:variable


title: MBcells_Ptc+-_Ink4c--_rep2

description:
Barcode used in pool: 5MLB
Raw data file: CSHL_FC12772_4_Medullo_3.fastq


title: MBcells_P53--_Ink4c--_rep3

description:
Barcode used in pool: 5MLA
Raw data file: CSHL_FC9506_4_Medullo_5.fastq


title: MBcells_Ptc+-_Ink4c--_rep5

description:
Barcode used in pool: 5MLG
Raw data file: CSHL_FC11273_8_Medullo_6.fastq


title: MBcells_Ptc+-_Ink4c--_rep3

description:
Barcode used in pool: 5MLC
Raw data file: CSHL_FC12772_4_Medullo_3.fastq


title: MBcells_Ptc+-_Ink4c--_rep4

description:
Barcode used in pool: 5MLB
Raw data file: CSHL_FC11273_8_Medullo_6.fastq


title: WholeCerebellum_1month_wt_rep2

description:
Barcode used in pool: 5MLC
Raw data file: CSHL_FC12772_5_Medullo_4.fastq

tag: Wild-type (C57BL/6), age 1 month

value: WT; Tissue:cerebellum; Age:1 month


title: WholeCerebellum_1month_wt_rep1

description:
Barcode used in pool: 5MLB
Raw data file: CSHL_FC12772_5_Medullo_4.fastq


title: MBcells_P53--_Ink4c--_rep5

description:
Barcode used in pool: 5MLI
Raw data file: CSHL_FC11273_8_Medullo_6.fastq


title: WholeCerebellum_1month_p53--_Ink4c--_rep2

description:
Barcode used in pool: 5MLF
Raw data file: CSHL_FC12772_5_Medullo_4.fastq


title: WholeCerebellum_1month_wt_rep3

description:
Barcode used in pool: 5MLD
Raw data file: CSHL_FC12772_5_Medullo_4.fastq


title: WholeCerebellum_1month_p53--_Ink4c--_rep1

description:
Barcode used in pool: 5MLE
Raw data file: CSHL_FC12772_5_Medullo_4.fastq


title: MBcells_P53--_Ink4c--_rep4

description:
Barcode used in pool: 5MLH
Raw data file: CSHL_FC11273_8_Medullo_6.fastq


title: WholeCerebellum_P6_Ptc+-_Ink4c--_rep5

description:
Barcode used in pool: 5MLJ
Raw data file: CSHL_FC9506_4_Medullo_5.fastq

value: Ptch1+/-, Ink4c (p18) -/-; Tissue:cerebellum; Age:P6


title: Placenta_2ndtri_9

source_name: Placenta at second trimester

value: normal


title: Cl34 ES cells, biological rep3

status: Public on Dec 19 2009

city: London

first: Ariane

last: Chapgier

address: 30 guilford street

department: Institute of Child Health

country: United Kingdom

institute: University College London

description: Gene expression data from mus musculus Hira-/- ES cells

hyb_protocol: To hybridize the sample to the array and wash and stain the arrays, an additional Hybridization wash and stain kit was used (Cat 900720).  The arrays were hybridized in the Hybridization oven 640, washed and stained using the Fluidics station 450.

scan_protocol: The arrays were scanned using the GCS3000, 7G.

data_processing: Bioconductor.  GCRMA normalized intensities (Zhijin Wu, Rafael A. Irizarry, Robert Gentleman, Francisco Martinez Murillo, and Forrest Spencer, A Model Based Background Adjustment for Oligonucleotide Expression Arrays (May 2004). Johns Hopkins University, Dept. of Biostatistics Working Papers. Working Paper 1. http://www.bepress.com/jhubiostat/paper1 )

source_name: Hira-/- derived ES cells

label_protocol: The Affymetrix protocol was used to prepare the samples using the GeneChip Mouse Gene 1.0 ST Array kit (Cat 9011780)

growth_protocol: ES cells were grown in KnockOut™ DMEM (Invitrogen) supplemented with 15% of FCS- ES Cell qualified (Chemicon), 1% Glutamax (Invitrogen), 1% of MEM NEAA (Invitrogen), 1% Penicillin-Streptomycin (Invitrogen), 0.1 mM of b-mercaptoetahnol (sigma), 1% of ESGRO (Chemicon)

treatment_protocol: ES cells were scrapped and collected in cold PBS1x, and then treated with 500 uL of Trizol (Invitrogen)

value: embryonic stem cell

value: Hira-/-


title: Cl34 ES cells, biological rep2


title: w9.5 ES cells, biological rep2

description: Gene expression data from mus musculus WT ES cells

source_name: WT parental ES cells


title: WholeCerebellum_1month_p53--_Ink4c--_rep3

description:
Barcode used in pool: 5MLG
Raw data file: CSHL_FC12772_5_Medullo_4.fastq


title: WholeCerebellum_1month_Ptc+-_Ink4c--_rep1

description:
Barcode used in pool: 5MLI
Raw data file: CSHL_FC12772_5_Medullo_4.fastq


title: w9.5 ES cells, biological rep1


title: Cl34 ES cells, biological rep1


title: WholeCerebellum_P6_Ptc+-_Ink4c--_rep3

description:
Barcode used in pool: 5MLH
Raw data file: CSHL_FC9506_4_Medullo_5.fastq


title: WholeCerebellum_P6_Ptc+-_Ink4c--_rep2

description:
Barcode used in pool: 5MLA
Raw data file: CSHL_FC12772_5_Medullo_4.fastq


title: WholeCerebellum_P6_Ptc+-_Ink4c--_rep4

description:
Barcode used in pool: 5MLI
Raw data file: CSHL_FC9506_4_Medullo_5.fastq


title: MBcells_P53--_Ink4c--_rep2

description:
Barcode used in pool: 5MLE
Raw data file: CSHL_FC12772_4_Medullo_3.fastq


title: WholeCerebellum_P6_p53--_Ink4c--_rep2

description:
Barcode used in pool: 5MLI
Raw data file: CSHL_FC12772_4_Medullo_3.fastq

value: P53-/-, Ink4c (p18) -/-; Tissue:cerebellum; Age:P6


title: WholeCerebellum_P6_Ptc+-_Ink4c--_rep1

description:
Barcode used in pool: 5MLJ
Raw data file: CSHL_FC12772_4_Medullo_3.fastq


title: WholeCerebellum_P6_p53--_Ink4c--_rep5

description:
Barcode used in pool: 5MLG
Raw data file: CSHL_FC9506_4_Medullo_5.fastq


title: WholeCerebellum_P6_p53--_Ink4c--_rep3

description:
Barcode used in pool: 5MLE
Raw data file: CSHL_FC9506_4_Medullo_5.fastq


title: WholeCerebellum_P6_wt_rep4

description:
Barcode used in pool: 5MLD
Raw data file: CSHL_FC9506_4_Medullo_5.fastq

tag: Wild-type (C57BL/6), age day 6 (P6)

value: WT; Tissue:cerebellum; Age:P6


title: WholeCerebellum_P6_wt_rep3

description:
Barcode used in pool: 5MLC
Raw data file: CSHL_FC9506_4_Medullo_5.fastq


title: WholeCerebellum_P6_p53--_Ink4c--_rep1

description:
Barcode used in pool: 5MLH
Raw data file: CSHL_FC12772_4_Medullo_3.fastq


title: CGNP_P6_Ptc+-_Ink4c--_rep4

description:
Barcode used in pool: 5MLJ
Raw data file: CSHL_FC9417_8_Medullo_2.2.fastq

source_name: Purified GNPs from cerebellum

value: Ptch1+/-, Ink4c (p18) -/-; Tissue:CGNP; Age:P6


title: CGNP_P6_Ptc+-_Ink4c--_rep5

description:
Barcode used in pool: 5MLB
Raw data file: CSHL_FC9506_4_Medullo_5.fastq


title: WholeCerebellum_P6_wt_rep1

description:
Barcode used in pool: 5MLF
Raw data file: CSHL_FC12772_4_Medullo_3.fastq


title: CGNP_P6_Ptc+-_Ink4c--_rep2

description:
Barcode used in pool: 5MLE
Raw data file: CSHL_FC9417_7_Medullo_1.2.fastq


title: WholeCerebellum_P6_wt_rep2

description:
Barcode used in pool: 5MLG
Raw data file: CSHL_FC12772_4_Medullo_3.fastq


title: w9.5 ES cells, biological rep3

description: Gene expression data from mus musculus WT ES cells


title: CGNP_P6_Ptc+-_Ink4c--_rep3

description:
Barcode used in pool: 5MLI
Raw data file: CSHL_FC9417_8_Medullo_2.2.fastq


title: CGNP_P6_p53--_Ink4c--_rep4

description:
Barcode used in pool: 5MLH
Raw data file: CSHL_FC9417_8_Medullo_2.2.fastq

value: P53-/-, Ink4c (p18) -/-; Tissue:CGNP; Age:P6


title: CGNP_P6_p53--_Ink4c--_rep5

description:
Barcode used in pool: 5MLA
Raw data file: CSHL_FC11273_8_Medullo_6.fastq


title: CGNP_P6_p53--_Ink4c--_rep3

description:
Barcode used in pool: 5MLG
Raw data file: CSHL_FC9417_8_Medullo_2.2.fastq


title: WholeCerebellum_P6_p53--_Ink4c--_rep4

description:
Barcode used in pool: 5MLF
Raw data file: CSHL_FC9506_4_Medullo_5.fastq


title: CGNP_P6_p53--_Ink4c--_rep2

description:
Barcode used in pool: 5MLC
Raw data file: CSHL_FC9417_7_Medullo_1.2.fastq


title: CGNP_P6_p53--_Ink4c--_rep1

description:
Barcode used in pool: 5MLF
Raw data file: CSHL_FC9417_8_Medullo_2.2.fastq


title: CGNP_P6_wt_rep4

description:
Barcode used in pool: 5MLC
Raw data file: CSHL_FC11273_8_Medullo_6.fastq

value: WT; Tissue:CGNP; Age:P6


title: CGNP_P6_wt_rep1

description:
Barcode used in pool: 5MLA
Raw data file: CSHL_FC9417_7_Medullo_1.2.fastq


title: CGNP_P6_wt_rep2

description:
Barcode used in pool: 5MLF
Raw data file: CSHL_FC11273_8_Medullo_6.fastq


title: CGNP_P6_wt_rep3

description:
Barcode used in pool: 5MLD
Raw data file: CSHL_FC11273_8_Medullo_6.fastq


title: CGNP_P6_Ptc+-_Ink4c--_rep1

description:
Barcode used in pool: 5MLD
Raw data file: CSHL_FC9417_7_Medullo_1.2.fastq